Plants are responsive to temperature, and can distinguish differences of 1ºC. In Arabidopsis, warmer temperature accelerates flowering and increases elongation growth (thermomorphogenesis). The mechanisms of temperature perception are however largely unknown. We describe a major thermosensory role for the phytochromes (red light receptors) during the night. Phytochrome null plants display a constitutive warm temperature response, and consistent with this, we show in this background that the warm temperature transcriptome 2 becomes de-repressed at low temperatures. We have discovered phytochrome B (phyB) directly associates with the promoters of key target genes in a temperature dependent manner.The rate of phyB inactivation is proportional to temperature in the dark, enabling phytochromes to function as thermal timers, integrating temperature information over the course of the night. One Sentence Summary:The plant temperature transcriptome is controlled at night by phytochromes, acting as thermoresponsive transcriptional repressors. Main Text:Plant development is responsive to temperature, and the phenology and distribution of crops and wild plants have already altered in response to climate change (1, 2). In Arabidopsis thaliana, warm temperature-mediated elongation growth and flowering is dependent on the bHLH transcription factors PHYTOCHROME INTERACTING FACTOR4 and 5 (PIF4 and 5) (3-6). Growth at 27ºC reduces the activity of the Evening Complex (EC) resulting in greater PIF4 transcription. The EC is a transcriptional repressor made up of the proteins EARLY FLOWERING3 (ELF3), ELF4 and LUX ARRHYTHMO (LUX) (7-9). To test if the EC is also required for hypocotyl elongation responses below 22ºC, we examined the behavior of elf3-1 and lux-4 at 12 and 17ºC. Hypocotyl elongation in elf3-1 and lux-4 is largely suppressed at lower temperatures (Fig. 1A, B), which is consistent with cold temperatures being able to suppress PIF4 overexpression phenotypes (10). Since PHYTOCHROME B (PHYB) was identified as a QTL for thermal responsiveness and PIF4 activity is regulated by phytochromes (8, 11), we investigated whether these red light receptors control hypocotyl elongation in the range 12 to 22ºC. Plants lacking phytochrome activity (12) show constitutively long hypocotyls at 12ºC and 17ºC. Thus phytochromes are essential for responding to temperature (Fig. 1C, D and Fig. S1).We used transcriptome analysis to determine whether disrupted thermomorphogenesis in phyABCDE is specific for temperature signaling or is a consequence of misregulated growth pathways. To capture diurnal variation in thermoresponsiveness, we sampled seedlings over 24 hours at 22 and 27ºC. Clustering analysis reveals 20 groups of transcripts ( Fig. 2A and Fig. S3; described in supplement). Thermomorphogenesis occurs predominantly at night and is driven by PIF4. Consistent with this, we observe PIF4 is present in cluster 20, which is more highly expressed at 27ºC during darkness. Clusters 15 and 16 represent the other major groups of 3 nighttim...

The two-component system (TCS), which works on the principle of histidine-aspartate phosphorelay signaling, is known to play an important role in diverse physiological processes in lower organisms and has recently emerged as an important signaling system in plants. Employing the tools of bioinformatics, we have characterized TCS signaling candidate genes in the genome of Oryza sativa L. subsp. japonica. We present a complete overview of TCS gene families in O. sativa, including gene structures, conserved motifs, chromosome locations, and phylogeny. Our analysis indicates a total of 51 genes encoding 73 putative TCS proteins. Fourteen genes encode 22 putative histidine kinases with a conserved histidine and other typical histidine kinase signature sequences, five phosphotransfer genes encoding seven phosphotransfer proteins, and 32 response regulator genes encoding 44 proteins. The variations seen between gene and protein numbers are assumed to result from alternative splicing. These putative proteins have high homology with TCS members that have been shown experimentally to participate in several important physiological phenomena in plants, such as ethylene and cytokinin signaling and phytochrome-mediated responses to light. We conclude that the overall architecture of the TCS machinery in O. sativa and Arabidopsis thaliana is similar, and our analysis provides insights into the conservation and divergence of this important signaling machinery in higher plants.

SummaryTemperature is a key environmental variable influencing plant growth and survival. Protection against high temperature stress in eukaryotes is coordinated by heat shock factors (HSFs), transcription factors that activate the expression of protective chaperones such as HEAT SHOCK PROTEIN 70 (HSP70); however, the pathway by which temperature is sensed and integrated with other environmental signals into adaptive responses is not well understood. Plants are exposed to considerable diurnal variation in temperature, and we have found that there is diurnal variation in thermotolerance in Arabidopsis thaliana, with maximal thermotolerance coinciding with higher HSP70 expression during the day. In a forward genetic screen, we identified a key role for the chloroplast in controlling this response, suggesting that light-induced chloroplast signaling plays a key role. Consistent with this, we are able to globally activate binding of HSFA1a to its targets by altering redox status in planta independently of a heat shock.