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BackgroundAs single-celled organisms, bacteria are very much at the mercy of their environment. They are frequently challenged with antimicrobial chemicals, host-defences and fluctuations in nutrient-availability, temperature, pH, osmolarity and redox.Transcriptional regulationTo survive and thrive in these circumstances a bacterial cell must rapidly adapt and react to prevailing conditions. To do this, bacteria frequently achieve this by differentially regulating the transcription of sets of genes. The classic model of transcriptional regulation in bacteria involves transcription factors (activators and/or repressors) that bind adjacent to the RNA polymerase (RNAP) binding site and thereby modulate transcriptional activity.Enhancer-dependent transcriptionBut there is an alternative mechanism: enhancer-dependent transcription. In this system RNAP interacts with an enhancer-binding protein , which is bound far upstream of the RNAP-binding site. involves a special form of RNAP that contains the sigma54 subunit rather than sigma70. The sigma54-containing RNAP shares several features in common with eukaryotic RNAPII. Sigma54 is also known as sigmaN, NtrA, and GlnF.Key questionsThis enhancer-dependent transcription system represents a sophisticated regulatory device. But it goes against the grain of how bacteria like to do things: it requires large intergenic spacer regions. Bacteria generally tend towards very compact genomes with little 'spacer' DNA. Therefore it is of interest to study how many genes are regulated in this way, what sorts of genes are regulated in this way, and why?Enhancer-dependent promoter DNA sequencesGenes that are regulated by enhancer-dependent transcription are preceded by a characteristic sequence motif . This sequence motif represents the binding site for sigma54-RNAP.The PromScan programThe original aim of the PromScan program was to scan DNA sequences for potential sigma54-RNAP-binding sites. However, it can be used to scan for any ungapped DNA sequence motif. All you need is an alignment of known sequences that is used to make a frequency matrix that can be plugged into PromScan. Click here for more information.The PromScan databaseAs new complete genome sequences become available, I scan the sequences for potential sigma54-RNAP-binding sites (promoters) and present these data here.Distribution and occurrence of enhancer-dependent transcription in bacteriaGenes encoding sigma54 and enhancer-binding proteins (EBPs) are found in a diverse range of bacteria. |
