In synthetic biology, we seek to engineer reliable and predictable behaviours in organisms by assembling a variety of ‘standardised’ genetic parts, But, as mentioned in our previous blog entry, biology is not an exact science, and implementing standardised genetic circuits does not guarantee the same “expected behaviour” in the organisms we want to control. One of the main reasons behind this phenomenon is that living organisms can reproduce, and therefore they are subject to heritable genetic changes. In other words, they evolve.
Evolution creates genetic variability which would help natural populations of microbes to adapt and endure. But these unpredictable changes can interfere with our synthetic circuits and their “defined purposes”, tearing their pieces apart and shutting them off in no time. Experiments, projects and funds can be lost due to the inability to preserve our synthetic circuits properly working in organisms.
If evolution is everywhere, are there any strategies to mitigate or avoid its effects? Yes, but in order to use them, it is necessary to understand how evolution can hamper progress in SynBio. For that purpose, let’s discuss some concepts explained in the work of James J. Bull and Jeffrey E. Barrick, two experts in systems and synthetic biology from the University of Texas at Austin [1].
Darwin, give us a break
Evolution does not necessary act only over a long period of time — short-term evolution is something we humans have been taking advantage of throughout our history on Earth, for example, through artificial selection in agriculture and farming. This ‘fast form’ of evolution can bring a number of drawbacks, such as the emergence of drug resistance in certain pathogens and parasites or the cancerous profile acquired by stem cells. Within SynBio, a common drawback of short-term evolution is the loss of function in cells used for biomanufacturing, which leads to an important decay of production.
To combat these unwanted side-effects, it is necessary to identify the pillars that sustain evolution, which can be summarised in three core concepts: mutation rates, selection and inheritance. When an organism is manipulated to behave in an artificial way, its native systems of survival are, in a way, compromised. So evolution plays around with population size, inactivating sequences and recombination, which may erase our synthetic circuits. Hence, these core elements must be tackled if we want to weaken evolutionary pressure in our devised organisms.
Arm-wrestling with evolution
Nowadays, there are several tools available to fight back against unwanted evolution in SynBio strategies.
First, there are traditional approaches based on population genetics principles without specifically using molecular tools. One good example of this kind of solution is growth limitation, where the population with unwanted mutations is discarded, either by directly removing it or by adding more elements of the unaltered population to outcompete them. This would keep mutation rates under control!
Another traditional strategy consists in adding competitors to keep population size and selection modulated. The main outcome of this is reduced chance of having adaptive mutations in a given population.
Beyond these classical solutions, SynBio has more alternatives to stop evolution: engineered approaches are focused on working directly with sequences and genetic parts to try to limit the action of evolution.
One of the main procedures within this category consists in reducing mutation rates [2]. This can be achieved by several strategies, but the most direct one is by eliminating volatile elements in circuits and/or in the host. Two good targets to tackle are, on one side, transposons—which can self-replicate and, therefore, easily disrupt our designed sequences—and repetitive DNA sequences, which can trigger homologous recombination systems that break large sets of genes of interest. By removing these genetic elements, we can notably reduce mutation rates, creating a more stable genetic landscape in our organisms.
There are more strategies to try to curb evolution that use genetic engineering principles. For instance, the incorporation of fail-safe genetic codes [3] to avoid mutations in protein-coding sequences or the use of overlapping genes [4] to co-encode our sequence of interest with an essential genetic part of the targeted genome and therefore decrease the potential evolutionary pressure around it. In addition, a combination of both traditional and engineering schemes looks like a promising route to follow in terms of efficacy and positive results.
This is just a warm up
Despite these breakthroughs, there is still a long road ahead to reach complete stability in a synthetic organism. Also, taking responsibility for the new behaviours that are introduced in living organisms is vital for people working in SynBio. Altering evolutionary ratios raises some ethical questions that are worth asking. Do we have enough data about long term outcomes of anti-evolution systems? Are we capable of controlling the possible scenarios derived from these kinds of genomes? [5]
In short, if we want to design truly effective solutions that can be used outside the lab, evolution remains a big challenge to the SynBio community — one that still demands our scientific and ethical attention.
References
[1] Bull, J. J., & Barrick, J. E. (2017). Arresting evolution. Trends in Genetics, 33(12), 910-920.
[2] Renda, B. A., Hammerling, M. J., & Barrick, J. E. (2014). Engineering reduced evolutionary potential for synthetic biology. Molecular BioSystems, 10(7), 1668-1678.
[3] Calles, J., Justice, I., Brinkley, D., Garcia, A., & Endy, D. (2019). Fail-safe genetic codes designed to intrinsically contain engineered organisms. Nucleic acids research, 47(19), 10439-10451.
[4] Blazejewski, T., Ho, H. I., & Wang, H. H. (2019). Synthetic sequence entanglement augments stability and containment of genetic information in cells. Science, 365(6453), 595-598.
[5] Anderson, J., Strelkowa, N., Stan, G. B., Douglas, T., Savulescu, J., Barahona, M., & Papachristodoulou, A. (2012). Engineering and ethical perspectives in synthetic biology: Rigorous, robust and predictable designs, public engagement and a modern ethical framework are vital to the continued success of synthetic biology. EMBO reports, 13(7), 584-590.