Clyde A. Hutchison, III, PhD

Distinguished Professor Emeritus

Clyde Hutchison, III, PhD, is a distinguished professor emeritus at the J. Craig Venter Institute in La Jolla, California, where he is a member of the Synthetic Biology Group. He is also a consultant for Synthetic Genomics, Inc. In 1995 he was elected to membership in the National Academy of Sciences. He graduated from Yale University in 1960, with a BS in Physics. His graduate studies were in the laboratory of Robert L. Sinsheimer at Cal Tech where he finished his PhD in 1968. He was a member of the faculty of The University of North Carolina at Chapel Hill from 1968 until 2005, where he now holds the title Kenan Professor Emeritus. He has worked on the molecular genetics of bacteriophage, bacteria, and mammals. In Fred Sanger's lab (1975-6) he helped determine the first complete sequence of a DNA molecule (phiX174). He developed site-directed mutagenesis with Michael Smith (1978). In 1990 he began work with mycoplasmas as models for the minimal cell. This led to collaboration with Smith and Venter, and his current work on synthetic genomics.

Research Priorities

Understanding the minimal requirements for life
  • Determining functions of all genes in the minimal cell, JCVI-syn3.0.
Developing methods for genome design
  • Extending the design of minimized genomes to simple eukaryotes.
Modeling the minimal cell
  • Collaborating with other labs to build a predictive computer model of JCVI-syn3.0.

Publications

The journal of physical chemistry. B. 2022-09-15; 126.36: 6820-6834.
Toward the Complete Functional Characterization of a Minimal Bacterial Proteome
Bianchi DM, Pelletier JF, Hutchison CA, Glass JI, Luthey-Schulten Z
PMID: 36048731
Cell. 2022-07-21; 185.15: 2708-2724.
Synthetic chromosomes, genomes, viruses, and cells
Venter JC, Glass JI, Hutchison CA, Vashee S
PMID: 35868275
Cell. 2022-01-20; 185.2: 345-360.e28.
Fundamental behaviors emerge from simulations of a living minimal cell
Thornburg ZR, Bianchi DM, Brier TA, Gilbert BR, Earnest TM, Melo MCR, Safronova N, Sáenz JP, Cook AT, Wise KS, Hutchison CA, Smith HO, Glass JI, Luthey-Schulten Z
PMID: 35063075
International journal of molecular sciences. 2020-09-26; 21.19:
Gross Chromosomal Rearrangements in Kluyveromyces marxianus Revealed by Illumina and Oxford Nanopore Sequencing
Ding L, Macdonald HD, Smith HO, Hutchison Iii CA, Merryman C, Michael TP, Abramson BW, Kannan K, Liang J, Gill J, Gibson DG, Glass JI
PMID: 32993167
Frontiers in molecular biosciences. 2019-11-28; 6.130.
Kinetic Modeling of the Genetic Information Processes in a Minimal Cell
Thornburg ZR, Melo MCR, Bianchi D, Brier TA, Crotty C, Breuer M, Smith HO, Hutchison CA, Glass JI, Luthey-Schulten Z
PMID: 31850364
Journal of bacteriology. 2019-10-01; 201.19:
Polar Effects of Transposon Insertion into a Minimal Bacterial Genome
Hutchison CA, Merryman C, Sun L, Assad-Garcia N, Richter RA, Smith HO, Glass JI
PMID: 31262838
eLife. 2019-01-18; 8.
Essential metabolism for a minimal cell
Breuer M, Earnest TM, Merryman C, Wise KS, Sun L, Lynott MR, Hutchison CA, Smith HO, Lapek JD, Gonzalez DJ, de Crécy-Lagard V, Haas D, Hanson AD, Labhsetwar P, Glass JI, Luthey-Schulten Z
PMID: 30657448
ACS synthetic biology. 2018-06-15; 7.6: 1538-1552.
Tuning Gene Activity by Inducible and Targeted Regulation of Gene Expression in Minimal Bacterial Cells
Mariscal AM, Kakizawa S, Hsu JY, Tanaka K, González-González L, Broto A, Querol E, Lluch-Senar M, Piñero-Lambea C, Sun L, Weyman PD, Wise KS, Merryman C, Tse G, Moore AJ, Hutchison CA, Smith HO, Tomita M, Venter JC, Glass JI, Piñol J, Suzuki Y
PMID: 29786424
Cold Spring Harbor perspectives in biology. 2017-12-01; 9.12:
Minimal Cells-Real and Imagined
Glass JI, Merryman C, Wise KS, Hutchison CA, Smith HO
PMID: 28348033
Scientific reports. 2016-08-04; 6.30714.
One step engineering of the small-subunit ribosomal RNA using CRISPR/Cas9
Kannan K, Tsvetanova B, Chuang RY, Noskov VN, Assad-Garcia N, Ma L, Hutchison Iii CA, Smith HO, Glass JI, Merryman C, Venter JC, Gibson DG
PMID: 27489041
Science (New York, N.Y.). 2016-03-25; 351.6280: aad6253.
Design and synthesis of a minimal bacterial genome
Hutchison CA, Chuang RY, Noskov VN, Assad-Garcia N, Deerinck TJ, Ellisman MH, Gill J, Kannan K, Karas BJ, Ma L, Pelletier JF, Qi ZQ, Richter RA, Strychalski EA, Sun L, Suzuki Y, Tsvetanova B, Wise KS, Smith HO, Glass JI, Merryman C, Gibson DG, Venter JC
PMID: 27013737
Genome research. 2015-03-01; 25.3: 435-44.
Bacterial genome reduction using the progressive clustering of deletions via yeast sexual cycling
Suzuki Y, Assad-Garcia N, Kostylev M, Noskov VN, Wise KS, Karas BJ, Stam J, Montague MG, Hanly TJ, Enriquez NJ, Ramon A, Goldgof GM, Richter RA, Vashee S, Chuang RY, Winzeler EA, Hutchison CA, Gibson DG, Smith HO, Glass JI, Venter JC
PMID: 25654978
Nature protocols. 2014-04-01; 9.4: 743-50.
Transferring whole genomes from bacteria to yeast spheroplasts using entire bacterial cells to reduce DNA shearing
Karas BJ, Jablanovic J, Irvine E, Sun L, Ma L, Weyman PD, Gibson DG, Glass JI, Venter JC, Hutchison CA, Smith HO, Suzuki Y
PMID: 24603933
Frontiers in microbiology. 2014-01-01; 5.369.
Rescue of mutant fitness defects using in vitro reconstituted designer transposons in Mycoplasma mycoides
Karas BJ, Wise KS, Sun L, Venter JC, Glass JI, Hutchison CA, Smith HO, Suzuki Y
PMID: 25101070
Journal of biological engineering. 2013-12-10; 7.1: 30.
Assembly of eukaryotic algal chromosomes in yeast
Karas BJ, Molparia B, Jablanovic J, Hermann WJ, Lin YC, Dupont CL, Tagwerker C, Yonemoto IT, Noskov VN, Chuang RY, Allen AE, Glass JI, Hutchison CA, Smith HO, Venter JC, Weyman PD
PMID: 24325901
Nature methods. 2013-05-01; 10.5: 410-2.
Direct transfer of whole genomes from bacteria to yeast
Karas BJ, Jablanovic J, Sun L, Ma L, Goldgof GM, Stam J, Ramon A, Manary MJ, Winzeler EA, Venter JC, Weyman PD, Gibson DG, Glass JI, Hutchison CA, Smith HO, Suzuki Y
PMID: 23542886
Nucleic acids research. 2012-11-01; 40.20: 10375-83.
Sequence analysis of a complete 1.66 Mb Prochlorococcus marinus MED4 genome cloned in yeast
Tagwerker C, Dupont CL, Karas BJ, Ma L, Chuang RY, Benders GA, Ramon A, Novotny M, Montague MG, Venepally P, Brami D, Schwartz A, Andrews-Pfannkoch C, Gibson DG, Glass JI, Smith HO, Venter JC, Hutchison CA
PMID: 22941652
ACS synthetic biology. 2012-07-20; 1.7: 267-73.
Assembly of large, high G+C bacterial DNA fragments in yeast
Noskov VN, Karas BJ, Young L, Chuang RY, Gibson DG, Lin YC, Stam J, Yonemoto IT, Suzuki Y, Andrews-Pfannkoch C, Glass JI, Smith HO, Hutchison CA, Venter JC, Weyman PD
PMID: 23651249
Nature methods. 2010-11-01; 7.11: 901-3.
Chemical synthesis of the mouse mitochondrial genome
Gibson DG, Smith HO, Hutchison CA, Venter JC, Merryman C
PMID: 20935651
Science (New York, N.Y.). 2010-07-02; 329.5987: 52-6.
Creation of a bacterial cell controlled by a chemically synthesized genome
Gibson DG, Glass JI, Lartigue C, Noskov VN, Chuang RY, Algire MA, Benders GA, Montague MG, Ma L, Moodie MM, Merryman C, Vashee S, Krishnakumar R, Assad-Garcia N, Andrews-Pfannkoch C, Denisova EA, Young L, Qi ZQ, Segall-Shapiro TH, Calvey CH, Parmar PP, Hutchison CA, Smith HO, Venter JC
PMID: 20488990
Nucleic acids research. 2010-05-01; 38.8: 2558-69.
Cloning whole bacterial genomes in yeast
Benders GA, Noskov VN, Denisova EA, Lartigue C, Gibson DG, Assad-Garcia N, Chuang RY, Carrera W, Moodie M, Algire MA, Phan Q, Alperovich N, Vashee S, Merryman C, Venter JC, Smith HO, Glass JI, Hutchison CA
PMID: 20211840
Science (New York, N.Y.). 2009-09-25; 325.5948: 1693-6.
Creating bacterial strains from genomes that have been cloned and engineered in yeast
Lartigue C, Vashee S, Algire MA, Chuang RY, Benders GA, Ma L, Noskov VN, Denisova EA, Gibson DG, Assad-Garcia N, Alperovich N, Thomas DW, Merryman C, Hutchison CA, Smith HO, Venter JC, Glass JI
PMID: 19696314
Nature methods. 2009-05-01; 6.5: 343-5.
Enzymatic assembly of DNA molecules up to several hundred kilobases
Gibson DG, Young L, Chuang RY, Venter JC, Hutchison CA, Smith HO
PMID: 19363495
Molecular systems biology. 2009-01-01; 5.330.
A systems biology tour de force for a near-minimal bacterium
Glass JI, Hutchison CA, Smith HO, Venter JC
PMID: 19953084
Proceedings of the National Academy of Sciences of the United States of America. 2008-12-23; 105.51: 20404-9.
One-step assembly in yeast of 25 overlapping DNA fragments to form a complete synthetic Mycoplasma genitalium genome
Gibson DG, Benders GA, Axelrod KC, Zaveri J, Algire MA, Moodie M, Montague MG, Venter JC, Smith HO, Hutchison CA
PMID: 19073939
Science (New York, N.Y.). 2008-02-29; 319.5867: 1215-20.
Complete chemical synthesis, assembly, and cloning of a Mycoplasma genitalium genome
Gibson DG, Benders GA, Andrews-Pfannkoch C, Denisova EA, Baden-Tillson H, Zaveri J, Stockwell TB, Brownley A, Thomas DW, Algire MA, Merryman C, Young L, Noskov VN, Glass JI, Venter JC, Hutchison CA, Smith HO
PMID: 18218864
Science (New York, N.Y.). 2007-08-03; 317.5838: 632-8.
Genome transplantation in bacteria: changing one species to another
Lartigue C, Glass JI, Alperovich N, Pieper R, Parmar PP, Hutchison CA, Smith HO, Venter JC
PMID: 17600181
Nucleic acids research. 2007-01-01; 35.Database issue: 6227-37.
DNA sequencing: bench to bedside and beyond
Hutchison CA
PMID: 17855400
Proceedings of the National Academy of Sciences of the United States of America. 2005-11-29; 102.48: 17332-6.
Cell-free cloning using phi29 DNA polymerase
Hutchison CA, Smith HO, Pfannkoch C, Venter JC
PMID: 16286637
Proceedings of the National Academy of Sciences of the United States of America. 2003-12-23; 100.26: 15440-5.
Generating a synthetic genome by whole genome assembly: phiX174 bacteriophage from synthetic oligonucleotides
Smith HO, Hutchison CA, Pfannkoch C, Venter JC
PMID: 14657399
Science (New York, N.Y.). 1999-12-10; 286.5447: 2165-9.
Global transposon mutagenesis and a minimal Mycoplasma genome
Hutchison CA, Peterson SN, Gill SR, Cline RT, White O, Fraser CM, Smith HO, Venter JC
PMID: 10591650
Science (New York, N.Y.). 1995-10-20; 270.5235: 397-403.
The minimal gene complement of Mycoplasma genitalium
Fraser CM, Gocayne JD, White O, Adams MD, Clayton RA, Fleischmann RD, Bult CJ, Kerlavage AR, Sutton G, Kelley JM, Fritchman RD, Weidman JF, Small KV, Sandusky M, Fuhrmann J, Nguyen D, Utterback TR, Saudek DM, Phillips CA, Merrick JM, Tomb JF, Dougherty BA, Bott KF, Hu PC, Lucier TS, Peterson SN, Smith HO, Hutchison CA, Venter JC
PMID: 7569993
Journal of bacteriology. 1993-12-01; 175.24: 7918-30.
A survey of the Mycoplasma genitalium genome by using random sequencing
Peterson SN, Hu PC, Bott KF, Hutchison CA
PMID: 8253680
Molecular and cellular biology. 1986-01-01; 6.1: 168-82.
The sequence of a large L1Md element reveals a tandemly repeated 5' end and several features found in retrotransposons
Loeb DD, Padgett RW, Hardies SC, Shehee WR, Comer MB, Edgell MH, Hutchison CA
PMID: 3023821
The Journal of biological chemistry. 1978-09-25; 253.18: 6551-60.
Mutagenesis at a specific position in a DNA sequence
Hutchison CA, Phillips S, Edgell MH, Gillam S, Jahnke P, Smith M
PMID: 681366
Nature. 1976-11-04; 264.5581: 34-41.
Overlapping genes in bacteriophage phiX174
Barrell BG, Air GM, Hutchison CA
PMID: 1004533
Nature. 1974-10-11; 251.5475: 536-8.
Maternal inheritance of mammalian mitochondrial DNA
Hutchison CA, Newbold JE, Potter SS, Edgell MH
PMID: 4423884

Research Priorities

Understanding the minimal requirements for life
  • Determining functions of all genes in the minimal cell, JCVI-syn3.0.
Developing methods for genome design
  • Extending the design of minimized genomes to simple eukaryotes.
Modeling the minimal cell
  • Collaborating with other labs to build a predictive computer model of JCVI-syn3.0.
21-Jul-2022
Press Release

Synthetic genomics advances and promise

Advances in DNA synthesis will enable extraordinary new opportunities in medicine, industry, agriculture, and research

20-Aug-2009
Press Release

J. Craig Venter Institute Researchers Clone and Engineer Bacterial Genomes in Yeast and Transplant Genomes Back into Bacterial Cells

New methods allow for the rapid engineering of bacterial chromosomes and the creation of extensively modified bacterial species; should also play key role in boot up of synthetic cell

24-Jan-2008
Press Release

Venter Institute Scientists Create First Synthetic Bacterial Genome

Publication Represents Largest Chemically Defined Structure Synthesized in the Lab

Team Completes Second Step in Three Step Process to Create Synthetic Organism

28-Jun-2007
Press Release

JCVI Scientists Publish First Bacterial Genome Transplantation Changing One Species to Another

Research is important step in further advancing field of synthetic genomics

13-Nov-2003
Press Release

IBEA Researchers Make Significant Advance in Methodology Toward Goal of a Synthetic Genome

Group Synthesizes Biologically Active Genome of Bacteriophage φX174

IBEA research, funded by Dept. of Energy, is an important advance toward the goal of a completely synthetic genome that could aid in carbon sequestration and energy production