Comparative genomics analysis of Chryseobacterium sp. KMC2 reveals metabolic pathways involved in keratinous utilization and natural product biosynthesis

Abstract

Several efforts have been made to valorize keratinous materials, an abundant and renewable resource. Despite these attempts to valorize products generated from keratin hydrolysate, either via chemical or microbial conversion, they generally remain with an overall low value. In this study, a promising keratinolytic strain from the genus Chryseobacterium (Chryseobacterium sp. KMC2) was investigated using comparative genomic tools against publicly available reference genomes to reveal the metabolic potential for biosynthesis of valuable secondary metabolites. Genome and metabolic features of four species were compared, shows different gene numbers but similar functional categories. We successfully mined eleven different secondary metabolite gene clusters of interest from the four genomes, including five common ones shared across all genomes. Among the common metabolites, we identified gene clusters involved in biosynthesis of flexirubin-type pigment, microviridin, and siderophore, all showing remarkable conservation across the four genomes. Unique secondary metabolite gene clusters were also discovered, for example, ladderane from Chryseobacterium sp. KMC2. Additionally, this study provides a more comprehensive understanding of the potential metabolic pathways of keratin utilization in Chryseobacterium sp. KMC2, with the involvement of amino acid metabolism, TCA cycle, glycolysis/gluconeogenesis, propanoate metabolism, and sulfate reduction. This work uncovers the biosynthesis of secondary metabolite gene clusters from four keratinolytic Chryseobacterium spp. and shades lights on the keratinolytic potential of Chryseobacterium sp. KMC2 from a genome-mining perspective, providing alternatives to valorize keratinous materials into high-value natural products. ImportanceKeratin is an abundant and renewable resource from slaughterhouses or the poultry industry. Low-value products such as animal feed and fertilizer were generated from these feedstocks based on conventional processing like chemical conversion. In fact, microorganisms possess the potential to synthesize valuable natural products. In this work, we explored the metabolic potential of Chryseobacterium sp. KMC2, which was isolated with efficient keratinolytic capacity from a previous study. Comparative genomics analysis displayed similar functional categories against three publicly available reference genomes of keratin-degrading Chryseobacterium spp.. Eleven different secondary metabolite gene clusters of interest were mined among four genomes, including five common and unique ones. Furthermore, we provide a more comprehensive understanding of metabolic pathways on keratin utilization in Chryseobacterium sp. KMC2, with the involvement of amino acid assimilation and sulfate reduction. These findings contribute to expanding the application of Chryseobacterium sp. KMC2 on the valorization of keratinous materials.