Dandruff-associated Malassezia genomes reveal convergent and divergent virulence traits shared with plant and human fungal pathogens

Abstract

Fungi in the genus Malassezia are ubiquitous skin residents of humans and other warm-blooded animals. Malassezia are involved in disorders including dandruff and seborrheic dermatitis, which together affect >50% of humans. Despite the importance of Malassezia in common skin diseases, remarkably little is known at the molecular level. We describe the genome, secretory proteome, and expression of selected genes of Malassezia globosa. Further, we report a comparative survey of the genome and secretory proteome of Malassezia restricta, a close relative implicated in similar skin disorders. Adaptation to the skin environment and associated pathogenicity may be due to unique metabolic limitations and capabilities. For example, the lipid dependence of M. globosa can be explained by the apparent absence of a fatty acid synthase gene. The inability to synthesize fatty acids may be complemented by the presence of multiple secreted lipases to aid in harvesting host lipids. In addition, an abundance of genes encoding secreted hydrolases (e.g., lipases, phospholipases, aspartyl proteases, and acid sphingomyelinases) was found in the M. globosa genome. In contrast, the phylogenetically closely related plant pathogen Ustilago maydis encodes a different arsenal of extracellular hydrolases with more copies of glycosyl hydrolase genes. M. globosa shares a similar arsenal of extracellular hydrolases with the phylogenetically distant human pathogen, Candida albicans, which occupies a similar niche, indicating the importance of host-specific adaptation. The M. globosa genome sequence also revealed the presence of mating-type genes, providing an indication that Malassezia may be capable of sex.

Fig. 1.

M. globosa does not have a traditional fungal fatty acid synthase. Ovals represent fatty acid synthase domains, with black connecting lines representing covalent connections, as predicted from the DNA sequences. FAS, fatty acid synthase; KS, β-ketoacyl synthase; AT, acetyl-CoA-ACP transacetylase; MT, malonyl-CoA-ACP-transacylase; DH, dehydratase; ER, β-enoyl reductase; KR, β-ketoacyl reductase; ACP, acyl carrier protein; PPT, phosphopantetheinyl transferase; MAT, malonyl-CoA-acetyl-CoA-ACP-transacylase; TE, thioesterase; PKS, polyketide synthase; TR, thioester reductase. The “?” next to DH activity of M. globosa PKS indicates the uncertainty of the activity based on homology alone. A domain name in parentheses represents a domain included in some, but not all, of this set of enzymes. Shown here is one example of type I PKS; many variations of this architecture exist. The two FAS subunits of U. maydis and several other fungi appear to be fused into a single polypeptide. See SI Tables 6–8 for more information.

Fig. 2.

Secreted proteins: gene expression and gene clusters. (A) Transcripts for lipase and phospholipase genes were detected from M. globosa cells isolated from scalp and from cells cultured in vitro. Isolated RNA was used for first-strand cDNA synthesis with reverse transcriptase and random hexamers and then PCR-amplified by using gene-specific primers, as described (17). (B) The 2D gel was stained with Coomassie blue. Multiple spots within a circle are different isoforms of the same protein. The dark spot in the bottom right corner of the gel (*) was resistant to multiple attempts at digestion and could not be identified. See also SI Tables 9 and 10. (C) Cyan symbols, proteins predicted to be secreted. Open symbols, proteins predicted not to be secreted. * in the middle of the gene indicates the protein was found in the extracellular fraction in the proteomics experiments. Lip, lipase family LIP; Lip3, lipase family LIP3; Plc, phospholipase C; Asp, aspartyl protease; Asm, acid sphingomyelinase. C1–6 refer to gene cluster names, with the contig numbers, gene numbers, and predicted gene functions listed in SI Table 12.

Fig. 3.

Similarities of phylogeny, mating type gene organization, and pathogenesis between Malassezia and Ustilago. (A) The phylogenetic tree based on 28 concatenated single-copy orthologous proteins present in 34 fungal genomes was prepared by using Maximum Likelihood (PHYML) by using JTT amino acid model substitution (SI Table 11). This tree depicts a small number of fungi; a more inclusive tree is shown (SI Fig. 4). (B) Schematic representation of the mating loci of U. hordei, U. maydis, and M. globosa. pra1: pheromone receptor 1; bW1: homeodomain transcription factor b west 1; bE1: homeodomain transcription factor b east 1. M. globosa mating-related genes: putative pheromone, MGL_0963; pra1, MGL_0964; bE1, MGL_0884; bW1, MGL_0883. (C) Illustration of the adaptations by Malassezia and Ustilago to take advantage of distinct host environments for survival. The model emphasizes the most prominent protein families based on the available data. The downward-pointing arrows represent the damage to the host substrate inflicted by secreted proteins, and the upward-pointing arrows represent the damaged host substrate that provides resources to support the growth and persistence of the fungal population. [Scale bars: 2 μm (Malassezia), 10 μm (Ustilago), and 1 cm (tumor formation).]