Implication of PKS type I gene and chromatographic strategy for the biodiscovery of antimicrobial polyketide metabolites from endosymbiotic Nocardiopsis prasina CLA68

Abstract

Advanced approach in probing for polyketide antimicrobials requires novel genomics and chromatographic strategies. An endophytic strain CLA68 was isolated from the root of Combretum latifolium Blume (Combretaceae) collected from the Western Ghats of Southern India. Strain CLA68 was then identified as Nocardiopsis prasina by its characteristic culture morphology and analysis of 16S rRNA gene sequence. Biosynthetic polyketide synthase genes were investigated using two pairs of degenerate primers. Ethyl acetate extract of CLA68 exhibited broad spectrum activity against a panel of test human pathogens. PKS type-I gene detection and chromatographic strategy yielded a robust polyketide antimicrobial compound which identified as nocapyrone E. Minimum inhibitory concentration of the purified compound against MRSA and other human pathogens ranged between 25 and 100 μg/ml. The present work highlights the utility of N. prasina CLA68 as potential source for antimicrobial polyketide nocapyrone E which could help to combat multidrug-resistant pathogens. This study demonstrates feasibility of PKS type-I gene-based molecular approach and chemical investigation by chromatographic approach is the best method for prediction and rapid discovery of novel polyketides from endosymbiotic actinomycetes. The sequence data of this endosymbiotic actinomycete is deposited in GenBank under the accession no. KP269077.

Chemogenomics driven discovery of endogenous polyketide anti-infective compounds from endosymbiotic Emericella variecolor CLB38 and their RNA secondary structure analysis

“…TOF-MS is a powerful tool for accurate and rapid identification of known compounds, i.e. dereplication which has a great importance towards discovery of new antimicrobial agents [ 61 – 63 ]. This strategy enables to minimize wasting attempt on isolation of known bioactive compounds.…”

Insights into the Variation in Bioactivities of Closely Related Streptomyces Strains from Marine Sediments of the Visayan Sea against ESKAPE and Ovarian Cancer

“…The production of secondary metabolites in Actinomycetes is driven by biosynthetic gene clusters (BGCs), a locally clustered group of two or more genes that encode a biosynthetic pathway [ 20 , 21 ]. Depending on the chemical entity of secondary metabolites, BGCs are differentiated according to different structural classes, including non-ribosomal peptide synthetases (NRPS), polyketide synthases (PKS), terpenes, and bacteriocins [ 22 , 23 , 24 , 25 , 26 , 27 ]. PKS and NRPS are popular BGC targets for natural product discovery.…”

“…They are known to synthesize diverse chemical structures with potential medicine applications such as antibiotics, anticancer, and immunosuppressants [ 23 , 27 , 28 , 29 , 30 , 31 ]. The PKS small metabolites such as erythromycin (antibiotic) and rapamycin (immunosuppressant) are encoded in Type I polyketide synthase (type I PKS) [ 24 ]. Type II polyketide synthase (type II PKS) gene clusters form compounds through aromatization and cyclization such as tetracycline (antibiotic) and doxorubicin (anticancer) [ 26 , 27 , 29 , 30 ].…”

Applications of microbial co‐cultures in polyketides production

“…Early co-cultures of different fungal species were carried out in solid-status media, in which the morphogenesis and metabolic changes were found at the leading edge of the fungal mycelia (Guo et al 2016). The patterns of interaction between the different species were also observed in these co-culture systems (Rao et al 2016;Chakraborty et al 2017;Charousova et al 2017;Govindarajan et al 2017). Up until recently, only co-cultures in solid-status media have been employed between different fungi, bacteria and protists.…”

“…The patterns of interaction between the different species were also observed in these co‐culture systems (Rao et al . 2016; Chakraborty et al . 2017; Charousova et al .…”