Martina Legris

Phytochrome B integrates light and temperature signals in Arabidopsis

Combining heat and light responses Plants integrate a variety of environmental signals to regulate growth patterns. Legris et al. and Jung et al. analyzed how the quality of light is interpreted through ambient temperature to regulate transcription and growth (see the Perspective by Halliday and Davis). The phytochromes responsible for reading the ratio of red to far-red light were also responsive to the small shifts in temperature that occur when dusk falls or when shade from neighboring plants cools the soil. Science, this issue p. 897, p. 886; see also p. 832 Red-light photoreceptors also act as temperature sensors in plants. Ambient temperature regulates many aspects of plant growth and development, but its sensors are unknown. Here, we demonstrate that the phytochrome B (phyB) photoreceptor participates in temperature perception through its temperature-dependent reversion from the active Pfr state to the inactive Pr state. Increased rates of thermal reversion upon exposing Arabidopsis seedlings to warm environments reduce both the abundance of the biologically active Pfr-Pfr dimer pool of phyB and the size of the associated nuclear bodies, even in daylight. Mathematical analysis of stem growth for seedlings expressing wild-type phyB or thermally stable variants under various combinations of light and temperature revealed that phyB is physiologically responsive to both signals. We therefore propose that in addition to its photoreceptor functions, phyB is a temperature sensor in plants.

Rapid Decline in Nuclear COSTITUTIVE PHOTOMORPHOGENESIS1 Abundance Anticipates the Stabilization of Its Target ELONGATED HYPOCOTYL5 in the Light

The classic view is challenged that the migration of the repressor of photomorphogenesis COP1 from the nucleus to the cytoplasm is too slow to participate in light-mediated developmental events.

COP1 re‐accumulates in the nucleus under shade

Shade-avoider plants typically respond to shade-light signals by increasing the rate of stem growth. CONSTITTUTIVE PHOTOMORPHOGENESIS 1 (COP1) is an E3 ligase involved in the ubiquitin labelling of proteins targeted for degradation. In dark-grown seedlings, COP1 accumulates in the nucleus and light exposure causes COP1 migration to the cytosol. Here, we show that in Arabidopsis thaliana, COP1 accumulates in the nucleus under natural or simulated shade, despite the presence of far-red light. In plants grown under white light, the transfer to shade-light conditions triggers an unexpectedly rapid re-accumulation of COP1 in the nucleus. The partial simulation of shade by lowering either blue or red light levels (maintaining far-red light) caused COP1 nuclear re-accumulation. Hypocotyl growth of wild-type seedlings is more sensitive to afternoon shade than to morning shade. A residual response to shade was observed in the cop1 mutant background, but these seedlings showed inverted sensitivity as they responded to morning shade and not to afternoon shade. COP1 overexpression exaggerated the wild-type pattern by enhancing afternoon sensitivity and making morning shade inhibitory of growth. COP1 nuclear re-accumulation also responded more strongly to afternoon shade than to morning shade. These results are consistent with a signalling role of COP1 in shade avoidance. We propose a function of COP1 in setting the daily patterns of sensitivity to shade in the fluctuating light environments of plant canopies.

Convergence of CONSTITUTIVE PHOTOMORPHOGENESIS 1 and PHYTOCHROME INTERACTING FACTOR signalling during shade avoidance

Shade-avoidance responses require CONSTITUTIVE PHOTOMORPHOGENESIS 1 (COP1) but the mechanisms of action of COP1 under shade have not been elucidated. Using simulated shade and control conditions, we analysed: the transcriptome and the auxin levels of cop1 and phytochrome interacting factor 1 (pif1) pif3 pif4 pif5 (pifq) mutants; the dynamics of ELONGATED HYPOCOTYL 5 (HY5) and LONG HYPOCOTYL IN FAR-RED (HFR1) proteins; and the epistatic relationships between cop1 and pif3, pif4, pif5, hy5 and hfr1 mutations in Arabidopsis thaliana. Despite severely impaired shade-avoidance responses, only a few genes that responded to shade in the wild-type failed to do so in cop1. Shade enhanced the convergence between cop1 and pifq transcriptomes, mainly on shade-avoidance marker genes. Shade failed to increase auxin levels in cop1. Residual shade avoidance in cop1 was not further reduced by the pif3, pif4 or pif5 mutations, suggesting convergent pathways. HFR1 stability decreased under shade in a COP1-dependent manner but shade increased HY5 stability. The cop1 mutant retains responses to shade and is more specifically impaired in shade avoidance. COP1 promotes the degradation of HFR1 under shade, thus increasing the ability of PIFs to control gene expression, increase auxin levels and promote stem growth.

Heat Shock–Induced Fluctuations in Clock and Light Signaling Enhance Phytochrome B–Mediated Arabidopsis Deetiolation

Transient exposures to high temperatures (heat shocks) in darkness make seedlings more responsive to subsequent light by rhythmically reducing the expression of repressors and by enhancing the nuclear abundance of positive regulators of photomorphogenesis. Moderately warm constant ambient temperatures tend to oppose light signals in the control of plant architecture. By contrast, here we show that brief heat shocks enhance the inhibition of hypocotyl growth induced by light perceived by phytochrome B in deetiolating Arabidopsis thaliana seedlings. In darkness, daily heat shocks transiently increased the expression of PSEUDO-RESPONSE REGULATOR7 (PRR7) and PRR9 and markedly enhanced the amplitude of the rhythms of LATE ELONGATED HYPOCOTYL (LHY) and CIRCADIAN CLOCK ASSOCIATED1 (CCA1) expression. In turn, these rhythms gated the hypocotyl response to red light, in part by changing the expression of PHYTOCHROME INTERACTING FACTOR4 (PIF4) and PIF5. After light exposure, heat shocks also reduced the nuclear abundance of CONSTITUTIVE PHOTOMORPHOGENIC1 (COP1) and increased the abundance of its target ELONGATED HYPOCOTYL5 (HY5). The synergism between light and heat shocks was deficient in the prr7 prr9, lhy cca1, pif4 pif5, cop1, and hy5 mutants. The evening element (binding site of LHY and CCA1) and G-box promoter motifs (binding site of PIFs and HY5) were overrepresented among genes with expression controlled by both heat shock and red light. The heat shocks experienced by buried seedlings approaching the surface of the soil prepare the seedlings for the impending exposure to light by rhythmically lowering LHY, CCA1, PIF4, and PIF5 expression and by enhancing HY5 stability.

Phytochrome B Nuclear Bodies Respond to the Low Red to Far-Red Ratio and to the Reduced Irradiance of Canopy Shade in Arabidopsis

Phytochrome B nuclear bodies perceive not only the low red to far-red ratio, but also the low irradiance of canopy shade. The current consensus is that plant responses to canopy shade involve the perception of low red to far-red ratios (R:FRs) by phytochrome B (phyB), which leads to the direct activation of auxin synthesis genes by PHYTOCHROME INTERACTING FACTORs (PIFs). In addition to its effect on R:FRs, shade also reduces irradiance, but whether shade-induced drops in irradiance affect phyB activity has not been demonstrated. To address this issue, we investigated whether irradiance and R:FRs have similar effects on the nuclear distribution of phyB in petiole cells of light-grown plants. Under high-irradiance white light, phyB formed large nuclear bodies. Lowering irradiance without changing R:FRs or lowering R:FRs by adding far-red light led to the appearance of small nuclear bodies containing phyB. Large nuclear bodies remained but with some concomitant reduction in diameter. The appearance of small nuclear bodies was rapid, stable, and reversible upon the return to high irradiance and high R:FRs. High levels of red light but not of blue light were enough to restrain the formation of small phyB nuclear bodies. Irradiance was effective within the range found in natural canopies and even under relatively low R:FRs. The promotion of leaf hyponasty by lowering irradiance was impaired in phyB and pif mutants, as previously reported for the response to R:FRs. The expression of auxin-related genes showed a similar hierarchy of response to low R:FRs and low irradiance. We propose that phyB is able to perceive not only the low R:FRs, but also the low irradiance of shade.

Perception and signalling of light and temperature cues in plants

Light and temperature patterns are often correlated under natural plant growth conditions. In this review, we analyse the perception and signalling mechanisms shared by both these environmental cues and discuss the functional implications of their convergence to control plant growth. The first point of integration is the phytochrome B (phyB) receptor, which senses light and temperature. Downstream of phyB, the signalling core comprises two branches, one involving PHYTOCHROME INTERACTING FACTOR 4 (PIF4) and the other CONSTITUTIVE PHOTOMORPHOGENIC 1 (COP1) and ELONGATED HYPOCOTYL 5 (HY5). The dynamics of accumulation and/or localization of each of these core signalling components depend on light and temperature conditions. These pathways are connected through COP1, which enhances the activity of PIF4. The circadian clock modulates this circuit, since EARLY FLOWERING 3 (ELF3), an essential component of the evening complex (EC), represses expression of the PIF4 gene and PIF4 transcriptional activity. Phytochromes are probably not the only entry point of temperature into this network, but other sensors remain to be established. The sharing of mechanisms of action for two distinct environmental cues is to some extent unexpected, as it renders these responses mutually dependent. There are nonetheless many ecological contexts in which such a mutual influence could be beneficial.

Rewiring of auxin signaling under persistent shade

Significance In agricultural crops, plants are cultivated in close proximity, exposed to mutual shading. Photosensory receptors perceive this light environment and initiate growth responses that adjust the position of plant organs within the canopy to maximize light capture. During the early hours under shade, these responses are mediated by elevated levels of the hormone auxin. Here we show that under prolonged shade, the PHYTOCHROME INTERACTING FACTOR 4 light-signaling transcription factor, selected auxin receptors, their upstream regulatory miRNA, and downstream transcriptional regulators change their abundance to enhance growth responses, while auxin levels return to those observed before shade. Thus, in the presence of persistent shade, plants elicit a system-level rearrangement of auxin signaling, which sustains growth without increased auxin. Light cues from neighboring vegetation rapidly initiate plant shade-avoidance responses. Despite our detailed knowledge of the early steps of this response, the molecular events under prolonged shade are largely unclear. Here we show that persistent neighbor cues reinforce growth responses in addition to promoting auxin-responsive gene expression in Arabidopsis and soybean. However, while the elevation of auxin levels is well established as an early event, in Arabidopsis, the response to prolonged shade occurs when auxin levels have declined to the prestimulation values. Remarkably, the sustained low activity of phytochrome B under prolonged shade led to (i) decreased levels of PHYTOCHROME INTERACTING FACTOR 4 (PIF4) in the cotyledons (the organs that supply auxin) along with increased levels in the vascular tissues of the stem, (ii) elevated expression of the PIF4 targets INDOLE-3-ACETIC ACID 19 (IAA19) and IAA29, which in turn reduced the expression of the growth-repressive IAA17 regulator, (iii) reduced abundance of AUXIN RESPONSE FACTOR 6, (iv) reduced expression of MIR393 and increased abundance of its targets, the auxin receptors, and (v) elevated auxin signaling as indicated by molecular markers. Mathematical and genetic analyses support the physiological role of this system-level rearrangement. We propose that prolonged shade rewires the connectivity between light and auxin signaling to sustain shade avoidance without enhanced auxin levels.

Long-day photoperiod enhances jasmonic acid-related plant defense

Long days perceived by photosensory receptors enhance jasmonic acid-dependent resistance in Arabidopsis. Agricultural crops are exposed to a range of daylengths, which act as important environmental cues for the control of developmental processes such as flowering. To explore the additional effects of daylength on plant function, we investigated the transcriptome of Arabidopsis (Arabidopsis thaliana) plants grown under short days (SD) and transferred to long days (LD). Compared with that under SD, the LD transcriptome was enriched in genes involved in jasmonic acid-dependent systemic resistance. Many of these genes exhibited impaired expression induction under LD in the phytochrome A (phyA), cryptochrome 1 (cry1), and cry2 triple photoreceptor mutant. Compared with that under SD, LD enhanced plant resistance to the necrotrophic fungus Botrytis cinerea. This response was reduced in the phyA cry1 cry2 triple mutant, in the constitutive photomorphogenic1 (cop1) mutant, in the myc2 mutant, and in mutants impaired in DELLA function. Plants grown under SD had an increased nuclear abundance of COP1 and decreased DELLA abundance, the latter of which was dependent on COP1. We conclude that growth under LD enhances plant defense by reducing COP1 activity and enhancing DELLA abundance and MYC2 expression.

Neighbor signals perceived by phytochrome B increase thermotolerance in Arabidopsis

Due to the preeminence of reductionist approaches, our understanding of plant responses to combined stresses is limited. We speculated that light-quality signals of neighboring vegetation might increase susceptibility to heat shocks because shade reduces tissue temperature and hence the likeness of heat shocks. In contrast, plants of Arabidopsis thaliana grown under low red / far-red ratios typical of shade were less damaged by heat stress than plants grown under simulated sunlight. Shade reduces the activity of phytochrome B (phyB) and the phyB mutant showed high tolerance to heat stress even under simulated sunlight. The enhanced heat tolerance under low red / far-red ratios failed in a multiple mutant of PHYTOCHROME INTERACTING FACTORs. The phyB mutant showed reduced expression of several fatty acid desaturase (FAD) genes, proportion of fully unsaturated fatty acids and electrolyte leakage of membranes exposed to a heat shock. Activation of phyB by red light also reduced thermotolerance of dark-grown (etiolated) seedlings but not via changes in FAD gene expression and membrane stability. We propose that the reduced photosynthetic capacity linked to thermotolerant membranes would be less costly under shade, where the light input itself limits photosynthesis.