Competition among seven Escherichia coli sigma subunits: relative binding affinities to the core RNA polymerase

Maeda, Hiroto; Fujita, Nobuyuki; Ishihama, Akira

doi:10.1093/nar/28.18.3497

Cited by 270 publications

(287 citation statements)

References 53 publications

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“…54 Binding-Even though the enhancer-dependent 54 and the enhancer-independent 70 bind the common RNAP with similar affinities and occupy similar positions within the RNAP holoenzyme (7,9,36), the ⌬flap mutation markedly reduces the activity of the RNAP to bind 54 and the stability of the resulting holoenzyme. In contrast, 70 binding and the stability of E 70 were not greatly affected by the ⌬flap mutation (13).…”

Section: Discussionmentioning

confidence: 99%

Multiple Roles of the RNA Polymerase β Subunit Flap Domain in ς54-Dependent Transcription

Wigneshweraraj

Kuznedelov²,

Severinov³

et al. 2003

Journal of Biological Chemistry

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Recent determinations of the structures of the bacterial RNA polymerase (RNAP) and promoter complex thereof establish that RNAP functions as a complex molecular machine that contains distinct structural modules that undergo major conformational changes during transcription. However, the contribution of the RNAP structural modules to transcription remains poorly understood. The bacterial core RNAP (␣ 2 ␤␤; E) associates with a sigma () subunit to form the holoenzyme (E Multisubunit DNA-dependent RNA polymerases (RNAP) 1 are complex molecular machines that synthesize a RNA copy from a DNA template. In Escherichia coli, five subunits (␣ 2 ␤␤Ј) form the RNAP catalytic core (E) that associates with a sigma () subunit to form the holoenzyme (E). The subunit imparts on the core RNAP the ability to specifically recognize and initiate transcription from promoters. Biochemical and structural studies indicate that the protein-protein contacts at the interface between core RNAP and , an extensive and functionally specialized sets of surfaces, govern the conformational changes that allow efficient promoter recognition and transcription initiation (1-3).Sequence comparisons reveal two unrelated families of RNAP factors. Members of the major family of factors form RNAP holoenzymes that recognize promoters and form transcriptionally competent promoter complexes in the absence of other factors or energy sources. This family, which includes most bacterial factors is named after the prototypical housekeeping of E. coli, 70 . Members of the second, minor family of factors, the 54 family, form RNAP holoenzymes that recognize promoters but require additional protein factors and a source of energy in the form of ATP or GTP hydrolysis for formation of transcriptionally competent promoter complexes (4 -6). Despite the differences in pathways that lead to transcription-competent open promoter complexes, both classes of factors occupy similar positions within their respective RNAP holoenzymes and appear to utilize some common RNAP surfaces for transcription initiation (7-10).Binding of a 70 family factor induces conformational changes within the core RNAP (2,11,12). Structural modules of the core RNAP, designated as the ␤Ј clamp, the ␤ flap, and the ␤ lobes, interact with a 70 family subunit ( A ) in the structures of Thermus aquaticus and Thermus thermophilus RNAP holoenzymes and undergo conformational changes, which orientate and position 70 DNA-binding domains within the RNAP holoenzyme to allow promoter recognition (2, 3). The importance of these conformational changes is underlined by our recent observation that removal of the E. coli RNAP ␤ flap domain abolished the ability of the mutant E 70 to recognize promoters of the Ϫ10/Ϫ35 class (13). E 54 recognizes and binds promoters containing conserved consensus elements centered around Ϫ24 and Ϫ12 nucleotides upstream of the transcription start site at ϩ1. These promoter elements can be considered as functional analogues of the Ϫ35/Ϫ10 consensus promoter elements recognized by E 70 cla...

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Section: Discussionmentioning

confidence: 99%

Multiple Roles of the RNA Polymerase β Subunit Flap Domain in ς54-Dependent Transcription

Wigneshweraraj

Kuznedelov²,

Severinov³

et al. 2003

Journal of Biological Chemistry

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“…3). It is likely that this apparently higher binding affinity by E 70 might depend on a higher affinity of 70 for the core RNA polymerase (43,44), which would result in more efficient assembly for E 70 than for E S . However, at a higher RNA polymerase concentration the E S form is clearly favored at both PaidB and PaidB(12C3 T), confirming that the C12T mutant of the aidB promoter also retains preferential binding by E S .…”

Section: Interaction Of the Wild Type And The C12t Mutant Aidb Promotmentioning

confidence: 99%

Nucleotides from –16 to –12 Determine Specific Promoter Recognition by Bacterial σS-RNA Polymerase

Lacour

Kolb

Landini

2003

Journal of Biological Chemistry

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The alternative sigma factor S , mainly active in stationary phase of growth, recognizes in vitro a ؊10 promoter sequence almost identical to the one for the main sigma factor, 70 , thus raising the problem of how specific promoter recognition by S -RNA polymerase (E S ) is achieved in vivo. We investigated the promoter features involved in selective recognition by E S at the strictly S -dependent aidB promoter. We show that the presence of a C nucleotide as first residue of the aidB ؊10 sequence (؊12C), instead of the T nucleotide canonical for 70 -dependent promoters, is the major determinant for selective recognition by E S . The presence of the ؊12C does not allow formation of an open complex fully proficient in transcription initiation by E 70 . The role of ؊12C as specific determinant for promoter recognition by E S was confirmed by sequence analysis of known E S -dependent promoters as well as site-directed mutagenesis at the promoters of the csgB and sprE genes. We propose that E S , unlike E 70 , can recognize both C and T as the first nucleotide in the ؊10 sequence. Additional promoter features such as the presence of a C nucleotide at position ؊13, contributing to open complex formation by E S , and a TG motif found at the unusual ؊16/؊15 location, possibly contributing to initial binding to the promoter, also represent important factors for S -dependent transcription. We propose a new sequence, TG(N) 0 -2 CCATA(c/a)T, as consensus ؊10 sequence for promoters exclusively recognized by E S .Bacterial cells adapt to changing environmental and physiological conditions by modulating gene expression. Sigma ( ) factors of RNA polymerase, as the subunits responsible for promoter recognition, play a major role in programming gene expression. At least seven different subunits have been identified in Escherichia coli; 70 is the main subunit and can carry out transcription from the majority of E. coli promoters. The alternative subunits can direct transcription toward specific sets of genes (i.e. heat-shock, extracellular proteins, etc.) whose transcription is directed by -specific promoter sequences. A partial exception to the typical role for alternative subunits is represented by S , the product of the rpoS gene, mainly expressed in the stationary phase of growth (1-3). Unlike the other subunits, S -RNA polymerase (E S ) 1 can initiate transcription from several promoters also recognized by E 70 , suggesting that they recognize similar promoter sequences (4). The recognition of similar promoter sequences by S and 70 is reflected by their strong similarity in the DNA binding domains (5). The alignment of E S -dependent promoters and the search for an optimal promoter for E S in vitro using the systematic evolution of ligands by exponential enrichment (SELEX) procedure have pointed to a Ϫ10 consensus sequence for E S , CTATA(c/a)T that is very similar to the canonical TATAAT sequence for 70 (6 -10). These results suggest that promoter selectivity between 70 and S might be determined by factors other than promote...

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“…RpoS has the lowest affinity of all σ factors for core polymerase (14). One of the ways that RpoS can overcome its lack of affinity for the core polymerase is by its interaction with its activator, the prosigma factor Crl.…”

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confidence: 99%

Transcriptional occlusion caused by overlapping promoters

Zafar

Carabetta

Mandel

et al. 2014

Proc. Natl. Acad. Sci. U.S.A.

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RpoS (σ 38 ) is required for cell survival under stress conditions, but it can inhibit growth if produced inappropriately and, consequently, its production and activity are elaborately regulated. Crl, a transcriptional activator that does not bind DNA, enhances RpoS activity by stimulating the interaction between RpoS and the core polymerase. The crl gene has two overlapping promoters, a housekeeping, RpoD-(σ 70 ) dependent promoter, and an RpoN (σ 54 ) promoter that is strongly up-regulated under nitrogen limitation. However, transcription from the RpoN promoter prevents transcription from the RpoD promoter, and the RpoN-dependent transcript lacks a ribosomebinding site. Thus, activation of the RpoN promoter produces a long noncoding RNA that silences crl gene expression simply by being made. This elegant and economical mechanism, which allows a near-instantaneous reduction in Crl synthesis without the need for transacting regulatory factors, restrains the activity of RpoS to allow faster growth under nitrogen-limiting conditions. transcriptional repression | lncRNA

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Competition among seven Escherichia coli sigma subunits: relative binding affinities to the core RNA polymerase

Cited by 270 publications

References 53 publications

Multiple Roles of the RNA Polymerase β Subunit Flap Domain in ς54-Dependent Transcription

Multiple Roles of the RNA Polymerase β Subunit Flap Domain in ς54-Dependent Transcription

Nucleotides from –16 to –12 Determine Specific Promoter Recognition by Bacterial σS-RNA Polymerase

Transcriptional occlusion caused by overlapping promoters

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