Whole-genome sequence analysis of penitrem A-producing Penicillium crustosum isolated from pears: secondary metabolite biosynthesis

Abstract

Penitrem A is a toxic secondary metabolite (SM) produced by Penicillium crustosum ( P. crustosum ) on various foods such as nuts, dairy products, and fruits. However, the biosynthetic gene clusters (BGCs) responsible for SMs including penitrem A in P. crustosum isolated from pears is largely unexplored. In the current study, we performed whole-genome sequencing of P. crustosum KACC 411287, which can produce penitrem A and roquefortine C, and identified its SM BGCs including BGCs of the toxins. Furthermore, we conducted a comparative analysis of the penitrem A and roquefortine C BGCs against those in other fungal strains. We also analyzed the carbohydrate-active enzyme-(CAZyme-) encoding genes in P. crustosum KACC 411287, and compared with those of other closely related fungal strains. The P. crustosum KACC 411287 genome is composed of five chromosomes, totaling approximately 32.37 Mb in size. Gene Ontology analysis using 8,520 functionally annotated proteins exhibited that the genome of P. crustosum KACC 411287 contains a significant abundance of genes involved in degradation of organonitrogen compounds including amino acids or carbohydrates and fungal self-protective mechanisms including SM biosynthesis. Of the 8,520 functionally annotated proteins, 546 predicted CAZymes were identified in P. crustosum KACC 411287. We also detected 68 SM BGCs including penitrem A and roquefortine C BGCs in P. crustosum KACC 411287. Furthermore, the conserved functionality analyses exhibited that each gene within the penitrem A BGC in P. crustosum KACC 411287 is highly conserved with the corresponding gene in four other penitrem A-producing Penicillium strains (above 77% amino acid sequence identity) except for ptmH in P. flavigenum IBT 14082 (20%). In contrast, the sequence identity decreased significantly (0–69% identity) in two penitrem A non-producing Penicillium strains. Our data strongly indicate that the penitrem A BGCs were highly conserved among P. crustosum KACC 411287 and three other penitrem A-producing Pencillium strains. Our findings expand our knowledge about the biosynthesis of SMs including penitrem A and roquefortine C in P. crustosum KACC 411287 that causes blue mold rot on pears. These results could provide new insight into the biosynthesis of penitrem A and roquefortine C in P. crustosum KACC 411287 to find potential approaches for alleviating penitrem A or roquefortine C contamination on pears.