Whole genome surveying and metabolomic profiling aided navigation of therapeutic plethora of Streptomyces melanogenes WPF1 isolated from Pinus patula rhizosphere

Rhizosphere microbial diversity from Western Ghats remains a relatively less explored source of therapeutic agents. Targeted screening of actinomycetes from an under studied area led to the isolation of 24 actinomycetes from Pinus patula rhizosphere. Screening led to identification of Streptomyces melanogenes WPF1 with strong therapeutic potential. Delineation of the whole genome of WPF1 and metabolic profiling of the partially purified active fraction (PF10) led to confirmation of kinamycin D, oleic acid, palmitic acid and other components. These molecules in unison can be correlated to the recorded biological activities of the active fraction. AntiSMASH analysis of the WPF1 genome identified 26 biosynthetic gene clusters (BGCs) associated with secondary metabolite biosynthesis, including one cluster exhibiting over 97% similarity to known Kinamycin biosynthetic pathway. LC-MS and high-resolution mass spectrometry (HRMS) analyses revealed presence of Kinamycin D in the partially purified fraction PF10. PF10 demonstrated selective antibacterial activity against Gram-positive human pathogens and effectively inhibited their biofilm formation. Additionally, PF10 suppressed the proliferation of cancer cell lines, with IC₅₀ values ranging from 2.0 to 2.5 µg/mL, and induced apoptosis, as evidenced by Poly (ADP-ribose) polymerase (PARP) cleavage, activation of caspase 3 and caspase 9 and Bax protein accumulation. These findings highlight S. melanogenes WPF1 as a promising source of bioactive secondary metabolites, and importance of rhizosphere microbial diversity for potential therapeutic discovery.