Daniel G. Gibson talks with
ScienceWatch.com and answers a few questions about
this month's Fast Breaking Paper in the Multidisciplinary
Article Title: Complete chemical synthesis,
assembly, and cloning of a Mycoplasma genitalium
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
Journal: SCIENCE, Volume: 319, Issue: 5867, Page: 1215-1220
Year: FEB 29 2008
* J Craig Venter Inst, Rockville, MD 20850 USA.
* J Craig Venter Inst, Rockville, MD 20850 USA.
Why do you think your paper is highly
This paper demonstrates, for the first time, the construction of a
synthetic bacterial genome, a critical step in our ambition to create a
synthetic cell. The only completely synthetic genomes reported, prior to
this work, have been from viruses; the 5.4 kb phiX genome, and the 7.5 kb
poliovirus genome. The largest stretch of synthetic DNA that was reported
in the literature was only 32 kb. Our synthetic genome is 18 times larger
than these examples.
Does it describe a new discovery, methodology, or
synthesis of knowledge?
"We believe the capacity to
synthesize cells will allow researchers to
design organisms that have extraordinary
properties such as the ability to produce
biofuels, pharmaceuticals, and textiles, and
the ability to capture carbon from the
We describe methods for synthesizing complete bacterial genomes. This work
demonstrates that we may soon have the ability to engineer synthetic cells
with properties that are defined by the genomes we synthesize. In the
meantime, synthetic biologists are metabolically engineering existing
organisms, such as E. coli and yeast, for the production of
biofuels, antibiotics, and industrial compounds. In most cases, this
involves constructing large DNA molecules. This paper describes efficient
methods for doing so.
Would you summarize the significance of your paper in
This paper describes the synthesis of a bacterial genome. The genome is
from a species called Mycoplasma genitalium and is 582,970 bp in
length. This is the largest chemically defined structure ever synthesized
in a laboratory. Complete genome synthesis is an essential step in our goal
to construct a synthetic bacterial cell.
How did you become involved in this research, and were
there any problems along the way?
A team led by
J. Craig Venter published the sequence of the
Mycoplasma genitalium genome in 1995. Because of its relatively
small size, they began to realize that it would be possible to
synthesize the entire genome from overlapping DNA cassettes that could
be joined by homologous recombination methods.
By 2003, they improved the methodology of assembling synthetic
oligonucleotides into DNA cassettes. All that remained was to learn how to
join these DNA cassettes into genome-size molecules.
I was fascinated by this research, and truly understood the significance of
creating a synthetic cell. In December 2004, I (Daniel G. Gibson) was hired
by the J. Craig Venter Institute (JCVI) as a post-doctoral fellow. I began
investigating methods that would allow overlapping DNA fragments to be
assembled. Within a year, we had a very good method in place for assembling
DNA molecules by in vitro recombination.
By this time, we purchased 101 overlapping DNA fragments that were about 6
kb each and began assembling them into the ~582 kb genome. For a very long
time, we had the genome assembled in four pieces but could not assemble
them any further. We realized that we needed a new method for assembling
such large DNA molecules. This was when we found that the yeast
Saccharomyces cerevisiae can take up these large pieces and join
them in vivo by using its natural homologous recombination
Where do you see your research leading in the
Experiments are in progress to isolate the synthetic genome from yeast and
activate it into a viable synthetic cell. We have already demonstrated that
one bacterial species can be converted to another by installing a donor
genome into a recipient cell. This work showed that it is the genome that
dictates the characteristics of a cell.
We should then be able to transplant the synthetic genome into a recipient
cell to create a synthetic cell that was designed by us at the nucleotide
level. Once we are able to do this, we will begin designing more useful and
Also, M. genitalium has the smallest genome of any known bacterium
capable of independent life. This is an excellent starting point for
creating a minimal cell, which has only the machinery necessary for life.
In a combinatorial fashion we hope to identify a minimal genome in which
all genes are essential. This will allow us to better understand life at
the cellular level.
Do you foresee any social or political implications for
We believe the capacity to synthesize cells will allow researchers to
design organisms that have extraordinary properties such as the ability to
produce biofuels, pharmaceuticals, and textiles, and the ability to capture
carbon from the atmosphere. Synthetically engineered cells with these
properties would offer great benefits to society.
Daniel G. Gibson, Ph.D.
Scientist, Synthetic Biology and Bioenergy
J. Craig Venter Institute, Rockville, Maryland, USA Web