title: Key features of σS required for specific recognition by Crl, a transcription factor promoting assembly of RNA polymerase holoenzyme.
abstract: Bacteria use multiple sigma factors to coordinate gene expression in response to environmental perturbations. In Escherichia coli and other γ-proteobacteria, the transcription factor Crl stimulates σ(S)-dependent transcription during times of cellular stress by promoting the association of σ(S) with core RNA polymerase. The molecular basis for specific recognition of σ(S) by Crl, rather than the homologous and more abundant primary sigma factor σ(70), is unknown. Here we use bacterial two-hybrid analysis in vivo and p-benzoyl-phenylalanine cross-linking in vitro to define the features in σ(S) responsible for specific recognition by Crl. We identify residues in σ(S) conserved domain 2 (σ(S)2) that are necessary and sufficient to allow recognition of σ(70) conserved domain 2 by Crl, one near the promoter-melting region and the other at the position where a large nonconserved region interrupts the sequence of σ(70). We then use luminescence resonance energy transfer to demonstrate directly that Crl promotes holoenzyme assembly using these specificity determinants on σ(S). Our results explain how Crl distinguishes between sigma factors that are largely homologous and activates discrete sets of promoters even though it does not bind to promoter DNA.
authors.affiliation: Department of Bacteriology and McArdle Laboratory for Cancer Research, University of Wisconsin-Madison, Madison, WI 53706.
authors.forename: Amy B
authors.initials: AB
authors.lastname: Banta
authors.forename: Robert S
authors.initials: RS
authors.lastname: Chumanov
authors.forename: Andy H
authors.initials: AH
authors.lastname: Yuan
authors.forename: Hueylie
authors.initials: H
authors.lastname: Lin
authors.forename: Elizabeth A
authors.initials: EA
authors.lastname: Campbell
authors.forename: Richard R
authors.initials: RR
authors.lastname: Burgess
authors.forename: Richard L
authors.initials: RL
authors.lastname: Gourse
mesh_terms: D001426:Bacterial Proteins / Q000378:metabolism*; D012321:DNA-Directed RNA Polymerases / Q000096:biosynthesis / Q000737:chemistry*; D004926:Escherichia coli / Q000378:metabolism*; D015964:Gene Expression Regulation, Bacterial / Q000502:physiology*; D020035:Holoenzymes / Q000096:biosynthesis; D009841:Oligonucleotides / Q000235:genetics; D025941:Protein Interaction Mapping; D012808:Sigma Factor / Q000737:chemistry*; D014157:Transcription Factors / Q000378:metabolism*
chemical_list: D001426:Bacterial Proteins; D020035:Holoenzymes; D009841:Oligonucleotides; D012808:Sigma Factor; D014157:Transcription Factors; C077481:Crl protein, Bacteria; D012321:DNA-Directed RNA Polymerases
keywords: RNAP formation; RpoS; bacterial stress response; curli fiber; transcription initiation
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