Chapter 3 66 3.2.5 Internode data revealed an FR-effect on growth-related GO terms To gain insight into the processes underpinning cell elongation and division that contribute to internode elongation, we focused on GO terms that could be associated with these processes. Firstly, we looked into GO term “nucleoside triphosphate catabolic process”, which refers to ATP and GTP breakdown or hydrolysis into their respective nucleoside diphosphate forms or even further into nucleoside monophosphates (https://www.ebi. ac.uk/QuickGO/term/GO:0009143). This process typically involves the release of energy stored within the high-energy phosphate bonds of these triphosphate molecules. This GO term is enriched among the initially upregulated DEGs in whole internode, and at the later timepoints, it is enriched specifically in the pith FR response (Figure 3.7). Secondly, we observed an enrichment of pathways linked to carbohydrate metabolism within the FR-upregulated DEGs, specifically carbohydrate metabolic process, nucleoside triphosphate catabolic process, nucleoside-triphosphate diphosphatase activity. This collective enrichment is an indication of FR enhancing growth. Furthermore, this pattern appears intermittently across specific timepoints throughout the entire internode. For cell division and enlargement to occur, it is imperative that cell walls undergo a loosening process. We noted that molecular components (GO terms: cellulose biosynthetic process, cellulose synthase (UDP-forming) activity, membrane, cell wall modification) linked with cell wall loosening are also enriched in FR-treated pith compared to whole internode (Figure 3.9). Similarly many transmembrane transport activities are enriched in FR-treated pith (Figure 3.9), potentially indicating changes in osmotic potential in pith. 3.2.6 At 6h FR treatment, energy exchanging activities were enriched The GO enrichment analysis (Figure 3.7) unveiled a noteworthy energy exchange pattern. Specifically, after 6 hours of FR treatment, we observed an enrichment in aerobic respiration and cytochrome-c oxidase activity within the internode upregulated DEGs. This signal of increased metabolic activity could indicate a more rapid respiration process, thereby providing increased energy for internode growth in response to FR. Furthermore, we identified enriched GO terms related to energy exchange activities essential for maintaining vital cell functions, including protein dimerization and pyruvate metabolism. In the context of protein dimerization, the synthesis of protein subunits demands energy, often in the form of ATP. However, the subsequent dimerization step
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