title: Synthesis, debugging, and effects of synthetic chromosome consolidation: synVI and beyond.
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 withinPRE4(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 theHIS2transcription 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.
authors.affiliation: Department of Biochemistry and Molecular Pharmacology, New York University Langone School of Medicine, New York, NY 10016, USA.|Institute for Systems Genetics, New York University Langone School of Medicine, New York, NY 10016, USA.
authors.forename: Leslie A
authors.identifier: 0000-0001-7869-9817
authors.initials: LA
authors.lastname: Mitchell
authors.affiliation: High Throughput Biology Center, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA.|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.
authors.forename: Ann
authors.initials: A
authors.lastname: Wang
authors.affiliation: High Throughput Biology Center, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA.|Department of Biomedical Engineering and Institute of Genetic Medicine, Whiting School of Engineering, Johns Hopkins University, Baltimore, MD 21218, USA.|School of Computer Science and Electronic Engineering, University of Essex, Wivenhoe Park, Colchester CO4 3SQ, UK.
authors.forename: Giovanni
authors.identifier: 0000-0001-9819-3645
authors.initials: G
authors.lastname: Stracquadanio
authors.affiliation: Department of Biochemistry and Molecular Pharmacology, New York University Langone School of Medicine, New York, NY 10016, USA.|Institute for Systems Genetics, New York University Langone School of Medicine, New York, NY 10016, USA.
authors.forename: Zheng
authors.identifier: 0000-0001-5855-8371
authors.initials: Z
authors.lastname: Kuang
authors.affiliation: Department of Biochemistry and Molecular Pharmacology, New York University Langone School of Medicine, New York, NY 10016, USA.|Institute for Systems Genetics, New York University Langone School of Medicine, New York, NY 10016, USA.
authors.forename: Xuya
authors.initials: X
authors.lastname: Wang
authors.affiliation: High Throughput Biology Center, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA.|Department of Biomedical Engineering and Institute of Genetic Medicine, Whiting School of Engineering, Johns Hopkins University, Baltimore, MD 21218, USA.
authors.forename: Kun
authors.identifier: 0000-0002-1060-8082
authors.initials: K
authors.lastname: Yang
authors.affiliation: High Throughput Biology Center, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA.|Department of Biomedical Engineering and Institute of Genetic Medicine, Whiting School of Engineering, Johns Hopkins University, Baltimore, MD 21218, USA.
authors.forename: Sarah
authors.identifier: 0000-0002-9820-9421
authors.initials: S
authors.lastname: Richardson
authors.affiliation: Department of Biochemistry and Molecular Pharmacology, New York University Langone School of Medicine, New York, NY 10016, USA.|Institute for Systems Genetics, New York University Langone School of Medicine, New York, NY 10016, USA.
authors.forename: J Andrew
authors.identifier: 0000-0002-7867-6997
authors.initials: JA
authors.lastname: Martin
authors.affiliation: Department of Biochemistry and Molecular Pharmacology, New York University Langone School of Medicine, New York, NY 10016, USA.|Institute for Systems Genetics, New York University Langone School of Medicine, New York, NY 10016, USA.
authors.forename: Yu
authors.identifier: 0000-0003-4659-9832
authors.initials: Y
authors.lastname: Zhao
authors.affiliation: Center for Synthetic and Systems Biology, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3JL, UK.
authors.forename: Roy
authors.identifier: 0000-0003-0960-4591
authors.initials: R
authors.lastname: Walker
authors.affiliation: Center for Synthetic and Systems Biology, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3JL, UK.
authors.forename: Yisha
authors.identifier: 0000-0002-4228-7527
authors.initials: Y
authors.lastname: Luo
authors.affiliation: GenScript, Piscataway, NJ 08854, USA.
authors.forename: Hongjiu
authors.initials: H
authors.lastname: Dai
authors.affiliation: GenScript, Piscataway, NJ 08854, USA.
authors.forename: Kang
authors.identifier: 0000-0003-4051-3233
authors.initials: K
authors.lastname: Dong
authors.affiliation: Department of Biochemistry and Molecular Pharmacology, New York University Langone School of Medicine, New York, NY 10016, USA.|Institute for Systems Genetics, New York University Langone School of Medicine, New York, NY 10016, USA.
authors.forename: Zuojian
authors.initials: Z
authors.lastname: Tang
authors.affiliation: Proteomics Resource Center, Office of Collaborative Science, New York University Langone School of Medicine, New York, NY 10016, USA.
authors.forename: Yanling
authors.initials: Y
authors.lastname: Yang
authors.affiliation: Center for Synthetic and Systems Biology, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3JL, UK.
authors.forename: Yizhi
authors.identifier: 0000-0003-1663-2865
authors.initials: Y
authors.lastname: Cai
authors.affiliation: Genome Technology Center, New York University Langone School of Medicine, New York, NY 10016, USA.
authors.forename: Adriana
authors.initials: A
authors.lastname: Heguy
authors.affiliation: Department of Biochemistry and Molecular Pharmacology, New York University Langone School of Medicine, New York, NY 10016, USA.|Proteomics Resource Center, Office of Collaborative Science, New York University Langone School of Medicine, New York, NY 10016, USA.
authors.forename: Beatrix
authors.identifier: 0000-0003-2512-0204
authors.initials: B
authors.lastname: Ueberheide
authors.affiliation: Department of Biochemistry and Molecular Pharmacology, New York University Langone School of Medicine, New York, NY 10016, USA.|Institute for Systems Genetics, New York University Langone School of Medicine, New York, NY 10016, USA.
authors.forename: David
authors.identifier: 0000-0001-5049-3825
authors.initials: D
authors.lastname: Fenyö
authors.affiliation: 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.
authors.forename: Junbiao
authors.identifier: 0000-0002-5299-4700
authors.initials: J
authors.lastname: Dai
authors.affiliation: High Throughput Biology Center, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA.|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.
authors.forename: Joel S
authors.identifier: 0000-0002-6020-4625
authors.initials: JS
authors.lastname: Bader
authors.affiliation: Department of Biochemistry and Molecular Pharmacology, New York University Langone School of Medicine, New York, NY 10016, USA. jef.boeke@nyumc.org.|Institute for Systems Genetics, New York University Langone School of Medicine, New York, NY 10016, USA.
authors.forename: Jef D
authors.identifier: 0000-0001-5322-4946
authors.initials: JD
authors.lastname: Boeke
mesh_terms: D058045:Artificial Cells / Q000378:metabolism; D018244:Chromosomes, Artificial, Yeast / Q000737:chemistry* / Q000235:genetics*; D020161:Physical Chromosome Mapping; D046988:Proteasome Endopeptidase Complex / Q000235:genetics; D040901:Proteomics; D012441:Saccharomyces cerevisiae / Q000235:genetics* / Q000254:growth & development; D029701:Saccharomyces cerevisiae Proteins / Q000235:genetics; D058615:Synthetic Biology / Q000379:methods*
chemical_list: D029701:Saccharomyces cerevisiae Proteins; C478799:PRE4 protein, S cerevisiae; D046988:Proteasome Endopeptidase Complex