Biotechnologists
engineer microorganisms to produce commodities by iterating
the
design-build-test cycle until, via continuously improving intermediates, the
highest
producers are
found. While the design and build capacities of the cycle are already
almost unlimited,
the addition of genetically encoded biosensors that can identify superior
producers also
endows the test phase of the cycle with high-throughput potential and
enables
scientists to evaluate billions of designs in a day.
Credit: Wyss Institute at
Harvard University
(February 17, 2016) Genetically
encoded fluorescent biosensors allow researchers to see how products form in
real time in microorganisms, and to test billions of candidates at a time
Synthetic biologists are learning to turn microbes and
unicellular organisms into highly productive factories by re-engineering their
metabolism to produce valued commodities such as fine chemicals, therapeutics
and biofuels. To speed up identification of the most efficient producers,
researchers at Harvard’s Wyss Institute for Biologically Inspired Engineering
describe new approaches to this process and demonstrate how genetically encoded
fluorescent biosensors can enable the generation and testing of billions of
individual variants of a metabolic pathway in record time. The discussion and
findings are reported in Trends in Biotechnology and the Proceedings of the
National Academy of Sciences (PNAS).
Biotechnologists that tinker with the metabolism of
microorganisms to produce valued products look at the engineering process
through the lens of the so-called 'design-build-test cycle.' The idea is that
multiple iterations of this cycle ultimately allow the identification of
combinations of genetic and metabolic elements that produce the highest levels
of a desired drug or chemical. Key to the cycle’s efficiency, however, is the
ability to construct and test the largest number of variants possible; in the
end, only a few of these variants will produce the product in industrially
attractive amounts.
Genetically
encoded fluorescent biosensors allow researchers to follow product
accumulation in
individual bacteria in real time and to filter the best producers out of
cultures with
billions of bacteria, each carrying a specific design.
Credit:
Henrik5000/iStock Photo
In the Trends in Biotechnology article, Wyss Institute
scientists George Church, Ph.D., and Jameson Rogers, Ph.D., lay out the current
state-of-the-art for designing, building and testing many variants at a time, a
methodology that bioengineers call 'multiplexing'. Church is a Wyss Institute
Core Faculty member and Professor of Genetics at Harvard Medical School and
Rogers, currently with the Boston Consulting Group, performed his work as a
Harvard Pierce Fellow and Doctoral Student mentored by Church.
Bioengineers thoroughly understand how metabolic pathways
work on the biochemical level and have a plethora of DNA sequences encoding
variants of all of the necessary enzymes at their disposal. Deploying these
sequences with the help of computational tools and regulating their expression
with an ever-growing number of genetic elements, gives them access to an almost
infinite pool of design possibilities. Similarly, revolutionary advances in
technologies enabling DNA synthesis and manipulation have made the construction
of billions of microorganisms, each containing a distinct design variant, a
routine process.