Surprisingly, we found that both and lines exhibited resistance to the BAP-mediated reduction of RAM

Surprisingly, we found that both and lines exhibited resistance to the BAP-mediated reduction of RAM. on the time point. BAP Regulates Carbohydrate and Energy Metabolism in the Shoot To gain an insight into the biological role of the BAP-regulated proteins in both tissues, we categorized the BAP-regulated proteins according to the classification introduced by Bevan et al. (1998) and mapped the proteins in the annotated pathway maps provided by the Kyoto Encyclopedia of Genes and Genomes (KEGG; http://www.genome.jp/kegg/). We were able to map 68 of the 104 proteins (65%) identified in this study (Supplemental Figs. S1 and S2; Supplemental Tables S1 and S2). Protein classification according to the functional categories Mcl1-IN-2 of Bevan et al. HDAC11 (1998) revealed that the major portion Mcl1-IN-2 of BAP-regulated proteins (both up- and down-regulated) in both tissues were proteins involved in processing metabolites of different pathways, such as amino acid, nitrogen, nucleotide, sugar, and lipid metabolism (Fig. 2B). In the shoot, the second major class of BAP-regulated proteins contained proteins involved in energy-associated (energy acquisition or storage) processes, such as glycolysis, gluconeogenesis, and photosynthesis. Accordingly, using the KEGG database, we mapped most of the BAP-regulated proteins in the shoot to carbohydrate metabolism and energy acquisition (Supplemental Fig. S1A; Supplemental Table S2). The roles of these proteins have been annotated in basic metabolic pathways, including starch and Suc metabolism, glycolysis, and gluconeogenesis (Supplemental Fig. S1B), pyruvate metabolism (Supplemental Fig. S1C), carbon fixation (Supplemental Fig. S1D), citrate cycle (Supplemental Fig. S1E), and oxidative phosphorylation, photosynthesis, and chlorophyll metabolism (Supplemental Table S2). Shoot-identified proteins that were Mcl1-IN-2 not mapped but have previously been described in the literature also indicate CK control over protein import in chloroplasts (AT5G16620, PDE120/ATTIC40; Bdard et al., 2007) or control of meristem size via correct folding and/or complex formation of CLV proteins (AT4G24190, SHD/AtHSP90.7; Ishiguro et al., 2002). With regard to the time specificity of the shoot response, most of the aforementioned processes were found to be predominantly regulated at the early-response time point, except for purine, porphyrin, and chlorophyll metabolism, which were found to be regulated during the delayed response (Supplemental Fig. S1). BAP Targets Protein Synthesis and Destination in the Root As in the shoot, the most abundant category of proteins regulated by BAP in the root related to metabolism. However, in contrast to the shoot response, the second most represented category in the root constituted proteins involved in protein destination and storage, such as protein folding, targeting, modification, and proteolysis. At the same frequency, BAP regulated proteins in the root associated with protein synthesis, like ribosomal proteins and tRNA synthases (Fig. 2B). With respect to KEGG mapped pathways, one of the most affected processes in the root was RNA transport (Supplemental Fig. S2A). Four of the BAP-regulated proteins have been annotated as proteasome components, three of which we identified in the root (Supplemental Fig. S2B). Several other BAP-regulated proteins in the root have been annotated as proteins involved in the proteasome-mediated regulation of protein stability (AT1G16190, AT5G22610), in protein folding (AT3G03960, AT3G18190), or in protein processing in the endoplasmic reticulum (ER; Supplemental Fig. S2C). Regarding metabolic processes, proteins Mcl1-IN-2 involved in amino sugar and nucleotide sugar metabolism (Supplemental Fig. S2D), as well as Cys and Met metabolism (Supplemental Fig. S2E), were also.