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J. Craig Venter Institute Researchers Publish Significant Advance in Genome Assembly Technology

Posted on: Thursday, 4 December 2008, 15:07 CST

Advance Allows for More Efficient Construction of Synthetic Genomes

ROCKVILLE, Md., Dec. 4 /PRNewswire-USNewswire/ -- Researchers at the J. Craig Venter Institute (JCVI), a not-for-profit genomic research organization, have published a paper describing a significant advance in genome assembly in which the team can now assemble the whole bacterial genome, Mycoplasma genitalium, in one step from 25 fragments of DNA. Lead author Daniel G. Gibson, Ph.D. and his team published their results in the online early edition of the journal Proceedings of the National Academy of Sciences (PNAS). The work was funded by the company Synthetic Genomics Inc. (SGI).

Today's publication represents major improvements in the methods that the team developed and described in their January 2008 publication of the first synthesis of a bacterial genome, M. genitalium. That publication outlined how the team synthesized in the laboratory the 582,970 base pair M. genitalium genome using the chemical building blocks of DNA -- adenine (A), guanine (G), cytosine (C) and thymine (T).

While this was a big advance, it took several years to come to fruition and in the end was a tedious, multi-stage process in which the team had to build the genome a quarter at a time using the bacterium Escherichia coli to clone and produce the DNA segments. During this building process the team found that E. coli had difficulty reproducing the large DNA segments, so they turned to the yeast Saccharomyces cerevisiae. They were then able to finish creating the synthetic bacterial genome using a method called homologous recombination (a process that cells naturally use to repair chromosome damage).

Realizing how robustly yeast performed, the team wondered if it could be used to build the entire M. genitalium genome from multiple, smaller, overlapping segments of DNA. For this study the team used DNA fragments that ranged in size from about 17,000 base pairs to 35,000 base pairs. These relatively short segments were inserted into yeast cells in one step and through the mechanism of homologous recombination were assembled into the synthetic M. genitalium genome. Several experiments were then done to confirm that all 25 pieces of the synthetic DNA had been correctly assembled in the yeast cells, and to show that the experiment could be successfully reproduced.

The JCVI team continues to explore the capacity for DNA assembly in yeast, and the various applications of this particular method. They conjecture that a variety of combinations of DNA molecules and genetic pathways could be manufactured in yeast, in essence turning yeast into a genetic factory for specifically designed and optimized processes. This advance is being used by scientists at the company SGI in making next generation biofuels and biochemicals more efficiently.

"We continue to be amazed by the capacity of yeast to simultaneously take up so many DNA pieces and assemble them into genome-size molecules," said lead author Dr. Gibson. "This capacity begs to be further explored and extended and will help accelerate progress in applications of synthetic genomics."

Senior author Clyde Hutchison, Ph.D., added, "I am astounded by our team's progress in assembling large DNA molecules. It remains to be seen how far we can push this yeast assembly platform but the team is hard at work exploring these methods as we work to boot up the synthetic chromosome."

Key Milestones/Ethical Background of JCVI's Synthetic Genomics Research

Mid-1990's: After sequencing the M. genitalium genome, Dr. Venter and colleagues begin work on the minimal genome project. This area of research, trying to understand the minimal genetic components necessary to sustain life, started with M. genitalium because it is a bacterium with the smallest genome known that can be grown in pure culture. This work was published in the journal Science in 1995.

2003: Drs. Venter, Smith and Hutchison (along with JCVI's Cynthia Andrews-Pfannkoch) made the first significant strides in the development of a synthetic genome by assembling the 5,386 base pair genome of bacteriophage phi X174 (phi X). They did so using short, single strands of synthetically produced, commercially available DNA (known as oligonucleotides) and using an adaptation of polymerase chain reaction (PCR), known as polymerase cycle assembly (PCA), to build the phi X genome. The team produced the synthetic phi X in just 14 days.

2007: JCVI researchers led by Carole Lartigue, Ph.D., announced the results of work published in the journal Science, which outlined the methods and techniques used to change one bacterial species, Mycoplasma capricolum, into another, Mycoplasma mycoides Large Colony (LC), by replacing one organism's genome with the other one's genome. Genome transplantation was the first essential enabling step in the field of synthetic genomics as it is a key mechanism by which chemically synthesized chromosomes can be activated into viable living cells.

January 2008: The second successful step in the JCVI teams' journey to create a cell controlled by synthetic DNA was completed when Gibson et al published in the journal Science, the synthetic M. genitalium genome. The team is still working on experiments to install a fully synthetic bacterial chromosome into a recipient cell and thus "boot up" a synthetic chromosome.

Ethical Considerations

Since the beginning of the quest to understand and build a synthetic genome, Dr. Venter and his team have been concerned with the societal issues surrounding the work. In 1995, while the team was doing the research on the minimal genome, the work underwent significant ethical review by a panel of experts at the University of Pennsylvania (Cho et al, Science December 1999:Vol. 286. no. 5447, pp. 2087 - 2090). The bioethical group's independent deliberations, published at the same time as the scientific minimal genome research, resulted in a unanimous decision that there were no strong ethical reasons why the work should not continue as long as the scientists involved continued to engage public discussion.

Dr. Venter and the team at JCVI continue to work with bioethicists, outside policy groups, legislative members and staff, and the public to encourage discussion and understanding about the societal implications of their work and the field of synthetic genomics generally. As such, the JCVI's policy team, along with the Center for Strategic & International Studies (CSIS), and the Massachusetts Institute of Technology (MIT), were funded by a grant from the Alfred P. Sloan Foundation for a 20-month study that explored the risks and benefits of this emerging technology, as well as possible safeguards to prevent abuse, including bioterrorism. After several workshops and public sessions the group published a report in October 2007 outlining options for the field and its researchers.

About the J. Craig Venter Institute

The JCVI is a not-for-profit research institute in Rockville, MD, and La Jolla, CA, dedicated to the advancement of the science of genomics; the understanding of its implications for society; and communication of those results to the scientific community, the public, and policymakers. Founded by J. Craig Venter, Ph.D., the JCVI is home to approximately 400 scientists and staff with expertise in human and evolutionary biology, genetics, bioinformatics/informatics, information technology, high-throughput DNA sequencing, genomic and environmental policy research, and public education in science and science policy. The legacy organizations of the JCVI are: The Institute for Genomic Research (TIGR), The Center for the Advancement of Genomics (TCAG), the Institute for Biological Energy Alternatives (IBEA), the Joint Technology Center (JTC), and the J. Craig Venter Science Foundation. The JCVI is a 501 (c) (3) organization. For additional information, please visit http://www.JCVI.org.

SOURCE J. Craig Venter Institute

Source: PR Newswire

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