Mining Biosynthetic Gene Clusters of Pseudomonas vancouverensis Utilizing Whole Genome Sequencing

Authors: Tamang, Prabin; UPADHAYA, ARJUN - Washington State University; PAUDEL, PRADEEP - US Department Of Agriculture (USDA); Meepagala, Kumudini; Cantrell, Charles

Submitted to: Microorganisms
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 3/6/2024
Publication Date: 3/9/2024
Citation: Tamang, P., Upadhaya, A., Paudel, P., Meepagala, K.M., Cantrell, C.L. 2024. Mining Biosynthetic Gene Clusters of Pseudomonas vancouverensis Utilizing Whole Genome Sequencing. Microorganisms. 12:1-17. https://doi.org/10.3390/microorganisms12030548.
DOI: https://doi.org/10.3390/microorganisms12030548

Interpretive Summary: In recent years, there has been a growing interest in natural product (NP)-based pesticides as an environmentally friendly alternative to traditional chemical fungicides in agriculture. This study explores the potential of NP-based pesticides, specifically focusing on the bacterium Pseudomonas vancouverensis, which exhibited antifungal activities against various crop fungal pathogens. The bacterium whole genome was sequenced, and biosynthetic gene clusters (BGCs) responsible for secondary metabolites or NPs were identified through genomic analysis. The analysis revealed a diverse range of biosynthetic gene clusters (BGCs) capable of producing various natural products, including non-ribosomal peptides (NRPs), polyketides (PKs), acyl homoserine lactone, cyclodipeptide, bacteriocins, and ribosomally synthesized and post-transcriptionally modified peptides (RiPPs). Notably, the bacterium was predicted to produce known compounds such as bovienimide-A and putidacin L1, suggesting the potential for novel and biologically active natural products. The findings suggest the promising biotechnological potential of P. vancouverensis in developing new and effective biopesticides. Future studies focusing on the antifungal activity of the identified compounds will provide valuable insights into the practical applications of these NPs for crop protection. This research contributes to the ongoing efforts in the agrochemical industry to explore sustainable and environmentally friendly approaches to safeguarding crops.

Technical Abstract: Natural product (NP)-based pesticides have emerged as a compelling alternative to traditional chemical fungicides, attracting substantial attention within the agrochemical industry as the world is pushing towards sustainable and environment-friendly approaches to safeguard crops. Microbes, both bacteria and fungi, are a huge source of diverse secondary metabolites with ver-satile applications across pharmaceuticals, agriculture, and the food industry. Microbial genome mining has been accelerated for pesticide/ drug discovery and development in recent years, driven by advancements in genome sequencing, bioinformatics, metabolom-ics/metabologenomics, and synthetic biology. Here, we isolated and identified Pseudomonas van-couverensis that had shown antifungal activities against crop fungal pathogens Colletotrichum fragariae, Botrytis cinerea, and Phomopsis obscurans in a dual plate culture and bioautography assay. Further, we sequenced the whole bacterial genome and mined the genome of this bacterium to identify secondary metabolites biosynthetic gene clusters (BGCs) using antiSMASH 7.0, PRISM 4, and BAGEL 4. The in-silico analysis suggests that P. vancouverensis possesses a rich repertoire of BGCs with the potential to produce diverse and novel NPs, including non-ribosomal peptides (NRPs), polyketides (PKs), acyl homoserine lactone, cyclodipeptide, bacteriocins, and riboso-mally synthesized and post-transcriptionally modified peptides (RiPPs). Bovienimide-A, an NRP, and putidacin L1, a lectin-like bacteriocin, were among the previously known predicted metabo-lites produced by this bacterium, suggesting that the NPs produced by this bacterium could have biological activities and be novel as well. Future studies on the antifungal activity of these compounds will elucidate the full biotechnological potential of P. vancouverensis.