3.4 Water deprivation caused extensive transcriptional
reprogramming in both WT and Fld-expressing leaves
Gene expression levels were determined after 3 days of water restriction
and transcripts displaying 2-fold or higher differences compared to
control well-watered conditions were classified as DE. Distribution of
these transcripts between treatments and genotypes (depicted as Venn
diagrams in Figure 4) indicates that 999 genes were induced by drought
in both lines, 1530 genes only in the non-transformed plants, and 698
uniquely in Stpfld 252 leaves (FC > 2, FDR
< 0.05). In contrast, 1505 genes were repressed by drought in
both lines, 1667 only in the wild type and 895 exclusively inStpfld 252 plants. In summary, drought induced 2529 genes in WT
plants against 1697 in Stpfld 252 siblings, and repressed 3172
genes in the wild type versus 2400 in the transformant. Hence, the
overall effect of Fld presence was to mitigate the changes in gene
expression driven by the drought treatment; either induction or
repression.
Functional enrichment analysis identified pathways and functional
categories that were significantly affected in response to water
withdrawal in the two genotypes. Among the categories that showed
drought-dependent induction in both WT and Stpfld 252 plants,
abiotic stress was over-represented. The opposite situation,e.g. , pathways repressed by water limitation in the two lines, is
exemplified by cell wall metabolism and kinase-dependent protein
modification and signaling (Figure 4, Supplementary Table S3).
Several DE genes showed differential stress responses in only one
genotype. Drought-dependent inactivation of photosynthesis in WT plants
(Figure 1b-d) was paralleled at the transcript level by widespread
down-regulation of genes encoding photosynthetic components. Repression
particularly impaired light reactions, and was largely prevented by
chloroplast Fld (Figure 4, Supplementary Table S3), correlating with the
protection of photosynthetic activities in the transformant (Figure
1b-d).
While the effect of drought on leaf gene expression was predominantly
repressive (Figure 4, Supplementary Table S3), stress-dependent
induction was also important in the wild type with more than 2500 genes
affected. Enriched functional categories included protein metabolism
with 98 DE genes (mostly ribosomal proteins), biotic stress and amino
acid synthesis (Figure 4, Supplementary Table S3). Differential
induction of all these pathways was totally or partially abolished by
Fld expression in chloroplasts, suggesting once again that the water
deficit regime had less impact in the transgenic plants than in their WT
siblings.
Finally, some functional categories were specifically over-represented
in the transformant, including drought-associated up-regulation of
membrane transport, sulfur assimilation and flavonoid synthesis (Figure
4, Supplementary Table S3).