In vivo hypermutation and continuous evolution

Rosana S. Molina; Gordon Rix; Amanuella A. Mengiste; Beatriz Álvarez; Daeje Seo; Haiqi Chen; Juan E. Hurtado; Qiong Zhang; Jorge Donato García-García; Zachary J. Heins; Patrick J. Almhjell; Frances H. Arnold; Ahmad S. Khalil; Andrew D. Hanson; John E. Dueber; David V. Schaffer; Fei Chen; Seokhee Kim; Luis Ángel Fernández; Matthew D. Shoulders; Chang C. Liu

doi:10.1038/s43586-022-00119-5

In vivo hypermutation and continuous evolution

Rosana S. Molina, Gordon Rix, Amanuella A. Mengiste, Beatriz Álvarez, Daeje Seo, Haiqi Chen, Juan E. Hurtado, Qiong Zhang, Jorge Donato García-García, Zachary J. Heins, Patrick J. Almhjell, Frances H. Arnold, Ahmad S. Khalil, Andrew D. Hanson, John E. Dueber, David V. Schaffer, Fei Chen, Seokhee Kim, Luis Ángel Fernández, Matthew D. ShouldersChang C. Liu

Research output: Contribution to journal › Review article › peer-review

24 Scopus citations

Abstract

Directed evolution has revolutionized biomolecular engineering by applying cycles of mutation, amplification and selection to genes of interest (GOIs). However, classical directed evolution methods that rely on manually staged evolutionary cycles constrain the scale and depth of the evolutionary search that is possible. We describe genetic systems that achieve cycles of rapid mutation, amplification and selection fully inside living cells, enabling the continuous evolution of GOIs as cells grow. These systems advance the scale, evolutionary search depth, ease and overall power of directed evolution and access important new areas of protein evolution and engineering.

Original language	English (US)
Article number	36
Journal	Nature Reviews Methods Primers
Volume	2
Issue number	1
DOIs	https://doi.org/10.1038/s43586-022-00119-5
State	Published - Dec 2022

ASJC Scopus subject areas

Biochemistry, Genetics and Molecular Biology(all)

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10.1038/s43586-022-00119-5

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Molina, R. S., Rix, G., Mengiste, A. A., Álvarez, B., Seo, D., Chen, H., Hurtado, J. E., Zhang, Q., García-García, J. D., Heins, Z. J., Almhjell, P. J., Arnold, F. H., Khalil, A. S., Hanson, A. D., Dueber, J. E., Schaffer, D. V., Chen, F., Kim, S., Fernández, L. Á., ... Liu, C. C. (2022). In vivo hypermutation and continuous evolution. Nature Reviews Methods Primers, 2(1), Article 36. https://doi.org/10.1038/s43586-022-00119-5

Molina, RS, Rix, G, Mengiste, AA, Álvarez, B, Seo, D, Chen, H, Hurtado, JE, Zhang, Q, García-García, JD, Heins, ZJ, Almhjell, PJ, Arnold, FH, Khalil, AS, Hanson, AD, Dueber, JE, Schaffer, DV, Chen, F, Kim, S, Fernández, LÁ, Shoulders, MD & Liu, CC 2022, 'In vivo hypermutation and continuous evolution', Nature Reviews Methods Primers, vol. 2, no. 1, 36. https://doi.org/10.1038/s43586-022-00119-5

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abstract = "Directed evolution has revolutionized biomolecular engineering by applying cycles of mutation, amplification and selection to genes of interest (GOIs). However, classical directed evolution methods that rely on manually staged evolutionary cycles constrain the scale and depth of the evolutionary search that is possible. We describe genetic systems that achieve cycles of rapid mutation, amplification and selection fully inside living cells, enabling the continuous evolution of GOIs as cells grow. These systems advance the scale, evolutionary search depth, ease and overall power of directed evolution and access important new areas of protein evolution and engineering.",

author = "Molina, {Rosana S.} and Gordon Rix and Mengiste, {Amanuella A.} and Beatriz {\'A}lvarez and Daeje Seo and Haiqi Chen and Hurtado, {Juan E.} and Qiong Zhang and Garc{\'i}a-Garc{\'i}a, {Jorge Donato} and Heins, {Zachary J.} and Almhjell, {Patrick J.} and Arnold, {Frances H.} and Khalil, {Ahmad S.} and Hanson, {Andrew D.} and Dueber, {John E.} and Schaffer, {David V.} and Fei Chen and Seokhee Kim and Fern{\'a}ndez, {Luis {\'A}ngel} and Shoulders, {Matthew D.} and Liu, {Chang C.}",

note = "Funding Information: The authors thank members of their groups for insightful discussions. This work was funded by National Institutes of Health (NIH) National Institute of General Medical Sciences (NIGMS) 1R35GM139513 (C.C.L.); NIH NIGMS 1R35GM136354 (M.D.S.); MIT Robert J Silbey Fellowship (A.A.M.); MIT School of Science Fund for Future of Science (A.A.M.); US Department of Energy, Office of Science, Basic Energy Sciences under Award DE-SC0020153 (A.D.H.); Innovative Genomics Institute and Laboratory for Genomics Research (J.E.H., J.E.D. and D.V.S.); UC Berkeley Miller Basic Research Fellowship (Q.Z.); NIH National Institute of Biomedical Imaging and Bioengineering (NIBIB) 1R01EB027793 (A.S.K.); Department of Defense (DoD) Vannevar Bush Faculty Fellowship N00014-20-1-2825 (A.S.K.); NIH NIGMS 1R01GM125887 (F.H.A.); and Ministerio de Ciencia e Innovaci{\'o}n - Consejo Superior de Investigaciones Cient{\'i}ficas (MICIN-CSIC) PTI + REC-EU SGL2103051 and EU Horizon 2020 research and innovation programme FET Open 965018-BIOCELLPHE (L.A.F.). The content is solely the responsibility of the authors and does not necessarily represent the official views of the NIH or other funding agencies. Publisher Copyright: {\textcopyright} 2022, Springer Nature Limited.",

year = "2022",

month = dec,

doi = "10.1038/s43586-022-00119-5",

language = "English (US)",

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T1 - In vivo hypermutation and continuous evolution

AU - Molina, Rosana S.

AU - Rix, Gordon

AU - Mengiste, Amanuella A.

AU - Álvarez, Beatriz

AU - Seo, Daeje

AU - Chen, Haiqi

AU - Hurtado, Juan E.

AU - Zhang, Qiong

AU - García-García, Jorge Donato

AU - Heins, Zachary J.

AU - Almhjell, Patrick J.

AU - Arnold, Frances H.

AU - Khalil, Ahmad S.

AU - Hanson, Andrew D.

AU - Dueber, John E.

AU - Schaffer, David V.

AU - Chen, Fei

AU - Kim, Seokhee

AU - Fernández, Luis Ángel

AU - Shoulders, Matthew D.

AU - Liu, Chang C.

N1 - Funding Information: The authors thank members of their groups for insightful discussions. This work was funded by National Institutes of Health (NIH) National Institute of General Medical Sciences (NIGMS) 1R35GM139513 (C.C.L.); NIH NIGMS 1R35GM136354 (M.D.S.); MIT Robert J Silbey Fellowship (A.A.M.); MIT School of Science Fund for Future of Science (A.A.M.); US Department of Energy, Office of Science, Basic Energy Sciences under Award DE-SC0020153 (A.D.H.); Innovative Genomics Institute and Laboratory for Genomics Research (J.E.H., J.E.D. and D.V.S.); UC Berkeley Miller Basic Research Fellowship (Q.Z.); NIH National Institute of Biomedical Imaging and Bioengineering (NIBIB) 1R01EB027793 (A.S.K.); Department of Defense (DoD) Vannevar Bush Faculty Fellowship N00014-20-1-2825 (A.S.K.); NIH NIGMS 1R01GM125887 (F.H.A.); and Ministerio de Ciencia e Innovación - Consejo Superior de Investigaciones Científicas (MICIN-CSIC) PTI + REC-EU SGL2103051 and EU Horizon 2020 research and innovation programme FET Open 965018-BIOCELLPHE (L.A.F.). The content is solely the responsibility of the authors and does not necessarily represent the official views of the NIH or other funding agencies. Publisher Copyright: © 2022, Springer Nature Limited.

PY - 2022/12

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N2 - Directed evolution has revolutionized biomolecular engineering by applying cycles of mutation, amplification and selection to genes of interest (GOIs). However, classical directed evolution methods that rely on manually staged evolutionary cycles constrain the scale and depth of the evolutionary search that is possible. We describe genetic systems that achieve cycles of rapid mutation, amplification and selection fully inside living cells, enabling the continuous evolution of GOIs as cells grow. These systems advance the scale, evolutionary search depth, ease and overall power of directed evolution and access important new areas of protein evolution and engineering.

AB - Directed evolution has revolutionized biomolecular engineering by applying cycles of mutation, amplification and selection to genes of interest (GOIs). However, classical directed evolution methods that rely on manually staged evolutionary cycles constrain the scale and depth of the evolutionary search that is possible. We describe genetic systems that achieve cycles of rapid mutation, amplification and selection fully inside living cells, enabling the continuous evolution of GOIs as cells grow. These systems advance the scale, evolutionary search depth, ease and overall power of directed evolution and access important new areas of protein evolution and engineering.

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DO - 10.1038/s43586-022-00119-5

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JO - Nature Reviews Methods Primers

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ER -

In vivo hypermutation and continuous evolution

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