Gene expression analysis of the biocontrol fungus Trichoderma harzianum in the presence of tomato plants, chitin, or glucose using a high-density oligonucleotide microarray

Abstract

BackgroundIt has recently been shown that the Trichoderma fungal species used for biocontrol of plant diseases are capable of interacting with plant roots directly, behaving as symbiotic microorganisms. With a view to providing further information at transcriptomic level about the early response of Trichoderma to a host plant, we developed a high-density oligonucleotide (HDO) microarray encompassing 14,081 Expressed Sequence Tag (EST)-based transcripts from eight Trichoderma spp. and 9,121 genome-derived transcripts of T. reesei, and we have used this microarray to examine the gene expression of T. harzianum either alone or in the presence of tomato plants, chitin, or glucose.ResultsGlobal microarray analysis revealed 1,617 probe sets showing differential expression in T. harzianum mycelia under at least one of the culture conditions tested as compared with one another. Hierarchical clustering and heat map representation showed that the expression patterns obtained in glucose medium clustered separately from the expression patterns observed in the presence of tomato plants and chitin. Annotations using the Blast2GO suite identified 85 of the 257 transcripts whose probe sets afforded up-regulated expression in response to tomato plants. Some of these transcripts were predicted to encode proteins related to Trichoderma-host (fungus or plant) associations, such as Sm1/Elp1 protein, proteases P6281 and PRA1, enchochitinase CHIT42, or QID74 protein, although previously uncharacterized genes were also identified, including those responsible for the possible biosynthesis of nitric oxide, xenobiotic detoxification, mycelium development, or those related to the formation of infection structures in plant tissues.ConclusionThe effectiveness of the Trichoderma HDO microarray to detect different gene responses under different growth conditions in the fungus T. harzianum strongly indicates that this tool should be useful for further assays that include different stages of plant colonization, as well as for expression studies in other Trichoderma spp. represented on it. Using this microarray, we have been able to define a number of genes probably involved in the transcriptional response of T. harzianum within the first hours of contact with tomato plant roots, which may provide new insights into the mechanisms and roles of this fungus in the Trichoderma-plant interaction.

Comparative study of Trichoderma gene expression in interactions with tomato plants using high-density oligonucleotide microarrays

“…TCTP/P23 overexpression in human cells leads to cell elongation resembling hyphal growth in fungi. In a previous study, the induction of the gene encoding the protein homologous to TCTP in T. harzianum T34 in contact with tomato roots was also observed (Samolski et al, 2009). These results suggest that P23 could be related to hyphal growth and the plant growth benefit derived from T7 and T34 root colonization.…”

“…A self-designed Trichoderma HDO microarray (Roche-NimbleGen) was constructed similarly to a previous Trichoderma HDO microarray (Samolski et al, 2009). The microarray was designed against 12 662 Trichoderma unique sequences (9510 singlets and 3152 contigs) (Samolski et al, 2009), 9129 genes of T. reesei QM6a, and 11 643 genes of T. virens Gv29-8 (T87).…”

“…The microarray was designed against 12 662 Trichoderma unique sequences (9510 singlets and 3152 contigs) (Samolski et al, 2009), 9129 genes of T. reesei QM6a, and 11 643 genes of T. virens Gv29-8 (T87). The 12 662 Trichoderma unique sequences came from 14 237 Trichoderma spp.…”

“…In the present study, an HDO microarray composed of 374 824 60-mer probes was constructed by adding 11 643 genes of the annotated genome of the biocontrol strain Trichoderma virens (Hypocrea virens) Gv29-8 to the previously described Trichoderma HDO microarray that encompassed 12 662 unique sequences derived from a Trichoderma expressed sequence tag (EST) collection obtained from 12 strains belonging to eight species (Vizcaíno et al, 2006(Vizcaíno et al, , 2007, and 9129 genes of Trichoderma reesei (Samolski et al, 2009), and was used to compare the transcriptional responses of Trichoderma hamatum IMI 224801 and T. harzianum CECT 2413, which both promote tomato growth, and T. virens Gv29-8, which showed detrimental effects in our study, during the early stages of their interactions with tomato roots.…”

“…Macroarray analyses have been applied to study the gene expression of four species of Trichoderma during their interaction with cacao seedlings (Bailey et al, 2006), and of Trichoderma harzianum during the early colonization of tomato roots (Chacó n et al, 2007), although one limitation to such studies has been the low number of genes tested. In a recent study, a Trichoderma high-density oligonucleotide (HDO) microarray was designed to analyse the gene expression of T. harzianum CECT 2413 under different growth conditions, including tomato root colonization (Samolski et al, 2009). …”