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Cited by 15Genomics and Chromatin DynamicsRNA Research and SplicingNuclear Structure and Function

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Structural basis of eukaryotic transcription termination by the Rat1 exonuclease complex

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Yanagisawa, Tatsuo, Murayama, Yuko, Ehara, Haruhiko, Goto, Mie, Aoki, Mari, Sekine, Shun-ichi·2024·Nature Communications
DOI 10.1038/s41467-024-52157-0PMC PMC11381523

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Abstract

Abstract The 5’-3’ exoribonuclease Rat1 (or Xrn2) plays a pivotal role in termination of mRNA transcription by eukaryotic RNA polymerase II (RNAPII). Rat1 forms a complex with its partner proteins, Rai1 and Rtt103, and acts as a “torpedo” to bind transcribing RNAPII and dissociate DNA/RNA from it. Here we report the cryo-electron microscopy structures of a Rat1-Rai1-Rtt103 complex and three Rat1-Rai1-associated RNAPII complexes (type-1, type-1b, and type-2) from the yeast Komagataella phaffii . The Rat1-Rai1-Rtt103 complex structure revealed that Rat1 and Rai1 form a heterotetramer, with a single Rtt103 bound between two Rai1 molecules. In the type-1 complex, Rat1-Rai1 forms a heterodimer and directly binds to the RNA exit site of transcribing RNAPII to extract RNA into the Rat1 nuclease active site. This interaction changes the RNA path in favor of termination (the “pre-termination” state). The type-1b and type-2 complexes have no bound DNA/RNA, likely representing the “post-termination” states. These structures shed light on the mechanism of eukaryotic mRNA transcription termination.

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Research works printed but not linked: 61

  1. Osman, S. & Cramer, P. Structural biology of RNA polymerase II transcription: 20 years on. Annu. Rev. Cell Dev. Biol. 36, 1–34 (2020). · DOI
  2. Kwak, H. & Lis, J. T. Control of transcriptional elongation. Annu. Rev. Genet. 47, 483–508 (2013). · DOI
  3. Komarnitsky, P., Cho, E. & Buratowski, S. Different phosphorylated forms of RNA polymerase II and associated mRNA processing factors during transcription. Genes Dev. 14, 2452–2460 (2000). · DOI
  4. Buratowski, S. The CTD code. Nat. Struct. Biol. 10, 679–680 (2003). · DOI
  5. Eick, D. & Geyer, M. The RNA polymerase II carboxy-terminal domain (CTD) code. Chem. Rev. 113, 8456–8490 (2013). · DOI
  6. Hsin, J. P. & Manley, J. L. The RNA polymerase II CTD coordinates transcription and RNA processing. Genes Dev. 26, 2119–2137 (2012). · DOI
  7. Jeronimo, C., Collin, P. & Robert, F. The RNA polymerase II CTD: the increasing complexity of a low-complexity protein domain. J. Mol. Biol. 428, 2607–2622 (2016). · DOI
  8. Mohamed, A. A., Vazquez Nunez, R. & Vos, S. M. Structural advances in transcription elongation. Curr. Opin. Struct. Biol. 75, 102422 (2022). · DOI
  9. Sekine, S., Ehara, H., Kujirai, T. & Kurumizaka, H. Structural perspectives on transcription in chromatin. Trends Cell Biol. 34, 211–224 (2023). · DOI
  10. Rodríguez-Molina, J., West, S. & Passmore, L. Knowing when to stop: transcription termination on protein-coding genes by eukaryotic RNAPII. Mol. Cell 83, 404–415 (2023). · DOI
  11. Eaton, J. & West, S. Termination of transcription by RNA Polymerase II: BOOM! Trends Genet. 36, 664–675 (2020). · DOI · Paper page
  12. Logan, J., Falck-Pedersen, E., Darnell, J. & Shenk, T. A poly(A) addition site and a downstream termination region are required for efficient cessation of transcription by RNA polymerase II in the mouse βmaj-globin gene. Proc. Natl Acad. Sci. USA 84, 8306–8310 (1987). · DOI · Paper page
  13. Proudfoot, N. How RNA polymerase II terminates transcription in higher eukaryotes. Trends Biochem. Sci. 14, 105–110 (1989). · DOI
  14. Connelly, S. & Manley, J. A functional mRNA polyadenylation signal is required for transcription termination by RNA polymerase II. Genes Dev. 2, 440–452 (1988). · DOI
  15. Birse, C., Minvielle-Sebastia, L., Lee, B., Keller, W. & Proudfoot, N. Coupling termination of transcription to messenger RNA maturation in yeast. Science 280, 298–301 (1998). · DOI
  16. Bentley, D. Rules of engagement: co-transcriptional recruitment of pre-mRNA processing factors. Curr. Opin. Cell Biol. 17, 251–256 (2005). · DOI
  17. Proudfoot, N. Ending the message: poly(A) signals then and now. Genes Dev. 25, 1770–1782 (2011). · DOI
  18. Porrua, O. & Libri, D. Transcription termination and the control of the transcriptome: why, where and how to stop. Nat. Rev. Mol. Cell Biol. 16, 190–202 (2015). · DOI
  19. Proudfoot, N. Transcriptional termination in mammals: stopping the RNA polymerase II juggernaut. Science 352, aad9926 (2016). · DOI
  20. West, S., Gromak, N. & Proudfoot, N. Human 5’→3’ exonuclease Xrn2 promotes transcription termination at co-transcriptional cleavage sites. Nature 432, 522–525 (2004). · DOI
  21. Kim, M. et al. Distinct pathways for snoRNA and mRNA termination. Mol. Cell 24, 723–734 (2006). · DOI
  22. Kilchert, C. & Vasiljeva, L. mRNA quality control goes transcriptional. Biochem. Soc. Trans. 41, 1666–1672 (2013). · DOI
  23. Nagarajan, V., Jones, C., Newbury, S. & Green, P. XRN 5’→3’ exoribonucleases: structure, mechanisms and functions. Biochim. Biophys. Acta 1829, 590–603 (2013). · DOI
  24. Stevens, A. & Poole, T. 5’-exonuclease-2 of Saccharomyces cerevisiae. Purification and features of ribonuclease activity with comparison to 5’-exonuclease-1. J. Biol. Chem. 270, 16063–16069 (1995). · DOI
  25. Xue, Y. et al. Saccharomyces cerevisiae RAI1 (YGL246c) is homologous to human DOM3Z and encodes a protein that binds the nuclear exoribonuclease Rat1p. Mol. Cell Biol. 20, 4006–4015 (2000). · DOI
  26. Kim, M. et al. The yeast Rat1 exonuclease promotes transcription termination by RNA polymerase II. Nature 432, 517–522 (2004). · DOI
  27. Lunde, B. et al. Cooperative interaction of transcription termination factors with the RNA polymerase II C-terminal domain. Nat. Struct. Mol. Biol. 17, 1195–1201 (2010). · DOI
  28. Connelly, S. & Manley, J. A CCAAT box sequence in the adenovirus major late promoter functions as part of an RNA polymerase II termination signal. Cell 57, 561–571 (1989). · DOI
  29. Han, Z. et al. DNA-directed termination of RNA polymerase II transcription. Mol. Cell 83, 3253–3267 (2023). · DOI
  30. Luo, W., Johnson, A. & Bentley, D. The role of Rat1 in coupling mRNA 3’-end processing to transcription termination: implications for a unified allosteric-torpedo model. Genes Dev. 20, 954–965 (2006). · DOI
  31. Eaton, J., Francis, L., Davidson, L. & West, S. A unified allosteric/torpedo mechanism for transcriptional termination on human protein-coding genes. Genes Dev. 34, 132–145 (2020). · DOI
  32. Ehara, H., Kujirai, T., Shirouzu, M., Kurumizaka, H. & Sekine, S. Structural basis of nucleosome disassembly and reassembly by RNAPII elongation complex with FACT. Science 377, eabp9466 (2022). · DOI
  33. Vos, S. et al. Structure of activated transcription complex Pol II-DSIF-PAF-SPT6. Nature 560, 607–612 (2018). · DOI · Paper page
  34. Xiang, S. et al. Structure and function of the 5’→3’ exoribonuclease Rat1 and its activating partner Rai1. Nature 458, 784–788 (2009). · DOI
  35. He, Y. et al. Near-atomic resolution visualization of human transcription promoter opening. Nature 533, 359–365 (2016). · DOI
  36. Plaschka, C. et al. Transcription initiation complex structures elucidate DNA opening. Nature 533, 353–358 (2016). · DOI
  37. Ehara, H. et al. Structure of the complete elongation complex of RNA polymerase II with basal factors. Science 357, 921–924 (2017). · DOI
  38. Ehara, H. et al. Structural insight into nucleosome transcription by RNA polymerase II with elongation factors. Science 363, 744–747 (2019). · DOI
  39. Crickard, J. B., Fu, J. & Reese, J. C. Biochemical analysis of yeast suppressor of Ty 4/5 (Spt4/5) reveals the importance of nucleic acid interactions in the prevention of RNA Polymerase II arrest. J. Biol. Chem. 291, 9853–9870 (2016). · DOI
  40. Zeng, Y., Zhang, H., Wu, X. & Zhang, Y. Structural basis of exoribonuclease-mediated mRNA transcription termination. Nature 628, 887–893 (2024). · DOI
  41. Braglia, P., Kawauchi, J. & Proudfoot, N. Co-transcriptional RNA cleavage provides a failsafe termination mechanism for yeast RNA polymerase I. Nucleic Acids Res. 39, 1439–1448 (2011). · DOI
  42. El Hage, A., Koper, M., Kufel, J. & Tollervey, D. Efficient termination of transcription by RNA polymerase I requires the 5’ exonuclease Rat1 in yeast. Genes Dev. 22, 1069–1081 (2008). · DOI
  43. Murayama, Y. et al. Structural basis of the transcription termination factor Rho engagement with transcribing RNA polymerase from Thermus thermophilus. Sci. Adv. 9, eade7093 (2023). · DOI
  44. Molodtsov, V., Wang, C., Firlar, E., Kaelber, J. & Ebright, R. Structural basis of Rho-dependent transcription termination. Nature 614, 367–374 (2023). · DOI
  45. Higo, T. et al. Development of a hexahistidine-3x FLAG-tandem affinity purification method for endogenous protein complexes in Pichia pastoris. J. Struct. Funct. Genomics 15, 191–199 (2014). · DOI
  46. Ehara, H., Umehara, T., Sekine, S.-I. & Yokoyama, S. Crystal structure of RNA polymerase II from Komagataella pastoris. Biochem. Biophys. Res. Commun. 487, 230–235 (2017). · DOI
  47. Mastronarde, D. N. Automated electron microscope tomography using robust prediction of specimen movements. J. Struct. Biol. 152, 36–51 (2005). · DOI
  48. Scheres, S. H. Processing of structurally heterogeneous cryo-EM data in RELION. Methods Enzymol. 579, 125–157 (2016). · DOI
  49. Scheres, S. A Bayesian view on cryo-EM structure determination. J. Mol. Biol. 415, 406–418 (2012). · DOI
  50. Rohou, A. & Grigorieff, N. CTFFIND4: fast and accurate defocus estimation from electron micrographs. J. Struct. Biol. 192, 216–221 (2015). · DOI
  51. Bepler, T. et al. Positive-unlabeled convolutional neural networks for particle picking in cryo-electron micrographs. Nat. Methods 16, 1153–1160 (2019). · DOI
  52. Tegunov, D. & Cramer, P. Real-time cryo-electron microscopy data preprocessing with Warp. Nat. Methods 16, 1146–1152 (2019). · DOI
  53. Kimanius, D. et al. Data-driven regularisation lowers the size barrier of cryo-EM structure determination. Nat. Methods 21, 1216–1221 (2024). · DOI
  54. Pettersen, E. F. et al. UCSF Chimera—a visualization system for exploratory research and analysis. J. Comput. Chem. 25, 1605–1612 (2004). · DOI
  55. Emsley, P., Lohkamp, B., Scott, W. G. & Cowtan, K. Features and development of Coot. Acta Crystallogr. D Biol. Crystallogr. 66, 486–501 (2010). · DOI · Paper page
  56. Croll, T. ISOLDE: a physically realistic environment for model building into low-resolution electron-density maps. Acta Crystallogr. D Struct. Biol. 74, 519–530 (2018). · DOI
  57. Afonine, P. et al. Towards automated crystallographic structure refinement with phenix.refine. Acta Crystallogr. D Biol. Crystallogr. 68, 352–367 (2012). · DOI · Paper page
  58. Davis, I. et al. MolProbity: all-atom contacts and structure validation for proteins and nucleic acids. Nucleic Acids Res. 35, W375–W383 (2007). · DOI
  59. CCP4. The CCP4 suite: programs for protein crystallography. Acta Crystallogr. D Biol. Crystallogr. 50, 760–763 (1994). · DOI
  60. Liebschner, D. et al. Macromolecular structure determination using X-rays, neutrons and electrons: recent developments in Phenix. Acta Crystallogr. D Struct. Biol. D75, 861–877 (2019). · DOI · Paper page
  61. Goddard, T. et al. UCSF ChimeraX: meeting modern challenges in visualization and analysis. Protein Sci. 27, 14–25 (2018). · DOI · Paper page

Metadata

Authors
Yanagisawa, T., Murayama, Y., Ehara, H., Goto, M., Aoki, M., & Sekine, S.-I.
Affiliations
RIKEN Center for Biosystems Dynamics Research (JP)
Corresponding author
Sekine, Shun-ichi
ORCID
Venue
Nature Communications
Publisher
Springer Science and Business Media LLC
Published
2024-09-08
Volume
15
Issue
1
Pages
7854-7854
ISSN
2041-1723 (ISSN-L)
DOI
10.1038/s41467-024-52157-0
PMC
PMC11381523
OpenAlex
W4402341346
Cited by
15
References
4
Citations by year
2026: 6 · 2025: 6 · 2024: 3
FWCI
2.04
Type
journal article
Language
en
Open access
Licence
Locations
  • Nature Communications (publishedVersion, cc-by-nc-nd)
  • bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion, cc-by-nc-nd)
  • PubMed Central (publishedVersion, cc-by-nc-nd)
  • PubMed (publishedVersion)
  • RePEc: Research Papers in Economics (submittedVersion)
  • DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion)
Funders
MEXT | Japan Society for the Promotion of Science (JP20H05690, JP20H05906, JP24H00062)
Topics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Chromatin Dynamics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › RNA Research and Splicing
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Nuclear Structure and Function
Keywords
RNA polymerase II, RAI1, 5'-3' exonuclease, Pichia pastoris, heterotetramer, cryo-EM structure
MeSH terms
Saccharomycetales, Exoribonucleases, Models, Molecular, Protein Binding, RNA, Messenger, Saccharomyces cerevisiae, Transcription, Genetic, Cryoelectron Microscopy, Saccharomyces cerevisiae Proteins, Transcription Termination, Genetic

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