Comparative Genomics Analysis of Keratin-Degrading Chryseobacterium Species Reveals Their Keratinolytic Potential for Secondary Metabolite Production.

Dingrong Kang,Søren J Sørensen,Rodrigo Ledesma-Amaro,Samuel Jacquiod,Saeed Shoaie

doi:10.3390/microorganisms9051042

Abstract

A promising keratin-degrading strain from the genus Chryseobacterium (Chryseobacterium sp. KMC2) was investigated using comparative genomic tools against three publicly available reference genomes to reveal the keratinolytic potential for biosynthesis of valuable secondary metabolites. Genomic features and metabolic potential of four species were compared, showing genomic differences but similar functional categories. Eleven different secondary metabolite gene clusters of interest were mined from the four genomes successfully, 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, 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 species and shades lights on the keratinolytic potential of Chryseobacterium sp. KMC2 from a genome-mining perspective, can provide alternatives to valorize keratinous materials into high-value bioactive natural products.

Highlights

IntroductionKeratin is the most abundant protein in epithelial cells, constituting the bulk of epidermal appendages such as hair and feather [1,2]
Secondary metabolite gene clusters of other eight Chryseobacterium genomes were predicted, consisting of 14 different candidates eight Chryseobacterium genomes were predicted, consisting of 14 different candidates (Supplementary Figure S2). These results demonstrate that various secondary metabolite (Supplementary Figure S2). These results demonstrate that various secondary metabolite gene clusters including both expected and unusual were discovered from Chryseobacterium gene clusters including both expected and unusual were discovered from Chryseobacterium genomes, which could turn into novel bioactive natural product sources
Common and unique secondary metabolite gene clusters were mined from Chryseobacterium genomes, suggesting the potential to generate high value

Summary

Introduction

Keratin is the most abundant protein in epithelial cells, constituting the bulk of epidermal appendages such as hair and feather [1,2]. Keratinous materials represent an abundant protein source, originating from the commercial slaughterhouses or poultry farms [3]. They contain peptides and amino acids, which are renewable natural resources with great potential in sustainable development [4]. Keratin is an insoluble protein with highly cross-linked disulfide bonds giving it a tough and recalcitrant structure [5]

Methods

Results

Conclusion