Abstract
Here we review recent findings and offer a perspective on how the major variant RNA polymerase of bacteria, which contains the sigma54 factor, functions for regulated gene expression. We consider what gaps exist in our understanding of its genetic, biochemical and biophysical functioning and how they might be addressed.
Highlights
Along with the recognition that bacterial RNA polymerases were heterogeneous with respect to their sigma factor content, came the finding that two classes of sigma factor existed in many different types of bacteria [1]
For example in the presence of sigma54 is the core enzyme in a catalytically competent state, and can smFRET data be reconciled with RNAP clamp opening and clamp closing, and the processive closed state of the core enzyme? Do the sigma54 and its activators take the RNAP
Genomics methods and RNAseq studies will no doubt offer us perspectives on why have sigma54 at all-is it a relic of a transcription repression mechanism, can it evolve in some cases to activator independence, and does it have repressive functionality alongside its gene activation responsiveness? Currently ChipSeq and RNAseq work with sigma54 and its holoenzyme to define its regulon suggests complexity in the roles of sigma54 [28,29]
Summary
Along with the recognition that bacterial RNA polymerases were heterogeneous with respect to their sigma factor content, came the finding that two classes of sigma factor existed in many different types of bacteria [1]. Unlike the major sigma class, the sigma class of factor was distinctive in being enhancer dependent and relying on a specialised class of transcription activator which used ATP binding and hydrolysis to catalyse the formation of open promoter complexes (RPO). Because the sigma factor controls important bacterial stress response genes in pathogenicity and in agriculture [5,6,7,8,9], there is considerable interest. What are the advantages the system may have over conventional repression and activation systems used by the sigma class of RNA polymerase holoenzymes?
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