Integrated genomics and proteomics analysis of Paenibacillus peoriae IBSD35 and insights into its antimicrobial characteristics

Abstract

Antimicrobial resistance has been developing fast and incurring a loss of human life, and there is a need for new antimicrobial agents. Naturally occurring antimicrobial peptides offer the characteristics to counter AMR because the resistance development is low or no resistance. Antimicrobial peptides from Paenibacillus peoriae IBSD35 cell-free supernatant were salted out and purified using chromatography and characterized with liquid chromatography–tandem-mass spectrometry. The extract has shown a high and broad spectrum of antimicrobial activity. Combining the strain IBSD35 genome sequence with its proteomic data enabled the prediction of biosynthetic gene clusters by connecting the peptide from LC–MS/MS data to the gene that encode. Antimicrobial peptide databases offered a platform for the effective search, prediction, and design of AMPs and expanded the studies on their isolation, structure elucidation, biological evaluation, and pathway engineering. The genome-based taxonomy and comparisons have shown that P. peoriae IBSD35 is closely related to Paenibacillus peoriae FSL J3-0120. P. peoriae IBSD35 harbored endophytic trait genes and nonribosomal peptide synthases biosynthetic gene clusters. The comparative genomics revealed evolutionary insights and facilitated the discovery of novel SMs using proteomics from the extract of P. peoriae IBSD35. It will increase the potential to find novel bio-molecules to counter AMR.

‘Multi-omics’ data integration: applications in probiotics studies

“…The proteome changes are determined using protein chips with antibodies, nucleic acid or other proteins that bind to protein targets 106 . The application of multi-omics enables the purification of antimicrobial peptides from microbes using liquid-chromatography tandem mass-spectrometry and the characterization of the genes encoding these compounds through integrated genomics and proteomics analysis 107 . Thus, enabling an evolutionary insight using comparative genomics and discovering novel antimicrobial compounds.…”