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 Wen; Fengji 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

doi:10.1126/science.aaf4791

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

Biomedical Engineering

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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.

Original language	English (US)
Article number	eaaf4791
Journal	Science
Volume	355
Issue number	6329
DOIs	https://doi.org/10.1126/science.aaf4791
State	Published - Mar 10 2017

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Shen, Y., Wang, Y., Chen, T., Gao, F., Gong, J., Abramczyk, D., Walker, R., Zhao, H., Chen, S., Liu, W., Luo, Y., Müller, C. A., Paul-Dubois-Taine, A., Alver, B., Stracquadanio, G., Mitchell, L. A., Luo, Z., Fan, Y., Zhou, B., ... Yang, H. (2017). Deep functional analysis of synII, a 770-kilobase synthetic yeast chromosome. Science, 355(6329), Article eaaf4791. https://doi.org/10.1126/science.aaf4791

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

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

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.",

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

year = "2017",

month = mar,

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doi = "10.1126/science.aaf4791",

language = "English (US)",

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T1 - Deep functional analysis of synII, a 770-kilobase synthetic yeast chromosome

AU - Shen, Yue

AU - Wang, Yun

AU - Chen, Tai

AU - Gao, Feng

AU - Gong, Jianhui

AU - Abramczyk, Dariusz

AU - Walker, Roy

AU - Zhao, Hongcui

AU - Chen, Shihong

AU - Liu, Wei

AU - Luo, Yisha

AU - Müller, Carolin A.

AU - Paul-Dubois-Taine, Adrien

AU - Alver, Bonnie

AU - Stracquadanio, Giovanni

AU - Mitchell, Leslie A.

AU - Luo, Zhouqing

AU - Fan, Yanqun

AU - Zhou, Baojin

AU - Wen, Bo

AU - Tan, Fengji

AU - Wang, Yujia

AU - Zi, Jin

AU - Xie, Zexiong

AU - Li, Bingzhi

AU - Yang, Kun

AU - Richardson, Sarah M.

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

AU - Boeke, Jef D.

AU - Xu, Xun

AU - Cai, Yizhi

AU - Yang, Huanming

PY - 2017/3/10

Y1 - 2017/3/10

N2 - 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.

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

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