Engineering biology in industrial biotech

Engineering biology is a tremendously powerful approach to finding sustainable alternatives to finite resources. However, it takes lots of time, money, and effort to develop the optimal microorganisms and bioprocesses for efficient and scalable production.

Stephen McColm, Team Leader, Molecular Automation, Ingenza Limited. Image Credit: Ingenza Limited

Advancements in technology, combined with new techniques, have changed the way engineering biology is performed in academia and industry on both small and large scales.

Several questions must be asked before starting a project, from what host to use to produce the product of interest to the commercially feasible conditions and scale of production.

This article discusses how these challenges can be tackled and how modern techniques and tools are helping to engineer microbes more efficiently and predictably for use in industrial bioprocesses.

Engineering biology is now widely recognized as a tremendously powerful approach to finding sustainable alternatives to finite resources, but it is not without its challenges. Often, large amounts of time, money and effort must be expended to identify suitable engineered microorganisms and bioprocesses for efficient and scalable production.

However, careful consideration of these aspects of the project in advance of embarking on any experimental work can help to overcome any issues before they are encountered.

Choose the right host

Researchers have traditionally turned to Escherichia coli and Saccharomyces cerevisiae, as these microbes are well understood, and a plethora of tools exist to manipulate them. However, this does not automatically make them the best choice for every project.

There are literally trillions of microorganisms to choose from, and it is important that researchers look at all the options and do not limit themselves to just these two when each process and application is different.

It is optimal to structure projects to include a number of different hosts, for example, using 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 approach provides the greatest chance of identifying the host that works best for a specific application.

Laboratories aiming to produce a protein-based drug molecule also need to consider how the host alters the target protein during post-translational modifications, as this may have a massive effect on its activity.

Yeast, for example, will add a lot of glycans, while E. coli will not add any. It is crucial to know and understand such details before starting a project and to have the correct tools to engineer multiple hosts for the target product.

Think about compatibility

Microorganisms evolve and, as a result, do not always act as anticipated in a bioprocess. However, this can be addressed with the right knowledge and by using the correct tools. How the host will cope with making the product and whether it already produces something similar are some considerations.

It is not uncommon for the high yields that are required for industrial biotechnology to be cytotoxic. In this situation, the host will find ways to expel or loop out the inserted DNA, giving that cell a selective advantage that will consequently lead to it taking over the culture as a non-producer.

It is important to routinely monitor potential hosts for this effect, as well as to ensure a good understanding of the tolerance to each target product. If a host already produces something similar to the required product, it is more likely to be tolerant and, therefore, could be a better option compared to instructing a cell to produce something it has never seen before.

Introducing genetic changes and host acceptance

Engineering microbes can involve a range of project-specific genetic changes, from deleting genes to up-regulating native genes, as well as adding recombinant genes or altering post-translational modifications.

Once these have been defined, those modifications must be built into the right host. Experience and know-how are crucial, as each technology and technique need to be tweaked depending on the host.

The genome of, for example, E. coli cannot be edited 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 available and, with the right expertise, can be efficiently and effectively applied to each microbe.

Streamlining and scaling up research

Traditional industrial biotechnology methods generally relied on treating hosts with UV light or chemicals to cause the DNA within the cell to mutate and rearrange, an approach that is non-targeted and, therefore, unpredictable.

The alternative was to create specific modifications, such as gene insertions or deletions, but this was slow and iterative using classical techniques.

Modern engineering biology has progressed from making one engineered microbe, testing it, and repeating it to making 100 or more bespoke microbes at a time, and this approach has been further amplified by laboratory automation.

Detecting the product of interest

One of the most important questions is how to screen for the target product. The screening process must not only be specific but also have an appropriate throughput that is compatible with the project needs, allowing rapid sorting of the engineered cells to identify the best hits to progress to the next stage.

The ideal scenario is to design and employ bespoke, high throughput screening strategies based on molecular biology, biochemistry and synthetic chemistry expertise.

Summary

Engineering biology has advanced in leaps and bounds over the years, offering an ever-improving approach to finding sustainable alternatives to finite resources.

While success depends on many different factors, careful consideration of the topics discussed above will go a long way towards time- and cost-effective identification of the optimal starting materials and processes for efficient and scalable production.

About Ingenza

Ingenza is an engineering biology company with an extensive and unique range of proprietary enabling technologies in microbial strain and mammalian cell-line engineering, protein production, fermentation and bioprocess development. Our staff span the disciplines of molecular genetics, biochemistry, fermentation and process/analytical chemistries in state-of-the-art facilities in Edinburgh, UK.

Our bacterial, yeast and mammalian cell platforms underpin competitive bioprocesses implemented worldwide by our customers and partners to manufacture (bio)pharmaceuticals, enzymes, chemicals, consumer products and sustainable fuels.

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