Genomic profiling of carbohydrate metabolism in the ectomycorrhizal fungus Tuber melanosporum

Abstract

Summary• Primary carbohydrate metabolism plays a special role related to carbon ⁄ nitrogen exchange, as well as metabolic support of fruiting body development, in ectomycorrhizal macrofungi. In this study, we used information retrieved from the recently sequenced Tuber melanosporum genome, together with transcriptome analysis data and targeted validation experiments, to construct the first genomewide catalogue of the proteins supporting carbohydrate metabolism in a plantsymbiotic ascomycete.• More than 100 genes coding for enzymes of the glycolysis, pentose phosphate, tricarboxylic acid, glyoxylate and methylcitrate pathways, glycogen, trehalose and mannitol metabolism and cell wall precursor were annotated. Transcriptional regulation of these pathways in different stages of the T. melanosporum lifecycle was investigated using whole-genome oligoarray expression data together with real-time reverse transcription-polymerase chain reaction analysis of selected genes.• The most significant results were the identification of methylcitrate cycle genes and of an acid invertase, the first enzyme of this kind to be described in a plantsymbiotic filamentous fungus.• A subset of transcripts coding for trehalose, glyoxylate and methylcitrate enzymes was up-regulated in fruiting bodies, whereas genes involved in mannitol and glycogen metabolism were preferentially expressed in mycelia and ectomycorrhizas, respectively. These data indicate a high degree of lifecycle stage specialization for particular branches of carbohydrate metabolism in T. melanosporum.

Simple Genetic Tools to Study Fruiting Body Development in Fungi

“…Fruiting body mutants are now available for many fungi other than P. anserina, including Sordaria macrospora [27], N. crassa [28], A. nidulans [29] and Coprinopsis cinerea (formely Coprinus cinereus) [30,31] and could be analyzed using similar methods. They are complementary to the now more widespread large scale analyses of transcriptomes during fruiting body development as performed in the ascomycetes Fusarium graminearum and Fusarium verticilloides [32][33][34], N. crassa [35,36], S. macrospora [37], Pyronema confluens [38], Tuber melanosporum [39][40][41], Cordyceps militaris [42] and Ophiocordyceps sinensis [43], as well as in the basidiomycetes C. cinerea [44], Moniliophthora perniciosa [45], Agrocybe aegerita [46], Lentinula edodes [47,48], Auricularia polytricha [49] and Ganoderma lucidum [50].…”

Truffle Research in the Post-Genomics Era

“…Interestingly, the presence of a gene coding for a secreted acid invertase has suggested that T. melanosporum is able to hydrolyze sucrose, unlike other ectomycorrhizal fungi, such as Laccaria bicolor (Martin et al 2008(Martin et al , 2010Ceccaroli et al 2011). In addition, transcripts of this gene have been reported to accumulate in the Hartig net compartment, i.e.…”

“…These data have improved the T. melanosporum genomic structural annotation and led to the identification of previously unidentified transcripts, exons, untranslated regions (UTRs) that extended in silico gene models and alternative splicing events. In addition, RNA-seq transcript profiling, which provides a global view on the transcriptome complexity, has been used for detailed analyses of specific gene groups (Balestrini et al 2012;Ceccaroli et al 2011;Montanini et al 2011;Rubini et al 2011a). More recently, the functional characterization of novel proteins has been obtained by Islam et al (2013).…”

“…The carbohydrate metabolism has been also investigated (Ceccaroli et al 2011), due to its special role related to nutrient exchange with the host plants and in metabolic support of fruiting body development. Interestingly, the presence of a gene coding for a secreted acid invertase has suggested that T. melanosporum is able to hydrolyze sucrose, unlike other ectomycorrhizal fungi, such as Laccaria bicolor (Martin et al 2008(Martin et al , 2010Ceccaroli et al 2011).…”

Current progress on truffle submerged fermentation: a promising alternative to its fruiting bodies

“…The genome sequence of the T. melanosporum black truffle fruiting body suggests that truffles possess all the genes needed to synthesize the key constituents of the truffle aroma (Martin et al 2010), and the Post-Genomics Era has been open to truffle research (Balestrini and Mello 2014;Kües and Martin 2011). Recently, the genomewide transcriptome studies have unraveled several developmental and metabolic pathways regulated by symbiosis and fruiting body formation, as well as environmental factors (Amicucci et al 2011;Bolchi et al 2011;Ceccaroli et al 2011;Montanini et al 2011;Zampieri et al 2011). However, the genes and enzymes involved in the biosynthesis of aroma active compounds, umami amino acids and 5′-nucleotides, and phytosterol are still unclear.…”