Figure find more 4 Expression profiles of five known genes of T. harzianum determined by Northern blot hybridization. The fungus was cultured in MS basal medium alone

or in the presence of tomato plants (MS-P), 2% glucose (MS-G), or 1% chitin (MS-Ch), as described in Methods. Fungal 18S rDNA was used as a loading control. Identification of T. harzianum genes expressed in response to tomato plants Since we were interested in identifying the genes induced in T. harzianum CECT 2413 by the presence of tomato plants, we selected the 257 probe sets affording significant differential expression in MS-P vs. MS (fold-change greater than 2.0 and FDR = 0.23; see additional file 3), and the corresponding transcript sequences were annotated according to the GO classification and the hierarchical structure using the Blast2GO suite [27]. GO categories were assigned to 85 of the 257 sequences examined (see additional file 4) whereas another 57 had no results after mapping or annotation processes (many of them were hypothetical proteins), and the remaining 115 sequences did not yield significant hits in the databases. As summarized in additional file 5, the annotated sequences represented a total of 46 different genes. Additionally, three sequences without Blast2GO annotation (T34C26, T34C242 and L10T34P112R10010)

but corresponding to three portions of the known protein QID74 [Prot: O74567] of T. harzianum CECT 2413 were also included in additional file 5. Within the genes identified as showing up-regulation in MS-P vs. MS, about 45% were

genes encoding homologues of proteins involved in metabolic pathways, mainly enzymes for carbohydrate, Doramapimod in vivo lipid and amino acid metabolism, but also enzymes for vitamin and cofactor biosynthesis, and energy- Rebamipide and detoxification- related processes. Interestingly, some of these up-regulated genes (encoding O-glycosyl hydrolase family 2, aldose 1-epimerase, dihydroxyacetone kinase, acid sphingomyelin phosphodiesterase, GTP cyclohydrolase I, glutathione-dependent formaldehyde-activating enzyme, plus two hypothetical proteins) were classified according to Blast2GO in the functional category “”growth or development of symbiont on or near host surface”" since their homologues in Magnaporte grisea were differentially expressed during appresorium formation [28]. Proteins related to carbohydrate metabolism included several enzymes of the glycolysis/gluconeogenesis pathways plus a phosphoketolase of the pentose phosphate pathway, and a 1,3-beta-glucan synthase involved in cell wall biosynthesis. The three up-regulated genes with homologues in lipid metabolism corresponded to a phosphatidylserine synthase participating in phospholipid biosynthesis; a dihydroxyacetone kinase involved in glycerolipid metabolism, and an acid sphingomyelin phosphodiesterase, responsible for breaking sphingomyelin down into phosphocholine and ceramide.

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