Datasets:

bigbio

/

bionlp_st_2011_id

like 1

[ { "id": "PMC2266911-02-Results_and_Discussion-04__text", "type": "abstract", "text": [ "Temperature-dependent genes \nTemperature is a key environmental signal to enable bacterial adaptation to diverse hosts. In Yersinia, temperature-dependent gene expression has been described to be an important theme in bacterial mechanisms of pathogenesis towards humans [116]. However, the biological role of genes repressed at body temperature, but induced at environmental temperature, has been underinvestigated so far. By data mining, we identified 32 genes or gene loci of Yersinia spp. that exhibit stronger expression with temperature decrease (Table 1). 19 of them have a homologue in P. luminescens. Most genes belong to the groups of offensive virulence factors, regulators, and metabolic enzymes. The data have derived from expression profiling in vitro and cannot directly be translated to the in vivo situation. Moreover, several genes induced at lower temperature such as inv, yst or yplA affect the virulence properties of Y. enterocolitica in mice [87]. However, low temperature-dependent expression of the genes in Table 1 suggests that they also play a role during the insect stage of Y. enterocolitica, or that they have evolved from bacteria-insect interaction and then adapted to pathogenicity towards mammals. Some of these low temperature-induced genes are restricted to a narrow spectrum of bacterial genera such as Burkholderia, Pseudomonas, Serratia, or Erwinia, all of which are known to be associated with soil, plants or insects. Other genes of Table 1 are present in a broader range of bacteria, and their expression might depend on regulatory mechanisms different from that of Y. enterocolitica. This pathogen is non-motile at body temperature, and a connection between motility and virulence is well-documented [116,117]. For example, a non-motile flhDC mutant of Y. enterocolitica secretes larger amounts of Yop proteins encoded by the pYV plasmid than the wild-type bacteria [118]. Recently, it was shown that the flagellar master-operon of X. nematophila regulates the expression of a novel hemolysin which is required for full virulence of X. nematophila against insects [119]. We therefore speculate that motility essentially contributes to the control of the Y. enterocolitica switch between two pathogenicity phases towards mammalians and invertebrates [120]. In evolutionary terms, environmental temperature, but not 37degreesC, appears as the ancient signal for the expression of many genes involved in pathogenicity, confirming the idea that the biological function of many virulence factors has been evolved during the association of bacteria with poikilothermic organisms (see below).\n" ], "offsets": [ [ 0, 2629 ] ] } ]

[ { "id": "PMC2266911-02-Results_and_Discussion-04_T1", "type": "Organism", "text": [ "Yersinia" ], "offsets": [ [ 123, 131 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-04_T2", "type": "Organism", "text": [ "humans" ], "offsets": [ [ 263, 269 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-04_T3", "type": "Organism", "text": [ "Yersinia spp." ], "offsets": [ [ 478, 491 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-04_T4", "type": "Organism", "text": [ "P. luminescens" ], "offsets": [ [ 593, 607 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-04_T5", "type": "Protein", "text": [ "inv" ], "offsets": [ [ 886, 889 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-04_T6", "type": "Protein", "text": [ "yst" ], "offsets": [ [ 891, 894 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-04_T7", "type": "Protein", "text": [ "yplA" ], "offsets": [ [ 898, 902 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-04_T8", "type": "Organism", "text": [ "Y. enterocolitica" ], "offsets": [ [ 938, 955 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-04_T9", "type": "Organism", "text": [ "mice" ], "offsets": [ [ 959, 963 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-04_T10", "type": "Organism", "text": [ "Y. enterocolitica" ], "offsets": [ [ 1103, 1120 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-04_T11", "type": "Organism", "text": [ "Burkholderia" ], "offsets": [ [ 1340, 1352 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-04_T12", "type": "Organism", "text": [ "Pseudomonas" ], "offsets": [ [ 1354, 1365 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-04_T13", "type": "Organism", "text": [ "Serratia" ], "offsets": [ [ 1367, 1375 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-04_T14", "type": "Organism", "text": [ "Erwinia" ], "offsets": [ [ 1380, 1387 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-04_T15", "type": "Organism", "text": [ "Y. enterocolitica" ], "offsets": [ [ 1608, 1625 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-04_T16", "type": "Organism", "text": [ "flhDC mutant" ], "offsets": [ [ 1780, 1792 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-04_T17", "type": "Protein", "text": [ "flhD" ], "offsets": [ [ 1780, 1784 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-04_T18", "type": "Protein", "text": [ "C" ], "offsets": [ [ 1784, 1785 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-04_T19", "type": "Organism", "text": [ "Y. enterocolitica" ], "offsets": [ [ 1796, 1813 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-04_T20", "type": "Organism", "text": [ "X. nematophila" ], "offsets": [ [ 1975, 1989 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-04_T21", "type": "Organism", "text": [ "X. nematophila" ], "offsets": [ [ 2076, 2090 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-04_T22", "type": "Organism", "text": [ "Y. enterocolitica" ], "offsets": [ [ 2197, 2214 ] ], "normalized": [] } ]

[ { "id": "PMC2266911-02-Results_and_Discussion-04_E1", "type": "Process", "trigger": { "text": [ "virulence" ], "offsets": [ [ 654, 663 ] ] }, "arguments": [] }, { "id": "PMC2266911-02-Results_and_Discussion-04_E2", "type": "Positive_regulation", "trigger": { "text": [ "induced" ], "offsets": [ [ 849, 856 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC2266911-02-Results_and_Discussion-04_T5" } ] }, { "id": "PMC2266911-02-Results_and_Discussion-04_E3", "type": "Positive_regulation", "trigger": { "text": [ "induced" ], "offsets": [ [ 849, 856 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC2266911-02-Results_and_Discussion-04_T6" } ] }, { "id": "PMC2266911-02-Results_and_Discussion-04_E4", "type": "Positive_regulation", "trigger": { "text": [ "induced" ], "offsets": [ [ 849, 856 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC2266911-02-Results_and_Discussion-04_T7" } ] }, { "id": "PMC2266911-02-Results_and_Discussion-04_E5", "type": "Regulation", "trigger": { "text": [ "affect" ], "offsets": [ [ 903, 909 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC2266911-02-Results_and_Discussion-04_E8" }, { "role": "Cause", "ref_id": "PMC2266911-02-Results_and_Discussion-04_E2" } ] }, { "id": "PMC2266911-02-Results_and_Discussion-04_E6", "type": "Regulation", "trigger": { "text": [ "affect" ], "offsets": [ [ 903, 909 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC2266911-02-Results_and_Discussion-04_E8" }, { "role": "Cause", "ref_id": "PMC2266911-02-Results_and_Discussion-04_E3" } ] }, { "id": "PMC2266911-02-Results_and_Discussion-04_E7", "type": "Regulation", "trigger": { "text": [ "affect" ], "offsets": [ [ 903, 909 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC2266911-02-Results_and_Discussion-04_E8" }, { "role": "Cause", "ref_id": "PMC2266911-02-Results_and_Discussion-04_E4" } ] }, { "id": "PMC2266911-02-Results_and_Discussion-04_E8", "type": "Process", "trigger": { "text": [ "virulence" ], "offsets": [ [ 914, 923 ] ] }, "arguments": [ { "role": "Participant", "ref_id": "PMC2266911-02-Results_and_Discussion-04_T8" } ] }, { "id": "PMC2266911-02-Results_and_Discussion-04_E9", "type": "Process", "trigger": { "text": [ "virulence" ], "offsets": [ [ 1714, 1723 ] ] }, "arguments": [] }, { "id": "PMC2266911-02-Results_and_Discussion-04_E10", "type": "Process", "trigger": { "text": [ "virulence" ], "offsets": [ [ 2063, 2072 ] ] }, "arguments": [ { "role": "Participant", "ref_id": "PMC2266911-02-Results_and_Discussion-04_T21" } ] }, { "id": "PMC2266911-02-Results_and_Discussion-04_E11", "type": "Process", "trigger": { "text": [ "virulence" ], "offsets": [ [ 2516, 2525 ] ] }, "arguments": [] } ]

[]

[]

[ { "id": "PMC2774163-02-Results-06__text", "type": "abstract", "text": [ "Mutant biofilms display protein and phosphorylation patterns indicative of stage-specific arrest of biofilm development \nBased on qualitative and quantitative analyses, BfiS (PA4197) and BfmR (PA4101) mutant biofilm architecture appeared to be the result of arrested biofilm formation following initial attachment, while inactivation of MifR (PA5511) coincided with biofilms impaired in microcolony formation at the maturation-1 stage. Since each of these biofilm developmental stages is characterized by a unique phosphorylation pattern (Figs. 1, 4, Table 1), we reasoned that if the mutant biofilms are indeed arrested in biofilm development, their phosphoproteomes will correspond to the stage at which they are arrested. We, therefore, analyzed the phosphorylation patterns of DeltabfiS, DeltabfmR, and DeltamifR biofilms grown for 144 hr in comparison to P. aeruginosa wild type biofilms grown for 8, 24, 72, and 144 hr. The phosphoproteomes were analyzed using two approaches, (i) immunoblot analysis of whole biofilm cell extracts and (ii) LC-MS/MS analysis in conjunction with cICAT labeling following MOAC purification. The phosphoproteome of DeltabfiS biofilms as determined by LC-MS/MS was 74% similar (26% difference) to planktonic cells while DeltabfmR biofilms shared 60% of all detected phosphorylation events with planktonic cells (40% difference). This is in contrast to the phosphoproteome of 144-hr-old P. aeruginosa wild type biofilms, which was 62-65% different from that of planktonic cells (Fig. 4A). Furthermore, both mutant biofilms failed to exhibit phosphorylation events typically observed during normal biofilm development following 144 hr of growth (see Fig. 1, Suppl. Table S2). For instance, DeltabfiS and DeltabfmR biofilms lacked all phosphorylated proteins typically found in mature, 144-hr-old biofilms. In addition, both mutant biofilms lacked evidence for MifR phosphorylation (phosphorylated following 72 hr of wild type growth, Table 1, Suppl. Fig. S3). Instead, DeltabfiS biofilms exhibited stage-specific phosphorylation events typically detected in 8-hr- and 24-hr-old wild type biofilms: the Ser/Thr phosphoproteome contained 15 out of 23 phosphorylated proteins and 2 out of 21 phosphorylated proteins that are specific for 8-hr- and 24-hr-old wild type biofilms, respectively (see Fig. 1, Suppl. Table S2). Similarly, the phosphorylation patterns of DeltabfmR biofilms indicated the presence of 24- and 72-hr stage-specific phosphorylated proteins (not shown). The phosphorylation patterns of 144-hr-old DeltamifR biofilms were 62% different relative to planktonic cells, but only shared 58% similarity with mature, 144-hr-old wild type biofilms (Fig. 4A). Furthermore, DeltamifR biofilms exhibited 8 out of 27 maturation-1 specific protein phosphorylation events, and only 16 out of 37 maturation-2 phosphorylation events (Suppl. Table S2, see Fig. 1). We further reasoned that if the mutant biofilms are indeed arrested in biofilm development, their whole proteomes will also correspond to the stage at which they are arrested. We therefore compared the protein production patterns of 144-hr-old DeltabfiS, DeltabfmR, and DeltamifR biofilms to the 2D-patterns of P. aeruginosa wild type biofilms grown for 24, 72 and 144 hr using 2D/PAGE, 2D ImageMaster Platinum software and heuristic clustering. As shown in Fig. 4B, cluster analysis based on protein similarity confirmed our previous findings obtained by microscopic and phosphoproteome analyses of mutant biofilms. DeltabfiS biofilms were more similar to 24-hr-old wild type biofilms than to wild type biofilms at more mature stages. The two protein patterns were more than 80% similar. In contrast, DeltabfmR biofilms were most similar to protein patterns obtained from 72-hr-old wild type biofilms (85% similarity), while those of DeltamifR biofilms were similar to both 72- and 144-hr-old biofilms sharing 76 and 82% similarity, respectively, to both protein patterns (Fig. 4B). Based on analyses of biofilm architecture, as well as of protein production and phosphorylation patterns, our findings indicate that DeltabfiS biofilms are arrested in the transition from reversible to the irreversible attachment stage (8 hr to 24-hr-old biofilms, respectively). Inactivation of MifR appeared to result in the arrest of biofilm development in the transition between the maturation-1 and -2 stages (72 to 144 hr) while DeltabfmR biofilms were arrested in the transition between irreversible attachment to maturation-1 stage.\n" ], "offsets": [ [ 0, 4525 ] ] } ]

[ { "id": "PMC2774163-02-Results-06_T1", "type": "Protein", "text": [ "BfiS" ], "offsets": [ [ 169, 173 ] ], "normalized": [] }, { "id": "PMC2774163-02-Results-06_T2", "type": "Protein", "text": [ "PA4197" ], "offsets": [ [ 175, 181 ] ], "normalized": [] }, { "id": "PMC2774163-02-Results-06_T3", "type": "Protein", "text": [ "BfmR" ], "offsets": [ [ 187, 191 ] ], "normalized": [] }, { "id": "PMC2774163-02-Results-06_T4", "type": "Protein", "text": [ "PA4101" ], "offsets": [ [ 193, 199 ] ], "normalized": [] }, { "id": "PMC2774163-02-Results-06_T5", "type": "Protein", "text": [ "MifR" ], "offsets": [ [ 337, 341 ] ], "normalized": [] }, { "id": "PMC2774163-02-Results-06_T6", "type": "Protein", "text": [ "PA5511" ], "offsets": [ [ 343, 349 ] ], "normalized": [] }, { "id": "PMC2774163-02-Results-06_T7", "type": "Organism", "text": [ "DeltabfiS" ], "offsets": [ [ 781, 790 ] ], "normalized": [] }, { "id": "PMC2774163-02-Results-06_T8", "type": "Protein", "text": [ "bfiS" ], "offsets": [ [ 786, 790 ] ], "normalized": [] }, { "id": "PMC2774163-02-Results-06_T9", "type": "Organism", "text": [ "DeltabfmR" ], "offsets": [ [ 792, 801 ] ], "normalized": [] }, { "id": "PMC2774163-02-Results-06_T10", "type": "Protein", "text": [ "bfmR" ], "offsets": [ [ 797, 801 ] ], "normalized": [] }, { "id": "PMC2774163-02-Results-06_T11", "type": "Organism", "text": [ "DeltamifR" ], "offsets": [ [ 807, 816 ] ], "normalized": [] }, { "id": "PMC2774163-02-Results-06_T12", "type": "Protein", "text": [ "mifR" ], "offsets": [ [ 812, 816 ] ], "normalized": [] }, { "id": "PMC2774163-02-Results-06_T13", "type": "Organism", "text": [ "P. aeruginosa" ], "offsets": [ [ 860, 873 ] ], "normalized": [] }, { "id": "PMC2774163-02-Results-06_T14", "type": "Organism", "text": [ "DeltabfiS" ], "offsets": [ [ 1152, 1161 ] ], "normalized": [] }, { "id": "PMC2774163-02-Results-06_T15", "type": "Protein", "text": [ "bfiS" ], "offsets": [ [ 1157, 1161 ] ], "normalized": [] }, { "id": "PMC2774163-02-Results-06_T16", "type": "Organism", "text": [ "DeltabfmR" ], "offsets": [ [ 1256, 1265 ] ], "normalized": [] }, { "id": "PMC2774163-02-Results-06_T17", "type": "Protein", "text": [ "bfmR" ], "offsets": [ [ 1261, 1265 ] ], "normalized": [] }, { "id": "PMC2774163-02-Results-06_T18", "type": "Organism", "text": [ "P. aeruginosa" ], "offsets": [ [ 1422, 1435 ] ], "normalized": [] }, { "id": "PMC2774163-02-Results-06_T19", "type": "Organism", "text": [ "DeltabfiS" ], "offsets": [ [ 1724, 1733 ] ], "normalized": [] }, { "id": "PMC2774163-02-Results-06_T20", "type": "Protein", "text": [ "bfiS" ], "offsets": [ [ 1729, 1733 ] ], "normalized": [] }, { "id": "PMC2774163-02-Results-06_T21", "type": "Organism", "text": [ "DeltabfmR" ], "offsets": [ [ 1738, 1747 ] ], "normalized": [] }, { "id": "PMC2774163-02-Results-06_T22", "type": "Protein", "text": [ "bfmR" ], "offsets": [ [ 1743, 1747 ] ], "normalized": [] }, { "id": "PMC2774163-02-Results-06_T23", "type": "Protein", "text": [ "MifR" ], "offsets": [ [ 1894, 1898 ] ], "normalized": [] }, { "id": "PMC2774163-02-Results-06_T24", "type": "Organism", "text": [ "DeltabfiS" ], "offsets": [ [ 2003, 2012 ] ], "normalized": [] }, { "id": "PMC2774163-02-Results-06_T25", "type": "Protein", "text": [ "bfiS" ], "offsets": [ [ 2008, 2012 ] ], "normalized": [] }, { "id": "PMC2774163-02-Results-06_T26", "type": "Organism", "text": [ "DeltabfmR" ], "offsets": [ [ 2396, 2405 ] ], "normalized": [] }, { "id": "PMC2774163-02-Results-06_T27", "type": "Protein", "text": [ "bfmR" ], "offsets": [ [ 2401, 2405 ] ], "normalized": [] }, { "id": "PMC2774163-02-Results-06_T28", "type": "Organism", "text": [ "DeltamifR" ], "offsets": [ [ 2550, 2559 ] ], "normalized": [] }, { "id": "PMC2774163-02-Results-06_T29", "type": "Protein", "text": [ "mifR" ], "offsets": [ [ 2555, 2559 ] ], "normalized": [] }, { "id": "PMC2774163-02-Results-06_T30", "type": "Organism", "text": [ "DeltamifR" ], "offsets": [ [ 2716, 2725 ] ], "normalized": [] }, { "id": "PMC2774163-02-Results-06_T31", "type": "Protein", "text": [ "mifR" ], "offsets": [ [ 2721, 2725 ] ], "normalized": [] }, { "id": "PMC2774163-02-Results-06_T32", "type": "Organism", "text": [ "DeltabfiS" ], "offsets": [ [ 3144, 3153 ] ], "normalized": [] }, { "id": "PMC2774163-02-Results-06_T33", "type": "Protein", "text": [ "bfiS" ], "offsets": [ [ 3149, 3153 ] ], "normalized": [] }, { "id": "PMC2774163-02-Results-06_T34", "type": "Organism", "text": [ "DeltabfmR" ], "offsets": [ [ 3155, 3164 ] ], "normalized": [] }, { "id": "PMC2774163-02-Results-06_T35", "type": "Protein", "text": [ "bfmR" ], "offsets": [ [ 3160, 3164 ] ], "normalized": [] }, { "id": "PMC2774163-02-Results-06_T36", "type": "Organism", "text": [ "DeltamifR" ], "offsets": [ [ 3170, 3179 ] ], "normalized": [] }, { "id": "PMC2774163-02-Results-06_T37", "type": "Protein", "text": [ "mifR" ], "offsets": [ [ 3175, 3179 ] ], "normalized": [] }, { "id": "PMC2774163-02-Results-06_T38", "type": "Organism", "text": [ "P. aeruginosa" ], "offsets": [ [ 3211, 3224 ] ], "normalized": [] }, { "id": "PMC2774163-02-Results-06_T39", "type": "Organism", "text": [ "DeltabfiS" ], "offsets": [ [ 3517, 3526 ] ], "normalized": [] }, { "id": "PMC2774163-02-Results-06_T40", "type": "Protein", "text": [ "bfiS" ], "offsets": [ [ 3522, 3526 ] ], "normalized": [] }, { "id": "PMC2774163-02-Results-06_T41", "type": "Organism", "text": [ "DeltabfmR" ], "offsets": [ [ 3702, 3711 ] ], "normalized": [] }, { "id": "PMC2774163-02-Results-06_T42", "type": "Protein", "text": [ "bfmR" ], "offsets": [ [ 3707, 3711 ] ], "normalized": [] }, { "id": "PMC2774163-02-Results-06_T43", "type": "Organism", "text": [ "DeltamifR" ], "offsets": [ [ 3835, 3844 ] ], "normalized": [] }, { "id": "PMC2774163-02-Results-06_T44", "type": "Protein", "text": [ "mifR" ], "offsets": [ [ 3840, 3844 ] ], "normalized": [] }, { "id": "PMC2774163-02-Results-06_T45", "type": "Organism", "text": [ "DeltabfiS" ], "offsets": [ [ 4117, 4126 ] ], "normalized": [] }, { "id": "PMC2774163-02-Results-06_T46", "type": "Protein", "text": [ "bfiS" ], "offsets": [ [ 4122, 4126 ] ], "normalized": [] }, { "id": "PMC2774163-02-Results-06_T47", "type": "Protein", "text": [ "MifR" ], "offsets": [ [ 4280, 4284 ] ], "normalized": [] }, { "id": "PMC2774163-02-Results-06_T48", "type": "Organism", "text": [ "DeltabfmR" ], "offsets": [ [ 4419, 4428 ] ], "normalized": [] }, { "id": "PMC2774163-02-Results-06_T49", "type": "Protein", "text": [ "bfmR" ], "offsets": [ [ 4424, 4428 ] ], "normalized": [] } ]

[ { "id": "PMC2774163-02-Results-06_E1", "type": "Negative_regulation", "trigger": { "text": [ "inactivation" ], "offsets": [ [ 321, 333 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC2774163-02-Results-06_T5" } ] }, { "id": "PMC2774163-02-Results-06_E2", "type": "Phosphorylation", "trigger": { "text": [ "phosphorylation" ], "offsets": [ [ 1899, 1914 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC2774163-02-Results-06_T23" } ] }, { "id": "PMC2774163-02-Results-06_E3", "type": "Phosphorylation", "trigger": { "text": [ "phosphorylated" ], "offsets": [ [ 1916, 1930 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC2774163-02-Results-06_T23" } ] }, { "id": "PMC2774163-02-Results-06_E4", "type": "Negative_regulation", "trigger": { "text": [ "Inactivation" ], "offsets": [ [ 4264, 4276 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC2774163-02-Results-06_T47" } ] } ]

[ { "id": "PMC2774163-02-Results-06_1", "entity_ids": [ "PMC2774163-02-Results-06_T1", "PMC2774163-02-Results-06_T2" ] }, { "id": "PMC2774163-02-Results-06_2", "entity_ids": [ "PMC2774163-02-Results-06_T3", "PMC2774163-02-Results-06_T4" ] }, { "id": "PMC2774163-02-Results-06_3", "entity_ids": [ "PMC2774163-02-Results-06_T5", "PMC2774163-02-Results-06_T6" ] } ]

[]

[ { "id": "PMC2816692-02-Results-02__text", "type": "abstract", "text": [ "SrcA contributes to Salmonella fitness in an animal host \nMost SsrB-regulated gene products contribute to the intracellular survival of Salmonella in a host. In comparative genomics analyses, srcA was found in all virulent strains of Salmonella enterica containing SPI-2, but was absent from the cold-blooded animal commensal, S. bongori, which lacks SPI-2 (Table S1). This suggested a co-evolution of srcA with the SPI-2 T3SS and a possible functional relationship. If so, we reasoned that SrcA should contribute to animal colonization because the SPI-2 T3SS is essential for host infection. To determine whether SrcA contributes to Salmonella fitness in a host, we created an unmarked in-frame srcA deletion in S. Typhimurium and competed this strain against wild type cells in mixed oral infections of mice [25]. After three days of infection the geometric mean competitive index (CI) for the mutant was 0.20 (95%CI 0.13-0.29) and 0.18 (95%CI 0.06-0.5) in the spleen and liver respectively (P<0.0001; Fig. 1D) indicating that bacteria lacking srcA were significantly out competed by wild type cells during systemic infection. To verify the role of srcA on this phenotype, we complemented the srcA mutant with a wild type srcA gene under the control of its endogenous promoter, which restored in vivo fitness to that of wild type (Fig. 1D). The level of attenuation of the srcA mutant was generally higher than most single effector gene mutants [26], which suggested to us that SrcA contributes to an important aspect of T3SS function in vivo.\n" ], "offsets": [ [ 0, 1546 ] ] } ]

[ { "id": "PMC2816692-02-Results-02_T1", "type": "Protein", "text": [ "SrcA" ], "offsets": [ [ 0, 4 ] ], "normalized": [] }, { "id": "PMC2816692-02-Results-02_T2", "type": "Organism", "text": [ "Salmonella" ], "offsets": [ [ 20, 30 ] ], "normalized": [] }, { "id": "PMC2816692-02-Results-02_T3", "type": "Organism", "text": [ "host" ], "offsets": [ [ 52, 56 ] ], "normalized": [] }, { "id": "PMC2816692-02-Results-02_T4", "type": "Protein", "text": [ "SsrB" ], "offsets": [ [ 63, 67 ] ], "normalized": [] }, { "id": "PMC2816692-02-Results-02_T5", "type": "Organism", "text": [ "Salmonella" ], "offsets": [ [ 136, 146 ] ], "normalized": [] }, { "id": "PMC2816692-02-Results-02_T6", "type": "Organism", "text": [ "host" ], "offsets": [ [ 152, 156 ] ], "normalized": [] }, { "id": "PMC2816692-02-Results-02_T7", "type": "Protein", "text": [ "srcA" ], "offsets": [ [ 192, 196 ] ], "normalized": [] }, { "id": "PMC2816692-02-Results-02_T8", "type": "Organism", "text": [ "Salmonella enterica" ], "offsets": [ [ 234, 253 ] ], "normalized": [] }, { "id": "PMC2816692-02-Results-02_T9", "type": "Organism", "text": [ "S. bongori" ], "offsets": [ [ 327, 337 ] ], "normalized": [] }, { "id": "PMC2816692-02-Results-02_T10", "type": "Protein", "text": [ "srcA" ], "offsets": [ [ 402, 406 ] ], "normalized": [] }, { "id": "PMC2816692-02-Results-02_T11", "type": "Protein", "text": [ "SrcA" ], "offsets": [ [ 491, 495 ] ], "normalized": [] }, { "id": "PMC2816692-02-Results-02_T12", "type": "Organism", "text": [ "host" ], "offsets": [ [ 577, 581 ] ], "normalized": [] }, { "id": "PMC2816692-02-Results-02_T13", "type": "Protein", "text": [ "SrcA" ], "offsets": [ [ 614, 618 ] ], "normalized": [] }, { "id": "PMC2816692-02-Results-02_T14", "type": "Organism", "text": [ "Salmonella" ], "offsets": [ [ 634, 644 ] ], "normalized": [] }, { "id": "PMC2816692-02-Results-02_T15", "type": "Organism", "text": [ "host" ], "offsets": [ [ 658, 662 ] ], "normalized": [] }, { "id": "PMC2816692-02-Results-02_T16", "type": "Protein", "text": [ "srcA" ], "offsets": [ [ 696, 700 ] ], "normalized": [] }, { "id": "PMC2816692-02-Results-02_T17", "type": "Organism", "text": [ "S. Typhimurium" ], "offsets": [ [ 713, 727 ] ], "normalized": [] }, { "id": "PMC2816692-02-Results-02_T18", "type": "Organism", "text": [ "mice" ], "offsets": [ [ 805, 809 ] ], "normalized": [] }, { "id": "PMC2816692-02-Results-02_T19", "type": "Protein", "text": [ "srcA" ], "offsets": [ [ 1046, 1050 ] ], "normalized": [] }, { "id": "PMC2816692-02-Results-02_T20", "type": "Protein", "text": [ "srcA" ], "offsets": [ [ 1151, 1155 ] ], "normalized": [] }, { "id": "PMC2816692-02-Results-02_T21", "type": "Organism", "text": [ "srcA mutant" ], "offsets": [ [ 1195, 1206 ] ], "normalized": [] }, { "id": "PMC2816692-02-Results-02_T22", "type": "Protein", "text": [ "srcA" ], "offsets": [ [ 1195, 1199 ] ], "normalized": [] }, { "id": "PMC2816692-02-Results-02_T23", "type": "Protein", "text": [ "srcA" ], "offsets": [ [ 1224, 1228 ] ], "normalized": [] }, { "id": "PMC2816692-02-Results-02_T24", "type": "Organism", "text": [ "srcA mutant" ], "offsets": [ [ 1375, 1386 ] ], "normalized": [] }, { "id": "PMC2816692-02-Results-02_T25", "type": "Protein", "text": [ "srcA" ], "offsets": [ [ 1375, 1379 ] ], "normalized": [] }, { "id": "PMC2816692-02-Results-02_T26", "type": "Protein", "text": [ "SrcA" ], "offsets": [ [ 1480, 1484 ] ], "normalized": [] } ]

[ { "id": "PMC2816692-02-Results-02_E1", "type": "Process", "trigger": { "text": [ "virulent" ], "offsets": [ [ 214, 222 ] ] }, "arguments": [ { "role": "Participant", "ref_id": "PMC2816692-02-Results-02_T8" } ] }, { "id": "PMC2816692-02-Results-02_E2", "type": "Process", "trigger": { "text": [ "infection" ], "offsets": [ [ 582, 591 ] ] }, "arguments": [] }, { "id": "PMC2816692-02-Results-02_E3", "type": "Process", "trigger": { "text": [ "infections" ], "offsets": [ [ 791, 801 ] ] }, "arguments": [ { "role": "Participant", "ref_id": "PMC2816692-02-Results-02_T17" } ] }, { "id": "PMC2816692-02-Results-02_E4", "type": "Process", "trigger": { "text": [ "infection" ], "offsets": [ [ 836, 845 ] ] }, "arguments": [] }, { "id": "PMC2816692-02-Results-02_E5", "type": "Process", "trigger": { "text": [ "infection" ], "offsets": [ [ 1118, 1127 ] ] }, "arguments": [] }, { "id": "PMC2816692-02-Results-02_E6", "type": "Process", "trigger": { "text": [ "attenuation" ], "offsets": [ [ 1356, 1367 ] ] }, "arguments": [ { "role": "Participant", "ref_id": "PMC2816692-02-Results-02_T24" } ] } ]

[]

[]

[ { "id": "PMC2639726-02-Results-01__text", "type": "abstract", "text": [ "Results \nSalmonella regulators required for systemic mouse infection Typhimurium encodes a surfeit of regulators (more than 330 based on annotation cited in NCBI) presumably because it can survive and replicate in many different environments, cause infection in diverse hosts, and can use multiple carbon sources and terminal electron acceptors. We focused on 83 regulators presumed to play roles in virulence, based on published data including negative selection experiments [13], [21]-[23]. We constructed non-polar in-frame deletions in which each regulator gene was replaced with a \"scar\" sequence using bacteriophage lambda-mediated recombination [24],[25]. The list of 83 regulator genes is provided in Supporting Information (Table S1). For the two-component regulator ssrA/ssrB we constructed in-frame deletions missing ssrA, ssrB or both; for the other two two-component regulators, phoP/phoQ and ompR/envZ, both the signal sensor and response regulator were deleted. As an initial screen two 4-6 weeks-old BALB/c mice were infected intraperitoneally (i.p.) with 200 colony forming units (CFU) of each deleted strain (about 100x the LD50). Mutations that resulted in either no deaths, one death, or delayed death of infected mice were retested with groups of 5 mice at the same dose (Figure 1A). Based on this preliminary screen we chose the regulators spvR, fruR, himD, phoP/phoQ, ssrA/ssrB, slyA, hnr, rpoE, smpB, csrA, rpoS, crp, ompR/envZ, and hfq for further investigation (see Figure 1 and Table 1 for references and descriptions; a complete list of virulence phenotypes is provided in Table S1). It is possible that additional regulators would be identified if a larger group of mice were used in the initial screen. The LD50 for each of the mutants was computed as shown in Figure 1B. Compared to the parental strain (ATCC14028), which has an LD50 of 1-2 cfu, all of the derivatives were attenuated for virulence. The 14 deletion strains lacking regulators reported in this study were selected from i.p. BALB/c mice infection to eliminate other regulators required only for gastrointestinal infection or persistence but most of these strains were avirulent in another strain of mice (129X1/SvJ) and by other route (intragastric) of infection (see Table S1). Therefore the regulators investigated in this study might be considered the most central regulators for virulence. In the other virulence assays, the 83 derivatives were tested for virulence by intragastric (i.g.) BALB/c infection and by a more sensitive competitive index (CI) experiment. In the competitive index experiment all mutants were co-administered to 129X1/SvJ mice and the number of each surviving mutant bacteria was determined 7 days after i.p. inoculation. BALB/c mice are missing natural resistance-associated macrophage protein (Nramp1) and thus succumb to Typhimurium infection within a week when mice are infected i.p. with less than 10 bacteria of the strain employed here (14028). Unlike BALB/c, 129X1/SvJ mice have a functional copy of Nramp1 and the bacteria persist for several weeks without killing the mouse [13],[26]. The CI test identified 30 (out of 83) regulator mutants that were attenuated in comparison to the wild type control (see Table S1). The 14 derivatives chosen for this study were among those showing the poorest survival by comparison to the parent in this competitive index experiment. The 14 regulators identified were diverse and included alternative sigma factors (rpoS and rpoE), two-component regulators (ompR/envZ, phoP/phoQ, and ssrA/ssrB), a response regulator for which the signal sensor is unknown (hnr or mviA), post-transcriptional regulators (csrA, hfq and smpB), a bending protein essential for some types of recombination (ihf) and an assortment of other DNA binding proteins (fruR, spvR, crp, and slyA). Transcription profiling was carried out for isogenic deletion mutants in each of these 14 genes under four different conditions and analyzed to infer a regulatory hierarchy during systemic infection. Salmonella transcription profiles for the following regulators have already been reported: rpoE [27]; phoP/phoQ [28]; ssrA/ssrB [29]; csrA [30]; slyA [31]; ihf [32]; hfq [33]. Our results closely match these published results. The large degree of attenuation we observed for an spvR mutation following i.p. infection was surprising, as most studies had limited its effect to the i.g. route of infection. To validate this result we complemented the spvR mutation in trans and found complete complementation in mouse virulence (Figure S1). The differences between our results and others are most likely related to the different strains of Salmonella used in the studies [34]. For the other mutations we have mobilized the mutation into a new genetic background by P22 transduction to ensure that there is no secondary mutation that influences the results [35].\n" ], "offsets": [ [ 0, 4898 ] ] } ]

[ { "id": "PMC2639726-02-Results-01_T1", "type": "Organism", "text": [ "Salmonella" ], "offsets": [ [ 9, 19 ] ], "normalized": [] }, { "id": "PMC2639726-02-Results-01_T2", "type": "Organism", "text": [ "mouse" ], "offsets": [ [ 53, 58 ] ], "normalized": [] }, { "id": "PMC2639726-02-Results-01_T3", "type": "Organism", "text": [ "Typhimurium" ], "offsets": [ [ 69, 80 ] ], "normalized": [] }, { "id": "PMC2639726-02-Results-01_T4", "type": "Chemical", "text": [ "carbon" ], "offsets": [ [ 298, 304 ] ], "normalized": [] }, { "id": "PMC2639726-02-Results-01_T5", "type": "Organism", "text": [ "bacteriophage lambda" ], "offsets": [ [ 608, 628 ] ], "normalized": [] }, { "id": "PMC2639726-02-Results-01_T6", "type": "Two-component-system", "text": [ "ssrA/ssrB" ], "offsets": [ [ 776, 785 ] ], "normalized": [] }, { "id": "PMC2639726-02-Results-01_T7", "type": "Protein", "text": [ "ssrA" ], "offsets": [ [ 776, 780 ] ], "normalized": [] }, { "id": "PMC2639726-02-Results-01_T8", "type": "Protein", "text": [ "ssrB" ], "offsets": [ [ 781, 785 ] ], "normalized": [] }, { "id": "PMC2639726-02-Results-01_T9", "type": "Protein", "text": [ "ssrA" ], "offsets": [ [ 828, 832 ] ], "normalized": [] }, { "id": "PMC2639726-02-Results-01_T10", "type": "Protein", "text": [ "ssrB" ], "offsets": [ [ 834, 838 ] ], "normalized": [] }, { "id": "PMC2639726-02-Results-01_T11", "type": "Two-component-system", "text": [ "phoP/phoQ" ], "offsets": [ [ 892, 901 ] ], "normalized": [] }, { "id": "PMC2639726-02-Results-01_T12", "type": "Protein", "text": [ "phoP" ], "offsets": [ [ 892, 896 ] ], "normalized": [] }, { "id": "PMC2639726-02-Results-01_T13", "type": "Protein", "text": [ "phoQ" ], "offsets": [ [ 897, 901 ] ], "normalized": [] }, { "id": "PMC2639726-02-Results-01_T14", "type": "Two-component-system", "text": [ "ompR/envZ" ], "offsets": [ [ 906, 915 ] ], "normalized": [] }, { "id": "PMC2639726-02-Results-01_T15", "type": "Protein", "text": [ "ompR" ], "offsets": [ [ 906, 910 ] ], "normalized": [] }, { "id": "PMC2639726-02-Results-01_T16", "type": "Protein", "text": [ "envZ" ], "offsets": [ [ 911, 915 ] ], "normalized": [] }, { "id": "PMC2639726-02-Results-01_T17", "type": "Organism", "text": [ "BALB/c mice" ], "offsets": [ [ 1016, 1027 ] ], "normalized": [] }, { "id": "PMC2639726-02-Results-01_T18", "type": "Organism", "text": [ "mice" ], "offsets": [ [ 1234, 1238 ] ], "normalized": [] }, { "id": "PMC2639726-02-Results-01_T19", "type": "Organism", "text": [ "mice" ], "offsets": [ [ 1270, 1274 ] ], "normalized": [] }, { "id": "PMC2639726-02-Results-01_T20", "type": "Protein", "text": [ "spvR" ], "offsets": [ [ 1362, 1366 ] ], "normalized": [] }, { "id": "PMC2639726-02-Results-01_T21", "type": "Protein", "text": [ "fruR" ], "offsets": [ [ 1368, 1372 ] ], "normalized": [] }, { "id": "PMC2639726-02-Results-01_T22", "type": "Protein", "text": [ "himD" ], "offsets": [ [ 1374, 1378 ] ], "normalized": [] }, { "id": "PMC2639726-02-Results-01_T23", "type": "Two-component-system", "text": [ "phoP/phoQ" ], "offsets": [ [ 1380, 1389 ] ], "normalized": [] }, { "id": "PMC2639726-02-Results-01_T24", "type": "Protein", "text": [ "phoP" ], "offsets": [ [ 1380, 1384 ] ], "normalized": [] }, { "id": "PMC2639726-02-Results-01_T25", "type": "Protein", "text": [ "phoQ" ], "offsets": [ [ 1385, 1389 ] ], "normalized": [] }, { "id": "PMC2639726-02-Results-01_T26", "type": "Two-component-system", "text": [ "ssrA/ssrB" ], "offsets": [ [ 1391, 1400 ] ], "normalized": [] }, { "id": "PMC2639726-02-Results-01_T27", "type": "Protein", "text": [ "ssrA" ], "offsets": [ [ 1391, 1395 ] ], "normalized": [] }, { "id": "PMC2639726-02-Results-01_T28", "type": "Protein", "text": [ "ssrB" ], "offsets": [ [ 1396, 1400 ] ], "normalized": [] }, { "id": "PMC2639726-02-Results-01_T29", "type": "Protein", "text": [ "slyA" ], "offsets": [ [ 1402, 1406 ] ], "normalized": [] }, { "id": "PMC2639726-02-Results-01_T30", "type": "Protein", "text": [ "hnr" ], "offsets": [ [ 1408, 1411 ] ], "normalized": [] }, { "id": "PMC2639726-02-Results-01_T31", "type": "Protein", "text": [ "rpoE" ], "offsets": [ [ 1413, 1417 ] ], "normalized": [] }, { "id": "PMC2639726-02-Results-01_T32", "type": "Protein", "text": [ "smpB" ], "offsets": [ [ 1419, 1423 ] ], "normalized": [] }, { "id": "PMC2639726-02-Results-01_T33", "type": "Protein", "text": [ "csrA" ], "offsets": [ [ 1425, 1429 ] ], "normalized": [] }, { "id": "PMC2639726-02-Results-01_T34", "type": "Protein", "text": [ "rpoS" ], "offsets": [ [ 1431, 1435 ] ], "normalized": [] }, { "id": "PMC2639726-02-Results-01_T35", "type": "Protein", "text": [ "crp" ], "offsets": [ [ 1437, 1440 ] ], "normalized": [] }, { "id": "PMC2639726-02-Results-01_T36", "type": "Two-component-system", "text": [ "ompR/envZ" ], "offsets": [ [ 1442, 1451 ] ], "normalized": [] }, { "id": "PMC2639726-02-Results-01_T37", "type": "Protein", "text": [ "ompR" ], "offsets": [ [ 1442, 1446 ] ], "normalized": [] }, { "id": "PMC2639726-02-Results-01_T38", "type": "Protein", "text": [ "envZ" ], "offsets": [ [ 1447, 1451 ] ], "normalized": [] }, { "id": "PMC2639726-02-Results-01_T39", "type": "Protein", "text": [ "hfq" ], "offsets": [ [ 1457, 1460 ] ], "normalized": [] }, { "id": "PMC2639726-02-Results-01_T40", "type": "Organism", "text": [ "mice" ], "offsets": [ [ 1695, 1699 ] ], "normalized": [] }, { "id": "PMC2639726-02-Results-01_T41", "type": "Organism", "text": [ "ATCC14028" ], "offsets": [ [ 1835, 1844 ] ], "normalized": [] }, { "id": "PMC2639726-02-Results-01_T42", "type": "Organism", "text": [ "BALB/c mice" ], "offsets": [ [ 2021, 2032 ] ], "normalized": [] }, { "id": "PMC2639726-02-Results-01_T43", "type": "Organism", "text": [ "mice" ], "offsets": [ [ 2195, 2199 ] ], "normalized": [] }, { "id": "PMC2639726-02-Results-01_T44", "type": "Organism", "text": [ "129X1/SvJ" ], "offsets": [ [ 2201, 2210 ] ], "normalized": [] }, { "id": "PMC2639726-02-Results-01_T45", "type": "Organism", "text": [ "BALB/c" ], "offsets": [ [ 2489, 2495 ] ], "normalized": [] }, { "id": "PMC2639726-02-Results-01_T46", "type": "Organism", "text": [ "129X1/SvJ mice" ], "offsets": [ [ 2637, 2651 ] ], "normalized": [] }, { "id": "PMC2639726-02-Results-01_T47", "type": "Organism", "text": [ "BALB/c mice" ], "offsets": [ [ 2747, 2758 ] ], "normalized": [] }, { "id": "PMC2639726-02-Results-01_T48", "type": "Protein", "text": [ "Nramp1" ], "offsets": [ [ 2821, 2827 ] ], "normalized": [] }, { "id": "PMC2639726-02-Results-01_T49", "type": "Organism", "text": [ "Typhimurium" ], "offsets": [ [ 2849, 2860 ] ], "normalized": [] }, { "id": "PMC2639726-02-Results-01_T50", "type": "Organism", "text": [ "mice" ], "offsets": [ [ 2890, 2894 ] ], "normalized": [] }, { "id": "PMC2639726-02-Results-01_T51", "type": "Organism", "text": [ "BALB/c" ], "offsets": [ [ 2984, 2990 ] ], "normalized": [] }, { "id": "PMC2639726-02-Results-01_T52", "type": "Organism", "text": [ "129X1/SvJ mice" ], "offsets": [ [ 2992, 3006 ] ], "normalized": [] }, { "id": "PMC2639726-02-Results-01_T53", "type": "Protein", "text": [ "Nramp1" ], "offsets": [ [ 3033, 3039 ] ], "normalized": [] }, { "id": "PMC2639726-02-Results-01_T54", "type": "Organism", "text": [ "mouse" ], "offsets": [ [ 3103, 3108 ] ], "normalized": [] }, { "id": "PMC2639726-02-Results-01_T55", "type": "Protein", "text": [ "rpoS" ], "offsets": [ [ 3487, 3491 ] ], "normalized": [] }, { "id": "PMC2639726-02-Results-01_T56", "type": "Protein", "text": [ "rpoE" ], "offsets": [ [ 3496, 3500 ] ], "normalized": [] }, { "id": "PMC2639726-02-Results-01_T57", "type": "Two-component-system", "text": [ "ompR/envZ" ], "offsets": [ [ 3529, 3538 ] ], "normalized": [] }, { "id": "PMC2639726-02-Results-01_T58", "type": "Protein", "text": [ "ompR" ], "offsets": [ [ 3529, 3533 ] ], "normalized": [] }, { "id": "PMC2639726-02-Results-01_T59", "type": "Protein", "text": [ "envZ" ], "offsets": [ [ 3534, 3538 ] ], "normalized": [] }, { "id": "PMC2639726-02-Results-01_T60", "type": "Two-component-system", "text": [ "phoP/phoQ" ], "offsets": [ [ 3540, 3549 ] ], "normalized": [] }, { "id": "PMC2639726-02-Results-01_T61", "type": "Protein", "text": [ "phoP" ], "offsets": [ [ 3540, 3544 ] ], "normalized": [] }, { "id": "PMC2639726-02-Results-01_T62", "type": "Protein", "text": [ "phoQ" ], "offsets": [ [ 3545, 3549 ] ], "normalized": [] }, { "id": "PMC2639726-02-Results-01_T63", "type": "Two-component-system", "text": [ "ssrA/ssrB" ], "offsets": [ [ 3555, 3564 ] ], "normalized": [] }, { "id": "PMC2639726-02-Results-01_T64", "type": "Protein", "text": [ "ssrA" ], "offsets": [ [ 3555, 3559 ] ], "normalized": [] }, { "id": "PMC2639726-02-Results-01_T65", "type": "Protein", "text": [ "ssrB" ], "offsets": [ [ 3560, 3564 ] ], "normalized": [] }, { "id": "PMC2639726-02-Results-01_T66", "type": "Protein", "text": [ "hnr" ], "offsets": [ [ 3628, 3631 ] ], "normalized": [] }, { "id": "PMC2639726-02-Results-01_T67", "type": "Protein", "text": [ "mviA" ], "offsets": [ [ 3635, 3639 ] ], "normalized": [] }, { "id": "PMC2639726-02-Results-01_T68", "type": "Protein", "text": [ "csrA" ], "offsets": [ [ 3675, 3679 ] ], "normalized": [] }, { "id": "PMC2639726-02-Results-01_T69", "type": "Protein", "text": [ "hfq" ], "offsets": [ [ 3681, 3684 ] ], "normalized": [] }, { "id": "PMC2639726-02-Results-01_T70", "type": "Protein", "text": [ "smpB" ], "offsets": [ [ 3689, 3693 ] ], "normalized": [] }, { "id": "PMC2639726-02-Results-01_T71", "type": "Protein", "text": [ "ihf" ], "offsets": [ [ 3757, 3760 ] ], "normalized": [] }, { "id": "PMC2639726-02-Results-01_T72", "type": "Protein", "text": [ "fruR" ], "offsets": [ [ 3811, 3815 ] ], "normalized": [] }, { "id": "PMC2639726-02-Results-01_T73", "type": "Protein", "text": [ "spvR" ], "offsets": [ [ 3817, 3821 ] ], "normalized": [] }, { "id": "PMC2639726-02-Results-01_T74", "type": "Protein", "text": [ "crp" ], "offsets": [ [ 3823, 3826 ] ], "normalized": [] }, { "id": "PMC2639726-02-Results-01_T75", "type": "Protein", "text": [ "slyA" ], "offsets": [ [ 3832, 3836 ] ], "normalized": [] }, { "id": "PMC2639726-02-Results-01_T76", "type": "Organism", "text": [ "Salmonella" ], "offsets": [ [ 4039, 4049 ] ], "normalized": [] }, { "id": "PMC2639726-02-Results-01_T77", "type": "Protein", "text": [ "rpoE" ], "offsets": [ [ 4130, 4134 ] ], "normalized": [] }, { "id": "PMC2639726-02-Results-01_T78", "type": "Two-component-system", "text": [ "phoP/phoQ" ], "offsets": [ [ 4141, 4150 ] ], "normalized": [] }, { "id": "PMC2639726-02-Results-01_T79", "type": "Protein", "text": [ "phoP" ], "offsets": [ [ 4141, 4145 ] ], "normalized": [] }, { "id": "PMC2639726-02-Results-01_T80", "type": "Protein", "text": [ "phoQ" ], "offsets": [ [ 4146, 4150 ] ], "normalized": [] }, { "id": "PMC2639726-02-Results-01_T81", "type": "Two-component-system", "text": [ "ssrA/ssrB" ], "offsets": [ [ 4157, 4166 ] ], "normalized": [] }, { "id": "PMC2639726-02-Results-01_T82", "type": "Protein", "text": [ "ssrA" ], "offsets": [ [ 4157, 4161 ] ], "normalized": [] }, { "id": "PMC2639726-02-Results-01_T83", "type": "Protein", "text": [ "ssrB" ], "offsets": [ [ 4162, 4166 ] ], "normalized": [] }, { "id": "PMC2639726-02-Results-01_T84", "type": "Protein", "text": [ "csrA" ], "offsets": [ [ 4173, 4177 ] ], "normalized": [] }, { "id": "PMC2639726-02-Results-01_T85", "type": "Protein", "text": [ "slyA" ], "offsets": [ [ 4184, 4188 ] ], "normalized": [] }, { "id": "PMC2639726-02-Results-01_T86", "type": "Protein", "text": [ "ihf" ], "offsets": [ [ 4195, 4198 ] ], "normalized": [] }, { "id": "PMC2639726-02-Results-01_T87", "type": "Protein", "text": [ "hfq" ], "offsets": [ [ 4205, 4208 ] ], "normalized": [] }, { "id": "PMC2639726-02-Results-01_T88", "type": "Protein", "text": [ "spvR" ], "offsets": [ [ 4317, 4321 ] ], "normalized": [] }, { "id": "PMC2639726-02-Results-01_T89", "type": "Protein", "text": [ "spvR" ], "offsets": [ [ 4487, 4491 ] ], "normalized": [] }, { "id": "PMC2639726-02-Results-01_T90", "type": "Organism", "text": [ "mouse" ], "offsets": [ [ 4548, 4553 ] ], "normalized": [] }, { "id": "PMC2639726-02-Results-01_T91", "type": "Organism", "text": [ "Salmonella" ], "offsets": [ [ 4676, 4686 ] ], "normalized": [] }, { "id": "PMC2639726-02-Results-01_T92", "type": "Protein", "text": [ "P22" ], "offsets": [ [ 4801, 4804 ] ], "normalized": [] } ]

[ { "id": "PMC2639726-02-Results-01_E1", "type": "Process", "trigger": { "text": [ "infection" ], "offsets": [ [ 59, 68 ] ] }, "arguments": [ { "role": "Participant", "ref_id": "PMC2639726-02-Results-01_T1" } ] }, { "id": "PMC2639726-02-Results-01_E2", "type": "Process", "trigger": { "text": [ "infection" ], "offsets": [ [ 249, 258 ] ] }, "arguments": [ { "role": "Participant", "ref_id": "PMC2639726-02-Results-01_T3" } ] }, { "id": "PMC2639726-02-Results-01_E3", "type": "Process", "trigger": { "text": [ "virulence" ], "offsets": [ [ 400, 409 ] ] }, "arguments": [] }, { "id": "PMC2639726-02-Results-01_E4", "type": "Process", "trigger": { "text": [ "infected" ], "offsets": [ [ 1033, 1041 ] ] }, "arguments": [] }, { "id": "PMC2639726-02-Results-01_E5", "type": "Process", "trigger": { "text": [ "infected" ], "offsets": [ [ 1225, 1233 ] ] }, "arguments": [] }, { "id": "PMC2639726-02-Results-01_E6", "type": "Process", "trigger": { "text": [ "virulence" ], "offsets": [ [ 1565, 1574 ] ] }, "arguments": [] }, { "id": "PMC2639726-02-Results-01_E7", "type": "Negative_regulation", "trigger": { "text": [ "attenuated" ], "offsets": [ [ 1905, 1915 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC2639726-02-Results-01_E8" } ] }, { "id": "PMC2639726-02-Results-01_E8", "type": "Process", "trigger": { "text": [ "virulence" ], "offsets": [ [ 1920, 1929 ] ] }, "arguments": [ { "role": "Participant", "ref_id": "PMC2639726-02-Results-01_T41" } ] }, { "id": "PMC2639726-02-Results-01_E9", "type": "Process", "trigger": { "text": [ "infection" ], "offsets": [ [ 2033, 2042 ] ] }, "arguments": [] }, { "id": "PMC2639726-02-Results-01_E10", "type": "Process", "trigger": { "text": [ "infection" ], "offsets": [ [ 2108, 2117 ] ] }, "arguments": [] }, { "id": "PMC2639726-02-Results-01_E11", "type": "Process", "trigger": { "text": [ "avirulent" ], "offsets": [ [ 2164, 2173 ] ] }, "arguments": [] }, { "id": "PMC2639726-02-Results-01_E12", "type": "Process", "trigger": { "text": [ "infection" ], "offsets": [ [ 2249, 2258 ] ] }, "arguments": [] }, { "id": "PMC2639726-02-Results-01_E13", "type": "Process", "trigger": { "text": [ "virulence" ], "offsets": [ [ 2379, 2388 ] ] }, "arguments": [] }, { "id": "PMC2639726-02-Results-01_E14", "type": "Process", "trigger": { "text": [ "virulence" ], "offsets": [ [ 2403, 2412 ] ] }, "arguments": [] }, { "id": "PMC2639726-02-Results-01_E15", "type": "Process", "trigger": { "text": [ "virulence" ], "offsets": [ [ 2456, 2465 ] ] }, "arguments": [] }, { "id": "PMC2639726-02-Results-01_E16", "type": "Process", "trigger": { "text": [ "infection" ], "offsets": [ [ 2496, 2505 ] ] }, "arguments": [] }, { "id": "PMC2639726-02-Results-01_E17", "type": "Process", "trigger": { "text": [ "resistance" ], "offsets": [ [ 2779, 2789 ] ] }, "arguments": [] }, { "id": "PMC2639726-02-Results-01_E18", "type": "Process", "trigger": { "text": [ "infection" ], "offsets": [ [ 2861, 2870 ] ] }, "arguments": [ { "role": "Participant", "ref_id": "PMC2639726-02-Results-01_T49" } ] }, { "id": "PMC2639726-02-Results-01_E19", "type": "Process", "trigger": { "text": [ "infected" ], "offsets": [ [ 2899, 2907 ] ] }, "arguments": [] }, { "id": "PMC2639726-02-Results-01_E20", "type": "Process", "trigger": { "text": [ "attenuated" ], "offsets": [ [ 3186, 3196 ] ] }, "arguments": [] }, { "id": "PMC2639726-02-Results-01_E21", "type": "Process", "trigger": { "text": [ "infection" ], "offsets": [ [ 4028, 4037 ] ] }, "arguments": [] }, { "id": "PMC2639726-02-Results-01_E22", "type": "Transcription", "trigger": { "text": [ "transcription" ], "offsets": [ [ 4050, 4063 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC2639726-02-Results-01_T77" } ] }, { "id": "PMC2639726-02-Results-01_E23", "type": "Transcription", "trigger": { "text": [ "transcription" ], "offsets": [ [ 4050, 4063 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC2639726-02-Results-01_T79" } ] }, { "id": "PMC2639726-02-Results-01_E24", "type": "Transcription", "trigger": { "text": [ "transcription" ], "offsets": [ [ 4050, 4063 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC2639726-02-Results-01_T80" } ] }, { "id": "PMC2639726-02-Results-01_E25", "type": "Transcription", "trigger": { "text": [ "transcription" ], "offsets": [ [ 4050, 4063 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC2639726-02-Results-01_T84" } ] }, { "id": "PMC2639726-02-Results-01_E26", "type": "Transcription", "trigger": { "text": [ "transcription" ], "offsets": [ [ 4050, 4063 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC2639726-02-Results-01_T85" } ] }, { "id": "PMC2639726-02-Results-01_E27", "type": "Transcription", "trigger": { "text": [ "transcription" ], "offsets": [ [ 4050, 4063 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC2639726-02-Results-01_T86" } ] }, { "id": "PMC2639726-02-Results-01_E28", "type": "Transcription", "trigger": { "text": [ "transcription" ], "offsets": [ [ 4050, 4063 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC2639726-02-Results-01_T87" } ] }, { "id": "PMC2639726-02-Results-01_E29", "type": "Transcription", "trigger": { "text": [ "transcription" ], "offsets": [ [ 4050, 4063 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC2639726-02-Results-01_T82" } ] }, { "id": "PMC2639726-02-Results-01_E30", "type": "Transcription", "trigger": { "text": [ "transcription" ], "offsets": [ [ 4050, 4063 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC2639726-02-Results-01_T83" } ] }, { "id": "PMC2639726-02-Results-01_E31", "type": "Process", "trigger": { "text": [ "attenuation" ], "offsets": [ [ 4286, 4297 ] ] }, "arguments": [] }, { "id": "PMC2639726-02-Results-01_E32", "type": "Process", "trigger": { "text": [ "infection" ], "offsets": [ [ 4346, 4355 ] ] }, "arguments": [] }, { "id": "PMC2639726-02-Results-01_E33", "type": "Process", "trigger": { "text": [ "infection" ], "offsets": [ [ 4432, 4441 ] ] }, "arguments": [] }, { "id": "PMC2639726-02-Results-01_E34", "type": "Process", "trigger": { "text": [ "virulence" ], "offsets": [ [ 4554, 4563 ] ] }, "arguments": [] } ]

[]

[]

[ { "id": "PMC2829055-02-Results-Discussion-04__text", "type": "abstract", "text": [ "Differential gene expression during the Y. pestis life cycle \nWith this study, the in vivo transcriptome of Y. pestis in blocked fleas and in the rat bubo [11] have now both been characterized. A comparison of normalized gene expression levels from the two data sets provides insight into the biology of the flea-mammal life cycle. About 15% of Y. pestis genes showed significantly higher relative expression levels or expression only in the flea than in the bubo; 24% were more highly expressed in the bubo than in the flea; and 61% were not differentially expressed in the two hosts (Fig. 3). Several virulence factors were differentially regulated in the two hosts, but others were not (Table 1). In addition to the known temperature-induced virulence factors, iron acquisition systems, including the ybt and yfe operons that are required for virulence; and oxidative and nitrosative stress response genes, including the hmp virulence factor, are highly upregulated in the rat bubo, but not the flea. The analysis also reinforces the model that Y. pestis produces a hexaacylated lipid A in the flea, and that the change to the less immunostimulatory tetraacylated form occurs only after transmission [32]. Other virulence and transmission factors were not differentially regulated, including the hms genes; and the Y. pestis plasminogen activator (pla), critical for dissemination from extravascular tissue at the fleabite site [33], and ymt were highly expressed in both hosts (Table S3 and [11]). The Y. pestis outer surface protein gene yadB, recently shown to be required for dissemination and bubonic plague pathogenesis from a subcutaneous inoculation site [34], was significantly upregulated in both the flea and the bubo compared to in vitro conditions (Tables 1, S1). Expression of genes in the pH 6 antigen locus (psaEFABC), responsible for the synthesis and transport of the PsaA fimbriae that enhance resistance to phagocytosis by macrophages [35],[36], were higher in the bubo than the flea, although the usher protein gene psaC was upregulated in the flea compared to in vitro growth (Tables 1, S1). The psa locus is regulated by RovA [36]. Consistent with these findings, rovA expression was downregulated in the flea; whereas expression of rovM, a negative regulator of rovA [37], was upregulated. The transcriptional regulator gene phoP of the PhoPQ two-component regulatory system and the PhoP-regulated mgtC gene were expressed at levels >2-fold higher in fleas than in any other condition (Tables 1, S1, S3). PhoP and MgtC are established virulence factors known to be important for survival of Y. pestis and other gram-negative bacteria in macrophages and for resistance to cationic antimicrobial peptides (CAMPs) of the mammalian innate immune response [38],[39],[40]. The PhoPQ system is induced in low Mg2+ or low pH environments, or by exposure to CAMPs [41],[42],[43]. The Mg2+ concentration and pH of the flea digestive tract have not been defined, so the inducing stimulus is unknown, but CAMPs are induced and secreted into the gut by blood feeding insects when they take a blood meal containing bacteria [44],[45]. X. cheopis fleas encode homologs of the insect CAMPs cecropin and defensin, and mount an inducible antibacterial response to infection (unpublished data). Thus, the PhoPQ regulatory system may be induced by the flea's immune system in response to Y. pestis in the midgut. Despite the upregulation of phoP in the flea, with the notable exception of mgtC there was little correlation between predicted PhoP-regulated genes in vitro and genes upregulated in the flea [39],[46],[47]. Differential regulation of members of the PhoP regulon may occur depending on the inducing stimulus, however [48].\n" ], "offsets": [ [ 0, 3743 ] ] } ]

[ { "id": "PMC2829055-02-Results-Discussion-04_T1", "type": "Organism", "text": [ "Y. pestis" ], "offsets": [ [ 40, 49 ] ], "normalized": [] }, { "id": "PMC2829055-02-Results-Discussion-04_T2", "type": "Organism", "text": [ "Y. pestis" ], "offsets": [ [ 108, 117 ] ], "normalized": [] }, { "id": "PMC2829055-02-Results-Discussion-04_T3", "type": "Organism", "text": [ "fleas" ], "offsets": [ [ 129, 134 ] ], "normalized": [] }, { "id": "PMC2829055-02-Results-Discussion-04_T4", "type": "Organism", "text": [ "rat" ], "offsets": [ [ 146, 149 ] ], "normalized": [] }, { "id": "PMC2829055-02-Results-Discussion-04_T5", "type": "Organism", "text": [ "flea" ], "offsets": [ [ 308, 312 ] ], "normalized": [] }, { "id": "PMC2829055-02-Results-Discussion-04_T6", "type": "Organism", "text": [ "Y. pestis" ], "offsets": [ [ 345, 354 ] ], "normalized": [] }, { "id": "PMC2829055-02-Results-Discussion-04_T7", "type": "Organism", "text": [ "flea" ], "offsets": [ [ 442, 446 ] ], "normalized": [] }, { "id": "PMC2829055-02-Results-Discussion-04_T8", "type": "Organism", "text": [ "flea" ], "offsets": [ [ 520, 524 ] ], "normalized": [] }, { "id": "PMC2829055-02-Results-Discussion-04_T9", "type": "Organism", "text": [ "hosts" ], "offsets": [ [ 579, 584 ] ], "normalized": [] }, { "id": "PMC2829055-02-Results-Discussion-04_T10", "type": "Organism", "text": [ "hosts" ], "offsets": [ [ 662, 667 ] ], "normalized": [] }, { "id": "PMC2829055-02-Results-Discussion-04_T11", "type": "Chemical", "text": [ "iron" ], "offsets": [ [ 764, 768 ] ], "normalized": [] }, { "id": "PMC2829055-02-Results-Discussion-04_T12", "type": "Regulon-operon", "text": [ "ybt" ], "offsets": [ [ 804, 807 ] ], "normalized": [] }, { "id": "PMC2829055-02-Results-Discussion-04_T13", "type": "Regulon-operon", "text": [ "yfe" ], "offsets": [ [ 812, 815 ] ], "normalized": [] }, { "id": "PMC2829055-02-Results-Discussion-04_T14", "type": "Protein", "text": [ "hmp virulence factor" ], "offsets": [ [ 924, 944 ] ], "normalized": [] }, { "id": "PMC2829055-02-Results-Discussion-04_T15", "type": "Organism", "text": [ "rat" ], "offsets": [ [ 976, 979 ] ], "normalized": [] }, { "id": "PMC2829055-02-Results-Discussion-04_T16", "type": "Organism", "text": [ "flea" ], "offsets": [ [ 998, 1002 ] ], "normalized": [] }, { "id": "PMC2829055-02-Results-Discussion-04_T17", "type": "Organism", "text": [ "Y. pestis" ], "offsets": [ [ 1048, 1057 ] ], "normalized": [] }, { "id": "PMC2829055-02-Results-Discussion-04_T18", "type": "Chemical", "text": [ "hexaacylated lipid A" ], "offsets": [ [ 1069, 1089 ] ], "normalized": [] }, { "id": "PMC2829055-02-Results-Discussion-04_T19", "type": "Organism", "text": [ "flea" ], "offsets": [ [ 1097, 1101 ] ], "normalized": [] }, { "id": "PMC2829055-02-Results-Discussion-04_T20", "type": "Chemical", "text": [ "tetraacylated" ], "offsets": [ [ 1153, 1166 ] ], "normalized": [] }, { "id": "PMC2829055-02-Results-Discussion-04_T21", "type": "Protein", "text": [ "Y. pestis plasminogen activator" ], "offsets": [ [ 1318, 1349 ] ], "normalized": [] }, { "id": "PMC2829055-02-Results-Discussion-04_T22", "type": "Protein", "text": [ "pla" ], "offsets": [ [ 1351, 1354 ] ], "normalized": [] }, { "id": "PMC2829055-02-Results-Discussion-04_T23", "type": "Protein", "text": [ "ymt" ], "offsets": [ [ 1441, 1444 ] ], "normalized": [] }, { "id": "PMC2829055-02-Results-Discussion-04_T24", "type": "Organism", "text": [ "hosts" ], "offsets": [ [ 1475, 1480 ] ], "normalized": [] }, { "id": "PMC2829055-02-Results-Discussion-04_T25", "type": "Organism", "text": [ "Y. pestis" ], "offsets": [ [ 1506, 1515 ] ], "normalized": [] }, { "id": "PMC2829055-02-Results-Discussion-04_T26", "type": "Protein", "text": [ "yadB" ], "offsets": [ [ 1543, 1547 ] ], "normalized": [] }, { "id": "PMC2829055-02-Results-Discussion-04_T27", "type": "Organism", "text": [ "flea" ], "offsets": [ [ 1714, 1718 ] ], "normalized": [] }, { "id": "PMC2829055-02-Results-Discussion-04_T28", "type": "Protein", "text": [ "psaE" ], "offsets": [ [ 1827, 1831 ] ], "normalized": [] }, { "id": "PMC2829055-02-Results-Discussion-04_T29", "type": "Protein", "text": [ "F" ], "offsets": [ [ 1831, 1832 ] ], "normalized": [] }, { "id": "PMC2829055-02-Results-Discussion-04_T30", "type": "Protein", "text": [ "A" ], "offsets": [ [ 1832, 1833 ] ], "normalized": [] }, { "id": "PMC2829055-02-Results-Discussion-04_T31", "type": "Protein", "text": [ "B" ], "offsets": [ [ 1833, 1834 ] ], "normalized": [] }, { "id": "PMC2829055-02-Results-Discussion-04_T32", "type": "Protein", "text": [ "C" ], "offsets": [ [ 1834, 1835 ] ], "normalized": [] }, { "id": "PMC2829055-02-Results-Discussion-04_T33", "type": "Protein", "text": [ "PsaA" ], "offsets": [ [ 1889, 1893 ] ], "normalized": [] }, { "id": "PMC2829055-02-Results-Discussion-04_T34", "type": "Organism", "text": [ "flea" ], "offsets": [ [ 2002, 2006 ] ], "normalized": [] }, { "id": "PMC2829055-02-Results-Discussion-04_T35", "type": "Protein", "text": [ "psaC" ], "offsets": [ [ 2040, 2044 ] ], "normalized": [] }, { "id": "PMC2829055-02-Results-Discussion-04_T36", "type": "Organism", "text": [ "flea" ], "offsets": [ [ 2068, 2072 ] ], "normalized": [] }, { "id": "PMC2829055-02-Results-Discussion-04_T37", "type": "Protein", "text": [ "RovA" ], "offsets": [ [ 2147, 2151 ] ], "normalized": [] }, { "id": "PMC2829055-02-Results-Discussion-04_T38", "type": "Protein", "text": [ "rovA" ], "offsets": [ [ 2190, 2194 ] ], "normalized": [] }, { "id": "PMC2829055-02-Results-Discussion-04_T39", "type": "Organism", "text": [ "flea" ], "offsets": [ [ 2231, 2235 ] ], "normalized": [] }, { "id": "PMC2829055-02-Results-Discussion-04_T40", "type": "Protein", "text": [ "rovM" ], "offsets": [ [ 2259, 2263 ] ], "normalized": [] }, { "id": "PMC2829055-02-Results-Discussion-04_T41", "type": "Protein", "text": [ "rovA" ], "offsets": [ [ 2289, 2293 ] ], "normalized": [] }, { "id": "PMC2829055-02-Results-Discussion-04_T42", "type": "Protein", "text": [ "phoP" ], "offsets": [ [ 2352, 2356 ] ], "normalized": [] }, { "id": "PMC2829055-02-Results-Discussion-04_T43", "type": "Two-component-system", "text": [ "PhoPQ" ], "offsets": [ [ 2364, 2369 ] ], "normalized": [] }, { "id": "PMC2829055-02-Results-Discussion-04_T44", "type": "Protein", "text": [ "PhoP" ], "offsets": [ [ 2364, 2368 ] ], "normalized": [] }, { "id": "PMC2829055-02-Results-Discussion-04_T45", "type": "Protein", "text": [ "Q" ], "offsets": [ [ 2368, 2369 ] ], "normalized": [] }, { "id": "PMC2829055-02-Results-Discussion-04_T46", "type": "Protein", "text": [ "PhoP" ], "offsets": [ [ 2410, 2414 ] ], "normalized": [] }, { "id": "PMC2829055-02-Results-Discussion-04_T47", "type": "Protein", "text": [ "mgtC" ], "offsets": [ [ 2425, 2429 ] ], "normalized": [] }, { "id": "PMC2829055-02-Results-Discussion-04_T48", "type": "Organism", "text": [ "fleas" ], "offsets": [ [ 2478, 2483 ] ], "normalized": [] }, { "id": "PMC2829055-02-Results-Discussion-04_T49", "type": "Protein", "text": [ "PhoP" ], "offsets": [ [ 2532, 2536 ] ], "normalized": [] }, { "id": "PMC2829055-02-Results-Discussion-04_T50", "type": "Protein", "text": [ "MgtC" ], "offsets": [ [ 2541, 2545 ] ], "normalized": [] }, { "id": "PMC2829055-02-Results-Discussion-04_T51", "type": "Organism", "text": [ "Y. pestis" ], "offsets": [ [ 2618, 2627 ] ], "normalized": [] }, { "id": "PMC2829055-02-Results-Discussion-04_T52", "type": "Two-component-system", "text": [ "PhoPQ" ], "offsets": [ [ 2798, 2803 ] ], "normalized": [] }, { "id": "PMC2829055-02-Results-Discussion-04_T53", "type": "Protein", "text": [ "PhoP" ], "offsets": [ [ 2798, 2802 ] ], "normalized": [] }, { "id": "PMC2829055-02-Results-Discussion-04_T54", "type": "Protein", "text": [ "Q" ], "offsets": [ [ 2802, 2803 ] ], "normalized": [] }, { "id": "PMC2829055-02-Results-Discussion-04_T55", "type": "Chemical", "text": [ "Mg2+" ], "offsets": [ [ 2829, 2833 ] ], "normalized": [] }, { "id": "PMC2829055-02-Results-Discussion-04_T56", "type": "Chemical", "text": [ "Mg2+" ], "offsets": [ [ 2902, 2906 ] ], "normalized": [] }, { "id": "PMC2829055-02-Results-Discussion-04_T57", "type": "Organism", "text": [ "flea" ], "offsets": [ [ 2935, 2939 ] ], "normalized": [] }, { "id": "PMC2829055-02-Results-Discussion-04_T58", "type": "Organism", "text": [ "X. cheopis fleas" ], "offsets": [ [ 3148, 3164 ] ], "normalized": [] }, { "id": "PMC2829055-02-Results-Discussion-04_T59", "type": "Protein", "text": [ "cecropin" ], "offsets": [ [ 3201, 3209 ] ], "normalized": [] }, { "id": "PMC2829055-02-Results-Discussion-04_T60", "type": "Protein", "text": [ "defensin" ], "offsets": [ [ 3214, 3222 ] ], "normalized": [] }, { "id": "PMC2829055-02-Results-Discussion-04_T61", "type": "Two-component-system", "text": [ "PhoPQ" ], "offsets": [ [ 3313, 3318 ] ], "normalized": [] }, { "id": "PMC2829055-02-Results-Discussion-04_T62", "type": "Protein", "text": [ "PhoP" ], "offsets": [ [ 3313, 3317 ] ], "normalized": [] }, { "id": "PMC2829055-02-Results-Discussion-04_T63", "type": "Protein", "text": [ "Q" ], "offsets": [ [ 3317, 3318 ] ], "normalized": [] }, { "id": "PMC2829055-02-Results-Discussion-04_T64", "type": "Organism", "text": [ "flea" ], "offsets": [ [ 3359, 3363 ] ], "normalized": [] }, { "id": "PMC2829055-02-Results-Discussion-04_T65", "type": "Organism", "text": [ "Y. pestis" ], "offsets": [ [ 3395, 3404 ] ], "normalized": [] }, { "id": "PMC2829055-02-Results-Discussion-04_T66", "type": "Protein", "text": [ "phoP" ], "offsets": [ [ 3448, 3452 ] ], "normalized": [] }, { "id": "PMC2829055-02-Results-Discussion-04_T67", "type": "Organism", "text": [ "flea" ], "offsets": [ [ 3460, 3464 ] ], "normalized": [] }, { "id": "PMC2829055-02-Results-Discussion-04_T68", "type": "Protein", "text": [ "mgtC" ], "offsets": [ [ 3496, 3500 ] ], "normalized": [] }, { "id": "PMC2829055-02-Results-Discussion-04_T69", "type": "Protein", "text": [ "PhoP" ], "offsets": [ [ 3548, 3552 ] ], "normalized": [] }, { "id": "PMC2829055-02-Results-Discussion-04_T70", "type": "Organism", "text": [ "flea" ], "offsets": [ [ 3607, 3611 ] ], "normalized": [] }, { "id": "PMC2829055-02-Results-Discussion-04_T72", "type": "Regulon-operon", "text": [ "PhoP" ], "offsets": [ [ 3670, 3674 ] ], "normalized": [] }, { "id": "PMC2829055-02-Results-Discussion-04_T71", "type": "Protein", "text": [ "PhoP" ], "offsets": [ [ 3670, 3674 ] ], "normalized": [] } ]

[ { "id": "PMC2829055-02-Results-Discussion-04_E1", "type": "Process", "trigger": { "text": [ "virulence" ], "offsets": [ [ 603, 612 ] ] }, "arguments": [] }, { "id": "PMC2829055-02-Results-Discussion-04_E2", "type": "Process", "trigger": { "text": [ "virulence" ], "offsets": [ [ 745, 754 ] ] }, "arguments": [] }, { "id": "PMC2829055-02-Results-Discussion-04_E3", "type": "Positive_regulation", "trigger": { "text": [ "required" ], "offsets": [ [ 833, 841 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC2829055-02-Results-Discussion-04_E5" }, { "role": "Cause", "ref_id": "PMC2829055-02-Results-Discussion-04_T12" } ] }, { "id": "PMC2829055-02-Results-Discussion-04_E4", "type": "Positive_regulation", "trigger": { "text": [ "required" ], "offsets": [ [ 833, 841 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC2829055-02-Results-Discussion-04_E5" }, { "role": "Cause", "ref_id": "PMC2829055-02-Results-Discussion-04_T13" } ] }, { "id": "PMC2829055-02-Results-Discussion-04_E5", "type": "Process", "trigger": { "text": [ "virulence" ], "offsets": [ [ 846, 855 ] ] }, "arguments": [] }, { "id": "PMC2829055-02-Results-Discussion-04_E6", "type": "Positive_regulation", "trigger": { "text": [ "upregulated" ], "offsets": [ [ 957, 968 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC2829055-02-Results-Discussion-04_T14" } ] }, { "id": "PMC2829055-02-Results-Discussion-04_E7", "type": "Process", "trigger": { "text": [ "virulence" ], "offsets": [ [ 1215, 1224 ] ] }, "arguments": [] }, { "id": "PMC2829055-02-Results-Discussion-04_E8", "type": "Gene_expression", "trigger": { "text": [ "expressed" ], "offsets": [ [ 1457, 1466 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC2829055-02-Results-Discussion-04_T23" } ] }, { "id": "PMC2829055-02-Results-Discussion-04_E9", "type": "Gene_expression", "trigger": { "text": [ "expressed" ], "offsets": [ [ 1457, 1466 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC2829055-02-Results-Discussion-04_T21" } ] }, { "id": "PMC2829055-02-Results-Discussion-04_E10", "type": "Positive_regulation", "trigger": { "text": [ "upregulated" ], "offsets": [ [ 1690, 1701 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC2829055-02-Results-Discussion-04_T26" } ] }, { "id": "PMC2829055-02-Results-Discussion-04_E11", "type": "Gene_expression", "trigger": { "text": [ "Expression" ], "offsets": [ [ 1780, 1790 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC2829055-02-Results-Discussion-04_T28" } ] }, { "id": "PMC2829055-02-Results-Discussion-04_E12", "type": "Gene_expression", "trigger": { "text": [ "Expression" ], "offsets": [ [ 1780, 1790 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC2829055-02-Results-Discussion-04_T29" } ] }, { "id": "PMC2829055-02-Results-Discussion-04_E13", "type": "Gene_expression", "trigger": { "text": [ "Expression" ], "offsets": [ [ 1780, 1790 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC2829055-02-Results-Discussion-04_T30" } ] }, { "id": "PMC2829055-02-Results-Discussion-04_E14", "type": "Gene_expression", "trigger": { "text": [ "Expression" ], "offsets": [ [ 1780, 1790 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC2829055-02-Results-Discussion-04_T31" } ] }, { "id": "PMC2829055-02-Results-Discussion-04_E15", "type": "Gene_expression", "trigger": { "text": [ "Expression" ], "offsets": [ [ 1780, 1790 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC2829055-02-Results-Discussion-04_T32" } ] }, { "id": "PMC2829055-02-Results-Discussion-04_E16", "type": "Positive_regulation", "trigger": { "text": [ "enhance" ], "offsets": [ [ 1908, 1915 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC2829055-02-Results-Discussion-04_E17" }, { "role": "Cause", "ref_id": "PMC2829055-02-Results-Discussion-04_T33" } ] }, { "id": "PMC2829055-02-Results-Discussion-04_E17", "type": "Process", "trigger": { "text": [ "resistance" ], "offsets": [ [ 1916, 1926 ] ] }, "arguments": [] }, { "id": "PMC2829055-02-Results-Discussion-04_E18", "type": "Positive_regulation", "trigger": { "text": [ "upregulated" ], "offsets": [ [ 2049, 2060 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC2829055-02-Results-Discussion-04_T35" } ] }, { "id": "PMC2829055-02-Results-Discussion-04_E19", "type": "Gene_expression", "trigger": { "text": [ "expression" ], "offsets": [ [ 2195, 2205 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC2829055-02-Results-Discussion-04_T38" } ] }, { "id": "PMC2829055-02-Results-Discussion-04_E20", "type": "Negative_regulation", "trigger": { "text": [ "downregulated" ], "offsets": [ [ 2210, 2223 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC2829055-02-Results-Discussion-04_E19" } ] }, { "id": "PMC2829055-02-Results-Discussion-04_E21", "type": "Gene_expression", "trigger": { "text": [ "expression" ], "offsets": [ [ 2245, 2255 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC2829055-02-Results-Discussion-04_T40" } ] }, { "id": "PMC2829055-02-Results-Discussion-04_E22", "type": "Positive_regulation", "trigger": { "text": [ "upregulated" ], "offsets": [ [ 2304, 2315 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC2829055-02-Results-Discussion-04_E21" } ] }, { "id": "PMC2829055-02-Results-Discussion-04_E23", "type": "Regulation", "trigger": { "text": [ "regulated" ], "offsets": [ [ 2415, 2424 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC2829055-02-Results-Discussion-04_T47" }, { "role": "Cause", "ref_id": "PMC2829055-02-Results-Discussion-04_T46" } ] }, { "id": "PMC2829055-02-Results-Discussion-04_E24", "type": "Gene_expression", "trigger": { "text": [ "expressed" ], "offsets": [ [ 2440, 2449 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC2829055-02-Results-Discussion-04_T42" } ] }, { "id": "PMC2829055-02-Results-Discussion-04_E25", "type": "Gene_expression", "trigger": { "text": [ "expressed" ], "offsets": [ [ 2440, 2449 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC2829055-02-Results-Discussion-04_T47" } ] }, { "id": "PMC2829055-02-Results-Discussion-04_E26", "type": "Process", "trigger": { "text": [ "virulence" ], "offsets": [ [ 2562, 2571 ] ] }, "arguments": [] }, { "id": "PMC2829055-02-Results-Discussion-04_E27", "type": "Process", "trigger": { "text": [ "resistance" ], "offsets": [ [ 2684, 2694 ] ] }, "arguments": [] }, { "id": "PMC2829055-02-Results-Discussion-04_E28", "type": "Positive_regulation", "trigger": { "text": [ "induced" ], "offsets": [ [ 2814, 2821 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC2829055-02-Results-Discussion-04_T52" } ] }, { "id": "PMC2829055-02-Results-Discussion-04_E29", "type": "Process", "trigger": { "text": [ "infection" ], "offsets": [ [ 3273, 3282 ] ] }, "arguments": [] }, { "id": "PMC2829055-02-Results-Discussion-04_E30", "type": "Positive_regulation", "trigger": { "text": [ "induced" ], "offsets": [ [ 3344, 3351 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC2829055-02-Results-Discussion-04_T61" } ] }, { "id": "PMC2829055-02-Results-Discussion-04_E31", "type": "Positive_regulation", "trigger": { "text": [ "upregulation" ], "offsets": [ [ 3432, 3444 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC2829055-02-Results-Discussion-04_T66" } ] }, { "id": "PMC2829055-02-Results-Discussion-04_E32", "type": "Regulation", "trigger": { "text": [ "regulation" ], "offsets": [ [ 3641, 3651 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC2829055-02-Results-Discussion-04_T72" } ] } ]

[ { "id": "PMC2829055-02-Results-Discussion-04_1", "entity_ids": [ "PMC2829055-02-Results-Discussion-04_T22", "PMC2829055-02-Results-Discussion-04_T21" ] } ]

[]

[ { "id": "PMC2682197-02-Results-01__text", "type": "abstract", "text": [ "Results \nMycobacterium tuberculosis Rv2623 regulates growth in vitro An rv2623-deletion mutant of the virulent M. tuberculosis Erdman strain was generated by specialized transduction [12]. The rv2623-specific allelic exchange construct was delivered via recombinant mycobacteriophage phAE159 and transformants were analyzed by Southern blot, confirming replacement of rv2623 with the hyg gene, which confers hygromycin resistance (Figure 1A). Aliquots of a single knockout clone, designated as Deltarv2623, were stored at -70degreesC. Deletion of rv2623 is not likely to affect transcription of neighboring genes, given the sequence-confirmed precise excision of the rv2623 coding region and the gene organization at the rv2623 locus (the downstream rv2624c is transcribed in the direction opposite to that of rv2623) (Figure 1B). Deletion of specific USPs in E. coli results in growth defects in vitro [8],[13],[14]. For example, an E. coli strain deficient for UspA exhibits reduced survival in stationary phase culture [14]. However, the in vitro growth kinetics of Deltarv2623 M. tuberculosis in OADC-supplemented Middlebrook 7H9 or minimal Sauton's medium is comparable to that of wildtype Erdman up to 14 days post-inoculation (Figure 2A). We reasoned that a potential growth-regulating attribute of Rv2623 might be masked by functional redundancy among the M. tuberculosis USP homologs. Indeed, partial functional overlap has been demonstrated among the E. coli USPs [9],[15]. We therefore examined the effect of overexpression of this USP in the rapidly growing M. smegmatis strain mc2155 [16]. As seen in Figure 2B, constitutive overexpression of M. tuberculosis rv2623 using the multi-copy plasmid pMV261 resulted in growth deficiency of the recipient strain both on solid medium (Middlebrook 7H10 agar) and in the liquid medium-based BD BACTEC 9000MB system. These results strongly suggest that M. tuberculosis Rv2623 regulates mycobacterial growth in vitro.\n" ], "offsets": [ [ 0, 1970 ] ] } ]

[ { "id": "PMC2682197-02-Results-01_T1", "type": "Organism", "text": [ "Mycobacterium tuberculosis" ], "offsets": [ [ 9, 35 ] ], "normalized": [] }, { "id": "PMC2682197-02-Results-01_T2", "type": "Protein", "text": [ "Rv2623" ], "offsets": [ [ 36, 42 ] ], "normalized": [] }, { "id": "PMC2682197-02-Results-01_T3", "type": "Organism", "text": [ "rv2623-deletion mutant" ], "offsets": [ [ 72, 94 ] ], "normalized": [] }, { "id": "PMC2682197-02-Results-01_T4", "type": "Protein", "text": [ "rv2623" ], "offsets": [ [ 72, 78 ] ], "normalized": [] }, { "id": "PMC2682197-02-Results-01_T5", "type": "Organism", "text": [ "M. tuberculosis Erdman strain" ], "offsets": [ [ 111, 140 ] ], "normalized": [] }, { "id": "PMC2682197-02-Results-01_T6", "type": "Protein", "text": [ "rv2623" ], "offsets": [ [ 193, 199 ] ], "normalized": [] }, { "id": "PMC2682197-02-Results-01_T7", "type": "Protein", "text": [ "rv2623" ], "offsets": [ [ 368, 374 ] ], "normalized": [] }, { "id": "PMC2682197-02-Results-01_T8", "type": "Chemical", "text": [ "hygromycin" ], "offsets": [ [ 408, 418 ] ], "normalized": [] }, { "id": "PMC2682197-02-Results-01_T9", "type": "Organism", "text": [ "Deltarv2623" ], "offsets": [ [ 494, 505 ] ], "normalized": [] }, { "id": "PMC2682197-02-Results-01_T10", "type": "Protein", "text": [ "rv2623" ], "offsets": [ [ 499, 505 ] ], "normalized": [] }, { "id": "PMC2682197-02-Results-01_T11", "type": "Protein", "text": [ "rv2623" ], "offsets": [ [ 547, 553 ] ], "normalized": [] }, { "id": "PMC2682197-02-Results-01_T12", "type": "Protein", "text": [ "rv2623" ], "offsets": [ [ 667, 673 ] ], "normalized": [] }, { "id": "PMC2682197-02-Results-01_T13", "type": "Protein", "text": [ "rv2623" ], "offsets": [ [ 721, 727 ] ], "normalized": [] }, { "id": "PMC2682197-02-Results-01_T14", "type": "Protein", "text": [ "rv2624" ], "offsets": [ [ 750, 756 ] ], "normalized": [] }, { "id": "PMC2682197-02-Results-01_T15", "type": "Protein", "text": [ "rv2623" ], "offsets": [ [ 810, 816 ] ], "normalized": [] }, { "id": "PMC2682197-02-Results-01_T16", "type": "Organism", "text": [ "E. coli" ], "offsets": [ [ 860, 867 ] ], "normalized": [] }, { "id": "PMC2682197-02-Results-01_T17", "type": "Organism", "text": [ "E. coli" ], "offsets": [ [ 934, 941 ] ], "normalized": [] }, { "id": "PMC2682197-02-Results-01_T18", "type": "Protein", "text": [ "UspA" ], "offsets": [ [ 963, 967 ] ], "normalized": [] }, { "id": "PMC2682197-02-Results-01_T19", "type": "Organism", "text": [ "Deltarv2623 M. tuberculosis" ], "offsets": [ [ 1069, 1096 ] ], "normalized": [] }, { "id": "PMC2682197-02-Results-01_T20", "type": "Protein", "text": [ "rv2623" ], "offsets": [ [ 1074, 1080 ] ], "normalized": [] }, { "id": "PMC2682197-02-Results-01_T21", "type": "Chemical", "text": [ "OADC" ], "offsets": [ [ 1100, 1104 ] ], "normalized": [] }, { "id": "PMC2682197-02-Results-01_T22", "type": "Organism", "text": [ "Erdman" ], "offsets": [ [ 1195, 1201 ] ], "normalized": [] }, { "id": "PMC2682197-02-Results-01_T23", "type": "Protein", "text": [ "Rv2623" ], "offsets": [ [ 1306, 1312 ] ], "normalized": [] }, { "id": "PMC2682197-02-Results-01_T24", "type": "Organism", "text": [ "M. tuberculosis" ], "offsets": [ [ 1364, 1379 ] ], "normalized": [] }, { "id": "PMC2682197-02-Results-01_T25", "type": "Organism", "text": [ "E. coli" ], "offsets": [ [ 1461, 1468 ] ], "normalized": [] }, { "id": "PMC2682197-02-Results-01_T26", "type": "Organism", "text": [ "M. smegmatis strain mc2155" ], "offsets": [ [ 1570, 1596 ] ], "normalized": [] }, { "id": "PMC2682197-02-Results-01_T27", "type": "Organism", "text": [ "M. tuberculosis" ], "offsets": [ [ 1656, 1671 ] ], "normalized": [] }, { "id": "PMC2682197-02-Results-01_T28", "type": "Protein", "text": [ "rv2623" ], "offsets": [ [ 1672, 1678 ] ], "normalized": [] }, { "id": "PMC2682197-02-Results-01_T29", "type": "Organism", "text": [ "M. tuberculosis" ], "offsets": [ [ 1906, 1921 ] ], "normalized": [] }, { "id": "PMC2682197-02-Results-01_T30", "type": "Protein", "text": [ "Rv2623" ], "offsets": [ [ 1922, 1928 ] ], "normalized": [] } ]

[ { "id": "PMC2682197-02-Results-01_E1", "type": "Process", "trigger": { "text": [ "virulent" ], "offsets": [ [ 102, 110 ] ] }, "arguments": [ { "role": "Participant", "ref_id": "PMC2682197-02-Results-01_T5" } ] }, { "id": "PMC2682197-02-Results-01_E2", "type": "Process", "trigger": { "text": [ "resistance" ], "offsets": [ [ 419, 429 ] ] }, "arguments": [] }, { "id": "PMC2682197-02-Results-01_E3", "type": "Transcription", "trigger": { "text": [ "transcribed" ], "offsets": [ [ 761, 772 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC2682197-02-Results-01_T14" } ] }, { "id": "PMC2682197-02-Results-01_E4", "type": "Gene_expression", "trigger": { "text": [ "overexpression" ], "offsets": [ [ 1638, 1652 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC2682197-02-Results-01_T28" } ] } ]

[]

[]

[ { "id": "PMC1913099-02-Results-Discussion-12__text", "type": "abstract", "text": [ "Neighbor Clustering and Operons \nAlthough neighbor clustering is not an operon-predicting method, we wanted to identify additional putative operons among the groupings since neighbor clusters by definition share certain operon characteristics (tandemly arranged genes, separated by <300 bp, with similar expression patterns). Although operon-modeling methods exist [54,55], we inspected clusters in silico for upstream regulatory elements and identified 17 candidates, including clusters such as streptolysin S that have been previously confirmed as operons [56]; the spy0127-0130 grouping, which was confirmed as an operon in this study; and others that have yet to be verified (Table S6). Experimental confirmation of each candidate is beyond the scope of this study, but Northern blot and RT-PCR analyses could provide such information.\n" ], "offsets": [ [ 0, 840 ] ] } ]

[ { "id": "PMC1913099-02-Results-Discussion-12_T1", "type": "Protein", "text": [ "streptolysin S" ], "offsets": [ [ 496, 510 ] ], "normalized": [] }, { "id": "PMC1913099-02-Results-Discussion-12_T2", "type": "Regulon-operon", "text": [ "spy0127-0130" ], "offsets": [ [ 568, 580 ] ], "normalized": [] }, { "id": "PMC1913099-02-Results-Discussion-12_T3", "type": "Protein", "text": [ "spy0127" ], "offsets": [ [ 568, 575 ] ], "normalized": [] }, { "id": "PMC1913099-02-Results-Discussion-12_T4", "type": "Protein", "text": [ "0130" ], "offsets": [ [ 576, 580 ] ], "normalized": [] } ]

[]

[]

[]

[ { "id": "PMC1974823-03-Results-01__text", "type": "abstract", "text": [ "Results \nRole of FimR in mfa1 expression The fimA gene is the only gene known to be tightly controlled by the FimS/FimR system. It was postulated that the expression of other genes may also be controlled by this two component regulatory system. To investigate effects of FimR on expression of the mfa1 gene, an insertional fimR mutant was constructed by allelic replacement. Expression of fimA and mfa1 in the fimR- mutant was determined using real-time PCR analysis. Statistically significant differences of the level of gene expression in 33277 and the fimR- mutant were calculated by a Student's t-test. As shown in Fig. 1a, expression of the fimA gene was abolished in the fimR- mutant strain FRE. This result is consistent with previous observations (Hayashi et al., 2000; Nishikawa et al., 2004). The striking finding is that expression of the mfa1 gene was also repressed threefold in the fimR- mutant, although not to the degree observed with the fimA expression. However, the fimR- mutation had no effect on expression of rgpA, a gene encoding the arginine-specific protease, or the P. gingivalis 16S RNA gene. This analysis suggests the FimS/FimR system is required for expression of both major and minor fimbriae. To determine production of long (major) and short (minor) fimbriae in the fimR- mutant, western blotting was performed with a polyclonal anti-FimA or anti-Mfa1 antibody to compare fimbrial production in wild-type strain (33277), the fimR- mutant (FRE), the fimA- mutant (FAT) and the mfa1- mutant (MFAE). Density of protein bands was determined by UVP Bioimaging System (UVP, CA). This analysis revealed that the expression of the fimA and mfa1 genes was consistent at the mRNA level and protein level (Fig. 1b). FimA protein was not detectable in the fimR- mutant, while a 50% lower level of Mfa1 protein was found in the fimR- mutant compared with that in wild-type strain 33277. Similarly, there was no apparent change in RgpA production in the fimR- mutant, which was detected by anti-RgpA serum.\n" ], "offsets": [ [ 0, 2026 ] ] } ]

[ { "id": "PMC1974823-03-Results-01_T1", "type": "Protein", "text": [ "FimR" ], "offsets": [ [ 17, 21 ] ], "normalized": [] }, { "id": "PMC1974823-03-Results-01_T2", "type": "Protein", "text": [ "mfa1" ], "offsets": [ [ 25, 29 ] ], "normalized": [] }, { "id": "PMC1974823-03-Results-01_T3", "type": "Protein", "text": [ "fimA" ], "offsets": [ [ 45, 49 ] ], "normalized": [] }, { "id": "PMC1974823-03-Results-01_T4", "type": "Two-component-system", "text": [ "FimS/FimR" ], "offsets": [ [ 110, 119 ] ], "normalized": [] }, { "id": "PMC1974823-03-Results-01_T5", "type": "Protein", "text": [ "FimS" ], "offsets": [ [ 110, 114 ] ], "normalized": [] }, { "id": "PMC1974823-03-Results-01_T6", "type": "Protein", "text": [ "FimR" ], "offsets": [ [ 115, 119 ] ], "normalized": [] }, { "id": "PMC1974823-03-Results-01_T7", "type": "Protein", "text": [ "FimR" ], "offsets": [ [ 271, 275 ] ], "normalized": [] }, { "id": "PMC1974823-03-Results-01_T8", "type": "Protein", "text": [ "mfa1" ], "offsets": [ [ 297, 301 ] ], "normalized": [] }, { "id": "PMC1974823-03-Results-01_T9", "type": "Organism", "text": [ "fimR mutant" ], "offsets": [ [ 323, 334 ] ], "normalized": [] }, { "id": "PMC1974823-03-Results-01_T10", "type": "Protein", "text": [ "fimR" ], "offsets": [ [ 323, 327 ] ], "normalized": [] }, { "id": "PMC1974823-03-Results-01_T11", "type": "Protein", "text": [ "fimA" ], "offsets": [ [ 389, 393 ] ], "normalized": [] }, { "id": "PMC1974823-03-Results-01_T12", "type": "Protein", "text": [ "mfa1" ], "offsets": [ [ 398, 402 ] ], "normalized": [] }, { "id": "PMC1974823-03-Results-01_T13", "type": "Organism", "text": [ "fimR- mutant" ], "offsets": [ [ 410, 422 ] ], "normalized": [] }, { "id": "PMC1974823-03-Results-01_T14", "type": "Protein", "text": [ "fimR" ], "offsets": [ [ 410, 414 ] ], "normalized": [] }, { "id": "PMC1974823-03-Results-01_T15", "type": "Organism", "text": [ "33277" ], "offsets": [ [ 541, 546 ] ], "normalized": [] }, { "id": "PMC1974823-03-Results-01_T16", "type": "Organism", "text": [ "fimR- mutant" ], "offsets": [ [ 555, 567 ] ], "normalized": [] }, { "id": "PMC1974823-03-Results-01_T17", "type": "Protein", "text": [ "fimR" ], "offsets": [ [ 555, 559 ] ], "normalized": [] }, { "id": "PMC1974823-03-Results-01_T18", "type": "Protein", "text": [ "fimA" ], "offsets": [ [ 646, 650 ] ], "normalized": [] }, { "id": "PMC1974823-03-Results-01_T19", "type": "Organism", "text": [ "fimR- mutant strain FRE" ], "offsets": [ [ 677, 700 ] ], "normalized": [] }, { "id": "PMC1974823-03-Results-01_T20", "type": "Protein", "text": [ "fimR" ], "offsets": [ [ 677, 681 ] ], "normalized": [] }, { "id": "PMC1974823-03-Results-01_T21", "type": "Protein", "text": [ "mfa1" ], "offsets": [ [ 850, 854 ] ], "normalized": [] }, { "id": "PMC1974823-03-Results-01_T22", "type": "Organism", "text": [ "fimR- mutant" ], "offsets": [ [ 896, 908 ] ], "normalized": [] }, { "id": "PMC1974823-03-Results-01_T23", "type": "Protein", "text": [ "fimR" ], "offsets": [ [ 896, 900 ] ], "normalized": [] }, { "id": "PMC1974823-03-Results-01_T24", "type": "Protein", "text": [ "fimA" ], "offsets": [ [ 955, 959 ] ], "normalized": [] }, { "id": "PMC1974823-03-Results-01_T25", "type": "Protein", "text": [ "fimR" ], "offsets": [ [ 985, 989 ] ], "normalized": [] }, { "id": "PMC1974823-03-Results-01_T26", "type": "Protein", "text": [ "rgpA" ], "offsets": [ [ 1031, 1035 ] ], "normalized": [] }, { "id": "PMC1974823-03-Results-01_T27", "type": "Organism", "text": [ "P. gingivalis" ], "offsets": [ [ 1092, 1105 ] ], "normalized": [] }, { "id": "PMC1974823-03-Results-01_T28", "type": "Protein", "text": [ "16S RNA" ], "offsets": [ [ 1106, 1113 ] ], "normalized": [] }, { "id": "PMC1974823-03-Results-01_T29", "type": "Two-component-system", "text": [ "FimS/FimR" ], "offsets": [ [ 1147, 1156 ] ], "normalized": [] }, { "id": "PMC1974823-03-Results-01_T30", "type": "Protein", "text": [ "FimS" ], "offsets": [ [ 1147, 1151 ] ], "normalized": [] }, { "id": "PMC1974823-03-Results-01_T31", "type": "Protein", "text": [ "FimR" ], "offsets": [ [ 1152, 1156 ] ], "normalized": [] }, { "id": "PMC1974823-03-Results-01_T32", "type": "Protein", "text": [ "minor fimbriae" ], "offsets": [ [ 1209, 1223 ] ], "normalized": [] }, { "id": "PMC1974823-03-Results-01_T33", "type": "Organism", "text": [ "fimR- mutant" ], "offsets": [ [ 1299, 1311 ] ], "normalized": [] }, { "id": "PMC1974823-03-Results-01_T34", "type": "Protein", "text": [ "fimR" ], "offsets": [ [ 1299, 1303 ] ], "normalized": [] }, { "id": "PMC1974823-03-Results-01_T35", "type": "Protein", "text": [ "FimA" ], "offsets": [ [ 1367, 1371 ] ], "normalized": [] }, { "id": "PMC1974823-03-Results-01_T36", "type": "Protein", "text": [ "Mfa1" ], "offsets": [ [ 1380, 1384 ] ], "normalized": [] }, { "id": "PMC1974823-03-Results-01_T37", "type": "Organism", "text": [ "33277" ], "offsets": [ [ 1446, 1451 ] ], "normalized": [] }, { "id": "PMC1974823-03-Results-01_T38", "type": "Organism", "text": [ "fimR- mutant" ], "offsets": [ [ 1458, 1470 ] ], "normalized": [] }, { "id": "PMC1974823-03-Results-01_T39", "type": "Protein", "text": [ "fimR" ], "offsets": [ [ 1458, 1462 ] ], "normalized": [] }, { "id": "PMC1974823-03-Results-01_T40", "type": "Organism", "text": [ "FRE" ], "offsets": [ [ 1472, 1475 ] ], "normalized": [] }, { "id": "PMC1974823-03-Results-01_T41", "type": "Organism", "text": [ "fimA- mutant" ], "offsets": [ [ 1482, 1494 ] ], "normalized": [] }, { "id": "PMC1974823-03-Results-01_T42", "type": "Protein", "text": [ "fimA" ], "offsets": [ [ 1482, 1486 ] ], "normalized": [] }, { "id": "PMC1974823-03-Results-01_T43", "type": "Organism", "text": [ "FAT" ], "offsets": [ [ 1496, 1499 ] ], "normalized": [] }, { "id": "PMC1974823-03-Results-01_T44", "type": "Organism", "text": [ "mfa1- mutant" ], "offsets": [ [ 1509, 1521 ] ], "normalized": [] }, { "id": "PMC1974823-03-Results-01_T45", "type": "Protein", "text": [ "mfa1" ], "offsets": [ [ 1509, 1513 ] ], "normalized": [] }, { "id": "PMC1974823-03-Results-01_T46", "type": "Organism", "text": [ "MFAE" ], "offsets": [ [ 1523, 1527 ] ], "normalized": [] }, { "id": "PMC1974823-03-Results-01_T47", "type": "Protein", "text": [ "fimA" ], "offsets": [ [ 1656, 1660 ] ], "normalized": [] }, { "id": "PMC1974823-03-Results-01_T48", "type": "Protein", "text": [ "mfa1" ], "offsets": [ [ 1665, 1669 ] ], "normalized": [] }, { "id": "PMC1974823-03-Results-01_T49", "type": "Protein", "text": [ "FimA" ], "offsets": [ [ 1738, 1742 ] ], "normalized": [] }, { "id": "PMC1974823-03-Results-01_T50", "type": "Organism", "text": [ "fimR- mutant" ], "offsets": [ [ 1777, 1789 ] ], "normalized": [] }, { "id": "PMC1974823-03-Results-01_T51", "type": "Protein", "text": [ "fimR" ], "offsets": [ [ 1777, 1781 ] ], "normalized": [] }, { "id": "PMC1974823-03-Results-01_T52", "type": "Protein", "text": [ "Mfa1" ], "offsets": [ [ 1818, 1822 ] ], "normalized": [] }, { "id": "PMC1974823-03-Results-01_T53", "type": "Organism", "text": [ "fimR- mutant" ], "offsets": [ [ 1848, 1860 ] ], "normalized": [] }, { "id": "PMC1974823-03-Results-01_T54", "type": "Protein", "text": [ "fimR" ], "offsets": [ [ 1848, 1852 ] ], "normalized": [] }, { "id": "PMC1974823-03-Results-01_T55", "type": "Organism", "text": [ "33277" ], "offsets": [ [ 1900, 1905 ] ], "normalized": [] }, { "id": "PMC1974823-03-Results-01_T56", "type": "Protein", "text": [ "RgpA" ], "offsets": [ [ 1950, 1954 ] ], "normalized": [] }, { "id": "PMC1974823-03-Results-01_T57", "type": "Organism", "text": [ "fimR- mutant" ], "offsets": [ [ 1973, 1985 ] ], "normalized": [] }, { "id": "PMC1974823-03-Results-01_T58", "type": "Protein", "text": [ "fimR" ], "offsets": [ [ 1973, 1977 ] ], "normalized": [] }, { "id": "PMC1974823-03-Results-01_T59", "type": "Protein", "text": [ "RgpA" ], "offsets": [ [ 2014, 2018 ] ], "normalized": [] } ]

[ { "id": "PMC1974823-03-Results-01_E1", "type": "Regulation", "trigger": { "text": [ "Role" ], "offsets": [ [ 9, 13 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC1974823-03-Results-01_E2" }, { "role": "Cause", "ref_id": "PMC1974823-03-Results-01_T1" } ] }, { "id": "PMC1974823-03-Results-01_E2", "type": "Gene_expression", "trigger": { "text": [ "expression" ], "offsets": [ [ 30, 40 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC1974823-03-Results-01_T2" } ] }, { "id": "PMC1974823-03-Results-01_E3", "type": "Regulation", "trigger": { "text": [ "controlled" ], "offsets": [ [ 92, 102 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC1974823-03-Results-01_T3" }, { "role": "Cause", "ref_id": "PMC1974823-03-Results-01_T4" } ] }, { "id": "PMC1974823-03-Results-01_E4", "type": "Regulation", "trigger": { "text": [ "effects" ], "offsets": [ [ 260, 267 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC1974823-03-Results-01_E5" }, { "role": "Cause", "ref_id": "PMC1974823-03-Results-01_T7" } ] }, { "id": "PMC1974823-03-Results-01_E5", "type": "Gene_expression", "trigger": { "text": [ "expression" ], "offsets": [ [ 279, 289 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC1974823-03-Results-01_T8" } ] }, { "id": "PMC1974823-03-Results-01_E6", "type": "Gene_expression", "trigger": { "text": [ "Expression" ], "offsets": [ [ 375, 385 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC1974823-03-Results-01_T11" } ] }, { "id": "PMC1974823-03-Results-01_E7", "type": "Gene_expression", "trigger": { "text": [ "Expression" ], "offsets": [ [ 375, 385 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC1974823-03-Results-01_T12" } ] }, { "id": "PMC1974823-03-Results-01_E8", "type": "Gene_expression", "trigger": { "text": [ "expression" ], "offsets": [ [ 628, 638 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC1974823-03-Results-01_T18" } ] }, { "id": "PMC1974823-03-Results-01_E9", "type": "Negative_regulation", "trigger": { "text": [ "abolished" ], "offsets": [ [ 660, 669 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC1974823-03-Results-01_E8" } ] }, { "id": "PMC1974823-03-Results-01_E10", "type": "Gene_expression", "trigger": { "text": [ "expression" ], "offsets": [ [ 832, 842 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC1974823-03-Results-01_T21" } ] }, { "id": "PMC1974823-03-Results-01_E11", "type": "Negative_regulation", "trigger": { "text": [ "repressed" ], "offsets": [ [ 869, 878 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC1974823-03-Results-01_E10" } ] }, { "id": "PMC1974823-03-Results-01_E12", "type": "Gene_expression", "trigger": { "text": [ "expression" ], "offsets": [ [ 960, 970 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC1974823-03-Results-01_T24" } ] }, { "id": "PMC1974823-03-Results-01_E13", "type": "Regulation", "trigger": { "text": [ "effect" ], "offsets": [ [ 1007, 1013 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC1974823-03-Results-01_E14" } ] }, { "id": "PMC1974823-03-Results-01_E14", "type": "Gene_expression", "trigger": { "text": [ "expression" ], "offsets": [ [ 1017, 1027 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC1974823-03-Results-01_T26" } ] }, { "id": "PMC1974823-03-Results-01_E15", "type": "Positive_regulation", "trigger": { "text": [ "required" ], "offsets": [ [ 1167, 1175 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC1974823-03-Results-01_E16" }, { "role": "Cause", "ref_id": "PMC1974823-03-Results-01_T29" } ] }, { "id": "PMC1974823-03-Results-01_E16", "type": "Gene_expression", "trigger": { "text": [ "expression" ], "offsets": [ [ 1180, 1190 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC1974823-03-Results-01_T32" } ] }, { "id": "PMC1974823-03-Results-01_E17", "type": "Gene_expression", "trigger": { "text": [ "expression" ], "offsets": [ [ 1638, 1648 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC1974823-03-Results-01_T47" } ] }, { "id": "PMC1974823-03-Results-01_E18", "type": "Gene_expression", "trigger": { "text": [ "expression" ], "offsets": [ [ 1638, 1648 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC1974823-03-Results-01_T48" } ] }, { "id": "PMC1974823-03-Results-01_E19", "type": "Gene_expression", "trigger": { "text": [ "production" ], "offsets": [ [ 1955, 1965 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC1974823-03-Results-01_T56" } ] } ]

[]

[]

[ { "id": "PMC2816692-01-Introduction__text", "type": "abstract", "text": [ "Introduction \nMany Gram-negative bacteria that colonize host animals use a type III secretion system (T3SS) to deliver effector proteins directly into host cells where their interaction with host proteins and membranes contribute to pathogenesis. Comprised of over 20 proteins, T3SS are complex structures with relation to the flagellar T3SS [1],[2] and include several central features; (i) inner and outer membrane ring structures, (ii) an extracellular needle structure with pore-forming proteins at the distal tip that engage a host cell membrane, (iii) an ATPase at the base of the apparatus with energetic and chaperone-effector recruitment roles, and (iv) a suite of chaperones to coordinate the assembly and function of the apparatus during infection. Secretion chaperones are proteins required for T3SS function with roles in apparatus assembly and effector delivery, but are not themselves subject to secretion [3]. These chaperones often have common physical features such as low molecular weight (<15 kDa), an acidic isoelectric point and a predicted amphipathic helix at the carboxyl terminus. Current literature groups secretion chaperones into three classes based on their physical interactions with cargo [3],[4]. Class I chaperones bind to translocated effector proteins at a chaperone binding domain (CBD) located in the amino terminus of the effector. Class I chaperones have a structural fold of five beta-strands and three alpha-helices, forming homodimers that bind to the CBD in a horseshoe-like structure. These chaperones have been further sub-classified based on their substrate repertoire and location with respect to the genes encoding the T3SS [3]. Class II chaperones bind to translocon proteins that make up the secretion pore in the host target membrane and class III chaperones bind the extracellular filament proteins (or flagellin rod in the orthologous flagellar system) that polymerize into a helical structure following secretion from the bacterial cell. Secondary structure predictions suggest class III chaperones adopt an extended alpha helical structure, which was confirmed by the crystal structure of the CesA chaperone in enteropathogenic E. coli that binds the EspA filament protein [5]. Much of the virulence potential of Salmonella enterica, a group of more than 2300 serotypes, is attributed to horizontally acquired genomic islands termed Salmonella Pathogenicity Islands (SPI). SPI-1 encodes a T3SS required for host cell invasion and SPI-2 encodes a second T3SS needed for intracellular survival and immune evasion [6],[7]. To date, 13 effectors have been identified as substrates of the SPI-1 T3SS and 21 effectors for the SPI-2 T3SS, although the chaperones orchestrating the latter system have been elusive. Whereas 80% of the effectors of the SPI-1 system have defined chaperones, only two effector-chaperone interactions are known for the SPI-2 system. These include the effector-chaperone pair of SseF-SscB, and the chaperone SseA that binds translocon components SseD and SseB [8],[9],[10]. Crystal structures have been determined for three chaperones that coordinate translocation of effectors through the SPI-1 T3SS (InvB [11], SicP [12] and SigE [13]). However no structures are available for the SPI-2 T3SS chaperones whose effector repertoire seems considerably larger than that of the SPI-1 system. In addition to maintaining a region of localized effector unfolding [12], T3SS chaperones have an emerging role as escorts that deliver their cargo to the cytoplasmic face of the inner membrane through physical interactions with an ATPase. These ATPases form a hexameric structure at the base of the T3SS [14] and are a conserved feature of both flagellar and non-flagellar type III systems to enhance secretion activity by promoting chaperone release and effector unfolding prior to secretion [15],[16],[17]. A chaperone-ATPase interaction for the SPI-2 T3SS has not been described previously and so whether this system conforms to the emerging escort paradigm is not known. The regulation of the SPI-2 T3SS and its associated effector genes is coordinated by environmental cues signifying the intracellular environment [18]. These cues activate a two-component signaling system encoded in the SPI-2 island comprising the SsrA sensor kinase and SsrB response regulator. In addition to activating all of the T3SS structural operons, transcriptional profiling has uncovered new genes in the SsrB regulon that are required for bacterial pathogenesis including a translocated effector, SseL [19],[20], and a gene of unknown function called srfN that is common to the Salmonella genus [21]. Using a reverse genetics approach we identified an SsrB-regulated gene (STM2138) that we named srcA (SsrB-regulated chaperone A), whose gene product satisfied several a priori predictions relating to the physical properties associated with T3SS chaperones. We solved the crystal structure of SrcA and performed additional biochemical, proteomic and in vivo experiments that revealed SrcA to be a class I chaperone required for bacterial fitness in the host environment. Despite being genetically disconnected from SPI-2, SrcA is integrated functionally with this system by binding to the T3SS ATPase, SsaN, and providing chaperone activity towards two important effectors, SseL (STM2287) and PipB2 (STM2780), necessary for immune escape and cell-to-cell transmission. These data reveal structural and biochemical insight into a T3SS secretion chaperone required for intracellular pathogenesis of Salmonella.\n" ], "offsets": [ [ 0, 5559 ] ] } ]

[ { "id": "PMC2816692-01-Introduction_T1", "type": "Organism", "text": [ "host" ], "offsets": [ [ 56, 60 ] ], "normalized": [] }, { "id": "PMC2816692-01-Introduction_T2", "type": "Organism", "text": [ "host" ], "offsets": [ [ 151, 155 ] ], "normalized": [] }, { "id": "PMC2816692-01-Introduction_T3", "type": "Organism", "text": [ "host" ], "offsets": [ [ 191, 195 ] ], "normalized": [] }, { "id": "PMC2816692-01-Introduction_T4", "type": "Organism", "text": [ "host" ], "offsets": [ [ 532, 536 ] ], "normalized": [] }, { "id": "PMC2816692-01-Introduction_T5", "type": "Chemical", "text": [ "carboxyl" ], "offsets": [ [ 1088, 1096 ] ], "normalized": [] }, { "id": "PMC2816692-01-Introduction_T6", "type": "Chemical", "text": [ "amino" ], "offsets": [ [ 1339, 1344 ] ], "normalized": [] }, { "id": "PMC2816692-01-Introduction_T7", "type": "Protein", "text": [ "CesA" ], "offsets": [ [ 2149, 2153 ] ], "normalized": [] }, { "id": "PMC2816692-01-Introduction_T8", "type": "Organism", "text": [ "E. coli" ], "offsets": [ [ 2184, 2191 ] ], "normalized": [] }, { "id": "PMC2816692-01-Introduction_T9", "type": "Protein", "text": [ "EspA" ], "offsets": [ [ 2207, 2211 ] ], "normalized": [] }, { "id": "PMC2816692-01-Introduction_T10", "type": "Organism", "text": [ "Salmonella enterica" ], "offsets": [ [ 2269, 2288 ] ], "normalized": [] }, { "id": "PMC2816692-01-Introduction_T11", "type": "Organism", "text": [ "host" ], "offsets": [ [ 2463, 2467 ] ], "normalized": [] }, { "id": "PMC2816692-01-Introduction_T12", "type": "Protein", "text": [ "SseF" ], "offsets": [ [ 2955, 2959 ] ], "normalized": [] }, { "id": "PMC2816692-01-Introduction_T13", "type": "Protein", "text": [ "SscB" ], "offsets": [ [ 2960, 2964 ] ], "normalized": [] }, { "id": "PMC2816692-01-Introduction_T14", "type": "Protein", "text": [ "SseA" ], "offsets": [ [ 2984, 2988 ] ], "normalized": [] }, { "id": "PMC2816692-01-Introduction_T15", "type": "Protein", "text": [ "SseD" ], "offsets": [ [ 3022, 3026 ] ], "normalized": [] }, { "id": "PMC2816692-01-Introduction_T16", "type": "Protein", "text": [ "SseB" ], "offsets": [ [ 3031, 3035 ] ], "normalized": [] }, { "id": "PMC2816692-01-Introduction_T17", "type": "Protein", "text": [ "InvB" ], "offsets": [ [ 3178, 3182 ] ], "normalized": [] }, { "id": "PMC2816692-01-Introduction_T18", "type": "Protein", "text": [ "SicP" ], "offsets": [ [ 3189, 3193 ] ], "normalized": [] }, { "id": "PMC2816692-01-Introduction_T19", "type": "Protein", "text": [ "SigE" ], "offsets": [ [ 3203, 3207 ] ], "normalized": [] }, { "id": "PMC2816692-01-Introduction_T20", "type": "Protein", "text": [ "SsrA" ], "offsets": [ [ 4287, 4291 ] ], "normalized": [] }, { "id": "PMC2816692-01-Introduction_T21", "type": "Protein", "text": [ "SsrB" ], "offsets": [ [ 4310, 4314 ] ], "normalized": [] }, { "id": "PMC2816692-01-Introduction_T22", "type": "Regulon-operon", "text": [ "SsrB regulon" ], "offsets": [ [ 4454, 4466 ] ], "normalized": [] }, { "id": "PMC2816692-01-Introduction_T23", "type": "Protein", "text": [ "SsrB" ], "offsets": [ [ 4454, 4458 ] ], "normalized": [] }, { "id": "PMC2816692-01-Introduction_T24", "type": "Protein", "text": [ "SseL" ], "offsets": [ [ 4547, 4551 ] ], "normalized": [] }, { "id": "PMC2816692-01-Introduction_T25", "type": "Protein", "text": [ "srfN" ], "offsets": [ [ 4601, 4605 ] ], "normalized": [] }, { "id": "PMC2816692-01-Introduction_T26", "type": "Organism", "text": [ "Salmonella" ], "offsets": [ [ 4628, 4638 ] ], "normalized": [] }, { "id": "PMC2816692-01-Introduction_T27", "type": "Protein", "text": [ "SsrB" ], "offsets": [ [ 4702, 4706 ] ], "normalized": [] }, { "id": "PMC2816692-01-Introduction_T28", "type": "Protein", "text": [ "STM2138" ], "offsets": [ [ 4723, 4730 ] ], "normalized": [] }, { "id": "PMC2816692-01-Introduction_T29", "type": "Protein", "text": [ "srcA" ], "offsets": [ [ 4746, 4750 ] ], "normalized": [] }, { "id": "PMC2816692-01-Introduction_T30", "type": "Protein", "text": [ "SsrB-regulated chaperone A" ], "offsets": [ [ 4752, 4778 ] ], "normalized": [] }, { "id": "PMC2816692-01-Introduction_T31", "type": "Protein", "text": [ "SrcA" ], "offsets": [ [ 4943, 4947 ] ], "normalized": [] }, { "id": "PMC2816692-01-Introduction_T32", "type": "Protein", "text": [ "SrcA" ], "offsets": [ [ 5034, 5038 ] ], "normalized": [] }, { "id": "PMC2816692-01-Introduction_T33", "type": "Protein", "text": [ "SrcA" ], "offsets": [ [ 5172, 5176 ] ], "normalized": [] }, { "id": "PMC2816692-01-Introduction_T34", "type": "Protein", "text": [ "SsaN" ], "offsets": [ [ 5252, 5256 ] ], "normalized": [] }, { "id": "PMC2816692-01-Introduction_T35", "type": "Protein", "text": [ "SseL" ], "offsets": [ [ 5324, 5328 ] ], "normalized": [] }, { "id": "PMC2816692-01-Introduction_T36", "type": "Protein", "text": [ "STM2287" ], "offsets": [ [ 5330, 5337 ] ], "normalized": [] }, { "id": "PMC2816692-01-Introduction_T37", "type": "Protein", "text": [ "PipB2" ], "offsets": [ [ 5343, 5348 ] ], "normalized": [] }, { "id": "PMC2816692-01-Introduction_T38", "type": "Protein", "text": [ "STM2780" ], "offsets": [ [ 5350, 5357 ] ], "normalized": [] }, { "id": "PMC2816692-01-Introduction_T39", "type": "Organism", "text": [ "Salmonella" ], "offsets": [ [ 5547, 5557 ] ], "normalized": [] } ]

[ { "id": "PMC2816692-01-Introduction_E1", "type": "Process", "trigger": { "text": [ "infection" ], "offsets": [ [ 749, 758 ] ] }, "arguments": [] }, { "id": "PMC2816692-01-Introduction_E2", "type": "Binding", "trigger": { "text": [ "binds" ], "offsets": [ [ 2197, 2202 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC2816692-01-Introduction_T7" }, { "role": "Theme", "ref_id": "PMC2816692-01-Introduction_T9" } ] }, { "id": "PMC2816692-01-Introduction_E3", "type": "Process", "trigger": { "text": [ "virulence" ], "offsets": [ [ 2246, 2255 ] ] }, "arguments": [ { "role": "Participant", "ref_id": "PMC2816692-01-Introduction_T10" } ] }, { "id": "PMC2816692-01-Introduction_E4", "type": "Binding", "trigger": { "text": [ "binds" ], "offsets": [ [ 2994, 2999 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC2816692-01-Introduction_T14" }, { "role": "Theme", "ref_id": "PMC2816692-01-Introduction_T15" } ] }, { "id": "PMC2816692-01-Introduction_E5", "type": "Binding", "trigger": { "text": [ "binds" ], "offsets": [ [ 2994, 2999 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC2816692-01-Introduction_T14" }, { "role": "Theme", "ref_id": "PMC2816692-01-Introduction_T16" } ] }, { "id": "PMC2816692-01-Introduction_E6", "type": "Regulation", "trigger": { "text": [ "regulated" ], "offsets": [ [ 4707, 4716 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC2816692-01-Introduction_T28" }, { "role": "Cause", "ref_id": "PMC2816692-01-Introduction_T27" } ] }, { "id": "PMC2816692-01-Introduction_E7", "type": "Binding", "trigger": { "text": [ "binding" ], "offsets": [ [ 5224, 5231 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC2816692-01-Introduction_T33" }, { "role": "Theme", "ref_id": "PMC2816692-01-Introduction_T34" } ] } ]

[ { "id": "PMC2816692-01-Introduction_1", "entity_ids": [ "PMC2816692-01-Introduction_T29", "PMC2816692-01-Introduction_T28", "PMC2816692-01-Introduction_T30" ] }, { "id": "PMC2816692-01-Introduction_2", "entity_ids": [ "PMC2816692-01-Introduction_T36", "PMC2816692-01-Introduction_T35" ] }, { "id": "PMC2816692-01-Introduction_3", "entity_ids": [ "PMC2816692-01-Introduction_T38", "PMC2816692-01-Introduction_T37" ] } ]

[]

[ { "id": "PMC2565068-02-Results-04__text", "type": "abstract", "text": [ "Impaired migration of PMN is due to degradation of IL-8 by serine proteinase ScpC \nAlthough NIH230slo lost the killing activity for PMN, migration of PMN in response to IL-8 in a transwell system was not restored in the presence of this mutant (Figure 4A), thereby, suggesting that severe invasive GAS blocks PMN migration by influence on IL-8 activity. Therefore, we quantified the amount of IL-8 in culture before and after co-culture with clinically isolated GAS or its mutants. Figure 4B shows that the amount of IL-8 was significantly reduced by 60-min co-culture with NIH230, as well as NIH230slo, but not with non-invasive GAS 1556. As previous reports suggested that the GAS envelope peptidase ScpC (also known as SpyCEP) degrades the CXC chemokines, such as human IL-8, Groalpha, murine KC and MIP-2 [17]-[19], we established a NIH230 mutant deficient with ScpC (NIH230scpC) and analyzed the property in a PMN migration assay. The results showed that NIH230scpC neither digested IL-8, like 1566 strain, (Figure 4B) nor abrogated the migration of PMN in response to IL-8, comparable to 1566 strain (Figure 4A), whereas the mutant killed the migrated PMN as well as the parent strain NIH230 (data not shown). These results demonstrate that clinically isolated invasive GAS impaired PMN recruitment and its survival, as a result of productions of ScpC and SLO, respectively.\n" ], "offsets": [ [ 0, 1381 ] ] } ]

[ { "id": "PMC2565068-02-Results-04_T1", "type": "Protein", "text": [ "IL-8" ], "offsets": [ [ 51, 55 ] ], "normalized": [] }, { "id": "PMC2565068-02-Results-04_T2", "type": "Protein", "text": [ "ScpC" ], "offsets": [ [ 77, 81 ] ], "normalized": [] }, { "id": "PMC2565068-02-Results-04_T3", "type": "Organism", "text": [ "NIH230slo" ], "offsets": [ [ 92, 101 ] ], "normalized": [] }, { "id": "PMC2565068-02-Results-04_T4", "type": "Protein", "text": [ "slo" ], "offsets": [ [ 98, 101 ] ], "normalized": [] }, { "id": "PMC2565068-02-Results-04_T5", "type": "Protein", "text": [ "IL-8" ], "offsets": [ [ 169, 173 ] ], "normalized": [] }, { "id": "PMC2565068-02-Results-04_T6", "type": "Organism", "text": [ "invasive GAS" ], "offsets": [ [ 289, 301 ] ], "normalized": [] }, { "id": "PMC2565068-02-Results-04_T7", "type": "Protein", "text": [ "IL-8" ], "offsets": [ [ 339, 343 ] ], "normalized": [] }, { "id": "PMC2565068-02-Results-04_T8", "type": "Protein", "text": [ "IL-8" ], "offsets": [ [ 393, 397 ] ], "normalized": [] }, { "id": "PMC2565068-02-Results-04_T9", "type": "Organism", "text": [ "GAS" ], "offsets": [ [ 462, 465 ] ], "normalized": [] }, { "id": "PMC2565068-02-Results-04_T10", "type": "Organism", "text": [ "its mutants" ], "offsets": [ [ 469, 480 ] ], "normalized": [] }, { "id": "PMC2565068-02-Results-04_T11", "type": "Protein", "text": [ "IL-8" ], "offsets": [ [ 517, 521 ] ], "normalized": [] }, { "id": "PMC2565068-02-Results-04_T12", "type": "Organism", "text": [ "NIH230" ], "offsets": [ [ 574, 580 ] ], "normalized": [] }, { "id": "PMC2565068-02-Results-04_T13", "type": "Organism", "text": [ "NIH230slo" ], "offsets": [ [ 593, 602 ] ], "normalized": [] }, { "id": "PMC2565068-02-Results-04_T14", "type": "Protein", "text": [ "slo" ], "offsets": [ [ 599, 602 ] ], "normalized": [] }, { "id": "PMC2565068-02-Results-04_T15", "type": "Organism", "text": [ "non-invasive GAS 1556" ], "offsets": [ [ 617, 638 ] ], "normalized": [] }, { "id": "PMC2565068-02-Results-04_T16", "type": "Organism", "text": [ "GAS" ], "offsets": [ [ 679, 682 ] ], "normalized": [] }, { "id": "PMC2565068-02-Results-04_T17", "type": "Protein", "text": [ "ScpC" ], "offsets": [ [ 702, 706 ] ], "normalized": [] }, { "id": "PMC2565068-02-Results-04_T18", "type": "Protein", "text": [ "SpyCEP" ], "offsets": [ [ 722, 728 ] ], "normalized": [] }, { "id": "PMC2565068-02-Results-04_T19", "type": "Organism", "text": [ "human" ], "offsets": [ [ 767, 772 ] ], "normalized": [] }, { "id": "PMC2565068-02-Results-04_T20", "type": "Protein", "text": [ "IL-8" ], "offsets": [ [ 773, 777 ] ], "normalized": [] }, { "id": "PMC2565068-02-Results-04_T21", "type": "Protein", "text": [ "Groalpha" ], "offsets": [ [ 779, 787 ] ], "normalized": [] }, { "id": "PMC2565068-02-Results-04_T22", "type": "Organism", "text": [ "murine" ], "offsets": [ [ 789, 795 ] ], "normalized": [] }, { "id": "PMC2565068-02-Results-04_T23", "type": "Protein", "text": [ "KC" ], "offsets": [ [ 796, 798 ] ], "normalized": [] }, { "id": "PMC2565068-02-Results-04_T24", "type": "Protein", "text": [ "MIP-2" ], "offsets": [ [ 803, 808 ] ], "normalized": [] }, { "id": "PMC2565068-02-Results-04_T25", "type": "Organism", "text": [ "NIH230 mutant" ], "offsets": [ [ 837, 850 ] ], "normalized": [] }, { "id": "PMC2565068-02-Results-04_T26", "type": "Protein", "text": [ "ScpC" ], "offsets": [ [ 866, 870 ] ], "normalized": [] }, { "id": "PMC2565068-02-Results-04_T27", "type": "Organism", "text": [ "NIH230scpC" ], "offsets": [ [ 872, 882 ] ], "normalized": [] }, { "id": "PMC2565068-02-Results-04_T28", "type": "Protein", "text": [ "scpC" ], "offsets": [ [ 878, 882 ] ], "normalized": [] }, { "id": "PMC2565068-02-Results-04_T29", "type": "Organism", "text": [ "NIH230scpC" ], "offsets": [ [ 960, 970 ] ], "normalized": [] }, { "id": "PMC2565068-02-Results-04_T30", "type": "Protein", "text": [ "scpC" ], "offsets": [ [ 966, 970 ] ], "normalized": [] }, { "id": "PMC2565068-02-Results-04_T31", "type": "Protein", "text": [ "IL-8" ], "offsets": [ [ 988, 992 ] ], "normalized": [] }, { "id": "PMC2565068-02-Results-04_T32", "type": "Organism", "text": [ "1566 strain" ], "offsets": [ [ 999, 1010 ] ], "normalized": [] }, { "id": "PMC2565068-02-Results-04_T33", "type": "Protein", "text": [ "IL-8" ], "offsets": [ [ 1074, 1078 ] ], "normalized": [] }, { "id": "PMC2565068-02-Results-04_T34", "type": "Organism", "text": [ "1566 strain" ], "offsets": [ [ 1094, 1105 ] ], "normalized": [] }, { "id": "PMC2565068-02-Results-04_T35", "type": "Organism", "text": [ "parent strain NIH230" ], "offsets": [ [ 1177, 1197 ] ], "normalized": [] }, { "id": "PMC2565068-02-Results-04_T36", "type": "Organism", "text": [ "invasive GAS" ], "offsets": [ [ 1267, 1279 ] ], "normalized": [] }, { "id": "PMC2565068-02-Results-04_T37", "type": "Protein", "text": [ "ScpC" ], "offsets": [ [ 1353, 1357 ] ], "normalized": [] }, { "id": "PMC2565068-02-Results-04_T38", "type": "Protein", "text": [ "SLO" ], "offsets": [ [ 1362, 1365 ] ], "normalized": [] } ]

[ { "id": "PMC2565068-02-Results-04_E1", "type": "Protein_catabolism", "trigger": { "text": [ "degradation" ], "offsets": [ [ 36, 47 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC2565068-02-Results-04_T1" } ] }, { "id": "PMC2565068-02-Results-04_E2", "type": "Positive_regulation", "trigger": { "text": [ "degradation" ], "offsets": [ [ 36, 47 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC2565068-02-Results-04_E1" }, { "role": "Cause", "ref_id": "PMC2565068-02-Results-04_T2" } ] }, { "id": "PMC2565068-02-Results-04_E3", "type": "Positive_regulation", "trigger": { "text": [ "degrades" ], "offsets": [ [ 730, 738 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC2565068-02-Results-04_E10" }, { "role": "Cause", "ref_id": "PMC2565068-02-Results-04_T17" } ] }, { "id": "PMC2565068-02-Results-04_E4", "type": "Protein_catabolism", "trigger": { "text": [ "degrades" ], "offsets": [ [ 730, 738 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC2565068-02-Results-04_T20" } ] }, { "id": "PMC2565068-02-Results-04_E5", "type": "Positive_regulation", "trigger": { "text": [ "degrades" ], "offsets": [ [ 730, 738 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC2565068-02-Results-04_E4" }, { "role": "Cause", "ref_id": "PMC2565068-02-Results-04_T17" } ] }, { "id": "PMC2565068-02-Results-04_E6", "type": "Protein_catabolism", "trigger": { "text": [ "degrades" ], "offsets": [ [ 730, 738 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC2565068-02-Results-04_T21" } ] }, { "id": "PMC2565068-02-Results-04_E7", "type": "Positive_regulation", "trigger": { "text": [ "degrades" ], "offsets": [ [ 730, 738 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC2565068-02-Results-04_E6" }, { "role": "Cause", "ref_id": "PMC2565068-02-Results-04_T17" } ] }, { "id": "PMC2565068-02-Results-04_E8", "type": "Protein_catabolism", "trigger": { "text": [ "degrades" ], "offsets": [ [ 730, 738 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC2565068-02-Results-04_T23" } ] }, { "id": "PMC2565068-02-Results-04_E9", "type": "Positive_regulation", "trigger": { "text": [ "degrades" ], "offsets": [ [ 730, 738 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC2565068-02-Results-04_E8" }, { "role": "Cause", "ref_id": "PMC2565068-02-Results-04_T17" } ] }, { "id": "PMC2565068-02-Results-04_E10", "type": "Protein_catabolism", "trigger": { "text": [ "degrades" ], "offsets": [ [ 730, 738 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC2565068-02-Results-04_T24" } ] }, { "id": "PMC2565068-02-Results-04_E11", "type": "Protein_catabolism", "trigger": { "text": [ "digested" ], "offsets": [ [ 979, 987 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC2565068-02-Results-04_T31" } ] }, { "id": "PMC2565068-02-Results-04_E12", "type": "Gene_expression", "trigger": { "text": [ "productions" ], "offsets": [ [ 1338, 1349 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC2565068-02-Results-04_T37" } ] }, { "id": "PMC2565068-02-Results-04_E13", "type": "Gene_expression", "trigger": { "text": [ "productions" ], "offsets": [ [ 1338, 1349 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC2565068-02-Results-04_T38" } ] } ]

[ { "id": "PMC2565068-02-Results-04_1", "entity_ids": [ "PMC2565068-02-Results-04_T17", "PMC2565068-02-Results-04_T18" ] } ]

[]

[ { "id": "PMC1974823-01-Introduction__text", "type": "abstract", "text": [ "Introduction \nPorphyromonas gingivalis is a gram-negative bacterium, which is considered to be a major periodontal pathogen (Socransky & Haffajee, 2005). It is also a pathogen that may be involved in coronary heart disease and preterm births (Boggess et al., 2005; Brodala et al., 2005; Chou et al., 2005). The ability of P. gingivalis to initiate a periodontal infection is mainly dependent on the expression of fimbriae (Malek et al., 1994). Two distinct fimbriae are found on the surface of the organism (Dickinson et al., 1988; Hamada et al., 1996). The long (major) filamentous structure is comprised of a FimA subunit protein encoded by the fimA gene. The short (minor) fimbriae are made up of a 67 kDa protein (Mfa1). Both fimbriae appear to be involved in bacterial pathogenicity (Amano et al., 2004). The function of the FimA protein and regulation of fimA expression have been extensively studied. The FimA protein is required for P. gingivalis colonization on salivary coated surfaces, and the early colonization of dental plaque (Malek et al., 1994; Levesque et al., 2003; Maeda et al., 2004). A P. gingivalis fimA mutant shows impaired invasion capability of epithelial cells compared with wild-type strain, suggesting the involvement of FimA in the bacterial interaction with surface receptor(s) on gingival cells (Weinberg et al., 1997). Earlier studies by the authors showed that FimA expression was modulated by environmental cues, including temperature and hemin concentration, and by the presence of Streptococcus cristatus, an early colonizer of dental plaque (Xie et al., 1997, 2000b). FimR, a response regulator of the fimS/fimR two-component system was identified, and FimA expression was found to be dramatically reduced in fimR mutants (Hayashi et al., 2000). Investigation of the mechanism of regulation of fimA by FimR indicates that FimR does not bind directly to the fimA promoter, but rather binds to the promoter region of the first gene (pg2130) in the fimA cluster, suggesting that PG2130 is the FimR target gene, which in turn regulates expression of other genes in the fimA cluster, including the fimA gene (Nishikawa et al., 2004). The short fimbriae (Mfa1) also contribute to P. gingivalis colonization. Coadhesion and biofilm development between P. gingivalis and Streptococcus gordonii require the interaction of Mfa1 with streptococcal protein SspB (Park et al., 2005). The authors have recently reported that the short fimbriae are required for P. gingivalis cell-cell aggregation, an essential step in microcolony formation (Lin et al., 2006). A mutant with a deficiency in minor fimbriae binds to a saliva-coated surface but does not form microcolonies as the wild-type strain does. Mfa1 expression appears to fluctuate under various growth conditions (Masuda et al., 2006). In a nutrient-limited medium, expression of FimA and Mfa1 are inhibited in P. gingivalis, whereas such differences are not found in gingipain expression. A recent study has shown that expression of mfa1 is repressed in the presence of some common oral plaque bacteria such as S. gordonii, Streptococcus sanguinis and Streptococcus mitis (Park et al., 2006). However, very little is known about regulatory mechanisms of mfa1 expression. In this study, it is demonstrated that FimR is a positive regulator of Mfa1 expression. Evidence is provided that unlike FimR-dependent fimA expression, FimR regulates mfa1 expression by directly binding to the promoter region of mfa1.\n" ], "offsets": [ [ 0, 3490 ] ] } ]

[ { "id": "PMC1974823-01-Introduction_T1", "type": "Organism", "text": [ "Porphyromonas gingivalis" ], "offsets": [ [ 14, 38 ] ], "normalized": [] }, { "id": "PMC1974823-01-Introduction_T2", "type": "Organism", "text": [ "P. gingivalis" ], "offsets": [ [ 322, 335 ] ], "normalized": [] }, { "id": "PMC1974823-01-Introduction_T3", "type": "Protein", "text": [ "FimA" ], "offsets": [ [ 611, 615 ] ], "normalized": [] }, { "id": "PMC1974823-01-Introduction_T4", "type": "Protein", "text": [ "fimA" ], "offsets": [ [ 647, 651 ] ], "normalized": [] }, { "id": "PMC1974823-01-Introduction_T5", "type": "Protein", "text": [ "Mfa1" ], "offsets": [ [ 718, 722 ] ], "normalized": [] }, { "id": "PMC1974823-01-Introduction_T6", "type": "Protein", "text": [ "FimA" ], "offsets": [ [ 830, 834 ] ], "normalized": [] }, { "id": "PMC1974823-01-Introduction_T7", "type": "Protein", "text": [ "fimA" ], "offsets": [ [ 861, 865 ] ], "normalized": [] }, { "id": "PMC1974823-01-Introduction_T8", "type": "Protein", "text": [ "FimA" ], "offsets": [ [ 912, 916 ] ], "normalized": [] }, { "id": "PMC1974823-01-Introduction_T9", "type": "Organism", "text": [ "P. gingivalis" ], "offsets": [ [ 941, 954 ] ], "normalized": [] }, { "id": "PMC1974823-01-Introduction_T10", "type": "Organism", "text": [ "P. gingivalis" ], "offsets": [ [ 1108, 1121 ] ], "normalized": [] }, { "id": "PMC1974823-01-Introduction_T11", "type": "Organism", "text": [ "fimA mutant" ], "offsets": [ [ 1122, 1133 ] ], "normalized": [] }, { "id": "PMC1974823-01-Introduction_T12", "type": "Protein", "text": [ "fimA" ], "offsets": [ [ 1122, 1126 ] ], "normalized": [] }, { "id": "PMC1974823-01-Introduction_T13", "type": "Protein", "text": [ "FimA" ], "offsets": [ [ 1251, 1255 ] ], "normalized": [] }, { "id": "PMC1974823-01-Introduction_T14", "type": "Protein", "text": [ "FimA" ], "offsets": [ [ 1396, 1400 ] ], "normalized": [] }, { "id": "PMC1974823-01-Introduction_T15", "type": "Chemical", "text": [ "hemin" ], "offsets": [ [ 1475, 1480 ] ], "normalized": [] }, { "id": "PMC1974823-01-Introduction_T16", "type": "Organism", "text": [ "Streptococcus cristatus" ], "offsets": [ [ 1519, 1542 ] ], "normalized": [] }, { "id": "PMC1974823-01-Introduction_T17", "type": "Protein", "text": [ "FimR" ], "offsets": [ [ 1607, 1611 ] ], "normalized": [] }, { "id": "PMC1974823-01-Introduction_T18", "type": "Two-component-system", "text": [ "fimS/fimR" ], "offsets": [ [ 1641, 1650 ] ], "normalized": [] }, { "id": "PMC1974823-01-Introduction_T19", "type": "Protein", "text": [ "fimS" ], "offsets": [ [ 1641, 1645 ] ], "normalized": [] }, { "id": "PMC1974823-01-Introduction_T20", "type": "Protein", "text": [ "fimR" ], "offsets": [ [ 1646, 1650 ] ], "normalized": [] }, { "id": "PMC1974823-01-Introduction_T21", "type": "Protein", "text": [ "FimA" ], "offsets": [ [ 1692, 1696 ] ], "normalized": [] }, { "id": "PMC1974823-01-Introduction_T22", "type": "Organism", "text": [ "fimR mutants" ], "offsets": [ [ 1748, 1760 ] ], "normalized": [] }, { "id": "PMC1974823-01-Introduction_T23", "type": "Protein", "text": [ "fimR" ], "offsets": [ [ 1748, 1752 ] ], "normalized": [] }, { "id": "PMC1974823-01-Introduction_T24", "type": "Protein", "text": [ "fimA" ], "offsets": [ [ 1833, 1837 ] ], "normalized": [] }, { "id": "PMC1974823-01-Introduction_T25", "type": "Protein", "text": [ "FimR" ], "offsets": [ [ 1841, 1845 ] ], "normalized": [] }, { "id": "PMC1974823-01-Introduction_T26", "type": "Protein", "text": [ "FimR" ], "offsets": [ [ 1861, 1865 ] ], "normalized": [] }, { "id": "PMC1974823-01-Introduction_T27", "type": "Protein", "text": [ "fimA" ], "offsets": [ [ 1896, 1900 ] ], "normalized": [] }, { "id": "PMC1974823-01-Introduction_T28", "type": "Protein", "text": [ "pg2130" ], "offsets": [ [ 1970, 1976 ] ], "normalized": [] }, { "id": "PMC1974823-01-Introduction_T29", "type": "Protein", "text": [ "fimA" ], "offsets": [ [ 1985, 1989 ] ], "normalized": [] }, { "id": "PMC1974823-01-Introduction_T30", "type": "Protein", "text": [ "PG2130" ], "offsets": [ [ 2015, 2021 ] ], "normalized": [] }, { "id": "PMC1974823-01-Introduction_T31", "type": "Protein", "text": [ "FimR" ], "offsets": [ [ 2029, 2033 ] ], "normalized": [] }, { "id": "PMC1974823-01-Introduction_T32", "type": "Protein", "text": [ "fimA" ], "offsets": [ [ 2104, 2108 ] ], "normalized": [] }, { "id": "PMC1974823-01-Introduction_T33", "type": "Protein", "text": [ "fimA" ], "offsets": [ [ 2132, 2136 ] ], "normalized": [] }, { "id": "PMC1974823-01-Introduction_T34", "type": "Protein", "text": [ "Mfa1" ], "offsets": [ [ 2188, 2192 ] ], "normalized": [] }, { "id": "PMC1974823-01-Introduction_T35", "type": "Organism", "text": [ "P. gingivalis" ], "offsets": [ [ 2213, 2226 ] ], "normalized": [] }, { "id": "PMC1974823-01-Introduction_T36", "type": "Organism", "text": [ "P. gingivalis" ], "offsets": [ [ 2284, 2297 ] ], "normalized": [] }, { "id": "PMC1974823-01-Introduction_T37", "type": "Organism", "text": [ "Streptococcus gordonii" ], "offsets": [ [ 2302, 2324 ] ], "normalized": [] }, { "id": "PMC1974823-01-Introduction_T38", "type": "Protein", "text": [ "Mfa1" ], "offsets": [ [ 2352, 2356 ] ], "normalized": [] }, { "id": "PMC1974823-01-Introduction_T39", "type": "Protein", "text": [ "SspB" ], "offsets": [ [ 2384, 2388 ] ], "normalized": [] }, { "id": "PMC1974823-01-Introduction_T40", "type": "Organism", "text": [ "P. gingivalis" ], "offsets": [ [ 2486, 2499 ] ], "normalized": [] }, { "id": "PMC1974823-01-Introduction_T41", "type": "Protein", "text": [ "Mfa1" ], "offsets": [ [ 2726, 2730 ] ], "normalized": [] }, { "id": "PMC1974823-01-Introduction_T42", "type": "Protein", "text": [ "FimA" ], "offsets": [ [ 2862, 2866 ] ], "normalized": [] }, { "id": "PMC1974823-01-Introduction_T43", "type": "Protein", "text": [ "Mfa1" ], "offsets": [ [ 2871, 2875 ] ], "normalized": [] }, { "id": "PMC1974823-01-Introduction_T44", "type": "Organism", "text": [ "P. gingivalis" ], "offsets": [ [ 2893, 2906 ] ], "normalized": [] }, { "id": "PMC1974823-01-Introduction_T45", "type": "Protein", "text": [ "mfa1" ], "offsets": [ [ 3016, 3020 ] ], "normalized": [] }, { "id": "PMC1974823-01-Introduction_T46", "type": "Organism", "text": [ "S. gordonii" ], "offsets": [ [ 3094, 3105 ] ], "normalized": [] }, { "id": "PMC1974823-01-Introduction_T47", "type": "Organism", "text": [ "Streptococcus sanguinis" ], "offsets": [ [ 3107, 3130 ] ], "normalized": [] }, { "id": "PMC1974823-01-Introduction_T48", "type": "Organism", "text": [ "Streptococcus mitis" ], "offsets": [ [ 3135, 3154 ] ], "normalized": [] }, { "id": "PMC1974823-01-Introduction_T49", "type": "Protein", "text": [ "mfa1" ], "offsets": [ [ 3237, 3241 ] ], "normalized": [] }, { "id": "PMC1974823-01-Introduction_T50", "type": "Protein", "text": [ "FimR" ], "offsets": [ [ 3293, 3297 ] ], "normalized": [] }, { "id": "PMC1974823-01-Introduction_T51", "type": "Protein", "text": [ "Mfa1" ], "offsets": [ [ 3325, 3329 ] ], "normalized": [] }, { "id": "PMC1974823-01-Introduction_T52", "type": "Protein", "text": [ "FimR" ], "offsets": [ [ 3375, 3379 ] ], "normalized": [] }, { "id": "PMC1974823-01-Introduction_T53", "type": "Protein", "text": [ "fimA" ], "offsets": [ [ 3390, 3394 ] ], "normalized": [] }, { "id": "PMC1974823-01-Introduction_T54", "type": "Protein", "text": [ "FimR" ], "offsets": [ [ 3407, 3411 ] ], "normalized": [] }, { "id": "PMC1974823-01-Introduction_T55", "type": "Protein", "text": [ "mfa1" ], "offsets": [ [ 3422, 3426 ] ], "normalized": [] }, { "id": "PMC1974823-01-Introduction_T56", "type": "Protein", "text": [ "mfa1" ], "offsets": [ [ 3484, 3488 ] ], "normalized": [] }, { "id": "PMC1974823-01-Introduction_T67", "type": "Entity", "text": [ "promoter" ], "offsets": [ [ 1901, 1909 ] ], "normalized": [] }, { "id": "PMC1974823-01-Introduction_T69", "type": "Entity", "text": [ "promoter region" ], "offsets": [ [ 1935, 1950 ] ], "normalized": [] }, { "id": "PMC1974823-01-Introduction_T90", "type": "Entity", "text": [ "promoter region" ], "offsets": [ [ 3465, 3480 ] ], "normalized": [] } ]

[ { "id": "PMC1974823-01-Introduction_E1", "type": "Process", "trigger": { "text": [ "infection" ], "offsets": [ [ 362, 371 ] ] }, "arguments": [ { "role": "Participant", "ref_id": "PMC1974823-01-Introduction_T2" } ] }, { "id": "PMC1974823-01-Introduction_E2", "type": "Positive_regulation", "trigger": { "text": [ "dependent" ], "offsets": [ [ 382, 391 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC1974823-01-Introduction_E1" } ] }, { "id": "PMC1974823-01-Introduction_E3", "type": "Regulation", "trigger": { "text": [ "regulation" ], "offsets": [ [ 847, 857 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC1974823-01-Introduction_E4" } ] }, { "id": "PMC1974823-01-Introduction_E4", "type": "Gene_expression", "trigger": { "text": [ "expression" ], "offsets": [ [ 866, 876 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC1974823-01-Introduction_T7" } ] }, { "id": "PMC1974823-01-Introduction_E5", "type": "Gene_expression", "trigger": { "text": [ "expression" ], "offsets": [ [ 1401, 1411 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC1974823-01-Introduction_T14" } ] }, { "id": "PMC1974823-01-Introduction_E6", "type": "Regulation", "trigger": { "text": [ "modulated" ], "offsets": [ [ 1416, 1425 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC1974823-01-Introduction_E5" } ] }, { "id": "PMC1974823-01-Introduction_E7", "type": "Gene_expression", "trigger": { "text": [ "expression" ], "offsets": [ [ 1697, 1707 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC1974823-01-Introduction_T21" } ] }, { "id": "PMC1974823-01-Introduction_E8", "type": "Negative_regulation", "trigger": { "text": [ "reduced" ], "offsets": [ [ 1737, 1744 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC1974823-01-Introduction_E7" } ] }, { "id": "PMC1974823-01-Introduction_E9", "type": "Regulation", "trigger": { "text": [ "regulation" ], "offsets": [ [ 1819, 1829 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC1974823-01-Introduction_T24" }, { "role": "Cause", "ref_id": "PMC1974823-01-Introduction_T25" } ] }, { "id": "PMC1974823-01-Introduction_E10", "type": "Binding", "trigger": { "text": [ "bind" ], "offsets": [ [ 1875, 1879 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC1974823-01-Introduction_T26" }, { "role": "Theme", "ref_id": "PMC1974823-01-Introduction_T27" }, { "role": "Site", "ref_id": "PMC1974823-01-Introduction_T67" } ] }, { "id": "PMC1974823-01-Introduction_E11", "type": "Binding", "trigger": { "text": [ "binds" ], "offsets": [ [ 1922, 1927 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC1974823-01-Introduction_T26" }, { "role": "Theme", "ref_id": "PMC1974823-01-Introduction_T28" }, { "role": "Site", "ref_id": "PMC1974823-01-Introduction_T69" } ] }, { "id": "PMC1974823-01-Introduction_E12", "type": "Regulation", "trigger": { "text": [ "regulates" ], "offsets": [ [ 2061, 2070 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC1974823-01-Introduction_E13" }, { "role": "Cause", "ref_id": "PMC1974823-01-Introduction_T30" } ] }, { "id": "PMC1974823-01-Introduction_E13", "type": "Gene_expression", "trigger": { "text": [ "expression" ], "offsets": [ [ 2071, 2081 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC1974823-01-Introduction_T33" } ] }, { "id": "PMC1974823-01-Introduction_E14", "type": "Binding", "trigger": { "text": [ "Coadhesion" ], "offsets": [ [ 2241, 2251 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC1974823-01-Introduction_T36" }, { "role": "Theme", "ref_id": "PMC1974823-01-Introduction_T37" } ] }, { "id": "PMC1974823-01-Introduction_E15", "type": "Positive_regulation", "trigger": { "text": [ "require" ], "offsets": [ [ 2325, 2332 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC1974823-01-Introduction_E14" }, { "role": "Cause", "ref_id": "PMC1974823-01-Introduction_E16" } ] }, { "id": "PMC1974823-01-Introduction_E16", "type": "Binding", "trigger": { "text": [ "interaction" ], "offsets": [ [ 2337, 2348 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC1974823-01-Introduction_T38" }, { "role": "Theme", "ref_id": "PMC1974823-01-Introduction_T39" } ] }, { "id": "PMC1974823-01-Introduction_E17", "type": "Gene_expression", "trigger": { "text": [ "expression" ], "offsets": [ [ 2731, 2741 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC1974823-01-Introduction_T41" } ] }, { "id": "PMC1974823-01-Introduction_E18", "type": "Regulation", "trigger": { "text": [ "fluctuate" ], "offsets": [ [ 2753, 2762 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC1974823-01-Introduction_E17" } ] }, { "id": "PMC1974823-01-Introduction_E19", "type": "Gene_expression", "trigger": { "text": [ "expression" ], "offsets": [ [ 2848, 2858 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC1974823-01-Introduction_T42" } ] }, { "id": "PMC1974823-01-Introduction_E20", "type": "Gene_expression", "trigger": { "text": [ "expression" ], "offsets": [ [ 2848, 2858 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC1974823-01-Introduction_T43" } ] }, { "id": "PMC1974823-01-Introduction_E21", "type": "Negative_regulation", "trigger": { "text": [ "inhibited" ], "offsets": [ [ 2880, 2889 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC1974823-01-Introduction_E19" } ] }, { "id": "PMC1974823-01-Introduction_E22", "type": "Negative_regulation", "trigger": { "text": [ "inhibited" ], "offsets": [ [ 2880, 2889 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC1974823-01-Introduction_E20" } ] }, { "id": "PMC1974823-01-Introduction_E23", "type": "Gene_expression", "trigger": { "text": [ "expression" ], "offsets": [ [ 3002, 3012 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC1974823-01-Introduction_T45" } ] }, { "id": "PMC1974823-01-Introduction_E24", "type": "Negative_regulation", "trigger": { "text": [ "repressed" ], "offsets": [ [ 3024, 3033 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC1974823-01-Introduction_E23" } ] }, { "id": "PMC1974823-01-Introduction_E25", "type": "Regulation", "trigger": { "text": [ "regulatory mechanisms" ], "offsets": [ [ 3212, 3233 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC1974823-01-Introduction_E26" } ] }, { "id": "PMC1974823-01-Introduction_E26", "type": "Gene_expression", "trigger": { "text": [ "expression" ], "offsets": [ [ 3242, 3252 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC1974823-01-Introduction_T49" } ] }, { "id": "PMC1974823-01-Introduction_E27", "type": "Positive_regulation", "trigger": { "text": [ "positive regulator" ], "offsets": [ [ 3303, 3321 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC1974823-01-Introduction_E28" }, { "role": "Cause", "ref_id": "PMC1974823-01-Introduction_T50" } ] }, { "id": "PMC1974823-01-Introduction_E28", "type": "Gene_expression", "trigger": { "text": [ "expression" ], "offsets": [ [ 3330, 3340 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC1974823-01-Introduction_T51" } ] }, { "id": "PMC1974823-01-Introduction_E29", "type": "Positive_regulation", "trigger": { "text": [ "dependent" ], "offsets": [ [ 3380, 3389 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC1974823-01-Introduction_E30" }, { "role": "Cause", "ref_id": "PMC1974823-01-Introduction_T52" } ] }, { "id": "PMC1974823-01-Introduction_E30", "type": "Gene_expression", "trigger": { "text": [ "expression" ], "offsets": [ [ 3395, 3405 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC1974823-01-Introduction_T53" } ] }, { "id": "PMC1974823-01-Introduction_E31", "type": "Regulation", "trigger": { "text": [ "regulates" ], "offsets": [ [ 3412, 3421 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC1974823-01-Introduction_E32" }, { "role": "Cause", "ref_id": "PMC1974823-01-Introduction_E33" } ] }, { "id": "PMC1974823-01-Introduction_E32", "type": "Gene_expression", "trigger": { "text": [ "expression" ], "offsets": [ [ 3427, 3437 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC1974823-01-Introduction_T55" } ] }, { "id": "PMC1974823-01-Introduction_E33", "type": "Binding", "trigger": { "text": [ "binding" ], "offsets": [ [ 3450, 3457 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC1974823-01-Introduction_T54" }, { "role": "Theme", "ref_id": "PMC1974823-01-Introduction_T56" }, { "role": "Site", "ref_id": "PMC1974823-01-Introduction_T90" } ] } ]

[]

[]

[ { "id": "PMC2774163-03-Discussion__text", "type": "abstract", "text": [ "Discussion \nEvidence showing that biofilm development is a coordinated series of events coinciding with distinct phenotypes has led to the assumption that the formation of biofilms is a regulated progression [11],[12],[66]. However, biofilm development has been considered to be distinct from other developmental processes including the programmed differentiation seen in spore formation in Bacillus subtilis or fruiting body formation in Myxococcus xanthus [11], mainly because no regulatory pathways have yet been identified that are responsible for regulating committed steps in the formation of biofilms with the exception of attachment. In this study we describe the identification and initial characterization of three novel two-component systems (TCS) essential in regulating three committed steps in biofilm development. Mutation in these regulatory pathways did not affect initial attachment, motility, or Pel and Psl polysaccharide production, but instead arrested biofilm development in the transition from reversible to irreversible attachment [8 hr to 24 hr, BfiRS (PA4196-4197)], from initial attachment to the maturation-1 stage [(24 hr to 72 hr, BfmRS (PA4101-4102)], and following the maturation-1 stage [72 hr to 144 hr, MifRS (PA5511-5512)] (Fig. 6). To our knowledge, this is the first description of a regulatory program for stage-specific biofilm development. The stage-specific arrest in biofilm formation of the mutant strains coincided with the timing of phosphorylation of the respective regulatory or sensory proteins indicating that the phosphorylation status of the three novel two-component systems is essential for their function in regulating biofilm development by P. aeruginosa. Furthermore, the phosphorylation of these two-component systems occurred in sequence with BfiS being phosphorylated first, followed by GacS, and lastly, MifR (Table 1, Fig. 6). The sequential phosphorylation of sensors/regulatory proteins is reminiscent of a regulatory cascade in which each phosphorylation event acts as a trigger for bacterial biofilm cells to transition to the next developmental stage (Fig. 6). Furthermore, the novel TCS systems described here appear to be linked via GacS to the multicomponent system RetS/LadS/GacAS/RsmA essential for regulating the switch between the planktonic and the sessile mode of growth. While it is not clear how the three two-component systems interact to form the observed sequential phosphorylation cascade, it is apparent from our observations that phosphorylation of each of the three novel TCS has to occur for P. aeruginosa biofilms to mature (Fig. 2). Possible scenarios for the sequential phosphorylation events to occur are by direct interaction or activation of a TCS system by one that is upstream in the cascade ( Fig. 6), or indirectly. Since inactivation of each TCS system resulted in altered or arrested biofilms which failed to exhibit stage-specific protein production and phosphorylation events (Figs. 1, 4, Suppl. Table S2), it is likely that the mutant biofilms in turn do not produce the necessary signal(s) to activate or phosphorylate TCS system(s) that are further downstream. Thus, it is likely that inactivation of one TCS system (in)directly results in altered or arrested phosphorylation patterns and thus, lack of phosphorylation of downstream TCS systems (as observed here). Independent of the mechanism, it is evident that inactivation not only disrupts the sequence of phosphorylation events but also leads to the collapse of mature biofilms to an earlier biofilm developmental stage at which the respective regulatory proteins play a role (Fig. 5, Table 3). This is even more important as this biofilm collapse was observed under two different nutritional conditions, when grown on minimal medium using either glutamate or citrate as a sole carbon source (see also Figs. 2 and 5 for comparison of LB and glutamate minimal medium). The finding suggests that while biofilm formation, architecture and cell-cell signaling is modulated by environmental and nutritional conditions resulting in biofilm development proceeding via distinctly different pathways [16], [55]-[63], it is possible that the novel regulatory proteins identified here play a role under more than one discrete culturing condition or pathway. The novelty of these TCS is further supported by the finding that a search for BfiS (PA4197) and BfmR (PA4101) homologues using BLAST (http://blast.ncbi.nlm.nih.gov/Blast.cgi) and BLINK (precomputed BLAST, [53]), did not reveal any proteins that have been previously characterized in the literature. However, BfiS-like sensory proteins with identities ranging between 28-68% were detected in a variety of Gram-negative bacteria, in particular in alpha-, beta-, and gamma-proteobacteria (Suppl. Table S3). No homologues, however, were detected in lambda-proteobacteria or E. coli, Klebsiella pneumoniae, and Enterobacter sp. Similarly, BfmR homologues were detected among proteobacteria including Yersinia sp., Burkholderia sp., Rhizobium sp., Vibrio sp, Geobacter sp., and M. xanthus with identities ranging between 50-92% (Suppl. Table S3). MifR homologues harboring a sigma-54 binding domain are present in both Gram-positive and Gram-negative bacteria including M. xanthus (Suppl. Table S3). The closest MifR homologue in M. xanthus was identified as the NtrC-like chemosensory regulator of development CrdA (48% identity). Inactivation of crdA has been shown to result in delayed M. xanthus multicellular development [67]. NtrC-like regulators belong to a family of transcriptional activators which control a variety of physiological processes in response to environmental signals [68]. This family of regulators control transcription from -12, -24 promoters recognized by RNA polymerase that utilizes the alternative sigma 54 factor encoded by rpoN and its analogs. At least 8 NtrC-like transcriptional regulators are involved in coordinating M. xanthus fruiting body formation at distinct stages of the developmental process [69]-[71]. The preponderance of developmental promoters with sigma 54 hallmarks led to the suggestion that NtrC-like activators are key components of the transcriptional machinery that coordinates gene expression during M. xanthus development [72]. While fruiting body formation is governed by a cascade of RpoN-dependent transcription factors in starving cells, endospore formation in B. subtilis requires the consecutive activity of multiple sigma factors including Sigma E, F, G, and K. Their activity is regulated by posttranslational processes, either by cleaving the precursor molecules or by sequestration of sigma factors by \"anti-sigma factor\" proteins in response to intercellular cues, and compartmentalization [68],[73]. Similarly, biofilm developmental processes appear to be controlled by sigma factors. Based on domain structure, two TCS regulatory proteins identified here regulate genes controlled by the sigma factors RpoD and RpoN [53],[74],[75]. BfiR harbors region 4 of Sigma-70 (RpoD)-like sigma factors, a domain involved in binding to -35 promoter elements. Activation of BfiR coincides with BfiS phosphorylation following 8 hours of surface attached growth and dephosphorylation of RpoD (Table 1). MifR harbors a sigma-54 binding (RpoN) binding domain and is dependent on the consecutive phosphorylation of BfiRS and BfmRS (see Suppl. Fig. S3). These results are consistent with the idea that biofilm development by P. aeruginosa is orchestrated by a regulatory cascade (Fig. 6) that is analogous to other developmental systems including spore formation in B. subtilis or fruiting body formation in M. xanthus, requiring the consecutive action of at least two sigma factors and three two-component regulatory systems in response to environmental signals. In summary, we have evidence of three novel regulatory systems playing a role in the progression of P. aeruginosa biofilm development in a stage-specific manner. The only other regulatory system having been identified to play a role at later stages of biofilm formation, in particular the formation of large microcolonies and fluid-filled channels, is the three-component system SadARS (RocS1RA1), probably by controlling the expression of fimbrial cup genes [66],[76]. In addition, coordinated transduction of phosphorylation events via two-component systems has also been shown to play a role in attachment. A multi-component switch composed of three unusual hybrid sensor kinases, RetS, LadS, and GacS, has recently been demonstrated to reciprocally orchestrate the transition from acute to chronic infection in P. aeruginosa, as well as to reciprocally regulate the transition between the planktonic and biofilm modes of growth by inversely coordinating repression of genes required for initial colonization, mainly genes responsible for exopolysaccharide components of the P. aeruginosa biofilm matrix [36],[37]. While our study did not result in the identification of RetS or LadS, we identified GacS by two different approaches and confirmed GacS phosphorylation by immunoblot analysis (Table 1). GacS acts as a suppressor of RetS (and vice versa) with RetS regulating the suppressor activity of the membrane-bound sensor GacS by directly modulating its phosphorylation state [38]. The finding is consistent with our observation of GacS playing a dual role in biofilm formation, with phosphorylation acting as a switch in the function of GacS (Fig. 3, Table 2): GacS participates in the planktonic/biofilm switch in its non-phosphorylated state, but limits/regulates the rate of biomass accumulation and biofilm development when phosphorylated. Since phosphorylation of GacS occurred following 8 hr of surface attached growth (Table 1) and since RetS directly modulates the phosphorylation state of GacS [38], the findings may suggest that RetS only remains functional for a period of 8 hours during initial attachment after which RetS is rendered non-functional. Here, GacS was found to be phosphorylated in a BfiS dependent manner. In turn, expression of the BfiS cognate response regulator, BfiR, was found to be RsmA dependent [77] (see Fig. 6). Taken together, our observations suggest a link between the multi-component switch RetS/LadS/GacAS/RsmA which reciprocally regulates virulence and the transition between the planktonic and the surface attached mode of growth and the previously undescribed signaling network which regulates developmental steps once P. aeruginosa has committed to the surface associated lifestyle (Fig. 6). Taken together, this work identifies a previously undescribed signal transduction network composed of BfiSR (PA4196-4197), BfmSR PA4101-4102), and MifSR (PA5511-5512) that sequentially regulates committed biofilm developmental steps following attachment by transcriptional and posttranscriptional mechanisms, which is linked via GacS and RsmA to the previously described multi-component switch RetS/LadS/GacAS/RsmA. Furthermore, the finding of sequential and essential regulatory steps in biofilm formation and the involvement of at least two sigma factors suggests that biofilm development is analogous to other programmed developmental processes. However, in contrast to known developmental processes, our findings suggest that both two-component regulatory systems and sigma factor dependent response regulators are key components of the transcriptional and regulatory machinery that coordinate gene expression during P. aeruginosa biofilm development.\n" ], "offsets": [ [ 0, 11520 ] ] } ]

[ { "id": "PMC2774163-03-Discussion_T1", "type": "Organism", "text": [ "Bacillus subtilis" ], "offsets": [ [ 391, 408 ] ], "normalized": [] }, { "id": "PMC2774163-03-Discussion_T2", "type": "Organism", "text": [ "Myxococcus xanthus" ], "offsets": [ [ 439, 457 ] ], "normalized": [] }, { "id": "PMC2774163-03-Discussion_T3", "type": "Protein", "text": [ "Pel" ], "offsets": [ [ 915, 918 ] ], "normalized": [] }, { "id": "PMC2774163-03-Discussion_T4", "type": "Protein", "text": [ "Psl" ], "offsets": [ [ 923, 926 ] ], "normalized": [] }, { "id": "PMC2774163-03-Discussion_T5", "type": "Two-component-system", "text": [ "BfiRS" ], "offsets": [ [ 1072, 1077 ] ], "normalized": [] }, { "id": "PMC2774163-03-Discussion_T6", "type": "Protein", "text": [ "BfiR" ], "offsets": [ [ 1072, 1076 ] ], "normalized": [] }, { "id": "PMC2774163-03-Discussion_T7", "type": "Protein", "text": [ "S" ], "offsets": [ [ 1076, 1077 ] ], "normalized": [] }, { "id": "PMC2774163-03-Discussion_T8", "type": "Two-component-system", "text": [ "PA4196-4197" ], "offsets": [ [ 1079, 1090 ] ], "normalized": [] }, { "id": "PMC2774163-03-Discussion_T9", "type": "Protein", "text": [ "PA4196" ], "offsets": [ [ 1079, 1085 ] ], "normalized": [] }, { "id": "PMC2774163-03-Discussion_T10", "type": "Protein", "text": [ "4197" ], "offsets": [ [ 1086, 1090 ] ], "normalized": [] }, { "id": "PMC2774163-03-Discussion_T11", "type": "Two-component-system", "text": [ "BfmRS" ], "offsets": [ [ 1162, 1167 ] ], "normalized": [] }, { "id": "PMC2774163-03-Discussion_T12", "type": "Protein", "text": [ "BfmR" ], "offsets": [ [ 1162, 1166 ] ], "normalized": [] }, { "id": "PMC2774163-03-Discussion_T13", "type": "Protein", "text": [ "S" ], "offsets": [ [ 1166, 1167 ] ], "normalized": [] }, { "id": "PMC2774163-03-Discussion_T14", "type": "Two-component-system", "text": [ "PA4101-4102" ], "offsets": [ [ 1169, 1180 ] ], "normalized": [] }, { "id": "PMC2774163-03-Discussion_T15", "type": "Protein", "text": [ "PA4101" ], "offsets": [ [ 1169, 1175 ] ], "normalized": [] }, { "id": "PMC2774163-03-Discussion_T16", "type": "Protein", "text": [ "4102" ], "offsets": [ [ 1176, 1180 ] ], "normalized": [] }, { "id": "PMC2774163-03-Discussion_T17", "type": "Two-component-system", "text": [ "MifRS" ], "offsets": [ [ 1239, 1244 ] ], "normalized": [] }, { "id": "PMC2774163-03-Discussion_T18", "type": "Protein", "text": [ "MifR" ], "offsets": [ [ 1239, 1243 ] ], "normalized": [] }, { "id": "PMC2774163-03-Discussion_T19", "type": "Protein", "text": [ "S" ], "offsets": [ [ 1243, 1244 ] ], "normalized": [] }, { "id": "PMC2774163-03-Discussion_T20", "type": "Two-component-system", "text": [ "PA5511-5512" ], "offsets": [ [ 1246, 1257 ] ], "normalized": [] }, { "id": "PMC2774163-03-Discussion_T21", "type": "Protein", "text": [ "PA5511" ], "offsets": [ [ 1246, 1252 ] ], "normalized": [] }, { "id": "PMC2774163-03-Discussion_T22", "type": "Protein", "text": [ "5512" ], "offsets": [ [ 1253, 1257 ] ], "normalized": [] }, { "id": "PMC2774163-03-Discussion_T23", "type": "Organism", "text": [ "P. aeruginosa" ], "offsets": [ [ 1698, 1711 ] ], "normalized": [] }, { "id": "PMC2774163-03-Discussion_T24", "type": "Protein", "text": [ "BfiS" ], "offsets": [ [ 1803, 1807 ] ], "normalized": [] }, { "id": "PMC2774163-03-Discussion_T25", "type": "Protein", "text": [ "GacS" ], "offsets": [ [ 1848, 1852 ] ], "normalized": [] }, { "id": "PMC2774163-03-Discussion_T26", "type": "Protein", "text": [ "MifR" ], "offsets": [ [ 1866, 1870 ] ], "normalized": [] }, { "id": "PMC2774163-03-Discussion_T27", "type": "Protein", "text": [ "GacS" ], "offsets": [ [ 2203, 2207 ] ], "normalized": [] }, { "id": "PMC2774163-03-Discussion_T28", "type": "Two-component-system", "text": [ "RetS/LadS" ], "offsets": [ [ 2237, 2246 ] ], "normalized": [] }, { "id": "PMC2774163-03-Discussion_T29", "type": "Protein", "text": [ "RetS" ], "offsets": [ [ 2237, 2241 ] ], "normalized": [] }, { "id": "PMC2774163-03-Discussion_T30", "type": "Protein", "text": [ "LadS" ], "offsets": [ [ 2242, 2246 ] ], "normalized": [] }, { "id": "PMC2774163-03-Discussion_T31", "type": "Protein", "text": [ "GacA" ], "offsets": [ [ 2247, 2251 ] ], "normalized": [] }, { "id": "PMC2774163-03-Discussion_T32", "type": "Protein", "text": [ "S" ], "offsets": [ [ 2251, 2252 ] ], "normalized": [] }, { "id": "PMC2774163-03-Discussion_T33", "type": "Protein", "text": [ "RsmA" ], "offsets": [ [ 2253, 2257 ] ], "normalized": [] }, { "id": "PMC2774163-03-Discussion_T34", "type": "Organism", "text": [ "P. aeruginosa" ], "offsets": [ [ 2579, 2592 ] ], "normalized": [] }, { "id": "PMC2774163-03-Discussion_T35", "type": "Chemical", "text": [ "glutamate" ], "offsets": [ [ 3807, 3816 ] ], "normalized": [] }, { "id": "PMC2774163-03-Discussion_T36", "type": "Chemical", "text": [ "citrate" ], "offsets": [ [ 3820, 3827 ] ], "normalized": [] }, { "id": "PMC2774163-03-Discussion_T37", "type": "Chemical", "text": [ "carbon" ], "offsets": [ [ 3838, 3844 ] ], "normalized": [] }, { "id": "PMC2774163-03-Discussion_T38", "type": "Protein", "text": [ "BfiS" ], "offsets": [ [ 4386, 4390 ] ], "normalized": [] }, { "id": "PMC2774163-03-Discussion_T39", "type": "Protein", "text": [ "PA4197" ], "offsets": [ [ 4392, 4398 ] ], "normalized": [] }, { "id": "PMC2774163-03-Discussion_T40", "type": "Protein", "text": [ "BfmR" ], "offsets": [ [ 4404, 4408 ] ], "normalized": [] }, { "id": "PMC2774163-03-Discussion_T41", "type": "Protein", "text": [ "PA4101" ], "offsets": [ [ 4410, 4416 ] ], "normalized": [] }, { "id": "PMC2774163-03-Discussion_T42", "type": "Protein", "text": [ "BfiS" ], "offsets": [ [ 4616, 4620 ] ], "normalized": [] }, { "id": "PMC2774163-03-Discussion_T43", "type": "Organism", "text": [ "E. coli" ], "offsets": [ [ 4878, 4885 ] ], "normalized": [] }, { "id": "PMC2774163-03-Discussion_T44", "type": "Organism", "text": [ "Klebsiella pneumoniae" ], "offsets": [ [ 4887, 4908 ] ], "normalized": [] }, { "id": "PMC2774163-03-Discussion_T45", "type": "Organism", "text": [ "Enterobacter sp" ], "offsets": [ [ 4914, 4929 ] ], "normalized": [] }, { "id": "PMC2774163-03-Discussion_T46", "type": "Protein", "text": [ "BfmR" ], "offsets": [ [ 4942, 4946 ] ], "normalized": [] }, { "id": "PMC2774163-03-Discussion_T47", "type": "Organism", "text": [ "Yersinia sp" ], "offsets": [ [ 5003, 5014 ] ], "normalized": [] }, { "id": "PMC2774163-03-Discussion_T48", "type": "Organism", "text": [ "Burkholderia sp" ], "offsets": [ [ 5017, 5032 ] ], "normalized": [] }, { "id": "PMC2774163-03-Discussion_T49", "type": "Organism", "text": [ "Rhizobium sp" ], "offsets": [ [ 5035, 5047 ] ], "normalized": [] }, { "id": "PMC2774163-03-Discussion_T50", "type": "Organism", "text": [ "Vibrio sp" ], "offsets": [ [ 5050, 5059 ] ], "normalized": [] }, { "id": "PMC2774163-03-Discussion_T51", "type": "Organism", "text": [ "Geobacter sp" ], "offsets": [ [ 5061, 5073 ] ], "normalized": [] }, { "id": "PMC2774163-03-Discussion_T52", "type": "Organism", "text": [ "M. xanthus" ], "offsets": [ [ 5080, 5090 ] ], "normalized": [] }, { "id": "PMC2774163-03-Discussion_T53", "type": "Protein", "text": [ "MifR" ], "offsets": [ [ 5149, 5153 ] ], "normalized": [] }, { "id": "PMC2774163-03-Discussion_T54", "type": "Organism", "text": [ "M. xanthus" ], "offsets": [ [ 5272, 5282 ] ], "normalized": [] }, { "id": "PMC2774163-03-Discussion_T55", "type": "Protein", "text": [ "MifR" ], "offsets": [ [ 5314, 5318 ] ], "normalized": [] }, { "id": "PMC2774163-03-Discussion_T56", "type": "Organism", "text": [ "M. xanthus" ], "offsets": [ [ 5332, 5342 ] ], "normalized": [] }, { "id": "PMC2774163-03-Discussion_T57", "type": "Protein", "text": [ "NtrC" ], "offsets": [ [ 5365, 5369 ] ], "normalized": [] }, { "id": "PMC2774163-03-Discussion_T58", "type": "Protein", "text": [ "CrdA" ], "offsets": [ [ 5413, 5417 ] ], "normalized": [] }, { "id": "PMC2774163-03-Discussion_T59", "type": "Protein", "text": [ "crdA" ], "offsets": [ [ 5450, 5454 ] ], "normalized": [] }, { "id": "PMC2774163-03-Discussion_T60", "type": "Organism", "text": [ "M. xanthus" ], "offsets": [ [ 5491, 5501 ] ], "normalized": [] }, { "id": "PMC2774163-03-Discussion_T61", "type": "Protein", "text": [ "NtrC" ], "offsets": [ [ 5534, 5538 ] ], "normalized": [] }, { "id": "PMC2774163-03-Discussion_T62", "type": "Protein", "text": [ "RNA polymerase" ], "offsets": [ [ 5784, 5798 ] ], "normalized": [] }, { "id": "PMC2774163-03-Discussion_T63", "type": "Protein", "text": [ "rpoN" ], "offsets": [ [ 5856, 5860 ] ], "normalized": [] }, { "id": "PMC2774163-03-Discussion_T64", "type": "Protein", "text": [ "NtrC" ], "offsets": [ [ 5889, 5893 ] ], "normalized": [] }, { "id": "PMC2774163-03-Discussion_T65", "type": "Organism", "text": [ "M. xanthus" ], "offsets": [ [ 5955, 5965 ] ], "normalized": [] }, { "id": "PMC2774163-03-Discussion_T66", "type": "Protein", "text": [ "NtrC" ], "offsets": [ [ 6145, 6149 ] ], "normalized": [] }, { "id": "PMC2774163-03-Discussion_T67", "type": "Organism", "text": [ "M. xanthus" ], "offsets": [ [ 6258, 6268 ] ], "normalized": [] }, { "id": "PMC2774163-03-Discussion_T68", "type": "Protein", "text": [ "RpoN" ], "offsets": [ [ 6345, 6349 ] ], "normalized": [] }, { "id": "PMC2774163-03-Discussion_T69", "type": "Organism", "text": [ "B. subtilis" ], "offsets": [ [ 6424, 6435 ] ], "normalized": [] }, { "id": "PMC2774163-03-Discussion_T70", "type": "Protein", "text": [ "Sigma E" ], "offsets": [ [ 6506, 6513 ] ], "normalized": [] }, { "id": "PMC2774163-03-Discussion_T71", "type": "Protein", "text": [ "F" ], "offsets": [ [ 6515, 6516 ] ], "normalized": [] }, { "id": "PMC2774163-03-Discussion_T72", "type": "Protein", "text": [ "G" ], "offsets": [ [ 6518, 6519 ] ], "normalized": [] }, { "id": "PMC2774163-03-Discussion_T73", "type": "Protein", "text": [ "K" ], "offsets": [ [ 6525, 6526 ] ], "normalized": [] }, { "id": "PMC2774163-03-Discussion_T74", "type": "Protein", "text": [ "RpoD" ], "offsets": [ [ 6974, 6978 ] ], "normalized": [] }, { "id": "PMC2774163-03-Discussion_T75", "type": "Protein", "text": [ "RpoN" ], "offsets": [ [ 6983, 6987 ] ], "normalized": [] }, { "id": "PMC2774163-03-Discussion_T76", "type": "Protein", "text": [ "BfiR" ], "offsets": [ [ 7004, 7008 ] ], "normalized": [] }, { "id": "PMC2774163-03-Discussion_T77", "type": "Protein", "text": [ "Sigma-70" ], "offsets": [ [ 7029, 7037 ] ], "normalized": [] }, { "id": "PMC2774163-03-Discussion_T78", "type": "Protein", "text": [ "RpoD" ], "offsets": [ [ 7039, 7043 ] ], "normalized": [] }, { "id": "PMC2774163-03-Discussion_T79", "type": "Protein", "text": [ "BfiR" ], "offsets": [ [ 7134, 7138 ] ], "normalized": [] }, { "id": "PMC2774163-03-Discussion_T80", "type": "Protein", "text": [ "BfiS" ], "offsets": [ [ 7154, 7158 ] ], "normalized": [] }, { "id": "PMC2774163-03-Discussion_T81", "type": "Protein", "text": [ "RpoD" ], "offsets": [ [ 7245, 7249 ] ], "normalized": [] }, { "id": "PMC2774163-03-Discussion_T82", "type": "Protein", "text": [ "MifR" ], "offsets": [ [ 7261, 7265 ] ], "normalized": [] }, { "id": "PMC2774163-03-Discussion_T83", "type": "Protein", "text": [ "sigma-54" ], "offsets": [ [ 7276, 7284 ] ], "normalized": [] }, { "id": "PMC2774163-03-Discussion_T84", "type": "Protein", "text": [ "RpoN" ], "offsets": [ [ 7294, 7298 ] ], "normalized": [] }, { "id": "PMC2774163-03-Discussion_T85", "type": "Two-component-system", "text": [ "BfiRS" ], "offsets": [ [ 7370, 7375 ] ], "normalized": [] }, { "id": "PMC2774163-03-Discussion_T86", "type": "Protein", "text": [ "BfiR" ], "offsets": [ [ 7370, 7374 ] ], "normalized": [] }, { "id": "PMC2774163-03-Discussion_T87", "type": "Protein", "text": [ "S" ], "offsets": [ [ 7374, 7375 ] ], "normalized": [] }, { "id": "PMC2774163-03-Discussion_T88", "type": "Two-component-system", "text": [ "BfmRS" ], "offsets": [ [ 7380, 7385 ] ], "normalized": [] }, { "id": "PMC2774163-03-Discussion_T89", "type": "Protein", "text": [ "BfmR" ], "offsets": [ [ 7380, 7384 ] ], "normalized": [] }, { "id": "PMC2774163-03-Discussion_T90", "type": "Protein", "text": [ "S" ], "offsets": [ [ 7384, 7385 ] ], "normalized": [] }, { "id": "PMC2774163-03-Discussion_T91", "type": "Organism", "text": [ "P. aeruginosa" ], "offsets": [ [ 7479, 7492 ] ], "normalized": [] }, { "id": "PMC2774163-03-Discussion_T92", "type": "Organism", "text": [ "B. subtilis" ], "offsets": [ [ 7620, 7631 ] ], "normalized": [] }, { "id": "PMC2774163-03-Discussion_T93", "type": "Organism", "text": [ "M. xanthus" ], "offsets": [ [ 7662, 7672 ] ], "normalized": [] }, { "id": "PMC2774163-03-Discussion_T94", "type": "Organism", "text": [ "P. aeruginosa" ], "offsets": [ [ 7918, 7931 ] ], "normalized": [] }, { "id": "PMC2774163-03-Discussion_T95", "type": "Protein", "text": [ "SadA" ], "offsets": [ [ 8197, 8201 ] ], "normalized": [] }, { "id": "PMC2774163-03-Discussion_T96", "type": "Protein", "text": [ "R" ], "offsets": [ [ 8201, 8202 ] ], "normalized": [] }, { "id": "PMC2774163-03-Discussion_T97", "type": "Protein", "text": [ "S" ], "offsets": [ [ 8202, 8203 ] ], "normalized": [] }, { "id": "PMC2774163-03-Discussion_T98", "type": "Protein", "text": [ "RocS1" ], "offsets": [ [ 8205, 8210 ] ], "normalized": [] }, { "id": "PMC2774163-03-Discussion_T99", "type": "Protein", "text": [ "RA" ], "offsets": [ [ 8210, 8212 ] ], "normalized": [] }, { "id": "PMC2774163-03-Discussion_T100", "type": "Protein", "text": [ "1" ], "offsets": [ [ 8212, 8213 ] ], "normalized": [] }, { "id": "PMC2774163-03-Discussion_T101", "type": "Protein", "text": [ "RetS" ], "offsets": [ [ 8502, 8506 ] ], "normalized": [] }, { "id": "PMC2774163-03-Discussion_T102", "type": "Protein", "text": [ "LadS" ], "offsets": [ [ 8508, 8512 ] ], "normalized": [] }, { "id": "PMC2774163-03-Discussion_T103", "type": "Protein", "text": [ "GacS" ], "offsets": [ [ 8518, 8522 ] ], "normalized": [] }, { "id": "PMC2774163-03-Discussion_T104", "type": "Organism", "text": [ "P. aeruginosa" ], "offsets": [ [ 8633, 8646 ] ], "normalized": [] }, { "id": "PMC2774163-03-Discussion_T105", "type": "Organism", "text": [ "P. aeruginosa" ], "offsets": [ [ 8896, 8909 ] ], "normalized": [] }, { "id": "PMC2774163-03-Discussion_T106", "type": "Protein", "text": [ "RetS" ], "offsets": [ [ 8992, 8996 ] ], "normalized": [] }, { "id": "PMC2774163-03-Discussion_T107", "type": "Protein", "text": [ "LadS" ], "offsets": [ [ 9000, 9004 ] ], "normalized": [] }, { "id": "PMC2774163-03-Discussion_T108", "type": "Protein", "text": [ "GacS" ], "offsets": [ [ 9020, 9024 ] ], "normalized": [] }, { "id": "PMC2774163-03-Discussion_T109", "type": "Protein", "text": [ "GacS" ], "offsets": [ [ 9067, 9071 ] ], "normalized": [] }, { "id": "PMC2774163-03-Discussion_T110", "type": "Protein", "text": [ "GacS" ], "offsets": [ [ 9122, 9126 ] ], "normalized": [] }, { "id": "PMC2774163-03-Discussion_T111", "type": "Protein", "text": [ "RetS" ], "offsets": [ [ 9151, 9155 ] ], "normalized": [] }, { "id": "PMC2774163-03-Discussion_T112", "type": "Protein", "text": [ "RetS" ], "offsets": [ [ 9178, 9182 ] ], "normalized": [] }, { "id": "PMC2774163-03-Discussion_T113", "type": "Protein", "text": [ "GacS" ], "offsets": [ [ 9247, 9251 ] ], "normalized": [] }, { "id": "PMC2774163-03-Discussion_T114", "type": "Protein", "text": [ "GacS" ], "offsets": [ [ 9357, 9361 ] ], "normalized": [] }, { "id": "PMC2774163-03-Discussion_T115", "type": "Protein", "text": [ "GacS" ], "offsets": [ [ 9463, 9467 ] ], "normalized": [] }, { "id": "PMC2774163-03-Discussion_T116", "type": "Protein", "text": [ "GacS" ], "offsets": [ [ 9487, 9491 ] ], "normalized": [] }, { "id": "PMC2774163-03-Discussion_T117", "type": "Protein", "text": [ "GacS" ], "offsets": [ [ 9695, 9699 ] ], "normalized": [] }, { "id": "PMC2774163-03-Discussion_T118", "type": "Protein", "text": [ "RetS" ], "offsets": [ [ 9771, 9775 ] ], "normalized": [] }, { "id": "PMC2774163-03-Discussion_T119", "type": "Protein", "text": [ "GacS" ], "offsets": [ [ 9824, 9828 ] ], "normalized": [] }, { "id": "PMC2774163-03-Discussion_T120", "type": "Protein", "text": [ "RetS" ], "offsets": [ [ 9865, 9869 ] ], "normalized": [] }, { "id": "PMC2774163-03-Discussion_T121", "type": "Protein", "text": [ "RetS" ], "offsets": [ [ 9956, 9960 ] ], "normalized": [] }, { "id": "PMC2774163-03-Discussion_T122", "type": "Protein", "text": [ "GacS" ], "offsets": [ [ 9995, 9999 ] ], "normalized": [] }, { "id": "PMC2774163-03-Discussion_T123", "type": "Protein", "text": [ "BfiS" ], "offsets": [ [ 10036, 10040 ] ], "normalized": [] }, { "id": "PMC2774163-03-Discussion_T124", "type": "Protein", "text": [ "BfiS" ], "offsets": [ [ 10086, 10090 ] ], "normalized": [] }, { "id": "PMC2774163-03-Discussion_T125", "type": "Protein", "text": [ "BfiR" ], "offsets": [ [ 10119, 10123 ] ], "normalized": [] }, { "id": "PMC2774163-03-Discussion_T126", "type": "Protein", "text": [ "RsmA" ], "offsets": [ [ 10141, 10145 ] ], "normalized": [] }, { "id": "PMC2774163-03-Discussion_T127", "type": "Protein", "text": [ "RetS" ], "offsets": [ [ 10258, 10262 ] ], "normalized": [] }, { "id": "PMC2774163-03-Discussion_T128", "type": "Protein", "text": [ "LadS" ], "offsets": [ [ 10263, 10267 ] ], "normalized": [] }, { "id": "PMC2774163-03-Discussion_T129", "type": "Protein", "text": [ "GacA" ], "offsets": [ [ 10268, 10272 ] ], "normalized": [] }, { "id": "PMC2774163-03-Discussion_T130", "type": "Protein", "text": [ "S" ], "offsets": [ [ 10272, 10273 ] ], "normalized": [] }, { "id": "PMC2774163-03-Discussion_T131", "type": "Protein", "text": [ "RsmA" ], "offsets": [ [ 10274, 10278 ] ], "normalized": [] }, { "id": "PMC2774163-03-Discussion_T132", "type": "Organism", "text": [ "P. aeruginosa" ], "offsets": [ [ 10490, 10503 ] ], "normalized": [] }, { "id": "PMC2774163-03-Discussion_T133", "type": "Two-component-system", "text": [ "BfiSR" ], "offsets": [ [ 10666, 10671 ] ], "normalized": [] }, { "id": "PMC2774163-03-Discussion_T134", "type": "Protein", "text": [ "BfiS" ], "offsets": [ [ 10666, 10670 ] ], "normalized": [] }, { "id": "PMC2774163-03-Discussion_T135", "type": "Protein", "text": [ "R" ], "offsets": [ [ 10670, 10671 ] ], "normalized": [] }, { "id": "PMC2774163-03-Discussion_T136", "type": "Two-component-system", "text": [ "PA4196-4197" ], "offsets": [ [ 10673, 10684 ] ], "normalized": [] }, { "id": "PMC2774163-03-Discussion_T137", "type": "Protein", "text": [ "PA4196" ], "offsets": [ [ 10673, 10679 ] ], "normalized": [] }, { "id": "PMC2774163-03-Discussion_T138", "type": "Protein", "text": [ "4197" ], "offsets": [ [ 10680, 10684 ] ], "normalized": [] }, { "id": "PMC2774163-03-Discussion_T139", "type": "Two-component-system", "text": [ "BfmSR" ], "offsets": [ [ 10687, 10692 ] ], "normalized": [] }, { "id": "PMC2774163-03-Discussion_T140", "type": "Protein", "text": [ "BfmS" ], "offsets": [ [ 10687, 10691 ] ], "normalized": [] }, { "id": "PMC2774163-03-Discussion_T141", "type": "Protein", "text": [ "R" ], "offsets": [ [ 10691, 10692 ] ], "normalized": [] }, { "id": "PMC2774163-03-Discussion_T142", "type": "Two-component-system", "text": [ "PA4101-4102" ], "offsets": [ [ 10693, 10704 ] ], "normalized": [] }, { "id": "PMC2774163-03-Discussion_T143", "type": "Protein", "text": [ "PA4101" ], "offsets": [ [ 10693, 10699 ] ], "normalized": [] }, { "id": "PMC2774163-03-Discussion_T144", "type": "Protein", "text": [ "4102" ], "offsets": [ [ 10700, 10704 ] ], "normalized": [] }, { "id": "PMC2774163-03-Discussion_T145", "type": "Two-component-system", "text": [ "MifSR" ], "offsets": [ [ 10711, 10716 ] ], "normalized": [] }, { "id": "PMC2774163-03-Discussion_T146", "type": "Protein", "text": [ "MifS" ], "offsets": [ [ 10711, 10715 ] ], "normalized": [] }, { "id": "PMC2774163-03-Discussion_T147", "type": "Protein", "text": [ "R" ], "offsets": [ [ 10715, 10716 ] ], "normalized": [] }, { "id": "PMC2774163-03-Discussion_T148", "type": "Two-component-system", "text": [ "PA5511-5512" ], "offsets": [ [ 10718, 10729 ] ], "normalized": [] }, { "id": "PMC2774163-03-Discussion_T149", "type": "Protein", "text": [ "PA5511" ], "offsets": [ [ 10718, 10724 ] ], "normalized": [] }, { "id": "PMC2774163-03-Discussion_T150", "type": "Protein", "text": [ "5512" ], "offsets": [ [ 10725, 10729 ] ], "normalized": [] }, { "id": "PMC2774163-03-Discussion_T151", "type": "Protein", "text": [ "GacS" ], "offsets": [ [ 10893, 10897 ] ], "normalized": [] }, { "id": "PMC2774163-03-Discussion_T152", "type": "Protein", "text": [ "RsmA" ], "offsets": [ [ 10902, 10906 ] ], "normalized": [] }, { "id": "PMC2774163-03-Discussion_T153", "type": "Protein", "text": [ "RetS" ], "offsets": [ [ 10958, 10962 ] ], "normalized": [] }, { "id": "PMC2774163-03-Discussion_T154", "type": "Protein", "text": [ "LadS" ], "offsets": [ [ 10963, 10967 ] ], "normalized": [] }, { "id": "PMC2774163-03-Discussion_T155", "type": "Protein", "text": [ "GacA" ], "offsets": [ [ 10968, 10972 ] ], "normalized": [] }, { "id": "PMC2774163-03-Discussion_T156", "type": "Protein", "text": [ "S" ], "offsets": [ [ 10972, 10973 ] ], "normalized": [] }, { "id": "PMC2774163-03-Discussion_T157", "type": "Protein", "text": [ "RsmA" ], "offsets": [ [ 10974, 10978 ] ], "normalized": [] }, { "id": "PMC2774163-03-Discussion_T158", "type": "Organism", "text": [ "P. aeruginosa" ], "offsets": [ [ 11485, 11498 ] ], "normalized": [] } ]

[ { "id": "PMC2774163-03-Discussion_E1", "type": "Phosphorylation", "trigger": { "text": [ "phosphorylated" ], "offsets": [ [ 1814, 1828 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC2774163-03-Discussion_T24" } ] }, { "id": "PMC2774163-03-Discussion_E2", "type": "Phosphorylation", "trigger": { "text": [ "phosphorylated" ], "offsets": [ [ 1814, 1828 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC2774163-03-Discussion_T25" } ] }, { "id": "PMC2774163-03-Discussion_E3", "type": "Phosphorylation", "trigger": { "text": [ "phosphorylated" ], "offsets": [ [ 1814, 1828 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC2774163-03-Discussion_T26" } ] }, { "id": "PMC2774163-03-Discussion_E4", "type": "Negative_regulation", "trigger": { "text": [ "Inactivation" ], "offsets": [ [ 5434, 5446 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC2774163-03-Discussion_T59" } ] }, { "id": "PMC2774163-03-Discussion_E5", "type": "Regulation", "trigger": { "text": [ "utilizes" ], "offsets": [ [ 5804, 5812 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC2774163-03-Discussion_T63" } ] }, { "id": "PMC2774163-03-Discussion_E6", "type": "Positive_regulation", "trigger": { "text": [ "Activation" ], "offsets": [ [ 7120, 7130 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC2774163-03-Discussion_T79" } ] }, { "id": "PMC2774163-03-Discussion_E7", "type": "Phosphorylation", "trigger": { "text": [ "phosphorylation" ], "offsets": [ [ 7159, 7174 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC2774163-03-Discussion_T80" } ] }, { "id": "PMC2774163-03-Discussion_E8", "type": "Positive_regulation", "trigger": { "text": [ "dependent" ], "offsets": [ [ 7322, 7331 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC2774163-03-Discussion_T82" } ] }, { "id": "PMC2774163-03-Discussion_E9", "type": "Process", "trigger": { "text": [ "infection" ], "offsets": [ [ 8620, 8629 ] ] }, "arguments": [ { "role": "Participant", "ref_id": "PMC2774163-03-Discussion_T104" } ] }, { "id": "PMC2774163-03-Discussion_E10", "type": "Phosphorylation", "trigger": { "text": [ "phosphorylation" ], "offsets": [ [ 9072, 9087 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC2774163-03-Discussion_T109" } ] }, { "id": "PMC2774163-03-Discussion_E11", "type": "Negative_regulation", "trigger": { "text": [ "suppressor" ], "offsets": [ [ 9137, 9147 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC2774163-03-Discussion_T111" }, { "role": "Cause", "ref_id": "PMC2774163-03-Discussion_T110" } ] }, { "id": "PMC2774163-03-Discussion_E12", "type": "Negative_regulation", "trigger": { "text": [ "vice versa" ], "offsets": [ [ 9161, 9171 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC2774163-03-Discussion_T110" }, { "role": "Cause", "ref_id": "PMC2774163-03-Discussion_T111" } ] }, { "id": "PMC2774163-03-Discussion_E13", "type": "Regulation", "trigger": { "text": [ "regulating" ], "offsets": [ [ 9183, 9193 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC2774163-03-Discussion_E15" }, { "role": "Cause", "ref_id": "PMC2774163-03-Discussion_T112" } ] }, { "id": "PMC2774163-03-Discussion_E14", "type": "Regulation", "trigger": { "text": [ "modulating" ], "offsets": [ [ 9264, 9274 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC2774163-03-Discussion_E15" }, { "role": "Cause", "ref_id": "PMC2774163-03-Discussion_T112" } ] }, { "id": "PMC2774163-03-Discussion_E15", "type": "Phosphorylation", "trigger": { "text": [ "phosphorylation" ], "offsets": [ [ 9279, 9294 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC2774163-03-Discussion_T113" } ] }, { "id": "PMC2774163-03-Discussion_E16", "type": "Phosphorylation", "trigger": { "text": [ "phosphorylation" ], "offsets": [ [ 9409, 9424 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC2774163-03-Discussion_T114" } ] }, { "id": "PMC2774163-03-Discussion_E17", "type": "Phosphorylation", "trigger": { "text": [ "non-phosphorylated" ], "offsets": [ [ 9545, 9563 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC2774163-03-Discussion_T116" } ] }, { "id": "PMC2774163-03-Discussion_E18", "type": "Phosphorylation", "trigger": { "text": [ "phosphorylated" ], "offsets": [ [ 9654, 9668 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC2774163-03-Discussion_T116" } ] }, { "id": "PMC2774163-03-Discussion_E19", "type": "Phosphorylation", "trigger": { "text": [ "phosphorylation" ], "offsets": [ [ 9676, 9691 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC2774163-03-Discussion_T117" } ] }, { "id": "PMC2774163-03-Discussion_E20", "type": "Regulation", "trigger": { "text": [ "modulates" ], "offsets": [ [ 9785, 9794 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC2774163-03-Discussion_E21" }, { "role": "Cause", "ref_id": "PMC2774163-03-Discussion_T118" } ] }, { "id": "PMC2774163-03-Discussion_E21", "type": "Phosphorylation", "trigger": { "text": [ "phosphorylation" ], "offsets": [ [ 9799, 9814 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC2774163-03-Discussion_T119" } ] }, { "id": "PMC2774163-03-Discussion_E22", "type": "Phosphorylation", "trigger": { "text": [ "phosphorylated" ], "offsets": [ [ 10016, 10030 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC2774163-03-Discussion_T122" } ] }, { "id": "PMC2774163-03-Discussion_E23", "type": "Positive_regulation", "trigger": { "text": [ "dependent" ], "offsets": [ [ 10041, 10050 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC2774163-03-Discussion_E22" }, { "role": "Cause", "ref_id": "PMC2774163-03-Discussion_T123" } ] }, { "id": "PMC2774163-03-Discussion_E24", "type": "Gene_expression", "trigger": { "text": [ "expression" ], "offsets": [ [ 10068, 10078 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC2774163-03-Discussion_T125" } ] }, { "id": "PMC2774163-03-Discussion_E25", "type": "Positive_regulation", "trigger": { "text": [ "dependent" ], "offsets": [ [ 10146, 10155 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC2774163-03-Discussion_E24" }, { "role": "Cause", "ref_id": "PMC2774163-03-Discussion_T126" } ] }, { "id": "PMC2774163-03-Discussion_E26", "type": "Regulation", "trigger": { "text": [ "regulates" ], "offsets": [ [ 10298, 10307 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC2774163-03-Discussion_E27" } ] }, { "id": "PMC2774163-03-Discussion_E27", "type": "Process", "trigger": { "text": [ "virulence" ], "offsets": [ [ 10308, 10317 ] ] }, "arguments": [] } ]

[ { "id": "PMC2774163-03-Discussion_1", "entity_ids": [ "PMC2774163-03-Discussion_T5", "PMC2774163-03-Discussion_T8" ] }, { "id": "PMC2774163-03-Discussion_2", "entity_ids": [ "PMC2774163-03-Discussion_T11", "PMC2774163-03-Discussion_T14" ] }, { "id": "PMC2774163-03-Discussion_3", "entity_ids": [ "PMC2774163-03-Discussion_T17", "PMC2774163-03-Discussion_T20" ] }, { "id": "PMC2774163-03-Discussion_4", "entity_ids": [ "PMC2774163-03-Discussion_T38", "PMC2774163-03-Discussion_T39" ] }, { "id": "PMC2774163-03-Discussion_5", "entity_ids": [ "PMC2774163-03-Discussion_T40", "PMC2774163-03-Discussion_T41" ] }, { "id": "PMC2774163-03-Discussion_6", "entity_ids": [ "PMC2774163-03-Discussion_T77", "PMC2774163-03-Discussion_T78" ] } ]

[]

[ { "id": "PMC2266911-03-Conclusion__text", "type": "abstract", "text": [ "Conclusion \nThe comparison of Y. enterocolitica and P. luminescens at the genomic level performed here provides the database for a better understanding of the genetic basis for their distinct behaviour towards invertebrates and mammals. Y. enterocolitica is expected to switch between two pathogenicity phases against insects and mammalians, while the genome of P. luminescens must contain the modulators and regulators necessary to change the bacterium from a state of symbiosis with nematodes to pathogenicity against insects, and also from symbiosis-proficient primary variants to symbiosis-deficient secondary variants [17]. Those adaptational processes must be precisely regulated by the bacteria. It was assumed that there are parallels in the regulation of pathogenicity in mammals and insect pathogens [41,123]. However, molecular components of the regulatory networks controlling pathogenicity and mutualism have recently been demonstrated to be very different between P. luminescens and X. nematophilus with similar life cycles [124]. Dissecting the genomes of Y. enterocolitica and P. luminescens for putative key regulators, we identified factor groups (AI-2, PAS-4/LuxR like receptors) possibly involved in pathogen-insect association only, those with members contributing to either insect or mammalian pathogenicity (QS, TKS, Usp), and c-di-GMP signalling probably not involved in regulation of activities against insects. Certainly, the question whether fundamental differences in regulatory networks reflect how each of these two bacteria specifically interacts with either the insect or the human host remains to be addressed in more detail. Bioconversion of its insect hosts is an important stage in the lifecycle of P. luminescens. This fact might explain the high number of antibacterial factors directed against possible competitors that are going to colonize the same insect cadaver or that are already present in the insect gut flora [17]. However, no corresponding determinants were identified in the genome of Y. enterocolitica. Moreover, P. luminescens is pathogenic to a variety of insect larvae, and a dose of <5 colony-forming units directly injected into the blood system is sufficient to kill within 48-72 h [124]. In contrast, only highly concentrated protein extracts of Y. enterocolitica are toxic for M. sexta [7], and a low insect larvae mortality has been observed following injection of approximately 3.5 x 106 Y. enterocolitica cells into the hemolymph (T. M. Fuchs, unpublished data). This data strongly suggests that Y. enterocolitica, similar to Y. pestis, has developed a strategy to infect and proliferate in insects, and use these organisms rather as transmission vectors than as pure nutrient source. Summarizing, Y. enterocolitica and P. luminescens have evolved partially different and partially similar and therefore probably conserved mechanisms to detect and to react on the insect host. Up to the present time, we are far away from understanding the complexity of bacteria-invertebrate interactions. With the genome comparison carried out here, however, we uncovered several genes which are promising candidate genes involved in insect association and pathogenicity, and therefore created a promising basis for future experimental work.\n" ], "offsets": [ [ 0, 3289 ] ] } ]

[ { "id": "PMC2266911-03-Conclusion_T1", "type": "Organism", "text": [ "Y. enterocolitica" ], "offsets": [ [ 30, 47 ] ], "normalized": [] }, { "id": "PMC2266911-03-Conclusion_T2", "type": "Organism", "text": [ "P. luminescens" ], "offsets": [ [ 52, 66 ] ], "normalized": [] }, { "id": "PMC2266911-03-Conclusion_T3", "type": "Organism", "text": [ "Y. enterocolitica" ], "offsets": [ [ 237, 254 ] ], "normalized": [] }, { "id": "PMC2266911-03-Conclusion_T4", "type": "Organism", "text": [ "P. luminescens" ], "offsets": [ [ 362, 376 ] ], "normalized": [] }, { "id": "PMC2266911-03-Conclusion_T5", "type": "Organism", "text": [ "P. luminescens" ], "offsets": [ [ 978, 992 ] ], "normalized": [] }, { "id": "PMC2266911-03-Conclusion_T6", "type": "Organism", "text": [ "X. nematophilus" ], "offsets": [ [ 997, 1012 ] ], "normalized": [] }, { "id": "PMC2266911-03-Conclusion_T7", "type": "Organism", "text": [ "Y. enterocolitica" ], "offsets": [ [ 1071, 1088 ] ], "normalized": [] }, { "id": "PMC2266911-03-Conclusion_T8", "type": "Organism", "text": [ "P. luminescens" ], "offsets": [ [ 1093, 1107 ] ], "normalized": [] }, { "id": "PMC2266911-03-Conclusion_T9", "type": "Protein", "text": [ "AI-2" ], "offsets": [ [ 1166, 1170 ] ], "normalized": [] }, { "id": "PMC2266911-03-Conclusion_T10", "type": "Protein", "text": [ "PAS-4" ], "offsets": [ [ 1172, 1177 ] ], "normalized": [] }, { "id": "PMC2266911-03-Conclusion_T11", "type": "Protein", "text": [ "LuxR" ], "offsets": [ [ 1178, 1182 ] ], "normalized": [] }, { "id": "PMC2266911-03-Conclusion_T12", "type": "Chemical", "text": [ "c-di-GMP" ], "offsets": [ [ 1350, 1358 ] ], "normalized": [] }, { "id": "PMC2266911-03-Conclusion_T13", "type": "Organism", "text": [ "human" ], "offsets": [ [ 1608, 1613 ] ], "normalized": [] }, { "id": "PMC2266911-03-Conclusion_T14", "type": "Organism", "text": [ "P. luminescens" ], "offsets": [ [ 1735, 1749 ] ], "normalized": [] }, { "id": "PMC2266911-03-Conclusion_T15", "type": "Organism", "text": [ "Y. enterocolitica" ], "offsets": [ [ 2035, 2052 ] ], "normalized": [] }, { "id": "PMC2266911-03-Conclusion_T16", "type": "Organism", "text": [ "P. luminescens" ], "offsets": [ [ 2064, 2078 ] ], "normalized": [] }, { "id": "PMC2266911-03-Conclusion_T17", "type": "Organism", "text": [ "Y. enterocolitica" ], "offsets": [ [ 2304, 2321 ] ], "normalized": [] }, { "id": "PMC2266911-03-Conclusion_T18", "type": "Organism", "text": [ "M. sexta" ], "offsets": [ [ 2336, 2344 ] ], "normalized": [] }, { "id": "PMC2266911-03-Conclusion_T19", "type": "Organism", "text": [ "Y. enterocolitica" ], "offsets": [ [ 2449, 2466 ] ], "normalized": [] }, { "id": "PMC2266911-03-Conclusion_T20", "type": "Organism", "text": [ "Y. enterocolitica" ], "offsets": [ [ 2558, 2575 ] ], "normalized": [] }, { "id": "PMC2266911-03-Conclusion_T21", "type": "Organism", "text": [ "Y. pestis" ], "offsets": [ [ 2588, 2597 ] ], "normalized": [] }, { "id": "PMC2266911-03-Conclusion_T22", "type": "Organism", "text": [ "Y. enterocolitica" ], "offsets": [ [ 2760, 2777 ] ], "normalized": [] }, { "id": "PMC2266911-03-Conclusion_T23", "type": "Organism", "text": [ "P. luminescens" ], "offsets": [ [ 2782, 2796 ] ], "normalized": [] } ]

[ { "id": "PMC2266911-03-Conclusion_E1", "type": "Process", "trigger": { "text": [ "infect" ], "offsets": [ [ 2627, 2633 ] ] }, "arguments": [ { "role": "Participant", "ref_id": "PMC2266911-03-Conclusion_T20" } ] } ]

[]

[]

[ { "id": "PMC1913099-02-Results-Discussion-09__text", "type": "abstract", "text": [ "Type II Clusters \nBased on the Type I cluster results, we speculated that genes contained in Type II clusters might be related by function or regulation. Type II groupings contain a combination of both known and unknown gene members and could provide preliminary clues about the function of unknown genes within a particular cluster by associating their expression with neighboring genes of known and defined function. Alternatively, co-expression of genes results from common regulation, and Type II associations may suggest shared regulatory mechanisms for clustered genes. We note, however, that despite the statistical framework with which groupings are assigned, experimental evidence is necessary to confirm functional or regulatory relatedness. We do not suggest simply assigning either based on cluster membership; rather, cluster associations may provide some preliminary functional or regulatory clues for gene members. A total of 18 (90%) of 20 Type II clusters (Table 3 and Figure S3) may not have been identified without neighbor clustering: eight (44.4%) of 18 gained additional gene members; the remaining ten comprised genes that demonstrated significant differential expression only after applying GenomeCrawler. Only two clusters (spy0127-0130 and spy1701-1704) could have been identified without neighbor clustering; however, a number of these genes were initially annotated as hypothetical proteins, so a potential relationship between the gene members may not have been readily apparent. The upregulated spy0127-0130 cluster is part of a larger genomic region known as FCT (for fibronectin- and collagen-binding proteins and T antigen-encoding loci), which spans spy0123-0136 in the SF370 genome and encodes surface proteins and transcriptional regulators [46]. A search of both the PFAM database [47] (http://pfam.wustl.edu) and sortase database (http://www.doe-mbi.ucla.edu/Services/Sortase) predicted that spy0129 encodes a sortase enzyme, which are transpeptidases that cleave protein substrates at conserved C-terminal motifs (often LPXTG) and then anchor these proteins to the bacterial cell wall [48,49]. Recently, it was reported that the four genes spanning spy0127-0130 encode, and are responsible for, the formation of surface-localized, trypsin-resistant pili that induce protective immunity against a lethal dose of group A streptococci in a mouse model of infection [36]. This same report provided the first experimental evidence supporting the sortase prediction, indicating that the gene product of spy0129 is responsible for the cell-wall sorting of the proteins encoded by both spy0128 (annotated as a Cpa homolog [50]) and spy0130 (annotated as a protein F homolog [14]). Furthermore, the spy0128-encoded protein is the structural backbone of the pili, and the gene product of spy0130 may be involved in stabilizing the structure [36]. Together with the identification of this cluster by GenomeCrawler, these results prompted us to study this cluster and the contributions of the gene products to pharyngeal cell adherence. We determined experimentally that cluster spy0127-0130 is an operon, verifying both related function and regulation of the gene members. Reverse transcription of SF370 RNA, with primer combinations that spanned all four genes, produced cDNA fragments of sizes that could only result from a polycistronic mRNA template (Figure 3). In silico sequence inspection identified a single putative promoter sequence upstream of spy0127 (see Table S6). Although GenomeCrawler is not an operon-identifying algorithm, these results show that it could (1) identify this commonly regulated gene cluster and (2) define the cluster boundaries, excluding other proximate genes, such as an additional sortase-encoding gene, spy0135.\n" ], "offsets": [ [ 0, 3779 ] ] } ]

[ { "id": "PMC1913099-02-Results-Discussion-09_T1", "type": "Regulon-operon", "text": [ "spy0127-0130" ], "offsets": [ [ 1249, 1261 ] ], "normalized": [] }, { "id": "PMC1913099-02-Results-Discussion-09_T2", "type": "Protein", "text": [ "spy0127" ], "offsets": [ [ 1249, 1256 ] ], "normalized": [] }, { "id": "PMC1913099-02-Results-Discussion-09_T3", "type": "Protein", "text": [ "0130" ], "offsets": [ [ 1257, 1261 ] ], "normalized": [] }, { "id": "PMC1913099-02-Results-Discussion-09_T4", "type": "Regulon-operon", "text": [ "spy1701-1704" ], "offsets": [ [ 1266, 1278 ] ], "normalized": [] }, { "id": "PMC1913099-02-Results-Discussion-09_T5", "type": "Protein", "text": [ "spy1701" ], "offsets": [ [ 1266, 1273 ] ], "normalized": [] }, { "id": "PMC1913099-02-Results-Discussion-09_T6", "type": "Protein", "text": [ "1704" ], "offsets": [ [ 1274, 1278 ] ], "normalized": [] }, { "id": "PMC1913099-02-Results-Discussion-09_T7", "type": "Regulon-operon", "text": [ "spy0127-0130" ], "offsets": [ [ 1525, 1537 ] ], "normalized": [] }, { "id": "PMC1913099-02-Results-Discussion-09_T8", "type": "Protein", "text": [ "spy0127" ], "offsets": [ [ 1525, 1532 ] ], "normalized": [] }, { "id": "PMC1913099-02-Results-Discussion-09_T9", "type": "Protein", "text": [ "0130" ], "offsets": [ [ 1533, 1537 ] ], "normalized": [] }, { "id": "PMC1913099-02-Results-Discussion-09_T10", "type": "Protein", "text": [ "spy0123" ], "offsets": [ [ 1684, 1691 ] ], "normalized": [] }, { "id": "PMC1913099-02-Results-Discussion-09_T11", "type": "Protein", "text": [ "0136" ], "offsets": [ [ 1692, 1696 ] ], "normalized": [] }, { "id": "PMC1913099-02-Results-Discussion-09_T12", "type": "Organism", "text": [ "SF370" ], "offsets": [ [ 1704, 1709 ] ], "normalized": [] }, { "id": "PMC1913099-02-Results-Discussion-09_T13", "type": "Protein", "text": [ "spy0129" ], "offsets": [ [ 1930, 1937 ] ], "normalized": [] }, { "id": "PMC1913099-02-Results-Discussion-09_T14", "type": "Regulon-operon", "text": [ "spy0127-0130" ], "offsets": [ [ 2188, 2200 ] ], "normalized": [] }, { "id": "PMC1913099-02-Results-Discussion-09_T15", "type": "Protein", "text": [ "spy0127" ], "offsets": [ [ 2188, 2195 ] ], "normalized": [] }, { "id": "PMC1913099-02-Results-Discussion-09_T16", "type": "Protein", "text": [ "0130" ], "offsets": [ [ 2196, 2200 ] ], "normalized": [] }, { "id": "PMC1913099-02-Results-Discussion-09_T17", "type": "Organism", "text": [ "group A streptococci" ], "offsets": [ [ 2350, 2370 ] ], "normalized": [] }, { "id": "PMC1913099-02-Results-Discussion-09_T18", "type": "Organism", "text": [ "mouse" ], "offsets": [ [ 2376, 2381 ] ], "normalized": [] }, { "id": "PMC1913099-02-Results-Discussion-09_T19", "type": "Protein", "text": [ "sortase" ], "offsets": [ [ 2480, 2487 ] ], "normalized": [] }, { "id": "PMC1913099-02-Results-Discussion-09_T20", "type": "Protein", "text": [ "spy0129" ], "offsets": [ [ 2536, 2543 ] ], "normalized": [] }, { "id": "PMC1913099-02-Results-Discussion-09_T21", "type": "Protein", "text": [ "spy0128" ], "offsets": [ [ 2617, 2624 ] ], "normalized": [] }, { "id": "PMC1913099-02-Results-Discussion-09_T22", "type": "Protein", "text": [ "Cpa" ], "offsets": [ [ 2641, 2644 ] ], "normalized": [] }, { "id": "PMC1913099-02-Results-Discussion-09_T23", "type": "Protein", "text": [ "spy0130" ], "offsets": [ [ 2663, 2670 ] ], "normalized": [] }, { "id": "PMC1913099-02-Results-Discussion-09_T24", "type": "Protein", "text": [ "protein F" ], "offsets": [ [ 2687, 2696 ] ], "normalized": [] }, { "id": "PMC1913099-02-Results-Discussion-09_T25", "type": "Protein", "text": [ "spy0128" ], "offsets": [ [ 2729, 2736 ] ], "normalized": [] }, { "id": "PMC1913099-02-Results-Discussion-09_T26", "type": "Protein", "text": [ "gene product" ], "offsets": [ [ 2801, 2813 ] ], "normalized": [] }, { "id": "PMC1913099-02-Results-Discussion-09_T27", "type": "Protein", "text": [ "spy0130" ], "offsets": [ [ 2817, 2824 ] ], "normalized": [] }, { "id": "PMC1913099-02-Results-Discussion-09_T28", "type": "Regulon-operon", "text": [ "spy0127-0130" ], "offsets": [ [ 3106, 3118 ] ], "normalized": [] }, { "id": "PMC1913099-02-Results-Discussion-09_T29", "type": "Protein", "text": [ "spy0127" ], "offsets": [ [ 3106, 3113 ] ], "normalized": [] }, { "id": "PMC1913099-02-Results-Discussion-09_T30", "type": "Protein", "text": [ "0130" ], "offsets": [ [ 3114, 3118 ] ], "normalized": [] }, { "id": "PMC1913099-02-Results-Discussion-09_T31", "type": "Organism", "text": [ "SF370" ], "offsets": [ [ 3226, 3231 ] ], "normalized": [] }, { "id": "PMC1913099-02-Results-Discussion-09_T32", "type": "Protein", "text": [ "spy0127" ], "offsets": [ [ 3483, 3490 ] ], "normalized": [] }, { "id": "PMC1913099-02-Results-Discussion-09_T33", "type": "Protein", "text": [ "spy0135" ], "offsets": [ [ 3770, 3777 ] ], "normalized": [] } ]

[ { "id": "PMC1913099-02-Results-Discussion-09_E1", "type": "Positive_regulation", "trigger": { "text": [ "upregulated" ], "offsets": [ [ 1513, 1524 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC1913099-02-Results-Discussion-09_T7" } ] }, { "id": "PMC1913099-02-Results-Discussion-09_E2", "type": "Process", "trigger": { "text": [ "infection" ], "offsets": [ [ 2391, 2400 ] ] }, "arguments": [ { "role": "Participant", "ref_id": "PMC1913099-02-Results-Discussion-09_T17" } ] } ]

[]

[]

[ { "id": "PMC2639726-02-Results-07__text", "type": "abstract", "text": [ "SsrB can complement other regulators of SPI-2 transcription \nSsrB binds within SPI-2 and activates SPI-2 genes for transcription. However the location of binding sites varies suggesting that SsrB regulation is unusual [52]. Some of the 14 regulators in this study have been previously shown to directly regulate ssrA/ssrB; OmpR binding to PssrA/ssrB [60],[61]; SlyA binding to PssrA [62]; PhoP binding to PssrB [45]. To distinguish direct from indirect effects, we carried out epistasis experiments and determined if ssrB expression could suppress the phenotype of the other regulators of SPI-2 expression. Each isogenic derivative was transformed with either pBAD30SsrB or the empty vector control. We investigated the same seven SPI-2 genes as in the qRT-PCR assays above, and results are shown in Figure 7A [52]. Expression of an episomal copy of ssrB resulted in expression of SPI-2 genes in each mutant background, suggesting that SsrB is epistatic to other regulators for SPI-2 transcription. This result is in agreement with the model shown in Figure 6 where all positive regulation takes place via either ssrB or slyA or both as tested further below. Furthermore, SsrB could complement all three deletions DeltassrB, DeltassrA, and DeltassrA/ssrB (Figure 7B), suggesting that over-expression of SsrB may compensate for differences in phosphorylation that normally play a role in regulation [52].\n" ], "offsets": [ [ 0, 1404 ] ] } ]

[ { "id": "PMC2639726-02-Results-07_T1", "type": "Protein", "text": [ "SsrB" ], "offsets": [ [ 0, 4 ] ], "normalized": [] }, { "id": "PMC2639726-02-Results-07_T2", "type": "Protein", "text": [ "SsrB" ], "offsets": [ [ 61, 65 ] ], "normalized": [] }, { "id": "PMC2639726-02-Results-07_T3", "type": "Protein", "text": [ "SsrB" ], "offsets": [ [ 191, 195 ] ], "normalized": [] }, { "id": "PMC2639726-02-Results-07_T4", "type": "Two-component-system", "text": [ "ssrA/ssrB" ], "offsets": [ [ 312, 321 ] ], "normalized": [] }, { "id": "PMC2639726-02-Results-07_T5", "type": "Protein", "text": [ "ssrA" ], "offsets": [ [ 312, 316 ] ], "normalized": [] }, { "id": "PMC2639726-02-Results-07_T6", "type": "Protein", "text": [ "ssrB" ], "offsets": [ [ 317, 321 ] ], "normalized": [] }, { "id": "PMC2639726-02-Results-07_T7", "type": "Protein", "text": [ "OmpR" ], "offsets": [ [ 323, 327 ] ], "normalized": [] }, { "id": "PMC2639726-02-Results-07_T8", "type": "Two-component-system", "text": [ "ssrA/ssrB" ], "offsets": [ [ 340, 349 ] ], "normalized": [] }, { "id": "PMC2639726-02-Results-07_T9", "type": "Protein", "text": [ "ssrA" ], "offsets": [ [ 340, 344 ] ], "normalized": [] }, { "id": "PMC2639726-02-Results-07_T10", "type": "Protein", "text": [ "ssrB" ], "offsets": [ [ 345, 349 ] ], "normalized": [] }, { "id": "PMC2639726-02-Results-07_T11", "type": "Protein", "text": [ "SlyA" ], "offsets": [ [ 361, 365 ] ], "normalized": [] }, { "id": "PMC2639726-02-Results-07_T12", "type": "Protein", "text": [ "ssrA" ], "offsets": [ [ 378, 382 ] ], "normalized": [] }, { "id": "PMC2639726-02-Results-07_T13", "type": "Protein", "text": [ "PhoP" ], "offsets": [ [ 389, 393 ] ], "normalized": [] }, { "id": "PMC2639726-02-Results-07_T14", "type": "Protein", "text": [ "ssrB" ], "offsets": [ [ 406, 410 ] ], "normalized": [] }, { "id": "PMC2639726-02-Results-07_T15", "type": "Protein", "text": [ "ssrB" ], "offsets": [ [ 517, 521 ] ], "normalized": [] }, { "id": "PMC2639726-02-Results-07_T16", "type": "Protein", "text": [ "SsrB" ], "offsets": [ [ 666, 670 ] ], "normalized": [] }, { "id": "PMC2639726-02-Results-07_T17", "type": "Protein", "text": [ "ssrB" ], "offsets": [ [ 850, 854 ] ], "normalized": [] }, { "id": "PMC2639726-02-Results-07_T18", "type": "Protein", "text": [ "SsrB" ], "offsets": [ [ 936, 940 ] ], "normalized": [] }, { "id": "PMC2639726-02-Results-07_T19", "type": "Protein", "text": [ "ssrB" ], "offsets": [ [ 1113, 1117 ] ], "normalized": [] }, { "id": "PMC2639726-02-Results-07_T20", "type": "Protein", "text": [ "slyA" ], "offsets": [ [ 1121, 1125 ] ], "normalized": [] }, { "id": "PMC2639726-02-Results-07_T21", "type": "Protein", "text": [ "SsrB" ], "offsets": [ [ 1172, 1176 ] ], "normalized": [] }, { "id": "PMC2639726-02-Results-07_T22", "type": "Organism", "text": [ "DeltassrB" ], "offsets": [ [ 1214, 1223 ] ], "normalized": [] }, { "id": "PMC2639726-02-Results-07_T23", "type": "Protein", "text": [ "ssrB" ], "offsets": [ [ 1219, 1223 ] ], "normalized": [] }, { "id": "PMC2639726-02-Results-07_T24", "type": "Organism", "text": [ "DeltassrA" ], "offsets": [ [ 1225, 1234 ] ], "normalized": [] }, { "id": "PMC2639726-02-Results-07_T25", "type": "Protein", "text": [ "ssrA" ], "offsets": [ [ 1230, 1234 ] ], "normalized": [] }, { "id": "PMC2639726-02-Results-07_T26", "type": "Organism", "text": [ "DeltassrA/ssrB" ], "offsets": [ [ 1240, 1254 ] ], "normalized": [] }, { "id": "PMC2639726-02-Results-07_T27", "type": "Two-component-system", "text": [ "ssrA/ssrB" ], "offsets": [ [ 1245, 1254 ] ], "normalized": [] }, { "id": "PMC2639726-02-Results-07_T28", "type": "Protein", "text": [ "ssrA" ], "offsets": [ [ 1245, 1249 ] ], "normalized": [] }, { "id": "PMC2639726-02-Results-07_T29", "type": "Protein", "text": [ "ssrB" ], "offsets": [ [ 1250, 1254 ] ], "normalized": [] }, { "id": "PMC2639726-02-Results-07_T30", "type": "Protein", "text": [ "SsrB" ], "offsets": [ [ 1303, 1307 ] ], "normalized": [] }, { "id": "PMC2639726-02-Results-07_T35", "type": "Entity", "text": [ "P" ], "offsets": [ [ 339, 340 ] ], "normalized": [] }, { "id": "PMC2639726-02-Results-07_T37", "type": "Entity", "text": [ "P" ], "offsets": [ [ 377, 378 ] ], "normalized": [] }, { "id": "PMC2639726-02-Results-07_T39", "type": "Entity", "text": [ "P" ], "offsets": [ [ 405, 406 ] ], "normalized": [] } ]

[ { "id": "PMC2639726-02-Results-07_E1", "type": "Binding", "trigger": { "text": [ "binds" ], "offsets": [ [ 66, 71 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC2639726-02-Results-07_T2" } ] }, { "id": "PMC2639726-02-Results-07_E2", "type": "Regulation", "trigger": { "text": [ "regulation" ], "offsets": [ [ 196, 206 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC2639726-02-Results-07_T3" } ] }, { "id": "PMC2639726-02-Results-07_E3", "type": "Regulation", "trigger": { "text": [ "regulate" ], "offsets": [ [ 303, 311 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC2639726-02-Results-07_T4" } ] }, { "id": "PMC2639726-02-Results-07_E4", "type": "Binding", "trigger": { "text": [ "binding" ], "offsets": [ [ 328, 335 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC2639726-02-Results-07_T7" }, { "role": "Theme", "ref_id": "PMC2639726-02-Results-07_T8" }, { "role": "Site", "ref_id": "PMC2639726-02-Results-07_T35" } ] }, { "id": "PMC2639726-02-Results-07_E5", "type": "Binding", "trigger": { "text": [ "binding" ], "offsets": [ [ 366, 373 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC2639726-02-Results-07_T11" }, { "role": "Theme", "ref_id": "PMC2639726-02-Results-07_T12" }, { "role": "Site", "ref_id": "PMC2639726-02-Results-07_T37" } ] }, { "id": "PMC2639726-02-Results-07_E6", "type": "Binding", "trigger": { "text": [ "binding" ], "offsets": [ [ 394, 401 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC2639726-02-Results-07_T13" }, { "role": "Theme", "ref_id": "PMC2639726-02-Results-07_T14" }, { "role": "Site", "ref_id": "PMC2639726-02-Results-07_T39" } ] }, { "id": "PMC2639726-02-Results-07_E7", "type": "Gene_expression", "trigger": { "text": [ "expression" ], "offsets": [ [ 522, 532 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC2639726-02-Results-07_T15" } ] }, { "id": "PMC2639726-02-Results-07_E8", "type": "Gene_expression", "trigger": { "text": [ "Expression" ], "offsets": [ [ 816, 826 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC2639726-02-Results-07_T17" } ] }, { "id": "PMC2639726-02-Results-07_E9", "type": "Positive_regulation", "trigger": { "text": [ "resulted" ], "offsets": [ [ 855, 863 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC2639726-02-Results-07_E8" } ] }, { "id": "PMC2639726-02-Results-07_E10", "type": "Gene_expression", "trigger": { "text": [ "over-expression" ], "offsets": [ [ 1284, 1299 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC2639726-02-Results-07_T30" } ] } ]

[]

[]

[ { "id": "PMC2581603-02-Results-01__text", "type": "abstract", "text": [ "Results \nExtracellular DNA has antimicrobial activity To study the role of the matrix component DNA on biofilm formation and biofilm-associated antibiotic resistance, we first examined the influence of extracellular DNA on P. aeruginosa growth in rich and defined media, LB and BM2, respectively. Addition of 0.5% (w/v) (5 mg/ml) or greater extracellular DNA to LB or 1% (w/v) or greater DNA to BM2 media inhibited growth of P. aeruginosa (Fig 1A and 1B). The kinetics of killing by extracellular DNA was determined by measuring the loss of luminescence from a chromosomally-tagged luminescent P. aeruginosa strain, PAO1::p16Slux. DNA-mediated killing was fast, within minutes, as measured by the rapid loss of luminescence upon exposure to 1.25% (w/v) DNA, or greater (Fig 1C). Killing was dose-dependent, with faster killing observed as the DNA concentration increased (Fig 1C). The rapid decrease in luminescence corresponded with a loss of bacterial viability, as determined by plating (Fig 1D). One percent (w/v) extracellular DNA in LB also inhibited the growth of Escherichia coli, Staphylococcus aureus and Burkholderia cenocepacia (data not shown), suggesting that the antimicrobial activity of DNA is not unique to P. aeruginosa.\n" ], "offsets": [ [ 0, 1240 ] ] } ]

[ { "id": "PMC2581603-02-Results-01_T1", "type": "Organism", "text": [ "P. aeruginosa" ], "offsets": [ [ 223, 236 ] ], "normalized": [] }, { "id": "PMC2581603-02-Results-01_T2", "type": "Organism", "text": [ "P. aeruginosa" ], "offsets": [ [ 425, 438 ] ], "normalized": [] }, { "id": "PMC2581603-02-Results-01_T3", "type": "Organism", "text": [ "P. aeruginosa" ], "offsets": [ [ 594, 607 ] ], "normalized": [] }, { "id": "PMC2581603-02-Results-01_T4", "type": "Organism", "text": [ "PAO1::p16Slux" ], "offsets": [ [ 616, 629 ] ], "normalized": [] }, { "id": "PMC2581603-02-Results-01_T5", "type": "Organism", "text": [ "Escherichia coli" ], "offsets": [ [ 1071, 1087 ] ], "normalized": [] }, { "id": "PMC2581603-02-Results-01_T6", "type": "Organism", "text": [ "Staphylococcus aureus" ], "offsets": [ [ 1089, 1110 ] ], "normalized": [] }, { "id": "PMC2581603-02-Results-01_T7", "type": "Organism", "text": [ "Burkholderia cenocepacia" ], "offsets": [ [ 1115, 1139 ] ], "normalized": [] }, { "id": "PMC2581603-02-Results-01_T8", "type": "Organism", "text": [ "P. aeruginosa" ], "offsets": [ [ 1225, 1238 ] ], "normalized": [] } ]

[ { "id": "PMC2581603-02-Results-01_E1", "type": "Process", "trigger": { "text": [ "resistance," ], "offsets": [ [ 155, 166 ] ] }, "arguments": [] } ]

[]

[]

[ { "id": "PMC2593050-01-INTRODUCTION__text", "type": "abstract", "text": [ "INTRODUCTION \nBacterial pathogens produce many two-component regulatory systems to regulate gene expression by specific environmental signals [1]. These systems consist of membrane protein sensors and cognate cytoplasmic response regulators. The regulator is phosphorylated by the sensor in response to a specific signal, activating or repressing the transcription of target genes. The two-component regulatory system VicRK or YycFG is specific for Gram-positive bacteria. The regulator component VicR is essential in Bacillus subtilis [2], Staphylococcus aureus [3], and Streptococcus pneumoniae [4-5] but appears not to be essential in Streptococcus pyogenes [6]. The deletion of the vicK gene can be readily inactivated in S. pneumoniae [7], Streptococcus mutans [8], and S. pyogenes [6] but not in B. subtilis [2] and S. aureus [3]. Conditional and unconditional vicRK mutants display various phenotypes, including defects in morphology and cell wall synthesis, decreased competence, sensitivity to antibiotics and fatty acids, defects in biofilm formation, and attenuated virulence, growth defect, and sensitivity to osmotic pressure [3, 6, 8-11]. The vicRK system of Gram-positive bacterium Streptococcus equi subspecies equi (S. equi) has not been studied. This pathogen causes equine strangles, a highly contagious purulent lymphadenitis [12-13]. The infection initially causes nasal discharge and fever and, then, leads to abscess formation in local lymph nodes, causing respiratory difficulty. Although the infection at the lymph nodes cause massive infiltration of polymorphoneuclear leukocytes (PMNs) [14], S. equi resists phagocytosis by PMNs and rapidly multiplies, forming an abscess of large numbers of degenerating PMNs and long chains of S. equi [15]. The hyaluronic acid capsule and S. equi M-like protein (SeM) are both required for the resistance to phagocytosis by PMNs [16-17]. Most horses recovered from strangles have immunity against S. equi reinfection for up to 5 years [18]. It is believed that the immunity is mediated by mucosal antibodies specific to SeM and other protective antigens. An intranasal vaccine made of live attenuated strain has been used in USA, which lacks the hyaluronic acid capsule, and various adverse effects, including pharyngeal lymphadenopathy, limb edema, and bastard strangles abscesses, have been reported [15]. This study aims at evaluating the importance of VicRK to S. equi virulence and the potential of a vicK deletion mutant as a live vaccine using mouse infection models. We found that the vicK deletion attenuated S. equi virulence in mouse models of subcutaneous and intranasal infections and that infection with a vicK deletion mutant confers protection against subsequent infection with wild-type S. equi and induces production of mucosal and systemic immunoglobins to SeM in nasal infection.\n" ], "offsets": [ [ 0, 2863 ] ] } ]

[ { "id": "PMC2593050-01-INTRODUCTION_T1", "type": "Two-component-system", "text": [ "VicRK" ], "offsets": [ [ 418, 423 ] ], "normalized": [] }, { "id": "PMC2593050-01-INTRODUCTION_T2", "type": "Protein", "text": [ "VicR" ], "offsets": [ [ 418, 422 ] ], "normalized": [] }, { "id": "PMC2593050-01-INTRODUCTION_T3", "type": "Protein", "text": [ "K" ], "offsets": [ [ 422, 423 ] ], "normalized": [] }, { "id": "PMC2593050-01-INTRODUCTION_T4", "type": "Two-component-system", "text": [ "YycFG" ], "offsets": [ [ 427, 432 ] ], "normalized": [] }, { "id": "PMC2593050-01-INTRODUCTION_T5", "type": "Protein", "text": [ "YycF" ], "offsets": [ [ 427, 431 ] ], "normalized": [] }, { "id": "PMC2593050-01-INTRODUCTION_T6", "type": "Protein", "text": [ "G" ], "offsets": [ [ 431, 432 ] ], "normalized": [] }, { "id": "PMC2593050-01-INTRODUCTION_T7", "type": "Protein", "text": [ "VicR" ], "offsets": [ [ 497, 501 ] ], "normalized": [] }, { "id": "PMC2593050-01-INTRODUCTION_T8", "type": "Organism", "text": [ "Bacillus subtilis" ], "offsets": [ [ 518, 535 ] ], "normalized": [] }, { "id": "PMC2593050-01-INTRODUCTION_T9", "type": "Organism", "text": [ "Staphylococcus aureus" ], "offsets": [ [ 541, 562 ] ], "normalized": [] }, { "id": "PMC2593050-01-INTRODUCTION_T10", "type": "Organism", "text": [ "Streptococcus pneumoniae" ], "offsets": [ [ 572, 596 ] ], "normalized": [] }, { "id": "PMC2593050-01-INTRODUCTION_T11", "type": "Organism", "text": [ "Streptococcus pyogenes" ], "offsets": [ [ 638, 660 ] ], "normalized": [] }, { "id": "PMC2593050-01-INTRODUCTION_T12", "type": "Protein", "text": [ "vicK" ], "offsets": [ [ 686, 690 ] ], "normalized": [] }, { "id": "PMC2593050-01-INTRODUCTION_T13", "type": "Organism", "text": [ "S. pneumoniae" ], "offsets": [ [ 726, 739 ] ], "normalized": [] }, { "id": "PMC2593050-01-INTRODUCTION_T14", "type": "Organism", "text": [ "Streptococcus mutans" ], "offsets": [ [ 745, 765 ] ], "normalized": [] }, { "id": "PMC2593050-01-INTRODUCTION_T15", "type": "Organism", "text": [ "S. pyogenes" ], "offsets": [ [ 775, 786 ] ], "normalized": [] }, { "id": "PMC2593050-01-INTRODUCTION_T16", "type": "Organism", "text": [ "B. subtilis" ], "offsets": [ [ 802, 813 ] ], "normalized": [] }, { "id": "PMC2593050-01-INTRODUCTION_T17", "type": "Organism", "text": [ "S. aureus" ], "offsets": [ [ 822, 831 ] ], "normalized": [] }, { "id": "PMC2593050-01-INTRODUCTION_T18", "type": "Two-component-system", "text": [ "vicRK" ], "offsets": [ [ 867, 872 ] ], "normalized": [] }, { "id": "PMC2593050-01-INTRODUCTION_T19", "type": "Protein", "text": [ "vicR" ], "offsets": [ [ 867, 871 ] ], "normalized": [] }, { "id": "PMC2593050-01-INTRODUCTION_T20", "type": "Protein", "text": [ "K" ], "offsets": [ [ 871, 872 ] ], "normalized": [] }, { "id": "PMC2593050-01-INTRODUCTION_T21", "type": "Two-component-system", "text": [ "vicRK" ], "offsets": [ [ 1157, 1162 ] ], "normalized": [] }, { "id": "PMC2593050-01-INTRODUCTION_T22", "type": "Protein", "text": [ "vicR" ], "offsets": [ [ 1157, 1161 ] ], "normalized": [] }, { "id": "PMC2593050-01-INTRODUCTION_T23", "type": "Protein", "text": [ "K" ], "offsets": [ [ 1161, 1162 ] ], "normalized": [] }, { "id": "PMC2593050-01-INTRODUCTION_T24", "type": "Organism", "text": [ "Streptococcus equi subspecies equi" ], "offsets": [ [ 1197, 1231 ] ], "normalized": [] }, { "id": "PMC2593050-01-INTRODUCTION_T25", "type": "Organism", "text": [ "S. equi" ], "offsets": [ [ 1233, 1240 ] ], "normalized": [] }, { "id": "PMC2593050-01-INTRODUCTION_T26", "type": "Organism", "text": [ "equine" ], "offsets": [ [ 1285, 1291 ] ], "normalized": [] }, { "id": "PMC2593050-01-INTRODUCTION_T27", "type": "Organism", "text": [ "S. equi" ], "offsets": [ [ 1619, 1626 ] ], "normalized": [] }, { "id": "PMC2593050-01-INTRODUCTION_T28", "type": "Organism", "text": [ "S. equi" ], "offsets": [ [ 1756, 1763 ] ], "normalized": [] }, { "id": "PMC2593050-01-INTRODUCTION_T29", "type": "Chemical", "text": [ "hyaluronic acid" ], "offsets": [ [ 1774, 1789 ] ], "normalized": [] }, { "id": "PMC2593050-01-INTRODUCTION_T30", "type": "Organism", "text": [ "S. equi" ], "offsets": [ [ 1802, 1809 ] ], "normalized": [] }, { "id": "PMC2593050-01-INTRODUCTION_T31", "type": "Protein", "text": [ "M-like protein" ], "offsets": [ [ 1810, 1824 ] ], "normalized": [] }, { "id": "PMC2593050-01-INTRODUCTION_T32", "type": "Protein", "text": [ "SeM" ], "offsets": [ [ 1826, 1829 ] ], "normalized": [] }, { "id": "PMC2593050-01-INTRODUCTION_T33", "type": "Organism", "text": [ "horses" ], "offsets": [ [ 1906, 1912 ] ], "normalized": [] }, { "id": "PMC2593050-01-INTRODUCTION_T34", "type": "Organism", "text": [ "S. equi" ], "offsets": [ [ 1960, 1967 ] ], "normalized": [] }, { "id": "PMC2593050-01-INTRODUCTION_T35", "type": "Protein", "text": [ "SeM" ], "offsets": [ [ 2083, 2086 ] ], "normalized": [] }, { "id": "PMC2593050-01-INTRODUCTION_T36", "type": "Chemical", "text": [ "hyaluronic acid" ], "offsets": [ [ 2209, 2224 ] ], "normalized": [] }, { "id": "PMC2593050-01-INTRODUCTION_T37", "type": "Two-component-system", "text": [ "VicRK" ], "offsets": [ [ 2419, 2424 ] ], "normalized": [] }, { "id": "PMC2593050-01-INTRODUCTION_T38", "type": "Protein", "text": [ "VicR" ], "offsets": [ [ 2419, 2423 ] ], "normalized": [] }, { "id": "PMC2593050-01-INTRODUCTION_T39", "type": "Protein", "text": [ "K" ], "offsets": [ [ 2423, 2424 ] ], "normalized": [] }, { "id": "PMC2593050-01-INTRODUCTION_T40", "type": "Organism", "text": [ "S. equi" ], "offsets": [ [ 2428, 2435 ] ], "normalized": [] }, { "id": "PMC2593050-01-INTRODUCTION_T41", "type": "Organism", "text": [ "vicK deletion mutant" ], "offsets": [ [ 2469, 2489 ] ], "normalized": [] }, { "id": "PMC2593050-01-INTRODUCTION_T42", "type": "Protein", "text": [ "vicK" ], "offsets": [ [ 2469, 2473 ] ], "normalized": [] }, { "id": "PMC2593050-01-INTRODUCTION_T43", "type": "Organism", "text": [ "mouse" ], "offsets": [ [ 2514, 2519 ] ], "normalized": [] }, { "id": "PMC2593050-01-INTRODUCTION_T44", "type": "Protein", "text": [ "vicK" ], "offsets": [ [ 2556, 2560 ] ], "normalized": [] }, { "id": "PMC2593050-01-INTRODUCTION_T45", "type": "Organism", "text": [ "S. equi" ], "offsets": [ [ 2581, 2588 ] ], "normalized": [] }, { "id": "PMC2593050-01-INTRODUCTION_T46", "type": "Organism", "text": [ "mouse" ], "offsets": [ [ 2602, 2607 ] ], "normalized": [] }, { "id": "PMC2593050-01-INTRODUCTION_T47", "type": "Organism", "text": [ "vicK deletion mutant" ], "offsets": [ [ 2683, 2703 ] ], "normalized": [] }, { "id": "PMC2593050-01-INTRODUCTION_T48", "type": "Protein", "text": [ "vicK" ], "offsets": [ [ 2683, 2687 ] ], "normalized": [] }, { "id": "PMC2593050-01-INTRODUCTION_T49", "type": "Organism", "text": [ "S. equi" ], "offsets": [ [ 2767, 2774 ] ], "normalized": [] }, { "id": "PMC2593050-01-INTRODUCTION_T50", "type": "Protein", "text": [ "SeM" ], "offsets": [ [ 2839, 2842 ] ], "normalized": [] } ]

[ { "id": "PMC2593050-01-INTRODUCTION_E1", "type": "Negative_regulation", "trigger": { "text": [ "inactivated" ], "offsets": [ [ 711, 722 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC2593050-01-INTRODUCTION_T12" } ] }, { "id": "PMC2593050-01-INTRODUCTION_E2", "type": "Negative_regulation", "trigger": { "text": [ "attenuated" ], "offsets": [ [ 1066, 1076 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC2593050-01-INTRODUCTION_E3" } ] }, { "id": "PMC2593050-01-INTRODUCTION_E3", "type": "Process", "trigger": { "text": [ "virulence" ], "offsets": [ [ 1077, 1086 ] ] }, "arguments": [] }, { "id": "PMC2593050-01-INTRODUCTION_E4", "type": "Process", "trigger": { "text": [ "infection" ], "offsets": [ [ 1359, 1368 ] ] }, "arguments": [] }, { "id": "PMC2593050-01-INTRODUCTION_E5", "type": "Process", "trigger": { "text": [ "infection" ], "offsets": [ [ 1517, 1526 ] ] }, "arguments": [] }, { "id": "PMC2593050-01-INTRODUCTION_E6", "type": "Process", "trigger": { "text": [ "resists" ], "offsets": [ [ 1627, 1634 ] ] }, "arguments": [ { "role": "Participant", "ref_id": "PMC2593050-01-INTRODUCTION_T27" } ] }, { "id": "PMC2593050-01-INTRODUCTION_E7", "type": "Process", "trigger": { "text": [ "resistance" ], "offsets": [ [ 1857, 1867 ] ] }, "arguments": [] }, { "id": "PMC2593050-01-INTRODUCTION_E8", "type": "Process", "trigger": { "text": [ "reinfection" ], "offsets": [ [ 1968, 1979 ] ] }, "arguments": [ { "role": "Participant", "ref_id": "PMC2593050-01-INTRODUCTION_T34" } ] }, { "id": "PMC2593050-01-INTRODUCTION_E9", "type": "Process", "trigger": { "text": [ "attenuated" ], "offsets": [ [ 2153, 2163 ] ] }, "arguments": [] }, { "id": "PMC2593050-01-INTRODUCTION_E10", "type": "Regulation", "trigger": { "text": [ "importance" ], "offsets": [ [ 2405, 2415 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC2593050-01-INTRODUCTION_E11" }, { "role": "Cause", "ref_id": "PMC2593050-01-INTRODUCTION_T37" } ] }, { "id": "PMC2593050-01-INTRODUCTION_E11", "type": "Process", "trigger": { "text": [ "virulence" ], "offsets": [ [ 2436, 2445 ] ] }, "arguments": [ { "role": "Participant", "ref_id": "PMC2593050-01-INTRODUCTION_T40" } ] }, { "id": "PMC2593050-01-INTRODUCTION_E12", "type": "Process", "trigger": { "text": [ "infection" ], "offsets": [ [ 2520, 2529 ] ] }, "arguments": [] }, { "id": "PMC2593050-01-INTRODUCTION_E13", "type": "Negative_regulation", "trigger": { "text": [ "attenuated" ], "offsets": [ [ 2570, 2580 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC2593050-01-INTRODUCTION_E14" } ] }, { "id": "PMC2593050-01-INTRODUCTION_E14", "type": "Process", "trigger": { "text": [ "virulence" ], "offsets": [ [ 2589, 2598 ] ] }, "arguments": [ { "role": "Participant", "ref_id": "PMC2593050-01-INTRODUCTION_T45" } ] }, { "id": "PMC2593050-01-INTRODUCTION_E15", "type": "Process", "trigger": { "text": [ "infections" ], "offsets": [ [ 2646, 2656 ] ] }, "arguments": [] }, { "id": "PMC2593050-01-INTRODUCTION_E16", "type": "Process", "trigger": { "text": [ "infection" ], "offsets": [ [ 2666, 2675 ] ] }, "arguments": [ { "role": "Participant", "ref_id": "PMC2593050-01-INTRODUCTION_T47" } ] }, { "id": "PMC2593050-01-INTRODUCTION_E17", "type": "Negative_regulation", "trigger": { "text": [ "protection" ], "offsets": [ [ 2712, 2722 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC2593050-01-INTRODUCTION_E18" }, { "role": "Cause", "ref_id": "PMC2593050-01-INTRODUCTION_E16" } ] }, { "id": "PMC2593050-01-INTRODUCTION_E18", "type": "Process", "trigger": { "text": [ "infection" ], "offsets": [ [ 2742, 2751 ] ] }, "arguments": [ { "role": "Participant", "ref_id": "PMC2593050-01-INTRODUCTION_T49" } ] }, { "id": "PMC2593050-01-INTRODUCTION_E19", "type": "Positive_regulation", "trigger": { "text": [ "induces" ], "offsets": [ [ 2779, 2786 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC2593050-01-INTRODUCTION_E20" }, { "role": "Cause", "ref_id": "PMC2593050-01-INTRODUCTION_E16" } ] }, { "id": "PMC2593050-01-INTRODUCTION_E20", "type": "Gene_expression", "trigger": { "text": [ "production" ], "offsets": [ [ 2787, 2797 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC2593050-01-INTRODUCTION_T50" } ] }, { "id": "PMC2593050-01-INTRODUCTION_E21", "type": "Process", "trigger": { "text": [ "infection" ], "offsets": [ [ 2852, 2861 ] ] }, "arguments": [] } ]

[ { "id": "PMC2593050-01-INTRODUCTION_1", "entity_ids": [ "PMC2593050-01-INTRODUCTION_T24", "PMC2593050-01-INTRODUCTION_T25" ] }, { "id": "PMC2593050-01-INTRODUCTION_2", "entity_ids": [ "PMC2593050-01-INTRODUCTION_T31", "PMC2593050-01-INTRODUCTION_T32" ] } ]

[]

[ { "id": "PMC2266911-00-TIAB__text", "type": "abstract", "text": [ "Comparative analysis of the Photorhabdus luminescens and the Yersinia enterocolitica genomes: uncovering candidate genes involved in insect pathogenicity \nBackground Photorhabdus luminescens and Yersinia enterocolitica are both enteric bacteria which are associated with insects. P. luminescens lives in symbiosis with soil nematodes and is highly pathogenic towards insects but not to humans. In contrast, Y. enterocolitica is widely found in the environment and mainly known to cause gastroenteritis in men, but has only recently been shown to be also toxic for insects. It is expected that both pathogens share an overlap of genetic determinants that play a role within the insect host. Results A selective genome comparison was applied. Proteins belonging to the class of two-component regulatory systems, quorum sensing, universal stress proteins, and c-di-GMP signalling have been analysed. The interorganismic synopsis of selected regulatory systems uncovered common and distinct signalling mechanisms of both pathogens used for perception of signals within the insect host. Particularly, a new class of LuxR-like regulators was identified, which might be involved in detecting insect-specific molecules. In addition, the genetic overlap unravelled a two-component system that is unique for the genera Photorhabdus and Yersinia and is therefore suggested to play a major role in the pathogen-insect relationship. Our analysis also highlights factors of both pathogens that are expressed at low temperatures as encountered in insects in contrast to higher (body) temperature, providing evidence that temperature is a yet under-investigated environmental signal for bacterial adaptation to various hosts. Common degradative metabolic pathways are described that might be used to explore nutrients within the insect gut or hemolymph, thus enabling the proliferation of P. luminescens and Y. enterocolitica in their invertebrate hosts. A strikingly higher number of genes encoding insecticidal toxins and other virulence factors in P. luminescens compared to Y. enterocolitica correlates with the higher virulence of P. luminescens towards insects, and suggests a putative broader insect host spectrum of this pathogen. Conclusion A set of factors shared by the two pathogens was identified including those that are involved in the host infection process, in persistence within the insect, or in host exploitation. Some of them might have been selected during the association with insects and then adapted to pathogenesis in mammalian hosts.\n" ], "offsets": [ [ 0, 2545 ] ] } ]

[ { "id": "PMC2266911-00-TIAB_T1", "type": "Organism", "text": [ "Photorhabdus luminescens" ], "offsets": [ [ 28, 52 ] ], "normalized": [] }, { "id": "PMC2266911-00-TIAB_T2", "type": "Organism", "text": [ "Yersinia enterocolitica" ], "offsets": [ [ 61, 84 ] ], "normalized": [] }, { "id": "PMC2266911-00-TIAB_T3", "type": "Organism", "text": [ "Photorhabdus luminescens" ], "offsets": [ [ 166, 190 ] ], "normalized": [] }, { "id": "PMC2266911-00-TIAB_T4", "type": "Organism", "text": [ "Yersinia enterocolitica" ], "offsets": [ [ 195, 218 ] ], "normalized": [] }, { "id": "PMC2266911-00-TIAB_T5", "type": "Organism", "text": [ "P. luminescens" ], "offsets": [ [ 280, 294 ] ], "normalized": [] }, { "id": "PMC2266911-00-TIAB_T6", "type": "Organism", "text": [ "humans" ], "offsets": [ [ 386, 392 ] ], "normalized": [] }, { "id": "PMC2266911-00-TIAB_T7", "type": "Organism", "text": [ "Y. enterocolitica" ], "offsets": [ [ 407, 424 ] ], "normalized": [] }, { "id": "PMC2266911-00-TIAB_T8", "type": "Organism", "text": [ "men" ], "offsets": [ [ 505, 508 ] ], "normalized": [] }, { "id": "PMC2266911-00-TIAB_T9", "type": "Chemical", "text": [ "c-di-GMP" ], "offsets": [ [ 857, 865 ] ], "normalized": [] }, { "id": "PMC2266911-00-TIAB_T10", "type": "Protein", "text": [ "LuxR" ], "offsets": [ [ 1111, 1115 ] ], "normalized": [] }, { "id": "PMC2266911-00-TIAB_T11", "type": "Organism", "text": [ "Photorhabdus" ], "offsets": [ [ 1309, 1321 ] ], "normalized": [] }, { "id": "PMC2266911-00-TIAB_T12", "type": "Organism", "text": [ "Yersinia" ], "offsets": [ [ 1326, 1334 ] ], "normalized": [] }, { "id": "PMC2266911-00-TIAB_T13", "type": "Organism", "text": [ "P. luminescens" ], "offsets": [ [ 1873, 1887 ] ], "normalized": [] }, { "id": "PMC2266911-00-TIAB_T14", "type": "Organism", "text": [ "Y. enterocolitica" ], "offsets": [ [ 1892, 1909 ] ], "normalized": [] }, { "id": "PMC2266911-00-TIAB_T15", "type": "Organism", "text": [ "P. luminescens" ], "offsets": [ [ 2035, 2049 ] ], "normalized": [] }, { "id": "PMC2266911-00-TIAB_T16", "type": "Organism", "text": [ "Y. enterocolitica" ], "offsets": [ [ 2062, 2079 ] ], "normalized": [] }, { "id": "PMC2266911-00-TIAB_T17", "type": "Organism", "text": [ "P. luminescens" ], "offsets": [ [ 2120, 2134 ] ], "normalized": [] } ]

[ { "id": "PMC2266911-00-TIAB_E1", "type": "Process", "trigger": { "text": [ "virulence" ], "offsets": [ [ 2014, 2023 ] ] }, "arguments": [] }, { "id": "PMC2266911-00-TIAB_E2", "type": "Process", "trigger": { "text": [ "virulence" ], "offsets": [ [ 2107, 2116 ] ] }, "arguments": [ { "role": "Participant", "ref_id": "PMC2266911-00-TIAB_T17" } ] }, { "id": "PMC2266911-00-TIAB_E3", "type": "Process", "trigger": { "text": [ "infection" ], "offsets": [ [ 2340, 2349 ] ] }, "arguments": [] } ]

[]

[]

[ { "id": "PMC2682197-02-Results-07__text", "type": "abstract", "text": [ "The growth-regulating property of M. tuberculosis Rv2623 is dependent on its ability to bind ATP \nWe next sought to probe the relationship between the nucleotide-binding capacity and growth regulation by this mycobacterial USP. Both the D15E and G117A mutant proteins were overexpressed in M. smegmatis mc2155 at levels equivalent to that of wild-type Rv2623 (Figure S4). Results of these studies demonstrated that while overexpression of wildtype Rv2623 retards the growth of the recipient strain relative to cells transformed with vector alone, growth of the strains overexpressing ATP-binding-deficient mutant Rv2623 are only minimally affected by overexpression as assessed by spotting serial dilutions of the cultures of the appropriate strains onto solid Middlebrook 7H10 agar (data not shown) as well as by monitoring the time to detection using the BD BACTEC 9000MB system (Figure 8A). The distinct effects exhibited by the wild type and the G117A and D15E mutants defective in ATP binding suggests a direct correlation between growth attenuation and ATP binding (Figure 7B). To examine whether the effects of overexpression of Rv2623 on M. smegmatis are operative in virulent M. tuberculosis, the growth kinetics of the Erdman strain overexpressing wildtype Rv2623, as well as the Rv2623G117A and the Rv2623D15E mutant proteins, were evaluated in vitro using the BACTEC 9000MB system (Figure 8B). As in the M. smegmatis studies, the results show that overexpression of Rv2623 in M. tuberculosis results in marked retardation of growth. Furthermore, this growth attenuation is not observed in M. tuberculosis strains overexpressing the G117A or the D15E mutant Rv2623 (Figure 8B). Taken together, these data strongly suggest that the ability of Rv2623 to regulate growth of M. smegmatis and M. tuberculosis is dependent on an ATP-dependent process.\n" ], "offsets": [ [ 0, 1857 ] ] } ]

[ { "id": "PMC2682197-02-Results-07_T1", "type": "Organism", "text": [ "M. tuberculosis" ], "offsets": [ [ 34, 49 ] ], "normalized": [] }, { "id": "PMC2682197-02-Results-07_T2", "type": "Protein", "text": [ "Rv2623" ], "offsets": [ [ 50, 56 ] ], "normalized": [] }, { "id": "PMC2682197-02-Results-07_T3", "type": "Chemical", "text": [ "ATP" ], "offsets": [ [ 93, 96 ] ], "normalized": [] }, { "id": "PMC2682197-02-Results-07_T4", "type": "Organism", "text": [ "M. smegmatis mc2155" ], "offsets": [ [ 290, 309 ] ], "normalized": [] }, { "id": "PMC2682197-02-Results-07_T5", "type": "Protein", "text": [ "Rv2623" ], "offsets": [ [ 352, 358 ] ], "normalized": [] }, { "id": "PMC2682197-02-Results-07_T6", "type": "Protein", "text": [ "Rv2623" ], "offsets": [ [ 448, 454 ] ], "normalized": [] }, { "id": "PMC2682197-02-Results-07_T7", "type": "Chemical", "text": [ "ATP" ], "offsets": [ [ 584, 587 ] ], "normalized": [] }, { "id": "PMC2682197-02-Results-07_T8", "type": "Protein", "text": [ "Rv2623" ], "offsets": [ [ 613, 619 ] ], "normalized": [] }, { "id": "PMC2682197-02-Results-07_T9", "type": "Organism", "text": [ "wild type" ], "offsets": [ [ 932, 941 ] ], "normalized": [] }, { "id": "PMC2682197-02-Results-07_T10", "type": "Organism", "text": [ "G117A" ], "offsets": [ [ 950, 955 ] ], "normalized": [] }, { "id": "PMC2682197-02-Results-07_T11", "type": "Organism", "text": [ "D15E mutants" ], "offsets": [ [ 960, 972 ] ], "normalized": [] }, { "id": "PMC2682197-02-Results-07_T12", "type": "Chemical", "text": [ "ATP" ], "offsets": [ [ 986, 989 ] ], "normalized": [] }, { "id": "PMC2682197-02-Results-07_T13", "type": "Chemical", "text": [ "ATP" ], "offsets": [ [ 1059, 1062 ] ], "normalized": [] }, { "id": "PMC2682197-02-Results-07_T14", "type": "Protein", "text": [ "Rv2623" ], "offsets": [ [ 1136, 1142 ] ], "normalized": [] }, { "id": "PMC2682197-02-Results-07_T15", "type": "Organism", "text": [ "M. smegmatis" ], "offsets": [ [ 1146, 1158 ] ], "normalized": [] }, { "id": "PMC2682197-02-Results-07_T16", "type": "Organism", "text": [ "M. tuberculosis" ], "offsets": [ [ 1185, 1200 ] ], "normalized": [] }, { "id": "PMC2682197-02-Results-07_T17", "type": "Organism", "text": [ "Erdman" ], "offsets": [ [ 1229, 1235 ] ], "normalized": [] }, { "id": "PMC2682197-02-Results-07_T18", "type": "Protein", "text": [ "Rv2623" ], "offsets": [ [ 1267, 1273 ] ], "normalized": [] }, { "id": "PMC2682197-02-Results-07_T19", "type": "Protein", "text": [ "Rv2623" ], "offsets": [ [ 1290, 1296 ] ], "normalized": [] }, { "id": "PMC2682197-02-Results-07_T20", "type": "Protein", "text": [ "Rv2623" ], "offsets": [ [ 1310, 1316 ] ], "normalized": [] }, { "id": "PMC2682197-02-Results-07_T21", "type": "Organism", "text": [ "M. smegmatis" ], "offsets": [ [ 1416, 1428 ] ], "normalized": [] }, { "id": "PMC2682197-02-Results-07_T22", "type": "Protein", "text": [ "Rv2623" ], "offsets": [ [ 1478, 1484 ] ], "normalized": [] }, { "id": "PMC2682197-02-Results-07_T23", "type": "Organism", "text": [ "M. tuberculosis" ], "offsets": [ [ 1488, 1503 ] ], "normalized": [] }, { "id": "PMC2682197-02-Results-07_T24", "type": "Organism", "text": [ "M. tuberculosis" ], "offsets": [ [ 1601, 1616 ] ], "normalized": [] }, { "id": "PMC2682197-02-Results-07_T25", "type": "Protein", "text": [ "Rv2623" ], "offsets": [ [ 1669, 1675 ] ], "normalized": [] }, { "id": "PMC2682197-02-Results-07_T26", "type": "Protein", "text": [ "Rv2623" ], "offsets": [ [ 1753, 1759 ] ], "normalized": [] }, { "id": "PMC2682197-02-Results-07_T27", "type": "Organism", "text": [ "M. smegmatis" ], "offsets": [ [ 1782, 1794 ] ], "normalized": [] }, { "id": "PMC2682197-02-Results-07_T28", "type": "Organism", "text": [ "M. tuberculosis" ], "offsets": [ [ 1799, 1814 ] ], "normalized": [] }, { "id": "PMC2682197-02-Results-07_T29", "type": "Chemical", "text": [ "ATP" ], "offsets": [ [ 1834, 1837 ] ], "normalized": [] } ]

[ { "id": "PMC2682197-02-Results-07_E1", "type": "Binding", "trigger": { "text": [ "bind" ], "offsets": [ [ 88, 92 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC2682197-02-Results-07_T2" }, { "role": "Theme", "ref_id": "PMC2682197-02-Results-07_T3" } ] }, { "id": "PMC2682197-02-Results-07_E2", "type": "Gene_expression", "trigger": { "text": [ "levels" ], "offsets": [ [ 313, 319 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC2682197-02-Results-07_T5" } ] }, { "id": "PMC2682197-02-Results-07_E3", "type": "Gene_expression", "trigger": { "text": [ "overexpression" ], "offsets": [ [ 421, 435 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC2682197-02-Results-07_T6" } ] }, { "id": "PMC2682197-02-Results-07_E4", "type": "Binding", "trigger": { "text": [ "binding" ], "offsets": [ [ 588, 595 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC2682197-02-Results-07_T7" }, { "role": "Theme", "ref_id": "PMC2682197-02-Results-07_T8" } ] }, { "id": "PMC2682197-02-Results-07_E5", "type": "Negative_regulation", "trigger": { "text": [ "deficient" ], "offsets": [ [ 596, 605 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC2682197-02-Results-07_E4" } ] }, { "id": "PMC2682197-02-Results-07_E6", "type": "Negative_regulation", "trigger": { "text": [ "defective" ], "offsets": [ [ 973, 982 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC2682197-02-Results-07_E7" } ] }, { "id": "PMC2682197-02-Results-07_E7", "type": "Binding", "trigger": { "text": [ "binding" ], "offsets": [ [ 990, 997 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC2682197-02-Results-07_T12" } ] }, { "id": "PMC2682197-02-Results-07_E8", "type": "Binding", "trigger": { "text": [ "binding" ], "offsets": [ [ 1063, 1070 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC2682197-02-Results-07_T13" } ] }, { "id": "PMC2682197-02-Results-07_E9", "type": "Gene_expression", "trigger": { "text": [ "overexpression" ], "offsets": [ [ 1118, 1132 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC2682197-02-Results-07_T14" } ] }, { "id": "PMC2682197-02-Results-07_E10", "type": "Process", "trigger": { "text": [ "virulent" ], "offsets": [ [ 1176, 1184 ] ] }, "arguments": [ { "role": "Participant", "ref_id": "PMC2682197-02-Results-07_T16" } ] }, { "id": "PMC2682197-02-Results-07_E11", "type": "Gene_expression", "trigger": { "text": [ "overexpressing" ], "offsets": [ [ 1243, 1257 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC2682197-02-Results-07_T18" } ] }, { "id": "PMC2682197-02-Results-07_E12", "type": "Gene_expression", "trigger": { "text": [ "overexpression" ], "offsets": [ [ 1460, 1474 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC2682197-02-Results-07_T22" } ] } ]

[]

[]

[ { "id": "PMC2593050-03-RESULTS-01__text", "type": "abstract", "text": [ "RESULTS \nS. equi vicK Deletion Mutant The S. equi vicRK genes were found by blasting the S. equi genome database (http://www.sanger.ac.uk/Projects/S_equi ) with the S. pyogenes vicRK sequence. Gene replacement strategy was used to generate vicK-deletion mutant (Fig. 1A). The vector pGRV has two genes aad and cmR for selections with spectinomycin and chloramphenicol, respectively. The two upstream and downstream flanking fragments of the internal vicK fragment from Tyr151 to Ser427 to be deleted were cloned at the upstream and downstream ends of the aad gene, respectively, resulting in suicide plasmid pGRV-DeltavicK. Single crossover between one flanking fragment in pGRV-DeltavicK and the homologous region in the genome would lead to the insertion of the whole plasmid into S. equi genome, resulting in strains resistant to both spectinomycin and chloramphenicol. Double crossoverat both of the flanking fragments would lead to the replacement of the vicK internal fragment with the aad gene, resulting in vicK deletion strains with resistance only to spectinomycin. The colonies on spectinomycin agar plates were tested for resistance to chloramphenicol. Three putative DeltavicK strains, which were spectinomycin-resistant and chloramphenicol-sensitive, were obtained. PCR analyses using the primers located beyond the deleted fragment resulted in the PCR product from these strains that were expectedly bigger than that from the wild-type strain because the replacing fragment was bigger than the displaced vicK fragment (Fig. 1B). DNA sequencing confirmed the desired deletion. One deletion strain was randomly chosen for further characterization.\n" ], "offsets": [ [ 0, 1661 ] ] } ]

[ { "id": "PMC2593050-03-RESULTS-01_T1", "type": "Organism", "text": [ "S. equi vicK Deletion Mutant" ], "offsets": [ [ 9, 37 ] ], "normalized": [] }, { "id": "PMC2593050-03-RESULTS-01_T2", "type": "Protein", "text": [ "vicK" ], "offsets": [ [ 17, 21 ] ], "normalized": [] }, { "id": "PMC2593050-03-RESULTS-01_T3", "type": "Organism", "text": [ "S. equi" ], "offsets": [ [ 42, 49 ] ], "normalized": [] }, { "id": "PMC2593050-03-RESULTS-01_T4", "type": "Two-component-system", "text": [ "vicRK" ], "offsets": [ [ 50, 55 ] ], "normalized": [] }, { "id": "PMC2593050-03-RESULTS-01_T5", "type": "Protein", "text": [ "vicR" ], "offsets": [ [ 50, 54 ] ], "normalized": [] }, { "id": "PMC2593050-03-RESULTS-01_T6", "type": "Protein", "text": [ "K" ], "offsets": [ [ 54, 55 ] ], "normalized": [] }, { "id": "PMC2593050-03-RESULTS-01_T7", "type": "Organism", "text": [ "S. equi" ], "offsets": [ [ 89, 96 ] ], "normalized": [] }, { "id": "PMC2593050-03-RESULTS-01_T8", "type": "Organism", "text": [ "S. pyogenes" ], "offsets": [ [ 165, 176 ] ], "normalized": [] }, { "id": "PMC2593050-03-RESULTS-01_T9", "type": "Two-component-system", "text": [ "vicRK" ], "offsets": [ [ 177, 182 ] ], "normalized": [] }, { "id": "PMC2593050-03-RESULTS-01_T10", "type": "Protein", "text": [ "vicR" ], "offsets": [ [ 177, 181 ] ], "normalized": [] }, { "id": "PMC2593050-03-RESULTS-01_T11", "type": "Protein", "text": [ "K" ], "offsets": [ [ 181, 182 ] ], "normalized": [] }, { "id": "PMC2593050-03-RESULTS-01_T12", "type": "Organism", "text": [ "vicK-deletion mutant" ], "offsets": [ [ 240, 260 ] ], "normalized": [] }, { "id": "PMC2593050-03-RESULTS-01_T13", "type": "Protein", "text": [ "vicK" ], "offsets": [ [ 240, 244 ] ], "normalized": [] }, { "id": "PMC2593050-03-RESULTS-01_T14", "type": "Protein", "text": [ "aad" ], "offsets": [ [ 302, 305 ] ], "normalized": [] }, { "id": "PMC2593050-03-RESULTS-01_T15", "type": "Protein", "text": [ "cmR" ], "offsets": [ [ 310, 313 ] ], "normalized": [] }, { "id": "PMC2593050-03-RESULTS-01_T16", "type": "Chemical", "text": [ "spectinomycin" ], "offsets": [ [ 334, 347 ] ], "normalized": [] }, { "id": "PMC2593050-03-RESULTS-01_T17", "type": "Chemical", "text": [ "chloramphenicol" ], "offsets": [ [ 352, 367 ] ], "normalized": [] }, { "id": "PMC2593050-03-RESULTS-01_T18", "type": "Protein", "text": [ "vicK" ], "offsets": [ [ 450, 454 ] ], "normalized": [] }, { "id": "PMC2593050-03-RESULTS-01_T19", "type": "Protein", "text": [ "aad" ], "offsets": [ [ 555, 558 ] ], "normalized": [] }, { "id": "PMC2593050-03-RESULTS-01_T20", "type": "Protein", "text": [ "vicK" ], "offsets": [ [ 618, 622 ] ], "normalized": [] }, { "id": "PMC2593050-03-RESULTS-01_T21", "type": "Protein", "text": [ "vicK" ], "offsets": [ [ 684, 688 ] ], "normalized": [] }, { "id": "PMC2593050-03-RESULTS-01_T22", "type": "Organism", "text": [ "S. equi" ], "offsets": [ [ 783, 790 ] ], "normalized": [] }, { "id": "PMC2593050-03-RESULTS-01_T23", "type": "Chemical", "text": [ "spectinomycin" ], "offsets": [ [ 838, 851 ] ], "normalized": [] }, { "id": "PMC2593050-03-RESULTS-01_T24", "type": "Chemical", "text": [ "chloramphenicol" ], "offsets": [ [ 856, 871 ] ], "normalized": [] }, { "id": "PMC2593050-03-RESULTS-01_T25", "type": "Protein", "text": [ "vicK" ], "offsets": [ [ 960, 964 ] ], "normalized": [] }, { "id": "PMC2593050-03-RESULTS-01_T26", "type": "Protein", "text": [ "aad" ], "offsets": [ [ 992, 995 ] ], "normalized": [] }, { "id": "PMC2593050-03-RESULTS-01_T27", "type": "Protein", "text": [ "vicK" ], "offsets": [ [ 1015, 1019 ] ], "normalized": [] }, { "id": "PMC2593050-03-RESULTS-01_T28", "type": "Chemical", "text": [ "spectinomycin" ], "offsets": [ [ 1061, 1074 ] ], "normalized": [] }, { "id": "PMC2593050-03-RESULTS-01_T29", "type": "Chemical", "text": [ "spectinomycin" ], "offsets": [ [ 1092, 1105 ] ], "normalized": [] }, { "id": "PMC2593050-03-RESULTS-01_T30", "type": "Chemical", "text": [ "chloramphenicol" ], "offsets": [ [ 1148, 1163 ] ], "normalized": [] }, { "id": "PMC2593050-03-RESULTS-01_T31", "type": "Protein", "text": [ "vicK" ], "offsets": [ [ 1185, 1189 ] ], "normalized": [] }, { "id": "PMC2593050-03-RESULTS-01_T32", "type": "Chemical", "text": [ "spectinomycin" ], "offsets": [ [ 1210, 1223 ] ], "normalized": [] }, { "id": "PMC2593050-03-RESULTS-01_T33", "type": "Chemical", "text": [ "chloramphenicol" ], "offsets": [ [ 1238, 1253 ] ], "normalized": [] }, { "id": "PMC2593050-03-RESULTS-01_T34", "type": "Protein", "text": [ "vicK" ], "offsets": [ [ 1519, 1523 ] ], "normalized": [] } ]

[ { "id": "PMC2593050-03-RESULTS-01_E1", "type": "Process", "trigger": { "text": [ "resistant" ], "offsets": [ [ 820, 829 ] ] }, "arguments": [] }, { "id": "PMC2593050-03-RESULTS-01_E2", "type": "Process", "trigger": { "text": [ "resistance" ], "offsets": [ [ 1042, 1052 ] ] }, "arguments": [] }, { "id": "PMC2593050-03-RESULTS-01_E3", "type": "Process", "trigger": { "text": [ "resistance" ], "offsets": [ [ 1134, 1144 ] ] }, "arguments": [] }, { "id": "PMC2593050-03-RESULTS-01_E4", "type": "Process", "trigger": { "text": [ "resistant" ], "offsets": [ [ 1224, 1233 ] ] }, "arguments": [] } ]

[]

[]

[ { "id": "PMC2639726-03-Discussion-04__text", "type": "abstract", "text": [ "Clustering analysis and co-expression \nThe complex regulatory network suggested by these studies has been partially confirmed. Complete elucidation of the virulence pathways must include proteomic studies to identify steps that require translational regulation, binding studies to distinguish direct from indirect effects and additional regulators not included in this preliminary group of 14. In this study, cluster analysis was used to identify genes that show similar expression profiles under a variety of environmental conditions and from the isogenic Salmonella regulatory mutants we describe. The average G+C content of the 92 genes outside of SPI-2 that show the same regulation as SPI-2 is 47% while the average for Salmonella is 52% (p<e-25). Most of these genes are not found in closely related non-pathogenic bacteria (overall comparison eliminating SPI-2 genes p<e-15). Thus application of the CLR algorithm identified a very interesting group of genes that are co-regulated with SPI-2 and were horizontally transferred to Salmonella. Analysis of microarrays and other expression data was used to construct a predictive model for how the regulators may interact and coordinate regulation within the host. A few of the predictions have been verified and more are being tested. The construction of a complete interaction network describing both the host and pathogen is a long-term goal of this and other related research efforts.\n" ], "offsets": [ [ 0, 1442 ] ] } ]

[ { "id": "PMC2639726-03-Discussion-04_T1", "type": "Organism", "text": [ "Salmonella" ], "offsets": [ [ 557, 567 ] ], "normalized": [] }, { "id": "PMC2639726-03-Discussion-04_T2", "type": "Organism", "text": [ "Salmonella" ], "offsets": [ [ 725, 735 ] ], "normalized": [] }, { "id": "PMC2639726-03-Discussion-04_T3", "type": "Organism", "text": [ "Salmonella" ], "offsets": [ [ 1036, 1046 ] ], "normalized": [] } ]

[ { "id": "PMC2639726-03-Discussion-04_E1", "type": "Process", "trigger": { "text": [ "virulence" ], "offsets": [ [ 155, 164 ] ] }, "arguments": [] } ]

[]

[]

[ { "id": "PMC2565068-01-Introduction__text", "type": "abstract", "text": [ "Introduction \nStreptococcus pyogenes (group A streptococcus; GAS) is one of the most common human pathogens. It causes a wide variety of infections ranging from uncomplicated pharyngitis and skin infections to severe and even life-threatening manifestations, such as necrotizing fasciitis (NF) and streptococcal toxic shock-like syndrome (STSS) [1], [2], with high mortality rates ranging from 20% to 60% [3]. Several streptococcal virulence factors, including streptolysin, and M protein, have been reported to be involved in these diseases, by genetic studies or animal-passaged models [1], [2], [4]-[6]. However, which of factors are involved in pathogenesis mediated by clinically isolated severe invasive GAS remains obscure. The strains of emm1 genotype, among more than 100 emm genes encoding the serotype-determinant M protein, are the predominant cause of severe GAS infections in Japan [7]. Recently, GAS with diverse emm genotypes, especially, emm49-genotype, have been isolated from patients of severe invasive GAS infections since 2000; however, these genotypes were not isolated before 1999 in Japan [8]. Therefore, emm49 GAS isolated from invasive infections seems to acquire the novel or altered virulence factors by mutations, genomic additions, or deletions. Epidemiological and pathological findings, including sporadic incidents of severe invasive GAS infections [9], high frequency of severe invasive infections in immunocompromised host [9], and aggregation of bacteria and a paucity of polymorphnuclear neutrophils (PMN) in foci of invasive GAS infection [10] suggest that host defense factors play an important role in the onset of invasive infections. These findings led us to postulate that invasive GAS infections hampered host innate immune defense, especially on PMN, providing the front-line defense against GAS infection by quick recruitment to infection site and clearance of bacteria following phagocytosis [11], [12]. So far, using animal-passaged GAS mutants, gene-manipulated GAS, many virulence-associated molecules are pointed out to play some roles in the bacterial evasion from phagocytic ingestion by neutrophils [13]. However, restricted availability of clinical isolates with the same serotypes fail to elucidate direct relationship between definitive genetic changes in clinically isolated severe invasive GAS and the lack of PMN at the site of bacterial growth. In the present study, we aimed to explore the crucial factors in the pathogenesis of severe invasive GAS infections in the context of PMN-GAS relationship, using a panel of emm49 clinical isolates from patients with or without severe invasive infection, and their gene-manipulated mutants. We now show a direct and previously unrecognized link between functional loss of a factor CsrS of two-component sensor/regulator system (CsrS/CsrR: also known as CovS/CovR) and escape from killing by PMN via inducing necrosis to them and digesting IL-8, a PMN-attracting chemokine. We further determined CsrS mutations in the severe invasive GAS was essential to control the expression of various virulence genes and contributed to the in vivo virulence and disease-specific pathophysiology in a mouse model. These data may participate in prediction of GAS potential for future invasive infection as well as risk assessment of patients by measuring PMN function.\n" ], "offsets": [ [ 0, 3360 ] ] } ]

[ { "id": "PMC2565068-01-Introduction_T1", "type": "Organism", "text": [ "Streptococcus pyogenes" ], "offsets": [ [ 14, 36 ] ], "normalized": [] }, { "id": "PMC2565068-01-Introduction_T2", "type": "Organism", "text": [ "group A streptococcus" ], "offsets": [ [ 38, 59 ] ], "normalized": [] }, { "id": "PMC2565068-01-Introduction_T3", "type": "Organism", "text": [ "GAS" ], "offsets": [ [ 61, 64 ] ], "normalized": [] }, { "id": "PMC2565068-01-Introduction_T4", "type": "Organism", "text": [ "human" ], "offsets": [ [ 92, 97 ] ], "normalized": [] }, { "id": "PMC2565068-01-Introduction_T5", "type": "Protein", "text": [ "M protein" ], "offsets": [ [ 479, 488 ] ], "normalized": [] }, { "id": "PMC2565068-01-Introduction_T6", "type": "Organism", "text": [ "invasive GAS" ], "offsets": [ [ 701, 713 ] ], "normalized": [] }, { "id": "PMC2565068-01-Introduction_T7", "type": "Organism", "text": [ "strains of emm1" ], "offsets": [ [ 735, 750 ] ], "normalized": [] }, { "id": "PMC2565068-01-Introduction_T8", "type": "Protein", "text": [ "emm1" ], "offsets": [ [ 746, 750 ] ], "normalized": [] }, { "id": "PMC2565068-01-Introduction_T9", "type": "Protein", "text": [ "emm" ], "offsets": [ [ 781, 784 ] ], "normalized": [] }, { "id": "PMC2565068-01-Introduction_T10", "type": "Protein", "text": [ "M protein" ], "offsets": [ [ 825, 834 ] ], "normalized": [] }, { "id": "PMC2565068-01-Introduction_T11", "type": "Organism", "text": [ "GAS" ], "offsets": [ [ 872, 875 ] ], "normalized": [] }, { "id": "PMC2565068-01-Introduction_T12", "type": "Organism", "text": [ "GAS with diverse emm genotypes" ], "offsets": [ [ 911, 941 ] ], "normalized": [] }, { "id": "PMC2565068-01-Introduction_T13", "type": "Protein", "text": [ "emm" ], "offsets": [ [ 928, 931 ] ], "normalized": [] }, { "id": "PMC2565068-01-Introduction_T14", "type": "Organism", "text": [ "emm49-genotype" ], "offsets": [ [ 955, 969 ] ], "normalized": [] }, { "id": "PMC2565068-01-Introduction_T15", "type": "Protein", "text": [ "emm49" ], "offsets": [ [ 955, 960 ] ], "normalized": [] }, { "id": "PMC2565068-01-Introduction_T16", "type": "Organism", "text": [ "patients" ], "offsets": [ [ 995, 1003 ] ], "normalized": [] }, { "id": "PMC2565068-01-Introduction_T17", "type": "Organism", "text": [ "invasive GAS" ], "offsets": [ [ 1014, 1026 ] ], "normalized": [] }, { "id": "PMC2565068-01-Introduction_T18", "type": "Organism", "text": [ "emm49 GAS" ], "offsets": [ [ 1130, 1139 ] ], "normalized": [] }, { "id": "PMC2565068-01-Introduction_T19", "type": "Protein", "text": [ "emm49" ], "offsets": [ [ 1130, 1135 ] ], "normalized": [] }, { "id": "PMC2565068-01-Introduction_T20", "type": "Organism", "text": [ "invasive GAS" ], "offsets": [ [ 1359, 1371 ] ], "normalized": [] }, { "id": "PMC2565068-01-Introduction_T21", "type": "Organism", "text": [ "invasive GAS" ], "offsets": [ [ 1555, 1567 ] ], "normalized": [] }, { "id": "PMC2565068-01-Introduction_T22", "type": "Organism", "text": [ "invasive GAS" ], "offsets": [ [ 1717, 1729 ] ], "normalized": [] }, { "id": "PMC2565068-01-Introduction_T23", "type": "Organism", "text": [ "GAS" ], "offsets": [ [ 1838, 1841 ] ], "normalized": [] }, { "id": "PMC2565068-01-Introduction_T24", "type": "Organism", "text": [ "GAS mutants" ], "offsets": [ [ 1982, 1993 ] ], "normalized": [] }, { "id": "PMC2565068-01-Introduction_T25", "type": "Organism", "text": [ "gene-manipulated GAS" ], "offsets": [ [ 1995, 2015 ] ], "normalized": [] }, { "id": "PMC2565068-01-Introduction_T26", "type": "Organism", "text": [ "invasive GAS" ], "offsets": [ [ 2341, 2353 ] ], "normalized": [] }, { "id": "PMC2565068-01-Introduction_T27", "type": "Organism", "text": [ "invasive GAS" ], "offsets": [ [ 2499, 2511 ] ], "normalized": [] }, { "id": "PMC2565068-01-Introduction_T28", "type": "Organism", "text": [ "emm49 clinical isolates" ], "offsets": [ [ 2580, 2603 ] ], "normalized": [] }, { "id": "PMC2565068-01-Introduction_T29", "type": "Protein", "text": [ "emm49" ], "offsets": [ [ 2580, 2585 ] ], "normalized": [] }, { "id": "PMC2565068-01-Introduction_T30", "type": "Organism", "text": [ "patients" ], "offsets": [ [ 2609, 2617 ] ], "normalized": [] }, { "id": "PMC2565068-01-Introduction_T31", "type": "Protein", "text": [ "CsrS" ], "offsets": [ [ 2787, 2791 ] ], "normalized": [] }, { "id": "PMC2565068-01-Introduction_T32", "type": "Two-component-system", "text": [ "CsrS/CsrR" ], "offsets": [ [ 2834, 2843 ] ], "normalized": [] }, { "id": "PMC2565068-01-Introduction_T33", "type": "Protein", "text": [ "CsrS" ], "offsets": [ [ 2834, 2838 ] ], "normalized": [] }, { "id": "PMC2565068-01-Introduction_T34", "type": "Protein", "text": [ "CsrR" ], "offsets": [ [ 2839, 2843 ] ], "normalized": [] }, { "id": "PMC2565068-01-Introduction_T35", "type": "Two-component-system", "text": [ "CovS/CovR" ], "offsets": [ [ 2859, 2868 ] ], "normalized": [] }, { "id": "PMC2565068-01-Introduction_T36", "type": "Protein", "text": [ "CovS" ], "offsets": [ [ 2859, 2863 ] ], "normalized": [] }, { "id": "PMC2565068-01-Introduction_T37", "type": "Protein", "text": [ "CovR" ], "offsets": [ [ 2864, 2868 ] ], "normalized": [] }, { "id": "PMC2565068-01-Introduction_T38", "type": "Protein", "text": [ "IL-8" ], "offsets": [ [ 2945, 2949 ] ], "normalized": [] }, { "id": "PMC2565068-01-Introduction_T39", "type": "Organism", "text": [ "CsrS mutations" ], "offsets": [ [ 3001, 3015 ] ], "normalized": [] }, { "id": "PMC2565068-01-Introduction_T40", "type": "Protein", "text": [ "CsrS" ], "offsets": [ [ 3001, 3005 ] ], "normalized": [] }, { "id": "PMC2565068-01-Introduction_T41", "type": "Organism", "text": [ "invasive GAS" ], "offsets": [ [ 3030, 3042 ] ], "normalized": [] }, { "id": "PMC2565068-01-Introduction_T42", "type": "Organism", "text": [ "mouse" ], "offsets": [ [ 3193, 3198 ] ], "normalized": [] }, { "id": "PMC2565068-01-Introduction_T43", "type": "Organism", "text": [ "GAS" ], "offsets": [ [ 3250, 3253 ] ], "normalized": [] }, { "id": "PMC2565068-01-Introduction_T44", "type": "Organism", "text": [ "patients" ], "offsets": [ [ 3324, 3332 ] ], "normalized": [] } ]

[ { "id": "PMC2565068-01-Introduction_E1", "type": "Process", "trigger": { "text": [ "infections" ], "offsets": [ [ 137, 147 ] ] }, "arguments": [] }, { "id": "PMC2565068-01-Introduction_E2", "type": "Process", "trigger": { "text": [ "infections" ], "offsets": [ [ 196, 206 ] ] }, "arguments": [] }, { "id": "PMC2565068-01-Introduction_E3", "type": "Process", "trigger": { "text": [ "virulence" ], "offsets": [ [ 432, 441 ] ] }, "arguments": [] }, { "id": "PMC2565068-01-Introduction_E4", "type": "Process", "trigger": { "text": [ "infections" ], "offsets": [ [ 876, 886 ] ] }, "arguments": [ { "role": "Participant", "ref_id": "PMC2565068-01-Introduction_T11" } ] }, { "id": "PMC2565068-01-Introduction_E5", "type": "Process", "trigger": { "text": [ "infections" ], "offsets": [ [ 1027, 1037 ] ] }, "arguments": [ { "role": "Participant", "ref_id": "PMC2565068-01-Introduction_T17" } ] }, { "id": "PMC2565068-01-Introduction_E6", "type": "Process", "trigger": { "text": [ "infections" ], "offsets": [ [ 1163, 1173 ] ] }, "arguments": [ { "role": "Participant", "ref_id": "PMC2565068-01-Introduction_T18" } ] }, { "id": "PMC2565068-01-Introduction_E7", "type": "Process", "trigger": { "text": [ "virulence" ], "offsets": [ [ 1212, 1221 ] ] }, "arguments": [] }, { "id": "PMC2565068-01-Introduction_E8", "type": "Process", "trigger": { "text": [ "infections" ], "offsets": [ [ 1372, 1382 ] ] }, "arguments": [ { "role": "Participant", "ref_id": "PMC2565068-01-Introduction_T20" } ] }, { "id": "PMC2565068-01-Introduction_E9", "type": "Process", "trigger": { "text": [ "infections" ], "offsets": [ [ 1422, 1432 ] ] }, "arguments": [] }, { "id": "PMC2565068-01-Introduction_E10", "type": "Process", "trigger": { "text": [ "infection" ], "offsets": [ [ 1568, 1577 ] ] }, "arguments": [ { "role": "Participant", "ref_id": "PMC2565068-01-Introduction_T21" } ] }, { "id": "PMC2565068-01-Introduction_E11", "type": "Process", "trigger": { "text": [ "infections" ], "offsets": [ [ 1665, 1675 ] ] }, "arguments": [] }, { "id": "PMC2565068-01-Introduction_E12", "type": "Process", "trigger": { "text": [ "infections" ], "offsets": [ [ 1730, 1740 ] ] }, "arguments": [ { "role": "Participant", "ref_id": "PMC2565068-01-Introduction_T22" } ] }, { "id": "PMC2565068-01-Introduction_E13", "type": "Process", "trigger": { "text": [ "infection" ], "offsets": [ [ 1842, 1851 ] ] }, "arguments": [ { "role": "Participant", "ref_id": "PMC2565068-01-Introduction_T23" } ] }, { "id": "PMC2565068-01-Introduction_E14", "type": "Process", "trigger": { "text": [ "infection" ], "offsets": [ [ 1876, 1885 ] ] }, "arguments": [] }, { "id": "PMC2565068-01-Introduction_E15", "type": "Process", "trigger": { "text": [ "virulence" ], "offsets": [ [ 2022, 2031 ] ] }, "arguments": [] }, { "id": "PMC2565068-01-Introduction_E16", "type": "Process", "trigger": { "text": [ "infections" ], "offsets": [ [ 2512, 2522 ] ] }, "arguments": [ { "role": "Participant", "ref_id": "PMC2565068-01-Introduction_T27" } ] }, { "id": "PMC2565068-01-Introduction_E17", "type": "Process", "trigger": { "text": [ "infection" ], "offsets": [ [ 2650, 2659 ] ] }, "arguments": [ { "role": "Participant", "ref_id": "PMC2565068-01-Introduction_T28" } ] }, { "id": "PMC2565068-01-Introduction_E18", "type": "Process", "trigger": { "text": [ "infection" ], "offsets": [ [ 2650, 2659 ] ] }, "arguments": [ { "role": "Participant", "ref_id": "PMC2565068-01-Introduction_T28" } ] }, { "id": "PMC2565068-01-Introduction_E19", "type": "Process", "trigger": { "text": [ "virulence" ], "offsets": [ [ 3094, 3103 ] ] }, "arguments": [] }, { "id": "PMC2565068-01-Introduction_E20", "type": "Process", "trigger": { "text": [ "virulence" ], "offsets": [ [ 3141, 3150 ] ] }, "arguments": [ { "role": "Participant", "ref_id": "PMC2565068-01-Introduction_T39" } ] }, { "id": "PMC2565068-01-Introduction_E21", "type": "Process", "trigger": { "text": [ "infection" ], "offsets": [ [ 3284, 3293 ] ] }, "arguments": [ { "role": "Participant", "ref_id": "PMC2565068-01-Introduction_T43" } ] } ]

[ { "id": "PMC2565068-01-Introduction_1", "entity_ids": [ "PMC2565068-01-Introduction_T2", "PMC2565068-01-Introduction_T3" ] }, { "id": "PMC2565068-01-Introduction_2", "entity_ids": [ "PMC2565068-01-Introduction_T32", "PMC2565068-01-Introduction_T35" ] } ]

[]

[ { "id": "PMC1913099-02-Results-Discussion-01__text", "type": "abstract", "text": [ "Results/Discussion \nAdherence-Mediated Differential Expression We developed spotted oligonucleotide arrays of the S. pyogenes SF370 (an M1 serotype) genome [14] and compared the transcriptomes of streptococci that adhere to Detroit 562 human pharyngeal cells to non-adherent (\"associated\") streptococci within the same experiment. Adherence assays were performed as described [15] with modifications to minimize eukaryotic cell disruption. We replicated experiments independently and used dye-swaps to incorporate biological and technical variation [16,17]. Following filtering and normalization [18,19], we analyzed data from four biological replicates [16] with robust summary statistics [20], Bayesian statistics [21,22], and permutation algorithms [19] to identify genes differentially expressed with significance during pharyngeal cell adherence. This analysis identified 79 genes (4% of the genome) exhibiting statistically significant fold changes in expression (PF value < 0.05) during adherence from 1,769 open reading frames represented on the array (Table 1). We refer to such genes as \"differentially expressed.\" We present the entire dataset from all experiments as Table S1. Genes demonstrating upregulation (n = 45) and downregulation (n = 34) included virulence factors, prophage-encoded transcripts, metabolic genes, and transcriptional regulators (Table 2). Undefined or hypothetical genes comprised 27% of differentially expressed genes (n = 21; 11 chromosomally encoded genes, ten phage-encoded genes).\n" ], "offsets": [ [ 0, 1523 ] ] } ]

[ { "id": "PMC1913099-02-Results-Discussion-01_T1", "type": "Organism", "text": [ "S. pyogenes SF370" ], "offsets": [ [ 114, 131 ] ], "normalized": [] }, { "id": "PMC1913099-02-Results-Discussion-01_T2", "type": "Organism", "text": [ "streptococci" ], "offsets": [ [ 196, 208 ] ], "normalized": [] }, { "id": "PMC1913099-02-Results-Discussion-01_T3", "type": "Organism", "text": [ "human" ], "offsets": [ [ 236, 241 ] ], "normalized": [] }, { "id": "PMC1913099-02-Results-Discussion-01_T4", "type": "Organism", "text": [ "streptococci" ], "offsets": [ [ 290, 302 ] ], "normalized": [] } ]

[ { "id": "PMC1913099-02-Results-Discussion-01_E1", "type": "Process", "trigger": { "text": [ "virulence" ], "offsets": [ [ 1268, 1277 ] ] }, "arguments": [] } ]

[]

[]

[ { "id": "PMC2774163-02-Results-04__text", "type": "abstract", "text": [ "TCS mutant biofilms are arrested in the transition to later biofilm developmental stages \nTo determine whether the altered biofilm structure was due to arrested biofilm formation or attachment defects, we first determined whether the P. aeruginosa mutants are defective in attachment. Inactivation of BfiS, BfmR, and MifR (PA4197, PA4101, PA5511, respectively) did not affect initial attachment to polystyrene compared to wild type biofilms as revealed by the crystal violet microtiter plate assay and confirmed by microscopy (not shown). Furthermore, no difference in growth in broth or defect with respect to twitching, swimming, and swarming or Pel and Psl polysaccharide production was detected for any of the mutant strains (not shown). In addition, no difference in transcript abundance, as determined by semi-quantitative RT-PCR, of genes involved in Pel and Psl polysaccharide biosynthesis compared to wild type was detected (not shown). However, a DeltagacS mutant showed 10-fold reduced initial attachment compared to the wild type (not shown), consistent with previous findings by Parkins and colleagues [65]. These findings implied that the novel regulatory proteins were involved in the regulation of biofilm formation at later stages following initial attachment. To determine the stage at which DeltabfiS and DeltabfmR mutant biofilms were arrested, the biofilm architecture of the mutant strains after 144 hr of growth was compared to the wild type P. aeruginosa biofilm architecture following 24, 72, and 144 hr of growth (Table 2). Based on the comparison of 5 biofilm variables, both mutant biofilms were more similar to 24-hr-old biofilms, with DeltabfmR forming more substantial biofilms than DeltabfiS or 24 hr wild type biofilms (Table 2). Arrest of biofilm formation at the 1-day time point correlated with the timing of BfiS and BfmR phosphorylation (Tables 1-2). Comparison of the DeltamifR biofilm architecture following 144 hr of growth to wild type biofilms indicated that DeltamifR biofilms were comparable to 72-hr-old biofilms. Since MifR was detected to be phosphorylated following 72 hr of biofilm growth (Table 1), our findings indicate that phosphorylation of MifR is essential for the progression of P. aeruginosa biofilms from the maturation-1 stage (72 hr) to the maturation-2 stage (144 hr). To exclude the possibility that the DeltabfiS, DeltabfmR, and DeltamifR mutant biofilms may have disaggregated prematurely, the formation of mutant biofilms was monitored daily by confocal microscopy over a period of 144 hr. The DeltabfiS and DeltabfmR biofilms resembled wild type biofilms with respect to biomass and overall architecture at the 24 hr time point (see Fig. 2A-B). However, while wild type biofilms continued to mature/develop upon prolonged incubation (see Fig. 2A), no additional biomass accumulation or alteration in architecture was observed for DeltabfiS and DeltabfmR biofilms post 24 hr of growth. Furthermore, for DeltamifR biofilms, the progression of biofilm formation was indistinguishable from wild type P. aeruginosa biofilm formation for the first 72 hr of growth. However, continued incubation did not result in increased DeltamifR biofilm growth (biomass, thickness) or microcolony formation typically seen in wild type biofilms at the maturation-2 stage (post 72 hr of growth, Table 2, Fig. 2). The findings clearly indicate that inactivation of these novel regulatory proteins did not cause biofilm disaggregation. Instead, our findings suggested that the mutant biofilms were incapable of progressing from the initial attachment stage to more mature biofilm stages.\n" ], "offsets": [ [ 0, 3633 ] ] } ]

[ { "id": "PMC2774163-02-Results-04_T1", "type": "Organism", "text": [ "P. aeruginosa" ], "offsets": [ [ 234, 247 ] ], "normalized": [] }, { "id": "PMC2774163-02-Results-04_T2", "type": "Protein", "text": [ "BfiS" ], "offsets": [ [ 301, 305 ] ], "normalized": [] }, { "id": "PMC2774163-02-Results-04_T3", "type": "Protein", "text": [ "BfmR" ], "offsets": [ [ 307, 311 ] ], "normalized": [] }, { "id": "PMC2774163-02-Results-04_T4", "type": "Protein", "text": [ "MifR" ], "offsets": [ [ 317, 321 ] ], "normalized": [] }, { "id": "PMC2774163-02-Results-04_T5", "type": "Protein", "text": [ "PA4197" ], "offsets": [ [ 323, 329 ] ], "normalized": [] }, { "id": "PMC2774163-02-Results-04_T6", "type": "Protein", "text": [ "PA4101" ], "offsets": [ [ 331, 337 ] ], "normalized": [] }, { "id": "PMC2774163-02-Results-04_T7", "type": "Protein", "text": [ "PA5511" ], "offsets": [ [ 339, 345 ] ], "normalized": [] }, { "id": "PMC2774163-02-Results-04_T8", "type": "Chemical", "text": [ "polystyrene" ], "offsets": [ [ 398, 409 ] ], "normalized": [] }, { "id": "PMC2774163-02-Results-04_T9", "type": "Protein", "text": [ "Pel" ], "offsets": [ [ 648, 651 ] ], "normalized": [] }, { "id": "PMC2774163-02-Results-04_T10", "type": "Protein", "text": [ "Psl" ], "offsets": [ [ 656, 659 ] ], "normalized": [] }, { "id": "PMC2774163-02-Results-04_T11", "type": "Protein", "text": [ "Pel" ], "offsets": [ [ 858, 861 ] ], "normalized": [] }, { "id": "PMC2774163-02-Results-04_T12", "type": "Protein", "text": [ "Psl" ], "offsets": [ [ 866, 869 ] ], "normalized": [] }, { "id": "PMC2774163-02-Results-04_T13", "type": "Organism", "text": [ "DeltagacS mutant" ], "offsets": [ [ 957, 973 ] ], "normalized": [] }, { "id": "PMC2774163-02-Results-04_T14", "type": "Protein", "text": [ "gacS" ], "offsets": [ [ 962, 966 ] ], "normalized": [] }, { "id": "PMC2774163-02-Results-04_T15", "type": "Organism", "text": [ "DeltabfiS" ], "offsets": [ [ 1310, 1319 ] ], "normalized": [] }, { "id": "PMC2774163-02-Results-04_T16", "type": "Protein", "text": [ "bfiS" ], "offsets": [ [ 1315, 1319 ] ], "normalized": [] }, { "id": "PMC2774163-02-Results-04_T17", "type": "Organism", "text": [ "DeltabfmR mutant" ], "offsets": [ [ 1324, 1340 ] ], "normalized": [] }, { "id": "PMC2774163-02-Results-04_T18", "type": "Protein", "text": [ "bfmR" ], "offsets": [ [ 1329, 1333 ] ], "normalized": [] }, { "id": "PMC2774163-02-Results-04_T19", "type": "Organism", "text": [ "P. aeruginosa" ], "offsets": [ [ 1465, 1478 ] ], "normalized": [] }, { "id": "PMC2774163-02-Results-04_T20", "type": "Organism", "text": [ "DeltabfmR" ], "offsets": [ [ 1665, 1674 ] ], "normalized": [] }, { "id": "PMC2774163-02-Results-04_T21", "type": "Protein", "text": [ "bfmR" ], "offsets": [ [ 1670, 1674 ] ], "normalized": [] }, { "id": "PMC2774163-02-Results-04_T22", "type": "Organism", "text": [ "DeltabfiS" ], "offsets": [ [ 1714, 1723 ] ], "normalized": [] }, { "id": "PMC2774163-02-Results-04_T23", "type": "Protein", "text": [ "bfiS" ], "offsets": [ [ 1719, 1723 ] ], "normalized": [] }, { "id": "PMC2774163-02-Results-04_T24", "type": "Protein", "text": [ "BfiS" ], "offsets": [ [ 1845, 1849 ] ], "normalized": [] }, { "id": "PMC2774163-02-Results-04_T25", "type": "Protein", "text": [ "BfmR" ], "offsets": [ [ 1854, 1858 ] ], "normalized": [] }, { "id": "PMC2774163-02-Results-04_T26", "type": "Organism", "text": [ "DeltamifR" ], "offsets": [ [ 1907, 1916 ] ], "normalized": [] }, { "id": "PMC2774163-02-Results-04_T27", "type": "Protein", "text": [ "mifR" ], "offsets": [ [ 1912, 1916 ] ], "normalized": [] }, { "id": "PMC2774163-02-Results-04_T28", "type": "Organism", "text": [ "DeltamifR" ], "offsets": [ [ 2002, 2011 ] ], "normalized": [] }, { "id": "PMC2774163-02-Results-04_T29", "type": "Protein", "text": [ "mifR" ], "offsets": [ [ 2007, 2011 ] ], "normalized": [] }, { "id": "PMC2774163-02-Results-04_T30", "type": "Protein", "text": [ "MifR" ], "offsets": [ [ 2066, 2070 ] ], "normalized": [] }, { "id": "PMC2774163-02-Results-04_T31", "type": "Protein", "text": [ "MifR" ], "offsets": [ [ 2196, 2200 ] ], "normalized": [] }, { "id": "PMC2774163-02-Results-04_T32", "type": "Organism", "text": [ "P. aeruginosa" ], "offsets": [ [ 2237, 2250 ] ], "normalized": [] }, { "id": "PMC2774163-02-Results-04_T33", "type": "Organism", "text": [ "DeltabfiS" ], "offsets": [ [ 2368, 2377 ] ], "normalized": [] }, { "id": "PMC2774163-02-Results-04_T34", "type": "Protein", "text": [ "bfiS" ], "offsets": [ [ 2373, 2377 ] ], "normalized": [] }, { "id": "PMC2774163-02-Results-04_T35", "type": "Organism", "text": [ "DeltabfmR" ], "offsets": [ [ 2379, 2388 ] ], "normalized": [] }, { "id": "PMC2774163-02-Results-04_T36", "type": "Protein", "text": [ "bfmR" ], "offsets": [ [ 2384, 2388 ] ], "normalized": [] }, { "id": "PMC2774163-02-Results-04_T37", "type": "Organism", "text": [ "DeltamifR mutant" ], "offsets": [ [ 2394, 2410 ] ], "normalized": [] }, { "id": "PMC2774163-02-Results-04_T38", "type": "Protein", "text": [ "mifR" ], "offsets": [ [ 2399, 2403 ] ], "normalized": [] }, { "id": "PMC2774163-02-Results-04_T39", "type": "Organism", "text": [ "DeltabfiS" ], "offsets": [ [ 2561, 2570 ] ], "normalized": [] }, { "id": "PMC2774163-02-Results-04_T40", "type": "Protein", "text": [ "bfiS" ], "offsets": [ [ 2566, 2570 ] ], "normalized": [] }, { "id": "PMC2774163-02-Results-04_T41", "type": "Organism", "text": [ "DeltabfmR" ], "offsets": [ [ 2575, 2584 ] ], "normalized": [] }, { "id": "PMC2774163-02-Results-04_T42", "type": "Protein", "text": [ "bfmR" ], "offsets": [ [ 2580, 2584 ] ], "normalized": [] }, { "id": "PMC2774163-02-Results-04_T43", "type": "Organism", "text": [ "DeltabfiS" ], "offsets": [ [ 2898, 2907 ] ], "normalized": [] }, { "id": "PMC2774163-02-Results-04_T44", "type": "Protein", "text": [ "bfiS" ], "offsets": [ [ 2903, 2907 ] ], "normalized": [] }, { "id": "PMC2774163-02-Results-04_T45", "type": "Organism", "text": [ "DeltabfmR" ], "offsets": [ [ 2912, 2921 ] ], "normalized": [] }, { "id": "PMC2774163-02-Results-04_T46", "type": "Protein", "text": [ "bfmR" ], "offsets": [ [ 2917, 2921 ] ], "normalized": [] }, { "id": "PMC2774163-02-Results-04_T47", "type": "Organism", "text": [ "DeltamifR" ], "offsets": [ [ 2970, 2979 ] ], "normalized": [] }, { "id": "PMC2774163-02-Results-04_T48", "type": "Protein", "text": [ "mifR" ], "offsets": [ [ 2975, 2979 ] ], "normalized": [] }, { "id": "PMC2774163-02-Results-04_T49", "type": "Organism", "text": [ "P. aeruginosa" ], "offsets": [ [ 3064, 3077 ] ], "normalized": [] }, { "id": "PMC2774163-02-Results-04_T50", "type": "Organism", "text": [ "DeltamifR" ], "offsets": [ [ 3185, 3194 ] ], "normalized": [] }, { "id": "PMC2774163-02-Results-04_T51", "type": "Protein", "text": [ "mifR" ], "offsets": [ [ 3190, 3194 ] ], "normalized": [] } ]

[ { "id": "PMC2774163-02-Results-04_E1", "type": "Negative_regulation", "trigger": { "text": [ "Inactivation" ], "offsets": [ [ 285, 297 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC2774163-02-Results-04_T2" } ] }, { "id": "PMC2774163-02-Results-04_E2", "type": "Negative_regulation", "trigger": { "text": [ "Inactivation" ], "offsets": [ [ 285, 297 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC2774163-02-Results-04_T3" } ] }, { "id": "PMC2774163-02-Results-04_E3", "type": "Negative_regulation", "trigger": { "text": [ "Inactivation" ], "offsets": [ [ 285, 297 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC2774163-02-Results-04_T4" } ] }, { "id": "PMC2774163-02-Results-04_E4", "type": "Regulation", "trigger": { "text": [ "affect" ], "offsets": [ [ 369, 375 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC2774163-02-Results-04_E7" }, { "role": "Cause", "ref_id": "PMC2774163-02-Results-04_E1" } ] }, { "id": "PMC2774163-02-Results-04_E5", "type": "Regulation", "trigger": { "text": [ "affect" ], "offsets": [ [ 369, 375 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC2774163-02-Results-04_E7" }, { "role": "Cause", "ref_id": "PMC2774163-02-Results-04_E2" } ] }, { "id": "PMC2774163-02-Results-04_E6", "type": "Regulation", "trigger": { "text": [ "affect" ], "offsets": [ [ 369, 375 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC2774163-02-Results-04_E7" }, { "role": "Cause", "ref_id": "PMC2774163-02-Results-04_E3" } ] }, { "id": "PMC2774163-02-Results-04_E7", "type": "Binding", "trigger": { "text": [ "attachment" ], "offsets": [ [ 384, 394 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC2774163-02-Results-04_T8" } ] }, { "id": "PMC2774163-02-Results-04_E8", "type": "Negative_regulation", "trigger": { "text": [ "reduced" ], "offsets": [ [ 989, 996 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC2774163-02-Results-04_E9" } ] }, { "id": "PMC2774163-02-Results-04_E9", "type": "Binding", "trigger": { "text": [ "attachment" ], "offsets": [ [ 1005, 1015 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC2774163-02-Results-04_T13" } ] }, { "id": "PMC2774163-02-Results-04_E10", "type": "Phosphorylation", "trigger": { "text": [ "phosphorylation" ], "offsets": [ [ 1859, 1874 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC2774163-02-Results-04_T24" } ] }, { "id": "PMC2774163-02-Results-04_E11", "type": "Phosphorylation", "trigger": { "text": [ "phosphorylation" ], "offsets": [ [ 1859, 1874 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC2774163-02-Results-04_T25" } ] }, { "id": "PMC2774163-02-Results-04_E12", "type": "Phosphorylation", "trigger": { "text": [ "phosphorylated" ], "offsets": [ [ 2090, 2104 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC2774163-02-Results-04_T30" } ] }, { "id": "PMC2774163-02-Results-04_E13", "type": "Phosphorylation", "trigger": { "text": [ "phosphorylation" ], "offsets": [ [ 2177, 2192 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC2774163-02-Results-04_T31" } ] } ]

[ { "id": "PMC2774163-02-Results-04_1", "entity_ids": [ "PMC2774163-02-Results-04_T2", "PMC2774163-02-Results-04_T5" ] }, { "id": "PMC2774163-02-Results-04_2", "entity_ids": [ "PMC2774163-02-Results-04_T3", "PMC2774163-02-Results-04_T6" ] }, { "id": "PMC2774163-02-Results-04_3", "entity_ids": [ "PMC2774163-02-Results-04_T4", "PMC2774163-02-Results-04_T7" ] } ]

[]

[ { "id": "PMC2829055-02-Results-Discussion-02__text", "type": "abstract", "text": [ "Y. pestis metabolic adaptation to the flea gut environment \nOf the 214 genes upregulated in the flea gut compared to all in vitro conditions, 78 are metabolic genes, 60 of which are involved in uptake and catabolism of amino acids and carbohydrates (Table S1). In particular, genes involved in transport and catabolism of the L-glutamate group of amino acids (Gln, His, Arg, and Pro) were specifically upregulated in the flea (Fig. 2). The degradation of these amino acids gives rise to L-glutamate and the TCA cycle intermediates succinate, formate, and alpha-ketoglutarate. The gabD and gabT genes involved in the production of succinate from gamma-aminobutyrate (GABA), another member of the L-glutamate group, were also highly induced in the flea. The gabD gene functions to produce succinate from both GABA and hydroxyphenylacetate (HPA), an aromatic degradation product of Tyr and Phe; and the HPA transport (hpaX) and catabolism (hpaCBIFHDE) genes of Y. pestis were also highly upregulated in the flea gut (Table S1, Fig. 2). As Y. pestis does not have homologs of genes required to produce GABA or HPA, these metabolites may be taken up from the flea digestive tract. Alternatively, the gabD and gabT gene products might act in the reverse direction to synthesize GABA, which has osmoprotective properties [13]. The central role of the L-glutamate family of amino acids may also confer this advantage in the flea gut, because Glu and Pro are osmoprotectants. Interestingly, both glutamate and GABA are important neurotransmitters at the neuromuscular junction of insects, and the concentration of glutamate is very low in insect hemolymph, suggesting that it is converted to glutamine before it is absorbed [14]. Insect midgut epithelium is typified by multiple amino acid transporters with specific substrates and rapid absorption kinetics, but different amino acids enter the hemocoel at different rates and amounts [14],[15]. Thus, Y. pestis metabolism in the flea may reflect the available pool of amino acids in the midgut. In contrast to the amino acids, hexoses do not appear to be an important energy source during infection of the flea. Only the genes encoding for chitobiose phosphotransferase (PTS) uptake and utilization systems (chbBC; chbF), and for a PTS system of unknown specificity (frwBCD) were significantly upregulated in the flea [16],[17]. Chitobiose could be present in the flea gut due to turnover of the chitin layer on the proventricular spines. Expression of the glucose PTS system was only slightly increased relative to LB cultures, and other PTS systems were downregulated (Table S2). Glycolytic pathways were not upregulated in the flea; instead, available hexoses and the gluconeogenesis pathway may be used to synthesize polysaccharide components required for cell growth. Upregulation of the actP and acs genes in the flea, which direct the uptake of acetate and its conversion to acetyl-CoA, also suggests that insufficient acetyl-CoA is produced by glycolysis to potentiate the TCA cycle. The switch from acetate secretion to acetate uptake is typical of growth in a glucose-limited, amino acid rich environment [18]. In contrast to hexose uptake systems, Y. pestis genes that encode permeases for the pentoses ribose, xylose, and arabinose were induced in the flea gut. Acquisition of pentoses from the environment may be important because Y. pestis does not possess glucose 6-phosphate dehydrogenase activity, the first step of the pentose phosphate pathway [19]. Although the flea gut contains lipid derived from the blood meal, Y. pestis does not appear to use it as a major energy source. None of the fatty acid uptake or catabolism genes were upregulated in the flea compared to growth in LB. However, genes for glycerol and glycerol-3-phosphate uptake and utilization were upregulated, suggesting that flea digestion products derived from blood glycerolipids may be used by Y. pestis. In summary, Y. pestis appears to use amino acids, particularly the L-glutamate family, as primary carbon, nitrogen, and energy sources in the flea. Amino acid carbon is presumably funneled into the TCA cycle, the genes for which are highly expressed in the flea (Table S3).\n" ], "offsets": [ [ 0, 4211 ] ] } ]

[ { "id": "PMC2829055-02-Results-Discussion-02_T1", "type": "Organism", "text": [ "Y. pestis" ], "offsets": [ [ 0, 9 ] ], "normalized": [] }, { "id": "PMC2829055-02-Results-Discussion-02_T2", "type": "Organism", "text": [ "flea" ], "offsets": [ [ 38, 42 ] ], "normalized": [] }, { "id": "PMC2829055-02-Results-Discussion-02_T3", "type": "Organism", "text": [ "flea" ], "offsets": [ [ 96, 100 ] ], "normalized": [] }, { "id": "PMC2829055-02-Results-Discussion-02_T4", "type": "Organism", "text": [ "flea" ], "offsets": [ [ 421, 425 ] ], "normalized": [] }, { "id": "PMC2829055-02-Results-Discussion-02_T5", "type": "Chemical", "text": [ "TCA" ], "offsets": [ [ 507, 510 ] ], "normalized": [] }, { "id": "PMC2829055-02-Results-Discussion-02_T6", "type": "Chemical", "text": [ "succinate" ], "offsets": [ [ 531, 540 ] ], "normalized": [] }, { "id": "PMC2829055-02-Results-Discussion-02_T7", "type": "Chemical", "text": [ "formate" ], "offsets": [ [ 542, 549 ] ], "normalized": [] }, { "id": "PMC2829055-02-Results-Discussion-02_T8", "type": "Chemical", "text": [ "alpha-ketoglutarate" ], "offsets": [ [ 555, 574 ] ], "normalized": [] }, { "id": "PMC2829055-02-Results-Discussion-02_T9", "type": "Protein", "text": [ "gabD" ], "offsets": [ [ 580, 584 ] ], "normalized": [] }, { "id": "PMC2829055-02-Results-Discussion-02_T10", "type": "Protein", "text": [ "gabT" ], "offsets": [ [ 589, 593 ] ], "normalized": [] }, { "id": "PMC2829055-02-Results-Discussion-02_T11", "type": "Chemical", "text": [ "succinate" ], "offsets": [ [ 630, 639 ] ], "normalized": [] }, { "id": "PMC2829055-02-Results-Discussion-02_T12", "type": "Chemical", "text": [ "gamma-aminobutyrate" ], "offsets": [ [ 645, 664 ] ], "normalized": [] }, { "id": "PMC2829055-02-Results-Discussion-02_T13", "type": "Chemical", "text": [ "GABA" ], "offsets": [ [ 666, 670 ] ], "normalized": [] }, { "id": "PMC2829055-02-Results-Discussion-02_T14", "type": "Organism", "text": [ "flea" ], "offsets": [ [ 746, 750 ] ], "normalized": [] }, { "id": "PMC2829055-02-Results-Discussion-02_T15", "type": "Protein", "text": [ "gabD" ], "offsets": [ [ 756, 760 ] ], "normalized": [] }, { "id": "PMC2829055-02-Results-Discussion-02_T16", "type": "Chemical", "text": [ "succinate" ], "offsets": [ [ 787, 796 ] ], "normalized": [] }, { "id": "PMC2829055-02-Results-Discussion-02_T17", "type": "Chemical", "text": [ "GABA" ], "offsets": [ [ 807, 811 ] ], "normalized": [] }, { "id": "PMC2829055-02-Results-Discussion-02_T18", "type": "Chemical", "text": [ "hydroxyphenylacetate" ], "offsets": [ [ 816, 836 ] ], "normalized": [] }, { "id": "PMC2829055-02-Results-Discussion-02_T19", "type": "Chemical", "text": [ "HPA" ], "offsets": [ [ 838, 841 ] ], "normalized": [] }, { "id": "PMC2829055-02-Results-Discussion-02_T20", "type": "Protein", "text": [ "HPA transport" ], "offsets": [ [ 900, 913 ] ], "normalized": [] }, { "id": "PMC2829055-02-Results-Discussion-02_T21", "type": "Protein", "text": [ "hpaX" ], "offsets": [ [ 915, 919 ] ], "normalized": [] }, { "id": "PMC2829055-02-Results-Discussion-02_T22", "type": "Protein", "text": [ "hpaC" ], "offsets": [ [ 937, 941 ] ], "normalized": [] }, { "id": "PMC2829055-02-Results-Discussion-02_T23", "type": "Protein", "text": [ "B" ], "offsets": [ [ 941, 942 ] ], "normalized": [] }, { "id": "PMC2829055-02-Results-Discussion-02_T24", "type": "Protein", "text": [ "I" ], "offsets": [ [ 942, 943 ] ], "normalized": [] }, { "id": "PMC2829055-02-Results-Discussion-02_T25", "type": "Protein", "text": [ "F" ], "offsets": [ [ 943, 944 ] ], "normalized": [] }, { "id": "PMC2829055-02-Results-Discussion-02_T26", "type": "Protein", "text": [ "H" ], "offsets": [ [ 944, 945 ] ], "normalized": [] }, { "id": "PMC2829055-02-Results-Discussion-02_T27", "type": "Protein", "text": [ "D" ], "offsets": [ [ 945, 946 ] ], "normalized": [] }, { "id": "PMC2829055-02-Results-Discussion-02_T28", "type": "Protein", "text": [ "E" ], "offsets": [ [ 946, 947 ] ], "normalized": [] }, { "id": "PMC2829055-02-Results-Discussion-02_T29", "type": "Organism", "text": [ "Y. pestis" ], "offsets": [ [ 958, 967 ] ], "normalized": [] }, { "id": "PMC2829055-02-Results-Discussion-02_T30", "type": "Organism", "text": [ "flea" ], "offsets": [ [ 1004, 1008 ] ], "normalized": [] }, { "id": "PMC2829055-02-Results-Discussion-02_T31", "type": "Organism", "text": [ "Y. pestis" ], "offsets": [ [ 1036, 1045 ] ], "normalized": [] }, { "id": "PMC2829055-02-Results-Discussion-02_T32", "type": "Chemical", "text": [ "GABA" ], "offsets": [ [ 1098, 1102 ] ], "normalized": [] }, { "id": "PMC2829055-02-Results-Discussion-02_T33", "type": "Chemical", "text": [ "HPA" ], "offsets": [ [ 1106, 1109 ] ], "normalized": [] }, { "id": "PMC2829055-02-Results-Discussion-02_T34", "type": "Organism", "text": [ "flea" ], "offsets": [ [ 1154, 1158 ] ], "normalized": [] }, { "id": "PMC2829055-02-Results-Discussion-02_T35", "type": "Protein", "text": [ "gabD" ], "offsets": [ [ 1195, 1199 ] ], "normalized": [] }, { "id": "PMC2829055-02-Results-Discussion-02_T36", "type": "Protein", "text": [ "gabT" ], "offsets": [ [ 1204, 1208 ] ], "normalized": [] }, { "id": "PMC2829055-02-Results-Discussion-02_T37", "type": "Chemical", "text": [ "GABA" ], "offsets": [ [ 1272, 1276 ] ], "normalized": [] }, { "id": "PMC2829055-02-Results-Discussion-02_T38", "type": "Organism", "text": [ "flea" ], "offsets": [ [ 1416, 1420 ] ], "normalized": [] }, { "id": "PMC2829055-02-Results-Discussion-02_T39", "type": "Chemical", "text": [ "glutamate" ], "offsets": [ [ 1487, 1496 ] ], "normalized": [] }, { "id": "PMC2829055-02-Results-Discussion-02_T40", "type": "Chemical", "text": [ "GABA" ], "offsets": [ [ 1501, 1505 ] ], "normalized": [] }, { "id": "PMC2829055-02-Results-Discussion-02_T41", "type": "Organism", "text": [ "Y. pestis" ], "offsets": [ [ 1943, 1952 ] ], "normalized": [] }, { "id": "PMC2829055-02-Results-Discussion-02_T42", "type": "Organism", "text": [ "flea" ], "offsets": [ [ 1971, 1975 ] ], "normalized": [] }, { "id": "PMC2829055-02-Results-Discussion-02_T43", "type": "Chemical", "text": [ "hexoses" ], "offsets": [ [ 2069, 2076 ] ], "normalized": [] }, { "id": "PMC2829055-02-Results-Discussion-02_T44", "type": "Organism", "text": [ "flea" ], "offsets": [ [ 2148, 2152 ] ], "normalized": [] }, { "id": "PMC2829055-02-Results-Discussion-02_T45", "type": "Protein", "text": [ "chitobiose phosphotransferase" ], "offsets": [ [ 2182, 2211 ] ], "normalized": [] }, { "id": "PMC2829055-02-Results-Discussion-02_T46", "type": "Protein", "text": [ "PTS" ], "offsets": [ [ 2213, 2216 ] ], "normalized": [] }, { "id": "PMC2829055-02-Results-Discussion-02_T47", "type": "Two-component-system", "text": [ "chbBC" ], "offsets": [ [ 2250, 2255 ] ], "normalized": [] }, { "id": "PMC2829055-02-Results-Discussion-02_T48", "type": "Protein", "text": [ "chbB" ], "offsets": [ [ 2250, 2254 ] ], "normalized": [] }, { "id": "PMC2829055-02-Results-Discussion-02_T49", "type": "Protein", "text": [ "C" ], "offsets": [ [ 2254, 2255 ] ], "normalized": [] }, { "id": "PMC2829055-02-Results-Discussion-02_T50", "type": "Protein", "text": [ "chbF" ], "offsets": [ [ 2257, 2261 ] ], "normalized": [] }, { "id": "PMC2829055-02-Results-Discussion-02_T51", "type": "Protein", "text": [ "frwB" ], "offsets": [ [ 2309, 2313 ] ], "normalized": [] }, { "id": "PMC2829055-02-Results-Discussion-02_T52", "type": "Protein", "text": [ "C" ], "offsets": [ [ 2313, 2314 ] ], "normalized": [] }, { "id": "PMC2829055-02-Results-Discussion-02_T53", "type": "Protein", "text": [ "D" ], "offsets": [ [ 2314, 2315 ] ], "normalized": [] }, { "id": "PMC2829055-02-Results-Discussion-02_T54", "type": "Organism", "text": [ "flea" ], "offsets": [ [ 2355, 2359 ] ], "normalized": [] }, { "id": "PMC2829055-02-Results-Discussion-02_T55", "type": "Protein", "text": [ "Chitobiose" ], "offsets": [ [ 2371, 2381 ] ], "normalized": [] }, { "id": "PMC2829055-02-Results-Discussion-02_T56", "type": "Organism", "text": [ "flea" ], "offsets": [ [ 2406, 2410 ] ], "normalized": [] }, { "id": "PMC2829055-02-Results-Discussion-02_T57", "type": "Chemical", "text": [ "glucose" ], "offsets": [ [ 2499, 2506 ] ], "normalized": [] }, { "id": "PMC2829055-02-Results-Discussion-02_T58", "type": "Organism", "text": [ "flea" ], "offsets": [ [ 2672, 2676 ] ], "normalized": [] }, { "id": "PMC2829055-02-Results-Discussion-02_T59", "type": "Chemical", "text": [ "hexoses" ], "offsets": [ [ 2697, 2704 ] ], "normalized": [] }, { "id": "PMC2829055-02-Results-Discussion-02_T60", "type": "Protein", "text": [ "actP" ], "offsets": [ [ 2835, 2839 ] ], "normalized": [] }, { "id": "PMC2829055-02-Results-Discussion-02_T61", "type": "Protein", "text": [ "acs" ], "offsets": [ [ 2844, 2847 ] ], "normalized": [] }, { "id": "PMC2829055-02-Results-Discussion-02_T62", "type": "Organism", "text": [ "flea" ], "offsets": [ [ 2861, 2865 ] ], "normalized": [] }, { "id": "PMC2829055-02-Results-Discussion-02_T63", "type": "Chemical", "text": [ "acetate" ], "offsets": [ [ 2894, 2901 ] ], "normalized": [] }, { "id": "PMC2829055-02-Results-Discussion-02_T64", "type": "Chemical", "text": [ "acetyl-CoA" ], "offsets": [ [ 2924, 2934 ] ], "normalized": [] }, { "id": "PMC2829055-02-Results-Discussion-02_T65", "type": "Chemical", "text": [ "acetyl-CoA" ], "offsets": [ [ 2968, 2978 ] ], "normalized": [] }, { "id": "PMC2829055-02-Results-Discussion-02_T66", "type": "Chemical", "text": [ "TCA" ], "offsets": [ [ 3023, 3026 ] ], "normalized": [] }, { "id": "PMC2829055-02-Results-Discussion-02_T67", "type": "Chemical", "text": [ "acetate" ], "offsets": [ [ 3050, 3057 ] ], "normalized": [] }, { "id": "PMC2829055-02-Results-Discussion-02_T68", "type": "Chemical", "text": [ "acetate" ], "offsets": [ [ 3071, 3078 ] ], "normalized": [] }, { "id": "PMC2829055-02-Results-Discussion-02_T69", "type": "Chemical", "text": [ "hexose" ], "offsets": [ [ 3178, 3184 ] ], "normalized": [] }, { "id": "PMC2829055-02-Results-Discussion-02_T70", "type": "Organism", "text": [ "Y. pestis" ], "offsets": [ [ 3201, 3210 ] ], "normalized": [] }, { "id": "PMC2829055-02-Results-Discussion-02_T71", "type": "Protein", "text": [ "permeases" ], "offsets": [ [ 3229, 3238 ] ], "normalized": [] }, { "id": "PMC2829055-02-Results-Discussion-02_T72", "type": "Chemical", "text": [ "pentoses ribose" ], "offsets": [ [ 3247, 3262 ] ], "normalized": [] }, { "id": "PMC2829055-02-Results-Discussion-02_T73", "type": "Chemical", "text": [ "xylose" ], "offsets": [ [ 3264, 3270 ] ], "normalized": [] }, { "id": "PMC2829055-02-Results-Discussion-02_T74", "type": "Chemical", "text": [ "arabinose" ], "offsets": [ [ 3276, 3285 ] ], "normalized": [] }, { "id": "PMC2829055-02-Results-Discussion-02_T75", "type": "Organism", "text": [ "flea" ], "offsets": [ [ 3306, 3310 ] ], "normalized": [] }, { "id": "PMC2829055-02-Results-Discussion-02_T76", "type": "Chemical", "text": [ "pentoses" ], "offsets": [ [ 3331, 3339 ] ], "normalized": [] }, { "id": "PMC2829055-02-Results-Discussion-02_T77", "type": "Organism", "text": [ "Y. pestis" ], "offsets": [ [ 3386, 3395 ] ], "normalized": [] }, { "id": "PMC2829055-02-Results-Discussion-02_T78", "type": "Protein", "text": [ "glucose 6-phosphate dehydrogenase" ], "offsets": [ [ 3413, 3446 ] ], "normalized": [] }, { "id": "PMC2829055-02-Results-Discussion-02_T79", "type": "Chemical", "text": [ "pentose phosphate" ], "offsets": [ [ 3479, 3496 ] ], "normalized": [] }, { "id": "PMC2829055-02-Results-Discussion-02_T80", "type": "Organism", "text": [ "flea" ], "offsets": [ [ 3524, 3528 ] ], "normalized": [] }, { "id": "PMC2829055-02-Results-Discussion-02_T81", "type": "Organism", "text": [ "Y. pestis" ], "offsets": [ [ 3577, 3586 ] ], "normalized": [] }, { "id": "PMC2829055-02-Results-Discussion-02_T82", "type": "Organism", "text": [ "flea" ], "offsets": [ [ 3713, 3717 ] ], "normalized": [] }, { "id": "PMC2829055-02-Results-Discussion-02_T83", "type": "Chemical", "text": [ "glycerol" ], "offsets": [ [ 3763, 3771 ] ], "normalized": [] }, { "id": "PMC2829055-02-Results-Discussion-02_T84", "type": "Chemical", "text": [ "glycerol-3-phosphate" ], "offsets": [ [ 3776, 3796 ] ], "normalized": [] }, { "id": "PMC2829055-02-Results-Discussion-02_T85", "type": "Organism", "text": [ "flea" ], "offsets": [ [ 3854, 3858 ] ], "normalized": [] }, { "id": "PMC2829055-02-Results-Discussion-02_T86", "type": "Chemical", "text": [ "glycerolipids" ], "offsets": [ [ 3897, 3910 ] ], "normalized": [] }, { "id": "PMC2829055-02-Results-Discussion-02_T87", "type": "Organism", "text": [ "Y. pestis" ], "offsets": [ [ 3926, 3935 ] ], "normalized": [] }, { "id": "PMC2829055-02-Results-Discussion-02_T88", "type": "Organism", "text": [ "Y. pestis" ], "offsets": [ [ 3949, 3958 ] ], "normalized": [] }, { "id": "PMC2829055-02-Results-Discussion-02_T89", "type": "Chemical", "text": [ "carbon" ], "offsets": [ [ 4035, 4041 ] ], "normalized": [] }, { "id": "PMC2829055-02-Results-Discussion-02_T90", "type": "Chemical", "text": [ "nitrogen" ], "offsets": [ [ 4043, 4051 ] ], "normalized": [] }, { "id": "PMC2829055-02-Results-Discussion-02_T91", "type": "Organism", "text": [ "flea" ], "offsets": [ [ 4079, 4083 ] ], "normalized": [] }, { "id": "PMC2829055-02-Results-Discussion-02_T92", "type": "Chemical", "text": [ "carbon" ], "offsets": [ [ 4096, 4102 ] ], "normalized": [] }, { "id": "PMC2829055-02-Results-Discussion-02_T93", "type": "Chemical", "text": [ "TCA" ], "offsets": [ [ 4135, 4138 ] ], "normalized": [] }, { "id": "PMC2829055-02-Results-Discussion-02_T94", "type": "Organism", "text": [ "flea" ], "offsets": [ [ 4194, 4198 ] ], "normalized": [] } ]

[ { "id": "PMC2829055-02-Results-Discussion-02_E1", "type": "Positive_regulation", "trigger": { "text": [ "induced" ], "offsets": [ [ 731, 738 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC2829055-02-Results-Discussion-02_T9" } ] }, { "id": "PMC2829055-02-Results-Discussion-02_E2", "type": "Positive_regulation", "trigger": { "text": [ "induced" ], "offsets": [ [ 731, 738 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC2829055-02-Results-Discussion-02_T10" } ] }, { "id": "PMC2829055-02-Results-Discussion-02_E3", "type": "Positive_regulation", "trigger": { "text": [ "upregulated" ], "offsets": [ [ 985, 996 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC2829055-02-Results-Discussion-02_T20" } ] }, { "id": "PMC2829055-02-Results-Discussion-02_E4", "type": "Positive_regulation", "trigger": { "text": [ "upregulated" ], "offsets": [ [ 985, 996 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC2829055-02-Results-Discussion-02_T22" } ] }, { "id": "PMC2829055-02-Results-Discussion-02_E5", "type": "Positive_regulation", "trigger": { "text": [ "upregulated" ], "offsets": [ [ 985, 996 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC2829055-02-Results-Discussion-02_T23" } ] }, { "id": "PMC2829055-02-Results-Discussion-02_E6", "type": "Positive_regulation", "trigger": { "text": [ "upregulated" ], "offsets": [ [ 985, 996 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC2829055-02-Results-Discussion-02_T24" } ] }, { "id": "PMC2829055-02-Results-Discussion-02_E7", "type": "Positive_regulation", "trigger": { "text": [ "upregulated" ], "offsets": [ [ 985, 996 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC2829055-02-Results-Discussion-02_T25" } ] }, { "id": "PMC2829055-02-Results-Discussion-02_E8", "type": "Positive_regulation", "trigger": { "text": [ "upregulated" ], "offsets": [ [ 985, 996 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC2829055-02-Results-Discussion-02_T26" } ] }, { "id": "PMC2829055-02-Results-Discussion-02_E9", "type": "Positive_regulation", "trigger": { "text": [ "upregulated" ], "offsets": [ [ 985, 996 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC2829055-02-Results-Discussion-02_T27" } ] }, { "id": "PMC2829055-02-Results-Discussion-02_E10", "type": "Positive_regulation", "trigger": { "text": [ "upregulated" ], "offsets": [ [ 985, 996 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC2829055-02-Results-Discussion-02_T28" } ] }, { "id": "PMC2829055-02-Results-Discussion-02_E11", "type": "Process", "trigger": { "text": [ "infection" ], "offsets": [ [ 2131, 2140 ] ] }, "arguments": [] }, { "id": "PMC2829055-02-Results-Discussion-02_E12", "type": "Positive_regulation", "trigger": { "text": [ "Upregulation" ], "offsets": [ [ 2815, 2827 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC2829055-02-Results-Discussion-02_T60" } ] }, { "id": "PMC2829055-02-Results-Discussion-02_E13", "type": "Localization", "trigger": { "text": [ "uptake" ], "offsets": [ [ 2884, 2890 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC2829055-02-Results-Discussion-02_T63" } ] }, { "id": "PMC2829055-02-Results-Discussion-02_E14", "type": "Localization", "trigger": { "text": [ "secretion" ], "offsets": [ [ 3058, 3067 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC2829055-02-Results-Discussion-02_T67" } ] }, { "id": "PMC2829055-02-Results-Discussion-02_E15", "type": "Localization", "trigger": { "text": [ "uptake" ], "offsets": [ [ 3079, 3085 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC2829055-02-Results-Discussion-02_T68" } ] }, { "id": "PMC2829055-02-Results-Discussion-02_E16", "type": "Localization", "trigger": { "text": [ "uptake" ], "offsets": [ [ 3185, 3191 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC2829055-02-Results-Discussion-02_T69" } ] }, { "id": "PMC2829055-02-Results-Discussion-02_E17", "type": "Localization", "trigger": { "text": [ "Acquisition" ], "offsets": [ [ 3316, 3327 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC2829055-02-Results-Discussion-02_T76" } ] }, { "id": "PMC2829055-02-Results-Discussion-02_E18", "type": "Localization", "trigger": { "text": [ "uptake" ], "offsets": [ [ 3797, 3803 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC2829055-02-Results-Discussion-02_T83" } ] }, { "id": "PMC2829055-02-Results-Discussion-02_E19", "type": "Localization", "trigger": { "text": [ "uptake" ], "offsets": [ [ 3797, 3803 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC2829055-02-Results-Discussion-02_T84" } ] } ]

[ { "id": "PMC2829055-02-Results-Discussion-02_1", "entity_ids": [ "PMC2829055-02-Results-Discussion-02_T13", "PMC2829055-02-Results-Discussion-02_T12" ] }, { "id": "PMC2829055-02-Results-Discussion-02_2", "entity_ids": [ "PMC2829055-02-Results-Discussion-02_T19", "PMC2829055-02-Results-Discussion-02_T18" ] }, { "id": "PMC2829055-02-Results-Discussion-02_3", "entity_ids": [ "PMC2829055-02-Results-Discussion-02_T21", "PMC2829055-02-Results-Discussion-02_T20" ] }, { "id": "PMC2829055-02-Results-Discussion-02_4", "entity_ids": [ "PMC2829055-02-Results-Discussion-02_T46", "PMC2829055-02-Results-Discussion-02_T45" ] } ]

[]

[ { "id": "PMC2430206-02-Results-01__text", "type": "abstract", "text": [ "Results \nThe graRS mutant shows altered cell surface charge but unaltered lysyl-phosphatidylglycerol (LPG) content In order to study if reduced expression of the dlt operon upon graRS disruption results in altered cell surface charge, we compared binding of the red-coloured, cationic protein cytochrome c to wild type S. aureus SA113 (WT), the isogenic graRS mutant, and the plasmid-complemented mutant. The graRS mutant bound significantly more cytochrome c than the WT or the complemented mutant (Fig. 1A), which is in accordance with the recently described reduced content of D-alanine residues in the teichoic acids of the mutant [10]. To analyse whether increased binding of cytochrome c by the graRS mutant is in fact due to altered cell surface charge by decreased teichoic acid alanylation or the altered expression of other surface-exposed molecules, we also examined binding of cytochrome c to a dltA deletion mutant, which completely lacks D-alanine substitution of teichoic acids [7], and a dltA/graRS double deletion mutant, which was generated by transducing the graRS mutation into the dltA mutant. Due to the high binding capacities of the dltA and the dltA/graRS mutant we modified the conditions in order to prevent limitation of applied cytochrome c. Deletion of the graRS genes in the dlt mutant background did not lead to further increased binding of cytochrome c compared to the dltA mutant (Fig. 1B). This finding indicates that the increased binding of cytochrome c by the graRS mutant is due to decreased alanylation of teichoic acids and that the resulting surface charge alteration does not result from other regulatory effects mediated by GraRS. Increased binding of cationic proteins may also result from reduced mprF expression and, accordingly, reduced lysylphosphatidylglycerol (LPG) content. To control for this possibility, we compared patterns of membrane lipids from log-phase bacteria by thin-layer chromatography. The amounts of LPG from WT and graRS mutant were indistinguishable (data not shown), which corroborates recent findings that mprF is not among the graRS-regulated genes in S. aureus SA113 [10]. The graRS mutant is more susceptible to killing by LL-37 and human neutrophil granulocytes in vitro In an attempt to test whether the increased affinity of the graRS mutant to cationic molecules leads to higher susceptibility to human host defense peptides, we compared inactivation of WT and graRS mutant by the human cathelicidin LL-37. This antimicrobial peptide is active against S. aureus at high concentrations or long exposure [15] but in this experiment we chose conditions under which the LL-37 did not affect viability of the S. aureus WT. Accordingly, the WT and complemented mutant strains showed no significant decrease in CFU following LL-37 exposure, whereas the number of graRS mutant bacteria recovered was only 25% of the original inoculum (Fig. 2A). Next we investigated whether the graRS mutant is killed faster than the parental strain by human neutrophils, which produce high amounts of LL-37 and other CAMPs as components of their antibacterial killing arsenal. The graRS mutant was killed by neutrophils considerably faster than the WT strain. After 15 and 30 min, the recovered CFU of the graRS mutant were significantly lower than those of the WT (Fig 2B). Of note, our previous studies had shown that altered alanylation of teichoic acids does not affect the rate of PMN phagocytosis [9]. Taken together, these data indicate that graRS-mediated control of CAMP resistance mechanisms is of importance for S. aureus evasion from neutrophil killing.\n" ], "offsets": [ [ 0, 3621 ] ] } ]

[ { "id": "PMC2430206-02-Results-01_T1", "type": "Organism", "text": [ "graRS mutant" ], "offsets": [ [ 13, 25 ] ], "normalized": [] }, { "id": "PMC2430206-02-Results-01_T2", "type": "Two-component-system", "text": [ "graRS" ], "offsets": [ [ 13, 18 ] ], "normalized": [] }, { "id": "PMC2430206-02-Results-01_T3", "type": "Protein", "text": [ "graR" ], "offsets": [ [ 13, 17 ] ], "normalized": [] }, { "id": "PMC2430206-02-Results-01_T4", "type": "Protein", "text": [ "S" ], "offsets": [ [ 17, 18 ] ], "normalized": [] }, { "id": "PMC2430206-02-Results-01_T5", "type": "Chemical", "text": [ "lysyl-phosphatidylglycerol" ], "offsets": [ [ 74, 100 ] ], "normalized": [] }, { "id": "PMC2430206-02-Results-01_T6", "type": "Chemical", "text": [ "LPG" ], "offsets": [ [ 102, 105 ] ], "normalized": [] }, { "id": "PMC2430206-02-Results-01_T7", "type": "Two-component-system", "text": [ "graRS" ], "offsets": [ [ 178, 183 ] ], "normalized": [] }, { "id": "PMC2430206-02-Results-01_T8", "type": "Protein", "text": [ "graR" ], "offsets": [ [ 178, 182 ] ], "normalized": [] }, { "id": "PMC2430206-02-Results-01_T9", "type": "Protein", "text": [ "S" ], "offsets": [ [ 182, 183 ] ], "normalized": [] }, { "id": "PMC2430206-02-Results-01_T10", "type": "Protein", "text": [ "cytochrome c" ], "offsets": [ [ 293, 305 ] ], "normalized": [] }, { "id": "PMC2430206-02-Results-01_T11", "type": "Organism", "text": [ "S. aureus SA113" ], "offsets": [ [ 319, 334 ] ], "normalized": [] }, { "id": "PMC2430206-02-Results-01_T12", "type": "Organism", "text": [ "graRS mutant" ], "offsets": [ [ 354, 366 ] ], "normalized": [] }, { "id": "PMC2430206-02-Results-01_T13", "type": "Two-component-system", "text": [ "graRS" ], "offsets": [ [ 354, 359 ] ], "normalized": [] }, { "id": "PMC2430206-02-Results-01_T14", "type": "Protein", "text": [ "graR" ], "offsets": [ [ 354, 358 ] ], "normalized": [] }, { "id": "PMC2430206-02-Results-01_T15", "type": "Protein", "text": [ "S" ], "offsets": [ [ 358, 359 ] ], "normalized": [] }, { "id": "PMC2430206-02-Results-01_T16", "type": "Organism", "text": [ "plasmid-complemented mutant" ], "offsets": [ [ 376, 403 ] ], "normalized": [] }, { "id": "PMC2430206-02-Results-01_T17", "type": "Organism", "text": [ "graRS mutant" ], "offsets": [ [ 409, 421 ] ], "normalized": [] }, { "id": "PMC2430206-02-Results-01_T18", "type": "Two-component-system", "text": [ "graRS" ], "offsets": [ [ 409, 414 ] ], "normalized": [] }, { "id": "PMC2430206-02-Results-01_T19", "type": "Protein", "text": [ "graR" ], "offsets": [ [ 409, 413 ] ], "normalized": [] }, { "id": "PMC2430206-02-Results-01_T20", "type": "Protein", "text": [ "S" ], "offsets": [ [ 413, 414 ] ], "normalized": [] }, { "id": "PMC2430206-02-Results-01_T21", "type": "Protein", "text": [ "cytochrome c" ], "offsets": [ [ 447, 459 ] ], "normalized": [] }, { "id": "PMC2430206-02-Results-01_T22", "type": "Chemical", "text": [ "teichoic acids" ], "offsets": [ [ 606, 620 ] ], "normalized": [] }, { "id": "PMC2430206-02-Results-01_T23", "type": "Protein", "text": [ "cytochrome c" ], "offsets": [ [ 681, 693 ] ], "normalized": [] }, { "id": "PMC2430206-02-Results-01_T24", "type": "Organism", "text": [ "graRS mutant" ], "offsets": [ [ 701, 713 ] ], "normalized": [] }, { "id": "PMC2430206-02-Results-01_T25", "type": "Two-component-system", "text": [ "graRS" ], "offsets": [ [ 701, 706 ] ], "normalized": [] }, { "id": "PMC2430206-02-Results-01_T26", "type": "Protein", "text": [ "graR" ], "offsets": [ [ 701, 705 ] ], "normalized": [] }, { "id": "PMC2430206-02-Results-01_T27", "type": "Protein", "text": [ "S" ], "offsets": [ [ 705, 706 ] ], "normalized": [] }, { "id": "PMC2430206-02-Results-01_T28", "type": "Chemical", "text": [ "teichoic acid" ], "offsets": [ [ 773, 786 ] ], "normalized": [] }, { "id": "PMC2430206-02-Results-01_T29", "type": "Protein", "text": [ "cytochrome c" ], "offsets": [ [ 889, 901 ] ], "normalized": [] }, { "id": "PMC2430206-02-Results-01_T30", "type": "Organism", "text": [ "dltA deletion mutant" ], "offsets": [ [ 907, 927 ] ], "normalized": [] }, { "id": "PMC2430206-02-Results-01_T31", "type": "Protein", "text": [ "dltA" ], "offsets": [ [ 907, 911 ] ], "normalized": [] }, { "id": "PMC2430206-02-Results-01_T32", "type": "Chemical", "text": [ "teichoic acids" ], "offsets": [ [ 978, 992 ] ], "normalized": [] }, { "id": "PMC2430206-02-Results-01_T33", "type": "Organism", "text": [ "dltA/graRS double deletion mutant" ], "offsets": [ [ 1004, 1037 ] ], "normalized": [] }, { "id": "PMC2430206-02-Results-01_T34", "type": "Protein", "text": [ "dltA" ], "offsets": [ [ 1004, 1008 ] ], "normalized": [] }, { "id": "PMC2430206-02-Results-01_T35", "type": "Two-component-system", "text": [ "graRS" ], "offsets": [ [ 1009, 1014 ] ], "normalized": [] }, { "id": "PMC2430206-02-Results-01_T36", "type": "Protein", "text": [ "graR" ], "offsets": [ [ 1009, 1013 ] ], "normalized": [] }, { "id": "PMC2430206-02-Results-01_T37", "type": "Protein", "text": [ "S" ], "offsets": [ [ 1013, 1014 ] ], "normalized": [] }, { "id": "PMC2430206-02-Results-01_T38", "type": "Two-component-system", "text": [ "graRS" ], "offsets": [ [ 1078, 1083 ] ], "normalized": [] }, { "id": "PMC2430206-02-Results-01_T39", "type": "Protein", "text": [ "graR" ], "offsets": [ [ 1078, 1082 ] ], "normalized": [] }, { "id": "PMC2430206-02-Results-01_T40", "type": "Protein", "text": [ "S" ], "offsets": [ [ 1082, 1083 ] ], "normalized": [] }, { "id": "PMC2430206-02-Results-01_T41", "type": "Organism", "text": [ "dltA mutant" ], "offsets": [ [ 1102, 1113 ] ], "normalized": [] }, { "id": "PMC2430206-02-Results-01_T42", "type": "Protein", "text": [ "dltA" ], "offsets": [ [ 1102, 1106 ] ], "normalized": [] }, { "id": "PMC2430206-02-Results-01_T43", "type": "Protein", "text": [ "dltA" ], "offsets": [ [ 1157, 1161 ] ], "normalized": [] }, { "id": "PMC2430206-02-Results-01_T44", "type": "Organism", "text": [ "dltA" ], "offsets": [ [ 1157, 1161 ] ], "normalized": [] }, { "id": "PMC2430206-02-Results-01_T45", "type": "Organism", "text": [ "dltA/graRS mutant" ], "offsets": [ [ 1170, 1187 ] ], "normalized": [] }, { "id": "PMC2430206-02-Results-01_T46", "type": "Protein", "text": [ "dltA" ], "offsets": [ [ 1170, 1174 ] ], "normalized": [] }, { "id": "PMC2430206-02-Results-01_T47", "type": "Two-component-system", "text": [ "graRS" ], "offsets": [ [ 1175, 1180 ] ], "normalized": [] }, { "id": "PMC2430206-02-Results-01_T48", "type": "Protein", "text": [ "graR" ], "offsets": [ [ 1175, 1179 ] ], "normalized": [] }, { "id": "PMC2430206-02-Results-01_T49", "type": "Protein", "text": [ "S" ], "offsets": [ [ 1179, 1180 ] ], "normalized": [] }, { "id": "PMC2430206-02-Results-01_T50", "type": "Protein", "text": [ "cytochrome c" ], "offsets": [ [ 1257, 1269 ] ], "normalized": [] }, { "id": "PMC2430206-02-Results-01_T51", "type": "Two-component-system", "text": [ "graRS" ], "offsets": [ [ 1287, 1292 ] ], "normalized": [] }, { "id": "PMC2430206-02-Results-01_T52", "type": "Protein", "text": [ "graR" ], "offsets": [ [ 1287, 1291 ] ], "normalized": [] }, { "id": "PMC2430206-02-Results-01_T53", "type": "Protein", "text": [ "S" ], "offsets": [ [ 1291, 1292 ] ], "normalized": [] }, { "id": "PMC2430206-02-Results-01_T54", "type": "Organism", "text": [ "dlt mutant" ], "offsets": [ [ 1306, 1316 ] ], "normalized": [] }, { "id": "PMC2430206-02-Results-01_T55", "type": "Protein", "text": [ "cytochrome c" ], "offsets": [ [ 1373, 1385 ] ], "normalized": [] }, { "id": "PMC2430206-02-Results-01_T56", "type": "Organism", "text": [ "dltA mutant" ], "offsets": [ [ 1402, 1413 ] ], "normalized": [] }, { "id": "PMC2430206-02-Results-01_T57", "type": "Protein", "text": [ "dltA" ], "offsets": [ [ 1402, 1406 ] ], "normalized": [] }, { "id": "PMC2430206-02-Results-01_T58", "type": "Protein", "text": [ "cytochrome c" ], "offsets": [ [ 1478, 1490 ] ], "normalized": [] }, { "id": "PMC2430206-02-Results-01_T59", "type": "Organism", "text": [ "graRS mutant" ], "offsets": [ [ 1498, 1510 ] ], "normalized": [] }, { "id": "PMC2430206-02-Results-01_T60", "type": "Two-component-system", "text": [ "graRS" ], "offsets": [ [ 1498, 1503 ] ], "normalized": [] }, { "id": "PMC2430206-02-Results-01_T61", "type": "Protein", "text": [ "graR" ], "offsets": [ [ 1498, 1502 ] ], "normalized": [] }, { "id": "PMC2430206-02-Results-01_T62", "type": "Protein", "text": [ "S" ], "offsets": [ [ 1502, 1503 ] ], "normalized": [] }, { "id": "PMC2430206-02-Results-01_T63", "type": "Chemical", "text": [ "teichoic acids" ], "offsets": [ [ 1546, 1560 ] ], "normalized": [] }, { "id": "PMC2430206-02-Results-01_T64", "type": "Two-component-system", "text": [ "GraRS" ], "offsets": [ [ 1668, 1673 ] ], "normalized": [] }, { "id": "PMC2430206-02-Results-01_T65", "type": "Protein", "text": [ "GraR" ], "offsets": [ [ 1668, 1672 ] ], "normalized": [] }, { "id": "PMC2430206-02-Results-01_T66", "type": "Protein", "text": [ "S" ], "offsets": [ [ 1672, 1673 ] ], "normalized": [] }, { "id": "PMC2430206-02-Results-01_T67", "type": "Protein", "text": [ "mprF" ], "offsets": [ [ 1743, 1747 ] ], "normalized": [] }, { "id": "PMC2430206-02-Results-01_T68", "type": "Chemical", "text": [ "lysylphosphatidylglycerol" ], "offsets": [ [ 1785, 1810 ] ], "normalized": [] }, { "id": "PMC2430206-02-Results-01_T69", "type": "Chemical", "text": [ "LPG" ], "offsets": [ [ 1812, 1815 ] ], "normalized": [] }, { "id": "PMC2430206-02-Results-01_T70", "type": "Chemical", "text": [ "LPG" ], "offsets": [ [ 1968, 1971 ] ], "normalized": [] }, { "id": "PMC2430206-02-Results-01_T71", "type": "Organism", "text": [ "graRS mutant" ], "offsets": [ [ 1984, 1996 ] ], "normalized": [] }, { "id": "PMC2430206-02-Results-01_T72", "type": "Two-component-system", "text": [ "graRS" ], "offsets": [ [ 1984, 1989 ] ], "normalized": [] }, { "id": "PMC2430206-02-Results-01_T73", "type": "Protein", "text": [ "graR" ], "offsets": [ [ 1984, 1988 ] ], "normalized": [] }, { "id": "PMC2430206-02-Results-01_T74", "type": "Protein", "text": [ "S" ], "offsets": [ [ 1988, 1989 ] ], "normalized": [] }, { "id": "PMC2430206-02-Results-01_T75", "type": "Protein", "text": [ "mprF" ], "offsets": [ [ 2078, 2082 ] ], "normalized": [] }, { "id": "PMC2430206-02-Results-01_T76", "type": "Two-component-system", "text": [ "graRS" ], "offsets": [ [ 2100, 2105 ] ], "normalized": [] }, { "id": "PMC2430206-02-Results-01_T77", "type": "Protein", "text": [ "graR" ], "offsets": [ [ 2100, 2104 ] ], "normalized": [] }, { "id": "PMC2430206-02-Results-01_T78", "type": "Protein", "text": [ "S" ], "offsets": [ [ 2104, 2105 ] ], "normalized": [] }, { "id": "PMC2430206-02-Results-01_T79", "type": "Organism", "text": [ "S. aureus SA113" ], "offsets": [ [ 2125, 2140 ] ], "normalized": [] }, { "id": "PMC2430206-02-Results-01_T80", "type": "Organism", "text": [ "graRS mutant" ], "offsets": [ [ 2151, 2163 ] ], "normalized": [] }, { "id": "PMC2430206-02-Results-01_T81", "type": "Two-component-system", "text": [ "graRS" ], "offsets": [ [ 2151, 2156 ] ], "normalized": [] }, { "id": "PMC2430206-02-Results-01_T82", "type": "Protein", "text": [ "graR" ], "offsets": [ [ 2151, 2155 ] ], "normalized": [] }, { "id": "PMC2430206-02-Results-01_T83", "type": "Protein", "text": [ "S" ], "offsets": [ [ 2155, 2156 ] ], "normalized": [] }, { "id": "PMC2430206-02-Results-01_T84", "type": "Protein", "text": [ "LL-37" ], "offsets": [ [ 2198, 2203 ] ], "normalized": [] }, { "id": "PMC2430206-02-Results-01_T85", "type": "Organism", "text": [ "human" ], "offsets": [ [ 2208, 2213 ] ], "normalized": [] }, { "id": "PMC2430206-02-Results-01_T86", "type": "Organism", "text": [ "graRS mutant" ], "offsets": [ [ 2307, 2319 ] ], "normalized": [] }, { "id": "PMC2430206-02-Results-01_T87", "type": "Two-component-system", "text": [ "graRS" ], "offsets": [ [ 2307, 2312 ] ], "normalized": [] }, { "id": "PMC2430206-02-Results-01_T88", "type": "Protein", "text": [ "graR" ], "offsets": [ [ 2307, 2311 ] ], "normalized": [] }, { "id": "PMC2430206-02-Results-01_T89", "type": "Protein", "text": [ "S" ], "offsets": [ [ 2311, 2312 ] ], "normalized": [] }, { "id": "PMC2430206-02-Results-01_T90", "type": "Organism", "text": [ "human" ], "offsets": [ [ 2376, 2381 ] ], "normalized": [] }, { "id": "PMC2430206-02-Results-01_T91", "type": "Organism", "text": [ "graRS mutant" ], "offsets": [ [ 2440, 2452 ] ], "normalized": [] }, { "id": "PMC2430206-02-Results-01_T92", "type": "Two-component-system", "text": [ "graRS" ], "offsets": [ [ 2440, 2445 ] ], "normalized": [] }, { "id": "PMC2430206-02-Results-01_T93", "type": "Protein", "text": [ "graR" ], "offsets": [ [ 2440, 2444 ] ], "normalized": [] }, { "id": "PMC2430206-02-Results-01_T94", "type": "Protein", "text": [ "S" ], "offsets": [ [ 2444, 2445 ] ], "normalized": [] }, { "id": "PMC2430206-02-Results-01_T95", "type": "Organism", "text": [ "human" ], "offsets": [ [ 2460, 2465 ] ], "normalized": [] }, { "id": "PMC2430206-02-Results-01_T96", "type": "Protein", "text": [ "LL-37" ], "offsets": [ [ 2479, 2484 ] ], "normalized": [] }, { "id": "PMC2430206-02-Results-01_T97", "type": "Organism", "text": [ "S. aureus" ], "offsets": [ [ 2531, 2540 ] ], "normalized": [] }, { "id": "PMC2430206-02-Results-01_T98", "type": "Protein", "text": [ "LL-37" ], "offsets": [ [ 2645, 2650 ] ], "normalized": [] }, { "id": "PMC2430206-02-Results-01_T99", "type": "Organism", "text": [ "S. aureus" ], "offsets": [ [ 2683, 2692 ] ], "normalized": [] }, { "id": "PMC2430206-02-Results-01_T100", "type": "Organism", "text": [ "complemented mutant strains" ], "offsets": [ [ 2721, 2748 ] ], "normalized": [] }, { "id": "PMC2430206-02-Results-01_T101", "type": "Protein", "text": [ "LL-37" ], "offsets": [ [ 2797, 2802 ] ], "normalized": [] }, { "id": "PMC2430206-02-Results-01_T102", "type": "Organism", "text": [ "graRS mutant" ], "offsets": [ [ 2835, 2847 ] ], "normalized": [] }, { "id": "PMC2430206-02-Results-01_T103", "type": "Two-component-system", "text": [ "graRS" ], "offsets": [ [ 2835, 2840 ] ], "normalized": [] }, { "id": "PMC2430206-02-Results-01_T104", "type": "Protein", "text": [ "graR" ], "offsets": [ [ 2835, 2839 ] ], "normalized": [] }, { "id": "PMC2430206-02-Results-01_T105", "type": "Protein", "text": [ "S" ], "offsets": [ [ 2839, 2840 ] ], "normalized": [] }, { "id": "PMC2430206-02-Results-01_T106", "type": "Organism", "text": [ "graRS mutant" ], "offsets": [ [ 2949, 2961 ] ], "normalized": [] }, { "id": "PMC2430206-02-Results-01_T107", "type": "Two-component-system", "text": [ "graRS" ], "offsets": [ [ 2949, 2954 ] ], "normalized": [] }, { "id": "PMC2430206-02-Results-01_T108", "type": "Protein", "text": [ "graR" ], "offsets": [ [ 2949, 2953 ] ], "normalized": [] }, { "id": "PMC2430206-02-Results-01_T109", "type": "Protein", "text": [ "S" ], "offsets": [ [ 2953, 2954 ] ], "normalized": [] }, { "id": "PMC2430206-02-Results-01_T110", "type": "Organism", "text": [ "human" ], "offsets": [ [ 3007, 3012 ] ], "normalized": [] }, { "id": "PMC2430206-02-Results-01_T111", "type": "Protein", "text": [ "LL-37" ], "offsets": [ [ 3056, 3061 ] ], "normalized": [] }, { "id": "PMC2430206-02-Results-01_T112", "type": "Organism", "text": [ "graRS mutant" ], "offsets": [ [ 3136, 3148 ] ], "normalized": [] }, { "id": "PMC2430206-02-Results-01_T113", "type": "Two-component-system", "text": [ "graRS" ], "offsets": [ [ 3136, 3141 ] ], "normalized": [] }, { "id": "PMC2430206-02-Results-01_T114", "type": "Protein", "text": [ "graR" ], "offsets": [ [ 3136, 3140 ] ], "normalized": [] }, { "id": "PMC2430206-02-Results-01_T115", "type": "Protein", "text": [ "S" ], "offsets": [ [ 3140, 3141 ] ], "normalized": [] }, { "id": "PMC2430206-02-Results-01_T116", "type": "Organism", "text": [ "graRS mutant" ], "offsets": [ [ 3261, 3273 ] ], "normalized": [] }, { "id": "PMC2430206-02-Results-01_T117", "type": "Two-component-system", "text": [ "graRS" ], "offsets": [ [ 3261, 3266 ] ], "normalized": [] }, { "id": "PMC2430206-02-Results-01_T118", "type": "Protein", "text": [ "graR" ], "offsets": [ [ 3261, 3265 ] ], "normalized": [] }, { "id": "PMC2430206-02-Results-01_T119", "type": "Protein", "text": [ "S" ], "offsets": [ [ 3265, 3266 ] ], "normalized": [] }, { "id": "PMC2430206-02-Results-01_T120", "type": "Two-component-system", "text": [ "graRS" ], "offsets": [ [ 3504, 3509 ] ], "normalized": [] }, { "id": "PMC2430206-02-Results-01_T121", "type": "Protein", "text": [ "graR" ], "offsets": [ [ 3504, 3508 ] ], "normalized": [] }, { "id": "PMC2430206-02-Results-01_T122", "type": "Protein", "text": [ "S" ], "offsets": [ [ 3508, 3509 ] ], "normalized": [] }, { "id": "PMC2430206-02-Results-01_T123", "type": "Organism", "text": [ "S. aureus" ], "offsets": [ [ 3578, 3587 ] ], "normalized": [] } ]

[ { "id": "PMC2430206-02-Results-01_E1", "type": "Binding", "trigger": { "text": [ "binding" ], "offsets": [ [ 247, 254 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC2430206-02-Results-01_T10" }, { "role": "Theme", "ref_id": "PMC2430206-02-Results-01_T11" } ] }, { "id": "PMC2430206-02-Results-01_E2", "type": "Binding", "trigger": { "text": [ "binding" ], "offsets": [ [ 247, 254 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC2430206-02-Results-01_T10" }, { "role": "Theme", "ref_id": "PMC2430206-02-Results-01_T12" } ] }, { "id": "PMC2430206-02-Results-01_E3", "type": "Binding", "trigger": { "text": [ "binding" ], "offsets": [ [ 247, 254 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC2430206-02-Results-01_T10" }, { "role": "Theme", "ref_id": "PMC2430206-02-Results-01_T16" } ] }, { "id": "PMC2430206-02-Results-01_E4", "type": "Binding", "trigger": { "text": [ "bound" ], "offsets": [ [ 422, 427 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC2430206-02-Results-01_T21" }, { "role": "Theme", "ref_id": "PMC2430206-02-Results-01_T17" } ] }, { "id": "PMC2430206-02-Results-01_E5", "type": "Binding", "trigger": { "text": [ "binding" ], "offsets": [ [ 670, 677 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC2430206-02-Results-01_T23" }, { "role": "Theme", "ref_id": "PMC2430206-02-Results-01_T24" } ] }, { "id": "PMC2430206-02-Results-01_E6", "type": "Binding", "trigger": { "text": [ "binding" ], "offsets": [ [ 878, 885 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC2430206-02-Results-01_T29" }, { "role": "Theme", "ref_id": "PMC2430206-02-Results-01_T33" } ] }, { "id": "PMC2430206-02-Results-01_E7", "type": "Binding", "trigger": { "text": [ "binding" ], "offsets": [ [ 878, 885 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC2430206-02-Results-01_T29" }, { "role": "Theme", "ref_id": "PMC2430206-02-Results-01_T30" } ] }, { "id": "PMC2430206-02-Results-01_E8", "type": "Binding", "trigger": { "text": [ "binding" ], "offsets": [ [ 1131, 1138 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC2430206-02-Results-01_T50" }, { "role": "Theme", "ref_id": "PMC2430206-02-Results-01_T45" } ] }, { "id": "PMC2430206-02-Results-01_E9", "type": "Binding", "trigger": { "text": [ "binding" ], "offsets": [ [ 1131, 1138 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC2430206-02-Results-01_T50" }, { "role": "Theme", "ref_id": "PMC2430206-02-Results-01_T44" } ] }, { "id": "PMC2430206-02-Results-01_E10", "type": "Positive_regulation", "trigger": { "text": [ "increased" ], "offsets": [ [ 1352, 1361 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC2430206-02-Results-01_E11" } ] }, { "id": "PMC2430206-02-Results-01_E11", "type": "Binding", "trigger": { "text": [ "binding" ], "offsets": [ [ 1362, 1369 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC2430206-02-Results-01_T55" } ] }, { "id": "PMC2430206-02-Results-01_E12", "type": "Positive_regulation", "trigger": { "text": [ "increased" ], "offsets": [ [ 1457, 1466 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC2430206-02-Results-01_E13" } ] }, { "id": "PMC2430206-02-Results-01_E13", "type": "Binding", "trigger": { "text": [ "binding" ], "offsets": [ [ 1467, 1474 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC2430206-02-Results-01_T58" }, { "role": "Theme", "ref_id": "PMC2430206-02-Results-01_T59" } ] }, { "id": "PMC2430206-02-Results-01_E14", "type": "Negative_regulation", "trigger": { "text": [ "reduced" ], "offsets": [ [ 1735, 1742 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC2430206-02-Results-01_E15" } ] }, { "id": "PMC2430206-02-Results-01_E15", "type": "Gene_expression", "trigger": { "text": [ "expression" ], "offsets": [ [ 1748, 1758 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC2430206-02-Results-01_T67" } ] }, { "id": "PMC2430206-02-Results-01_E16", "type": "Negative_regulation", "trigger": { "text": [ "inactivation" ], "offsets": [ [ 2417, 2429 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC2430206-02-Results-01_T91" }, { "role": "Cause", "ref_id": "PMC2430206-02-Results-01_T96" } ] }, { "id": "PMC2430206-02-Results-01_E17", "type": "Gene_expression", "trigger": { "text": [ "produce" ], "offsets": [ [ 3032, 3039 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC2430206-02-Results-01_T111" } ] } ]

[]

[]

[ { "id": "PMC1913099-02-Results-Discussion-10__text", "type": "abstract", "text": [ "Allelic Replacement of spy0129 \nWe created a spy0129 deletion mutant in strain SF370 (SF370Deltaspy0129) to determine if genes contained within the spy0127-0130 cluster were directly involved in adherence to pharyngeal cells. We posited that a deletion in the spy0129 sortase gene may have the greatest overall effect on the production and processing of the gene products of this cluster, since both the spy0128 and spy0130 gene products do not localize to the cell-wall surface in the absence of the sortase enzyme [36]. Allelic replacement created two putative deletion mutants; however, RT-PCR analysis (Figure 4A) revealed that only one such clone (SF370Deltaspy0129.2) was a true knock-out for the spy0129 gene and useful for further study. Because the gene cluster is also an operon, expression of the downstream gene spy0130, encoding the protein F homolog/pilus protein, was also eliminated in this mutant (Figure 4A). In vitro pharyngeal cell adherence assays revealed that the SF370Deltaspy0129.2 mutant was approximately 66% less adherent than the parental control strain, SF370 (Figure 4B; p = 0.03 as determined by the Student's t-test). These results suggest that either the spy0130 gene product is involved directly in adherence, or that due to the elimination of the sortase, the pili, which may function in their entirety as adhesins, were not assembled on the surface of the mutant. Because the spy0129 gene product is not expected to be found on the streptococcal surface (i.e., it lacks a cell-wall anchoring motif), it is not likely to be involved directly in adherence. We are working to produce an in-frame deletion of spy0128 and a spy0130 single knock-out mutant to delineate the contribution of each individual clustered gene product to adherence. These results show that neighbor clustering is able to identify biologically relevant gene clusters. This attribute may be particularly important for datasets in which the relationship between clustered genes is not obvious, and may facilitate the organization of larger datasets into more manageable packages.\n" ], "offsets": [ [ 0, 2085 ] ] } ]

[ { "id": "PMC1913099-02-Results-Discussion-10_T1", "type": "Protein", "text": [ "spy0129" ], "offsets": [ [ 23, 30 ] ], "normalized": [] }, { "id": "PMC1913099-02-Results-Discussion-10_T2", "type": "Organism", "text": [ "spy0129 deletion mutant" ], "offsets": [ [ 45, 68 ] ], "normalized": [] }, { "id": "PMC1913099-02-Results-Discussion-10_T3", "type": "Protein", "text": [ "spy0129" ], "offsets": [ [ 45, 52 ] ], "normalized": [] }, { "id": "PMC1913099-02-Results-Discussion-10_T4", "type": "Organism", "text": [ "SF370" ], "offsets": [ [ 79, 84 ] ], "normalized": [] }, { "id": "PMC1913099-02-Results-Discussion-10_T5", "type": "Organism", "text": [ "SF370Deltaspy0129" ], "offsets": [ [ 86, 103 ] ], "normalized": [] }, { "id": "PMC1913099-02-Results-Discussion-10_T6", "type": "Protein", "text": [ "spy0129" ], "offsets": [ [ 96, 103 ] ], "normalized": [] }, { "id": "PMC1913099-02-Results-Discussion-10_T7", "type": "Regulon-operon", "text": [ "spy0127-0130" ], "offsets": [ [ 148, 160 ] ], "normalized": [] }, { "id": "PMC1913099-02-Results-Discussion-10_T8", "type": "Protein", "text": [ "spy0127" ], "offsets": [ [ 148, 155 ] ], "normalized": [] }, { "id": "PMC1913099-02-Results-Discussion-10_T9", "type": "Protein", "text": [ "0130" ], "offsets": [ [ 156, 160 ] ], "normalized": [] }, { "id": "PMC1913099-02-Results-Discussion-10_T10", "type": "Protein", "text": [ "spy0129" ], "offsets": [ [ 260, 267 ] ], "normalized": [] }, { "id": "PMC1913099-02-Results-Discussion-10_T11", "type": "Protein", "text": [ "spy0128" ], "offsets": [ [ 404, 411 ] ], "normalized": [] }, { "id": "PMC1913099-02-Results-Discussion-10_T12", "type": "Protein", "text": [ "spy0130" ], "offsets": [ [ 416, 423 ] ], "normalized": [] }, { "id": "PMC1913099-02-Results-Discussion-10_T13", "type": "Protein", "text": [ "sortase" ], "offsets": [ [ 501, 508 ] ], "normalized": [] }, { "id": "PMC1913099-02-Results-Discussion-10_T14", "type": "Organism", "text": [ "SF370Deltaspy0129.2" ], "offsets": [ [ 653, 672 ] ], "normalized": [] }, { "id": "PMC1913099-02-Results-Discussion-10_T15", "type": "Protein", "text": [ "spy0129" ], "offsets": [ [ 663, 670 ] ], "normalized": [] }, { "id": "PMC1913099-02-Results-Discussion-10_T16", "type": "Protein", "text": [ "spy0129" ], "offsets": [ [ 703, 710 ] ], "normalized": [] }, { "id": "PMC1913099-02-Results-Discussion-10_T17", "type": "Protein", "text": [ "spy0130" ], "offsets": [ [ 824, 831 ] ], "normalized": [] }, { "id": "PMC1913099-02-Results-Discussion-10_T18", "type": "Organism", "text": [ "SF370Deltaspy0129.2 mutant" ], "offsets": [ [ 987, 1013 ] ], "normalized": [] }, { "id": "PMC1913099-02-Results-Discussion-10_T19", "type": "Protein", "text": [ "spy0129" ], "offsets": [ [ 997, 1004 ] ], "normalized": [] }, { "id": "PMC1913099-02-Results-Discussion-10_T20", "type": "Organism", "text": [ "SF370" ], "offsets": [ [ 1084, 1089 ] ], "normalized": [] }, { "id": "PMC1913099-02-Results-Discussion-10_T21", "type": "Protein", "text": [ "spy0130" ], "offsets": [ [ 1189, 1196 ] ], "normalized": [] }, { "id": "PMC1913099-02-Results-Discussion-10_T22", "type": "Protein", "text": [ "sortase" ], "offsets": [ [ 1283, 1290 ] ], "normalized": [] }, { "id": "PMC1913099-02-Results-Discussion-10_T23", "type": "Protein", "text": [ "spy0129" ], "offsets": [ [ 1413, 1420 ] ], "normalized": [] }, { "id": "PMC1913099-02-Results-Discussion-10_T24", "type": "Protein", "text": [ "spy0128" ], "offsets": [ [ 1642, 1649 ] ], "normalized": [] }, { "id": "PMC1913099-02-Results-Discussion-10_T25", "type": "Protein", "text": [ "spy0130" ], "offsets": [ [ 1656, 1663 ] ], "normalized": [] }, { "id": "PMC1913099-02-Results-Discussion-10_T27", "type": "Entity", "text": [ "cell-wall surface" ], "offsets": [ [ 461, 478 ] ], "normalized": [] } ]

[ { "id": "PMC1913099-02-Results-Discussion-10_E1", "type": "Localization", "trigger": { "text": [ "localize" ], "offsets": [ [ 445, 453 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC1913099-02-Results-Discussion-10_T11" }, { "role": "AtLoc", "ref_id": "PMC1913099-02-Results-Discussion-10_T27" } ] }, { "id": "PMC1913099-02-Results-Discussion-10_E2", "type": "Localization", "trigger": { "text": [ "localize" ], "offsets": [ [ 445, 453 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC1913099-02-Results-Discussion-10_T12" }, { "role": "AtLoc", "ref_id": "PMC1913099-02-Results-Discussion-10_T27" } ] }, { "id": "PMC1913099-02-Results-Discussion-10_E3", "type": "Gene_expression", "trigger": { "text": [ "expression" ], "offsets": [ [ 790, 800 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC1913099-02-Results-Discussion-10_T17" } ] }, { "id": "PMC1913099-02-Results-Discussion-10_E4", "type": "Negative_regulation", "trigger": { "text": [ "eliminated" ], "offsets": [ [ 888, 898 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC1913099-02-Results-Discussion-10_E3" } ] }, { "id": "PMC1913099-02-Results-Discussion-10_E5", "type": "Negative_regulation", "trigger": { "text": [ "elimination" ], "offsets": [ [ 1264, 1275 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC1913099-02-Results-Discussion-10_T22" } ] } ]

[]

[]

[ { "id": "PMC2266911-02-Results_and_Discussion-03-02__text", "type": "abstract", "text": [ "Iron uptake \nBacteria use two different strategies to acquire sufficient amounts of iron, namely the expression and secretion of high-affinity iron-binding compounds called siderophores, and the production of receptors for iron carriers such as heme. Genes involved in the biosynthesis, transport and regulation of the siderophore yersiniabactin are clustered in the high pathogenicity island of Y. enterocolitica [103] and have counterparts in P. luminescens (plu2316-2324). Remarkably, yersiniabactin is absent in all Y. enterocolitica strains beside biovar 1B. Present in both bacterial organisms compared here are also genes encoding a hemine uptake system (ye0323-0332/plu2631-2636), the YfeABCD transporter system of chelated iron, the ferrous (Fe2+) iron transporter proteins FeoAB, the AfuABC/SfuABC ferric (Fe3+) transporter, the enterobactin and its transporter (FepBDCG), the FecABCDE ABC transporter system, and several putative hemin/siderophore/iron uptake proteins (YE1459-1461/Plu2850-2852), YE3190/Plu2853, and YE0555/Plu3738). The proteins encoded by the P. luminescens fecIRABCDE operon are similar to the components of the E. coli Fe3+-dicitrate transport system. Homologues are present in the genome of Y. enterocolitica, but scattered over the chromosome. In addition, Y. enterocolitica produces two heme-protein acquisition sytems (YE0123-126, YE2180-2182), a second SfuABC system, the ferrichrome binding and transport proteins (YE0730-0732), a putative siderophore (YE0704), and a hemin storage system (YE2481-2484). None of these iron acquisition systems is present in P. luminescens which in contrast produces the siderophore photobactin [104]. Furthermore, P. luminescens encodes two putative heme-binding hemopexin-like proteins, the photopexins PpxA (Plu4242) and PpxB (Plu4243), which are the first hemopexins found in bacteria. It is suggested that the photopexins may be used by P. luminescens to scavenge iron containing compounds from insects [105]. Interestingly, three gene loci involved in iron acquisition, namely the genes encoding the hemin storage system, the yersiniabactin and the enterobactin transporter FepG, have been demonstrated to be up-regulated upon temperature decrease in Y. pestis or Y. ruckeri, respectively (Table 1). This large set of iron, hemin, heme and siderophore transporters underlines the importance of iron availability for the life cycles of P. luminescens and Y. enterocolitica. It also indicates that iron acquisition is a prerequisite for the infection process of pathogenic bacteria not only in mammalian, but also in invertebrate hosts, and underlines the suggestion that genetic determinants of invertebrate pathogens such as P. luminescens include the progenitors of virulence factors against vertebrates [79,106].\n" ], "offsets": [ [ 0, 2791 ] ] } ]

[ { "id": "PMC2266911-02-Results_and_Discussion-03-02_T1", "type": "Chemical", "text": [ "Iron" ], "offsets": [ [ 0, 4 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-03-02_T2", "type": "Chemical", "text": [ "iron" ], "offsets": [ [ 84, 88 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-03-02_T3", "type": "Chemical", "text": [ "iron" ], "offsets": [ [ 143, 147 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-03-02_T4", "type": "Chemical", "text": [ "iron" ], "offsets": [ [ 223, 227 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-03-02_T5", "type": "Chemical", "text": [ "heme" ], "offsets": [ [ 245, 249 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-03-02_T6", "type": "Chemical", "text": [ "yersiniabactin" ], "offsets": [ [ 331, 345 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-03-02_T7", "type": "Organism", "text": [ "Y. enterocolitica" ], "offsets": [ [ 396, 413 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-03-02_T8", "type": "Organism", "text": [ "P. luminescens" ], "offsets": [ [ 445, 459 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-03-02_T9", "type": "Organism", "text": [ "Y. enterocolitica" ], "offsets": [ [ 520, 537 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-03-02_T10", "type": "Organism", "text": [ "1B" ], "offsets": [ [ 560, 562 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-03-02_T11", "type": "Chemical", "text": [ "hemine" ], "offsets": [ [ 640, 646 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-03-02_T12", "type": "Protein", "text": [ "ye0323" ], "offsets": [ [ 662, 668 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-03-02_T13", "type": "Protein", "text": [ "0332" ], "offsets": [ [ 669, 673 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-03-02_T14", "type": "Protein", "text": [ "plu2631" ], "offsets": [ [ 674, 681 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-03-02_T15", "type": "Protein", "text": [ "2636" ], "offsets": [ [ 682, 686 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-03-02_T16", "type": "Protein", "text": [ "YfeA" ], "offsets": [ [ 693, 697 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-03-02_T17", "type": "Protein", "text": [ "B" ], "offsets": [ [ 697, 698 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-03-02_T18", "type": "Protein", "text": [ "C" ], "offsets": [ [ 698, 699 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-03-02_T19", "type": "Protein", "text": [ "D" ], "offsets": [ [ 699, 700 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-03-02_T20", "type": "Chemical", "text": [ "iron" ], "offsets": [ [ 732, 736 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-03-02_T21", "type": "Chemical", "text": [ "ferrous (Fe2+) iron" ], "offsets": [ [ 742, 761 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-03-02_T22", "type": "Protein", "text": [ "FeoA" ], "offsets": [ [ 783, 787 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-03-02_T23", "type": "Protein", "text": [ "B" ], "offsets": [ [ 787, 788 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-03-02_T24", "type": "Protein", "text": [ "AfuA" ], "offsets": [ [ 794, 798 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-03-02_T25", "type": "Protein", "text": [ "B" ], "offsets": [ [ 798, 799 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-03-02_T26", "type": "Protein", "text": [ "C" ], "offsets": [ [ 799, 800 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-03-02_T27", "type": "Protein", "text": [ "SfuA" ], "offsets": [ [ 801, 805 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-03-02_T28", "type": "Protein", "text": [ "B" ], "offsets": [ [ 805, 806 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-03-02_T29", "type": "Protein", "text": [ "C" ], "offsets": [ [ 806, 807 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-03-02_T30", "type": "Chemical", "text": [ "ferric" ], "offsets": [ [ 808, 814 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-03-02_T31", "type": "Chemical", "text": [ "Fe3+" ], "offsets": [ [ 816, 820 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-03-02_T32", "type": "Chemical", "text": [ "enterobactin" ], "offsets": [ [ 839, 851 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-03-02_T33", "type": "Protein", "text": [ "FepB" ], "offsets": [ [ 873, 877 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-03-02_T34", "type": "Protein", "text": [ "D" ], "offsets": [ [ 877, 878 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-03-02_T35", "type": "Protein", "text": [ "C" ], "offsets": [ [ 878, 879 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-03-02_T36", "type": "Protein", "text": [ "G" ], "offsets": [ [ 879, 880 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-03-02_T37", "type": "Protein", "text": [ "FecA" ], "offsets": [ [ 887, 891 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-03-02_T38", "type": "Protein", "text": [ "B" ], "offsets": [ [ 891, 892 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-03-02_T39", "type": "Protein", "text": [ "C" ], "offsets": [ [ 892, 893 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-03-02_T40", "type": "Protein", "text": [ "D" ], "offsets": [ [ 893, 894 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-03-02_T41", "type": "Protein", "text": [ "E" ], "offsets": [ [ 894, 895 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-03-02_T42", "type": "Chemical", "text": [ "hemin" ], "offsets": [ [ 941, 946 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-03-02_T43", "type": "Chemical", "text": [ "siderophore" ], "offsets": [ [ 947, 958 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-03-02_T44", "type": "Chemical", "text": [ "iron" ], "offsets": [ [ 959, 963 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-03-02_T45", "type": "Protein", "text": [ "YE1459" ], "offsets": [ [ 981, 987 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-03-02_T46", "type": "Protein", "text": [ "1461" ], "offsets": [ [ 988, 992 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-03-02_T47", "type": "Protein", "text": [ "Plu2850" ], "offsets": [ [ 993, 1000 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-03-02_T48", "type": "Protein", "text": [ "2852" ], "offsets": [ [ 1001, 1005 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-03-02_T49", "type": "Protein", "text": [ "YE3190" ], "offsets": [ [ 1008, 1014 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-03-02_T50", "type": "Protein", "text": [ "Plu2853" ], "offsets": [ [ 1015, 1022 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-03-02_T51", "type": "Protein", "text": [ "YE0555" ], "offsets": [ [ 1028, 1034 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-03-02_T52", "type": "Protein", "text": [ "Plu3738" ], "offsets": [ [ 1035, 1042 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-03-02_T53", "type": "Organism", "text": [ "P. luminescens" ], "offsets": [ [ 1073, 1087 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-03-02_T54", "type": "Regulon-operon", "text": [ "fecIRABCDE" ], "offsets": [ [ 1088, 1098 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-03-02_T55", "type": "Protein", "text": [ "fecI" ], "offsets": [ [ 1088, 1092 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-03-02_T56", "type": "Protein", "text": [ "R" ], "offsets": [ [ 1092, 1093 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-03-02_T57", "type": "Protein", "text": [ "A" ], "offsets": [ [ 1093, 1094 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-03-02_T58", "type": "Protein", "text": [ "B" ], "offsets": [ [ 1094, 1095 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-03-02_T59", "type": "Protein", "text": [ "C" ], "offsets": [ [ 1095, 1096 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-03-02_T60", "type": "Protein", "text": [ "D" ], "offsets": [ [ 1096, 1097 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-03-02_T61", "type": "Protein", "text": [ "E" ], "offsets": [ [ 1097, 1098 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-03-02_T62", "type": "Organism", "text": [ "E. coli" ], "offsets": [ [ 1143, 1150 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-03-02_T63", "type": "Chemical", "text": [ "Fe3+" ], "offsets": [ [ 1151, 1155 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-03-02_T64", "type": "Organism", "text": [ "Y. enterocolitica" ], "offsets": [ [ 1224, 1241 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-03-02_T65", "type": "Organism", "text": [ "Y. enterocolitica" ], "offsets": [ [ 1291, 1308 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-03-02_T66", "type": "Chemical", "text": [ "heme" ], "offsets": [ [ 1322, 1326 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-03-02_T67", "type": "Protein", "text": [ "YE0123" ], "offsets": [ [ 1355, 1361 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-03-02_T68", "type": "Protein", "text": [ "126" ], "offsets": [ [ 1362, 1365 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-03-02_T69", "type": "Protein", "text": [ "YE2180" ], "offsets": [ [ 1367, 1373 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-03-02_T70", "type": "Protein", "text": [ "2182" ], "offsets": [ [ 1374, 1378 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-03-02_T71", "type": "Protein", "text": [ "SfuA" ], "offsets": [ [ 1390, 1394 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-03-02_T72", "type": "Protein", "text": [ "B" ], "offsets": [ [ 1394, 1395 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-03-02_T73", "type": "Protein", "text": [ "C" ], "offsets": [ [ 1395, 1396 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-03-02_T74", "type": "Chemical", "text": [ "ferrichrome" ], "offsets": [ [ 1409, 1420 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-03-02_T75", "type": "Protein", "text": [ "YE0730" ], "offsets": [ [ 1453, 1459 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-03-02_T76", "type": "Protein", "text": [ "0732" ], "offsets": [ [ 1460, 1464 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-03-02_T77", "type": "Chemical", "text": [ "siderophore" ], "offsets": [ [ 1478, 1489 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-03-02_T78", "type": "Protein", "text": [ "YE0704" ], "offsets": [ [ 1491, 1497 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-03-02_T79", "type": "Chemical", "text": [ "hemin" ], "offsets": [ [ 1506, 1511 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-03-02_T80", "type": "Protein", "text": [ "YE2481" ], "offsets": [ [ 1528, 1534 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-03-02_T81", "type": "Protein", "text": [ "2484" ], "offsets": [ [ 1535, 1539 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-03-02_T82", "type": "Chemical", "text": [ "iron" ], "offsets": [ [ 1556, 1560 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-03-02_T83", "type": "Organism", "text": [ "P. luminescens" ], "offsets": [ [ 1595, 1609 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-03-02_T84", "type": "Chemical", "text": [ "siderophore" ], "offsets": [ [ 1641, 1652 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-03-02_T85", "type": "Organism", "text": [ "P. luminescens" ], "offsets": [ [ 1685, 1699 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-03-02_T86", "type": "Chemical", "text": [ "heme" ], "offsets": [ [ 1721, 1725 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-03-02_T87", "type": "Protein", "text": [ "PpxA" ], "offsets": [ [ 1775, 1779 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-03-02_T88", "type": "Protein", "text": [ "Plu4242" ], "offsets": [ [ 1781, 1788 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-03-02_T89", "type": "Protein", "text": [ "PpxB" ], "offsets": [ [ 1794, 1798 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-03-02_T90", "type": "Protein", "text": [ "Plu4243" ], "offsets": [ [ 1800, 1807 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-03-02_T91", "type": "Organism", "text": [ "P. luminescens" ], "offsets": [ [ 1912, 1926 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-03-02_T92", "type": "Chemical", "text": [ "iron" ], "offsets": [ [ 1939, 1943 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-03-02_T93", "type": "Chemical", "text": [ "iron" ], "offsets": [ [ 2028, 2032 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-03-02_T94", "type": "Chemical", "text": [ "hemin" ], "offsets": [ [ 2076, 2081 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-03-02_T95", "type": "Chemical", "text": [ "yersiniabactin" ], "offsets": [ [ 2102, 2116 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-03-02_T96", "type": "Chemical", "text": [ "enterobactin" ], "offsets": [ [ 2125, 2137 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-03-02_T97", "type": "Protein", "text": [ "FepG" ], "offsets": [ [ 2150, 2154 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-03-02_T98", "type": "Organism", "text": [ "Y. pestis" ], "offsets": [ [ 2227, 2236 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-03-02_T99", "type": "Organism", "text": [ "Y. ruckeri" ], "offsets": [ [ 2240, 2250 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-03-02_T100", "type": "Chemical", "text": [ "iron" ], "offsets": [ [ 2294, 2298 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-03-02_T101", "type": "Chemical", "text": [ "hemin" ], "offsets": [ [ 2300, 2305 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-03-02_T102", "type": "Chemical", "text": [ "heme" ], "offsets": [ [ 2307, 2311 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-03-02_T103", "type": "Chemical", "text": [ "iron" ], "offsets": [ [ 2370, 2374 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-03-02_T104", "type": "Organism", "text": [ "P. luminescens" ], "offsets": [ [ 2411, 2425 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-03-02_T105", "type": "Organism", "text": [ "Y. enterocolitica" ], "offsets": [ [ 2430, 2447 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-03-02_T106", "type": "Chemical", "text": [ "iron" ], "offsets": [ [ 2472, 2476 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-03-02_T107", "type": "Organism", "text": [ "P. luminescens" ], "offsets": [ [ 2701, 2715 ] ], "normalized": [] } ]

[ { "id": "PMC2266911-02-Results_and_Discussion-03-02_E1", "type": "Gene_expression", "trigger": { "text": [ "produces" ], "offsets": [ [ 1309, 1317 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC2266911-02-Results_and_Discussion-03-02_T67" } ] }, { "id": "PMC2266911-02-Results_and_Discussion-03-02_E2", "type": "Gene_expression", "trigger": { "text": [ "produces" ], "offsets": [ [ 1309, 1317 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC2266911-02-Results_and_Discussion-03-02_T75" } ] }, { "id": "PMC2266911-02-Results_and_Discussion-03-02_E3", "type": "Gene_expression", "trigger": { "text": [ "produces" ], "offsets": [ [ 1309, 1317 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC2266911-02-Results_and_Discussion-03-02_T76" } ] }, { "id": "PMC2266911-02-Results_and_Discussion-03-02_E4", "type": "Gene_expression", "trigger": { "text": [ "produces" ], "offsets": [ [ 1309, 1317 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC2266911-02-Results_and_Discussion-03-02_T78" } ] }, { "id": "PMC2266911-02-Results_and_Discussion-03-02_E5", "type": "Gene_expression", "trigger": { "text": [ "produces" ], "offsets": [ [ 1309, 1317 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC2266911-02-Results_and_Discussion-03-02_T80" } ] }, { "id": "PMC2266911-02-Results_and_Discussion-03-02_E6", "type": "Gene_expression", "trigger": { "text": [ "produces" ], "offsets": [ [ 1309, 1317 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC2266911-02-Results_and_Discussion-03-02_T81" } ] }, { "id": "PMC2266911-02-Results_and_Discussion-03-02_E7", "type": "Gene_expression", "trigger": { "text": [ "produces" ], "offsets": [ [ 1309, 1317 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC2266911-02-Results_and_Discussion-03-02_T68" } ] }, { "id": "PMC2266911-02-Results_and_Discussion-03-02_E8", "type": "Gene_expression", "trigger": { "text": [ "produces" ], "offsets": [ [ 1309, 1317 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC2266911-02-Results_and_Discussion-03-02_T69" } ] }, { "id": "PMC2266911-02-Results_and_Discussion-03-02_E9", "type": "Gene_expression", "trigger": { "text": [ "produces" ], "offsets": [ [ 1309, 1317 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC2266911-02-Results_and_Discussion-03-02_T70" } ] }, { "id": "PMC2266911-02-Results_and_Discussion-03-02_E10", "type": "Gene_expression", "trigger": { "text": [ "produces" ], "offsets": [ [ 1309, 1317 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC2266911-02-Results_and_Discussion-03-02_T71" } ] }, { "id": "PMC2266911-02-Results_and_Discussion-03-02_E11", "type": "Gene_expression", "trigger": { "text": [ "produces" ], "offsets": [ [ 1309, 1317 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC2266911-02-Results_and_Discussion-03-02_T72" } ] }, { "id": "PMC2266911-02-Results_and_Discussion-03-02_E12", "type": "Gene_expression", "trigger": { "text": [ "produces" ], "offsets": [ [ 1309, 1317 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC2266911-02-Results_and_Discussion-03-02_T73" } ] }, { "id": "PMC2266911-02-Results_and_Discussion-03-02_E13", "type": "Binding", "trigger": { "text": [ "binding" ], "offsets": [ [ 1421, 1428 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC2266911-02-Results_and_Discussion-03-02_T75" } ] }, { "id": "PMC2266911-02-Results_and_Discussion-03-02_E14", "type": "Binding", "trigger": { "text": [ "binding" ], "offsets": [ [ 1421, 1428 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC2266911-02-Results_and_Discussion-03-02_T76" } ] }, { "id": "PMC2266911-02-Results_and_Discussion-03-02_E15", "type": "Positive_regulation", "trigger": { "text": [ "up-regulated" ], "offsets": [ [ 2185, 2197 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC2266911-02-Results_and_Discussion-03-02_T97" } ] }, { "id": "PMC2266911-02-Results_and_Discussion-03-02_E16", "type": "Process", "trigger": { "text": [ "infection" ], "offsets": [ [ 2515, 2524 ] ] }, "arguments": [] }, { "id": "PMC2266911-02-Results_and_Discussion-03-02_E17", "type": "Process", "trigger": { "text": [ "virulence" ], "offsets": [ [ 2743, 2752 ] ] }, "arguments": [] } ]

[ { "id": "PMC2266911-02-Results_and_Discussion-03-02_1", "entity_ids": [ "PMC2266911-02-Results_and_Discussion-03-02_T30", "PMC2266911-02-Results_and_Discussion-03-02_T31" ] }, { "id": "PMC2266911-02-Results_and_Discussion-03-02_2", "entity_ids": [ "PMC2266911-02-Results_and_Discussion-03-02_T87", "PMC2266911-02-Results_and_Discussion-03-02_T88" ] }, { "id": "PMC2266911-02-Results_and_Discussion-03-02_3", "entity_ids": [ "PMC2266911-02-Results_and_Discussion-03-02_T89", "PMC2266911-02-Results_and_Discussion-03-02_T90" ] } ]

[]

[ { "id": "PMC2639726-00-TIAB__text", "type": "abstract", "text": [ "Coordinated Regulation of Virulence during Systemic Infection of Salmonella enterica Serovar Typhimurium \nTo cause a systemic infection, Salmonella must respond to many environmental cues during mouse infection and express specific subsets of genes in a temporal and spatial manner, but the regulatory pathways are poorly established. To unravel how micro-environmental signals are processed and integrated into coordinated action, we constructed in-frame non-polar deletions of 83 regulators inferred to play a role in Salmonella enteriditis Typhimurium (STM) virulence and tested them in three virulence assays (intraperitoneal [i.p.], and intragastric [i.g.] infection in BALB/c mice, and persistence in 129X1/SvJ mice). Overall, 35 regulators were identified whose absence attenuated virulence in at least one assay, and of those, 14 regulators were required for systemic mouse infection, the most stringent virulence assay. As a first step towards understanding the interplay between a pathogen and its host from a systems biology standpoint, we focused on these 14 genes. Transcriptional profiles were obtained for deletions of each of these 14 regulators grown under four different environmental conditions. These results, as well as publicly available transcriptional profiles, were analyzed using both network inference and cluster analysis algorithms. The analysis predicts a regulatory network in which all 14 regulators control the same set of genes necessary for Salmonella to cause systemic infection. We tested the regulatory model by expressing a subset of the regulators in trans and monitoring transcription of 7 known virulence factors located within Salmonella pathogenicity island 2 (SPI-2). These experiments validated the regulatory model and showed that the response regulator SsrB and the MarR type regulator, SlyA, are the terminal regulators in a cascade that integrates multiple signals. Furthermore, experiments to demonstrate epistatic relationships showed that SsrB can replace SlyA and, in some cases, SlyA can replace SsrB for expression of SPI-2 encoded virulence factors.\n" ], "offsets": [ [ 0, 2107 ] ] } ]

[ { "id": "PMC2639726-00-TIAB_T1", "type": "Organism", "text": [ "Salmonella enterica Serovar Typhimurium" ], "offsets": [ [ 65, 104 ] ], "normalized": [] }, { "id": "PMC2639726-00-TIAB_T2", "type": "Organism", "text": [ "Salmonella" ], "offsets": [ [ 137, 147 ] ], "normalized": [] }, { "id": "PMC2639726-00-TIAB_T3", "type": "Organism", "text": [ "mouse" ], "offsets": [ [ 195, 200 ] ], "normalized": [] }, { "id": "PMC2639726-00-TIAB_T4", "type": "Organism", "text": [ "Salmonella enteriditis Typhimurium" ], "offsets": [ [ 520, 554 ] ], "normalized": [] }, { "id": "PMC2639726-00-TIAB_T5", "type": "Organism", "text": [ "STM" ], "offsets": [ [ 556, 559 ] ], "normalized": [] }, { "id": "PMC2639726-00-TIAB_T6", "type": "Organism", "text": [ "BALB/c mice" ], "offsets": [ [ 675, 686 ] ], "normalized": [] }, { "id": "PMC2639726-00-TIAB_T7", "type": "Organism", "text": [ "129X1/SvJ mice" ], "offsets": [ [ 707, 721 ] ], "normalized": [] }, { "id": "PMC2639726-00-TIAB_T8", "type": "Organism", "text": [ "mouse" ], "offsets": [ [ 876, 881 ] ], "normalized": [] }, { "id": "PMC2639726-00-TIAB_T9", "type": "Organism", "text": [ "Salmonella" ], "offsets": [ [ 1476, 1486 ] ], "normalized": [] }, { "id": "PMC2639726-00-TIAB_T10", "type": "Organism", "text": [ "Salmonella" ], "offsets": [ [ 1670, 1680 ] ], "normalized": [] }, { "id": "PMC2639726-00-TIAB_T11", "type": "Protein", "text": [ "SsrB" ], "offsets": [ [ 1801, 1805 ] ], "normalized": [] }, { "id": "PMC2639726-00-TIAB_T12", "type": "Protein", "text": [ "MarR" ], "offsets": [ [ 1814, 1818 ] ], "normalized": [] }, { "id": "PMC2639726-00-TIAB_T13", "type": "Protein", "text": [ "SlyA" ], "offsets": [ [ 1835, 1839 ] ], "normalized": [] }, { "id": "PMC2639726-00-TIAB_T14", "type": "Protein", "text": [ "SsrB" ], "offsets": [ [ 1992, 1996 ] ], "normalized": [] }, { "id": "PMC2639726-00-TIAB_T15", "type": "Protein", "text": [ "SlyA" ], "offsets": [ [ 2009, 2013 ] ], "normalized": [] }, { "id": "PMC2639726-00-TIAB_T16", "type": "Protein", "text": [ "SlyA" ], "offsets": [ [ 2034, 2038 ] ], "normalized": [] }, { "id": "PMC2639726-00-TIAB_T17", "type": "Protein", "text": [ "SsrB" ], "offsets": [ [ 2051, 2055 ] ], "normalized": [] } ]

[ { "id": "PMC2639726-00-TIAB_E1", "type": "Process", "trigger": { "text": [ "Virulence" ], "offsets": [ [ 26, 35 ] ] }, "arguments": [ { "role": "Participant", "ref_id": "PMC2639726-00-TIAB_T1" } ] }, { "id": "PMC2639726-00-TIAB_E2", "type": "Process", "trigger": { "text": [ "Infection" ], "offsets": [ [ 52, 61 ] ] }, "arguments": [ { "role": "Participant", "ref_id": "PMC2639726-00-TIAB_T1" } ] }, { "id": "PMC2639726-00-TIAB_E3", "type": "Process", "trigger": { "text": [ "infection" ], "offsets": [ [ 126, 135 ] ] }, "arguments": [] }, { "id": "PMC2639726-00-TIAB_E4", "type": "Process", "trigger": { "text": [ "infection" ], "offsets": [ [ 201, 210 ] ] }, "arguments": [ { "role": "Participant", "ref_id": "PMC2639726-00-TIAB_T2" } ] }, { "id": "PMC2639726-00-TIAB_E5", "type": "Process", "trigger": { "text": [ "virulence" ], "offsets": [ [ 561, 570 ] ] }, "arguments": [ { "role": "Participant", "ref_id": "PMC2639726-00-TIAB_T4" } ] }, { "id": "PMC2639726-00-TIAB_E6", "type": "Process", "trigger": { "text": [ "virulence" ], "offsets": [ [ 596, 605 ] ] }, "arguments": [] }, { "id": "PMC2639726-00-TIAB_E7", "type": "Negative_regulation", "trigger": { "text": [ "attenuated" ], "offsets": [ [ 777, 787 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC2639726-00-TIAB_E8" } ] }, { "id": "PMC2639726-00-TIAB_E8", "type": "Process", "trigger": { "text": [ "virulence" ], "offsets": [ [ 788, 797 ] ] }, "arguments": [] }, { "id": "PMC2639726-00-TIAB_E9", "type": "Process", "trigger": { "text": [ "infection" ], "offsets": [ [ 882, 891 ] ] }, "arguments": [] }, { "id": "PMC2639726-00-TIAB_E10", "type": "Process", "trigger": { "text": [ "virulence" ], "offsets": [ [ 912, 921 ] ] }, "arguments": [] }, { "id": "PMC2639726-00-TIAB_E11", "type": "Process", "trigger": { "text": [ "infection" ], "offsets": [ [ 1505, 1514 ] ] }, "arguments": [ { "role": "Participant", "ref_id": "PMC2639726-00-TIAB_T9" } ] }, { "id": "PMC2639726-00-TIAB_E12", "type": "Process", "trigger": { "text": [ "virulence" ], "offsets": [ [ 1637, 1646 ] ] }, "arguments": [] }, { "id": "PMC2639726-00-TIAB_E13", "type": "Process", "trigger": { "text": [ "virulence" ], "offsets": [ [ 2088, 2097 ] ] }, "arguments": [] } ]

[ { "id": "PMC2639726-00-TIAB_1", "entity_ids": [ "PMC2639726-00-TIAB_T4", "PMC2639726-00-TIAB_T5" ] } ]

[]

[ { "id": "PMC2858072-01-Introduction__text", "type": "abstract", "text": [ "Introduction \nFacultative intracellular bacteria such as Brucella must survive in varied and changing conditions ranging from the open environment to the intracellular medium. For this, the bacterium must coordinate an intricate network of factors to generate a suitable adaptive response to the various signals. This attribute is often accomplished by two-component transduction systems, consisting of a sensor kinase and a response regulator. These regulatory systems are highly conserved among bacteria and widely used for controlling gene expression in response to environmental signals. In response to stimuli, the sensor kinase autophosphorylates, then transfers its phosphate to its cognate response regulator to control the transcription of target genes [1]. Up to now, BvrR/BvrS is the best characterized two-component regulatory system of Brucella [2]-[4]. BvrS is a membrane-bound homodimeric protein that has three conserved regions frequently found in members of the histidine protein kinase superfamily: an amino-terminal periplasmic sensing domain with transmembrane segments, a cytoplasmic dimerisation domain with a specific His residue, and the carboxy-terminal ATP-binding kinase domain [5]. BvrR is a cytoplasmic protein that shows significant similarity to OmpR/PhoB subfamily of response regulator proteins with a specific Asp residue located within a conserved regulatory domain and an effector domain with DNA-binding activity [5]. Although genome sequencing has revealed 21 putative two-component regulatory systems in the Brucella genus, the best characterized one implicated in virulence is the BvrR/BvrS system. BvrR/bvrS mutants are avirulent in mice, have increased susceptibility to killing by nonimmune serum, show reduced invasiveness to epithelial cells and macrophages, and are incapable of inhibiting lysosome fusion and of intracellular replication [4]. As demonstrated for other two-component systems, multiple genes are expected to be under the control of BvrR/BvrS [1]. B. abortus mutants in this system were more susceptible to bactericidal polycationic substances like polymyxin B, melittin or poly-L-lysine, and displayed a more hydrophobic outer membrane surface than the parental strain [4]. This evidence suggests an altered outer membrane structure. Later studies demonstrated that the BvrR/BvrS system regulates transcription of at least two major outer membrane proteins, Omp22 (Omp3b) and Omp25a (Omp3a). Changes in non-protein envelope molecules such as lipid A underacylation and increased LPS acyl-chain fluidity have been also found in these mutants [3]. To further understand the role of the BvrR/BvrS two-component signal transduction system, global gene expression profiles were analyzed by using ORFeome-based Brucella whole-genome DNA microarrays and confirmed by reverse transcription-PCR (RT-PCR). Our results link the regulation of carbon and nitrogen metabolism to the expression of cell envelope components and suggest the existence of a complex regulatory network with the interplay of several transcriptional regulators.\n" ], "offsets": [ [ 0, 3087 ] ] } ]

[ { "id": "PMC2858072-01-Introduction_T1", "type": "Organism", "text": [ "Brucella" ], "offsets": [ [ 57, 65 ] ], "normalized": [] }, { "id": "PMC2858072-01-Introduction_T2", "type": "Chemical", "text": [ "phosphate" ], "offsets": [ [ 673, 682 ] ], "normalized": [] }, { "id": "PMC2858072-01-Introduction_T3", "type": "Two-component-system", "text": [ "BvrR/BvrS" ], "offsets": [ [ 778, 787 ] ], "normalized": [] }, { "id": "PMC2858072-01-Introduction_T4", "type": "Protein", "text": [ "BvrR" ], "offsets": [ [ 778, 782 ] ], "normalized": [] }, { "id": "PMC2858072-01-Introduction_T5", "type": "Protein", "text": [ "BvrS" ], "offsets": [ [ 783, 787 ] ], "normalized": [] }, { "id": "PMC2858072-01-Introduction_T6", "type": "Organism", "text": [ "Brucella" ], "offsets": [ [ 849, 857 ] ], "normalized": [] }, { "id": "PMC2858072-01-Introduction_T7", "type": "Protein", "text": [ "BvrS" ], "offsets": [ [ 867, 871 ] ], "normalized": [] }, { "id": "PMC2858072-01-Introduction_T8", "type": "Chemical", "text": [ "ATP" ], "offsets": [ [ 1180, 1183 ] ], "normalized": [] }, { "id": "PMC2858072-01-Introduction_T9", "type": "Protein", "text": [ "BvrR" ], "offsets": [ [ 1211, 1215 ] ], "normalized": [] }, { "id": "PMC2858072-01-Introduction_T10", "type": "Two-component-system", "text": [ "OmpR/PhoB" ], "offsets": [ [ 1278, 1287 ] ], "normalized": [] }, { "id": "PMC2858072-01-Introduction_T11", "type": "Protein", "text": [ "OmpR" ], "offsets": [ [ 1278, 1282 ] ], "normalized": [] }, { "id": "PMC2858072-01-Introduction_T12", "type": "Protein", "text": [ "PhoB" ], "offsets": [ [ 1283, 1287 ] ], "normalized": [] }, { "id": "PMC2858072-01-Introduction_T13", "type": "Organism", "text": [ "Brucella" ], "offsets": [ [ 1548, 1556 ] ], "normalized": [] }, { "id": "PMC2858072-01-Introduction_T14", "type": "Two-component-system", "text": [ "BvrR/BvrS" ], "offsets": [ [ 1622, 1631 ] ], "normalized": [] }, { "id": "PMC2858072-01-Introduction_T15", "type": "Protein", "text": [ "BvrR" ], "offsets": [ [ 1622, 1626 ] ], "normalized": [] }, { "id": "PMC2858072-01-Introduction_T16", "type": "Protein", "text": [ "BvrS" ], "offsets": [ [ 1627, 1631 ] ], "normalized": [] }, { "id": "PMC2858072-01-Introduction_T17", "type": "Organism", "text": [ "BvrR/bvrS mutants" ], "offsets": [ [ 1640, 1657 ] ], "normalized": [] }, { "id": "PMC2858072-01-Introduction_T18", "type": "Two-component-system", "text": [ "BvrR/bvrS" ], "offsets": [ [ 1640, 1649 ] ], "normalized": [] }, { "id": "PMC2858072-01-Introduction_T19", "type": "Protein", "text": [ "BvrR" ], "offsets": [ [ 1640, 1644 ] ], "normalized": [] }, { "id": "PMC2858072-01-Introduction_T20", "type": "Protein", "text": [ "bvrS" ], "offsets": [ [ 1645, 1649 ] ], "normalized": [] }, { "id": "PMC2858072-01-Introduction_T21", "type": "Organism", "text": [ "mice" ], "offsets": [ [ 1675, 1679 ] ], "normalized": [] }, { "id": "PMC2858072-01-Introduction_T22", "type": "Two-component-system", "text": [ "BvrR/BvrS" ], "offsets": [ [ 1995, 2004 ] ], "normalized": [] }, { "id": "PMC2858072-01-Introduction_T23", "type": "Protein", "text": [ "BvrR" ], "offsets": [ [ 1995, 1999 ] ], "normalized": [] }, { "id": "PMC2858072-01-Introduction_T24", "type": "Protein", "text": [ "BvrS" ], "offsets": [ [ 2000, 2004 ] ], "normalized": [] }, { "id": "PMC2858072-01-Introduction_T25", "type": "Organism", "text": [ "B. abortus mutants" ], "offsets": [ [ 2010, 2028 ] ], "normalized": [] }, { "id": "PMC2858072-01-Introduction_T26", "type": "Chemical", "text": [ "polymyxin B" ], "offsets": [ [ 2111, 2122 ] ], "normalized": [] }, { "id": "PMC2858072-01-Introduction_T27", "type": "Chemical", "text": [ "melittin" ], "offsets": [ [ 2124, 2132 ] ], "normalized": [] }, { "id": "PMC2858072-01-Introduction_T28", "type": "Chemical", "text": [ "poly-L-lysine" ], "offsets": [ [ 2136, 2149 ] ], "normalized": [] }, { "id": "PMC2858072-01-Introduction_T29", "type": "Two-component-system", "text": [ "BvrR/BvrS" ], "offsets": [ [ 2333, 2342 ] ], "normalized": [] }, { "id": "PMC2858072-01-Introduction_T30", "type": "Protein", "text": [ "BvrR" ], "offsets": [ [ 2333, 2337 ] ], "normalized": [] }, { "id": "PMC2858072-01-Introduction_T31", "type": "Protein", "text": [ "BvrS" ], "offsets": [ [ 2338, 2342 ] ], "normalized": [] }, { "id": "PMC2858072-01-Introduction_T32", "type": "Protein", "text": [ "Omp22" ], "offsets": [ [ 2421, 2426 ] ], "normalized": [] }, { "id": "PMC2858072-01-Introduction_T33", "type": "Protein", "text": [ "Omp3b" ], "offsets": [ [ 2428, 2433 ] ], "normalized": [] }, { "id": "PMC2858072-01-Introduction_T34", "type": "Protein", "text": [ "Omp25a" ], "offsets": [ [ 2439, 2445 ] ], "normalized": [] }, { "id": "PMC2858072-01-Introduction_T35", "type": "Protein", "text": [ "Omp3a" ], "offsets": [ [ 2447, 2452 ] ], "normalized": [] }, { "id": "PMC2858072-01-Introduction_T36", "type": "Chemical", "text": [ "lipid A" ], "offsets": [ [ 2505, 2512 ] ], "normalized": [] }, { "id": "PMC2858072-01-Introduction_T37", "type": "Chemical", "text": [ "LPS" ], "offsets": [ [ 2542, 2545 ] ], "normalized": [] }, { "id": "PMC2858072-01-Introduction_T38", "type": "Two-component-system", "text": [ "BvrR/BvrS" ], "offsets": [ [ 2647, 2656 ] ], "normalized": [] }, { "id": "PMC2858072-01-Introduction_T39", "type": "Protein", "text": [ "BvrR" ], "offsets": [ [ 2647, 2651 ] ], "normalized": [] }, { "id": "PMC2858072-01-Introduction_T40", "type": "Protein", "text": [ "BvrS" ], "offsets": [ [ 2652, 2656 ] ], "normalized": [] }, { "id": "PMC2858072-01-Introduction_T41", "type": "Organism", "text": [ "Brucella" ], "offsets": [ [ 2768, 2776 ] ], "normalized": [] }, { "id": "PMC2858072-01-Introduction_T42", "type": "Chemical", "text": [ "carbon" ], "offsets": [ [ 2894, 2900 ] ], "normalized": [] }, { "id": "PMC2858072-01-Introduction_T43", "type": "Chemical", "text": [ "nitrogen" ], "offsets": [ [ 2905, 2913 ] ], "normalized": [] } ]

[ { "id": "PMC2858072-01-Introduction_E1", "type": "Regulation", "trigger": { "text": [ "implicated" ], "offsets": [ [ 1591, 1601 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC2858072-01-Introduction_E2" }, { "role": "Cause", "ref_id": "PMC2858072-01-Introduction_T14" } ] }, { "id": "PMC2858072-01-Introduction_E2", "type": "Process", "trigger": { "text": [ "virulence" ], "offsets": [ [ 1605, 1614 ] ] }, "arguments": [ { "role": "Participant", "ref_id": "PMC2858072-01-Introduction_T13" } ] }, { "id": "PMC2858072-01-Introduction_E3", "type": "Process", "trigger": { "text": [ "avirulent" ], "offsets": [ [ 1662, 1671 ] ] }, "arguments": [ { "role": "Participant", "ref_id": "PMC2858072-01-Introduction_T17" } ] }, { "id": "PMC2858072-01-Introduction_E4", "type": "Regulation", "trigger": { "text": [ "regulates" ], "offsets": [ [ 2350, 2359 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC2858072-01-Introduction_E6" }, { "role": "Cause", "ref_id": "PMC2858072-01-Introduction_T29" } ] }, { "id": "PMC2858072-01-Introduction_E5", "type": "Regulation", "trigger": { "text": [ "regulates" ], "offsets": [ [ 2350, 2359 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC2858072-01-Introduction_E7" }, { "role": "Cause", "ref_id": "PMC2858072-01-Introduction_T29" } ] }, { "id": "PMC2858072-01-Introduction_E6", "type": "Transcription", "trigger": { "text": [ "transcription" ], "offsets": [ [ 2360, 2373 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC2858072-01-Introduction_T32" } ] }, { "id": "PMC2858072-01-Introduction_E7", "type": "Transcription", "trigger": { "text": [ "transcription" ], "offsets": [ [ 2360, 2373 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC2858072-01-Introduction_T34" } ] } ]

[ { "id": "PMC2858072-01-Introduction_1", "entity_ids": [ "PMC2858072-01-Introduction_T32", "PMC2858072-01-Introduction_T33" ] }, { "id": "PMC2858072-01-Introduction_2", "entity_ids": [ "PMC2858072-01-Introduction_T34", "PMC2858072-01-Introduction_T35" ] } ]

[]

[ { "id": "PMC2565068-02-Results-02__text", "type": "abstract", "text": [ "Severe invasive GAS rapidly induce necrosis to human PMN \nIn an acute bacterial infection, PMN were quickly recruited at the site of infectious foci according to the gradient of chemoattractants. Therefore, we examined whether GAS clinically isolated from severe invasive infections could affect the migration ability of PMN in response to chemokines. As a model of local infection of the initial phase, we utilized a transwell system and added IL-8 and GAS in culture medium within the lower wells. PMN were applied in the upper wells and subsequently incubated for 90 min. As shown in Figure 2A and 2B, a substantial number of PMN, consisted largely of viable cells, was detected in the lower wells consisted of IL-8 and non-invasive GAS, as a control. Contrarily, number of PMN was significantly low in the presence of severe invasive GAS (p=0.016) compared to that of control culture. Flow cytometry analysis suggested that although PMN was detected in the lower well consisted of IL-8 and severe invasive GAS, but most of them were dead as defined by propidium iodine staining (p=0.016) (Figure 2A and 2C) demonstrating that severe invasive GAS affected survival of PMN and its migration activity in a transwell system.\n" ], "offsets": [ [ 0, 1225 ] ] } ]

[ { "id": "PMC2565068-02-Results-02_T1", "type": "Organism", "text": [ "invasive GAS" ], "offsets": [ [ 7, 19 ] ], "normalized": [] }, { "id": "PMC2565068-02-Results-02_T2", "type": "Organism", "text": [ "human" ], "offsets": [ [ 47, 52 ] ], "normalized": [] }, { "id": "PMC2565068-02-Results-02_T3", "type": "Organism", "text": [ "GAS" ], "offsets": [ [ 227, 230 ] ], "normalized": [] }, { "id": "PMC2565068-02-Results-02_T4", "type": "Protein", "text": [ "IL-8" ], "offsets": [ [ 445, 449 ] ], "normalized": [] }, { "id": "PMC2565068-02-Results-02_T5", "type": "Organism", "text": [ "GAS" ], "offsets": [ [ 454, 457 ] ], "normalized": [] }, { "id": "PMC2565068-02-Results-02_T6", "type": "Protein", "text": [ "IL-8" ], "offsets": [ [ 714, 718 ] ], "normalized": [] }, { "id": "PMC2565068-02-Results-02_T7", "type": "Organism", "text": [ "non-invasive GAS" ], "offsets": [ [ 723, 739 ] ], "normalized": [] }, { "id": "PMC2565068-02-Results-02_T8", "type": "Organism", "text": [ "invasive GAS" ], "offsets": [ [ 829, 841 ] ], "normalized": [] }, { "id": "PMC2565068-02-Results-02_T9", "type": "Protein", "text": [ "IL-8" ], "offsets": [ [ 985, 989 ] ], "normalized": [] }, { "id": "PMC2565068-02-Results-02_T10", "type": "Organism", "text": [ "invasive GAS" ], "offsets": [ [ 1001, 1013 ] ], "normalized": [] }, { "id": "PMC2565068-02-Results-02_T11", "type": "Chemical", "text": [ "propidium iodine" ], "offsets": [ [ 1056, 1072 ] ], "normalized": [] }, { "id": "PMC2565068-02-Results-02_T12", "type": "Organism", "text": [ "invasive GAS" ], "offsets": [ [ 1137, 1149 ] ], "normalized": [] } ]

[ { "id": "PMC2565068-02-Results-02_E1", "type": "Process", "trigger": { "text": [ "infection" ], "offsets": [ [ 80, 89 ] ] }, "arguments": [] }, { "id": "PMC2565068-02-Results-02_E2", "type": "Process", "trigger": { "text": [ "infectious" ], "offsets": [ [ 133, 143 ] ] }, "arguments": [] }, { "id": "PMC2565068-02-Results-02_E3", "type": "Process", "trigger": { "text": [ "infections" ], "offsets": [ [ 272, 282 ] ] }, "arguments": [ { "role": "Participant", "ref_id": "PMC2565068-02-Results-02_T3" } ] }, { "id": "PMC2565068-02-Results-02_E4", "type": "Process", "trigger": { "text": [ "infection" ], "offsets": [ [ 372, 381 ] ] }, "arguments": [] } ]

[]

[]

[ { "id": "PMC2885601-03-RESULTS-03__text", "type": "abstract", "text": [ "Endopeptidase Activity of SeMac against Horse IgG1 and Human IgG \nGAS Mac can cleave the heavy chain of human IgG at the lower hinge region between Fab and Fc fragments. A catalytic triad of Cys94, His262, and Asp284 residues is critical for the enzymatic activity of GAS Mac [7, 8]. SeMac possesses putative catalytic residues of Cys102, His272, and Asp294 (Fig. 1). To determine whether SeMac also is a cysteine endopeptidase targeting IgG, Cys102 and His272 or Asp294 of SeMac were replaced with Ser and Ala, respectively, by site-directed mutagenesis, and wild-type and mutant (SeMacCys102Ser, SeMacHis272Ala and SeMacAsp294Ala) SeMac proteins expressed in E. coli were tested for IgG endopeptidase activity using human IgG. Wild-type SeMac cleaved the heavy chain of human IgG, while SeMacCys102Ser and SeMacHis272Ala completely lost the IgG endopeptidase activity, and SeMacAsp294Ala had dramatically lower enzymatic activity than the wild-type protein (Fig. 4A). The results indicate that SeMac is a cysteine endopeptidase, which uses Cys102, His272 and Asp294 as its catalytic triad to cleave human IgG. Purified recombinant SeMac and GAS Mac were then tested for activity to cleave horse IgG. While both proteins cleaved human IgG efficiently, only a small fraction of horse IgG was cleaved by either protein (Fig. 4B), suggesting that SeMac or GAS Mac cannot digest all subgroups of horse IgG. To test this possibility, available horse IgG1 and a mixture of IgG1 and IgG4 were treated with SeMac or GAS Mac. SeMac or GAS Mac cleaved a small portion of the IgG1/IgG4 mixture, but not IgG4. Therefore, the Mac proteins can cleave IgG1 but not IgG4. Due to the unavailability of other purified subgroup IgG, it is not known whether SeMac cleaves the other IgG subgroups.\n" ], "offsets": [ [ 0, 1778 ] ] } ]

[ { "id": "PMC2885601-03-RESULTS-03_T1", "type": "Protein", "text": [ "SeMac" ], "offsets": [ [ 26, 31 ] ], "normalized": [] }, { "id": "PMC2885601-03-RESULTS-03_T2", "type": "Organism", "text": [ "Horse" ], "offsets": [ [ 40, 45 ] ], "normalized": [] }, { "id": "PMC2885601-03-RESULTS-03_T3", "type": "Protein", "text": [ "IgG1" ], "offsets": [ [ 46, 50 ] ], "normalized": [] }, { "id": "PMC2885601-03-RESULTS-03_T4", "type": "Organism", "text": [ "Human" ], "offsets": [ [ 55, 60 ] ], "normalized": [] }, { "id": "PMC2885601-03-RESULTS-03_T5", "type": "Protein", "text": [ "IgG" ], "offsets": [ [ 61, 64 ] ], "normalized": [] }, { "id": "PMC2885601-03-RESULTS-03_T6", "type": "Organism", "text": [ "GAS" ], "offsets": [ [ 66, 69 ] ], "normalized": [] }, { "id": "PMC2885601-03-RESULTS-03_T7", "type": "Protein", "text": [ "Mac" ], "offsets": [ [ 70, 73 ] ], "normalized": [] }, { "id": "PMC2885601-03-RESULTS-03_T8", "type": "Organism", "text": [ "human" ], "offsets": [ [ 104, 109 ] ], "normalized": [] }, { "id": "PMC2885601-03-RESULTS-03_T9", "type": "Protein", "text": [ "IgG" ], "offsets": [ [ 110, 113 ] ], "normalized": [] }, { "id": "PMC2885601-03-RESULTS-03_T10", "type": "Organism", "text": [ "GAS" ], "offsets": [ [ 268, 271 ] ], "normalized": [] }, { "id": "PMC2885601-03-RESULTS-03_T11", "type": "Protein", "text": [ "Mac" ], "offsets": [ [ 272, 275 ] ], "normalized": [] }, { "id": "PMC2885601-03-RESULTS-03_T12", "type": "Protein", "text": [ "SeMac" ], "offsets": [ [ 284, 289 ] ], "normalized": [] }, { "id": "PMC2885601-03-RESULTS-03_T13", "type": "Protein", "text": [ "SeMac" ], "offsets": [ [ 389, 394 ] ], "normalized": [] }, { "id": "PMC2885601-03-RESULTS-03_T14", "type": "Protein", "text": [ "IgG" ], "offsets": [ [ 438, 441 ] ], "normalized": [] }, { "id": "PMC2885601-03-RESULTS-03_T15", "type": "Protein", "text": [ "SeMac" ], "offsets": [ [ 474, 479 ] ], "normalized": [] }, { "id": "PMC2885601-03-RESULTS-03_T16", "type": "Protein", "text": [ "SeMacCys102Ser" ], "offsets": [ [ 582, 596 ] ], "normalized": [] }, { "id": "PMC2885601-03-RESULTS-03_T17", "type": "Protein", "text": [ "SeMacHis272Ala" ], "offsets": [ [ 598, 612 ] ], "normalized": [] }, { "id": "PMC2885601-03-RESULTS-03_T18", "type": "Protein", "text": [ "SeMacAsp294Ala" ], "offsets": [ [ 617, 631 ] ], "normalized": [] }, { "id": "PMC2885601-03-RESULTS-03_T19", "type": "Protein", "text": [ "SeMac" ], "offsets": [ [ 633, 638 ] ], "normalized": [] }, { "id": "PMC2885601-03-RESULTS-03_T20", "type": "Organism", "text": [ "E. coli" ], "offsets": [ [ 661, 668 ] ], "normalized": [] }, { "id": "PMC2885601-03-RESULTS-03_T21", "type": "Protein", "text": [ "IgG endopeptidase" ], "offsets": [ [ 685, 702 ] ], "normalized": [] }, { "id": "PMC2885601-03-RESULTS-03_T22", "type": "Organism", "text": [ "human" ], "offsets": [ [ 718, 723 ] ], "normalized": [] }, { "id": "PMC2885601-03-RESULTS-03_T23", "type": "Protein", "text": [ "IgG" ], "offsets": [ [ 724, 727 ] ], "normalized": [] }, { "id": "PMC2885601-03-RESULTS-03_T24", "type": "Protein", "text": [ "SeMac" ], "offsets": [ [ 739, 744 ] ], "normalized": [] }, { "id": "PMC2885601-03-RESULTS-03_T25", "type": "Organism", "text": [ "human" ], "offsets": [ [ 772, 777 ] ], "normalized": [] }, { "id": "PMC2885601-03-RESULTS-03_T26", "type": "Protein", "text": [ "IgG" ], "offsets": [ [ 778, 781 ] ], "normalized": [] }, { "id": "PMC2885601-03-RESULTS-03_T27", "type": "Protein", "text": [ "SeMacCys102Ser" ], "offsets": [ [ 789, 803 ] ], "normalized": [] }, { "id": "PMC2885601-03-RESULTS-03_T28", "type": "Protein", "text": [ "SeMacHis272Ala" ], "offsets": [ [ 808, 822 ] ], "normalized": [] }, { "id": "PMC2885601-03-RESULTS-03_T29", "type": "Protein", "text": [ "IgG endopeptidase" ], "offsets": [ [ 843, 860 ] ], "normalized": [] }, { "id": "PMC2885601-03-RESULTS-03_T30", "type": "Protein", "text": [ "SeMacAsp294Ala" ], "offsets": [ [ 875, 889 ] ], "normalized": [] }, { "id": "PMC2885601-03-RESULTS-03_T31", "type": "Protein", "text": [ "SeMac" ], "offsets": [ [ 996, 1001 ] ], "normalized": [] }, { "id": "PMC2885601-03-RESULTS-03_T32", "type": "Protein", "text": [ "cysteine endopeptidase" ], "offsets": [ [ 1007, 1029 ] ], "normalized": [] }, { "id": "PMC2885601-03-RESULTS-03_T33", "type": "Organism", "text": [ "human" ], "offsets": [ [ 1101, 1106 ] ], "normalized": [] }, { "id": "PMC2885601-03-RESULTS-03_T34", "type": "Protein", "text": [ "IgG" ], "offsets": [ [ 1107, 1110 ] ], "normalized": [] }, { "id": "PMC2885601-03-RESULTS-03_T35", "type": "Protein", "text": [ "SeMac" ], "offsets": [ [ 1133, 1138 ] ], "normalized": [] }, { "id": "PMC2885601-03-RESULTS-03_T36", "type": "Organism", "text": [ "GAS" ], "offsets": [ [ 1143, 1146 ] ], "normalized": [] }, { "id": "PMC2885601-03-RESULTS-03_T37", "type": "Protein", "text": [ "Mac" ], "offsets": [ [ 1147, 1150 ] ], "normalized": [] }, { "id": "PMC2885601-03-RESULTS-03_T38", "type": "Organism", "text": [ "horse" ], "offsets": [ [ 1191, 1196 ] ], "normalized": [] }, { "id": "PMC2885601-03-RESULTS-03_T39", "type": "Protein", "text": [ "IgG" ], "offsets": [ [ 1197, 1200 ] ], "normalized": [] }, { "id": "PMC2885601-03-RESULTS-03_T40", "type": "Organism", "text": [ "human" ], "offsets": [ [ 1230, 1235 ] ], "normalized": [] }, { "id": "PMC2885601-03-RESULTS-03_T41", "type": "Protein", "text": [ "IgG" ], "offsets": [ [ 1236, 1239 ] ], "normalized": [] }, { "id": "PMC2885601-03-RESULTS-03_T42", "type": "Organism", "text": [ "horse" ], "offsets": [ [ 1278, 1283 ] ], "normalized": [] }, { "id": "PMC2885601-03-RESULTS-03_T43", "type": "Protein", "text": [ "IgG" ], "offsets": [ [ 1284, 1287 ] ], "normalized": [] }, { "id": "PMC2885601-03-RESULTS-03_T44", "type": "Protein", "text": [ "SeMac" ], "offsets": [ [ 1345, 1350 ] ], "normalized": [] }, { "id": "PMC2885601-03-RESULTS-03_T45", "type": "Organism", "text": [ "GAS" ], "offsets": [ [ 1354, 1357 ] ], "normalized": [] }, { "id": "PMC2885601-03-RESULTS-03_T46", "type": "Protein", "text": [ "Mac" ], "offsets": [ [ 1358, 1361 ] ], "normalized": [] }, { "id": "PMC2885601-03-RESULTS-03_T47", "type": "Organism", "text": [ "horse" ], "offsets": [ [ 1393, 1398 ] ], "normalized": [] }, { "id": "PMC2885601-03-RESULTS-03_T48", "type": "Protein", "text": [ "IgG" ], "offsets": [ [ 1399, 1402 ] ], "normalized": [] }, { "id": "PMC2885601-03-RESULTS-03_T49", "type": "Organism", "text": [ "horse" ], "offsets": [ [ 1440, 1445 ] ], "normalized": [] }, { "id": "PMC2885601-03-RESULTS-03_T50", "type": "Protein", "text": [ "IgG1" ], "offsets": [ [ 1446, 1450 ] ], "normalized": [] }, { "id": "PMC2885601-03-RESULTS-03_T51", "type": "Protein", "text": [ "IgG1" ], "offsets": [ [ 1468, 1472 ] ], "normalized": [] }, { "id": "PMC2885601-03-RESULTS-03_T52", "type": "Protein", "text": [ "IgG4" ], "offsets": [ [ 1477, 1481 ] ], "normalized": [] }, { "id": "PMC2885601-03-RESULTS-03_T53", "type": "Protein", "text": [ "SeMac" ], "offsets": [ [ 1500, 1505 ] ], "normalized": [] }, { "id": "PMC2885601-03-RESULTS-03_T54", "type": "Organism", "text": [ "GAS" ], "offsets": [ [ 1509, 1512 ] ], "normalized": [] }, { "id": "PMC2885601-03-RESULTS-03_T55", "type": "Protein", "text": [ "Mac" ], "offsets": [ [ 1513, 1516 ] ], "normalized": [] }, { "id": "PMC2885601-03-RESULTS-03_T56", "type": "Protein", "text": [ "SeMac" ], "offsets": [ [ 1518, 1523 ] ], "normalized": [] }, { "id": "PMC2885601-03-RESULTS-03_T57", "type": "Organism", "text": [ "GAS" ], "offsets": [ [ 1527, 1530 ] ], "normalized": [] }, { "id": "PMC2885601-03-RESULTS-03_T58", "type": "Protein", "text": [ "Mac" ], "offsets": [ [ 1531, 1534 ] ], "normalized": [] }, { "id": "PMC2885601-03-RESULTS-03_T59", "type": "Protein", "text": [ "IgG1" ], "offsets": [ [ 1566, 1570 ] ], "normalized": [] }, { "id": "PMC2885601-03-RESULTS-03_T60", "type": "Protein", "text": [ "IgG4" ], "offsets": [ [ 1571, 1575 ] ], "normalized": [] }, { "id": "PMC2885601-03-RESULTS-03_T61", "type": "Protein", "text": [ "IgG4" ], "offsets": [ [ 1593, 1597 ] ], "normalized": [] }, { "id": "PMC2885601-03-RESULTS-03_T62", "type": "Protein", "text": [ "Mac" ], "offsets": [ [ 1614, 1617 ] ], "normalized": [] }, { "id": "PMC2885601-03-RESULTS-03_T63", "type": "Protein", "text": [ "IgG1" ], "offsets": [ [ 1638, 1642 ] ], "normalized": [] }, { "id": "PMC2885601-03-RESULTS-03_T64", "type": "Protein", "text": [ "IgG4" ], "offsets": [ [ 1651, 1655 ] ], "normalized": [] }, { "id": "PMC2885601-03-RESULTS-03_T65", "type": "Protein", "text": [ "IgG" ], "offsets": [ [ 1710, 1713 ] ], "normalized": [] }, { "id": "PMC2885601-03-RESULTS-03_T66", "type": "Protein", "text": [ "SeMac" ], "offsets": [ [ 1739, 1744 ] ], "normalized": [] }, { "id": "PMC2885601-03-RESULTS-03_T67", "type": "Protein", "text": [ "IgG" ], "offsets": [ [ 1763, 1766 ] ], "normalized": [] } ]

[ { "id": "PMC2885601-03-RESULTS-03_E1", "type": "Protein_catabolism", "trigger": { "text": [ "cleave" ], "offsets": [ [ 78, 84 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC2885601-03-RESULTS-03_T9" } ] }, { "id": "PMC2885601-03-RESULTS-03_E2", "type": "Positive_regulation", "trigger": { "text": [ "cleave" ], "offsets": [ [ 78, 84 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC2885601-03-RESULTS-03_E1" }, { "role": "Cause", "ref_id": "PMC2885601-03-RESULTS-03_T7" } ] }, { "id": "PMC2885601-03-RESULTS-03_E3", "type": "Gene_expression", "trigger": { "text": [ "expressed" ], "offsets": [ [ 648, 657 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC2885601-03-RESULTS-03_T16" } ] }, { "id": "PMC2885601-03-RESULTS-03_E4", "type": "Gene_expression", "trigger": { "text": [ "expressed" ], "offsets": [ [ 648, 657 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC2885601-03-RESULTS-03_T17" } ] }, { "id": "PMC2885601-03-RESULTS-03_E5", "type": "Gene_expression", "trigger": { "text": [ "expressed" ], "offsets": [ [ 648, 657 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC2885601-03-RESULTS-03_T18" } ] }, { "id": "PMC2885601-03-RESULTS-03_E6", "type": "Protein_catabolism", "trigger": { "text": [ "cleaved" ], "offsets": [ [ 745, 752 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC2885601-03-RESULTS-03_T26" } ] }, { "id": "PMC2885601-03-RESULTS-03_E7", "type": "Positive_regulation", "trigger": { "text": [ "cleaved" ], "offsets": [ [ 745, 752 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC2885601-03-RESULTS-03_E6" }, { "role": "Cause", "ref_id": "PMC2885601-03-RESULTS-03_T24" } ] }, { "id": "PMC2885601-03-RESULTS-03_E8", "type": "Protein_catabolism", "trigger": { "text": [ "cleave" ], "offsets": [ [ 1094, 1100 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC2885601-03-RESULTS-03_T34" } ] }, { "id": "PMC2885601-03-RESULTS-03_E9", "type": "Positive_regulation", "trigger": { "text": [ "cleave" ], "offsets": [ [ 1094, 1100 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC2885601-03-RESULTS-03_E8" }, { "role": "Cause", "ref_id": "PMC2885601-03-RESULTS-03_T31" } ] }, { "id": "PMC2885601-03-RESULTS-03_E10", "type": "Protein_catabolism", "trigger": { "text": [ "cleave" ], "offsets": [ [ 1184, 1190 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC2885601-03-RESULTS-03_T39" } ] }, { "id": "PMC2885601-03-RESULTS-03_E11", "type": "Positive_regulation", "trigger": { "text": [ "cleave" ], "offsets": [ [ 1184, 1190 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC2885601-03-RESULTS-03_E10" }, { "role": "Cause", "ref_id": "PMC2885601-03-RESULTS-03_T35" } ] }, { "id": "PMC2885601-03-RESULTS-03_E12", "type": "Positive_regulation", "trigger": { "text": [ "cleave" ], "offsets": [ [ 1184, 1190 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC2885601-03-RESULTS-03_E10" }, { "role": "Cause", "ref_id": "PMC2885601-03-RESULTS-03_T37" } ] }, { "id": "PMC2885601-03-RESULTS-03_E13", "type": "Protein_catabolism", "trigger": { "text": [ "cleaved" ], "offsets": [ [ 1222, 1229 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC2885601-03-RESULTS-03_T41" } ] }, { "id": "PMC2885601-03-RESULTS-03_E14", "type": "Positive_regulation", "trigger": { "text": [ "cleaved" ], "offsets": [ [ 1222, 1229 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC2885601-03-RESULTS-03_E13" }, { "role": "Cause", "ref_id": "PMC2885601-03-RESULTS-03_T35" } ] }, { "id": "PMC2885601-03-RESULTS-03_E15", "type": "Positive_regulation", "trigger": { "text": [ "cleaved" ], "offsets": [ [ 1222, 1229 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC2885601-03-RESULTS-03_E13" }, { "role": "Cause", "ref_id": "PMC2885601-03-RESULTS-03_T37" } ] }, { "id": "PMC2885601-03-RESULTS-03_E16", "type": "Protein_catabolism", "trigger": { "text": [ "cleaved" ], "offsets": [ [ 1292, 1299 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC2885601-03-RESULTS-03_T43" } ] }, { "id": "PMC2885601-03-RESULTS-03_E17", "type": "Positive_regulation", "trigger": { "text": [ "cleaved" ], "offsets": [ [ 1292, 1299 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC2885601-03-RESULTS-03_E16" }, { "role": "Cause", "ref_id": "PMC2885601-03-RESULTS-03_T35" } ] }, { "id": "PMC2885601-03-RESULTS-03_E18", "type": "Positive_regulation", "trigger": { "text": [ "cleaved" ], "offsets": [ [ 1292, 1299 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC2885601-03-RESULTS-03_E16" }, { "role": "Cause", "ref_id": "PMC2885601-03-RESULTS-03_T37" } ] }, { "id": "PMC2885601-03-RESULTS-03_E19", "type": "Protein_catabolism", "trigger": { "text": [ "digest" ], "offsets": [ [ 1369, 1375 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC2885601-03-RESULTS-03_T48" } ] }, { "id": "PMC2885601-03-RESULTS-03_E20", "type": "Positive_regulation", "trigger": { "text": [ "digest" ], "offsets": [ [ 1369, 1375 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC2885601-03-RESULTS-03_E19" }, { "role": "Cause", "ref_id": "PMC2885601-03-RESULTS-03_T44" } ] }, { "id": "PMC2885601-03-RESULTS-03_E21", "type": "Positive_regulation", "trigger": { "text": [ "digest" ], "offsets": [ [ 1369, 1375 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC2885601-03-RESULTS-03_E19" }, { "role": "Cause", "ref_id": "PMC2885601-03-RESULTS-03_T46" } ] }, { "id": "PMC2885601-03-RESULTS-03_E22", "type": "Protein_catabolism", "trigger": { "text": [ "cleaved" ], "offsets": [ [ 1535, 1542 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC2885601-03-RESULTS-03_T59" } ] }, { "id": "PMC2885601-03-RESULTS-03_E23", "type": "Protein_catabolism", "trigger": { "text": [ "cleaved" ], "offsets": [ [ 1535, 1542 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC2885601-03-RESULTS-03_T60" } ] }, { "id": "PMC2885601-03-RESULTS-03_E24", "type": "Protein_catabolism", "trigger": { "text": [ "cleaved" ], "offsets": [ [ 1535, 1542 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC2885601-03-RESULTS-03_T61" } ] }, { "id": "PMC2885601-03-RESULTS-03_E25", "type": "Positive_regulation", "trigger": { "text": [ "cleaved" ], "offsets": [ [ 1535, 1542 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC2885601-03-RESULTS-03_E22" }, { "role": "Cause", "ref_id": "PMC2885601-03-RESULTS-03_T56" } ] }, { "id": "PMC2885601-03-RESULTS-03_E26", "type": "Positive_regulation", "trigger": { "text": [ "cleaved" ], "offsets": [ [ 1535, 1542 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC2885601-03-RESULTS-03_E22" }, { "role": "Cause", "ref_id": "PMC2885601-03-RESULTS-03_T58" } ] }, { "id": "PMC2885601-03-RESULTS-03_E27", "type": "Positive_regulation", "trigger": { "text": [ "cleaved" ], "offsets": [ [ 1535, 1542 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC2885601-03-RESULTS-03_E23" }, { "role": "Cause", "ref_id": "PMC2885601-03-RESULTS-03_T56" } ] }, { "id": "PMC2885601-03-RESULTS-03_E28", "type": "Positive_regulation", "trigger": { "text": [ "cleaved" ], "offsets": [ [ 1535, 1542 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC2885601-03-RESULTS-03_E23" }, { "role": "Cause", "ref_id": "PMC2885601-03-RESULTS-03_T58" } ] }, { "id": "PMC2885601-03-RESULTS-03_E29", "type": "Positive_regulation", "trigger": { "text": [ "cleaved" ], "offsets": [ [ 1535, 1542 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC2885601-03-RESULTS-03_E24" }, { "role": "Cause", "ref_id": "PMC2885601-03-RESULTS-03_T56" } ] }, { "id": "PMC2885601-03-RESULTS-03_E30", "type": "Positive_regulation", "trigger": { "text": [ "cleaved" ], "offsets": [ [ 1535, 1542 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC2885601-03-RESULTS-03_E24" }, { "role": "Cause", "ref_id": "PMC2885601-03-RESULTS-03_T58" } ] }, { "id": "PMC2885601-03-RESULTS-03_E31", "type": "Protein_catabolism", "trigger": { "text": [ "cleave" ], "offsets": [ [ 1631, 1637 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC2885601-03-RESULTS-03_T63" } ] }, { "id": "PMC2885601-03-RESULTS-03_E32", "type": "Positive_regulation", "trigger": { "text": [ "cleave" ], "offsets": [ [ 1631, 1637 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC2885601-03-RESULTS-03_E31" }, { "role": "Cause", "ref_id": "PMC2885601-03-RESULTS-03_T62" } ] }, { "id": "PMC2885601-03-RESULTS-03_E33", "type": "Protein_catabolism", "trigger": { "text": [ "cleave" ], "offsets": [ [ 1631, 1637 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC2885601-03-RESULTS-03_T64" } ] }, { "id": "PMC2885601-03-RESULTS-03_E34", "type": "Positive_regulation", "trigger": { "text": [ "cleave" ], "offsets": [ [ 1631, 1637 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC2885601-03-RESULTS-03_E33" }, { "role": "Cause", "ref_id": "PMC2885601-03-RESULTS-03_T62" } ] }, { "id": "PMC2885601-03-RESULTS-03_E35", "type": "Protein_catabolism", "trigger": { "text": [ "cleaves" ], "offsets": [ [ 1745, 1752 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC2885601-03-RESULTS-03_T67" } ] }, { "id": "PMC2885601-03-RESULTS-03_E36", "type": "Positive_regulation", "trigger": { "text": [ "cleaves" ], "offsets": [ [ 1745, 1752 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC2885601-03-RESULTS-03_E35" }, { "role": "Cause", "ref_id": "PMC2885601-03-RESULTS-03_T66" } ] } ]

[]

[]

[ { "id": "PMC2682197-00-TIAB__text", "type": "abstract", "text": [ "Mycobacterium tuberculosis Universal Stress Protein Rv2623 Regulates Bacillary Growth by ATP-Binding: Requirement for Establishing Chronic Persistent Infection \nTuberculous latency and reactivation play a significant role in the pathogenesis of tuberculosis, yet the mechanisms that regulate these processes remain unclear. The Mycobacterium tuberculosis universal stress protein (USP) homolog, rv2623, is among the most highly induced genes when the tubercle bacillus is subjected to hypoxia and nitrosative stress, conditions thought to promote latency. Induction of rv2623 also occurs when M. tuberculosis encounters conditions associated with growth arrest, such as the intracellular milieu of macrophages and in the lungs of mice with chronic tuberculosis. Therefore, we tested the hypothesis that Rv2623 regulates tuberculosis latency. We observed that an Rv2623-deficient mutant fails to establish chronic tuberculous infection in guinea pigs and mice, exhibiting a hypervirulence phenotype associated with increased bacterial burden and mortality. Consistent with this in vivo growth-regulatory role, constitutive overexpression of rv2623 attenuates mycobacterial growth in vitro. Biochemical analysis of purified Rv2623 suggested that this mycobacterial USP binds ATP, and the 2.9-A-resolution crystal structure revealed that Rv2623 engages ATP in a novel nucleotide-binding pocket. Structure-guided mutagenesis yielded Rv2623 mutants with reduced ATP-binding capacity. Analysis of mycobacteria overexpressing these mutants revealed that the in vitro growth-inhibitory property of Rv2623 correlates with its ability to bind ATP. Together, the results indicate that i) M. tuberculosis Rv2623 regulates mycobacterial growth in vitro and in vivo, and ii) Rv2623 is required for the entry of the tubercle bacillus into the chronic phase of infection in the host; in addition, iii) Rv2623 binds ATP; and iv) the growth-regulatory attribute of this USP is dependent on its ATP-binding activity. We propose that Rv2623 may function as an ATP-dependent signaling intermediate in a pathway that promotes persistent infection.\n" ], "offsets": [ [ 0, 2126 ] ] } ]

[ { "id": "PMC2682197-00-TIAB_T1", "type": "Organism", "text": [ "Mycobacterium tuberculosis" ], "offsets": [ [ 0, 26 ] ], "normalized": [] }, { "id": "PMC2682197-00-TIAB_T2", "type": "Protein", "text": [ "Rv2623" ], "offsets": [ [ 52, 58 ] ], "normalized": [] }, { "id": "PMC2682197-00-TIAB_T3", "type": "Chemical", "text": [ "ATP" ], "offsets": [ [ 89, 92 ] ], "normalized": [] }, { "id": "PMC2682197-00-TIAB_T4", "type": "Organism", "text": [ "Mycobacterium tuberculosis" ], "offsets": [ [ 328, 354 ] ], "normalized": [] }, { "id": "PMC2682197-00-TIAB_T5", "type": "Protein", "text": [ "rv2623" ], "offsets": [ [ 395, 401 ] ], "normalized": [] }, { "id": "PMC2682197-00-TIAB_T6", "type": "Organism", "text": [ "tubercle bacillus" ], "offsets": [ [ 451, 468 ] ], "normalized": [] }, { "id": "PMC2682197-00-TIAB_T7", "type": "Protein", "text": [ "rv2623" ], "offsets": [ [ 569, 575 ] ], "normalized": [] }, { "id": "PMC2682197-00-TIAB_T8", "type": "Organism", "text": [ "M. tuberculosis" ], "offsets": [ [ 593, 608 ] ], "normalized": [] }, { "id": "PMC2682197-00-TIAB_T9", "type": "Organism", "text": [ "mice" ], "offsets": [ [ 730, 734 ] ], "normalized": [] }, { "id": "PMC2682197-00-TIAB_T10", "type": "Protein", "text": [ "Rv2623" ], "offsets": [ [ 803, 809 ] ], "normalized": [] }, { "id": "PMC2682197-00-TIAB_T11", "type": "Organism", "text": [ "Rv2623-deficient mutant" ], "offsets": [ [ 862, 885 ] ], "normalized": [] }, { "id": "PMC2682197-00-TIAB_T12", "type": "Protein", "text": [ "Rv2623" ], "offsets": [ [ 862, 868 ] ], "normalized": [] }, { "id": "PMC2682197-00-TIAB_T13", "type": "Organism", "text": [ "guinea pigs" ], "offsets": [ [ 938, 949 ] ], "normalized": [] }, { "id": "PMC2682197-00-TIAB_T14", "type": "Organism", "text": [ "mice" ], "offsets": [ [ 954, 958 ] ], "normalized": [] }, { "id": "PMC2682197-00-TIAB_T15", "type": "Protein", "text": [ "rv2623" ], "offsets": [ [ 1140, 1146 ] ], "normalized": [] }, { "id": "PMC2682197-00-TIAB_T16", "type": "Protein", "text": [ "Rv2623" ], "offsets": [ [ 1222, 1228 ] ], "normalized": [] }, { "id": "PMC2682197-00-TIAB_T17", "type": "Chemical", "text": [ "ATP" ], "offsets": [ [ 1273, 1276 ] ], "normalized": [] }, { "id": "PMC2682197-00-TIAB_T18", "type": "Protein", "text": [ "Rv2623" ], "offsets": [ [ 1335, 1341 ] ], "normalized": [] }, { "id": "PMC2682197-00-TIAB_T19", "type": "Chemical", "text": [ "ATP" ], "offsets": [ [ 1350, 1353 ] ], "normalized": [] }, { "id": "PMC2682197-00-TIAB_T20", "type": "Protein", "text": [ "Rv2623" ], "offsets": [ [ 1429, 1435 ] ], "normalized": [] }, { "id": "PMC2682197-00-TIAB_T21", "type": "Chemical", "text": [ "ATP" ], "offsets": [ [ 1457, 1460 ] ], "normalized": [] }, { "id": "PMC2682197-00-TIAB_T22", "type": "Organism", "text": [ "mycobacteria" ], "offsets": [ [ 1491, 1503 ] ], "normalized": [] }, { "id": "PMC2682197-00-TIAB_T23", "type": "Protein", "text": [ "Rv2623" ], "offsets": [ [ 1590, 1596 ] ], "normalized": [] }, { "id": "PMC2682197-00-TIAB_T24", "type": "Chemical", "text": [ "ATP" ], "offsets": [ [ 1633, 1636 ] ], "normalized": [] }, { "id": "PMC2682197-00-TIAB_T25", "type": "Organism", "text": [ "M. tuberculosis" ], "offsets": [ [ 1677, 1692 ] ], "normalized": [] }, { "id": "PMC2682197-00-TIAB_T26", "type": "Protein", "text": [ "Rv2623" ], "offsets": [ [ 1693, 1699 ] ], "normalized": [] }, { "id": "PMC2682197-00-TIAB_T27", "type": "Protein", "text": [ "Rv2623" ], "offsets": [ [ 1761, 1767 ] ], "normalized": [] }, { "id": "PMC2682197-00-TIAB_T28", "type": "Organism", "text": [ "tubercle bacillus" ], "offsets": [ [ 1801, 1818 ] ], "normalized": [] }, { "id": "PMC2682197-00-TIAB_T29", "type": "Protein", "text": [ "Rv2623" ], "offsets": [ [ 1886, 1892 ] ], "normalized": [] }, { "id": "PMC2682197-00-TIAB_T30", "type": "Chemical", "text": [ "ATP" ], "offsets": [ [ 1899, 1902 ] ], "normalized": [] }, { "id": "PMC2682197-00-TIAB_T31", "type": "Chemical", "text": [ "ATP" ], "offsets": [ [ 1976, 1979 ] ], "normalized": [] }, { "id": "PMC2682197-00-TIAB_T32", "type": "Protein", "text": [ "Rv2623" ], "offsets": [ [ 2014, 2020 ] ], "normalized": [] }, { "id": "PMC2682197-00-TIAB_T33", "type": "Chemical", "text": [ "ATP" ], "offsets": [ [ 2040, 2043 ] ], "normalized": [] } ]

[ { "id": "PMC2682197-00-TIAB_E1", "type": "Binding", "trigger": { "text": [ "Binding" ], "offsets": [ [ 93, 100 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC2682197-00-TIAB_T2" }, { "role": "Theme", "ref_id": "PMC2682197-00-TIAB_T3" } ] }, { "id": "PMC2682197-00-TIAB_E2", "type": "Positive_regulation", "trigger": { "text": [ "induced" ], "offsets": [ [ 428, 435 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC2682197-00-TIAB_T5" } ] }, { "id": "PMC2682197-00-TIAB_E3", "type": "Positive_regulation", "trigger": { "text": [ "Induction" ], "offsets": [ [ 556, 565 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC2682197-00-TIAB_T7" } ] }, { "id": "PMC2682197-00-TIAB_E4", "type": "Process", "trigger": { "text": [ "infection" ], "offsets": [ [ 925, 934 ] ] }, "arguments": [ { "role": "Participant", "ref_id": "PMC2682197-00-TIAB_T11" } ] }, { "id": "PMC2682197-00-TIAB_E5", "type": "Gene_expression", "trigger": { "text": [ "overexpression" ], "offsets": [ [ 1122, 1136 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC2682197-00-TIAB_T15" } ] }, { "id": "PMC2682197-00-TIAB_E6", "type": "Binding", "trigger": { "text": [ "binds" ], "offsets": [ [ 1267, 1272 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC2682197-00-TIAB_T16" }, { "role": "Theme", "ref_id": "PMC2682197-00-TIAB_T17" } ] }, { "id": "PMC2682197-00-TIAB_E7", "type": "Binding", "trigger": { "text": [ "engages" ], "offsets": [ [ 1342, 1349 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC2682197-00-TIAB_T18" }, { "role": "Theme", "ref_id": "PMC2682197-00-TIAB_T19" } ] }, { "id": "PMC2682197-00-TIAB_E8", "type": "Binding", "trigger": { "text": [ "binding" ], "offsets": [ [ 1461, 1468 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC2682197-00-TIAB_T21" } ] }, { "id": "PMC2682197-00-TIAB_E9", "type": "Binding", "trigger": { "text": [ "bind" ], "offsets": [ [ 1628, 1632 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC2682197-00-TIAB_T23" }, { "role": "Theme", "ref_id": "PMC2682197-00-TIAB_T24" } ] }, { "id": "PMC2682197-00-TIAB_E10", "type": "Positive_regulation", "trigger": { "text": [ "required" ], "offsets": [ [ 1771, 1779 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC2682197-00-TIAB_E11" }, { "role": "Cause", "ref_id": "PMC2682197-00-TIAB_T27" } ] }, { "id": "PMC2682197-00-TIAB_E11", "type": "Process", "trigger": { "text": [ "infection" ], "offsets": [ [ 1845, 1854 ] ] }, "arguments": [ { "role": "Participant", "ref_id": "PMC2682197-00-TIAB_T28" } ] }, { "id": "PMC2682197-00-TIAB_E12", "type": "Binding", "trigger": { "text": [ "binds" ], "offsets": [ [ 1893, 1898 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC2682197-00-TIAB_T29" }, { "role": "Theme", "ref_id": "PMC2682197-00-TIAB_T30" } ] }, { "id": "PMC2682197-00-TIAB_E13", "type": "Positive_regulation", "trigger": { "text": [ "dependent" ], "offsets": [ [ 2044, 2053 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC2682197-00-TIAB_T32" }, { "role": "Cause", "ref_id": "PMC2682197-00-TIAB_T33" } ] } ]

[]

[]

[ { "id": "PMC1913099-01-Introduction__text", "type": "abstract", "text": [ "Introduction \nMicroarray technology is now commonly used to reveal genome-wide transcriptional changes in bacterial pathogens during interactions with the host. Several factors, however, limit the power of such analyses, including inadequate statistical analysis and insufficient sample replication, both of which do not account for experimental variability, and often result in arbitrary thresholds for significance [1,2]. In addition, unknown bacterial genes can confound the interpretation of expression profiles, restricting many microarray studies to the differential expression of well-characterized genes. Several methods are available to organize gene expression profiles and to assist in extracting functional or regulatory gene information from microarray datasets. Clustering algorithms group genes by similarities in expression patterns, based on the assumption that co-expressed genes share common function or regulation [3,4]; however, clustering solely by co-expression patterns may not reveal a considerable amount of information contained in array data. These methods often: (1) produce unreliable data by missing known gene members of biological pathways; (2) fail to distinguish truly related gene clusters from coincidental groupings; and (3) identify clusters containing only unknown genes that may lack either common function or regulation, a considerable limitation for genomes containing a large percentage of undefined genes [1,2]. Because no tools exist to interpret unknown gene clusters or to assess their significance and completeness, a significant portion of bacterial expression profiles are not interpretable using current clustering methods. We introduce neighbor clustering as a new tool for analyzing bacterial microarray data that addresses some of these limitations by incorporating the physical position of genes on the bacterial chromosome into the analysis of expression data. Information about gene function and regulation is stored intrinsically in the bacterial genome structure, as genes with common function or regulation tend to be physically proximate on the chromosome and often linked as operons [5,6]. We incorporated these positional data into a series of neighbor clustering algorithms, named GenomeCrawler, that identifies groupings of potentially related genes from array data by combining two informative characteristics of bacterial genes that share common function or regulation [3-6]: (1) similar gene expression profiles (i.e., co-expression); and (2) physical proximity of genes on the chromosome. The algorithms also recalculate the statistical significance of each gene as a member of a particular cluster, as well as the significance of each resulting grouping as a whole, to ensure accuracy of cluster assignments. This process ultimately identifies significant clusters of co-expressed gene neighbors that likely share common function or regulation. We used this approach to analyze microarray expression data from group A streptococci (Streptococcus pyogenes) during adherence to human pharyngeal cells, the first overt infection step [7]. The ability of all bacterial pathogens to infect the human host depends upon coordinated regulation of diverse gene sets that are required for survival in host environments. Although recent microarray studies have highlighted the molecular responses of streptococci in relevant host conditions [8-10], characterizing differentially expressed loci during pharyngeal cell adherence is critical for understanding the molecular basis for host colonization. Studies from our laboratory [11,12] and others [13] have demonstrated that in vitro association with pharyngeal cells results in streptococcal phage induction and the increased expression of phage-encoded virulence factors. Although the mechanisms mediating these responses are not known, the results of these studies indicate that streptococci sense and, on a transcriptional level, respond to various signals and cues in the pharyngeal cell environment. We undertook the present study to understand and to assess more accurately the genome-wide transcriptional responses of streptococci during one of the earliest recognized stages of infection, namely adherence to human pharyngeal cells. We compared data generated before and after neighbor clustering to show that this method provides a more comprehensive view of transcription by: (1) identifying more differentially expressed genes than even traditional, rigorous statistical analyses; (2) reconstructing intact biological pathways that statistical significance analysis could not reconstruct; and (3) providing preliminary insight and clues about the function or regulation of uncharacterized genes by associating their co-expression with physically proximate, functionally defined genes.\n" ], "offsets": [ [ 0, 4807 ] ] } ]

[ { "id": "PMC1913099-01-Introduction_T1", "type": "Organism", "text": [ "group A streptococci" ], "offsets": [ [ 2981, 3001 ] ], "normalized": [] }, { "id": "PMC1913099-01-Introduction_T2", "type": "Organism", "text": [ "Streptococcus pyogenes" ], "offsets": [ [ 3003, 3025 ] ], "normalized": [] }, { "id": "PMC1913099-01-Introduction_T3", "type": "Organism", "text": [ "human" ], "offsets": [ [ 3047, 3052 ] ], "normalized": [] }, { "id": "PMC1913099-01-Introduction_T4", "type": "Organism", "text": [ "human" ], "offsets": [ [ 3160, 3165 ] ], "normalized": [] }, { "id": "PMC1913099-01-Introduction_T5", "type": "Organism", "text": [ "streptococci" ], "offsets": [ [ 3360, 3372 ] ], "normalized": [] }, { "id": "PMC1913099-01-Introduction_T6", "type": "Organism", "text": [ "streptococci" ], "offsets": [ [ 3892, 3904 ] ], "normalized": [] }, { "id": "PMC1913099-01-Introduction_T7", "type": "Organism", "text": [ "streptococci" ], "offsets": [ [ 4136, 4148 ] ], "normalized": [] }, { "id": "PMC1913099-01-Introduction_T8", "type": "Organism", "text": [ "human" ], "offsets": [ [ 4228, 4233 ] ], "normalized": [] } ]

[ { "id": "PMC1913099-01-Introduction_E1", "type": "Process", "trigger": { "text": [ "infection" ], "offsets": [ [ 3087, 3096 ] ] }, "arguments": [] }, { "id": "PMC1913099-01-Introduction_E2", "type": "Process", "trigger": { "text": [ "infect" ], "offsets": [ [ 3149, 3155 ] ] }, "arguments": [] }, { "id": "PMC1913099-01-Introduction_E3", "type": "Process", "trigger": { "text": [ "virulence" ], "offsets": [ [ 3765, 3774 ] ] }, "arguments": [] }, { "id": "PMC1913099-01-Introduction_E4", "type": "Process", "trigger": { "text": [ "infection" ], "offsets": [ [ 4197, 4206 ] ] }, "arguments": [] } ]

[]

[]

[ { "id": "PMC2266911-02-Results_and_Discussion-01-04__text", "type": "abstract", "text": [ "Regulation via c-di-GMP as a second messenger \nCyclic diguanylate (c-di-GMP) is a bacterial second messenger that activates biofilm formation while inhibiting motility, thus regulating the switch between a planktonic and a sessile lifestyle. In addition to phenotypes that affect virulence properties indirectly, c-di-GMP can also directly regulate virulence factors [56,57]. Proteins containing a so-called GGDEF domain are responsible for the synthesis of c-di-GMP, and those with a so-called EAL domain for its degradation. The expression and activity of those GGDEF and EAL domain containing proteins is regulated by factors with a PilZ domain that binds c-di-GMP. The PilZ domain is found as a stand-alone domain or in combination with GGDEF, EAL and other domains, thus assumed to function also as an allosteric domain to control other regulatory enzymes [58,59]. In Y. enterocolitica, we identified 22 putative proteins containing GGDEF and EAL domains. Eleven of these proteins solely contain a GGDEF-domain and six solely an EAL-domain, and both domains are found in tandem in five proteins. The protein AdrA (YE3010, GGDEF domain) is annotated as a putative diguanylate cyclase, YE2278 (GGDEF+EAL) as a putative phosphodiesterase, YE3818 (GGDEF) as a putative regulator, and YE3806 (GGDEF+EAL) as a putative exported protein. All other GGDEF and EAL domain-containing proteins are of unknown function. Furthermore, two proteins with PilZ domain exist in Y. enterocolitica, namely YE3197 and BcsA (YE4074), a putative cellulose synthase. Cellulose synthesis in bacteria has been identified to be important for the protection from chemical or mechanical stress by forming a hydrophobic extracellular matrix [60]. The expression of two of those EAL-domain containing proteins, YE4063 and YE1324, is induced at low temperature (Tab. 1). These two factors might therefore be important for insect colonization instead for virulence against mammals. The presence of c-di-GMP mediated regulation in Y. enterocolitica is therefore suggested to play a central role in switching from biofilm formation to the human as well as to the insect environment. P. luminescens contains no protein with GGDEF, EAL or PilZ domain. This phenomenon is quite surprising, because with few exceptions such as Helicobacter pylori, nearly all pathogenic bacteria use c-di-GMP as a second messenger. It has been reported that P. luminescens forms biofilms in vitro, and that a luxS-deficient mutant unable to synthesize the quorum-sensing inducer AI-2 showed a decreased biofilm formation [42]. The lack of these protein domains in P. luminescens reveals that c-di-GMP signalling plays a major role in pathogenic bacteria when colonizing a mammalian host, and a minor for invertebrate colonization of entomopathogenic or entomoinfecting bacteria.\n" ], "offsets": [ [ 0, 2827 ] ] } ]

[ { "id": "PMC2266911-02-Results_and_Discussion-01-04_T1", "type": "Chemical", "text": [ "c-di-GMP" ], "offsets": [ [ 15, 23 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-01-04_T2", "type": "Chemical", "text": [ "Cyclic diguanylate" ], "offsets": [ [ 47, 65 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-01-04_T3", "type": "Chemical", "text": [ "c-di-GMP" ], "offsets": [ [ 67, 75 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-01-04_T4", "type": "Chemical", "text": [ "c-di-GMP" ], "offsets": [ [ 313, 321 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-01-04_T5", "type": "Protein", "text": [ "GGDEF" ], "offsets": [ [ 408, 413 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-01-04_T6", "type": "Chemical", "text": [ "c-di-GMP" ], "offsets": [ [ 458, 466 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-01-04_T7", "type": "Protein", "text": [ "EAL" ], "offsets": [ [ 495, 498 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-01-04_T8", "type": "Protein", "text": [ "GGDEF" ], "offsets": [ [ 564, 569 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-01-04_T9", "type": "Protein", "text": [ "EAL" ], "offsets": [ [ 574, 577 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-01-04_T10", "type": "Protein", "text": [ "PilZ" ], "offsets": [ [ 636, 640 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-01-04_T11", "type": "Chemical", "text": [ "c-di-GMP" ], "offsets": [ [ 659, 667 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-01-04_T12", "type": "Protein", "text": [ "PilZ" ], "offsets": [ [ 673, 677 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-01-04_T13", "type": "Protein", "text": [ "GGDEF" ], "offsets": [ [ 741, 746 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-01-04_T14", "type": "Protein", "text": [ "EAL" ], "offsets": [ [ 748, 751 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-01-04_T15", "type": "Organism", "text": [ "Y. enterocolitica" ], "offsets": [ [ 873, 890 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-01-04_T16", "type": "Protein", "text": [ "GGDEF" ], "offsets": [ [ 938, 943 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-01-04_T17", "type": "Protein", "text": [ "EAL" ], "offsets": [ [ 948, 951 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-01-04_T18", "type": "Protein", "text": [ "GGDEF" ], "offsets": [ [ 1003, 1008 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-01-04_T19", "type": "Protein", "text": [ "EAL" ], "offsets": [ [ 1034, 1037 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-01-04_T20", "type": "Protein", "text": [ "AdrA" ], "offsets": [ [ 1113, 1117 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-01-04_T21", "type": "Protein", "text": [ "YE3010" ], "offsets": [ [ 1119, 1125 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-01-04_T22", "type": "Protein", "text": [ "GGDEF" ], "offsets": [ [ 1127, 1132 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-01-04_T23", "type": "Chemical", "text": [ "diguanylate" ], "offsets": [ [ 1168, 1179 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-01-04_T24", "type": "Protein", "text": [ "YE2278" ], "offsets": [ [ 1189, 1195 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-01-04_T25", "type": "Protein", "text": [ "GGDEF" ], "offsets": [ [ 1197, 1202 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-01-04_T26", "type": "Protein", "text": [ "EAL" ], "offsets": [ [ 1203, 1206 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-01-04_T27", "type": "Protein", "text": [ "YE3818" ], "offsets": [ [ 1241, 1247 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-01-04_T28", "type": "Protein", "text": [ "GGDEF" ], "offsets": [ [ 1249, 1254 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-01-04_T29", "type": "Protein", "text": [ "YE3806" ], "offsets": [ [ 1285, 1291 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-01-04_T30", "type": "Protein", "text": [ "GGDEF" ], "offsets": [ [ 1293, 1298 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-01-04_T31", "type": "Protein", "text": [ "EAL" ], "offsets": [ [ 1299, 1302 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-01-04_T32", "type": "Protein", "text": [ "GGDEF" ], "offsets": [ [ 1346, 1351 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-01-04_T33", "type": "Protein", "text": [ "EAL" ], "offsets": [ [ 1356, 1359 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-01-04_T34", "type": "Protein", "text": [ "PilZ" ], "offsets": [ [ 1443, 1447 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-01-04_T35", "type": "Organism", "text": [ "Y. enterocolitica" ], "offsets": [ [ 1464, 1481 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-01-04_T36", "type": "Protein", "text": [ "YE3197" ], "offsets": [ [ 1490, 1496 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-01-04_T37", "type": "Protein", "text": [ "BcsA" ], "offsets": [ [ 1501, 1505 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-01-04_T38", "type": "Protein", "text": [ "YE4074" ], "offsets": [ [ 1507, 1513 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-01-04_T39", "type": "Protein", "text": [ "EAL" ], "offsets": [ [ 1752, 1755 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-01-04_T40", "type": "Protein", "text": [ "YE4063" ], "offsets": [ [ 1784, 1790 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-01-04_T41", "type": "Protein", "text": [ "YE1324" ], "offsets": [ [ 1795, 1801 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-01-04_T42", "type": "Chemical", "text": [ "c-di-GMP" ], "offsets": [ [ 1969, 1977 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-01-04_T43", "type": "Organism", "text": [ "Y. enterocolitica" ], "offsets": [ [ 2001, 2018 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-01-04_T44", "type": "Organism", "text": [ "human" ], "offsets": [ [ 2108, 2113 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-01-04_T45", "type": "Organism", "text": [ "P. luminescens" ], "offsets": [ [ 2152, 2166 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-01-04_T46", "type": "Protein", "text": [ "GGDEF" ], "offsets": [ [ 2192, 2197 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-01-04_T47", "type": "Protein", "text": [ "EAL" ], "offsets": [ [ 2199, 2202 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-01-04_T48", "type": "Protein", "text": [ "PilZ" ], "offsets": [ [ 2206, 2210 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-01-04_T49", "type": "Organism", "text": [ "Helicobacter pylori" ], "offsets": [ [ 2292, 2311 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-01-04_T50", "type": "Chemical", "text": [ "c-di-GMP" ], "offsets": [ [ 2348, 2356 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-01-04_T51", "type": "Organism", "text": [ "P. luminescens" ], "offsets": [ [ 2406, 2420 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-01-04_T52", "type": "Organism", "text": [ "luxS-deficient mutant" ], "offsets": [ [ 2457, 2478 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-01-04_T53", "type": "Protein", "text": [ "luxS" ], "offsets": [ [ 2457, 2461 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-01-04_T54", "type": "Protein", "text": [ "AI-2" ], "offsets": [ [ 2527, 2531 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-01-04_T55", "type": "Organism", "text": [ "P. luminescens" ], "offsets": [ [ 2612, 2626 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-01-04_T56", "type": "Chemical", "text": [ "c-di-GMP" ], "offsets": [ [ 2640, 2648 ] ], "normalized": [] } ]

[ { "id": "PMC2266911-02-Results_and_Discussion-01-04_E1", "type": "Regulation", "trigger": { "text": [ "affect" ], "offsets": [ [ 273, 279 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC2266911-02-Results_and_Discussion-01-04_E2" } ] }, { "id": "PMC2266911-02-Results_and_Discussion-01-04_E2", "type": "Process", "trigger": { "text": [ "virulence" ], "offsets": [ [ 280, 289 ] ] }, "arguments": [] }, { "id": "PMC2266911-02-Results_and_Discussion-01-04_E3", "type": "Process", "trigger": { "text": [ "virulence" ], "offsets": [ [ 349, 358 ] ] }, "arguments": [] }, { "id": "PMC2266911-02-Results_and_Discussion-01-04_E4", "type": "Gene_expression", "trigger": { "text": [ "expression" ], "offsets": [ [ 1725, 1735 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC2266911-02-Results_and_Discussion-01-04_T40" } ] }, { "id": "PMC2266911-02-Results_and_Discussion-01-04_E5", "type": "Gene_expression", "trigger": { "text": [ "expression" ], "offsets": [ [ 1725, 1735 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC2266911-02-Results_and_Discussion-01-04_T41" } ] }, { "id": "PMC2266911-02-Results_and_Discussion-01-04_E6", "type": "Positive_regulation", "trigger": { "text": [ "induced" ], "offsets": [ [ 1806, 1813 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC2266911-02-Results_and_Discussion-01-04_E4" } ] }, { "id": "PMC2266911-02-Results_and_Discussion-01-04_E7", "type": "Positive_regulation", "trigger": { "text": [ "induced" ], "offsets": [ [ 1806, 1813 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC2266911-02-Results_and_Discussion-01-04_E5" } ] }, { "id": "PMC2266911-02-Results_and_Discussion-01-04_E8", "type": "Process", "trigger": { "text": [ "virulence" ], "offsets": [ [ 1926, 1935 ] ] }, "arguments": [] }, { "id": "PMC2266911-02-Results_and_Discussion-01-04_E9", "type": "Gene_expression", "trigger": { "text": [ "synthesize" ], "offsets": [ [ 2489, 2499 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC2266911-02-Results_and_Discussion-01-04_T54" } ] } ]

[ { "id": "PMC2266911-02-Results_and_Discussion-01-04_1", "entity_ids": [ "PMC2266911-02-Results_and_Discussion-01-04_T2", "PMC2266911-02-Results_and_Discussion-01-04_T3" ] }, { "id": "PMC2266911-02-Results_and_Discussion-01-04_2", "entity_ids": [ "PMC2266911-02-Results_and_Discussion-01-04_T20", "PMC2266911-02-Results_and_Discussion-01-04_T21" ] }, { "id": "PMC2266911-02-Results_and_Discussion-01-04_3", "entity_ids": [ "PMC2266911-02-Results_and_Discussion-01-04_T37", "PMC2266911-02-Results_and_Discussion-01-04_T38" ] } ]

[]

[ { "id": "PMC2829055-00-TIAB__text", "type": "abstract", "text": [ "Transit through the Flea Vector Induces a Pretransmission Innate Immunity Resistance Phenotype in Yersinia pestis \nYersinia pestis, the agent of plague, is transmitted to mammals by infected fleas. Y. pestis exhibits a distinct life stage in the flea, where it grows in the form of a cohesive biofilm that promotes transmission. After transmission, the temperature shift to 37degreesC induces many known virulence factors of Y. pestis that confer resistance to innate immunity. These factors are not produced in the low-temperature environment of the flea, however, suggesting that Y. pestis is vulnerable to the initial encounter with innate immune cells at the flea bite site. In this study, we used whole-genome microarrays to compare the Y. pestis in vivo transcriptome in infective fleas to in vitro transcriptomes in temperature-matched biofilm and planktonic cultures, and to the previously characterized in vivo gene expression profile in the rat bubo. In addition to genes involved in metabolic adaptation to the flea gut and biofilm formation, several genes with known or predicted roles in resistance to innate immunity and pathogenicity in the mammal were upregulated in the flea. Y. pestis from infected fleas were more resistant to phagocytosis by macrophages than in vitro-grown bacteria, in part attributable to a cluster of insecticidal-like toxin genes that were highly expressed only in the flea. Our results suggest that transit through the flea vector induces a phenotype that enhances survival and dissemination of Y. pestis after transmission to the mammalian host.\n" ], "offsets": [ [ 0, 1589 ] ] } ]

[ { "id": "PMC2829055-00-TIAB_T1", "type": "Organism", "text": [ "Flea" ], "offsets": [ [ 20, 24 ] ], "normalized": [] }, { "id": "PMC2829055-00-TIAB_T2", "type": "Organism", "text": [ "Yersinia pestis" ], "offsets": [ [ 98, 113 ] ], "normalized": [] }, { "id": "PMC2829055-00-TIAB_T3", "type": "Organism", "text": [ "Yersinia pestis" ], "offsets": [ [ 115, 130 ] ], "normalized": [] }, { "id": "PMC2829055-00-TIAB_T4", "type": "Organism", "text": [ "fleas" ], "offsets": [ [ 191, 196 ] ], "normalized": [] }, { "id": "PMC2829055-00-TIAB_T5", "type": "Organism", "text": [ "Y. pestis" ], "offsets": [ [ 198, 207 ] ], "normalized": [] }, { "id": "PMC2829055-00-TIAB_T6", "type": "Organism", "text": [ "flea" ], "offsets": [ [ 246, 250 ] ], "normalized": [] }, { "id": "PMC2829055-00-TIAB_T7", "type": "Organism", "text": [ "Y. pestis" ], "offsets": [ [ 425, 434 ] ], "normalized": [] }, { "id": "PMC2829055-00-TIAB_T8", "type": "Organism", "text": [ "flea" ], "offsets": [ [ 551, 555 ] ], "normalized": [] }, { "id": "PMC2829055-00-TIAB_T9", "type": "Organism", "text": [ "Y. pestis" ], "offsets": [ [ 582, 591 ] ], "normalized": [] }, { "id": "PMC2829055-00-TIAB_T10", "type": "Organism", "text": [ "flea" ], "offsets": [ [ 663, 667 ] ], "normalized": [] }, { "id": "PMC2829055-00-TIAB_T11", "type": "Organism", "text": [ "Y. pestis" ], "offsets": [ [ 742, 751 ] ], "normalized": [] }, { "id": "PMC2829055-00-TIAB_T12", "type": "Organism", "text": [ "fleas" ], "offsets": [ [ 787, 792 ] ], "normalized": [] }, { "id": "PMC2829055-00-TIAB_T13", "type": "Organism", "text": [ "rat" ], "offsets": [ [ 951, 954 ] ], "normalized": [] }, { "id": "PMC2829055-00-TIAB_T14", "type": "Organism", "text": [ "flea" ], "offsets": [ [ 1022, 1026 ] ], "normalized": [] }, { "id": "PMC2829055-00-TIAB_T15", "type": "Organism", "text": [ "flea" ], "offsets": [ [ 1187, 1191 ] ], "normalized": [] }, { "id": "PMC2829055-00-TIAB_T16", "type": "Organism", "text": [ "Y. pestis" ], "offsets": [ [ 1193, 1202 ] ], "normalized": [] }, { "id": "PMC2829055-00-TIAB_T17", "type": "Organism", "text": [ "fleas" ], "offsets": [ [ 1217, 1222 ] ], "normalized": [] }, { "id": "PMC2829055-00-TIAB_T18", "type": "Organism", "text": [ "flea" ], "offsets": [ [ 1410, 1414 ] ], "normalized": [] }, { "id": "PMC2829055-00-TIAB_T19", "type": "Organism", "text": [ "flea" ], "offsets": [ [ 1461, 1465 ] ], "normalized": [] }, { "id": "PMC2829055-00-TIAB_T20", "type": "Organism", "text": [ "Y. pestis" ], "offsets": [ [ 1537, 1546 ] ], "normalized": [] }, { "id": "PMC2829055-00-TIAB_T21", "type": "Organism", "text": [ "host" ], "offsets": [ [ 1583, 1587 ] ], "normalized": [] } ]

[ { "id": "PMC2829055-00-TIAB_E1", "type": "Process", "trigger": { "text": [ "Resistance" ], "offsets": [ [ 74, 84 ] ] }, "arguments": [ { "role": "Participant", "ref_id": "PMC2829055-00-TIAB_T2" } ] }, { "id": "PMC2829055-00-TIAB_E2", "type": "Process", "trigger": { "text": [ "infected" ], "offsets": [ [ 182, 190 ] ] }, "arguments": [ { "role": "Participant", "ref_id": "PMC2829055-00-TIAB_T3" } ] }, { "id": "PMC2829055-00-TIAB_E3", "type": "Process", "trigger": { "text": [ "virulence" ], "offsets": [ [ 404, 413 ] ] }, "arguments": [ { "role": "Participant", "ref_id": "PMC2829055-00-TIAB_T7" } ] }, { "id": "PMC2829055-00-TIAB_E4", "type": "Process", "trigger": { "text": [ "resistance" ], "offsets": [ [ 447, 457 ] ] }, "arguments": [] }, { "id": "PMC2829055-00-TIAB_E5", "type": "Process", "trigger": { "text": [ "infective" ], "offsets": [ [ 777, 786 ] ] }, "arguments": [ { "role": "Participant", "ref_id": "PMC2829055-00-TIAB_T12" } ] }, { "id": "PMC2829055-00-TIAB_E6", "type": "Process", "trigger": { "text": [ "resistance" ], "offsets": [ [ 1101, 1111 ] ] }, "arguments": [] }, { "id": "PMC2829055-00-TIAB_E7", "type": "Process", "trigger": { "text": [ "infected" ], "offsets": [ [ 1208, 1216 ] ] }, "arguments": [ { "role": "Participant", "ref_id": "PMC2829055-00-TIAB_T16" } ] }, { "id": "PMC2829055-00-TIAB_E8", "type": "Process", "trigger": { "text": [ "resistant" ], "offsets": [ [ 1233, 1242 ] ] }, "arguments": [ { "role": "Participant", "ref_id": "PMC2829055-00-TIAB_T17" } ] } ]

[]

[]

[ { "id": "PMC2242835-02-Results-04__text", "type": "abstract", "text": [ "Virulence Studies of H37Ra Complemented Mutants in a Mouse Model \nFurther assessment of the in vivo growth of different H37Ra knock-in strains was carried out by intravenous infection of severe combined immuno-deficient (SCID) mice. Complementation of H37Ra with the PhoP-expressing cosmid increased the virulence of the H37Ra::phoP recombinant relative to H37Ra, resulting in a 1.0 log and 0.5 log increase in CFU number in lungs and spleens, respectively. In contrast, no effects on the virulence were observed when H37Ra was complemented with fadE5 (Figure 2) or rpsL (unpublished data). However, as already observed in macrophages, integration of phoP did not restore levels of virulence to those of the reference strain H37Rv (Figure 2). This situation is also reflected in the sizes of spleens, which correlate with the CFU data in spleens (Figure S4). Together with the data from the macrophage infection assay, the results from the mouse infection show that the S219L mutation in the phoP gene definitely represents one genetic lesion that contributed to the attenuation of the H37Ra strain.\n" ], "offsets": [ [ 0, 1100 ] ] } ]

[ { "id": "PMC2242835-02-Results-04_T1", "type": "Organism", "text": [ "H37Ra" ], "offsets": [ [ 21, 26 ] ], "normalized": [] }, { "id": "PMC2242835-02-Results-04_T2", "type": "Organism", "text": [ "Mouse" ], "offsets": [ [ 53, 58 ] ], "normalized": [] }, { "id": "PMC2242835-02-Results-04_T3", "type": "Organism", "text": [ "H37Ra" ], "offsets": [ [ 120, 125 ] ], "normalized": [] }, { "id": "PMC2242835-02-Results-04_T4", "type": "Organism", "text": [ "severe combined immuno-deficient (SCID) mice" ], "offsets": [ [ 187, 231 ] ], "normalized": [] }, { "id": "PMC2242835-02-Results-04_T5", "type": "Organism", "text": [ "H37Ra" ], "offsets": [ [ 252, 257 ] ], "normalized": [] }, { "id": "PMC2242835-02-Results-04_T6", "type": "Protein", "text": [ "PhoP" ], "offsets": [ [ 267, 271 ] ], "normalized": [] }, { "id": "PMC2242835-02-Results-04_T7", "type": "Organism", "text": [ "H37Ra::phoP" ], "offsets": [ [ 321, 332 ] ], "normalized": [] }, { "id": "PMC2242835-02-Results-04_T8", "type": "Protein", "text": [ "phoP" ], "offsets": [ [ 328, 332 ] ], "normalized": [] }, { "id": "PMC2242835-02-Results-04_T9", "type": "Organism", "text": [ "H37Ra" ], "offsets": [ [ 357, 362 ] ], "normalized": [] }, { "id": "PMC2242835-02-Results-04_T10", "type": "Organism", "text": [ "H37Ra" ], "offsets": [ [ 518, 523 ] ], "normalized": [] }, { "id": "PMC2242835-02-Results-04_T11", "type": "Protein", "text": [ "fadE5" ], "offsets": [ [ 546, 551 ] ], "normalized": [] }, { "id": "PMC2242835-02-Results-04_T12", "type": "Protein", "text": [ "rpsL" ], "offsets": [ [ 566, 570 ] ], "normalized": [] }, { "id": "PMC2242835-02-Results-04_T13", "type": "Protein", "text": [ "phoP" ], "offsets": [ [ 651, 655 ] ], "normalized": [] }, { "id": "PMC2242835-02-Results-04_T14", "type": "Organism", "text": [ "H37Rv" ], "offsets": [ [ 725, 730 ] ], "normalized": [] }, { "id": "PMC2242835-02-Results-04_T15", "type": "Organism", "text": [ "mouse" ], "offsets": [ [ 940, 945 ] ], "normalized": [] }, { "id": "PMC2242835-02-Results-04_T16", "type": "Protein", "text": [ "phoP" ], "offsets": [ [ 992, 996 ] ], "normalized": [] }, { "id": "PMC2242835-02-Results-04_T17", "type": "Organism", "text": [ "H37Ra" ], "offsets": [ [ 1086, 1091 ] ], "normalized": [] } ]

[ { "id": "PMC2242835-02-Results-04_E1", "type": "Process", "trigger": { "text": [ "Virulence" ], "offsets": [ [ 0, 9 ] ] }, "arguments": [ { "role": "Participant", "ref_id": "PMC2242835-02-Results-04_T1" } ] }, { "id": "PMC2242835-02-Results-04_E2", "type": "Process", "trigger": { "text": [ "infection" ], "offsets": [ [ 174, 183 ] ] }, "arguments": [ { "role": "Participant", "ref_id": "PMC2242835-02-Results-04_T3" } ] }, { "id": "PMC2242835-02-Results-04_E3", "type": "Positive_regulation", "trigger": { "text": [ "increased" ], "offsets": [ [ 290, 299 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC2242835-02-Results-04_E5" } ] }, { "id": "PMC2242835-02-Results-04_E4", "type": "Process", "trigger": { "text": [ "virulence" ], "offsets": [ [ 304, 313 ] ] }, "arguments": [ { "role": "Participant", "ref_id": "PMC2242835-02-Results-04_T9" } ] }, { "id": "PMC2242835-02-Results-04_E5", "type": "Process", "trigger": { "text": [ "virulence" ], "offsets": [ [ 304, 313 ] ] }, "arguments": [ { "role": "Participant", "ref_id": "PMC2242835-02-Results-04_T7" } ] }, { "id": "PMC2242835-02-Results-04_E6", "type": "Regulation", "trigger": { "text": [ "effects" ], "offsets": [ [ 474, 481 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC2242835-02-Results-04_E7" } ] }, { "id": "PMC2242835-02-Results-04_E7", "type": "Process", "trigger": { "text": [ "virulence" ], "offsets": [ [ 489, 498 ] ] }, "arguments": [ { "role": "Participant", "ref_id": "PMC2242835-02-Results-04_T10" } ] }, { "id": "PMC2242835-02-Results-04_E8", "type": "Positive_regulation", "trigger": { "text": [ "restore" ], "offsets": [ [ 664, 671 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC2242835-02-Results-04_E10" } ] }, { "id": "PMC2242835-02-Results-04_E9", "type": "Process", "trigger": { "text": [ "virulence" ], "offsets": [ [ 682, 691 ] ] }, "arguments": [ { "role": "Participant", "ref_id": "PMC2242835-02-Results-04_T14" } ] }, { "id": "PMC2242835-02-Results-04_E10", "type": "Process", "trigger": { "text": [ "virulence" ], "offsets": [ [ 682, 691 ] ] }, "arguments": [ { "role": "Participant", "ref_id": "PMC2242835-02-Results-04_T10" } ] }, { "id": "PMC2242835-02-Results-04_E11", "type": "Process", "trigger": { "text": [ "infection" ], "offsets": [ [ 902, 911 ] ] }, "arguments": [] }, { "id": "PMC2242835-02-Results-04_E12", "type": "Process", "trigger": { "text": [ "infection" ], "offsets": [ [ 946, 955 ] ] }, "arguments": [ { "role": "Participant", "ref_id": "PMC2242835-02-Results-04_T17" } ] } ]

[]

[]

[ { "id": "PMC2266911-02-Results_and_Discussion-02-01-01__text", "type": "abstract", "text": [ "Virulence factors \nSo-called offensive virulence factors actively contribute to a successful infection by colonization of and toxicity towards the host organism. We compared both genomes with respect to genes encoding toxins, adhesins or invasines that are common to both pathogens. All virulence factors described in the following are summarized in Fig. 4. Toxins Insecticidal toxins The insecticidal toxin complex (Tc) proteins were first purified from P. luminescens [61]. Tc homologues have also been described to be present in Yersinia spp. and in other insect-associated bacteria such as Serratia entomophila and Xenorhabdus nematophilus [62,63]. The respective genes encoding four high molecular weight toxin complexes are termed tca, tcb, tcc and tcd. Further experiments supported the hypothesis that TccC-like proteins might act as universal activators of, or chaperons for, different toxin proteins, while Tca-like and Tcd-like proteins contribute predominantly to the oral toxicity of bacterial supernatants [17]. It is speculated that the Tc toxins are active against different tissues within individual hosts, namely Tcb against hemocytes and Tcd and Tca against cells of the insect gut. In Y. enterocolitica, the insecticidal toxin genes are located on a distinct genomic island termed tc-PAIYe of 21 kb, and are low-temperature induced [7]. Similar islands in which regulatory genes are followed by three tca genes, phage-related genes and one or two tccC genes, are present in the genomes of Y. pseudotuberculosis IP32953 and Y. pestis KIM. In P. luminescens, the insecticidal genes are organized in the tcd island harbouring nine tcd- and tcc-like genes and several non tc-like genes, while further nine tcc-like genes are scattered over the chromosome [24]. The reason for the over-represence of tc-like genes in the P. luminescens genome might reflect the different strategies followed by both bacteria within insects, namely the rapid killing for exploiting the victim as a food source in case of P. luminescens, and infection of and persistance within the invertebrate host as possibly preferred by Y. enterocolitica.\n" ], "offsets": [ [ 0, 2140 ] ] } ]

[ { "id": "PMC2266911-02-Results_and_Discussion-02-01-01_T1", "type": "Organism", "text": [ "P. luminescens" ], "offsets": [ [ 455, 469 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-02-01-01_T2", "type": "Organism", "text": [ "Yersinia" ], "offsets": [ [ 532, 540 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-02-01-01_T3", "type": "Organism", "text": [ "Serratia entomophila" ], "offsets": [ [ 594, 614 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-02-01-01_T4", "type": "Organism", "text": [ "Xenorhabdus nematophilus" ], "offsets": [ [ 619, 643 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-02-01-01_T5", "type": "Protein", "text": [ "TccC" ], "offsets": [ [ 810, 814 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-02-01-01_T6", "type": "Organism", "text": [ "Y. enterocolitica" ], "offsets": [ [ 1205, 1222 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-02-01-01_T7", "type": "Protein", "text": [ "tccC" ], "offsets": [ [ 1467, 1471 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-02-01-01_T8", "type": "Organism", "text": [ "Y. pseudotuberculosis IP32953" ], "offsets": [ [ 1509, 1538 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-02-01-01_T9", "type": "Organism", "text": [ "Y. pestis KIM" ], "offsets": [ [ 1543, 1556 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-02-01-01_T10", "type": "Organism", "text": [ "P. luminescens" ], "offsets": [ [ 1561, 1575 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-02-01-01_T11", "type": "Organism", "text": [ "P. luminescens" ], "offsets": [ [ 1836, 1850 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-02-01-01_T12", "type": "Organism", "text": [ "P. luminescens" ], "offsets": [ [ 2018, 2032 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-02-01-01_T13", "type": "Organism", "text": [ "Y. enterocolitica" ], "offsets": [ [ 2121, 2138 ] ], "normalized": [] } ]

[ { "id": "PMC2266911-02-Results_and_Discussion-02-01-01_E1", "type": "Process", "trigger": { "text": [ "Virulence" ], "offsets": [ [ 0, 9 ] ] }, "arguments": [] }, { "id": "PMC2266911-02-Results_and_Discussion-02-01-01_E2", "type": "Process", "trigger": { "text": [ "virulence" ], "offsets": [ [ 39, 48 ] ] }, "arguments": [] }, { "id": "PMC2266911-02-Results_and_Discussion-02-01-01_E3", "type": "Process", "trigger": { "text": [ "infection" ], "offsets": [ [ 93, 102 ] ] }, "arguments": [] }, { "id": "PMC2266911-02-Results_and_Discussion-02-01-01_E4", "type": "Process", "trigger": { "text": [ "virulence" ], "offsets": [ [ 287, 296 ] ] }, "arguments": [] }, { "id": "PMC2266911-02-Results_and_Discussion-02-01-01_E5", "type": "Process", "trigger": { "text": [ "infection" ], "offsets": [ [ 2038, 2047 ] ] }, "arguments": [ { "role": "Participant", "ref_id": "PMC2266911-02-Results_and_Discussion-02-01-01_T13" } ] } ]

[]

[]

[ { "id": "PMC2266911-02-Results_and_Discussion-01-02-01__text", "type": "abstract", "text": [ "Quorum sensing-like gene regulation \nRegulation by AHL-LuxR-like receptors Virulence, bioluminescence, mutualism, antibiotic production and biofilm formation are often regulated by LuxI/LuxR quorum sensing systems in Gram-negative bacteria. They produce membrane diffusible signalling molecules, acyl homoserine lactones (AHLs), which are sensed by the receptor/regulator LuxR when exceeding a threshold concentration. These AHLs are produced by an autoinductor synthase named LuxI. Upon autoinductor-binding, the receptor LuxR binds to the promoter/operator regions of the target genes or operons, resulting in the regulation of gene expression in response to the cell number [33]. Y. enterocolitica possesses a typical quorum sensing pair of homologues, YenI/YenR (YE1600/YE1599), and it has recently been shown that swimming and swarming motility is regulated by 3-oxo-C6-AHL and C6-AHL, which are synthesized by YenI [34]. In Y. pestis, the production of YspI and YspR, the homologues of YenI and YenR, is induced at 26degreesC (Table 1). Moreover, we identified a second AHL-LuxR regulator, YE1026, which lacks a separate AHL synthase (Fig. 3). It is not known if this receptor also binds the AHLs produced by YenI. In the genome of P. luminescens, two genes encoding putative AHL-LuxR-like receptors, plu0320 and plu4562, but no luxI genes are present (Fig. 3). This suggests that P. luminescens does not produce its own AHL signalling molecule, but might be able to sense those produced by other bacteria and therefore to detect mixed microbial communities as demonstrated for Salmonella enterica and Escherichia coli [35-37]. A similar function in Y. enterocolitica might be provided by YE1026. It is interesting to note that Sodalis glossinidius strain morsitans, an endosymbiont of the tse tse fly Glossina morsitans morsitans [38], also has two pontential AHL-LuxR receptors, SG1740 and SG0285, but no luxI homologue (Fig. 3). Instead of producing AHLs to regulate quorum dependent genes, a common strategy of insect-colonizing bacteria might be the detection of AHLs as a signal for the presence of other bacteria such as those colonizing the insect intestinal tract or living in soil.\n" ], "offsets": [ [ 0, 2198 ] ] } ]

[ { "id": "PMC2266911-02-Results_and_Discussion-01-02-01_T1", "type": "Chemical", "text": [ "AHL" ], "offsets": [ [ 51, 54 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-01-02-01_T2", "type": "Protein", "text": [ "LuxR" ], "offsets": [ [ 55, 59 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-01-02-01_T3", "type": "Two-component-system", "text": [ "LuxI/LuxR" ], "offsets": [ [ 181, 190 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-01-02-01_T4", "type": "Protein", "text": [ "LuxI" ], "offsets": [ [ 181, 185 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-01-02-01_T5", "type": "Protein", "text": [ "LuxR" ], "offsets": [ [ 186, 190 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-01-02-01_T6", "type": "Chemical", "text": [ "acyl homoserine lactones" ], "offsets": [ [ 296, 320 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-01-02-01_T7", "type": "Chemical", "text": [ "AHLs" ], "offsets": [ [ 322, 326 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-01-02-01_T8", "type": "Protein", "text": [ "LuxR" ], "offsets": [ [ 372, 376 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-01-02-01_T9", "type": "Chemical", "text": [ "AHLs" ], "offsets": [ [ 425, 429 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-01-02-01_T10", "type": "Protein", "text": [ "LuxI" ], "offsets": [ [ 477, 481 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-01-02-01_T11", "type": "Protein", "text": [ "LuxR" ], "offsets": [ [ 523, 527 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-01-02-01_T12", "type": "Organism", "text": [ "Y. enterocolitica" ], "offsets": [ [ 683, 700 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-01-02-01_T13", "type": "Two-component-system", "text": [ "YenI/YenR" ], "offsets": [ [ 756, 765 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-01-02-01_T14", "type": "Protein", "text": [ "YenI" ], "offsets": [ [ 756, 760 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-01-02-01_T15", "type": "Protein", "text": [ "YenR" ], "offsets": [ [ 761, 765 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-01-02-01_T16", "type": "Two-component-system", "text": [ "YE1600/YE1599" ], "offsets": [ [ 767, 780 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-01-02-01_T17", "type": "Protein", "text": [ "YE1600" ], "offsets": [ [ 767, 773 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-01-02-01_T18", "type": "Protein", "text": [ "YE1599" ], "offsets": [ [ 774, 780 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-01-02-01_T19", "type": "Chemical", "text": [ "3-oxo-C6-AHL" ], "offsets": [ [ 866, 878 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-01-02-01_T20", "type": "Chemical", "text": [ "C6-AHL" ], "offsets": [ [ 883, 889 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-01-02-01_T21", "type": "Protein", "text": [ "YenI" ], "offsets": [ [ 916, 920 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-01-02-01_T22", "type": "Organism", "text": [ "Y. pestis" ], "offsets": [ [ 930, 939 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-01-02-01_T23", "type": "Protein", "text": [ "YspI" ], "offsets": [ [ 959, 963 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-01-02-01_T24", "type": "Protein", "text": [ "YspR" ], "offsets": [ [ 968, 972 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-01-02-01_T25", "type": "Protein", "text": [ "YenI" ], "offsets": [ [ 992, 996 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-01-02-01_T26", "type": "Protein", "text": [ "YenR" ], "offsets": [ [ 1001, 1005 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-01-02-01_T27", "type": "Chemical", "text": [ "AHL" ], "offsets": [ [ 1076, 1079 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-01-02-01_T28", "type": "Protein", "text": [ "LuxR" ], "offsets": [ [ 1080, 1084 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-01-02-01_T29", "type": "Protein", "text": [ "YE1026" ], "offsets": [ [ 1096, 1102 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-01-02-01_T30", "type": "Chemical", "text": [ "AHL" ], "offsets": [ [ 1127, 1130 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-01-02-01_T31", "type": "Chemical", "text": [ "AHLs" ], "offsets": [ [ 1198, 1202 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-01-02-01_T32", "type": "Protein", "text": [ "YenI" ], "offsets": [ [ 1215, 1219 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-01-02-01_T33", "type": "Organism", "text": [ "P. luminescens" ], "offsets": [ [ 1238, 1252 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-01-02-01_T34", "type": "Chemical", "text": [ "AHL" ], "offsets": [ [ 1282, 1285 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-01-02-01_T35", "type": "Protein", "text": [ "LuxR" ], "offsets": [ [ 1286, 1290 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-01-02-01_T36", "type": "Protein", "text": [ "plu0320" ], "offsets": [ [ 1307, 1314 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-01-02-01_T37", "type": "Protein", "text": [ "plu4562" ], "offsets": [ [ 1319, 1326 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-01-02-01_T38", "type": "Protein", "text": [ "luxI" ], "offsets": [ [ 1335, 1339 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-01-02-01_T39", "type": "Organism", "text": [ "P. luminescens" ], "offsets": [ [ 1387, 1401 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-01-02-01_T40", "type": "Chemical", "text": [ "AHL" ], "offsets": [ [ 1427, 1430 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-01-02-01_T41", "type": "Organism", "text": [ "Salmonella enterica" ], "offsets": [ [ 1584, 1603 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-01-02-01_T42", "type": "Organism", "text": [ "Escherichia coli" ], "offsets": [ [ 1608, 1624 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-01-02-01_T43", "type": "Organism", "text": [ "Y. enterocolitica" ], "offsets": [ [ 1656, 1673 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-01-02-01_T44", "type": "Protein", "text": [ "YE1026" ], "offsets": [ [ 1695, 1701 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-01-02-01_T45", "type": "Organism", "text": [ "Sodalis glossinidius strain morsitans" ], "offsets": [ [ 1734, 1771 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-01-02-01_T46", "type": "Organism", "text": [ "tse tse fly Glossina morsitans morsitans" ], "offsets": [ [ 1796, 1836 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-01-02-01_T47", "type": "Chemical", "text": [ "AHL" ], "offsets": [ [ 1867, 1870 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-01-02-01_T48", "type": "Protein", "text": [ "LuxR" ], "offsets": [ [ 1871, 1875 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-01-02-01_T49", "type": "Protein", "text": [ "SG1740" ], "offsets": [ [ 1887, 1893 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-01-02-01_T50", "type": "Protein", "text": [ "SG0285" ], "offsets": [ [ 1898, 1904 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-01-02-01_T51", "type": "Protein", "text": [ "luxI" ], "offsets": [ [ 1913, 1917 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-01-02-01_T52", "type": "Chemical", "text": [ "AHLs" ], "offsets": [ [ 1959, 1963 ] ], "normalized": [] }, { "id": "PMC2266911-02-Results_and_Discussion-01-02-01_T53", "type": "Chemical", "text": [ "AHLs" ], "offsets": [ [ 2074, 2078 ] ], "normalized": [] } ]

[ { "id": "PMC2266911-02-Results_and_Discussion-01-02-01_E1", "type": "Process", "trigger": { "text": [ "Virulence" ], "offsets": [ [ 75, 84 ] ] }, "arguments": [] }, { "id": "PMC2266911-02-Results_and_Discussion-01-02-01_E2", "type": "Regulation", "trigger": { "text": [ "regulated" ], "offsets": [ [ 168, 177 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC2266911-02-Results_and_Discussion-01-02-01_E1" }, { "role": "Cause", "ref_id": "PMC2266911-02-Results_and_Discussion-01-02-01_T3" } ] }, { "id": "PMC2266911-02-Results_and_Discussion-01-02-01_E3", "type": "Binding", "trigger": { "text": [ "binds" ], "offsets": [ [ 528, 533 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC2266911-02-Results_and_Discussion-01-02-01_T11" } ] }, { "id": "PMC2266911-02-Results_and_Discussion-01-02-01_E4", "type": "Gene_expression", "trigger": { "text": [ "production" ], "offsets": [ [ 945, 955 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC2266911-02-Results_and_Discussion-01-02-01_T23" } ] }, { "id": "PMC2266911-02-Results_and_Discussion-01-02-01_E5", "type": "Gene_expression", "trigger": { "text": [ "production" ], "offsets": [ [ 945, 955 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC2266911-02-Results_and_Discussion-01-02-01_T24" } ] }, { "id": "PMC2266911-02-Results_and_Discussion-01-02-01_E6", "type": "Positive_regulation", "trigger": { "text": [ "induced" ], "offsets": [ [ 1010, 1017 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC2266911-02-Results_and_Discussion-01-02-01_E4" } ] }, { "id": "PMC2266911-02-Results_and_Discussion-01-02-01_E7", "type": "Positive_regulation", "trigger": { "text": [ "induced" ], "offsets": [ [ 1010, 1017 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC2266911-02-Results_and_Discussion-01-02-01_E5" } ] } ]

[ { "id": "PMC2266911-02-Results_and_Discussion-01-02-01_1", "entity_ids": [ "PMC2266911-02-Results_and_Discussion-01-02-01_T6", "PMC2266911-02-Results_and_Discussion-01-02-01_T7" ] } ]

[]

[ { "id": "PMC2581603-02-Results-05__text", "type": "abstract", "text": [ "Expression of the CAP resistance operon PA3552-PA3559 is induced in biofilms in response to extracellular DNA \nTo determine the influence of extracellular DNA on PA3553 gene expression in biofilms, DNA-enriched biofilms were cultivated on the surface of polystyrene pegs. Consistent with previous reports that DNA is a component of biofilms [50],[51], we observed DNA in 24 h old peg-adhered biofilms (Fig 5A and 5B). Double staining of P. aeruginosa with syto9 (stains viable cells green) and the extracellular DNA stain DDAO (red) [51] was used to visualize DNA as a loose lattice in biofilms formed on polystyrene pegs after 24 h (Fig 5A). DNA was also visualized (PI stained) as a mesh-like DNA matrix in 1 day-old peg-adhered biofilm monolayers (Fig 5B), which resembled the thread-like projections of genomic DNA observed in DNA or EDTA-lysed cells (Fig 2B). These localization patterns of extracellular DNA are suggestive of DNA gradients within biofilms. Biofilm formation was inhibited at extracellular DNA concentrations >/=0.5% (w/v) (Fig 6A). This is consistent with the observed growth inhibition of planktonic cells at similar DNA concentrations (Fig 1A). One-day old PA3553::lux biofilms were washed to remove non-adhered cells and gene expression was measured from the cells adhered to the polystyrene peg surface. PA3553 gene expression was strongly induced, up to 20-fold, in peg-adhered biofilms, with the highest induction at 0.5% (w/v) extracellular DNA (Fig 6B). Although gene expression was measured in a mutant background, both PAO1 and PA3553::lux had similar biofilm phenotypes in each condition tested (Fig 6A). In biofilms cultivated in the presence of extracellular DNA supplemented with excess Mg2+ (5 mM), PA3553 gene expression was completely repressed (data not shown).\n" ], "offsets": [ [ 0, 1803 ] ] } ]

[ { "id": "PMC2581603-02-Results-05_T1", "type": "Chemical", "text": [ "CAP" ], "offsets": [ [ 18, 21 ] ], "normalized": [] }, { "id": "PMC2581603-02-Results-05_T2", "type": "Regulon-operon", "text": [ "PA3552-PA3559" ], "offsets": [ [ 40, 53 ] ], "normalized": [] }, { "id": "PMC2581603-02-Results-05_T3", "type": "Protein", "text": [ "PA3552" ], "offsets": [ [ 40, 46 ] ], "normalized": [] }, { "id": "PMC2581603-02-Results-05_T4", "type": "Protein", "text": [ "PA3559" ], "offsets": [ [ 47, 53 ] ], "normalized": [] }, { "id": "PMC2581603-02-Results-05_T5", "type": "Protein", "text": [ "PA3553" ], "offsets": [ [ 162, 168 ] ], "normalized": [] }, { "id": "PMC2581603-02-Results-05_T6", "type": "Chemical", "text": [ "polystyrene" ], "offsets": [ [ 254, 265 ] ], "normalized": [] }, { "id": "PMC2581603-02-Results-05_T7", "type": "Organism", "text": [ "P. aeruginosa" ], "offsets": [ [ 437, 450 ] ], "normalized": [] }, { "id": "PMC2581603-02-Results-05_T8", "type": "Chemical", "text": [ "syto9" ], "offsets": [ [ 456, 461 ] ], "normalized": [] }, { "id": "PMC2581603-02-Results-05_T9", "type": "Chemical", "text": [ "DDAO" ], "offsets": [ [ 522, 526 ] ], "normalized": [] }, { "id": "PMC2581603-02-Results-05_T10", "type": "Chemical", "text": [ "polystyrene" ], "offsets": [ [ 605, 616 ] ], "normalized": [] }, { "id": "PMC2581603-02-Results-05_T11", "type": "Chemical", "text": [ "PI" ], "offsets": [ [ 668, 670 ] ], "normalized": [] }, { "id": "PMC2581603-02-Results-05_T12", "type": "Chemical", "text": [ "EDTA" ], "offsets": [ [ 838, 842 ] ], "normalized": [] }, { "id": "PMC2581603-02-Results-05_T13", "type": "Organism", "text": [ "PA3553::lux" ], "offsets": [ [ 1182, 1193 ] ], "normalized": [] }, { "id": "PMC2581603-02-Results-05_T14", "type": "Protein", "text": [ "PA3553" ], "offsets": [ [ 1182, 1188 ] ], "normalized": [] }, { "id": "PMC2581603-02-Results-05_T15", "type": "Protein", "text": [ "lux" ], "offsets": [ [ 1190, 1193 ] ], "normalized": [] }, { "id": "PMC2581603-02-Results-05_T16", "type": "Chemical", "text": [ "polystyrene" ], "offsets": [ [ 1306, 1317 ] ], "normalized": [] }, { "id": "PMC2581603-02-Results-05_T17", "type": "Protein", "text": [ "PA3553" ], "offsets": [ [ 1331, 1337 ] ], "normalized": [] }, { "id": "PMC2581603-02-Results-05_T18", "type": "Organism", "text": [ "PAO1" ], "offsets": [ [ 1552, 1556 ] ], "normalized": [] }, { "id": "PMC2581603-02-Results-05_T19", "type": "Organism", "text": [ "PA3553::lux" ], "offsets": [ [ 1561, 1572 ] ], "normalized": [] }, { "id": "PMC2581603-02-Results-05_T20", "type": "Protein", "text": [ "PA3553" ], "offsets": [ [ 1561, 1567 ] ], "normalized": [] }, { "id": "PMC2581603-02-Results-05_T21", "type": "Protein", "text": [ "lux" ], "offsets": [ [ 1569, 1572 ] ], "normalized": [] }, { "id": "PMC2581603-02-Results-05_T22", "type": "Chemical", "text": [ "Mg2+" ], "offsets": [ [ 1724, 1728 ] ], "normalized": [] }, { "id": "PMC2581603-02-Results-05_T23", "type": "Protein", "text": [ "PA3553" ], "offsets": [ [ 1737, 1743 ] ], "normalized": [] } ]

[ { "id": "PMC2581603-02-Results-05_E1", "type": "Gene_expression", "trigger": { "text": [ "Expression" ], "offsets": [ [ 0, 10 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC2581603-02-Results-05_T2" } ] }, { "id": "PMC2581603-02-Results-05_E2", "type": "Process", "trigger": { "text": [ "resistance" ], "offsets": [ [ 22, 32 ] ] }, "arguments": [] }, { "id": "PMC2581603-02-Results-05_E3", "type": "Positive_regulation", "trigger": { "text": [ "induced" ], "offsets": [ [ 57, 64 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC2581603-02-Results-05_E1" } ] }, { "id": "PMC2581603-02-Results-05_E4", "type": "Gene_expression", "trigger": { "text": [ "expression" ], "offsets": [ [ 174, 184 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC2581603-02-Results-05_T5" } ] }, { "id": "PMC2581603-02-Results-05_E5", "type": "Gene_expression", "trigger": { "text": [ "expression" ], "offsets": [ [ 1252, 1262 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC2581603-02-Results-05_T14" } ] }, { "id": "PMC2581603-02-Results-05_E6", "type": "Gene_expression", "trigger": { "text": [ "expression" ], "offsets": [ [ 1252, 1262 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC2581603-02-Results-05_T15" } ] }, { "id": "PMC2581603-02-Results-05_E7", "type": "Gene_expression", "trigger": { "text": [ "expression" ], "offsets": [ [ 1343, 1353 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC2581603-02-Results-05_T17" } ] }, { "id": "PMC2581603-02-Results-05_E8", "type": "Positive_regulation", "trigger": { "text": [ "induced" ], "offsets": [ [ 1367, 1374 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC2581603-02-Results-05_E7" } ] }, { "id": "PMC2581603-02-Results-05_E9", "type": "Gene_expression", "trigger": { "text": [ "expression" ], "offsets": [ [ 1499, 1509 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC2581603-02-Results-05_T20" } ] }, { "id": "PMC2581603-02-Results-05_E10", "type": "Gene_expression", "trigger": { "text": [ "expression" ], "offsets": [ [ 1499, 1509 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC2581603-02-Results-05_T21" } ] }, { "id": "PMC2581603-02-Results-05_E11", "type": "Gene_expression", "trigger": { "text": [ "expression" ], "offsets": [ [ 1749, 1759 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC2581603-02-Results-05_T23" } ] }, { "id": "PMC2581603-02-Results-05_E12", "type": "Negative_regulation", "trigger": { "text": [ "repressed" ], "offsets": [ [ 1775, 1784 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC2581603-02-Results-05_E11" }, { "role": "Cause", "ref_id": "PMC2581603-02-Results-05_T22" } ] } ]

[]

[]

[ { "id": "PMC2593050-03-RESULTS-05__text", "type": "abstract", "text": [ "DeltavicK Infection Confers Protection of Mice against Reinfection with Wild-Type S. equi \nTo test whether DeltavicK infection confers immunity against S. equi infection, the seven mice recovered from the subcutaneous DeltavicK infection was reinfected subcutaneously with 1.5 x 108 cfu wild-type S. equi 30 days after the first infection and monitored for 18 days. Six of the 7 mice survived the reinfection (Fig. 4A), suggesting that the DeltavicK infection induces immunity against S. equi infection.\n" ], "offsets": [ [ 0, 504 ] ] } ]

[ { "id": "PMC2593050-03-RESULTS-05_T1", "type": "Organism", "text": [ "DeltavicK" ], "offsets": [ [ 0, 9 ] ], "normalized": [] }, { "id": "PMC2593050-03-RESULTS-05_T2", "type": "Protein", "text": [ "vicK" ], "offsets": [ [ 5, 9 ] ], "normalized": [] }, { "id": "PMC2593050-03-RESULTS-05_T3", "type": "Organism", "text": [ "Mice" ], "offsets": [ [ 42, 46 ] ], "normalized": [] }, { "id": "PMC2593050-03-RESULTS-05_T4", "type": "Organism", "text": [ "S. equi" ], "offsets": [ [ 82, 89 ] ], "normalized": [] }, { "id": "PMC2593050-03-RESULTS-05_T5", "type": "Organism", "text": [ "DeltavicK" ], "offsets": [ [ 107, 116 ] ], "normalized": [] }, { "id": "PMC2593050-03-RESULTS-05_T6", "type": "Protein", "text": [ "vicK" ], "offsets": [ [ 112, 116 ] ], "normalized": [] }, { "id": "PMC2593050-03-RESULTS-05_T7", "type": "Organism", "text": [ "S. equi" ], "offsets": [ [ 152, 159 ] ], "normalized": [] }, { "id": "PMC2593050-03-RESULTS-05_T8", "type": "Organism", "text": [ "mice" ], "offsets": [ [ 181, 185 ] ], "normalized": [] }, { "id": "PMC2593050-03-RESULTS-05_T9", "type": "Organism", "text": [ "DeltavicK" ], "offsets": [ [ 218, 227 ] ], "normalized": [] }, { "id": "PMC2593050-03-RESULTS-05_T10", "type": "Protein", "text": [ "vicK" ], "offsets": [ [ 223, 227 ] ], "normalized": [] }, { "id": "PMC2593050-03-RESULTS-05_T11", "type": "Organism", "text": [ "S. equi" ], "offsets": [ [ 297, 304 ] ], "normalized": [] }, { "id": "PMC2593050-03-RESULTS-05_T12", "type": "Organism", "text": [ "mice" ], "offsets": [ [ 379, 383 ] ], "normalized": [] }, { "id": "PMC2593050-03-RESULTS-05_T13", "type": "Organism", "text": [ "DeltavicK" ], "offsets": [ [ 440, 449 ] ], "normalized": [] }, { "id": "PMC2593050-03-RESULTS-05_T14", "type": "Protein", "text": [ "vicK" ], "offsets": [ [ 445, 449 ] ], "normalized": [] }, { "id": "PMC2593050-03-RESULTS-05_T15", "type": "Organism", "text": [ "S. equi" ], "offsets": [ [ 485, 492 ] ], "normalized": [] } ]

[ { "id": "PMC2593050-03-RESULTS-05_E1", "type": "Process", "trigger": { "text": [ "Infection" ], "offsets": [ [ 10, 19 ] ] }, "arguments": [ { "role": "Participant", "ref_id": "PMC2593050-03-RESULTS-05_T1" } ] }, { "id": "PMC2593050-03-RESULTS-05_E2", "type": "Negative_regulation", "trigger": { "text": [ "Protection" ], "offsets": [ [ 28, 38 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC2593050-03-RESULTS-05_E3" }, { "role": "Cause", "ref_id": "PMC2593050-03-RESULTS-05_E1" } ] }, { "id": "PMC2593050-03-RESULTS-05_E3", "type": "Process", "trigger": { "text": [ "Reinfection" ], "offsets": [ [ 55, 66 ] ] }, "arguments": [ { "role": "Participant", "ref_id": "PMC2593050-03-RESULTS-05_T4" } ] }, { "id": "PMC2593050-03-RESULTS-05_E4", "type": "Process", "trigger": { "text": [ "infection" ], "offsets": [ [ 117, 126 ] ] }, "arguments": [ { "role": "Participant", "ref_id": "PMC2593050-03-RESULTS-05_T5" } ] }, { "id": "PMC2593050-03-RESULTS-05_E5", "type": "Process", "trigger": { "text": [ "infection" ], "offsets": [ [ 160, 169 ] ] }, "arguments": [ { "role": "Participant", "ref_id": "PMC2593050-03-RESULTS-05_T7" } ] }, { "id": "PMC2593050-03-RESULTS-05_E6", "type": "Process", "trigger": { "text": [ "infection" ], "offsets": [ [ 228, 237 ] ] }, "arguments": [ { "role": "Participant", "ref_id": "PMC2593050-03-RESULTS-05_T9" } ] }, { "id": "PMC2593050-03-RESULTS-05_E7", "type": "Process", "trigger": { "text": [ "reinfected" ], "offsets": [ [ 242, 252 ] ] }, "arguments": [ { "role": "Participant", "ref_id": "PMC2593050-03-RESULTS-05_T11" } ] }, { "id": "PMC2593050-03-RESULTS-05_E8", "type": "Process", "trigger": { "text": [ "infection" ], "offsets": [ [ 329, 338 ] ] }, "arguments": [] }, { "id": "PMC2593050-03-RESULTS-05_E9", "type": "Process", "trigger": { "text": [ "reinfection" ], "offsets": [ [ 397, 408 ] ] }, "arguments": [] }, { "id": "PMC2593050-03-RESULTS-05_E10", "type": "Process", "trigger": { "text": [ "infection" ], "offsets": [ [ 450, 459 ] ] }, "arguments": [ { "role": "Participant", "ref_id": "PMC2593050-03-RESULTS-05_T13" } ] }, { "id": "PMC2593050-03-RESULTS-05_E11", "type": "Process", "trigger": { "text": [ "infection" ], "offsets": [ [ 493, 502 ] ] }, "arguments": [ { "role": "Participant", "ref_id": "PMC2593050-03-RESULTS-05_T15" } ] } ]

[]

[]

[ { "id": "PMC1913099-02-Results-Discussion-05__text", "type": "abstract", "text": [ "Allelic Replacement of speH \nIncreased expression of speH during pharyngeal cell adherence suggests that the SpeH exotoxin is either necessary for adherence, or is a component of a downstream infection process. Adherence-mediated upregulation of speH is likely not the result of phage induction, as the remaining phage 370.2 genes identified in our analysis were downregulated. To determine if SpeH plays a direct role in the adherence process, we created a deletion mutant in strain SF370 (SF370DeltaspeH), which was confirmed by PCR (unpublished data) and RT-PCR (Figure 1A) and tested in vitro for adherence to human pharyngeal cells. We observed no significant difference in adherence between the wild-type (SF370) and mutant strains (Figure 1B), indicating that SpeH is not involved directly in attachment to the pharyngeal cell. The significant upregulation of the speH gene during adherence suggests that the gene product may function instead during a subsequent stage of infection.\n" ], "offsets": [ [ 0, 990 ] ] } ]

[ { "id": "PMC1913099-02-Results-Discussion-05_T1", "type": "Protein", "text": [ "speH" ], "offsets": [ [ 23, 27 ] ], "normalized": [] }, { "id": "PMC1913099-02-Results-Discussion-05_T2", "type": "Protein", "text": [ "speH" ], "offsets": [ [ 53, 57 ] ], "normalized": [] }, { "id": "PMC1913099-02-Results-Discussion-05_T3", "type": "Protein", "text": [ "SpeH" ], "offsets": [ [ 109, 113 ] ], "normalized": [] }, { "id": "PMC1913099-02-Results-Discussion-05_T4", "type": "Protein", "text": [ "speH" ], "offsets": [ [ 246, 250 ] ], "normalized": [] }, { "id": "PMC1913099-02-Results-Discussion-05_T5", "type": "Protein", "text": [ "SpeH" ], "offsets": [ [ 394, 398 ] ], "normalized": [] }, { "id": "PMC1913099-02-Results-Discussion-05_T6", "type": "Organism", "text": [ "SF370" ], "offsets": [ [ 484, 489 ] ], "normalized": [] }, { "id": "PMC1913099-02-Results-Discussion-05_T7", "type": "Organism", "text": [ "SF370DeltaspeH" ], "offsets": [ [ 491, 505 ] ], "normalized": [] }, { "id": "PMC1913099-02-Results-Discussion-05_T8", "type": "Protein", "text": [ "speH" ], "offsets": [ [ 501, 505 ] ], "normalized": [] }, { "id": "PMC1913099-02-Results-Discussion-05_T9", "type": "Organism", "text": [ "human" ], "offsets": [ [ 614, 619 ] ], "normalized": [] }, { "id": "PMC1913099-02-Results-Discussion-05_T10", "type": "Organism", "text": [ "SF370" ], "offsets": [ [ 712, 717 ] ], "normalized": [] }, { "id": "PMC1913099-02-Results-Discussion-05_T11", "type": "Protein", "text": [ "SpeH" ], "offsets": [ [ 767, 771 ] ], "normalized": [] }, { "id": "PMC1913099-02-Results-Discussion-05_T12", "type": "Protein", "text": [ "speH" ], "offsets": [ [ 871, 875 ] ], "normalized": [] } ]

[ { "id": "PMC1913099-02-Results-Discussion-05_E1", "type": "Positive_regulation", "trigger": { "text": [ "Increased" ], "offsets": [ [ 29, 38 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC1913099-02-Results-Discussion-05_E2" } ] }, { "id": "PMC1913099-02-Results-Discussion-05_E2", "type": "Gene_expression", "trigger": { "text": [ "expression" ], "offsets": [ [ 39, 49 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC1913099-02-Results-Discussion-05_T2" } ] }, { "id": "PMC1913099-02-Results-Discussion-05_E3", "type": "Process", "trigger": { "text": [ "infection" ], "offsets": [ [ 192, 201 ] ] }, "arguments": [] }, { "id": "PMC1913099-02-Results-Discussion-05_E4", "type": "Positive_regulation", "trigger": { "text": [ "upregulation" ], "offsets": [ [ 230, 242 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC1913099-02-Results-Discussion-05_T4" } ] }, { "id": "PMC1913099-02-Results-Discussion-05_E5", "type": "Positive_regulation", "trigger": { "text": [ "upregulation" ], "offsets": [ [ 851, 863 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC1913099-02-Results-Discussion-05_T12" } ] }, { "id": "PMC1913099-02-Results-Discussion-05_E6", "type": "Process", "trigger": { "text": [ "infection" ], "offsets": [ [ 979, 988 ] ] }, "arguments": [] } ]

[]

[]

[ { "id": "PMC2816692-02-Results-04__text", "type": "abstract", "text": [ "SrcA interacts with the SPI-2 T3SS ATPase \nAn emerging function for T3SS chaperones is delivery of cargo to the base of the apparatus through interactions with an ATPase. This was shown for the flagellar T3SS [17] and later in the virulence-associated T3SS in E. coli [16],[27] and the SPI-1 T3SS in Salmonella [15]. However, analogous interactions have not been described for the SPI-2 T3SS. Since srcA expression was co-regulated with genes in SPI-2, we hypothesized that it had a functional role in this system. To address this biochemically we purified SrcA and the predicted ATPase for the SPI-2 T3SS, SsaN, and performed binding experiments and gel filtration chromatography of the protein mixtures. SsaN contains conserved amino acid residues characteristic of Walker-A and Walker-B motifs of P-loop nucleoside triphosphate hydrolases, as well as a number of residues shown to contribute to ATP binding or ring stacking with the adenine base of ATP in the E. coli orthologue, EscN, (Q412, E191, R366) (Fig. S1). Since SsaN had not been characterized biochemically we first verified that our purified protein had ATPase activity (Fig. S1). We then mixed SrcA and SsaN proteins and resolved the protein complexes by gel filtration chromatography. By itself, SrcA existed as a dimer in solution (Fig. 4A) with no higher oligomers present, substantiating the stoichiometry obtained from our crystal data. SsaN existed as a monomer with a minor population eluting in a volume consistent with a probable dimer (Fig. 4B). When SrcA was mixed with SsaN, a new protein complex of high molecular weight was observed, along with diminished peaks corresponding to the SrcA dimer and SsaN monomer (Fig. 4C). This new complex elutes with a Stokes radius consistent with an apparent molecular mass of approximately600 kDa. We verified the identities of protein originating from each peak by western blot (Fig. 4D) and LC-MS/MS, which showed the new complex was comprised of both SsaN and SrcA.\n" ], "offsets": [ [ 0, 1986 ] ] } ]

[ { "id": "PMC2816692-02-Results-04_T1", "type": "Protein", "text": [ "SrcA" ], "offsets": [ [ 0, 4 ] ], "normalized": [] }, { "id": "PMC2816692-02-Results-04_T2", "type": "Organism", "text": [ "E. coli" ], "offsets": [ [ 260, 267 ] ], "normalized": [] }, { "id": "PMC2816692-02-Results-04_T3", "type": "Organism", "text": [ "Salmonella" ], "offsets": [ [ 300, 310 ] ], "normalized": [] }, { "id": "PMC2816692-02-Results-04_T4", "type": "Protein", "text": [ "srcA" ], "offsets": [ [ 399, 403 ] ], "normalized": [] }, { "id": "PMC2816692-02-Results-04_T5", "type": "Protein", "text": [ "SrcA" ], "offsets": [ [ 557, 561 ] ], "normalized": [] }, { "id": "PMC2816692-02-Results-04_T6", "type": "Protein", "text": [ "SsaN" ], "offsets": [ [ 607, 611 ] ], "normalized": [] }, { "id": "PMC2816692-02-Results-04_T7", "type": "Protein", "text": [ "SsaN" ], "offsets": [ [ 706, 710 ] ], "normalized": [] }, { "id": "PMC2816692-02-Results-04_T8", "type": "Protein", "text": [ "nucleoside triphosphate hydrolases" ], "offsets": [ [ 807, 841 ] ], "normalized": [] }, { "id": "PMC2816692-02-Results-04_T9", "type": "Chemical", "text": [ "ATP" ], "offsets": [ [ 898, 901 ] ], "normalized": [] }, { "id": "PMC2816692-02-Results-04_T10", "type": "Chemical", "text": [ "adenine" ], "offsets": [ [ 936, 943 ] ], "normalized": [] }, { "id": "PMC2816692-02-Results-04_T11", "type": "Chemical", "text": [ "ATP" ], "offsets": [ [ 952, 955 ] ], "normalized": [] }, { "id": "PMC2816692-02-Results-04_T12", "type": "Organism", "text": [ "E. coli" ], "offsets": [ [ 963, 970 ] ], "normalized": [] }, { "id": "PMC2816692-02-Results-04_T13", "type": "Protein", "text": [ "EscN" ], "offsets": [ [ 983, 987 ] ], "normalized": [] }, { "id": "PMC2816692-02-Results-04_T14", "type": "Protein", "text": [ "SsaN" ], "offsets": [ [ 1025, 1029 ] ], "normalized": [] }, { "id": "PMC2816692-02-Results-04_T15", "type": "Protein", "text": [ "SrcA" ], "offsets": [ [ 1160, 1164 ] ], "normalized": [] }, { "id": "PMC2816692-02-Results-04_T16", "type": "Protein", "text": [ "SsaN" ], "offsets": [ [ 1169, 1173 ] ], "normalized": [] }, { "id": "PMC2816692-02-Results-04_T17", "type": "Protein", "text": [ "SrcA" ], "offsets": [ [ 1263, 1267 ] ], "normalized": [] }, { "id": "PMC2816692-02-Results-04_T18", "type": "Protein", "text": [ "SsaN" ], "offsets": [ [ 1408, 1412 ] ], "normalized": [] }, { "id": "PMC2816692-02-Results-04_T19", "type": "Protein", "text": [ "SrcA" ], "offsets": [ [ 1527, 1531 ] ], "normalized": [] }, { "id": "PMC2816692-02-Results-04_T20", "type": "Protein", "text": [ "SsaN" ], "offsets": [ [ 1547, 1551 ] ], "normalized": [] }, { "id": "PMC2816692-02-Results-04_T21", "type": "Protein", "text": [ "SrcA" ], "offsets": [ [ 1663, 1667 ] ], "normalized": [] }, { "id": "PMC2816692-02-Results-04_T22", "type": "Protein", "text": [ "SsaN" ], "offsets": [ [ 1678, 1682 ] ], "normalized": [] }, { "id": "PMC2816692-02-Results-04_T23", "type": "Protein", "text": [ "SsaN" ], "offsets": [ [ 1971, 1975 ] ], "normalized": [] }, { "id": "PMC2816692-02-Results-04_T24", "type": "Protein", "text": [ "SrcA" ], "offsets": [ [ 1980, 1984 ] ], "normalized": [] } ]

[ { "id": "PMC2816692-02-Results-04_E1", "type": "Binding", "trigger": { "text": [ "interacts" ], "offsets": [ [ 5, 14 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC2816692-02-Results-04_T1" } ] }, { "id": "PMC2816692-02-Results-04_E2", "type": "Process", "trigger": { "text": [ "virulence" ], "offsets": [ [ 231, 240 ] ] }, "arguments": [] }, { "id": "PMC2816692-02-Results-04_E3", "type": "Gene_expression", "trigger": { "text": [ "expression" ], "offsets": [ [ 404, 414 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC2816692-02-Results-04_T4" } ] }, { "id": "PMC2816692-02-Results-04_E4", "type": "Regulation", "trigger": { "text": [ "regulated" ], "offsets": [ [ 422, 431 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC2816692-02-Results-04_E3" } ] }, { "id": "PMC2816692-02-Results-04_E5", "type": "Binding", "trigger": { "text": [ "binding" ], "offsets": [ [ 627, 634 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC2816692-02-Results-04_T5" }, { "role": "Theme", "ref_id": "PMC2816692-02-Results-04_T6" } ] }, { "id": "PMC2816692-02-Results-04_E6", "type": "Binding", "trigger": { "text": [ "binding" ], "offsets": [ [ 902, 909 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC2816692-02-Results-04_T7" }, { "role": "Theme", "ref_id": "PMC2816692-02-Results-04_T9" } ] }, { "id": "PMC2816692-02-Results-04_E7", "type": "Binding", "trigger": { "text": [ "complex" ], "offsets": [ [ 1567, 1574 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC2816692-02-Results-04_T19" }, { "role": "Theme", "ref_id": "PMC2816692-02-Results-04_T20" } ] }, { "id": "PMC2816692-02-Results-04_E8", "type": "Binding", "trigger": { "text": [ "complex" ], "offsets": [ [ 1941, 1948 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC2816692-02-Results-04_T23" }, { "role": "Theme", "ref_id": "PMC2816692-02-Results-04_T24" } ] } ]

[]

[]

[ { "id": "PMC2639726-02-Results-03__text", "type": "abstract", "text": [ "Transcription profiling of avirulent strains \nBecause some of the Typhimurium regulator mutants survived so poorly within macrophages that preparing mRNA from intracellular bacteria was not possible we have used in vitro growth conditions that duplicate some of the intracellular conditions (low pH, minimal media; [47],[48]). The 14 virulence regulators, whose absence was identified by attenuated virulence in vivo in this study, presumably sense specific environmental signals within the host and respond by expressing the appropriate complement of virulence factors. However the specific environmental signals are not known and therefore each strain was grown in four different conditions; to log phase or stationary phase in Luria-Bertani (LB) broth and in a low pH/low magnesium, minimal medium [47],[48]. Two different minimal media conditions were used depending only on pre-growth conditions as described in the Materials and Methods (called acidic minimal media (AMM)1 and AMM2 here); these conditions are identical to conditions previously reported for expression of SPI-2; [47],[48]. The fate of intracellular Typhimurium is determined by pre-growth conditions prior to macrophage infection and for that reason we used both conditions AMM1 and 2 [49]. To identify global transcriptional changes for each regulator, mRNAs were isolated from each strain grown under the four conditions, converted to cDNA, and used to probe a spotted non-redundant pan-Salmonella orf microarray using hybridization of total genomic Salmonella DNA as an internal control [50]. Each microarray was probed with RNA from the parent or an isogenic deletion of one of the regulator mutants prepared from bacterial cells grown under one of the four conditions. In all there were 4 biological replicates of the parent strain but one for each mutant under each growth condition. Transcriptional profiles were significantly different from the parent for known virulence factors required during systemic infection, but only if cells were grown in acidic minimal media (AMM1 or AMM2; see Figure 3; complete microarray data available at http://www.ohsu.edu/microbiology/heffron/r01.html). Z-scores ((score-mean)/standard deviation) were computed for each gene in the Typhimurium genome in each mutant background under each growth condition (Table S2). Statistical analysis of the complete transcriptional data for gene expression in AMM1 identified at least 237 genes that were reduced 4-fold or more in common comparing the mutations to the parent strain (at least 3 standard deviation based on the technical replicates). Because transcription is reduced in the mutant compared to the parent, it suggests that normally the regulator activates transcription of these genes as is shown dramatically in Figure 3 for all SPI-2 encoded virulence genes. Conversely, only 45 genes showed a 4-fold or more up-regulation in the mutant backgrounds when cells were prepared under the same growth condition, suggesting that the regulator normally represses these genes. A more precise statistical analysis of genes that are co-regulated with SPI-2 is provided below (Table 2). All in all, these results suggest that the normal function of each of the 14 regulators is to activate transcription of virulence factors necessary for systemic infection but only under specific environmental conditions. Acidic minimal media (AMM1) provides the best induction condition of those that were examined.\n" ], "offsets": [ [ 0, 3462 ] ] } ]

[ { "id": "PMC2639726-02-Results-03_T1", "type": "Organism", "text": [ "Typhimurium" ], "offsets": [ [ 66, 77 ] ], "normalized": [] }, { "id": "PMC2639726-02-Results-03_T2", "type": "Chemical", "text": [ "magnesium" ], "offsets": [ [ 775, 784 ] ], "normalized": [] }, { "id": "PMC2639726-02-Results-03_T3", "type": "Organism", "text": [ "Typhimurium" ], "offsets": [ [ 1122, 1133 ] ], "normalized": [] }, { "id": "PMC2639726-02-Results-03_T4", "type": "Organism", "text": [ "Salmonella" ], "offsets": [ [ 1462, 1472 ] ], "normalized": [] }, { "id": "PMC2639726-02-Results-03_T5", "type": "Organism", "text": [ "Salmonella" ], "offsets": [ [ 1525, 1535 ] ], "normalized": [] }, { "id": "PMC2639726-02-Results-03_T6", "type": "Organism", "text": [ "Typhimurium" ], "offsets": [ [ 2247, 2258 ] ], "normalized": [] } ]

[ { "id": "PMC2639726-02-Results-03_E1", "type": "Process", "trigger": { "text": [ "avirulent" ], "offsets": [ [ 27, 36 ] ] }, "arguments": [] }, { "id": "PMC2639726-02-Results-03_E2", "type": "Process", "trigger": { "text": [ "virulence" ], "offsets": [ [ 334, 343 ] ] }, "arguments": [] }, { "id": "PMC2639726-02-Results-03_E3", "type": "Negative_regulation", "trigger": { "text": [ "attenuated" ], "offsets": [ [ 388, 398 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC2639726-02-Results-03_E4" } ] }, { "id": "PMC2639726-02-Results-03_E4", "type": "Process", "trigger": { "text": [ "virulence" ], "offsets": [ [ 399, 408 ] ] }, "arguments": [] }, { "id": "PMC2639726-02-Results-03_E5", "type": "Process", "trigger": { "text": [ "virulence" ], "offsets": [ [ 552, 561 ] ] }, "arguments": [] }, { "id": "PMC2639726-02-Results-03_E6", "type": "Process", "trigger": { "text": [ "virulence" ], "offsets": [ [ 1943, 1952 ] ] }, "arguments": [] }, { "id": "PMC2639726-02-Results-03_E7", "type": "Process", "trigger": { "text": [ "infection" ], "offsets": [ [ 1986, 1995 ] ] }, "arguments": [] }, { "id": "PMC2639726-02-Results-03_E8", "type": "Process", "trigger": { "text": [ "virulence" ], "offsets": [ [ 2812, 2821 ] ] }, "arguments": [] }, { "id": "PMC2639726-02-Results-03_E9", "type": "Process", "trigger": { "text": [ "virulence" ], "offsets": [ [ 3266, 3275 ] ] }, "arguments": [] } ]

[]

[]

[ { "id": "PMC2829055-02-Results-Discussion-06__text", "type": "abstract", "text": [ "Does transit through the flea vector preadapt Y. pestis to resist mammalian innate immunity? \nWhen Y. pestis is transmitted into the dermis by an infected flea, it is immediately exposed to the mammalian innate immune system. The most important antiphagocytic virulence factors, the cytotoxic Yersinia outer proteins (Yops), part of the T3SS encoded by the Y. pestis virulence plasmid and the F1 capsule encoded by the pMT1 plasmid, are not present at this initial stage of infection. Their expression is strictly temperature-regulated and are not produced in vivo until 3-5 hours after the temperature shift to 37degreesC that accompanies transmission [1],[3],[53],[54]. Consequently, Y. pestis grown at <28degreesC in vitro are initially susceptible to in vivo uptake and killing by phagocytes until the Yop and F1 virulence factors are produced, effectively preventing further phagocytosis [53],[54]. Our results indicate that Y. pestis entering the mammal from an infective flea is relatively resistant to macrophages, as well as PMNs [7]; a vector-specific phenotype that is not related to the T3SS or capsule. Coming from the flea, Y. pestis is also associated with the biofilm ECM, identical or closely related to the poly-beta-1,6-N-acetyl glucosamine ECM of staphylococcal biofilms, which has been shown to provide protection from innate immune components [55],[56]. In addition, although the antiphagocytic F1 capsule and Psa fimbriae do not appear to be produced in the flea, upregulation in the flea of most F1 genes in the cafRcaf1M1A1 locus and the Psa usher protein gene psaC (Tables 1, S1) suggests that components of the F1 and Psa translocation system are made, which may prime Y. pestis for rapid secretion of these extracellular virulence factors after transmission. The upregulation of the innate immunity resistance genes phoP and mgtC suggest that those Y. pestis that are phagocytized may be prepared for resistance to CAMPs and intracellular survival while still in the flea vector. Finally, the major essential virulence factors yadBC and pla, essential for Y. pestis dissemination from the dermis, were maximally or very highly expressed in the flea (Tables 1, S3). Besides degrading plasminogen, the Pla protease may also inactivate CAMPs, particularly when the F1 capsule is not present [57], which matches the phenotype of Y. pestis in the flea. In summary, Y. pestis appears to be prepared for pathogenesis in the mammal while still in the flea vector. The biofilm phenotype of Y. pestis and the virulence factors upregulated or highly expressed in the flea may enhance the earliest stages of plague pathogenesis while the full complement of temperature-shift-regulated virulence factors is still being induced. Increased resistance to innate immunity that is preinduced in the flea vector may be critical to productive transmission because blocked fleas transmit relatively few bacteria, often below the LD50 of Y. pestis grown in vitro at <28degreesC [1],[52].\n" ], "offsets": [ [ 0, 2994 ] ] } ]

[ { "id": "PMC2829055-02-Results-Discussion-06_T1", "type": "Organism", "text": [ "flea" ], "offsets": [ [ 25, 29 ] ], "normalized": [] }, { "id": "PMC2829055-02-Results-Discussion-06_T2", "type": "Organism", "text": [ "Y. pestis" ], "offsets": [ [ 46, 55 ] ], "normalized": [] }, { "id": "PMC2829055-02-Results-Discussion-06_T3", "type": "Organism", "text": [ "Y. pestis" ], "offsets": [ [ 99, 108 ] ], "normalized": [] }, { "id": "PMC2829055-02-Results-Discussion-06_T4", "type": "Organism", "text": [ "flea" ], "offsets": [ [ 155, 159 ] ], "normalized": [] }, { "id": "PMC2829055-02-Results-Discussion-06_T5", "type": "Organism", "text": [ "Y. pestis" ], "offsets": [ [ 357, 366 ] ], "normalized": [] }, { "id": "PMC2829055-02-Results-Discussion-06_T6", "type": "Organism", "text": [ "Y. pestis" ], "offsets": [ [ 686, 695 ] ], "normalized": [] }, { "id": "PMC2829055-02-Results-Discussion-06_T7", "type": "Organism", "text": [ "Y. pestis" ], "offsets": [ [ 930, 939 ] ], "normalized": [] }, { "id": "PMC2829055-02-Results-Discussion-06_T8", "type": "Organism", "text": [ "flea" ], "offsets": [ [ 978, 982 ] ], "normalized": [] }, { "id": "PMC2829055-02-Results-Discussion-06_T9", "type": "Organism", "text": [ "flea" ], "offsets": [ [ 1132, 1136 ] ], "normalized": [] }, { "id": "PMC2829055-02-Results-Discussion-06_T10", "type": "Organism", "text": [ "Y. pestis" ], "offsets": [ [ 1138, 1147 ] ], "normalized": [] }, { "id": "PMC2829055-02-Results-Discussion-06_T11", "type": "Chemical", "text": [ "poly-beta-1,6-N-acetyl glucosamine" ], "offsets": [ [ 1225, 1259 ] ], "normalized": [] }, { "id": "PMC2829055-02-Results-Discussion-06_T12", "type": "Organism", "text": [ "staphylococcal" ], "offsets": [ [ 1267, 1281 ] ], "normalized": [] }, { "id": "PMC2829055-02-Results-Discussion-06_T13", "type": "Organism", "text": [ "flea" ], "offsets": [ [ 1481, 1485 ] ], "normalized": [] }, { "id": "PMC2829055-02-Results-Discussion-06_T14", "type": "Organism", "text": [ "flea" ], "offsets": [ [ 1507, 1511 ] ], "normalized": [] }, { "id": "PMC2829055-02-Results-Discussion-06_T15", "type": "Protein", "text": [ "cafR" ], "offsets": [ [ 1536, 1540 ] ], "normalized": [] }, { "id": "PMC2829055-02-Results-Discussion-06_T16", "type": "Protein", "text": [ "caf1M" ], "offsets": [ [ 1540, 1545 ] ], "normalized": [] }, { "id": "PMC2829055-02-Results-Discussion-06_T17", "type": "Protein", "text": [ "1A" ], "offsets": [ [ 1545, 1547 ] ], "normalized": [] }, { "id": "PMC2829055-02-Results-Discussion-06_T18", "type": "Protein", "text": [ "1" ], "offsets": [ [ 1547, 1548 ] ], "normalized": [] }, { "id": "PMC2829055-02-Results-Discussion-06_T19", "type": "Protein", "text": [ "psaC" ], "offsets": [ [ 1586, 1590 ] ], "normalized": [] }, { "id": "PMC2829055-02-Results-Discussion-06_T20", "type": "Organism", "text": [ "Y. pestis" ], "offsets": [ [ 1696, 1705 ] ], "normalized": [] }, { "id": "PMC2829055-02-Results-Discussion-06_T21", "type": "Protein", "text": [ "phoP" ], "offsets": [ [ 1844, 1848 ] ], "normalized": [] }, { "id": "PMC2829055-02-Results-Discussion-06_T22", "type": "Protein", "text": [ "mgtC" ], "offsets": [ [ 1853, 1857 ] ], "normalized": [] }, { "id": "PMC2829055-02-Results-Discussion-06_T23", "type": "Organism", "text": [ "Y. pestis" ], "offsets": [ [ 1877, 1886 ] ], "normalized": [] }, { "id": "PMC2829055-02-Results-Discussion-06_T24", "type": "Organism", "text": [ "flea" ], "offsets": [ [ 1995, 1999 ] ], "normalized": [] }, { "id": "PMC2829055-02-Results-Discussion-06_T25", "type": "Protein", "text": [ "yadBC" ], "offsets": [ [ 2055, 2060 ] ], "normalized": [] }, { "id": "PMC2829055-02-Results-Discussion-06_T26", "type": "Protein", "text": [ "pla" ], "offsets": [ [ 2065, 2068 ] ], "normalized": [] }, { "id": "PMC2829055-02-Results-Discussion-06_T27", "type": "Organism", "text": [ "Y. pestis" ], "offsets": [ [ 2084, 2093 ] ], "normalized": [] }, { "id": "PMC2829055-02-Results-Discussion-06_T28", "type": "Organism", "text": [ "flea" ], "offsets": [ [ 2172, 2176 ] ], "normalized": [] }, { "id": "PMC2829055-02-Results-Discussion-06_T29", "type": "Protein", "text": [ "Pla" ], "offsets": [ [ 2228, 2231 ] ], "normalized": [] }, { "id": "PMC2829055-02-Results-Discussion-06_T30", "type": "Organism", "text": [ "Y. pestis" ], "offsets": [ [ 2353, 2362 ] ], "normalized": [] }, { "id": "PMC2829055-02-Results-Discussion-06_T31", "type": "Organism", "text": [ "flea" ], "offsets": [ [ 2370, 2374 ] ], "normalized": [] }, { "id": "PMC2829055-02-Results-Discussion-06_T32", "type": "Organism", "text": [ "Y. pestis" ], "offsets": [ [ 2388, 2397 ] ], "normalized": [] }, { "id": "PMC2829055-02-Results-Discussion-06_T33", "type": "Organism", "text": [ "flea" ], "offsets": [ [ 2471, 2475 ] ], "normalized": [] }, { "id": "PMC2829055-02-Results-Discussion-06_T34", "type": "Organism", "text": [ "Y. pestis" ], "offsets": [ [ 2509, 2518 ] ], "normalized": [] }, { "id": "PMC2829055-02-Results-Discussion-06_T35", "type": "Organism", "text": [ "flea" ], "offsets": [ [ 2584, 2588 ] ], "normalized": [] }, { "id": "PMC2829055-02-Results-Discussion-06_T36", "type": "Organism", "text": [ "flea" ], "offsets": [ [ 2809, 2813 ] ], "normalized": [] }, { "id": "PMC2829055-02-Results-Discussion-06_T37", "type": "Organism", "text": [ "fleas" ], "offsets": [ [ 2880, 2885 ] ], "normalized": [] }, { "id": "PMC2829055-02-Results-Discussion-06_T38", "type": "Organism", "text": [ "Y. pestis" ], "offsets": [ [ 2944, 2953 ] ], "normalized": [] } ]

[ { "id": "PMC2829055-02-Results-Discussion-06_E1", "type": "Process", "trigger": { "text": [ "resist" ], "offsets": [ [ 59, 65 ] ] }, "arguments": [ { "role": "Participant", "ref_id": "PMC2829055-02-Results-Discussion-06_T2" } ] }, { "id": "PMC2829055-02-Results-Discussion-06_E2", "type": "Process", "trigger": { "text": [ "infected" ], "offsets": [ [ 146, 154 ] ] }, "arguments": [ { "role": "Participant", "ref_id": "PMC2829055-02-Results-Discussion-06_T3" } ] }, { "id": "PMC2829055-02-Results-Discussion-06_E3", "type": "Process", "trigger": { "text": [ "virulence" ], "offsets": [ [ 260, 269 ] ] }, "arguments": [] }, { "id": "PMC2829055-02-Results-Discussion-06_E4", "type": "Process", "trigger": { "text": [ "virulence" ], "offsets": [ [ 367, 376 ] ] }, "arguments": [] }, { "id": "PMC2829055-02-Results-Discussion-06_E5", "type": "Process", "trigger": { "text": [ "infection" ], "offsets": [ [ 474, 483 ] ] }, "arguments": [] }, { "id": "PMC2829055-02-Results-Discussion-06_E6", "type": "Process", "trigger": { "text": [ "virulence" ], "offsets": [ [ 817, 826 ] ] }, "arguments": [] }, { "id": "PMC2829055-02-Results-Discussion-06_E7", "type": "Process", "trigger": { "text": [ "infective" ], "offsets": [ [ 968, 977 ] ] }, "arguments": [] }, { "id": "PMC2829055-02-Results-Discussion-06_E8", "type": "Process", "trigger": { "text": [ "resistant" ], "offsets": [ [ 997, 1006 ] ] }, "arguments": [] }, { "id": "PMC2829055-02-Results-Discussion-06_E9", "type": "Positive_regulation", "trigger": { "text": [ "upregulation" ], "offsets": [ [ 1487, 1499 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC2829055-02-Results-Discussion-06_T17" } ] }, { "id": "PMC2829055-02-Results-Discussion-06_E10", "type": "Positive_regulation", "trigger": { "text": [ "upregulation" ], "offsets": [ [ 1487, 1499 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC2829055-02-Results-Discussion-06_T18" } ] }, { "id": "PMC2829055-02-Results-Discussion-06_E11", "type": "Positive_regulation", "trigger": { "text": [ "upregulation" ], "offsets": [ [ 1487, 1499 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC2829055-02-Results-Discussion-06_T19" } ] }, { "id": "PMC2829055-02-Results-Discussion-06_E12", "type": "Positive_regulation", "trigger": { "text": [ "upregulation" ], "offsets": [ [ 1487, 1499 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC2829055-02-Results-Discussion-06_T15" } ] }, { "id": "PMC2829055-02-Results-Discussion-06_E13", "type": "Positive_regulation", "trigger": { "text": [ "upregulation" ], "offsets": [ [ 1487, 1499 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC2829055-02-Results-Discussion-06_T16" } ] }, { "id": "PMC2829055-02-Results-Discussion-06_E14", "type": "Process", "trigger": { "text": [ "virulence" ], "offsets": [ [ 1749, 1758 ] ] }, "arguments": [] }, { "id": "PMC2829055-02-Results-Discussion-06_E15", "type": "Positive_regulation", "trigger": { "text": [ "upregulation" ], "offsets": [ [ 1791, 1803 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC2829055-02-Results-Discussion-06_T21" } ] }, { "id": "PMC2829055-02-Results-Discussion-06_E16", "type": "Positive_regulation", "trigger": { "text": [ "upregulation" ], "offsets": [ [ 1791, 1803 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC2829055-02-Results-Discussion-06_T22" } ] }, { "id": "PMC2829055-02-Results-Discussion-06_E17", "type": "Process", "trigger": { "text": [ "resistance" ], "offsets": [ [ 1827, 1837 ] ] }, "arguments": [] }, { "id": "PMC2829055-02-Results-Discussion-06_E18", "type": "Process", "trigger": { "text": [ "resistance" ], "offsets": [ [ 1929, 1939 ] ] }, "arguments": [] }, { "id": "PMC2829055-02-Results-Discussion-06_E19", "type": "Process", "trigger": { "text": [ "virulence" ], "offsets": [ [ 2037, 2046 ] ] }, "arguments": [] }, { "id": "PMC2829055-02-Results-Discussion-06_E20", "type": "Gene_expression", "trigger": { "text": [ "expressed" ], "offsets": [ [ 2155, 2164 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC2829055-02-Results-Discussion-06_T25" } ] }, { "id": "PMC2829055-02-Results-Discussion-06_E21", "type": "Gene_expression", "trigger": { "text": [ "expressed" ], "offsets": [ [ 2155, 2164 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC2829055-02-Results-Discussion-06_T26" } ] }, { "id": "PMC2829055-02-Results-Discussion-06_E22", "type": "Process", "trigger": { "text": [ "virulence" ], "offsets": [ [ 2527, 2536 ] ] }, "arguments": [] }, { "id": "PMC2829055-02-Results-Discussion-06_E23", "type": "Process", "trigger": { "text": [ "virulence" ], "offsets": [ [ 2701, 2710 ] ] }, "arguments": [] }, { "id": "PMC2829055-02-Results-Discussion-06_E24", "type": "Process", "trigger": { "text": [ "resistance" ], "offsets": [ [ 2753, 2763 ] ] }, "arguments": [] } ]

[]

[]

[ { "id": "PMC2565068-03-Discussion__text", "type": "abstract", "text": [ "Discussion \nIt have been demonstrated that CsrS/R is a member of the two-component regulatory systems for regulating the multipe virulence factors of GAS, by using genetically- manipulated GAS mutants [20]. The present study demonstrate that the loss-of-functional mutations in csrS gene which were accumulated in clinically isolated GAS from patients with severe invasive infections, but not with emm-matched non-invasive strains. The csrS mutations enhanced the expression of scpC and slo, associated with the evasion of PMN functions and in vivo virulence. Introduction of the intact csrS gene into the severe invasive GAS restored the susceptibility to the killing by PMN and abrogated the activity for inhibition of PMN recruitment and survival, thus, demonstrating an instructional role of the loss-of-functional mutations in csrS gene for the evasion of PMN functions, providing unique pathophysiology of invasive GAS infections. Previous studies using animal-passaged GAS have shown that mutations in both csrS and csrR gene are important for the invasive phenotype [5], [6], and mutation frequency of csrS and csrR seems to be the same [21]. However, the severe invasive isolates analyzed in this study accumulated mutations in the csrS gene but not in the csrR gene (Figure 5B and data not shown). Then we further examined whether severe invasive isolates of other than emm49 genotype have the mutation of the csrS and the csrR genes. The frequency of the mutation in the csrS gene is higher than that in csrR (csrS mutation:csrR mutation=59:19) (manuscript in preparation), suggesting the csrS mutation is more important in comparison with that of csrR in the clinical isolates regardless of emm genotypes. Furthermore, the expression of some human invasive disease-associated genes [5] including slo was enhanced in the csrS mutant (Figure 5B), but not in the csrR mutant [20]. On the contrary of a dogma that CsrS/R is a definitive member of the two-component regulatory systems, which involve a coordinate pair of proteins known as the sensor kinase and the response regulator [20], CsrS may transmit a signal not only to CsrR but also to other regulators. This dominant role of CsrS is the first important observation in this study, and its mutation is possibly more important than that of csrR in terms of etiopathogenesis of human severe invasive diseases. Numbers of studies has pointed out virulent factors to evade host defense using genetically-manipulated GAS and animal models [18], [22], [23], although the significance of each factor to invasive infection is diverse and sometimes controversial, perhaps due to lack of proper non-invasive counterpart. As examples, SpeB [22] and SLS [23] have been proposed as an invasive infection-associated factor by its cytotoxic effect, however, speB and sagA expression is not enhanced in any csrS-mutated severe invasive GAS isolate used in this study and others [5], [24]. Furthermore, SLS hemolytic activity of invasive GAS is significantly decreased as compared with non-invasive strains (data not shown) and SLS-deletion in invasive GAS did not affect PMN survival at all, excluding the possibility for the role of SLS in PMN necrosis seen in this study. Extracellular deoxyribonuclease (DNase) is a virulence factor that protects emm1 type GAS against neutrophil killing by degrading the DNA framework of neutrophil extracelluar traps (NETs) [25], [26]. However, we confirmed that addition of DNase in the culture did not alter the level of PI-positive PMN, meaning bright PI staining of PMN is not due to release of NETs from PMN (Figure S1A). DNase activity of the emm49 severe invasive GAS was lower than that of non-invasive GAS (Figure S1B), possibly due to the difference of emm type. The expression of DNase as well as the slo and the scpC genes in emm1-genotype strains was enhanced under the csrS mutation [5]. These suggest that DNase may be important but redundant for induction of invasive diseases. Therefore, the second important observation in the present study is that an essential requirement of csrS mutation for invasive infection is associated with increased expression of ScpC and SLO and in vitro evasion of PMN functions, though we do not exclude the possibility that other CsrS-regulating factors contribute to the escape of invasive GAS from host defense. SLO and ScpC independently enable GAS to escape from PMN functions; Present data using clinical isolated GAS and a scpC-deletion mutant (Figure 4A and 4B) show that enhanced production of serine proteinase ScpC in virulent GAS is essential to impair PMN migration in vitro by degradation of IL-8, as others partially have demonstrated [17]-[19]. The present study also uncovers that increased activity of SLO from invasive GAS isolates induces rapid and extensive necrosis to human PMN. SLO is a cholesterol-binding pore-forming hemolysin as well as cytotoxic for other cells [15]. A study has demonstrated SLO from invasive GAS lyse PMN [27], however this effect is likely due to complement activation by SLO [28] or PMN activation [29] but not due to cytotoxity of SLO itself as judged by their flow cytometry profiles which are distinct from ours (Figure 2A). In the present study, we observed that SLO concentration in a short-time culture with severe invasive GAS did not reach the threshold level to kill PMN by formation of pores (data not shown) and that PMN did not undergo necrosis upon incubation with culture media of severe invasive GAS (Figure 3B), leading to the novel possibility that PMN are probably killed following encounter with invasive GAS in a contact-dependent manner. PMN-binding GAS may make a small interface containing a high concentration of SLO between bacteria and PMN, which resembles to killing mechanism of killer cells to target cells [30]. Collaboration of SLO with other toxins may be critical to induce PMN necrosis as similarly mechanism has been reported [31], although it remains to be examined whether there exist explore interaction-associated molecules on both host and bacterial membrane is needed. In contrast to the previous view [18], we observed that both of ScpC and SLO together, but not each of them, mediated sufficient in vivo virulence (Table 1), thus compatible with the notion that plural virulence-associated factors under the regulation of csrS abrogate PMN bactericidal functions and induce invasive diseases in in vivo animal model. Consistently, the high mortality and histopathological findings which lacks PMN infiltration in mice tissues infected with csrS-mutated GAS (Figure 7) are similar to those seen in clinical invasive GAS infections [32]. Thus, these results suggest that the ability of incompetence for PMN functions by individual GAS strain may determine the induction and clinical outcome of invasive diseases. Several clinical reports seem to support this hypothesis; Leukocytopenia seen in patients with STSS is more severe than that with non-STSS [33], and invasive GAS-infected patients with leukocytopenia show worse prognosis than those without leukocytopenia [33], [34]. Furthermore, predisposing factors for severe invasive GAS infection [9], such as diabetes mellitus [35], liver cirrhosis [36], and congestive heart failure [37] are known to impair PMN function. These evidences suggest that the level of PMN function is one of the critical factors to determine the threshold for the onset of invasive GAS infection, which may be the reason for rare outbreaks of invasive GAS infections. Thus, enhanced expression of virulence factors that could evade PMN function is a key issue at first step to cause invasive bacterial infections. A further study in which collates clinical with bacterial/immunological data may provide with novel clues for early diagnosis and therapeutics of invasive bacterial infections.\n" ], "offsets": [ [ 0, 7850 ] ] } ]

[ { "id": "PMC2565068-03-Discussion_T1", "type": "Two-component-system", "text": [ "CsrS/R" ], "offsets": [ [ 43, 49 ] ], "normalized": [] }, { "id": "PMC2565068-03-Discussion_T2", "type": "Protein", "text": [ "CsrS" ], "offsets": [ [ 43, 47 ] ], "normalized": [] }, { "id": "PMC2565068-03-Discussion_T3", "type": "Protein", "text": [ "R" ], "offsets": [ [ 48, 49 ] ], "normalized": [] }, { "id": "PMC2565068-03-Discussion_T4", "type": "Organism", "text": [ "GAS" ], "offsets": [ [ 150, 153 ] ], "normalized": [] }, { "id": "PMC2565068-03-Discussion_T5", "type": "Organism", "text": [ "genetically- manipulated GAS" ], "offsets": [ [ 164, 192 ] ], "normalized": [] }, { "id": "PMC2565068-03-Discussion_T6", "type": "Protein", "text": [ "csrS" ], "offsets": [ [ 278, 282 ] ], "normalized": [] }, { "id": "PMC2565068-03-Discussion_T7", "type": "Organism", "text": [ "GAS" ], "offsets": [ [ 334, 337 ] ], "normalized": [] }, { "id": "PMC2565068-03-Discussion_T8", "type": "Organism", "text": [ "patients" ], "offsets": [ [ 343, 351 ] ], "normalized": [] }, { "id": "PMC2565068-03-Discussion_T9", "type": "Protein", "text": [ "csrS" ], "offsets": [ [ 436, 440 ] ], "normalized": [] }, { "id": "PMC2565068-03-Discussion_T10", "type": "Protein", "text": [ "scpC" ], "offsets": [ [ 478, 482 ] ], "normalized": [] }, { "id": "PMC2565068-03-Discussion_T11", "type": "Protein", "text": [ "slo" ], "offsets": [ [ 487, 490 ] ], "normalized": [] }, { "id": "PMC2565068-03-Discussion_T12", "type": "Protein", "text": [ "csrS" ], "offsets": [ [ 587, 591 ] ], "normalized": [] }, { "id": "PMC2565068-03-Discussion_T13", "type": "Organism", "text": [ "invasive GAS" ], "offsets": [ [ 613, 625 ] ], "normalized": [] }, { "id": "PMC2565068-03-Discussion_T14", "type": "Protein", "text": [ "csrS" ], "offsets": [ [ 832, 836 ] ], "normalized": [] }, { "id": "PMC2565068-03-Discussion_T15", "type": "Organism", "text": [ "GAS" ], "offsets": [ [ 921, 924 ] ], "normalized": [] }, { "id": "PMC2565068-03-Discussion_T16", "type": "Organism", "text": [ "GAS" ], "offsets": [ [ 976, 979 ] ], "normalized": [] }, { "id": "PMC2565068-03-Discussion_T17", "type": "Protein", "text": [ "csrS" ], "offsets": [ [ 1014, 1018 ] ], "normalized": [] }, { "id": "PMC2565068-03-Discussion_T18", "type": "Protein", "text": [ "csrR" ], "offsets": [ [ 1023, 1027 ] ], "normalized": [] }, { "id": "PMC2565068-03-Discussion_T19", "type": "Protein", "text": [ "csrS" ], "offsets": [ [ 1110, 1114 ] ], "normalized": [] }, { "id": "PMC2565068-03-Discussion_T20", "type": "Protein", "text": [ "csrR" ], "offsets": [ [ 1119, 1123 ] ], "normalized": [] }, { "id": "PMC2565068-03-Discussion_T21", "type": "Protein", "text": [ "csrS" ], "offsets": [ [ 1241, 1245 ] ], "normalized": [] }, { "id": "PMC2565068-03-Discussion_T22", "type": "Protein", "text": [ "csrR" ], "offsets": [ [ 1266, 1270 ] ], "normalized": [] }, { "id": "PMC2565068-03-Discussion_T23", "type": "Protein", "text": [ "emm49" ], "offsets": [ [ 1380, 1385 ] ], "normalized": [] }, { "id": "PMC2565068-03-Discussion_T24", "type": "Protein", "text": [ "csrS" ], "offsets": [ [ 1420, 1424 ] ], "normalized": [] }, { "id": "PMC2565068-03-Discussion_T25", "type": "Protein", "text": [ "csrR" ], "offsets": [ [ 1433, 1437 ] ], "normalized": [] }, { "id": "PMC2565068-03-Discussion_T26", "type": "Protein", "text": [ "csrS" ], "offsets": [ [ 1482, 1486 ] ], "normalized": [] }, { "id": "PMC2565068-03-Discussion_T27", "type": "Protein", "text": [ "csrR" ], "offsets": [ [ 1515, 1519 ] ], "normalized": [] }, { "id": "PMC2565068-03-Discussion_T28", "type": "Protein", "text": [ "csrS" ], "offsets": [ [ 1521, 1525 ] ], "normalized": [] }, { "id": "PMC2565068-03-Discussion_T29", "type": "Protein", "text": [ "csrR" ], "offsets": [ [ 1535, 1539 ] ], "normalized": [] }, { "id": "PMC2565068-03-Discussion_T30", "type": "Protein", "text": [ "csrS" ], "offsets": [ [ 1600, 1604 ] ], "normalized": [] }, { "id": "PMC2565068-03-Discussion_T31", "type": "Protein", "text": [ "csrR" ], "offsets": [ [ 1659, 1663 ] ], "normalized": [] }, { "id": "PMC2565068-03-Discussion_T32", "type": "Protein", "text": [ "emm" ], "offsets": [ [ 1703, 1706 ] ], "normalized": [] }, { "id": "PMC2565068-03-Discussion_T33", "type": "Organism", "text": [ "human" ], "offsets": [ [ 1754, 1759 ] ], "normalized": [] }, { "id": "PMC2565068-03-Discussion_T34", "type": "Protein", "text": [ "slo" ], "offsets": [ [ 1808, 1811 ] ], "normalized": [] }, { "id": "PMC2565068-03-Discussion_T35", "type": "Organism", "text": [ "csrS mutant" ], "offsets": [ [ 1832, 1843 ] ], "normalized": [] }, { "id": "PMC2565068-03-Discussion_T36", "type": "Protein", "text": [ "csrS" ], "offsets": [ [ 1832, 1836 ] ], "normalized": [] }, { "id": "PMC2565068-03-Discussion_T37", "type": "Organism", "text": [ "csrR mutant" ], "offsets": [ [ 1872, 1883 ] ], "normalized": [] }, { "id": "PMC2565068-03-Discussion_T38", "type": "Protein", "text": [ "csrR" ], "offsets": [ [ 1872, 1876 ] ], "normalized": [] }, { "id": "PMC2565068-03-Discussion_T39", "type": "Two-component-system", "text": [ "CsrS/R" ], "offsets": [ [ 1922, 1928 ] ], "normalized": [] }, { "id": "PMC2565068-03-Discussion_T40", "type": "Protein", "text": [ "CsrS" ], "offsets": [ [ 1922, 1926 ] ], "normalized": [] }, { "id": "PMC2565068-03-Discussion_T41", "type": "Protein", "text": [ "R" ], "offsets": [ [ 1927, 1928 ] ], "normalized": [] }, { "id": "PMC2565068-03-Discussion_T42", "type": "Protein", "text": [ "CsrS" ], "offsets": [ [ 2097, 2101 ] ], "normalized": [] }, { "id": "PMC2565068-03-Discussion_T43", "type": "Protein", "text": [ "CsrR" ], "offsets": [ [ 2136, 2140 ] ], "normalized": [] }, { "id": "PMC2565068-03-Discussion_T44", "type": "Protein", "text": [ "CsrS" ], "offsets": [ [ 2193, 2197 ] ], "normalized": [] }, { "id": "PMC2565068-03-Discussion_T45", "type": "Protein", "text": [ "csrR" ], "offsets": [ [ 2305, 2309 ] ], "normalized": [] }, { "id": "PMC2565068-03-Discussion_T46", "type": "Organism", "text": [ "human" ], "offsets": [ [ 2342, 2347 ] ], "normalized": [] }, { "id": "PMC2565068-03-Discussion_T47", "type": "Organism", "text": [ "GAS" ], "offsets": [ [ 2478, 2481 ] ], "normalized": [] }, { "id": "PMC2565068-03-Discussion_T48", "type": "Protein", "text": [ "SpeB" ], "offsets": [ [ 2690, 2694 ] ], "normalized": [] }, { "id": "PMC2565068-03-Discussion_T49", "type": "Protein", "text": [ "SLS" ], "offsets": [ [ 2704, 2707 ] ], "normalized": [] }, { "id": "PMC2565068-03-Discussion_T50", "type": "Protein", "text": [ "speB" ], "offsets": [ [ 2809, 2813 ] ], "normalized": [] }, { "id": "PMC2565068-03-Discussion_T51", "type": "Protein", "text": [ "sagA" ], "offsets": [ [ 2818, 2822 ] ], "normalized": [] }, { "id": "PMC2565068-03-Discussion_T52", "type": "Organism", "text": [ "csrS-mutated severe invasive GAS" ], "offsets": [ [ 2857, 2889 ] ], "normalized": [] }, { "id": "PMC2565068-03-Discussion_T53", "type": "Protein", "text": [ "csrS" ], "offsets": [ [ 2857, 2861 ] ], "normalized": [] }, { "id": "PMC2565068-03-Discussion_T54", "type": "Protein", "text": [ "SLS" ], "offsets": [ [ 2952, 2955 ] ], "normalized": [] }, { "id": "PMC2565068-03-Discussion_T55", "type": "Organism", "text": [ "invasive GAS" ], "offsets": [ [ 2978, 2990 ] ], "normalized": [] }, { "id": "PMC2565068-03-Discussion_T56", "type": "Organism", "text": [ "non-invasive strains" ], "offsets": [ [ 3035, 3055 ] ], "normalized": [] }, { "id": "PMC2565068-03-Discussion_T57", "type": "Organism", "text": [ "SLS-deletion in invasive GAS" ], "offsets": [ [ 3077, 3105 ] ], "normalized": [] }, { "id": "PMC2565068-03-Discussion_T58", "type": "Protein", "text": [ "SLS" ], "offsets": [ [ 3077, 3080 ] ], "normalized": [] }, { "id": "PMC2565068-03-Discussion_T59", "type": "Protein", "text": [ "SLS" ], "offsets": [ [ 3184, 3187 ] ], "normalized": [] }, { "id": "PMC2565068-03-Discussion_T60", "type": "Protein", "text": [ "Extracellular deoxyribonuclease" ], "offsets": [ [ 3224, 3255 ] ], "normalized": [] }, { "id": "PMC2565068-03-Discussion_T61", "type": "Protein", "text": [ "DNase" ], "offsets": [ [ 3257, 3262 ] ], "normalized": [] }, { "id": "PMC2565068-03-Discussion_T62", "type": "Organism", "text": [ "emm1 type GAS" ], "offsets": [ [ 3300, 3313 ] ], "normalized": [] }, { "id": "PMC2565068-03-Discussion_T63", "type": "Protein", "text": [ "emm1" ], "offsets": [ [ 3300, 3304 ] ], "normalized": [] }, { "id": "PMC2565068-03-Discussion_T64", "type": "Protein", "text": [ "DNase" ], "offsets": [ [ 3463, 3468 ] ], "normalized": [] }, { "id": "PMC2565068-03-Discussion_T65", "type": "Chemical", "text": [ "PI" ], "offsets": [ [ 3511, 3513 ] ], "normalized": [] }, { "id": "PMC2565068-03-Discussion_T66", "type": "Chemical", "text": [ "PI" ], "offsets": [ [ 3543, 3545 ] ], "normalized": [] }, { "id": "PMC2565068-03-Discussion_T67", "type": "Protein", "text": [ "DNase" ], "offsets": [ [ 3615, 3620 ] ], "normalized": [] }, { "id": "PMC2565068-03-Discussion_T68", "type": "Organism", "text": [ "emm49 severe invasive GAS" ], "offsets": [ [ 3637, 3662 ] ], "normalized": [] }, { "id": "PMC2565068-03-Discussion_T69", "type": "Protein", "text": [ "emm49" ], "offsets": [ [ 3637, 3642 ] ], "normalized": [] }, { "id": "PMC2565068-03-Discussion_T70", "type": "Organism", "text": [ "non-invasive GAS" ], "offsets": [ [ 3686, 3702 ] ], "normalized": [] }, { "id": "PMC2565068-03-Discussion_T71", "type": "Protein", "text": [ "DNase" ], "offsets": [ [ 3779, 3784 ] ], "normalized": [] }, { "id": "PMC2565068-03-Discussion_T72", "type": "Protein", "text": [ "slo" ], "offsets": [ [ 3800, 3803 ] ], "normalized": [] }, { "id": "PMC2565068-03-Discussion_T73", "type": "Protein", "text": [ "scpC" ], "offsets": [ [ 3812, 3816 ] ], "normalized": [] }, { "id": "PMC2565068-03-Discussion_T74", "type": "Organism", "text": [ "emm1-genotype strains" ], "offsets": [ [ 3826, 3847 ] ], "normalized": [] }, { "id": "PMC2565068-03-Discussion_T75", "type": "Protein", "text": [ "emm1" ], "offsets": [ [ 3826, 3830 ] ], "normalized": [] }, { "id": "PMC2565068-03-Discussion_T76", "type": "Protein", "text": [ "csrS" ], "offsets": [ [ 3871, 3875 ] ], "normalized": [] }, { "id": "PMC2565068-03-Discussion_T77", "type": "Protein", "text": [ "DNase" ], "offsets": [ [ 3909, 3914 ] ], "normalized": [] }, { "id": "PMC2565068-03-Discussion_T78", "type": "Protein", "text": [ "csrS" ], "offsets": [ [ 4083, 4087 ] ], "normalized": [] }, { "id": "PMC2565068-03-Discussion_T79", "type": "Protein", "text": [ "ScpC" ], "offsets": [ [ 4163, 4167 ] ], "normalized": [] }, { "id": "PMC2565068-03-Discussion_T80", "type": "Protein", "text": [ "SLO" ], "offsets": [ [ 4172, 4175 ] ], "normalized": [] }, { "id": "PMC2565068-03-Discussion_T81", "type": "Protein", "text": [ "CsrS" ], "offsets": [ [ 4267, 4271 ] ], "normalized": [] }, { "id": "PMC2565068-03-Discussion_T82", "type": "Organism", "text": [ "invasive GAS" ], "offsets": [ [ 4319, 4331 ] ], "normalized": [] }, { "id": "PMC2565068-03-Discussion_T83", "type": "Protein", "text": [ "SLO" ], "offsets": [ [ 4351, 4354 ] ], "normalized": [] }, { "id": "PMC2565068-03-Discussion_T84", "type": "Protein", "text": [ "ScpC" ], "offsets": [ [ 4359, 4363 ] ], "normalized": [] }, { "id": "PMC2565068-03-Discussion_T85", "type": "Organism", "text": [ "GAS" ], "offsets": [ [ 4385, 4388 ] ], "normalized": [] }, { "id": "PMC2565068-03-Discussion_T86", "type": "Organism", "text": [ "GAS" ], "offsets": [ [ 4456, 4459 ] ], "normalized": [] }, { "id": "PMC2565068-03-Discussion_T87", "type": "Organism", "text": [ "scpC-deletion mutant" ], "offsets": [ [ 4466, 4486 ] ], "normalized": [] }, { "id": "PMC2565068-03-Discussion_T88", "type": "Protein", "text": [ "scpC" ], "offsets": [ [ 4466, 4470 ] ], "normalized": [] }, { "id": "PMC2565068-03-Discussion_T89", "type": "Protein", "text": [ "ScpC" ], "offsets": [ [ 4557, 4561 ] ], "normalized": [] }, { "id": "PMC2565068-03-Discussion_T90", "type": "Organism", "text": [ "GAS" ], "offsets": [ [ 4574, 4577 ] ], "normalized": [] }, { "id": "PMC2565068-03-Discussion_T91", "type": "Protein", "text": [ "IL-8" ], "offsets": [ [ 4642, 4646 ] ], "normalized": [] }, { "id": "PMC2565068-03-Discussion_T92", "type": "Protein", "text": [ "SLO" ], "offsets": [ [ 4756, 4759 ] ], "normalized": [] }, { "id": "PMC2565068-03-Discussion_T93", "type": "Organism", "text": [ "GAS" ], "offsets": [ [ 4774, 4777 ] ], "normalized": [] }, { "id": "PMC2565068-03-Discussion_T94", "type": "Organism", "text": [ "human" ], "offsets": [ [ 4827, 4832 ] ], "normalized": [] }, { "id": "PMC2565068-03-Discussion_T95", "type": "Protein", "text": [ "SLO" ], "offsets": [ [ 4838, 4841 ] ], "normalized": [] }, { "id": "PMC2565068-03-Discussion_T96", "type": "Chemical", "text": [ "cholesterol" ], "offsets": [ [ 4847, 4858 ] ], "normalized": [] }, { "id": "PMC2565068-03-Discussion_T97", "type": "Protein", "text": [ "SLO" ], "offsets": [ [ 4958, 4961 ] ], "normalized": [] }, { "id": "PMC2565068-03-Discussion_T98", "type": "Organism", "text": [ "GAS" ], "offsets": [ [ 4976, 4979 ] ], "normalized": [] }, { "id": "PMC2565068-03-Discussion_T99", "type": "Protein", "text": [ "SLO" ], "offsets": [ [ 5057, 5060 ] ], "normalized": [] }, { "id": "PMC2565068-03-Discussion_T100", "type": "Protein", "text": [ "SLO" ], "offsets": [ [ 5118, 5121 ] ], "normalized": [] }, { "id": "PMC2565068-03-Discussion_T101", "type": "Protein", "text": [ "SLO" ], "offsets": [ [ 5253, 5256 ] ], "normalized": [] }, { "id": "PMC2565068-03-Discussion_T102", "type": "Organism", "text": [ "invasive GAS" ], "offsets": [ [ 5307, 5319 ] ], "normalized": [] }, { "id": "PMC2565068-03-Discussion_T103", "type": "Organism", "text": [ "invasive GAS" ], "offsets": [ [ 5488, 5500 ] ], "normalized": [] }, { "id": "PMC2565068-03-Discussion_T104", "type": "Organism", "text": [ "invasive GAS" ], "offsets": [ [ 5601, 5613 ] ], "normalized": [] }, { "id": "PMC2565068-03-Discussion_T105", "type": "Organism", "text": [ "GAS" ], "offsets": [ [ 5657, 5660 ] ], "normalized": [] }, { "id": "PMC2565068-03-Discussion_T106", "type": "Protein", "text": [ "SLO" ], "offsets": [ [ 5723, 5726 ] ], "normalized": [] }, { "id": "PMC2565068-03-Discussion_T107", "type": "Protein", "text": [ "SLO" ], "offsets": [ [ 5845, 5848 ] ], "normalized": [] }, { "id": "PMC2565068-03-Discussion_T108", "type": "Protein", "text": [ "ScpC" ], "offsets": [ [ 6160, 6164 ] ], "normalized": [] }, { "id": "PMC2565068-03-Discussion_T109", "type": "Protein", "text": [ "SLO" ], "offsets": [ [ 6169, 6172 ] ], "normalized": [] }, { "id": "PMC2565068-03-Discussion_T110", "type": "Protein", "text": [ "csrS" ], "offsets": [ [ 6351, 6355 ] ], "normalized": [] }, { "id": "PMC2565068-03-Discussion_T111", "type": "Organism", "text": [ "mice" ], "offsets": [ [ 6542, 6546 ] ], "normalized": [] }, { "id": "PMC2565068-03-Discussion_T112", "type": "Organism", "text": [ "csrS-mutated GAS" ], "offsets": [ [ 6569, 6585 ] ], "normalized": [] }, { "id": "PMC2565068-03-Discussion_T113", "type": "Protein", "text": [ "csrS" ], "offsets": [ [ 6569, 6573 ] ], "normalized": [] }, { "id": "PMC2565068-03-Discussion_T114", "type": "Organism", "text": [ "invasive GAS" ], "offsets": [ [ 6635, 6647 ] ], "normalized": [] }, { "id": "PMC2565068-03-Discussion_T115", "type": "Organism", "text": [ "GAS" ], "offsets": [ [ 6758, 6761 ] ], "normalized": [] }, { "id": "PMC2565068-03-Discussion_T116", "type": "Organism", "text": [ "patients" ], "offsets": [ [ 6921, 6929 ] ], "normalized": [] }, { "id": "PMC2565068-03-Discussion_T117", "type": "Organism", "text": [ "invasive GAS" ], "offsets": [ [ 6989, 7001 ] ], "normalized": [] }, { "id": "PMC2565068-03-Discussion_T118", "type": "Organism", "text": [ "patients" ], "offsets": [ [ 7011, 7019 ] ], "normalized": [] }, { "id": "PMC2565068-03-Discussion_T119", "type": "Organism", "text": [ "invasive GAS" ], "offsets": [ [ 7152, 7164 ] ], "normalized": [] }, { "id": "PMC2565068-03-Discussion_T120", "type": "Organism", "text": [ "invasive GAS" ], "offsets": [ [ 7432, 7444 ] ], "normalized": [] }, { "id": "PMC2565068-03-Discussion_T121", "type": "Organism", "text": [ "invasive GAS" ], "offsets": [ [ 7502, 7514 ] ], "normalized": [] } ]

[ { "id": "PMC2565068-03-Discussion_E1", "type": "Process", "trigger": { "text": [ "virulence" ], "offsets": [ [ 129, 138 ] ] }, "arguments": [ { "role": "Participant", "ref_id": "PMC2565068-03-Discussion_T4" } ] }, { "id": "PMC2565068-03-Discussion_E2", "type": "Process", "trigger": { "text": [ "infections" ], "offsets": [ [ 373, 383 ] ] }, "arguments": [ { "role": "Participant", "ref_id": "PMC2565068-03-Discussion_T7" } ] }, { "id": "PMC2565068-03-Discussion_E3", "type": "Positive_regulation", "trigger": { "text": [ "enhanced" ], "offsets": [ [ 451, 459 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC2565068-03-Discussion_E5" } ] }, { "id": "PMC2565068-03-Discussion_E4", "type": "Positive_regulation", "trigger": { "text": [ "enhanced" ], "offsets": [ [ 451, 459 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC2565068-03-Discussion_E6" } ] }, { "id": "PMC2565068-03-Discussion_E5", "type": "Gene_expression", "trigger": { "text": [ "expression" ], "offsets": [ [ 464, 474 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC2565068-03-Discussion_T10" } ] }, { "id": "PMC2565068-03-Discussion_E6", "type": "Gene_expression", "trigger": { "text": [ "expression" ], "offsets": [ [ 464, 474 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC2565068-03-Discussion_T11" } ] }, { "id": "PMC2565068-03-Discussion_E7", "type": "Process", "trigger": { "text": [ "virulence" ], "offsets": [ [ 549, 558 ] ] }, "arguments": [] }, { "id": "PMC2565068-03-Discussion_E8", "type": "Gene_expression", "trigger": { "text": [ "Introduction" ], "offsets": [ [ 560, 572 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC2565068-03-Discussion_T12" } ] }, { "id": "PMC2565068-03-Discussion_E9", "type": "Process", "trigger": { "text": [ "infections" ], "offsets": [ [ 925, 935 ] ] }, "arguments": [ { "role": "Participant", "ref_id": "PMC2565068-03-Discussion_T15" } ] }, { "id": "PMC2565068-03-Discussion_E10", "type": "Gene_expression", "trigger": { "text": [ "expression" ], "offsets": [ [ 1735, 1745 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC2565068-03-Discussion_T34" } ] }, { "id": "PMC2565068-03-Discussion_E11", "type": "Positive_regulation", "trigger": { "text": [ "enhanced" ], "offsets": [ [ 1816, 1824 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC2565068-03-Discussion_E10" } ] }, { "id": "PMC2565068-03-Discussion_E12", "type": "Process", "trigger": { "text": [ "virulent" ], "offsets": [ [ 2409, 2417 ] ] }, "arguments": [] }, { "id": "PMC2565068-03-Discussion_E13", "type": "Process", "trigger": { "text": [ "infection" ], "offsets": [ [ 2571, 2580 ] ] }, "arguments": [] }, { "id": "PMC2565068-03-Discussion_E14", "type": "Process", "trigger": { "text": [ "infection" ], "offsets": [ [ 2747, 2756 ] ] }, "arguments": [] }, { "id": "PMC2565068-03-Discussion_E15", "type": "Gene_expression", "trigger": { "text": [ "expression" ], "offsets": [ [ 2823, 2833 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC2565068-03-Discussion_T50" } ] }, { "id": "PMC2565068-03-Discussion_E16", "type": "Gene_expression", "trigger": { "text": [ "expression" ], "offsets": [ [ 2823, 2833 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC2565068-03-Discussion_T51" } ] }, { "id": "PMC2565068-03-Discussion_E17", "type": "Positive_regulation", "trigger": { "text": [ "enhanced" ], "offsets": [ [ 2841, 2849 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC2565068-03-Discussion_E15" } ] }, { "id": "PMC2565068-03-Discussion_E18", "type": "Positive_regulation", "trigger": { "text": [ "enhanced" ], "offsets": [ [ 2841, 2849 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC2565068-03-Discussion_E16" } ] }, { "id": "PMC2565068-03-Discussion_E19", "type": "Process", "trigger": { "text": [ "virulence" ], "offsets": [ [ 3269, 3278 ] ] }, "arguments": [] }, { "id": "PMC2565068-03-Discussion_E20", "type": "Gene_expression", "trigger": { "text": [ "expression" ], "offsets": [ [ 3765, 3775 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC2565068-03-Discussion_T71" } ] }, { "id": "PMC2565068-03-Discussion_E21", "type": "Gene_expression", "trigger": { "text": [ "expression" ], "offsets": [ [ 3765, 3775 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC2565068-03-Discussion_T72" } ] }, { "id": "PMC2565068-03-Discussion_E22", "type": "Gene_expression", "trigger": { "text": [ "expression" ], "offsets": [ [ 3765, 3775 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC2565068-03-Discussion_T73" } ] }, { "id": "PMC2565068-03-Discussion_E23", "type": "Positive_regulation", "trigger": { "text": [ "enhanced" ], "offsets": [ [ 3852, 3860 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC2565068-03-Discussion_E20" } ] }, { "id": "PMC2565068-03-Discussion_E24", "type": "Positive_regulation", "trigger": { "text": [ "enhanced" ], "offsets": [ [ 3852, 3860 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC2565068-03-Discussion_E21" } ] }, { "id": "PMC2565068-03-Discussion_E25", "type": "Positive_regulation", "trigger": { "text": [ "enhanced" ], "offsets": [ [ 3852, 3860 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC2565068-03-Discussion_E22" } ] }, { "id": "PMC2565068-03-Discussion_E26", "type": "Process", "trigger": { "text": [ "infection" ], "offsets": [ [ 4110, 4119 ] ] }, "arguments": [] }, { "id": "PMC2565068-03-Discussion_E27", "type": "Positive_regulation", "trigger": { "text": [ "increased" ], "offsets": [ [ 4139, 4148 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC2565068-03-Discussion_E29" } ] }, { "id": "PMC2565068-03-Discussion_E28", "type": "Positive_regulation", "trigger": { "text": [ "increased" ], "offsets": [ [ 4139, 4148 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC2565068-03-Discussion_E30" } ] }, { "id": "PMC2565068-03-Discussion_E29", "type": "Gene_expression", "trigger": { "text": [ "expression" ], "offsets": [ [ 4149, 4159 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC2565068-03-Discussion_T79" } ] }, { "id": "PMC2565068-03-Discussion_E30", "type": "Gene_expression", "trigger": { "text": [ "expression" ], "offsets": [ [ 4149, 4159 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC2565068-03-Discussion_T80" } ] }, { "id": "PMC2565068-03-Discussion_E31", "type": "Process", "trigger": { "text": [ "virulent" ], "offsets": [ [ 4565, 4573 ] ] }, "arguments": [ { "role": "Participant", "ref_id": "PMC2565068-03-Discussion_T90" } ] }, { "id": "PMC2565068-03-Discussion_E32", "type": "Process", "trigger": { "text": [ "virulence" ], "offsets": [ [ 6233, 6242 ] ] }, "arguments": [] }, { "id": "PMC2565068-03-Discussion_E33", "type": "Process", "trigger": { "text": [ "virulence" ], "offsets": [ [ 6298, 6307 ] ] }, "arguments": [] }, { "id": "PMC2565068-03-Discussion_E34", "type": "Regulation", "trigger": { "text": [ "regulation" ], "offsets": [ [ 6337, 6347 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC2565068-03-Discussion_T110" } ] }, { "id": "PMC2565068-03-Discussion_E35", "type": "Process", "trigger": { "text": [ "infected" ], "offsets": [ [ 6555, 6563 ] ] }, "arguments": [ { "role": "Participant", "ref_id": "PMC2565068-03-Discussion_T112" } ] }, { "id": "PMC2565068-03-Discussion_E36", "type": "Process", "trigger": { "text": [ "infections" ], "offsets": [ [ 6648, 6658 ] ] }, "arguments": [ { "role": "Participant", "ref_id": "PMC2565068-03-Discussion_T114" } ] }, { "id": "PMC2565068-03-Discussion_E37", "type": "Process", "trigger": { "text": [ "infected" ], "offsets": [ [ 7002, 7010 ] ] }, "arguments": [ { "role": "Participant", "ref_id": "PMC2565068-03-Discussion_T117" } ] }, { "id": "PMC2565068-03-Discussion_E38", "type": "Process", "trigger": { "text": [ "infection" ], "offsets": [ [ 7165, 7174 ] ] }, "arguments": [ { "role": "Participant", "ref_id": "PMC2565068-03-Discussion_T119" } ] }, { "id": "PMC2565068-03-Discussion_E39", "type": "Process", "trigger": { "text": [ "infection" ], "offsets": [ [ 7445, 7454 ] ] }, "arguments": [ { "role": "Participant", "ref_id": "PMC2565068-03-Discussion_T120" } ] }, { "id": "PMC2565068-03-Discussion_E40", "type": "Process", "trigger": { "text": [ "infections" ], "offsets": [ [ 7515, 7525 ] ] }, "arguments": [ { "role": "Participant", "ref_id": "PMC2565068-03-Discussion_T121" } ] }, { "id": "PMC2565068-03-Discussion_E41", "type": "Process", "trigger": { "text": [ "virulence" ], "offsets": [ [ 7556, 7565 ] ] }, "arguments": [] }, { "id": "PMC2565068-03-Discussion_E42", "type": "Process", "trigger": { "text": [ "infections" ], "offsets": [ [ 7661, 7671 ] ] }, "arguments": [] }, { "id": "PMC2565068-03-Discussion_E43", "type": "Process", "trigger": { "text": [ "infections" ], "offsets": [ [ 7838, 7848 ] ] }, "arguments": [] } ]

[ { "id": "PMC2565068-03-Discussion_1", "entity_ids": [ "PMC2565068-03-Discussion_T60", "PMC2565068-03-Discussion_T61" ] } ]

[]

[ { "id": "PMC2682197-02-Results-03__text", "type": "abstract", "text": [ "Effects of environmental stress on growth of M. tuberculosis Deltarv2623 in vitro \nAlthough the functions of universal stress proteins have yet to be completely defined, there is evidence that many USPs play differential roles in protecting microbes against various environmental stresses [9]. Therefore, the hypervirulence of Deltarv2623 in guinea pigs and susceptible mice is intriguing; if Rv2623 provides M. tuberculosis protection against stress, it might be expected that the Rv2623-deficient mutant would be attenuated in vivo. The growth kinetics and survival of the Deltarv2623 strain was examined under various stress conditions, including those likely to be present during M. tuberculosis infection. These included oxidative stress (superoxide anion, O2-), DNA damage (UV irradiation, mitomycin C), heat shock (53degreesC), and acidic culture (pH 4.0). The use of streptonigrin, an antibiotic whose toxicity correlates with levels of free iron, was based on the observation that the intracellular environment of macrophages can induce a iron-scavenging response in mycobacteria [25], perhaps as a means of maintaining adequate levels of this important growth factor, and that an E. coli USP was shown to regulate iron uptake [9]. The results showed that the mutant strain was no more susceptible to growth inhibition than was wild type Erdman under all of the stress conditions tested (Figure S2). These results support the notion that it is unlikely that M. tuberculosis Rv2623 is essential for resistance to stresses encountered in the host, which is consistent with the observed in vivo hypervirulence phenotype of Deltarv2623.\n" ], "offsets": [ [ 0, 1642 ] ] } ]

[ { "id": "PMC2682197-02-Results-03_T1", "type": "Organism", "text": [ "M. tuberculosis Deltarv2623" ], "offsets": [ [ 45, 72 ] ], "normalized": [] }, { "id": "PMC2682197-02-Results-03_T2", "type": "Protein", "text": [ "rv2623" ], "offsets": [ [ 66, 72 ] ], "normalized": [] }, { "id": "PMC2682197-02-Results-03_T3", "type": "Organism", "text": [ "Deltarv2623" ], "offsets": [ [ 327, 338 ] ], "normalized": [] }, { "id": "PMC2682197-02-Results-03_T4", "type": "Protein", "text": [ "rv2623" ], "offsets": [ [ 332, 338 ] ], "normalized": [] }, { "id": "PMC2682197-02-Results-03_T5", "type": "Organism", "text": [ "guinea pigs" ], "offsets": [ [ 342, 353 ] ], "normalized": [] }, { "id": "PMC2682197-02-Results-03_T6", "type": "Organism", "text": [ "mice" ], "offsets": [ [ 370, 374 ] ], "normalized": [] }, { "id": "PMC2682197-02-Results-03_T7", "type": "Protein", "text": [ "Rv2623" ], "offsets": [ [ 393, 399 ] ], "normalized": [] }, { "id": "PMC2682197-02-Results-03_T8", "type": "Organism", "text": [ "M. tuberculosis" ], "offsets": [ [ 409, 424 ] ], "normalized": [] }, { "id": "PMC2682197-02-Results-03_T9", "type": "Organism", "text": [ "Rv2623-deficient mutant" ], "offsets": [ [ 482, 505 ] ], "normalized": [] }, { "id": "PMC2682197-02-Results-03_T10", "type": "Protein", "text": [ "Rv2623" ], "offsets": [ [ 482, 488 ] ], "normalized": [] }, { "id": "PMC2682197-02-Results-03_T11", "type": "Organism", "text": [ "Deltarv2623" ], "offsets": [ [ 575, 586 ] ], "normalized": [] }, { "id": "PMC2682197-02-Results-03_T12", "type": "Protein", "text": [ "rv2623" ], "offsets": [ [ 580, 586 ] ], "normalized": [] }, { "id": "PMC2682197-02-Results-03_T13", "type": "Organism", "text": [ "M. tuberculosis" ], "offsets": [ [ 684, 699 ] ], "normalized": [] }, { "id": "PMC2682197-02-Results-03_T14", "type": "Chemical", "text": [ "superoxide anion" ], "offsets": [ [ 744, 760 ] ], "normalized": [] }, { "id": "PMC2682197-02-Results-03_T15", "type": "Chemical", "text": [ "O2-" ], "offsets": [ [ 762, 765 ] ], "normalized": [] }, { "id": "PMC2682197-02-Results-03_T16", "type": "Chemical", "text": [ "mitomycin C" ], "offsets": [ [ 796, 807 ] ], "normalized": [] }, { "id": "PMC2682197-02-Results-03_T17", "type": "Chemical", "text": [ "streptonigrin" ], "offsets": [ [ 875, 888 ] ], "normalized": [] }, { "id": "PMC2682197-02-Results-03_T18", "type": "Chemical", "text": [ "iron" ], "offsets": [ [ 950, 954 ] ], "normalized": [] }, { "id": "PMC2682197-02-Results-03_T19", "type": "Chemical", "text": [ "iron" ], "offsets": [ [ 1048, 1052 ] ], "normalized": [] }, { "id": "PMC2682197-02-Results-03_T20", "type": "Organism", "text": [ "E. coli" ], "offsets": [ [ 1190, 1197 ] ], "normalized": [] }, { "id": "PMC2682197-02-Results-03_T21", "type": "Chemical", "text": [ "iron" ], "offsets": [ [ 1224, 1228 ] ], "normalized": [] }, { "id": "PMC2682197-02-Results-03_T22", "type": "Organism", "text": [ "Erdman" ], "offsets": [ [ 1347, 1353 ] ], "normalized": [] }, { "id": "PMC2682197-02-Results-03_T23", "type": "Organism", "text": [ "M. tuberculosis" ], "offsets": [ [ 1467, 1482 ] ], "normalized": [] }, { "id": "PMC2682197-02-Results-03_T24", "type": "Protein", "text": [ "Rv2623" ], "offsets": [ [ 1483, 1489 ] ], "normalized": [] }, { "id": "PMC2682197-02-Results-03_T25", "type": "Organism", "text": [ "Deltarv2623" ], "offsets": [ [ 1629, 1640 ] ], "normalized": [] }, { "id": "PMC2682197-02-Results-03_T26", "type": "Protein", "text": [ "rv2623" ], "offsets": [ [ 1634, 1640 ] ], "normalized": [] } ]

[ { "id": "PMC2682197-02-Results-03_E1", "type": "Process", "trigger": { "text": [ "hypervirulence" ], "offsets": [ [ 309, 323 ] ] }, "arguments": [ { "role": "Participant", "ref_id": "PMC2682197-02-Results-03_T3" } ] }, { "id": "PMC2682197-02-Results-03_E2", "type": "Process", "trigger": { "text": [ "infection" ], "offsets": [ [ 700, 709 ] ] }, "arguments": [ { "role": "Participant", "ref_id": "PMC2682197-02-Results-03_T13" } ] }, { "id": "PMC2682197-02-Results-03_E3", "type": "Positive_regulation", "trigger": { "text": [ "essential" ], "offsets": [ [ 1493, 1502 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC2682197-02-Results-03_E4" }, { "role": "Cause", "ref_id": "PMC2682197-02-Results-03_T24" } ] }, { "id": "PMC2682197-02-Results-03_E4", "type": "Process", "trigger": { "text": [ "resistance" ], "offsets": [ [ 1507, 1517 ] ] }, "arguments": [] }, { "id": "PMC2682197-02-Results-03_E5", "type": "Process", "trigger": { "text": [ "hypervirulence" ], "offsets": [ [ 1601, 1615 ] ] }, "arguments": [ { "role": "Participant", "ref_id": "PMC2682197-02-Results-03_T25" } ] } ]

[ { "id": "PMC2682197-02-Results-03_1", "entity_ids": [ "PMC2682197-02-Results-03_T14", "PMC2682197-02-Results-03_T15" ] } ]

[]

[ { "id": "PMC1913099-02-Results-Discussion-14__text", "type": "abstract", "text": [ "Concluding Remarks \nAlthough GenomeCrawler improves bacterial array analyses, it has limitations: it cannot identify regulons comprising genes dispersed throughout the genome by virtue of its design, it does not specifically interrogate single-gene operons, and it only applies to genomes with available and accurate experimental information (expression data and gene annotations). We recognize that incorporating intergenic distance and transcription direction into the algorithms would reduce processing time. Adding available clusters of orthologous groups (COG) information into a downstream processing step could decrease errors by minimizing clustering of unrelated genes. Nonetheless, neighbor clustering provided a more comprehensive view of the transcriptome of group A streptococci during adherence to human pharyngeal cells, a critical step in the infection program of this organism. We found that even a rigorous statistical analysis of well-replicated microarray data produced a dataset that was somewhat limited, although certainly more informative than assigning arbitrary thresholds for significance. As described in other microarray reports, we had initially identified a number of incomplete biological pathways in which we did not detect the differential expression of a number of known pathway members. Neighbor clustering was able to extend the results by identifying more differentially expressed genes and reconstructing more intact biological pathways. Neighbor clustering, despite the statistical framework with which it assigns groupings, would be valuable to microarray data analysis only if it produced biologically relevant data. Although biological testing of every identified gene or cluster is unrealistic, we provided evidence, through the creation and testing of isogenic deletion mutants and through the identification of clusters of known, functionally related genes from a published streptococcal array study, that the algorithms produce results that are pertinent to the biology of streptococci. This may be of particular importance for data in which the relationship between clustered genes is not obvious, and may facilitate the organization of larger datasets into more meaningful packages. It is also possible that GenomeCrawler (in its current form) could be used to interrogate intergenic portions of the genome (such as those encoding small noncoding RNAs or sRNAs), if probes representing such regions were included on the microarray, and experimental conditions were designed to promote their differential expression. Finally, because of the common architecture of bacterial chromosomes, the neighbor clustering algorithms may be applicable to microarray datasets from other prokaryotes.\n" ], "offsets": [ [ 0, 2735 ] ] } ]

[ { "id": "PMC1913099-02-Results-Discussion-14_T1", "type": "Organism", "text": [ "group A streptococci" ], "offsets": [ [ 771, 791 ] ], "normalized": [] }, { "id": "PMC1913099-02-Results-Discussion-14_T2", "type": "Organism", "text": [ "human" ], "offsets": [ [ 812, 817 ] ], "normalized": [] }, { "id": "PMC1913099-02-Results-Discussion-14_T3", "type": "Organism", "text": [ "streptococci" ], "offsets": [ [ 2020, 2032 ] ], "normalized": [] } ]

[ { "id": "PMC1913099-02-Results-Discussion-14_E1", "type": "Process", "trigger": { "text": [ "infection" ], "offsets": [ [ 859, 868 ] ] }, "arguments": [] } ]

[]

[]

[ { "id": "PMC1974823-03-Results-03__text", "type": "abstract", "text": [ "Binding of FimR to the promoter region of mfa1 \nThe previous study has shown that the mechanism of FimR activation of the fimA gene involves a regulatory cascade (Nishikawa et al., 2004). It was postulated that different mechanisms might be involved in FimR-mediated mfa1 expression, since expression regulation of mfa1 by FimR was not controlled as tightly as observed for fimA expression. One possibility is that FimR modulates mfa1 expression by directly binding to the promoter region of mfa1. To test this hypothesis, electrophoretic mobility shift assays were performed. The mfa1 promoter (positioned from +18 to -138), fimA promoter (positioned from -22 to-190) (Xie & Lamont, 1999) and mfa1 coding DNA (positioned from +1253 to +1373) were generated by PCR with the 5' biotin-labeled primers (Table 1). The recombinant FimR (rFimR) was expressed in pET expression system and purified from E. coli. The rHGP44 protein, a binding domain of P. gingivalis gingipains (Xie et al., 2006), expressed in the same system and purified by the same procedures as rFimR was used as a control. Cold competitor chase experiments with a 100-fold excess of unlabeled DNA probe as a specific competitor were also used to demonstrate the specificity of rFimR binding. As shown in Fig. 3, the DNA fragment of the mfa1 promoter region was shifted in the presence of the rFimR. Retarded mfa1 promoter-rFimR complex was detected with as little as 10 pmol muL-1 rFimR (Fig. 3). As the concentration of rFimR increased, the retarded protein-DNA complex became evident, with complete loss of the mfa1 promoter DNA. The unlabeled mfa1 promoter fragments effectively competed with the labeled fragment, suggesting a specific interaction between rFimA and the mfa1 promoter. To investigate the role of phosphorylation of FimR in its binding to the mfa1 promoter region, EMSA experiments were also performed with the phosphorylated rFimR. No significant difference was detected in the level of DNA binding between the phosphorylated rFimR and unphosphorylated rFimR (data not shown). In agreement with a previous report (Nishikawa et al., 2004), rFimR did not bind to the fimA promoter region, suggesting that regulation of fimA expression by FimR is through a different mechanism. Moreover, incubation of rHGP44 with mfa1 promoter fragment did not retard the DNA movement in polyacrylamide gel. There was also no DNA shift detected when rFimR was incubated with the coding region of mfa1. These data clearly show that FimR protein can bind specifically to the mfa1 promoter region, acting as an activator of mfa1 transcription. EMSA experiments were also performed to examine whether the rFimR binds to the other promoter region identified by Park et al. (2006). The biotin-labeled DNA fragment corresponding to this promoter region did not shift in the presence of the rFimA protein (data not shown), suggesting that only the promoter identified here is involved for mfa1 expression mediated by FimR.\n" ], "offsets": [ [ 0, 2981 ] ] } ]

[ { "id": "PMC1974823-03-Results-03_T1", "type": "Protein", "text": [ "FimR" ], "offsets": [ [ 11, 15 ] ], "normalized": [] }, { "id": "PMC1974823-03-Results-03_T2", "type": "Protein", "text": [ "mfa1" ], "offsets": [ [ 42, 46 ] ], "normalized": [] }, { "id": "PMC1974823-03-Results-03_T3", "type": "Protein", "text": [ "FimR" ], "offsets": [ [ 99, 103 ] ], "normalized": [] }, { "id": "PMC1974823-03-Results-03_T4", "type": "Protein", "text": [ "fimA" ], "offsets": [ [ 122, 126 ] ], "normalized": [] }, { "id": "PMC1974823-03-Results-03_T5", "type": "Protein", "text": [ "FimR" ], "offsets": [ [ 253, 257 ] ], "normalized": [] }, { "id": "PMC1974823-03-Results-03_T6", "type": "Protein", "text": [ "mfa1" ], "offsets": [ [ 267, 271 ] ], "normalized": [] }, { "id": "PMC1974823-03-Results-03_T7", "type": "Protein", "text": [ "mfa1" ], "offsets": [ [ 315, 319 ] ], "normalized": [] }, { "id": "PMC1974823-03-Results-03_T8", "type": "Protein", "text": [ "FimR" ], "offsets": [ [ 323, 327 ] ], "normalized": [] }, { "id": "PMC1974823-03-Results-03_T9", "type": "Protein", "text": [ "fimA" ], "offsets": [ [ 374, 378 ] ], "normalized": [] }, { "id": "PMC1974823-03-Results-03_T10", "type": "Protein", "text": [ "FimR" ], "offsets": [ [ 415, 419 ] ], "normalized": [] }, { "id": "PMC1974823-03-Results-03_T11", "type": "Protein", "text": [ "mfa1" ], "offsets": [ [ 430, 434 ] ], "normalized": [] }, { "id": "PMC1974823-03-Results-03_T12", "type": "Protein", "text": [ "mfa1" ], "offsets": [ [ 492, 496 ] ], "normalized": [] }, { "id": "PMC1974823-03-Results-03_T13", "type": "Protein", "text": [ "mfa1" ], "offsets": [ [ 581, 585 ] ], "normalized": [] }, { "id": "PMC1974823-03-Results-03_T14", "type": "Protein", "text": [ "fimA" ], "offsets": [ [ 626, 630 ] ], "normalized": [] }, { "id": "PMC1974823-03-Results-03_T15", "type": "Protein", "text": [ "mfa1" ], "offsets": [ [ 694, 698 ] ], "normalized": [] }, { "id": "PMC1974823-03-Results-03_T16", "type": "Protein", "text": [ "FimR" ], "offsets": [ [ 827, 831 ] ], "normalized": [] }, { "id": "PMC1974823-03-Results-03_T17", "type": "Protein", "text": [ "rFimR" ], "offsets": [ [ 833, 838 ] ], "normalized": [] }, { "id": "PMC1974823-03-Results-03_T18", "type": "Organism", "text": [ "E. coli" ], "offsets": [ [ 897, 904 ] ], "normalized": [] }, { "id": "PMC1974823-03-Results-03_T19", "type": "Protein", "text": [ "rHGP44" ], "offsets": [ [ 910, 916 ] ], "normalized": [] }, { "id": "PMC1974823-03-Results-03_T20", "type": "Organism", "text": [ "P. gingivalis" ], "offsets": [ [ 946, 959 ] ], "normalized": [] }, { "id": "PMC1974823-03-Results-03_T21", "type": "Protein", "text": [ "rFimR" ], "offsets": [ [ 1059, 1064 ] ], "normalized": [] }, { "id": "PMC1974823-03-Results-03_T22", "type": "Protein", "text": [ "rFimR" ], "offsets": [ [ 1242, 1247 ] ], "normalized": [] }, { "id": "PMC1974823-03-Results-03_T23", "type": "Protein", "text": [ "mfa1" ], "offsets": [ [ 1301, 1305 ] ], "normalized": [] }, { "id": "PMC1974823-03-Results-03_T24", "type": "Protein", "text": [ "rFimR" ], "offsets": [ [ 1357, 1362 ] ], "normalized": [] }, { "id": "PMC1974823-03-Results-03_T25", "type": "Protein", "text": [ "mfa1" ], "offsets": [ [ 1373, 1377 ] ], "normalized": [] }, { "id": "PMC1974823-03-Results-03_T26", "type": "Protein", "text": [ "rFimR" ], "offsets": [ [ 1387, 1392 ] ], "normalized": [] }, { "id": "PMC1974823-03-Results-03_T27", "type": "Protein", "text": [ "rFimR" ], "offsets": [ [ 1446, 1451 ] ], "normalized": [] }, { "id": "PMC1974823-03-Results-03_T28", "type": "Protein", "text": [ "rFimR" ], "offsets": [ [ 1486, 1491 ] ], "normalized": [] }, { "id": "PMC1974823-03-Results-03_T29", "type": "Protein", "text": [ "mfa1" ], "offsets": [ [ 1578, 1582 ] ], "normalized": [] }, { "id": "PMC1974823-03-Results-03_T30", "type": "Protein", "text": [ "mfa1" ], "offsets": [ [ 1611, 1615 ] ], "normalized": [] }, { "id": "PMC1974823-03-Results-03_T31", "type": "Protein", "text": [ "rFimA" ], "offsets": [ [ 1725, 1730 ] ], "normalized": [] }, { "id": "PMC1974823-03-Results-03_T32", "type": "Protein", "text": [ "mfa1" ], "offsets": [ [ 1739, 1743 ] ], "normalized": [] }, { "id": "PMC1974823-03-Results-03_T33", "type": "Protein", "text": [ "FimR" ], "offsets": [ [ 1800, 1804 ] ], "normalized": [] }, { "id": "PMC1974823-03-Results-03_T34", "type": "Protein", "text": [ "mfa1" ], "offsets": [ [ 1827, 1831 ] ], "normalized": [] }, { "id": "PMC1974823-03-Results-03_T35", "type": "Protein", "text": [ "rFimR" ], "offsets": [ [ 1910, 1915 ] ], "normalized": [] }, { "id": "PMC1974823-03-Results-03_T36", "type": "Protein", "text": [ "rFimR" ], "offsets": [ [ 2011, 2016 ] ], "normalized": [] }, { "id": "PMC1974823-03-Results-03_T37", "type": "Protein", "text": [ "rFimR" ], "offsets": [ [ 2038, 2043 ] ], "normalized": [] }, { "id": "PMC1974823-03-Results-03_T38", "type": "Protein", "text": [ "rFimR" ], "offsets": [ [ 2124, 2129 ] ], "normalized": [] }, { "id": "PMC1974823-03-Results-03_T39", "type": "Protein", "text": [ "fimA" ], "offsets": [ [ 2150, 2154 ] ], "normalized": [] }, { "id": "PMC1974823-03-Results-03_T40", "type": "Protein", "text": [ "fimA" ], "offsets": [ [ 2202, 2206 ] ], "normalized": [] }, { "id": "PMC1974823-03-Results-03_T41", "type": "Protein", "text": [ "FimR" ], "offsets": [ [ 2221, 2225 ] ], "normalized": [] }, { "id": "PMC1974823-03-Results-03_T42", "type": "Protein", "text": [ "rHGP44" ], "offsets": [ [ 2284, 2290 ] ], "normalized": [] }, { "id": "PMC1974823-03-Results-03_T43", "type": "Protein", "text": [ "mfa1" ], "offsets": [ [ 2296, 2300 ] ], "normalized": [] }, { "id": "PMC1974823-03-Results-03_T44", "type": "Protein", "text": [ "rFimR" ], "offsets": [ [ 2416, 2421 ] ], "normalized": [] }, { "id": "PMC1974823-03-Results-03_T45", "type": "Protein", "text": [ "mfa1" ], "offsets": [ [ 2462, 2466 ] ], "normalized": [] }, { "id": "PMC1974823-03-Results-03_T46", "type": "Protein", "text": [ "FimR" ], "offsets": [ [ 2497, 2501 ] ], "normalized": [] }, { "id": "PMC1974823-03-Results-03_T47", "type": "Protein", "text": [ "mfa1" ], "offsets": [ [ 2539, 2543 ] ], "normalized": [] }, { "id": "PMC1974823-03-Results-03_T48", "type": "Protein", "text": [ "mfa1" ], "offsets": [ [ 2587, 2591 ] ], "normalized": [] }, { "id": "PMC1974823-03-Results-03_T49", "type": "Protein", "text": [ "rFimR" ], "offsets": [ [ 2667, 2672 ] ], "normalized": [] }, { "id": "PMC1974823-03-Results-03_T50", "type": "Protein", "text": [ "rFimA" ], "offsets": [ [ 2849, 2854 ] ], "normalized": [] }, { "id": "PMC1974823-03-Results-03_T51", "type": "Protein", "text": [ "mfa1" ], "offsets": [ [ 2947, 2951 ] ], "normalized": [] }, { "id": "PMC1974823-03-Results-03_T52", "type": "Protein", "text": [ "FimR" ], "offsets": [ [ 2975, 2979 ] ], "normalized": [] }, { "id": "PMC1974823-03-Results-03_T54", "type": "Entity", "text": [ "promoter region" ], "offsets": [ [ 23, 38 ] ], "normalized": [] }, { "id": "PMC1974823-03-Results-03_T65", "type": "Entity", "text": [ "promoter region" ], "offsets": [ [ 473, 488 ] ], "normalized": [] }, { "id": "PMC1974823-03-Results-03_T69", "type": "Entity", "text": [ "promoter" ], "offsets": [ [ 1378, 1386 ] ], "normalized": [] }, { "id": "PMC1974823-03-Results-03_T72", "type": "Entity", "text": [ "promoter" ], "offsets": [ [ 1744, 1752 ] ], "normalized": [] }, { "id": "PMC1974823-03-Results-03_T76", "type": "Entity", "text": [ "promoter region" ], "offsets": [ [ 1832, 1847 ] ], "normalized": [] }, { "id": "PMC1974823-03-Results-03_T81", "type": "Entity", "text": [ "promoter region" ], "offsets": [ [ 2155, 2170 ] ], "normalized": [] }, { "id": "PMC1974823-03-Results-03_T85", "type": "Entity", "text": [ "promoter region" ], "offsets": [ [ 2544, 2559 ] ], "normalized": [] } ]

[ { "id": "PMC1974823-03-Results-03_E1", "type": "Binding", "trigger": { "text": [ "Binding" ], "offsets": [ [ 0, 7 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC1974823-03-Results-03_T1" }, { "role": "Theme", "ref_id": "PMC1974823-03-Results-03_T2" }, { "role": "Site", "ref_id": "PMC1974823-03-Results-03_T54" } ] }, { "id": "PMC1974823-03-Results-03_E2", "type": "Positive_regulation", "trigger": { "text": [ "activation" ], "offsets": [ [ 104, 114 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC1974823-03-Results-03_T4" }, { "role": "Cause", "ref_id": "PMC1974823-03-Results-03_T3" } ] }, { "id": "PMC1974823-03-Results-03_E3", "type": "Regulation", "trigger": { "text": [ "mediated" ], "offsets": [ [ 258, 266 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC1974823-03-Results-03_E4" }, { "role": "Cause", "ref_id": "PMC1974823-03-Results-03_T5" } ] }, { "id": "PMC1974823-03-Results-03_E4", "type": "Gene_expression", "trigger": { "text": [ "expression" ], "offsets": [ [ 272, 282 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC1974823-03-Results-03_T6" } ] }, { "id": "PMC1974823-03-Results-03_E5", "type": "Gene_expression", "trigger": { "text": [ "expression" ], "offsets": [ [ 290, 300 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC1974823-03-Results-03_T7" } ] }, { "id": "PMC1974823-03-Results-03_E6", "type": "Regulation", "trigger": { "text": [ "regulation" ], "offsets": [ [ 301, 311 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC1974823-03-Results-03_E5" }, { "role": "Cause", "ref_id": "PMC1974823-03-Results-03_T8" } ] }, { "id": "PMC1974823-03-Results-03_E7", "type": "Regulation", "trigger": { "text": [ "controlled" ], "offsets": [ [ 336, 346 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC1974823-03-Results-03_E8" } ] }, { "id": "PMC1974823-03-Results-03_E8", "type": "Gene_expression", "trigger": { "text": [ "expression" ], "offsets": [ [ 379, 389 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC1974823-03-Results-03_T9" } ] }, { "id": "PMC1974823-03-Results-03_E9", "type": "Regulation", "trigger": { "text": [ "modulates" ], "offsets": [ [ 420, 429 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC1974823-03-Results-03_E10" }, { "role": "Cause", "ref_id": "PMC1974823-03-Results-03_E11" } ] }, { "id": "PMC1974823-03-Results-03_E10", "type": "Gene_expression", "trigger": { "text": [ "expression" ], "offsets": [ [ 435, 445 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC1974823-03-Results-03_T11" } ] }, { "id": "PMC1974823-03-Results-03_E11", "type": "Binding", "trigger": { "text": [ "binding" ], "offsets": [ [ 458, 465 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC1974823-03-Results-03_T10" }, { "role": "Theme", "ref_id": "PMC1974823-03-Results-03_T12" }, { "role": "Site", "ref_id": "PMC1974823-03-Results-03_T65" } ] }, { "id": "PMC1974823-03-Results-03_E12", "type": "Gene_expression", "trigger": { "text": [ "expressed" ], "offsets": [ [ 844, 853 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC1974823-03-Results-03_T17" } ] }, { "id": "PMC1974823-03-Results-03_E13", "type": "Gene_expression", "trigger": { "text": [ "expressed" ], "offsets": [ [ 991, 1000 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC1974823-03-Results-03_T19" } ] }, { "id": "PMC1974823-03-Results-03_E14", "type": "Binding", "trigger": { "text": [ "binding" ], "offsets": [ [ 1248, 1255 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC1974823-03-Results-03_T22" } ] }, { "id": "PMC1974823-03-Results-03_E15", "type": "Binding", "trigger": { "text": [ "complex" ], "offsets": [ [ 1393, 1400 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC1974823-03-Results-03_T26" }, { "role": "Theme", "ref_id": "PMC1974823-03-Results-03_T25" }, { "role": "Site", "ref_id": "PMC1974823-03-Results-03_T69" } ] }, { "id": "PMC1974823-03-Results-03_E16", "type": "Binding", "trigger": { "text": [ "interaction" ], "offsets": [ [ 1705, 1716 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC1974823-03-Results-03_T31" }, { "role": "Theme", "ref_id": "PMC1974823-03-Results-03_T32" }, { "role": "Site", "ref_id": "PMC1974823-03-Results-03_T72" } ] }, { "id": "PMC1974823-03-Results-03_E17", "type": "Regulation", "trigger": { "text": [ "role" ], "offsets": [ [ 1773, 1777 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC1974823-03-Results-03_E19" }, { "role": "Cause", "ref_id": "PMC1974823-03-Results-03_E18" } ] }, { "id": "PMC1974823-03-Results-03_E18", "type": "Phosphorylation", "trigger": { "text": [ "phosphorylation" ], "offsets": [ [ 1781, 1796 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC1974823-03-Results-03_T33" } ] }, { "id": "PMC1974823-03-Results-03_E19", "type": "Binding", "trigger": { "text": [ "binding" ], "offsets": [ [ 1812, 1819 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC1974823-03-Results-03_T33" }, { "role": "Theme", "ref_id": "PMC1974823-03-Results-03_T34" }, { "role": "Site", "ref_id": "PMC1974823-03-Results-03_T76" } ] }, { "id": "PMC1974823-03-Results-03_E20", "type": "Binding", "trigger": { "text": [ "binding" ], "offsets": [ [ 1976, 1983 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC1974823-03-Results-03_T36" } ] }, { "id": "PMC1974823-03-Results-03_E21", "type": "Binding", "trigger": { "text": [ "binding" ], "offsets": [ [ 1976, 1983 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC1974823-03-Results-03_T37" } ] }, { "id": "PMC1974823-03-Results-03_E22", "type": "Phosphorylation", "trigger": { "text": [ "phosphorylated" ], "offsets": [ [ 1996, 2010 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC1974823-03-Results-03_T36" } ] }, { "id": "PMC1974823-03-Results-03_E23", "type": "Phosphorylation", "trigger": { "text": [ "unphosphorylated" ], "offsets": [ [ 2021, 2037 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC1974823-03-Results-03_T37" } ] }, { "id": "PMC1974823-03-Results-03_E24", "type": "Binding", "trigger": { "text": [ "bind" ], "offsets": [ [ 2138, 2142 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC1974823-03-Results-03_T38" }, { "role": "Theme", "ref_id": "PMC1974823-03-Results-03_T39" }, { "role": "Site", "ref_id": "PMC1974823-03-Results-03_T81" } ] }, { "id": "PMC1974823-03-Results-03_E25", "type": "Regulation", "trigger": { "text": [ "regulation" ], "offsets": [ [ 2188, 2198 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC1974823-03-Results-03_E26" }, { "role": "Cause", "ref_id": "PMC1974823-03-Results-03_T41" } ] }, { "id": "PMC1974823-03-Results-03_E26", "type": "Gene_expression", "trigger": { "text": [ "expression" ], "offsets": [ [ 2207, 2217 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC1974823-03-Results-03_T40" } ] }, { "id": "PMC1974823-03-Results-03_E27", "type": "Binding", "trigger": { "text": [ "bind" ], "offsets": [ [ 2514, 2518 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC1974823-03-Results-03_T46" }, { "role": "Theme", "ref_id": "PMC1974823-03-Results-03_T47" }, { "role": "Site", "ref_id": "PMC1974823-03-Results-03_T85" } ] }, { "id": "PMC1974823-03-Results-03_E28", "type": "Positive_regulation", "trigger": { "text": [ "activator" ], "offsets": [ [ 2574, 2583 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC1974823-03-Results-03_E29" }, { "role": "Cause", "ref_id": "PMC1974823-03-Results-03_T46" } ] }, { "id": "PMC1974823-03-Results-03_E29", "type": "Transcription", "trigger": { "text": [ "transcription" ], "offsets": [ [ 2592, 2605 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC1974823-03-Results-03_T48" } ] }, { "id": "PMC1974823-03-Results-03_E30", "type": "Binding", "trigger": { "text": [ "binds" ], "offsets": [ [ 2673, 2678 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC1974823-03-Results-03_T49" } ] }, { "id": "PMC1974823-03-Results-03_E31", "type": "Gene_expression", "trigger": { "text": [ "expression" ], "offsets": [ [ 2952, 2962 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC1974823-03-Results-03_T51" } ] }, { "id": "PMC1974823-03-Results-03_E32", "type": "Positive_regulation", "trigger": { "text": [ "mediated" ], "offsets": [ [ 2963, 2971 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC1974823-03-Results-03_E31" }, { "role": "Cause", "ref_id": "PMC1974823-03-Results-03_T52" } ] } ]

[]

[]

[ { "id": "PMC2858072-02-Results_and_Discussion-01__text", "type": "abstract", "text": [ "Results and Discussion \nBrucella mutants in the BvrR/BvrS two-component regulatory system are pleiotropic [3]-[6]. Whole-genome microarray analysis was made to determine the effect of the mutation in BvrR/BvrS in the gene expression pattern of Brucella. B. abortus RNA was obtained from three independent cultures of each wild type and bvrR mutant cells grown in the same conditions. To confirm the reproducibility of the gene expression data, the array experiment was composed of six slides (three for each type of cells) yielding six measurements per gene, representing three biological replicates (since each gene is present twice on each slide). The ORFeome-based Brucella whole-genome DNA microarray used in this study has been previously validated for the analysis of gene expression under any experimental conditions [7]. The microarray experimental design was made according to the MIAME recommendations [8]. A change in gene expression was considered both statistically and biologically significant if the p-value was less than 0.01. The statistical analysis resulted in the identification of a total of 127 genes differentially transcribed in the bvrR mutant versus the wild type. Eighty three genes (65%) were up- and 44 (35%) were down-regulated (the complete list of differentially expressed genes in the bvrR mutant versus the wild type is show in Table S1). Twenty three % of the differentially transcribed genes (30) encoded for hypothetical proteins. For genes of annotated function, 59 appeared to be up regulated and 38 down regulated in the bvrR mutant. Genes encoding proteins involved in metabolism and cellular process are among the most up regulated genes, and those encoding proteins involved in membrane transport are among the most down regulated (Figure 1). To further validate some data generated in the microarray experiment, forty-eight differentially expressed genes were chosen to be analyzed by real-time quantitative reverse transcription-PCR (RT-PCR). Total RNA from both Brucella strains were reverse transcribed into cDNA. The reactions were made by triplicate from at least two independent cultures, and the cycle of threshold (Ct) was determined for each reaction. Data were normalized by the 2-DeltaDeltaCt method [9] using the IF-1 housekeeping gene of Brucella as reference (Table 1). Transcriptional data of forty-one (85%) of the genes selected gave identical tendency by both methods microarray and RT-PCR: 22 were up and 19 were down regulated in the bvrR mutant. Interestingly, the level of transcription obtained by RT-PCR of the flagellar genes fliM (BAB2_0124) and motB (BAB2_1103), and the pckA gene (BAB1_2091) were the highest in the bvrR mutant. On the other hand, exoR (BAB1_0891), omp25a (BAB1_0722), hpr-K (BAB1_2094), bvrS (BAB1_2093) and the lipoproteins (BAB1_2147, BAB1_0589, BAB1_0358) were among the less expressed genes (Table 1). These results confirmed a good correlation between microarray and RT-PCR data, thus validating the model. Next, we will focus on the genes differentially expressed in the bvrR mutant (a complete representation of the differentially expressed genes is show in Figure 2). Cell envelope modulation It is well know that the transcription of omp25a y omp22 genes is under the control of the BvrR/BvrS system, and that bvrR/bvrS mutants have increased amount of underacylated lipid A species in the LPS [2], [3]. In addition, proteomic analysis of Brucella outer membrane fragments demonstrated that the expression of several OMPs, lipoproteins and chaperones was altered in these mutants [6]. These observations led to the hypothesis that the BvrR/BvrS system is involved in cell envelope changes required for adaptation to the intracellular environment. Our microarray results demonstrated several genes directly involved in cell envelope or outer membrane biogenesis differentially expressed in the bvrR mutant. As expected, these included genes that encoded OMPs like Omp25a (BAB1_0722) and Omp25d (BAB1_0115) which were down-regulated. Other bvrR regulated genes related with cell envelope were: three lipoprotein genes (BAB1_0358; BAB1_0589; BAB1_2147), which were down-regulated; six genes for periplasmic proteins and chaperones (htpX, heat shock protein, BAB1_1821; clpA and clpB, stress response proteins, BAB1_1573 and BAB1_1868, respectively; BAB2_1107; BAB1_0505; BAB1_1022), which were all up-regulated; one gene related with LPS biosynthesis (glycosyl transferase, BAB1_1620), which was up-regulated; and five genes for fatty acids biosynthesis (fabG, ketoacyl-acyl-carrier-protein reductase, BAB1_2043; fabF, oxoacyl-acyl-carrier-protein synthase, BAB1_0872; fadD, fatty-acyl-CoA synthase, BAB1_0320; cfa, cyclopropane-fatty-acyl-phospholipid synthase, BAB1_0476; BAB1_1357). These data confirm that BvrR/BvrS regulates bacterial envelope changes that could modify surface properties relevant for Brucella virulence [6].\n" ], "offsets": [ [ 0, 4927 ] ] } ]

[ { "id": "PMC2858072-02-Results_and_Discussion-01_T1", "type": "Organism", "text": [ "Brucella mutants" ], "offsets": [ [ 24, 40 ] ], "normalized": [] }, { "id": "PMC2858072-02-Results_and_Discussion-01_T2", "type": "Two-component-system", "text": [ "BvrR/BvrS" ], "offsets": [ [ 48, 57 ] ], "normalized": [] }, { "id": "PMC2858072-02-Results_and_Discussion-01_T3", "type": "Protein", "text": [ "BvrR" ], "offsets": [ [ 48, 52 ] ], "normalized": [] }, { "id": "PMC2858072-02-Results_and_Discussion-01_T4", "type": "Protein", "text": [ "BvrS" ], "offsets": [ [ 53, 57 ] ], "normalized": [] }, { "id": "PMC2858072-02-Results_and_Discussion-01_T5", "type": "Two-component-system", "text": [ "BvrR/BvrS" ], "offsets": [ [ 200, 209 ] ], "normalized": [] }, { "id": "PMC2858072-02-Results_and_Discussion-01_T6", "type": "Protein", "text": [ "BvrR" ], "offsets": [ [ 200, 204 ] ], "normalized": [] }, { "id": "PMC2858072-02-Results_and_Discussion-01_T7", "type": "Protein", "text": [ "BvrS" ], "offsets": [ [ 205, 209 ] ], "normalized": [] }, { "id": "PMC2858072-02-Results_and_Discussion-01_T8", "type": "Organism", "text": [ "Brucella" ], "offsets": [ [ 244, 252 ] ], "normalized": [] }, { "id": "PMC2858072-02-Results_and_Discussion-01_T9", "type": "Organism", "text": [ "B. abortus" ], "offsets": [ [ 254, 264 ] ], "normalized": [] }, { "id": "PMC2858072-02-Results_and_Discussion-01_T10", "type": "Organism", "text": [ "bvrR mutant" ], "offsets": [ [ 336, 347 ] ], "normalized": [] }, { "id": "PMC2858072-02-Results_and_Discussion-01_T11", "type": "Protein", "text": [ "bvrR" ], "offsets": [ [ 336, 340 ] ], "normalized": [] }, { "id": "PMC2858072-02-Results_and_Discussion-01_T12", "type": "Organism", "text": [ "Brucella" ], "offsets": [ [ 668, 676 ] ], "normalized": [] }, { "id": "PMC2858072-02-Results_and_Discussion-01_T13", "type": "Organism", "text": [ "bvrR mutant" ], "offsets": [ [ 1157, 1168 ] ], "normalized": [] }, { "id": "PMC2858072-02-Results_and_Discussion-01_T14", "type": "Protein", "text": [ "bvrR" ], "offsets": [ [ 1157, 1161 ] ], "normalized": [] }, { "id": "PMC2858072-02-Results_and_Discussion-01_T15", "type": "Organism", "text": [ "bvrR mutant" ], "offsets": [ [ 1318, 1329 ] ], "normalized": [] }, { "id": "PMC2858072-02-Results_and_Discussion-01_T16", "type": "Protein", "text": [ "bvrR" ], "offsets": [ [ 1318, 1322 ] ], "normalized": [] }, { "id": "PMC2858072-02-Results_and_Discussion-01_T17", "type": "Organism", "text": [ "bvrR mutant" ], "offsets": [ [ 1561, 1572 ] ], "normalized": [] }, { "id": "PMC2858072-02-Results_and_Discussion-01_T18", "type": "Protein", "text": [ "bvrR" ], "offsets": [ [ 1561, 1565 ] ], "normalized": [] }, { "id": "PMC2858072-02-Results_and_Discussion-01_T19", "type": "Organism", "text": [ "Brucella" ], "offsets": [ [ 2008, 2016 ] ], "normalized": [] }, { "id": "PMC2858072-02-Results_and_Discussion-01_T20", "type": "Organism", "text": [ "Brucella" ], "offsets": [ [ 2295, 2303 ] ], "normalized": [] }, { "id": "PMC2858072-02-Results_and_Discussion-01_T21", "type": "Organism", "text": [ "bvrR mutant" ], "offsets": [ [ 2498, 2509 ] ], "normalized": [] }, { "id": "PMC2858072-02-Results_and_Discussion-01_T22", "type": "Protein", "text": [ "bvrR" ], "offsets": [ [ 2498, 2502 ] ], "normalized": [] }, { "id": "PMC2858072-02-Results_and_Discussion-01_T23", "type": "Protein", "text": [ "fliM" ], "offsets": [ [ 2595, 2599 ] ], "normalized": [] }, { "id": "PMC2858072-02-Results_and_Discussion-01_T24", "type": "Protein", "text": [ "BAB2_0124" ], "offsets": [ [ 2601, 2610 ] ], "normalized": [] }, { "id": "PMC2858072-02-Results_and_Discussion-01_T25", "type": "Protein", "text": [ "motB" ], "offsets": [ [ 2616, 2620 ] ], "normalized": [] }, { "id": "PMC2858072-02-Results_and_Discussion-01_T26", "type": "Protein", "text": [ "BAB2_1103" ], "offsets": [ [ 2622, 2631 ] ], "normalized": [] }, { "id": "PMC2858072-02-Results_and_Discussion-01_T27", "type": "Protein", "text": [ "pckA" ], "offsets": [ [ 2642, 2646 ] ], "normalized": [] }, { "id": "PMC2858072-02-Results_and_Discussion-01_T28", "type": "Protein", "text": [ "BAB1_2091" ], "offsets": [ [ 2653, 2662 ] ], "normalized": [] }, { "id": "PMC2858072-02-Results_and_Discussion-01_T29", "type": "Organism", "text": [ "bvrR mutant" ], "offsets": [ [ 2688, 2699 ] ], "normalized": [] }, { "id": "PMC2858072-02-Results_and_Discussion-01_T30", "type": "Protein", "text": [ "bvrR" ], "offsets": [ [ 2688, 2692 ] ], "normalized": [] }, { "id": "PMC2858072-02-Results_and_Discussion-01_T31", "type": "Protein", "text": [ "exoR" ], "offsets": [ [ 2720, 2724 ] ], "normalized": [] }, { "id": "PMC2858072-02-Results_and_Discussion-01_T32", "type": "Protein", "text": [ "BAB1_0891" ], "offsets": [ [ 2726, 2735 ] ], "normalized": [] }, { "id": "PMC2858072-02-Results_and_Discussion-01_T33", "type": "Protein", "text": [ "omp25a" ], "offsets": [ [ 2738, 2744 ] ], "normalized": [] }, { "id": "PMC2858072-02-Results_and_Discussion-01_T34", "type": "Protein", "text": [ "BAB1_0722" ], "offsets": [ [ 2746, 2755 ] ], "normalized": [] }, { "id": "PMC2858072-02-Results_and_Discussion-01_T35", "type": "Protein", "text": [ "hpr-K" ], "offsets": [ [ 2758, 2763 ] ], "normalized": [] }, { "id": "PMC2858072-02-Results_and_Discussion-01_T36", "type": "Protein", "text": [ "BAB1_2094" ], "offsets": [ [ 2765, 2774 ] ], "normalized": [] }, { "id": "PMC2858072-02-Results_and_Discussion-01_T37", "type": "Protein", "text": [ "bvrS" ], "offsets": [ [ 2777, 2781 ] ], "normalized": [] }, { "id": "PMC2858072-02-Results_and_Discussion-01_T38", "type": "Protein", "text": [ "BAB1_2093" ], "offsets": [ [ 2783, 2792 ] ], "normalized": [] }, { "id": "PMC2858072-02-Results_and_Discussion-01_T39", "type": "Protein", "text": [ "BAB1_2147" ], "offsets": [ [ 2816, 2825 ] ], "normalized": [] }, { "id": "PMC2858072-02-Results_and_Discussion-01_T40", "type": "Protein", "text": [ "BAB1_0589" ], "offsets": [ [ 2827, 2836 ] ], "normalized": [] }, { "id": "PMC2858072-02-Results_and_Discussion-01_T41", "type": "Protein", "text": [ "BAB1_0358" ], "offsets": [ [ 2838, 2847 ] ], "normalized": [] }, { "id": "PMC2858072-02-Results_and_Discussion-01_T42", "type": "Organism", "text": [ "bvrR mutant" ], "offsets": [ [ 3067, 3078 ] ], "normalized": [] }, { "id": "PMC2858072-02-Results_and_Discussion-01_T43", "type": "Protein", "text": [ "bvrR" ], "offsets": [ [ 3067, 3071 ] ], "normalized": [] }, { "id": "PMC2858072-02-Results_and_Discussion-01_T44", "type": "Protein", "text": [ "omp25a" ], "offsets": [ [ 3233, 3239 ] ], "normalized": [] }, { "id": "PMC2858072-02-Results_and_Discussion-01_T45", "type": "Protein", "text": [ "omp22" ], "offsets": [ [ 3242, 3247 ] ], "normalized": [] }, { "id": "PMC2858072-02-Results_and_Discussion-01_T46", "type": "Two-component-system", "text": [ "BvrR/BvrS" ], "offsets": [ [ 3282, 3291 ] ], "normalized": [] }, { "id": "PMC2858072-02-Results_and_Discussion-01_T47", "type": "Protein", "text": [ "BvrR" ], "offsets": [ [ 3282, 3286 ] ], "normalized": [] }, { "id": "PMC2858072-02-Results_and_Discussion-01_T48", "type": "Protein", "text": [ "BvrS" ], "offsets": [ [ 3287, 3291 ] ], "normalized": [] }, { "id": "PMC2858072-02-Results_and_Discussion-01_T49", "type": "Organism", "text": [ "bvrR/bvrS mutants" ], "offsets": [ [ 3309, 3326 ] ], "normalized": [] }, { "id": "PMC2858072-02-Results_and_Discussion-01_T50", "type": "Two-component-system", "text": [ "bvrR/bvrS" ], "offsets": [ [ 3309, 3318 ] ], "normalized": [] }, { "id": "PMC2858072-02-Results_and_Discussion-01_T51", "type": "Protein", "text": [ "bvrR" ], "offsets": [ [ 3309, 3313 ] ], "normalized": [] }, { "id": "PMC2858072-02-Results_and_Discussion-01_T52", "type": "Protein", "text": [ "bvrS" ], "offsets": [ [ 3314, 3318 ] ], "normalized": [] }, { "id": "PMC2858072-02-Results_and_Discussion-01_T53", "type": "Chemical", "text": [ "lipid A" ], "offsets": [ [ 3366, 3373 ] ], "normalized": [] }, { "id": "PMC2858072-02-Results_and_Discussion-01_T54", "type": "Chemical", "text": [ "LPS" ], "offsets": [ [ 3389, 3392 ] ], "normalized": [] }, { "id": "PMC2858072-02-Results_and_Discussion-01_T55", "type": "Organism", "text": [ "Brucella" ], "offsets": [ [ 3438, 3446 ] ], "normalized": [] }, { "id": "PMC2858072-02-Results_and_Discussion-01_T56", "type": "Two-component-system", "text": [ "BvrR/BvrS" ], "offsets": [ [ 3634, 3643 ] ], "normalized": [] }, { "id": "PMC2858072-02-Results_and_Discussion-01_T57", "type": "Protein", "text": [ "BvrR" ], "offsets": [ [ 3634, 3638 ] ], "normalized": [] }, { "id": "PMC2858072-02-Results_and_Discussion-01_T58", "type": "Protein", "text": [ "BvrS" ], "offsets": [ [ 3639, 3643 ] ], "normalized": [] }, { "id": "PMC2858072-02-Results_and_Discussion-01_T59", "type": "Organism", "text": [ "bvrR mutant" ], "offsets": [ [ 3892, 3903 ] ], "normalized": [] }, { "id": "PMC2858072-02-Results_and_Discussion-01_T60", "type": "Protein", "text": [ "bvrR" ], "offsets": [ [ 3892, 3896 ] ], "normalized": [] }, { "id": "PMC2858072-02-Results_and_Discussion-01_T61", "type": "Protein", "text": [ "Omp25a" ], "offsets": [ [ 3962, 3968 ] ], "normalized": [] }, { "id": "PMC2858072-02-Results_and_Discussion-01_T62", "type": "Protein", "text": [ "BAB1_0722" ], "offsets": [ [ 3970, 3979 ] ], "normalized": [] }, { "id": "PMC2858072-02-Results_and_Discussion-01_T63", "type": "Protein", "text": [ "Omp25d" ], "offsets": [ [ 3985, 3991 ] ], "normalized": [] }, { "id": "PMC2858072-02-Results_and_Discussion-01_T64", "type": "Protein", "text": [ "BAB1_0115" ], "offsets": [ [ 3993, 4002 ] ], "normalized": [] }, { "id": "PMC2858072-02-Results_and_Discussion-01_T65", "type": "Protein", "text": [ "bvrR" ], "offsets": [ [ 4037, 4041 ] ], "normalized": [] }, { "id": "PMC2858072-02-Results_and_Discussion-01_T66", "type": "Protein", "text": [ "BAB1_0358" ], "offsets": [ [ 4116, 4125 ] ], "normalized": [] }, { "id": "PMC2858072-02-Results_and_Discussion-01_T67", "type": "Protein", "text": [ "BAB1_0589" ], "offsets": [ [ 4127, 4136 ] ], "normalized": [] }, { "id": "PMC2858072-02-Results_and_Discussion-01_T68", "type": "Protein", "text": [ "BAB1_2147" ], "offsets": [ [ 4138, 4147 ] ], "normalized": [] }, { "id": "PMC2858072-02-Results_and_Discussion-01_T69", "type": "Protein", "text": [ "htpX" ], "offsets": [ [ 4228, 4232 ] ], "normalized": [] }, { "id": "PMC2858072-02-Results_and_Discussion-01_T70", "type": "Protein", "text": [ "BAB1_1821" ], "offsets": [ [ 4254, 4263 ] ], "normalized": [] }, { "id": "PMC2858072-02-Results_and_Discussion-01_T71", "type": "Protein", "text": [ "clpA" ], "offsets": [ [ 4265, 4269 ] ], "normalized": [] }, { "id": "PMC2858072-02-Results_and_Discussion-01_T72", "type": "Protein", "text": [ "clpB" ], "offsets": [ [ 4274, 4278 ] ], "normalized": [] }, { "id": "PMC2858072-02-Results_and_Discussion-01_T73", "type": "Protein", "text": [ "BAB1_1573" ], "offsets": [ [ 4306, 4315 ] ], "normalized": [] }, { "id": "PMC2858072-02-Results_and_Discussion-01_T74", "type": "Protein", "text": [ "BAB1_1868" ], "offsets": [ [ 4320, 4329 ] ], "normalized": [] }, { "id": "PMC2858072-02-Results_and_Discussion-01_T75", "type": "Protein", "text": [ "BAB2_1107" ], "offsets": [ [ 4345, 4354 ] ], "normalized": [] }, { "id": "PMC2858072-02-Results_and_Discussion-01_T76", "type": "Protein", "text": [ "BAB1_0505" ], "offsets": [ [ 4356, 4365 ] ], "normalized": [] }, { "id": "PMC2858072-02-Results_and_Discussion-01_T77", "type": "Protein", "text": [ "BAB1_1022" ], "offsets": [ [ 4367, 4376 ] ], "normalized": [] }, { "id": "PMC2858072-02-Results_and_Discussion-01_T78", "type": "Chemical", "text": [ "LPS" ], "offsets": [ [ 4430, 4433 ] ], "normalized": [] }, { "id": "PMC2858072-02-Results_and_Discussion-01_T79", "type": "Protein", "text": [ "BAB1_1620" ], "offsets": [ [ 4470, 4479 ] ], "normalized": [] }, { "id": "PMC2858072-02-Results_and_Discussion-01_T80", "type": "Protein", "text": [ "fabG" ], "offsets": [ [ 4551, 4555 ] ], "normalized": [] }, { "id": "PMC2858072-02-Results_and_Discussion-01_T81", "type": "Protein", "text": [ "BAB1_2043" ], "offsets": [ [ 4598, 4607 ] ], "normalized": [] }, { "id": "PMC2858072-02-Results_and_Discussion-01_T82", "type": "Protein", "text": [ "fabF" ], "offsets": [ [ 4609, 4613 ] ], "normalized": [] }, { "id": "PMC2858072-02-Results_and_Discussion-01_T83", "type": "Protein", "text": [ "BAB1_0872" ], "offsets": [ [ 4654, 4663 ] ], "normalized": [] }, { "id": "PMC2858072-02-Results_and_Discussion-01_T84", "type": "Protein", "text": [ "fadD" ], "offsets": [ [ 4665, 4669 ] ], "normalized": [] }, { "id": "PMC2858072-02-Results_and_Discussion-01_T85", "type": "Chemical", "text": [ "fatty-acyl-CoA" ], "offsets": [ [ 4671, 4685 ] ], "normalized": [] }, { "id": "PMC2858072-02-Results_and_Discussion-01_T86", "type": "Protein", "text": [ "BAB1_0320" ], "offsets": [ [ 4696, 4705 ] ], "normalized": [] }, { "id": "PMC2858072-02-Results_and_Discussion-01_T87", "type": "Protein", "text": [ "cfa" ], "offsets": [ [ 4707, 4710 ] ], "normalized": [] }, { "id": "PMC2858072-02-Results_and_Discussion-01_T88", "type": "Chemical", "text": [ "cyclopropane-fatty-acyl-phospholipid" ], "offsets": [ [ 4712, 4748 ] ], "normalized": [] }, { "id": "PMC2858072-02-Results_and_Discussion-01_T89", "type": "Protein", "text": [ "BAB1_0476" ], "offsets": [ [ 4759, 4768 ] ], "normalized": [] }, { "id": "PMC2858072-02-Results_and_Discussion-01_T90", "type": "Protein", "text": [ "BAB1_1357" ], "offsets": [ [ 4770, 4779 ] ], "normalized": [] }, { "id": "PMC2858072-02-Results_and_Discussion-01_T91", "type": "Two-component-system", "text": [ "BvrR/BvrS" ], "offsets": [ [ 4806, 4815 ] ], "normalized": [] }, { "id": "PMC2858072-02-Results_and_Discussion-01_T92", "type": "Protein", "text": [ "BvrR" ], "offsets": [ [ 4806, 4810 ] ], "normalized": [] }, { "id": "PMC2858072-02-Results_and_Discussion-01_T93", "type": "Protein", "text": [ "BvrS" ], "offsets": [ [ 4811, 4815 ] ], "normalized": [] }, { "id": "PMC2858072-02-Results_and_Discussion-01_T94", "type": "Organism", "text": [ "Brucella" ], "offsets": [ [ 4903, 4911 ] ], "normalized": [] } ]

[ { "id": "PMC2858072-02-Results_and_Discussion-01_E1", "type": "Transcription", "trigger": { "text": [ "transcription" ], "offsets": [ [ 2539, 2552 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC2858072-02-Results_and_Discussion-01_T23" } ] }, { "id": "PMC2858072-02-Results_and_Discussion-01_E2", "type": "Transcription", "trigger": { "text": [ "transcription" ], "offsets": [ [ 2539, 2552 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC2858072-02-Results_and_Discussion-01_T25" } ] }, { "id": "PMC2858072-02-Results_and_Discussion-01_E3", "type": "Transcription", "trigger": { "text": [ "transcription" ], "offsets": [ [ 2539, 2552 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC2858072-02-Results_and_Discussion-01_T27" } ] }, { "id": "PMC2858072-02-Results_and_Discussion-01_E4", "type": "Gene_expression", "trigger": { "text": [ "expressed" ], "offsets": [ [ 2869, 2878 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC2858072-02-Results_and_Discussion-01_T41" } ] }, { "id": "PMC2858072-02-Results_and_Discussion-01_E5", "type": "Gene_expression", "trigger": { "text": [ "expressed" ], "offsets": [ [ 2869, 2878 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC2858072-02-Results_and_Discussion-01_T31" } ] }, { "id": "PMC2858072-02-Results_and_Discussion-01_E6", "type": "Gene_expression", "trigger": { "text": [ "expressed" ], "offsets": [ [ 2869, 2878 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC2858072-02-Results_and_Discussion-01_T33" } ] }, { "id": "PMC2858072-02-Results_and_Discussion-01_E7", "type": "Gene_expression", "trigger": { "text": [ "expressed" ], "offsets": [ [ 2869, 2878 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC2858072-02-Results_and_Discussion-01_T35" } ] }, { "id": "PMC2858072-02-Results_and_Discussion-01_E8", "type": "Gene_expression", "trigger": { "text": [ "expressed" ], "offsets": [ [ 2869, 2878 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC2858072-02-Results_and_Discussion-01_T37" } ] }, { "id": "PMC2858072-02-Results_and_Discussion-01_E9", "type": "Gene_expression", "trigger": { "text": [ "expressed" ], "offsets": [ [ 2869, 2878 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC2858072-02-Results_and_Discussion-01_T39" } ] }, { "id": "PMC2858072-02-Results_and_Discussion-01_E10", "type": "Gene_expression", "trigger": { "text": [ "expressed" ], "offsets": [ [ 2869, 2878 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC2858072-02-Results_and_Discussion-01_T40" } ] }, { "id": "PMC2858072-02-Results_and_Discussion-01_E11", "type": "Transcription", "trigger": { "text": [ "transcription" ], "offsets": [ [ 3216, 3229 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC2858072-02-Results_and_Discussion-01_T44" } ] }, { "id": "PMC2858072-02-Results_and_Discussion-01_E12", "type": "Transcription", "trigger": { "text": [ "transcription" ], "offsets": [ [ 3216, 3229 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC2858072-02-Results_and_Discussion-01_T45" } ] }, { "id": "PMC2858072-02-Results_and_Discussion-01_E13", "type": "Regulation", "trigger": { "text": [ "control" ], "offsets": [ [ 3267, 3274 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC2858072-02-Results_and_Discussion-01_E11" }, { "role": "Cause", "ref_id": "PMC2858072-02-Results_and_Discussion-01_T46" } ] }, { "id": "PMC2858072-02-Results_and_Discussion-01_E14", "type": "Regulation", "trigger": { "text": [ "control" ], "offsets": [ [ 3267, 3274 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC2858072-02-Results_and_Discussion-01_E12" }, { "role": "Cause", "ref_id": "PMC2858072-02-Results_and_Discussion-01_T46" } ] }, { "id": "PMC2858072-02-Results_and_Discussion-01_E15", "type": "Negative_regulation", "trigger": { "text": [ "down-regulated" ], "offsets": [ [ 4015, 4029 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC2858072-02-Results_and_Discussion-01_T61" } ] }, { "id": "PMC2858072-02-Results_and_Discussion-01_E16", "type": "Negative_regulation", "trigger": { "text": [ "down-regulated" ], "offsets": [ [ 4015, 4029 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC2858072-02-Results_and_Discussion-01_T63" } ] }, { "id": "PMC2858072-02-Results_and_Discussion-01_E17", "type": "Regulation", "trigger": { "text": [ "regulated" ], "offsets": [ [ 4042, 4051 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC2858072-02-Results_and_Discussion-01_T80" }, { "role": "Cause", "ref_id": "PMC2858072-02-Results_and_Discussion-01_T65" } ] }, { "id": "PMC2858072-02-Results_and_Discussion-01_E18", "type": "Regulation", "trigger": { "text": [ "regulated" ], "offsets": [ [ 4042, 4051 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC2858072-02-Results_and_Discussion-01_T82" }, { "role": "Cause", "ref_id": "PMC2858072-02-Results_and_Discussion-01_T65" } ] }, { "id": "PMC2858072-02-Results_and_Discussion-01_E19", "type": "Regulation", "trigger": { "text": [ "regulated" ], "offsets": [ [ 4042, 4051 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC2858072-02-Results_and_Discussion-01_T84" }, { "role": "Cause", "ref_id": "PMC2858072-02-Results_and_Discussion-01_T65" } ] }, { "id": "PMC2858072-02-Results_and_Discussion-01_E20", "type": "Regulation", "trigger": { "text": [ "regulated" ], "offsets": [ [ 4042, 4051 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC2858072-02-Results_and_Discussion-01_T87" }, { "role": "Cause", "ref_id": "PMC2858072-02-Results_and_Discussion-01_T65" } ] }, { "id": "PMC2858072-02-Results_and_Discussion-01_E21", "type": "Regulation", "trigger": { "text": [ "regulated" ], "offsets": [ [ 4042, 4051 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC2858072-02-Results_and_Discussion-01_T90" }, { "role": "Cause", "ref_id": "PMC2858072-02-Results_and_Discussion-01_T65" } ] }, { "id": "PMC2858072-02-Results_and_Discussion-01_E22", "type": "Negative_regulation", "trigger": { "text": [ "regulated" ], "offsets": [ [ 4042, 4051 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC2858072-02-Results_and_Discussion-01_T66" }, { "role": "Cause", "ref_id": "PMC2858072-02-Results_and_Discussion-01_T65" } ] }, { "id": "PMC2858072-02-Results_and_Discussion-01_E23", "type": "Negative_regulation", "trigger": { "text": [ "regulated" ], "offsets": [ [ 4042, 4051 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC2858072-02-Results_and_Discussion-01_T67" }, { "role": "Cause", "ref_id": "PMC2858072-02-Results_and_Discussion-01_T65" } ] }, { "id": "PMC2858072-02-Results_and_Discussion-01_E24", "type": "Negative_regulation", "trigger": { "text": [ "regulated" ], "offsets": [ [ 4042, 4051 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC2858072-02-Results_and_Discussion-01_T68" }, { "role": "Cause", "ref_id": "PMC2858072-02-Results_and_Discussion-01_T65" } ] }, { "id": "PMC2858072-02-Results_and_Discussion-01_E25", "type": "Positive_regulation", "trigger": { "text": [ "regulated" ], "offsets": [ [ 4042, 4051 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC2858072-02-Results_and_Discussion-01_T69" }, { "role": "Cause", "ref_id": "PMC2858072-02-Results_and_Discussion-01_T65" } ] }, { "id": "PMC2858072-02-Results_and_Discussion-01_E26", "type": "Positive_regulation", "trigger": { "text": [ "regulated" ], "offsets": [ [ 4042, 4051 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC2858072-02-Results_and_Discussion-01_T71" }, { "role": "Cause", "ref_id": "PMC2858072-02-Results_and_Discussion-01_T65" } ] }, { "id": "PMC2858072-02-Results_and_Discussion-01_E27", "type": "Positive_regulation", "trigger": { "text": [ "regulated" ], "offsets": [ [ 4042, 4051 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC2858072-02-Results_and_Discussion-01_T72" }, { "role": "Cause", "ref_id": "PMC2858072-02-Results_and_Discussion-01_T65" } ] }, { "id": "PMC2858072-02-Results_and_Discussion-01_E28", "type": "Positive_regulation", "trigger": { "text": [ "regulated" ], "offsets": [ [ 4042, 4051 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC2858072-02-Results_and_Discussion-01_T75" }, { "role": "Cause", "ref_id": "PMC2858072-02-Results_and_Discussion-01_T65" } ] }, { "id": "PMC2858072-02-Results_and_Discussion-01_E29", "type": "Positive_regulation", "trigger": { "text": [ "regulated" ], "offsets": [ [ 4042, 4051 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC2858072-02-Results_and_Discussion-01_T76" }, { "role": "Cause", "ref_id": "PMC2858072-02-Results_and_Discussion-01_T65" } ] }, { "id": "PMC2858072-02-Results_and_Discussion-01_E30", "type": "Positive_regulation", "trigger": { "text": [ "regulated" ], "offsets": [ [ 4042, 4051 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC2858072-02-Results_and_Discussion-01_T77" }, { "role": "Cause", "ref_id": "PMC2858072-02-Results_and_Discussion-01_T65" } ] }, { "id": "PMC2858072-02-Results_and_Discussion-01_E31", "type": "Positive_regulation", "trigger": { "text": [ "regulated" ], "offsets": [ [ 4042, 4051 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC2858072-02-Results_and_Discussion-01_T79" }, { "role": "Cause", "ref_id": "PMC2858072-02-Results_and_Discussion-01_T65" } ] }, { "id": "PMC2858072-02-Results_and_Discussion-01_E32", "type": "Negative_regulation", "trigger": { "text": [ "down-regulated" ], "offsets": [ [ 4161, 4175 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC2858072-02-Results_and_Discussion-01_T66" }, { "role": "Cause", "ref_id": "PMC2858072-02-Results_and_Discussion-01_T65" } ] }, { "id": "PMC2858072-02-Results_and_Discussion-01_E33", "type": "Negative_regulation", "trigger": { "text": [ "down-regulated" ], "offsets": [ [ 4161, 4175 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC2858072-02-Results_and_Discussion-01_T67" }, { "role": "Cause", "ref_id": "PMC2858072-02-Results_and_Discussion-01_T65" } ] }, { "id": "PMC2858072-02-Results_and_Discussion-01_E34", "type": "Negative_regulation", "trigger": { "text": [ "down-regulated" ], "offsets": [ [ 4161, 4175 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC2858072-02-Results_and_Discussion-01_T68" }, { "role": "Cause", "ref_id": "PMC2858072-02-Results_and_Discussion-01_T65" } ] }, { "id": "PMC2858072-02-Results_and_Discussion-01_E35", "type": "Positive_regulation", "trigger": { "text": [ "up-regulated" ], "offsets": [ [ 4394, 4406 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC2858072-02-Results_and_Discussion-01_T69" }, { "role": "Cause", "ref_id": "PMC2858072-02-Results_and_Discussion-01_T65" } ] }, { "id": "PMC2858072-02-Results_and_Discussion-01_E36", "type": "Positive_regulation", "trigger": { "text": [ "up-regulated" ], "offsets": [ [ 4394, 4406 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC2858072-02-Results_and_Discussion-01_T71" }, { "role": "Cause", "ref_id": "PMC2858072-02-Results_and_Discussion-01_T65" } ] }, { "id": "PMC2858072-02-Results_and_Discussion-01_E37", "type": "Positive_regulation", "trigger": { "text": [ "up-regulated" ], "offsets": [ [ 4394, 4406 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC2858072-02-Results_and_Discussion-01_T72" }, { "role": "Cause", "ref_id": "PMC2858072-02-Results_and_Discussion-01_T65" } ] }, { "id": "PMC2858072-02-Results_and_Discussion-01_E38", "type": "Positive_regulation", "trigger": { "text": [ "up-regulated" ], "offsets": [ [ 4394, 4406 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC2858072-02-Results_and_Discussion-01_T75" }, { "role": "Cause", "ref_id": "PMC2858072-02-Results_and_Discussion-01_T65" } ] }, { "id": "PMC2858072-02-Results_and_Discussion-01_E39", "type": "Positive_regulation", "trigger": { "text": [ "up-regulated" ], "offsets": [ [ 4394, 4406 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC2858072-02-Results_and_Discussion-01_T76" }, { "role": "Cause", "ref_id": "PMC2858072-02-Results_and_Discussion-01_T65" } ] }, { "id": "PMC2858072-02-Results_and_Discussion-01_E40", "type": "Positive_regulation", "trigger": { "text": [ "up-regulated" ], "offsets": [ [ 4394, 4406 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC2858072-02-Results_and_Discussion-01_T77" }, { "role": "Cause", "ref_id": "PMC2858072-02-Results_and_Discussion-01_T65" } ] }, { "id": "PMC2858072-02-Results_and_Discussion-01_E41", "type": "Positive_regulation", "trigger": { "text": [ "up-regulated" ], "offsets": [ [ 4492, 4504 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC2858072-02-Results_and_Discussion-01_T79" }, { "role": "Cause", "ref_id": "PMC2858072-02-Results_and_Discussion-01_T65" } ] }, { "id": "PMC2858072-02-Results_and_Discussion-01_E42", "type": "Process", "trigger": { "text": [ "virulence" ], "offsets": [ [ 4912, 4921 ] ] }, "arguments": [ { "role": "Participant", "ref_id": "PMC2858072-02-Results_and_Discussion-01_T94" } ] } ]

[ { "id": "PMC2858072-02-Results_and_Discussion-01_1", "entity_ids": [ "PMC2858072-02-Results_and_Discussion-01_T23", "PMC2858072-02-Results_and_Discussion-01_T24" ] }, { "id": "PMC2858072-02-Results_and_Discussion-01_2", "entity_ids": [ "PMC2858072-02-Results_and_Discussion-01_T25", "PMC2858072-02-Results_and_Discussion-01_T26" ] }, { "id": "PMC2858072-02-Results_and_Discussion-01_3", "entity_ids": [ "PMC2858072-02-Results_and_Discussion-01_T27", "PMC2858072-02-Results_and_Discussion-01_T28" ] }, { "id": "PMC2858072-02-Results_and_Discussion-01_4", "entity_ids": [ "PMC2858072-02-Results_and_Discussion-01_T31", "PMC2858072-02-Results_and_Discussion-01_T32" ] }, { "id": "PMC2858072-02-Results_and_Discussion-01_5", "entity_ids": [ "PMC2858072-02-Results_and_Discussion-01_T33", "PMC2858072-02-Results_and_Discussion-01_T34" ] }, { "id": "PMC2858072-02-Results_and_Discussion-01_6", "entity_ids": [ "PMC2858072-02-Results_and_Discussion-01_T35", "PMC2858072-02-Results_and_Discussion-01_T36" ] }, { "id": "PMC2858072-02-Results_and_Discussion-01_7", "entity_ids": [ "PMC2858072-02-Results_and_Discussion-01_T37", "PMC2858072-02-Results_and_Discussion-01_T38" ] }, { "id": "PMC2858072-02-Results_and_Discussion-01_8", "entity_ids": [ "PMC2858072-02-Results_and_Discussion-01_T61", "PMC2858072-02-Results_and_Discussion-01_T62" ] }, { "id": "PMC2858072-02-Results_and_Discussion-01_9", "entity_ids": [ "PMC2858072-02-Results_and_Discussion-01_T63", "PMC2858072-02-Results_and_Discussion-01_T63" ] }, { "id": "PMC2858072-02-Results_and_Discussion-01_10", "entity_ids": [ "PMC2858072-02-Results_and_Discussion-01_T69", "PMC2858072-02-Results_and_Discussion-01_T70" ] }, { "id": "PMC2858072-02-Results_and_Discussion-01_11", "entity_ids": [ "PMC2858072-02-Results_and_Discussion-01_T71", "PMC2858072-02-Results_and_Discussion-01_T73" ] }, { "id": "PMC2858072-02-Results_and_Discussion-01_12", "entity_ids": [ "PMC2858072-02-Results_and_Discussion-01_T72", "PMC2858072-02-Results_and_Discussion-01_T74" ] }, { "id": "PMC2858072-02-Results_and_Discussion-01_13", "entity_ids": [ "PMC2858072-02-Results_and_Discussion-01_T80", "PMC2858072-02-Results_and_Discussion-01_T81" ] }, { "id": "PMC2858072-02-Results_and_Discussion-01_14", "entity_ids": [ "PMC2858072-02-Results_and_Discussion-01_T82", "PMC2858072-02-Results_and_Discussion-01_T83" ] }, { "id": "PMC2858072-02-Results_and_Discussion-01_15", "entity_ids": [ "PMC2858072-02-Results_and_Discussion-01_T84", "PMC2858072-02-Results_and_Discussion-01_T86" ] }, { "id": "PMC2858072-02-Results_and_Discussion-01_16", "entity_ids": [ "PMC2858072-02-Results_and_Discussion-01_T87", "PMC2858072-02-Results_and_Discussion-01_T89" ] } ]

[]

[ { "id": "PMC2565068-02-Results-06__text", "type": "abstract", "text": [ "csrS mutation is important in the pathogenesis of invasive infections in a mouse model \nIn order to elucidate the role of csrS, in infections in vivo, we compared the virulence of GAS isolates using a mouse model which infected GAS intraperitoneally. The non-invasive 1566 strain displayed the LD50 value approximately 100-fold higher than that of the severe invasive NIH230 strain (Table 1), whereas a csrS deletion (1566DeltacsrS) caused an increase in the LD50 value comparable to that of the NIH230 strain. Consistently, an introduction of the intact csrS gene into the NIH230 strain (NIH230::csrS+) reduced the LD50 value to the level observed in the non-invasive strain. These results indicate that csrS is an important virulence factor in the mouse model of lethal infections. As shown in Figure 7A, the NIH230 strain caused bacteremia in mice 24 h after intraperitoneal injection whereas the bacteremia was barely detected in mice infected with NIH230::csrS+as well as the 1566 strain (p=0.005 compared with non-invasive isolates, and p=0.005 compared with invasive isolates +CsrS). Histopathologically, in the mice injected with the NIH230 strain, bacteria formed clusters in interstitial tissues in the kidneys and the lungs, accompanied congestion and no inflammatory cells at infectious foci (Figure 7B, 7C and data not shown). Contrarily, no significant pathological alterations were observed in the mice injected with the 1566 and NIH230::csrS+ strains (Figure 7B and 7C). Figure 7D shows that subcutaneous infection of NIH230 formed the infected lesions with area significantly larger than those of 1566 and NIH230::csrS+. These results suggest that the invasive GAS isolates are more virulent in vivo than non-invasive GAS, and impair PMN function in vivo, owing, at least in part, to the mutations in the csrS gene.\n" ], "offsets": [ [ 0, 1833 ] ] } ]

[ { "id": "PMC2565068-02-Results-06_T1", "type": "Protein", "text": [ "csrS" ], "offsets": [ [ 0, 4 ] ], "normalized": [] }, { "id": "PMC2565068-02-Results-06_T2", "type": "Organism", "text": [ "mouse" ], "offsets": [ [ 75, 80 ] ], "normalized": [] }, { "id": "PMC2565068-02-Results-06_T3", "type": "Protein", "text": [ "csrS" ], "offsets": [ [ 122, 126 ] ], "normalized": [] }, { "id": "PMC2565068-02-Results-06_T4", "type": "Organism", "text": [ "GAS" ], "offsets": [ [ 180, 183 ] ], "normalized": [] }, { "id": "PMC2565068-02-Results-06_T5", "type": "Organism", "text": [ "mouse" ], "offsets": [ [ 201, 206 ] ], "normalized": [] }, { "id": "PMC2565068-02-Results-06_T6", "type": "Organism", "text": [ "GAS" ], "offsets": [ [ 228, 231 ] ], "normalized": [] }, { "id": "PMC2565068-02-Results-06_T7", "type": "Organism", "text": [ "non-invasive 1566" ], "offsets": [ [ 255, 272 ] ], "normalized": [] }, { "id": "PMC2565068-02-Results-06_T8", "type": "Organism", "text": [ "invasive NIH230" ], "offsets": [ [ 359, 374 ] ], "normalized": [] }, { "id": "PMC2565068-02-Results-06_T9", "type": "Organism", "text": [ "csrS deletion" ], "offsets": [ [ 403, 416 ] ], "normalized": [] }, { "id": "PMC2565068-02-Results-06_T10", "type": "Protein", "text": [ "csrS" ], "offsets": [ [ 403, 407 ] ], "normalized": [] }, { "id": "PMC2565068-02-Results-06_T11", "type": "Organism", "text": [ "1566DeltacsrS" ], "offsets": [ [ 418, 431 ] ], "normalized": [] }, { "id": "PMC2565068-02-Results-06_T12", "type": "Protein", "text": [ "csrS" ], "offsets": [ [ 427, 431 ] ], "normalized": [] }, { "id": "PMC2565068-02-Results-06_T13", "type": "Organism", "text": [ "NIH230" ], "offsets": [ [ 496, 502 ] ], "normalized": [] }, { "id": "PMC2565068-02-Results-06_T14", "type": "Protein", "text": [ "csrS" ], "offsets": [ [ 555, 559 ] ], "normalized": [] }, { "id": "PMC2565068-02-Results-06_T15", "type": "Organism", "text": [ "NIH230" ], "offsets": [ [ 574, 580 ] ], "normalized": [] }, { "id": "PMC2565068-02-Results-06_T16", "type": "Organism", "text": [ "NIH230::csrS+" ], "offsets": [ [ 589, 602 ] ], "normalized": [] }, { "id": "PMC2565068-02-Results-06_T17", "type": "Protein", "text": [ "csrS+" ], "offsets": [ [ 597, 602 ] ], "normalized": [] }, { "id": "PMC2565068-02-Results-06_T18", "type": "Organism", "text": [ "non-invasive strain" ], "offsets": [ [ 656, 675 ] ], "normalized": [] }, { "id": "PMC2565068-02-Results-06_T19", "type": "Protein", "text": [ "csrS" ], "offsets": [ [ 705, 709 ] ], "normalized": [] }, { "id": "PMC2565068-02-Results-06_T20", "type": "Organism", "text": [ "mouse" ], "offsets": [ [ 750, 755 ] ], "normalized": [] }, { "id": "PMC2565068-02-Results-06_T21", "type": "Organism", "text": [ "NIH230" ], "offsets": [ [ 811, 817 ] ], "normalized": [] }, { "id": "PMC2565068-02-Results-06_T22", "type": "Organism", "text": [ "mice" ], "offsets": [ [ 846, 850 ] ], "normalized": [] }, { "id": "PMC2565068-02-Results-06_T23", "type": "Organism", "text": [ "mice" ], "offsets": [ [ 934, 938 ] ], "normalized": [] }, { "id": "PMC2565068-02-Results-06_T24", "type": "Organism", "text": [ "NIH230::csrS+" ], "offsets": [ [ 953, 966 ] ], "normalized": [] }, { "id": "PMC2565068-02-Results-06_T25", "type": "Protein", "text": [ "csrS+" ], "offsets": [ [ 961, 966 ] ], "normalized": [] }, { "id": "PMC2565068-02-Results-06_T26", "type": "Organism", "text": [ "1566" ], "offsets": [ [ 981, 985 ] ], "normalized": [] }, { "id": "PMC2565068-02-Results-06_T27", "type": "Organism", "text": [ "non-invasive" ], "offsets": [ [ 1016, 1028 ] ], "normalized": [] }, { "id": "PMC2565068-02-Results-06_T28", "type": "Organism", "text": [ "invasive isolates +CsrS" ], "offsets": [ [ 1065, 1088 ] ], "normalized": [] }, { "id": "PMC2565068-02-Results-06_T29", "type": "Protein", "text": [ "CsrS" ], "offsets": [ [ 1084, 1088 ] ], "normalized": [] }, { "id": "PMC2565068-02-Results-06_T30", "type": "Organism", "text": [ "mice" ], "offsets": [ [ 1119, 1123 ] ], "normalized": [] }, { "id": "PMC2565068-02-Results-06_T31", "type": "Organism", "text": [ "NIH230" ], "offsets": [ [ 1142, 1148 ] ], "normalized": [] }, { "id": "PMC2565068-02-Results-06_T32", "type": "Organism", "text": [ "mice" ], "offsets": [ [ 1413, 1417 ] ], "normalized": [] }, { "id": "PMC2565068-02-Results-06_T33", "type": "Organism", "text": [ "1566" ], "offsets": [ [ 1436, 1440 ] ], "normalized": [] }, { "id": "PMC2565068-02-Results-06_T34", "type": "Organism", "text": [ "NIH230::csrS+" ], "offsets": [ [ 1445, 1458 ] ], "normalized": [] }, { "id": "PMC2565068-02-Results-06_T35", "type": "Protein", "text": [ "csrS+" ], "offsets": [ [ 1453, 1458 ] ], "normalized": [] }, { "id": "PMC2565068-02-Results-06_T36", "type": "Organism", "text": [ "NIH230" ], "offsets": [ [ 1534, 1540 ] ], "normalized": [] }, { "id": "PMC2565068-02-Results-06_T37", "type": "Organism", "text": [ "1566" ], "offsets": [ [ 1614, 1618 ] ], "normalized": [] }, { "id": "PMC2565068-02-Results-06_T38", "type": "Organism", "text": [ "NIH230::csrS+" ], "offsets": [ [ 1623, 1636 ] ], "normalized": [] }, { "id": "PMC2565068-02-Results-06_T39", "type": "Protein", "text": [ "csrS+" ], "offsets": [ [ 1631, 1636 ] ], "normalized": [] }, { "id": "PMC2565068-02-Results-06_T40", "type": "Organism", "text": [ "invasive GAS" ], "offsets": [ [ 1669, 1681 ] ], "normalized": [] }, { "id": "PMC2565068-02-Results-06_T41", "type": "Organism", "text": [ "non-invasive GAS" ], "offsets": [ [ 1722, 1738 ] ], "normalized": [] }, { "id": "PMC2565068-02-Results-06_T42", "type": "Protein", "text": [ "csrS" ], "offsets": [ [ 1822, 1826 ] ], "normalized": [] } ]

[ { "id": "PMC2565068-02-Results-06_E1", "type": "Process", "trigger": { "text": [ "infections" ], "offsets": [ [ 59, 69 ] ] }, "arguments": [] }, { "id": "PMC2565068-02-Results-06_E2", "type": "Process", "trigger": { "text": [ "infections" ], "offsets": [ [ 131, 141 ] ] }, "arguments": [] }, { "id": "PMC2565068-02-Results-06_E3", "type": "Process", "trigger": { "text": [ "virulence" ], "offsets": [ [ 167, 176 ] ] }, "arguments": [ { "role": "Participant", "ref_id": "PMC2565068-02-Results-06_T4" } ] }, { "id": "PMC2565068-02-Results-06_E4", "type": "Process", "trigger": { "text": [ "infected" ], "offsets": [ [ 219, 227 ] ] }, "arguments": [ { "role": "Participant", "ref_id": "PMC2565068-02-Results-06_T6" } ] }, { "id": "PMC2565068-02-Results-06_E5", "type": "Positive_regulation", "trigger": { "text": [ "introduction" ], "offsets": [ [ 528, 540 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC2565068-02-Results-06_T14" } ] }, { "id": "PMC2565068-02-Results-06_E6", "type": "Process", "trigger": { "text": [ "virulence" ], "offsets": [ [ 726, 735 ] ] }, "arguments": [] }, { "id": "PMC2565068-02-Results-06_E7", "type": "Process", "trigger": { "text": [ "infections" ], "offsets": [ [ 772, 782 ] ] }, "arguments": [] }, { "id": "PMC2565068-02-Results-06_E8", "type": "Process", "trigger": { "text": [ "infected" ], "offsets": [ [ 939, 947 ] ] }, "arguments": [ { "role": "Participant", "ref_id": "PMC2565068-02-Results-06_T24" } ] }, { "id": "PMC2565068-02-Results-06_E9", "type": "Process", "trigger": { "text": [ "infection" ], "offsets": [ [ 1521, 1530 ] ] }, "arguments": [ { "role": "Participant", "ref_id": "PMC2565068-02-Results-06_T36" } ] }, { "id": "PMC2565068-02-Results-06_E10", "type": "Process", "trigger": { "text": [ "infected" ], "offsets": [ [ 1552, 1560 ] ] }, "arguments": [ { "role": "Participant", "ref_id": "PMC2565068-02-Results-06_T36" } ] }, { "id": "PMC2565068-02-Results-06_E11", "type": "Process", "trigger": { "text": [ "infected" ], "offsets": [ [ 1552, 1560 ] ] }, "arguments": [ { "role": "Participant", "ref_id": "PMC2565068-02-Results-06_T37" } ] }, { "id": "PMC2565068-02-Results-06_E12", "type": "Process", "trigger": { "text": [ "infected" ], "offsets": [ [ 1552, 1560 ] ] }, "arguments": [ { "role": "Participant", "ref_id": "PMC2565068-02-Results-06_T38" } ] }, { "id": "PMC2565068-02-Results-06_E13", "type": "Process", "trigger": { "text": [ "virulent" ], "offsets": [ [ 1700, 1708 ] ] }, "arguments": [ { "role": "Participant", "ref_id": "PMC2565068-02-Results-06_T40" } ] }, { "id": "PMC2565068-02-Results-06_E14", "type": "Process", "trigger": { "text": [ "virulent" ], "offsets": [ [ 1700, 1708 ] ] }, "arguments": [ { "role": "Participant", "ref_id": "PMC2565068-02-Results-06_T41" } ] } ]

[ { "id": "PMC2565068-02-Results-06_1", "entity_ids": [ "PMC2565068-02-Results-06_T9", "PMC2565068-02-Results-06_T11" ] } ]

[]

[ { "id": "PMC2816692-03-Discussion-01__text", "type": "abstract", "text": [ "Discussion \nStructural features of SrcA We used a reverse genetics approach to define a new secretion chaperone in S. Typhimurium that is integrated functionally with the T3SS encoded by SPI-2, a system well described for its role in immune subversion and intracellular infection during host colonization. Consistent with other class I secretion chaperones, SrcA has extensive electronegative charge distributed over the surface of the molecule. The exact function of this charge distribution is not known, but data from other systems suggests a docking recognition function with other components of the type III apparatus, possibly the T3SS-accociated ATPase. For instance, electronegative surface residues on the SigE chaperone in the SPI-1-encoded T3SS negatively affect cargo secretion, but not cargo stability [30]. In enteropathogenic E. coli, a surface-exposed electronegative residue in the CesT chaperone (Glu142) likewise contributes to Tir secretion but not Tir binding [16], suggesting a role in either targeting bound cargo to the T3SS or in the secretion process itself. Interestingly, SrcA lacks 17-amino acids that make up the carboxyl terminus of CesT, which includes Glu142, and yet it still retains effector binding, ATPase binding and effector secretion functionalities. Thus, it is likely that other surface charged residues of SrcA are involved in these functions or that SrcA targets effector cargo to the secretion apparatus through a mechanism distinct from CesT. The interface for the SrcA homodimer is extensive and is more in keeping with the structural features of single-effector class IA chaperones (approximately1100-1300 A2) compared to the reduced dimer interface of Spa15, a multi-cargo class IB chaperone from Shigella [31]. Similar to CesT and SicP, the dimer interface of SrcA adopts a parallel configuration when comparing alpha2 helices of opposing subunits. In contrast, the subunits of Spa15 undergo a significant relative rotation (80degrees) about the alpha2-axis resulting in a different interface. These features may relate to biological function in the SPI2 T3SS and/or in vetting effector cargo amongst the >30 effectors identified in Salmonella. We found no evidence of interactions between SrcA and translocon components of the SPI-2 T3SS and so it appears as though SrcA functions specifically in effector translocation events.\n" ], "offsets": [ [ 0, 2379 ] ] } ]

[ { "id": "PMC2816692-03-Discussion-01_T1", "type": "Protein", "text": [ "SrcA" ], "offsets": [ [ 35, 39 ] ], "normalized": [] }, { "id": "PMC2816692-03-Discussion-01_T2", "type": "Organism", "text": [ "S. Typhimurium" ], "offsets": [ [ 115, 129 ] ], "normalized": [] }, { "id": "PMC2816692-03-Discussion-01_T3", "type": "Organism", "text": [ "host" ], "offsets": [ [ 287, 291 ] ], "normalized": [] }, { "id": "PMC2816692-03-Discussion-01_T4", "type": "Protein", "text": [ "SrcA" ], "offsets": [ [ 358, 362 ] ], "normalized": [] }, { "id": "PMC2816692-03-Discussion-01_T5", "type": "Protein", "text": [ "SigE" ], "offsets": [ [ 715, 719 ] ], "normalized": [] }, { "id": "PMC2816692-03-Discussion-01_T6", "type": "Organism", "text": [ "E. coli" ], "offsets": [ [ 841, 848 ] ], "normalized": [] }, { "id": "PMC2816692-03-Discussion-01_T7", "type": "Protein", "text": [ "CesT" ], "offsets": [ [ 899, 903 ] ], "normalized": [] }, { "id": "PMC2816692-03-Discussion-01_T8", "type": "Protein", "text": [ "Tir" ], "offsets": [ [ 947, 950 ] ], "normalized": [] }, { "id": "PMC2816692-03-Discussion-01_T9", "type": "Protein", "text": [ "Tir" ], "offsets": [ [ 969, 972 ] ], "normalized": [] }, { "id": "PMC2816692-03-Discussion-01_T10", "type": "Protein", "text": [ "SrcA" ], "offsets": [ [ 1100, 1104 ] ], "normalized": [] }, { "id": "PMC2816692-03-Discussion-01_T11", "type": "Chemical", "text": [ "carboxyl" ], "offsets": [ [ 1143, 1151 ] ], "normalized": [] }, { "id": "PMC2816692-03-Discussion-01_T12", "type": "Protein", "text": [ "CesT" ], "offsets": [ [ 1164, 1168 ] ], "normalized": [] }, { "id": "PMC2816692-03-Discussion-01_T13", "type": "Protein", "text": [ "SrcA" ], "offsets": [ [ 1349, 1353 ] ], "normalized": [] }, { "id": "PMC2816692-03-Discussion-01_T14", "type": "Protein", "text": [ "SrcA" ], "offsets": [ [ 1394, 1398 ] ], "normalized": [] }, { "id": "PMC2816692-03-Discussion-01_T15", "type": "Protein", "text": [ "CesT" ], "offsets": [ [ 1483, 1487 ] ], "normalized": [] }, { "id": "PMC2816692-03-Discussion-01_T16", "type": "Protein", "text": [ "SrcA" ], "offsets": [ [ 1511, 1515 ] ], "normalized": [] }, { "id": "PMC2816692-03-Discussion-01_T17", "type": "Protein", "text": [ "Spa15" ], "offsets": [ [ 1701, 1706 ] ], "normalized": [] }, { "id": "PMC2816692-03-Discussion-01_T18", "type": "Organism", "text": [ "Shigella" ], "offsets": [ [ 1746, 1754 ] ], "normalized": [] }, { "id": "PMC2816692-03-Discussion-01_T19", "type": "Protein", "text": [ "CesT" ], "offsets": [ [ 1772, 1776 ] ], "normalized": [] }, { "id": "PMC2816692-03-Discussion-01_T20", "type": "Protein", "text": [ "SicP" ], "offsets": [ [ 1781, 1785 ] ], "normalized": [] }, { "id": "PMC2816692-03-Discussion-01_T21", "type": "Protein", "text": [ "SrcA" ], "offsets": [ [ 1810, 1814 ] ], "normalized": [] }, { "id": "PMC2816692-03-Discussion-01_T22", "type": "Protein", "text": [ "Spa15" ], "offsets": [ [ 1928, 1933 ] ], "normalized": [] }, { "id": "PMC2816692-03-Discussion-01_T23", "type": "Organism", "text": [ "Salmonella" ], "offsets": [ [ 2183, 2193 ] ], "normalized": [] }, { "id": "PMC2816692-03-Discussion-01_T24", "type": "Protein", "text": [ "SrcA" ], "offsets": [ [ 2240, 2244 ] ], "normalized": [] }, { "id": "PMC2816692-03-Discussion-01_T25", "type": "Protein", "text": [ "SrcA" ], "offsets": [ [ 2317, 2321 ] ], "normalized": [] } ]

[ { "id": "PMC2816692-03-Discussion-01_E1", "type": "Process", "trigger": { "text": [ "infection" ], "offsets": [ [ 270, 279 ] ] }, "arguments": [ { "role": "Participant", "ref_id": "PMC2816692-03-Discussion-01_T2" } ] }, { "id": "PMC2816692-03-Discussion-01_E2", "type": "Binding", "trigger": { "text": [ "binding" ], "offsets": [ [ 973, 980 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC2816692-03-Discussion-01_T7" }, { "role": "Theme", "ref_id": "PMC2816692-03-Discussion-01_T9" } ] }, { "id": "PMC2816692-03-Discussion-01_E3", "type": "Binding", "trigger": { "text": [ "binding" ], "offsets": [ [ 1227, 1234 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC2816692-03-Discussion-01_T10" } ] }, { "id": "PMC2816692-03-Discussion-01_E4", "type": "Binding", "trigger": { "text": [ "binding" ], "offsets": [ [ 1243, 1250 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC2816692-03-Discussion-01_T10" } ] }, { "id": "PMC2816692-03-Discussion-01_E5", "type": "Binding", "trigger": { "text": [ "interactions" ], "offsets": [ [ 2219, 2231 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMC2816692-03-Discussion-01_T24" } ] } ]

[]

[]