February 17, 2016

Fluorescent biosensors light up high-throughput metabolic engineering

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.

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