Synthetic Genome

A fully synthesized genome transforms one species of bacterium into another.

A chemical marker (blue) shows the ability of a single bacterium with synthesized genome to spawn a viable colony. Credit: Science/AAAS

Scientists have built a bacterial genome from scratch and used it to ‘reboot’ a cell from a different species of bacterium.

Daniel Gibson and his colleagues at the J. Craig Venter Institute in Rockville, Maryland, synthesized the genome of the bacterium Mycoplasma mycoides, consisting of about 1.1 million base pairs. Having assembled the genome inside a yeast cell, they transplanted it into a cell from a closely related species, Mycoplasma capricolum. After the newly made cell had divided, the cells of the bacterial colony that it formed contained only proteins characteristic of M. mycoides.

The success clears the way for developing and testing new variants of existing organisms.

"With this approach we now have the ability to start with a DNA sequence and design organisms exactly like we want," says Gibson. "We can get down to the very nucleotide level and make any changes we want to a genome."

Scientists have already developed many good ways of engineering genes, he adds, but this technique provides an unprecedented ability to make many changes to a genome at once, and to add segments of DNA that aren’t found in nature but might be designed to perform useful functions.

Step by step

Colonies of Mycoplasma mycoides bacterium from an experiment in 2007. Credit: J. Craig Venter Institute

Creating a ‘synthetic cell’, as described in a report published online in Science, meant putting together a series of previously developed steps. First, the team established a method for transplanting natural DNA from M. mycoides into M. capricolum (see ‘Genome transplant makes species switch‘). Then, working with Mycoplasma genitalium, a species whose genome is about half the length of that of M. mycoides, the group stitched together a synthetic donor genome and cloned it in a yeast cell (see ‘Genome stitched together by hand‘).

But the scientists couldn’t transplant the newly made DNA into a different bacterial species. Bacteria recognize foreign invaders by the lack of chemical marks called methyl groups on their DNA; synthetic DNA would share the same deficit. To get around the problem, the group developed a way to add methyl groups to an engineered genome. They also disabled the destructive enzyme in the recipient M. capricolum cell (see ‘Scientists devise new way to modify organisms‘).

The custom-built genome is a near-exact replica of its natural counterpart, with just a few nonessential genes removed and a small number of sequence errors that don’t affect the organism’s function. The group also added four special ‘watermark sequences’ to help to distinguish it from the original version. The sequences contain a hidden code of names and sentences, along with a URL and an e-mail address for would-be decoders to contact.

"It’s a pretty significant achievement," says Christopher Voigt, a synthetic biologist at the University of California, San Francisco. "What’s neat here is that it’s really the first time in which the information from a genome is all that was required to rebuild the DNA and convert that into a living cell."

New toolkit

Daniel G. Gibson was the lead author on the Science publication. Credit: J. Craig Venter Institute

So far, it’s not clear how being able to engineer a whole, functioning genome will be useful, researchers say. James Collins, a biomedical engineer and a Howard Hughes Medical Institute investigator at Boston University in Massachusetts, says that, in principle, "it potentially makes it considerably easier to make large-scale changes to a genome, and to introduce large-scale pathways of interest into an organism". That might mean, for example, engineering large networks of genes into bacteria which will make biofuels or proteins for treating disease.

But researchers don’t yet understand enough about genetic networks to design them in this way. "There needs to be a lot of work in understanding how to go about designing a genetic system at the scale of the genome," Voigt says. "We don’t really have a framework to think at that level."

Also, says Collins, synthesizing DNA is expensive and, at least for now, most groups don’t have the resources to engineer whole genomes.

Gibson says that his team is now trying to make different types of synthetic cell, using different pairs of bacteria. The group also plans to use the approach to continue work on its project to create a ‘minimal’ cell that contains only the genes necessary for a cell’s most basic survival. "We finally have an assay for determining the functionality of a genome," says Gibson. "So we want to start whittling away at this genome and try to determine the smallest number of genes needed to sustain life."

Nature asked eight experts about the implications of the J. Craig Venter Institute’s latest creation.

A synthesized genome has been assembled, modified and implanted into a DNA-free bacterial shell to make a self-replicating Mycoplasma mycoides bacterium1. Here, Nature presents short extracts from eight comment pieces on what this achievement means for biotechnology, evolutionary biology, regulation and philosophy. The full-length comments are available to read here.

Mark Bedau, professor of philosophy and humanities, Reed College, Oregon. Credit: S. K. Timmermann

Mark Bedau

"The ability to make prosthetic genomes marks a significant advance over traditional genetic engineering of individual genes. It raises important scientific and societal issues: we now have an unprecedented opportunity to learn about life. We must develop and perfect new methods for engineering emergence, as this calls for fundamental innovations in precautionary thinking and risk analysis. It will revitalize perennial questions about the significance of life — what it is, why it is important, and what role humans should have in its future."

George Church, geneticist, Harvard Medical School. Credit: S. Ogden

George Church

"With regard to regulations to prevent the release of hazardous life forms made in ways akin to the new Mycoplasma or by other means, there are two scenarios: bioerror and bioterror. For the former, licensing and surveillance, handled by computers, minimally inconvenience researchers, while sensitively detecting deviations from normal practice and smoothly integrating new risk scenarios. For bioterror avoidance, realistic lab ecosystems should be standardized to test the ability of new synthetic genomes to persist or exchange genes in the wild."

David Deamer, professor of biomolecular engineering, University of California, Santa Cruz

David Deamer

"Now that the JCVI has demonstrated how to reassemble a microbial genome, it may be possible to answer one of the great remaining questions of biology: how did life begin? Using the tools of synthetic biology, perhaps DNA and proteins can be discarded — RNA itself can act both as a genetic molecule and as a catalyst. If a synthetic RNA can be designed to catalyse its own reproduction within an artificial membrane, we really will have created life in the laboratory, perhaps resembling the first forms of life on Earth nearly four billion years ago."

Arthur Caplan, professor of bioethics, University of Pennsylvania. Credit: D. Burke

Arthur Caplan

"Venter and his colleagues have shown that the material world can be manipulated to produce what we recognize as life. In doing so they bring to an end a debate about the nature of life that has lasted thousands of years. Their achievement undermines a fundamental belief about the nature of life that is likely to prove as momentous to our view of ourselves and our place in the Universe as the discoveries of Galileo, Copernicus, Darwin and Einstein."

Steen Rasmussen, Center for Fundamental Living Technology, University of Southern Denmark. Credit: J. Rudiger

Steen Rasmussen

"Implementing a synthetic genome in a modern cell is a significant milestone in understanding life today. However, the radical ‘top-down’ genetic engineering that Venter’s team has done, does not quite constitute a "synthetic cell" by my definition. ‘Bottom-up’ researchers, like myself, aim to assemble life — including the hardware and the program — as simply as possible, even if the result is different from what we think of as life. Constructing life using different materials and blueprints will teach us more about the nature of life than will reproducing life as we know it."

Jim Collins, professor of Biomedical Engineering, Boston University. Credit: R. E. Klein/AP/HHMI

Jim Collins

"This is an important advance in our ability to re-engineer organisms, not make new life from scratch. Frankly, scientists don’t know enough about biology to create life. Although the Human Genome Project has expanded the parts list for cells, there is no instruction manual for putting them together to produce a living cell. It is like trying to assemble an operational jumbo jet from its parts list — impossible. Although some of us in synthetic biology have delusions of grandeur, our goals are much more modest."

Steven Benner, Foundation for Applied Molecular Evolution, Florida. Credit: P. Benner

Steven Benner

"The JCVI work may help to link chemistry to natural history. The sequences of the genomes of extinct ancestral Mycoplasma species might be inferred from the sequences of various modern mycoplasmae, including M. capricolum, M. genitalium and M. mycoides — the three bacteria that Venter and his colleagues’ synthesis started with. The new synthetic technology allows resurrection of such ancient bacteria, whose behaviour should inform us about planetary and ecological environments 100 million years ago."

Martin Fussenegger, professor of Biotechnology and Bioengineering, ETH Zurich in Basel.

Martin Fussenegger

"It is a technical advance, not a conceptual one. Chimeric organisms have long been created through breeding and, more recently, through the transfer of native genomes into denucleated target cells. Chimeric organisms with synthetic genomes contain engineered but natural genetic components. They are subject to evolution, a natural law that cannot be tricked. Whether these organisms will face natural limits, such as impaired reproduction or a shortened lifespan, remains to be seen."

The full-length comment pieces from Nature are available here.