Direct binding of TFEα opens DNA binding cleft of RNA polymerase

Sung-Hoon Jun (), Jaekyung Hyun, Jeong Seok Cha, Hoyoung Kim, Michael S. Bartlett, Hyun-Soo Cho () and Katsuhiko S. Murakami ()
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Sung-Hoon Jun: Korea Basic Science Institute
Jaekyung Hyun: Korea Basic Science Institute
Jeong Seok Cha: College of Life Science and Biotechnology, Yonsei University
Hoyoung Kim: College of Life Science and Biotechnology, Yonsei University
Michael S. Bartlett: the Portland State University
Hyun-Soo Cho: College of Life Science and Biotechnology, Yonsei University
Katsuhiko S. Murakami: The Pennsylvania State University

Nature Communications, 2020, vol. 11, issue 1, 1-12

Abstract: 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-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 while maintaining the TFEα 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 TFEα interacts with promoter DNA to stabilize the transcription bubble. This study provides a structural basis for the functions of TFEα 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.

Date: 2020
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DOI: 10.1038/s41467-020-19998-x

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