Local and global regulation of transcription initiation in bacteria

Key Points Transcription initiation involves the interaction of DNA-dependent RNA polymerase with promoters. In bacteria, this is a highly regulated process. Many regulators interact directly with the bacterial DNA-dependent RNA polymerase, whereas other regulators interact directly with promoters. Regulation of transcription initiation occurs in the context of folding and compaction of bacterial chromosomes. A very wide range of different strategies are used to regulate transcription initiation in bacteria and these differ between species. In this Review, Browning and Busby describe the advances that have been made in recent years in understanding the molecular details of how transcription initiation is regulated to fine tune gene expression, highlighting factors that relate both to the RNA polymerase and to the promoter. Gene expression in bacteria relies on promoter recognition by the DNA-dependent RNA polymerase and subsequent transcription initiation. Bacterial cells are able to tune their transcriptional programmes to changing environments, through numerous mechanisms that regulate the activity of RNA polymerase, or change the set of promoters to which the RNA polymerase can bind. In this Review, we outline our current understanding of the different factors that direct the regulation of transcription initiation in bacteria, whether by interacting with promoters, with RNA polymerase or with both, and we discuss the diverse molecular mechanisms that are used by these factors to regulate gene expression.