Biosynthetic Potential-Based Strain Prioritization for Natural Product Discovery: A Showcase for Diterpenoid-Producing Actinomycetes

Abstract

Natural products remain the best sources of drugs and drug leads and serve as outstanding small molecule probes to dissect fundamental biological processes. A great challenge for the natural product community is to discover novel natural products efficiently and cost effectively. Here we report the development of a practical method to survey biosynthetic potential in microorganisms, thereby identifying the most promising strains and prioritizing them for natural product discovery. Central to our approach is the innovative preparation, by a two-tiered PCR method, of a pool of pathway-specific probes, thereby allowing the survey of all variants of the biosynthetic machineries for the targeted class of natural products. The utility of the method was demonstrated by surveying 100 strains, randomly selected from our actinomycete collection, for their biosynthetic potential of four classes of natural products, aromatic polyketides, reduced polyketides, nonribosomal peptides, and diterpenoids, identifying 16 talented strains. One of the talented strains, Streptomyces griseus CB00830, was finally chosen to showcase the discovery of the targeted classes of natural products, resulting in the isolation of three diterpenoids, six nonribosomal peptides and related metabolites, and three polyketides. Variations of this method should be applicable to the discovery of other classes of natural products.

Angucyclines and Angucyclinones from Streptomyces sp. CB01913 Featuring C-Ring Cleavage and Expansion

“…We recently reported methods to guide strain prioritization for natural product discovery by surveying the biosynthetic gene clusters for the targeted class of natural products. 17 While these genomics-based methods are effective in prioritizing strains according to the biosynthetic potential, it is far from certain that the predicted biosynthetic machinery will be functional under the fermentation conditions of investigation for natural product production and isolation. The method reported here, chemical profiling of extracts, complements the genomics-based strain prioritization strategies and allows direct assessment of natural products produced under the conditions of investigation.…”

“…As a part of the Natural Products Library Initiative (NPLI) at The Scripps Research Institute (TSRI) dedicated to the discovery of natural products from our Actinomycetales strain collection, 13–17 we report the discovery of 14 angucyclinones and two angucyclines ( 1–16 ) from Streptomyces sp. CB01913, including 12 new compounds with (i) various oxidations on rings A and C ( 1, 2 , and 4 ), (ii) different glycosylations on rings A and B ( 3 and 6 ), and (iii) C-ring cleavage ( 5 and 10–14 ) and expansion ( 8 ).…”

New isofuranonaphthoquinones and isoindolequinones from Streptomyces sp. CB01883

“…It grows and sporulates well on ISP4 agar medium, and was classified as a Streptomyces species on the basis of a phylogenetic analysis using the concatenated partial sequences of three housekeeping genes 16 S rRNA, rpoB and trpB (Genebank accession number KT722854, KT736417 and KT793843, respectively). [14][15][16] In our continued effort Isofuranonaphthoquinones from Streptomyces sp. CB01883 Z Guo et al to study the biosynthesis of hybrid peptide-polyketide natural products, [19][20][21] we sequenced the genome of Streptomyces sp.…”

“…The NPLI biases natural products from Actinomycetales that are isolated from unexplored or underexplored ecological niches and unavailable in public strain collections. [7][8][9][10][11][12][13][14][15][16][17] The current library at TSRI consists of (i) purified natural products with fully assigned structures, (ii) C-18 mediumpressure liquid chromatography fractions, and (iii) crude extracts of microbial fermentation. Typically, strains were fermented in multiple media and subjected to HPLC and LC-MS analysis.…”

Exploring the diversity and metabolic potential of actinomycetes from temperate marine sediments from Newfoundland, Canada

“…These results argue strongly for the continued development of metabolomics screening methodologies and their further integration in NP discovery programs. Future coupling of metabolomics discovery work flows with novel strain prioritization approaches [85] will further invigorate NP discovery pipelines.…”