Comparative analysis of the heat stable proteome of radicles of Medicago truncatula seeds during germination identifies late embryogenesis abundant proteins associated with desiccation tolerance

Liquid-liquid phase separation in plants: Advances and perspectives from model species to crops

Membraneless biomolecular condensates play important roles in both normal biological activities and responses to environmental stimuli in living organisms. Liquid‒liquid phase separation (LLPS) is an organizational mechanism that has emerged in recent years to explain the formation of biomolecular condensates. In the past decade, advances in LLPS research have contributed to breakthroughs in disease fields. By contrast, although LLPS research in plants has progressed over the past 5 years, it has been concentrated on the model plant Arabidopsis, which has limited relevance to agricultural production. In this review, we provide an overview of recently reported advances in LLPS in plants, with a particular focus on photomorphogenesis, flowering, and abiotic and biotic stress responses. We propose that many potential LLPS proteins also exist in crops and may affect crop growth, development, and stress resistance. This possibility presents a great challenge as well as an opportunity for rigorous scientific research on the biological functions and applications of LLPS in crops.

Identification of the Maize LEA Gene Family and Its Relationship with Kernel Dehydration

Maize, the most widely planted and highest yielding of the three major crops in the world, requires the development and breeding of new varieties to accommodate the shift towards mechanized harvesting. However, the moisture content of kernels during harvest poses a significant challenge to mechanized harvesting, leading to seed breakage and increased storage costs. Previous studies highlighted the importance of LEA (Late Embryogenesis Abundant) members in regulating kernel dehydration. In this study, we aimed to gain a better understanding of the relationship between the LEA family and grain dehydration in maize. Through expression pattern analysis of maize, we identified 52 LEA genes (ZmLEAs) distributed across 10 chromosomes, organized into seven subgroups based on phylogenetic analysis, gene structure, and conserved motifs. Evolutionary and selective pressure analysis revealed that the amplification of ZmLEA genes primarily resulted from whole-genome or fragment replication events, with strong purifying selection effects during evolution. Furthermore, the transcriptome data of kernels of two maize inbred lines with varying dehydration rates at different developmental stages showed that 14 ZmLEA genes were expressed differentially in the two inbreds. This suggested that the ZmLEA genes might participate in regulating the kernel dehydration rate (KDR) in maize. Overall, this study enhances our understanding of the ZmLEA family and provides a foundation for further research into its role in regulating genes associated with grain dehydration in maize.

Chromatin dynamics associated with seed desiccation tolerance/sensitivity at early germination in Medicago truncatula

Desiccation tolerance (DT) has contributed greatly to the adaptation of land plants to severe water-deficient conditions. DT is mostly observed in reproductive parts in flowering plants such as seeds. The seed DT is lost at early post germination stage but is temporally re-inducible in 1 mm radicles during the so-called DT window following a PEG treatment before being permanently silenced in 5 mm radicles of germinating seeds. The molecular mechanisms that activate/reactivate/silence DT in developing and germinating seeds have not yet been elucidated. Here, we analyzed chromatin dynamics related to re-inducibility of DT before and after the DT window at early germination in Medicago truncatula radicles to determine if DT-associated genes were transcriptionally regulated at the chromatin levels. Comparative transcriptome analysis of these radicles identified 948 genes as DT re-induction-related genes, positively correlated with DT re-induction. ATAC-Seq analyses revealed that the chromatin state of genomic regions containing these genes was clearly modulated by PEG treatment and affected by growth stages with opened chromatin in 1 mm radicles with PEG (R1P); intermediate openness in 1 mm radicles without PEG (R1); and condensed chromatin in 5 mm radicles without PEG (R5). In contrast, we also showed that the 103 genes negatively correlated with the re-induction of DT did not show any transcriptional regulation at the chromatin level. Additionally, ChIP-Seq analyses for repressive marks H2AK119ub and H3K27me3 detected a prominent signal of H3K27me3 on the DT re-induction-related gene sequences at R5 but not in R1 and R1P. Moreover, no clear H2AK119ub marks was observed on the DT re-induction-related gene sequences at both developmental radicle stages, suggesting that silencing of DT process after germination will be mainly due to H3K27me3 marks by the action of the PRC2 complex, without involvement of PRC1 complex. The dynamic of chromatin changes associated with H3K27me3 were also confirmed on seed-specific genes encoding potential DT-related proteins such as LEAs, oleosins and transcriptional factors. However, several transcriptional factors did not show a clear link between their decrease of chromatin openness and H3K27me3 levels, suggesting that their accessibility may also be regulated by additional factors, such as other histone modifications. Finally, in order to make these comprehensive genome-wide analyses of transcript and chromatin dynamics useful to the scientific community working on early germination and DT, we generated a dedicated genome browser containing all these data and publicly available at https://iris.angers.inrae.fr/mtseedepiatlas/jbrowse/?data=Mtruncatula.

SK, Sheoran S, K. UB, K. BN, Kumar S, Singh AN, Singh HV. Seed Longevity in Legumes: Deeper Insights Into Mechanisms and Molecular Perspectives

Sustainable agricultural production largely depends upon the viability and longevity of high-quality seeds during storage. Legumes are considered as rich source of dietary protein that helps to ensure nutritional security, but associated with poor seed longevity that hinders their performance and productivity in farmer's fields. Seed longevity is the key determinant to assure proper seed plant value and crop yield. Thus, maintenance of seed longevity during storage is of prime concern and a pre-requisite for enhancing crop productivity of legumes. Seed longevity is significantly correlated with other seed quality parameters such as germination, vigor, viability and seed coat permeability that affect crop growth and development, consequently distressing crop yield. Therefore, information on genetic basis and regulatory networks associated with seed longevity, as well as molecular dissection of traits linked to longevity could help in developing crop varieties with good storability. Keeping this in view, the present review focuses towards highlighting the molecular basis of seed longevity, with special emphasis on candidate genes and proteins associated with seed longevity and their interplay with other quality parameters. Further, an attempt was made to provide information on 3D structures of various genetic loci (genes/proteins) associated to seed longevity that could facilitate in understanding the interactions taking place within the seed at molecular level. This review compiles and provides information on genetic and genomic approaches for the identification of molecular pathways and key players involved in the maintenance of seed longevity in legumes, in a holistic manner. Finally, a hypothetical fast-forward breeding pipeline has been provided, that could assist the breeders to successfully develop varieties with improved seed longevity in legumes.

The heat stable protein fraction from Opuntia ficus indica seeds exhibits an enzyme protective effect against thermal denaturation and an antibacterial activity

Desiccation tolerance in developing seeds occurs through several mechanisms among which, a common group of proteins named dehydrins has received considerable attention. So far, there is no information dealing with the accumulation of dehydrins in seeds of Opuntia ficus-indica. We have initiated here an extraction protocol based on two critical steps: heat and acid treatments, and the purity of this fraction was analyzed by FTIR spectroscopy. Western blot analysis of the heat-stable protein fraction (HSF) revealed two main bands of approximately 45 and 44 kDa, while three others of ∼40, 32, and 31 kDa were faintly visible, which were recognized by anti-dehydrin antibodies. This fraction exhibited a Cu²⁺ -dependent resistance to protease treatments. Next, we performed a series of assays to compare the functional properties of the HSF with those of the previously characterized wheat dehydrin (DHN-5). Antibacterial assays revealed that HSF exhibits only moderate antibacterial activities against gram-negative and gram-positive bacteria, with a minimum inhibition concentration ranging from 0.25 to 1 mg/ml. However, in vitro assays revealed that compared to DHN-5, HSF exhibits higher protective activities of the lactate dehydrogenase (LDH) when exposed to heat, freezing, and dehydration stresses. The protective role of HSF seems to be linked to its best ability to minimize protein aggregation.

Mechanistic insights derived from re-establishment of desiccation tolerance in germinating xerophytic seeds: Caragana korshinskii as an example

Germplasm conservation strongly depends on the desiccation tolerance (DT) of seeds. Xerophytic seeds have strong desiccation resistance, which makes them excellent models to study DT. Although some experimental strategies have been applied previously, most methods are difficult to apply to xerophytic seeds. In this review, we attempted to synthesize current strategies for the study of seed DT and provide an in-depth look at Caragana korshinskii as an example. First, we analyze congenital advantages of xerophytes in the study of seed DT. Second, we summarize several strategies used to study DT and illustrate a suitable strategy for xerophytic species. Then, based on our previous studies work with C. korshinskii, a feasible technical strategy for DT re-establishment is provided and we provide illustrate some special molecular mechanisms seen in xerophytic seeds. Finally, several steps to unveil the DT mechanism of xerophytic seeds are suggested, and three scientific questions that the field should consider are listed. We hope to optimize and utilize this strategy for more xerophytic species to more systematically decipher the physiological and molecular processes of seed DT and provide more candidate genes for molecular breeding.

The Orthodox Dry Seeds Are Alive: A Clear Example of Desiccation Tolerance

To survive in the dry state, orthodox seeds acquire desiccation tolerance. As maturation progresses, the seeds gradually acquire longevity, which is the total timespan during which the dry seeds remain viable. The desiccation-tolerance mechanism(s) allow seeds to remain dry without losing their ability to germinate. This adaptive trait has played a key role in the evolution of land plants. Understanding the mechanisms for seed survival after desiccation is one of the central goals still unsolved. That is, the cellular protection during dry state and cell repair during rewatering involves a not entirely known molecular network(s). Although desiccation tolerance is retained in seeds of higher plants, resurrection plants belonging to different plant lineages keep the ability to survive desiccation in vegetative tissue. Abscisic acid (ABA) is involved in desiccation tolerance through tight control of the synthesis of unstructured late embryogenesis abundant (LEA) proteins, heat shock thermostable proteins (sHSPs), and non-reducing oligosaccharides. During seed maturation, the progressive loss of water induces the formation of a so-called cellular "glass state". This glassy matrix consists of soluble sugars, which immobilize macromolecules offering protection to membranes and proteins. In this way, the secondary structure of proteins in dry viable seeds is very stable and remains preserved. ABA insensitive-3 (ABI3), highly conserved from bryophytes to Angiosperms, is essential for seed maturation and is the only transcription factor (TF) required for the acquisition of desiccation tolerance and its re-induction in germinated seeds. It is noteworthy that chlorophyll breakdown during the last step of seed maturation is controlled by ABI3. This update contains some current results directly related to the physiological, genetic, and molecular mechanisms involved in survival to desiccation in orthodox seeds. In other words, the mechanisms that facilitate that an orthodox dry seed is a living entity.

Subcellular Localization of Seed-Expressed LEA_4 Proteins Reveals Liquid-Liquid Phase Separation for LEA9 and for LEA48 Homo- and LEA42-LEA48 Heterodimers

LEA proteins are involved in plant stress tolerance. In Arabidopsis, the LEA_4 Pfam group is the biggest group with the majority of its members being expressed in dry seeds. To assess subcellular localization in vivo, we investigated 11 seed-expressed LEA_4 proteins in embryos dissected from dry seeds expressing LEA_4 fusion proteins under its native promoters with the Venus fluorescent protein (proLEA_4::LEA_4:Venus). LEA_4 proteins were shown to be localized in the endoplasmic reticulum, nucleus, mitochondria, and plastids. LEA9, in addition to the nucleus, was also found in cytoplasmic condensates in dry seeds dependent on cellular hydration level. Most investigated LEA_4 proteins were detected in 4-d-old seedlings. In addition, we assessed bioinformatic tools for predicting subcellular localization and promoter motifs of 11 seed-expressed LEA_4 proteins. Ratiometric bimolecular fluorescence complementation assays showed that LEA7, LEA29, and LEA48 form homodimers while heterodimers were formed between LEA7-LEA29 and LEA42-LEA48 in tobacco leaves. Interestingly, LEA48 homodimers and LEA42-LEA48 heterodimers formed droplets structures with liquid-like behavior. These structures, along with LEA9 cytoplasmic condensates, may have been formed through liquid-liquid phase separation. These findings suggest possible important roles of LLPS for LEA protein functions.

Characterization of the Heat-Stable Proteome during Seed Germination in Arabidopsis with Special Focus on LEA Proteins

During seed germination, desiccation tolerance is lost in the radicle with progressing radicle protrusion and seedling establishment. This process is accompanied by comprehensive changes in the metabolome and proteome. Germination of Arabidopsis seeds was investigated over 72 h with special focus on the heat-stable proteome including late embryogenesis abundant (LEA) proteins together with changes in primary metabolites. Six metabolites in dry seeds known to be important for seed longevity decreased during germination and seedling establishment, while all other metabolites increased simultaneously with activation of growth and development. Thermo-stable proteins were associated with a multitude of biological processes. In the heat-stable proteome, a relatively similar proportion of fully ordered and fully intrinsically disordered proteins (IDP) was discovered. Highly disordered proteins were found to be associated with functional categories development, protein, RNA and stress. As expected, the majority of LEA proteins decreased during germination and seedling establishment. However, four germination-specific dehydrins were identified, not present in dry seeds. A network analysis of proteins, metabolites and amino acids generated during the course of germination revealed a highly connected LEA protein network.

Proteomic Analysis of Desiccation Tolerance and Its Re-Establishment in Different Embryo Axis Tissues of Germinated Pea Seeds

The model of loss and re-establishment of desiccation tolerance (DT) in germinated seeds has been well developed to explore the mechanisms associated with DT, but little attention has been paid to the tissue variation in this model. Herein, we investigated DT in different embryo axis tissues of germinated pea seeds and its re-establishment by poly(ethylene glycol) (PEG) treatment and then employed an iTRAQ-based proteomic method to explore the underlying mechanisms. DT varied among the four embryo axis parts of germinated seeds: epicotyl > hypocotyl-E (hypocotyl part attached to the epicotyl) > hypocotyl-R (hypocotyl part attached to the radicle) > radicle. Meanwhile, PEG treatment of germinated seeds resulted in a differential extent of DT re-establishment in these tissues. Proteins involved in detoxification and stress response were enriched in desiccation-tolerant hypocotyls-E and epicotyls of germinated seeds, respectively. Upon rehydration, proteome change during dehydration was recovered in the hypocotyls-E but not in the radicles. PEG treatment of germinated seeds led to numerous changes in proteins, in abundance in desiccation-sensitive radicles and hypocotyls-R, of which many accumulated in the hypocotyls-E and epicotyls before the treatment. We hypothesized that accumulation of groups 1 and 5 LEA proteins and proteins related to detoxification, ABA, ethylene, and calcium signaling contributed mainly to the variation of DT in different tissues and its re-establishment.

Stabilization of Dry Sucrose Glasses by Four LEA_4 Proteins from Arabidopsis thaliana

Cells of many organisms and organs can withstand an (almost) total water loss (anhydrobiosis). Sugars play an essential role in desiccation tolerance due to their glass formation ability during dehydration. In addition, intrinsically disordered LEA proteins contribute to cellular survival under such conditions. One possible mechanism of LEA protein function is the stabilization of sugar glasses. However, little is known about the underlying mechanisms. Here we used FTIR spectroscopy to investigate sucrose (Suc) glass stability dried from water or from two buffer components in the presence of four recombinant LEA and globular reference proteins. Buffer ions influenced the strength of the Suc glass in the order Suc < Suc/Tris < Suc/NaP. LEA proteins strengthened the sugar H-bonded network and the molecular structure in the glassy state. The position of νOH peak and the wavenumber–temperature coefficient (WTC_g) provided similar information about the H-bonded network. Protein aggregation of LEA proteins was reduced in the desiccation-induced Suc glassy state. Detailed knowledge about the role of LEA proteins in the stabilization of dry sugar glasses yields information about their role in anhydrobiosis. This may open the possibility to use such proteins in biotechnical applications requiring dry storage of biologicals such as proteins, cells or tissues.

Proteomics reveals commitment to germination in barley seeds is marked by loss of stress response proteins and mobilisation of nutrient reservoirs

Germination is a critical process in the reproduction and propagation of flowering plants, and is also the key stage of industrial grain malting. Germination commences when seeds are steeped in water, followed by degradation of the endosperm cell walls, enzymatic digestion of starch and proteins to provide nutrients for the growing plant, and emergence of the radicle from the seed. Dormancy is a state where seeds fail to germinate upon steeping, but which prevents inappropriate premature germination of the seeds before harvest from the field. This can result in inefficiencies in industrial malting. We used Sequential Window Acquisition of all THeoretical ions Mass Spectrometry (SWATH-MS) proteomics to measure changes in the barley seed proteome throughout germination. We found a large number of proteins involved in desiccation tolerance and germination inhibition rapidly decreased in abundance after imbibition. This was followed by a decrease in proteins involved in lipid, protein and nutrient reservoir storage, consistent with induction and activation of systems for nutrient mobilisation to provide nutrients to the growing embryo. Dormant seeds that failed to germinate showed substantial biochemical activity distinct from that of seeds undergoing germination, with differences in sulfur metabolic enzymes, endogenous alpha-amylase/trypsin inhibitors, and histone proteins. We verified our findings with analysis of germinating barley seeds from two commercial malting facilities, demonstrating that key features of the dynamic proteome of germinating barley seeds were conserved between laboratory and industrial scales. The results provide a more detailed understanding of the changes in the barley proteome during germination and give possible target proteins for testing or to inform selective breeding to enhance germination or control dormancy. SIGNIFICANCE: Germination is critical to the reproduction and propagation of flowering plants, and in industrial malting. Dormancy, where seeds fail to germinate upon steeping, can result in inefficiencies in industrial malting. Our DIA/SWATH-MS proteomics analyses identified key changes during germination, including an initial loss of proteins involved in desiccation tolerance and germination inhibition, followed by decreases in lipid, protein and nutrient reservoir storage. These changes were consistent between laboratory and industrial malting scales, and therefore demonstrate the utility of laboratory-scale barley germination as a model system for industrial malt house processes. We also showed that dormant seeds that failed to germinate showed substantial biochemical activity distinct from that of seeds undergoing germination, consistent with dormancy being an actively regulated state. Our results provide a more detailed understanding of the changes in the barley proteome during germination and give possible target proteins for testing or to inform selective breeding to enhance germination or control dormancy.

Liquid-liquid phase separation promotes animal desiccation tolerance

Proteinaceous liquid-liquid phase separation (LLPS) occurs when a polypeptide coalesces into a dense phase to form a liquid droplet (i.e., condensate) in aqueous solution. In vivo, functional protein-based condensates are often referred to as membraneless organelles (MLOs), which have roles in cellular processes ranging from stress responses to regulation of gene expression. Late embryogenesis abundant (LEA) proteins containing seed maturation protein domains (SMP; PF04927) have been linked to storage tolerance of orthodox seeds. The mechanism by which anhydrobiotic longevity is improved is unknown. Interestingly, the brine shrimp Artemia franciscana is the only animal known to express such a protein (AfrLEA6) in its anhydrobiotic embryos. Ectopic expression of AfrLEA6 (AWM11684) in insect cells improves their desiccation tolerance and a fraction of the protein is sequestered into MLOs, while aqueous AfrLEA6 raises the viscosity of the cytoplasm. LLPS of AfrLEA6 is driven by the SMP domain, while the size of formed MLOs is regulated by a domain predicted to engage in protein binding. AfrLEA6 condensates formed in vitro selectively incorporate target proteins based on their surface charge, while cytoplasmic MLOs formed in AfrLEA6-transfected insect cells behave like stress granules. We suggest that AfrLEA6 promotes desiccation tolerance by engaging in two distinct molecular mechanisms: by raising cytoplasmic viscosity at even modest levels of water loss to promote cell integrity during drying and by forming condensates that may act as protective compartments for desiccation-sensitive proteins. Identifying and understanding the molecular mechanisms that govern anhydrobiosis will lead to significant advancements in preserving biological samples.

A Short Peptide Designed from Late Embryogenesis Abundant Protein Enhances Acid Tolerance in Escherichia coli

Unsuitable pH is a major limiting factor for all organisms, and a low pH can lead to organism death. Late embryogenesis abundant (LEA) peptides confer tolerance to abiotic stresses including salinity, drought, high and low temperature, and ultraviolet radiation same as the LEA proteins from which they originate. In this study, LEA peptides derived from group 3 LEA proteins of Polypedilum vanderplanki were used to enhance low pH tolerance. Recombinant Escherichia coli BL21 (DE3) cells expressing the five designed LEA peptides were grown at pH 4, 3, and 2. The transformants showed higher growth capacity at low pH as compared to control cells. These results indicate that LEA peptide could prevent E. coli cell death under low pH conditions.

Seed comparative genomics in three coffee species identify desiccation tolerance mechanisms in intermediate seeds

In contrast to desiccation-tolerant 'orthodox' seeds, so-called 'intermediate' seeds cannot survive complete drying and are short-lived. All species of the genus Coffea produce intermediate seeds, but they show a considerable variability in seed desiccation tolerance (DT), which may help to decipher the molecular basis of seed DT in plants. We performed a comparative transcriptome analysis of developing seeds in three coffee species with contrasting desiccation tolerance. Seeds of all species shared a major transcriptional switch during late maturation that governs a general slow-down of metabolism. However, numerous key stress-related genes, including those coding for the late embryogenesis abundant protein EM6 and the osmosensitive calcium channel ERD4, were up-regulated during DT acquisition in the two species with high seed DT, C. arabica and C. eugenioides. By contrast, we detected up-regulation of numerous genes involved in the metabolism, transport, and perception of auxin in C. canephora seeds with low DT. Moreover, species with high DT showed a stronger down-regulation of the mitochondrial machinery dedicated to the tricarboxylic acid cycle and oxidative phosphorylation. Accordingly, respiration measurements during seed dehydration demonstrated that intermediate seeds with the highest DT are better prepared to cease respiration and avoid oxidative stresses.

Structural Plasticity of Intrinsically Disordered LEA Proteins from Xerophyta schlechteri Provides Protection In Vitro and In Vivo

Late embryogenesis abundant (LEA) proteins are essential to the ability of resurrection plants and orthodox seeds to protect the subcellular milieu against irreversible damage associated with desiccation. In this work, we investigated the structure and function of six LEA proteins expressed during desiccation in the monocot resurrection species Xerophyta schlechteri (XsLEAs). In silico analyses suggested that XsLEAs are hydrophilic proteins with variable intrinsically disordered protein (IDP) properties. Circular dichroism (CD) analysis indicated that these proteins are mostly unstructured in water but acquire secondary structure in hydrophobic solution, suggesting that structural dynamics may play a role in their function in the subcellular environment. The protective property of XsLEAs was demonstrated by their ability to preserve the activity of the enzyme lactate dehydrogenase (LDH) against desiccation, heat and oxidative stress, as well as growth of Escherichia coli upon exposure to osmotic and salt stress. Subcellular localization analysis indicated that XsLEA recombinant proteins are differentially distributed in the cytoplasm, membranes and nucleus of Nicotiana benthamiana leaves. Interestingly, a LEA_1 family protein (XsLEA1-8), showing the highest disorder-to-order propensity and protective ability in vitro and in vivo, was also able to enhance salt and drought stress tolerance in Arabidopsis thaliana. Together, our results suggest that the structural plasticity of XsLEAs is essential for their protective activity to avoid damage of various subcellular components caused by water deficit stress. XsLEA1-8 constitutes a potential model protein for engineering structural stability in vitro and improvement of water-deficit stress tolerance in plants.

Proteomic Comparison of Three Extraction Methods Reveals the Abundance of Protease Inhibitors in the Seeds of Grass Pea, a Unique Orphan Legume

Grass pea is an orphan legume that is grown in many places in the world. It is a high-protein, drought-tolerant legume that is capable of surviving extreme environmental challenges and can be a sole food source during famine. However, grass pea produces the neurotoxin β-N-oxalyl-L-α,β-diaminopropionic acid (β-ODAP), which can cause a neurological disease. This crop is promising as a food source for both animals and humans if β-ODAP levels and other antinutritional factors such as protease inhibitors are lowered or removed. To understand more about these proteins, a proteomic analysis of grass pea was conducted using three different extraction methods to determine which was more efficient at isolating antinutritional factors. Seed proteins extracted with Tris-buffered saline (TBS), 30% ethanol, and 50% isopropanol were identified by mass spectrometry, resulting in the documentation of the most abundant proteins for each extraction method. Mass spectrometry spectral data and BLAST2GO analysis led to the identification of 1376 proteins from all extraction methods. The molecular function of the extracted proteins revealed distinctly different protein functional profiles. The majority of the TBS-extracted proteins were annotated with nutrient reservoir activity, while the isopropanol extraction yielded the highest percentage of endopeptidase proteinase inhibitors. Our results demonstrate that the 50% isopropanol extraction method was the most efficient at isolating antinutritional factors including protease inhibitors.

Heat Stress in Legume Seed Setting: Effects, Causes, and Future Prospects

Grain legumes provide a rich resource of plant nutrition to human diets and are vital for food security and sustainable cropping. Heat stress during flowering has a detrimental effect on legume seed yield, mainly due to irreversible loss of seed number. To start with, we provide an overview of the developmental and physiological basis of controlling seed setting in response to heat stress. It is shown that every single process of seed setting including male and female gametophyte development, fertilization, and early seed/fruit development is sensitive to heat stress, in particular male reproductive development in legume crops is especially susceptible. A series of physiochemical processes including heat shock proteins, antioxidants, metabolites, and hormones centered with sugar starvation are proposed to play a key role in regulating legume seed setting in response to heat stress. The exploration of the molecular mechanisms underlying reproductive heat tolerance is in its infancy. Medicago truncatula, with a small diploid genome, and well-established transformation system and molecular platforms, has become a valuable model for testing gene function that can be applied to advance the physiological and molecular understanding of legume reproductive heat tolerance.

Influence of seed priming with iron and/or zinc in the nucleolar activity and protein content of bread wheat

Seed priming with iron (Fe) and/or zinc (Zn) can overcome the reduced availability of these micronutrients in soils and crops, but suitable dosages should be predetermined. Nucleolus responds to stress, such as cytotoxicity, with alterations perceivable by cytogenetic analyses. This work intends to study how seed priming with Fe and/or Zn affects the nucleolar activity in roots and the total soluble protein content in the flour of bread wheat cv. 'Jordão'. Seven priming treatments with 0 mg L^-1 to 8 mg L^-1 of Fe and/or Zn were performed. In all treatments, each metaphase cell presented a maximum of six nucleolar organizer regions positively stained with silver nitrate (Ag-NORs). Also, a maximum number of six nucleoli per nucleus were observed in all treatments, except in the hydroprimed seeds (used as control) that showed a maximum of five nucleoli, probably due to nucleolar fusion. Irregular interphases were frequent in treatments with the highest dosage of micronutrients (8 mg L^-1 Fe and/or 8 mg L^-1 Zn). The nucleolar area reduced (p < 0.001) as the number of nucleoli increased, and it was lower in treatments with a combination of Fe and Zn. However, the combinations of Fe and Zn showed the highest concentrations of total soluble protein (p ≤ 0.001). Although a reduced nucleolar area represents low ribosomal RNA gene transcription and ribosomal production, the significant increase of the number of nucleoli in the seeds primed with Fe and Zn enhanced the total soluble protein content as compared to the hydroprimed seeds (control) probably due to an increase of nucleolar surface-to-volume ratio that improved the protein synthesis. Overall, this work revealed that priming of bread wheat seeds with suited dosages of Fe and Zn can improve the nutritional value of flour, and the nucleolar number, morphology, and area can be useful biomarkers in cytotoxicity studies.

Characterization of Dehydrin protein, CdDHN4-L and CdDHN4-S, and their differential protective roles against abiotic stress in vitro

BACKGROUND

Dehydrins play positive roles in regulating plant abiotic stress responses. The objective of this study was to characterize two dehydrin genes, CdDHN4-L and CdDHN4-S, generated by alternative splicing of CdDHN4 in bermudagrass.

RESULTS

Overexpression of CdDHN4-L with φ-segment and CdDHN4-S lacking of φ-segment in Arabidopsis significantly increased tolerance against abiotic stresses. The growth phenotype of Arabidopsis exposed to NaCl at 100 mM was better in plants overexpressing CdDHN4-L than those overexpressing CdDHN4-S, as well as better in E.coli cells overexpressing CdDHN4-L than those overexpressing CdDHN4-S in 300 and 400 mM NaCl, and under extreme temperature conditions at - 20 °C and 50 °C. The CdDHN4-L had higher disordered characterization on structures than CdDHN4-S at temperatures from 10 to 90 °C. The recovery activities of lactic dehydrogenase (LDH) and alcohol dehydrogenase (ADH) in presence of CdDHN4-L and CdDHN4-S were higher than that of LDH and ADH alone under freeze-thaw damage and heat. Protein-binding and bimolecular fluorescence complementation showed that both proteins could bind to proteins with positive isoelectric point via electrostatic forces.

CONCLUSIONS

These results indicate that CdDHN4-L has higher protective ability against abiotic stresses due to its higher flexible unfolded structure and thermostability in comparison with CdDHN4-S. These provided direct evidence of the function of the φ-segment in dehydrins for protecting plants against abiotic stress and to show the electrostatic interaction between dehydrins and client proteins.

Toward characterizing germination and early growth in the non-orthodox forest tree species Quercus ilex through complementary gel and gel-free proteomic analysis of embryo and seedlings

By using two complementary proteomics, gel-based and gel-free (shotgun) approaches, the protein profiles of the non-orthodox forest tree species Quercus ilex seeds during germination and early seedling growth have been compared. Proteins were extracted from embryo axis, radicle and shoot tissues at different developmental stages. Proteins were subjected to one- and two-dimensional gel electrophoresis. A multivariate analysis (PCA) revealed that SDS-PAGE clearly separated germination (0-24 h post-imbibition), postgermination (72-216 h post-imbibition) and early seedling growth stages (2 weeks post-imbibition). Image analysis of the two-dimensional gels revealed a total of 732 spots, 103 of which were significantly variable among developmental stages. After MALDI-TOF/TOF MS analysis, 90 spots were identified, belonging to six main functional categories: carbohydrate, amino acids, energy, and protein metabolism, biosynthesis of secondary metabolites, and redox processes. The gel-based approach disclosed important metabolic changes that occurred in the holm oak seed after the germination. However, few proteins were significantly altered during the germination period (from 0 h to 24 h post imbibition) and, because of that, a further shotgun analysis was therefore used to analyse changes in the protein profile during seed germination. Up to 1250 proteins could be confidently identified, with 153 being variable. They belonged to the main functional categories of carbohydrate, amino acids and secondary metabolism, protein degradation, and responses to abiotic stress. The accumulation of proteases and amino acids metabolism proteins in mature seeds can be reflecting the production of energy from the mobilization of storage proteins to start germination. These results, therefore, corroborate the hypothesis that the mature non-orthodox seeds of Q. ilex have all the machinery necessary for rapidly resuming metabolic activities and starting the germination process, in contrast to that occurs in orthodox seeds, which metabolic activity ceases in mature dry seeds. The use of a genus-specific database combined with the public Viridiplantae database improved the quality and quantity of protein identification in this orphan species. In addition, both proteomics approaches (gel-based and shotgun) were complementary, with shotgun increasing by over two-fold the coverage of the proteome analysed. Both approaches provided similar results and supported the same conclusions on the metabolic switch experienced by the seed upon germination. SIGNIFICANCE: The optimal seed germination is a prerequisite for successful seedling establishment and plant vigour, being of great relevance in the case of crops and commercial woody plants. By using a complementary gel-based and gel-free proteomic strategy we have study the protein profiles of the non-orthodox forest tree species Quercus ilex seeds during germination and early seedling growth. The contribution of this work is of great importance, due to the complemented proteomic approaches giving similar clues to the metabolic state of the mature Q. ilex seed before the germination starts, and the metabolic switch experienced by the imbibed acorn until the seedling is established.

Identification of a seed maturation protein gene from Coffea arabica (CaSMP) and analysis of its promoter activity in tomato

A seed maturation protein gene (CaSMP) from Coffea arabica is expressed in the endosperm of yellow/green fruits. The CaSMP promoter drives reporter expression in the seeds of immature tomato fruits. In this report, an expressed sequence tag-based approach was used to identify a seed-specific candidate gene for promoter isolation in Coffea arabica. The tissue-specific expression of the cognate gene (CaSMP), which encodes a yet uncharacterized coffee seed maturation protein, was validated by RT-qPCR. Additional expression analysis during coffee fruit development revealed higher levels of CaSMP transcript accumulation in the yellow/green phenological stage. Moreover, CaSMP was preferentially expressed in the endosperm and was down-regulated during water imbibition of the seeds. The presence of regulatory cis-elements known to be involved in seed- and endosperm-specific expression was observed in the CaSMP 5'-upstream region amplified by genome walking (GW). Additional histochemical analysis of transgenic tomato (cv. Micro-Tom) lines harboring the GW-amplified fragment (~ 1.4 kb) fused to uidA reporter gene confirmed promoter activity in the ovule of immature tomato fruits, while no activity was observed in the seeds of ripening fruits and in the other organs/tissues examined. These results indicate that the CaSMP promoter can be used to drive transgene expression in coffee beans and tomato seeds, thus representing a promising biotechnological tool.

Does water stress promote the proteome-wide adjustment of intrinsically disordered proteins in plants?

Plant response to water stress involves the activation of mechanisms expected to help them cope with water scarcity. Among these mechanisms, proteome-wide adjustment is well known. This includes actions to save energy, protect cellular and molecular components, and maintain vital functions of the cell. Intrinsically disordered proteins, which are proteins without a rigid three-dimensional structure, are seen as emerging multifunctional cellular components of proteomes. They are highly abundant in eukaryotic proteomes, and numerous functions for these proteins have been proposed. Here, we discuss several reasons why the collection of intrinsically disordered proteins in a proteome (disordome) could be subjected to an active regulation during conditions of water scarcity in plants. We also discuss the potential misinterpretations of disordome content estimations made so far due to bias-prone data and the need for reliable analysis based on experimental data in order to acknowledge the plasticity nature of the disordome.

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.

Combined QTL mapping, physiological and transcriptomic analyses to identify candidate genes involved in Brassica napus seed aging

Seed aging is an inevitable problem in the germplasm conservation of oil crops. Thus, clarifying the genetic mechanism of seed aging is important for rapeseed breeding. In this study, Brassica napus seeds were exposed to an artificial aging environment (40 °C and 90% relative humidity). Using a population of 172 recombinant inbred lines, 13 QTLs were detected on 8 chromosomes, which explained ~ 9.05% of the total phenotypic variation. The QTLs q2015AGIA-C08 and q2016AGI-C08-2 identified in the two environments were considered the same QTL. After artificial aging, lower germination index, increased relative electrical conductivity, malondialdehyde and proline content, and reduced soluble sugar, protein content and antioxidant enzyme activities were detected. Furthermore, seeds of extreme lines that were either left untreated (R0 and S0) or subjected to 15 days of artificial aging (R15 and S15) were used for transcriptome sequencing. In total, 2843, 1084, 429 and 1055 differentially expressed genes were identified in R15 vs. R0, S15 vs. S0, R0 vs. S0 and R15 vs. S15, respectively. Through integrated QTL mapping and RNA-sequencing analyses, seven genes, such as BnaA03g37460D, encoding heat shock transcription factor C1, and BnaA03g40360D, encoding phosphofructokinase 4, were screened as candidate genes involved in seed aging. Further researches on these candidate genes could broaden our understanding of the regulatory mechanisms of seed aging.

Escherichia coli tolerance of ultraviolet radiation by in vivo expression of a short peptide designed from late embryogenesis abundant protein

Ultraviolet (UV) radiation causes damage in all living organisms, including DNA damage that leads to cell death. Herein, we provide a new technique for UV radiation protection through intracellular short peptide expression. The late embryogenesis abundant (LEA) peptide, which functions as a shield that protects macromolecules from various abiotic stress, was obtained from the Polypedilum vanderplanki group 3 LEA protein. Recombinant Escherichia coli BL21 (DE3) expressing functional LEA short peptide in vivo were exposed to UVA and UVC radiation for 4, 6, and 8 h. E. coli transformants expressing the LEA peptide showed higher cell viability under both UVA and UVC treatment at all time points as compared with that of the control. Furthermore, the cells expressing LEA peptide showed a higher number of colony-forming units per dilution under UVA and UVC treatment. These results suggested that expression of the short peptide could be useful for the development of genetically modified organisms and in applications that require resilience of organisms to UV radiation.

Integrative analysis of the late maturation programme and desiccation tolerance mechanisms in intermediate coffee seeds

The 'intermediate seed' category was defined in the early 1990s using coffee (Coffea arabica) as a model. In contrast to orthodox seeds, intermediate seeds cannot survive complete drying, which is a major constraint for seed storage and has implications for both biodiversity conservation and agricultural purposes. However, intermediate seeds are considerably more tolerant to drying than recalcitrant seeds, which are highly sensitive to desiccation. To gain insight into the mechanisms governing such differences, changes in desiccation tolerance (DT), hormone contents, and the transcriptome were analysed in developing coffee seeds. Acquisition of DT coincided with a dramatic transcriptional switch characterised by the repression of primary metabolism, photosynthesis, and respiration, and the up-regulation of genes coding for late-embryogenesis abundant (LEA) proteins, heat-shock proteins (HSPs), and antioxidant enzymes. Analysis of the heat-stable proteome in mature coffee seeds confirmed the accumulation of LEA proteins identified at the transcript level. Transcriptome analysis also suggested a major role for ABA and for the transcription factors CaHSFA9, CaDREB2G, CaANAC029, CaPLATZ, and CaDOG-like in DT acquisition. The ability of CaHSFA9 and CaDREB2G to trigger HSP gene transcription was validated by Agrobacterium-mediated transformation of coffee somatic embryos.

Selection Mapping Identifies Loci Underpinning Autumn Dormancy in Alfalfa (Medicago sativa)

Autumn dormancy in alfalfa (Medicago sativa) is associated with agronomically important traits including regrowth rate, maturity, and winter survival. Historical recurrent selection experiments have been able to manipulate the dormancy response. We hypothesized that artificial selection for dormancy phenotypes in these experiments had altered allele frequencies of dormancy-related genes. Here, we follow this hypothesis and analyze allele frequency changes using genome-wide polymorphisms in the pre- and postselection populations from one historical selection experiment. We screened the nondormant cultivar CUF 101 and populations developed by three cycles of recurrent phenotypic selection for taller and shorter plants in autumn with markers derived from genotyping-by-sequencing (GBS). We validated the robustness of our GBS-derived allele frequency estimates using an empirical approach. Our results suggest that selection mapping is a powerful means of identifying genomic regions associated with traits, and that it can be exploited to provide regions on which to focus further mapping and cloning projects.

Uncovering the basis of viability loss in desiccation sensitive Trichilia dregeana seeds using differential quantitative protein expression profiling by iTRAQ

Recalcitrant seeds, unlike orthodox types, are desiccation sensitive and hence, cannot be stored using conventional seed storage methods In this study, relative changes of protein expression in T. dregeana seeds during desiccation and hydrated storage (a short- to medium-term storage method) were analysed to understand the basis of their desiccation- and storage-induced viability loss. Isobaric Tags for Relative and Absolute Quantitation (iTRAQ) were used to compare (selected) protein expression levels across fresh, partially dehydrated and stored seeds. A total of 114 proteins were significantly differentially expressed in embryonic axes of fresh seeds and those seeds exposed to dehydration and hydrated storage (which exposed seeds to a mild dehydration stress). Proteins involved in protein synthesis were up-regulated in stored and dehydrated seeds, possibly in response to dehydration-induced repair processes and/or germinative development. A range of proteins related to antioxidant protection were variably up- and down-regulated in stored and dehydrated seeds, respectively. Additionally, a class I heat shock protein was down-regulated in dehydrated and stored seeds; no late embryogenesis abundant proteins were identified in both stored and dehydrated seeds; and storage and dehydration up-regulated proteins involved in the provision of energy for cell survival. The results suggest that dehydration- and storage-induced viability loss in recalcitrant seeds may be based on proteomic changes that lead to cellular redox imbalance and increased cell energy demands. This, together with the absence/down-regulation of proteins associated with desiccation tolerance in plant tissues may form part of the proteomic footprint for desiccation sensitivity in seeds.

Intrinsically Disordered Proteins as Important Players during Desiccation Stress of Soybean Radicles

Intrinsically disordered proteins (IDPs) play a variety of important physiological roles in all living organisms. However, there is no comprehensive analysis of the abundance of IDPs associated with environmental stress in plants. Here, we show that a set of heat-stable proteins (i.e., proteins that do not denature after boiling at 100 °C for 10 min) was present in R0mm and R15mm radicles (i.e., before radicle emergence and 15 mm long radicles) of soybean (Glycine max) seeds. This set of 795 iTRAQ-quantified heat-stable proteins contained a high proportion of wholly or highly disordered proteins (15%), which was significantly higher than that estimated for the whole soybean proteome containing 55,787 proteins (9%). The heat-stable proteome of soybean radicles that contain many IDPs could protect lactate dehydrogenase (LDH) during freeze-thaw cycles. Comparison of the 795 heat-stable proteins in the R0mm and R15mm soybean radicles revealed that many of these proteins changed abundance during seedling growth with 170 and 89 proteins being more abundant in R0mm and R15mm, respectively. KEGG analysis identified 18 proteins from the cysteine and methionine metabolism pathways and nine proteins from the phenylpropanoid biosynthesis pathway. As an important type of IDP related to stress, 30 late embryogenesis abundant proteins were also found. Ten selected proteins with high levels of predicted intrinsic disorder were able to efficiently protect LDH from the freeze-thaw-induced inactivation, but the protective ability was not correlated with the disorder content of these proteins. These observations suggest that protection of the enzymes and other proteins in a stressed cell can be one of the biological functions of plant IDPs.

SmLEA2, a gene for late embryogenesis abundant protein isolated from Salvia miltiorrhiza, confers tolerance to drought and salt stress in Escherichia coli and S. miltiorrhiza

Abiotic stresses, such as drought and high salinity, are major factors that limit plant growth and productivity. Late embryogenesis abundant (LEA) proteins are members of a diverse, multigene family closely associated with tolerance to abiotic stresses in numerous organisms. We examined the function of SmLEA2, previously isolated from Salvia miltiorrhiza, in defense responses to drought and high salinity. Phylogenetic analysis indicated that SmLEA2 belongs to the LEA_2 subfamily. Its overexpression in Escherichia coli improved growth performance when compared with the control under salt and drought stresses. We further characterized its roles in S. miltiorrhiza through overexpression and RNAi-mediated silencing. In response to drought and salinity treatments, transgenic plants overexpressing SmLEA2 exhibited significantly increased superoxide dismutase activity, reduced levels of lipid peroxidation, and more vigorous growth than empty-vector control plants did. However, transgenic lines in which expression was suppressed showed the opposite results. Our data demonstrate that SmLEA2 plays an important role in the abiotic stress response and its overexpression in transgenic S. miltiorrhiza improves tolerance to excess salt and drought conditions.

Late seed maturation: drying without dying

Besides the deposition of storage reserves, seed maturation is characterized by the acquisition of functional traits including germination, desiccation tolerance, dormancy, and longevity. After seed filling, seed longevity increases up to 30-fold, concomitant with desiccation that brings the embryo to a quiescent state. The period that we define as late maturation phase can represent 10-78% of total seed development time, yet it remains overlooked. Its importance is underscored by the fact that in the seed production chain, the stage of maturity at harvest is the primary factor that influences seed longevity and seedling establishment. This review describes the major events and regulatory pathways underlying the acquisition of seed longevity, focusing on key indicators of maturity such as chlorophyll degradation, accumulation of raffinose family oligosaccharides, late embryogenesis abundant proteins, and heat shock proteins. We discuss how these markers are correlated with or contribute to seed longevity, and highlight questions that merit further attention. We present evidence suggesting that molecular players involved in biotic defence also have a regulatory role in seed longevity. We also explore how the concept of plasticity can help understand the acquisition of longevity.

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.

ABI5 Is a Regulator of Seed Maturation and Longevity in Legumes

The preservation of our genetic resources and production of high-quality seeds depends on their ability to remain viable and vigorous during storage. In a quantitative trait locus analysis on seed longevity in Medicago truncatula, we identified the bZIP transcription factor ABSCISIC ACID INSENSITIVE5 (ABI5). Characterization of Mt-abi5 insertion mutant seeds revealed that both the acquisition of longevity and dormancy were severely impaired. Using transcriptomes of developing Mt-abi5 seeds, we created a gene coexpression network and revealed ABI5 as a regulator of gene modules with functions related to raffinose family oligosaccharide (RFO) metabolism, late embryogenesis abundant (LEA) proteins, and photosynthesis-associated nuclear genes (PhANGs). Lower RFO contents in Mt-abi5 seeds were linked to the regulation of SEED IMBIBITION PROTEIN1 Proteomic analysis confirmed that a set of LEA polypeptides was reduced in mature Mt-abi5 seeds, whereas the absence of repression of PhANG in mature Mt-abi5 seeds was accompanied by chlorophyll and carotenoid retention. This resulted in a stress response in Mt-abi5 seeds, evident from an increase in α-tocopherol and upregulation of genes related to programmed cell death and protein folding. Characterization of abi5 mutants in a second legume species, pea (Pisum sativum), confirmed a role for ABI5 in the regulation of longevity, seed degreening, and RFO accumulation, identifying ABI5 as a prominent regulator of late seed maturation in legumes.

Role of Proteomics in Crop Stress Tolerance

Plants often experience various biotic and abiotic stresses during their life cycle. The abiotic stresses include mainly drought, salt, temperature (low/high), flooding and nutritional deficiency/excess which hamper crop growth and yield to a great extent. In view of a projection 50% of the crop loss is attributable to abiotic stresses. However, abiotic stresses cause a myriad of changes in physiological, molecular and biochemical processes operating in plants. It is now widely reported that several proteins respond to these stresses at pre- and post-transcriptional and translational levels. By knowing the role of these stress inducible proteins, it would be easy to comprehensively expound the processes of stress tolerance in plants. The proteomics study offers a new approach to discover proteins and pathways associated with crop physiological and stress responses. Thus, studying the plants at proteomic levels could help understand the pathways involved in stress tolerance. Furthermore, improving the understanding of the identified key metabolic proteins involved in tolerance can be implemented into biotechnological applications, regarding recombinant/transgenic formation. Additionally, the investigation of identified metabolic processes ultimately supports the development of antistress strategies. In this review, we discussed the role of proteomics in crop stress tolerance. We also discussed different abiotic stresses and their effects on plants, particularly with reference to stress-induced expression of proteins, and how proteomics could act as vital biotechnological tools for improving stress tolerance in plants.

A LEA 4 protein up-regulated by ABA is involved in drought response in maize roots

Late embryogenesis abundant (LEA) proteins are hydrophilic proteins that accumulate to high concentrations during the late stages of seeds development, which are integral to desiccation tolerance. LEA proteins also play a protective role under other abiotic stresses. We analyzed in silico a maize protein predicted to be highly hydrophilic and intrinsically disordered. This prediction was experimentally corroborated by solubility assays under denaturing conditions. Based on its amino acid sequence, we propose that this protein belongs to group four of the LEA proteins. The accumulation pattern of this protein was similar to that of dehydrins during the desiccation process that takes place during seed development. This protein was induced by exogenous abscisic acid in immature embryos, but during imbibition was down-regulated by gibberellins. It was also induced in maize roots under osmotic stress. So far, this is the first member of the LEA proteins belonging to group four to be characterized in maize, and it plays a role in the response to osmotic stress.

Physiological and biochemical changes during the loss of desiccation tolerance in germinating Adenanthera pavonina L. seeds

ABSTRACT We investigated the loss of desiccation tolerance (DT) in Adenanthera pavonina seeds during germination. Seeds were subjected to imbibition for 0, 24, 36, 48, 60 and 81 h, then dried to their initial moisture content (13%), rehydrated and evaluated for survival (resumption of growth and development of normal seedlings) and membrane system integrity (electrolyte leakage). Embryonic axes of seeds subjected only to imbibition during the same early time periods were used to investigate the electrophoretic patterns of heat-stable proteins and the relative nuclear DNA content. In A. pavonina seeds, DT remained unchanged until 36 h of imbibition (resulting in germination and 82% normal seedlings), after which it was progressively lost, and seeds with a protruded radicle length of 1 mm did not withstand dehydration. The loss of desiccation tolerance could not be related to either membrane damage caused by drying or the resumption of the cell cycle during germination. However, the decrease in heat-stable protein contents observed throughout germination may be related to the loss of DT in A. pavonina seeds.

Seedling survival of Handroanthus impetiginosus (Mart ex DC) Mattos in a semi-arid environment through modified germination speed and post-germination desiccation tolerance

Uniform rapid seed germination generally forms a great risk for the plant population if subsequent intermittent precipitation causes desiccation and seedling death. Handroanthus impetiginosus can be found commonly in a wide range of biomes within Brazil including those that are semi-arid. Germination and early growth was studied to understand how germinated seeds survive under these stringent conditions. Accessions were sampled from four seasonally dry biomes in Brazil. Precipitation at the start of the rainy season in the Caatinga, a semi-arid biome, is less predictable and the number of successive dry days per dry interval in the first four months of the rainy season was higher than in the other studied biomes. Plants from the Caatinga produced thicker seeds and this trait concurred with slow germination and stronger osmotic inhibition of germination across the accessions, forming a stress avoidance mechanism in the Caatinga. Post-germination desiccation tolerance was high in the Caatinga accession, could be re-induced in accessions from biomes with more regular precipitation (Cerrado and transition zone), but remained poor in the Cerradão accession; thus forming a stress tolerance mechanism. Production of adventitious roots ascertained survival of all tested individuals from all four locations, even if protruded radicles did not survive desiccation, forming an additional stress tolerance mechanism. A sequence of stress avoidance and stress tolerance mechanisms in seeds and germinated seeds was associated with precipitation patterns in different biomes. These mechanisms purportedly allow rapid seedling establishment when conditions are suitable and enable survival of the young seedling when conditions are adverse.

A proteomic analysis of seeds from Bt-transgenic Brassica napus and hybrids with wild B. juncea

Transgene insertions might have unintended side effects on the transgenic host, both crop and hybrids with wild relatives that harbor transgenes. We employed proteomic approaches to assess protein abundance changes in seeds from Bt-transgenic oilseed rape (Brassica napus) and its hybrids with wild mustard (B. juncea). A total of 24, 15 and 34 protein spots matching to 23, 13 and 31 unique genes were identified that changed at least 1.5 fold (p < 0.05, Student’s t-test) in abundance between transgenic (tBN) and non-transgenic (BN) oilseed rape, between hybrids of B. juncea (BJ) × tBN (BJtBN) and BJ × BN (BJBN) and between BJBN and BJ, respectively. Eight proteins had higher abundance in tBN than in BN. None of these proteins was toxic or nutritionally harmful to human health, which is not surprising since the seeds are not known to produce toxic proteins. Protein spots varying in abundance between BJtBN and BJBN seeds were the same or homologous to those in the respective parents. None of the differentially-accumulated proteins between BJtBN and BJBN were identical to those between tBN and BN. Results indicated that unintended effects resulted from transgene flow fell within the range of natural variability of hybridization and those found in the native host proteomes.

Heat shock transcription factors involved in seed desiccation tolerance and longevity retard vegetative senescence in transgenic tobacco

MAIN CONCLUSION

Transcription factors normally expressed in sunflower seeds delayed vegetative senescence induced by severe stress in transgenic tobacco. This revealed a novel connection between seed heat shock factors, desiccation tolerance and vegetative longevity. HaHSFA9 and HaHSFA4a coactivate a genetic program that, in sunflower (Helianthus annuus L.), contributes to seed longevity and desiccation tolerance. We have shown that overexpression of HaHSFA9 in transgenic tobacco seedlings resulted in tolerance to drastic dehydration and oxidative stress. Overexpression of HaHSFA9 alone was linked to a remarkable protection of the photosynthetic apparatus. In addition, the combined overexpression of HaHSFA9 and HaHSFA4a enhanced all these stress-resistance phenotypes. Here, we find that HaHSFA9 confers protection against damage induced by different stress conditions that accelerate vegetative senescence during different stages of development. Seedlings and plants that overexpress HaHSFA9 survived lethal treatments of dark-induced senescence. HaHSFA9 overexpression induced resistance to effects of culture under darkness for several weeks. Only some homoiochlorophyllous resurrection plants are able to withstand this experimental severe stress condition. The combined overexpression of HaHSFA9 and HaHSFA4a did not result in further slowing of dark-induced seedling senescence. However, combined expression of the two transcription factors caused improved recovery of the photosynthetic organs of seedlings after lethal dark treatments. At later stages of vegetative development, HaHSFA9 delayed the appearance of senescence symptoms in leaves of plants grown under normal illumination. This delay was observed under either control or stress treatments. Thus, HaHSFA9 delayed both natural and stress-induced leaf senesce. These novel observations connect transcription factors involved in desiccation tolerance with leaf longevity.

Variability within a pea core collection of LEAM and HSP22, two mitochondrial seed proteins involved in stress tolerance

LEAM, a late embryogenesis abundant protein, and HSP22, a small heat shock protein, were shown to accumulate in the mitochondria during pea (Pisum sativum L.) seed development, where they are expected to contribute to desiccation tolerance. Here, their expression was examined in seeds of 89 pea genotypes by Western blot analysis. All genotypes expressed LEAM and HSP22 in similar amounts. In contrast with HSP22, LEAM displayed different isoforms according to apparent molecular mass. Each of the 89 genotypes harboured a single LEAM isoform. Genomic and RT-PCR analysis revealed four LEAM genes differing by a small variable indel in the coding region. These variations were consistent with the apparent molecular mass of each isoform. Indels, which occurred in repeated domains, did not alter the main properties of LEAM. Structural modelling indicated that the class A α-helix structure, which allows interactions with the mitochondrial inner membrane in the dry state, was preserved in all isoforms, suggesting functionality is maintained. The overall results point out the essential character of LEAM and HSP22 in pea seeds. LEAM variability is discussed in terms of pea breeding history as well as LEA gene evolution mechanisms.

Comparative proteome analysis of embryo and endosperm reveals central differential expression proteins involved in wheat seed germination

BACKGROUND

Wheat seeds provide a staple food and an important protein source for the world's population. Seed germination is vital to wheat growth and development and directly affects grain yield and quality. In this study, we performed the first comparative proteomic analysis of wheat embryo and endosperm during seed germination.

RESULTS

The proteomic changes in embryo and endosperm during the four different seed germination stages of elite Chinese bread wheat cultivar Zhengmai 9023 were first investigated. In total, 74 and 34 differentially expressed protein (DEP) spots representing 63 and 26 unique proteins were identified in embryo and endosperm, respectively. Eight common DEP were present in both tissues, and 55 and 18 DEP were specific to embryo and endosperm, respectively. These identified DEP spots could be sorted into 13 functional groups, in which the main group was involved in different metabolism pathways, particularly in the reserves necessary for mobilization in preparation for seed germination. The DEPs from the embryo were mainly related to carbohydrate metabolism, proteometabolism, amino acid metabolism, nucleic acid metabolism, and stress-related proteins, whereas those from the endosperm were mainly involved in protein storage, carbohydrate metabolism, inhibitors, stress response, and protein synthesis. During seed germination, both embryo and endosperm had a basic pattern of oxygen consumption, so the proteins related to respiration and energy metabolism were up-regulated or down-regulated along with respiration of wheat seeds. When germination was complete, most storage proteins from the endosperm began to be mobilized, but only a small amount was degraded during germination. Transcription expression of six representative DEP genes at the mRNA level was consistent with their protein expression changes.

CONCLUSION

Wheat seed germination is a complex process with imbibition, stirring, and germination stages, which involve a series of physiological, morphological, and proteomic changes. The first process is a rapid water uptake, in which the seed coat becomes softer and the physical state of storage materials change gradually. Then the germinated seed enters the second process (a plateau phase) and the third process (the embryonic axes elongation). Seed embryo and endosperm display distinct differentially expressed proteins, and their synergistic expression mechanisms provide a basis for the normal germination of wheat seeds.

Proteome analysis of dormancy-released seeds of Fraxinus mandshurica Rupr. in response to re-dehydration under different conditions

Desiccation tolerance is the ability of orthodox seeds to achieve equilibrium with atmospheric relative humidity and to survive in this state. Understanding how orthodox seeds respond to dehydration is important for improving quality and long-term storage of seeds under low temperature and drought stress conditions. Long-term storage of seeds is an artificial situation, because in most natural situations a seed that has been shed may not remain in a desiccated state for very long, and if dormant it may undergo repeated cycles of hydration. Different types of seeds are differentially sensitive to desiccation and this directly affects long-term storage. For these reasons, many researchers are investigating loss of desiccation tolerance during orthodox seed development to understand how it is acquired. In this study, the orthodox seed proteome response of Fraxinus mandshurica Rupr. to dehydration (to a relative water content of 10%, which mimics seed dehydration) was investigated under four different conditions viz. 20 °C; 20 °C with silica gel; 1 °C; and 1 °C after pretreatment with Ca2+. Proteins from seeds dehydrated under different conditions were extracted and separated by two-dimensional difference gel electrophoresis (2D-DIGE). A total of 2919 protein spots were detected, and high-resolution 2D-DIGE indicated there were 27 differentially expressed. Seven of these were identified using MALDI TOF/TOF mass spectrometry. Inferences from bioinformatics annotations of these proteins established the possible involvement of detoxifying enzymes, transport proteins, and nucleotide metabolism enzymes in response to dehydration. Of the seven differentially abundant proteins, the amounts of six were down-regulated and one was up-regulated. Also, a putative acyl-coenzyme A oxidase of the glyoxylate cycle increased in abundance. In particular, the presence of kinesin-1, a protein important for regulation and cargo interaction, was up-regulated in seeds exposed to low temperature dehydration. Kinesin-1 is present in all major lineages, but it is rarely detected in seed desiccation tolerance of woody species. These observations provide new insight into the proteome of seeds in deep dormancy under different desiccation conditions.

Acquisition and loss of desiccation tolerance in seeds: from experimental model to biological relevance

Besides being an important model to study desiccation tolerance, the induction of desiccation tolerance in germinated seeds may also play an ecological role in seedling establishment. Desiccation tolerance (DT) is the ability of certain organisms to survive extreme water losses without accumulation of lethal damage. This was a key feature in the conquering of dry land and is currently found in all taxa including bacteria, fungi, roundworms and plants. Not surprisingly, studies in various fields have been performed to unravel this intriguing phenomenon. In flowering plants, DT is rare in whole plants (vegetative tissues), yet is common in seeds. In this review, we present our current understanding of the evolution of DT in plants. We focus on the acquisition of DT in seeds and the subsequent loss during and after germination by highlighting and comparing research in two model plants Medicago truncatula and Arabidopsis thaliana. Finally, we discuss the ability of seeds to re-establish DT during post-germination, the possible ecological meaning of this phenomenon, and the hypothesis that DT, in combination with dormancy, optimizes seedling establishment.

Proteomics of seed development, desiccation tolerance, germination and vigor

Proteomics, the large-scale study of the total complement of proteins in a given sample, has been applied to all aspects of seed biology mainly using model species such as Arabidopsis or important agricultural crops such as corn and rice. Proteins extracted from the sample have typically been separated and quantified by 2-dimensional polyacrylamide gel electrophoresis followed by liquid chromatography and mass spectrometry to identify the proteins in the gel spots. In this way, qualitative and quantitative changes in the proteome during seed development, desiccation tolerance, germination, dormancy release, vigor alteration and responses to environmental factors have all been studied. Many proteins or biological processes potentially important for each seed process have been highlighted by these studies, which greatly expands our knowledge of seed biology. Proteins that have been identified to be particularly important for at least two of the seed processes are involved in detoxification of reactive oxygen species, the cytoskeleton, glycolysis, protein biosynthesis, post-translational modifications, methionine metabolism, and late embryogenesis-abundant (LEA) proteins. It will be useful for molecular biologists and molecular plant breeders to identify and study genes encoding particularly interesting target proteins with the aim to improve the yield, stress tolerance or other critical properties of our crop species.