Proteome analysis of Norway maple (Acer platanoides L.) seeds dormancy breaking and germination: influence of abscisic and gibberellic acids

Spatial specificity of metabolism regulation of abscisic acid-imposed seed germination inhibition in Korean pine (Pinus koraiensis sieb et zucc)

Introduction

Abscisic acid (ABA) can negatively regulate seed germination, but the mechanisms of ABA-mediated metabolism modulation are not well understood. Moreover, it remains unclear whether metabolic pathways vary with the different tissue parts of the embryo, such as the radicle, hypocotyl and cotyledon.

Methods

In this report, we performed the first comprehensive metabolome analysis of the radicle and hypocotyl + cotyledon in Pinus koraiensis seeds in response to ABA treatment during germination.

Results and discussion

Metabolome profiling showed that following ABA treatment, 67 significantly differentially accumulated metabolites in the embryo were closely associated with pyrimidine metabolism, phenylalanine metabolism, cysteine and methionine metabolism, galactose metabolism, terpenoid backbone biosynthesis, and glutathione metabolism. Meanwhile, 62 metabolites in the hypocotyl + cotyledon were primarily involved in glycerophospholipid metabolism and glycolysis/gluconeogenesis. We can conclude that ABA may inhibit Korean pine seed germination primarily by disrupting the biosynthesis of certain plant hormones mediated by cysteine and methionine metabolism and terpenoid backbone biosynthesis, as well as reducing the reactive oxygen species scavenging ability regulated by glutathione metabolism and shikimate pathway in radicle. ABA may strongly disrupt the structure and function of cellular membranes due to alterations in glycerophospholipid metabolism, and weaken glycolysis/gluconeogenesis in the hypocotyl + cotyledon, both of which are major contributors to ABA-mediated inhibition of seed germination. These results highlight that the spatial modulation of metabolic pathways in Pinus koraiensis seeds underlies the germination response to ABA.

Comparative transcriptome analysis reveals the potential mechanism of GA3-induced dormancy release in Suaeda glauca black seeds

Suaeda glauca Bunge produces dimorphic seeds on the same plant, with brown seeds displaying non-dormant characteristics and black seeds exhibiting intermediate physiological dormancy traits. Previous studies have shown that black seeds have a very low germination rate under natural conditions, but exogenous GA3 effectively enhanced the germination rate of black seeds. However, the physiological and molecular mechanisms underlying the effects of GA3 on S. glauca black seeds are still unclear. In this study, transcriptomic profiles of seeds at different germination stages with and without GA3 treatment were analyzed and compared, and the TTF, H2O2, O2 -, starch, and soluble sugar contents of the corresponding seed samples were determined. The results indicated that exogenous GA3 treatment significantly increased seed vigor, H2O2, and O2 - contents but decreased starch and soluble sugar contents of S. glauca black seeds during seed dormancy release. RNA-seq results showed that a total of 1136 DEGs were identified in three comparison groups and were involved mainly in plant hormone signal transduction, diterpenoid biosynthesis, flavonoid biosynthesis, phenylpropanoid biosynthesis, and carbohydrate metabolism pathway. Among them, the DEGs related to diterpenoid biosynthesis (SgGA3ox1, SgKAO and SgGA2ox8) and ABA signal transduction (SgPP2Cs) could play important roles during seed dormancy release. Most genes involved in phenylpropanoid biosynthesis were activated under GA3 treatment conditions, especially many SgPER genes encoding peroxidase. In addition, exogenous GA3 treatment also significantly enhanced the expression of genes involved in flavonoid synthesis, which might be beneficial to seed dormancy release. In accordance with the decline in starch and soluble sugar contents, 15 genes involved in carbohydrate metabolism were significantly up-regulated during GA3-induced dormancy release, such as SgBAM, SgHXK2, and SgAGLU, etc. In a word, exogenous GA3 effectively increased the germination rate and seed vigor of S. glauca black seeds by mediating the metabolic process or signal transduction of plant hormones, phenylpropanoid and flavonoid biosynthesis, and carbohydrate metabolism processes. Our results provide novel insights into the transcriptional regulation mechanism of exogenous GA3 on the dormancy release of S. glauca black seeds. The candidate genes identified in this study may be further studied and used to enrich our knowledge of seed dormancy and germination.

Methodological and Physiological Study during Seed Dormancy Release of Symplocos paniculata

Symplocos paniculata are reported to exhibit seed dormancy, which impedes its cultivation and widespread adoption. In this study, a comprehensive method was established to overcome seed dormancy by subjecting seeds to scarification in 98% H2SO4 for 10 min, followed by 1000 mg·L-1 GA3 soaking for 48 h and stratification at 4 °C for 100 days. The seed germination percentage has increased significantly, to a peak of 42.67%, though the seeds could not germinate timely by NaOH scarification. Additionally, the dynamic changes of key stored substances (proteins, soluble sugars, starches, and fats), associated enzyme activities (amylases, peroxidase, and catalase), and endogenous hormones (abscisic acid, gibberellic acid, and indole-3-acetic acid) in seeds were investigated. The results demonstrated a continuous degradation of starch and fat in S. paniculata seeds, while the levels of protein and soluble sugar exhibited fluctuations, which probably facilitated seed dormancy breaking through energy supply and transformation. The enzymatic activities underwent rapid changes, accompanied by a gradual decrease in ABA content within the seeds with increasing stratification time. Notably, GA3, GA3/ABA, and (GA3 + IAA)/ABA showed significant increases, indicating their positive regulatory roles in seed germination. This study clarified the dormancy mechanism and established an effective method for the release dormancy of S. paniculata seeds.

ABA Inhibits Rice Seed Aging by Reducing H2O2 Accumulation in the Radicle of Seeds

The seed, a critical organ in higher plants, serves as a primary determinant of agricultural productivity, with its quality directly influencing crop yield. Improper storage conditions can diminish seed vigor, adversely affecting seed germination and seedling establishment. Therefore, understanding the seed-aging process and exploring strategies to enhance seed-aging resistance are paramount. In this study, we observed that seed aging during storage leads to a decline in seed vigor and can coincide with the accumulation of hydrogen peroxide (H2O2) in the radicle, resulting in compromised or uneven germination and asynchronous seedling emergence. We identified the abscisic acid (ABA) catabolism gene, abscisic acid 8'-hydroxylase 2 (OsABA8ox2), as significantly induced by aging treatment. Interestingly, transgenic seeds overexpressing OsABA8ox2 exhibited reduced seed vigor, while gene knockout enhanced seed vigor, suggesting its role as a negative regulator. Similarly, seeds pretreated with ABA or diphenyleneiodonium chloride (DPI, an H2O2 inhibitor) showed increased resistance to aging, with more robust early seedling establishment. Both OsABA8ox2 mutant seeds and seeds pretreated with ABA or DPI displayed lower H2O2 content during aging treatment. Overall, our findings indicate that ABA mitigates rice seed aging by reducing H2O2 accumulation in the radicle. This study offers valuable germplasm resources and presents a novel approach to enhancing seed resistance against aging.

Comparative proteomic analysis between mature and germinating seeds in Paris polyphylla var. yunnanensis

The long dormancy period of Paris polyphylla var. yunnanensis seeds affects the supply of this scarce plant, which is used as an important traditional Chinese medicine. Mature seeds with a globular embryo and germinating seeds with developed embryo were used to explore the mechanisms of seed germination in this species. The protein profiles between the mature and germinating seeds were compared using the isobaric tags for relative and absolute quantification (iTRAQ) approach. Of the 4,488 proteins identified, a total of 1,305 differentially expressed proteins (DEPs) were detected. A Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis of these DEPs indicated that metabolic pathways and the biosynthesis of secondary metabolites were the two top pathways. Additionally, phytohormone quantification shows that the abscisic acid (ABA) level significantly decreased, whereas the GA₃ level dramatically increased among nine endogenous gibberellins (GAs), resulting in a significant increase of the GA₃/ABA ratio in germinating seeds. The biosynthesis pathways of carotenoid as a precursor for ABA production and GA were further analyzed, and showed that proteinic expressions of the candidate genes in the two pathways did not correlate with the transcriptional abundances. However, 9-cis-epoxycarotenoid dioxygenase (NCED), a rate limited enzyme for ABA biosynthesis, was significantly decreased in mRNA levels in germinating seeds. By contrast, gibberellin 20-oxidase (GA20ox), a key enzyme GA biosynthesis, exhibited the major increase in one copy and a slight decrease in three others at the protentional level in germinating seeds. Gibberellin 2-oxidase (GA2ox), an inactivate enzyme in bioactive GAs, has the tendency to down-regulate in mRNA or at the proteinic level in germinating seeds. Altogether, these results suggested that the analyses of ABA and GA levels, the GA₃/ABA ratio, and the expressional patterns of their regulatory genes may provide a novel mechanistic understanding of how phytohormones regulate seed germination in P. polyphylla var. yunnanensis.

Embryo transcriptome and miRNA analyses reveal the regulatory network of seed dormancy in Ginkgo biloba

Seed dormancy is crucial for plant survival and prevents seed germination out of season. However, little is known about the regulatory mechanism of morphophysiological seed dormancy. Ginkgo biloba L. is one of the most ancient gymnosperms, and the completion of seed germination in this species requires cold and moist stratification. Here, we observed that at the mature seed stage, the embryo was not fully developed in G. biloba seeds. During dormancy stages, the length and weight of the embryo significantly increased, and nutrients accumulated in cotyledons. We further found that abscisic acid (ABA), gibberellic acid (GA), cytokinin and ethylene were integrated in the seed dormancy induction, maintenance and release processes, and GA biosynthesis and signaling transduction specifically act on dormancy release. Combining mRNA and miRNA analyses, we demonstrated that miRNA156 is involved in the regulation of morphophysiological dormancy. Our analyses revealed that G. biloba seed dormancy belongs to the ancestral morphophysiological dormancy type, which is not only regulated by the balance of ABA/GA, but also by other hormones associated with embryo morphological development, as well as genes related to embryo differentiation and development. These findings helped with elucidating the comprehensive regulatory network of morphophysiological dormancy in tree seeds.

Involvement of the MetO/Msr System in Two Acer Species That Display Contrasting Characteristics during Germination

The levels of methionine sulfoxide (MetO) and the abundances of methionine sulfoxide reductases (Msrs) were reported as important for the desiccation tolerance of Acer seeds. To determine whether the MetO/Msrs system is related to reactive oxygen species (ROS) and involved in the regulation of germination in orthodox and recalcitrant seeds, Norway maple and sycamore were investigated. Changes in water content, MetO content, the abundance of MsrB1 and MsrB2 in relation to ROS content and the activity of reductases depending on nicotinamide adenine dinucleotides were monitored. Acer seeds differed in germination speed-substantially higher in sycamore-hydration dynamics, levels of hydrogen peroxide, superoxide anion radicals (O2•-) and hydroxyl radicals (•OH), which exhibited peaks at different stages of germination. The MetO level dynamically changed, particularly in sycamore embryonic axes, where it was positively correlated with the levels of O2•- and the abundance of MsrB1 and negatively with the levels of •OH and the abundance of MsrB2. The MsrB2 abundance increased upon sycamore germination; in contrast, it markedly decreased in Norway maple. We propose that the ROS-MetO-Msr redox system, allowing balanced Met redox homeostasis, participates in the germination process in sycamore, which is characterized by a much higher speed compared to Norway maple.

Temperature Regulation of Primary and Secondary Seed Dormancy in Rosa canina L.: Findings from Proteomic Analysis

Temperature is a key environmental factor restricting seed germination. Rose (Rosa canina L.) seeds are characterized by physical/physiological dormancy, which is broken during warm, followed by cold stratification. Exposing pretreated seeds to 20 °C resulted in the induction of secondary dormancy. The aim of this study was to identify and functionally characterize the proteins associated with dormancy control of rose seeds. Proteins from primary dormant, after warm and cold stratification (nondormant), and secondary dormant seeds were analyzed using 2-D electrophoresis. Proteins that varied in abundance were identified by mass spectrometry. Results showed that cold stratifications affected the variability of the highest number of spots, and there were more common spots with secondary dormancy than with warm stratification. The increase of mitochondrial proteins and actin during dormancy breaking suggests changes in cell functioning and seed preparation to germination. Secondary dormant seeds were characterized by low levels of legumin, metabolic enzymes, and actin, suggesting the consumption of storage materials, a decrease in metabolic activity, and cell elongation. Breaking the dormancy of rose seeds increased the abundance of cellular and metabolic proteins that promote germination. Induction of secondary dormancy caused a decrease in these proteins and germination arrest.

Cellular alteration and differential protein profile explain effects of GA3 and ABA and their inhibitor on Trichocline catharinensis (Asteraceae) seed germination

Seed physiology of wild species has not been studied as deeply as that of domesticated crop species. Trichocline catharinensis (Asteraceae) is an endemic wildflower species from the high-altitude fields of southern Brazil. This species is of interest as a source of genes to improve cultivated Asteraceae because of its ornamental features, disease resistance and ability to tolerate drought and poor soil conditions. We studied the effects of abscisic acid (ABA) and gibberellic acid (GA₃ ) and their inhibitors, fluridone (FLU) and paclobutrazol (PAC), on seed germination. We individually assessed ultrastructural changes and differential protein accumulation. The principal component analysis explained 69.66% of differential accumulation for 32 proteins at phase II of seed germination in response to hormone and inhibitor treatment. GA₃ -imbibed seed germination (98.75%) resulted in increased protein accumulation to meet energy demand, redox regulation, and reserve metabolism activation. FLU-imbibed seeds showed a higher germination speed index as a consequence of metabolism activation. ABA-imbibed seeds (58.75%) showed osmotolerance and flattened cells in the hypocotyl-radicular axis, suggesting that ABA inhibits cell expansion. PAC-imbibed seeds remained at phase II for 300 h, and germination was suppressed (7.5%) because of the increased signaling proteins and halted reserve mobilization. Therefore, our findings provide insight into the behavior of Asteraceae non-dormant seed germination, which broadens our knowledge of seed germination in a wild and endemic plant species from a threatened ecosystem.

What Do We Know About the Genetic Basis of Seed Desiccation Tolerance and Longevity?

Long-term seed storage is important for protecting both economic interests and biodiversity. The extraordinary properties of seeds allow us to store them in the right conditions for years. However, not all types of seeds are resilient, and some do not tolerate extreme desiccation or low temperature. Seeds can be divided into three categories: (1) orthodox seeds, which tolerate water losses of up to 7% of their water content and can be stored at low temperature; (2) recalcitrant seeds, which require a humidity of 27%; and (3) intermediate seeds, which lose their viability relatively quickly compared to orthodox seeds. In this article, we discuss the genetic bases for desiccation tolerance and longevity in seeds and the differences in gene expression profiles between the mentioned types of seeds.

Tuberomics: a molecular profiling for the adaption of edible fungi (Tuber magnatum Pico) to different natural environments

BACKGROUND

Truffles are symbiotic fungi that develop underground in association with plant roots, forming ectomycorrhizae. They are primarily known for the organoleptic qualities of their hypogeous fruiting bodies. Primarily, Tuber magnatum Pico is a greatly appreciated truffle species mainly distributed in Italy and Balkans. Its price and features are mostly depending on its geographical origin. However, the genetic variation within T. magnatum has been only partially investigated as well as its adaptation to several environments.

RESULTS

Here, we applied an integrated omic strategy to T. magnatum fruiting bodies collected during several seasons from three different areas located in the North, Center and South of Italy, with the aim to distinguish them according to molecular and biochemical traits and to verify the impact of several environments on these properties. With the proteomic approach based on two-dimensional electrophoresis (2-DE) followed by mass spectrometry, we were able to identify proteins specifically linked to the sample origin. We further associated the proteomic results to an RNA-seq profiling, which confirmed the possibility to differentiate samples according to their source and provided a basis for the detailed analysis of genes involved in sulfur metabolism. Finally, geographical specificities were associated with the set of volatile compounds produced by the fruiting bodies, as quantitatively and qualitatively determined through proton transfer reaction-mass spectrometry (PTR-MS) and gas-chromatography-mass spectrometry (GC-MS). In particular, a partial least squares-discriminant analysis (PLS-DA) model built from the latter data was able to return high confidence predictions of sample source.

CONCLUSIONS

Results provide a characterization of white fruiting bodies by a wide range of different molecules, suggesting the role for specific compounds in the responses and adaptation to distinct environments.

Regulation of thiol metabolism as a factor that influences the development and storage capacity of beech seeds

Seeds are the basis of propagation for the common beech (Fagus sylvatica L.), but the seed set of the beech is unsteady, with 5-10 years between abundant crops. Beech seeds are very difficult to store and lose their viability quickly even in optimum storage conditions. To date, it has not been possible to determine factors indicative of the aging process and the loss of viability of beech seeds during storage. To address this important economic challenge and interesting scientific problem, we analyzed the adjustment of the redox state during the development and storage of seeds. Many metabolic processes are based on reduction and oxidation reactions. Thiol proteins control and react to the redox state in the cells. The level of thiol proteins increased during seed maturation and decreased during storage. Gel-based redox proteomics identified 17 proteins in beech seeds during development. The proteins could be assigned to processes like metabolism and antioxidant functions. During storage, the number of proteins decreased to only six, i.e., oxidoreductases, peptidases, hydrolases and isomerases. The occurrence of peroxiredoxins (PRX) as thiol peroxidases and redox regulators indicates an important role of cytosolic 1CysPRX and PRXIIC, mitochondrial PRXIIF, and plastidic PRXIIE, 2CysPRX, and PRXQ in beech seeds during development and storage. Particularly, 2CysPRX was present in beech seeds during development and storage and may perform an important function in regulation of the redox state during both seed development and storage. The role of thiol proteins in the regulation of the redox state during the development and storage of beech seeds is discussed.

Comparative transcriptome analysis revealing the potential mechanism of seed germination stimulated by exogenous gibberellin in Fraxinus hupehensis

BACKGROUND

Fraxinus hupehensis is an endangered tree species that is endemic to in China; the species has very high commercial value because of its intricate shape and potential to improve and protect the environment. Its seeds show very low germination rates in natural conditions. Preliminary experiments indicated that gibberellin (GA₃) effectively stimulated the seed germination of F. hupehensis. However, little is known about the physiological and molecular mechanisms underlying the effect of GA₃ on F. hupehensis seed germination.

RESULTS

We compared dormant seeds (CK group) and germinated seeds after treatment with water (W group) and GA₃ (G group) in terms of seed vigor and several other physiological indicators related to germination, hormone content, and transcriptomics. Results showed that GA₃ treatment increases seed vigor, energy requirements, and trans-Zetain (ZT) and GA₃ contents but decreases sugar and abscisic acid (ABA) contents. A total of 116,932 unigenes were obtained from F. hupehensis transcriptome. RNA-seq analysis identified 31,856, 33,188 and 2056 differentially expressed genes (DEGs) between the W and CK groups, the G and CK groups, and the G and W groups, respectively. Up-regulation of eight selected DEGs of the glycolytic pathway accelerated the oxidative decomposition of sugar to release energy for germination. Up-regulated genes involved in ZT (two genes) and GA₃ (one gene) biosynthesis, ABA degradation pathway (one gene), and ABA signal transduction (two genes) may contribute to seed germination. Two down-regulated genes associated with GA₃ signal transduction were also observed in the G group. GA₃-regulated genes may alter hormone levels to facilitate germination. Candidate transcription factors played important roles in GA₃-promoted F. hupehensis seed germination, and Quantitative Real-time PCR (qRT-PCR) analysis verified the expression patterns of these genes.

CONCLUSION

Exogenous GA₃ increased the germination rate, vigor, and water absorption rate of F. hupehensis seeds. Our results provide novel insights into the transcriptional regulation mechanism of effect of exogenous GA₃ on F. hupehensis seed germination. The transcriptome data generated in this study may be used for further molecular research on this unique species.

Profiling of Seed Proteome in Pea (Pisum sativum L.) Lines Characterized with High and Low Responsivity to Combined Inoculation with Nodule Bacteria and Arbuscular Mycorrhizal Fungi

Legume crops represent the major source of food protein and contribute to human nutrition and animal feeding. An essential improvement of their productivity can be achieved by symbiosis with beneficial soil microorganisms-rhizobia (Rh) and arbuscular mycorrhizal (AM) fungi. The efficiency of these interactions depends on plant genotype. Recently, we have shown that, after simultaneous inoculation with Rh and AM, the productivity gain of pea (Pisum sativum L) line K-8274, characterized by high efficiency of interaction with soil microorganisms (EIBSM), was higher in comparison to a low-EIBSM line K-3358. However, the molecular mechanisms behind this effect are still uncharacterized. Therefore, here, we address the alterations in pea seed proteome, underlying the symbiosis-related productivity gain, and identify 111 differentially expressed proteins in the two lines. The high-EIBSM line K-8274 responded to inoculation by prolongation of seed maturation, manifested by up-regulation of proteins involved in cellular respiration, protein biosynthesis, and down-regulation of late-embryogenesis abundant (LEA) proteins. In contrast, the low-EIBSM line K-3358 demonstrated lower levels of the proteins, related to cell metabolism. Thus, we propose that the EIBSM trait is linked to prolongation of seed filling that needs to be taken into account in pulse crop breeding programs. The raw data have been deposited to the ProteomeXchange with identifier PXD013479.

Comparative physiological and leaf proteome analysis between drought-tolerant chickpea Cicer reticulatum and drought-sensitive chickpea C. arietinum

Comparative physiological and proteomic analysis were performed to understand the stress responses of two chickpea species (C. reticulatum and C. arietinum) against drought. Our study revealed that drought stress reduced root length, leaf water content, and enhanced free proline content in both species. Effect of drought stress appeared to be greater in C. arietinum compared to C. reticulatum. A total of 24 differently expressed proteins were identified by using MALDI-TOF/ TOF-MS/MS in response to drought. The proteins involved in photosynthesis and energy mechanisms were up-regulated in C. reticulatum and down-regulated in C. arietinum under drought. Our results suggest that the photosynthesis capacity of C. reticulatum is greater than that of C. arietinum under drought stress. Abundance of proline and sucrose biosynthesis related proteins, glutamine synthetase and cyctosolic fructose-bisphosphate aldolase, respectively, also increased in C. reticulatum under drought stress. The findings of this proteome analysis will help in understanding the mechanism of drought resistance in chickpea and may be also helpful in developing drought-resistant transgenic plants.

DNA synthesis pattern, proteome, and ABA and GA signalling in developing seeds of Norway maple (Acer platanoides)

Mature seeds of Norway maple exhibit desiccation tolerance and deep physiological dormancy. Flow cytometry, proteomics, and immunodetection have been combined to investigate seed development of this species. DNA content analysis revealed that cell cycle/endoreduplication activity differs between seed organs and developmental stages. In the embryo axis, the proportion of the nuclei with the highest DNA content (4C) increases at the beginning of maturation (17 weeks after flowering; WAF), and then is stable until the end of maturation, to increase again after drying. In cotyledons, during maturation endopolyploid nuclei (8C) occur and the intensity of endoreduplication increases up to 21 WAF, and then is stable until development is completed. In dry mature seeds, the proportion of 4C nuclei is high, and reaches 36% in the embryo axis and 52% in cotyledons. Proteomic studies revealed that energy and carbon metabolism, fatty acid biosynthesis, storage and antioxidant proteins are associated with seed development. Study of the ABI5 protein, a transcription factor involved in ABA signalling, and the RGL2 protein, a repressor of the GA signalling indicates that the highest accumulation of these proteins occurs in fully-matured and dried seeds. It is suggested that this increase in accumulation can be associated with completion of maturation, mainly with desiccation and dormancy acquisition.

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.

Comparative proteomics illustrates the molecular mechanism of potato (Solanum tuberosum L.) tuberization inhibited by exogenous gibberellins in vitro

Among the multiple environmental signals and hormonal factors regulating potato tuberization, gibberellins (GAs) are important components of the signaling pathways in these processes. To understand the GAs-signaling response mechanism of potato tuberization, a comparative proteomics approach was applied to analyze proteome change of potato tuberization in vitro subjected to a range of exogenous GA₃ treatments (0, 0.01, 0.1 and 1.0 μM) using two-dimensional gel electrophoresis. Quantitative image analyses showed that a total of 37 protein spots have their abundance significantly altered more than 2-fold. Among these proteins, 13 proteins were up-regulated, 13 proteins were down-regulated, one protein was absent and 10 proteins were induced after treatment by exogenous GA₃ . The MALDI-TOF/TOF MS analyses led to the identification of differentially abundant proteins that are mainly involved in bioenergy and metabolism, storage, signaling, cell defense and rescue, transcription, chaperones, transport. Furthermore, the comparative analysis of GA₃ -responsive proteome allowed for general elucidation of underlying molecular mechanisms of potato tuberization inhibited by exogenous GA₃ . Most of these cellular processes were not conducive to the transition from stolon elongation to tuber formation, including a blockage of starch and storage protein accumulation, the accelerated carbohydrate catabolism, a blockage of JA biosynthesis but an elevated endogenous GAs level, the amplification of GA₃ signal transduction by other signaling pathways, and the regulation of cellular RNA metabolism for controlling tuberization. Our results firstly integrated physiology and proteome data to provide new insights into GA₃ -signaling response mechanisms of potato tuberization in vitro.

Proteome-Level Analysis of Metabolism- and Stress-Related Proteins during Seed Dormancy and Germination in Gnetum parvifolium

Gnetum parvifolium is a rich source of materials for traditional medicines, food, and oil, but little is known about the mechanism underlying its seed dormancy and germination. In this study, we analyzed the proteome-level changes in its seeds during germination using isobaric tags for relative and absolute quantitation. In total, 1,040 differentially expressed proteins were identified, and cluster analysis revealed the distinct time points during which signal transduction and oxidation-reduction activity changed. Gene Ontology analysis showed that "carbohydrate metabolic process" and "response to oxidative stress" were the main enriched terms. Proteins associated with starch degradation and antioxidant enzymes were important for dormancy-release, while proteins associated with energy metabolism and protein synthesis were up-regulated during germination. Moreover, protein-interaction networks were mainly associated with heat-shock proteins. Furthermore, in accord with changes in the energy metabolism- and antioxidant-related proteins, indole-3-acetic acid, Peroxidase, and soluble sugar content increased, and the starch content decreased in almost all six stages of dormancy and germination analyzed (S1-S6). The activity of superoxide dismutase, abscisic acid, and malondialdehyde content increased in the dormancy stages (S1-S3) and then decreased in the germination stages (S4-S6). Our results provide new insights into G. parvifolium seed dormancy and germination at the proteome and physiological levels, with implications for improving seed propagation.

The sRNAome mining revealed existence of unique signature small RNAs derived from 5.8SrRNA from Piper nigrum and other plant lineages

Small RNAs derived from ribosomal RNAs (srRNAs) are rarely explored in the high-throughput data of plant systems. Here, we analyzed srRNAs from the deep-sequenced small RNA libraries of Piper nigrum, a unique magnoliid plant. The 5' end of the putative long form of 5.8S rRNA (5.8S_LrRNA) was identified as the site for biogenesis of highly abundant srRNAs that are unique among the Piperaceae family of plants. A subsequent comparative analysis of the ninety-seven sRNAomes of diverse plants successfully uncovered the abundant existence and precise cleavage of unique rRF signature small RNAs upstream of a novel 5' consensus sequence of the 5.8S rRNA. The major cleavage process mapped identically among the different tissues of the same plant. The differential expression and cleavage of 5'5.8S srRNAs in Phytophthora capsici infected P. nigrum tissues indicated the critical biological functions of these srRNAs during stress response. The non-canonical short hairpin precursor structure, the association with Argonaute proteins, and the potential targets of 5'5.8S srRNAs reinforced their regulatory role in the RNAi pathway in plants. In addition, this novel lineage specific small RNAs may have tremendous biological potential in the taxonomic profiling of plants.

Proteome changes associated with dormancy release of Dongxiang wild rice seeds

Seed dormancy provides optimum timing for seed germination and subsequent seedling growth, but the mechanism of seed dormancy is still poorly understood. Here, we used Dongxiang wild rice (DXWR) seeds to investigate the dormancy behavior and the differentially changed proteome in embryo and endosperm during dormancy release. DXWR seed dormancy was caused by interaction of embryo and its surrounding structure, and was an intermediate physiological dormancy. During seed dormancy release, a total of 109 and 97 protein spots showed significant change in abundance and were successfully identified in embryo and endosperm, respectively. As a result of dormancy release, the abundance of nine proteins involved in storage protein, cell defense and rescue and energy changed in the same way in both embryo and endosperm, while 67 and 49 protein spots changed differentially in embryo and endosperm, respectively. Dormancy release of DXWR seeds was closely associated with degradation of storage proteins in both embryo and endosperm. At the same time, the abundance of proteins involved in metabolism, glycolysis and TCA cycle, cell growth and division, protein synthesis and destination and signal transduction increased in embryos while staying constant or decreasing in endosperms.

Analysis of the embryo proteome of sycamore (Acer pseudoplatanus L.) seeds reveals a distinct class of proteins regulating dormancy release

Acer pseudoplatanus seeds are characterized by a deep physiological embryo dormancy that requires a few weeks of cold stratification in order to promote germination. Understanding the function of proteins and their related metabolic pathways, in conjunction with the plant hormones implicated in the breaking of seed dormancy, would expand our knowledge pertaining to this process. In this study, a proteomic approach was used to analyze the changes occurring in seeds in response to cold stratification, which leads to dormancy release. In addition, the involvement of abscisic (ABA) and gibberellic acids (GA) was also examined. Fifty-three proteins showing significant changes were identified by mass spectrometry. An effect of ABA on protein variation was observed at the beginning of stratification, while the influence of GA on protein abundance was observed during the middle phase of stratification. The majority of proteins associated with dormancy breaking in the presence of only water, and also ABA or GA, were classified as being involved in metabolism and genetic information processing. For metabolic-related proteins, the effect of ABA on protein abundance was stimulatory for half of the proteins and inhibitory for half of the proteins. On the other hand, the effect on genetic information processing related proteins was stimulatory. GA was found to upregulate both metabolic-related and genetic information processing-related proteins. While seed dormancy breaking depends on proteins involved in a variety of processes, proteins associated with methionine metabolism (adenosine kinase, methionine synthase) and glycine-rich RNA binding proteins appear to be of particular importance.

Protein profile of cotyledon, tegument, and embryonic axis of mature acorns from a non-orthodox plant species: Quercus ilex

Contrary to the orthodox seeds, recalcitrant Holm oak seeds possess the enzymatic machinery to start germination during the maturation phase. The protein profile of the different parts, mature seeds, of the Holm oak, a non-orthodox plant species, has been characterized using one- and two-dimensional gel electrophoresis coupled to matrix-assisted laser desorption ionization-time of flight mass spectrometry. Protein content and profiles of the three seed tissues (cotyledon, embryonic axis and tegument) were quite different. The embryonic axis showed 4-fold and 20-fold higher protein content than the cotyledon and the tegument, respectively. Two hundred and twenty-six variable proteins among the three seed parts were identified, being classified according to their function into eight main groups. The cotyledon presented the highest number of metabolic and storage proteins (89% of them are legumin) compared to the embryonic axis and tegument. The embryonic axis had the highest number of the species within the protein fate group. The tegument presented the largest number of the defense-/stress-related and cytoskeleton proteins. This distribution is in good agreement with the biological role of the tissues. The study of the seed tissue proteome demonstrated a compartmentalization of pathways and a division of metabolic tasks between embryonic axis, cotyledon and tegument. This compartmentalization uncovered in our study should provide a starting point for understanding, at the molecular level, the particularities of the recalcitrant seeds.

Plant Structure and Specificity - Challenges and Sample Preparation Considerations for Proteomics

Plants are considered as a simple structured organism when compared to humans and other vertebrates. The number of organs and tissue types is very limited. Instead the origin of the complexity comes from the high number and variety of plant species that exist, with >300,000 compared to 5000 in mammals. Proteomics, defined as the large-scale study of the proteins present in a tissue, cell or cellular compartment at a defined time point, was introduced in 1994. However, the first publications reported in the plant proteomics field only appeared at the beginning of the twenty-first century. Since these early years, the increase of proteomic studies in plants has only followed a linear trend. The main reason for this stems from the challenges specific to studying plants, those of protein extraction from cells with variously strengthened cellulosic cell walls, and a high abundance of interfering compounds, such as phenolic compounds and pigments located in plastids throughout the plant. Indeed, the heterogeneity between different organs and tissue types, between species and different developmental stages, requires the use of optimized plant protein extraction methods as described in this section. The second bottleneck of plant proteomics, which will not be discussed or reviewed here, is the lack of genomic information. Without sequence databases of the >300,000 species, proteomic studies of plants, especially of those that are not considered economically relevant, are impossible to accomplish.

Role of the proteome in phytohormonal signaling

Phytohormones are orchestrators of plant growth and development. A lot of time and effort has been invested in attempting to comprehend their complex signaling pathways but despite success in elucidating some key components, molecular mechanisms in the transduction pathways are far from being resolved. The last decade has seen a boom in the analysis of phytohormone-responsive proteins. Abscisic acid, auxin, brassinosteroids, cytokinin, ethylene, gibberellins, nitric oxide, oxylipins, strigolactones, salicylic acid--all have been analyzed to various degrees. For this review, we collected data from proteome-wide analyses resulting in a list of over 2000 annotated proteins from Arabidopsis proteomics and nearly 500 manually filtered protein families merged from all the data available from different species. We present the currently accepted model of phytohormone signaling, highlight the contributions made by proteomic-based research and describe the key nodes in phytohormone signaling networks, as revealed by proteome analysis. These include ubiquitination and proteasome mediated degradation, calcium ion signaling, redox homeostasis, and phosphoproteome dynamics. Finally, we discuss potential pitfalls and future perspectives in the field. This article is part of a Special Issue entitled: Plant Proteomics--a bridge between fundamental processes and crop production, edited by Dr. Hans-Peter Mock.

Effects of moist cold stratification on germination, plant growth regulators, metabolites and embryo ultrastructure in seeds of Acer morrisonense (Sapindaceae)

Breaking of seed dormancy by moist cold stratification involves complex interactions in cells. To assess the effect of moist cold stratification on dormancy break in seeds of Acer morrisonense, we monitored percentages and rates of germination and changes in plant growth regulators, sugars, amino acids and embryo ultrastructure after various periods of cold stratification. Fresh seeds incubated at 25/15 °C for 24 weeks germinated to 61%, while those cold stratified at 5 °C for 12 weeks germinated to 87% in 1 week. Neither exogenous GA3 nor GA4 pretreatment significantly increased final seed germination percentage. Total ABA content of seeds cold stratified for 12 weeks was reduced about 3.3-fold, to a concentration similar to that in germinated seeds (radicle emergence). Endogenous GA3 and GA7 were detected in 8-week and 12-week cold stratified seeds but not in fresh seeds. Numerous protein and lipid bodies were present in the plumule, first true leaves and cotyledons of fresh seeds. Protein and lipid bodies decreased greatly during cold stratification, and concentrations of total soluble sugars and amino acids increased. The major non-polar sugars in fresh seeds were sucrose and fructose, but sucrose increased and fructose decreased significantly during cold stratification. The major free amino acids were proline and tryptophan in fresh seeds, and proline increased and tryptophan decreased during cold stratification. Thus, as dormancy break occurs during cold stratification seeds of A. morrisonense undergo changes in plant growth regulators, proteins, lipids, sugars, amino acids and cell ultrastructure.

Proteomic changes during tuber dormancy release process revealed by iTRAQ quantitative proteomics in potato

Given that limited information is available with regard to tuber dormancy release related proteome, we conducted proteome analysis of tuber dormancy release process at dormant tuber (DT), dormancy release tuber (DRT) and sprouting tuber (ST) using the iTRAQ technology. A total of 1,752 proteins were identified. Among them, a subset of 316 proteins was screened as significant up- (137) and down regulated (179) between DT vs DRT. A subset of 120 proteins experienced significant up- (40) or down-regulation (80) between DRT vs ST. The differentially expressed proteins were grouped into 11 functional categories. Proteins enriched in functional categories of major carbohydrate (CHO) metabolism, glycolysis, fermentation, amino acid metabolism, protein and transport were highly up-regulated, while functional categories of photosynthesis and RNA were down-regulated between DT vs DRT. Proteins enriched in functional groups of protein, cell wall, lipid metabolism, miscellaneous, and signaling were strongly up-regulated, while functional categories of photosynthesis, hormone metabolism and protein were down-regulated between DRT vs ST. Consistent with previous documented differentially expressed genes, most of differentially expressed proteins were also identified between DT and DRT, indicating the metabolism shift from growth suspension to growth activation as tubers dormancy breaking. The changes in protein profiles showed lower concordance with corresponding alterations in transcript levels, indicating possible transcriptional and posttranscriptional regulation. Furthermore, the possible mechanism of tuber dormancy release was discussed in relation to what was known in transcripts change and other plant models from carbohydrate metabolism, protein metabolism, stress response, redox regulation, transcription regulation, DNA metabolism, amino acid metabolism, development, signaling as well as hormone metabolism.

Gel-based comparative phosphoproteomic analysis on rice embryo during germination

Seed germination is a well regulated process, which incorporates many events including signal transduction, mobilization of reserves, reactive oxygen species scavenging and cell division. Although many transcriptomic and proteomic studies have been conducted on this process, regulation of protein modification has not been studied. To better understand the mechanism, a gel-based comparative phosphoproteomic study was performed on rice embryo during the germination process. In total, 168 protein spots exhibited significantly changed Pro-Q staining intensity during germination. Using matrix-assisted laser deionization-time of flight/time of flight mass spectrometry (MALDI-TOF/TOF MS) analysis, 193 proteins were identified. By combining Pro-Q and Coomassie brilliant blue stain intensity analyses, 109 proteins were verified to be phosphorylation regulation proteins. Functional analyses indicated that phosphorylation of proteins involved in stress response and storage was gradually enhanced. Phosphorylation of signal transduction proteins was mainly activated during the early stage of germination, while stress response and storage protein phosphorylation were enhanced at the late stage. Enzyme assays proved that the phosphorylation of fructokinase, pyruvate kinase, malate dehydrogenase, GDP-mannose 3,5-epimerase1, ascorbate peroxidase and glutathione S-transferase could consistently enhance their activity. This study showed the dynamic changes of protein phosphorylation status in rice embryo during germination and provided new insight into understanding the mechanism underlying this process.

Comparative proteomic analysis of somatic embryo maturation in Carica papaya L

Background

Somatic embryogenesis is a complex process regulated by numerous factors. The identification of proteins that are differentially expressed during plant development could result in the development of molecular markers of plant metabolism and provide information contributing to the monitoring and understanding of different biological responses. In addition, the identification of molecular markers could lead to the optimization of protocols allowing the use of biotechnology for papaya propagation and reproduction. This work aimed to investigate the effects of polyethylene glycol (PEG) on somatic embryo development and the protein expression profile during somatic embryo maturation in papaya (Carica papaya L.).

Results

The maturation treatment supplemented with 6% PEG (PEG6) resulted in the greatest number of somatic embryos and induced differential protein expression compared with cultures grown under the control treatment. Among 135 spots selected for MS/MS analysis, 76 spots were successfully identified, 38 of which were common to both treatments, while 14 spots were unique to the control treatment, and 24 spots were unique to the PEG6 treatment. The identified proteins were assigned to seven categories or were unclassified. The most representative class of proteins observed in the control treatment was associated with the stress response (25.8%), while those under PEG6 treatment were carbohydrate and energy metabolism (18.4%) and the stress response (18.4%).

Conclusions

The differential expression of three proteins (enolase, esterase and ADH3) induced by PEG6 treatment could play an important role in maturation, and these proteins could be characterized as candidate biomarkers of somatic embryogenesis in papaya.

Proteomic analysis of embryogenesis and the acquisition of seed dormancy in Norway maple (Acer platanoides L.)

The proteome of zygotic embryos of Acer platanoides L. was analyzed via high-resolution 2D-SDS-PAGE and MS/MS in order to: (1) identify significant physiological processes associated with embryo development; and (2) identify changes in the proteome of the embryo associated with the acquisition of seed dormancy. Seventeen spots were identified as associated with morphogenesis at 10 to 13 weeks after flowering (WAF). Thirty-three spots were associated with maturation of the embryo at 14 to 22 WAF. The greatest changes in protein abundance occurred at 22 WAF, when seeds become fully mature. Overall, the stage of morphogenesis was characterized by changes in the abundance of proteins (tubulins and actin) associated with the growth and development of the embryo. Enzymes related to energy supply were especially elevated, most likely due to the energy demand associated with rapid growth and cell division. The stage of maturation is crucial to the establishment of seed dormancy and is associated with a higher abundance of proteins involved in genetic information processing, energy and carbon metabolism and cellular and antioxidant processes. Results indicated that a glycine-rich RNA-binding protein and proteasome proteins may be directly involved in dormancy acquisition control, and future studies are warranted to verify this association.

A systematic proteomic analysis of NaCl-stressed germinating maize seeds

Salt (NaCl) is a common physiological stressor of plants. To better understand how germinating seeds respond to salt stress, we examined the changes that occurred in the proteome of maize seeds during NaCl-treated germination. Phenotypically, salt concentrations less than 0.2 M appear to delay germination, while higher concentrations disrupt development completely, leading to seed death. The identities of 96 proteins with expression levels altered by NaCl-incubation were established using 2-DE-MALDI-TOF-MS and 2-DE-MALDI-TOF-MS/MS. Of these 96 proteins, 79 were altered greater than twofold when incubated with a 0.2 M salt solution, while 51 were altered when incubated with a 0.1 M salt solution. According to their functional annotations in the Swiss-Prot protein-sequence databases, these proteins are mainly involved in seed storage, energy metabolism, stress response, and protein metabolism. Notably, the expression of proteins that respond to abscisic acid signals increased in response to salt stress. The results of this study provide important clues as to how NaCl stresses the physiology of germinating maize seeds.

Proteomic insights into seed germination in response to environmental factors

Seed germination is a critical process in the life cycle of higher plants. During germination, the imbibed mature seed is highly sensitive to different environmental factors.However, knowledge about the molecular and physiological mechanisms underlying the environmental effects on germination has been lacking. Recent proteomic work has provided invaluable insight into the molecular processes in germinating seeds of Arabidopsis, rice (Oryza sativa), soybean (Glycine max), barley (Hordeum vulgare), maize (Zeamays), tea (Camellia sinensis), European beech (Fagus sylvatica), and Norway maple (Acer platanoides) under different treatments including metal ions (e.g. copper and cadmium), drought, low temperature, hormones, and chemicals (gibberellic acid, abscisic acid, salicylic acid, and α-amanitin), as well as Fusarium graminearum infection. A total of 561 environmental factor-responsive proteins have been identified with various expression patterns in germinating seeds. The data highlight diverse regulatory and metabolic mechanisms upon seed germination, including induction of environmental factor-responsive signaling pathways, seed storage reserve mobilization and utilization, enhancement of DNA repair and modification, regulation of gene expression and protein synthesis, modulation of cell structure, and cell defense. In this review, we summarize the interesting findings and discuss the relevance and significance for our understanding of environmental regulation of seed germination.

The involvement of the mitochondrial peroxiredoxin PRXIIF in defining physiological differences between orthodox and recalcitrant seeds of two Acer species

Norway maple (Acer platanoides L., orthodox) and sycamore (Acer pseudoplatanus L., recalcitrant) belong to the same genus and grow under similar climatic conditions, but their seeds differ in their tolerance to desiccation. The initial water content (WC) of the seeds used in this study was 50%, and they were dried to 40, 20 and 7%. The mitochondrial peroxiredoxin IIF (PRXIIF) was identified in seeds of both species by immunoblotting. Semiquantitative RT-PCR analyses indicated that the transcript level of PRXIIF in both types of seeds increased during different stages of desiccation and was higher in seeds of Norway maple than in sycamore. General proteome analyses showed important differences between orthodox and recalcitrant seeds. In sycamore seeds that had been desiccated to a 7% WC, the number of protein spots and the levels of those spots were lower than in desiccation-tolerant Norway maple seeds. Post-translational modifications of PRXIIF in seeds at a 50% WC were detected via 2D electrophoresis and subsequent western blot analysis. The detected shift in the pI values (± 0.3) in A. pseudoplatanus was possibly caused by phosphorylation because several potential phosphorylation sites were predicted in silico for that protein. The gene and amino acid sequences were obtained and aligned with known sequences of other plant PRXIIF genes and proteins. High values of sequence identity were noted between the PRXIIF protein sequences of Acer species, Populus trichocarpa Torr. & A. Gray and Arabidopsis thaliana (L.) Heynh. The involvement of PRXIIF in defining the physiological differences between desiccation-tolerant and desiccation-sensitive Acer seeds is discussed in the context of its role in mitochondrial redox homeostasis.

Changes in the protein patterns in pea (Pisum sativum L.) roots under the influence of long- and short-term chilling stress and post-stress recovery

Amongst many factors restricting geographical distribution of plants and crop productivity, low temperature is one of the most important. To gain better understanding of the molecular response of germinating pea (Pisum sativum L.) to low temperature, we investigated the influence of long and short chilling stress as well as post-stress recovery on the alterations in the root proteomes. The impact of long stress was examined on the pea seeds germinating in the continuous chilling conditions of 10 °C for 8 days (LS). To examine the impact of short stress, pea seeds germinating for 72 h in the optimal temperature of 20 °C were subjected to 24-h chilling (SS). Additionally, both stress treatments were followed by 24 h of recovery in the optimal conditions (accordingly LSR and SR). Using the 2D gel electrophoresis and MALDI-TOF MS protein identification, it was revealed, that most of the proteins undergoing regulation under the applied conditions were implicated in metabolism, protection against stress, cell cycle regulation, cell structure maintenance and hormone synthesis, which altogether may influence root growth and development in the early stages of plant life. The obtained results have shown that most of detected alterations in the proteome patterns of pea roots are dependent on stress duration. However, there are some analogical response pathways which are triggered regardless of stress length. The functions of proteins which accumulation has been changed by chilling stress and post-stress recovery are discussed here in relation to their impact on pea roots development.

Integrated analysis of seed proteome and mRNA oxidation reveals distinct post-transcriptional features regulating dormancy in wheat (Triticum aestivum L.)

Wheat seeds can be released from a dormant state by after-ripening; however, the underlying molecular mechanisms are still mostly unknown. We previously identified transcriptional programmes involved in the regulation of after-ripening-mediated seed dormancy decay in wheat (Triticum aestivum L.). Here, we show that seed dormancy maintenance and its release by dry after-ripening in wheat is associated with oxidative modification of distinct seed-stored mRNAs that mainly correspond to oxidative phosphorylation, ribosome biogenesis, nutrient reservoir and α-amylase inhibitor activities, suggesting the significance of post-transcriptional repression of these biological processes in regulating seed dormancy. We further show that after-ripening induced seed dormancy release in wheat is mediated by differential expression of specific proteins in both dry and hydrated states, including those involved in proteolysis, cellular signalling, translation and energy metabolism. Among the genes corresponding to these proteins, the expression of those encoding α-amylase/trypsin inhibitor and starch synthase appears to be regulated by mRNA oxidation. Co-expression analysis of the probesets differentially expressed and oxidized during dry after-ripening along with those corresponding to proteins differentially regulated between dormant and after-ripened seeds produced three co-expressed gene clusters containing more candidate genes potentially involved in the regulation of seed dormancy in wheat. Two of the three clusters are enriched with elements that are either abscisic acid (ABA) responsive or recognized by ABA-regulated transcription factors, indicating the association between wheat seed dormancy and ABA sensitivity.

Suppression Subtractive Hybridization Analysis of Genes Regulated by Application of Exogenous Abscisic Acid in Pepper Plant (Capsicum annuum L.) Leaves under Chilling Stress

Low temperature is one of the major factors limiting pepper (Capsicum annuum L.) production during winter and early spring in non-tropical regions. Application of exogenous abscisic acid (ABA) effectively alleviates the symptoms of chilling injury, such as wilting and formation of necrotic lesions on pepper leaves; however, the underlying molecular mechanism is not understood. The aim of this study was to identify genes that are differentially up- or downregulated in ABA-pretreated hot pepper seedlings incubated at 6°C for 48 h, using a suppression subtractive hybridization (SSH) method. A total of 235 high-quality ESTs were isolated, clustered and assembled into a collection of 73 unigenes including 18 contigs and 55 singletons. A total of 37 unigenes (50.68%) showed similarities to genes with known functions in the non-redundant database; the other 36 unigenes (49.32%) showed low similarities or unknown functions. Gene ontology analysis revealed that the 37 unigenes could be classified into nine functional categories. The expression profiles of 18 selected genes were analyzed using quantitative RT-PCR; the expression levels of 10 of these genes were at least two-fold higher in the ABA-pretreated seedlings under chilling stress than water-pretreated (control) plants under chilling stress. In contrast, the other eight genes were downregulated in ABA-pretreated seedlings under chilling stress, with expression levels that were one-third or less of the levels observed in control seedlings under chilling stress. These results suggest that ABA can positively and negatively regulate genes in pepper plants under chilling stress.

Differential expression of proteins associated with seasonal bud dormancy at four critical stages in Japanese apricot

Dormancy is of great significance in the growth and development of deciduous fruit trees. We used a combination of two-dimensional gel electrophoresis (2-DE) and matrix-assisted laser desorption/ionisation time of flight/time of flight mass spectrometry (MALDI-TOF/TOF MS) to identify the differentially expressed proteome of Japanese apricot flower buds at four critical stages, from paradormancy before leaf fall to dormancy release. More than 400 highly reproducible protein spots (P < 0.05) were detected: 34 protein spots showed a greater than twofold difference in expression values, of which 32 protein spots were confidently identified from databases. Identified proteins were classified into six functional categories: stress response and defence (11), energy metabolism (ten), protein metabolism (five), cell structure (three), transcription (one) and unclassified (two). The glyoxalase I homologue could help Japanese apricot survival under various abiotic and biotic stresses, greatly contributing to its dormancy. Enolase, thioredoxin family proteins and triose phosphate isomerase provide adequate energy to complete consecutive dormancy release and bud break in Japanese apricot. Cinnamyl alcohol dehydrogenase 9 and arginase enhance the resilience of plants, enabling them to complete dormancy safely. Analysis of functions of identified proteins and related metabolic pathways will increase our knowledge of dormancy in woody plants.

Proteomics research on forest trees, the most recalcitrant and orphan plant species

The contribution of proteomics to the knowledge of forest tree (the most recalcitrant and almost forgotten plant species) biology is being reviewed and discussed, based on the author's own research work and papers published up to November 2010. This review is organized in four introductory sections starting with the definition of forest trees (1), the description of the environmental and economic importance (2) and its derived current priorities and research lines for breeding and conservation (3) including forest tree genomics (4). These precede the main body of this review: a general overview to proteomics (5) for introducing the forest tree proteomics section (6). Proteomics, defined as scientific discipline or experimental approach, it will be discussed both from a conceptual and methodological point of view, commenting on realities, challenges and limitations. Proteomics research in woody plants is limited to a reduced number of genera, including Pinus, Picea, Populus, Eucalyptus, and Fagus, mainly using first-generation approaches, e.g., those based on two-dimensional electrophoresis coupled to mass spectrometry. This area joins the own limitations of the technique and the difficulty and recalcitrance of the plant species as an experimental system. Furthermore, it contributes to a deeper knowledge of some biological processes, namely growth, development, organogenesis, and responses to stresses, as it is also used in the characterization and cataloguing of natural populations and biodiversity (proteotyping) and in assisting breeding programmes.

Using proteomics to study sexual reproduction in angiosperms

While a relative latecomer to the postgenomics era of functional biology, the application of mass spectrometry-based proteomic analysis has increased exponentially over the past 10 years. Some of this increase is the result of transition of chemists, physicists, and mathematicians to the study of biology, and some is due to improved methods, increased instrument sensitivity, and better techniques of bioinformatics-based data analysis. Proteomic Biological processes are typically studied in isolation, and seldom are efforts made to coordinate results obtained using structural, biochemical, and molecular-genetic strategies. Mass spectrometry-based proteomic analysis can serve as a platform to bridge these disparate results and to additionally incorporate both temporal and anatomical considerations. Recently, proteomic analyses have transcended their initial purely descriptive applications and are being employed extensively in studies of posttranslational protein modifications, protein interactions, and control of metabolic networks. Herein, we provide a brief introduction to sample preparation, comparison of gel-based versus gel-free methods, and explanation of data analysis emphasizing plant reproductive applications. We critically review the results from the relatively small number of extant proteomics-based analyses of angiosperm reproduction, from flowers to seedlings, and speculate on the utility of this strategy for future developments and directions.

Proteomic approach to analyze dormancy breaking of tree seeds

In forest broadleaves from the temperate zone, a large number of species exhibit seed dormancy phenomena. Tree seeds show some of the most pronounced and complicated forms of dormancy in the plant kingdom. Many seeds are deeply physiologically dormant whatever their moisture level and age. However, dormancy can usually be overcome by a cold or warm stratification for several months. The transition from seed dormancy to germination is a multi-step process. In combination with the availability of genome sequence data, proteomics has opened up enormous possibilities for identifying the total set of expressed proteins as well as expression changes during dormancy breaking. The proteomic approach used for analysis of dormancy breaking of tree seeds offers new data allowing better understanding of the mechanism of deep physiological dormancy. The results of proteomic studies on dormancy breaking and the presence of abscisic and gibberellic acids in tree seeds (beech Fagus sylvatica L., Norway maple Acer platanoides L. and sycamore Acer pseudoplatanus L.), help to explain this process better. Most of the changes in protein expression were observed at the end of stratification and in the germinated seeds. This is the most active period of dormancy breaking when seeds pass from the quiescent state to germination. The analysis of the proteins' function showed that the mechanism of seed dormancy breaking involves many processes. Energy metabolism, proteasome, transcription, protein synthesis, signal transduction and methionine metabolism proteins have a special importance.

The role of abscisic acid and auxin in the response of poplar to abiotic stress

The plant hormones auxin and abscisic acid may at first sight appear to be a conflicting pair of plant regulators. Abscisic acid content increases during stress and protects plant water status. The content of free auxin in the developing xylem of poplar declines during stress, while auxin conjugates increase. This indicates that specific down-regulation of a signal transduction chain is important in plant adaptation to stress. Diminished auxin content may be a factor that adapts growth and wood development of poplar during adverse environmental conditions. To allow integration of environmental signals, abscisic acid and auxin must interact. Data are accumulating that abscisic acid-auxin cross-talk exists in plants. However, knowledge of the role of plant hormones in the response of trees to stress is scarce. Our data show that differences in the localisation of ABA synthesis exist between the annual, herbaceous plant Arabidopsis and the perennial woody species, poplar.