title: Design and synthesis of a minimal bacterial genome.
abstract: We used whole-genome design and complete chemical synthesis to minimize the 1079-kilobase pair synthetic genome of Mycoplasma mycoides JCVI-syn1.0. An initial design, based on collective knowledge of molecular biology combined with limited transposon mutagenesis data, failed to produce a viable cell. Improved transposon mutagenesis methods revealed a class of quasi-essential genes that are needed for robust growth, explaining the failure of our initial design. Three cycles of design, synthesis, and testing, with retention of quasi-essential genes, produced JCVI-syn3.0 (531 kilobase pairs, 473 genes), which has a genome smaller than that of any autonomously replicating cell found in nature. JCVI-syn3.0 retains almost all genes involved in the synthesis and processing of macromolecules. Unexpectedly, it also contains 149 genes with unknown biological functions. JCVI-syn3.0 is a versatile platform for investigating the core functions of life and for exploring whole-genome design.
authors.affiliation: J. Craig Venter Institute, La Jolla, CA 92037, USA.
authors.forename: Clyde A
authors.initials: CA
authors.lastname: Hutchison
authors.affiliation: J. Craig Venter Institute, La Jolla, CA 92037, USA.
authors.forename: Ray-Yuan
authors.initials: RY
authors.lastname: Chuang
authors.affiliation: J. Craig Venter Institute, La Jolla, CA 92037, USA.
authors.forename: Vladimir N
authors.initials: VN
authors.lastname: Noskov
authors.affiliation: J. Craig Venter Institute, La Jolla, CA 92037, USA.
authors.forename: Nacyra
authors.initials: N
authors.lastname: Assad-Garcia
authors.affiliation: National Center for Microscopy and Imaging Research, University of California-San Diego, La Jolla, CA 92037, USA.
authors.forename: Thomas J
authors.initials: TJ
authors.lastname: Deerinck
authors.affiliation: National Center for Microscopy and Imaging Research, University of California-San Diego, La Jolla, CA 92037, USA.
authors.forename: Mark H
authors.initials: MH
authors.lastname: Ellisman
authors.affiliation: Synthetic Genomics, La Jolla, CA 92037, USA.
authors.forename: John
authors.initials: J
authors.lastname: Gill
authors.affiliation: Synthetic Genomics, La Jolla, CA 92037, USA.
authors.forename: Krishna
authors.initials: K
authors.lastname: Kannan
authors.affiliation: J. Craig Venter Institute, La Jolla, CA 92037, USA.
authors.forename: Bogumil J
authors.initials: BJ
authors.lastname: Karas
authors.affiliation: J. Craig Venter Institute, La Jolla, CA 92037, USA.
authors.forename: Li
authors.initials: L
authors.lastname: Ma
authors.affiliation: National Institute of Standards and Technology, Gaithersburg, MD 20899, USA.
authors.forename: James F
authors.initials: JF
authors.lastname: Pelletier
authors.affiliation: Synthetic Genomics, La Jolla, CA 92037, USA.
authors.forename: Zhi-Qing
authors.initials: ZQ
authors.lastname: Qi
authors.affiliation: J. Craig Venter Institute, La Jolla, CA 92037, USA.
authors.forename: R Alexander
authors.initials: RA
authors.lastname: Richter
authors.affiliation: National Institute of Standards and Technology, Gaithersburg, MD 20899, USA.
authors.forename: Elizabeth A
authors.initials: EA
authors.lastname: Strychalski
authors.affiliation: J. Craig Venter Institute, La Jolla, CA 92037, USA.
authors.forename: Lijie
authors.initials: L
authors.lastname: Sun
authors.affiliation: J. Craig Venter Institute, La Jolla, CA 92037, USA.
authors.forename: Yo
authors.initials: Y
authors.lastname: Suzuki
authors.affiliation: Synthetic Genomics, La Jolla, CA 92037, USA.
authors.forename: Billyana
authors.initials: B
authors.lastname: Tsvetanova
authors.affiliation: J. Craig Venter Institute, La Jolla, CA 92037, USA.
authors.forename: Kim S
authors.initials: KS
authors.lastname: Wise
authors.affiliation: J. Craig Venter Institute, La Jolla, CA 92037, USA. Synthetic Genomics, La Jolla, CA 92037, USA.
authors.forename: Hamilton O
authors.initials: HO
authors.lastname: Smith
authors.affiliation: J. Craig Venter Institute, La Jolla, CA 92037, USA.
authors.forename: John I
authors.initials: JI
authors.lastname: Glass
authors.affiliation: J. Craig Venter Institute, La Jolla, CA 92037, USA.
authors.forename: Chuck
authors.initials: C
authors.lastname: Merryman
authors.affiliation: J. Craig Venter Institute, La Jolla, CA 92037, USA. Synthetic Genomics, La Jolla, CA 92037, USA.
authors.forename: Daniel G
authors.initials: DG
authors.lastname: Gibson
authors.affiliation: J. Craig Venter Institute, La Jolla, CA 92037, USA. Synthetic Genomics, La Jolla, CA 92037, USA.
authors.forename: J Craig
authors.initials: JC
authors.lastname: Venter
mesh_terms: D058045:Artificial Cells; D003062:Codon / Q000235:genetics; D004251:DNA Transposable Elements; D004269:DNA, Bacterial / Q000138:chemical synthesis* / Q000235:genetics; D020043:Genes, Essential; D005813:Genes, Synthetic / Q000235:genetics / Q000502:physiology*; D016680:Genome, Bacterial; D016296:Mutagenesis; D009176:Mycoplasma mycoides / Q000235:genetics*; D011506:Proteins / Q000235:genetics; D012313:RNA / Q000235:genetics; D058615:Synthetic Biology
chemical_list: D003062:Codon; D004251:DNA Transposable Elements; D004269:DNA, Bacterial; D011506:Proteins; D012313:RNA