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

• Published in: Fermentation (Basel) 2023-01, Vol.9 (1), p.65
• Main Authors: Rehan, Medhat, Gueddou, Abdellatif, Alharbi, Abdulaziz, Ben Abdelmalek, Imen
• Format: Article
• Language: English
• Subjects: Antibiotics; Antifungal activity; arid soil; Bacteria; BGCs; Bioinformatics; data mining; Drugs; Gene clusters; genome sequencing; Genomes; Gram-positive bacteria; Insecticides; Metabolism; Metabolites; Natural products; Open reading frames; Operons; Phylogenetics; Polyketide synthase; Post-translation; rRNA 16S; rRNA 23S; rRNA 5S; Sandy soils; Secondary metabolites; Soybeans; Staphylococcus infections; Streptococcus infections; Streptomyces; tRNA
• ISSN: 2311-5637; 2311-5637
• DOI: 10.3390/fermentation9010065

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.