High-5 elements of a successful synthetic biology project
Ingenza’s Stephen McColm recently wrote this blog piece highlighting five things to consider before starting a synthetic biology project.
Stephen McColm, Ingenza
Synthetic biology is a tremendously powerful approach to finding sustainable alternatives to finite resources, but it can still take huge amounts of time, money and effort to find the suitable starting materials and processes for efficient and scalable production.
So, what are the five things you should really consider before you start a synthetic biology project?
1. Choose your host wisely
Traditionally, Escherichia coli and Saccharomyces cerevisiae are the go-to microbes. They are well understood, and there are a plethora of tools to manipulate them, but by no means are they the best choice for every project. There are literally millions of microorganisms out there – okay, it’s impossible to choose from the entire smorgasbord – and you should not be limited to just two when each process and application is different.
Now we’re not implying that E. coli and S. cerevisiae aren’t fine hosts, and many times they are the best and easiest option, but it’s optimal to structure your project to include a number of different hosts. At Ingenza, we use a panel of around ten microorganisms – including E. coli and S. cerevisiae – along with other yeasts and bacteria, both Gram-negative and Gram-positive. This way, we have the greatest chance to identify the host that works best for your application.
And if you’re aiming to produce a protein-based drug molecule, you also need to consider how the host alters your target protein during post-translational modifications, as it will have a massive effect on its activity. Yeast, for example, will add a lot of glycans, while E. coli will add none. Knowing these details before starting, and having the correct tools to engineer multiple hosts for your target product, are therefore crucial factors before you start your project.
2. Compatibility questionnaire
Microorganisms have been around a while, meaning they sometimes evolve in unexpected ways, and don’t always do as they’re told. But if you know how to ask – using the right tools – they can adhere to your demands and be tolerant of your work. You must therefore ask yourself more important questions:
I. How will the host cope with making your product? Quite often, the high yields that are required for industrial biotechnology are cytotoxic. In this case, they will find ways to expel or loop out your inserted DNA or mutate, giving that cell an advantage that will consequently take over the culture as a non-producer. This is something to look out for, and is routinely monitored across a suite of potential hosts at Ingenza, to give us a good understanding of tolerance to each target product.
II. Does a host already produce something similar to your product? If so, it is more likely to be tolerant, and therefore a better option compared to instructing a cell to produce something it has never seen before.
3. What are the genetic changes you need to introduce? And how will each host accept them?
This can span a range of options, from deleting genes to up-regulating native genes, as well as adding recombinant genes or modifying post-translational modifications. Once you’ve defined your genetic changes, you need to have a good way to build that strain in the right host. This is where experience and knowhow enter the conversation – as each technology and technique needs to be tweaked depending on the host. You can’t just edit the genome of E. coli in the same fashion as Bacillus subtilis; the individual needs of each organism must be addressed. Even something as fundamental as transporting DNA into the cell needs to be carefully considered. The underpinning technologies are certainly available, and we have the expertise to apply them efficiently and effectively to each microbe.
4. How can technologies help to further streamline and scale up your research?
Traditional industrial biotechnology methods usually relied on either blasting hosts with UV light or treating them with chemicals to cause the DNA within the cell to mutate and rearrange. This scattergun approach can work, but is non-targeted, making it unpredictable. The alternative approach was to create specific modifications – like inserting or deleting a gene of interest – but this made it a slow and iterative technique.
Modern synthetic biology has broken free from this limited landscape, so rather than making one construct and testing it, we can now make 100. Laboratory automation has amplified this approach further. A scientist at a bench pipetting one microlitre into a little tube is slow, but liquid handling robots perform these repetitive and time-consuming tasks with ease, meaning we can now screen thousands of genes in the same timeframe.
5. How are you going to detect your product of interest?
One of the most important questions – yet one that is often overlooked – is how to screen for your target product. You need a screening process that is not only specific, but also has a throughput that is compatible with your needs. This allows you to rapidly sort through all the engineered cells, find the hits and take them to the next stage. This is something we have invested a lot of time in at Ingenza, and we have designed bespoke, high throughput screening strategies combining our expertise in molecular biology, biochemistry and synthetic chemistry.
Of course, there are more considerations beyond the five we discussed today, but this is a blog after all, and is here to entice more in-depth discussion about synthetic biology and your applications. Please get in touch to continue this conversation.