IDEAS home Printed from https://ideas.repec.org/a/nat/natcom/v13y2022i1d10.1038_s41467-022-35275-5.html
   My bibliography  Save this article

Structural basis for the non-self RNA-activated protease activity of the type III-E CRISPR nuclease-protease Craspase

Author

Listed:
  • Ning Cui

    (Southern University of Science and Technology)

  • Jun-Tao Zhang

    (Southern University of Science and Technology)

  • Zhuolin Li

    (Southern University of Science and Technology)

  • Xiao-Yu Liu

    (Southern University of Science and Technology)

  • Chongyuan Wang

    (Chinese Academy of Science
    Chinese Academy of Science)

  • Hongda Huang

    (Southern University of Science and Technology)

  • Ning Jia

    (Southern University of Science and Technology
    Guangdong Provincial Key Laboratory of Cell Microenvironment and Disease Research, Southern University of Science and Technology
    Key University Laboratory of Metabolism and Health of Guangdong, Southern University of Science and Technology)

Abstract

The RNA-targeting type III-E CRISPR-gRAMP effector interacts with a caspase-like protease TPR-CHAT to form the CRISPR-guided caspase complex (Craspase), but their functional mechanism is unknown. Here, we report cryo-EM structures of the type III-E gRAMPcrRNA and gRAMPcrRNA-TPR-CHAT complexes, before and after either self or non-self RNA target binding, and elucidate the mechanisms underlying RNA-targeting and non-self RNA-induced protease activation. The associated TPR-CHAT adopted a distinct conformation upon self versus non-self RNA target binding, with nucleotides at positions −1 and −2 of the CRISPR-derived RNA (crRNA) serving as a sensor. Only binding of the non-self RNA target activated the TPR-CHAT protease, leading to cleavage of Csx30 protein. Furthermore, TPR-CHAT structurally resembled eukaryotic separase, but with a distinct mechanism for protease regulation. Our findings should facilitate the development of gRAMP-based RNA manipulation tools, and advance our understanding of the virus-host discrimination process governed by a nuclease-protease Craspase during type III-E CRISPR-Cas immunity.

Suggested Citation

  • Ning Cui & Jun-Tao Zhang & Zhuolin Li & Xiao-Yu Liu & Chongyuan Wang & Hongda Huang & Ning Jia, 2022. "Structural basis for the non-self RNA-activated protease activity of the type III-E CRISPR nuclease-protease Craspase," Nature Communications, Nature, vol. 13(1), pages 1-13, December.
  • Handle: RePEc:nat:natcom:v:13:y:2022:i:1:d:10.1038_s41467-022-35275-5
    DOI: 10.1038/s41467-022-35275-5
    as

    Download full text from publisher

    File URL: https://www.nature.com/articles/s41467-022-35275-5
    File Function: Abstract
    Download Restriction: no

    File URL: https://libkey.io/10.1038/s41467-022-35275-5?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. Ole Niewoehner & Carmela Garcia-Doval & Jakob T. Rostøl & Christian Berk & Frank Schwede & Laurent Bigler & Jonathan Hall & Luciano A. Marraffini & Martin Jinek, 2017. "Type III CRISPR–Cas systems produce cyclic oligoadenylate second messengers," Nature, Nature, vol. 548(7669), pages 543-548, August.
    2. Alexandra East-Seletsky & Mitchell R. O’Connell & Spencer C. Knight & David Burstein & Jamie H. D. Cate & Robert Tjian & Jennifer A. Doudna, 2016. "Two distinct RNase activities of CRISPR-C2c2 enable guide-RNA processing and RNA detection," Nature, Nature, vol. 538(7624), pages 270-273, October.
    3. Ahsen Özcan & Rohan Krajeski & Eleonora Ioannidi & Brennan Lee & Apolonia Gardner & Kira S. Makarova & Eugene V. Koonin & Omar O. Abudayyeh & Jonathan S. Gootenberg, 2021. "Programmable RNA targeting with the single-protein CRISPR effector Cas7-11," Nature, Nature, vol. 597(7878), pages 720-725, September.
    4. Tomohiro Miyoshi & Kosuke Ito & Ryo Murakami & Toshio Uchiumi, 2016. "Structural basis for the recognition of guide RNA and target DNA heteroduplex by Argonaute," Nature Communications, Nature, vol. 7(1), pages 1-12, September.
    5. Luciano A. Marraffini & Erik J. Sontheimer, 2010. "Self versus non-self discrimination during CRISPR RNA-directed immunity," Nature, Nature, vol. 463(7280), pages 568-571, January.
    6. Zhonghui Lin & Xuelian Luo & Hongtao Yu, 2016. "Structural basis of cohesin cleavage by separase," Nature, Nature, vol. 532(7597), pages 131-134, April.
    7. Jun Yu & Pierre Raia & Chloe M. Ghent & Tobias Raisch & Yashar Sadian & Simone Cavadini & Pramod M. Sabale & David Barford & Stefan Raunser & David O. Morgan & Andreas Boland, 2021. "Structural basis of human separase regulation by securin and CDK1–cyclin B1," Nature, Nature, vol. 596(7870), pages 138-142, August.
    8. Alexander J. Meeske & Sandra Nakandakari-Higa & Luciano A. Marraffini, 2019. "Cas13-induced cellular dormancy prevents the rise of CRISPR-resistant bacteriophage," Nature, Nature, vol. 570(7760), pages 241-245, June.
    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. Antonios Apostolopoulos & Naohiro Kawamoto & Siu Yu A. Chow & Hitomi Tsuiji & Yoshiho Ikeuchi & Yuichi Shichino & Shintaro Iwasaki, 2024. "dCas13-mediated translational repression for accurate gene silencing in mammalian cells," Nature Communications, Nature, vol. 15(1), pages 1-18, December.
    2. Lidiya Lisitskaya & Yeonoh Shin & Aleksei Agapov & Anna Olina & Ekaterina Kropocheva & Sergei Ryazansky & Alexei A. Aravin & Daria Esyunina & Katsuhiko S. Murakami & Andrey Kulbachinskiy, 2022. "Programmable RNA targeting by bacterial Argonaute nucleases with unconventional guide binding and cleavage specificity," Nature Communications, Nature, vol. 13(1), pages 1-15, December.
    3. Anna Nemudraia & Artem Nemudryi & Murat Buyukyoruk & Andrew M. Scherffius & Trevor Zahl & Tanner Wiegand & Shishir Pandey & Joseph E. Nichols & Laina N. Hall & Aidan McVey & Helen H. Lee & Royce A. Wi, 2022. "Sequence-specific capture and concentration of viral RNA by type III CRISPR system enhances diagnostic," Nature Communications, Nature, vol. 13(1), pages 1-12, December.
    4. Shunsuke Kawasaki & Hiroki Ono & Moe Hirosawa & Takeru Kuwabara & Shunsuke Sumi & Suji Lee & Knut Woltjen & Hirohide Saito, 2023. "Programmable mammalian translational modulators by CRISPR-associated proteins," Nature Communications, Nature, vol. 14(1), pages 1-17, December.
    5. Devashish Dwivedi & Daniela Harry & Patrick Meraldi, 2023. "Mild replication stress causes premature centriole disengagement via a sub-critical Plk1 activity under the control of ATR-Chk1," Nature Communications, Nature, vol. 14(1), pages 1-16, December.
    6. Grace N. Hibshman & Jack P. K. Bravo & Matthew M. Hooper & Tyler L. Dangerfield & Hongshan Zhang & Ilya J. Finkelstein & Kenneth A. Johnson & David W. Taylor, 2024. "Unraveling the mechanisms of PAMless DNA interrogation by SpRY-Cas9," Nature Communications, Nature, vol. 15(1), pages 1-15, December.
    7. Feiyu Zhao & Tao Zhang & Xiaodi Sun & Xiyun Zhang & Letong Chen & Hejun Wang & Jinze Li & Peng Fan & Liangxue Lai & Tingting Sui & Zhanjun Li, 2023. "A strategy for Cas13 miniaturization based on the structure and AlphaFold," Nature Communications, Nature, vol. 14(1), pages 1-13, December.
    8. Pengdbamba Dieudonné Zongo & Nicolas Cabanel & Guilhem Royer & Florence Depardieu & Alain Hartmann & Thierry Naas & Philippe Glaser & Isabelle Rosinski-Chupin, 2024. "An antiplasmid system drives antibiotic resistance gene integration in carbapenemase-producing Escherichia coli lineages," Nature Communications, Nature, vol. 15(1), pages 1-15, December.
    9. Hongrui Zhao & Yan Sheng & Tenghua Zhang & Shujun Zhou & Yuqing Zhu & Feiyang Qian & Meiru Liu & Weixue Xu & Dengsong Zhang & Jiaming Hu, 2024. "The CRISPR-Cas13a Gemini System for noncontiguous target RNA activation," Nature Communications, Nature, vol. 15(1), pages 1-11, December.
    10. Jack P. K. Bravo & Cristian Aparicio-Maldonado & Franklin L. Nobrega & Stan J. J. Brouns & David W. Taylor, 2022. "Structural basis for broad anti-phage immunity by DISARM," Nature Communications, Nature, vol. 13(1), pages 1-11, December.
    11. Yuqian Guo & Yaofeng Zhou & Hong Duan & Derong Xu & Min Wei & Yuhao Wu & Ying Xiong & Xirui Chen & Siyuan Wang & Daofeng Liu & Xiaolin Huang & Hongbo Xin & Yonghua Xiong & Ben Zhong Tang, 2024. "CRISPR/Cas-mediated “one to more” lighting-up nucleic acid detection using aggregation-induced emission luminogens," Nature Communications, Nature, vol. 15(1), pages 1-16, December.
    12. Evan A. Schwartz & Tess M. McBride & Jack P. K. Bravo & Daniel Wrapp & Peter C. Fineran & Robert D. Fagerlund & David W. Taylor, 2022. "Structural rearrangements allow nucleic acid discrimination by type I-D Cascade," Nature Communications, Nature, vol. 13(1), pages 1-11, December.
    13. Pierre Aldag & Marius Rutkauskas & Julene Madariaga-Marcos & Inga Songailiene & Tomas Sinkunas & Felix Kemmerich & Dominik Kauert & Virginijus Siksnys & Ralf Seidel, 2023. "Dynamic interplay between target search and recognition for a Type I CRISPR-Cas system," Nature Communications, Nature, vol. 14(1), pages 1-14, December.
    14. Xiangkai Zhen & Xiaolong Xu & Le Ye & Song Xie & Zhijie Huang & Sheng Yang & Yanhui Wang & Jinyu Li & Feng Long & Songying Ouyang, 2024. "Structural basis of antiphage immunity generated by a prokaryotic Argonaute-associated SPARSA system," Nature Communications, Nature, vol. 15(1), pages 1-13, December.
    15. M. Alejandra Zeballos C. & Hayden J. Moore & Tyler J. Smith & Jackson E. Powell & Najah S. Ahsan & Sijia Zhang & Thomas Gaj, 2023. "Mitigating a TDP-43 proteinopathy by targeting ataxin-2 using RNA-targeting CRISPR effector proteins," Nature Communications, Nature, vol. 14(1), pages 1-17, December.
    16. Gabriel Magno Freitas Almeida & Ville Hoikkala & Janne Ravantti & Noora Rantanen & Lotta-Riina Sundberg, 2022. "Mucin induces CRISPR-Cas defense in an opportunistic pathogen," Nature Communications, Nature, vol. 13(1), pages 1-12, December.
    17. Xinmi Song & Sheng Lei & Shunhang Liu & Yanqiu Liu & Pan Fu & Zhifeng Zeng & Ke Yang & Yu Chen & Ming Li & Qunxin She & Wenyuan Han, 2023. "Catalytically inactive long prokaryotic Argonaute systems employ distinct effectors to confer immunity via abortive infection," Nature Communications, Nature, vol. 14(1), pages 1-16, December.
    18. Chu Chen & Valentina Piano & Amal Alex & Simon J. Y. Han & Pim J. Huis in ’t Veld & Babhrubahan Roy & Daniel Fergle & Andrea Musacchio & Ajit P. Joglekar, 2023. "The structural flexibility of MAD1 facilitates the assembly of the Mitotic Checkpoint Complex," Nature Communications, Nature, vol. 14(1), pages 1-11, December.
    19. Shirin Fatma & Arpita Chakravarti & Xuankun Zeng & Raven H. Huang, 2021. "Molecular mechanisms of the CdnG-Cap5 antiphage defense system employing 3′,2′-cGAMP as the second messenger," Nature Communications, Nature, vol. 12(1), pages 1-9, December.
    20. Hung-Che Kuo & Joshua Prupes & Chia-Wei Chou & Ilya J. Finkelstein, 2024. "Massively parallel profiling of RNA-targeting CRISPR-Cas13d," Nature Communications, Nature, vol. 15(1), pages 1-13, December.

    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:13:y:2022:i:1:d:10.1038_s41467-022-35275-5. 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.