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

ROCKVILLE, MD (November 13, 2003). Researchers from the Institute for Biological Energy Alternatives (IBEA), led by J. Craig Venter, Ph.D., have significantly advanced methods to improve the speed and accuracy of genomic synthesis. The IBEA researchers assembled the 5,386 base pair bacteriophage φX174 (phi X), from short, single strands of synthetically produced, commercially available DNA (known as oligonucleotides) using an adaptation of polymerase chain reaction (PCR), known as polymerase cycle assembly (PCA), to build the phi X genome. Like PCR, PCA is a technique that produces double-stranded copies of individual gene sequences based on single-stranded templates. The IBEA team produced the synthetic phi X in just 14 days. The research, accepted for publication and in press with the Proceedings of the National Academy of Sciences (PNAS), was announced today at a press conference with Secretary of the Department of Energy, Spencer Abraham and Dr. Venter.

Bacteriophages are viruses that infect bacteria and are not harmful to humans, animals, or plants. The authors of the PNAS paper, Hamilton O. Smith, M.D., scientific director of IBEA; Clyde A. Hutchison, Ph.D., University of North Carolina, Chapel Hill; Cynthia Pfannkoch, IBEA; and J. Craig Venter, Ph.D., president of IBEA, chose phi X for several reasons. First, working with this bacteriophage poses no health or ethical concerns. Second, phi X has been well studied in the laboratory and in 1978 it was the first DNA completely sequenced. Finally, its unique genetic code arrangement (overlapping genes), requires very high accuracy making it easy to verify whether exact synthesis has occurred. IBEA researchers hope that by making synthetic organisms they can rapidly and effectively harness all energy in the organism toward either energy production, likely in the form of hydrogen, or carbon sequestration.

"Synthesis of phi X by Ham Smith, Clyde Hutchison and the IBEA team is an important step toward our ultimate goal of synthesizing a complete cellular genome," said Dr. Venter. "Work in creating a synthetic chromosome/genome will at its most basic level give us a better understanding of basic cellular processes. Genome composition, regulatory circuits, signaling pathways and numerous other aspects of organism gene and protein function will be better understood through construction of a synthetic genome. Not only will this basic research lead to better understanding of these pathways and components in the particular organisms IBEA scientists are working on, but also better understanding of human biology. The ability to construct synthetic genomes may lead to extraordinary advances in our ability to engineer microorganisms for many vital energy and environmental purposes."

"Researchers have made an exciting scientific advance that may speed our ability to develop biology-based solutions for some of our most pressing energy and environmental challenges," Secretary Abraham said. "With this advance it is easier to imagine, in the not-too-distant future, a colony of specially designed microbes living within the emission-control system of a coal-fired plant, consuming its pollution and its carbon dioxide, or employing microbes to radically reduce water pollution or to reduce the toxic effects of radioactive waste."

Both Secretary Abraham and Dr. Venter stressed that because scientific advance in this area could raise the possibility of harmful misuse of this new technology, leaders in the scientific and national security communities already are engaged in concerted deliberations to determine the path forward that will maximize scientific progress and take proper account of any and all ethical and security concerns. Abraham also announced that he is creating a special subcommittee of the department.s Biological and Environmental Research Advisory Committee to conduct a thorough review of IBEA.s research and to recommend ways to accelerate this research and identify the full range of potential benefits to energy missions as well as other areas of vital importance. The new subcommittee will be chaired by Dr. Ray Gesteland, vice president of research and professor of genetics at the University of Utah.

Background

This latest advance toward IBEA.s goal of constructing a cellular synthetic genome was a direct result of early work done in the mid-to-late 1990's at The Institute for Genomic Research (TIGR) by Dr. Venter and colleagues on Mycoplasma genitalium and the minimal genome project. This area of research, trying to understand the minimal genetic components necessary to sustain life, underwent significant ethical review by a panel of experts at the University of Pennsylvania. 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.

When IBEA applied for a grant from the Department of Energy in 2002 (as part of the Genomes to Life initiative), the group outlined a project to construct an artificial chromosome. The goal of this work was to develop an artificial construct that could serve as a carrier for genes that encode expanded metabolic pathways and capabilities of naturally-occurring microorganisms. Ultimately, the goal is to have microorganisms engineered to be more efficient for specific processes related to biofuel production (e.g., methane and hydrogen) and carbon sequestration (e.g., from industrial waste streams).

The first stage toward the ultimate goal of genomic engineered organisms has now been accomplished with the successful construction of synthetic phi X. This work has potential application as an efficient, simple carrier vehicle for the production of proteins and genes of importance for health, environmental and other commercial applications.

Benefits of Synthetic Genomes/Synthetic phi X

Dr. Venter and the authors on the PNAS manuscript outline the potential uses and benefits of synthetic genomics. The group foresees a day when, "synthetic genomics will become commonplace and provide the potential for a vast array of new and complex chemistries altering our approaches to production of energy, pharmaceuticals, and textiles." Here are examples of some of the specific benefits of synthetic genomics/synthetic phi X:

• Better, faster gene synthesis.thus any biotech product that is derived from or uses a 10kb or less gene product could benefit from the IBEA developed synthesis technique.
• Faster, more accurate DNA-based vaccine production
• Improved phage therapy, for example, for treating antibiotic resistant infections
• Improved biological agent detection/deterrent
• Clean energy production.hydrogen through engineered photosynthetic process
• Eventual construction of "cassette-based" organisms — eventually we will be able to produce "cassettes" of particular genes or pathways that could be inserted into host organisms to conduct many types of functions. For example, extrapolating from the IBEA work and the work that has been done at Dupont with E. coli, organisms could be engineered to improve production in a more environmentally sound way in pharmaceutical, textiles, and plastics manufacture, replacing the use of petrochemicals. Likewise, microbes for cleaning up oil spills, radioactive waste, etc. could be improved through this technique.

The work in constructing a synthetic phi X genome was funded through the Department of Energy's (DOE) Genomes to Life program and the J. Craig Venter Science Foundation.

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The Institute for Biological Energy Alternatives (IBEA) is a not-for-profit, 501 (c) (3), research-based institution dedicated to employing the tools of genomics to develop cost-effective biological fuels and other biological approaches to greenhouse mitigation and exploring solutions for carbon sequestration using microbes, microbial pathways, and plants. For example, IBEA will develop and use microbial pathways and microbial metabolism to produce carbon-neutral fuels in an environmentally sound fashion. IBEA will undertake genome engineering to better understand the evolution of cellular life and how these cell components function together in a living system. More information about IBEA is available at www.bioenergyalts.org

DOE's Genomes to Life program aims to use the department's unique computational capabilities and research facilities to understand the activities of single-cell organisms on three levels: the proteins and multi-molecular machines that perform most of the cell's work; the gene regulatory networks that control these processes; and microbial associations or communities in which groups of different microbes carry out fundamental functions in nature. Once researchers understand how life functions at the microbial level, they hope to use the capabilities of these organisms to help meet many of our national challenges in energy and the environment. The program will combine research in biology, engineering and computation with the development of novel facilities for high-throughput biology projects. More information on the Genomes to Life program is on the Web at www.doegenomestolife.org

Contact

Heather Kowalski
Kowalski Communications
202-294-9206
[email protected]

Jeff Sherwood, DOE 202-586-5806 [email protected]