IDEAS home Printed from https://ideas.repec.org/a/nat/natcom/v16y2025i1d10.1038_s41467-025-58671-z.html
   My bibliography  Save this article

Molecular basis for the interaction between Saccharomyces cerevisiae Rtt103 and the Rat1-Rai1 complex

Author

Listed:
  • Hsu-Feng Chu

    (Columbia University)

  • Liang Tong

    (Columbia University)

Abstract

The Rat1 5’-3’ exoribonuclease together with its partner Rai1 have important roles in Saccharomyces cerevisiae RNA polymerase II transcription termination. Rtt103 copurifies with Rat1-Rai1 in S. cerevisiae, but its mechanism of interaction with them is not known. We report here the cryo-EM structure of the S. cerevisiae Rat1-Rai1-Rtt103 ternary complex at 2.9 Å resolution. We found that a short segment of Rtt103 is in close contact with Rai1, while the rest of Rtt103, including its RNA polymerase II C-terminal domain interaction domain, shows no interactions with Rai1 or Rat1. This is in contrast to the observations on the Komagataella phaffii Rat1-Rai1-Rtt103 complex, where only the RNA polymerase II C-terminal domain interaction domain of Rtt103 has contacts with Rai1. Our structure reveals that S. cerevisiae Rtt103 Pro261 and Tyr263 have important contacts with Rai1, and we show that the P261G/Y263A mutation of Rtt103 blocks the interaction with Rat1-Rai1. Our structure suggests that, in yeast, this segment of Rtt103, which we have named the Rai1 interaction segment, likely helps the recruitment of Rat1-Rai1 to RNA polymerase II for termination.

Suggested Citation

  • Hsu-Feng Chu & Liang Tong, 2025. "Molecular basis for the interaction between Saccharomyces cerevisiae Rtt103 and the Rat1-Rai1 complex," Nature Communications, Nature, vol. 16(1), pages 1-7, December.
    • Handle: RePEc:nat:natcom:v:16:y:2025:i:1:d:10.1038_s41467-025-58671-z
    DOI: 10.1038/s41467-025-58671-z
    as

    Download full text from publisher

    File URL: https://www.nature.com/articles/s41467-025-58671-z
    File Function: Abstract
    Download Restriction: no
    File URL: https://libkey.io/10.1038/s41467-025-58671-z?utm_source=ideas
    LibKey link: if access is restricted and if your library uses this service, LibKey will redirect you to where you can use your library subscription to access this item
    ---><---

    References listed on IDEAS

    as
    1. Tatsuo Yanagisawa & Yuko Murayama & Haruhiko Ehara & Mie Goto & Mari Aoki & Shun-ichi Sekine, 2024. "Structural basis of eukaryotic transcription termination by the Rat1 exonuclease complex," Nature Communications, Nature, vol. 15(1), pages 1-12, December.
    2. Xinfu Jiao & Song Xiang & ChanSeok Oh & Charles E. Martin & Liang Tong & Megerditch Kiledjian, 2010. "Identification of a quality-control mechanism for mRNA 5′-end capping," Nature, Nature, vol. 467(7315), pages 608-611, September.
    3. Yuan Zeng & Hong-Wei Zhang & Xiao-Xian Wu & Yu Zhang, 2024. "Structural basis of exoribonuclease-mediated mRNA transcription termination," Nature, Nature, vol. 628(8009), pages 887-893, April.
    4. Minkyu Kim & Nevan J. Krogan & Lidia Vasiljeva & Oliver J. Rando & Eduard Nedea & Jack F. Greenblatt & Stephen Buratowski, 2004. "The yeast Rat1 exonuclease promotes transcription termination by RNA polymerase II," Nature, Nature, vol. 432(7016), pages 517-522, November.
    Full references (including those not matched with items on IDEAS)

    Most related items

    These are the items that most often cite the same works as this one and are cited by the same works as this one.
    1. Krzysztof Kuś & Loic Carrique & Tea Kecman & Marjorie Fournier & Sarah Sayed Hassanein & Ebru Aydin & Cornelia Kilchert & Jonathan M. Grimes & Lidia Vasiljeva, 2025. "DSIF factor Spt5 coordinates transcription, maturation and exoribonucleolysis of RNA polymerase II transcripts," Nature Communications, Nature, vol. 16(1), pages 1-19, December.
    2. Tatsuo Yanagisawa & Yuko Murayama & Haruhiko Ehara & Mie Goto & Mari Aoki & Shun-ichi Sekine, 2024. "Structural basis of eukaryotic transcription termination by the Rat1 exonuclease complex," Nature Communications, Nature, vol. 15(1), pages 1-12, December.
    3. François-Xavier Stubbe & Pauline Ponsard & Florian A. Steiner & Damien Hermand, 2025. "SSUP-72/PINN-1 coordinates RNA-polymerase II 3′ pausing and developmental gene expression in C. elegans," Nature Communications, Nature, vol. 16(1), pages 1-11, December.
    4. Konstantin Axt & Sarah L French & Ann L Beyer & David Tollervey, 2014. "Kinetic Analysis Demonstrates a Requirement for the Rat1 Exonuclease in Cotranscriptional Pre-rRNA Cleavage," PLOS ONE, Public Library of Science, vol. 9(2), pages 1-11, February.
    5. Ebru Aydin & Silke Schreiner & Jacqueline Böhme & Birte Keil & Jan Weber & Bojan Žunar & Timo Glatter & Cornelia Kilchert, 2024. "DEAD-box ATPase Dbp2 is the key enzyme in an mRNP assembly checkpoint at the 3’-end of genes and involved in the recycling of cleavage factors," Nature Communications, Nature, vol. 15(1), pages 1-20, December.
    6. Ying Xiong & Weijing Han & Chunhua Xu & Jing Shi & Lisha Wang & Taoli Jin & Qi Jia & Ying Lu & Shuxin Hu & Shuo-Xing Dou & Wei Lin & Terence R. Strick & Shuang Wang & Ming Li, 2024. "Single-molecule reconstruction of eukaryotic factor-dependent transcription termination," Nature Communications, Nature, vol. 15(1), pages 1-12, December.
    7. Krishanpal Anamika & Àkos Gyenis & Laetitia Poidevin & Olivier Poch & Làszlò Tora, 2012. "RNA Polymerase II Pausing Downstream of Core Histone Genes Is Different from Genes Producing Polyadenylated Transcripts," PLOS ONE, Public Library of Science, vol. 7(6), pages 1-14, June.

    More about this item

    Statistics

    Access and download statistics

    Corrections

    All material on this site has been provided by the respective publishers and authors. You can help correct errors and omissions. When requesting a correction, please mention this item's handle: RePEc:nat:natcom:v:16:y:2025:i:1:d:10.1038_s41467-025-58671-z. See general information about how to correct material in RePEc.

    If you have authored this item and are not yet registered with RePEc, we encourage you to do it here. This allows to link your profile to this item. It also allows you to accept potential citations to this item that we are uncertain about.

    If CitEc recognized a bibliographic reference but did not link an item in RePEc to it, you can help with this form .

    If you know of missing items citing this one, you can help us creating those links by adding the relevant references in the same way as above, for each refering item. If you are a registered author of this item, you may also want to check the "citations" tab in your RePEc Author Service profile, as there may be some citations waiting for confirmation.

    For technical questions regarding this item, or to correct its authors, title, abstract, bibliographic or download information, contact: Sonal Shukla or Springer Nature Abstracting and Indexing (email available below). General contact details of provider: http://www.nature.com .

    Please note that corrections may take a couple of weeks to filter through the various RePEc services.

    IDEAS is a RePEc service. RePEc uses bibliographic data supplied by the respective publishers.