Comparative genomics, proteomics and transcriptomics give new insight into the exoproteome of the basidiomycete Hebeloma cylindrosporum and its involvement in ectomycorrhizal symbiosis

Abstract

SummaryExtracellular proteins play crucial roles in the interaction between mycorrhizal fungi and their environment. Computational prediction and experimental detection allowed identification of 869 proteins constituting the exoproteome of Hebeloma cylindrosporum. Small secreted proteins (SSPs) and carbohydrate-active enzymes (CAZymes) were the two major classes of extracellular proteins.Twenty-eight per cent of the SSPs were secreted by free-living mycelia and five of the 10 most abundant extracellular proteins were SSPs. By contrast, 63-75% of enzymes involved in nutrient acquisition were secreted.A total of 150 extracellular protein-coding genes were differentially expressed between mycorrhizas and free-living mycelia. SSPs were the most affected. External environmental conditions also affected expression of 199 exoproteome genes in mycorrhizas. SSPs displayed different patterns of regulation in response to presence of a host plant or other environmental signals. Several of the genes most overexpressed in the presence of organic matter encoded oxidoreductases.Hebeloma cylindrosporum has not fully lost its ancestral saprotrophic capacities but rather adapted them not to harm its hosts and to use soil organic nitrogen. The complex and divergent patterns of regulation of SSPs in response to a symbiotic partner and/or organic matter suggest various roles in the biology of mycorrhizal fungi.

Reflection on Molecular Approaches Influencing State-of-the-Art Bioremediation Design: Culturing to Microbial Community Fingerprinting to Omics

“…Chemical analyses of proteins (proteomics) and metabolites (metabolomics) are beginning to be used to complement genomic and transcriptomic studies. For example, Dore et al predicted the proteins and extracellular enzymes secreted by a fungus from analyzing the genome and transcriptome and then used liquid chromatography combined with mass spectrometry to detect what was actually secreted by the fungus under environmental conditions (Dore et al 2015). In another study, Konopka and Wilkins used meta-transcriptomics and meta-proteomics to predict and verify Geobacter spp.…”

Genomic Data Quality Impacts Automated Detection of Lateral Gene Transfer in Fungi

“…Lower quality genomes were excluded based on sequencing read coverage, number of scaffolds, and sizes of the longest scaffolds, with the exception of the endophytes, which were all retained. These species include: symbiotic endophytic fungi [ Daldinia eschscholtzii , Rhodotorula graminis (Firrincieli et al 2015), Xylona heveae (Gazis et al 2016)], mycorrhizal fungi [ Cenococcum geophilum , Choiromyces venosus , Cortinarius glaucopus , Gyrodon lividus , Hebeloma cylindrosporum (Kohler et al 2015; Dore et al 2015), Laccaria bicolor (Martin et al 2008), Meliniomyces bicolor (Grelet et al 2009), Oidiodendron maius (Kohler et al 2015), Paxillus involutus (Kohler et al 2015), Pisolithus tinctorius (Kohler et al 2015), Terfezia boudieri , Tuber melanosporum (Martin et al 2010), and Wilcoxina mikolae )] and plant pathogens [ Bipolaris sorokiniana (Ohm et al 2012; Condon et al 2013), Blumeria graminis (Spanu et al 2010), Botryosphaeria dothidea , Botrytis cinerea (Staats and van Kan 2012; Amselem et al 2011), Cercospora zeae-maydis , Colletotrichum graminicola (O’Connell et al 2012), Cronartium quercuum , Didymella exigua , Fomitiporia mediterranea (Floudas et al 2012), Fusarium graminearum (Cuomo et al 2007), Leptosphaeria maculans (Rouxel et al 2011), Magnaporthe oryzae (Dean et al 2005), Mixia osmundae (Toome et al 2014), Passalora fulva (de Wit et al 2012; Ohm et al 2012), Phaeosphaeria nodorum (Hane et al 2007), Sclerotinia sclerotiorum (Amselem et al 2011), Setosphaeria turcica (Ohm et al 2012; Condon et al 2013), Sporisorium reilianum (Schirawski et al 2010), Verticillium alfalfae (Klosterman et al 2011), and Zopfia rhizophila ]. Transcript sequences were downloaded for all species, also from the JGI database.…”

Comparative Analysis of Secretomes from Ectomycorrhizal Fungi with an Emphasis on Small-Secreted Proteins

“…Pellegrin et al (2015) and previous large-scale studies highlighted many other SSPs with unknown function (Martin et al, 2008; Doré et al, 2015; Kohler et al, 2015). …”

“…Later, SSPs have been identified in the secretome of the ECM fungi L. bicolor and Hebeloma cylindrosporum cultured without their host (Vincent et al, 2012; Doré et al, 2015). Pellegrin et al (2015) predicted SSPs that are shared by ECM, saprotrophic, and pathogenic fungi, suggesting conserved mechanisms in hyphal development, fruiting body formation, or interaction with other soil organisms and the environment.…”