Molecular diversity of LysM carbohydrate-binding motifs in fungi

Akçapınar, Günseli Bayram; Kappel, Lisa; Sezerman, Uğur; Seidl‐Seiboth, Verena

doi:10.1007/s00294-014-0471-9

Cited by 91 publications

(96 citation statements)

References 52 publications

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“…1a, Supplementary Table 5). In other plant pathogens, these are involved in modifying fungal cell wall composition and/or capturing chitin residues to mask chitin-triggered immune signals and evade detection by the host plants [21][22][23][24][25] , suggesting similar roles in Armillaria.…”

Section: Resultsmentioning

confidence: 99%

Genome expansion and lineage-specific genetic innovations in the forest pathogenic fungi Armillaria

et al. 2017

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T he genus Armillaria causes root rot disease in both gymnoand angiosperms, in forests, parks, and even vineyards in more than 500 host plant species 1 across the world. Most Armillaria species are facultative necrotrophs, which, after colonizing and killing the root cambium, transition to a saprobic phase, decomposing dead woody tissues of the host. As saprotrophs, Armillaria spp. are white rot (WR) fungi, which can efficiently decompose all components of plant cell walls, including lignin, (hemi-)cellulose and pectin 2 . They produce fleshy fruiting bodies (honey mushrooms) that appear in large clumps around infected plants and produce sexual spores. The vegetative phase of Armillaria is predominantly diploid rather than dikaryotic like most basidiomycetes.Individuals of Armillaria can reach immense sizes and include the 'humongous fungus' , one of the largest terrestrial organisms on Earth 3 , measuring up to 965 hectares and 600 tons 4 , and can display a mutation rate ≅ 3 orders of magnitude lower than most filamentous fungi 5 . Individuals reach this immense size via growing rhizomorphs, dark mycelial strings 1-4 mm wide that allow the fungus to bridge gaps between food sources or host plants 1,6 (hence the name shoestring root rot). Rhizomorphs develop through the aggregation and coordinated parallel growth of hyphae, similar to some fruiting body tissues 7,8 . As migratory and exploratory organs, rhizomorphs can grow approximately 1 m yr −1 and cross several metres underground in search for new hosts, although roles in uptake and longrange translocation of nutrients have also been proposed 1,9,10 . Root contact by rhizomorphs is the main mode of infection by the fungus, which makes the prevention of recurrent infection in Armillariacontaminated areas particularly difficult 1 . Despite their huge impact on forestry, horticulture and agriculture, the genetics of the pathogenicity of Armillaria species is poorly understood. The only -omics data published so far have highlighted a substantial repertoire of plant cell wall degrading enzymes (PCWDE) and secreted proteins, among others, in A. mellea and A. solidipes 11,12 , while analyses of the genomes of other pathogenic basidiomycetes (such as Moniliophthora 13,14 , Heterobasidion 15 and Rhizoctonia 16 ) identified genes coding for PCWDEs, secreted and effector proteins or secondary metabolism (SM) as putative pathogenicity factors. However, the lifecycle and unique dispersal strategy of Armillaria prefigure other evolutionary routes to pathogenicity, which, along with other potential genomic factors (such as transposable elements 17 ) are not yet known.Here, we investigate genome evolution and the origin of pathogenicity in Armillaria using comparative genomics, transcriptomics

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Section: Resultsmentioning

confidence: 99%

Genome expansion and lineage-specific genetic innovations in the forest pathogenic fungi Armillaria

et al. 2017

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“…We identified other putative chitin-related proteins that have carbohydrate-binding module family 50 domains (CBM50, known as the LysM domain). Several LysM domains have chitin-binding ability, and several chitinases contain LysM domains (50). We found 7 proteins containing CMB50 domains; 5 of 7 such proteins were increased after harvest, and 2 of 5 were identified as DEGs in the fruiting body after harvest (g6653.t1 and g8231.t1) ( Table 4).…”

Section: Resultsmentioning

confidence: 87%

Lentinula edodes Genome Survey and Postharvest Transcriptome Analysis

Sakamoto

Nakade

Sato

et al. 2017

Appl Environ Microbiol

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Lentinula edodes is a popular, cultivated edible and medicinal mushroom. Lentinula edodes is susceptible to postharvest problems, such as gill browning, fruiting body softening, and lentinan degradation. We constructed a de novo assembly draft genome sequence and performed gene prediction for Lentinula edodes. De novo assembly was carried out using short reads from paired-end and mate-paired libraries and by using long reads by PacBio, resulting in a contig number of 1,951 and an N 50 of 1 Mb. Furthermore, we predicted genes by Augustus using transcriptome sequencing (RNA-seq) data from the whole life cycle of Lentinula edodes, resulting in 12,959 predicted genes. This analysis revealed that Lentinula edodes lacks lignin peroxidase. To reveal genes involved in the loss of quality of Lentinula edodes postharvest fruiting bodies, transcriptome analysis was carried out using serial analysis of gene expression (SuperSAGE). This analysis revealed that many cell wall-related enzymes are upregulated after harvest, such as ␤-1,3-1,6-glucan-degrading enzymes in glycoside hydrolase (GH) families GH5, GH16, GH30, GH55, and GH128, and thaumatin-like proteins. In addition, we found that several chitin-related genes are upregulated, such as putative chitinases in GH family 18, exochitinases in GH20, and a putative chitosanase in GH family 75. The results suggest that cell wall-degrading enzymes synergistically cooperate for rapid fruiting body autolysis. Many putative transcription factor genes were upregulated postharvest, such as genes containing high-mobility-group (HMG) domains and zinc finger domains. Several cell deathrelated proteins were also upregulated postharvest.IMPORTANCE Our data collectively suggest that there is a rapid fruiting body autolysis system in Lentinula edodes. The genes for the loss of postharvest quality newly found in this research will be targets for the future breeding of strains that keep fresh longer than present strains. De novo Lentinula edodes genome assembly data will be used for the construction of a complete Lentinula edodes chromosome map for future breeding.

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“…6%). Among these the LysM motif (CBM50) has attracted most attention [56]. This module has general N-acetylglucosamine binding properties and is therefore able to bind to chitin or chitin-like carbohydrates [57].…”

Section: Resultsmentioning

confidence: 99%

Comparative genomics to explore phylogenetic relationship, cryptic sexual potential and host specificity of Rhynchosporium species on grasses

et al. 2016

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BackgroundThe Rhynchosporium species complex consists of hemibiotrophic fungal pathogens specialized to different sweet grass species including the cereal crops barley and rye. A sexual stage has not been described, but several lines of evidence suggest the occurrence of sexual reproduction. Therefore, a comparative genomics approach was carried out to disclose the evolutionary relationship of the species and to identify genes demonstrating the potential for a sexual cycle. Furthermore, due to the evolutionary very young age of the five species currently known, this genus appears to be well-suited to address the question at the molecular level of how pathogenic fungi adapt to their hosts.ResultsThe genomes of the different Rhynchosporium species were sequenced, assembled and annotated using ab initio gene predictors trained on several fungal genomes as well as on Rhynchosporium expressed sequence tags. Structures of the rDNA regions and genome-wide single nucleotide polymorphisms provided a hypothesis for intra-genus evolution. Homology screening detected core meiotic genes along with most genes crucial for sexual recombination in ascomycete fungi. In addition, a large number of cell wall-degrading enzymes that is characteristic for hemibiotrophic and necrotrophic fungi infecting monocotyledonous hosts were found. Furthermore, the Rhynchosporium genomes carry a repertoire of genes coding for polyketide synthases and non-ribosomal peptide synthetases. Several of these genes are missing from the genome of the closest sequenced relative, the poplar pathogen Marssonina brunnea, and are possibly involved in adaptation to the grass hosts. Most importantly, six species-specific genes coding for protein effectors were identified in R. commune. Their deletion yielded mutants that grew more vigorously in planta than the wild type.ConclusionBoth cryptic sexuality and secondary metabolites may have contributed to host adaptation. Most importantly, however, the growth-retarding activity of the species-specific effectors suggests that host adaptation of R. commune aims at extending the biotrophic stage at the expense of the necrotrophic stage of pathogenesis. Like other apoplastic fungi Rhynchosporium colonizes the intercellular matrix of host leaves relatively slowly without causing symptoms, reminiscent of the development of endophytic fungi. Rhynchosporium may therefore become an object for studying the mutualism-parasitism transition.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-016-3299-5) contains supplementary material, which is available to authorized users.

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Molecular diversity of LysM carbohydrate-binding motifs in fungi

Cited by 91 publications

References 52 publications

Genome expansion and lineage-specific genetic innovations in the forest pathogenic fungi Armillaria

Genome expansion and lineage-specific genetic innovations in the forest pathogenic fungi Armillaria

Lentinula edodes Genome Survey and Postharvest Transcriptome Analysis

Comparative genomics to explore phylogenetic relationship, cryptic sexual potential and host specificity of Rhynchosporium species on grasses

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