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

• Published in: Plant physiology (Bethesda) 2011-05, Vol.156 (1), p.357-372
• Main Authors: Nozue, Kazunari, Harmer, Stacey L., Maloof, Julin N.
• Format: Article
• Language: English
• Subjects: Arabidopsis - genetics; Arabidopsis - growth & development; Arabidopsis - physiology; Arabidopsis - radiation effects; Arabidopsis Proteins - genetics; Arabidopsis Proteins - metabolism; Arabidopsis thaliana; Basic Helix-Loop-Helix Transcription Factors - genetics; Basic Helix-Loop-Helix Transcription Factors - metabolism; Biological and medical sciences; Circadian Clocks - genetics; Circadian Rhythm - genetics; Fundamental and applied biological sciences. Psychology; Genomics; Gibberellins - metabolism; Hypocotyl - genetics; Hypocotyl - growth & development; Hypocotyl - physiology; Hypocotyl - radiation effects; Indoleacetic Acids - metabolism; Light; Photoperiod; Phytochrome - metabolism; Plant physiology and development; Plants, Genetically Modified; Seedlings - genetics; Seedlings - growth & development; Seedlings - physiology; Seedlings - radiation effects; Signal Transduction; SYSTEMS BIOLOGY, MOLOCULAR BIOLOGY, AND GENE REGULATION
• ISSN: 0032-0889; 1532-2548; 1532-2548
• DOI: 10.1104/pp.111.172684

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 realtime 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.