Although Trichoderma is widely used in the field to control plant diseases and its commercialization has significantly increased, our understanding of the mechanisms used by Trichoderma to antagonize phytopathogenic fungi is still very limited.

Little is known on the signaling pathways that determine host recognition, although there is evidence of the involvement of conserved signaling pathways such as heterotrimeric G proteins in hyphal coiling. At later stages of the interaction, MAPK pathways appear to participate in the regulation of the expression of MRGs. However, we are still just beginning to untangle the networks determining host recognition.

An important number of genes encoding cell-wall degrading enzymes have been cloned. In most cases, their expression correlates with conditions that simulate the actual interaction with the host and some of them have even been used to generate improved strains. However, the fact that several of the cloned MRGs respond to multiple environmental signals that they are subjected to catabolite repression, and that none of them is expressed specifically at the sites of interaction, suggests that these genes maybe part of a specialized saprophytic response. Thus, the corresponding enzymes are more likely to participate in the utilization of the host's cellular components as a food supply at the end of the parasitic process. An alternative explanation is that the interaction of Trichoderma with a host is interpreted by the parasite as a stress signal and that MRGs are in fact stress responsive genes. It is likely that genes coding for key enzymes such as those expressed specifically at the site of interaction where penetration or cell wall perforations are observed, have not been yet identified. The use of functional genomics strategies will certainly be a major step towards the identification of genes playing key roles in mycoparasitism by Trichoderma. Trichoderma has already proven to be an important source of genes for engineering plants for pathogen resistance. Yet, there is still a complete battery of genes that should be tested for this purpose, as well as combinatory strategies using several Trichoderma genes. Induction of defense responses in host plants and plant growth promotion are important attributes of Trichoderma, whose study was neglected for a long time. The recent evidence on these two aspects makes Trichoderma an even more attractive organism for large-scale application as a biological control agent. In spite of our limited knowledge on the mechanisms underlying the mycoparasitic activity of Trichoderma, it is clear that it is an excellent model system for the study of interfungal parasitic relationships and that it has an enormous potential for a variety of biotechnological applications.

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