Transcriptome changes of tomato internode elongation induced by far-red light 3 83 3.3.1 Auxin could be the key regulator for elongation in tomato SAS “Response to auxin” GO term was highly enriched in our GO analysis, largely due to many SAURs (Small Auxin-Up-regulated RNAs) upregulated in our data. The actual auxin pathway DEGs had changes of up to 38-fold. Auxin function in cell elongation and stem elongation has already been reported before (Kutschera and Niklas, 2007; Bou-Torrent et al., 2014), but here, we also found auxin response upregulated specifically in pith, linked to the pith cell elongation and division patterns that we reported in the Chapter 2. ATP and ADP activity and carbohydrate metabolism pathways were also enriched in FR-upregulated DEGs in pith (Figure 3.7), which might indicate auxin-induced the cell division and expansion activities are especially active in pith compared to the whole internode. SAURs are a class of small, non-coding RNAs that are involved in the regulation of auxin signaling in plants. SAURs have been implicated in a wide range of physiological processes in plants, including growth, development, and stress responses (Ren and Gray, 2015; Stortenbeker and Bemer, 2019). In the context of SAS, SAURs have been shown to be upregulated in response to low R:FR ratio in Arabidopsis. Specifically, SAUR19 and SAUR20 have been identified as key regulators of hypocotyl elongation in Arabidopsis under low R:FR. SAURs are thought to act downstream of the phytochrome signaling pathway, and their upregulation is possibly driven by PIF-regulated auxin, which is also involved in SAS (Devlin et al., 2003; Vandenbussche et al., 2007; Franklin and Quail, 2010). SAUR genes, a prominent family of early auxin-response genes, have demonstrated their rapid upregulation by auxin in various plant species, including Arabidopsis, rice, and tomato, suggesting a conserved role in auxin responses (Ren and Gray, 2015). Specifically, many SAURs in Arabidopsis exhibit swift induction in response to shade treatment, implicating their involvement in the shade avoidance response (Devlin et al., 2003; Kohnen et al., 2016a). Notably, overexpressing SAUR19 in the pif4 mutant background effectively rescued impaired hypocotyl elongation at high temperatures, and SAUR36 overexpression also promoted hypocotyl elongation (Franklin et al., 2011; Stamm et al., 2013). SAUR proteins play a crucial role in regulating cell elongation by affecting proton pumps and subsequently activating cell wall modifying enzymes. The mechanism underlying SAUR-mediated cell expansion involves the interaction of SAUR proteins with PP2C.D phosphatases, which leads to the activation of plasma membrane H+-ATPases, thus promoting cell expansion. This process results in the acidification of the cell wall and the subsequent activation of cell wall modifying enzymes, which facilitate cell
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