Abstract
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.
Highlights
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
Examining categories defined by MapMan (Supplemental Table S11A), we found that auxin metabolism genes and transcription factors (TFs) subgroups including homeobox genes (BINCODE 27.3.22, such as ATHB2, -7, -12, -52, and HOMEOBOX FROM ARABIDOPSIS THALIANA2) were overrepresented in upG and PHYTOCHROME-INTERACTING FACTOR4 (PIF4) or PIF5 up-regulated genes (Supplemental Table S11A)
Since overrepresentation analysis (ORA) of hormone signaling genes (Supplemental Table S6) and hormone-responsive genes (Supplemental Table S7) predict the involvement of gibberellic acid (GA) pathways in rhythmic growth, we tested whether reduced GA biosynthesis could result in retarded rhythmic growth
Summary
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). 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. Light is an important regulator of plant growth; early in development, it inhibits the elongation of the young plant stem, or hypocotyl. This response is mediated by phytochromes and cryptochromes, photoreceptors that sense red and far-red light or blue. Investigating the mechanism underlying normal diurnal growth, we found that the clock and light signaling pathways converge to control two transcription factors (TFs) via transcriptional and posttranscriptional regulation. The transcriptional targets downstream of PIF4 and PIF5 that cause these daily growth rhythms have yet to be identified
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