LNK genes integrate light and clock signaling networks at the core of the Arabidopsis oscillator

Abstract

Light signaling pathways and the circadian clock interact to help organisms synchronize physiological and developmental processes with periodic environmental cycles. The plant photoreceptors responsible for clock resetting have been characterized, but signaling components that link the photoreceptors to the clock remain to be identified. Here we describe a family of night lightinducible and clock-regulated genes (LNK) that play a key role linking light regulation of gene expression to the control of daily and seasonal rhythms in Arabidopsis thaliana. A genomewide transcriptome analysis revealed that most light-induced genes respond more strongly to light during the subjective day, which is consistent with the diurnal nature of most physiological processes in plants. However, a handful of genes, including the homologous genes LNK1 and LNK2, are more strongly induced by light in the middle of the night, when the clock is most responsive to this signal. Further analysis revealed that the morning phased LNK1 and LNK2 genes control circadian rhythms, photomorphogenic responses, and photoperiodic dependent flowering, most likely by regulating a subset of clock and flowering time genes in the afternoon. LNK1 and LNK2 themselves are directly repressed by members of the TIMING OF CAB1 EXPRESSION/PSEUDO RESPONSE REGULATOR family of core-clock genes in the afternoon and early night. Thus, LNK1 and LNK2 integrate early light signals with temporal information provided by core oscillator components to control the expression of afternoon genes, allowing plants to keep track of seasonal changes in day length.

Genome-wide identification of CCA1 targets uncovers an expanded clock network inArabidopsis

“…This inclusive target list identified NIGHT LIGHT-INDUCIBLE AND CLOCK-REGULATED3 (LNK3) as a CCA1 target, and the severely altered LNK3 transcript level in CCA1-OX and cca1-1/lhy-21 plants in LL confirms that it is indeed regulated by CCA1 (Fig. S5 B-D) (53). We therefore prepared a more inclusive list of CCA1 targets and made the ChIP-Seq data available on the Integrated Genome Browser (IGB) Quickload site (bioviz.org/igb/index.html) (54) and through the AnnoJ browser (neomorph.salk.edu/Kay_CCA1.php) (55) to enable researchers to browse for potential CCA1 peaks near the promoters of their favorite gene (Dataset S4).…”

FBH1 affects warm temperature responses in the Arabidopsis circadian clock

“…The clock can be entrained by both thermocycles and photocycles to set the pace and phase of the clock under natural conditions and can compensate for changes in ambient temperature and light to maintain this periodicity (12,13). Although several photoreceptors that play a role in entrainment and light perception are known, very little is known mechanistically about how temperature signals are perceived and integrated into the clock network (14)(15)(16)(17)(18). A well-studied and important characteristic of the clock is the ability to buffer against temperature changes.…”

CO-EXPRESSED WITH CLOCK GENES LHY AND CCA1 1 (CEC1) is regulated by LHY and CCA1 and plays a key role in phase setting of GI in Arabidopsis thaliana

“…LNK1 (At5g64170) was not present in the LHY/CCA1 co-expression networks. LNK1 and LNK2 might regulate the expression of clock genes such as PRR5 and ELF4 (Rugnone et al 2013). While lnk2 single mutants showed an early flowering phenotype under LD as did cec1 in this work, the lnk1;lnk2 double mutant showed late flowering under LD (Rugnone et al 2013).…”

“…LNK1 and LNK2 might regulate the expression of clock genes such as PRR5 and ELF4 (Rugnone et al 2013). While lnk2 single mutants showed an early flowering phenotype under LD as did cec1 in this work, the lnk1;lnk2 double mutant showed late flowering under LD (Rugnone et al 2013). In general, phenotypes of double mutants are thought to be much more severe than those of the corresponding single mutants.…”

“…The reason why the lnk1;lnk2 double mutant showed a phenotype opposite to the single mutants has not been elucidated (Rugnone et al 2013). Therefore, further genetic and biochemical analyses including the examination of double, triple, and quadruple mutants of the LNK1, LNK2/CEC1, LNK3/CEC2, and LNK4/CEC3 genes are required.…”