This review will focus on mechanisms specific to group 1 σ-containing holoenzymes. Expression of σ factors can be regulated based on environmental conditions either at the gene or protein level ( 13, 17), resulting in temporal concentration changes and permitting competition in binding of RNAP core to form σ-specific holoenzymes ( 18, – 21). ![]() In the case of group 4, these stress signals are often generated outside the cell, leading to their designation of extracytoplasmic function (ECF) σ factors ( 14, – 16). Group 1 includes the essential housekeeping σ factor (σ 70) and contains all four structural domains group 2 includes σ 38 (σ S) which lacks σ 1.1 and plays important roles in stress responses and survival but can also transcribe housekeeping genes ( 10, – 13) group 3 (usually containing σ 2, σ 3, σ 4) and group 4 (containing only σ 2 and σ 4) generally transcribe smaller sets of genes in response to specific stresses. Within the σ 70 family, a further group classification is made based on the presence or absence of four structural domains (σ 1.1, σ 2, σ 3, and σ 4) ( 8, 9). This review focuses on mechanisms specific to Escherichia coli σ 70 ( 6) those of σ 54 are distinct and require ATP-dependent remodeling by bacterial enhancer-binding proteins ( 7). Bacterial σ factors are classified into two families based on homology, called σ 70 and σ 54 ( 5). ![]() For RNAP to initiate promoter specific transcription, it must first assemble with a σ factor to form RNAP holoenzyme ( 3, 4). The bacterial RNA polymerase (RNAP) core enzyme, composed of β, β′, and ω subunits, along with an α dimer subunit, represents the catalytic machinery responsible for DNA-templated RNA synthesis ( 1, 2). Finally, we describe how individual transcription factors take advantage of the broad distribution of sequence-dependent basal kinetics to either increase or decrease RNA flux. Instead, the entire series of linked, sequence-dependent structural transitions must be considered holistically. By calculating the steady-state flux of RNA production as a function of these effects, we illustrate that the presence/absence of a consensus promoter motif cannot be used in isolation to make conclusions regarding promoter strength. In this review, we aim to provide the required background to understand how promoter sequence motifs may affect initiation kinetics during promoter recognition and binding, subsequent conformational changes which lead to DNA opening around the transcription start site, and promoter escape. The time required to complete the initiation phase can vary by orders of magnitude and is ultimately dictated by the DNA sequence of the promoter. The initiation phase encompasses the binding of RNA polymerase (RNAP) to promoter DNA and a series of coupled protein-DNA conformational changes prior to entry into processive elongation. Kinetic regulation of transcription initiation is a key step in modulating the levels of transcribed genes to promote bacterial survival. ![]() The fitness of an individual bacterial cell is highly dependent upon the temporal tuning of gene expression levels when subjected to different environmental cues.
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