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

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

Research output: Contribution to journalArticle

Abstract

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.

Original languageEnglish (US)
Article numbereaaf4791
JournalScience
Volume355
Issue number6329
DOIs
StatePublished - Mar 10 2017

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Chromosomes
Yeasts
Glycerol
Biological Phenomena
Chromosome Segregation
Transfer RNA
Proteomics
Osmolar Concentration
Up-Regulation
Growth

ASJC Scopus subject areas

  • Medicine(all)
  • General

Cite this

Shen, Y., Wang, Y., Chen, T., Gao, F., Gong, J., Abramczyk, D., ... Yang, H. (2017). Deep functional analysis of synII, a 770-kilobase synthetic yeast chromosome. Science, 355(6329), [eaaf4791]. https://doi.org/10.1126/science.aaf4791

Deep functional analysis of synII, a 770-kilobase synthetic yeast chromosome. / Shen, Yue; Wang, Yun; Chen, Tai; Gao, Feng; Gong, Jianhui; Abramczyk, Dariusz; Walker, Roy; Zhao, Hongcui; Chen, Shihong; Liu, Wei; Luo, Yisha; Müller, Carolin A.; Paul-Dubois-Taine, Adrien; Alver, Bonnie; Stracquadanio, Giovanni; Mitchell, Leslie A.; Luo, Zhouqing; Fan, Yanqun; Zhou, Baojin; Wen, Bo; Tan, Fengji; Wang, Yujia; Zi, Jin; Xie, Zexiong; Li, Bingzhi; Yang, Kun; Richardson, Sarah M.; Jiang, Hui; French, Christopher E.; Nieduszynski, Conrad A.; Koszul, Romain; Marston, Adele L.; Yuan, Yingjin; Wang, Jian; Bader, Joel S.; Dai, Junbiao; Boeke, Jef D.; Xu, Xun; Cai, Yizhi; Yang, Huanming.

In: Science, Vol. 355, No. 6329, eaaf4791, 10.03.2017.

Research output: Contribution to journalArticle

Shen, Y, Wang, Y, Chen, T, Gao, F, Gong, J, Abramczyk, D, Walker, R, Zhao, H, Chen, S, Liu, W, Luo, Y, Müller, CA, Paul-Dubois-Taine, A, Alver, B, Stracquadanio, G, Mitchell, LA, Luo, Z, Fan, Y, Zhou, B, Wen, B, Tan, F, Wang, Y, Zi, J, Xie, Z, Li, B, Yang, K, Richardson, SM, Jiang, H, French, CE, Nieduszynski, CA, Koszul, R, Marston, AL, Yuan, Y, Wang, J, Bader, JS, Dai, J, Boeke, JD, Xu, X, Cai, Y & Yang, H 2017, 'Deep functional analysis of synII, a 770-kilobase synthetic yeast chromosome', Science, vol. 355, no. 6329, eaaf4791. https://doi.org/10.1126/science.aaf4791
Shen Y, Wang Y, Chen T, Gao F, Gong J, Abramczyk D et al. Deep functional analysis of synII, a 770-kilobase synthetic yeast chromosome. Science. 2017 Mar 10;355(6329). eaaf4791. https://doi.org/10.1126/science.aaf4791
Shen, Yue ; Wang, Yun ; Chen, Tai ; Gao, Feng ; Gong, Jianhui ; Abramczyk, Dariusz ; Walker, Roy ; Zhao, Hongcui ; Chen, Shihong ; Liu, Wei ; Luo, Yisha ; Müller, Carolin A. ; Paul-Dubois-Taine, Adrien ; Alver, Bonnie ; Stracquadanio, Giovanni ; Mitchell, Leslie A. ; Luo, Zhouqing ; Fan, Yanqun ; Zhou, Baojin ; Wen, Bo ; Tan, Fengji ; Wang, Yujia ; Zi, Jin ; Xie, Zexiong ; Li, Bingzhi ; Yang, Kun ; Richardson, Sarah M. ; Jiang, Hui ; French, Christopher E. ; Nieduszynski, Conrad A. ; Koszul, Romain ; Marston, Adele L. ; Yuan, Yingjin ; Wang, Jian ; Bader, Joel S. ; Dai, Junbiao ; Boeke, Jef D. ; Xu, Xun ; Cai, Yizhi ; Yang, Huanming. / Deep functional analysis of synII, a 770-kilobase synthetic yeast chromosome. In: Science. 2017 ; Vol. 355, No. 6329.
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abstract = "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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AU - Walker, Roy

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AU - Luo, Zhouqing

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AU - Jiang, Hui

AU - French, Christopher E.

AU - Nieduszynski, Conrad A.

AU - Koszul, Romain

AU - Marston, Adele L.

AU - Yuan, Yingjin

AU - Wang, Jian

AU - Bader, Joel S.

AU - Dai, Junbiao

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