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High throughput gene expression profiling of yeast colonies with microgel-culture Drop-seq.

ABSTRACT: Yeast can be engineered into "living foundries" for non-natural chemical production by reprogramming them via a "design-build-test" cycle. While methods for "design" and "build" are relatively scalable and efficient, "test" remains a bottleneck, limiting the effectiveness of the procedure. Here we describe isogenic colony sequencing (ICO-seq), a massively-parallel strategy to assess the gene expression, and thus engineered pathway efficacy, of large numbers of genetically distinct yeast colonies. We use the approach to characterize opaque-white switching in 658 C. albicans colonies. By profiling the transcriptomes of 1642 engineered S. cerevisiae strains, we assess gene expression heterogeneity in a protein mutagenesis library. Our approach will accelerate synthetic biology by allowing facile and cost-effective transcriptional profiling of large numbers of genetically distinct yeast strains.

SUBMITTER: Liu L

PROVIDER: S-EPMC7909483 | biostudies-literature | 2019 May

REPOSITORIES: biostudies-literature

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High throughput gene expression profiling of yeast colonies with microgel-culture Drop-seq.

Liu Leqian L Dalal Chiraj K CK Heineike Benjamin M BM Abate Adam R AR

Lab on a chip 20190501 10

Yeast can be engineered into "living foundries" for non-natural chemical production by reprogramming them via a "design-build-test" cycle. While methods for "design" and "build" are relatively scalable and efficient, "test" remains a bottleneck, limiting the effectiveness of the procedure. Here we describe isogenic colony sequencing (ICO-seq), a massively-parallel strategy to assess the gene expression, and thus engineered pathway efficacy, of large numbers of genetically distinct yeast colonies ...[more]

PMID: 31020292

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