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

Jee Loon Foo; Shohei Kitano; Adelia Vicanatalita Susanto; Zhu Jin; Yicong Lin; Zhouqing Luo; Linsen Huang; Zhenzhen Liang; Leslie A. Mitchell; Kun Yang; Adison Wong; Yizhi Cai; Jitong Cai; Giovanni Stracquadanio; Joel S. Bader; Jef D. Boeke; Junbiao Dai; Matthew Wook Chang

doi:10.1016/j.xgen.2023.100435

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

Jee Loon Foo, Shohei Kitano, Adelia Vicanatalita Susanto, Zhu Jin, Yicong Lin, Zhouqing Luo, Linsen Huang, Zhenzhen Liang, Leslie A. Mitchell, Kun Yang, Adison Wong, Yizhi Cai, Jitong Cai, Giovanni Stracquadanio, Joel S. Bader, Jef D. Boeke, Junbiao Dai, Matthew Wook Chang

Biomedical Engineering

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

Abstract

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

Original language	English (US)
Article number	100435
Journal	Cell Genomics
Volume	3
Issue number	11
DOIs	https://doi.org/10.1016/j.xgen.2023.100435
State	Published - Nov 8 2023

Keywords

CRISPR-Cas9
Saccharomyces cerevisiae
chromosome reconfiguration
design-build-test-learn
mitotic recombination
synthetic biology
synthetic chromosome
synthetic genomics
synthetic yeast

ASJC Scopus subject areas

Biochemistry, Genetics and Molecular Biology (miscellaneous)
Genetics

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Foo, J. L., Kitano, S., Susanto, A. V., Jin, Z., Lin, Y., Luo, Z., Huang, L., Liang, Z., Mitchell, L. A., Yang, K., Wong, A., Cai, Y., Cai, J., Stracquadanio, G., Bader, J. S., Boeke, J. D., Dai, J., & Chang, M. W. (2023). Establishing chromosomal design-build-test-learn through a synthetic chromosome and its combinatorial reconfiguration. Cell Genomics, 3(11), Article 100435. https://doi.org/10.1016/j.xgen.2023.100435

Foo, JL, Kitano, S, Susanto, AV, Jin, Z, Lin, Y, Luo, Z, Huang, L, Liang, Z, Mitchell, LA, Yang, K, Wong, A, Cai, Y, Cai, J, Stracquadanio, G, Bader, JS, Boeke, JD, Dai, J & Chang, MW 2023, 'Establishing chromosomal design-build-test-learn through a synthetic chromosome and its combinatorial reconfiguration', Cell Genomics, vol. 3, no. 11, 100435. https://doi.org/10.1016/j.xgen.2023.100435

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

keywords = "CRISPR-Cas9, Saccharomyces cerevisiae, chromosome reconfiguration, design-build-test-learn, mitotic recombination, synthetic biology, synthetic chromosome, synthetic genomics, synthetic yeast",

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AU - Foo, Jee Loon

AU - Kitano, Shohei

AU - Susanto, Adelia Vicanatalita

AU - Jin, Zhu

AU - Lin, Yicong

AU - Luo, Zhouqing

AU - Huang, Linsen

AU - Liang, Zhenzhen

AU - Mitchell, Leslie A.

AU - Yang, Kun

AU - Wong, Adison

AU - Cai, Yizhi

AU - Cai, Jitong

AU - Stracquadanio, Giovanni

AU - Bader, Joel S.

AU - Boeke, Jef D.

AU - Dai, Junbiao

AU - Chang, Matthew Wook

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N2 - Chromosome-level design-build-test-learn cycles (chrDBTLs) allow systematic combinatorial reconfiguration of chromosomes with ease. Here, we established chrDBTL with a redesigned synthetic Saccharomyces cerevisiae chromosome XV, synXV. We designed and built synXV to harbor strategically inserted features, modified elements, and synonymously recoded genes throughout the chromosome. Based on the recoded chromosome, we developed a method to enable chrDBTL: CRISPR-Cas9-mediated mitotic recombination with endoreduplication (CRIMiRE). CRIMiRE allowed the creation of customized wild-type/synthetic combinations, accelerating genotype-phenotype mapping and synthetic chromosome redesign. We also leveraged synXV as a “build-to-learn” model organism for translation studies by ribosome profiling. We conducted a locus-to-locus comparison of ribosome occupancy between synXV and the wild-type chromosome, providing insight into the effects of codon changes and redesigned features on translation dynamics in vivo. Overall, we established synXV as a versatile reconfigurable system that advances chrDBTL for understanding biological mechanisms and engineering strains.

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

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KW - Saccharomyces cerevisiae

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KW - synthetic yeast

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

Abstract

Keywords

ASJC Scopus subject areas

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