IDEAS home Printed from https://ideas.repec.org/a/nat/natcom/v15y2024i1d10.1038_s41467-024-47800-9.html
   My bibliography  Save this article

CoCas9 is a compact nuclease from the human microbiome for efficient and precise genome editing

Author

Listed:
  • Eleonora Pedrazzoli

    (University of Trento)

  • Michele Demozzi

    (University of Trento)

  • Elisabetta Visentin

    (University of Trento)

  • Matteo Ciciani

    (University of Trento)

  • Ilaria Bonuzzi

    (University of Trento)

  • Laura Pezzè

    (Alia Therapeutics)

  • Lorenzo Lucchetta

    (University of Trento)

  • Giulia Maule

    (University of Trento)

  • Simone Amistadi

    (University of Trento
    INSERM)

  • Federica Esposito

    (Telethon Institute of Genetics and Medicine (TIGEM))

  • Mariangela Lupo

    (Telethon Institute of Genetics and Medicine (TIGEM))

  • Annarita Miccio

    (INSERM)

  • Alberto Auricchio

    (Telethon Institute of Genetics and Medicine (TIGEM)
    University of Naples “Federico II”)

  • Antonio Casini

    (Alia Therapeutics)

  • Nicola Segata

    (University of Trento)

  • Anna Cereseto

    (University of Trento)

Abstract

The expansion of the CRISPR-Cas toolbox is highly needed to accelerate the development of therapies for genetic diseases. Here, through the interrogation of a massively expanded repository of metagenome-assembled genomes, mostly from human microbiomes, we uncover a large variety (n = 17,173) of type II CRISPR-Cas loci. Among these we identify CoCas9, a strongly active and high-fidelity nuclease with reduced molecular size (1004 amino acids) isolated from an uncultivated Collinsella species. CoCas9 is efficiently co-delivered with its sgRNA through adeno associated viral (AAV) vectors, obtaining efficient in vivo editing in the mouse retina. With this study we uncover a collection of previously uncharacterized Cas9 nucleases, including CoCas9, which enriches the genome editing toolbox.

Suggested Citation

  • Eleonora Pedrazzoli & Michele Demozzi & Elisabetta Visentin & Matteo Ciciani & Ilaria Bonuzzi & Laura Pezzè & Lorenzo Lucchetta & Giulia Maule & Simone Amistadi & Federica Esposito & Mariangela Lupo &, 2024. "CoCas9 is a compact nuclease from the human microbiome for efficient and precise genome editing," Nature Communications, Nature, vol. 15(1), pages 1-12, December.
    • Handle: RePEc:nat:natcom:v:15:y:2024:i:1:d:10.1038_s41467-024-47800-9
    DOI: 10.1038/s41467-024-47800-9
    as

    Download full text from publisher

    File URL: https://www.nature.com/articles/s41467-024-47800-9
    File Function: Abstract
    Download Restriction: no
    File URL: https://libkey.io/10.1038/s41467-024-47800-9?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. Benjamin P. Kleinstiver & Michelle S. Prew & Shengdar Q. Tsai & Ved V. Topkar & Nhu T. Nguyen & Zongli Zheng & Andrew P. W. Gonzales & Zhuyun Li & Randall T. Peterson & Jing-Ruey Joanna Yeh & Martin J, 2015. "Engineered CRISPR-Cas9 nucleases with altered PAM specificities," Nature, Nature, vol. 523(7561), pages 481-485, July.
    2. Anuska Das & Travis H. Hand & Chardasia L. Smith & Ethan Wickline & Michael Zawrotny & Hong Li, 2020. "The molecular basis for recognition of 5′-NNNCC-3′ PAM and its methylation state by Acidothermus cellulolyticus Cas9," Nature Communications, Nature, vol. 11(1), pages 1-11, December.
    3. F. Ann Ran & Le Cong & Winston X. Yan & David A. Scott & Jonathan S. Gootenberg & Andrea J. Kriz & Bernd Zetsche & Ophir Shalem & Xuebing Wu & Kira S. Makarova & Eugene V. Koonin & Phillip A. Sharp & , 2015. "In vivo genome editing using Staphylococcus aureus Cas9," Nature, Nature, vol. 520(7546), pages 186-191, April.
    4. 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.
    5. Eunji Kim & Taeyoung Koo & Sung Wook Park & Daesik Kim & Kyoungmi Kim & Hee-Yeon Cho & Dong Woo Song & Kyu Jun Lee & Min Hee Jung & Seokjoong Kim & Jin Hyoung Kim & Jeong Hun Kim & Jin-Soo Kim, 2017. "In vivo genome editing with a small Cas9 orthologue derived from Campylobacter jejuni," Nature Communications, Nature, vol. 8(1), pages 1-12, April.
    6. Matteo Ciciani & Michele Demozzi & Eleonora Pedrazzoli & Elisabetta Visentin & Laura Pezzè & Lorenzo Federico Signorini & Aitor Blanco-Miguez & Moreno Zolfo & Francesco Asnicar & Antonio Casini & Anna, 2022. "Automated identification of sequence-tailored Cas9 proteins using massive metagenomic data," Nature Communications, Nature, vol. 13(1), pages 1-8, December.
    7. Jennifer A. Doudna, 2020. "The promise and challenge of therapeutic genome editing," Nature, Nature, vol. 578(7794), pages 229-236, February.
    8. Alexandre Almeida & Alex L. Mitchell & Miguel Boland & Samuel C. Forster & Gregory B. Gloor & Aleksandra Tarkowska & Trevor D. Lawley & Robert D. Finn, 2019. "A new genomic blueprint of the human gut microbiota," Nature, Nature, vol. 568(7753), pages 499-504, April.
    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. 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.
    2. Zhaohui Zhong & Guanqing Liu & Zhongjie Tang & Shuyue Xiang & Liang Yang & Lan Huang & Yao He & Tingting Fan & Shishi Liu & Xuelian Zheng & Tao Zhang & Yiping Qi & Jian Huang & Yong Zhang, 2023. "Efficient plant genome engineering using a probiotic sourced CRISPR-Cas9 system," Nature Communications, Nature, vol. 14(1), pages 1-16, December.
    3. 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.
    4. Matteo Ciciani & Michele Demozzi & Eleonora Pedrazzoli & Elisabetta Visentin & Laura Pezzè & Lorenzo Federico Signorini & Aitor Blanco-Miguez & Moreno Zolfo & Francesco Asnicar & Antonio Casini & Anna, 2022. "Automated identification of sequence-tailored Cas9 proteins using massive metagenomic data," Nature Communications, Nature, vol. 13(1), pages 1-8, December.
    5. 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.
    6. 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.
    7. Péter István Kulcsár & András Tálas & Zoltán Ligeti & Eszter Tóth & Zsófia Rakvács & Zsuzsa Bartos & Sarah Laura Krausz & Ágnes Welker & Vanessza Laura Végi & Krisztina Huszár & Ervin Welker, 2023. "A cleavage rule for selection of increased-fidelity SpCas9 variants with high efficiency and no detectable off-targets," Nature Communications, Nature, vol. 14(1), pages 1-20, December.
    8. Dawn G. L. Thean & Hoi Yee Chu & John H. C. Fong & Becky K. C. Chan & Peng Zhou & Cynthia C. S. Kwok & Yee Man Chan & Silvia Y. L. Mak & Gigi C. G. Choi & Joshua W. K. Ho & Zongli Zheng & Alan S. L. W, 2022. "Machine learning-coupled combinatorial mutagenesis enables resource-efficient engineering of CRISPR-Cas9 genome editor activities," Nature Communications, Nature, vol. 13(1), pages 1-14, December.
    9. Jeremy Vicencio & Carlos Sánchez-Bolaños & Ismael Moreno-Sánchez & David Brena & Charles E. Vejnar & Dmytro Kukhtar & Miguel Ruiz-López & Mariona Cots-Ponjoan & Alejandro Rubio & Natalia Rodrigo Meler, 2022. "Genome editing in animals with minimal PAM CRISPR-Cas9 enzymes," Nature Communications, Nature, vol. 13(1), pages 1-13, December.
    10. Shiran Abadi & Winston X Yan & David Amar & Itay Mayrose, 2017. "A machine learning approach for predicting CRISPR-Cas9 cleavage efficiencies and patterns underlying its mechanism of action," PLOS Computational Biology, Public Library of Science, vol. 13(10), pages 1-24, October.
    11. Maarten H. Geurts & Shashank Gandhi & Matteo G. Boretto & Ninouk Akkerman & Lucca L. M. Derks & Gijs Son & Martina Celotti & Sarina Harshuk-Shabso & Flavia Peci & Harry Begthel & Delilah Hendriks & Pa, 2023. "One-step generation of tumor models by base editor multiplexing in adult stem cell-derived organoids," Nature Communications, Nature, vol. 14(1), pages 1-18, December.
    12. 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.
    13. Lin Zhao & Sabrina R. T. Koseki & Rachel A. Silverstein & Nadia Amrani & Christina Peng & Christian Kramme & Natasha Savic & Martin Pacesa & Tomás C. Rodríguez & Teodora Stan & Emma Tysinger & Lauren , 2023. "PAM-flexible genome editing with an engineered chimeric Cas9," Nature Communications, Nature, vol. 14(1), pages 1-8, December.
    14. Xiaoguang Pan & Kunli Qu & Hao Yuan & Xi Xiang & Christian Anthon & Liubov Pashkova & Xue Liang & Peng Han & Giulia I. Corsi & Fengping Xu & Ping Liu & Jiayan Zhong & Yan Zhou & Tao Ma & Hui Jiang & J, 2022. "Massively targeted evaluation of therapeutic CRISPR off-targets in cells," Nature Communications, Nature, vol. 13(1), pages 1-14, December.
    15. Li Zhang & Karen R. Jonscher & Zuyuan Zhang & Yi Xiong & Ryan S. Mueller & Jacob E. Friedman & Chongle Pan, 2022. "Islet autoantibody seroconversion in type-1 diabetes is associated with metagenome-assembled genomes in infant gut microbiomes," Nature Communications, Nature, vol. 13(1), pages 1-14, December.
    16. Jae-Chang Cho, 2021. "Human microbiome privacy risks associated with summary statistics," PLOS ONE, Public Library of Science, vol. 16(4), pages 1-11, April.
    17. Fang Liang & Yu Zhang & Lin Li & Yexin Yang & Ji-Feng Fei & Yanmei Liu & Wei Qin, 2022. "SpG and SpRY variants expand the CRISPR toolbox for genome editing in zebrafish," Nature Communications, Nature, vol. 13(1), pages 1-10, December.
    18. Xiangjun He & Zhenjie Zhang & Junyi Xue & Yaofeng Wang & Siqi Zhang & Junkang Wei & Chenzi Zhang & Jue Wang & Brian Anugerah Urip & Chun Christopher Ngan & Junjiang Sun & Yuefeng Li & Zhiqian Lu & Hui, 2022. "Low-dose AAV-CRISPR-mediated liver-specific knock-in restored hemostasis in neonatal hemophilia B mice with subtle antibody response," Nature Communications, Nature, vol. 13(1), pages 1-17, December.
    19. Xiangyang Li & Guiquan Zhang & Shisheng Huang & Yao Liu & Jin Tang & Mingtian Zhong & Xin Wang & Wenjun Sun & Yuan Yao & Quanjiang Ji & Xiaolong Wang & Jianghuai Liu & Shiqiang Zhu & Xingxu Huang, 2023. "Development of a versatile nuclease prime editor with upgraded precision," Nature Communications, Nature, vol. 14(1), pages 1-13, December.
    20. Margot Karlikow & Evan Amalfitano & Xiaolong Yang & Jennifer Doucet & Abigail Chapman & Peivand Sadat Mousavi & Paige Homme & Polina Sutyrina & Winston Chan & Sofia Lemak & Alexander F. Yakunin & Adam, 2023. "CRISPR-induced DNA reorganization for multiplexed nucleic acid detection," Nature Communications, Nature, vol. 14(1), pages 1-11, 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_s41467-024-47800-9. 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.