Escherichia coli σ 70 senses sequence and conformation of the promoter spacer region

Abstract

In bacteria, promoter identification by RNA polymerase is mediated by a dissociable σ factor. The housekeeping σ 70 factor of Escherichia coli recognizes two well characterized DNA sequence elements, known as the '-10' and '-35' hexamers. These elements are separated by 'spacer' DNA, the sequence of which is generally considered unimportant. Here, we use a combination of bioinformatics, genetics and biochemistry to show that σ 70 can sense the sequence and conformation of the promoter spacer region. Our data illustrate how alterations in spacer region sequence can increase promoter activity. This stimulatory effect requires σ 70 side chain R451, which is located in close proximity to the non-template strand at promoter position-18. Conversely, R451 is not required to mediate transcriptional stimulation by improvement of the-10 element. Mutation of σ 70 residue R451, which is highly conserved, results in reduced growth rate, consistent with a central role in promoter recognition. © 2011 The Author(s).