Identification of Mycoparasitism-Related Genes in Trichoderma atroviride

Abstract

A high-throughput sequencing approach was utilized to carry out a comparative transcriptome analysis of Trichoderma atroviride IMI206040 during mycoparasitic interactions with the plant-pathogenic fungus Rhizoctonia solani. In this study, transcript fragments of 7,797 Trichoderma genes were sequenced, 175 of which were host responsive. According to the functional annotation of these genes by KOG (eukaryotic orthologous groups), the most abundant group during direct contact was "metabolism." Quantitative reverse transcription (RT)-PCR confirmed the differential transcription of 13 genes (including swo1, encoding an expansin-like protein; axe1, coding for an acetyl xylan esterase; and homologs of genes encoding the aspartyl protease papA and a trypsin-like protease, pra1) in the presence of R. solani. An additional relative gene expression analysis of these genes, conducted at different stages of mycoparasitism against Botrytis cinerea and Phytophthora capsici, revealed a synergistic transcription of various genes involved in cell wall degradation. The similarities in expression patterns and the occurrence of regulatory binding sites in the corresponding promoter regions suggest a possible analog regulation of these genes during the mycoparasitism of T. atroviride. Furthermore, a chitin-and distance-dependent induction of pra1 was demonstrated.Due to hazardous chemical fungicides affecting human health (4) and the environment (9), the application of biological control agents like Trichoderma spp. is a promising alternative for plant protection (17). Members of the genus Trichoderma (teleomorph Hypocrea) are potent mycoparasitic fungi that not only compete for nutrients but also secrete cell wall-degrading enzymes (CWDEs) such as chitinases, glucanases, and proteases, among others, and excrete secondary metabolites that are active against a number of plant-pathogenic fungi (15,28,29,41,58). In addition to an increase in enzyme secretion during interactions with host fungi, it was shown previously that differentiation processes occur, leading to morphological changes and the formation of penetration structures in mycoparasitic Trichoderma spp. (7,22). Interestingly, mycoparasitism is not a mere result of physical contact but may be proceeded by an early recognition process that leads to the induction of gene expression of hydrolytic enzymes (e.g., prb1 [18] and ech42 [67]).In recent years, a number of studies have identified enzymes and effectors involved in host recognition and the mycoparasitic responses of Trichoderma (40, 46, 51); however, their modes of action and the mechanisms determining host specificity remain poorly understood. Mainly expressed-sequencetag (EST) libraries of different Trichoderma strains obtained under various growth conditions have contributed significantly to the large-scale identification of active genes (63, 64). Additionally, diverse DNA array experiments have determined that an expansin-like protein, aspartyl proteases, and hydrophobins, among others, are involved in the biocontrol a...

The Genomes of Three Uneven Siblings: Footprints of the Lifestyles of Three Trichoderma Species

“…In a plate confrontation assay, another ABC transporter of T. atroviride, TA_289170, was slightly downregulated before physical contact with the host compared to the control samples. Interestingly, genes involved in transport and metabolism of secondary metabolites were shown to be downregulated during mycoparasitic interactions (355). No homologs of TA_289170 were predicted in the genome of T. reesei or T. virens.…”

“…Mycoparasitism-related genes of T. atroviride were identified in a comparative transcriptome analysis during confrontation of T. atroviride with R. solani (355). Two genes encoding sugar transporters (TA_133590 and TA_150280) were shown to be downregulated compared to control conditions, independent of physical distance.…”

“…Genome-wide gene expression during mycoparasitism has been studied, mainly with microarray and EST-based approaches (22,25,355,356). Besides more indirect growth conditions related to mycoparasitism, e.g., growth on fungal cell walls or chitin as carbon source, the experimental design often used to study mycoparasitism entails plate confrontation assays.…”

Trichoderma Research in the Genome Era

“…An extensive survey of Trichoderma genomes revealed the presence of three types of peptaibol synthetases: the long (18-20 modules), medium (14 modules), and short (7 modules) (30, 96). One of the most interesting findings driven by genomics was the ability of Tex2, the 14-module NRPS, to synthesize 11-and 14-residue peptaibols in T. virens (102), later confirmed in T. reesei (38). On the basis of sequence alignment and the absence of an 11-module peptaibol synthase in either of the genomes, module skipping is suggested to be the mechanism of synthesis of these two classes …”

“…Using a high-throughput transcriptome analysis, 175 genes from T. atroviride were identified that responded to the presence of R. solani. Strongly upregulated genes include swo1 and axe1 as well as genes encoding aspartyl protease PapA and a trypsin-like protease Pra1 (102).…”