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

TOR and SnRK1 signaling pathways manipulation for improving postharvest fruits and vegetables marketability

During postharvest life, intracellular sugar insufficiency accompanied by insufficient intracellular ATP and NADPH supply, intracellular ROS overaccumulation along with intracellular ABA accumulation arising from water shortage could be responsible for accelerating fruits and vegetables deterioration through promoting SnRK1 and SnRK2 signaling pathways while preventing TOR signaling pathway. By TOR and SnRK1 signaling pathways manipulation, sufficient intracellular ATP and NADPH providing, supporting phenols, flavonoids and anthocyanins accumulation accompanied by improving DPPH, FRAP, and ABTS scavenging capacity by enhancing phenylpropanoid pathway activity, stimulating endogenous salicylic acid accumulation and NPR1-TGA-PRs signaling pathway, enhancing fatty acids biosynthesis, elongation and unsaturation, suppressing intracellular ROS overaccumulation, and promoting endogenous sucrose accumulation could be responsible for chilling injury palliating, fungal decay alleviating, senescence delaying and sensory and nutritional quality preservation in fruits and vegetables. Therefore, TOR and SnRK1 signaling pathways manipulation during postharvest shelf life by employing eco-friendly approaches such as exogenous trehalose and ATP application or engaging biotechnological approaches such as genome editing CRISPR-Cas9 or sprayable double-stranded RNA-based RNA interference would be applicable for improving fruits and vegetables marketability.

Bioinformatic insights into sugar signaling pathways in sugarcane growth

The SnRK1, hexokinase, and TORC1 (TOR, LST8, RAPTOR) are three pivotal kinases at the core of sugar level sensing, significantly impacting plant metabolism and development. We retrieved and analyzed protein sequences of these three kinase pathways from seven sugarcane transcriptome and genome datasets, identifying protein domains, phylogenetic relationships, sequence ancestry, and in silico expression levels. Additionally, we predicted HXK subcellular localization and assessed its enzymatic activity in sugarcane leaves and culms along development in the field. We retrieved 11 TOR, 23 RAPTOR, 55 LST8, 95 SnRK1α, 98 HXK, and 14 HXK-like putative full-length sequences containing all the conserved domains. Most of these transcripts seem to share a common origin with the three ancestral species of sugarcane: Saccharum officinarum, Saccharum spontaneum, and Saccharum barberi. We accessed the expression profile of sequences from one sugarcane transcriptome. We found the highest enzymatic activity of HXK in culms in the first month, which, at this stage, provides carbon (sucrose) and nitrogen (amino acids) for initial plant development. Our approach places novel sugar sensing sequences that work as a guideline for further research into the underlying signaling mechanisms and biotechnology applications in sugarcane.

Recent advances in response to environmental signals during Arabidopsis root development

Plants grow by anchoring their roots in the soil, acquiring essential water and nutrients for growth, and interacting with other signaling factors in the soil. Root systems are crucial for both the basic growth and development of plants and their response to external environmental stimuli. Under different environmental conditions, the configuration of root systems in plants can undergo significant changes, with their strength determining the plant's ability to adapt to the environment. Therefore, understanding the mechanisms by which environmental factors regulate root development is essential for crop root architecture improvement and breeding for stress resistance. This paper summarizes the research progress in genetic regulation of root development of the model plant Arabidopsis thaliana (L.) Heynh. amidst diverse environmental stimuli over the past five years. Specifically, it focuses on the regulatory networks of environmental signals, encompassing light, energy, temperature, water, nutrients, and reactive oxygen species, on root development. Furthermore, it provides prospects for the application of root architecture improvement in crop breeding for stress resistance and nutrient efficiency.

Sugar signaling modulates SHOOT MERISTEMLESS expression and meristem function in Arabidopsis

In plants, development of all above-ground tissues relies on the shoot apical meristem (SAM) which balances cell proliferation and differentiation to allow life-long growth. To maximize fitness and survival, meristem activity is adjusted to the prevailing conditions through a poorly understood integration of developmental signals with environmental and nutritional information. Here, we show that sugar signals influence SAM function by altering the protein levels of SHOOT MERISTEMLESS (STM), a key regulator of meristem maintenance. STM is less abundant in inflorescence meristems with lower sugar content, resulting from plants being grown or treated under limiting light conditions. Additionally, sucrose but not light is sufficient to sustain STM accumulation in excised inflorescences. Plants overexpressing the α1-subunit of SUCROSE-NON-FERMENTING1-RELATED KINASE 1 (SnRK1) accumulate less STM protein under optimal light conditions, despite higher sugar accumulation in the meristem. Furthermore, SnRK1α1 interacts physically with STM and inhibits its activity in reporter assays, suggesting that SnRK1 represses STM protein function. Contrasting the absence of growth defects in SnRK1α1 overexpressors, silencing SnRK1α in the SAM leads to meristem dysfunction and severe developmental phenotypes. This is accompanied by reduced STM transcript levels, suggesting indirect effects on STM. Altogether, we demonstrate that sugars promote STM accumulation and that the SnRK1 sugar sensor plays a dual role in the SAM, limiting STM function under unfavorable conditions but being required for overall meristem organization and integrity under favorable conditions. This highlights the importance of sugars and SnRK1 signaling for the proper coordination of meristem activities.

Direct and indirect responses of the Arabidopsis transcriptome to an induced increase in trehalose 6-phosphate

Trehalose 6-phosphate (Tre6P) is an essential signal metabolite that regulates the level of sucrose, linking growth and development to the metabolic status. We hypothesized that Tre6P plays a role in mediating the regulation of gene expression by sucrose. To test this, we performed transcriptomic profiling on Arabidopsis (Arabidopsis thaliana) plants that expressed a bacterial TREHALOSE 6-PHOSPHATE SYNTHASE (TPS) under the control of an ethanol-inducible promoter. Induction led to a 4-fold rise in Tre6P levels, a concomitant decrease in sucrose, significant changes (FDR ≤ 0.05) of over 13,000 transcripts, and 2-fold or larger changes of over 5,000 transcripts. Comparison with nine published responses to sugar availability allowed some of these changes to be linked to the rise in Tre6P, while others were probably due to lower sucrose or other indirect effects. Changes linked to Tre6P included repression of photosynthesis-related gene expression and induction of many growth-related processes including ribosome biogenesis. About 500 starvation-related genes are known to be induced by SUCROSE-NON-FERMENTING-1-RELATED KINASE 1 (SnRK1). They were largely repressed by Tre6P in a manner consistent with SnRK1 inhibition by Tre6P. SnRK1 also represses many genes that are involved in biosynthesis and growth. These responded to Tre6P in a more complex manner, pointing toward Tre6P interacting with other C-signaling pathways. Additionally, elevated Tre6P modified the expression of genes encoding regulatory subunits of the SnRK1 complex and TPS class II and FCS-LIKE ZINC FINGER proteins that are thought to modulate SnRK1 function and genes involved in circadian, TARGET OF RAPAMYCIN, light, abscisic acid, and other hormone signaling.

Sugar sensing in C4 source leaves: a gap that needs to be filled

Plant growth depends on sugar production and export by photosynthesizing source leaves and sugar allocation and import by sink tissues (grains, roots, stems, and young leaves). Photosynthesis and sink demand are tightly coordinated through metabolic (substrate, allosteric) feedback and signalling (sugar, hormones) mechanisms. Sugar signalling integrates sugar production with plant development and environmental cues. In C3 plants (e.g. wheat and rice), it is well documented that sugar accumulation in source leaves, due to source-sink imbalance, negatively feeds back on photosynthesis and plant productivity. However, we have a limited understanding about the molecular mechanisms underlying those feedback regulations, especially in C4 plants (e.g. maize, sorghum, and sugarcane). Recent work with the C4 model plant Setaria viridis suggested that C4 leaves have different sugar sensing thresholds and behaviours relative to C3 counterparts. Addressing this research priority is critical because improving crop yield requires a better understanding of how plants coordinate source activity with sink demand. Here we review the literature, present a model of action for sugar sensing in C4 source leaves, and suggest ways forward.

A natural variation in OsDSK2a modulates plant growth and salt tolerance through phosphorylation by SnRK1A in rice

Plants grow rapidly for maximal production under optimal conditions; however, they adopt a slower growth strategy to maintain survival when facing environmental stresses. As salt stress restricts crop architecture and grain yield, identifying genetic variations associated with growth and yield responses to salinity is critical for breeding optimal crop varieties. OsDSK2a is a pivotal modulator of plant growth and salt tolerance via the modulation of gibberellic acid (GA) metabolism; however, its regulation remains unclear. Here, we showed that OsDSK2a can be phosphorylated at the second amino acid (S2) to maintain its stability. The gene-edited mutant osdsk2aS2G showed decreased plant height and enhanced salt tolerance. SnRK1A modulated OsDSK2a-S2 phosphorylation and played a substantial role in GA metabolism. Genetic analysis indicated that SnRK1A functions upstream of OsDSK2a and affects plant growth and salt tolerance. Moreover, SnRK1A activity was suppressed under salt stress, resulting in decreased phosphorylation and abundance of OsDSK2a. Thus, SnRK1A preserves the stability of OsDSK2a to maintain plant growth under normal conditions, and reduces the abundance of OsDSK2a to limit growth under salt stress. Haplotype analysis using 3 K-RG data identified a natural variation in OsDSK2a-S2. The allele of OsDSK2a-G downregulates plant height and improves salt-inhibited grain yield. Thus, our findings revealed a new mechanism for OsDSK2a stability and provided a valuable target for crop breeding to overcome yield limitations under salinity stress.

Physiological and molecular responses in phosphorus-hyperaccumulating Polygonum species to high phosphorus exposure

Phosphorus (P)-hyperaccumulators for phytoextraction from P-polluted areas generally show rapid growth and accumulate large amounts of P without any toxicity symptom, which depends on a range of physiological processes and gene expression patterns that have never been explored. We investigated growth, leaf element concentrations, P fractions, photosynthetic traits, and leaf metabolome and transcriptome response in amphibious P-hyperaccumulators, Polygonum hydropiper and P. lapathifolium, to high-P exposure (5 mmol L-1), with 0.05 mmol L-1 as the control. Under high-P exposure, both species demonstrated good growth, allocating more P to metabolite P and inorganic P (Pi) accompanied by high potassium and calcium. The expression of a cluster of unigenes associated with photosynthesis was maintained or increased in P. lapathifolium, explaining the increase in net photosynthetic rate and the rapid growth under high-P exposure. Metabolites of trehalose metabolism, including trehalose 6-phosphate and trehalose, were sharply increased in both species by the high-P exposure, in line with the enhanced expression of associated unigenes, indicating that trehalose metabolic pathway was closely related to high-P tolerance. These findings elucidated the physiological and molecular responses involved in the photosynthesis and trehalose metabolism in P-hyperaccumulators to high-P exposure, and provides potential regulatory pathways to improve the P-phytoextraction capability.

Spliceosomal complex components are critical for adjusting the C:N balance during high-light acclimation

Plant acclimation to an ever-changing environment is decisive for growth, reproduction, and survival. Light availability limits biomass production on both ends of the intensity spectrum. Therefore, the adjustment of plant metabolism is central to high-light (HL) acclimation, and the accumulation of photoprotective anthocyanins is commonly observed. However, mechanisms and factors regulating the HL acclimation response are less clear. Two Arabidopsis mutants of spliceosome components exhibiting a pronounced anthocyanin overaccumulation in HL were isolated from a forward genetic screen for new factors crucial for plant acclimation. Time-resolved physiological, transcriptome, and metabolome analysis revealed a vital function of the spliceosome components for rapidly adjusting gene expression and metabolism. Deficiency of INCREASED LEVEL OF POLYPLOIDY1 (ILP1), NTC-RELATED PROTEIN1 (NTR1), and PLEIOTROPIC REGULATORY LOCUS1 (PRL1) resulted in a marked overaccumulation of carbohydrates and strongly diminished amino acid biosynthesis in HL. While not generally limited in N-assimilation, ilp1, ntr1, and prl1 showed higher glutamate levels and reduced amino acid biosynthesis in HL. The comprehensive analysis reveals a function of the spliceosome components in the conditional regulation of the carbon:nitrogen balance and the accumulation of anthocyanins during HL acclimation. The importance of gene expression, metabolic regulation, and re-direction of carbon towards anthocyanin biosynthesis for HL acclimation are discussed.

A comprehensive assessment of photosynthetic acclimation to shade in C4 grass (Cynodon dactylon (L.) Pers.)

BACKGROUND

Light deficit in shaded environment critically impacts the growth and development of turf plants. Despite this fact, past research has predominantly concentrated on shade avoidance rather than shade tolerance. To address this, our study examined the photosynthetic adjustments of Bermudagrass when exposed to varying intensities of shade to gain an integrative understanding of the shade response of C4 turfgrass.

RESULTS

We observed alterations in photosynthetic pigment-proteins, electron transport and its associated carbon and nitrogen assimilation, along with ROS-scavenging enzyme activity in shaded conditions. Mild shade enriched Chl b and LHC transcripts, while severe shade promoted Chl a, carotenoids and photosynthetic electron transfer beyond QA- (ET0/RC, φE0, Ψ0). The study also highlighted differential effects of shade on leaf and root components. For example, Soluble sugar content varied between leaves and roots as shade diminished SPS, SUT1 but upregulated BAM. Furthermore, we observed that shading decreased the transcriptional level of genes involving in nitrogen assimilation (e.g. NR) and SOD, POD, CAT enzyme activities in leaves, even though it increased in roots.

CONCLUSIONS

As shade intensity increased, considerable changes were noted in light energy conversion and photosynthetic metabolism processes along the electron transport chain axis. Our study thus provides valuable theoretical groundwork for understanding how C4 grass acclimates to shade tolerance.

MORF9-dependent specific plastid RNA editing inhibits root growth under sugar starvation in Arabidopsis

Multiple organellar RNA editing factor (MORF) complex was shown to be highly associated with C-to-U RNA editing of vascular plant editosome. However, mechanisms by which MORF9-dependent plastid RNA editing controls plant development and responses to environmental alteration remain obscure. In this study, we found that loss of MORF9 function impaired PSII efficiency, NDH activity, and carbohydrate production, rapidly promoted nuclear gene expression including sucrose transporter and sugar/energy responsive genes, and attenuated root growth under sugar starvation conditions. Sugar repletion increased MORF9 and MORF2 expression in wild-type seedlings and reduced RNA editing of matK-706, accD-794, ndhD-383 and ndhF-290 in the morf9 mutant. RNA editing efficiency of ndhD-383 and ndhF-290 sites was diminished in the gin2/morf9 double mutants, and that of matK-706, accD-794, ndhD-383 and ndhF-290 sites were significantly diminished in the snrk1/morf9 double mutants. In contrast, overexpressing HXK1 or SnRK1 promoted RNA editing rate of matK-706, accD-794, ndhD-383 and ndhF-290 in leaves of morf9 mutants, suggesting that HXK1 partially impacts MORF9 mediated ndhD-383 and ndhF-290 editing, while SnRK1 may only affect MORF9-mediated ndhF-290 site editing. Collectively, these findings suggest that sugar and/or its intermediary metabolites impair MORF9-dependent plastid RNA editing resulting in derangements of plant root development.

Sensing and regulation of C and N metabolism - novel features and mechanisms of the TOR and SnRK1 signaling pathways

Carbon (C) and nitrogen (N) metabolisms are tightly integrated to allow proper plant growth and development. Photosynthesis is dependent on N invested in chlorophylls, enzymes, and structural components of the photosynthetic machinery, while N uptake and assimilation rely on ATP, reducing equivalents, and C-skeletons provided by photosynthesis. The direct connection between N availability and photosynthetic efficiency allows the synthesis of precursors for all metabolites and building blocks in plants. Thus, the capacity to sense and respond to sudden changes in C and N availability is crucial for plant survival and is mediated by complex yet efficient signaling pathways such as TARGET OF RAPAMYCIN (TOR) and SUCROSE-NON-FERMENTING-1-RELATED PROTEIN KINASE 1 (SnRK1). In this review, we present recent advances in mechanisms involved in sensing C and N status as well as identifying current gaps in our understanding. We finally attempt to provide new perspectives and hypotheses on the interconnection of diverse signaling pathways that will allow us to understand the integration and orchestration of the major players governing the regulation of the CN balance.

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.

GRIK phosphorylates and activates KIN10 which also promotes its degradation

The sensor kinase Sucrose Non-fermenting-1-Related Kinase 1 (SnRK1) plays a central role in energy and metabolic homeostasis. KIN10 is a major catalytic (α) kinase subunit of SnRK1 regulated by transcription, posttranslational modification, targeted protein degradation, and its subcellular localization. Geminivirus Rep Interacting Kinase 1 and 2 (GRIK1 and 2) are immediate upstream kinases of KIN10. In the transient protein expression assays carried out in Nicotiana benthamiana (N. benthamiana) leaves, GRIK1 not only phosphorylates KIN10 but also simultaneously initiates its degradation. Posttranslational GRIK-mediated KIN10 degradation is dependent on both GRIK kinase activity and phosphorylation of the KIN10 T-loop. KIN10 proteins are significantly enriched in the grik1-1 grik2-1 double mutant, consistent with the transient assays in N. benthamiana. Interestingly. Among the enriched KIN10 proteins from grik1-1 grik2-1, is a longer isoform, putatively derived by alternative splicing which is barely detectable in wild-type plants. The reduced stability of KIN10 upon phosphorylation and activation by GRIK represents a mechanism that enables the KIN10 activity to be rapidly reduced when the levels of intracellular sugar/energy are restored to their set point, representing an important homeostatic control that prevents a metabolic overreaction to low-sugar conditions. Since GRIKs are activating kinases of KIN10, KIN10s in the grik1 grik2 double null mutant background remain un-phosphorylated, with only their basal level of activity, are more stable, and therefore increase in abundance, which also explains the longer isoform KIN10L which is a minor isoform in wild type is clearly detected in the grik1 grik2 double mutant.

Physcomitrium patens response to elevated CO2 is flexible and determined by an interaction between sugar and nitrogen availability

Mosses hold a unique position in plant evolution and are crucial for protecting natural, long-term carbon storage systems such as permafrost and bogs. Due to small stature, mosses grow close to the soil surface and are exposed to high levels of CO2 , produced by soil respiration. However, the impact of elevated CO2 (eCO2 ) levels on mosses remains underexplored. We determined the growth responses of the moss Physcomitrium patens to eCO2 in combination with different nitrogen levels and characterized the underlying physiological and metabolic changes. Three distinct growth characteristics, an early transition to caulonema, the development of longer, highly pigmented rhizoids, and increased biomass, define the phenotypic responses of P. patens to eCO2 . Elevated CO2 impacts growth by enhancing the level of a sugar signaling metabolite, T6P. The quantity and form of nitrogen source influences these metabolic and phenotypic changes. Under eCO2 , P. patens exhibits a diffused growth pattern in the presence of nitrate, but ammonium supplementation results in dense growth with tall gametophores, demonstrating high phenotypic plasticity under different environments. These results provide a framework for comparing the eCO2 responses of P. patens with other plant groups and provide crucial insights into moss growth that may benefit climate change models.

Genome-wide identification of TPS and TPP genes in cultivated peanut (Arachis hypogaea) and functional characterization of AhTPS9 in response to cold stress

Introduction

Trehalose is vital for plant metabolism, growth, and stress resilience, relying on Trehalose-6-phosphate synthase (TPS) and Trehalose-6-phosphate phosphatase (TPP) genes. Research on these genes in cultivated peanuts (Arachis hypogaea) is limited.

Methods

This study employed bioinformatics to identify and analyze AhTPS and AhTPP genes in cultivated peanuts, with subsequent experimental validation of AhTPS9's role in cold tolerance.

Results

In the cultivated peanut genome, a total of 16 AhTPS and 17 AhTPP genes were identified. AhTPS and AhTPP genes were observed in phylogenetic analysis, closely related to wild diploid peanuts, respectively. The evolutionary patterns of AhTPS and AhTPP genes were predominantly characterized by gene segmental duplication events and robust purifying selection. A variety of hormone-responsive and stress-related cis-elements were unveiled in our analysis of cis-regulatory elements. Distinct expression patterns of AhTPS and AhTPP genes across different peanut tissues, developmental stages, and treatments were revealed, suggesting potential roles in growth, development, and stress responses. Under low-temperature stress, qPCR results showcased upregulation in AhTPS genes (AhTPS2-5, AhTPS9-12, AhTPS14, AhTPS15) and AhTPP genes (AhTPP1, AhTPP6, AhTPP11, AhTPP13). Furthermore, AhTPS9, exhibiting the most significant expression difference under cold stress, was obviously induced by cold stress in cultivated peanut, and AhTPS9-overexpression improved the cold tolerance of Arabidopsis by protect the photosynthetic system of plants, and regulates sugar-related metabolites and genes.

Discussion

This comprehensive study lays the groundwork for understanding the roles of AhTPS and AhTPP gene families in trehalose regulation within cultivated peanuts and provides valuable insights into the mechanisms related to cold stress tolerance.

Oligosaccharide production and signaling correlate with delayed flowering in an Arabidopsis genotype grown and selected in high [CO2]

Since industrialization began, atmospheric CO2 ([CO2]) has increased from 270 to 415 ppm and is projected to reach 800-1000 ppm this century. Some Arabidopsis thaliana (Arabidopsis) genotypes delayed flowering in elevated [CO2] relative to current [CO2], while others showed no change or accelerations. To predict genotype-specific flowering behaviors, we must understand the mechanisms driving flowering response to rising [CO2]. [CO2] changes alter photosynthesis and carbohydrates in plants. Plants sense carbohydrate levels, and exogenous carbohydrate application influences flowering time and flowering transcript levels. We asked how organismal changes in carbohydrates and transcription correlate with changes in flowering time under elevated [CO2]. We used a genotype (SG) of Arabidopsis that was selected for high fitness at elevated [CO2] (700 ppm). SG delays flowering under elevated [CO2] (700 ppm) relative to current [CO2] (400 ppm). We compared SG to a closely related control genotype (CG) that shows no [CO2]-induced flowering change. We compared metabolomic and transcriptomic profiles in these genotypes at current and elevated [CO2] to assess correlations with flowering in these conditions. While both genotypes altered carbohydrates in response to elevated [CO2], SG had higher levels of sucrose than CG and showed a stronger increase in glucose and fructose in elevated [CO2]. Both genotypes demonstrated transcriptional changes, with CG increasing genes related to fructose 1,6-bisphosphate breakdown, amino acid synthesis, and secondary metabolites; and SG decreasing genes related to starch and sugar metabolism, but increasing genes involved in oligosaccharide production and sugar modifications. Genes associated with flowering regulation within the photoperiod, vernalization, and meristem identity pathways were altered in these genotypes. Elevated [CO2] may alter carbohydrates to influence transcription in both genotypes and delayed flowering in SG. Changes in the oligosaccharide pool may contribute to delayed flowering in SG. This work extends the literature exploring genotypic-specific flowering responses to elevated [CO2].

Comparative Physiological and Transcriptome Analyses of Tolerant and Susceptible Cultivars Reveal the Molecular Mechanism of Cold Tolerance in Anthurium andraeanum

Anthurium andraeanum is a tropical ornamental flower. The cost of Anthurium production is higher under low temperature (non-freezing) conditions; therefore, it is important to increase its cold tolerance. However, the molecular mechanisms underlying the response of Anthurium to cold stress remain elusive. In this study, comparative physiological and transcriptome sequencing analyses of two cultivars with contrasting cold tolerances were conducted to evaluate the cold stress response at the flowering stage. The activities of superoxide dismutase and peroxidase and the contents of proline, soluble sugar, and malondialdehyde increased under cold stress in the leaves of the cold tolerant cultivar Elegang (E) and cold susceptible cultivar Menghuang (MH), while the soluble protein content decreased in MH and increased in E. Using RNA sequencing, 24,695 differentially expressed genes (DEGs) were identified from comparisons between cultivars under the same conditions or between the treatment and control groups of a single cultivar, 9132 of which were common cold-responsive DEGs. Heat-shock proteins and pectinesterases were upregulated in E and downregulated in MH, indicating that these proteins are essential for Anthurium cold tolerance. Furthermore, four modules related to cold treatment were obtained by weighted gene co-expression network analysis. The expression of the top 20 hub genes in these modules was induced by cold stress in E or MH, suggesting they might be crucial contributors to cold tolerance. DEGs were significantly enriched in plant hormone signal transduction pathways, trehalose metabolism, and ribosomal proteins, suggesting these processes play important roles in Anthurium's cold stress response. This study provides a basis for elucidating the mechanism of cold tolerance in A. andraeanum and potential targets for molecular breeding.

Functions of sucrose and trehalose 6-phosphate in controlling plant development

Plants exhibit enormous plasticity in regulating their architecture to be able to adapt to a constantly changing environment and carry out vital functions such as photosynthesis, anchoring, and nutrient uptake. Phytohormones play a role in regulating these responses, but sugar signalling mechanisms are also crucial. Sucrose is not only an important source of carbon and energy fuelling plant growth, but it also functions as a signalling molecule that influences various developmental processes. Trehalose 6-phosphate (Tre6P), a sucrose-specific signalling metabolite, is emerging as an important regulator in plant metabolism and development. Key players involved in sucrose and Tre6P signalling pathways, including MAX2, SnRK1, bZIP11, and TOR, have been implicated in processes such as flowering, branching, and root growth. We will summarize our current knowledge of how these pathways shape shoot and root architecture and highlight how sucrose and Tre6P signalling are integrated with known signalling networks in shaping plant growth.

Trehalose metabolism coordinates transcriptional regulatory control and metabolic requirements to trigger the onset of cassava storage root initiation

Cassava storage roots (SR) are an important source of food energy and raw material for a wide range of applications. Understanding SR initiation and the associated regulation is critical to boosting tuber yield in cassava. Decades of transcriptome studies have identified key regulators relevant to SR formation, transcriptional regulation and sugar metabolism. However, there remain uncertainties over the roles of the regulators in modulating the onset of SR development owing to the limitation of the widely applied differential gene expression analysis. Here, we aimed to investigate the regulation underlying the transition from fibrous (FR) to SR based on Dynamic Network Biomarker (DNB) analysis. Gene expression analysis during cassava root initiation showed the transition period to SR happened in FR during 8 weeks after planting (FR8). Ninety-nine DNB genes associated with SR initiation and development were identified. Interestingly, the role of trehalose metabolism, especially trehalase1 (TRE1), in modulating metabolites abundance and coordinating regulatory signaling and carbon substrate availability via the connection of transcriptional regulation and sugar metabolism was highlighted. The results agree with the associated DNB characters of TRE1 reported in other transcriptome studies of cassava SR initiation and Attre1 loss of function in literature. The findings help fill the knowledge gap regarding the regulation underlying cassava SR initiation.

The trehalose 6-phosphate phosphatase family in plants

Trehalose 6-phosphate (Tre6P), the intermediate of trehalose biosynthesis, is an essential signalling metabolite linking plant growth and development to carbon metabolism. While recent work has focused predominantly on the enzymes that produce Tre6P, little is known about the proteins that catalyse its degradation, the trehalose 6-phosphate phosphatases (TPPs). Often occurring in large protein families, TPPs exhibit cell-, tissue- and developmental stage-specific expression patterns, suggesting important regulatory functions in controlling local levels of Tre6P and trehalose as well as Tre6P signalling. Furthermore, growing evidence through gene expression studies and transgenic approaches shows that TPPs play an important role in integrating environmental signals with plant metabolism. This review highlights the large diversity of TPP isoforms in model and crop plants and identifies how modulating Tre6P metabolism in certain cell types, tissues, and at different developmental stages may promote stress tolerance, resilience and increased crop yield.

Natural variation of warm temperature-induced raffinose accumulation identifies TREHALOSE-6-PHOSPHATE SYNTHASE 1 as a modulator of thermotolerance

High-temperature stress limits plant growth and reproduction. Exposure to high temperature, however, also elicits a physiological response, which protects plants from the damage evoked by heat. This response involves a partial reconfiguration of the metabolome including the accumulation of the trisaccharide raffinose. In this study, we explored the intraspecific variation of warm temperature-induced raffinose accumulation as a metabolic marker for temperature responsiveness with the aim to identify genes that contribute to thermotolerance. By combining raffinose measurements in 250 Arabidopsis thaliana accessions following a mild heat treatment with genome-wide association studies, we identified five genomic regions that were associated with the observed trait variation. Subsequent functional analyses confirmed a causal relationship between TREHALOSE-6-PHOSPHATE SYNTHASE 1 (TPS1) and warm temperature-dependent raffinose synthesis. Moreover, complementation of the tps1-1 null mutant with functionally distinct TPS1 isoforms differentially affected carbohydrate metabolism under more severe heat stress. While higher TPS1 activity was associated with reduced endogenous sucrose levels and thermotolerance, disruption of trehalose 6-phosphate signalling resulted in higher accumulation of transitory starch and sucrose and was associated with enhanced heat resistance. Taken together, our findings suggest a role of trehalose 6-phosphate in thermotolerance, most likely through its regulatory function in carbon partitioning and sucrose homoeostasis.

HEXOKINASE1 and glucose-6-phosphate fuel plant growth and development

As photoautotrophic organisms, plants produce an incredible spectrum of pigments, anti-herbivory compounds, structural materials and energic intermediates. These biosynthetic routes help plants grow, reproduce and mitigate stress. HEXOKINASE1 (HXK1), a metabolic enzyme and glucose sensor, catalyzes the phosphorylation of hexoses, a key introductory step for many of these pathways. However, previous studies have largely focused on the glucose sensing and signaling functions of HXK1, and the importance of the enzyme's catalytic function is only recently being connected to plant development. In this brief Spotlight, we describe the developmental significance of plant HXK1 and its role in plant metabolic pathways, specifically in glucose-6-phosphate production. Furthermore, we describe the emerging connections between metabolism and development and suggest that HXK1 signaling and catalytic activity regulate discrete areas of plant development.

Overexpression of OsSnRK1a through a green tissue-specific promoter improves rice yield by accelerating sheath-to-panicle transport of nonstructural carbohydrates and increasing leaf photosynthesis

The redistribution of nonstructural carbohydrates (NSCs) in rice (Oryza sativa) sheaths contributes greatly to grain filling. Sucrose nonfermenting-1-related protein kinase 1 (SnRK1) regulates sheath-to-panicle transport of NSCs during rice grain filling; however, it is unknown whether elevated activity of SnRK1 in sheaths improves NSC transport and grain filling. Expression of OsSnRK1a is mainly responsible for regulating SnRK1 activity in rice sheaths. Analysis of transgenic rice plants containing the OsSnRK1a promoter::GUS construct indicated that OsSnRK1a is widely expressed in rice. Notably, OsSnRK1a is highly expressed in mesophyll cells of sheaths. Therefore, a green tissue promoter specifically expressed in sheaths and leaf parenchyma cells and phloem tissue was used to over-express OsSnRK1a in japonica rice. The transgenic lines exhibited increased SnRK1a expression and SnRK1 activity in sheaths. The NSC and starch in the transgenic lines and WT all showed accumulation before heading and during the early-filling stage, and declining at the peak filling stage. But the starch and NSC content in transgenic lines was lower than that of WT. Moreover, the transgenic lines showed lower sucrose contents and higher sucrose efflux rates. The accelerated sheath NSC transport improved grain filling, and stimulated panicle development in transgenic lines. SnRK1a expression and SnRK1 activity were also increased in the leaves of transgenic lines, which improved leaf photosynthetic activity and contributed to optimal grain filling and panicle development. These results verify the promotion of high SnRK1 activity in sheath NSC transport, and also provide a new approach to improving sheath NSC transport and rice yield.

The Inferior Grain Filling Initiation Promotes the Source Strength of Rice Leaves

Poor grain-filling initiation in inferior spikelets severely impedes rice yield improvement, while photo-assimilates from source leaves can greatly stimulate the initiation of inferior grain-filling (sink). To investigate the underlying mechanism of source-sink interaction, a two-year field experiment was conducted in 2019 and 2020 using two large-panicle rice cultivars (CJ03 and W1844). The treatments included intact panicles and partial spikelet removal. These two cultivars showed no significant difference in the number of spikelets per panicle. However, after removing spikelet, W1844 showed higher promotion on 1000-grain weight and seed-setting rate than CJ03, particularly for inferior spikelets. The reason was that the better sink activity of W1844 led to a more effective initiation of inferior grain-filling compared to CJ03. The inferior grain weight of CJ03 and W1844 did not show a significant increase until 8 days poster anthesis (DPA), which follows a similar pattern to the accumulation of photo-assimilates in leaves. After removing spikelets, the source leaves of W1844 exhibited lower photosynthetic inhibition compared to CJ03, as well as stronger metabolism and transport of photo-assimilates. Although T6P levels remained constant in both cultivars under same conditions, the source leaves of W1844 showed notable downregulation of SnRK1 activity and upregulation of phytohormones (such as abscisic acid, cytokinins, and auxin) after removing spikelets. Hence, the high sink strength of inferior spikelets plays a role in triggering the enhancement of source strength in rice leaves, thereby fulfilling grain-filling initiation demands.

Coordination of carbon assimilation, allocation, and utilization for systemic improvement of cereal yield

The growth of yield outputs is dwindling after the first green revolution, which cannot meet the demand for the projected population increase by the mid-century, especially with the constant threat from extreme climates. Cereal yield requires carbon (C) assimilation in the source for subsequent allocation and utilization in the sink. However, whether the source or sink limits yield improvement, a crucial question for strategic orientation in future breeding and cultivation, is still under debate. To narrow the knowledge gap and capture the progress, we focus on maize, rice, and wheat by briefly reviewing recent advances in yield improvement by modulation of i) leaf photosynthesis; ii) primary C allocation, phloem loading, and unloading; iii) C utilization and grain storage; and iv) systemic sugar signals (e.g., trehalose 6-phosphate). We highlight strategies for optimizing C allocation and utilization to coordinate the source-sink relationships and promote yields. Finally, based on the understanding of these physiological mechanisms, we envisage a future scenery of "smart crop" consisting of flexible coordination of plant C economy, with the goal of yield improvement and resilience in the field population of cereals crops.

Carbohydrate dynamics in Populus trees under drought: An expression atlas of genes related to sensing, translocation, and metabolism across organs

In trees, nonstructural carbohydrates (NSCs) serve as long-term carbon storage and long-distance carbon transport from source to sink. NSC management in response to drought stress is key to our understanding of drought acclimation. However, the molecular mechanisms underlying these processes remain unclear. By combining a transcriptomic approach with NSC quantification in the leaves, stems, and roots of Populus alba under drought stress, we analyzed genes from 29 gene families related to NSC signaling, translocation, and metabolism. We found starch depletion across organs and accumulation of soluble sugars (SS) in the leaves. Activation of the trehalose-6-phosphate/SNF1-related protein kinase (SnRK1) signaling pathway across organs via the suppression of class I TREHALOSE-PHOSPHATE SYNTHASE (TPS) and the expression of class II TPS genes suggested an active response to drought. The expression of SnRK1α and β subunits, and SUCROSE SYNTHASE6 supported SS accumulation in leaves. The upregulation of active transporters and the downregulation of most passive transporters implied a shift toward active sugar transport and enhanced regulation over partitioning. SS accumulation in vacuoles supports osmoregulation in leaves. The increased expression of sucrose synthesis genes and reduced expression of sucrose degradation genes in the roots did not coincide with sucrose levels, implying local sucrose production for energy. Moreover, the downregulation of invertases in the roots suggests limited sucrose allocation from the aboveground organs. This study provides an expression atlas of NSC-related genes that respond to drought in poplar trees, and can be tested in tree improvement programs for adaptation to drought conditions.

Interaction between sugar transport and plant development

Endogenous programs and constant interaction with the environment regulate the development of the plant organism and its individual organs. Sugars are necessary building blocks for plant and organ growth and at the same time act as critical integrators of the metabolic state into the developmental program. There is a growing recognition that the specific type of sugar and its subcellular or tissue distribution is sensed and translated to developmental responses. Therefore, the transport of sugars across membranes is a key process in adapting plant organ properties and overall development to the nutritional state of the plant. In this review, we discuss how plants exploit various sugar transporters to signal growth responses, for example, to control the development of sink organs such as roots or fruits. We highlight which sugar transporters are involved in root and shoot growth and branching, how intracellular sugar allocation can regulate senescence, and, for example, control fruit development. We link the important transport processes to downstream signaling cascades and elucidate the factors responsible for the integration of sugar signaling and plant hormone responses.

SnRK1 inhibits anthocyanin biosynthesis through both transcriptional regulation and direct phosphorylation and dissociation of the MYB/bHLH/TTG1 MBW complex

Plants have evolved an extensive specialized secondary metabolism. The colorful flavonoid anthocyanins, for example, not only stimulate flower pollination and seed dispersal, but also protect different tissues against high light, UV and oxidative stress. Their biosynthesis is highly regulated by environmental and developmental cues and induced by high sucrose levels. Expression of the biosynthetic enzymes involved is controlled by a transcriptional MBW complex, comprising (R2R3) MYB- and bHLH-type transcription factors and the WD40 repeat protein TTG1. Anthocyanin biosynthesis is not only useful, but also carbon- and energy-intensive and non-vital. Consistently, the SnRK1 protein kinase, a metabolic sensor activated in carbon- and energy-depleting stress conditions, represses anthocyanin biosynthesis. Here we show that Arabidopsis SnRK1 represses MBW complex activity both at the transcriptional and post-translational level. In addition to repressing expression of the key transcription factor MYB75/PAP1, SnRK1 activity triggers MBW complex dissociation, associated with loss of target promoter binding, MYB75 protein degradation and nuclear export of TTG1. We also provide evidence for direct interaction with and phosphorylation of multiple MBW complex proteins. These results indicate that repression of expensive anthocyanin biosynthesis is an important strategy to save energy and redirect carbon flow to more essential processes for survival in metabolic stress conditions.

Heterologous Overexpression of Apple MdKING1 Promotes Fruit Ripening in Tomato

Fruit ripening is governed by a complex regulatory network, and ethylene plays an important role in this process. MdKING1 is a γ subunit of SNF1-related protein kinases (SnRKs), but the function was unclear. Here, we characterized the role of MdKING1 during fruit ripening, which can promote fruit ripening through the ethylene pathway. Our findings reveal that MdKING1 has higher expression in early-ripening cultivars than late-ripening during the early stage of apple fruit development, and its transcription level significantly increased during apple fruit ripening. Overexpression of MdKING1 (MdKING1 OE) in tomatoes could promote early ripening of fruits, with the increase in ethylene content and the loss of fruit firmness. Ethylene inhibitor treatment could delay the fruit ripening of both MdKING1 OE and WT fruits. However, MdKING1 OE fruits turned fruit ripe faster, with an increase in carotenoid content compared with WT. In addition, the expression of genes involved in ethylene biosynthesis (SlACO1, SlACS2, and SlACS4), carotenoid biosynthesis (SlPSY1 and SlGgpps2a), and fruit firmness regulation (SlPG2a, SlPL, and SlCEL2) was also increased in the fruits of MdKING1 OE plants. In conclusion, our results suggest that MdKING1 plays a key role in promoting tomato fruit ripening, thus providing a theoretical basis for apple fruit quality improvement by genetic engineering in the future.

Spatial expression patterns of genes encoding sugar sensors in leaves of C4 and C3 grasses

BACKGROUND AND AIMS

The mechanisms of sugar sensing in grasses remain elusive, especially those using C4 photosynthesis even though a large proportion of the world's agricultural crops utilize this pathway. We addressed this gap by comparing the expression of genes encoding components of sugar sensors in C3 and C4 grasses, with a focus on source tissues of C4 grasses. Given C4 plants evolved into a two-cell carbon fixation system, it was hypothesized this may have also changed how sugars were sensed.

METHODS

For six C3 and eight C4 grasses, putative sugar sensor genes were identified for target of rapamycin (TOR), SNF1-related kinase 1 (SnRK1), hexokinase (HXK) and those involved in the metabolism of the sugar sensing metabolite trehalose-6-phosphate (T6P) using publicly available RNA deep sequencing data. For several of these grasses, expression was compared in three ways: source (leaf) versus sink (seed), along the gradient of the leaf, and bundle sheath versus mesophyll cells.

KEY RESULTS

No positive selection of codons associated with the evolution of C4 photosynthesis was identified in sugar sensor proteins here. Expressions of genes encoding sugar sensors were relatively ubiquitous between source and sink tissues as well as along the leaf gradient of both C4 and C3 grasses. Across C4 grasses, SnRK1β1 and TPS1 were preferentially expressed in the mesophyll and bundle sheath cells, respectively. Species-specific differences of gene expression between the two cell types were also apparent.

CONCLUSIONS

This comprehensive transcriptomic study provides an initial foundation for elucidating sugar-sensing genes within major C4 and C3 crops. This study provides some evidence that C4 and C3 grasses do not differ in how sugars are sensed. While sugar sensor gene expression has a degree of stability along the leaf, there are some contrasts between the mesophyll and bundle sheath cells.

SnRK1 kinase-mediated phosphorylation of transcription factor bZIP39 regulates sorbitol metabolism in apple

Sorbitol is a major photosynthate produced in leaves and transported through the phloem of apple (Malus domestica) and other tree fruits in Rosaceae. Sorbitol stimulates its own metabolism, but the underlying molecular mechanism remains unknown. Here, we show that sucrose nonfermenting 1 (SNF1)-related protein kinase 1 (SnRK1) is involved in regulating the sorbitol-responsive expression of both SORBITOL DEHYDROGENASE 1 (SDH1) and ALDOSE-6-PHOSPHATE REDUCTASE (A6PR), encoding 2 key enzymes in sorbitol metabolism. SnRK1 expression is increased by feeding of exogenous sorbitol but decreased by sucrose. SnRK1 interacts with and phosphorylates the basic leucine zipper (bZIP) transcription factor bZIP39. bZIP39 binds to the promoters of both SDH1 and A6PR and activates their expression. Overexpression of SnRK1 in 'Royal Gala' apple increases its protein level and activity, upregulating transcript levels of both SDH1 and A6PR without altering the expression of bZIP39. Of all the sugars tested, sorbitol is the only 1 that stimulates SDH1 and A6PR expression, and this stimulation is blocked by RNA interference (RNAi)-induced repression of either SnRK1 or bZIP39. These findings reveal that sorbitol acts as a signal regulating its own metabolism via SnRK1-mediated phosphorylation of bZIP39, which integrates sorbitol signaling into the SnRK1-mediated sugar signaling network to modulate plant carbohydrate metabolism.

A bittersweet symphony: Metabolic signals in the circadian system

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

Metabolic regulation of quiescence in plants

Quiescence is a crucial survival attribute in which cell division is repressed in a reversible manner. Although quiescence has long been viewed as an inactive state, recent studies have shown that it is an actively monitored process that is influenced by environmental stimuli. Here, we provide a perspective of the quiescent state and discuss how this process is tuned by energy, nutrient and oxygen status, and the pathways that sense and transmit these signals. We not only highlight the governance of canonical regulators and signalling mechanisms that respond to changes in nutrient and energy status, but also consider the central significance of mitochondrial functions and cues as key regulators of nuclear gene expression. Furthermore, we discuss how reactive oxygen species and the associated redox processes, which are intrinsically linked to energy carbohydrate metabolism, also play a key role in the orchestration of quiescence.

Singlet oxygen-induced signalling depends on the metabolic status of the Chlamydomonas reinhardtii cell

Using a mutant screen, we identified trehalose 6-phosphate phosphatase 1 (TSPP1) as a functional enzyme dephosphorylating trehalose 6-phosphate (Tre6P) to trehalose in Chlamydomonas reinhardtii. The tspp1 knock-out results in reprogramming of the cell metabolism via altered transcriptome. As a secondary effect, tspp1 also shows impairment in ¹O₂-induced chloroplast retrograde signalling. From transcriptomic analysis and metabolite profiling, we conclude that accumulation or deficiency of certain metabolites directly affect ¹O₂-signalling. ¹O₂-inducible GLUTATHIONE PEROXIDASE 5 (GPX5) gene expression is suppressed by increased content of fumarate and 2-oxoglutarate, intermediates in the tricarboxylic acid cycle (TCA cycle) in mitochondria and dicarboxylate metabolism in the cytosol, but also myo-inositol, involved in inositol phosphate metabolism and phosphatidylinositol signalling system. Application of another TCA cycle intermediate, aconitate, recovers ¹O₂-signalling and GPX5 expression in otherwise aconitate-deficient tspp1. Genes encoding known essential components of chloroplast-to-nucleus ¹O₂-signalling, PSBP2, MBS, and SAK1, show decreased transcript levels in tspp1, which also can be rescued by exogenous application of aconitate. We demonstrate that chloroplast retrograde signalling involving ¹O₂ depends on mitochondrial and cytosolic processes and that the metabolic status of the cell determines the response to ¹O₂.

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.

Comparative Metabolomics Profiling Reveals Key Metabolites and Associated Pathways Regulating Tuber Dormancy in White Yam (Dioscorea rotundata Poir.)

Yams are economic and medicinal crops with a long growth cycle, spanning between 9-11 months due to their prolonged tuber dormancy. Tuber dormancy has constituted a major constraint in yam production and genetic improvement. In this study, we performed non-targeted comparative metabolomic profiling of tubers of two white yam genotypes, (Obiaoturugo and TDr1100873), to identify metabolites and associated pathways that regulate yam tuber dormancy using gas chromatography-mass spectrometry (GC-MS). Yam tubers were sampled between 42 days after physiological maturity (DAPM) till tuber sprouting. The sampling points include 42-DAPM, 56-DAPM, 87DAPM, 101-DAPM, 115-DAPM, and 143-DAPM. A total of 949 metabolites were annotated, 559 in TDr1100873 and 390 in Obiaoturugo. A total of 39 differentially accumulated metabolites (DAMs) were identified across the studied tuber dormancy stages in the two genotypes. A total of 27 DAMs were conserved between the two genotypes, whereas 5 DAMs were unique in the tubers of TDr1100873 and 7 DAMs were in the tubers of Obiaoturugo. The differentially accumulated metabolites (DAMs) spread across 14 major functional chemical groups. Amines and biogenic polyamines, amino acids and derivatives, alcohols, flavonoids, alkaloids, phenols, esters, coumarins, and phytohormone positively regulated yam tuber dormancy induction and maintenance, whereas fatty acids, lipids, nucleotides, carboxylic acids, sugars, terpenoids, benzoquinones, and benzene derivatives positively regulated dormancy breaking and sprouting in tubers of both yam genotypes. Metabolite set enrichment analysis (MSEA) revealed that 12 metabolisms were significantly enriched during yam tuber dormancy stages. Metabolic pathway topology analysis further revealed that six metabolic pathways (linoleic acid metabolic pathway, phenylalanine metabolic pathway, galactose metabolic pathway, starch and sucrose metabolic pathway, alanine-aspartate-glutamine metabolic pathways, and purine metabolic pathway) exerted significant impact on yam tuber dormancy regulation. This result provides vital insights into molecular mechanisms regulating yam tuber dormancy.

Rice ubiquitin-conjugating enzyme OsUbc13 negatively regulates immunity against pathogens by enhancing the activity of OsSnRK1a

Ubc13 is required for Lys63-linked polyubiquitination and innate immune responses in mammals, but its functions in plant immunity still remain largely unknown. Here, we used molecular biological, pathological, biochemical, and genetic approaches to evaluate the roles of rice OsUbc13 in response to pathogens. The OsUbc13-RNA interference (RNAi) lines with lesion mimic phenotypes displayed a significant increase in the accumulation of flg22- and chitin-induced reactive oxygen species, and in defence-related genes expression or hormones as well as resistance to Magnaporthe oryzae and Xanthomonas oryzae pv oryzae. Strikingly, OsUbc13 directly interacts with OsSnRK1a, which is the α catalytic subunit of SnRK1 (sucrose non-fermenting-1-related protein kinase-1) and acts as a positive regulator of broad-spectrum disease resistance in rice. In the OsUbc13-RNAi plants, although the protein level of OsSnRK1a did not change, its activity and ABA sensitivity were obviously enhanced, and the K63-linked polyubiquitination was weaker than that of wild-type Dongjin (DJ). Overexpression of the deubiquitinase-encoding gene OsOTUB1.1 produced similar effects with inhibition of OsUbc13 in affecting immunity responses, M. oryzae resistance, OsSnRK1a ubiquitination, and OsSnRK1a activity. Furthermore, re-interfering with OsSnRK1a in one OsUbc13-RNAi line (Ri-3) partially restored its M. oryzae resistance to a level between those of Ri-3 and DJ. Our data demonstrate OsUbc13 negatively regulates immunity against pathogens by enhancing the activity of OsSnRK1a.

Identification of a stable major sucrose-related QTL and diagnostic marker for flavor improvement in peanut

An InDel marker closely linked with a major and stable quantitative trait locus (QTL) on chromosome A08, qSUCA08.2, controlling sucrose content will benefit peanut flavor improvement. Sucrose is the main soluble sugar in mature peanut kernel, and its content is a key determinant of flavor. However, the genetic basis of sucrose content in peanut remains poorly understood, which limits the progress of flavor improvement. In the present study, two genomic regions (qSUCA08a and qSUCB06a) for sucrose content on chromosomes A08 and B06 were identified by QTL-seq in a RIL population derived from a cross between Zhonghua 10 and ICG 12625. In the interval of qSUCB06a, QTL qSUCB06.2 was detected through QTL mapping in a single environment. The qSUCA08a was further dissected into 3 adjacent genomic regions using linkage analysis including a major QTL qSUCA08.2 explaining 5.43-17.84% phenotypic variation across five environments. A 61-bp insertion at position 35,099,320 in the higher sucrose parent ICG 12625 was found in qSUCA08.2. An InDel marker SUC.InDel.A08 based on the insertion/deletion polymorphism was developed and validated within a natural population containing 172 peanut cultivars in two environments. The mean sucrose content of 93 cultivars with ICG 12625 allele was significantly higher than that of 79 cultivars with Zhonghua 10 allele. The qSUCA08.2 corresponding to a 2.11 Mb interval harbored 110 genes. Among these genes, a total of 19 genes were considered as candidate genes including 5 non-synonymous mutation genes and 14 differentially expressed genes during seed development. These results provide new insights into the genetic basis of sucrose regulation in peanut and benefit the breeding program for developing new varieties with excellent flavor.

Photosynthetic acclimation to changing environments

Plants are exposed to environments that fluctuate of timescales varying from seconds to months. Leaves that develop in one set of conditions optimise their metabolism to the conditions experienced, in a process called developmental acclimation. However, when plants experience a sustained change in conditions, existing leaves will also acclimate dynamically to the new conditions. Typically this process takes several days. In this review, we discuss this dynamic acclimation process, focussing on the responses of the photosynthetic apparatus to light and temperature. We briefly discuss the principal changes occurring in the chloroplast, before examining what is known, and not known, about the sensing and signalling processes that underlie acclimation, identifying likely regulators of acclimation.

Vacuolar Phosphate Transporter1 (VPT1) may transport sugar in response to soluble sugar status of grape fruits

Vacuolar Phosphate Transporter1 (VPT1)-mediated phosphate uptake in the vacuoles is essential to plant development and fruit ripening. Interestingly, here we find that the VPT1 may transport sugar in response to soluble sugar status of fruits. The VvVPT1 protein isolated from grape (Vitis vinifera) berries was tonoplast-localized and contains SPX (Syg1/Pho81/XPR1) and MFS (major facilitator superfamily) domains. Its mRNA expression was significantly increased during fruit ripening and induced by sucrose. Functional analyses based on transient transgenic systems in grape berry showed that VvVPT1 positively regulated berry ripening and significantly affected hexose contents, fruit firmness, and ripening-related gene expression. The VPT1 proteins (Grape VvVPT1, strawberry FaVPT1, and Arabidopsis AtVPT1) all showed low affinity for phosphate verified in yeast system, while they appear different in sugar transport capacity, consistent with fruit sugar status. Thus, our findings reveal a role for VPT1 in fruit ripening, associated to its SPX and MFS domains in direct transport of soluble sugar available into the vacuole, and open potential avenues for genetic improvement in fleshy fruit.

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.

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.

Evidence that mitochondrial alternative oxidase respiration supports carbon balance in source leaves of Nicotiana tabacum

Alternative oxidase (AOX) represents a non-energy conserving pathway within the mitochondrial electron transport chain. One potential physiological role of AOX could be to manage leaf carbohydrate amounts by supporting respiratory carbon oxidation reactions. In this study, several approaches tested the hypothesis that AOX1a gene expression in Nicotiana tabacum leaf is enhanced in conditions expected to promote an increased leaf carbohydrate status. These approaches included supplying leaves with exogenous carbohydrates, comparing plants grown at different atmospheric CO₂ concentrations, comparing sink leaves with source leaves, comparing plants with different ratios of source to sink activity, and examining gene expression over the diel cycle. In each case, the pattern of AOX1a gene expression was compared with that of other genes known to respond to carbohydrates and/or other factors related to source:sink activity. These included GPT1 and GPT3 (that encode chloroplast glucose 6-phosphate/phosphate translocators), SPS (that encodes sucrose phosphate synthase), SUT1 (that encodes a sucrose/H⁺ symporter involved in phloem loading) and UCP1 (that encodes a mitochondrial uncoupling protein). The AOX1a transcript amount was higher following the leaf sink-to-source transition, and in plants with higher source relative to sink activity due to increasing plant age. Further, these effects were amplified in plants grown at elevated CO₂ to stimulate source activity, particularly at end-of-day time periods. The AOX1a transcript amount was also higher following treatment of leaves with carbohydrate, in particular sucrose. Overall, the results provide evidence that, while source leaf sucrose accumulation may signal for a down-regulation of sucrose synthesis and transport, it also signals for means to manage the excess cytosolic carbohydrate pools. This includes increased AOX respiration to support carbon oxidation pathways even if energy charge is high, in combination perhaps with some return flux of carbohydrate from cytosol to stroma through the GPT3 translocator. As discussed, these activities could contribute to maintaining plant source:sink balance, as well as photosynthetic and phloem loading capacity.

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.

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

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

Trehalose 6-Phosphate/SnRK1 Signaling Participates in Harvesting-Stimulated Rubber Production in the Hevea Tree

Trehalose 6-phosphate (T6P), the intermediate of trehalose biosynthesis and a signaling molecule, affects crop yield via targeting sucrose allocation and utilization. As there have been no reports of T6P signaling affecting secondary metabolism in a crop plant, the rubber tree Hevea brasiliensis serves as an ideal model in this regard. Sucrose metabolism critically influences the productivity of natural rubber, a secondary metabolite of industrial importance. Here, we report on the characterization of the T6P synthase (TPS) gene family and the T6P/SNF1-related protein kinase1 (T6P/SnRK1) signaling components in Hevea laticifers under tapping (rubber harvesting), an agronomic manipulation that itself stimulates rubber production. A total of fourteen TPS genes were identified, among which a class II TPS gene, HbTPS5, seemed to have evolved with a function specialized in laticifers. T6P and trehalose increased when the trees were tapped, this being consistent with the observed enhanced activities of TPS and T6P phosphatase (TPP) and expression of an active TPS-encoding gene, HbTPS1. On the other hand, SnRK1 activities decreased, suggesting the inhibition of elevated T6P on SnRK1. Expression profiles of the SnRK1 marker genes coincided with elevated T6P and depressed SnRK1. Interestingly, HbTPS5 expression decreased significantly with the onset of tapping, suggesting a regulatory function in the T6P pathway associated with latex production in laticifers. In brief, transcriptional, enzymatic, and metabolic evidence supports the participation of T6P/SnRK1 signaling in rubber formation, thus providing a possible avenue to increasing the yield of a valuable secondary metabolite by targeting T6P in specific cells.

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

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

Nutrient Supply Is Essential for Shifting Tree Peony Reflowering Ahead in Autumn and Sugar Signaling Is Involved

The flowering time of tree peony is short and concentrated in spring, which limits the development of its industry. We previously achieved tree peony reflowering in autumn. Here, we further shifted its reflowering time ahead through proper gibberellin (GA) treatment plus nutrient supply. GA treatment alone initiated bud differentiation, but it aborted later, whereas GA plus nutrient (G + N) treatment completed the opening process 38 days before the control group. Through microstructural observation of bud differentiation and starch grains, we concluded that GA plays a triggering role in flowering induction, whereas the nutriment supply ensured the continuous developing for final opening, and both are necessary. We further determined the expression of five floral induction pathway genes and found that PsSOC1 and PsLFY probably played key integral roles in flowering induction and nutrient supply, respectively. Considering the GA signaling, PsGA2ox may be mainly involved in GA regulation, whereas PsGAI may regulate further flower formation after nutrient application. Furthermore, G + N treatment, but not GA alone, inhibited the expression of PsTPS1, a key restricting enzyme in sugar signaling, at the early stage, indicating that sugar signaling is also involved in this process; in addition, GA treatment induced high expression of PsSnRK1, a major nutrient insufficiency indicator, and the induction of PsHXK1, a rate-limiting enzyme for synthesis of sugar signaling substances, further confirmed the nutrient shortage. In short, besides GA application, exogenous nutrient supply is essential to shift tree peony reflowering ahead in autumn under current forcing culture technologies.

The OsNAC23-Tre6P-SnRK1a feed-forward loop regulates sugar homeostasis and grain yield in rice

Tre6P (trehalose-6-phosphate) mediates sensing of carbon availability to maintain sugar homeostasis in plants, which underpins crop yield and resilience. However, how Tre6P responds to fluctuations in sugar levels and regulates the utilization of sugars for growth remains to be addressed. Here, we report that the sugar-inducible rice NAC transcription factor OsNAC23 directly represses the transcription of the Tre6P phosphatase gene TPP1 to simultaneously elevate Tre6P and repress trehalose levels, thus facilitating carbon partitioning from source to sink organs. Meanwhile, OsNAC23 and Tre6P suppress the transcription and enzyme activity of SnRK1a, a low-carbon sensor and antagonist of OsNAC23, to prevent the SnRK1a-mediated phosphorylation and degradation of OsNAC23. Thus, OsNAC23, Tre6P, and SnRK1a form a feed-forward loop to sense sugar and maintain sugar homeostasis by transporting sugars to sink organs. Importantly, plants over-expressing OsNAC23 exhibited an elevated photosynthetic rate, sugar transport, and sink organ size, which consistently increased rice yields by 13%-17% in three elite-variety backgrounds and two locations, suggesting that manipulation of OsNAC23 expression has great potential for rice improvement. Collectively, these findings enhance our understanding of Tre6P-mediated sugar signaling and homeostasis, and provide a new strategy for genetic improvement of rice and possibly also other crops.