Establishing chromosomal design-build-test-learn through a synthetic chromosome and its combinatorial reconfiguration

• DOI: 10.1016/j.xgen.2023.100435
• Publication Date: 2023-11-09T16:50:50Z
• Authors: Jee Loon Foo; Shohei Kitano; Adelia Vicanatali...; Zhu Jin; Yicong Lin; Zhouqing Luo; Linsen Huang; Zhenzhen Liang; Leslie A. Mitchell; Kun Yang; Adison Wong; Yizhi Cai; Jitong Cai; Giovanni Stracqua...; Joel S. Bader; Jef D. Boeke; Junbiao Dai; Matthew Wook Chang
• Keywords: Synthetic Biology; Chromosome engineering

Chromosome-level design-build-test-learn cycles (chrDBTLs) allow systematic combinatorial reconfiguration of chromosomes with ease. Here, we established chrDBTL a redesigned synthetic Saccharomyces cerevisiae chromosome XV, synXV. We designed and built synXV to harbor strategically inserted features, modified elements, synonymously recoded genes throughout the chromosome. Based on chromosome, developed method enable chrDBTL: CRISPR-Cas9-mediated mitotic recombination endoreduplication (CRIMiRE). CRIMiRE allowed creation customized wild-type/synthetic combinations, accelerating genotype-phenotype mapping redesign. also leveraged as "build-to-learn" model organism for translation studies by ribosome profiling. conducted locus-to-locus comparison occupancy between wild-type providing insight into effects codon changes features dynamics in vivo. Overall, versatile reconfigurable system that advances understanding biological mechanisms engineering strains.