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

Research output: Contribution to journalArticlepeer-review


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 languageEnglish (US)
Article number100379
JournalCell Genomics
Issue number11
StatePublished - Nov 8 2023


  • 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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