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

Mohd Shukri Baba,Siti Junaidah Ahmad,Nuraziemah Ahmad,Fazren Azmi,Noor Wini Mazlan,Syarul Nataqain Baharum,Noraziah Mohamad Zin

doi:10.3390/antibiotics10080969

Abstract

Streptomyces sp. has been known to be a major antibiotic producer since the 1940s. As the number of cases related to resistance pathogens infection increases yearly, discovering the biosynthesis pathways of antibiotic has become important. In this study, we present the streamline of a project report summary; the genome data and metabolome data of newly isolated Streptomyces SUK 48 strain are also analyzed. The antibacterial activity of its crude extract is also determined. To obtain genome data, the genomic DNA of SUK 48 was extracted using a commercial kit (Promega) and sent for sequencing (Pac Biosciences technology platform, Menlo Park, CA, USA). The raw data were assembled and polished using Hierarchical Genome Assembly Process 4.0 (HGAP 4.0). The assembled data were structurally predicted using tRNAscan-SE and rnammer. Then, the data were analyzed using Kyoto Encyclopedia of Genes and Genomes (KEGG) database and antiSMASH analysis. Meanwhile, the metabolite profile of SUK 48 was determined using liquid chromatography-mass spectrophotometry (LC-MS) for both negative and positive modes. The results showed that the presence of kanamycin and gentamicin, as well as the other 11 antibiotics. Nevertheless, the biosynthesis pathways of aurantioclavine were also found. The cytotoxicity activity showed IC50 value was at 0.35 ± 1.35 mg/mL on the cell viability of HEK 293. In conclusion, Streptomyces sp. SUK 48 has proven to be a non-toxic antibiotic producer such as auranticlavine and gentamicin.

Highlights

Coronamycin was reported by Strobel et al in 2004, isolated from endophytic Streptomyces sp. from Monstera sp. in Amazon, Peru which acts as an antiplasmodial agent against Plasmodium falciparum with the IC50 value of 9 ng/mL [4]
A putative aurantioclavine was found in positive mode through metabolomics analysis which was reported as a potential anti-plasmodial agent [42]
We found that kanamycin and gentamycin were identified in metabolomics analysis and BGC of kanamycin was found in genomics analysis (Figure 1)

Summary

Introduction

Was known as an antibiotic producer 80 years back [1]. Streptomyces was the large group of genus Actinomycetes and filamentous aerobic Gram-positive bacteria [2,3] and was known to produce many remarkable secondary metabolites that can have antibacterial, antifungal, antiplasmodial, and antiviral functions [4,5]. Genome is the fact that its biosynthetic genes cluster encodes enzymes that responsible for secondary metabolites production [6]. Streptomyces kebangsaanensis contains phz enzymes to produce novel metabolite, 6-((2-hydroxyl-4metoxylphenoxylcarbonyl)phenazine-1-carboxylic acid HCPCA) (tubermycin B) which acts as an antibacterial agent [7,8]. Coronamycin was reported by Strobel et al in 2004, isolated from endophytic Streptomyces sp. The coronamycin had cytotoxicity effects against primary mammary epithelial cells (HMEC), which was a similar effect to taxol, an anti-cancer drug [4]

Methods

Results

Conclusion