This week in synthetic biology

This was another incredible week for synthetic biology community, again several peer reviewed papers made their way to This week in synthetic biology (TWiSB). This was a week of riboswitches, biofuels and biological nanofactories which we will be discussing in next section. For now (as usual) if you have a synthetic biology story which you want to share with us you can send an email to post@syntheticfuture.posterous.com.

Engineered orthogonal selectivity of the riboswitches
Riboswitches are strctural element typically found in the 5′-UTRs (untranslated regions) of bacterial or eukaryotic mRNAs. These riboswitches generally dictate the the gene expression of corresponding genes by interacting or binding with the small target molecules or metabolites. Binding of naturally occuring metabolite to aptamer domain of riboswitch mRNA cause the structural change in the gene expression machinery leading to regulation of gene expression levels. Now researchers from The University of Manchester have developed riboswitches that allow orthogonally selective, tuneable, and dose-dependent control of gene expression in response to nonnatural synthetic small molecule. A news release from the university office suggest that this is very first rewire of genetic switches, although not everyone is convinced with that and it can be considered as first rewire of genetic riboswitches. Christina Agapakis has an interesting review for this paper on her blog. The findings are reported by the group let by Dr Neil Dixon in the latest edition of Proceedings of the National Academy of Sciences (PNAS). As Dr Neil Dixon suggest that the next big thing will be to realise the real potential of this research by tweaking the important biological pathway and replicate this technology for human cells.

Combining the best of synthetic biology and nanotechnology
Seems like my picks from futurama of science are coming true. George Church assertion that nano-tech in combination with synthetic biology will be offering unseen endeavors can not wait for 2020, it’s already here. Scientists at the University of Maryland (UMD) have now demonstrated how engineered biological nanofactories can trigger quorum sensing responses in targeted bacterial population which will help us to combat the bacterial infections without antibiotics by hijacking bacterial communication network. In a recent research published in advance online edition of journal Nature Nanotechnology William E. Bentley and team report self-assembled, self-guided and self-destructible biological nanofactories which not only target a specific population in bacterial co-cultures selectively but also trigger communication between two bacterial populations that do not communicate in normal conditions. Not all bacteria are bad some are beneficial for us and potentially this kind of differential behavior of nanofactories can help us selectively protect the good bacteria while same time targeting the harmful bacteria (pathogen) by switching off their triggering activities. Normally this kind of selective is missing in antibiotics and hence they have unwanted side effects. These nanofactories are functinally modular, they have targeting module , and sensing, synthesis and assembly modules (last 3 modules make a single unit, a fusion protein). One important aspect of research was use of biofabrication to assemble antibodies on to the fusion protein unit, which enables targeting. Interestingly these nanofactories can self-destruct upon completion of the task.

Following their addition to bacterial cultures, nanofactories bind specifically to the targeted bacteria (green circle), synthesize and deliver AI-2 (yellow circles) at their cell surfaces and trigger the quorum sensing response.

Synthetically engineered bacterium can make biofuel directly from biomass
Since the article has already been reviewed to death in mainstream media, I am just going to give a quick overview. Researchers throughout the world are working to produce biofuel using synthetic engineered microbes in a cost effective way. Scaling up these different solution holds the key for their success. To this end scientists are trying different novel approaches, for example very recently the Lionetti et. al reported that genetic modification of plant cell wall may scale-up biofuel production and now researchers from the University of California, Berkeley, and the biotech firm LS9 of South San Francisco, California report another cost-effective route for direct biofuel production from grass or crop waste.

A more scalable, controllable and economic route to this important class of chemicals would be through the microbial conversion of renewable feedstocks, such as biomass-derived carbohydrates. Here we demonstrate the engineering of Escherichia coli to produce structurally tailored fatty esters (biodiesel), fatty alcohols, and waxes directly from simple sugars. Furthermore, we show engineering of the biodiesel-producing cells to express hemicellulases, a step towards producing these compounds directly from hemicellulose, a major component of plant-derived biomass.

By using an array of genetic modifications they not only diverted the metabolic flux in desired direction to produce non-native products but they also improved the yields of these products within an order of magnitude of that required for commercial production. Currently this approach converts the simple sugar or hemicellulose component of biomass into biofuesl, they are targetting to scale up this process by producing biofuels directly from cellulose. This will eventually r
equire the synthetically engineered cells those can express cellulases- a diverse group of enzymes that hydrolyze or degrade celluloses into simple forms.

Solazyme in Red Herring’s Global 100 of Tech Startups

Solazyme, a renewable oil production company in algal synthetic biology, received the Red Herring Global 100 award, placing the company among a list of startups.

Minimizing the Risks of Synthetic DNA

On January 11, 2010, the AAAS CSTSP hosted a meeting to discuss the draft U.S. Sequence Framework for Synthesis of Double Stranded DNA providers with the scientific community and gene synthesis providers. Stakeholders from academia, private industry, and the gene synthesis industry all support the voluntary guidance. Although meeting participants identified specific concerns and offered specific recommendations to address some of those concerns, the overall sentiment was that the guidance is well thought out, facilitates advances in scientific knowledge, and allows for international engagement.

That’s all for this week. Next week TWiSB will be back with few more interesting stories.