Julia Foreman

Prediction of Photoperiodic Regulators from Quantitative Gene Circuit Models

Photoperiod sensors allow physiological adaptation to the changing seasons. The prevalent hypothesis is that day length perception is mediated through coupling of an endogenous rhythm with an external light signal. Sufficient molecular data are available to test this quantitatively in plants, though not yet in mammals. In Arabidopsis, the clock-regulated genes CONSTANS (CO) and FLAVIN, KELCH, F-BOX (FKF1) and their light-sensitive proteins are thought to form an external coincidence sensor. Here, we model the integration of light and timing information by CO, its target gene FLOWERING LOCUS T (FT), and the circadian clock. Among other predictions, our models show that FKF1 activates FT. We demonstrate experimentally that this effect is independent of the known activation of CO by FKF1, thus we locate a major, novel controller of photoperiodism. External coincidence is part of a complex photoperiod sensor: modeling makes this complexity explicit and may thus contribute to crop improvement.

Light receptor action is critical for maintaining plant biomass at warm ambient temperatures

The ability to withstand environmental temperature variation is essential for plant survival. Former studies in Arabidopsis revealed that light signalling pathways had a potentially unique role in shielding plant growth and development from seasonal and daily fluctuations in temperature. In this paper we describe the molecular circuitry through which the light receptors cry1 and phyB buffer the impact of warm ambient temperatures. We show that the light signalling component HFR1 acts to minimise the potentially devastating effects of elevated temperature on plant physiology. Light is known to stabilise levels of HFR1 protein by suppressing proteasome-mediated destruction of HFR1. We demonstrate that light-dependent accumulation and activity of HFR1 are highly temperature dependent. The increased potency of HFR1 at warmer temperatures provides an important restraint on PIF4 that drives elongation growth. We show that warm ambient temperatures promote the accumulation of phosphorylated PIF4. However, repression of PIF4 activity by phyB and cry1 (via HFR1) is critical for controlling growth and maintaining physiology as temperatures rise. Loss of this light-mediated restraint has severe consequences for adult plants which have greatly reduced biomass.

Network balance via CRY signalling controls the Arabidopsis circadian clock over ambient temperatures

Circadian clocks exhibit ‘temperature compensation’, meaning that they show only small changes in period over a broad temperature range. Several clock genes have been implicated in the temperature‐dependent control of period in Arabidopsis. We show that blue light is essential for this, suggesting that the effects of light and temperature interact or converge upon common targets in the circadian clock. Our data demonstrate that two cryptochrome photoreceptors differentially control circadian period and sustain rhythmicity across the physiological temperature range. In order to test the hypothesis that the targets of light regulation are sufficient to mediate temperature compensation, we constructed a temperature‐compensated clock model by adding passive temperature effects into only the light‐sensitive processes in the model. Remarkably, this model was not only capable of full temperature compensation and consistent with mRNA profiles across a temperature range, but also predicted the temperature‐dependent change in the level of LATE ELONGATED HYPOCOTYL, a key clock protein. Our analysis provides a systems‐level understanding of period control in the plant circadian oscillator.

Linked circadian outputs control elongation growth and flowering in response to photoperiod and temperature

Clock‐regulated pathways coordinate the response of many developmental processes to changes in photoperiod and temperature. We model two of the best‐understood clock output pathways in Arabidopsis, which control key regulators of flowering and elongation growth. In flowering, the model predicted regulatory links from the clock to CYCLING DOF FACTOR 1 (CDF1) and FLAVIN‐BINDING, KELCH REPEAT, F‐BOX 1 (FKF1) transcription. Physical interaction data support these links, which create threefold feed‐forward motifs from two clock components to the floral regulator FT. In hypocotyl growth, the model described clock‐regulated transcription of PHYTOCHROME‐INTERACTING FACTOR 4 and 5 (PIF4, PIF5), interacting with post‐translational regulation of PIF proteins by phytochrome B (phyB) and other light‐activated pathways. The model predicted bimodal and end‐of‐day PIF activity profiles that are observed across hundreds of PIF‐regulated target genes. In the response to temperature, warmth‐enhanced PIF4 activity explained the observed hypocotyl growth dynamics but additional, temperature‐dependent regulators were implicated in the flowering response. Integrating these two pathways with the clock model highlights the molecular mechanisms that coordinate plant development across changing conditions.

Arabidopsis cell expansion is controlled by a photothermal switch

In Arabidopsis, the seedling hypocotyl has emerged as an exemplar model system to study light and temperature control of cell expansion. Light sensitivity of this organ is epitomized in the fluence rate response where suppression of hypocotyl elongation increases incrementally with light intensity. This finely calibrated response is controlled by the photoreceptor, phytochrome B, through the deactivation and proteolytic destruction of phytochrome-interacting factors (PIFs). Here we show that this classical light response is strictly temperature dependent: a shift in temperature induces a dramatic reversal of response from inhibition to promotion of hypocotyl elongation by light. Applying an integrated experimental and mathematical modelling approach, we show how light and temperature coaction in the circuitry drives a molecular switch in PIF activity and control of cell expansion. This work provides a paradigm to understand the importance of signal convergence in evoking different or non-intuitive alterations in molecular signalling.

Paths through the phytochrome network.

Since the discovery of the physical interaction between phytochrome B and the basic helix-loop-helix (bHLH) transcription factor (TF) PIF3 a decade ago, plant phytochrome-signalling research has largely focused on understanding the mechanisms through which phytochromes and members of this bHLH family signal. This concerted effort has revealed how phytochrome and bHLH TF control gene expression and plant growth, and has assigned precise roles to a number of genes in the PIF3-like bHLH TF clade. This work has focused largely on cell autonomous signalling events; however, to synchronize plant growth and developmental events at the tissue and organ level, temporal and spatial signal integration is crucial. This review brings together current knowledge of phytochrome signalling through phytochrome-interacting factors (PIFs)/phytochrome-interacting factor-like (PILs), and it evaluates the current evidence for cross-tissue signal integration.

HIGH EXPRESSION OF OSMOTICALLY RESPONSIVE GENES1 Is Required for Circadian Periodicity through the Promotion of Nucleo-Cytoplasmic mRNA Export in Arabidopsis

This work shows that HOS1, previously characterized as a nuclear pore–associated E3 ubiquitin ligase, is required for nucleo-cytoplasmic mRNA export. This study demonstrates that this reduction in nucleo-cytoplasmic export by hos1, or mutations to other previously characterized nuclear pore–associated proteins, leads to altered RNA levels and rhythms, circadian clock function, and cold signaling. Cold acclimation has been shown to be attenuated by the degradation of the INDUCER OF CBF EXPRESSION1 protein by the E3 ubiquitin ligase HIGH EXPRESSION OF OSMOTICALLY RESPONSIVE GENES1 (HOS1). However, recent work has suggested that HOS1 may have a wider range of roles in plants than previously appreciated. Here, we show that hos1 mutants are affected in circadian clock function, exhibiting a long-period phenotype in a wide range of temperature and light environments. We demonstrate that hos1 mutants accumulate polyadenylated mRNA in the nucleus and that the circadian defect in hos1 is shared by multiple mutants with aberrant mRNA export, but not in a mutant attenuated in nucleo-cytoplasmic transport of microRNAs. As revealed by RNA sequencing, hos1 exhibits gross changes to the transcriptome with genes in multiple functional categories being affected. In addition, we show that hos1 and other previously described mutants with altered mRNA export affect cold signaling in a similar manner. Our data support a model in which altered mRNA export is important for the manifestation of hos1 circadian clock defects and suggest that HOS1 may indirectly affect cold signaling through disruption of the circadian clock.

Inference on periodicity of circadian time series

Estimation of the period length of time-course data from cyclical biological processes, such as those driven by the circadian pacemaker, is crucial for inferring the properties of the biological clock found in many living organisms. We propose a methodology for period estimation based on spectrum resampling (SR) techniques. Simulation studies show that SR is superior and more robust to non-sinusoidal and noisy cycles than a currently used routine based on Fourier approximations. In addition, a simple fit to the oscillations using linear least squares is available, together with a non-parametric test for detecting changes in period length which allows for period estimates with different variances, as frequently encountered in practice. The proposed methods are motivated by and applied to various data examples from chronobiology.

The plant‐specific CDKB1‐CYCB1 complex mediates homologous recombination repair in Arabidopsis

Upon DNA damage, cyclin‐dependent kinases (CDKs) are typically inhibited to block cell division. In many organisms, however, it has been found that CDK activity is required for DNA repair, especially for homology‐dependent repair (HR), resulting in the conundrum how mitotic arrest and repair can be reconciled. Here, we show that Arabidopsis thaliana solves this dilemma by a division of labor strategy. We identify the plant‐specific B1‐type CDKs (CDKB1s) and the class of B1‐type cyclins (CYCB1s) as major regulators of HR in plants. We find that RADIATION SENSITIVE 51 (RAD51), a core mediator of HR, is a substrate of CDKB1‐CYCB1 complexes. Conversely, mutants in CDKB1 and CYCB1 fail to recruit RAD51 to damaged DNA. CYCB1;1 is specifically activated after DNA damage and we show that this activation is directly controlled by SUPPRESSOR OF GAMMA RESPONSE 1 (SOG1), a transcription factor that acts similarly to p53 in animals. Thus, while the major mitotic cell‐cycle activity is blocked after DNA damage, CDKB1‐CYCB1 complexes are specifically activated to mediate HR.

Shedding light on flower development: Phytochrome B regulates gynoecium formation in association with the transcription factor SPATULA

Accurate development of the gynoecium, the female reproductive organ, is necessary to achieve efficient fertilization. In Arabidopsis, the correct patterning of the apical-basal axis of the gynoecium requires the establishment of a morphogenic gradient of auxin. This allows the production of specialized tissues, whose roles consist of attracting pollen, allowing pollen tube growth and protecting the ovules within the ovaries. Mutations in the bHLH transcription factor SPATULA (SPT) are known to impair the development of the apical tissues of the gynoecium. Here, we show that the spt phenotype is rescued by the removal of phytochrome B, and discuss how light signaling may control flower development.