Differential association of primary and alternative σ factors with RNA polymerase of <i>Mycobacterium tuberculosis</i> during transcription elongation

In response to environmental cues, bacteria alter gene expression by switching σ factor(s) that recognize a specific set of promoters. This 'σ-cycle', in which σ binds to RNA polymerase (RNAP) to initiate transcription and is released during transcription elongation, is thought to be an essential step for σ-switching. Studies in Escherichia coli provide evidence that σ70 is stochastically released from the elongation complex. This 'σ-cycle' became a general model for all σ factors of all bacteria. Here, using three distinct groups of σ factors in Mycobacterium tuberculosis, we show that although a significant fraction of σA and σE are stochastically or immediately released from RNAP during the transition from transcription initiation to elongation, most of σF are retained. We also show that NusA facilitates σA release from elongation complexes at specific genes but does not affect the release of σE and σF. Our results further indicate that σF remains bound at the elongation complex despite the displacement of σ4, as σ2 and σ3 remain associated with RNAP. Our study demonstrates that σ-release is not a universal phenomenon-the release or retention of σ factor depends on its domain architecture.