PIF7 is a master regulator of thermomorphogenesis in shade.

The size of plant organs is highly responsive to environmental conditions. The plant's embryonic stem, or hypocotyl, displays phenotypic plasticity, in response to light and temperature. The hypocotyl of shade avoiding species elongates to outcompete neighboring plants and secure access to sunlight. Similar elongation occurs in high temperature. However, it is poorly understood how environmental light and temperature cues interact to effect plant growth. We found that shade combined with warm temperature produces a synergistic hypocotyl growth response that dependent on PHYTOCHROME-INTERACTING FACTOR 7 (PIF7) and auxin. This unique but agriculturally relevant scenario was almost totally independent on PIF4 activity. We show that warm temperature is sufficient to promote PIF7 DNA binding but not transcriptional activation and we demonstrate that additional, unknown factor/s must be working downstream of the phyB-PIF-auxin module. Our findings will improve the predictions of how plants will respond to increased ambient temperatures when grown at high density.

Local HY5 Activity Mediates Hypocotyl Growth and Shoot-to-Root Communication.

Plants optimize their growth in fluctuating environments using information acquired by different organs. This information is then transmitted through the rest of the plant using both short- and long-distance signals, including hormones and mobile proteins. Although a few of these signals have been characterized, long-distance signaling is not well understood in plants. Recently, the light-regulated transcription factor HY5 was reported to move from the shoot to the root to regulate root growth. We generated a cell-type specifically expressed HY5 fusion protein that could not be detected outside the tissue in which it was targeted. By expressing this DOF-HY5 protein in specific cell types of the hypocotyl, we showed that its local activity was sufficient to regulate hypocotyl growth. We also found that, although DOF-HY5 was expressed specifically in the shoot and not detected in the roots, it could rescue hy5 growth defects in primary roots but not in lateral roots. We therefore conclude that HY5 protein mobility is not required in the hypocotyl or for shoot-to-root communication. Our results indicate that a signal downstream of, or in parallel with, HY5 in the shoot is mobile and links shoot and root growth.

Chimeric Activators and Repressors Define HY5 Activity and Reveal a Light-Regulated Feedback Mechanism.

The first exposure to light marks a crucial transition in plant development. This transition relies on the transcription factor HY5 controlling a complex downstream growth program. Despite its importance, its function in transcription remains unclear. Previous studies have generated lists of thousands of potential target genes and competing models of HY5 transcription regulation. In this work, we carry out detailed phenotypic and molecular analysis of constitutive activator and repressor HY5 fusion proteins. Using this strategy, we were able to filter out large numbers of genes that are unlikely to be direct targets, allowing us to eliminate several proposed models of HY5's mechanism of action. We demonstrate that the primary activity of HY5 is promoting transcription and that this function relies on other, likely light-regulated, factors. In addition, this approach reveals a molecular feedback loop via the COP1/SPA E3 ubiquitin ligase complex, suggesting a mechanism that maintains low HY5 in the dark, primed for rapid accumulation to reprogram growth upon light exposure. Our strategy is broadly adaptable to the study of transcription factor activity. Lastly, we show that modulating this feedback loop can generate significant phenotypic diversity in both Arabidopsis (Arabidopsis thaliana) and tomato (Solanum lycopersicum).

Dancing in the dark: darkness as a signal in plants.

Daily cycles of light and dark provide an organizing principle and temporal constraints under which life on Earth evolved. While light is often the focus of plant studies, it is only half the story. Plants continuously adjust to their surroundings, taking both dawn and dusk as cues to organize their growth, development and metabolism to appropriate times of day. In this review, we examine the effects of darkness on plant physiology and growth. We describe the similarities and differences between seedlings grown in the dark versus those grown in light-dark cycles, and the evolution of etiolated growth. We discuss the integration of the circadian clock into other processes, looking carefully at the points of contact between clock genes and growth-promoting gene-regulatory networks in temporal gating of growth. We also examine daily starch accumulation and degradation, and the possible contribution of dark-specific metabolic controls in regulating energy and growth. Examining these studies together reveals a complex and continuous balancing act, with many signals, dark included, contributing information and guiding the plant through its life cycle. The extraordinary interconnection between light and dark is manifest during cycles of day and night and during seedling emergence above versus below the soil surface.

Dual PDF signaling pathways reset clocks via TIMELESS and acutely excite target neurons to control circadian behavior.

Molecular circadian clocks are interconnected via neural networks. In Drosophila, PIGMENT-DISPERSING FACTOR (PDF) acts as a master network regulator with dual functions in synchronizing molecular oscillations between disparate PDF(+) and PDF(-) circadian pacemaker neurons and controlling pacemaker neuron output. Yet the mechanisms by which PDF functions are not clear. We demonstrate that genetic inhibition of protein kinase A (PKA) in PDF(-) clock neurons can phenocopy PDF mutants while activated PKA can partially rescue PDF receptor mutants. PKA subunit transcripts are also under clock control in non-PDF DN1p neurons. To address the core clock target of PDF, we rescued per in PDF neurons of arrhythmic per°¹ mutants. PDF neuron rescue induced high amplitude rhythms in the clock component TIMELESS (TIM) in per-less DN1p neurons. Complete loss of PDF or PKA inhibition also results in reduced TIM levels in non-PDF neurons of per°¹ flies. To address how PDF impacts pacemaker neuron output, we focally applied PDF to DN1p neurons and found that it acutely depolarizes and increases firing rates of DN1p neurons. Surprisingly, these effects are reduced in the presence of an adenylate cyclase inhibitor, yet persist in the presence of PKA inhibition. We have provided evidence for a signaling mechanism (PKA) and a molecular target (TIM) by which PDF resets and synchronizes clocks and demonstrates an acute direct excitatory effect of PDF on target neurons to control neuronal output. The identification of TIM as a target of PDF signaling suggests it is a multimodal integrator of cell autonomous clock, environmental light, and neural network signaling. Moreover, these data reveal a bifurcation of PKA-dependent clock effects and PKA-independent output effects. Taken together, our results provide a molecular and cellular basis for the dual functions of PDF in clock resetting and pacemaker output.

The CRYPTOCHROME photoreceptor gates PDF neuropeptide signaling to set circadian network hierarchy in Drosophila.

Circadian clocks in the brain are organized as coupled oscillators that integrate seasonal cues such as light and temperature to time daily behaviors. In Drosophila, the PIGMENT DISPERSING FACTOR (PDF) neuropeptide-expressing morning (M) and non-PDF evening (E) cells are coupled cell groups important for morning and evening behavior, respectively. Depending on day length, either M cells (short days) or E cells (long days) dictate both the morning and the evening phase, a phenomenon that we term network hierarchy. To examine the role of PDF in light-dark conditions, we examined flies lacking both the PDF receptor (PDFR) and the circadian photoreceptor CRYPTOCHROME (CRY). We found that subsets of E cells exhibit molecular oscillations antiphase to those of wild-type flies, single cry mutants, or single Pdfr mutants, demonstrating a potent role for PDF in light-mediated entrainment, specifically in the absence of CRY. Moreover, we find that the evening behavioral phase is more strongly reset by PDF(+) M cells in the absence of CRY. On the basis of our findings, we propose that CRY can gate PDF signaling to determine behavioral phase and network hierarchy.