TY - JOUR

T1 - Comparative Genomics Analysis of Keratin-Degrading Chryseobacterium Species Reveals Their Keratinolytic Potential for Secondary Metabolite Production

AU - Kang, Dingrong

AU - Shoaie, Saeed

AU - Jacquiod, Samuel

AU - Sørensen, Søren J.

AU - Ledesma-Amaro, Rodrigo

N1 - Funding Information: This research was funded by the Innovation Fund Denmark (Grant Number 1308-00015B, Keratin2Protein) and also under the support of the Chinese Scholarship Council Program. R.L.-A. received funding from BBSRC (BB/R01602X/1), 19-ERACoBioTech-33 SyCoLim BB/T011408/1, BBSRC BB/T013176/1, British Council 527429894, European Research Council (ERC) under the European Union?s Horizon 2020 research and innovation programme (DEUSBIO-949080). S.S. was supported by Engineering and Physical Sciences Research Council (EPSRC) (EP/S001301/1), Biotechnology Biological Sciences Research Council (BBSRC) (BB/S016899/1), and Science for Life Laboratory (SciLifeLab). Publisher Copyright: © 2021 by the authors. Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (https:// creativecommons.org/licenses/by/ 4.0/).

PY - 2021

Y1 - 2021

N2 - 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.

AB - 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.

KW - Degradation pathways

KW - Gene clusters

KW - Genome mining

KW - Keratinous materials

KW - Metabolic potential

U2 - 10.3390/microorganisms9051042

DO - 10.3390/microorganisms9051042

M3 - Journal article

C2 - 34066089

AN - SCOPUS:85105663521

VL - 9

JO - Microorganisms

JF - Microorganisms

SN - 2076-2607

IS - 5

M1 - 1042

ER -