Clyde A. Hutchison III

Last updated
Clyde A. Hutchison III
NationalityAmerican
Education Yale University
Alma mater California Institute of Technology
Known forResearch on site-directed mutagenesis and synthetic biology
Scientific career
Fields Biochemistry, microbiology
Institutions University of North Carolina at Chapel Hill, J. Craig Venter Institute

Clyde A. Hutchison III is an American biochemist and microbiologist notable for his research on site-directed mutagenesis and synthetic biology. He is Professor Emeritus of Microbiology and Immunology at the University of North Carolina at Chapel Hill, distinguished professor at the J Craig Venter Institute, a member of the National Academy of Sciences, and a fellow of the American Academy of Arts and Sciences. [1]

Contents

Early research

Hutchison graduated from Yale University in 1960, with a B.S. degree in physics. He studied for his PhD at Caltech, working on the bacteriophage ΦX174. While at Caltech he began a long-term collaboration with Marshall Edgell. [1] In 1968 he moved to UNC-Chapel Hill. Hutchison and Edgell used restriction enzymes for the analysis of ΦX174 and mammalian DNA.

Hutchison participated in the determination of the first complete sequence of a DNA molecule (ΦX174) when he spent a year sabbatical at the Frederick Sanger's laboratory in 1975/1976. [2]

Site-directed mutagenesis

In 1971, Clyde Hutchison and Marshall Edgell showed that it is possible to produce mutants with small fragments of bacteriophage ϕX174 and restriction nucleases. [3] [4] Hutchison later collaborated with Michael Smith and developed a more general method of site-directed mutagenesis using a mutant oligonucleotide primer and DNA polymerase. Smith and Hutchison used a 12-nucleotide oligomer with a centrally positioned single mismatched nucleotide as primer, a circular single-stranded ϕX174 DNA as template, and E. coli DNA polymerase I in which the 5'-exonuclease had been inactivated by subtilisin. The polymerization with the primer annealed to the template generated a double-stranded DNA product that contained a mutation and could be converted to a closed circular duplex by enzymatic ligation. [5] Transfection of E. coli with this molecule produced a mixed population of wild-type and mutated phage DNA. For his part in the development of this process, Michael Smith later shared the Nobel Prize in Chemistry in 1993 with Kary B. Mullis, who invented polymerase chain reaction. [6]

Hutchison later developed methods for "complete mutagenesis" in which each residue in a protein is individually altered. [7]

Synthetic biology

In 1990 Hutchison began work on Mycoplasma genitalium , which has the smallest known genome that can constitute a cell. It led to a collaboration with The Institute for Genomic Research (TIGR) to sequence the entire genome of the organism in 1995. In 1996 Hutchison spent a sabbatical year at TIGR; there he discussed with Hamilton Smith and Craig Venter the idea of a minimum cell - cell with the minimal set of genes required for survival. [8] They speculated that they may need to synthesize the genome to test them in recipient cell, thereby creating a synthetic cell.

In 2003 Hutchison began a collaboration with Hamilton Smith on the assembly of a synthetic minimal cellular genome, and successfully synthesized the small genome (5386 base pairs) of the bacteriophage ΦX174. The M. genitalium genome however is over 100 times larger than that of ΦX174. In 2007, a chemically synthesized genome of 582,970 base pairs based on M. genitalium, intended for the creation of an organism christened Mycoplasma laboratorium , was successfully assembled. [9] M. genitalium however is slow-growing and attempts at transplanting its genome to another species became protracted and proved unsuccessful. The synthetic-cell team however showed that it is possible to transplant the natural genome of Mycoplasma mycoides , whose genome is twice the size of M. genitalium, into a related species Mycoplasma capricolum . [10] The team therefore decided to switch to the faster-growing M. mycoides as the donor species. In March 2010, a synthesized M. mycoides genome was successfully transplanted into M. capricolum . [8] [11] The resulting organism was called "Synthia" by the popular press. [8] In 2016, the team revealed a further pared-down version of the organism with 473 genes, 149 of which whose functions are completely unknown. [12]

Work on creating the minimal cell is currently in progress. New versions of the synthetic genome with genes removed are transplanted into recipient cells, and the resultant cells' growth rates and their colony size are monitored. Other more complex bacteria such as cyanobacteria are also being assessed for the feasibility of genome transplantation. [8]

Related Research Articles

<span class="mw-page-title-main">Mycoplasma genitalium</span> Species of bacterium

Mycoplasma genitalium is a sexually transmitted, small and pathogenic bacterium that lives on the mucous epithelial cells of the urinary and genital tracts in humans. Medical reports published in 2007 and 2015 state that Mgen is becoming increasingly common. Resistance to multiple antibiotics, including the macrolide azithromycin, which until recently was the most reliable treatment, is becoming prevalent. The bacteria was first isolated from the urogenital tract of humans in 1981, and was eventually identified as a new species of Mycoplasma in 1983. It can cause negative health effects in men and women. It also increases the risk factor for HIV spread with higher occurrences in those previously treated with the azithromycin antibiotics.

<span class="mw-page-title-main">Genomics</span> Discipline in genetics

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<span class="mw-page-title-main">Michael Smith (chemist)</span> British-born Canadian biochemist, businessman and Nobel Prize laureate (1932–2000)

Michael Smith was a British-born Canadian biochemist and businessman. He shared the 1993 Nobel Prize in Chemistry with Kary Mullis for his work in developing site-directed mutagenesis. Following a PhD in 1956 from the University of Manchester, he undertook postdoctoral research with Har Gobind Khorana at the British Columbia Research Council in Vancouver, British Columbia, Canada. Subsequently, Smith worked at the Fisheries Research Board of Canada Laboratory in Vancouver before being appointed a professor of biochemistry in the UBC Faculty of Medicine in 1966. Smith's career included roles as the founding director of the UBC Biotechnology Laboratory and the founding scientific leader of the Protein Engineering Network of Centres of Excellence (PENCE). In 1996 he was named Peter Wall Distinguished Professor of Biotechnology. Subsequently, he became the founding director of the Genome Sequencing Centre at the BC Cancer Research Centre.

<i>Mycoplasma</i> Genus of bacteria

Mycoplasma is a genus of bacteria that, like the other members of the class Mollicutes, lack a cell wall around their cell membranes. Peptidoglycan (murein) is absent. This characteristic makes them naturally resistant to antibiotics that target cell wall synthesis. They can be parasitic or saprotrophic. Several species are pathogenic in humans, including M. pneumoniae, which is an important cause of "walking" pneumonia and other respiratory disorders, and M. genitalium, which is believed to be involved in pelvic inflammatory diseases. Mycoplasma species are among the smallest organisms yet discovered, can survive without oxygen, and come in various shapes. For example, M. genitalium is flask-shaped, while M. pneumoniae is more elongated, many Mycoplasma species are coccoid. Hundreds of Mycoplasma species infect animals.

<i>Nanoarchaeum equitans</i> Species of archaeon

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Site-directed mutagenesis is a molecular biology method that is used to make specific and intentional mutating changes to the DNA sequence of a gene and any gene products. Also called site-specific mutagenesis or oligonucleotide-directed mutagenesis, it is used for investigating the structure and biological activity of DNA, RNA, and protein molecules, and for protein engineering.

<span class="mw-page-title-main">Synthetic biology</span> Interdisciplinary branch of biology and engineering

Synthetic biology (SynBio) is a multidisciplinary field of science that focuses on living systems and organisms, and it applies engineering principles to develop new biological parts, devices, and systems or to redesign existing systems found in nature.

<span class="mw-page-title-main">J. Craig Venter Institute</span> Non-profit genomics research institute

The J. Craig Venter Institute (JCVI) is a non-profit genomics research institute founded by J. Craig Venter, Ph.D. in October 2006. The institute was the result of consolidating four organizations: the Center for the Advancement of Genomics, The Institute for Genomic Research (TIGR), the Institute for Biological Energy Alternatives, and the J. Craig Venter Science Foundation Joint Technology Center. It has facilities in Rockville, Maryland and San Diego, California.

Microviridae is a family of bacteriophages with a single-stranded DNA genome. The name of this family is derived from the ancient Greek word μικρός (mikrós), meaning "small". This refers to the size of their genomes, which are among the smallest of the DNA viruses. Enterobacteria, intracellular parasitic bacteria, and spiroplasma serve as natural hosts. There are 22 species in this family, divided among seven genera and two subfamilies.

<span class="mw-page-title-main">Phi X 174</span> A single-stranded DNA virus that infects bacteria

The phi X 174 bacteriophage is a single-stranded DNA (ssDNA) virus that infects Escherichia coli. This virus was isolated in 1935 by Nicolas Bulgakov in Félix d'Hérelle's laboratory at the Pasteur Institute, from samples collected in Paris sewers. Its characterization and the study of its replication mechanism were carried out from the 1950s onwards. It was the first DNA-based genome to be sequenced. This work was completed by Fred Sanger and his team in 1977. In 1962, Walter Fiers and Robert Sinsheimer had already demonstrated the physical, covalently closed circularity of ΦX174 DNA. Nobel prize winner Arthur Kornberg used ΦX174 as a model to first prove that DNA synthesized in a test tube by purified enzymes could produce all the features of a natural virus, ushering in the age of synthetic biology. In 1972–1974, Jerard Hurwitz, Sue Wickner, and Reed Wickner with collaborators identified the genes required to produce the enzymes to catalyze conversion of the single stranded form of the virus to the double stranded replicative form. In 2003, it was reported by Craig Venter's group that the genome of ΦX174 was the first to be completely assembled in vitro from synthesized oligonucleotides. The ΦX174 virus particle has also been successfully assembled in vitro. In 2012, it was shown how its highly overlapping genome can be fully decompressed and still remain functional.

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Artificial gene synthesis, or simply gene synthesis, refers to a group of methods that are used in synthetic biology to construct and assemble genes from nucleotides de novo. Unlike DNA synthesis in living cells, artificial gene synthesis does not require template DNA, allowing virtually any DNA sequence to be synthesized in the laboratory. It comprises two main steps, the first of which is solid-phase DNA synthesis, sometimes known as DNA printing. This produces oligonucleotide fragments that are generally under 200 base pairs. The second step then involves connecting these oligonucleotide fragments using various DNA assembly methods. Because artificial gene synthesis does not require template DNA, it is theoretically possible to make a completely synthetic DNA molecule with no limits on the nucleotide sequence or size.

Mycoplasma laboratorium or Synthia refers to a synthetic strain of bacterium. The project to build the new bacterium has evolved since its inception. Initially the goal was to identify a minimal set of genes that are required to sustain life from the genome of Mycoplasma genitalium, and rebuild these genes synthetically to create a "new" organism. Mycoplasma genitalium was originally chosen as the basis for this project because at the time it had the smallest number of genes of all organisms analyzed. Later, the focus switched to Mycoplasma mycoides and took a more trial-and-error approach.

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Φ29 DNA polymerase is an enzyme from the bacteriophage Φ29. It is being increasingly used in molecular biology for multiple displacement DNA amplification procedures, and has a number of features that make it particularly suitable for this application. It was discovered and characterized by Spanish scientists Luis Blanco and Margarita Salas.

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Synthetic genome is a synthetically built genome whose formation involves either genetic modification on pre-existing life forms or artificial gene synthesis to create new DNA or entire lifeforms. The field that studies synthetic genomes is called synthetic genomics.

References

  1. 1 2 "Clyde A. Hutchison III - a brief career sketch". University of North Carolina at Chapel Hill.
  2. ↑ Sanger F, Coulson AR, Friedmann T, Air GM, Barrell BG, Brown NL, Fiddes JC, Hutchison CA 3rd, Slocombe PM, Smith M (1978). "The nucleotide sequence of bacteriophage phiX174". Journal of Molecular Biology. 125 (2): 225–46. doi:10.1016/0022-2836(78)90346-7. PMID   731693.
  3. ↑ Hutchison III, C. A.; Edgell, M. H. (1971). "Genetic Assay for Small Fragments of Bacteriophage φX174 Deoxyribonucleic Acid". Journal of Virology. 8 (2): 181–189. doi:10.1128/JVI.8.2.181-189.1971. PMC   356229 . PMID   4940243.
  4. ↑ Marshall H. Edgell; Clyde A. Hutchison & III, Morton Sclair (1972). "Specific Endonuclease R Fragments of Bacteriophage X174 Deoxyribonucleic Acid". Journal of Virology. 9 (4): 574–582. doi:10.1128/JVI.9.4.574-582.1972. PMC   356341 . PMID   4553678.
  5. ↑ Hutchison, C.A.; Phillips, S.; Edgell, M.H.; Gillham, S.; Jahnke, P.; Smith, M. (1978). "Mutagenesis at a Specific Position in a DNA Sequence" (PDF). Journal of Biological Chemistry. 253 (18): 551–6560. doi: 10.1016/S0021-9258(19)46967-6 . PMID   681366.
  6. ↑ Nicole Kresge; Robert D. Simoni; Robert L. Hill. "The Development of Site-directed Mutagenesis by Michael Smith" (PDF). Journal of Biological Chemistry. 281 (39).
  7. ↑ Hutchison, C.A. III; Swanstrom, R. & Loeb, D.D. (1991). Complete Mutagenesis of Protein Coding Domains . Methods in Enzymology. Vol. 202. pp.  356–390. doi:10.1016/0076-6879(91)02019-6. ISBN   9780121821036. PMID   1784182.
  8. 1 2 3 4 Roberta Kwok (2010). "Genomics: DNA's master craftsmen". Nature. 468 (7320): 22–5. Bibcode:2010Natur.468...22K. doi: 10.1038/468022a . PMID   21048740.
  9. ↑ Ed Pilkington (6 October 2007). "I am creating artificial life, declares US gene pioneer". Guardian.
  10. ↑ Lartigue C, Glass JI, Alperovich N, Pieper R, Parmar PP, Hutchison CA 3rd, Smith HO, Venter JC (2007). "Genome transplantation in bacteria: changing one species to another". Science. 317 (5838): 632–8. Bibcode:2007Sci...317..632L. CiteSeerX   10.1.1.395.4374 . doi:10.1126/science.1144622. PMID   17600181. S2CID   83956478.
  11. ↑ 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 3rd, Smith HO, Venter JC (2010). "Creation of a bacterial cell controlled by a chemically synthesized genome". Science. 329 (5987): 52–6. Bibcode:2010Sci...329...52G. doi: 10.1126/science.1190719 . PMID   20488990.
  12. ↑ Ed Yong (March 24, 2016). "The Mysterious Thing About a Marvelous New Synthetic Cell".
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