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 1,153 records · Page 64Linked to original sources

PubMed1985

Genetic dissection of stringent control and nutritional shift-up response of the Escherichia coli S10 ribosomal protein operon.

The S10 operon of Escherichia coli is autogenously regulated by L4, one of 11 ribosomal proteins encoded by the operon. We have previously shown that L4 regulates transcription of the operon by modulating the level of read-through at an attenuator in the S10 leader. To determine the physiological roles of both L4-mediated attenuation and the regulation of transcription initiation, we have constructed mutations eliminating their two regulatory targets, the S10 leader and the S10 promoter. Our results indicate that stringent control requires only the S10 promoter and therefore is mediated at the level of initiation. However, growth-medium-dependent control after a nutritional shift-up involves regulation of both initiation of transcription at the promoter and transcription read-through at the attenuator.

Bacterial Proteins↗

PubMed1985

Transcriptional regulation of a periodically controlled flagellar gene operon in Caulobacter crescentus.

Temporal regulation of flagellar gene expression in Caulobacter crescentus has been examined by a detailed analysis of the flbG-flaJ-flbH-flaK hook operon. The approximate location of the promoter for this 4.4 X 10(3) base-pair transcriptional unit was determined by deletion mapping, and the flaK gene was shown by nucleotide sequencing to code for the hook protein. flaK messenger RNA was quantified by S1 nuclease mapping with an internal restriction fragment of the gene as the 5'-labeled DNA probe. The results of these assays provide the first direct evidence that periodic expression of a flagellar gene in the C. crescentus cell cycle is regulated at the transcriptional level. The effect of altering the time of gene duplication in the cell cycle was examined by subcloning the complete hook operon on a plasmid that replicates throughout the S phase. The normal periodicity of flaK transcription and translation was maintained in this merodiploid strain, which suggests that replication alone is not sufficient to initiate flagellar gene expression. We also show that the three adjacent transcriptional units III, IV and V are required in trans for transcription of the book operon, and we discuss the possible role of these genes in the hierarchical regulation of the flagellar gene expression.

Bacterial Proteins↗

PubMed1986

malM, a new gene of the maltose regulon in Escherichia coli K12. I. malM is the last gene of the malK-lamB operon and encodes a periplasmic protein.

The structure and expression of the distal part of the malK-lamB operon in Escherichia coli was studied. DNA sequencing was performed as far as a HinfI restriction site located 1313 base-pairs downstream from gene lamB. The open reading frame, formerly called molA, which begins 245 base-pairs downstream from gene lamB, is longer than was initially thought, and was renamed malM. It could encode a protein of 306 amino acid residues. The complete malM open reading frame was cloned under control of the tac 12 promoter. In maxicells, the resulting plasmid permitted tac12-promoted synthesis of two polypeptides, encoded by gene malM, with apparent molecular weights of 37 X 10(3) and 34.5 X 10(3). We provide strong evidence that the 34.5 X 10(3) Mr protein is derived from the 37 X 10(3) Mr protein by processing at the amino-terminal end, and that this processed form is located in the periplasmic space. We show that the chromosomal malM gene is expressed as part of the malK-lamB operon, and that its product is periplasmic. Finally, we demonstrate with nuclease S1 mapping experiments that the mRNA terminates at a typical rho-independent terminator located about 45 base-pairs beyond the end of gene malM, which is thus the last gene of the malK-lamB operon.

Amino Acid Sequence↗

PubMed1986

Transcription termination and processing sites in the bacteriophage lambda pL operon.

S1 nuclease mapping was performed on transcripts from the major leftward operon of the bacteriophage lambda in order to locate the 3' ends of stable RNA species produced in vivo. The analysis was carried out on RNA purified from either an induced lambda prophage or bacteria carrying a plasmid containing a large segment of lambda including the intact PL operon through the bet gene. The S1 nuclease mapping was performed on transcripts produced in the presence and the absence of the N antitermination function, and in the presence and the absence of either the RNase III processing enzyme or the Rho factor. The results of this work indicate that the intercistronic region between the N and ral genes of lambda contains three sites at which transcripts end under N-Rho+ conditions (positions on the lambda sequence: 34,826, 34,558 and 34,393). The distal two correspond to the two sites previously described in this region as tL1 (on both sides of the BamHI site). In the region between ral and Ea10, we mapped the 3' ends of three species of RNA. The 3' end of one species was found to be located 90 nucleotides proximal to tL2a, at 34,000 in the lambda sequence. The terminator at this site may be partially N-resistant. In an RNase III deficient host, an additional RNA species is formed. The 3' end of this RNA species is located at tL2a (33,910 on the lambda sequence). In the presence of the antitermination N gene product, the readthrough transcripts are processed to form a 3' end at position 33,980 on the lambda sequence. These results suggest that elongation of transcription of the lambda PL operon is reduced gradually by clusters of termination located between genes and that the expression of the terminated products is further controlled by processing of the mRNA.

Bacteriophage lambda↗

PubMed1987

Primary structure of the bc1 complex of Rhodopseudomonas capsulata. Nucleotide sequence of the pet operon encoding the Rieske cytochrome b, and cytochrome c1 apoproteins.

The nucleotide sequence of the pet operon of Rhodopseudomonas capsulata strain SB1003 has been determined. This operon consists of the petA, petB and petC genes, which encode the Rieske Fe-S protein, cytochrome b and cytochrome c1, respectively, all components of the ubiquinol-cytochrome c2 oxidoreductase. The deduced amino acid sequences of the pet genes show homology to the corresponding proteins from other organisms, and particularly high homologies (over 90% for amino acid and nucleotide sequences) to the previously described fbc operon from a strain previously identified as Rhodopseudomonas spheroides GA. The amino acid sequences of the pet proteins are discussed with reference to the structure and function of the ubiquinol-cytochrome c2 oxidoreductase.

Amino Acid Sequence↗

PubMed1987

Transcription termination sites at the distal end of the leu operon of Salmonella typhimurium.

Transcription terminates at two different sites at the distal end of the leucine operon of Salmonella typhimurium. The first of these sites (leut), located 140 base-pairs past the end of leuD, contains a G + C-rich palindrome followed by a run of T residues in the non-coding strand. Termination at leut, both in vitro and in vivo, is independent of rho protein, but is stimulated by the NusA protein. The second termination site (leut'), located 145 base-pairs beyond the first, is rho-dependent both in vitro and in vivo, and is not influenced by NusA protein. The organization of transcription termination sites at the distal end of the leu operon (a rho-independent site followed by a rho-dependent site) is similar to that for the trp operon of Escherichia coli.

Acetyltransferases↗

PubMed1988

Structure and regulation of controlling sequences for the Streptomyces coelicolor glycerol operon.

The pathway for glycerol catabolism in Streptomyces coelicolor is determined by the gylABX operon. The sequence of about 1500 base-pairs (bp) preceding the structural genes of the operon has been determined, and related to a detailed transcriptional analysis of this region. The gylABX operon contains two major promoters, gylP1 and gylP2, separated by 50 bp. Both promoters are glycerol-inducible and glucose-repressible. A 900-base transcription unit, gylR, is situated immediately upstream of the gylABX promoter region and contains an open reading frame for a 27,600 Mr protein. The predicted sequence of this protein contains a region that is similar to the helix-turn-helix domains of certain DNA-binding proteins. Transcription of gylR is also glycerol-inducible, but is only weakly glucose-repressible, and initiates predominantly from a single promoter, gylRp. The three promoters, gylRP, gylP1 and gylP2, each resemble the "typical" prokaryotic consensus promoter sequence. The DNA sequence of the gylR and gylABX promoter regions share some striking features. These include almost identical operator-like elements (segments of which are tandemly repeated around gylRP) and tracts of alternating purine-pyrimidine residues.

Base Sequence↗

PubMed1988

Translational regulation of the spc operon in Escherichia coli. Identification and structural analysis of the target site for S8 repressor protein.

The spc ribosomal protein operon of Escherichia coli is feedback-regulated by ribosomal protein S8, a translational repressor. We have analyzed the region of the spc mRNA that is responsible for this regulation. First, we have established that the S8 target site on the mRNA is near the translation start site of the third gene encoding ribosomal protein L5 in the operon. This was done by constructing hybrid plasmids carrying spc operon ribosomal protein genes under lac transcriptional control, as well as their deletion derivatives, and carrying out both in vivo and in vitro protein synthesis experiments. Next, the secondary structure of this region was studied by analyzing 5' end-labeled RNA synthesized from the phage SP6 promoter using structure-specific nucleases. A secondary structure model consistent with the results was deduced with the aid of a computer prediction of RNA folding. In addition, we cloned and sequenced the corresponding region from Salmonella typhimurium, Proteus vulgaris and Serratia marcescens and found five "compensating" substitutions that support some of the deduced helical structures of mRNA. None of the base changes was inconsistent with the deduced secondary structure model. Finally, site-directed mutagenesis experiments have identified bases important for regulation, including two base-paired sites representing each of two helical regions. This has led to the conclusion that some specific nucleotide residues located between these two helical regions are directly involved in S8 recognition, and that the function of the two helical regions is to maintain the proper orientation of these nucleotide residues. Comparison of the structure of the S8 target site on the spc mRNA with the known S8 binding site on rRNA has revealed a striking similarity in both primary and secondary structures. In particular, primary sequences of rRNA conserved among distantly related bacterial species in this region is found to be identical with the sequences at the corresponding positions in mRNA. These results suggest that the same structural features of the S8 repressor protein are involved in the interaction with both 16 S rRNA and the mRNA target site.

Base Sequence↗

PubMed1989

Cleavage by RNase III in the transcripts of the met Y-nus-A-infB operon of Escherichia coli releases the tRNA and initiates the decay of the downstream mRNA.

The metY gene coding for a minor form of the initiator tRNA is the first gene of a complex polycistronic operon also encoding the transcription termination factor NusA and the translation initiation factor IF2. The mixed tRNA-mRNA polycistronic transcript is cleaved by RNase III in a hairpin structure downstream from the tRNA. This cleavage separates the tRNA from the mRNA and initiates the rapid degradation of the 5' extremity of the downstream mRNA. Dissociation of the structural (tRNA) and informational (mRNA) RNAs from this operon is also achieved by independent transcription in vivo. The presence of two transcription terminators located downstream from metY produces a small tRNAMetf2 precursor transcript, whereas an internal promoter situated between metY and the first open reading frame directs the transcription of only the protein-coding part of the operon.

Bacterial Proteins↗

PubMed1990

Escherichia coli cell division inhibitor DicF-RNA of the dicB operon. Evidence for its generation in vivo by transcription termination and by RNase III and RNase E-dependent processing.

We have established that the long non-coding intercistronic region of the dicB operon of Escherichia coli expresses a trans-acting division inhibitor specified by a region dicF, at most 65 nucleotides-long. The present study deals with the processing of dicBF operon mRNA in vivo, and identifies the dicF gene product as a 53 nucleotide RNA species. A sequence at the end of DicF resembles, and behaves as, a Rho-independent terminator, but further processing of readthrough transcripts, presumably by RNase III, followed by a limited 3' to 5' degradation, appears to generate additional DicF-RNA 3' ends. For the 5' end of DicF-RNA, our results show that a 190 nucleotide precursor DicF-RNA species is formed by cleavage at an RNase III site, while the 53 nucleotide minimal DicF-RNA is generated by further processing requiring the presence of an active form of RNase E in vivo. These data indicate that an untranslated product derived from an operon RNA can have a regulatory activity by affecting cell division.

Base Sequence↗

PubMed1990

Closely spaced and divergent promoters for an aminoacyl-tRNA synthetase gene and a tRNA operon in Escherichia coli. Transcriptional and post-transcriptional regulation of gltX, valU and alaW.

The transcription of the gltX gene encoding the glutamyl-tRNA synthetase and of the adjacent valU and alaW tRNA operons of Escherichia coli K-12 has been studied. The alaW operon containing two tRNA(GGCAla) genes, is 800 base-pairs downstream from the gltX terminator and is transcribed from the same strand. The valU operon, containing three tRNA(UACVal) and one tRNA(UUULys) (the wild-type allele of supN) genes, is adjacent to gltX and is transcribed from the opposite strand. Its only promoter is upstream from the gltX promoters. The gltX gene transcript is monocistronic and its transcription initiates at three promoters, P1, P2 and P3. The transcripts from one or more of these promoters are processed by RNase E to generate two major species of gltX mRNA, which are stable and whose relative abundance varies with growth conditions. The stability of gltX mRNA decreases in an RNase E- strain and its level increases with growth rate about three times more than that of the glutamyl-tRNA synthetase. The 5' region of these mRNAs can adopt a stable secondary structure (close to the ribosome binding site) that is similar to the anticodon and part of the dihydroU stems and loops of tRNA(Glu), and which might be involved in translational regulation of GluRS synthesis. The gltX and valU promoters share the same AT-rich and bent upstream region, whose position coincides with the position of the upstream activating sequences of tRNA and rRNA promoters to which they are similar. This suggests that gltX and valU share transcriptional regulatory mechanisms.

Amino Acyl-tRNA Synthetases↗

PubMed1992

Developmental regulation of transcription of the Bacillus subtilis ftsAZ operon.

The products of the ftsA and ftsZ genes play a major role in septum formation in Escherichia coli. Their homologues have been found in various bacterial species, such as Bacillus subtilis where they are involved in septation during vegetative growth as well as during sporulation, a developmental process that is initiated by the formation of an asymmetrically positioned septum. Transcription of the B. subtilis ftsAZ operon was studied during exponential growth and sporulation by monitoring beta-galactosidase synthesis in strains harboring fusions of the E. coli lacZ gene with various fragments of the ftsAZ regulatory region. Transcription of the ftsAZ operon was found to be controlled by three promoters which were mapped by primer extension and characterized by their temporal pattern of expression. Two of these promoters, P1 and P3, are dependent on sigma A, the major vegetative sigma factor, and are expressed mainly during growth. The third one, P2, is recognized by sigma H associated RNA polymerase and its activity increases three- to four-fold around the onset of sporulation. The post-exponential enhancement of P2-driven transcription is abolished in a spo0A mutant but partially restored in an abrB spo0A double mutant. After inactivation by oligonucleotide-directed mutagenesis mutated copies of P1 and P2 were introduced into the chromosome upstream from the ftsAZ operon. Transformants could be obtained only when ftsAZ transcription was controlled by a combination of two intact promoters, neither P1, P2 nor P3 being essential for viability. The sporulation efficiency was found to be dependent on the level of transcription of ftsAZ, the absence of P2 still allowing 30% of the normal sporulation rate. Therefore the post-exponential burst of synthesis of the FtsA and FtsZ proteins is not an absolute requirement for the successful completion of the asymmetric septum.

Bacillus subtilis↗

PubMed1992

Regulation of open complex formation at the Escherichia coli galactose operon promoters. Simultaneous interaction of RNA polymerase, gal repressor and CAP/cAMP.

The regulation of open complex formation at the Escherichia coli galactose operon promoters by galactose repressor and catabolite activator protein/cyclic AMP (CAP/cAMP) was investigated in DNA-binding and kinetic experiments performed in vitro. We found that gal repressor and CAP/cAMP bind to the gal regulatory region independently, resulting in simultaneous occupancy of the two gal operators and the CAP/cAMP binding site. Both CAP/cAMP and gal repressor altered the partitioning of RNA polymerase between the two overlapping gal promoters. Open complexes formed in the absence of added regulatory proteins were partitioned between gal P1 and P2 with occupancies of 25% and 75%, respectively. CAP/cAMP caused open complexes to be formed nearly exclusively at P1 (98% occupancy). gal repressor caused a co-ordinated, but incomplete, switch in promoter partitioning from P1 to P2 in both the absence and presence of CAP/cAMP. We measured the kinetic constants governing open complex formation and decay at the gal promoters in the absence and presence of gal repressor and CAP/cAMP. CAP/cAMP had the largest effect on the kinetics of open complex formation, resulting in a 30-fold increase in the apparent binding constant. We conclude that the regulation of open complex formation at the gal promoters does not result from competition between gal repressor, CAP/cAMP and RNA polymerase for binding at the gal operon regulatory region, but instead results from the interactions of the three proteins during the formation of a nucleoprotein complex on the gal DNA fragment. Finally, we present a kinetic model for the regulation of open complex formation at the gal operon.

Base Sequence↗

PubMed1979

Identification of initiation sites for the in vitro transcription of rRNA operons rrnE and rrnA in E. coli.

The transcription initiation sites of E. coli rRNA operons were determined using various DNA fragments derived from transducing phage lambda metA20 carrying rrnE and from hybrid plasmid pLC19-3 carrying rrnA. In vitro transcription products were analyzed for their 5' end sequences and their oligonucleotide compositions. The results are in full agreement with the nuceotide sequences of the DNA templates described in an accompanying paper (de Boer, Gilbert and Nomura, 1979) and allow us to make the following conclusions. First, there are two transcription, start sites on each of the rRNA operons; they are 109 bp apart in the case of rrnE and 117 +/- 1 bp aprart in rrnA. Second, the first start site is 283 bp upstream from the m16S rRNA coding region in the case of rrnE, while is 291 bp upstream in rrnA. Initiation starts with ATP in both cases. Finally, the second start sites are 174 and 174 +/- 1 bp from the m16S rRNA genes in rrnE and rrnA, respectively. Initiation starts with CTP in both cases. We have also shown that in the present in vitro transcription system, guanosine tetraphosphate (ppGpp) inhibits the synthesis of full-sized RNAs from both start sites in each rRNA operon.

Base Sequence↗

PubMed1980

Insertions of Tn 10 into an E. coli ribosomal RNA operon are incompletely polar.

Insertions of the transposon Tn 10 have been obtained in an E. coli ribosomal RNA operon (rrnX). These insertions were used to determine whether present models of polarity are sufficient to explain transcriptional properties of operon which are transcribed but not translated. Most models of polarity suggest that transcription of mRNA requires simultaneous translation of nascent mRNA, or else premature termination of transcription will result. This model as stated does not encompass rrn operons. In this study three Tn 10 insertions into rrnX were characterized. All three Tn 10 insertions do not completely eliminate in vivo transcription of the most distal tRNA gene of rrnX. In ultraviolet-irradiated cells one Tn 10 insertion reduces synthesis of downstream portions of rrnX by at most 2--3 fold. Two other insertions may have more extensive polar effects, although the exact level of polarity is difficult to evaluate because these Tn 10 insertions may affect RNA maturation and stability.

DNA Transposable Elements↗

PubMed1982

A previously unidentified gene in the spc operon of Escherichia coli K12 specifies a component of the protein export machinery.

The gene prlA codes for a factor that appears to function in the export of proteins in Escherichia coli. This conclusion is based on the finding that mutations altering the prlA gene product restore export of envelope proteins with defective signal sequences. Previous results showed that the prlA gene lies in an operon (spc) known to code for ten different ribosomal proteins. Our studies show that the prlA gene lies promoter-distal to the last known ribosomal protein gene in this operon. Evidence from gene fusions constructed in vitro suggests that prlA codes for a protein containing at least 300 amino acids. Thus a heretofore unidentified protein specified by a gene within the spc operon appears to be a component of the cellular protein export machinery.

Bacterial Proteins↗

PubMed1983

Expression of rRNA and tRNA genes in Escherichia coli: evidence for feedback regulation by products of rRNA operons.

We have tested a model for global ribosome biosynthesis by examining the effects of increased gene dosage on the synthesis of rRNA. Increasing gene dosage does not lead to a significant increase in total rRNA transcription; i.e., rRNA synthesis from individual rRNA operons is reduced to keep total rRNA production unchanged. In contrast, when the plasmid-encoded rRNA operons used to increase gene dosage contain deletions within the rRNA coding region, rRNA transcription is gene-dosage-dependent; i.e., rRNA regulation is relieved. We find that the syntheses of most, if not all, tRNAs are also subject to the same controls as rRNA transcription. We conclude that the production of functional rRNA is monitored by the regulatory system that controls rRNA and tRNA transcription. We propose that rRNA and tRNA are negatively controlled by products of rRNA operons and discuss evidence suggesting that ribosomes are the key element involved in the postulated feedback regulation.

Chromosome Deletion↗

PubMed1983

Differential stringent control of the tandem E. coli ribosomal RNA promoters from the rrnA operon expressed in vivo in multicopy plasmids.

The tandem P1, P2 promoter region of the rrnA ribosomal operon has been fused to the t1, t2 terminator region of the rrnB operon in pBR322 plasmid derivatives. This deletes most internal RNA structural elements ordinarily processed out of ribosomal operon transcripts. In vivo as well as in vitro transcripts arising from both promoters terminate predominantly in the t1 terminator region about 40 base pairs beyond the mature rrnB 5S RNA gene. Stringent control of the P1 and P2 promoted transcripts has been assessed in vivo. In these plasmid fusions, the upstream (P1) promoter activity was subject to stringent control, while the downstream (P2) promoter activity was inhibited by amino acid starvation in both stringent and relaxed hosts. A plasmid with an additional deletion of the P2 region also showed stringent regulation of the P1 promoter.

Amino Acids↗