IDEAS home Printed from https://ideas.repec.org/a/nat/natcom/v15y2024i1d10.1038_s41467-024-54491-9.html
   My bibliography  Save this article

Cas12e orthologs evolve variable structural elements to facilitate dsDNA cleavage

Author

Listed:
  • Danyuan Li

    (Tsinghua University
    Tsinghua University)

  • Shouyue Zhang

    (Chinese Academy of Sciences
    University of Chinese Academy of Sciences)

  • Shuo Lin

    (Tsinghua University
    Tsinghua University)

  • Wenjing Xing

    (Tsinghua University)

  • Yun Yang

    (Tsinghua University
    Tsinghua University)

  • Fengxia Zhu

    (Peking University Institute of Advanced Agricultural Sciences)

  • Dingding Su

    (Peking University Institute of Advanced Agricultural Sciences)

  • Chunlai Chen

    (Tsinghua University)

  • Jun-Jie Gogo Liu

    (Tsinghua University
    Tsinghua University)

Abstract

Exceptionally diverse type V CRISPR-Cas systems provide numerous RNA-guided nucleases as powerful tools for DNA manipulation. Two known Cas12e nucleases, DpbCas12e and PlmCas12e, are both effective in genome editing. However, many differences exist in their in vitro dsDNA cleavage activities, reflecting the diversity in Cas12e’s enzymatic properties. To comprehensively understand the Cas12e family, we identify and characterize six unreported Cas12e members that vary in their CRISPR-locus architectures, PAM preferences, and cleavage efficacies. Interestingly, among all variants, PlmCas12e exhibits the most robust trans-cleavage activity and the lowest salt sensitivity in cis-cleavage. Further structural comparisons reveal that the unique NTSB domain in PlmCas12e is beneficial to DNA unwinding at high salt concentrations, while some NTSB-lacking Cas12e proteins rely on positively charged loops for dsDNA unwinding. These findings demonstrate how divergent evolution of structural elements shapes the nuclease diversity within the Cas12e family, potentially contributing to their adaptations to varying environmental conditions.

Suggested Citation

  • Danyuan Li & Shouyue Zhang & Shuo Lin & Wenjing Xing & Yun Yang & Fengxia Zhu & Dingding Su & Chunlai Chen & Jun-Jie Gogo Liu, 2024. "Cas12e orthologs evolve variable structural elements to facilitate dsDNA cleavage," Nature Communications, Nature, vol. 15(1), pages 1-14, December.
    • Handle: RePEc:nat:natcom:v:15:y:2024:i:1:d:10.1038_s41467-024-54491-9
    DOI: 10.1038/s41467-024-54491-9
    as

    Download full text from publisher

    File URL: https://www.nature.com/articles/s41467-024-54491-9
    File Function: Abstract
    Download Restriction: no
    File URL: https://libkey.io/10.1038/s41467-024-54491-9?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. Giedrius Gasiunas & Joshua K. Young & Tautvydas Karvelis & Darius Kazlauskas & Tomas Urbaitis & Monika Jasnauskaite & Mantvyda M. Grusyte & Sushmitha Paulraj & Po-Hao Wang & Zhenglin Hou & Shane K. Do, 2020. "A catalogue of biochemically diverse CRISPR-Cas9 orthologs," Nature Communications, Nature, vol. 11(1), pages 1-10, December.
    2. Carolin Anders & Ole Niewoehner & Alessia Duerst & Martin Jinek, 2014. "Structural basis of PAM-dependent target DNA recognition by the Cas9 endonuclease," Nature, Nature, vol. 513(7519), pages 569-573, September.
    3. Liyang Zhang & John A. Zuris & Ramya Viswanathan & Jasmine N. Edelstein & Rolf Turk & Bernice Thommandru & H. Tomas Rube & Steve E. Glenn & Michael A. Collingwood & Nicole M. Bode & Sarah F. Beaudoin , 2021. "AsCas12a ultra nuclease facilitates the rapid generation of therapeutic cell medicines," Nature Communications, Nature, vol. 12(1), pages 1-15, December.
    4. David Burstein & Lucas B. Harrington & Steven C. Strutt & Alexander J. Probst & Karthik Anantharaman & Brian C. Thomas & Jennifer A. Doudna & Jillian F. Banfield, 2017. "New CRISPR–Cas systems from uncultivated microbes," Nature, Nature, vol. 542(7640), pages 237-241, February.
    5. Elitza Deltcheva & Krzysztof Chylinski & Cynthia M. Sharma & Karine Gonzales & Yanjie Chao & Zaid A. Pirzada & Maria R. Eckert & Jörg Vogel & Emmanuelle Charpentier, 2011. "CRISPR RNA maturation by trans-encoded small RNA and host factor RNase III," Nature, Nature, vol. 471(7340), pages 602-607, March.
    6. Jun-Jie Liu & Natalia Orlova & Benjamin L. Oakes & Enbo Ma & Hannah B. Spinner & Katherine L. M. Baney & Jonathan Chuck & Dan Tan & Gavin J. Knott & Lucas B. Harrington & Basem Al-Shayeb & Alexander W, 2019. "CasX enzymes comprise a distinct family of RNA-guided genome editors," Nature, Nature, vol. 566(7743), pages 218-223, February.
    7. Bo Zhang & Diyin Luo & Yu Li & Vanja Perčulija & Jing Chen & Jinying Lin & Yangmiao Ye & Songying Ouyang, 2021. "Mechanistic insights into the R-loop formation and cleavage in CRISPR-Cas12i1," Nature Communications, Nature, vol. 12(1), pages 1-13, December.
    8. Liyang Zhang & John A. Zuris & Ramya Viswanathan & Jasmine N. Edelstein & Rolf Turk & Bernice Thommandru & H. Tomas Rube & Steve E. Glenn & Michael A. Collingwood & Nicole M. Bode & Sarah F. Beaudoin , 2021. "Author Correction: AsCas12a ultra nuclease facilitates the rapid generation of therapeutic cell medicines," Nature Communications, Nature, vol. 12(1), pages 1-1, December.
    9. Singh, Amar & Singh, Navin, 2015. "Effect of salt concentration on the stability of heterogeneous DNA," Physica A: Statistical Mechanics and its Applications, Elsevier, vol. 419(C), pages 328-334.
    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. Changchang Xin & Jianhang Yin & Shaopeng Yuan & Liqiong Ou & Mengzhu Liu & Weiwei Zhang & Jiazhi Hu, 2022. "Comprehensive assessment of miniature CRISPR-Cas12f nucleases for gene disruption," Nature Communications, Nature, vol. 13(1), pages 1-10, December.
    2. Burcu Bestas & Sandra Wimberger & Dmitrii Degtev & Alexandra Madsen & Antje K. Rottner & Fredrik Karlsson & Sergey Naumenko & Megan Callahan & Julia Liz Touza & Margherita Francescatto & Carl Ivar Möl, 2023. "A Type II-B Cas9 nuclease with minimized off-targets and reduced chromosomal translocations in vivo," Nature Communications, Nature, vol. 14(1), pages 1-15, December.
    3. Daphne Collias & Elena Vialetto & Jiaqi Yu & Khoa Co & Éva d. H. Almási & Ann-Sophie Rüttiger & Tatjana Achmedov & Till Strowig & Chase L. Beisel, 2023. "Systematically attenuating DNA targeting enables CRISPR-driven editing in bacteria," Nature Communications, Nature, vol. 14(1), pages 1-12, December.
    4. Colin McGaw & Anthony J. Garrity & Gabrielle Z. Munoz & Jeffrey R. Haswell & Sejuti Sengupta & Elise Keston-Smith & Pratyusha Hunnewell & Alexa Ornstein & Mishti Bose & Quinton Wessells & Noah Jakimo , 2022. "Engineered Cas12i2 is a versatile high-efficiency platform for therapeutic genome editing," Nature Communications, Nature, vol. 13(1), pages 1-11, December.
    5. Hang Su & Yuanchun Wang & Jin Xu & Ahmad A. Omar & Jude W. Grosser & Milica Calovic & Liyang Zhang & Yu Feng & Christopher A. Vakulskas & Nian Wang, 2023. "Generation of the transgene-free canker-resistant Citrus sinensis using Cas12a/crRNA ribonucleoprotein in the T0 generation," Nature Communications, Nature, vol. 14(1), pages 1-12, December.
    6. Raed Ibraheim & Phillip W. L. Tai & Aamir Mir & Nida Javeed & Jiaming Wang & Tomás C. Rodríguez & Suk Namkung & Samantha Nelson & Eraj Shafiq Khokhar & Esther Mintzer & Stacy Maitland & Zexiang Chen &, 2021. "Self-inactivating, all-in-one AAV vectors for precision Cas9 genome editing via homology-directed repair in vivo," Nature Communications, Nature, vol. 12(1), pages 1-17, December.
    7. Ying-Ying Jin & Peng Zhang & Le-Le Liu & Xiang Zhao & Xiao-Qing Hu & Si-Zhe Liu & Ze-Kun Li & Qian Liu & Jian-Qiao Wang & De-Long Hao & Zhu-Qin Zhang & Hou-Zao Chen & De-Pei Liu, 2024. "Enhancing homology-directed repair efficiency with HDR-boosting modular ssDNA donor," Nature Communications, Nature, vol. 15(1), pages 1-14, December.
    8. Guanhua Xun & Zhixin Zhu & Nilmani Singh & Jingxia Lu & Piyush K. Jain & Huimin Zhao, 2024. "Harnessing noncanonical crRNA for highly efficient genome editing," Nature Communications, Nature, vol. 15(1), pages 1-13, December.
    9. Daniela S. Aliaga Goltsman & Lisa M. Alexander & Jyun-Liang Lin & Rodrigo Fregoso Ocampo & Benjamin Freeman & Rebecca C. Lamothe & Andres Perez Rivas & Morayma M. Temoche-Diaz & Shailaja Chadha & Nata, 2022. "Compact Cas9d and HEARO enzymes for genome editing discovered from uncultivated microbes," Nature Communications, Nature, vol. 13(1), pages 1-11, December.
    10. Yin Liu & Xinyi Liu & Dongyi Wei & Lu Dang & Xiaoran Xu & Shisheng Huang & Liwen Li & Sanyun Wu & Jinxian Wu & Xiaoyan Liu & Wenjun Sun & Wanyu Tao & Yongchang Wei & Xingxu Huang & Kui Li & Xinjie Wan, 2024. "CoHIT: a one-pot ultrasensitive ERA-CRISPR system for detecting multiple same-site indels," Nature Communications, Nature, vol. 15(1), pages 1-14, December.
    11. Yang Liu & Filipe Pinto & Xinyi Wan & Zhugen Yang & Shuguang Peng & Mengxi Li & Jonathan M. Cooper & Zhen Xie & Christopher E. French & Baojun Wang, 2022. "Reprogrammed tracrRNAs enable repurposing of RNAs as crRNAs and sequence-specific RNA biosensors," Nature Communications, Nature, vol. 13(1), pages 1-12, December.
    12. Dalton T. Ham & Tyler S. Browne & Pooja N. Banglorewala & Tyler L. Wilson & Richard K. Michael & Gregory B. Gloor & David R. Edgell, 2023. "A generalizable Cas9/sgRNA prediction model using machine transfer learning with small high-quality datasets," Nature Communications, Nature, vol. 14(1), pages 1-16, December.
    13. 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.
    14. Ulaganathan, Kandasamy & Goud, Sravanthi & Reddy, Madhavi & Kayalvili, Ulaganathan, 2017. "Genome engineering for breaking barriers in lignocellulosic bioethanol production," Renewable and Sustainable Energy Reviews, Elsevier, vol. 74(C), pages 1080-1107.
    15. 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.
    16. Jian Wang & Yuxi Teng & Ruihua Zhang & Yifei Wu & Lei Lou & Yusong Zou & Michelle Li & Zhong-Ru Xie & Yajun Yan, 2021. "Engineering a PAM-flexible SpdCas9 variant as a universal gene repressor," Nature Communications, Nature, vol. 12(1), pages 1-10, December.
    17. Danielle Miller & Adi Stern & David Burstein, 2022. "Deciphering microbial gene function using natural language processing," Nature Communications, Nature, vol. 13(1), pages 1-11, December.
    18. Boris Kantor & Bernadette O’Donovan & Joseph Rittiner & Dellila Hodgson & Nicholas Lindner & Sophia Guerrero & Wendy Dong & Austin Zhang & Ornit Chiba-Falek, 2024. "The therapeutic implications of all-in-one AAV-delivered epigenome-editing platform in neurodegenerative disorders," Nature Communications, Nature, vol. 15(1), pages 1-15, December.
    19. Kazuki Kato & Sae Okazaki & Soumya Kannan & Han Altae-Tran & F. Esra Demircioglu & Yukari Isayama & Junichiro Ishikawa & Masahiro Fukuda & Rhiannon K. Macrae & Tomohiro Nishizawa & Kira S. Makarova & , 2022. "Structure of the IscB–ωRNA ribonucleoprotein complex, the likely ancestor of CRISPR-Cas9," Nature Communications, Nature, vol. 13(1), pages 1-10, December.
    20. Wenhui Li & Xianyue Jiang & Wuke Wang & Liya Hou & Runze Cai & Yongqian Li & Qiuxi Gu & Qinchang Chen & Peixiang Ma & Jin Tang & Menghao Guo & Guohui Chuai & Xingxu Huang & Jun Zhang & Qi Liu, 2024. "Discovering CRISPR-Cas system with self-processing pre-crRNA capability by foundation models," Nature Communications, Nature, vol. 15(1), pages 1-14, 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:15:y:2024:i:1:d:10.1038_s41467-024-54491-9. 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.