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Mutational analysis of Escherichia coli σ 28 and its target promoters reveals recognition of a composite −10 region, comprised of an ‘extended −10’ motif and a core −10 element
Author(s) -
Koo ByoungMo,
Rhodius Virgil A.,
Campbell Elizabeth A.,
Gross Carol A.
Publication year - 2009
Publication title -
molecular microbiology
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.857
H-Index - 247
eISSN - 1365-2958
pISSN - 0950-382X
DOI - 10.1111/j.1365-2958.2009.06691.x
Subject(s) - biology , promoter , genetics , gene , motif (music) , escherichia coli , conserved sequence , recognition sequence , computational biology , gene expression , peptide sequence , restriction enzyme , physics , acoustics
Summary σ 28 controls the expression of flagella‐related genes and is the most widely distributed alternative σ factor, present in motile Gram‐positive and Gram‐negative bacteria. The distinguishing feature of σ 28 promoters is a long −10 region (GCCGATAA). Despite the fact that the upstream GC is highly conserved, previous studies have not indicated a functional role for this motif. Here we examine the functional relevance of the GCCG motif and determine which residues in σ 28 participate in its recognition. We find that the GCCG motif is a functionally important composite element. The upstream GC constitutes an extended −10 motif and is recognized by R91, a residue in Domain 3 of σ 28 . The downstream CG is the upstream edge of −10 region of the promoter; two residues in Region 2.4, D81 and R84, participate in its recognition. Consistent with their role in base‐specific recognition of the promoter, R91, D81 and D84 are universally conserved in σ 28 orthologues. σ 28 is the second Group 3 σ shown to use an extended −10 region in promoter recognition, raising the possibility that other Group 3 σs will do so as well.