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Programming cells by multiplex genome engineering and accelerated evolution

Author

Listed:
  • Harris H. Wang

    (Harvard Medical School, Boston, Massachusetts 02115, USA
    Program in Biophysics, Harvard University, Cambridge, Massachusetts 02138, USA
    Program in Medical Engineering Medical Physics)

  • Farren J. Isaacs

    (Harvard Medical School, Boston, Massachusetts 02115, USA)

  • Peter A. Carr

    (The Center for Bits and Atoms,
    Media Lab, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA)

  • Zachary Z. Sun

    (Harvard College, Cambridge, Massachusetts 02138, USA)

  • George Xu

    (Harvard College, Cambridge, Massachusetts 02138, USA)

  • Craig R. Forest

    (George W. Woodruff School of Mechanical Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332, USA)

  • George M. Church

    (Harvard Medical School, Boston, Massachusetts 02115, USA)

Abstract

Generating genomic diversity Genomic diversity is difficult to generate in the laboratory in an efficient way. A new technique called MAGE (multiplex automated genome engineering), described here, simultaneously targets many locations on the chromosome for modification in a single cell or across a population of cells, thereby producing combinatorial genomic diversity. This is an automated and efficient approach that expedites the design and evolution of organisms with new and improved properties.

Suggested Citation

  • 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.
    • Handle: RePEc:nat:nature:v:460:y:2009:i:7257:d:10.1038_nature08187
    DOI: 10.1038/nature08187
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    Cited by:

    1. 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.
    2. Molly F. Parsons & Matthew F. Allan & Shanshan Li & Tyson R. Shepherd & Sakul Ratanalert & Kaiming Zhang & Krista M. Pullen & Wah Chiu & Silvi Rouskin & Mark Bathe, 2023. "3D RNA-scaffolded wireframe origami," Nature Communications, Nature, vol. 14(1), pages 1-14, December.
    3. Timothy P. Newing & Jodi L. Brewster & Lucy J. Fitschen & James C. Bouwer & Nikolas P. Johnston & Haibo Yu & Gökhan Tolun, 2022. "Redβ177 annealase structure reveals details of oligomerization and λ Red-mediated homologous DNA recombination," Nature Communications, Nature, vol. 13(1), pages 1-14, December.
    4. Einat Shaer Tamar & Roy Kishony, 2022. "Multistep diversification in spatiotemporal bacterial-phage coevolution," Nature Communications, Nature, vol. 13(1), pages 1-12, December.
    5. Jack M. Moen & Kyle Mohler & Svetlana Rogulina & Xiaojian Shi & Hongying Shen & Jesse Rinehart, 2022. "Enhanced access to the human phosphoproteome with genetically encoded phosphothreonine," Nature Communications, Nature, vol. 13(1), pages 1-14, December.
    6. 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.
    7. Brian J. Caldwell & Andrew S. Norris & Caroline F. Karbowski & Alyssa M. Wiegand & Vicki H. Wysocki & Charles E. Bell, 2022. "Structure of a RecT/Redβ family recombinase in complex with a duplex intermediate of DNA annealing," Nature Communications, Nature, vol. 13(1), pages 1-14, December.
    8. Carolyn N. Bayer & Maja Rennig & Anja K. Ehrmann & Morten H. H. Nørholm, 2021. "A standardized genome architecture for bacterial synthetic biology (SEGA)," Nature Communications, Nature, vol. 12(1), pages 1-13, December.
    9. 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.
    10. Sabarathinam Shanmugam & Anjana Hari & Arivalagan Pugazhendhi & Timo Kikas, 2023. "Integrated Catalytic Upgrading of Biomass-Derived Alcohols for Advanced Biofuel Production," Energies, MDPI, vol. 16(13), pages 1-24, June.
    11. 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.
    12. Joshua Tasoff & Michael T Mee & Harris H Wang, 2015. "An Economic Framework of Microbial Trade," PLOS ONE, Public Library of Science, vol. 10(7), pages 1-20, July.
    13. Marc Teufel & Carlo A. Klein & Maurice Mager & Patrick Sobetzko, 2022. "A multifunctional system for genome editing and large-scale interspecies gene transfer," Nature Communications, Nature, vol. 13(1), pages 1-19, December.
    14. Shanmugam, Sabarathinam & Ngo, Huu-Hao & Wu, Yi-Rui, 2020. "Advanced CRISPR/Cas-based genome editing tools for microbial biofuels production: A review," Renewable Energy, Elsevier, vol. 149(C), pages 1107-1119.
    15. Daniel Mark Shapiro & Gunasheil Mandava & Sibel Ebru Yalcin & Pol Arranz-Gibert & Peter J. Dahl & Catharine Shipps & Yangqi Gu & Vishok Srikanth & Aldo I. Salazar-Morales & J. Patrick O’Brien & Koen V, 2022. "Protein nanowires with tunable functionality and programmable self-assembly using sequence-controlled synthesis," Nature Communications, Nature, vol. 13(1), pages 1-10, December.
    16. T. Kuiken & G. Dana & K. Oye & D. Rejeski, 2014. "Shaping ecological risk research for synthetic biology," Journal of Environmental Studies and Sciences, Springer;Association of Environmental Studies and Sciences, vol. 4(3), pages 191-199, September.
    17. Das, Manali & Patra, Pradipta & Ghosh, Amit, 2020. "Metabolic engineering for enhancing microbial biosynthesis of advanced biofuels," Renewable and Sustainable Energy Reviews, Elsevier, vol. 119(C).
    18. 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.
    19. Michael B. Doud & Animesh Gupta & Victor Li & Sarah J. Medina & Caesar A. Fuente & Justin R. Meyer, 2024. "Competition-driven eco-evolutionary feedback reshapes bacteriophage lambda’s fitness landscape and enables speciation," Nature Communications, Nature, vol. 15(1), pages 1-12, December.

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