RNA-aptamers-in-droplets (RAPID) high-throughput screening for secretory phenotypes

Joseph Abatemarco, Maen F. Sarhan, James M. Wagner, Jyun-Liang Lin, Leqian Liu, Wafa Hassouneh, Shuo-Fu Yuan, Hal S. Alper () and Adam R. Abate ()
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Joseph Abatemarco: The University of Texas at Austin
Maen F. Sarhan: University of California San Francisco
James M. Wagner: The University of Texas at Austin
Jyun-Liang Lin: The University of Texas at Austin
Leqian Liu: University of California San Francisco
Wafa Hassouneh: University of California San Francisco
Shuo-Fu Yuan: The University of Texas at Austin
Hal S. Alper: The University of Texas at Austin
Adam R. Abate: University of California San Francisco

Nature Communications, 2017, vol. 8, issue 1, 1-9

Abstract: Abstract Synthetic biology and metabolic engineering seek to re-engineer microbes into “living foundries” for the production of high value chemicals. Through a “design-build-test” cycle paradigm, massive libraries of genetically engineered microbes can be constructed and tested for metabolite overproduction and secretion. However, library generation capacity outpaces the rate of high-throughput testing and screening. Well plate assays are flexible but with limited throughput, whereas droplet microfluidic techniques are ultrahigh-throughput but require a custom assay for each target. Here we present RNA-aptamers-in-droplets (RAPID), a method that greatly expands the generality of ultrahigh-throughput microfluidic screening. Using aptamers, we transduce extracellular product titer into fluorescence, allowing ultrahigh-throughput screening of millions of variants. We demonstrate the RAPID approach by enhancing production of tyrosine and secretion of a recombinant protein in Saccharomyces cerevisiae by up to 28- and 3-fold, respectively. Aptamers-in-droplets affords a general approach for evolving microbes to synthesize and secrete value-added chemicals.

Date: 2017
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DOI: 10.1038/s41467-017-00425-7

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