The metabolic sensor AKIN10 modulates the Arabidopsis circadian clock in a light-dependent manner

Stable and dynamic gene expression patterns over diurnal and developmental timescales in Arabidopsis thaliana

Developmental processes are known to be circadian-regulated in plants. For instance, the circadian clock regulates genes involved in the photoperiodic flowering pathway and the initiation of leaf senescence. Furthermore, signals that entrain the circadian clock, such as energy availability, are known to vary in strength over plant development. However, diel oscillations of the Arabidopsis transcriptome have typically been measured in seedlings. We collected RNA sequencing (RNA-seq) data from Arabidopsis leaves over developmental and diel timescales, concurrently: every 4 h d-1, on three separate days after a synchronised vegetative-to-reproductive transition. Gene expression varied more over the developmental timescale than on the diel timescale, including genes related to a key energy sensor: the sucrose nonfermenting-1-related protein kinase complex. Moreover, regulatory targets of core clock genes displayed changes in rhythmicity and amplitude of expression over development. Cell-type-specific expression showed diel patterns that varied in amplitude, but not phase, over development. Some previously identified reverse transcription quantitative polymerase chain reaction housekeeping genes display undesirable levels of variation over both timescales. We identify which common reverse transcription quantitative polymerase chain reaction housekeeping genes are most stable across developmental and diel timescales. In summary, we establish the patterns of circadian transcriptional regulation over plant development, demonstrating how diel patterns of expression change over developmental timescales.

Cytochrome c levels link mitochondrial function to plant growth and stress responses through changes in SnRK1 pathway activity

Energy is required for growth as well as for multiple cellular processes. During evolution, plants developed regulatory mechanisms to adapt energy consumption to metabolic reserves and cellular needs. Reduced growth is often observed under stress, leading to a growth-stress trade-off that governs plant performance under different conditions. In this work, we report that plants with reduced levels of the mitochondrial respiratory chain component cytochrome c (CYTc), required for electron transport coupled to oxidative phosphorylation and ATP production, show impaired growth and increased global expression of stress-responsive genes, similar to those observed after inhibiting the respiratory chain or the mitochondrial ATP synthase. CYTc-deficient plants also show activation of the SnRK1 pathway, which regulates growth, metabolism, and stress responses under carbon starvation conditions, even though their carbohydrate levels are not significantly different from wild-type. Notably, loss-of-function of the gene encoding the SnRK1α1 subunit restores the growth of CYTc-deficient plants, as well as autophagy, free amino acid and TOR pathway activity levels, which are affected in these plants. Moreover, increasing CYTc levels decreases SnRK1 pathway activation, reflected in reduced SnRK1α1 phosphorylation, with no changes in total SnRK1α1 protein levels. Under stress imposed by mannitol, the growth of CYTc-deficient plants is relatively less affected than that of wild-type plants, which is also related to the activation of the SnRK1 pathway. Our results indicate that SnRK1 function is affected by CYTc levels, thus providing a molecular link between mitochondrial function and plant growth under normal and stress conditions.

Exploring sugar allocation and metabolic shifts in cassava plants infected with Cassava common mosaic virus (CsCMV) under long-day photoperiod: diel changes in source and sink leaves

Cassava common mosaic virus (CsCMV) is a potexvirus that impairs chloroplast and metabolism, causing significant yield losses to cassava crops. Crop yield depends on diel rhythms, influencing carbon allocation and growth, and sugar signaling also impacting light-dark rhythms. This study aimed to elucidate the early impact of CsCMV infection on diel carbon allocation, metabolism, and defense mechanisms in both source and sink cassava leaves before storage root bulking. Soluble sugar and starch concentrations were examined over a 24-h cycle (16:8 photoperiod) in CsCMV-infected plants. The expression of an array of genes-carbohydrate metabolism, SnRK1 activity marker, defense, circadian marker-was analyzed at ZT6, ZT16 and ZT24/ZT0. In CsCMV-infected source leaves, at ZT6, sucrose increased whereas glucose, fructose and sucrose rose at night. An increase in Suc:hexose ratio and upregulation of SnRK1 activity marker genes and PR1 transcripts were found in infected leaves, suggesting a combination of altered carbon metabolism and defense response mechanisms against the viral infection. GIGANTEA, a clock-controlled gene, showed a reduced expression in infected leaves at ZT6 and ZT24/ZT0, suggesting a circadian phase shift compared with uninfected control plants. Additionally, starch mobilization transcripts were downregulated at ZT24/ZT0, though starch content remained unchanged during the 24-h cycle. In sink leaves, a transient peak of maltose (ZT6) was observed. Our findings suggest that CsCMV disrupts the plant's natural rhythms of sugar metabolism and allocation. Spikes in sucrose levels may serve as infection signals in the internal daily clock of the plant, influencing plant responses during the cassava-CsCMV interaction.

Similar chilling response of dormant buds in potato tuber and woody perennials

Bud dormancy is a survival strategy that plants have developed in their native habitats. It helps them endure harsh seasonal changes by temporarily halting growth and activity until conditions become more favorable. Research has primarily focused on bud dormancy in tree species and the ability to halt growth in vegetative tissues, particularly in meristems. Various plant species, such as potato, have developed specialized storage organs, enabling them to become dormant during their yearly growth cycle. Deciduous trees and potato tubers exhibit a similar type of bud endodormancy, where the bud meristem will not initiate growth, even under favorable environmental conditions. Chilling accumulation activates C-repeat/dehydration responsive element binding (DREB) factors (CBFs) transcription factors that modify the expression of dormancy-associated genes. Chilling conditions shorten the duration of endodormancy by influencing plant hormones and sugar metabolism, which affect the timing and rate of bud growth. Sugar metabolism and signaling pathways can interact with abscisic acid, affecting the symplastic connection of dormant buds. This review explores how chilling affects endodormancy duration and explores the similarity of the chilling response of dormant buds in potato tubers and woody perennials.

The critical roles of three sugar-related proteins (HXK, SnRK1, TOR) in regulating plant growth and stress responses

Sugar signaling is one of the most critical regulatory signals in plants, and its metabolic network contains multiple regulatory factors. Sugar signal molecules regulate cellular activities and organism development by combining with other intrinsic regulatory factors and environmental inputs. HXK, SnRK1, and TOR are three fundamental proteins that have a pivotal role in the metabolism of sugars in plants. HXK, being the initial glucose sensor discovered in plants, is renowned for its multifaceted characteristics. Recent investigations have unveiled that HXK additionally assumes a significant role in plant hormonal signaling and abiotic stress. SnRK1 serves as a vital regulator of growth under energy-depleted circumstances, whereas TOR, a large protein, acts as a central integrator of signaling pathways that govern cell metabolism, organ development, and transcriptome reprogramming in response to diverse stimuli. Together, these two proteins work to sense upstream signals and modulate downstream signals to regulate cell growth and proliferation. In recent years, there has been an increasing amount of research on these three proteins, particularly on TOR and SnRK1. Furthermore, studies have found that these three proteins not only regulate sugar signaling but also exhibit certain signal crosstalk in regulating plant growth and development. This review provides a comprehensive overview and summary of the basic functions and regulatory networks of these three proteins. It aims to serve as a reference for further exploration of the interactions between these three proteins and their involvement in co-regulatory networks.

GIGANTEA Unveiled: Exploring Its Diverse Roles and Mechanisms

GIGANTEA (GI) is a conserved nuclear protein crucial for orchestrating the clock-associated feedback loop in the circadian system by integrating light input, modulating gating mechanisms, and regulating circadian clock resetting. It serves as a core component which transmits blue light signals for circadian rhythm resetting and overseeing floral initiation. Beyond circadian functions, GI influences various aspects of plant development (chlorophyll accumulation, hypocotyl elongation, stomatal opening, and anthocyanin metabolism). GI has also been implicated to play a pivotal role in response to stresses such as freezing, thermomorphogenic stresses, salinity, drought, and osmotic stresses. Positioned at the hub of complex genetic networks, GI interacts with hormonal signaling pathways like abscisic acid (ABA), gibberellin (GA), salicylic acid (SA), and brassinosteroids (BRs) at multiple regulatory levels. This intricate interplay enables GI to balance stress responses, promoting growth and flowering, and optimize plant productivity. This review delves into the multifaceted roles of GI, supported by genetic and molecular evidence, and recent insights into the dynamic interplay between flowering and stress responses, which enhance plants' adaptability to environmental challenges.

A bittersweet symphony: Metabolic signals in the circadian system

Plants must match their metabolism to daily and seasonal fluctuations in their environment to maximise performance in natural conditions. Circadian clocks enable organisms to anticipate and adapt to these predictable and unpredictable environmental challenges. Metabolism is increasingly recognised as an integrated feature of the plant circadian system. Metabolism is an important circadian-regulated output but also provides input to this dynamic timekeeping mechanism. The spatial organisation of metabolism within cells and between tissues, and the temporal features of metabolism across days, seasons and development, raise interesting questions about how metabolism influences circadian timekeeping. The various mechanisms by which metabolic signals influence the transcription-translation feedback loops of the circadian oscillator are emerging. These include roles for major metabolic signalling pathways, various retrograde signals, and direct metabolic modifications of clock genes or proteins. Such metabolic feedback loops enable intra- and intercellular coordination of rhythmic metabolism, and recent discoveries indicate these contribute to diverse aspects of daily, developmental and seasonal timekeeping.

In vivo protein kinase activity of SnRK1 fluctuates in Arabidopsis rosettes during light-dark cycles

Sucrose-nonfermenting 1 (SNF1)-related kinase 1 (SnRK1) is a central hub in carbon and energy signaling in plants, and is orthologous with SNF1 in yeast and the AMP-activated protein kinase (AMPK) in animals. Previous studies of SnRK1 relied on in vitro activity assays or monitoring of putative marker gene expression. Neither approach gives unambiguous information about in vivo SnRK1 activity. We have monitored in vivo SnRK1 activity using Arabidopsis (Arabidopsis thaliana) reporter lines that express a chimeric polypeptide with an SNF1/SnRK1/AMPK-specific phosphorylation site. We investigated responses during an equinoctial diel cycle and after perturbing this cycle. As expected, in vivo SnRK1 activity rose toward the end of the night and rose even further when the night was extended. Unexpectedly, although sugars rose after dawn, SnRK1 activity did not decline until about 12 h into the light period. The sucrose signal metabolite, trehalose 6-phosphate (Tre6P), has been shown to inhibit SnRK1 in vitro. We introduced the SnRK1 reporter into lines that harbored an inducible trehalose-6-phosphate synthase construct. Elevated Tre6P decreased in vivo SnRK1 activity in the light period, but not at the end of the night. Reporter polypeptide phosphorylation was sometimes negatively correlated with Tre6P, but a stronger and more widespread negative correlation was observed with glucose-6-phosphate. We propose that SnRK1 operates within a network that controls carbon utilization and maintains diel sugar homeostasis, that SnRK1 activity is regulated in a context-dependent manner by Tre6P, probably interacting with further inputs including hexose phosphates and the circadian clock, and that SnRK1 signaling is modulated by factors that act downstream of SnRK1.

Root PRR7 Improves the Accuracy of the Shoot Circadian Clock through Nutrient Transport

The circadian clock allows plants to anticipate and adapt to periodic environmental changes. Organ- and tissue-specific properties of the circadian clock and shoot-to-root circadian signaling have been reported. While this long-distance signaling is thought to coordinate physiological functions across tissues, little is known about the feedback regulation of the root clock on the shoot clock in the hierarchical circadian network. Here, we show that the plant circadian clock conveys circadian information between shoots and roots through sucrose and K+. We also demonstrate that K+ transport from roots suppresses the variance of period length in shoots and then improves the accuracy of the shoot circadian clock. Sucrose measurements and qPCR showed that root sucrose accumulation was regulated by the circadian clock. Furthermore, root circadian clock genes, including PSEUDO-RESPONSE REGULATOR7 (PRR7), were regulated by sucrose, suggesting the involvement of sucrose from the shoot in the regulation of root clock gene expression. Therefore, we performed time-series measurements of xylem sap and micrografting experiments using prr7 mutants and showed that root PRR7 regulates K+ transport and suppresses variance of period length in the shoot. Our modeling analysis supports the idea that root-to-shoot signaling contributes to the precision of the shoot circadian clock. We performed micrografting experiments that illustrated how root PRR7 plays key roles in maintaining the accuracy of shoot circadian rhythms. We thus present a novel directional signaling pathway for circadian information from roots to shoots and propose that plants modulate physiological events in a timely manner through various timekeeping mechanisms.

Mapping of the plant SnRK1 kinase signalling network reveals a key regulatory role for the class II T6P synthase-like proteins

The central metabolic regulator SnRK1 controls plant growth and survival upon activation by energy depletion, but detailed molecular insight into its regulation and downstream targets is limited. Here we used phosphoproteomics to infer the sucrose-dependent processes targeted upon starvation by kinases as SnRK1, corroborating the relation of SnRK1 with metabolic enzymes and transcriptional regulators, while also pointing to SnRK1 control of intracellular trafficking. Next, we integrated affinity purification, proximity labelling and crosslinking mass spectrometry to map the protein interaction landscape, composition and structure of the SnRK1 heterotrimer, providing insight in its plant-specific regulation. At the intersection of this multi-dimensional interactome, we discovered a strong association of SnRK1 with class II T6P synthase (TPS)-like proteins. Biochemical and cellular assays show that TPS-like proteins function as negative regulators of SnRK1. Next to stable interactions with the TPS-like proteins, similar intricate connections were found with known regulators, suggesting that plants utilize an extended kinase complex to fine-tune SnRK1 activity for optimal responses to metabolic stress.

TIME FOR COFFEE regulates phytochrome A-mediated hypocotyl growth through dawn-phased signaling

To enhance plant fitness under natural conditions, the circadian clock is synchronized and entrained by light via photoreceptors. In turn, the circadian clock exquisitely regulates the abundance and activity of photoreceptors via largely uncharacterized mechanisms. Here we show that the clock regulator TIME FOR COFFEE (TIC) controls the activity of the far-red light photoreceptor phytochrome A (phyA) at multiple levels in Arabidopsis thaliana. Null mutants of TIC displayed dramatically increased sensitivity to light irradiation with respect to hypocotyl growth, especially to far-red light. RNA-sequencing demonstrated that TIC and phyA play largely opposing roles in controlling light-regulated gene expression at dawn. Additionally, TIC physically interacts with the transcriptional repressor TOPLESS (TPL), which was associated with the significantly increased PHYA transcript levels in the tic-2 and tpl-1 mutants. Moreover, TIC interacts with phyA in the nucleus, thereby affecting phyA protein turnover and the formation of phyA nuclear speckles following light irradiation. Genetically, phyA was found to act downstream of TIC in regulating far red light-inhibited growth. Taken together, these findings indicate that TIC acts as a major negative regulator of phyA by integrating transcriptional and post-translational mechanisms at multiple levels.

Impaired KIN10 function restores developmental defects in the Arabidopsis trehalose 6-phosphate synthase1 (tps1) mutant

Sensing carbohydrate availability is essential for plants to coordinate their growth and development. In Arabidopsis thaliana, TREHALOSE 6-PHOSPHATE SYNTHASE 1 (TPS1) and its product, trehalose 6-phosphate (T6P), are important for the metabolic control of development. tps1 mutants are embryo-lethal and unable to flower when embryogenesis is rescued. T6P regulates development in part through inhibition of SUCROSE NON-FERMENTING1 RELATED KINASE1 (SnRK1). Here, we explored the role of SnRK1 in T6P-mediated plant growth and development using a combination of a mutant suppressor screen and genetic, cellular and transcriptomic approaches. We report nonsynonymous amino acid substitutions in the catalytic KIN10 and regulatory SNF4 subunits of SnRK1 that can restore both embryogenesis and flowering of tps1 mutant plants. The identified SNF4 point mutations disrupt the interaction with the catalytic subunit KIN10. Contrary to the common view that the two A. thaliana SnRK1 catalytic subunits act redundantly, we found that loss-of-function mutations in KIN11 are unable to restore embryogenesis and flowering, highlighting the important role of KIN10 in T6P signalling.

Impact of the SnRK1 protein kinase on sucrose homeostasis and the transcriptome during the diel cycle

SNF1-related Kinase 1 (SnRK1) is an evolutionarily conserved protein kinase with key functions in energy management during stress responses in plants. To address a potential role of SnRK1 under favorable conditions, we performed a metabolomic and transcriptomic characterization of rosettes of 20-d-old Arabidopsis (Arabidopsis thaliana) plants of SnRK1 gain- and loss-of-function mutants during the regular diel cycle. Our results show that SnRK1 manipulation alters the sucrose and trehalose 6-phosphate (Tre6P) relationship, influencing how the sucrose content is translated into Tre6P accumulation and modulating the flux of carbon to the tricarboxylic acid cycle downstream of Tre6P signaling. On the other hand, daily cycles of Tre6P accumulation were accompanied by changes in SnRK1 signaling, leading to a maximum in the expression of SnRK1-induced genes at the end of the night, when Tre6P levels are lowest, and to a minimum at the end of the day, when Tre6P levels peak. The expression of SnRK1-induced genes was strongly reduced by transient Tre6P accumulation in an inducible Tre6P synthase (otsA) line, further suggesting the involvement of Tre6P in the diel oscillations in SnRK1 signaling. Transcriptional profiling of wild-type plants and SnRK1 mutants also uncovered defects that are suggestive of an iron sufficiency response and of a matching induction of sulfur acquisition and assimilation when SnRK1 is depleted. In conclusion, under favorable growth conditions, SnRK1 plays a role in sucrose homeostasis and transcriptome remodeling in autotrophic tissues and its activity is influenced by diel fluctuations in Tre6P levels.

The circadian clock gene circuit controls protein and phosphoprotein rhythms in Arabidopsis thaliana

Twenty-four-hour, circadian rhythms control many eukaryotic mRNA levels, whereas the levels of their more stable proteins are not expected to reflect the RNA rhythms, emphasizing the need to test the circadian regulation of protein abundance and modification. Here we present circadian proteomic and phosphoproteomic time series from Arabidopsis thaliana plants under constant light conditions, estimating that just 0.4% of quantified proteins but a much larger proportion of quantified phospho-sites were rhythmic. Approximately half of the rhythmic phospho-sites were most phosphorylated at subjective dawn, a pattern we term the “phospho-dawn.” Members of the SnRK/CDPK family of protein kinases are candidate regulators. A CCA1-overexpressing line that disables the clock gene circuit lacked most circadian protein phosphorylation. However, the few phospho-sites that fluctuated despite CCA1-overexpression still tended to peak in abundance close to subjective dawn, suggesting that the canonical clock mechanism is necessary for most but perhaps not all protein phosphorylation rhythms. To test the potential functional relevance of our datasets, we conducted phosphomimetic experiments using the bifunctional enzyme fructose-6-phosphate-2-kinase/phosphatase (F2KP), as an example. The rhythmic phosphorylation of diverse protein targets is controlled by the clock gene circuit, implicating posttranslational mechanisms in the transmission of circadian timing information in plants.

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Circadian (phospho)proteomics time courses of plants with or without functional clock.

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Most protein abundance/phosphorylation rhythms require a transcriptional oscillator.

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The majority of rhythmic phosphosites peak around subjective dawn (“phospho-dawn”).

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A phosphorylated serine of the metabolic enzyme F2KP has functional relevance.

SNF1-related protein kinase 1: the many-faced signaling hub regulating developmental plasticity in plants

The Snf1-related protein kinase 1 (SnRK1) is the plant homolog of the heterotrimeric AMP-activated protein kinase/sucrose non-fermenting 1 (AMPK/Snf1), which works as a major regulator of growth under nutrient-limiting conditions in eukaryotes. Along with its conserved role as a master regulator of sugar starvation responses, SnRK1 is involved in controlling the developmental plasticity and resilience under diverse environmental conditions in plants. In this review, through mining and analyzing the interactome and phosphoproteome data of SnRK1, we are highlighting its role in fundamental cellular processes such as gene regulation, protein synthesis, primary metabolism, protein trafficking, nutrient homeostasis, and autophagy. Along with the well-characterized molecular interaction in SnRK1 signaling, our analysis highlights several unchartered regions of SnRK1 signaling in plants such as its possible communication with chromatin remodelers, histone modifiers, and inositol phosphate signaling. We also discuss potential reciprocal interactions of SnRK1 signaling with other signaling pathways and cellular processes, which could be involved in maintaining flexibility and homeostasis under different environmental conditions. Overall, this review provides a comprehensive overview of the SnRK1 signaling network in plants and suggests many novel directions for future research.

Superoxide is promoted by sucrose and affects amplitude of circadian rhythms in the evening

Plants must coordinate photosynthetic metabolism with the daily environment and adapt rhythmic physiology and development to match carbon availability. Circadian clocks drive biological rhythms which adjust to environmental cues. Products of photosynthetic metabolism, including sugars and reactive oxygen species (ROS), are closely associated with the plant circadian clock, and sugars have been shown to provide metabolic feedback to the circadian oscillator. Here, we report a comprehensive sugar-regulated transcriptome of Arabidopsis and identify genes associated with redox and ROS processes as a prominent feature of the transcriptional response. We show that sucrose increases levels of superoxide (O₂ ^-), which is required for transcriptional and growth responses to sugar. We identify circadian rhythms of O₂ ^--regulated transcripts which are phased around dusk and find that O₂ ^- is required for sucrose to promote expression of TIMING OF CAB1 (TOC1) in the evening. Our data reveal a role for O₂ ^- as a metabolic signal affecting transcriptional control of the circadian oscillator in Arabidopsis.

An early-morning gene network controlled by phytochromes and cryptochromes regulates photomorphogenesis pathways in Arabidopsis

Light perception at dawn plays a key role in coordinating multiple molecular processes and in entraining the plant circadian clock. The Arabidopsis mutant lacking the main photoreceptors, however, still shows clock entrainment, indicating that the integration of light into the morning transcriptome is not well understood. In this study, we performed a high-resolution RNA-sequencing time-series experiment, sampling every 2 min beginning at dawn. In parallel experiments, we perturbed temperature, the circadian clock, photoreceptor signaling, and chloroplast-derived light signaling. We used these data to infer a gene network that describes the gene expression dynamics after light stimulus in the morning, and then validated key edges. By sampling time points at high density, we are able to identify three light- and temperature-sensitive bursts of transcription factor activity, one of which lasts for only about 8 min. Phytochrome and cryptochrome mutants cause a delay in the transcriptional bursts at dawn, and completely remove a burst of expression in key photomorphogenesis genes (HY5 and BBX family). Our complete network is available online (http://www-users.york.ac.uk/∼de656/dawnBurst/dawnBurst.html). Taken together, our results show that phytochrome and cryptochrome signaling is required for fine-tuning the dawn transcriptional response to light, but separate pathways can robustly activate much of the program in their absence.

A Novel Signaling Pathway Required for Arabidopsis Endodermal Root Organization Shapes the Rhizosphere Microbiome

The Casparian strip (CS) constitutes a physical diffusion barrier to water and nutrients in plant roots, which is formed by the polar deposition of lignin polymer in the endodermis tissue. The precise pattern of lignin deposition is determined by the scaffolding activity of membrane-bound Casparian Strip domain proteins (CASPs), but little is known of the mechanism(s) directing this process. Here, we demonstrate that Endodermis-specific Receptor-like Kinase 1 (ERK1) and, to a lesser extent, ROP Binding Kinase1 (RBK1) are also involved in regulating CS formation, with the former playing an essential role in lignin deposition as well as in the localization of CASP1. We show that ERK1 is localized to the cytoplasm and nucleus of the endodermis and that together with the circadian clock regulator, Time for Coffee (TIC), forms part of a novel signaling pathway necessary for correct CS organization and suberization of the endodermis, with their single or combined loss of function resulting in altered root microbiome composition. In addition, we found that other mutants displaying defects in suberin deposition at the CS also display altered root exudates and microbiome composition. Thus, our work reveals a complex network of signaling factors operating within the root endodermis that establish both the CS diffusion barrier and influence the microbial composition of the rhizosphere.

Growing in time: exploring the molecular mechanisms of tree growth

Trees cover vast areas of the Earth's landmasses. They mitigate erosion, capture carbon dioxide, produce oxygen and support biodiversity, and also are a source of food, raw materials and energy for human populations. Understanding the growth cycles of trees is fundamental for many areas of research. Trees, like most other organisms, have evolved a circadian clock to synchronize their growth and development with the daily and seasonal cycles of the environment. These regular changes in light, daylength and temperature are perceived via a range of dedicated receptors and cause resetting of the circadian clock to local time. This allows anticipation of daily and seasonal fluctuations and enables trees to co-ordinate their metabolism and physiology to ensure vital processes occur at the optimal times. In this review, we explore the current state of knowledge concerning the regulation of growth and seasonal dormancy in trees, using information drawn from model systems such as Populus spp.

Arabidopsis SnRK1 negatively regulates phenylpropanoid metabolism via Kelch domain-containing F-box proteins

Phenylpropanoid metabolism represents a substantial metabolic sink for photosynthetically fixed carbon. The evolutionarily conserved Sucrose Non-Fermenting Related Kinase 1 (SnRK1) is a major metabolic sensor that reprograms metabolism upon carbon deprivation. However, it is not clear if and how the SnRK1-mediated sugar signaling pathway controls phenylpropanoid metabolism. Here, we show that Arabidopsis SnRK1 negatively regulates phenylpropanoid biosynthesis via a group of Kelch domain-containing F-box (KFB) proteins that are responsible for the ubiquitination and degradation of phenylalanine ammonia lyase (PAL). Downregulation of AtSnRK1 significantly promoted the accumulation of soluble phenolics and lignin polymers and drastically increased PAL cellular accumulation but only slightly altered its transcription level. Co-expression of SnRK1α with PAL in Nicotiana benthamiana leaves resulted in the severe attenuation of the latter's protein level, but protein interaction assays suggested PAL is not a direct substrate of SnRK1. Furthermore, up or downregulation of AtSnRK1 positively affected KFB^PALs gene expression, and energy starvation upregulated KFB^PAL expression, which partially depends on AtSnRK1. Collectively, our study reveals that SnRK1 negatively regulates phenylpropanoid biosynthesis, and KFB^PALs act as regulatory components of the SnRK1 signaling network, transcriptionally regulated by SnRK1 and subsequently mediate proteasomal degradation of PAL in response to the cellular carbon availability.

A temperature regime that disrupts clock-controlled starch mobilization induces transient carbohydrate starvation, resulting in compact growth

In nature plants are usually subjected to a light/temperature regime of warm day and cold night (referred to as +DIF). Compared to growth under +DIF, Arabidopsis plants show compact growth under the same photoperiod, but with an inverse temperature regime (cold day and warm night: -DIF). Here we show that -DIF differentially affects the phase and amplitude of core clock gene expression. Under -DIF the phase of the morning clock gene CIRCADIAN CLOCK ASSOCIATED 1 (CCA1) is delayed, similar to that of plants grown on low sucrose. Indeed, under -DIF carbohydrate (CHO) starvation marker genes are specifically upregulated at the End of the Night (EN) in Arabidopsis rosettes. However, only in inner-rosette tissue (small sink leaves and petioles of older leaves) sucrose levels are lower under -DIF compared to under +DIF, suggesting that sucrose in source leaf blades is not sensed for CHO status and that sucrose transport from source to sink may be impaired at EN. CHO-starvation under -DIF correlated with increased starch breakdown during the night and decreased starch accumulation during the day. Moreover, we demonstrate that different ways of inducing CHO-starvation all link to reduced growth of sink leaves. Practical implications for control of plant growth in horticulture are discussed.

The Arabidopsis Circadian Clock and Metabolic Energy: A Question of Time

A fundamental principle shared by all organisms is the metabolic conversion of nutrients into energy for cellular processes and structural building blocks. A highly precise spatiotemporal programming is required to couple metabolic capacity with energy allocation. Cellular metabolism is also able to adapt to the external time, and the mechanisms governing such an adaptation rely on the circadian clock. Virtually all photosensitive organisms have evolved a self-sustained timekeeping mechanism or circadian clock that anticipates and responds to the 24-h environmental changes that occur during the day and night cycle. This endogenous timing mechanism works in resonance with the environment to control growth, development, responses to stress, and also metabolism. Here, we briefly describe the prevalent role for the circadian clock controlling the timing of mitochondrial activity and cellular energy in Arabidopsis thaliana. Evidence that metabolic signals can in turn feedback to the clock place the spotlight onto the molecular mechanisms and components linking the circadian function with metabolic homeostasis and energy.

SnRK1 and trehalose 6-phosphate - two ancient pathways converge to regulate plant metabolism and growth

SUCROSE-NON-FERMENTING1-RELATED KINASE1 (SnRK1) belongs to a family of protein kinases that originated in the earliest eukaryotes and plays a central role in energy and metabolic homeostasis. Trehalose 6-phosphate (Tre6P) is the intermediate of trehalose biosynthesis, and has even more ancient roots, being found in all three domains of life - Archaea, Bacteria and Eukarya. In plants, the function of SnRK1 has diverged from its orthologues in fungi and animals, evolving new roles in signalling of nutrient status and abiotic stress. Tre6P has also acquired a novel function in plants as a signal and homeostatic regulator of sucrose, the dominant sugar in plant metabolism. These two ancient pathways have converged in a unique way in plants, enabling them to coordinate their metabolism, growth, and development with their environment, which is essential for their autotrophic and sessile lifestyle.

Starch: A Flexible, Adaptable Carbon Store Coupled to Plant Growth

Research in the past decade has uncovered new and surprising information about the pathways of starch synthesis and degradation. This includes the discovery of previously unsuspected protein families required both for processes and for the long-sought mechanism of initiation of starch granules. There is also growing recognition of the central role of leaf starch turnover in making carbon available for growth across the day-night cycle. Sophisticated systems-level control mechanisms involving the circadian clock set rates of nighttime starch mobilization that maintain a steady supply of carbon until dawn and modulate partitioning of photosynthate into starch in the light, optimizing the fraction of assimilated carbon that can be used for growth. These discoveries also uncover complexities: Results from experiments with Arabidopsis leaves in conventional controlled environments are not necessarily applicable to other organs or species or to growth in natural, fluctuating environments.

TRANSPARENT TESTA GLABRA 1 participates in flowering time regulation in Arabidopsis thaliana

Pleiotropic regulatory factors mediate concerted responses of the plant’s trait network to endogenous and exogenous cues. TRANSPARENT TESTA GLABRA 1 (TTG1) is such a factor that has been predominantly described as a regulator of early developmental traits. Although its closest homologs LIGHT-REGULATED WD1 (LWD1) and LWD2 affect photoperiodic flowering, a role of TTG1 in flowering time regulation has not been reported. Here we reveal that TTG1 is a regulator of flowering time in Arabidopsis thaliana and changes transcript levels of different targets within the flowering time regulatory pathway. TTG1 mutants flower early and TTG1 overexpression lines flower late at long-day conditions. Consistently, TTG1 can suppress the transcript levels of the floral integrators FLOWERING LOCUS T and SUPPRESSOR OF OVEREXPRESSION OF CO1 and can act as an activator of circadian clock components. Moreover, TTG1 might form feedback loops at the protein level. The TTG1 protein interacts with PSEUDO RESPONSE REGULATOR (PRR)s and basic HELIX-LOOP-HELIX 92 (bHLH92) in yeast. In planta, the respective pairs exhibit interesting patterns of localization including a recruitment of TTG1 by PRR5 to subnuclear foci. This mechanism proposes additional layers of regulation by TTG1 and might aid to specify the function of bHLH92. Within another branch of the pathway, TTG1 can elevate FLOWERING LOCUS C (FLC) transcript levels. FLC mediates signals from the vernalization, ambient temperature and autonomous pathway and the circadian clock is pivotal for the plant to synchronize with diurnal cycles of environmental stimuli like light and temperature. Our results suggest an unexpected positioning of TTG1 upstream of FLC and upstream of the circadian clock. In this light, this points to an adaptive value of the role of TTG1 in respect to flowering time regulation.

Circadian Regulation of the Plant Transcriptome Under Natural Conditions

Circadian rhythms produce a biological measure of the time of day. In plants, circadian regulation forms an essential adaptation to the fluctuating environment. Most of our knowledge of the molecular aspects of circadian regulation in plants is derived from laboratory experiments that are performed under controlled conditions. However, it is emerging that the circadian clock has complex roles in the coordination of the transcriptome under natural conditions, in both naturally occurring populations of plants and in crop species. In this review, we consider recent insights into circadian regulation under natural conditions. We examine how circadian regulation is integrated with the acute responses of plants to the daily and seasonally fluctuating environment that also presents environmental stresses, in order to coordinate the transcriptome and dynamically adapt plants to their continuously changing environment.

SnRK1 activation, signaling, and networking for energy homeostasis

The SnRK1 kinases are key regulators of the plant energy balance, but how their activity is regulated by metabolic status is still unclear. While the heterotrimeric kinase complex is well conserved among plants, fungi, and animals, plants appear to have modified its regulation to better fit their unique physiology and lifestyle. The SnRK1 kinases control metabolism, growth, and development, and stress tolerance by direct phosphorylation of metabolic enzymes and regulatory proteins and by extensive transcriptional regulation. Diverse types of transcription factors have already been implicated, with a well-studied role for the heterodimerizing group C and group S1 bZIPs. SnRK1 is also part of a more elaborate metabolic and stress signaling network, which includes the TOR kinase and the ABA-signaling SnRK2 kinases.

Physiological and Genetic Dissection of Sucrose Inputs to the Arabidopsis thaliana Circadian System

Circadian rhythms allow an organism to synchronize internal physiological responses to the external environment. Perception of external signals such as light and temperature are critical in the entrainment of the oscillator. However, sugar can also act as an entraining signal. In this work, we have confirmed that sucrose accelerates the circadian period, but this observed effect is dependent on the reporter gene used. This observed response was dependent on sucrose being available during free-running conditions. If sucrose was applied during entrainment, the circadian period was only temporally accelerated, if any effect was observed at all. We also found that sucrose acts to stabilize the robustness of the circadian period under red light or blue light, in addition to its previously described role in stabilizing the robustness of rhythms in the dark. Finally, we also found that CCA1 is required for both a short- and long-term response of the circadian oscillator to sucrose, while LHY acts to attenuate the effects of sucrose on circadian period. Together, this work highlights new pathways for how sucrose could be signaling to the oscillator and reveals further functional separation of CCA1 and LHY.

The Plant Circadian Oscillator

It has been nearly 300 years since the first scientific demonstration of a self-sustaining circadian clock in plants. It has become clear that plants are richly rhythmic, and many aspects of plant biology, including photosynthetic light harvesting and carbon assimilation, resistance to abiotic stresses, pathogens, and pests, photoperiodic flower induction, petal movement, and floral fragrance emission, exhibit circadian rhythmicity in one or more plant species. Much experimental effort, primarily, but not exclusively in Arabidopsis thaliana, has been expended to characterize and understand the plant circadian oscillator, which has been revealed to be a highly complex network of interlocked transcriptional feedback loops. In addition, the plant circadian oscillator has employed a panoply of post-transcriptional regulatory mechanisms, including alternative splicing, adjustable rates of translation, and regulated protein activity and stability. This review focuses on our present understanding of the regulatory network that comprises the plant circadian oscillator. The complexity of this oscillatory network facilitates the maintenance of robust rhythmicity in response to environmental extremes and permits nuanced control of multiple clock outputs. Consistent with this view, the clock is emerging as a target of domestication and presents multiple targets for targeted breeding to improve crop performance.

Retrograde signalling as an informant of circadian timing

Contents Summary 1749 I. The circadian system is responsive to environmental change 1749 II. Photoassimilates regulate circadian timing 1750 III. Retrograde signals contribute to circadian timing 1750 IV. Conclusions 1752 Acknowledgements 1752 References 1752 SUMMARY: The circadian system comprises interlocking transcriptional-translational feedback loops that regulate gene expression and consequently modulate plant development and physiology. In order to maximize utility, the circadian system is entrained by changes in temperature and light, allowing endogenous rhythms to be synchronized with both daily and seasonal environmental change. Although a great deal of environmental information is decoded by a suite of photoreceptors, it is also becoming apparent that changes in cellular metabolism also contribute to circadian timing, through either the stimulation of metabolic pathways or the accumulation of metabolic intermediates as a consequence of environmental stress. As the source of many of these metabolic byproducts, mitochondria and chloroplasts have begun to be viewed as environmental sensors, and rapid advancement of this field is revealing the complex web of signalling pathways initiated by organelle perturbation. This review highlights recent advances in our understanding of how this metabolic regulation influences circadian timing.

Multiple circadian clock outputs regulate diel turnover of carbon and nitrogen reserves

Plants accumulate reserves in the daytime to support growth at night. Circadian regulation of diel reserve turnover was investigated by profiling starch, sugars, glucose 6-phosphate, organic acids, and amino acids during a light-dark cycle and after transfer to continuous light in Arabidopsis wild types and in mutants lacking dawn (lhy cca1), morning (prr7 prr9), dusk (toc1, gi), or evening (elf3) clock components. The metabolite time series were integrated with published time series for circadian clock transcripts to identify circadian outputs that regulate central metabolism. (a) Starch accumulation was slower in elf3 and prr7 prr9. It is proposed that ELF3 positively regulates starch accumulation. (b) Reducing sugars were high early in the T-cycle in elf3, revealing that ELF3 negatively regulates sucrose recycling. (c) The pattern of starch mobilization was modified in all five mutants. A model is proposed in which dawn and dusk/evening components interact to pace degradation to anticipated dawn. (d) An endogenous oscillation of glucose 6-phosphate revealed that the clock buffers metabolism against the large influx of carbon from photosynthesis. (e) Low levels of organic and amino acids in lhy cca1 and high levels in prr7 prr9 provide evidence that the dawn components positively regulate the accumulation of amino acid reserves.

Low doses of triazine xenobiotics mobilize ABA and cytokinin regulations in a stress- and low-energy-dependent manner

The extent of residual contaminations of pesticides through drift, run-off and leaching is a potential threat to non-target plant communities. Arabidopsis thaliana responds to low doses of the herbicide atrazine, and of its degradation products, desethylatrazine and hydroxyatrazine, not only in the long term, but also under conditions of short-term exposure. In order to investigate underlying molecular mechanisms of low-dose responses and to decipher commonalities and specificities between different chemical treatments, parallel transcriptomic studies of the early effects of the atrazine-desethylatrazine-hydroxyatrazine chemical series were undertaken using whole-genome microarrays. All of the triazines under study produced coordinated and specific changes in gene expression. Hydroxyatrazine-responsive genes were mainly linked to root development, whereas atrazine and desethylatrazine mostly affected molecular signaling networks implicated in stress and hormone responses. Analysis of signaling-related genes, promoter sites and shared-function interaction networks highlighted the involvement of energy-, stress-, abscisic acid- and cytokinin-regulated processes, and emphasized the importance of cold-, heat- and drought-related signaling in the perception of low doses of triazines. These links between low-dose xenobiotic impacts and stress-hormone crosstalk pathways give novel insights into plant-pesticide interactions and plant-pollution interactions that are essential for toxicity evaluation in the context of environmental risk assessment.

Circadian Entrainment in Arabidopsis by the Sugar-Responsive Transcription Factor bZIP63

Synchronization of circadian clocks to the day-night cycle ensures the correct timing of biological events. This entrainment process is essential to ensure that the phase of the circadian oscillator is synchronized with daily events within the environment [1], to permit accurate anticipation of environmental changes [2, 3]. Entrainment in plants requires phase changes in the circadian oscillator, through unidentified pathways, which alter circadian oscillator gene expression in response to light, temperature, and sugars [4, 5, 6]. To determine how circadian clocks respond to metabolic rhythms, we investigated the mechanisms by which sugars adjust the circadian phase in Arabidopsis [5]. We focused upon metabolic regulation because interactions occur between circadian oscillators and metabolism in several experimental systems [5, 7, 8, 9], but the molecular mechanisms are unidentified. Here, we demonstrate that the transcription factor BASIC LEUCINE ZIPPER63 (bZIP63) regulates the circadian oscillator gene PSEUDO RESPONSE REGULATOR7 (PRR7) to change the circadian phase in response to sugars. We find that SnRK1, a sugar-sensing kinase that regulates bZIP63 activity and circadian period [10, 11, 12, 13, 14] is required for sucrose-induced changes in circadian phase. Furthermore, TREHALOSE-6-PHOSPHATE SYNTHASE1 (TPS1), which synthesizes the signaling sugar trehalose-6-phosphate, is required for circadian phase adjustment in response to sucrose. We demonstrate that daily rhythms of energy availability can entrain the circadian oscillator through the function of bZIP63, TPS1, and the KIN10 subunit of the SnRK1 energy sensor. This identifies a molecular mechanism that adjusts the circadian phase in response to sugars.

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The transcription factor bZIP63 binds and regulates the circadian clock gene PRR7

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bZIP63 is required for adjustment of circadian period by sugars

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Trehalose-6-phosphate metabolism and KIN10 signaling regulate circadian period

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Sugar signals establish the correct circadian phase in light and dark cycles

Feedback regulation by trehalose 6-phosphate slows down starch mobilization below the rate that would exhaust starch reserves at dawn in Arabidopsis leaves

Trehalose 6-phosphate (Tre6P), a sucrose signaling metabolite, inhibits transitory starch breakdown in Arabidopsis (Arabidopsis thaliana) leaves and potentially links starch turnover to leaf sucrose status and demand from sink organs (Plant Physiology, 163, 2013, 1142). To investigate this relationship further, we compared diel patterns of starch turnover in ethanol-inducible Tre6P synthase (iTPS) lines, which have high Tre6P and low sucrose after induction, with those in sweet11;12 sucrose export mutants, which accumulate sucrose in their leaves and were predicted to have high Tre6P. Short-term changes in irradiance were used to investigate whether the strength of inhibition by Tre6P depends on starch levels. sweet11;12 mutants had twofold higher levels of Tre6P and restricted starch mobilization. The relationship between Tre6P and starch mobilization was recapitulated in iTPS lines, pointing to a dominant role for Tre6P in feedback regulation of starch mobilization. Tre6P restricted mobilization across a wide range of conditions. However, there was no correlation between the level of Tre6P and the absolute rate of starch mobilization. Rather, Tre6P depressed the rate of mobilization below that required to exhaust starch at dawn, leading to incomplete use of starch. It is discussed how Tre6P interacts with the clock to set the rate of starch mobilization.

Arabidopsis ANGUSTIFOLIA3 (AN3) is associated with the promoter of CONSTITUTIVE PHOTOMORPHOGENIC1 (COP1) to regulate light-mediated stomatal development

Light signals are perceived by multiple photoreceptors that converge to suppress the RING E3 ubiquitin ligase CONSTITUTIVE PHOTOMORPHOGENIC1 (COP1) for the regulation of stomatal development. Thus, COP1 is a point of integration between light signaling and stomatal patterning. However, how light signaling is collected into COP1 for the production and spacing of stomata is still unknown. Here, we report that the loss-of-function mutant of ANGUSTIFOLIA3 (AN3) delays asymmetric cell division, which leads to decreased stomatal index. Furthermore, overexpression of AN3 accelerates asymmetric cell division, which results in clusters of stomata. In addition, the stomatal development through AN3 regulation is mediated by light signaling. Finally, we find that an3 is a light-signaling mutant, and that AN3 protein is light regulated. Self-activation by AN3 contributes to the control of AN3 expression. Thus, AN3 is a point of collection between light signaling and stomatal patterning. Target-gene analysis indicates that AN3 is associated with COP1 promoter for the regulation of light-controlling stomatal development. Together, these components for regulating stomatal development form an AN3-COP1-E3 ubiquitin ligase complex, allowing the integration of light signaling into the production and spacing of stomata.

Circadian clock components control daily growth activities by modulating cytokinin levels and cell division-associated gene expression in Populus trees

Trees are carbon dioxide sinks and major producers of terrestrial biomass with distinct seasonal growth patterns. Circadian clocks enable the coordination of physiological and biochemical temporal activities, optimally regulating multiple traits including growth. To dissect the clock's role in growth, we analysed Populus tremula × P. tremuloides trees with impaired clock function due to down-regulation of central clock components. late elongated hypocotyl (lhy-10) trees, in which expression of LHY1 and LHY2 is reduced by RNAi, have a short free-running period and show disrupted temporal regulation of gene expression and reduced growth, producing 30-40% less biomass than wild-type trees. Genes important in growth regulation were expressed with an earlier phase in lhy-10, and CYCLIN D3 expression was misaligned and arrhythmic. Levels of cytokinins were lower in lhy-10 trees, which also showed a change in the time of peak expression of genes associated with cell division and growth. However, auxin levels were not altered in lhy-10 trees, and the size of the lignification zone in the stem showed a relative increase. The reduced growth rate and anatomical features of lhy-10 trees were mainly caused by misregulation of cell division, which may have resulted from impaired clock function.

AKIN10 activity as a cellular link between metabolism and circadian-clock entrainment in Arabidopsis thaliana

AKIN10, the catalytic subunit of the Snf1 (sucrose non-fermenting 1)-related kinase 1 (SnRK1) complex, acts as an energy sensor in plants. We showed that AKIN10-induced expression affects the pace of the circadian clock and particularly the phase of expression of GIGANTEA (GI). The AKIN10 effect on period length required TIME FOR COFFEE (TIC), a circadian-clock component with developmental and metabolic roles. Here we expand on the possible interactions between AKIN10, whose activity is involved in transcriptional reprogramming, and clock elements GI and TIC. We hypothesize how they could participate in clock entrainment through a metabolic signal derived from carbon pools and starch metabolism. Additionally, we consider further the role of cellular energy status to the clock through the formation of a hypothetical protein complex. We also demonstrate the role of AKIN10, but not its sequence-related kinase AKIN11, on clock periodicity. Altogether we present a model of action of these elements in metabolic-related clock entrainment.

Involvement of the SnRK1 subunit KIN10 in sucrose-induced hypocotyl elongation

A mechanism participating in energy sensing and signalling in plants involves the regulation of sucrose non-fermenting1 (Snf1)-related protein kinase 1 (SnRK1) activity in response to sugar availability. SnRK1 is thought to regulate the activity of both metabolic enzymes and transcription factors in response to changes in energy availability, with trehalose-6-phospate functioning as a signalling sugar that suppresses SnRK1 activity under sugar-replete conditions. Sucrose supplementation increases the elongation of hypocotyls of developing Arabidopsis seedlings, and this response to sucrose involves both the SnRK1 subunit KIN10 and also TREHALOSE-6-PHOSPHATE SYNTHASE1 (TPS1). Here, we measured sucrose-induced hypocotyl elongation in two insertional mutants of KIN10 (akin10 and akin10-2). Under short photoperiods, sucrose supplementation caused great proportional hypocotyl elongation in these KIN10 mutants compared with the wild type, and these mutants had shorter hypocotyls than the wild type in the absence of sucrose supplementation. One interpretation is that SnRK1 activity might suppress hypocotyl elongation in the presence of sucrose, because KIN10 overexpression inhibits sucrose-induced hypocotyl elongation and akin10 mutants enhance sucrose-induced hypocotyl elongation.

Beyond Histones: New Substrate Proteins of Lysine Deacetylases in Arabidopsis Nuclei

The reversible acetylation of lysine residues is catalyzed by the antagonistic action of lysine acetyltransferases and deacetylases, which can be considered as master regulators of their substrate proteins. Lysine deacetylases, historically referred to as histone deacetylases, have profound functions in regulating stress defenses and development in plants. Lysine acetylation of the N-terminal histone tails promotes gene transcription and decondensation of chromatin, rendering the DNA more accessible to the transcription machinery. In plants, the classical lysine deacetylases from the RPD3/HDA1-family have thus far mainly been studied in the context of their deacetylating activities on histones, and their versatility in molecular activities is still largely unexplored. Here we discuss the potential impact of lysine acetylation on the recently identified nuclear substrate proteins of lysine deacetylases from the Arabidopsis RPD3/HDA1-family. Among the deacetylase substrate proteins, many interesting candidates involved in nuclear protein import, transcriptional regulation, and chromatin remodeling have been identified. These candidate proteins represent key starting points for unraveling new molecular functions of the Arabidopsis lysine deacetylases. Site-directed engineering of lysine acetylation sites on these target proteins might even represent a new approach for optimizing plant growth under climate change conditions.

Shining a light on the Arabidopsis circadian clock

The circadian clock provides essential timing information to ensure optimal growth to prevailing external environmental conditions. A major time-setting mechanism (zeitgeber) in clock synchronization is light. Differing light wavelengths, intensities, and photoperiodic duration are processed for the clock-setting mechanism. Many studies on light-input pathways to the clock have focused on Arabidopsis thaliana. Photoreceptors are specific chromic proteins that detect light signals and transmit this information to the central circadian oscillator through a number of different signalling mechanisms. The most well-characterized clock-mediating photoreceptors are cryptochromes and phytochromes, detecting blue, red, and far-red wavelengths of light. Ultraviolet and shaded light are also processed signals to the oscillator. Notably, the clock reciprocally generates rhythms of photoreceptor action leading to so-called gating of light responses. Intermediate proteins, such as Phytochrome interacting factors (PIFs), constitutive photomorphogenic 1 (COP1) and EARLY FLOWERING 3 (ELF3), have been established in signalling pathways downstream of photoreceptor activation. However, the precise details for these signalling mechanisms are not fully established. This review highlights both historical and recent efforts made to understand overall light input to the oscillator, first looking at how each wavelength of light is detected, this is then related to known input mechanisms and their interactions.

Phosphorylation of Ribosomal Protein RPS6 Integrates Light Signals and Circadian Clock Signals

The translation of mRNA into protein is tightly regulated by the light environment as well as by the circadian clock. Although changes in translational efficiency have been well documented at the level of mRNA-ribosome loading, the underlying mechanisms are unclear. The reversible phosphorylation of RIBOSOMAL PROTEIN OF THE SMALL SUBUNIT 6 (RPS6) has been known for 40 years, but the biochemical significance of this event remains unclear to this day. Here, we confirm using a clock-deficient strain of Arabidopsis thaliana that RPS6 phosphorylation (RPS6-P) is controlled by the diel light-dark cycle with a peak during the day. Strikingly, when wild-type, clock-enabled, seedlings that have been entrained to a light-dark cycle are placed under free-running conditions, the circadian clock drives a cycle of RPS6-P with an opposite phase, peaking during the subjective night. We show that in wild-type seedlings under a light-dark cycle, the incoherent light and clock signals are integrated by the plant to cause an oscillation in RPS6-P with a reduced amplitude with a peak during the day. Sucrose can stimulate RPS6-P, as seen when sucrose in the medium masks the light response of etiolated seedlings. However, the diel cycles of RPS6-P are observed in the presence of 1% sucrose and in its absence. Sucrose at a high concentration of 3% appears to interfere with the robust integration of light and clock signals at the level of RPS6-P. Finally, we addressed whether RPS6-P occurs uniformly in polysomes, non-polysomal ribosomes and their subunits, and non-ribosomal protein. It is the polysomal RPS6 whose phosphorylation is most highly stimulated by light and repressed by darkness. These data exemplify a striking case of contrasting biochemical regulation between clock signals and light signals. Although the physiological significance of RPS6-P remains unknown, our data provide a mechanistic basis for the future understanding of this enigmatic event.