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

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.

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.

ATP homeostasis and signaling in plants

ATP is the primary form of energy for plants, and a shortage of cellular ATP is generally acknowledged to pose a threat to plant growth and development, stress resistance, and crop quality. The overall metabolic processes that contribute to the ATP pool, from production, dissipation, and transport to elimination, have been studied extensively. Considerable evidence has revealed that in addition to its role in energy supply, ATP also acts as a regulatory signaling molecule to activate global metabolic responses. Identification of the eATP receptor DORN1 contributed to a better understanding of how plants cope with disruption of ATP homeostasis and of the key points at which ATP signaling pathways intersect in cells or whole organisms. The functions of SnRK1α, the master regulator of the energy management network, in restoring the equilibrium of the ATP pool have been demonstrated, and the vast and complex metabolic network mediated by SnRK1α to adapt to fluctuating environments has been characterized. This paper reviews recent advances in understanding the regulatory control of the cellular ATP pool and discusses possible interactions among key regulators of ATP-pool homeostasis and crosstalk between iATP/eATP signaling pathways. Perception of ATP deficit and modulation of cellular ATP homeostasis mediated by SnRK1α in plants are discussed at the physiological and molecular levels. Finally, we suggest future research directions for modulation of plant cellular ATP homeostasis.

Trehalose-6-phosphate synthase 8 increases photosynthesis and seed yield in Brassica napus

Trehalose-6-phosphate (T6P) functions as a vital proxy for assessing carbohydrate status in plants. While class II T6P synthases (TPS) do not exhibit TPS activity, they are believed to play pivotal regulatory roles in trehalose metabolism. However, their precise functions in carbon metabolism and crop yield have remained largely unknown. Here, BnaC02.TPS8, a class II TPS gene, is shown to be specifically expressed in mature leaves and the developing pod walls of Brassica napus. Overexpression of BnaC02.TPS8 increased photosynthesis and the accumulation of sugars, starch, and biomass compared to wild type. Metabolomic analysis of BnaC02.TPS8 overexpressing lines and CRISPR/Cas9 mutants indicated that BnaC02.TPS8 enhanced the partitioning of photoassimilate into starch and sucrose, as opposed to glycolytic intermediates and organic acids, which might be associated with TPS activity. Furthermore, the overexpression of BnaC02.TPS8 not only increased seed yield but also enhanced seed oil accumulation and improved the oil fatty acid composition in B. napus under both high nitrogen (N) and low N conditions in the field. These results highlight the role of class II TPS in impacting photosynthesis and seed yield of B. napus, and BnaC02.TPS8 emerges as a promising target for improving B. napus seed yield.

A transposon insertion in the promoter of OsUBC12 enhances cold tolerance during japonica rice germination

Low-temperature germination (LTG) is an important agronomic trait for rice (Oryza sativa). Japonica rice generally has greater capacity for germination at low temperatures than the indica subpopulation. However, the genetic basis and molecular mechanisms underlying this complex trait are poorly understood. Here, we report that OsUBC12, encoding an E2 ubiquitin-conjugating enzyme, increases low-temperature germinability in japonica, owing to a transposon insertion in its promoter enhancing its expression. Natural variation analysis reveals that transposon insertion in the OsUBC12 promoter mainly occurs in the japonica lineage. The variation detected in eight representative two-line male sterile lines suggests the existence of this allele introgression by indica-japonica hybridization breeding, and varieties carrying the japonica OsUBC12 locus (transposon insertion) have higher low-temperature germinability than varieties without the locus. Further molecular analysis shows that OsUBC12 negatively regulate ABA signaling. OsUBC12-regulated seed germination and ABA signaling mainly depend on a conserved active site required for ubiquitin-conjugating enzyme activity. Furthermore, OsUBC12 directly associates with rice SUCROSE NON-FERMENTING 1-RELATED PROTEIN KINASE 1.1 (OsSnRK1.1), promoting its degradation. OsSnRK1.1 inhibits LTG by enhancing ABA signaling and acts downstream of OsUBC12. These findings shed light on the underlying mechanisms of UBC12 regulating LTG and provide genetic reference points for improving LTG in indica rice.

Deciphering the regulatory role of PheSnRK genes in Moso bamboo: insights into hormonal, energy, and stress responses

The SnRK (sucrose non-fermentation-related protein kinase) plays an important role in regulating various signals in plants. However, as an important bamboo shoot and wood species, the response mechanism of PheSnRK in Phyllostachys edulis to hormones, low energy and stress remains unclear. In this paper, we focused on the structure, expression, and response of SnRK to hormones and sugars. In this study, we identified 75 PheSnRK genes from the Moso bamboo genome, which can be divided into three groups according to the evolutionary relationship. Cis-element analysis has shown that the PheSnRK gene can respond to various hormones, light, and stress. The PheSnRK2.9 proteins were localized in the nucleus and cytoplasm. Transgenic experiments showed that overexpression of PheSnRK2.9 inhibited root development, the plants were salt-tolerant and exhibited slowed starch consumption in Arabidopsis in the dark. The results of yeast one-hybrid and dual luciferase assay showed that PheIAAs and PheNACs can regulate PheSnRK2.9 gene expression by binding to the promoter of PheSnRK2.9. This study provided a comprehensive understanding of PheSnRK genes of Moso bamboo, which provides valuable information for further research on energy regulation mechanism and stress response during the growth and development of Moso bamboo.

Sucrose homeostasis: Mechanisms and opportunity in crop yield improvement

Sugar homeostasis is a critical feature of biological systems. In humans, raised and dysregulated blood sugar is a serious health issue. In plants, directed changes in sucrose homeostasis and allocation represent opportunities in crop improvement. Plant tissue sucrose varies more than blood glucose and is found at higher concentrations (cytosol and phloem ca. 100 mM v 3.9-6.9 mM for blood glucose). Tissue sucrose varies with developmental stage and environment, but cytosol and phloem exhibit tight sucrose control. Sucrose homeostasis is a consequence of the integration of photosynthesis, synthesis of storage end-products such as starch, transport of sucrose to sinks and sink metabolism. Trehalose 6-phosphate (T6P)-SnRK1 and TOR play central, still emerging roles in regulating and coordinating these processes. Overall, tissue sucrose levels are more strongly related to growth than to photosynthesis. As a key sucrose signal, T6P regulates sucrose levels, transport and metabolic pathways to coordinate source and sink at a whole plant level. Emerging evidence shows that T6P interacts with meristems. With careful targeting, T6P manipulation through exploiting natural variation, chemical intervention and genetic modification is delivering benefits for crop yields. Regulation of cereal grain set, filling and retention may be the most strategically important aspect of sucrose allocation and homeostasis for food security.

DOMAIN OF UNKNOWN FUNCTION581-9 negatively regulates SnRK1 kinase activity

In plants, sucrose nonfermenting 1 (SNF1)-related protein kinase 1 (SnRK1) is a key energy sensor that orchestrates large-scale transcriptional reprograming to maintain cellular homeostasis under energy deficit. SnRK1 activity is under tight negative control, although the exact mechanisms leading to its activation are not well understood. We show that the Arabidopsis (Arabidopsis thaliana) DOMAIN OF UNKNOWN FUNCTION (DUF581) protein DUF581-9/FCS-like zinc finger 3 binds to the catalytic SnRK1.1 α subunit (KIN10) to inhibit its activation by geminivirus rep-interacting kinase (GRIK)-dependent T-loop phosphorylation. Overexpression of DUF581-9 in Arabidopsis dampens SnRK1 signaling and interferes with adaptation to dark-induced starvation. The presence of DUF581-9 significantly reduced SnRK1 activity in protoplasts and in vitro. This was accompanied by a reduction in T175 T-loop phosphorylation and also diminished KIN10 auto-phosphorylation. Furthermore, DUF581-9 reduced binding of the upstream activating kinase GRIK2 to KIN10, explaining the reduced KIN10 T-loop phosphorylation. Ectopically expressed DUF581-9 protein was rapidly turned over by the proteasome when Arabidopsis plants were subjected to starvation treatment, likely releasing its inhibitory activity on the SnRK1 complex. Taken together, our results support a model in which DUF581-9 negatively regulates SnRK1 activity under energy sufficient conditions. Turnover of the protein provides a rapid way for SnRK1 activation under energy deficit without the need of de novo protein synthesis.

Identification of Ossnrk1a-1 Regulated Genes Associated with Rice Immunity and Seed Set

Sucrose non-fermenting-1-related protein kinase-1 (SnRK1) is a highly conserved serine-threonine kinase complex regulating plants' energy metabolisms and resistance to various types of stresses. However, the downstream genes regulated by SnRK1 in these plant physiological processes still need to be explored. In this study, we found that the knockout of OsSnRK1a resulted in no obvious defects in rice growth but notably decreased the seed setting rate. The ossnrk1a mutants were more sensitive to blast fungus (Magnaporthe oryzae) infection and showed compromised immune responses. Transcriptome analyses revealed that SnRK1a was an important intermediate in the energy metabolism and response to biotic stress. Further investigation confirmed that the transcription levels of OsNADH-GOGAT2, which positively controls rice yield, and the defense-related gene pathogenesis-related protein 1b (OsPR1b) were remarkably decreased in the ossnrk1a mutant. Moreover, we found that OsSnRK1a directly interacted with the regulatory subunits OsSnRK1β1 and OsSnRK1β3, which responded specifically to blast fungus infection and starvation stresses, respectively. Taken together, our findings provide an insight into the mechanism of OsSnRK1a, which forms a complex with specific β subunits, contributing to rice seed set and resistance by regulating the transcription of related genes.

A sucrose non-fermenting-1-related protein kinase 1 gene from wheat, TaSnRK1α regulates starch biosynthesis by modulating AGPase activity

Major portion of wheat grain consist of carbohydrate, mainly starch. The proportion of amylose and amylopectin in starch greatly influence the end product quality. Advancement in understanding starch biosynthesis pathway and modulating key genes has enabled the genetic modification of crops resulting in enhanced starch quality. However, the regulation of starch biosynthesis genes still remains unexplored. So, to expand the limited knowledge, here, we characterized a Ser/Thr kinase, SnRK1α in wheat and determined its role in regulating starch biosynthesis. SnRK1 is an evolutionary conserved protein kinase and share homology to yeast SNF1. Yeast complementation assay suggests TaSnRK1α restores growth defect and promotes glycogen accumulation. Domain analysis and complementation assay with truncated domain proteins suggest the importance of ATP-binding and UBA domain in TaSnRK1α activity. Sub-cellular localization identified nuclear and cytoplasmic localization of TaSnRK1α in tobacco leaves. Further, heterologous over-expression (O/E) of TaSnRK1α in Arabidopsis not only led to increase in starch content but also enlarges the starch granules. TaSnRK1α was found to restore starch accumulation in Arabidopsis kin10. Remarkably, TaSnRK1α O/E increases the AGPase activity suggesting the direct regulation of rate limiting enzyme AGPase involved in starch biosynthesis. Furthermore, in vitro and in vivo interaction assay reveal that TaSnRK1α interacts with AGPase large sub-unit. Overall, our findings indicate that TaSnRK1α plays a role in starch biosynthesis by regulating AGPase activity.

Quinoa panicles contribute to carbon assimilation and are more tolerant to salt stress than leaves

Contribution of inflorescences to seed filling have attracted great attention given the resilience of this photosynthetic organ to stressful conditions. However, studies have been almost exclusively focused to small grain cereals. In this study, we aimed to explore these responses in quinoa, as a climate resilient seed crop of elevated economic and nutritious potential. We compared the physiological and metabolic performance of panicles and leaves of two quinoa cultivars growing under contrasting salinity levels. Plant growth, photosynthetic and transpiratory gas exchange and chlorophyll fluorescence were monitored in inflorescences and leaves throughout the experiment. At flowering stage, young and mature leaves and panicles were sampled for key metabolic markers related to carbon, nitrogen and secondary metabolisms. When subjected to salt stress, panicles showed attenuated declines on photosynthesis, water use, pigments, amino acids, and protein levels as compared to leaves. In fact, the assimilation rates, together with a high hexose content evidenced an active photosynthetic role of the panicle under optimal and salt stress conditions. Moreover, we also found significant genotypic variability for physiological and metabolic traits of panicles and leaves, which emphasizes the study of genotype-dependent stress responses at the whole plant level. We conclude that quinoa panicles are less affected by salt stress than leaves, which encourages further research and exploitation of this organ for crop improvement and stress resilience considering the high natural diversity.

Genome-Wide Identification of Trehalose-6-phosphate Synthase (TPS) Gene Family Reveals the Potential Role in Carbohydrate Metabolism in Peach

Trehalose-6-phosphate synthase (TPS) is essential for plant growth and development, linking trehalose-6-phosphate (T6P) to carbon metabolism. However, little is known about the TPS gene family in peaches and their potential roles in regulating carbohydrates in peach fruit. In this study, nine TPS genes were identified in the peach genome and named according to the homologous genes in Arabidopsis. Phylogenetic analysis showed that three subfamilies were identified, including TPSI, TPSII-1, and TPSII-2, which were also consistent with gene structure analysis. Considerable cis-elements were enriched in the promoters, including plant hormone-related elements. Tissue-specific analysis showed that these TPS genes were mainly expressed in leaves, stems, and fruit, showing different expression patterns for each gene. In addition, during fruit development, the content of trehalose-6-phosphate (T6P) was positively correlated with the expression of PpTPS7a and negatively with sucrose non-fermenting-1-related kinase 1 (SnRK1) activity. Transient overexpression and silencing of PpTPS7a in peach fruit validated its function in regulating T6P content and SnRK1 activity.

Assessing the impacts of genetic defects on starch metabolism in Arabidopsis plants using the carbon homeostasis model

Starch serves as an important carbon storage mechanism for many plant species, facilitating their adaptation to the cyclic variations in the light environment, including day-night cycles as well as seasonal changes in photoperiod. By dynamically adjusting starch accumulation and degradation rates, plants maintain carbon homeostasis, enabling continuous growth under fluctuating environmental conditions. To understand dynamic nature of starch metabolism at the molecular level, it is necessary to integrate empirical knowledge from genetic defects in specific regulatory pathways into the dynamical system of starch metabolism. To achieve this, we evaluated the impact of genetic defects in the circadian clock, sugar sensing and starch degradation pathways using the carbon homeostasis model that encompasses the interplay between these pathways. Through the collection of starch metabolism data from 10 Arabidopsis mutants, we effectively fitted the experimental data to the model. The system-level assessment revealed that genetic defects in both circadian clock components and sugar sensing pathway hindered the appropriate adjustment of the starch degradation rate, particularly under long-day conditions. These findings not only confirmed the previous empirical findings but also provide the novel insights into the role of each gene within the gene regulatory network on the emergence of carbon homeostasis.

The rice SnRK family: biological roles and cell signaling modules

Stimulus-activated signaling pathways orchestrate cellular responses to control plant growth and development and mitigate the effects of adverse environmental conditions. During this process, signaling components are modulated by central regulators of various signal transduction pathways. Protein phosphorylation by kinases is one of the most important events transmitting signals downstream, via the posttranslational modification of signaling components. The plant serine and threonine kinase SNF1-related protein kinase (SnRK) family, which is classified into three subgroups, is highly conserved in plants. SnRKs participate in a wide range of signaling pathways and control cellular processes including plant growth and development and responses to abiotic and biotic stress. Recent notable discoveries have increased our understanding of how SnRKs control these various processes in rice (Oryza sativa). In this review, we summarize current knowledge of the roles of OsSnRK signaling pathways in plant growth, development, and stress responses and discuss recent insights. This review lays the foundation for further studies on SnRK signal transduction and for developing strategies to enhance stress tolerance in plants.

SNF1-RELATED KINASE 1 and TARGET OF RAPAMYCIN control light-responsive splicing events and developmental characteristics in etiolated Arabidopsis seedlings

The kinases SNF1-RELATED KINASE 1 (SnRK1) and TARGET OF RAPAMYCIN (TOR) are central sensors of the energy status, linking this information via diverse regulatory mechanisms to plant development and stress responses. Despite the well-studied functions of SnRK1 and TOR under conditions of limited or ample energy availability, respectively, little is known about the extent to which the 2 sensor systems function and how they are integrated in the same molecular process or physiological context. Here, we demonstrate that both SnRK1 and TOR are required for proper skotomorphogenesis in etiolated Arabidopsis (Arabidopsis thaliana) seedlings, light-induced cotyledon opening, and regular development in light. Furthermore, we identify SnRK1 and TOR as signaling components acting upstream of light- and sugar-regulated alternative splicing events, expanding the known action spectra for these 2 key players in energy signaling. Our findings imply that concurring SnRK1 and TOR activities are required throughout various phases of plant development. Based on the current knowledge and our findings, we hypothesize that turning points in the activities of these sensor kinases, as expected to occur upon illumination of etiolated seedlings, instead of signaling thresholds reflecting the nutritional status may modulate developmental programs in response to altered energy availability.

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.

Triose phosphate export from chloroplasts and cellular sugar content regulate anthocyanin biosynthesis during high light acclimation

Plants have evolved multiple strategies to cope with rapid changes in the environment. During high light (HL) acclimation, the biosynthesis of photoprotective flavonoids, such as anthocyanins, is induced. However, the exact nature of the signal and downstream factors for HL induction of flavonoid biosynthesis (FB) is still under debate. Here, we show that carbon fixation in chloroplasts, subsequent export of photosynthates by triose phosphate/phosphate translocator (TPT), and rapid increase in cellular sugar content permit the transcriptional and metabolic activation of anthocyanin biosynthesis during HL acclimation. In combination with genetic and physiological analysis, targeted and whole-transcriptome gene expression studies suggest that reactive oxygen species and phytohormones play only a minor role in rapid HL induction of the anthocyanin branch of FB. In addition to transcripts of FB, sugar-responsive genes showed delayed repression or induction in tpt-2 during HL treatment, and a significant overlap with transcripts regulated by SNF1-related protein kinase 1 (SnRK1) was observed, including a central transcription factor of FB. Analysis of mutants with increased and repressed SnRK1 activity suggests that sugar-induced inactivation of SnRK1 is required for HL-mediated activation of anthocyanin biosynthesis. Our study emphasizes the central role of chloroplasts as sensors for environmental changes as well as the vital function of sugar signaling in plant acclimation.

The time course of acclimation to the stress of triose phosphate use limitation

Triose phosphate utilisation (TPU) limits the maximum rate at which plants can photosynthesise. However, TPU is almost never found to be limiting photosynthesis under ambient conditions for plants. This, along with previous results showing adaptability of TPU at low temperature, suggest that TPU capacity is regulated to be just above the photosynthetic rate achievable under the prevailing conditions. A set of experiments were performed to study the adaptability of TPU capacity when plants are acclimated to elevated CO₂ concentrations. Plants held at 1500 ppm CO₂ were initially TPU limited. After 30 h they no longer exhibited TPU limitations but they did not elevate their TPU capacity. Instead, the maximum rates of carboxylation and electron transport declined. A timecourse of regulatory responses was established. A step increase of CO₂ first caused PSI to be oxidised but after 40 s both PSI and PSII had excess electrons as a result of acceptor-side limitations. Electron flow to PSI slowed and the proton motive force increased. Eventually, non-photochemical quenching reduced electron flow sufficiently to balance the TPU limitation. Over several minutes rubisco deactivated contributing to regulation of metabolism to overcome the TPU limitation.

Phosphorylation of DPE2 at S786 partially regulates starch degradation

In plants, transitory starch is synthetized during the day and degraded at night to provide the continuous carbon needed for growth and development. Starch metabolism is highly coordinated, as the starch degradation rate must be coupled to the amount of starch synthetized during the day. Maltose is one of the chloroplastic products obtained from starch degradation, and maltose is exported to the cytosol where disproportionating enzyme-2 (DPE2) is responsible for its metabolism. The amount of DPE2 remained unchanged throughout the day, but its activity notably increased at the end of the day (7 p.m.), suggesting that posttranslational modification drives the mechanism underlying the regulatory activity of this enzyme. Sucrose nonfermenting-related kinase-1 (SnRK1), a protein kinase that controls the activity of several metabolic enzymes, was able to interact and phosphorylate DPE2 at three different residues localized in the α-glucanotransferase domain. This phosphorylation acts as a positive regulator of DPE2, increasing its activity. Complementation of dpe2-deficient mutants with the wild-type (WT) and S786A forms of DPE2 showed that the nonphosphorylated form of DPE2 only partially restored starch degradation, suggesting that phosphorylation at S786 is involved in enzyme regulation.

Management of plant central metabolism by SnRK1 protein kinases

SUCROSE NON-FERMENTING1 (SNF1)-RELATED KINASE 1 (SnRK1) is an evolutionarily conserved protein kinase with key roles in plant stress responses. SnRK1 is activated when energy levels decline during stress, reconfiguring metabolism and gene expression to favour catabolism over anabolism, and ultimately to restore energy balance and homeostasis. The capacity to efficiently redistribute resources is crucial to cope with adverse environmental conditions and, accordingly, genetic manipulations that increase SnRK1 activity are generally associated with enhanced tolerance to stress. In addition to its well-established function in stress responses, an increasing number of studies implicate SnRK1 in the homeostatic control of metabolism during the regular day-night cycle and in different organs and developmental stages. Here, we review how the genetic manipulation of SnRK1 alters central metabolism in several plant species and tissue types. We complement this with studies that provide mechanistic insight into how SnRK1 modulates metabolism, identifying changes in transcripts of metabolic components, altered enzyme activities, or direct regulation of enzymes or transcription factors by SnRK1 via phosphorylation. We identify patterns of response that centre on the maintenance of sucrose levels, in an analogous manner to the role described for its mammalian orthologue in the control of blood glucose homeostasis. Finally, we highlight several knowledge gaps and technical limitations that will have to be addressed in future research aiming to fully understand how SnRK1 modulates metabolism at the cellular and whole-plant levels.

A reactive oxygen species Ca2+ signalling pathway identified from a chemical screen for modifiers of sugar-activated circadian gene expression

Sugars are essential metabolites for energy and anabolism that can also act as signals to regulate plant physiology and development. Experimental tools to disrupt major sugar signalling pathways are limited. We performed a chemical screen for modifiers of activation of circadian gene expression by sugars to discover pharmacological tools to investigate and manipulate plant sugar signalling. Using a library of commercially available bioactive compounds, we identified 75 confident hits that modified the response of a circadian luciferase reporter to sucrose in dark-adapted Arabidopsis thaliana seedlings. We validated the transcriptional effect on a subset of the hits and measured their effects on a range of sugar-dependent phenotypes for 13 of these chemicals. Chemicals were identified that appear to influence known and unknown sugar signalling pathways. Pentamidine isethionate was identified as a modifier of a sugar-activated Ca²⁺ signal that acts as a calmodulin inhibitor downstream of superoxide in a metabolic signalling pathway affecting circadian rhythms, primary metabolism and plant growth. Our data provide a resource of new experimental tools to manipulate plant sugar signalling and identify novel components of these pathways.

Insight into the regulatory networks underlying the high lipid perennial ryegrass growth under different irradiances

Under favourable conditions, perennial ryegrass (Lolium perenne) engineered to accumulated high lipid (HL) carbon sink in their leaves was previously shown to also enhance photosynthesis and growth. The greater aboveground biomass was found to be diminished in a dense canopy compared to spaced pots. Besides, the underlying genetic regulatory network linking between leaf lipid sinks and these physiological changes remains unknown. In this study, we demonstrated that the growth advantage was not displayed in HL Lolium grown in spaced pots under low lights. Under standard lights, analysis of differentiating transcripts in HL Lolium reveals that the plants had elevated transcripts involved in lipid metabolism, light capturing, photosynthesis, and sugar signalling while reduced expression of genes participating in sugar biosynthesis and transportation. The plants also had altered several transcripts involved in mitochondrial oxidative respiration and redox potential. Many of the above upregulated or downregulated transcript levels were found to be complemented by growing the plants under low light. Overall, this study emphasizes the importance of carbon and energy homeostatic regulatory mechanisms to overall productivity of the HL Lolium through photosynthesis, most of which are significantly impacted by low irradiances.

CAN OF SPINACH, a novel long non-coding RNA, affects iron deficiency responses in Arabidopsis thaliana

Long non-coding RNAs (lncRNAs) are RNA molecules with functions independent of any protein-coding potential. A whole transcriptome (RNA-seq) study of Arabidopsis shoots under iron sufficient and deficient conditions was carried out to determine the genes that are iron-regulated in the shoots. We identified two previously unannotated transcripts on chromosome 1 that are significantly iron-regulated. We have called this iron-regulated lncRNA, CAN OF SPINACH (COS). cos mutants have altered iron levels in leaves and seeds. Despite the low iron levels in the leaves, cos mutants have higher chlorophyll levels than WT plants. Moreover, cos mutants have abnormal development during iron deficiency. Roots of cos mutants are longer than those of WT plants, when grown on iron deficient medium. In addition, cos mutant plants accumulate singlet oxygen during iron deficiency. The mechanism through which COS affects iron deficiency responses is unclear, but small regions of sequence similarity to several genes involved in iron deficiency responses occur in COS, and small RNAs from these regions have been detected. We hypothesize that COS is required for normal adaptation to iron deficiency conditions.

Increasing SnRK1 activity with the AMPK activator A-769662 accelerates seed germination in rice

Sucrose non-fermenting-1-related protein kinase 1 (SnRK1) plays a key role in rice germination. The small molecule drug, A-769662, activates AMP-activated protein kinase, a mammalian homolog of SnRK1. However, it is unknown whether A-769662 activates SnRK1, thereby affecting germination. SnRK1 in desalted extracts from germinating rice seeds was strongly activated by adding A-769662 in vitro. Applying 50 or 100 μM A-769662 accelerated germination and increased the root length, shoot length, and seedling fresh weight. 50 μM A-769662 treatment increased the catalytic activity and phosphorylation of SnRK1 during germination. Transcriptome analysis and biochemical validation were performed to investigate the mechanism whereby A-769662 treatment promoted rice germination. A-769662 treatment promoted starch hydrolysis by increasing the expression and activity of amylase and inhibited starch biosynthesis by decreasing the expression of OsAGPL2, OsAGPS2a, Wx, and SSIIa. The abscisic acid (ABA) level and gene expression of ABA-induced transcription factors, including OsNF-YC9, OsNF-YC12, OsWRKY24, OsPYL8, OsMKKK62, and OsMKKK63, which reduced the inhibition of germination by ABA were decreased under 50 μM A-769662 treatment. The increased expression of the OsACO3 and OsACO5 genes and increased ethylene levels under A-769662 treatment, which counteracted the inhibition of ABA on germination and, thus, promoted germination. These results demonstrate the activation of A-769662 on SnRK1 and further reveal the regulatory mechanism of A-769662 in rice seed germination and nutrient remobilization.

Sucrose nonfermenting-1-related protein kinase 1 regulates sheath-to-panicle transport of nonstructural carbohydrates during rice grain filling

The remobilization of nonstructural carbohydrates (NSCs) reserved in rice (Oryza sativa) sheaths is essential for grain filling. This assimilate distribution between plant tissues and organs is determined by sucrose non-fermenting-1-related protein kinase 1 (SnRK1). However, the SnRK1-mediated mechanism regulating the sheath-to-panicle transport of NSCs in rice remains unknown. In this study, leaf cutting treatment was used to accelerate NSC transport in the rice sheaths. Accelerated NSC transport was accompanied by increased levels of OsSnRK1a mRNA expression, SnRK1a protein expression, catalytic subunit phosphorylation of SnRK1, and SnRK1 activity, indicating that SnRK1 activity plays an important role in sheath NSC transport. We also discovered that trehalose-6-phosphate, a signal of sucrose availability, slightly reduced SnRK1 activity in vitro. Since SnRK1 activity is mostly regulated by OsSnRK1a transcription in response to low sucrose content, we constructed an snrk1a mutant to verify the function of SnRK1 in NSC transport. NSCs accumulated in the sheaths of snrk1a mutant plants and resulted in a low seed setting rate and grain weight, verifying that SnRK1 activity is essential for NSC remobilization. Using phosphoproteomics and parallel reaction monitoring, we identified 20 SnRK1-dependent phosphosites that are involved in NSC transport. In addition, the SnRK1-mediated phosphorylation of the phosphosites directly affected starch degradation, sucrose metabolism, phloem transport, sugar transport across the tonoplast, and glycolysis in rice sheaths to promote NSC transport. Therefore, our findings reveal the importance, function, and possible regulatory mechanism of SnRK1 in the sheath-to-panicle transport of NSCs in rice.

Sugars and the speed of life-Metabolic signals that determine plant growth, development and death

Plant growth and development depend on the availability of carbohydrates synthesised in photosynthesis (source activity) and utilisation of these carbohydrates for growth (sink activity). External conditions, such as temperature, nutrient availability and stress, can affect source as well as sink activity. Optimal utilisation of resources is under circadian clock control. This molecular timekeeper ensures that growth responses are adjusted to different photoperiod and temperature settings by modulating starch accumulation and degradation accordingly. For example, during the night, starch degradation is required to provide sugars for growth. Under favourable growth conditions, high sugar availability stimulates growth and development, resulting in an overall accelerated life cycle of annual plants. Key signalling components include trehalose-6-phosphate (Tre6P), which reflects sucrose availability and stimulates growth and branching when the conditions are favourable. Under sink limitation, Tre6P does, however, inhibit night-time starch degradation. Tre6P interacts with Sucrose-non-fermenting1-Related Kinase1 (SnRK1), a protein kinase that inhibits growth under starvation and stress conditions and delays development (including flowering and senescence). Tre6P inhibits SnRK1 activity, but SnRK1 increases the Tre6P to sucrose ratio under favourable conditions. Alongside Tre6P, Target of Rapamycin (TOR) stimulates processes such as protein synthesis and growth when sugar availability is high. In annual plants, an accelerated life cycle results in early leaf and plant senescence, thus shortening the lifespan. While the availability of carbohydrates in the form of sucrose and other sugars also plays an important role in seasonal life cycle events (phenology) of perennial plants, the sugar signalling pathways in perennials are less well understood.

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.

Imperative role of trehalose metabolism and trehalose-6-phosphate signaling on salt stress responses in plants

Sugar transport and distribution have a direct impact on the growth and development of plants. Many sugars significantly influence salt stress response. The sensing of salt stress signals triggers a wide array of complicated network transduction pathways in plants. Trehalose and its intermediate compounds effectively modulate salt response and salt tolerance. Sugars such as trehalose and its derivatives not only serve as metabolic resources and structural components of cells in plants but also exhibit hormone-like regulating properties. Trehalose has an important physiological role in improving plant tolerance against salinity stresses in different plants. Plants finely adjust their cytoplasmic compatible solute pool to cope with high salinity. Salt stress induces a variety of structural, anatomical, molecular, biochemical, and physiological changes in plants, all of which have a detrimental influence on plant growth and development. This review highlights the recent developments in understanding trehalose and trehalose-6-phosphate signaling processes in plants, especially their impacts on plants growing in salty environments.