Genomic and Proteomic Dissection of the Ubiquitous Plant Pathogen, <i>Armillaria mellea</i>: Toward a New Infection Model System

Armillaria mellea is a major plant pathogen. Yet, no large-scale “-omics” data are available to enable new studies, and limited experimental models are available to investigate basidiomycete pathogenicity. Here we reveal that the <i>A. mellea</i> genome comprises 58.35 Mb, contains 14473 gene models, of average length 1575 bp (4.72 introns/gene). Tandem mass spectrometry identified 921 mycelial (<i>n</i> = 629 unique) and secreted (<i>n</i> = 183 unique) proteins. Almost 100 mycelial proteins were either species-specific or previously unidentified at the protein level. A number of proteins (<i>n</i> = 111) was detected in both mycelia and culture supernatant extracts. Signal sequence occurrence was 4-fold greater for secreted (50.2%) compared to mycelial (12%) proteins. Analyses revealed a rich reservoir of carbohydrate degrading enzymes, laccases, and lignin peroxidases in the <i>A. mellea</i> proteome, reminiscent of both basidiomycete and ascomycete glycodegradative arsenals. We discovered that <i>A. mellea</i> exhibits a specific killing effect against Candida albicans during coculture. Proteomic investigation of this interaction revealed the unique expression of defensive and potentially offensive <i>A. mellea</i> proteins (<i>n</i> = 30). Overall, our data reveal new insights into the origin of basidiomycete virulence and we present a new model system for further studies aimed at deciphering fungal pathogenic mechanisms

Genomic and Proteomic Dissection of the Ubiquitous Plant Pathogen, <i>Armillaria mellea</i>: Toward a New Infection Model System

Armillaria mellea is a major plant pathogen. Yet, no large-scale “-omics” data are available to enable new studies, and limited experimental models are available to investigate basidiomycete pathogenicity. Here we reveal that the <i>A. mellea</i> genome comprises 58.35 Mb, contains 14473 gene models, of average length 1575 bp (4.72 introns/gene). Tandem mass spectrometry identified 921 mycelial (<i>n</i> = 629 unique) and secreted (<i>n</i> = 183 unique) proteins. Almost 100 mycelial proteins were either species-specific or previously unidentified at the protein level. A number of proteins (<i>n</i> = 111) was detected in both mycelia and culture supernatant extracts. Signal sequence occurrence was 4-fold greater for secreted (50.2%) compared to mycelial (12%) proteins. Analyses revealed a rich reservoir of carbohydrate degrading enzymes, laccases, and lignin peroxidases in the <i>A. mellea</i> proteome, reminiscent of both basidiomycete and ascomycete glycodegradative arsenals. We discovered that <i>A. mellea</i> exhibits a specific killing effect against Candida albicans during coculture. Proteomic investigation of this interaction revealed the unique expression of defensive and potentially offensive <i>A. mellea</i> proteins (<i>n</i> = 30). Overall, our data reveal new insights into the origin of basidiomycete virulence and we present a new model system for further studies aimed at deciphering fungal pathogenic mechanisms

Genomic and Proteomic Dissection of the Ubiquitous Plant Pathogen, <i>Armillaria mellea</i>: Toward a New Infection Model System

Armillaria mellea is a major plant pathogen. Yet, no large-scale “-omics” data are available to enable new studies, and limited experimental models are available to investigate basidiomycete pathogenicity. Here we reveal that the <i>A. mellea</i> genome comprises 58.35 Mb, contains 14473 gene models, of average length 1575 bp (4.72 introns/gene). Tandem mass spectrometry identified 921 mycelial (<i>n</i> = 629 unique) and secreted (<i>n</i> = 183 unique) proteins. Almost 100 mycelial proteins were either species-specific or previously unidentified at the protein level. A number of proteins (<i>n</i> = 111) was detected in both mycelia and culture supernatant extracts. Signal sequence occurrence was 4-fold greater for secreted (50.2%) compared to mycelial (12%) proteins. Analyses revealed a rich reservoir of carbohydrate degrading enzymes, laccases, and lignin peroxidases in the <i>A. mellea</i> proteome, reminiscent of both basidiomycete and ascomycete glycodegradative arsenals. We discovered that <i>A. mellea</i> exhibits a specific killing effect against Candida albicans during coculture. Proteomic investigation of this interaction revealed the unique expression of defensive and potentially offensive <i>A. mellea</i> proteins (<i>n</i> = 30). Overall, our data reveal new insights into the origin of basidiomycete virulence and we present a new model system for further studies aimed at deciphering fungal pathogenic mechanisms

The Mating Type-like Locus in <i>D</i>. <i>catenulata</i>.

<p>A. Gene order around <i>MTL</i>α in <i>M</i>. <i>guilliermondii</i> and <i>D</i>. <i>catenulata</i>. Orthologous genes are connected with gray lines. Mating-type genes are filled in pink, and other genes associated with the <i>MTL</i> are edged in pink. The assembly of the <i>D</i>. <i>catenulata</i> contig stops at <i>OBP</i>. B. Phylogenetic relationship of <i>PAP</i>α and <i>PAP</i><b>a</b> from the indicated species from the Debaryomycetaceae/Metschnikowiaceae clade. The <i>PAP</i> protein from <i>D</i>. <i>catenulata</i> (which is not found at the <i>MTL</i> locus) is more closely related to <i>PAP</i><b>a</b> than to <i>PAP</i>α alleles. Alignments and phylogenetic trees were constructed using PhyML in SeaView [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0198957#pone.0198957.ref039" target="_blank">39</a>].</p

<i>D</i>. <i>catenulata</i> translates CUG codons as serine.

<p>A. Bar plot showing frequencies of amino acid matches to CUG codons in the <i>D</i>. <i>catenulata</i> genome. The values on the Y-axis represent the number of CUG codon sites that align with the amino acid residues shown on the X-axis in the YGOB protein database [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0198957#pone.0198957.ref041" target="_blank">41</a>]. Analysis of all codons is shown in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0198957#pone.0198957.s002" target="_blank">S1 File</a>. B. Comparison of tRNA^Ser(CAG) from <i>D</i>. <i>catenulata</i> with the same tRNA encoded by other species in the Debaryomycetaceae/Metschnikowiaceae. The discriminator base at the 3’ end (highlighted in red) is G in tRNA^Ser(CAG), and A in most tRNA^Leu(CAG) molecules. The G base just 5’ to the anticodon (highlighted in blue) also reduces leucylation [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0198957#pone.0198957.ref054" target="_blank">54</a>].</p

<i>Diutina catenulata</i> is a member of the Debaryomycetaceae/Metschnikowiaceae clade.

<p>The phylogenetic tree was inferred from a superalignment of 204 ubiquitous gene families from 42 species. A consensus Bayesian supermatrix phylogeny was generated using PhyloBayes [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0198957#pone.0198957.ref038" target="_blank">38</a>]. Clades within the Saccharomycotina (Debaryomycetaceae/Metschnikowiaceae, Pichiaceae, Phaffomycetaceae, Saccharomycodaceae and Saccharomycetaceae) are highlighted in color. Species within the Lodderomyces clade in the Debaryomycetaceae/Metschnikowiaceae are surrounded with a gray box. The exact definition of the Lodderomyces clade is not clear, and it may include <i>Spathaspora</i> species [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0198957#pone.0198957.ref048" target="_blank">48</a>]. The branch supports show Bayesian Posterior Probabilities.</p