Protein Farnesylation Takes Part in Arabidopsis Seed Development.

Protein farnesylation is a post-translational modification regulated by the ERA1 (Enhanced Response to ABA 1) gene encoding the ß-subunit of the protein farnesyltransferase in Arabidopsis. The era1 mutants have been described for over two decades and exhibit severe pleiotropic phenotypes, affecting vegetative and flower development. We further investigated the development and quality of era1 seeds. While the era1 ovary contains numerous ovules, the plant produces fewer seeds but larger and heavier, with higher protein contents and a modified fatty acid distribution. Furthermore, era1 pollen grains show lower germination rates and, at flower opening, the pistils are immature and the ovules require one additional day to complete the embryo sac. Hand pollinated flowers confirmed that pollination is a major obstacle to era1 seed phenotypes, and a near wild-type seed morphology was thus restored. Still, era1 seeds conserved peculiar storage protein contents and altered fatty acid distributions. The multiplicity of era1 phenotypes reflects the diversity of proteins targeted by the farnesyltransferase. Our work highlights the involvement of protein farnesylation in seed development and in the control of traits of agronomic interest.

Novel Cytonuclear Combinations Modify Arabidopsis thaliana Seed Physiology and Vigor.

Dormancy and germination vigor are complex traits of primary importance for adaptation and agriculture. Intraspecific variation in cytoplasmic genomes and cytonuclear interactions were previously reported to affect germination in Arabidopsis using novel cytonuclear combinations that disrupt co-adaptation between natural variants of nuclear and cytoplasmic genomes. However, specific aspects of dormancy and germination vigor were not thoroughly explored, nor the parental contributions to the genetic effects. Here, we specifically assessed dormancy, germination performance and longevity of seeds from Arabidopsis plants with natural and new genomic compositions. All three traits were modified by cytonuclear reshuffling. Both depth and release rate of dormancy could be modified by a changing of cytoplasm. Significant changes on dormancy and germination performance due to specific cytonuclear interacting combinations mainly occurred in opposite directions, consistent with the idea that a single physiological consequence of the new genetic combination affected both traits oppositely. However, this was not always the case. Interestingly, the ability of parental accessions to contribute to significant cytonuclear interactions modifying the germination phenotype was different depending on whether they provided the nuclear or cytoplasmic genetic compartment. The observed deleterious effects of novel cytonuclear combinations (in comparison with the nuclear parent) were consistent with a contribution of cytonuclear interactions to germination adaptive phenotypes. More surprisingly, we also observed favorable effects of novel cytonuclear combinations, suggesting suboptimal genetic combinations exist in natural populations for these traits. Reduced sensitivity to exogenous ABA and faster endogenous ABA decay during germination were observed in a novel cytonuclear combination that also exhibited enhanced longevity and better germination performance, compared to its natural nuclear parent. Taken together, our results strongly support that cytoplasmic genomes represent an additional resource of natural variation for breeding seed vigor traits.

Combined Proteomic and Metabolomic Profiling of the Arabidopsis thaliana vps29 Mutant Reveals Pleiotropic Functions of the Retromer in Seed Development.

The retromer is a multiprotein complex conserved from yeast to humans, which is involved in intracellular protein trafficking and protein recycling. Selection of cargo proteins transported by the retromer depends on the core retromer subunit composed of the three vacuolar protein sorting (VPS) proteins, namely VPS26, VPS29, and VPS35. To gain a better knowledge of the importance of the plant retromer in protein sorting, we carried out a comparative proteomic and metabolomic analysis of Arabidopsis thaliana seeds from the wild-type and the null-retromer mutant vps29. Here, we report that the retromer mutant displays major alterations in the maturation of seed storage proteins and synthesis of lipid reserves, which are accompanied by severely impaired seed vigor and longevity. We also show that the lack of retromer components is counterbalanced by an increase in proteins involved in intracellular trafficking, notably members of the Ras-related proteins in brain (RAB) family proteins. Our study suggests that loss of the retromer stimulates energy metabolism, affects many metabolic pathways, including that of cell wall biogenesis, and triggers an osmotic stress response, underlining the importance of retromer function in seed biology.

An Integrated "Multi-Omics" Comparison of Embryo and Endosperm Tissue-Specific Features and Their Impact on Rice Seed Quality.

Although rice is a key crop species, few studies have addressed both rice seed physiological and nutritional quality, especially at the tissue level. In this study, an exhaustive "multi-omics" dataset on the mature rice seed was obtained by combining transcriptomics, label-free shotgun proteomics and metabolomics from embryo and endosperm, independently. These high-throughput analyses provide a new insight on the tissue-specificity related to rice seed quality. Foremost, we pinpointed that extensive post-transcriptional regulations occur at the end of rice seed development such that the embryo proteome becomes much more diversified than the endosperm proteome. Secondly, we observed that survival in the dry state in each seed compartment depends on contrasted metabolic and enzymatic apparatus in the embryo and the endosperm, respectively. Thirdly, it was remarkable to identify two different sets of starch biosynthesis enzymes as well as seed storage proteins (glutelins) in both embryo and endosperm consistently with the supernumerary embryo hypothesis origin of the endosperm. The presence of a putative new glutelin with a possible embryonic favored abundance is described here for the first time. Finally, we quantified the rate of mRNA translation into proteins. Consistently, the embryonic panel of protein translation initiation factors is much more diverse than that of the endosperm. This work emphasizes the value of tissue-specificity-centered "multi-omics" study in the seed to highlight new features even from well-characterized pathways. It paves the way for future studies of critical genetic determinants of rice seed physiological and nutritional 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.

Compartmentation and dynamics of flavone metabolism in dry and germinated rice seeds.

Among secondary metabolites, flavonoids are particularly important for the plant life cycle and could be beneficial for human health. The study of Arabidopsis thaliana transparent testa mutants showed that seed flavonoids are important for environmental adaptation, reactive oxygen species homeostasis, dormancy and longevity. Compared with Arabidopsis and maize (Zea mays L.), far less research has been conducted on rice (Oryza sativa L.) particularly for cultivars with non-pigmented seeds. In this study, we describe the localization, nature and relative abundance of flavonoids in mature and germinated non-pigmented Nipponbare seeds using a combination of confocal microscopy, mass spectrometry and gene expression analysis. The mature seed exclusively accumulates flavones mostly in the embryo and to a lesser extent in the pericarp/testa. Due to the variety of flavone conjugation patterns, 21 different flavones were identified, including sulfated flavones never mentioned before in cereals. Schaftoside (apigenin-6-C-glucoside-8-C-arabinoside) and its two isomers represent nearly 50% of all rice seed flavones and are the only flavonoids accumulated in the pericarp/testa seed compartment. These 21 conjugated flavones showed a very stable profile during rice seed germination sensu stricto, while expression of key flavone synthesis genes strongly increases before the completion of germination. We discuss the potential roles of these rice seed flavones in a seed biology context.

Nitric oxide implication in the control of seed dormancy and germination.

Germination ability is regulated by a combination of environmental and endogenous signals with both synergistic and antagonistic effects. Nitric oxide (NO) is a potent dormancy-releasing agent in many species, including Arabidopsis, and has been suggested to behave as an endogenous regulator of this physiological blockage. Distinct reports have also highlighted a positive impact of NO on seed germination under sub-optimal conditions. However, its molecular mode of action in the context of seed biology remains poorly documented. This review aims to focus on the implications of this radical in the control of seed dormancy and germination. The consequences of NO chemistry on the investigations on both its signaling and its targets in seeds are discussed. NO-dependent protein post-translational modifications are proposed as a key mechanism underlying NO signaling during early seed germination.

Cold stratification and exogenous nitrates entail similar functional proteome adjustments during Arabidopsis seed dormancy release.

Despite having very similar initial pools of stored mRNAs and proteins in the dry state, mature Arabidopsis seeds can either proceed toward radicle protrusion or stay in a dormant state upon imbibition. Dormancy breaking, a prerequisite to germination completion, can be induced by different treatments though the underlying mechanisms remain elusive. Thus, we investigated the consequence of such treatments on the seed proteome. Two unrelated dormancy-releasing treatments were applied to dormant seeds, namely, cold stratification and exogenous nitrates, in combination with differential proteomic tools to highlight the specificities of the imbibed dormant state. The results reveal that both treatments lead to highly similar proteome adjustments. In the imbibed dormant state, enzymes involved in reserve mobilization are less accumulated and it appears that several energetically costly processes associated to seed germination and preparation for subsequent seedling establishment are repressed. Our data suggest that dormancy maintenance is associated to an abscisic-acid-dependent recapitulation of the late maturation program resulting in a higher potential to cope with environmental stresses. The comparison of the present results with previously published -omic data sets reinforces and extends the assumption that post-transcriptional, translational, and post-translational regulations are determinant for seed germination.

Proteomics and posttranslational proteomics of seed dormancy and germination.

The seed is the dispersal unit of plants and must survive the vagaries of the environment. It is the object of intense genetic and genomic studies because processes related to seed quality affect crop yield and the seed itself provides food for humans and animals. Presently, the general aim of postgenomics analyses is to understand the complex biochemical and molecular processes underlying seed quality, longevity, dormancy, and vigor. Due to advances in functional genomics, the recent past years have seen a tremendous progress in our understanding of several aspects of seed development and germination. Here, we describe the proteomics protocols (from protein extraction to mass spectrometry) that can be used to investigate several aspects of seed physiology, including germination and its hormonal regulation, dormancy release, and seed longevity. These techniques can be applied to the study of both model plants (such as Arabidopsis) and crops.

Protein damage and repair controlling seed vigor and longevity.

The formation of abnormal isoaspartyl residues derived from aspartyl or asparaginyl residues is a major source of spontaneous protein misfolding in cells. The repair enzyme protein L: -isoaspartyl methyltransferase (PIMT) counteracts such damage by catalyzing the conversion of abnormal isoaspartyl residues to their normal aspartyl forms. Thus, this enzyme contributes to the survival of many organisms, including plants. Analysis of the accumulation of isoaspartyl-containing proteins and its modulation by the PIMT repair pathway, using germination tests, immunodetection, enzymatic assays, and HPLC analysis, gives new insights in understanding controlling mechanisms of seed longevity and vigor.

Reboot the system thanks to protein post-translational modifications and proteome diversity: How quiescent seeds restart their metabolism to prepare seedling establishment.

Once liberated in their environment, orthodox seeds live in a quiescent dehydrated state not totally exempt of essential molecular events as, for example, the capacity of breaking dormancy during after-ripening. Upon imbibition, if internal regulatory padlocks are released and given adequate external conditions, the quiescent seed is able to "reboot" its system and, thus, germinate. Recent studies unraveled the crucial importance of protein PTMs in seed dormancy, longevity and vigor. As compared to other plant developmental stages, the seed proteome appears quite unique and diverse. Seed proteins encompass several functional classes from primary and secondary metabolism to structural and antimicrobial defense. In the dry state, oxidative damages can occur due to reactive oxygen and nitrogen species produced by non-enzymatic reactions. These reactive species can affect proteins by the oxidation of their amino acids in a post-translational manner. The hormone abscisic acid regulates major aspects of seed life including dormancy and germination. This signaling pathway has been shown to rely on several PTMs such as protein phosphorylation or ubiquitination.

[Seed aging and survival mechanisms]. / Vieillissement des semences et mécanismes de survie.

Aging and death are universal to living systems. In temperate climate latitudes the mature seeds of higher plants are exposed to aging and have developed resistance mechanisms allowing survival and plant propagation. In addition to the physicochemical properties of the seed that confer stress resistance, the protein metabolism contributes importantly to longevity mechanisms. Recently, genetic studies have demonstrated the occurrence of the Protein L-isoaspartyl methyltransferase repair enzyme in controlling age-related protein damages and seed survival. These protective mechanisms by protein repair are widespread in all kingdoms, so that the use of seeds as models to study these controlling processes offers the prospect of understanding longevity mechanisms better.

Protein repair L-isoaspartyl methyltransferase 1 is involved in both seed longevity and germination vigor in Arabidopsis.

The formation of abnormal amino acid residues is a major source of spontaneous age-related protein damage in cells. The protein l-isoaspartyl methyltransferase (PIMT) combats protein misfolding resulting from l-isoaspartyl formation by catalyzing the conversion of abnormal l-isoaspartyl residues to their normal l-aspartyl forms. In this way, the PIMT repair enzyme system contributes to longevity and survival in bacterial and animal kingdoms. Despite the discovery of PIMT activity in plants two decades ago, the role of this enzyme during plant stress adaptation and in seed longevity remains undefined. In this work, we have isolated Arabidopsis thaliana lines exhibiting altered expression of PIMT1, one of the two genes encoding the PIMT enzyme in Arabidopsis. PIMT1 overaccumulation reduced the accumulation of l-isoaspartyl residues in seed proteins and increased both seed longevity and germination vigor. Conversely, reduced PIMT1 accumulation was associated with an increase in the accumulation of l-isoaspartyl residues in the proteome of freshly harvested dry mature seeds, thus leading to heightened sensitivity to aging treatments and loss of seed vigor under stressful germination conditions. These data implicate PIMT1 as a major endogenous factor that limits abnormal l-isoaspartyl accumulation in seed proteins, thereby improving seed traits such as longevity and vigor. The PIMT repair pathway likely works in concert with other anti-aging pathways to actively eliminate deleterious protein products, thus enabling successful seedling establishment and strengthening plant proliferation in natural environments.

Rate and mechanism of the reaction of alkenes with aryl palladium complexes ligated by a bidentate P,P ligand in Heck reactions.

The regioselectivity of the Heck reaction is supposed to be highly affected by the electronic properties of the alkene and the ionic or neutral character of the aryl palladium(II) complexes involved in the reaction with alkenes. In Heck reactions performed in dmf, [Pd(dppp){dppp(O)}Ph](+) (dppp=1,2-bis(diphenylphosphino)propane) is generated in the oxidative addition of PhI with [Pd(0)(dppp)(OAc)](-) formed in situ from Pd(OAc)(2) associated to two equivalents of dppp. [Pd(dppp){dppp(O)}Ph](+) is not very reactive with alkenes (styrene or methyl acrylate); however, it reacts with iodide ions (released in the catalytic reactions) to give [Pd(dppp)IPh] and with acetate ions (used as base) to give [Pd(dppp)(OAc)Ph]. [Pd(dppp)(OAc)Ph] reacts with styrene and methyl acrylate exclusively by an ionic mechanism, that is, via the cationic complex [Pd(dppp)(dmf)Ph](+) formed by dissociation of the acetate ion. The reaction of [Pd(dppp)IPh] is more complex and substrate dependent. It reacts with styrene exclusively by the ionic mechanism via [Pd(dppp)(dmf)Ph](+). [Pd(dppp)IPh] (neutral mechanism) and [Pd(dppp)(dmf)Ph](+) (ionic mechanism) react in parallel with methyl acrylate. [Pd(dppp)(dmf)Ph](+) is more reactive than [Pd(dppp)IPh] but is always generated at lower concentration.

Coordination chemistry of the hexavacant tungstophosphate [H2P(2W12O48]12-: synthesis and characterization of iron(III) complexes derived from the unprecedented {P2W14O54} fragment.

Clusters which display the rare cubic Fe8 topology have been obtained by reaction of the metastable hexavacant polyoxotungstate [H2P2W12O48]12- with basic trinuclear metal acetates.

Gene expression analysis by cDNA-AFLP highlights a set of new signaling networks and translational control during seed dormancy breaking in Nicotiana plumbaginifolia.

Seed dormancy in Nicotiana plumbaginifolia is characterized by an abscisic acid accumulation linked to a pronounced germination delay. Dormancy can be released by 1 year after-ripening treatment. Using a cDNA-amplified fragment length polymorphism (cDNA-AFLP) approach we compared the gene expression patterns of dormant and after-ripened seeds, air-dry or during one day imbibition and analyzed 15,000 cDNA fragments. Among them 1020 were found to be differentially regulated by dormancy. Of 412 sequenced cDNA fragments, 83 were assigned to a known function by search similarities to public databases. The functional categories of the identified dormancy maintenance and breaking responsive genes, give evidence that after-ripening turns in the air-dry seed to a new developmental program that modulates, at the RNA level, components of translational control, signaling networks, transcriptional control and regulated proteolysis.

Maternal synthesis of abscisic acid controls seed development and yield in Nicotiana plumbaginifolia.

The role of maternally derived abscisic acid (ABA) during seed development has been studied using ABA-deficient mutants of Nicotiana plumbaginifolia Viviani. ABA deficiency induced seed abortion, resulting in reduced seed yield, and delayed growth of the remaining embryos. Mutant grafting onto wild-type stocks and reciprocal crosses indicated that maternal ABA, synthesized in maternal vegetative tissues and translocated to the seed, promoted early seed development and growth. Moreover ABA deficiency delayed both seed coat pigmentation and capsule dehiscence. Mutant grafting did not restore these phenotypes, indicating that ABA synthesized in the seed coat and capsule envelope may have a positive effect on capsule and testa maturation. Together these results shed light on the positive role of maternal ABA during N. plumbaginifolia seed development.