Genomic Analysis of Circadian Clock-, Light-, and Growth-Correlated Genes Reveals PHYTOCHROME-INTERACTING FACTOR5 as a Modulator of Auxin Signaling in Arabidopsis

Mar 25, 2011Plant physiology

Genetic study of daily rhythm, light, and growth genes identifies a key regulator of plant growth signals in Arabidopsis

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Abstract

Genome-wide analysis revealed significant overlap between light, clock, and growth-related gene pathways in plants.

PIF4 and PIF5 are key transcription factors that integrate light and circadian signals for regulating plant growth.
Auxin and gibberellic acid hormone pathways are predicted to play roles in controlling diurnal plant growth.
Mutations in gibberellic acid biosynthesis genes slowed down rhythmic growth, indicating their involvement in growth regulation.
Auxin pathway and response genes are more significantly regulated by PIF4 and PIF5 compared to gibberellic acid-responsive genes.
The impact on auxin response is greater than that on gibberellic acid response in specific mutant and overexpressing plant lines.

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Plants exhibit daily rhythms in their growth, providing an ideal system for the study of interactions between environmental stimuli such as light and internal regulators such as the circadian clock. We previously found that two basic loop-helix-loop transcription factors, PHYTOCHROME-INTERACTING FACTOR4 (PIF4) and PIF5, integrate light and circadian clock signaling to generate rhythmic plant growth in Arabidopsis (Arabidopsis thaliana). Here, we use expression profiling and real-time growth assays to identify growth regulatory networks downstream of PIF4 and PIF5. Genome-wide analysis of light-, clock-, or growth-correlated genes showed significant overlap between the transcriptomes of clock-, light-, and growth-related pathways. Overrepresentation analysis of growth-correlated genes predicted that the auxin and gibberellic acid (GA) hormone pathways both contribute to diurnal growth control. Indeed, lesions of GA biosynthesis genes retarded rhythmic growth. Surprisingly, GA-responsive genes are not enriched among genes regulated by PIF4 and PIF5, whereas auxin pathway and response genes are. Consistent with this finding, the auxin response is more severely affected than the GA response in pif4 pif5 double mutants and in PIF5-overexpressing lines. We conclude that at least two downstream modules participate in diurnal rhythmic hypocotyl growth: PIF4 and/or PIF5 modulation of auxin-related pathways and PIF-independent regulation of the GA pathway.

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Genomic Analysis of Circadian Clock-, Light-, and Growth-Correlated Genes Reveals PHYTOCHROME-INTERACTING FACTOR5 as a Modulator of Auxin Signaling in Arabidopsis

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