The primary σ factor in Escherichia coli can access the transcription elongation complex from solution in vivo

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Abstract

The σ subunit of bacterial RNA polymerase (RNAP) confers on the enzyme the ability to initiate promoter-specific transcription. Although σ factors are generally classified as initiation factors, σ can also remain associated with, and modulate the behavior of, RNAP during elongation. Here we establish that the primary σ factor in Escherichia coli, σ⁷⁰, can function as an elongation factor in vivo by loading directly onto the transcription elongation complex (TEC) in trans. We demonstrate that σ⁷⁰ can bind in trans to TECs that emanate from either a σ⁷⁰-dependent promoter or from a promoter that is controlled by an alternative σ factor. We further demonstrate that binding of σ⁷⁰ to the TEC in trans can have a particularly large impact on the dynamics of transcription elongation during stationary phase. Our findings establish a mechanism whereby the primary σ factor can exert direct effects on the composition of the entire transcriptome, not just that portion that is produced under the control of σ⁷⁰-dependent promoters.

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Seth R Goldman

Department of Microbiology and Immunobiology, Harvard Medical School, Boston, United States

Competing interests
The authors declare that no competing interests exist.
Nikhil U Nair

Department of Microbiology and Immunobiology, Harvard Medical School, Boston, United States

Competing interests
The authors declare that no competing interests exist.
Christopher D Wells

Department of Microbiology and Immunobiology, Harvard Medical School, Boston, United States

Competing interests
The authors declare that no competing interests exist.
Bryce E Nickels

Department of Genetics, Waksman Institute, Rutgers University, New Brunswick, United States

Competing interests
The authors declare that no competing interests exist.
Ann Hochschild

Department of Microbiology and Immunobiology, Harvard Medical School, Boston, United States

For correspondence
ahochschild@hms.harvard.edu

Competing interests
The authors declare that no competing interests exist.

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