Parallel laboratory evolution and rational debugging reveal genomic plasticity to S. cerevisiae synthetic chromosome XIV defects

Thomas C. Williams; Heinrich Kroukamp; Xin Xu; Elizabeth L.I. Wightman; Briardo Llorente; Anthony R. Borneman; Alexander C. Carpenter; Niel Van Wyk; Felix Meier; Thomas R.V. Collier; Monica I. Espinosa; Elizabeth L. Daniel; Roy S.K. Walker; Yizhi Cai; Helena K.M. Nevalainen; Natalie C. Curach; Ira W. Deveson; Timothy R. Mercer; Daniel L. Johnson; Leslie A. Mitchell; Joel S. Bader; Giovanni Stracquadanio; Jef D. Boeke; Hugh D. Goold; Isak S. Pretorius; Ian T. Paulsen

doi:10.1016/j.xgen.2023.100379

Parallel laboratory evolution and rational debugging reveal genomic plasticity to S. cerevisiae synthetic chromosome XIV defects

Thomas C. Williams, Heinrich Kroukamp, Xin Xu, Elizabeth L.I. Wightman, Briardo Llorente, Anthony R. Borneman, Alexander C. Carpenter, Niel Van Wyk, Felix Meier, Thomas R.V. Collier, Monica I. Espinosa, Elizabeth L. Daniel, Roy S.K. Walker, Yizhi Cai, Helena K.M. Nevalainen, Natalie C. Curach, Ira W. Deveson, Timothy R. Mercer, Daniel L. Johnson, Leslie A. MitchellJoel S. Bader, Giovanni Stracquadanio, Jef D. Boeke, Hugh D. Goold, Isak S. Pretorius, Ian T. Paulsen

Biomedical Engineering

Research output: Contribution to journal › Article › peer-review

Abstract

Synthetic chromosome engineering is a complex process due to the need to identify and repair growth defects and deal with combinatorial gene essentiality when rearranging chromosomes. To alleviate these issues, we have demonstrated novel approaches for repairing and rearranging synthetic Saccharomyces cerevisiae genomes. We have designed, constructed, and restored wild-type fitness to a synthetic 753,096-bp version of S. cerevisiae chromosome XIV as part of the Synthetic Yeast Genome project. In parallel to the use of rational engineering approaches to restore wild-type fitness, we used adaptive laboratory evolution to generate a general growth-defect-suppressor rearrangement in the form of increased TAR1 copy number. We also extended the utility of the synthetic chromosome recombination and modification by loxPsym-mediated evolution (SCRaMbLE) system by engineering synthetic-wild-type tetraploid hybrid strains that buffer against essential gene loss, highlighting the plasticity of the S. cerevisiae genome in the presence of rational and non-rational modifications.

Original language	English (US)
Article number	100379
Journal	Cell Genomics
Volume	3
Issue number	11
DOIs	https://doi.org/10.1016/j.xgen.2023.100379
State	Published - Nov 8 2023

Keywords

SCRaMbLE
TAR1
adaptive laboratory evolution
directed evolution
synthetic biology
synthetic genome
yeast

ASJC Scopus subject areas

Biochemistry, Genetics and Molecular Biology (miscellaneous)
Genetics

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10.1016/j.xgen.2023.100379

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Williams, T. C., Kroukamp, H., Xu, X., Wightman, E. L. I., Llorente, B., Borneman, A. R., Carpenter, A. C., Van Wyk, N., Meier, F., Collier, T. R. V., Espinosa, M. I., Daniel, E. L., Walker, R. S. K., Cai, Y., Nevalainen, H. K. M., Curach, N. C., Deveson, I. W., Mercer, T. R., Johnson, D. L., ... Paulsen, I. T. (2023). Parallel laboratory evolution and rational debugging reveal genomic plasticity to S. cerevisiae synthetic chromosome XIV defects. Cell Genomics, 3(11), Article 100379. https://doi.org/10.1016/j.xgen.2023.100379

Williams, TC, Kroukamp, H, Xu, X, Wightman, ELI, Llorente, B, Borneman, AR, Carpenter, AC, Van Wyk, N, Meier, F, Collier, TRV, Espinosa, MI, Daniel, EL, Walker, RSK, Cai, Y, Nevalainen, HKM, Curach, NC, Deveson, IW, Mercer, TR, Johnson, DL, Mitchell, LA, Bader, JS, Stracquadanio, G, Boeke, JD, Goold, HD, Pretorius, IS & Paulsen, IT 2023, 'Parallel laboratory evolution and rational debugging reveal genomic plasticity to S. cerevisiae synthetic chromosome XIV defects', Cell Genomics, vol. 3, no. 11, 100379. https://doi.org/10.1016/j.xgen.2023.100379

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title = "Parallel laboratory evolution and rational debugging reveal genomic plasticity to S. cerevisiae synthetic chromosome XIV defects",

abstract = "Synthetic chromosome engineering is a complex process due to the need to identify and repair growth defects and deal with combinatorial gene essentiality when rearranging chromosomes. To alleviate these issues, we have demonstrated novel approaches for repairing and rearranging synthetic Saccharomyces cerevisiae genomes. We have designed, constructed, and restored wild-type fitness to a synthetic 753,096-bp version of S. cerevisiae chromosome XIV as part of the Synthetic Yeast Genome project. In parallel to the use of rational engineering approaches to restore wild-type fitness, we used adaptive laboratory evolution to generate a general growth-defect-suppressor rearrangement in the form of increased TAR1 copy number. We also extended the utility of the synthetic chromosome recombination and modification by loxPsym-mediated evolution (SCRaMbLE) system by engineering synthetic-wild-type tetraploid hybrid strains that buffer against essential gene loss, highlighting the plasticity of the S. cerevisiae genome in the presence of rational and non-rational modifications.",

keywords = "SCRaMbLE, TAR1, adaptive laboratory evolution, directed evolution, synthetic biology, synthetic genome, yeast",

author = "Williams, {Thomas C.} and Heinrich Kroukamp and Xin Xu and Wightman, {Elizabeth L.I.} and Briardo Llorente and Borneman, {Anthony R.} and Carpenter, {Alexander C.} and {Van Wyk}, Niel and Felix Meier and Collier, {Thomas R.V.} and Espinosa, {Monica I.} and Daniel, {Elizabeth L.} and Walker, {Roy S.K.} and Yizhi Cai and Nevalainen, {Helena K.M.} and Curach, {Natalie C.} and Deveson, {Ira W.} and Mercer, {Timothy R.} and Johnson, {Daniel L.} and Mitchell, {Leslie A.} and Bader, {Joel S.} and Giovanni Stracquadanio and Boeke, {Jef D.} and Goold, {Hugh D.} and Pretorius, {Isak S.} and Paulsen, {Ian T.}",

note = "Publisher Copyright: {\textcopyright} 2023 The Author(s)",

year = "2023",

month = nov,

day = "8",

doi = "10.1016/j.xgen.2023.100379",

language = "English (US)",

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T1 - Parallel laboratory evolution and rational debugging reveal genomic plasticity to S. cerevisiae synthetic chromosome XIV defects

AU - Williams, Thomas C.

AU - Kroukamp, Heinrich

AU - Xu, Xin

AU - Wightman, Elizabeth L.I.

AU - Llorente, Briardo

AU - Borneman, Anthony R.

AU - Carpenter, Alexander C.

AU - Van Wyk, Niel

AU - Meier, Felix

AU - Collier, Thomas R.V.

AU - Espinosa, Monica I.

AU - Daniel, Elizabeth L.

AU - Walker, Roy S.K.

AU - Cai, Yizhi

AU - Nevalainen, Helena K.M.

AU - Curach, Natalie C.

AU - Deveson, Ira W.

AU - Mercer, Timothy R.

AU - Johnson, Daniel L.

AU - Mitchell, Leslie A.

AU - Bader, Joel S.

AU - Stracquadanio, Giovanni

AU - Boeke, Jef D.

AU - Goold, Hugh D.

AU - Pretorius, Isak S.

AU - Paulsen, Ian T.

PY - 2023/11/8

Y1 - 2023/11/8

N2 - Synthetic chromosome engineering is a complex process due to the need to identify and repair growth defects and deal with combinatorial gene essentiality when rearranging chromosomes. To alleviate these issues, we have demonstrated novel approaches for repairing and rearranging synthetic Saccharomyces cerevisiae genomes. We have designed, constructed, and restored wild-type fitness to a synthetic 753,096-bp version of S. cerevisiae chromosome XIV as part of the Synthetic Yeast Genome project. In parallel to the use of rational engineering approaches to restore wild-type fitness, we used adaptive laboratory evolution to generate a general growth-defect-suppressor rearrangement in the form of increased TAR1 copy number. We also extended the utility of the synthetic chromosome recombination and modification by loxPsym-mediated evolution (SCRaMbLE) system by engineering synthetic-wild-type tetraploid hybrid strains that buffer against essential gene loss, highlighting the plasticity of the S. cerevisiae genome in the presence of rational and non-rational modifications.

AB - Synthetic chromosome engineering is a complex process due to the need to identify and repair growth defects and deal with combinatorial gene essentiality when rearranging chromosomes. To alleviate these issues, we have demonstrated novel approaches for repairing and rearranging synthetic Saccharomyces cerevisiae genomes. We have designed, constructed, and restored wild-type fitness to a synthetic 753,096-bp version of S. cerevisiae chromosome XIV as part of the Synthetic Yeast Genome project. In parallel to the use of rational engineering approaches to restore wild-type fitness, we used adaptive laboratory evolution to generate a general growth-defect-suppressor rearrangement in the form of increased TAR1 copy number. We also extended the utility of the synthetic chromosome recombination and modification by loxPsym-mediated evolution (SCRaMbLE) system by engineering synthetic-wild-type tetraploid hybrid strains that buffer against essential gene loss, highlighting the plasticity of the S. cerevisiae genome in the presence of rational and non-rational modifications.

KW - SCRaMbLE

KW - TAR1

KW - adaptive laboratory evolution

KW - directed evolution

KW - synthetic biology

KW - synthetic genome

KW - yeast

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JO - Cell Genomics

JF - Cell Genomics

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M1 - 100379

ER -

Parallel laboratory evolution and rational debugging reveal genomic plasticity to S. cerevisiae synthetic chromosome XIV defects

Abstract

Keywords

ASJC Scopus subject areas

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