Structural basis of ECF-σ-factor-dependent transcription initiation

Extracytoplasmic (ECF) sigma factors, the largest class of alternative s factors, are related to primary sigma factors, but have simpler structures, comprising only two of six conserved functional modules 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 s 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 s factors, show that the connector between sigma R2 and sigma R4 of the ECF sigma factor-although shorter and 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 s factors. The results define protein-protein and protein-DNA interactions involved in ECF-sigma-factor-dependent transcription initiation.