Data on DNA-seq analysis of Endophytic Streptomyces sp. SUK 48

Abstract

The data genome sequence of SUK 48 consists of 8,341,706 bp, comprising of one contig with a high G + C content of 72.33%. The genome sequence encodes for 67 tRNAs and 21 rRNAs in one contig. SUK48 was found to have low similarities with other Streptomyces sp. (81–93% ANI indices) indicating that the isolated strain has a unique genome property and is presumably a novel species. This genome includes 34 genetic clusters responsible for the synthesis of secondary metabolites, including two polyketide synthase (PKS) clusters; one PKS type II cluster gene, one PKS gene cluster type III, five NRPS genetic clusters, and five PKS/NRPS hybrid clusters.

Antibiotic Biosynthesis Pathways from Endophytic Streptomyces SUK 48 through Metabolomics and Genomics Approaches

“…The bioinformatics analysis using Kyoto Encyclopedia of Genes and Genomes (KEGG) database ( Figure 1 ) and antiSMASH analysis shows that Streptomyces sp. SUK 48 had a pathway of putative kanamycin biosynthesis [ 41 ]. This result was supported by position region number one of this biosynthesis in the gene cluster [ 41 ].…”

“…SUK 48 had a pathway of putative kanamycin biosynthesis [ 41 ]. This result was supported by position region number one of this biosynthesis in the gene cluster [ 41 ]. In addition, instead of in positive mode ( Table S1 ), putative kanamycin A compound (483.2323 m / z , t = 6.71) and putative gentamicin (492.3036 m / z , t = 12.26) were found in negative mode ( Table S2 ).…”

“…There were 34 gene clusters that were responsible for producing secondary metabolites in Streptomyces sp. SUK 48, including polyketide synthase (PKS) type I, II and III, as well as nonribosomal peptide synthase (NRPS) and hybrid NRPS/PKS [ 41 ]. PKS genes were encoding polyketide metabolites that had multiple antimicrobials targets, such as tetracycline and antifungal amphotericin B [ 43 , 44 ].…”

“…Only enzyme glucokinase was detected during the analysis that initiated the reaction of kanamycin and gentamicin biosynthesis. To prove the biosynthesis, the kanamycin gene cluster was found at 1% homolog with the reference cluster indicating the unique cluster of this kanamycin cluster [ 41 ]. However, further study on validation of metabolomics data could be carried out by using LC-MS/MS and Nuclear Magnetic Resonance (NMR) to confirm the presence of the metabolites.…”

“…However, further study on validation of metabolomics data could be carried out by using LC-MS/MS and Nuclear Magnetic Resonance (NMR) to confirm the presence of the metabolites. Additionally, BCG for the kirromycin gene has been identified as two different clusters, which were the 12th cluster with 16% homolog, and the 34th cluster with 3% homolog [ 41 ]. Interestingly, these clusters encoded the production of an antiplasmodial compound that inhibits the synthesis of protein in the Plasmodium falciparum [ 42 , 49 ].…”