Genome-design contest aims to engineer cress for commercial uses.
A Japanese competition launched last week is aiming to help the burgeoning science of synthetic biology to deliver commercial applications.
Last month's unveiling of the first fully functioning cell with a synthetic genome (see 'Researchers start up cell with synthetic genome') marked a milestone in scientists' ability to manipulate the code of life. But efforts to engineer specific genetic sequences and integrate them with bacteria or plant genomes so that they perform useful functions have faced a variety of hurdles.
These genetic sequences can give the host organisms the ability to make proteins with useful properties: producing useful chemicals such as biofuels or drugs; acting as biochemical sensors; or breaking down environmental pollutants, for example. But when these genes are integrated into living cells, they are often frustratingly unpredictable and sometimes incompatible with the host organism (see 'Five hard truths for synthetic biology').
The International Rational Genome-Design Contest (GenoCon), launched by the Yokohama-based Bioinformatics and Systems Engineering (BASE) division of Japan's RIKEN research institute, is now hoping that its participants will optimize genetic sequences so that they can be used practically. No prize money has been offered; honour, it seems, should be sufficient reward.
The inaugural challenge asks contestants to genetically redesign thale cress (Arabidopsis thaliana) so that it can metabolize the airborne pollutant formaldehyde. Researchers have previously inserted genes into thale cress that give it a limited ability to absorb formaldehyde, and GenoCon's goal is to improve on this.
GenoCon is not the first synthetic biology contest. Since 2004, the annual International Genetically Engineered Machine (iGEM) competition, run by the Massachusetts Institute of Technology, Cambridge, has asked teams of undergraduates to use genetic components that give bacteria novel features. In the past, contestants have produced microbes that act as biosensors for arsenic; or that smell of bananas or wintergreen; or that come in a rainbow of different hues.
Many of the genetic parts that confer these properties are developed anew by competitors, and must be registered in a growing, open-access repository.
But GenoCon is taking a different tack. Whereas iGEM's participants get to choose how they transform bacteria, GenoCon will focus on specific challenges that have a clear environmental application. BASE director Tetsuro Toyoda hopes that this will spark wider interest among scientists, the public and industry, and prove the value of synthetic biology to funders.
The competition also hopes to attract researchers familiar with bioinformatics who perhaps lack the experimental resources to build what they design. Participants have until the end of September to assemble genetic code — within a 'virtual laboratory' on BASE's website — that will make thale cress an effective formaldehyde detoxifier. Judges will pick the most promising 20 or 30 sequences, which RIKEN and affiliated research institutes will use to create plants with the given sequences integrated into the cress genome. The plants will be housed together in a formaldehyde-rich environment — normally toxic to the plants — and tested for their ability to survive. Next year, the prize will go to the design of the best drought-resistant cress, and participants will also be invited to improve on winning designs from previous contests.
Masayuki Yamamura, a bioinformatics researcher at the Tokyo Institute of Technology, whose group received gold medals from iGEM in 2007, 2008 and 2009, believes that GenoCon will make a huge contribution to synthetic biology, both in Japan and internationally. He points out that because iGEM's parts registry is open access, the sequences cannot be used in patents. This has deterred the biotech industry from getting deeply involved in iGEM, argues Yamamura: "Those from industry have mostly just been looking on from the sidelines."
By contrast, GenoCon is "expecting small-scale business groups and university people with patented DNA sequences to use our platform to find much more optimized versions of the sequences claimed in the patent", Toyoda says. Results will normally be made public, but participating companies will have the option to keep sequences secret if they are negotiating joint patent or licensing agreements with other businesses. "This framework is what we call open-optimization research," says Toyoda. Randy Rettberg, director of iGEM, declined to comment on the GenoCon competition.
The organizers hope that GenoCon will attract budding scientists through its separate category for high-school students. Yutaka Mizokami, a biology teacher at the Yokohama Science Frontier High School (see 'Reading, writing and nanofabrication'), says that he expects several teams from his school to join, and thinks that most of the other 125 Super Science High Schools in Japan (which are given extra funding to accelerate science teaching) will also put up teams.
Adam Arkin, a bioengineering expert based at the University of California, Berkeley, and at the Lawrence Berkeley National Laboratory, says that GenoCon "beautifully refocuses students and their mentors on the design aspects of synthetic biology".
Arkin is also co-director of the International Open Facility Advancing Biotechnology (BIOFAB), based at the Joint BioEnergy Institute in Emeryville, which bills itself as "the world's first biological design-build facility". He and other BIOFAB scientists are helping to coordinate another nascent synthetic-biology competition to improve biological parts, called Critical Assessment of Genetically Engineering Networks (CAGEN), which will see its first competition run until 2012.
"This constellation of competitions — iGEM, CAGEN and GenoCon — will drive a great deal of international conversation and collaboration, and this can only be stimulating for the field as a whole," says Arkin.