3.7 Genes whose drought response was ameliorated by chloroplast Fld
A significant number of genes showed different expression patterns under water stress conditions depending on the presence of Fld, exhibiting lower induction (clusters 5 and 6) or repression (clusters 7 and 8) inStpfld 252 leaves relative to WT counterparts (Figure 5, Supplementary Table S6). These four clusters comprise 33% of total DE transcripts (1611 genes), and collectively represent the most common response to treatment and genotype. Cluster 5 contained 546 genes whose drought-dependent induction was completely abolished by Fld, while for 274 genes of cluster 6 the effect of Fld was only partial.
Cluster 5 contained genes involved in sucrose metabolism, including several sucrose synthase isoforms (Figure 5, Supplementary Table S6). It also harbored genes involved in the regulation of isoprenoid metabolism. Isoprenoids are a large and diverse group of molecules that include photosynthetic pigments (chlorophylls and carotenoids), components of different electron transport chains (plastoquinone, ubiquinone), hormones (abscisic acid, gibberellins, cytokinins and brassinosteroids), membrane-associated phytosterols and antimicrobials (phytoalexins).
Cluster 6 was enriched in pathways related to abiotic stress responses, including various heat-responsive transcription factors and heat-shock proteins (Figure 5, Supplementary Table S6). Most members of this category function as chaperones involved in protein folding, assembly and translocation.
Clusters 7 and 8 exhibit a remarkable over-representation of genes associated to photosynthesis, including components of the light-harvesting complexes, the photosynthetic electron transport chain (PETC) and the Calvin-Benson cycle (Figure 5, Supplementary Table S6). In addition, cluster 7 (528 genes) includes transcripts encoding glycolytic enzymes (e.g. , phosphoglycerate kinase) and enzymes involved in homoserine and γ-aminobutyrate (GABA) synthesis. Cluster 8 (263 genes), in turn, contained transcripts related to cell wall metabolism, although most of the genes belonging to this functional category were grouped in cluster 2.
A small number of genes showed drought responsiveness only inpfld 252 plants (Figure 6a, Supplementary Table S7). Cluster 9 contained 111 induced genes, with over-representation of transcripts associated to isoprenoid metabolism, whereas cluster 10 included 117 drought-repressed genes, and was enriched in transcripts related to the auxin and minor carbohydrate categories, particularly raffinose synthesis (Figure 6a, Supplementary Table S7).