Structural basis for transcription activation by Crl through tethering of ?S and RNA polymerase.

ABSTRACT: In bacteria, a primary ?-factor associates with the core RNA polymerase (RNAP) to control most transcription initiation, while alternative ?-factors are used to coordinate expression of additional regulons in response to environmental conditions. Many alternative ?-factors are negatively regulated by anti-?-factors. In Escherichia coli, Salmonella enterica, and many other ?-proteobacteria, the transcription factor Crl positively regulates the alternative ?S-regulon by promoting the association of ?S with RNAP without interacting with promoter DNA. The molecular mechanism for Crl activity is unknown. Here, we determined a single-particle cryo-electron microscopy structure of Crl-?S-RNAP in an open promoter complex with a ?S-regulon promoter. In addition to previously predicted interactions between Crl and domain 2 of ?S (?S 2), the structure, along with p-benzoylphenylalanine cross-linking, reveals that Crl interacts with a structural element of the RNAP ?'-subunit that we call the ?'-clamp-toe (?'CT). Deletion of the ?'CT decreases activation by Crl without affecting basal transcription, highlighting the functional importance of the Crl-?'CT interaction. We conclude that Crl activates ?S-dependent transcription in part through stabilizing ?S-RNAP by tethering ?S 2 and the ?'CT. We propose that Crl, and other transcription activators that may use similar mechanisms, be designated ?-activators.

SUBMITTER: Cartagena AJ 

PROVIDER: S-EPMC6754549 | biostudies-literature | 2019 Sep

REPOSITORIES: biostudies-literature