Info

1,504

chs2/wild type

1,523

1,717

3,240

chs3/wild type

1,293

1,426

2,719

Data include numbers of probe sets on the Affymetrix ATH1 Genome Array differentially expressed at p < 0.05 and induced or repressed by a factor of at least 4

Data include numbers of probe sets on the Affymetrix ATH1 Genome Array differentially expressed at p < 0.05 and induced or repressed by a factor of at least 4

plants. Doing so, led to the identification of 1,504, 3,240, and 2,719 probe sets whose expression significantly changed after exposure to chilling in chsl, chs2, and chs3 mutants, respectively (Table 7.1).

To define the degree of similarity and differences between gene expression patterns in the various class 1 chs mutants in response to chilling, we conducted a Venn diagram comparison (Fig. 7.7). It was found that the expression of a large group of 1,426 probe sets was similarly affected by chilling in all class 1 chs mutants, and that of 1,207 additionally genes were similarly affected in both chs2 and chs3 mutants (Fig. 7.7). Thus, chs1, chs2, and chs3 mutants endure similar molecular responses following exposure to chilling stress.

In order to assign the chilling-induced differentially expressed genes in chsl, chs2, and chs3 mutants into corresponding molecular functions, we performed functional categorization analysis using the MapMan software (Thimm et al. 2004). Doing so revealed that the main functional categories up-regulated by chilling in the mutants were "stress," "protein," and "signaling," whereas the main categories down-regulated by chilling chsl chs2

(1504 probe sets) (3240 probe sets)

chsl chs2

(1504 probe sets) (3240 probe sets)

chs3 (2719 probe sets)

Fig. 7.7 Venn diagram illustrating the overlapping and differences in gene expression patterns among the various chsl, chs2, and chs3 chilling-responsive regulons. The numbers on the diagram indicate the amount of overlapped probe sets chs3 (2719 probe sets)

Fig. 7.7 Venn diagram illustrating the overlapping and differences in gene expression patterns among the various chsl, chs2, and chs3 chilling-responsive regulons. The numbers on the diagram indicate the amount of overlapped probe sets were "photosynthesis" and "tetrapyrrole synthesis," "major carbohydrate metabolism," "cell wall," and "lipid metabolism" (Table 7.2). A more or less similar response consisting differential expression of stress, photosynthesis, and protein, carbohydrate and lipid metabolism genes, following exposure to chilling were reported also in several other chilling-sensitive commodities, such as rice, sunflower and potato as well as chilling-tolerant poplar trees (Yan et al. 2006; Fernandez et al. 2008; Oufir et al. 2008; Maestrini et al. 2009). The up-regulated category of "protein" included massive up-regulation of genes involved in protein degradation, and particularly transcripts encoding members of RING finger and F-BOX proteins belonging to the ubiquitin protein degradation pathway. In addition, the "protein" category further included massive down-regulation of genes involved in protein synthesis. The up-regulated category of "signaling" included mainly up-regulation of receptor kinase genes and calcium signaling genes, as previously reported (Bhattacharjee 2009) . The observed down-regulation in "lipid metabolism"

genes included mainly suppression of transcripts involved in fatty acid synthesis and desaturation; the latter is known to be a crucial factor required for adaptation to chilling (Murata et al. 1992; Nishida and Murata 1996).

The overall meanings of these findings are that under chilling conditions class 1 chs mutants are defective in normal gene expression related to the photosynthesis machinery and carbohydrate metabolism, and cell wall and lipid metabolism. In addition, the chs mutants were in severe stress as indicated by massive up-regulation of stress genes, and suffered from imbalanced protein metabolism (suppression of protein synthesis and induction of protein degradation).

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