Including the transcription factors discussed above involved in the regulation of lipid metabolism and pleiotropic drug resistance, in total more than 30 transcription factors were up-regulated in response to pterostilbene (see Additional file 3: List of pterostilbene-responding genes in the "cell wall," "transcription factor activity," and "mitochondrion" categories). Of particular interest are genes encoding transcription factors involved in mitochondrial function (RTG1 and RTG2), cell wall-related functions (RLM1), and methionine metabolism (MET4 and MET31), considering that these functional categories were over-represented in the gene ontology analysis (Table (Table3).3). Thus, the genes present in these functional categories include transcription factors as well as their cognate targets, suggesting the modulation of these processes, at least in part, via altered levels of these specific transcription factors in response to pterostilbene exposure.
In the Cellular Component-based ontology analysis, genes required for mitochondrial and cell wall-related functions were also over-represented (Table (Table3).3). The cell wall category had a z-score of 8.22 (Table (Table3),3), and most of the genes assigned within this category were down-regulated by pterostilbene treatment (Table (Table3).3). The majority of these genes are involved in mating responses [e.g., FIG1, FIG2, SAG1, AGA1, MF(ALPHA)1, and MF(ALPHA)2, see Additional file 3: op. cit.], which is also in agreement with the over-representation of the gene ontology term "reproduction" in the Biological Process category (z-score of 3.01, Table Table3).3). Additional down-regulated cell wall-related genes included chitin synthase 2(CHS2), cell wall mannoproteins (TIP1, CWP1) and a major exo-1,3-beta-glucanase of the cell wall (EXG1) (see Additional file 3: op. cit.). These genes are responsible for the biosynthesis of three major constituents (chitin, mannoproteins and glucan) found in yeast cell walls [38]. The gene BAG7 (Rho GTPase activating protein), however, was induced by ~137-fold in pterostilbene treated cells (see Additional file 3: op. cit.). It has been reported that Bag7p plays a role in the control of cell wall synthesis and is involved in regulating key components of the cell wall stress-response pathway [39].
With respect to mitochondrial genes, it is interesting to note that more than 100 genes involved in diverse mitochondrial functions were up-regulated by pterostilbene treatment (Table (Table3,3, and Additional file 3: op. cit.). These genes play important roles in respiration, electron transport, mitochondrial protein targeting, and mitochondrial protein synthesis (see Additional file 3: op. cit.).
Of particular interest was the finding that a group of genes involved in sulfur metabolism was significantly over-represented, generating a z-score of 10.5 for the category "sulfur amino acid metabolism," (the highest score obtained in the present study). Within this category, a subset of genes assigned to the ontology term "methionine metabolism" (z-score of 11.78) were down-regulated upon exposure to pterostilbene (Table (Table3).3). Of the 21 genes assigned to this ontology term on the array, eleven were differentially regulated. As shown in Figure Figure22 and Table Table6,6, all responsive genes involved in sulfur-containing amino acid biosynthesis were down-regulated, with the exception of MET4 (transcriptional activator) and MET31 (transcriptional regulator), which were up-regulated (Table 6).