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Key features of σ S required for specific recognition by Crl, a transcription factor promoting assembly of RNA polymerase holoenzyme

Amy B. Banta, Robert S. Chumanov, Andy H. Yuan, Hueylie Lin, Elizabeth A. Campbell, Richard R. Burgess and Richard L. Gourse
Proceedings of the National Academy of Sciences of the United States of America
Vol. 110, No. 40 (October 1, 2013), pp. 15955-15960
Stable URL: http://www.jstor.org/stable/23749695
Page Count: 6
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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 σS-dependent transcription during times of cellular stress by promoting the association of σS with core RNA polymerase. The molecular basis for specific recognition of σS by Crl, rather than the homologous and more abundant primary sigma factor σ70, is unknown. Here we use bacterial two-hybrid analysis in vivo and p-benzoylphenylalanine cross-linking in vitro to define the features in σS responsible for specific recognition by Crl. We identify residues in σS conserved domain 2 (σS2) that are necessary and sufficient to allow recognition of σ70 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 σ70. We then use luminescence resonance energy transfer to demonstrate directly that Crl promotes holoenzyme assembly using these specificity determinants on σS. 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.

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