A Full-Length Group 1 Bacterial Sigma Factor Adopts a Compact Structure Incompatible with DNA Binding

Schwartz, Edmund C.; Shekhtman, Alexander; Dutta, Kaushik; Pratt, Matthew R.; Cowburn, David; Darst, Seth A.; Muir, Tom W.

doi:10.1016/j.chembiol.2008.09.008

Cited by 55 publications

(66 citation statements)

References 44 publications

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“…Given its flexible nature, 1.1 has not been solved in all Thermus RNAP holoenzyme crystal structures that have been reported (5, 9 -12). Only an NMR structure of 1.1 from Thermotoga maritima has been reported, and it consists of three ␣ helices with a compact hydrophobic core formed by highly conserved hydrophobic residues (6).…”

Section: Rna Polymerase (Rnap)mentioning

confidence: 99%

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X-ray Crystal Structure of Escherichia coli RNA Polymerase σ70 Holoenzyme

Murakami

2013

Journal of Biological Chemistry

184

221

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Background: A crystal structure of Escherichia coli RNA polymerase (RNAP) has not been determined. Results: The 1.1 and ␣ subunit C-terminal domain structures have been determined in the context of an intact RNAP. Conclusion: 1.1 localizes within the RNAP DNA-binding channel and must disengage from this site to form an open complex. Significance: This work enables future structure determination of bacterial RNAP mutants.

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Section: Rna Polymerase (Rnap)mentioning

confidence: 99%

“…In addition to the 2, 3, and 4 domains, the group 1 family contains an ϳ100-amino acid N-terminal extension, 1.1 , which is a negatively charged ␣ helical domain (6). The 1.1 domain has been shown to accelerate the formation of the open complex at some promoters and suggested to reside inside the RNAP main channel (7).…”

Section: Rna Polymerase (Rnap)mentioning

confidence: 99%

X-ray Crystal Structure of Escherichia coli RNA Polymerase σ70 Holoenzyme

Murakami

2013

Journal of Biological Chemistry

184

221

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“…Fitting statistics are provided in Table S1. Coordinates for 70 region 1.1 (35) were not fitted to the map, because density could not be unambiguously assigned for this small domain. Second, a homology model for E. coli RNAP was generated from the heterogeneous fitted RNAP fragments.…”

Section: Design Assembly and Imaging Of A Class I Cap-rnap-promotermentioning

confidence: 99%

Three-dimensional EM structure of an intact activator-dependent transcription initiation complex

Hudson

Quispe

Lara-González³

et al. 2009

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

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We present the experimentally determined 3D structure of an intact activator-dependent transcription initiation complex comprising the Escherichia coli catabolite activator protein (CAP), RNA polymerase holoenzyme (RNAP), and a DNA fragment containing positions ؊78 to ؉20 of a Class I CAP-dependent promoter with a CAP site at position ؊61.5 and a premelted transcription bubble. A 20-Å electron microscopy reconstruction was obtained by iterative projection-based matching of single particles visualized in carbonsandwich negative stain and was fitted using atomic coordinate sets for CAP, RNAP, and DNA. The structure defines the organization of a Class I CAP-RNAP-promoter complex and supports previously proposed interactions of CAP with RNAP ␣ subunit C-terminal domain (␣CTD), interactions of ␣CTD with 70 region 4, interactions of CAP and RNAP with promoter DNA, and phased-DNAbend-dependent partial wrapping of DNA around the complex. The structure also reveals the positions and shapes of species-specific domains within the RNAP ␤ , ␤, and 70 subunits.catabolite activator protein ͉ deoxyribonucleic acid ͉ RNA polymerase holoenzyme ͉ gene regulation ͉ electron microscopy

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“…These results suggest a role for crl in the appearance of rpoS mutants and raise the possibility that a number of rpoS mutations in bacterial populations have escaped our attention due to the capacity of Crl to rescue the activity of the corresponding S mutant proteins. There is no three-dimensional structure available for fulllength free , but several lines of evidence suggest that free adopts a compact (closed) conformation that is incompatible with promoter recognition and different from its open structure in E complexes (7,43). Indeed, binding to E induces large movements of the domains (5,7,29), switching into an active conformation in which the DNA binding determinants in 2 and 4 are exposed (29).…”

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confidence: 99%

Crl Binds to Domain 2 of σ ^S and Confers a Competitive Advantage on a Natural rpoS Mutant of Salmonella enterica Serovar Typhi

et al. 2010

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The RpoS sigma factor ( S ) is the master regulator of the bacterial response to a variety of stresses. Mutants in rpoS arise in bacterial populations in the absence of stress, probably as a consequence of a subtle balance between self-preservation and nutritional competence. We characterized here one natural rpoS mutant of Salmonella enterica serovar Typhi (Ty19). We show that the rpoS allele of Ty19 (rpoS Ty19 ) led to the synthesis of a S Ty19 protein carrying a single glycine-to-valine substitution at position 282 in S domain 4, which was much more dependent than the wild-type S protein on activation by Crl, a chaperone-like protein that increases the affinity of S for the RNA polymerase core enzyme (E). We used the bacterial adenylate cyclase two-hybrid system to demonstrate that Crl bound to residues 72 to 167 of S domain 2 and that G282V substitution did not directly affect Crl binding. However, this substitution drastically reduced the ability of S Ty19 to bind E in a surface plasmon resonance assay, a defect partially rescued by Crl. The modeled structure of the E S holoenzyme suggested that substitution G282V could directly disrupt a favorable interaction between S and E. The rpoS Ty19 allele conferred a competitive fitness when the bacterial population was wild type for crl but was outcompeted in ⌬crl populations. Thus, these results indicate that the competitive advantage of the rpoS Ty19 mutant is dependent on Crl and suggest that crl plays a role in the appearance of rpoS mutants in bacterial populations.In bacteria, transcription depends on a RNA polymerase (RNAP) consisting of a catalytically active core enzyme (E) with a subunit structure ␣ 2 ␤␤Ј that associates with any one of several factors to form different E holoenzymes. The subunit is required for specific promoter binding, and different factors direct RNAP to different classes of promoters, thereby modulating the gene expression patterns (17). The holoenzyme containing the 70 subunit is responsible for the transcription of most genes during exponential growth (17). When cells enter stationary phase or undergo specific stress conditions (high osmolarity, low pH, or high and low temperatures) during exponential growth, S , which is encoded by the rpoS gene, becomes more abundant, associates with E, and directs the transcription of genes essential for the general stress response (17,18,21). In Salmonella and Escherichia coli, the S regulon comprises more than 300 genes contributing to survival during stationary phase, adaptive stress responses, biofilm formation, and virulence of S. enterica serovar Typhimurium, a wide-host-range pathogen and a major cause of human gastroenteritis and food-borne disease (2, 48). However, the precise function of nearly half of the genes in the regulon is unknown.An intriguing aspect of S is the allelic variation of rpoS in E.coli and Salmonella (9,13,36,38,50). Because of its role in general stress resistance and its high position in the hierarchy of transcriptional regulators, one might expect S to be conser...

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A Full-Length Group 1 Bacterial Sigma Factor Adopts a Compact Structure Incompatible with DNA Binding

Cited by 55 publications

References 44 publications

X-ray Crystal Structure of Escherichia coli RNA Polymerase σ70 Holoenzyme

X-ray Crystal Structure of Escherichia coli RNA Polymerase σ70 Holoenzyme

Three-dimensional EM structure of an intact activator-dependent transcription initiation complex

Crl Binds to Domain 2 of σ ^S and Confers a Competitive Advantage on a Natural rpoS Mutant of Salmonella enterica Serovar Typhi

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A Full-Length Group 1 Bacterial Sigma Factor Adopts a Compact Structure Incompatible with DNA Binding

Cited by 55 publications

References 44 publications

X-ray Crystal Structure of Escherichia coli RNA Polymerase σ70 Holoenzyme

X-ray Crystal Structure of Escherichia coli RNA Polymerase σ70 Holoenzyme

Three-dimensional EM structure of an intact activator-dependent transcription initiation complex

Crl Binds to Domain 2 of σ S and Confers a Competitive Advantage on a Natural rpoS Mutant of Salmonella enterica Serovar Typhi

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Crl Binds to Domain 2 of σ ^S and Confers a Competitive Advantage on a Natural rpoS Mutant of Salmonella enterica Serovar Typhi