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Title: Functional Profiling Reveals that Only a Small Number of Phytochrome-Regulated Early-Response Genes in Arabidopsis Are Necessary for Optimal Deetiolation

Author
item KHANNA, RAJNISH - UCB-ARS PLNT GEN EXP CTR
item SHEN, YU - UCB-ARS PLNT GENE EXP CTR
item TOLEDO-ORTIZ, GABRIELA - UCB-ARS PLNT GENE EXP CTR
item KIKIS, ELISA - UCB-ARS PLNT GENE EXP CTR
item JOHANNESSON, HENRIK - UCB-ARS PLNT GENE EXP CTR
item HWANG, YONG-SIC - UCB-ARS PLNT GENE EXP CTR
item QUAIL, PETER - UCB-ARS PLNT GENE EXP CTR

Submitted to: The Plant Cell
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 7/3/2006
Publication Date: 8/4/2006
Citation: Khanna, R., Shen, Y., Toledo-Ortiz, G., Kikis, E.A., Johannesson, H., Hwang, Y., Quail, P.H. 2006. Functional Profiling Reveals that Only a Small Number of Phytochrome-Regulated Early-Response Genes in Arabidopsis Are Necessary for Optimal Deetiolation. The Plant Cell. 18:2157-2171.

Interpretive Summary: Systematic assessment of the effects of specific, targeted gene-disruptions is a powerful approach to determining the functional importance of genes putatively involved in signaling and transcriptional networks. We identified 32 genes encoding putative transcription factors, signaling components, and unknown proteins, rapidly and robustly induced by phytochrome (phy)-mediated light signals and obtained knockout mutations in each. Surprisingly, we found that only about 20% of these genes were important to light signaling, indicating possible functional redundancy in the remaining 80%.

Technical 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.