Possible roles of σ-dependent RNA polymerase pausing in transcription regulation

The sigma subunit of bacterial RNA polymerase is required for promoter recognition during transcription initiation but may also regulate transcription elongation. The principal sigma(70) subunit of Escherichia coli was shown to travel with RNA polymerase and induce transcriptional pausing at promoter-like motifs, with potential regulatory output. We recently demonstrated that an alternative sigma(38) subunit can also induce RNA polymerase pausing. Here, we outline proposed regulatory roles of sigma-dependent pausing in bacteria and discuss possible interplay between alternative s variants and regulatory factors during transcription elongation.