Draft genome and secondary metabolite biosynthetic gene clusters of Streptomyces sp. strain 196
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ORIGINAL ARTICLE
Draft genome and secondary metabolite biosynthetic gene clusters of Streptomyces sp. strain 196 Prateek Kumar1 · Anjali Chauhan2,3 · Munendra Kumar1 · Bijoy K. Kuanr3 · Renu Solanki4 · Monisha Khanna Kapur1 Received: 13 January 2020 / Accepted: 17 August 2020 © Springer Nature B.V. 2020
Abstract Emergence of MDR ‘superbugs’ inflamed a severe sense of urgency amongst scientists aiming at the discovery of novel potential drug molecules. Bacteria of the genus Streptomyces are really worth investigating for their immense potential to produce natural compounds of pharmaceutical importance. In the present study, the genome of Streptomyces sp. strain 196 was sequenced, studied and secondary metabolite biosynthetic gene clusters (smBGCs) were detected. FAME analysis was used for taxonomic validation of strain 196. Genome of strain 196 was sequenced using the Illumina NextSeq system which has resulted in a draft genome of 7.4 Mb. Rapid annotation using subsystem technology (RAST) results revealed the presence of 6682 CDS, 64 tRNA genes and 7 rRNA genes. Comparative studies revealed that strain 196 have 93.5% nucleotide and 96% protein level similarities with Streptomyces rhizosphaericola 1AS2c. Genome mining using antiSMASH predicted the presence of BGCs responsible for diverse bioactive compound production. The detected gene clusters were two PKS-III, one PKS-I, five NRPS, two hybrid PKS-I/NRPS, one thiopeptide/LAP, and one bacteriocin types. Furthermore, many other types BGCs such as three ectoine, two siderophore, one arylpolyene, two butyrolactone, one lassopeptide, one lanthipeptide and one melanin were also found. The results of this study provides information about genome and BGCs of strain 196, this information is valuable for researchers who are interested in isolation of bioactive compounds and working on heterologous expression of cryptic BGCs for novel bioactive compounds production. Keywords Draft genome · Streptomyces · Bioactive compounds · Biosynthetic gene clusters · AntiSMASH · PKS and NRPS
Introduction Antimicrobial resistance has resulted in a global health crisis where both common and deadly infections becoming incurable [1]. The rise in these incidences and reduction in drug discovery is greatly limiting the therapeutic options. Natural products from microbes have the potential for the * Monisha Khanna Kapur [email protected] 1
Microbial Technology Lab, Acharya Narendra Dev College, University of Delhi, Govindpuri, Kalkaji, New Delhi 110 019, India
2
School of Life Sciences, Jawaharlal Nehru University, New Delhi, India
3
Special Centre for Nanoscience, Jawaharlal Nehru University, New Delhi, India
4
Deen Dayal Upadhyaya College, University of Delhi, New Delhi, India
development of new remedial options. Natural products from actinomycetes are considered as excellent reserves of bioactive compounds and lead molecules [2]. Upto the mid-1990s, more than 50% of drugs were obtained from natural products [3, 4]. After that, the use of these products decreased
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