By Stephen Casper
Right now in biology, environmental remediation, gene drives, antibiotics, and pest-resistance are all the rage. And they should be—synthetic biology is a powerful tool for engineering the world around us in positive ways. The next century or two might come to be known as the time in human history when we strategically altered the biology of our agriculture and ecosystems to help ourselves and life on Earth. But we shouldn’t get ahead of ourselves. The next chapter in biology could also become the time when we brought about tragic unintended consequences as our microbes escaped or leaked their genes. Mistakes may not be apocalyptic, but given the very harmful impacts of invasive species and biodiversity loss on the world that we can plainly see, we should probably be more afraid of understating environmental risks than overstating them. Furthermore, a single mistake could set the field of ecoengineering back by years. Recall that in 1999, when a single person was killed in an irresponsible gene therapy trial, popular outrage stalled gene therapy research and left a stain on the field that research still suffers from to this day. Certainly, more lives have been lost from the impeded development of gene therapies than the one from 1999, but the public perception of science isn’t shaped by counterfactuals. A single environmental blunder could lead to an avalanche of bad press, slashed funding, and hostile policy that could turn back the clock on progress. We can’t afford to mess up.
Enter MIT researcher, Jim Collins: one of the big names in synthetic biology whose lab has been working on solutions to make systems robust to bio-escape. In June 2018, the Collins lab published in Nature a paper titled Next-generation biocontainment systems for engineered organisms which gives an overview of current research in biocontainment. It’s cutting edge, from a leading lab, and discusses essential, accessible techniques for biosafety: an amazing read for any iGEM student looking for a project or just curious about learning more.
The paper first dives into criteria for effective biocontainment systems, and the name of the game is to make the proportion of cells (or their genes) that escape from where we want them ridiculously small—many orders of magnitude less than the number-1 we deploy. We need systems that are robust, stable, and redundant. Some effective strategies have already been demonstrated. For example, preventing survival or reproduction absent a specific inducer via auxotrophy is widely used—especially with engineered plants. And when it comes to microbes, a common technique is toxin-antitoxin pairing between plasmids so that both versions need to be in a cell for it to survive. This makes horizontal gene transfer much less likely to cause the escape of engineered genes. Recent years have also seen the development of dynamic approaches to biocontainment with genetic circuits that make cells viable only given the presence or absence of certain chemical (or physical) combinations of inputs.
The publication also outlines a set of future directions for biocontainment. Cas-9 proteins, most commonly used for creating targeted breaks in DNA for gene editing, are rapidly being used for a diverse set of purposes including the precise cutting of genes that develop certain hazardous mutations to revert cells away from dangerous genotypes. Another strategy for reducing mutation could be through modifying polymerases and DNA repair machinery to reduce the unwanted evolution of engineered cells. When it comes to the challenge of keeping cells from escaping the group, a promising approach is to make them dependent on a secreted molecule that is only present in sufficient concentrations in a quorum.
Beyond the immediate future, the publication discusses two of my favorite prospects for biocontainment. First, cells that use orthogonal mechanisms for life (such as XNA, o-promoters, o-polymerases, o-ribosomes, different genetic codes, or even molecules with reversed chirality) would give us cells whose genes couldn’t interact horizontally with natural life because of fundamentally incompatible hardware. These offer a particularly powerful mechanism for preventing horizontal escape of engineered genes. But secondly, who even needs cells? If our goal is to get a biochemical job done, we might be able to do so with simplified vesicles protocells, or just solutions of biomolecules.
All in all, this Collins publication is a good introduction to pressing challenges and cutting-edge innovations in biocontainment. There might be inspiration for a dozen or more iGEM project ideas inside. Not only is experimenting with the elements of an effective biocontainment system well-within an iGEM team’s capabilities, but it’s an important intersectional area where prototyping matter a great deal. A team can make a great project and impact by demonstrating one or more of these strategies (remember—redundancy is everything) in bacteria or yeast.
Camacho DM, Collins KM, Powers RK, Costello JC and Collins JJ. Next-generation machine learning for biological networks. Cell 173: 1581-1592 (2018)
