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^*

^*Corresponding author for this work

School of Natural Sciences

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

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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
Article number	100379
Pages (from-to)	1-16.e7
Number of pages	24
Journal	Cell Genomics
Volume	3
Issue number	11
DOIs	https://doi.org/10.1016/j.xgen.2023.100379
Publication status	Published - 8 Nov 2023

Bibliographical note

Copyright the Author(s) 2023. Version archived for private and non-commercial use with the permission of the author/s and according to publisher conditions. For further rights please contact the publisher.

Keywords

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

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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), 1-16.e7. Article 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 = "adaptive laboratory evolution, directed evolution, SCRaMbLE, synthetic biology, synthetic genome, TAR1, 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 = "Copyright the Author(s) 2023. Version archived for private and non-commercial use with the permission of the author/s and according to publisher conditions. For further rights please contact the publisher. ",

year = "2023",

month = nov,

day = "8",

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

language = "English",

volume = "3",

pages = "1--16.e7",

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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, pp. 1-16.e7. https://doi.org/10.1016/j.xgen.2023.100379

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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.

N1 - Copyright the Author(s) 2023. Version archived for private and non-commercial use with the permission of the author/s and according to publisher conditions. For further rights please contact the publisher.

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 - adaptive laboratory evolution

KW - directed evolution

KW - SCRaMbLE

KW - synthetic biology

KW - synthetic genome

KW - TAR1

KW - yeast

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UR - http://purl.org/au-research/grants/arc/DP200100717

U2 - 10.1016/j.xgen.2023.100379

DO - 10.1016/j.xgen.2023.100379

M3 - Article

C2 - 38020977

AN - SCOPUS:85175637016

SN - 2666-979X

VL - 3

SP - 1-16.e7

JO - Cell Genomics

JF - Cell Genomics

IS - 11

M1 - 100379

ER -

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

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Keywords

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