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 757 records · Page 42Linked to original sources

PubMed1985

Studies on deo operon regulation in Escherichia coli: cloning and expression of the cytR structural gene.

The structural gene that encodes one repressor (the cytR-encoded repressor) of the Escherichia coli deo operon has been cloned from a lambda dmet transducing phage into the multicopy plasmid pBR322 by selecting for ApR, Lac- transformants of E. coli SS110(delta lac, cytR, tsx::lac). Restriction maps for the cytR+ plasmids have been generated and the position of the cytR gene on the cloned insert of these plasmids has been determined through deletion analysis. Results from maxicell experiments employing pCB001 and its cytR- derivatives suggest that the cytR gene encodes a protein with a subunit Mr of 37 000. In contrast to the complete repression of the deo operon obtained when deoR+ plasmids were introduced into E. coli SS201 (deoR, cytR), transformation of this DeoR-, CytR- strain with any of the cytR+ plasmids yields only clones which have phenotypes and Deo enzyme levels characteristic of a DeoR- single mutant. The data presented in this study are consistent with the interpretation that, in E. coli, the deoR-encoded repressor controls deo operon transcription initiating from both deo promoter-operator sites, PO1 and PO2. In contrast, the cytR-encoded repressor regulates deo operon expression only through deo promoter-operator site PO2.

Bacteriophage lambda↗

PubMed1985

Transcriptional control of the nah and sal hydrocarbon-degradation operons by the nahR gene product.

The positively regulated nah and sal operons of the NAH7 plasmid from Pseudomonas putida encode the enzymes for metabolism of naphthalene via salicylate. To study their coordinate regulation, a 6-kb DNA fragment containing the entire nahA gene (encoding naphthalene dioxygenase), the gene of the nah operon, was cloned into a RSF1010 plasmid derivative. Analysis of expression of nahA from the nah promoter in either Escherichia coli or Pseudomonas putida showed that a 1.6-kb DNA fragment from the nahR (nah operon regulatory locus) region was required in trans for (i) induction by salicylate; (ii) high-level expression of nahA, and (iii) complementation of nahR- mutants. Measurement of transcription in induced and uninduced P. putida showed that induction of the nah and sal operons occurred at the transcriptional level. The trans-acting positive regulatory gene, nahR, however, was constitutively transcribed.

Cloning, Molecular↗

PubMed1986

Reconstitution of an operon from overlapping fragments: use of the lambda SV2 integrative cloning system.

We have used the lambda SV2 system [Howard and Gottesman. In Gluzman (Ed.), Eukaryotic Viral Vectors. Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, 1982, pp. 211-216; in Inouye, M. (Ed.) Experimental Manipulations of Gene Expression. Academic Press, New York, 1983, pp. 137-153] to reconstitute the Salmonella typhimurium his operon from overlapping fragments. lambda SV2 can be propagated as an autonomously replicating plasmid or as a prophage integrated in the Escherichia coli chromosome at the lambda attachment site; our reconstitution was accomplished in the integrated state. We first inserted a portion of the his operon into lambda SV2 and integrated the resulting plasmid by site-specific recombination into the E. coli chromosome. This was achieved by brief induction of a resident prophage. The lysogen was then transformed with DNA from a lambda SV2 clone carrying the remainder of the his operon on an overlapping DNA fragment. The second plasmid was forced to integrate into the first by homologous recombination. When this recombination occurs at the his overlap, a lysogen carrying two lambda SV2 prophages is produced. One prophage carries the entire his operon and the other carries the his overlap region. The latter is removed by site-specific recombination, permitting further contiguous sequences to be sequentially added to the remaining prophage. This method should be applicable for the reconstitution and maintenance of large genes or gene clusters in the E. coli genome.

Alleles↗

PubMed1989

Duplication of the phycocyanin operon in the unicellular cyanobacterium Anacystis nidulans R2.

Two phycocyanin (PC) operons, each containing alpha- and beta-subunit genes, have been isolated from the unicellular cyanobacterium Anacystis nidulans R2. Using oligodeoxyribonucleotide probes for the PC-coding regions, three PstI fragments were obtained and shown to contain the two operons, which are 2.7 kb apart, with a proposed gene order of 5'-(beta I-alpha I)-(beta II-alpha II)-3'. The nucleotide sequences of both alpha-subunit genes are identical, as are the beta-sequences and the 51-bp intergenic regions. However, significant nucleotide sequence differences are found in both the 5' and 3' untranslated regions of the two operons. Two mRNA species of 1.65 and 1.5 kb were detected in A. nidulans R2 RNA when probed with either the alpha-specific or the beta-specific probe. The results demonstrate the existence of two PC operons which are both transcriptionally active.

Base Sequence↗

PubMed1991

Gene-specific transposon mutagenesis of the biphenyl/polychlorinated biphenyl-degradation-controlling bph operon in soil bacteria.

A transposon, Tn5-B21, was gene-specifically inserted into the chromosomal biphenyl/polychlorinated biphenyl-catabolic operon (bph operon) of soil bacteria. The cloned bphA, bphB and bphC genes of Pseudomonas pseudoalcaligenes KF707, coding for conversion of biphenyl into a ring meta-cleavage product (2-hydroxy-6-oxo-6-phenylhexa-2,4-dienoic acid), carried random insertions of Tn5-B21. The mutagenized bphABC DNA, carried by a suicide plasmid, was introduced back into the parent strain KF707, resulting in the appearance of gene-specific transposon mutants by double crossover homologous recombination: the bphA::Tn5-B21 mutant did not attack 4-chlorobiphenyl, the bphB::Tn5-B21 mutant accumulated dihydrodiol, and the bphC::Tn5-B21 mutant produced dihydroxy compound. Gene-specific transposon mutants of the bph operon were also obtained for some other biphenyl-utilizing strains which possess bph operons nearly identical to that of KF707.

Biphenyl Compounds↗

PubMed1993

The lumazine protein-encoding gene in Photobacterium leiognathi is linked to the lux operon.

The nucleotide (nt) sequence of the lumP (EMBL accession No. X65612) gene of Photobacterium leiognathi PL741 was determined and the amino acid (aa) sequence deduced. The encoded aa sequence of lumP was identified as that of the lumazine protein (LumP) by homology with that of Photobacterium phosphoreum (56%). This small protein has a calculated M(r) of 19,997 and comprises 186 aa residues. Biochemical studies suggested that LumP is the protein which, when combined with luciferase, is responsible for the bioluminescent spectrum shift from blue-green light (490-505 nm) to blue (470 nm) in P. leiognathi. The nt sequence of the flanking region showed that lumP is linked to the lux operon but runs in the opposite direction. The gene order of the lumP and lux operon is as follows: <--lumP-R&R-luxC-luxD-luxA-luxB-luxN-lu xE-->; the R&R regulatory region sequence included two promoter systems, PR for the lux operon and PL for the lumP or the lum operon.

Amino Acid Sequence↗

PubMed1993

Cloning and sequencing of the Lactococcus lactis subsp. lactis groESL operon.

The operon (groESL) coding for the Lactococcus lactis subsp. lactis heat-shock proteins GroEL and GroES, has been isolated and its complete nucleotide (nt) sequence determined. A set of degenerate PCR primers, deduced from amino acids which are conserved in a number of prokaryotic GroELs, were synthesized and used to amplify a 957-bp fragment. This PCR fragment was used as a probe to isolate a 5.0-kb EcoRI chromosomally derived fragment. A region of this 5.0-kb EcoRI fragment was sequenced and revealed that the groES gene was located 5' to groEL. This sequence was then used to design a set of inverse PCR primers and a 2.5-kb HindIII fragment was cloned which contained the region 5' to groEL. The complete nt sequence of the groESL operon was determined from overlapping fragments. It revealed that the groESL operon was preceded by a stem-loop structure and the promoter appears similar to most L. lactis subsp. lactis and other Gram+ bacterial promoters. Northern analysis demonstrated that the groESL operon is under tight regulation and a dramatic induction of mRNA synthesis occurs within 15 min after heat shock.

Amino Acid Sequence↗

PubMed1995

Two different operons for the same function: comparison of the Salmonella typhimurium nrdAB and nrdEF genes.

By using a P22 phage-mediated cloning system, the nrdAB genes of Salmonella typhimurium (St), encoding a ribonucleotide reductase (RR) of class I, have been isolated. The coding regions of the St nrdAB operon show a very high identity with those of the homologous operon of Escherichia coli (Ec). Nevertheless, there are significant differences in their promoter regions since, although the promoters of both operons present two DnaA boxes, these boxes are located downstream from the transcription start point in St, being upstream in Ec. Moreover, the deduced amino-acid sequences of the St nrdAB showed a very limited overall identity (28%) with the products of St nrdEF, which encode a second class-I RR. Expression of St nrdAB and nrdEF is inducible by hydroxyurea, an inhibitor of RR activity. Alignment of the promoter regions of the nrdAB and nrdEF operons of both St and Ec reveals the presence of a consensus sequence. St is the first organism from which two different RR belonging to the same biochemical class are known.

Base Sequence↗

PubMed1989

The nucleotide sequence of the first two genes of the CFA/I fimbrial operon of human enterotoxigenic Escherichia coli.

An oligonucleotide probe, derived from the N-terminal amino acid sequence of the CFA/I fimbrial subunit protein, was used to identify the gene encoding this protein within a cloned DNA fragment encoding CFA/I fimbriae. The gene (cfa b) was found and sequenced. Flanking it upstream was a gene (cfa a) encoding a protein of 206 amino acids and downstream a gene (cfa c) probably encoding an 85 kDa protein was found. This genetic organisation of the CFA/I operon differs from that of other fimbrial operons in Escherichia coli. All three proteins have signal peptides. The nucleotide sequence was analysed for homology with other sequences, secondary structure, ribosomal binding sites and possible promoter sequences. A region of dyad symmetry probably involved in the regulation of translation of the cfa c gene was found at the 5' end of this gene. A region of dyad symmetry was also observed within the cfa b gene. In front of the CFA/I operon part of insertion sequence IS2 was found. This IS2 sequence was found in a number of CFA/I plasmids, obtained from strains isolated from various geographic locations. The insertion of the IS2 element in the CFA/I operon therefore probably happened rather early during evolution of CFA/I producing Escherichia coli strains.

Amino Acid Sequence↗

PubMed2006

A theoretical steady state analysis indicates that induction of Escherichia coli glnALG operon can display all-or-none behavior.

The nitrogen starvation response in Escherichia coli is characterized by the enhanced expression of Ntr regulon, comprising hundreds of genes including the one coding for nitrogen-assimilating glutamine synthetase (GS) enzyme. The biosynthesis and activity of GS is regulated mainly by nitrogen and carbon levels in the cell and monitored by three functionally separable interconnected modules. Here, we present the steady-state modular analysis of this intricate network made up of a GS bicyclic closed-loop cascade, a NRII-NRI two-component system, and an autoregulated glnALG operon encoding genes for GS, NRII, and NRI. Our simulation results indicate that the transcriptional output of glnALG operon is discrete and switch-like, whereas the activation of transcription factor NRI is graded, and the inactivation of GS is moderately ultrasensitive to input stimulus glutamine. The autoregulation of the NRII-NRI two-component system was found to be essential for the all-or-none induction of the glnALG operon. Furthermore, we show that the autoregulated two-component system modulates the total active GS by delineating the GS activity from its biosynthetic regulation. Our analysis indicates that the exclusive relationship between GS activity and its synthesis is brought about by the autoregulated two-component system. The modularity of the network endows the system to respond differently to nitrogen depending on the carbon status of the cell. Through a system-level quantification, we conclude that the discrete switch-like transcriptional response of the E. coli glnALG operon to nutrient starvation prevents the premature initiation of transcription and may represent the desperate attempt by the cell to survive in limiting conditions.

Bacterial Physiological Phenomena↗

PubMed2004

The fdh operon of Sulfurospirillum multivorans.

The complete single copy fdh operon (approximately 5.7 kb) encoding the formate dehydrogenase subunits of the gram negative, reductively dehalogenating anaerobe Sulfurospirillum multivorans was sequenced and analyzed. The gene fdhA encoding the catalytically active periplasmic subunit is part of an operon (fdhEABCD) containing additional structural genes. The genes fdhEABCD were cotranscribed as indicated by RT-PCR and primer extension experiments. Two mRNAs for fdhEABCD and fdhABCD were either transcribed independently from two transcription start sites upstream of fdhE and fdhA or might result from posttranscriptional processing of the full-length fdhEABCD mRNA. The operon shows a high degree of similarity to the fdh operons of Campylobacter jejuni and Wolinella succinogenes in terms of architecture and putative cofactor binding motifs of the gene products.

Amino Acid Sequence↗

PubMed2004

Identification of an operon involved in tyrosinase activity and melanin synthesis in Marinomonas mediterranea.

The genomic region of Marinomonas mediterranea containing the genes required for tyrosinase activity and melanin synthesis has been cloned by marker rescue using the transposon-generated, amelanogenic strain T105. Five ORFs, two incomplete and three complete, have been sequenced in the genomic region where the transposon was inserted. RT-PCR analysis indicates that ORF 3, coding for tyrosinase, and ORF4, coding for a protein of 250 amino acids, are in the same transcriptional unit, constituting an operon whose promoter region has been determined by 5'-RACE. This operon has been sequenced in the wild-type and several mutant strains, indicating that both ORFs are required for expression of tyrosinase activity and melanin synthesis. The nitrosoguanidine generated, amelanogenic mutant ng56, shows a nonsense mutation in ORF3 coding for the tyrosinase. On the other hand, in the strain T105 the transposon is inserted in ORF4. The product of this gene is related to copper metabolism, since the addition of this metal ion to cell extracts or culture media partially restores melanin synthesis and tyrosinase activity in the strain T105. However, it does not show significant sequence similarity to previously characterized metallochaperones and hence may be an example of a new kind of those proteins. The operon has been denoted as ppoB, taking into consideration that ppoA denotes the M. mediterranea gene coding for the previously cloned polyphenol oxidase with laccase activity. This is the first demonstration of the tyrosinase gene forming part of an operon in a Gram-negative bacterium.

Amino Acid Sequence↗

PubMed2025

The SinR·SlrR Heteromer Attenuates Transcription of a Long Operon of Flagellar Genes in Bacillus subtilis.

During growth, Bacillus subtilis differentiates into subpopulations of motile individuals and non-motile chains, associated with dispersal and biofilm formation, respectively. The two cell types are dictated by the activity of the alternative sigma factor SigD encoded as the penultimate gene of the 27-kb long fla/che flagellar operon. The frequency of SigD-ON motile cells is increased by the heteromeric transcription factor SwrA·DegU that activates the fla/che promoter. Conversely, the frequency of motile cells is decreased by the heteromeric transcription factor SinR·SlrR, but the mechanism and location of inhibition is poorly understood. Here, using ChIP-Seq analysis, we determine the binding sites of the SinR·SlrR heteromer on the genome. We identified two sites within the fla/che operon that were necessary and sufficient to attenuate transcript abundance by causing premature termination upstream of the gene that encodes SigD. Thus, cell motility and the transition to biofilm formation depend on the expression of a long operon governed by two opposing heteromeric transcription factors that operate at two different stages of the transcription cycle. More broadly, our study serves as a model for transcription factors that control transcriptional elongation and the regulation of long operons in bacteria.

Bacillus subtilis↗

PubMed2006

An operon in Streptococcus pneumoniae containing a putative alkylhydroperoxidase D homologue contributes to virulence and the response to oxidative stress.

Analysis of the pneumococcal genome sequences from strains R6 and TIGR4 identified a putative alkylhydroperoxidase homologue RT-PCR showed this gene to be expressed in an operon with the downstream open reading frame. No probable function for this second gene is suggested although it appears to be an integral membrane protein. An allelic replacement mutant lacking this two-gene operon in strain D39 was attenuated in competitive infections with the wild type parent. This operon is, therefore, a novel pneumococcal virulence determinant. In line with a role in the response to oxidative stress, this mutant showed enhanced resistance to killing by hydrogen peroxide, a phenotype shared by alkylhydroperoxidase mutants in other bacterial species. The analysis of non-polar single mutants shows that both genes contribute to these phenotypes. Finally, an important role in pneumococcal biology is suggested by the presence of this operon in all 20 clinical isolates examined and the highly conserved sequence of the two genes.

Amino Acid Sequence↗

PubMed2004

Transcriptional analysis of the groE and dnaK heat-shock operons of Enterococcus faecalis.

Enterococcus faecalis is able to survive in extremely adverse conditions, and its ability to resist stress is considered a key virulence attribute. Here, we conducted a detailed transcriptional analysis of the groE and dnaK operons of E. faecalis. The dnaK operon is comprised of four genes (hrcA-grpE-dnaK-dnaJ) preceded by two conserved CIRCE sequences. The dnaK operon is expressed from a sigmaA-type promoter located upstream of hrcA and multiple transcripts are detectable, possibly due to mRNA processing. The groE operon (groES-groEL) is transcribed as a single mRNA from a sigmaA-type promoter located immediately upstream of a CIRCE element. Induction of dnaK and groEL occurs in response to heat shock and exposure to NaCl, SDS and H(2)O(2).

Bacterial Proteins↗

PubMed2005

Organization of heat shock dnaK and groE operons of the nosocomial pathogen Enterococcus faecium.

Enterococcus faecium is a frequently antibiotic-resistant opportunistic pathogen that is commonly recovered from hospitalized patients. The genetic organization of the dnaK operon was analyzed and was shown to consist of at least four heat shock genes, hrcA-grpE-dnaK-dnaJ. The dnaK/J intergenic region was 140 bp shorter than in E. faecalis. The dnaK operon was expressed from a putative sigma(A)-type promoter (PhrcA) upstream of the hrcA start codon and was preceded by two conserved CIRCE sequences. Northern hybridization revealed the presence of multiple mRNAs in the dnaK operon. Conversely, the groE operon was transcribed as a single mRNA. Induction of dnaK and groEL genes occurred in response to either heat shock or exposure to other stress agents.

Bacterial Proteins↗

PubMed2006

Structure and expression of the atp operon coding for F1F0-ATP synthase from the antibiotic-producing actinomycete Nonomuraea sp. ATCC 39727.

Nonomuraea sp. ATCC 39727 is a poorly characterized actinomycete, producer of the glycopeptide antibiotic A40926. In this study, the nucleotide sequence of the atp operon coding for F1F0-ATP synthase of Nonomuraea sp. ATCC 39727 was determined. It consisted of ten open reading frames arranged in the order atpI (encoding the i protein), orfX, atpB (a subunit), atpE (c subunit), atpF (b subunit), atpH (delta subunit), atpA (alpha subunit), atpG (gamma subunit), atpD (beta subunit) and atpC (epsilon subunit). The orfX coded for a putative small hydrophobic 71 amino acid peptide of unknown function related to several bacterial permeases. Its presence appeared to be a distinctive feature of the atp operon of phylogenetically distant actinobacteria. Transcription of the atp operon was evaluated. The results of northern blot and RT-PCR experiments demonstrated that the atp genes were co-transcribed into a single polycistronic mRNA. Real-time RT-PCR data provided evidence showing that transcription of the atp operon was biphasic during Nonomuraea growth. The amount of the atpD transcript decreased at the end of the exponential growth phase, and then moderately increased during the early stationary phase when, in contrast, the levels of ctaC, encoding the cytochrome c oxidase subunit II, progressively decreased. Western blot analysis confirmed that ATP synthase was also present in the membrane during the stationary phase. These results together with previous data demonstrate that oligomycin-sensitive ATP-driven proton pumping activity remained constant in the stationary phase; in contrast, the activity and cytochrome content of the respiratory enzymes became negligible.

Actinomycetales↗

PubMed2004

The different roles of tryptophan transfer RNA in regulating trp operon expression in E. coli versus B. subtilis.

Escherichia coli and Bacillus subtilis use different mechanisms of sensing and responding to tryptophan and uncharged tRNA(Trp) as regulatory signals. In E. coli, tryptophan activates a repressor that binds to the trp promoter- operator, inhibiting transcription initiation. In B. subtilis, tryptophan activates an RNA-binding protein, TRAP, which binds to the trp operon leader RNA, causing transcription termination. In E. coli uncharged tRNA(Trp) accumulation stalls the ribosome attempting translation of tandem Trp codons in the leader-peptide coding region of the operon. This stalling permits the formation of an RNA antiterminator structure, preventing transcription termination. In B. subtilis uncharged tRNA(Trp) accumulation activates transcription and translation of the at operon. AT protein inhibits tryptophan-activated TRAP, thereby preventing TRAP-mediated transcription termination. These differences might reflect the unique organizational features of the respective trp operons and their ancestry.

Bacillus subtilis↗