The inhibitor protein of phosphorylated nitrate reductase from spinach (Spinacia oleracea) leaves is a 14-3-3 protein

Comparative Proteomic Analysis Provides New Insights into Improved Grain-filling in Ratoon Season Rice

Grain-filling of rice spikelets (particularly for the later flowering inferior spikelets) is an important characteristic that affects both quality and yield. Rice ratooning technology is used to cultivate a second crop from dormant buds that sprout from stubble left after the first harvest. This study used two rice varieties, the conventional indica rice 'Jinhui 809' and the hybrid indica-japonica rice 'Yongyou 1540', to assess the impact of rice ratooning on grain-filling. The results indicated that the grain-filling process in inferior spikelets of ratoon season rice (ISR) showed significant improvement compared to inferior spikelets of main crop (late season) rice (ISL). This improvement was evident in the earlier onset of rapid grain-filling, higher seed-setting percentage, and improved grain quality. A label-free quantitative proteomic analysis using mass spectrometry identified 1724 proteins with significant abundance changes, shedding light on the molecular mechanisms behind the improved grain-filling in ISR. The functional analysis of these proteins indicated that ratooning stimulated the metabolic processes of sucrose-starch, trehalose, and hormones in rice inferior spikelets, leading to enhanced enzyme activities related to starch synthesis, elevated concentrations of trehalose-6-phosphate (T6P), indole-3-acetic acid (IAA) and zeatin riboside (ZR) during the active grain-filling phase. This research highlighted the importance of the GF14f protein as a key regulator in the grain-filling process of ISR. It revealed that GF14f transcriptional and protein levels declined more rapidly in ISR compared to ISL during grain-filling. Additionally, the GF14f-RNAi plants specific to the endosperm exhibited improved quality in inferior spikelets. These findings suggest that the enhancement of starch synthesis, increased levels of IAA, ZR, and T6P, along with the rapid decrease in GF14f protein, play a role in enhancing grain-filling in ratoon season rice.

Overexpression of peanut (Arachis hypogaea L.) AhGRFi gene enhanced root growth inhibition under exogenous NAA treatment in Arabidopsis thaliana

The 14-3-3 protein is a kind of evolutionary ubiquitous protein family highly conserved in eukaryotes. Initially, 14-3-3 proteins were reported in mammalian nervous tissues, but in the last decade, their role in various metabolic pathways in plants established the importance of 14-3-3 proteins. In the present study, a total of 22 14-3-3 genes, also called general regulatory factors (GRF), were identified in the peanut (Arachis hypogaea) genome, out of which 12 belonged to the ε group, whereas 10 of them belonged to the non- ε-group. Tissue-specific expression of identified 14-3-3 genes were studied using transcriptome analysis. The peanut AhGRFi gene was cloned and transformed into Arabidopsis thaliana. The investigation of subcellular localization indicated that AhGRFi is localized in the cytoplasm. Overexpression of the AhGRFi gene in transgenic Arabidopsis showed that under exogenous 1-naphthaleneacetic acid (NAA) treatment, root growth inhibition in transgenic plants was enhanced. Further analysis indicated that the expression of auxin-responsive genes IAA3, IAA7, IAA17, and SAUR-AC1 was upregulated and GH3.2 and GH3.3 were downregulated in transgenic plants, but the expression of GH3.2, GH3.3, and SAUR-AC1 showed opposite trends of change under NAA treatment. These results suggest that AhGRFi may be involved in auxin signaling during seedling root development. An in-depth study of the molecular mechanism of this process remains to be further explored.

Role of protein phosphatases in the regulation of nitrogen nutrition in plants

The reversible protein phosphorylation and dephosphorylation mediated by protein kinases and phosphatases regulate different biological processes and their response to environmental cues, including nitrogen (N) availability. Nitrate assimilation is under the strict control of phosphorylation-dephosphorylation mediated post-translational regulation. The protein phosphatase family with approximately 150 members in Arabidopsis and around 130 members in rice is a promising player in N uptake and assimilation pathways. Protein phosphatase 2A (PP2A) enhances the activation of nitrate reductase (NR) by deactivating SnRK1 and reduces the binding of inhibitory 14-3-3 proteins on NR. The functioning of nitrate transporter NPF6.3 is regulated by phosphorylation of CBL9 (Calcineurin B like protein 9) and CIPK23 (CBL interacting protein kinase 23) module. Phosphorylation by CIPK23 inhibits the activity of NPF6.3, whereas protein phosphatases (PP2C) enhance the NPF6.3-dependent nitrate sensing. PP2Cs and CIPK23 also regulate ammonium transporters (AMTs). Under either moderate ammonium supply or high N demand, CIPK23 is bound and inactivated by PP2Cs. Ammonium uptake is mediated by nonphosphorylated and active AMT1s. Whereas, under high ammonium availability, CIPK23 gets activated and phosphorylate AMT1;1 and AMT1;2 rendering them inactive. Recent reports suggest the critical role of protein phosphatases in regulating N use efficiency (NUE). In rice, PP2C9 regulates NUE by improving N uptake and assimilation. Comparative leaf proteome of wild type and PP2C9 over-expressing transgenic rice lines showed 30 differentially expressed proteins under low N level. These proteins are involved in photosynthesis, N metabolism, signalling, and defence.

Nitrate triggered phosphoproteome changes and a PIN2 phosphosite modulating root system architecture

Nitrate commands genome‐wide gene expression changes that impact metabolism, physiology, plant growth, and development. In an effort to identify new components involved in nitrate responses in plants, we analyze the Arabidopsis thaliana root phosphoproteome in response to nitrate treatments via liquid chromatography coupled to tandem mass spectrometry. 176 phosphoproteins show significant changes at 5 or 20 min after nitrate treatments. Proteins identified by 5 min include signaling components such as kinases or transcription factors. In contrast, by 20 min, proteins identified were associated with transporter activity or hormone metabolism functions, among others. The phosphorylation profile of NITRATE TRANSPORTER 1.1 (NRT1.1) mutant plants was significantly altered as compared to wild‐type plants, confirming its key role in nitrate signaling pathways that involves phosphorylation changes. Integrative bioinformatics analysis highlights auxin transport as an important mechanism modulated by nitrate signaling at the post‐translational level. We validated a new phosphorylation site in PIN2 and provide evidence that it functions in primary and lateral root growth responses to nitrate.

Synchronization of developmental, molecular and metabolic aspects of source-sink interactions

Plants have evolved a multitude of strategies to adjust their growth according to external and internal signals. Interconnected metabolic and phytohormonal signalling networks allow adaption to changing environmental and developmental conditions and ensure the survival of species in fluctuating environments. In agricultural ecosystems, many of these adaptive responses are not required or may even limit crop yield, as they prevent plants from realizing their fullest potential. By lifting source and sink activities to their maximum, massive yield increases can be foreseen, potentially closing the future yield gap resulting from an increasing world population and the transition to a carbon-neutral economy. To do so, a better understanding of the interplay between metabolic and developmental processes is required. In the past, these processes have been tackled independently from each other, but coordinated efforts are required to understand the fine mechanics of source-sink relations and thus optimize crop yield. Here, we describe approaches to design high-yielding crop plants utilizing strategies derived from current metabolic concepts and our understanding of the molecular processes determining sink development.

14-3-3 Proteins in Plant Hormone Signaling: Doing Several Things at Once

In this review we highlight the advances achieved in the investigation of the role of 14-3-3 proteins in hormone signaling, biosynthesis, and transport. 14-3-3 proteins are a family of conserved molecules that target a number of protein clients through their ability to recognize well-defined phosphorylated motifs. As a result, they regulate several cellular processes, ranging from metabolism to transport, growth, development, and stress response. High-throughput proteomic data and two-hybrid screen demonstrate that 14-3-3 proteins physically interact with many protein clients involved in the biosynthesis or signaling pathways of the main plant hormones, while increasing functional evidence indicates that 14-3-3-target interactions play pivotal regulatory roles. These advances provide a framework of our understanding of plant hormone action, suggesting that 14-3-3 proteins act as hubs of a cellular web encompassing different signaling pathways, transducing and integrating diverse hormone signals in the regulation of physiological processes.

Nitrate signaling and early responses in Arabidopsis roots

Nitrogen (N) is an essential macronutrient that impacts many aspects of plant physiology, growth, and development. Besides its nutritional role, N nutrient and metabolites act as signaling molecules that regulate the expression of a wide range of genes and biological processes. In this review, we describe recent advances in the understanding of components of the nitrate signaling pathway. Recent evidence posits that in one nitrate signaling pathway, nitrate sensed by NRT1.1 activates a phospholipase C activity that is necessary for increased cytosolic calcium levels. The nitrate-elicited calcium increase presumably activates calcium sensors, kinases, or phosphatases, resulting in changes in expression of primary nitrate response genes. Consistent with this model, nitrate treatments elicit proteome-wide changes in phosphorylation patterns in a wide range of proteins, including transporters, metabolic enzymes, kinases, phosphatases, and other regulatory proteins. Identifying and characterizing the function of the different players involved in this and other nitrate signaling pathways and their functional relationships is the next step to understand N responses in plants.

CDPKs and 14-3-3 Proteins: Emerging Duo in Signaling

Calcium-dependent protein kinases (CDPKs) are Ca²⁺-sensors that play pivotal roles in plant development and stress responses. They have the unique ability to directly translate intracellular Ca²⁺ signals into reversible phosphorylation events of diverse substrates which can mediate interactions with 14-3-3 proteins to modulate protein functions. Recent studies have revealed roles for the coordinated action of CDPKs and 14-3-3s in regulating diverse aspects of plant biology including metabolism, development, and stress responses. We review here the underlying interaction and cross-regulation of the two signaling proteins, and we discuss how this insight has led to the emerging concept of CDPK/14-3-3 signaling modules that could contribute to response specificity.

Spinach 14-3-3 protein interacts with the plasma membrane H(+)-ATPase and nitrate reductase in response to excess nitrate stress

To investigate the function of 14-3-3 protein in response to excess nitrate stress, a 14-3-3 protein, designated as So14-3-3, was isolated from spinach. Phylogenetic analysis demonstrated that So14-3-3 belongs to non-ε group of 14-3-3 superfamily. Real time-quantitative RT-PCR and western blot analysis showed that So14-3-3 was induced by excess nitrate stress in spinach roots and leaves. After nitrate treatment, the phosphorylated H(+)-ATPase and nitrate reductase (NR) increased and decreased respectively. Co-Immunoprecipitation (Co-IP) suggested that the interaction of So14-3-3 with the phosphorylated H(+)-ATPase enhanced, but reduced with phosphorylated NR in spinach roots after nitrate treatment. Besides, 5 proteins interacted with So14-3-3 were found by Co-IP and LC-MS/MS analysis. So14-3-3 overexpressing transgenic tobacco plants showed enhanced tolerance to nitrate treatment at the germination and young seedlings stage. The transgenic plants showed longer root length, lower malondialdehyde (MDA), H2O2, protein carbonyl contents, relatively higher soluble sugar and protein contents, than the WT plants after nitrate treatment. The phosphorylation levels of H(+)-ATPase in transgenic plants were higher than the WT plants after nitrate treatment, whereas NR were lower. Additionally, in transgenic plants, the interaction of So14-3-3 with phosphorylated H(+)-ATPase and NR increased and decreased more than the WT plants under nitrate stress, leading to higher H(+)-ATPase and NR activities in transgenic plants. These data suggested that So14-3-3 might be involved in nitrate stress response by interacting with H(+)-ATPase and NR.

Quantitative Proteomic Analysis of the Response to Zinc, Magnesium, and Calcium Deficiency in Specific Cell Types of Arabidopsis Roots

The proteome profiles of specific cell types have recently been investigated using techniques such as fluorescence activated cell sorting and laser capture microdissection. However, quantitative proteomic analysis of specific cell types has not yet been performed. In this study, to investigate the response of the proteome to zinc, magnesium, and calcium deficiency in specific cell types of Arabidopsis thaliana roots, we performed isobaric tags for relative and absolute quantification (iTRAQ)-based quantitative proteomics using GFP-expressing protoplasts collected by fluorescence-activated cell sorting. Protoplasts were collected from the pGL2-GFPer and pMGP-GFPer marker lines for epidermis or inner cell lines (pericycle, endodermis, and cortex), respectively. To increase the number of proteins identified, iTRAQ-labeled peptides were separated into 24 fractions by OFFGFEL electrophoresis prior to high-performance liquid chromatography coupled with mass spectrometry analysis. Overall, 1039 and 737 proteins were identified and quantified in the epidermal and inner cell lines, respectively. Interestingly, the expression of many proteins was decreased in the epidermis by mineral deficiency, although a weaker effect was observed in inner cell lines such as the pericycle, endodermis, and cortex. Here, we report for the first time the quantitative proteomics of specific cell types in Arabidopsis roots.

Regulation of the Regulators: Post-Translational Modifications, Subcellular, and Spatiotemporal Distribution of Plant 14-3-3 Proteins

14-3-3 proteins bind to and modulate the activity of phosphorylated proteins that regulate a variety of metabolic processes in eukaryotes. Multiple 14-3-3 isoforms are expressed in most organisms and display redundancy in both sequence and function. Plants contain the largest number of 14-3-3 isoforms. For example, Arabidopsis thaliana contains thirteen 14-3-3 genes, each of which is expressed. Interest in the plant 14-3-3 field has swelled over the past decade, largely due to the vast number of possibilities for 14-3-3 metabolic regulation. As the field progresses, it is essential to understand these proteins' activities at both the spatiotemporal and subcellular levels. This review summarizes current knowledge of 14-3-3 proteins in plants, including 14-3-3 interactions, regulatory functions, isoform specificity, and post-translational modifications. We begin with a historical overview and structural analysis of 14-3-3 proteins, which describes the basic principles of 14-3-3 function, and then discuss interactions and regulatory effects of plant 14-3-3 proteins in specific tissues and subcellular compartments. We conclude with a summary of 14-3-3 phosphorylation and current knowledge of the functional effects of this modification in plants.

Higher order Arabidopsis 14-3-3 mutants show 14-3-3 involvement in primary root growth both under control and abiotic stress conditions

Arabidopsis 14-3-3 proteins are a family of conserved proteins that interact with numerous partner proteins in a phospho-specific manner, and can affect the target proteins in a number of ways; e.g. modification of enzymatic activity. We isolated T-DNA insertion lines in six 14-3-3 genes within the non-epsilon group that phylogenetically group in three closely related gene pairs. In total, 6 single, 3 double, 12 triple, and 3 quadruple mutants were generated. The mutants were phenotyped for primary root growth on control plates: single and double mutants were indistinguishable from WT, whereas six triples and all quadruples showed a shorter primary root. In addition, length of the first epidermal cell with a visible root hair bulge (LEH) was used to determine primary root elongation on medium containing mannitol and 1-aminocyclopropane-1-carboxylic acid (ACC). This analysis showed clear differences depending on the stress and 14-3-3 gene combinations. Next to the phenotypic growth analyses, a 14-3-3 pull-down assay on roots treated with and without mannitol showed that mannitol stress strongly affects the 14-3-3 interactome. In conclusion, we show gene specificity and functional redundancy among 14-3-3 proteins in primary root elongation under control and under abiotic stress conditions and changes in the 14-3-3 interactome during the onset of stress adaptation.

Nitrogen control of developmental phase transitions in Arabidopsis thaliana

Nitrogen (N) is an essential macronutrient and a key structural component of macromolecules in plants. N nutrients and metabolites can act as signals that impact on many aspects of plant biology. The plant life cycle involves a series of developmental phase transitions that must be tightly coordinated to external and internal cues in order to ensure plant survival and reproduction. N availability is one of the factors controlling phase changes. In this review, we integrate and summarize the known effects of N over different developmental stages in plants. Substantial advances have been made in our understanding of signalling and N-responsive gene regulatory networks. We focus on the molecular mechanisms underlying N regulation of developmental transitions and the role of putative new regulators that might link N availability to pathways controlling Arabidopsis growth and development from seed germination through the plant reproductive transition.

Phosphorylation of Arabidopsis ubiquitin ligase ATL31 is critical for plant carbon/nitrogen nutrient balance response and controls the stability of 14-3-3 proteins

Ubiquitin ligase plays a fundamental role in regulating multiple cellular events in eukaryotes by fine-tuning the stability and activity of specific target proteins. We have previously shown that ubiquitin ligase ATL31 regulates plant growth in response to nutrient balance between carbon and nitrogen (C/N) in Arabidopsis. Subsequent study demonstrated that ATL31 targets 14-3-3 proteins for ubiquitination and modulates the protein abundance in response to C/N-nutrient status. However, the underlying mechanism for the targeting of ATL31 to 14-3-3 proteins remains unclear. Here, we show that ATL31 interacts with 14-3-3 proteins in a phosphorylation-dependent manner. We identified Thr(209), Ser(247), Ser(270), and Ser(303) as putative 14-3-3 binding sites on ATL31 by motif analysis. Mutation of these Ser/Thr residues to Ala in ATL31 inhibited the interaction with 14-3-3 proteins, as demonstrated by yeast two-hybrid and co-immunoprecipitation analyses. Additionally, we identified in vivo phosphorylation of Thr(209) and Ser(247) on ATL31 by MS analysis. A peptide competition assay showed that the application of synthetic phospho-Thr(209) peptide, but not the corresponding unphosphorylated peptide, suppresses the interaction between ATL31 and 14-3-3 proteins. Moreover, Arabidopsis plants overexpressing mutated ATL31, which could not bind to 14-3-3 proteins, showed accumulation of 14-3-3 proteins and growth arrest in disrupted C/N-nutrient conditions similar to wild-type plants, although overexpression of intact ATL31 resulted in repression of 14-3-3 accumulation and tolerance to the conditions. Together, these results demonstrate that the physiological role of phosphorylation at 14-3-3 binding sites on ATL31 is to modulate the binding ability and stability of 14-3-3 proteins to control plant C/N-nutrient response.

Multisite phosphorylation of 14-3-3 proteins by calcium-dependent protein kinases

Plant 14-3-3 proteins are phosphorylated at multiple sites in vivo; however, the protein kinase(s) responsible are unknown. Of the 34 CPK (calcium-dependent protein kinase) paralogues in Arabidopsis thaliana, three (CPK1, CPK24 and CPK28) contain a canonical 14-3-3-binding motif. These three, in addition to CPK3, CPK6 and CPK8, were tested for activity against recombinant 14-3-3 proteins χ and ε. Using an MS-based quantitative assay we demonstrate phosphorylation of 14-3-3 χ and ε at a total of seven sites, one of which is an in vivo site discovered in Arabidopsis. CPK autophosphorylation was also comprehensively monitored by MS and revealed a total of 45 sites among the six CPKs analysed, most of which were located within the N-terminal variable and catalytic domains. Among these CPK autophosphorylation sites was Tyr463 within the calcium-binding EF-hand domain of CPK28. Of all CPKs assayed, CPK28, which contained an autophosphorylation site (Ser43) within a canonical 14-3-3-binding motif, showed the highest activity against 14-3-3 proteins. Phosphomimetic mutagenesis of Ser72 to aspartate on 14-3-3χ, which is adjacent to the 14-3-3-binding cleft and conserved among all 14-3-3 isoforms, prevented 14-3-3-mediated inhibition of phosphorylated nitrate reductase.

Ubiquitin ligase ATL31 functions in leaf senescence in response to the balance between atmospheric CO2 and nitrogen availability in Arabidopsis

Carbon (C) and nitrogen (N) are essential elements for metabolism, and their availability, called the C/N balance, must be tightly coordinated for optimal growth in plants. Previously, we have identified the ubiquitin ligase CNI1/ATL31 as a novel C/N regulator by screening plants grown on C/N stress medium containing excess sugar and limited N. To elucidate further the effect of C/N balance on plant growth and to determine the physiological function of ATL31, we performed C/N response analysis using an atmospheric CO2 manipulation system. Under conditions of elevated CO2 and sufficient N, plant biomass and total sugar and starch dramatically increased. In contrast, elevated CO2 with limited N did not increase plant biomass but promoted leaf chlorosis, with anthocyanin accumulation and increased senescence-associated gene expression. Similar results were obtained with plants grown in medium containing excess sugar and limited N, suggesting that disruption of the C/N balance affects senescence progression. In ATL31-overexpressing plants, promotion of senescence under disrupted CO2/N conditions was repressed, whereas in the loss-of-function mutant it was enhanced. The ATL31 gene was transcriptionally up-regulated under N deficiency and in senescent leaves, and ATL31 expression was highly correlated with WRKY53 expression, a key regulator of senescence. Furthermore, transient protoplast analysis implicated the direct activation of ATL31 expression by WRKY53, which was in accordance with the results of WRKY53 overexpression experiments. Together, these results demonstrate the importance of C/N balance in leaf senescence and the involvement of ubiquitin ligase ATL31 in the process of senescence in Arabidopsis.

A complex containing SNF1-related kinase (SnRK1) and adenosine kinase in Arabidopsis

SNF1-related kinase (SnRK1) in plants belongs to a conserved family that includes sucrose non-fermenting 1 kinase (SNF1) in yeast and AMP-activated protein kinase (AMPK) in animals. These kinases play important roles in the regulation of cellular energy homeostasis and in response to stresses that deplete ATP, they inhibit energy consuming anabolic pathways and promote catabolism. Energy stress is sensed by increased AMP:ATP ratios and in plants, 5′-AMP inhibits inactivation of phosphorylated SnRK1 by phosphatase. In previous studies, we showed that geminivirus pathogenicity proteins interact with both SnRK1 and adenosine kinase (ADK), which phosphorylates adenosine to generate 5′-AMP. This suggested a relationship between SnRK1 and ADK, which we investigate in the studies described here. We demonstrate that SnRK1 and ADK physically associate in the cytoplasm, and that SnRK1 stimulates ADK in vitro by an unknown, non-enzymatic mechanism. Further, altering SnRK1 or ADK activity in transgenic plants altered the activity of the other kinase, providing evidence for in vivo linkage but also revealing that in vivo regulation of these activities is complex. This study establishes the existence of SnRK1-ADK complexes that may play important roles in energy homeostasis and cellular responses to biotic and abiotic stress.

Mathematical modeling reveals that metabolic feedback regulation of SnRK1 and hexokinase is sufficient to control sugar homeostasis from energy depletion to full recovery

Sucrose and trehalose-6-phosphate (T6P) are central compounds in the regulation and orchestration of whole plant metabolism, growth, development, and flowering. To evaluate their highly complex and regulatory interaction with the two conserved sugar and energy sensors Snf1-related protein kinase 1 (SnRK1), an AMPK-related protein kinase, and hexokinase (Hxk), we developed a kinetic model which demonstrates the subtle metabolic control of sugar homeostasis in a wide range of concentrations without the need for changes in gene expression or protein concentrations. Our model approach is based on a comprehensive set of published metabolite concentrations under various conditions and coupled enzyme kinetics accounting for the role of SnRK1 and Hxk in the sugar and energy homeostasis. This allowed us to investigate interactions between sugar phosphates, such as T6P, which are metabolic inhibitors of SnRK1 and Hxk, and sucrose synthesis during the transition from carbon deficiency to availability. Model simulations and sensitivity analyses indicated that slight changes in SnRK1 activity induced by allosteric effectors may be sufficient to explain a dramatic readjustment of metabolic homeostasis. This may comprise up to 10-fold changes in metabolite concentrations. Further, the Hxk/T6P/SnRK1 interaction implemented in the model supports the interpretation of phenotypic and transcriptomic changes observed in Hxk overexpressing plants. Finally, our approach presents a theoretical framework to kinetically link metabolic networks to underlying regulatory instances.

In silico characterization of a nitrate reductase gene family and analysis of the predicted proteins from the moss Physcomitrella patens

Assimilatory nitrate reductase (NR; EC 1.7.1.1-3) catalyzes the reduction of nitrate to nitrite. This enzyme has a conserved structure common to fungi, algae and plants. However, some differences in the amino acid sequence between plant and algal NR suggest that the activity regulation mechanisms have changed during plant evolution. Since only NRs from angiosperms have been studied, the search and analysis of NR genes and proteins from the moss Physcomitrella patens, a basal land plant, was performed to widen the knowledge of land plant NR structure. A family of three nr genes, named ppnia1;1, ppnia1;2 and ppnia2, was localized in the P. patens genome. The predicted proteins are canonical NRs with the conserved domains Molybdene-Cytochorme b -Cytochrome b reductase and possess 20 amino acid residues important for the enzymatic function conserved in plant and algal NRs. Interestingly, moss NRs lack a consensus sequence, common to angiosperm NRs, that is a target for posttranslational regulation. A phylogenetic tree with embryophyte and green algae NR sequences was constructed and P. patens NRs localized at the base of embryophyte NR evolution. The data presented here suggest that bryophytes and vascular plants have different systems to regulate NR activity.

Responses of barley root and shoot proteomes to long-term nitrogen deficiency, short-term nitrogen starvation and ammonium

Cereals are major crops worldwide, and improvement of their nitrogen use efficiency is a crucial challenge. In this study proteins responding to N supply in barley roots and shoots were analysed using a proteomics approach, to provide insight into mechanisms of N uptake and assimilation. Control plants grown hydroponically for 33 d with 5 mm nitrate, plants grown under N deficiency (0.5 mm nitrate, 33 d) or short-term N starvation (28 d with 5 mm nitrate followed by 5 d with no N source) were compared. N deficiency caused changes in C and N metabolism and ascorbate-glutathione cycle enzymes in shoots and roots. N starvation altered proteins of amino acid metabolism in roots. Both treatments caused proteome changes in roots that could affect growth. Shoots of plants grown with ammonium as N source (28 d with 5 mm nitrate followed by 5 d with 5 mm ammonium) showed responses similar to N deficient shoots, characterized by turnover of ribulose 1·5-bisphosphate carboxylase/oxygenase (Rubisco) and increases in proteins of the chloroplastic transcription and translation machinery. Identified proteins in 67 and 49 varying spots in roots and shoots respectively, corresponded to 62 functions and over 80 gene products, considerably advancing knowledge of N responses in barley.

Determining novel functions of Arabidopsis 14-3-3 proteins in central metabolic processes

Background

14-3-3 proteins are considered master regulators of many signal transduction cascades in eukaryotes. In plants, 14-3-3 proteins have major roles as regulators of nitrogen and carbon metabolism, conclusions based on the studies of a few specific 14-3-3 targets.

Results

In this study, extensive novel roles of 14-3-3 proteins in plant metabolism were determined through combining the parallel analyses of metabolites and enzyme activities in 14-3-3 overexpression and knockout plants with studies of protein-protein interactions. Decreases in the levels of sugars and nitrogen-containing-compounds and in the activities of known 14-3-3-interacting-enzymes were observed in 14-3-3 overexpression plants. Plants overexpressing 14-3-3 proteins also contained decreased levels of malate and citrate, which are intermediate compounds of the tricarboxylic acid (TCA) cycle. These modifications were related to the reduced activities of isocitrate dehydrogenase and malate dehydrogenase, which are key enzymes of TCA cycle. In addition, we demonstrated that 14-3-3 proteins interacted with one isocitrate dehydrogenase and two malate dehydrogenases. There were also changes in the levels of aromatic compounds and the activities of shikimate dehydrogenase, which participates in the biosynthesis of aromatic compounds.

Conclusion

Taken together, our findings indicate that 14-3-3 proteins play roles as crucial tuners of multiple primary metabolic processes including TCA cycle and the shikimate pathway.

Identification of 14-3-3 proteins as a target of ATL31 ubiquitin ligase, a regulator of the C/N response in Arabidopsis

The balance between carbon (C) and nitrogen (N) availability is an important determinant for various phases of plant growth; however, the detailed mechanisms regulating the C/N response are not well understood. We previously described two related ubiquitin ligases, ATL31 and ATL6, that function in the C/N response in Arabidopsis thaliana. Here, we used FLAG tag affinity purification and MS analysis to identify proteins targeted by ATL31, and thus likely to be involved in regulating the phase transition checkpoint based on C/N status. This analysis revealed that 14-3-3 proteins were associated with ATL31, and one of these, 14-3-3χ, was selected for detailed characterization. The interaction between ATL31 and 14-3-3χ was confirmed by yeast two-hybrid and co-immunoprecipitation analyses. In vitro assays showed that ubiquitination of 14-3-3χ is catalyzed by ATL31. Degradation of 14-3-3χin vivo was shown to be correlated with ATL31 activity, and to occur in a proteasome-dependent manner. Furthermore, 14-3-3 protein accumulation was induced by a shift to high-C/N stress conditions in Arabidopsis seedlings, and this regulated response required both ATL31 and ATL6. It was also shown that over-expression of 14-3-3χ leads to hypersensitivity of Arabidopsis seedlings to C/N stress conditions. These results indicate that ATL31 targets and ubiquitinates 14-3-3 proteins for degradation via the ubiquitin-proteasome system during the response to cellular C/N status.

Carbon and nitrogen metabolism regulated by the ubiquitin-proteasome system

The ubiquitin-proteasome system (UPS) is a unique protein degradation mechanism conserved in the eukaryotic cell. In addition to the control of protein quality, UPS regulates diverse cellular signal transduction via the fine-tuning of target protein degradation. Protein ubiquitylation and subsequent degradation by the 26S proteasome are involved in almost all aspects of plant growth and development and response to biotic and abiotic stresses. Recent studies reveal that the UPS plays an essential role in adaptation to carbon and nitrogen availability in plants. Here we highlight ubiquitin ligase ATL31 and the homologue ATL6 target 14-3-3 proteins for ubiquitylation to be degraded, which control signaling for carbon and nitrogen metabolisms and C/N balance response. We also give an overview of the UPS function involved in carbon and nitrogen metabolisms.

The role of protein disorder in the 14-3-3 interaction network

Disordered regions are segments of a protein that do not fold completely and thus remain flexible. These regions have key physiological roles, particularly in phospho-proteins, which are enriched in disorder-promoting residues surrounding their phosphorylation sites. 14-3-3 proteins are ordered hubs that interact with multiple and diverse intrinsically disordered phosphorylated targets. This provides 14-3-3 with the ability to participate in and to regulate multiple signalling networks. Here, I review the effect of structural disorder on the mechanism involved in 14-3-3 protein-protein interactions and how 14-3-3 impacts cell biology through disordered ligands. How 14-3-3 proteins constitute an advantageous system to identify novel classes of biological tools is discussed with a special emphasis on a particular-and innovative-use of small molecules to stabilize 14-3-3 protein complexes, useful to study gene expression, cancer signalling and neurodegenerative diseases.

14-3-3 proteins in plant physiology

Plant 14-3-3 isoforms, like their highly conserved homologues in mammals, function by binding to phosphorylated client proteins to modulate their function. Through the regulation of a diverse range of proteins including kinases, transcription factors, structural proteins, ion channels and pathogen defense-related proteins, they are being implicated in an expanding catalogue of physiological functions in plants. 14-3-3s themselves are affected, both transcriptionally and functionally, by the extracellular and intracellular environment of the plant. They can modulate signaling pathways that transduce inputs from the environment and also the downstream proteins that elicit the physiological response. This review covers some of the key emerging roles for plant 14-3-3s including their role in the response to the plant extracellular environment, particularly environmental stress, pathogens and light conditions. We also address potential key roles in primary metabolism, hormone signaling, growth and cell division.

Root morphological and proteomic responses to growth restriction in maize plants supplied with sufficient N

The primary objective of this study was to better understand how root morphological alteration stimulates N uptake in maize plants after root growth restriction, by investigating the changes in length and number of lateral roots, (15)NO(3)(-) influx, the expression level of the low-affinity Nitrate transporter ZmNrt1.1, and proteomic composition of primary roots. Maize seedlings were hydroponically cultured with three different types of root systems: an intact root system, embryonic roots only, or primary roots only. In spite of sufficient N supply, root growth restriction stimulated compensatory growth of remaining roots, as indicated by the increased lateral root number and root density. On the other hand, there was no significant difference in (15)NO(3)(-) influx between control and primary root plants; neither in ZmNrt1.1 expression levels in primary roots of different treatments. Our data suggested that increased N uptake by maize seedlings experiencing root growth restriction is attributed to root morphological adaptation, rather than explained by the variation in N uptake activity. Eight proteins were differentially accumulated in embryonic and primary root plants compared to control plants. These differentially accumulated proteins were closely related to signal transduction and increased root growth.

Transcriptional regulation of CDP1 and CYG56 is required for proper NH4+ sensing in Chlamydomonas

The assimilation of inorganic nitrogen is an essential process for all plant-like organisms. In the presence of ammonium and nitrate as nitrogen sources, Chlamydomonas reinhardtii preferentially assimilates ammonium and represses the nitrate assimilation pathway through an unknown mechanism that in part involves the guanylate cyclase CYG56. It is demonstrated that cells not only respond quantitatively to the NH(4)(+) signal but are also able to sense a balance between both nitrogen sources. This quantitative response was altered in a collection of mutants that were partially insensitive to NH(4)(+). In one of these mutants, reduced function of a gene named CDP1 encoding a cysteine domain-containing protein was genetically linked to NH(4)(+) insensitivity. Alteration of CYG56 or CDP1 transcription was detected in several mutants, and combined down-regulation of both genes seemed to enhance the incapacity to sense NH(4)(+) properly. These results suggest that transcriptional regulation of CYG56 and CDP1 are central and independent steps of the NH(4)(+) signalling pathway.

Kinetic analysis of 14-3-3-inhibited Arabidopsis thaliana nitrate reductase

Eukaryotic assimilatory nitrate reductase (NR) is a dimeric multidomain molybdo-heme-flavo protein that catalyzes the first and rate-limiting step in the nitrate assimilation of plants, algae, and fungi. Nitrate reduction takes place at the N-terminal molybdenum cofactor-containing domain. Reducing equivalents are derived from NADH, which reduce the C-terminal FAD domain followed by single-electron transfer steps via the middle heme domain to the molybdenum center. In plants, nitrate reduction is post-translationally inhibited by phosphorylation and subsequent binding of 14-3-3 protein to a conserved phosphoserine located in the surface-exposed hinge between the catalytic and heme domain. Here we investigated Arabidopsis thaliana NR activity upon phosphorylation and 14-3-3 binding by using a fully defined in vitro system with purified proteins. We demonstrate that among different calcium-dependent protein kinases (CPKs), CPK-17 efficiently phosphorylates Ser534 in NR. Out of eight purified Arabidopsis 14-3-3 proteins, isoforms ω, κ, and λ exhibited the strongest inhibition of NR. The kinetic parameters of noninhibited, phosphorylated NR (pNR) and pNR in a complex with 14-3-3 were investigated. An 18-fold reduction in k(cat) and a decrease in the apparent K(M)(nitrate) (from 280 to 141 μM) were observed upon binding of 14-3-3 to pNR, suggesting a noncompetitive inhibition with a preferential binding to the substrate-bound state of the enzyme. Recording partial activities of NR demonstrated that the transfer of electrons to the heme is not affected by 14-3-3 binding. The Ser534Ala variant of NR was not inhibited by 14-3-3 proteins. We propose that 14-3-3 binding to Ser534 blocks the transfer of electrons from heme to nitrate by arresting the domain movement via hinge 1.

A new client for 14-3-3 proteins: GmMYB176, an R1 MYB transcription factor

We recently identified a novel R1 MYB transcription factor, GmMYB176, which regulates the CHS8 gene expression and influences isoflavonoid biosynthesis in soybeans. GmMYB176 recognizes a unique sequence motif [TAGT(T/A)(A/T)] in CHS8 promoter and binds with it. The in planta role of GmMYB176 was established by RNAi silencing of GmMYB176 in soybean hairy roots. Silencing of GmMYB176 reduced the expression of CHS8 gene expression and isoflavonoid accumulation in hairy roots. However, the overexpression of GmMYB176 did not lead to increase in both CHS8 expression and isoflavonoid level in hairy roots suggesting that GmMYB176 is essential but not sufficient for CHS8 gene activation.

14-3-3 and FHA domains mediate phosphoprotein interactions

Many aspects of plant growth and development require specific protein interactions to carry out biochemical and cellular functions. Several proteins mediate these interactions, two of which specifically recognize phosphoproteins: 14-3-3 proteins and proteins with FHA domains. These are the only phosphobinding domains identified in plants. Both domains are present in animals and plants, and are used by plant proteins to regulate metabolic, developmental, and signaling pathways. 14-3-3s regulate sugar metabolism, proton gradients, and control transcription factor localization. FHA domains are modular domains often found in multidomain proteins that are involved in signal transduction and plant development.

14-3-3-dependent inhibition of the deubiquitinating activity of UBPY and its cancellation in the M phase

The deubiquitinating enzyme UBPY, also known as USP8, regulates cargo sorting and membrane traffic at early endosomes. Here we demonstrate the regulatory mechanism of the UBPY catalytic activity. We identified 14-3-3 epsilon, gamma, and zeta as UBPY-binding proteins using co-immunoprecipitation followed by mass spectrometric analysis. The 14-3-3 binding of UBPY was inhibited by mutating the consensus 14-3-3-binding motif RSYS(680)SP, by phosphatase treatment, and by competition with the Ser(680)-phosphorylated RSYS(680)SP peptide. Metabolic labeling with [(32)P]orthophosphate and immunoblotting using antibody against the phosphorylated 14-3-3-binding motif showed that Ser(680) is a major phosphorylation site in UBPY. These results indicated that 14-3-3s bind to the region surrounding Ser(680) in a phosphorylation-dependent manner. The mutation at Ser(680) led to enhanced ubiquitin isopeptidase activity of UBPY toward poly-ubiquitin chains and a cellular substrate, epidermal growth factor receptor, in vitro and in vivo. Moreover, addition of 14-3-3epsilon inhibited the UBPY activity in vitro. Finally, UBPY was dephosphorylated at Ser(680) and dissociated from 14-3-3s in the M phase, resulting in enhanced activity of UBPY during cell division. We conclude that UBPY is catalytically inhibited in a phosphorylation-dependent manner by 14-3-3s during the interphase, and this regulation is cancelled in the M phase.

Virus-induced gene silencing of 14-3-3 genes abrogates dark repression of nitrate reductase activity in Nicotiana benthamiana

In order to study the effect of repression of 14-3-3 genes on actual activity of the nitrate reductase (NR) in Nicotiana benthamiana leaves, Nb14-3-3a gene was silenced by virus-induced gene silencing (VIGS) method using potato virus X (PVX). Expression of Nb14-3-3a as well as Nb14-3-3b genes was altogether repressed in the leaves of PVX-14-3a-infected plants. Furthermore, two-dimensional gel electrophoresis and immunoblot analysis with anti-14-3-3 antiserum suggested that the expressions of Nb14-3-3a and Nb14-3-3b proteins are accordingly repressed in PVX-14-3a-infected plants. It is well known that binding of 14-3-3 proteins to phosphorylated NR leads to substantial decrease in NR activity of leaves under darkness. Therefore, we studied the changes in NR activity in response to light/dark transitions in the leaves of PVX-14-3a-infected plants. NR activation state was kept at a high level under darkness in PVX-14-3a-infected plants, but not in PVX-green fluorescent protein (GFP)-infected and control plants. This result suggests that Nb14-3-3a and/or Nb14-3-3b proteins are indeed involved in the inactivation of NR activity under darkness in N. benthamiana.

Evidence for increased proton dissociation in low-activity forms of dephosphorylated squash-leaf nitrate reductase

The pH dependence of squash-leaf nitrate reductase has been studied. It has been found that high- and low-activity forms of purified nitrate reductase (both forms dephosphorylated) have different optimum pH values. A high-activity form has always a higher pH optimum compared with a low-activity form. Model computations show that the decrease in activity and the corresponding change of the pH optimum is apparently due to a conformation-dependent increase of proton dissociation of the enzyme. As previously shown, this behavior is also observed in leaf extracts during the conversion (and probably phosphorylation of nitrate reductase) from a high-active form to a low-active form when plants are transferred from light to darkness.

Divalent Cation Effects on Interactions between Multiple Arabidopsis 14-3-3 Isoforms and Phosphopeptide Targets

Oscillations in cellular divalent cation concentrations are key events that can trigger signal transduction cascades. Common cellular divalent cations, such as calcium and magnesium, interact with 14-3-3 proteins. The metal ion interaction causes a conformational change in the 14-3-3 proteins, which is manifested as an increase in hydrophobicity. In this study, the effect of divalent cations on the interaction between 14-3-3 proteins and target peptides was investigated using surface plasmon resonance and isothermal titration calorimetry. The binding between ten recombinant Arabidopsis 14-3-3 isoforms and two synthetic target peptides was observed in the presence of various physiologically relevant concentrations of calcium or magnesium, from 1 microM to 1 mM or from 1 microM to 5 mM, respectively. The synthetic target peptides were based on sequences from Arabidopsis nitrate reductase (NR2) and the plasma membrane proton pump (AHA2) representing fundamentally different target classes. Isoforms representing every branch of the Arabidopsis 14-3-3 phylogenetic tree were tested. The general result for all cases is that an increased concentration of divalent cations in solution causes an increase in the concentration of 14-3-3 protein interacting with the respective phosphopeptide.

14-3-3 proteins: a historic overview

This chapter includes a historic overview of 14-3-3 proteins with an emphasis on the differences between potentially cancer-relevant isoforms on the genomic, protein and functional level. The focus will therefore be on mammalian 14-3-3s although many important developments in the field have involved Drosophila 14-3-3 proteins for example and the cross-fertilisation from parallel studies on plant 14-3-3 should not be underestimated. In the major part of this review I will attempt to focus on some novel data and aspects of 14-3-3 structure and function, in particular regulation of 14-3-3 isoforms by oncogene-related protein kinase phosphorylation and aspects of 14-3-3 research with which newcomers to the field may be less familiar.

Protein-protein interactions of tandem affinity purification-tagged protein kinases in rice

Forty-one rice cDNAs encoding protein kinases were fused to the tandem affinity purification (TAP) tag and expressed in transgenic rice plants. The TAP-tagged kinases and interacting proteins were purified from the T1 progeny of the transgenic rice plants and identified by mass spectrometry. Ninety-five percent of the TAP-tagged kinases were recovered. Fifty-six percent of the TAP-tagged kinases were found to interact with other rice proteins. A number of these interactions were consistent with known protein complexes found in other species, validating the TAP-tag method in rice plants. Phosphorylation sites were identified on four of the kinases that interacted with either 14-3-3 proteins or cyclins.

Nitrate assimilation in the forage legume Lotus japonicus L

Nitrate assimilation in the model legume, Lotus japonicus, has been investigated using a variety of approaches. A gene encoding a nitrate-inducible nitrate reductase (NR) has been cloned and appears to be the only NR gene present in the genome. Most of the nitrate reductase activity (NRA) is found in the roots and the plant assimilates the bulk of its nitrogen in that tissue. We calculate that the observed rates of nitrate reduction are compatible with the growth requirement for reduced nitrogen. The NR mRNA, NRA and the nitrate content do not show a strong diurnal rhythm in the roots and assimilation continues during the dark period although export of assimilated N to the shoot is lower during this time. In shoots, the previous low NR activity may be further inactivated during the dark either by a phosphorylation mechanism or due to reduced nitrate flux coincident with a decreased delivery through the transpiration stream. From nitrate-sufficient conditions, the removal of nitrate from the external medium causes a rapid drop in hydraulic conductivity and a decline in nitrate and reduced-N export. Root nitrate content, NR and nitrate transporter (NRT2) mRNA decline over a period of 2 days to barely detectable levels. On resupply, a coordinated increase of NR and NRT2 mRNA, and NRA is seen within hours.

Exposed loop domains of complexed 14-3-3 proteins contribute to structural diversity and functional specificity

The 14-3-3 family of proteins functions through protein:phosphoprotein interactions, the nature of which has been elucidated using x-ray crystallography. However, some key structural features in nonconserved regions have yet to be fully resolved, leaving open questions regarding the functional selectivity of 14-3-3 family members for diverse clients. In an effort to study surface accessible structural features in 14-3-3 containing macromolecular complexes and to illuminate important structure/function variations among the 14-3-3 isoforms, we determined the epitopes for three unique monoclonal antibodies (mAbs) developed against the Arabidopsis (Arabidopsis thaliana) G-box DNA:protein complex. The epitopes mapped to different loops in a phylogenetically important subset of the 13 14-3-3 family members. All three epitopes were on a common exposed face of complexed 14-3-3s. Two of the mAbs recognized linear sequences within loops 5 and 6, while the third mAb recognized 14-3-3 residues surrounding the pivotal medial Gly in the divalent cation-binding domain of loop 8, together with distal residue(s) in the putative dynamic 10th helix that has yet to be determined by crystallography. Gly at this loop 8 position is unique to nonepsilon 14-3-3 isoforms of the plant kingdom, suggesting that this region constitutes a plant-specific key functional 14-3-3 feature and highlighting that the loop 8 region is functionally significant. Mutagenesis of the medial amino acid in the loop 8 domain changed the flexibility of the C terminus and altered client peptide-binding selectivity, demonstrating the functional significance of the surface accessible, evolutionarily distinct loop 8 domain.

Single amino acid variation in barley 14-3-3 proteins leads to functional isoform specificity in the regulation of nitrate reductase

The highly conserved family of 14-3-3 proteins function in the regulation of a wide variety of cellular processes. The presence of multiple 14-3-3 isoforms and the diversity of cellular processes regulated by 14-3-3 suggest functional isoform specificity of 14-3-3 isoforms in the regulation of target proteins. Indeed, several studies observed differences in affinity and functionality of 14-3-3 isoforms. However, the structural variation by which isoform specificity is accomplished remains unclear. Because other reports suggest that specificity is found in differential expression and availability of 14-3-3 isoforms, we used the nitrate reductase (NR) model system to analyse the availability and functionality of the three barley 14-3-3 isoforms. We found that 14-3-3C is unavailable in dark harvested barley leaf extract and 14-3-3A is functionally not capable to efficiently inhibit NR activity, leaving 14-3-3B as the only characterized isoform able to regulate NR in barley. Further, using site directed mutagenesis, we identified a single amino acid variation (Gly versus Ser) in loop 8 of the 14-3-3 proteins that plays an important role in the observed isoform specificity. Mutating the Gly residue of 14-3-3A to the alternative residue, as found in 14-3-3B and 14-3-3C, turned it into a potent inhibitor of NR activity. Using surface plasmon resonance, we show that the ability of 14-3-3A and the mutated version to inhibit NR activity correlates well with their binding affinity for the 14-3-3 binding motif in the NR protein, indicating involvement of this residue in ligand discrimination. These results suggest that both the availability of 14-3-3 isoforms as well as binding affinity determine isoform-specific regulation of NR activity.

14-3-3 proteins: a number of functions for a numbered protein

Many signal transduction events are orchestrated by specific interactions of proteins mediated through discrete phosphopeptide-binding motifs. Although several phosphospecific-binding domains are now known, 14-3-3s were the first proteins recognized to specifically bind a discrete phosphoserine or phosphothreonine motif. The 14-3-3 proteins are a family of ubiquitously expressed, exclusively eukaryotic proteins with an astonishingly large number of binding partners. Consequently, 14-3-3s modulate an enormous and diverse group of cellular processes. The effects of 14-3-3 proteins on their targets can be broadly defined using three categories: (i) conformational change; (ii) physical occlusion of sequence-specific or structural protein features; and (iii) scaffolding. This review will describe the current state of knowledge on 14-3-3 proteins, highlighting several important advances, and will attempt to provide a framework by which 14-3-3 functions can be understood.

14-3-3 proteins: a number of functions for a numbered protein

Many signal transduction events are orchestrated by specific interactions of proteins mediated through discrete phosphopeptide-binding motifs. Although several phosphospecific-binding domains are now known, 14-3-3s were the first proteins recognized to specifically bind a discrete phosphoserine or phosphothreonine motif. The 14-3-3 proteins are a family of ubiquitously expressed, exclusively eukaryotic proteins with an astonishingly large number of binding partners. Consequently, 14-3-3s modulate an enormous and diverse group of cellular processes. The effects of 14-3-3 proteins on their targets can be broadly defined using three categories: (i) conformational change; (ii) physical occlusion of sequence-specific or structural protein features; and (iii) scaffolding. This review will describe the current state of knowledge on 14-3-3 proteins, highlighting several important advances, and will attempt to provide a framework by which 14-3-3 functions can be understood.

Carbon metabolite sensing and signalling

The regulation of carbon metabolism in plant cells responds sensitively to the levels of carbon metabolites that are available. The sensing and signalling systems that are involved in this process form a complex web that comprises metabolites, transporters, enzymes, transcription factors and hormones. Exactly which metabolites are sensed is not yet known, but candidates include sucrose, glucose and other hexoses, glucose-6-phosphate, trehalose-6-phosphate, trehalose and adenosine monophosphate. Important components of the signalling pathways include sucrose non-fermenting-1-related protein kinase-1 (SnRK1) and hexokinase; sugar transporters are also implicated. A battery of genes and enzymes involved in carbohydrate metabolism, secondary metabolism, nitrogen assimilation and photosynthesis are under the control of these pathways and fundamental developmental processes such as germination, sprouting, pollen development and senescence are affected by them. Here we review the current knowledge of carbon metabolite sensing and signalling in plants, drawing comparisons with homologous and analogous systems in animals and fungi. We also review the evidence for cross-talk between carbon metabolite and other major signalling systems in plant cells and the prospects for manipulating this fundamentally important aspect of metabolic regulation for crop improvement.

The C-terminal tail of Arabidopsis 14-3-3omega functions as an autoinhibitor and may contain a tenth alpha-helix

The eukaryotic regulatory protein 14-3-3 is involved in many important plant cellular processes including regulation of nitrate assimilation through inhibition of phosphorylated nitrate reductase (pNR) in darkened leaves. Divalent metal cations (Me2+) and some polyamines interact with the loop 8 region of the 14-3-3 proteins and allow them to bind and inhibit pNR in vitro. The role of the highly variant C-terminal regions of the 14-3-3 isoforms in regulation by polycations is not clear. In this study, we carried out structural analyses on the C-terminal tail of the Arabidopsis 14-3-3omega isoform and evaluated its contributions to the inhibition of pNR. Nested C-terminal truncations of the recombinant 14-3-3omega protein revealed that the removal of the C-terminal tail renders the protein partially Mg2+-independent in both pNR binding and inhibition of activity, suggesting that the C-terminus functions as an autoinhibitor. The C-terminus of 14-3-3omega appears to undergo a conformational change in the presence of polycations as demonstrated by its increased trypsin cleavage at Lys-247. C-terminal truncation of 14-3-3omega at Thr-255 increased its interaction with antibodies to the C-terminus of 14-3-3omega in non-denaturing conditions, but not in denaturing conditions, suggesting that the C-terminal tail contains ordered structures that might be disrupted by the truncation. Circular dichroism (CD) analysis of a C-terminal peptide, from Trp-234 to Lys-249, revealed that the C-terminal tail might contain a tenth alpha-helix, in agreement with the in silico predictions. The function of the putative tenth alpha-helix is not clear because substituting two prolyl residues within the predicted helix (E245P/I246P mutant), which prevented the corresponding peptide from adopting a helical conformation, did not affect the inhibition of pNR activity in the presence or absence of Mg2+. We propose that in the absence of polycations, access of target proteins to their binding groove in the 14-3-3 protein is restricted by the C-terminus, which acts as part of a gate that opens with the binding of polycations to loop 8.

14-3-3 isoforms and pattern formation during barley microspore embryogenesis

The members of the 14-3-3 isoform family have been shown to be developmentally regulated during animal embryogenesis, where they take part in cell differentiation processes. 14-3-3 isoform-specific expression patterns were studied in plant embryogenic processes, using barley (Hordeum vulgare L.) microspore embryogenesis as a model system. After embryogenesis induction by stress, microspores with enlarged morphology showed higher viability than non-enlarged ones. Following microspore culture, cell division was only observed among the enlarged microspores. Western blot and immunolocalization of three barley 14-3-3 isoforms, 14-3-3A, 14-3-3B and 14-3-3C were carried out using isoform-specific antibodies. The level of 14-3-3C protein was higher in enlarged microspores than in non-enlarged ones. A processed form of 14-3-3A was associated with the death pathway of the non-enlarged microspores. In the early embryogenesis stage, 14-3-3 subcellular localization differed among dividing and non-dividing microspores and the microspore-derived multicellular structures showed a polarized expression pattern of 14-3-3C and a higher 14-3-3A signal in epidermis primordia. In the late embryogenesis stage, 14-3-3C was specifically expressed underneath the L(1) layer of the shoot apical meristem and in the scutellum of embryo-like structures (ELSs). 14-3-3C was also expressed in the scutellum and underneath the L(1) layer of the shoot apical meristem of 21 d after pollination (DAP) zygotic embryos. These results reveal that 14-3-3A processing and 14-3-3C isoform tissue-specific expression are closely related to cell fate and initiation of specific cell type differentiation, providing a new insight into the study of 14-3-3 proteins in plant embryogenesis.

Metabolic signalling and carbon partitioning: role of Snf1-related (SnRK1) protein kinase

A protein kinase that plays a key role in the global control of plant carbon metabolism is SnRK1 (sucrose non-fermenting-1-related protein kinase 1), so-called because of its homology and functional similarity with sucrose non-fermenting 1 (SNF1) of yeast. This article reviews studies on the characterization of SnRK1 gene families, SnRK1 regulation and function, interacting proteins, and the effects of manipulating SnRK1 activity on carbon metabolism and development.

Function and specificity of 14-3-3 proteins in the regulation of carbohydrate and nitrogen metabolism

Protein phosphorylation is key to the regulation of many proteins. Altered protein activity often requires the interaction of the phosphorylated protein with a class of "adapters" known as 14-3-3 proteins. This review will cover aspects of 14-3-3 interaction with key proteins of carbon and nitrogen metabolism such as nitrate reductase, glutamine synthetase and sucrose-phosphate synthase. It will also address 14-3-3 involvement in signal transduction pathways with emphasis on the regulation of plant metabolism. To date, 14-3-3 proteins have been identified and studied in many diverse systems, yielding a plethora of data, requiring careful analysis and interpretation. Problems such as these are not uncommon when dealing with multigene families. The number of isoforms makes the question of redundancy versus specificity of 14-3-3 proteins a crucial one. This issue is discussed in relation to structure, function and expression of 14-3-3 proteins.

Markers and signals associated with nitrogen assimilation in higher plants

A key concept underpinning current understanding of the carbon/nitrogen (C/N) interaction in plants is that the capacity for N assimilation is aligned to nutrient availability and requirements by the integrated perception of signals from hormones, nitrate, sugars, organic acids, and amino acids. Studies on the nature and integration of these signals over the last ten years has revealed a complex network of controls brokered by an interplay of C and N signals. These controls not only act to orchestrate the relative rates of C and N assimilation and carbohydrate and amino acid production, but they also have a significant influence on plant development. Amino acids are the hub around which the processes of N assimilation, associated C metabolism, photorespiration, export of organic N from the leaf, and the synthesis of nitrogenous end-products revolve. Since specific major amino acids or their relative ratios are modulated differentially by photorespiration and N assimilation, even though these processes are tightly intermeshed, they are potentially powerful markers for metabolite profiling and metabolomics approaches to the study of plant biology. Moreover, while minor amino acids show marked diurnal rhythms, their contents fluctuate in a co-ordinated manner. It is probable that factors associated with early events and processes in C and N assimilation influence the relative composition of minor amino acids.

Photosynthetic electron transport determines nitrate reductase gene expression and activity in higher plants

The influence of photosynthetic electron flow in chloroplasts on the expression and enzyme activity of the cytosolic nitrate reductase (NR) was studied. Using light sources that predominantly excite either photosystem I (PSI) or photosystem II (PSII), we modulated photosynthetic electron transport in tobacco, Arabidopsis, and Lemna sprouts. In all instances, oxidation of components of photosynthetic electron flow by PSI light correlated with an increase in NR activity and/or transcription. This is confirmed by experiments with electron transport inhibitors 3-(3',4'-dichlorophenyl)-1,1'-dimethyl urea and 2,5-dibromo-3-methyl-6-isopropyl-p-benzoquinone. In addition, a Lemna mutant deficient in the cytochrome b(6)/f complex failed to respond to the different light sources and exhibited a constitutively high level of NR activity. These data indicate that NR is activated by the oxidized state of an electron transport component located after the plastoquinone pool. An involvement of the cytoplasmic photoreceptor phytochrome A in this light regulation could be excluded, since an Arabidopsis phytochrome A mutant exhibited a wild-type like response. The observation that NR activity in the cytoplasm and the expression of its gene in the nucleus is controlled by signals from photosynthetic electron flow adds a new facet to the intracellular cross-talk between chloroplasts and the nucleus.

A protein kinase activated by darkness phosphorylates nitrate reductase in Komatsuna (Brassica campestris) leaves

Although it has been shown that leaf nitrate reductase (NR: EC 1.6.6.1) is phosphorylated by subjecting plants to darkness, there is no evidence for the existence of dark-activated or dark-induced NR kinase. This study was undertaken to investigate the occurrence of a protein kinase phosphorylating NR in response to dark treatments. Immediately after transferring Komatsuna (Brassica campestris L.) plants to darkness, we observed rapid increases in the phosphorylating activity of the synthetic peptide, which is designed for the amino acid sequence surrounding the regulatory serine residue of the hinge 1 region of Komatsuna NR, in crude extracts from leaves. The activity reached a maximum after 10 min of darkness. Inactivation states of NR estimated from relative activities with or without Mg2+ were correlated to activities of the putative dark-activated protein kinase. Using the synthetic peptide as a substrate, we purified a protein kinase from dark-treated leaves by means of successive chromatographies on Q-Sepharose, Blue Sepharose, FPLC Q-Sepharose, and ATP-gamma-Sepharose columns. The purified kinase had an apparent molecular mass of 150 kDa with a catalytic subunit of 55 kDa, and it was Ca2+-independent. The purified kinase phosphorylated a recombinant cytochrome c reductase protein, a partial protein of NR, and holo NR, and inactivated NR in the presence of both 14-3-3 protein and Mg2+. The kinase also phosphorylated synthetic peptide substrates designed for sucrose phosphate synthase and 3-hydroxy-3-methylglutaryl-Coenzyme A reductase. Among inhibitors tested, only K252a, a potent and specific serine/threonine kinase inhibitor, completely inhibited the activity of the dark-activated kinase. The activity of the purified kinase was also specifically inhibited by K252a. Taken together with these findings, results obtained suggest that the putative dark-activated protein kinase may be the purified kinase itself, and may be responsible for in vivo phosphorylation of NR and its inactivation during darkness.