Comparative and functional genomics provide insights into the pathogenicity of dermatophytic fungi

ABSTRACT: BACKGROUND: Millions of humans and animals suffer from superficial infections caused by a group of highly specialized filamentous fungi, the dermatophytes, which exclusively infect keratinized host structures. To provide broad insights into the molecular basis of the pathogenicity-associated traits, we report the first genome sequences of two closely phylogenetically related dermatophytes, Arthroderma benhamiae and Trichophyton verrucosum, both of which induce highly inflammatory infections in humans. RESULTS: 97% of the 22.5 megabase genome sequences of A. benhamiae and T. verrucosum are unambiguously alignable and collinear. To unravel dermatophyte-specific virulence-associated traits, we compared sets of potentially pathogenicity-associated proteins, such as secreted proteases and enzymes involved in secondary metabolite production, with those of closely related onygenales (Coccidioides species) and the mould Aspergillus fumigatus. The comparisons revealed expansion of several gene families in dermatophytes and disclosed the peculiarities of the dermatophyte secondary metabolite gene sets. Secretion of proteases and other hydrolytic enzymes by A. benhamiae was proven experimentally by a global secretome analysis during keratin degradation. Molecular insights into the interaction of A. benhamiae with human keratinocytes were obtained for the first time by global transcriptome profiling. Given that A. benhamiae is able to undergo mating, a detailed comparison of the genomes further unraveled the genetic basis of sexual reproduction in this species. CONCLUSIONS: Our results enlighten the genetic basis of fundamental and putatively virulence-related traits of dermatophytes, advancing future research on these medically important pathogens

Dataset of cocoa aspartic protease cleavage sites

The data provide information in support of the research article, “The cleavage specificity of the aspartic protease of cocoa beans involved in the generation of the cocoa-specific aroma precursors” (Janek et al., 2016) [1]. Three different protein substrates were partially digested with the aspartic protease isolated from cocoa beans and commercial pepsin, respectively. The obtained peptide fragments were analyzed by matrix-assisted laser-desorption/ionization time-of-flight mass spectrometry (MALDI-TOF/TOF-MS/MS) and identified using the MASCOT server. The N- and C-terminal ends of the peptide fragments were used to identify the corresponding in-vitro cleavage sites by comparison with the amino acid sequences of the substrate proteins. The same procedure was applied to identify the cleavage sites used by the cocoa aspartic protease during cocoa fermentation starting from the published amino acid sequences of oligopeptides isolated from fermented cocoa beans. Keywords: Aspartic protease, Cleavage sites, Cocoa, In-vitro proteolysis, Mass spectrometry, Peptide

The fate of mitochondria after infection of the Mucoralean fungus <i>Absidia glauca</i> by the fusion parasite <i>Parasitella parasitica</i>: comparison of mitochondrial genomes in zygomycetes

<p><i>Absidia glauca</i> and <i>Parasitella parasitica</i> constitute a versatile experimental system for studying horizontal gene transfer between a mucoralean host and its fusion parasite. The <i>A. glauca</i> chondriome has a length of approximately 63 kb and a GC content of 28%. The chondriome of <i>P. parasitica</i> is larger, 83 kb, and contains 31% GC base pairs. These mtDNAs contain the standard fungal mitochondrial gene set, small and large subunit rRNAs, plus ribonuclease P RNA. Comparing zygomycete chondriomes reveals an unusually high number of homing endonuclease genes in <i>P. parasitica</i>, substantiating the mobility of intron elements independent of host-parasite interactions.</p

Identification and Isolation of Two Ascomycete Fungi from Spores of the Arbuscular Mycorrhizal Fungus Scutellospora castanea

Two filamentous fungi with different phenotypes were isolated from crushed healthy spores or perforated dead spores of the arbuscular mycorrhizal fungus (AMF) Scutellospora castanea. Based on comparative sequence analysis of 5.8S ribosomal DNA and internal transcribed spacer fragments, one isolate, obtained from perforated dead spores only, was assigned to the genus Nectria, and the second, obtained from both healthy and dead spores, was assigned to Leptosphaeria, a genus that also contains pathogens of plants in the Brassicaceae. PCR and randomly amplified polymorphic DNA-PCR analyses, however, did not indicate similarities between pathogens and the isolate. The presence of the two isolates in both healthy spores and perforated dead spores of S. castanea was finally confirmed by transmission electron microscopy by using distinctive characteristics of the isolates and S. castanea. The role of this fungus in S. castanea spores remains unclear, but the results serve as a strong warning that sequences obtained from apparently healthy AMF spores cannot be presumed to be of glomalean origin and that this could present problems for studies on AMF genes

Cocoa-specific flavor components and their peptide precursors

Essential precursors of the cocoa-specific roasting-flavor notes were formed during proteolysis of the cocoa vicilin-class(7S) globulin by a mixture of cocoa aspartic protease and carboxypeptidase. These could be partially purified by ligand-exchange chromatography. Many constituents of this peptide fraction were destroyed by posttreatment with pepsin, but the cocoa-specific flavor-precursor peptides were largely resistant against pepsin treatment. However, these peptides were not generated when the cocoa vicilin-class(7S) globulin was digested with a mixture of pepsin and carboxypeptidase. By nano-liquid chromatography mass spectrometry, the peptide composition of these peptide fractions were compared in order to identify the putative precursors of the cocoaspecific flavor components. These peptides were assigned to five regions of the cocoa vicilin-class(7S) globulin. Analyzing the roasting products of the different protein fractions by headspace solid-phase microextraction, followed by gas chromatography mass spectrometry, eight volatile compounds were detected, whose occurrence correlated with the sensory detection of cocoa-specific flavor notes.Fil: Scalone, Gustavo Luis Leonardo. University of Ghent; Bélgica. Consejo Nacional de Investigaciones Científicas y Técnicas; ArgentinaFil: Textoris Taube, Kathrin. Universität Medizin Berlin; AlemaniaFil: De Meulenaer, Bruno. University of Ghent; BélgicaFil: De Kimpe, Norbert. University of Ghent; BélgicaFil: Wöstemeyer, Johannes. Universitat Jena; AlemaniaFil: Voigt, Jürgen. Universitat Jena; Alemani

Mating Type Gene Homologues and Putative Sex Pheromone-Sensing Pathway in Arbuscular Mycorrhizal Fungi, a Presumably Asexual Plant Root Symbiont

<div><p>The fungal kingdom displays a fascinating diversity of sex-determination systems. Recent advances in genomics provide insights into the molecular mechanisms of sex, mating type determination, and evolution of sexual reproduction in many fungal species in both ancient and modern phylogenetic lineages. All major fungal groups have evolved sexual differentiation and recombination pathways. However, sexuality is unknown in arbuscular mycorrhizal fungi (AMF) of the phylum Glomeromycota, an ecologically vital group of obligate plant root symbionts. AMF are commonly considered an ancient asexual lineage dating back to the Ordovician, approximately 460 M years ago. In this study, we used genomic and transcriptomic surveys of several AMF species to demonstrate the presence of conserved putative sex pheromone-sensing mitogen-activated protein (MAP) kinases, comparable to those described in Ascomycota and Basidiomycota. We also find genes for high mobility group (HMG) transcription factors, homologous to <i>SexM</i> and <i>SexP</i> genes in the Mucorales. The <i>SexM</i> genes show a remarkable sequence diversity among multiple copies in the genome, while only a single <i>SexP</i> sequence was detected in some isolates of <i>Rhizophagus irregularis</i>. In the Mucorales and Microsporidia, the <i>sexM</i> gene is flanked by genes for a triosephosphate transporter (TPT) and a RNA helicase, but we find no evidence for synteny in the vicinity of the <i>Sex</i> locus in AMF. Nonetheless, our results, together with previous observations on meiotic machinery, suggest that AMF could undergo a complete sexual reproduction cycle.</p> </div

3D structure comparison of XYL1, XYL2 and TSP1.

<p>Structure alignment of XYL1 (pink), XYL2 (brown) and TSP1 (blue), showing that XYL protein shares all protein domains with TSP1, known to belong to the aldo/keto group of dehydrogenases.</p

Phylogenetic tree of mating type transcription factors.

<p>Maximum likelihood of amino acid sequences of <i>SexM</i> and <i>SexP</i> analysed with the LG+G+F (with four distinct gamma categories) phylogenetic model of mating type HMG-box proteins. The <i>Rhizophagus </i><i>spp.</i> sequences are highlighted in blue, mucoralean <i>SexM</i> sequences in green, and <i>SexP</i> in orange. The ascomycotan, basidiomycotan, as well as the human outgroup sequences are in black. The numbers at branches correspond to bootstrap support values generated with 1,000 bootstrap replicates. As previously described [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0080729#B21" target="_blank">21</a>,<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0080729#B56" target="_blank">56</a>], internal nodes are not statistically supported due to high evolutionary rates of mating type proteins [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0080729#B57" target="_blank">57</a>], leading to poorly supported topologies. However, the <i>R. irregularis</i> sequences s12765 and mucoralean <i>SexP</i> proteins fall into the same clade, while other <i>Rhizophagus </i><i>spp.</i> sequences are grouped together in the star-shaped cluster with mucoralean <i>SexM</i> and other fungal domains mating type proteins.</p