Synthesis, debugging, and effects of synthetic chromosome consolidation: synVI and beyond

Leslie A Mitchell^{1

2}, Ann Wang^{3

4}, Giovanni Stracquadanio^{3

5

6}, Zheng Kuang^{1

2}, Xuya Wang^{1

2}, Kun Yang^{3

5}, Sarah Richardson^{3

5}, J Andrew Martin^{1

2}, Yu Zhao^{1

2}, Roy Walker⁷, Yisha Luo⁷, Hongjiu Dai⁸, Kang Dong⁸, Zuojian Tang^{1

2}, Yanling Yang⁹, Yizhi Cai⁷, Adriana Heguy¹⁰, Beatrix Ueberheide^{1

9}, David Fenyö^{1

2}, Junbiao Dai⁴, Joel S Bader^{3

4}, Jef D Boeke^{11

2}

Affiliations

¹ Department of Biochemistry and Molecular Pharmacology, New York University Langone School of Medicine, New York, NY 10016, USA.
² Institute for Systems Genetics, New York University Langone School of Medicine, New York, NY 10016, USA.
³ High Throughput Biology Center, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA.
⁴ Key Laboratory for Industrial Biocatalysis (Ministry of Education), Key Laboratory of Bioinformatics (Ministry of Education), Center for Synthetic and Systems Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China.
⁵ Department of Biomedical Engineering and Institute of Genetic Medicine, Whiting School of Engineering, Johns Hopkins University, Baltimore, MD 21218, USA.
⁶ School of Computer Science and Electronic Engineering, University of Essex, Wivenhoe Park, Colchester CO4 3SQ, UK.
⁷ Center for Synthetic and Systems Biology, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3JL, UK.
⁸ GenScript, Piscataway, NJ 08854, USA.
⁹ Proteomics Resource Center, Office of Collaborative Science, New York University Langone School of Medicine, New York, NY 10016, USA.
¹⁰ Genome Technology Center, New York University Langone School of Medicine, New York, NY 10016, USA.
¹¹ Department of Biochemistry and Molecular Pharmacology, New York University Langone School of Medicine, New York, NY 10016, USA. jef.boeke@nyumc.org.

PMID: 28280154
DOI: 10.1126/science.aaf4831

Synthesis, debugging, and effects of synthetic chromosome consolidation: synVI and beyond

Leslie A Mitchell et al. Science. 2017.

. 2017 Mar 10;355(6329):eaaf4831.

doi: 10.1126/science.aaf4831.

Authors

Affiliations

¹ Department of Biochemistry and Molecular Pharmacology, New York University Langone School of Medicine, New York, NY 10016, USA.
² Institute for Systems Genetics, New York University Langone School of Medicine, New York, NY 10016, USA.
³ High Throughput Biology Center, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA.
⁴ Key Laboratory for Industrial Biocatalysis (Ministry of Education), Key Laboratory of Bioinformatics (Ministry of Education), Center for Synthetic and Systems Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China.
⁵ Department of Biomedical Engineering and Institute of Genetic Medicine, Whiting School of Engineering, Johns Hopkins University, Baltimore, MD 21218, USA.
⁶ School of Computer Science and Electronic Engineering, University of Essex, Wivenhoe Park, Colchester CO4 3SQ, UK.
⁷ Center for Synthetic and Systems Biology, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3JL, UK.
⁸ GenScript, Piscataway, NJ 08854, USA.
⁹ Proteomics Resource Center, Office of Collaborative Science, New York University Langone School of Medicine, New York, NY 10016, USA.
¹⁰ Genome Technology Center, New York University Langone School of Medicine, New York, NY 10016, USA.
¹¹ Department of Biochemistry and Molecular Pharmacology, New York University Langone School of Medicine, New York, NY 10016, USA. jef.boeke@nyumc.org.

PMID: 28280154
DOI: 10.1126/science.aaf4831

Abstract

We describe design, rapid assembly, and characterization of synthetic yeast Sc2.0 chromosome VI (synVI). A mitochondrial defect in the synVI strain mapped to synonymous coding changes within PRE4 (YFR050C), encoding an essential proteasome subunit; Sc2.0 coding changes reduced Pre4 protein accumulation by half. Completing Sc2.0 specifies consolidation of 16 synthetic chromosomes into a single strain. We investigated phenotypic, transcriptional, and proteomewide consequences of Sc2.0 chromosome consolidation in poly-synthetic strains. Another "bug" was discovered through proteomic analysis, associated with alteration of the HIS2 transcription start due to transfer RNA deletion and loxPsym site insertion. Despite extensive genetic alterations across 6% of the genome, no major global changes were detected in the poly-synthetic strain "omics" analyses. This work sets the stage for completion of a designer, synthetic eukaryotic genome.

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Comment in

Synthetic yeast chromosomes help probe mysteries of evolution.
Maxmen A. Maxmen A. Nature. 2017 Mar 9;543(7645):298-299. doi: 10.1038/nature.2017.21615. Nature. 2017. PMID: 28300123 No abstract available.
How dare you call us diplomats.
Moro-Martín A. Moro-Martín A. Nature. 2017 Mar 14;543(7645):289. doi: 10.1038/543289a. Nature. 2017. PMID: 28300124 No abstract available.
Synthetic Biology: Building a custom eukaryotic genome de novo.
Burgess DJ. Burgess DJ. Nat Rev Genet. 2017 Apr 12;18(5):274. doi: 10.1038/nrg.2017.30. Nat Rev Genet. 2017. PMID: 28400600 No abstract available.

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Synthesis, debugging, and effects of synthetic chromosome consolidation: synVI and beyond

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Synthesis, debugging, and effects of synthetic chromosome consolidation: synVI and beyond

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Affiliations

Abstract

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