In Silico Prediction of Secondary Metabolites and Biosynthetic Gene Clusters Analysis of Streptomyces thinghirensis HM3 Isolated from Arid Soil

Abstract

Natural products produced by microorganisms are considered an important resource of bioactive secondary metabolites, such as anticancer, antifungal, antibiotic, and immunosuppressive molecules. Streptomyces are the richest source of bioactive natural products via possessing a wide number of secondary metabolite biosynthetic gene clusters (SM-BGCs). Based on rapid development in sequencing technologies with advances in genome mining, exploring the newly isolated Streptomyces species for possible new secondary metabolites is mandatory to find novel natural products. The isolated Streptomyces thinghirensis strain HM3 from arid and sandy texture soil in Qassim, SA, exerted inhibition activity against tested animal pathogenic Gram-positive bacteria and pathogenic fungal species. In this study, we report the draft genome of S. thinghirensis strain HM3, which consists of 7,139,324 base pairs (bp), with an average G+C content of 71.49%, predicting 7949 open reading frames, 12 rRNA operons (5S, 16S, 23S) and 60 tRNAs. An in silico analysis of strain HM3 genome by the antiSMASH and PRISM 4 online software for SM-BGCs predicted 16 clusters, including four terpene, one lantipeptide, one siderophore, two polyketide synthase (PKS), two non-ribosomal peptide synthetase (NRPS) cluster)/NRPS-like fragment, two RiPP/RiPP-like (ribosomally synthesised and post-translationally modified peptide product), two butyrolactone, one CDPS (tRNA-dependent cyclodipeptide synthases), and one other (cluster containing a secondary metabolite-related protein that does not fit into any other category) BGC. The presented BGCs inside the genome, along with antibacterial and antifungal activity, indicate that HM3 may represent an invaluable source for new secondary metabolites.

A Practical Toolkit for the Detection, Isolation, Quantification, and Characterization of Siderophores and Metallophores in Microorganisms

“…PRISM is linked to the “Genomes-to-Natural Products” platform (GNP), which matches these predictions with MS/MS data, as well as the GRAPE/GARLIC tools, which match such predictions to chemical databases . A recent study explored the newly isolated Streptomyces thinghirensis strain HM3 for possible new secondary metabolites to find novel natural products . The in silico analysis by the antiSMASH and PRISM 4 online software for SM-BGCs predicted 16 clusters, including four terpene, one lantipeptide, one siderophore, two polyketide synthase, two NRPS cluster/NRPS-like fragments, two ribosomally synthesized and post-translationally modified peptide products, two butyrolactones, one tRNA-dependent cyclodipeptide synthase, and one other BGC .…”

“…This study highlighted that S. thinghirensis strain HM3 presents a potential new source of secondary metabolites and the usefulness of these genomic approaches …”

“… 122 A recent study explored the newly isolated Streptomyces thinghirensis strain HM3 for possible new secondary metabolites to find novel natural products. 128 The in silico analysis by the antiSMASH and PRISM 4 online software for SM-BGCs predicted 16 clusters, including four terpene, one lantipeptide, one siderophore, two polyketide synthase, two NRPS cluster/NRPS-like fragments, two ribosomally synthesized and post-translationally modified peptide products, two butyrolactones, one tRNA-dependent cyclodipeptide synthase, and one other BGC. 128 This study highlighted that S. thinghirensis strain HM3 presents a potential new source of secondary metabolites and the usefulness of these genomic approaches.…”