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Escherichia coli σ⁷⁰ senses sequence and conformation of the promoter spacer region

Singh, Shivani S., Typas, Athanasios, Hengge, Regine, Grainger, David C.
Nucleic acids research 2011 v.39 no.12 pp. 5109-5118
DNA, DNA-directed RNA polymerase, Escherichia coli, bacteria, bioinformatics, mutation, nucleotide sequences, transcription (genetics)
In bacteria, promoter identification by RNA polymerase is mediated by a dissociable σ factor. The housekeeping σ⁷⁰ 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 σ⁷⁰ 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 σ⁷⁰ 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 σ⁷⁰ residue R451, which is highly conserved, results in reduced growth rate, consistent with a central role in promoter recognition.