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Direct binding of TFE? opens DNA binding cleft of RNA polymerase.

ABSTRACT: Opening of the DNA binding cleft of cellular RNA polymerase (RNAP) is necessary for transcription initiation but the underlying molecular mechanism is not known. Here, we report on the cryo-electron microscopy structures of the RNAP, RNAP-TFE? binary, and RNAP-TFE?-promoter DNA ternary complexes from archaea, Thermococcus kodakarensis (Tko). The structures reveal that TFE? bridges the RNAP clamp and stalk domains to open the DNA binding cleft. Positioning of promoter DNA into the cleft closes it while maintaining the TFE? interactions with the RNAP mobile modules. The structures and photo-crosslinking results also suggest that the conserved aromatic residue in the extended winged-helix domain of TFE? interacts with promoter DNA to stabilize the transcription bubble. This study provides a structural basis for the functions of TFE? and elucidates the mechanism by which the DNA binding cleft is opened during transcription initiation in the stalk-containing RNAPs, including archaeal and eukaryotic RNAPs.

SUBMITTER: Jun SH 

PROVIDER: S-EPMC7704642 | biostudies-literature | 2020 Nov

REPOSITORIES: biostudies-literature

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Direct binding of TFEα opens DNA binding cleft of RNA polymerase.

Jun Sung-Hoon SH   Hyun Jaekyung J   Cha Jeong Seok JS   Kim Hoyoung H   Bartlett Michael S MS   Cho Hyun-Soo HS   Murakami Katsuhiko S KS  

Nature communications 20201130 1

Opening of the DNA binding cleft of cellular RNA polymerase (RNAP) is necessary for transcription initiation but the underlying molecular mechanism is not known. Here, we report on the cryo-electron microscopy structures of the RNAP, RNAP-TFEα binary, and RNAP-TFEα-promoter DNA ternary complexes from archaea, Thermococcus kodakarensis (Tko). The structures reveal that TFEα bridges the RNAP clamp and stalk domains to open the DNA binding cleft. Positioning of promoter DNA into the cleft closes it  ...[more]

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