Engineering the ribosomal DNA in a megabase synthetic chromosome

Weimin Zhang; Guanghou Zhao; Zhouqing Luo; Yicong Lin; Lihui Wang; Yakun Guo; Ann Wang; Shuangying Jiang; Qingwen Jiang; Jianhui Gong; Yun Wang; Sha Hou; Jing Huang; Tianyi Li; Yiran Qin; Junkai Dong; Qin Qin; Jiaying Zhang; Xinzhi Zou; Xi He; Li Zhao; Yibo Xiao; Meng Xu; Erchao Cheng; Ning Huang; Tong Zhou; Yue Shen; Roy Walker; Yisha Luo; Zheng Kuang; Leslie A Mitchell; Kun Yang; Sarah M Richardson; Yi Wu; Bing-Zhi Li; Ying-Jin Yuan; Huanming Yang; Jiwei Lin; Guo-Qiang Chen; Qingyu Wu; Joel S Bader; Yizhi Cai; Jef D Boeke; Junbiao Dai

doi:10.1126/science.aaf3981

Engineering the ribosomal DNA in a megabase synthetic chromosome

Weimin Zhang, Guanghou Zhao, Zhouqing Luo, Yicong Lin, Lihui Wang, Yakun Guo, Ann Wang, Shuangying Jiang, Qingwen Jiang, Jianhui Gong, Yun Wang, Sha Hou, Jing Huang, Tianyi Li, Yiran Qin, Junkai Dong, Qin Qin, Jiaying Zhang, Xinzhi Zou, Xi HeLi Zhao, Yibo Xiao, Meng Xu, Erchao Cheng, Ning Huang, Tong Zhou, Yue Shen, Roy Walker, Yisha Luo, Zheng Kuang, Leslie A Mitchell, Kun Yang, Sarah M Richardson, Yi Wu, Bing-Zhi Li, Ying-Jin Yuan, Huanming Yang, Jiwei Lin, Guo-Qiang Chen, Qingyu Wu, Joel S Bader, Yizhi Cai, Jef D Boeke, Junbiao Dai

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Abstract

We designed and synthesized a 976,067-base pair linear chromosome, synXII, based on native chromosome XII in Saccharomyces cerevisiae SynXII was assembled using a two-step method, specified by successive megachunk integration and meiotic recombination-mediated assembly, producing a functional chromosome in S. cerevisiae. Minor growth defect "bugs" detected in synXII, caused by deletion of tRNA genes, were rescued by introducing an ectopic copy of a single tRNA gene. The ribosomal gene cluster (rDNA) on synXII was left intact during the assembly process and subsequently replaced by a modified rDNA unit used to regenerate rDNA at three distinct chromosomal locations. The signature sequences within rDNA, which can be used to determine species identity, were swapped to generate a Saccharomyces synXII strain that would be identified as Saccharomyces bayanus by standard DNA barcoding procedures.

Original language	English
Article number	eaaf3981
Journal	Science
Volume	355
Issue number	6329
DOIs	https://doi.org/10.1126/science.aaf3981
Publication status	Published - 10 Mar 2017

Keywords

Journal Article
Research Support, Non-U.S. Gov't

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10.1126/science.aaf3981

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title = "Engineering the ribosomal DNA in a megabase synthetic chromosome",

abstract = "We designed and synthesized a 976,067-base pair linear chromosome, synXII, based on native chromosome XII in Saccharomyces cerevisiae SynXII was assembled using a two-step method, specified by successive megachunk integration and meiotic recombination-mediated assembly, producing a functional chromosome in S. cerevisiae. Minor growth defect {"}bugs{"} detected in synXII, caused by deletion of tRNA genes, were rescued by introducing an ectopic copy of a single tRNA gene. The ribosomal gene cluster (rDNA) on synXII was left intact during the assembly process and subsequently replaced by a modified rDNA unit used to regenerate rDNA at three distinct chromosomal locations. The signature sequences within rDNA, which can be used to determine species identity, were swapped to generate a Saccharomyces synXII strain that would be identified as Saccharomyces bayanus by standard DNA barcoding procedures.",

keywords = "Journal Article, Research Support, Non-U.S. Gov't",

author = "Weimin Zhang and Guanghou Zhao and Zhouqing Luo and Yicong Lin and Lihui Wang and Yakun Guo and Ann Wang and Shuangying Jiang and Qingwen Jiang and Jianhui Gong and Yun Wang and Sha Hou and Jing Huang and Tianyi Li and Yiran Qin and Junkai Dong and Qin Qin and Jiaying Zhang and Xinzhi Zou and Xi He and Li Zhao and Yibo Xiao and Meng Xu and Erchao Cheng and Ning Huang and Tong Zhou and Yue Shen and Roy Walker and Yisha Luo and Zheng Kuang and Mitchell, {Leslie A} and Kun Yang and Richardson, {Sarah M} and Yi Wu and Bing-Zhi Li and Ying-Jin Yuan and Huanming Yang and Jiwei Lin and Guo-Qiang Chen and Qingyu Wu and Bader, {Joel S} and Yizhi Cai and Boeke, {Jef D} and Junbiao Dai",

note = "Copyright {\textcopyright} 2017, American Association for the Advancement of Science.",

year = "2017",

month = mar,

day = "10",

doi = "10.1126/science.aaf3981",

language = "English",

volume = "355",

journal = "Science",

issn = "0036-8075",

publisher = "American Association for the Advancement of Science (A A A S)",

number = "6329",

}

Zhang, W, Zhao, G, Luo, Z, Lin, Y, Wang, L, Guo, Y, Wang, A, Jiang, S, Jiang, Q, Gong, J, Wang, Y, Hou, S, Huang, J, Li, T, Qin, Y, Dong, J, Qin, Q, Zhang, J, Zou, X, He, X, Zhao, L, Xiao, Y, Xu, M, Cheng, E, Huang, N, Zhou, T, Shen, Y, Walker, R, Luo, Y, Kuang, Z, Mitchell, LA, Yang, K, Richardson, SM, Wu, Y, Li, B-Z, Yuan, Y-J, Yang, H, Lin, J, Chen, G-Q, Wu, Q, Bader, JS, Cai, Y, Boeke, JD & Dai, J 2017, 'Engineering the ribosomal DNA in a megabase synthetic chromosome', Science, vol. 355, no. 6329, eaaf3981. https://doi.org/10.1126/science.aaf3981

TY - JOUR

T1 - Engineering the ribosomal DNA in a megabase synthetic chromosome

AU - Zhang, Weimin

AU - Zhao, Guanghou

AU - Luo, Zhouqing

AU - Lin, Yicong

AU - Wang, Lihui

AU - Guo, Yakun

AU - Wang, Ann

AU - Jiang, Shuangying

AU - Jiang, Qingwen

AU - Gong, Jianhui

AU - Wang, Yun

AU - Hou, Sha

AU - Huang, Jing

AU - Li, Tianyi

AU - Qin, Yiran

AU - Dong, Junkai

AU - Qin, Qin

AU - Zhang, Jiaying

AU - Zou, Xinzhi

AU - He, Xi

AU - Zhao, Li

AU - Xiao, Yibo

AU - Xu, Meng

AU - Cheng, Erchao

AU - Huang, Ning

AU - Zhou, Tong

AU - Shen, Yue

AU - Walker, Roy

AU - Luo, Yisha

AU - Kuang, Zheng

AU - Mitchell, Leslie A

AU - Yang, Kun

AU - Richardson, Sarah M

AU - Wu, Yi

AU - Li, Bing-Zhi

AU - Yuan, Ying-Jin

AU - Yang, Huanming

AU - Lin, Jiwei

AU - Chen, Guo-Qiang

AU - Wu, Qingyu

AU - Bader, Joel S

AU - Cai, Yizhi

AU - Boeke, Jef D

AU - Dai, Junbiao

PY - 2017/3/10

Y1 - 2017/3/10

N2 - We designed and synthesized a 976,067-base pair linear chromosome, synXII, based on native chromosome XII in Saccharomyces cerevisiae SynXII was assembled using a two-step method, specified by successive megachunk integration and meiotic recombination-mediated assembly, producing a functional chromosome in S. cerevisiae. Minor growth defect "bugs" detected in synXII, caused by deletion of tRNA genes, were rescued by introducing an ectopic copy of a single tRNA gene. The ribosomal gene cluster (rDNA) on synXII was left intact during the assembly process and subsequently replaced by a modified rDNA unit used to regenerate rDNA at three distinct chromosomal locations. The signature sequences within rDNA, which can be used to determine species identity, were swapped to generate a Saccharomyces synXII strain that would be identified as Saccharomyces bayanus by standard DNA barcoding procedures.

AB - We designed and synthesized a 976,067-base pair linear chromosome, synXII, based on native chromosome XII in Saccharomyces cerevisiae SynXII was assembled using a two-step method, specified by successive megachunk integration and meiotic recombination-mediated assembly, producing a functional chromosome in S. cerevisiae. Minor growth defect "bugs" detected in synXII, caused by deletion of tRNA genes, were rescued by introducing an ectopic copy of a single tRNA gene. The ribosomal gene cluster (rDNA) on synXII was left intact during the assembly process and subsequently replaced by a modified rDNA unit used to regenerate rDNA at three distinct chromosomal locations. The signature sequences within rDNA, which can be used to determine species identity, were swapped to generate a Saccharomyces synXII strain that would be identified as Saccharomyces bayanus by standard DNA barcoding procedures.

KW - Journal Article

KW - Research Support, Non-U.S. Gov't

U2 - 10.1126/science.aaf3981

DO - 10.1126/science.aaf3981

M3 - Article

C2 - 28280149

SN - 0036-8075

VL - 355

JO - Science

JF - Science

IS - 6329

M1 - eaaf3981

ER -

Engineering the ribosomal DNA in a megabase synthetic chromosome

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