Comparative genome analysis of Trichophyton rubrum and related dermatophytes reveals candidate genes involved in infection

Abstract

The major cause of athlete's foot is Trichophyton rubrum, a dermatophyte or fungal pathogen of human skin. To facilitate molecular analyses of the dermatophytes, we sequenced T. rubrum and four related species, Trichophyton tonsurans, Trichophyton equinum, Microsporum canis, and Microsporum gypseum. These species differ in host range, mating, and disease progression. The dermatophyte genomes are highly colinear yet contain gene family expansions not found in other human-associated fungi. Dermatophyte genomes are enriched for gene families containing the LysM domain, which binds chitin and potentially related carbohydrates. These LysM domains differ in sequence from those in other species in regions of the peptide that could affect substrate binding. The dermatophytes also encode novel sets of fungus-specific kinases with unknown specificity, including nonfunctional pseudokinases, which may inhibit phosphorylation by competing for kinase sites within substrates, acting as allosteric effectors, or acting as scaffolds for signaling. The dermatophytes are also enriched for a large number of enzymes that synthesize secondary metabolites, including dermatophyte-specific genes that could synthesize novel compounds. Finally, dermatophytes are enriched in several classes of proteases that are necessary for fungal growth and nutrient acquisition on keratinized tissues. Despite differences in mating ability, genes involved in mating and meiosis are conserved across species, suggesting the possibility of cryptic mating in species where it has not been previously detected. These genome analyses identify gene families that are important to our understanding of how dermatophytes cause chronic infections, how they interact with epithelial cells, and how they respond to the host immune response.

FIG 1

(A) Phylogenetic relationship and gene conservation of the dermatophytes and other species compared in this study; (B) section of the phylogeny in Fig. 1A comprising the dermatophytes; (C) shared and unique ortholog groups (see Materials and Methods) for the seven dermatophyte genomes grouped by host or ecological niche preference. Ortholog groups in this figure include paralogous duplications; therefore, total gene counts including paralogs are higher. The number of genes unique to each species (not contained in any other species in panel A) is shown in parentheses after the species name.

FIG 2

IPR domains most enriched in dermatophytes compared to all nondermatophytes in the study. Values are colored along a blue (low) to red (high) color scale, with color scaling relative to the low and high values of each row. IPR categories are sorted by P value within each supercategory. IPR domain enrichments shown have P values of at least 3e−8.

FIG 3

Phylogenetic tree of all fungal proteins containing LysM domains. Phylogeny was estimated using RAxML (see Materials and Methods). Two major clades were identified and labeled clade A (black gene names) and clade B (green gene names). Clade B may have arisen differently, as the majority of proteins in clade B do not have chitinase domains. Clade C contains LysM domains that have evidence of recent intergene duplication of the LysM domain, accounting for the high number of LysM domains in this group. Genes in clade D contain polysaccharide deacetylase domains in combination with the LysM domain. This combination is found only in dermatophytes. Genes in clade E contain the WA/GW signature in the LysM domain, typically the domain closest to the chitinase domain. Clade E.1 (labeled in the phylogeny tree) is a recently expanded group of genes that do not contain the WA/GW phylogenetically embedded within the WA/GW signature-containing group.

FIG 4

Eukaryotic protein kinase superfamily members (kinomes) of the dermatophytes compared with the kinomes of other fungi. Kinases from established families are shown on the left of the black line, while novel or recently discovered kinases are shown on the right. Kinases are classified into major groups shown as colored blocks (76). Abbreviations: Aben, A. benhamie; Tver, T. verrucosum; Trub, T. rubrum; Tton, T. tonsurans; Tequ, T. equinum; Mgyp, M. gypseum; Mcan, M. canis; Cimi, C. immitis; Anid, A. nidulans; Afum, A. fumigatus; Scer, S. cerevisiae; AGC, protein kinases A, G, and C; CAMK, calcium/calmodulin-dependent kinases; CK1, casein kinase 1; CMGC, cyclin-dependent kinases (CDK), mitogen-activated, glycogen-synthase, and CDK-like kinases; STE, sterile phenotype kinases; FunK1, fungal-specific kinase 1; SRPKL, serine/arginine-rich protein-specific kinase-like; other, kinases not falling into major groups.