SEARCH · PubMed Health

Results for “Operon”

Explore indexed PubMed citations for clinical trials, systematic reviews and public health research. Read source abstracts and follow each citation to its original PubMed record.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 667 records · Page 37Linked to original sources

PubMed1999

Structure and transcriptional control of the flagellar master operon of Salmonella typhimurium.

The flhD and flhC genes constitute the flagellar master operon whose products are required for expression of all the remaining flagellar operons in Salmonella typhimurium. Here we report the molecular structure and in vivo and in vitro expression of the flhD operon. Nucleotide sequence analysis revealed that the upstream region of this operon contains the consensus sequence for the cAMP-CRP binding site. Primer extension analysis demonstrated six possible transcription start sites for this operon. They include CRP-dependent and CRP-repressible transcription start sites. The CRP-dependent transcription start site is located 203 bp upstream of the initiation codon of the flhD gene and preceded by the consensus sequences of the -10 and -35 regions of the sigma 70-dependent promoter. The putative cAMP-CRP binding site is located centered 70 bp upstream of this start site. The CRP-repressible transcription start site is located within this putative cAMP-CRP binding site. These two start sites were confirmed by in vitro transcription experiments using sigma 70-RNA polymerase with or without cAMP-CRP.

Amino Acid Sequence↗

PubMed1999

Promoter analysis of the class 2 flagellar operons of Salmonella.

The Salmonella flagellar operons are divided into three classes with reference to their relative positions in the transcriptional hierarchy. Expression of the class 2 operons requires the class 1 gene products, FlhD and FlhC, and is enhanced by an unknown mechanism in the presence of the class 3-specific sigma factor, FliA, and in the absence of its cognate anti-sigma factor, FlgM. In this study, the transcriptional start site mapping was performed by primer extension analysis for five class 2 operons, flgA, flgB, flhB, fliE and fliL. In all cases, one or a few major transcriptional start sites were identified. These start signals disappeared in the flhDC-mutant background, and their intensity decreased and increased in the fliA-mutant and flgM-mutant backgrounds, respectively. Therefore, we conclude that the FlhD/FlhC-dependent transcription is responsible for the FliA-dependent enhancement. Sequence comparison revealed that an imperfect inverted repetitious sequence is conserved upstream of the class 2 operons. Truncation of this sequence from the flgB promoter reduced its transcriptional activity to the background level, indicating that this is an essential cis-acting element for transcription of the class 2 operons.

Bacterial Proteins↗

PubMed1991

Sequence and features of the tryptophan operon of Vibrio parahemolyticus.

The nucleotide sequence of the trp operon of the marine enteric bacterium Vibrio parahemolyticus is presented. The gene order E, G, D, C(F), B, A is identical to that of other enterics. The structural genes of the operon are preceded by a long leader region encoding a 41-residue peptide containing five tryptophan residues. The organization of the leader region suggests that transcription of the operon is subject to attenuation control. The promoter-operator region of the V. parahemolyticus trp operon is almost identical to the corresponding promoter-operator of E. coli. The similarities suggest that promoter strength and operator function are identical in the two species, and that transcription initiation is regulated by repression. The operon appears to lack the internal promoter within trpD that is common in terrestrial enteric species.

Base Sequence↗

PubMed2006

Cop-like operon: structure and organization in species of the Lactobacillale order.

Copper is an essential and toxic trace metal for bacteria and, therefore, must be tightly regulated in the cell. Enterococcus hirae is a broadly studied model for copper homeostasis. The intracellular copper levels in E. hirae are regulated by the cop operon, which is formed by four genes: copA and copB that encode ATPases for influx and efflux of copper, respectively; copZ that encodes a copper chaperone; and copY, a copper responsive repressor. Since the complete genome sequence for E. hirae is not available, it is possible that other genes may encode proteins involved in copper homeostasis. Here, we identified a cop-like operon in nine species of Lactobacillale order with a known genome sequence. All of them always encoded a CopY-like repressor and a copper ATPase. The alignment of the cop-like operon promoter region revealed two CopY binding sites, one of which was conserved in all strains, and the second was only present in species of Streptococcus genus and L. johnsonii. Additional proteins associated to copper metabolism, CutC and Cupredoxin, also were detected. This study allowed for the description of the structure and organization of the cop operon and discussion of a phylogenetic hypothesis based on the differences observed in this operon's organization and its regulation in Lactobacillale order.

Adenosine Triphosphatases↗

PubMedDate not supplied

[Computer analysis of regulatory signals in complete bacterial genomes. Translation initiation of ribosomal protein operons].

Signals of translation initiation of operons of Haemophilus influenzae ribosomal proteins were predicted. This process is regulated by the formation of secondary RNA structures to which one of the proteins encoded in a particular operon binds. In some cases, these structures imitate the region of protein binding to rRNA. Predictions are made by comparing with homologous operons of Escherichia coli and analogous regions of rRNA and by estimating the energy of secondary structure formation. It is shown that this regulatory mechanism occurs: in operons L11, S10, S15, spc, and alpha of H.influenzae and, probably, in operon S15 of Helicobacter pylori, Bacillus subtilis, and Mycoplasma genitalium.

Base Sequence↗

PubMed2000

Phosphoenolpyruvate is a signal metabolite in transcriptional control of the cbb CO2 fixation operons in Ralstonia eutropha.

The two highly homologous cbb operons of the facultative chemoautotroph Ralstonia eutropha H16 encode most enzymes of the Calvin-Benson-Bassham carbon reduction cycle. Their transcriptional regulation was investigated both in vitro and in vivo to identify a metabolic signal involved in this process. For this purpose an in vitro transcription system employing the DNA-dependent RNA polymerase purified from R. eutropha was established. The enzyme from Escherichia coli was also used in verifying comparative studies. Plasmid DNA carrying the control region of the chromosomal cbb operon served as template. In the homologous as well as the heterologous system specific transcripts synthesized under the control of the operon promoter PcbbL were observed, depending on the structure of the tested promoter variant as well as the presence or absence of the activator protein CbbR. Unlike mutationally improved PcbbL variants, the wild-type promoter remained inactive, even in the presence of CbbR together with various potential signal metabolites. CbbR stimulated PcbbL mutants with intermediate basal activity. Phosphoenolpyruvate (PEP) was identified as a negative effector of CbbR that inhibited PcbbL-directed transcription and increased the operator-binding affinity of the protein. This CbbR-mediated inhibition was confirmed by assaying wild-type PcbbL operon fusions in glucose- or succinate-grown cells of E. coli, which contain greatly different concentrations of PEP. It is concluded that at least one additional protein must participate in the overall control of the cbb operons in R. eutropha.

Bacterial Proteins↗

PubMed2001

Molecular cloning and characterization of groESL operon in Streptococcus pneumoniae.

GroEL is a major target of the immune defense in infection and seems to be negatively regulated by HrcA in gram-positive organisms. However, HrcA's mechanism has not been elucidated. To elucidate the role of groEL in Streptococcus pneumoniae, the groESL operon was cloned in Escherichia coli. The promoter region of the pneumococcal groESL operon contained a sigmaA type promoter and an inverted repeat (CIRCE). A Northern blot analysis of the groESL operon demonstrated that the groESL operon is transcribed as a bicistronic mRNA, and reached maximum expression 7.5 to 10 min after heat shock. A primer extension analysis showed a potential transcription start point at 155 bp upstream of the translation start site, preceding the groES gene. The putative negative regulator of the groEL gene, hrcA, of S. pneumoniae was recovered by PCR-based chromosomal walking from grpE locus. A sequence analysis showed a sigmaA type promoter flanked by 2 CIRCE elements. His-tagged HrcA was overexpressed as a soluble form in E. coli and bound to the CIRCE regions in the promoter of both groESL and dnaK operons in vitro. Additionally, a helix-loop helix motif, a putative DNA binding domain, was found at the C-terminal of HrcA. These results will help to determine the nature of HrcA in the groESL repression.

Amino Acid Sequence↗

PubMed2001

[Transcription regulation in the ribosomal RNA operon of mycobacteria].

Tuberculosis is a extremely important infectious disease, caused by the bacilli Mycobacterium tuberculosis. One of the characteristic of this bacteria is its very slow rate of growth, that allows it to survive for long periods of time inside the host cells. Among the genetic elements involved in growth regulation the operon rrn is of extreme importance. This operon contains the genes that code the three rRNA molecules, essential components of the bacterial ribosome. The tuberculosis bacilli, differently from most of the microorganisms, has a single copy of the rrn operon per genome, meaning that it must be submitted to very strict control mechanisms. Another important conclusion is that the sequences of the rrn operon constitute ideal targets for anti-mycobacterial drugs. In this work we have studied some of the elements involved in transcription control in M. tuberculosis, particularly those present in the leader region of the operon. By using basic molecular biology techniques we have identified sequence elements in the leader region that seem to be involved in the control of transcription elongation, by a mechanism related to anti-termination.

Base Sequence↗

PubMed1992

Characterization of the mmsAB operon of Pseudomonas aeruginosa PAO encoding methylmalonate-semialdehyde dehydrogenase and 3-hydroxyisobutyrate dehydrogenase.

A 5417-base pair (bp) region of Pseudomonas aeruginosa PAO chromosomal DNA containing the mmsAB operon and an upstream regulatory gene (mmsR) has been cloned and characterized. The operon contains two structural genes involved in valine metabolism: mmsA, which encodes methylmalonate-semialdehyde dehydrogenase; and mmsB, which encodes 3-hydroxyisobutyrate dehydrogenase. mmsA and mmsB share the same orientation and are separated by a 16-bp noncoding region. The transcriptional start site for the operon has been pinpointed to a cytidine residue located 77 bp from the translational start site of the operon. mmsR is located on the opposite strand and begins 134 bp from the translational start site of mmsA. MmsR has been identified as a member of the XylS/AraC family of transcriptional regulators and appears to act as a positive regulator of the mmsAB operon. Sequence comparison of MmsA to other proteins in the data bases revealed that MmsA belongs to the aldehyde dehydrogenase (NAD+) superfamily. MmsB shares a 44% amino acid identity with 3-hydroxyisobutyrate dehydrogenase from rat liver. Mutants with insertionally inactivated mmsR, mmsA, and mmsB grow slowly on valine/isoleucine medium and exhibit reduced enzyme activity in cell-free extracts compared to P. aeruginosa PAO.

Alcohol Oxidoreductases↗

PubMed2004

Computational prediction of operons in Synechococcus sp. WH8102.

We computationally predict operons in the Synechococcus sp. WH8102 genome based on three types of genomic data: intergenic distances, COG gene functions and phylogenetic profiles. In the proposed method, we first estimate a log-likelihood distribution for each type of genomic data, and then fuse these distribution information by a perceptron to discriminate pairs of genes within operons (WO pairs) from those across transcription unit borders (TUB pairs). Computational experiments demonstrated that WO pairs tend to have shorter intergenic distances, a higher probability being in the same COG functional categories and more similar phylogenetic profiles than TUB pairs, indicating their powerful capabilities for operon prediction. By testing the method on 236 known operons of Escherichia coli K12, an overall accuracy of 83.8% is obtained by joint learning from multiple types of genomic data, whereas individual information source yields accuracies of 80.4%, 74.4%, and 70.6% respectively. We have applied this new approach, in conjunction with our previous comparative genome analysis-based approach, to predict 556 (putative) operons in WH8102. All predicted data are available at (http://www.cs.ucr.edu/~xin/operons.htm) for public use.

Computational Biology↗

PubMed1986

Origin of the mRNA stoichiometry of the puf operon in Rhodobacter sphaeroides.

The LH-I structural genes are located 5' of the RC-L and -M structural genes on what has been designated as the puf operon of Rhodobacter sphaeroides. Analysis of puf operon expression in R. sphaeroides by Northern hybridization with probes specific for individual structural gene has identified two transcripts encoded by this operon. The large (2.6 kilobase pairs (kb] transcript contains sequences for all four polypeptides of the puf operon, whereas the small (0.5 kb) transcript, which is more abundant (10-15-fold) than the large transcript under photosynthetic growth, is homologous only to the two LH-I structural genes. Transcription of the puf operon during photosynthetic growth under saturating light conditions is increased approximately 3-fold relative to growth in the presence of oxygen while the relative ratio of these two transcripts is independent of the incident light intensity. Analysis of the turnover of the two transcripts (t1/2 of 9 and 20 min for the large and small transcripts, respectively) indicates that 5' processing is the initial step in the degradation of the large transcript and that the molar excess of the small transcript cannot be accounted for by differences in the rates of turnover of these two mRNA species. Analysis of the 5' ends of the 2.6- and 0.5-kb transcripts, their relative abundance, and stabilities indicates that these two transcripts have different 5'-ends corresponding to 75 and 104 base pairs upstream from the start of the LH-I beta structural gene, respectively. Northern hybridization analysis with specific synthetic deoxyoligonucleotide probes confirmed that the two transcripts differ by 29 bases at their 5'-ends, suggesting that differential transcript initiation may be involved in regulating the relative levels of these two mRNA species in vivo, although we cannot rule out complex mechanisms of post-transcriptional processing.

Bacterial Proteins↗

PubMed1987

Rho-dependent transcriptional polarity in the ilvGMEDA operon of wild-type Escherichia coli K12.

It has been generally accepted that transcriptional polarity in prokaryotic systems is due to an uncoupling of translation and transcription which unmasks latent rho-dependent termination sites in a polycistronic messenger RNA. In this report, we identify and characterize rho-dependent termination sites responsible for transcriptional polarity in the ilvGMEDA operon of wild-type Escherichia coli K12. The ilvG gene in the wild-type E. coli K12 ilvGMEDA operon contains a frameshift site which results in termination of translation in the middle of the gene. Mutations have been characterized which restore the reading frame of this gene. In addition to allowing full-length expression of the ilvG product, these mutations cause a 3-4-fold elevation in the expression of the operon distal genes. This transcriptional polarity effect on operon distal genes also has been shown to be relieved by rho suppressor mutations. We have used in vitro transcription experiments to identify rho-dependent transcriptional termination sites downstream of the frameshift site in the ilvG gene. Three tandem rho-dependent sites have been located in the ilv'GM' gene region using transcription reactions containing linear or supercoiled plasmid DNA templates. Accumulatively, these rho-dependent termination sites account for about 80% in vitro transcription termination, which is in agreement with the in vivo measurements of transcriptional polarity on operon distal gene expression. These transcriptional experiments provide in vitro confirmation for the latent rho-dependent termination site model of transcriptional polarity.

Bacterial Proteins↗

PubMed1988

[Metabolic regulation of the histidine operon in Escherichia coli and Salmonella typhimurium].

Expression of the histidine operon in Escherichia coli cells in contrast to the one in Salmonella typhimurium is changed proportionally to cells growth rate on the different carbon sources. The specific activity of histidinol-dehydrogenase is repressed by addition of 19 amino acids both in Escherichia coli and Salmonella typhimurium independent of the growth medium used. Using of Escherichia coli and Salmonella typhimurium strains containing the heterologous histidine operons made possible to demonstrate the dependence of the histidine operon metabolic regulation to be determined by the operon itself but not by the specificity of the recipient cells. ppGpp was shown to be a positive regulator of the histidine operon expression in Escherichia coli.

Alcohol Oxidoreductases↗

PubMed1988

Purification and characterization of a repressor for the Bacillus subtilis gnt operon.

The GntR protein is a negative regulator involved in gluconate-inducible expression of the Bacillus subtilis gnt operon which is responsible for gluconate metabolism. The GntR protein has been purified to homogeneity from an overproducing Escherichia coli strain harboring a gntR gene-carrying plasmid. The total amino acid composition and the NH2-terminal amino acid sequence of the purified protein were essentially the same as those deduced from the nucleotide sequence of the gntR gene. Molecular weight determination by gel filtration revealed that the purified protein is in a highly polymerized form, but it likely exists as a dimer when highly diluted. The purified GntR protein was found to be specifically bound to DNA fragments carrying the promoter of the gnt operon in an electrophoretic mobility shift assay. This binding was specifically inhibited by the addition of gluconate or glucono-delta-lactone. The purified protein repressed in vitro transcription from the promoter of the gnt operon. This repression was suppressed by gluconate or glucono-delta-lactone. These results indicate that the GntR protein is a repressor for the gnt operon and that gluconate and glucono-delta-lactone are inducers for this operon.

Bacillus subtilis↗

PubMed1987

The hisT-purF region of the Escherichia coli K-12 chromosome. Identification of additional genes of the hisT and purF operons.

A 9.7-kilobase pair segment of the Escherichia coli chromosome spanning the hisT and purF loci has been characterized. Six genes were identified in this region by complete DNA sequence analysis, in vivo expression in maxicells, and RNA transcript analysis. S1 nuclease analysis has demonstrated that some of these genes are part of the hisT or purF operons. Two of the newly identified genes, dedA and dedB, were localized immediately downstream of hisT in the hisT operon. Two other genes, denoted dedC and dedD, have been localized between the hisT and purF operons. The other two genes, dedE and dedF flank the purF gene. dedE has been previously described as the first gene in the purF operon (Makaroff, C.A., and Zalkin, H. (1985) J. Biol. Chem. 260, 10378-10387). dedF was localized downstream from purF and is part of the purF operon. In addition, dedF is homologous to the ubiX gene of Salmonella typhimurium. Adjacent to dedF is the E. coli homologue of the S. typhimurium argT locus encoding the lysine/arginine/ornithine-binding protein. All of the genes in this region of the chromosome were found to be transcribed in a counter-clockwise direction on the E. coli map which revises the direction of purF transcription.

Base Sequence↗

PubMed1995

Transcriptional regulation of puc operon expression in Rhodobacter sphaeroides. Analysis of the cis-acting downstream regulatory sequence.

Both site-directed and spontaneous mutagenesis have been used to investigate the role of the cis-acting regulatory region between -92 and -1 base pair (bp) of the puc operon of Rhodobacter sphaeroides. The DNA sequence from -84 to -66 bp upstream of the 5' end of the start site of puc operon transcription is essential for normal puc operon expression. This regulatory effect was exerted irrespective of the presence or absence of additional upstream regulatory sequences extending from -629 to -93 bp. It is likely that this region is involved in activator binding. Additionally, two regions of dyad symmetry centered at -42 and -17 bp are shown to be involved in oxygen repression of puc operon expression. Mutations within these regions of dyad symmetry were further subdivided on the basis of whether or not the upstream regulatory region was required to observe the mutant phenotype. Based upon these observations we conclude that these regions of dyad symmetry possessing the motif TGT-N12-ACA (where N represents any nucleotide) are involved in repressor binding with the puc operon promoter overlapping each of these dyad symmetries.

Base Sequence↗

PubMed1994

[Decrease in the level of DeoR-dependent repression of the deo operon as a result of integration of foreign DNA fragments into the interoperator deoO1-deoO2 region of the Escherichia coli chromosome].

Two heterologous DNA fragments encoding the genes Kanr and cat were integrated into the regulatory region of the deo operon of Escherichia coli, located in a recombinant plasmid. As a result, plasmids pD5K and pD5C were obtained, in which the distance between the deoO1 and deoO2 operators increased from 599 bp in the deo operon of the wild type to 2019 and 1398 bp in case of integration of Kanr and cat, respectively. Then, linearized DNA of plasmids pD5K and pD5C was incorporated into the deo locus of the chromosome of E. coli through homologous recombination by the use of a recipient strain recBC sbcB. The constructed strains contained insertions in the interoperator region of the deo operon. Expression of the deo operon was studied in these strains, on a different genetic background with respect to the genes deoR, cytR, and cyaA. An increase in the interoperator distance was shown to increase the basal level of gene expression of the deo operon and to disturb cooperative interaction of the DeoR repressor and operator sites.

Chromosomes, Bacterial↗

PubMed1994

Purification and characterization of a novel organometallic receptor protein regulating the expression of the broad spectrum mercury-resistant operon of plasmid pDU1358.

The narrow spectrum mercury-resistant (mer) operons of transposons Tn21 and Tn501 are inducible by inorganic mercury salts. The major regulatory gene merR is transcribed divergently from the other mer genes, which are cotranscribed. The MerR protein represses its own expression, as well as the expression of the other mer genes in the absence of the inducers. The synthesis of the polycistronic mer message is stimulated by MerR in the presence of the inducers. The MerRBS protein encoded by the broad spectrum mer operon of plasmid pDU1358 was characterized as a novel organomercurial receptor, distinguishing it from the narrow spectrum MerRNS proteins, described above. Several organomercurial compounds directly effected cellular activation of the mer operon transcription via the receptor protein MerRBS, but not by MerRNS. The merR gene from pDU1358 was cloned under the tac promoter, and the overexpressed MerRBS protein was soluble in buffer solutions containing 0.5 M NaCl at pH 7.5, but precipitated when NaCl concentration was reduced to 0.1 M (MerRBS concentrations at or above 0.1 mg/ml). MerRBS was purified to near homogeneity by selective precipitation and solubilization by varying the salt concentration in buffer solutions, followed by Sephadex G-75 column chromatography. Both MerRBS and Tn21-encoded MerRNS bound with DNA fragments containing the pDU1358 mer operator sequence with comparable affinities. In vitro run-off transcription studies revealed that MerRBS activated mer operon expression in the presence of Hg2+ or phenylmercuric acetate. Phenylmercuric acetate did not induce mer operon expression when the MerRNS was used in the assay.

Bacterial Proteins↗