Engineering biology approaches for enhanced gene control in bioprocessing and therapeutic applications

Engineering (or synthetic) biology is emerging into a large, multidisciplinary field that has enveloped many of the modern scientific disciplines born out of the post-genomics era, including bioinformatics, systems biology, functional genomics and big data science, as well as organic chemistry, nanotechnology, microfluidics and robotics

It truly does comprise all aspects of both modern and traditional natural sciences and, in the burgeoning field of industrial biotechnology, has been heralded as the solution to many of society’s most pressing problems in energy, food and medicine.

The recent construction of the first living synthetic organism at the J. Craig Venter Institute has stimulated a flurry of activity in this field, driving scientists to uncover the minimal set of genes required to sustain simple life forms and better define how biological systems can be rationally applied to more efficiently drive industrial-scale processes.

Paramount to developing new synthetic biology systems and, in particular, the development of larger, more complex synthetic organisms, it is essential that new transcription programmes are assembled that can be used to control the gene expression of various pathway and system components. One means of achieving this goal is the construction and application of synthetic gene regulators, or synthetic promoters.

In lower prokaryotic organisms, such as the widely used workhorse organism E. coli, synthetic gene regulators are created through promoter sequence mutagenesis; but, for higher species, including plants, yeast, mammals and humans, more elegant solutions are required, given the complexity of eukaryotic gene regulation.

This is a key focus of research currently under way at Synpromics (a UK company leading the area of synthetic promoter design).

Since the emergence of functional genomics, following the sequencing of the human genome in the early 2000s, large collaborative efforts comprising consortia of leading academic centres have driven efforts to better understand how genomes are regulated.

Of importance are the ENCODE consortium (the Encyclopedia of DNA Elements), subsequently expanded into the Epigenomics Roadmap, and Riken’s FANTOM5 project, each of which aim to identify all the regulatory motifs encoded within the human genome. The research emanating from these consortia has vastly improved our understanding of eukaryotic gene regulation.1–3

In the industrial biotechnology sector, the development of a toolset of promoters for individual chassis organisms enables the pathway engineering of host strains, allowing the creation of metabolic pathways through the expression of multiple enzymes, which can be used to drive the synthesis of high value chemical entities.

For bioprocessing applications, pathway engineering can be employed to boost productivity by easing the metabolic burden induced by excessive protein production and can further improve glycosylation, processing and export of the protein that is being manufactured.

In pharmaceutical development, novel synthetic promoters can be used to enhance the efficiency and safety of cell and gene therapies by enabling construct optimisation of therapeutic expression cassettes.

This allows the transcriptional targeting of different cell types and raises the possibility of regulatable gene expression wherein expression is induced by the addition of small molecule drugs or in response to environmental or pathological conditions.

If synthetic biology is to be employed outside of the industrial biotechnology sector and into pharmaceutical development, then it is key that we continue to gain a deeper understanding of how a cell’s genotype determines its phenotype. As we achieve this, we can improve our ability to create the biological parts that are needed to form standardised building blocks that will enable the true engineering of biology.

References

1. The ENCODE Consortium, “An Integrated Encyclopedia of DNA Elements in the Human Genome,” Nature 489, 57–74 (2012).

2. C.E. Romanoski, et al.<.i>, “Epigenomics: Roadmap for Regulation,” Nature 518, 314–316 (2015).

3. The FANTOM Consortium and the RIKEN PMI and CLST (DGT), “A Promoter-Level Mammalian Expression Atlas,” Nature 507, 462–470 (2014).

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