Phytochrome B dynamics departs from photoequilibrium in the field

The interactive effects between far-red light and temperature on lettuce growth and morphology diminish at high light intensity

Phytochromes (PHYs) play a dual role in sensing light spectral quality and temperature. PHYs can interconvert between the active Pfr form and inactive Pr form upon absorption of red (R) and far-red (FR) light (Photoconversion). In addition, active Pfr can be converted to inactive Pr in a temperature-dependent manner (Thermal Reversion). Recent studies have shown that FR light and temperature can interactively affect plant growth and morphology through co-regulating phytochrome activities. These studies were primarily conducted under relatively low light intensities. As light intensity increases, the impact of thermal reversion on phytochrome dynamics decreases. However, the light intensity dependency of the interactive effects between FR light and temperature on plant growth and morphology has not been characterized. In this study, lettuce (Lactuca sativa L.) 'Rex' was grown under two total photon flux densities (TPFD; 400-800 nm) (150 and 300 μmol m-2 s-1) x three temperatures (20, 24, and 28°C) x two light spectra (0 and 20% of FR light in TPFD). Our results showed that the effects of FR light on leaf, stem, and root elongation, leaf number, and leaf expansion were dependent on temperature at lower TPFD. However, the magnitude of the interactive effects between FR light and temperature on plant morphology decreased at higher TPFD. Particularly, at a lower TPFD, FR light stimulated leaf expansion and canopy photon capture only under a cooler temperature of 20°C. However, at a higher TPFD, FR light consistently increased total leaf area across all three temperatures. Plant biomass was more strongly correlated with the total number of photons intercepted by the leaves than with the photosynthetic activities of individual leaves. FR light decreased the contents of chlorophylls, carotenoids, flavonoids, and phenolics, as well as the total antioxidant capacity. In contrast, warmer temperatures and high light intensity increased the values of these parameters. We concluded that the interactive effects between FR light and temperature on plant growth and morphology diminished as total light intensity increased. Additionally, the combination of high light intensity, warm temperature, and FR light resulted in the highest crop yield and antioxidant capacity in lettuce.

Plant Thermosensors

Plants are exposed to temperature conditions that fluctuate over different time scales, including those inherent to global warming. In the face of these variations, plants sense temperature to adjust their functions and minimize the negative consequences. Transcriptome responses underlie changes in growth, development, and biochemistry (thermomorphogenesis and acclimation to extreme temperatures). We are only beginning to understand temperature sensation by plants. Multiple thermosensors convey complementary temperature information to a given signaling network to control gene expression. Temperature-induced changes in protein or transcript structure and/or in the dynamics of biomolecular condensates are the core sensing mechanisms of known thermosensors, but temperature impinges on their activities via additional indirect pathways. The diversity of plant responses to temperature anticipates that many new thermosensors and eventually novel sensing mechanisms will be uncovered soon.

UV RESISTANCE LOCUS 8-Mediated UV-B Response Is Required Alongside CRYPTOCHROME 1 for Plant Survival in Sunlight under Field Conditions

As sessile, photoautotrophic organisms, plants are subjected to fluctuating sunlight that includes potentially detrimental ultraviolet-B (UV-B) radiation. Experiments under controlled conditions have shown that the UV-B photoreceptor UV RESISTANCE LOCUS 8 (UVR8) controls acclimation and tolerance to UV-B in Arabidopsis thaliana; however, its long-term impact on plant fitness under naturally fluctuating environments remain poorly understood. Here, we quantified the survival and reproduction of different Arabidopsis mutant genotypes under diverse field and laboratory conditions. We found that uvr8 mutants produced more fruits than wild type when grown in growth chambers under artificial low-UV-B conditions but not under natural field conditions, indicating a fitness cost in the absence of UV-B stress. Importantly, independent double mutants of UVR8 and the blue light photoreceptor gene CRYPTOCHROME 1 (CRY1) in two genetic backgrounds showed a drastic reduction in fitness in the field. Experiments with UV-B attenuation in the field and with supplemental UV-B in growth chambers demonstrated that UV-B caused the cry1 uvr8 conditional lethal phenotype. Using RNA-seq data of field-grown single and double mutants, we explicitly identified genes showing significant statistical interaction of UVR8 and CRY1 mutations in the presence of UV-B in the field. They were enriched in Gene Ontology categories related to oxidative stress, photoprotection and DNA damage repair in addition to UV-B response. Our study demonstrates the functional importance of the UVR8-mediated response across life stages in natura, which is partially redundant with that of cry1. Moreover, these data provide an integral picture of gene expression associated with plant responses under field conditions.

On the contrasting morphological response to far-red at high and low photon fluxes

Plants compete for sunlight and have evolved to perceive shade through both relative increases in the flux of far-red photons (FR; 700 to 750 nm) and decreases in the flux of all photons (intensity). These two signals interact to control stem elongation and leaf expansion. Although the interacting effects on stem elongation are well quantified, responses for leaf expansion are poorly characterized. Here we report a significant interaction between far-red fraction and total photon flux. Extended photosynthetic photon flux density (ePPFD; 400 to 750 nm) was maintained at three levels (50/100, 200 and 500 µmol m^-2 s^-1), each with a range of 2 to 33% FR. Increasing FR increased leaf expansion in three cultivars of lettuce at the highest ePPFD but decreased expansion at the lowest ePPFD. This interaction was attributed to differences in biomass partitioning between leaves and stems. Increased FR favored stem elongation and biomass partitioning to stems at low ePPFD and favored leaf expansion at high ePPFD. In cucumber, leaf expansion was increased with increasing percent FR under all ePPFD levels showing minimal interaction. The interactions (and lack thereof) have important implications for horticulture and warrant further study for plant ecology.

The adaptive nature of the plant circadian clock in natural environments

The plant circadian clock coordinates developmental, physiological, and metabolic processes with diel changes in light and temperature throughout the year. The balance between the persistence and plasticity of the clock in response to predictable and unpredictable environmental changes may be key to the clock's adaptive nature across temporal and spatial scales. Studies under controlled conditions have uncovered critical signaling pathways involved in light and temperature perception by the clock; however, they don't account for the natural lag of temperature behind photoperiod. Studies in natural environments provide key insights into the clock's adaptive advantage under more complex natural settings. Here, we discuss the role of the circadian clock in light and temperature perception and signaling, how the clock integrates these signals for a coordinated and adaptive response, and the adaptive advantage conferred by the clock across time and space in natural environments.

PIFs- and COP1-HY5-mediated temperature signaling in higher plants

Plants have to cope with the surrounding changing environmental stimuli to optimize their physiological and developmental response throughout their entire life cycle. Light and temperature are two critical environmental cues that fluctuate greatly during day-night cycles and seasonal changes. These two external signals coordinately control the plant growth and development. Distinct spectrum of light signals are perceived by a group of wavelength-specific photoreceptors in plants. PIFs and COP1-HY5 are two predominant signaling hubs that control the expression of a large number of light-responsive genes and subsequent light-mediated development in plants. In parallel, plants also transmit low or warm temperature signals to these two regulatory modules that precisely modulate the responsiveness of low or warm temperatures. The core component of circadian clock ELF3 integrates signals from light and warm temperatures to regulate physiological and developmental processes in plants. In this review, we summarize and discuss recent advances and progresses on PIFs-, COP1-HY5- and ELF3-mediated light, low or warm temperature signaling, and highlight emerging insights regarding the interactions between light and low or warm temperature signal transduction pathways in the control of plant growth.

EARLY FLOWERING 3 represses the nighttime growth response to sucrose in Arabidopsis

Plant growth depends on the supply of carbohydrates produced by photosynthesis. Exogenously applied sucrose promotes the growth of the hypocotyl in Arabidopsis thaliana seedlings grown under short days. Whether this effect of sucrose is stronger under the environmental conditions where the light input for photosynthesis is limiting remains unknown. We characterised the effects of exogenous sucrose on hypocotyl growth rates under light compared to simulated shade, during different portions of the daily cycle. The strongest effects of exogenous sucrose occurred under shade and during the night; i.e., the conditions where there is reduced or no photosynthesis. Conversely, a faster hypocotyl growth rate, predicted to enhance the demand of carbohydrates, did not associate to a stronger sucrose effect. The early flowering 3 (elf3) mutation strongly enhanced the impact of sucrose on hypocotyl growth during the night of a white-light day. This effect occurred under short, but not under long days. The addition of sucrose enhanced the fluorescence intensity of ELF3 nuclear speckles. The elf3 mutant showed increased abundance of PHYTOCHROME INTERACTING FACTOR4 (PIF4), which is a transcription factor required for a full response to sucrose. Sucrose increased PIF4 protein abundance by post-transcriptional mechanisms. Under shade, elf3 showed enhanced daytime and reduced nighttime effects of sucrose. We conclude that ELF3 modifies the responsivity to sucrose according to the time of the daily cycle and the prevailing light or shade conditions.

Organ-specific COP1 control of BES1 stability adjusts plant growth patterns under shade or warmth

Under adverse conditions such as shade or elevated temperatures, cotyledon expansion is reduced and hypocotyl growth is promoted to optimize plant architecture. The mechanisms underlying the repression of cotyledon cell expansion remain unknown. Here, we report that the nuclear abundance of the BES1 transcription factor decreased in the cotyledons and increased in the hypocotyl in Arabidopsis thaliana under shade or warmth. Brassinosteroid levels did not follow the same trend. PIF4 and COP1 increased their nuclear abundance in both organs under shade or warmth. PIF4 directly bound the BES1 promoter to enhance its activity but indirectly reduced BES1 expression. COP1 physically interacted with the BES1 protein, promoting its proteasome degradation in the cotyledons. COP1 had the opposite effect in the hypocotyl, demonstrating organ-specific regulatory networks. Our work indicates that shade or warmth reduces BES1 activity by transcriptional and post-translational regulation to inhibit cotyledon cell expansion.

Hysteresis in PHYTOCHROME-INTERACTING FACTOR 4 and EARLY-FLOWERING 3 dynamics dominates warm daytime memory in Arabidopsis

Despite the identification of temperature sensors and downstream components involved in promoting stem growth by warm temperatures, when and how previous temperatures affect current plant growth remain unclear. Here we show that hypocotyl growth in Arabidopsis thaliana during the night responds not only to the current temperature but also to preceding daytime temperatures, revealing a short-term memory of previous conditions. Daytime temperature affected the levels of PHYTOCHROME-INTERACTING FACTOR 4 (PIF4) and LONG HYPOCOTYL 5 (HY5) in the nucleus during the next night. These factors jointly accounted for the observed growth kinetics, whereas nighttime memory of prior daytime temperature was impaired in pif4 and hy5 mutants. PIF4 promoter activity largely accounted for the temperature-dependent changes in PIF4 protein levels. Notably, the decrease in PIF4 promoter activity triggered by cooling required a stronger temperature shift than the increase caused by warming, representing a typical hysteretic effect; this hysteretic pattern required EARLY-FLOWERING 3 (ELF3). Warm temperatures promoted the formation of nuclear condensates of ELF3 in hypocotyl cells during the afternoon but not in the morning. These nuclear speckles showed poor sensitivity to subsequent cooling. We conclude that ELF3 achieves hysteresis and drives the PIF4 promoter into the same behavior, enabling a short-term memory of daytime temperature conditions.

Functional convergence of growth responses to shade and warmth in Arabidopsis

Shade and warmth promote the growth of the stem, but the degree of mechanistic convergence and functional association between these responses is not clear. We analysed the quantitative impact of mutations and natural genetic variation on the hypocotyl growth responses of Arabidopsis thaliana to shade and warmth, the relationship between the abundance of PHYTOCHROME INTERACTING FACTOR 4 (PIF4) and growth stimulation by shade or warmth, the effects of both cues on the transcriptome and the consequences of warm temperature on carbon balance. Growth responses to shade and warmth showed strong genetic linkage and similar dependence on PIF4 levels. Temperature increased growth and phototropism even within a range where damage by extreme high temperatures is unlikely to occur in nature. Both cues enhanced the expression of growth-related genes and reduced the expression of photosynthetic genes. However, only warmth enhanced the expression of genes involved in responses to heat. Warm temperatures substantially increased the amount of light required to compensate for the daily carbon dioxide balance. We propose that the main ecological function of hypocotyl growth responses to warmth is to increase the access of shaded photosynthetic organs to light, which implies functional convergence with shade avoidance.

Photons from NIR LEDs can delay flowering in short-day soybean and Cannabis: Implications for phytochrome activity

Photons during the dark period delay flowering in short-day plants (SDP). Red photons applied at night convert phytochromes to the active far-red absorbing form (Pfr), leading to inhibition of flowering. Far-red photons (greater than 700 nm) re-induce flowering when applied after a pulse of red photons during the dark period. However, far-red photons at sufficiently high intensity and duration delay flowering in sensitive species. Mechanistically, this response occurs because phytochrome-red (Pr) absorbance is not zero beyond 700 nm. We applied nighttime photons from near infrared (NIR) LEDs (peak 850 nm) over a 12 h dark period. Flowering was delayed in Glycine max and Cannabis sativa (two photosensitive species) by 3 and 12 days, respectively, as the flux of photons from NIR LEDs was increased up to 83 and 116 μmol m-2 s-1. This suggests that long wavelength photons from NIR LEDs can activate phytochromes (convert Pr to Pfr) and thus alter plant development.

Improving the Predictive Value of Phytochrome Photoequilibrium: Consideration of Spectral Distortion Within a Leaf

The ratio of active phytochrome (Pfr) to total phytochrome (Pr + Pfr), called phytochrome photo-equilibrium (PPE; also called phytochrome photostationary state, PSS) has been used to explain shade avoidance responses in both natural and controlled environments. PPE is commonly estimated using measurements of the spectral photon distribution (SPD) above the canopy and photoconversion coefficients. This approach has effectively predicted morphological responses when only red and far-red (FR) photon fluxes have varied, but controlled environment research often utilizes unique ratios of wavelengths so a more rigorous evaluation of the predictive ability of PPE on morphology is warranted. Estimations of PPE have rarely incorporated the optical effects of spectral distortion within a leaf caused by pigment absorbance and photon scattering. We studied stem elongation rate in the model plant cucumber under diverse spectral backgrounds over a range of one to 45% FR (total photon flux density, 400-750 nm, of 400 μmol m^-2 s^-1) and found that PPE was not predictive when blue and green varied. Preferential absorption of red and blue photons by chlorophyll results in an SPD that is relatively enriched in green and FR at the phytochrome molecule within a cell. This can be described by spectral distortion functions for specific layers of a leaf. Multiplying the photoconversion coefficients by these distortion functions yields photoconversion weighting factors that predict phytochrome conversion at the site of photon perception within leaf tissue. Incorporating spectral distortion improved the predictive value of PPE when phytochrome was assumed to be homogeneously distributed within the whole leaf. In a supporting study, the herbicide norflurazon was used to remove chlorophyll in seedlings. Using distortion functions unique to either green or white cotyledons, we came to the same conclusions as with whole plants in the longer-term study. Leaves of most species have similar spectral absorbance so this approach for predicting PPE should be broadly applicable. We provide a table of the photoconversion weighting factors. Our analysis indicates that the simple, intuitive ratio of FR (700-750 nm) to total photon flux (far-red fraction) is also a reliable predictor of morphological responses like stem length.

Phytochrome B links the environment to transcription

Phytochrome B (phyB) senses the difference between darkness and light, the level of irradiance, the red/far-red ratio, and temperature. Thanks to these sensory capacities, phyB perceives whether plant organs are buried in the soil, exposed to full sunlight, in the presence of nearby vegetation, and/or under risk of heat stress. In some species, phyB perceives seasonal daylength cues. phyB affects the activity of several transcriptional regulators either by direct physical interaction or indirectly by physical interaction with proteins involved in the turnover of transcriptional regulators. Typically, interaction of a protein with phyB has either negative or positive effects on the interaction of the latter with a third party, this being another protein or DNA. Thus, phyB mediates the context-dependent modulation of the transcriptome underlying changes in plant morphology, physiology, and susceptibility to biotic and abiotic stress. phyB operates as a dynamic switch that improves carbon balance, prioritizing light interception and photosynthetic capacity in open places and the projection of the shoot towards light in the soil, under shade and in warm conditions.

Auxin-Environment Integration in Growth Responses to Forage for Resources

Plant fitness depends on the adequate morphological adjustment to the prevailing conditions of the environment. Therefore, plants sense environmental cues through their life cycle, including the presence of full darkness, light, or shade, the range of ambient temperatures, the direction of light and gravity vectors, and the presence of water and mineral nutrients (such as nitrate and phosphate) in the soil. The environmental information impinges on different aspects of the auxin system such as auxin synthesis, degradation, transport, perception, and downstream transcriptional regulation to modulate organ growth. Although a single environmental cue can affect several of these points, the relative impacts differ significantly among the various growth processes and cues. While stability in the generation of precise auxin gradients serves to guide the basic developmental pattern, dynamic changes in the auxin system fine-tune body shape to optimize the capture of environmental resources.

Phytochrome B and PCH1 protein dynamics store night temperature information

Plants experience temperature fluctuations during the course of the daily cycle, and although stem growth responds rapidly to these changes we largely ignore whether there is a short-term memory of previous conditions. Here we show that nighttime temperatures affect the growth of the hypocotyl of Arabidopsis thaliana seedlings not only during the night but also during the subsequent photoperiod. Active phytochrome B (phyB) represses nighttime growth and warm temperatures reduce active phyB via thermal reversion. The function of PHOTOPERIODIC CONTROL OF HYPOCOTYL1 (PCH1) is to stabilise active phyB in nuclear bodies but, surprisingly, warmth reduces PCH1 gene expression and PCH1 stability. When phyB was active at the beginning of the night, warm night temperatures enhanced the levels of nuclear phyB and reduced hypocotyl growth rate during the following day. However, when end-of-day far-red light minimised phyB activity, warm night temperatures reduced the levels of nuclear phyB and enhanced the hypocotyl growth rate during the following day. This complex growth pattern was absent in the phyB mutant. We propose that temperature-induced changes in the levels of PCH1 and in the size of the physiologically relevant nuclear pool of phyB amplify the impact of phyB-mediated temperature sensing.

Shade avoidance responses become more aggressive in warm environments

When exposed to neighbour cues, competitive plants increase stem growth to reduce the degree of current or future shade. The aim of this work is to investigate the impact of weather conditions on the magnitude of shade avoidance responses in Arabidopsis thaliana. We first generated a growth rate database under controlled conditions and elaborated a model that predicts daytime hypocotyl growth as a function of the activity of the main photosensory receptors (phytochromes A and B, cryptochromes 1 and 2) in combination with light and temperature inputs. We then incorporated the action of thermal amplitude to account for its effect on selected genotypes, which correlates with the dynamics of the growth-promoting transcription factor PHYTOCHROME-INTERACTING FACTOR 4. The model predicted growth rate in the field with reasonable accuracy. Thus, we used the model in combination with a worldwide data set of current and future whether conditions. The analysis predicted enhanced shade avoidance responses as a result of higher temperatures due to the geographical location or global warming. Irradiance and thermal amplitude had no effects. These trends were also observed for our local growth rate measurements. We conclude that, if water and nutrients do not become limiting, warm environments enhance the shade avoidance response.

Photosynthetic Acclimation to Fluctuating Irradiance in Plants

Unlike the short-term responses of photosynthesis to fluctuating irradiance, the long-term response (i.e., acclimation) at the chloroplast, leaf, and plant level has received less attention so far. The ability of plants to acclimate to irradiance fluctuations and the speed at which this acclimation occurs are potential limitations to plant growth under field conditions, and therefore this process deserves closer study. In the first section of this review, we look at the sources of natural irradiance fluctuations, their effects on short-term photosynthesis, and the interaction of these effects with circadian rhythms. This is followed by an overview of the mechanisms that are involved in acclimation to fluctuating (or changes of) irradiance. We highlight the chain of events leading to acclimation: retrograde signaling, systemic acquired acclimation (SAA), gene transcription, and changes in protein abundance. We also review how fluctuating irradiance is applied in experiments and highlight the fact that they are significantly slower than natural fluctuations in the field, although the technology to achieve realistic fluctuations exists. Finally, we review published data on the effects of growing plants under fluctuating irradiance on different plant traits, across studies, spatial scales, and species. We show that, when plants are grown under fluctuating irradiance, the chlorophyll a/b ratio and plant biomass decrease, specific leaf area increases, and photosynthetic capacity as well as root/shoot ratio are, on average, unaffected.

Differential phosphorylation of the N-terminal extension regulates phytochrome B signaling

Phytochrome B (phyB) is an excellent light quality and quantity sensor that can detect subtle changes in the light environment. The relative amounts of the biologically active photoreceptor (phyB Pfr) are determined by the light conditions and light independent thermal relaxation of Pfr into the inactive phyB Pr, termed thermal reversion. Little is known about the regulation of thermal reversion and how it affects plants' light sensitivity. In this study we identified several serine/threonine residues on the N-terminal extension (NTE) of Arabidopsis thaliana phyB that are differentially phosphorylated in response to light and temperature, and examined transgenic plants expressing nonphosphorylatable and phosphomimic phyB mutants. The NTE of phyB is essential for thermal stability of the Pfr form, and phosphorylation of S86 particularly enhances the thermal reversion rate of the phyB Pfr-Pr heterodimer in vivo. We demonstrate that S86 phosphorylation is especially critical for phyB signaling compared with phosphorylation of the more N-terminal residues. Interestingly, S86 phosphorylation is reduced in light, paralleled by a progressive Pfr stabilization under prolonged irradiation. By investigating other phytochromes (phyD and phyE) we provide evidence that acceleration of thermal reversion by phosphorylation represents a general mechanism for attenuating phytochrome signaling.

Molecular mechanisms underlying phytochrome-controlled morphogenesis in plants

Phytochromes are bilin-binding photosensory receptors which control development over a broad range of environmental conditions and throughout the whole plant life cycle. Light-induced conformational changes enable phytochromes to interact with signaling partners, in particular transcription factors or proteins that regulate them, resulting in large-scale transcriptional reprograming. Phytochromes also regulate promoter usage, mRNA splicing and translation through less defined routes. In this review we summarize our current understanding of plant phytochrome signaling, emphasizing recent work performed in Arabidopsis. We compare and contrast phytochrome responses and signaling mechanisms among land plants and highlight open questions in phytochrome research.