Functional Profiling Reveals That Only a Small Number of Phytochrome-Regulated Early-Response Genes inArabidopsisAre Necessary for Optimal Deetiolation

Abstract

In previous time-resolved microarray-based expression profiling, we identified 32 genes encoding putative transcription factors, signaling components, and unknown proteins that are rapidly and robustly induced by phytochrome (phy)-mediated light signals. Postulating that they are the most likely to be direct targets of phy signaling and to function in the primary phy regulatory circuitry, we examined the impact of targeted mutations in these genes on the phy-induced seedling deetiolation process in Arabidopsis thaliana. Using light-imposed concomitant inhibition of hypocotyl and stimulation of cotyledon growth as diagnostic criteria for normal deetiolation, we identified three major mutant response categories. Seven (22%) lines displayed statistically significant, reciprocal, aberrant photoresponsiveness in the two organs, suggesting disruption of normal deetiolation; 13 (41%) lines displayed significant defects either unidirectionally in both organs or in hypocotyls only, suggesting global effects not directly related to photomorphogenic signaling; and 12 (37%) lines displayed no significant difference in photoresponsiveness from the wild type. Potential reasons for the high proportion of rapidly light-responsive genes apparently unnecessary for the deetiolation phenotype are discussed. One of the seven disrupted genes displaying a significant mutant phenotype, the basic helix-loop-helix factor-encoding PHYTOCHROME-INTERACTING FACTOR3-LIKE1 gene, was found to be necessary for rapid light-induced expression of the photomorphogenesis-and circadian-related PSEUDO-RESPONSE REGULATOR9 gene, indicating a regulatory function in the early phy-induced transcriptional network.

BBX32, an Arabidopsis B-Box Protein, Functions in Light Signaling by Suppressing HY5-Regulated Gene Expression and Interacting with STH2/BBX21

“…1E). These data are consistent with the conclusions from a previous study, where it was found that a large percentage of loss-of-function mutations in single genes implicated in light signaling do not result in any significant defects in deetiolation (Khanna et al, 2006). Here, we show that overexpression of BBX32 resulted in seedlings with elongated hypocotyls along with smaller cotyledons, consistent with phenotypes linked to an altered photomorphogenic response.…”

“…For plate-based assays, seeds were sterilized and grown on plates containing growth medium without Suc as described (Khanna et al, 2006). An E-30LED plant growth chamber (Percival) was used for red, far-red, and blue light treatments, and an AR75L chamber (Percival) was used for white light.…”

Arabidopsis SAURs are critical for differential light regulation of the development of various organs

“…Deetiolation is an excellent model process to study differential light effects on various organs. Although certain organ-specific light-regulated genes have already been identified (8)(9)(10), the core components and molecular mechanisms connecting signals to development were lacking. In our study, by analyzing light-responsive genes in cotyledons and hypocotyls separately, we identified a group of lirSAURs that were oppositely regulated by light in these two organs and that might play key roles in the differential light regulation of various organs (Figs.…”

“…At the molecular level, the Arabidopsis tubulin gene TUB1 was demonstrated to be down-regulated by light specifically in hypocotyls (8). Mutants affected in several phytochrome-regulated early light response genes exhibited phenotypic differences only in hypocotyls, which indicated that these genes had specific functions in these organs (9). Microarray analysis of dissected organs from Arabidopsis seedlings grown in the dark or in white light found that the expression of hundreds of light-responsive genes was specific to certain organs (10).…”

The BBX subfamily IV

“…61 The homolog of BBX24, BBX25, has been reported to function as a negative regulator of hypocotyl elongation under red and farred light. 39,62 The phenotype described for bbx25 mutants is weak, insights on the probable relation of the members to the major regulators of photomorphogenesis and light signaling.…”