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Deep functional analysis of synII, a 770-kilobase synthetic yeast chromosome

by Gong, Jianhui , Paul-Dubois-Taine, Adrien , Richardson, Sarah M. , Fan, Yanqun , Xu, Xun , Abramczyk, Dariusz , Alver, Bonnie , Cai, Yizhi , Nieduszynski, Conrad A. , Bader, Joel S. , Chen, Shihong , Walker, Roy , French, Christopher E. , Xie, Zexiong , Zi, Jin , Stracquadanio, Giovanni , Müller, Carolin A. , Wang, Yujia , Luo, Yisha , Gao, Feng , Wen, Bo , Yuan, Yingjin , Li, Bingzhi , Boeke, Jef D. , Yang, Huanming , Wang, Jian , Liu, Wei , Mitchell, Leslie A. , Zhou, Baojin , Shen, Yue , Yang, Kun , Jiang, Hui , Dai, Junbiao , Zhao, Hongcui , Luo, Zhouqing , Chen, Tai , Koszul, Romain , Marston, Adele L. , Wang, Yun , Tan, Fengji

in Anaphase / Artificial chromosomes / Assaying / Biological activity / Biological evolution / Carbon sources / Cell cycle / Chromosome 2 / Chromosome Segregation / Chromosomes / Chromosomes, Artificial, Yeast - chemistry / Chromosomes, Artificial, Yeast - genetics / Chromosomes, Artificial, Yeast - physiology / Clonal deletion / Colonies / Complementation / Complexity / Copy number / Culture Media - chemistry / Debugging / Defects / Deletion / Deoxyribonucleic acid / Design / DNA / DNA biosynthesis / DNA Replication / Evolution / Functional analysis / Gene regulation / Gene sequencing / Genes / Genome, Fungal / Genomes / Glycerol / Glycerols / High temperature / Homologous recombination / In vivo methods and tests / Integration / Life Sciences / Literary Devices / Logical Thinking / Meiosis / Metabolomics / Metaphase / Origins / Osmolarity / Phenotyping / Proteomics / Replication / RESEARCH ARTICLE SUMMARY / Ribonucleic acid / RNA / Saccharomyces cerevisiae - genetics / Saccharomyces cerevisiae - growth & development / Segregations / Sequence Analysis, DNA / Spindles / Swine / Synthetic Biology / Temperature effects / Transcriptome / Translation / tRNA / Yeast

2017

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Deep functional analysis of synII, a 770-kilobase synthetic yeast chromosome

2017

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Deep functional analysis of synII, a 770-kilobase synthetic yeast chromosome

2017

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Journal Article

Deep functional analysis of synII, a 770-kilobase synthetic yeast chromosome

Gong, Jianhui,

Paul-Dubois-Taine, Adrien,

Richardson, Sarah M.,

Fan, Yanqun,

Xu, Xun,

Abramczyk, Dariusz,

Alver, Bonnie,

Cai, Yizhi,

Nieduszynski, Conrad A.,

Bader, Joel S.,

Chen, Shihong,

Walker, Roy,

French, Christopher E.,

Xie, Zexiong,

Zi, Jin,

Stracquadanio, Giovanni,

Müller, Carolin A.,

Wang, Yujia,

Luo, Yisha,

Gao, Feng,

Wen, Bo,

Yuan, Yingjin,

Li, Bingzhi,

Boeke, Jef D.,

Yang, Huanming,

Wang, Jian,

Liu, Wei,

Mitchell, Leslie A.,

Zhou, Baojin,

Shen, Yue,

Yang, Kun,

Jiang, Hui,

Dai, Junbiao,

Zhao, Hongcui,

Luo, Zhouqing,

Chen, Tai,

Koszul, Romain,

Marston, Adele L.,

Wang, Yun,

Tan, Fengji

2017

Overview

Here, we report the successful design, construction, and characterization of a 770-kilobase synthetic yeast chromosome II (synII). Our study incorporates characterization at multiple levels—including phenomics, transcriptomics, proteomics, chromosome segregation, and replication analysis—to provide a thorough and comprehensive analysis of a synthetic chromosome. Our Trans-Omics analyses reveal a modest but potentially relevant pervasive up-regulation of translational machinery observed in synII, mainly caused by the deletion of 13 transfer RNAs. By both complementation assays and SCRaMbLE (synthetic chromosome rearrangement and modification by loxP -mediated evolution), we targeted and debugged the origin of a growth defect at 37°C in glycerol medium, which is related to misregulation of the high-osmolarity glycerol response. Despite the subtle differences, the synII strain shows highly consistent biological processes comparable to the native strain.

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Publisher

American Association for the Advancement of Science,The American Association for the Advancement of Science,American Association for the Advancement of Science (AAAS)

Subject

Anaphase

/ Artificial chromosomes

/ Assaying

/ Biological activity

/ Biological evolution

/ Carbon sources

/ Cell cycle

/ Chromosome 2

/ Chromosome Segregation

/ Chromosomes

/ Chromosomes, Artificial, Yeast - chemistry