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

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.

doi:10.1021/acschembio.1c00157

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

Journal Article · Thu May 06 00:00:00 EDT 2021 · ACS Chemical Biology

DOI:https://doi.org/10.1021/acschembio.1c00157· OSTI ID:1844526

Kim, Woojoo E. ^[1]; Charov, Katherine ^[1]; Džunková, Mária ^[2]; Becraft, Eric D. ^[3]; Brown, Julia ^[4]; Schulz, Frederik ^[2]; Woyke, Tanja ^[2]; La Clair, James J. ^[1]; Stepanauskas, Ramunas ^[4]; ^[1]

Univ. of California, San Diego, La Jolla, CA (United States)
Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)
Bigelow Lab. for Ocean Sciences, East Boothbay, ME (United States); Univ. of North Alabama, Florence, AL (United States)
Bigelow Lab. for Ocean Sciences, East Boothbay, ME (United States)

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 in vivo biosynthetic functionality. Using fluorescent in situ 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 Oceanospirillales 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. Furthermore, this demonstrates activity-guided single-cell genomics as a tool to guide novel biosynthetic discovery.

View Accepted Manuscript (DOE)

Research Organization:: Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States)

Sponsoring Organization:: USDOE Office of Science (SC), Basic Energy Sciences (BES). Scientific User Facilities Division

Grant/Contract Number:: AC02-05CH11231

OSTI ID:: 1844526

Journal Information:: ACS Chemical Biology, Journal Name: ACS Chemical Biology Journal Issue: 5 Vol. 16; ISSN 1554-8929

Publisher:: American Chemical Society (ACS)Copyright Statement

Country of Publication:: United States

Language:: English

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