Trichoderma proteins with an ankyrin domain

Species of the multicellular fungus Trichoderma are among the most frequent mitosporic fungi (teleomorph Hypocrea, Hypocreales, Ascomycota, Dykaria) commonly detected in cultivation-based surveys. They have been isolated from an innumerable diversity of natural and artificial substrata what demonstrates their high opportunistic potential and adaptability to various ecological conditions. Recent genome sequencing and evolutionary analysis has revealed that the innate nature of Trichoderma is that of a mycotrophic fungus, but that this trait gave rise to development of a broad environmental opportunism from biotrophic interactions with plants and animals to saprotrophic nutrition. Systematic analysis of the genome content of Trichoderma revealed a unique inventory among the Pezizomycotina. The most striking finding is an enrichment of genes coding proteins with ankyrin domains that outnumbers all other fungi, and the combination of these ankyrin domains with HET and NACHT domains. In this project, we are therefore planning a systematic investigation of the ankyrin repertoire of Trichoderma, using a transcriptomic (deep RNA sequencing) and cell biological (gene knock out, gene overexpression) approach to learn the involvement of these proteins in the various life-styles of Trichoderma.

Molds in the genus Trichoderma (Ascomycota, Hypocreales) display a unique nutritional versatility. They can feed on other fungi, attack animals, and degrade plant debris. The later property is so efficient that one species (T. reesei) is commercially used for the production of cellulolytic enzymes required for making biofuels and other industry. Within the realm of this project, we compiled the current knowledge on T. reesei ecology, physiology, and genomics to present a holistic view on the natural behavior of the organism. This is critical for science-driven further improvement of the biotechnological applications of this fungus. The findings will be helpful for the further development of highly efficient enzyme mixtures for lignocellulosic biomass conversion. The core of the project further reported an extensive study about the evolution of plant cell wall degrading carbohydrate active enzymes in Trichoderma by comparing 9 whole genomes of Trichoderma (6 of which were sequenced under this project) with 12 other reference hypocrealean genomes. The major outcome of this study was the detection of the massive lateral transfer of genes required for the degradation of plant biomass to Trichoderma genomes from fungi that Trichoderma can parasitize. These exciting results allowed us to propose a concept of adelphoparasitism (parasitism on closely related organisms) as an important factor contributing to the architecture of Trichoderma genomes and prompted the follow-up research on the lateral gene transfer (LGT) in fungi. We also published the detailed evolutionary and LGT assessment of all Trichoderma cellulolytic enzymes that may serve as a reference for the scientists researching these genes for industrial applications. Subsequently, LGT was also hypothesized as one of the probable reason for expansion of Ankyrin domain containing proteins in Trichoderma. Through large scale comparative genomics, we investigated the expansion of Ankyrin domain containing (ANKdc) proteins in most aggressive Trichoderma spp. All ANKdc genes were manually re-annotated in 18 hypocrealean genomes (including 10 Trichoderma spp.). The proportion of genes containing ANK-domain as the only identified domain (pure ankyrins ) was revealed. It was also revealed that about 50% of Ankyrins in genus Trichoderma are orphomes (all the proteins in a genome/group of genomes that do not have homologs in close taxonomic relatives). Further, owing to Trichodermas carbohydrate degrading enzymes, species like T. aggressivum and T. pleuroti are also known for causing serious losses in mushroom production worldwide. NRPS genes that enables biosynthesis of peptaibols, potential growth inhibitors of mushroom mycelia, were characterized in genomes of both of these fungi. In contrary, the property of Trichoderma species to be able to attack other fungi, is also employed in biocontrol. We genetically characterized the use of T. guizhouense NJAU 4742 (Harzianum clade) for suppressing the causative agent of banana wild disease Fusarium oxysporum f. sp. cubense 4 (Foc4). Additionally, in a book chapter, we focussed on both potential benefits and pitfalls of applications of mycoparasitic fungi for protection of agricultural crops were discussed.