Pseudozyma saprotrophic yeasts have retained a large effector arsenal, including functional Pep1 orthologs

Abstract

SummaryThe basidiomycete smut fungi are predominantly plant parasitic, causing severe losses in some crops. Most species feature a saprotrophic haploid yeast stage, and several smut fungi are only known from this stage, with some isolated from habitats without suitable hosts, e.g. from Antarctica. Thus, these species are generally believed to be apathogenic, but recent findings that some of these might have a plant pathogenic sexual counterpart, casts doubts on the validity of this hypothesis. Here, four Pseudozyma genomes were re-annotated and compared to published smut pathogens and the well-characterised effector gene Pep1 from these species was checked for its ability to complement a Pep1 deletion strain of Ustilago maydis. It was found that 113 high-confidence putative effector proteins were conserved among smut and Pseudozyma genomes. Among these were several validated effector proteins, including Pep1. By genetic complementation we show that Pep1 homologs from the supposedly apathogenic yeasts restore virulence in Pep1-deficient mutants Ustilago maydis. Thus, it is concluded that Pseudozyma species have retained a suite of effectors. This hints at the possibility that Pseudozyma species have kept an unknown plant pathogenic stage for sexual recombination or that these effectors have positive effects when colonising plant surfaces.

Comparative genomics reveals low levels of inter- and intraspecies diversity in the causal agents of dwarf and common bunt of wheat and hint at conspecificity of Tilletia caries and T. laevis

“…Out of 56 sequences of functionally characterized proteins, only six putative orthologous genes were identified by a tBLASTn search (at least 60% coverage and > 20% identity). These genes included (1) Clp1 required for the proliferation of dikaryotic filaments in planta (Scherer et al 2006 ); (2) defense-suppressing virulence effector Pep1 (Doehlemann et al 2009 ; Hemetsberger et al 2012 , 2015 ; Sharma et al 2018 ); (3) Pep4 involved in dimorphism and pathogenesis (Soberanes-Gutiérrez et al 2015 ); (4) precursor of the peptide conferring surface hydrophobicity to hyphae Rep1 (Wösten et al 1996 ; Müller et al 2008 ; Teertstra et al 2009 ); (5) peroxisomal sterol carrier protein Scp2 (Krombach et al 2018 ); and (6) high-affinity sucrose transporter required for virulence Srt1 (Wahl et al 2010 ).…”

Diversity of Moesziomyces (Ustilaginales, Ustilaginomycotina) on Echinochloa and Leersia (Poaceae)

“…There is genomic evidence that some saprobic ustilaginalean yeasts, e.g. M.antarcticus , Kalmanozymabrasiliensis (= P.brasiliensis ), Pseudozymahubeiensis , and the yeast stage of M.bullatus (= P.aphidis ), have retained the capacity to produce effector proteins, which hints at the possibility that undiscovered plant pathogenic stages may exist for these fungi (Sharma et al 2018). Indeed, a teleomorph for M.antarcticus (= P.antarctica ) was recently reported for the first time on Echinochloacrus-galli (Tanaka et al 2019).…”

Molecular Interactions Between Smut Fungi and Their Host Plants

“…The Anthracocystis flocculosa (previously Pseudozyma flocculosa) genome contains a similar number of repeats (13.9%) and predicted effector genes (554, strict method) as the smut species U. hordei (16.5%) and U. maydis (553, strict method), respectively (30). Furthermore, the A. flocculosa genome is also compartmentalized with 54 predicted effectors residing in gene clusters, which are fewer genes than U. maydis (101) but more than U. hordei, which has none (30). In general, genes encoding for the secretome of Pseudozyma species strongly correspond with that of pathogenic smut species (97).…”

“…Furthermore, Moesziomyces antarcticus still contains 21 of the 24 identified core effector candidates of smut pathogens, which caused Schuster et al (97) to hypothesize that M. antarcticus may still have the ability to infect plants. Comparative genome analysis performed by Sharma et al (101) has shown that 113 of a core set of 211 putative effector proteins were conserved among all pathogenic smut species and four tested Pseudozyma genomes. Furthermore, they also showed that U. maydis Pep1 homologs from the supposedly nonpathogenic yeasts are fully functional in U. maydis (101).…”

“…Comparative genome analysis performed by Sharma et al (101) has shown that 113 of a core set of 211 putative effector proteins were conserved among all pathogenic smut species and four tested Pseudozyma genomes. Furthermore, they also showed that U. maydis Pep1 homologs from the supposedly nonpathogenic yeasts are fully functional in U. maydis (101). These results indicate that the Pseudozyma species known only for their yeast stage may retain the potential to be a pathogen or lost pathogenicity only recently.…”