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PubMed1995

The recA gene of Streptococcus pneumoniae is part of a competence-induced operon and controls lysogenic induction.

The recently identified recA gene of the naturally transformable bacterium Streptococcus pneumoniae has been further characterized by constructing a recA null mutation and by investigating its regulation. The recA mutation has been shown to confer both DNA repair (as judged from sensitivity to u.v. and methyl methane sulphonate) and recombination deficiencies. Plasmid transformation into the recA mutant was also drastically reduced. Western blotting established that recA gene expression is increased several fold at the onset of competence for genetic transformation. Increased expression was associated with the appearance of a recA-specific transcript, approximately 5.7 kb long. This transcript indicated that recA is part of a competence-inducible (cin) operon. The major (about 4.3 kb) transcript detected from non-competent cells did not include cinA, the first gene in the operon, suggesting that this gene could be specifically required at some stage in the transformation process. Detection of small amounts of the 5.7 kb polycistronic mRNA in cells treated with mitomycin C suggested that the operon could also be damage inducible. In addition, mitomycin C treatment of a recA- lysogenic strain did not lead to prophage induction and cell lysis. This is unlike the situation of a recA+ lysogen. Together these results demonstrate that RecA controls lysogenic induction and suggest the existence of a SOS repair system in S. pneumoniae.

Bacterial Proteins↗

PubMed1995

A gene required for nutritional repression of the Bacillus subtilis dipeptide permease operon.

An insertion mutation was isolated that resulted in derepressed expression of the Bacillus subtillis dipeptide transport operon (dpp) during the exponential growth phase in rich medium. DNA flanking the site of insertion was found to encode an operon (codVWXY) of four potential open reading frames (ORFs). The deduced product of the codV ORF is similar to members of the lambda Int family; CodW and CodX are homologous to HsIV and HsIU, two putative heat-shock proteins from Escherichia coli, and to LapC and LapA, two gene products of unknown function from Pasteurella haemolytica. CodX also shares homology with a family of ATPases, including ClpX, a regulatory subunit of the E. coli ClpP protease. CodY does not have any homologues in the data-bases. The insertion mutation and all previously isolated spontaneous cod mutations were found to map in codY. In-frame deletion mutations in each of the other cod genes revealed that only codY is required for repression of dpp in nutrient-rich medium. The codY mutations partially relieved amino acid repression of the histidine utilization (hut) operon but had no effect on regulation of certain other early stationary phase-induced genes, such as spoVG and gsiA.

Amino Acid Sequence↗

PubMed1995

Organization of tcp, acf, and toxT genes within a ToxT-dependent operon.

The toxin coregulated pilus (TCP) is required for Vibrio cholerae to colonize the human intestine. The expression of the pilin gene, tcpA, is dependent upon ToxR and upon ToxT. The toxT gene was recently mapped within the TCP biogenesis gene cluster and shown to be capable of activating a tcpA::TnphoA fusion when cloned in Escherichia coli. In this study, we determined that ToxR/ToxT activation occurs at the level of tcpA transcription. ToxT expressed in E. coli could activate a tcp operon fusion, while ToxR, ToxR with ToxS, or a ToxR-PhoA fusion failed to activate the tcp operon fusion and we could not demonstrate binding of a ToxR extract to the tcpA promoter region in DNA mobility-shift assays. The start site for the regulated promoter was shown by primer extension to lie 75 bp upstream of the first codon of tcpA. An 800-base tcpA message was identified, by Northern analysis, that correlates by size to the distance between the transcriptional start and a hairpin-loop sequence between tcpA and tcpB. The more-sensitive assay of RNase protection analysis demonstrated that a regulated transcript probably extends through the rest of the downstream tcp genes, including toxT and the adjacent accessory colonization factor (acf) genes. An in-frame tcpA deletion, but not a polar tcpA::TnphoA fusion, could be complemented for pilus surface expression by providing tcpA in trans. This evidence suggests that the tcp genes, including toxT, are organized in an operon directly activated by ToxT in a ToxR-dependent manner. Most of the toxT expression under induced conditions requires transcription of the tcpA promoter. Further investigation of how tcp::TnphoA insertions that are polar on toxT expression retain regulation showed that a low basal level of toxT expression is present in toxR and tcp::TnphoA strains. Overall, these observations support the ToxR/ToxT cascade of regulation for tcp. Once induced, toxT expression becomes autoregulatory via the tcp promoter, linking tcp expression to that of additional colonization factors, exotoxin production, and genes of unknown function in cholera pathogenesis.

Amino Acid Sequence↗

PubMed1996

A glutamate/glutamine/aspartate/asparagine transport operon in Rhodobacter capsulatus.

A mutant of Rhodobacter capsulatus was identified in which an operon encoding a binding-protein-dependent transporter was interrupted by Tn5 transposition. Cloning and sequence analysis of the wild-type operon revealed a four-gene cluster with similarities to genes encoding periplasmic binding proteins (BztA), integral membrane proteins (BztB and BztC), and ATP-binding proteins (BztD). To assess the function of this putative binding-protein-dependent transport system, a mutant was constructed in which most of the bztABCD operon was deleted and replaced by an antibiotic-resistance marker. The deletion mutant grew more slowly than the wild type in NH4(+)-free medium supplemented by glutamate, glutamine, aspartate or asparagine; it was resistant to toxic analogues of Glu, Asp, and Asn at concentrations that inhibited growth of the wild type; and it was defective in the uptake of Glu, Gln, and Asp. A complementing plasmid containing the wildtype copy of bztABCD was able to rescue all the mutant phenotypes. Taken together, these results indicate that the proteins encoded by bztABCD are active in the uptake of Glu, Gln, Asp, and Asn. In addition, competition experiments, in which the ability of each of the four amino acids to compete for the transport of one another was examined, demonstrated that all four substrates share at least one component of this transport system.

Amino Acid Sequence↗

PubMed2004

The histone-like nucleoid structuring protein H-NS represses the Escherichia coli bgl operon downstream of the promoter.

Specificity of repression by the histone-like nucleoid structuring protein and pleiotropic regulator, H-NS, is exceptionally high in case of the Escherichia coli bgl (beta-glucoside) operon. Here we present evidence that H-NS represses the operon at two levels. The binding of H-NS to an upstream silencer results in an approximately threefold repression of the catabolite gene regulator protein (CRP) dependent bgl promoter. In addition, H-NS binds to a silencer region located approximately 600-700 base pairs downstream of the promoter, within the coding region of first gene, bglG, resulting in a approximately sevenfold further decrease of expression. Repression by H-NS at the downstream silencer requires termination factor Rho and is reduced by translation of the bglG mRNA, but is independent of the promoter. This suggests that H-NS induces polarity of transcription by acting as a roadblock to the elongating RNA polymerase. The control of the bgl operon by H-NS at two levels results in a highly specific repression.

Bacterial Proteins↗

PubMed2005

Elaborate transcription regulation of the Bacillus subtilis ilv-leu operon involved in the biosynthesis of branched-chain amino acids through global regulators of CcpA, CodY and TnrA.

The Bacillus subtilis ilv-leu operon involved in the biosynthesis of branched-chain amino acids is under negative regulation mediated by TnrA and CodY, which recognize and bind to their respective cis-elements located upstream of the ilv-leu promoter. This operon is known to be under CcpA-dependent positive regulation. We have currently identified a catabolite-responsive element (cre) for this positive regulation (bases -96 to -82; +1 is the ilv-leu transcription initiation base) by means of DNase I-footprinting in vitro, and deletion and base-substitution analyses of cre. Under nitrogen-rich growth conditions in glucose-minimal medium supplemented with glutamine and amino acids, CcpA and CodY exerted positive and negative regulation of ilv-leu, respectively, but TnrA did not function. Moreover, CcpA and CodY were able to function without their counteracting regulation of each other, although the CcpA-dependent positive regulation did not overcome the CodY-dependent negative regulation. Furthermore, under nitrogen-limited conditions in glucose-minimal medium with glutamate as the sole nitrogen source, CcpA and TnrA exerted positive and negative regulation, respectively, but CodY did not function. This CcpA-dependent positive regulation occurred without the TnrA-dependent negative regulation. However, the TnrA-dependent negative regulation did not occur without the CcpA-dependent positive regulation, raising the possibility that this negative regulation might decrease the CcpA-dependent positive regulation. The physiological role of this elaborate transcription regulation of the B. subtilis ilv-leu operon in overall metabolic regulation in this organism is discussed.

Amino Acids, Branched-Chain↗

PubMed2006

The role of proton motive force in expression of the Staphylococcus aureus cid and lrg operons.

The Staphylococcus aureus cidABC and lrgAB operons have been shown to play a key role in the regulation of murein hydrolase activity and cell death in a manner thought to be analogous to bacteriophage-encoded holins and anti-holins respectively. Because of these functions, it has been proposed that the regulation of these operons is tightly controlled and responsive to key metabolic signals. The current study revealed the presence of two overlapping regulatory pathways controlling cidABC and lrgAB expression, one dependent on acetic acid and the other dependent on proton motive force (PMF). The latter pathway was analysed using agents that affect various aspects of the PMF. Gramicidin and carbonyl cyanide m-chlorophenylhydrazone (CCCP), antimicrobial agents that dissipate the DeltapH and membrane potential (DeltaPsi), both enhanced lrgAB expression. Restoration of the PMF by incubation of the bacteria in the presence of glucose restored lrgAB expression back to the uninduced state. In addition, valinomycin, which specifically collapses the DeltaPsi, also induced lrgAB expression. In contrast, nigericin, which dissipates the DeltapH component of the PMF, was found to have a minimal effect on DeltaPsi and lrgAB transcription. Finally, the DeltaPsi-inducible expression of lrgAB was shown to be dependent on the previously characterized LytSR two-component regulatory system that is involved in the regulation of autolysis. The results of this study support a model in which the LytSR regulatory system responds to a collapse in DeltaPsi by inducing the transcription of the lrgAB operon.

Acids↗

PubMed1997

Cloning and sequencing of part of the S10 operon from Actinobacillus actinomycetemcomitans FDC Y4.

We have cloned and sequenced the 5.2 kb EcoRI fragment that contained part of the S10 operon from Actinobacillus actinomycetemcomitans FDC Y4. The order of the ribosomal protein genes was identical to that of the S10 operon of Haemophilus influenzae and Escherichia coli. The deduced amino acid sequences of ribosomal proteins in this operon displayed significant homologies (65.3%-100%) to those of H. influenzae, E. coli, Yersinia enterocolitica and Yersinia pseudotuberculosis. Phylogenetic trees obtained for these ribosomal proteins were similar to that obtained for 16S rRNA.

Aggregatibacter actinomycetemcomitans↗

PubMed1997

Transcriptional analysis of the groESL operon from Porphyromonas gingivalis.

Transcriptional analysis of the groESL operon from Porphyromonas gingivalis, one of the obligative anaerobic oral microorganisms implicated in adult periodontitis, was performed. P. gingivalis 381 cultured at 37 degrees C was shifted to 42 degrees C, 45 degrees C or 48 degrees C for 10 mins. Northern hybridization analysis revealed that a band with 2.1-kb (kilo base pair) was observed, and the transcripts increased greatly by heat shock. Primer extension and S1 mapping detected four different 5'-ending sites of the mRNAs at the upstream region of the groES. Three sites out of the four were heat-inducible. There were inverted repeats and a Escherichia coli sigma 32-recognizing consensus sequence in the promoter region of the groESL, which may be relevant to the regulation of transcription of groESL operon in P. gingivalis. Both a heat shock promoter and inverted repeats may be relevant to the transcriptional regulation of the groESL operon in P. gingivalis.

Bacterial Proteins↗

PubMed2004

Role of a Streptococcus gordonii copper-transport operon, copYAZ, in biofilm detachment.

Streptococcus gordonii is a pioneer oral bacterium that is associated with the initiation of dental plaque development. Located downstream of the S. gordonii adc operon, which is involved in competence and biofilm formation, were three open reading frames, designated copY, copA and copZ. These open reading frames were homologous to the copYAZ genes in Streptococcus mutans that are involved in copper homeostasis and biofilm detachment. This study examined whether copYAZ genes play any role in the biofilm formation and detachment of S. gordonii. The copY gene encodes a 143-amino acid protein homologous to the negative transcriptional regulator of a copper-transport operon, copA encodes a 748-amino acid copper-transporting P-type ATPase, and copZ encodes a 69-amino acid putative metallochaperone protein in S. mutans. Each open reading frame in the copYAZ operon in S. gordonii was inactivated by insertional mutation and the growth, biofilm formation and detachment of each mutant were examined. S. gordonii copY::specR, copA::specR, and copZ::specR mutants were able to form biofilms on both polystyrene and glass surfaces. However, inactivation of copZ and to a lesser extent copY resulted in phenotypes that were defective in biofilm detachment, which is consistent with previous observations in S. mutans and suggests that the trace element copper might influence biofilm detachment of bacterial biofilms.

Bacterial Adhesion↗

PubMed1987

Nucleotide sequence and comparative analysis of the frd operon encoding the fumarate reductase of Proteus vulgaris. Extensive sequence divergence of the membrane anchors and absence of an frd-linked ampC cephalosporinase gene.

The fumarate reductase of Escherichia coli is a bioenergetically important membrane-bound flavoenzyme consisting of four subunits. A and B comprise a membrane-extrinsic catalytic domain whereas C and D are hydrophobic polypeptides which link the catalytic centres to the electron-transport chain. The nucleotide sequence of the frd operon encoding the fumarate reductase of the distantly related bacterium, Proteus vulgaris has been determined and used to predict the primary structures of the respective subunits. Extensive amino acid sequence identity (greater than 80%) was found between the fumarate reductase A and B subunits of P. vulgaris and E. coli. In contrast, the primary structures of the P. vulgaris and E. coli C and D proteins are much less closely related (about 60% homology) although the overall hydrophobicity of their three membrane-spanning segments has been conserved. In most enteric bacteria, the frd operon is followed by genes, ampR and/or ampC, required for the genetic regulation and biosynthesis of a cephalosporinase. The corresponding region of the P. vulgaris genome is occupied by an operon (orf A'BCD) containing at least four genes which are clearly unrelated to the ampC system. Intriguingly the primary structures of the OrfA and OrfD proteins suggest that, like fumarate reductase, they may be components of a membrane-bound enzyme complex involved in energy metabolism.

Amino Acid Sequence↗

PubMed1988

Nucleotide sequence of the carA gene and regulation of the carAB operon in Salmonella typhimurium.

The carAB operon of Salmonella typhimurium encoding carbamoyl-phosphate synthetase (CPSase) has been cloned, and the nucleotide sequence of the first gene of the operon, carA, together with 760 base pairs of the 5'-flanking region was determined. The product of the carA gene is the small subunit of CPSase. It catalyzes the transfer of the amide group from glutamine to an NH3-site on the heavy subunit. Primer extension and S1 nuclease mapping of in vivo carAB transcripts revealed that transcription is similar to that of Escherichia coli [Piette, J. et al. (1984) Proc. Natl Acad. Sci. USA 81, 4134-4138] in its initiation at two promoters, P1 and P2, controlled by pyrimidines and arginine, respectively. The arginine control is mediated through binding to the arginine repressor (argR). The involvement of titratable regulatory elements is indicated by the escape from both arginine and pyrimidine control, when the operon is present in multicopies on a plasmid. Measurements of CPSase levels in mutants which allows independent manipulation of the intracellular uracil and cytosine nucleotide pools show, that both uracil and cytosine nucleotides are required for full repression and that limitation of either nucleotide results in derepression of CPSase synthesis. Deletion analyses indicate that regions upstream of the P1 promoter are required for normal expression from this promoter but not from P2.

Amino Acid Sequence↗

PubMed2005

Aerobic anoxygenic photosynthesis genes and operons in uncultured bacteria in the Delaware River.

Photosynthesis genes and operons of aerobic anoxygenic photosynthetic (AAP) bacteria have been examined in a variety of marine habitats, but genomic information about freshwater AAP bacteria is lacking. The goal of this study was to examine photosynthesis genes of AAP bacteria in the Delaware River. In a fosmid library, we found two clones bearing photosynthesis gene clusters with unique gene content and organization. Both clones contained 37 open reading frames, with most of those genes encoding known AAP bacterial proteins. The genes in one fosmid were most closely related to those of AAP bacteria in the Rhodobacter genus. The genes of the other clone were related to those of freshwater beta-proteobacteria. Both clones contained the acsF gene, which is required for aerobic bacteriochlorophyll synthesis, suggesting that these bacteria are not anaerobes. The beta-proteobacterial fosmid has the puf operon B-A-L-M-C and is the first example of an uncultured bacterium with this operon structure. The alpha-3-proteobacterial fosmid has a rare gene order (Q-B-A-L-M-X), previously observed only in the Rhodobacter genus. Phylogenetic analyses of photosynthesis genes revealed a possible freshwater cluster of AAP beta-proteobacteria. The data from both Delaware River clones suggest there are groups of freshwater or estuarine AAP bacteria distinct from those found in marine environments.

Aerobiosis↗

PubMed2004

Presence of the ica operon in clinical isolates of Staphylococcus epidermidis and its role in biofilm production.

Staphylococcus epidermidis is an important cause of catheter-associated infections, which are attributed to its ability to form a multilayered biofilm on polymeric surfaces. This ability depends, in part, on the activity of the icaADBC locus and the icaR gene, which are involved in the production of the polysaccharide intercellular adhesin (PIA) that is functionally necessary for cell-to-cell adhesion and biofilm accumulation. The present study determined: (1) the prevalence of the icaADBC operon in S. epidermidis isolates from catheter-related and other nosocomial infections; (2) the correlation between the presence of this operon, biofilm production and resistance to antibiotics; (3) the expression of ica genes and biofilm production; and (4) the genetic relatedness of the isolates. The results showed that icaRADBC was present in 45% of the isolates included in the study, and that such isolates were significantly more resistant to the main antibiotics tested than were ica-negative isolates. The presence of the entire cluster did not always correlate with biofilm production, determined under different culture conditions, but there was evidence to suggest a correlation when at least two genes (icaAD) were co-transcribed. Eight of 18 ica-positive isolates had the entire operon in the same restriction fragment after pulsed-field gel electrophoresis, but the isolates were not clonal. Estimation of genetic relatedness indicated that ica-positive S. epidermidis isolates belonged to different lineages, distributed in only one of two major clusters, with a genetic distance of c. 0.12.

Bacterial Adhesion↗

PubMed2006

Assessment of ica operon carriage and biofilm production in Staphylococcus epidermidis isolates causing bacteraemia in bone marrow transplant recipients.

The clinical significance of coagulase-negative staphylococci isolated from blood culture is typically assessed on the basis of a combination of clinical and microbiological criteria. However, these criteria are difficult to apply to haematology patients who are highly immunosuppressed and from whom blood cultures are obtained most frequently through a central venous catheter. This study analysed 112 episodes of Staphylococcus epidermidis bacteraemia that occurred in 79 bone marrow transplant recipients. In 73 (65%) episodes, only one blood culture set was positive for S. epidermidis, while 39 (35%) episodes grew S. epidermidis from multiple blood cultures. Nine patients had two or more episodes of bacteraemia with the same strain, as determined by pulsed-field gel electrophoresis (PFGE). The PFGE method also showed that 34 (31%) isolates belonged to seven clusters, indicating the persistence of certain clones in the environment. Of the 109 isolates analysed, 59 (54%) produced biofilm and 91 (83.5%) carried the ica operon. Isolates that produced biofilm were observed to colonise central venous catheters faster than non-biofilm-producing isolates (18 vs. 37 days; p 0.03). No clinical features were associated with carriage of the ica operon, but the ica operon was carried more frequently by the isolates that formed clusters.

Adhesins, Bacterial↗

PubMed1993

Identification of the transcriptional start site of the cyd operon from Escherichia coli.

The cydAB operon encodes the two subunits of the cytochrome bd ubiquinol oxidase from Escherichia coli. This enzyme is one of two terminal oxidases in the aerobic respiratory chain of E. coli. It has been demonstrated that expression of the cyd operon is transcriptionally regulated by oxygen via both the fnr and arcA gene products. Whereas arcA clearly serves as a positive regulator at low oxygen tension, there is no consensus concerning the role of the fnr gene product (FNR). In this paper, the transcriptional start site of the cyd operon is identified at position -287 with respect to the translational start. This is located 53 basepairs downstream from the center of dyad symmetry of the putative FNR recognition sequence.

Base Sequence↗

PubMed1995

rRNA operon restriction derived taxa for Streptomyces (RiDiTS).

A method for grouping Streptomyces strains by fingerprints of their rRNA operons is described. In polyacrylamide gels, multicopy rRNA operon fragments in Streptomyces genomic MseI fingerprints produced intense bands which are well resolved from the less conspicuous low copy fragments interspersed between them. The high intensity multicopy rRNA bands are easily distinguished from the low intensity bands, eliminating the need for Southern blot hybridization to visualize the rRNA fragments. Direct evidence that the high-intensity bands in these polyacrylamide gels originated from rRNA operons was provided by a 'differential' Southern blot technique. We have used this method to assign 98 strains to 11 rRNA fingerprint type groups. This clustering method may be applicable to any prokaryote with a high G+C content genome.

Blotting, Southern↗

PubMed1996

The arsenical resistance operon of IncN plasmid R46.

The arsenical resistance operon of the IncN plasmid R46 consists of 4696 bp and starts with predicted transcriptional control and initiation signals, followed by five genes, arsD, arsA, and arsC. The corresponding Escherichia coli chromosomal ars operon and two staphylococcal ars operons lack arsA and arsD genes. The R46 system contains only the second known versions of arsA and arsD, after those of plasmid R773. Western blot analysis identified the R46 proteins using antibodies against R773 ArsA, ArsD and ArsR.

Adenosine Triphosphatases↗