Structural basis of exoribonuclease-mediated mRNA transcription termination

Efficient termination is required for robust gene transcription. Eukaryotic organisms use a conserved exoribonuclease-mediated mechanism to terminate the mRNA transcription by RNA polymerase II (Pol II) 1,2,3,4,5 . Here we report two cryogenic electron microscopy structures of Saccharomyces cerevisiae Pol II pre-termination transcription complexes bound to the 5′-to-3′ exoribonuclease Rat1 and its partner Rai1. Our structures show that Rat1 displaces the elongation factor Spt5 to dock at the Pol II stalk domain. Rat1 shields the RNA exit channel of Pol II, guides the nascent RNA towards its active centre and stacks three nucleotides at the 5′ terminus of the nascent RNA. The structures further show that Rat1 rotates towards Pol II as it shortens RNA. Our results provide the structural mechanism for the Rat1-mediated termination of mRNA transcription by Pol II in yeast and the exoribonuclease-mediated termination of mRNA transcription in other eukaryotes.

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Data availability

Atomic coordinates have been deposited in the PDB under the accession codes 8JCH (Pol II Rat1–PTTC1) and 8K5P (Pol II Rat1–PTTC2). Corresponding cryo-EM density maps have been deposited in the Electron Microscopy Data Bank under the accession codes EMD-36162 (Pol II Rat1–PTTC1) and EMD-36908 (Pol II Rat1–PTTC2). Source data are provided with this paper.

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Acknowledgements

The work was supported by the National Key Research and Development Program of China 2018YFA0900701 (Y. Zhang) and the Basic Research Zone Program of Shanghai JCYJ-SHFY-2022-012 (Y. Zhang). We thank L. Kong, F. Wang, G. Li, J. Duan at electron microscopy system at the National Facility for Protein Science in Shanghai (NFPS), M. Zhang at the electron microscopy center in Interdisciplinary Research Center on Biology and Chemistry (IRCBC), and staffs X. Men, F. Liu, and S. Wang at electron microscopy center at Shuimu Biosciences in Hangzhou for providing technical support and assistance in cryo-EM data collection. We thank M. Zhang and Z. Zhang at the core facility of the Center for Excellence in Molecular Plant Sciences (CEMPS) for technical support and assistance in screening cryo-EM samples. The S. cerevisiae BJ2168 strain was a gift from G. Cai. The pESC-his vector was a gift from Z. Zhou.

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Authors and Affiliations

  1. Key Laboratory of Synthetic Biology, National Key Laboratory of Plant Design, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China Yuan Zeng, Hong-Wei Zhang, Xiao-Xian Wu & Yu Zhang
  2. University of Chinese Academy of Sciences, Beijing, China Yuan Zeng & Hong-Wei Zhang
  1. Yuan Zeng