Recent progress in molecular genetics and omics-driven research in seed biology.

Elucidating the mechanisms that control seed development, metabolism, and physiology is a fundamental issue in biology. Michel Caboche had long been a catalyst for seed biology research in France up until his untimely passing away last year. To honour his memory, we have updated a review written under his coordination in 2010 entitled "Arabidopsis seed secrets unravelled after a decade of genetic and omics-driven research". This review encompassed different molecular aspects of seed development, reserve accumulation, dormancy and germination, that are studied in the lab created by M. Caboche. We have extended the scope of this review to highlight original experimental approaches implemented in the field over the past decade such as omics approaches aimed at investigating the control of gene expression, protein modifications, primary and specialized metabolites at the tissue or even cellular level, as well as seed biodiversity and the impact of the environment on seed quality.

L'élucidation des mécanismes qui contrôlent le développement, le métabolisme et la physiologie des graines est une question fondamentale en biologie. Michel Caboche a longtemps été un catalyseur de la recherche en biologie des graines en France jusqu'à son décès prématuré l'année dernière. Pour honorer sa mémoire, nous avons mis à jour une revue écrite sous sa coordination en 2010 intitulée « Arabidopsis seed secrets unravelled after a decade of genetic and omics-driven research ¼. Cette revue englobait différents aspects moléculaires du développement des graines, de l'accumulation des réserves, de la dormance et de la germination, qui sont étudiés dans le laboratoire créé par M. Caboche. Nous avons étendu la portée de cette revue pour mettre en évidence des approches expérimentales originales mises en œuvre dans le domaine au cours de la dernière décennie, telles que les approches omiques visant à étudier le contrôle de l'expression des gènes, les modifications des protéines, les métabolites primaires et spécialisés au niveau des tissus ou même des cellules, tout en tenant compte de la biodiversité des graines et de l'impact de l'environnement sur leur qualité.

Are Methionine Sulfoxide-Containing Proteins Related to Seed Longevity? A Case Study of Arabidopsisthaliana Dry Mature Seeds Using Cyanogen Bromide Attack and Two-Dimensional-Diagonal Electrophoresis.

In recent years, several reports pointed out the role of protein oxidation in seed longevity, notably regarding the oxidation of methionine (Met) residues to methionine sulfoxide (MetO) in proteins. To further consider this question, we present a handy proteomic method based on the use of two-dimensional diagonal electrophoresis (2Dd) and cyanogen bromide (CNBr) cleavage, which we refer to as 2Dd-CNBr. CNBr treatment of proteins causes the non-enzymatic hydrolysis of peptide bonds on the carboxyl side of reduced Met residues. However, Met oxidation causes a lack of cleavage, thus modifying the electrophoretic mobility of CNBr-induced peptides. This approach was first validated using bovine serum albumin as a model protein, which confirmed the possibility of distinguishing between oxidized and non-oxidized forms of Met-containing peptides in gels. Then, the 2Dd-CNBr method was applied to the Arabidopsis thaliana seed protein extract in a control (non-oxidized) condition and in an oxidized one (as obtained following hypochlorous acid treatment). Twenty-four oxidized Met residues in 19 proteins identified by mass spectrometry were found to be surface exposed in these proteins. In the three-dimensional environment of the oxidized Met, we detected amino acid residues that could be converted by oxidation (carbonylation) or by phosphorylation, suggesting a possible interplay between Met oxidation and the other protein modifications. The identification of the proteins oxidatively modified in Met residues revealed the finding that MetO-containing proteins are related to seed longevity. Based on these results, we suggest that the method presently described also has the potential for wider applications.

ScreenSeed as a novel high throughput seed germination phenotyping method.

A high throughput phenotyping tool for seed germination, the ScreenSeed technology, was developed with the aim of screening genotype responsiveness and chemical drugs. This technology was presently used with Arabidopsis thaliana seeds to allow characterizing seed samples germination behavior by incubating seeds in 96-well microplates under defined conditions and detecting radicle protrusion through the seed coat by automated image analysis. This study shows that this technology provides a fast procedure allowing to handle thousands of seeds without compromising repeatability or accuracy of the germination measurements. Potential biases of the experimental protocol were assessed through statistical analyses of germination kinetics. Comparison of the ScreenSeed procedure with commonly used germination tests based upon visual scoring displayed very similar germination kinetics.

Systems-Based Approaches to Unravel Networks and Individual Elements Involved in Apple Superficial Scald.

Superficial scald is a major physiological disorder in apple fruit that is induced by cold storage and is mainly expressed as brown necrotic patches on peel tissue. However, a global view of the gene-protein-metabolite interactome underlying scald prevention/sensitivity is currently missing. Herein, we have found for the first time that cold storage in an atmosphere enriched with ozone (O3) induced scald symptoms in 'Granny Smith' apple fruits during subsequent ripening at room temperature. In contrast, treatment with the ethylene perception inhibitor 1-methylcyclopropene (1-MCP) reversed this O3-induced scald effect. Amino acids, including branched-chain amino acids, were the most strongly induced metabolites in peel tissue of 1-MCP treated fruits. Proteins involved in oxidative stress and protein trafficking were differentially accumulated prior to and during scald development. Genes involved in photosynthesis, flavonoid biosynthesis and ethylene signaling displayed significant alterations in response to 1-MCP and O3. Analysis of regulatory module networks identified putative transcription factors (TFs) that could be involved in scald. Subsequently, a transcriptional network of the genes-proteins-metabolites and the connected TFs was constructed. This approach enabled identification of several genes coregulated by TFs, notably encoding glutathione S-transferase (GST) protein(s) with distinct signatures following 1-MCP and O3 treatments. Overall, this study is an important contribution to future functional studies and breeding programs for this fruit, aiding to the development of improved apple cultivars to superficial scald.

The Multiple Facets of Plant-Fungal Interactions Revealed Through Plant and Fungal Secretomics.

The plant secretome is usually considered in the frame of proteomics, aiming at characterizing extracellular proteins, their biological roles and the mechanisms accounting for their secretion in the extracellular space. In this review, we aim to highlight recent results pertaining to secretion through the conventional and unconventional protein secretion pathways notably those involving plant exosomes or extracellular vesicles. Furthermore, plants are well known to actively secrete a large array of different molecules from polymers (e.g. extracellular RNA and DNA) to small compounds (e.g. ATP, phytochemicals, secondary metabolites, phytohormones). All of these play pivotal roles in plant-fungi (or oomycetes) interactions, both for beneficial (mycorrhizal fungi) and deleterious outcomes (pathogens) for the plant. For instance, recent work reveals that such secretion of small molecules by roots is of paramount importance to sculpt the rhizospheric microbiota. Our aim in this review is to extend the definition of the plant and fungal secretomes to a broader sense to better understand the functioning of the plant/microorganisms holobiont. Fundamental perspectives will be brought to light along with the novel tools that should support establishing an environment-friendly and sustainable agriculture.

Patterns of protein carbonylation during Medicago truncatula seed maturation.

Seeds mainly acquire their physiological quality during maturation, whereas oxidative conditions reign within cells triggering protein carbonylation. To better understand the role of this protein modification in legume seeds, we compared by proteomics patterns of carbonylated proteins in maturing seeds of Medicago truncatula naturally desiccated or prematurely dried, a treatment known to impair seed quality acquisition. In both cases, protein carbonylation increased in these seeds, accompanying water removal. We identified several proteins whose extent of carbonylation varied when comparing natural desiccation and premature drying and that could therefore be responsible for the impairment of seed quality acquisition or expression. In particular, we focused on PM34, a protein specific to seeds exhibiting a high sensitivity to carbonylation and of which function in dicotyledons was not known before. PM34 proved to have a cellulase activity presumably associated with cell elongation, a process required for germination and subsequent seedling growth. We discuss the possibility that PM34 (abundance or redox state) could be used to assess crop seed quality.

A Combination of Histological, Physiological, and Proteomic Approaches Shed Light on Seed Desiccation Tolerance of the Basal Angiosperm Amborella trichopoda.

Desiccation tolerance allows plant seeds to remain viable in a dry state for years and even centuries. To reveal potential evolutionary processes of this trait, we have conducted a shotgun proteomic analysis of isolated embryo and endosperm from mature seeds of Amborella trichopoda, an understory shrub endemic to New Caledonia that is considered to be the basal extant angiosperm. The present analysis led to the characterization of 415 and 69 proteins from the isolated embryo and endosperm tissues, respectively. The role of these proteins is discussed in terms of protein evolution and physiological properties of the rudimentary, underdeveloped, Amborella embryos, notably considering that the acquisition of desiccation tolerance corresponds to the final developmental stage of mature seeds possessing large embryos.

Citrus Plants: A Model System for Unlocking the Secrets of NO and ROS-Inspired Priming Against Salinity and Drought.

Plants treated with chemical compounds can develop an enhanced capacity to resist long after being subjected to (a)biotic stress, a phenomenon known as priming. Evidence suggests that reactive oxygen species (ROS) and reactive nitrogen species (RNS) coordinately regulate plant stress responses to adverse environmental conditions; however, the mechanisms underlying this function remain unknown. Based on the observation that pre-exposure of citrus (Citrus aurantium L.) roots to the NO donor sodium nitroprusside (SNP) or to H2O2 prior to NaCl application can induce acclimation against subsequent stress we characterized the changes occurring in primed citrus tissues using several approaches. Herein, using this experimental model system, we provide an overview of our current knowledge of the possible mechanisms associated with NO and H2O2 priming to abiotic stresses, particularly concerning salinity and drought. The data and ideas presented here introduce six aspects of priming behavior in citrus under abiotic stress that provide knowledge necessary to exploit priming syndrome in the context of sustainable agriculture.

Beyond plant defense: insights on the potential of salicylic and methylsalicylic acid to contain growth of the phytopathogen Botrytis cinerea.

Using Botrytis cinerea we confirmed in the present work several previous studies showing that salicylic acid, a main plant hormone, inhibits fungal growth in vitro. Such an inhibitory effect was also observed for the two salicylic acid derivatives, methylsalicylic and acetylsalicylic acid. In marked contrast, 5-sulfosalicylic acid was totally inactive. Comparative proteomics from treated vs. control mycelia showed that both the intracellular and extracellular proteomes were affected in the presence of salicylic acid or methylsalicylic acid. These data suggest several mechanisms that could potentially account for the observed fungal growth inhibition, notably pH regulation, metal homeostasis, mitochondrial respiration, ROS accumulation and cell wall remodeling. The present observations support a role played by the phytohormone SA and derivatives in directly containing the pathogen. Data are available via ProteomeXchange with identifier PXD002873.

The Amborella vacuolar processing enzyme family.

Most vacuolar proteins are synthesized on rough endoplasmic reticulum as proprotein precursors and then transported to the vacuoles, where they are converted into their respective mature forms by vacuolar processing enzymes (VPEs). In the case of the seed storage proteins, this process is of major importance, as it conditions the establishment of vigorous seedlings. Toward the goal of identifying proteome signatures that could be associated with the origin and early diversification of angiosperms, we previously characterized the 11S-legumin-type seed storage proteins from Amborella trichopoda, a rainforest shrub endemic to New Caledonia that is also the probable sister to all other angiosperms (Amborella Genome Project, 2013). In the present study, proteomic and genomic approaches were used to characterize the VPE family in this species. Three genes were found to encode VPEs in the Amborella's genome. Phylogenetic analyses showed that the Amborella sequences grouped within two major clades of angiosperm VPEs, indicating that the duplication that generated the ancestors of these clades occurred before the most recent common ancestor of living angiosperms. A further important duplication within the VPE family appears to have occurred in common ancestor of the core eudicots, while many more recent duplications have also occurred in specific taxa, including both Arabidopsis thaliana and Amborella. An analysis of natural genetic variation for each of the three Amborella VPE genes revealed the absence of selective forces acting on intronic and exonic single-nucleotide polymorphisms among several natural Amborella populations in New Caledonia.

INPPO2014, First INPPO World Congress on "Plant Proteomics: Methodology to Biology"-A global platform for involving, gathering and disseminating knowledge.

The International Plant Proteomics Organization (INPPO) is a global platform of the plant proteomics community or, more generally, the scientific community that uses proteomics to address plant biology. Organizing an international conference is one of its initiatives to promote plant proteomics by involving and gathering scientists/researchers/students and by disseminating the acquired knowledge. In this fourth INPPO Highlights, the first INPPO World Congress 2014 (INPPO2014) is described and discussed. The INPPO2014 was held at the University of Hamburg (Germany) with the title "Plant Proteomics: Methodology to Biology" under the leadership of Sabine Lüthje (Germany). Participants (around 150) from 38 nations attended this congress covering all continents. The four-day scientific program comprised 52 lectures and 61 poster presentations in a highly professional and friendly atmosphere on mass spectrometry and gel-based proteomics. Two round-table open discussions deliberated on plant proteomics, its associated international organizations/initiatives and future INPPO perspectives. The Second INPPO World Congress 2016 (INPPO2016) "The Quest for Tolerant Varieties-Phenotyping at Plant and Cellular Level" is planned to be organized in Bratislava (Slovakia) under the leadership of Martin Hajduch (Slovak Republic) and Sébastien Carpentier (Belgium) and cosponsored by the COST action FA1306.

Dynamic proteomics emphasizes the importance of selective mRNA translation and protein turnover during Arabidopsis seed germination.

During seed germination, the transition from a quiescent metabolic state in a dry mature seed to a proliferative metabolic state in a vigorous seedling is crucial for plant propagation as well as for optimizing crop yield. This work provides a detailed description of the dynamics of protein synthesis during the time course of germination, demonstrating that mRNA translation is both sequential and selective during this process. The complete inhibition of the germination process in the presence of the translation inhibitor cycloheximide established that mRNA translation is critical for Arabidopsis seed germination. However, the dynamics of protein turnover and the selectivity of protein synthesis (mRNA translation) during Arabidopsis seed germination have not been addressed yet. Based on our detailed knowledge of the Arabidopsis seed proteome, we have deepened our understanding of seed mRNA translation during germination by combining two-dimensional gel-based proteomics with dynamic radiolabeled proteomics using a radiolabeled amino acid precursor, namely [(35)S]-methionine, in order to highlight de novo protein synthesis, stability, and turnover. Our data confirm that during early imbibition, the Arabidopsis translatome keeps reflecting an embryonic maturation program until a certain developmental checkpoint. Furthermore, by dividing the seed germination time lapse into discrete time windows, we highlight precise and specific patterns of protein synthesis. These data refine and deepen our knowledge of the three classical phases of seed germination based on seed water uptake during imbibition and reveal that selective mRNA translation is a key feature of seed germination. Beyond the quantitative control of translational activity, both the selectivity of mRNA translation and protein turnover appear as specific regulatory systems, critical for timing the molecular events leading to successful germination and seedling establishment.

Polyamines reprogram oxidative and nitrosative status and the proteome of citrus plants exposed to salinity stress.

The interplay among polyamines (PAs) and reactive oxygen and nitrogen species (RNS and ROS) is emerging as a key issue in plant responses to salinity. To address this question, we analysed the impact of exogenous PAs [putrescine (Put), spermidine (Spd) and spermine (Spm)] on the oxidative and nitrosative status in citrus plants exposed to salinity. PAs partially reversed the NaCl-induced phenotypic and physiological disturbances. The expression of PA biosynthesis (ADC, SAMDC, SPDS and SPMS) and catabolism (DAO and PAO) genes was systematically up-regulated by PAs. In addition, PAs altered the oxidative status in salt-stressed plants as inferred by changes in ROS production and redox status accompanied by regulation of transcript expression and activities of various antioxidant enzymes. Furthermore, NaCl-induced up-regulation of NO-associated genes, such as NR, NADde, NOS-like and AOX, along with S-nitrosoglutathione reductase and nitrate reductase activities, was partially restored by PAs. Protein carbonylation and tyrosine nitration are depressed by specific PAs whereas protein S-nitrosylation was elicited by all PAs. Furthermore, we identified 271 S-nitrosylated proteins that were commonly or preferentially targeted by salinity and individual PAs. This work helps improve our knowledge on the plant's response to environmental challenge.

Role of protein and mRNA oxidation in seed dormancy and germination.

Reactive oxygen species (ROS) are key players in the regulation of seed germination and dormancy. Although their regulated accumulation is a prerequisite for germination, the cellular basis of their action remains unknown, but very challenging to elucidate due to the lack of specificity of these compounds that can potentially react with all biomolecules. Among these, nucleic acids and proteins are very prone to oxidative damage. RNA is highly sensitive to oxidation because of its single-stranded structure and the absence of a repair system. Oxidation of mRNAs induces their decay through processing bodies or results in the synthesis of aberrant proteins through altered translation. Depending on the oxidized amino acid, ROS damage of proteins can be irreversible (i.e., carbonylation) thus triggering the degradation of the oxidized proteins by the cytosolic 20S proteasome or can be reversed through the action of thioredoxins, peroxiredoxins, or glutaredoxins (cysteine oxidation) or by methionine sulfoxide reductase (methionine oxidation). Seed dormancy alleviation in the dry state, referred to as after-ripening, requires both selective mRNA oxidation and protein carbonylation. Similarly, seed imbibition of non-dormant seeds is associated with targeted oxidation of a subset of proteins. Altogether, these specific features testify that such oxidative modifications play important role in commitment of the cellular functioning toward germination completion.

Secretomes: the fungal strike force.

Microorganisms, although being very diverse because they comprise prokaryotic organisms such as bacteria or eukaryotic organisms such as fungi, all share an essential exodigester function. The consequence is their essential need to have a secretome adapted to their environment. The selection pressure exerted by environmental constraints led to the emergence of species with varying complexity in terms of composition of their secretomes. This review on fungal secretomes highlights the extraordinary variability among these organisms, even within the same species, and hence the absolute necessity to fully characterize all their components in the aims of understanding the fundamental mechanisms responsible for secretome plasticity and developing applications notably toward a better control of diseases caused by these pathogens.

A decade of plant proteomics and mass spectrometry: translation of technical advancements to food security and safety issues.

Tremendous progress in plant proteomics driven by mass spectrometry (MS) techniques has been made since 2000 when few proteomics reports were published and plant proteomics was in its infancy. These achievements include the refinement of existing techniques and the search for new techniques to address food security, safety, and health issues. It is projected that in 2050, the world's population will reach 9-12 billion people demanding a food production increase of 34-70% (FAO, 2009) from today's food production. Provision of food in a sustainable and environmentally committed manner for such a demand without threatening natural resources, requires that agricultural production increases significantly and that postharvest handling and food manufacturing systems become more efficient requiring lower energy expenditure, a decrease in postharvest losses, less waste generation and food with longer shelf life. There is also a need to look for alternative protein sources to animal based (i.e., plant based) to be able to fulfill the increase in protein demands by 2050. Thus, plant biology has a critical role to play as a science capable of addressing such challenges. In this review, we discuss proteomics especially MS, as a platform, being utilized in plant biology research for the past 10 years having the potential to expedite the process of understanding plant biology for human benefits. The increasing application of proteomics technologies in food security, analysis, and safety is emphasized in this review. But, we are aware that no unique approach/technology is capable to address the global food issues. Proteomics-generated information/resources must be integrated and correlated with other omics-based approaches, information, and conventional programs to ensure sufficient food and resources for human development now and in the future.

Plant proteomics in India and Nepal: current status and challenges ahead.

Plant proteomics has made tremendous contributions in understanding the complex processes of plant biology. Here, its current status in India and Nepal is discussed. Gel-based proteomics is predominantly utilized on crops and non-crops to analyze majorly abiotic (49 %) and biotic (18 %) stress, development (11 %) and post-translational modifications (7 %). Rice is the most explored system (36 %) with major focus on abiotic mainly dehydration (36 %) stress. In spite of expensive proteomics setup and scarcity of trained workforce, output in form of publications is encouraging. To boost plant proteomics in India and Nepal, researchers have discussed ground level issues among themselves and with the International Plant Proteomics Organization (INPPO) to act in priority on concerns like food security. Active collaboration may help in translating this knowledge to fruitful applications.