Large Scale Identification and Quantitative Profiling of Phosphoproteins Expressed during Seed Filling in Oilseed Rape

KiC assay: a quantitative mass spectrometry-based approach for kinase client screening and activity analysis [corrected]

Protein phosphorylation is one of the most important posttranslational modifications (PTMs) involved in the transduction of cellular signals. The number of kinases in eukaryotic genomes ranges from several hundred to over one thousand. And with rapidly evolving mass spectrometry (MS)-based approaches, thousands to tens of thousands of phosphorylation sites (phosphosites) have been reported from various eukaryotic organisms, from man to plants. In this relative context, few bona fide kinase-client relationships have been identified to date. To merge the gap between these phosphosites and the cognate kinases that beget these events, comparable large-scale methodologies are required. We describe in detail a MS-based method for identifying kinase-client interactions and quantifying kinase activity. We term this novel Kinase-Client assay, the KiC assay. The KiC assay relies upon the fact that substrate specificities of many kinases are largely determined by primary amino acid sequence or phosphorylation motifs, which consist of key amino acids surrounding the phosphorylation sites. The workflow for detecting kinase-substrate interactions includes four major steps: (1) preparation of purified kinases and synthetic peptide library, (2) in vitro kinase peptide library assay, (3) liquid chromatography (LC)-tandem MS (MS/MS) analysis, and (4) data processing and interpretation. Kinase activity is quantified with the KiC assay by monitoring spectral counts of phosphorylated and unphosphorylated peptides as the readout from LC-tandem mass spectrometry. The KiC assay can be applied as a discovery assay to screen kinases against a synthetic peptide library to find kinase-client relationships or as a targeted assay to characterize kinase kinetics.

Daily changes in the phosphoproteome of the dinoflagellate Lingulodinium

The dinoflagellate Lingulodinium has a large number of daily rhythms, many of which have no biochemical correlates. We examined the possibility that changes in protein phosphorylation may mediate some of the rhythmic changes by comparing proteins prepared from midday (LD6) and midnight (LD18) cultures. We used two different methods, one a 2D gel protocol in which phosphoproteins were identified after staining with ProQ Diamond, and the other an LC-MS/MS identification of tryptic phosphopeptides that had been purified by TiO(2) chromatography. Two differentially phosphorylated proteins, a light harvesting complex protein and Rad24, were identified using the 2D gel protocol. Six differentially phosphorylated proteins, a polyketide synthase, an uncharacterized transporter, a LIM (actin binding) domain and three RNA binding domain proteins, were identified using the phosphopeptide enrichment protocol. We conclude that changes in protein phosphorylation may underlie some of the rhythmic behavior of Lingulodinium.

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 and analysis of phosphorylation status of proteins in dormant terminal buds of poplar

BACKGROUND

Although there has been considerable progress made towards understanding the molecular mechanisms of bud dormancy, the roles of protein phosphorylation in the process of dormancy regulation in woody plants remain unclear.

RESULTS

We used mass spectrometry combined with TiO₂ phosphopeptide-enrichment strategies to investigate the phosphoproteome of dormant terminal buds (DTBs) in poplar (Populus simonii × P. nigra). There were 161 unique phosphorylated sites in 161 phosphopeptides from 151 proteins; 141 proteins have orthologs in Arabidopsis, and 10 proteins are unique to poplar. Only 34 sites in proteins in poplar did not match well with the equivalent phosphorylation sites of their orthologs in Arabidopsis, indicating that regulatory mechanisms are well conserved between poplar and Arabidopsis. Further functional classifications showed that most of these phosphoproteins were involved in binding and catalytic activity. Extraction of the phosphorylation motif using Motif-X indicated that proline-directed kinases are a major kinase group involved in protein phosphorylation in dormant poplar tissues.

CONCLUSIONS

This study provides evidence about the significance of protein phosphorylation during dormancy, and will be useful for similar studies on other woody plants.

Structure, function and membrane interactions of plant annexins: an update

Knowledge accumulated over the past 15 years on plant annexins clearly indicates that this disparate group of proteins builds on the common annexin function of membrane association, but possesses divergent molecular mechanisms. Functionally, the current literature agrees on a key role of plant annexins in stress response processes such as wound healing and drought tolerance. This is contrasted by only few established details of the molecular level mechanisms that are driving these activities. In this review, we appraise the current knowledge of plant annexin molecular, functional and structural properties with a special emphasis on topics of less coverage in recent past overviews. In particular, plant annexin post-translational modification, roles in polar growth and membrane stabilisation processes are discussed.

Agricultural recovery of a formerly radioactive area: I. Establishment of high-resolution quantitative protein map of mature flax seeds harvested from the remediated Chernobyl area

In recent years there has been an increasing tendency toward remediation of contaminated areas for agriculture purposes. The study described herein is part of a comprehensive, long-term characterization of crop plants grown in the area formerly contaminated with radioactivity. As a first step, we have established a quantitative map of proteins isolated from mature flax (Linum usitatissimum L.) seeds harvested from plants grown in a remediated plot localized directly in Chernobyl town. Flax was selected because it is a crop of economic and historical importance, despite the relative paucity of molecular resources. We used 2-dimensional electrophoresis followed by tandem mass spectrometry to establish a high-resolution seed proteome map. This approach yielded quantitative information for 318 protein spots. Genomic sequence resources for flax are very limited, leaving us with an "unknown function" annotation for 38% of the proteins analyzed including several that comprise very large spots. In addition to the seed storage proteins, we were able to reliably identify 82 proteins many of which are involved with central metabolism.

Using multiplex-staining to study changes in the maize leaf phosphoproteome in response to mechanical wounding

Mechanical wounding of 2-week-old maize (Zea mays L.) leaves, one of the first steps in both pathogen infection and herbivore attack, stimulates metabolism and activates signal transduction pathways dedicated to defense and recovery. The signaling pathways include reversible protein phosphorylation which can modulate protein activities, and transmit signals within cellular pathways and networks. We have used multiplex-staining of high-resolution 2D gels for protein (Sypro Ruby) and phosphorylation (Pro-Q Diamond) as a strategy for quantifying changes in the stoichiometry of phosphorylation after wounding for 270 protein spots. Rigorous statistical analysis of the time-index data allowed us to accept patterns of change in 125 of the spots as non-random, and these patterns were assigned to five clusters. A reliable identity was assigned to 21 selected proteins, most of which have been previously described as phospho-proteins. The results suggest that analysis of protein spots from high-resolution 2D gels by multiplex-staining for protein plus phosphorylation is a strategy that can be broadly useful for study of how the phospho-proteome responds to abiotic stress.

Systems biology approaches to abscisic acid signaling

Recent advances in our understanding of abscisic acid (ABA) signaling have identified a core pathway consisting of receptors (PYR/PYL/RCAR), protein phosphatases (PP2C), protein kinases (SnRK2), and several downstream factors that will lead to the next stage of ABA research. Systems biology will be an important concept for further understanding ABA responses in plants. In this review, two practical approaches of systems biology to ABA signaling are presented: the one is 'transcriptome analysis', which covers coding genes as well as unannotated transcripts, and the other is 'phosphoproteomics'. The latter technology will offer an unprecedented overview of the regulatory networks involved in ABA signaling because protein phosphorylation/dephosphorylation is a major center of such regulation. Systematic studies will contribute to our understanding of the network structure and dynamics of ABA signaling; moreover, systems biology will facilitate ABA signaling studies as well as future biotechnological applications in crops or trees.

Next generation functional proteomics in non-model plants: A survey on techniques and applications for the analysis of protein complexes and post-translational modifications

The congruent development of computational technology, bioinformatics and analytical instrumentation makes proteomics ready for the next leap. Present-day state of the art proteomics grew from a descriptive method towards a full stake holder in systems biology. High throughput and genome wide studies are now made at the functional level. These include quantitative aspects, functional aspects with respect to protein interactions as well as post translational modifications and advanced computational methods that aid in predicting protein function and mapping these functionalities across the species border. In this review an overview is given of the current status of these aspects in plant studies with special attention to non-genomic model plants.

Genotypic variation in sulphur assimilation and metabolism of onion (Allium cepa L.). II: Characterisation of ATP sulphurylase activity

To investigate the regulation of sulphur (S)-assimilation in onion further at the biochemical level, the pungent cultivar W202A and the milder cultivar Texas Grano 438 PVP (TG) have been grown in S-sufficient (S(+); 4meqS(-1)) or S-deficient (S(-); 0.1meqS(-1)) growth conditions, and tissues excised at the seedling stage (pre-bulbing; ca. 10-weeks-old) and at the mature stage (bulbing; ca. 16-weeks-old). S-supply negatively influenced adenosine-5'-phosphosulphate (APS) reductase (APR) enzyme activity in both cultivars at bulbing only, and a higher abundance of APR was observed in both cultivars at bulbing in response to low S-supply. In contrast, S-supply significantly influenced ATP sulphurylase (ATPS) activity in leaf tissues of W202A only, and only at bulbing, while an increase in abundance in response to high S-supply was observed for both cultivars at bulbing. To investigate the regulation of the ATPS enzyme activity and accumulation further, activity was shown to decrease significantly in roots at bulbing in the S-deficient treatment in both cultivars, a difference that was only supported by western analyses in W202A. Phylogenetic analysis revealed that AcATPS1 groups in a broad monocot clade with the closest sequences identified in Sorghum bicolour, Zea mays and Oryza sativa, but with some support for a divergence of AcATPS1. Detection of ATPS in leaf extracts after two dimensional gel electrophoresis (2-DE) revealed that the protein may undergo post-translational modification with a differential pattern of ATPS accumulation detected in both cultivars over the developmental progression from the seedling to the bulbing stage. Treatment of leaf extracts of W202A to dephosphorylate proteins resulted in the loss of immuno-recognised ATPS spots after 2-DE separation, although enzyme activity was not influenced. These results are discussed in terms of the tiers of control that operate at the biochemical level in the reductive S-assimilation pathway in a S-accumulating species particularly during the high-S-demanding bulbing stage.

Quantitative phosphoproteomics strategies for understanding protein kinase-mediated signal transduction pathways

Protein phosphorylation is a central regulatory mechanism of cell signaling pathways. This highly controlled biochemical process is involved in most cellular functions, and defects in protein kinases and phosphatases have been implicated in many diseases, highlighting the importance of understanding phosphorylation-mediated signaling networks. However, phosphorylation is a transient modification, and phosphorylated proteins are often less abundant. Therefore, the large-scale identification and quantification of phosphoproteins and their phosphorylation sites under different conditions are one of the most interesting and challenging tasks in the field of proteomics. Both 2D gel electrophoresis and liquid chromatography-tandem mass spectrometry serve as key phosphoproteomic technologies in combination with prefractionation, such as enrichment of phosphorylated proteins/peptides. Recently, new possibilities for quantitative phosphoproteomic analysis have been offered by technical advances in sample preparation, enrichment, separation, instrumentation, quantification and informatics. In this article, we present an overview of several strategies for quantitative phosphoproteomics and discuss how phosphoproteomic analysis can help to elucidate signaling pathways that regulate various cellular processes.

Comparative proteomics of seed maturation in oilseeds reveals differences in intermediary metabolism

Proteomics is increasingly being used to understand enzyme expression and regulatory mechanisms involved in the accumulation of storage reserves in crops with sequenced genomes. During the past six years, considerable progress has been made to characterize proteomes of both mature and developing seeds, particularly oilseeds - plants which accumulate principally oil and protein as storage reserves. This review summarizes the emerging proteomics data, with emphasis on seed filling in soy, rapeseed, castor and Arabidopsis as each of these oilseeds were analyzed using very similar proteomic strategies. These parallel studies provide a comprehensive view of source-sink relationships, specifically sucrose assimilation into organic acid intermediates for de novo amino acid and fatty acid synthesis. We map these biochemical processes for seed maturation and illustrate the differences and similarities among the four oilseeds. For example, while the four oilseeds appear capable of producing cytosolic phosphoenolpyruvate as the principal carbon intermediate, soybean and castor also express malic enzymes and malate dehydrogenase, together capable of producing malate that has been previously proposed to be the major intermediate for fatty acid synthesis in castor. We discuss these and other differences in the context of intermediary metabolism for developing oilseeds.

Soybean 14-3-3 gene family: identification and molecular characterization

The 14-3-3s are a group of proteins that are ubiquitously found in eukaryotes. Plant 14-3-3 proteins are encoded by a large multigene family and are involved in signaling pathways to regulate plant development and protection from stress. Recent studies in Arabidopsis and rice have demonstrated the isoform specificity in 14-3-3s and their client protein interactions. However, detailed characterization of 14-3-3 gene family in legumes has not been reported. In this study, soybean 14-3-3 proteins were identified and their molecular characterization performed. Data mining of soybean genome and expressed sequence tag databases identified 18 14-3-3 genes, of them 16 are transcribed. All 16 SGF14s have higher expression in embryo tissues suggesting their potential role in seed development. Subcellular localization of all transcribed SGF14s demonstrated that 14-3-3 proteins in soybean have isoform specificity, however, some overlaps were also observed between closely related isoforms. A comparative analysis of SGF14s with Arabidopsis and rice 14-3-3s indicated that SGF14s also group into epsilon and non-epsilon classes. However, unlike Arabidopsis and rice 14-3-3s, SGF14s contained only one kind of gene structure belonging to each class. Overall, soybean consists of the largest family of 14-3-3 proteins characterized to date. Our results provide a solid framework for further investigations into the role of SGF14s and their involvement in legume-specific functions.

Annexins

Annexins are multifunctional lipid-binding proteins. Plant annexins are expressed throughout the life cycle and are under environmental control. Their association or insertion into membranes may be governed by a range of local conditions (Ca(2+), pH, voltage or lipid identity) and nonclassical sorting motifs. Protein functions include exocytosis, actin binding, peroxidase activity, callose synthase regulation and ion transport. As such, annexins appear capable of linking Ca(2+), redox and lipid signalling to coordinate development with responses to the biotic and abiotic environment. Significant advances in plant annexin research have been made in the past 2 yr. Here, we review the basis of annexin multifunctionality and suggest how these proteins may operate in the life and death of a plant cell.

Phosphoproteomics using iTRAQ

The identification of phosphorylation on proteins has become practicable for many laboratories in recent years, largely due to improvements in mass spectrometry (MS) and the development of methods to selectively enrich for phosphorylated peptides and proteins. However, phosphorylation is a dynamic and reversible modification which plays a central role in many biological processes including intracellular signalling. Therefore, the quantitative analysis of phosphorylated proteins and peptides is a subject of intense interest. We discuss three applications of isobaric tags for relative and absolute quantitation (iTRAQ) to the analysis of phosphopeptides from a variety of sample materials.

Phosphorylation of maize eukaryotic translation initiation factor 5A (eIF5A) by casein kinase 2: identification of phosphorylated residue and influence on intracellular localization of eIF5A

Maize eukaryotic translation initiation factor 5A (ZmeIF5A) co-purifies with the catalytic alpha subunit of protein kinase CK2 and is phosphorylated by this enzyme. Phosphorylated ZmeIF5A was also identified after separation of maize leaf proteins by two-dimensional electrophoresis. Multiple sequence alignment of eIF5A proteins showed that in monocots, in contrast to other eukaryotes, there are two serine/threonine residues that could potentially be phosphorylated by CK2. To identify the phosphorylation site(s) of ZmeIF5A, the serine residues potentially phosphorylated by CK2 were mutated. ZmeIF5A and its mutated variants S2A and S4A were expressed in Escherichia coli and purified. Of these recombinant proteins, only ZmeIF5A-S2A was not phosphorylated by maize CK2. Also, Arabidopsis thaliana and Saccharomyces cerevisiae eIF5A-S2A mutants were not phosphorylated despite effective phosphorylation of wild-type variants. A newly developed method exploiting the specificity of thrombin cleavage was used to confirm that Ser(2) in ZmeIF5A is indeed phosphorylated. To find a role of the Ser(2) phosphorylation, ZmeIF5A and its variants mutated at Ser(2) (S2A and S2D) were transiently expressed in maize protoplasts. The expressed fluorescence labeled proteins were visualized by confocal microscopy. Although wild-type ZmeIF5A and its S2A variant were distributed evenly between the nucleus and cytoplasm, the variant with Ser(2) replaced by aspartic acid, which mimics a phosphorylated serine, was sequestered in the nucleus. These results suggests that phosphorylation of Ser(2) plays a role in regulation of nucleocytoplasmic shuttling of eIF5A in plant cells.

Physiological and molecular changes in Oryza meridionalis Ng., a heat-tolerant species of wild rice

Oryza meridionalis Ng. is a wild relative of Oryza sativa L. found throughout northern Australia where temperatures regularly exceed 35 degrees C in the monsoon growing season. Heat tolerance in O. meridionalis was established by comparing leaf elongation and photosynthetic rates at 45 degrees C with plants maintained at 27 degrees C. By comparison with O. sativa ssp. japonica cv. Amaroo, O. meridionalis was heat tolerant. Elongation rates of the third leaf of O. meridionalis declined by 47% over 24 h at 45 degrees C compared with a 91% decrease for O. sativa. Net photosynthesis was significantly higher in O. sativa at 27 degrees C whereas the two species had the same assimilation rates at 45 degrees C. The leaf proteome and expression levels of individual heat-responsive genes provided insight into the heat response of O. meridionalis. After 24 h of heat exposure, many enzymes involved in the Calvin Cycle were more abundant, while mRNA of their genes generally decreased. Ferredoxin-NADP(H) oxidoreductase, a key enzyme in photosynthetic electron transport had both reduced abundance and gene expression, suggesting light reactions were highly susceptible to heat stress. Rubisco activase was strongly up-regulated after 24 h of heat, with the large isoform having the largest relative increase in protein abundance and a significant increase in gene expression. The protective proteins Cpn60, Hsp90, and Hsp70 all increased in both protein abundance and gene expression. A thiamine biosynthesis protein (THI1), previously shown to act protectively against stress, increased in abundance during heat, even as thiamine levels fell in O. meridionalis.

Plant phosphoproteomics: an update

Phosphoproteomics involves identification of phosphoproteins, precise mapping, and quantification of phosphorylation sites, and eventually, revealing their biological function. In plants, several systematic phosphoproteomic analyses have recently been performed to optimize in vitro and in vivo technologies to reveal components of the phosphoproteome. The discovery of novel substrates for specific protein kinases is also an important issue. Development of a new tool has enabled rapid identification of potential kinase substrates such as kinase assays using plant protein microarrays. Progress has also been made in quantitative and dynamic analysis of mapped phosphorylation sites. Increased quantity of experimentally verified phosphorylation sites in plants has prompted the creation of dedicated web-resources for plant-specific phosphoproteomics data. This resulted in development of computational prediction methods yielding significantly improved sensitivity and specificity for the detection of phosphorylation sites in plants when compared to methods trained on less plant-specific data. In this review, we present an update on phosphoproteomic studies in plants and summarize the recent progress in the computational prediction of plant phosphorylation sites. The application of the experimental and computed results in understanding the phosphoproteomic networks of cellular and metabolic processes in plants is discussed. This is a continuation of our comprehensive review series on plant phosphoproteomics.

Proteomics tools and resources for investigating protein allergens in oilseeds

Oilseeds are important renewable sources of natural products including protein and oil which are produced during the maturation (or seed filling) phase of embryo development. My lab employed high-resolution, two-dimensional gel electrophoresis (2-DE) and mass spectrometry to profile and identify over 500 proteins expressed during seed filling in various oilseeds including soybean, canola, castor, and Arabidopsis. The principal objective of these studies was to develop predictive models for carbon assimilation for comparison among the four oilseeds. Other uses for these large proteomic datasets have come to light including characterization of the diversity and expression of known and yet-to-be-discovered protein allergens as they accumulate during seed development. Legume oilseeds such as soybean and peanut present a human and animal health concern for a small percentage of the population that are allergic to one or more of the seed proteins. Information about the expression and diversity of 2-DE spots that map to individual genes or gene families of allergens can prove useful for breeding- or biotechnology-based approaches aimed at silencing allergen expression. We have begun releasing these proteomics datasets for public access on the Oilseed Proteomics web portal, www.oilseedproteomics.missouri.edu. I will present the status of these projects and the website with specific emphasis on soybean.

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.

Plant proteomics: concepts, applications, and novel strategies for data interpretation

Proteomics is an essential source of information about biological systems because it generates knowledge about the concentrations, interactions, functions, and catalytic activities of proteins, which are the major structural and functional determinants of cells. In the last few years significant technology development has taken place both at the level of data analysis software and mass spectrometry hardware. Conceptual progress in proteomics has made possible the analysis of entire proteomes at previously unprecedented density and accuracy. New concepts have emerged that comprise quantitative analyses of full proteomes, database-independent protein identification strategies, targeted quantitative proteomics approaches with proteotypic peptides and the systematic analysis of an increasing number of posttranslational modifications at high temporal and spatial resolution. Although plant proteomics is making progress, there are still several analytical challenges that await experimental and conceptual solutions. With this review I will highlight the current status of plant proteomics and put it into the context of the aforementioned conceptual progress in the field, illustrate some of the plant-specific challenges and present my view on the great opportunities for plant systems biology offered by proteomics.

A high-resolution two dimensional Gel- and Pro-Q DPS-based proteomics workflow for phosphoprotein identification and quantitative profiling

The two-dimensional (2-D) gel-based proteomics platform remains the workhorse for proteomics and is fueled by a number of key improvements, including fluorescence-based stains for detection and quantification of proteins and phosphoproteins with high sensitivity and linear dynamic ranges. One such stain is Pro-Q diamond phosphoprotein stain (Pro-Q DPS), which binds to the phosphate moiety of phospho-proteins irrespective of the phosphoamino acid. We recently introduced a modified Pro-Q DPS protocol to detect phosphoprotein spots on 2-D gels with very low background addressing some prime concerns, including high cost and reproducibility of Pro-Q DPS. The major modifications were a threefold dilution of Pro-Q DPS and the use of threefold less volume of the diluted staining solution. In this chapter, use of the modified Pro-Q DPS protocol along with the 2-D gel-based proteomics for phosphoprotein detection and quantification is described in detail. This 2-D gel- and Pro-Q DPS-based proteomics workflow has seven major steps: preparation of total protein, separation of proteins by 2-D gel electrophoresis, detection of phosphoprotein and total protein, image analysis and quantitative expression profiling, excision of 2-D spots, mass spectrometry analysis, and data processing and organization. Involvement of the modified Pro-Q DPS protocol in this proteomics workflow alone reduces the overall cost by at least ninefold for conducting phospho-proteomics analysis on a global scale, thereby making this entire process economically attractive to the scientific community.

Differential regulation of proteins and phosphoproteins in rice under drought stress

Drought is the largest constraint on rice production in Asia. Protein phosphorylation has been recognized as an important mechanism for environmental stress signaling. However, the differential expression of proteins and phosphoproteins induced by drought in rice is still largely unknown. In this paper, we report the identification of differentially expressed proteins and phosphoproteins induced by drought in rice using proteomic approaches. Three drought-responsive proteins were identified. Late embryogenesis abundant (LEA)-like protein and chloroplast Cu-Zn superoxide dismutase (SOD) were up-regulated by drought whereas Rieske Fe-S precursor protein was down-regulated. Ten drought-responsive phosphoproteins were identified: NAD-malate dehydrogenase, OSJNBa0084K20.14 protein, abscisic acid- and stress-inducible protein, ribosomal protein, drought-induced S-like ribonuclease, ethylene-inducible protein, guanine nucleotide-binding protein beta subunit-like protein, r40c1 protein, OSJNBb0039L24.13 protein and germin-like protein 1. Seven of these phosphoproteins have not previously been reported to be involved in rice drought stress. These results provide new insight into the regulatory mechanism of drought-induced proteins and implicate several previously unrecognized proteins in response to drought stress.

Purification and proteomic characterization of plastids from Brassica napus developing embryos

Plastids are functionally and structurally diverse organelles responsible for numerous biosynthetic reactions within the plant cell. Plastids from embryos have a range of properties depending upon the plant source but compared to other plastid types are poorly understood and therefore, we term them embryoplasts. Isolating intact plastids from developing embryos is challenging due to large starch granules within the stroma and the prevalence of nonplastid, storage organelles (oil bodies and protein storage vacuoles) which compromise plastid integrity and purity, respectively. To characterize rapeseed embryoplasts it was necessary to develop an improved isolation procedure. A new method is presented for the isolation of intact plastids from developing embryos of Brassica napus seeds. Intactness and purity of embryoplast preparations was determined using phase-contrast and transmission electron microscopy, immunoblotting, and multidimensional protein identification technology (MudPIT) MS/MS. Eighty nonredundant proteins were identified by MudPIT analysis of embryoplast preparations. Approximately 53% of these proteins were components of photosystem, light harvesting, cytochrome b/f, and ATP synthase complexes, suggesting ATP and NADPH production are important functions for this plastid type.

A shotgun phosphoproteomics analysis of embryos in germinated maize seeds

To better understand the role that reversible protein phosphorylation plays in seed germination, we initiated a phosphoproteomic investigation of embryos of germinated maize seeds. A total of 776 proteins including 39 kinases, 16 phosphatases, and 33 phosphoproteins containing 36 precise in vivo phosphorylation sites were identified. All the phosphorylation sites identified, with the exception of the phosphorylation site on HSP22, have not been reported previously (Lund et al. in J Biol Chem, 276, 29924-29929, 2001). Assayed with QRT-PCR, the transcripts of ten kinase genes were found to be dramatically up-regulated during seed germination and those of four phosphatase genes were up-regulated after germination, which indicated that reversible protein phosphorylation occurred and complex regulating networks were activated during this period. At least one-third of these phosphoproteins are key components involved in biological processes which relate to seed germination, such as DNA repair, gene transcription, RNA splicing and protein translation, suggesting that protein phosphorylation plays an important role in seed germination. As far as we know, this is the first phosphoproteomic study on a monocot and it will lay a solid foundation for further study of the molecular mechanisms of seed germination and seedling development.

P3DB: a plant protein phosphorylation database

P(3)DB (http://www.p3db.org/) provides a resource of protein phosphorylation data from multiple plants. The database was initially constructed with a dataset from oilseed rape, including 14,670 nonredundant phosphorylation sites from 6382 substrate proteins, representing the largest collection of plant phosphorylation data to date. Additional protein phosphorylation data are being deposited into this database from large-scale studies of Arabidopsis thaliana and soybean. Phosphorylation data from current literature are also being integrated into the P(3)DB. With a web-based user interface, the database is browsable, downloadable and searchable by protein accession number, description and sequence. A BLAST utility was integrated and a phosphopeptide BLAST browser was implemented to allow users to query the database for phosphopeptides similar to protein sequences of their interest. With the large-scale phosphorylation data and associated web-based tools, P(3)DB will be a valuable resource for both plant and nonplant biologists in the field of protein phosphorylation.

A simple and rapid technique for detecting protein phosphorylation using one-dimensional isoelectric focusing gels and immunoblot analysis

We report a technique for detecting protein phosphorylation that involves isoelectric focusing in a vertical mini-gel format followed by immunoblot detection of the target protein. This method uses standard protein gel equipment, allows sensitive detection of protein phosphorylation when phosphospecific antibodies are not available, and provides a stoichiometric measure of phosphorylation. We demonstrate the application of this method for observing phosphorylation of an Arabidopsis thaliana protein in response to biotic stress.

In-depth investigation of the soybean seed-filling proteome and comparison with a parallel study of rapeseed

To better understand the metabolic processes of seed filling in soybean (Glycine max), two complementary proteomic approaches, two-dimensional gel electrophoresis (2-DGE) and semicontinuous multidimensional protein identification technology (Sec-MudPIT) coupled with liquid chromatography-mass spectrometry, were employed to analyze whole seed proteins at five developmental stages. 2-DGE and Sec-MudPIT analyses collectively identified 478 nonredundant proteins with only 70 proteins common to both datasets. 2-DGE data revealed that 38% of identified proteins were represented by multiple 2-DGE species. Identified proteins belonged to 13 (2-DGE) and 15 (Sec-MudPIT) functional classes. Proteins involved in metabolism, protein destination and storage, and energy were highly represented, collectively accounting for 61.1% (2-DGE) and 42.2% (Sec-MudPIT) of total identified proteins. Membrane proteins, based upon transmembrane predictions, were 3-fold more prominent in Sec-MudPIT than 2-DGE. Data were integrated into an existing soybean proteome database (www.oilseedproteomics.missouri.edu). The integrated quantitative soybean database was compared to a parallel study of rapeseed (Brassica napus) to further understand the regulation of intermediary metabolism in protein-rich versus oil-rich seeds. Comparative analyses revealed (1) up to 3-fold higher expression of fatty acid biosynthetic proteins during seed filling in rapeseed compared to soybean; and (2) approximately a 48% higher number of protein species and a net 80% higher protein abundance for carbon assimilatory and glycolytic pathways leading to fatty acid synthesis in rapeseed versus soybean. Increased expression of glycolytic and fatty acid biosynthetic proteins in rapeseed compared to soybean suggests that a possible mechanistic basis for higher oil in rapeseed involves the concerted commitment of hexoses to glycolysis and eventual de novo fatty acid synthesis pathways.

Proteomic analysis of phosphoproteins regulated by abscisic acid in rice leaves

Abscisic acid (ABA) is a hormone that regulates plant development and adaptation to environmental stresses. Protein phosphorylation has been recognized as an important mechanism for ABA signaling. However, the target phosphoproteins regulated by ABA are still largely unknown. Here, we report the identification of ABA-regulated phosphoproteins in rice using proteomic approaches. Six ABA-regulated phosphoproteins were identified as G protein beta subunit-like protein, ascorbate peroxidase, manganese superoxide dismutase, triosephosphate isomerase, putative Ca(2+)/H(+) antiporter regulator protein, and glyoxysomal malate dehydrogenase. These results provide new insight into the regulatory mechanism for some ABA signaling proteins and implicate several previously unrecognized proteins in ABA action.

Site-specific phosphorylation profiling of Arabidopsis proteins by mass spectrometry and peptide chip analysis

An estimated one-third of all proteins in higher eukaryotes are regulated by phosphorylation by protein kinases (PKs). Although plant genomes encode more than 1000 PKs, the substrates of only a small fraction of these kinases are known. By mass spectrometry of peptides from cytoplasmic- and nuclear-enriched fractions, we determined 303 in vivo phosphorylation sites in Arabidopsis proteins. Among 21 different PKs, 12 were phosphorylated in their activation loops, suggesting that they were in their active state. Immunoblotting and mutational analysis confirmed a tyrosine phosphorylation site in the activation loop of a GSK3/shaggy-like kinase. Analysis of phosphorylation motifs in the substrates suggested links between several of these PKs and many target sites. To perform quantitative phosphorylation analysis, peptide arrays were generated with peptides corresponding to in vivo phosphorylation sites. These peptide chips were used for kinome profiling of subcellular fractions as well as H 2O 2-treated Arabidopsis cells. Different peptide phosphorylation profiles indicated the presence of overlapping but distinct PK activities in cytosolic and nuclear compartments. Among different H 2O 2-induced PK targets, a peptide of the serine/arginine-rich (SR) splicing factor SCL30 was most strongly affected. SRPK4 (SR protein-specific kinase 4) and MAPKs (mitogen-activated PKs) were found to phosphorylate this peptide, as well as full-length SCL30. However, whereas SRPK4 was constitutively active, MAPKs were activated by H 2O 2. These results suggest that SCL30 is targeted by different PKs. Together, our data demonstrate that a combination of mass spectrometry with peptide chip phosphorylation profiling has a great potential to unravel phosphoproteome dynamics and to identify PK substrates.

Advances in the analysis of protein phosphorylation

Phosphorylation is one of the most relevant and ubiquitous post-translational modifications. Despite its relevance, the analysis of protein phosphorylation has been revealed as one of the most challenging tasks due to its highly dynamic nature and low stoichiometry. However, the development and introduction of new analytical methods are modifying rapidly and substantially this field. Especially important has been the introduction of more sensitive and specific methods for phosphoprotein and phosphopeptide purification as well as the use of more sensitive and accurate MS-based analytical methods. The integration of both approaches has enabled large-scale phosphoproteome studies to be performed, an unimaginable task few years ago. Additionally, methods originally developed for differential proteomics have been adapted making the study of the highly dynamic nature of protein phosphorylation feasible. This review aims at offering an overview on the most frequently used methods in phosphoprotein and phosphopeptide enrichment as well as on the most recent MS-based analysis strategies. Current strategies for quantitative phosphoproteomics and the study of the dynamics of protein phosphorylation are highlighted.

A phosphomimetic mutation in the Sall1 repression motif disrupts recruitment of the nucleosome remodeling and deacetylase complex and repression of Gbx2

The multizinc finger transcription factor Sall1 is a critical developmental regulator that mediates repression through the recruitment of the nucleosome remodeling and deacetylase (NuRD) complex. Although a short conserved peptide motif in Sall1 is sufficient to recruit NuRD, its ability to regulate native Sall1 target genes in vivo has not been demonstrated. In this report, we demonstrate an in vivo role for the Sall1 repression motif and describe a novel direct target gene of Sall1, Gbx2, that is directly repressed in a NuRD-dependent fashion. The ability of Sall1 to repress Gbx2 was impaired in Xenopus embryos expressing mutant forms of Sall1 that are defective for NuRD binding. Finally, we demonstrate that protein kinase C phosphorylates serine 2 of the Sall1 repression motif and reveal that a phosphomimetic mutation of serine 2 disrupts the ability of Sall1 to repress Gbx2 in cell culture and Xenopus embryos. Together, these studies establish that Sall1 recruits NuRD via the Sall1 repression motif to mediate repression of a native target gene and suggest a model in which dynamic control of gene expression by Sall1 is modulated by serine phosphorylation of the Sall1 repression motif.

Phosphoenolpyruvate carboxylase protein kinase from developing castor oil seeds: partial purification, characterization, and reversible control by photosynthate supply

Phosphoenolpyruvate carboxylase (PEPC, EC 4.1.1.31) protein kinase (PPCK) was purified approximately 1,500-fold from developing castor oil seeds (COS). Gel filtration and immunoblotting with anti-(rice PPCK2)-immune serum indicated that this Ca2+-insensitive PPCK exists as a 31-kDa monomer. COS PPCK-mediated rephosphorylation of the 107-kDa subunit (p107) of COS PEPC1 (Km = 2.2 microM) activated PEPC1 by approximately 80% when assayed under suboptimal conditions (pH 7.3, 0.2 mM PEP, and 0.125 mM malate). COS PPCK displayed remarkable selectivity for phosphorylating COS PEPC1 (relative to tobacco, sorghum, or maize PEPCs), exhibited a broad pH-activity optima of approximately pH 8.5, and at pH 7.3 was activated 40-65% by 1 mM PEP, or 10 mM Gln or Asn, but inhibited 65% by 10 mM L-malate. The possible control of COS PPCK by disulfide-dithiol interconversion was suggested by its rapid inactivation and subsequent reactivation when incubated with oxidized glutathione and then dithiothreitol. In vitro PPCK activity correlated with in vivo p107 phosphorylation status, with both peaking in mid-cotyledon to full-cotyledon developing COS. Notably, PPCK activity and p107 phosphorylation of developing COS were eliminated following pod excision or prolonged darkness of intact plants. Both effects were fully reversed 12 h following reillumination of darkened plants. These results implicate a direct relationship between the up-regulation of COS PPCK and p107 phosphorylation during the recommencement of photosynthate delivery from illuminated leaves to the non-photosynthetic COS. Overall, the results support the hypothesis that PEPC and PPCK participate in the control of photosynthate partitioning into C-skeletons needed as precursors for key biosynthetic pathways of developing COS.

Using phosphoproteomics to reveal signalling dynamics in plants

To ensure appropriate responses to stimuli, organisms have evolved signalling networks that rely on post-translational modifications of their components. Among these, protein phosphorylation has a prominent role and much research in plants has focused on protein kinases and phosphatases, which, respectively, catalyse phosphorylation and dephosphorylation of specific substrates. Technical limitations, however, have hampered the identification of these substrates. As reviewed here, novel mass spectrometry-based techniques have enabled the large-scale mapping of in vivo phosphorylation sites. Alternatively, methods based on peptide and protein microarrays have revealed protein kinase activities in cell extracts, in addition to kinase substrates. A combined phosphoproteomic approach of mass spectrometry and microarray technology could enhance the construction of dynamic plant signalling networks that underlie plant biology.

Combined networks regulating seed maturation

Seed maturation is an important phase of seed development during which embryo growth ceases, storage products accumulate, the protective tegument differentiates and tolerance to desiccation develops, leading to seed dormancy. The spatial and temporal regulation of all these processes requires the concerted action of several signaling pathways that integrate information from genetic programs, and both hormonal and metabolic signals. Recent genetic studies have identified some of the interactions that occur between four master regulators in Arabidopsis, increasing our knowledge of the control of the transcriptional program involved in seed maturation. Moreover, several recent breakthroughs have led to a better understanding of the role of abscisic acid signal modulation and the importance of metabolic regulation in the maternal to filial switch leading to the maturation phase.

Proteomic technologies in the study of kinases: novel tools for the investigation of PKC in the heart

Recent developments in the field of protein separation allows for the analysis of qualitative and quantitative global protein changes in a particular state of a biological system. Due to the enormous number of proteins potentially present in a cell, sub-fractionation and the enrichment of specific organelles are emerging as a necessary step to allow a more comprehensive representation of the protein content. The proteomic studies demonstrate that a key to understand the mechanisms underlying physiological or pathological phenotypes lies, at least in part, in post-translational modifications (PTMs), including phosphorylation of proteins. Rapid improvements in proteomic characterization of amino acid modifications are further expanding our comprehension of the importance of these mechanisms. The present review will provide an overview of technologies available for the study of a proteome, including tools to assess changes in protein quantity (abundance) as well as in quality (PTM forms). Examples of the recent application of these technologies and strategies in the field of kinase signalling will be provided with particular attention on the role of PKC in the heart. Studies of PKC-mediated phosphorylation of cytoskeletal, myofilament and mitochondrial proteins in the heart have provided great insight into the phenotypes of heart failure, hypertrophy and cardioprotection. Proteomics studies of the mitochondria have provided novel evidences for kinase signalling cascades localized to the mitochondria, some of which are known to involve various isoforms of PKC. Proteomics technologies allow for the identification of the different PTM forms of specific proteins and this information is likely to provide insight into the determinants of morphological as well as metabolic mal-adaptations, both in the heart and other tissues.

Proteome and phosphoproteome dynamic change during cell dedifferentiation inArabidopsis

Cell dedifferentiation is a cell fate switching process in which a differentiated cell reverts to a status with competence for cell division and organ regeneration like an embryonic stem cell. Although the phenomenon of cell dedifferentiation has been known for over two and a half centuries in plants, little is known of the underlying mechanisms. Here, we have established the proteome map of Arabidopsis cotyledons and investigated the dynamic change of the cotyledon proteome in the time course of cell dedifferentiation. Among the 353 distinct genes, corresponding to 500 2-DE gel protein spots identified with high confidence, 12% have over twofold differential regulations within the first 48 h of induction of cell dedifferentiation. The distributions of these genes among different Gene Ontology categories and gene differential regulations within each of the categories have been examined. In addition, we have investigated the cotyledon phosphoproteome using Pro-Q Diamond Phosphoprotein in Gel Stain followed by mass spectrometry analyses. Among the 53 identified putative phosphoproteins, nine are differentially regulated during cell dedifferentiation. These studies have provided significant new insight into protein and phosphoprotein differential expression during cell dedifferentiation in plants.

Phosphoproteomic identification of targets of the Arabidopsis sucrose nonfermenting-like kinase SnRK2.8 reveals a connection to metabolic processes

SnRK2.8 is a member of the sucrose nonfermenting-related kinase family that is down-regulated when plants are deprived of nutrients and growth is reduced. When this kinase is over expressed in Arabidopsis, the plants grow larger. To understand how this kinase modulates growth, we identified some of the proteins that are phosphorylated by this kinase. A new phosphoproteomic method was used in which total protein from plants overexpressing the kinase was compared with total protein from plants in which the kinase was inactivated. Protein profiles were compared on two-dimensional gels following staining by a dye that recognizes phosphorylated amino acids. Candidate target proteins were confirmed with in vitro phosphorylation assays, using the kinase and target proteins that were purified from Escherichia coli. Seven target proteins were confirmed as being phosphorylated by SnRK2.8. Certain targets, such as 14-3-3 proteins, regulate as yet unidentified proteins, whereas other targets, such as glyoxalase I and ribose 5-phosphate isomerase, detoxify byproducts from glycolysis and catalyze one of the final steps in carbon fixation, respectively. Also, adenosine kinase and 60S ribosomal protein were confirmed as targets of SnRK2.8. Using mass spectrometry, we identified phosphorylated residues in the SnRK2.8, the 14-3-3kappa, and the 14-3-3chi. These data show that the expression of SnRK2.8 is correlated with plant growth, which may in part be due to the phosphorylation of enzymes involved in metabolic processes.

Proteome and Phosphoproteome Differential Expression under Salinity Stress in Rice (Oryza sativa) Roots

Salinity stress is a major abiotic stress that limits agriculture productivity worldwide. Rice is a model plant of monocotyledons, including cereal crops. Studies have suggested a critical role of protein phosphorylation in salt stress response in plants. However, the phosphoproteome in rice, particularly under salinity stress, has not been well studied. Here, we use Pro-Q Diamond Phosphoprotein Stain to study rice phosphoproteome differential expression under salt stress. Seventeen differentially upregulated and 11 differentially downregulated putative phosphoproteins have been identified. Further analyses indicate that 10 of the 17 upregulated proteins are probably upregulated at post-translational level instead of the protein concentration. Meanwhile, we have identified 31 salt stress differentially regulated proteins using SYPRO Ruby stain. While eight of them are known salt stress response proteins, the majority has not been reported in the literature. Our studies have provided valuable new insight into plant response to salinity stress.