Adjustment of carbon fluxes to light conditions regulates the daily turnover of starch in plants: a computational model

Integrated multi-omic analysis reveals the carbon metabolism-mediated regulation of polysaccharide biosynthesis by suitable light intensity in Bletilla striata leaves

Bletilla striata, valued for its medicinal and ornamental properties, remains largely unexplored in terms of how light intensity affects its physiology, biochemistry, and polysaccharide formation. In this 5-month study, B. striata plants were exposed to three different light intensities: low light (LL) (5-20 μmol m-2·s-1), middle light (ML) (200 μmol m-2·s-1), and high light (HL) (400 μmol m-2·s-1). The comprehensive assessment included growth, photosynthetic apparatus, chlorophyll fluorescence electron transport, and analysis of differential metabolites based on the transcriptome and metabolome data. The results indicated that ML resulted in the highest plant height and total polysaccharide content, enhanced photosynthetic apparatus performance and light energy utilization, and stimulated carbon metabolism and carbohydrate accumulation. HL reduced Chl content and photosynthetic apparatus functionality, disrupted OEC activity and electron transfer, stimulated carbon metabolism and starch and glucose accumulation, and hindered energy metabolism related to carbohydrate degradation and oxidation. In contrast, LL facilitated leaf growth and increased chlorophyll content but decreased plant height and total polysaccharide content, compromised the photosynthetic apparatus, hampered light energy utilization, stimulated energy metabolism related to carbohydrate degradation and oxidation, and inhibited carbon metabolism and carbohydrate synthesis. Numerous genes in carbon metabolism were strongly related to polysaccharide metabolites. The katE and cysK genes in carbon metabolism were strongly related not only to polysaccharide metabolites, but also to genes involved in polysaccharide biosynthesis. Our results highlight that light intensity plays a crucial role in affecting polysaccharide biosynthesis in B. striata, with carbon metabolism acting as a mediator under suitable light intensity conditions.

The end game(s) of photosynthetic carbon metabolism

The year 2024 marks 70 years since the general outline of the carbon pathway in photosynthesis was published. Although several alternative pathways are now known, it is remarkable how many organisms use the reaction sequence described 70 yrs ago, which is now known as the Calvin-Benson cycle or variants such as the Calvin-Benson-Bassham cycle or Benson-Calvin cycle. However, once the carbon has entered the Calvin-Benson cycle and is converted to a 3-carbon sugar, it has many potential fates. This review will examine the last stages of photosynthetic metabolism in leaves. In land plants, this process mostly involves the production of sucrose provided by an endosymbiont (the chloroplast) to its host for use and transport to the rest of the plant. Photosynthetic metabolism also usually involves the synthesis of starch, which helps maintain respiration in the dark and enables the symbiont to supply sugars during both the day and night. Other end products made in the chloroplast are closely tied to photosynthetic CO2 assimilation. These include serine from photorespiration and various amino acids, fatty acids, isoprenoids, and shikimate pathway products. I also describe 2 pathways that can short circuit parts of the Calvin-Benson cycle. These final processes of photosynthetic metabolism play many important roles in plants.

Dynamic interactions between SPX proteins, the ubiquitination machinery, and signalling molecules for stress adaptation at a whole-plant level

The plant macronutrient phosphorus is a scarce resource and plant-available phosphate is limiting in most soil types. Generally, a gene regulatory module called the phosphate starvation response (PSR) enables efficient phosphate acquisition by roots and translocation to other organs. Plants growing on moderate to nutrient-rich soils need to co-ordinate availability of different nutrients and repress the highly efficient PSR to adjust phosphate acquisition to the availability of other macro- and micronutrients, and in particular nitrogen. PSR repression is mediated by a small family of single SYG1/Pho81/XPR1 (SPX) domain proteins. The SPX domain binds higher order inositol pyrophosphates that signal cellular phosphorus status and modulate SPX protein interaction with PHOSPHATE STARVATION RESPONSE1 (PHR1), the central transcriptional regulator of PSR. Sequestration by SPX repressors restricts PHR1 access to PSR gene promoters. Here we focus on SPX4 that primarily acts in shoots and sequesters many transcription factors other than PHR1 in the cytosol to control processes beyond the classical PSR, such as nitrate, auxin, and jasmonic acid signalling. Unlike SPX1 and SPX2, SPX4 is subject to proteasomal degradation not only by singular E3 ligases, but also by SCF-CRL complexes. Emerging models for these different layers of control and their consequences for plant acclimation to the environment will be discussed.

Artificial warming affects sugar signals and flavonoid accumulation to improve female willows' growth faster than males

Increasing global warming is severely affecting tree growth and development. However, research on the sex-specific responses of dioecious trees to warming is scarce. Here, male and female Salix paraplesia were selected for artificial warming (an increase of 4 °C relative to ambient temperature) to investigate the effects on morphological, physiological, biochemical and molecular responses. The results showed that warming significantly promoted the growth of female and male S. paraplesia, but females grew faster than males. Warming affected photosynthesis, chloroplast structures, peroxidase activity, proline, flavonoids, nonstructural carbohydrates (NSCs) and phenolic contents in both sexes. Interestingly, warming increased flavonoid accumulation in female roots and male leaves but inhibited it in female leaves and male roots. The transcriptome and proteome results indicated that differentially expressed genes and proteins were significantly enriched in sucrose and starch metabolism and flavonoid biosynthesis pathways. The integrative analysis of transcriptomic, proteomic, biochemical and physiological data revealed that warming changed the expression of SpAMY, SpBGL, SpEGLC and SpAGPase genes, resulting in the reduction of NSCs and starch and the activation of sugar signaling, particularly SpSnRK1s, in female roots and male leaves. These sugar signals subsequently altered the expression of SpHCTs, SpLAR and SpDFR in the flavonoid biosynthetic pathway, ultimately leading to the differential accumulation of flavonoids in female and male S. paraplesia. Therefore, warming causes sexually differential responses of S. paraplesia, with females performing better than males.

The circadian clock mutant lhy cca1 elf3 paces starch mobilization to dawn despite severely disrupted circadian clock function

Many plants, including Arabidopsis (Arabidopsis thaliana), accumulate starch in the daytime and remobilize it to support maintenance and growth at night. Starch accumulation is increased when carbon is in short supply, for example, in short photoperiods. Mobilization is paced to exhaust starch around dawn, as anticipated by the circadian clock. This diel pattern of turnover is largely robust against loss of day, dawn, dusk, or evening clock components. Here, we investigated diel starch turnover in the triple circadian clock mutant lhy cca1 elf3, which lacks the LATE ELONGATED HYPOCOTYL and the CIRCADIAN CLOCK-ASSOCIATED1 (CCA1) dawn components and the EARLY FLOWERING3 (ELF3) evening components of the circadian clock. The diel oscillations of transcripts for the remaining clock components and related genes like REVEILLE and PHYTOCHROME-INTERACING FACTOR family members exhibited attenuated amplitudes and altered peak time, weakened dawn dominance, and decreased robustness against changes in the external light-dark cycle. The triple mutant was unable to increase starch accumulation in short photoperiods. However, it was still able to pace starch mobilization to around dawn in different photoperiods and growth irradiances and to around 24 h after the previous dawn in T17 and T28 cycles. The triple mutant was able to slow down starch mobilization after a sudden low-light day or a sudden early dusk, although in the latter case it did not fully compensate for the lengthened night. Overall, there was a slight trend to less linear mobilization of starch. Thus, starch mobilization can be paced rather robustly to dawn despite a major disruption of the transcriptional clock. It is proposed that temporal information can be delivered from clock components or a semi-autonomous oscillator.

Transcriptome analysis reveals the main metabolic pathway of c-GMP induced by salt stress in tomato (Solanum lycopersicum) seedlings

Tomato (Solanum lycopersicum L.) is a model crop as well as an important food worldwide. In arid areas, increasing soil salinity has limited higher yields in tomato production. As a second messenger molecule, cyclic guanosine monophosphate (c-GMP) plays an indispensable role in plant response to salt stress by regulating cell processes to promote plant growth and development. However, this mechanism has not been fully explored in tomato seedlings. In this experiment, tomato seeds were cultured in four treatments: (1) distilled water (CK); (2) 20μM c-GMP (T1); (3) 50mM NaCl (T2); and (4) 20μM c-GMP+50mM NaCl (T3). The results show that 20μM c-GMP effectively alleviated the inhibitory effect of 50mM NaCl on growth and development, and induced the expression of 1580 differentially expressed genes (DEGs). Seedlings in the CK vs T1 shared 95 upregulated and 442 downregulated DEGs, whereas T2 vs T3 shared 271 upregulated and 772 downregulated DEGs. Based on KEGG (Kyoto Encyclopaedia of Genes and Genomes) analysis, the majority of DEGs were involved in metabolism; exogenous c-GMP induced significant enrichment of pathways associated with carbohydrates, phenylpropanoids and fatty acid metabolism. Most PMEs , acCoA , PAL , PODs , FADs , and AD were upregulated, and GAPDHs , PL , PG , BXL4 , and β-G were downregulated, which reduced susceptibility of tomato seedlings to salt and promoted their salt tolerance. The application of c-GMP increased soluble sugar, flavonoid and lignin contents, reduced accumulation of malondialdehyde (MDA), and enhanced the activity of peroxidase (POD). Thus, our results provide insights into the molecular mechanisms associated with salt tolerance of tomato seedlings.

Turning the Knobs: The Impact of Post-translational Modifications on Carbon Metabolism

Plants rely on the carbon fixed by photosynthesis into sugars to grow and reproduce. However, plants often face non-ideal conditions caused by biotic and abiotic stresses. These constraints impose challenges to managing sugars, the most valuable plant asset. Hence, the precise management of sugars is crucial to avoid starvation under adverse conditions and sustain growth. This review explores the role of post-translational modifications (PTMs) in the modulation of carbon metabolism. PTMs consist of chemical modifications of proteins that change protein properties, including protein-protein interaction preferences, enzymatic activity, stability, and subcellular localization. We provide a holistic view of how PTMs tune resource distribution among different physiological processes to optimize plant fitness.

How Stress Affects Your Budget-Stress Impacts on Starch Metabolism

Starch is a polysaccharide that is stored to be used in different timescales. Transitory starch is used during nighttime when photosynthesis is unavailable. Long-term starch is stored to support vegetative or reproductive growth, reproduction, or stress responses. Starch is not just a reserve of energy for most plants but also has many other roles, such as promoting rapid stomatal opening, making osmoprotectants, cryoprotectants, scavengers of free radicals and signals, and reverting embolised vessels. Biotic and abiotic stress vary according to their nature, strength, duration, developmental stage of the plant, time of the day, and how gradually they develop. The impact of stress on starch metabolism depends on many factors: how the stress impacts the rate of photosynthesis, the affected organs, how the stress impacts carbon allocation, and the energy requirements involved in response to stress. Under abiotic stresses, starch degradation is usually activated, but starch accumulation may also be observed when growth is inhibited more than photosynthesis. Under biotic stresses, starch is usually accumulated, but the molecular mechanisms involved are largely unknown. In this mini-review, we explore what has been learned about starch metabolism and plant stress responses and discuss the current obstacles to fully understanding their interactions.

Data Management and Modeling in Plant Biology

The study of plant-environment interactions is a multidisciplinary research field. With the emergence of quantitative large-scale and high-throughput techniques, amount and dimensionality of experimental data have strongly increased. Appropriate strategies for data storage, management, and evaluation are needed to make efficient use of experimental findings. Computational approaches of data mining are essential for deriving statistical trends and signatures contained in data matrices. Although, current biology is challenged by high data dimensionality in general, this is particularly true for plant biology. Plants as sessile organisms have to cope with environmental fluctuations. This typically results in strong dynamics of metabolite and protein concentrations which are often challenging to quantify. Summarizing experimental output results in complex data arrays, which need computational statistics and numerical methods for building quantitative models. Experimental findings need to be combined by computational models to gain a mechanistic understanding of plant metabolism. For this, bioinformatics and mathematics need to be combined with experimental setups in physiology, biochemistry, and molecular biology. This review presents and discusses concepts at the interface of experiment and computation, which are likely to shape current and future plant biology. Finally, this interface is discussed with regard to its capabilities and limitations to develop a quantitative model of plant-environment interactions.

The sugar-responsive circadian clock regulator bZIP63 modulates plant growth

Adjustment to energy starvation is crucial to ensure growth and survival. In Arabidopsis thaliana (Arabidopsis), this process relies in part on the phosphorylation of the circadian clock regulator bZIP63 by SUCROSE non-fermenting RELATED KINASE1 (SnRK1), a key mediator of responses to low energy. We investigated the effects of mutations in bZIP63 on plant carbon (C) metabolism and growth. Results from phenotypic, transcriptomic and metabolomic analysis of bZIP63 mutants prompted us to investigate the starch accumulation pattern and the expression of genes involved in starch degradation and in the circadian oscillator. bZIP63 mutation impairs growth under light-dark cycles, but not under constant light. The reduced growth likely results from the accentuated C depletion towards the end of the night, which is caused by the accelerated starch degradation of bZIP63 mutants. The diel expression pattern of bZIP63 is dictated by both the circadian clock and energy levels, which could determine the changes in the circadian expression of clock and starch metabolic genes observed in bZIP63 mutants. We conclude that bZIP63 composes a regulatory interface between the metabolic and circadian control of starch breakdown to optimize C usage and plant growth.

Biotechnological Potential of Cephalaria uralensis (Murray) Roem. & Schult. and C. gigantea (Ledeb.) Bobrov-Comparative Analysis of Plant Anatomy and the Content of Biologically Active Substances

Studies conducted to date have shown that Cephalaria uralensis and C. gigantea have high contents of substances with antibacterial, anti-inflammatory, and antioxidant properties; hence, they are attractive plants from the pharmaceutical point of view. However, despite their multifarious desirable biotechnological aspects, the knowledge of these plants is insufficient. The present study focused on the analysis of the morphological, anatomical, and histological structure of aboveground parts of the plants, the identification of the distribution of biologically active compounds in the tissues, and quantitative phytochemical analyses of polyphenolic compounds contained in their aboveground organs. Importantly, the phenological and morphological features of the aboveground organs in the analyzed species were maintained, as in the same plant species growing in different climatic conditions. The analysis of primary metabolites and phenolic compounds in the tissues revealed their distribution in the aboveground organs, which has never been described before. The comparative analyses of the content of total phenolics, total phenolic acids, and total flavonoids in the aboveground organs showed that the level of these substances differed not only between the species but also between the organs. It should be emphasized that the level of these compounds is higher than in many other medicinal plants.

Theoretical and experimental approaches to understand the biosynthesis of starch granules in a physiological context

Starch, a plant-derived insoluble carbohydrate composed of glucose polymers, is the principal carbohydrate in our diet and a valuable raw material for industry. The properties of starch depend on the arrangement of glucose units within the constituent polymers. However, key aspects of starch structure and the underlying biosynthetic processes are not well understood, limiting progress towards targeted improvement of our starch crops. In particular, the major component of starch, amylopectin, has a complex three-dimensional, branched architecture. This architecture stems from the combined actions of a multitude of enzymes, each having broad specificities that are difficult to capture experimentally. In this review, we reflect on experimental approaches and limitations to decipher the enzymes' specificities and explore possibilities for in silico simulations of these activities. We believe that the synergy between experimentation and simulation is needed for the correct interpretation of experimental data and holds the potential to greatly advance our understanding of the overall starch biosynthetic process. We furthermore propose that the formation of glucan secondary structures, concomitant with its synthesis, is a previously overlooked factor that directly affects amylopectin architecture through its impact on enzyme function.

Transient Carbon Reserves in Barley: Malate, Sucrose and Starch Are the Main Players, Their Quantitative Involvement Being Light Intensity Dependant

Under natural environment plants experience different light intensities which can affect photosynthesis and consequently the availability of carbohydrates for daytime growth and their transient storage to supply night growth. We grew a spring barley cultivar, Propino, under three different light intensities under warm days and nights, and evaluated the spatial and diurnal adjustments occurring in the transient carbon stores. Leaves under high light at the end of the day accumulated mainly sucrose (30%) and malate (35%), with lower content of hexoses (5%), starch (15%) and fructans (15%). Under low light, plants presented reduced photosynthesis, with lower metabolite contents at end of day. The malate represented 51% of the total carbon accumulated at end of the day, at the expense of sucrose (12%), other metabolite contributions remaining similar to high light. The percentage of metabolites consumed at night was similar for all light intensities with around 75% of the sucrose and starch being mobilized whilst malate and fructans were only partially mobilized with 56 and 44%, respectively. Altogether, sucrose and malate were the main contributors of the total carbon used at night by barley plants, sucrose being predominant under high light (35% vs. 27%), but malate being the major metabolite used under low light with 40% of the total carbon consumed. Interestingly, light intensity also influenced the location of the C transient stores, the plants under low light prioritizing the accumulation of the metabolites, mostly malate, in the youngest tissues. Therefore, light influences quantitatively, but also qualitatively and spatially the carbon stores in the spring barley cv. Propino, suggesting a tight regulation of the primary metabolism.

Dynamics of Plant Metabolism during Cold Acclimation

Plants have evolved strategies to tightly regulate metabolism during acclimation to a changing environment. Low temperature significantly constrains distribution, growth and yield of many temperate plant species. Exposing plants to low but non-freezing temperature induces a multigenic processes termed cold acclimation, which eventually results in an increased freezing tolerance. Cold acclimation comprises reprogramming of the transcriptome, proteome and metabolome and affects communication and signaling between subcellular organelles. Carbohydrates play a central role in this metabolic reprogramming. This review summarizes current knowledge about the role of carbohydrate metabolism in plant cold acclimation with a focus on subcellular metabolic reprogramming, its thermodynamic constraints under low temperature and mathematical modelling of metabolism.

Elevated temperature differently affects growth, photosynthetic capacity, nutrient absorption and leaf ultrastructure of Abies faxoniana and Picea purpurea under intra- and interspecific competition

There is a limited understanding of the impacts of global warming on intra- and interspecific plant competition. Resolving this knowledge gap is important for predicting the potential influence of global warming on forests, particularly on high-altitude trees, which are more sensitive to warming. In the present study, effects of intra- and interspecific competition on plant growth and associated physiological, structural and chemical traits were investigated in Abies faxoniana and Picea purpurea seedlings under control (ambient temperature) and elevated temperature (ET, 2 °C above ambient temperature) conditions for 2 years. We found that A. faxoniana and P. purpurea grown under intra- and interspecific competition showed significant differences in dry matter accumulation (DMA), photosynthetic capacity, nutrient absorption, non-structural carbohydrate (NSC) contents and leaf ultrastructure under ET conditions. ET increased leaf, stem and root DMA of both conifers under both competition patterns. Moreover, under ET and interspecific competition, P. purpurea had overall superior competitive capacity characterized by higher organ (leaf, stem and root) and total DMA, height growth rate, net photosynthetic rate, specific leaf area, water use efficiency (δ13C), leaf and root N and NSC concentrations and greater plasticity for absorption of different soil N forms. Thus, the growth of P. purpurea benefitted from the presence of A. faxoniana under ET. Our results demonstrated that ET significantly affects the asymmetric competition patterns in subalpine conifer species. Potential alteration of plant competitive interactions by global warming can influence the composition, structure and functioning of subalpine coniferous forests.

Exploring regulatory networks in plants: transcription factors of starch metabolism

Biological networks are complex (non-linear), redundant (cyclic) and compartmentalized at the subcellular level. Rational manipulation of plant metabolism may have failed due to inherent difficulties of a comprehensive understanding of regulatory loops. We first need to identify key factors controlling the regulatory loops of primary metabolism. The paradigms of plant networks are revised in order to highlight the differences between metabolic and transcriptional networks. Comparison between animal and plant transcription factors (TFs) reveal some important differences. Plant transcriptional networks function at a lower hierarchy compared to animal regulatory networks. Plant genomes contain more TFs than animal genomes, but plant proteins are smaller and have less domains as animal proteins which are often multifunctional. We briefly summarize mutant analysis and co-expression results pinpointing some TFs regulating starch enzymes in plants. Detailed information is provided about biochemical reactions, TFs and cis regulatory motifs involved in sucrose-starch metabolism, in both source and sink tissues. Examples about coordinated responses to hormones and environmental cues in different tissues and species are listed. Further advancements require combined data from single-cell transcriptomic and metabolomic approaches. Cell fractionation and subcellular inspection may provide valuable insights. We propose that shuffling of promoter elements might be a promising strategy to improve in the near future starch content, crop yield or food quality.

Continuous dynamic adjustment of the plant circadian oscillator

The clockwork of plant circadian oscillators has been resolved through investigations in Arabidopsis thaliana. The circadian oscillator is an important regulator of much of plant physiology, though many of the mechanisms are unclear. New findings demonstrate that the oscillator adjusts phase and period in response to abiotic and biotic signals, providing insight in to how the plant circadian oscillator integrates with the biology of the cell and entrains to light, dark and temperature cycles. We propose that the plant circadian oscillator is dynamically plastic, in constant adjustment, rather than being an isolated clock impervious to cellular events.

Mathematical modeling of diurnal patterns of carbon allocation to shoot and root in Arabidopsis thaliana

We developed a mathematical model to simulate dynamics of central carbon metabolism over complete diurnal cycles for leaves of Arabidopsis thaliana exposed to either normal (120 µmol m-2 s-1) or high light intensities (1200 µmol m- 2 s-1). The main objective was to obtain a high-resolution time series for metabolite dynamics as well as for shoot structural carbon formation (compounds with long residence time) and assimilate export of aerial organs to the sink tissue. Model development comprised a stepwise increment of complexity to finally approach the in vivo situation. The correct allocation of assimilates to either sink export or shoot structural carbon formation was a central goal of model development. Diurnal gain of structural carbon was calculated based on the daily increment in total photosynthetic carbon fixation, and this was the only parameter for structural carbon formation implemented in the model. Simulations of the dynamics of central metabolite pools revealed that shoot structural carbon formation occurred solely during the light phase but not during the night. The model allowed simulation of shoot structural carbon formation as a function of central leaf carbon metabolism under different environmental conditions without structural modifications. Model simulations were performed for the accession Landsberg erecta (Ler) and its hexokinase null-mutant gin2-1. This mutant displays a slow growth phenotype especially at increasing light intensities. Comparison of simulations revealed that the retarded shoot growth in the mutant resulted from an increased assimilate transport to sink organs. Due to its central function in sucrose cycling and sugar signaling, our findings suggest an important role of hexokinase-1 for carbon allocation to either shoot growth or assimilate export.

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.

Parallel analysis of Arabidopsis circadian clock mutants reveals different scales of transcriptome and proteome regulation

The circadian clock regulates physiological processes central to growth and survival. To date, most plant circadian clock studies have relied on diurnal transcriptome changes to elucidate molecular connections between the circadian clock and observable phenotypes in wild-type plants. Here, we have integrated RNA-sequencing and protein mass spectrometry data to comparatively analyse the lhycca1, prr7prr9, gi and toc1 circadian clock mutant rosette at the end of day and end of night. Each mutant affects specific sets of genes and proteins, suggesting that the circadian clock regulation is modular. Furthermore, each circadian clock mutant maintains its own dynamically fluctuating transcriptome and proteome profile specific to subcellular compartments. Most of the measured protein levels do not correlate with changes in their corresponding transcripts. Transcripts and proteins that have coordinated changes in abundance are enriched for carbohydrate- and cold-responsive genes. Transcriptome changes in all four circadian clock mutants also affect genes encoding starch degradation enzymes, transcription factors and protein kinases. The comprehensive transcriptome and proteome datasets demonstrate that future system-driven research of the circadian clock requires multi-level experimental approaches. Our work also shows that further work is needed to elucidate the roles of post-translational modifications and protein degradation in the regulation of clock-related processes.

To grow or not to grow, a power-saving program induced in dormant buds

Plant shoot branching patterns determine leaf, flower and fruit production, and thus reproductive success and yield. Branch primordia, or axillary buds, arise in the axils of leaves and their decision to either grow or enter dormancy is coordinated at the whole plant level. Comparisons of transcriptional profiles of axillary buds entering dormancy have identified a shared set of responses that closely resemble a Low Energy Syndrome. This syndrome is aimed at saving carbon use to support essential maintenance functions, rather than additional growth, and involves growth arrest (thus dormancy), metabolic reprogramming and hormone signalling. This response is widely conserved in distantly related woody and herbaceous species, and not only underlies but also precedes the growth-to-dormancy transition induced in buds by different stimuli.

The Importance of the Circadian Clock in Regulating Plant Metabolism

Carbohydrates are the primary energy source for plant development. Plants synthesize sucrose in source organs and transport them to sink organs during plant growth. This metabolism is sensitive to environmental changes in light quantity, quality, and photoperiod. In the daytime, the synthesis of sucrose and starch accumulates, and starch is degraded at nighttime. The circadian clock genes provide plants with information on the daily environmental changes and directly control many developmental processes, which are related to the path of primary metabolites throughout the life cycle. The circadian clock mechanism and processes of metabolism controlled by the circadian rhythm were studied in the model plant Arabidopsis and in the crops potato and rice. However, the translation of molecular mechanisms obtained from studies of model plants to crop plants is still difficult. Crop plants have specific organs such as edible seed and tuber that increase the size or accumulate valuable metabolites by harvestable metabolic components. Human consumers are interested in the regulation and promotion of these agriculturally significant crops. Circadian clock manipulation may suggest various strategies for the increased productivity of food crops through using environmental signal or overcoming environmental stress.

Photosynthate partitioning to starch in Arabidopsis thaliana is insensitive to light intensity but sensitive to photoperiod due to a restriction on growth in the light in short photoperiods

Photoperiod duration can be predicted from previous days, but irradiance fluctuates in an unpredictable manner. To investigate how allocation to starch responds to changes in these two environmental variables, Arabidopsis Col-0 was grown in a 6 h and a 12 h photoperiod at three different irradiances. The absolute rate of starch accumulation increased when photoperiod duration was shortened and when irradiance was increased. The proportion of photosynthate allocated to starch increased strongly when photoperiod duration was decreased but only slightly when irradiance was decreased. There was a small increase in the daytime level of sucrose and twofold increases in glucose, fructose and glucose 6-phosphate at a given irradiance in short photoperiods compared to long photoperiods. The rate of starch accumulation correlated strongly with sucrose and glucose levels in the light, irrespective of whether these sugars were responding to a change in photoperiod or irradiance. Whole plant carbon budget modelling revealed a selective restriction of growth in the light period in short photoperiods. It is proposed that photoperiod sensing, possibly related to the duration of the night, restricts growth in the light period in short photoperiods, increasing allocation to starch and providing more carbon reserves to support metabolism and growth in the long night.

Adjustment of the Arabidopsis circadian oscillator by sugar signalling dictates the regulation of starch metabolism

Arabidopsis plants store part of the carbon fixed by photosynthesis as starch to sustain growth at night. Two competing hypotheses have been proposed to explain this diel starch turnover based on either the measurement of starch abundance with respect to circadian time, or the sensing of sugars to feedback to the circadian oscillator to dynamically adjust the timing of starch turnover. We report a phase oscillator model that permitted derivation of the ideal responses of the circadian regulation of starch breakdown to maintain sucrose homeostasis. Testing the model predictions using a sugar-unresponsive mutant of Arabidopsis demonstrated that the dynamics of starch turnover arise from the circadian clock measuring and responding to the rate of change of cellular sucrose. Our theory and experiments suggest that starch turnover is controlled by the circadian clock acting as a dynamic homeostat responding to sucrose signals to maintain carbon homeostasis.

Effects of Elevated Carbon Dioxide on Photosynthesis and Carbon Partitioning: A Perspective on Root Sugar Sensing and Hormonal Crosstalk

Plant responses to atmospheric carbon dioxide will be of great concern in the future, as carbon dioxide concentrations ([CO2]) are predicted to continue to rise. Elevated [CO2] causes increased photosynthesis in plants, which leads to greater production of carbohydrates and biomass. Which organ the extra carbohydrates are allocated to varies between species, but also within species. These carbohydrates are a major energy source for plant growth, but they also act as signaling molecules and have a range of uses beyond being a source of carbon and energy. Currently, there is a lack of information on how the sugar sensing and signaling pathways of plants are affected by the higher content of carbohydrates produced under elevated [CO2]. Particularly, the sugar signaling pathways of roots are not well understood, along with how they are affected by elevated [CO2]. At elevated [CO2], some plants allocate greater amounts of sugars to roots where they are likely to act on gene regulation and therefore modify nutrient uptake and transport. Glucose and sucrose also promote root growth, an effect similar to what occurs under elevated [CO2]. Sugars also crosstalk with hormones to regulate root growth, but also affect hormone biosynthesis. This review provides an update on the role of sugars as signaling molecules in plant roots and thus explores the currently known functions that may be affected by elevated [CO2].

A Conserved Carbon Starvation Response Underlies Bud Dormancy in Woody and Herbaceous Species

Plant shoot systems give rise to characteristic above-ground plant architectures. Shoots are formed from axillary meristems and buds, whose growth and development is modulated by systemic and local signals. These cues convey information about nutrient and water availability, light quality, sink/source organ activity and other variables that determine the timeliness and competence to maintain development of new shoots. This information is translated into a local response, in meristems and buds, of growth or quiescence. Although some key genes involved in the onset of bud latency have been identified, the gene regulatory networks (GRNs) controlled by these genes are not well defined. Moreover, it has not been determined whether bud dormancy induced by environmental cues, such as a low red-to-far-red light ratio, shares genetic mechanisms with bud latency induced by other causes, such as apical dominance or a short-day photoperiod. Furthermore, the evolution and conservation of these GRNs throughout angiosperms is not well established. We have reanalyzed public transcriptomic datasets that compare quiescent and active axillary buds of Arabidopsis, with datasets of axillary buds of the woody species Vitis vinifera (grapevine) and apical buds of Populus tremula x Populus alba (poplar) during the bud growth-to-dormancy transition. Our aim was to identify potentially common GRNs induced during the process that leads to bud para-, eco- and endodormancy. In Arabidopsis buds that are entering eco- or paradormancy, we have identified four induced interrelated GRNs that correspond to a carbon (C) starvation syndrome, typical of tissues undergoing low C supply. This response is also detectable in poplar and grapevine buds before and during the transition to dormancy. In all eukaryotes, C-limiting conditions are coupled to growth arrest and latency like that observed in dormant axillary buds. Bud dormancy might thus be partly a consequence of the underlying C starvation syndrome triggered by environmental and endogenous cues that anticipate or signal conditions unfavorable for sustained shoot growth.

Photoperiod-dependent changes in the phase of core clock transcripts and global transcriptional outputs at dawn and dusk in Arabidopsis

Plants use the circadian clock to sense photoperiod length. Seasonal responses like flowering are triggered at a critical photoperiod when a light-sensitive clock output coincides with light or darkness. However, many metabolic processes, like starch turnover, and growth respond progressively to photoperiod duration. We first tested the photoperiod response of 10 core clock genes and two output genes. qRT-PCR analyses of transcript abundance under 6, 8, 12 and 18 h photoperiods revealed 1-4 h earlier peak times under short photoperiods and detailed changes like rising PRR7 expression before dawn. Clock models recapitulated most of these changes. We explored the consequences for global gene expression by performing transcript profiling in 4, 6, 8, 12 and 18 h photoperiods. There were major changes in transcript abundance at dawn, which were as large as those between dawn and dusk in a given photoperiod. Contributing factors included altered timing of the clock relative to dawn, light signalling and changes in carbon availability at night as a result of clock-dependent regulation of starch degradation. Their interaction facilitates coordinated transcriptional regulation of key processes like starch turnover, anthocyanin, flavonoid and glucosinolate biosynthesis and protein synthesis and underpins the response of metabolism and growth to photoperiod.

Modeling the diversion of primary carbon flux into secondary metabolism under variable nitrate and light/dark conditions

In plants, the partitioning of carbon resources between growth and defense is detrimental for their development. From a metabolic viewpoint, growth is mainly related to primary metabolism including protein, amino acid and lipid synthesis, whereas defense is based notably on the biosynthesis of a myriad of secondary metabolites. Environmental factors, such as nitrate fertilization, impact the partitioning of carbon resources between growth and defense. Indeed, experimental data showed that a shortage in the nitrate fertilization resulted in a reduction of the plant growth, whereas some secondary metabolites involved in plant defense, such as phenolic compounds, accumulated. Interestingly, sucrose, a key molecule involved in the transport and partitioning of carbon resources, appeared to be under homeostatic control. Based on the inflow/outflow properties of sucrose homeostatic regulation we propose a global model on how the diversion of the primary carbon flux into the secondary phenolic pathways occurs at low nitrate concentrations. The model can account for the accumulation of starch during the light phase and the sucrose remobilization by starch degradation during the night. Day-length sensing mechanisms for variable light-dark regimes are discussed, showing that growth is proportional to the length of the light phase. The model can describe the complete starch consumption during the night for plants adapted to a certain light/dark regime when grown on sufficient nitrate and can account for an increased accumulation of starch observed under nitrate limitation.

Can cyanobacteria serve as a model of plant photorespiration? - a comparative meta-analysis of metabolite profiles

Photorespiration is a process that is crucial for the survival of oxygenic phototrophs in environments that favour the oxygenation reaction of Rubisco. While photorespiration is conserved among cyanobacteria, algae, and embryophytes, it evolved to different levels of complexity in these phyla. The highest complexity is found in embryophytes, where the pathway involves four cellular compartments and respective transport processes. The complexity of photorespiration in embryophytes raises the question whether a simpler system, such as cyanobacteria, may serve as a model to facilitate our understanding of the common key aspects of photorespiration. In this study, we conducted a meta-analysis of publicly available metabolite profiles from the embryophyte Arabidopsis thaliana and the cyanobacterium Synechocystis sp. PCC 6803 grown under conditions that either activate or suppress photorespiration. The comparative meta-analysis evaluated the similarity of metabolite profiles, the variability of metabolite pools, and the patterns of metabolite ratios. Our results show that the metabolic signature of photorespiration is in part conserved between the compared model organisms under conditions that favour the oxygenation reaction. Therefore, our findings support the claim that cyanobacteria can serve as prokaryotic models of photorespiration in embryophytes.

Approximating the stabilization of cellular metabolism by compartmentalization

Biochemical regulation in compartmentalized metabolic networks is highly complex and non-intuitive. This is particularly true for cells of higher plants showing one of the most compartmentalized cellular structures across all kingdoms of life. The interpretation and testable hypothesis generation from experimental data on such complex systems is a challenging step in biological research and biotechnological applications. While it is known that subcellular compartments provide defined reaction spaces within a cell allowing for the tight coordination of complex biochemical reaction sequences, its role in the coordination of metabolic signals during metabolic reprogramming due to environmental fluctuations is less clear. In the present study, we numerically analysed the effects of environmental fluctuations in a subcellular metabolic network with regard to the stability of an experimentally observed steady state in the genetic model plant Arabidopsis thaliana. Applying a method for kinetic parameter normalization, several millions of probable enzyme kinetic parameter constellations were simulated and evaluated with regard to the stability information of the metabolic homeostasis. Information about the stability of the metabolic steady state was derived from real parts of eigenvalues of Jacobian matrices. Our results provide evidence for a differential stabilizing contribution of different subcellular compartments. We could identify stabilizing and destabilizing network components which we could classify according to their subcellular localization. The findings prove that a highly dynamic interplay between intracellular compartments is preliminary for an efficient stabilization of a metabolic homeostasis after environmental perturbation. Further, our results provide evidence that feedback-inhibition originating from the cytosol and plastid seem to stabilize the sucrose homeostasis more efficiently than vacuolar control. In summary, our results indicate stabilizing and destabilizing network components in context of their subcellular organization.

A Strategy for Functional Interpretation of Metabolomic Time Series Data in Context of Metabolic Network Information

The functional connection of experimental metabolic time series data with biochemical network information is an important, yet complex, issue in systems biology. Frequently, experimental analysis of diurnal, circadian, or developmental dynamics of metabolism results in a comprehensive and multidimensional data matrix comprising information about metabolite concentrations, protein levels, and/or enzyme activities. While, irrespective of the type of organism, the experimental high-throughput analysis of the transcriptome, proteome, and metabolome has become a common part of many systems biological studies, functional data integration in a biochemical and physiological context is still challenging. Here, an approach is presented which addresses the functional connection of experimental time series data with biochemical network information which can be inferred, for example, from a metabolic network reconstruction. Based on a time-continuous and variance-weighted regression analysis of experimental data, metabolic functions, i.e., first-order derivatives of metabolite concentrations, were related to time-dependent changes in other biochemically relevant metabolic functions, i.e., second-order derivatives of metabolite concentrations. This finally revealed time points of perturbed dependencies in metabolic functions indicating a modified biochemical interaction. The approach was validated using previously published experimental data on a diurnal time course of metabolite levels, enzyme activities, and metabolic flux simulations. To support and ease the presented approach of functional time series analysis, a graphical user interface including a test data set and a manual is provided which can be run within the numerical software environment Matlab®.

Effects of phosphorus application on photosynthetic carbon and nitrogen metabolism, water use efficiency and growth of dwarf bamboo (Fargesia rufa) subjected to water deficit

Dwarf bamboo (Fargesia rufa Yi), one of the staple foods for the endangered giant pandas, is highly susceptible to water deficit due to its shallow roots. In the face of climate change, maintenance and improvement in its productivity is very necessary for the management of the giant pandas' habitats. However, the regulatory mechanisms underlying plant responses to water deficit are poorly known. To investigate the effects of P application on photosynthetic C and N metabolism, water use efficiency (WUE) and growth of dwarf bamboo under water deficit, a completely randomized design with two factors of two watering (well-watered and water-stressed) and two P regimes (with and without P fertilization) was arranged. P application hardly changed growth, net CO2 assimilation rate (P(n)) and WUE in well-watered plants but significantly increased relative growth rate (RGR) and P(n) in water-stressed plants. The effect of P application on RGR under water stress was mostly associated with physiological adjustments rather than with differences in biomass allocation. P application maintained the balance of C metabolism in well-watered plants, but altered the proportion of nitrogenous compounds in N metabolism. By contrast, P application remarkably increased sucrose-metabolizing enzymes activities with an obvious decrease in sucrose content in water-stressed plants, suggesting an accelerated sucrose metabolism. Activation of nitrogen-metabolizing enzymes in water-stressed plants was attenuated after P application, thus slowing nitrate reduction and ammonium assimilation. P application hardly enlarged the phenotypic plasticity of dwarf bamboo in response to water in the short term. Generally, these examined traits of dwarf bamboo displayed weak or negligible responses to water-P interaction. In conclusion, P application could accelerate P(n) and sucrose metabolism and slow N metabolism in water-stressed dwarf bamboo, and as a result improved RGR and alleviated damage from soil water deficit.

Mathematical modelling of diurnal regulation of carbohydrate allocation by osmo-related processes in plants

Plants synthesize sucrose in source tissues (mainly mature leafs) and supply it for growth of sink tissues (young leafs). Sucrose is derived from photosynthesis during daytime and from starch at night. Because the diurnal regulation of sucrose fluxes is not completely understood, we built a mathematical model designed to reproduce all key experimental observations. For this, assumptions were made about the molecular mechanisms underlying the regulations, which are all motivated by experimental facts. The key regulators in our model are two kinases (SnRK1 and osmo-sensitive kinase OsmK) under the control of the circadian clock. SnRK1 is activated in the night to prepare for regularly occurring carbon-limiting conditions, whereas OsmK is activated during the day to prepare for water deficit, which often occurs in the afternoon. Decrease of SnRK1 and increase of OsmK result in partitioning of carbon towards sucrose to supply growing sink tissues. Concomitantly, increasing levels of the growth regulator trehalose-6-phosphate stimulates the development of new sink tissues and thus sink demand, which further activates sucrose supply in a positive feedback loop. We propose that OsmK acts as a timer to measure the length of the photoperiod and suggest experiments how this hypothesis can be validated.

Mathematical modelling of the diurnal regulation of the MEP pathway in Arabidopsis

Isoprenoid molecules are essential elements of plant metabolism. Many important plant isoprenoids, such as chlorophylls, carotenoids, tocopherols, prenylated quinones and hormones are synthesised in chloroplasts via the 2-C-methyl-d-erythritol 4-phosphate (MEP) pathway. Here we develop a mathematical model of diurnal regulation of the MEP pathway in Arabidopsis thaliana. We used both experimental and theoretical approaches to integrate mechanisms potentially involved in the diurnal control of the pathway. Our data show that flux through the MEP pathway is accelerated in light due to the photosynthesis-dependent supply of metabolic substrates of the pathway and the transcriptional regulation of key biosynthetic genes by the circadian clock. We also demonstrate that feedback regulation of both the activity and the abundance of the first enzyme of the MEP pathway (1-deoxy-D-xylulose 5-phosphate synthase, DXS) by pathway products stabilizes the flux against changes in substrate supply and adjusts the flux according to product demand under normal growth conditions. These data illustrate the central relevance of photosynthesis, the circadian clock and feedback control of DXS for the diurnal regulation of the MEP pathway.

Understanding circadian regulation of carbohydrate metabolism in Arabidopsis using mathematical models

C3 plants assimilate carbon by photosynthesis only during the day, but carbon resources are also required for growth and maintenance at night. To avoid carbon starvation, many plants store a part of photosynthetic carbon in starch during the day, and degrade it to supply sugars for growth at night. In Arabidopsis, starch accumulation in the day and degradation at night occur almost linearly, with the shape of this diel starch profile adaptively changing to allow continuous supply of sugar even in long-night conditions. The anticipation of dawn required to ensure linear consumption of starch to almost zero at dawn presumably requires the circadian clock. We review the links between carbon metabolism and the circadian clock, and mathematical models aimed at explaining the diel starch profile. These models can be considered in two classes, those that assume the level of available starch is sensed and the system ensures linearity of starch availability, and those in which sugar sensing is assumed, yielding linearity of starch availability as an emergent property of sucrose homeostasis. In the second class of model the feedback from starch metabolism to the circadian clock is considered to be essential for adaptive response to diverse photoperiods, consistent with recent empirical data demonstrating entrainment of the circadian clock by photosynthesis. Knowledge concerning the mechanisms regulating the dynamics of starch metabolism and sugar homeostasis in plants is required to develop new theories about the limitations of growth and biomass accumulation.

How plants manage food reserves at night: quantitative models and open questions

In order to cope with night-time darkness, plants during the day allocate part of their photosynthate for storage, often as starch. This stored reserve is then degraded at night to sustain metabolism and growth. However, night-time starch degradation must be tightly controlled, as over-rapid turnover results in premature depletion of starch before dawn, leading to starvation. Recent experiments in Arabidopsis have shown that starch degradation proceeds at a constant rate during the night and is set such that starch reserves are exhausted almost precisely at dawn. Intriguingly, this pattern is robust with the degradation rate being adjusted to compensate for unexpected changes in the time of darkness onset. While a fundamental role for the circadian clock is well-established, the underlying mechanisms controlling starch degradation remain poorly characterized. Here, we discuss recent quantitative models that have been proposed to explain how plants can compute the appropriate starch degradation rate, a process that requires an effective arithmetic division calculation. We review experimental confirmation of the models, and describe aspects that require further investigation. Overall, the process of night-time starch degradation necessitates a fundamental metabolic role for the circadian clock and, more generally, highlights how cells process information in order to optimally manage their resources.

The relationship between leaf area growth and biomass accumulation in Arabidopsis thaliana

Leaf area growth determines the light interception capacity of a crop and is often used as a surrogate for plant growth in high-throughput phenotyping systems. The relationship between leaf area growth and growth in terms of mass will depend on how carbon is partitioned among new leaf area, leaf mass, root mass, reproduction, and respiration. A model of leaf area growth in terms of photosynthetic rate and carbon partitioning to different plant organs was developed and tested with Arabidopsis thaliana L. Heynh. ecotype Columbia (Col-0) and a mutant line, gigantea-2 (gi-2), which develops very large rosettes. Data obtained from growth analysis and gas exchange measurements was used to train a genetic programming algorithm to parameterize and test the above model. The relationship between leaf area and plant biomass was found to be non-linear and variable depending on carbon partitioning. The model output was sensitive to the rate of photosynthesis but more sensitive to the amount of carbon partitioned to growing thicker leaves. The large rosette size of gi-2 relative to that of Col-0 resulted from relatively small differences in partitioning to new leaf area vs. leaf thickness.

Multiscale digital Arabidopsis predicts individual organ and whole-organism growth

Understanding how dynamic molecular networks affect whole-organism physiology, analogous to mapping genotype to phenotype, remains a key challenge in biology. Quantitative models that represent processes at multiple scales and link understanding from several research domains can help to tackle this problem. Such integrated models are more common in crop science and ecophysiology than in the research communities that elucidate molecular networks. Several laboratories have modeled particular aspects of growth in Arabidopsis thaliana, but it was unclear whether these existing models could productively be combined. We test this approach by constructing a multiscale model of Arabidopsis rosette growth. Four existing models were integrated with minimal parameter modification (leaf water content and one flowering parameter used measured data). The resulting framework model links genetic regulation and biochemical dynamics to events at the organ and whole-plant levels, helping to understand the combined effects of endogenous and environmental regulators on Arabidopsis growth. The framework model was validated and tested with metabolic, physiological, and biomass data from two laboratories, for five photoperiods, three accessions, and a transgenic line, highlighting the plasticity of plant growth strategies. The model was extended to include stochastic development. Model simulations gave insight into the developmental control of leaf production and provided a quantitative explanation for the pleiotropic developmental phenotype caused by overexpression of miR156, which was an open question. Modular, multiscale models, assembling knowledge from systems biology to ecophysiology, will help to understand and to engineer plant behavior from the genome to the field.