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

The sigma subunit of bacterial RNA polymerase (RNAP) confers on the enzyme the ability to initiate promoter-specific transcription. Although sigma factors are generally classified as initiation factors, sigma can also remain associated with, and modulate the behavior of, RNAP during elongation. Here we establish that the primary sigma factor in Escherichia coli, sigma(70), can function as an elongation factor in vivo by loading directly onto the transcription elongation complex (TEC) in trans. We demonstrate that sigma(70) can bind in trans to TECs that emanate from either a sigma(70)-dependent promoter or a promoter that is controlled by an alternative sigma factor. We further demonstrate that binding of sigma(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 s factor can exert direct effects on the composition of the entire transcriptome, not just that portion that is produced under the control of sigma(70)-dependent promoters.