Comparative Interactomics: Analysis of Arabidopsis 14-3-3 Complexes Reveals Highly Conserved 14-3-3 Interactions between Humans and Plants

Is 14-3-3 the Combination to Unlock New Pathways to Improve Metabolic Homeostasis and β-Cell Function?

Since their discovery nearly five decades ago, molecular scaffolds belonging to the 14-3-3 protein family have been recognized as pleiotropic regulators of diverse cellular and physiological functions. With their ability to bind to proteins harboring specific serine and threonine phosphorylation motifs, 14-3-3 proteins can interact with and influence the function of docking proteins, enzymes, transcription factors, and transporters that have essential roles in metabolism and glucose homeostasis. Here, we will discuss the regulatory functions of 14-3-3 proteins that will be of great interest to the fields of metabolism, pancreatic β-cell biology, and diabetes. We first describe how 14-3-3 proteins play a central role in glucose and lipid homeostasis by modulating key pathways of glucose uptake, glycolysis, oxidative phosphorylation, and adipogenesis. This is followed by a discussion of the contributions of 14-3-3 proteins to calcium-dependent exocytosis and how this relates to insulin secretion from β-cells. As 14-3-3 proteins are major modulators of apoptosis and cell cycle progression, we will explore if 14-3-3 proteins represent a viable target for promoting β-cell regeneration and discuss the feasibility of targeting 14-3-3 proteins to treat metabolic diseases such as diabetes.

ARTICLE HIGHLIGHTS

14-3-3 proteins are ubiquitously expressed scaffolds with multiple roles in glucose homeostasis and metabolism. 14-3-3ζ regulates adipogenesis via distinct mechanisms and is required for postnatal adiposity and adipocyte function. 14-3-3ζ controls glucose-stimulated insulin secretion from pancreatic β-cells by regulating mitochondrial function and ATP synthesis as well as facilitating cross talk between β-cells and α-cells.

Physiological and interactomic analysis reveals versatile functions of Arabidopsis 14-3-3 quadruple mutants in response to Fe deficiency

To date, few phenotypes have been described for Arabidopsis 14-3-3 mutants or the phenotypes showing the role of 14-3-3 in plant responding to abiotic stress. Although one member of the 14-3-3 protein family (14-3-3 omicron) was shown to be involved in the proper operation of Fe acquisition mechanisms at physiological and gene expression levels in Arabidopsis thaliana, it remains to be explored whether other members play a role in regulating iron acquisition. To more directly and effectively observe whether members of 14-3-3 non-epsilon group have a function in Fe-deficiency adaptation, three higher order quadruple KOs, kappa/lambda/phi/chi (klpc), kappa/lambda/upsilon/nu(klun), and upsilon/nu/phi/chi (unpc) were generated and studied for physiological analysis in this study. The analysis of iron-utilization efficiency, root phenotyping, and transcriptional level of Fe-responsive genes suggested that the mutant with kl background showed different phenotypes from Wt when plants suffered Fe starved, while these phenotypes were absent in the unpc mutant. Moreover, the absence of the four 14-3-3 isoforms in the klun mutant has a clear impact on the 14-3-3 interactome upon Fe deficiency. Dynamics of 14-3-3-client interactions analysis showed that 27 and 17 proteins differentially interacted with 14-3-3 in Wt and klun roots caused by Fe deficiency, respectively. Many of these Fe responsive proteins have a role in glycolysis, oxidative phosphorylation and TCA cycle, the FoF1-synthase and in the cysteine/methionine synthesis. A clear explanation for the observed phenotypes awaits a more detailed analysis of the functional aspects of 14-3-3 binding to the target proteins identified in this study.

The protein 14-3-3: A functionally versatile molecule in Giardia duodenalis

Giardia duodenalis is a cosmopolitan zoonotic protozoan parasite causing giardiasis, one of the most common diarrhoeal diseases in human and animals. Beyond its public health relevance, Giardia represents a valuable and fascinating model microorganism. The deep-branching phylogenetic position of Giardia, its simple life cycle and its minimalistic genomic and cellular organization provide a unique opportunity to define basal and "ancestral" eukaryotic functions. The eukaryotic 14-3-3 protein family represents a distinct example of phosphoserine/phosphothreonine-binding proteins. The extended network of protein-protein interactions established by 14-3-3 proteins place them at the crossroad of multiple signalling pathways that regulate physiological and pathological cellular processes. Despite the remarkable insight on 14-3-3 protein in different organisms, from yeast to humans, so far little attention was given to the study of this protein in protozoan parasites. However, in the last years, research efforts have provided evidences on unique properties of the single 14-3-3 protein of Giardia and on its association in key aspects of Giardia life cycle. In the first part of this chapter, a general overview of the features commonly shared among 14-3-3 proteins in different organisms (i.e. structure, target recognition, mode of action and regulatory mechanisms) is included. The second part focus on the current knowledge on the biochemistry and biology of the Giardia 14-3-3 protein and on the possibility to use this protein as target to propose new strategies for developing innovative antigiardial therapy.

Regulation of ABI5 expression by ABF3 during salt stress responses in Arabidopsis thaliana

Background

Basic region/leucine zippers (bZIPs) are transcription factors (TFs) encoded by a large gene family in plants. ABF3 and ABI5 are Group A bZIP TFs that are known to be important in abscisic acid (ABA) signaling. However, questions of whether ABF3 regulates ABI5 are still present.

Results

In vitro kinase assay results showed that Thr-128, Ser-134, and Thr-451 of ABF3 are calcium-dependent protein kinase phosphorylation sites. Bimolecular fluorescence complementation (BiFC) analysis results showed a physical interaction between ABF3 and 14-3-3ω. A Thr-451 to Ala point mutation abolished the interaction but did not change the subcellular localization. In addition, the Arabidopsis protoplast transactivation assay using a luciferase reporter exhibited ABI5 activation by either ABF3 alone or by co-expression of ABF3 and 14-3-3ω. Moreover, chromatin immunoprecipitation-qPCR results showed that in Arabidopsis, ABI5 ABA-responsive element binding proteins (ABREs) of the promoter region (between − 1376 and − 455) were enriched by ABF3 binding under normal and 150 mM NaCl salt stress conditions.

Conclusion

Taken together, our results demonstrated that ABI5 expression is regulated by ABF3, which could contribute to salt stress tolerance in Arabidopsis thaliana.

Electronic supplementary material

The online version of this article (10.1186/s40529-019-0264-z) contains supplementary material, which is available to authorized users.

Affinity chromatography revealed 14-3-3 interactome of tomato (Solanum lycopersicum L.) during blue light-induced de-etiolation

De-etiolation is the first developmental process under light control allowing the heterotrophic seedling to become autotrophic. The phytohormones cytokinins (CKs) largely contribute to this process. Reversible phosphorylation is a key event of cell signaling, allowing proteins to become active or generating a binding site for specific protein interaction. 14-3-3 proteins regulate a variety of plant responses. The expression, hormonal regulation, and proteomic network under the control of 14-3-3s were addressed in tomato (Solanum lycopersicum L.) during blue light-induced photomorphogenesis. Two isoforms were specifically investigated due to their high expression during tomato de-etiolation. The multidisciplinary approach demonstrated that TFT9 expression, but not TFT6, was regulated by CKs and identified cis-regulating elements required for this response. Our study revealed >130 potential TFT6/9 interactors. Their functional annotation predicted that TFTs might regulate the activity of proteins involved notably in cell wall strengthening or primary metabolism. Several potential interactors were also predicted to be CK-responsive. For the first time, the 14-3-3 interactome linked to de-etiolation was investigated and evidenced that 14-3-3s might be involved in CK signaling pathway, cell expansion inhibition and steady-state growth rate establishment, and reprograming from heterotrophy to autotrophy. BIOLOGICAL SIGNIFICANCE: Tomato (Solanum lycopersicum L.) is one of the most important vegetables consumed all around the world and represents probably the most preferred garden crop. Regulation of hypocotyl growth by light plays an important role in the early development of a seedling, and consequently the homogeneity of the culture. The present study focuses on the importance of tomato 14-3-3/TFT proteins in this process. We provide here the first report of 14-3-3 interactome in the regulation of light-induced de-etiolation and subsequent photomorphogenesis. Our data provide new insights into light-induced de-etiolation and open new horizons for dissecting the post-transcriptional regulations.

Molecular characterization of the 14-3-3 gene family in rice and its expression studies under abiotic stress

14-3-3 isoforms were relatively less conserved at the C-terminal region across plant groups. Both Os 14-3-3f and Os 14-3-3g were inducible with differential gene expression levels under different abiotic stress and developmental stages in sensitive and tolerant indica rice cultivars as confirmed both at transcript and protein level. Plant 14-3-3s has been well characterized to function in several signaling pathways, biotic as well as abiotic stress and nutrient metabolism. We attempted comprehensive analysis of 14-3-3 genes in different plant lineages such as green algae (Chlamydomonas reinhardtii), moss (Physcomitrella patens) and lycophyte (Selaginella moellendorffii), dicot Arabidopsis thaliana and monocot Oryza sativa sub sp. japonica at the gene and protein level. Sequence alignment results revealed that 14-3-3 isoforms were evolutionarily conserved across all taxa with variable C-terminal end. Phylogenetic analysis indicated that the majority of 14-3-3 isoforms in rice belong to the non-epsilon group that clustered separately from the dicot group. Segmental duplication event played a significant role in the expansion of both, Arabidopsis and rice, 14-3-3 isoforms as revealed by synteny studies. In silico gene expression using Massive Parallel Signature Sequencing and microarray analysis revealed that 14-3-3 isoforms have variable expression in different tissue types and under different abiotic stress regime in Arabidopsis and japonica rice. Both, semi-quantitative and qPCR results, confirmed that Os14-3-3f and Os14-3-3g were inducible under abiotic stress in lamina and roots of indica rice and relatively higher under salinity and cold stress in Nonabokra, under dehydration stress in N-22 and under exogenous ABA in IR-29 usually after 3-6 h of treatment. Both, 14-3-3f and 14-3-3g, were highly expressed in flag leaves, stems and panicles and mature roots. These results were further confirmed by immunoblot analysis of rice cultivars using Os14-3-3f antibody generated from recombinant Os14-3-3f protein. The results provide the first comprehensive report of Os14-3-3 gene expression in indica rice cultivars which differ in tolerance to abiotic stress that might be useful for further research.

Protein sumoylation and phosphorylation intersect in Arabidopsis signaling

Conjugation of the small ubiquitin-related modifier (SUMO) to protein substrates has an impact on stress responses and on development. We analyzed the proteome and phosphoproteome of mutants in this pathway. The mutants chosen had defects in SUMO ligase SIZ1, which catalyzes attachment of single SUMO moieties onto substrates, and in ligases PIAL1 and PIAL2, which are known to form SUMO chains. A total of 2657 proteins and 550 phosphopeptides were identified and quantified. Approximately 40% of the proteins and 20% of the phosphopeptides showed differences in abundance in at least one of the analyzed genotypes, demonstrating the influence of SUMO conjugation on protein abundance and phosphorylation. The data show that PIAL1 and PIAL2 are integral parts of the SUMO conjugation system with an impact on stress response, and confirm the involvement of SIZ1 in plant defense. We find a high abundance of predicted SUMO attachment sites in phosphoproteins (70% versus 40% in the total proteome), suggesting convergence of phosphorylation and sumoylation signals onto a set of common targets.

Characterization of ubiquitin ligase SlATL31 and proteomic analysis of 14-3-3 targets in tomato fruit tissue (Solanum lycopersicum L.)

The 14-3-3 proteins participate in many aspects of plant physiology by interacting with phosphorylated proteins and thereby regulating target protein functions. In Arabidopsis plant, the ubiquitin ligase ATL31 controls 14-3-3 stability via both direct interaction and ubiquitination, and this consequently regulates post-germinative growth in response to carbon and nitrogen nutrient availability. Since 14-3-3 proteins regulate the activities of many key enzymes related to nutrient metabolism, one would anticipate that they should play an essential role not only in vegetative but also in reproductive tissue. Because fruit yield largely depends on carbon and nitrogen availability and their utilization, the function of 14-3-3 proteins was analyzed in tomato fruit tissue. Here, we isolated and characterized an ubiquitin ligase SlATL31 (Solyc03g112340) from tomato and demonstrated that SlATL31 has ubiquitin ligase activity as well as interaction with tomato 14-3-3 proteins, suggesting the possibility that the SlATL31 functions as an ubiquitin ligase for 14-3-3 similarly to its Arabidopsis ortholog. Furthermore, we performed proteomic analysis of 14-3-3 interacting proteins and identified 106 proteins as putative 14-3-3 targets including key enzymes for carbon metabolism and photosynthesis. This 14-3-3 interactome result and available transcriptome profile suggest a considerable yet complex role of 14-3-3 proteins in tomato fruit tissue.

BIOLOGICAL SIGNIFICANCE

Considerable cumulative evidence exists which implies that 14-3-3 proteins are involved in the regulation of plant primary metabolism. Here we provide the first report of 14-3-3 interactome analysis and identify putative 14-3-3 targets in tomato fruit tissue, which may be highly important given the documented metabolic shifts, which occur during fruit development and ripening. These data open future research avenues by which to understand the regulation of the role of post-translational regulation in tomato fruit development.

Genome-Wide Identification and Expression Analysis of the 14-3-3 Family Genes in Medicago truncatula

The 14-3-3 gene family, which is conserved in eukaryotes, is involved in protein-protein interactions and mediates signal transduction. However, detailed investigations of the 14-3-3 gene family in Medicago truncatula are largely unknown. In this study, the identification and study of M. truncatula 14-3-3-family genes were performed based on the latest M. truncatula genome. In the M. truncatula genome, 10 14-3-3 family genes were identified, and they can be grouped into ε and non-ε groups. An exon-intron analysis showed that the gene structures are conserved in the same group. The protein structure analysis showed that 14-3-3 proteins in M. truncatula are composed of nine typical antiparallel α-helices. The expression patterns of Mt14-3-3 genes indicated that they are expressed in all tissues. Furthermore, the gene expression levels of Mt14-3-3 under hormone treatment and Sinorhizobium meliloti infection showed that the Mt14-3-3 genes were involve in nodule formation. Our findings lay a solid foundation for further functional studies of 14-3-3 in M. truncatula.

Phosphomimetic mutation of a conserved serine residue in Arabidopsis thaliana 14-3-3ω suggests a regulatory role of phosphorylation in dimerization and target interactions

14-3-3s are evolutionarily conserved eukaryotic regulatory proteins that are involved in diverse biological processes. The common mode of action for the 14-3-3 proteins is through the binding of phosphorylated target proteins. In many species, multiple 14-3-3 isoforms exist and these different isoforms can exhibit distinct ranges of target interactions. The dimerization of 14-3-3s is central to their function. 14-3-3 isoforms can form different combinations of homo- and heterodimers, which contribute to the broad functional diversity of the family. In this study, we showed that phosphomimetic mutation of a conserved serine residue in the dimerization interface of 14-3-3 isoforms, Ser-62, not only affects the ability of Arabidopsis 14-3-3ω to form homodimers, but alters the range of 14-3-3 family members with which it can form heterodimers. Furthermore, we demonstrated that the phosphorylation status of Ser-62 can regulate the binding of 14-3-3ω to target proteins, suggesting that Ser-62 might be a conserved key element to modulate target binding in both plants and animals.

Identification and characterization of the 14-3-3 gene family in Hevea brasiliensis

The 14-3-3 proteins are a family of conserved phospho-specific binding proteins involved in diverse physiological processes. Although the genome-wide analysis of this family has been carried out in certain plant species, little is known about 14-3-3 protein genes in rubber tree (Hevea brasiliensis). In this study, we identified 10 14-3-3 protein genes (designated as HbGF14a to HbGF14j) in the latest rubber tree genome. A phylogenetic tree was constructed and found to demonstrate that HbGF14s can be divided into two major groups. Tissue-specific expression profiles showed that 10 HbGF14 were expressed in at least one of the tissues, which suggested that HbGF14s participated in numerous cellular processes. The 10 HbGF14s responded to jasmonic acid (JA) and ethylene (ET) treatment, which suggested that these HbGF14s were involved in response to JA and ET signaling. The target of HbGF14c protein was related to small rubber particle protein, a major rubber particle protein that is involved in rubber biosynthesis. These findings suggested that 14-3-3 proteins may be involved in the regulation of natural rubber biosynthesis.

Purification of protein complexes and characterization of protein-protein interactions

In plants and all other multicellular organisms, both the intra- and extracellular environments are filled with dynamic biomolecular interactions that control many biological processes. Most of these interactions are biochemical in nature and often exist between proteins. For instance, many protein-protein interactions assist in sustained cellular homeostasis but also allow for rapid intracellular communication in response to stimuli. Thus, the discovery and validation of protein-protein interactions, and the consequent formation of protein complexes, is an integral and essential component of plant biology research. The ability to efficiently and accurately determine existing protein networks is necessary to further our understanding of plant biology. However, discovering protein networks represents a challenge for both present and future researchers. Here we have outlined several straightforward methods aimed at first discovering protein-protein interactions and then characterizing them utilizing additional approaches. We first describe methods for rate-zonal centrifugation, in vitro binding assays, and co-immunoprecipitation experiments in the context of discovering novel protein-protein interactions. Next, we discuss methods for characterizing and validating these interactions using alternative approaches: yeast two-hybrid, in vitro pull-down assays, and bimolecular fluorescence complementation (BiFC). Obviously each of these methods need not be performed in parallel; rather our goal was to describe several approaches, some of which may be more appropriate for increasingly specialized laboratory environments.

Phosphorylation-related modification at the dimer interface of 14-3-3ω dramatically alters monomer interaction dynamics

14-3-3 proteins are generally believed to function as dimers in a broad range of eukaryotic signaling pathways. The consequences of altering dimer stability are not fully understood. Phosphorylation at Ser58 in the dimer interface of mammalian 14-3-3 isoforms has been reported to destabilise dimers. An equivalent residue, Ser62, is present across most Arabidopsis isoforms but the effects of phosphorylation have not been studied in plants. Here, we assessed the effects of phosphorylation at the dimer interface of Arabidopsis 14-3-3ω. Protein kinase A phosphorylated 14-3-3ω at Ser62 and also at a previously unreported residue, Ser67, resulting in a monomer-sized band on native-PAGE. Phosphorylation at Ser62 alone, or with additional Ser67 phosphorylation, was investigated using phosphomimetic versions of 14-3-3ω. In electrophoretic and chromatographic analyses, these mutants showed mobilities intermediate between dimers and monomers. Mobility was increased by detergents, by reducing protein concentration, or by increasing pH or temperature. Urea gradient gels showed complex structural transitions associated with alterations of dimer stability, including a previously unreported 14-3-3 aggregation phenomenon. Overall, our analyses showed that dimer interface modifications such as phosphorylation reduce dimer stability, dramatically affecting the monomer-dimer equilibrium and denaturation trajectory. These findings may have dramatic implications for 14-3-3 structure and function in vivo.

Plant 14-3-3 proteins as spiders in a web of phosphorylation

Protein phosphorylation is essential for many aspects of plant growth and development. To fully modulate the activity of specific proteins after phosphorylation, interaction with members of the 14-3-3 family is necessary. 14-3-3 Proteins are important for many processes because they "assist" a wide range of target proteins with divergent functions. In this review, we will describe how plant 14-3-3 proteins are as spiders in a web of phosphorylation: they act as sensors for phospho-motifs, they themselves are phosphorylated with unknown consequences and they have kinases as target, where some of these phosphorylate 14-3-3 binding motifs in other proteins. Two specific classes of 14-3-3 targets, protein kinases and transcription factors of the bZIP and basic helix-loop-helix-like families, with important and diverse functions in the plant as a whole will be discussed. An important question to be addressed in the near future is how the interaction with 14-3-3 proteins has diverged, both structurally and functionally, between different members of the same protein family, like the kinases and transcription factors.

Subcellular localization of class II HDAs in Arabidopsis thaliana: nucleocytoplasmic shuttling of HDA15 is driven by light

Class II histone deacetylases in humans and other model organisms undergo nucleocytoplasmic shuttling. This unique functional regulatory mechanism has been well elucidated in eukaryotic organisms except in plant systems. In this study, we have paved the baseline evidence for the cytoplasmic and nuclear localization of Class II HDAs as well as their mRNA expression patterns. RT-PCR analysis on the different vegetative parts and developmental stages reveal that Class II HDAs are ubiquitously expressed in all tissues with minimal developmental specificity. Moreover, stable and transient expression assays using HDA-YFP/GFP fusion constructs indicate cytoplasmic localization of HDA5, HDA8, and HDA14 further suggesting their potential for nuclear transport and deacetylating organellar and cytoplasmic proteins. Organelle markers and stains confirm HDA14 to abound in the mitochondria and chloroplasts while HDA5 localizes in the ER. HDA15, on the other hand, shuttles in and out of the nucleus upon light exposure. In the absence of light, it is exported out of the nucleus where further re-exposition to light treatments signals its nuclear import. Unlike HDA5 which binds with 14-3-3 proteins, HDA15 fails to interact with these chaperones. Instead, HDA15 relies on its own nuclear localization and export signals to navigate its subcellular compartmentalization classifying it as a Class IIb HDA. Our study indicates that nucleocytoplasmic shuttling is indeed a hallmark for all eukaryotic Class II histone deacetylases.

Induction of expression of a 14-3-3 gene in response to copper exposure in the marine alga, Fucus vesiculosus

The macro-alga Fucus vesiculosus has a broad global and estuarine distribution and exhibits exceptional resistance to toxic metals, the molecular basis of which is poorly understood. To address this issue a cDNA library was constructed from an environmental isolate of F. vesiculosus growing in an area with chronic copper pollution. Characterisation of this library led to the identification of a cDNA encoding a protein known to be synthesised in response to toxicity, a full length 14-3-3 exhibiting a 71% identity to human/mouse epsilon isoform, 70-71% identity to yeast BMH1/2 and 95 and 71% identity to the Ectocarpus siliculosus 14-3-3 isoforms 1 and 2 respectively. Preliminary characterisation of the expression profile of the 14-3-3 indicated concentration- and time-dependent inductions on acute exposure of F. vesiculosus of copper (3-30 μg/l). Higher concentrations of copper (≥150 μg/l) did not elicit significant induction of the 14-3-3 gene compared with the control even though levels of both intracellular copper and the expression of a cytosolic metal chaperone, metallothionein, continued to rise. Analysis of gene expression within environmental isolates demonstrated up-regulation of the 14-3-3 gene associated with the known copper pollution gradient. Here we report for the first time, identification of a gene encoding a putative 14-3-3 protein in a multicellular alga and provide preliminary evidence to link the induction of this 14-3-3 gene to copper exposure in this alga. Interestingly, the threshold exposure profile may be associated with a decrease in the organism's ability to control copper influx so that it perceives copper as a toxic response.

Proteomics investigation of endogenous S-nitrosylation in Arabidopsis

S-Nitrosylation emerges as an important protein modification in many processes. However, most data were obtained at the protein level after addition of a NO donor, particularly in plants where information about the cysteines nitrosylated in these proteins is scarce. An adapted work-flow, combining the classical biotin switch method and labeling with isotope-coded affinity tags (ICAT), is proposed. Without addition of NO donor, a total of 53 endogenous nitrosocysteines was identified in Arabidopsis cells, in proteins belonging to all cell territories, including membranes, and covering a large panel of functions. This first repertoire of nitrosothiols in plants enabled also preliminary structural description. Three apolar motifs, not located in close vicinity of cysteines and accounting for half the dataset, were detected and are proposed to complement nitrosylation prediction algorithms, poorly trained with plant data to date. Analysis of changes induced by a brief salt stress showed that NaCl modified the nitrosylation level of a small proportion of endogenously nitrosylated proteins and did not concern all nitrosothiols in these proteins. The possible role of some NO targets in the response to salt stress was discussed.

Identification of testis 14-3-3 binding proteins by tandem affinity purification

The 14-3-3 family of proteins interacts with various cellular phosphoproteins and regulates multiple cell signaling cascades. Identification of 14-3-3 interactors is important to define 14-3-3 functions in various biological pathways. The binding partners of protein 14-3-3 in testis are not known. The main goal of this study was to identify the 14-3-3 interactome in testis to determine the 14-3-3 regulated cellular processes in testis. We used transgenic mice expressing tandem affinity tagged 14-3-3ζ (TAP-14-3-3ζ) driven by the ubiquitin promoter to isolate 14-3-3 binding proteins. The 14-3-3 complexes in testis were isolated using a two-step tandem affinity purification (TAP) followed by identification with liquid chromatography/tandem mass spectrometry (LC-MS/MS). A total of 135 proteins were found to be associated with 14-3-3 in vivo in testis. Comparison of the testis 14-3-3 proteome with known 14-3-3 binding proteins showed that 71 of the proteins identified in this study are novel 14-3-3 interactors. Eight of these novel 14-3-3 interacting proteins are predominantly expressed in testis. The 14-3-3 interactors predominant in testis are: protein phosphatase1γ2 (PP1γ2), spermatogenesis associated 18 (SPATA18), phosphoglycerate kinase-2 (PGK2), testis specific gene A-2 (TSGA-2), dead box polypeptide 4 (DDX4), piwi homolog 1, protein kinase NYD-SP25 and EAN57. The fact that some of these proteins are indispensable for spermatogenesis suggests that their binding to 14-3-3 may be important for their function in germ cell division and maturation. These findings are discussed in context of the putative functions of 14-3-3 in spermatogenesis.

Studying protein-protein affinity and immobilized ligand-protein affinity interactions using MS-based methods

This review discusses the most important current methods employing mass spectrometry (MS) analysis for the study of protein affinity interactions. The methods are discussed in depth with particular reference to MS-based approaches for analyzing protein-protein and protein-immobilized ligand interactions, analyzed either directly or indirectly. First, we introduce MS methods for the study of intact protein complexes in the gas phase. Next, pull-down methods for affinity-based analysis of protein-protein and protein-immobilized ligand interactions are discussed. Presently, this field of research is often called interactomics or interaction proteomics. A slightly different approach that will be discussed, chemical proteomics, allows one to analyze selectivity profiles of ligands for multiple drug targets and off-targets. Additionally, of particular interest is the use of surface plasmon resonance technologies coupled with MS for the study of protein interactions. The review addresses the principle of each of the methods with a focus on recent developments and the applicability to lead compound generation in drug discovery as well as the elucidation of protein interactions involved in cellular processes. The review focuses on the analysis of bioaffinity interactions of proteins with other proteins and with ligands, where the proteins are considered as the bioactives analyzed by MS.

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.

Visualization and biochemical analyses of the emerging mammalian 14-3-3-phosphoproteome

Hundreds of candidate 14-3-3-binding (phospho)proteins have been reported in publications that describe one interaction at a time, as well as high-throughput 14-3-3-affinity and mass spectrometry-based studies. Here, we transcribed these data into a common format, deposited the collated data from low-throughput studies in MINT (http://mint.bio.uniroma2.it/mint), and compared the low- and high-throughput data in VisANT graphs that are easy to analyze and extend. Exploring the graphs prompted questions about technical and biological specificity, which were addressed experimentally, resulting in identification of phosphorylated 14-3-3-binding sites in the mitochondrial import sequence of the iron-sulfur cluster assembly enzyme (ISCU), cytoplasmic domains of the mitochondrial fission factor (MFF), and endoplasmic reticulum-tethered receptor expression-enhancing protein 4 (REEP4), RNA regulator SMAUG2, and cytoskeletal regulatory proteins, namely debrin-like protein (DBNL) and kinesin light chain (KLC) isoforms. Therefore, 14-3-3s undergo physiological interactions with proteins that are destined for diverse subcellular locations. Graphing and validating interactions underpins efforts to use 14-3-3-phosphoproteomics to identify mechanisms and biomarkers for signaling pathways in health and disease.

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.

Quantitative proteomic analysis of the interaction between the endophytic plant-growth-promoting bacterium Gluconacetobacter diazotrophicus and sugarcane

Gluconacetobacter diazotrophicus is a plant-growth-promoting bacterium that colonizes sugarcane. In order to investigate molecular aspects of the G. diazotrophicus-sugarcane interaction, we performed a quantitative mass spectrometry-based proteomic analysis by (15)N metabolic labeling of bacteria, root samples, and co-cultures. Overall, more than 400 proteins were analyzed and 78 were differentially expressed between the plant-bacterium interaction model and control cultures. A comparative analysis of the G. diazotrophicus in interaction with two distinct genotypes of sugarcane, SP70-1143 and Chunee, revealed proteins with fundamental roles in cellular recognition. G. diazotrophicus presented proteins involved in adaptation to atypical conditions and signaling systems during the interaction with both genotypes. However, SP70-1143 and Chunee, sugarcane genotypes with high and low contribution of biological nitrogen fixation, showed divergent responses in contact with G. diazotrophicus. The SP70-1143 genotype overexpressed proteins from signaling cascades and one from a lipid metabolism pathway, whereas Chunee differentially synthesized proteins involved in chromatin remodeling and protein degradation pathways. In addition, we have identified 30 bacterial proteins in the roots of the plant samples; from those, nine were specifically induced by plant signals. This is the first quantitative proteomic analysis of a bacterium-plant interaction, which generated insights into early signaling of the G. diazotrophicus-sugarcane interaction.

Arabidopsis 14-3-3 proteins: fascinating and less fascinating aspects

14-3-3 Dimers are well known to interact with diverse target proteins throughout eukaryotes. Most notably, association of 14-3-3s commonly requires phosphorylation of a serine or threonine residue within a specific sequence motif of the client protein. Studies with a focus on individual target proteins have unequivocally demonstrated 14-3-3s to be the crucial factors modifying the client's activity state upon phosphorylation and, thus, finishing the job initiated by a kinase. In this respect, a recent in-depth analysis of the rice transcription factor FLOWERING LOCUS D1 (OsFD1) revealed 14-3-3s to be essential players in floral induction. Such fascinating discoveries, however, can often be ascribed to the random identification of 14-3-3 as an interaction partner of the favorite protein. In contrast, our understanding of 14-3-3 function in higher organisms is frustratingly limited, mainly due to an overwhelming spectrum of putative targets in combination with the existence of a multigene 14-3-3 family. In this review we will discuss our current understanding of the function of plant 14-3-3 proteins, taking into account recent surveys of the Arabidopsis 14-3-3 interactome.

14-3-3 proteins fine-tune plant nutrient metabolism

14-3-3 Proteins regulate many cellular processes by binding to phosphorylated proteins. Previous findings suggest a connection between three 14-3-3 isoforms and plant nutrient signaling. To better understand how these 14-3-3s regulate metabolism in response to changes in plant nutrient status, putative new targets involved in nitrogen (N) and sulfur (S) metabolisms have been identified. The interactions between these 14-3-3s and multiple proteins involved in N and S metabolism and altered activity of the target proteins were confirmed in planta. Using a combination of methods, this work elucidates how 14-3-3s function as modulators of plant N and S metabolic pathways.

Towards proteome scale antibody selections using phage display

In vitro antibody generation by panning a large universal gene library with phage display was employed to generate antibodies to more than 60 different antigens. Of particular interest was a comparison of pannings on 20 different SH2 domains provided by the Structural Genomics Consortium (SGC). Streamlined methods for high throughput antibody generation developed within the 'Antibody Factory' of the German National Genome Research Network (NGFN) were demonstrated to minimise effort and provide a reliable and robust source for antibodies. For the SH2 domains, in two successive series of selections, 2668 clones were analysed, resulting in 347 primary hits in ELISA. Half of these hits were further analysed, and more than 90 different scFv antibodies to all antigens were identified. The validation of selected antibodies by cross-reactivity ELISA, western blot and on protein microarrays demonstrated the versatility of the in vitro antibody selection pipeline to generate a renewable resource of highly specific monoclonal binders in proteome scale numbers with substantially reduced effort and time.