Structural basis of ECF-sigma-factor-dependent transcription initiation.

Extracytoplasmic (ECF) {sigma} factors, the largest class of alternative {sigma} factors, are related to primary {sigma} factors, but have simpler structures, comprising only two of the six conserved functional modules present in primary {sigma} factors: region 2 ({sigma}R2) and region 4 ({sigma}R4). Here, we report crystal structures of transcription initiation complexes containing Mycobacterium tuberculosis RNA polymerase (RNAP), M. tuberculosis ECF {sigma} factor {sigma}L, and promoter DNA. The structures show that {sigma}R2 and {sigma}R4 of the ECF {sigma} factor occupy the same sites on RNAP as in primary {sigma} factors, show that the connector between {sigma}R2 and {sigma}R4 of the ECF {sigma} factor--although unrelated in sequence--follows the same path through RNAP as in primary {sigma} factors, and show that the ECF {sigma} factor uses the same strategy to bind and unwind promoter DNA as primary {sigma} factors. The results define protein-protein and protein-DNA interactions involved in ECF-{sigma}-factor-dependent transcription initiation.