IDEAS home Printed from https://ideas.repec.org/a/nat/natcom/v14y2023i1d10.1038_s41467-023-39087-z.html
   My bibliography  Save this article

A Cas3-base editing tool for targetable in vivo mutagenesis

Author

Listed:
  • Anna Zimmermann

    (VIB-KU Leuven Center for Microbiology
    KU Leuven)

  • Julian E. Prieto-Vivas

    (VIB-KU Leuven Center for Microbiology
    KU Leuven)

  • Charlotte Cautereels

    (VIB-KU Leuven Center for Microbiology
    KU Leuven)

  • Anton Gorkovskiy

    (VIB-KU Leuven Center for Microbiology
    KU Leuven)

  • Jan Steensels

    (VIB-KU Leuven Center for Microbiology
    KU Leuven)

  • Yves Peer

    (Ghent University
    VIB Center for Plant Systems Biology
    University of Pretoria
    Nanjing Agricultural University)

  • Kevin J. Verstrepen

    (VIB-KU Leuven Center for Microbiology
    KU Leuven)

Abstract

The generation of genetic diversity via mutagenesis is routinely used for protein engineering and pathway optimization. Current technologies for random mutagenesis often target either the whole genome or relatively narrow windows. To bridge this gap, we developed CoMuTER (Confined Mutagenesis using a Type I-E CRISPR-Cas system), a tool that allows inducible and targetable, in vivo mutagenesis of genomic loci of up to 55 kilobases. CoMuTER employs the targetable helicase Cas3, signature enzyme of the class 1 type I-E CRISPR-Cas system, fused to a cytidine deaminase to unwind and mutate large stretches of DNA at once, including complete metabolic pathways. The tool increases the number of mutations in the target region 350-fold compared to the rest of the genome, with an average of 0.3 mutations per kilobase. We demonstrate the suitability of CoMuTER for pathway optimization by doubling the production of lycopene in Saccharomyces cerevisiae after a single round of mutagenesis.

Suggested Citation

  • Anna Zimmermann & Julian E. Prieto-Vivas & Charlotte Cautereels & Anton Gorkovskiy & Jan Steensels & Yves Peer & Kevin J. Verstrepen, 2023. "A Cas3-base editing tool for targetable in vivo mutagenesis," Nature Communications, Nature, vol. 14(1), pages 1-16, December.
  • Handle: RePEc:nat:natcom:v:14:y:2023:i:1:d:10.1038_s41467-023-39087-z
    DOI: 10.1038/s41467-023-39087-z
    as

    Download full text from publisher

    File URL: https://www.nature.com/articles/s41467-023-39087-z
    File Function: Abstract
    Download Restriction: no

    File URL: https://libkey.io/10.1038/s41467-023-39087-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. Peter Edge & Vikas Bansal, 2019. "Longshot enables accurate variant calling in diploid genomes from single-molecule long read sequencing," Nature Communications, Nature, vol. 10(1), pages 1-10, December.
    2. Harris H. Wang & Farren J. Isaacs & Peter A. Carr & Zachary Z. Sun & George Xu & Craig R. Forest & George M. Church, 2009. "Programming cells by multiplex genome engineering and accelerated evolution," Nature, Nature, vol. 460(7257), pages 894-898, August.
    3. C. J. Paddon & P. J. Westfall & D. J. Pitera & K. Benjamin & K. Fisher & D. McPhee & M. D. Leavell & A. Tai & A. Main & D. Eng & D. R. Polichuk & K. H. Teoh & D. W. Reed & T. Treynor & J. Lenihan & H., 2013. "High-level semi-synthetic production of the potent antimalarial artemisinin," Nature, Nature, vol. 496(7446), pages 528-532, April.
    4. Kazuto Yoshimi & Kohei Takeshita & Noriyuki Kodera & Satomi Shibumura & Yuko Yamauchi & Mine Omatsu & Kenichi Umeda & Yayoi Kunihiro & Masaki Yamamoto & Tomoji Mashimo, 2022. "Dynamic mechanisms of CRISPR interference by Escherichia coli CRISPR-Cas3," Nature Communications, Nature, vol. 13(1), pages 1-14, December.
    5. Bates, Douglas & Mächler, Martin & Bolker, Ben & Walker, Steve, 2015. "Fitting Linear Mixed-Effects Models Using lme4," Journal of Statistical Software, Foundation for Open Access Statistics, vol. 67(i01).
    6. Aaron Cravens & Osman K. Jamil & Deze Kong & Jonathan T. Sockolosky & Christina D. Smolke, 2021. "Polymerase-guided base editing enables in vivo mutagenesis and rapid protein engineering," Nature Communications, Nature, vol. 12(1), pages 1-12, December.
    7. Lenth, Russell V., 2016. "Least-Squares Means: The R Package lsmeans," Journal of Statistical Software, Foundation for Open Access Statistics, vol. 69(i01).
    8. Beatriz Álvarez & Mario Mencía & Víctor Lorenzo & Luis Ángel Fernández, 2020. "In vivo diversification of target genomic sites using processive base deaminase fusions blocked by dCas9," Nature Communications, Nature, vol. 11(1), pages 1-14, December.
    9. Kevin M. Esvelt & Jacob C. Carlson & David R. Liu, 2011. "A system for the continuous directed evolution of biomolecules," Nature, Nature, vol. 472(7344), pages 499-503, April.
    10. Shakked O. Halperin & Connor J. Tou & Eric B. Wong & Cyrus Modavi & David V. Schaffer & John E. Dueber, 2018. "CRISPR-guided DNA polymerases enable diversification of all nucleotides in a tunable window," Nature, Nature, vol. 560(7717), pages 248-252, August.
    11. Alexis C. Komor & Yongjoo B. Kim & Michael S. Packer & John A. Zuris & David R. Liu, 2016. "Programmable editing of a target base in genomic DNA without double-stranded DNA cleavage," Nature, Nature, vol. 533(7603), pages 420-424, May.
    12. Hiroyuki Morisaka & Kazuto Yoshimi & Yuya Okuzaki & Peter Gee & Yayoi Kunihiro & Ekasit Sonpho & Huaigeng Xu & Noriko Sasakawa & Yuki Naito & Shinichiro Nakada & Takashi Yamamoto & Shigetoshi Sano & A, 2019. "CRISPR-Cas3 induces broad and unidirectional genome editing in human cells," Nature Communications, Nature, vol. 10(1), pages 1-13, December.
    13. Nathan Crook & Joseph Abatemarco & Jie Sun & James M. Wagner & Alexander Schmitz & Hal S. Alper, 2016. "In vivo continuous evolution of genes and pathways in yeast," Nature Communications, Nature, vol. 7(1), pages 1-14, December.
    14. André B. Canelas & Nicola Harrison & Alessandro Fazio & Jie Zhang & Juha-Pekka Pitkänen & Joost van den Brink & Barbara M. Bakker & Lara Bogner & Jildau Bouwman & Juan I. Castrillo & Ayca Cankorur & P, 2010. "Integrated multilaboratory systems biology reveals differences in protein metabolism between two reference yeast strains," Nature Communications, Nature, vol. 1(1), pages 1-8, December.
    15. Xiaozhou Luo & Michael A. Reiter & Leo d’Espaux & Jeff Wong & Charles M. Denby & Anna Lechner & Yunfeng Zhang & Adrian T. Grzybowski & Simon Harth & Weiyin Lin & Hyunsu Lee & Changhua Yu & John Shin &, 2019. "Complete biosynthesis of cannabinoids and their unnatural analogues in yeast," Nature, Nature, vol. 567(7746), pages 123-126, March.
    Full references (including those not matched with items on IDEAS)

    Citations

    Citations are extracted by the CitEc Project, subscribe to its RSS feed for this item.
    as


    Cited by:

    1. Meiling Lu & Chenlin Yu & Yuwen Zhang & Wenjun Ju & Zhi Ye & Chenyang Hua & Jinze Mao & Chunyi Hu & Zhenhuang Yang & Yibei Xiao, 2024. "Structure and genome editing of type I-B CRISPR-Cas," Nature Communications, Nature, vol. 15(1), pages 1-12, December.
    2. Charlotte Cautereels & Jolien Smets & Peter Bircham & Dries De Ruysscher & Anna Zimmermann & Peter De Rijk & Jan Steensels & Anton Gorkovskiy & Joleen Masschelein & Kevin J. Verstrepen, 2024. "Combinatorial optimization of gene expression through recombinase-mediated promoter and terminator shuffling in yeast," Nature Communications, Nature, vol. 15(1), pages 1-17, December.
    3. Jing Guo & Luyao Gong & Haiying Yu & Ming Li & Qiaohui An & Zhenquan Liu & Shuru Fan & Changjialian Yang & Dahe Zhao & Jing Han & Hua Xiang, 2024. "Engineered minimal type I CRISPR-Cas system for transcriptional activation and base editing in human cells," Nature Communications, Nature, vol. 15(1), pages 1-16, December.

    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. Enrico Orsi & Lennart Schada von Borzyskowski & Stephan Noack & Pablo I. Nikel & Steffen N. Lindner, 2024. "Automated in vivo enzyme engineering accelerates biocatalyst optimization," Nature Communications, Nature, vol. 15(1), pages 1-14, December.
    2. Sean Coogan & Zhixian Sui & David Raubenheimer, 2018. "Gluttony and guilt: monthly trends in internet search query data are comparable with national-level energy intake and dieting behavior," Palgrave Communications, Palgrave Macmillan, vol. 4(1), pages 1-9, December.
    3. Claire H Luby & Julie C Dawson & Irwin L Goldman, 2016. "Assessment and Accessibility of Phenotypic and Genotypic Diversity of Carrot (Daucus carota L. var. sativus) Cultivars Commercially Available in the United States," PLOS ONE, Public Library of Science, vol. 11(12), pages 1-19, December.
    4. Muhammad Javed ASIF & Deivaseeno Dorairaj & Ratnam Wickneswari, 2017. "Characterization of natural provenances of Acacia mangium Willd. and Acacia auriculiformis A. Cunn. ex Benth. in Malaysia based on phenotypic traits," Journal of Forest Science, Czech Academy of Agricultural Sciences, vol. 63(12), pages 562-576.
    5. Emily Zhang & Monica E. Neugebauer & Nicholas A. Krasnow & David R. Liu, 2024. "Phage-assisted evolution of highly active cytosine base editors with enhanced selectivity and minimal sequence context preference," Nature Communications, Nature, vol. 15(1), pages 1-13, December.
    6. Belinda A Wilson & Maldwyn J Evans & William G Batson & Sam C Banks & Iain J Gordon & Donald B Fletcher & Claire Wimpenny & Jenny Newport & Emily Belton & Annette Rypalski & Tim Portas & Adrian D Mann, 2020. "Adapting reintroduction tactics in successive trials increases the likelihood of establishment for an endangered carnivore in a fenced sanctuary," PLOS ONE, Public Library of Science, vol. 15(6), pages 1-17, June.
    7. Jack Chun-Ting Liu & Ricardo De La Peña & Christian Tocol & Elizabeth S. Sattely, 2024. "Reconstitution of early paclitaxel biosynthetic network," Nature Communications, Nature, vol. 15(1), pages 1-11, December.
    8. Sławomir Kujawski & Agnieszka Kujawska & Mariusz Kozakiewicz & Djordje G. Jakovljevic & Błażej Stankiewicz & Julia L. Newton & Kornelia Kędziora-Kornatowska & Paweł Zalewski, 2022. "Effects of Sitting Callisthenic Balance and Resistance Exercise Programs on Cognitive Function in Older Participants," IJERPH, MDPI, vol. 19(22), pages 1-18, November.
    9. Ayse Ilkay Isik & Edward A Vessel, 2019. "Continuous ratings of movie watching reveal idiosyncratic dynamics of aesthetic enjoyment," PLOS ONE, Public Library of Science, vol. 14(10), pages 1-21, October.
    10. Duško Lainšček & Vida Forstnerič & Veronika Mikolič & Špela Malenšek & Peter Pečan & Mojca Benčina & Matjaž Sever & Helena Podgornik & Roman Jerala, 2022. "Coiled-coil heterodimer-based recruitment of an exonuclease to CRISPR/Cas for enhanced gene editing," Nature Communications, Nature, vol. 13(1), pages 1-12, December.
    11. Philip Amoah & Noah Adamtey & Olufunke Cofie, 2017. "Effect of Urine, Poultry Manure, and Dewatered Faecal Sludge on Agronomic Characteristics of Cabbage in Accra, Ghana," Resources, MDPI, vol. 6(2), pages 1-14, May.
    12. Jozef N. Coppelmans & Fieke M. A. Wagemans & Lotte F. Dillen, 2024. "An empirical investigation of emotion and the criminal law: towards a “criminalization bias”?," Palgrave Communications, Palgrave Macmillan, vol. 11(1), pages 1-17, December.
    13. Jo Dorning & Stephen Harris, 2017. "Dominance, gender, and season influence food patch use in a group-living, solitary foraging canid," Behavioral Ecology, International Society for Behavioral Ecology, vol. 28(5), pages 1302-1313.
    14. Daniel C. Volke & Román A. Martino & Ekaterina Kozaeva & Andrea M. Smania & Pablo I. Nikel, 2022. "Modular (de)construction of complex bacterial phenotypes by CRISPR/nCas9-assisted, multiplex cytidine base-editing," Nature Communications, Nature, vol. 13(1), pages 1-14, December.
    15. Mary S. Morrison & Tina Wang & Aditya Raguram & Colin Hemez & David R. Liu, 2021. "Disulfide-compatible phage-assisted continuous evolution in the periplasmic space," Nature Communications, Nature, vol. 12(1), pages 1-14, December.
    16. Ng'ombe, John, 2019. "Economics of the Greenseeder Hand Planter, Discrete Choice Modeling, and On-Farm Field Experimentation," Thesis Commons jckt7, Center for Open Science.
    17. Patrizia Piotti & Juliane Kaminski, 2016. "Do Dogs Provide Information Helpfully?," PLOS ONE, Public Library of Science, vol. 11(8), pages 1-19, August.
    18. Peter N. Ciaccia & Zhuobin Liang & Anabel Y. Schweitzer & Eli Metzner & Farren J. Isaacs, 2024. "Enhanced eMAGE applied to identify genetic factors of nuclear hormone receptor dysfunction via combinatorial gene editing," Nature Communications, Nature, vol. 15(1), pages 1-11, December.
    19. Siwei Li & Jingjing An & Yaqiu Li & Xiagu Zhu & Dongdong Zhao & Lixian Wang & Yonghui Sun & Yuanzhao Yang & Changhao Bi & Xueli Zhang & Meng Wang, 2022. "Automated high-throughput genome editing platform with an AI learning in situ prediction model," Nature Communications, Nature, vol. 13(1), pages 1-11, December.
    20. Karis J. McFarlane & Daniela F. Cusack & Lee H. Dietterich & Alexandra L. Hedgpeth & Kari M. Finstad & Andrew T. Nottingham, 2024. "Experimental warming and drying increase older carbon contributions to soil respiration in lowland tropical forests," Nature Communications, Nature, vol. 15(1), pages 1-10, 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:14:y:2023:i:1:d:10.1038_s41467-023-39087-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.