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PubMed1991

A DNA sequence upstream of the puf operon of Rhodobacter capsulatus is involved in its oxygen-dependent regulation and functions as a protein binding site.

The transcription of the polycistronic puf operon which encodes pigment binding proteins of the reaction center and light-harvesting complex I of Rhodobacter capsulatus is regulated by the oxygen tension in the culture. A DNA sequence upstream of the puf transcriptional start was identified as a protein binding site. A DNA fragment carrying this DNA sequence participated in the formation of two DNA-protein complexes. The relative amounts of the two complexes were dependent on the oxygen tension in cultures from which the cytosolic fraction used for the in vitro binding studies was isolated. A single base pair transition within the protein binding site affected the oxygen-dependent expression of puf in vivo and the formation of DNA-protein complexes in vitro. The data suggest that the formation of specific DNA-protein complexes is involved in the oxygen-dependent regulation of the puf promoter. A DNA fragment containing the promoter region of the puc operon that encodes proteins of the light-harvesting complex II acted as a competitor for the formation of the DNA-protein complexes with the puf-specific fragment, indicating coregulation of the two operons.

Bacterial Proteins↗

PubMed1994

Amplification of the groESL operon in Pseudomonas putida increases siderophore gene promoter activity.

Pseudobactin 358 is the yellow-green fluorescent siderophore [microbial iron(III) transport agent] produced by Pseudomonas putida WCS358 under iron-limiting conditions. The genes encoding pseudobactin 358 biosynthesis are iron-regulated at the level of transcription. In this study, the molecular characterization is reported of a cosmid clone of WCS358 DNA that can stimulate, in an iron-dependent manner, the activity of a WCS358 siderophore gene promoter in the heterologous Pseudomonas strain A225. The functional region in the clone was identified by subcloning, transposon mutagenesis and DNA sequencing as the groESL operon of strain WCS358. This increase in promoter activity was not observed when the groESL genes of strain WCS358 were integrated via a transposon vector into the genome of Pseudomonas A225, indicating that multiple copies of the operon are necessary for the increase in siderophore gene promoter activity. Amplification of the Escherichia coli and WCS358 groESL genes also increased iron-regulated promoter activity in the parent strain WCS358. The groESL operon codes for the chaperone proteins GroES and GroEL, which are responsible for mediating the folding and assembly of many proteins.

Amino Acid Sequence↗

PubMed1991

Intercistronic group III introns in polycistronic ribosomal protein operons of chloroplasts.

A novel ribosomal protein operon in the Euglena gracilis chloroplast genome was characterized. It encodes the genes for ribosomal proteins S4 and S11 (rps4 and rps11). The coding region of the rps11 gene is interrupted by two introns of 107 and 100 bp. The introns belong to a distinct class known as group III introns. The major transcript from this operon was characterized as a fully spliced dicistronic rps4-rps11 mRNA by RNA blot analysis, primer extension sequencing, and cDNA cloning and sequencing. An additional 95 nucleotide (nt) group III intron was identified in the 123 nt rps4-rps11 intercistronic region. The identification of the intercistronic intron between the rps4 and rps11 genes was unexpected. Other RNA transcripts from regions of the genome that could potentially contain intercistronic introns were re-examined and two other intercistronic, group III introns were found. These are located in a large ribosomal protein operon between the genes for the ribosomal proteins L23 and L2, and between L14 and L5. There are at least 50 group III introns in the E. gracilis chloroplast genome. All but 6 are found in genes encoding protein components of the transcriptional and translational apparatus. The distribution of group III introns and the unusual location of intercistronic group III introns may reflect some aspect of gene expression, or provide some insight into the mechanism of their splicing.

Amino Acid Sequence↗

PubMed1995

Detection and characterization of the African citrus greening liberobacter by amplification, cloning, and sequencing of the rplKAJL-rpoBC operon.

Greening disease of citrus is caused by a phloem-restricted, uncultured bacterium, recently characterized and named Liberobacter. As shown previously, a probe encoding ribosomal protein genes (rplKAJL-rpoBC operon) from an Asian liberobacter could detect all Asian liberobacter strains tested, but not African strains. Using the sequence of the rplKAJL-rpoBC operon of the Asian liberobacter strain from Poona (India), we have defined primers for PCR amplification of the equivalent genes of an African liberobacter strain. The amplified fragment was cloned in pUC18 and successfully used as a probe to detect African liberobacter strains by Southern and dot hybridizations. Sequence comparisons of the African and Asian liberobacter operons indicate that they represent two different species in the proposed genus Liberobacter.

Base Sequence↗

PubMed1982

The structural gene (trmD) for the tRNA(m1G)methyltransferase is part of a four polypeptide operon in Escherichia coli K-12.

The trmD gene, which is the structural gene for the tRNA(m1G)-methyltransferase, is shown to be part of a polycistronic operon. A 4.6 kb SalI-EcoRI chromosomal DNA fragment contains the trmD gene (Byström and Björk 1982). Subclonings, deletion mapping and Tn5 insertions into plasmid pBY03 have established the gene organization of the trmD area on the Escherichia coli chromosome. The different plasmid derivatives were analysed for expression of protein products using the minicell system. Such analyses established the organisation of genes encoding six polypeptides to be SalI1-48 K-13 K-25 K-31 K-15 K-16 K-EcoRI1. The 31 K polypeptide was shown to be the tRNA(m1G)methyltransferase. The trmD operon encodes for four polypeptides; 13 K-25 K-31 K(trmD)-15 K and the direction of transcription is from 13 K (promoter proximal) to 15 K (promoter distal). However, there might be a weak internal promoter between the trmD gene and the gene encoding the 15 K product. The level of expression from this operon in the minicell system does not seem to follow normal polarity since we observed high expression of 13 K, 25 K, and 15 K products but low expression of the internal trmD gene.

Chromosome Deletion↗

PubMed1985

Characterization of the 3' end of the leucine operon of Salmonella typhimurium.

The nucleotide sequence of the leuD gene of Salmonella typhimurium and of the downstream flanking region are presented. S1 mapping experiments identified 3' endpoints of leu mRNA 140 and 285 nucleotides downstream of the UAA stop codon of leuD mRNA. Experiments employing pulse-labeled RNA suggest that these endpoints result from transcription termination rather than RNA processing. Our results indicate that the organization of the 3' non-translated region of the leu operon from S. typhimurium resembles that of the trp operon of Escherichia coli. Further, our results suggest that the leu operon of S. typhimurium does not contain structural genes other than those identified by genetic experiments, i.e. leu, A,B,C and D.

Amino Acid Sequence↗

PubMed1989

Characterization of the str operon genes from Spirulina platensis and their evolutionary relationship to those of other prokaryotes.

A 5.3 kb DNA segment containing the str operon (ca. 4.5 kb) of the cyanobacterium Spirulina platensis has been sequenced. The str operon includes the structural genes rpsL (ribosomal protein S12), rpsG (ribosomal protein S7), fus (translation elongation factor EF-G) and tuf (translation elongation factor EF-Tu). From the nucleotide sequence of this operon, the primary structures of the four gene products have been derived and compared with the available corresponding structures from eubacteria, archaebacteria and chloroplasts. Extensive homologies were found in almost all cases and in the order S12 greater than EF-Tu greater than EF-G greater than S7; the largest homologies were generally found between the cyanobacterial proteins and the corresponding chloroplast gene products. Overall codon usage in S. platensis was found to be rather unbiased.

Amino Acid Sequence↗

PubMed1987

The xylS gene positive regulator of TOL plasmid pWWO: identification, sequence analysis and overproduction leading to constitutive expression of meta cleavage operon.

The Pseudomonas putida TOL plasmid pWWO carries an operon that specifies a meta-cleavage pathway for the catabolism of benzoate and toluates whose transcription is positively regulated by the xylS gene product. Stimulation of transcription of the operon is thought to result from activation of this protein by pathway substrates/effectors. In the present study, overexpression of the xylS gene has led to identification of the regulator as a 33 kDa protein. Overexpression of xylS also resulted in partially constitutive, i.e. effector-independent expression of the meta-cleavage operon. Determination of the polynucleotide sequence of the xylS gene revealed amino acid sequence homology with several DNA binding proteins, particularly with the araC products of Escherichia coli and Salmonella typhimurium and with the nifA and ntrC products of Klebsiella pneumoniae. Homologous sequences were mainly located in an alpha-helix-turn-alpha-helix domain of the polypeptide. Interestingly, amino acid sequence homology was also found with sigma factors of E. coli (ntrA and htpR products) and Bacillus subtilis (spoIIG and phage SPOI Gp34 products) and other RNA polymerase core-interacting proteins, such as the E. coli nusA product.

Amino Acid Sequence↗

PubMed1985

Molecular characterisation of the colicin E2 operon and identification of its products.

The DNA sequence of the entire colicin E2 operon was determined. The operon comprises the colicin activity gene, ceaB, the colicin immunity gene, ceiB, and the lysis gene, celB, which is essential for colicin release from producing cells. A potential LexA binding site is located immediately upstream from ceaB, and a rho-independent terminator structure is located immediately downstream from celB. A comparison of the predicted amino acid sequences of colicin E2 and cloacin DF13 revealed extensive stretches of homology. These colicins have different modes of action and recognise different cell surface receptors; the two major regions of heterology at the carboxy terminus, and in the carboxy-terminal end of the central region probably correspond to the catalytic and receptor-recognition domains, respectively. Sequence homologies between colicins E2, A and E1 were less striking, and the colicin E2 immunity protein was not found to share extensive homology with the colicin E3 or cloacin DF13 immunity proteins. The lysis proteins of the ColE2, ColE1 and CloDF13 plasmids are almost identical except in the aminoterminal regions, which themselves have overall similarity with lipoprotein signal peptides. Processing of the ColE2 prolysis protein to the mature form was prevented by globomycin, a specific inhibitor of the lipoprotein signal peptidase. The mature ColE2 lysis protein was located in the cell envelope. The results are discussed in terms of the functional organisation of the colicin operons and the colicin proteins, and the way in which colicins are released from producing cells.

Amino Acid Sequence↗

PubMed1978

New regulatory mutations affecting the expression of the threonine operon in Escherichia coli K-12.

The promoter of the threonine operon was joined to the structural genes of the lac operon in Escherichia coli K 12. The synthesis of beta-galactosidase was thus repressed by threonine plus isoleucine in the fusion strains. To isolate mutations which affect the expression of the threonine operon, alterations in the level of expression of the lacZ gene were selected. A new type of regulatory mutation was discovered.

Escherichia coli↗

PubMed1978

Fine structure analysis of the threonine operon in Escherichia coli K-12.

A fine structure analysis of the threonine operon in Escherichia coli K-12 was performed by deletion mapping. Lambda transducing bacteriophages carrying various parts of the threonine operon were isolated from strains in which the lacZ gene was fused to a thr gene. We tested for recombination between deletions of the threonine promotor extending into the threonine operon, carried by the phage, and bacterial thr auxotrophs. The relative order of thrO (operator) mutations was established. We propose that an operator region is located between a promoter region and the structural genes. Mutations leading to the desensitization of the aspartokinase I-homoserine dehydrogenase I towards threonine were localized in two different regions of the thrA gene.

Aspartokinase Homoserine Dehydrogenase↗

PubMed1983

Selective inhibition of transcription of the E. coli tufB operon by guanosine-5'-diphosphate-3'-diphosphate.

We have studied the effect of guanosine-5'-diphosphate-3'-diphosphate (ppGpp) on the transcription of the E. coli tufB and recA operons in a cell-free system containing of purified RNA polymerase holoenzyme. The transcription of the tufB operon which is under stringent control, was markedly inhibited by 0.5 mM ppGpp, and the extent of this inhibition was found to be greatly influenced by the Mg2+ and K+ concentrations in the reaction mixture. Maximal inhibition was obtained in the presence of 2 mM Mg2+ and 80-120 mM K+, whereas at higher concentrations of Mg2+ or lower concentrations of K+, practically no inhibition was observed. In contrast, transcription of the recA operon which is not subject to stringent control, was little affected by ppGpp at any of Mg2+ and K+ concentrations tested. The nucleotide inhibited initiation of transcription of tufB, while the rate of RNA chain elongation was not greatly inhibited in the presence of ppGpp.

Bacterial Proteins↗

PubMed1976

Supra-operonic clustering of genes specifying glucose dissimilation in Pseudomonas putida.

The linkage arrangements of genes governing glucolysis in Pseudomonas putida have been determined by transductional analysis. Five genes (gdh, kgtA, kgtB, edd and eda), comprising at least three operons, are contransducible with each other, but not with ggu (glucose and gluconate uptake) nor with genes of a known supra-operonic cluster of genes specifying enzymes of other dissimilatory pathways, nor with a biochemically uncharacterized his marker. It thus appears that P. putida may have more than one chromosomal region in which genes with dissimilatory function are clustered in a supro-operonic fashion.

Gene Frequency↗

PubMed1981

Internal promoters of the rpoBC operon of Escherichia coli.

Four ribosomal protein genes, rplA, rplJ, rplK and rplL form an operon in E. coli together with the genes rpoB and rpoC which encode the beta and beta' subunits of RNA polymerase. Transcription is initiated principally at two promoters, PL11 and Pl, the overall structure of the operon being (in the direction of transcription) PL11 rplK rplA Pl rplJ rplL rpoB rpoC. Here we describe studies of phage lambda derivatives carrying various segments of this operon, which demonstrate the existence of at least three additional weak internal promoters, and help to define their positions and strengths.

Bacteriophage lambda↗

PubMed1991

rps10, unreported for plastid DNAs, is located on the cyanelle genome of Cyanophora paradoxa and is cotranscribed with the str operon genes.

rps10, encoding the plastid ribosomal protein S10, is a nuclear gene in higher plants and green algae, and is missing from the large ribosomal protein gene cluster of chlorophyll b-type plastids that contains components of the prokaryotic S10, spc and alpha operons. The cyanelle genome of Cyanophora paradoxa is shown to harbor rps10 as another specific feature of its organization. However, this novel plastid gene is not contiguous with the genes of the "S10" operon, but is adjacent to, and cotranscribed with, the str operon, a trait also found in archaebacteria.

Amino Acid Sequence↗

PubMed1994

Gene structure and expression of a novel Euglena gracilis chloroplast operon encoding cytochrome b6 and the beta and epsilon subunits of the H(+)-ATP synthase complex.

The genes encoding cytochrome b6 of the chloroplast cytochrome b6/f complex (petB) and the ATP synthase CF1-beta subunit (atpB) and epsilon-subunit (atpE) were identified on the EcoD fragment of the Euglena gracilis chloroplast genome. The complete nucleotide sequence of these three genes was determined. The petB-atpB-atpE genes are cotranscribed as a tricistronic operon. This gene organization differs from that of land plants in which atpB-atpE form a discistronic operon, and petB is within the psbB-ycf8-psbH-petB-petD operon. Euglena cytochrome b6 and the beta-subunit of the chloroplast ATP synthase are very similar in derived amino acid sequence to the corresponding gene products from other organisms. The epsilon-subunit of the chloroplast ATP synthase complex is more divergent. In Euglena, the petB-atpB-atpE genes contain introns, including two twintrons, at eight different positions. All of the intron positions were confirmed by analysis of cDNAs. Two independent intercistronic RNA processing events and 11 splicing reactions lead to the accumulation of the mature petB, atpB and atpE monocistronic mRNAs.

Amino Acid Sequence↗

PubMed1976

The site for catabolite deactivation in the L-arabinose BAD operon in Escherichia coli B/r.

A series of deletions beginning in the leu operon and continuing into the araC gene and also into the ara controlling site region were analyzed in reciprocal merodiploids, e.g., F' A2Cc67/B24delta719, F' B24delta719/A2Cc67, for their effects on catabolite deactivation (CD). The results of these experiments are consistent with placing the catabolite gene activator-cyclic AMP sensitive site in the controlling site region between araB and araO. With a deletion mutant, delta1109, that places araBAD under leu control when transcription begins at leuP, the araBAD operon is immune to CD even though araCGA, araP and araI are intact and functional. To focus attention on the fine structure and related functions of this region we propose that the three proteins that function therein have separate sites of action: araI (initiator-site for activator), araP (promoter-site for RNA polymerase) and ara(CGA) (catabolite gene activator-site for CGA-cAMP). None of the eighteen initiator constitutive mutants (Ic) tested have any significant effect on catabolite derepression or on the maximal level of expression of the operon supporting the view that the araI site may be distinct from araP and ARA(CGA). A series of constitutive mutants in the araC gene (Cc) also have no pronounced effect on catabolite deactivation.

Arabinose↗

PubMed1987

Regulation of the ban gene containing operon of prophage P1.

A physical map of the ban gene of P1 and sites relevant to its regulation has been deduced from cloning of the appropriate regions of P1 wild-type and of P1 ban regulatory mutants. The cloning required the presence of P1 repressor in the cell confirming the existence of a repressible ban operon (Austin et al. 1978). Evidence for additional member(s) of that operon is presented. Of particular interest for understanding the regulation of ban are the relative positions of a binding site for the P1 repressor and of the regulatory mutations bac and crr that render ban expression constitutive. The results reveal a repressible operon-like structure of about 4 kb within the P1 EcoRI-3 fragment that comprises a c1 repressor binding site/bac - additional gene(s) - crr/ban in the clockwise direction of the circular map of P1.

Bacterial Proteins↗