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PubMed2001

Genetic organization of the Pantoea stewartii subsp. stewartii hrp gene cluster and sequence analysis of the hrpA, hrpC, hrpN, and wtsE operons.

The hrp/wts gene cluster of Pantoea stewartii subsp. stewartii is required for pathogenicity on sweet corn and the ability to elicit a hypersensitive response (HR) in tobacco. Site-directed transposon mutagenesis and nucleotide sequencing were used to identify hrp/wts genes within the left 20 kb of this cluster. Seventeen open reading frames (ORFs) comprise seven genetic complementation groups. These ORFs share homology with hrp and dsp genes from Erwinia amylovora, Erwinia chrysanthemi, and Pseudomonas syringae pathovars and have been designated, in map order, wtsF, wtsE, hrpN, hrpV, hrpT, hrcC, hrpG, hrpF, hrpE, hrpD, hrcJ, hrpB, hrpA, hrpS, hrpY, hrpX, and hrpL. Putative hrp consensus promoter sequences were identified upstream of hrpA, hrpF, hrpN, and wtsE. Expression of the hrpA, hrpC, and wtsE operons was regulated by HrpS. Transposon mutations in all of the hrp operons abolished pathogenicity and HR elicitation, except for the hrpN and hrpV mutants, which were still pathogenic. hrpS, hrpXY, and hrpL regulatory mutations abolished HrpN synthesis, whereas secretory mutations in the hrpC, hrpA, and hrpJ operons permitted intracellular HrpN synthesis. wtsEF mutants were not pathogenic but still produced HrpN and elicited the HR. wtsE encodes a 201-kDa protein that is similar to DspE in E. amylovora and AvrE in P. syringae pv. tomato, suggesting that this protein is a major virulence factor involved in the elicitation of water-soaked lesions.

Bacterial Outer Membrane Proteins↗

PubMed2003

Genetic analysis of a pH-regulated operon from Rhizobium tropici CIAT899 involved in acid tolerance and nodulation competitiveness.

Rhizobium tropici CIAT899 is highly acid tolerant and a good competitor for Phaseolus vulgaris nodule occupancy at low pH values. Using Tn5 mutagenesis, we identified an operon required for acid tolerance and nodulation competitiveness. The insertion was mapped to the 5' end of atvA, encoding a product with high sequence identity to the agro-bacterial AcvB virulence protein. Complementation analyses indicated that atvA is an ortholog of acvB, both genes being required for acid tolerance. A Ser/Ala substitution in the LIPASE_SER motif of AtvA resulted in an acid sensitive Fix+ but very poorly competing strain, demonstrating that Ser-313 is essential for AtvA function. atvA is the second gene in an operon that is transcriptionally upregulated by acid shock. The acid-responsive promoter was mapped to a 469-bp intergenic region located upstream of lpiA, the first gene in the operon. lpiA-like genes are found in several alpha, beta, and gamma Proteobacteria that interact with eukaryotic host cells, and they are predicted to encode membrane proteins related to the FmtC/MprF family from low G+C Firmicutes. The latter proteins are involved in resistance to cationic antimicrobial peptides. A nonpolar deletion in lpiA caused a sevenfold decrease in relative nodulation competitiveness.

Adaptation, Physiological↗

PubMed1996

Phylogeny of Methanopyrus kandleri based on methyl coenzyme M reductase operons.

The mcrBDCGA operon that encodes methyl coenzyme M reductase (MR) in the hyperthermophile Methanopyrus kandleri was cloned and sequenced. The results of a phylogenetic analysis of the nine MR sequences now available support the position that M. kandleri is a separate methanogen lineage. As in other methanogens, the M. kandleri mcr operon is located immediately upstream of the mtrE gene, the promoter-proximal gene in an operon that encodes the N5-methyltetrahydromethanopterin:coenzyme M methyltransferase that catalyzes the step preceding the MR-catalyzed reaction in methanogenesis. In contrast to other methanogens and hyperthermophilic members of the Archaea, CG dinucleotides and CG-containing codons occur frequently in M. kandleri DNA. The MR subunit-encoding genes are preceded by sequences consistent with ribosome binding sites, indicating that mRNA-rRNA base pairing can still direct translation initiation in cells growing at temperatures above 100 degrees C.

Euryarchaeota↗

PubMed1988

Comparison of the meta pathway operons on NAH plasmid pWW60-22 and TOL plasmid pWW53-4 and its evolutionary significance.

The regulated meta pathway operon for the catabolism of salicylate on the naphthalene plasmid pWW60-22 was cloned into the broad-host-range vector pKT230 on a 17.5 kbp BamHI fragment. The recombinant plasmid conferred the ability to grow on salicylate when mobilized into plasmid-free Pseudomonas putida PaW130. A detailed restriction map of the insert was derived and the locations of some of the genes were determined by subcloning and assaying for their gene products in Escherichia coli and P. putida hosts. The existence of a regulatory gene was demonstrated by the induction of enzyme activities in the presence of salicylate. DNA-DNA hybridization indicated a high degree of structural homology between the pWW60-22 operon and the analogous meta pathway operon on TOL plasmid pWW53-4. The data are consistent with the structural genes being arranged in an identical linear array and suggest an evolutionary link between the two catabolic systems.

Biological Evolution↗

PubMed1991

Analysis of the Serratia marcescens proBA operon and feedback control of proline biosynthesis.

The proBA operon, coding for gamma-glutamyl kinase (GK) and gamma-glutamyl phosphate reductase (GPR), was cloned from the chromosome of the wild-type strain of Serratia marcescens Sr41. From our sequence data the proB (1101 bp) and proA (1472 bp) genes were shown to code for two proteins of Mr 39,169 and 44,640, respectively. Analysis of expression of the lacZ structural gene fused with the proBA promoter showed that the proBA operon is not subject to proline-mediated feedback repression. Amplification of the proBA operon enabled us to determine GK activity, which was inhibited in the presence of a low concentration of L-proline. Comparison of the amino acid sequences of the S. marcescens GK and GPR proteins with those of the GK and GPR proteins from E. coli revealed extensive similarities.

Aldehyde Oxidoreductases↗

PubMed1992

Analysis of the mutant proBA operon from a proline-producing strain of Serratia marcescens.

The nucleotide sequence of the proBA operon from a proline-hyperproducing mutant of Serratia marcescens was determined. Two base substitutions were found: one in the proB structural gene, coding for gamma-glutamyl kinase (GK), and a second one in the promoter region of the operon. The former base substitution led to a change of the predicted amino acid at position 117 from an alanine to a valine in GK. This mutation rendered GK 700-fold less sensitive to proline-mediated feedback inhibition than the wild-type enzyme. The other base substitution, a transversion from a G-C to an A-T, was located in the spacer region between the '-35' and '-10' sequences of the promoter, and it increased the transcriptional activity of this operon fourfold. Both these two base substitutions, which were acquired at the step of selecting mutants resistant to a toxic proline analogue, 3,4-dehydroproline, confer upon cells a high proline productivity and an increased osmotolerance.

Amino Acid Sequence↗

PubMed1992

The nucleotide sequence of the promoter, 16S rRNA and spacer region of the ribosomal RNA operon of Mycobacterium tuberculosis and comparison with Mycobacterium leprae precursor rRNA.

Mycobacterium tuberculosis H37Rv has a single rrn (ribosomal RNA) operon. The operon was cloned and a region of 1536 nucleotides was sequenced, starting 621 bp upstream from the 5'-end of the 16S rRNA coding region and continuing to the start of the 23S rRNA coding region. The 16S rRNA sequence inferred from the gene sequence was found to differ in one position from Mycobacterium bovis (nucleotide 1443) and from Mycobacterium microti (nucleotide 427). A single putative promoter was identified on the basis of similarities with the sequence of rrn operons of Bacillus subtilis and Escherichia coli. The regions of similarity include a -35 box, a -10 box, a stringent response element, antitermination signals, potential RNAase III processing sites and features of precursor rRNA secondary structure. Sequences upstream from the 5'-end of Mycobacterium leprae 16S rRNA were also investigated. Homologous schemes of secondary structure were deduced for precursor rRNA of both M. tuberculosis and M. leprae; although the principal features are common to both species there are notable differences.

Base Sequence↗

PubMed1998

The mabA gene from the inhA operon of Mycobacterium tuberculosis encodes a 3-ketoacyl reductase that fails to confer isoniazid resistance.

A target of the anti-tuberculosis drugs isoniazid (INH) and ethionamide (ETH) has been shown to be an enoyl reductase, encoded by the inhA gene. The mabA (mycolic acid biosynthesis A) gene is located immediately upstream of inhA in Mycobacterium tuberculosis, Mycobacterium bovis and Mycobacterium smegmatis. The MabA protein from M. tuberculosis was expressed in Escherichia coli and shown to have 3-ketoacyl reductase activity, consistent with a role in mycolic acid biosynthesis. In M. smegmatis, inhA and mabA are independently transcribed, but in M. tuberculosis and M. bovis BCG, mabA and inhA constitute a single operon. Several INH-ETH-resistant M. tuberculosis clinical isolates contain point mutations in the ribosome-binding site of mabA in the mabA-inhA operon. However, genetic dissection of this operon reveals that the INH-ETH-resistance phenotype is encoded only by inhA, and not by mabA.

3-Oxoacyl-(Acyl-Carrier-Protein) Reductase↗

PubMed1998

Transcription of the trp operon in Lactococcus lactis is controlled by antitermination in the leader region.

The regulatory functions of the leader region preceding the Lactococcus lactis trp operon have been studied by mutagenesis analysis. This leader presents striking similarity to 'T-box' leaders found upstream of many Gram-positive aminoacyl-tRNA synthetase genes and some amino acid biosynthesis operons, which are controlled by antitermination through interaction of the leader transcript with cognate uncharged tRNA. A region of the L. lactis leader transcript also contains a series of (G/U) AG repeats which, in Bacillus, are involved in the binding of the trp RNA-binding protein (TRAP) which controls trp transcription. A screen was developed for the isolation of regulatory mutants affected in the leader region. All spontaneous mutants contained deletions; point mutations were only obtained after UV-induced mutagenesis. All mutations affected the putative transcription terminator upstream of the trp operon, demonstrating that trp is indeed controlled by transcription antitermination.

Base Sequence↗

PubMed1999

Transcriptional analysis of the Bacillus subtilis teichuronic acid operon.

The cell walls of Gram-positive bacteria consist primarily of a macromolecular matrix comprising similar amounts of peptidoglycan and covalently attached anionic polymers. Under most growth conditions the anionic polymers of Bacillus subtilis are principally teichoic acids; in strain 168 these include a polyglycerol teichoic acid and a glucose/galactosamine-containing teichoic acid. However, when cultures are subjected to phosphate stress the bacterium induces a complex series of responses, one of which is the replacement of at least part of the wall teichoic acid with teichuronic acid, a non-phosphate-containing anionic polymer. In this paper the construction of a transcriptional reporter strain that facilitates the monitoring of the promoter region upstream of the tua operon involved in teichuronic acid synthesis and its controlled expression are reported. The expression of the tua operon was monitored in both phosphate-starved, non-growing batch cultures and phosphate-limited continuous cultures. We show that the transcription of the operon correlates well with the anionic polymer composition of the cell walls.

Bacillus subtilis↗

PubMed2000

Catabolite repression of dra-nupC-pdp operon expression in Bacillus subtilis.

Expression of the Bacillus subtilis dra-nupC-pdp operon is subject to catabolite repression by glucose. It was shown that a cis-acting catabolite-responsive element (CRE) sequence located 64 bp downstream of the transcription-start site mediated catabolite repression of the dra-nupC-pdp operon as it does for many other B. subtilis genes. Point mutations in the CRE sequence caused the loss of catabolite repression of the operon. Catabolite repression of dra-nupC-pdp expression was relieved in a ccpA mutant and was found to be dependent on both HPr and the HPr-like protein Crh. Furthermore, a transcription-repair coupling factor, Mfd, was also found to be involved in the glucose repression of dra-nupC-pdp expression. By the use of in vitro gel mobility shift analysis, a specific HPr-P dependent binding of CcpA to the dra CRE site was demonstrated.

Bacillus subtilis↗

PubMed2000

The gene encoding IIAB(Man)L in Streptococcus salivarius is part of a tetracistronic operon encoding a phosphoenolpyruvate: mannose/glucose phosphotransferase system.

Glucose and mannose are transported in streptococci by the mannose-PTS (phosphoenolpyruvate:mannose phosphotransferase system), which consists of a cytoplasmic IIAB protein, called IIAB(Man), and an uncharacterized membrane permease. This paper reports the characterization of the man operon encoding the specific components of the mannose-PTS of Streptococcus salivarius. The man operon was composed of four genes, manL, manM, manN and manO. These genes were transcribed from a canonical promoter (Pman) into a 3.6 kb polycistronic mRNA that contained a 5'-UTR (untranslated region). The predicted manL gene product encoded a 35.5 kDa protein and contained the amino acid sequences of the IIA and IIB phosphorylation sites already determined from purified S. salivarius IIAB(Man)L. Expression of manL in Escherichia coli generated a 35 kDa protein that reacted with anti-IIAB(Man)L antibodies. The predicted ManM protein had an estimated size of 27.2 kDa. ManM had similarity with IIC domains of the mannose-EII family, but did not possess the signature proposed for mannose-IIC proteins from Gram-negative bacteria. From multiple alignment analyses of sequences available in current databases, the following modified IIC(Man) signature is proposed: GX3G[DNH]X3G[LIVM]2XG2[STL][LT][EQ]. The deduced product of manN was a hydrophobic protein with a predicted molecular mass of 33.4 kDa. The ManN protein contained an amino acid sequence similar to the signature sequence of the IID domains of the mannose-EII family. manO encoded a 13.7 kDa protein. This gene was also transcribed as a monocistronic mRNA from a promoter located in the manN-manO intergenic region. A search of current databases revealed the presence of IIAB(Man)L, ManM, ManN and ManO orthologues in Streptococcus mutans, Streptococcus pyogenes, Streptococcus pneumoniae and Enterococcus faecalis. This work has elucidated the molecular structure of the mannose PTS in streptococci and enterococci, and demonstrated the presence of a putative regulatory protein (ManO) within the man operon.

Amino Acid Sequence↗

PubMed2001

Molecular analysis of the mannitol operon of Clostridium acetobutylicum encoding a phosphotransferase system and a putative PTS-modulated regulator.

Clostridium acetobutylicum DSM 792 accumulates and phosphorylates mannitol via a phosphoenolpyruvate (PEP)-dependent phosphotransferase system (PTS). PEP-dependent mannitol phosphorylation by extracts of cells grown on mannitol required both soluble and membrane fractions. Neither the soluble nor the membrane fraction could be complemented by the opposite fraction prepared from glucose-grown cells, indicating that the mannitol-specific PTS consists of both a soluble (IIA) and a membrane-bound (IICB) component. The mannitol (mtl) operon of C. acetobutylicum DSM 792 comprises four genes in the order mtlARFD. Sequence analysis of deduced protein products indicated that the mtlA and mtlF genes respectively encode the IICB and IIA components of the mannitol PTS, which is a member of the fructose-mannitol (Fru) family. The mtlD gene product is a mannitol-1-phosphate dehydrogenase, while mtlR encodes a putative transcriptional regulator. MtlR contains two PTS regulatory domains (PRDs), which have been found in a number of DNA-binding transcriptional regulators and in transcriptional antiterminators of the Escherichia coli BglG family. Also, near the C-terminus is a well-conserved signature motif characteristic of members of the IIA(Fru)/IIA(Mtl)/IIA(Ntr) PTS protein family. These regions are probably the sites of PTS-dependent phosphorylation to regulate the activity of the protein. A helix-turn-helix DNA-binding motif was not found in MtlR. Transcriptional analysis of the mtl genes by Northern blotting indicated that the genes were transcribed as a polycistronic operon, expression of which was induced by mannitol and repressed by glucose. Primer extension experiments identified a transcriptional start point 42 bp upstream of the mtlA start codon. Two catabolite-responsive elements (CREs), one of which overlapped the putative -35 region of the promoter, were located within the 100 bp upstream of the start codon. These sequences may be involved in regulation of expression of the operon.

Amino Acid Sequence↗

PubMed2001

The bio operon on the acquired symbiosis island of Mesorhizobium sp. strain R7A includes a novel gene involved in pimeloyl-CoA synthesis.

The symbiosis island of Mesorhizobium sp. strain R7A is a 500 kb chromosomal genetic element that upon transfer converts nonsymbiotic mesorhizobia to symbionts able to nodulate and fix nitrogen with Lotus corniculatus. Four genomic species of nonsymbiotic mesorhizobia have been isolated. All were auxotrophic for thiamin and biotin and three were auxotrophic for nicotinate, whereas derivatives of the strains containing the symbiosis island were prototrophic for all three vitamins. In this work, a 13.2 kb region of the island that converts the nonsymbionts to nicotinate and biotin prototrophy was characterized. The region contained orthologues of the Escherichia coli bioBFD and A genes arranged in an operon with a novel gene, bioZ, a nadABC operon, the nitrogen-fixation regulatory gene nifA, and a homologue of the pantothenate biosynthesis gene panD. The bioZ gene product was similar to beta-ketoacyl-acyl carrier protein synthase III (FabH). bioZ::Tn5 mutants grew poorly in the absence of biotin and the bioZ gene complemented an E. coli bioH mutant, suggesting that its product is involved in the synthesis of pimeloyl-COA: The bio operon was not required for symbiosis, as only mutants in the nifA gene were impaired in symbiosis, and a bioA::Tn5 mutant was not impaired in rhizosphere colonization. The rationale for the vitamin biosynthetic loci being located on an acquired genetic element that is absent from nonsymbiotic mesorhizobia remains to be determined.

Acyl Coenzyme A↗

PubMed2002

The divergent chromosomal ars operon of Acidithiobacillus ferrooxidans is regulated by an atypical ArsR protein.

The chromosomal arsenic-resistance (ars) operon of Acidithiobacillus ferrooxidans is atypical in that it is divergent, with its arsCR and arsBH genes transcribed in opposite directions. Furthermore, the amino-acid sequence of the putative ArsR-like regulator of the ars operon is not conserved in regions that have been shown to be responsible for binding to arsenic. Instead, the ArsR-like protein of At. ferrooxidans is related to a group of unstudied ArsR-like proteins that have been found to be associated with chromosomal ars-like operons identified during genome-sequencing projects. Using arsB-lacZ, arsR-lacZ and arsC-lacZ fusions, it was shown that the ArsR-like protein of At. ferrooxidans is a repressor of the arsBH and arsRC genes of this organism, and that induction of gene expression took place when either AsIII (arsenite) or AsV (arsenate) were added. Deletion of 19 aa from the C terminus of the 118 aa ArsR protein did not affect the regulation of its activity, but deletion of an additional 28 aa inactivated ArsR. Northern-blot hybridization suggested that on induction of expression, the arsRC genes were transcribed in greater quantities than the arsBH genes, but that the level of induction was not affected by the form of arsenic added (AsIII or AsV).

Amino Acid Sequence↗

PubMed2002

Molecular characterization of an operon, cueAR, encoding a putative P1-type ATPase and a MerR-type regulatory protein involved in copper homeostasis in Pseudomonas putida.

The authors have characterized a chromosomally localized two-gene operon, cueAR, which encodes a putative P1-type ATPase, CueA, and a MerR-type metalloregulatory protein, CueR, in Pseudomonas putida PNL-MK25. Disruption of cueAR by the insertion of mini-Tn5::gfp into the wild-type strain led to a mutant strain with a sixfold reduction in its tolerance to copper; however, the tolerance of this mutant strain to the other seven related transition metals tested was not affected. The sensitivity of the mutant strain was attributed to a higher level of accumulation of intracellular copper, suggesting the involvement of CueA in copper export. Insertion of the cloned cueAR operon into the copper-sensitive mutant strain fully restored its tolerance to copper. cueA::gfp expression studies confirmed that the cueAR operon was transcriptionally regulated by copper and CueR. Studies done on the mutant strain complemented with cueR and cueA revealed partial functional redundancy of cueA and cueR, respectively, in copper tolerance. Thus, the results of this study clearly suggest the involvement of cueAR in copper homeostasis in P. putida.

Adenosine Triphosphatases↗

PubMed1994

Sequence and analysis of the citrulline biosynthetic operon argC-F from Bacillus subtilis.

The citrulline biosynthetic operon argC-F located at 100 degrees on the Bacillus subtilis chromosome contains seven open reading frames which encode all the enzymes required for the biosynthesis of citrulline. The operon is transcribed as a single transcription unit. The second cistron of the operon is homologous to ArgJ (ornithine acetyltransferase) from Bacillus stearothermophilus and Neisseria gonorrhoeae, suggesting that the acetylation of glutamate and the deacetylation of acetylornithine are carried out by a single enzyme in a cyclical pathway. The argF gene is an orthologue of argF from Pseudomonas aeruginosa and a paralogue of arcB from P. aeruginosa and argF/argI from Escherichia coli.

Amino Acid Sequence↗

PubMed1995

I-CeuI recognition sites in the rrn operons of the Bacillus subtilis 168 chromosome: inherent landmarks for genome analysis.

The Bacillus subtilis 168 circular chromosome yielded ten fragments on I-CeuI endonuclease digestion. I-CeuI recognizes a 26 bp sequence that is located within the gene encoding the 23S subunit of the rRNA in Chlamydomonas eugametos, Escherichia coli and Salmonella typhimurium. The precise locations of the I-CeuI sites of the B. subtilis chromosome were determined on a NotI-SfiI physical map by (i) double digestion analyses with I-CeuI and SfiI, (ii) comparison of mutant strains lacking a specific rrn operon, (iii) using an I-CeuI linking clone and (iv) analysis of nucleotide sequence data of some rrn operons. In conclusion, all the I-CeuI sites were located within the B. subtilis rrn operons and the I-CeuI sites were conserved in all the B. subtilis 168 derivatives tested. Thus, variations in size of the I-CeuI fragments must be due to genome alterations. A B. subtilis 168 strain was investigated with I-CeuI. We demonstrated that the aberrant structure was the outcome of the inversion of an approximately 1700 kb DNA segment.

Bacillus subtilis↗