Structures and mechanism of transcription initiation by bacterial ECF factors

Bacterial RNA polymerase (RNAP) forms distinct holoenzymes with extra-cytoplasmic function (ECF) sigma factors to initiate specific gene expression programs. In this study, we report a cryo-EM structure at 4.0 angstrom of Escherichia coli transcription initiation complex comprising sigma(E)-the most-studied bacterial ECF sigma factor (Ec sigma(E)-RPo), and a crystal structure at 3.1 angstrom of Mycobacterium tuberculosis transcription initiation complex with a chimeric sigma(H/E) (Mtb sigma(H/E)-RPo). The structure of Ec sigma(E)-RPo reveals key interactions essential for assembly of E. coli sigma(E)-RNAP holoenzyme and for promoter recognition and unwinding by E. coli sigma(E). Moreover, both structures show that the non-conserved linkers (sigma(2)/sigma(4) linker) of the two ECF sigma factors are inserted into the active-center cleft and exit through the RNA-exit channel. We performed secondary-structure prediction of 27,670 ECF sigma factors and find that their non-conserved linkers probably reach into and exit from RNAP active-center cleft in a similar manner. Further biochemical results suggest that such sigma(2)/sigma(4) linker plays an important role in RPo formation, abortive production and promoter escape during ECF sigma factors-mediated transcription initiation.