bluuebunny/crossref_metadata_2025_split huggingface dataset:
Anaerobic growth and cyanide synthesis of Pseudomonas aeruginosa depend on anr, a regulatory gene homologous with fnr of Escherichia coli
Authors: Zimmermann A. , Reimmann C. , Galimand M. , Haas D. 
Published: October 2006

SummaryAnaerobic growth of Pseudomonas aeruginosa on nitrate or arginine requires the anr gene, which codes for a positive control element (ANR) capable of functionally complementing an fnr mutation in Escherichia coli. The anr gene was sequenced; it showed 51% identity with the fnr gene at the amino acid sequence level. Four cysteine residues known to be essential in the FNR protein are conserved in ANR. The anr gene product (deduced Mr 27129) was visualized by the maxicell method and migrated like a 32kDa protein in gel electrophoresis under denaturing conditions. An anr mutant of P. aeruginosa constructed by gene replacement was defective in nitrate respiration, arginine deiminase activity, and hydrogen cyanide biosynthesis, underscoring the diverse metabolic functions of ANR during oxygen limitation. Pseudomonas fluorescens, Pseudomonas putida, Pseudomonas syringae, and Pseudomonas mendocina all had a functional analogue of ANR, indicating that similar anaerobic control mechanisms exist in these bacteria.
The Rhizobium meliloti exoZl exoB fragment of megaplasmid 2: ExoB functions as a UDP‐glucose 4‐epimerase and ExoZ shows homology to NodX of Rhizobium leguminosarum biovar viciae strain TOM
Authors: Buendia A. M. , Enenkel B. , Köplin R. , Niehaus K. , Arnold W. , Pünier A. 
Published: October 2006

SummaryA 2.6kb Clal‐Bam HI DNA fragment of megaplasmid 2 of Rhizobium meliloti 2011 was found to carry genes involved in exopolysaccharide synthesis and infection of alfalfa nodules. The analysis of the nucleotide sequence of this DNA fragment revealed the existence of two open reading frames (ORFs) running in opposite directions. Plasmid integration mutagenesis showed that these ORFs are organized as two monocistronic transcription units. One of the ORFs represents a new exo gene designated exoZ, which is involved in, but not essential for, the production of acidic exopolysaccharide. However, exoZ is not necessary for nodule formation with alfalfa. The ExoZ protein was found to show homology (23.3%) to the NodX protein of the R. leguminosarum biovar viciae strain TOM, known to be essential for nodulating the primitive Afghanistan pea. The second identified ORF corresponds to the exoB locus. The deduced amino acid sequence of the ExoB protein is homologous (39.6%) to that of the Escherichia coli GalE protein. In R meliloti, exoB codes for a UDP‐glucose 4‐epimerase. A deficiency in the activity of this enzyme fully accounts for all the multiple carbohydrate defects that have been observed in exoB mutants.
Structure of two retrons of Escherichia coli and their common chromosomal insertion site
Authors: Lim D. 
Published: October 2006

SummaryIt has been shown that certain strains of myxobacteria and of Escherichia coli have a genetic element encoding a reverse transcriptase (RT). This element, called a ‘retron’, produces a covalently linked RNA–DNA compound (msDNA–RNA). Here, I report the complete nucleotide sequence of retron EC‐86, the retron in E. coli B, together with its flanking regions. Retron EC‐86 contains genes for msDNA–RNA (msd, and msr), a gene for RT (ret) and a gene for an open reading frame whose function is unknown. The upstream junction is composed of the sequence GCGCGCGC, but there are no direct or inverted repeats at the retron–host junctions. It is also shown that another retron of E. coli, EC‐67, which was isolated originally from the clinical strain CL1 and was later found to be present also in a clinical E. coli isolate from Brazil, is inserted at the same chromosomal site as retron EC‐66. Retron EC‐67 contains only msd, msr, and ret. I suggest that these two retrons were independently inserted into the same site of their host strains via a novel mechanism of integration.
Complement activation and antibody binding by pneumolysin via a region of the toxin homologous to a human acute‐phase protein
Authors: Mitchell T. J. , Andrew P. W. , Saunders F. K. , Smith A. N. , Boulnois G. J. 
Published: October 2006

SummaryPneumolysin, a membrane‐damaging toxin, is known to activate the classical complement pathway. We have shown that 1 μg ml−1 of pneumolysin can activate complement, which is a much lower level than observed previously. We have identified two distinct regions of pneumolysin which show homology with a contiguous sequence within acute‐phase proteins, including human C‐reactive protein (CRP). Site‐directed mutagenesis of the pneumolysin gene was used to change residues common to pneumolysin and CRP. Some of the modified toxins had a reduced ability both to activate complement and bind antibody. We suggest that the ability of pneumolysin to activate complement is related to its ability to bind the Fc portion of immunoglobulin G.
Characterization of a Legionella pneumophila gene encoding a lipoprotein antigen
Authors: Engleberg N. C. , Howe D. C. , Rogers J. E. , Arroyo J. , Eisenstein B. I. 
Published: October 2006

SummaryA prominent 19kDa surface antigen of Legionella pneumophila, cloned in Escherichia coli, was found to be intimately associated with peptidoglycan. The DNA region encoding this antigen was mapped on an 11.9kb plasmid by means of deletion analysis and transposon mutagenesis. PhoA+ gene fusions, generated by TnphoA insertions into this region, confirmed the presence of a gene encoding a secreted protein. PhoA+ transposon insertions were also associated with loss of the 19 kDa antigen in immunoassay s using a monoclonal antibody (mAb1E9) and the replacement of the 19kDa antigen with larger fusion proteins in immunoblots using Legionella immune serum. A 1540bp PstI fragment carrying the gene was sequenced, and the open reading frame encoding the antigen was identified. The gene encodes a polypeptide 176 amino acid residues long and 18913Da in size. The presence of a signal sequence of 22 amino acids with a consensus sequence for cleavage by signal peptidase II indicates that the antigen is a lipoprotein, and striking similarity with peptidoglycan‐associated lipoproteins (PALs) from E. coli (51% amino acid homology) and Haemophilus influenzae (55% homology) is noted. We conclude that the 19kDa antigen of L. pneumophila is the structural equivalent of the PAL found in other Gram‐negative species and suggest that its post‐translational acylation may explain its potency as an immunogen.
Evolved neomycin phosphotransferase from an isolate of Klebsiella pneumoniae
Authors: Lee K.‐Y. , Hopkins J. D. , Syvanen M. 
Published: October 2006

SummaryA new aminoglycoside resistance gene (aphA 1‐IA6) confers high‐level resistance to neomycin. The sequence of apA 1‐IAB is closely related to aphA 1 found in the transposons Tn4352, 7n903 and Tn602. For example, aphA 1‐IAB differs from aphA 1–903 at five nucleotides that result in four amino acid replacements. The enzyme encoded by aphA 1‐IAB has a significantly higher turnover number with neomycin, kanamycin and G418 as substrates than does the aphA 1–903 enzyme. A parsimonious phylogenetic tree suggests that aphA 1‐IAB evolved from an ancestral form that is closely related or identical to the aphA 1 found in Tn903. The excess of replacement substitutions over silent substitutions in aphA I‐IAB, as well as its convergence toward aphA 3 from Staphylococcus aureus, is indicative of selective evolution. Our hypothesis to explain these results is that aphA 1‐IAB evolved under the selective pressure of neomycin use in relatively recent times.
Repression and induction of the nag regulon of Escherichia coll K‐12: the roles of nagC and nagA in maintenance of the uninduced state
Authors: Plumbridge J. A. 
Published: October 2006

SummaryThe nag regulon located at 15.5 min on the Escherichia coli chromosome consists of two divergent operons, nagE and nagBACD, encoding genes involved in the uptake and metabolism of N‐acetylglucosamine. Null mutations have been created in each of the genes by insertion of antibiotic resistance cartridges. The phenotypes of the strains carrying the insertions in nagE, B and A were consistent with the previous identification of gene products: nagE, EIINag, the N‐acetylglucosamine specific transporter of the phosphotransferase system and nagB and nagA, the two enzymes necessary for the degradation of N‐acetylglucosamine. Insertions in the napC result in derepression of the nag genes, which is consistent with earlier observations that the nagC gene encodes the repressor of the regulon. Insertions in nagA also provoke a derepression, implying that nagA has a role in the regulation of the expression of the nag regulon as well as in the degradation of the amino‐sugars. N‐acetylglucosamine‐6‐phosphate, the intra‐cellular product of N‐acetylglucosamine transport and the substrate of the nagA gene product, is shown to be an inducer of the regulon and this suggests how nagA mutations result in derepression: the absence of N‐acetylglucosamine‐6‐phosphate deacetylase allows N‐acetylglucosamine‐6‐phosphate to accumulate and induce the regulon.
Partial deletion of the Rhizobium phaseoli CFN23 symbiotic plasmid implies a concomitant amplification of plasmid DNA sequences
Authors: Soberón‐Chávez G. , Nájera R. , Calva E. , Fernández M. 
Published: October 2006

Summary Rhizobium leguminosarum biovar phaseol CFN23 loses its ability to nodulate beans at a high frequency because of a deletion of part of its symbiotic (pSym) plasmid (Soberón‐Chávez et al., 1986). We report here that at least 80kb of pSym are deleted upon loss of the symbiotic phenotype; the deletion removes the nitrogenase structural nifHDK and the common nod ABC genes. The size of the deleted pSym is not reduced, since it is accompanied by an amplification of other pSym plasmid sequences. This genetic rearrangement is similar to the deletion and amplification of yeast mitochondrial DNA leading to‘petite’mutations.
Complementation of DNA repair‐deficient Escherichia coli by the yeast Apn1 apurinic/apyrimidinic endonuclease gene
Authors: Ramotar D. , Popoff S. C. , Demple B. 
Published: October 2006

SummaryThe Saccharomyces cerevisiae APN1 gene encoding an AP endonuclease/3′ ‐diesterase was engineered in vitro for expression in Escherichia coli. The expression vector directs the synthesis in E. coli of a Mr 40500 protein that reacts with anti‐Apn1 antibodies and has the DNA‐repair activities characteristic of Apn1 isolated from yeast. A band corresponding to Apn1 was observed in DNA repair activity gels only with extracts of E. coli harbouring the APN1 expression plasmid. Expression of Apn1 conferred resistance to oxidants and alkylating agents in E. coli lacking exonuclease III and endonuclease IV. For H2O2 damage, this rescue effect was correlated with the repair of oxidative lesions in the bacterial chromosome by the Apn1 protein. Thus, Apn1 can function in bacteria in a manner similar to its proposed multiple functions in yeast.
Evidence that the entire length of a kinetoplast DNA minicircle is transcribed in Trypanosoma cruzi
Authors: Thertulien R. , Harth G. , Haidaris C. G. 
Published: October 2006

SummaryA 1.3kb cDNA (cDNA52) was derived from Trypanosoma cruzi trypomastigote mRNA. Using single stranded probes in Northern blots, we identified the putative coding strand of cDNA52. In addition, a minor band was detected in RNA from epimastigotes that was absent in RNA from trypomastigotes. Nucleotide sequence analysis revealed that cDNA52 was highly homologous to T. cruzi kinetoplast DNA minicircle sequences. All four conserved regions of T. cruzi minicircles were identified in cDNA52. Using several criteria, we demonstrated that the hybridization signals were not caused by contaminating minicircle DNA in the RNA preparations. The data provide direct evidence for the unprecedented finding that the entire length of a kDNA minicircle is transcribed in T. cruzi.
Expression of the gene encoding glycerol‐3‐phosphate dehydrogenase (glpD) in Bacillus subtilis is controlled by antitermination
Authors: Holmberg C. , Rutberg B. 
Published: October 2006

SummaryThe Bacillus subtilis glpD gene encodes glycerol‐3‐phosphate (G3P) dehydrogenase. A sigma A type promoter and the transcriptional startpoint for glpD were identified. Between the transcriptional start‐point and glpD there is an inverted repeat followed by a run of T residues. The inverted repeat prevents expression of a reporter gene, xylE, when positioned between this gene and a constitutive promoter. Expression of xylE, like expression of glpD, is induced by G3P and repressed by glucose. Induction also requires the product of the glpP gene. Our results suggest that glpD expression is controlled by antitermination of transcription. The inverted repeat appears to be a target for induction by G3P and GlpP. We speculate that glucose repression is mediated via an inhibitory effect on synthesis or activity of GlpP.
Prevalence of gene sequences coding for hypervariable regions of Opa (protein II) in Neisseria gonorrhoeae
Authors: Brooks G. F. , Olinger L. , Lammel C. J. , Bhat K. S. , Calvello C. A. , Palmer M. L. , Knapp J. S. , Stephens R. S. 
Published: October 2006

SummaryOpas (protein IIs) are a family of surface‐exposed proteins of Neisseria gonorrhoeae. Each strain of N. gonorrhoeae has multiple (10–11) genes encoding for Opas. Identifiable elements in opa genes include the coding repeat within the signal sequence, conserved 5′ and 3′ regions, and hypervariable regions (HV1 and HV2) located within the structural gene. N. gonorrhoeae strains appear to have many biological properties in common that are either HV‐region‐mediated or associated with the presence of specific HV regions, suggesting that HV regions could be found in many clinical isolates. Oligonucleotides from three source strains representing three conserved regions of opa, 12 HV1 regions, and 14 HV2 regions were used by dot blot analysis to probe 120 clinicial isolates of N. gonorrhoeae. The probe for the coding repeat hybridized to all 120 strains, the 3′ conserved‐region probe reacted with 98% of the strains, and the 5′ conserved‐region probe with 90% of the strains. Nine HV1 probes hybridized to 3.3–39.2% of the strains, and 13 of the HV2 probes hybridized to 1.7–25% of the isolates. Analysis of the number of probes that hybridized to each of the isolates showed that 19% did not hybridize with any of the HV1 probes and 25% did not hybridize with any of the HV2 probes. Approximately three‐quarters of the isolates hybridized with one, two or three of the HV1 probes or one, two or three of the HV2 probes; 89% of the isolates hybridized to least one HV1 or oe HV2 probe. The data indicate that some genes encoding HV regions of N. gonorhoeae Opa proteins are widely distributed in nature.
A class of gyrB mutants, substantially unaffected in DNA topology, suppresses the Escherichia coli K12 fts Z84 mutation
Authors: Ruberti I. , Crescenzi F. , Paolozzi L. , Ghelardini P. 
Published: October 2006

SummaryPrevious work in our laboratory suggested that DNA topology could be implicated in the regulation of the division gene ftsZ. To settle this question, we have selected and characterized mutants in the gyrB gene able to phenotypically suppress the defects of the ftsZ84 mutation. No strict correlation was found between the degree of plasmid DNA relaxation and the level of suppression of the thermosensitivity of the ftsZ84 strain. Interestingly, the class of mutants that shows maximal suppression is substantially unaffected in DNA topology. In addition, the amount of ffsZ‐specific mRNA in this class of mutants is comparable to that present in the ftsZ84 strain. These results hint that the ability of these gyrB mutants to correct the effects of the ftsZ84 mutation is largely unrelated to the function of the GyrB (as a part of DNA gyrase) in the control of DNA superhelicity and suggest hitherto unsuspected interaction between the ftsZ and gyrB gene products.
Analysis of the gluconate (gnt) operon of Bacillus subtilis
Authors: Reizer A. , Deutscher J. , Saier M. H. , Reizer J. 
Published: October 2006

SummaryThe gluconate (gnt) operon of Bacillus subtilis includes the gntR, gntK, gntP, and gntZ genes, respectively encoding the transcriptional repressor of the operon, gluconate kinase, the gluconate permease, and an unidentified open reading frame (Fujita and Fujita, 1987). We have compared the proteins encoded by the gnt operon of B. subtilis with published sequences and showed that (i) the gluconate repressor is homologous to several putative regulatory proteins in Escherichia coli, (ii) the gluconate kinase of B. subtilis is homologous to xylulose kinase, glycerol kinase and fucose kinase in E. coli (20‐26% identity; 12‐59 S.D.), (iii) the gluconate permease exhibits a C‐terminal domain which is homologous to a hydrophobic protein encoded by an unidentified open reading frame (dsdAp) which precedes the dsdA gene of E. coli (39% identity; 19 S.D.), and (iv) the gntZ gene product is homologous to 6‐phosphogluconate dehydrogenases of other bacteria and of animals (48‐56%; 82‐178 S.D.), thereby suggesting that the B. subtilis gntZ encodes 6‐phosphogluconate dehydro‐genase. Several conserved regions of the sequenced 6‐phosphogluconate dehydrogenases can serve as signature patterns of this protein. Computer analyses have indicated that the previously reported sequences of the porcine and ovine 6‐phosphogluconate dehydrogenases, as well as the hypothetical DsdAp protein, are probably erroneous. The probable reasons for the errors are reported along with the proposed revised sequences.
Identification and characterization of a conserved outer‐membrane protein of Neisseria gonorrhoeae
Authors: Judd R. C. , Strange J. C. , Pettit R. K. , Shafer W. M. 
Published: October 2006

SummaryA previous study in our laboratory identified a surface‐exposed peptidoglycan‐associated protein of Neisseria gonorrhoeae which had an apparent molecular mass of 44000 daltons (44kDa) (Hill and Judd, 1989). This paper reports results which confirm that the 44 kDa protein is surface‐exposed, and that the protein is expressed in, and is structurally invariant among, 14 strains of N. gonorrhoeae. The fact that the 44kDa outer‐membrane protein is found in a conserved form in all gonococci examined strongly suggests that ft is crucial to the bacterium's survival. Moreover, it appears that this protein is a penicillin‐binding protein (PBP3) (Shafer and Judd, 1991). This invariant, surface‐exposed, peptidoglycan‐associated outer‐membrane protein deserves further investigation to elucidate its role in the immunobiology of N. gonorrhoeae, and its possible use as an immunoprophylactic reagent.
The cephamycin biosynthetic genes pcbAB, encoding a large multidomain peptide synthetase, and pcbC of Nocardia lactamdurans are clustered together in an organization different from the same genes in Acremonium chrysogenum and Penicillium chrysogenum
Authors: Coque J. J. R. , Martin J. F. , Calzada J. G. , Liras P. 
Published: October 2006

SummaryA 34 kb fragment of the Nocardia lactamdurans DNA carrying the cluster of early cephamycin biosynthetic genes was cloned in λ EMBL3 by hybridization with probes internal to the pcbAB and pcbC genes of Penicillium chrysogenum and Streptomyces griseus. The pcbAB and pcbC genes were found to be closely linked together in the genome of N. lactamdurans. The pcbAB gene of N. lactamdurans showed the same orientation as the pcbC gene, in contrast to the divergent expression of the genes in the pcbAB‐pcbC cluster of P. chrysogenum and Acremonium chrysogenum. The pcbAB gene encodes a large (3649 amino acids) multidomain δ‐(L‐α‐aminoadipyl)‐L‐cysteinyl‐D‐valine synthetase with a deduced Mr, of 404134. This enzyme contains three repeated domains and a consensus thioesterase active‐site sequence. The pcbC gene encodes a protein of 328 amino acids with a deduced Mr of 37469, which is similar to other isopenicillin N synthases except that it lacks one of two cysteine residues conserved in all other isopenicillin N synthases. The different organization of the pcbAB‐pcbC gene cluster in N. lactamadurans and Streptomyces clavuligerus relative to P. chrysogenum and A. chrysogenum is intriguing in relation to the hypothesis of horizontal transference of these genes from actinomycetes to filamentous fungi by a single transfer event.
Nucleotide sequence of the endoglucanase C gene (cenC) of Cellulomonas fimi, its high‐level expression in Escherichia coli, and characterization of its products
Authors: Coutinho J. B. , Moser B. , Kilburn D. G. , Warren R. A. J. , Miller R. C. 
Published: October 2006

SummaryThe cenC gene of Cellulomonas fimi, encoding endoglucanase CenC, has an open reading frame of 1101 codons closely followed by a 9bp inverted repeat. The predicted amino acid sequence of mature CenC, which is 1069 amino acids long, is very unusual in that it has a 150‐amino‐acid tandem repeat at the N‐terminus and an unrelated 100‐amino‐acid tandem repeat at the C‐terminus. CenC belongs to subfamily E1 of the β‐1,4‐glycanases. High‐level expression in Escherichia coli of cenC from a 3.6kbp fragment of C. fimi DNA leads to levels of CenC which exceed 10% of total cell protein. Most of the CenC is in the cytoplasm in an inactive form. About 60% of the active fraction of CenC is in the periplasm. The catalytic properties of the active CenC are indistinguishable from those of native CenC from C. fimi. The Mr of CenC from E. coli and C. fimi is approximately 130 kDa. E. coli and C. fimi also produce an endoglucanase, CenC', of approximate Mr, 120kDa and with the same N‐terminal amino acid sequence and catalytic properties as CenC. CenC’appears to be a proteolytic product of CenC. CenC and CenC’can bind to cellulose and to Sephadex. CenC is the most active component of the C. fimi cellulase system isolated to date.
Topographic analysis of the toxic Gef protein from Escherichia coli
Authors: Poulsen L. K. , Refn A. , Molin S. , Andersson P. 
Published: October 2006

SummaryThe chromosomal gef gene of Escherichia coli is a member of the gef gene family which encodes strongly toxic proteins of about 50 amino acids. We demonstrate here that the Gef protein is detectable by anti‐peptide antibodies. Furthermore, we show that Gef is anchored in the cytoplasmic membrane by the N‐terminal part of the protein, and that the C‐terminal part is localized in the periplasm in a dimeric form with at least one disulphide bond. By mutagenesis of gef it is shown that the periplasmic portion of Gef encodes the toxic domain and that the dimerization of Gef is not essential for the toxic effect.
Possible role of calmodulin in the secretion of Entamoeba histolytica electron‐dense granules containing collagenase
Authors: Muñoz M. de L. , Moreno M. A. , Pérez‐Garcia J. N. , Tovar G. R. , Hernandez V. I. 
Published: October 2006

Summary Entamoeba histolytica cells secrete electron‐dense granules (EDGs) that have collagenase activity. To study the possible involvement of calmodulin (CaM) on EDG secretion, the effect of several CaM antagonists (TFP, R24571, W‐7, W‐5, dibucaine and DL‐propranolol) was tested on this cellular function. Except for W‐5 and dibucaine, the rest of these compounds inhibited EDG secretion. Transmission electron microscopy of collagen‐activated trophozoites showed numerous EDGs located in or near the surface membrane. In contrast, trophozoites incubated with TFP showed no EDGs. Protein kinase C inhibitors (H‐7, ML‐9) had no effect on EDG secretion, suggesting that CaM antagonists acted by selectively inhibiting CaM. These results suggest that a CaM‐dependent process is involved in EDG secretion.