Synthase-Selective Exploration of a Tunicate Microbiome by Activity-Guided Single-Cell Genomics

While thousands of environmental metagenomes have been mined for the presence of novel biosynthetic gene clusters, such computational predictions do not provide evidence of their biosynthetic functionality. Using fluorescent enzyme assay targeting carrier proteins common to polyketide (PKS) and nonr...

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Bibliographic Details
Published in:ACS chemical biology 2021-05, Vol.16 (5), p.813-819
Main Authors: Kim, Woojoo E, Charov, Katherine, Džunková, Mária, Becraft, Eric D, Brown, Julia, Schulz, Frederik, Woyke, Tanja, La Clair, James J, Stepanauskas, Ramunas, Burkart, Michael D
Format: Article
Language:English
Subjects:
Animals
Bacillus subtilis - genetics
Bacteria
BASIC BIOLOGICAL SCIENCES
Carrier Proteins - chemistry
Carrier Proteins - genetics
Ciona intestinalis - metabolism
Cluster chemistry
Computational Biology
Escherichia coli - genetics
Flow Cytometry
Fluorescence
Genomics
Genomics - methods
INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CHEMISTRY
Microbiota - genetics
Multigene Family - genetics
Peptide Synthases - metabolism
Phylogeny
Polyketides - chemistry
Probes
Secondary Metabolism
Siderophores - chemistry
Siderophores - genetics
Single-Cell Analysis
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Summary:While thousands of environmental metagenomes have been mined for the presence of novel biosynthetic gene clusters, such computational predictions do not provide evidence of their biosynthetic functionality. Using fluorescent enzyme assay targeting carrier proteins common to polyketide (PKS) and nonribosomal peptide synthetases (NRPS), we applied fluorescence-activated cell sorting to tunicate microbiome to enrich for microbes with active secondary metabolic capabilities. Single-cell genomics uncovered the genetic basis for a wide biosynthetic diversity in the enzyme-active cells and revealed a member of marine harboring a novel NRPS gene cluster with high similarity to phylogenetically distant marine and terrestrial bacteria. Interestingly, this synthase belongs to a larger class of siderophore biosynthetic gene clusters commonly associated with pestilence and disease. This demonstrates activity-guided single-cell genomics as a tool to guide novel biosynthetic discovery.
ISSN:1554-8929
1554-8937
DOI:10.1021/acschembio.1c00157