Synthetic Biology Gone Wild? Probably Not. An interview with Tom Ellis.

August 26, 2014 PLOS Blogs Uncategorized

By Prashant Bhat

The first annual Synthetic Biology: Engineering, Evolution & Design (SEED) conference was held last month in Manhattan Beach, CA. Both new and veteran star-studded synthetic biologists shared the podium for four days to showcase cutting-edge technologies being developed in their respective labs. Talks covering metabolic engineering, sensors, genetic circuits, and nanotechnology highlighted the diverse and interdisciplinary nature of SynBio research. In particular, a common theme involved research addressing issues of bio-safety and the potential ecological ramifications of synthetic biology. On the first day of SEED, I interviewed presenter Dr. Tom Ellis, to talk about his research and his views concerning SynBio research.

Tom Ellis at SEED 2014. Dr. Ellis and colleagues developed GeneGuard, an environmentally safe method to perform experiments with engineered bacterial cells. Image credit: Prashant Bhat

Public concern over manipulating ecosystems, such as genetically modifying crops and plants, is a growing problem that many scientists often fail to take into account when creating the next weather-insect-pesticide-resistant mega-crop. Inadvertently creating “superbugs” or spreading unwanted genes through fragile ecosystems are ongoing concerns that need to be addressed. Many synthetic biology researchers are developing creative methods to make their research safer for the environment and better for the general public good.

Guarding our ecosystem with GeneGuard

Dr Tom Ellis, a Lecturer and Research Leader at Imperial College London, developed GeneGuard, a tool that enables researchers to perform environmentally safe experiments with engineered bacterial cells that are ultimately released into the environment. GeneGuard relies on a new type of plasmid, a circular piece of DNA that researchers use to transfer genes between cells. Ellis describes, “Regular plasmids have not really changed in the past 30 to 40 years. They encode an origin of replication and an antibiotic resistance marker. And those are really the only two things you need. The antibiotic resistance marker makes sure [the plasmid] is kept within the inside of the cell by providing an antibiotic the whole time. And the origin of replication allows the plasmid to self-replicate.”

Similarly, GeneGuard is a DNA plasmid system that works in a specific E. coli strain and prevents plasmid DNA from replicating unless it follows three controlled conditions. One of the conditions is to use dependence on externally supplied nutrients (auxotrophy) instead of antibiotic resistance to select for the plasmid to keep it in the cell. Second, the plasmid will only multiply if the host cell provides an essential protein that the plasmid requires to replicate (conditional origin of replication). And the final condition is the use of a toxin-antitoxin pair that exists in nature. “The difference with the GeneGuard system is no antibiotics,” Ellis explains. “Instead, the selection is through auxotrophy. There is an origin of replication but it is conditional. So it only works if a protein is provided in trans, which is provided by the cell. And we have the extra facet added to it with the toxin molecule to lower the attractiveness of the DNA to other organisms.”

fig1 — GeneGuard schematic. The three conditions include conditional origin of replication (COR), auxotrophy (AUXO), and toxin-antitoxin systems. Image credit: http://openwetware.org/wiki/Ellis:Publications

The real story about risks

Does synthetic biology run the risk of going wild? Ellis responds, “Personally, I don’t think there is much of chance of 99.9% of synthetic biology research being a danger or even a danger of going wild. Engineered microbes do pretty badly in the wild. They get outcompeted pretty quickly. If you look six months after seeding these bacteria all over the soil, they aren’t there anymore. They’re gone. They’re caput.” However, although the living bacteria may not be there, the plasmid DNA can linger on for years and adds potential risks of spreading. Ellis explains, “The GeneGuard system is not designed to prevent live bacteria engineered with the GeneGuard system from being able to go wild. We think they will still be able to grow, just like any engineered bacteria, but they won’t grow as well as wild type because of all the extra DNA we put inside them.” I asked Dr Ellis whether there were potential complications with GeneGuard plasmids backfiring if released into the environment.

“We really put a lot of thought in choosing genes for our system that are natural genes already present. There is no reason why particular combinations of toxin-antitoxins could cause trouble… Also, if you scoop a hand full of soil and check what bacteria are in there, we have some of the nastiest bacteria we know! Botulism bacteria and all of these other horrible bacteria do horizontal gene transfer between each other quite a lot in nature. We certainly don’t freak out and go sterilize our soil every few days because we are afraid the botulism gene has gotten into the Salmonella.”

Horizontal gene transfer. When bacteria come into contact, they can exchange DNA, sometimes conferring selective advantages to weaker bacteria so that they may survive in the presence of certain antibiotics or toxins. Image credit link: http://fac.ksu.edu.sa/sites/default/files/2-Competent_Cells_Formation_and_Transformation_of_Competent_Cells.pdf

Dr Todd Kuiken at SEED 2014. His talk called for synthetic biologists and other scientists to be more involved in public and policy-making. Image Credit: Prashant Bhat

Other Bio-safety measures

Dr Todd Kuiken, Senior Program Associate with the Science and Technology Innovation Program at the Woodrow Wilson International Center, learned about GeneGuard when Ellis and his team of undergraduate researchers first presented it at the 2011 iGEM competition. Kuiken explains, “GeneGuard is a system that is being developed as an effective application for small and controlled environments.” Kuiken’s concern is whether “GeneGuard [plasmids] will actually work if they are out in an environment where they are interacting with multitudes of different variables.” Although he thinks GeneGuard carries promising potential for controlled environments like large fermentation reactors, he thinks there needs to be more development for larger, less controlled areas.

Public Support

The potential for GeneGuard and other similar, environmentally friendly research tools to be implemented are largely dependent on public and political support. Ellis thinks, “synthetic biologists have done a pretty good job so far interacting with the public. We’ve done all sorts of things for public dialogue within the UK. In the UK, we have very high profile in synthetic biology in terms of public understanding of such a small and young field. So I think we have done a good job and I think we need to because ultimately taxpayers pay for the vast majority of our work. It’s members of the public paying for our research, so it’s their right to have a voice of where it goes!”

The views expressed in this post belong to the author and/or his subjects and do not necessarily represent those of PLOS.

Prashant Bhat is a recent biochemistry and molecular biology graduate from the University of California, Berkeley where he served as Editor-in-Chief of Berkeley Scientific Journal.