Transcriptional Programs Related to Phytochrome A Function in Arabidopsis Seed Germination

Abstract

In Arabidopsis seeds, germination is promoted only by phytochromes, principally phytochrome B (phyB) and phytochrome A (phyA). Despite the abundant information concerning the molecular basis of phyB signaling downstream of PIF1/PIL5, the signaling network inducing germination by phyA is poorly known. Here, we describe the influence of phyA on the transcriptome of Arabidopsis seeds when germination is induced by a far-red (FR) pulse. The expression of 11% of the genome was significantly regulated by phyA. Most of the genes were up-regulated and the changes noted late (i.e. 5 h after a FR pulse), whereas changes in down-regulated genes were more abundant earlier (i.e. 0.5 h after a FR pulse). Auxin- and GA-associated elements were overrepresented in the genes that were modified by phyA. A significant number of genes whose expression was affected by phyA had not been previously reported to be dependent on PIL5. Among them, homozygotic mutant seeds of MYB66, a SAUR-like protein, PIN7, and GASA4 showed an impaired promotion of germination by phyA. Natural variation at the transcriptional level was found in early signaling and GA metabolic genes, but not in ABA metabolic and expansin genes between Columbia and Landsberg erecta accessions. Although phyA and phyB/PIL5 signaling pathways share some molecular components, our data suggest that phyA signaling is partially independent of PIL5 when germination is promoted by very low fluences of light.

DOF AFFECTING GERMINATION 2 is a positive regulator of light-mediated seed germination and is repressed by DOF AFFECTING GERMINATION 1

“…We then verified whether expression of some factors known to be involved in the phyA-signalling pathway [27] may be affected in dag2 mutant seeds. In particular, we analysed expression of the FR light-regulated ARABIDOPSIS THALIANA HOMEOBOX PROTEIN 2 ( ATHB2) and PHYTOCHROME INTERACTING FACTOR 3-LIKE 2 ( PIL2 ) genes, of the GA-regulated GA-STIMULATED ARABIDOPSIS 4 and 6 ( GASA4 and GASA6 ), and of the ABA signalling gene ABA INSENSITIVE 4 ( ABI4) .…”

HFR1 Sequesters PIF1 to Govern the Transcriptional Network Underlying Light-Initiated Seed Germination in Arabidopsis

“…In addition, our results suggest that the auxin efflux carriers also play important roles in promoting seed germination. Previous studies showed that three auxin transport proteins (PIN1, PIN2, and PIN7) are involved in phyA-dependent germination and pin7 showed germination defects upon FR (Ibarra et al, 2013). Also, auxin influx transport AUX1 functions in ABA-dependent repression of embryonic axis elongation in the early seedling development (Belin et al, 2009).…”

Seed-specific transcription factor HSFA9 links late embryogenesis and early photomorphogenesis

“…Indeed, >60% of early FRc and Rc light-induced genes have been found to be direct HY5-binding targets (Lee et al , 2007). In Arabidopsis, only PHYA modulates the expression of 11% of the genome; this includes a diversity of TFs involved in light-signalling cascades in imbibed seeds (Ibarra et al , 2013). Therefore, HSFA9, through PHYA and PHYB , could enhance a widespread transcriptional effect after the first exposure of seedlings to light.…”

“…Underlying part of the observed effects, HSFA9 would enhance light responses that depend at least on PHYA and PHYB . Such responses are critical to the transition from heterotrophic seedling growth from stored reserves to the biogenesis of photosynthetic active plastids, which allows autotrophic plant growth (Franklin and Quail, 2010; Ibarra et al , 2013; Casal et al , 2014, and references therein). In all, our results uncover a novel transcriptional link between seed maturation and early photomorphogenesis.…”