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

School of Biological Sciences

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

164 Citations (Scopus)

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
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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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), [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.

@article{7fb1ab97fc5c4d4dbeaf2d142692d7ba,

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",

note = "Funding Information: The project was funded by China National High Technology Research and Development Program ({"}863{"} Program: 2012AA02A708) to H.Y. and National Natural Science Foundation of China (21621004 and 21390203) to Y.Y.; a Chancellor's Fellowship from the University of Edinburgh, a start-up fund from Scottish Universities Life Sciences Alliance and Biotechnology and Biological Sciences Research Council grants (BB/M005690/1, BB/M025640/1, and BB/M00029X/1) to Y.C.; the Wellcome Trust to A.M. (090903 and 092076); U.S. NSF grants MCB-1026068 and MCB-1158201 to J.D.B.; U.S. NSF grant MCB-1445545 to J.S.B.; and U.S. Department of Energy grant DE-FG02097ER25308 to S.M.R. Work at Tsinghua University was supported by National Science Foundation of China grant 31471254 and Chinese Ministry of Science and Technology grant 2012CB725201 to J.D. Funding from ERASynBio and Agence Nationale pour la Recherche (IESY ANR-14-SYNB-0001-03) to R.K. We thank W. Zhang for many comments on the manuscript. J.D.B. and J.S.B. are founders and directors of Neochromosome Inc. J.D.B. serves as a scientific advisor to Recombinetics Inc. and Sample6, Inc. These arrangements are reviewed and managed by the committees on conflict of interest at New York University Langone Medical Center (J.D.B.) and Johns Hopkins University (J.S.B.). Y.C., H.Y., and J.D.B. conceived the concept and designed the experiments. L.M., G.S., S.M.R., J.S.B., and J.D.B. designed the synII chromosome. Y.S., Y.W., T.C.,J.G.,Y.L.,andY.C.designedexperiments.T.C.,F.G.,H.Z.,Y.S., S.C., D.A., Z.L., R.W., W.L., and F.T. performed experiments. Y.W. and J.G. analyzed genomic and RNA-seq data. Y.F., B.Z., and J.G. analyzed mass spectrometry and LC-MS data. Y.S. and D.A. analyzed synII cell cycle data. C.M. and C.N. analyzed synII replication timing profiles. G.M., H.M., and R.K. analyzed synII 3C/3D structure. The manuscript was written by Y.S., Y.W., T.C., F.G., J.D., and Y.C., with input from C.M., C.N., R.K., C.F., A.M., J.S.B, J.D.B., and H.Y. and with comments provided by all other authors. SynII genomic sequencing data and RNA-seq data have been deposited in the Sequence Read Archive (SRA) sequence database (www.ncbi.nlm.nih.gov/sra/), accession code SRP062892. Proteomics data have been submitted to the ProteomeXchange (www.proteomexchange.org/), accession code PXD003435. The metabolomics and lipidomics data have been deposited to the MetaboLights metabolomics repository (accession number MTBLS296; accessed via link www.ebi.ac.uk/metabolights/MTBLS296). The designed and sequenced synII information is uploaded with accession codes CP013607 and CP013608 on GenBank. Additional information [synII design diagram, PCRTag sequences, variants in physical strain (yeast-chr02-9-01), PCR primers, and summary of megachunks, chunks, and minichunks] related to synII can be accessed on the Sc2.0 website (www.syntheticyeast.org). Publisher Copyright: {\textcopyright} 2017, American Association for the Advancement of Science. All rights reserved.",

year = "2017",

month = mar,

day = "10",

doi = "10.1126/science.aaf4791",

language = "English",

volume = "355",

journal = "Science",

issn = "0036-8075",

publisher = "American Association for the Advancement of Science",

number = "6329",

}

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

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 journal › Article › peer-review

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 - 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

N1 - Funding Information: The project was funded by China National High Technology Research and Development Program ("863" Program: 2012AA02A708) to H.Y. and National Natural Science Foundation of China (21621004 and 21390203) to Y.Y.; a Chancellor's Fellowship from the University of Edinburgh, a start-up fund from Scottish Universities Life Sciences Alliance and Biotechnology and Biological Sciences Research Council grants (BB/M005690/1, BB/M025640/1, and BB/M00029X/1) to Y.C.; the Wellcome Trust to A.M. (090903 and 092076); U.S. NSF grants MCB-1026068 and MCB-1158201 to J.D.B.; U.S. NSF grant MCB-1445545 to J.S.B.; and U.S. Department of Energy grant DE-FG02097ER25308 to S.M.R. Work at Tsinghua University was supported by National Science Foundation of China grant 31471254 and Chinese Ministry of Science and Technology grant 2012CB725201 to J.D. Funding from ERASynBio and Agence Nationale pour la Recherche (IESY ANR-14-SYNB-0001-03) to R.K. We thank W. Zhang for many comments on the manuscript. J.D.B. and J.S.B. are founders and directors of Neochromosome Inc. J.D.B. serves as a scientific advisor to Recombinetics Inc. and Sample6, Inc. These arrangements are reviewed and managed by the committees on conflict of interest at New York University Langone Medical Center (J.D.B.) and Johns Hopkins University (J.S.B.). Y.C., H.Y., and J.D.B. conceived the concept and designed the experiments. L.M., G.S., S.M.R., J.S.B., and J.D.B. designed the synII chromosome. Y.S., Y.W., T.C.,J.G.,Y.L.,andY.C.designedexperiments.T.C.,F.G.,H.Z.,Y.S., S.C., D.A., Z.L., R.W., W.L., and F.T. performed experiments. Y.W. and J.G. analyzed genomic and RNA-seq data. Y.F., B.Z., and J.G. analyzed mass spectrometry and LC-MS data. Y.S. and D.A. analyzed synII cell cycle data. C.M. and C.N. analyzed synII replication timing profiles. G.M., H.M., and R.K. analyzed synII 3C/3D structure. The manuscript was written by Y.S., Y.W., T.C., F.G., J.D., and Y.C., with input from C.M., C.N., R.K., C.F., A.M., J.S.B, J.D.B., and H.Y. and with comments provided by all other authors. SynII genomic sequencing data and RNA-seq data have been deposited in the Sequence Read Archive (SRA) sequence database (www.ncbi.nlm.nih.gov/sra/), accession code SRP062892. Proteomics data have been submitted to the ProteomeXchange (www.proteomexchange.org/), accession code PXD003435. The metabolomics and lipidomics data have been deposited to the MetaboLights metabolomics repository (accession number MTBLS296; accessed via link www.ebi.ac.uk/metabolights/MTBLS296). The designed and sequenced synII information is uploaded with accession codes CP013607 and CP013608 on GenBank. Additional information [synII design diagram, PCRTag sequences, variants in physical strain (yeast-chr02-9-01), PCR primers, and summary of megachunks, chunks, and minichunks] related to synII can be accessed on the Sc2.0 website (www.syntheticyeast.org). Publisher Copyright: © 2017, American Association for the Advancement of Science. All rights reserved.

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.

UR - http://www.scopus.com/inward/record.url?scp=85014855090&partnerID=8YFLogxK

U2 - 10.1126/science.aaf4791

DO - 10.1126/science.aaf4791

M3 - Article

C2 - 28280153

AN - SCOPUS:85014855090

VL - 355

JO - Science

JF - Science

SN - 0036-8075

IS - 6329

M1 - eaaf4791

ER -

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

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