A comparative metabologenomic approach reveals mechanistic insights into Streptomyces antibiotic crypticity.

Publisher: National Academy of Sciences Country of Publication: United States NLM ID: 7505876 Publication Model: Print Cited Medium: Internet ISSN: 1091-6490 (Electronic) Linking ISSN: 00278424 NLM ISO Abbreviation: Proc Natl Acad Sci U S A Subsets: MEDLINE

Original Publication: Washington, DC : National Academy of Sciences

Genomics*; Anti-Bacterial Agents/*metabolism ; Streptomyces/*metabolism; Gene Deletion ; Gene Expression Regulation, Bacterial/physiology ; Genome, Bacterial ; Promoter Regions, Genetic ; Streptomyces/genetics

Streptomyces genomes harbor numerous, biosynthetic gene clusters (BGCs) encoding for drug-like compounds. While some of these BGCs readily yield expected products, many do not. Biosynthetic crypticity represents a significant hurdle to drug discovery, and the biological mechanisms that underpin it remain poorly understood. Polycyclic tetramate macrolactam (PTM) antibiotic production is widespread within the Streptomyces genus, and examples of active and cryptic PTM BGCs are known. To reveal further insights into the causes of biosynthetic crypticity, we employed a PTM-targeted comparative metabologenomics approach to analyze a panel of S. griseus clade strains that included both poor and robust PTM producers. By comparing the genomes and PTM production profiles of these strains, we systematically mapped the PTM promoter architecture within the group, revealed that these promoters are directly activated via the global regulator AdpA, and discovered that small promoter insertion-deletion lesions (indels) differentiate weaker PTM producers from stronger ones. We also revealed an unexpected link between robust PTM expression and griseorhodin pigment coproduction, with weaker S. griseus -clade PTM producers being unable to produce the latter compound. This study highlights promoter indels and biosynthetic interactions as important, genetically encoded factors that impact BGC outputs, providing mechanistic insights that will undoubtedly extend to other Streptomyces BGCs. We highlight comparative metabologenomics as a powerful approach to expose genomic features that differentiate strong, antibiotic producers from weaker ones. This should prove useful for rational discovery efforts and is orthogonal to current engineering and molecular signaling approaches now standard in the field.
Competing Interests: Competing interest statement: J.A.V.B. was a former employee, consultant, and advisory member of Warp Drive Bio, Inc. Warp Drive Bio is now a wholly owned subsidiary of Revolution Medicines where J.A.V.B. is a minority shareholder.
(Copyright © 2021 the Author(s). Published by PNAS.)

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Keywords: Streptomyces griseus; cryptic metabolism; metabologenomics; regulation; tetramic acid

0 (Anti-Bacterial Agents)

Date Created: 20210730 Date Completed: 20211209 Latest Revision: 20211214

20240829

PMC8346890

10.1073/pnas.2103515118

34326261