An overview of prokaryotic transcription factors : a summary of function and occurrence in bacterial genomes

Transcriptional initiation is arguably the most important control point for gene expression. It is regulated by a combination of factors, including DNA sequence and its three-dimensional topology, proteins and small molecules. In this chapter, we focus on the trans-acting factors of bacterial regulation. Initiation begins with the recruitment of the RNA polymerase holoenzyme to a specific locus upstream of the gene known as its promoter. The sigma factor, which is a component of the holoenzyme, provides the most fundamental mechanisms for orchestrating broad changes in gene expression state. It is responsible for promoter recognition as well as recruiting the holoenzyme to the promoter. Distinct sigma factors compete with for binding to a common pool of RNA polymerases, thus achieving condition-dependent differential expression. Another important class of bacterial regulators is transcription factors, which activate or repress transcription of target genes typically in response to an environmental or cellular trigger. These factors may be global or local depending on the number of genes and range of cellular functions that they target. The activities of both global and local transcription factors may be regulated either at a post-transcriptional level via signal-sensing protein domains or at the level of their own expression. In addition to modulating polymerase recruitment to promoters, several global factors are considered as "nucleoid-associated proteins" that impose structural constraints on the chromosome by altering the conformation of the bound DNA, thus influencing other processes involving DNA such as replication and recombination. This chapter concludes with a discussion of how regulatory interactions between transcription factors and their target genes can be represented as a network.