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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 , σ 70 , can function as an elongation factor in vivo by loading directly onto the transcription elongation complex (TEC)  in trans . We demonstrate that σ 70  can bind  in trans  to TECs that emanate from either a σ 70 -dependent promoter or a promoter that is controlled by an alternative σ factor. We further demonstrate that binding of σ 70  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 σ 70 -dependent promoters.

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