In Streptomyces coelicolor SigR, methionine at the -35 element interacting region 4 confers the -31′-adenine base selectivity

In Gram-positive Streptomyces coelicolor A3(2), SigR (Sc σR) of the group IV ECF sigma factor singly activates expression of more than 30 oxidation responsive genes. Of the two promoter-binding domains – individually called region 2 and region 4 – within Sc σR, we hereby report a 2.6 à resolution structure of the -35 element interacting carboxyl-terminal region 4 (Sc σR4). Structural comparison of Sc σR4 with the Escherichia coli SigE (Ec σE) in complex with Ec σE -35 element suggested that a single residue (Sc σR Met188 and Ec σE Arg171) may be responsible for distinguishing the one-base pair difference of the -35 elements – Sc σR−31′ATTCC−35′ (−31′A) vs. Ec σE−31′GTTCC−35′ (−31′G) – by interacting with the -31′-base. Further studies using expressed Sc σR indicate that the wild-type Sc σR with Met188 selectively interacted with the −31′A sequence over the −31′G sequence, whereas a mutation of Met188 to arginine resulted in interaction with both −31′A and −31′G sequences. Hence, we conclude that Met188 of Sc σR confers the −31′A-selectivity in -35 element interaction by disfavoured interaction with the −31′G base.