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Wu Y, Li BZ, Zhao M, Mitchell LA, Xie ZX, Lin QH, Wang X, Xiao WH, Wang Y, Zhou X, Liu H, Li X, Ding MZ, Liu D, Zhang L, Liu BL, Wu XL, Li FF, Dong XT, Jia B, Zhang WZ, Jiang GZ, Liu Y, Bai X, Song TQ, Chen Y, Zhou SJ, Zhu RY, Gao F, Kuang Z, Wang X, Shen M, Yang K, Stracquadanio G, Richardson SM, Lin Y, Wang L, Walker R, Luo Y, Ma PS, Yang H, Cai Y, Dai J, Bader JS, Boeke JD, Yuan YJ. Bug mapping and fitness testing of chemically synthesized chromosome X. Science 2017; 355:355/6329/eaaf4706. [PMID: 28280152 DOI: 10.1126/science.aaf4706] [Citation(s) in RCA: 141] [Impact Index Per Article: 20.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2016] [Accepted: 02/01/2017] [Indexed: 01/03/2023]
Abstract
Debugging a genome sequence is imperative for successfully building a synthetic genome. As part of the effort to build a designer eukaryotic genome, yeast synthetic chromosome X (synX), designed as 707,459 base pairs, was synthesized chemically. SynX exhibited good fitness under a wide variety of conditions. A highly efficient mapping strategy called pooled PCRTag mapping (PoPM), which can be generalized to any watermarked synthetic chromosome, was developed to identify genetic alterations that affect cell fitness ("bugs"). A series of bugs were corrected that included a large region bearing complex amplifications, a growth defect mapping to a recoded sequence in FIP1, and a loxPsym site affecting promoter function of ATP2 PoPM is a powerful tool for synthetic yeast genome debugging and an efficient strategy for phenotype-genotype mapping.
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Affiliation(s)
- Yi Wu
- Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, PR China.,SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin University, Tianjin, 300072, PR China
| | - Bing-Zhi Li
- Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, PR China.,SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin University, Tianjin, 300072, PR China
| | - Meng Zhao
- Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, PR China.,SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin University, Tianjin, 300072, PR China
| | - Leslie A Mitchell
- Institute for Systems Genetics and Department of Biochemistry and Molecular Pharmacology, New York University (NYU) Langone Medical Center, New York City, NY 10016, USA
| | - Ze-Xiong Xie
- Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, PR China.,SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin University, Tianjin, 300072, PR China
| | - Qiu-Hui Lin
- Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, PR China.,SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin University, Tianjin, 300072, PR China
| | - Xia Wang
- Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, PR China.,SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin University, Tianjin, 300072, PR China
| | - Wen-Hai Xiao
- Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, PR China.,SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin University, Tianjin, 300072, PR China
| | - Ying Wang
- Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, PR China.,SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin University, Tianjin, 300072, PR China
| | - Xiao Zhou
- Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, PR China.,SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin University, Tianjin, 300072, PR China
| | - Hong Liu
- Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, PR China.,SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin University, Tianjin, 300072, PR China
| | - Xia Li
- Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, PR China.,SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin University, Tianjin, 300072, PR China
| | - Ming-Zhu Ding
- Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, PR China.,SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin University, Tianjin, 300072, PR China
| | - Duo Liu
- Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, PR China.,SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin University, Tianjin, 300072, PR China
| | - Lu Zhang
- Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, PR China.,SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin University, Tianjin, 300072, PR China
| | - Bao-Li Liu
- Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, PR China.,SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin University, Tianjin, 300072, PR China
| | - Xiao-Le Wu
- Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, PR China.,SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin University, Tianjin, 300072, PR China
| | - Fei-Fei Li
- Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, PR China.,SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin University, Tianjin, 300072, PR China
| | - Xiu-Tao Dong
- Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, PR China.,SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin University, Tianjin, 300072, PR China
| | - Bin Jia
- Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, PR China.,SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin University, Tianjin, 300072, PR China
| | - Wen-Zheng Zhang
- Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, PR China.,SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin University, Tianjin, 300072, PR China
| | - Guo-Zhen Jiang
- Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, PR China.,SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin University, Tianjin, 300072, PR China
| | - Yue Liu
- Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, PR China.,SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin University, Tianjin, 300072, PR China
| | - Xue Bai
- Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, PR China.,SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin University, Tianjin, 300072, PR China
| | - Tian-Qing Song
- Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, PR China.,SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin University, Tianjin, 300072, PR China
| | - Yan Chen
- Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, PR China.,SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin University, Tianjin, 300072, PR China
| | - Si-Jie Zhou
- Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, PR China.,SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin University, Tianjin, 300072, PR China
| | - Rui-Ying Zhu
- Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, PR China.,SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin University, Tianjin, 300072, PR China
| | - Feng Gao
- Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, PR China.,SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin University, Tianjin, 300072, PR China
| | - Zheng Kuang
- Institute for Systems Genetics and Department of Biochemistry and Molecular Pharmacology, New York University (NYU) Langone Medical Center, New York City, NY 10016, USA
| | - Xuya Wang
- Institute for Systems Genetics and Department of Biochemistry and Molecular Pharmacology, New York University (NYU) Langone Medical Center, New York City, NY 10016, USA
| | - Michael Shen
- Institute for Systems Genetics and Department of Biochemistry and Molecular Pharmacology, New York University (NYU) Langone Medical Center, New York City, NY 10016, USA
| | - Kun Yang
- High Throughput Biology Center and Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD 21205, USA
| | - Giovanni Stracquadanio
- High Throughput Biology Center and Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD 21205, USA.,School of Computer Science and Electronic Engineering, University of Essex, Wivenhoe Park, Colchester CO4 3SQ, UK
| | - Sarah M Richardson
- High Throughput Biology Center and Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD 21205, USA
| | - Yicong Lin
- Key laboratory of Industrial Biocatalysis (Ministry of Education), Center for Synthetic and Systems Biology, School of Life Sciences, Tsinghua University, Beijing, 100084, PR China
| | - Lihui Wang
- Key laboratory of Industrial Biocatalysis (Ministry of Education), Center for Synthetic and Systems Biology, School of Life Sciences, Tsinghua University, Beijing, 100084, PR China
| | - Roy Walker
- School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3BF, Scotland, UK
| | - Yisha Luo
- School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3BF, Scotland, UK
| | - Ping-Sheng Ma
- Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, PR China.,SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin University, Tianjin, 300072, PR China
| | - Huanming Yang
- BGI-Shenzhen, Shenzhen, 518083, PR China.,James D. Watson Institute of Genome Sciences, Hangzhou 310058, PR China
| | - Yizhi Cai
- School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3BF, Scotland, UK
| | - Junbiao Dai
- Key laboratory of Industrial Biocatalysis (Ministry of Education), Center for Synthetic and Systems Biology, School of Life Sciences, Tsinghua University, Beijing, 100084, PR China
| | - Joel S Bader
- High Throughput Biology Center and Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD 21205, USA
| | - Jef D Boeke
- Institute for Systems Genetics and Department of Biochemistry and Molecular Pharmacology, New York University (NYU) Langone Medical Center, New York City, NY 10016, USA
| | - Ying-Jin Yuan
- Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, PR China. .,SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin University, Tianjin, 300072, PR China
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