Sigma Factors R.R. Burgess, in Encyclopedia of Genetics, 2001 History Sigma factors are subunits of all bacterial RNA polymerases. They are responsible for determining the specificity of promoter DNA binding and control how efficiently RNA synthesis (transcription) is initiated. The first sigma factor discovered was the sigma70 (σ70) of the highly studied bacterium Escherichia coli. Its discovery in 1968 was an unexpected outcome of attempts to understand the subunit structure of RNA polymerase. It was found that RNA polymerase activity was associated with two protein species. A core polymerase (with subunit structure α2ββ′) can transcribe DNA into RNA inefficiently and nonspecifically. When the sigma subunit, σ 70, is added, it can bind to core forming a holoenzyme (α2ββ′σ) that is capable of specific engagement with duplex DNA at the beginning of genes (promoters) as well as efficient initiation of transcription. It was hypothesized that multiple sigma factors would be found in E. coli, each capable of directing the core polymerase to transcribe a specific set of genes. In this way, by regulating the level of each active sigma factor, the cell could coordinately regulate groups of genes with common functions. During the last 25 years, multiple sigma factors have indeed been found. The seven sigma factors of E. coli are listed in Table 1 along with their gene names, molecular weights, consensus promoter DNA binding sites, and classes of genes they regulate. Sigma factors have also been discovered that are encoded by bacteriophage. By binding to core polymerase these proteins cause preferential transcription of phage genes. In the sporulating bacterium Bacillus subtilis, ten sigma factors have been discovered and characterized. These proteins not only regulate classes of genes during vegetative growth, but also orchestrate the development of the spore, in response to nutrient starvation. E. coli σ 70 was essentially the first positive transcription activation factor whose basic mode of action was understood. The concept that groups of genes could be coordinately regulated by transcription initiation factors spurred successful searches for numerous transcription factors in both bacteria and higher organisms.

Table 1. The seven sigma factors of Escherichia coli

Number of amino Size Factora Gene Consensus binding siteb Genes regulated acid residues (kDa)

70 D σ (σ ) rpoD 613 70 TTGACA–N17–TATAAT Housekeeping Number of amino Size Factora Gene Consensus binding siteb Genes regulated acid residues (kDa)

rpoN Nitrogen σ54 (σN) 477 54 CTGGCAC–N –TTGCA (ntrA) 5 metabolism

rpoS TTGACA–N – σS 362 38 12 Stationary phase (katF) TGTGCTATACT

rpoH CTTGAA–N – σ32 (σH) 284 32 14 Heat shock (htpR) CCCCATNT

F 28 σ (σ ) fliA 239 28 TAAA–N15–GCCGATAA Flagellar proteins

Extreme heat σE rpoE 191 24 GAACTT–N –TCTGA 16 shock

fecI σ fecI 173 19 GGAAAT–N17–TC Iron transport

a.. Alternative names are given in parenthesis.

b....Nx indicates any x number of nucleotides.

Encyclopedia of Genetics, Genomics, Proteomics and Informatics 2008 Edition Pribnow Box (TATA box) First Online: 16 July 2016 DOI: https://doi.org/10.1007/978-1-4020-6754-9_13407

5′-TATAATG-3′ (or similar) consensus preceding the prokaryotic transcription initiation sites by 5–7 nucleotides in the promoter region at about −10 position from the translation initiation site. Separated by 17 bp there is another conserved element (called extended promoter) in prokaryotes at −35 (TTGACA). The eukaryotic homolog of the Pribnow box is the Hogness box. Search ScienceDirect Advanced

Reference Module in Life Sciences 2017

Hogness Box☆

Author links open overlay panelM.PonomarenkoV.MironovaK.GunbinP.PonomarenkoV.SuslovL.Savinko va Show more https://doi.org/10.1016/B978-0-12-809633-8.06530-4Get rights and content Abstract

The Hogness box, also known as the Goldberg–Hogness box, the ATA box, and, on most occasions, the TATA box, is the binding site in protists, metazoans, fungi, and eukaryotic viruses for the TATA-binding protein (TBP), a subunit of transcription factor II D (TFIID). In the gene transcribed by RNA polymerase II, the first base of the Hogness box, the consensus sequence TATA(t/a)A(t/a), is located approximately 30 bp upstream of the transcription start sites. The affinity of TBP for the Hogness box is an important characteristic of gene promoters, because its predicted values correlate with the values of many molecular genetic characteristics such as the transcription reinitiation rates, levels of transcriptional activity, gene expression levels, and norms of reaction. Hogness box polymorphisms have been associated with hereditary diseases, plant and animals traits valuable in breeding practices, and trends in the current acquired immunodeficiency syndrome (AIDS) pandemic. Eukaryotic promoters are commonly classed into TATA-containing promoters and TATA-less promoters depending on the Hogness box score in Bucher’s position-weight matrix. In mammals, switchovers from TATA-containing promoters to TATA-less promoters in the Gli1 and Gli3 genes correlate with switchovers from r-selection to K-selection in the course of evolution.

Hogness Box A.J. Berk, in Encyclopedia of Genetics, 2001

Also known as the ‘TATA box,’ the Hogness box is an 8-bp AT-rich promoter sequence in eukaryotes and Archaea that is the binding site for the TATA-box binding protein (TBP), a subunit of the TFIID initiation factor in metazoans. TBP functions as an initiation factor without additional TBP-associated factors in Archaea and at many promoters in Saccharomyces cerevisiae. The first base of the sense strand consensus sequence T-A-T-A-T/A-A-T/A-N is approximately 30 bp upstream of RNA polymerase II transcription start sites in metazoans, Archaea, and some fungi. In S. cerevisiae the Hogness (TATA) box occurs ∼90 bp upstream of the transcription start site. The match to the consensus sequence (determining the affinity for TBP) is an important determinant of promoter strength.