Datasets:

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bionlp_st_2011_id

like 1

[ { "id": "PMC2565068-02-Results-07__text", "type": "abstract", "text": [ "scpC and slo are insufficient singly for the pathogenesis of invasive infections \nFinally, we assessed the influence of enhanced expression of the scpC or the slo gene on the virulence in a mouse model. As shown in Table 1, NIH230scpC and NIH230slo exerted the LD50 value 3-10 fold lower than that of the non-invasive isolate 1566, but 10-30 fold higher than that of severe invasive isolates. Subcutaneous inoculation of NIH230scpC and NIH230slo yielded the local infected lesions with area comparable to those of 1566 and NIH230::csrS+ during the course of infection (Figure 7D). These results suggest that enhanced expression of ScpC and SLO in invasive GAS plays an important role in vivo virulence of GAS infection.\n" ], "offsets": [ [ 0, 720 ] ] } ]

[ { "id": "PMC2565068-02-Results-07_T1", "type": "Protein", "text": [ "scpC" ], "offsets": [ [ 0, 4 ] ], "normalized": [] }, { "id": "PMC2565068-02-Results-07_T2", "type": "Protein", "text": [ "slo" ], "offsets": [ [ 9, 12 ] ], "normalized": [] }, { "id": "PMC2565068-02-Results-07_T3", "type": "Protein", "text": [ "scpC" ], "offsets": [ [ 147, 151 ] ], "normalized": [] }, { "id": "PMC2565068-02-Results-07_T4", "type": "Protein", "text": [ "slo" ], "offsets": [ [ 159, 162 ] ], "normalized": [] }, { "id": "PMC2565068-02-Results-07_T5", "type": "Organism", "text": [ "mouse" ], "offsets": [ [ 190, 195 ] ], "normalized": [] }, { "id": "PMC2565068-02-Results-07_T6", "type": "Organism", "text": [ "NIH230scpC" ], "offsets": [ [ 224, 234 ] ], "normalized": [] }, { "id": "PMC2565068-02-Results-07_T7", "type": "Protein", "text": [ "scpC" ], "offsets": [ [ 230, 234 ] ], "normalized": [] }, { "id": "PMC2565068-02-Results-07_T8", "type": "Organism", "text": [ "NIH230slo" ], "offsets": [ [ 239, 248 ] ], "normalized": [] }, { "id": "PMC2565068-02-Results-07_T9", "type": "Protein", "text": [ "slo" ], "offsets": [ [ 245, 248 ] ], "normalized": [] }, { "id": "PMC2565068-02-Results-07_T10", "type": "Organism", "text": [ "non-invasive isolate 1566" ], "offsets": [ [ 305, 330 ] ], "normalized": [] }, { "id": "PMC2565068-02-Results-07_T11", "type": "Organism", "text": [ "NIH230scpC" ], "offsets": [ [ 421, 431 ] ], "normalized": [] }, { "id": "PMC2565068-02-Results-07_T12", "type": "Protein", "text": [ "scpC" ], "offsets": [ [ 427, 431 ] ], "normalized": [] }, { "id": "PMC2565068-02-Results-07_T13", "type": "Organism", "text": [ "NIH230slo" ], "offsets": [ [ 436, 445 ] ], "normalized": [] }, { "id": "PMC2565068-02-Results-07_T14", "type": "Protein", "text": [ "slo" ], "offsets": [ [ 442, 445 ] ], "normalized": [] }, { "id": "PMC2565068-02-Results-07_T15", "type": "Organism", "text": [ "1566" ], "offsets": [ [ 514, 518 ] ], "normalized": [] }, { "id": "PMC2565068-02-Results-07_T16", "type": "Organism", "text": [ "NIH230::csrS+" ], "offsets": [ [ 523, 536 ] ], "normalized": [] }, { "id": "PMC2565068-02-Results-07_T17", "type": "Protein", "text": [ "csrS+" ], "offsets": [ [ 531, 536 ] ], "normalized": [] }, { "id": "PMC2565068-02-Results-07_T18", "type": "Protein", "text": [ "ScpC" ], "offsets": [ [ 631, 635 ] ], "normalized": [] }, { "id": "PMC2565068-02-Results-07_T19", "type": "Protein", "text": [ "SLO" ], "offsets": [ [ 640, 643 ] ], "normalized": [] }, { "id": "PMC2565068-02-Results-07_T20", "type": "Organism", "text": [ "invasive GAS" ], "offsets": [ [ 647, 659 ] ], "normalized": [] }, { "id": "PMC2565068-02-Results-07_T21", "type": "Organism", "text": [ "GAS" ], "offsets": [ [ 705, 708 ] ], "normalized": [] } ]

[ { "id": "PMC2565068-02-Results-07_E1", "type": "Process", "trigger": { "text": [ "infections" ], "offsets": [ [ 70, 80 ] ] }, "arguments": [] }, { "id": "PMC2565068-02-Results-07_E2", "type": "Regulation", "trigger": { "text": [ "influence" ], "offsets": [ [ 107, 116 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC2565068-02-Results-07_E8" }, { "role": "Cause", "ref_id": "PMC2565068-02-Results-07_E4" } ] }, { "id": "PMC2565068-02-Results-07_E3", "type": "Regulation", "trigger": { "text": [ "influence" ], "offsets": [ [ 107, 116 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC2565068-02-Results-07_E8" }, { "role": "Cause", "ref_id": "PMC2565068-02-Results-07_E5" } ] }, { "id": "PMC2565068-02-Results-07_E4", "type": "Positive_regulation", "trigger": { "text": [ "enhanced" ], "offsets": [ [ 120, 128 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC2565068-02-Results-07_E6" } ] }, { "id": "PMC2565068-02-Results-07_E5", "type": "Positive_regulation", "trigger": { "text": [ "enhanced" ], "offsets": [ [ 120, 128 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC2565068-02-Results-07_E7" } ] }, { "id": "PMC2565068-02-Results-07_E6", "type": "Gene_expression", "trigger": { "text": [ "expression" ], "offsets": [ [ 129, 139 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC2565068-02-Results-07_T3" } ] }, { "id": "PMC2565068-02-Results-07_E7", "type": "Gene_expression", "trigger": { "text": [ "expression" ], "offsets": [ [ 129, 139 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC2565068-02-Results-07_T4" } ] }, { "id": "PMC2565068-02-Results-07_E8", "type": "Process", "trigger": { "text": [ "virulence" ], "offsets": [ [ 175, 184 ] ] }, "arguments": [] }, { "id": "PMC2565068-02-Results-07_E9", "type": "Process", "trigger": { "text": [ "infected" ], "offsets": [ [ 464, 472 ] ] }, "arguments": [ { "role": "Participant", "ref_id": "PMC2565068-02-Results-07_T13" } ] }, { "id": "PMC2565068-02-Results-07_E10", "type": "Process", "trigger": { "text": [ "infected" ], "offsets": [ [ 464, 472 ] ] }, "arguments": [ { "role": "Participant", "ref_id": "PMC2565068-02-Results-07_T15" } ] }, { "id": "PMC2565068-02-Results-07_E11", "type": "Process", "trigger": { "text": [ "infected" ], "offsets": [ [ 464, 472 ] ] }, "arguments": [ { "role": "Participant", "ref_id": "PMC2565068-02-Results-07_T16" } ] }, { "id": "PMC2565068-02-Results-07_E12", "type": "Process", "trigger": { "text": [ "infected" ], "offsets": [ [ 464, 472 ] ] }, "arguments": [ { "role": "Participant", "ref_id": "PMC2565068-02-Results-07_T11" } ] }, { "id": "PMC2565068-02-Results-07_E13", "type": "Process", "trigger": { "text": [ "infection" ], "offsets": [ [ 558, 567 ] ] }, "arguments": [] }, { "id": "PMC2565068-02-Results-07_E14", "type": "Positive_regulation", "trigger": { "text": [ "enhanced" ], "offsets": [ [ 608, 616 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC2565068-02-Results-07_E16" } ] }, { "id": "PMC2565068-02-Results-07_E15", "type": "Positive_regulation", "trigger": { "text": [ "enhanced" ], "offsets": [ [ 608, 616 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC2565068-02-Results-07_E17" } ] }, { "id": "PMC2565068-02-Results-07_E16", "type": "Gene_expression", "trigger": { "text": [ "expression" ], "offsets": [ [ 617, 627 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC2565068-02-Results-07_T18" } ] }, { "id": "PMC2565068-02-Results-07_E17", "type": "Gene_expression", "trigger": { "text": [ "expression" ], "offsets": [ [ 617, 627 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC2565068-02-Results-07_T19" } ] }, { "id": "PMC2565068-02-Results-07_E18", "type": "Regulation", "trigger": { "text": [ "important role" ], "offsets": [ [ 669, 683 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC2565068-02-Results-07_E20" }, { "role": "Cause", "ref_id": "PMC2565068-02-Results-07_E14" } ] }, { "id": "PMC2565068-02-Results-07_E19", "type": "Regulation", "trigger": { "text": [ "important role" ], "offsets": [ [ 669, 683 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC2565068-02-Results-07_E20" }, { "role": "Cause", "ref_id": "PMC2565068-02-Results-07_E15" } ] }, { "id": "PMC2565068-02-Results-07_E20", "type": "Process", "trigger": { "text": [ "virulence" ], "offsets": [ [ 692, 701 ] ] }, "arguments": [ { "role": "Participant", "ref_id": "PMC2565068-02-Results-07_T21" } ] }, { "id": "PMC2565068-02-Results-07_E21", "type": "Process", "trigger": { "text": [ "infection" ], "offsets": [ [ 709, 718 ] ] }, "arguments": [ { "role": "Participant", "ref_id": "PMC2565068-02-Results-07_T21" } ] } ]

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[ { "id": "PMC2816692-03-Discussion-02__text", "type": "abstract", "text": [ "Implications for type III secretion function \nThe interaction between SrcA and SsaN supports an emerging paradigm whereby secretion chaperones bring effector cargo to the T3SS through physical interaction with the hexameric ATPase at the base of the apparatus [14]. This was demonstrated for chaperone-ATPase components in the flagellar type III system [17] and in non-flagellar type III systems in E. coli [27] and the SPI-1 system in Salmonella [15]. Our work shows the first chaperone-ATPase interaction for a T3SS functioning from within an intracellular vacuolar compartment and supports this interaction as a more generalize feature of type III secretion function. In our experiments, we could induce the ATPase domain of SsaN to oligomerize in the presence of SrcA, but not in its absence, which was intriguing because the purified enzyme lacked a domain at the carboxyl terminus thought to be involved in oligomer stability, at least for E. coli EscN [14]. These data suggest that type III chaperones might have an as yet undefined role in assembly of the ATPase homohexamer that gives rise to efficient effector translocation. This will be an important area for further experimentation in this and other systems.\n" ], "offsets": [ [ 0, 1222 ] ] } ]

[ { "id": "PMC2816692-03-Discussion-02_T1", "type": "Protein", "text": [ "SrcA" ], "offsets": [ [ 70, 74 ] ], "normalized": [] }, { "id": "PMC2816692-03-Discussion-02_T2", "type": "Protein", "text": [ "SsaN" ], "offsets": [ [ 79, 83 ] ], "normalized": [] }, { "id": "PMC2816692-03-Discussion-02_T3", "type": "Organism", "text": [ "E. coli" ], "offsets": [ [ 399, 406 ] ], "normalized": [] }, { "id": "PMC2816692-03-Discussion-02_T4", "type": "Organism", "text": [ "Salmonella" ], "offsets": [ [ 436, 446 ] ], "normalized": [] }, { "id": "PMC2816692-03-Discussion-02_T5", "type": "Protein", "text": [ "SsaN" ], "offsets": [ [ 728, 732 ] ], "normalized": [] }, { "id": "PMC2816692-03-Discussion-02_T6", "type": "Protein", "text": [ "SrcA" ], "offsets": [ [ 767, 771 ] ], "normalized": [] }, { "id": "PMC2816692-03-Discussion-02_T7", "type": "Chemical", "text": [ "carboxyl" ], "offsets": [ [ 869, 877 ] ], "normalized": [] }, { "id": "PMC2816692-03-Discussion-02_T8", "type": "Organism", "text": [ "E. coli" ], "offsets": [ [ 946, 953 ] ], "normalized": [] }, { "id": "PMC2816692-03-Discussion-02_T9", "type": "Protein", "text": [ "EscN" ], "offsets": [ [ 954, 958 ] ], "normalized": [] }, { "id": "PMC2816692-03-Discussion-02_T12", "type": "Entity", "text": [ "ATPase domain" ], "offsets": [ [ 711, 724 ] ], "normalized": [] } ]

[ { "id": "PMC2816692-03-Discussion-02_E1", "type": "Binding", "trigger": { "text": [ "interaction" ], "offsets": [ [ 50, 61 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC2816692-03-Discussion-02_T1" }, { "role": "Theme", "ref_id": "PMC2816692-03-Discussion-02_T2" } ] }, { "id": "PMC2816692-03-Discussion-02_E2", "type": "Positive_regulation", "trigger": { "text": [ "induce" ], "offsets": [ [ 700, 706 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC2816692-03-Discussion-02_E3" } ] }, { "id": "PMC2816692-03-Discussion-02_E3", "type": "Binding", "trigger": { "text": [ "oligomerize" ], "offsets": [ [ 736, 747 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC2816692-03-Discussion-02_T5" }, { "role": "Site", "ref_id": "PMC2816692-03-Discussion-02_T12" } ] } ]

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[ { "id": "PMC2858072-02-Results_and_Discussion-02__text", "type": "abstract", "text": [ "Regulation of carbon and nitrogen metabolism \nOne of the remarkable findings observed in our microarray analysis was that several genes related with metabolism were also differentially expressed. These included twelve genes encoding ABC transport systems (matE, BAB1_0340; dctM, BAB1_0372; fhuD, BAB1_1366; yadH, BAB1_1368; oppA, BAB1_1601; oppC, BAB2_1051; oppD, BAB2_0817; potC, BAB1_ 1624; ssuB, BAB2_0917; ugpC, BAB2_1143; BAB2_0794; BAB2_1139), ten genes related with carbohydrate, amino or fatty acids metabolism and five related with nitrogen metabolism. Interestingly, all genes related with carbohydrate, amino or fatty acids metabolism were up-regulated in the bvrR mutant. These included the first enzyme in gluconeogenesis (pckA, phosphoenolpyruvate carboxykinase, BAB1_2091), four genes involved in TCA cycle and pyruvate metabolism (fumB, fumarate hydratase, BAB1_0977; lpdA, dihydrolipoamide dehydrogenase, BAB2_0712; pyruvate dehydrogenase, BAB2_0032; acetyl-CoA acetyltransferase, BAB2_0443), three genes involved in amino or fatty acid metabolism (aldehyde dehydrogenases, BAB2_1130, BAB2_1114; hydroxymethylglutaryl-CoA lyase, BAB1_0017), and two genes involve in benzoate degradation (pcaC, carboxymuconolactone decarboxylase, BAB2_0597; pcaI, coenzyme A transferase, BAB2_0604). In addition, the complete maltose transport system of Brucella, which consists in a large operon containing thirteen genes (BAB1_0236-0248) was also affected. Ten of these genes, including malK, malG, malF, malE and an iclR regulator, were down-regulated suggesting that the complete operon was negatively regulated in the bvrR mutant. Although it has been showed that the mutants in the BvrR/BvrS system have no obvious defects with regard to the ability to grow on standard media [4], our microarray results suggests that the BvrR/BvrS system controls elements directly involved in adjusting the Brucella metabolism to the nutrient shift expected to occur during the transit to the intracellular niche. To determine if the BvrR/BvrS system affects the metabolism, bvrR mutant and wild type strains were grown in synthetic minimal media. As show in Figure 3, growth of the bvrR mutant was significantly reduced in minimal media. Other genes differentially expressed in the bvrR mutant included denitrification genes. The nitrite reductase gene ( nirK, BAB2_0943) was down regulated and the nitric oxide and nitrous oxide reductases genes ( nor C, BAB2_0955; nosZ, BAB2_0928) were up regulated. On the other hand, two deaminases (glutaminase, BAB2_0863; guanine deaminase, BAB1_0383) were also affected. Since Brucella is an intracellular facultative pathogen, the bacteria could use these denitrification reactions to grow under low-oxygen condition by respiration of nitrate. Brucella may also take advantage of denitrification to cope with nitric oxide (NO) production in the macrophage during the innate response against infection. In fact, some of these denitrification genes have been related with the virulence in mice [10], [11]. Interestingly, our experiments to study the intracellular transcriptional level of BvrR/BvrS controlled genes (see below) showed that whereas norC was induced intracellularly, nirK and nosZ were less expressed. Taken together all these data support the proposal that one role of the BvrR/BvrS system could be neutralize the production of toxic reactive nitrogen molecules, as NO, by the host. These results also demonstrated a connection between carbon and nitrogen metabolism and BvrR/BvrS in Brucella. Our results also demonstrated that gene hpr-K (BAB1_2094), a member of the Brucella phosphotransferase system (PTS; BAB1_2097-2094) adjacent to the bvrR/bvrS, was down-regulated. As mentioned before, phosphoenolpyruvate carboxykinase gene (pckA, BAB1_2091) which is located upstream of the regulatory gene bvrR and divergently expressed was up-regulated. Comparative genome analysis revealed that in addition to the bvrR/bvrS genes, the genome structure around these genes is essentially the same for all the alpha-proteobacteria [5]. Genes encoding proteins related to the PTS, including a HPr Ser-kinase, an EIIA permease of the mannose family and a HPr homologue precede those of the two-component regulatory system. In most of these loci, upstream of the regulatory gene the pckA is divergently expressed (Figure 2). This gene catalyzes the reversible decarboxylation and phosphorylation of oxaloacetate to form phosphoenolpyruvate. In alpha-proteobacteria, it has been proposed that HPr might control the phosphorylation state of the transcription regulator [12]-[14]. In this regard, Letesson and col. [15] have suggested that in Brucella the PTS could interact with the BvrS sensor kinase, which in turn phosphorylates the response regulator. Then, the BvrR could control transcription of the pckA gene, which encodes an essential control enzyme of the gluconeogenesis and Krebs cycle. This hypothesis could explain the observation that mutants in the regulatory gene bvrR were inhibited in minimal media (see above). According to this, it has been demonstrated that in A. tumefaciens the pckA genes is indeed under the control of ChvG/ChvI [16] and that null mutants in S. meliloti exoS and chvI have pleiotropic growth defects and were unable to grow on several carbon sources [17]. A link between carbon and nitrogen metabolism, PTS and two-component regulatory systems have been proposed for some bacteria [18], and our microarray results strongly suggest that same relationship could be made for Brucella.\n" ], "offsets": [ [ 0, 5563 ] ] } ]

[ { "id": "PMC2858072-02-Results_and_Discussion-02_T1", "type": "Chemical", "text": [ "carbon" ], "offsets": [ [ 14, 20 ] ], "normalized": [] }, { "id": "PMC2858072-02-Results_and_Discussion-02_T2", "type": "Chemical", "text": [ "nitrogen" ], "offsets": [ [ 25, 33 ] ], "normalized": [] }, { "id": "PMC2858072-02-Results_and_Discussion-02_T3", "type": "Protein", "text": [ "matE" ], "offsets": [ [ 256, 260 ] ], "normalized": [] }, { "id": "PMC2858072-02-Results_and_Discussion-02_T4", "type": "Protein", "text": [ "BAB1_0340" ], "offsets": [ [ 262, 271 ] ], "normalized": [] }, { "id": "PMC2858072-02-Results_and_Discussion-02_T5", "type": "Protein", "text": [ "dctM" ], "offsets": [ [ 273, 277 ] ], "normalized": [] }, { "id": "PMC2858072-02-Results_and_Discussion-02_T6", "type": "Protein", "text": [ "BAB1_0372" ], "offsets": [ [ 279, 288 ] ], "normalized": [] }, { "id": "PMC2858072-02-Results_and_Discussion-02_T7", "type": "Protein", "text": [ "fhuD" ], "offsets": [ [ 290, 294 ] ], "normalized": [] }, { "id": "PMC2858072-02-Results_and_Discussion-02_T8", "type": "Protein", "text": [ "BAB1_1366" ], "offsets": [ [ 296, 305 ] ], "normalized": [] }, { "id": "PMC2858072-02-Results_and_Discussion-02_T9", "type": "Protein", "text": [ "yadH" ], "offsets": [ [ 307, 311 ] ], "normalized": [] }, { "id": "PMC2858072-02-Results_and_Discussion-02_T10", "type": "Protein", "text": [ "BAB1_1368" ], "offsets": [ [ 313, 322 ] ], "normalized": [] }, { "id": "PMC2858072-02-Results_and_Discussion-02_T11", "type": "Protein", "text": [ "oppA" ], "offsets": [ [ 324, 328 ] ], "normalized": [] }, { "id": "PMC2858072-02-Results_and_Discussion-02_T12", "type": "Protein", "text": [ "BAB1_1601" ], "offsets": [ [ 330, 339 ] ], "normalized": [] }, { "id": "PMC2858072-02-Results_and_Discussion-02_T13", "type": "Protein", "text": [ "oppC" ], "offsets": [ [ 341, 345 ] ], "normalized": [] }, { "id": "PMC2858072-02-Results_and_Discussion-02_T14", "type": "Protein", "text": [ "BAB2_1051" ], "offsets": [ [ 347, 356 ] ], "normalized": [] }, { "id": "PMC2858072-02-Results_and_Discussion-02_T15", "type": "Protein", "text": [ "oppD" ], "offsets": [ [ 358, 362 ] ], "normalized": [] }, { "id": "PMC2858072-02-Results_and_Discussion-02_T16", "type": "Protein", "text": [ "BAB2_0817" ], "offsets": [ [ 364, 373 ] ], "normalized": [] }, { "id": "PMC2858072-02-Results_and_Discussion-02_T17", "type": "Protein", "text": [ "potC" ], "offsets": [ [ 375, 379 ] ], "normalized": [] }, { "id": "PMC2858072-02-Results_and_Discussion-02_T18", "type": "Protein", "text": [ "BAB1_ 1624" ], "offsets": [ [ 381, 391 ] ], "normalized": [] }, { "id": "PMC2858072-02-Results_and_Discussion-02_T19", "type": "Protein", "text": [ "ssuB" ], "offsets": [ [ 393, 397 ] ], "normalized": [] }, { "id": "PMC2858072-02-Results_and_Discussion-02_T20", "type": "Protein", "text": [ "BAB2_0917" ], "offsets": [ [ 399, 408 ] ], "normalized": [] }, { "id": "PMC2858072-02-Results_and_Discussion-02_T21", "type": "Protein", "text": [ "ugpC" ], "offsets": [ [ 410, 414 ] ], "normalized": [] }, { "id": "PMC2858072-02-Results_and_Discussion-02_T22", "type": "Protein", "text": [ "BAB2_1143" ], "offsets": [ [ 416, 425 ] ], "normalized": [] }, { "id": "PMC2858072-02-Results_and_Discussion-02_T23", "type": "Protein", "text": [ "BAB2_0794" ], "offsets": [ [ 427, 436 ] ], "normalized": [] }, { "id": "PMC2858072-02-Results_and_Discussion-02_T24", "type": "Protein", "text": [ "BAB2_1139" ], "offsets": [ [ 438, 447 ] ], "normalized": [] }, { "id": "PMC2858072-02-Results_and_Discussion-02_T25", "type": "Organism", "text": [ "bvrR mutant" ], "offsets": [ [ 671, 682 ] ], "normalized": [] }, { "id": "PMC2858072-02-Results_and_Discussion-02_T26", "type": "Protein", "text": [ "bvrR" ], "offsets": [ [ 671, 675 ] ], "normalized": [] }, { "id": "PMC2858072-02-Results_and_Discussion-02_T27", "type": "Protein", "text": [ "pckA" ], "offsets": [ [ 736, 740 ] ], "normalized": [] }, { "id": "PMC2858072-02-Results_and_Discussion-02_T28", "type": "Chemical", "text": [ "phosphoenolpyruvate" ], "offsets": [ [ 742, 761 ] ], "normalized": [] }, { "id": "PMC2858072-02-Results_and_Discussion-02_T29", "type": "Protein", "text": [ "BAB1_2091" ], "offsets": [ [ 777, 786 ] ], "normalized": [] }, { "id": "PMC2858072-02-Results_and_Discussion-02_T30", "type": "Chemical", "text": [ "pyruvate" ], "offsets": [ [ 826, 834 ] ], "normalized": [] }, { "id": "PMC2858072-02-Results_and_Discussion-02_T31", "type": "Protein", "text": [ "fumB" ], "offsets": [ [ 847, 851 ] ], "normalized": [] }, { "id": "PMC2858072-02-Results_and_Discussion-02_T32", "type": "Chemical", "text": [ "fumarate" ], "offsets": [ [ 853, 861 ] ], "normalized": [] }, { "id": "PMC2858072-02-Results_and_Discussion-02_T33", "type": "Protein", "text": [ "BAB1_0977" ], "offsets": [ [ 873, 882 ] ], "normalized": [] }, { "id": "PMC2858072-02-Results_and_Discussion-02_T34", "type": "Protein", "text": [ "lpdA" ], "offsets": [ [ 884, 888 ] ], "normalized": [] }, { "id": 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[]

[ { "id": "PMC2639726-02-Results-04__text", "type": "abstract", "text": [ "Validation of SPI-2 regulation \nSPI-2 encodes a type III secretion system and secreted effectors required for systemic mouse infection [8],[9]. To assess the effects of growth conditions on expression of the SPI-2 secretion apparatus we constructed a lacZ transcriptional fusion to ssaG, a component of the secretion apparatus, and tested expression in each mutant background under each of the four growth conditions. At the same time we determined transcript levels via quantitative real-time PCR (qRT-PCR), using transcripts from rpoD and gyrB as controls [51]. We observed that the results determined by these two methods matched closely (Figure S2) and that the level of transcription of ssaG was highest when Salmonella was grown in minimal acidic media. In agreement with the microarrays, the effect of these regulators on ssaG expression was minimal if the bacteria were grown in rich media (LB broth). Because the type III secretion system and associated virulence factors encoded within SPI-2 were most highly expressed in acidic minimal media we therefore focused on growth in this media and used qRT-PCR to measure transcript levels. To validate the transcriptional profiles we prepared RNA from mutants and parent bacteria grown in acidic minimal medium and used as template for qRT-PCR. Six promoters have been identified for the type III secretion system encoded within SPI-2 (see Figure 4; [52]). We monitored transcription of seven genes within SPI-2, covering each operon at least once, and used gyrB transcript as an internal control. We observed a decrease in transcription of all 7 genes in 11 of the 14 mutants. The three exceptions were spvR, fruR, and rpoS. Strains containing mutations in phoP/phoQ, ssrA/ssrB, slyA, and ompR/envZ showed at least 100-fold decreases in transcription of all SPI-2 genes (Figure 4). Mutations of ihf (himD) and csrA showed an intermediate level of 8-16-fold decreased transcription whereas hnr, rpoE, smpB, crp and hfq showed a modest decrease of 2-8-fold. The results of this analysis are generally concordant with the microarray results although the dynamic range was larger for qRT-PCR than for the microarrays as has been observed before [53]. Note that rpoE and hfq mutants showed a dramatic reduction in macrophage survival, but little difference in transcription of SPI-2 genes during growth in AMM. It has recently been reported that the translational regulator Hfq, regulates translation of RpoE explaining in part why the two mutations behave similarly [54]. Furthermore, Hfq regulates translation of more than 20% of all Salmonella proteins explaining why a mutation in this gene has such a dramatic phenotype ([54]; Charles Ansong, Hyunjin Yoon, Steffen Porwollik, Heather Mottaz-Brewer, Briana Ogata-Petritis, Navdeep Jaitly, Joshua N. Adkins, Michael McClelland, Fred Heffron, and Richard D. Smith; Global systems-level analysis of small RNA-mediated translational regulation: Implications for virulence and global protein translation; Submitted).\n" ], "offsets": [ [ 0, 3017 ] ] } ]

[ { "id": "PMC2639726-02-Results-04_T1", "type": "Organism", "text": [ "mouse" ], "offsets": [ [ 119, 124 ] ], "normalized": [] }, { "id": "PMC2639726-02-Results-04_T2", "type": "Protein", "text": [ "lacZ" ], "offsets": [ [ 251, 255 ] ], "normalized": [] }, { "id": "PMC2639726-02-Results-04_T3", "type": "Protein", "text": [ "ssaG" ], "offsets": [ [ 282, 286 ] ], "normalized": [] }, { "id": "PMC2639726-02-Results-04_T4", "type": "Protein", "text": [ "rpoD" ], "offsets": [ [ 532, 536 ] ], "normalized": [] }, { "id": "PMC2639726-02-Results-04_T5", "type": "Protein", "text": [ "gyrB" ], "offsets": [ [ 541, 545 ] ], "normalized": [] }, { "id": "PMC2639726-02-Results-04_T6", "type": "Protein", "text": [ "ssaG" ], "offsets": [ [ 692, 696 ] ], "normalized": [] }, { "id": "PMC2639726-02-Results-04_T7", "type": "Organism", "text": [ "Salmonella" ], "offsets": [ [ 714, 724 ] ], "normalized": [] }, { "id": "PMC2639726-02-Results-04_T8", "type": "Protein", "text": [ "ssaG" ], "offsets": [ [ 829, 833 ] ], "normalized": [] }, { "id": "PMC2639726-02-Results-04_T9", "type": "Protein", "text": [ "gyrB" ], "offsets": [ [ 1513, 1517 ] ], "normalized": [] }, { "id": "PMC2639726-02-Results-04_T10", "type": "Protein", "text": [ "spvR" ], "offsets": [ [ 1659, 1663 ] ], "normalized": [] }, { "id": "PMC2639726-02-Results-04_T11", "type": "Protein", "text": [ "fruR" ], "offsets": [ [ 1665, 1669 ] ], "normalized": [] }, { "id": "PMC2639726-02-Results-04_T12", "type": "Protein", "text": [ "rpoS" ], "offsets": [ [ 1675, 1679 ] ], "normalized": [] }, { "id": "PMC2639726-02-Results-04_T13", "type": "Two-component-system", "text": [ "phoP/phoQ" ], "offsets": [ [ 1713, 1722 ] ], "normalized": [] }, { "id": "PMC2639726-02-Results-04_T14", "type": "Protein", "text": [ "phoP" ], "offsets": [ [ 1713, 1717 ] ], "normalized": [] }, { "id": "PMC2639726-02-Results-04_T15", "type": "Protein", "text": [ "phoQ" ], "offsets": [ [ 1718, 1722 ] ], "normalized": [] }, { "id": "PMC2639726-02-Results-04_T16", "type": "Two-component-system", "text": [ "ssrA/ssrB" ], "offsets": [ [ 1724, 1733 ] ], "normalized": [] }, { "id": "PMC2639726-02-Results-04_T17", "type": "Protein", "text": [ "ssrA" ], "offsets": [ [ 1724, 1728 ] ], "normalized": [] }, { "id": "PMC2639726-02-Results-04_T18", "type": "Protein", "text": [ "ssrB" ], "offsets": [ [ 1729, 1733 ] ], "normalized": [] }, { "id": "PMC2639726-02-Results-04_T19", "type": "Protein", "text": [ "slyA" ], "offsets": [ [ 1735, 1739 ] ], "normalized": [] }, { "id": "PMC2639726-02-Results-04_T20", "type": "Two-component-system", "text": [ "ompR/envZ" ], "offsets": [ [ 1745, 1754 ] ], "normalized": [] }, { "id": "PMC2639726-02-Results-04_T21", "type": "Protein", "text": [ "ompR" ], "offsets": [ [ 1745, 1749 ] ], "normalized": [] }, { "id": "PMC2639726-02-Results-04_T22", "type": "Protein", "text": [ "envZ" ], "offsets": [ [ 1750, 1754 ] ], "normalized": [] }, { "id": "PMC2639726-02-Results-04_T23", "type": "Protein", "text": [ "ihf" ], "offsets": [ [ 1851, 1854 ] ], "normalized": [] }, { "id": "PMC2639726-02-Results-04_T24", "type": "Protein", "text": [ "himD" ], "offsets": [ [ 1856, 1860 ] ], "normalized": [] }, { "id": "PMC2639726-02-Results-04_T25", "type": "Protein", "text": [ "csrA" ], "offsets": [ [ 1866, 1870 ] ], "normalized": [] }, { "id": "PMC2639726-02-Results-04_T26", "type": "Protein", "text": [ "hnr" ], "offsets": [ [ 1945, 1948 ] ], "normalized": [] }, { "id": "PMC2639726-02-Results-04_T27", "type": "Protein", "text": [ "rpoE" ], "offsets": [ [ 1950, 1954 ] ], "normalized": [] }, { "id": "PMC2639726-02-Results-04_T28", "type": "Protein", "text": [ "smpB" ], "offsets": [ [ 1956, 1960 ] ], "normalized": [] }, { "id": "PMC2639726-02-Results-04_T29", "type": "Protein", "text": [ "crp" ], "offsets": [ [ 1962, 1965 ] ], "normalized": [] }, { "id": "PMC2639726-02-Results-04_T30", "type": "Protein", "text": [ "hfq" ], "offsets": [ [ 1970, 1973 ] ], "normalized": [] }, { "id": "PMC2639726-02-Results-04_T31", "type": "Protein", "text": [ "rpoE" ], "offsets": [ [ 2213, 2217 ] ], "normalized": [] }, { "id": "PMC2639726-02-Results-04_T32", "type": "Organism", "text": [ "rpoE" ], "offsets": [ [ 2213, 2217 ] ], "normalized": [] }, { "id": "PMC2639726-02-Results-04_T33", "type": "Organism", "text": [ "hfq mutants" ], "offsets": [ [ 2222, 2233 ] ], "normalized": [] }, { "id": "PMC2639726-02-Results-04_T34", "type": "Protein", "text": [ "hfq" ], "offsets": [ [ 2222, 2225 ] ], "normalized": [] }, { "id": "PMC2639726-02-Results-04_T35", "type": "Protein", "text": [ "Hfq" ], "offsets": [ [ 2425, 2428 ] ], "normalized": [] }, { "id": "PMC2639726-02-Results-04_T36", "type": "Protein", "text": [ "RpoE" ], "offsets": [ [ 2455, 2459 ] ], "normalized": [] }, { "id": "PMC2639726-02-Results-04_T37", "type": "Protein", "text": [ "Hfq" ], "offsets": [ [ 2537, 2540 ] ], "normalized": [] }, { "id": "PMC2639726-02-Results-04_T38", "type": "Organism", "text": [ "Salmonella" ], "offsets": [ [ 2587, 2597 ] ], "normalized": [] } ]

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] }, "arguments": [ { "role": "Theme", "ref_id": "PMC2639726-02-Results-04_T6" } ] }, { "id": "PMC2639726-02-Results-04_E6", "type": "Regulation", "trigger": { "text": [ "effect" ], "offsets": [ [ 799, 805 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC2639726-02-Results-04_E7" } ] }, { "id": "PMC2639726-02-Results-04_E7", "type": "Gene_expression", "trigger": { "text": [ "expression" ], "offsets": [ [ 834, 844 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC2639726-02-Results-04_T8" } ] }, { "id": "PMC2639726-02-Results-04_E8", "type": "Process", "trigger": { "text": [ "virulence" ], "offsets": [ [ 963, 972 ] ] }, "arguments": [] }, { "id": "PMC2639726-02-Results-04_E9", "type": "Transcription", "trigger": { "text": [ "transcript" ], "offsets": [ [ 1518, 1528 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC2639726-02-Results-04_T9" } ] }, { "id": "PMC2639726-02-Results-04_E10", "type": "Negative_regulation", "trigger": { "text": [ "decreased" ], "offsets": [ [ 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[ 1990, 1998 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC2639726-02-Results-04_E13" } ] }, { "id": "PMC2639726-02-Results-04_E20", "type": "Negative_regulation", "trigger": { "text": [ "decrease" ], "offsets": [ [ 1990, 1998 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC2639726-02-Results-04_E14" } ] }, { "id": "PMC2639726-02-Results-04_E21", "type": "Negative_regulation", "trigger": { "text": [ "decrease" ], "offsets": [ [ 1990, 1998 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC2639726-02-Results-04_E15" } ] }, { "id": "PMC2639726-02-Results-04_E22", "type": "Negative_regulation", "trigger": { "text": [ "decrease" ], "offsets": [ [ 1990, 1998 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC2639726-02-Results-04_E16" } ] }, { "id": "PMC2639726-02-Results-04_E23", "type": "Negative_regulation", "trigger": { "text": [ "decrease" ], "offsets": [ [ 1990, 1998 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC2639726-02-Results-04_E17" } ] }, { 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[ { "id": "PMC2816692-02-Results-05__text", "type": "abstract", "text": [ "SrcA binds effector cargo destined for the SPI-2 T3SS \nSince structural and biochemical data unambiguously defined SrcA as a T3SS-associated chaperone, we used two experimental approaches to identify SrcA cargo(s). First, we used stable isotope labeling of amino acids in cell culture (SILAC) [28] in conjunction with quantitative mass spectrometry-based proteomics to identify cargo immunoprecipitated with SrcA from Salmonella. For this series of experiments we constructed a mutant in which the srcA gene was replaced on the chromosome with srcA-FLAG to enable immunoprecipitation from cell lysates. Lysates prepared from wild type cells grown in 2H4-Lys and 13C6-Arg containing SILAC medium (heavy) and srcA mutant cells grown in medium containing natural amino acids of Lys and Arg (light) were mixed and subjected to an immunoprecipitation procedure with an anti-FLAG antibody followed by quantitative mass spectrometry. Peptides originating from wild type cells contained heavy atom-substituted lysine and arginine such that putative SrcA cargo proteins would generate low heavy:light SILAC peptide ratios from the complex mixtures (Fig. 5A). In these experiments the T3SS effector protein SseL was identified by quantitative SILAC mass spectrometry as a specific SrcA cargo protein (Fig. 5B). SseL was immunoprecipitated specifically along with SrcA-FLAG with a SILAC ratio of 0.08, whereas additional abundant proteins displayed SILAC ratios closer to approximately1 (OmpF is shown, Fig. 5B) (mean SILAC ratio of all other peptides identified was 0.93 (Dataset S1). Secondly, to verify the mass spectrometry data and to identify other possible effector cargo, we examined the secretion profiles of wild type cells and an srcA mutant that each expressed HA-tagged effector genes, the products of which are secreted by the SPI-2-encoded T3SS. Using this approach SseL-HA and PipB2-HA were depleted from the secreted protein fraction of srcA mutant cells (Fig. 5C) but reached similar levels in the bacterial cytoplasm (Fig. 5D). As expected from data with the complemented mutant in vivo, expression of srcA in trans restored effector secretion in the srcA mutant (data not shown).\n" ], "offsets": [ [ 0, 2189 ] ] } ]

[ { "id": "PMC2816692-02-Results-05_T1", "type": "Protein", "text": [ "SrcA" ], "offsets": [ [ 0, 4 ] ], "normalized": [] }, { "id": "PMC2816692-02-Results-05_T2", "type": "Protein", "text": [ "SrcA" ], "offsets": [ [ 115, 119 ] ], "normalized": [] }, { "id": "PMC2816692-02-Results-05_T3", "type": "Protein", "text": [ "SrcA" ], "offsets": [ [ 200, 204 ] ], "normalized": [] }, { "id": "PMC2816692-02-Results-05_T4", "type": "Protein", "text": [ "SrcA" ], "offsets": [ [ 408, 412 ] ], "normalized": [] }, { "id": "PMC2816692-02-Results-05_T5", "type": "Organism", "text": [ "Salmonella" ], "offsets": [ [ 418, 428 ] ], "normalized": [] }, { "id": "PMC2816692-02-Results-05_T6", "type": "Protein", "text": [ "srcA" ], "offsets": [ [ 498, 502 ] ], "normalized": [] }, { "id": "PMC2816692-02-Results-05_T7", "type": "Protein", "text": [ "srcA" ], "offsets": [ [ 544, 548 ] ], "normalized": [] }, { "id": "PMC2816692-02-Results-05_T8", "type": "Organism", "text": [ "srcA mutant" ], "offsets": [ [ 707, 718 ] ], "normalized": [] }, { "id": "PMC2816692-02-Results-05_T9", "type": "Protein", "text": [ "srcA" ], "offsets": [ [ 707, 711 ] ], "normalized": [] }, { "id": "PMC2816692-02-Results-05_T10", "type": "Protein", "text": [ "SrcA" ], "offsets": [ [ 1041, 1045 ] ], "normalized": [] }, { "id": "PMC2816692-02-Results-05_T11", "type": "Protein", "text": [ "SseL" ], "offsets": [ [ 1197, 1201 ] ], "normalized": [] }, { "id": "PMC2816692-02-Results-05_T12", "type": "Protein", "text": [ "SrcA" ], "offsets": [ [ 1271, 1275 ] ], "normalized": [] }, { "id": "PMC2816692-02-Results-05_T13", "type": "Protein", "text": [ "SseL" ], "offsets": [ [ 1301, 1305 ] ], "normalized": [] }, { "id": "PMC2816692-02-Results-05_T14", "type": "Protein", "text": [ "SrcA" ], "offsets": [ [ 1353, 1357 ] ], "normalized": [] }, { "id": "PMC2816692-02-Results-05_T15", "type": "Protein", "text": [ "OmpF" ], "offsets": [ [ 1477, 1481 ] ], "normalized": [] }, { "id": "PMC2816692-02-Results-05_T16", "type": "Organism", "text": [ "srcA mutant" ], "offsets": [ [ 1730, 1741 ] ], "normalized": [] }, { "id": "PMC2816692-02-Results-05_T17", "type": "Protein", "text": [ "srcA" ], "offsets": [ [ 1730, 1734 ] ], "normalized": [] }, { "id": "PMC2816692-02-Results-05_T18", "type": "Protein", "text": [ "SseL" ], "offsets": [ [ 1870, 1874 ] ], "normalized": [] }, { "id": "PMC2816692-02-Results-05_T19", "type": "Protein", "text": [ "PipB2" ], "offsets": [ [ 1882, 1887 ] ], "normalized": [] }, { "id": "PMC2816692-02-Results-05_T20", "type": "Organism", "text": [ "srcA mutant" ], "offsets": [ [ 1943, 1954 ] ], "normalized": [] }, { "id": "PMC2816692-02-Results-05_T21", "type": "Protein", "text": [ "srcA" ], "offsets": [ [ 1943, 1947 ] ], "normalized": [] }, { "id": "PMC2816692-02-Results-05_T22", "type": "Protein", "text": [ "srcA" ], "offsets": [ [ 2110, 2114 ] ], "normalized": [] }, { "id": "PMC2816692-02-Results-05_T23", "type": "Organism", "text": [ "srcA mutant" ], "offsets": [ [ 2159, 2170 ] ], "normalized": [] }, { "id": "PMC2816692-02-Results-05_T24", "type": "Protein", "text": [ "srcA" ], "offsets": [ [ 2159, 2163 ] ], "normalized": [] } ]

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[]

[ { "id": "PMC1913099-02-Results-Discussion-06__text", "type": "abstract", "text": [ "Differential Expression of Genes from Diverse Functional Categories \nWe identified a number of genes encoding proteins involved in housekeeping processes (such as carbohydrate and coenzyme metabolism) that were differentially expressed, indicating a shift in metabolic processes due to host cell adherence (Tables 1 and 2). For example, genes encoding proteins involved in folate biosynthesis [40] were upregulated, suggesting that certain cofactors that may be necessary during adherence were unavailable. Also upregulated were genes encoding subunits of the F0F1 ATPase [41] (discussed in more detail later), which may indicate an acid stress response to maintain cytoplasmic pH or a need to generate ATP in response to increased energy requirements. We also identified the adherence-mediated upregulation of four transcriptional regulators (Table 1), suggestive of an adaptive response to host cell contact that is dynamic and complex. For example, RopB (encoded by spy2042), a member of the Rgg family of response regulators, interacts with a number of regulatory networks throughout the streptococcal genome (e.g., mga, csrRS, sagA, and fasBCA), affecting the transcription of numerous proteins, virulence factors, and two-component regulatory systems [42,43]. Although the delineation of genes influenced by RopB (or any identified transcriptional regulator) is beyond the scope of this study, our initial analysis did identify the upregulation of a two-component regulatory system, encoded by spy1236-1237. The functions of these particular loci are not yet known, and their adherence-mediated upregulation represents new targets in the study of regulators that function during host cell contact.\n" ], "offsets": [ [ 0, 1704 ] ] } ]

[ { "id": "PMC1913099-02-Results-Discussion-06_T1", "type": "Chemical", "text": [ "folate" ], "offsets": [ [ 373, 379 ] ], "normalized": [] }, { "id": "PMC1913099-02-Results-Discussion-06_T2", "type": "Chemical", "text": [ "ATP" ], "offsets": [ [ 703, 706 ] ], "normalized": [] }, { "id": "PMC1913099-02-Results-Discussion-06_T3", "type": "Protein", "text": [ "RopB" ], "offsets": [ [ 952, 956 ] ], "normalized": [] }, { "id": "PMC1913099-02-Results-Discussion-06_T4", "type": "Protein", "text": [ "spy2042" ], "offsets": [ [ 969, 976 ] ], "normalized": [] }, { "id": "PMC1913099-02-Results-Discussion-06_T5", "type": "Protein", "text": [ "Rgg" ], "offsets": [ [ 995, 998 ] ], "normalized": [] }, { "id": "PMC1913099-02-Results-Discussion-06_T6", "type": "Protein", "text": [ "mga" ], "offsets": [ [ 1120, 1123 ] ], "normalized": [] }, { "id": "PMC1913099-02-Results-Discussion-06_T7", "type": "Two-component-system", "text": [ "csrRS" ], "offsets": [ [ 1125, 1130 ] ], "normalized": [] }, { "id": "PMC1913099-02-Results-Discussion-06_T8", "type": "Protein", "text": [ "csrR" ], "offsets": [ [ 1125, 1129 ] ], "normalized": [] }, { "id": "PMC1913099-02-Results-Discussion-06_T9", "type": "Protein", "text": [ "S" ], "offsets": [ [ 1129, 1130 ] ], "normalized": [] }, { "id": "PMC1913099-02-Results-Discussion-06_T10", "type": "Protein", "text": [ "sagA" ], "offsets": [ [ 1132, 1136 ] ], "normalized": [] }, { "id": "PMC1913099-02-Results-Discussion-06_T11", "type": "Regulon-operon", "text": [ "fasBCA" ], "offsets": [ [ 1142, 1148 ] ], "normalized": [] }, { "id": "PMC1913099-02-Results-Discussion-06_T12", "type": "Protein", "text": [ "fasB" ], "offsets": [ [ 1142, 1146 ] ], "normalized": [] }, { "id": "PMC1913099-02-Results-Discussion-06_T13", "type": "Protein", "text": [ "C" ], "offsets": [ [ 1146, 1147 ] ], "normalized": [] }, { "id": "PMC1913099-02-Results-Discussion-06_T14", "type": "Protein", "text": [ "A" ], "offsets": [ [ 1147, 1148 ] ], "normalized": [] }, { "id": "PMC1913099-02-Results-Discussion-06_T15", "type": "Protein", "text": [ "RopB" ], "offsets": [ [ 1314, 1318 ] ], "normalized": [] }, { "id": "PMC1913099-02-Results-Discussion-06_T16", "type": "Two-component-system", "text": [ "spy1236-1237" ], "offsets": [ [ 1500, 1512 ] ], "normalized": [] }, { "id": "PMC1913099-02-Results-Discussion-06_T17", "type": "Protein", "text": [ "spy1236" ], "offsets": [ [ 1500, 1507 ] ], "normalized": [] }, { "id": "PMC1913099-02-Results-Discussion-06_T18", "type": "Protein", "text": [ "1237" ], "offsets": [ [ 1508, 1512 ] ], "normalized": [] } ]

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[ { "id": "PMC1913099-02-Results-Discussion-06_1", "entity_ids": [ "PMC1913099-02-Results-Discussion-06_T4", "PMC1913099-02-Results-Discussion-06_T3" ] } ]

[]

[ { "id": "PMC2682197-02-Results-04__text", "type": "abstract", "text": [ "M. tuberculosis Rv2623 is a nucleotide-binding protein \nWe began a biochemical characterization of Rv2623 in order to gain insight into the relationship between the molecular structure/function of this USP and it's growth-regulatory properties. M. tuberculosis Rv2623 was expressed in E. coli and purified to homogeneity for biochemical studies. SDS-PAGE analysis of affinity-purified His6-Rv2623 revealed a single band that approximates the predicted molecular mass of approximately31.6 kDa, which was identified by immunoblotting as Rv2623 (Figure S3). Gel filtration analysis of native His6-Rv2623 revealed that the purified protein exists primarily as a single species with an apparent molecular mass of 61+/-1 kDa; suggesting that Rv2623 is a dimer under native conditions (Figure S3), an observation that was later confirmed using nano electrospray ionization (nano ESI) mass spectrometry (data not shown). The nucleotide-binding capacity of a subset of USPs was discovered following the observation that MJ0577, a single-domain USP from Methanococcus jannaschii, co-purifies and co-crystallizes with ATP [26]. On the basis of structures of ATP-binding and non-ATP-binding USPs, a G-2X-G-9X-G(S/T) motif was suggested to be essential for the binding of ATP [27]. The presence of this motif in each of the two tandem USP domains of Rv2623 [7] raised the possibility that this protein possesses ATP binding activity. An HPLC-based examination of supernatants from boiled samples of His6-Rv2623 demonstrated that His6-Rv2623 co-purifies with both ATP and ADP (Figure 5). Analysis of E. coli-expressed Rv2623 using nano ESI mass spectrometry also demonstrated that an ATP-saturated form of dimeric Rv2623 (composed of 2 bound ATP molecules per monomer) constitutes at least half of the purified sample (data not shown). Measurement of the binding stoichiometry, which comprised HPLC-based quantification of adenine nucleotides from the boiled supernatant and spectral analysis of heat denatured Rv2623 following reconstitution in 6 M guanidine-HCl, yields 1.4+/-0.2 nucleotide equivalents/monomer with an overall content of 86+/-4% ATP (14+/-4% ADP). Thus, Rv2623 binds endogenous adenine nucleotides in E. coli, and the association is sufficiently tight that nearly 75% of the nucleotide binding sites are occupied upon purification. Indeed, nucleotide did not completely dissociate from the protein following an extensive, two-week dialysis with multiple changes against nucleotide-free buffer (approximately 0.3 nucleotide equivalents per monomer remain). It is conceivable that the presence of ADP is the consequence of an Rv2623-associated ATP activity and this putative ATPase function is currently under investigation.\n" ], "offsets": [ [ 0, 2728 ] ] } ]

[ { "id": "PMC2682197-02-Results-04_T1", "type": "Organism", "text": [ "M. tuberculosis" ], "offsets": [ [ 0, 15 ] ], "normalized": [] }, { "id": "PMC2682197-02-Results-04_T2", "type": "Protein", "text": [ "Rv2623" ], "offsets": [ [ 16, 22 ] ], "normalized": [] }, { "id": "PMC2682197-02-Results-04_T3", "type": "Protein", "text": [ "Rv2623" ], "offsets": [ [ 99, 105 ] ], "normalized": [] }, { "id": "PMC2682197-02-Results-04_T4", "type": "Organism", "text": [ "M. tuberculosis" ], "offsets": [ [ 245, 260 ] ], "normalized": [] }, { "id": "PMC2682197-02-Results-04_T5", "type": "Protein", "text": [ "Rv2623" ], "offsets": [ [ 261, 267 ] ], "normalized": [] }, { "id": "PMC2682197-02-Results-04_T6", "type": "Organism", "text": [ "E. coli" ], "offsets": [ [ 285, 292 ] ], "normalized": [] }, { "id": "PMC2682197-02-Results-04_T7", "type": "Protein", "text": [ "Rv2623" ], "offsets": [ [ 390, 396 ] ], "normalized": [] }, { "id": "PMC2682197-02-Results-04_T8", "type": "Protein", "text": [ "Rv2623" ], "offsets": [ [ 535, 541 ] ], "normalized": [] }, { "id": "PMC2682197-02-Results-04_T9", "type": "Protein", "text": [ "Rv2623" ], "offsets": [ [ 594, 600 ] ], "normalized": [] }, { "id": "PMC2682197-02-Results-04_T10", "type": "Protein", "text": [ "Rv2623" ], "offsets": [ [ 736, 742 ] ], "normalized": [] }, { "id": "PMC2682197-02-Results-04_T11", "type": "Protein", "text": [ "MJ0577" ], "offsets": [ [ 1011, 1017 ] ], "normalized": [] }, { "id": "PMC2682197-02-Results-04_T12", "type": "Organism", "text": [ "Methanococcus jannaschii" ], "offsets": [ [ 1044, 1068 ] ], "normalized": [] }, { "id": "PMC2682197-02-Results-04_T13", "type": "Chemical", "text": [ "ATP" ], "offsets": [ [ 1107, 1110 ] ], "normalized": [] }, { "id": "PMC2682197-02-Results-04_T14", "type": "Chemical", "text": [ "ATP" ], "offsets": [ [ 1147, 1150 ] ], "normalized": [] }, { "id": "PMC2682197-02-Results-04_T15", "type": "Chemical", "text": [ "ATP" ], "offsets": [ [ 1167, 1170 ] ], "normalized": [] }, { "id": "PMC2682197-02-Results-04_T16", "type": "Chemical", "text": [ "ATP" ], "offsets": [ [ 1259, 1262 ] ], "normalized": [] }, { "id": "PMC2682197-02-Results-04_T17", "type": "Protein", "text": [ "Rv2623" ], "offsets": [ [ 1337, 1343 ] ], "normalized": [] }, { "id": "PMC2682197-02-Results-04_T18", "type": "Chemical", "text": [ "ATP" ], "offsets": [ [ 1399, 1402 ] ], "normalized": [] }, { "id": "PMC2682197-02-Results-04_T19", "type": "Protein", "text": [ "Rv2623" ], "offsets": [ [ 1491, 1497 ] ], "normalized": [] }, { "id": "PMC2682197-02-Results-04_T20", "type": "Protein", "text": [ "Rv2623" ], "offsets": [ [ 1521, 1527 ] ], "normalized": [] }, { "id": "PMC2682197-02-Results-04_T21", "type": "Chemical", "text": [ "ATP" ], "offsets": [ [ 1550, 1553 ] ], "normalized": [] }, { "id": "PMC2682197-02-Results-04_T22", "type": "Chemical", "text": [ "ADP" ], "offsets": [ [ 1558, 1561 ] ], "normalized": [] }, { "id": "PMC2682197-02-Results-04_T23", "type": "Organism", "text": [ "E. coli" ], "offsets": [ [ 1586, 1593 ] ], "normalized": [] }, { "id": "PMC2682197-02-Results-04_T24", "type": "Protein", "text": [ "Rv2623" ], "offsets": [ [ 1604, 1610 ] ], "normalized": [] }, { "id": "PMC2682197-02-Results-04_T25", "type": "Chemical", "text": [ "ATP" ], "offsets": [ [ 1670, 1673 ] ], "normalized": [] }, { "id": "PMC2682197-02-Results-04_T26", "type": "Protein", "text": [ "Rv2623" ], "offsets": [ [ 1700, 1706 ] ], "normalized": [] }, { "id": "PMC2682197-02-Results-04_T27", "type": "Chemical", "text": [ "ATP" ], "offsets": [ [ 1728, 1731 ] ], "normalized": [] }, { "id": "PMC2682197-02-Results-04_T28", "type": "Protein", "text": [ "Rv2623" ], "offsets": [ [ 1997, 2003 ] ], "normalized": [] }, { "id": "PMC2682197-02-Results-04_T29", "type": "Chemical", "text": [ "guanidine-HCl" ], "offsets": [ [ 2036, 2049 ] ], "normalized": [] }, { "id": "PMC2682197-02-Results-04_T30", "type": "Chemical", "text": [ "ATP" ], "offsets": [ [ 2134, 2137 ] ], "normalized": [] }, { "id": "PMC2682197-02-Results-04_T31", "type": "Protein", "text": [ "Rv2623" ], "offsets": [ [ 2159, 2165 ] ], "normalized": [] }, { "id": "PMC2682197-02-Results-04_T32", "type": "Organism", "text": [ "E. coli" ], "offsets": [ [ 2206, 2213 ] ], "normalized": [] }, { "id": "PMC2682197-02-Results-04_T33", "type": "Chemical", "text": [ "ADP" ], "offsets": [ [ 2600, 2603 ] ], "normalized": [] }, { "id": "PMC2682197-02-Results-04_T34", "type": "Protein", "text": [ "Rv2623" ], "offsets": [ [ 2629, 2635 ] ], "normalized": [] }, { "id": "PMC2682197-02-Results-04_T35", "type": "Chemical", "text": [ "ATP" ], "offsets": [ [ 2647, 2650 ] ], "normalized": [] }, { "id": "PMC2682197-02-Results-04_T36", "type": "Chemical", "text": [ "ATP" ], "offsets": [ [ 2678, 2681 ] ], "normalized": [] } ]

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[]

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[ { "id": "PMC2639726-03-Discussion-01__text", "type": "abstract", "text": [ "Discussion \nDuring systemic mouse infection, Salmonella processes multiple environmental cues via more than 14 regulators We performed virulence assays on 83 regulators previously identified as required for Salmonella enteriditis virulence by one or more negative selection experiments in various hosts including calves, chickens, and mice [13], [21]-[23]. The mutant strains devoid of 83 regulators were tested in three mouse virulence assays to identify a subset of 14 that were most highly attenuated in a systemic mouse infection model. These 14 regulators are very diverse including alternative sigma factors (rpoS and rpoE), two-component regulators (ompR/envZ, phoP/phoQ, and ssrA/ssrB), post-transcriptional regulators (csrA, hfq and smpB), a bending protein (ihf) and an assortment of other DNA binding proteins (fruR, spvR, crp, slyA, and hnr; see Table 1 for references). Salmonella follows a short course of infection after intraperitoneal infection, as we have used here, passing through the lymph nodes in the peritoneal cavity to the blood stream and then colonizing and replicating within the spleen and liver. During this entire trip the bacteria are located within cells either neutrophiles or monocytes although at lower numbers in B and T cells and dendritic cells of every subclass [16],[37],[38],[65],[66]. Because the bacteria are exclusively intracellular we tested the hypothesis that replication in macrophages could be a surrogate for systemic mouse infection. Mutations that were attenuated for growth in primary macrophages were also attenuated in the mouse but the converse was not always true. Next, we used expression profiling to define the regulatory pathways. Transcriptional profiles from intracellular bacteria at different times after infection are likely to match most closely the environments encountered by Salmonella during infection. However, isolation of RNA from intracellular bacteria was not used because we wished to test a spectrum of regulatory mutants several of which simply did not survive within cells long enough to allow RNA preparation. RNA was therefore prepared using four laboratory growth conditions two of which partially mimic the intracellular environment (acidic minimal media). We compared the transcriptional profiles we observed using laboratory growth conditions that mimic intracellular conditions, to those that have been performed during intracellular replication within J774 macrophage like cells. We computed the z-score for each Salmonella gene from our data and from the data provided by Eriksson et al. [67] thus providing a value that can be compared across different experiments. To compare the two sets of data we subtracted the z-scores computed from our data for AMM1 from that computed from expression profiles of intracellular Salmonella. As the expression pattern changes with time after infection we computed the difference for each time as well as an average for all three-time points reported (4, 8, and 12 hours after infection). There were 102 genes where the difference in z-score was 2 or greater, and 54 genes of 102 were annotated as putative, hypothetical, or conserved hypothetical. Four of the 5 most strongly differentially induced genes include magnesium transporters (mgtB and mgtC), an acid shock protein (STM1485), and a high affinity phosphate transporter (pstS) suggesting that the acidic minimal media we used may not be low enough in magnesium, phosphate, or may not be sufficiently acidic. Many genes are transcribed inside cells but may be only weakly transcribed or not at all transcribed in acidic minimal media. Examples of such genes include sifA and the operon STM3117-3120. This operon encodes some of the most abundantly expressed proteins by intracellular Salmonella. This result is striking, given that STM3117-3120 are not transcribed under a variety of in vitro conditions including AMM1 and 2 and the many conditions corresponding to the transcriptional profiles reported for microarrays archived in GEO ([68], J. McDermott and L Shi, Unpubl. Obs.). The nature of the inducing signal(s) that results in expression of these genes during intracellular growth is not known. The regulatory network controlling expression of the genes necessary for systemic infection is complex. In our transcriptional network each pink node represents a regulator (Figure 6 B) and lines represent positive or negative transcriptional interactions (positive in red and negative in blue). In E. coli most regulation has been shown to follow one of three motifs: feedforward in which a regulator controls a second regulator, single input in which a regulator uniquely controls a set of downstream genes, and so called dense overlapping regulons in which there are multiple regulatory inputs to a single operon [69]. A feedforward loop can act as an electronic \"AND-gate\" preventing expression except when two or more signals are sensed as we see for slyA (upstream) and ssrB (downstream); fruR (upstream) and crp (downstream). Many of these predicted relationships have been demonstrated already but some are new and merit further investigation. The single input motif is found in systems of genes that form a protein complex such as both of the type III secretion systems in Salmonella. For SPI-2 ssrB plays this role and for SPI-1 hilA is the central regulator. The multiple promoters located within SPI-2 presumably respond to differences in ssrB/slyA activation, perhaps establishing part of the temporal order of expression following phagocytosis of Salmonella. There are other regulators required for systemic infection in BALB/c mice, including those whose absence reduces viability without a compensating mutation (hns; [70]), those that require deletion of two unlinked genes for inactivation (ppGpp; reviewed in [71] and ydgT/hha [48]), or those that were simply missed in the screens (STM0410; [72]); these regulators will be included in subsequent analyses.\n" ], "offsets": [ [ 0, 5967 ] ] } ]

[ { "id": "PMC2639726-03-Discussion-01_T1", "type": "Organism", "text": [ "mouse" ], "offsets": [ [ 28, 33 ] ], "normalized": [] }, { "id": "PMC2639726-03-Discussion-01_T2", "type": "Organism", "text": [ "Salmonella" ], "offsets": [ [ 45, 55 ] ], "normalized": [] }, { "id": "PMC2639726-03-Discussion-01_T3", "type": "Organism", "text": [ "Salmonella enteriditis" ], "offsets": [ [ 207, 229 ] ], "normalized": [] }, { "id": "PMC2639726-03-Discussion-01_T4", "type": "Organism", "text": [ "calves" ], "offsets": [ [ 313, 319 ] ], "normalized": [] }, { "id": "PMC2639726-03-Discussion-01_T5", "type": "Organism", "text": [ "chickens" ], "offsets": [ [ 321, 329 ] ], "normalized": [] }, { "id": "PMC2639726-03-Discussion-01_T6", "type": "Organism", "text": [ "mice" ], "offsets": [ [ 335, 339 ] ], "normalized": [] }, { "id": "PMC2639726-03-Discussion-01_T7", "type": "Organism", "text": [ "mouse" ], "offsets": [ [ 421, 426 ] ], "normalized": [] }, { "id": "PMC2639726-03-Discussion-01_T8", "type": "Organism", "text": [ "mouse" ], "offsets": [ [ 518, 523 ] ], "normalized": [] }, { "id": "PMC2639726-03-Discussion-01_T9", "type": "Protein", "text": [ "rpoS" ], "offsets": [ [ 615, 619 ] ], "normalized": [] }, { "id": "PMC2639726-03-Discussion-01_T10", "type": "Protein", "text": [ "rpoE" ], "offsets": [ [ 624, 628 ] ], "normalized": [] }, { "id": "PMC2639726-03-Discussion-01_T11", "type": "Two-component-system", "text": [ "ompR/envZ" ], "offsets": [ [ 657, 666 ] ], "normalized": [] }, { "id": "PMC2639726-03-Discussion-01_T12", "type": "Protein", "text": [ "ompR" ], "offsets": [ [ 657, 661 ] ], "normalized": [] }, { "id": "PMC2639726-03-Discussion-01_T13", "type": "Protein", "text": [ "envZ" ], "offsets": [ [ 662, 666 ] ], "normalized": [] }, { "id": "PMC2639726-03-Discussion-01_T14", "type": "Two-component-system", "text": [ "phoP/phoQ" ], "offsets": [ [ 668, 677 ] ], "normalized": [] }, { "id": "PMC2639726-03-Discussion-01_T15", "type": "Protein", "text": [ "phoP" ], "offsets": [ [ 668, 672 ] ], "normalized": [] }, { "id": "PMC2639726-03-Discussion-01_T16", "type": "Protein", "text": [ "phoQ" ], "offsets": [ [ 673, 677 ] ], "normalized": [] }, { "id": "PMC2639726-03-Discussion-01_T17", "type": "Two-component-system", "text": [ "ssrA/ssrB" ], "offsets": [ [ 683, 692 ] ], "normalized": [] }, { "id": "PMC2639726-03-Discussion-01_T18", "type": "Protein", "text": [ "ssrA" ], "offsets": [ [ 683, 687 ] ], "normalized": [] }, { "id": "PMC2639726-03-Discussion-01_T19", "type": "Protein", "text": [ "ssrB" ], "offsets": [ [ 688, 692 ] ], "normalized": [] }, { "id": "PMC2639726-03-Discussion-01_T20", "type": "Protein", "text": [ "csrA" ], "offsets": [ [ 728, 732 ] ], "normalized": [] }, { "id": "PMC2639726-03-Discussion-01_T21", "type": "Protein", "text": [ "hfq" ], "offsets": [ [ 734, 737 ] ], "normalized": [] }, { "id": "PMC2639726-03-Discussion-01_T22", "type": "Protein", "text": [ "smpB" ], "offsets": [ [ 742, 746 ] ], "normalized": [] }, { "id": "PMC2639726-03-Discussion-01_T23", "type": "Protein", "text": [ "ihf" ], "offsets": [ [ 768, 771 ] ], "normalized": [] }, { "id": "PMC2639726-03-Discussion-01_T24", "type": "Protein", "text": [ "fruR" ], "offsets": [ [ 822, 826 ] ], "normalized": [] }, { "id": "PMC2639726-03-Discussion-01_T25", "type": "Protein", "text": [ "spvR" ], "offsets": [ [ 828, 832 ] ], "normalized": [] }, { "id": "PMC2639726-03-Discussion-01_T26", "type": "Protein", "text": [ "crp" ], "offsets": [ [ 834, 837 ] ], "normalized": [] }, { "id": "PMC2639726-03-Discussion-01_T27", "type": "Protein", "text": [ "slyA" ], "offsets": [ [ 839, 843 ] ], "normalized": [] }, { "id": "PMC2639726-03-Discussion-01_T28", "type": "Protein", "text": [ "hnr" ], "offsets": [ [ 849, 852 ] ], "normalized": [] }, { "id": "PMC2639726-03-Discussion-01_T29", "type": "Organism", "text": [ "Salmonella" ], "offsets": [ [ 883, 893 ] ], "normalized": [] }, { "id": "PMC2639726-03-Discussion-01_T30", "type": "Organism", "text": [ "mouse" ], "offsets": [ [ 1471, 1476 ] ], "normalized": [] }, { "id": "PMC2639726-03-Discussion-01_T31", "type": "Organism", "text": [ "mouse" ], "offsets": [ [ 1581, 1586 ] ], "normalized": [] }, { "id": "PMC2639726-03-Discussion-01_T32", "type": "Organism", "text": [ "Salmonella" ], "offsets": [ [ 1848, 1858 ] ], "normalized": [] }, { "id": "PMC2639726-03-Discussion-01_T33", "type": "Organism", "text": [ "Salmonella" ], "offsets": [ [ 2504, 2514 ] ], "normalized": [] }, { "id": "PMC2639726-03-Discussion-01_T34", "type": "Organism", "text": [ "Salmonella" ], "offsets": [ [ 2811, 2821 ] ], "normalized": [] }, { "id": "PMC2639726-03-Discussion-01_T35", "type": "Chemical", "text": [ "magnesium" ], "offsets": [ [ 3244, 3253 ] ], "normalized": [] }, { "id": "PMC2639726-03-Discussion-01_T36", "type": "Protein", "text": [ "mgtB" ], "offsets": [ [ 3268, 3272 ] ], "normalized": [] }, { "id": "PMC2639726-03-Discussion-01_T37", "type": "Protein", "text": [ "mgtC" ], "offsets": [ [ 3277, 3281 ] ], "normalized": [] }, { "id": "PMC2639726-03-Discussion-01_T38", "type": "Protein", "text": [ "STM1485" ], "offsets": [ [ 3307, 3314 ] ], "normalized": [] }, { "id": "PMC2639726-03-Discussion-01_T39", "type": "Chemical", "text": [ "phosphate" ], "offsets": [ [ 3337, 3346 ] ], "normalized": [] }, { "id": "PMC2639726-03-Discussion-01_T40", "type": "Protein", "text": [ "pstS" ], "offsets": [ [ 3360, 3364 ] ], "normalized": [] }, { "id": "PMC2639726-03-Discussion-01_T41", "type": "Chemical", "text": [ "magnesium" ], "offsets": [ [ 3440, 3449 ] ], "normalized": [] }, { "id": "PMC2639726-03-Discussion-01_T42", "type": "Chemical", "text": [ "phosphate" ], "offsets": [ [ 3451, 3460 ] ], "normalized": [] }, { "id": "PMC2639726-03-Discussion-01_T43", "type": "Protein", "text": [ "sifA" ], "offsets": [ [ 3654, 3658 ] ], "normalized": [] }, { "id": "PMC2639726-03-Discussion-01_T44", "type": "Regulon-operon", "text": [ "STM3117-3120" ], "offsets": [ [ 3674, 3686 ] ], "normalized": [] }, { "id": "PMC2639726-03-Discussion-01_T45", "type": "Protein", "text": [ "STM3117" ], "offsets": [ [ 3674, 3681 ] ], "normalized": [] }, { "id": "PMC2639726-03-Discussion-01_T46", "type": "Protein", "text": [ "3120" ], "offsets": [ [ 3682, 3686 ] ], "normalized": [] }, { "id": "PMC2639726-03-Discussion-01_T47", "type": "Organism", "text": [ "Salmonella" ], "offsets": [ [ 3772, 3782 ] ], "normalized": [] }, { "id": "PMC2639726-03-Discussion-01_T48", "type": "Regulon-operon", "text": [ "STM3117-3120" ], "offsets": [ [ 3820, 3832 ] ], "normalized": [] }, { "id": "PMC2639726-03-Discussion-01_T49", "type": "Protein", "text": [ "STM3117" ], "offsets": [ [ 3820, 3827 ] ], "normalized": [] }, { "id": "PMC2639726-03-Discussion-01_T50", "type": "Protein", "text": [ "3120" ], "offsets": [ [ 3828, 3832 ] ], "normalized": [] }, { "id": "PMC2639726-03-Discussion-01_T51", "type": "Organism", "text": [ "E. coli" ], "offsets": [ [ 4490, 4497 ] ], "normalized": [] }, { "id": "PMC2639726-03-Discussion-01_T52", 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[]

[]

[ { "id": "PMC2593050-00-TIAB__text", "type": "abstract", "text": [ "The Two-Component Regulatory System VicRK is Important to Virulence of Streptococcus equi Subspecies equi \nThis study aims at evaluating the importance of the two-component regulatory system VicRK to virulence of the horse pathogen Streptococcus equi subspecies equi and the potential of a vicK mutant as a live vaccine candidate using mouse infection models. The vicK gene was deleted by gene replacement. The DeltavicK mutant is attenuated in virulence in both subcutaneous and intranasal infections in mice. DeltavicK grows less slowly than the parent strain but retains the ability of S. equi to resist to phagocytosis by polymorphoneuclear leukocytes, suggesting that the vicK deletion causes growth defect. DeltavicK infection protects mice against reinfection with a wild-type S. equi strain. Intranasal DeltavicK infection induces production of anti-SeM mucosal IgA and systemic IgG. These results indicate that VicRK is important to S. equi growth and virulence and suggest that DeltavicK has the potential to be developed as a live S. equi vaccine.\n" ], "offsets": [ [ 0, 1059 ] ] } ]

[ { "id": "PMC2593050-00-TIAB_T1", "type": "Two-component-system", "text": [ "VicRK" ], "offsets": [ [ 36, 41 ] ], "normalized": [] }, { "id": "PMC2593050-00-TIAB_T2", "type": "Protein", "text": [ "VicR" ], "offsets": [ [ 36, 40 ] ], "normalized": [] }, { "id": "PMC2593050-00-TIAB_T3", "type": "Protein", "text": [ "K" ], "offsets": [ [ 40, 41 ] ], "normalized": [] }, { "id": "PMC2593050-00-TIAB_T4", "type": "Organism", "text": [ "Streptococcus equi Subspecies equi" ], "offsets": [ [ 71, 105 ] ], "normalized": [] }, { "id": "PMC2593050-00-TIAB_T5", "type": "Two-component-system", "text": [ "VicRK" ], "offsets": [ [ 191, 196 ] ], "normalized": [] }, { "id": "PMC2593050-00-TIAB_T6", "type": "Protein", "text": [ "VicR" ], "offsets": [ [ 191, 195 ] ], "normalized": [] }, { "id": "PMC2593050-00-TIAB_T7", "type": "Protein", "text": [ "K" ], "offsets": [ [ 195, 196 ] ], "normalized": [] }, { "id": "PMC2593050-00-TIAB_T8", "type": "Organism", "text": [ "horse" ], "offsets": [ [ 217, 222 ] ], "normalized": [] }, { "id": "PMC2593050-00-TIAB_T9", "type": "Organism", "text": [ "Streptococcus equi subspecies equi" ], "offsets": [ [ 232, 266 ] ], "normalized": [] }, { "id": "PMC2593050-00-TIAB_T10", "type": "Protein", "text": [ "vicK" ], "offsets": [ [ 290, 294 ] ], "normalized": [] }, { "id": "PMC2593050-00-TIAB_T11", "type": "Organism", "text": [ "mouse" ], "offsets": [ [ 336, 341 ] ], "normalized": [] }, { "id": "PMC2593050-00-TIAB_T12", "type": "Protein", "text": [ "vicK" ], "offsets": [ [ 364, 368 ] ], "normalized": [] }, { "id": "PMC2593050-00-TIAB_T13", "type": "Organism", "text": [ "DeltavicK mutant" ], "offsets": [ [ 411, 427 ] ], "normalized": [] }, { "id": "PMC2593050-00-TIAB_T14", "type": "Protein", "text": [ "vicK" ], "offsets": [ [ 416, 420 ] ], "normalized": [] }, { "id": "PMC2593050-00-TIAB_T15", "type": "Organism", "text": [ "mice" ], "offsets": [ [ 505, 509 ] ], "normalized": [] }, { "id": "PMC2593050-00-TIAB_T16", "type": "Organism", "text": [ "DeltavicK" ], "offsets": [ [ 511, 520 ] ], "normalized": [] }, { "id": "PMC2593050-00-TIAB_T17", "type": "Protein", "text": [ "vicK" ], "offsets": [ [ 516, 520 ] ], "normalized": [] }, { "id": "PMC2593050-00-TIAB_T18", "type": "Organism", "text": [ "S. equi" ], "offsets": [ [ 589, 596 ] ], "normalized": [] }, { "id": "PMC2593050-00-TIAB_T19", "type": "Protein", "text": [ "vicK" ], "offsets": [ [ 677, 681 ] ], "normalized": [] }, { "id": "PMC2593050-00-TIAB_T20", "type": "Organism", "text": [ "DeltavicK" ], "offsets": [ [ 713, 722 ] ], "normalized": [] }, { "id": "PMC2593050-00-TIAB_T21", "type": "Protein", "text": [ "vicK" ], "offsets": [ [ 718, 722 ] ], "normalized": [] }, { "id": "PMC2593050-00-TIAB_T22", "type": "Organism", "text": [ "mice" ], "offsets": [ [ 742, 746 ] ], "normalized": [] }, { "id": "PMC2593050-00-TIAB_T23", "type": "Organism", "text": [ "S. equi" ], "offsets": [ [ 784, 791 ] ], "normalized": [] }, { "id": "PMC2593050-00-TIAB_T24", "type": "Organism", "text": [ "DeltavicK" ], "offsets": [ [ 811, 820 ] ], "normalized": [] }, { "id": "PMC2593050-00-TIAB_T25", "type": "Protein", "text": [ "vicK" ], "offsets": [ [ 816, 820 ] ], "normalized": [] }, { "id": "PMC2593050-00-TIAB_T26", "type": "Protein", "text": [ "SeM" ], "offsets": [ [ 858, 861 ] ], "normalized": [] }, { "id": "PMC2593050-00-TIAB_T27", "type": "Protein", "text": [ "IgA" ], "offsets": [ [ 870, 873 ] ], "normalized": [] }, { "id": "PMC2593050-00-TIAB_T28", "type": "Protein", "text": [ "IgG" ], "offsets": [ [ 887, 890 ] ], "normalized": [] }, { "id": "PMC2593050-00-TIAB_T29", "type": "Two-component-system", "text": [ "VicRK" ], "offsets": [ [ 920, 925 ] ], "normalized": [] }, { "id": "PMC2593050-00-TIAB_T30", "type": "Protein", "text": [ "VicR" ], "offsets": [ [ 920, 924 ] ], "normalized": [] }, { "id": "PMC2593050-00-TIAB_T31", "type": "Protein", "text": [ "K" ], "offsets": [ [ 924, 925 ] ], "normalized": [] }, { "id": "PMC2593050-00-TIAB_T32", "type": "Organism", "text": [ "S. equi" ], "offsets": [ [ 942, 949 ] ], "normalized": [] }, { "id": "PMC2593050-00-TIAB_T33", "type": "Organism", "text": [ "DeltavicK" ], "offsets": [ [ 988, 997 ] ], "normalized": [] }, { "id": "PMC2593050-00-TIAB_T34", "type": "Protein", "text": [ "vicK" ], "offsets": [ [ 993, 997 ] ], "normalized": [] }, { "id": "PMC2593050-00-TIAB_T35", "type": "Organism", "text": [ "S. equi" ], "offsets": [ [ 1042, 1049 ] ], "normalized": [] } ]

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[]

[]

[ { "id": "PMC2774163-02-Results-01__text", "type": "abstract", "text": [ "Results \nThe formation of biofilms has been proposed to be controlled in response to environmental signals [39]. Given that protein phosphorylation is a common modification system used in signal transduction that changes the function of proteins in response to environmental stimuli [38], we chose a phosphoproteomic approach for the detection and identification of regulatory pathways active following the transition to the surface attached mode of growth. Detection of differentially phosphorylated proteins over the course of biofilm formation While phosphoproteomic analyses have become widespread in studies of regulation, signaling, development, the characterization of bacterial species and host responses during pathogenesis [40]-[49], only a limited number of studies have demonstrated that bacterial phosphoproteomes are dynamic [44],[46],[48]. We therefore used a combination of 2D/PAGE and immunoblot analysis using commercially available anti-phospho Ser/Thr antibodies (see Suppl. Fig. S1A-B for an example) to probe for the presence of signal transduction events that occur over the course of biofilm formation. Immunoblots of whole cell extracts obtained from planktonic cells and biofilm cells representing five developmental stages (reversibly and irreversibly attached cells, maturation-1 and -2 and dispersion stage; following 8, 24, 72, 144, and 216 hr of growth, respectively, see [12],[50] for timing of biofilm stages) were thus analyzed for the presence of planktonic- and biofilm-specific phosphorylation events. The planktonic mode of growth coincided with 24 phosphorylated proteins that were not phosphorylated following the transition of P. aeruginosa to surface-associated mode of growth (Fig. 1A, stage-specific events). Additional stage-specific events were detected for biofilms differing in age. For instance, 8 hr and 24 hr old biofilms displayed 23 and 21 phosphorylation events, respectively, not detected at any other stage. Regardless of the biofilm developmental stage, 7 phosphorylation events were detected that were absent in planktonic cells (Fig. 1A, biofilm-specific events). In both modes of growth, 26 proteins were constitutively phosphorylated. In addition to biofilm stage-specific phosphorylation of proteins, protein phosphorylation events were detectable at more than one biofilm growth stage indicating that the transition to surface-associated growth coincides with distinct protein phosphorylation and dephosphorylation events. As shown in Fig. 1A, these phosphorylation events are subcategorized as occurring during the reversible and irreversible attachment, biofilm formation and maturation stage depending on when and for how long protein phosphorylation was detected. For instance, four proteins were phosphorylated both in planktonic and reversible attached cells (8 hr biofilms) but not at any other biofilm stage (Fig. 1A, reversible attachment) while 4 different proteins were phosphorylated only in planktonic cells and biofilm cells after 8 hr and 24 hr of growth under flowing conditions (Fig. 1A, irreversible attachment). Furthermore, evidence of proteins being dephosphorylated over the course of biofilm formation was detected. Multiple proteins were found to be dephosphorylated at either a single or at multiple stages over the course of biofilm formation and maturation (Fig. 1B). Moreover, the similarity of the biofilm phosphoproteome to the planktonic phosphorylation patterns decreased from 59% in 8-hr-old biofilms to 35% in 144-hr-old, mature biofilms. The reduced similarity in phosphorylation events between biofilms and planktonic cells was mainly due to biofilm specific phosphorylation events detected at one or more stages of development. Dispersion-stage biofilms (216-hr-old) shared 43% similarity with the phosphorylation patterns of planktonically-grown P. aeruginosa cells (not shown). The increase in similarity between the planktonic and the 216-hr-old biofilm phosphoproteomes is consistent with previous reports indicating that cells within dispersion-stage biofilms are returning to the planktonic mode of growth [12],[50]. Protein phosphorylation in bacteria is not restricted to serine and threonine amino acid residues; however, the analysis of phosphorylation events by immunoblotting is limited to the availability of anti-phospho Ser/Thr (and tyrosine) antibodies. We therefore also purified phosphorylated proteins using metal oxide affinity chromatography (MOAC, see Fig. S1), a gel-independent approach allowing for the enrichment of phosphoproteins independent of the phosphorylation site with an up to 100% specificity [51],[52], followed by cleavable isotope coded affinity tag (cICAT) labeling and analysis by liquid chromatography tandem mass spectrometry (LC-MS/MS). This quantitative mass spectrometric approach was used to analyze protein phosphorylation patterns of biofilm cells grown to the reversible, irreversible, maturation-1 and maturation-2 biofilm stages (8-, 24-, 7-2, and 144-hr-old biofilms, respectively [12]) in comparison to those of planktonic cells. Similarly to the results obtained via immunoblot analysis, the changes in phosphorylation events over the course of biofilm development detected using LC-MS-MS analysis appeared to be stage-specific (two examples are shown in Suppl. Fig. S2), with the similarity to the planktonic patterns decreasing from 72% in 8 hr biofilms to 38% in 144 hr biofilms (Fig. 1C). The overall stage-specific (de)phosphorylation events as well as the differences in the phosphoproteome were similar to those detected by immunoblot analysis using anti-Ser/Thr antibodies. This is the first description of the dynamic changes of the phosphoproteome occurring during biofilm development. The combination of approaches used here has not been previously used to identify phosphorylated proteins in biofilms.\n" ], "offsets": [ [ 0, 5869 ] ] } ]

[ { "id": "PMC2774163-02-Results-01_T1", "type": "Organism", "text": [ "P. aeruginosa" ], "offsets": [ [ 1668, 1681 ] ], "normalized": [] }, { "id": "PMC2774163-02-Results-01_T2", "type": "Organism", "text": [ "P. aeruginosa" ], "offsets": [ [ 3847, 3860 ] ], "normalized": [] } ]

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[ { "id": "PMC2242835-02-Results-05__text", "type": "abstract", "text": [ "Link between Mutation in phoP and Secretion of ESAT-6 \nAs PhoP fulfills important regulatory functions in M. tuberculosis [21,22], it was of primary interest to identify and study potential effector molecules whose involvement in host pathogen interaction were influenced by the point mutation in phoP of H37Ra. Since secreted proteins of the ESX-1 system of M. tuberculosis constitute a major interface between the bacterium and its host [23], we analyzed the different strains for their potential to induce T cell responses against ESAT-6 and its binding partner, the 10-kD culture filtrate protein CFP-10. Groups of C57BL/6 mice were subcutaneously inoculated with H37Rv, H37Ra, or one of three recombinant H37Ra strains complemented with phoP, fadE5, or rpsL, respectively. Two weeks after vaccination we assessed the interferon-gamma (IFN-gamma) production of splenocytes mounted against ESX-1 antigens or controls. As anticipated, all tested strains induced IFN-gamma production in response to purified protein derivative (PPD) but not to a control peptide (Mal-E), indicating successful vaccination (Figure 3). Most importantly, the various strains differed extensively in their potential to induce antigen specific T cell responses towards ESAT-6 and CFP-10. As shown in Figure 3, splenocytes from mice that were inoculated with H37Rv produced high amounts of IFN-gamma upon stimulation with ESAT-6 or CFP-10, whereas the responses of H37Ra, H37Ra::fadE5, and H37Ra::rpsL infected mice were extremely weak. In contrast, splenocytes from H37Ra::phoP inoculated mice showed very strong IFN-gamma production in response to incubation with ESAT-6 and CFP-10. Exactly the same trend was observed when a highly sensitive T cell hybridoma assay was used to investigate ESAT-6 secretion. This test is based on the presentation of the immunodominant epitope contained in the first 20 amino acids of ESAT-6 by H37Ra, recombinant H37Ra, or H37Rv infected bone marrow-derived dendritic cells (BM-DC) to an ESAT-6-specific T cell hybridoma (NB11), restricted by I-Ab. Figure 4A shows that infection of BM-DC with H37Ra or H37Ra::rpsL induced no stimulation of the hybridoma as judged by IL-2 production, while H37Ra::phoP or H37Rv triggered high amounts of IL-2 production in this very sensitive and specific test. All strains behaved comparably towards the Ag85A:241-260 control, emphasizing the specificity of the observed phenomenon for ESAT-6 (Figure 4B). To further evaluate the involvement of phoP and the ESX-1 system in immunogenicity, C57BL/6 mice were vaccinated with additional strains. Firstly, we constructed a partially diploid H37Ra knock-in strain carrying cosmid RD1-ppe68-ko that, in BCG yields the greatest amounts of ESAT-6 expression and secretion [24]. However, in H37Ra the presence of this cosmid could not increase the weak ESAT-6 and CFP-10 T cell responses (Figure 3B) in the splenocyte IFN-gamma assay. Secondly, we also tested the previously described M. tuberculosis MT103 phoP knock-out (ko) strain SO2 [14,25] in this assay and found that this strain induced a potent PPD response as previously reported [25]. However, in comparison to the corresponding MT103 wild-type strain, the SO2 strain showed a strongly reduced ESAT-6 and CFP-10 specific T cell response, corresponding to a similar low level as the H37Ra strain (Figure 3B). Altogether, our data obtained from multiple replicate experiments indicate that a direct link exists between a fully functional PhoP and the ability to generate T cell responses against ESAT-6 and CFP-10.\n" ], "offsets": [ [ 0, 3565 ] ] } ]

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"offsets": [ [ 534, 540 ] ], "normalized": [] }, { "id": "PMC2242835-02-Results-05_T9", "type": "Protein", "text": [ "CFP-10" ], "offsets": [ [ 601, 607 ] ], "normalized": [] }, { "id": "PMC2242835-02-Results-05_T10", "type": "Organism", "text": [ "C57BL/6 mice" ], "offsets": [ [ 619, 631 ] ], "normalized": [] }, { "id": "PMC2242835-02-Results-05_T11", "type": "Organism", "text": [ "H37Rv" ], "offsets": [ [ 668, 673 ] ], "normalized": [] }, { "id": "PMC2242835-02-Results-05_T12", "type": "Organism", "text": [ "H37Ra" ], "offsets": [ [ 675, 680 ] ], "normalized": [] }, { "id": "PMC2242835-02-Results-05_T13", "type": "Organism", "text": [ "H37Ra" ], "offsets": [ [ 710, 715 ] ], "normalized": [] }, { "id": "PMC2242835-02-Results-05_T14", "type": "Protein", "text": [ "phoP" ], "offsets": [ [ 742, 746 ] ], "normalized": [] }, { "id": "PMC2242835-02-Results-05_T15", "type": "Protein", "text": [ "fadE5" ], "offsets": [ [ 748, 753 ] ], "normalized": [] }, { "id": "PMC2242835-02-Results-05_T16", "type": "Protein", "text": [ "rpsL" ], "offsets": [ [ 758, 762 ] ], "normalized": [] }, { "id": "PMC2242835-02-Results-05_T17", "type": "Protein", "text": [ "interferon-gamma" ], "offsets": [ [ 822, 838 ] ], "normalized": [] }, { "id": "PMC2242835-02-Results-05_T18", "type": "Protein", "text": [ "IFN-gamma" ], "offsets": [ [ 840, 849 ] ], "normalized": [] }, { "id": "PMC2242835-02-Results-05_T19", "type": "Protein", "text": [ "IFN-gamma" ], "offsets": [ [ 964, 973 ] ], "normalized": [] }, { "id": "PMC2242835-02-Results-05_T20", "type": "Protein", "text": [ "ESAT-6" ], "offsets": [ [ 1248, 1254 ] ], "normalized": [] }, { "id": "PMC2242835-02-Results-05_T21", "type": "Protein", "text": [ "CFP-10" ], "offsets": [ [ 1259, 1265 ] ], "normalized": [] }, { "id": "PMC2242835-02-Results-05_T22", "type": "Organism", "text": [ "mice" ], "offsets": [ [ 1306, 1310 ] ], "normalized": [] }, { "id": "PMC2242835-02-Results-05_T23", "type": "Organism", "text": [ "H37Rv" ], "offsets": [ [ 1337, 1342 ] ], "normalized": [] }, { "id": "PMC2242835-02-Results-05_T24", "type": "Protein", "text": [ "IFN-gamma" ], "offsets": [ [ 1368, 1377 ] ], "normalized": [] }, { "id": "PMC2242835-02-Results-05_T25", "type": "Protein", "text": [ "ESAT-6" ], "offsets": [ [ 1400, 1406 ] ], "normalized": [] }, { "id": "PMC2242835-02-Results-05_T26", "type": "Protein", "text": [ "CFP-10" ], "offsets": [ [ 1410, 1416 ] ], "normalized": [] }, { "id": "PMC2242835-02-Results-05_T27", "type": "Organism", "text": [ "H37Ra" ], "offsets": [ [ 1443, 1448 ] ], "normalized": [] }, { "id": "PMC2242835-02-Results-05_T28", "type": "Organism", "text": [ "H37Ra::fadE5" ], "offsets": [ [ 1450, 1462 ] ], "normalized": [] }, { "id": "PMC2242835-02-Results-05_T29", "type": "Protein", "text": [ "fadE5" ], "offsets": [ [ 1457, 1462 ] ], "normalized": [] }, { "id": "PMC2242835-02-Results-05_T30", "type": "Organism", "text": [ "H37Ra::rpsL" ], "offsets": [ [ 1468, 1479 ] ], "normalized": [] }, { "id": "PMC2242835-02-Results-05_T31", "type": "Protein", "text": [ "rpsL" ], "offsets": [ [ 1475, 1479 ] ], "normalized": [] }, { "id": "PMC2242835-02-Results-05_T32", "type": "Organism", "text": [ "mice" ], "offsets": [ [ 1489, 1493 ] ], "normalized": [] }, { "id": "PMC2242835-02-Results-05_T33", "type": "Organism", "text": [ "H37Ra::phoP" ], "offsets": [ [ 1545, 1556 ] ], "normalized": [] }, { "id": "PMC2242835-02-Results-05_T34", "type": "Protein", "text": [ "phoP" ], "offsets": [ [ 1552, 1556 ] ], "normalized": [] }, { "id": "PMC2242835-02-Results-05_T35", "type": "Organism", "text": [ "mice" ], "offsets": [ [ 1568, 1572 ] ], "normalized": [] }, { "id": "PMC2242835-02-Results-05_T36", "type": "Protein", "text": [ "IFN-gamma" ], "offsets": [ [ 1592, 1601 ] ], "normalized": [] }, { "id": "PMC2242835-02-Results-05_T37", "type": "Protein", "text": [ "ESAT-6" ], "offsets": [ [ 1644, 1650 ] ], "normalized": [] }, { "id": "PMC2242835-02-Results-05_T38", "type": "Protein", "text": [ "CFP-10" ], "offsets": [ [ 1655, 1661 ] ], "normalized": [] }, { "id": "PMC2242835-02-Results-05_T39", "type": "Protein", "text": [ "ESAT-6" ], "offsets": [ [ 1770, 1776 ] ], "normalized": [] }, { "id": "PMC2242835-02-Results-05_T40", "type": "Protein", "text": [ "ESAT-6" ], "offsets": [ [ 1898, 1904 ] ], "normalized": [] }, { "id": "PMC2242835-02-Results-05_T41", "type": "Organism", "text": [ "H37Ra" ], "offsets": [ [ 1908, 1913 ] ], "normalized": [] }, { "id": "PMC2242835-02-Results-05_T42", "type": "Organism", "text": [ "H37Ra" ], "offsets": [ [ 1927, 1932 ] ], "normalized": [] }, { "id": "PMC2242835-02-Results-05_T43", "type": "Organism", "text": [ "H37Rv" ], "offsets": [ [ 1937, 1942 ] ], "normalized": [] }, { "id": "PMC2242835-02-Results-05_T44", "type": "Organism", "text": [ "ESAT-6" ], "offsets": [ [ 2002, 2008 ] ], "normalized": [] }, { "id": "PMC2242835-02-Results-05_T45", "type": "Organism", "text": [ "H37Ra" ], "offsets": [ [ 2108, 2113 ] ], "normalized": [] }, { "id": "PMC2242835-02-Results-05_T46", "type": "Organism", "text": [ "H37Ra::rpsL" ], "offsets": [ [ 2117, 2128 ] ], "normalized": [] }, { "id": "PMC2242835-02-Results-05_T47", "type": "Protein", "text": [ "rpsL" ], "offsets": [ [ 2124, 2128 ] ], "normalized": [] }, { "id": "PMC2242835-02-Results-05_T48", "type": "Protein", "text": [ "IL-2" ], "offsets": [ [ 2182, 2186 ] ], "normalized": [] }, { "id": "PMC2242835-02-Results-05_T49", "type": "Organism", "text": [ "H37Ra::phoP" ], "offsets": [ [ 2205, 2216 ] ], "normalized": [] }, { "id": "PMC2242835-02-Results-05_T50", "type": "Protein", "text": [ "phoP" ], "offsets": [ [ 2212, 2216 ] ], "normalized": [] }, { "id": "PMC2242835-02-Results-05_T51", "type": "Organism", "text": [ "H37Rv" ], "offsets": [ [ 2220, 2225 ] ], "normalized": [] }, { "id": "PMC2242835-02-Results-05_T52", "type": "Protein", "text": [ "IL-2" ], "offsets": [ [ 2252, 2256 ] ], "normalized": [] }, { "id": "PMC2242835-02-Results-05_T53", "type": "Protein", "text": [ "ESAT-6" ], "offsets": [ [ 2435, 2441 ] ], "normalized": [] }, { "id": "PMC2242835-02-Results-05_T54", "type": "Protein", "text": [ "phoP" ], "offsets": [ [ 2494, 2498 ] ], "normalized": [] }, { "id": "PMC2242835-02-Results-05_T55", "type": "Organism", "text": [ "C57BL/6 mice" ], "offsets": [ [ 2539, 2551 ] ], "normalized": [] }, { "id": "PMC2242835-02-Results-05_T56", "type": "Organism", "text": [ "H37Ra" ], "offsets": [ [ 2637, 2642 ] ], "normalized": [] }, { "id": "PMC2242835-02-Results-05_T57", "type": "Protein", "text": [ "ppe68" ], "offsets": [ [ 2679, 2684 ] ], "normalized": [] }, { "id": "PMC2242835-02-Results-05_T58", "type": "Organism", "text": [ "BCG" ], "offsets": [ [ 2697, 2700 ] ], "normalized": [] }, { "id": "PMC2242835-02-Results-05_T59", "type": "Protein", "text": [ "ESAT-6" ], "offsets": [ [ 2732, 2738 ] ], "normalized": [] }, { "id": "PMC2242835-02-Results-05_T60", "type": "Organism", "text": [ "H37Ra" ], "offsets": [ [ 2782, 2787 ] ], "normalized": [] }, { "id": "PMC2242835-02-Results-05_T61", "type": "Protein", "text": [ "ESAT-6" ], "offsets": [ [ 2844, 2850 ] ], "normalized": [] }, { "id": "PMC2242835-02-Results-05_T62", "type": "Protein", "text": [ "CFP-10" ], "offsets": [ [ 2855, 2861 ] ], "normalized": [] }, { "id": "PMC2242835-02-Results-05_T63", "type": "Protein", "text": [ "IFN-gamma" ], "offsets": [ [ 2909, 2918 ] ], "normalized": [] }, { "id": "PMC2242835-02-Results-05_T64", "type": "Organism", "text": [ "M. tuberculosis MT103 phoP knock-out (ko) strain SO2" ], "offsets": [ [ 2976, 3028 ] ], "normalized": [] }, { "id": "PMC2242835-02-Results-05_T65", "type": "Protein", "text": [ "phoP" ], "offsets": [ [ 2998, 3002 ] ], "normalized": [] }, { "id": "PMC2242835-02-Results-05_T66", "type": "Organism", "text": [ "MT103" ], "offsets": [ [ 3181, 3186 ] ], "normalized": [] }, { "id": "PMC2242835-02-Results-05_T67", "type": "Organism", "text": [ "SO2" ], "offsets": [ [ 3209, 3212 ] ], "normalized": [] }, { "id": "PMC2242835-02-Results-05_T68", "type": "Protein", "text": [ "ESAT-6" ], "offsets": [ [ 3246, 3252 ] ], "normalized": [] }, { "id": "PMC2242835-02-Results-05_T69", "type": "Protein", "text": [ "CFP-10" ], "offsets": [ [ 3257, 3263 ] ], "normalized": [] }, { "id": "PMC2242835-02-Results-05_T70", "type": "Organism", "text": [ "H37Ra" ], "offsets": [ [ 3334, 3339 ] ], "normalized": [] }, { "id": "PMC2242835-02-Results-05_T71", "type": "Protein", "text": [ "PhoP" ], "offsets": [ [ 3488, 3492 ] ], "normalized": [] }, { "id": "PMC2242835-02-Results-05_T72", "type": "Protein", "text": [ "ESAT-6" ], "offsets": [ [ 3546, 3552 ] ], "normalized": [] }, { "id": "PMC2242835-02-Results-05_T73", "type": "Protein", "text": [ "CFP-10" ], "offsets": [ [ 3557, 3563 ] ], "normalized": [] } ]

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[ { "id": "PMC2593050-04-DISCUSSION__text", "type": "abstract", "text": [ "DISCUSSION \nVicK is essential in B. subtilis [2] and S. aureus [3] but not in S. pneumoniae [7], S. mutans [8], and S. pyogenes [6]. We successfully deleted the vicK gene of S. equi. Thus, VicK is not essential in S. equi. However, the DeltavicK mutant is attenuated in virulence in both mouse models of subcutaneous and intranasal S. equi infections, indicating that VicRK is important to virulence. The results provide the further evidence for the importance of VicRK to virulence of Gram-positive pathogens. S. equi DeltavicK mutant does not grow as well as the wild-type strain in both THY and blood, suggesting that the vicK deletion causes defect in growth, a plausible reason that likely contributes to the attenuation of S. equi virulence in the mouse infection models. This suggestion is further supported by the observations that both the wild-type and DeltavicK mutant strains are resistant to phagocytosis by PMNs, which suggest that VicRK is not required for the evasion of S. equi to the innate immunity. As introduced earlier, the various phenotypes have been described for the vicRK mutants of the various pathogens. Whether the phenotypes are specific to particular organisms is not known. The phenotypes of the S. equi DeltavicK mutant are similar to those of the S. pyogenes DeltavicK mutant [6], suggesting that the growth defect phenotype may be a common feature of the vicRK mutants of various Gram-positive pathogens. The DeltavicK mutant appears to possess the properties of a potential live vaccine. First, it is attenuated in virulence in the mouse infection models. Secondly, DeltavicK inoculation protects mice against subsequent infection with wild-type S. equi. Thirdly, most of the mice with intranasal DeltavicK infection produce mucosal IgA and systemic IgG specific to protective antigen SeM. However, whether DeltavicK can be an effective live vaccine and whether the DeltavicK mutant has any advantages over the current live S. equi vaccine require the test of the mutant in horses since S. equi does not naturally infect mice. We hope to perform this expensive test in future when funds are available\n" ], "offsets": [ [ 0, 2138 ] ] } ]

[ { "id": "PMC2593050-04-DISCUSSION_T1", "type": "Protein", "text": [ "VicK" ], "offsets": [ [ 12, 16 ] ], "normalized": [] }, { "id": "PMC2593050-04-DISCUSSION_T2", "type": "Organism", "text": [ "B. subtilis" ], "offsets": [ [ 33, 44 ] ], "normalized": [] }, { "id": "PMC2593050-04-DISCUSSION_T3", "type": "Organism", "text": [ "S. aureus" ], "offsets": [ [ 53, 62 ] ], "normalized": [] }, { "id": "PMC2593050-04-DISCUSSION_T4", "type": "Organism", "text": [ "S. pneumoniae" ], "offsets": [ [ 78, 91 ] ], "normalized": [] }, { "id": "PMC2593050-04-DISCUSSION_T5", "type": "Organism", "text": [ "S. mutans" ], "offsets": [ [ 97, 106 ] ], "normalized": [] }, { "id": "PMC2593050-04-DISCUSSION_T6", "type": "Organism", "text": [ "S. pyogenes" ], "offsets": [ [ 116, 127 ] ], "normalized": [] }, { "id": "PMC2593050-04-DISCUSSION_T7", "type": "Protein", "text": [ "vicK" ], "offsets": [ [ 161, 165 ] ], "normalized": [] }, { "id": "PMC2593050-04-DISCUSSION_T8", "type": "Organism", "text": [ "S. equi" ], "offsets": [ [ 174, 181 ] ], "normalized": [] }, { "id": "PMC2593050-04-DISCUSSION_T9", "type": "Protein", "text": [ "VicK" ], "offsets": [ [ 189, 193 ] ], "normalized": [] }, { "id": "PMC2593050-04-DISCUSSION_T10", "type": "Organism", "text": [ "S. equi" ], "offsets": [ [ 214, 221 ] ], "normalized": [] }, { "id": "PMC2593050-04-DISCUSSION_T11", "type": "Organism", "text": [ "DeltavicK mutant" ], "offsets": [ [ 236, 252 ] ], "normalized": [] }, { "id": "PMC2593050-04-DISCUSSION_T12", "type": "Protein", "text": [ "vicK" ], "offsets": [ [ 241, 245 ] ], "normalized": [] }, { "id": "PMC2593050-04-DISCUSSION_T13", "type": "Organism", "text": [ "mouse" ], "offsets": [ [ 288, 293 ] ], "normalized": [] }, { "id": "PMC2593050-04-DISCUSSION_T14", "type": "Organism", "text": [ "S. equi" ], "offsets": [ [ 332, 339 ] ], "normalized": [] }, { "id": "PMC2593050-04-DISCUSSION_T15", "type": "Two-component-system", "text": [ "VicRK" ], "offsets": [ [ 368, 373 ] ], "normalized": [] }, { "id": "PMC2593050-04-DISCUSSION_T16", "type": "Protein", "text": [ "VicR" ], "offsets": [ [ 368, 372 ] ], "normalized": [] }, { "id": "PMC2593050-04-DISCUSSION_T17", "type": "Protein", "text": [ "K" ], "offsets": [ [ 372, 373 ] ], "normalized": [] }, { "id": "PMC2593050-04-DISCUSSION_T18", "type": "Two-component-system", "text": [ "VicRK" ], "offsets": [ [ 464, 469 ] ], "normalized": [] }, { "id": "PMC2593050-04-DISCUSSION_T19", "type": "Protein", "text": [ "VicR" ], "offsets": [ [ 464, 468 ] ], "normalized": [] }, { "id": "PMC2593050-04-DISCUSSION_T20", "type": "Protein", "text": [ "K" ], "offsets": [ [ 468, 469 ] ], "normalized": [] }, { "id": "PMC2593050-04-DISCUSSION_T21", "type": "Organism", "text": [ "S. equi DeltavicK mutant" ], "offsets": [ [ 511, 535 ] ], "normalized": [] }, { "id": "PMC2593050-04-DISCUSSION_T22", "type": "Protein", "text": [ "vicK" ], "offsets": [ [ 524, 528 ] ], "normalized": [] }, { "id": "PMC2593050-04-DISCUSSION_T23", "type": "Protein", "text": [ "vicK" ], "offsets": [ [ 625, 629 ] ], "normalized": [] }, { "id": "PMC2593050-04-DISCUSSION_T24", "type": "Organism", "text": [ "S. equi" ], "offsets": [ [ 729, 736 ] ], "normalized": [] }, { "id": "PMC2593050-04-DISCUSSION_T25", "type": "Organism", "text": [ "mouse" ], "offsets": [ [ 754, 759 ] ], "normalized": [] }, { "id": "PMC2593050-04-DISCUSSION_T26", "type": "Organism", "text": [ "DeltavicK mutant" ], "offsets": [ [ 863, 879 ] ], "normalized": [] }, { "id": "PMC2593050-04-DISCUSSION_T27", "type": "Protein", "text": [ "vicK" ], "offsets": [ [ 868, 872 ] ], "normalized": [] }, { "id": "PMC2593050-04-DISCUSSION_T28", "type": "Two-component-system", "text": [ "VicRK" ], "offsets": [ [ 946, 951 ] ], "normalized": [] }, { "id": "PMC2593050-04-DISCUSSION_T29", "type": "Protein", "text": [ "VicR" ], "offsets": [ [ 946, 950 ] ], "normalized": [] }, { "id": "PMC2593050-04-DISCUSSION_T30", "type": "Protein", "text": [ "K" ], "offsets": [ [ 950, 951 ] ], "normalized": [] }, { "id": "PMC2593050-04-DISCUSSION_T31", "type": "Organism", "text": [ "S. equi" ], "offsets": [ [ 987, 994 ] ], "normalized": [] }, { "id": "PMC2593050-04-DISCUSSION_T32", "type": "Two-component-system", "text": [ "vicRK" ], "offsets": [ [ 1093, 1098 ] ], "normalized": [] }, { "id": "PMC2593050-04-DISCUSSION_T33", "type": "Protein", "text": [ "vicR" ], "offsets": [ [ 1093, 1097 ] ], "normalized": [] }, { "id": "PMC2593050-04-DISCUSSION_T34", "type": "Protein", "text": [ "K" ], "offsets": [ [ 1097, 1098 ] ], "normalized": [] }, { "id": "PMC2593050-04-DISCUSSION_T35", "type": "Organism", "text": [ "S. equi DeltavicK mutant" ], "offsets": [ [ 1229, 1253 ] ], "normalized": [] }, { "id": "PMC2593050-04-DISCUSSION_T36", "type": "Protein", "text": [ "vicK" ], "offsets": [ [ 1242, 1246 ] ], "normalized": [] }, { "id": "PMC2593050-04-DISCUSSION_T37", "type": "Organism", "text": [ "S. pyogenes DeltavicK mutant" ], "offsets": [ [ 1282, 1310 ] ], "normalized": [] }, { "id": "PMC2593050-04-DISCUSSION_T38", "type": "Protein", "text": [ "vicK" ], "offsets": [ [ 1299, 1303 ] ], "normalized": [] }, { "id": "PMC2593050-04-DISCUSSION_T39", "type": "Two-component-system", "text": [ "vicRK" ], "offsets": [ [ 1391, 1396 ] ], "normalized": [] }, { "id": "PMC2593050-04-DISCUSSION_T40", "type": "Protein", "text": [ "vicR" ], "offsets": [ [ 1391, 1395 ] ], "normalized": [] }, { "id": "PMC2593050-04-DISCUSSION_T41", "type": "Protein", "text": [ "K" ], "offsets": [ [ 1395, 1396 ] ], "normalized": [] }, { "id": "PMC2593050-04-DISCUSSION_T42", "type": "Organism", "text": [ "DeltavicK mutant" ], "offsets": [ [ 1445, 1461 ] ], "normalized": [] }, { "id": "PMC2593050-04-DISCUSSION_T43", "type": "Protein", "text": [ "vicK" ], "offsets": [ [ 1450, 1454 ] ], "normalized": [] }, { "id": "PMC2593050-04-DISCUSSION_T44", "type": "Organism", "text": [ "mouse" ], "offsets": [ [ 1569, 1574 ] ], "normalized": [] }, { "id": "PMC2593050-04-DISCUSSION_T45", "type": "Organism", "text": [ "DeltavicK" ], "offsets": [ [ 1603, 1612 ] ], "normalized": [] }, { "id": "PMC2593050-04-DISCUSSION_T46", "type": "Protein", "text": [ "vicK" ], "offsets": [ [ 1608, 1612 ] ], "normalized": [] }, { "id": "PMC2593050-04-DISCUSSION_T47", "type": "Organism", "text": [ "mice" ], "offsets": [ [ 1634, 1638 ] ], "normalized": [] }, { "id": "PMC2593050-04-DISCUSSION_T48", "type": "Organism", "text": [ "S. equi" ], "offsets": [ [ 1683, 1690 ] ], "normalized": [] }, { "id": "PMC2593050-04-DISCUSSION_T49", "type": "Organism", "text": [ "mice" ], "offsets": [ [ 1713, 1717 ] ], "normalized": [] }, { "id": "PMC2593050-04-DISCUSSION_T50", "type": "Organism", "text": [ "DeltavicK" ], "offsets": [ [ 1734, 1743 ] ], "normalized": [] }, { "id": "PMC2593050-04-DISCUSSION_T51", "type": "Protein", "text": [ "vicK" ], "offsets": [ [ 1739, 1743 ] ], "normalized": [] }, { "id": "PMC2593050-04-DISCUSSION_T52", "type": "Protein", "text": [ "IgA" ], "offsets": [ [ 1770, 1773 ] ], "normalized": [] }, { "id": "PMC2593050-04-DISCUSSION_T53", "type": "Protein", "text": [ "IgG" ], "offsets": [ [ 1787, 1790 ] ], "normalized": [] }, { "id": "PMC2593050-04-DISCUSSION_T54", "type": "Protein", "text": [ "SeM" ], "offsets": [ [ 1822, 1825 ] ], "normalized": [] }, { "id": "PMC2593050-04-DISCUSSION_T55", "type": "Organism", "text": [ "DeltavicK" ], "offsets": [ [ 1844, 1853 ] ], "normalized": [] }, { "id": "PMC2593050-04-DISCUSSION_T56", "type": "Protein", "text": [ "vicK" ], "offsets": [ [ 1849, 1853 ] ], "normalized": [] }, { "id": "PMC2593050-04-DISCUSSION_T57", "type": "Organism", "text": [ "DeltavicK mutant" ], "offsets": [ [ 1903, 1919 ] ], "normalized": [] }, { "id": "PMC2593050-04-DISCUSSION_T58", "type": "Protein", "text": [ "vicK" ], "offsets": [ [ 1908, 1912 ] ], "normalized": [] }, { "id": "PMC2593050-04-DISCUSSION_T59", "type": "Organism", "text": [ "S. equi" ], "offsets": [ [ 1961, 1968 ] ], "normalized": [] }, { "id": "PMC2593050-04-DISCUSSION_T60", "type": "Organism", "text": [ "horses" ], "offsets": [ [ 2011, 2017 ] ], "normalized": [] }, { "id": "PMC2593050-04-DISCUSSION_T61", "type": "Organism", "text": [ "S. equi" ], "offsets": [ [ 2024, 2031 ] ], "normalized": [] }, { "id": "PMC2593050-04-DISCUSSION_T62", "type": "Organism", "text": [ "mice" ], "offsets": [ [ 2058, 2062 ] ], "normalized": [] } ]

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[]

[]

[ { "id": "PMC2581603-03-Discussion__text", "type": "abstract", "text": [ "Discussion \nInfections caused by P. aeruginosa continue to be a leading cause of mortality among immunocompromised patients. The ability of P. aeruginosa to form biofilms promotes survival of the bacteria in the presence of antimicrobials and host defense mechanisms and is thought to contribute significantly to its ability to survive long-term within the hostile environment of chronically-infected patients. Understanding the mechanisms underlying antibiotic resistance and especially biofilm-specific antimicrobial resistance is of significant importance in the development of new treatment options and/or strategies. We have identified a novel mechanism of biofilm-associated antibiotic resistance in which the presence of DNA in the extracellular matrix of biofilms creates a localized cation-limited environment that is detected by P. aeruginosa leading to the induction of LPS modification genes and resistance to antimicrobials. Magnesium limitation has long been known as an in vitro signal that induces resistance to CAPs in P. aeruginosa [59]. As an intracellular pathogen, the PhoPQ system of Salmonella typhimurium is activated by limiting magnesium in vitro and phoP-regulated genes are also induced after invasion of macrophages and epithelial cells [65]. These observations suggested that Mg2+ is limiting within host cells, but it was recently shown that vacuole acidification and low pH is the crucial environmental trigger of PhoPQ activation [66]. Many extracellular pathogens possess homologs of the cation-sensing PhoPQ TCS that responds to magnesium limitation and induces genes necessary for surviving this environmental challenge [65]. However, to date the identification of a relevant in vivo environment for P. aeruginosa which is cation limited has remained elusive. We have demonstrated that DNA-rich environments, such as biofilms, are cation limited. While Mg2+ limitation has been identified as a signal involved in induced resistance to aminoglycosides in P. aeruginosa [59], the contribution of the PhoPQ-regulated LPS modifications has not been clearly determined. PhoQ mutants, which constitutively express phoP and are constitutively resistant to cationic antimicrobial peptides, are also more resistant to aminoglycosides [43]. In S. typhimurium, PhoPQ regulates multiple LPS modifications that decrease the OM permeability to membrane cationic dyes, bile salts and antibiotics, including gentamicin [67]. We report here that DNA-induces aminoglycoside resistance in P. aeruginosa biofilms, and this resistance is partially dependent on the LPS modification operon PA3552-PA3559. The aminoarabinose modification likely blocks the self-promoted uptake of aminoglycosides, which normally bind and displace cations that crosslink adjacent LPS molecules [68]. Previous reports have documented the involvement of P. aeruginosa PmrAB [49] and the E. coli PmrAB homologs BasRS [69] in regulating the formation of an antimicrobial peptide-tolerant subpopulation within biofilms. In pure culture P. aeruginosa biofilms, genomic DNA localizes throughout the biofilm surface monolayer and surrounds the mushroom-shaped microcolonies [51]. This coincides with the localization of a CAP-tolerant subpopulation of bacteria that expresses the PA3552-PA3559 operon along the surface of mushroom-structured P. aeruginosa biofilms [49]. To date, it was thought unlikely that a biofilm environment may be cation limited. However, our data indicates that the presence of DNA in biofilms does indeed result in a cation-limited environment, resulting in the induction of the LPS modification operon PA3552-PA3559. To our knowledge this is the first report to identify the antimicrobial properties of DNA. Above certain concentrations (approximately0.5% (w/v)) extracellular DNA inhibited planktonic growth and biofilm formation. Recently, a novel host defense mechanism was discovered whereby stimulated neutrophils ejected a mesh-like net of intracellular DNA and proteins that functions to trap and kill pathogens [70]. The antimicrobial property of neutrophil nets was attributed to DNA-associated histones and other antimicrobial peptides [70]. However, our results demonstrate that above certain concentrations, the DNA itself is antimicrobial due to cation chelation. In principle, cation chelation by DNA is similar to another recently identified host defense mechanism, where the Mn2+ and Zn2+ metal chelation properties of the host innate-immune protein calprotectin was shown to limit Staphylococcus aureus growth in tissue abscesses [71]. Staining of peg-adhered biofilms indicated that DNA was present throughout the biofilm. (Fig 5B). This data supports the hypothesis that the release of genomic DNA by lysed cells following exposure to inhibitory concentrations of extracellular DNA may result in a continual release of DNA by dying cells and a DNA gradient within the biofilm. Our observation that DNA imposes a cation gradient in biofilm is also consistent with previous reports of oxygen and nutrient gradients within biofilms, which result in diverse physiological cellular states within a biofilm community [72]. Although DNA is toxic at high concentrations, it functions as a double-edged sword whereby sub-inhibitory DNA concentrations serve to protect bacteria from antibiotic exposure, either from the host immune response or from antimicrobial treatment. It has previously been reported that Mg2+ concentrations within the airway surface fluid are high (2.2 mM) [73],[74]. However, sputum samples from the lungs of CF patients have very high concentrations of DNA, up to 20 mg/ml (2% (w/v)) [75],[76]. It is likely that within the CF lung, localized cation limited environments exist within DNA-rich microcolonies. It is also known that CF airway fluid contains high levels of neutrophil defensins [77] and that sub-lethal doses of CAPs induce PA3553 gene expression, although independently of PhoPQ and PmrAB [45]. Therefore, it appears that there are multiple environmental signals in the CF lung that can induce the expression the PA3552-PA3559 operon, which may explain why many P. aeruginosa CF isolates show LPS modifications such as aminoarabinose addition to lipid A [78]. As many P. aeruginosa strains isolated from the CF lung overproduce the negatively charged EPS alginate, we hypothesized that alginate may also be a relevant in vivo signal inducing expression of the PA3552-PA3559 operon. However, induction of PA3553 gene expression does not occur in the presence of alginate (data not shown). The observation that DNA is present in the lungs of CF patients has prompted the use of DNAseI as a therapeutic agent to reduce the sputum viscosity and improve lung function [75],[76]. However, our data suggests that the success of DNAseI therapy may, in part, be attributed to the degradation of DNA and subsequent disarming of the PhoPQ/PmrAB response and antibiotic resistance mechanisms. While previous studies have shown the biofilm matrix to function as a diffusion barrier to antibiotics, these results demonstrate a novel function of the biofilm matrix component DNA, where the cation chelating properties of DNA in biofilms induces resistance to host-derived or therapeutic antimicrobials. Furthermore, these findings indicate that DNA-rich environments, such as bacterial biofilms or the CF lung, may represent the natural setting where bacterial growth is cation limited, and highlight the importance of the PhoPQ/PmrAB controlled response and LPS modifications in antibiotic resistance in biofilms.\n" ], "offsets": [ [ 0, 7563 ] ] } ]

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"text": [ "LPS" ], "offsets": [ [ 3592, 3595 ] ], "normalized": [] }, { "id": "PMC2581603-03-Discussion_T68", "type": "Regulon-operon", "text": [ "PA3552-PA3559" ], "offsets": [ [ 3616, 3629 ] ], "normalized": [] }, { "id": "PMC2581603-03-Discussion_T69", "type": "Protein", "text": [ "PA3552" ], "offsets": [ [ 3616, 3622 ] ], "normalized": [] }, { "id": "PMC2581603-03-Discussion_T70", "type": "Protein", "text": [ "PA3559" ], "offsets": [ [ 3623, 3629 ] ], "normalized": [] }, { "id": "PMC2581603-03-Discussion_T71", "type": "Chemical", "text": [ "Mn2+" ], "offsets": [ [ 4405, 4409 ] ], "normalized": [] }, { "id": "PMC2581603-03-Discussion_T72", "type": "Chemical", "text": [ "Zn2+" ], "offsets": [ [ 4414, 4418 ] ], "normalized": [] }, { "id": "PMC2581603-03-Discussion_T73", "type": "Organism", "text": [ "Staphylococcus aureus" ], "offsets": [ [ 4512, 4533 ] ], "normalized": [] }, { "id": "PMC2581603-03-Discussion_T74", "type": "Chemical", "text": [ "oxygen" ], "offsets": [ [ 5016, 5022 ] ], "normalized": [] }, { "id": "PMC2581603-03-Discussion_T75", "type": "Chemical", "text": [ "Mg2+" ], "offsets": [ [ 5434, 5438 ] ], "normalized": [] }, { "id": "PMC2581603-03-Discussion_T76", "type": "Organism", "text": [ "patients" ], "offsets": [ [ 5560, 5568 ] ], "normalized": [] }, { "id": "PMC2581603-03-Discussion_T77", "type": "Protein", "text": [ "PA3553" ], "offsets": [ [ 5886, 5892 ] ], "normalized": [] }, { "id": "PMC2581603-03-Discussion_T78", "type": "Two-component-system", "text": [ "PhoPQ" ], "offsets": [ [ 5936, 5941 ] ], "normalized": [] }, { "id": "PMC2581603-03-Discussion_T79", "type": "Protein", "text": [ "PhoP" ], "offsets": [ [ 5936, 5940 ] ], "normalized": [] }, { "id": "PMC2581603-03-Discussion_T80", "type": "Protein", "text": [ "Q" ], "offsets": [ [ 5940, 5941 ] ], "normalized": [] }, { "id": "PMC2581603-03-Discussion_T81", "type": "Two-component-system", "text": [ "PmrAB" ], "offsets": [ [ 5946, 5951 ] ], "normalized": [] }, { "id": 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"lipid A" ], "offsets": [ [ 6209, 6216 ] ], "normalized": [] }, { "id": "PMC2581603-03-Discussion_T90", "type": "Organism", "text": [ "P. aeruginosa" ], "offsets": [ [ 6231, 6244 ] ], "normalized": [] }, { "id": "PMC2581603-03-Discussion_T91", "type": "Chemical", "text": [ "EPS alginate" ], "offsets": [ [ 6314, 6326 ] ], "normalized": [] }, { "id": "PMC2581603-03-Discussion_T92", "type": "Chemical", "text": [ "alginate" ], "offsets": [ [ 6349, 6357 ] ], "normalized": [] }, { "id": "PMC2581603-03-Discussion_T93", "type": "Regulon-operon", "text": [ "PA3552-PA3559" ], "offsets": [ [ 6423, 6436 ] ], "normalized": [] }, { "id": "PMC2581603-03-Discussion_T94", "type": "Protein", "text": [ "PA3552" ], "offsets": [ [ 6423, 6429 ] ], "normalized": [] }, { "id": "PMC2581603-03-Discussion_T95", "type": "Protein", "text": [ "PA3559" ], "offsets": [ [ 6430, 6436 ] ], "normalized": [] }, { "id": "PMC2581603-03-Discussion_T96", "type": "Protein", "text": [ "PA3553" ], "offsets": [ [ 6467, 6473 ] ], "normalized": [] }, { "id": "PMC2581603-03-Discussion_T97", "type": "Chemical", "text": [ "alginate" ], "offsets": [ [ 6524, 6532 ] ], "normalized": [] }, { "id": "PMC2581603-03-Discussion_T98", "type": "Organism", "text": [ "patients" ], "offsets": [ [ 6606, 6614 ] ], "normalized": [] }, { "id": "PMC2581603-03-Discussion_T99", "type": "Two-component-system", "text": [ "PhoPQ" ], "offsets": [ [ 6885, 6890 ] ], "normalized": [] }, { "id": "PMC2581603-03-Discussion_T100", "type": "Protein", "text": [ "PhoP" ], "offsets": [ [ 6885, 6889 ] ], "normalized": [] }, { "id": "PMC2581603-03-Discussion_T101", "type": "Protein", "text": [ "Q" ], "offsets": [ [ 6889, 6890 ] ], "normalized": [] }, { "id": "PMC2581603-03-Discussion_T102", "type": "Two-component-system", "text": [ "PmrAB" ], "offsets": [ [ 6891, 6896 ] ], "normalized": [] }, { "id": "PMC2581603-03-Discussion_T103", "type": "Protein", "text": [ "PmrA" ], "offsets": [ [ 6891, 6895 ] ], "normalized": [] }, { "id": "PMC2581603-03-Discussion_T104", "type": "Protein", "text": [ "B" ], "offsets": [ [ 6895, 6896 ] ], "normalized": [] }, { "id": "PMC2581603-03-Discussion_T105", "type": "Two-component-system", "text": [ "PhoPQ" ], "offsets": [ [ 7471, 7476 ] ], "normalized": [] }, { "id": "PMC2581603-03-Discussion_T106", "type": "Protein", "text": [ "PhoP" ], "offsets": [ [ 7471, 7475 ] ], "normalized": [] }, { "id": "PMC2581603-03-Discussion_T107", "type": "Protein", "text": [ "Q" ], "offsets": [ [ 7475, 7476 ] ], "normalized": [] }, { "id": "PMC2581603-03-Discussion_T108", "type": "Two-component-system", "text": [ "PmrAB" ], "offsets": [ [ 7477, 7482 ] ], "normalized": [] }, { "id": "PMC2581603-03-Discussion_T109", "type": "Protein", "text": [ "PmrA" ], "offsets": [ [ 7477, 7481 ] ], "normalized": [] }, { "id": "PMC2581603-03-Discussion_T110", "type": "Protein", "text": [ "B" ], "offsets": [ [ 7481, 7482 ] ], "normalized": [] }, { "id": "PMC2581603-03-Discussion_T111", "type": "Chemical", "text": [ "LPS" ], "offsets": [ [ 7507, 7510 ] ], "normalized": [] } ]

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[ { "id": "PMC2266911-02-Results_and_Discussion-02-01-02__text", "type": "abstract", "text": [ "Hemolysins or hemagglutinin-related proteins \nThese extracellular toxins target red blood cells to provide access to iron, but often show activity against immune cells, thus contributing to the bacterial response to the immune system of hosts, including phagocytosis by insect blood cells [64]. Hemolysins or surface-associated adhesins, together with their transporters, are sometimes organized as two-partner secretion (TPS) systems, a specialized mechanism for the delivery of large exoproteins [65]. TPS systems have been characterized mainly in pathogenic bacteria, but are also present in other microorganisms. P. luminescens and Y. enterocolitica TPS systems include the calcium-independent hemolysin PhlA that is transported through the outer membrane and activated by PhlB. Remarkably, their expression is induced by low iron concentration as encountered in the insect host, and phlA/phlB are up-regulated at 18degreesC compared to 28degreesC in Y. ruckeri [66]. Eight other TPS systems are present in P. luminescens, namely Plu0225/Plu0226, Plu0548/Plu0549, Plu1149/Plu1150, Plu1367/Plu1368, Plu3064/Plu3065, Plu3125-3127/3128, Plu3667/Plu3668, and Plu3718/Plu3719, and further three genes for which the partner locus has not been identified (Fig. 4). In the genome of Y. enterocolitica, only three complete TPS systems are present, namely YE0479/YE0480, YE2407/YE2408, (YE4084)YE4085/YE4086, and YE3454 which lacks the activator partner. Except YE0479/YE0480, all have counterparts in the P. luminescens genome. Recently, we have shown that a luciferase reporter insertion into YE0480 is induced at low temperature [67], indicating that this TPS system might contribute to insect pathogenicity and possibly to the host-specificity of Y. enterocolitica. The genomes of both pathogens also carry three and five, respectively, further hemolysin/hemagglutinin-related proteins which are absent in the other pathogen (Fig. 4). FhaC which belongs to a family of hemolysin activator proteins related to ShlA from Serratia marcescens is present in both pathogens and also induced at low temperature [67]. The genome sequence of P. luminescens exhibits more toxin genes than found in any other bacterial genome sequenced yet, including the genome of Y. enterocolitica. Hemolysin-related factors and their transporters discussed above are an example for this redundancy. However, the majority of these P. luminescens toxins exhibit highly significant similarities to those of Y. enterocolitica, suggesting common progenitors of hemolysins. It is therefore tempting to speculate that hemolytic activities of bacteria had been evolved during the association with insects and then adapted to mammalian hosts. Although it can not be excluded that the hemolysins of Y. enterocolitica act on the immune systems of both the insect and the mammalian host, the genetic overlap of this group of virulence factor between both pathogens, and the low-temperature expression of YE0479/YE0480 and fhaC, indicates the presence of insect-specific hemolysins in the genome of Y. enterocolitica.\n" ], "offsets": [ [ 0, 3078 ] ] } ]

[ { "id": "PMC2266911-02-Results_and_Discussion-02-01-02_T1", "type": "Chemical", "text": [ "iron" ], "offsets": [ [ 117, 121 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-02-01-02_T2", "type": "Organism", "text": [ "P. luminescens" ], "offsets": [ [ 617, 631 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-02-01-02_T3", "type": "Organism", "text": [ "Y. enterocolitica" ], "offsets": [ [ 636, 653 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-02-01-02_T4", "type": "Chemical", "text": [ "calcium" ], "offsets": [ [ 678, 685 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-02-01-02_T5", "type": "Protein", "text": [ "PhlA" ], "offsets": [ [ 708, 712 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-02-01-02_T6", "type": "Protein", "text": [ "PhlB" ], "offsets": [ [ 777, 781 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-02-01-02_T7", "type": "Chemical", "text": [ "iron" ], "offsets": [ [ 830, 834 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-02-01-02_T8", "type": "Two-component-system", "text": [ "phlA/phlB" ], "offsets": [ [ 888, 897 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-02-01-02_T9", "type": "Protein", "text": [ "phlA" ], "offsets": [ [ 888, 892 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-02-01-02_T10", "type": "Protein", "text": [ "phlB" ], "offsets": [ [ 893, 897 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-02-01-02_T11", "type": "Organism", "text": [ "Y. ruckeri" ], "offsets": [ [ 955, 965 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-02-01-02_T12", "type": "Organism", "text": [ "P. luminescens" ], "offsets": [ [ 1011, 1025 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-02-01-02_T13", "type": "Two-component-system", "text": [ "Plu0225/Plu0226" ], "offsets": [ [ 1034, 1049 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-02-01-02_T14", "type": "Protein", "text": [ "Plu0225" ], "offsets": [ [ 1034, 1041 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-02-01-02_T15", "type": "Protein", "text": [ "Plu0226" ], "offsets": [ [ 1042, 1049 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-02-01-02_T16", "type": "Two-component-system", "text": [ "Plu0548/Plu0549" ], "offsets": [ [ 1051, 1066 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-02-01-02_T17", "type": "Protein", "text": [ "Plu0548" ], "offsets": [ [ 1051, 1058 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-02-01-02_T18", "type": "Protein", "text": [ "Plu0549" ], "offsets": [ [ 1059, 1066 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-02-01-02_T19", "type": "Two-component-system", "text": [ "Plu1149/Plu1150" ], "offsets": [ [ 1068, 1083 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-02-01-02_T20", "type": "Protein", "text": [ "Plu1149" ], "offsets": [ [ 1068, 1075 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-02-01-02_T21", "type": "Protein", "text": [ "Plu1150" ], "offsets": [ [ 1076, 1083 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-02-01-02_T22", "type": "Two-component-system", "text": [ "Plu1367/Plu1368" ], "offsets": [ [ 1085, 1100 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-02-01-02_T23", "type": "Protein", "text": [ "Plu1367" ], "offsets": [ [ 1085, 1092 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-02-01-02_T24", "type": "Protein", "text": [ "Plu1368" ], "offsets": [ [ 1093, 1100 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-02-01-02_T25", "type": "Two-component-system", "text": [ "Plu3064/Plu3065" ], "offsets": [ [ 1102, 1117 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-02-01-02_T26", "type": "Protein", "text": [ "Plu3064" ], "offsets": [ [ 1102, 1109 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-02-01-02_T27", "type": "Protein", "text": [ "Plu3065" ], "offsets": [ [ 1110, 1117 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-02-01-02_T28", "type": "Two-component-system", "text": [ "Plu3125-3127/3128" ], "offsets": [ [ 1119, 1136 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-02-01-02_T29", "type": "Protein", "text": [ "Plu3125" ], "offsets": [ [ 1119, 1126 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-02-01-02_T30", "type": "Protein", "text": [ "3127" ], "offsets": [ [ 1127, 1131 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-02-01-02_T31", "type": "Protein", "text": [ "3128" ], "offsets": [ [ 1132, 1136 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-02-01-02_T32", "type": "Two-component-system", "text": [ "Plu3667/Plu3668" ], "offsets": [ [ 1138, 1153 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-02-01-02_T33", "type": "Protein", "text": [ "Plu3667" ], "offsets": [ [ 1138, 1145 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-02-01-02_T34", "type": "Protein", "text": [ "Plu3668" ], "offsets": [ [ 1146, 1153 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-02-01-02_T35", "type": "Two-component-system", "text": [ "Plu3718/Plu3719" ], "offsets": [ [ 1159, 1174 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-02-01-02_T36", "type": "Protein", "text": [ "Plu3718" ], "offsets": [ [ 1159, 1166 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-02-01-02_T37", "type": "Protein", "text": [ "Plu3719" ], "offsets": [ [ 1167, 1174 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-02-01-02_T38", "type": "Organism", "text": [ "Y. enterocolitica" ], "offsets": [ [ 1279, 1296 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-02-01-02_T39", "type": "Two-component-system", "text": [ "YE0479/YE0480" ], "offsets": [ [ 1350, 1363 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-02-01-02_T40", "type": "Protein", "text": [ "YE0479" ], "offsets": [ [ 1350, 1356 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-02-01-02_T41", "type": "Protein", "text": [ "YE0480" ], "offsets": [ [ 1357, 1363 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-02-01-02_T42", "type": "Two-component-system", "text": [ "YE2407/YE2408" ], "offsets": [ [ 1365, 1378 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-02-01-02_T43", "type": "Protein", "text": [ "YE2407" ], "offsets": [ [ 1365, 1371 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-02-01-02_T44", "type": "Protein", "text": [ "YE2408" ], "offsets": [ [ 1372, 1378 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-02-01-02_T45", "type": "Two-component-system", "text": [ "(YE4084)YE4085/YE4086" ], "offsets": [ [ 1380, 1401 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-02-01-02_T46", "type": "Protein", "text": [ "YE4084" ], "offsets": [ [ 1381, 1387 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-02-01-02_T47", "type": "Protein", "text": [ "YE4085" ], "offsets": [ [ 1388, 1394 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-02-01-02_T48", "type": "Protein", "text": [ "YE4086" ], "offsets": [ [ 1395, 1401 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-02-01-02_T49", "type": "Protein", "text": [ "YE3454" ], "offsets": [ [ 1407, 1413 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-02-01-02_T50", "type": "Two-component-system", "text": [ "YE0479/YE0480" ], "offsets": [ [ 1456, 1469 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-02-01-02_T51", "type": "Protein", "text": [ "YE0479" ], "offsets": [ [ 1456, 1462 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-02-01-02_T52", "type": "Protein", "text": [ "YE0480" ], "offsets": [ [ 1463, 1469 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-02-01-02_T53", "type": "Organism", "text": [ "P. luminescens" ], "offsets": [ [ 1500, 1514 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-02-01-02_T54", "type": "Protein", "text": [ "YE0480" ], "offsets": [ [ 1589, 1595 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-02-01-02_T55", "type": "Organism", "text": [ "Y. enterocolitica" ], "offsets": [ [ 1745, 1762 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-02-01-02_T56", "type": "Protein", "text": [ "FhaC" ], "offsets": [ [ 1933, 1937 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-02-01-02_T57", "type": "Protein", "text": [ "ShlA" ], "offsets": [ [ 2007, 2011 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-02-01-02_T58", "type": "Organism", "text": [ "Serratia marcescens" ], "offsets": [ [ 2017, 2036 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-02-01-02_T59", "type": "Organism", "text": [ "P. luminescens" ], "offsets": [ [ 2131, 2145 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-02-01-02_T60", "type": "Organism", "text": [ "Y. enterocolitica" ], "offsets": [ [ 2252, 2269 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-02-01-02_T61", "type": "Organism", "text": [ "P. luminescens" ], "offsets": [ [ 2403, 2417 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-02-01-02_T62", "type": "Organism", "text": [ "Y. enterocolitica" ], "offsets": [ [ 2477, 2494 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-02-01-02_T63", "type": "Organism", "text": [ "Y. enterocolitica" ], "offsets": [ [ 2762, 2779 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-02-01-02_T64", "type": "Two-component-system", "text": [ "YE0479/YE0480" ], "offsets": [ [ 2965, 2978 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-02-01-02_T65", "type": "Protein", "text": [ "YE0479" ], "offsets": [ [ 2965, 2971 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-02-01-02_T66", "type": "Protein", "text": [ "YE0480" ], "offsets": [ [ 2972, 2978 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-02-01-02_T67", "type": "Protein", "text": [ "fhaC" ], "offsets": [ [ 2983, 2987 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-02-01-02_T68", "type": "Organism", "text": [ "Y. enterocolitica" ], "offsets": [ [ 3059, 3076 ] ], "normalized": [] } ]

[ { "id": "PMC2266911-02-Results_and_Discussion-02-01-02_E1", "type": "Localization", "trigger": { "text": [ "transported" ], "offsets": [ [ 721, 732 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC2266911-02-Results_and_Discussion-02-01-02_T5" } ] }, { "id": "PMC2266911-02-Results_and_Discussion-02-01-02_E2", "type": "Positive_regulation", "trigger": { "text": [ "activated" ], "offsets": [ [ 764, 773 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC2266911-02-Results_and_Discussion-02-01-02_T5" }, { "role": "Cause", "ref_id": "PMC2266911-02-Results_and_Discussion-02-01-02_T6" } ] }, { "id": "PMC2266911-02-Results_and_Discussion-02-01-02_E3", "type": "Gene_expression", "trigger": { "text": [ "expression" ], "offsets": [ [ 801, 811 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC2266911-02-Results_and_Discussion-02-01-02_T5" } ] }, { "id": "PMC2266911-02-Results_and_Discussion-02-01-02_E4", "type": "Gene_expression", "trigger": { "text": [ "expression" ], "offsets": [ [ 801, 811 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC2266911-02-Results_and_Discussion-02-01-02_T6" } ] }, { "id": "PMC2266911-02-Results_and_Discussion-02-01-02_E5", "type": "Positive_regulation", "trigger": { "text": [ "up-regulated" ], "offsets": [ [ 902, 914 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC2266911-02-Results_and_Discussion-02-01-02_T8" } ] }, { "id": "PMC2266911-02-Results_and_Discussion-02-01-02_E6", "type": "Positive_regulation", "trigger": { "text": [ "induced" ], "offsets": [ [ 2075, 2082 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC2266911-02-Results_and_Discussion-02-01-02_T56" } ] }, { "id": "PMC2266911-02-Results_and_Discussion-02-01-02_E7", "type": "Process", "trigger": { "text": [ "virulence" ], "offsets": [ [ 2886, 2895 ] ] }, "arguments": [] }, { "id": "PMC2266911-02-Results_and_Discussion-02-01-02_E8", "type": "Gene_expression", "trigger": { "text": [ "expression" ], "offsets": [ [ 2951, 2961 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC2266911-02-Results_and_Discussion-02-01-02_T67" } ] }, { "id": "PMC2266911-02-Results_and_Discussion-02-01-02_E9", "type": "Gene_expression", "trigger": { "text": [ "expression" ], "offsets": [ [ 2951, 2961 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC2266911-02-Results_and_Discussion-02-01-02_T65" } ] }, { "id": "PMC2266911-02-Results_and_Discussion-02-01-02_E10", "type": "Gene_expression", "trigger": { "text": [ "expression" ], "offsets": [ [ 2951, 2961 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC2266911-02-Results_and_Discussion-02-01-02_T66" } ] } ]

[]

[]

[ { "id": "PMC2565068-00-TIAB__text", "type": "abstract", "text": [ "Incompetence of Neutrophils to Invasive Group A streptococcus Is Attributed to Induction of Plural Virulence Factors by Dysfunction of a Regulator \nGroup A streptococcus (GAS) causes variety of diseases ranging from common pharyngitis to life-threatening severe invasive diseases, including necrotizing fasciitis and streptococcal toxic shock-like syndrome. The characteristic of invasive GAS infections has been thought to attribute to genetic changes in bacteria, however, no clear evidence has shown due to lack of an intriguingly study using serotype-matched isolates from clinical severe invasive GAS infections. In addition, rare outbreaks of invasive infections and their distinctive pathology in which infectious foci without neutrophil infiltration hypothesized us invasive GAS could evade host defense, especially neutrophil functions. Herein we report that a panel of serotype-matched GAS, which were clinically isolated from severe invasive but not from non-invaive infections, could abrogate functions of human polymorphnuclear neutrophils (PMN) in at least two independent ways; due to inducing necrosis to PMN by enhanced production of a pore-forming toxin streptolysin O (SLO) and due to impairment of PMN migration via digesting interleukin-8, a PMN attracting chemokine, by increased production of a serine protease ScpC. Expression of genes was upregulated by a loss of repressive function with the mutation of csrS gene in the all emm49 severe invasive GAS isolates. The csrS mutants from clinical severe invasive GAS isolates exhibited high mortality and disseminated infection with paucity of neutrophils, a characteristic pathology seen in human invasive GAS infection, in a mouse model. However, GAS which lack either SLO or ScpC exhibit much less mortality than the csrS-mutated parent invasive GAS isolate to the infected mice. These results suggest that the abilities of GAS to abrogate PMN functions can determine the onset and severity of invasive GAS infection.\n" ], "offsets": [ [ 0, 1992 ] ] } ]

[ { "id": "PMC2565068-00-TIAB_T1", "type": "Organism", "text": [ "Invasive Group A streptococcus" ], "offsets": [ [ 31, 61 ] ], "normalized": [] }, { "id": "PMC2565068-00-TIAB_T2", "type": "Organism", "text": [ "Group A streptococcus" ], "offsets": [ [ 148, 169 ] ], "normalized": [] }, { "id": "PMC2565068-00-TIAB_T3", "type": "Organism", "text": [ "GAS" ], "offsets": [ [ 171, 174 ] ], "normalized": [] }, { "id": "PMC2565068-00-TIAB_T4", "type": "Organism", "text": [ "invasive GAS" ], "offsets": [ [ 380, 392 ] ], "normalized": [] }, { "id": "PMC2565068-00-TIAB_T5", "type": "Organism", "text": [ "invasive GAS" ], "offsets": [ [ 593, 605 ] ], "normalized": [] }, { "id": "PMC2565068-00-TIAB_T6", "type": "Organism", "text": [ "invasive GAS" ], "offsets": [ [ 774, 786 ] ], "normalized": [] }, { "id": "PMC2565068-00-TIAB_T7", "type": "Organism", "text": [ "GAS" ], "offsets": [ [ 896, 899 ] ], "normalized": [] }, { "id": "PMC2565068-00-TIAB_T8", "type": "Organism", "text": [ "human" ], "offsets": [ [ 1018, 1023 ] ], "normalized": [] }, { "id": "PMC2565068-00-TIAB_T9", "type": "Protein", "text": [ "streptolysin O" ], "offsets": [ [ 1172, 1186 ] ], "normalized": [] }, { "id": "PMC2565068-00-TIAB_T10", "type": "Protein", "text": [ "SLO" ], "offsets": [ [ 1188, 1191 ] ], "normalized": [] }, { "id": "PMC2565068-00-TIAB_T11", "type": "Protein", "text": [ "interleukin-8" ], "offsets": [ [ 1246, 1259 ] ], "normalized": [] }, { "id": "PMC2565068-00-TIAB_T12", "type": "Protein", "text": [ "ScpC" ], "offsets": [ [ 1334, 1338 ] ], "normalized": [] }, { "id": "PMC2565068-00-TIAB_T13", "type": "Protein", "text": [ "csrS" ], "offsets": [ [ 1430, 1434 ] ], "normalized": [] }, { "id": "PMC2565068-00-TIAB_T14", "type": "Protein", "text": [ "emm49" ], "offsets": [ [ 1451, 1456 ] ], "normalized": [] }, { "id": "PMC2565068-00-TIAB_T15", "type": "Organism", "text": [ "invasive GAS" ], "offsets": [ [ 1464, 1476 ] ], "normalized": [] }, { "id": "PMC2565068-00-TIAB_T16", "type": "Organism", "text": [ "csrS mutants" ], "offsets": [ [ 1491, 1503 ] ], "normalized": [] }, { "id": "PMC2565068-00-TIAB_T17", "type": "Protein", "text": [ "csrS" ], "offsets": [ [ 1491, 1495 ] ], "normalized": [] }, { "id": "PMC2565068-00-TIAB_T18", "type": "Organism", "text": [ "invasive GAS" ], "offsets": [ [ 1525, 1537 ] ], "normalized": [] }, { "id": "PMC2565068-00-TIAB_T19", "type": "Organism", "text": [ "human" ], "offsets": [ [ 1663, 1668 ] ], "normalized": [] }, { "id": "PMC2565068-00-TIAB_T20", "type": "Organism", "text": [ "invasive GAS" ], "offsets": [ [ 1669, 1681 ] ], "normalized": [] }, { "id": "PMC2565068-00-TIAB_T21", "type": "Organism", "text": [ "mouse" ], "offsets": [ [ 1698, 1703 ] ], "normalized": [] }, { "id": "PMC2565068-00-TIAB_T22", "type": "Organism", "text": [ "GAS" ], "offsets": [ [ 1720, 1723 ] ], "normalized": [] }, { "id": "PMC2565068-00-TIAB_T23", "type": "Protein", "text": [ "SLO" ], "offsets": [ [ 1742, 1745 ] ], "normalized": [] }, { "id": "PMC2565068-00-TIAB_T24", "type": "Protein", "text": [ "ScpC" ], "offsets": [ [ 1749, 1753 ] ], "normalized": [] }, { "id": "PMC2565068-00-TIAB_T25", "type": "Organism", "text": [ "csrS-mutated parent invasive GAS" ], "offsets": [ [ 1791, 1823 ] ], "normalized": [] }, { "id": "PMC2565068-00-TIAB_T26", "type": "Protein", "text": [ "csrS" ], "offsets": [ [ 1791, 1795 ] ], "normalized": [] }, { "id": "PMC2565068-00-TIAB_T27", "type": "Organism", "text": [ "mice" ], "offsets": [ [ 1848, 1852 ] ], "normalized": [] }, { "id": "PMC2565068-00-TIAB_T28", "type": "Organism", "text": [ "GAS" ], "offsets": [ [ 1898, 1901 ] ], "normalized": [] }, { "id": "PMC2565068-00-TIAB_T29", "type": "Organism", "text": [ "invasive GAS" ], "offsets": [ [ 1968, 1980 ] ], "normalized": [] } ]

[ { "id": "PMC2565068-00-TIAB_E1", "type": "Process", "trigger": { "text": [ "Virulence" ], "offsets": [ [ 99, 108 ] ] }, "arguments": [] }, { "id": "PMC2565068-00-TIAB_E2", "type": "Process", "trigger": { "text": [ "infections" ], "offsets": [ [ 393, 403 ] ] }, "arguments": [ { "role": "Participant", "ref_id": "PMC2565068-00-TIAB_T4" } ] }, { "id": "PMC2565068-00-TIAB_E3", "type": "Process", "trigger": { "text": [ "infections" ], "offsets": [ [ 606, 616 ] ] }, "arguments": [ { "role": "Participant", "ref_id": "PMC2565068-00-TIAB_T5" } ] }, { "id": "PMC2565068-00-TIAB_E4", "type": "Process", "trigger": { "text": [ "infections" ], "offsets": [ [ 658, 668 ] ] }, "arguments": [] }, { "id": "PMC2565068-00-TIAB_E5", "type": "Process", "trigger": { "text": [ "infections" ], "offsets": [ [ 978, 988 ] ] }, "arguments": [ { "role": "Participant", "ref_id": "PMC2565068-00-TIAB_T7" } ] }, { "id": "PMC2565068-00-TIAB_E6", "type": "Gene_expression", "trigger": { "text": [ "production" ], "offsets": [ [ 1137, 1147 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC2565068-00-TIAB_T9" } ] }, { "id": "PMC2565068-00-TIAB_E7", "type": "Positive_regulation", "trigger": { "text": [ "increased" ], "offsets": [ [ 1292, 1301 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC2565068-00-TIAB_E8" } ] }, { "id": "PMC2565068-00-TIAB_E8", "type": "Gene_expression", "trigger": { "text": [ "production" ], "offsets": [ [ 1302, 1312 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC2565068-00-TIAB_T12" } ] }, { "id": "PMC2565068-00-TIAB_E9", "type": "Process", "trigger": { "text": [ "infection" ], "offsets": [ [ 1589, 1598 ] ] }, "arguments": [ { "role": "Participant", "ref_id": "PMC2565068-00-TIAB_T16" } ] }, { "id": "PMC2565068-00-TIAB_E10", "type": "Process", "trigger": { "text": [ "infection" ], "offsets": [ [ 1682, 1691 ] ] }, "arguments": [ { "role": "Participant", "ref_id": "PMC2565068-00-TIAB_T20" } ] }, { "id": "PMC2565068-00-TIAB_E11", "type": "Process", "trigger": { "text": [ "infected" ], "offsets": [ [ 1839, 1847 ] ] }, "arguments": [ { "role": "Participant", "ref_id": "PMC2565068-00-TIAB_T22" } ] }, { "id": "PMC2565068-00-TIAB_E12", "type": "Process", "trigger": { "text": [ "infection" ], "offsets": [ [ 1981, 1990 ] ] }, "arguments": [ { "role": "Participant", "ref_id": "PMC2565068-00-TIAB_T29" } ] } ]

[ { "id": "PMC2565068-00-TIAB_1", "entity_ids": [ "PMC2565068-00-TIAB_T2", "PMC2565068-00-TIAB_T3" ] }, { "id": "PMC2565068-00-TIAB_2", "entity_ids": [ "PMC2565068-00-TIAB_T9", "PMC2565068-00-TIAB_T10" ] } ]

[]

[ { "id": "PMC1913099-00-TIAB__text", "type": "abstract", "text": [ "Novel Algorithms Reveal Streptococcal Transcriptomes and Clues about Undefined Genes \nBacteria-host interactions are dynamic processes, and understanding transcriptional responses that directly or indirectly regulate the expression of genes involved in initial infection stages would illuminate the molecular events that result in host colonization. We used oligonucleotide microarrays to monitor (in vitro) differential gene expression in group A streptococci during pharyngeal cell adherence, the first overt infection stage. We present neighbor clustering, a new computational method for further analyzing bacterial microarray data that combines two informative characteristics of bacterial genes that share common function or regulation: (1) similar gene expression profiles (i.e., co-expression); and (2) physical proximity of genes on the chromosome. This method identifies statistically significant clusters of co-expressed gene neighbors that potentially share common function or regulation by coupling statistically analyzed gene expression profiles with the chromosomal position of genes. We applied this method to our own data and to those of others, and we show that it identified a greater number of differentially expressed genes, facilitating the reconstruction of more multimeric proteins and complete metabolic pathways than would have been possible without its application. We assessed the biological significance of two identified genes by assaying deletion mutants for adherence in vitro and show that neighbor clustering indeed provides biologically relevant data. Neighbor clustering provides a more comprehensive view of the molecular responses of streptococci during pharyngeal cell adherence.\n" ], "offsets": [ [ 0, 1718 ] ] } ]

[ { "id": "PMC1913099-00-TIAB_T1", "type": "Organism", "text": [ "group A streptococci" ], "offsets": [ [ 440, 460 ] ], "normalized": [] }, { "id": "PMC1913099-00-TIAB_T2", "type": "Organism", "text": [ "streptococci" ], "offsets": [ [ 1671, 1683 ] ], "normalized": [] } ]

[ { "id": "PMC1913099-00-TIAB_E1", "type": "Process", "trigger": { "text": [ "infection" ], "offsets": [ [ 261, 270 ] ] }, "arguments": [] }, { "id": "PMC1913099-00-TIAB_E2", "type": "Process", "trigger": { "text": [ "infection" ], "offsets": [ [ 511, 520 ] ] }, "arguments": [] } ]

[]

[]

[ { "id": "PMC2593050-03-RESULTS-06__text", "type": "abstract", "text": [ "Intranasal DeltavicK Infection Induces SeM-Specific Mucosal IgA and Systemic IgG \nTo examine the humoral immune responses in the intranasal DeltavicK infection, nasal wash and serum samples were collected from the 8 mice infected intranasally with DeltavicK and 3 surviving mice infected with the wild-type S. equi 30 days after infection. Half of the nasal wash samples from the mice infected with DeltavicK had similar levels of SeM38-260-IgA reactivity with those from the mice infected with the wild-type strains. Similarly, these 4 mice with higher IgA levels also had higher levels of SeM-specific systemic IgG (Fig. 5B). Western blotting analysis was used to confirm the presence of SeM-specific IgG. The wild-type sera and 5 of the 8 DeltavicK samples had strong immunoreactions with SeM38-260 in Western blotting analysis (Fig. 5C). Thus, the DeltavicK mutant has the ability to induce mucosal and systemic immune responses, though there was host variation in these responses caused by DeltavicK infection.\n" ], "offsets": [ [ 0, 1016 ] ] } ]

[ { "id": "PMC2593050-03-RESULTS-06_T1", "type": "Organism", "text": [ "DeltavicK" ], "offsets": [ [ 11, 20 ] ], "normalized": [] }, { "id": "PMC2593050-03-RESULTS-06_T2", "type": "Protein", "text": [ "vicK" ], "offsets": [ [ 16, 20 ] ], "normalized": [] }, { "id": "PMC2593050-03-RESULTS-06_T3", "type": "Protein", "text": [ "SeM" ], "offsets": [ [ 39, 42 ] ], "normalized": [] }, { "id": "PMC2593050-03-RESULTS-06_T4", "type": "Protein", "text": [ "IgA" ], "offsets": [ [ 60, 63 ] ], "normalized": [] }, { "id": "PMC2593050-03-RESULTS-06_T5", "type": "Protein", "text": [ "IgG" ], "offsets": [ [ 77, 80 ] ], "normalized": [] }, { "id": "PMC2593050-03-RESULTS-06_T6", "type": "Organism", "text": [ "DeltavicK" ], "offsets": [ [ 140, 149 ] ], "normalized": [] }, { "id": "PMC2593050-03-RESULTS-06_T7", "type": "Protein", "text": [ "vicK" ], "offsets": [ [ 145, 149 ] ], "normalized": [] }, { "id": "PMC2593050-03-RESULTS-06_T8", "type": "Organism", "text": [ "mice" ], "offsets": [ [ 216, 220 ] ], "normalized": [] }, { "id": "PMC2593050-03-RESULTS-06_T9", "type": "Organism", "text": [ "DeltavicK" ], "offsets": [ [ 248, 257 ] ], "normalized": [] }, { "id": "PMC2593050-03-RESULTS-06_T10", "type": "Protein", "text": [ "vicK" ], "offsets": [ [ 253, 257 ] ], "normalized": [] }, { "id": "PMC2593050-03-RESULTS-06_T11", "type": "Organism", "text": [ "mice" ], "offsets": [ [ 274, 278 ] ], "normalized": [] }, { "id": "PMC2593050-03-RESULTS-06_T12", "type": "Organism", "text": [ "S. equi" ], "offsets": [ [ 307, 314 ] ], "normalized": [] }, { "id": "PMC2593050-03-RESULTS-06_T13", "type": "Organism", "text": [ "mice" ], "offsets": [ [ 380, 384 ] ], "normalized": [] }, { "id": "PMC2593050-03-RESULTS-06_T14", "type": "Organism", "text": [ "DeltavicK" ], "offsets": [ [ 399, 408 ] ], "normalized": [] }, { "id": "PMC2593050-03-RESULTS-06_T15", "type": "Protein", "text": [ "vicK" ], "offsets": [ [ 404, 408 ] ], "normalized": [] }, { "id": "PMC2593050-03-RESULTS-06_T16", "type": "Protein", "text": [ "SeM38" ], "offsets": [ [ 431, 436 ] ], "normalized": [] }, { "id": "PMC2593050-03-RESULTS-06_T17", "type": "Protein", "text": [ "260" ], "offsets": [ [ 437, 440 ] ], "normalized": [] }, { "id": "PMC2593050-03-RESULTS-06_T18", "type": "Protein", "text": [ "IgA" ], "offsets": [ [ 441, 444 ] ], "normalized": [] }, { "id": "PMC2593050-03-RESULTS-06_T19", "type": "Organism", "text": [ "mice" ], "offsets": [ [ 476, 480 ] ], "normalized": [] }, { "id": "PMC2593050-03-RESULTS-06_T20", "type": "Organism", "text": [ "mice" ], "offsets": [ [ 537, 541 ] ], "normalized": [] }, { "id": "PMC2593050-03-RESULTS-06_T21", "type": "Protein", "text": [ "IgA" ], "offsets": [ [ 554, 557 ] ], "normalized": [] }, { "id": "PMC2593050-03-RESULTS-06_T22", "type": "Protein", "text": [ "SeM" ], "offsets": [ [ 591, 594 ] ], "normalized": [] }, { "id": "PMC2593050-03-RESULTS-06_T23", "type": "Protein", "text": [ "IgG" ], "offsets": [ [ 613, 616 ] ], "normalized": [] }, { "id": "PMC2593050-03-RESULTS-06_T24", "type": "Protein", "text": [ "SeM" ], "offsets": [ [ 690, 693 ] ], "normalized": [] }, { "id": "PMC2593050-03-RESULTS-06_T25", "type": "Protein", "text": [ "IgG" ], "offsets": [ [ 703, 706 ] ], "normalized": [] }, { "id": "PMC2593050-03-RESULTS-06_T26", "type": "Organism", "text": [ "DeltavicK" ], "offsets": [ [ 742, 751 ] ], "normalized": [] }, { "id": "PMC2593050-03-RESULTS-06_T27", "type": "Protein", "text": [ "vicK" ], "offsets": [ [ 747, 751 ] ], "normalized": [] }, { "id": "PMC2593050-03-RESULTS-06_T28", "type": "Protein", "text": [ "SeM38" ], "offsets": [ [ 792, 797 ] ], "normalized": [] }, { "id": "PMC2593050-03-RESULTS-06_T29", "type": "Protein", "text": [ "260" ], "offsets": [ [ 798, 801 ] ], "normalized": [] }, { "id": "PMC2593050-03-RESULTS-06_T30", "type": "Organism", "text": [ "DeltavicK mutant" ], "offsets": [ [ 852, 868 ] ], "normalized": [] }, { "id": "PMC2593050-03-RESULTS-06_T31", "type": "Protein", "text": [ "vicK" ], "offsets": [ [ 857, 861 ] ], "normalized": [] }, { "id": "PMC2593050-03-RESULTS-06_T32", "type": "Organism", "text": [ "DeltavicK" ], "offsets": [ [ 995, 1004 ] ], "normalized": [] }, { "id": "PMC2593050-03-RESULTS-06_T33", "type": "Protein", "text": [ "vicK" ], "offsets": [ [ 1000, 1004 ] ], "normalized": [] } ]

[ { "id": "PMC2593050-03-RESULTS-06_E1", "type": "Process", "trigger": { "text": [ "Infection" ], "offsets": [ [ 21, 30 ] ] }, "arguments": [ { "role": "Participant", "ref_id": "PMC2593050-03-RESULTS-06_T1" } ] }, { "id": "PMC2593050-03-RESULTS-06_E2", "type": "Positive_regulation", "trigger": { "text": [ "Induces" ], "offsets": [ [ 31, 38 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC2593050-03-RESULTS-06_T4" }, { "role": "Cause", "ref_id": "PMC2593050-03-RESULTS-06_E1" } ] }, { "id": "PMC2593050-03-RESULTS-06_E3", "type": "Positive_regulation", "trigger": { "text": [ "Induces" ], "offsets": [ [ 31, 38 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC2593050-03-RESULTS-06_T5" }, { "role": "Cause", "ref_id": "PMC2593050-03-RESULTS-06_E1" } ] }, { "id": "PMC2593050-03-RESULTS-06_E4", "type": "Process", "trigger": { "text": [ "infection" ], "offsets": [ [ 150, 159 ] ] }, "arguments": [ { "role": "Participant", "ref_id": "PMC2593050-03-RESULTS-06_T6" } ] }, { "id": "PMC2593050-03-RESULTS-06_E5", "type": "Process", "trigger": { "text": [ "infected" ], "offsets": [ [ 221, 229 ] ] }, "arguments": [ { "role": "Participant", "ref_id": "PMC2593050-03-RESULTS-06_T9" } ] }, { "id": "PMC2593050-03-RESULTS-06_E6", "type": "Process", "trigger": { "text": [ "infected" ], "offsets": [ [ 279, 287 ] ] }, "arguments": [ { "role": "Participant", "ref_id": "PMC2593050-03-RESULTS-06_T12" } ] }, { "id": "PMC2593050-03-RESULTS-06_E7", "type": "Process", "trigger": { "text": [ "infection" ], "offsets": [ [ 329, 338 ] ] }, "arguments": [] }, { "id": "PMC2593050-03-RESULTS-06_E8", "type": "Process", "trigger": { "text": [ "infected" ], "offsets": [ [ 385, 393 ] ] }, "arguments": [ { "role": "Participant", "ref_id": "PMC2593050-03-RESULTS-06_T14" } ] }, { "id": "PMC2593050-03-RESULTS-06_E9", "type": "Process", "trigger": { "text": [ "infected" ], "offsets": [ [ 481, 489 ] ] }, "arguments": [] }, { "id": "PMC2593050-03-RESULTS-06_E10", "type": "Process", "trigger": { "text": [ "infection" ], "offsets": [ [ 1005, 1014 ] ] }, "arguments": [ { "role": "Participant", "ref_id": "PMC2593050-03-RESULTS-06_T32" } ] } ]

[]

[]

[ { "id": "PMC2266911-02-Results_and_Discussion-01-01__text", "type": "abstract", "text": [ "Results and Discussion \nThe genomes of P. luminescens ssp. laumondii TT01 and Y. enterocolitica 8081 have completely been sequenced. The genome of the latter strain has a size of ~4.6 Mbp and encodes 4037 putative proteins [23]. Its genome size is exceeded by the ~5.7 Mbp genome of P. luminescens encoding 4839 putative proteins [24]. To uncover candidate genes which are involved in insect pathogenicity, a total of 424 (P. luminescens) and 386 (Y. enterocolitica) genes and proteins predicted to belong to one of the functional categories described in the text were analysed for their presence or absence in both organisms, and for their degree of similarity. House-keeping genes and genes of unknown function were not considered. The set of shared genes or proteins, respectively, indicates mechanisms of regulation, virulence and metabolic pathways similar for both pathogens, and moreover unraveled novel candidate genes/proteins which presumably are involved in insect association and/or pathogenicity. Proteins which are solely present in either one of the organisms suggest a distinct function of these factors, or different strategies followed by the two pathogens during their life cycles. Sensing, signalling, and regulation Bacteria have evolved several regulation mechanisms to ensure a proper answer to changing environments. Upon entering their insect hosts, P. luminescens and Y. enterocolitica are challenged by varying and detrimental surrounding conditions which they have to sense and adapt to for further persistence. In addition, both pathogens must be capable to withstand the insect's immune response. In the following chapter we compare sensing and regulating mechanisms of the two insect-associated organisms, P. luminescens and Y. enterocolitica, thus identifying strategies which might be important for insect colonization and pathogenicity. Two-component signal transduction To sense their environment and to react rapidly to changing surrounding conditions, bacteria have evolved so called two-component systems (TCSs) [25] which have been found to be involved in the control of virulence or symbiosis, in metabolite utilization, and also in the adaptation to various stress factors [26]. A basic TCS consists of two proteins, a sensor histidine kinase and a response regulator performing a His-Asp phosphotransfer. The consisting domains or proteins can also be organized as more complex systems using a His-Asp-His-Asp phosphorelay. The number of TCSs ranges from zero in Mycoplasma genitalium to 80 in Syncheocystes spp. [25,27]. Eighteen of these TCSs are present in P. luminescens, and 28 in Y. enterocolitica, of which 17 are shared by both organisms (Fig. 2, depicted in grey). The additional set of eleven TCSs in Y. enterocolitica (Fig. 2, shown in red) might reflect the high number of different environments this pathogen is exposed to during its life cycle, namely soil, water and invertebrates as well as mammalian hosts. In contrast, P. luminescens cells are primarily restricted to symbiosis with the nematode species H. bacteriophora and the insect larvae as hosts, thus encountering a more homeostatic milieu. Among the eleven TCSs of Y. enterocolitica not shared by P. luminescens are duplicates of the CitA/CitB system (YE2505/YE2506 and YE2654/YE2655) and of the LytS/LytR system (YE1228/YE1227 and YE4014/YE4015). The principal biological reason for this redundancy remains unclear. Interestingly, one TCS (Plu0102/Plu103 and YE4185/YE4186) is unique for the genera Photorhabdus and Yersinia. Both sensor kinases Plu0102 and YE4185 are of moderate similarity (31.5% identity, 48.5% homology). They are anchored to the membrane with one transmembrane domain, and have a large periplasmic sensing domain which is proposed to bind a specific ligand. Therefore, Plu0102 and YE4185 are interesting candidates for unravelling invertebrate-specific signals. The putative target genes of Plu0102/Plu0103 and Ye4185/Ye4186, plu0104 and ye4187, respectively, are homologues and encode putative secreted proteins which might act in a similar, yet unknown manner. All TCSs present in both organisms are depicted in grey in Fig. 2, and include PhoP/PhoQ, and AstS/AstR (BvgS/BvgR) which have been identified to be involved in virulence [28]. The role of PhoP/PhoQ in regulating virulence gene expression has been characterized mainly in Salmonella species, but has also been shown, in addition to three other TCSs, to be important for virulence of Y. pseudotuberculosis [29,30]. In P. luminescens, this TCS controls the expression of the pbgPE operon which is involved in lipid A modification and thus plays a role in colonization and infection of the invertebrate hosts [18,31]. Furthermore, PhoP has also been found to be important for virulence of Y. pestis [32], but its function in Y. enterocolitica during its insect-associated phase remains hypothetical. The AstS/AstR TCS is required for the correct timing of phase variant switching in P. luminescens [28]. BvgS/BvgR is the TCS of Y. enterocolitica that corresponds to AstS/AstR. Because Y. enterocolitica is not known to switch to another phenotypic variant, the possible role in virulence regulation still remains to be elucidated. Both Y. enterocolitica and P. luminescens produce the KdpD/KdpE system that regulates K+ homeostasis and osmotic stress. It has recently been found that the Kdp-system of P. luminescens is important for insect pathogenicity (S. E. Reynolds and N. R. Waterfield, University of Bath, UK, personal communication). Therefore, the KdpD/KdpE system is also a further candidate system which might be involved in the regulation of insecticidal activity of Y. enterocolitica. The only TCS of P. luminescens absent in Y. enterocolitica is TctE/TctD (Fig. 2, marked in blue), which, however, is found in the genomes of Y. intermedia and Y. frederiksenii. Beside these microorganisms, TctE/TctD homologues controlling the transport of tricarboxylic acid (see section \"Tricarboxylate utilization\") are present in the genera Salmonella, Burkholderia, Agrobacterium, Bordetella, Collinsella, Xylella, Xanthomonas, and Pseudomonas, particularly P. entomophila, all of which are found in association with eukaryotes. To summarize, the comparison of the P. luminescens and the Y. enterocolitica TCSs reveals a basal set of signal sensing mechanisms which are used by both organisms. Whether the stimulons or regulons which are regulated by these sets of TCSs are also similar remains to be examined. In comparison to P. luminescens, Y. enterocolitica uses an expanded set of TCSs, possibly to adapt to its various hosts (Fig. 1).\n" ], "offsets": [ [ 0, 6644 ] ] } ]

[ { "id": "PMC2266911-02-Results_and_Discussion-01-01_T1", "type": "Organism", "text": [ "P. luminescens ssp. laumondii TT01" ], "offsets": [ [ 39, 73 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-01-01_T2", "type": "Organism", "text": [ "Y. enterocolitica 8081" ], "offsets": [ [ 78, 100 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-01-01_T3", "type": "Organism", "text": [ "P. luminescens" ], "offsets": [ [ 283, 297 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-01-01_T4", "type": "Organism", "text": [ "P. luminescens" ], "offsets": [ [ 423, 437 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-01-01_T5", "type": "Organism", "text": [ "Y. enterocolitica" ], "offsets": [ [ 448, 465 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-01-01_T6", "type": "Organism", "text": [ "P. luminescens" ], "offsets": [ [ 1375, 1389 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-01-01_T7", "type": "Organism", "text": [ "Y. enterocolitica" ], "offsets": [ [ 1394, 1411 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-01-01_T8", "type": "Organism", "text": [ "P. luminescens" ], "offsets": [ [ 1737, 1751 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-01-01_T9", "type": "Organism", "text": [ "Y. enterocolitica" ], "offsets": [ [ 1756, 1773 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-01-01_T10", "type": "Organism", "text": [ "Mycoplasma genitalium" ], "offsets": [ [ 2505, 2526 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-01-01_T11", "type": "Organism", "text": [ "Syncheocystes spp" ], "offsets": [ [ 2536, 2553 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-01-01_T12", "type": "Organism", "text": [ "P. luminescens" ], "offsets": [ [ 2602, 2616 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-01-01_T13", "type": "Organism", "text": [ "Y. enterocolitica" ], "offsets": [ [ 2628, 2645 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-01-01_T14", "type": "Organism", "text": [ "Y. enterocolitica" ], "offsets": [ [ 2753, 2770 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-01-01_T15", "type": "Organism", "text": [ "P. luminescens" ], "offsets": [ [ 2979, 2993 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-01-01_T16", "type": "Organism", "text": [ "H. bacteriophora" ], "offsets": [ [ 3064, 3080 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-01-01_T17", "type": "Organism", "text": [ "Y. enterocolitica" ], "offsets": [ [ 3183, 3200 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-01-01_T18", "type": "Organism", "text": [ "P. luminescens" ], "offsets": [ [ 3215, 3229 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-01-01_T19", "type": "Two-component-system", "text": [ "CitA/CitB" ], "offsets": [ [ 3252, 3261 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-01-01_T20", "type": "Protein", "text": [ "CitA" ], "offsets": [ [ 3252, 3256 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-01-01_T21", "type": "Protein", "text": [ "CitB" ], "offsets": [ [ 3257, 3261 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-01-01_T22", "type": "Two-component-system", "text": [ "YE2505/YE2506" ], "offsets": [ [ 3270, 3283 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-01-01_T23", "type": "Protein", "text": [ "YE2505" ], "offsets": [ [ 3270, 3276 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-01-01_T24", "type": "Protein", "text": [ "YE2506" ], "offsets": [ [ 3277, 3283 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-01-01_T25", "type": "Two-component-system", "text": [ "YE2654/YE2655" ], "offsets": [ [ 3288, 3301 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-01-01_T26", "type": "Protein", "text": [ "YE2654" ], "offsets": [ [ 3288, 3294 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-01-01_T27", "type": "Protein", "text": [ "YE2655" ], "offsets": [ [ 3295, 3301 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-01-01_T28", "type": "Two-component-system", "text": [ "LytS/LytR" ], "offsets": [ [ 3314, 3323 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-01-01_T29", "type": "Protein", "text": [ "LytS" ], "offsets": [ [ 3314, 3318 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-01-01_T30", "type": "Protein", "text": [ "LytR" ], "offsets": [ [ 3319, 3323 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-01-01_T31", "type": "Two-component-system", "text": [ "YE1228/YE1227" ], "offsets": [ [ 3332, 3345 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-01-01_T32", "type": "Protein", "text": [ "YE1228" ], "offsets": [ [ 3332, 3338 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-01-01_T33", "type": "Protein", "text": [ "YE1227" ], "offsets": [ [ 3339, 3345 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-01-01_T34", "type": "Two-component-system", "text": [ "YE4014/YE4015" ], "offsets": [ [ 3350, 3363 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-01-01_T35", "type": "Protein", "text": [ "YE4014" ], "offsets": [ [ 3350, 3356 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-01-01_T36", "type": "Protein", "text": [ "YE4015" ], "offsets": [ [ 3357, 3363 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-01-01_T37", "type": "Two-component-system", "text": [ "Plu0102/Plu103" ], "offsets": [ [ 3459, 3473 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-01-01_T38", "type": "Protein", "text": [ "Plu0102" ], "offsets": [ [ 3459, 3466 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-01-01_T39", "type": "Protein", "text": [ "Plu103" ], "offsets": [ [ 3467, 3473 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-01-01_T40", "type": "Two-component-system", "text": [ "YE4185/YE4186" ], "offsets": [ [ 3478, 3491 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-01-01_T41", "type": "Protein", "text": [ "YE4185" ], "offsets": [ [ 3478, 3484 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-01-01_T42", "type": "Protein", "text": [ "YE4186" ], "offsets": [ [ 3485, 3491 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-01-01_T43", "type": "Organism", "text": [ "Photorhabdus" ], "offsets": [ [ 3518, 3530 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-01-01_T44", "type": "Organism", "text": [ "Yersinia" ], "offsets": [ [ 3535, 3543 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-01-01_T45", "type": "Protein", "text": [ "Plu0102" ], "offsets": [ [ 3565, 3572 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-01-01_T46", "type": "Protein", "text": [ "YE4185" ], "offsets": [ [ 3577, 3583 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-01-01_T47", "type": "Protein", "text": [ "Plu0102" ], "offsets": [ [ 3810, 3817 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-01-01_T48", "type": "Protein", "text": [ "YE4185" ], "offsets": [ [ 3822, 3828 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-01-01_T49", "type": "Two-component-system", "text": [ "Plu0102/Plu0103" ], "offsets": [ [ 3932, 3947 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-01-01_T50", "type": "Protein", "text": [ "Plu0102" ], "offsets": [ [ 3932, 3939 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-01-01_T51", "type": "Protein", "text": [ "Plu0103" ], "offsets": [ [ 3940, 3947 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-01-01_T52", "type": "Two-component-system", "text": [ "Ye4185/Ye4186" ], "offsets": [ [ 3952, 3965 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-01-01_T53", "type": "Protein", "text": [ "Ye4185" ], "offsets": [ [ 3952, 3958 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-01-01_T54", "type": "Protein", "text": [ "Ye4186" ], "offsets": [ [ 3959, 3965 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-01-01_T55", "type": "Protein", "text": [ "plu0104" ], "offsets": [ [ 3967, 3974 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-01-01_T56", "type": "Protein", "text": [ "ye4187" ], "offsets": [ [ 3979, 3985 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-01-01_T57", "type": "Two-component-system", "text": [ "PhoP/PhoQ" ], "offsets": [ [ 4183, 4192 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-01-01_T58", "type": "Protein", "text": [ "PhoP" ], "offsets": [ [ 4183, 4187 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-01-01_T59", "type": "Protein", "text": [ "PhoQ" ], "offsets": [ [ 4188, 4192 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-01-01_T60", "type": "Two-component-system", "text": [ "AstS/AstR" ], "offsets": [ [ 4198, 4207 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-01-01_T61", "type": "Protein", "text": [ "AstS" ], "offsets": [ [ 4198, 4202 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-01-01_T62", "type": "Protein", "text": [ "AstR" ], "offsets": [ [ 4203, 4207 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-01-01_T63", "type": "Two-component-system", "text": [ "BvgS/BvgR" ], "offsets": [ [ 4209, 4218 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-01-01_T64", "type": "Protein", "text": [ "BvgS" ], "offsets": [ [ 4209, 4213 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-01-01_T65", "type": "Protein", "text": [ "BvgR" ], "offsets": [ [ 4214, 4218 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-01-01_T66", "type": "Two-component-system", "text": [ "PhoP/PhoQ" ], "offsets": [ [ 4293, 4302 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-01-01_T67", "type": "Protein", "text": [ "PhoP" ], "offsets": [ [ 4293, 4297 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-01-01_T68", "type": "Protein", "text": [ "PhoQ" ], "offsets": [ [ 4298, 4302 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-01-01_T69", "type": "Organism", "text": [ "Salmonella" ], "offsets": [ [ 4376, 4386 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-01-01_T70", "type": "Organism", "text": [ "Y. pseudotuberculosis" ], "offsets": [ [ 4487, 4508 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-01-01_T71", "type": "Organism", "text": [ "P. luminescens" ], "offsets": [ [ 4521, 4535 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-01-01_T72", "type": "Regulon-operon", "text": [ "pbgPE" ], "offsets": [ [ 4577, 4582 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-01-01_T73", "type": "Protein", "text": [ "pbgP" ], "offsets": [ [ 4577, 4581 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-01-01_T74", "type": "Protein", "text": [ "E" ], "offsets": [ [ 4581, 4582 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-01-01_T75", "type": "Chemical", "text": [ "lipid A" ], "offsets": [ [ 4611, 4618 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-01-01_T76", "type": "Protein", "text": [ "PhoP" ], "offsets": [ [ 4732, 4736 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-01-01_T77", "type": "Organism", "text": [ "Y. pestis" ], "offsets": [ [ 4790, 4799 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-01-01_T78", "type": "Organism", "text": [ "Y. enterocolitica" ], "offsets": [ [ 4826, 4843 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-01-01_T79", "type": "Two-component-system", "text": [ "AstS/AstR" ], "offsets": [ [ 4905, 4914 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-01-01_T80", "type": "Protein", "text": [ "AstS" ], "offsets": [ [ 4905, 4909 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-01-01_T81", "type": "Protein", "text": [ "AstR" ], "offsets": [ [ 4910, 4914 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-01-01_T82", "type": "Organism", "text": [ "P. luminescens" ], "offsets": [ [ 4984, 4998 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-01-01_T83", "type": "Two-component-system", "text": [ "BvgS/BvgR" ], "offsets": [ [ 5005, 5014 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-01-01_T84", "type": "Protein", "text": [ "BvgS" ], "offsets": [ [ 5005, 5009 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-01-01_T85", "type": "Protein", "text": [ "BvgR" ], "offsets": [ [ 5010, 5014 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-01-01_T86", "type": "Organism", "text": [ "Y. enterocolitica" ], "offsets": [ [ 5029, 5046 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-01-01_T87", "type": "Two-component-system", "text": [ "AstS/AstR" ], "offsets": [ [ 5067, 5076 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-01-01_T88", "type": "Protein", "text": [ "AstS" ], "offsets": [ [ 5067, 5071 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-01-01_T89", "type": "Protein", "text": [ "AstR" ], "offsets": [ [ 5072, 5076 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-01-01_T90", "type": "Organism", "text": [ "Y. enterocolitica" ], "offsets": [ [ 5086, 5103 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-01-01_T91", "type": "Organism", "text": [ "Y. enterocolitica" ], "offsets": [ [ 5237, 5254 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-01-01_T92", "type": "Organism", "text": [ "P. luminescens" ], "offsets": [ [ 5259, 5273 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-01-01_T93", "type": "Two-component-system", "text": [ "KdpD/KdpE" ], "offsets": [ [ 5286, 5295 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-01-01_T94", "type": "Protein", "text": [ "KdpD" ], "offsets": [ [ 5286, 5290 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-01-01_T95", "type": "Protein", "text": [ "KdpE" ], "offsets": [ [ 5291, 5295 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-01-01_T96", "type": "Organism", "text": [ "P. luminescens" ], "offsets": [ [ 5403, 5417 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-01-01_T97", "type": "Two-component-system", "text": [ "KdpD/KdpE" ], "offsets": [ [ 5558, 5567 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-01-01_T98", "type": "Protein", "text": [ "KdpD" ], "offsets": [ [ 5558, 5562 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-01-01_T99", "type": "Protein", "text": [ "KdpE" ], "offsets": [ [ 5563, 5567 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-01-01_T100", "type": "Organism", "text": [ "Y. enterocolitica" ], "offsets": [ [ 5680, 5697 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-01-01_T101", "type": "Organism", "text": [ "P. luminescens" ], "offsets": [ [ 5715, 5729 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-01-01_T102", "type": "Organism", "text": [ "Y. enterocolitica" ], "offsets": [ [ 5740, 5757 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-01-01_T103", "type": "Two-component-system", "text": [ "TctE/TctD" ], "offsets": [ [ 5761, 5770 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-01-01_T104", "type": "Protein", "text": [ "TctE" ], "offsets": [ [ 5761, 5765 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-01-01_T105", "type": "Protein", "text": [ "TctD" ], "offsets": [ [ 5766, 5770 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-01-01_T106", "type": "Organism", "text": [ "Y. intermedia" ], "offsets": [ [ 5840, 5853 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-01-01_T107", "type": "Organism", "text": [ "Y. frederiksenii" ], "offsets": [ [ 5858, 5874 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-01-01_T108", "type": "Two-component-system", "text": [ "TctE/TctD" ], "offsets": [ [ 5905, 5914 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-01-01_T109", "type": "Protein", "text": [ "TctE" ], "offsets": [ [ 5905, 5909 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-01-01_T110", "type": "Protein", "text": [ "TctD" ], "offsets": [ [ 5910, 5914 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-01-01_T111", "type": "Organism", "text": [ "Salmonella" ], "offsets": [ [ 6043, 6053 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-01-01_T112", "type": "Organism", "text": [ "Burkholderia" ], "offsets": [ [ 6055, 6067 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-01-01_T113", "type": "Organism", "text": [ "Agrobacterium" ], "offsets": [ [ 6069, 6082 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-01-01_T114", "type": "Organism", "text": [ "Bordetella" ], "offsets": [ [ 6084, 6094 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-01-01_T115", "type": "Organism", "text": [ "Collinsella" ], "offsets": [ [ 6096, 6107 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-01-01_T116", "type": "Organism", "text": [ "Xylella" ], "offsets": [ [ 6109, 6116 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-01-01_T117", "type": "Organism", "text": [ "Xanthomonas" ], "offsets": [ [ 6118, 6129 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-01-01_T118", "type": "Organism", "text": [ "Pseudomonas" ], "offsets": [ [ 6135, 6146 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-01-01_T119", "type": "Organism", "text": [ "P. entomophila" ], "offsets": [ [ 6161, 6175 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-01-01_T120", "type": "Organism", "text": [ "P. luminescens" ], "offsets": [ [ 6268, 6282 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-01-01_T121", "type": "Organism", "text": [ "Y. enterocolitica" ], "offsets": [ [ 6291, 6308 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-01-01_T122", "type": "Organism", "text": [ "P. luminescens" ], "offsets": [ [ 6531, 6545 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-01-01_T123", "type": "Organism", "text": [ "Y. enterocolitica" ], "offsets": [ [ 6547, 6564 ] ], "normalized": [] } ]

[ { "id": "PMC2266911-02-Results_and_Discussion-01-01_E1", "type": "Process", "trigger": { "text": [ "challenged" ], "offsets": [ [ 1416, 1426 ] ] }, "arguments": [ { "role": "Participant", "ref_id": "PMC2266911-02-Results_and_Discussion-01-01_T6" } ] }, { "id": "PMC2266911-02-Results_and_Discussion-01-01_E2", "type": "Process", "trigger": { "text": [ "challenged" ], "offsets": [ [ 1416, 1426 ] ] }, "arguments": [ { "role": "Participant", "ref_id": "PMC2266911-02-Results_and_Discussion-01-01_T7" } ] }, { "id": "PMC2266911-02-Results_and_Discussion-01-01_E3", "type": "Process", "trigger": { "text": [ "virulence" ], "offsets": [ [ 2110, 2119 ] ] }, "arguments": [] }, { "id": "PMC2266911-02-Results_and_Discussion-01-01_E4", "type": "Regulation", "trigger": { "text": [ "involved" ], "offsets": [ [ 4253, 4261 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC2266911-02-Results_and_Discussion-01-01_E7" }, { "role": "Cause", "ref_id": "PMC2266911-02-Results_and_Discussion-01-01_T57" } ] }, { "id": "PMC2266911-02-Results_and_Discussion-01-01_E5", "type": "Regulation", "trigger": { "text": [ "involved" ], "offsets": [ [ 4253, 4261 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC2266911-02-Results_and_Discussion-01-01_E7" }, { "role": "Cause", "ref_id": "PMC2266911-02-Results_and_Discussion-01-01_T60" } ] }, { "id": "PMC2266911-02-Results_and_Discussion-01-01_E6", "type": "Regulation", "trigger": { "text": [ "involved" ], "offsets": [ [ 4253, 4261 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC2266911-02-Results_and_Discussion-01-01_E7" }, { "role": "Cause", "ref_id": "PMC2266911-02-Results_and_Discussion-01-01_T63" } ] }, { "id": "PMC2266911-02-Results_and_Discussion-01-01_E7", "type": "Process", "trigger": { "text": [ "virulence" ], "offsets": [ [ 4265, 4274 ] ] }, "arguments": [] }, { "id": "PMC2266911-02-Results_and_Discussion-01-01_E8", "type": "Process", "trigger": { "text": [ "virulence" ], "offsets": [ [ 4317, 4326 ] ] }, "arguments": [] }, { "id": "PMC2266911-02-Results_and_Discussion-01-01_E9", "type": "Process", "trigger": { "text": [ "virulence" ], "offsets": [ [ 4474, 4483 ] ] }, "arguments": [ { "role": "Participant", "ref_id": "PMC2266911-02-Results_and_Discussion-01-01_T70" } ] }, { "id": "PMC2266911-02-Results_and_Discussion-01-01_E10", "type": "Gene_expression", "trigger": { "text": [ "expression" ], "offsets": [ [ 4559, 4569 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC2266911-02-Results_and_Discussion-01-01_T72" } ] }, { "id": "PMC2266911-02-Results_and_Discussion-01-01_E11", "type": "Regulation", "trigger": { "text": [ "plays a role" ], "offsets": [ [ 4641, 4653 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC2266911-02-Results_and_Discussion-01-01_E12" }, { "role": "Cause", "ref_id": "PMC2266911-02-Results_and_Discussion-01-01_E10" } ] }, { "id": "PMC2266911-02-Results_and_Discussion-01-01_E12", "type": "Process", "trigger": { "text": [ "infection" ], "offsets": [ [ 4674, 4683 ] ] }, "arguments": [ { "role": "Participant", "ref_id": "PMC2266911-02-Results_and_Discussion-01-01_T71" } ] }, { "id": "PMC2266911-02-Results_and_Discussion-01-01_E13", "type": "Process", "trigger": { "text": [ "virulence" ], "offsets": [ [ 4777, 4786 ] ] }, "arguments": [ { "role": "Participant", "ref_id": "PMC2266911-02-Results_and_Discussion-01-01_T77" } ] }, { "id": "PMC2266911-02-Results_and_Discussion-01-01_E14", "type": "Process", "trigger": { "text": [ "virulence" ], "offsets": [ [ 5179, 5188 ] ] }, "arguments": [] }, { "id": "PMC2266911-02-Results_and_Discussion-01-01_E15", "type": "Regulation", "trigger": { "text": [ "regulation" ], "offsets": [ [ 5189, 5199 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC2266911-02-Results_and_Discussion-01-01_E14" } ] } ]

[]

[]

[ { "id": "PMC2266911-02-Results_and_Discussion-01-02-02__text", "type": "abstract", "text": [ "Regulation by AI-2 \nBeside AHL, other putative quorum sensing signalling molecules have been identified. One of them is autoinductor 2 (AI-2), furanosyl borate diester, which is synthesized by the luxS product [39,40] of which homologues are present in P. luminescens and Y. enterocolitica (plu1253, ye0839). It has been shown that the luxS pathway negatively controls the expression of genes for carbapenem antibiotic biosynthesis in P. luminescens [41]. Overall, more than 300 AI-2 regulated genes involved in regulation, metabolic activity, stress response and pathogenicity are known in P. luminescens [42]. For example, the expression of tcdA1 and tccC1 encoding subunits of the insecticidal toxin complexes and the production of mcf2 encoding the \"Makes caterpillar floppy\" toxin was identified to be luxS dependent. The DeltaluxS mutant also showed decreased expression of virulence factors such as the cytotoxic protein CcdB, the hemolysin secretion protein HlyD (Plu0635), and the toxin ABC transporter subunits RtxD/RtxB. Homologues of these proteins are present in Y. enterocolitica (see chapter 2), suggesting their possible regulation by AI-2 also in this bacterium. Furthermore, the P. luminescens luxS-negative strain exhibited decreased biofilm formation, increased type IV/V pilus-dependent twitching motility, and attenuated virulence against insect larvae [42]. Taken together, a similar and AI-2 dependent mechanism for the regulation of insect colonization and insect pathogenicity might be used by both organisms. Whether they sense self-produced or external AI-2, or a combination of both, indicating a quorum sensing mechanism or a regulation similar to AHL as described above, remains to be elucidated.\n" ], "offsets": [ [ 0, 1728 ] ] } ]

[ { "id": "PMC2266911-02-Results_and_Discussion-01-02-02_T1", "type": "Chemical", "text": [ "AI-2" ], "offsets": [ [ 14, 18 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-01-02-02_T2", "type": "Chemical", "text": [ "AHL" ], "offsets": [ [ 27, 30 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-01-02-02_T3", "type": "Chemical", "text": [ "autoinductor 2" ], "offsets": [ [ 120, 134 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-01-02-02_T4", "type": "Chemical", "text": [ "AI-2" ], "offsets": [ [ 136, 140 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-01-02-02_T5", "type": "Chemical", "text": [ "furanosyl borate diester" ], "offsets": [ [ 143, 167 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-01-02-02_T6", "type": "Protein", "text": [ "luxS" ], "offsets": [ [ 197, 201 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-01-02-02_T7", "type": "Organism", "text": [ "P. luminescens" ], "offsets": [ [ 253, 267 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-01-02-02_T8", "type": "Organism", "text": [ "Y. enterocolitica" ], "offsets": [ [ 272, 289 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-01-02-02_T9", "type": "Protein", "text": [ "plu1253" ], "offsets": [ [ 291, 298 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-01-02-02_T10", "type": "Protein", "text": [ "ye0839" ], "offsets": [ [ 300, 306 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-01-02-02_T11", "type": "Protein", "text": [ "luxS" ], "offsets": [ [ 336, 340 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-01-02-02_T12", "type": "Chemical", "text": [ "carbapenem" ], "offsets": [ [ 397, 407 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-01-02-02_T13", "type": "Organism", "text": [ "P. luminescens" ], "offsets": [ [ 435, 449 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-01-02-02_T14", "type": "Chemical", "text": [ "AI-2" ], "offsets": [ [ 479, 483 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-01-02-02_T15", "type": "Organism", "text": [ "P. luminescens" ], "offsets": [ [ 591, 605 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-01-02-02_T16", "type": "Protein", "text": [ "tcdA1" ], "offsets": [ [ 643, 648 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-01-02-02_T17", "type": "Protein", "text": [ "tccC1" ], "offsets": [ [ 653, 658 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-01-02-02_T18", "type": "Protein", "text": [ "mcf2" ], "offsets": [ [ 735, 739 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-01-02-02_T19", "type": "Protein", "text": [ "luxS" ], "offsets": [ [ 807, 811 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-01-02-02_T20", "type": "Organism", "text": [ "DeltaluxS mutant" ], "offsets": [ [ 827, 843 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-01-02-02_T21", "type": "Protein", "text": [ "luxS" ], "offsets": [ [ 832, 836 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-01-02-02_T22", "type": "Protein", "text": [ "CcdB" ], "offsets": [ [ 928, 932 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-01-02-02_T23", "type": "Protein", "text": [ "HlyD" ], "offsets": [ [ 966, 970 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-01-02-02_T24", "type": "Protein", "text": [ "Plu0635" ], "offsets": [ [ 972, 979 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-01-02-02_T25", "type": "Two-component-system", "text": [ "RtxD/RtxB" ], "offsets": [ [ 1021, 1030 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-01-02-02_T26", "type": "Protein", "text": [ "RtxD" ], "offsets": [ [ 1021, 1025 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-01-02-02_T27", "type": "Protein", "text": [ "RtxB" ], "offsets": [ [ 1026, 1030 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-01-02-02_T28", "type": "Organism", "text": [ "Y. enterocolitica" ], "offsets": [ [ 1076, 1093 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-01-02-02_T29", "type": "Chemical", "text": [ "AI-2" ], "offsets": [ [ 1151, 1155 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-01-02-02_T30", "type": "Organism", "text": [ "P. luminescens luxS-negative strain" ], "offsets": [ [ 1197, 1232 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-01-02-02_T31", "type": "Protein", "text": [ "luxS" ], "offsets": [ [ 1212, 1216 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-01-02-02_T32", "type": "Chemical", "text": [ "AI-2" ], "offsets": [ [ 1411, 1415 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-01-02-02_T33", "type": "Chemical", "text": [ "AI-2" ], "offsets": [ [ 1581, 1585 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-01-02-02_T34", "type": "Chemical", "text": [ "AHL" ], "offsets": [ [ 1678, 1681 ] ], "normalized": [] } ]

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[]

[ { "id": "PMC2581603-02-Results-06__text", "type": "abstract", "text": [ "DNA chelation of Mg2+, Ca2+ or Mn2+ but not Zn2+ induces PA3553 expression \nAt lethal concentrations, extracellular DNA induced cell lysis by chelating cations from the OM. This antimicrobial activity can be prevented if DNA is pre-loaded with Mg2+, Ca2+ or Mn2+, but not Zn2+, prior to treatment of cells (Fig 3A and 3B). To determine the specificity of cation chelation, flame atomic absorption spectroscopy was employed to quantitate DNA-dependent removal of cations from buffer containing known concentrations of Mg2+, Ca2+, Mn2+ or Zn2+ and a combination of all four cations. DNA was capable of binding all four cations at similar levels (80-88%), whether alone (Fig 7A) or in combination (data not shown). To ensure binding was specific to DNA a negative control was included. The concentration of Mg2+ that bound to the column in the absence of DNA is indicated. At sub-lethal concentrations, extracellular DNA imposes a cation limitation that leads to induction of PA3553 (Fig 4A), which can be repressed by excess Mg2+ (Fig 4B), indicating that P. aeruginosa senses Mg2+. The P. aeruginosa PhoQ sensor kinase protein has been shown to bind to and be repressed by Mg2+ and Ca2+ cations [63],[64]. Under limiting Mg2+ conditions, the addition of excess Mg2+, Ca2+ or Mn2+, but not Zn2+, repressed PA3553 expression (Fig 7B). Taken together, these data indicate that P. aeruginosa can sense the presence of Mg2+, Ca2+ or Mn2+ and that chelation of these same cations by DNA results in induction of the PA3552-PA3559 LPS modification operon.\n" ], "offsets": [ [ 0, 1547 ] ] } ]

[ { "id": "PMC2581603-02-Results-06_T1", "type": "Chemical", "text": [ "Mg2+" ], "offsets": [ [ 17, 21 ] ], "normalized": [] }, { "id": "PMC2581603-02-Results-06_T2", "type": "Chemical", "text": [ "Ca2+" ], "offsets": [ [ 23, 27 ] ], "normalized": [] }, { "id": "PMC2581603-02-Results-06_T3", "type": "Chemical", "text": [ "Mn2+" ], "offsets": [ [ 31, 35 ] ], "normalized": [] }, { "id": "PMC2581603-02-Results-06_T4", "type": "Chemical", "text": [ "Zn2+" ], "offsets": [ [ 44, 48 ] ], "normalized": [] }, { "id": "PMC2581603-02-Results-06_T5", "type": "Protein", "text": [ "PA3553" ], "offsets": [ [ 57, 63 ] ], "normalized": [] }, { "id": "PMC2581603-02-Results-06_T6", "type": "Chemical", "text": [ "Mg2+" ], "offsets": [ [ 244, 248 ] ], "normalized": [] }, { "id": "PMC2581603-02-Results-06_T7", "type": "Chemical", "text": [ "Ca2+" ], "offsets": [ [ 250, 254 ] ], "normalized": [] }, { "id": "PMC2581603-02-Results-06_T8", "type": "Chemical", "text": [ "Mn2+" ], "offsets": [ [ 258, 262 ] ], "normalized": [] }, { "id": "PMC2581603-02-Results-06_T9", "type": "Chemical", "text": [ "Zn2+" ], "offsets": [ [ 272, 276 ] ], "normalized": [] }, { "id": "PMC2581603-02-Results-06_T10", "type": "Chemical", "text": [ "Mg2+" ], "offsets": [ [ 517, 521 ] ], "normalized": [] }, { "id": "PMC2581603-02-Results-06_T11", "type": "Chemical", "text": [ "Ca2+" ], "offsets": [ [ 523, 527 ] ], "normalized": [] }, { "id": "PMC2581603-02-Results-06_T12", "type": "Chemical", "text": [ "Mn2+" ], "offsets": [ [ 529, 533 ] ], "normalized": [] }, { "id": "PMC2581603-02-Results-06_T13", "type": "Chemical", "text": [ "Zn2+" ], "offsets": [ [ 537, 541 ] ], "normalized": [] }, { "id": "PMC2581603-02-Results-06_T14", "type": "Chemical", "text": [ "Mg2+" ], "offsets": [ [ 804, 808 ] ], "normalized": [] }, { "id": "PMC2581603-02-Results-06_T15", "type": "Protein", "text": [ "PA3553" ], "offsets": [ [ 973, 979 ] ], "normalized": [] }, { "id": "PMC2581603-02-Results-06_T16", "type": "Chemical", "text": [ "Mg2+" ], "offsets": [ [ 1023, 1027 ] ], "normalized": [] }, { "id": "PMC2581603-02-Results-06_T17", "type": "Organism", "text": [ "P. aeruginosa" ], "offsets": [ [ 1054, 1067 ] ], "normalized": [] }, { "id": "PMC2581603-02-Results-06_T18", "type": "Chemical", "text": [ "Mg2+" ], "offsets": [ [ 1075, 1079 ] ], "normalized": [] }, { "id": "PMC2581603-02-Results-06_T19", "type": "Organism", "text": [ "P. aeruginosa" ], "offsets": [ [ 1085, 1098 ] ], "normalized": [] }, { "id": "PMC2581603-02-Results-06_T20", "type": "Protein", "text": [ "PhoQ" ], "offsets": [ [ 1099, 1103 ] ], "normalized": [] }, { "id": "PMC2581603-02-Results-06_T21", "type": "Chemical", "text": [ "Mg2+" ], "offsets": [ [ 1172, 1176 ] ], "normalized": [] }, { "id": "PMC2581603-02-Results-06_T22", "type": "Chemical", "text": [ "Ca2+" ], "offsets": [ [ 1181, 1185 ] ], "normalized": [] }, { "id": "PMC2581603-02-Results-06_T23", "type": "Chemical", "text": [ "Mg2+" ], "offsets": [ [ 1220, 1224 ] ], "normalized": [] }, { "id": "PMC2581603-02-Results-06_T24", "type": "Chemical", "text": [ "Mg2+" ], "offsets": [ [ 1260, 1264 ] ], "normalized": [] }, { "id": "PMC2581603-02-Results-06_T25", "type": "Chemical", "text": [ "Ca2+" ], "offsets": [ [ 1266, 1270 ] ], "normalized": [] }, { "id": "PMC2581603-02-Results-06_T26", "type": "Chemical", "text": [ "Mn2+" ], "offsets": [ [ 1274, 1278 ] ], "normalized": [] }, { "id": "PMC2581603-02-Results-06_T27", "type": "Chemical", "text": [ "Zn2+" ], "offsets": [ [ 1288, 1292 ] ], "normalized": [] }, { "id": "PMC2581603-02-Results-06_T28", "type": "Protein", "text": [ "PA3553" ], "offsets": [ [ 1304, 1310 ] ], "normalized": [] }, { "id": "PMC2581603-02-Results-06_T29", "type": "Organism", "text": [ "P. aeruginosa" ], "offsets": [ [ 1373, 1386 ] ], "normalized": [] }, { "id": "PMC2581603-02-Results-06_T30", "type": "Chemical", "text": [ "Mg2+" ], "offsets": [ [ 1413, 1417 ] ], "normalized": [] }, { "id": "PMC2581603-02-Results-06_T31", "type": "Chemical", "text": [ "Ca2+" ], "offsets": [ [ 1419, 1423 ] ], "normalized": [] }, { "id": "PMC2581603-02-Results-06_T32", "type": "Chemical", "text": [ "Mn2+" ], "offsets": [ [ 1427, 1431 ] ], "normalized": [] }, { "id": "PMC2581603-02-Results-06_T33", "type": "Regulon-operon", "text": [ "PA3552-PA3559" ], "offsets": [ [ 1508, 1521 ] ], "normalized": [] }, { "id": "PMC2581603-02-Results-06_T34", "type": "Protein", "text": [ "PA3552" ], "offsets": [ [ 1508, 1514 ] ], "normalized": [] }, { "id": "PMC2581603-02-Results-06_T35", "type": "Protein", "text": [ "PA3559" ], "offsets": [ [ 1515, 1521 ] ], "normalized": [] }, { "id": "PMC2581603-02-Results-06_T36", "type": "Chemical", "text": [ "LPS" ], "offsets": [ [ 1522, 1525 ] ], "normalized": [] } ]

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[]

[]

[ { "id": "PMC2858072-00-TIAB__text", "type": "abstract", "text": [ "Transcriptome Analysis of the Brucella abortus BvrR/BvrS Two-Component Regulatory System \nBackground The two-component BvrR/BvrS system is essential for Brucella abortus virulence. It was shown previously that its dysfunction alters the expression of some major outer membrane proteins and the pattern of lipid A acylation. To determine the genes regulated by BvrR/BvrS, we performed a whole-genome microarray analysis using B. abortus RNA obtained from wild type and bvrR mutant cells grown in the same conditions. Methodology/Principal Findings A total of 127 differentially expressed genes were found: 83 were over expressed and 44 were less expressed in the bvrR mutant. Two operons, the phosphotransferase system and the maltose transport system, were down-regulated. Several genes involved in cell envelope or outer membrane biogenesis were differentially expressed: genes for outer membrane proteins (omp25a, omp25d), lipoproteins, LPS and fatty acid biosynthesis, stress response proteins, chaperones, flagellar genes, and twelve genes encoding ABC transport systems. Ten genes related with carbon metabolism (pckA and fumB among others) were up-regulated in the bvrR mutant, and denitrification genes (nirK, norC and nosZ) were also regulated. Notably, seven transcriptional regulators were affected, including VjbR, ExoR and OmpR that were less expressed in the bvrR mutant. Finally, the expression of eleven genes which have been previously related with Brucella virulence was also altered. Conclusions/Significance All these data corroborate the impact of BvrR/BvrS on cell envelope modulation, confirm that this system controls the carbon and nitrogen metabolism, and suggest a cross-talk among some regulators to adjust the Brucella physiology to the shift expected to occur during the transit from the extracellular to the intracellular niche.\n" ], "offsets": [ [ 0, 1859 ] ] } ]

[ { "id": "PMC2858072-00-TIAB_T1", "type": "Organism", "text": [ "Brucella abortus" ], "offsets": [ [ 30, 46 ] ], "normalized": [] }, { "id": "PMC2858072-00-TIAB_T2", "type": "Two-component-system", "text": [ "BvrR/BvrS" ], "offsets": [ [ 47, 56 ] ], "normalized": [] }, { "id": "PMC2858072-00-TIAB_T3", "type": "Protein", "text": [ "BvrR" ], "offsets": [ [ 47, 51 ] ], "normalized": [] }, { "id": "PMC2858072-00-TIAB_T4", "type": "Protein", "text": [ "BvrS" ], "offsets": [ [ 52, 56 ] ], "normalized": [] }, { "id": "PMC2858072-00-TIAB_T5", "type": "Two-component-system", "text": [ "BvrR/BvrS" ], "offsets": [ [ 119, 128 ] ], "normalized": [] }, { "id": "PMC2858072-00-TIAB_T6", "type": "Protein", "text": [ "BvrR" ], "offsets": [ [ 119, 123 ] ], "normalized": [] }, { "id": "PMC2858072-00-TIAB_T7", "type": "Protein", "text": [ "BvrS" ], "offsets": [ [ 124, 128 ] ], "normalized": [] }, { "id": "PMC2858072-00-TIAB_T8", "type": "Organism", "text": [ "Brucella abortus" ], "offsets": [ [ 153, 169 ] ], "normalized": [] }, { "id": "PMC2858072-00-TIAB_T9", "type": "Chemical", "text": [ "lipid A" ], "offsets": [ [ 305, 312 ] ], "normalized": [] }, { "id": "PMC2858072-00-TIAB_T10", "type": "Two-component-system", "text": [ "BvrR/BvrS" ], "offsets": [ [ 360, 369 ] ], "normalized": [] }, { "id": "PMC2858072-00-TIAB_T11", "type": "Protein", "text": [ "BvrR" ], "offsets": [ [ 360, 364 ] ], "normalized": [] }, { "id": "PMC2858072-00-TIAB_T12", "type": "Protein", "text": [ "BvrS" ], "offsets": [ [ 365, 369 ] ], "normalized": [] }, { "id": "PMC2858072-00-TIAB_T13", "type": "Organism", "text": [ "B. abortus" ], "offsets": [ [ 425, 435 ] ], "normalized": [] }, { "id": "PMC2858072-00-TIAB_T14", "type": "Organism", "text": [ "bvrR mutant" ], "offsets": [ [ 468, 479 ] ], "normalized": [] }, { "id": "PMC2858072-00-TIAB_T15", "type": "Protein", "text": [ "bvrR" ], "offsets": [ [ 468, 472 ] ], "normalized": [] }, { "id": "PMC2858072-00-TIAB_T16", "type": "Organism", "text": [ "bvrR mutant" ], "offsets": [ [ 662, 673 ] ], "normalized": [] }, { "id": "PMC2858072-00-TIAB_T17", "type": "Protein", "text": [ "bvrR" ], "offsets": [ [ 662, 666 ] ], "normalized": [] }, { "id": "PMC2858072-00-TIAB_T18", "type": "Protein", "text": [ "omp25a" ], "offsets": [ [ 908, 914 ] ], "normalized": [] }, { "id": "PMC2858072-00-TIAB_T19", "type": "Protein", "text": [ "omp25d" ], "offsets": [ [ 916, 922 ] ], "normalized": [] }, { "id": "PMC2858072-00-TIAB_T20", "type": "Chemical", "text": [ "LPS" ], "offsets": [ [ 939, 942 ] ], "normalized": [] }, { "id": "PMC2858072-00-TIAB_T21", "type": "Chemical", "text": [ "fatty acid" ], "offsets": [ [ 947, 957 ] ], "normalized": [] }, { "id": "PMC2858072-00-TIAB_T22", "type": "Chemical", "text": [ "carbon" ], "offsets": [ [ 1099, 1105 ] ], "normalized": [] }, { "id": "PMC2858072-00-TIAB_T23", "type": "Protein", "text": [ "pckA" ], "offsets": [ [ 1118, 1122 ] ], "normalized": [] }, { "id": "PMC2858072-00-TIAB_T24", "type": "Protein", "text": [ "fumB" ], "offsets": [ [ 1127, 1131 ] ], "normalized": [] }, { "id": "PMC2858072-00-TIAB_T25", "type": "Organism", "text": [ "bvrR mutant" ], "offsets": [ [ 1171, 1182 ] ], "normalized": [] }, { "id": "PMC2858072-00-TIAB_T26", "type": "Protein", "text": [ "bvrR" ], "offsets": [ [ 1171, 1175 ] ], "normalized": [] }, { "id": "PMC2858072-00-TIAB_T27", "type": "Protein", "text": [ "nirK" ], "offsets": [ [ 1211, 1215 ] ], "normalized": [] }, { "id": "PMC2858072-00-TIAB_T28", "type": "Protein", "text": [ "norC" ], "offsets": [ [ 1217, 1221 ] ], "normalized": [] }, { "id": "PMC2858072-00-TIAB_T29", "type": "Protein", "text": [ "nosZ" ], "offsets": [ [ 1226, 1230 ] ], "normalized": [] }, { "id": "PMC2858072-00-TIAB_T30", "type": "Protein", "text": [ "VjbR" ], "offsets": [ [ 1320, 1324 ] ], "normalized": [] }, { "id": "PMC2858072-00-TIAB_T31", "type": "Protein", "text": [ "ExoR" ], "offsets": [ [ 1326, 1330 ] ], "normalized": [] }, { "id": "PMC2858072-00-TIAB_T32", "type": "Protein", "text": [ "OmpR" ], "offsets": [ [ 1335, 1339 ] ], "normalized": [] }, { "id": "PMC2858072-00-TIAB_T33", "type": "Organism", "text": [ "bvrR mutant" ], "offsets": [ [ 1372, 1383 ] ], "normalized": [] }, { "id": "PMC2858072-00-TIAB_T34", "type": "Protein", "text": [ "bvrR" ], "offsets": [ [ 1372, 1376 ] ], "normalized": [] }, { "id": "PMC2858072-00-TIAB_T35", "type": "Organism", "text": [ "Brucella" ], "offsets": [ [ 1465, 1473 ] ], "normalized": [] }, { "id": "PMC2858072-00-TIAB_T36", "type": "Two-component-system", "text": [ "BvrR/BvrS" ], "offsets": [ [ 1568, 1577 ] ], "normalized": [] }, { "id": "PMC2858072-00-TIAB_T37", "type": "Protein", "text": [ "BvrR" ], "offsets": [ [ 1568, 1572 ] ], "normalized": [] }, { "id": "PMC2858072-00-TIAB_T38", "type": "Protein", "text": [ "BvrS" ], "offsets": [ [ 1573, 1577 ] ], "normalized": [] }, { "id": "PMC2858072-00-TIAB_T39", "type": "Chemical", "text": [ "carbon" ], "offsets": [ [ 1645, 1651 ] ], "normalized": [] }, { "id": "PMC2858072-00-TIAB_T40", "type": "Chemical", "text": [ "nitrogen" ], "offsets": [ [ 1656, 1664 ] ], "normalized": [] }, { "id": "PMC2858072-00-TIAB_T41", "type": "Organism", "text": [ "Brucella" ], "offsets": [ [ 1738, 1746 ] ], "normalized": [] } ]

[ { "id": "PMC2858072-00-TIAB_E1", "type": "Positive_regulation", "trigger": { "text": [ "essential" ], "offsets": [ [ 139, 148 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC2858072-00-TIAB_E2" }, { "role": "Cause", "ref_id": "PMC2858072-00-TIAB_T5" } ] }, { "id": "PMC2858072-00-TIAB_E2", "type": "Process", "trigger": { "text": [ "virulence" ], "offsets": [ [ 170, 179 ] ] }, "arguments": [ { "role": "Participant", "ref_id": "PMC2858072-00-TIAB_T8" } ] }, { "id": "PMC2858072-00-TIAB_E3", "type": "Gene_expression", "trigger": { "text": [ "expressed" ], "offsets": [ [ 862, 871 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC2858072-00-TIAB_T18" } ] }, { "id": "PMC2858072-00-TIAB_E4", "type": "Gene_expression", "trigger": { "text": [ "expressed" ], "offsets": [ [ 862, 871 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC2858072-00-TIAB_T19" } ] }, { "id": "PMC2858072-00-TIAB_E5", "type": "Positive_regulation", "trigger": { "text": [ "up-regulated" ], "offsets": [ [ 1151, 1163 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC2858072-00-TIAB_T23" } ] }, { "id": "PMC2858072-00-TIAB_E6", "type": "Positive_regulation", "trigger": { "text": [ "up-regulated" ], "offsets": [ [ 1151, 1163 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC2858072-00-TIAB_T24" } ] }, { "id": "PMC2858072-00-TIAB_E7", "type": "Regulation", "trigger": { "text": [ "regulated" ], "offsets": [ [ 1242, 1251 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC2858072-00-TIAB_T27" } ] }, { "id": "PMC2858072-00-TIAB_E8", "type": "Regulation", "trigger": { "text": [ "regulated" ], "offsets": [ [ 1242, 1251 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC2858072-00-TIAB_T28" } ] }, { "id": "PMC2858072-00-TIAB_E9", "type": "Regulation", "trigger": { "text": [ "regulated" ], "offsets": [ [ 1242, 1251 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC2858072-00-TIAB_T29" } ] }, { "id": "PMC2858072-00-TIAB_E10", "type": "Regulation", "trigger": { "text": [ "affected" ], "offsets": [ [ 1300, 1308 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC2858072-00-TIAB_T30" } ] }, { "id": "PMC2858072-00-TIAB_E11", "type": "Regulation", "trigger": { "text": [ "affected" ], "offsets": [ [ 1300, 1308 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC2858072-00-TIAB_T31" } ] }, { "id": "PMC2858072-00-TIAB_E12", "type": "Regulation", "trigger": { "text": [ "affected" ], "offsets": [ [ 1300, 1308 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC2858072-00-TIAB_T32" } ] }, { "id": "PMC2858072-00-TIAB_E13", "type": "Gene_expression", "trigger": { "text": [ "expressed" ], "offsets": [ [ 1355, 1364 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC2858072-00-TIAB_T30" } ] }, { "id": "PMC2858072-00-TIAB_E14", "type": "Gene_expression", "trigger": { "text": [ "expressed" ], "offsets": [ [ 1355, 1364 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC2858072-00-TIAB_T31" } ] }, { "id": "PMC2858072-00-TIAB_E15", "type": "Gene_expression", "trigger": { "text": [ "expressed" ], "offsets": [ [ 1355, 1364 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC2858072-00-TIAB_T32" } ] }, { "id": "PMC2858072-00-TIAB_E16", "type": "Process", "trigger": { "text": [ "virulence" ], "offsets": [ [ 1474, 1483 ] ] }, "arguments": [ { "role": "Participant", "ref_id": "PMC2858072-00-TIAB_T35" } ] } ]

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[ { "id": "PMC2242835-02-Results-01__text", "type": "abstract", "text": [ "Results \nMicroarray-Based Comparative Genome Sequencing of M. tuberculosis H37Ra The genome-wide comparative mutational analysis of H37Ra and H37Rv was carried out by NimbleGen Systems following a previously published method [13]. Putative SNPs with high probability scores were separated into synonymous and non-synonymous SNPs of which the latter were verified by conventional dye terminator cycle sequencing. By this combined approach we identified 13 non-synonymous SNPs that differed between the H37Ra and H37Rv strains used (Table S1). We were particularly interested in a C to T mutation responsible for the serine to leucine replacement at position 219, S219L, of the two-component regulator PhoP as this protein is well known for its involvement in the virulent phenotype of M. tuberculosis [14]. Importantly, on inspection of the structure of the PhoP-ortholog from Bacillus subtilis, it was found that the equivalent residue Ser 207 is a main residue in the DNA-binding domain, helix alpha3 [15]. For the other 13 genes we found no indication that would identify them as potential virulence genes, as none of them belong to the 5% of genes that were previously determined by transposon site hybridization (TraSH) as being essential for in vivo growth of M. tuberculosis [16]. While writing this article, the whole genome sequence of H37Ra became publicly available (NC_009525), and comparison of the SNP data obtained from the H37Ra strain used in our laboratory (Table S1) with the NC_009525 data, showed that some differences existed between the H37Ra strains, a phenomenon which was also previously observed for BCG [4] and H37Rv [17]. Nevertheless, the S129L mutation in PhoP, which we consider an important SNP involved in the attenuation and reduced immunogenicity of H37Ra, is identical in all H37Ra strains.\n" ], "offsets": [ [ 0, 1827 ] ] } ]

[ { "id": "PMC2242835-02-Results-01_T1", "type": "Organism", "text": [ "M. tuberculosis H37Ra" ], "offsets": [ [ 59, 80 ] ], "normalized": [] }, { "id": "PMC2242835-02-Results-01_T2", "type": "Organism", "text": [ "H37Ra" ], "offsets": [ [ 132, 137 ] ], "normalized": [] }, { "id": "PMC2242835-02-Results-01_T3", "type": "Organism", "text": [ "H37Rv" ], "offsets": [ [ 142, 147 ] ], "normalized": [] }, { "id": "PMC2242835-02-Results-01_T4", "type": "Organism", "text": [ "H37Ra" ], "offsets": [ [ 501, 506 ] ], "normalized": [] }, { "id": "PMC2242835-02-Results-01_T5", "type": "Organism", "text": [ "H37Rv" ], "offsets": [ [ 511, 516 ] ], "normalized": [] }, { "id": "PMC2242835-02-Results-01_T6", "type": "Protein", "text": [ "PhoP" ], "offsets": [ [ 700, 704 ] ], "normalized": [] }, { "id": "PMC2242835-02-Results-01_T7", "type": "Organism", "text": [ "M. tuberculosis" ], "offsets": [ [ 784, 799 ] ], "normalized": [] }, { "id": "PMC2242835-02-Results-01_T8", "type": "Protein", "text": [ "PhoP" ], "offsets": [ [ 857, 861 ] ], "normalized": [] }, { "id": "PMC2242835-02-Results-01_T9", "type": "Organism", "text": [ "Bacillus subtilis" ], "offsets": [ [ 876, 893 ] ], "normalized": [] }, { "id": "PMC2242835-02-Results-01_T10", "type": "Organism", "text": [ "M. tuberculosis" ], "offsets": [ [ 1265, 1280 ] ], "normalized": [] }, { "id": "PMC2242835-02-Results-01_T11", "type": "Organism", "text": [ "H37Ra" ], "offsets": [ [ 1344, 1349 ] ], "normalized": [] }, { "id": "PMC2242835-02-Results-01_T12", "type": "Organism", "text": [ "H37Ra" ], "offsets": [ [ 1438, 1443 ] ], "normalized": [] }, { "id": "PMC2242835-02-Results-01_T13", "type": "Organism", "text": [ "H37Ra" ], "offsets": [ [ 1559, 1564 ] ], "normalized": [] }, { "id": "PMC2242835-02-Results-01_T14", "type": "Organism", "text": [ "BCG" ], "offsets": [ [ 1626, 1629 ] ], "normalized": [] }, { "id": "PMC2242835-02-Results-01_T15", "type": "Organism", "text": [ "H37Rv" ], "offsets": [ [ 1638, 1643 ] ], "normalized": [] }, { "id": "PMC2242835-02-Results-01_T16", "type": "Protein", "text": [ "PhoP" ], "offsets": [ [ 1686, 1690 ] ], "normalized": [] }, { "id": "PMC2242835-02-Results-01_T17", "type": "Organism", "text": [ "H37Ra" ], "offsets": [ [ 1785, 1790 ] ], "normalized": [] }, { "id": "PMC2242835-02-Results-01_T18", "type": "Organism", "text": [ "H37Ra" ], "offsets": [ [ 1812, 1817 ] ], "normalized": [] } ]

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[ { "id": "PMC2266911-01-Background__text", "type": "abstract", "text": [ "Background \nPathogenicity as well as symbiosis plays a key role in the interaction of bacteria with their hosts including invertebrates. Despite the relevance of this relationship for the evolution of bacterial pathogenicity, few studies have addressed this subject at the genomic level. We therefore decided to perform a comparative study of the genomes of Photorhabdus luminescens and Yersinia enterocolitica. The former bacterium is a representative of pathogens highly virulent towards insects, but apathogenic against men. Y. enterocolitica, an example of a primarily human pathogen, also confers toxicity to insects, but is less toxic towards these hosts than P. luminescens. Members of the genus Yersinia are primarily considered as mammalian pathogens. However, Y. pestis, a blood-borne pathogen and the etiological agent of human plague, has long been known to be transmitted by insects, specifically by rat fleas. Y. enterocolitica strains have been isolated from flies that are assumed to play an important role in food contamination by this pathogen [1-3], and Y. pseudotuberculosis strains were recovered from fly larvae isolated in the wild [4]. More recent data strongly support the idea that yersiniae are capable to interact with insects. Loci encoding the insecticidal toxin complexes (Tc) have been identified in the genomes of Y. pestis KIM [5], Y. pseudotuberculosis [6], and Y. enterocolitica [7]. Y. pseudotuberculosis, in contrast to Y. pestis, has been shown to be orally toxic to flea [8]. This toxicity revealed to be independent of tc genes, suggesting that loss of one or more insect gut toxins is a critical step in the change of the Y. pestis lifestyle compared with the Y. pseudotuberculosis and thus in evolution of flea-borne transmission [8]. While Y. enterocolitica and Y. pseudotuberculosis have diverged within the last 200 million years, Y. pestis has emerged from Y. pseudotuberculosis only 1,500-20,000 years ago [9]. Bacterial lysates both of Y. enterocolitica and Y. pseudotuberculosis are toxic for Manduca sexta neonates, and significant levels of natively or heterologously expressed toxins were observed in both species at 15degreesC, but not at mammalian body temperature [7,10]. Furthermore, Y. pseudotuberculosis and Y. enterocolitica have been demonstrated to adhere to and invade cultivated insect cells [10]. Thus, the interaction of Y. enterocolitica with insects is an important link in the ecological range of bacteria-host interactions extending from entomopathogenic to humanpathogenic bacteria. In contrast, Photorhabdus luminescens is predominantly an insect pathogenic enterobacterium which maintains a mutualistic interaction with heterorhabditid nematodes, and can infect a wide range of insects [11,12]. Interestingly, another Photorhabdus species, P. asymbiotica, has been described as a human pathogen. It was isolated from human clinical specimens where the cells caused locally invasive soft tissue infections [13,14]. It is assumed that these strains are associated with spiders, because spider bites where attended with Photorhabdus human infections [15]. However, bacteria of the species P. luminescens are exclusively known to be associated with nematodes and insects. Generally, the bacteria colonise the gut of the infective juvenile stage of the nematode Heterorhabditis bacteriophora. Upon entering an insect host, the nematodes release the bacteria by regurgiation directly into the insect hemocoel, the open circulatory system of the insect. Once inside the hemocoel, the bacteria replicate rapidly and establish a lethal septemica in the host by the production of virulence factors such as the insecticidal toxin complexes that kill the insect within 48 hours. Bioconversion of the insect's body by P. luminescens produces a rich food source for the bacteria as well as for the nematodes. Nematode reproduction is supported by the bacteria, probably by providing essential nutrients that are required for efficient nematode proliferation [16]. Further properties of P. luminescens are the production of many antimicrobial substances to defend the insect cadaver from bacterial competitors, and glowing due to bacterial luciferase production. When the insect cadaver is depleted, the nematodes and bacteria reassociate and emerge from the carcass in search of a new insect host (Fig. 1, right circle)[17,18]. Photorhabdus species exist in two forms, designated as primary and secondary phenotypic colony variants, which differ in morphological and physiological traits. Primary variants are found to produce extracellular protease, extracellular lipase, intracellular protein crystals CipA and CipB, antibiotics, and are bioluminescent. Secondary variants lack protease, lipase and antibiotic activity, and bioluminescence is strongly decreased. They also differ in colony morphology, pigmentation, dye adsorption, metabolism, and the ability to support growth and reproduction of the nematodes. It is assumed that primary variants correspond to the nematode-associated form, and secondary variants to the insect-associated form of the bacteria [19,20]. Therefore, P. luminescens serves as an ideal model to study the switch from a symbiotic state with nematodes to one in which the bacterium is pathogenic to insects [21,22]. In the following comparative genome analysis, we examined the extent to which P. luminescens and Y. enterocolitica share factors that are probably attributed to insect association. We identified genes and the corresponding proteins involved in signalling, regulation, pathogenicity, as well as in metabolism, and suggest their possible function during colonization and infection of non-mammals. The results obtained not only improve our understanding of the biology of both pathogens, but also reveal some implications on the evolution of invertebrate and vertebrate virulence factors.\n" ], "offsets": [ [ 0, 5891 ] ] } ]

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"PMC2266911-01-Background_T8", "type": "Organism", "text": [ "Y. pestis" ], "offsets": [ [ 770, 779 ] ], "normalized": [] }, { "id": "PMC2266911-01-Background_T9", "type": "Organism", "text": [ "human" ], "offsets": [ [ 833, 838 ] ], "normalized": [] }, { "id": "PMC2266911-01-Background_T10", "type": "Organism", "text": [ "rat" ], "offsets": [ [ 913, 916 ] ], "normalized": [] }, { "id": "PMC2266911-01-Background_T11", "type": "Organism", "text": [ "Y. enterocolitica" ], "offsets": [ [ 924, 941 ] ], "normalized": [] }, { "id": "PMC2266911-01-Background_T12", "type": "Organism", "text": [ "Y. pseudotuberculosis" ], "offsets": [ [ 1073, 1094 ] ], "normalized": [] }, { "id": "PMC2266911-01-Background_T13", "type": "Organism", "text": [ "Y. pestis KIM" ], "offsets": [ [ 1347, 1360 ] ], "normalized": [] }, { "id": "PMC2266911-01-Background_T14", "type": "Organism", "text": [ "Y. pseudotuberculosis" ], "offsets": [ [ 1366, 1387 ] ], "normalized": [] }, { "id": "PMC2266911-01-Background_T15", "type": "Organism", "text": [ "Y. enterocolitica" ], "offsets": [ [ 1397, 1414 ] ], "normalized": [] }, { "id": "PMC2266911-01-Background_T16", "type": "Organism", "text": [ "Y. pseudotuberculosis" ], "offsets": [ [ 1420, 1441 ] ], "normalized": [] }, { "id": "PMC2266911-01-Background_T17", "type": "Organism", "text": [ "Y. pestis" ], "offsets": [ [ 1458, 1467 ] ], "normalized": [] }, { "id": "PMC2266911-01-Background_T18", "type": "Organism", "text": [ "Y. pestis" ], "offsets": [ [ 1664, 1673 ] ], "normalized": [] }, { "id": "PMC2266911-01-Background_T19", "type": "Organism", "text": [ "Y. pseudotuberculosis" ], "offsets": [ [ 1702, 1723 ] ], "normalized": [] }, { "id": "PMC2266911-01-Background_T20", "type": "Organism", "text": [ "Y. enterocolitica" ], "offsets": [ [ 1784, 1801 ] ], "normalized": [] }, { "id": "PMC2266911-01-Background_T21", "type": "Organism", "text": [ "Y. pseudotuberculosis" ], "offsets": [ [ 1806, 1827 ] ], "normalized": [] }, { "id": "PMC2266911-01-Background_T22", "type": "Organism", "text": [ "Y. pestis" ], "offsets": [ [ 1877, 1886 ] ], "normalized": [] }, { "id": "PMC2266911-01-Background_T23", "type": "Organism", "text": [ "Y. pseudotuberculosis" ], "offsets": [ [ 1904, 1925 ] ], "normalized": [] }, { "id": "PMC2266911-01-Background_T24", "type": "Organism", "text": [ "Y. enterocolitica" ], "offsets": [ [ 1985, 2002 ] ], "normalized": [] }, { "id": "PMC2266911-01-Background_T25", "type": "Organism", "text": [ "Y. pseudotuberculosis" ], "offsets": [ [ 2007, 2028 ] ], "normalized": [] }, { "id": "PMC2266911-01-Background_T26", "type": "Organism", "text": [ "Manduca sexta" ], "offsets": [ [ 2043, 2056 ] ], "normalized": [] }, { "id": "PMC2266911-01-Background_T27", "type": "Organism", "text": [ "Y. pseudotuberculosis" ], "offsets": [ [ 2241, 2262 ] ], "normalized": [] }, { "id": "PMC2266911-01-Background_T28", "type": "Organism", "text": [ "Y. enterocolitica" ], "offsets": [ [ 2267, 2284 ] ], "normalized": [] }, { "id": "PMC2266911-01-Background_T29", "type": "Organism", "text": [ "Y. enterocolitica" ], "offsets": [ [ 2387, 2404 ] ], "normalized": [] }, { "id": "PMC2266911-01-Background_T30", "type": "Organism", "text": [ "Photorhabdus luminescens" ], "offsets": [ [ 2567, 2591 ] ], "normalized": [] }, { "id": "PMC2266911-01-Background_T31", "type": "Organism", "text": [ "heterorhabditid nematodes" ], "offsets": [ [ 2693, 2718 ] ], "normalized": [] }, { "id": "PMC2266911-01-Background_T32", "type": "Organism", "text": [ "Photorhabdus" ], "offsets": [ [ 2791, 2803 ] ], "normalized": [] }, { "id": "PMC2266911-01-Background_T33", "type": "Organism", "text": [ "P. asymbiotica" ], "offsets": [ [ 2813, 2827 ] ], "normalized": [] }, { "id": "PMC2266911-01-Background_T34", "type": "Organism", "text": [ "human" ], "offsets": [ [ 2853, 2858 ] ], "normalized": [] }, { "id": "PMC2266911-01-Background_T35", "type": "Organism", "text": [ "human" ], "offsets": [ [ 2890, 2895 ] ], "normalized": [] }, { "id": "PMC2266911-01-Background_T36", "type": "Organism", "text": [ "Photorhabdus" ], "offsets": [ [ 3090, 3102 ] ], "normalized": [] }, { "id": "PMC2266911-01-Background_T37", "type": "Organism", "text": [ "human" ], "offsets": [ [ 3103, 3108 ] ], "normalized": [] }, { "id": "PMC2266911-01-Background_T38", "type": "Organism", "text": [ "P. luminescens" ], "offsets": [ [ 3159, 3173 ] ], "normalized": [] }, { "id": "PMC2266911-01-Background_T39", "type": "Organism", "text": [ "Heterorhabditis bacteriophora" ], "offsets": [ [ 3330, 3359 ] ], "normalized": [] }, { "id": "PMC2266911-01-Background_T40", "type": "Organism", "text": [ "P. luminescens" ], "offsets": [ [ 3778, 3792 ] ], "normalized": [] }, { "id": "PMC2266911-01-Background_T41", "type": "Organism", "text": [ "P. luminescens" ], "offsets": [ [ 4045, 4059 ] ], "normalized": [] }, { "id": "PMC2266911-01-Background_T42", "type": "Organism", "text": [ "Photorhabdus" ], "offsets": [ [ 4387, 4399 ] ], "normalized": [] }, { "id": "PMC2266911-01-Background_T43", "type": "Protein", "text": [ "CipA" ], "offsets": [ [ 4663, 4667 ] ], "normalized": [] }, { "id": "PMC2266911-01-Background_T44", "type": "Protein", "text": [ "CipB" ], "offsets": [ [ 4672, 4676 ] ], "normalized": [] }, { "id": "PMC2266911-01-Background_T45", "type": "Organism", "text": [ "P. luminescens" ], "offsets": [ [ 5143, 5157 ] ], "normalized": [] }, { "id": "PMC2266911-01-Background_T46", "type": "Organism", "text": [ "P. luminescens" ], "offsets": [ [ 5383, 5397 ] ], "normalized": [] }, { "id": "PMC2266911-01-Background_T47", "type": "Organism", "text": [ "Y. enterocolitica" ], "offsets": [ [ 5402, 5419 ] ], "normalized": [] } ]

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[ { "id": "PMC2581603-01-Introduction__text", "type": "abstract", "text": [ "Introduction \nPseudomonas aeruginosa is an opportunistic pathogen capable of causing both acute and chronic infections. It is the third-leading cause of nosocomial infections and is the predominant pathogen associated with morbidity and mortality of CF patients [1],[2]. The biofilm-forming ability of P. aeruginosa, and indeed other bacteria, is thought to contribute to their ability to thrive in hostile host environments and result in chronic infection [3],[4]. Biofilms are multicellular surface-associated microbial communities encased in an extracellular matrix which display a characteristic structure and increased resistance to antimicrobial compounds and environmental stresses. P. aeruginosa biofilms are up to 1000-fold more antibiotic tolerant than planktonic cells, to single and combination antibiotics [5]-[7]. As acute CF exacerbations caused by P. aeruginosa are often treated with combination antibiotic therapy [8]-[10], the increased resistance of biofilms to combination antibiotics is of direct clinical relevance. Eighty five percent of P. aeruginosa strains isolated from the lungs of CF patients with advanced stages of disease have a distinctive mucoid colony morphology [11]. This mucoid phenotype is a result of overproduction of the alginate exopolysaccharide (EPS) [1],[12]. Alginate production has been shown to inhibit phagocytic killing of Pseudomonas, to protect from antibiotic exposure [13],[14], and is associated with poor prognosis for the infected patients [15],[16]. The direct observation of P. aeruginosa microcolonies encased in an alginate matrix in microscopy studies of CF bronchial samples [17], along with a large body of additional in vitro and in vivo data [7], [18]-[21] suggests that P. aeruginosa forms biofilms in the lungs of CF patients. The mechanisms of biofilm-associated antibiotic resistance are distinct from the well studied intrinsic resistance mechanisms such as drug efflux, drug inactivation, membrane permeability and target site alterations. Although the basis of biofilm-associated antibiotic resistance is not fully understood, it is likely that multiple mechanisms operate simultaneously in biofilms to contribute to antibiotic resistance. Cells in a biofilm may be protected from antibiotic exposure due to the restricted penetration of antibiotics through the biofilm matrix [19]. However, while the biofilm matrix may limit diffusion initially for certain antibiotics such as beta-lactams and aminoglycosides [14],[22], the penetration of fluoroquinolones occurs immediately and without delay [23]-[25]. The rate of diffusion through the matrix is presumably dependent on binding of the antibiotic molecules to the EPS matrix. Once the matrix becomes saturated, diffusion and antimicrobial activity of the drug will resume [26]. It is the general consensus that reduced diffusion through the biofilm matrix only provides a short-term protective effect and does not play a significant role during long-term antibiotic exposure [26]. Other resistance mechanisms include the presence of subpopulations of multidrug tolerant persister cells [27]-[29], drug indifference of slow-growing, nutrient-limited cells [30], and unique resistance mechanisms specifically associated with biofilms [31],[32]. Despite the fact that biofilms are recognized as the predominant mode of bacterial growth in nature and are responsible for the majority of refractory bacterial infections [19], little is known regarding the mechanisms of biofilm-specific antibiotic resistance. Furthering our understanding of the mechanisms underlying biofilm-associated antibiotic resistance will significantly improve the treatment options available to patients with chronic bacterial infections. Signal transduction systems have been documented to be involved in the regulation of biofilm formation in multiple bacterial species including P. aeruginosa, S. aureus, E. coli and V. fischeri [33]-[38]. These two component systems (TCS) are comprised of an membrane-anchored histidine kinase sensor and a cytoplasmic response regulator. After detecting specific environmental signals, a signal transduction cascade is initiated that results in phosphorylation of the response regulator, which activates or represses the necessary target genes. A number of regulatory systems that influence biofilm formation have been described. These include, but are not limited to, the global virulence factor regulator GacA, mutation of which results in a 10-fold decrease in biofilm formation and failure to form microcolony structures [33]. Additionally, the hybrid sensor kinases, LadS and RetS appear to work upstream of GacA to possibly control the switch to a biofilm lifestyle [34],[35]. Mutations in algR, a response regulator protein required for synthesis of alginate, which is a major component of the matrix of biofilms in the cystic fibrosis lung [1] results in a P. aeruginosa strain that has decreased type IV pili-dependent motility and biofilm formation [39]. The three-component system SadARS which regulates the formation of mature microcolonies [40] and PvrR, a response regulator involved in the switch from planktonic to antibiotic-resistant biofilm cells in P. aeruginosa are additional examples of regulators of biofilm formation [41]. During the course of an infection, one of the first lines of defense encountered by colonizing bacteria is the production of cationic antimicrobial peptides (CAPs) by a variety of host cells including neutrophils, platelets and epithelia. CAPs are short, amphipathic peptides that bind to and disrupt both the outer and cytoplasmic membranes resulting in cell death. The broad-spectrum antimicrobial activity of CAPs against Gram-negative and Gram-positive bacteria accounts for their role as an essential component of the innate immune response of humans, animals and insects. Cationic peptides, which have antimicrobial and immunomodulatory activities, are being developed as a promising new class of therapeutically relevant drugs [42]. In P. aeruginosa, resistance to CAPs is inducible by the PhoPQ and PmrAB TCSs, both of which are activated independently in response to limiting Mg2+ [43]-[46]. Under conditions of limiting magnesium, PhoP and PmrA bind to the promoter of the CAP resistance operon PA3552-PA3559 (arnBCADTEF-ugd) and induce its expression [45]-[47]. These genes encode an LPS modification pathway required for the addition of aminoarabinose to lipid A, which reduces the OM permeability to CAPs [48]. The PhoPQ and PmrAB regulatory systems are well studied in planktonic cultures and have been shown to induce modest resistance to CAPs (8-fold) under low Mg2+ conditions [45]. However, while the PA3552-PA3559 operon has been reported to be expressed in biofilms cultivated in flowcells, and is required for survival in response to colistin treatment [49], little else is known regarding these systems and the role they may play in biofilm-associated antibiotic resistance. The extracellular matrix of P. aeruginosa biofilms includes extracellular DNA [50],[51], multiple bacterial exopolysaccharides and host proteins [4],[52]. Extracellular DNA, which is a matrix component of both Gram-positive and Gram-negative bacterial biofilms [51],[53], functions to maintain the 3D biofilm architecture by acting as a cell-cell interconnecting compound [50]. Genomic DNA has been shown to localize to the biofilm surface, surrounding the mushroom-shaped microcolonies [51]. DNA in the biofilm matrix is likely released by dead bacteria or immune cells. It has been reported that prophage-mediated cell death is an important mechanism in the differentiation and dispersal of biofilms [54],[55]. Additional sources of DNA in biofilms may include the quorum sensing regulated release of DNA [51] and/or DNA contained within outer membrane vesicles (OMV) that bleb and are released from the OM of living P. aeruginosa cells [56],[57]. Furthermore, while a specific mechanism of DNA release has not been reported for P. aeruginosa it is possible that such a method may exist, similar to the autolysin-mediated DNA release observed in Staphylococcus epidermidis biofilms [53]. In this study we sought to examine if the presence of DNA in biofilms may contribute to biofilm-specific antibiotic resistance. Here we identify a novel cation chelating property of DNA, which has several important consequences for biofilm physiology and antibiotic resistance in biofilms.\n" ], "offsets": [ [ 0, 8464 ] ] } ]

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[]

[ { "id": "PMC2639726-02-Results-08__text", "type": "abstract", "text": [ "SlyA can complement other regulators for SPI-2 expression \nThe number of inputs at each regulator shown in Figure 6B corresponds to the number of regulators that directly or indirectly control its expression. The number of regulators that act on slyA was surprising. Quantitative RT-PCR confirmed that slyA transcription was reduced in 11 of 14 mutant backgrounds (Figure 6A). slyA transcriptional activation by PhoP has been reported [63],[64]. The complementation result suggests that many of the regulators may function on SPI-2 through SlyA activation of ssrB or alternatively via both regulators (slyA and ssrB) acting together. To determine epistatic relationships, we introduced a slyA-expressing plasmid, pBAD30SlyA, into each regulatory mutant and examined complementation in each mutant background compared to an empty vector control (Figure 7C). The construct strongly complemented ompR/envZ, phoP/phoQ, csrA and himD, suggesting that the effect of these regulators on SPI-2 expression may be indirect via regulation of slyA. Surprisingly, the expression of SPI-2 genes depended upon slyA even in an ssrA/ssrB deleted strain. This suggests that slyA can regulate expression of SPI-2 in a way that is independent of ssrB. To test this possibility we constructed double deletions of ssrAB/ompRenvZ, ssrAB/phoPQ, ssrAB/csrA and ssrAB/himD. As shown in Figure 7D, slyA is capable of activating expression of SPI-2 genes independently of ssrB, ompR/envZ, phoP/phoQ, csrA and himD (ihf), although the effects are not as strong as ssrB. Furthermore there was a clear dichotomy in expression between the first two SPI-2 operons encoding ssaB-ssaE and sseA-sseG and the operons further downstream (ssaG-ssaQ) suggesting that slyA may act at different sites within SPI-2. However, these experiments are based on over-expression of slyA that may complicate the analysis because of binding to sites that would normally not be occupied.\n" ], "offsets": [ [ 0, 1935 ] ] } ]

[ { "id": "PMC2639726-02-Results-08_T1", "type": "Protein", "text": [ "SlyA" ], "offsets": [ [ 0, 4 ] ], "normalized": [] }, { "id": "PMC2639726-02-Results-08_T2", "type": "Protein", "text": [ "slyA" ], "offsets": [ [ 246, 250 ] ], "normalized": [] }, { "id": "PMC2639726-02-Results-08_T3", "type": "Protein", "text": [ "slyA" ], "offsets": [ [ 302, 306 ] ], "normalized": [] }, { "id": "PMC2639726-02-Results-08_T4", "type": "Protein", "text": [ "slyA" ], "offsets": [ [ 377, 381 ] ], "normalized": [] }, { "id": "PMC2639726-02-Results-08_T5", "type": "Protein", "text": [ "PhoP" ], "offsets": [ [ 412, 416 ] ], "normalized": [] }, { "id": "PMC2639726-02-Results-08_T6", "type": "Protein", "text": [ "SlyA" ], "offsets": [ [ 540, 544 ] ], "normalized": [] }, { "id": "PMC2639726-02-Results-08_T7", "type": "Protein", "text": [ "ssrB" ], "offsets": [ [ 559, 563 ] ], "normalized": [] }, { "id": "PMC2639726-02-Results-08_T8", "type": "Protein", "text": [ "slyA" ], "offsets": [ [ 602, 606 ] ], "normalized": [] }, { "id": "PMC2639726-02-Results-08_T9", "type": "Protein", "text": [ "ssrB" ], "offsets": [ [ 611, 615 ] ], "normalized": [] }, { "id": "PMC2639726-02-Results-08_T10", "type": "Protein", "text": [ "slyA" ], "offsets": [ [ 688, 692 ] ], "normalized": [] }, { "id": "PMC2639726-02-Results-08_T11", "type": "Protein", "text": [ "SlyA" ], "offsets": [ [ 719, 723 ] ], "normalized": [] }, { "id": "PMC2639726-02-Results-08_T12", "type": "Two-component-system", "text": [ "ompR/envZ" ], "offsets": [ [ 893, 902 ] ], "normalized": [] }, { "id": "PMC2639726-02-Results-08_T13", "type": "Protein", "text": [ "ompR" ], "offsets": [ [ 893, 897 ] ], "normalized": [] }, { "id": "PMC2639726-02-Results-08_T14", "type": "Protein", "text": [ "envZ" ], "offsets": [ [ 898, 902 ] ], "normalized": [] }, { "id": "PMC2639726-02-Results-08_T15", "type": "Two-component-system", "text": [ "phoP/phoQ" ], "offsets": [ [ 904, 913 ] ], "normalized": [] }, { "id": "PMC2639726-02-Results-08_T16", "type": "Protein", "text": [ "phoP" ], "offsets": [ [ 904, 908 ] ], "normalized": [] }, { "id": "PMC2639726-02-Results-08_T17", "type": "Protein", "text": [ "phoQ" ], "offsets": [ [ 909, 913 ] ], "normalized": [] }, { "id": "PMC2639726-02-Results-08_T18", "type": "Protein", "text": [ "csrA" ], "offsets": [ [ 915, 919 ] ], "normalized": [] }, { "id": "PMC2639726-02-Results-08_T19", "type": "Protein", "text": [ "himD" ], "offsets": [ [ 924, 928 ] ], "normalized": [] }, { "id": "PMC2639726-02-Results-08_T20", "type": "Protein", "text": [ "slyA" ], "offsets": [ [ 1031, 1035 ] ], "normalized": [] }, { "id": "PMC2639726-02-Results-08_T21", "type": "Protein", "text": [ "slyA" ], "offsets": [ [ 1095, 1099 ] ], "normalized": [] }, { "id": "PMC2639726-02-Results-08_T22", "type": "Two-component-system", "text": [ "ssrA/ssrB" ], "offsets": [ [ 1111, 1120 ] ], "normalized": [] }, { "id": "PMC2639726-02-Results-08_T23", "type": "Protein", "text": [ "ssrA" ], "offsets": [ [ 1111, 1115 ] ], "normalized": [] }, { "id": "PMC2639726-02-Results-08_T24", "type": "Protein", "text": [ "ssrB" ], "offsets": [ [ 1116, 1120 ] ], "normalized": [] }, { "id": "PMC2639726-02-Results-08_T25", "type": "Protein", "text": [ "slyA" ], "offsets": [ [ 1156, 1160 ] ], "normalized": [] }, { "id": "PMC2639726-02-Results-08_T26", "type": "Protein", "text": [ "ssrB" ], "offsets": [ [ 1226, 1230 ] ], "normalized": [] }, { "id": "PMC2639726-02-Results-08_T27", "type": "Organism", "text": [ "ssrAB/ompRenvZ" ], "offsets": [ [ 1292, 1306 ] ], "normalized": [] }, { "id": "PMC2639726-02-Results-08_T28", "type": "Two-component-system", "text": [ "ssrAB" ], "offsets": [ [ 1292, 1297 ] ], "normalized": [] }, { "id": "PMC2639726-02-Results-08_T29", "type": "Protein", "text": [ "ssrA" ], "offsets": [ [ 1292, 1296 ] ], "normalized": [] }, { "id": "PMC2639726-02-Results-08_T30", "type": "Protein", "text": [ "B" ], "offsets": [ [ 1296, 1297 ] ], "normalized": [] }, { "id": "PMC2639726-02-Results-08_T31", "type": "Two-component-system", "text": [ "ompRenvZ" ], "offsets": [ [ 1298, 1306 ] ], "normalized": [] }, { "id": "PMC2639726-02-Results-08_T32", "type": "Protein", "text": [ "ompR" ], "offsets": [ [ 1298, 1302 ] ], "normalized": [] }, { "id": "PMC2639726-02-Results-08_T33", "type": "Protein", "text": [ "envZ" ], "offsets": [ [ 1302, 1306 ] ], "normalized": [] }, { "id": "PMC2639726-02-Results-08_T34", "type": "Organism", "text": [ "ssrAB/phoPQ" ], "offsets": [ [ 1308, 1319 ] ], "normalized": [] }, { "id": "PMC2639726-02-Results-08_T35", "type": "Two-component-system", "text": [ "ssrAB" ], "offsets": [ [ 1308, 1313 ] ], "normalized": [] }, { "id": "PMC2639726-02-Results-08_T36", "type": "Protein", "text": [ "ssrA" ], "offsets": [ [ 1308, 1312 ] ], "normalized": [] }, { "id": "PMC2639726-02-Results-08_T37", "type": "Protein", "text": [ "B" ], "offsets": [ [ 1312, 1313 ] ], "normalized": [] }, { "id": "PMC2639726-02-Results-08_T38", "type": "Two-component-system", "text": [ "phoPQ" ], "offsets": [ [ 1314, 1319 ] ], "normalized": [] }, { "id": "PMC2639726-02-Results-08_T39", "type": "Protein", "text": [ "phoP" ], "offsets": [ [ 1314, 1318 ] ], "normalized": [] }, { "id": "PMC2639726-02-Results-08_T40", "type": "Protein", "text": [ "Q" ], "offsets": [ [ 1318, 1319 ] ], "normalized": [] }, { "id": "PMC2639726-02-Results-08_T41", "type": "Organism", "text": [ "ssrAB/csrA" ], "offsets": [ [ 1321, 1331 ] ], "normalized": [] }, { "id": "PMC2639726-02-Results-08_T42", "type": "Two-component-system", "text": [ "ssrAB" ], "offsets": [ [ 1321, 1326 ] ], "normalized": [] }, { "id": "PMC2639726-02-Results-08_T43", "type": "Protein", "text": [ "ssrA" ], "offsets": [ [ 1321, 1325 ] ], "normalized": [] }, { "id": "PMC2639726-02-Results-08_T44", "type": "Protein", "text": [ "B" ], "offsets": [ [ 1325, 1326 ] ], "normalized": [] }, { "id": "PMC2639726-02-Results-08_T45", "type": "Protein", "text": [ "csrA" ], "offsets": [ [ 1327, 1331 ] ], "normalized": [] }, { "id": "PMC2639726-02-Results-08_T46", "type": "Organism", "text": [ "ssrAB/himD" ], "offsets": [ [ 1336, 1346 ] ], "normalized": [] }, { "id": "PMC2639726-02-Results-08_T47", "type": "Two-component-system", "text": [ "ssrAB" ], "offsets": [ [ 1336, 1341 ] ], "normalized": [] }, { "id": "PMC2639726-02-Results-08_T48", "type": "Protein", "text": [ "ssrA" ], "offsets": [ [ 1336, 1340 ] ], "normalized": [] }, { "id": "PMC2639726-02-Results-08_T49", "type": "Protein", "text": [ "B" ], "offsets": [ [ 1340, 1341 ] ], "normalized": [] }, { "id": "PMC2639726-02-Results-08_T50", "type": "Protein", "text": [ "himD" ], "offsets": [ [ 1342, 1346 ] ], "normalized": [] }, { "id": "PMC2639726-02-Results-08_T51", "type": "Protein", "text": [ "slyA" ], "offsets": [ [ 1371, 1375 ] ], "normalized": [] }, { "id": "PMC2639726-02-Results-08_T52", "type": "Protein", "text": [ "ssrB" ], "offsets": [ [ 1444, 1448 ] ], "normalized": [] }, { "id": "PMC2639726-02-Results-08_T53", "type": "Two-component-system", "text": [ "ompR/envZ" ], "offsets": [ [ 1450, 1459 ] ], "normalized": [] }, { "id": "PMC2639726-02-Results-08_T54", "type": "Protein", "text": [ "ompR" ], "offsets": [ [ 1450, 1454 ] ], "normalized": [] }, { "id": "PMC2639726-02-Results-08_T55", "type": "Protein", "text": [ "envZ" ], "offsets": [ [ 1455, 1459 ] ], "normalized": [] }, { "id": "PMC2639726-02-Results-08_T56", "type": "Two-component-system", "text": [ "phoP/phoQ" ], "offsets": [ [ 1461, 1470 ] ], "normalized": [] }, { "id": "PMC2639726-02-Results-08_T57", "type": "Protein", "text": [ "phoP" ], "offsets": [ [ 1461, 1465 ] ], "normalized": [] }, { "id": "PMC2639726-02-Results-08_T58", "type": "Protein", "text": [ "phoQ" ], "offsets": [ [ 1466, 1470 ] ], "normalized": [] }, { "id": "PMC2639726-02-Results-08_T59", "type": "Protein", "text": [ "csrA" ], "offsets": [ [ 1472, 1476 ] ], "normalized": [] }, { "id": "PMC2639726-02-Results-08_T60", "type": "Protein", "text": [ "himD" ], "offsets": [ [ 1481, 1485 ] ], "normalized": [] }, { "id": "PMC2639726-02-Results-08_T61", "type": "Protein", "text": [ "ihf" ], "offsets": [ [ 1487, 1490 ] ], "normalized": [] }, { "id": "PMC2639726-02-Results-08_T62", "type": "Protein", "text": [ "ssrB" ], "offsets": [ [ 1535, 1539 ] ], "normalized": [] }, { "id": "PMC2639726-02-Results-08_T63", "type": "Regulon-operon", "text": [ "ssaB-ssaE" ], "offsets": [ [ 1640, 1649 ] ], "normalized": [] }, { "id": "PMC2639726-02-Results-08_T64", "type": "Protein", "text": [ "ssaB" ], "offsets": [ [ 1640, 1644 ] ], "normalized": [] }, { "id": "PMC2639726-02-Results-08_T65", "type": "Protein", "text": [ "ssaE" ], "offsets": [ [ 1645, 1649 ] ], "normalized": [] }, { "id": "PMC2639726-02-Results-08_T66", "type": "Regulon-operon", "text": [ "sseA-sseG" ], "offsets": [ [ 1654, 1663 ] ], "normalized": [] }, { "id": "PMC2639726-02-Results-08_T67", "type": "Protein", "text": [ "sseA" ], "offsets": [ [ 1654, 1658 ] ], "normalized": [] }, { "id": "PMC2639726-02-Results-08_T68", "type": "Protein", "text": [ "sseG" ], "offsets": [ [ 1659, 1663 ] ], "normalized": [] }, { "id": "PMC2639726-02-Results-08_T69", "type": "Regulon-operon", "text": [ "ssaG-ssaQ" ], "offsets": [ [ 1700, 1709 ] ], "normalized": [] }, { "id": "PMC2639726-02-Results-08_T70", "type": "Protein", "text": [ "ssaG" ], "offsets": [ [ 1700, 1704 ] ], "normalized": [] }, { "id": "PMC2639726-02-Results-08_T71", "type": "Protein", "text": [ "ssaQ" ], "offsets": [ [ 1705, 1709 ] ], "normalized": [] }, { "id": "PMC2639726-02-Results-08_T72", "type": "Protein", "text": [ "slyA" ], "offsets": [ [ 1727, 1731 ] ], "normalized": [] }, { "id": "PMC2639726-02-Results-08_T73", "type": "Protein", "text": [ "slyA" ], "offsets": [ [ 1832, 1836 ] ], "normalized": [] } ]

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[]

[]

[ { "id": "PMC2593050-03-RESULTS-02__text", "type": "abstract", "text": [ "Growth of DeltavicK in THY and Rabbit Blood \nThe growth curve of the DeltavicK mutant in THY displays a longer early growth phase and smaller slope in the exponential growth phase than that of the parent strain (Fig. 2A), indicating that the vicK deletion detrimentally affects S. equi growth. The effect of the deletion on S. equi growth in blood was also examined. The wild-type and DeltavicK S. equi strains were inoculated into 1 ml heparinized rabbit blood at an inoculum of approximately 20,000 cfu. The samples were incubated for 4 h, and the numbers of the bacteria in the samples and inocula at time zero were determined by plating. The growth factors, the ratio of cfu in the sample at 4 h over cfu at time zero, were 250 and 66 for the wild type and DeltavicK strains, respectively (Fig. 2B). Thus, the DeltavicK mutant has significantly reduced ability to grow in rabbit blood (P <0.0001).\n" ], "offsets": [ [ 0, 902 ] ] } ]

[ { "id": "PMC2593050-03-RESULTS-02_T1", "type": "Organism", "text": [ "DeltavicK" ], "offsets": [ [ 10, 19 ] ], "normalized": [] }, { "id": "PMC2593050-03-RESULTS-02_T2", "type": "Protein", "text": [ "vicK" ], "offsets": [ [ 15, 19 ] ], "normalized": [] }, { "id": "PMC2593050-03-RESULTS-02_T3", "type": "Organism", "text": [ "DeltavicK mutant" ], "offsets": [ [ 69, 85 ] ], "normalized": [] }, { "id": "PMC2593050-03-RESULTS-02_T4", "type": "Protein", "text": [ "vicK" ], "offsets": [ [ 74, 78 ] ], "normalized": [] }, { "id": "PMC2593050-03-RESULTS-02_T5", "type": "Protein", "text": [ "vicK" ], "offsets": [ [ 242, 246 ] ], "normalized": [] }, { "id": "PMC2593050-03-RESULTS-02_T6", "type": "Organism", "text": [ "S. equi" ], "offsets": [ [ 278, 285 ] ], "normalized": [] }, { "id": "PMC2593050-03-RESULTS-02_T7", "type": "Organism", "text": [ "S. equi" ], "offsets": [ [ 324, 331 ] ], "normalized": [] }, { "id": "PMC2593050-03-RESULTS-02_T8", "type": "Organism", "text": [ "DeltavicK S. equi" ], "offsets": [ [ 385, 402 ] ], "normalized": [] }, { "id": "PMC2593050-03-RESULTS-02_T9", "type": "Protein", "text": [ "vicK" ], "offsets": [ [ 390, 394 ] ], "normalized": [] }, { "id": "PMC2593050-03-RESULTS-02_T10", "type": "Organism", "text": [ "DeltavicK" ], "offsets": [ [ 761, 770 ] ], "normalized": [] }, { "id": "PMC2593050-03-RESULTS-02_T11", "type": "Protein", "text": [ "vicK" ], "offsets": [ [ 766, 770 ] ], "normalized": [] }, { "id": "PMC2593050-03-RESULTS-02_T12", "type": "Organism", "text": [ "DeltavicK mutant" ], "offsets": [ [ 814, 830 ] ], "normalized": [] }, { "id": "PMC2593050-03-RESULTS-02_T13", "type": "Protein", "text": [ "vicK" ], "offsets": [ [ 819, 823 ] ], "normalized": [] } ]

[]

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[]

[ { "id": "PMC2581603-02-Results-02__text", "type": "abstract", "text": [ "Extracellular DNA induces cell death by membrane perturbation and cell lysis \nDNA is a highly anionic polymer due to the phosphates in the deoxyribose backbone. This property, in combination with the fast-killing observed in response to extracellular DNA led us to hypothesize that addition of exogenous DNA resulted in the loss of membrane integrity through cation chelation, in a manner similar to that observed with the known cation chelator EDTA [58]. The OM of P. aeruginosa contains a 20:1 ratio of Mg2+:Ca2+ cations [59], which bind to and stabilize LPS in the outer leaflet of the OM [58]. EDTA treatment of cells resulted in chelation and removal of divalent cations from the OM, leading to disruption of the OM [58]. To determine the effect of DNA on membrane integrity, microscopic analysis in response to lethal concentrations of DNA and relevant controls was performed. Lipoproteins are lipid-modified proteins anchored in the outer leaflet of the IM or the inner leaflet of the OM. P. aeruginosa cells producing mCherry fluorescent membrane-anchored lipoproteins (lipoChFP) that are localized to either the OM or IM [60],[61] were used as markers of OM and IM integrity. LipoChFP-labelled P. aeruginosa cells showed dramatic membrane perturbations when exposed to 2% (w/v) DNA, but showed uniform membrane staining patterns in untreated cells (Fig 2A). The OM perturbations in DNA-exposed cells included regions of patchy fluorescence and the release of OMVs, while the IM perturbations were visualized simply as patchy and irregular regions of membrane fluorescence (Fig 2A). EDTA, the known cation chelator caused comparable IM and OM perturbations as those observed in cells exposed to extracellular DNA. Propidium iodide (PI) stains extracellular DNA and DNA in dead cells. PI staining was observed in cells exposed to DNA and EDTA, confirming that this treatment was lethal (Fig 2B). PI staining also revealed the presence of long strands of genomic DNA, presumably as a consequence of the loss of membrane integrity, cell lysis and release of cytoplasmic contents, including DNA (Fig 2B). The DNA released by lysed cells formed a mesh-like coating surrounding and connecting individual bacterial cells (Fig 2B). Degradation of these strands by DNAse treatment of lysed cells confirmed that these fibres were composed of DNA (Fig S1). Pseudomonas specific semi-quantitative PCR (qPCR) was also performed to confirm that the DNA released following DNA or EDTA treated cells was in fact genomic DNA from P. aeruginosa (Fig 2C). Buffer treated control cells showed intense green staining with syto9 (indicating viability) and a lack of PI staining (indicating no dead/dying cells or DNA release) (Fig S1).\n" ], "offsets": [ [ 0, 2722 ] ] } ]

[ { "id": "PMC2581603-02-Results-02_T1", "type": "Chemical", "text": [ "EDTA" ], "offsets": [ [ 445, 449 ] ], "normalized": [] }, { "id": "PMC2581603-02-Results-02_T2", "type": "Organism", "text": [ "P. aeruginosa" ], "offsets": [ [ 466, 479 ] ], "normalized": [] }, { "id": "PMC2581603-02-Results-02_T3", "type": "Chemical", "text": [ "Mg2+" ], "offsets": [ [ 505, 509 ] ], "normalized": [] }, { "id": "PMC2581603-02-Results-02_T4", "type": "Chemical", "text": [ "Ca2+" ], "offsets": [ [ 510, 514 ] ], "normalized": [] }, { "id": "PMC2581603-02-Results-02_T5", "type": "Chemical", "text": [ "LPS" ], "offsets": [ [ 557, 560 ] ], "normalized": [] }, { "id": "PMC2581603-02-Results-02_T6", "type": "Chemical", "text": [ "EDTA" ], "offsets": [ [ 598, 602 ] ], "normalized": [] }, { "id": "PMC2581603-02-Results-02_T7", "type": "Organism", "text": [ "P. aeruginosa" ], "offsets": [ [ 996, 1009 ] ], "normalized": [] }, { "id": "PMC2581603-02-Results-02_T8", "type": "Organism", "text": [ "P. aeruginosa" ], "offsets": [ [ 1203, 1216 ] ], "normalized": [] }, { "id": "PMC2581603-02-Results-02_T9", "type": "Chemical", "text": [ "EDTA" ], "offsets": [ [ 1591, 1595 ] ], "normalized": [] }, { "id": "PMC2581603-02-Results-02_T10", "type": "Chemical", "text": [ "Propidium iodide" ], "offsets": [ [ 1722, 1738 ] ], "normalized": [] }, { "id": "PMC2581603-02-Results-02_T11", "type": "Chemical", "text": [ "PI" ], "offsets": [ [ 1740, 1742 ] ], "normalized": [] }, { "id": "PMC2581603-02-Results-02_T12", "type": "Chemical", "text": [ "PI" ], "offsets": [ [ 1792, 1794 ] ], "normalized": [] }, { "id": "PMC2581603-02-Results-02_T13", "type": "Chemical", "text": [ "EDTA" ], "offsets": [ [ 1845, 1849 ] ], "normalized": [] }, { "id": "PMC2581603-02-Results-02_T14", "type": "Chemical", "text": [ "PI" ], "offsets": [ [ 1903, 1905 ] ], "normalized": [] }, { "id": "PMC2581603-02-Results-02_T15", "type": "Organism", "text": [ "Pseudomonas" ], "offsets": [ [ 2354, 2365 ] ], "normalized": [] }, { "id": "PMC2581603-02-Results-02_T16", "type": "Chemical", "text": [ "EDTA" ], "offsets": [ [ 2473, 2477 ] ], "normalized": [] }, { "id": "PMC2581603-02-Results-02_T17", "type": "Organism", "text": [ "P. aeruginosa" ], "offsets": [ [ 2521, 2534 ] ], "normalized": [] }, { "id": "PMC2581603-02-Results-02_T18", "type": "Chemical", "text": [ "syto9" ], "offsets": [ [ 2609, 2614 ] ], "normalized": [] }, { "id": "PMC2581603-02-Results-02_T19", "type": "Chemical", "text": [ "PI" ], "offsets": [ [ 2652, 2654 ] ], "normalized": [] } ]

[ { "id": "PMC2581603-02-Results-02_E1", "type": "Binding", "trigger": { "text": [ "bind" ], "offsets": [ [ 535, 539 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC2581603-02-Results-02_T3" }, { "role": "Theme", "ref_id": "PMC2581603-02-Results-02_T5" } ] }, { "id": "PMC2581603-02-Results-02_E2", "type": "Binding", "trigger": { "text": [ "bind" ], "offsets": [ [ 535, 539 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC2581603-02-Results-02_T4" }, { "role": "Theme", "ref_id": "PMC2581603-02-Results-02_T5" } ] } ]

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[]

[ { "id": "PMC2774163-02-Results-05__text", "type": "abstract", "text": [ "GacS plays a dual role in P. aeruginosa biofilm development \nSince GacS was found to be phosphorylated in a BfiS-dependent manner following 8 hrs of growth, we asked whether a DeltagacS mutant forms biofilms similar in architecture to DeltabfiS biofilms. Inactivation of gacS resulted in the formation of biofilms following 144 hr of growth that were similar in appearance to 24-hr-old wild type biofilms. Closer inspection of biofilm formation by DeltagacS over a period of 144 hr, however, indicated that the biofilm architecture (seen after 144 hr) was due to accelerated biofilm growth followed by premature disaggregation of biofilms as compared to wild type biofilms. DeltagacS mutant biofilms were significantly thicker than wild type biofilms following 1 and 72 hr of growth under flowing conditions, forming microcolonies and clusters exceeding 150 microm in diameter (Fig. 3). At both time points, DeltagacS biofilms not only exceeded the average microcolony size typically seen for wild type biofilms of the same age, but also the biomass and thickness of wild type biofilms at more mature ages (Fig. 3, Table 2). Continued growth for more than 72 hr, however, resulted in the disaggregation of DeltagacS mutant biofilms as indicated by the presence of large, detached clusters floating in the bulk liquid, and a significantly reduced attached biofilm biomass and biofilm thickness (Fig. 3, Table 2). Thus, while growth of DeltagacS mutant biofilms following 24 hr post attachment was accelerated (Fig. 3), initial attachment was significantly reduced in this mutant (not shown). These findings suggest that GacS may play a dual role in regulating biofilm formation, which in turn may be dependent on the phosphorylation status of GacS (Table 1).\n" ], "offsets": [ [ 0, 1758 ] ] } ]

[ { "id": "PMC2774163-02-Results-05_T1", "type": "Protein", "text": [ "GacS" ], "offsets": [ [ 0, 4 ] ], "normalized": [] }, { "id": "PMC2774163-02-Results-05_T2", "type": "Organism", "text": [ "P. aeruginosa" ], "offsets": [ [ 26, 39 ] ], "normalized": [] }, { "id": "PMC2774163-02-Results-05_T3", "type": "Protein", "text": [ "GacS" ], "offsets": [ [ 67, 71 ] ], "normalized": [] }, { "id": "PMC2774163-02-Results-05_T4", "type": "Protein", "text": [ "BfiS" ], "offsets": [ [ 108, 112 ] ], "normalized": [] }, { "id": "PMC2774163-02-Results-05_T5", "type": "Organism", "text": [ "DeltagacS mutant" ], "offsets": [ [ 176, 192 ] ], "normalized": [] }, { "id": "PMC2774163-02-Results-05_T6", "type": "Protein", "text": [ "gacS" ], "offsets": [ [ 181, 185 ] ], "normalized": [] }, { "id": "PMC2774163-02-Results-05_T7", "type": "Organism", "text": [ "DeltabfiS" ], "offsets": [ [ 235, 244 ] ], "normalized": [] }, { "id": "PMC2774163-02-Results-05_T8", "type": "Protein", "text": [ "bfiS" ], "offsets": [ [ 240, 244 ] ], "normalized": [] }, { "id": "PMC2774163-02-Results-05_T9", "type": "Protein", "text": [ "gacS" ], "offsets": [ [ 271, 275 ] ], "normalized": [] }, { "id": "PMC2774163-02-Results-05_T10", "type": "Organism", "text": [ "DeltagacS" ], "offsets": [ [ 448, 457 ] ], "normalized": [] }, { "id": "PMC2774163-02-Results-05_T11", "type": "Protein", "text": [ "gacS" ], "offsets": [ [ 453, 457 ] ], "normalized": [] }, { "id": "PMC2774163-02-Results-05_T12", "type": "Organism", "text": [ "DeltagacS" ], "offsets": [ [ 674, 683 ] ], "normalized": [] }, { "id": "PMC2774163-02-Results-05_T13", "type": "Protein", "text": [ "gacS" ], "offsets": [ [ 679, 683 ] ], "normalized": [] }, { "id": "PMC2774163-02-Results-05_T14", "type": "Organism", "text": [ "DeltagacS" ], "offsets": [ [ 908, 917 ] ], "normalized": [] }, { "id": "PMC2774163-02-Results-05_T15", "type": "Protein", "text": [ "gacS" ], "offsets": [ [ 913, 917 ] ], "normalized": [] }, { "id": "PMC2774163-02-Results-05_T16", "type": "Organism", "text": [ "DeltagacS" ], "offsets": [ [ 1206, 1215 ] ], "normalized": [] }, { "id": "PMC2774163-02-Results-05_T17", "type": "Protein", "text": [ "gacS" ], "offsets": [ [ 1211, 1215 ] ], "normalized": [] }, { "id": "PMC2774163-02-Results-05_T18", "type": "Organism", "text": [ "DeltagacS" ], "offsets": [ [ 1434, 1443 ] ], "normalized": [] }, { "id": "PMC2774163-02-Results-05_T19", "type": "Protein", "text": [ "gacS" ], "offsets": [ [ 1439, 1443 ] ], "normalized": [] }, { "id": "PMC2774163-02-Results-05_T20", "type": "Protein", "text": [ "GacS" ], "offsets": [ [ 1619, 1623 ] ], "normalized": [] }, { "id": "PMC2774163-02-Results-05_T21", "type": "Protein", "text": [ "GacS" ], "offsets": [ [ 1742, 1746 ] ], "normalized": [] } ]

[ { "id": "PMC2774163-02-Results-05_E1", "type": "Phosphorylation", "trigger": { "text": [ "phosphorylated" ], "offsets": [ [ 88, 102 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC2774163-02-Results-05_T3" } ] }, { "id": "PMC2774163-02-Results-05_E2", "type": "Positive_regulation", "trigger": { "text": [ "dependent" ], "offsets": [ [ 113, 122 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC2774163-02-Results-05_E1" }, { "role": "Cause", "ref_id": "PMC2774163-02-Results-05_T4" } ] }, { "id": "PMC2774163-02-Results-05_E3", "type": "Negative_regulation", "trigger": { "text": [ "Inactivation" ], "offsets": [ [ 255, 267 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC2774163-02-Results-05_T9" } ] }, { "id": "PMC2774163-02-Results-05_E4", "type": "Phosphorylation", "trigger": { "text": [ "phosphorylation" ], "offsets": [ [ 1716, 1731 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC2774163-02-Results-05_T21" } ] } ]

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[ { "id": "PMC2816692-02-Results-01__text", "type": "abstract", "text": [ "Results \nIdentification of an SsrB-regulated secretion chaperone Transcriptional profiling of SsrB-regulated genes in S. enterica serovar Typhimurium (S. Typhimurium) [22] identified a hypothetical gene, STM2138 (named srcA hereafter), that was co-regulated with genes in SPI-2 and repressed approximately20-fold in an ssrB mutant compared to wild type. This gene was also down regulated in Salmonella mutants lacking the SsrA sensor kinase [20], and was predicted to encode a possible chaperone in a bioinformatics-based screen [23]. The srcA gene is not located in the vicinity of the T3SS encoded by SPI-2 (STM1378-STM1425), but is 713 genes downstream on the chromosome (STM numbers are based on the LT2 genome and ordered sequentially on the chromosome beginning at STM0001, thrL). The predicted srcA gene product was a small protein approximately16 kDa with a pI of 4.6, similar to secretion chaperones associated with T3SS. To verify SsrB input on srcA expression, we analyzed SsrB binding in vivo at the region of DNA surrounding srcA using genome-wide ChIP-on-chip [21] (and unpublished data). This analysis revealed a strong SsrB binding site spanning 10 syntenic probes within the intergenic region (IGR) upstream of srcA, that together with the transcriptional data corroborated a direct regulatory role for SsrB on srcA expression (Fig. 1A). To determine the cellular distribution of SrcA we constructed a srcA-HA allele and expressed this gene in wild type and in ssrB mutant cells under conditions that activate the SPI-2 T3SS [24]. In whole cell lysates, SrcA protein was reduced approximately10-fold in DeltassrB cells compared to wild type (Fig. 1B) and the protein was not detected in the secreted fraction from wild type cells (Fig. 1C), consistent with the expected properties of a T3SS chaperone. As a positive control, SseC, an SsrB-regulated translocon protein of the SPI-2 T3SS was present in the secreted fraction from wild type cells but not from an ssrB mutant.\n" ], "offsets": [ [ 0, 1990 ] ] } ]

[ { "id": "PMC2816692-02-Results-01_T1", "type": "Protein", "text": [ "SsrB" ], "offsets": [ [ 30, 34 ] ], "normalized": [] }, { "id": "PMC2816692-02-Results-01_T2", "type": "Protein", "text": [ "SsrB" ], "offsets": [ [ 94, 98 ] ], "normalized": [] }, { "id": "PMC2816692-02-Results-01_T3", "type": "Organism", "text": [ "S. enterica serovar Typhimurium" ], "offsets": [ [ 118, 149 ] ], "normalized": [] }, { "id": "PMC2816692-02-Results-01_T4", "type": "Organism", "text": [ "S. Typhimurium" ], "offsets": [ [ 151, 165 ] ], "normalized": [] }, { "id": "PMC2816692-02-Results-01_T5", "type": "Protein", "text": [ "STM2138" ], "offsets": [ [ 204, 211 ] ], "normalized": [] }, { "id": "PMC2816692-02-Results-01_T6", "type": "Protein", "text": [ "srcA" ], "offsets": [ [ 219, 223 ] ], "normalized": [] }, { "id": "PMC2816692-02-Results-01_T7", "type": "Organism", "text": [ "ssrB mutant" ], "offsets": [ [ 319, 330 ] ], "normalized": [] }, { "id": "PMC2816692-02-Results-01_T8", "type": "Protein", "text": [ "ssrB" ], "offsets": [ [ 319, 323 ] ], "normalized": [] }, { "id": "PMC2816692-02-Results-01_T9", "type": "Organism", "text": [ "Salmonella" ], "offsets": [ [ 391, 401 ] ], "normalized": [] }, { "id": "PMC2816692-02-Results-01_T10", "type": "Protein", "text": [ "SsrA" ], "offsets": [ [ 422, 426 ] ], "normalized": [] }, { "id": "PMC2816692-02-Results-01_T11", "type": "Protein", "text": [ "srcA" ], "offsets": [ [ 539, 543 ] ], "normalized": [] }, { "id": "PMC2816692-02-Results-01_T12", "type": "Protein", "text": [ "STM1378" ], "offsets": [ [ 610, 617 ] ], "normalized": [] }, { "id": "PMC2816692-02-Results-01_T13", "type": "Protein", "text": [ "STM1425" ], "offsets": [ [ 618, 625 ] ], "normalized": [] }, { "id": "PMC2816692-02-Results-01_T14", "type": "Protein", "text": [ "thrL" ], "offsets": [ [ 780, 784 ] ], "normalized": [] }, { "id": "PMC2816692-02-Results-01_T15", "type": "Protein", "text": [ "srcA" ], "offsets": [ [ 801, 805 ] ], "normalized": [] }, { "id": "PMC2816692-02-Results-01_T16", "type": "Protein", "text": [ "SsrB" ], "offsets": [ [ 941, 945 ] ], "normalized": [] }, { "id": "PMC2816692-02-Results-01_T17", "type": "Protein", "text": [ "srcA" ], "offsets": [ [ 955, 959 ] ], "normalized": [] }, { "id": "PMC2816692-02-Results-01_T18", "type": "Protein", "text": [ "SsrB" ], "offsets": [ [ 984, 988 ] ], "normalized": [] }, { "id": "PMC2816692-02-Results-01_T19", "type": "Protein", "text": [ "srcA" ], "offsets": [ [ 1038, 1042 ] ], "normalized": [] }, { "id": "PMC2816692-02-Results-01_T20", "type": "Protein", "text": [ "SsrB" ], "offsets": [ [ 1135, 1139 ] ], "normalized": [] }, { "id": "PMC2816692-02-Results-01_T21", "type": "Protein", "text": [ "srcA" ], "offsets": [ [ 1228, 1232 ] ], "normalized": [] }, { "id": "PMC2816692-02-Results-01_T22", "type": "Protein", "text": [ "SsrB" ], "offsets": [ [ 1320, 1324 ] ], "normalized": [] }, { "id": "PMC2816692-02-Results-01_T23", "type": "Protein", "text": [ "srcA" ], "offsets": [ [ 1328, 1332 ] ], "normalized": [] }, { "id": "PMC2816692-02-Results-01_T24", "type": "Protein", "text": [ "1A" ], "offsets": [ [ 1350, 1352 ] ], "normalized": [] }, { "id": "PMC2816692-02-Results-01_T25", "type": "Protein", "text": [ "SrcA" ], "offsets": [ [ 1397, 1401 ] ], "normalized": [] }, { "id": "PMC2816692-02-Results-01_T26", "type": "Protein", "text": [ "srcA" ], "offsets": [ [ 1419, 1423 ] ], "normalized": [] }, { "id": "PMC2816692-02-Results-01_T27", "type": "Organism", "text": [ "ssrB mutant" ], "offsets": [ [ 1478, 1489 ] ], "normalized": [] }, { "id": "PMC2816692-02-Results-01_T28", "type": "Protein", "text": [ "ssrB" ], "offsets": [ [ 1478, 1482 ] ], "normalized": [] }, { "id": "PMC2816692-02-Results-01_T29", "type": "Protein", "text": [ "SrcA" ], "offsets": [ [ 1571, 1575 ] ], "normalized": [] }, { "id": "PMC2816692-02-Results-01_T30", "type": "Organism", "text": [ "DeltassrB" ], "offsets": [ [ 1620, 1629 ] ], "normalized": [] }, { "id": "PMC2816692-02-Results-01_T31", "type": "Protein", "text": [ "SseC" ], "offsets": [ [ 1842, 1846 ] ], "normalized": [] }, { "id": "PMC2816692-02-Results-01_T32", "type": "Protein", "text": [ "SsrB" ], "offsets": [ [ 1851, 1855 ] ], "normalized": [] }, { "id": "PMC2816692-02-Results-01_T33", "type": "Organism", "text": [ "ssrB mutant" ], "offsets": [ [ 1977, 1988 ] ], "normalized": [] }, { "id": "PMC2816692-02-Results-01_T34", "type": "Protein", "text": [ "ssrB" ], "offsets": [ [ 1977, 1981 ] ], "normalized": [] }, { "id": "PMC2816692-02-Results-01_T42", "type": "Entity", "text": [ "intergenic region (IGR)" ], "offsets": [ [ 1192, 1215 ] ], "normalized": [] } ]

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[ { "id": "PMC1913099-02-Results-Discussion-02__text", "type": "abstract", "text": [ "Verification by Quantitative Real-Time PCR \nWe conducted TaqMan (qRT-PCR) analysis [23] of 11 differentially expressed genes to validate selected microarray hybridization results (see Table S2 for genes and primer-probe sequences). Five genes chosen for validation demonstrated statistically significant fold changes in expression by microarray analysis (PF value < 0.05; two upregulated, three downregulated). The remaining six genes (four upregulated, two downregulated) did not have significant PF values, but were statistically significant as members of particular neighbor clusters in subsequent analyses (PE < 0.05) as detailed in later sections). We averaged the data to generate a value for each gene, creating a set of 11 paired values from quantitative real-time (qRT)-PCR and microarray analyses (Table S3). Results of standard linear regression analysis demonstrated a strong positive correlation (r = 0.9) between data obtained using the different techniques (see Figure S1).\n" ], "offsets": [ [ 0, 989 ] ] } ]

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[ { "id": "PMC2430206-02-Results-02__text", "type": "abstract", "text": [ "Deletion of graRS leads to attenuated virulence in a mouse infection model \nTo investigate the impact of reduced resistance of the graRS mutant to neutrophil and CAMP-mediated killing on the ability of the bacteria to cause infections in vivo, we compared the virulence of WT and mutant bacteria in a mouse challenge model. Therefore female BALB/c mice (12 to 15 weeks old) were infected with S. aureus WT or graRS mutant bacteria. 72 h after infection numbers of CFU/kidney were determined. Significantly less bacteria were detected in the kidneys of animals, which had been infected with the graRS mutant than those infected with the WT bacteria. (Fig. 3) This finding is in coincidence with the increased susceptibility to clearance by CAMPs and neutrophils, corroborating the central importance of these host factors in innate defense.\n" ], "offsets": [ [ 0, 840 ] ] } ]

[ { "id": "PMC2430206-02-Results-02_T1", "type": "Two-component-system", "text": [ "graRS" ], "offsets": [ [ 12, 17 ] ], "normalized": [] }, { "id": "PMC2430206-02-Results-02_T2", "type": "Protein", "text": [ "graR" ], "offsets": [ [ 12, 16 ] ], "normalized": [] }, { "id": "PMC2430206-02-Results-02_T3", "type": "Protein", "text": [ "S" ], "offsets": [ [ 16, 17 ] ], "normalized": [] }, { "id": "PMC2430206-02-Results-02_T4", "type": "Organism", "text": [ "mouse" ], "offsets": [ [ 53, 58 ] ], "normalized": [] }, { "id": "PMC2430206-02-Results-02_T5", "type": "Organism", "text": [ "graRS mutant" ], "offsets": [ [ 131, 143 ] ], "normalized": [] }, { "id": "PMC2430206-02-Results-02_T6", "type": "Two-component-system", "text": [ "graRS" ], "offsets": [ [ 131, 136 ] ], "normalized": [] }, { "id": "PMC2430206-02-Results-02_T7", "type": "Protein", "text": [ "graR" ], "offsets": [ [ 131, 135 ] ], "normalized": [] }, { "id": "PMC2430206-02-Results-02_T8", "type": "Protein", "text": [ "S" ], "offsets": [ [ 135, 136 ] ], "normalized": [] }, { "id": "PMC2430206-02-Results-02_T9", "type": "Organism", "text": [ "mouse" ], "offsets": [ [ 301, 306 ] ], "normalized": [] }, { "id": "PMC2430206-02-Results-02_T10", "type": "Organism", "text": [ "BALB/c mice" ], "offsets": [ [ 341, 352 ] ], "normalized": [] }, { "id": "PMC2430206-02-Results-02_T11", "type": "Organism", "text": [ "S. aureus" ], "offsets": [ [ 393, 402 ] ], "normalized": [] }, { "id": "PMC2430206-02-Results-02_T12", "type": "Organism", "text": [ "graRS mutant" ], "offsets": [ [ 409, 421 ] ], "normalized": [] }, { "id": "PMC2430206-02-Results-02_T13", "type": "Two-component-system", "text": [ "graRS" ], "offsets": [ [ 409, 414 ] ], "normalized": [] }, { "id": "PMC2430206-02-Results-02_T14", "type": "Protein", "text": [ "graR" ], "offsets": [ [ 409, 413 ] ], "normalized": [] }, { "id": "PMC2430206-02-Results-02_T15", "type": "Protein", "text": [ "S" ], "offsets": [ [ 413, 414 ] ], "normalized": [] }, { "id": "PMC2430206-02-Results-02_T16", "type": "Organism", "text": [ "graRS mutant" ], "offsets": [ [ 594, 606 ] ], "normalized": [] }, { "id": "PMC2430206-02-Results-02_T17", "type": "Two-component-system", "text": [ "graRS" ], "offsets": [ [ 594, 599 ] ], "normalized": [] }, { "id": "PMC2430206-02-Results-02_T18", "type": "Protein", "text": [ "graR" ], "offsets": [ [ 594, 598 ] ], "normalized": [] }, { "id": "PMC2430206-02-Results-02_T19", "type": "Protein", "text": [ "S" ], "offsets": [ [ 598, 599 ] ], "normalized": [] } ]

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[ { "id": "PMC2266911-02-Results_and_Discussion-02-04__text", "type": "abstract", "text": [ "Secretion and exoenzymes \nIn Y. enterocolitica, two type-III secretion systems (T3SS) essential for virulence in the mammalian host are encoded on pYV and by the ysa operon (YE3533-3561) [23,82]. The P. luminescens genome encodes one T3SS which is highly similar to the plasmid-encoded T3SS of Y. enterocolitica and probably involved in the secretion of virulence proteins or in immunomodulation of the insect response to an infection. Interestingly, the T3SS of Y. pestis has recently been demonstrated to translocate insecticidal toxins, providing evidence that they support the transmission of the plague agent by insects [83]. Furthermore, the flagellar export apparatus of Y. pseudotuberculosis functions as a secretion system for the virulence-associated phospholipase YplA [84]. The typical effector proteins of Y. enterocolitica are also present in P. luminescens. The P. luminescens Lop effector proteins are homologs of the Yop effector proteins of Y. enterocolitica [85]. The LopT effector protein of P. luminescens can be injected by Y. enterocolitica into mammal cells [86], underlining the idea that both T3SS act similarly. Furthermore, we found homologues of the Y. enterocolitica low-calcium-response genes (lcrH, lcrV, and lrcD) in P. luminescens (plu3757, plu3758, sctV) which further supports this hypothesis. The fact that Y. enterocolitica a second T3SS (Ysa) is not shared by P. luminescens confirms its solely role in human pathogenicity [87]. Both P. luminesens and Y. enterocolitica share a Sec protein translocation system that belongs to the type-II secretion systems (T2SS). These are substrate-specific secretion machineries that share a similar architecture and secretion mechanism [88]. Proteins secreted by these systems are mainly virulence determinants such as exotoxins like the Cholera toxin of Vibrio cholerae, pili, and S-layer components (see [89] for review). Additionally to the Sec-system, Y. enterocolitica produces a T2SS named Yts1, which has been found to be important for virulence in mice [90]. Because there is no counterpart of Yts1 present in P. luminescens, one can speculate that the major parts of type-II dependent secreted proteins which are important for insect association of Y. enterocolitica are translocated via the Sec system. Recently, a novel protein secretion mechanism translocating proteins without an N-terminal leader sequence has been described, termed type-VI secretion system, T6SS (see [91] for review). The genes encoding these kinds of secretion systems were named vas (virulence associated secretion), and homologues are widespread in Gram-negative bacteria. VAS-dependent secretion has been found to be important for virulence of Vibrio cholerae [92] as well as for Pseudomonas aeruginosa [93], and T6SS are assumed to play a major role in virulence in many Gram-negative bacteria [91]. P. luminescens as well as Y. enterocolitica harbour homologues of the vas genes, indicating that several proteins involved in virulence are secreted via this pathway. Both pathogens secrete lipases and proteases that are assumed to contribute to immunosuppression, degradation of insect tissues or antibacterial peptides, and host bioconversion (Fig. 4). One of those exoenzymes is the phospholipase A (YplA) with an accessory protein (YplB) of Y. enterocolitica (YE1005/YE1006) which are also present in P. luminescens (Plu3370/Plu3369). YplA contributes to pathogenesis of Y. enterocolitica in a mouse model [94], suggesting a role in virulence against insects for the P. luminescens homologue. Remarkably, yplA is induced at low temperature (Table 1), and its expression is known to be regulated by the master regulator FlhDC [94], indicating that YplA plays a role in pathogenicity both against human and insect hosts. Two additional phospholipases are present in Y. enterocolitica, namely PdlA (YE0203) and PdlB (YE0207), the latter one a homologue of Plu4619. This overlap is another example for Y. enterocolitica enzymes probably involved rather in the association with invertebrates than in pathogenicity towards mammalians. Plu1971 of P. luminescens is a protein which contains two phospholipase D motifs. Furthermore, it shares homologies to the plasmid (pMT1)-encoded murine toxin (Ymt) of Y. pestis. It was suggested that ymt has been acquired by Y. pestis from P. luminescens or a close relative [24]. Ymt is essential for flea colonization by Y. pestis and is regulated by AHL both in Y. pestis [95] and P. luminescens (R. Heermann, unpublished data), indicating that Ymt is also required for insect colonization by P. luminescens. Due to its absence in Y. enterocolitica, Ymt is another example for the high diversity of genetic determinants that are used by closely related bacterial pathogens to interact with their insect hosts. There are several other exoenzymes present either in Y. enterocolitica or in P. luminescens, which do not have a homologue counterpart in the other bacterium. Examples are the ten triacylglycerol lipases of P. luminescens or the three identified lipases of Y. enterocolitica. However, homologies are observed for six secreted proteases of both organisms. Among them is PrtA (Plu0655/YE4052), a zinc metalloprotease that is involved in the immunosuppressive activity of X. nematophila [96], and that has also been shown to be involved in insect gut colonization of P. luminescens [97]. Further examples for shared proteases are another Zn-dependent protease (Plu0306/YE4066), the protease III (Plu0631/YE3311), and DegQ/DegS (YE3744/YE3745/Plu4018/Plu4022). The high number of homologs in both organisms suggests an important and similar role of these exoproteases in the infection process. We also identified two proteases in each pathogen (Plu4291, Plu0631, YE0320, and YE2087) without a homologue in the other bacterium. We speculate that these Y. enterocolitica proteases could be involved in the infection process in mammals, whereas the P. luminescens proteases are rather used for nutrient bioconversion than for the infection process.\n" ], "offsets": [ [ 0, 6054 ] ] } ]

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"text": [ "Y. enterocolitica" ], "offsets": [ [ 294, 311 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-02-04_T8", "type": "Organism", "text": [ "Y. pestis" ], "offsets": [ [ 463, 472 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-02-04_T9", "type": "Organism", "text": [ "Y. pseudotuberculosis" ], "offsets": [ [ 678, 699 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-02-04_T10", "type": "Protein", "text": [ "YplA" ], "offsets": [ [ 775, 779 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-02-04_T11", "type": "Organism", "text": [ "Y. enterocolitica" ], "offsets": [ [ 819, 836 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-02-04_T12", "type": "Organism", "text": [ "P. luminescens" ], "offsets": [ [ 857, 871 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-02-04_T13", "type": "Organism", "text": [ "P. luminescens" ], "offsets": [ [ 877, 891 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-02-04_T14", "type": "Organism", "text": [ "Y. enterocolitica" ], "offsets": [ [ 959, 976 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-02-04_T15", "type": "Protein", "text": [ "LopT" ], "offsets": [ [ 987, 991 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-02-04_T16", "type": "Organism", "text": [ "P. luminescens" ], "offsets": [ [ 1012, 1026 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-02-04_T17", "type": "Organism", "text": [ "Y. enterocolitica" ], "offsets": [ [ 1046, 1063 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-02-04_T18", "type": "Organism", "text": [ "Y. enterocolitica" ], "offsets": [ [ 1179, 1196 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-02-04_T19", "type": "Chemical", "text": [ "calcium" ], "offsets": [ [ 1201, 1208 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-02-04_T20", "type": "Protein", "text": [ "lcrH" ], "offsets": [ [ 1225, 1229 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-02-04_T21", "type": "Protein", "text": [ "lcrV" ], "offsets": [ [ 1231, 1235 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-02-04_T22", "type": "Protein", "text": [ "lrcD" ], "offsets": [ [ 1241, 1245 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-02-04_T23", "type": "Organism", "text": [ "P. luminescens" ], "offsets": [ [ 1250, 1264 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-02-04_T24", "type": "Protein", "text": [ "plu3757" ], "offsets": [ [ 1266, 1273 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-02-04_T25", "type": "Protein", "text": [ "plu3758" ], "offsets": [ [ 1275, 1282 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-02-04_T26", "type": "Protein", "text": [ "sctV" ], "offsets": [ [ 1284, 1288 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-02-04_T27", "type": "Organism", "text": [ "Y. enterocolitica" ], "offsets": [ [ 1344, 1361 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-02-04_T28", "type": "Organism", "text": [ "P. luminescens" ], "offsets": [ [ 1399, 1413 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-02-04_T29", "type": "Organism", "text": [ "human" ], "offsets": [ [ 1442, 1447 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-02-04_T30", "type": "Organism", "text": [ "P. luminesens" ], "offsets": [ [ 1473, 1486 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-02-04_T31", "type": "Organism", "text": [ "Y. enterocolitica" ], "offsets": [ [ 1491, 1508 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-02-04_T32", "type": "Organism", "text": [ "Vibrio cholerae" ], "offsets": [ [ 1832, 1847 ] ], "normalized": [] 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"Organism", "text": [ "Vibrio cholerae" ], "offsets": [ [ 2708, 2723 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-02-04_T40", "type": "Organism", "text": [ "Pseudomonas aeruginosa" ], "offsets": [ [ 2744, 2766 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-02-04_T41", "type": "Organism", "text": [ "P. luminescens" ], "offsets": [ [ 2865, 2879 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-02-04_T42", "type": "Organism", "text": [ "Y. enterocolitica" ], "offsets": [ [ 2891, 2908 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-02-04_T43", "type": "Protein", "text": [ "phospholipase A" ], "offsets": [ [ 3251, 3266 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-02-04_T44", "type": "Protein", "text": [ "YplA" ], "offsets": [ [ 3268, 3272 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-02-04_T45", "type": "Protein", "text": [ "YplB" ], "offsets": [ [ 3301, 3305 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-02-04_T46", "type": "Organism", "text": [ "Y. enterocolitica" ], "offsets": [ [ 3310, 3327 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-02-04_T47", "type": "Protein", "text": [ "YE1005" ], "offsets": [ [ 3329, 3335 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-02-04_T48", "type": "Protein", "text": [ "YE1006" ], "offsets": [ [ 3336, 3342 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-02-04_T49", "type": "Organism", "text": [ "P. luminescens" ], "offsets": [ [ 3370, 3384 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-02-04_T50", "type": "Protein", "text": [ "Plu3370" ], "offsets": [ [ 3386, 3393 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-02-04_T51", "type": "Protein", "text": [ "Plu3369" ], "offsets": [ [ 3394, 3401 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-02-04_T52", "type": "Protein", "text": [ "YplA" ], "offsets": [ [ 3404, 3408 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-02-04_T53", "type": "Organism", "text": [ "Y. enterocolitica" ], "offsets": [ [ 3440, 3457 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-02-04_T54", "type": "Organism", "text": [ "mouse" ], "offsets": [ [ 3463, 3468 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-02-04_T55", "type": "Organism", "text": [ "P. luminescens" ], "offsets": [ [ 3536, 3550 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-02-04_T56", "type": "Protein", "text": [ "yplA" ], "offsets": [ [ 3574, 3578 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-02-04_T57", "type": "Two-component-system", "text": [ "FlhDC" ], "offsets": [ [ 3688, 3693 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-02-04_T58", "type": "Protein", "text": [ "FlhD" ], "offsets": [ [ 3688, 3692 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-02-04_T59", "type": "Protein", "text": [ "C" ], "offsets": [ [ 3692, 3693 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-02-04_T60", "type": "Protein", "text": [ "YplA" ], "offsets": [ [ 3716, 3720 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-02-04_T61", "type": "Organism", "text": [ "human" ], "offsets": [ [ 3764, 3769 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-02-04_T62", "type": "Organism", "text": [ "Y. enterocolitica" ], "offsets": [ [ 3833, 3850 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-02-04_T63", "type": "Protein", "text": [ "PdlA" ], "offsets": [ [ 3859, 3863 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-02-04_T64", "type": "Protein", "text": [ "YE0203" ], "offsets": [ [ 3865, 3871 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-02-04_T65", "type": "Protein", "text": [ "PdlB" ], "offsets": [ [ 3877, 3881 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-02-04_T66", "type": "Protein", "text": [ "YE0207" ], "offsets": [ [ 3883, 3889 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-02-04_T67", "type": "Protein", "text": [ "Plu4619" ], "offsets": [ [ 3922, 3929 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-02-04_T68", "type": "Organism", "text": [ "Y. enterocolitica" ], "offsets": [ [ 3967, 3984 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-02-04_T69", "type": "Protein", "text": [ "Plu1971" ], "offsets": [ [ 4098, 4105 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-02-04_T70", "type": "Organism", "text": [ "P. luminescens" ], "offsets": [ [ 4109, 4123 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-02-04_T71", "type": "Protein", "text": [ "phospholipase D" ], "offsets": [ [ 4156, 4171 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-02-04_T72", "type": "Organism", "text": [ "murine" ], "offsets": [ [ 4244, 4250 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-02-04_T73", "type": "Protein", "text": [ "Ymt" ], "offsets": [ [ 4258, 4261 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-02-04_T74", "type": "Organism", "text": [ "Y. pestis" ], "offsets": [ [ 4266, 4275 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-02-04_T75", "type": "Protein", "text": [ "ymt" ], "offsets": [ [ 4299, 4302 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-02-04_T76", "type": "Organism", "text": [ "Y. pestis" ], "offsets": [ [ 4324, 4333 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-02-04_T77", "type": "Organism", "text": [ "P. luminescens" ], "offsets": [ [ 4339, 4353 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-02-04_T78", "type": "Protein", "text": [ "Ymt" ], "offsets": [ [ 4380, 4383 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-02-04_T79", "type": "Organism", "text": [ "Y. pestis" ], "offsets": [ [ 4422, 4431 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-02-04_T80", "type": "Chemical", "text": [ "AHL" ], "offsets": [ [ 4452, 4455 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-02-04_T81", "type": "Organism", "text": [ "Y. pestis" ], "offsets": [ [ 4464, 4473 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-02-04_T82", "type": "Organism", "text": [ "P. luminescens" ], "offsets": [ [ 4483, 4497 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-02-04_T83", "type": "Protein", "text": [ "Ymt" ], "offsets": [ [ 4547, 4550 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-02-04_T84", "type": "Organism", "text": [ "P. luminescens" ], "offsets": [ [ 4595, 4609 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-02-04_T85", "type": "Organism", "text": [ "Y. enterocolitica" ], "offsets": [ [ 4633, 4650 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-02-04_T86", "type": "Protein", "text": [ "Ymt" ], "offsets": [ [ 4652, 4655 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-02-04_T87", "type": "Organism", "text": [ "Y. enterocolitica" ], "offsets": [ [ 4865, 4882 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-02-04_T88", "type": "Organism", "text": [ "P. luminescens" ], "offsets": [ [ 4889, 4903 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-02-04_T89", "type": "Chemical", "text": [ "triacylglycerol" ], "offsets": [ [ 4992, 5007 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-02-04_T90", "type": "Organism", "text": [ "P. luminescens" ], "offsets": [ [ 5019, 5033 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-02-04_T91", "type": "Organism", "text": [ "Y. enterocolitica" ], "offsets": [ [ 5069, 5086 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-02-04_T92", "type": "Protein", "text": [ "PrtA" ], "offsets": [ [ 5181, 5185 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-02-04_T93", "type": "Protein", "text": [ "Plu0655" ], "offsets": [ [ 5187, 5194 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-02-04_T94", "type": "Protein", "text": [ "YE4052" ], "offsets": [ [ 5195, 5201 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-02-04_T95", "type": "Organism", "text": [ "X. nematophila" ], "offsets": [ [ 5281, 5295 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-02-04_T96", "type": "Organism", "text": [ "P. luminescens" ], "offsets": [ [ 5376, 5390 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-02-04_T97", "type": "Protein", "text": [ "Plu0306" ], "offsets": [ [ 5470, 5477 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-02-04_T98", "type": "Protein", "text": [ "YE4066" ], "offsets": [ [ 5478, 5484 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-02-04_T99", "type": "Protein", "text": [ "Plu0631" ], "offsets": [ [ 5505, 5512 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-02-04_T100", "type": "Protein", "text": [ "YE3311" ], "offsets": [ [ 5513, 5519 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-02-04_T101", "type": "Two-component-system", "text": [ "DegQ/DegS" ], "offsets": [ [ 5526, 5535 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-02-04_T102", "type": "Protein", "text": [ "DegQ" ], "offsets": [ [ 5526, 5530 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-02-04_T103", "type": "Protein", "text": [ 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[ { "id": "PMC2829055-02-Results-Discussion-03__text", "type": "abstract", "text": [ "Y. pestis genes involved in infection and biofilm formation in the flea \nBecause blockage of the flea vector is essentially a biofilm phenomenon, Y. pestis genes whose expression patterns are significantly upregulated in the flea and flowcell biofilms relative to planktonic cultures (Table S4) might indicate that they are transmission factors. Several studies comparing the transcriptional profiles of Escherichia coli and other gram negative bacteria during biofilm and planktonic growth in vitro have been published [20],[21],[22],[23]. Certain genes whose mutational loss resulted in an altered biofilm phenotype have been identified in these studies; but in general a consistent, distinct biofilm gene expression profile has not emerged. This is probably because different media and experimental systems have been employed and the fact that a biofilm consists of a physiologically heterogeneous community [24],[25]. Nevertheless, common biofilm-related adaptations include the repression of motility and the induction of specific adhesins, an extracellular polysaccharide matrix (ECM), and an envelope stress response (ESR) [10],[23]. However, Y. pestis is constitutively nonmotile, and synthesis of the Hms-dependent biofilm ECM is regulated post-translationally [26]. The ymt gene was among the most highly expressed genes in the flea (Table S3), but neither it nor the known transmission factors (hmsHFRS, hmsT, hmsP, and gmhA) showed significantly higher expression in the flea than in vitro at 21degreesC, indicating that they are induced primarily by low temperature, and not by environmental factors specific to the flea gut. Y. pestis homologs of two genes with previously identified roles in biofilm, yidE, which encodes a hyperadherence factor in E. coli [27], and cpxP, a member of the cpxPAR ESR system, were upregulated in the flowcell; but predicted adhesin genes were not upregulated. The transcriptional profile of Y. pestis in blocked fleas showed greater similarity to the transcriptional profile reported for E. coli in mature, four-day-old in vitro biofilms [23]. In addition to yidE and cpxP, other Y. pestis predicted adhesins and components of an ESR were upregulated in the flea. The Y. pestis homologs of Pseudomonas aeruginosa cupA1 and cupA3 in a predicted fimbrial biosynthesis operon and yapL, a predicted autotransporter adhesin similar to E. coli tibA, were specifically upregulated in the flea (Table S1). The cupA fimbrial locus and tibA are important for surface adherence and for biofilm formation in P. aeruginosa and E. coli, respectively [28],[29]. Evidence for induction of an ESR in the flea included the high expression levels of rpoE, the gene for the alternate transcription factor sigmaE (as well as the anti-sigmaE negative regulator genes rseA and rseB), cpxP; and pspA and pspG, components of the phage-shock protein (Psp) response (Tables S1 and S3). These genes were also found to be upregulated in mature E. coli biofilms [23], suggesting that the three prominent ESR systems are important for integrating signals required for survival in a biofilm. Because homologs of the yidE, cpxP, tibA (yapL), cupA fimbriae, and pspABC genes were upregulated in the flea and have been shown to be involved in biofilm formation in other bacteria [23],[27],[28],[29], we made a series of Y. pestis strains containing deletions of these loci. However, the single loss of any of these genes did not result in a noticeable defect in biofilm formation in vitro, or in flea infection or blockage (data not shown). These genes may contribute to biofilm formation, but are not individually essential for this phenotype. Although genes in the polyamine transport gabTpotDBC locus are among the most highly induced genes in the flea (Table S1) and polyamines are essential for Y. pestis biofilm formation [30], we have previously reported that a Y. pestis Deltapot mutant has no defect in flea infection or blockage [31]. This is likely due to the fact that Y. pestis is able to synthesize polyamines de novo.\n" ], "offsets": [ [ 0, 4044 ] ] } ]

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"id": "PMC2829055-02-Results-Discussion-03_T8", "type": "Protein", "text": [ "ymt" ], "offsets": [ [ 1280, 1283 ] ], "normalized": [] }, { "id": "PMC2829055-02-Results-Discussion-03_T9", "type": "Organism", "text": [ "flea" ], "offsets": [ [ 1338, 1342 ] ], "normalized": [] }, { "id": "PMC2829055-02-Results-Discussion-03_T10", "type": "Protein", "text": [ "hmsH" ], "offsets": [ [ 1406, 1410 ] ], "normalized": [] }, { "id": "PMC2829055-02-Results-Discussion-03_T11", "type": "Protein", "text": [ "F" ], "offsets": [ [ 1410, 1411 ] ], "normalized": [] }, { "id": "PMC2829055-02-Results-Discussion-03_T12", "type": "Protein", "text": [ "R" ], "offsets": [ [ 1411, 1412 ] ], "normalized": [] }, { "id": "PMC2829055-02-Results-Discussion-03_T13", "type": "Protein", "text": [ "S" ], "offsets": [ [ 1412, 1413 ] ], "normalized": [] }, { "id": "PMC2829055-02-Results-Discussion-03_T14", "type": "Protein", "text": [ "hmsT" ], "offsets": [ [ 1415, 1419 ] ], "normalized": [] }, { "id": "PMC2829055-02-Results-Discussion-03_T15", "type": "Protein", "text": [ "hmsP" ], "offsets": [ [ 1421, 1425 ] ], "normalized": [] }, { "id": "PMC2829055-02-Results-Discussion-03_T16", "type": "Protein", "text": [ "gmhA" ], "offsets": [ [ 1431, 1435 ] ], "normalized": [] }, { "id": "PMC2829055-02-Results-Discussion-03_T17", "type": "Organism", "text": [ "flea" ], "offsets": [ [ 1483, 1487 ] ], "normalized": [] }, { "id": "PMC2829055-02-Results-Discussion-03_T18", "type": "Organism", "text": [ "flea" ], "offsets": [ [ 1629, 1633 ] ], "normalized": [] }, { "id": "PMC2829055-02-Results-Discussion-03_T19", "type": "Organism", "text": [ "Y. pestis" ], "offsets": [ [ 1639, 1648 ] ], "normalized": [] }, { "id": "PMC2829055-02-Results-Discussion-03_T20", "type": "Protein", "text": [ "yidE" ], "offsets": [ [ 1716, 1720 ] ], "normalized": [] }, { "id": "PMC2829055-02-Results-Discussion-03_T21", "type": "Organism", "text": [ "E. coli" ], "offsets": [ [ 1763, 1770 ] ], "normalized": [] }, { "id": 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"normalized": [] }, { "id": "PMC2829055-02-Results-Discussion-03_T36", "type": "Protein", "text": [ "cupA3" ], "offsets": [ [ 2269, 2274 ] ], "normalized": [] }, { "id": "PMC2829055-02-Results-Discussion-03_T37", "type": "Protein", "text": [ "yapL" ], "offsets": [ [ 2323, 2327 ] ], "normalized": [] }, { "id": "PMC2829055-02-Results-Discussion-03_T38", "type": "Organism", "text": [ "E. coli" ], "offsets": [ [ 2376, 2383 ] ], "normalized": [] }, { "id": "PMC2829055-02-Results-Discussion-03_T39", "type": "Protein", "text": [ "tibA" ], "offsets": [ [ 2384, 2388 ] ], "normalized": [] }, { "id": "PMC2829055-02-Results-Discussion-03_T40", "type": "Organism", "text": [ "flea" ], "offsets": [ [ 2427, 2431 ] ], "normalized": [] }, { "id": "PMC2829055-02-Results-Discussion-03_T41", "type": "Protein", "text": [ "cupA" ], "offsets": [ [ 2448, 2452 ] ], "normalized": [] }, { "id": "PMC2829055-02-Results-Discussion-03_T42", "type": "Protein", "text": [ "tibA" ], "offsets": [ [ 2472, 2476 ] ], 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], "normalized": [] }, { "id": "PMC2829055-02-Results-Discussion-03_T50", "type": "Protein", "text": [ "cpxP" ], "offsets": [ [ 2807, 2811 ] ], "normalized": [] }, { "id": "PMC2829055-02-Results-Discussion-03_T51", "type": "Protein", "text": [ "pspA" ], "offsets": [ [ 2817, 2821 ] ], "normalized": [] }, { "id": "PMC2829055-02-Results-Discussion-03_T52", "type": "Protein", "text": [ "pspG" ], "offsets": [ [ 2826, 2830 ] ], "normalized": [] }, { "id": "PMC2829055-02-Results-Discussion-03_T53", "type": "Organism", "text": [ "E. coli" ], "offsets": [ [ 2961, 2968 ] ], "normalized": [] }, { "id": "PMC2829055-02-Results-Discussion-03_T54", "type": "Protein", "text": [ "yidE" ], "offsets": [ [ 3130, 3134 ] ], "normalized": [] }, { "id": "PMC2829055-02-Results-Discussion-03_T55", "type": "Protein", "text": [ "cpxP" ], "offsets": [ [ 3136, 3140 ] ], "normalized": [] }, { "id": "PMC2829055-02-Results-Discussion-03_T56", "type": "Protein", "text": [ "tibA" ], "offsets": [ [ 3142, 3146 ] ], "normalized": [] }, { "id": "PMC2829055-02-Results-Discussion-03_T57", "type": "Protein", "text": [ "yapL" ], "offsets": [ [ 3148, 3152 ] ], "normalized": [] }, { "id": "PMC2829055-02-Results-Discussion-03_T58", "type": "Protein", "text": [ "cupA fimbriae" ], "offsets": [ [ 3155, 3168 ] ], "normalized": [] }, { "id": "PMC2829055-02-Results-Discussion-03_T59", "type": "Protein", "text": [ "pspABC" ], "offsets": [ [ 3174, 3180 ] ], "normalized": [] }, { "id": "PMC2829055-02-Results-Discussion-03_T60", "type": "Organism", "text": [ "flea" ], "offsets": [ [ 3211, 3215 ] ], "normalized": [] }, { "id": "PMC2829055-02-Results-Discussion-03_T61", "type": "Organism", "text": [ "Y. pestis" ], "offsets": [ [ 3331, 3340 ] ], "normalized": [] }, { "id": "PMC2829055-02-Results-Discussion-03_T62", "type": "Organism", "text": [ "flea" ], "offsets": [ [ 3507, 3511 ] ], "normalized": [] }, { "id": "PMC2829055-02-Results-Discussion-03_T63", "type": "Protein", "text": [ "gabT" ], "offsets": [ [ 3698, 3702 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[]

[ { "id": "PMC2266911-02-Results_and_Discussion-03-03__text", "type": "abstract", "text": [ "Tricarboxylate utilization \nThe TctE/TctD system is the only TCS of P. luminescens without homologue in Y. enterocolitica (see section \"Two-component signal transduction\", Fig. 2). It controls the expression of the tctCBA operon encoding the tricarboxylic acid transport system TctCBA [107]. The transporter is supposed to facilitate uptake of citrate, fluorocitrate, isocitrate and cis-acconitate for aerobic utilization [108,109]. The Na+ dependent citrate symporter CitS of S. enterica, which the Y. enterocolitica protein YE2507 is homologous to, is induced by the CitA/CitB system for fermentation of citrate under anoxic conditions [110], indicating a general difference of citrate utilization in P. luminescens and Y. enterocolitica. While Y. enterocolitica explores citrate for anaerobic metabolism, it is most likely that the specific uptake of citrate and other tricarboxylic acids by TctCBA is used by P. luminescens upon entering the insect host where enough citrate is available. The specific up-regulation of the tricarboxylic acid cycle (TCA) enzymes within a host has also been described for other microorganisms. For example, sucA encoding a subunit of alpha-ketoglutarate synthase and acnA encoding the aconitase have been found to be induced in V. cholerae during host infection [111,112], and a complete TCA cycle is also required for S. typhimurium virulence [113]. We also observed induction of sucA in P. luminescens in the insect host Galleria mellonella (R. Heermann, unpublished data). This finding underlines the hypothesis that the citric cycle enzymes used under aerobic conditions are up-regulated as a specific adaptation of the metabolic activity in the nutrient rich insect host. To guarantee an optimal amount of tricarboxylic acids within the cell, TctE might specifically sense the presence of tricarboxylic acids and/or signals of the host. Y. enterocolitica and Y. pestis, in contrast exhibit upregulation of all TCA genes upon temperature shift from 26degreesC to 37degreesC [114,115]. Therefore, it is obvious that Y. enterocolitica and P. luminescens use different sensing and utilization strategies for tricarboxylates.\n" ], "offsets": [ [ 0, 2162 ] ] } ]

[ { "id": "PMC2266911-02-Results_and_Discussion-03-03_T1", "type": "Two-component-system", "text": [ "TctE/TctD" ], "offsets": [ [ 32, 41 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-03-03_T2", "type": "Protein", "text": [ "TctE" ], "offsets": [ [ 32, 36 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-03-03_T3", "type": "Protein", "text": [ "TctD" ], "offsets": [ [ 37, 41 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-03-03_T4", "type": "Organism", "text": [ "P. luminescens" ], "offsets": [ [ 68, 82 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-03-03_T5", "type": "Organism", "text": [ "Y. enterocolitica" ], "offsets": [ [ 104, 121 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-03-03_T6", "type": "Regulon-operon", "text": [ "tctCBA" ], "offsets": [ [ 215, 221 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-03-03_T7", "type": "Protein", "text": [ "tctC" ], "offsets": [ [ 215, 219 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-03-03_T8", "type": "Protein", "text": [ "B" ], "offsets": [ [ 219, 220 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-03-03_T9", "type": "Protein", "text": [ "A" ], "offsets": [ [ 220, 221 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-03-03_T10", "type": "Chemical", "text": [ "tricarboxylic acid" ], "offsets": [ [ 242, 260 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-03-03_T11", "type": "Protein", "text": [ "TctC" ], "offsets": [ [ 278, 282 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-03-03_T12", "type": "Protein", "text": [ "B" ], "offsets": [ [ 282, 283 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-03-03_T13", "type": "Protein", "text": [ "A" ], "offsets": [ [ 283, 284 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-03-03_T14", "type": "Chemical", "text": [ "citrate" ], "offsets": [ [ 344, 351 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-03-03_T15", "type": "Chemical", "text": [ "fluorocitrate" ], "offsets": [ [ 353, 366 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-03-03_T16", "type": "Chemical", "text": [ "isocitrate" ], "offsets": [ [ 368, 378 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-03-03_T17", "type": "Chemical", "text": [ "cis-acconitate" ], "offsets": [ [ 383, 397 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-03-03_T18", "type": "Chemical", "text": [ "Na+" ], "offsets": [ [ 437, 440 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-03-03_T19", "type": "Chemical", "text": [ "citrate" ], "offsets": [ [ 451, 458 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-03-03_T20", "type": "Protein", "text": [ "CitS" ], "offsets": [ [ 469, 473 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-03-03_T21", "type": "Organism", "text": [ "S. enterica" ], "offsets": [ [ 477, 488 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-03-03_T22", "type": "Organism", "text": [ "Y. enterocolitica" ], "offsets": [ [ 500, 517 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-03-03_T23", "type": "Protein", "text": [ "YE2507" ], "offsets": [ [ 526, 532 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-03-03_T24", "type": "Two-component-system", "text": [ "CitA/CitB" ], "offsets": [ [ 569, 578 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-03-03_T25", "type": "Protein", "text": [ "CitA" ], "offsets": [ [ 569, 573 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-03-03_T26", "type": "Protein", "text": [ "CitB" ], "offsets": [ [ 574, 578 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-03-03_T27", "type": "Chemical", "text": [ "citrate" ], "offsets": [ [ 606, 613 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-03-03_T28", "type": "Chemical", "text": [ "citrate" ], "offsets": [ [ 680, 687 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-03-03_T29", "type": "Organism", "text": [ "P. luminescens" ], "offsets": [ [ 703, 717 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-03-03_T30", "type": "Organism", "text": [ "Y. enterocolitica" ], "offsets": [ [ 722, 739 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-03-03_T31", "type": "Organism", "text": [ "Y. enterocolitica" ], "offsets": [ [ 747, 764 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-03-03_T32", "type": "Chemical", "text": [ "citrate" ], "offsets": [ [ 774, 781 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-03-03_T33", "type": "Chemical", "text": [ "citrate" ], "offsets": [ [ 854, 861 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-03-03_T34", "type": "Chemical", "text": [ "tricarboxylic acids" ], "offsets": [ [ 872, 891 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-03-03_T35", "type": "Chemical", "text": [ "TctC" ], "offsets": [ [ 895, 899 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-03-03_T36", "type": "Chemical", "text": [ "B" ], "offsets": [ [ 899, 900 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-03-03_T37", "type": "Chemical", "text": [ "A" ], "offsets": [ [ 900, 901 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-03-03_T38", "type": "Organism", "text": [ "P. luminescens" ], "offsets": [ [ 913, 927 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-03-03_T39", "type": "Chemical", "text": [ "citrate" ], "offsets": [ [ 971, 978 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-03-03_T40", "type": "Chemical", "text": [ "tricarboxylic acid" ], "offsets": [ [ 1027, 1045 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-03-03_T41", "type": "Protein", "text": [ "sucA" ], "offsets": [ [ 1143, 1147 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-03-03_T42", "type": "Chemical", "text": [ "alpha-ketoglutarate" ], "offsets": [ [ 1170, 1189 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-03-03_T43", "type": "Protein", "text": [ "acnA" ], "offsets": [ [ 1203, 1207 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-03-03_T44", "type": "Organism", "text": [ "V. cholerae" ], "offsets": [ [ 1264, 1275 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-03-03_T45", "type": "Chemical", "text": [ "TCA" ], "offsets": [ [ 1324, 1327 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-03-03_T46", "type": "Organism", "text": [ "S. typhimurium" ], "offsets": [ [ 1355, 1369 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-03-03_T47", "type": "Protein", "text": [ "sucA" ], "offsets": [ [ 1417, 1421 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-03-03_T48", "type": "Organism", "text": [ "P. luminescens" ], "offsets": [ [ 1425, 1439 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-03-03_T49", "type": "Organism", "text": [ "Galleria mellonella" ], "offsets": [ [ 1459, 1478 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-03-03_T50", "type": "Chemical", "text": [ "tricarboxylic acids" ], "offsets": [ [ 1747, 1766 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-03-03_T51", "type": "Protein", "text": [ "TctE" ], "offsets": [ [ 1784, 1788 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-03-03_T52", "type": "Chemical", "text": [ "tricarboxylic acids" ], "offsets": [ [ 1830, 1849 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-03-03_T53", "type": "Organism", "text": [ "Y. enterocolitica" ], "offsets": [ [ 1878, 1895 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-03-03_T54", "type": "Organism", "text": [ "Y. pestis" ], "offsets": [ [ 1900, 1909 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-03-03_T55", "type": "Organism", "text": [ "Y. enterocolitica" ], "offsets": [ [ 2055, 2072 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-03-03_T56", "type": "Organism", "text": [ "P. luminescens" ], "offsets": [ [ 2077, 2091 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-03-03_T57", "type": "Chemical", "text": [ "tricarboxylates" ], "offsets": [ [ 2145, 2160 ] ], "normalized": [] } ]

[ { "id": "PMC2266911-02-Results_and_Discussion-03-03_E1", "type": "Regulation", "trigger": { "text": [ "controls" ], "offsets": [ [ 184, 192 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC2266911-02-Results_and_Discussion-03-03_E2" } ] }, { "id": "PMC2266911-02-Results_and_Discussion-03-03_E2", "type": "Gene_expression", "trigger": { "text": [ "expression" ], "offsets": [ [ 197, 207 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC2266911-02-Results_and_Discussion-03-03_T6" } ] }, { "id": "PMC2266911-02-Results_and_Discussion-03-03_E3", "type": "Positive_regulation", "trigger": { "text": [ "induced" ], "offsets": [ [ 554, 561 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC2266911-02-Results_and_Discussion-03-03_T20" }, { "role": "Cause", "ref_id": "PMC2266911-02-Results_and_Discussion-03-03_T24" } ] }, { "id": "PMC2266911-02-Results_and_Discussion-03-03_E4", "type": "Positive_regulation", "trigger": { "text": [ "induced" ], "offsets": [ [ 1253, 1260 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC2266911-02-Results_and_Discussion-03-03_T41" } ] }, { "id": "PMC2266911-02-Results_and_Discussion-03-03_E5", "type": "Positive_regulation", "trigger": { "text": [ "induced" ], "offsets": [ [ 1253, 1260 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC2266911-02-Results_and_Discussion-03-03_T43" } ] }, { "id": "PMC2266911-02-Results_and_Discussion-03-03_E6", "type": "Process", "trigger": { "text": [ "infection" ], "offsets": [ [ 1288, 1297 ] ] }, "arguments": [] }, { "id": "PMC2266911-02-Results_and_Discussion-03-03_E7", "type": "Positive_regulation", "trigger": { "text": [ "required" ], "offsets": [ [ 1342, 1350 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC2266911-02-Results_and_Discussion-03-03_E8" } ] }, { "id": "PMC2266911-02-Results_and_Discussion-03-03_E8", "type": "Process", "trigger": { "text": [ "virulence" ], "offsets": [ [ 1370, 1379 ] ] }, "arguments": [ { "role": "Participant", "ref_id": "PMC2266911-02-Results_and_Discussion-03-03_T46" } ] }, { "id": "PMC2266911-02-Results_and_Discussion-03-03_E9", "type": "Positive_regulation", "trigger": { "text": [ "induction" ], "offsets": [ [ 1404, 1413 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC2266911-02-Results_and_Discussion-03-03_T47" } ] } ]

[]

[]

[ { "id": "PMC1913099-02-Results-Discussion-11__text", "type": "abstract", "text": [ "Additional Type II Cluster Example \nAnother cluster, spy1725-1719, contained six genes that together (though not individually) exhibited significant downregulation. The genes spy1724, spy1722, spy1721, and spy1719 share transcriptional order and predicted function with homologs in the nusA-infB protein biosynthesis operon of Bacillus subtilis and Escherichia coli [51]. We examined the spy1725 and spy1723 gene products (annotated as hypothetical proteins [14]) for similarities with known proteins that might indicate a role for these gene products in protein biosynthesis. BlastP analysis aligned the spy1725 gene product, which has homologs in all sequenced streptococcal genomes, with the SP14.3 protein from S. pneumoniae [52] (80% sequence similarity; 67% identity). Based on structural characterization, SP14.3 is a predicted RNA-binding protein. The spy1723 gene product has similar domain structure to the YlxR protein of S. pneumoniae, an RNA-binding protein implicated in transcription termination [53]. These results indicate that both genes likely encode RNA-binding proteins, in agreement with their functionally defined cluster members. Although domain and homology searches yielded the functional predictions, their membership within a protein biosynthetic cluster provided the initial indication of common function or regulation.\n" ], "offsets": [ [ 0, 1349 ] ] } ]

[ { "id": "PMC1913099-02-Results-Discussion-11_T1", "type": "Regulon-operon", "text": [ "spy1725-1719" ], "offsets": [ [ 53, 65 ] ], "normalized": [] }, { "id": "PMC1913099-02-Results-Discussion-11_T2", "type": "Protein", "text": [ "spy1725" ], "offsets": [ [ 53, 60 ] ], "normalized": [] }, { "id": "PMC1913099-02-Results-Discussion-11_T3", "type": "Protein", "text": [ "1719" ], "offsets": [ [ 61, 65 ] ], "normalized": [] }, { "id": "PMC1913099-02-Results-Discussion-11_T4", "type": "Protein", "text": [ "spy1724" ], "offsets": [ [ 175, 182 ] ], "normalized": [] }, { "id": "PMC1913099-02-Results-Discussion-11_T5", "type": "Protein", "text": [ "spy1722" ], "offsets": [ [ 184, 191 ] ], "normalized": [] }, { "id": "PMC1913099-02-Results-Discussion-11_T6", "type": "Protein", "text": [ "spy1721" ], "offsets": [ [ 193, 200 ] ], "normalized": [] }, { "id": "PMC1913099-02-Results-Discussion-11_T7", "type": "Protein", "text": [ "spy1719" ], "offsets": [ [ 206, 213 ] ], "normalized": [] }, { "id": "PMC1913099-02-Results-Discussion-11_T8", "type": "Regulon-operon", "text": [ "nusA-infB" ], "offsets": [ [ 286, 295 ] ], "normalized": [] }, { "id": "PMC1913099-02-Results-Discussion-11_T9", "type": "Protein", "text": [ "nusA" ], "offsets": [ [ 286, 290 ] ], "normalized": [] }, { "id": "PMC1913099-02-Results-Discussion-11_T10", "type": "Protein", "text": [ "infB" ], "offsets": [ [ 291, 295 ] ], "normalized": [] }, { "id": "PMC1913099-02-Results-Discussion-11_T11", "type": "Organism", "text": [ "Bacillus subtilis" ], "offsets": [ [ 327, 344 ] ], "normalized": [] }, { "id": "PMC1913099-02-Results-Discussion-11_T12", "type": "Organism", "text": [ "Escherichia coli" ], "offsets": [ [ 349, 365 ] ], "normalized": [] }, { "id": "PMC1913099-02-Results-Discussion-11_T13", "type": "Protein", "text": [ "spy1725" ], "offsets": [ [ 388, 395 ] ], "normalized": [] }, { "id": "PMC1913099-02-Results-Discussion-11_T14", "type": "Protein", "text": [ "spy1723" ], "offsets": [ [ 400, 407 ] ], "normalized": [] }, { "id": "PMC1913099-02-Results-Discussion-11_T15", "type": "Protein", "text": [ "spy1725" ], "offsets": [ [ 605, 612 ] ], "normalized": [] }, { "id": "PMC1913099-02-Results-Discussion-11_T16", "type": "Protein", "text": [ "SP14.3" ], "offsets": [ [ 695, 701 ] ], "normalized": [] }, { "id": "PMC1913099-02-Results-Discussion-11_T17", "type": "Organism", "text": [ "S. pneumoniae" ], "offsets": [ [ 715, 728 ] ], "normalized": [] }, { "id": "PMC1913099-02-Results-Discussion-11_T18", "type": "Protein", "text": [ "SP14.3" ], "offsets": [ [ 813, 819 ] ], "normalized": [] }, { "id": "PMC1913099-02-Results-Discussion-11_T19", "type": "Protein", "text": [ "spy1723" ], "offsets": [ [ 860, 867 ] ], "normalized": [] }, { "id": "PMC1913099-02-Results-Discussion-11_T20", "type": "Protein", "text": [ "YlxR" ], "offsets": [ [ 917, 921 ] ], "normalized": [] }, { "id": "PMC1913099-02-Results-Discussion-11_T21", "type": "Organism", "text": [ "S. pneumoniae" ], "offsets": [ [ 933, 946 ] ], "normalized": [] }, { "id": "PMC1913099-02-Results-Discussion-11_T22", "type": "Protein", "text": [ "domain" ], "offsets": [ [ 1163, 1169 ] ], "normalized": [] } ]

[ { "id": "PMC1913099-02-Results-Discussion-11_E1", "type": "Negative_regulation", "trigger": { "text": [ "downregulation" ], "offsets": [ [ 149, 163 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC1913099-02-Results-Discussion-11_T1" } ] } ]

[]

[]

[ { "id": "PMC2565068-02-Results-03__text", "type": "abstract", "text": [ "PMN were killed by streptolysin O (SLO) from severe invasive GAS \nPMN death was induced shortly after encounter with severe invasive GAS, and PMN were not in apoptotic death because of low frequency of cells positive for annexin V (data not shown), which was seen in the case of cytolysin-dependent cell injury [15]. GAS produce two cytolysins that may contribute to pathogenesis. Streptolysin S (SLS) is an oxygen-stable beta-hemolysin and Streptolysin O (SLO) is a pore-forming cholesterol-binding toxin [16]. Therefore, to know the mechanism underlying GAS-mediated killing of PMN, we investigated whether SLO produced by invasive GAS affect survival of PMN in an in vitro migration assay system. Figure 3A shows that PMN killing by invasive GAS was blocked by anti-SLO Ab in culture medium within lower wells of a transwell system (p=0.018 compared with control Ig), at similar extent by adding free cholesterol in the medium (data not shown). Furthermore, an SLO deficient mutant from a STSS isolate NIH230 (NIH230slo) lost the killing activity for PMN (Figure 3A), thereby, strongly suggesting that SLO is a key element for PMN killing mediated by invasive GAS. Contrarily, SLS-deficient mutant from NIH230 strain (NIH230sagA) killed PMN, as efficiently as did parent strain, indicating that SLS is dispensable for killing of PMN mediated by invasive GAS. SLO and SLS double mutant GAS from NIH230 strain (NIH230slosagA) displayed the killing activity indistinguishable from that of NIH230slo, confirming the primarily role of SLO for GAS-mediated PMN killing. As shown in Figure 3B, incubation of PMN with supernatant from co-culture of IL-8 and invasive or non-invasive GAS did not affect PMN viability, suggesting that severe invasive GAS causes PMN killing following encounter with bacteria in a contact-dependent manner. To confirm that SLO activity is increased in invasive GAS strain, we measured SLO hemolytic activity of GAS strains used in this study. As shown in Figure 3C, SLO activity of severe invasive isolate NIH230 is increased as twice as that of non-invasive strain 1566 (p=0.017).\n" ], "offsets": [ [ 0, 2107 ] ] } ]

[ { "id": "PMC2565068-02-Results-03_T1", "type": "Protein", "text": [ "streptolysin O" ], "offsets": [ [ 19, 33 ] ], "normalized": [] }, { "id": "PMC2565068-02-Results-03_T2", "type": "Protein", "text": [ "SLO" ], "offsets": [ [ 35, 38 ] ], "normalized": [] }, { "id": "PMC2565068-02-Results-03_T3", "type": "Organism", "text": [ "invasive GAS" ], "offsets": [ [ 52, 64 ] ], "normalized": [] }, { "id": "PMC2565068-02-Results-03_T4", "type": "Organism", "text": [ "invasive GAS" ], "offsets": [ [ 124, 136 ] ], "normalized": [] }, { "id": "PMC2565068-02-Results-03_T5", "type": "Protein", "text": [ "annexin V" ], "offsets": [ [ 221, 230 ] ], "normalized": [] }, { "id": "PMC2565068-02-Results-03_T6", "type": "Chemical", "text": [ "cytolysin" ], "offsets": [ [ 279, 288 ] ], "normalized": [] }, { "id": "PMC2565068-02-Results-03_T7", "type": "Organism", "text": [ "GAS" ], "offsets": [ [ 317, 320 ] ], "normalized": [] }, { "id": "PMC2565068-02-Results-03_T8", "type": "Chemical", "text": [ "cytolysins" ], "offsets": [ [ 333, 343 ] ], "normalized": [] }, { "id": "PMC2565068-02-Results-03_T9", "type": "Protein", "text": [ "Streptolysin S" ], "offsets": [ [ 381, 395 ] ], "normalized": [] }, { "id": "PMC2565068-02-Results-03_T10", "type": "Protein", "text": [ "SLS" ], "offsets": [ [ 397, 400 ] ], "normalized": [] }, { "id": "PMC2565068-02-Results-03_T11", "type": "Chemical", "text": [ "oxygen" ], "offsets": [ [ 408, 414 ] ], "normalized": [] }, { "id": "PMC2565068-02-Results-03_T12", "type": "Chemical", "text": [ "beta-hemolysin" ], "offsets": [ [ 422, 436 ] ], "normalized": [] }, { "id": "PMC2565068-02-Results-03_T13", "type": "Protein", "text": [ "Streptolysin O" ], "offsets": [ [ 441, 455 ] ], "normalized": [] }, { "id": "PMC2565068-02-Results-03_T14", "type": "Protein", "text": [ "SLO" ], "offsets": [ [ 457, 460 ] ], "normalized": [] }, { "id": "PMC2565068-02-Results-03_T15", "type": "Chemical", "text": [ "cholesterol" ], "offsets": [ [ 480, 491 ] ], "normalized": [] }, { "id": "PMC2565068-02-Results-03_T16", "type": "Organism", "text": [ "GAS" ], "offsets": [ [ 556, 559 ] ], "normalized": [] }, { "id": "PMC2565068-02-Results-03_T17", "type": "Protein", "text": [ "SLO" ], "offsets": [ [ 609, 612 ] ], "normalized": [] }, { "id": "PMC2565068-02-Results-03_T18", "type": "Organism", "text": [ "invasive GAS" ], "offsets": [ [ 625, 637 ] ], "normalized": [] }, { "id": "PMC2565068-02-Results-03_T19", "type": "Organism", "text": [ "invasive GAS" ], "offsets": [ [ 736, 748 ] ], "normalized": [] }, { "id": "PMC2565068-02-Results-03_T20", "type": "Protein", "text": [ "SLO" ], "offsets": [ [ 769, 772 ] ], "normalized": [] }, { "id": "PMC2565068-02-Results-03_T21", "type": "Chemical", "text": [ "cholesterol" ], "offsets": [ [ 904, 915 ] ], "normalized": [] }, { "id": "PMC2565068-02-Results-03_T22", "type": "Organism", "text": [ "SLO deficient mutant" ], "offsets": [ [ 964, 984 ] ], "normalized": [] }, { "id": "PMC2565068-02-Results-03_T23", "type": "Protein", "text": [ "SLO" ], "offsets": [ [ 964, 967 ] ], "normalized": [] }, { "id": "PMC2565068-02-Results-03_T24", "type": "Organism", "text": [ "NIH230" ], "offsets": [ [ 1005, 1011 ] ], "normalized": [] }, { "id": "PMC2565068-02-Results-03_T25", "type": "Organism", "text": [ "NIH230slo" ], "offsets": [ [ 1013, 1022 ] ], "normalized": [] }, { "id": "PMC2565068-02-Results-03_T26", "type": "Protein", "text": [ "slo" ], "offsets": [ [ 1019, 1022 ] ], "normalized": [] }, { "id": "PMC2565068-02-Results-03_T27", "type": "Protein", "text": [ "SLO" ], "offsets": [ [ 1105, 1108 ] ], "normalized": [] }, { "id": "PMC2565068-02-Results-03_T28", "type": "Organism", "text": [ "invasive GAS" ], "offsets": [ [ 1154, 1166 ] ], "normalized": [] }, { "id": "PMC2565068-02-Results-03_T29", "type": "Organism", "text": [ "SLS-deficient mutant" ], "offsets": [ [ 1180, 1200 ] ], "normalized": [] }, { "id": "PMC2565068-02-Results-03_T30", "type": "Protein", "text": [ "SLS" ], "offsets": [ [ 1180, 1183 ] ], "normalized": [] }, { "id": "PMC2565068-02-Results-03_T31", "type": "Organism", "text": [ "NIH230" ], "offsets": [ [ 1206, 1212 ] ], "normalized": [] }, { "id": "PMC2565068-02-Results-03_T32", "type": "Organism", "text": [ "NIH230sagA" ], "offsets": [ [ 1221, 1231 ] ], "normalized": [] }, { "id": "PMC2565068-02-Results-03_T33", "type": "Protein", "text": [ "sagA" ], "offsets": [ [ 1227, 1231 ] ], "normalized": [] }, { "id": "PMC2565068-02-Results-03_T34", "type": "Protein", "text": [ "SLS" ], "offsets": [ [ 1298, 1301 ] ], "normalized": [] }, { "id": "PMC2565068-02-Results-03_T35", "type": "Organism", "text": [ "invasive GAS" ], "offsets": [ [ 1348, 1360 ] ], "normalized": [] }, { "id": "PMC2565068-02-Results-03_T36", "type": "Organism", "text": [ "SLO and SLS double mutant GAS" ], "offsets": [ [ 1362, 1391 ] ], "normalized": [] }, { "id": "PMC2565068-02-Results-03_T37", "type": "Protein", "text": [ "SLO" ], "offsets": [ [ 1362, 1365 ] ], "normalized": [] }, { "id": "PMC2565068-02-Results-03_T38", "type": "Protein", "text": [ "SLS" ], "offsets": [ [ 1370, 1373 ] ], "normalized": [] }, { "id": "PMC2565068-02-Results-03_T39", "type": "Organism", "text": [ "NIH230" ], "offsets": [ [ 1397, 1403 ] ], "normalized": [] }, { "id": "PMC2565068-02-Results-03_T40", "type": "Organism", "text": [ "NIH230slosagA" ], "offsets": [ [ 1412, 1425 ] ], "normalized": [] }, { "id": "PMC2565068-02-Results-03_T41", "type": "Protein", "text": [ "slo" ], "offsets": [ [ 1418, 1421 ] ], "normalized": [] }, { "id": "PMC2565068-02-Results-03_T42", "type": "Protein", "text": [ "sagA" ], "offsets": [ [ 1421, 1425 ] ], "normalized": [] }, { "id": "PMC2565068-02-Results-03_T43", "type": "Organism", "text": [ "NIH230slo" ], "offsets": [ [ 1489, 1498 ] ], "normalized": [] }, { "id": "PMC2565068-02-Results-03_T44", "type": "Protein", "text": [ "slo" ], "offsets": [ [ 1495, 1498 ] ], "normalized": [] }, { "id": "PMC2565068-02-Results-03_T45", "type": "Protein", "text": [ "SLO" ], "offsets": [ [ 1533, 1536 ] ], "normalized": [] }, { "id": "PMC2565068-02-Results-03_T46", "type": "Organism", "text": [ "GAS" ], "offsets": [ [ 1541, 1544 ] ], "normalized": [] }, { "id": "PMC2565068-02-Results-03_T47", "type": "Protein", "text": [ "IL-8" ], "offsets": [ [ 1644, 1648 ] ], "normalized": [] }, { "id": "PMC2565068-02-Results-03_T48", "type": "Organism", "text": [ "invasive" ], "offsets": [ [ 1653, 1661 ] ], "normalized": [] }, { "id": "PMC2565068-02-Results-03_T49", "type": "Organism", "text": [ "non-invasive GAS" ], "offsets": [ [ 1665, 1681 ] ], "normalized": [] }, { "id": "PMC2565068-02-Results-03_T50", "type": "Organism", "text": [ "invasive GAS" ], "offsets": [ [ 1735, 1747 ] ], "normalized": [] }, { "id": "PMC2565068-02-Results-03_T51", "type": "Protein", "text": [ "SLO" ], "offsets": [ [ 1848, 1851 ] ], "normalized": [] }, { "id": "PMC2565068-02-Results-03_T52", "type": "Organism", "text": [ "invasive GAS" ], "offsets": [ [ 1877, 1889 ] ], "normalized": [] }, { "id": "PMC2565068-02-Results-03_T53", "type": "Protein", "text": [ "SLO" ], "offsets": [ [ 1910, 1913 ] ], "normalized": [] }, { "id": "PMC2565068-02-Results-03_T54", "type": "Organism", "text": [ "GAS" ], "offsets": [ [ 1936, 1939 ] ], "normalized": [] }, { "id": "PMC2565068-02-Results-03_T55", "type": "Protein", "text": [ "SLO" ], "offsets": [ [ 1991, 1994 ] ], "normalized": [] }, { "id": "PMC2565068-02-Results-03_T56", "type": "Organism", "text": [ "NIH230" ], "offsets": [ [ 2031, 2037 ] ], "normalized": [] }, { "id": "PMC2565068-02-Results-03_T57", "type": "Organism", "text": [ "non-invasive strain 1566" ], "offsets": [ [ 2071, 2095 ] ], "normalized": [] } ]

[ { "id": "PMC2565068-02-Results-03_E1", "type": "Gene_expression", "trigger": { "text": [ "produced" ], "offsets": [ [ 613, 621 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC2565068-02-Results-03_T17" } ] }, { "id": "PMC2565068-02-Results-03_E2", "type": "Positive_regulation", "trigger": { "text": [ "increased" ], "offsets": [ [ 1864, 1873 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC2565068-02-Results-03_T51" } ] }, { "id": "PMC2565068-02-Results-03_E3", "type": "Positive_regulation", "trigger": { "text": [ "increased" ], "offsets": [ [ 2041, 2050 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC2565068-02-Results-03_T55" } ] } ]

[ { "id": "PMC2565068-02-Results-03_1", "entity_ids": [ "PMC2565068-02-Results-03_T1", "PMC2565068-02-Results-03_T2" ] } ]

[]

[ { "id": "PMC2885601-03-RESULTS-04__text", "type": "abstract", "text": [ "SeMac does not Inhibit Opsonophagocytosis of S. equi by Horse PMN \nA whole blood based phagocytosis assay [13, 14] was used to test whether SeMac inhibits opsonophagocytosis of S. equi by horse PMNs. The bacteria were labeled with FITC, treated with S. equi-specific horse convalescent serum in the absence or presence of SeMac, and incubated with horse blood. Percentage of PMNs with phagocytosed S. equi was determined by flow cytometry. As expected, percentage of PMNs with phagocytosed S. equi with the serum treatment was significantly higher than that for S. equi without serum treatment. But the inclusion of SeMac in the assay did not affect opsonophagocytosis of S. equi (Fig. 5A), suggesting that SeMac does not inhibit opsonophagocytosis of S. equi by horse PMNs. The inability of SeMac to inhibit S. equi opsonophagocytosis by horse PMNs may be due to its inability to cleave the majority of horse IgG. If this is true, SeMac should inhibit opsonophagocytosis of GAS by human PMNs, since SeMac efficiently cleaves human IgG. To test this idea, the phagocytosis assay was repeated using GAS and human blood. SeMac indeed inhibits the opsonophagocytosis of GAS by human PMNs (Fig. 5B). These results suggest that IgG endopeptidase activity of SeMac is critical for inhibition of phagocytosis.\n" ], "offsets": [ [ 0, 1303 ] ] } ]

[ { "id": "PMC2885601-03-RESULTS-04_T1", "type": "Protein", "text": [ "SeMac" ], "offsets": [ [ 0, 5 ] ], "normalized": [] }, { "id": "PMC2885601-03-RESULTS-04_T2", "type": "Organism", "text": [ "S. equi" ], "offsets": [ [ 45, 52 ] ], "normalized": [] }, { "id": "PMC2885601-03-RESULTS-04_T3", "type": "Organism", "text": [ "Horse" ], "offsets": [ [ 56, 61 ] ], "normalized": [] }, { "id": "PMC2885601-03-RESULTS-04_T4", "type": "Protein", "text": [ "SeMac" ], "offsets": [ [ 140, 145 ] ], "normalized": [] }, { "id": "PMC2885601-03-RESULTS-04_T5", "type": "Organism", "text": [ "S. equi" ], "offsets": [ [ 177, 184 ] ], "normalized": [] }, { "id": "PMC2885601-03-RESULTS-04_T6", "type": "Organism", "text": [ "horse" ], "offsets": [ [ 188, 193 ] ], "normalized": [] }, { "id": "PMC2885601-03-RESULTS-04_T7", "type": "Organism", "text": [ "S. equi" ], "offsets": [ [ 250, 257 ] ], "normalized": [] }, { "id": "PMC2885601-03-RESULTS-04_T8", "type": "Organism", "text": [ "horse" ], "offsets": [ [ 267, 272 ] ], "normalized": [] }, { "id": "PMC2885601-03-RESULTS-04_T9", "type": "Protein", "text": [ "SeMac" ], "offsets": [ [ 322, 327 ] ], "normalized": [] }, { "id": "PMC2885601-03-RESULTS-04_T10", "type": "Organism", "text": [ "horse" ], "offsets": [ [ 348, 353 ] ], "normalized": [] }, { "id": "PMC2885601-03-RESULTS-04_T11", "type": "Organism", "text": [ "S. equi" ], "offsets": [ [ 398, 405 ] ], "normalized": [] }, { "id": "PMC2885601-03-RESULTS-04_T12", "type": "Organism", "text": [ "S. equi" ], "offsets": [ [ 490, 497 ] ], "normalized": [] }, { "id": "PMC2885601-03-RESULTS-04_T13", "type": "Organism", "text": [ "S. equi" ], "offsets": [ [ 562, 569 ] ], "normalized": [] }, { "id": "PMC2885601-03-RESULTS-04_T14", "type": "Protein", "text": [ "SeMac" ], "offsets": [ [ 616, 621 ] ], "normalized": [] }, { "id": "PMC2885601-03-RESULTS-04_T15", "type": "Organism", "text": [ "S. equi" ], "offsets": [ [ 672, 679 ] ], "normalized": [] }, { "id": "PMC2885601-03-RESULTS-04_T16", "type": "Protein", "text": [ "SeMac" ], "offsets": [ [ 707, 712 ] ], "normalized": [] }, { "id": "PMC2885601-03-RESULTS-04_T17", "type": "Organism", "text": [ "S. equi" ], "offsets": [ [ 752, 759 ] ], "normalized": [] }, { "id": "PMC2885601-03-RESULTS-04_T18", "type": "Organism", "text": [ "horse" ], "offsets": [ [ 763, 768 ] ], "normalized": [] }, { "id": "PMC2885601-03-RESULTS-04_T19", "type": "Protein", "text": [ "SeMac" ], "offsets": [ [ 792, 797 ] ], "normalized": [] }, { "id": "PMC2885601-03-RESULTS-04_T20", "type": "Organism", "text": [ "S. equi" ], "offsets": [ [ 809, 816 ] ], "normalized": [] }, { "id": "PMC2885601-03-RESULTS-04_T21", "type": "Organism", "text": [ "horse" ], "offsets": [ [ 839, 844 ] ], "normalized": [] }, { "id": "PMC2885601-03-RESULTS-04_T22", "type": "Organism", "text": [ "horse" ], "offsets": [ [ 904, 909 ] ], "normalized": [] }, { "id": "PMC2885601-03-RESULTS-04_T23", "type": "Protein", "text": [ "IgG" ], "offsets": [ [ 910, 913 ] ], "normalized": [] }, { "id": "PMC2885601-03-RESULTS-04_T24", "type": "Protein", "text": [ "SeMac" ], "offsets": [ [ 932, 937 ] ], "normalized": [] }, { "id": "PMC2885601-03-RESULTS-04_T25", "type": "Organism", "text": [ "GAS" ], "offsets": [ [ 975, 978 ] ], "normalized": [] }, { "id": "PMC2885601-03-RESULTS-04_T26", "type": "Organism", "text": [ "human" ], "offsets": [ [ 982, 987 ] ], "normalized": [] }, { "id": "PMC2885601-03-RESULTS-04_T27", "type": "Protein", "text": [ "SeMac" ], "offsets": [ [ 1000, 1005 ] ], "normalized": [] }, { "id": "PMC2885601-03-RESULTS-04_T28", "type": "Organism", "text": [ "human" ], "offsets": [ [ 1026, 1031 ] ], "normalized": [] }, { "id": "PMC2885601-03-RESULTS-04_T29", "type": "Protein", "text": [ "IgG" ], "offsets": [ [ 1032, 1035 ] ], "normalized": [] }, { "id": "PMC2885601-03-RESULTS-04_T30", "type": "Organism", "text": [ "GAS" ], "offsets": [ [ 1098, 1101 ] ], "normalized": [] }, { "id": "PMC2885601-03-RESULTS-04_T31", "type": "Organism", "text": [ "human" ], "offsets": [ [ 1106, 1111 ] ], "normalized": [] }, { "id": "PMC2885601-03-RESULTS-04_T32", "type": "Protein", "text": [ "SeMac" ], "offsets": [ [ 1119, 1124 ] ], "normalized": [] }, { "id": "PMC2885601-03-RESULTS-04_T33", "type": "Organism", "text": [ "GAS" ], "offsets": [ [ 1167, 1170 ] ], "normalized": [] }, { "id": "PMC2885601-03-RESULTS-04_T34", "type": "Organism", "text": [ "human" ], "offsets": [ [ 1174, 1179 ] ], "normalized": [] }, { "id": "PMC2885601-03-RESULTS-04_T35", "type": "Protein", "text": [ "IgG endopeptidase" ], "offsets": [ [ 1223, 1240 ] ], "normalized": [] }, { "id": "PMC2885601-03-RESULTS-04_T36", "type": "Protein", "text": [ "SeMac" ], "offsets": [ [ 1253, 1258 ] ], "normalized": [] } ]

[ { "id": "PMC2885601-03-RESULTS-04_E1", "type": "Protein_catabolism", "trigger": { "text": [ "cleaves" ], "offsets": [ [ 1018, 1025 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC2885601-03-RESULTS-04_T29" } ] }, { "id": "PMC2885601-03-RESULTS-04_E2", "type": "Positive_regulation", "trigger": { "text": [ "cleaves" ], "offsets": [ [ 1018, 1025 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC2885601-03-RESULTS-04_E1" }, { "role": "Cause", "ref_id": "PMC2885601-03-RESULTS-04_T27" } ] } ]

[]

[]

[ { "id": "PMC2858072-02-Results_and_Discussion-04__text", "type": "abstract", "text": [ "Virulence and the adaptation to intracellular growth \nBvrR/bvrS mutants are unable to multiply intracellularly and are avirulent in the mouse model [4]. Our microarray results demonstrated that at least 127 genes were differentially expressed in the bvrR mutant. Although this general expression changes could explain the complete loss of virulence of these mutants, it was remarkable the presence among them of ten genes, in addition to bvrS, whose products are already known to be associated with Brucella virulence [10], [11], [33], [34]. These included the already mentioned vjbR, but also motB (BAB2_1103), malK (BAB1_0241), norC (BAB2_0955), oppA (BAB1_1601), aspB (BAB1_1397), mosA (BAB1_0666) and three genes encoding hypothetical proteins (BAB1_1717, BAB1_0597 y BAB2_1127). B. melitensis malK mutant and B. suis aspB mutant were attenuated in cellular model of infection, and B. melitensis mutants in vjbR, motB, oppA, mosA and the hypothetical proteins BAB1_0597, BAB1_1717, BAB2_1127 were attenuated in both cellular and mouse models of infection (for a review see [33], [34]). In addition, it has been demonstrated that some denitrification genes of the nor operon are required for Brucella virulence: norD in B. suis and norB in B. melitensis [10], [11]. Most of the genes candidate to be regulated by BvrR/BvrS identified in our microarray experiments can be involved with the changes needed for intracellular survival of Brucella. In order to investigate if the BvrR/BvrS controlled genes were expressed intracellularly, bacterial RNA was obtained from B. abortus wild type recovered from infected cells as described in Material and Methods. The amount of bacterial RNA was not enough to perform microarray hybridizations. For this reason, the analysis of intracellular expression of 32 selected genes was done by RT-PCR by using total RNA from intracellular bacteria and from the same strain (B. abortus 2308) grown in laboratory conditions (Table 2). VirB8 (BAB2_0061) was used as control of intracellularly expressed gene [35]. The results showed significant differences in the expression of at least fifteen genes controlled by BvrR/BvrS. The expression of genes vjbR, malF, norC, pckA, fumB, BAB1_0017 (fatty acids metabolism) and BAB1_1620 (LPS glycosyl transferase) were induced intracellularly. On the other hand, two genes for cell envelope proteins (omp25d and one lipoprotein) and three denitrification genes (norC, nirK and glutaminase BAB2_0863) were less expressed intracellularly. In conclusion, all these results and previous findings support the proposal that BvrR/BvrS controls a significantly broad set of phenotypes and define an important and coordinate gateway between the free-living and intracellular states of Brucella. However, 30 of the genes differentially expressed in the bvrR mutant compared with the parental strain have a yet uncharacterized function. This group may contain unknown essential information to completely understand the regulatory role of the BvrR/BvrS two-component regulatory system.\n" ], "offsets": [ [ 0, 3049 ] ] } ]

[ { "id": "PMC2858072-02-Results_and_Discussion-04_T1", "type": "Organism", "text": [ "BvrR/bvrS mutants" ], "offsets": [ [ 54, 71 ] ], "normalized": [] }, { "id": "PMC2858072-02-Results_and_Discussion-04_T2", "type": "Two-component-system", "text": [ "BvrR/bvrS" ], "offsets": [ [ 54, 63 ] ], "normalized": [] }, { "id": "PMC2858072-02-Results_and_Discussion-04_T3", "type": "Protein", "text": [ "BvrR" ], "offsets": [ [ 54, 58 ] ], "normalized": [] }, { "id": "PMC2858072-02-Results_and_Discussion-04_T4", "type": "Protein", "text": [ "bvrS" ], "offsets": [ [ 59, 63 ] ], "normalized": [] }, { "id": "PMC2858072-02-Results_and_Discussion-04_T5", "type": "Organism", "text": [ "mouse" ], "offsets": [ [ 136, 141 ] ], "normalized": [] }, { "id": "PMC2858072-02-Results_and_Discussion-04_T6", "type": "Organism", "text": [ "bvrR mutant" ], "offsets": [ [ 250, 261 ] ], "normalized": [] }, { "id": "PMC2858072-02-Results_and_Discussion-04_T7", "type": "Protein", "text": [ "bvrR" ], "offsets": [ [ 250, 254 ] ], "normalized": [] }, { "id": "PMC2858072-02-Results_and_Discussion-04_T8", "type": "Protein", "text": [ "bvrS" ], "offsets": [ [ 438, 442 ] ], "normalized": [] }, { "id": "PMC2858072-02-Results_and_Discussion-04_T9", "type": "Organism", "text": [ "Brucella" ], "offsets": [ [ 499, 507 ] ], "normalized": [] }, { "id": "PMC2858072-02-Results_and_Discussion-04_T10", "type": "Protein", "text": [ "vjbR" ], "offsets": [ [ 579, 583 ] ], "normalized": [] }, { "id": "PMC2858072-02-Results_and_Discussion-04_T11", "type": "Protein", "text": [ "motB" ], "offsets": [ [ 594, 598 ] ], "normalized": [] }, { "id": "PMC2858072-02-Results_and_Discussion-04_T12", "type": "Protein", "text": [ "BAB2_1103" ], "offsets": [ [ 600, 609 ] ], "normalized": [] }, { "id": "PMC2858072-02-Results_and_Discussion-04_T13", "type": "Protein", "text": [ "malK" ], "offsets": [ [ 612, 616 ] ], "normalized": [] }, { "id": "PMC2858072-02-Results_and_Discussion-04_T14", "type": "Protein", "text": [ "BAB1_0241" ], "offsets": [ [ 618, 627 ] ], "normalized": [] }, { "id": "PMC2858072-02-Results_and_Discussion-04_T15", "type": "Protein", "text": [ "norC" ], "offsets": [ [ 630, 634 ] ], "normalized": [] }, { "id": "PMC2858072-02-Results_and_Discussion-04_T16", "type": "Protein", "text": [ "BAB2_0955" ], "offsets": [ [ 636, 645 ] ], "normalized": [] }, { "id": "PMC2858072-02-Results_and_Discussion-04_T17", "type": "Protein", "text": [ "oppA" ], "offsets": [ [ 648, 652 ] ], "normalized": [] }, { "id": "PMC2858072-02-Results_and_Discussion-04_T18", "type": "Protein", "text": [ "BAB1_1601" ], "offsets": [ [ 654, 663 ] ], "normalized": [] }, { "id": "PMC2858072-02-Results_and_Discussion-04_T19", "type": "Protein", "text": [ "aspB" ], "offsets": [ [ 666, 670 ] ], "normalized": [] }, { "id": "PMC2858072-02-Results_and_Discussion-04_T20", "type": "Protein", "text": [ "BAB1_1397" ], "offsets": [ [ 672, 681 ] ], "normalized": [] }, { "id": "PMC2858072-02-Results_and_Discussion-04_T21", "type": "Protein", "text": [ "mosA" ], "offsets": [ [ 684, 688 ] ], "normalized": [] }, { "id": "PMC2858072-02-Results_and_Discussion-04_T22", "type": "Protein", "text": [ "BAB1_0666" ], "offsets": [ [ 690, 699 ] ], "normalized": [] }, { "id": "PMC2858072-02-Results_and_Discussion-04_T23", "type": "Protein", "text": [ "BAB1_1717" ], "offsets": [ [ 749, 758 ] ], "normalized": [] }, { "id": "PMC2858072-02-Results_and_Discussion-04_T24", "type": "Protein", "text": [ "BAB1_0597" ], "offsets": [ [ 760, 769 ] ], "normalized": [] }, { "id": "PMC2858072-02-Results_and_Discussion-04_T25", "type": "Protein", "text": [ "BAB2_1127" ], "offsets": [ [ 772, 781 ] ], "normalized": [] }, { "id": "PMC2858072-02-Results_and_Discussion-04_T26", "type": "Organism", "text": [ "B. melitensis malK mutant" ], "offsets": [ [ 784, 809 ] ], "normalized": [] }, { "id": "PMC2858072-02-Results_and_Discussion-04_T27", "type": "Protein", "text": [ "malK" ], "offsets": [ [ 798, 802 ] ], "normalized": [] }, { "id": "PMC2858072-02-Results_and_Discussion-04_T28", "type": "Organism", "text": [ "B. suis aspB mutant" ], "offsets": [ [ 814, 833 ] ], "normalized": [] }, { "id": "PMC2858072-02-Results_and_Discussion-04_T29", "type": "Protein", "text": [ "aspB" ], "offsets": [ [ 822, 826 ] ], "normalized": [] }, { "id": "PMC2858072-02-Results_and_Discussion-04_T30", "type": "Organism", "text": [ "B. melitensis mutants" ], "offsets": [ [ 886, 907 ] ], "normalized": [] }, { "id": "PMC2858072-02-Results_and_Discussion-04_T31", "type": "Protein", "text": [ "vjbR" ], "offsets": [ [ 911, 915 ] ], "normalized": [] }, { "id": "PMC2858072-02-Results_and_Discussion-04_T32", "type": "Protein", "text": [ "motB" ], "offsets": [ [ 917, 921 ] ], "normalized": [] }, { "id": "PMC2858072-02-Results_and_Discussion-04_T33", "type": "Protein", "text": [ "oppA" ], "offsets": [ [ 923, 927 ] ], "normalized": [] }, { "id": "PMC2858072-02-Results_and_Discussion-04_T34", "type": "Protein", "text": [ "mosA" ], "offsets": [ [ 929, 933 ] ], "normalized": [] }, { "id": "PMC2858072-02-Results_and_Discussion-04_T35", "type": "Protein", "text": [ "BAB1_0597" ], "offsets": [ [ 964, 973 ] ], "normalized": [] }, { "id": "PMC2858072-02-Results_and_Discussion-04_T36", "type": "Protein", "text": [ "BAB1_1717" ], "offsets": [ [ 975, 984 ] ], "normalized": [] }, { "id": "PMC2858072-02-Results_and_Discussion-04_T37", "type": "Protein", "text": [ "BAB2_1127" ], "offsets": [ [ 986, 995 ] ], "normalized": [] }, { "id": "PMC2858072-02-Results_and_Discussion-04_T38", "type": "Organism", "text": [ "mouse" ], "offsets": [ [ 1033, 1038 ] ], "normalized": [] }, { "id": "PMC2858072-02-Results_and_Discussion-04_T39", "type": "Regulon-operon", "text": [ "nor operon" ], "offsets": [ [ 1167, 1177 ] ], "normalized": [] }, { "id": "PMC2858072-02-Results_and_Discussion-04_T40", "type": "Protein", "text": [ "nor" ], "offsets": [ [ 1167, 1170 ] ], "normalized": [] }, { "id": "PMC2858072-02-Results_and_Discussion-04_T41", "type": "Organism", "text": [ "Brucella" ], "offsets": [ [ 1195, 1203 ] ], "normalized": [] }, { "id": "PMC2858072-02-Results_and_Discussion-04_T42", "type": "Protein", "text": [ "norD" ], "offsets": [ [ 1215, 1219 ] ], "normalized": [] }, { "id": "PMC2858072-02-Results_and_Discussion-04_T43", "type": "Organism", "text": [ "B. suis" ], "offsets": [ [ 1223, 1230 ] ], "normalized": [] }, { "id": "PMC2858072-02-Results_and_Discussion-04_T44", "type": "Protein", "text": [ "norB" ], "offsets": [ [ 1235, 1239 ] ], "normalized": [] }, { "id": "PMC2858072-02-Results_and_Discussion-04_T45", "type": "Organism", "text": [ "B. melitensis" ], "offsets": [ [ 1243, 1256 ] ], "normalized": [] }, { "id": "PMC2858072-02-Results_and_Discussion-04_T46", "type": "Two-component-system", "text": [ "BvrR/BvrS" ], "offsets": [ [ 1316, 1325 ] ], "normalized": [] }, { "id": "PMC2858072-02-Results_and_Discussion-04_T47", "type": "Protein", "text": [ "BvrR" ], "offsets": [ [ 1316, 1320 ] ], "normalized": [] }, { "id": "PMC2858072-02-Results_and_Discussion-04_T48", "type": "Protein", "text": [ "BvrS" ], "offsets": [ [ 1321, 1325 ] ], "normalized": [] }, { "id": "PMC2858072-02-Results_and_Discussion-04_T49", "type": "Organism", "text": [ "Brucella" ], "offsets": [ [ 1437, 1445 ] ], "normalized": [] }, { "id": "PMC2858072-02-Results_and_Discussion-04_T50", "type": "Two-component-system", "text": [ "BvrR/BvrS" ], "offsets": [ [ 1478, 1487 ] ], "normalized": [] }, { "id": "PMC2858072-02-Results_and_Discussion-04_T51", "type": "Protein", "text": [ "BvrR" ], "offsets": [ [ 1478, 1482 ] ], "normalized": [] }, { "id": "PMC2858072-02-Results_and_Discussion-04_T52", "type": "Protein", "text": [ "BvrS" ], "offsets": [ [ 1483, 1487 ] ], "normalized": [] }, { "id": "PMC2858072-02-Results_and_Discussion-04_T53", "type": "Organism", "text": [ "B. abortus" ], "offsets": [ [ 1569, 1579 ] ], "normalized": [] }, { "id": "PMC2858072-02-Results_and_Discussion-04_T54", "type": "Organism", "text": [ "B. abortus 2308" ], 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"type": "Protein", "text": [ "malF" ], "offsets": [ [ 2189, 2193 ] ], "normalized": [] }, { "id": "PMC2858072-02-Results_and_Discussion-04_T62", "type": "Protein", "text": [ "norC" ], "offsets": [ [ 2195, 2199 ] ], "normalized": [] }, { "id": "PMC2858072-02-Results_and_Discussion-04_T63", "type": "Protein", "text": [ "pckA" ], "offsets": [ [ 2201, 2205 ] ], "normalized": [] }, { "id": "PMC2858072-02-Results_and_Discussion-04_T64", "type": "Protein", "text": [ "fumB" ], "offsets": [ [ 2207, 2211 ] ], "normalized": [] }, { "id": "PMC2858072-02-Results_and_Discussion-04_T65", "type": "Protein", "text": [ "BAB1_0017" ], "offsets": [ [ 2213, 2222 ] ], "normalized": [] }, { "id": "PMC2858072-02-Results_and_Discussion-04_T66", "type": "Protein", "text": [ "BAB1_1620" ], "offsets": [ [ 2252, 2261 ] ], "normalized": [] }, { "id": "PMC2858072-02-Results_and_Discussion-04_T67", "type": "Chemical", "text": [ "LPS" ], "offsets": [ [ 2263, 2266 ] ], "normalized": [] }, { "id": "PMC2858072-02-Results_and_Discussion-04_T68", "type": "Protein", "text": [ "omp25d" ], "offsets": [ [ 2376, 2382 ] ], "normalized": [] }, { "id": "PMC2858072-02-Results_and_Discussion-04_T69", "type": "Protein", "text": [ "norC" ], "offsets": [ [ 2437, 2441 ] ], "normalized": [] }, { "id": "PMC2858072-02-Results_and_Discussion-04_T70", "type": "Protein", "text": [ "nirK" ], "offsets": [ [ 2443, 2447 ] ], "normalized": [] }, { "id": "PMC2858072-02-Results_and_Discussion-04_T71", "type": "Protein", "text": [ "BAB2_0863" ], "offsets": [ [ 2464, 2473 ] ], "normalized": [] }, { "id": "PMC2858072-02-Results_and_Discussion-04_T72", "type": "Two-component-system", "text": [ "BvrR/BvrS" ], "offsets": [ [ 2593, 2602 ] ], "normalized": [] }, { "id": "PMC2858072-02-Results_and_Discussion-04_T73", "type": "Protein", "text": [ "BvrR" ], "offsets": [ [ 2593, 2597 ] ], "normalized": [] }, { "id": "PMC2858072-02-Results_and_Discussion-04_T74", "type": "Protein", "text": [ "BvrS" ], "offsets": [ [ 2598, 2602 ] ], "normalized": [] }, { "id": "PMC2858072-02-Results_and_Discussion-04_T75", "type": "Organism", "text": [ "Brucella" ], "offsets": [ [ 2751, 2759 ] ], "normalized": [] }, { "id": "PMC2858072-02-Results_and_Discussion-04_T76", "type": "Organism", "text": [ "bvrR mutant" ], "offsets": [ [ 2818, 2829 ] ], "normalized": [] }, { "id": "PMC2858072-02-Results_and_Discussion-04_T77", "type": "Protein", "text": [ "bvrR" ], "offsets": [ [ 2818, 2822 ] ], "normalized": [] }, { "id": "PMC2858072-02-Results_and_Discussion-04_T78", "type": "Two-component-system", "text": [ "BvrR/BvrS" ], "offsets": [ [ 3006, 3015 ] ], "normalized": [] }, { "id": "PMC2858072-02-Results_and_Discussion-04_T79", "type": "Protein", "text": [ "BvrR" ], "offsets": [ [ 3006, 3010 ] ], "normalized": [] }, { "id": "PMC2858072-02-Results_and_Discussion-04_T80", "type": "Protein", "text": [ "BvrS" ], "offsets": [ [ 3011, 3015 ] ], "normalized": [] } ]

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[]

[ { "id": "PMC2682197-03-Discussion__text", "type": "abstract", "text": [ "Discussion \nDespite the significance of M. tuberculosis latency in pathogenesis, the mechanisms by which the tubercle bacillus establishes and maintains the latent state remain incompletely defined. Identification of M. tuberculosis genes that are induced by hypoxia and nitric oxide (NO) in vitro provides a framework for understanding the physiology of dormant bacilli [3],[4],[5]. These genes, referred to as the dormancy regulon, are transcriptionally regulated by the mycobacterial two-component system DosR-DosS under hypoxic conditions [4]. Indeed, it has been shown that both the cognate sensor histidine kinase DosS (a member of the dormancy regulon) as well as an \"orphan\" kinase, DosT, functioning as redox and hypoxia sensors, respectively; can regulate DosR activity, and that O2, NO, and CO can modulate the activity of these two kinases via interaction with a haem prosthetic group [28],[29],[30],[31],[32]. The biological significance of the dormancy regulon has been underscored by in vitro studies of dosR mutants of BCG and M. tuberculosis, which demonstrated the requirement of this transcription factor for survival under hypoxic conditions [3],[33]. Further, upregulation of the expression of certain dormancy regulon genes have been implicated in tuberculosis transmission as well as the virulence of the epidemiologically important W-Beijing lineage of M. tuberculosis [34],[35]. There are eight genes in the M. tuberculosis genome annotated to encode USP family proteins [7]. We studied the M. tuberculosis USP rv2623 because it is one of the most highly induced genes in the dormancy regulon when bacilli are subjected to hypoxia and nitrosative stress [3],[4],[5],[36],[37]. More important, rv2623 was also shown to be up-regulated when the tubercle bacillus is internalized by human and mouse macrophages [10],[38] as well as in the lungs of mice with persistent M. tuberculosis infection [11]. These latter observations suggest that the induction of rv2623 may have biological relevance. The precise mechanisms by which Rv2623 expression is regulated remain to be defined. Recent transcriptional analysis of Rv2623, while confirming the essentiality of the two 18 bp palindromic DosR-binding motifs that are present in the promoter region of this gene [38] for induction of Rv2623 under low oxygen conditions, also demonstrated the presence of additional regulatory elements within the rv2623 5'-untranslated region [18]. These results suggest that the regulation of Rv2623 is likely complex. The M. tuberculosis dormancy response features a dramatic decrease in metabolic activity, resulting in a rapid decrease in bacterial replication [39]. Therefore, it is possible that deficiency in certain members of the dormancy regulon could result in inability of the tubercle bacillus to enter a latent state in the infected host, leading to unrestrained growth and thus, hypervirulence. Indeed, specific members of the M. tuberculosis dormancy regulon whose insufficiency results in a hypervirulence phenotype have been reported [40],[41]. In certain experimental tuberculosis animal models, DosR deficiency has been associated with a hypervirulence phenotype [41]. However, DosR deficiency has also been reported to have no effect on M. tuberculosis virulence or to lead to an attenuated phenotype [42],[43]. The discrepancies regarding M. tuberculosis virulence in these DosR studies are unclear, but could be due to differences in experimental systems employed. Insufficiency of the chaperone-like alpha-crystallin encoded by M. tuberculosis hspX (acr) has also been shown to be associated with hypervirulence in a BALB/c mouse model of tuberculosis [40]. In the present study, an rv2623 knockout mutant of virulent M. tuberculosis Erdman fails to establish a chronic persistent infection, displaying a hypervirulent phenotype in susceptible hosts, as assessed by lung bacterial burden, histopathology, and mortality. Results of the complementation studies indicate that the phenotype is Rv2623-specific. This growth-regulating phenomenon is echoed by the observation that ectopic overexpression of Rv2623 results in attenuation of mycobacterial growth. Together, these data strongly suggest that the M. tuberculosis USP Rv2623 has the ability to regulate growth in vitro and in vivo, and is required for the establishment of a persistent infection. Intriguingly, ectopic overexpression of HspX by the same means employed by our study also resulted in an attenuated growth phenotype compared with LacZ-overexpressing controls [44], suggesting that these two tightly co-regulated \"stress\" proteins might have similar growth-regulatory roles during dormancy. Bioinformatic and experimental evidence suggest that nucleotide-binding capacity represents a discriminating biochemical feature that facilitates USP protein classification. Putative functional differences between USPs are implied by their assignment to two subclasses: one whose members do not bind ATP and another whose constituents bind and hydrolyze adenine nucleotide substrates [8],[26],[27],[45],[46]. A structural comparison between the prototypic members of the two subclasses, the non-ATP-binding UspA homolog (H. influenzae, PDB ID 1JMV) and the ATP-binding USP, MJ0577 (M. jannaschii, PDB ID 1MJH) revealed that while both proteins exhibit a similar fold, conserved glycine residues within the ATP-binding loop of the latter are substituted with bulky amino acids that preclude ATP recognition in the former [26],[27]. The unique nucleotide-binding pocket of this protein family is structurally distinct from those commonly encountered in ATP-binding proteins [26],[47],[48]. Specific roles for USP family proteins are just beginning to be characterized, and early functional classifications have been informed by ATP-binding capacity [9]. While the non-ATP-binding UspA homologs appear to play diverse roles in promoting survival under a variety of environmental insults [15],[49],[50],[51], the function(s) of ATP-binding type USPs remain unclear [9]. Based on in silico analyses, Florczyk et al. classified Rv2623 as belonging to a novel class of ATPases [52], although formal evidence for ATP binding by this protein has not been reported. This study has provided substantial biochemical and structural evidence that M. tuberculosis Rv2623 is a bona fide nucleotide-binding USP: i) E. coli-expressed His6-Rv2623 co-purifies with tightly bound ATP and ADP; ii) analysis of the 2.9 A -resolution Rv2623 crystal structure, the first molecular model of a tandem-type USP, reveals four ATP-bound nucleotide-binding pockets; and iii) point mutations (D15E, G117A) within the conserved L1 (D15E) and beta4 (G117A) regions of the structure, which were predicted to disrupt nucleotide-binding, yielded mutant proteins with attenuated ATP-binding capacity. Furthermore, given that the attenuated growth phenotype caused by overexpression of Rv2623 could be abrogated by mutations that interfere with the binding of this protein to its nucleotide substrate, it is likely that the mycobacterial growth-regulatory faculty of Rv2623 is mediated by an ATP-dependent function. In summary, the results of the present study have revealed that the M. tuberculosis USP Rv2623 has the ability to regulate mycobacterial growth, as evident by the in vivo hypervirulence phenotype of Deltarv2623, which fails to establish a persistent infection in susceptible hosts, as well as the growth attenuation observed in mycobacteria overexpressing this USP. Thus, M. tuberculosis Rv2623 may serve the function of promoting mycobacterial transition into latency. The latent state allows persistence in infected individuals of tubercle bacilli that can reactivate to cause active disease and to disseminate when the immune status of the host is compromised. As a result, Rv2623 may contribute significantly to the propagation of the tubercle bacillus in the human host and the difficulties in eradicating tuberculosis. Mechanistically, results of the mutagenesis studies have shown that Rv2623 regulates growth through ATP-dependent function. Clearly, much remains to be learned regarding how the ATP-dependent function of Rv2623 contributes to growth regulation. It has been proposed that a nucleotide-binding USP from M. jannaschii, MJ0577, whose ability to hydrolyze ATP is dependent on interaction with factor(s) present in the cell extract of this hyperthermophile [26], functions as a molecular switch much like the Ras protein family, whose GTP hydrolysis ability is modulated by interaction with a number of regulatory proteins [53],[54],[55]. The fact that E. coli-expressed Rv2623 co-purifies with ADP as well as ATP suggests the possibility that this mycobacterial USP, like MJ0577, is capable of ATP hydrolysis. It is therefore conceivable that M. tuberculosis Rv2623, as a component of the yet-to-be defined dormancy signaling pathway(s), functions as a molecular switch by virtue of its ATP-binding and putative ATP-hydrolyzing properties, to mediate the establishment of tuberculous latency. Experiments designed to investigate the potential ATP-hydrolyzing activity of Rv2623 are currently underway. Recent identification of the DosR-dependent dormancy regulon [3],[4],[5]; the DosR-independent enduring hypoxic response, which involves over 200 mycobacterial genes, including those known to regulate bacteriostasis [42]; and the demonstration that M. tuberculosis redox and hypoxia sensors can interact with multiple ligands that differentially modulate the activity of these important kinases [28],[29],[30],[31],[32], predict a complex regulatory network for tuberculous latency. Elucidation of how ATP-binding and, potentially, the hydrolysis of ATP by Rv2623 regulate M. tuberculosis dormancy-signaling pathways will likely illuminate the mechanisms by which the tubercle bacillus establishes persistence.\n" ], "offsets": [ [ 0, 9895 ] ] } ]

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[]

[ { "id": "PMC2639726-02-Results-06__text", "type": "abstract", "text": [ "Computer aided analysis of the regulatory network \nThe fact that all of the 14 regulators in this study have biological functions during infection suggests they could be part of a coordinated network. Acidic minimal medium is a well-established in vitro condition for SPI-2 expression; accordingly, we focused on examining regulation of genes expressed under these conditions [47],[48],[58]. To identify coordinated regulation we compared expression of each regulator in each mutant background when grown in minimal acidic medium (Figure 6A). RNA samples were prepared from three separate cultures and used as a template in separate qRT-PCR experiments. A matrix with 14 mutants in columns and 14 regulatory genes and SPI-2 genes (6 genes except for ssrB as used in Figure 4) in rows was constructed based on qRT-PCR data and z-scores were calculated based on average and standard deviations from columns and rows. A network among regulators and SPI-2 was mapped as described in Lee et al. by sorting out values that changed in a specific mutant background [59]. We visualized the resulting relationships using Cytoscape [57]. Nodes indicate regulators or SPI-2 and red and blue arrows indicate activation and repression respectively (see Figure 6B). In the computed network multiple regulators act both directly and indirectly to control SPI-2 expression. However, direct or indirect regulation cannot be distinguished without additional experimental verification. So, in Figure 6B all regulatory effects on SPI-2 have been removed except for those mediated directly by slyA and ssrB based on additional genetic data as described below. The network suggests that both slyA and ssrA/ssrB could coordinate regulation of SPI-2 and other virulence factors by integrating signals from multiple regulators as was tested next. An overall network was also generated by integrating 4 data sets; two CLR algorithm data from the complete microarray results and GSE2456 public microarray database and two matrix analysis data from the transcription profiles and qRT-PCR results (Figure S3; the limitation is that no distinction is made between positive and negative regulation in CLR algorithm data). The consensus network combining all data reported in this study includes the network computed from qRT-PCR (Figure 6B) in part and suggests a predictive regulatory cascade that merits a test.\n" ], "offsets": [ [ 0, 2382 ] ] } ]

[ { "id": "PMC2639726-02-Results-06_T1", "type": "Protein", "text": [ "ssrB" ], "offsets": [ [ 750, 754 ] ], "normalized": [] }, { "id": "PMC2639726-02-Results-06_T2", "type": "Protein", "text": [ "slyA" ], "offsets": [ [ 1571, 1575 ] ], "normalized": [] }, { "id": "PMC2639726-02-Results-06_T3", "type": "Protein", "text": [ "ssrB" ], "offsets": [ [ 1580, 1584 ] ], "normalized": [] }, { "id": "PMC2639726-02-Results-06_T4", "type": "Protein", "text": [ "slyA" ], "offsets": [ [ 1669, 1673 ] ], "normalized": [] }, { "id": "PMC2639726-02-Results-06_T5", "type": "Two-component-system", "text": [ "ssrA/ssrB" ], "offsets": [ [ 1678, 1687 ] ], "normalized": [] }, { "id": "PMC2639726-02-Results-06_T6", "type": "Protein", "text": [ "ssrA" ], "offsets": [ [ 1678, 1682 ] ], "normalized": [] }, { "id": "PMC2639726-02-Results-06_T7", "type": "Protein", "text": [ "ssrB" ], "offsets": [ [ 1683, 1687 ] ], "normalized": [] } ]

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[]

[]

[ { "id": "PMC1913099-02-Results-Discussion-08__text", "type": "abstract", "text": [ "Type I Clusters: Intact Metabolic Pathways and Multimeric Proteins \nWe measured the performance of our algorithm by examining whether it identified gene groupings known to be functionally related (Type I clusters). Only four (16%) of 25 Type I clusters (spy0080-0081, spy1236-1237, spy1707-1711, spy2041-2042) could have been identified in entirety by significance analysis because all clustered genes exhibited significant differential expression (PF value < 0.05). A total of 11 (52.4%) of the remaining 21 clusters would not have been identified in their entirety without GenomeCrawler because we initially identified significant fold-changes in only a subset of genes necessary to encode particular pathways or loci; this is intuitively unreasonable if all genes are essential for functionality. GenomeCrawler expanded these clusters to contain more genes that encode intact loci (Table 3). For example, we initially identified (Table 1) the significant upregulation of three of the five known gene members of the folate biosynthetic pathway [40] (spy1096-1100), but GenomeCrawler identified a significant cluster containing all five genes (Table 3 and Figure 2B). We obtained a similar result for the eight-gene operon encoding the F0F1-type proton translocating ATPase [41] (spy0754-0761). The initial significance analysis identified only four atp genes (Table 1), but neighbor clustering identified a significant cluster containing all eight genes necessary to encode a functional ATPase (Table 3). Each of the 11 neighbor clusters that could have been only partially identified by our initial analysis alone gained gene members after application of the algorithms and became more complete sets of functionally related genes than initially identified (Table 3). These clusters encompass various metabolic processes, including purine biosynthesis (spy0025-0028), lactose metabolism (spy1916-1923), fatty acid biosynthesis (spy1743-1747), lipoteichoic acid synthesis (spy1308-1312), and sugar phosphotransferase transport (spy1058-1060) [14], suggesting that specific changes occur in the streptococcal metabolic program as the bacteria adhere to human pharyngeal cells in vitro. Notably, the remaining ten Type I clusters were composed entirely of genes that individually were not significant; however, after applying our algorithms, the combined contribution of each gene resulted in a significant cluster. For example, the nine-gene operon that spans genes spy0738-0746 encodes streptolysin S, a potent cytolytic toxin that promotes internalization and host tissue dissemination [25,44]. Though the differential expression of the individual genes was not significant following our initial statistical analysis, GenomeCrawler identified a significant downregulated cluster containing all nine genes (Table 3). Adherence-induced downregulation of streptolysin S is consistent with its previously determined role in host cell internalization [25]; however, without neighbor clustering, expression of this operon was not evident immediately. Although individual gene members of Type I clusters may not be statistically significant as a result of technical variability within experiments [17], the genetic structure of certain Type I operons may provide an alternative explanation. For example, the streptolysin operon encodes an internal terminator downstream of the sagA gene (the first gene in the operon), which modulates the abundance of particular mRNA species (e.g., sagA mRNA versus the polycistronic message for all nine genes) under different environmental conditions [45]. If transcription is internally disrupted by such a terminator, the abundance of the sagA transcript may be much greater than the polycistronic message; such disproportionate transcript levels would affect log2-fold change values and impact the statistical significance of individual genes within these types of clusters. Thus, in addition to helping resolve clusters that would not be easily recognized because of experimental technical variability, the neighbor clustering method may help to resolve operons with such internal terminators and regulators. These results demonstrate that neighbor clustering effectively reconstructed a number of complete pathways and loci from processed array data. Importantly, because functional gene data are not incorporated into its algorithms, GenomeCrawler is not biased toward identifying \"expected\" clusters. Curating the dataset following its application may make the algorithms less user-friendly; however, the elimination of such bias is essential for this type of analysis.\n" ], "offsets": [ [ 0, 4608 ] ] } ]

[ { "id": "PMC1913099-02-Results-Discussion-08_T1", "type": "Regulon-operon", "text": [ "spy0080-0081" ], "offsets": [ [ 254, 266 ] ], "normalized": [] }, { "id": "PMC1913099-02-Results-Discussion-08_T2", "type": "Protein", "text": [ "spy0080" ], "offsets": [ [ 254, 261 ] ], "normalized": [] }, { "id": "PMC1913099-02-Results-Discussion-08_T3", "type": "Protein", "text": [ "0081" ], "offsets": [ [ 262, 266 ] ], "normalized": [] }, { "id": "PMC1913099-02-Results-Discussion-08_T4", "type": "Regulon-operon", "text": [ "spy1236-1237" ], "offsets": [ [ 268, 280 ] ], "normalized": [] }, { "id": "PMC1913099-02-Results-Discussion-08_T5", "type": "Protein", "text": [ "spy1236" ], "offsets": [ [ 268, 275 ] ], "normalized": [] }, { "id": "PMC1913099-02-Results-Discussion-08_T6", "type": "Protein", "text": [ "1237" ], "offsets": [ [ 276, 280 ] ], "normalized": [] }, { "id": "PMC1913099-02-Results-Discussion-08_T7", "type": "Regulon-operon", "text": [ "spy1707-1711" ], "offsets": [ [ 282, 294 ] ], "normalized": [] }, { "id": "PMC1913099-02-Results-Discussion-08_T8", "type": "Protein", "text": [ "spy1707" ], "offsets": [ [ 282, 289 ] ], "normalized": [] }, { "id": "PMC1913099-02-Results-Discussion-08_T9", "type": "Protein", "text": [ "1711" ], "offsets": [ [ 290, 294 ] ], "normalized": [] }, { "id": "PMC1913099-02-Results-Discussion-08_T10", "type": "Regulon-operon", "text": [ "spy2041-2042" ], "offsets": [ [ 296, 308 ] ], "normalized": [] }, { "id": "PMC1913099-02-Results-Discussion-08_T11", "type": "Protein", "text": [ "spy2041" ], "offsets": [ [ 296, 303 ] ], "normalized": [] }, { "id": "PMC1913099-02-Results-Discussion-08_T12", "type": "Protein", "text": [ "2042" ], "offsets": [ [ 304, 308 ] ], "normalized": [] }, { "id": "PMC1913099-02-Results-Discussion-08_T13", "type": "Chemical", "text": [ "folate" ], "offsets": [ [ 1018, 1024 ] ], "normalized": [] }, { "id": "PMC1913099-02-Results-Discussion-08_T14", "type": "Protein", "text": [ "spy1096" ], "offsets": [ [ 1052, 1059 ] ], "normalized": [] }, { "id": "PMC1913099-02-Results-Discussion-08_T15", "type": "Protein", "text": [ "1100" ], "offsets": [ [ 1060, 1064 ] ], "normalized": [] }, { "id": "PMC1913099-02-Results-Discussion-08_T16", "type": "Regulon-operon", "text": [ "spy0754-0761" ], "offsets": [ [ 1281, 1293 ] ], "normalized": [] }, { "id": "PMC1913099-02-Results-Discussion-08_T17", "type": "Protein", "text": [ "spy0754" ], "offsets": [ [ 1281, 1288 ] ], "normalized": [] }, { "id": "PMC1913099-02-Results-Discussion-08_T18", "type": "Protein", "text": [ "0761" ], "offsets": [ [ 1289, 1293 ] ], "normalized": [] }, { "id": "PMC1913099-02-Results-Discussion-08_T19", "type": "Regulon-operon", "text": [ "spy0025-0028" ], "offsets": [ [ 1855, 1867 ] ], "normalized": [] }, { "id": "PMC1913099-02-Results-Discussion-08_T20", "type": "Protein", "text": [ "spy0025" ], "offsets": [ [ 1855, 1862 ] ], "normalized": [] }, { "id": "PMC1913099-02-Results-Discussion-08_T21", "type": "Protein", "text": [ "0028" ], "offsets": [ [ 1863, 1867 ] ], "normalized": [] }, { "id": "PMC1913099-02-Results-Discussion-08_T22", "type": "Chemical", "text": [ "lactose" ], "offsets": [ [ 1870, 1877 ] ], "normalized": [] }, { "id": "PMC1913099-02-Results-Discussion-08_T23", "type": "Regulon-operon", "text": [ "spy1916-1923" ], "offsets": [ [ 1890, 1902 ] ], "normalized": [] }, { "id": "PMC1913099-02-Results-Discussion-08_T24", "type": "Protein", "text": [ "spy1916" ], "offsets": [ [ 1890, 1897 ] ], "normalized": [] }, { "id": "PMC1913099-02-Results-Discussion-08_T25", "type": "Protein", "text": [ "1923" ], "offsets": [ [ 1898, 1902 ] ], "normalized": [] }, { "id": "PMC1913099-02-Results-Discussion-08_T26", "type": "Regulon-operon", "text": [ "spy1743-1747" ], "offsets": [ [ 1930, 1942 ] ], "normalized": [] }, { "id": "PMC1913099-02-Results-Discussion-08_T27", "type": "Protein", "text": [ "spy1743" ], "offsets": [ [ 1930, 1937 ] ], "normalized": [] }, { "id": "PMC1913099-02-Results-Discussion-08_T28", "type": "Protein", "text": [ "1747" ], "offsets": [ [ 1938, 1942 ] ], "normalized": [] }, { "id": "PMC1913099-02-Results-Discussion-08_T29", "type": "Chemical", "text": [ "lipoteichoic acid" ], "offsets": [ [ 1945, 1962 ] ], "normalized": [] }, { "id": "PMC1913099-02-Results-Discussion-08_T30", "type": "Regulon-operon", "text": [ "spy1308-1312" ], "offsets": [ [ 1974, 1986 ] ], "normalized": [] }, { "id": "PMC1913099-02-Results-Discussion-08_T31", "type": "Protein", "text": [ "spy1308" ], "offsets": [ [ 1974, 1981 ] ], "normalized": [] }, { "id": "PMC1913099-02-Results-Discussion-08_T32", "type": "Protein", "text": [ "1312" ], "offsets": [ [ 1982, 1986 ] ], "normalized": [] }, { "id": "PMC1913099-02-Results-Discussion-08_T33", "type": "Regulon-operon", "text": [ "spy1058-1060" ], "offsets": [ [ 2029, 2041 ] ], "normalized": [] }, { "id": "PMC1913099-02-Results-Discussion-08_T34", "type": "Protein", "text": [ "spy1058" ], "offsets": [ [ 2029, 2036 ] ], "normalized": [] }, { "id": "PMC1913099-02-Results-Discussion-08_T35", "type": "Protein", "text": [ "1060" ], "offsets": [ [ 2037, 2041 ] ], "normalized": [] }, { "id": "PMC1913099-02-Results-Discussion-08_T36", "type": "Organism", "text": [ "human" ], "offsets": [ [ 2153, 2158 ] ], "normalized": [] }, { "id": "PMC1913099-02-Results-Discussion-08_T37", "type": "Regulon-operon", "text": [ "spy0738-0746" ], "offsets": [ [ 2466, 2478 ] ], "normalized": [] }, { "id": "PMC1913099-02-Results-Discussion-08_T38", "type": "Protein", "text": [ "spy0738" ], "offsets": [ [ 2466, 2473 ] ], "normalized": [] }, { "id": "PMC1913099-02-Results-Discussion-08_T39", "type": "Protein", "text": [ "0746" ], "offsets": [ [ 2474, 2478 ] ], "normalized": [] }, { "id": "PMC1913099-02-Results-Discussion-08_T40", "type": "Protein", "text": [ "streptolysin S" ], "offsets": [ [ 2487, 2501 ] ], "normalized": [] }, { "id": "PMC1913099-02-Results-Discussion-08_T41", "type": "Protein", "text": [ "streptolysin S" ], "offsets": [ [ 2854, 2868 ] ], "normalized": [] }, { "id": "PMC1913099-02-Results-Discussion-08_T42", "type": "Regulon-operon", "text": [ "streptolysin operon" ], "offsets": [ [ 3303, 3322 ] ], "normalized": [] }, { "id": "PMC1913099-02-Results-Discussion-08_T43", "type": "Protein", "text": [ "sagA" ], "offsets": [ [ 3372, 3376 ] ], "normalized": [] }, { "id": "PMC1913099-02-Results-Discussion-08_T44", "type": "Protein", "text": [ "sagA" ], "offsets": [ [ 3478, 3482 ] ], "normalized": [] }, { "id": "PMC1913099-02-Results-Discussion-08_T45", "type": "Protein", "text": [ "sagA" ], "offsets": [ [ 3672, 3676 ] ], "normalized": [] } ]

[ { "id": "PMC1913099-02-Results-Discussion-08_E1", "type": "Regulation", "trigger": { "text": [ "modulates" ], "offsets": [ [ 3420, 3429 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC1913099-02-Results-Discussion-08_T44" }, { "role": "Cause", "ref_id": "PMC1913099-02-Results-Discussion-08_T42" } ] } ]

[]

[]

[ { "id": "PMC1974823-04-Discussion__text", "type": "abstract", "text": [ "Discussion \nThe two-component regulatory system is a major mechanism of signal transduction and is widespread in bacteria. Six putative two-component regulatory systems were detected by surveying the P. gingivalis W83 genome database for homologues of the two-component sensor histidine kinase (Hasegawa et al., 2003). Although most target genes of P. gingivalis two-component systems are unknown, the role of the FimS/FimR in expression of the fimA gene is well defined. Expression of minor fimbriae (mfa1) in a fimR mutanthas been investigated. A comparison of the transcriptional level of the mfa1 in P. gingivalis wild-type strain and in the fimR mutant indicates that the FimS/FimR system is a positive regulator for the mfa1 gene, although the system controls two fimbrial genes at different levels. It is hypothesized that the FimS/FimR system regulates expression of each fimbrial gene through a unique mechanism. The previous study suggested that regulation of fimA expression by FimR is through a regulation cascade involving interaction of FimR and the promoter region of the first gene in the fimA cluster (Nishikawa et al., 2004). Here it is demonstrated that FimR binds directly to the promoter region of the mfa1 gene, suggesting a direct role of FimR in activation of mfa1 expression. It has also been reported previously that the transcriptional activity of fimA was reduced in the fimA mutant, indicating multiple levels of control of fimA expression in P. gingivalis (Xie et al., 2000a). This may explain the much tighter control of fimA expression by FimR. However, the possibility cannot be excluded that other regulatory elements are also involved in expression of the mfa1 gene. A two-component regulatory system typically contains a membrane-bound histidine kinase sensor and a cytosolic response regulator. Phosphorylation, mediated by histidine kinase at a specific aspartate residue, activates DNA-binding activity of the response regulator and initiates the corresponding cellular response. However, no apparent difference was found in DNA-binding affinity between rFimRs with or without acetyl phosphate treatment. Observation suggests that different mechanisms may be involved in P. gingivalis FimR activation. Activation of a regulatory protein not corresponding to phosphorylation was also observed in Streptococcus mutans (Biswas & Biswas, 2006). Phosphorylation of CovR, a global response regulator, had no effect on its DNA-binding affinity. The fact that FimR was not activated by phosphorylation may also be due to the short lifetime of the phosphorylated state, which has been observed in other bacteria (Stock et al., 2000). The transcriptional start site of the mfa1 gene located at 434 bp upstream of the putative start codon was detected, which is also 390 bp upstream of the site previously reported (Park et al., 2006). The transcriptional site revealed here is confirmed by RT-PCR analysis. Data of this study suggest that transcription of the mfa1 gene originated at a distal upstream transcriptional start site and read through the promoter region suggested by Park et al. (2006). Moreover, FimR appears to act on the promoter region identified here, suggesting that this promoter may make significant contributions toward mfa1 expression through the FimS/FimR system. Gene expression under the control of two promoters is not uncommon in bacteria. In E. coli, two promoters direct transcription of acs encoding, an acetate-scavenging enzyme required for fitness during periods of carbon starvation - the distal acsP1 and the proximal acsP2 (Beatty et al., 2003). It is suggested that each promoter may interact with different regulatory elements. Two promoter regions in the P. gingivalis fimA gene were also reported (Xie & Lamont, 1999; Nishikawa et al., 2004). A cascade regulation starting with FimR appears to act on the upstream promoter (Nishikawa et al., 2004). The observations that FimR binds only to the upstream promoter region of the mfa1 gene and that activity of the downstream promoter is inhibited by S. gordonii, S. sanguinis and S. mitis (Park et al., 2006) imply the complexity of regulation of mfa1 expression. It is possible that two promoters of mfa1 are regulated in response to different environmental signals. The hypothesis is currently under investigation. In conclusion, P. gingivalis fimbriae play a predominant role in the attachment of the organism to a variety of oral surfaces (Lamont & Jenkinson, 2000; Amano et al., 2004), although other surface proteins, such as gingipains, may also be involved in the bacterial colonization (Tokuda et al., 1996; Chen et al., 2001). It has been recently reported by the authors that both major fimbriae and minor fimbriae contribute to the formation of P. gingivalis biofilm (Lin et al., 2006). Major fimbriae are required for initial attachment and the minor fimbriae appear to play an important role in microcolony formation by facilitating cell-cell interactions. The data presented here provide evidence that these two distinct fimbriae are under the control of a two-component regulatory system: FimS/FimR. Expression of major fimbriae (FimA) is extremely low in the fimR mutant, and minor fimbriae production in this mutant is inhibited by least 50%. Therefore, it is proposed that FimR can be an attractive target for inhibition of P. gingivalis colonization.\n" ], "offsets": [ [ 0, 5387 ] ] } ]

[ { "id": "PMC1974823-04-Discussion_T1", "type": "Organism", "text": [ "P. gingivalis W83" ], "offsets": [ [ 200, 217 ] ], "normalized": [] }, { "id": "PMC1974823-04-Discussion_T2", "type": "Organism", "text": [ "P. gingivalis" ], "offsets": [ [ 349, 362 ] ], "normalized": [] }, { "id": "PMC1974823-04-Discussion_T3", "type": "Two-component-system", "text": [ "FimS/FimR" ], "offsets": [ [ 414, 423 ] ], "normalized": [] }, { "id": "PMC1974823-04-Discussion_T4", "type": "Protein", "text": [ "FimS" ], "offsets": [ [ 414, 418 ] ], "normalized": [] }, { "id": "PMC1974823-04-Discussion_T5", "type": "Protein", "text": [ "FimR" ], "offsets": [ [ 419, 423 ] ], "normalized": [] }, { "id": "PMC1974823-04-Discussion_T6", "type": "Protein", "text": [ "fimA" ], "offsets": [ [ 445, 449 ] ], "normalized": [] }, { "id": "PMC1974823-04-Discussion_T7", "type": "Protein", "text": [ "minor fimbriae" ], "offsets": [ [ 486, 500 ] ], "normalized": [] }, { "id": "PMC1974823-04-Discussion_T8", "type": "Protein", "text": [ "mfa1" ], "offsets": [ [ 502, 506 ] ], "normalized": [] }, { "id": "PMC1974823-04-Discussion_T9", "type": "Organism", "text": [ "fimR mutant" ], "offsets": [ [ 513, 524 ] ], "normalized": [] }, { "id": "PMC1974823-04-Discussion_T10", "type": "Protein", "text": [ "fimR" ], "offsets": [ [ 513, 517 ] ], "normalized": [] }, { "id": "PMC1974823-04-Discussion_T11", "type": "Protein", "text": [ "mfa1" ], "offsets": [ [ 596, 600 ] ], "normalized": [] }, { "id": "PMC1974823-04-Discussion_T12", "type": "Organism", "text": [ "P. gingivalis" ], "offsets": [ [ 604, 617 ] ], "normalized": [] }, { "id": "PMC1974823-04-Discussion_T13", "type": "Organism", "text": [ "fimR mutant" ], "offsets": [ [ 646, 657 ] ], "normalized": [] }, { "id": "PMC1974823-04-Discussion_T14", "type": "Protein", "text": [ "fimR" ], "offsets": [ [ 646, 650 ] ], "normalized": [] }, { "id": "PMC1974823-04-Discussion_T15", "type": "Two-component-system", "text": [ "FimS/FimR" ], "offsets": [ [ 677, 686 ] ], "normalized": [] }, { "id": "PMC1974823-04-Discussion_T16", "type": "Protein", "text": [ "FimS" ], "offsets": [ [ 677, 681 ] ], "normalized": [] }, { "id": "PMC1974823-04-Discussion_T17", "type": "Protein", "text": [ "FimR" ], "offsets": [ [ 682, 686 ] ], "normalized": [] }, { "id": "PMC1974823-04-Discussion_T18", "type": "Protein", "text": [ "mfa1" ], "offsets": [ [ 726, 730 ] ], "normalized": [] }, { "id": "PMC1974823-04-Discussion_T19", "type": "Two-component-system", "text": [ "FimS/FimR" ], "offsets": [ [ 834, 843 ] ], "normalized": [] }, { "id": "PMC1974823-04-Discussion_T20", "type": "Protein", "text": [ "FimS" ], "offsets": [ [ 834, 838 ] ], "normalized": [] }, { "id": "PMC1974823-04-Discussion_T21", "type": "Protein", "text": [ "FimR" ], "offsets": [ [ 839, 843 ] ], "normalized": [] }, { "id": "PMC1974823-04-Discussion_T22", "type": "Protein", "text": [ "fimA" ], "offsets": [ [ 970, 974 ] ], "normalized": [] }, { "id": "PMC1974823-04-Discussion_T23", "type": "Protein", "text": [ "FimR" ], "offsets": [ [ 989, 993 ] ], "normalized": [] }, { "id": "PMC1974823-04-Discussion_T24", "type": "Protein", "text": [ "FimR" ], "offsets": [ [ 1051, 1055 ] ], "normalized": [] }, { "id": "PMC1974823-04-Discussion_T25", "type": "Protein", "text": [ "fimA" ], "offsets": [ [ 1105, 1109 ] ], "normalized": [] }, { "id": "PMC1974823-04-Discussion_T26", "type": "Protein", "text": [ "FimR" ], "offsets": [ [ 1173, 1177 ] ], "normalized": [] }, { "id": "PMC1974823-04-Discussion_T27", "type": "Protein", "text": [ "mfa1" ], "offsets": [ [ 1223, 1227 ] ], "normalized": [] }, { "id": "PMC1974823-04-Discussion_T28", "type": "Protein", "text": [ "FimR" ], "offsets": [ [ 1262, 1266 ] ], "normalized": [] }, { "id": "PMC1974823-04-Discussion_T29", "type": "Protein", "text": [ "mfa1" ], "offsets": [ [ 1284, 1288 ] ], "normalized": [] }, { "id": "PMC1974823-04-Discussion_T30", "type": "Protein", "text": [ "fimA" ], "offsets": [ [ 1375, 1379 ] ], "normalized": [] }, { "id": "PMC1974823-04-Discussion_T31", "type": "Protein", "text": [ "fimA" ], "offsets": [ [ 1399, 1403 ] ], "normalized": [] }, { "id": "PMC1974823-04-Discussion_T32", "type": "Protein", "text": [ "fimA" ], "offsets": [ [ 1453, 1457 ] ], "normalized": [] }, { "id": "PMC1974823-04-Discussion_T33", "type": "Organism", "text": [ "P. gingivalis" ], "offsets": [ [ 1472, 1485 ] ], "normalized": [] }, { "id": "PMC1974823-04-Discussion_T34", "type": "Protein", "text": [ "fimA" ], "offsets": [ [ 1552, 1556 ] ], "normalized": [] }, { "id": "PMC1974823-04-Discussion_T35", "type": "Protein", "text": [ "FimR" ], "offsets": [ [ 1571, 1575 ] ], "normalized": [] }, { "id": "PMC1974823-04-Discussion_T36", "type": "Protein", "text": [ "mfa1" ], "offsets": [ [ 1691, 1695 ] ], "normalized": [] }, { "id": "PMC1974823-04-Discussion_T37", "type": "Protein", "text": [ "rFimR" ], "offsets": [ [ 2093, 2098 ] ], "normalized": [] }, { "id": "PMC1974823-04-Discussion_T38", "type": "Chemical", "text": [ "acetyl phosphate" ], "offsets": [ [ 2116, 2132 ] ], "normalized": [] }, { "id": "PMC1974823-04-Discussion_T39", "type": "Organism", "text": [ "P. gingivalis" ], "offsets": [ [ 2210, 2223 ] ], "normalized": [] }, { "id": "PMC1974823-04-Discussion_T40", "type": "Protein", "text": [ "FimR" ], "offsets": [ [ 2224, 2228 ] ], "normalized": [] }, { "id": "PMC1974823-04-Discussion_T41", "type": "Organism", "text": [ "Streptococcus mutans" ], "offsets": [ [ 2334, 2354 ] ], "normalized": [] }, { "id": "PMC1974823-04-Discussion_T42", "type": "Protein", "text": [ "CovR" ], "offsets": [ [ 2399, 2403 ] ], "normalized": [] }, { "id": "PMC1974823-04-Discussion_T43", "type": "Protein", "text": [ "FimR" ], "offsets": [ [ 2491, 2495 ] ], "normalized": [] }, { "id": "PMC1974823-04-Discussion_T44", "type": "Protein", "text": [ "mfa1" ], "offsets": [ [ 2702, 2706 ] ], "normalized": [] }, { "id": "PMC1974823-04-Discussion_T45", "type": "Protein", "text": [ "mfa1" ], "offsets": [ [ 2989, 2993 ] ], "normalized": [] 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[]

[ { "id": "PMC2682197-02-Results-06__text", "type": "abstract", "text": [ "Generation and analysis of ATP-binding-deficient Rv2623 mutants \nTo explore the relationship between the putative ATP-dependent biochemical function of Rv2623 and the growth-regulating attribute of Rv2623, we engineered mutations within the L1 (D15E) and beta4 (G117A) conserved residues that were predicted, on the basis of the crystal structure, to disrupt ATP recognition (Figure 7A). In silico replacement of the beta4 G117 side chain hydrogen with a methyl group suggested that any residue larger than glycine at this position is likely to perturb both of the conserved loop regions in contact with the nucleotide. Similarly, extension of the D15 side chain to glutamate was also predicted to interfere with the ATP-binding conformation (Figure 7A). HPLC analysis of nucleotides extracted from Rv2623D15E and Rv2623G117A revealed that the mutant proteins are indeed deficient in ATP-binding, exhibiting approximately34% (p<0.001) and approximately29% (p=0.0018) of the amount of ATP bound by wild-type Rv2623, respectively (Figure 7B). Likewise, following an overnight incubation with [alpha-33P] ATP at 4degreesC, the amount of protein-bound radioactivity, which represented a very small fraction of the total ATP binding sites, was significantly less for the mutant proteins than wild-type Rv2623 (data not shown). Importantly, thermal denaturation profiles of wild-type Rv2623, Rv2623D15E and Rv2623G117A demonstrated virtually identical Tm values, implying that the native Rv2623 fold was not destabilized by these mutations (Figure 7C). It is therefore likely that the D15E and G117A mutations produced local structural changes in the ATP binding loops that contributed directly to the reduced levels of bound ATP in comparing to wild-type Rv2623.\n" ], "offsets": [ [ 0, 1758 ] ] } ]

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[]

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[ { "id": "PMC2639726-03-Discussion-03__text", "type": "abstract", "text": [ "SlyA and SsrA/SsrB together activate transcription of the SPI-2 encoded secretion apparatus \nSlyA is a DNA-binding protein with high affinity for inverted repeat sequences [79] and the binding ability of SlyA to the ssrA promoter region was previously reported [62]. SlyA binds to a specific palindromic sequence, but also to other binding sites that do not fit a consensus sequence [79],[80]. Similarly SsrB binds upstream of ssrA in a region of the promoter typical of response regulators but has no obvious recognition site and binds within the operons that encode structural components of the type III secretion system [52],[81]. Four nucleoid-like proteins in enteric bacteria, H-NS, StpA, Hha, and YdgT have a predilection for binding to A+T rich sequences and repress transcription of SPI-2 genes (rev. in [14]). These proteins have a degenerate recognition sequence and the ability to polymerize along and bridge adjacent stretches of DNA repressing transcription apparently by occlusion of RNA polymerase. It has been shown that virulence regulator slyA, and close homologues rovA [82] and toxT [83] act to relieve the repression caused by H-NS at specific promoters [48],[70],[84],[85]. SPI-2 regulation by SsrB and SlyA may be explained in a similar mechanism where both SlyA and SsrB counteract the silencing activity of H-NS/YdgT/Hha by competing for binding to the same target sequences or by altering the structure of the DNA to promote transcription for SPI-2. Walthers et al. [52] and Feng et al. [81] found that there was no consensus SsrB binding site or distance relative to the transcription start sites and Walthers (ibid) proposes that different promoters may be activated by distinct SsrB mechanisms. Our results support this conclusion and extend the observation to slyA at least for specific SPI-2 transcripts. A proposed mechanism for activation is that SlyA competes with a repressor for binding to the promoter and subsequently facilitates RNA polymerase access [80]. This model is supported by SlyA binding sites that are located downstream of transcriptional start sites [31],[86], which is unusual for a traditional transcriptional activator. In agreement with this model, SlyA and PhoP counteract H-NS silencing at pagC [85],[87]. Thus, one explanation for the transcription we observe following over-expression of ssrB or slyA may be that both SlyA and SsrB counteract binding of small nucleoid-like proteins including both H-NS and YdgD/Hha in this A+T rich SPI-2 region [70]. This possibility may be reflected in the differences in expression of the five operons within SPI-2 following ssrB and slyA over-expression.\n" ], "offsets": [ [ 0, 2653 ] ] } ]

[ { "id": "PMC2639726-03-Discussion-03_T1", "type": "Protein", "text": [ "SlyA" ], "offsets": [ [ 0, 4 ] ], "normalized": [] }, { "id": "PMC2639726-03-Discussion-03_T2", "type": "Two-component-system", "text": [ "SsrA/SsrB" ], "offsets": [ [ 9, 18 ] ], "normalized": [] }, { "id": "PMC2639726-03-Discussion-03_T3", "type": "Protein", "text": [ "SsrA" ], "offsets": [ [ 9, 13 ] ], "normalized": [] }, { "id": "PMC2639726-03-Discussion-03_T4", "type": "Protein", "text": [ "SsrB" ], "offsets": [ [ 14, 18 ] ], "normalized": [] }, { "id": "PMC2639726-03-Discussion-03_T5", "type": "Protein", "text": [ "SlyA" ], "offsets": [ [ 93, 97 ] ], "normalized": [] }, { "id": "PMC2639726-03-Discussion-03_T6", "type": "Protein", "text": [ "SlyA" ], "offsets": [ [ 204, 208 ] ], "normalized": [] }, { "id": "PMC2639726-03-Discussion-03_T7", "type": "Protein", "text": [ "ssrA" ], "offsets": [ [ 216, 220 ] ], "normalized": [] }, { "id": "PMC2639726-03-Discussion-03_T8", "type": "Protein", "text": [ "SlyA" ], "offsets": [ [ 267, 271 ] ], "normalized": [] }, { "id": "PMC2639726-03-Discussion-03_T9", "type": "Protein", "text": [ "SsrB" ], "offsets": [ [ 404, 408 ] ], "normalized": [] }, { "id": "PMC2639726-03-Discussion-03_T10", "type": "Protein", "text": [ "ssrA" ], "offsets": [ [ 427, 431 ] ], "normalized": [] }, { "id": "PMC2639726-03-Discussion-03_T11", "type": "Protein", "text": [ "H-NS" ], "offsets": [ [ 683, 687 ] ], "normalized": [] }, { "id": "PMC2639726-03-Discussion-03_T12", "type": "Protein", "text": [ "StpA" ], "offsets": [ [ 689, 693 ] ], "normalized": [] }, { "id": "PMC2639726-03-Discussion-03_T13", "type": "Protein", "text": [ "Hha" ], "offsets": [ [ 695, 698 ] ], "normalized": [] }, { "id": "PMC2639726-03-Discussion-03_T14", "type": "Protein", "text": [ "YdgT" ], "offsets": [ [ 704, 708 ] ], "normalized": [] }, { "id": "PMC2639726-03-Discussion-03_T15", "type": "Protein", "text": [ "slyA" ], "offsets": [ [ 1058, 1062 ] ], "normalized": [] }, { "id": "PMC2639726-03-Discussion-03_T16", "type": "Protein", "text": [ "rovA" ], "offsets": [ [ 1085, 1089 ] ], "normalized": [] }, { "id": "PMC2639726-03-Discussion-03_T17", "type": "Protein", "text": [ "toxT" ], "offsets": [ [ 1099, 1103 ] ], "normalized": [] }, { "id": "PMC2639726-03-Discussion-03_T18", "type": "Protein", "text": [ "H-NS" ], "offsets": [ [ 1149, 1153 ] ], "normalized": [] }, { "id": "PMC2639726-03-Discussion-03_T19", "type": "Protein", "text": [ "SsrB" ], "offsets": [ [ 1217, 1221 ] ], "normalized": [] }, { "id": "PMC2639726-03-Discussion-03_T20", "type": "Protein", "text": [ "SlyA" ], "offsets": [ [ 1226, 1230 ] ], "normalized": [] }, { "id": "PMC2639726-03-Discussion-03_T21", "type": "Protein", "text": [ "SlyA" ], "offsets": [ [ 1282, 1286 ] ], "normalized": [] }, { "id": "PMC2639726-03-Discussion-03_T22", "type": "Protein", "text": [ "SsrB" ], "offsets": [ [ 1291, 1295 ] ], "normalized": [] }, { "id": "PMC2639726-03-Discussion-03_T23", "type": "Protein", "text": [ "H-NS" ], "offsets": [ [ 1333, 1337 ] ], "normalized": [] }, { "id": "PMC2639726-03-Discussion-03_T24", "type": "Protein", "text": [ "YdgT" ], "offsets": [ [ 1338, 1342 ] ], "normalized": [] }, { "id": "PMC2639726-03-Discussion-03_T25", "type": "Protein", "text": [ "Hha" ], "offsets": [ [ 1343, 1346 ] ], "normalized": [] }, { "id": "PMC2639726-03-Discussion-03_T26", "type": "Protein", "text": [ "SsrB" ], "offsets": [ [ 1553, 1557 ] ], "normalized": [] }, { "id": "PMC2639726-03-Discussion-03_T27", "type": "Protein", "text": [ "SsrB" ], "offsets": [ [ 1708, 1712 ] ], "normalized": [] }, { "id": "PMC2639726-03-Discussion-03_T28", "type": "Protein", "text": [ "slyA" ], "offsets": [ [ 1791, 1795 ] ], "normalized": [] }, { "id": "PMC2639726-03-Discussion-03_T29", "type": "Protein", "text": [ "SlyA" ], "offsets": [ [ 1881, 1885 ] ], "normalized": [] }, { "id": "PMC2639726-03-Discussion-03_T30", "type": "Protein", "text": [ "SlyA" ], "offsets": [ [ 2024, 2028 ] ], "normalized": [] }, { "id": "PMC2639726-03-Discussion-03_T31", "type": "Protein", "text": [ "SlyA" ], "offsets": [ [ 2205, 2209 ] ], "normalized": [] }, { "id": "PMC2639726-03-Discussion-03_T32", "type": "Protein", "text": [ "PhoP" ], "offsets": [ [ 2214, 2218 ] ], "normalized": [] }, { "id": "PMC2639726-03-Discussion-03_T33", "type": "Protein", "text": [ "H-NS" ], "offsets": [ [ 2230, 2234 ] ], "normalized": [] }, { "id": "PMC2639726-03-Discussion-03_T34", "type": "Protein", "text": [ "pagC" ], "offsets": [ [ 2248, 2252 ] ], "normalized": [] }, { "id": "PMC2639726-03-Discussion-03_T35", "type": "Protein", "text": [ "ssrB" ], "offsets": [ [ 2348, 2352 ] ], "normalized": [] }, { "id": "PMC2639726-03-Discussion-03_T36", "type": "Protein", "text": [ "slyA" ], "offsets": [ [ 2356, 2360 ] ], "normalized": [] }, { "id": "PMC2639726-03-Discussion-03_T37", "type": "Protein", "text": [ "SlyA" ], "offsets": [ [ 2378, 2382 ] ], "normalized": [] }, { "id": "PMC2639726-03-Discussion-03_T38", "type": "Protein", "text": [ "SsrB" ], "offsets": [ [ 2387, 2391 ] ], "normalized": [] }, { "id": "PMC2639726-03-Discussion-03_T39", "type": "Protein", "text": [ "H-NS" ], "offsets": [ [ 2458, 2462 ] ], "normalized": [] }, { "id": "PMC2639726-03-Discussion-03_T40", "type": "Protein", "text": [ "YdgD" ], "offsets": [ [ 2467, 2471 ] ], "normalized": [] }, { "id": "PMC2639726-03-Discussion-03_T41", "type": "Protein", "text": [ "Hha" ], "offsets": [ [ 2472, 2475 ] ], "normalized": [] }, { "id": "PMC2639726-03-Discussion-03_T42", "type": "Protein", "text": [ "ssrB" ], "offsets": [ [ 2622, 2626 ] ], "normalized": [] }, { "id": "PMC2639726-03-Discussion-03_T43", "type": "Protein", "text": [ "slyA" ], "offsets": [ [ 2631, 2635 ] ], "normalized": [] }, { "id": "PMC2639726-03-Discussion-03_T45", "type": "Entity", "text": [ "promoter region" ], "offsets": [ [ 221, 236 ] ], "normalized": [] }, { "id": "PMC2639726-03-Discussion-03_T48", "type": "Entity", "text": [ "promoter" ], "offsets": [ [ 451, 459 ] ], "normalized": [] }, { "id": "PMC2639726-03-Discussion-03_T59", "type": "Entity", "text": [ "A+T rich SPI-2 region" ], "offsets": [ [ 2484, 2505 ] ], "normalized": [] } ]

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[ "counteract" ], "offsets": [ [ 1296, 1306 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC2639726-03-Discussion-03_T23" }, { "role": "Cause", "ref_id": "PMC2639726-03-Discussion-03_E15" } ] }, { "id": "PMC2639726-03-Discussion-03_E10", "type": "Negative_regulation", "trigger": { "text": [ "counteract" ], "offsets": [ [ 1296, 1306 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC2639726-03-Discussion-03_T24" }, { "role": "Cause", "ref_id": "PMC2639726-03-Discussion-03_E16" } ] }, { "id": "PMC2639726-03-Discussion-03_E11", "type": "Negative_regulation", "trigger": { "text": [ "counteract" ], "offsets": [ [ 1296, 1306 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC2639726-03-Discussion-03_T25" }, { "role": "Cause", "ref_id": "PMC2639726-03-Discussion-03_E17" } ] }, { "id": "PMC2639726-03-Discussion-03_E12", "type": "Negative_regulation", "trigger": { "text": [ "counteract" ], "offsets": [ [ 1296, 1306 ] ] }, "arguments": [ { "role": "Theme", "ref_id": 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] }, "arguments": [ { "role": "Theme", "ref_id": "PMC2639726-03-Discussion-03_E28" }, { "role": "Cause", "ref_id": "PMC2639726-03-Discussion-03_T32" } ] }, { "id": "PMC2639726-03-Discussion-03_E28", "type": "Negative_regulation", "trigger": { "text": [ "silencing" ], "offsets": [ [ 2235, 2244 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC2639726-03-Discussion-03_T34" }, { "role": "Cause", "ref_id": "PMC2639726-03-Discussion-03_T33" } ] }, { "id": "PMC2639726-03-Discussion-03_E29", "type": "Gene_expression", "trigger": { "text": [ "over-expression" ], "offsets": [ [ 2329, 2344 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC2639726-03-Discussion-03_T35" } ] }, { "id": "PMC2639726-03-Discussion-03_E30", "type": "Gene_expression", "trigger": { "text": [ "over-expression" ], "offsets": [ [ 2329, 2344 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC2639726-03-Discussion-03_T36" } ] }, { "id": "PMC2639726-03-Discussion-03_E31", "type": "Negative_regulation", "trigger": 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"PMC2639726-03-Discussion-03_E37" }, { "role": "Cause", "ref_id": "PMC2639726-03-Discussion-03_T38" } ] }, { "id": "PMC2639726-03-Discussion-03_E35", "type": "Negative_regulation", "trigger": { "text": [ "counteract" ], "offsets": [ [ 2392, 2402 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC2639726-03-Discussion-03_E38" }, { "role": "Cause", "ref_id": "PMC2639726-03-Discussion-03_T38" } ] }, { "id": "PMC2639726-03-Discussion-03_E36", "type": "Negative_regulation", "trigger": { "text": [ "counteract" ], "offsets": [ [ 2392, 2402 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC2639726-03-Discussion-03_E39" }, { "role": "Cause", "ref_id": "PMC2639726-03-Discussion-03_T38" } ] }, { "id": "PMC2639726-03-Discussion-03_E37", "type": "Binding", "trigger": { "text": [ "binding" ], "offsets": [ [ 2403, 2410 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC2639726-03-Discussion-03_T39" }, { "role": "Site", "ref_id": "PMC2639726-03-Discussion-03_T59" } ] }, { "id": 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[]

[ { "id": "PMC2242835-00-TIAB__text", "type": "abstract", "text": [ "Control of M. tuberculosis ESAT-6 Secretion and Specific T Cell Recognition by PhoP \nAnalysis of mycobacterial strains that have lost their ability to cause disease is a powerful approach to identify yet unknown virulence determinants and pathways involved in tuberculosis pathogenesis. Two of the most widely used attenuated strains in the history of tuberculosis research are Mycobacterium bovis BCG (BCG) and Mycobacterium tuberculosis H37Ra (H37Ra), which both lost their virulence during in vitro serial passage. Whereas the attenuation of BCG is due mainly to loss of the ESAT-6 secretion system, ESX-1, the reason why H37Ra is attenuated remained unknown. However, here we show that a point mutation (S219L) in the predicted DNA binding region of the regulator PhoP is involved in the attenuation of H37Ra via a mechanism that impacts on the secretion of the major T cell antigen ESAT-6. Only H37Ra \"knock-ins\" that carried an integrated cosmid with the wild-type phoP gene from M. tuberculosis H37Rv showed changes in colony morphology, increased virulence, ESAT-6 secretion, and induction of specific T cell responses, whereas other H37Ra constructs did not. This finding established a link between the PhoP regulator and ESAT-6 secretion that opens exciting new perspectives for elucidating virulence regulation in M. tuberculosis.\n" ], "offsets": [ [ 0, 1342 ] ] } ]

[ { "id": "PMC2242835-00-TIAB_T1", "type": "Organism", "text": [ "M. tuberculosis" ], "offsets": [ [ 11, 26 ] ], "normalized": [] }, { "id": "PMC2242835-00-TIAB_T2", "type": "Protein", "text": [ "ESAT-6" ], "offsets": [ [ 27, 33 ] ], "normalized": [] }, { "id": "PMC2242835-00-TIAB_T3", "type": "Protein", "text": [ "PhoP" ], "offsets": [ [ 79, 83 ] ], "normalized": [] }, { "id": "PMC2242835-00-TIAB_T4", "type": "Organism", "text": [ "mycobacterial strains" ], "offsets": [ [ 97, 118 ] ], "normalized": [] }, { "id": "PMC2242835-00-TIAB_T5", "type": "Organism", "text": [ "Mycobacterium bovis BCG" ], "offsets": [ [ 378, 401 ] ], "normalized": [] }, { "id": "PMC2242835-00-TIAB_T6", "type": "Organism", "text": [ "BCG" ], "offsets": [ [ 403, 406 ] ], "normalized": [] }, { "id": "PMC2242835-00-TIAB_T7", "type": "Organism", "text": [ "Mycobacterium tuberculosis H37Ra" ], "offsets": [ [ 412, 444 ] ], "normalized": [] }, { "id": "PMC2242835-00-TIAB_T8", "type": "Organism", "text": [ "H37Ra" ], "offsets": [ [ 446, 451 ] ], "normalized": [] }, { "id": "PMC2242835-00-TIAB_T9", "type": "Organism", "text": [ "BCG" ], "offsets": [ [ 545, 548 ] ], "normalized": [] }, { "id": "PMC2242835-00-TIAB_T10", "type": "Protein", "text": [ "ESAT-6" ], "offsets": [ [ 578, 584 ] ], "normalized": [] }, { "id": "PMC2242835-00-TIAB_T11", "type": "Protein", "text": [ "ESX-1" ], "offsets": [ [ 603, 608 ] ], "normalized": [] }, { "id": "PMC2242835-00-TIAB_T12", "type": "Organism", "text": [ "H37Ra" ], "offsets": [ [ 625, 630 ] ], "normalized": [] }, { "id": "PMC2242835-00-TIAB_T13", "type": "Protein", "text": [ "PhoP" ], "offsets": [ [ 768, 772 ] ], "normalized": [] }, { "id": "PMC2242835-00-TIAB_T14", "type": "Organism", "text": [ "H37Ra" ], "offsets": [ [ 807, 812 ] ], "normalized": [] }, { "id": "PMC2242835-00-TIAB_T15", "type": "Protein", "text": [ "ESAT-6" ], "offsets": [ [ 887, 893 ] ], "normalized": [] }, { "id": "PMC2242835-00-TIAB_T16", "type": "Organism", "text": [ "H37Ra" ], "offsets": [ [ 900, 905 ] ], "normalized": [] }, { "id": "PMC2242835-00-TIAB_T17", "type": "Protein", "text": [ "phoP" ], "offsets": [ [ 971, 975 ] ], "normalized": [] }, { "id": "PMC2242835-00-TIAB_T18", "type": "Organism", "text": [ "M. tuberculosis H37Rv" ], "offsets": [ [ 986, 1007 ] ], "normalized": [] }, { "id": "PMC2242835-00-TIAB_T19", "type": "Protein", "text": [ "ESAT-6" ], "offsets": [ [ 1066, 1072 ] ], "normalized": [] }, { "id": "PMC2242835-00-TIAB_T20", "type": "Organism", "text": [ "H37Ra" ], "offsets": [ [ 1142, 1147 ] ], "normalized": [] }, { "id": "PMC2242835-00-TIAB_T21", "type": "Protein", "text": [ "PhoP" ], "offsets": [ [ 1212, 1216 ] ], "normalized": [] }, { "id": "PMC2242835-00-TIAB_T22", "type": "Protein", "text": [ "ESAT-6" ], "offsets": [ [ 1231, 1237 ] ], "normalized": [] }, { "id": "PMC2242835-00-TIAB_T23", "type": "Organism", "text": [ "M. tuberculosis" ], "offsets": [ [ 1325, 1340 ] ], "normalized": [] } ]

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[ { "id": "PMC2242835-00-TIAB_1", "entity_ids": [ "PMC2242835-00-TIAB_T5", "PMC2242835-00-TIAB_T6" ] }, { "id": "PMC2242835-00-TIAB_2", "entity_ids": [ "PMC2242835-00-TIAB_T7", "PMC2242835-00-TIAB_T8" ] } ]

[]

[ { "id": "PMC2774163-02-Results-03__text", "type": "abstract", "text": [ "Inactivation of two-component regulatory systems that are phosphorylated in a stage-specific manner leads to altered biofilm formation \nAs differential and sequential phosphorylation of regulatory proteins was detected over the course of P. aeruginosa biofilm development, we asked whether inactivation of these regulatory proteins would alter or affect the stage-specific progression of biofilm formation. We therefore focused on biofilm-specific regulatory proteins. Since the proteins PA4101, PA4197, and PA5511 were found to be phosphorylated following 8, 24, and 72 hr of biofilm growth, respectively (Table 1), corresponding to three biofilm developmental stages [9],[12], mutants in these three genes were chosen and allowed to form biofilms for 144 hr in flow cells to test for biofilm formation defects. Under the conditions tested, wild type P. aeruginosa biofilms reached maturity following 144 hr of growth as characterized by biofilms being composed of large microcolonies exceeding 100 microm in diameter (Fig. 2A). In contrast, PA4197 and PA4101 mutant biofilms lacked microcolonies after 144 hr of growth (Fig. 2B) and were only composed of a thin layer of cells at the substratum with an average height of 0.5 and 1.4 microm, respectively (Table 2). However, in contrast to PA4197 mutant biofilms, PA4101 mutant biofilms demonstrated the formation of some cellular aggregates which were less than 10 microm in height (Fig. 2B). Furthermore, the mutant biofilms differed significantly from wild type biofilms with respect to biomass, surface coverage, and roughness coefficient. Complementation of both PA4101 and PA4197 mutants restored biofilm formation to wild type levels (Fig. 2C, Table 2). These results allowed us to firmly conclude that the mutant biofilm phenotypes are caused by a defect in the PA4197 and PA4101 ORF. Based on the role of PA4197 in the initiation of biofilm formation, we named the PA4197 ORF Biofilm initiation Sensor (BfiS). BfiS is an unusual sensor that harbors a His kinase A domain typically found in two-component system (TCS) sensor proteins, a Histidine kinase-like ATPase domain involved in autophosphorylation but also in protein dephosphorylation events, and a PAS signal receiver domain [53]. The cognate response regulator BfiR (PA4196) harbors a CheY-like signal receiver domain and a LuxR-like DNA binding domain, which is also present in the quorum-sensing regulatory proteins LasR, RhlR, and QscR and in response regulators with established roles in biofilm formation (GacA, RocA1/SadA) [53]. BfiR also harbors region 4 of Sigma-70 (RpoD)-like sigma factors, a domain involved in binding to -35 promoter elements [53]. Due to its role in biofilm maturation, we named the PA4101 ORF Biofilm maturation Regulator (BfmR). The protein harbors an OmpR-like transcriptional regulator domain encompassing the common signal receiver and DNA-binding effector domains [53]. The cognate sensor BfmS (PA4102) is unusual in that it lacks an autophosphorylation site typically found in sensor kinases [53]. As shown in Table 1, the probable TCS regulatory protein PA5511 was phosphorylated following 72 hr of surface-associated growth. PA5511 mutant biofilms grown for 144 hr lacked clusters and microcolonies typically found in wild type biofilms following 72-144 hr of growth (Fig. 2A-B). Complementation restored biofilm formation to wild type levels (Fig. 2C, Table 2). However, when placed in a PAO1 background (PAO1/pJN5511), overexpression of PA5511 resulted in biofilms composed of large microcolonies exceeding 250 microm in diameter (compared to an average cluster diameter of 150 microm in P. aeruginosa PAO1, Fig. 2A, D). Since cluster formation correlated with PA5511 expression levels, we named PA5511 Microcolony formation Regulator (MifR). MifR harbors a CheY-like receiver and a sigma-54 interaction domain [53]. The protein is on average 30-50% identical to known P. aeruginosa NtrC-like enhancer binding proteins including PilR, FleQ, FleR, AlgB, CbrB, and NtrC [53],[54]. The cognate sensor (MifS, PA5512) is a typical sensor kinase harboring both a His kinase A and a His kinase-like ATPase domain [53]. Since individual carbon and nitrogen sources have been demonstrated to modulate P. aeruginosa in vitro biofilm development and architecture [16], [55]-[58], surface motility [59] and P. aeruginosa cell-cell signaling (quorum sensing) [60]-[63], the biofilm architecture of all four mutant biofilms was tested using three different media including LB medium and two minimal media containing glutamate [17] or citrate [64] as sole carbon source. Under the conditions tested, the biofilm architecture of all three mutants was similar to the biofilm architecture shown in Fig. 2 independent of the media used.\n" ], "offsets": [ [ 0, 4778 ] ] } ]

[ { "id": "PMC2774163-02-Results-03_T1", "type": "Organism", "text": [ "P. aeruginosa" ], "offsets": [ [ 238, 251 ] ], "normalized": [] }, { "id": "PMC2774163-02-Results-03_T2", "type": "Protein", "text": [ "PA4101" ], "offsets": [ [ 488, 494 ] ], "normalized": [] }, { "id": "PMC2774163-02-Results-03_T3", "type": "Protein", "text": [ "PA4197" ], "offsets": [ [ 496, 502 ] ], "normalized": [] }, { "id": "PMC2774163-02-Results-03_T4", "type": "Protein", "text": [ "PA5511" ], "offsets": [ [ 508, 514 ] ], "normalized": [] }, { "id": "PMC2774163-02-Results-03_T5", "type": "Organism", "text": [ "P. aeruginosa" ], "offsets": [ [ 852, 865 ] ], "normalized": [] }, { "id": "PMC2774163-02-Results-03_T6", "type": "Protein", "text": [ "PA4197" ], "offsets": [ [ 1043, 1049 ] ], "normalized": [] }, { "id": "PMC2774163-02-Results-03_T7", "type": "Organism", "text": [ "PA4197" ], "offsets": [ [ 1043, 1049 ] ], "normalized": [] }, { "id": "PMC2774163-02-Results-03_T8", "type": "Organism", "text": [ "PA4101 mutant" ], "offsets": [ [ 1054, 1067 ] ], "normalized": [] }, { "id": "PMC2774163-02-Results-03_T9", "type": "Protein", "text": [ "PA4101" ], "offsets": [ [ 1054, 1060 ] ], "normalized": [] }, { "id": "PMC2774163-02-Results-03_T10", "type": "Organism", "text": [ "PA4197 mutant" ], "offsets": [ [ 1291, 1304 ] ], "normalized": [] }, { "id": "PMC2774163-02-Results-03_T11", "type": "Protein", "text": [ "PA4197" ], "offsets": [ [ 1291, 1297 ] ], "normalized": [] }, { "id": "PMC2774163-02-Results-03_T12", "type": "Organism", "text": [ "PA4101 mutant" ], "offsets": [ [ 1315, 1328 ] ], "normalized": [] }, { "id": "PMC2774163-02-Results-03_T13", "type": "Protein", "text": [ "PA4101" ], "offsets": [ [ 1315, 1321 ] ], "normalized": [] }, { "id": "PMC2774163-02-Results-03_T14", "type": "Protein", "text": [ "PA4101" ], "offsets": [ [ 1619, 1625 ] ], "normalized": [] }, { "id": "PMC2774163-02-Results-03_T15", "type": "Organism", "text": [ "PA4101" ], "offsets": [ [ 1619, 1625 ] ], "normalized": [] }, { "id": "PMC2774163-02-Results-03_T16", "type": "Organism", "text": [ "PA4197 mutants" ], "offsets": [ [ 1630, 1644 ] ], "normalized": [] }, { "id": "PMC2774163-02-Results-03_T17", "type": "Protein", "text": [ "PA4197" ], "offsets": [ [ 1630, 1636 ] ], "normalized": [] }, { "id": "PMC2774163-02-Results-03_T18", "type": "Protein", "text": [ "PA4197" ], "offsets": [ [ 1821, 1827 ] ], "normalized": [] }, { "id": "PMC2774163-02-Results-03_T19", "type": "Protein", "text": [ "PA4101" ], "offsets": [ [ 1832, 1838 ] ], "normalized": [] }, { "id": "PMC2774163-02-Results-03_T20", "type": "Protein", "text": [ "PA4197" ], "offsets": [ [ 1865, 1871 ] ], "normalized": [] }, { "id": "PMC2774163-02-Results-03_T21", "type": "Protein", "text": [ "PA4197" ], "offsets": [ [ 1925, 1931 ] ], "normalized": [] }, { "id": "PMC2774163-02-Results-03_T22", "type": "Protein", "text": [ "BfiS" ], "offsets": [ [ 1970, 1974 ] ], "normalized": [] }, { "id": "PMC2774163-02-Results-03_T23", "type": "Protein", "text": [ "BfiR" ], "offsets": [ [ 2280, 2284 ] ], "normalized": [] }, { "id": "PMC2774163-02-Results-03_T24", "type": "Protein", "text": [ "PA4196" ], "offsets": [ [ 2286, 2292 ] ], "normalized": [] }, { "id": "PMC2774163-02-Results-03_T25", "type": "Protein", "text": [ "LuxR" ], "offsets": [ [ 2343, 2347 ] ], "normalized": [] }, { "id": "PMC2774163-02-Results-03_T26", "type": "Protein", "text": [ "LasR" ], "offsets": [ [ 2437, 2441 ] ], "normalized": [] }, { "id": "PMC2774163-02-Results-03_T27", "type": "Protein", "text": [ "RhlR" ], "offsets": [ [ 2443, 2447 ] ], "normalized": [] }, { "id": "PMC2774163-02-Results-03_T28", "type": "Protein", "text": [ "QscR" ], "offsets": [ [ 2453, 2457 ] ], "normalized": [] }, { "id": "PMC2774163-02-Results-03_T29", "type": "Protein", "text": [ "GacA" ], "offsets": [ [ 2530, 2534 ] ], "normalized": [] }, { "id": "PMC2774163-02-Results-03_T30", "type": "Protein", "text": [ "RocA1" ], "offsets": [ [ 2536, 2541 ] ], "normalized": [] }, { "id": "PMC2774163-02-Results-03_T31", "type": "Protein", "text": [ "SadA" ], "offsets": [ [ 2542, 2546 ] ], "normalized": [] }, { "id": "PMC2774163-02-Results-03_T32", "type": "Protein", "text": [ "BfiR" ], "offsets": [ [ 2554, 2558 ] ], "normalized": [] }, { "id": "PMC2774163-02-Results-03_T33", "type": "Protein", "text": [ "Sigma-70" ], "offsets": [ [ 2584, 2592 ] ], "normalized": [] }, { "id": "PMC2774163-02-Results-03_T34", "type": "Protein", "text": [ "RpoD" ], "offsets": [ [ 2594, 2598 ] ], "normalized": [] }, { "id": "PMC2774163-02-Results-03_T35", "type": "Protein", "text": [ "PA4101" ], "offsets": [ [ 2732, 2738 ] ], "normalized": [] }, { "id": "PMC2774163-02-Results-03_T36", "type": "Protein", "text": [ "BfmR" ], "offsets": [ [ 2773, 2777 ] ], "normalized": [] }, { "id": "PMC2774163-02-Results-03_T37", "type": "Protein", "text": [ "OmpR" ], "offsets": [ [ 2803, 2807 ] ], "normalized": [] }, { "id": "PMC2774163-02-Results-03_T38", "type": "Protein", "text": [ "BfmS" ], "offsets": [ [ 2944, 2948 ] ], "normalized": [] }, { "id": "PMC2774163-02-Results-03_T39", "type": "Protein", "text": [ "PA4102" ], "offsets": [ [ 2950, 2956 ] ], "normalized": [] }, { "id": "PMC2774163-02-Results-03_T40", "type": "Protein", "text": [ "PA5511" ], "offsets": [ [ 3111, 3117 ] ], "normalized": [] }, { "id": "PMC2774163-02-Results-03_T41", "type": "Protein", "text": [ "PA5511" ], "offsets": [ [ 3183, 3189 ] ], "normalized": [] }, { "id": "PMC2774163-02-Results-03_T42", "type": "Organism", "text": [ "PAO1" ], "offsets": [ [ 3447, 3451 ] ], "normalized": [] }, { "id": "PMC2774163-02-Results-03_T43", "type": "Organism", "text": [ "PAO1/pJN5511" ], "offsets": [ [ 3464, 3476 ] ], "normalized": [] }, { "id": "PMC2774163-02-Results-03_T44", "type": "Protein", "text": [ "PA5511" ], "offsets": [ [ 3497, 3503 ] ], "normalized": [] }, { "id": "PMC2774163-02-Results-03_T45", "type": "Organism", "text": [ "P. aeruginosa PAO1" ], "offsets": [ [ 3648, 3666 ] ], "normalized": [] }, { "id": "PMC2774163-02-Results-03_T46", "type": "Protein", "text": [ "PA5511" ], "offsets": [ [ 3721, 3727 ] ], "normalized": [] }, { "id": "PMC2774163-02-Results-03_T47", "type": "Protein", "text": [ "PA5511" ], "offsets": [ [ 3756, 3762 ] ], "normalized": [] }, { "id": "PMC2774163-02-Results-03_T48", "type": "Protein", "text": [ "MifR" ], "offsets": [ [ 3796, 3800 ] ], "normalized": [] }, { "id": "PMC2774163-02-Results-03_T49", "type": "Protein", "text": [ "MifR" ], "offsets": [ [ 3803, 3807 ] ], "normalized": [] }, { "id": "PMC2774163-02-Results-03_T50", "type": "Protein", "text": [ "CheY" ], "offsets": [ [ 3818, 3822 ] ], "normalized": [] }, { "id": "PMC2774163-02-Results-03_T51", "type": "Protein", "text": [ "sigma-54" ], "offsets": [ [ 3843, 3851 ] ], "normalized": [] }, { "id": "PMC2774163-02-Results-03_T52", "type": "Organism", "text": [ "P. aeruginosa" ], "offsets": [ [ 3929, 3942 ] ], "normalized": [] }, { "id": "PMC2774163-02-Results-03_T53", "type": "Protein", "text": [ "NtrC" ], "offsets": [ [ 3943, 3947 ] ], "normalized": [] }, { "id": "PMC2774163-02-Results-03_T54", "type": "Protein", "text": [ "PilR" ], "offsets": [ [ 3989, 3993 ] ], "normalized": [] }, { "id": "PMC2774163-02-Results-03_T55", "type": "Protein", "text": [ "FleQ" ], "offsets": [ [ 3995, 3999 ] ], "normalized": [] }, { "id": "PMC2774163-02-Results-03_T56", "type": "Protein", "text": [ "FleR" ], "offsets": [ [ 4001, 4005 ] ], "normalized": [] }, { "id": "PMC2774163-02-Results-03_T57", "type": "Protein", "text": [ "AlgB" ], "offsets": [ [ 4007, 4011 ] ], "normalized": [] }, { "id": "PMC2774163-02-Results-03_T58", "type": "Protein", "text": [ "CbrB" ], "offsets": [ [ 4013, 4017 ] ], "normalized": [] }, { "id": "PMC2774163-02-Results-03_T59", "type": "Protein", "text": [ "NtrC" ], "offsets": [ [ 4023, 4027 ] ], "normalized": [] }, { "id": "PMC2774163-02-Results-03_T60", "type": "Protein", "text": [ "MifS" ], "offsets": [ [ 4059, 4063 ] ], "normalized": [] }, { "id": "PMC2774163-02-Results-03_T61", "type": "Protein", "text": [ "PA5512" ], "offsets": [ [ 4065, 4071 ] ], "normalized": [] }, { "id": "PMC2774163-02-Results-03_T62", "type": "Chemical", "text": [ "carbon" ], "offsets": [ [ 4189, 4195 ] ], "normalized": [] }, { "id": "PMC2774163-02-Results-03_T63", "type": "Chemical", "text": [ "nitrogen" ], "offsets": [ [ 4200, 4208 ] ], "normalized": [] }, { "id": "PMC2774163-02-Results-03_T64", "type": "Organism", "text": [ "P. aeruginosa" ], "offsets": [ [ 4252, 4265 ] ], "normalized": [] }, { "id": "PMC2774163-02-Results-03_T65", "type": "Organism", "text": [ "P. aeruginosa" ], "offsets": [ [ 4355, 4368 ] ], "normalized": [] }, { "id": "PMC2774163-02-Results-03_T66", "type": "Chemical", "text": [ "carbon" ], "offsets": [ [ 4601, 4607 ] ], "normalized": [] } ]

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[]

[ { "id": "PMC2266911-02-Results_and_Discussion-02-03-02__text", "type": "abstract", "text": [ "Oxygenases and hydrolases \nP. luminescens produces proteins similar to monooxygenases, dioxygenases and hydroxylases that have been suggested to play a role in rapid elimination of insect polyphenols or in the detoxification of reactive oxygen species generated by the invaded host [24]. Examples are the product of plu4258, adjacent to a gene encoding glutathione transferase (plu4259), a putative steroid monooxygenase (Plu4232), and a glycine oxidase (Plu2242), all of which have no counterparts in Y. enterocolitica. Factors present in both pathogens are two monooxigenases encoded by ye1945/hpaC (plu0974) and ye3394/plu3599, and two hydroxylases encoded by ubiH (ye3395/plu3600) and ubiF (ye2984/plu1313). It is therefore possible that the Y. enterocolitica homologues of these enzymes are involved in persistence within the insect, a mechanism which is also used by P. luminescens.\n" ], "offsets": [ [ 0, 889 ] ] } ]

[ { "id": "PMC2266911-02-Results_and_Discussion-02-03-02_T1", "type": "Organism", "text": [ "P. luminescens" ], "offsets": [ [ 27, 41 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-02-03-02_T2", "type": "Chemical", "text": [ "polyphenols" ], "offsets": [ [ 188, 199 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-02-03-02_T3", "type": "Chemical", "text": [ "reactive oxygen species" ], "offsets": [ [ 228, 251 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-02-03-02_T4", "type": "Protein", "text": [ "plu4258" ], "offsets": [ [ 316, 323 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-02-03-02_T5", "type": "Chemical", "text": [ "glutathione" ], "offsets": [ [ 353, 364 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-02-03-02_T6", "type": "Protein", "text": [ "plu4259" ], "offsets": [ [ 378, 385 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-02-03-02_T7", "type": "Chemical", "text": [ "steroid" ], "offsets": [ [ 399, 406 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-02-03-02_T8", "type": "Protein", "text": [ "Plu4232" ], "offsets": [ [ 422, 429 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-02-03-02_T9", "type": "Protein", "text": [ "Plu2242" ], "offsets": [ [ 455, 462 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-02-03-02_T10", "type": "Organism", "text": [ "Y. enterocolitica" ], "offsets": [ [ 502, 519 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-02-03-02_T11", "type": "Protein", "text": [ "ye1945" ], "offsets": [ [ 589, 595 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-02-03-02_T12", "type": "Protein", "text": [ "hpaC" ], "offsets": [ [ 596, 600 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-02-03-02_T13", "type": "Protein", "text": [ "plu0974" ], "offsets": [ [ 602, 609 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-02-03-02_T14", "type": "Protein", "text": [ "ye3394" ], "offsets": [ [ 615, 621 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-02-03-02_T15", "type": "Protein", "text": [ "plu3599" ], "offsets": [ [ 622, 629 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-02-03-02_T16", "type": "Protein", "text": [ "ubiH" ], "offsets": [ [ 663, 667 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-02-03-02_T17", "type": "Protein", "text": [ "ye3395" ], "offsets": [ [ 669, 675 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-02-03-02_T18", "type": "Protein", "text": [ "plu3600" ], "offsets": [ [ 676, 683 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-02-03-02_T19", "type": "Protein", "text": [ "ubiF" ], "offsets": [ [ 689, 693 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-02-03-02_T20", "type": "Protein", "text": [ "ye2984" ], "offsets": [ [ 695, 701 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-02-03-02_T21", "type": "Protein", "text": [ "plu1313" ], "offsets": [ [ 702, 709 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-02-03-02_T22", "type": "Organism", "text": [ "Y. enterocolitica" ], "offsets": [ [ 746, 763 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-02-03-02_T23", "type": "Organism", "text": [ "P. luminescens" ], "offsets": [ [ 873, 887 ] ], "normalized": [] } ]

[ { "id": "PMC2266911-02-Results_and_Discussion-02-03-02_E1", "type": "Gene_expression", "trigger": { "text": [ "produces" ], "offsets": [ [ 42, 50 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC2266911-02-Results_and_Discussion-02-03-02_T4" } ] }, { "id": "PMC2266911-02-Results_and_Discussion-02-03-02_E2", "type": "Gene_expression", "trigger": { "text": [ "produces" ], "offsets": [ [ 42, 50 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC2266911-02-Results_and_Discussion-02-03-02_T6" } ] }, { "id": "PMC2266911-02-Results_and_Discussion-02-03-02_E3", "type": "Gene_expression", "trigger": { "text": [ "produces" ], "offsets": [ [ 42, 50 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC2266911-02-Results_and_Discussion-02-03-02_T8" } ] }, { "id": "PMC2266911-02-Results_and_Discussion-02-03-02_E4", "type": "Gene_expression", "trigger": { "text": [ "produces" ], "offsets": [ [ 42, 50 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC2266911-02-Results_and_Discussion-02-03-02_T9" } ] } ]

[]

[]

[ { "id": "PMC2430206-01-Background__text", "type": "abstract", "text": [ "Background \nStaphylococcus aureus, a frequent cause of human infections, is highly resistant to antimicrobial factors of the innate immune system such as cationic antimicrobial peptides (CAMPs) [1,2] which are produced by epithelial cells and neutrophils [3,4]. These peptides generally contain 10-50 amino acids and have positive net charges [5]. Due to their cationic properties, CAMPs can easily bind to the highly negatively charged bacterial cell envelope and inactivate bacteria, e.g. by forming pores in the bacterial membrane leading to bacterial lysis [6]. S. aureus has evolved mechanisms to alter the anionic charge of cell surface components to gain resistance to a broad variety of cationic antimicrobial factors such as CAMPs [7], phospholipase A2 [8], myeloperoxidase [9], or lysozyme [10]. One such mechanism is based upon modification of phospholipids in the cytoplasmic membrane by introducing a positively charged lysyl group into anionic phosphatidylglycerol by the MprF protein, thereby neutralizing the net charge of the membrane surface [11,12]. A similar reaction is mediated by products of the dltABCD operon, which are responsible for attachment of positively charged D-alanine residues into negatively charged phosphate groups in the backbone of teichoic acids [7,9]. Mechanisms involved in the regulation of these resistance factors are not yet well understood in Gram-positive bacteria. Herbert et al. recently found that the S. aureus two-component regulatory system graRS positively regulates expression of the dlt operon. In a S. aureus SA113 graRS deletion mutant, the content of D-alanine in teichoic acids was reduced by 47% and the mutant showed reduced resistance to various antibiotics including polymyxin B, gallidermin, and vancomycin [10,13]. Accordingly, graRS have previously been implicated in regulation of vancomycin intermediary resistance [14]. As the dlt operon plays a key role in S. aureus resistance to cationic antimicrobial host molecules, the graRS system may be important in evasion of host defense mechanisms such as cationic antimicrobial peptides and neutrophil killing.\n" ], "offsets": [ [ 0, 2130 ] ] } ]

[ { "id": "PMC2430206-01-Background_T1", "type": "Organism", "text": [ "Staphylococcus aureus" ], "offsets": [ [ 12, 33 ] ], "normalized": [] }, { "id": "PMC2430206-01-Background_T2", "type": "Organism", "text": [ "human" ], "offsets": [ [ 55, 60 ] ], "normalized": [] }, { "id": "PMC2430206-01-Background_T3", "type": "Organism", "text": [ "S. aureus" ], "offsets": [ [ 566, 575 ] ], "normalized": [] }, { "id": "PMC2430206-01-Background_T4", "type": "Protein", "text": [ "phospholipase A2" ], "offsets": [ [ 745, 761 ] ], "normalized": [] }, { "id": "PMC2430206-01-Background_T5", "type": "Protein", "text": [ "myeloperoxidase" ], "offsets": [ [ 767, 782 ] ], "normalized": [] }, { "id": "PMC2430206-01-Background_T6", "type": "Chemical", "text": [ "phosphatidylglycerol" ], "offsets": [ [ 958, 978 ] ], "normalized": [] }, { "id": "PMC2430206-01-Background_T7", "type": "Protein", "text": [ "MprF" ], "offsets": [ [ 986, 990 ] ], "normalized": [] }, { "id": "PMC2430206-01-Background_T8", "type": "Regulon-operon", "text": [ "dltABCD" ], "offsets": [ [ 1119, 1126 ] ], "normalized": [] }, { "id": "PMC2430206-01-Background_T9", "type": "Protein", "text": [ "dltA" ], "offsets": [ [ 1119, 1123 ] ], "normalized": [] }, { "id": "PMC2430206-01-Background_T10", "type": "Protein", "text": [ "B" ], "offsets": [ [ 1123, 1124 ] ], "normalized": [] }, { "id": "PMC2430206-01-Background_T11", "type": "Protein", "text": [ "C" ], "offsets": [ [ 1124, 1125 ] ], "normalized": [] }, { "id": "PMC2430206-01-Background_T12", "type": "Protein", "text": [ "D" ], "offsets": [ [ 1125, 1126 ] ], "normalized": [] }, { "id": "PMC2430206-01-Background_T13", "type": "Chemical", "text": [ "teichoic acids" ], "offsets": [ [ 1273, 1287 ] ], "normalized": [] }, { "id": "PMC2430206-01-Background_T14", "type": "Organism", "text": [ "S. aureus" ], "offsets": [ [ 1455, 1464 ] ], "normalized": [] }, { "id": "PMC2430206-01-Background_T15", "type": "Two-component-system", "text": [ "graRS" ], "offsets": [ [ 1497, 1502 ] ], "normalized": [] }, { "id": "PMC2430206-01-Background_T16", "type": "Protein", "text": [ "graR" ], "offsets": [ [ 1497, 1501 ] ], "normalized": [] }, { "id": "PMC2430206-01-Background_T17", "type": "Protein", "text": [ "S" ], "offsets": [ [ 1501, 1502 ] ], "normalized": [] }, { "id": "PMC2430206-01-Background_T18", "type": "Regulon-operon", "text": [ "dlt" ], "offsets": [ [ 1542, 1545 ] ], "normalized": [] }, { "id": "PMC2430206-01-Background_T19", "type": "Organism", "text": [ "S. aureus SA113 graRS deletion mutant" ], "offsets": [ [ 1559, 1596 ] ], "normalized": [] }, { "id": "PMC2430206-01-Background_T20", "type": "Two-component-system", "text": [ "graRS" ], "offsets": [ [ 1575, 1580 ] ], "normalized": [] }, { "id": "PMC2430206-01-Background_T21", "type": "Protein", "text": [ "graR" ], "offsets": [ [ 1575, 1579 ] ], "normalized": [] }, { "id": "PMC2430206-01-Background_T22", "type": "Protein", "text": [ "S" ], "offsets": [ [ 1579, 1580 ] ], "normalized": [] }, { "id": "PMC2430206-01-Background_T23", "type": "Chemical", "text": [ "teichoic acids" ], "offsets": [ [ 1626, 1640 ] ], "normalized": [] }, { "id": "PMC2430206-01-Background_T24", "type": "Chemical", "text": [ "polymyxin B" ], "offsets": [ [ 1734, 1745 ] ], "normalized": [] }, { "id": "PMC2430206-01-Background_T25", "type": "Chemical", "text": [ "gallidermin" ], "offsets": [ [ 1747, 1758 ] ], "normalized": [] }, { "id": "PMC2430206-01-Background_T26", "type": "Chemical", "text": [ "vancomycin" ], "offsets": [ [ 1764, 1774 ] ], "normalized": [] }, { "id": "PMC2430206-01-Background_T27", "type": "Two-component-system", "text": [ "graRS" ], "offsets": [ [ 1797, 1802 ] ], "normalized": [] }, { "id": "PMC2430206-01-Background_T28", "type": "Protein", "text": [ "graR" ], "offsets": [ [ 1797, 1801 ] ], "normalized": [] }, { "id": "PMC2430206-01-Background_T29", "type": "Protein", "text": [ "S" ], "offsets": [ [ 1801, 1802 ] ], "normalized": [] }, { "id": "PMC2430206-01-Background_T30", "type": "Chemical", "text": [ "vancomycin" ], "offsets": [ [ 1852, 1862 ] ], "normalized": [] }, { "id": "PMC2430206-01-Background_T31", "type": "Regulon-operon", "text": [ "dlt" ], "offsets": [ [ 1900, 1903 ] ], "normalized": [] }, { "id": "PMC2430206-01-Background_T32", "type": "Organism", "text": [ "S. aureus" ], "offsets": [ [ 1931, 1940 ] ], "normalized": [] }, { "id": "PMC2430206-01-Background_T33", "type": "Two-component-system", "text": [ "graRS" ], "offsets": [ [ 1998, 2003 ] ], "normalized": [] }, { "id": "PMC2430206-01-Background_T34", "type": "Protein", "text": [ "graR" ], "offsets": [ [ 1998, 2002 ] ], "normalized": [] }, { "id": "PMC2430206-01-Background_T35", "type": "Protein", "text": [ "S" ], "offsets": [ [ 2002, 2003 ] ], "normalized": [] } ]

[ { "id": "PMC2430206-01-Background_E1", "type": "Process", "trigger": { "text": [ "infections" ], "offsets": [ [ 61, 71 ] ] }, "arguments": [ { "role": "Participant", "ref_id": "PMC2430206-01-Background_T1" } ] }, { "id": "PMC2430206-01-Background_E2", "type": "Process", "trigger": { "text": [ "resistant" ], "offsets": [ [ 83, 92 ] ] }, "arguments": [ { "role": "Participant", "ref_id": "PMC2430206-01-Background_T1" } ] }, { "id": "PMC2430206-01-Background_E3", "type": "Process", "trigger": { "text": [ "resistance" ], "offsets": [ [ 662, 672 ] ] }, "arguments": [ { "role": "Participant", "ref_id": "PMC2430206-01-Background_T3" } ] }, { "id": "PMC2430206-01-Background_E4", "type": "Positive_regulation", "trigger": { "text": [ "responsible" ], "offsets": [ [ 1145, 1156 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC2430206-01-Background_T8" } ] }, { "id": "PMC2430206-01-Background_E5", "type": "Process", "trigger": { "text": [ "resistance" ], "offsets": [ [ 1342, 1352 ] ] }, "arguments": [] }, { "id": "PMC2430206-01-Background_E6", "type": "Positive_regulation", "trigger": { "text": [ "positively regulates" ], "offsets": [ [ 1503, 1523 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC2430206-01-Background_E7" }, { "role": "Cause", "ref_id": "PMC2430206-01-Background_T15" } ] }, { "id": "PMC2430206-01-Background_E7", "type": "Gene_expression", "trigger": { "text": [ "expression" ], "offsets": [ [ 1524, 1534 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC2430206-01-Background_T18" } ] }, { "id": "PMC2430206-01-Background_E8", "type": "Negative_regulation", "trigger": { "text": [ "reduced" ], "offsets": [ [ 1682, 1689 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC2430206-01-Background_E9" } ] }, { "id": "PMC2430206-01-Background_E9", "type": "Process", "trigger": { "text": [ "resistance" ], "offsets": [ [ 1690, 1700 ] ] }, "arguments": [ { "role": "Participant", "ref_id": "PMC2430206-01-Background_T19" } ] }, { "id": "PMC2430206-01-Background_E10", "type": "Regulation", "trigger": { "text": [ "regulation" ], "offsets": [ [ 1838, 1848 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC2430206-01-Background_E11" }, { "role": "Cause", "ref_id": "PMC2430206-01-Background_T27" } ] }, { "id": "PMC2430206-01-Background_E11", "type": "Process", "trigger": { "text": [ "resistance" ], "offsets": [ [ 1876, 1886 ] ] }, "arguments": [] }, { "id": "PMC2430206-01-Background_E12", "type": "Regulation", "trigger": { "text": [ "plays a key role" ], "offsets": [ [ 1911, 1927 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC2430206-01-Background_E13" }, { "role": "Cause", "ref_id": "PMC2430206-01-Background_T31" } ] }, { "id": "PMC2430206-01-Background_E13", "type": "Process", "trigger": { "text": [ "resistance" ], "offsets": [ [ 1941, 1951 ] ] }, "arguments": [ { "role": "Participant", "ref_id": "PMC2430206-01-Background_T32" } ] } ]

[]

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[ { "id": "PMC2829055-02-Results-Discussion-01__text", "type": "abstract", "text": [ "Results/Discussion \nTranscriptional profile of Y. pestis in the flea Little is known about the environmental conditions in the flea digestive tract, how Y. pestis adapts to them, or the physiological state of the bacteria at transmission when they exit the flea and enter the mammal. Adult fleas are obligate blood feeders and take frequent blood meals, consisting primarily of protein and lipid with relatively little carbohydrate. Flea proteases, lipases, and other digestive enzymes begin to process the blood meal in the midgut immediately after feeding, yielding amino acids and peptides, glycerol, fatty acids, and simple carbohydrates [12]. This provides the \"medium\" for Y. pestis growth, but these and other factors such as pH, oxygen tension, osmolarity, and flea antibacterial immune components are poorly defined. During the first week after being ingested in an infectious blood meal, Y. pestis grows rapidly in the flea midgut to form large bacterial aggregates. Bacterial load peaks at about 106 cells per flea as the Y. pestis biofilm accumulates in the proventriculus to cause blockage, and then plateaus [2],[3]. In this study, we determined the Y. pestis gene expression profile in infective, blocked fleas, in which the proventriculus was occluded with a mature bacterial biofilm. Y. pestis KIM6+, which lacks the 70-kb virulence plasmid that is not required for flea infection or blockage [3] was used for this analysis. Blockage occurred between 1.5 and 3.5 weeks after the initial infectious blood meal, during which time the fleas fed on uninfected mice twice weekly. The Y. pestis in vivo biofilm transcriptome was compared to the transcriptomes of in vitro biofilm and planktonic cultures grown at 21degreesC, the same temperature at which the fleas were maintained. Expression of 55% of Y. pestis ORFs was detected in the flea samples; and 74 to 79% in the in vitro biofilm, exponential phase planktonic and stationary phase planktonic cultures. Principal component analysis to visualize overall clustering of the microarray data showed that the transcriptional profiles were reproducible and discrete for the in vitro and in vivo conditions (Fig. 1A). Profiles of the exponential and stationary phase planktonic cultures clustered most closely, whereas the profiles from in vitro and in vivo biofilm growth were more distinct from each other and from the planktonic culture profiles. There were 214 Y. pestis genes whose expression was significantly upregulated and 56 genes downregulated in the flea compared to all in vitro growth conditions (Fig. 1B; Tables S1 and S2). Quantitative RT-PCR analysis of a subset of Y. pestis genes differentially expressed in the flea was confirmatory of the microarray results (Fig. S2).\n" ], "offsets": [ [ 0, 2752 ] ] } ]

[ { "id": "PMC2829055-02-Results-Discussion-01_T1", "type": "Organism", "text": [ "Y. pestis" ], "offsets": [ [ 47, 56 ] ], "normalized": [] }, { "id": "PMC2829055-02-Results-Discussion-01_T2", "type": "Organism", "text": [ "flea" ], "offsets": [ [ 64, 68 ] ], "normalized": [] }, { "id": "PMC2829055-02-Results-Discussion-01_T3", "type": "Organism", "text": [ "flea" ], "offsets": [ [ 127, 131 ] ], "normalized": [] }, { "id": "PMC2829055-02-Results-Discussion-01_T4", "type": "Organism", "text": [ "Y. pestis" ], "offsets": [ [ 153, 162 ] ], "normalized": [] }, { "id": "PMC2829055-02-Results-Discussion-01_T5", "type": "Organism", "text": [ "flea" ], "offsets": [ [ 257, 261 ] ], "normalized": [] }, { "id": "PMC2829055-02-Results-Discussion-01_T6", "type": "Organism", "text": [ "fleas" ], "offsets": [ [ 290, 295 ] ], "normalized": [] }, { "id": "PMC2829055-02-Results-Discussion-01_T7", "type": "Organism", "text": [ "Flea" ], "offsets": [ [ 433, 437 ] ], "normalized": [] }, { "id": "PMC2829055-02-Results-Discussion-01_T8", "type": "Chemical", "text": [ "glycerol" ], "offsets": [ [ 594, 602 ] ], "normalized": [] }, { "id": "PMC2829055-02-Results-Discussion-01_T9", "type": "Organism", "text": [ "Y. pestis" ], "offsets": [ [ 679, 688 ] ], "normalized": [] }, { "id": "PMC2829055-02-Results-Discussion-01_T10", "type": "Chemical", "text": [ "oxygen" ], "offsets": [ [ 737, 743 ] ], "normalized": [] }, { "id": "PMC2829055-02-Results-Discussion-01_T11", "type": "Organism", "text": [ "flea" ], "offsets": [ [ 769, 773 ] ], "normalized": [] }, { "id": "PMC2829055-02-Results-Discussion-01_T12", "type": "Organism", "text": [ "Y. pestis" ], "offsets": [ [ 898, 907 ] ], "normalized": [] }, { "id": "PMC2829055-02-Results-Discussion-01_T13", "type": "Organism", "text": [ "flea" ], "offsets": [ [ 929, 933 ] ], "normalized": [] }, { "id": "PMC2829055-02-Results-Discussion-01_T14", "type": "Organism", "text": [ "flea" ], "offsets": [ [ 1021, 1025 ] ], "normalized": [] }, { "id": "PMC2829055-02-Results-Discussion-01_T15", "type": "Organism", "text": [ "Y. pestis" ], "offsets": [ [ 1033, 1042 ] ], "normalized": [] }, { "id": "PMC2829055-02-Results-Discussion-01_T16", "type": "Organism", "text": [ "Y. pestis" ], "offsets": [ [ 1164, 1173 ] ], "normalized": [] }, { "id": "PMC2829055-02-Results-Discussion-01_T17", "type": "Organism", "text": [ "fleas" ], "offsets": [ [ 1220, 1225 ] ], "normalized": [] }, { "id": "PMC2829055-02-Results-Discussion-01_T18", "type": "Organism", "text": [ "Y. pestis KIM6+" ], "offsets": [ [ 1301, 1316 ] ], "normalized": [] }, { "id": "PMC2829055-02-Results-Discussion-01_T19", "type": "Organism", "text": [ "flea" ], "offsets": [ [ 1383, 1387 ] ], "normalized": [] }, { "id": "PMC2829055-02-Results-Discussion-01_T20", "type": "Organism", "text": [ "fleas" ], "offsets": [ [ 1549, 1554 ] ], "normalized": [] }, { "id": "PMC2829055-02-Results-Discussion-01_T21", "type": "Organism", "text": [ "mice" ], "offsets": [ [ 1573, 1577 ] ], "normalized": [] }, { "id": "PMC2829055-02-Results-Discussion-01_T22", "type": "Organism", "text": [ "Y. pestis" ], "offsets": [ [ 1596, 1605 ] ], "normalized": [] }, { "id": "PMC2829055-02-Results-Discussion-01_T23", "type": "Organism", "text": [ "fleas" ], "offsets": [ [ 1770, 1775 ] ], "normalized": [] }, { "id": "PMC2829055-02-Results-Discussion-01_T24", "type": "Organism", "text": [ "Y. pestis" ], "offsets": [ [ 1814, 1823 ] ], "normalized": [] }, { "id": "PMC2829055-02-Results-Discussion-01_T25", "type": "Organism", "text": [ "flea" ], "offsets": [ [ 1849, 1853 ] ], "normalized": [] }, { "id": "PMC2829055-02-Results-Discussion-01_T26", "type": "Organism", "text": [ "Y. pestis" ], "offsets": [ [ 2427, 2436 ] ], "normalized": [] }, { "id": "PMC2829055-02-Results-Discussion-01_T27", "type": "Organism", "text": [ "flea" ], "offsets": [ [ 2524, 2528 ] ], "normalized": [] }, { "id": "PMC2829055-02-Results-Discussion-01_T28", "type": "Organism", "text": [ "Y. pestis" ], "offsets": [ [ 2645, 2654 ] ], "normalized": [] }, { "id": "PMC2829055-02-Results-Discussion-01_T29", "type": "Organism", "text": [ "flea" ], "offsets": [ [ 2693, 2697 ] ], "normalized": [] } ]

[ { "id": "PMC2829055-02-Results-Discussion-01_E1", "type": "Process", "trigger": { "text": [ "infectious" ], "offsets": [ [ 875, 885 ] ] }, "arguments": [] }, { "id": "PMC2829055-02-Results-Discussion-01_E2", "type": "Process", "trigger": { "text": [ "infective" ], "offsets": [ [ 1201, 1210 ] ] }, "arguments": [ { "role": "Participant", "ref_id": "PMC2829055-02-Results-Discussion-01_T16" } ] }, { "id": "PMC2829055-02-Results-Discussion-01_E3", "type": "Process", "trigger": { "text": [ "virulence" ], "offsets": [ [ 1340, 1349 ] ] }, "arguments": [] }, { "id": "PMC2829055-02-Results-Discussion-01_E4", "type": "Process", "trigger": { "text": [ "infection" ], "offsets": [ [ 1388, 1397 ] ] }, "arguments": [] }, { "id": "PMC2829055-02-Results-Discussion-01_E5", "type": "Process", "trigger": { "text": [ "infectious" ], "offsets": [ [ 1504, 1514 ] ] }, "arguments": [] }, { "id": "PMC2829055-02-Results-Discussion-01_E6", "type": "Process", "trigger": { "text": [ "uninfected" ], "offsets": [ [ 1562, 1572 ] ] }, "arguments": [] } ]

[]

[]

[ { "id": "PMC2266911-02-Results_and_Discussion-02-02__text", "type": "abstract", "text": [ "Adhesins and invasins \nColonization and penetration of epithelial cells, and interaction with immune cells, are key steps during the host infection by pathogens. Many of the pathogen-receptor molecules such as Toll-like receptors or integrins are conserved between invertebrates and mammalians [79]. We therefore investigated if P. luminescens and Y. enterocolitica that interact with the midgut of diverse hosts use the same adhesion and invasive factors. The most prominent protein of Y. enterocolitica involved in attachment to and invasion of mammalian cells is Ail (YE1820) that is homologue to three P. luminescens proteins encoded by plu2481, plu2480, and plu1967, and InvA (YE2564) with high similarity to Plu2057. Further invasin genes of Y. enterocolitica with counterparts in P. luminescens are ysaV (ye3546/plu3761) and invF (ye3549/plu3775). Y. enterocolitica genes not present in P. luminescens are ye1873 encoding the adhesin YadA which is maximally expressed at 37degreesC, and the invasin genes invE, ysaH, ye3550, and ye3555. The function of the latter two in cell recognition is predicted, but has not yet been demonstrated experimentally. In contrast, P. luminescens produces several factors involved in host cell interaction without homologues in Y. enterocolitica, namely Plu2096 which is similar to lectin PA-I, Plu1561 with strong homology to a Ca2+ dependent adhesion molecule, the adhesin Plu2433 similar to a virulence factor of the Gram-negative plant pathogen Erwinia carotovora, EvF, which is involved in colonisation of the D. melanogaster gut epithelium [80], and the putative invasin Plu2064. In P. luminescens, eleven fimbrial gene cluster have been identified, four of which (V, VII, IX and X) are also present in Y. enterocolitica. Unique for the human pathogen in comparison to P. luminescens are the two fimbrial gene cluster ye2664-2668 and ye2692-2700, both of yet hypothetical function. Thus, invasin and adhesin homologues similar in the two pathogens might contribute to the infection of insect or mammalian hosts, but candidates for insect- and mammalian-specific colonization factors have also been revealed by the genome comparison performed here.\n" ], "offsets": [ [ 0, 2194 ] ] } ]

[ { "id": "PMC2266911-02-Results_and_Discussion-02-02_T1", "type": "Organism", "text": [ "P. luminescens" ], "offsets": [ [ 329, 343 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-02-02_T2", "type": "Organism", "text": [ "Y. enterocolitica" ], "offsets": [ [ 348, 365 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-02-02_T3", "type": "Organism", "text": [ "Y. enterocolitica" ], "offsets": [ [ 487, 504 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-02-02_T4", "type": "Protein", "text": [ "Ail" ], "offsets": [ [ 566, 569 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-02-02_T5", "type": "Protein", "text": [ "YE1820" ], "offsets": [ [ 571, 577 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-02-02_T6", "type": "Organism", "text": [ "P. luminescens" ], "offsets": [ [ 606, 620 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-02-02_T7", "type": "Protein", "text": [ "plu2481" ], "offsets": [ [ 641, 648 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-02-02_T8", "type": "Protein", "text": [ "plu2480" ], "offsets": [ [ 650, 657 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-02-02_T9", "type": "Protein", "text": [ "plu1967" ], "offsets": [ [ 663, 670 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-02-02_T10", "type": "Protein", "text": [ "InvA" ], "offsets": [ [ 676, 680 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-02-02_T11", "type": "Protein", "text": [ "YE2564" ], "offsets": [ [ 682, 688 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-02-02_T12", "type": "Protein", "text": [ "Plu2057" ], "offsets": [ [ 714, 721 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-02-02_T13", "type": "Organism", "text": [ "Y. enterocolitica" ], "offsets": [ [ 748, 765 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-02-02_T14", "type": "Organism", "text": [ "P. luminescens" ], "offsets": [ [ 787, 801 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-02-02_T15", "type": "Protein", "text": [ "ysaV" ], "offsets": [ [ 806, 810 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-02-02_T16", "type": "Protein", "text": [ "ye3546" ], "offsets": [ [ 812, 818 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-02-02_T17", "type": "Protein", "text": [ "plu3761" ], "offsets": [ [ 819, 826 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-02-02_T18", "type": "Protein", "text": [ "invF" ], "offsets": [ [ 832, 836 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-02-02_T19", "type": "Protein", "text": [ "ye3549" ], "offsets": [ [ 838, 844 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-02-02_T20", "type": "Protein", "text": [ "plu3775" ], "offsets": [ [ 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[]

[ { "id": "PMC2829055-01-Introduction__text", "type": "abstract", "text": [ "Introduction \nArthropod-borne transmission of bacterial pathogens is somewhat rare but has evolved in a phylogenetically diverse group that includes the rickettsiae, Borrelia spirochetes, and the gram-negative bacteria Francisella tularensis and Yersinia pestis, the plague bacillus. Y. pestis circulates among many species of wild rodents, its primary reservoir hosts, via flea bite. As it alternates between fleas and mammals, it is postulated that Y. pestis regulates gene expression appropriately to adapt to the two disparate host environments, and that different sets of genes are required to produce a transmissible infection in the flea and disease in the mammal. Many important Y. pestis virulence factors that are required for plague in mammals have been identified, and most of them are induced by a temperature shift from <26degreesC to 37degreesC, which mimics the transition from a flea to the warm-blooded host [1]. To date, only three transmission factors (genes specifically required to produce a transmissible infection in the flea) have been characterized. One, the yersinia murine toxin (ymt) gene, encodes a phospholipase D that is required for survival in the flea midgut [2]. The other two, (hmsHFRS and gmhA), are responsible for an extracellular polysaccharide and a lipopolysaccharide (LPS) core modification that are required for normal biofilm formation and blockage in the flea [3],[4]. Biofilm development in the flea digestive tract is important for biological transmission [5],[6],[7]. After being taken up in a blood meal, Y. pestis proliferates in the lumen of the flea midgut to form cohesive multicellular biofilm aggregates. In some infected fleas, the proventricular valve between the midgut and esophagus is colonized. The subsequent growth and consolidation of the adherent Y. pestis biofilm amongst the rows of cuticle-covered spines that line the proventriculus interferes with normal blood feeding, resulting in regurgitation of bacteria and transmission. Fleas with a completely blocked proventriculus make prolonged, repeated attempts to feed, increasing the opportunities for transmission. Formation of a Y. pestis biofilm in vitro and in the flea proventriculus depends on synthesis of an extracellular polysaccharide matrix (ECM) that is synthesized only at temperatures below 26degreesC [3],[7]. In common with many other bacteria, ECM synthesis in Y. pestis is controlled by intracellular levels of cyclic di-GMP, which are determined by competing activities of the hmsT diguanylate cyclase and hmsP phosphodiesterase gene products [8],[9]. Bacterial adhesins are typically required for initial adherence and autoaggregation in biofilm development [10], but such factors have yet to be identified in Y. pestis. In a previous study, we reported the in vivo gene expression profile of Y. pestis during bubonic plague in rats [11]. In this study, we characterized the Y. pestis transcriptome in blocked Xenopsylla cheopis rat fleas, an important vector of plague to humans. Comparing the Y. pestis gene expression profile in the flea to those of in vitro biofilm and planktonic cells cultured at the low temperature typical of the flea implicated several genes in a flea-specific adaptive response and in proventricular blockage. In addition, comparing the gene expression patterns in the flea and in the rat bubo confirmed that distinct subsets of genes are differentially expressed during the Y. pestis life cycle. Notably, several genes with known or predicted roles in protection against the mammalian innate immune system and in pathogenesis were upregulated in the flea, suggesting that transit through the insect vector preinduces a phenotype that enhances Y. pestis survival and dissemination in the mammal after flea-borne transmission.\n" ], "offsets": [ [ 0, 3794 ] ] } ]

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"PMC2829055-01-Introduction_T8", "type": "Organism", "text": [ "fleas" ], "offsets": [ [ 410, 415 ] ], "normalized": [] }, { "id": "PMC2829055-01-Introduction_T9", "type": "Organism", "text": [ "Y. pestis" ], "offsets": [ [ 451, 460 ] ], "normalized": [] }, { "id": "PMC2829055-01-Introduction_T10", "type": "Organism", "text": [ "host" ], "offsets": [ [ 531, 535 ] ], "normalized": [] }, { "id": "PMC2829055-01-Introduction_T11", "type": "Organism", "text": [ "flea" ], "offsets": [ [ 640, 644 ] ], "normalized": [] }, { "id": "PMC2829055-01-Introduction_T12", "type": "Organism", "text": [ "Y. pestis" ], "offsets": [ [ 687, 696 ] ], "normalized": [] }, { "id": "PMC2829055-01-Introduction_T13", "type": "Organism", "text": [ "flea" ], "offsets": [ [ 896, 900 ] ], "normalized": [] }, { "id": "PMC2829055-01-Introduction_T14", "type": "Organism", "text": [ "flea" ], "offsets": [ [ 1045, 1049 ] ], "normalized": [] }, { "id": "PMC2829055-01-Introduction_T15", "type": "Protein", "text": [ "yersinia murine toxin" ], "offsets": [ [ 1086, 1107 ] ], "normalized": [] }, { "id": "PMC2829055-01-Introduction_T16", "type": "Protein", "text": [ "ymt" ], "offsets": [ [ 1109, 1112 ] ], "normalized": [] }, { "id": "PMC2829055-01-Introduction_T17", "type": "Protein", "text": [ "phospholipase D" ], "offsets": [ [ 1130, 1145 ] ], "normalized": [] }, { "id": "PMC2829055-01-Introduction_T18", "type": "Organism", "text": [ "flea" ], "offsets": [ [ 1183, 1187 ] ], "normalized": [] }, { "id": "PMC2829055-01-Introduction_T19", "type": "Regulon-operon", "text": [ "hmsHFRS" ], "offsets": [ [ 1216, 1223 ] ], "normalized": [] }, { "id": "PMC2829055-01-Introduction_T20", "type": "Protein", "text": [ "gmhA" ], "offsets": [ [ 1228, 1232 ] ], "normalized": [] }, { "id": "PMC2829055-01-Introduction_T21", "type": "Chemical", "text": [ "lipopolysaccharide" ], "offsets": [ [ 1293, 1311 ] ], "normalized": [] }, { "id": "PMC2829055-01-Introduction_T22", "type": "Chemical", "text": [ "LPS" ], "offsets": [ [ 1313, 1316 ] ], "normalized": [] }, { "id": "PMC2829055-01-Introduction_T23", "type": "Organism", "text": [ "flea" ], "offsets": [ [ 1403, 1407 ] ], "normalized": [] }, { "id": "PMC2829055-01-Introduction_T24", "type": "Organism", "text": [ "flea" ], "offsets": [ [ 1444, 1448 ] ], "normalized": [] }, { "id": "PMC2829055-01-Introduction_T25", "type": "Organism", "text": [ "Y. pestis" ], "offsets": [ [ 1557, 1566 ] ], "normalized": [] }, { "id": "PMC2829055-01-Introduction_T26", "type": "Organism", "text": [ "flea" ], "offsets": [ [ 1600, 1604 ] ], "normalized": [] }, { "id": "PMC2829055-01-Introduction_T27", "type": "Organism", "text": [ "fleas" ], "offsets": [ [ 1680, 1685 ] ], "normalized": [] }, { "id": "PMC2829055-01-Introduction_T28", "type": "Organism", "text": [ "Y. pestis" ], "offsets": [ [ 1815, 1824 ] ], "normalized": [] }, { "id": "PMC2829055-01-Introduction_T29", "type": "Organism", "text": [ "Fleas" ], "offsets": [ [ 2000, 2005 ] ], "normalized": [] }, { "id": "PMC2829055-01-Introduction_T30", "type": "Organism", "text": [ "Y. pestis" ], "offsets": [ [ 2152, 2161 ] ], "normalized": [] }, { "id": "PMC2829055-01-Introduction_T31", "type": "Organism", "text": [ "flea" ], "offsets": [ [ 2190, 2194 ] ], "normalized": [] }, { "id": "PMC2829055-01-Introduction_T32", "type": "Organism", "text": [ "Y. pestis" ], "offsets": [ [ 2399, 2408 ] ], "normalized": [] }, { "id": "PMC2829055-01-Introduction_T33", "type": "Chemical", "text": [ "di-GMP" ], "offsets": [ [ 2457, 2463 ] ], "normalized": [] }, { "id": "PMC2829055-01-Introduction_T34", "type": "Protein", "text": [ "hmsT" ], "offsets": [ [ 2517, 2521 ] ], "normalized": [] }, { "id": "PMC2829055-01-Introduction_T35", "type": "Protein", "text": [ "diguanylate cyclase" ], "offsets": [ [ 2522, 2541 ] ], "normalized": [] }, { "id": "PMC2829055-01-Introduction_T36", "type": "Protein", "text": [ "hmsP" ], "offsets": [ [ 2546, 2550 ] ], "normalized": [] }, { "id": "PMC2829055-01-Introduction_T37", "type": "Protein", "text": [ "phosphodiesterase" ], "offsets": [ [ 2551, 2568 ] ], "normalized": [] }, { "id": "PMC2829055-01-Introduction_T38", "type": "Organism", "text": [ "Y. pestis" ], "offsets": [ [ 2751, 2760 ] ], "normalized": [] }, { "id": "PMC2829055-01-Introduction_T39", "type": "Organism", "text": [ "Y. pestis" ], "offsets": [ [ 2834, 2843 ] ], "normalized": [] }, { "id": "PMC2829055-01-Introduction_T40", "type": "Organism", "text": [ "rats" ], "offsets": [ [ 2869, 2873 ] ], "normalized": [] }, { "id": "PMC2829055-01-Introduction_T41", "type": "Organism", "text": [ "Y. pestis" ], "offsets": [ [ 2916, 2925 ] ], "normalized": [] }, { "id": "PMC2829055-01-Introduction_T42", "type": "Organism", "text": [ "Xenopsylla cheopis rat fleas" ], "offsets": [ [ 2951, 2979 ] ], "normalized": [] }, { "id": "PMC2829055-01-Introduction_T43", "type": "Organism", "text": [ "humans" ], "offsets": [ [ 3014, 3020 ] ], "normalized": [] }, { "id": "PMC2829055-01-Introduction_T44", "type": "Organism", 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"normalized": [] }, { "id": "PMC2829055-01-Introduction_T52", "type": "Organism", "text": [ "Y. pestis" ], "offsets": [ [ 3712, 3721 ] ], "normalized": [] }, { "id": "PMC2829055-01-Introduction_T53", "type": "Organism", "text": [ "flea" ], "offsets": [ [ 3769, 3773 ] ], "normalized": [] } ]

[ { "id": "PMC2829055-01-Introduction_E1", "type": "Process", "trigger": { "text": [ "infection" ], "offsets": [ [ 623, 632 ] ] }, "arguments": [] }, { "id": "PMC2829055-01-Introduction_E2", "type": "Process", "trigger": { "text": [ "virulence" ], "offsets": [ [ 697, 706 ] ] }, "arguments": [ { "role": "Participant", "ref_id": "PMC2829055-01-Introduction_T12" } ] }, { "id": "PMC2829055-01-Introduction_E3", "type": "Process", "trigger": { "text": [ "infection" ], "offsets": [ [ 1028, 1037 ] ] }, "arguments": [] }, { "id": "PMC2829055-01-Introduction_E4", "type": "Regulation", "trigger": { "text": [ "responsible" ], "offsets": [ [ 1239, 1250 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC2829055-01-Introduction_T19" } ] }, { "id": "PMC2829055-01-Introduction_E5", "type": "Regulation", "trigger": { "text": [ "responsible" ], "offsets": [ [ 1239, 1250 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC2829055-01-Introduction_T20" } ] }, { "id": "PMC2829055-01-Introduction_E6", "type": "Process", "trigger": { "text": [ "infected" ], "offsets": [ [ 1671, 1679 ] ] }, "arguments": [] }, { "id": "PMC2829055-01-Introduction_E7", "type": "Negative_regulation", "trigger": { "text": [ "competing" ], "offsets": [ [ 2489, 2498 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC2829055-01-Introduction_T34" }, { "role": "Cause", "ref_id": "PMC2829055-01-Introduction_T33" } ] }, { "id": "PMC2829055-01-Introduction_E8", "type": "Negative_regulation", "trigger": { "text": [ "competing" ], "offsets": [ [ 2489, 2498 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC2829055-01-Introduction_T36" }, { "role": "Cause", "ref_id": "PMC2829055-01-Introduction_T33" } ] } ]

[ { "id": "PMC2829055-01-Introduction_1", "entity_ids": [ "PMC2829055-01-Introduction_T16", "PMC2829055-01-Introduction_T15" ] }, { "id": "PMC2829055-01-Introduction_2", "entity_ids": [ "PMC2829055-01-Introduction_T21", "PMC2829055-01-Introduction_T22" ] } ]

[]

[ { "id": "PMC2266911-02-Results_and_Discussion-03-01__text", "type": "abstract", "text": [ "Metabolism \nWhile many specific virulence factors, which enable the microbes to overcome the various physical and biochemical barriers of the infected hosts, have been investigated in detail, little attention has been given to the metabolic requirements and substrate availability of bacteria in vivo. Both in insects and mammals, pathogens get access to host-specific nutrients, but also encounter substrate limitations such as low iron concentration. In this chapter, we focus on metabolic pathways of P. luminescens and Y. enterocolitica absent in E. coli, induced at low temperature, or already known to be virulence-associated. Degradative pathways P. luminescens and Y. enterocolitica share loci encoding several common degradation pathways that are absent in E. coli K-12, including the urease operon (ureABCEFGD), the genes involved in myo-inositol degradation, and the histidine degradation operon (hutHUCGI). These pathways might help the bacteria to gain access to sufficient amounts of substrates and thus to proliferate in the hemolymph of the insect larvae. We recently reported that the genes of the urease operon as well as a histidine ammonia lyase (ye3021/plu1240), which deaminates histidine to urocanic acid, are highly induced in Y. enterocolitica upon temperature decrease [67]. Beside arginine (5.17 mumol/g), lysine (12.23 mumol/g), serine (6.77 mumol/g) and proline (6.40 mumol/g), histidine (5.04 mumol/g) is the most abundant free amino acids in the Hyalophora gloveri fat body [98]. The synthesis of vitamin B12 that occurs only anaerobically is required for the degradation of 1,2-propanediol by the products of the pdu operon, as well as of ethanolamine by the eutABC-encoded enzymes. The cobalamine-dependent anaerobic growth of Salmonella typhimurium on both these substrates has been shown to be supported by the alternative electron acceptor tetrathionate whose respiration is facilitated by the tetrathionate reductase gene cluster ttr [99,100]. Beside S. typhimurium, all these genetic determinants were found only in few other bacteria, namely the human pathogens Listeria monocytogenes, and Clostridium perfringens [101]. Y. enterocolitica carries the genes encoding tetrathionate reductase (ttrABC) and the TCS TtrRS (YE1613-1617). The gene clusters for cobalamin synthesis and propanediol degradation are located on a 40-kb genomic island (ye2707-2750), but the eutABC operon is missing. Propanediol degradation by Y. enterocolitica might also be supported by YE4187 with a putative GlcG domain which is predicted to be involved in glycolate and propanediol utilization. The cobalamine synthesis genes and the eutABC operon, but not ttrC, ttrR, ttrS and the propanediol utilization gene cluster, are also present in the genome of P. luminescens, suggesting the degradation of phosphatidylethanolamine as additional energy source in the insect host [102]. Further metabolic genes common to both pathogens are dctA responsible for transport of C4- dicarboxylates across the membrane, the UhpABC regulatory system controlling the hexose phosphate transport by UhpT, and the three Mg2+ transport systems CorA, MgtA and MgtB. The uhpABC operon as well as mgtC encoding the Mg2+ transport ATPase subunit have been found to be induced at low temperature in Y. enterocolitica [67], indicating a relevance for these metabolic genes for P. luminescens and Y. enterocolitica during insect infection. Another gene, gltP encoding a glutamate-aspartate symporter, is also up-regulated at low temperature in Y. enterocolitica, but lacks a counterpart in P. luminescens. Furthermore, both insecticidal bacteria produce a chitin-binding-like protein (Plu2352, YE3576), but chitinase-like proteins (Plu2235, Plu2458 and Plu2461) are without homologues in Y. enterocolitica. This fact correlates once more with the separate lifestyle of both bacteria, e.g. association with the host and persistence for Y. enterocolitica, and association and bioconversion of the insect in case of P. luminescens.\n" ], "offsets": [ [ 0, 4018 ] ] } ]

[ { "id": "PMC2266911-02-Results_and_Discussion-03-01_T1", "type": "Organism", "text": [ "P. luminescens" ], "offsets": [ [ 504, 518 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-03-01_T2", "type": "Organism", "text": [ "Y. enterocolitica" ], "offsets": [ [ 523, 540 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-03-01_T3", "type": "Organism", "text": [ "E. coli" ], "offsets": [ [ 551, 558 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-03-01_T4", "type": "Organism", "text": [ "P. luminescens" ], "offsets": [ [ 654, 668 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-03-01_T5", "type": "Organism", "text": [ "Y. enterocolitica" ], "offsets": [ [ 673, 690 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-03-01_T6", "type": "Organism", "text": [ "E. coli K-12" ], "offsets": [ [ 766, 778 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-03-01_T7", "type": "Regulon-operon", "text": [ "ureABCEFGD" ], "offsets": [ [ 809, 819 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-03-01_T8", "type": "Protein", "text": [ "ureA" ], "offsets": [ [ 809, 813 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-03-01_T9", "type": "Protein", "text": [ "B" ], "offsets": [ [ 813, 814 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-03-01_T10", "type": "Protein", "text": [ "C" ], "offsets": [ [ 814, 815 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-03-01_T11", "type": "Protein", "text": [ "E" ], "offsets": [ [ 815, 816 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-03-01_T12", "type": "Protein", "text": [ "F" ], "offsets": [ [ 816, 817 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-03-01_T13", "type": "Protein", "text": [ "G" ], "offsets": [ [ 817, 818 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-03-01_T14", "type": "Protein", "text": [ "D" ], "offsets": [ [ 818, 819 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-03-01_T15", "type": "Regulon-operon", "text": [ "hutHUCGI" ], "offsets": [ [ 908, 916 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-03-01_T16", "type": "Protein", "text": [ "hutH" ], "offsets": [ [ 908, 912 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-03-01_T17", "type": "Protein", "text": [ "U" ], "offsets": [ [ 912, 913 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-03-01_T18", "type": "Protein", "text": [ "C" ], "offsets": [ [ 913, 914 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-03-01_T19", "type": "Protein", "text": [ "G" ], "offsets": [ [ 914, 915 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-03-01_T20", "type": "Protein", "text": [ "I" ], "offsets": [ [ 915, 916 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-03-01_T21", "type": "Chemical", "text": [ "ammonia" ], "offsets": [ [ 1152, 1159 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-03-01_T22", "type": "Protein", "text": [ "ye3021" ], "offsets": [ [ 1167, 1173 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-03-01_T23", "type": "Protein", "text": [ "plu1240" ], "offsets": [ [ 1174, 1181 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-03-01_T24", "type": "Chemical", "text": [ "urocanic acid" ], "offsets": [ [ 1214, 1227 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-03-01_T25", "type": "Organism", "text": [ "Y. enterocolitica" ], "offsets": [ [ 1251, 1268 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-03-01_T26", "type": "Organism", "text": [ "Hyalophora gloveri" ], "offsets": [ [ 1477, 1495 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-03-01_T27", "type": "Chemical", "text": [ "vitamin B12" ], "offsets": [ [ 1528, 1539 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-03-01_T28", "type": "Chemical", "text": [ "1,2-propanediol" ], "offsets": [ [ 1606, 1621 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-03-01_T29", "type": "Regulon-operon", "text": [ "pdu" ], "offsets": [ [ 1645, 1648 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-03-01_T30", "type": "Chemical", "text": [ "ethanolamine" ], "offsets": [ [ 1671, 1683 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-03-01_T31", "type": "Protein", "text": [ "eutA" ], "offsets": [ [ 1691, 1695 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-03-01_T32", "type": "Protein", "text": [ "B" ], "offsets": [ [ 1695, 1696 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-03-01_T33", "type": "Protein", "text": [ "C" ], "offsets": [ [ 1696, 1697 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-03-01_T34", "type": "Chemical", "text": [ "cobalamine" ], "offsets": [ [ 1719, 1729 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-03-01_T35", "type": "Organism", "text": [ "Salmonella typhimurium" ], "offsets": [ [ 1760, 1782 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-03-01_T36", "type": "Chemical", "text": [ "tetrathionate" ], "offsets": [ [ 1876, 1889 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-03-01_T37", "type": "Chemical", "text": [ "tetrathionate" ], "offsets": [ [ 1930, 1943 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-03-01_T38", "type": "Organism", "text": [ "S. typhimurium" ], "offsets": [ [ 1988, 2002 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-03-01_T39", "type": "Organism", "text": [ "human" ], "offsets": [ [ 2085, 2090 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-03-01_T40", "type": "Organism", "text": [ "Listeria monocytogenes" ], "offsets": [ [ 2101, 2123 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-03-01_T41", "type": "Organism", "text": [ "Clostridium perfringens" ], "offsets": [ [ 2129, 2152 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-03-01_T42", "type": "Organism", "text": [ "Y. enterocolitica" ], "offsets": [ [ 2160, 2177 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-03-01_T43", "type": "Chemical", "text": [ "tetrathionate" ], "offsets": [ [ 2205, 2218 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-03-01_T44", "type": "Protein", "text": [ "ttrA" ], "offsets": [ [ 2230, 2234 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-03-01_T45", "type": "Protein", "text": [ "B" ], "offsets": [ [ 2234, 2235 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-03-01_T46", "type": "Protein", "text": [ "C" ], "offsets": [ [ 2235, 2236 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-03-01_T47", "type": "Two-component-system", "text": [ "TtrRS" ], "offsets": [ [ 2250, 2255 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-03-01_T48", "type": "Protein", "text": [ "TtrR" ], "offsets": [ [ 2250, 2254 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-03-01_T49", "type": "Protein", "text": [ "S" ], "offsets": [ [ 2254, 2255 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-03-01_T50", "type": "Protein", "text": [ "YE1613" ], "offsets": [ [ 2257, 2263 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-03-01_T51", "type": "Protein", "text": [ "1617" ], "offsets": [ [ 2264, 2268 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-03-01_T52", "type": "Chemical", "text": [ "cobalamin" ], "offsets": [ [ 2293, 2302 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-03-01_T53", "type": "Chemical", "text": [ "propanediol" ], "offsets": [ [ 2317, 2328 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-03-01_T54", "type": "Protein", "text": [ "ye2707" ], "offsets": [ [ 2380, 2386 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-03-01_T55", "type": "Protein", "text": [ "2750" ], "offsets": [ [ 2387, 2391 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-03-01_T56", "type": "Regulon-operon", "text": [ "eutABC" ], "offsets": [ [ 2402, 2408 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-03-01_T57", "type": "Protein", "text": [ "eutA" ], "offsets": [ [ 2402, 2406 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-03-01_T58", "type": "Protein", "text": [ "B" ], "offsets": [ [ 2406, 2407 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-03-01_T59", "type": "Protein", "text": [ "C" ], "offsets": [ [ 2407, 2408 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-03-01_T60", "type": "Chemical", "text": [ "Propanediol" ], "offsets": [ [ 2428, 2439 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-03-01_T61", "type": "Organism", "text": [ "Y. enterocolitica" ], "offsets": [ [ 2455, 2472 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-03-01_T62", "type": "Protein", "text": [ "YE4187" ], "offsets": [ [ 2500, 2506 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-03-01_T63", "type": "Protein", "text": [ "GlcG" ], "offsets": [ [ 2523, 2527 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-03-01_T64", "type": "Chemical", "text": [ "glycolate" ], "offsets": [ [ 2572, 2581 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-03-01_T65", "type": "Chemical", "text": [ "propanediol" ], "offsets": [ [ 2586, 2597 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-03-01_T66", "type": "Chemical", "text": [ "cobalamine" ], "offsets": [ [ 2615, 2625 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-03-01_T67", "type": "Regulon-operon", "text": [ "eutABC" ], "offsets": [ [ 2650, 2656 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-03-01_T68", "type": "Protein", "text": [ "eutA" ], "offsets": [ [ 2650, 2654 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-03-01_T69", "type": "Protein", "text": [ "B" ], "offsets": [ [ 2654, 2655 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-03-01_T70", "type": "Protein", "text": [ "C" ], "offsets": [ [ 2655, 2656 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-03-01_T71", "type": "Protein", "text": [ "ttrC" ], "offsets": [ [ 2673, 2677 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-03-01_T72", "type": "Protein", "text": [ "ttrR" ], "offsets": [ [ 2679, 2683 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-03-01_T73", "type": "Protein", "text": [ "ttrS" ], "offsets": [ [ 2685, 2689 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-03-01_T74", "type": "Chemical", "text": [ "propanediol" ], "offsets": [ [ 2698, 2709 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-03-01_T75", "type": "Organism", "text": [ "P. luminescens" ], "offsets": [ [ 2770, 2784 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-03-01_T76", "type": "Chemical", "text": [ "phosphatidylethanolamine" ], "offsets": [ [ 2816, 2840 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-03-01_T77", "type": "Protein", "text": [ "dctA" ], "offsets": [ [ 2948, 2952 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-03-01_T78", "type": "Chemical", "text": [ "C4- dicarboxylates" ], "offsets": [ [ 2982, 3000 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-03-01_T79", "type": "Protein", "text": [ "UhpA" ], "offsets": [ [ 3026, 3030 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-03-01_T80", "type": "Protein", "text": [ "B" ], "offsets": [ [ 3030, 3031 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-03-01_T81", "type": "Protein", "text": [ "C" ], "offsets": [ [ 3031, 3032 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-03-01_T82", "type": "Chemical", "text": [ "hexose phosphate" ], "offsets": [ [ 3067, 3083 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-03-01_T83", "type": "Protein", "text": [ "UhpT" ], "offsets": [ [ 3097, 3101 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-03-01_T84", "type": "Chemical", "text": [ "Mg2+" ], "offsets": [ [ 3117, 3121 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-03-01_T85", "type": "Protein", "text": [ "CorA" ], "offsets": [ [ 3140, 3144 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-03-01_T86", "type": "Protein", "text": [ "MgtA" ], "offsets": [ [ 3146, 3150 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-03-01_T87", "type": "Protein", "text": [ "MgtB" ], "offsets": [ [ 3155, 3159 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-03-01_T88", "type": "Regulon-operon", "text": [ "uhpABC" ], "offsets": [ [ 3165, 3171 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-03-01_T89", "type": "Protein", "text": [ "uhpA" ], "offsets": [ [ 3165, 3169 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-03-01_T90", "type": "Protein", "text": [ "B" ], "offsets": [ [ 3169, 3170 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-03-01_T91", "type": "Protein", "text": [ "C" ], "offsets": [ [ 3170, 3171 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-03-01_T92", "type": "Protein", "text": [ "mgtC" ], "offsets": [ [ 3190, 3194 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-03-01_T93", "type": "Chemical", "text": [ "Mg2+" ], "offsets": [ [ 3208, 3212 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-03-01_T94", "type": "Organism", "text": [ "Y. enterocolitica" ], "offsets": [ [ 3290, 3307 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-03-01_T95", "type": "Organism", "text": [ "P. luminescens" ], "offsets": [ [ 3367, 3381 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-03-01_T96", "type": "Organism", "text": [ "Y. enterocolitica" ], "offsets": [ [ 3386, 3403 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-03-01_T97", "type": "Protein", "text": [ "gltP" ], "offsets": [ [ 3443, 3447 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-03-01_T98", "type": "Organism", "text": [ "Y. enterocolitica" ], "offsets": [ [ 3533, 3550 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-03-01_T99", "type": "Organism", "text": [ "P. luminescens" ], "offsets": [ [ 3579, 3593 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-03-01_T100", "type": "Chemical", "text": [ "chitin" ], "offsets": [ [ 3645, 3651 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-03-01_T101", "type": "Protein", "text": [ "Plu2352" ], "offsets": [ [ 3674, 3681 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-03-01_T102", "type": "Protein", "text": [ "YE3576" ], "offsets": [ [ 3683, 3689 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-03-01_T103", "type": "Protein", "text": [ "Plu2235" ], "offsets": [ [ 3721, 3728 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-03-01_T104", "type": "Protein", "text": [ "Plu2458" ], "offsets": [ [ 3730, 3737 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-03-01_T105", "type": "Protein", "text": [ "Plu2461" ], "offsets": [ [ 3742, 3749 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-03-01_T106", "type": "Organism", "text": [ "Y. enterocolitica" ], "offsets": [ [ 3777, 3794 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-03-01_T107", "type": "Organism", "text": [ "Y. enterocolitica" ], "offsets": [ [ 3924, 3941 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-03-01_T108", "type": "Organism", "text": [ "P. luminescens" ], "offsets": [ [ 4002, 4016 ] ], "normalized": [] } ]

[ { "id": "PMC2266911-02-Results_and_Discussion-03-01_E1", "type": "Process", "trigger": { "text": [ "virulence" ], "offsets": [ [ 32, 41 ] ] }, "arguments": [] }, { "id": "PMC2266911-02-Results_and_Discussion-03-01_E2", "type": "Process", "trigger": { "text": [ "infected" ], "offsets": [ [ 142, 150 ] ] }, "arguments": [] }, { "id": "PMC2266911-02-Results_and_Discussion-03-01_E3", "type": "Process", "trigger": { "text": [ "virulence" ], "offsets": [ [ 611, 620 ] ] }, "arguments": [] }, { "id": "PMC2266911-02-Results_and_Discussion-03-01_E4", "type": "Positive_regulation", "trigger": { "text": [ "induced" ], "offsets": [ [ 3260, 3267 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC2266911-02-Results_and_Discussion-03-01_T88" } ] }, { "id": "PMC2266911-02-Results_and_Discussion-03-01_E5", "type": "Positive_regulation", "trigger": { "text": [ "induced" ], "offsets": [ [ 3260, 3267 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC2266911-02-Results_and_Discussion-03-01_T92" } ] }, { "id": "PMC2266911-02-Results_and_Discussion-03-01_E6", "type": "Process", "trigger": { "text": [ "infection" ], "offsets": [ [ 3418, 3427 ] ] }, "arguments": [ { "role": "Participant", "ref_id": "PMC2266911-02-Results_and_Discussion-03-01_T95" } ] }, { "id": "PMC2266911-02-Results_and_Discussion-03-01_E7", "type": "Process", "trigger": { "text": [ "infection" ], "offsets": [ [ 3418, 3427 ] ] }, "arguments": [ { "role": "Participant", "ref_id": "PMC2266911-02-Results_and_Discussion-03-01_T96" } ] }, { "id": "PMC2266911-02-Results_and_Discussion-03-01_E8", "type": "Positive_regulation", "trigger": { "text": [ "up-regulated" ], "offsets": [ [ 3498, 3510 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC2266911-02-Results_and_Discussion-03-01_T97" } ] } ]

[]

[]

[ { "id": "PMC1974823-00-TIAB__text", "type": "abstract", "text": [ "Porphyromonas gingivalis short fimbriae are regulated by a FimS/FimR two-component system \nPorphyromonas gingivalis possesses two distinct fimbriae. The long (FimA) fimbriae have been extensively studied. Expression of the fimA gene is tightly controlled by a two-component system (FimS/FimR) through a cascade regulation. The short (Mfa1) fimbriae are less understood. The authors have recently demonstrated that both fimbriae are required for formation of P. gingivalis biofilms. Here, the novel finding that FimR, a member of the two-component regulatory system, is a transcriptional activator of the mfa1 gene is promoted. Unlike the regulatory mechanism of FimA by FimR, this regulation of the mfa1 gene is accomplished by FimR directly binding to the promoter region of mfa1.\n" ], "offsets": [ [ 0, 782 ] ] } ]

[ { "id": "PMC1974823-00-TIAB_T1", "type": "Organism", "text": [ "Porphyromonas gingivalis" ], "offsets": [ [ 0, 24 ] ], "normalized": [] }, { "id": "PMC1974823-00-TIAB_T2", "type": "Two-component-system", "text": [ "FimS/FimR" ], "offsets": [ [ 59, 68 ] ], "normalized": [] }, { "id": "PMC1974823-00-TIAB_T3", "type": "Protein", "text": [ "FimS" ], "offsets": [ [ 59, 63 ] ], "normalized": [] }, { "id": "PMC1974823-00-TIAB_T4", "type": "Protein", "text": [ "FimR" ], "offsets": [ [ 64, 68 ] ], "normalized": [] }, { "id": "PMC1974823-00-TIAB_T5", "type": "Organism", "text": [ "Porphyromonas gingivalis" ], "offsets": [ [ 91, 115 ] ], "normalized": [] }, { "id": "PMC1974823-00-TIAB_T6", "type": "Protein", "text": [ "FimA" ], "offsets": [ [ 159, 163 ] ], "normalized": [] }, { "id": "PMC1974823-00-TIAB_T7", "type": "Protein", "text": [ "fimA" ], "offsets": [ [ 223, 227 ] ], "normalized": [] }, { "id": "PMC1974823-00-TIAB_T8", "type": "Two-component-system", "text": [ "FimS/FimR" ], "offsets": [ [ 282, 291 ] ], "normalized": [] }, { "id": "PMC1974823-00-TIAB_T9", "type": "Protein", "text": [ "FimS" ], "offsets": [ [ 282, 286 ] ], "normalized": [] }, { "id": "PMC1974823-00-TIAB_T10", "type": "Protein", "text": [ "FimR" ], "offsets": [ [ 287, 291 ] ], "normalized": [] }, { "id": "PMC1974823-00-TIAB_T11", "type": "Protein", "text": [ "Mfa1" ], "offsets": [ [ 334, 338 ] ], "normalized": [] }, { "id": "PMC1974823-00-TIAB_T12", "type": "Organism", "text": [ "P. gingivalis" ], "offsets": [ [ 458, 471 ] ], "normalized": [] }, { "id": "PMC1974823-00-TIAB_T13", "type": "Protein", "text": [ "FimR" ], "offsets": [ [ 511, 515 ] ], "normalized": [] }, { "id": "PMC1974823-00-TIAB_T14", "type": "Protein", "text": [ "mfa1" ], "offsets": [ [ 604, 608 ] ], "normalized": [] }, { "id": "PMC1974823-00-TIAB_T15", "type": "Protein", "text": [ "FimA" ], "offsets": [ [ 662, 666 ] ], "normalized": [] }, { "id": "PMC1974823-00-TIAB_T16", "type": "Protein", "text": [ "FimR" ], "offsets": [ [ 670, 674 ] ], "normalized": [] }, { "id": "PMC1974823-00-TIAB_T17", "type": "Protein", "text": [ "mfa1" ], "offsets": [ [ 699, 703 ] ], "normalized": [] }, { "id": "PMC1974823-00-TIAB_T18", "type": "Protein", "text": [ "FimR" ], "offsets": [ [ 728, 732 ] ], "normalized": [] }, { "id": "PMC1974823-00-TIAB_T19", "type": "Protein", "text": [ "mfa1" ], "offsets": [ [ 776, 780 ] ], "normalized": [] }, { "id": "PMC1974823-00-TIAB_T26", "type": "Entity", "text": [ "promoter region" ], "offsets": [ [ 757, 772 ] ], "normalized": [] } ]

[ { "id": "PMC1974823-00-TIAB_E1", "type": "Gene_expression", "trigger": { "text": [ "Expression" ], "offsets": [ [ 205, 215 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC1974823-00-TIAB_T7" } ] }, { "id": "PMC1974823-00-TIAB_E2", "type": "Regulation", "trigger": { "text": [ "controlled" ], "offsets": [ [ 244, 254 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC1974823-00-TIAB_E1" }, { "role": "Cause", "ref_id": "PMC1974823-00-TIAB_T8" } ] }, { "id": "PMC1974823-00-TIAB_E3", "type": "Positive_regulation", "trigger": { "text": [ "promoted" ], "offsets": [ [ 617, 625 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC1974823-00-TIAB_T13" } ] }, { "id": "PMC1974823-00-TIAB_E4", "type": "Regulation", "trigger": { "text": [ "regulatory mechanism" ], "offsets": [ [ 638, 658 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC1974823-00-TIAB_T15" }, { "role": "Cause", "ref_id": "PMC1974823-00-TIAB_T16" } ] }, { "id": "PMC1974823-00-TIAB_E5", "type": "Regulation", "trigger": { "text": [ "regulation" ], "offsets": [ [ 681, 691 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC1974823-00-TIAB_T17" } ] }, { "id": "PMC1974823-00-TIAB_E6", "type": "Binding", "trigger": { "text": [ "binding" ], "offsets": [ [ 742, 749 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC1974823-00-TIAB_T18" }, { "role": "Theme", "ref_id": "PMC1974823-00-TIAB_T19" }, { "role": "Site", "ref_id": "PMC1974823-00-TIAB_T26" } ] } ]

[]

[]

[ { "id": "PMC2266911-02-Results_and_Discussion-01-03__text", "type": "abstract", "text": [ "Universal stress proteins \nUniversal stress proteins (Usp) are small soluble proteins found in bacteria, archaea and plants. The production of these proteins is induced upon global stress conditions such as nutrient starvation, heat stress, osmotic stress, oxidative stress, or the presence of toxic compounds. The protein family is divided into the UspA subfamily and the UspFG subfamily. The functional mechanism of these Usp proteins is not known [48]. Because P. luminescens and Y. enterocolitica are exposed to those stresses upon infecting and colonizing the insect host, we compared their set of Usp proteins (Table 2). Both genomes share an UspA-like (Plu0121 and YE4050) and an UspE-like (Plu2178 and YE2076) homologue. In E. coli, the sequence motif of Usp proteins is not highly conserved: UspA and UspC show a sequence identity of 37% and a homology of 57%, for example. In contrast, the UspA and the UspE homologues of P. luminescens and Y. enterocolitica are nearly similar, indicating that an identical stress response is regulated by these proteins. Homologues of these proteins are also present in P. aeruginosa, namely PA4352 and PA3309, a tandem-type Usp protein and a UspA-like protein, respectively. They are essential for survival under anaerobic growth and therefore biofilm formation, a situation cells are exposed to when colonizing the cystic fibrosis lung in hosts [49,50]. The Usp homologues of P. luminescens and Y. enterocolitica might also be important during infection of the insect host. In P. luminescens, expression of UspA has been shown to be under control of the AstS/AstR TCS, which is important for the correct timing of phase variant switching [28]. It is discussed that the AstS/AstR-system prevents or delays phenotypic variation by protecting the cell from stress [18]. Because Y. enterocolitica produces the corresponding TCS BvgS/BvgR, but is not known to switch to another phenotypic variant, the possible role of UspA in global regulation still remains to be elucidated. Phenotypic variation and thus the switch between mutualism and pathogenicity in P. luminescens is proposed to be regulated by a Ner-like and a HexA-like regulator that repress primary variant specific genes in the stage of the secondary variant [17]. Therefore, UspA might have a global importance in P. luminescens notifying stress and transmitting signals for HexA [18]. In Y. enterocolitica, the transcriptional repressor RovM (YE1343) is similar to HexA of P. luminescens (61% identity and 75% homology), and has only recently been shown to control cell invasion, virulence and motility in Y. pseudotuberculosis, Y. pestis and Y. enterocolitica [51-53]. This fact suggests a similar UspA-dependent regulatory mechanism used by the two bacteria compared here. P. luminescens, but not Y. enterocolitica, produces two members of the UspFG family, the UspG homologues Plu2030 and Plu2032 (Tab. 2), indicating a global stress response induced by those Usp proteins that is different in both organisms. It is known that UspG of E. coli interacts with the chaperonin GroEL [54], which promotes the correct folding of many cytosolic proteins [55]. A GroEL homologue is present in P. luminescens (Plu4134) which the P. luminescens UspG homologues might interact with. In contrast to P. luminescens, Y. enterocolitica encodes another member of the UspA subfamily, the UspC homologue YE2583 (Tab. 2), which is not present in P. luminescens. Therefore, an UspC mediated stress response is not assumed to play a major role in insect pathogenicity. Summarizing, the set of the shared and different Usp proteins reveals a partially similar and a partially different (fine)-regulation of the global stress response modules in P. luminescens and Y. enterocolitica. This pattern corresponds to the overlapping life cycles of both pathogens (Fig. 1). The UspA and the UspE homologues are predicted here to be relevant for insect infection, whereas UspC is assumed be more important for Y. enterocolitica in other environments/hosts. The two UspG homologues might constitute a set of Usp proteins that play a specific role in P. luminescens infection or in symbiosis with the nematode host.\n" ], "offsets": [ [ 0, 4194 ] ] } ]

[ { "id": "PMC2266911-02-Results_and_Discussion-01-03_T1", "type": "Protein", "text": [ "UspA" ], "offsets": [ [ 350, 354 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-01-03_T2", "type": "Protein", "text": [ "UspF" ], "offsets": [ [ 373, 377 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-01-03_T3", "type": "Protein", "text": [ "G" ], "offsets": [ [ 377, 378 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-01-03_T4", "type": "Organism", "text": [ "P. luminescens" ], "offsets": [ [ 464, 478 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-01-03_T5", "type": "Organism", "text": [ "Y. enterocolitica" ], "offsets": [ [ 483, 500 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-01-03_T6", "type": "Protein", "text": [ "UspA" ], "offsets": [ [ 649, 653 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-01-03_T7", "type": "Protein", "text": [ "Plu0121" ], "offsets": [ [ 660, 667 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-01-03_T8", "type": "Protein", "text": [ "YE4050" ], "offsets": [ [ 672, 678 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-01-03_T9", "type": "Protein", "text": [ "UspE" ], "offsets": [ [ 687, 691 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-01-03_T10", "type": "Protein", "text": [ "Plu2178" ], "offsets": [ [ 698, 705 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-01-03_T11", "type": "Protein", "text": [ "YE2076" ], "offsets": [ [ 710, 716 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-01-03_T12", "type": "Organism", "text": [ "E. coli" ], "offsets": [ [ 732, 739 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-01-03_T13", "type": "Protein", "text": [ "UspA" ], "offsets": [ [ 801, 805 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-01-03_T14", "type": "Protein", "text": [ "UspC" ], "offsets": [ [ 810, 814 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-01-03_T15", "type": "Protein", "text": [ "UspA" ], "offsets": [ [ 900, 904 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-01-03_T16", "type": "Protein", "text": [ "UspE" ], "offsets": [ [ 913, 917 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-01-03_T17", "type": "Organism", "text": [ "P. luminescens" ], "offsets": [ [ 932, 946 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-01-03_T18", "type": "Organism", "text": [ "Y. enterocolitica" ], "offsets": [ [ 951, 968 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-01-03_T19", "type": "Organism", "text": [ "P. aeruginosa" ], "offsets": [ [ 1115, 1128 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-01-03_T20", "type": "Protein", "text": [ "PA4352" ], "offsets": [ [ 1137, 1143 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-01-03_T21", "type": "Protein", "text": [ "PA3309" ], "offsets": [ [ 1148, 1154 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-01-03_T22", "type": "Protein", "text": [ "UspA" ], "offsets": [ [ 1188, 1192 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-01-03_T23", "type": "Organism", "text": [ "P. luminescens" ], "offsets": [ [ 1423, 1437 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-01-03_T24", "type": "Organism", "text": [ "Y. enterocolitica" ], "offsets": [ [ 1442, 1459 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-01-03_T25", "type": "Organism", "text": [ "P. luminescens" ], "offsets": [ [ 1524, 1538 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-01-03_T26", "type": "Protein", "text": [ "UspA" ], "offsets": [ [ 1554, 1558 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-01-03_T27", "type": "Two-component-system", "text": [ "AstS/AstR" ], "offsets": [ [ 1601, 1610 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-01-03_T28", "type": "Protein", "text": [ "AstS" ], "offsets": [ [ 1601, 1605 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-01-03_T29", "type": "Protein", "text": [ "AstR" ], "offsets": [ [ 1606, 1610 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-01-03_T30", "type": "Two-component-system", "text": [ "AstS/AstR" ], "offsets": [ [ 1716, 1725 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-01-03_T31", "type": "Protein", "text": [ "AstS" ], "offsets": [ [ 1716, 1720 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-01-03_T32", "type": "Protein", "text": [ "AstR" ], "offsets": [ [ 1721, 1725 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-01-03_T33", "type": "Organism", "text": [ "Y. enterocolitica" ], "offsets": [ [ 1822, 1839 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-01-03_T34", "type": "Two-component-system", "text": [ "BvgS/BvgR" ], "offsets": [ [ 1871, 1880 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-01-03_T35", "type": "Protein", "text": [ "BvgS" ], "offsets": [ [ 1871, 1875 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-01-03_T36", "type": "Protein", "text": [ "BvgR" ], "offsets": [ [ 1876, 1880 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-01-03_T37", "type": "Protein", "text": [ "UspA" ], "offsets": [ [ 1961, 1965 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-01-03_T38", "type": "Organism", "text": [ "P. luminescens" ], "offsets": [ [ 2099, 2113 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-01-03_T39", "type": "Protein", "text": [ "Ner" ], "offsets": [ [ 2147, 2150 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-01-03_T40", "type": "Protein", "text": [ "HexA" ], "offsets": [ [ 2162, 2166 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-01-03_T41", "type": "Protein", "text": [ "UspA" ], "offsets": [ [ 2281, 2285 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-01-03_T42", "type": "Organism", "text": [ "P. luminescens" ], "offsets": [ [ 2320, 2334 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-01-03_T43", "type": "Protein", "text": [ "HexA" ], "offsets": [ [ 2381, 2385 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-01-03_T44", "type": "Organism", "text": [ "Y. enterocolitica" ], "offsets": [ [ 2395, 2412 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-01-03_T45", "type": "Protein", "text": [ "RovM" ], "offsets": [ [ 2444, 2448 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-01-03_T46", "type": "Protein", "text": [ "YE1343" ], "offsets": [ [ 2450, 2456 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-01-03_T47", "type": "Protein", "text": [ "HexA" ], "offsets": [ [ 2472, 2476 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-01-03_T48", "type": "Organism", "text": [ "P. luminescens" ], "offsets": [ [ 2480, 2494 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-01-03_T49", "type": "Organism", "text": [ "Y. pseudotuberculosis" ], "offsets": [ [ 2613, 2634 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-01-03_T50", "type": "Organism", "text": [ "Y. pestis" ], "offsets": [ [ 2636, 2645 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-01-03_T51", "type": "Organism", "text": [ "Y. enterocolitica" ], "offsets": [ [ 2650, 2667 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-01-03_T52", "type": "Protein", "text": [ "UspA" ], "offsets": [ [ 2706, 2710 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-01-03_T53", "type": "Organism", "text": [ "P. luminescens" ], "offsets": [ [ 2782, 2796 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-01-03_T54", "type": "Organism", "text": [ "Y. enterocolitica" ], "offsets": [ [ 2806, 2823 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-01-03_T55", "type": "Protein", "text": [ "UspF" ], "offsets": [ [ 2853, 2857 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-01-03_T56", "type": "Protein", "text": [ "G" ], "offsets": [ [ 2857, 2858 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-01-03_T57", "type": "Protein", "text": [ "UspG" ], "offsets": [ [ 2871, 2875 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-01-03_T58", "type": "Protein", "text": [ "Plu2030" ], "offsets": [ [ 2887, 2894 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-01-03_T59", "type": "Protein", "text": [ "Plu2032" ], "offsets": [ [ 2899, 2906 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-01-03_T60", "type": "Protein", "text": [ "UspG" ], "offsets": [ [ 3037, 3041 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-01-03_T61", "type": "Organism", "text": [ "E. coli" ], "offsets": [ [ 3045, 3052 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-01-03_T62", "type": "Protein", "text": [ "GroEL" ], "offsets": [ [ 3083, 3088 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-01-03_T63", "type": "Protein", "text": [ "GroEL" ], "offsets": [ [ 3165, 3170 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-01-03_T64", "type": "Organism", "text": [ "P. luminescens" ], "offsets": [ [ 3195, 3209 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-01-03_T65", "type": "Protein", "text": [ "Plu4134" ], "offsets": [ [ 3211, 3218 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-01-03_T66", "type": "Organism", "text": [ "P. luminescens" ], "offsets": [ [ 3230, 3244 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-01-03_T67", "type": "Protein", "text": [ "UspG" ], "offsets": [ [ 3245, 3249 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-01-03_T68", "type": "Organism", "text": [ "P. luminescens" ], "offsets": [ [ 3297, 3311 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-01-03_T69", "type": "Organism", "text": [ "Y. enterocolitica" ], "offsets": [ [ 3313, 3330 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-01-03_T70", "type": "Protein", "text": [ "UspA" ], "offsets": [ [ 3361, 3365 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-01-03_T71", "type": "Protein", "text": [ "UspC" ], "offsets": [ [ 3381, 3385 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-01-03_T72", "type": "Protein", "text": [ "YE2583" ], "offsets": [ [ 3396, 3402 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-01-03_T73", "type": "Organism", "text": [ "P. luminescens" ], "offsets": [ [ 3437, 3451 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-01-03_T74", "type": "Protein", "text": [ "UspC" ], "offsets": [ [ 3467, 3471 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-01-03_T75", "type": "Organism", "text": [ "P. luminescens" ], "offsets": [ [ 3733, 3747 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-01-03_T76", "type": "Organism", "text": [ "Y. enterocolitica" ], "offsets": [ [ 3752, 3769 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-01-03_T77", "type": "Protein", "text": [ "UspA" ], "offsets": [ [ 3859, 3863 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-01-03_T78", "type": "Protein", "text": [ "UspE" ], "offsets": [ [ 3872, 3876 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-01-03_T79", "type": "Protein", "text": [ "UspC" ], "offsets": [ [ 3952, 3956 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-01-03_T80", "type": "Organism", "text": [ "Y. enterocolitica" ], "offsets": [ [ 3990, 4007 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-01-03_T81", "type": "Protein", "text": [ "UspG" ], "offsets": [ [ 4045, 4049 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-01-03_T82", "type": "Organism", "text": [ "P. luminescens" ], "offsets": [ [ 4129, 4143 ] ], "normalized": [] } ]

[ { "id": "PMC2266911-02-Results_and_Discussion-01-03_E1", "type": "Process", "trigger": { "text": [ "infecting" ], "offsets": [ [ 536, 545 ] ] }, "arguments": [ { "role": "Participant", "ref_id": "PMC2266911-02-Results_and_Discussion-01-03_T4" } ] }, { "id": "PMC2266911-02-Results_and_Discussion-01-03_E2", "type": "Process", "trigger": { "text": [ "infecting" ], "offsets": [ [ 536, 545 ] ] }, "arguments": [ { "role": "Participant", "ref_id": "PMC2266911-02-Results_and_Discussion-01-03_T5" } ] }, { "id": "PMC2266911-02-Results_and_Discussion-01-03_E3", "type": "Process", "trigger": { "text": [ "infection" ], "offsets": [ [ 1491, 1500 ] ] }, "arguments": [ { "role": "Participant", "ref_id": "PMC2266911-02-Results_and_Discussion-01-03_T23" } ] }, { "id": "PMC2266911-02-Results_and_Discussion-01-03_E4", "type": "Process", "trigger": { "text": [ "infection" ], "offsets": [ [ 1491, 1500 ] ] }, "arguments": [ { "role": "Participant", "ref_id": "PMC2266911-02-Results_and_Discussion-01-03_T24" } ] }, { "id": "PMC2266911-02-Results_and_Discussion-01-03_E5", "type": "Gene_expression", "trigger": { "text": [ "expression" ], "offsets": [ [ 1540, 1550 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC2266911-02-Results_and_Discussion-01-03_T26" } ] }, { "id": "PMC2266911-02-Results_and_Discussion-01-03_E6", "type": "Regulation", "trigger": { "text": [ "control" ], "offsets": [ [ 1586, 1593 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC2266911-02-Results_and_Discussion-01-03_E5" }, { "role": "Cause", "ref_id": "PMC2266911-02-Results_and_Discussion-01-03_T27" } ] }, { "id": "PMC2266911-02-Results_and_Discussion-01-03_E7", "type": "Regulation", "trigger": { "text": [ "control" ], "offsets": [ [ 2564, 2571 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC2266911-02-Results_and_Discussion-01-03_E10" }, { "role": "Cause", "ref_id": "PMC2266911-02-Results_and_Discussion-01-03_T45" } ] }, { "id": "PMC2266911-02-Results_and_Discussion-01-03_E8", "type": "Regulation", "trigger": { "text": [ "control" ], "offsets": [ [ 2564, 2571 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC2266911-02-Results_and_Discussion-01-03_E11" }, { "role": "Cause", "ref_id": "PMC2266911-02-Results_and_Discussion-01-03_T45" } ] }, { "id": "PMC2266911-02-Results_and_Discussion-01-03_E9", "type": "Regulation", "trigger": { "text": [ "control" ], "offsets": [ [ 2564, 2571 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC2266911-02-Results_and_Discussion-01-03_E12" }, { "role": "Cause", "ref_id": "PMC2266911-02-Results_and_Discussion-01-03_T45" } ] }, { "id": "PMC2266911-02-Results_and_Discussion-01-03_E10", "type": "Process", "trigger": { "text": [ "virulence" ], "offsets": [ [ 2587, 2596 ] ] }, "arguments": [ { "role": "Participant", "ref_id": "PMC2266911-02-Results_and_Discussion-01-03_T49" } ] }, { "id": "PMC2266911-02-Results_and_Discussion-01-03_E11", "type": "Process", "trigger": { "text": [ "virulence" ], "offsets": [ [ 2587, 2596 ] ] }, "arguments": [ { "role": "Participant", "ref_id": "PMC2266911-02-Results_and_Discussion-01-03_T50" } ] }, { "id": "PMC2266911-02-Results_and_Discussion-01-03_E12", "type": "Process", "trigger": { "text": [ "virulence" ], "offsets": [ [ 2587, 2596 ] ] }, "arguments": [ { "role": "Participant", "ref_id": "PMC2266911-02-Results_and_Discussion-01-03_T51" } ] }, { "id": "PMC2266911-02-Results_and_Discussion-01-03_E13", "type": "Gene_expression", "trigger": { "text": [ "produces" ], "offsets": [ [ 2825, 2833 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC2266911-02-Results_and_Discussion-01-03_T58" } ] }, { "id": "PMC2266911-02-Results_and_Discussion-01-03_E14", "type": "Gene_expression", "trigger": { "text": [ "produces" ], "offsets": [ [ 2825, 2833 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC2266911-02-Results_and_Discussion-01-03_T59" } ] }, { "id": "PMC2266911-02-Results_and_Discussion-01-03_E15", "type": "Gene_expression", "trigger": { "text": [ "produces" ], "offsets": [ [ 2825, 2833 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC2266911-02-Results_and_Discussion-01-03_T58" } ] }, { "id": "PMC2266911-02-Results_and_Discussion-01-03_E16", "type": "Gene_expression", "trigger": { "text": [ "produces" ], "offsets": [ [ 2825, 2833 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC2266911-02-Results_and_Discussion-01-03_T59" } ] }, { "id": "PMC2266911-02-Results_and_Discussion-01-03_E17", "type": "Binding", "trigger": { "text": [ "interacts" ], "offsets": [ [ 3053, 3062 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC2266911-02-Results_and_Discussion-01-03_T60" }, { "role": "Theme", "ref_id": "PMC2266911-02-Results_and_Discussion-01-03_T62" } ] }, { "id": "PMC2266911-02-Results_and_Discussion-01-03_E18", "type": "Process", "trigger": { "text": [ "infection" ], "offsets": [ [ 3933, 3942 ] ] }, "arguments": [] }, { "id": "PMC2266911-02-Results_and_Discussion-01-03_E19", "type": "Process", "trigger": { "text": [ "infection" ], "offsets": [ [ 4144, 4153 ] ] }, "arguments": [ { "role": "Participant", "ref_id": "PMC2266911-02-Results_and_Discussion-01-03_T82" } ] } ]

[ { "id": "PMC2266911-02-Results_and_Discussion-01-03_1", "entity_ids": [ "PMC2266911-02-Results_and_Discussion-01-03_T45", "PMC2266911-02-Results_and_Discussion-01-03_T46" ] } ]

[]

[ { "id": "PMC2565068-02-Results-01__text", "type": "abstract", "text": [ "Results \nGroup A streptococcus isolates from severe invasive infections is resistant to killing by human PMN To examine whether emm49 GAS isolated from severe invasive infection might alter human PMN function, we performed phagocytosis assay in vitro. As non-opsonized GAS was resistant to the phagocytosis by PMN [14], we opsonized GAS with human plasma in advance to the assay. As shown in Figure 1A, there was no significant difference between GAS that were isolated from non-invasive and severe invasive infections in phagocytosis by PMN (p=0.5556). However, as shown in Figure 1B, in vitro killing assay revealed that PMN killed non-invasive GAS, resulting in 15-42% of initial number of bacteria, but not invasive GAS (p=0.019). The similar results were obtained when opsonized with either FCS or human serum regardless of complements immobilization (data not shown). These results were common among all PMN donors. These data indicated that clinically isolated severe invasive GAS were phagocytosed, but escaped from killing by human PMN.\n" ], "offsets": [ [ 0, 1046 ] ] } ]

[ { "id": "PMC2565068-02-Results-01_T1", "type": "Organism", "text": [ "Group A streptococcus" ], "offsets": [ [ 9, 30 ] ], "normalized": [] }, { "id": "PMC2565068-02-Results-01_T2", "type": "Organism", "text": [ "human" ], "offsets": [ [ 99, 104 ] ], "normalized": [] }, { "id": "PMC2565068-02-Results-01_T3", "type": "Organism", "text": [ "emm49 GAS" ], "offsets": [ [ 128, 137 ] ], "normalized": [] }, { "id": "PMC2565068-02-Results-01_T4", "type": "Protein", "text": [ "emm49" ], "offsets": [ [ 128, 133 ] ], "normalized": [] }, { "id": "PMC2565068-02-Results-01_T5", "type": "Organism", "text": [ "human" ], "offsets": [ [ 190, 195 ] ], "normalized": [] }, { "id": "PMC2565068-02-Results-01_T6", "type": "Organism", "text": [ "GAS" ], "offsets": [ [ 269, 272 ] ], "normalized": [] }, { "id": "PMC2565068-02-Results-01_T7", "type": "Organism", "text": [ "GAS" ], "offsets": [ [ 333, 336 ] ], "normalized": [] }, { "id": "PMC2565068-02-Results-01_T8", "type": "Organism", "text": [ "human" ], "offsets": [ [ 342, 347 ] ], "normalized": [] }, { "id": "PMC2565068-02-Results-01_T9", "type": "Organism", "text": [ "GAS" ], "offsets": [ [ 447, 450 ] ], "normalized": [] }, { "id": "PMC2565068-02-Results-01_T10", "type": "Organism", "text": [ "non-invasive GAS" ], "offsets": [ [ 634, 650 ] ], "normalized": [] }, { "id": "PMC2565068-02-Results-01_T11", "type": "Organism", "text": [ "invasive GAS" ], "offsets": [ [ 711, 723 ] ], "normalized": [] }, { "id": "PMC2565068-02-Results-01_T12", "type": "Organism", "text": [ "human" ], "offsets": [ [ 803, 808 ] ], "normalized": [] }, { "id": "PMC2565068-02-Results-01_T13", "type": "Organism", "text": [ "invasive GAS" ], "offsets": [ [ 975, 987 ] ], "normalized": [] }, { "id": "PMC2565068-02-Results-01_T14", "type": "Organism", "text": [ "human" ], "offsets": [ [ 1035, 1040 ] ], "normalized": [] } ]

[ { "id": "PMC2565068-02-Results-01_E1", "type": "Process", "trigger": { "text": [ "infections" ], "offsets": [ [ 61, 71 ] ] }, "arguments": [ { "role": "Participant", "ref_id": "PMC2565068-02-Results-01_T1" } ] }, { "id": "PMC2565068-02-Results-01_E2", "type": "Process", "trigger": { "text": [ "infection" ], "offsets": [ [ 168, 177 ] ] }, "arguments": [ { "role": "Participant", "ref_id": "PMC2565068-02-Results-01_T3" } ] }, { "id": "PMC2565068-02-Results-01_E3", "type": "Process", "trigger": { "text": [ "infections" ], "offsets": [ [ 508, 518 ] ] }, "arguments": [ { "role": "Participant", "ref_id": "PMC2565068-02-Results-01_T9" } ] } ]

[]

[]

[ { "id": "PMC2885601-03-RESULTS-02__text", "type": "abstract", "text": [ "Recombinant SeMac and In Vitro and In Vivo Expression of SeMac \nTo characterize SeMac, the fragment of S. equi mac gene encoding mature SeMac was cloned, and recombinant SeMac was purified to >95% purity as assessed by SDS-PAGE (Fig. 3A). To assess the in vitro production of SeMac, culture supernatant of the 10 S. equi strains was prepared by the method of Lei et al. [16], resolved by SDS-PAGE, and probed by Western immunoblot with anti-SeMac mouse antisera. No SeMac was detected in all the samples (data not shown), suggesting that SeMac is not produced in vitro. To test whether SeMac is produced in vivo during S. equi infection, the presence of SeMac-specific antibody was assessed by Western immunoblot analysis with convalescent sera from 3 horses suffered from strangles and mice with experimental S. equi infection. All the convalescent sera tested had SeMac-specific antibody (Fig. 3B), indicating that SeMac is produced in vivo during infection.\n" ], "offsets": [ [ 0, 961 ] ] } ]

[ { "id": "PMC2885601-03-RESULTS-02_T1", "type": "Protein", "text": [ "SeMac" ], "offsets": [ [ 12, 17 ] ], "normalized": [] }, { "id": "PMC2885601-03-RESULTS-02_T2", "type": "Protein", "text": [ "SeMac" ], "offsets": [ [ 57, 62 ] ], "normalized": [] }, { "id": "PMC2885601-03-RESULTS-02_T3", "type": "Protein", "text": [ "SeMac" ], "offsets": [ [ 80, 85 ] ], "normalized": [] }, { "id": "PMC2885601-03-RESULTS-02_T4", "type": "Organism", "text": [ "S. equi" ], "offsets": [ [ 103, 110 ] ], "normalized": [] }, { "id": "PMC2885601-03-RESULTS-02_T5", "type": "Protein", "text": [ "mac" ], "offsets": [ [ 111, 114 ] ], "normalized": [] }, { "id": "PMC2885601-03-RESULTS-02_T6", "type": "Protein", "text": [ "SeMac" ], "offsets": [ [ 136, 141 ] ], "normalized": [] }, { "id": "PMC2885601-03-RESULTS-02_T7", "type": "Protein", "text": [ "SeMac" ], "offsets": [ [ 170, 175 ] ], "normalized": [] }, { "id": "PMC2885601-03-RESULTS-02_T8", "type": "Protein", "text": [ "SeMac" ], "offsets": [ [ 276, 281 ] ], "normalized": [] }, { "id": "PMC2885601-03-RESULTS-02_T9", "type": "Organism", "text": [ "S. equi" ], "offsets": [ [ 313, 320 ] ], "normalized": [] }, { "id": "PMC2885601-03-RESULTS-02_T10", "type": "Protein", "text": [ "SeMac" ], "offsets": [ [ 441, 446 ] ], "normalized": [] }, { "id": "PMC2885601-03-RESULTS-02_T11", "type": "Organism", "text": [ "mouse" ], "offsets": [ [ 447, 452 ] ], "normalized": [] }, { "id": "PMC2885601-03-RESULTS-02_T12", "type": "Protein", "text": [ "SeMac" ], "offsets": [ [ 466, 471 ] ], "normalized": [] }, { "id": "PMC2885601-03-RESULTS-02_T13", "type": "Protein", "text": [ "SeMac" ], "offsets": [ [ 538, 543 ] ], "normalized": [] }, { "id": "PMC2885601-03-RESULTS-02_T14", "type": "Protein", "text": [ "SeMac" ], "offsets": [ [ 586, 591 ] ], "normalized": [] }, { "id": "PMC2885601-03-RESULTS-02_T15", "type": "Organism", "text": [ "S. equi" ], "offsets": [ [ 619, 626 ] ], "normalized": [] }, { "id": "PMC2885601-03-RESULTS-02_T16", "type": "Protein", "text": [ "SeMac" ], "offsets": [ [ 654, 659 ] ], "normalized": [] }, { "id": "PMC2885601-03-RESULTS-02_T17", "type": "Organism", "text": [ "horses" ], "offsets": [ [ 752, 758 ] ], "normalized": [] }, { "id": "PMC2885601-03-RESULTS-02_T18", "type": "Organism", "text": [ "mice" ], "offsets": [ [ 787, 791 ] ], "normalized": [] }, { "id": "PMC2885601-03-RESULTS-02_T19", "type": "Organism", "text": [ "S. equi" ], "offsets": [ [ 810, 817 ] ], "normalized": [] }, { "id": "PMC2885601-03-RESULTS-02_T20", "type": "Protein", "text": [ "SeMac" ], "offsets": [ [ 866, 871 ] ], "normalized": [] }, { "id": "PMC2885601-03-RESULTS-02_T21", "type": "Protein", "text": [ "SeMac" ], "offsets": [ [ 917, 922 ] ], "normalized": [] } ]

[ { "id": "PMC2885601-03-RESULTS-02_E1", "type": "Gene_expression", "trigger": { "text": [ "Expression" ], "offsets": [ [ 43, 53 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC2885601-03-RESULTS-02_T2" } ] }, { "id": "PMC2885601-03-RESULTS-02_E2", "type": "Gene_expression", "trigger": { "text": [ "production" ], "offsets": [ [ 262, 272 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC2885601-03-RESULTS-02_T8" } ] }, { "id": "PMC2885601-03-RESULTS-02_E3", "type": "Gene_expression", "trigger": { "text": [ "produced" ], "offsets": [ [ 551, 559 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC2885601-03-RESULTS-02_T13" } ] }, { "id": "PMC2885601-03-RESULTS-02_E4", "type": "Gene_expression", "trigger": { "text": [ "produced" ], "offsets": [ [ 595, 603 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC2885601-03-RESULTS-02_T14" } ] }, { "id": "PMC2885601-03-RESULTS-02_E5", "type": "Process", "trigger": { "text": [ "infection" ], "offsets": [ [ 627, 636 ] ] }, "arguments": [ { "role": "Participant", "ref_id": "PMC2885601-03-RESULTS-02_T15" } ] }, { "id": "PMC2885601-03-RESULTS-02_E6", "type": "Process", "trigger": { "text": [ "infection" ], "offsets": [ [ 818, 827 ] ] }, "arguments": [ { "role": "Participant", "ref_id": "PMC2885601-03-RESULTS-02_T19" } ] }, { "id": "PMC2885601-03-RESULTS-02_E7", "type": "Gene_expression", "trigger": { "text": [ "produced" ], "offsets": [ [ 926, 934 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC2885601-03-RESULTS-02_T21" } ] }, { "id": "PMC2885601-03-RESULTS-02_E8", "type": "Process", "trigger": { "text": [ "infection" ], "offsets": [ [ 950, 959 ] ] }, "arguments": [] } ]

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[ { "id": "PMC2266911-02-Results_and_Discussion-01-02-04__text", "type": "abstract", "text": [ "Regulation by uncommon LuxR-like receptors \nLuxR-like receptors in Y. enterocolitica with a yet unidentified signalling binding-site are YE2705 and YE3014, both of which are also present in Y. pestis (YPO2955 and YPO2593) and in S. glossinidius (SGP1_007, SG1174, SG1480, and SG1698), but not in P. luminescens (Fig. 3). It might be possible that signalling molecules of mammals and hormones of adult insects are sensed via these receptors by Y. enterocolitica and S. glossinidius, respectively, hosts which P. luminescens does not specifically interact with during its life cycle. In P. luminescens, two LuxR-like receptors with a yet unidentified signalling binding site are present, Plu4274 and Plu1817, the latter of which is shared by Y. enterocolitica (YE1621), but not by S. glossinidius.\n" ], "offsets": [ [ 0, 796 ] ] } ]

[ { "id": "PMC2266911-02-Results_and_Discussion-01-02-04_T1", "type": "Protein", "text": [ "LuxR" ], "offsets": [ [ 23, 27 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-01-02-04_T2", "type": "Protein", "text": [ "LuxR" ], "offsets": [ [ 44, 48 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-01-02-04_T3", "type": "Organism", "text": [ "Y. enterocolitica" ], "offsets": [ [ 67, 84 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-01-02-04_T4", "type": "Protein", "text": [ "YE2705" ], "offsets": [ [ 137, 143 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-01-02-04_T5", "type": "Protein", "text": [ "YE3014" ], "offsets": [ [ 148, 154 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-01-02-04_T6", "type": "Organism", "text": [ "Y. pestis" ], "offsets": [ [ 190, 199 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-01-02-04_T7", "type": "Protein", "text": [ "YPO2955" ], "offsets": [ [ 201, 208 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-01-02-04_T8", "type": "Protein", "text": [ "YPO2593" ], "offsets": [ [ 213, 220 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-01-02-04_T9", "type": "Organism", "text": [ "S. glossinidius" ], "offsets": [ [ 229, 244 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-01-02-04_T10", "type": "Protein", "text": [ "SGP1_007" ], "offsets": [ [ 246, 254 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-01-02-04_T11", "type": "Protein", "text": [ "SG1174" ], "offsets": [ [ 256, 262 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-01-02-04_T12", "type": "Protein", "text": [ "SG1480" ], "offsets": [ [ 264, 270 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-01-02-04_T13", "type": "Protein", "text": [ "SG1698" ], "offsets": [ [ 276, 282 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-01-02-04_T14", "type": "Organism", "text": [ "P. luminescens" ], "offsets": [ [ 296, 310 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-01-02-04_T15", "type": "Organism", "text": [ "Y. enterocolitica" ], "offsets": [ [ 443, 460 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-01-02-04_T16", "type": "Organism", "text": [ "S. glossinidius" ], "offsets": [ [ 465, 480 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-01-02-04_T17", "type": "Organism", "text": [ "P. luminescens" ], "offsets": [ [ 508, 522 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-01-02-04_T18", "type": "Organism", "text": [ "P. luminescens" ], "offsets": [ [ 585, 599 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-01-02-04_T19", "type": "Protein", "text": [ "LuxR" ], "offsets": [ [ 605, 609 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-01-02-04_T20", "type": "Protein", "text": [ "Plu4274" ], "offsets": [ [ 686, 693 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-01-02-04_T21", "type": "Protein", "text": [ "Plu1817" ], "offsets": [ [ 698, 705 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-01-02-04_T22", "type": "Organism", "text": [ "Y. enterocolitica" ], "offsets": [ [ 740, 757 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-01-02-04_T23", "type": "Protein", "text": [ "YE1621" ], "offsets": [ [ 759, 765 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-01-02-04_T24", "type": "Organism", "text": [ "S. glossinidius" ], "offsets": [ [ 779, 794 ] ], "normalized": [] } ]

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[ { "id": "PMC2816692-00-TIAB__text", "type": "abstract", "text": [ "Structural and Biochemical Characterization of SrcA, a Multi-Cargo Type III Secretion Chaperone in Salmonella Required for Pathogenic Association with a Host \nMany Gram-negative bacteria colonize and exploit host niches using a protein apparatus called a type III secretion system (T3SS) that translocates bacterial effector proteins into host cells where their functions are essential for pathogenesis. A suite of T3SS-associated chaperone proteins bind cargo in the bacterial cytosol, establishing protein interaction networks needed for effector translocation into host cells. In Salmonella enterica serovar Typhimurium, a T3SS encoded in a large genomic island (SPI-2) is required for intracellular infection, but the chaperone complement required for effector translocation by this system is not known. Using a reverse genetics approach, we identified a multi-cargo secretion chaperone that is functionally integrated with the SPI-2-encoded T3SS and required for systemic infection in mice. Crystallographic analysis of SrcA at a resolution of 2.5 A revealed a dimer similar to the CesT chaperone from enteropathogenic E. coli but lacking a 17-amino acid extension at the carboxyl terminus. Further biochemical and quantitative proteomics data revealed three protein interactions with SrcA, including two effector cargos (SseL and PipB2) and the type III-associated ATPase, SsaN, that increases the efficiency of effector translocation. Using competitive infections in mice we show that SrcA increases bacterial fitness during host infection, highlighting the in vivo importance of effector chaperones for the SPI-2 T3SS.\n" ], "offsets": [ [ 0, 1627 ] ] } ]

[ { "id": "PMC2816692-00-TIAB_T1", "type": "Protein", "text": [ "SrcA" ], "offsets": [ [ 47, 51 ] ], "normalized": [] }, { "id": "PMC2816692-00-TIAB_T2", "type": "Organism", "text": [ "Salmonella" ], "offsets": [ [ 99, 109 ] ], "normalized": [] }, { "id": "PMC2816692-00-TIAB_T3", "type": "Organism", "text": [ "Host" ], "offsets": [ [ 153, 157 ] ], "normalized": [] }, { "id": "PMC2816692-00-TIAB_T4", "type": "Organism", "text": [ "host" ], "offsets": [ [ 208, 212 ] ], "normalized": [] }, { "id": "PMC2816692-00-TIAB_T5", "type": "Organism", "text": [ "host" ], "offsets": [ [ 339, 343 ] ], "normalized": [] }, { "id": "PMC2816692-00-TIAB_T6", "type": "Organism", "text": [ "host" ], "offsets": [ [ 568, 572 ] ], "normalized": [] }, { "id": "PMC2816692-00-TIAB_T7", "type": "Organism", "text": [ "Salmonella enterica serovar Typhimurium" ], "offsets": [ [ 583, 622 ] ], "normalized": [] }, { "id": "PMC2816692-00-TIAB_T8", "type": "Organism", "text": [ "mice" ], "offsets": [ [ 990, 994 ] ], "normalized": [] }, { "id": "PMC2816692-00-TIAB_T9", "type": "Protein", "text": [ "SrcA" ], "offsets": [ [ 1025, 1029 ] ], "normalized": [] }, { "id": "PMC2816692-00-TIAB_T10", "type": "Protein", "text": [ "CesT" ], "offsets": [ [ 1087, 1091 ] ], "normalized": [] }, { "id": "PMC2816692-00-TIAB_T11", "type": "Organism", "text": [ "E. coli" ], "offsets": [ [ 1124, 1131 ] ], "normalized": [] }, { "id": "PMC2816692-00-TIAB_T12", "type": "Chemical", "text": [ "carboxyl" ], "offsets": [ [ 1177, 1185 ] ], "normalized": [] }, { "id": "PMC2816692-00-TIAB_T13", "type": "Protein", "text": [ "SrcA" ], "offsets": [ [ 1290, 1294 ] ], "normalized": [] }, { "id": "PMC2816692-00-TIAB_T14", "type": "Protein", "text": [ "SseL" ], "offsets": [ [ 1327, 1331 ] ], "normalized": [] }, { "id": "PMC2816692-00-TIAB_T15", "type": "Protein", "text": [ "PipB2" ], "offsets": [ [ 1336, 1341 ] ], "normalized": [] }, { "id": "PMC2816692-00-TIAB_T16", "type": "Protein", "text": [ "SsaN" ], "offsets": [ [ 1379, 1383 ] ], "normalized": [] }, { "id": "PMC2816692-00-TIAB_T17", "type": "Organism", "text": [ "mice" ], "offsets": [ [ 1474, 1478 ] ], "normalized": [] }, { "id": "PMC2816692-00-TIAB_T18", "type": "Protein", "text": [ "SrcA" ], "offsets": [ [ 1492, 1496 ] ], "normalized": [] }, { "id": "PMC2816692-00-TIAB_T19", "type": "Organism", "text": [ "host" ], "offsets": [ [ 1532, 1536 ] ], "normalized": [] } ]

[ { "id": "PMC2816692-00-TIAB_E1", "type": "Process", "trigger": { "text": [ "infection" ], "offsets": [ [ 703, 712 ] ] }, "arguments": [] }, { "id": "PMC2816692-00-TIAB_E2", "type": "Process", "trigger": { "text": [ "infection" ], "offsets": [ [ 977, 986 ] ] }, "arguments": [] }, { "id": "PMC2816692-00-TIAB_E3", "type": "Binding", "trigger": { "text": [ "interactions" ], "offsets": [ [ 1272, 1284 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC2816692-00-TIAB_T13" }, { "role": "Theme", "ref_id": "PMC2816692-00-TIAB_T14" } ] }, { "id": "PMC2816692-00-TIAB_E4", "type": "Binding", "trigger": { "text": [ "interactions" ], "offsets": [ [ 1272, 1284 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC2816692-00-TIAB_T13" }, { "role": "Theme", "ref_id": "PMC2816692-00-TIAB_T15" } ] }, { "id": "PMC2816692-00-TIAB_E5", "type": "Binding", "trigger": { "text": [ "interactions" ], "offsets": [ [ 1272, 1284 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC2816692-00-TIAB_T13" }, { "role": "Theme", "ref_id": "PMC2816692-00-TIAB_T16" } ] }, { "id": "PMC2816692-00-TIAB_E6", "type": "Process", "trigger": { "text": [ "infections" ], "offsets": [ [ 1460, 1470 ] ] }, "arguments": [] }, { "id": "PMC2816692-00-TIAB_E7", "type": "Process", "trigger": { "text": [ "infection" ], "offsets": [ [ 1537, 1546 ] ] }, "arguments": [] } ]

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[ { "id": "PMC2242835-02-Results-03__text", "type": "abstract", "text": [ "Ex Vivo Virulence Studies \nChanges in the regulatory potential of a pathogen are often accompanied by altered virulence. In a first attempt to determine the virulence of the complemented H37Ra knock-in strains relative to wild-type H37Ra and H37Rv, bone marrow-derived murine macrophages (BMM) were infected with the different strains at a multiplicity of infection (MOI) of 1:1 and 10:1 bacteria per cell. As depicted in Figure 1, macrophages were able to control ex vivo growth of H37Ra, but failed to control growth of H37Rv, confirming results from Freeman and colleagues [20]. When H37Ra knock-ins were tested, important differences in their ex vivo growth characteristics were found. Whereas H37Ra::fadE5 (Figure 1) and H37Ra::rpsL (unpublished data) showed very little or no growth over the 7-d period, the H37Ra::phoP mutant grew more vigorously, with a 7.5-fold increase in colony-forming units (CFU) over the 7-d period. From these experiments we concluded that complementation of H37Ra with the phoP wild-type copy partially restored its virulence, but not to the extent of the fully virulent H37Rv strain.\n" ], "offsets": [ [ 0, 1118 ] ] } ]

[ { "id": "PMC2242835-02-Results-03_T1", "type": "Organism", "text": [ "H37Ra" ], "offsets": [ [ 187, 192 ] ], "normalized": [] }, { "id": "PMC2242835-02-Results-03_T2", "type": "Organism", "text": [ "H37Ra" ], "offsets": [ [ 232, 237 ] ], "normalized": [] }, { "id": "PMC2242835-02-Results-03_T3", "type": "Organism", "text": [ "H37Rv" ], "offsets": [ [ 242, 247 ] ], "normalized": [] }, { "id": "PMC2242835-02-Results-03_T4", "type": "Organism", "text": [ "H37Ra" ], "offsets": [ [ 483, 488 ] ], "normalized": [] }, { "id": "PMC2242835-02-Results-03_T5", "type": "Organism", "text": [ "H37Rv" ], "offsets": [ [ 522, 527 ] ], "normalized": [] }, { "id": "PMC2242835-02-Results-03_T6", "type": "Organism", "text": [ "H37Ra" ], "offsets": [ [ 587, 592 ] ], "normalized": [] }, { "id": "PMC2242835-02-Results-03_T7", "type": "Organism", "text": [ "H37Ra::fadE5" ], "offsets": [ [ 698, 710 ] ], "normalized": [] }, { "id": "PMC2242835-02-Results-03_T8", "type": "Protein", "text": [ "fadE5" ], "offsets": [ [ 705, 710 ] ], "normalized": [] }, { "id": "PMC2242835-02-Results-03_T9", "type": "Organism", "text": [ "H37Ra::rpsL" ], "offsets": [ [ 726, 737 ] ], "normalized": [] }, { "id": "PMC2242835-02-Results-03_T10", "type": "Protein", "text": [ "rpsL" ], "offsets": [ [ 733, 737 ] ], "normalized": [] }, { "id": "PMC2242835-02-Results-03_T11", "type": "Organism", "text": [ "H37Ra::phoP" ], "offsets": [ [ 814, 825 ] ], "normalized": [] }, { "id": "PMC2242835-02-Results-03_T12", "type": "Protein", "text": [ "phoP" ], "offsets": [ [ 821, 825 ] ], "normalized": [] }, { "id": "PMC2242835-02-Results-03_T13", "type": "Organism", "text": [ "H37Ra" ], "offsets": [ [ 991, 996 ] ], "normalized": [] }, { "id": "PMC2242835-02-Results-03_T14", "type": "Protein", "text": [ "phoP" ], "offsets": [ [ 1006, 1010 ] ], "normalized": [] }, { "id": "PMC2242835-02-Results-03_T15", "type": "Organism", "text": [ "H37Rv" ], "offsets": [ [ 1104, 1109 ] ], "normalized": [] } ]

[ { "id": "PMC2242835-02-Results-03_E1", "type": "Process", "trigger": { "text": [ "Virulence" ], "offsets": [ [ 8, 17 ] ] }, "arguments": [] }, { "id": "PMC2242835-02-Results-03_E2", "type": "Process", "trigger": { "text": [ "virulence" ], "offsets": [ [ 110, 119 ] ] }, "arguments": [] }, { "id": "PMC2242835-02-Results-03_E3", "type": "Process", "trigger": { "text": [ "virulence" ], "offsets": [ [ 157, 166 ] ] }, "arguments": [ { "role": "Participant", "ref_id": "PMC2242835-02-Results-03_T3" } ] }, { "id": "PMC2242835-02-Results-03_E4", "type": "Process", "trigger": { "text": [ "virulence" ], "offsets": [ [ 157, 166 ] ] }, "arguments": [ { "role": "Participant", "ref_id": "PMC2242835-02-Results-03_T1" } ] }, { "id": "PMC2242835-02-Results-03_E5", "type": "Process", "trigger": { "text": [ "virulence" ], "offsets": [ [ 157, 166 ] ] }, "arguments": [ { "role": "Participant", "ref_id": "PMC2242835-02-Results-03_T2" } ] }, { "id": "PMC2242835-02-Results-03_E6", "type": "Process", "trigger": { "text": [ "infected" ], "offsets": [ [ 299, 307 ] ] }, "arguments": [ { "role": "Participant", "ref_id": "PMC2242835-02-Results-03_T2" } ] }, { "id": "PMC2242835-02-Results-03_E7", "type": "Process", "trigger": { "text": [ "infected" ], "offsets": [ [ 299, 307 ] ] }, "arguments": [ { "role": "Participant", "ref_id": "PMC2242835-02-Results-03_T3" } ] }, { "id": "PMC2242835-02-Results-03_E8", "type": "Process", "trigger": { "text": [ "infected" ], "offsets": [ [ 299, 307 ] ] }, "arguments": [ { "role": "Participant", "ref_id": "PMC2242835-02-Results-03_T1" } ] }, { "id": "PMC2242835-02-Results-03_E9", "type": "Process", "trigger": { "text": [ "infection" ], "offsets": [ [ 356, 365 ] ] }, "arguments": [] }, { "id": "PMC2242835-02-Results-03_E10", "type": "Positive_regulation", "trigger": { "text": [ "restored" ], "offsets": [ [ 1036, 1044 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC2242835-02-Results-03_E11" } ] }, { "id": "PMC2242835-02-Results-03_E11", "type": "Process", "trigger": { "text": [ "virulence" ], "offsets": [ [ 1049, 1058 ] ] }, "arguments": [ { "role": "Participant", "ref_id": "PMC2242835-02-Results-03_T13" } ] }, { "id": "PMC2242835-02-Results-03_E12", "type": "Process", "trigger": { "text": [ "virulent" ], "offsets": [ [ 1095, 1103 ] ] }, "arguments": [ { "role": "Participant", "ref_id": "PMC2242835-02-Results-03_T15" } ] } ]

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[ { "id": "PMC2593050-03-RESULTS-04__text", "type": "abstract", "text": [ "Attenuation of S. equi Virulence by vicK Deletion \nGroup of 8 mice were subcutaneously inoculated with 1.1 x 108 cfu wild-type or DeltavicK mutant strains. Seven of the 8 mice infected with the wild-type S. equi strain died, whereas 7 of the 8 mice inoculated with DeltavicK survived (Fig. 4A). The infection was performed in a model of intranasal infection as well. All the 8 mice infected with DeltavicK survived, whereas 5 of the 8 mice infected with the wild-type S. equi strain died (Fig. 4B). These results indicate that the vicK deletion significantly attenuated S. equi virulence in both mouse models of subcutaneous (P = 0.0066) and nasal (P = 0.0085) infections.\n" ], "offsets": [ [ 0, 673 ] ] } ]

[ { "id": "PMC2593050-03-RESULTS-04_T1", "type": "Organism", "text": [ "S. equi" ], "offsets": [ [ 15, 22 ] ], "normalized": [] }, { "id": "PMC2593050-03-RESULTS-04_T2", "type": "Protein", "text": [ "vicK" ], "offsets": [ [ 36, 40 ] ], "normalized": [] }, { "id": "PMC2593050-03-RESULTS-04_T3", "type": "Organism", "text": [ "mice" ], "offsets": [ [ 62, 66 ] ], "normalized": [] }, { "id": "PMC2593050-03-RESULTS-04_T4", "type": "Organism", "text": [ "DeltavicK mutant" ], "offsets": [ [ 130, 146 ] ], "normalized": [] }, { "id": "PMC2593050-03-RESULTS-04_T5", "type": "Protein", "text": [ "vicK" ], "offsets": [ [ 135, 139 ] ], "normalized": [] }, { "id": "PMC2593050-03-RESULTS-04_T6", "type": "Organism", "text": [ "mice" ], "offsets": [ [ 171, 175 ] ], "normalized": [] }, { "id": "PMC2593050-03-RESULTS-04_T7", "type": "Organism", "text": [ "S. equi" ], "offsets": [ [ 204, 211 ] ], "normalized": [] }, { "id": "PMC2593050-03-RESULTS-04_T8", "type": "Organism", "text": [ "mice" ], "offsets": [ [ 244, 248 ] ], "normalized": [] }, { "id": "PMC2593050-03-RESULTS-04_T9", "type": "Organism", "text": [ "DeltavicK" ], "offsets": [ [ 265, 274 ] ], "normalized": [] }, { "id": "PMC2593050-03-RESULTS-04_T10", "type": "Protein", "text": [ "vicK" ], "offsets": [ [ 270, 274 ] ], "normalized": [] }, { "id": "PMC2593050-03-RESULTS-04_T11", "type": "Organism", "text": [ "mice" ], "offsets": [ [ 377, 381 ] ], "normalized": [] }, { "id": "PMC2593050-03-RESULTS-04_T12", "type": "Organism", "text": [ "DeltavicK" ], "offsets": [ [ 396, 405 ] ], "normalized": [] }, { "id": "PMC2593050-03-RESULTS-04_T13", "type": "Protein", "text": [ "vicK" ], "offsets": [ [ 401, 405 ] ], "normalized": [] }, { "id": "PMC2593050-03-RESULTS-04_T14", "type": "Organism", "text": [ "mice" ], "offsets": [ [ 435, 439 ] ], "normalized": [] }, { "id": "PMC2593050-03-RESULTS-04_T15", "type": "Organism", "text": [ "S. equi" ], "offsets": [ [ 468, 475 ] ], "normalized": [] }, { "id": "PMC2593050-03-RESULTS-04_T16", "type": "Protein", "text": [ "vicK" ], "offsets": [ [ 531, 535 ] ], "normalized": [] }, { "id": "PMC2593050-03-RESULTS-04_T17", "type": "Organism", "text": [ "S. equi" ], "offsets": [ [ 570, 577 ] ], "normalized": [] }, { "id": "PMC2593050-03-RESULTS-04_T18", "type": "Organism", "text": [ "mouse" ], "offsets": [ [ 596, 601 ] ], "normalized": [] } ]

[ { "id": "PMC2593050-03-RESULTS-04_E1", "type": "Negative_regulation", "trigger": { "text": [ "Attenuation" ], "offsets": [ [ 0, 11 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC2593050-03-RESULTS-04_E2" } ] }, { "id": "PMC2593050-03-RESULTS-04_E2", "type": "Process", "trigger": { "text": [ "Virulence" ], "offsets": [ [ 23, 32 ] ] }, "arguments": [ { "role": "Participant", "ref_id": "PMC2593050-03-RESULTS-04_T1" } ] }, { "id": "PMC2593050-03-RESULTS-04_E3", "type": "Process", "trigger": { "text": [ "infected" ], "offsets": [ [ 176, 184 ] ] }, "arguments": [ { "role": "Participant", "ref_id": "PMC2593050-03-RESULTS-04_T7" } ] }, { "id": "PMC2593050-03-RESULTS-04_E4", "type": "Process", "trigger": { "text": [ "infection" ], "offsets": [ [ 299, 308 ] ] }, "arguments": [] }, { "id": "PMC2593050-03-RESULTS-04_E5", "type": "Process", "trigger": { "text": [ "infection" ], "offsets": [ [ 348, 357 ] ] }, "arguments": [] }, { "id": "PMC2593050-03-RESULTS-04_E6", "type": "Process", "trigger": { "text": [ "infected" ], "offsets": [ [ 382, 390 ] ] }, "arguments": [ { "role": "Participant", "ref_id": "PMC2593050-03-RESULTS-04_T12" } ] }, { "id": "PMC2593050-03-RESULTS-04_E7", "type": "Process", "trigger": { "text": [ "infected" ], "offsets": [ [ 440, 448 ] ] }, "arguments": [ { "role": "Participant", "ref_id": "PMC2593050-03-RESULTS-04_T15" } ] }, { "id": "PMC2593050-03-RESULTS-04_E8", "type": "Negative_regulation", "trigger": { "text": [ "attenuated" ], "offsets": [ [ 559, 569 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC2593050-03-RESULTS-04_E9" } ] }, { "id": "PMC2593050-03-RESULTS-04_E9", "type": "Process", "trigger": { "text": [ "virulence" ], "offsets": [ [ 578, 587 ] ] }, "arguments": [ { "role": "Participant", "ref_id": "PMC2593050-03-RESULTS-04_T17" } ] }, { "id": "PMC2593050-03-RESULTS-04_E10", "type": "Process", "trigger": { "text": [ "infections" ], "offsets": [ [ 661, 671 ] ] }, "arguments": [] } ]

[]

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[ { "id": "PMC2581603-02-Results-04__text", "type": "abstract", "text": [ "Extracellular DNA induces expression of the PA3552-PA3559 CAP resistance operon in planktonic cultures \nIn P. aeruginosa, the PhoPQ and PmrAB-controlled response to magnesium limitation includes the induction of the PA3552 and its neighbouring genes. The genes PA3552-PA3559 are co-regulated under low Mg2+ conditions and are thought to be organized as an operon [45]-[47]. These genes encode an LPS modification pathway required for the addition of aminoarabinose to lipid A, which reduces the OM permeability to CAPs, thus conferring resistance [48]. To determine if extracellular DNA imposes Mg2+ limitation, we measured the gene expression of a chromosomally encoded transcriptional lux (bioluminescence) fusion to PA3553, as a measure of the CAP resistance operon expression in planktonic cultures. PA3553::lux expression was strongly induced (up to 10-fold) by sub-inhibitory concentrations of low molecular weight salmon sperm DNA (Fig 4A). Induction of the CAP resistance operon was dose-dependent with increasing DNA concentrations up to 0.5% (w/v) DNA, at which growth is inhibited (Fig 4A). Addition of excess Mg2+ (5 mM) to the growth medium completely repressed the expression of PA3553 in cultures supplemented with DNA, except at the highest DNA concentration tested (0.5% (w/v)) (Fig 4B). A similar induction profile of PA3553::lux was observed following exposure to high molecular weight P. aeruginosa genomic DNA (not shown) or P. aeruginosa genomic DNA that was mechanically sheared by sonication (Fig 4C). P. aeruginosa genomic DNA inhibited growth at similar concentrations as salmon sperm DNA. Thus, the ability of extracellular DNA to chelate magnesium is independent of origin and molecular weight, indicating that chelation is a general property of this negatively charged polymer. To ensure that induction of PA3553 expression was specific to the ability of DNA to chelate cations, DNAse treated DNA was assessed for its ability to induce PA3553 gene expression (Fig 4D). DNAse treated DNA failed to induce PA3553 gene expression. However the addition of DNAse buffer to cells in our buffer control experiment also abolished induction of PA3553. This is due to the addition of excess Mg2+ ions as part of the DNAse buffer, which is required for DNAse activity. Thus, it is impossible to determine conclusively if DNAse treatment of DNA abolished PA3553 gene expression.\n" ], "offsets": [ [ 0, 2396 ] ] } ]

[ { "id": "PMC2581603-02-Results-04_T1", "type": "Regulon-operon", "text": [ "PA3552-PA3559" ], "offsets": [ [ 44, 57 ] ], "normalized": [] }, { "id": "PMC2581603-02-Results-04_T2", "type": "Protein", "text": [ "PA3552" ], "offsets": [ [ 44, 50 ] ], "normalized": [] }, { "id": "PMC2581603-02-Results-04_T3", "type": "Protein", "text": [ "PA3559" ], "offsets": [ [ 51, 57 ] ], "normalized": [] }, { "id": "PMC2581603-02-Results-04_T4", "type": "Chemical", "text": [ "CAP" ], "offsets": [ [ 58, 61 ] ], "normalized": [] }, { "id": "PMC2581603-02-Results-04_T5", "type": "Organism", "text": [ "P. aeruginosa" ], "offsets": [ [ 107, 120 ] ], "normalized": [] }, { "id": "PMC2581603-02-Results-04_T6", "type": "Two-component-system", "text": [ "PhoPQ" ], "offsets": [ [ 126, 131 ] ], "normalized": [] }, { "id": "PMC2581603-02-Results-04_T7", "type": "Protein", "text": [ "PhoP" ], "offsets": [ [ 126, 130 ] ], "normalized": [] }, { "id": "PMC2581603-02-Results-04_T8", "type": "Protein", "text": [ "Q" ], "offsets": [ [ 130, 131 ] ], "normalized": [] }, { "id": "PMC2581603-02-Results-04_T9", "type": "Two-component-system", "text": [ "PmrAB" ], "offsets": [ [ 136, 141 ] ], "normalized": [] }, { "id": "PMC2581603-02-Results-04_T10", "type": "Protein", "text": [ "PmrA" ], "offsets": [ [ 136, 140 ] ], "normalized": [] }, { "id": "PMC2581603-02-Results-04_T11", "type": "Protein", "text": [ "B" ], "offsets": [ [ 140, 141 ] ], "normalized": [] }, { "id": "PMC2581603-02-Results-04_T12", "type": "Chemical", "text": [ "magnesium" ], "offsets": [ [ 165, 174 ] ], "normalized": [] }, { "id": "PMC2581603-02-Results-04_T13", "type": "Protein", "text": [ "PA3552" ], "offsets": [ [ 216, 222 ] ], "normalized": [] }, { "id": "PMC2581603-02-Results-04_T14", "type": "Regulon-operon", "text": [ "PA3552-PA3559" ], "offsets": [ [ 261, 274 ] ], "normalized": [] }, { "id": "PMC2581603-02-Results-04_T15", "type": "Protein", "text": [ "PA3552" ], "offsets": [ [ 261, 267 ] ], "normalized": [] }, { "id": "PMC2581603-02-Results-04_T16", "type": "Protein", "text": [ "PA3559" ], "offsets": [ [ 268, 274 ] ], "normalized": [] }, { "id": "PMC2581603-02-Results-04_T17", "type": "Chemical", "text": [ "Mg2+" ], "offsets": [ [ 302, 306 ] ], "normalized": [] }, { "id": "PMC2581603-02-Results-04_T18", "type": "Chemical", "text": [ "LPS" ], "offsets": [ [ 396, 399 ] ], "normalized": [] }, { "id": "PMC2581603-02-Results-04_T19", "type": "Chemical", "text": [ "lipid A" ], "offsets": [ [ 468, 475 ] ], "normalized": [] }, { "id": "PMC2581603-02-Results-04_T20", "type": "Chemical", "text": [ "CAPs" ], "offsets": [ [ 514, 518 ] ], "normalized": [] }, { "id": "PMC2581603-02-Results-04_T21", "type": "Chemical", "text": [ "Mg2+" ], "offsets": [ [ 595, 599 ] ], "normalized": [] }, { "id": "PMC2581603-02-Results-04_T22", "type": "Protein", "text": [ "lux" ], "offsets": [ [ 687, 690 ] ], "normalized": [] }, { "id": "PMC2581603-02-Results-04_T23", "type": "Protein", "text": [ "PA3553" ], "offsets": [ [ 719, 725 ] ], "normalized": [] }, { "id": "PMC2581603-02-Results-04_T24", "type": "Chemical", "text": [ "CAP" ], "offsets": [ [ 747, 750 ] ], "normalized": [] }, { "id": "PMC2581603-02-Results-04_T25", "type": "Protein", "text": [ "PA3553" ], "offsets": [ [ 804, 810 ] ], "normalized": [] }, { "id": "PMC2581603-02-Results-04_T26", "type": "Protein", "text": [ "lux" ], "offsets": [ [ 812, 815 ] ], "normalized": [] }, { "id": "PMC2581603-02-Results-04_T27", "type": "Chemical", "text": [ "CAP" ], "offsets": [ [ 965, 968 ] ], "normalized": [] }, { "id": "PMC2581603-02-Results-04_T28", "type": "Chemical", "text": [ "Mg2+" ], "offsets": [ [ 1121, 1125 ] ], "normalized": [] }, { "id": "PMC2581603-02-Results-04_T29", "type": "Protein", "text": [ "PA3553" ], "offsets": [ [ 1193, 1199 ] ], "normalized": [] }, { "id": "PMC2581603-02-Results-04_T30", "type": "Protein", "text": [ "PA3553" ], "offsets": [ [ 1336, 1342 ] ], "normalized": [] }, { "id": "PMC2581603-02-Results-04_T31", "type": "Protein", "text": [ "lux" ], "offsets": [ [ 1344, 1347 ] ], "normalized": [] }, { "id": "PMC2581603-02-Results-04_T32", "type": "Organism", "text": [ "P. aeruginosa" ], "offsets": [ [ 1405, 1418 ] ], "normalized": [] }, { "id": "PMC2581603-02-Results-04_T33", "type": "Organism", "text": [ "P. aeruginosa" ], "offsets": [ [ 1446, 1459 ] ], "normalized": [] }, { "id": "PMC2581603-02-Results-04_T34", "type": "Organism", "text": [ "P. aeruginosa" ], "offsets": [ [ 1526, 1539 ] ], "normalized": [] }, { "id": "PMC2581603-02-Results-04_T35", "type": "Organism", "text": [ "salmon" ], "offsets": [ [ 1598, 1604 ] ], "normalized": [] }, { "id": "PMC2581603-02-Results-04_T36", "type": "Chemical", "text": [ "magnesium" ], "offsets": [ [ 1666, 1675 ] ], "normalized": [] }, { "id": "PMC2581603-02-Results-04_T37", "type": "Protein", "text": [ "PA3553" ], "offsets": [ [ 1835, 1841 ] ], "normalized": [] }, { "id": "PMC2581603-02-Results-04_T38", "type": "Protein", "text": [ "PA3553" ], "offsets": [ [ 1965, 1971 ] ], "normalized": [] }, { "id": "PMC2581603-02-Results-04_T39", "type": "Protein", "text": [ "PA3553" ], "offsets": [ [ 2033, 2039 ] ], "normalized": [] }, { "id": "PMC2581603-02-Results-04_T40", "type": "Protein", "text": [ "PA3553" ], "offsets": [ [ 2164, 2170 ] ], "normalized": [] }, { "id": "PMC2581603-02-Results-04_T41", "type": "Chemical", "text": [ "Mg2+" ], "offsets": [ [ 2210, 2214 ] ], "normalized": [] }, { "id": "PMC2581603-02-Results-04_T42", "type": "Protein", "text": [ "PA3553" ], "offsets": [ [ 2372, 2378 ] ], "normalized": [] } ]

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"role": "Theme", "ref_id": "PMC2581603-02-Results-04_E6" }, { "role": "Cause", "ref_id": "PMC2581603-02-Results-04_T9" } ] }, { "id": "PMC2581603-02-Results-04_E6", "type": "Positive_regulation", "trigger": { "text": [ "induction" ], "offsets": [ [ 199, 208 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC2581603-02-Results-04_T13" } ] }, { "id": "PMC2581603-02-Results-04_E7", "type": "Regulation", "trigger": { "text": [ "co-regulated" ], "offsets": [ [ 279, 291 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC2581603-02-Results-04_T14" } ] }, { "id": "PMC2581603-02-Results-04_E8", "type": "Process", "trigger": { "text": [ "resistance" ], "offsets": [ [ 536, 546 ] ] }, "arguments": [] }, { "id": "PMC2581603-02-Results-04_E9", "type": "Gene_expression", "trigger": { "text": [ "expression" ], "offsets": [ [ 633, 643 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC2581603-02-Results-04_T22" } ] }, { "id": "PMC2581603-02-Results-04_E10", "type": "Gene_expression", "trigger": { "text": [ "expression" ], "offsets": [ [ 633, 643 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC2581603-02-Results-04_T23" } ] }, { "id": "PMC2581603-02-Results-04_E11", "type": "Process", "trigger": { "text": [ "resistance" ], "offsets": [ [ 751, 761 ] ] }, "arguments": [] }, { "id": "PMC2581603-02-Results-04_E12", "type": "Gene_expression", "trigger": { "text": [ "expression" ], "offsets": [ [ 816, 826 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC2581603-02-Results-04_T25" } ] }, { "id": "PMC2581603-02-Results-04_E13", "type": "Gene_expression", "trigger": { "text": [ "expression" ], "offsets": [ [ 816, 826 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC2581603-02-Results-04_T26" } ] }, { "id": "PMC2581603-02-Results-04_E14", "type": "Positive_regulation", "trigger": { "text": [ "induced" ], "offsets": [ [ 840, 847 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC2581603-02-Results-04_E12" } ] }, { "id": "PMC2581603-02-Results-04_E15", "type": "Positive_regulation", "trigger": { "text": [ "induced" ], "offsets": [ [ 840, 847 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC2581603-02-Results-04_E13" } ] }, { "id": "PMC2581603-02-Results-04_E16", "type": "Process", "trigger": { "text": [ "resistance" ], "offsets": [ [ 969, 979 ] ] }, "arguments": [] }, { "id": "PMC2581603-02-Results-04_E17", "type": "Negative_regulation", "trigger": { "text": [ "repressed" ], "offsets": [ [ 1165, 1174 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC2581603-02-Results-04_E18" }, { "role": "Cause", "ref_id": "PMC2581603-02-Results-04_T28" } ] }, { "id": "PMC2581603-02-Results-04_E18", "type": "Gene_expression", "trigger": { "text": [ "expression" ], "offsets": [ [ 1179, 1189 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC2581603-02-Results-04_T29" } ] }, { "id": "PMC2581603-02-Results-04_E19", "type": "Positive_regulation", "trigger": { "text": [ "induction" ], "offsets": [ [ 1315, 1324 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC2581603-02-Results-04_T30" } ] }, { "id": "PMC2581603-02-Results-04_E20", "type": "Positive_regulation", "trigger": { "text": [ "induction" ], "offsets": [ [ 1315, 1324 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC2581603-02-Results-04_T31" } ] }, { "id": "PMC2581603-02-Results-04_E21", "type": "Positive_regulation", "trigger": { "text": [ "induction" ], "offsets": [ [ 1822, 1831 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC2581603-02-Results-04_E22" } ] }, { "id": "PMC2581603-02-Results-04_E22", "type": "Gene_expression", "trigger": { "text": [ "expression" ], "offsets": [ [ 1842, 1852 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC2581603-02-Results-04_T37" } ] }, { "id": "PMC2581603-02-Results-04_E23", "type": "Positive_regulation", "trigger": { "text": [ "induce" ], "offsets": [ [ 1958, 1964 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC2581603-02-Results-04_E24" } ] }, { "id": "PMC2581603-02-Results-04_E24", "type": "Gene_expression", "trigger": { "text": [ "gene expression" ], "offsets": [ [ 1972, 1987 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC2581603-02-Results-04_T38" } ] }, { "id": "PMC2581603-02-Results-04_E25", "type": "Positive_regulation", "trigger": { "text": [ "induce" ], "offsets": [ [ 2026, 2032 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC2581603-02-Results-04_E26" } ] }, { "id": "PMC2581603-02-Results-04_E26", "type": "Gene_expression", "trigger": { "text": [ "gene expression" ], "offsets": [ [ 2040, 2055 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC2581603-02-Results-04_T39" } ] }, { "id": "PMC2581603-02-Results-04_E27", "type": "Negative_regulation", "trigger": { "text": [ "abolished" ], "offsets": [ [ 2141, 2150 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC2581603-02-Results-04_E28" } ] }, { "id": "PMC2581603-02-Results-04_E28", "type": "Positive_regulation", "trigger": { "text": [ "induction" ], "offsets": [ [ 2151, 2160 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC2581603-02-Results-04_T40" } ] }, { "id": "PMC2581603-02-Results-04_E29", "type": "Negative_regulation", "trigger": { "text": [ "abolished" ], "offsets": [ [ 2362, 2371 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC2581603-02-Results-04_E30" } ] }, { "id": "PMC2581603-02-Results-04_E30", "type": "Gene_expression", "trigger": { "text": [ "gene expression" ], "offsets": [ [ 2379, 2394 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC2581603-02-Results-04_T42" } ] } ]

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[]

[ { "id": "PMC2885601-00-TIAB__text", "type": "abstract", "text": [ "IgG Endopeptidase SeMac does not Inhibit Opsonophagocytosis of Streptococcus equi Subspecies equi by Horse Polymorphonuclear Leukocytes \nThe secreted Mac protein made by group A Streptococcus (GAS) inhibits opsonophagocytosis of GAS by human polymorphonuclear leukocytes (PMNs). This protein also has the endopeptidase activity against human immunoglobulin G (IgG), and the Cys94, His262 and Asp284 are critical for the enzymatic activity. The horse pathogen Streptococcus equi subspecies equi produces a homologue of Mac (SeMac). SeMac was characterized to determine whether SeMac has IgG endopeptidase activity and inhibits opsonophagocytosis of S. equi by horse PMNs. The gene was cloned and recombinant SeMac was overexpressed in Escherichia coli and purified to homogeneity. Mice with experimental S. equi infection and horses with strangles caused by S. equi seroconverted to SeMac, indicating that SeMac is produced in vivo during infection. SeMac has endopeptidase activity against human IgG. However, the protein just cleaves a small fraction, which may be IgG1 only, of horse IgG. Replacement of Cys102 with Ser or His272 with Ala abolishes the enzymatic activity of SeMac, and the Asp294Ala mutation greatly decreases the enzymatic activity. SeMac does not inhibit opsonophagocytosis of S. equi by horse PMNs but opsonophagocytosis of GAS by human PMNs. Thus, SeMac is a cysteine endopeptidase with a limited activity against horse IgG and must have other function.\n" ], "offsets": [ [ 0, 1477 ] ] } ]

[ { "id": "PMC2885601-00-TIAB_T1", "type": "Protein", "text": [ "IgG Endopeptidase" ], "offsets": [ [ 0, 17 ] ], "normalized": [] }, { "id": "PMC2885601-00-TIAB_T2", "type": "Protein", "text": [ "SeMac" ], "offsets": [ [ 18, 23 ] ], "normalized": [] }, { "id": "PMC2885601-00-TIAB_T3", "type": "Organism", "text": [ "Streptococcus equi Subspecies equi" ], "offsets": [ [ 63, 97 ] ], "normalized": [] }, { "id": "PMC2885601-00-TIAB_T4", "type": "Organism", "text": [ "Horse" ], "offsets": [ [ 101, 106 ] ], "normalized": [] }, { "id": "PMC2885601-00-TIAB_T5", "type": "Protein", "text": [ "Mac" ], "offsets": [ [ 150, 153 ] ], "normalized": [] }, { "id": "PMC2885601-00-TIAB_T6", "type": "Organism", "text": [ "group A Streptococcus" ], "offsets": [ [ 170, 191 ] ], "normalized": [] }, { "id": "PMC2885601-00-TIAB_T7", "type": "Organism", "text": [ "GAS" ], "offsets": [ [ 193, 196 ] ], "normalized": [] }, { "id": "PMC2885601-00-TIAB_T8", "type": "Protein", "text": [ "GAS" ], "offsets": [ [ 229, 232 ] ], "normalized": [] }, { "id": "PMC2885601-00-TIAB_T9", "type": "Organism", "text": [ "human" ], "offsets": [ [ 236, 241 ] ], "normalized": [] }, { "id": "PMC2885601-00-TIAB_T10", "type": "Organism", "text": [ "human" ], "offsets": [ [ 336, 341 ] ], "normalized": [] }, { "id": "PMC2885601-00-TIAB_T11", "type": "Protein", "text": [ "immunoglobulin G" ], "offsets": [ [ 342, 358 ] ], "normalized": [] }, { "id": "PMC2885601-00-TIAB_T12", "type": "Protein", "text": [ "IgG" ], "offsets": [ [ 360, 363 ] ], "normalized": [] }, { "id": "PMC2885601-00-TIAB_T13", "type": "Organism", "text": [ "horse" ], "offsets": [ [ 444, 449 ] ], "normalized": [] }, { "id": "PMC2885601-00-TIAB_T14", "type": "Organism", "text": [ "Streptococcus equi subspecies equi" ], "offsets": [ [ 459, 493 ] ], "normalized": [] }, { "id": "PMC2885601-00-TIAB_T15", "type": "Protein", "text": [ "Mac" ], "offsets": [ [ 518, 521 ] ], "normalized": [] }, { "id": "PMC2885601-00-TIAB_T16", "type": "Protein", "text": [ "SeMac" ], "offsets": [ [ 523, 528 ] ], "normalized": [] }, { "id": "PMC2885601-00-TIAB_T17", "type": "Protein", "text": [ "SeMac" ], "offsets": [ [ 531, 536 ] ], "normalized": [] }, { "id": "PMC2885601-00-TIAB_T18", "type": "Protein", "text": [ "SeMac" ], "offsets": [ [ 576, 581 ] ], "normalized": [] }, { "id": "PMC2885601-00-TIAB_T19", "type": "Protein", "text": [ "IgG endopeptidase" ], "offsets": [ [ 586, 603 ] ], "normalized": [] }, { "id": "PMC2885601-00-TIAB_T20", "type": "Organism", "text": [ "S. equi" ], "offsets": [ [ 648, 655 ] ], "normalized": [] }, { "id": "PMC2885601-00-TIAB_T21", "type": "Organism", "text": [ "horse" ], "offsets": [ [ 659, 664 ] ], "normalized": [] }, { "id": "PMC2885601-00-TIAB_T22", "type": "Protein", "text": [ "SeMac" ], "offsets": [ [ 707, 712 ] ], "normalized": [] }, { "id": "PMC2885601-00-TIAB_T23", "type": "Organism", "text": [ "Escherichia coli" ], "offsets": [ [ 734, 750 ] ], "normalized": [] }, { "id": "PMC2885601-00-TIAB_T24", "type": "Organism", "text": [ "Mice" ], "offsets": [ [ 780, 784 ] ], "normalized": [] }, { "id": "PMC2885601-00-TIAB_T25", "type": "Organism", "text": [ "S. equi" ], "offsets": [ [ 803, 810 ] ], "normalized": [] }, { "id": "PMC2885601-00-TIAB_T26", "type": "Organism", "text": [ "horses" ], "offsets": [ [ 825, 831 ] ], "normalized": [] }, { "id": "PMC2885601-00-TIAB_T27", "type": "Organism", "text": [ "S. equi" ], "offsets": [ [ 857, 864 ] ], "normalized": [] }, { "id": "PMC2885601-00-TIAB_T28", "type": "Protein", "text": [ "SeMac" ], "offsets": [ [ 882, 887 ] ], "normalized": [] }, { "id": "PMC2885601-00-TIAB_T29", "type": "Protein", "text": [ "SeMac" ], "offsets": [ [ 905, 910 ] ], "normalized": [] }, { "id": "PMC2885601-00-TIAB_T30", "type": "Protein", "text": [ "SeMac" ], "offsets": [ [ 949, 954 ] ], "normalized": [] }, { "id": "PMC2885601-00-TIAB_T31", "type": "Organism", "text": [ "human" ], "offsets": [ [ 990, 995 ] ], "normalized": [] }, { "id": "PMC2885601-00-TIAB_T32", "type": "Protein", "text": [ "IgG" ], "offsets": [ [ 996, 999 ] ], "normalized": [] }, { "id": "PMC2885601-00-TIAB_T33", "type": "Protein", "text": [ "IgG1" ], "offsets": [ [ 1066, 1070 ] ], "normalized": [] }, { "id": "PMC2885601-00-TIAB_T34", "type": "Organism", "text": [ "horse" ], "offsets": [ [ 1080, 1085 ] ], "normalized": [] }, { "id": "PMC2885601-00-TIAB_T35", "type": "Protein", "text": [ "IgG" ], "offsets": [ [ 1086, 1089 ] ], "normalized": [] }, { "id": "PMC2885601-00-TIAB_T36", "type": "Protein", "text": [ "SeMac" ], "offsets": [ [ 1177, 1182 ] ], "normalized": [] }, { "id": "PMC2885601-00-TIAB_T37", "type": "Protein", "text": [ "SeMac" ], "offsets": [ [ 1253, 1258 ] ], "normalized": [] }, { "id": "PMC2885601-00-TIAB_T38", "type": "Organism", "text": [ "S. equi" ], "offsets": [ [ 1298, 1305 ] ], "normalized": [] }, { "id": "PMC2885601-00-TIAB_T39", "type": "Organism", "text": [ "horse" ], "offsets": [ [ 1309, 1314 ] ], "normalized": [] }, { "id": "PMC2885601-00-TIAB_T40", "type": "Organism", "text": [ "GAS" ], "offsets": [ [ 1346, 1349 ] ], "normalized": [] }, { "id": "PMC2885601-00-TIAB_T41", "type": "Organism", "text": [ "human" ], "offsets": [ [ 1353, 1358 ] ], "normalized": [] }, { "id": "PMC2885601-00-TIAB_T42", "type": "Protein", "text": [ "SeMac" ], "offsets": [ [ 1371, 1376 ] ], "normalized": [] }, { "id": "PMC2885601-00-TIAB_T43", "type": "Protein", "text": [ "cysteine endopeptidase" ], "offsets": [ [ 1382, 1404 ] ], "normalized": [] }, { "id": "PMC2885601-00-TIAB_T44", "type": "Organism", "text": [ "horse" ], "offsets": [ [ 1437, 1442 ] ], "normalized": [] }, { "id": "PMC2885601-00-TIAB_T45", "type": "Protein", "text": [ "IgG" ], "offsets": [ [ 1443, 1446 ] ], "normalized": [] } ]

[ { "id": "PMC2885601-00-TIAB_E1", "type": "Localization", "trigger": { "text": [ "secreted" ], "offsets": [ [ 141, 149 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC2885601-00-TIAB_T5" } ] }, { "id": "PMC2885601-00-TIAB_E2", "type": "Gene_expression", "trigger": { "text": [ "produces" ], "offsets": [ [ 494, 502 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC2885601-00-TIAB_T16" } ] }, { "id": "PMC2885601-00-TIAB_E3", "type": "Gene_expression", "trigger": { "text": [ "overexpressed" ], "offsets": [ [ 717, 730 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC2885601-00-TIAB_T22" } ] }, { "id": "PMC2885601-00-TIAB_E4", "type": "Process", "trigger": { "text": [ "infection" ], "offsets": [ [ 811, 820 ] ] }, "arguments": [ { "role": "Participant", "ref_id": "PMC2885601-00-TIAB_T25" } ] }, { "id": "PMC2885601-00-TIAB_E5", "type": "Gene_expression", "trigger": { "text": [ "produced" ], "offsets": [ [ 914, 922 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC2885601-00-TIAB_T29" } ] }, { "id": "PMC2885601-00-TIAB_E6", "type": "Process", "trigger": { "text": [ "infection" ], "offsets": [ [ 938, 947 ] ] }, "arguments": [] }, { "id": "PMC2885601-00-TIAB_E7", "type": "Protein_catabolism", "trigger": { "text": [ "cleaves" ], "offsets": [ [ 1027, 1034 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC2885601-00-TIAB_T33" } ] }, { "id": "PMC2885601-00-TIAB_E8", "type": "Positive_regulation", "trigger": { "text": [ "cleaves" ], "offsets": [ [ 1027, 1034 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC2885601-00-TIAB_E7" }, { "role": "Cause", "ref_id": "PMC2885601-00-TIAB_T30" } ] } ]

[ { "id": "PMC2885601-00-TIAB_1", "entity_ids": [ "PMC2885601-00-TIAB_T6", "PMC2885601-00-TIAB_T7" ] }, { "id": "PMC2885601-00-TIAB_2", "entity_ids": [ "PMC2885601-00-TIAB_T11", "PMC2885601-00-TIAB_T12" ] } ]

[]

[ { "id": "PMC2774163-00-TIAB__text", "type": "abstract", "text": [ "A Novel Signaling Network Essential for Regulating Pseudomonas aeruginosa Biofilm Development \nThe important human pathogen Pseudomonas aeruginosa has been linked to numerous biofilm-related chronic infections. Here, we demonstrate that biofilm formation following the transition to the surface attached lifestyle is regulated by three previously undescribed two-component systems: BfiSR (PA4196-4197) harboring an RpoD-like domain, an OmpR-like BfmSR (PA4101-4102), and MifSR (PA5511-5512) belonging to the family of NtrC-like transcriptional regulators. These two-component systems become sequentially phosphorylated during biofilm formation. Inactivation of bfiS, bfmR, and mifR arrested biofilm formation at the transition to the irreversible attachment, maturation-1 and -2 stages, respectively, as indicated by analyses of biofilm architecture, and protein and phosphoprotein patterns. Moreover, discontinuation of bfiS, bfmR, and mifR expression in established biofilms resulted in the collapse of biofilms to an earlier developmental stage, indicating a requirement for these regulatory systems for the development and maintenance of normal biofilm architecture. Interestingly, inactivation did not affect planktonic growth, motility, polysaccharide production, or initial attachment. Further, we demonstrate the interdependency of this two-component systems network with GacS (PA0928), which was found to play a dual role in biofilm formation. This work describes a novel signal transduction network regulating committed biofilm developmental steps following attachment, in which phosphorelays and two sigma factor-dependent response regulators appear to be key components of the regulatory machinery that coordinates gene expression during P. aeruginosa biofilm development in response to environmental cues.\n" ], "offsets": [ [ 0, 1819 ] ] } ]

[ { "id": "PMC2774163-00-TIAB_T1", "type": "Organism", "text": [ "Pseudomonas aeruginosa" ], "offsets": [ [ 51, 73 ] ], "normalized": [] }, { "id": "PMC2774163-00-TIAB_T2", "type": "Organism", "text": [ "human" ], "offsets": [ [ 109, 114 ] ], "normalized": [] }, { "id": "PMC2774163-00-TIAB_T3", "type": "Organism", "text": [ "Pseudomonas aeruginosa" ], "offsets": [ [ 124, 146 ] ], "normalized": [] }, { "id": "PMC2774163-00-TIAB_T4", "type": "Two-component-system", "text": [ "BfiSR" ], "offsets": [ [ 382, 387 ] ], "normalized": [] }, { "id": "PMC2774163-00-TIAB_T5", "type": "Protein", "text": [ "BfiS" ], "offsets": [ [ 382, 386 ] ], "normalized": [] }, { "id": "PMC2774163-00-TIAB_T6", "type": "Protein", "text": [ "R" ], "offsets": [ [ 386, 387 ] ], "normalized": [] }, { "id": "PMC2774163-00-TIAB_T7", "type": "Two-component-system", "text": [ "PA4196-4197" ], "offsets": [ [ 389, 400 ] ], "normalized": [] }, { "id": "PMC2774163-00-TIAB_T8", "type": "Protein", "text": [ "PA4196" ], "offsets": [ [ 389, 395 ] ], "normalized": [] }, { "id": "PMC2774163-00-TIAB_T9", "type": "Protein", "text": [ "4197" ], "offsets": [ [ 396, 400 ] ], "normalized": [] }, { "id": "PMC2774163-00-TIAB_T10", "type": "Protein", "text": [ "RpoD" ], "offsets": [ [ 415, 419 ] ], "normalized": [] }, { "id": "PMC2774163-00-TIAB_T11", "type": "Protein", "text": [ "OmpR" ], "offsets": [ [ 436, 440 ] ], "normalized": [] }, { "id": "PMC2774163-00-TIAB_T12", "type": "Two-component-system", "text": [ "BfmSR" ], "offsets": [ [ 446, 451 ] ], "normalized": [] }, { "id": "PMC2774163-00-TIAB_T13", "type": "Protein", "text": [ "BfmS" ], "offsets": [ [ 446, 450 ] ], "normalized": [] }, { "id": "PMC2774163-00-TIAB_T14", "type": "Protein", "text": [ "R" ], "offsets": [ [ 450, 451 ] ], "normalized": [] }, { "id": "PMC2774163-00-TIAB_T15", "type": "Two-component-system", "text": [ "PA4101-4102" ], "offsets": [ [ 453, 464 ] ], "normalized": [] }, { "id": "PMC2774163-00-TIAB_T16", "type": "Protein", "text": [ "PA4101" ], "offsets": [ [ 453, 459 ] ], "normalized": [] }, { "id": "PMC2774163-00-TIAB_T17", "type": "Protein", "text": [ "4102" ], "offsets": [ [ 460, 464 ] ], "normalized": [] }, { "id": "PMC2774163-00-TIAB_T18", "type": "Two-component-system", "text": [ "MifSR" ], "offsets": [ [ 471, 476 ] ], "normalized": [] }, { "id": "PMC2774163-00-TIAB_T19", "type": "Protein", "text": [ "MifS" ], "offsets": [ [ 471, 475 ] ], "normalized": [] }, { "id": "PMC2774163-00-TIAB_T20", "type": "Protein", "text": [ "R" ], "offsets": [ [ 475, 476 ] ], "normalized": [] }, { "id": "PMC2774163-00-TIAB_T21", "type": "Two-component-system", "text": [ "PA5511-5512" ], "offsets": [ [ 478, 489 ] ], "normalized": [] }, { "id": "PMC2774163-00-TIAB_T22", "type": "Protein", "text": [ "PA5511" ], "offsets": [ [ 478, 484 ] ], "normalized": [] }, { "id": "PMC2774163-00-TIAB_T23", "type": "Protein", "text": [ "5512" ], "offsets": [ [ 485, 489 ] ], "normalized": [] }, { "id": "PMC2774163-00-TIAB_T24", "type": "Protein", "text": [ "NtrC" ], "offsets": [ [ 518, 522 ] ], "normalized": [] }, { "id": "PMC2774163-00-TIAB_T25", "type": "Protein", "text": [ "bfiS" ], "offsets": [ [ 661, 665 ] ], "normalized": [] }, { "id": "PMC2774163-00-TIAB_T26", "type": "Protein", "text": [ "bfmR" ], "offsets": [ [ 667, 671 ] ], "normalized": [] }, { "id": "PMC2774163-00-TIAB_T27", "type": "Protein", "text": [ "mifR" ], "offsets": [ [ 677, 681 ] ], "normalized": [] }, { "id": "PMC2774163-00-TIAB_T28", "type": "Protein", "text": [ "bfiS" ], "offsets": [ [ 921, 925 ] ], "normalized": [] }, { "id": "PMC2774163-00-TIAB_T29", "type": "Protein", "text": [ "bfmR" ], "offsets": [ [ 927, 931 ] ], "normalized": [] }, { "id": "PMC2774163-00-TIAB_T30", "type": "Protein", "text": [ "mifR" ], "offsets": [ [ 937, 941 ] ], "normalized": [] }, { "id": "PMC2774163-00-TIAB_T31", "type": "Protein", "text": [ "GacS" ], "offsets": [ [ 1380, 1384 ] ], "normalized": [] }, { "id": "PMC2774163-00-TIAB_T32", "type": "Protein", "text": [ "PA0928" ], "offsets": [ [ 1386, 1392 ] ], "normalized": [] }, { "id": "PMC2774163-00-TIAB_T33", "type": "Organism", "text": [ "P. aeruginosa" ], "offsets": [ [ 1750, 1763 ] ], "normalized": [] } ]

[ { "id": "PMC2774163-00-TIAB_E1", "type": "Process", "trigger": { "text": [ "infections" ], "offsets": [ [ 199, 209 ] ] }, "arguments": [ { "role": "Participant", "ref_id": "PMC2774163-00-TIAB_T3" } ] }, { "id": "PMC2774163-00-TIAB_E2", "type": "Negative_regulation", "trigger": { "text": [ "Inactivation" ], "offsets": [ [ 645, 657 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC2774163-00-TIAB_T25" } ] }, { "id": "PMC2774163-00-TIAB_E3", "type": "Negative_regulation", "trigger": { "text": [ "Inactivation" ], "offsets": [ [ 645, 657 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC2774163-00-TIAB_T26" } ] }, { "id": "PMC2774163-00-TIAB_E4", "type": "Negative_regulation", "trigger": { "text": [ "Inactivation" ], "offsets": [ [ 645, 657 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC2774163-00-TIAB_T27" } ] }, { "id": "PMC2774163-00-TIAB_E5", "type": "Negative_regulation", "trigger": { "text": [ "discontinuation" ], "offsets": [ [ 902, 917 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC2774163-00-TIAB_E9" } ] }, { "id": "PMC2774163-00-TIAB_E6", "type": "Negative_regulation", "trigger": { "text": [ "discontinuation" ], "offsets": [ [ 902, 917 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC2774163-00-TIAB_E10" } ] }, { "id": "PMC2774163-00-TIAB_E7", "type": "Negative_regulation", "trigger": { "text": [ "discontinuation" ], "offsets": [ [ 902, 917 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC2774163-00-TIAB_E8" } ] }, { "id": "PMC2774163-00-TIAB_E8", "type": "Gene_expression", "trigger": { "text": [ "expression" ], "offsets": [ [ 942, 952 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC2774163-00-TIAB_T30" } ] }, { "id": "PMC2774163-00-TIAB_E9", "type": "Gene_expression", "trigger": { "text": [ "expression" ], "offsets": [ [ 942, 952 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC2774163-00-TIAB_T28" } ] }, { "id": "PMC2774163-00-TIAB_E10", "type": "Gene_expression", "trigger": { "text": [ "expression" ], "offsets": [ [ 942, 952 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC2774163-00-TIAB_T29" } ] } ]

[ { "id": "PMC2774163-00-TIAB_1", "entity_ids": [ "PMC2774163-00-TIAB_T4", "PMC2774163-00-TIAB_T7" ] }, { "id": "PMC2774163-00-TIAB_2", "entity_ids": [ "PMC2774163-00-TIAB_T12", "PMC2774163-00-TIAB_T15" ] }, { "id": "PMC2774163-00-TIAB_3", "entity_ids": [ "PMC2774163-00-TIAB_T18", "PMC2774163-00-TIAB_T21" ] }, { "id": "PMC2774163-00-TIAB_4", "entity_ids": [ "PMC2774163-00-TIAB_T31", "PMC2774163-00-TIAB_T32" ] } ]

[]

[ { "id": "PMC2639726-02-Results-02__text", "type": "abstract", "text": [ "The ability of Salmonella to survive and replicate in macrophages is necessary but not sufficient for mouse virulence \nPrevious work demonstrated that Salmonella mutants that were unable to survive within elicited peritoneal macrophages were attenuated for virulence during systemic mouse infection [36]. In fact, fluorescence-activated cell sorting analysis of infected blood and spleen using Salmonella that expresses green fluorescent protein does not identify any extracellular bacteria [16],[37],[38]. Salmonella is within blood monocytes and in other WBC in the spleen including neutrophils, dendritic cells, and B and T cells in these reports (ibid). It is possible that growth in cells types other than macrophages is necessary for Salmonella to cause a systemic infection in mice following i.p. administration. Thus, some of the regulatory mutations described here may affect growth in cells types other than macrophages. We therefore wished to determine if there is a direct relationship between growth in macrophages and mouse virulence. In these studies we used primary bone marrow-derived macrophages (BMDM) from the same strain of mouse as used in the original identification of attenuated regulatory mutants (BALB/c). The identical number of input bacteria and the identical number of macrophages were used in every infection experiment. As observed by others, following phagocytosis there is some bacterial killing that varied from strain to strain followed by intracellular growth. We monitored the number of intracellular bacteria at an early time (30 min) to determine the number of bacteria internalized (Figure 2). Even at the shortest time few intracellular bacteria were recovered from macrophage infection with an rpoE mutant, suggesting that this strain is very sensitive to microbicidal factors released by macrophages on contact with bacteria or doesn't get internalized very well. At 2.0 hrs post infection there was a decrease in bacterial numbers that varied from strain to strain presumably reflecting variation in the sensitivity to bacterial killing by the oxidative burst, acidic pH, and antimicrobial peptides. Finally, at 18 hrs bacterial numbers were enumerated to monitor intracellular replication as well as the ability to withstand nitrous oxide oxidation and other late antimicrobial factors [39],[40]. No effect was found at any time point for a mutant in the plasmid-encoded regulator spvR in murine macrophages in agreement with other investigators [41],[42]. Small differences in intracellular growth were observed for ssrA/ssrB and slyA compared to the parent although larger differences have been observed previously [43]-[45] perhaps reflecting BMDM preparation techniques, bacterial strain differences, or opsonization differences [46]. Mutations of himD, rpoE, crp, or hfq drastically reduce the number of viable bacteria that can be recovered from macrophages even at short times (Figure 2). These results also demonstrated that growth in macrophages per se does not duplicate in vivo infection and that some regulator mutants that were totally avirulent in the mouse showed no differences in growth in these primary macrophages.\n" ], "offsets": [ [ 0, 3181 ] ] } ]

[ { "id": "PMC2639726-02-Results-02_T1", "type": "Organism", "text": [ "Salmonella" ], "offsets": [ [ 15, 25 ] ], "normalized": [] }, { "id": "PMC2639726-02-Results-02_T2", "type": "Organism", "text": [ "mouse" ], "offsets": [ [ 102, 107 ] ], "normalized": [] }, { "id": "PMC2639726-02-Results-02_T3", "type": "Organism", "text": [ "Salmonella" ], "offsets": [ [ 151, 161 ] ], "normalized": [] }, { "id": "PMC2639726-02-Results-02_T4", "type": "Organism", "text": [ "mouse" ], "offsets": [ [ 283, 288 ] ], "normalized": [] }, { "id": "PMC2639726-02-Results-02_T5", "type": "Organism", "text": [ "Salmonella" ], "offsets": [ [ 394, 404 ] ], "normalized": [] }, { "id": "PMC2639726-02-Results-02_T6", "type": "Organism", "text": [ "Salmonella" ], "offsets": [ [ 507, 517 ] ], "normalized": [] }, { "id": "PMC2639726-02-Results-02_T7", "type": "Organism", "text": [ "Salmonella" ], "offsets": [ [ 740, 750 ] ], "normalized": [] }, { "id": "PMC2639726-02-Results-02_T8", "type": "Organism", "text": [ "mice" ], "offsets": [ [ 784, 788 ] ], "normalized": [] }, { "id": "PMC2639726-02-Results-02_T9", "type": "Organism", "text": [ "mouse" ], "offsets": [ [ 1032, 1037 ] ], "normalized": [] }, { "id": "PMC2639726-02-Results-02_T10", "type": "Organism", "text": [ "mouse" ], "offsets": [ [ 1145, 1150 ] ], "normalized": [] }, { "id": "PMC2639726-02-Results-02_T11", "type": "Organism", "text": [ "BALB/c" ], "offsets": [ [ 1224, 1230 ] ], "normalized": [] }, { "id": "PMC2639726-02-Results-02_T12", "type": "Protein", "text": [ "rpoE" ], "offsets": [ [ 1738, 1742 ] ], "normalized": [] }, { "id": "PMC2639726-02-Results-02_T13", "type": "Protein", "text": [ "spvR" ], "offsets": [ [ 2428, 2432 ] ], "normalized": [] }, { "id": "PMC2639726-02-Results-02_T14", "type": "Organism", "text": [ "murine" ], "offsets": [ [ 2436, 2442 ] ], "normalized": [] }, { "id": "PMC2639726-02-Results-02_T15", "type": "Two-component-system", "text": [ "ssrA/ssrB" ], "offsets": [ [ 2564, 2573 ] ], "normalized": [] }, { "id": "PMC2639726-02-Results-02_T16", "type": "Protein", "text": [ "ssrA" ], "offsets": [ [ 2564, 2568 ] ], "normalized": [] }, { "id": "PMC2639726-02-Results-02_T17", "type": "Protein", "text": [ "ssrB" ], "offsets": [ [ 2569, 2573 ] ], "normalized": [] }, { "id": "PMC2639726-02-Results-02_T18", "type": "Protein", "text": [ "slyA" ], "offsets": [ [ 2578, 2582 ] ], "normalized": [] }, { "id": "PMC2639726-02-Results-02_T19", "type": "Protein", "text": [ "himD" ], "offsets": [ [ 2799, 2803 ] ], "normalized": [] }, { "id": "PMC2639726-02-Results-02_T20", "type": "Protein", "text": [ "rpoE" ], "offsets": [ [ 2805, 2809 ] ], "normalized": [] }, { "id": "PMC2639726-02-Results-02_T21", "type": "Protein", "text": [ "crp" ], "offsets": [ [ 2811, 2814 ] ], "normalized": [] }, { "id": "PMC2639726-02-Results-02_T22", "type": "Protein", "text": [ "hfq" ], "offsets": [ [ 2819, 2822 ] ], "normalized": [] }, { "id": "PMC2639726-02-Results-02_T23", "type": "Organism", "text": [ "mouse" ], "offsets": [ [ 3113, 3118 ] ], "normalized": [] } ]

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[]

[]

[ { "id": "PMC2816692-02-Results-03__text", "type": "abstract", "text": [ "Crystal structure of SrcA \nSequence analysis showed 59% amino acid identity between SrcA and CesT, a secretion chaperone in enteropathogenic E. coli (EPEC) (Fig. 2A). As a means to address the biological function of SrcA, we solved the crystal structure at 2.5-A resolution (PDB 3EPU). A summary of crystallographic data collection and model refinement statistics is in Table 1. The structure was solved by molecular replacement using an initial model based on CesT (PDB 1K3E) [13]. SrcA crystallized in space group C2 with two molecules related by a 2-fold symmetry axis in each asymmetric unit (Fig. 2B). Each monomer consisted of a small and large domain. The smaller domain formed by alpha1 and the extended loop region preceding beta1 adopts a distinct conformation in each subunit. The larger domain mediates dimerization and is comprised of a twisted anti-parallel beta-sheet (beta1-beta2-beta3-beta5-beta4) flanked by alpha-helices alpha2 and alpha3. The dimer interface formed between SrcA monomers occurs primarily through reciprocal hydrophobic interactions between alpha2 and alpha2' with additional interface-stabilizing interactions occurring between the alpha2 helix of one monomer and beta4 and beta5 strands of the opposing monomer (Fig. 2B). The total surface area buried at the dimer interface is 1258 A2, suggesting that SrcA would exist as a dimer in solution, which we confirmed by gel filtration analysis (see below). A structure similarity search with SrcA revealed proteins identified as T3SS secretion chaperones. CesT and SicP were the most structurally similar to SrcA, aligning with RMSD of 1.8 A and 2.2 A respectively. With the exception of CesT, SrcA has weak overall sequence identity (<20%) with other T3SS chaperones. CesT, SicP and SrcA contain several clusters of highly conserved amino acids notable on primary sequence alignments (Fig. 2A). Most of these conserved sites are located in the alpha2-interface helix and in strands beta4 and beta5 that help stabilize this interface. Although the N-terminus of these proteins is conserved structurally, the tertiary structures differ for each protein. In CesT, alpha1 and beta1 adopt an extended conformation while the equivalent domain in SicP remains closely packed against the dimerization domain [12]. In SrcA, both extended and closely packed conformations are observed in separate subunits of the same dimer within the asymmetric unit. In the extended conformation the N-terminal helix from one dimer interacts with the beta4 region of an adjacent dimer, similar to a domain swap seen in CesT [13]. At this time, the possible biological relevance for such a domain swap is unclear and may reflect an artifact of crystallization as critically discussed [13]. A comparison of the SrcA dimer interface with other class I chaperone family members indicates the overall similarity of quaternary structure shared between SrcA, CesT and SicP (Fig. 3A). This is in contrast to the class II chaperone interface of Spa15, which despite having similar tertiary structure to SrcA adopts a distinct dimer interface. A structural alignment of SrcA and Spa15 generated through alignment of single monomers shows the relative difference in subunit orientation between SrcA and Spa15 reflected by the positions of each monomer in the dimer configuration. These unique orientations produce an 80degrees rotational offset between respective subunits and could be expected to influence the mode of effector interactions utilized by these proteins. To evaluate the potential for an effector-binding surface on SrcA, the structure of SicP in complex with its effector SptP was aligned with SrcA and represented as a space-filling model (Fig. 3B). Binding of SptP occurs primarily in the N-terminus of SicP [12], which is similar to the effector binding surface for SrcA predicted in silico. This surface contains several conserved hydrophobic residues including L16, D24, N26, and I32 (Fig. 2A), which is consistent with SrcA using a similar mechanism for interaction with effectors.\n" ], "offsets": [ [ 0, 4053 ] ] } ]

[ { "id": "PMC2816692-02-Results-03_T1", "type": "Protein", "text": [ "SrcA" ], "offsets": [ [ 21, 25 ] ], "normalized": [] }, { "id": "PMC2816692-02-Results-03_T2", "type": "Protein", "text": [ "SrcA" ], "offsets": [ [ 84, 88 ] ], "normalized": [] }, { "id": "PMC2816692-02-Results-03_T3", "type": "Protein", "text": [ "CesT" ], "offsets": [ [ 93, 97 ] ], "normalized": [] }, { "id": "PMC2816692-02-Results-03_T4", "type": "Organism", "text": [ "enteropathogenic E. coli" ], "offsets": [ [ 124, 148 ] ], "normalized": [] }, { "id": "PMC2816692-02-Results-03_T5", "type": "Organism", "text": [ "EPEC" ], "offsets": [ [ 150, 154 ] ], "normalized": [] }, { "id": "PMC2816692-02-Results-03_T6", "type": "Protein", "text": [ "SrcA" ], "offsets": [ [ 216, 220 ] ], "normalized": [] }, { "id": "PMC2816692-02-Results-03_T7", "type": "Protein", "text": [ "PDB 3EPU" ], "offsets": [ [ 275, 283 ] ], "normalized": [] }, { "id": "PMC2816692-02-Results-03_T8", "type": "Protein", "text": [ "CesT" ], "offsets": [ [ 461, 465 ] ], "normalized": [] }, { "id": "PMC2816692-02-Results-03_T9", "type": "Protein", "text": [ "PDB 1K3E" ], "offsets": [ [ 467, 475 ] ], "normalized": [] }, { "id": "PMC2816692-02-Results-03_T10", "type": "Protein", "text": [ "SrcA" ], "offsets": [ [ 483, 487 ] ], "normalized": [] }, { "id": "PMC2816692-02-Results-03_T11", "type": "Protein", "text": [ "SrcA" ], "offsets": [ [ 994, 998 ] ], "normalized": [] }, { "id": "PMC2816692-02-Results-03_T12", "type": "Protein", "text": [ "SrcA" ], "offsets": [ [ 1341, 1345 ] ], "normalized": [] }, { "id": "PMC2816692-02-Results-03_T13", "type": "Protein", "text": [ "SrcA" ], "offsets": [ [ 1476, 1480 ] ], "normalized": [] }, { "id": "PMC2816692-02-Results-03_T14", "type": "Protein", "text": [ "CesT" ], "offsets": [ [ 1540, 1544 ] ], "normalized": [] }, { "id": "PMC2816692-02-Results-03_T15", "type": "Protein", "text": [ "SicP" ], "offsets": [ [ 1549, 1553 ] ], "normalized": [] }, { "id": "PMC2816692-02-Results-03_T16", "type": "Protein", "text": [ "SrcA" ], "offsets": [ [ 1592, 1596 ] ], "normalized": [] }, { "id": "PMC2816692-02-Results-03_T17", "type": "Protein", "text": [ "CesT" ], "offsets": [ [ 1672, 1676 ] ], "normalized": [] }, { "id": "PMC2816692-02-Results-03_T18", "type": "Protein", "text": [ "SrcA" ], "offsets": [ [ 1678, 1682 ] ], "normalized": [] }, { "id": "PMC2816692-02-Results-03_T19", "type": "Protein", "text": [ "CesT" ], "offsets": [ [ 1753, 1757 ] ], "normalized": [] }, { "id": "PMC2816692-02-Results-03_T20", "type": "Protein", "text": [ "SicP" ], "offsets": [ [ 1759, 1763 ] ], "normalized": [] }, { "id": "PMC2816692-02-Results-03_T21", "type": "Protein", "text": [ "SrcA" ], "offsets": [ [ 1768, 1772 ] ], "normalized": [] }, { "id": "PMC2816692-02-Results-03_T22", "type": "Protein", "text": [ "CesT" ], "offsets": [ [ 2140, 2144 ] ], "normalized": [] }, { "id": "PMC2816692-02-Results-03_T23", "type": "Protein", "text": [ "SicP" ], "offsets": [ [ 2225, 2229 ] ], "normalized": [] }, { "id": "PMC2816692-02-Results-03_T24", "type": "Protein", "text": [ "SrcA" ], "offsets": [ [ 2294, 2298 ] ], "normalized": [] }, { "id": "PMC2816692-02-Results-03_T25", "type": "Protein", "text": [ "CesT" ], "offsets": [ [ 2579, 2583 ] ], "normalized": [] }, { "id": "PMC2816692-02-Results-03_T26", "type": "Protein", "text": [ "SrcA" ], "offsets": [ [ 2769, 2773 ] ], "normalized": [] }, { "id": "PMC2816692-02-Results-03_T27", "type": "Protein", "text": [ "SrcA" ], "offsets": [ [ 2906, 2910 ] ], "normalized": [] }, { "id": "PMC2816692-02-Results-03_T28", "type": "Protein", "text": [ "CesT" ], "offsets": [ [ 2912, 2916 ] ], "normalized": [] }, { "id": "PMC2816692-02-Results-03_T29", "type": "Protein", "text": [ "SicP" ], "offsets": [ [ 2921, 2925 ] ], "normalized": [] }, { "id": "PMC2816692-02-Results-03_T30", "type": "Protein", "text": [ "Spa15" ], "offsets": [ [ 2996, 3001 ] ], "normalized": [] }, { "id": "PMC2816692-02-Results-03_T31", "type": "Protein", "text": [ "SrcA" ], "offsets": [ [ 3054, 3058 ] ], "normalized": [] }, { "id": "PMC2816692-02-Results-03_T32", "type": "Protein", "text": [ "SrcA" ], "offsets": [ [ 3120, 3124 ] ], "normalized": [] }, { "id": "PMC2816692-02-Results-03_T33", "type": "Protein", "text": [ "Spa15" ], "offsets": [ [ 3129, 3134 ] ], "normalized": [] }, { "id": "PMC2816692-02-Results-03_T34", "type": "Protein", "text": [ "SrcA" ], "offsets": [ [ 3243, 3247 ] ], "normalized": [] }, { "id": "PMC2816692-02-Results-03_T35", "type": "Protein", "text": [ "Spa15" ], "offsets": [ [ 3252, 3257 ] ], "normalized": [] }, { "id": "PMC2816692-02-Results-03_T36", "type": "Protein", "text": [ "SrcA" ], "offsets": [ [ 3580, 3584 ] ], "normalized": [] }, { "id": "PMC2816692-02-Results-03_T37", "type": "Protein", "text": [ "SicP" ], "offsets": [ [ 3603, 3607 ] ], "normalized": [] }, { "id": "PMC2816692-02-Results-03_T38", "type": "Protein", "text": [ "SptP" ], "offsets": [ [ 3637, 3641 ] ], "normalized": [] }, { "id": "PMC2816692-02-Results-03_T39", "type": "Protein", "text": [ "SrcA" ], "offsets": [ [ 3659, 3663 ] ], "normalized": [] }, { "id": "PMC2816692-02-Results-03_T40", "type": "Protein", "text": [ "SptP" ], "offsets": [ [ 3727, 3731 ] ], "normalized": [] }, { "id": "PMC2816692-02-Results-03_T41", "type": "Protein", "text": [ "SicP" ], "offsets": [ [ 3770, 3774 ] ], "normalized": [] }, { "id": "PMC2816692-02-Results-03_T42", "type": "Protein", "text": [ "SrcA" ], "offsets": [ [ 3834, 3838 ] ], "normalized": [] }, { "id": "PMC2816692-02-Results-03_T43", "type": "Protein", "text": [ "SrcA" ], "offsets": [ [ 3990, 3994 ] ], "normalized": [] }, { "id": "PMC2816692-02-Results-03_T46", "type": "Entity", "text": [ "N-terminus" ], "offsets": [ [ 3756, 3766 ] ], "normalized": [] } ]

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[]

[ { "id": "PMC2774163-02-Results-07__text", "type": "abstract", "text": [ "Expression of bfiS, bfmR, and mifR is required for maintenance of normal biofilm architecture while loss of expression results in biofilm architecture collapse \nOur observations indicated that BfiS (PA4197), BfmR (PA4101) and MifR (PA5511) are essential in the stage-specific development of P. aeruginosa biofilm formation. To determine whether these regulatory proteins are only essential during biofilm formation or are also necessary for the maintenance of established biofilms, we asked whether inactivation of these regulatory proteins in mature biofilms would affect biofilm architecture. Complemented mutant strains, harboring the respective regulator genes under the control of the arabinose-inducible PBAD promoter, were allowed to grow for 144 hr in flow cells to maturity (Fig. 2C, Fig. 5-0 hr) in the presence of arabinose, after which time arabinose was removed from the growth medium to stop the transcription of the respective genes. The resulting biofilm architecture was viewed over a period of 144 hr post arabinose removal using confocal microscopy. P. aeruginosa wild type harboring an empty pJN105 vector was used as control. Loss of bfiS, bfmR, and mifR expression due to arabinose removal resulted in the collapse of the mutant biofilm architecture within three days. For DeltabfiS and DeltabfmR mutant biofilms, biofilm disaggregation was noticeable as early as 24 hr post arabinose removal (not shown). The collapse was apparent by significant reduction (P<0.05) of biofilm variables including biofilm biomass and thickness, which further decreased upon continued incubation (Fig. 5, Table 3). Post 144 hr of arabinose removal, the biofilm architecture of the complemented mutants was similar to mutant biofilms lacking the respective regulatory gene (Figs. 2, 5). In contrast, no reduction of the wild type biofilm architecture was observed (Fig. 5, Table 3). These findings indicated that the three novel regulators are not only essential for the stage-specific progression of P. aeruginosa biofilms but also in the maintenance of the biofilm structure.\n" ], "offsets": [ [ 0, 2081 ] ] } ]

[ { "id": "PMC2774163-02-Results-07_T1", "type": "Protein", "text": [ "bfiS" ], "offsets": [ [ 14, 18 ] ], "normalized": [] }, { "id": "PMC2774163-02-Results-07_T2", "type": "Protein", "text": [ "bfmR" ], "offsets": [ [ 20, 24 ] ], "normalized": [] }, { "id": "PMC2774163-02-Results-07_T3", "type": "Protein", "text": [ "mifR" ], "offsets": [ [ 30, 34 ] ], "normalized": [] }, { "id": "PMC2774163-02-Results-07_T4", "type": "Protein", "text": [ "BfiS" ], "offsets": [ [ 193, 197 ] ], "normalized": [] }, { "id": "PMC2774163-02-Results-07_T5", "type": "Protein", "text": [ "PA4197" ], "offsets": [ [ 199, 205 ] ], "normalized": [] }, { "id": "PMC2774163-02-Results-07_T6", "type": "Protein", "text": [ "BfmR" ], "offsets": [ [ 208, 212 ] ], "normalized": [] }, { "id": "PMC2774163-02-Results-07_T7", "type": "Protein", "text": [ "PA4101" ], "offsets": [ [ 214, 220 ] ], "normalized": [] }, { "id": "PMC2774163-02-Results-07_T8", "type": "Protein", "text": [ "MifR" ], "offsets": [ [ 226, 230 ] ], "normalized": [] }, { "id": "PMC2774163-02-Results-07_T9", "type": "Protein", "text": [ "PA5511" ], "offsets": [ [ 232, 238 ] ], "normalized": [] }, { "id": "PMC2774163-02-Results-07_T10", "type": "Organism", "text": [ "P. aeruginosa" ], "offsets": [ [ 291, 304 ] ], "normalized": [] }, { "id": "PMC2774163-02-Results-07_T11", "type": "Chemical", "text": [ "arabinose" ], "offsets": [ [ 825, 834 ] ], "normalized": [] }, { "id": "PMC2774163-02-Results-07_T12", "type": "Chemical", "text": [ "arabinose" ], "offsets": [ [ 853, 862 ] ], "normalized": [] }, { "id": "PMC2774163-02-Results-07_T13", "type": "Organism", "text": [ "P. aeruginosa" ], "offsets": [ [ 1069, 1082 ] ], "normalized": [] }, { "id": "PMC2774163-02-Results-07_T14", "type": "Protein", "text": [ "bfiS" ], "offsets": [ [ 1155, 1159 ] ], "normalized": [] }, { "id": "PMC2774163-02-Results-07_T15", "type": "Protein", "text": [ "bfmR" ], "offsets": [ [ 1161, 1165 ] ], "normalized": [] }, { "id": "PMC2774163-02-Results-07_T16", "type": "Protein", "text": [ "mifR" ], "offsets": [ [ 1171, 1175 ] ], "normalized": [] }, { "id": "PMC2774163-02-Results-07_T17", "type": "Chemical", "text": [ "arabinose" ], "offsets": [ [ 1194, 1203 ] ], "normalized": [] }, { "id": "PMC2774163-02-Results-07_T18", "type": "Organism", "text": [ "DeltabfiS" ], "offsets": [ [ 1295, 1304 ] ], "normalized": [] }, { "id": "PMC2774163-02-Results-07_T19", "type": "Protein", "text": [ "bfiS" ], "offsets": [ [ 1300, 1304 ] ], "normalized": [] }, { "id": "PMC2774163-02-Results-07_T20", "type": "Organism", "text": [ "DeltabfmR mutant" ], "offsets": [ [ 1309, 1325 ] ], "normalized": [] }, { "id": "PMC2774163-02-Results-07_T21", "type": "Protein", "text": [ "bfmR" ], "offsets": [ [ 1314, 1318 ] ], "normalized": [] }, { "id": "PMC2774163-02-Results-07_T22", "type": "Chemical", "text": [ "arabinose" ], "offsets": [ [ 1397, 1406 ] ], "normalized": [] }, { "id": "PMC2774163-02-Results-07_T23", "type": "Chemical", "text": [ "arabinose" ], "offsets": [ [ 1634, 1643 ] ], "normalized": [] }, { "id": "PMC2774163-02-Results-07_T24", "type": "Organism", "text": [ "P. aeruginosa" ], "offsets": [ [ 2004, 2017 ] ], "normalized": [] } ]

[ { "id": "PMC2774163-02-Results-07_E1", "type": "Gene_expression", "trigger": { "text": [ "Expression" ], "offsets": [ [ 0, 10 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC2774163-02-Results-07_T1" } ] }, { "id": "PMC2774163-02-Results-07_E2", "type": "Gene_expression", "trigger": { "text": [ "Expression" ], "offsets": [ [ 0, 10 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC2774163-02-Results-07_T2" } ] }, { "id": "PMC2774163-02-Results-07_E3", "type": "Gene_expression", "trigger": { "text": [ "Expression" ], "offsets": [ [ 0, 10 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC2774163-02-Results-07_T3" } ] }, { "id": "PMC2774163-02-Results-07_E4", "type": "Negative_regulation", "trigger": { "text": [ "inactivation" ], "offsets": [ [ 499, 511 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC2774163-02-Results-07_T4" } ] }, { "id": "PMC2774163-02-Results-07_E5", "type": "Negative_regulation", "trigger": { "text": [ "inactivation" ], "offsets": [ [ 499, 511 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC2774163-02-Results-07_T6" } ] }, { "id": "PMC2774163-02-Results-07_E6", "type": "Negative_regulation", "trigger": { "text": [ "inactivation" ], "offsets": [ [ 499, 511 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC2774163-02-Results-07_T8" } ] }, { "id": "PMC2774163-02-Results-07_E7", "type": "Negative_regulation", "trigger": { "text": [ "Loss" ], "offsets": [ [ 1147, 1151 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC2774163-02-Results-07_E10" } ] }, { "id": "PMC2774163-02-Results-07_E8", "type": "Negative_regulation", "trigger": { "text": [ "Loss" ], "offsets": [ [ 1147, 1151 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC2774163-02-Results-07_E11" } ] }, { "id": "PMC2774163-02-Results-07_E9", "type": "Negative_regulation", "trigger": { "text": [ "Loss" ], "offsets": [ [ 1147, 1151 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC2774163-02-Results-07_E12" } ] }, { "id": "PMC2774163-02-Results-07_E10", "type": "Gene_expression", "trigger": { "text": [ "expression" ], "offsets": [ [ 1176, 1186 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC2774163-02-Results-07_T14" } ] }, { "id": "PMC2774163-02-Results-07_E11", "type": "Gene_expression", "trigger": { "text": [ "expression" ], "offsets": [ [ 1176, 1186 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC2774163-02-Results-07_T15" } ] }, { "id": "PMC2774163-02-Results-07_E12", "type": "Gene_expression", "trigger": { "text": [ "expression" ], "offsets": [ [ 1176, 1186 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC2774163-02-Results-07_T16" } ] } ]

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[]

[ { "id": "PMC1913099-02-Results-Discussion-04__text", "type": "abstract", "text": [ "Phage-Encoded Genes \nSF370 contains one inducible prophage (370.1) and three defective prophages (370.2, 370.3, and 370.4) that produce no infectious phage [39]. We identified 11 differentially expressed phage 370.2 genes, suggesting that this defective phage is not transcriptionally silent (Table 1). The speH gene (spy1008) was induced, and the remaining genes, hypothetically involved in replication and regulation [39], were downregulated. The speH gene encodes a mitogenic exotoxin [38] reportedly induced during polymorphonuclear leukocyte phagocytosis [8] but not implicated previously in adherence.\n" ], "offsets": [ [ 0, 608 ] ] } ]

[ { "id": "PMC1913099-02-Results-Discussion-04_T1", "type": "Organism", "text": [ "SF370" ], "offsets": [ [ 21, 26 ] ], "normalized": [] }, { "id": "PMC1913099-02-Results-Discussion-04_T2", "type": "Protein", "text": [ "speH" ], "offsets": [ [ 307, 311 ] ], "normalized": [] }, { "id": "PMC1913099-02-Results-Discussion-04_T3", "type": "Protein", "text": [ "spy1008" ], "offsets": [ [ 318, 325 ] ], "normalized": [] }, { "id": "PMC1913099-02-Results-Discussion-04_T4", "type": "Protein", "text": [ "speH" ], "offsets": [ [ 449, 453 ] ], "normalized": [] } ]

[ { "id": "PMC1913099-02-Results-Discussion-04_E1", "type": "Process", "trigger": { "text": [ "infectious" ], "offsets": [ [ 139, 149 ] ] }, "arguments": [] }, { "id": "PMC1913099-02-Results-Discussion-04_E2", "type": "Positive_regulation", "trigger": { "text": [ "induced" ], "offsets": [ [ 331, 338 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC1913099-02-Results-Discussion-04_T2" } ] }, { "id": "PMC1913099-02-Results-Discussion-04_E3", "type": "Positive_regulation", "trigger": { "text": [ "induced" ], "offsets": [ [ 504, 511 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC1913099-02-Results-Discussion-04_T4" } ] } ]

[ { "id": "PMC1913099-02-Results-Discussion-04_1", "entity_ids": [ "PMC1913099-02-Results-Discussion-04_T3", "PMC1913099-02-Results-Discussion-04_T2" ] } ]

[]

[ { "id": "PMC2266911-02-Results_and_Discussion-05__text", "type": "abstract", "text": [ "Evolution of pathogenicity \nIt has been suggested that bacteria-invertebrate interactions do not only play a role in the transmission of human pathogens but have also shaped their evolution [79]. We identified several common loci representing ancestral clusters of genes important in Y. enterocolitica and P. luminescens pathogenesis that might have evolved during the association of bacteria with invertebrates, the so-called \"pre-vertebrate\" pathosphere [121] and then been adapted to more recent pathologies in mammalians. Examples are yersiniabactin, quorum sensing-like regulators, or the urease operon. The complexity of this evolutionary concept is also demonstrated by the fact that the immune systems both of invertebrates and vertebrates are based on phagocytic cells that are attacked by hemolysins, T3SS effector proteins, and many other toxins described above. Thus, it can not be excluded that these virulence factors are able to act on both immune systems [121]. The fact that P. asymbiotica has been found to be pathogenic against humans [14] strengthens this hypothesis. Thus, P. asymbiotica might be an evolutionary link that is evolving from an insect to a mammal-pathogen. Another example that might enlighten the evolution of bacterial pathogenicity is the plasticity zone (PZ) of Y. enterocolitica, a 199 kb key locus for high pathogenicity that includes YAPIYe, secretion systems, hydrogenase loci essential for gut colonization of S. typhimurium and H. pylori [122], and iron acquisition systems. A second flagellar cluster, Flag-2, is also located within the PZ of Y. enterocolitica biotypes 2-5 [120]. It is assumed that the PZ has not been acquired by a single event of gene transfer, but through a series of independent insertions [23]. A comparison of the PZ sequence with the genome of P. luminescens is depicted in Fig. 5. A region highly similar to YAPIYe is the genome island plu0958-1166 carrying a hemolysin, hypothetical genes, the toxin/antitoxin system CcdA/CcdB, and the type IV pilus. Only few other genes or operons of the PZ are also present in P. luminescens, namely a chitinase, two iron acquisition systems, and three ysa genes, thus confirming the idea of a patchwork of horizontally acquired genes within the PZ [23]. However, given the extensive transfer of virulence factors between bacteria, the history of pathogen evolution still requires further investigation.\n" ], "offsets": [ [ 0, 2414 ] ] } ]

[ { "id": "PMC2266911-02-Results_and_Discussion-05_T1", "type": "Organism", "text": [ "human" ], "offsets": [ [ 137, 142 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-05_T2", "type": "Organism", "text": [ "Y. enterocolitica" ], "offsets": [ [ 284, 301 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-05_T3", "type": "Organism", "text": [ "P. luminescens" ], "offsets": [ [ 306, 320 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-05_T4", "type": "Organism", "text": [ "yersiniabactin" ], "offsets": [ [ 539, 553 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-05_T5", "type": "Organism", "text": [ "P. asymbiotica" ], "offsets": [ [ 992, 1006 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-05_T6", "type": "Organism", "text": [ "humans" ], "offsets": [ [ 1047, 1053 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-05_T7", "type": "Organism", "text": [ "P. asymbiotica" ], "offsets": [ [ 1094, 1108 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-05_T8", "type": "Organism", "text": [ "Y. enterocolitica" ], "offsets": [ [ 1302, 1319 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-05_T9", "type": "Organism", "text": [ "S. typhimurium" ], "offsets": [ [ 1455, 1469 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-05_T10", "type": "Organism", "text": [ "H. pylori" ], "offsets": [ [ 1474, 1483 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-05_T11", "type": "Chemical", "text": [ "iron" ], "offsets": [ [ 1495, 1499 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-05_T12", "type": "Protein", "text": [ "Flag-2" ], "offsets": [ [ 1549, 1555 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-05_T13", "type": "Organism", "text": [ "Y. enterocolitica" ], "offsets": [ [ 1590, 1607 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-05_T14", "type": "Organism", "text": [ "P. luminescens" ], "offsets": [ [ 1816, 1830 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-05_T15", "type": "Protein", "text": [ "plu0958" ], "offsets": [ [ 1909, 1916 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-05_T16", "type": "Protein", "text": [ "1166" ], "offsets": [ [ 1917, 1921 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-05_T17", "type": "Two-component-system", "text": [ "CcdA/CcdB" ], "offsets": [ [ 1991, 2000 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-05_T18", "type": "Protein", "text": [ "CcdA" ], "offsets": [ [ 1991, 1995 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-05_T19", "type": "Protein", "text": [ "CcdB" ], "offsets": [ [ 1996, 2000 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-05_T20", "type": "Organism", "text": [ "P. luminescens" ], "offsets": [ [ 2087, 2101 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-05_T21", "type": "Chemical", "text": [ "iron" ], "offsets": [ [ 2127, 2131 ] ], "normalized": [] } ]

[ { "id": "PMC2266911-02-Results_and_Discussion-05_E1", "type": "Process", "trigger": { "text": [ "virulence" ], "offsets": [ [ 914, 923 ] ] }, "arguments": [] }, { "id": "PMC2266911-02-Results_and_Discussion-05_E2", "type": "Process", "trigger": { "text": [ "virulence" ], "offsets": [ [ 2306, 2315 ] ] }, "arguments": [] } ]

[]

[]

[ { "id": "PMC2885601-04-DISCUSSION__text", "type": "abstract", "text": [ "DISCUSSION \nIn this study we describe that SeMac is a cysteine endopeptidase with limited activity against horse IgG and is unable to inhibit opsonophagocytosis of S. equi by horse PMNs in a whole blood assay. SeMac efficiently cleaves the heavy chain of human IgG. The residues of Cys102 and His272 are essential and Asp294 important for the enzymatic activity of SeMac. Thus, like GAS M1 Mac [7,8], SeMac is a cysteine endopeptidase. Although both SeMac and GAS Mac efficiently cleave human IgG, they cannot cleave the majority of total horse IgG. The peptide fragment, PELLGG, in the lower hinge region is proposed to bind to the active site of Mac [9], and the cleavage occurs between the two Gly residues (Table 1). This lower hinge region is not well conserved in the seven subgroups of horse IgG [17] (Table 1). Cleavable horse IgG1 has PELLGG, while the non-cleavable horse IgG4 has PECLSVG in the same region, suggesting that the amino acid sequences of the lower hinge region are important for cleavability by SeMac and GAS Mac. If this is true, horse IgG3 may be also cleavable by SeMac, while the other five horse IgG subgroups may not be cleaved. These horse IgG antibodies that cannot be cleaved by SeMac thus still can mediate the opsonophagocytosis of S. equi. SeMac and GAS M1 Mac show similar enzymatic specificity (Fig. 4 and Table 1), confirming the previous finding [18]. SeMac can cleave human IgG and inhibit the opsonophagocytosis of GAS by human PMNs, but it has limited enzymatic activity against horse IgG and is unable to inhibit opsonophagocytosis of S. equi by horse PMNs. Thus, there is a correlation between the enzymatic activity of SeMac and its ability to inhibit opsonophagocytosis, suggesting that SeMac functions like GAS M1 Mac in the inhibition of opsonophagocytosis of GAS by human PMNs. Timoney et al. recently reported that IdeE/SeMac reduces the bactericidal activity of isolated equine PMNs for S. equi [19]. Our results suggest that the inhibition of the bactericidal activity of PMNs may not be mediated by opsonophagocytosis or may be insignificant in whole blood. SeMac is not produced in vitro, whereas GAS Mac is [16]. The mac gene is controlled by the two-component regulatory system CovRS [5], which also controls the expression of many virulence factors including the hyaluronic capsule [20]. The hyaluronic capsule of S. equi is highly produced in vitro. These observations suggest that the semac and mac genes are regulated by different mechanisms. This suggestion is supported by only 29% DNA sequence identity between S. equi and M1 GAS in the upstream region of the semac and mac genes. S. equi is a horse pathogen. The fact that SeMac does not inhibit opsonophagocytosis of S. equi by horse PMNs indicates that SeMac is not involved in the evasion of the acquired horse immunity against S. equi. This suggests that SeMac has other unknown function.\n" ], "offsets": [ [ 0, 2909 ] ] } ]

[ { "id": "PMC2885601-04-DISCUSSION_T1", "type": "Protein", "text": [ "SeMac" ], "offsets": [ [ 43, 48 ] ], "normalized": [] }, { "id": "PMC2885601-04-DISCUSSION_T2", "type": "Protein", "text": [ "cysteine endopeptidase" ], "offsets": [ [ 54, 76 ] ], "normalized": [] }, { "id": "PMC2885601-04-DISCUSSION_T3", "type": "Organism", "text": [ "horse" ], "offsets": [ [ 107, 112 ] ], "normalized": [] }, { "id": "PMC2885601-04-DISCUSSION_T4", "type": "Protein", "text": [ "IgG" ], "offsets": [ [ 113, 116 ] ], "normalized": [] }, { "id": "PMC2885601-04-DISCUSSION_T5", "type": "Organism", "text": [ "S. equi" ], "offsets": [ [ 164, 171 ] ], "normalized": [] }, { "id": "PMC2885601-04-DISCUSSION_T6", "type": "Organism", "text": [ "horse" ], "offsets": [ [ 175, 180 ] ], "normalized": [] }, { "id": "PMC2885601-04-DISCUSSION_T7", "type": "Protein", "text": [ "SeMac" ], "offsets": [ [ 210, 215 ] ], "normalized": [] }, { "id": "PMC2885601-04-DISCUSSION_T8", "type": "Organism", "text": [ "human" ], "offsets": [ [ 255, 260 ] ], "normalized": [] }, { "id": "PMC2885601-04-DISCUSSION_T9", "type": "Protein", "text": [ "IgG" ], "offsets": [ [ 261, 264 ] ], "normalized": [] }, { "id": "PMC2885601-04-DISCUSSION_T10", "type": "Protein", "text": [ "SeMac" ], "offsets": [ [ 365, 370 ] ], "normalized": [] }, { "id": "PMC2885601-04-DISCUSSION_T11", "type": "Organism", "text": [ "GAS" ], "offsets": [ [ 383, 386 ] ], "normalized": [] }, { "id": "PMC2885601-04-DISCUSSION_T12", "type": "Protein", "text": [ "Mac" ], "offsets": [ [ 390, 393 ] ], "normalized": [] }, { "id": "PMC2885601-04-DISCUSSION_T13", "type": "Protein", "text": [ "SeMac" ], "offsets": [ [ 401, 406 ] ], "normalized": [] }, { "id": "PMC2885601-04-DISCUSSION_T14", "type": "Protein", "text": [ "cysteine endopeptidase" ], "offsets": [ [ 412, 434 ] ], "normalized": [] }, { "id": "PMC2885601-04-DISCUSSION_T15", "type": "Protein", "text": [ "SeMac" ], "offsets": [ [ 450, 455 ] ], "normalized": [] }, { "id": "PMC2885601-04-DISCUSSION_T16", "type": "Organism", "text": [ "GAS" ], "offsets": [ [ 460, 463 ] ], "normalized": [] }, { "id": "PMC2885601-04-DISCUSSION_T17", "type": "Protein", "text": [ "Mac" ], "offsets": [ [ 464, 467 ] ], "normalized": [] }, { "id": "PMC2885601-04-DISCUSSION_T18", "type": "Organism", "text": [ "human" ], "offsets": [ [ 487, 492 ] ], "normalized": [] }, { "id": "PMC2885601-04-DISCUSSION_T19", "type": "Protein", "text": [ "IgG" ], "offsets": [ [ 493, 496 ] ], "normalized": [] }, { "id": "PMC2885601-04-DISCUSSION_T20", "type": "Organism", "text": [ "horse" ], "offsets": [ [ 539, 544 ] ], "normalized": [] }, { "id": "PMC2885601-04-DISCUSSION_T21", "type": "Protein", "text": [ "IgG" ], "offsets": [ [ 545, 548 ] ], "normalized": [] }, { "id": "PMC2885601-04-DISCUSSION_T22", "type": "Protein", "text": [ "Mac" ], "offsets": [ [ 648, 651 ] ], "normalized": [] }, { "id": "PMC2885601-04-DISCUSSION_T23", "type": "Organism", "text": [ "horse" ], "offsets": [ [ 793, 798 ] ], "normalized": [] }, { "id": "PMC2885601-04-DISCUSSION_T24", "type": "Protein", "text": [ "IgG" ], "offsets": [ [ 799, 802 ] ], "normalized": [] }, { "id": "PMC2885601-04-DISCUSSION_T25", "type": "Organism", "text": [ "horse" ], "offsets": [ [ 829, 834 ] ], "normalized": [] }, { "id": "PMC2885601-04-DISCUSSION_T26", "type": "Protein", "text": [ "IgG1" ], "offsets": [ [ 835, 839 ] ], "normalized": [] }, { "id": "PMC2885601-04-DISCUSSION_T27", "type": "Organism", "text": [ "horse" ], "offsets": [ [ 876, 881 ] ], "normalized": [] }, { "id": "PMC2885601-04-DISCUSSION_T28", "type": "Protein", "text": [ "IgG4" ], "offsets": [ [ 882, 886 ] ], "normalized": [] }, { "id": "PMC2885601-04-DISCUSSION_T29", "type": "Protein", "text": [ "SeMac" ], "offsets": [ [ 1020, 1025 ] ], "normalized": [] }, { "id": "PMC2885601-04-DISCUSSION_T30", "type": "Organism", "text": [ "GAS" ], "offsets": [ [ 1030, 1033 ] ], "normalized": [] }, { "id": "PMC2885601-04-DISCUSSION_T31", "type": "Protein", "text": [ "Mac" 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[]

[]

[ { "id": "PMC2682197-02-Results-02__text", "type": "abstract", "text": [ "Rv2623 regulates mycobacterial growth in vivo \nAlthough USP family proteins are expressed by many bacterial pathogens [7],[8], to date, there has only been one in vivo study, which showed that a Salmonella USP promotes virulence in mice [17]. The observation that Rv2623 modulates mycobacterial growth in vitro prompted us to examine the effect of this USP on the in vivo kinetics of M. tuberculosis infection. Low dose aerosol infection of outbred Hartley guinea pigs with approximately30 CFU revealed a clear growth advantage of the Deltarv2623 mutant strain relative to wildtype. As early as 20 days post-infection, the number of M. tuberculosis bacilli present in the lungs of Deltarv2623-infected guinea pigs was approximately10-fold higher (p<0.05) than those infected with wildtype Erdman, and continued to rise, attaining a 15-fold (p<0.001) difference by 60 days post-infection (Figure 3A). Guinea pigs are able to control the growth of Erdman bacilli following the onset of adaptive immunity at approximately3 weeks post-infection, as evident by the relatively stable pulmonary bacterial burden beyond the 3 week time point, yet levels of Deltarv2623 bacilli continued to increase at a reduced but steady rate resulting in a rapidly progressing infection. Moreover, Deltarv2623-infected guinea pigs were moribund at 60 days post-infection, while those challenged with wildtype Erdman remained relatively healthy, providing further evidence that the mutant strain is hypervirulent in this model. Finally, complementation with a single integrated copy of rv2623 expressed from a constitutive mycobacterial promoter (Deltarv2623 attB::Phsp60Rv2623) abrogated the growth advantage of the deletion mutant (Figure 3A). Also consistent with the fulminate disease progression displayed by Deltarv2623-infected guinea pigs are the more severe pathological changes observed as early as 20 days post-infection in the lungs of these animals, as assessed by histopathological studies, including the semi-quantitative Total Lung Score analysis (Figure 3B and Protocol S1). Overall, the progression of pulmonic lesions was accelerated in Deltarv2623-infected animals compared to those infected with wildtype Erdman, accompanied by more extensive necrosis and widespread fibrosis. This increase in lung pathology was also largely reversed in animals infected with the complemented Deltarv2623 attB::Phsp60Rv2623 strain (Figure 3B and C). Results of the complementation experiments were further validated using a complemented strain Deltarv2623 attB::Prv2623Rv2623, whose expression of the wildtype universal stress protein is driven by the native rv2623 promoter [18] (Figure 3D and E). In contrast to the result of the guinea pig study, we observed no difference in the kinetics of infection between C57BL/6 mice infected with wildtype M. tuberculosis, Deltarv2623, or the attB::Phsp60 Rv2623 complemented strain in a low dose aerogenic model [19], as assessed by lung bacterial burden (Figure 4A). However, the mouse is a relatively resistant host to M. tuberculosis, particularly in strains such as C57BL/6 [20],[21]. In fact, evidence exists that M. tuberculosis triggers an immune response in mice that is in excess of that required for controlling the infection [22],[23]. Thus, the hypervirulence phenotype of Deltarv2623 observed in the susceptible guinea pig model could have been masked in the C57BL/6 mice. Consequently, we examined the virulence of Deltarv2623 in the relatively susceptible C3H/HeJ mouse strain [24]. Indeed, the Deltarv2623 mutant was markedly more virulent relative to wildtype Erdman M. tuberculosis following aerogenic infection, as assessed by the mean survival time of C3H/HeJ mice infected with these strains (62 and 25.5 days post infection for Erdman- and Deltarv2623-infected mice, respectively, p=0.0014; Figure 4B). In agreement with the survival data, quantification of tissue bacterial burden revealed a growth advantage for the Rv2623-deficient mutant relative to wildtype M. tuberculosis Erdman (Figure 4C). Manifestation of this hypervirulence phenotype is apparent as early as 3 weeks post-infection, with the lung bacterial burden of mice infected with Deltarv2623 M. tuberculosis approximately100 fold higher than that in the wildtype-infected animals. As in the guinea pig studies, results of complementation experiments involving the reintroduction of a single copy of wildtype rv2623 into Deltarv2623 M.tuberculosis reverses the hypervirulence (Figure 4C) exhibited in the C3H/HeJ model, thus indicating that the observed growth phenotype of the tubercle bacillus deficient for the universal stress protein is rv2623-specific. Finally, survival of Deltarv2623-infected mice was also significantly reduced in another susceptible mouse strain, C3HeB/FeJ (Figure S1). Together, the animal studies provide strong evidence that Rv2623 regulates the growth of M. tuberculosis in vivo: in the absence of Rv2623, the tubercle bacillus fails to establish a chronic persistent infection, exhibiting a hypervirulent phenotype.\n" ], "offsets": [ [ 0, 5062 ] ] } ]

[ { "id": "PMC2682197-02-Results-02_T1", "type": "Protein", "text": [ "Rv2623" ], "offsets": [ [ 0, 6 ] ], "normalized": [] }, { "id": "PMC2682197-02-Results-02_T2", "type": "Organism", "text": [ "Salmonella" ], "offsets": [ [ 195, 205 ] ], "normalized": [] }, { "id": "PMC2682197-02-Results-02_T3", "type": "Organism", "text": [ "mice" ], "offsets": [ [ 232, 236 ] ], "normalized": [] }, { "id": "PMC2682197-02-Results-02_T4", "type": "Protein", "text": [ "Rv2623" ], "offsets": [ [ 264, 270 ] ], "normalized": [] }, { "id": "PMC2682197-02-Results-02_T5", "type": "Organism", "text": [ "M. tuberculosis" ], "offsets": [ [ 384, 399 ] ], "normalized": [] }, { "id": "PMC2682197-02-Results-02_T6", "type": "Organism", "text": [ "guinea pigs" ], "offsets": [ [ 457, 468 ] ], "normalized": [] }, { "id": "PMC2682197-02-Results-02_T7", "type": "Organism", "text": [ "Deltarv2623" ], "offsets": [ [ 535, 546 ] ], "normalized": [] }, { "id": "PMC2682197-02-Results-02_T8", "type": "Protein", "text": [ 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"Theme", "ref_id": "PMC2682197-02-Results-02_E36" }, { "role": "Cause", "ref_id": "PMC2682197-02-Results-02_E34" } ] }, { "id": "PMC2682197-02-Results-02_E36", "type": "Process", "trigger": { "text": [ "hypervirulence" ], "offsets": [ [ 4475, 4489 ] ] }, "arguments": [ { "role": "Participant", "ref_id": "PMC2682197-02-Results-02_T78" } ] }, { "id": "PMC2682197-02-Results-02_E37", "type": "Process", "trigger": { "text": [ "infection" ], "offsets": [ [ 5013, 5022 ] ] }, "arguments": [ { "role": "Participant", "ref_id": "PMC2682197-02-Results-02_T90" } ] }, { "id": "PMC2682197-02-Results-02_E38", "type": "Process", "trigger": { "text": [ "hypervirulent" ], "offsets": [ [ 5037, 5050 ] ] }, "arguments": [ { "role": "Participant", "ref_id": "PMC2682197-02-Results-02_T90" } ] } ]

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[ { "id": "PMC2829055-02-Results-Discussion-05__text", "type": "abstract", "text": [ "Induction of a phagocytosis-resistant phenotype in the flea \nSoon after transmission, Y. pestis would be expected to encounter rapidly-responding phagocytic cells in the dermis. To assess the overall effect of the flea-specific phenotype on this encounter, we compared the interaction of Y. pestis recovered from infected fleas and from in vitro cultures with murine bone marrow macrophages. Bacteria from fleas showed significantly lower levels of phagocytosis (Fig. 4A). We have previously reported analogous findings using human polymorphonuclear leukocytes (PMNs) [7]. The yit and yip genes in a Y. pestis locus (y0181-0191) that encode predicted insecticidal-like toxins of the toxin complex (Tc) family and three linked phage-related genes were upregulated 4- to 50-fold in the flea midgut (Tables 1 and S1). We previously reported that the genes for these Tc-like proteins are highly expressed in fleas, but that their products are nontoxic to fleas [49]. yitR, a LysR-type regulator that activates the Tc-like yit genes [50], was upregulated >10-fold in the flea, but its expression was not detected in the rat bubo (Table 1). The specific induction in the flea of yitR and genes in the adjacent Tc-like yit and yip loci suggests that they are involved in adaptation to and colonization of the flea. However, deletion of yitR or yitA-yipB (y0183-y0191) does not affect the ability of Y. pestis KIM6+ to infect or block fleas (data not shown). These observations, and the fact that the Yersinia Tc proteins have toxicity to certain eukaryotic cell lines in vitro [50],[51], prompted us to investigate a possible post-transmission antiphagocytic role for these proteins in the mammalian host. To determine if the insecticidal-like toxins were involved in resistance to phagocytosis, we repeated the macrophage experiments with a Y. pestis DeltayitR mutant, which as expected showed greatly reduced expression of the yit and yip genes in vitro and in the flea (Fig. 4B). Loss of yitR significantly reduced the increased resistance to phagocytosis of Y. pestis isolated from infected fleas (Fig. 4C). Since the yit and yip genes are not required for Y. pestis to produce a transmissible infection in fleas, it was possible to compare the virulence of wild-type and DeltayitR Y. pestis following transmission by fleabite. The incidence rate and time to disease onset were identical for both Y. pestis strains, demonstrating that expression of yit and yip is not essential for flea-borne transmission or disease (data not shown). On average, the mice challenged with Y. pestis DeltayitR-infected fleas, both those that developed disease and those that did not, received a higher cumulative number of bites from blocked fleas than the mice challenged with Y. pestis-infected fleas, but this difference was not statistically significant (Fig. 5). However, it was not possible to detect any relatively minor difference in LD50 because the number of bacteria transmitted by a blocked flea varies widely [1],[52]. Even a small decrease in LD50 provided by the Yit-Yip proteins would be significant at the ecological level in the maintenance of plague transmission cycles, because the transmission efficiency of blocked fleas is very low- often only a few or no bacterial cells are transmitted in an individual fleabite [52]. Because phoP is required by Y. pestis to produce a transmissible infection in fleas (unpublished data), it was not possible to similarly assess the effect on disease transmission of phoP induction in the flea.\n" ], "offsets": [ [ 0, 3532 ] ] } ]

[ { "id": "PMC2829055-02-Results-Discussion-05_T1", "type": "Organism", "text": [ "flea" ], "offsets": [ [ 55, 59 ] ], "normalized": [] }, { "id": "PMC2829055-02-Results-Discussion-05_T2", "type": "Organism", "text": [ "Y. pestis" ], "offsets": [ [ 86, 95 ] ], "normalized": [] }, { "id": "PMC2829055-02-Results-Discussion-05_T3", "type": "Organism", "text": [ "flea" ], "offsets": [ [ 214, 218 ] ], "normalized": [] }, { "id": "PMC2829055-02-Results-Discussion-05_T4", "type": "Organism", "text": [ "Y. pestis" ], "offsets": [ [ 288, 297 ] ], "normalized": [] }, { "id": "PMC2829055-02-Results-Discussion-05_T5", "type": "Organism", "text": [ "fleas" ], "offsets": [ [ 322, 327 ] ], "normalized": [] }, { "id": "PMC2829055-02-Results-Discussion-05_T6", "type": "Organism", "text": [ "murine" ], "offsets": [ [ 360, 366 ] ], "normalized": [] }, { "id": "PMC2829055-02-Results-Discussion-05_T7", "type": "Organism", "text": [ "fleas" ], "offsets": [ [ 406, 411 ] ], "normalized": [] }, { "id": "PMC2829055-02-Results-Discussion-05_T8", "type": "Organism", "text": [ "human" ], "offsets": [ [ 526, 531 ] ], "normalized": [] }, { "id": "PMC2829055-02-Results-Discussion-05_T9", "type": "Organism", "text": [ "Y. pestis" ], "offsets": [ [ 600, 609 ] ], "normalized": [] }, { "id": "PMC2829055-02-Results-Discussion-05_T10", "type": "Organism", "text": [ "flea" ], "offsets": [ [ 784, 788 ] ], "normalized": [] }, { "id": "PMC2829055-02-Results-Discussion-05_T11", "type": "Organism", "text": [ "fleas" ], "offsets": [ [ 904, 909 ] ], "normalized": [] }, { "id": "PMC2829055-02-Results-Discussion-05_T12", "type": "Organism", "text": [ "fleas" ], "offsets": [ [ 951, 956 ] ], "normalized": [] }, { "id": "PMC2829055-02-Results-Discussion-05_T13", "type": "Protein", "text": [ "yitR" ], "offsets": [ [ 963, 967 ] ], "normalized": [] }, { "id": "PMC2829055-02-Results-Discussion-05_T14", "type": "Organism", "text": [ "flea" ], "offsets": [ [ 1066, 1070 ] ], "normalized": [] }, { "id": "PMC2829055-02-Results-Discussion-05_T15", "type": "Organism", "text": [ "rat" ], "offsets": [ [ 1115, 1118 ] ], "normalized": [] }, { "id": "PMC2829055-02-Results-Discussion-05_T16", "type": "Organism", "text": [ "flea" ], "offsets": [ [ 1165, 1169 ] ], "normalized": [] }, { "id": "PMC2829055-02-Results-Discussion-05_T17", "type": "Protein", "text": [ "yitR" ], "offsets": [ [ 1173, 1177 ] ], "normalized": [] }, { "id": "PMC2829055-02-Results-Discussion-05_T18", "type": "Organism", "text": [ "flea" ], "offsets": [ [ 1302, 1306 ] ], "normalized": [] }, { "id": "PMC2829055-02-Results-Discussion-05_T19", "type": "Protein", "text": [ "yitR" ], "offsets": [ [ 1329, 1333 ] ], "normalized": [] }, { "id": "PMC2829055-02-Results-Discussion-05_T20", "type": "Protein", "text": [ "yitA" ], "offsets": [ [ 1337, 1341 ] ], "normalized": [] }, { "id": "PMC2829055-02-Results-Discussion-05_T21", "type": "Protein", "text": [ "yipB" ], "offsets": [ [ 1342, 1346 ] ], "normalized": [] }, { "id": "PMC2829055-02-Results-Discussion-05_T22", "type": "Organism", "text": [ "Y. pestis KIM6+" ], "offsets": [ [ 1392, 1407 ] ], "normalized": [] }, { "id": "PMC2829055-02-Results-Discussion-05_T23", "type": "Organism", "text": [ "fleas" ], "offsets": [ [ 1427, 1432 ] ], "normalized": [] }, { "id": "PMC2829055-02-Results-Discussion-05_T24", "type": "Organism", "text": [ "host" ], "offsets": [ [ 1693, 1697 ] ], "normalized": [] }, { "id": "PMC2829055-02-Results-Discussion-05_T25", "type": "Organism", "text": [ "Y. pestis DeltayitR" ], "offsets": [ [ 1835, 1854 ] ], "normalized": [] }, { "id": "PMC2829055-02-Results-Discussion-05_T26", "type": "Organism", "text": [ "flea" ], "offsets": [ [ 1960, 1964 ] ], "normalized": [] }, { "id": "PMC2829055-02-Results-Discussion-05_T27", "type": "Protein", "text": [ "yitR" ], "offsets": [ [ 1984, 1988 ] ], "normalized": [] }, { "id": "PMC2829055-02-Results-Discussion-05_T28", "type": "Organism", "text": [ "Y. pestis" ], "offsets": [ [ 2055, 2064 ] ], "normalized": [] }, { "id": "PMC2829055-02-Results-Discussion-05_T29", "type": "Organism", "text": [ "fleas" ], "offsets": [ [ 2088, 2093 ] ], "normalized": [] }, { "id": "PMC2829055-02-Results-Discussion-05_T30", "type": "Organism", "text": [ "Y. pestis" ], "offsets": [ [ 2154, 2163 ] ], "normalized": [] }, { "id": "PMC2829055-02-Results-Discussion-05_T31", "type": "Organism", "text": [ "fleas" ], "offsets": [ [ 2204, 2209 ] ], "normalized": [] }, { "id": "PMC2829055-02-Results-Discussion-05_T32", "type": "Organism", "text": [ "DeltayitR Y. pestis" ], "offsets": [ [ 2269, 2288 ] ], "normalized": [] }, { "id": "PMC2829055-02-Results-Discussion-05_T33", "type": "Organism", "text": [ "Y. pestis" ], "offsets": [ [ 2394, 2403 ] ], "normalized": [] }, { "id": "PMC2829055-02-Results-Discussion-05_T34", "type": "Organism", "text": [ "flea" ], "offsets": [ [ 2479, 2483 ] ], "normalized": [] }, { "id": "PMC2829055-02-Results-Discussion-05_T35", "type": "Organism", "text": [ "mice" ], "offsets": [ [ 2548, 2552 ] ], "normalized": [] }, { "id": "PMC2829055-02-Results-Discussion-05_T36", "type": "Organism", "text": [ "Y. pestis DeltayitR-infected fleas" ], "offsets": [ [ 2569, 2603 ] ], "normalized": [] }, { "id": "PMC2829055-02-Results-Discussion-05_T37", "type": "Organism", "text": [ "fleas" ], "offsets": [ [ 2721, 2726 ] ], "normalized": [] }, { "id": "PMC2829055-02-Results-Discussion-05_T38", "type": "Organism", "text": [ "mice" ], "offsets": [ [ 2736, 2740 ] ], "normalized": [] }, { "id": "PMC2829055-02-Results-Discussion-05_T39", "type": "Organism", "text": [ "Y. pestis" ], "offsets": [ [ 2757, 2766 ] ], "normalized": [] }, { "id": "PMC2829055-02-Results-Discussion-05_T40", "type": "Organism", "text": [ "fleas" ], "offsets": [ [ 2776, 2781 ] ], "normalized": [] }, { "id": "PMC2829055-02-Results-Discussion-05_T41", "type": "Organism", "text": [ "flea" ], "offsets": [ [ 2982, 2986 ] ], "normalized": [] }, { "id": "PMC2829055-02-Results-Discussion-05_T42", "type": "Organism", "text": [ "fleas" ], "offsets": [ [ 3216, 3221 ] ], "normalized": [] }, { "id": "PMC2829055-02-Results-Discussion-05_T43", "type": "Protein", "text": [ "phoP" ], "offsets": [ [ 3330, 3334 ] ], "normalized": [] }, { "id": "PMC2829055-02-Results-Discussion-05_T44", "type": "Organism", "text": [ "Y. pestis" ], "offsets": [ [ 3350, 3359 ] ], "normalized": [] }, { "id": "PMC2829055-02-Results-Discussion-05_T45", "type": "Organism", "text": [ "fleas" ], "offsets": [ [ 3400, 3405 ] ], "normalized": [] }, { "id": "PMC2829055-02-Results-Discussion-05_T46", "type": "Protein", "text": [ "phoP" ], "offsets": [ [ 3504, 3508 ] ], "normalized": [] }, { "id": "PMC2829055-02-Results-Discussion-05_T47", "type": "Organism", "text": [ "flea" ], "offsets": [ [ 3526, 3530 ] ], "normalized": [] } ]

[ { "id": "PMC2829055-02-Results-Discussion-05_E1", "type": "Positive_regulation", "trigger": { "text": [ "Induction" ], "offsets": [ [ 0, 9 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC2829055-02-Results-Discussion-05_E2" } ] }, { "id": "PMC2829055-02-Results-Discussion-05_E2", "type": "Process", "trigger": { "text": [ "resistant" ], "offsets": [ [ 28, 37 ] ] }, "arguments": [] }, { "id": "PMC2829055-02-Results-Discussion-05_E3", "type": "Process", "trigger": { "text": [ "infected" ], "offsets": [ [ 313, 321 ] ] }, "arguments": [ { "role": "Participant", "ref_id": "PMC2829055-02-Results-Discussion-05_T4" } ] }, { "id": "PMC2829055-02-Results-Discussion-05_E4", "type": "Positive_regulation", "trigger": { "text": [ "upregulated" ], "offsets": [ [ 1038, 1049 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC2829055-02-Results-Discussion-05_T13" } ] }, { "id": "PMC2829055-02-Results-Discussion-05_E5", "type": "Gene_expression", "trigger": { "text": [ "expression" ], "offsets": [ [ 1080, 1090 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC2829055-02-Results-Discussion-05_T13" } ] }, { "id": "PMC2829055-02-Results-Discussion-05_E6", "type": "Positive_regulation", "trigger": { "text": [ "induction" ], "offsets": [ [ 1148, 1157 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC2829055-02-Results-Discussion-05_T17" } ] }, { "id": "PMC2829055-02-Results-Discussion-05_E7", "type": "Process", "trigger": { "text": [ "infect" ], "offsets": [ [ 1411, 1417 ] ] }, "arguments": [ { "role": "Participant", "ref_id": "PMC2829055-02-Results-Discussion-05_T22" } ] }, { "id": "PMC2829055-02-Results-Discussion-05_E8", "type": "Process", "trigger": { "text": [ "resistance" ], "offsets": [ [ 1761, 1771 ] ] }, "arguments": [] }, { "id": "PMC2829055-02-Results-Discussion-05_E9", "type": "Process", "trigger": { "text": [ "resistance" ], "offsets": [ [ 2025, 2035 ] ] }, "arguments": [ { "role": "Participant", "ref_id": "PMC2829055-02-Results-Discussion-05_T28" } ] }, { "id": "PMC2829055-02-Results-Discussion-05_E10", "type": "Process", "trigger": { "text": [ "infected" ], "offsets": [ [ 2079, 2087 ] ] }, "arguments": [] }, { "id": "PMC2829055-02-Results-Discussion-05_E11", "type": "Process", "trigger": { "text": [ "infection" ], "offsets": [ [ 2191, 2200 ] ] }, "arguments": [] }, { "id": "PMC2829055-02-Results-Discussion-05_E12", "type": "Process", "trigger": { "text": [ "virulence" ], "offsets": [ [ 2242, 2251 ] ] }, "arguments": [ { "role": "Participant", "ref_id": "PMC2829055-02-Results-Discussion-05_T32" } ] }, { "id": "PMC2829055-02-Results-Discussion-05_E13", "type": "Process", "trigger": { "text": [ "infected" ], "offsets": [ [ 2767, 2775 ] ] }, "arguments": [ { "role": "Participant", "ref_id": "PMC2829055-02-Results-Discussion-05_T39" } ] }, { "id": "PMC2829055-02-Results-Discussion-05_E14", "type": "Positive_regulation", "trigger": { "text": [ "required" ], "offsets": [ [ 3338, 3346 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC2829055-02-Results-Discussion-05_E15" }, { "role": "Cause", "ref_id": "PMC2829055-02-Results-Discussion-05_T43" } ] }, { "id": "PMC2829055-02-Results-Discussion-05_E15", "type": "Process", "trigger": { "text": [ "infection" ], "offsets": [ [ 3387, 3396 ] ] }, "arguments": [ { "role": "Participant", "ref_id": "PMC2829055-02-Results-Discussion-05_T44" } ] }, { "id": "PMC2829055-02-Results-Discussion-05_E16", "type": "Positive_regulation", "trigger": { "text": [ "induction" ], "offsets": [ [ 3509, 3518 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC2829055-02-Results-Discussion-05_T46" } ] } ]

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[ { "id": "PMC1974823-03-Results-02__text", "type": "abstract", "text": [ "Identification of the transcriptional start site of the mfa1 gene \nTo identify the promoter region of mfa1, the transcriptional start site was first determined. The RACE experiment was first conducted with mfa1-specific reverse primers MfaTSR1 located at 135 bp up-stream of the potential start codon and MfaTSR2 located at 37 bp downstream of the potential start codon (Fig. 2a). The transcriptional start site (the A) of mfa1 was at 434 bp upstream from the potential start codon (Fig. 2b). To verify the result, the RACE experiment was repeated with mfa1-specific reverse primers MfaTSR3 and MfaTSR4 located at 237 bp upstream of the potential start codon. The same transcriptional start site was identified. To confirm the result of RACE, reverse-transcriptional PCR using three sets of primers was performed. As shown in Fig. 2c, the PCR product was generated only with primers MfaTSF1 (corresponding to +6 to +25) and MfaTSR5 (+805 to +824). There was no PCR product generated from RT-PCR using the primers (MfaTSF3, from -139 to -121 or MfaTSF2, from -66 to -47) which correspond to the DNA sequences upstream from the transcriptional start site. This transcriptional start site is 390 bp upstream of the site previously reported (Park et al., 2006). It is likely that mfa1 gene possesses two functional promoters, which are also detected in the fimA gene of P. gingivalis (Xie & Lamont, 1999; Nishikawa et al., 2004).\n" ], "offsets": [ [ 0, 1426 ] ] } ]

[ { "id": "PMC1974823-03-Results-02_T1", "type": "Protein", "text": [ "mfa1" ], "offsets": [ [ 56, 60 ] ], "normalized": [] }, { "id": "PMC1974823-03-Results-02_T2", "type": "Protein", "text": [ "mfa1" ], "offsets": [ [ 102, 106 ] ], "normalized": [] }, { "id": "PMC1974823-03-Results-02_T3", "type": "Protein", "text": [ "mfa1" ], "offsets": [ [ 206, 210 ] ], "normalized": [] }, { "id": "PMC1974823-03-Results-02_T4", "type": "Protein", "text": [ "mfa1" ], "offsets": [ [ 423, 427 ] ], "normalized": [] }, { "id": "PMC1974823-03-Results-02_T5", "type": "Protein", "text": [ "mfa1" ], "offsets": [ [ 553, 557 ] ], "normalized": [] }, { "id": "PMC1974823-03-Results-02_T6", "type": "Protein", "text": [ "mfa1" ], "offsets": [ [ 1276, 1280 ] ], "normalized": [] }, { "id": "PMC1974823-03-Results-02_T7", "type": "Protein", "text": [ "fimA" ], "offsets": [ [ 1353, 1357 ] ], "normalized": [] }, { "id": "PMC1974823-03-Results-02_T8", "type": "Organism", "text": [ "P. gingivalis" ], "offsets": [ [ 1366, 1379 ] ], "normalized": [] } ]

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[]

[ { "id": "PMC1913099-02-Results-Discussion-13__text", "type": "abstract", "text": [ "Analysis of Previously Published Array Data \nWe applied the statistical analysis and the GenomeCrawler algorithms to data from a recently published streptococcal microarray study that is relevant for comparison to our own data (same streptococcal strain, similar array platform) [57]. In this study, the transciptomes of S. pyogenes strain SF370 and an isogenic mutant deficient for the Mga regulon were compared during exponential growth in culture broth. The Mga regulator is a growth-phase mediator of a number of surface-exposed molecules and secreted proteins involved in colonization and immune evasion during infection [58]. Although the authors of that study did not provide a statistical analysis of their data, we compared the published results for the magnitude and direction of fold-changes for each gene reported in this study with those obtained from our initial significance analysis of this dataset (presented as Table S7). A total of 256 genes reported in this study were also detected by our analysis, and the magnitude and log2-fold change were found to be in agreement for 81% of the genes. We suspect that this discrepancy results from different normalization methods used, or from different methods that were applied to analyze the ratio of signal intensities between sample and control (i.e., we analyzed the ratios of the median rather than the ratios of the mean [57]). Although the published report did not include statistical analysis of the data, we note that the statistical analysis that we performed identified four genes with significant log2-fold changes in expression (PF < 0.05; Table S8). We applied the GenomeCrawler algorithms to the statistically analyzed dataset, which identified an expanded group of genes (107 versus four) contained within 36 statistically significant clusters (PK < 0.05; Table S9). These groupings included clusters of genes that have been shown previously in streptococci to be functionally related, indicating that the algorithms were performing as expected. Two of the identified upregulated clusters (spy2009-2010 and spy2039-2040) encoding the well-studied virulence factors, C5a peptidase and SpeB, respectively, showed consistently large log2-fold changes of the genes across replicates [57]. GenomeCrawler confirmed these results by identifying both groupings as statistically significant neighbor clusters. GenomeCrawler also identified a number of clusters that contained genes known to share common function or regulation; however, they were not as apparent in the dataset without its application. For example, the algorithm identified a significant neighbor cluster spanning spy0711-0712. This grouping encodes two known virulence factors, pyrogenic exotoxin SpeC and the MF2 DNase, previously shown to be commonly regulated as an operon [11]. The algorithm also identified other neighbor clusters containing genes known to be functionally related, including spy0098-0100 (encoding the beta and beta' subunits of DNA-dependent RNA polymerase), spy2159-2160 (encoding the 50S ribosomal subunit proteins L32 and L33), and spy0741-0746 (six of the nine streptolysin S-encoding genes) [14]. Although the analysis of this previously published dataset did not reveal as many intact biological pathways as were identified from the pharyngeal cell adherence data, the inclusion of more replicates in the analysis to increase statistical power could resolve such loci. However, these results provided further supporting evidence that the GenomeCrawler algorithms can identify (1) a larger group of genes than a rigorous statistical analysis alone and (2) biologically relevant groupings in other microarray datasets, even if they contain fewer replicates than presented in our study.\n" ], "offsets": [ [ 0, 3749 ] ] } ]

[ { "id": "PMC1913099-02-Results-Discussion-13_T1", "type": "Organism", "text": [ "streptococcal strain" ], "offsets": [ [ 233, 253 ] ], "normalized": [] }, { "id": "PMC1913099-02-Results-Discussion-13_T2", "type": "Organism", "text": [ "S. pyogenes strain SF370" ], "offsets": [ [ 321, 345 ] ], "normalized": [] }, { "id": "PMC1913099-02-Results-Discussion-13_T3", "type": "Regulon-operon", "text": [ "Mga regulon" ], "offsets": [ [ 387, 398 ] ], "normalized": [] }, { "id": "PMC1913099-02-Results-Discussion-13_T4", "type": "Protein", "text": [ "Mga" ], "offsets": [ [ 387, 390 ] ], "normalized": [] }, { "id": "PMC1913099-02-Results-Discussion-13_T5", "type": "Protein", "text": [ "Mga" ], "offsets": [ [ 461, 464 ] ], "normalized": [] }, { "id": "PMC1913099-02-Results-Discussion-13_T6", "type": "Organism", "text": [ "streptococci" ], "offsets": [ [ 1922, 1934 ] ], "normalized": [] }, { "id": "PMC1913099-02-Results-Discussion-13_T7", "type": "Regulon-operon", "text": [ "spy2009-2010" ], "offsets": [ [ 2067, 2079 ] ], "normalized": [] }, { "id": "PMC1913099-02-Results-Discussion-13_T8", "type": "Protein", "text": [ "spy2009" ], "offsets": [ [ 2067, 2074 ] ], "normalized": [] }, { "id": "PMC1913099-02-Results-Discussion-13_T9", "type": "Protein", "text": [ "2010" ], "offsets": [ [ 2075, 2079 ] ], "normalized": [] }, { "id": "PMC1913099-02-Results-Discussion-13_T10", "type": "Regulon-operon", "text": [ "spy2039-2040" ], "offsets": [ [ 2084, 2096 ] ], "normalized": [] }, { "id": "PMC1913099-02-Results-Discussion-13_T11", "type": "Protein", "text": [ "spy2039" ], "offsets": [ [ 2084, 2091 ] ], "normalized": [] }, { "id": "PMC1913099-02-Results-Discussion-13_T12", "type": "Protein", "text": [ "2040" ], "offsets": [ [ 2092, 2096 ] ], "normalized": [] }, { "id": "PMC1913099-02-Results-Discussion-13_T13", "type": "Protein", "text": [ "C5a peptidase" ], "offsets": [ [ 2143, 2156 ] ], "normalized": [] }, { "id": "PMC1913099-02-Results-Discussion-13_T14", "type": "Protein", "text": [ "SpeB" ], "offsets": [ [ 2161, 2165 ] ], "normalized": [] }, { "id": "PMC1913099-02-Results-Discussion-13_T15", "type": "Protein", "text": [ "spy0711" ], "offsets": [ [ 2649, 2656 ] ], "normalized": [] }, { "id": "PMC1913099-02-Results-Discussion-13_T16", "type": "Protein", "text": [ "0712" ], "offsets": [ [ 2657, 2661 ] ], "normalized": [] }, { "id": "PMC1913099-02-Results-Discussion-13_T17", "type": "Protein", "text": [ "SpeC" ], "offsets": [ [ 2733, 2737 ] ], "normalized": [] }, { "id": "PMC1913099-02-Results-Discussion-13_T18", "type": "Protein", "text": [ "MF2" ], "offsets": [ [ 2746, 2749 ] ], "normalized": [] }, { "id": "PMC1913099-02-Results-Discussion-13_T19", "type": "Regulon-operon", "text": [ "spy0098-0100" ], "offsets": [ [ 2933, 2945 ] ], "normalized": [] }, { "id": "PMC1913099-02-Results-Discussion-13_T20", "type": "Protein", "text": [ "spy0098" ], "offsets": [ [ 2933, 2940 ] ], "normalized": [] }, { "id": "PMC1913099-02-Results-Discussion-13_T21", "type": "Protein", "text": [ "0100" ], "offsets": [ [ 2941, 2945 ] ], "normalized": [] }, { "id": "PMC1913099-02-Results-Discussion-13_T22", "type": "Regulon-operon", "text": [ "spy2159-2160" ], "offsets": [ [ 3018, 3030 ] ], "normalized": [] }, { "id": "PMC1913099-02-Results-Discussion-13_T23", "type": "Protein", "text": [ "spy2159" ], "offsets": [ [ 3018, 3025 ] ], "normalized": [] }, { "id": "PMC1913099-02-Results-Discussion-13_T24", "type": "Protein", "text": [ "2160" ], "offsets": [ [ 3026, 3030 ] ], "normalized": [] }, { "id": "PMC1913099-02-Results-Discussion-13_T25", "type": "Protein", "text": [ "L32" ], "offsets": [ [ 3076, 3079 ] ], "normalized": [] }, { "id": "PMC1913099-02-Results-Discussion-13_T26", "type": "Protein", "text": [ "L33" ], "offsets": [ [ 3084, 3087 ] ], "normalized": [] }, { "id": "PMC1913099-02-Results-Discussion-13_T27", "type": "Regulon-operon", "text": [ "spy0741-0746" ], "offsets": [ [ 3094, 3106 ] ], "normalized": [] }, { "id": "PMC1913099-02-Results-Discussion-13_T28", "type": "Protein", "text": [ "spy0741" ], "offsets": [ [ 3094, 3101 ] ], "normalized": [] }, { "id": "PMC1913099-02-Results-Discussion-13_T29", "type": "Protein", "text": [ "0746" ], "offsets": [ [ 3102, 3106 ] ], "normalized": [] }, { "id": "PMC1913099-02-Results-Discussion-13_T30", "type": "Protein", "text": [ "streptolysin S" ], "offsets": [ [ 3124, 3138 ] ], "normalized": [] } ]

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[ { "id": "PMC2682197-01-Introduction__text", "type": "abstract", "text": [ "Introduction \nMycobacterium tuberculosis, one of the most successful human pathogens, infects one-third of the world's population, causing nearly two million deaths per year [1]. Epidemiological data estimate that, in the immunocompetent host, only approximately10% of M. tuberculosis infection progress to active pulmonary disease. The remaining 90% of the infected individuals are asymptomatic, and are generally believed to harbor latent bacilli that can reactivate to cause tuberculous diseases, sometimes decades after the initial infection. Recrudescence of latent bacilli contributes significantly to the incidence of adult tuberculosis [2], yet the physiological state of latent bacilli and the signals that promote dormancy in the host remain incompletely defined. Understanding the dynamic interaction between host and pathogen during the establishment of persistent M. tuberculosis infection will guide the design of novel treatment for the latently infected population. An intracellular pathogen, M. tuberculosis must possess a finely tuned signaling network to sense and transduce complex environmental signals, ensuring survival of the bacilli within host cells. Nitric oxide (NO) produced by infected macrophages and relative hypoxia are signals likely to be encountered within tuberculous lesions that are believed, based on in vitro studies, to promote latency by prompting the M. tuberculosis dormancy response. Exposure to these stimuli results in the induction of approximately50 M. tuberculosis genes, designated the dormancy regulon, via the two-component regulatory system DosR-DosS (see Table S1 for accession numbers) [3],[4],[5]. Among this set of genes is rv2623, one of eight M. tuberculosis genes annotated as containing the universal stress protein (USP) domain [6],[7]. Members of this ancient and conserved family of proteins are found in all forms of life and can be induced by a variety of environmental stresses [8],[9]. However, the roles of USP proteins in microbial pathogenesis are incompletely understood. Interestingly, rv2623 is one of the most strongly induced transcripts of the dormancy regulon [3],[4],[5]. Increased expression of rv2623 was also observed following phagocytosis by macrophages [10] and in the lungs of chronically infected mice [11], supporting a functional role during persistent M. tuberculosis infection. The present study reveals that: i) deletion of rv2623 confers hypervirulence on the tubercle bacillus in animal models, suggesting that expression of Rv2623 may be conducive to the establishment of persistence in vivo; ii) overexpression of Rv2623 results in growth retardation of recipient strains in vitro, further supporting a growth-regulatory role; iii) Rv2623 binds ATP; and finally, through mutagenesis study guided by crystallographic analysis of Rv2623 (the first such study for a tandem-domain USP), we show that iv) the growth-regulating attribute of this M. tuberculosis USP is linked to its ATP-binding capacity.\n" ], "offsets": [ [ 0, 2997 ] ] } ]

[ { "id": "PMC2682197-01-Introduction_T1", "type": "Organism", "text": [ "Mycobacterium tuberculosis" ], "offsets": [ [ 14, 40 ] ], "normalized": [] }, { "id": "PMC2682197-01-Introduction_T2", "type": "Organism", "text": [ "human" ], "offsets": [ [ 69, 74 ] ], "normalized": [] }, { "id": "PMC2682197-01-Introduction_T3", "type": "Organism", "text": [ "M. tuberculosis" ], "offsets": [ [ 269, 284 ] ], "normalized": [] }, { "id": "PMC2682197-01-Introduction_T4", "type": "Organism", "text": [ "M. tuberculosis" ], "offsets": [ [ 877, 892 ] ], "normalized": [] }, { "id": "PMC2682197-01-Introduction_T5", "type": "Organism", "text": [ "M. tuberculosis" ], "offsets": [ [ 1009, 1024 ] ], "normalized": [] }, { "id": "PMC2682197-01-Introduction_T6", "type": "Chemical", "text": [ "Nitric oxide" ], "offsets": [ [ 1177, 1189 ] ], "normalized": [] }, { "id": "PMC2682197-01-Introduction_T7", "type": "Chemical", "text": [ "NO" ], "offsets": [ [ 1191, 1193 ] ], "normalized": [] }, { "id": "PMC2682197-01-Introduction_T8", "type": "Organism", "text": [ "M. tuberculosis" ], "offsets": [ [ 1395, 1410 ] ], "normalized": [] }, { "id": "PMC2682197-01-Introduction_T9", "type": "Organism", "text": [ "M. tuberculosis" ], "offsets": [ [ 1500, 1515 ] ], "normalized": [] }, { "id": "PMC2682197-01-Introduction_T10", "type": "Two-component-system", "text": [ "DosR-DosS" ], "offsets": [ [ 1596, 1605 ] ], "normalized": [] }, { "id": "PMC2682197-01-Introduction_T11", "type": "Protein", "text": [ "DosR" ], "offsets": [ [ 1596, 1600 ] ], "normalized": [] }, { "id": "PMC2682197-01-Introduction_T12", "type": "Protein", "text": [ "DosS" ], "offsets": [ [ 1601, 1605 ] ], "normalized": [] }, { "id": "PMC2682197-01-Introduction_T13", "type": "Protein", "text": [ "rv2623" ], "offsets": [ [ 1683, 1689 ] ], "normalized": [] }, { "id": "PMC2682197-01-Introduction_T14", "type": "Organism", "text": [ "M. tuberculosis" ], "offsets": [ [ 1704, 1719 ] ], "normalized": [] }, { "id": "PMC2682197-01-Introduction_T15", "type": "Protein", "text": [ "rv2623" ], "offsets": [ [ 2061, 2067 ] ], "normalized": [] }, { "id": "PMC2682197-01-Introduction_T16", "type": "Protein", "text": [ "rv2623" ], "offsets": [ [ 2177, 2183 ] ], "normalized": [] }, { "id": "PMC2682197-01-Introduction_T17", "type": "Organism", "text": [ "mice" ], "offsets": [ [ 2286, 2290 ] ], "normalized": [] }, { "id": "PMC2682197-01-Introduction_T18", "type": "Organism", "text": [ "M. tuberculosis" ], "offsets": [ [ 2344, 2359 ] ], "normalized": [] }, { "id": "PMC2682197-01-Introduction_T19", "type": "Protein", "text": [ "rv2623" ], "offsets": [ [ 2418, 2424 ] ], "normalized": [] }, { "id": "PMC2682197-01-Introduction_T20", "type": "Organism", "text": [ "tubercle bacillus" ], "offsets": [ [ 2455, 2472 ] ], "normalized": [] }, { "id": "PMC2682197-01-Introduction_T21", "type": "Protein", "text": [ "Rv2623" ], "offsets": [ [ 2521, 2527 ] ], "normalized": [] }, { "id": "PMC2682197-01-Introduction_T22", "type": "Protein", "text": [ "Rv2623" ], "offsets": [ [ 2612, 2618 ] ], "normalized": [] }, { "id": "PMC2682197-01-Introduction_T23", "type": "Protein", "text": [ "Rv2623" ], "offsets": [ [ 2730, 2736 ] ], "normalized": [] }, { "id": "PMC2682197-01-Introduction_T24", "type": "Chemical", "text": [ "ATP" ], "offsets": [ [ 2743, 2746 ] ], "normalized": [] }, { "id": "PMC2682197-01-Introduction_T25", "type": "Protein", "text": [ "Rv2623" ], "offsets": [ [ 2826, 2832 ] ], "normalized": [] }, { "id": "PMC2682197-01-Introduction_T26", "type": "Organism", "text": [ "M. tuberculosis" ], "offsets": [ [ 2938, 2953 ] ], "normalized": [] }, { "id": "PMC2682197-01-Introduction_T27", "type": "Chemical", "text": [ "ATP" ], "offsets": [ [ 2975, 2978 ] ], "normalized": [] } ]

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[ { "id": "PMC2639726-01-Introduction__text", "type": "abstract", "text": [ "Introduction \nGastrointestinal infections are the second most common cause of childhood mortality in the developing world and Typhoid alone (caused by serovar Typhi) is estimated to result in 500,000 deaths per year [1]. In addition to fluid and electrolyte loss, non-typhoidal Salmonella often results in septicemia in children and in HIV infected adults in developing countries with a fatality rate of 25% or greater [2]. Salmonella enteriditis serotype Typhimurium (referred to simply as Salmonella or Typhimurium below) is a paradigm for understanding intracellular pathogenesis because of its established genetics and simple and inexpensive animal model - the mouse. All strains of Salmonella enteriditis share at least 95% sequence identity; the differences are associated with growth in a specific host or survival in an environmental niche. More than 4% of the entire genome is required for Typhimurium to infect the mouse [3]. These genes are widely distributed around the entire circular chromosome including many genes not involved in metabolic processes nor required for growth under laboratory conditions. Numerous studies have assigned a small fraction of these genes to specific steps in mouse infection but most are still a mystery. Many virulence genes are attributable to horizontally acquired DNA sequences that are not present in nonpathogenic but related bacteria. These regions include two 40 kb stretches of DNA termed Salmonella pathogenicity islands 1 (SPI-1) and 2 (SPI-2) [4]-[9]. SPI-1 and SPI-2 encode a secretion apparatus resembling a needle and related to the bacterial flagella that uses the proton motive force to secrete proteins directly into the cytoplasm of the eukaryotic cell [10]. Secretion can take place from extracellular bacteria that are juxtaposed to the surface of the cell or from intracellular bacteria located in vacuoles. The two type III secretion systems are expressed under different environmental conditions and play distinct roles in pathogenesis. SPI-2 is known to be required for systemic infection whereas SPI-1 plays an essential role during intestinal infection and in mouse persistence [11]-[14]. During the course of systemic infection in mice, bacteria are found within neutrophils, monocytes, dendritic cells, and B and T cells but are not found extracellularly until the last one or two days immediately before death of the mouse [15]-[17]. How Salmonella survives and replicates within the host and how it expresses virulence genes at the appropriate time during systemic infection is little understood and the subject of this work. Technological advances in the last 10 years such as microarrays, whole genome sequences, and global proteomics have provided a more complete picture of gene expression for a number of bacteria. The goal of the current work is to develop a predictive model for host-pathogen interactions that will provide insight into how Salmonella responds to specific conditions in the host. This approach was based on identification of regulators that were necessary for Salmonella to cause a systemic infection and transcriptional profiling of isogenic derivatives missing the regulator under a variety of growth conditions. The transcriptional profiles provided more than 300,000 data point, necessitating computer analysis. We have used SEBINI (Software Environment for Biological Network Inference; [18]) to directly compare multiple network algorithms. The network inference algorithm that we have used is the context likelihood of relatedness (CLR) to analyze the gene expression profiles [19]. CLR is an extension of the relevance network class of machine learning algorithms [20] and provides the highest precision of several algorithms tested [19]. At a 60% true positive rate, CLR identified 1,079 regulatory interactions in E. coli, of which 338 were in previously known networks and 741 were novel predictions (ibid). The analysis of our data provided a testable regulatory hierarchy and a list of genes with similar expression profiles as described below.\n" ], "offsets": [ [ 0, 4057 ] ] } ]

[ { "id": "PMC2639726-01-Introduction_T1", "type": "Organism", "text": [ "Typhi" ], "offsets": [ [ 159, 164 ] ], "normalized": [] }, { "id": "PMC2639726-01-Introduction_T2", "type": "Organism", "text": [ "Salmonella" ], "offsets": [ [ 278, 288 ] ], "normalized": [] }, { "id": "PMC2639726-01-Introduction_T3", "type": "Organism", "text": [ "children" ], "offsets": [ [ 320, 328 ] ], "normalized": [] }, { "id": "PMC2639726-01-Introduction_T4", "type": "Organism", "text": [ "HIV infected adults" ], "offsets": [ [ 336, 355 ] ], "normalized": [] }, { "id": "PMC2639726-01-Introduction_T5", "type": "Organism", "text": [ "HIV" ], "offsets": [ [ 336, 339 ] ], "normalized": [] }, { "id": "PMC2639726-01-Introduction_T6", "type": "Organism", "text": [ "Salmonella enteriditis serotype Typhimurium" ], "offsets": [ [ 424, 467 ] ], "normalized": [] }, { "id": "PMC2639726-01-Introduction_T7", "type": "Organism", "text": [ "Salmonella" ], "offsets": [ [ 491, 501 ] ], "normalized": [] }, { "id": "PMC2639726-01-Introduction_T8", "type": "Organism", "text": [ "Typhimurium" ], "offsets": [ [ 505, 516 ] ], "normalized": [] }, { "id": "PMC2639726-01-Introduction_T9", "type": "Organism", "text": [ "mouse" ], "offsets": [ [ 665, 670 ] ], "normalized": [] }, { "id": "PMC2639726-01-Introduction_T10", "type": "Organism", "text": [ "Salmonella enteriditis" ], "offsets": [ [ 687, 709 ] ], "normalized": [] }, { "id": "PMC2639726-01-Introduction_T11", "type": "Organism", "text": [ "Typhimurium" ], "offsets": [ [ 899, 910 ] ], "normalized": [] }, { "id": "PMC2639726-01-Introduction_T12", "type": "Organism", "text": [ "mouse" ], "offsets": [ [ 925, 930 ] ], "normalized": [] }, { "id": "PMC2639726-01-Introduction_T13", "type": "Organism", "text": [ "mouse" ], "offsets": [ [ 1203, 1208 ] ], "normalized": [] }, { "id": "PMC2639726-01-Introduction_T14", "type": "Organism", "text": [ "Salmonella" ], "offsets": [ [ 1442, 1452 ] ], "normalized": [] }, { "id": "PMC2639726-01-Introduction_T15", "type": "Organism", "text": [ "mouse" ], "offsets": [ [ 2131, 2136 ] ], "normalized": [] }, { "id": "PMC2639726-01-Introduction_T16", "type": "Organism", "text": [ "mice" ], "offsets": [ [ 2203, 2207 ] ], "normalized": [] }, { "id": "PMC2639726-01-Introduction_T17", "type": "Organism", "text": [ "mouse" ], "offsets": [ [ 2391, 2396 ] ], "normalized": [] }, { "id": "PMC2639726-01-Introduction_T18", "type": "Organism", "text": [ "Salmonella" ], "offsets": [ [ 2412, 2422 ] ], "normalized": [] }, { "id": "PMC2639726-01-Introduction_T19", "type": "Organism", "text": [ "Salmonella" ], "offsets": [ [ 2923, 2933 ] ], "normalized": [] }, { "id": "PMC2639726-01-Introduction_T20", "type": "Organism", "text": [ "Salmonella" ], "offsets": [ [ 3059, 3069 ] ], "normalized": [] }, { "id": "PMC2639726-01-Introduction_T21", "type": "Organism", "text": [ "E. coli" ], "offsets": [ [ 3823, 3830 ] ], "normalized": [] } ]

[ { "id": "PMC2639726-01-Introduction_E1", "type": "Process", "trigger": { "text": [ "infections" ], "offsets": [ [ 31, 41 ] ] }, "arguments": [] }, { "id": "PMC2639726-01-Introduction_E2", "type": "Process", "trigger": { "text": [ "infect" ], "offsets": [ [ 914, 920 ] ] }, "arguments": [ { "role": "Participant", "ref_id": "PMC2639726-01-Introduction_T11" } ] }, { "id": "PMC2639726-01-Introduction_E3", "type": "Process", "trigger": { "text": [ "infection" ], "offsets": [ [ 1209, 1218 ] ] }, "arguments": [] }, { "id": "PMC2639726-01-Introduction_E4", "type": "Process", "trigger": { "text": [ "virulence" ], "offsets": [ [ 1254, 1263 ] ] }, "arguments": [] }, { "id": "PMC2639726-01-Introduction_E5", "type": "Process", "trigger": { "text": [ "infection" ], "offsets": [ [ 2114, 2123 ] ] }, "arguments": [] }, { "id": "PMC2639726-01-Introduction_E6", "type": "Process", "trigger": { "text": [ "infection" ], "offsets": [ [ 2190, 2199 ] ] }, "arguments": [] }, { "id": "PMC2639726-01-Introduction_E7", "type": "Process", "trigger": { "text": [ "virulence" ], "offsets": [ [ 2484, 2493 ] ] }, "arguments": [] }, { "id": "PMC2639726-01-Introduction_E8", "type": "Process", "trigger": { "text": [ "infection" ], "offsets": [ [ 2540, 2549 ] ] }, "arguments": [ { "role": "Participant", "ref_id": "PMC2639726-01-Introduction_T18" } ] }, { "id": "PMC2639726-01-Introduction_E9", "type": "Process", "trigger": { "text": [ "infection" ], "offsets": [ [ 3090, 3099 ] ] }, "arguments": [ { "role": "Participant", "ref_id": "PMC2639726-01-Introduction_T20" } ] } ]

[]

[]

[ { "id": "PMC2565068-02-Results-05__text", "type": "abstract", "text": [ "Enhanced expression of the slo and the scpC genes in severe invasive GAS is attributed to mutation of a transcriptional regulator CsrS \nAlthough sequences of the slo gene and the scpC gene were identical among clinically isolated non-invasive and severe invasive GAS (data not shown), Figure 5A shows that the slo and the scpC genes were expressed in the severe invasive GAS greater in extent than those in the non-invasive GAS. The expression of the other virulence-associated genes, such as IgG degrading protease of GAS, Mac-1-like protein (mac), nicotine adenine dinucleotide glycohydrolase (nga), polysaccharide capsule production (hasA), and C5a peptidase (scpA), was also upregulted in the severe invasive GAS, greater than that detected in the non-invasive GAS (Figure 5A). Contrarily, the levels of streptococcal pyrogenic endotoxin (speB), SLS (sagA), and mitogenic factor (speF) genes were downregulated in the severe invasive GAS, compared to that found in the non-invasive GAS (Figure 5A and data not shown). These results demonstrate the prominent changes in the transcriptional profile of several virulence-associated genes, including the slo and the scpC, in the all severe invasive GAS. Mutation of csrR or csrS can cause significant alterations in virulence in mouse models of infection,either increasing lethality or the severity of localized soft tissue lesions [5], [6]. GAS isolates from mice with severe invasive disease had mutations in csrS, raising the notion that CsrR/S function is important in modulating gene expression during infection. Therefore, we analyzed the linkage between the csrS and/or csrR genes and the property of invasive GAS infection by sequencing these genes in the emm49 strains used in this study. The nucleotide sequence of the csrR gene was identical in all the isolates, and that of the csrS gene was identical among the all non-invasive GAS isolates (data not shown). However, as shown in Figure 5B, the csrS genes of all clinically isolated severe invasive GAS had a deletion, a point mutation, or an insertion, thereby, resulting in the creation of translational stop codons (NIH147, NIH226, NIH230, and NIH269) or in a mutation in the presumed kinase domain (NIH200). In order to clarify the role of CsrS regarding expression of the virulence-associated genes and resistance to PMN killing, we introduced the intact csrS gene of the 1566 strain into the severe invasive GAS (see Figure 5A). The csrS-introduced severe invasive GAS reduced the expression levels of the slo and the scpC genes, comparable to those detected in the non-invasive GAS. In contrast, the expression of speB was upregulated to the level observed in the non-invasive GAS (Figure 5A). In parallel with the expression profile of slo and scpC in the severe invasive GAS, introduction of the intact csrS gene into the severe invasive GAS restored the susceptibility to the killing by PMN (p=0.015 compared with severe invasive isolates +CsrS) (Figure 6A), abrogated the inhibition of PMN migration by degradation of IL-8 (p=0.002 compared with invasive isolates +CsrS) (Figure 4A, 4B, and 6B), and diminished the killing activity for PMN by necrosis (p=0.00016 compared with invasive isolates +CsrS) (Figure 3A, 3C, and 6C), These results strongly suggest that mutations in the csrS gene correspond to the immunocompromized activity in the severe invasive isolates, associated with inhibition of PMN recruitment and survival.\n" ], "offsets": [ [ 0, 3452 ] ] } ]

[ { "id": "PMC2565068-02-Results-05_T1", "type": "Protein", "text": [ "slo" ], "offsets": [ [ 27, 30 ] ], "normalized": [] }, { "id": "PMC2565068-02-Results-05_T2", "type": "Protein", "text": [ "scpC" ], "offsets": [ [ 39, 43 ] ], "normalized": [] }, { "id": "PMC2565068-02-Results-05_T3", "type": "Organism", "text": [ "invasive GAS" ], "offsets": [ [ 60, 72 ] ], "normalized": [] }, { "id": "PMC2565068-02-Results-05_T4", "type": "Protein", "text": [ "CsrS" ], "offsets": [ [ 130, 134 ] ], "normalized": [] }, { "id": "PMC2565068-02-Results-05_T5", "type": "Protein", "text": [ "slo" ], "offsets": [ [ 162, 165 ] ], "normalized": [] }, { "id": "PMC2565068-02-Results-05_T6", "type": "Protein", "text": [ "scpC" ], "offsets": [ [ 179, 183 ] ], "normalized": [] }, { "id": "PMC2565068-02-Results-05_T7", "type": "Organism", "text": [ "non-invasive" ], "offsets": [ [ 230, 242 ] ], "normalized": [] }, { "id": "PMC2565068-02-Results-05_T8", "type": "Organism", "text": [ "invasive GAS" ], "offsets": [ [ 254, 266 ] ], "normalized": [] }, { "id": "PMC2565068-02-Results-05_T9", "type": "Protein", "text": [ "slo" ], "offsets": [ [ 310, 313 ] ], "normalized": [] }, { "id": "PMC2565068-02-Results-05_T10", "type": "Protein", "text": [ "scpC" ], "offsets": [ [ 322, 326 ] ], "normalized": [] }, { "id": "PMC2565068-02-Results-05_T11", "type": "Organism", "text": [ "invasive GAS" ], "offsets": [ [ 362, 374 ] ], "normalized": [] }, { "id": "PMC2565068-02-Results-05_T12", "type": "Organism", "text": [ "non-invasive GAS" ], "offsets": [ [ 411, 427 ] ], "normalized": [] }, { "id": "PMC2565068-02-Results-05_T13", "type": "Protein", "text": [ "IgG" ], "offsets": [ [ 493, 496 ] ], "normalized": [] }, { "id": "PMC2565068-02-Results-05_T14", "type": "Protein", "text": [ "GAS" ], "offsets": [ [ 519, 522 ] ], "normalized": [] }, { "id": "PMC2565068-02-Results-05_T15", "type": "Protein", "text": [ "Mac-1" ], "offsets": [ [ 524, 529 ] ], "normalized": [] }, { "id": "PMC2565068-02-Results-05_T16", "type": "Protein", "text": [ "mac" ], "offsets": [ [ 544, 547 ] ], "normalized": [] }, { "id": "PMC2565068-02-Results-05_T17", "type": "Chemical", "text": [ "nicotine adenine dinucleotide" ], "offsets": [ [ 550, 579 ] ], "normalized": [] }, { "id": "PMC2565068-02-Results-05_T18", "type": "Protein", "text": [ "nga" ], "offsets": [ [ 596, 599 ] ], "normalized": [] }, { "id": "PMC2565068-02-Results-05_T19", "type": "Chemical", "text": [ "polysaccharide capsule" ], "offsets": [ [ 602, 624 ] ], "normalized": [] }, { "id": "PMC2565068-02-Results-05_T20", "type": "Protein", "text": [ "hasA" ], "offsets": [ [ 637, 641 ] ], "normalized": [] }, { "id": "PMC2565068-02-Results-05_T21", "type": "Protein", "text": [ "scpA" ], "offsets": [ [ 663, 667 ] ], "normalized": [] }, { "id": "PMC2565068-02-Results-05_T22", "type": "Organism", "text": [ "invasive GAS" ], "offsets": [ [ 704, 716 ] ], "normalized": [] }, { "id": "PMC2565068-02-Results-05_T23", "type": "Organism", "text": [ "non-invasive GAS" ], "offsets": [ [ 752, 768 ] ], "normalized": [] }, { "id": "PMC2565068-02-Results-05_T24", "type": "Protein", "text": [ "speB" ], "offsets": [ [ 843, 847 ] ], "normalized": [] }, { "id": "PMC2565068-02-Results-05_T25", "type": "Protein", "text": [ "SLS" ], "offsets": [ [ 850, 853 ] ], "normalized": [] }, { "id": "PMC2565068-02-Results-05_T26", "type": "Protein", "text": [ "sagA" ], "offsets": [ [ 855, 859 ] ], "normalized": [] }, { "id": "PMC2565068-02-Results-05_T27", "type": "Protein", "text": [ "speF" ], "offsets": [ [ 884, 888 ] ], "normalized": [] }, { "id": "PMC2565068-02-Results-05_T28", "type": "Organism", "text": [ "invasive GAS" ], "offsets": [ [ 929, 941 ] ], "normalized": [] }, { "id": "PMC2565068-02-Results-05_T29", "type": "Organism", "text": [ "non-invasive GAS" ], "offsets": [ [ 973, 989 ] ], "normalized": [] }, { "id": "PMC2565068-02-Results-05_T30", "type": "Protein", "text": [ "slo" ], "offsets": [ [ 1154, 1157 ] ], "normalized": [] }, { "id": "PMC2565068-02-Results-05_T31", "type": "Protein", "text": [ "scpC" ], "offsets": [ [ 1166, 1170 ] ], "normalized": [] }, { "id": "PMC2565068-02-Results-05_T32", "type": "Organism", "text": [ "invasive GAS" ], "offsets": [ [ 1190, 1202 ] ], "normalized": [] }, { "id": "PMC2565068-02-Results-05_T33", "type": "Protein", "text": [ "csrR" ], "offsets": [ [ 1216, 1220 ] ], "normalized": [] }, { "id": "PMC2565068-02-Results-05_T34", "type": "Protein", "text": [ "csrS" ], "offsets": [ [ 1224, 1228 ] ], "normalized": [] }, { "id": "PMC2565068-02-Results-05_T35", "type": "Organism", "text": [ "mouse" ], "offsets": [ [ 1279, 1284 ] ], "normalized": [] }, { "id": "PMC2565068-02-Results-05_T36", "type": "Organism", "text": [ "GAS" ], "offsets": [ [ 1392, 1395 ] ], "normalized": [] }, { "id": "PMC2565068-02-Results-05_T37", "type": "Organism", "text": [ "mice" ], "offsets": [ [ 1410, 1414 ] ], "normalized": [] }, { "id": "PMC2565068-02-Results-05_T38", "type": "Protein", "text": [ "csrS" ], "offsets": [ [ 1461, 1465 ] ], "normalized": [] }, { "id": "PMC2565068-02-Results-05_T39", "type": "Two-component-system", "text": [ "CsrR/S" ], "offsets": [ [ 1491, 1497 ] ], "normalized": [] }, { "id": "PMC2565068-02-Results-05_T40", "type": "Protein", "text": [ "CsrR" ], "offsets": [ [ 1491, 1495 ] ], "normalized": [] }, { "id": "PMC2565068-02-Results-05_T41", "type": "Protein", "text": [ "S" ], "offsets": [ [ 1496, 1497 ] ], "normalized": [] }, { "id": "PMC2565068-02-Results-05_T42", "type": "Protein", "text": [ "csrS" ], "offsets": [ [ 1615, 1619 ] ], "normalized": [] }, { "id": "PMC2565068-02-Results-05_T43", "type": "Protein", "text": [ "csrR" ], "offsets": [ [ 1627, 1631 ] ], "normalized": [] }, { "id": "PMC2565068-02-Results-05_T44", "type": "Organism", "text": [ "invasive GAS" ], "offsets": [ [ 1658, 1670 ] ], "normalized": [] }, { "id": "PMC2565068-02-Results-05_T45", "type": "Organism", "text": [ "emm49 strains" ], "offsets": [ [ 1714, 1727 ] ], "normalized": [] }, { "id": "PMC2565068-02-Results-05_T46", "type": "Protein", "text": [ "emm49" ], "offsets": [ [ 1714, 1719 ] ], "normalized": [] }, { "id": "PMC2565068-02-Results-05_T47", "type": "Protein", "text": [ "csrR" ], "offsets": [ [ 1779, 1783 ] ], "normalized": [] }, { "id": "PMC2565068-02-Results-05_T48", "type": "Protein", "text": [ "csrS" ], "offsets": [ [ 1840, 1844 ] ], "normalized": [] }, { "id": "PMC2565068-02-Results-05_T49", "type": "Organism", "text": [ "non-invasive GAS" ], "offsets": [ [ 1878, 1894 ] ], "normalized": [] }, { "id": "PMC2565068-02-Results-05_T50", "type": "Protein", "text": [ "csrS" ], "offsets": [ [ 1958, 1962 ] ], "normalized": [] }, { "id": "PMC2565068-02-Results-05_T51", "type": "Organism", "text": [ "invasive GAS" ], "offsets": [ [ 2003, 2015 ] ], "normalized": [] }, { "id": "PMC2565068-02-Results-05_T52", "type": "Organism", "text": [ "NIH147" ], "offsets": [ [ 2132, 2138 ] ], "normalized": [] }, { "id": "PMC2565068-02-Results-05_T53", "type": "Organism", "text": [ "NIH226" ], "offsets": [ [ 2140, 2146 ] ], "normalized": [] }, { "id": "PMC2565068-02-Results-05_T54", "type": "Organism", "text": [ "NIH230" ], "offsets": [ [ 2148, 2154 ] ], "normalized": [] }, { "id": "PMC2565068-02-Results-05_T55", "type": "Organism", "text": [ "NIH269" ], "offsets": [ [ 2160, 2166 ] ], "normalized": [] }, { "id": "PMC2565068-02-Results-05_T56", "type": "Organism", "text": [ "NIH200" ], "offsets": [ [ 2216, 2222 ] ], "normalized": [] }, { "id": "PMC2565068-02-Results-05_T57", "type": "Protein", "text": [ "CsrS" ], "offsets": [ [ 2257, 2261 ] ], "normalized": [] }, { "id": "PMC2565068-02-Results-05_T58", "type": "Protein", "text": [ "csrS" ], "offsets": [ [ 2373, 2377 ] ], "normalized": [] }, { "id": "PMC2565068-02-Results-05_T59", "type": "Organism", "text": [ "1566" ], "offsets": [ [ 2390, 2394 ] ], "normalized": [] }, { "id": "PMC2565068-02-Results-05_T60", "type": "Organism", "text": [ "invasive GAS" ], "offsets": [ [ 2418, 2430 ] ], "normalized": [] }, { "id": "PMC2565068-02-Results-05_T61", "type": "Organism", "text": [ "csrS-introduced severe invasive GAS" ], "offsets": [ [ 2452, 2487 ] ], "normalized": [] }, { "id": "PMC2565068-02-Results-05_T62", "type": "Protein", "text": [ "csrS" ], "offsets": [ [ 2452, 2456 ] ], "normalized": [] }, { "id": "PMC2565068-02-Results-05_T63", "type": "Protein", "text": [ "slo" ], "offsets": [ [ 2525, 2528 ] ], "normalized": [] }, { "id": "PMC2565068-02-Results-05_T64", "type": "Protein", "text": [ "scpC" ], "offsets": [ [ 2537, 2541 ] ], "normalized": [] }, { "id": "PMC2565068-02-Results-05_T65", "type": "Organism", "text": [ "non-invasive GAS" ], "offsets": [ [ 2585, 2601 ] ], "normalized": [] }, { "id": "PMC2565068-02-Results-05_T66", "type": "Protein", "text": [ "speB" ], "offsets": [ [ 2634, 2638 ] ], "normalized": [] }, { "id": "PMC2565068-02-Results-05_T67", "type": "Organism", "text": [ "non-invasive GAS" ], "offsets": [ [ 2684, 2700 ] ], "normalized": [] }, { "id": "PMC2565068-02-Results-05_T68", "type": "Protein", "text": [ "slo" ], "offsets": [ [ 2757, 2760 ] ], "normalized": [] }, { "id": "PMC2565068-02-Results-05_T69", "type": "Protein", "text": [ "scpC" ], "offsets": [ [ 2765, 2769 ] ], "normalized": [] }, { "id": "PMC2565068-02-Results-05_T70", "type": "Organism", "text": [ "invasive GAS" ], "offsets": [ [ 2784, 2796 ] ], "normalized": [] }, { "id": "PMC2565068-02-Results-05_T71", "type": "Protein", "text": [ "csrS" ], "offsets": [ [ 2825, 2829 ] ], "normalized": [] }, { "id": "PMC2565068-02-Results-05_T72", "type": "Organism", "text": [ "invasive GAS" ], "offsets": [ [ 2851, 2863 ] ], "normalized": [] }, { "id": "PMC2565068-02-Results-05_T73", "type": "Organism", "text": [ "invasive isolates +CsrS" ], "offsets": [ [ 2944, 2967 ] ], "normalized": [] }, { "id": "PMC2565068-02-Results-05_T74", "type": "Protein", "text": [ "CsrS" ], "offsets": [ [ 2963, 2967 ] ], "normalized": [] }, { "id": "PMC2565068-02-Results-05_T75", "type": "Protein", "text": [ "IL-8" ], "offsets": [ [ 3042, 3046 ] ], "normalized": [] }, { "id": "PMC2565068-02-Results-05_T76", "type": "Organism", "text": [ "invasive isolates +CsrS" ], "offsets": [ [ 3070, 3093 ] ], "normalized": [] }, { "id": "PMC2565068-02-Results-05_T77", "type": "Protein", "text": [ "CsrS" ], "offsets": [ [ 3089, 3093 ] ], "normalized": [] }, { "id": "PMC2565068-02-Results-05_T78", "type": "Organism", "text": [ "invasive isolates +CsrS" ], "offsets": [ [ 3201, 3224 ] ], "normalized": [] }, { "id": "PMC2565068-02-Results-05_T79", "type": "Protein", "text": [ "CsrS" ], "offsets": [ [ 3220, 3224 ] ], "normalized": [] }, { "id": "PMC2565068-02-Results-05_T80", "type": "Protein", "text": [ "csrS" ], "offsets": [ [ 3304, 3308 ] ], "normalized": [] } ]

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], "offsets": [ [ 901, 914 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC2565068-02-Results-05_T24" } ] }, { "id": "PMC2565068-02-Results-05_E24", "type": "Negative_regulation", "trigger": { "text": [ "downregulated" ], "offsets": [ [ 901, 914 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC2565068-02-Results-05_T25" } ] }, { "id": "PMC2565068-02-Results-05_E25", "type": "Negative_regulation", "trigger": { "text": [ "downregulated" ], "offsets": [ [ 901, 914 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC2565068-02-Results-05_T27" } ] }, { "id": "PMC2565068-02-Results-05_E26", "type": "Transcription", "trigger": { "text": [ "transcriptional profile" ], "offsets": [ [ 1077, 1100 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC2565068-02-Results-05_T30" } ] }, { "id": "PMC2565068-02-Results-05_E27", "type": "Transcription", "trigger": { "text": [ "transcriptional profile" ], "offsets": [ [ 1077, 1100 ] ] }, "arguments": [ { "role": "Theme", "ref_id": 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[ "infection" ], "offsets": [ [ 1671, 1680 ] ] }, "arguments": [ { "role": "Participant", "ref_id": "PMC2565068-02-Results-05_T44" } ] }, { "id": "PMC2565068-02-Results-05_E34", "type": "Process", "trigger": { "text": [ "virulence" ], "offsets": [ [ 2290, 2299 ] ] }, "arguments": [] }, { "id": "PMC2565068-02-Results-05_E35", "type": "Process", "trigger": { "text": [ "resistance" ], "offsets": [ [ 2321, 2331 ] ] }, "arguments": [] }, { "id": "PMC2565068-02-Results-05_E36", "type": "Negative_regulation", "trigger": { "text": [ "reduced" ], "offsets": [ [ 2488, 2495 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC2565068-02-Results-05_E38" } ] }, { "id": "PMC2565068-02-Results-05_E37", "type": "Negative_regulation", "trigger": { "text": [ "reduced" ], "offsets": [ [ 2488, 2495 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC2565068-02-Results-05_E39" } ] }, { "id": "PMC2565068-02-Results-05_E38", "type": "Gene_expression", "trigger": { "text": [ "expression" ], "offsets": [ 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[]

[ { "id": "PMC2581603-00-TIAB__text", "type": "abstract", "text": [ "Extracellular DNA Chelates Cations and Induces Antibiotic Resistance in Pseudomonas aeruginosa Biofilms \nBiofilms are surface-adhered bacterial communities encased in an extracellular matrix composed of DNA, bacterial polysaccharides and proteins, which are up to 1000-fold more antibiotic resistant than planktonic cultures. To date, extracellular DNA has been shown to function as a structural support to maintain Pseudomonas aeruginosa biofilm architecture. Here we show that DNA is a multifaceted component of P. aeruginosa biofilms. At physiologically relevant concentrations, extracellular DNA has antimicrobial activity, causing cell lysis by chelating cations that stabilize lipopolysaccharide (LPS) and the outer membrane (OM). DNA-mediated killing occurred within minutes, as a result of perturbation of both the outer and inner membrane (IM) and the release of cytoplasmic contents, including genomic DNA. Sub-inhibitory concentrations of DNA created a cation-limited environment that resulted in induction of the PhoPQ- and PmrAB-regulated cationic antimicrobial peptide resistance operon PA3552-PA3559 in P. aeruginosa. Furthermore, DNA-induced expression of this operon resulted in up to 2560-fold increased resistance to cationic antimicrobial peptides and 640-fold increased resistance to aminoglycosides, but had no effect on beta-lactam and fluoroquinolone resistance. Thus, the presence of extracellular DNA in the biofilm matrix contributes to cation gradients, genomic DNA release and inducible antibiotic resistance. DNA-rich environments, including biofilms and other infection sites like the CF lung, are likely the in vivo environments where extracellular pathogens such as P. aeruginosa encounter cation limitation.\n" ], "offsets": [ [ 0, 1742 ] ] } ]

[ { "id": "PMC2581603-00-TIAB_T1", "type": "Organism", "text": [ "Pseudomonas aeruginosa" ], "offsets": [ [ 72, 94 ] ], "normalized": [] }, { "id": "PMC2581603-00-TIAB_T2", "type": "Organism", "text": [ "Pseudomonas aeruginosa" ], "offsets": [ [ 416, 438 ] ], "normalized": [] }, { "id": "PMC2581603-00-TIAB_T3", "type": "Organism", "text": [ "P. aeruginosa" ], "offsets": [ [ 514, 527 ] ], "normalized": [] }, { "id": "PMC2581603-00-TIAB_T4", "type": "Chemical", "text": [ "lipopolysaccharide" ], "offsets": [ [ 683, 701 ] ], "normalized": [] }, { "id": "PMC2581603-00-TIAB_T5", "type": "Chemical", "text": [ "LPS" ], "offsets": [ [ 703, 706 ] ], "normalized": [] }, { "id": "PMC2581603-00-TIAB_T6", "type": "Two-component-system", "text": [ "PhoPQ" ], "offsets": [ [ 1025, 1030 ] ], "normalized": [] }, { "id": "PMC2581603-00-TIAB_T7", "type": "Protein", "text": [ "PhoP" ], "offsets": [ [ 1025, 1029 ] ], "normalized": [] }, { "id": "PMC2581603-00-TIAB_T8", "type": "Protein", "text": [ "Q" ], "offsets": [ [ 1029, 1030 ] ], "normalized": [] }, { "id": "PMC2581603-00-TIAB_T9", "type": "Two-component-system", "text": [ "PmrAB" ], "offsets": [ [ 1036, 1041 ] ], "normalized": [] }, { "id": "PMC2581603-00-TIAB_T10", "type": "Protein", "text": [ "PmrA" ], "offsets": [ [ 1036, 1040 ] ], "normalized": [] }, { "id": "PMC2581603-00-TIAB_T11", "type": "Protein", "text": [ "B" ], "offsets": [ [ 1040, 1041 ] ], "normalized": [] }, { "id": "PMC2581603-00-TIAB_T12", "type": "Regulon-operon", "text": [ "PA3552-PA3559" ], "offsets": [ [ 1101, 1114 ] ], "normalized": [] }, { "id": "PMC2581603-00-TIAB_T13", "type": "Protein", "text": [ "PA3552" ], "offsets": [ [ 1101, 1107 ] ], "normalized": [] }, { "id": "PMC2581603-00-TIAB_T14", "type": "Protein", "text": [ "PA3559" ], "offsets": [ [ 1108, 1114 ] ], "normalized": [] }, { "id": "PMC2581603-00-TIAB_T15", "type": "Organism", "text": [ "P. aeruginosa" ], "offsets": [ [ 1118, 1131 ] ], "normalized": [] }, { "id": "PMC2581603-00-TIAB_T16", "type": "Chemical", "text": [ "aminoglycosides" ], "offsets": [ [ 1305, 1320 ] ], "normalized": [] }, { "id": "PMC2581603-00-TIAB_T17", "type": "Chemical", "text": [ "beta-lactam" ], "offsets": [ [ 1343, 1354 ] ], "normalized": [] }, { "id": "PMC2581603-00-TIAB_T18", "type": "Chemical", "text": [ "fluoroquinolone" ], "offsets": [ [ 1359, 1374 ] ], "normalized": [] }, { "id": "PMC2581603-00-TIAB_T19", "type": "Organism", "text": [ "P. aeruginosa" ], "offsets": [ [ 1699, 1712 ] ], "normalized": [] } ]

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[]

[ { "id": "PMC2816692-03-Discussion-03__text", "type": "abstract", "text": [ "Genetic and functional integration of SrcA with type III secretion \nThe genes encoding the srcA chaperone and the effector cargos (pipB2 and sseL) are found in all serotypes of Salmonella enterica that contain the SPI-2-encoded T3SS. Conversely, these genes are absent from S. bongori, which lacks the SPI-2-encoded T3SS. The expression of srcA is coordinated with T3SS transcriptional activity via the SsrA-SsrB two-component regulatory system encoded in SPI-2. The direct binding of SsrB to the promoter region upstream of srcA, along with SsrB-regulation of both sseL [19],[20] and pipB2 [32] is indicative of multiple cis-regulatory mutation events that have allowed for functional coordination of the distributed secretion apparatus, chaperone and effector cargos. We recently described this type of regulatory evolution for pathogenic adaptation of Salmonella to its host [21] and srcA is consistent with regulatory evolution of chaperone-effector gene pairs that are not co-transcribed in operons. Due to low G+C base content compared to the genome average of 52%, it's likely that srcA (32% G+C) and an adjacent gene, STM2137 (37% G+C), were acquired as a foreign islet that was retained in organisms containing the SPI-2 T3SS due to the selective advantage afforded by the new protein interactions so created. Interestingly, STM2137 (also known as SseK2) is a likely paralog of SseK1, an effector translocated by the SPI-2 T3SS [33]. SseK2 is also regulated by the SsrA-SsrB two-component system but compared to SseK1, it is translocated in much less abundance into host cells [33]. Using the methods described here, we were not able to detect SseK2 secretion or a physical interaction with SrcA, however it remains possible that SrcA also chaperones SseK2 for low-level translocation. SrcA is unique among other multi-effector chaperones most closely related to it in that it is unlinked from the T3SS genomic island. For example, InvB and SicP (Salmonella SPI-1), CesT (enteropathogenic E. coli locus of enterocyte effacement) and Spa15 (Shigella mxi/spa virulence plasmid region) chaperones are all encoded within the T3SS structural operons, implying they have co-evolved as a single genetic entity from a common ancestor. Given its genetic neighborhood, srcA appears to be a genetic acquisition separate from SPI-2 that functionally links some effectors to the T3SS apparatus via the ATPase. The role of horizontal gene transfer and regulatory evolution in allowing for uncoupling of chaperones, effectors and the T3SS has many possible implications for T3SS function, including plasticity in chaperone-effector interaction networks, expansion of effector repertoires, and alterations to the kinetics and hierarchical delivery of effectors to a host cell. These events may improve host adaptability or even expand the host range of bacteria that acquire and integrate new functional secretion chaperones.\n" ], "offsets": [ [ 0, 2919 ] ] } ]

[ { "id": "PMC2816692-03-Discussion-03_T1", "type": "Protein", "text": [ "SrcA" ], "offsets": [ [ 38, 42 ] ], "normalized": [] }, { "id": "PMC2816692-03-Discussion-03_T2", "type": "Protein", "text": [ "srcA" ], "offsets": [ [ 91, 95 ] ], "normalized": [] }, { "id": "PMC2816692-03-Discussion-03_T3", "type": "Protein", "text": [ "pipB2" ], "offsets": [ [ 131, 136 ] ], "normalized": [] }, { "id": "PMC2816692-03-Discussion-03_T4", "type": "Protein", "text": [ "sseL" ], "offsets": [ [ 141, 145 ] ], "normalized": [] }, { "id": "PMC2816692-03-Discussion-03_T5", "type": "Organism", "text": [ "Salmonella enterica" ], "offsets": [ [ 177, 196 ] ], "normalized": [] }, { "id": "PMC2816692-03-Discussion-03_T6", "type": "Organism", "text": [ "S. bongori" ], "offsets": [ [ 274, 284 ] ], "normalized": [] }, { "id": "PMC2816692-03-Discussion-03_T7", "type": "Protein", "text": [ "srcA" ], "offsets": [ [ 340, 344 ] ], "normalized": [] }, { "id": "PMC2816692-03-Discussion-03_T8", "type": "Two-component-system", "text": [ "SsrA-SsrB" ], "offsets": [ [ 403, 412 ] ], "normalized": [] }, { "id": "PMC2816692-03-Discussion-03_T9", "type": "Protein", "text": [ "SsrA" ], "offsets": [ [ 403, 407 ] ], "normalized": [] }, { "id": "PMC2816692-03-Discussion-03_T10", "type": "Protein", "text": [ "SsrB" ], "offsets": [ [ 408, 412 ] ], "normalized": [] }, { "id": "PMC2816692-03-Discussion-03_T11", "type": "Protein", "text": [ "SsrB" ], "offsets": [ [ 485, 489 ] ], "normalized": [] }, { "id": "PMC2816692-03-Discussion-03_T12", "type": "Protein", "text": [ "srcA" ], "offsets": [ [ 525, 529 ] ], "normalized": [] }, { "id": "PMC2816692-03-Discussion-03_T13", "type": "Protein", "text": [ "SsrB" ], "offsets": [ [ 542, 546 ] ], "normalized": [] }, { "id": "PMC2816692-03-Discussion-03_T14", "type": "Protein", "text": [ "sseL" ], "offsets": [ [ 566, 570 ] ], "normalized": [] }, { "id": "PMC2816692-03-Discussion-03_T15", "type": "Protein", "text": [ "pipB2" ], "offsets": [ [ 585, 590 ] ], "normalized": [] }, { "id": "PMC2816692-03-Discussion-03_T16", "type": "Organism", "text": [ "Salmonella" ], "offsets": [ [ 855, 865 ] ], "normalized": [] }, { "id": "PMC2816692-03-Discussion-03_T17", "type": "Organism", "text": [ "host" ], "offsets": [ [ 873, 877 ] ], "normalized": [] }, { "id": "PMC2816692-03-Discussion-03_T18", "type": "Protein", "text": [ "srcA" ], "offsets": [ [ 887, 891 ] ], "normalized": [] }, { "id": "PMC2816692-03-Discussion-03_T19", "type": "Protein", "text": [ "srcA" ], "offsets": [ [ 1089, 1093 ] ], "normalized": [] }, { "id": "PMC2816692-03-Discussion-03_T20", "type": "Protein", "text": [ "STM2137" ], "offsets": [ [ 1126, 1133 ] ], "normalized": [] }, { "id": "PMC2816692-03-Discussion-03_T21", "type": "Protein", "text": [ "STM2137" ], "offsets": [ [ 1334, 1341 ] ], "normalized": [] }, { "id": "PMC2816692-03-Discussion-03_T22", "type": "Protein", "text": [ "SseK2" ], "offsets": [ [ 1357, 1362 ] ], "normalized": [] }, { "id": "PMC2816692-03-Discussion-03_T23", "type": "Protein", "text": [ "SseK1" ], "offsets": [ [ 1387, 1392 ] ], "normalized": [] }, { "id": "PMC2816692-03-Discussion-03_T24", "type": "Protein", "text": [ "SseK2" ], "offsets": [ [ 1443, 1448 ] ], "normalized": [] }, { "id": "PMC2816692-03-Discussion-03_T25", "type": "Two-component-system", "text": [ "SsrA-SsrB" ], "offsets": [ [ 1474, 1483 ] ], "normalized": [] }, { "id": "PMC2816692-03-Discussion-03_T26", "type": "Protein", "text": [ "SsrA" ], "offsets": [ [ 1474, 1478 ] ], "normalized": [] }, { "id": "PMC2816692-03-Discussion-03_T27", "type": "Protein", "text": [ "SsrB" ], "offsets": [ [ 1479, 1483 ] ], "normalized": [] }, { "id": "PMC2816692-03-Discussion-03_T28", "type": "Protein", "text": [ "SseK1" ], "offsets": [ [ 1521, 1526 ] ], "normalized": [] }, { "id": "PMC2816692-03-Discussion-03_T29", "type": "Protein", "text": [ "SseK2" ], "offsets": [ [ 1653, 1658 ] ], "normalized": [] }, { "id": "PMC2816692-03-Discussion-03_T30", "type": "Protein", "text": [ "SrcA" ], "offsets": [ [ 1700, 1704 ] ], "normalized": [] }, { "id": "PMC2816692-03-Discussion-03_T31", "type": "Protein", "text": [ "SrcA" ], "offsets": [ [ 1739, 1743 ] ], "normalized": [] }, { "id": "PMC2816692-03-Discussion-03_T32", "type": "Protein", "text": [ "SseK2" ], "offsets": [ [ 1760, 1765 ] ], "normalized": [] }, { "id": "PMC2816692-03-Discussion-03_T33", "type": "Protein", "text": [ "SrcA" ], "offsets": [ [ 1795, 1799 ] ], "normalized": [] }, { "id": "PMC2816692-03-Discussion-03_T34", "type": "Protein", "text": [ "InvB" ], "offsets": [ [ 1941, 1945 ] ], "normalized": [] }, { "id": "PMC2816692-03-Discussion-03_T35", "type": "Protein", "text": [ "SicP" ], "offsets": [ [ 1950, 1954 ] ], "normalized": [] }, { "id": "PMC2816692-03-Discussion-03_T36", "type": "Organism", "text": [ "Salmonella" ], "offsets": [ [ 1956, 1966 ] ], "normalized": [] }, { "id": "PMC2816692-03-Discussion-03_T37", "type": "Protein", "text": [ "CesT" ], "offsets": [ [ 1975, 1979 ] ], "normalized": [] }, { "id": "PMC2816692-03-Discussion-03_T38", "type": "Organism", "text": [ "E. coli" ], "offsets": [ [ 1998, 2005 ] ], "normalized": [] }, { "id": "PMC2816692-03-Discussion-03_T39", "type": "Organism", "text": [ "Shigella" ], "offsets": [ [ 2049, 2057 ] ], "normalized": [] }, { "id": "PMC2816692-03-Discussion-03_T40", "type": "Protein", "text": [ "srcA" ], "offsets": [ [ 2268, 2272 ] ], "normalized": [] }, { "id": "PMC2816692-03-Discussion-03_T44", "type": "Entity", "text": [ "promoter region" ], "offsets": [ [ 497, 512 ] ], "normalized": [] }, { "id": "PMC2816692-03-Discussion-03_T49", "type": "Entity", "text": [ "host cells" ], "offsets": [ [ 1575, 1585 ] ], "normalized": [] } ]

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[ { "id": "PMC2816692-03-Discussion-03_1", "entity_ids": [ "PMC2816692-03-Discussion-03_T22", "PMC2816692-03-Discussion-03_T21" ] } ]

[]

[ { "id": "PMC2858072-02-Results_and_Discussion-03__text", "type": "abstract", "text": [ "BvrR/BvrS and the expression of other transcriptional regulators \nNotably, seven transcriptional regulators genes were also differentially expressed in the bvrR mutant compared to parental strain: BAB1_0237, BAB1_0891 (exoR), BAB1_1397, BAB2_0118 (vjbR), BAB2_0762 (ompR), BAB2_1127 and BAB2_1152. Three of these, namely exoR, ompR and vjbR are down regulated and have been previously implicated in Brucella virulence. B. melitensis vjbR mutant is highly attenuated in both cellular and mouse models of infection [19]. VjbR has been described as a transcriptional regulator able to activate directly the secretion system virB operon and the flagellar genes, both virulence factors associated to the surface of the bacteria [20], [21]. Moreover, it has been demonstrated that VjbR controls the synthesis of exopolysaccharides and the productions of several OMPs, some of which are also involved in virulence [22]. Interestingly, our results also showed that the expression of vjbR was also induced intracellularly (see below). All these data suggest that VjbR, similarly to the BvrR/BvrS system, is involved in the control of outer membrane composition and virulence. In addition, DeJong and col [20] have demonstrated that among the promoters which expression is dependent of the VjbR regulator, is the ompR gene, the regulator of the OmpR/EnvZ two component system. E. coli OmpR/EnvZ system controls the transcription of the outer membrane porins OmpF and OmpC in response to osmolarity [23]. Moreover, a systematically transcriptome analysis of all two component regulatory systems in E. coli has demonstrated that the OmpR/EnvZ system also controls the metabolism of amino acids, flagellar synthesis and nutrient transport [24]. As we have show in this study, the expression of at least three flagellar genes (fliM, BAB2_0124/5; flgJ, BAB1_0260; motB, BAB2_1103) were increased also in the bvrR mutant (Figure 2). The two-regulatory systems ChvG(ExoS)/ChvI in S. meliloti and A. tumefaciens posses a high level of identity with the Brucella BvrR/BvrS [25], [26]. Chaves-Olarte et al have reported that B. abortus bvrS mutant complemented with the ExoS protein recuperated the ability to invade and replicated successfully in HeLa and macrophage cells [27], suggesting that the BvrR/BvrS system is functionally interchangeable with the ExoS/ChvI system. A. tumefaciens ChvI/ChvG system controls the expression of the Aop, an OMP homologous to Brucella Omp25a [28], and in S. meliloti, ExoS/ChvI is a key regulator of gene expression for exopolysaccharide synthesis, motility and nutrient utilization [26]. It has been described in S. meliloti that exoR gene encodes a global regulator of transcription and that ExoR interacts genetically with both ExoS and ChvI and inhibits ExoS/ChvI activity [29], [30]. Further analysis indicated that both the ExoR protein and the ExoS/ChvI two-component regulatory system are involved in the regulation of both polysaccharides and flagellum biosynthesis [31]. In addition, the transcription of the S. meliloti lpsS gene, that encodes a sulfotransferase that modifies LPS, is dependent on the exoR gene [32]. Other authors [29] suggest that ExoR is an inhibitor of two-component signaling that may be conserved in a large number of alpha-proteobacteria. Our results also support this hypothesis: the functional relationship between the exoR gene and the BvrR/BvrS system. Based on all these findings, obvious comparison about the function of all these regulators in Brucella could be made. The fact that the expression of VjbR, OmpR and ExoR was altered in the bvrR mutant demonstrated for the first time an interaction or cross-talk among these global regulators, all involved in the control of composition and structure of the cell envelope (OMPs, LPS, chaperones, flagella, em).\n" ], "offsets": [ [ 0, 3821 ] ] } ]

[ { "id": "PMC2858072-02-Results_and_Discussion-03_T1", "type": "Two-component-system", "text": [ "BvrR/BvrS" ], "offsets": [ [ 0, 9 ] ], "normalized": [] }, { "id": "PMC2858072-02-Results_and_Discussion-03_T2", "type": "Protein", "text": [ "BvrR" ], "offsets": [ [ 0, 4 ] ], "normalized": [] }, { "id": "PMC2858072-02-Results_and_Discussion-03_T3", "type": "Protein", "text": [ "BvrS" ], "offsets": [ [ 5, 9 ] ], "normalized": [] }, { "id": "PMC2858072-02-Results_and_Discussion-03_T4", "type": "Organism", "text": [ "bvrR mutant" ], "offsets": [ [ 156, 167 ] ], "normalized": [] }, { "id": "PMC2858072-02-Results_and_Discussion-03_T5", "type": "Protein", "text": [ "bvrR" ], "offsets": [ [ 156, 160 ] ], "normalized": [] }, { "id": "PMC2858072-02-Results_and_Discussion-03_T6", "type": "Protein", "text": [ "BAB1_0237" ], "offsets": [ [ 197, 206 ] ], "normalized": [] }, { "id": "PMC2858072-02-Results_and_Discussion-03_T7", "type": "Protein", "text": [ "BAB1_0891" ], "offsets": [ [ 208, 217 ] ], "normalized": [] }, { "id": "PMC2858072-02-Results_and_Discussion-03_T8", "type": "Protein", "text": [ "exoR" ], "offsets": [ [ 219, 223 ] ], "normalized": [] }, { "id": "PMC2858072-02-Results_and_Discussion-03_T9", "type": "Protein", "text": [ "BAB1_1397" ], "offsets": [ [ 226, 235 ] ], "normalized": [] }, { "id": "PMC2858072-02-Results_and_Discussion-03_T10", "type": "Protein", "text": [ "BAB2_0118" ], "offsets": [ [ 237, 246 ] ], "normalized": [] }, { "id": "PMC2858072-02-Results_and_Discussion-03_T11", "type": "Protein", "text": [ "vjbR" ], "offsets": [ [ 248, 252 ] ], "normalized": [] }, { "id": "PMC2858072-02-Results_and_Discussion-03_T12", "type": "Protein", "text": [ "BAB2_0762" ], "offsets": [ [ 255, 264 ] ], "normalized": [] }, { "id": "PMC2858072-02-Results_and_Discussion-03_T13", "type": "Protein", "text": [ "ompR" ], "offsets": [ [ 266, 270 ] ], "normalized": [] }, { "id": "PMC2858072-02-Results_and_Discussion-03_T14", "type": "Protein", "text": [ "BAB2_1127" ], "offsets": [ [ 273, 282 ] ], "normalized": [] }, { "id": "PMC2858072-02-Results_and_Discussion-03_T15", "type": "Protein", "text": [ "BAB2_1152" ], "offsets": [ [ 287, 296 ] ], "normalized": [] }, { "id": "PMC2858072-02-Results_and_Discussion-03_T16", "type": "Protein", "text": [ "exoR" ], "offsets": [ [ 321, 325 ] ], "normalized": [] }, { "id": "PMC2858072-02-Results_and_Discussion-03_T17", "type": "Protein", "text": [ "ompR" ], "offsets": [ [ 327, 331 ] ], "normalized": [] }, { "id": "PMC2858072-02-Results_and_Discussion-03_T18", "type": "Protein", "text": [ "vjbR" ], "offsets": [ [ 336, 340 ] ], "normalized": [] }, { "id": "PMC2858072-02-Results_and_Discussion-03_T19", "type": "Organism", "text": [ "Brucella" ], "offsets": [ [ 399, 407 ] ], "normalized": [] }, { "id": "PMC2858072-02-Results_and_Discussion-03_T20", "type": "Organism", "text": [ "B. melitensis vjbR mutant" ], "offsets": [ [ 419, 444 ] ], "normalized": [] }, { "id": "PMC2858072-02-Results_and_Discussion-03_T21", "type": "Protein", "text": [ "vjbR" ], "offsets": [ [ 433, 437 ] ], "normalized": [] }, { "id": "PMC2858072-02-Results_and_Discussion-03_T22", "type": "Organism", "text": [ "mouse" ], "offsets": [ [ 487, 492 ] ], "normalized": [] }, { "id": "PMC2858072-02-Results_and_Discussion-03_T23", "type": "Protein", "text": [ "VjbR" ], "offsets": [ [ 519, 523 ] ], "normalized": [] }, { "id": "PMC2858072-02-Results_and_Discussion-03_T24", "type": "Regulon-operon", "text": [ "virB operon" ], "offsets": [ [ 621, 632 ] ], "normalized": [] }, { "id": "PMC2858072-02-Results_and_Discussion-03_T25", "type": "Protein", "text": [ "virB" ], "offsets": [ [ 621, 625 ] ], "normalized": [] }, { "id": "PMC2858072-02-Results_and_Discussion-03_T26", "type": "Protein", "text": [ "VjbR" ], "offsets": [ [ 775, 779 ] ], "normalized": [] }, { "id": "PMC2858072-02-Results_and_Discussion-03_T27", "type": "Protein", "text": [ "vjbR" ], "offsets": [ [ 975, 979 ] ], "normalized": [] }, { "id": "PMC2858072-02-Results_and_Discussion-03_T28", "type": "Protein", "text": [ "VjbR" ], "offsets": [ [ 1054, 1058 ] ], "normalized": [] }, { "id": "PMC2858072-02-Results_and_Discussion-03_T29", "type": "Two-component-system", "text": [ "BvrR/BvrS" ], "offsets": [ [ 1077, 1086 ] ], "normalized": [] }, { "id": "PMC2858072-02-Results_and_Discussion-03_T30", "type": "Protein", "text": [ "BvrR" ], "offsets": [ [ 1077, 1081 ] ], "normalized": [] }, { "id": "PMC2858072-02-Results_and_Discussion-03_T31", "type": "Protein", "text": [ "BvrS" ], "offsets": [ [ 1082, 1086 ] ], "normalized": [] }, { "id": "PMC2858072-02-Results_and_Discussion-03_T32", "type": "Protein", "text": [ "VjbR" ], "offsets": [ [ 1280, 1284 ] ], "normalized": [] }, { "id": "PMC2858072-02-Results_and_Discussion-03_T33", "type": "Protein", "text": [ "ompR" ], "offsets": [ [ 1303, 1307 ] ], "normalized": [] }, { "id": "PMC2858072-02-Results_and_Discussion-03_T34", "type": "Two-component-system", "text": [ "OmpR/EnvZ" ], "offsets": [ [ 1335, 1344 ] ], "normalized": [] }, { "id": "PMC2858072-02-Results_and_Discussion-03_T35", "type": "Protein", "text": [ "OmpR" ], "offsets": [ [ 1335, 1339 ] ], "normalized": [] }, { "id": "PMC2858072-02-Results_and_Discussion-03_T36", "type": "Protein", "text": [ "EnvZ" ], "offsets": [ [ 1340, 1344 ] ], "normalized": [] }, { "id": "PMC2858072-02-Results_and_Discussion-03_T37", "type": "Organism", "text": [ "E. coli" ], "offsets": [ [ 1367, 1374 ] ], "normalized": [] }, { "id": "PMC2858072-02-Results_and_Discussion-03_T38", "type": "Two-component-system", "text": [ "OmpR/EnvZ" ], "offsets": [ [ 1375, 1384 ] ], "normalized": [] }, { "id": "PMC2858072-02-Results_and_Discussion-03_T39", "type": "Protein", "text": [ "OmpR" ], "offsets": [ [ 1375, 1379 ] ], "normalized": [] }, { "id": "PMC2858072-02-Results_and_Discussion-03_T40", "type": "Protein", "text": [ "EnvZ" ], "offsets": [ [ 1380, 1384 ] ], "normalized": [] }, { "id": "PMC2858072-02-Results_and_Discussion-03_T41", "type": "Protein", "text": [ "OmpF" ], "offsets": [ [ 1448, 1452 ] ], "normalized": [] }, { "id": "PMC2858072-02-Results_and_Discussion-03_T42", "type": "Protein", "text": [ "OmpC" ], "offsets": [ [ 1457, 1461 ] ], "normalized": [] }, { "id": "PMC2858072-02-Results_and_Discussion-03_T43", "type": "Organism", "text": [ "E. coli" ], "offsets": [ [ 1587, 1594 ] ], "normalized": [] }, { "id": "PMC2858072-02-Results_and_Discussion-03_T44", "type": "Two-component-system", "text": [ "OmpR/EnvZ" ], "offsets": [ [ 1621, 1630 ] ], "normalized": [] }, { "id": "PMC2858072-02-Results_and_Discussion-03_T45", "type": "Protein", "text": [ "OmpR" ], "offsets": [ [ 1621, 1625 ] ], "normalized": [] }, { "id": "PMC2858072-02-Results_and_Discussion-03_T46", "type": "Protein", "text": [ "EnvZ" ], "offsets": [ [ 1626, 1630 ] ], "normalized": [] }, { "id": "PMC2858072-02-Results_and_Discussion-03_T47", "type": "Protein", "text": [ "fliM" ], "offsets": [ [ 1813, 1817 ] ], "normalized": [] }, { "id": "PMC2858072-02-Results_and_Discussion-03_T48", "type": "Protein", "text": [ "BAB2_0124/5" ], "offsets": [ [ 1819, 1830 ] ], "normalized": [] }, { "id": "PMC2858072-02-Results_and_Discussion-03_T49", "type": "Protein", "text": [ "flgJ" ], "offsets": [ [ 1832, 1836 ] ], "normalized": [] }, { "id": "PMC2858072-02-Results_and_Discussion-03_T50", "type": "Protein", "text": [ "BAB1_0260" ], "offsets": [ [ 1838, 1847 ] ], "normalized": [] }, { "id": "PMC2858072-02-Results_and_Discussion-03_T51", "type": "Protein", "text": [ "motB" ], "offsets": [ [ 1849, 1853 ] ], "normalized": [] }, { "id": "PMC2858072-02-Results_and_Discussion-03_T52", "type": "Protein", "text": [ "BAB2_1103" ], "offsets": [ [ 1855, 1864 ] ], "normalized": [] }, { "id": "PMC2858072-02-Results_and_Discussion-03_T53", "type": "Organism", "text": [ "bvrR mutant" ], "offsets": [ [ 1893, 1904 ] ], "normalized": [] }, { "id": "PMC2858072-02-Results_and_Discussion-03_T54", "type": "Protein", "text": [ "bvrR" ], "offsets": [ [ 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"PMC2858072-02-Results_and_Discussion-03_T61", "type": "Organism", "text": [ "Brucella" ], "offsets": [ [ 2035, 2043 ] ], "normalized": [] }, { "id": "PMC2858072-02-Results_and_Discussion-03_T62", "type": "Two-component-system", "text": [ "BvrR/BvrS" ], "offsets": [ [ 2044, 2053 ] ], "normalized": [] }, { "id": "PMC2858072-02-Results_and_Discussion-03_T63", "type": "Protein", "text": [ "BvrR" ], "offsets": [ [ 2044, 2048 ] ], "normalized": [] }, { "id": "PMC2858072-02-Results_and_Discussion-03_T64", "type": "Protein", "text": [ "BvrS" ], "offsets": [ [ 2049, 2053 ] ], "normalized": [] }, { "id": "PMC2858072-02-Results_and_Discussion-03_T65", "type": "Organism", "text": [ "B. abortus" ], "offsets": [ [ 2105, 2115 ] ], "normalized": [] }, { "id": "PMC2858072-02-Results_and_Discussion-03_T66", "type": "Organism", "text": [ "bvrS mutant" ], "offsets": [ [ 2116, 2127 ] ], "normalized": [] }, { "id": "PMC2858072-02-Results_and_Discussion-03_T67", "type": "Protein", "text": [ "bvrS" ], 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"role": "Theme", "ref_id": "PMC2858072-02-Results_and_Discussion-03_T79" } ] }, { "id": "PMC2858072-02-Results_and_Discussion-03_E39", "type": "Regulation", "trigger": { "text": [ "interacts" ], "offsets": [ [ 2718, 2727 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC2858072-02-Results_and_Discussion-03_T89" }, { "role": "Cause", "ref_id": "PMC2858072-02-Results_and_Discussion-03_T88" } ] }, { "id": "PMC2858072-02-Results_and_Discussion-03_E40", "type": "Regulation", "trigger": { "text": [ "interacts" ], "offsets": [ [ 2718, 2727 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC2858072-02-Results_and_Discussion-03_T90" }, { "role": "Cause", "ref_id": "PMC2858072-02-Results_and_Discussion-03_T88" } ] }, { "id": "PMC2858072-02-Results_and_Discussion-03_E41", "type": "Negative_regulation", "trigger": { "text": [ "inhibits" ], "offsets": [ [ 2768, 2776 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC2858072-02-Results_and_Discussion-03_T91" }, { "role": "Cause", 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"altered" ], "offsets": [ [ 3585, 3592 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC2858072-02-Results_and_Discussion-03_E46" } ] } ]

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[ { "id": "PMC1913099-02-Results-Discussion-07__text", "type": "abstract", "text": [ "Neighbor Clustering \nOur initial analysis revealed the differential expression of a wide range of functionally diverse genes and provided insight into the adaptive response of streptococci to host cell contact. However, despite a rigorous statistical approach, this analysis, like many previous microarray studies, identified the differential expression of a large number of unknown genes (n = 21) and a number of incomplete biological pathways (e.g., F0F1 ATPase [41] and folate biosynthesis [40]) by failing to detect the differential expression of a number of known gene pathway members (Table 1). To overcome these limitations and to extract more functional information from the array dataset (including more complete biological pathways), we developed the neighbor clustering algorithms to combine the physical position of genes on the streptococcal chromosome with gene expression data. Neighbor clustering was designed to identify expanded groupings of potentially related genes from our array data by incorporating two reliable predictors of genes that share common function or regulation, namely physical proximity and similar expression profiles [5,6]. We implemented this approach by developing an algorithm with dynamic windowing (GenomeCrawler) that sequentially stepped through the microarray data and identified clusters of adjacent genes exhibiting similar fold changes in expression. Because the genome contains many possible clusters, we restricted the algorithm's search space to identify only spatially related clusters. GenomeCrawler applied a separate permutation algorithm, using the sum of each gene's t-statistics to calculate adjusted P values (PK) for each cluster, which corresponded to the probability of assembling a cluster by chance. Significance was assigned to clusters with PK < 0.05, and the resulting groupings are listed in Table 3. Because individual genes could be members of many different significant clusters, GenomeCrawler then applied a distinct permutation algorithm to calculate the probability (PC) that a gene was clustered coincidentally. Calculation of PC values relies on Bayes' Theorem, in which the probability of a gene's log2-fold change (PF value) is combined with the cluster probability itself (PK value). We stress that PC reflects the significance of a gene based on its cluster context rather than a recapitulation of PF. This ensures a strong dependency between PF and PC, preventing a gene with a relatively low log2-fold change from being scored as significant simply because it is clustered with a gene with a highly significant PF value. Finally, GenomeCrawler calculated the overall significance of differentially expressed genes (PE values) by integrating differential expression probabilities (PF) and cluster context probabilities (PC). We developed a plotting application (GenomeSpyer) that represents the chromosome as a linear molecule to visualize GenomeCrawler output, with genes displayed on the x-axis and their log2-fold change magnitudes on the y-axis. Applications and all datasets are available for download at http://www.rockefeller.edu/vaf/streparray.php. We visually inspected the resulting clusters and disqualified those that violated our neighbor cluster definition (see Methods for details). All output prior to cluster disqualifications is included for comparison (see Table S4). Of the 309 qualifying clusters (Table S5), 197 (63.8%) were composed entirely of known, functionally defined genes; however, 26 (13%) of these were incorrectly assembled, as they contained known genes that are functionally unrelated. Because we did not incorporate functional annotations of genes into the algorithms (i.e., to keep the analysis \"blind\"), we anticipated the possibility that some groupings could be assembled incorrectly despite the statistical framework for assigning clusters. Of the remaining 283 (91.6%) groupings, a number of differently sized clusters contained the same gene (Table S5). We report such clusters first by highest significance (lowest PK value), then by largest number of genes. Thus, if clusters containing a particular gene were of equal significance, we report the cluster with the most gene members. This method identified 47 significant clusters containing 173 differentially expressed genes (listed in Table 3 and visualized in Figures 2 and S2-S4), a considerably larger group than could have been compiled using only the initial 79 significant genes. A total of 56 of the original 79 significant genes became components of significant clusters, whereas 23 remained unclustered. We subdivided all clusters into three qualitative types based on the functional annotation of gene members. We present examples of Type I and II clusters: Type I clusters (n = 25) contained only functionally defined and functionally related genes (as reported in published studies), such as biological pathways components (Figures 2B and S2); Type II clusters (n = 20) included both known and unknown genes (Figures 2C and S3). Type III clusters (n = 2) were composed entirely of unknown genes (Figures 2D and S4), and are not discussed in detail.\n" ], "offsets": [ [ 0, 5141 ] ] } ]

[ { "id": "PMC1913099-02-Results-Discussion-07_T1", "type": "Chemical", "text": [ "folate" ], "offsets": [ [ 473, 479 ] ], "normalized": [] } ]

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[ { "id": "PMC2816692-02-Results-06__text", "type": "abstract", "text": [ "SrcA is required for PipB2-dependent centrifugal displacement of the Salmonella-containing vacuole \nTo further show a role for SrcA in chaperoning PipB2, we set up experiments to test whether deleting srcA would phenocopy DeltapipB2 cells for PipB2-dependent centrifugal displacement of the Salmonella containing vacuole (SCV) in epithelial cells, an event linked to cell-to-cell transfer during infection in vitro [29]. At 10 h after infection the majority of SCVs were situated near the nucleus in accordance with previous work (Fig. 6A) [29]. By 24 h after infection SCVs containing wild type bacteria were displaced centrifugally towards the cell periphery whereas SCVs containing either pipB2 or srcA mutant bacteria remained juxtaposed to the nucleus (Fig. 6A). The average distance from the nucleus of LAMP1+ SCVs containing wild type bacteria was 2.19 microm at 10h post infection and increased to 7.86 microm by 24 h after infection. Conversely, SCVs containing either DeltapipB2 cells or DeltasrcA cells were 1.38 microm and 2.09 microm at 10h but lacked centrifugal displacement at 24 h (2.23 microm and 2.85 microm, respectively) (Fig. 6B).\n" ], "offsets": [ [ 0, 1153 ] ] } ]

[ { "id": "PMC2816692-02-Results-06_T1", "type": "Protein", "text": [ "SrcA" ], "offsets": [ [ 0, 4 ] ], "normalized": [] }, { "id": "PMC2816692-02-Results-06_T2", "type": "Protein", "text": [ "PipB2" ], "offsets": [ [ 21, 26 ] ], "normalized": [] }, { "id": "PMC2816692-02-Results-06_T3", "type": "Organism", "text": [ "Salmonella" ], "offsets": [ [ 69, 79 ] ], "normalized": [] }, { "id": "PMC2816692-02-Results-06_T4", "type": "Protein", "text": [ "SrcA" ], "offsets": [ [ 127, 131 ] ], "normalized": [] }, { "id": "PMC2816692-02-Results-06_T5", "type": "Protein", "text": [ "PipB2" ], "offsets": [ [ 147, 152 ] ], "normalized": [] }, { "id": "PMC2816692-02-Results-06_T6", "type": "Protein", "text": [ "srcA" ], "offsets": [ [ 201, 205 ] ], "normalized": [] }, { "id": "PMC2816692-02-Results-06_T7", "type": "Organism", "text": [ "DeltapipB2" ], "offsets": [ [ 222, 232 ] ], "normalized": [] }, { "id": "PMC2816692-02-Results-06_T8", "type": "Protein", "text": [ "PipB2" ], "offsets": [ [ 243, 248 ] ], "normalized": [] }, { "id": "PMC2816692-02-Results-06_T9", "type": "Organism", "text": [ "Salmonella" ], "offsets": [ [ 291, 301 ] ], "normalized": [] }, { "id": "PMC2816692-02-Results-06_T10", "type": "Protein", "text": [ "pipB2" ], "offsets": [ [ 692, 697 ] ], "normalized": [] }, { "id": "PMC2816692-02-Results-06_T11", "type": "Organism", "text": [ "srcA mutant" ], "offsets": [ [ 701, 712 ] ], "normalized": [] }, { "id": "PMC2816692-02-Results-06_T12", "type": "Protein", "text": [ "srcA" ], "offsets": [ [ 701, 705 ] ], "normalized": [] }, { "id": "PMC2816692-02-Results-06_T13", "type": "Organism", "text": [ "DeltapipB2" ], "offsets": [ [ 978, 988 ] ], "normalized": [] }, { "id": "PMC2816692-02-Results-06_T14", "type": "Organism", "text": [ "DeltasrcA" ], "offsets": [ [ 998, 1007 ] ], "normalized": [] } ]

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[ { "id": "PMC2639726-02-Results-05__text", "type": "abstract", "text": [ "Cluster analysis identifies additional genes that are co-regulated with known virulence factors \nThe results from the microarray analysis identified many genes that appeared to be coordinately regulated including all SPI-2 encoded genes that are part of the type III secretion system (Table S2). We searched for additional previously unidentified virulence factors encoded elsewhere on the chromosome that show the same pattern of expression as those located within SPI-2. A systematic way of identifying co-regulation is with one of several computer algorithms that group genes together if their expression is similarly changed under like conditions. The diverse growth conditions used in this study, as well as differences between isogenic strains containing mutations in virulence regulators, make our data set ideal for this type of analysis. In addition, we also performed cluster analysis using public data sets acquired from the NIH sponsored public repository of microarray data, gene expression omnibus (GEO). We chose 120 transcriptional profiles from GEO that were derived by extracting RNA from the same parent Salmonella strain grown under a wide variety of culture conditions (GSE2456; G. Yun et al., unpublished data). Expression profiles for all genes were uploaded to SEBINI (Software Environment for Biological Network Inference [18]). SEBINI incorporates statistical and network algorithms into a framework for network inference [55],[56]. To detect dependencies among genes over different conditions we employed the context likelihood of relatedness algorithm (CLR; [19]), which is a plugin for SEBINI. The results were visualized as a network of similarity relationships using Cytoscape [57]. A recent study with E. coli shows that the CLR algorithm was the most accurate in computing the correct network for experimentally verified regulatory interactions [19]. The results shown in Figure 5 use a force-directed network layout algorithm where genes (shown as small colored circles) are generally closer together when their statistical association, and thus degree of predicted co-regulation, is stronger (the cutoff for the genes shown is 5 standard deviations from the mean or greater; p<.0001). All SPI-2 secretion apparatus genes as well as associated effectors and chaperones were found to very tightly cluster in the network. In support of this conclusion, the cluster analyses based on our data and based on publicly available data sets are consistent. The cluster analysis identified 92 genes that are co-regulated with the SPI-2 encoded type III secretion system but not located within SPI-2. This includes known SPI-2 secreted effectors encoded elsewhere on the chromosome as well as many genes for which no function has been assigned (all total 123 genes; see Table 2). Several of these genes are A+T rich (>60% compared to 48% for the Salmonella chromosome) and located within sequences that are not present in close relatives of Salmonella suggesting that they may be unidentified secreted effectors or other virulence determinants that have been acquired from other pathogens. All in all, the implication of the cluster data is that the genes shown in Table 2 are co-regulated with SPI-2. One interesting point is that the algorithm does not distinguish between positive and negative regulation only that it is coincident. We analyzed expression of each of the 123 genes and found that only two genes (pepA and mopB) are negatively regulated; the remaining 121 are positively regulated.\n" ], "offsets": [ [ 0, 3523 ] ] } ]

[ { "id": "PMC2639726-02-Results-05_T1", "type": "Organism", "text": [ "Salmonella" ], "offsets": [ [ 1123, 1133 ] ], "normalized": [] }, { "id": "PMC2639726-02-Results-05_T2", "type": "Organism", "text": [ "E. coli" ], "offsets": [ [ 1734, 1741 ] ], "normalized": [] }, { "id": "PMC2639726-02-Results-05_T3", "type": "Organism", "text": [ "Salmonella" ], "offsets": [ [ 2869, 2879 ] ], "normalized": [] }, { "id": "PMC2639726-02-Results-05_T4", "type": "Organism", "text": [ "Salmonella" ], "offsets": [ [ 2964, 2974 ] ], "normalized": [] }, { "id": "PMC2639726-02-Results-05_T5", "type": "Protein", "text": [ "pepA" ], "offsets": [ [ 3438, 3442 ] ], "normalized": [] }, { "id": "PMC2639726-02-Results-05_T6", "type": "Protein", "text": [ "mopB" ], "offsets": [ [ 3447, 3451 ] ], "normalized": [] } ]

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[ { "id": "PMC2682197-02-Results-05__text", "type": "abstract", "text": [ "The crystal structure of M. tuberculosis Rv2623: Dimer assembly and ATP-binding capacity \nTo examine the biochemical mechanisms responsible for Rv2623 function, we determined the crystal structure of wild-type Rv2623 at a resolution of 2.9 A. The structure reveals a compact, 2-fold symmetric dimer. Each monomer is composed of tandem USP domains [residues 6-154 (domain 1), 155-294 (domain2)] that share 26% sequence identity and significant structural homology (residues 6-154 and 155-294 comprise domains 1 and 2, respectively; interdomain rms=2.04 A for 140 equivalent Calpha's). Individual domains, which consist of a twisted, five-stranded, parallel beta sheet flanked by four alpha helices, unite through an antiparallel, cross-strand (beta5-beta10) interaction that produces a central dyad axis between beta5/beta10 and a continuous, ten-stranded, mixed beta sheet in the complete monomer. Each domain possesses a pair of conserved betaalphabeta motifs (domain 1: beta1-L1-alpha1- beta2, beta4-L2-alpha4-beta5; domain 2: beta6-L3-alpha5-beta7, beta9-L4-alpha8-beta10) that encompass four loops (designated L1-L4) responsible for ATP recognition (Figure 6A and C). A \"U-shaped\" ATP molecule that lies within a cleft near the monomer surface is stabilized by 1) a cluster of hydrophobic residues (I14, V41, H42, V116/132/261/277/281, L136, A175) that forge the adenine/ribose-binding scaffold, 2) a pair of conserved L1/L3 aspartates (D15-L1/D167-L3), and 3) small phosphoryl/ribosyl-binding residues within the G-2X-G-9X-G (S/T) motifs that comprise L2/L4 (G120/265/267/268 and S131/276) (Figures 6A,C and 7A). Dimerization of Rv2623 occurs along a 2-fold axis orthogonal to the intramonomer dyad and juxtaposes ATP binding pockets from opposing monomers (Figure 6B). Phylogenomic analysis places Rv2623 in a Uniprot/TrEMBL family (Q5YVE7) of 370 tandem-domain USPs, and a 113-member subfamily (N631) that consists almost exclusively of actinobacterial representatives (Text S1). Structure-based sequence alignments of both Rv2623 domains with the N631 consensus suggest that domain 2, which exhibits significantly higher conservation than domain 1 across global and ATP-binding subfamily consensus sequences, represents the ancestral domain among ATP-binding USPs with tandem-type architectures. Interestingly, the domain fold and interdomain organization observed for Rv2623 is broadly conserved: these features are shared among single domain USP structures, both monomeric and dimeric, that are presently represented within the PDB. As this manuscript was under preparation, a second, lower resolution (3.2 A) crystal form of Rv2623 (PDB ID 2JAX) was released for public access. This structure is nearly identical to the present model as demonstrated by superposition over the ATP ligands and the monomeric and dimeric forms (rmsds are 0.57 and 0.81 for 258 and 517 matched CA's, respectively). The differences localize primarily to flexible loop regions (residues 44-58, 150-159) that, while disordered in 2JAX, are partially stabilized in the present structure by local crystal contacts. To gain insight into the ATP-binding mode(s) exhibited by Rv2623, the structural features of the ATP-binding pocket of domains 1/2 were compared to the monomer fold of the representative ATP-binding USP, MJ0577 (PDBID 1MJH) [26]. Overlay of these structures reveals very considerable similarity for the residues that form the binding pockets and the associated ATP molecules, for which the triphosphoryl moieties assume virtually indistinguishable conformations. Relatively subtle structural and phylogenetic differences that exist between the ATP-binding pockets might nevertheless confer divergent binding and/or regulatory properties to the tandem domains.\n" ], "offsets": [ [ 0, 3760 ] ] } ]

[ { "id": "PMC2682197-02-Results-05_T1", "type": "Organism", "text": [ "M. tuberculosis" ], "offsets": [ [ 25, 40 ] ], "normalized": [] }, { "id": "PMC2682197-02-Results-05_T2", "type": "Protein", "text": [ "Rv2623" ], "offsets": [ [ 41, 47 ] ], "normalized": [] }, { "id": "PMC2682197-02-Results-05_T3", "type": "Chemical", "text": [ "ATP" ], "offsets": [ [ 68, 71 ] ], "normalized": [] }, { "id": "PMC2682197-02-Results-05_T4", "type": "Protein", "text": [ "Rv2623" ], "offsets": [ [ 144, 150 ] ], "normalized": [] }, { "id": "PMC2682197-02-Results-05_T5", "type": "Protein", "text": [ "Rv2623" ], "offsets": [ [ 210, 216 ] ], "normalized": [] }, { "id": "PMC2682197-02-Results-05_T6", "type": "Chemical", "text": [ "ATP" ], "offsets": [ [ 1137, 1140 ] ], "normalized": [] }, { "id": "PMC2682197-02-Results-05_T7", "type": "Chemical", "text": [ "ATP" ], "offsets": [ [ 1185, 1188 ] ], "normalized": [] }, { "id": "PMC2682197-02-Results-05_T8", "type": "Protein", "text": [ "Rv2623" ], "offsets": [ [ 1634, 1640 ] ], "normalized": [] }, { "id": "PMC2682197-02-Results-05_T9", "type": "Chemical", "text": [ "ATP" ], "offsets": [ [ 1719, 1722 ] ], "normalized": [] }, { "id": "PMC2682197-02-Results-05_T10", "type": "Protein", "text": [ "Rv2623" ], "offsets": [ [ 1804, 1810 ] ], "normalized": [] }, { "id": "PMC2682197-02-Results-05_T11", "type": "Protein", "text": [ "Rv2623" ], "offsets": [ [ 2031, 2037 ] ], "normalized": [] }, { "id": "PMC2682197-02-Results-05_T12", "type": "Chemical", "text": [ "ATP" ], "offsets": [ [ 2174, 2177 ] ], "normalized": [] }, { "id": "PMC2682197-02-Results-05_T13", "type": "Chemical", "text": [ "ATP" ], "offsets": [ [ 2255, 2258 ] ], "normalized": [] }, { "id": "PMC2682197-02-Results-05_T14", "type": "Protein", "text": [ "Rv2623" ], "offsets": [ [ 2377, 2383 ] ], "normalized": [] }, { "id": "PMC2682197-02-Results-05_T15", "type": "Protein", "text": [ "Rv2623" ], "offsets": [ [ 2636, 2642 ] ], "normalized": [] }, { "id": "PMC2682197-02-Results-05_T16", "type": "Chemical", "text": [ "ATP" ], "offsets": [ [ 2787, 2790 ] ], "normalized": [] }, { "id": "PMC2682197-02-Results-05_T17", "type": "Chemical", "text": [ "ATP" ], "offsets": [ [ 3125, 3128 ] ], "normalized": [] }, { "id": "PMC2682197-02-Results-05_T18", "type": "Protein", "text": [ "Rv2623" ], "offsets": [ [ 3158, 3164 ] ], "normalized": [] }, { "id": "PMC2682197-02-Results-05_T19", "type": "Chemical", "text": [ "ATP" ], "offsets": [ [ 3197, 3200 ] ], "normalized": [] }, { "id": "PMC2682197-02-Results-05_T20", "type": "Chemical", "text": [ "ATP" ], "offsets": [ [ 3287, 3290 ] ], "normalized": [] }, { "id": "PMC2682197-02-Results-05_T21", "type": "Protein", "text": [ "MJ0577" ], "offsets": [ [ 3304, 3310 ] ], "normalized": [] }, { "id": "PMC2682197-02-Results-05_T22", "type": "Chemical", "text": [ "ATP" ], "offsets": [ [ 3461, 3464 ] ], "normalized": [] }, { "id": "PMC2682197-02-Results-05_T23", "type": "Chemical", "text": [ "ATP" ], "offsets": [ [ 3644, 3647 ] ], "normalized": [] } ]

[ { "id": "PMC2682197-02-Results-05_E1", "type": "Binding", "trigger": { "text": [ "binding" ], "offsets": [ [ 72, 79 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC2682197-02-Results-05_T3" }, { "role": "Theme", "ref_id": "PMC2682197-02-Results-05_T2" } ] }, { "id": "PMC2682197-02-Results-05_E2", "type": "Binding", "trigger": { "text": [ "Dimerization" ], "offsets": [ [ 1618, 1630 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC2682197-02-Results-05_T8" } ] }, { "id": "PMC2682197-02-Results-05_E3", "type": "Binding", "trigger": { "text": [ "binding" ], "offsets": [ [ 2259, 2266 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC2682197-02-Results-05_T13" } ] }, { "id": "PMC2682197-02-Results-05_E4", "type": "Binding", "trigger": { "text": [ "binding" ], "offsets": [ [ 3129, 3136 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC2682197-02-Results-05_T17" }, { "role": "Theme", "ref_id": "PMC2682197-02-Results-05_T18" } ] }, { "id": "PMC2682197-02-Results-05_E5", "type": "Binding", "trigger": { "text": [ "binding" ], "offsets": [ [ 3291, 3298 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC2682197-02-Results-05_T20" }, { "role": "Theme", "ref_id": "PMC2682197-02-Results-05_T21" } ] }, { "id": "PMC2682197-02-Results-05_E6", "type": "Binding", "trigger": { "text": [ "associated" ], "offsets": [ [ 3450, 3460 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC2682197-02-Results-05_T22" } ] } ]

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[]

[ { "id": "PMC2639726-03-Discussion-02__text", "type": "abstract", "text": [ "What are the signals being sensed during systemic infection and how are they integrated to express virulence factors appropriately? \nThere have been several studies to identify environmental factors that regulate expression of the type III secretion system encoded within SPI-2. Carbon limitation, low concentrations of Mg2+ or Ca2+ [73], and acidic pH [47],[61] induce SPI-2 expression in vitro. Inside professional phagocytic cells divalent cation concentrations and the presence of defensin-like molecules signal through phoP/phoQ [74],[75], and acidic pH and osmolarity signal through ompR/envZ [76]. OmpR has been shown to respond to acidic pH via cadC [77]. The signal(s) received by SsrA, the sensor of the SsrA/SsrB system, is not yet established. It is surprising that over-expression of ssrB can compensate for a deletion of ssrA or ssrA/ssrB. Previous results have shown that a conservative replacement of the amino acid that is the essential phosphate acceptor eliminated expression of SPI-2 genes suggesting that SsrB requires phosphorylation for activity. Yet, expression of ssrB without ssrA results in expression of all 7 SPI-2 genes examined (Figure 7A). It is possible that SsrB can be phosphorylated from other sources as noted by Walthers et al. [52] or that the over-expression results in dimerization and self activation similar to what has been observed for PhoP [78]. Mutations in rpoE, smpB, rpoS, and hfq showed only small decreases in SPI-2 gene transcription during growth in minimal acidic media but some of them showed large defects in survival assays performed in murine macrophages. For rpoE and rpoS it is possible that the environmental conditions that distinguish growth in minimal media from those in the SCV inside hosts are sensed via these two alternative sigma factors. Figure 6B shows that there is a close relationship between these two regulators and that they can both affect each other through the ompR/envZ two-component regulator. Post-transcriptional SPI-2 regulation is a likely explanation for the large intracellular growth defects observed in the mutant smpB and hfq derivatives despite relative small transcriptional effects. Strains containing mutations in spvR and hnr showed comparable survival levels to wild-type in macrophages from BALB/c mice despite the fact that they are attenuated in the same mouse strain. Perhaps these regulators are selected during growth in other cell types or within phagocytic cells that are activated as a consequence of the inflammatory response generated by the bacteria.\n" ], "offsets": [ [ 0, 2562 ] ] } ]

[ { "id": "PMC2639726-03-Discussion-02_T1", "type": "Chemical", "text": [ "Carbon" ], "offsets": [ [ 279, 285 ] ], "normalized": [] }, { "id": "PMC2639726-03-Discussion-02_T2", "type": "Chemical", "text": [ "Mg2+" ], "offsets": [ [ 320, 324 ] ], "normalized": [] }, { "id": "PMC2639726-03-Discussion-02_T3", "type": "Chemical", "text": [ "Ca2+" ], "offsets": [ [ 328, 332 ] ], "normalized": [] }, { "id": "PMC2639726-03-Discussion-02_T4", "type": "Two-component-system", "text": [ "phoP/phoQ" ], "offsets": [ [ 524, 533 ] ], "normalized": [] }, { "id": "PMC2639726-03-Discussion-02_T5", "type": "Protein", "text": [ "phoP" ], "offsets": [ [ 524, 528 ] ], "normalized": [] }, { "id": "PMC2639726-03-Discussion-02_T6", "type": "Protein", "text": [ "phoQ" ], "offsets": [ [ 529, 533 ] ], "normalized": [] }, { "id": "PMC2639726-03-Discussion-02_T7", "type": "Two-component-system", "text": [ "ompR/envZ" ], "offsets": [ [ 589, 598 ] ], "normalized": [] }, { "id": "PMC2639726-03-Discussion-02_T8", "type": "Protein", "text": [ "ompR" ], "offsets": [ [ 589, 593 ] ], "normalized": [] }, { "id": "PMC2639726-03-Discussion-02_T9", "type": "Protein", "text": [ "envZ" ], "offsets": [ [ 594, 598 ] ], "normalized": [] }, { "id": "PMC2639726-03-Discussion-02_T10", "type": "Protein", "text": [ "OmpR" ], "offsets": [ [ 605, 609 ] ], "normalized": [] }, { "id": "PMC2639726-03-Discussion-02_T11", "type": "Protein", "text": [ "cadC" ], "offsets": [ [ 653, 657 ] ], "normalized": [] }, { "id": "PMC2639726-03-Discussion-02_T12", "type": "Protein", "text": [ "SsrA" ], "offsets": [ [ 690, 694 ] ], "normalized": [] }, { "id": "PMC2639726-03-Discussion-02_T13", "type": "Two-component-system", "text": [ "SsrA/SsrB" ], "offsets": [ [ 714, 723 ] ], "normalized": [] }, { "id": "PMC2639726-03-Discussion-02_T14", "type": "Protein", "text": [ "SsrA" ], "offsets": [ [ 714, 718 ] ], "normalized": [] }, { "id": "PMC2639726-03-Discussion-02_T15", "type": "Protein", "text": [ "SsrB" ], "offsets": [ [ 719, 723 ] ], "normalized": [] }, { "id": "PMC2639726-03-Discussion-02_T16", "type": "Protein", "text": [ "ssrB" ], "offsets": [ [ 797, 801 ] ], "normalized": [] }, { "id": "PMC2639726-03-Discussion-02_T17", "type": "Protein", "text": [ "ssrA" ], "offsets": [ [ 835, 839 ] ], "normalized": [] }, { "id": "PMC2639726-03-Discussion-02_T18", "type": "Two-component-system", "text": [ "ssrA/ssrB" ], "offsets": [ [ 843, 852 ] ], "normalized": [] }, { "id": "PMC2639726-03-Discussion-02_T19", "type": "Protein", "text": [ "ssrA" ], "offsets": [ [ 843, 847 ] ], "normalized": [] }, { "id": "PMC2639726-03-Discussion-02_T20", "type": "Protein", "text": [ "ssrB" ], "offsets": [ [ 848, 852 ] ], "normalized": [] }, { "id": "PMC2639726-03-Discussion-02_T21", "type": "Chemical", "text": [ "phosphate" ], "offsets": [ [ 954, 963 ] ], "normalized": [] }, { "id": "PMC2639726-03-Discussion-02_T22", "type": "Protein", "text": [ "SsrB" ], "offsets": [ [ 1026, 1030 ] ], "normalized": [] }, { "id": "PMC2639726-03-Discussion-02_T23", "type": "Protein", "text": [ "ssrB" ], "offsets": [ [ 1089, 1093 ] ], "normalized": [] }, { "id": "PMC2639726-03-Discussion-02_T24", "type": "Protein", "text": [ "ssrA" ], "offsets": [ [ 1102, 1106 ] ], "normalized": [] }, { "id": "PMC2639726-03-Discussion-02_T25", "type": "Protein", "text": [ "SsrB" ], "offsets": [ [ 1192, 1196 ] ], "normalized": [] }, { "id": "PMC2639726-03-Discussion-02_T26", "type": "Protein", "text": [ "PhoP" ], "offsets": [ [ 1381, 1385 ] ], "normalized": [] }, { "id": "PMC2639726-03-Discussion-02_T27", "type": "Protein", "text": [ "rpoE" ], "offsets": [ [ 1405, 1409 ] ], "normalized": [] }, { "id": "PMC2639726-03-Discussion-02_T28", "type": "Protein", "text": [ "smpB" ], "offsets": [ [ 1411, 1415 ] ], "normalized": [] }, { "id": "PMC2639726-03-Discussion-02_T29", "type": "Protein", "text": [ "rpoS" ], "offsets": [ [ 1417, 1421 ] ], "normalized": [] }, { "id": "PMC2639726-03-Discussion-02_T30", "type": "Protein", "text": [ "hfq" ], "offsets": [ [ 1427, 1430 ] ], "normalized": [] }, { "id": "PMC2639726-03-Discussion-02_T31", "type": "Organism", "text": [ "murine" ], "offsets": [ [ 1595, 1601 ] ], "normalized": [] }, { "id": "PMC2639726-03-Discussion-02_T32", "type": "Protein", "text": [ "rpoE" ], "offsets": [ [ 1619, 1623 ] ], "normalized": [] }, { "id": "PMC2639726-03-Discussion-02_T33", "type": "Protein", "text": [ "rpoS" ], "offsets": [ [ 1628, 1632 ] ], "normalized": [] }, { "id": "PMC2639726-03-Discussion-02_T34", "type": "Organism", "text": [ "SCV" ], "offsets": [ [ 1741, 1744 ] ], "normalized": [] }, { "id": "PMC2639726-03-Discussion-02_T35", "type": "Two-component-system", "text": [ "ompR/envZ" ], "offsets": [ [ 1943, 1952 ] ], "normalized": [] }, { "id": "PMC2639726-03-Discussion-02_T36", "type": "Protein", "text": [ "ompR" ], "offsets": [ [ 1943, 1947 ] ], "normalized": [] }, { "id": "PMC2639726-03-Discussion-02_T37", "type": "Protein", "text": [ "envZ" ], "offsets": [ [ 1948, 1952 ] ], "normalized": [] }, { "id": "PMC2639726-03-Discussion-02_T38", "type": "Protein", "text": [ "smpB" ], "offsets": [ [ 2106, 2110 ] ], "normalized": [] }, { "id": "PMC2639726-03-Discussion-02_T39", "type": "Protein", "text": [ "hfq" ], "offsets": [ [ 2115, 2118 ] ], "normalized": [] }, { "id": "PMC2639726-03-Discussion-02_T40", "type": "Protein", "text": [ "spvR" ], "offsets": [ [ 2211, 2215 ] ], "normalized": [] }, { "id": "PMC2639726-03-Discussion-02_T41", "type": "Protein", "text": [ "hnr" ], "offsets": [ [ 2220, 2223 ] ], "normalized": [] }, { "id": "PMC2639726-03-Discussion-02_T42", "type": "Organism", "text": [ "BALB/c mice" ], "offsets": [ [ 2291, 2302 ] ], "normalized": [] }, { "id": "PMC2639726-03-Discussion-02_T43", "type": "Organism", "text": [ "mouse" ], "offsets": [ [ 2357, 2362 ] ], "normalized": [] } ]

[ { "id": "PMC2639726-03-Discussion-02_E1", "type": "Positive_regulation", "trigger": { "text": [ "respond" ], "offsets": [ [ 628, 635 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC2639726-03-Discussion-02_T10" }, { "role": "Cause", "ref_id": "PMC2639726-03-Discussion-02_T11" } ] }, { "id": "PMC2639726-03-Discussion-02_E2", "type": "Gene_expression", "trigger": { "text": [ "over-expression" ], "offsets": [ [ 778, 793 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC2639726-03-Discussion-02_T16" } ] }, { "id": "PMC2639726-03-Discussion-02_E3", "type": "Positive_regulation", "trigger": { "text": [ "requires" ], "offsets": [ [ 1031, 1039 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC2639726-03-Discussion-02_T22" }, { "role": "Cause", "ref_id": "PMC2639726-03-Discussion-02_E4" } ] }, { "id": "PMC2639726-03-Discussion-02_E4", "type": "Phosphorylation", "trigger": { "text": [ "phosphorylation" ], "offsets": [ [ 1040, 1055 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC2639726-03-Discussion-02_T22" } ] }, { "id": "PMC2639726-03-Discussion-02_E5", "type": "Gene_expression", "trigger": { "text": [ "expression" ], "offsets": [ [ 1075, 1085 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC2639726-03-Discussion-02_T23" } ] }, { "id": "PMC2639726-03-Discussion-02_E6", "type": "Phosphorylation", "trigger": { "text": [ "phosphorylated" ], "offsets": [ [ 1204, 1218 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC2639726-03-Discussion-02_T25" } ] }, { "id": "PMC2639726-03-Discussion-02_E7", "type": "Gene_expression", "trigger": { "text": [ "over-expression" ], "offsets": [ [ 1283, 1298 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC2639726-03-Discussion-02_T25" } ] }, { "id": "PMC2639726-03-Discussion-02_E8", "type": "Positive_regulation", "trigger": { "text": [ "activation" ], "offsets": [ [ 1332, 1342 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC2639726-03-Discussion-02_T25" }, { "role": "Cause", "ref_id": "PMC2639726-03-Discussion-02_E7" } ] }, { "id": "PMC2639726-03-Discussion-02_E9", "type": "Regulation", "trigger": { "text": [ "affect" ], "offsets": [ [ 1913, 1919 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC2639726-03-Discussion-02_T35" }, { "role": "Cause", "ref_id": "PMC2639726-03-Discussion-02_T33" } ] }, { "id": "PMC2639726-03-Discussion-02_E10", "type": "Regulation", "trigger": { "text": [ "affect" ], "offsets": [ [ 1913, 1919 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC2639726-03-Discussion-02_T33" }, { "role": "Cause", "ref_id": "PMC2639726-03-Discussion-02_E12" } ] }, { "id": "PMC2639726-03-Discussion-02_E11", "type": "Regulation", "trigger": { "text": [ "affect" ], "offsets": [ [ 1913, 1919 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC2639726-03-Discussion-02_T32" }, { "role": "Cause", "ref_id": "PMC2639726-03-Discussion-02_E9" } ] }, { "id": "PMC2639726-03-Discussion-02_E12", "type": "Regulation", "trigger": { "text": [ "affect" ], "offsets": [ [ 1913, 1919 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC2639726-03-Discussion-02_T35" }, { "role": "Cause", "ref_id": "PMC2639726-03-Discussion-02_T32" } ] }, { "id": "PMC2639726-03-Discussion-02_E13", "type": "Process", "trigger": { "text": [ "attenuated" ], "offsets": [ [ 2334, 2344 ] ] }, "arguments": [] } ]

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[]

[ { "id": "PMC2266911-02-Results_and_Discussion-02-03-01__text", "type": "abstract", "text": [ "Defensive mechanisms \nAntimicrobials The production of antibiotics is mainly restricted to P. luminescens, whereas factors combating antimicrobial host substances play an important role during the infection process of both pathogens compared here. In the genome of P. luminescens ssp. laumondii strain TT01, many loci involved in the defense of the insect cadaver against different microbial competitors are present, including nearly 50 genes encoding proteins such as polyketide and peptide synthases putatively involved in antibiotic synthesis and efflux. Interestingly, none of these genes showed significant similarities to sequences of the Y. enterocolitica genome. Phage-derived bacteriocins in entomopathogenic bacteria are also presumed to eliminate competing bacteria. More than twenty colicin/pyocin-like factors and putative immunity proteins are unique to P. luminescens in comparison to Y. enterocolitica. Remarkable exceptions are the toxin/antitoxin system ccdA/ccdB, the tolQRAB/pal operon involved in group A colicin translocation, and a colicin production and secretion system (Plu3168/Plu3869; YE0791/YE1314). Recently, it was reported that PrtS (Plu1382) secreted by P. luminescens, a metalloprotease without counterpart in Y. enterocolitica, specifically induces melanization of the hemolymph, probably to circumvent the innate immune response of the insect [81].\n" ], "offsets": [ [ 0, 1385 ] ] } ]

[ { "id": "PMC2266911-02-Results_and_Discussion-02-03-01_T1", "type": "Organism", "text": [ "P. luminescens" ], "offsets": [ [ 91, 105 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-02-03-01_T2", "type": "Organism", "text": [ "P. luminescens ssp. laumondii strain TT01" ], "offsets": [ [ 265, 306 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-02-03-01_T3", "type": "Organism", "text": [ "Y. enterocolitica" ], "offsets": [ [ 645, 662 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-02-03-01_T4", "type": "Organism", "text": [ "P. luminescens" ], "offsets": [ [ 868, 882 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-02-03-01_T5", "type": "Organism", "text": [ "Y. enterocolitica" ], "offsets": [ [ 900, 917 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-02-03-01_T6", "type": "Two-component-system", "text": [ "ccdA/ccdB" ], "offsets": [ [ 972, 981 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-02-03-01_T7", "type": "Protein", "text": [ "ccdA" ], "offsets": [ [ 972, 976 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-02-03-01_T8", "type": "Protein", "text": [ "ccdB" ], "offsets": [ [ 977, 981 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-02-03-01_T9", "type": "Regulon-operon", "text": [ "tolQRAB/pal" ], "offsets": [ [ 987, 998 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-02-03-01_T10", "type": "Protein", "text": [ "tolQ" ], "offsets": [ [ 987, 991 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-02-03-01_T11", "type": "Protein", "text": [ "R" ], "offsets": [ [ 991, 992 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-02-03-01_T12", "type": "Protein", "text": [ "A" ], "offsets": [ [ 992, 993 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-02-03-01_T13", "type": "Protein", "text": [ "B" ], "offsets": [ [ 993, 994 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-02-03-01_T14", "type": "Protein", "text": [ "pal" ], "offsets": [ [ 995, 998 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-02-03-01_T15", "type": "Two-component-system", "text": [ "Plu3168/Plu3869" ], "offsets": [ [ 1096, 1111 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-02-03-01_T16", "type": "Protein", "text": [ "Plu3168" ], "offsets": [ [ 1096, 1103 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-02-03-01_T17", "type": "Protein", "text": [ "Plu3869" ], "offsets": [ [ 1104, 1111 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-02-03-01_T18", "type": "Two-component-system", "text": [ "YE0791/YE1314" ], "offsets": [ [ 1113, 1126 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-02-03-01_T19", "type": "Protein", "text": [ "YE0791" ], "offsets": [ [ 1113, 1119 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-02-03-01_T20", "type": "Protein", "text": [ "YE1314" ], "offsets": [ [ 1120, 1126 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-02-03-01_T21", "type": "Protein", "text": [ "PrtS" ], "offsets": [ [ 1160, 1164 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-02-03-01_T22", "type": "Protein", "text": [ "Plu1382" ], "offsets": [ [ 1166, 1173 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-02-03-01_T23", "type": "Organism", "text": [ "P. luminescens" ], "offsets": [ [ 1187, 1201 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-02-03-01_T24", "type": "Organism", "text": [ "Y. enterocolitica" ], "offsets": [ [ 1244, 1261 ] ], "normalized": [] } ]

[ { "id": "PMC2266911-02-Results_and_Discussion-02-03-01_E1", "type": "Regulation", "trigger": { "text": [ "play an important role" ], "offsets": [ [ 163, 185 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC2266911-02-Results_and_Discussion-02-03-01_E2" } ] }, { "id": "PMC2266911-02-Results_and_Discussion-02-03-01_E2", "type": "Process", "trigger": { "text": [ "infection" ], "offsets": [ [ 197, 206 ] ] }, "arguments": [] }, { "id": "PMC2266911-02-Results_and_Discussion-02-03-01_E3", "type": "Localization", "trigger": { "text": [ "secreted" ], "offsets": [ [ 1175, 1183 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC2266911-02-Results_and_Discussion-02-03-01_T21" } ] } ]

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[]

[ { "id": "PMC2774163-02-Results-02__text", "type": "abstract", "text": [ "Identification of regulatory proteins involved in sensing environmental signals associated with planktonic and biofilm growth \nThe quantitative mass spectrometric approach by LC-MS/MS allowed for the simultaneous determination of peptide amino acid sequences by collision-induced dissociation (CID) in the MS/MS mode. Examples of two CID spectra are shown in Suppl. Fig. S2. Proteins that were confirmed to be phosphorylated by immunoblot analysis were identified using a mass spectrometric approach as well. We thus identified 48 proteins that were differentially phosphorylated at one or more biofilm developmental stage including elongation factors, ribosomal proteins, several enzymes including reductases and GMP synthase, sigma factor RpoD (Suppl. Table S1) and 11 regulatory proteins (Table 1). The majority of regulatory proteins found to be uniquely phosphorylated during planktonic growth were transcriptional regulators, while with the exception of PA2096, all regulatory proteins found to be phosphorylated during surface attached growth were identified as belonging to two-component systems (TCS) (Table 1). Of those, the sensor/response regulator hybrid GacS and PA4197 (BfiS) were found to be phosphorylated as soon as 8 hr following attachment, and PA2096 and PA4101 (BfmR) following 24 hr of surface-associated growth (Table 1). Interestingly, PA4102 (BfmS), the cognate sensor of PA4101, was found to be phosphorylated following PA4101 phosphorylation after 72 hr of biofilm growth (Table 1). The reason for the difference in the timing of phosphorylation between sensor and response regulator is unclear. It is possible that this due to the different detection methods used. The probable TCS regulatory protein PA5511 (MifR) was phosphorylated following 72 hr of surface-associated growth. The stage-specific detection and phosphorylation of PA5511 as determined by LC-MS/MS analysis in conjunction with cICAT as well as the CID spectra of a tryptic peptide of PA5511 is shown in Suppl. Fig. S2. Neither the cognate sensory protein PA5512 nor the response regulator PA4196 were identified in this study. This may be due to detection limitation (low protein concentrations, poor protein solubility, poor ionization) and/or limitation in the number of phosphorylated proteins identified (see Suppl. Tables S1 and S2 for comparison). As PA4197, PA4101 and GacS were all phosphorylated by 24 hr of biofilm growth, we asked whether the three proteins are modified simultaneously or in a sequential manner. We reasoned that if protein phosphorylation occurs in sequence, inactivation of one of the proteins would potentially prevent phosphorylation of the other proteins of the phosphorelay. We therefore analyzed GacS, PA4101, and PA4197 mutant biofilm phosphorylation patterns for the presence/absence of these regulators. No evidence of phosphorylation of PA4197, PA4101, or GacS was detected in DeltaPA4197 mutant biofilm phosphorylation patterns. However, phosphorylation of both GacS and PA4197 was detected in DeltaPA4101 mutant biofilms, indicating that PA4101 phosphorylation may occur downstream of GacS and PA4197. DeltagacS biofilm phosphorylation patterns showed an intermediate phosphorylation phenotype with PA4197 being phosphorylated but PA4101 phosphorylation lacking (not shown). PA5511 was not detected in any of the mutant biofilms analyzed (Suppl. Fig. S3). The findings suggest that phosphorylation of regulatory proteins occurs in a sequential (but probably indirect) manner over the course of biofilm formation. To determine whether phosphorylation coincided with de novo gene expression or reflected biofilm-specific patterns of posttranslational modification, RT-PCR was used. PA4101 expression was detected to be biofilm-specific, while PA4197 and PA5511 were constitutively expressed regardless of the mode of growth (Suppl. Fig. S4). Similarly, retS and ladS were also constitutively expressed indicating that posttranslational modifications are essential for their activity.\n" ], "offsets": [ [ 0, 4019 ] ] } ]

[ { "id": "PMC2774163-02-Results-02_T1", "type": "Protein", "text": [ "RpoD" ], "offsets": [ [ 741, 745 ] ], "normalized": [] }, { "id": "PMC2774163-02-Results-02_T2", "type": "Protein", "text": [ "PA2096" ], "offsets": [ [ 960, 966 ] ], "normalized": [] }, { "id": "PMC2774163-02-Results-02_T3", "type": "Protein", "text": [ "GacS" ], "offsets": [ [ 1168, 1172 ] ], "normalized": [] }, { "id": "PMC2774163-02-Results-02_T4", "type": "Protein", "text": [ "PA4197" ], "offsets": [ [ 1177, 1183 ] ], "normalized": [] }, { "id": "PMC2774163-02-Results-02_T5", "type": "Protein", "text": [ "BfiS" ], "offsets": [ [ 1185, 1189 ] ], "normalized": [] }, { "id": "PMC2774163-02-Results-02_T6", "type": "Protein", "text": [ "PA2096" ], "offsets": [ [ 1265, 1271 ] ], "normalized": [] }, { "id": "PMC2774163-02-Results-02_T7", "type": "Protein", "text": [ "PA4101" ], "offsets": [ [ 1276, 1282 ] ], "normalized": [] }, { "id": "PMC2774163-02-Results-02_T8", "type": "Protein", "text": [ "BfmR" ], "offsets": [ [ 1284, 1288 ] ], "normalized": [] }, { "id": "PMC2774163-02-Results-02_T9", "type": "Protein", "text": [ "PA4102" ], "offsets": [ [ 1361, 1367 ] ], "normalized": [] }, { "id": "PMC2774163-02-Results-02_T10", "type": "Protein", "text": [ "BfmS" ], "offsets": [ [ 1369, 1373 ] ], "normalized": [] }, { "id": "PMC2774163-02-Results-02_T11", "type": "Protein", "text": [ "PA4101" ], "offsets": [ [ 1398, 1404 ] ], "normalized": [] }, { "id": "PMC2774163-02-Results-02_T12", "type": "Protein", "text": [ "PA4101" ], "offsets": [ [ 1447, 1453 ] ], "normalized": [] }, { "id": "PMC2774163-02-Results-02_T13", "type": "Protein", "text": [ "PA5511" ], "offsets": [ [ 1730, 1736 ] ], "normalized": [] }, { "id": "PMC2774163-02-Results-02_T14", "type": "Protein", "text": [ "MifR" ], "offsets": [ [ 1738, 1742 ] ], "normalized": [] }, { "id": "PMC2774163-02-Results-02_T15", "type": "Protein", "text": [ "PA5511" ], "offsets": [ [ 1861, 1867 ] ], "normalized": [] }, { "id": "PMC2774163-02-Results-02_T16", "type": "Protein", "text": [ "PA5511" ], "offsets": [ [ 1980, 1986 ] ], "normalized": [] }, { "id": "PMC2774163-02-Results-02_T17", "type": "Protein", "text": [ "PA5512" ], "offsets": [ [ 2051, 2057 ] ], "normalized": [] }, { "id": "PMC2774163-02-Results-02_T18", "type": "Protein", "text": [ "PA4196" ], "offsets": [ [ 2085, 2091 ] ], "normalized": [] }, { "id": "PMC2774163-02-Results-02_T19", "type": "Protein", "text": [ "PA4197" ], "offsets": [ [ 2353, 2359 ] ], "normalized": [] }, { "id": "PMC2774163-02-Results-02_T20", "type": "Protein", "text": [ "PA4101" ], "offsets": [ [ 2361, 2367 ] ], "normalized": [] }, { "id": "PMC2774163-02-Results-02_T21", "type": "Protein", "text": [ "GacS" ], "offsets": [ [ 2372, 2376 ] ], "normalized": [] }, { "id": "PMC2774163-02-Results-02_T22", "type": "Protein", "text": [ "GacS" ], "offsets": [ [ 2727, 2731 ] ], "normalized": [] }, { "id": "PMC2774163-02-Results-02_T23", "type": "Protein", "text": [ "PA4101" ], "offsets": [ [ 2733, 2739 ] ], "normalized": [] }, { "id": "PMC2774163-02-Results-02_T24", "type": "Protein", "text": [ "PA4197" ], "offsets": [ [ 2745, 2751 ] ], "normalized": [] }, { "id": "PMC2774163-02-Results-02_T25", "type": "Protein", "text": [ "PA4197" ], "offsets": [ [ 2872, 2878 ] ], "normalized": [] }, { "id": "PMC2774163-02-Results-02_T26", "type": "Protein", "text": [ "PA4101" ], "offsets": [ [ 2880, 2886 ] ], "normalized": [] }, { "id": "PMC2774163-02-Results-02_T27", "type": "Protein", "text": [ "GacS" ], "offsets": [ [ 2891, 2895 ] ], "normalized": [] }, { "id": "PMC2774163-02-Results-02_T28", "type": "Organism", "text": [ "DeltaPA4197 mutant" ], "offsets": [ [ 2912, 2930 ] ], "normalized": [] }, { "id": "PMC2774163-02-Results-02_T29", "type": "Protein", "text": [ "PA4197" ], "offsets": [ [ 2917, 2923 ] ], "normalized": [] }, { "id": "PMC2774163-02-Results-02_T30", "type": "Protein", "text": [ "GacS" ], "offsets": [ [ 2998, 3002 ] ], "normalized": [] }, { "id": "PMC2774163-02-Results-02_T31", "type": "Protein", "text": [ "PA4197" ], "offsets": [ [ 3007, 3013 ] ], "normalized": [] }, { "id": "PMC2774163-02-Results-02_T32", "type": "Organism", "text": [ "DeltaPA4101 mutant" ], "offsets": [ [ 3030, 3048 ] ], "normalized": [] }, { "id": "PMC2774163-02-Results-02_T33", "type": "Protein", "text": [ "PA4101" ], "offsets": [ [ 3035, 3041 ] ], "normalized": [] }, { "id": "PMC2774163-02-Results-02_T34", "type": "Protein", "text": [ "PA4101" ], "offsets": [ [ 3075, 3081 ] ], "normalized": [] }, { "id": "PMC2774163-02-Results-02_T35", "type": "Protein", "text": [ "GacS" ], "offsets": [ [ 3122, 3126 ] ], "normalized": [] }, { "id": "PMC2774163-02-Results-02_T36", "type": "Protein", "text": [ "PA4197" ], "offsets": [ [ 3131, 3137 ] ], "normalized": [] }, { "id": "PMC2774163-02-Results-02_T37", "type": "Organism", "text": [ "DeltagacS" ], "offsets": [ [ 3139, 3148 ] ], "normalized": [] }, { "id": "PMC2774163-02-Results-02_T38", "type": "Protein", "text": [ "gacS" ], "offsets": [ [ 3144, 3148 ] ], "normalized": [] }, { "id": "PMC2774163-02-Results-02_T39", "type": "Protein", "text": [ "PA4197" ], "offsets": [ [ 3236, 3242 ] ], "normalized": [] }, { "id": "PMC2774163-02-Results-02_T40", "type": "Protein", "text": [ "PA4101" ], "offsets": [ [ 3268, 3274 ] ], "normalized": [] }, { "id": "PMC2774163-02-Results-02_T41", "type": "Protein", "text": [ "PA5511" ], "offsets": [ [ 3312, 3318 ] ], "normalized": [] }, { "id": "PMC2774163-02-Results-02_T42", "type": "Protein", "text": [ "PA4101" ], "offsets": [ [ 3717, 3723 ] ], "normalized": [] }, { "id": "PMC2774163-02-Results-02_T43", "type": "Protein", "text": [ "PA4197" ], "offsets": [ [ 3778, 3784 ] ], "normalized": [] }, { "id": "PMC2774163-02-Results-02_T44", "type": "Protein", "text": [ "PA5511" ], "offsets": [ [ 3789, 3795 ] ], "normalized": [] }, { "id": "PMC2774163-02-Results-02_T45", "type": "Protein", "text": [ "retS" ], "offsets": [ [ 3888, 3892 ] ], "normalized": [] }, { "id": "PMC2774163-02-Results-02_T46", "type": "Protein", "text": [ "ladS" ], "offsets": [ [ 3897, 3901 ] ], "normalized": [] } ]

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[ { "id": "PMC2242835-02-Results-06__text", "type": "abstract", "text": [ "Functional Characterization of Knock-In Mutants \nWe have previously shown that antigen-specific IFN-gamma production of splenocytes is a reliable readout system to evaluate whether or not ESAT-6 was secreted by recombinant strains [23,24,26]. Thus, in order to determine the reason for the observed failure of H37Ra to induce ESAT-6-specific responses, H37Rv and H37Ra strains were tested for their potential to express and secrete ESAT-6 in vitro. The western blot analysis presented in Figure 5 shows that the cell lysates of H37Ra and H37Ra::rpsL contain large amounts of ESAT-6, indicating that the antigen is properly expressed. However, hardly any ESAT-6 was present in the culture filtrates of these cultures, indicating that these strains were unable to secrete ESAT-6 under the in vitro conditions employed in spite of proper expression. Similar results were obtained for H37Ra::fadE5 (unpublished data). In contrast, from examination of the western blots of M. tuberculosis H37Ra::phoP and H37Rv it is clear that a large portion of their ESAT-6 protein is secreted into the culture filtrates. Analysis of the M. tuberculosis MT103 phoP ko strain SO2 showed strong expression of ESAT-6, but only very little secreted ESAT-6 (Figure 5). In a previous report [25], the presence of ESAT-6 in cell free extracts was described for this strain, but no secretion assay was performed. Together, our findings correlate perfectly with the in vivo data described above and suggest that the lack of ESAT-6 specific T cell recognition for H37Ra, H37Ra::fadE5, H37Ra::rpsL, and SO2 is not caused by a loss of ESAT-6 expression, but rather due to a failure of (phoP dependent) ESAT-6 secretion. The observation that knocking-in the ESX-1 region of H37Rv into H37Ra (H37Ra::RD1-ppe68-ko), and the resultant diploidy, did not improve the ESAT-6-specific T cell responses (Figure 3B), further argues that PhoP-dependent ESAT-secretion might be regulated via a mechanism that lies outside the RD1 region. As closer inspection of the available literature on transcriptional analyses of a H37Rv-phoP ko strain [21] and H37Ra [12] suggested that the expression of gene cluster rv3612c-rv3616c is reduced in both strains, we evaluated the expression level of rv3614c in H37Rv, H37Ra, and H37Ra::phoP by quantitative real time PCR (qRT-PCR). In previous studies rv3614c, rv3615c, rv3616c (espA) were independently shown to be essential for proper ESAT-6 secretion [27,28]. We confirmed the trend that rv3614c was expressed much lower in H37Ra compared to H37Rv by qRT-PCR (Figure 6), whereas expression of rv3614c in H37Ra::phoP was restored to wild-type levels, suggesting that the rv3612c-rv3616c gene cluster is regulated by PhoP. Interestingly, expression of phoP was higher in H37Ra than in H37Rv (Figure 6). These findings are consistent with data from a previous transcriptional study [12] and suggest that the proposed ability of PhoP to downregulate its own expression [22] is affected by the S219L phoP mutation [29]. They also indicate that it is not a lack of phoP expression that is causing the phoP-associated effects in H37Ra.\n" ], "offsets": [ [ 0, 3127 ] ] } ]

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[ 528, 533 ] ], "normalized": [] }, { "id": "PMC2242835-02-Results-06_T9", "type": "Organism", "text": [ "H37Ra::rpsL" ], "offsets": [ [ 538, 549 ] ], "normalized": [] }, { "id": "PMC2242835-02-Results-06_T10", "type": "Protein", "text": [ "rpsL" ], "offsets": [ [ 545, 549 ] ], "normalized": [] }, { "id": "PMC2242835-02-Results-06_T11", "type": "Protein", "text": [ "ESAT-6" ], "offsets": [ [ 575, 581 ] ], "normalized": [] }, { "id": "PMC2242835-02-Results-06_T12", "type": "Protein", "text": [ "ESAT-6" ], "offsets": [ [ 654, 660 ] ], "normalized": [] }, { "id": "PMC2242835-02-Results-06_T13", "type": "Protein", "text": [ "ESAT-6" ], "offsets": [ [ 770, 776 ] ], "normalized": [] }, { "id": "PMC2242835-02-Results-06_T14", "type": "Organism", "text": [ "H37Ra::fadE5" ], "offsets": [ [ 881, 893 ] ], "normalized": [] }, { "id": "PMC2242835-02-Results-06_T15", "type": "Protein", "text": [ "fadE5" ], "offsets": [ [ 888, 893 ] ], "normalized": [] }, { "id": "PMC2242835-02-Results-06_T16", "type": "Organism", "text": [ "M. tuberculosis H37Ra::phoP" ], "offsets": [ [ 968, 995 ] ], "normalized": [] }, { "id": "PMC2242835-02-Results-06_T17", "type": "Protein", "text": [ "phoP" ], "offsets": [ [ 991, 995 ] ], "normalized": [] }, { "id": "PMC2242835-02-Results-06_T18", "type": "Organism", "text": [ "H37Rv" ], "offsets": [ [ 1000, 1005 ] ], "normalized": [] }, { "id": "PMC2242835-02-Results-06_T19", "type": "Protein", "text": [ "ESAT-6" ], "offsets": [ [ 1048, 1054 ] ], "normalized": [] }, { "id": "PMC2242835-02-Results-06_T20", "type": "Organism", "text": [ "M. tuberculosis MT103 phoP ko strain SO2" ], "offsets": [ [ 1119, 1159 ] ], "normalized": [] }, { "id": "PMC2242835-02-Results-06_T21", "type": "Protein", "text": [ "ESAT-6" ], "offsets": [ [ 1188, 1194 ] ], "normalized": [] }, { "id": "PMC2242835-02-Results-06_T22", "type": "Protein", "text": [ "ESAT-6" ], "offsets": [ [ 1226, 1232 ] ], "normalized": [] }, { "id": "PMC2242835-02-Results-06_T23", "type": "Protein", "text": [ "ESAT-6" ], "offsets": [ [ 1288, 1294 ] ], "normalized": [] }, { "id": "PMC2242835-02-Results-06_T24", "type": "Protein", "text": [ "ESAT-6" ], "offsets": [ [ 1496, 1502 ] ], "normalized": [] }, { "id": "PMC2242835-02-Results-06_T25", "type": "Organism", "text": [ "H37Ra" ], "offsets": [ [ 1535, 1540 ] ], "normalized": [] }, { "id": "PMC2242835-02-Results-06_T26", "type": "Organism", "text": [ "H37Ra::fadE5" ], "offsets": [ [ 1542, 1554 ] ], "normalized": [] }, { "id": "PMC2242835-02-Results-06_T27", "type": "Protein", "text": [ "fadE5" ], "offsets": [ [ 1549, 1554 ] ], "normalized": [] }, { "id": "PMC2242835-02-Results-06_T28", "type": "Organism", "text": [ "H37Ra::rpsL" ], "offsets": [ [ 1556, 1567 ] ], "normalized": [] }, { "id": "PMC2242835-02-Results-06_T29", "type": "Protein", "text": [ "rpsL" ], "offsets": [ [ 1563, 1567 ] ], "normalized": [] }, { "id": "PMC2242835-02-Results-06_T30", "type": "Organism", "text": [ "SO2" ], "offsets": [ [ 1573, 1576 ] ], "normalized": [] }, { "id": "PMC2242835-02-Results-06_T31", "type": "Protein", "text": [ "ESAT-6" ], "offsets": [ [ 1604, 1610 ] ], "normalized": [] }, { "id": "PMC2242835-02-Results-06_T32", "type": "Protein", "text": [ "phoP" ], "offsets": [ [ 1655, 1659 ] ], "normalized": [] }, { "id": "PMC2242835-02-Results-06_T33", "type": "Protein", "text": [ "ESAT-6" ], "offsets": [ [ 1671, 1677 ] ], "normalized": [] }, { "id": "PMC2242835-02-Results-06_T34", "type": "Protein", "text": [ "ESX-1" ], "offsets": [ [ 1726, 1731 ] ], "normalized": [] }, { "id": "PMC2242835-02-Results-06_T35", "type": "Organism", "text": [ "H37Rv" ], "offsets": [ [ 1742, 1747 ] ], "normalized": [] }, { "id": "PMC2242835-02-Results-06_T36", "type": "Organism", "text": [ "H37Ra" ], "offsets": [ [ 1753, 1758 ] ], "normalized": [] }, { "id": "PMC2242835-02-Results-06_T37", "type": "Organism", "text": [ "H37Ra::RD1-ppe68-ko" ], "offsets": [ [ 1760, 1779 ] ], "normalized": [] }, { "id": "PMC2242835-02-Results-06_T38", "type": "Protein", "text": [ "RD1" ], "offsets": [ [ 1767, 1770 ] ], "normalized": [] }, { "id": "PMC2242835-02-Results-06_T39", "type": "Protein", "text": [ "ppe68" ], "offsets": [ [ 1771, 1776 ] ], "normalized": [] }, { "id": "PMC2242835-02-Results-06_T40", "type": "Protein", "text": [ "ESAT-6" ], "offsets": [ [ 1830, 1836 ] ], "normalized": [] }, { "id": "PMC2242835-02-Results-06_T41", "type": "Protein", "text": [ "PhoP" ], "offsets": [ [ 1896, 1900 ] ], "normalized": [] }, { "id": "PMC2242835-02-Results-06_T42", "type": "Organism", "text": [ "H37Rv-phoP ko" ], "offsets": [ [ 2077, 2090 ] ], "normalized": [] }, { "id": "PMC2242835-02-Results-06_T43", "type": "Protein", "text": [ "phoP" ], "offsets": [ [ 2083, 2087 ] ], "normalized": [] }, { "id": "PMC2242835-02-Results-06_T44", "type": "Organism", "text": [ "H37Ra" ], "offsets": [ [ 2107, 2112 ] ], "normalized": [] }, { "id": "PMC2242835-02-Results-06_T45", "type": "Protein", "text": [ "rv3612c" ], "offsets": [ [ 2164, 2171 ] ], "normalized": [] }, { 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"rv3615c" ], "offsets": [ [ 2356, 2363 ] ], "normalized": [] }, { "id": "PMC2242835-02-Results-06_T54", "type": "Protein", "text": [ "rv3616c" ], "offsets": [ [ 2365, 2372 ] ], "normalized": [] }, { "id": "PMC2242835-02-Results-06_T55", "type": "Protein", "text": [ "espA" ], "offsets": [ [ 2374, 2378 ] ], "normalized": [] }, { "id": "PMC2242835-02-Results-06_T56", "type": "Protein", "text": [ "ESAT-6" ], "offsets": [ [ 2432, 2438 ] ], "normalized": [] }, { "id": "PMC2242835-02-Results-06_T57", "type": "Protein", "text": [ "rv3614c" ], "offsets": [ [ 2486, 2493 ] ], "normalized": [] }, { "id": "PMC2242835-02-Results-06_T58", "type": "Organism", "text": [ "H37Ra" ], "offsets": [ [ 2522, 2527 ] ], "normalized": [] }, { "id": "PMC2242835-02-Results-06_T59", "type": "Organism", "text": [ "H37Rv" ], "offsets": [ [ 2540, 2545 ] ], "normalized": [] }, { "id": "PMC2242835-02-Results-06_T60", "type": "Protein", "text": [ "rv3614c" ], "offsets": [ [ 2591, 2598 ] ], "normalized": [] }, { "id": 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[ { "id": "PMC2266911-02-Results_and_Discussion-02-01-03__text", "type": "abstract", "text": [ "Repeats-in-toxin (RTX) and other toxins \nRTX proteins constitute another family of toxins that may contribute to the insecticidal activity of the two pathogens. A putative RTX-family toxin transporter is common to both pathogens (YE1998-2000, Plu0634/Plu0635). The P. luminescens genome comprises a gene cluster encoding RTX proteins, namely plu1330-1369. Further RTX toxins are encoded by plu3217, plu3324 (both RTX A-family), plu4117 (own family), and plu3668 (RTX cytotoxin), none of which is present in Y. enterocolitica. This pathogen produces only one RTX protein (YE1322) for which a truncated homologue is found in P. luminescens (Plu3209). Other examples of toxins common for both bacterial species compared here are homologues of XaxAB, an apoptotic AB toxin of X. nematophila [68], and proteins encoded by the macrophage toxin (mt)-like genes Plu2288 and Plu0359 with high similarity to YE2685. cnf encoding the cytonecrosis factor-like toxin is present in Y. enterocolitica (YE2091) and P. luminescens ssp. akhurstii strain W14, but not in P. luminescens ssp. laumondii strain TT01 (Fig. 4). P. luminescens produces a series of proteins similar to toxins that have been identified in other bacteria, but are absent in Y. enterocolitica. Examples identified are Txp40, a 40 kD insecticidal toxin [69], the nematicidal toxin (Xnp2) first described in X. bovienii (accession number AJ296651.1), galA (plu0840) similar to the enterotoxin Ast of Aeromonas hydrophila which is involved in carbohydrate transport and metabolism [70], and two dermonecrotizing toxin-(dnt-) like factors (plu2400 and plu2420). In addition, neither the crystal proteins encoded by cipA and cipB in P. luminescens nor a Bt-like toxin (plu1537) could be found in Y. enterocolitica. A cytonecrosis factor (CNF)-like protein, Pnf, was identified in P. luminescens ssp. akhurstii strain W14, but not in P. luminescens ssp. laumondii strain TT01. In P. luminescens, the two paralogs plu4092 and plu4436 encode juvenile hormone esterases (JHE) for which insect toxicity has already been demonstrated [24]. Additionally, neither the locus mcf that confers insecticidal activity of P. luminescens towards M. sexta [71] by inducing apoptosis [72], nor the homologous gene locus mcf2 (plu3128) [73] are present in the genome of Y. enterocolitica. Most of these toxins probably contribute to the higher insect toxicity of P. luminescens against the tobacco hornworm in comparison with Y. enterocolitica. No homologues of the Y. pestis gene coding for enhancin (YPO0339) could be found for which a role in flea colonization was predicted [74]. We also identified several virulence genes and operons that are present in Y. enterocolitica, but not in P. luminescens, suggesting that they have been acquired by horizontal gene transfer from other bacteria and do not play a role in bacteria-insect association. Examples are SopB, a host cell invasion factor translocated via the type-III secretion system that is present in the emerging human pathogen P. asymbiotica, but not in the insect pathogen P. luminescens [14], a putative effector protein (YE2447) with proteolytic activity, and a homologue of SrfA which is negatively regulated by PhoP in S. typhimurium [75]. The SrfA homologue has been demonstrated to be up-regulated by environmental temperature [67]. Other virulence factors absent in P. luminescens are the opg cluster (YE1604-1606) and ProP (YE3594), both involved in osmoprotection [76], cellulose biosynthesis (YE4072-4078) associated with protection from chemical and mechanical stress [60], the methionine-salvage pathway (YE3228-3235) also involved in AHL production [23], the putative ADP-ribosyltransferase toxin encoded by ytxAB (ye2124/ye2123) [77], and the Yersinia heat-stable toxin Yst [78] which is stronger expressed at 28degreesC than at 37degreesC (Table 1). Summarizing, the large variety of diverse toxins present in P. luminescens, but absent in Y. enterocolitica, might contribute to the higher toxicity towards insects of P. luminescens in comparison to Y. enterocolitica. Toxins only present in Y. enterocolitica are assumed to play a major role in its pathogenicity towards mammalians, and some of them might have been acquired by horizontal gene transfer. Examples of those factors are shown in Fig. 5.\n" ], "offsets": [ [ 0, 4312 ] ] } ]

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"1369" ], "offsets": [ [ 350, 354 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-02-01-03_T8", "type": "Protein", "text": [ "plu3217" ], "offsets": [ [ 390, 397 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-02-01-03_T9", "type": "Protein", "text": [ "plu3324" ], "offsets": [ [ 399, 406 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-02-01-03_T10", "type": "Protein", "text": [ "plu4117" ], "offsets": [ [ 428, 435 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-02-01-03_T11", "type": "Protein", "text": [ "plu3668" ], "offsets": [ [ 454, 461 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-02-01-03_T12", "type": "Organism", "text": [ "Y. enterocolitica" ], "offsets": [ [ 507, 524 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-02-01-03_T13", "type": "Protein", "text": [ "YE1322" ], "offsets": [ [ 571, 577 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-02-01-03_T14", "type": "Organism", "text": [ "P. luminescens" ], "offsets": [ [ 623, 637 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-02-01-03_T15", "type": "Protein", "text": [ "Plu3209" ], "offsets": [ [ 639, 646 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-02-01-03_T16", "type": "Protein", "text": [ "XaxA" ], "offsets": [ [ 740, 744 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-02-01-03_T17", "type": "Protein", "text": [ "B" ], "offsets": [ [ 744, 745 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-02-01-03_T18", "type": "Organism", "text": [ "X. nematophila" ], "offsets": [ [ 772, 786 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-02-01-03_T19", "type": "Protein", "text": [ "Plu2288" ], "offsets": [ [ 854, 861 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-02-01-03_T20", "type": "Protein", "text": [ "Plu0359" ], "offsets": [ [ 866, 873 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-02-01-03_T21", "type": "Protein", "text": [ "YE2685" ], "offsets": [ [ 898, 904 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-02-01-03_T22", "type": "Organism", "text": [ "Y. enterocolitica" ], "offsets": [ [ 968, 985 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-02-01-03_T23", "type": "Protein", "text": [ "YE2091" ], "offsets": [ [ 987, 993 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-02-01-03_T24", "type": "Organism", "text": [ "P. luminescens ssp. akhurstii strain W14" ], "offsets": [ [ 999, 1039 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-02-01-03_T25", "type": "Organism", "text": [ "P. luminescens ssp. laumondii strain TT01" ], "offsets": [ [ 1052, 1093 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-02-01-03_T26", "type": "Organism", "text": [ "P. luminescens" ], "offsets": [ [ 1104, 1118 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-02-01-03_T27", "type": "Organism", "text": [ "Y. enterocolitica" ], "offsets": [ [ 1230, 1247 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-02-01-03_T28", "type": "Protein", "text": [ "Txp40" ], "offsets": [ [ 1273, 1278 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-02-01-03_T29", "type": "Protein", "text": [ "Xnp2" ], "offsets": [ [ 1336, 1340 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-02-01-03_T30", "type": "Organism", "text": [ "X. bovienii" ], "offsets": [ [ 1361, 1372 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-02-01-03_T31", "type": "Protein", "text": [ "galA" ], "offsets": [ [ 1404, 1408 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-02-01-03_T32", "type": "Protein", "text": [ "plu0840" ], "offsets": [ [ 1410, 1417 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-02-01-03_T33", "type": "Organism", "text": [ "Aeromonas hydrophila" ], "offsets": [ [ 1453, 1473 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-02-01-03_T34", "type": "Protein", "text": [ "plu2400" ], "offsets": [ [ 1591, 1598 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-02-01-03_T35", "type": "Protein", "text": [ "plu2420" ], "offsets": [ [ 1603, 1610 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-02-01-03_T36", "type": "Protein", "text": [ "cipA" ], "offsets": [ [ 1666, 1670 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-02-01-03_T37", "type": "Protein", "text": [ "cipB" ], "offsets": [ [ 1675, 1679 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-02-01-03_T38", "type": "Organism", "text": [ "P. luminescens" ], "offsets": [ [ 1683, 1697 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-02-01-03_T39", 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[]

[ { "id": "PMC2774163-01-Introduction__text", "type": "abstract", "text": [ "Introduction \nBiofilms are composed of microorganisms attached to a solid surface and encased in a hydrated polymeric matrix of their own synthesis. Biofilms form when bacteria adhere to surfaces in moist environments. Biofilm-associated microorganisms have been shown to colonize a wide variety of medical devices and have been implicated in over 80% of chronic inflammatory and infectious diseases including chronic otitis media, native valve endocarditis, gastrointestinal ulcers, urinary tract and middle ear infections, and chronic lung infections in cystic fibrosis (CF) patients [1],[2]. The human pathogen Pseudomonas aeruginosa is considered one of the primary causes of mortality in patients with CF, the most common life-threatening hereditary disease in Caucasians [3],[4]. In addition, P. aeruginosa causes a variety of diseases in individuals predisposed to infections as the result of severe burns, wounds, urinary tract or corneal injury, or immunocompromised status [5]-[8]. Biofilm cells differ from their planktonic counterparts in the genes and proteins that they express, resulting in distinct phenotypes including altered resistance to antibiotics and the human immune system [2],[9],[10]. Thus, it is not surprising that biofilms are considered to be differentiated communities compared to their planktonic counterparts [9],[11]. This is supported by the finding that various microorganisms, including P. aeruginosa have been shown to form biofilms in a stage-specific and coordinated manner. Biofilm formation is initiated with surface attachment by planktonic bacteria, followed by formation of clusters and microcolonies and subsequent development of differentiated structures in which individual bacteria as well as the entire community are surrounded by exopolysaccharides. The biofilm developmental cycle comes full circle when biofilms disperse [12],[13]. This process has been shown to be governed by the activities of regulatory networks that coordinate the temporal expression of various motility, adhesion, and exopolysaccharide genes in response to inter- and intracellular signaling molecules and environmental cues. Vallet et al. [14] described a transcriptional regulator MvaT in P. aeruginosa that represses the expression of cup genes involved in the chaperone-usher fimbrial assembly pathway. MvaT deletion mutants exhibited enhanced attachment. In contrast, type IV pili and flagella deletion mutants exhibited reduced attachment indicating that attachment and biofilm formation are mediated by extracellular appendages [12], [15]-[17]. Furthermore, the intracellular signaling molecule bis-(3'-5')-cyclic diguanylic guanosine monophosphate (cyclic-di-GMP), first described to control extracellular cellulose biosynthesis in Acetobacter xylinum [18],[19], has been demonstrated in several microorganisms to modulate biofilm formation via the production of exopolysaccharides or matrix components, control auto-aggregation of planktonic cells, and regulate swarming motility [20]-[32]. In P. aeruginosa, at least two pathways have been identified to modulate cyclic-di-GMP and thus, biofilm formation. These are the wsp chemosensory signal transduction pathway [25] and a genetic pathway composed of the phosphodiesterase BifA, the inner membrane-localized diguanylate cyclase SadC and the cytoplasmic protein SadB [20],[21],[33]. Both are involved in the reciprocal cyclic-di-GMP-dependent regulation of Pel and Psl exopolysaccharide production as P. aeruginosa transitions from a planktonic to a surface associated lifestyle. Both Pel and Psl exopolysaccharides contribute to the overall architecture of biofilms and are essential for surface interaction and biofilm initiation [34],[35]. Expression of the pel and psl genes is coordinated by the global regulator RetS, a hybrid sensor kinase-response regulator protein, that plays a key role in the reciprocal regulation of virulence factors and biofilm formation required for acute versus chronic infection [36]. RetS belongs to the family of two-component regulatory systems (TCS) which translate external signals into adaptive responses by a variety of mechanisms, including control of gene expression and methylation of target proteins. RetS is postulated to act in concert with two other TCS sensor kinase-response regulator hybrids, GacS and LadS, to coordinate the expression of determinants involved in biofilm formation and the production of determinants required for cytotoxicity in P. aeruginosa via the small regulatory RNA rsmZ [36],[37]. Inactivation of RetS results in reduced cytotoxicity but increased attachment and biofilm formation, while inactivation of both LadS and GacS results in increased virulence but decreased biofilm formation capacity [36],[37]. This multi-component switch thus orchestrates the transition from the planktonic to the biofilm mode of growth by P. aeruginosa via phosphorylation events of the two-component regulatory system GacA/GacS [36]-[38]. Overall, the findings suggest that the transition to a surface associated lifestyle proceeds via several pathways, probably in response to environmental cues or signals present during attachment, and involves the coordinated transduction of phosphorylation events via two-component regulatory systems (TCS). This raises the question of whether the transition to later stages of biofilm formation, which coincide with distinct phenotypes compared to planktonic and initial attached bacterial cells, also involves sensing of environmental signal(s) and requires the coordinated transduction of phosphorylation events (phosphorelays). Here we demonstrate that P. aeruginosa exhibits distinct protein phosphorylation patterns at various stages of biofilm development. Furthermore, we report the identification of three novel two-component regulatory systems named BfiRS (PA4196-4197), BfmRS (PA4101-4102), and MifRS (PA5511-5512) that coordinate phosphorylation events required for the progression of P. aeruginosa biofilm development in a stage-specific manner. These systems together form a coordinated signaling network that regulates three committed steps of the P. aeruginosa biofilm life cycle, in particular the transition to three later biofilm developmental stages following initial attachment, namely initiation of biofilm formation (BfiRS), biofilm maturation (BfmRS), and microcolony formation (MifRS).\n" ], "offsets": [ [ 0, 6397 ] ] } ]

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"PMC2774163-01-Introduction_T8", "type": "Protein", "text": [ "MvaT" ], "offsets": [ [ 2210, 2214 ] ], "normalized": [] }, { "id": "PMC2774163-01-Introduction_T9", "type": "Organism", "text": [ "P. aeruginosa" ], "offsets": [ [ 2218, 2231 ] ], "normalized": [] }, { "id": "PMC2774163-01-Introduction_T10", "type": "Protein", "text": [ "MvaT" ], "offsets": [ [ 2334, 2338 ] ], "normalized": [] }, { "id": "PMC2774163-01-Introduction_T11", "type": "Organism", "text": [ "type IV pili" ], "offsets": [ [ 2400, 2412 ] ], "normalized": [] }, { "id": "PMC2774163-01-Introduction_T12", "type": "Organism", "text": [ "flagella deletion mutants" ], "offsets": [ [ 2417, 2442 ] ], "normalized": [] }, { "id": "PMC2774163-01-Introduction_T13", "type": "Chemical", "text": [ "bis-(3'-5')-cyclic diguanylic guanosine monophosphate" ], "offsets": [ [ 2629, 2682 ] ], "normalized": [] }, { "id": "PMC2774163-01-Introduction_T14", "type": "Chemical", "text": [ "cyclic-di-GMP" ], "offsets": [ [ 2684, 2697 ] ], "normalized": [] }, { "id": "PMC2774163-01-Introduction_T15", "type": "Organism", "text": [ "Acetobacter xylinum" ], "offsets": [ [ 2767, 2786 ] ], "normalized": [] }, { "id": "PMC2774163-01-Introduction_T16", "type": "Organism", "text": [ "P. aeruginosa" ], "offsets": [ [ 3030, 3043 ] ], "normalized": [] }, { "id": "PMC2774163-01-Introduction_T17", "type": "Chemical", "text": [ "cyclic-di-GMP" ], "offsets": [ [ 3100, 3113 ] ], "normalized": [] }, { "id": "PMC2774163-01-Introduction_T18", "type": "Protein", "text": [ "BifA" ], "offsets": [ [ 3263, 3267 ] ], "normalized": [] }, { "id": "PMC2774163-01-Introduction_T19", "type": "Protein", "text": [ "SadC" ], "offsets": [ [ 3318, 3322 ] ], "normalized": [] }, { "id": "PMC2774163-01-Introduction_T20", "type": "Protein", "text": [ "SadB" ], "offsets": [ [ 3351, 3355 ] ], "normalized": [] }, { "id": "PMC2774163-01-Introduction_T21", "type": "Chemical", "text": [ "cyclic-di-GMP" ], "offsets": [ [ 3408, 3421 ] ], "normalized": [] }, { "id": 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"offsets": [ [ 3807, 3811 ] ], "normalized": [] }, { "id": "PMC2774163-01-Introduction_T30", "type": "Protein", "text": [ "RetS" ], "offsets": [ [ 4008, 4012 ] ], "normalized": [] }, { "id": "PMC2774163-01-Introduction_T31", "type": "Protein", "text": [ "RetS" ], "offsets": [ [ 4235, 4239 ] ], "normalized": [] }, { "id": "PMC2774163-01-Introduction_T32", "type": "Protein", "text": [ "GacS" ], "offsets": [ [ 4333, 4337 ] ], "normalized": [] }, { "id": "PMC2774163-01-Introduction_T33", "type": "Protein", "text": [ "LadS" ], "offsets": [ [ 4342, 4346 ] ], "normalized": [] }, { "id": "PMC2774163-01-Introduction_T34", "type": "Organism", "text": [ "P. aeruginosa" ], "offsets": [ [ 4487, 4500 ] ], "normalized": [] }, { "id": "PMC2774163-01-Introduction_T35", "type": "Protein", "text": [ "rsmZ" ], "offsets": [ [ 4530, 4534 ] ], "normalized": [] }, { "id": "PMC2774163-01-Introduction_T36", "type": "Protein", "text": [ "RetS" ], "offsets": [ [ 4562, 4566 ] ], "normalized": [] }, { "id": "PMC2774163-01-Introduction_T37", "type": "Protein", "text": [ "LadS" ], "offsets": [ [ 4674, 4678 ] ], "normalized": [] }, { "id": "PMC2774163-01-Introduction_T38", "type": "Protein", "text": [ "GacS" ], "offsets": [ [ 4683, 4687 ] ], "normalized": [] }, { "id": "PMC2774163-01-Introduction_T39", "type": "Organism", "text": [ "P. aeruginosa" ], "offsets": [ [ 4885, 4898 ] ], "normalized": [] }, { "id": "PMC2774163-01-Introduction_T40", "type": "Two-component-system", "text": [ "GacA/GacS" ], "offsets": [ [ 4965, 4974 ] ], "normalized": [] }, { "id": "PMC2774163-01-Introduction_T41", "type": "Protein", "text": [ "GacA" ], "offsets": [ [ 4965, 4969 ] ], "normalized": [] }, { "id": "PMC2774163-01-Introduction_T42", "type": "Protein", "text": [ "GacS" ], "offsets": [ [ 4970, 4974 ] ], "normalized": [] }, { "id": "PMC2774163-01-Introduction_T43", "type": "Organism", "text": [ "P. aeruginosa" ], "offsets": [ [ 5643, 5656 ] ], "normalized": [] }, { "id": "PMC2774163-01-Introduction_T44", "type": "Two-component-system", "text": [ "BfiRS" ], "offsets": [ [ 5846, 5851 ] ], "normalized": [] }, { "id": "PMC2774163-01-Introduction_T45", "type": "Protein", "text": [ "BfiR" ], "offsets": [ [ 5846, 5850 ] ], "normalized": [] }, { "id": "PMC2774163-01-Introduction_T46", "type": "Protein", "text": [ "S" ], "offsets": [ [ 5850, 5851 ] ], "normalized": [] }, { "id": "PMC2774163-01-Introduction_T47", "type": "Protein", "text": [ "PA4196" ], "offsets": [ [ 5853, 5859 ] ], "normalized": [] }, { "id": "PMC2774163-01-Introduction_T48", "type": "Protein", "text": [ "4197" ], "offsets": [ [ 5860, 5864 ] ], "normalized": [] }, { "id": "PMC2774163-01-Introduction_T49", "type": "Two-component-system", "text": [ "BfmRS" ], "offsets": [ [ 5867, 5872 ] ], "normalized": [] }, { "id": "PMC2774163-01-Introduction_T50", "type": "Protein", "text": [ "BfmR" ], "offsets": [ [ 5867, 5871 ] ], "normalized": [] }, { "id": "PMC2774163-01-Introduction_T51", "type": "Protein", "text": [ "S" ], "offsets": [ [ 5871, 5872 ] ], "normalized": [] }, { "id": "PMC2774163-01-Introduction_T52", "type": "Protein", "text": [ "PA4101" ], "offsets": [ [ 5874, 5880 ] ], "normalized": [] }, { "id": "PMC2774163-01-Introduction_T53", "type": "Protein", "text": [ "4102" ], "offsets": [ [ 5881, 5885 ] ], "normalized": [] }, { "id": "PMC2774163-01-Introduction_T54", "type": "Two-component-system", "text": [ "MifRS" ], "offsets": [ [ 5892, 5897 ] ], "normalized": [] }, { "id": "PMC2774163-01-Introduction_T55", "type": "Protein", "text": [ "MifR" ], "offsets": [ [ 5892, 5896 ] ], "normalized": [] }, { "id": "PMC2774163-01-Introduction_T56", "type": "Protein", "text": [ "S" ], "offsets": [ [ 5896, 5897 ] ], "normalized": [] }, { "id": "PMC2774163-01-Introduction_T57", "type": "Protein", "text": [ "PA5511" ], "offsets": [ [ 5899, 5905 ] ], "normalized": [] }, { "id": "PMC2774163-01-Introduction_T58", "type": "Protein", "text": [ "5512" ], "offsets": [ [ 5906, 5910 ] ], "normalized": [] }, { "id": "PMC2774163-01-Introduction_T59", "type": "Organism", "text": [ "P. aeruginosa" ], "offsets": [ [ 5983, 5996 ] ], "normalized": [] }, { "id": "PMC2774163-01-Introduction_T60", "type": "Organism", "text": [ "P. aeruginosa" ], "offsets": [ [ 6149, 6162 ] ], "normalized": [] }, { "id": "PMC2774163-01-Introduction_T61", "type": "Two-component-system", "text": [ "BfiRS" ], "offsets": [ [ 6326, 6331 ] ], "normalized": [] }, { "id": "PMC2774163-01-Introduction_T62", "type": "Protein", "text": [ "BfiR" ], "offsets": [ [ 6326, 6330 ] ], "normalized": [] }, { "id": "PMC2774163-01-Introduction_T63", "type": "Protein", "text": [ "S" ], "offsets": [ [ 6330, 6331 ] ], "normalized": [] }, { "id": "PMC2774163-01-Introduction_T64", "type": "Two-component-system", "text": [ "BfmRS" ], "offsets": [ [ 6354, 6359 ] ], "normalized": [] }, { "id": "PMC2774163-01-Introduction_T65", "type": "Protein", "text": [ "BfmR" ], "offsets": [ [ 6354, 6358 ] ], "normalized": [] }, { "id": "PMC2774163-01-Introduction_T66", "type": "Protein", "text": [ "S" ], "offsets": [ [ 6358, 6359 ] ], "normalized": [] }, { "id": "PMC2774163-01-Introduction_T67", "type": "Two-component-system", "text": [ "MifRS" ], "offsets": [ [ 6389, 6394 ] ], "normalized": [] }, { "id": "PMC2774163-01-Introduction_T68", "type": "Protein", "text": [ "MifR" ], "offsets": [ [ 6389, 6393 ] ], "normalized": [] }, { "id": "PMC2774163-01-Introduction_T69", "type": "Protein", "text": [ "S" ], "offsets": [ [ 6393, 6394 ] ], "normalized": [] } ]

[ { "id": "PMC2774163-01-Introduction_E1", "type": "Process", "trigger": { "text": [ "infections" ], "offsets": [ [ 513, 523 ] ] }, "arguments": [] }, { "id": "PMC2774163-01-Introduction_E2", "type": "Process", "trigger": { "text": [ "infections" ], "offsets": [ [ 542, 552 ] ] }, "arguments": [] }, { "id": "PMC2774163-01-Introduction_E3", "type": "Process", "trigger": { "text": [ "infections" ], "offsets": [ [ 872, 882 ] ] }, "arguments": [ { "role": "Participant", "ref_id": "PMC2774163-01-Introduction_T5" } ] }, { "id": "PMC2774163-01-Introduction_E4", "type": "Process", "trigger": { "text": [ "resistance" ], "offsets": [ [ 1144, 1154 ] ] }, "arguments": [] }, { "id": "PMC2774163-01-Introduction_E5", "type": "Regulation", "trigger": { "text": [ "modulate" ], "offsets": [ [ 3091, 3099 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC2774163-01-Introduction_T17" } ] }, { "id": "PMC2774163-01-Introduction_E6", "type": "Positive_regulation", "trigger": { "text": [ "dependent" ], "offsets": [ [ 3422, 3431 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC2774163-01-Introduction_E8" }, { "role": "Cause", "ref_id": "PMC2774163-01-Introduction_T21" } ] }, { "id": "PMC2774163-01-Introduction_E7", "type": "Positive_regulation", "trigger": { "text": [ "dependent" ], "offsets": [ [ 3422, 3431 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC2774163-01-Introduction_E9" }, { "role": "Cause", "ref_id": "PMC2774163-01-Introduction_T21" } ] }, { "id": "PMC2774163-01-Introduction_E8", "type": "Regulation", "trigger": { "text": [ "regulation" ], "offsets": [ [ 3432, 3442 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC2774163-01-Introduction_T22" } ] }, { "id": "PMC2774163-01-Introduction_E9", "type": "Regulation", "trigger": { "text": [ "regulation" ], "offsets": [ [ 3432, 3442 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC2774163-01-Introduction_T23" } ] }, { "id": "PMC2774163-01-Introduction_E10", "type": "Gene_expression", "trigger": { "text": [ "Expression" ], "offsets": [ [ 3732, 3742 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC2774163-01-Introduction_T28" } ] }, { "id": "PMC2774163-01-Introduction_E11", "type": "Gene_expression", "trigger": { "text": [ "Expression" ], "offsets": [ [ 3732, 3742 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC2774163-01-Introduction_T27" } ] }, { "id": "PMC2774163-01-Introduction_E12", "type": "Regulation", "trigger": { "text": [ "coordinated" ], "offsets": [ [ 3771, 3782 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC2774163-01-Introduction_E11" }, { "role": "Cause", "ref_id": "PMC2774163-01-Introduction_T29" } ] }, { "id": "PMC2774163-01-Introduction_E13", "type": "Regulation", "trigger": { "text": [ "coordinated" ], "offsets": [ [ 3771, 3782 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC2774163-01-Introduction_E10" }, { "role": "Cause", "ref_id": "PMC2774163-01-Introduction_T29" } ] }, { "id": "PMC2774163-01-Introduction_E14", "type": "Process", "trigger": { "text": [ "virulence" ], "offsets": [ [ 3918, 3927 ] ] }, "arguments": [] }, { "id": "PMC2774163-01-Introduction_E15", "type": "Process", "trigger": { "text": [ "infection" ], "offsets": [ [ 3992, 4001 ] ] }, "arguments": [] }, { "id": "PMC2774163-01-Introduction_E16", "type": "Negative_regulation", "trigger": { "text": [ "Inactivation" ], "offsets": [ [ 4546, 4558 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC2774163-01-Introduction_T36" } ] }, { "id": "PMC2774163-01-Introduction_E17", "type": "Negative_regulation", "trigger": { "text": [ "inactivation" ], "offsets": [ [ 4653, 4665 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC2774163-01-Introduction_T37" } ] }, { "id": "PMC2774163-01-Introduction_E18", "type": "Negative_regulation", "trigger": { "text": [ "inactivation" ], "offsets": [ [ 4653, 4665 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC2774163-01-Introduction_T38" } ] }, { "id": "PMC2774163-01-Introduction_E19", "type": "Positive_regulation", "trigger": { "text": [ "results" ], "offsets": [ [ 4688, 4695 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC2774163-01-Introduction_E21" }, { "role": "Cause", "ref_id": "PMC2774163-01-Introduction_E17" } ] }, { "id": "PMC2774163-01-Introduction_E20", "type": "Positive_regulation", "trigger": { "text": [ "results" ], "offsets": [ [ 4688, 4695 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC2774163-01-Introduction_E21" }, { "role": "Cause", "ref_id": "PMC2774163-01-Introduction_E18" } ] }, { "id": "PMC2774163-01-Introduction_E21", "type": "Positive_regulation", "trigger": { "text": [ "increased" ], "offsets": [ [ 4699, 4708 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC2774163-01-Introduction_E22" } ] }, { "id": "PMC2774163-01-Introduction_E22", "type": "Process", "trigger": { "text": [ "virulence" ], "offsets": [ [ 4709, 4718 ] ] }, "arguments": [] } ]

[ { "id": "PMC2774163-01-Introduction_1", "entity_ids": [ "PMC2774163-01-Introduction_T13", "PMC2774163-01-Introduction_T14" ] } ]

[]

[ { "id": "PMC2430206-00-TIAB__text", "type": "abstract", "text": [ "The GraRS regulatory system controls Staphylococcus aureus susceptibility to antimicrobial host defenses \nBackground Modification of teichoic acids with D-alanine by the products of the dlt operon protects Gram-positive bacteria against major antimicrobial host defense molecules such as defensins, cathelicidins, myeloperoxidase or phospholipase. The graRS regulatory genes have recently been implicated in the control of D-alanylation in Staphylococcus aureus. Results To determine the impact of the GraRS regulatory system on resistance to antimicrobial host defense mechanisms and virulence of S. aureus, we compared inactivation of S. aureus SA113 wild type and its isogenic graRS deletion mutant by the human cathelicidin LL-37 or human neutrophil granulocytes in vitro, and the ability to cause infection in vivo. We show here that graRS deletion considerably alters bacterial surface charge, increases susceptibility to killing by human neutrophils or the defense peptide LL-37, and attenuates virulence of S. aureus in a mouse infection model. Conclusion Our results indicate that S. aureus can regulate its surface properties in order to overcome innate host defenses.\n" ], "offsets": [ [ 0, 1179 ] ] } ]

[ { "id": "PMC2430206-00-TIAB_T1", "type": "Two-component-system", "text": [ "GraRS" ], "offsets": [ [ 4, 9 ] ], "normalized": [] }, { "id": "PMC2430206-00-TIAB_T2", "type": "Protein", "text": [ "GraR" ], "offsets": [ [ 4, 8 ] ], "normalized": [] }, { "id": "PMC2430206-00-TIAB_T3", "type": "Protein", "text": [ "S" ], "offsets": [ [ 8, 9 ] ], "normalized": [] }, { "id": "PMC2430206-00-TIAB_T4", "type": "Organism", "text": [ "Staphylococcus aureus" ], "offsets": [ [ 37, 58 ] ], "normalized": [] }, { "id": "PMC2430206-00-TIAB_T5", "type": "Regulon-operon", "text": [ "dlt" ], "offsets": [ [ 186, 189 ] ], "normalized": [] }, { "id": "PMC2430206-00-TIAB_T6", "type": "Organism", "text": [ "Gram-positive bacteria" ], "offsets": [ [ 206, 228 ] ], "normalized": [] }, { "id": "PMC2430206-00-TIAB_T7", "type": "Protein", "text": [ "myeloperoxidase" ], "offsets": [ [ 314, 329 ] ], "normalized": [] }, { "id": "PMC2430206-00-TIAB_T8", "type": "Two-component-system", "text": [ "graRS" ], "offsets": [ [ 352, 357 ] ], "normalized": [] }, { "id": "PMC2430206-00-TIAB_T9", "type": "Protein", "text": [ "graR" ], "offsets": [ [ 352, 356 ] ], "normalized": [] }, { "id": "PMC2430206-00-TIAB_T10", "type": "Protein", "text": [ "S" ], "offsets": [ [ 356, 357 ] ], "normalized": [] }, { "id": "PMC2430206-00-TIAB_T11", "type": "Organism", "text": [ "Staphylococcus aureus" ], "offsets": [ [ 440, 461 ] ], "normalized": [] }, { "id": "PMC2430206-00-TIAB_T12", "type": "Two-component-system", "text": [ "GraRS" ], "offsets": [ [ 502, 507 ] ], "normalized": [] }, { "id": "PMC2430206-00-TIAB_T13", "type": "Protein", "text": [ "GraR" ], "offsets": [ [ 502, 506 ] ], "normalized": [] }, { "id": "PMC2430206-00-TIAB_T14", "type": "Protein", "text": [ "S" ], "offsets": [ [ 506, 507 ] ], "normalized": [] }, { "id": "PMC2430206-00-TIAB_T15", "type": "Organism", "text": [ "S. aureus" ], "offsets": [ [ 598, 607 ] ], "normalized": [] }, { "id": "PMC2430206-00-TIAB_T16", "type": "Organism", "text": [ "S. aureus SA113 wild type" ], "offsets": [ [ 637, 662 ] ], "normalized": [] }, { "id": "PMC2430206-00-TIAB_T17", "type": "Organism", "text": [ "graRS deletion mutant" ], "offsets": [ [ 680, 701 ] ], "normalized": [] }, { "id": "PMC2430206-00-TIAB_T18", "type": "Two-component-system", "text": [ "graRS" ], "offsets": [ [ 680, 685 ] ], "normalized": [] }, { "id": "PMC2430206-00-TIAB_T19", "type": "Protein", "text": [ "graR" ], "offsets": [ [ 680, 684 ] ], "normalized": [] }, { "id": "PMC2430206-00-TIAB_T20", "type": "Protein", "text": [ "S" ], "offsets": [ [ 684, 685 ] ], "normalized": [] }, { "id": "PMC2430206-00-TIAB_T21", "type": "Protein", "text": [ "LL-37" ], "offsets": [ [ 728, 733 ] ], "normalized": [] }, { "id": "PMC2430206-00-TIAB_T22", "type": "Two-component-system", "text": [ "graRS" ], "offsets": [ [ 839, 844 ] ], "normalized": [] }, { "id": "PMC2430206-00-TIAB_T23", "type": "Protein", "text": [ "graR" ], "offsets": [ [ 839, 843 ] ], "normalized": [] }, { "id": "PMC2430206-00-TIAB_T24", "type": "Protein", "text": [ "S" ], "offsets": [ [ 843, 844 ] ], "normalized": [] }, { "id": "PMC2430206-00-TIAB_T25", "type": "Organism", "text": [ "human" ], "offsets": [ [ 939, 944 ] ], "normalized": [] }, { "id": "PMC2430206-00-TIAB_T26", "type": "Protein", "text": [ "LL-37" ], "offsets": [ [ 980, 985 ] ], "normalized": [] }, { "id": "PMC2430206-00-TIAB_T27", "type": "Organism", "text": [ "S. aureus" ], "offsets": [ [ 1015, 1024 ] ], "normalized": [] }, { "id": "PMC2430206-00-TIAB_T28", "type": "Organism", "text": [ "mouse" ], "offsets": [ [ 1030, 1035 ] ], "normalized": [] }, { "id": "PMC2430206-00-TIAB_T29", "type": "Organism", "text": [ "S. aureus" ], "offsets": [ [ 1090, 1099 ] ], "normalized": [] } ]

[ { "id": "PMC2430206-00-TIAB_E1", "type": "Process", "trigger": { "text": [ "resistance" ], "offsets": [ [ 529, 539 ] ] }, "arguments": [] }, { "id": "PMC2430206-00-TIAB_E2", "type": "Process", "trigger": { "text": [ "virulence" ], "offsets": [ [ 585, 594 ] ] }, "arguments": [ { "role": "Participant", "ref_id": "PMC2430206-00-TIAB_T15" } ] }, { "id": "PMC2430206-00-TIAB_E3", "type": "Negative_regulation", "trigger": { "text": [ "inactivation" ], "offsets": [ [ 621, 633 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC2430206-00-TIAB_T16" }, { "role": "Cause", "ref_id": "PMC2430206-00-TIAB_T21" } ] }, { "id": "PMC2430206-00-TIAB_E4", "type": "Negative_regulation", "trigger": { "text": [ "inactivation" ], "offsets": [ [ 621, 633 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC2430206-00-TIAB_T17" }, { "role": "Cause", "ref_id": "PMC2430206-00-TIAB_T21" } ] }, { "id": "PMC2430206-00-TIAB_E5", "type": "Negative_regulation", "trigger": { "text": [ "attenuates" ], "offsets": [ [ 991, 1001 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC2430206-00-TIAB_E6" } ] }, { "id": "PMC2430206-00-TIAB_E6", "type": "Process", "trigger": { "text": [ "virulence" ], "offsets": [ [ 1002, 1011 ] ] }, "arguments": [ { "role": "Participant", "ref_id": "PMC2430206-00-TIAB_T22" } ] }, { "id": "PMC2430206-00-TIAB_E7", "type": "Process", "trigger": { "text": [ "infection" ], "offsets": [ [ 1036, 1045 ] ] }, "arguments": [] } ]

[]

[]

[ { "id": "PMC2885601-03-RESULTS-01__text", "type": "abstract", "text": [ "RESULTS \nS. equi Mac Gene S. equi genome encodes a Mac homologue SeMac. The protein shares 62.4% identity in amino acid sequence with Mac made by serotype M1 GAS and a putative secretion signal sequence (amino acids 1-34), and the catalytic residues of GAS Mac consisting of Cys94, His262 and Asp284 are conserved in SeMac (Cys102, His272 and Asp 294) (Fig. 1). To test whether other S. equi strains have the mac gene, 10 S. equi isolates representing various geographic locations were tested with PCR using mac-specific primers. All the strains tested had the mac gene (Fig. 2). DNA sequencing found that the mac gene is 100% conserved in DNA sequence in these strains.\n" ], "offsets": [ [ 0, 671 ] ] } ]

[ { "id": "PMC2885601-03-RESULTS-01_T1", "type": "Organism", "text": [ "S. equi" ], "offsets": [ [ 9, 16 ] ], "normalized": [] }, { "id": "PMC2885601-03-RESULTS-01_T2", "type": "Protein", "text": [ "Mac" ], "offsets": [ [ 17, 20 ] ], "normalized": [] }, { "id": "PMC2885601-03-RESULTS-01_T3", "type": "Organism", "text": [ "S. equi" ], "offsets": [ [ 26, 33 ] ], "normalized": [] }, { "id": "PMC2885601-03-RESULTS-01_T4", "type": "Protein", "text": [ "Mac" ], "offsets": [ [ 51, 54 ] ], "normalized": [] }, { "id": "PMC2885601-03-RESULTS-01_T5", "type": "Protein", "text": [ "SeMac" ], "offsets": [ [ 65, 70 ] ], "normalized": [] }, { "id": "PMC2885601-03-RESULTS-01_T6", "type": "Protein", "text": [ "Mac" ], "offsets": [ [ 134, 137 ] ], "normalized": [] }, { "id": "PMC2885601-03-RESULTS-01_T7", "type": "Organism", "text": [ "serotype M1 GAS" ], "offsets": [ [ 146, 161 ] ], "normalized": [] }, { "id": "PMC2885601-03-RESULTS-01_T8", "type": "Organism", "text": [ "GAS" ], "offsets": [ [ 253, 256 ] ], "normalized": [] }, { "id": "PMC2885601-03-RESULTS-01_T9", "type": "Protein", "text": [ "Mac" ], "offsets": [ [ 257, 260 ] ], "normalized": [] }, { "id": "PMC2885601-03-RESULTS-01_T10", "type": "Protein", "text": [ "SeMac" ], "offsets": [ [ 317, 322 ] ], "normalized": [] }, { "id": "PMC2885601-03-RESULTS-01_T11", "type": "Organism", "text": [ "S. equi" ], "offsets": [ [ 384, 391 ] ], "normalized": [] }, { "id": "PMC2885601-03-RESULTS-01_T12", "type": "Protein", "text": [ "mac" ], "offsets": [ [ 409, 412 ] ], "normalized": [] }, { "id": "PMC2885601-03-RESULTS-01_T13", "type": "Organism", "text": [ "S. equi" ], "offsets": [ [ 422, 429 ] ], "normalized": [] }, { "id": "PMC2885601-03-RESULTS-01_T14", "type": "Protein", "text": [ "mac" ], "offsets": [ [ 508, 511 ] ], "normalized": [] }, { "id": "PMC2885601-03-RESULTS-01_T15", "type": "Protein", "text": [ "mac" ], "offsets": [ [ 561, 564 ] ], "normalized": [] }, { "id": "PMC2885601-03-RESULTS-01_T16", "type": "Protein", "text": [ "mac" ], "offsets": [ [ 610, 613 ] ], "normalized": [] } ]

[]

[]

[]

[ { "id": "PMC2581603-02-Results-07__text", "type": "abstract", "text": [ "DNA induces resistance to CAPs and aminoglycosides \nTo determine if DNA-induced expression of PA3552-PA3559 resulted in increased resistance to antimicrobials, antibiotic susceptibility testing of P. aeruginosa biofilms grown in the presence and absence of extracellular DNA was performed. Biofilms were cultivated on 96-well format, polystyrene pegs submerged in BM2 defined media, with or without sub-inhibitory concentrations of extracellular DNA (0.75% (w/v)), and challenged with antibiotics. After antibiotic challenge, this assay allows for determination of both the minimum inhibitory concentration (MIC) of planktonic cultures and the minimum biofilm eradication concentration (MBEC). Consistent with previous results reporting on the antibiotic resistance phenotype of bacterial biofilms [6],[19], the MBEC values of biofilms cultivated in magnesium-replete conditions and treated with CAPs (polymyxin B, colistin) or aminoglycosides (gentamycin, tobramycin) were up to 64-fold higher than the MIC values of planktonic cultures (Table 1). The MBEC values of biofilms supplemented with extracellular DNA were 8 and 64-fold more CAP and aminoglycoside resistant than biofilms without exogenous DNA, respectively (Table 1). DNA-enriched biofilms were dramatically more resistant than planktonic cultures, up to 256-fold, and this resistance phenotype to CAPs and aminoglycosides was also observed in planktonic cultures supplemented with DNA. The simple addition of sub-inhibitory DNA amounts to planktonic cultures closely simulated the resistance-inducing effects of DNA in a biofilm (Table 1). The MIC values for polymyxin B and gentamicin are equal to 1 microg/ml and 2 microg/ml, respectively, using the standard microbroth dilution method for antimicrobial susceptibility testing (National Committee on Clinical Laboratory Standards (NCCLS) protocol) (data not shown). Thus, depending on the method used to determine the MIC (CBD or NCCLS protocol), DNA-enriched biofilms can be up to 2560-fold more polymyxin B resistant and up to 640-fold more aminoglycoside resistant than planktonic cultures. DNA-enriched biofilms did not show an increased tolerance to ceftazidime (beta-lactam) or ciprofloxacin (fluoroquinolone) (data not shown). Since extracellular DNA is a natural matrix component of PAO1 biofilms (Fig 5A and 5B), DNA-induced antibiotic resistance is likely to be a phenomenon unique to biofilms or other DNA rich environments. The presence of DNA in peg-cultivated biofilms (Fig 5A), grown in the absence of exogenous DNA, likely contributes to the increased antibiotic resistance generally observed in biofilms (Table 1). We have shown previously that the PA3552-PA3559 operon is required for resistance to cationic antimicrobial peptides in planktonic cultures grown in limiting magnesium conditions [47]. To determine if DNA-induced resistance requires these genes in biofilms, the resistance phenotype of the PA3553::lux mutant was determined. PA3553::lux had no significant DNA-induced CAP resistance in biofilm or planktonic cultures, confirming that these genes are essential for CAP resistance in the presence of extracellular DNA (Table 1). The PA3553 mutant also displayed decreased DNA-induced resistance to aminoglycosides compared to PAO1. The differences observed between CAP and aminoglycoside resistance in PA3553::lux suggests that DNA-induced resistance to aminoglycosides is not limited to PA3553 induction. The biofilms formed by the PA3553::lux mutant were unaltered compared to PAO1 biofilms under these conditions, ensuring that the difference observed was not due to an altered biofilm phenotype (Fig 6B). The CAP resistance phenotype of biofilms grown in limiting magnesium (20 microM) was similar to biofilms grown in DNA, confirming that DNA imposes a magnesium limitation stress (Table 2). Biofilms that were exposed to DNA during either the cultivation or challenge stages only, showed similar resistance profiles to biofilms grown and challenged in magnesium-replete conditions (Tables 1-2). Therefore, the DNA-induced resistance of biofilms requires both the cultivation and challenge under cation-limiting conditions. These latter two observations rule out the possibility that negatively charged DNA simply interacts with cationic antimicrobial peptides and prevents their access to bacterial cells.\n" ], "offsets": [ [ 0, 4358 ] ] } ]

[ { "id": "PMC2581603-02-Results-07_T1", "type": "Chemical", "text": [ "CAPs" ], "offsets": [ [ 26, 30 ] ], "normalized": [] }, { "id": "PMC2581603-02-Results-07_T2", "type": "Chemical", "text": [ "aminoglycosides" ], "offsets": [ [ 35, 50 ] ], "normalized": [] }, { "id": "PMC2581603-02-Results-07_T3", "type": "Regulon-operon", "text": [ "PA3552-PA3559" ], "offsets": [ [ 94, 107 ] ], "normalized": [] }, { "id": "PMC2581603-02-Results-07_T4", "type": "Protein", "text": [ "PA3552" ], "offsets": [ [ 94, 100 ] ], "normalized": [] }, { "id": "PMC2581603-02-Results-07_T5", "type": "Protein", "text": [ "PA3559" ], "offsets": [ [ 101, 107 ] ], "normalized": [] }, { "id": "PMC2581603-02-Results-07_T6", "type": "Organism", "text": [ "P. aeruginosa" ], "offsets": [ [ 197, 210 ] ], "normalized": [] }, { "id": "PMC2581603-02-Results-07_T7", "type": "Chemical", "text": [ "magnesium" ], "offsets": [ [ 850, 859 ] ], "normalized": [] }, { "id": "PMC2581603-02-Results-07_T8", "type": "Chemical", "text": [ "CAPs" ], "offsets": [ [ 896, 900 ] ], "normalized": [] }, { "id": "PMC2581603-02-Results-07_T9", "type": "Chemical", "text": [ "polymyxin B" ], "offsets": [ [ 902, 913 ] ], "normalized": [] }, { "id": "PMC2581603-02-Results-07_T10", "type": "Chemical", "text": [ "colistin" ], "offsets": [ [ 915, 923 ] ], "normalized": [] }, { "id": "PMC2581603-02-Results-07_T11", "type": "Chemical", "text": [ "aminoglycosides" ], "offsets": [ [ 928, 943 ] ], "normalized": [] }, { "id": "PMC2581603-02-Results-07_T12", "type": "Chemical", "text": [ "gentamycin" ], "offsets": [ [ 945, 955 ] ], "normalized": [] }, { "id": "PMC2581603-02-Results-07_T13", "type": "Chemical", "text": [ "tobramycin" ], "offsets": [ [ 957, 967 ] ], "normalized": [] }, { "id": "PMC2581603-02-Results-07_T14", "type": "Chemical", "text": [ "CAP" ], "offsets": [ [ 1137, 1140 ] ], "normalized": [] }, { "id": "PMC2581603-02-Results-07_T15", "type": "Chemical", "text": [ "aminoglycoside" ], "offsets": [ [ 1145, 1159 ] ], "normalized": [] }, { "id": "PMC2581603-02-Results-07_T16", "type": "Chemical", "text": [ "CAPs" ], "offsets": [ [ 1361, 1365 ] ], "normalized": [] }, { "id": "PMC2581603-02-Results-07_T17", "type": "Chemical", "text": [ "aminoglycosides" ], "offsets": [ [ 1370, 1385 ] ], "normalized": [] }, { "id": "PMC2581603-02-Results-07_T18", "type": "Chemical", "text": [ "polymyxin B" ], "offsets": [ [ 1623, 1634 ] ], "normalized": [] }, { "id": "PMC2581603-02-Results-07_T19", "type": "Chemical", "text": [ "gentamicin" ], "offsets": [ [ 1639, 1649 ] ], "normalized": [] }, { "id": "PMC2581603-02-Results-07_T20", "type": "Chemical", "text": [ "polymyxin B" ], "offsets": [ [ 2013, 2024 ] ], "normalized": [] }, { "id": "PMC2581603-02-Results-07_T21", "type": "Chemical", "text": [ "aminoglycoside" ], "offsets": [ [ 2059, 2073 ] ], "normalized": [] }, { "id": "PMC2581603-02-Results-07_T22", "type": "Chemical", "text": [ "ceftazidime" ], "offsets": [ [ 2171, 2182 ] ], "normalized": [] }, { "id": "PMC2581603-02-Results-07_T23", "type": "Chemical", "text": [ "beta-lactam" ], "offsets": [ [ 2184, 2195 ] ], "normalized": [] }, { "id": "PMC2581603-02-Results-07_T24", "type": "Chemical", "text": [ "ciprofloxacin" ], "offsets": [ [ 2200, 2213 ] ], "normalized": [] }, { "id": "PMC2581603-02-Results-07_T25", "type": "Chemical", "text": [ "fluoroquinolone" ], "offsets": [ [ 2215, 2230 ] ], "normalized": [] }, { "id": "PMC2581603-02-Results-07_T26", "type": "Organism", "text": [ "PAO1" ], "offsets": [ [ 2307, 2311 ] ], "normalized": [] }, { "id": "PMC2581603-02-Results-07_T27", "type": "Regulon-operon", "text": [ "PA3552-PA3559" ], "offsets": [ [ 2682, 2695 ] ], "normalized": [] }, { "id": "PMC2581603-02-Results-07_T28", "type": "Protein", "text": [ "PA3552" ], "offsets": [ [ 2682, 2688 ] ], "normalized": [] }, { "id": "PMC2581603-02-Results-07_T29", "type": "Protein", "text": [ "PA3559" ], "offsets": [ [ 2689, 2695 ] ], "normalized": [] }, { "id": "PMC2581603-02-Results-07_T30", "type": "Chemical", "text": [ "magnesium" ], "offsets": [ [ 2806, 2815 ] ], "normalized": [] }, { "id": "PMC2581603-02-Results-07_T31", "type": "Organism", "text": [ "PA3553::lux mutant" ], "offsets": [ [ 2938, 2956 ] ], "normalized": [] }, { "id": "PMC2581603-02-Results-07_T32", "type": "Protein", "text": [ "PA3553" ], "offsets": [ [ 2938, 2944 ] ], "normalized": [] }, { "id": "PMC2581603-02-Results-07_T33", "type": "Protein", "text": [ "lux" ], "offsets": [ [ 2946, 2949 ] ], "normalized": [] }, { "id": "PMC2581603-02-Results-07_T34", "type": "Organism", "text": [ "PA3553::lux" ], "offsets": [ [ 2973, 2984 ] ], "normalized": [] }, { "id": "PMC2581603-02-Results-07_T35", "type": "Protein", "text": [ "PA3553" ], "offsets": [ [ 2973, 2979 ] ], "normalized": [] }, { "id": "PMC2581603-02-Results-07_T36", "type": "Protein", "text": [ "lux" ], "offsets": [ [ 2981, 2984 ] ], "normalized": [] }, { "id": "PMC2581603-02-Results-07_T37", "type": "Chemical", "text": [ "CAP" ], "offsets": [ [ 3016, 3019 ] ], "normalized": [] }, { "id": "PMC2581603-02-Results-07_T38", "type": "Chemical", "text": [ "CAP" ], "offsets": [ [ 3112, 3115 ] ], "normalized": [] }, { "id": "PMC2581603-02-Results-07_T39", "type": "Organism", "text": [ "PA3553 mutant" ], "offsets": [ [ 3179, 3192 ] ], "normalized": [] }, { "id": "PMC2581603-02-Results-07_T40", "type": "Protein", "text": [ "PA3553" ], "offsets": [ [ 3179, 3185 ] ], "normalized": [] }, { "id": "PMC2581603-02-Results-07_T41", "type": "Chemical", "text": [ "aminoglycosides" ], "offsets": [ [ 3244, 3259 ] ], "normalized": [] }, { "id": "PMC2581603-02-Results-07_T42", "type": "Organism", "text": [ "PAO1" ], "offsets": [ [ 3272, 3276 ] ], "normalized": [] }, { "id": "PMC2581603-02-Results-07_T43", "type": "Chemical", "text": [ "CAP" ], "offsets": [ [ 3311, 3314 ] ], "normalized": [] }, { "id": "PMC2581603-02-Results-07_T44", "type": "Chemical", "text": [ "aminoglycoside" ], "offsets": [ [ 3319, 3333 ] ], "normalized": [] }, { "id": "PMC2581603-02-Results-07_T45", "type": "Organism", "text": [ "PA3553::lux" ], "offsets": [ [ 3348, 3359 ] ], "normalized": [] }, { "id": "PMC2581603-02-Results-07_T46", "type": "Protein", "text": [ "PA3553" ], "offsets": [ [ 3348, 3354 ] ], "normalized": [] }, { "id": "PMC2581603-02-Results-07_T47", "type": "Protein", "text": [ "lux" ], "offsets": [ [ 3356, 3359 ] ], "normalized": [] }, { "id": "PMC2581603-02-Results-07_T48", "type": "Chemical", "text": [ "aminoglycosides" ], "offsets": [ [ 3400, 3415 ] ], "normalized": [] }, { "id": "PMC2581603-02-Results-07_T49", "type": "Protein", "text": [ "PA3553" ], "offsets": [ [ 3434, 3440 ] ], "normalized": [] }, { "id": "PMC2581603-02-Results-07_T50", "type": "Organism", "text": [ "PA3553::lux mutant" ], "offsets": [ [ 3479, 3497 ] ], "normalized": [] }, { "id": "PMC2581603-02-Results-07_T51", "type": "Protein", "text": [ "PA3553" ], "offsets": [ [ 3479, 3485 ] ], "normalized": [] }, { "id": "PMC2581603-02-Results-07_T52", "type": "Protein", "text": [ "lux" ], "offsets": [ [ 3487, 3490 ] ], "normalized": [] }, { "id": "PMC2581603-02-Results-07_T53", "type": "Organism", "text": [ "PAO1" ], "offsets": [ [ 3525, 3529 ] ], "normalized": [] }, { "id": "PMC2581603-02-Results-07_T54", "type": "Chemical", "text": [ "CAP" ], "offsets": [ [ 3659, 3662 ] ], "normalized": [] }, { "id": "PMC2581603-02-Results-07_T55", "type": "Chemical", "text": [ "magnesium" ], "offsets": [ [ 3714, 3723 ] ], "normalized": [] }, { "id": "PMC2581603-02-Results-07_T56", "type": "Chemical", "text": [ "magnesium" ], "offsets": [ [ 3804, 3813 ] ], "normalized": [] }, { "id": "PMC2581603-02-Results-07_T57", "type": "Chemical", "text": [ "magnesium" ], "offsets": [ [ 4004, 4013 ] ], "normalized": [] } ]

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[]

[]

[ { "id": "PMC2266911-02-Results_and_Discussion-01-02-03__text", "type": "abstract", "text": [ "Regulation by PAS_4/LuxR-like receptors \nIn P. luminescens, the amount of luxR-like genes is overrepresented with 39 copies in the genome. 35 of these potential LuxR-like receptors exhibit PAS_4 signal binding domains instead of an AHL-binding domain, and two have a signalling domain with a yet unidentified motif (Fig. 3). Most of the genes are located in two large gene clusters (plu0918-0925 and plu2001-2019). Interestingly, eleven of those LuxR-like receptors are present in Y. enterocolitica of which five are located in a cluster (ye0035-0039). Nine of these have a so-called PAS_4 signal binding domains of yet unknown function. It is interesting to note that there is only one bacterium else, the insect colonizing S. glossinidius, whose genome also carries a series of unclustered genes coding for PAS_4/LuxR-like receptors, indicating that this kind of receptors plays a role during insect infection. PAS-domains have been suspected to act as insect juvenile hormone (JH) receptors in the fruit fly Drosophila melanogaster [43,44]. The methoprene-tolerant gene (met, also called Resistance to Juvenile Hormone Rst1JH) of D. melanogaster encodes a helix-loop-helix transcriptional regulator combined with a PAS_3 domain [45]. Met has been shown to bind JH at physiological concentrations and is therefore suspected to act as a JH receptor [46,47]. Therefore, the potential PAS_4/LuxR-like receptors of P. luminescens, Y. enterocolitica, and S. glossinidius might sense JH or other eukaryotic hormones of the insect to adapt their gene expression to the insect host. The high number of 35 highly homologous receptor proteins in P. luminescens might be the reason for the wide insect host spectrum this pathogen is capable to infect. Although Y. enterocolitica protein extracts confer toxicity against M. sexta larvae [7], its host spectrum still remains to be defined. The difference in the number of the uncommon LuxR-like receptors (35 in P. luminescens, nine in Y. enterocolitica) gives rise to speculations that the insect host spectrum is constricted for Y. enterocolitica compared with P. luminescens. This hypothesis is underlined by the fact that not more than five PAS_4/LuxR-like receptors are present in S. glossinidius for which only one insect host has been reported.\n" ], "offsets": [ [ 0, 2291 ] ] } ]

[ { "id": "PMC2266911-02-Results_and_Discussion-01-02-03_T1", "type": "Protein", "text": [ "PAS_4" ], "offsets": [ [ 14, 19 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-01-02-03_T2", "type": "Protein", "text": [ "LuxR" ], "offsets": [ [ 20, 24 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-01-02-03_T3", "type": "Organism", "text": [ "P. luminescens" ], "offsets": [ [ 44, 58 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-01-02-03_T4", "type": "Protein", "text": [ "luxR" ], "offsets": [ [ 74, 78 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-01-02-03_T5", "type": "Protein", "text": [ "LuxR" ], "offsets": [ [ 161, 165 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-01-02-03_T6", "type": "Protein", "text": [ "PAS_4" ], "offsets": [ [ 189, 194 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-01-02-03_T7", "type": "Chemical", "text": [ "AHL" ], "offsets": [ [ 232, 235 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-01-02-03_T8", "type": "Protein", "text": [ "plu0918" ], "offsets": [ [ 383, 390 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-01-02-03_T9", "type": "Protein", "text": [ "0925" ], "offsets": [ [ 391, 395 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-01-02-03_T10", "type": "Protein", "text": [ "plu2001" ], "offsets": [ [ 400, 407 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-01-02-03_T11", "type": "Protein", "text": [ "2019" ], "offsets": [ [ 408, 412 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-01-02-03_T12", "type": "Protein", "text": [ "LuxR" ], "offsets": [ [ 446, 450 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-01-02-03_T13", "type": "Organism", "text": [ "Y. enterocolitica" ], "offsets": [ [ 481, 498 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-01-02-03_T14", "type": "Protein", "text": [ "ye0035" ], "offsets": [ [ 539, 545 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-01-02-03_T15", "type": "Protein", "text": [ "0039" ], "offsets": [ [ 546, 550 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-01-02-03_T16", "type": "Protein", "text": [ "PAS_4" ], "offsets": [ [ 584, 589 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-01-02-03_T17", "type": "Organism", "text": [ "S. glossinidius" ], "offsets": [ [ 725, 740 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-01-02-03_T18", "type": "Protein", "text": [ "PAS_4" ], "offsets": [ [ 809, 814 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-01-02-03_T19", "type": "Protein", "text": [ "LuxR" ], "offsets": [ [ 815, 819 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-01-02-03_T20", "type": "Organism", "text": [ "fruit fly Drosophila melanogaster" ], "offsets": [ [ 1001, 1034 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-01-02-03_T21", "type": "Chemical", "text": [ "methoprene" ], "offsets": [ [ 1048, 1058 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-01-02-03_T22", "type": "Protein", "text": [ "met" ], "offsets": [ [ 1074, 1077 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-01-02-03_T23", "type": "Protein", "text": [ "Rst1JH" ], "offsets": [ [ 1122, 1128 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-01-02-03_T24", "type": "Organism", "text": [ "D. melanogaster" ], "offsets": [ [ 1133, 1148 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-01-02-03_T25", "type": "Protein", "text": [ "PAS_3" ], "offsets": [ [ 1218, 1223 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-01-02-03_T26", "type": "Protein", "text": [ "Met" ], "offsets": [ [ 1237, 1240 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-01-02-03_T27", "type": "Protein", "text": [ "PAS_4" ], "offsets": [ [ 1384, 1389 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-01-02-03_T28", "type": "Protein", "text": [ "LuxR" ], "offsets": [ [ 1390, 1394 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-01-02-03_T29", "type": "Organism", "text": [ "P. luminescens" ], "offsets": [ [ 1413, 1427 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-01-02-03_T30", "type": "Organism", "text": [ "Y. enterocolitica" ], "offsets": [ [ 1429, 1446 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-01-02-03_T31", "type": "Organism", "text": [ "S. glossinidius" ], "offsets": [ [ 1452, 1467 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-01-02-03_T32", "type": "Organism", "text": [ "P. luminescens" ], "offsets": [ [ 1638, 1652 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-01-02-03_T33", "type": "Organism", "text": [ "Y. enterocolitica" ], "offsets": [ [ 1752, 1769 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-01-02-03_T34", "type": "Organism", "text": [ "M. sexta" ], "offsets": [ [ 1811, 1819 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-01-02-03_T35", "type": "Protein", "text": [ "LuxR" ], "offsets": [ [ 1924, 1928 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-01-02-03_T36", "type": "Organism", "text": [ "P. luminescens" ], "offsets": [ [ 1951, 1965 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-01-02-03_T37", "type": "Organism", "text": [ "Y. enterocolitica" ], "offsets": [ [ 1975, 1992 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-01-02-03_T38", "type": "Organism", "text": [ "Y. enterocolitica" ], "offsets": [ [ 2070, 2087 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-01-02-03_T39", "type": "Organism", "text": [ "P. luminescens" ], "offsets": [ [ 2102, 2116 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-01-02-03_T40", "type": "Protein", "text": [ "PAS_4" ], "offsets": [ [ 2184, 2189 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-01-02-03_T41", "type": "Protein", "text": [ "LuxR" ], "offsets": [ [ 2190, 2194 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-01-02-03_T42", "type": "Organism", "text": [ "S. glossinidius" ], "offsets": [ [ 2225, 2240 ] ], "normalized": [] } ]

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[]

[ { "id": "PMC2885601-01-INTRODUCTION__text", "type": "abstract", "text": [ "INTRODUCTION \nGram-positive bacterium Streptococcus equi subspeices equi (S. equi) causes equine strangles, a highly contagious purulent lymphadenitis and one of the most common infectious diseases in horses [1,2]. The infection initially causes nasal discharge and fever and, then, leads to abscess formation in local lymph nodes, causing enormous pain and respiratory difficulty. There is massive infiltration of polymorphonuclear leukocytes (PMNs) to the infection site. However, S. equi effectively evades the horse innate immunity by being resistant to phagocytosis by PMNs. Horses recovered from strangles acquire immunity against S. equi reinfection [3]. The immunity is primarily mediated by protective antibodies [4], which opsonize and thus enhance phagocytosis of S. equi by horse PMNs. To survive in hosts, bacterial pathogens have evolved multiple mechanisms to evade host defense. For examples, both S. equi and group A Streptococcus (GAS) produce the hyaluronic acid capsule and surface protein M protein to contribute to resistance to phagocytosis by PMNs. We found that GAS produces a secreted Mac protein (also known as IdeE), which inhibits opsonophagocytosis of GAS by human PMNs [5]. This protein can cleave the heavy chain of human immunoglobulin G (IgG) using Cys94, His262 and Asp284 as its catalytic triad [6-8]. There are two kinds of Mac produced by GAS isolates [7], which use different mechanisms to block the interaction between IgG and Fc receptor on the surface of PMNs. The type-1 Mac, such as M1 Mac produced by serotype M1 GAS strains, has high enzymatic activity and low affinity to Fc receptor on the surface of PMNs, while the type-2 Mac can bind to the Fc receptor and has lower enzymatic activity [9]. S. equi has a homologue of GAS M1 Mac (designated SeMac). In this study, SeMac was prepared and characterized. The results indicate that SeMac is a cysteine endopeptidase but does not inhibit opsonophagocytosis of S. equi by horse PMNs, suggesting that SeMac has function other than evading horse acquired immunity against S. equi infection.\n" ], "offsets": [ [ 0, 2084 ] ] } ]

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"Organism", "text": [ "S. equi" ], "offsets": [ [ 637, 644 ] ], "normalized": [] }, { "id": "PMC2885601-01-INTRODUCTION_T9", "type": "Organism", "text": [ "S. equi" ], "offsets": [ [ 775, 782 ] ], "normalized": [] }, { "id": "PMC2885601-01-INTRODUCTION_T10", "type": "Organism", "text": [ "horse" ], "offsets": [ [ 786, 791 ] ], "normalized": [] }, { "id": "PMC2885601-01-INTRODUCTION_T11", "type": "Organism", "text": [ "S. equi" ], "offsets": [ [ 914, 921 ] ], "normalized": [] }, { "id": "PMC2885601-01-INTRODUCTION_T12", "type": "Organism", "text": [ "group A Streptococcus" ], "offsets": [ [ 926, 947 ] ], "normalized": [] }, { "id": "PMC2885601-01-INTRODUCTION_T13", "type": "Organism", "text": [ "GAS" ], "offsets": [ [ 949, 952 ] ], "normalized": [] }, { "id": "PMC2885601-01-INTRODUCTION_T14", "type": "Chemical", "text": [ "hyaluronic acid" ], "offsets": [ [ 966, 981 ] ], "normalized": [] }, { "id": "PMC2885601-01-INTRODUCTION_T15", "type": "Protein", "text": [ "M protein" ], "offsets": [ [ 1010, 1019 ] ], "normalized": [] }, { "id": "PMC2885601-01-INTRODUCTION_T16", "type": "Organism", "text": [ "GAS" ], "offsets": [ [ 1087, 1090 ] ], "normalized": [] }, { "id": "PMC2885601-01-INTRODUCTION_T17", "type": "Protein", "text": [ "Mac" ], "offsets": [ [ 1111, 1114 ] ], "normalized": [] }, { "id": "PMC2885601-01-INTRODUCTION_T18", "type": "Protein", "text": [ "IdeE" ], "offsets": [ [ 1138, 1142 ] ], "normalized": [] }, { "id": "PMC2885601-01-INTRODUCTION_T19", "type": "Organism", "text": [ "GAS" ], "offsets": [ [ 1182, 1185 ] ], "normalized": [] }, { "id": "PMC2885601-01-INTRODUCTION_T20", "type": "Organism", "text": [ "human" ], "offsets": [ [ 1189, 1194 ] ], "normalized": [] }, { "id": "PMC2885601-01-INTRODUCTION_T21", "type": "Organism", "text": [ "human" ], "offsets": [ [ 1248, 1253 ] ], "normalized": [] }, { "id": "PMC2885601-01-INTRODUCTION_T22", "type": "Protein", "text": [ "immunoglobulin G" ], "offsets": [ [ 1254, 1270 ] ], "normalized": [] }, { "id": "PMC2885601-01-INTRODUCTION_T23", "type": "Protein", "text": [ "IgG" ], "offsets": [ [ 1272, 1275 ] ], "normalized": [] }, { "id": "PMC2885601-01-INTRODUCTION_T24", "type": "Protein", "text": [ "Mac" ], "offsets": [ [ 1361, 1364 ] ], "normalized": [] }, { "id": "PMC2885601-01-INTRODUCTION_T25", "type": "Organism", "text": [ "GAS" ], "offsets": [ [ 1377, 1380 ] ], "normalized": [] }, { "id": "PMC2885601-01-INTRODUCTION_T26", "type": "Protein", "text": [ "IgG" ], "offsets": [ [ 1459, 1462 ] ], "normalized": [] }, { "id": "PMC2885601-01-INTRODUCTION_T27", "type": "Protein", "text": [ "Fc receptor" ], "offsets": [ [ 1467, 1478 ] ], "normalized": [] }, { "id": "PMC2885601-01-INTRODUCTION_T28", "type": "Protein", "text": [ "Mac" ], "offsets": [ [ 1514, 1517 ] ], "normalized": [] }, { "id": "PMC2885601-01-INTRODUCTION_T29", "type": "Protein", "text": [ "Mac" ], "offsets": [ [ 1530, 1533 ] ], "normalized": [] }, { "id": "PMC2885601-01-INTRODUCTION_T30", "type": "Organism", "text": [ "serotype M1 GAS" ], "offsets": [ [ 1546, 1561 ] ], "normalized": [] }, { "id": "PMC2885601-01-INTRODUCTION_T31", "type": "Protein", "text": [ "Fc receptor" ], "offsets": [ [ 1619, 1630 ] ], "normalized": [] }, { "id": "PMC2885601-01-INTRODUCTION_T32", "type": "Protein", "text": [ "Mac" ], "offsets": [ [ 1672, 1675 ] ], "normalized": [] }, { "id": "PMC2885601-01-INTRODUCTION_T33", "type": "Protein", "text": [ "Fc receptor" ], "offsets": [ [ 1692, 1703 ] ], "normalized": [] }, { "id": "PMC2885601-01-INTRODUCTION_T34", "type": "Organism", "text": [ "S. equi" ], "offsets": [ [ 1742, 1749 ] ], "normalized": [] }, { "id": "PMC2885601-01-INTRODUCTION_T35", "type": "Organism", "text": [ "GAS" ], "offsets": [ [ 1769, 1772 ] ], "normalized": [] }, { "id": "PMC2885601-01-INTRODUCTION_T36", "type": "Protein", "text": [ "Mac" ], "offsets": [ [ 1776, 1779 ] ], "normalized": [] }, { "id": "PMC2885601-01-INTRODUCTION_T37", "type": "Protein", "text": [ "SeMac" ], "offsets": [ [ 1792, 1797 ] ], "normalized": [] }, { "id": "PMC2885601-01-INTRODUCTION_T38", "type": "Protein", "text": [ "SeMac" ], "offsets": [ [ 1815, 1820 ] ], "normalized": [] }, { "id": "PMC2885601-01-INTRODUCTION_T39", "type": "Protein", "text": [ "SeMac" ], "offsets": [ [ 1879, 1884 ] ], "normalized": [] }, { "id": "PMC2885601-01-INTRODUCTION_T40", "type": "Protein", "text": [ "cysteine endopeptidase" ], "offsets": [ [ 1890, 1912 ] ], "normalized": [] }, { "id": "PMC2885601-01-INTRODUCTION_T41", "type": "Organism", "text": [ "S. equi" ], "offsets": [ [ 1956, 1963 ] ], "normalized": [] }, { "id": "PMC2885601-01-INTRODUCTION_T42", "type": "Organism", "text": [ "horse" ], "offsets": [ [ 1967, 1972 ] ], "normalized": [] }, { "id": "PMC2885601-01-INTRODUCTION_T43", "type": "Protein", "text": [ "SeMac" ], "offsets": [ [ 1995, 2000 ] ], "normalized": [] }, { "id": "PMC2885601-01-INTRODUCTION_T44", "type": "Organism", "text": [ "horse" ], "offsets": [ [ 2033, 2038 ] ], "normalized": [] }, { "id": "PMC2885601-01-INTRODUCTION_T45", "type": "Organism", "text": [ "S. equi" ], "offsets": [ [ 2065, 2072 ] ], "normalized": [] } ]

[ { "id": "PMC2885601-01-INTRODUCTION_E1", "type": "Process", "trigger": { "text": [ "infection" ], "offsets": [ [ 219, 228 ] ] }, "arguments": [] }, { "id": "PMC2885601-01-INTRODUCTION_E2", "type": "Process", "trigger": { "text": [ "infection" ], "offsets": [ [ 458, 467 ] ] }, "arguments": [] }, { "id": "PMC2885601-01-INTRODUCTION_E3", "type": "Process", "trigger": { "text": [ "resistant" ], "offsets": [ [ 545, 554 ] ] }, "arguments": [] }, { "id": "PMC2885601-01-INTRODUCTION_E4", "type": "Process", "trigger": { "text": [ "reinfection" ], "offsets": [ [ 645, 656 ] ] }, "arguments": [ { "role": "Participant", "ref_id": "PMC2885601-01-INTRODUCTION_T8" } ] }, { "id": "PMC2885601-01-INTRODUCTION_E5", "type": "Gene_expression", "trigger": { "text": [ "produce" ], "offsets": [ [ 954, 961 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC2885601-01-INTRODUCTION_T15" } ] }, { "id": "PMC2885601-01-INTRODUCTION_E6", "type": "Process", "trigger": { "text": [ "resistance" ], "offsets": [ [ 1037, 1047 ] ] }, "arguments": [] }, { "id": "PMC2885601-01-INTRODUCTION_E7", "type": "Gene_expression", "trigger": { "text": [ "produces" ], "offsets": [ [ 1091, 1099 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC2885601-01-INTRODUCTION_T17" } ] }, { "id": "PMC2885601-01-INTRODUCTION_E8", "type": "Localization", "trigger": { "text": [ "secreted" ], "offsets": [ [ 1102, 1110 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC2885601-01-INTRODUCTION_T17" } ] }, { "id": "PMC2885601-01-INTRODUCTION_E9", "type": "Positive_regulation", "trigger": { "text": [ "cleave" ], "offsets": [ [ 1222, 1228 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC2885601-01-INTRODUCTION_E10" }, { "role": "Cause", "ref_id": "PMC2885601-01-INTRODUCTION_T17" } ] }, { "id": "PMC2885601-01-INTRODUCTION_E10", "type": "Protein_catabolism", "trigger": { "text": [ "cleave" ], "offsets": [ [ 1222, 1228 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC2885601-01-INTRODUCTION_T22" } ] }, { "id": "PMC2885601-01-INTRODUCTION_E11", "type": "Gene_expression", "trigger": { "text": [ "produced" ], "offsets": [ [ 1365, 1373 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC2885601-01-INTRODUCTION_T24" } ] }, { "id": "PMC2885601-01-INTRODUCTION_E12", "type": "Negative_regulation", "trigger": { "text": [ "block" ], "offsets": [ [ 1429, 1434 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC2885601-01-INTRODUCTION_E13" } ] }, { "id": "PMC2885601-01-INTRODUCTION_E13", "type": "Binding", "trigger": { "text": [ "interaction" ], "offsets": [ [ 1439, 1450 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC2885601-01-INTRODUCTION_T26" }, { "role": "Theme", "ref_id": "PMC2885601-01-INTRODUCTION_T27" } ] }, { "id": "PMC2885601-01-INTRODUCTION_E14", "type": "Gene_expression", "trigger": { "text": [ "produced" ], "offsets": [ [ 1534, 1542 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC2885601-01-INTRODUCTION_T29" } ] }, { "id": "PMC2885601-01-INTRODUCTION_E15", "type": "Binding", "trigger": { "text": [ "bind" ], "offsets": [ [ 1680, 1684 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC2885601-01-INTRODUCTION_T32" }, { "role": "Theme", "ref_id": "PMC2885601-01-INTRODUCTION_T33" } ] }, { "id": "PMC2885601-01-INTRODUCTION_E16", "type": "Process", "trigger": { "text": [ "infection" ], "offsets": [ [ 2073, 2082 ] ] }, "arguments": [ { "role": "Participant", "ref_id": "PMC2885601-01-INTRODUCTION_T45" } ] } ]

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[]

[ { "id": "PMC2242835-03-Discussion__text", "type": "abstract", "text": [ "Discussion \nThe attenuated H37Ra strain was obtained at the Trudeau Institute in the 1930s in an attempt to dissociate virulent and avirulent forms of the tubercle bacillus H37. Steenken et al. have shown that the virulence of the H37 strain was associated with colony morphology and that the avirulent variant H37Ra failed to propagate in an ordinarily susceptible host while the virulent variant H37Rv was able to proliferate [6]. Although these different H37 daughter strains have been available for many years now and belong to the standard strain collections of almost every tuberculosis diagnostic or research laboratory in the world [30,31], the genetic basis of the decreased virulence of H37Ra remained unknown. The identification of the amino acid change S219L in the predicted DNA binding region of the C-terminal effector domain of PhoP [15,22] in H37Ra was therefore a particularly exciting finding that has the potential to explain part of the attenuation of the H37Ra strain and to elucidate the PhoP/PhoR associated complex regulatory network in M. tuberculosis. In the bacterial world the PhoP/PhoR like two-component systems are widely distributed and fulfill a large variety of functions including sensing phosphate and magnesium [32,33], or regulating virulence genes [34]. For M. tuberculosis, several studies have described a link between the inactivation of phoP and loss of virulence, suggesting that the phoP gene is required for intracellular growth of M. tuberculosis [14,25]. It was also found that the PhoP-PhoR system controls the biosynthesis of polyketide-derived lipids [35] and determines the amount of triacylated and monoacylated lipoarabinomannans in M. tuberculosis [36]. However, according to very recent information, these polyketide-derived (Pks2-4) lipids do not have a strong impact on the virulence of M. tuberculosis [29]. Finally, microarray-based trancriptome analysis using the wild-type versus a phoP ko mutant of H37Rv has provided an overview of the transcriptional regulation linked to PhoP [21]. That study identified 44 genes in the phoP-ko strain that were expressed at least 2.5-fold lower in the mutant than their counterparts in the M. tuberculosis wild-type strain. Most interestingly, about two thirds of these 44 genes were also found substantially lower expressed in H37Ra in comparison to H37Rv, when the transcriptional profiles of H37Ra and H37Rv cultures grown in various media were examined [12]. This finding argues that the PhoP S219L mutation likely has a broad impact on gene regulation in H37Ra with effects similar to those seen for complete inactivation of phoP. Among the genes expressed at low level in the phoP-ko strain and in H37Ra were several that are involved in lipid metabolism; for example, the polyketide synthases pks2 (rv3825c) or the Pks-associated protein papA1 (rv3824c). There were also several ppe genes that seem to be regulated by phoP but not ppe68 [21]. In addition, NirA (Rv2391), a putative nitrite reductase and MmpL10-FadD21 (Rv1183-85c), which were all identified by TraSH analysis as potentially implicated in virulence [16], seem to be regulated by PhoP [12,21]. However, the most striking link in relation to our results on phoP and ESAT-6 secretion that was revealed by these two transcriptional analyses, were the data on gene cluster rv3612c-rv3616c. Closer inspection of the data published in the corresponding supplemental materials showed that rv3612c-rv3616c were strongly downregulated in the H37Rv phoP ko mutant as well as in H37Ra [12,21]. These transcriptome data corroborate our results obtained by quantitative RT-PCR using probe rv3614c, which showed that gene rv3614c was definitely expressed much lower in H37Ra than in H37Rv and H37Ra::phoP strains (Figure 6). Since in previous, independent studies it has been demonstrated that functions of the rv3614c-rv3616c (espA) gene cluster were essential for the secretion of ESAT-6 and CFP-10 [27,28], it is quite probable that the lack of ESAT-6-specific T cell responses observed for strains H37Ra and SO2 (Figure 3) might be caused by the insufficient expression of rv3612c-rv3616c, which results from the lack of a fully functional PhoP in these strains. Moreover, the expression values of genes rv3612c-rv3616c in H37Rv described in the article by Gao et al. [12] show substantial differences between cultures grown in roller bottles relative to cultures grown in shake flasks, arguing that this gene cluster might be regulated by environmental conditions through the PhoP/PhoR system. It is not clear yet which factors might contribute to this effect. However, upregulation of phoP and rv3614c-rv3616c was observed after incubation of M. tuberculosis in 5mM H2O2 [37]. Furthermore, rv3614c-rv3616c were reported to be transiently upregulated in the phagosome and under acidic stress [38]. Altogether, from these reports it seems plausible that the pleiotropic regulator PhoP is involved in the regulation of rv3612c-rv3616c expression and thereby influences ESAT-6 secretion and virulence [16], but to unambiguously answer this question, virulence tests with recombinant H37Ra and/or phoP ko strains that express rv3616c-3612c under a constitutive promoter or a tetracycline inducable expression system [39] will be needed. Construction of such strains has recently been initiated as a first step of a future study to gain deeper insight into signaling events and regulation of the ESX-1 secretion system in different tubercle bacilli, including members of the putative progenitor species Mycobacterium prototuberculosis [40]. As in previous DNA/DNA microarray analyses [10], and from inspection of the very recently released genome sequence of H37Ra, no significant differences in the ESX-1 encoding region were found, the assumption that the observed lack of ESAT-6 secretion in H37Ra may be caused by factors outside of the RD1 region is very plausible. In contrast, in another transcriptome analysis, Mostowy and colleagues [11] found several genes of the RD1 region, including that encoding ESAT-6, among the genes that were at least 2.5-fold lower expressed in H37Ra than in H37Rv. Our results obtained for ESAT-6 expression (Figure 5) and the transcriptome data from Gao and colleagues [12] argue against direct downregulation of ESAT-6 in H37Ra. However, it is also possible that the observed differences may be caused by variations of in vitro culture conditions. In conclusion, in this work we report the identification and profound consequences of the PhoP S219L mutation on the widely used H37Ra strain. BLASTP comparisons of the PhoP sequence showed that the predicted DNA binding region, where the mutation occurred, is perfectly conserved among a wide range of actinobacteria, with H37Ra being the only strain showing such a mutation. By complementation with the wild-type copy of PhoP, we obtained a significant increase in virulence in ex vivo and animal models as well as restoration of ESAT-6 secretion and the accompanying antigen-specific immunological recognition by sensitized splenocytes or T cell hybridomas. It should be mentioned here that the SO2 phoP ko strain, which showed strong ESAT-6 expression but little ESAT-6 secretion (Figure 5), induced only very reduced ESAT-6- specific T cell responses (Figure 3). This strain was previously used to vaccinate mice and guinea pigs and conferred good protection against a challenge with virulent M. tuberculosis [25]. As ESAT-6-specific T cell responses induced by this strain are low, ESAT-6-based IFN-gamma production assays might be used to differentiate between vaccination with SO2 and infection with wild-type M. tuberculosis. With its well documented role in virulence and strong T cell antigenicity, ESAT-6 is one of the most important proteins of M. tuberculosis involved in host pathogen interaction [5,41-43]. However, as previously observed in complementation studies of BCG [18], the level of virulence displayed by the phoP complemented H37Ra strain was still substantially below that of wild-type H37Rv, arguing that the strong attenuation of the H37Ra strain is likely based on several different genetic lesions, such as the one responsible for the absence of phthiocerol dimycocerosates (PDIM) [29], that were probably introduced into this strain during years of continued culture following the original event of attenuation described by Steenken et al. in 1934 [6]. Indeed, preliminary comparison of the 4.4-Mb genome of H37Rv [7] (NC_000962) with the recently accessible H37Ra genome (NC_009525) revealed 194 differences, including 126 SNPs, 16 deletions, 27 insertions, and 25 substitutions. At present, we do not know how many of these differences actually contribute to the attenuation of H37Ra, and it also remains to be determined how many differences exist among the various H37Ra strains that are presently used in the worldwide tuberculosis research laboratories. The link described here between mutation of phoP and consequences on ESAT-6 secretion, however, appears to be one factor that significantly contributes to attenuation. Finally, it is intriguing that both BCG and H37Ra, the two most often used attenuated tubercle bacilli, are attenuated for reasons linked to loss of ESAT-6 functions. Thus, our results once more emphasize the great importance of the ESX-1 system for tubercle bacilli and provide important new information about the phoP-associated virulence regulation in M. tuberculosis.\n" ], "offsets": [ [ 0, 9479 ] ] } ]

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[]

[ { "id": "PMC2242835-02-Results-02__text", "type": "abstract", "text": [ "Rationale for Knock-Ins \nTo evaluate the phenotypic effect of the different SNPs and to assess their potential contribution to the attenuation process, we undertook functional genomic analyses using knock-ins of H37Ra, as described previously [18]. Clones spanning the different genomic regions of non-synonymous SNPs were selected from an ordered H37Rv library of integrating shuttle cosmids [7,19] and individually electroporated into H37Ra, where they inserted stably into the attB site. By this approach we obtained appropriately complemented transformants for the SNPs in genes fadE5, rpsL, and phoP (Table S1), using cosmids I230, I563, and I36, respectively. Based on the known role of phoP in virulence [14], the H37Ra strain complemented with I36 (H37Ra::phoP) was accorded highest priority for further molecular characterization and functional analyses, whereas the two other recombinants (H37Ra::fadE5, H37Ra::rpsL) served as controls. Figure S1 shows part of the nucleotide sequence of a PCR-amplified fragment obtained from H37Ra::phoP. It is clearly visible that at nucleotide position 656 of phoP two peaks exist, one originating from the SNP present in H37Ra and one from the integrated cosmid I36 carrying the H37Rv wild-type copy of phoP. Similar results were also obtained for the SNPs in fadE5 and rpsL using cosmids I230 and I563, respectively (Figure S1). Correct integration of I36 was also confirmed by Southern blot. As depicted in Figure S2, hybridization of SpeI-digested genomic DNA with a 32P labeled phoP probe resulted in two bands of different sizes, one corresponding to the SpeI fragment harboring the H37Ra phoP gene (50 kb), and the other to the larger SpeI fragment created by integration of the I36 cosmid into the genome of H37Ra at the attB site. The successful integration of the cosmid was also reflected by a change in colony morphology that is shown in Figure S3. Indeed, Steenken and colleagues originally selected the H37Ra mutants mainly on the basis of the changes in colony morphology [6].\n" ], "offsets": [ [ 0, 2039 ] ] } ]

[ { "id": "PMC2242835-02-Results-02_T1", "type": "Organism", "text": [ "H37Ra" ], "offsets": [ [ 212, 217 ] ], "normalized": [] }, { "id": "PMC2242835-02-Results-02_T2", "type": "Organism", "text": [ "H37Rv" ], "offsets": [ [ 348, 353 ] ], "normalized": [] }, { "id": "PMC2242835-02-Results-02_T3", "type": "Organism", "text": [ "H37Ra" ], "offsets": [ [ 437, 442 ] ], "normalized": [] }, { "id": "PMC2242835-02-Results-02_T4", "type": "Protein", "text": [ "fadE5" ], "offsets": [ [ 583, 588 ] ], "normalized": [] }, { "id": "PMC2242835-02-Results-02_T5", "type": "Protein", "text": [ "rpsL" ], "offsets": [ [ 590, 594 ] ], "normalized": [] }, { "id": "PMC2242835-02-Results-02_T6", "type": "Protein", "text": [ "phoP" ], "offsets": [ [ 600, 604 ] ], "normalized": [] }, { "id": "PMC2242835-02-Results-02_T7", "type": "Protein", "text": [ "phoP" ], "offsets": [ [ 693, 697 ] ], "normalized": [] }, { "id": "PMC2242835-02-Results-02_T8", "type": "Organism", "text": [ "H37Ra" ], "offsets": [ [ 721, 726 ] ], "normalized": [] }, { "id": "PMC2242835-02-Results-02_T9", "type": "Organism", "text": [ "H37Ra::phoP" ], "offsets": [ [ 757, 768 ] ], "normalized": [] }, { "id": "PMC2242835-02-Results-02_T10", "type": "Protein", "text": [ "phoP" ], "offsets": [ [ 764, 768 ] ], "normalized": [] }, { "id": "PMC2242835-02-Results-02_T11", "type": "Organism", "text": [ "H37Ra::fadE5" ], "offsets": [ [ 900, 912 ] ], "normalized": [] }, { "id": "PMC2242835-02-Results-02_T12", "type": "Protein", "text": [ "fadE5" ], "offsets": [ [ 907, 912 ] ], "normalized": [] }, { "id": "PMC2242835-02-Results-02_T13", "type": "Organism", "text": [ "H37Ra::rpsL" ], "offsets": [ [ 914, 925 ] ], "normalized": [] }, { "id": "PMC2242835-02-Results-02_T14", "type": "Protein", "text": [ "rpsL" ], "offsets": [ [ 921, 925 ] ], "normalized": [] }, { "id": "PMC2242835-02-Results-02_T15", "type": "Organism", "text": [ "H37Ra::phoP" ], "offsets": [ [ 1037, 1048 ] ], "normalized": [] }, { "id": "PMC2242835-02-Results-02_T16", "type": "Protein", "text": [ "phoP" ], "offsets": [ [ 1044, 1048 ] ], "normalized": [] }, { "id": "PMC2242835-02-Results-02_T17", "type": "Protein", "text": [ "phoP" ], "offsets": [ [ 1107, 1111 ] ], "normalized": [] }, { "id": "PMC2242835-02-Results-02_T18", "type": "Organism", "text": [ "H37Ra" ], "offsets": [ [ 1169, 1174 ] ], "normalized": [] }, { "id": "PMC2242835-02-Results-02_T19", "type": "Organism", "text": [ "H37Rv" ], "offsets": [ [ 1227, 1232 ] ], "normalized": [] }, { "id": "PMC2242835-02-Results-02_T20", "type": "Protein", "text": [ "phoP" ], "offsets": [ [ 1251, 1255 ] ], "normalized": [] }, { "id": "PMC2242835-02-Results-02_T21", "type": "Protein", "text": [ "fadE5" ], "offsets": [ [ 1308, 1313 ] ], "normalized": [] }, { "id": "PMC2242835-02-Results-02_T22", "type": "Protein", "text": [ "rpsL" ], "offsets": [ [ 1318, 1322 ] ], "normalized": [] }, { "id": "PMC2242835-02-Results-02_T23", "type": "Protein", "text": [ "SpeI" ], "offsets": [ [ 1485, 1489 ] ], "normalized": [] }, { "id": "PMC2242835-02-Results-02_T24", "type": "Protein", "text": [ "phoP" ], "offsets": [ [ 1530, 1534 ] ], "normalized": [] }, { "id": "PMC2242835-02-Results-02_T25", "type": "Protein", "text": [ "SpeI" ], "offsets": [ [ 1608, 1612 ] ], "normalized": [] }, { "id": "PMC2242835-02-Results-02_T26", "type": "Organism", "text": [ "H37Ra" ], "offsets": [ [ 1636, 1641 ] ], "normalized": [] }, { "id": "PMC2242835-02-Results-02_T27", "type": "Protein", "text": [ "phoP" ], "offsets": [ [ 1642, 1646 ] ], "normalized": [] }, { "id": "PMC2242835-02-Results-02_T28", "type": "Protein", "text": [ "SpeI" ], "offsets": [ [ 1689, 1693 ] ], "normalized": [] }, { "id": "PMC2242835-02-Results-02_T29", "type": "Organism", "text": [ "H37Ra" ], "offsets": [ [ 1763, 1768 ] ], "normalized": [] }, { "id": "PMC2242835-02-Results-02_T30", "type": "Organism", "text": [ "H37Ra" ], "offsets": [ [ 1964, 1969 ] ], "normalized": [] } ]

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[]

[ { "id": "PMC2242835-01-Introduction__text", "type": "abstract", "text": [ "Introduction \n125 years of intense research on the major human pathogen Mycobacterium tuberculosis have passed since its discovery by Robert Koch, resulting in a huge body of knowledge. In spite of the great progress that has been made in the understanding of some basic features of its pathogenesis, tuberculosis remains a major threat to human life in most parts of the world. Indeed, M. tuberculosis has retained many secrets of its so successful pathogenic lifecycle. Among the different possibilities to obtain new insight into the mechanisms employed by M. tuberculosis to infect its host, the analysis of attenuated strains is one promising approach, and there are some well-documented examples of laboratory-attenuated strains. One of them is the \"Bacille de Calmette et Guerin\" (BCG), which was originally derived in 1921 from a virulent Mycobacterium bovis strain by 230 passages on potato-glycerol-ox bile medium [1]. The genetic lesions of BCG have recently been determined [2-4], revealing that the loss of region of difference 1 (RD1), which encodes part of the ESX-1 secretion system [5], was one of the key events in its attenuation. Another famous example of an attenuated strain is M. tuberculosis H37Ra (\"a\" for avirulent) (H37Ra). This strain was obtained in 1934 by serial passage of patient isolate M. tuberculosis H37 through media with different pHs [6] and since then has been widely used in many laboratories in the world. Despite its long use, the reasons for its stable attenuation have not yet been elucidated. As H37Ra is derived from the same parent strain as M. tuberculosis H37Rv (\"v\" for virulent) (H37Rv), the sequenced paradigm strain of tuberculosis research [7], genomic comparisons of the attenuated and virulent variants of M. tuberculosis H37 are particularly interesting and have the potential to identify subtle genetic changes that might be responsible for the phenotypic differences observed between the two strains. In a previous study we have tried to reveal these determinants [8], but the methods employed only identified large genetic polymorphisms, associated with IS6110, which were not found to be responsible for the attenuation of H37Ra [8]. In another study, Pascopella et al. [9] transformed a cosmid library of H37Rv into H37Ra and then selected for clones that were enriched on passage through the mouse. A number of overlapping cosmid clones that gave enhanced growth and survival in the spleens of infected mice relative to that of wild-type H37Ra were identified [9]. However, the effects of these complementation attempts on virulence remained limited, and no sequence information was described, which makes it difficult now to identify the genes implicated. H37Ra was also the subject of extensive micro-array based analyses, including whole genome comparative DNA/DNA analyses [10] and transcriptional studies [11,12], which have identified some candidate genes that were consistently downregulated. However, a definitive conclusion about the molecular determinants of the attenuation could not be drawn. As all these previous attempts have failed to identify the genetic basis for the attenuation, we subjected H37Ra to microarray-based DNA re-sequencing (NimbleGen Systems). This technique has previously permitted single nucleotide polymorphisms (SNPs) of a PA-824 drug resistant mutant strain of H37Rv to be detected [13]. This approach was combined with gene \"knock-in\" strategies, to complement selected lesions, that allowed recombinant H37Ra strains to be engineered, whose virulence and immunogenicity were then evaluated in in vitro, ex vivo and animal models. This strategy led us to identify and characterize a point mutation in the phoP/phoR two-component regulatory system of H37Ra that has uncovered novel regulatory links, which impact on the secretion and T cell recognition of the major T cell antigens ESAT-6 and CFP-10.\n" ], "offsets": [ [ 0, 3905 ] ] } ]

[ { "id": "PMC2242835-01-Introduction_T1", "type": "Organism", "text": [ "human" ], "offsets": [ [ 57, 62 ] ], "normalized": [] }, { "id": "PMC2242835-01-Introduction_T2", "type": "Organism", "text": [ "Mycobacterium tuberculosis" ], "offsets": [ [ 72, 98 ] ], "normalized": [] }, { "id": "PMC2242835-01-Introduction_T3", "type": "Organism", "text": [ "human" ], "offsets": [ [ 340, 345 ] ], "normalized": [] }, { "id": "PMC2242835-01-Introduction_T4", "type": "Organism", "text": [ "M. tuberculosis" ], "offsets": [ [ 387, 402 ] ], "normalized": [] }, { "id": "PMC2242835-01-Introduction_T5", "type": "Organism", "text": [ "M. tuberculosis" ], "offsets": [ [ 560, 575 ] ], "normalized": [] }, { "id": "PMC2242835-01-Introduction_T6", "type": "Organism", "text": [ "Bacille de Calmette et Guerin" ], "offsets": [ [ 756, 785 ] ], "normalized": [] }, { "id": "PMC2242835-01-Introduction_T7", "type": "Organism", "text": [ "BCG" ], "offsets": [ [ 788, 791 ] ], "normalized": [] }, { "id": "PMC2242835-01-Introduction_T8", "type": "Organism", "text": [ "Mycobacterium bovis" ], "offsets": [ [ 847, 866 ] ], "normalized": [] }, { "id": "PMC2242835-01-Introduction_T9", "type": "Organism", "text": [ "BCG" ], "offsets": [ [ 952, 955 ] ], "normalized": [] }, { "id": "PMC2242835-01-Introduction_T10", "type": "Organism", "text": [ "M. tuberculosis H37Ra" ], "offsets": [ [ 1200, 1221 ] ], "normalized": [] }, { "id": "PMC2242835-01-Introduction_T11", "type": "Organism", "text": [ "H37Ra" ], "offsets": [ [ 1243, 1248 ] ], "normalized": [] }, { "id": "PMC2242835-01-Introduction_T12", "type": "Organism", "text": [ "patient" ], "offsets": [ [ 1305, 1312 ] ], "normalized": [] }, { "id": "PMC2242835-01-Introduction_T13", "type": "Organism", "text": [ "M. tuberculosis H37" ], "offsets": [ [ 1321, 1340 ] ], "normalized": [] }, { "id": "PMC2242835-01-Introduction_T14", "type": "Organism", "text": [ "H37Ra" ], "offsets": [ [ 1543, 1548 ] ], "normalized": [] }, { "id": "PMC2242835-01-Introduction_T15", "type": "Organism", "text": [ "M. tuberculosis H37Rv" ], "offsets": [ [ 1591, 1612 ] ], "normalized": [] }, { "id": "PMC2242835-01-Introduction_T16", "type": "Organism", "text": [ "H37Rv" ], "offsets": [ [ 1633, 1638 ] ], "normalized": [] }, { "id": "PMC2242835-01-Introduction_T17", "type": "Organism", "text": [ "M. tuberculosis H37" ], "offsets": [ [ 1764, 1783 ] ], "normalized": [] }, { "id": "PMC2242835-01-Introduction_T18", "type": "Organism", "text": [ "H37Ra" ], "offsets": [ [ 2186, 2191 ] ], "normalized": [] }, { "id": "PMC2242835-01-Introduction_T19", "type": "Organism", "text": [ "H37Rv" ], "offsets": [ [ 2269, 2274 ] ], "normalized": [] }, { "id": "PMC2242835-01-Introduction_T20", "type": "Organism", "text": [ "H37Ra" ], "offsets": [ [ 2280, 2285 ] ], "normalized": [] }, { "id": "PMC2242835-01-Introduction_T21", "type": "Organism", "text": [ "mouse" ], "offsets": [ [ 2357, 2362 ] ], "normalized": [] }, { "id": "PMC2242835-01-Introduction_T22", "type": "Organism", "text": [ "mice" ], "offsets": [ [ 2468, 2472 ] ], "normalized": [] }, { "id": "PMC2242835-01-Introduction_T23", "type": "Organism", "text": [ "H37Ra" ], "offsets": [ [ 2503, 2508 ] ], "normalized": [] }, { "id": "PMC2242835-01-Introduction_T24", "type": "Organism", "text": [ "H37Ra" ], "offsets": [ [ 2722, 2727 ] ], "normalized": [] }, { "id": "PMC2242835-01-Introduction_T25", "type": "Organism", "text": [ "H37Ra" ], "offsets": [ [ 3177, 3182 ] ], "normalized": [] }, { "id": "PMC2242835-01-Introduction_T26", "type": "Chemical", "text": [ "PA-824" ], "offsets": [ [ 3326, 3332 ] ], "normalized": [] }, { "id": "PMC2242835-01-Introduction_T27", "type": "Organism", "text": [ "H37Rv" ], "offsets": [ [ 3365, 3370 ] ], "normalized": [] }, { "id": "PMC2242835-01-Introduction_T28", "type": "Organism", "text": [ "H37Ra" ], "offsets": [ [ 3509, 3514 ] ], "normalized": [] }, { "id": "PMC2242835-01-Introduction_T29", "type": "Two-component-system", "text": [ "phoP/phoR" ], "offsets": [ [ 3710, 3719 ] ], "normalized": [] }, { "id": "PMC2242835-01-Introduction_T30", "type": "Protein", "text": [ "phoP" ], "offsets": [ [ 3710, 3714 ] ], "normalized": [] }, { "id": "PMC2242835-01-Introduction_T31", "type": "Protein", "text": [ "phoR" ], "offsets": [ [ 3715, 3719 ] ], "normalized": [] }, { "id": "PMC2242835-01-Introduction_T32", "type": "Organism", "text": [ "H37Ra" ], "offsets": [ [ 3755, 3760 ] ], "normalized": [] }, { "id": "PMC2242835-01-Introduction_T33", "type": "Protein", "text": [ "ESAT-6" ], "offsets": [ [ 3886, 3892 ] ], "normalized": [] }, { "id": "PMC2242835-01-Introduction_T34", "type": "Protein", "text": [ "CFP-10" ], "offsets": [ [ 3897, 3903 ] ], "normalized": [] } ]

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[ { "id": "PMC2581603-02-Results-03__text", "type": "abstract", "text": [ "DNA has cation chelating activity \nThe observation that DNA disrupted the integrity of the cell envelope causing cell lysis suggested that DNA was acting as a cation chelator. To confirm that DNA-mediated killing was a result of cation chelation, excess Mg2+, Ca2+, Mn2+, and Zn2+ were added to P. aeruginosa cultures. The rapidity of DNA-induced cell death ruled out the possibility that death, or lack of growth, was simply due to cation starvation. Addition of excess cations to planktonic cultures inhibited the fast-acting antimicrobial effects of DNA (Fig 3A). Protection was measured in response to a range of cation concentrations, where the highest concentration tested was that which remained soluble in the presence of DNA (3.125-25 mM). The concentration at which maximal protection was obtained for each cation is represented in Fig 3A (25 mM Mg2+; 6.25 mM Ca2+; 6.25 Mn2+; 3.125 mM Zn2+). Kill curve assays indicated that the addition of Mg2+, Ca2+ or Mn2+ provided protection from DNA-induced lysis, however, the addition of Zn2+ did not protect from DNA-mediated killing (Fig 3A). In a similar manner, the addition of excess Mg2+, Ca2+ and Mn2+ restored growth of P. aeruginosa in BM2 media. Only partial restoration of growth was observed in the presence of Zn2+ (Fig 3B). The increased protection observed following addition of Mg2+ and Ca2+ is likely due to their importance in membrane integrity where they function to stabilize the OM by crosslinking adjacent LPS molecules [58]. Cations play diverse physiologically important roles within a cell; from detoxification of reactive oxygen species and co-factors for enzymes to the stabilization of macromolecules within the cell [62]. Since Mg2+ limitation has been shown to be associated with CAP resistance in P. aeruginosa [44],[45],[47], we sought to determine if Mg2+ chelation by DNA may account, at least in part, for the increased antibiotic resistance observed in biofilms.\n" ], "offsets": [ [ 0, 1952 ] ] } ]

[ { "id": "PMC2581603-02-Results-03_T1", "type": "Chemical", "text": [ "Mg2+" ], "offsets": [ [ 254, 258 ] ], "normalized": [] }, { "id": "PMC2581603-02-Results-03_T2", "type": "Chemical", "text": [ "Ca2+" ], "offsets": [ [ 260, 264 ] ], "normalized": [] }, { "id": "PMC2581603-02-Results-03_T3", "type": "Chemical", "text": [ "Mn2+" ], "offsets": [ [ 266, 270 ] ], "normalized": [] }, { "id": "PMC2581603-02-Results-03_T4", "type": "Chemical", "text": [ "Zn2+" ], "offsets": [ [ 276, 280 ] ], "normalized": [] }, { "id": "PMC2581603-02-Results-03_T5", "type": "Organism", "text": [ "P. aeruginosa" ], "offsets": [ [ 295, 308 ] ], "normalized": [] }, { "id": "PMC2581603-02-Results-03_T6", "type": "Chemical", "text": [ "Mg2+" ], "offsets": [ [ 856, 860 ] ], "normalized": [] }, { "id": "PMC2581603-02-Results-03_T7", "type": "Chemical", "text": [ "Ca2+" ], "offsets": [ [ 870, 874 ] ], "normalized": [] }, { "id": "PMC2581603-02-Results-03_T8", "type": "Chemical", "text": [ "Mn2+" ], "offsets": [ [ 881, 885 ] ], "normalized": [] }, { "id": "PMC2581603-02-Results-03_T9", "type": "Chemical", "text": [ "Zn2+" ], "offsets": [ [ 896, 900 ] ], "normalized": [] }, { "id": "PMC2581603-02-Results-03_T10", "type": "Chemical", "text": [ "Mg2+" ], "offsets": [ [ 952, 956 ] ], "normalized": [] }, { "id": "PMC2581603-02-Results-03_T11", "type": "Chemical", "text": [ "Ca2+" ], "offsets": [ [ 958, 962 ] ], "normalized": [] }, { "id": "PMC2581603-02-Results-03_T12", "type": "Chemical", "text": [ "Mn2+" ], "offsets": [ [ 966, 970 ] ], "normalized": [] }, { "id": "PMC2581603-02-Results-03_T13", "type": "Chemical", "text": [ "Zn2+" ], "offsets": [ [ 1040, 1044 ] ], "normalized": [] }, { "id": "PMC2581603-02-Results-03_T14", "type": "Chemical", "text": [ "Mg2+" ], "offsets": [ [ 1141, 1145 ] ], "normalized": [] }, { "id": "PMC2581603-02-Results-03_T15", "type": "Chemical", "text": [ "Ca2+" ], "offsets": [ [ 1147, 1151 ] ], "normalized": [] }, { "id": "PMC2581603-02-Results-03_T16", "type": "Chemical", "text": [ "Mn2+" ], "offsets": [ [ 1156, 1160 ] ], "normalized": [] }, { "id": "PMC2581603-02-Results-03_T17", "type": "Organism", "text": [ "P. aeruginosa" ], "offsets": [ [ 1180, 1193 ] ], "normalized": [] }, { "id": "PMC2581603-02-Results-03_T18", "type": "Chemical", "text": [ "Zn2+" ], "offsets": [ [ 1275, 1279 ] ], "normalized": [] }, { "id": "PMC2581603-02-Results-03_T19", "type": "Chemical", "text": [ "Mg2+" ], "offsets": [ [ 1346, 1350 ] ], "normalized": [] }, { "id": "PMC2581603-02-Results-03_T20", "type": "Chemical", "text": [ "Ca2+" ], "offsets": [ [ 1355, 1359 ] ], "normalized": [] }, { "id": "PMC2581603-02-Results-03_T21", "type": "Chemical", "text": [ "LPS" ], "offsets": [ [ 1481, 1484 ] ], "normalized": [] }, { "id": "PMC2581603-02-Results-03_T22", "type": "Chemical", "text": [ "reactive oxygen species" ], "offsets": [ [ 1592, 1615 ] ], "normalized": [] }, { "id": "PMC2581603-02-Results-03_T23", "type": "Chemical", "text": [ "Mg2+" ], "offsets": [ [ 1710, 1714 ] ], "normalized": [] }, { "id": "PMC2581603-02-Results-03_T24", "type": "Chemical", "text": [ "CAP" ], "offsets": [ [ 1763, 1766 ] ], "normalized": [] }, { "id": "PMC2581603-02-Results-03_T25", "type": "Organism", "text": [ "P. aeruginosa" ], "offsets": [ [ 1781, 1794 ] ], "normalized": [] }, { "id": "PMC2581603-02-Results-03_T26", "type": "Chemical", "text": [ "Mg2+" ], "offsets": [ [ 1837, 1841 ] ], "normalized": [] } ]

[ { "id": "PMC2581603-02-Results-03_E1", "type": "Process", "trigger": { "text": [ "resistance" ], "offsets": [ [ 1767, 1777 ] ] }, "arguments": [ { "role": "Participant", "ref_id": "PMC2581603-02-Results-03_T25" } ] }, { "id": "PMC2581603-02-Results-03_E2", "type": "Process", "trigger": { "text": [ "resistance" ], "offsets": [ [ 1919, 1929 ] ] }, "arguments": [] } ]

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[ { "id": "PMC2593050-03-RESULTS-03__text", "type": "abstract", "text": [ "No Effect of the vicK Deletion on Resistance of S. equi to Phagocytosis by PMNs \nTo determine whether the DeltavicK deletion affects the resistance of S. equi to phagocytosis by PMNs, the phagocytosis of wild-type and DeltavicK bacteria by PMNs in non-immune horse and rabbit blood was compared. FITC-labeled wild-type S. equi, DeltavicK mutant, and S. pyogenes spy1718::aad mutant were incubated with heparinized horse or rabbit blood for 5 and 15 min, and percentages of PMNs associated with fluorescent bacteria were quantified using flow cytometry analysis. The spy1718::aad mutant of S. pyogenes, which is no longer resistant to phagocytosis by PMNs, was used as a positive control in the assay. The percentages of PMNs with associated wild-type S. equi and spy1718::aad were low and high, respectively, indicating that the assay worked well to evaluate resistance of the bacteria to phagocytosis. There was no significant difference in the percentages of PMNs associated with wild-type and DeltavicK bacteria at both time points and in both horse and rabbit blood (Fig. 3), indicating that the DeltavicK mutant retains the ability of S. equi to resist to phagocytosis by PMNs.\n" ], "offsets": [ [ 0, 1183 ] ] } ]

[ { "id": "PMC2593050-03-RESULTS-03_T1", "type": "Protein", "text": [ "vicK" ], "offsets": [ [ 17, 21 ] ], "normalized": [] }, { "id": "PMC2593050-03-RESULTS-03_T2", "type": "Organism", "text": [ "S. equi" ], "offsets": [ [ 48, 55 ] ], "normalized": [] }, { "id": "PMC2593050-03-RESULTS-03_T3", "type": "Protein", "text": [ "vicK" ], "offsets": [ [ 111, 115 ] ], "normalized": [] }, { "id": "PMC2593050-03-RESULTS-03_T4", "type": "Organism", "text": [ "S. equi" ], "offsets": [ [ 151, 158 ] ], "normalized": [] }, { "id": "PMC2593050-03-RESULTS-03_T5", "type": "Organism", "text": [ "DeltavicK" ], "offsets": [ [ 218, 227 ] ], "normalized": [] }, { "id": "PMC2593050-03-RESULTS-03_T6", "type": "Protein", "text": [ "vicK" ], "offsets": [ [ 223, 227 ] ], "normalized": [] }, { "id": "PMC2593050-03-RESULTS-03_T7", "type": "Organism", "text": [ "S. equi" ], "offsets": [ [ 319, 326 ] ], "normalized": [] }, { "id": "PMC2593050-03-RESULTS-03_T8", "type": "Organism", "text": [ "DeltavicK mutant" ], "offsets": [ [ 328, 344 ] ], "normalized": [] }, { "id": "PMC2593050-03-RESULTS-03_T9", "type": "Protein", "text": [ "vicK" ], "offsets": [ [ 333, 337 ] ], "normalized": [] }, { "id": "PMC2593050-03-RESULTS-03_T10", "type": "Organism", "text": [ "spy1718::aad mutant" ], "offsets": [ [ 362, 381 ] ], "normalized": [] }, { "id": "PMC2593050-03-RESULTS-03_T11", "type": "Protein", "text": [ "spy1718" ], "offsets": [ [ 362, 369 ] ], "normalized": [] }, { "id": "PMC2593050-03-RESULTS-03_T12", "type": "Protein", "text": [ "aad" ], "offsets": [ [ 371, 374 ] ], "normalized": [] }, { "id": "PMC2593050-03-RESULTS-03_T13", "type": "Organism", "text": [ "spy1718::aad mutant" ], "offsets": [ [ 566, 585 ] ], "normalized": [] }, { "id": "PMC2593050-03-RESULTS-03_T14", "type": "Protein", "text": [ "spy1718" ], "offsets": [ [ 566, 573 ] ], "normalized": [] }, { "id": "PMC2593050-03-RESULTS-03_T15", "type": "Protein", "text": [ "aad" ], "offsets": [ [ 575, 578 ] ], "normalized": [] }, { "id": "PMC2593050-03-RESULTS-03_T16", "type": "Organism", "text": [ "S. pyogenes" ], "offsets": [ [ 589, 600 ] ], "normalized": [] }, { "id": "PMC2593050-03-RESULTS-03_T17", "type": "Organism", "text": [ "S. equi" ], "offsets": [ [ 751, 758 ] ], "normalized": [] }, { "id": "PMC2593050-03-RESULTS-03_T18", "type": "Organism", "text": [ "spy1718::aad" ], "offsets": [ [ 763, 775 ] ], "normalized": [] }, { "id": "PMC2593050-03-RESULTS-03_T19", "type": "Protein", "text": [ "spy1718" ], "offsets": [ [ 763, 770 ] ], "normalized": [] }, { "id": "PMC2593050-03-RESULTS-03_T20", "type": "Protein", "text": [ "aad" ], "offsets": [ [ 772, 775 ] ], "normalized": [] }, { "id": "PMC2593050-03-RESULTS-03_T21", "type": "Organism", "text": [ "DeltavicK" ], "offsets": [ [ 996, 1005 ] ], "normalized": [] }, { "id": "PMC2593050-03-RESULTS-03_T22", "type": "Protein", "text": [ "vicK" ], "offsets": [ [ 1001, 1005 ] ], "normalized": [] }, { "id": "PMC2593050-03-RESULTS-03_T23", "type": "Organism", "text": [ "DeltavicK mutant" ], "offsets": [ [ 1100, 1116 ] ], "normalized": [] }, { "id": "PMC2593050-03-RESULTS-03_T24", "type": "Protein", "text": [ "vicK" ], "offsets": [ [ 1105, 1109 ] ], "normalized": [] }, { "id": "PMC2593050-03-RESULTS-03_T25", "type": "Organism", "text": [ "S. equi" ], "offsets": [ [ 1140, 1147 ] ], "normalized": [] } ]

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[ { "id": "PMC1913099-02-Results-Discussion-03__text", "type": "abstract", "text": [ "Virulence Factors \nStreptococci elaborate several factors implicated in infection, including surface-exposed adhesins and secreted toxigenic proteins (reviewed in [7,14,24]). The initial statistical analysis identified four differentially expressed virulence genes (Tables 1 and 2). Genes encoding streptolysin O (slo or spy0167) and the SpeB protease (spy2039) were downregulated, while genes encoding pyrogenic exotoxin H (speH or spy1008) and a putative fibronectin-binding protein (spy0130) were upregulated. We verified the differential expression of spy2039 and spy0130 by qRT-PCR. The downregulation of virulence loci during presumably inappropriate stages of infection was not surprising. Streptolysin O is a cytotoxin that damages human tissue and increases host cell cytotoxicity [7,25]. The resulting cellular damage, particularly to polymorphonuclear leukocytes [26], decreases internalization and subsequent intracellular killing of streptococci [27]. Based on its downregulation during adherence, we infer that slo was transcribed during pre-adherence associations, perhaps, as previously reported, to protect streptococci from phagocytic killing in vivo [27]. However, once adhered, our data suggest that streptococci downregulate production of this cytotoxin, presumably to prevent further host tissue destruction that could interfere with adherence. SpeB (encoded by spy2039) is a multifunctional cysteine protease implicated in numerous infection strategies [28,29]. Although few studies have examined gene expression patterns during adherence, SpeB production (as detected by Western blot analysis) decreases during co-culture with human peripheral blood mononuclear cells [30] and in a mouse infection model [31]. When SpeB expression is limited, several streptococcal proteins necessary for adherence remain intact [24,32,33]; thus, decreased SpeB production (as indicated here) may promote pharyngeal cell attachment. Furthermore, SpeB abolishes internalization (following adherence) of certain streptococcal strains by epithelial cells (including Detroit 562 cells), a process mediated in part by the fibronectin-binding protein F [34,35]. We observed significant upregulation of the gene spy0130, encoding a protein recently found to be associated with the production of surface-exposed pili on strain SF370 [36]. The protein shares 60% sequence similarity to protein F, suggesting that it may coordinate a similar internalization mechanism or may be involved directly in adherence (discussed later in detail). SpeB downregulation also coincides with increased expression of pyrogenic exotoxins [33,37] that reportedly increase streptococcal survival in vivo. We observed that the exotoxin-encoding speH gene [38] was upregulated. Taken together, our results agree with previous reports on SpeB production during host cell interactions, suggesting that decreased expression may promote streptococcal adherence (by preventing proteolytic degradation of key virulence factors or adhesins), enhance internalization (perhaps through a fibronectin-mediated pathway), and increase survival (through increased pyrogenic exotoxin production, discussed below).\n" ], "offsets": [ [ 0, 3176 ] ] } ]

[ { "id": "PMC1913099-02-Results-Discussion-03_T1", "type": "Organism", "text": [ "Streptococci" ], "offsets": [ [ 19, 31 ] ], "normalized": [] }, { "id": "PMC1913099-02-Results-Discussion-03_T2", "type": "Protein", "text": [ "streptolysin O" ], "offsets": [ [ 298, 312 ] ], "normalized": [] }, { "id": "PMC1913099-02-Results-Discussion-03_T3", "type": "Protein", "text": [ "slo" ], "offsets": [ [ 314, 317 ] ], "normalized": [] }, { "id": "PMC1913099-02-Results-Discussion-03_T4", "type": "Protein", "text": [ "spy0167" ], "offsets": [ [ 321, 328 ] ], "normalized": [] }, { "id": "PMC1913099-02-Results-Discussion-03_T5", "type": "Protein", "text": [ "SpeB" ], "offsets": [ [ 338, 342 ] ], "normalized": [] }, { "id": "PMC1913099-02-Results-Discussion-03_T6", "type": "Protein", "text": [ "spy2039" ], "offsets": [ [ 353, 360 ] ], "normalized": [] }, { "id": "PMC1913099-02-Results-Discussion-03_T7", "type": "Protein", "text": [ "pyrogenic exotoxin H" ], "offsets": [ [ 403, 423 ] ], "normalized": [] }, { "id": "PMC1913099-02-Results-Discussion-03_T8", "type": "Protein", "text": [ "speH" ], "offsets": [ [ 425, 429 ] ], "normalized": [] }, { "id": "PMC1913099-02-Results-Discussion-03_T9", "type": "Protein", "text": [ "spy1008" ], "offsets": [ [ 433, 440 ] ], "normalized": [] }, { "id": "PMC1913099-02-Results-Discussion-03_T10", "type": "Protein", "text": [ "putative fibronectin-binding protein" ], "offsets": [ [ 448, 484 ] ], "normalized": [] }, { "id": "PMC1913099-02-Results-Discussion-03_T11", "type": "Protein", "text": [ "spy0130" ], "offsets": [ [ 486, 493 ] ], "normalized": [] }, { "id": "PMC1913099-02-Results-Discussion-03_T12", "type": "Protein", "text": [ "spy2039" ], "offsets": [ [ 556, 563 ] ], "normalized": [] }, { "id": "PMC1913099-02-Results-Discussion-03_T13", "type": "Protein", "text": [ "spy0130" ], "offsets": [ [ 568, 575 ] ], "normalized": [] }, { "id": "PMC1913099-02-Results-Discussion-03_T14", "type": "Protein", "text": [ "Streptolysin O" ], "offsets": [ [ 697, 711 ] ], "normalized": [] }, { "id": "PMC1913099-02-Results-Discussion-03_T15", "type": "Organism", "text": [ "human" ], "offsets": [ [ 740, 745 ] ], "normalized": [] }, { "id": "PMC1913099-02-Results-Discussion-03_T16", "type": "Organism", "text": [ "streptococci" ], "offsets": [ [ 946, 958 ] ], "normalized": [] }, { "id": "PMC1913099-02-Results-Discussion-03_T17", "type": "Protein", "text": [ "slo" ], "offsets": [ [ 1025, 1028 ] ], "normalized": [] }, { "id": "PMC1913099-02-Results-Discussion-03_T18", "type": "Organism", "text": [ "streptococci" ], "offsets": [ [ 1124, 1136 ] ], "normalized": [] }, { "id": "PMC1913099-02-Results-Discussion-03_T19", "type": "Organism", "text": [ "streptococci" ], "offsets": [ [ 1220, 1232 ] ], "normalized": [] }, { "id": "PMC1913099-02-Results-Discussion-03_T20", "type": "Protein", "text": [ "SpeB" ], "offsets": [ [ 1367, 1371 ] ], "normalized": [] }, { "id": "PMC1913099-02-Results-Discussion-03_T21", "type": "Protein", "text": [ "spy2039" ], "offsets": [ [ 1384, 1391 ] ], "normalized": [] }, { "id": "PMC1913099-02-Results-Discussion-03_T22", "type": "Protein", "text": [ "cysteine protease" ], "offsets": [ [ 1414, 1431 ] ], "normalized": [] }, { "id": "PMC1913099-02-Results-Discussion-03_T23", "type": "Protein", "text": [ "SpeB" ], "offsets": [ [ 1563, 1567 ] ], "normalized": [] }, { "id": "PMC1913099-02-Results-Discussion-03_T24", "type": "Organism", "text": [ "human" ], "offsets": [ [ 1651, 1656 ] ], "normalized": [] }, { "id": "PMC1913099-02-Results-Discussion-03_T25", "type": "Organism", "text": [ "mouse" ], "offsets": [ [ 1706, 1711 ] ], "normalized": [] }, { "id": "PMC1913099-02-Results-Discussion-03_T26", "type": "Protein", "text": [ "SpeB" ], "offsets": [ [ 1739, 1743 ] ], "normalized": [] }, { "id": "PMC1913099-02-Results-Discussion-03_T27", "type": "Protein", "text": [ "SpeB" ], "offsets": [ [ 1864, 1868 ] ], "normalized": [] }, { "id": "PMC1913099-02-Results-Discussion-03_T28", "type": "Protein", "text": [ "SpeB" ], "offsets": [ [ 1953, 1957 ] ], "normalized": [] }, { "id": "PMC1913099-02-Results-Discussion-03_T29", "type": "Organism", "text": [ "streptococcal strains" ], "offsets": [ [ 2017, 2038 ] ], "normalized": [] }, { "id": "PMC1913099-02-Results-Discussion-03_T30", "type": "Protein", "text": [ "fibronectin-binding protein F" ], "offsets": [ [ 2124, 2153 ] ], "normalized": [] }, { "id": "PMC1913099-02-Results-Discussion-03_T31", "type": "Protein", "text": [ "spy0130" ], "offsets": [ [ 2212, 2219 ] ], "normalized": [] }, { "id": "PMC1913099-02-Results-Discussion-03_T32", "type": "Organism", "text": [ "SF370" ], "offsets": [ [ 2326, 2331 ] ], "normalized": [] }, { "id": "PMC1913099-02-Results-Discussion-03_T33", "type": "Protein", "text": [ "protein F" ], "offsets": [ [ 2384, 2393 ] ], "normalized": [] }, { "id": "PMC1913099-02-Results-Discussion-03_T34", "type": "Protein", "text": [ "SpeB" ], "offsets": [ [ 2535, 2539 ] ], "normalized": [] }, { "id": "PMC1913099-02-Results-Discussion-03_T35", "type": "Protein", "text": [ "speH" ], "offsets": [ [ 2723, 2727 ] ], "normalized": [] }, { "id": "PMC1913099-02-Results-Discussion-03_T36", "type": "Protein", "text": [ "SpeB" ], "offsets": [ [ 2814, 2818 ] ], "normalized": [] } ]

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