The Circadian Clock in Arabidopsis Roots Is a Simplified Slave Version of the Clock in Shoots

Abstract

The circadian oscillator in eukaryotes consists of several interlocking feedback loops through which the expression of clock genes is controlled. It is generally assumed that all plant cells contain essentially identical and cell-autonomous multiloop clocks. Here, we show that the circadian clock in the roots of mature Arabidopsis plants differs markedly from that in the shoots and that the root clock is synchronized by a photosynthesis-related signal from the shoot. Two of the feedback loops of the plant circadian clock are disengaged in roots, because two key clock components, the transcription factors CCA1 and LHY, are able to inhibit gene expression in shoots but not in roots. Thus, the plant clock is organ-specific but not organ-autonomous.

Organ specificity in the plant circadian system is explained by different light inputs to the shoot and root clocks

“…(2008), who found that only the morning loop genes were scored as rhythmic in roots of plants under LL. The discrepancy was not caused by the difference in ecotype (Ws in Fig.…”

“…Thus, these data confirm and extend the organ specificity of the plant circadian system (James et al ., 2008): the root clock has a longer FRP under LL than the shoot clock irrespective of whether roots are illuminated. In addition, the relative amplitude of clock gene expression is lower in dark‐grown roots compared with shoots or light‐grown roots, and direct exposure to light can increase relative amplitude in roots.…”

“…S1). Hydroponic culture was essentially as described previously (James et al ., 2008), except that plants were harvested between 4 and 5 wk after sowing. Tissue was collected under a green safety light, immediately frozen in liquid nitrogen and stored at −80°C until use.…”

“…RNA extraction, cDNA synthesis and qPCR were performed as described previously (James et al ., 2008), with modifications. Total RNA was extracted with the RNeasy Plant Mini kit (Qiagen) and DNase treated (DNA‐free; Ambion).…”

“…Exposure of seedling roots to LD cycles entrained them independently of shoots (Thain et al ., 2000). However, roots are not usually exposed to direct light; we therefore compared the root and shoot clocks in hydroponically grown plants with the roots in darkness (James et al ., 2008). Using quantitative real‐time (RT‐q)PCR measurement of gene expression, we showed that the free‐running period (FRP) of the root clock in constant light (LL) was longer than that in shoots, although the organs were synchronized in LD, suggesting that roots can be entrained by a signal from shoots.…”