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 Luo; Yisha Luo; Carolin A Müller; Adrien Paul-Dubois-Taine; Bonnie Alver; Giovanni Stracquadanio; Leslie A Mitchell; Zhouqing  Lou; Yanqun Fan; Baojin Zhou; Bo Wen; Fengji Tan; Yujia Wang; Jin Zi; Zexiong Xie; Bingzhi Li; Kun Yang; Sarah M Richardson; Hui Jiang; Christopher French; Conrad A. Nieduszynski; Romain Koszul; Adele Marston; Yuan Yingjin; 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 Luo, Yisha Luo, Carolin A Müller, Adrien Paul-Dubois-Taine, Bonnie Alver, Giovanni Stracquadanio, Leslie A Mitchell, Zhouqing Lou, Yanqun Fan, Baojin Zhou, Bo WenFengji Tan, Yujia Wang, Jin Zi, Zexiong Xie, Bingzhi Li, Kun Yang, Sarah M Richardson, Hui Jiang, Christopher French, Conrad A. Nieduszynski, Romain Koszul, Adele Marston, Yuan Yingjin, Jian Wang, Joel S Bader, Junbiao Dai, Jef D Boeke, Xun Xu, Yizhi Cai, Huanming Yang

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

Abstract

Herein we report the successful design, construction and characterization of a 770 kb 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 significant pervasive up-regulation of translational machinery observed in synII is mainly caused by the deletion of 13 tRNAs. By both complementation assays and SCRaMbLE, we targeted and debuged the origin of a growth defect at 37°C in glycerol medium, which is related to misregulation of the HOG response. Despite the subtle differences, the synII strain shows highly consistent biological processes comparable to the native strain.

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

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10.1126/science.aaf4791

YangEtalS2017DeepFunctionalAnalysisOfSynIIA770-KilobaseSyntheticYeastChromosomeAccepted author manuscript, 1.98 MBLicence: Other

Building national hardware and software infrastructure for UK DNA foundries
Cai, Y. & Rosser, S.
BBSRC
13/02/15 → 30/11/16
Project: Research
14 ERASynBio - IESY - Inducible Evolution of Synthetic Yeast genomes
Calvert, J. & Frow, E.
BBSRC
1/01/15 → 31/12/17
Project: Research
Edinburgh Genome Foundry
Rosser, S. & Cai, Y.
BBSRC
16/09/14 → 15/09/15
Project: Research

Chris French
- C.Frenched.acuk
- School of Biological Sciences - Personal Chair of Microbial Biotechnology
- Centre for Engineering Biology
Person: Academic: Research Active
Giovanni Stracquadanio
- School of Biological Sciences - Personal Chair in Engineering Biology
- Centre for Engineering Biology
Person: Academic: Research Active

Cite this

Shen, Y., Wang, Y., Chen, T., Gao, F., Gong, J., Abramczyk, D., Walker, R., Zhao, H., Chen, S., Luo, W., Luo, Y., Müller, C. A., Paul-Dubois-Taine, A., Alver, B., Stracquadanio, G., Mitchell, L. A., Lou, 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

@article{ebc24d9bcc7042a389ce5e4eb96ef94f,

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

abstract = "Herein we report the successful design, construction and characterization of a 770 kb 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 significant pervasive up-regulation of translational machinery observed in synII is mainly caused by the deletion of 13 tRNAs. By both complementation assays and SCRaMbLE, we targeted and debuged the origin of a growth defect at 37°C in glycerol medium, which is related to misregulation of the HOG 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 Luo 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 Lou 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 Christopher French and Nieduszynski, {Conrad A.} and Romain Koszul and Adele Marston and Yuan Yingjin 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,

day = "10",

doi = "10.1126/science.aaf4791",

language = "English",

volume = "355",

journal = "Science",

issn = "0036-8075",

publisher = "AMER ASSOC ADVANCEMENT SCIENCE",

number = "6329",

}

Shen, Y, Wang, Y, Chen, T, Gao, F, Gong, J, Abramczyk, D, Walker, R, Zhao, H, Chen, S, Luo, W, Luo, Y, Müller, CA, Paul-Dubois-Taine, A, Alver, B, Stracquadanio, G, Mitchell, LA, Lou, Z, Fan, Y, Zhou, B, Wen, B, Tan, F, Wang, Y, Zi, J, Xie, Z, Li, B, Yang, K, Richardson, SM, Jiang, H, French, C, Nieduszynski, CA, Koszul, R, Marston, A, Yingjin, 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

TY - JOUR

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 - Luo, Wei

AU - Luo, Yisha

AU - Müller, Carolin A

AU - Paul-Dubois-Taine, Adrien

AU - Alver, Bonnie

AU - Stracquadanio, Giovanni

AU - Mitchell, Leslie A

AU - Lou, 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

AU - Nieduszynski, Conrad A.

AU - Koszul, Romain

AU - Marston, Adele

AU - Yingjin, Yuan

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 - Herein we report the successful design, construction and characterization of a 770 kb 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 significant pervasive up-regulation of translational machinery observed in synII is mainly caused by the deletion of 13 tRNAs. By both complementation assays and SCRaMbLE, we targeted and debuged the origin of a growth defect at 37°C in glycerol medium, which is related to misregulation of the HOG response. Despite the subtle differences, the synII strain shows highly consistent biological processes comparable to the native strain.

AB - Herein we report the successful design, construction and characterization of a 770 kb 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 significant pervasive up-regulation of translational machinery observed in synII is mainly caused by the deletion of 13 tRNAs. By both complementation assays and SCRaMbLE, we targeted and debuged the origin of a growth defect at 37°C in glycerol medium, which is related to misregulation of the HOG response. Despite the subtle differences, the synII strain shows highly consistent biological processes comparable to the native strain.

U2 - 10.1126/science.aaf4791

DO - 10.1126/science.aaf4791

M3 - Article

SN - 0036-8075

VL - 355

JO - Science

JF - Science

IS - 6329

M1 - eaaf4791

ER -

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

Abstract

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Projects

Building national hardware and software infrastructure for UK DNA foundries

14 ERASynBio - IESY - Inducible Evolution of Synthetic Yeast genomes

Edinburgh Genome Foundry

Profiles

Chris French

Giovanni Stracquadanio

Cite this