ABSTRACT
Although the enzymes for dissimilatory sulfate reduction by microbes have been studied, the mechanisms for transcriptional regulation of the encoding genes remain unknown. In a number of bacteria the transcriptional regulator Rex has been shown to play a key role as a repressor of genes producing proteins involved in energy conversion. In the model sulfate-reducing microbe Desulfovibrio vulgaris Hildenborough, the gene DVU_0916 was observed to resemble other known Rex proteins. Therefore, the DVU_0916 protein has been predicted to be a transcriptional repressor of genes encoding proteins that function in the process of sulfate reduction in D. vulgaris Hildenborough. Examination of the deduced DVU_0916 protein identified two domains, one a winged helix DNA-binding domain common for transcription factors, and the other a Rossman fold that could potentially interact with pyridine nucleotides. A deletion of the putative rex gene was made in D. vulgaris Hildenborough, and transcript expression studies of sat, encoding sulfate adenylyl transferase, showed increased levels in the D. vulgaris Hildenborough Rex (RexDvH) mutant relative to the parental strain. The RexDvH-binding site upstream of sat was identified, confirming RexDvH to be a repressor of sat. We established in vitro that the presence of elevated NADH disrupted the interaction between RexDvH and DNA. Examination of the 5' transcriptional start site for the sat mRNA revealed two unique start sites, one for respiring cells that correlated with the RexDvH-binding site and a second for fermenting cells. Collectively, these data support the role of RexDvH as a transcription repressor for sat that senses the redox status of the cell.
Subject(s)
Bacterial Proteins/metabolism , Desulfovibrio vulgaris/metabolism , Gene Expression Regulation, Enzymologic/physiology , NAD/metabolism , Sulfate Adenylyltransferase/metabolism , Bacterial Proteins/genetics , Base Sequence , Binding Sites , Desulfovibrio vulgaris/genetics , Gene Deletion , Gene Expression Regulation, Bacterial/physiology , Sulfate Adenylyltransferase/antagonists & inhibitors , Sulfate Adenylyltransferase/geneticsABSTRACT
We searched for new members of the TnrA and GlnR regulons controlling assimilation of nitrogen in gram-positive bacteria. We identified the regulatory signals for these transcription factors with consensuses ATGTNAWWWWWWWTNACAT for GlnR and TGTNAWWWWWWWTNACA for TnrA. We described the structure and found new potential members for the TnrA/GlnR regulons in Bacillus subtilis, B. licheniformis, Geobacillus kaustophilus, Oceanobacillus iheyensis, for the TnrA regulon in B. halodurans and for the GlnR regulons in Lactococcus lactis, Lactobacillus plantarum, Streptococcus pyogenes, S. pneumoniae, S. mutans, S. agalactiae, Enterococcus faecalis, Listeria monocytogenes, Staphylococcus aureus and St. epidermidis.
Subject(s)
Gene Expression Regulation, Bacterial , Gram-Positive Bacteria/metabolism , Nitrogen/metabolism , Amino Acid Sequence , Bacillus subtilis/genetics , Bacillus subtilis/metabolism , Bacterial Proteins/genetics , Bacterial Proteins/metabolism , DNA-Binding Proteins/genetics , DNA-Binding Proteins/metabolism , Genome, Bacterial , Gram-Positive Bacteria/genetics , Molecular Sequence Data , Operon/genetics , Regulon/genetics , Signal Transduction , Trans-Activators/genetics , Trans-Activators/metabolismABSTRACT
In Bacillus subtilis, utilisation of xylose, arabinose and ribose is controlled by the transcriptional factors XylR, AraR and RbsR, respectively. Here we apply the comparative approach to the analysis of these regulons in the Bacillus/Clostridium group. Evolutionary variability of operon structures is demonstrated and operator sites for the main transcription factors are predicted. The consensus sequences for the XylR and RbsR binding sites vary in different subgroups of genomes. The functional coupling of gene clusters and the conservation of regulatory sites allow for detection of non-orthologous gene displacement of ribulose kinase in Enterococcus faecium and Clostridium acetobutylicum. Moreover, candidate catabolite responsive elements found upstream of most pentose-utilising genes suggest CcpA-mediated catabolite repression.
Subject(s)
Bacillus/genetics , Bacterial Proteins , Clostridium/genetics , Genes, Bacterial , Pentoses/metabolism , AraC Transcription Factor , Bacillus/classification , Bacillus/metabolism , Binding Sites , Clostridium/metabolism , DNA-Binding Proteins/genetics , Genes, Regulator , Operon , Phylogeny , Repressor Proteins/genetics , Transcription Factors/genetics , Transcription, GeneticABSTRACT
Comparative approach is a powerful tool for analysis of gene regulation in bacterial genomes. Here we apply it to analysis of regulation of the multidrug resistance transport (MDRT) systems in enterobacteria Escherichia coli, Salmonella typhi, Klebsiella pneumoniae and Yersinia pestis. Comparison of nucleotide sequences upstream of MDRT genes was performed in order to predict new regulatory sites (operators) and identify candidate regulons. Since the regulatory sites diverge slower than the non-coding regions in general, they are visible as strongly conserved islands. This analysis resulted in description of a regulatory network for known and hypothetical MDRT systems and porins. New candidate members of the MarA regulon were detected. Putative binding sites for EmrR and AcrR were suggested. A new hypothetical MarX regulon was described that includes some multidrug transporters and porins.
Subject(s)
Drug Resistance, Microbial , Drug Resistance, Multiple , Escherichia coli Proteins , Gammaproteobacteria/genetics , Gene Expression Regulation, Bacterial , Genome, Bacterial , Bacterial Proteins/genetics , Base Sequence , Conserved Sequence , DNA-Binding Proteins/genetics , Escherichia coli/genetics , Gammaproteobacteria/drug effects , Genetic Variation , Klebsiella pneumoniae/genetics , Molecular Sequence Data , Regulon , Repressor Proteins/genetics , Salmonella typhi/genetics , Sequence Alignment , Sequence Homology, Nucleic Acid , Trans-Activators/genetics , Yersinia pestis/geneticsABSTRACT
Comparative approach to computer analysis of regulatory signals allows one to predict new signals in bacterial genomes with high accuracy. A prediction is reliable whenever candidate signals are consistently observed in several related genomes. We applied comparative approach to the analysis of the Fnr regulon of gamma-proteobacteria. Responding to changes in the aerobic/anaerobic state of the medium, the transcriptional factor Fnr regulates expression of many genes. We predicted Fnr binding-sites in 12 genes regulated by Fnr, and identified 17 new operons as potential members of the Fnr regulon of Escherichia coli. In addition, we described the Fnr regulon of other gamma-proteobacteria.
Subject(s)
Bacterial Proteins/metabolism , Computers , Escherichia coli Proteins , Genome, Bacterial , Iron-Sulfur Proteins/metabolism , Regulatory Sequences, Nucleic Acid , Transcription Factors/metabolism , Bacterial Proteins/genetics , Binding Sites , Escherichia coli/genetics , Iron-Sulfur Proteins/genetics , Operon , Transcription Factors/geneticsABSTRACT
The comparative approach is a powerful tool for the analysis of gene regulation in bacterial genomes. It can be applied to the analysis of regulons that have been studied experimentally as well as that of regulons for which no known regulatory sites are available. It is assumed that the set of co-regulated genes and the regulatory signal itself are conserved in related genomes. Here, we use genomic comparisons to study the regulation of transport and utilization systems for sugar acids in gamma purple bacteria Escherichia coli, Salmonella typhi, Klebsiella pneumoniae, Yersinia pestis, Erwinia chrysanthemi, Haemophilus influenzae and Vibrio cholerae. The variability of the operon structure and the location of the operator sites for the main transcription factors are demonstrated. The common metabolic map is combined with known and predicted regulatory interactions. It includes all known and predicted members of the GntR, UxuR/ExuR, KdgR, UidR and IdnR regulons. Moreover, most members of these regulons seem to be under catabolite repression mediated by CRP. The candidate UxuR/ExuR signal is proposed, the KdgR consensus is extended, and new operators for all transcription factors are identified in all studied genomes. Two new members of the KdgR regulon, a hypothetical ATP-dependent transport system OgtABCD and YjgK protein with unknown function, are detected. The former is likely to be the transport system for the products of pectin degradation, oligogalacturonides.