An increase in pectin methyl esterase activity accompanies dormancy breakage and germination of yellow cedar seeds

Mutation of AtPME2, a pH-Dependent Pectin Methylesterase, Affects Cell Wall Structure and Hypocotyl Elongation

Pectin methylesterases (PMEs) modify homogalacturonan's chemistry and play a key role in regulating primary cell wall mechanical properties. Here, we report on Arabidopsis AtPME2, which we found to be highly expressed during lateral root emergence and dark-grown hypocotyl elongation. We showed that dark-grown hypocotyl elongation was reduced in knock-out mutant lines as compared to the control. The latter was related to the decreased total PME activity as well as increased stiffness of the cell wall in the apical part of the hypocotyl. To relate phenotypic analyses to the biochemical specificity of the enzyme, we produced the mature active enzyme using heterologous expression in Pichia pastoris and characterized it through the use of a generic plant PME antiserum. AtPME2 is more active at neutral compared to acidic pH, on pectins with a degree of 55-70% methylesterification. We further showed that the mode of action of AtPME2 can vary according to pH, from high processivity (at pH8) to low processivity (at pH5), and relate these observations to the differences in electrostatic potential of the protein. Our study brings insights into how the pH-dependent regulation by PME activity could affect the pectin structure and associated cell wall mechanical properties.

Exogenous spraying of IAA improved the efficiency of microspore embryogenesis in Wucai (Brassica campestris L.) by affecting the balance of endogenous hormones, energy metabolism, and cell wall degradation

BACKGROUND

Microspore embryogenesis is an extraordinarily complicated process, comprehensively regulated by a composite network of physiological and molecular factors, among which hormone is one of the most crucial factors. Auxin is required for stress-induced microspore reprogramming, however, the mechanism of its regulation of microspore embryogenesis is still unclear.

RESULTS

In this study, we found exogenously spraying 100 mg·L^- 1 IAA on the buds of Wucai significantly increased the rate of microspore embryogenesis, and moreover accelerated the process of embryogenesis. Physiological and biochemical tests showed that the contents of amino acids, soluble total sugar, soluble protein, and starch were significantly increased after IAA treatment. Furthermore, exogenously spraying 100 mg·L^- 1 IAA significantly enhanced IAA, GA₄, and GA₉ content, increased catalase (CAT) and malondialdehyde (MDA) activity, and reduced abscisic acid (ABA), MDA and soluble protopectin content, H₂O₂ and O₂·^- production rate in the bud with the largest population of late-uninucleate-stage microspores. Transcriptome sequencing was performed on buds respectively treated with 100 mg·L^- 1 IAA and fresh water. A total of 2004 DEGs were identified, of which 79 were involved in micropores development, embryonic development and cell wall formation and modification, most of which were upregulated. KEGG and GO analysis revealed that 9.52% of DEGs were enriched in plant hormone synthesis and signal transduction pathways, pentose and glucuronic acid exchange pathways, and oxidative phosphorylation pathways.

CONCLUSIONS

These findings indicated that exogenous IAA altered the contents of endogenous hormone content, total soluble sugar, amino acid, starch, soluble protein, MDA and protopectin, the activities of CAT and peroxidase (POD), and the production rate of H₂O₂ and O₂·^-. Combined with transcriptome analysis, it was found that most genes related to gibberellin (GA) and Auxin (IAA) synthesis and signal transduction, pectin methylase (PME) and polygalacturonase (PGs) genes and genes related to ATP synthesis and electron transport chain were upregulated, and genes related to ABA synthesis and signal transduction were downregulated. These results indicated that exogenous IAA treatment could change the balance of endogenous hormones, accelerate cell wall degradation, promote ATP synthesis and nutrient accumulation, inhibit ROS accumulation, which ultimately promote microspore embryogenesis.

Escaping drought: The pectin methylesterase inhibitor gene Slpmei27 can significantly change drought resistance in tomato

Drought stress will lead to a decrease in tomato yield and poor flavour, yield and quality, resulting in economic losses in agricultural production. Mining the key genes regulating tomato drought resistance is of great significance to improve the drought resistance of tomato plants. The cell wall can directly participate in the plant drought stress response as one of the main components of the cell wall, and the regulation of pectin content in plant drought resistance is still unclear. Here, the candidate gene Solyc08g006690 (Slpmei27) was obtained by fine mapping based on genome sequencing technology (BSA-seq) of late-maturing stress-resistant tomato mutants found in the field. Slpmei27 is expressed in the cell wall. The transient silencing of Slpmei27 by VIGS significantly improved the drought resistance of tomato. Meanwhile, Slpmei27 silencing could significantly change the cell wall structure of plants, change the stomatal pass rate, reduce the water loss rate of plants, improve the scavenging ability of reactive oxygen species, change the redox balance in plants, and thus improve the drought resistance of tomato. The promoter region of this gene contains a large number of hormone-response and stress-response binding sites. The promoter region of the Slpmei27 gene in the mutant could lower the expression of downstream genes. Through this study, the mechanism by which Slpmei27 improves tomato drought resistance was revealed, and the relationship between pectin methyl ester metabolism and plant drought resistance was established, providing a theoretical basis for the production of high-quality tomato materials with high drought resistance.

The metaxenia effects of different pollen grains on secondary metabolites enzymes and sugars of 'Piarom' date palm fruit

In this research, the characteristics of pollen were studied in eight pollinating cultivars of date palm, namely, ‘Shahani’, ‘Kabkab’, ‘Zahedi’, ‘Beraem’, ‘Faryab’, ‘Sheikhali’, ‘Fard’ and ‘Jarvis’. The characteristics were compared and metaxenia effects were evaluated on secondary metabolites, enzymes and other biochemical compounds of ‘Piarom’ date fruits. The evaluations were carried out during four stages of fruit growth and development. The pollen of these eight pollinating cultivars were compared in terms of carbohydrates, proteins, starch, total phenol, flavonoids, pectin methyl esterase, and amylase enzymes. According to the results, the pollen of ‘Sheikhali’, ‘Fard’, ‘Zahedi’ and ‘Shahani’ cultivars contained more of the above compounds, compared to the other cultivars. Regarding the effects of pollen on the composition of ‘Piarom’ date fruits, ‘Fard’ and ‘Sheikhali’ pollen produced the lowest amount of soluble tannin, which resulted in a better quality of ‘Piarom’ date fruits. Pollen was also obtained from ‘Sheikhali’ and ‘Fard’ cultivars for evaluations, showing that they led to the highest amounts of glucose and fructose in the fruits. Regarding the sucrose amount, ‘Jarvis’ and ‘Shikhali’ produced the best results. Pollen of ‘Sheikhali’ and ‘Fard’ cultivars caused the lowest amount of chlorophyll at the different stages of fruit growth, indicating a better decomposition of fruit chlorophyll and, as a result, better fruit quality. Pollen of ‘Sheikhali’ and ‘Fard’ cultivars produced the highest amounts of secondary metabolites such as total phenol, carotenoids and anthocyanin at the different stages of fruit development. The pollen of ‘Fard’ and ‘Sheikhali’ cultivars produced the highest levels of polygalacturonase, cellulase and invertase enzymes at different growth stages of the ‘Piarom’ date fruit. Regarding cellulase enzyme, fruits of the ‘Zahedi’ cultivar had more cellulase than the fruits of ‘Sheikhali’. In general, the pollen of ‘Fard’ and ‘Sheikhali, in comparison with other cultivars, improved the quantity and quality of ‘Piarom’ date fruits, due to their metaxenia properties.

Endosperm weakening: The gateway to a seed's new life

Seed germination is a crucial stage in a plant's life cycle, during which the embryo, surrounded by several tissues, undergoes a transition from the quiescent to a highly active state. Endosperm weakening, a key step in this transition, plays an important role in radicle protrusion. Endosperm weakening is initiated upon water uptake, followed by multiple key molecular events occurring within and outside endosperm cells. Although available transcriptomes have provided information about pivotal genes involved in this process, a complete understanding of the signaling pathways are yet to be elucidated. Much remains to be learnt about the diverse intercellular signals, such as reactive oxygen species-mediated redox signals, phytohormone crosstalk, environmental cue-dependent oxidative phosphorylation, peroxisomal-mediated pectin degradation, and storage protein mobilization during endosperm cell wall loosening. This review discusses the evidences from recent researches into the mechanism of endosperm weakening. Further, given that the endosperm has great potential for manipulation by crop breeding and biotechnology, we offer several novel insights, which will be helpful in this research field and in its application to the improvement of crop production.

Effects of Exogenous Phthalic Acid on Seed Germination, Root Physiological Characteristics, and Mineral Element Absorption of Watermelon

To understand the effect of exogenous PA on the watermelon root system, the watermelon variety ‘Zaojia 84–24’ was used as experimental material. This study investigated the effects of allelochemicals DIBP and DOP at varying different concentrations (0, 0.05, 0.1, 0.5, 1, and 4 mmol·L−1) on the physiological characteristics and mineral content of watermelon roots. The results revealed that proper PA treatment concentrations (0.05~0.1 mmol·L−1) promoted seed germination, increased the number of RBCs and the survival rate of RBCs, and enhanced the activities of PME and dehydrogenase in watermelon roots. In addition, proper PA treatment concentrations (0.05~0.1 mmol·L−1) promoted the activities of SOD, POD, CAT, and NR in watermelon roots. The contents of MDA and soluble protein were increased at 0.05~4 mmol·L−1 PA. In addition, proper PA treatment concentrations promoted the absorption and accumulation of P, K, Ca, Fe, Cu, and Zn elements in watermelon roots. These results indicate that PA at a concentration of 0.05~0.5 mmol·L−1 can promote watermelon seed germination, improve antioxidant enzyme activity of watermelon roots, and maintain normal physiological activities of watermelon by affecting absorption and accumulation of mineral elements in the root system.

The SNF5-type protein BUSHY regulates seed germination via the gibberellin pathway and is dependent on HUB1 in Arabidopsis

The SNF5-type protein BUSHY plays a role in the regulation of seed germination via the gibberellin pathway dependent on HUB1 in Arabidopsis thaliana. SWITCH/SUCROSE NONFERMENTING (SWI/SNF) complexes play diverse roles in plant development. Some components have roles in embryo development and seed maturation, however, whether the SNF5-type protein BUSHY (BSH), one of the components, plays a role in Arabidopsis seed related traits is presently unclear. In our study, we show that a loss-of-function mutation in BSH causes increased seed germination in Arabidopsis. BSH transcription was induced by the gibberellin (GA) inhibitor paclobutrazol (PAC) in the seed, and BSH regulates the expression of GA pathway genes, such as Gibberellin 3-Oxidase 1 (GA3OX1), Gibberellic Acid-Stimulated Arabidopsis 4 (GASA4), and GASA6 during seed germination. A genetic analysis showed that seed germination was distinctly improved in the bshga3ox1ga3ox2 triple mutant, indicating that BSH acts partially downstream of GA3OX1 and GA3OX2. Moreover, the regulation of seed germination by BSH in response to PAC is dependent on HUB1. These results provide new insights and clues to understand the mechanisms of phytohormones in the regulation of seed germination.

Genome-wide identification of PME genes, evolution and expression analyses in soybean (Glycine max L.)

BACKGROUND

Pectin methylesterase (PME) is one of pectin-modifying enzyme that affects the pectin homeostasis in cell wall and regulates plant growth and diverse biological processes. The PME genes have been well explored and characterized in different plants. Nevertheless, systematic research on the soybean (Glycine max L.) PME genes remain lacking.

RESULTS

We identified 127 Glycine max PME genes (GmPME) from the soybean Wm82.a2.v1 genome, which unevenly distributed on 20 soybean chromosomes. Phylogenetic analysis classified the GmPME genes into four clades (Group I, Group II, Group III and Group IV). GmPME gene members in the same clades displayed similar gene structures and motif patterns. The gene family expansion analysis demonstrated that segmental duplication was the major driving force to acquire novel GmPME genes compared to the tandem duplication events. Further synteny and evolution analyses showed that the GmPME gene family experienced strong purifying selective pressures during evolution. The cis-element analyses together with the expression patterns of the GmPME genes in various tissues suggested that the GmPME genes broadly participate in distinct biological processes and regulate soybean developments. Importantly, based on the transcriptome data and quantitative RT-PCR validations, we examined the potential roles of the GmPME genes in regulating soybean flower bud development and seed germination.

CONCLUSION

In conclusion, we provided a comprehensive characterization of the PME genes in soybean, and our work laid a foundation for the functional study of GmPME genes in the future.

Volatile signature indicates viability of dormant orthodox seeds

All seeds eventually die even under optimal storage conditions. The moment of viability loss is difficult to predict and detect. In order to differentiate between dead and viable dormant orthodox seeds, GC-MS analysis was used to non-invasively evaluate the volatile signature of seeds of Pyrus communis L. and Sorbus aucuparia L. Dormant seeds are capable of extended metabolic depression. However, their low metabolic rate remains largely unquantified, and there are no measurements of metabolites, i.e. volatile organic compounds (VOC) for physiologically dormant seeds during storage. Therefore, to address this issue, seeds were stored at a broad range of moisture content (MC) ranging from 2 to 30% under cryogenic (-196°C), cool (5°C) and elevated (40°C) temperatures. Volatile emission was highly dependent on seed MC and storage temperature and was higher under conditions associated with seed viability loss. However, changes in the emission of volatiles entrapped in seeds and released during 24 h after storage were detected for all conditions, providing insight into the processes occurring in dry dormant seeds. Among the 36 volatiles identified, three (acetaldehyde, ethanol, ethyl acetate) were highly correlated with seed germinability and show potential for the non-invasive screening of viability. Significantly, all three VOC are derived mostly from glycolysis and peroxidation and were detected even under very low moisture and temperature storage conditions. This is the first study to report on VOC accumulation and emission from physiologically dormant seeds and provide a broader view into their viability.

Exogenous salicylic acid regulates cell wall polysaccharides synthesis and pectin methylation to reduce Cd accumulation of tomato

Cadmium (Cd) is harmful to plant growth and can be easily transferred from soil to plants. Plant cell wall plays important role in preventing Cd from entering cells. Salicylic acid (SA) mediated defense response increases plant resistance to heavy metals. In this study, all tomato seedlings were pre-treated with 100 μM SA for 3 d, then seedlings were used to analyze the role of SA in regulating plant cell wall resistance to Cd stress. The results showed that exogenous SA significantly reduced Cd accumulation in tomato plants and changed Cd distribution. By analyzing the cell wall composition, it was found cellulose, hemicellulose, pectin, and lignin were induced by SA. Interestingly, the content of Cd in pectin decreased by SA pretreatment, however it was increased in cellulose. Gene expression analysis showed SA up-regulated the expression level of lignin and cellulose synthase genes, but down-regulated the expression of pectin methylesterase related genes. In addition, SA down-regulated the activity of pectin methylesterase. These results indicated that SA pretreatment up-regulated cell wall polysaccharide synthesis and related gene expression to thicken the cell wall and block Cd from passing through. Furthermore, SA decreased pectin methylesterase activity and content to reduce cell wall Cd accumulation and change the Cd partition ratio.

A Molecular Signal Integration Network Underpinning Arabidopsis Seed Germination

Seed dormancy is an adaptive trait defining where and when plants are established. Diverse signals from the environment are used to decide when to initiate seed germination, a process driven by the expansion of cells within the embryo. How these signals are integrated and transduced into the biomechanical changes that drive embryo growth remains poorly understood. Using Arabidopsis seeds, we demonstrate that cell-wall-loosening EXPANSIN (EXPA) genes promote gibberellic acid (GA)-mediated germination, identifying EXPAs as downstream molecular targets of this developmental phase transition. Molecular interaction screening identified transcription factors (TFs) that bind to both EXPA promoter fragments and DELLA GA-response regulators. A subset of these TFs is targeted each by nitric oxide (NO) and the phytochrome-interacting TF PIL5. This molecular interaction network therefore directly links the perception of an external environmental signal (light) and internal hormonal signals (GA and NO) with downstream germination-driving EXPA gene expression. Experimental validation of this network established that many of these TFs mediate GA-regulated germination, including TCP14/15, RAP2.2/2.3/2.12, and ZML1. The reduced germination phenotype of the tcp14 tcp15 mutant seed was partially rescued through ectopic expression of their direct target EXPA9. The GA-mediated control of germination by TCP14/15 is regulated through EXPA-mediated control of cell wall loosening, providing a mechanistic explanation for this phenotype and a previously undescribed role for TCPs in the control of cell expansion. This network reveals the paths of signal integration that culminate in seed germination and provides a resource to uncover links between the genetic and biomechanical bases of plant growth.

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The network linking integration of environmental signals to seed growth is mapped

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EXPANSIN gene expression is redundantly regulated and promotes GA-mediated germination

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The TCP14 transcription factor directly regulates EXPANSIN9 expression

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The tcp14/15 germination phenotype is complemented by EXPANSIN9 expression

Maternal environment alters dead pericarp biochemical properties of the desert annual plant Anastatica hierochuntica L

The dead organs enclosing embryos (DOEEs) emerge as central components of the dispersal unit (DU) capable for long-term storage of active proteins and other substances that affect seed performance and fate. We studied the effect of maternal environment (salt and salt+heat) on progeny DU (dry indehiscent fruit) focusing on pericarp properties of Anastatica hierochuntica. Stressed plants displayed increased seed abortion and low level and rate of germination. Hydrated pericarps released antimicrobial factors and allelopathic substances that inhibit germination of heterologous species. Proteome analysis of dead pericarps revealed hundreds of proteins, among them nucleases, chitinases and proteins involved in reactive oxygen species detoxification and cell wall modification. Salt treatment altered the composition and level of proteins stored in the pericarp. We observed changes in protein profile released from seeds of salt-treated plants with a notable increase in a small anti-fungal protein, defensin. The levels of phytohormones including IAA, ABA and salicylic acid were reduced in dead pericarps of stressed plants. The data presented here highlighted the predominant effects of maternal environment on progeny DUs of the desert plant A. hierochuntica, particularly on pericarp properties, which in turn might affect seed performance and fate, soil fertility and consequently plant biodiversity.

The leaf extract of crofton weed (Eupatorium adenophorum) inhibits primary root growth by inducing cell death in maize root border cells

The extract of crofton weed (Eupatorium adenophorum) inhibits seed germination and weed growth; however, the physiological mechanisms underlying the effect of crofton weed extract on the modulation of seedling growth and root system development remain largely unclear. In this study, we investigated the effects of the leaf extract of crofton weed (LECW) on primary root (PR) growth in maize seedlings. Treatment with LECW markedly inhibited seed germination and seedling growth in a dose-dependent manner. Physiological analysis indicated that the LECW induced reactive oxygen species (ROS) accumulation in root tips, thereby leading to cell swelling and deformation both in the root cap and elongation zone of root tips, finally leading to cell death in root border cells (RBCs) and PR growth inhibition. The LECW also inhibited pectin methyl esterase (PME) activity, thereby decreasing the RBC number. Taken together, our results indicated that the LECW inhibited PR growth by inducing ROS accumulation and subsequent cell death in RBCs. The present study provides a better understanding of how the LECW modifies root system development and provides insight for evaluating the toxicity of crofton weed extracts in plants.

Aeration Increases Cadmium (Cd) Retention by Enhancing Iron Plaque Formation and Regulating Pectin Synthesis in the Roots of Rice (Oryza sativa) Seedlings

BACKGROUND

Aeration and water management increasing rhizosphere oxygen amount significantly promote rice (Oryza sativa) growth and yield, but the effect of root aeration on cadmium (Cd) toxicity and accumulation in rice seedlings under hydroponic culture remains unclear.

RESULTS

Results showed that aeration promoted rice seedling growth and alleviated Cd toxicity. Transverse section discovered that Cd accelerated root mature and senescence while aeration delayed the mature and senescence of roots. Non-invasive Micro-test Technology (NMT) showed that aeration increased net O2 and Cd2+ influxes on the surface of roots while decreased net Cd2+ influx in xylem. Perls blue staining showed that aeration and Cd treatments increased iron plaque formation on the surface of roots. Results of metal concentration analysis showed that besides increasing Cd retention in iron plaque, aeration also increasing Cd retention in the cell wall of rice roots. Cell wall component analysis showed that aeration not only increased pectin content but also decreased pectin methylesterification degree (PMD) by increasing pectin methylesterase (PME) activity.

CONCLUSIONS

All of these results indicate that aeration not only delays root mature and senescence but also increases Cd retention in roots by enhancing iron plaque formation and regulating pectin synthesis in the roots of rice seedlings.

Seed germination and dormancy: The classic story, new puzzles, and evolution

This review highlights recent progresses in seed germination and dormancy research. Research on the weakening of the endosperm during germination, which is almost a classic theme in seed biology, was resumed by α-xylosidase studies. Strong genetic evidence was presented to suggest that the quality control of xyloglucan biosynthesis in the endosperm (and the embryo) plays a critical role in germination. Further analyses on the endosperm and the adjacent layers have suggested that the cutin coat in the endosperm-testa interphase negatively affects germination while the endosperm-embryo interphase produces a sheath that facilitates germination. These progresses significantly advanced our understanding of seed germination mechanisms. A breakthrough in dormancy research, on the other hand, revealed the unique abscisic acid signaling pathway that is regulated by DELAY OF GERMINATION1 (DOG1). The detailed analysis of DOG1 expression uncovered the intriguing story of reciprocal regulation of the sense-antisense pair, which generated new questions. Recent studies also suggested that the DOG1 function is not limited to dormancy but extended through general seed maturation, which provokes questions about the evolution of DOG1 family proteins. Seed biology is becoming more exciting with the classic stories being revitalized and new puzzles emerging from the frontier.

Gene expression analysis of bud burst process in European hazelnut (Corylus avellana L.) using RNA-Seq

The control of bud burst process depending on temperature is crucial factor in woody perennial plants to survive in unfavorable ecological conditions. Although it has important economic and agronomic values, little information is available on the molecular mechanism of the bud burst process in Corylus avellana. Here for the first time, we conducted a de novo transcriptome-based experiment using eco-dormant leaf bud tissues. Four transcriptome libraries were constructed from the leaf bud tissues and sequenced via Illumina platform. Transcriptome analysis revealed 86,394 unigenes with a mean length of 1189 nt and an N50 of 1916 nt. Among these unigenes, 63,854 (73.78%) of them were annotated by at least one database. De novo assembled transcripts were enriched in phenylpropanoid metabolism, phytohormone biosynthesis and signal transduction pathways. Analyses of phytohormone-associated genes revealed important changes during bud burst, in response to gibberellic acid, auxin, and brassinosteroids. Approximately 2163 putative transcription factors were predicted, of which the largest number of unique transcripts belonged to the MYB transcription factor family. These results contribute to a better understanding of the regulation of bud burst genes in perennial plants.

Pooled whole-genome sequencing of interspecific chestnut (Castanea) hybrids reveals loci associated with differences in caching behavior of fox squirrels (Sciurus niger L.)

Dispersal of seeds by scatter-hoarding rodents is common among tropical and temperate tree species, including chestnuts in the genus Castanea. Backcrossed (BC) interspecific hybrid chestnuts exhibit wide variation in seed traits: as the parent species (Castanea dentata and C. mollissima) have distinct seed phenotypes and tend to be handled differently by seed dispersers, phenotypic variation in BC trees is likely due to inheritance of genes that have undergone divergent evolution in the parent species. To identify candidate genomic regions for interspecific differences in seed dispersal, we used tagged seeds to measure average dispersal distance for seeds of third-generation BC chestnuts and sequenced pooled whole genomes of mother trees with contrasting seed dispersal: high caching rate/long distance; low caching rate/short distance; no caching. Candidate regions affecting seed dispersal were identified as loci with more C. mollissima alleles in the high caching rate/ long-distance pool than expected by chance and observed in the other two pools. Functional annotations of candidate regions included predicted lipid metabolism, dormancy regulation, seed development, and carbohydrate metabolism genes. The results support the hypothesis that perception of seed dormancy is a predominant factor in squirrel caching decisions, and also indicate profitable directions for future work on the evolutionary genomics of trees and coevolved seed dispersers.

The Dead Can Nurture: Novel Insights into the Function of Dead Organs Enclosing Embryos

Plants have evolved a variety of dispersal units whereby the embryo is enclosed by various dead protective layers derived from maternal organs of the reproductive system including seed coats (integuments), pericarps (ovary wall, e.g., indehiscent dry fruits) as well as floral bracts (e.g., glumes) in grasses. Commonly, dead organs enclosing embryos (DOEEs) are assumed to provide a physical shield for embryo protection and means for dispersal in the ecosystem. In this review article, we highlight recent studies showing that DOEEs of various species across families also have the capability for long-term storage of various substances including active proteins (hydrolases and ROS detoxifying enzymes), nutrients and metabolites that have the potential to support the embryo during storage in the soil and assist in germination and seedling establishment. We discuss a possible role for DOEEs as natural coatings capable of "engineering" the seed microenvironment for the benefit of the embryo, the seedling and the growing plant.

Seed Dormancy Involves a Transcriptional Program That Supports Early Plastid Functionality during Imbibition

Red rice fully dormant seeds do not germinate even under favorable germination conditions. In several species, including rice, seed dormancy can be removed by dry-afterripening (warm storage); thus, dormant and non-dormant seeds can be compared for the same genotype. A weedy (red) rice genotype with strong dormancy was used for mRNA expression profiling, by RNA-Seq, of dormant and non-dormant dehulled caryopses (here addressed as seeds) at two temperatures (30 °C and 10 °C) and two durations of incubation in water (8 h and 8 days). Aim of the study was to highlight the differences in the transcriptome of dormant and non-dormant imbibed seeds. Transcript data suggested important differences between these seeds (at least, as inferred by expression-based metabolism reconstruction): dry-afterripening seems to impose a respiratory impairment onto non-dormant seeds, thus glycolysis is deduced to be preferentially directed to alcoholic fermentation in non-dormant seeds but to alanine production in dormant ones; phosphoenolpyruvate carboxykinase, pyruvate phosphate dikinase and alanine aminotransferase pathways appear to have an important gluconeogenetic role associated with the restoration of plastid functions in the dormant seed following imbibition; correspondingly, co-expression analysis pointed out a commitment to guarantee plastid functionality in dormant seeds. At 8 h of imbibition, as inferred by gene expression, dormant seeds appear to preferentially use carbon and nitrogen resources for biosynthetic processes in the plastid, including starch and proanthocyanidins accumulation. Chromatin modification appears to be a possible mechanism involved in the transition from dormancy to germination. Non-dormant seeds show higher expression of genes related to cell wall modification, suggesting they prepare for acrospire/radicle elongation.

Structural and dynamical characterization of the pH-dependence of the pectin methylesterase-pectin methylesterase inhibitor complex

Pectin methylesterases (PMEs) catalyze the demethylesterification of pectin, one of the main polysaccharides in the plant cell wall, and are of critical importance in plant development. PME activity generates highly negatively charged pectin and mutates the physiochemical properties of the plant cell wall such that remodeling of the plant cell can occur. PMEs are therefore tightly regulated by proteinaceous inhibitors (PMEIs), some of which become active upon changes in cellular pH. Nevertheless, a detailed picture of how this pH-dependent inhibition of PME occurs at the molecular level is missing. Herein, using an interdisciplinary approach that included homology modeling, MD simulations, and biophysical and biochemical characterizations, we investigated the molecular basis of PME3 inhibition by PMEI7 in Arabidopsis thaliana Our complementary approach uncovered how changes in the protonation of amino acids at the complex interface shift the network of interacting residues between intermolecular and intramolecular. These shifts ultimately regulate the stability of the PME3-PMEI7 complex and the inhibition of the PME as a function of the pH. These findings suggest a general model of how pH-dependent proteinaceous inhibitors function. Moreover, they enhance our understanding of how PMEs may be regulated by pH and provide new insights into how this regulation may control the physical properties and structure of the plant cell wall.

PECTIN METHYLESTERASE34 Contributes to Heat Tolerance through Its Role in Promoting Stomatal Movement

Pectin, a major component of the primary cell wall, is synthesized in the Golgi apparatus and exported to the cell wall in a highly methylesterified form, then is partially demethylesterified by pectin methylesterases (PMEs; EC 3.1.1.11). PME activity on the status of pectin methylesterification profoundly affects the properties of pectin and, thereby, is critical for plant development and the plant defense response, although the roles of PMEs under heat stress (HS) are poorly understood. Functional genome annotation predicts that at least 66 potential PME genes are contained in Arabidopsis (Arabidopsis thaliana). Thermotolerance assays of PME gene T-DNA insertion lines revealed two null mutant alleles of PME34 (At3g49220) that both consistently showed reduced thermotolerance. Nevertheless, their impairment was independently associated with the expression of HS-responsive genes. It was also observed that PME34 transcription was induced by abscisic acid and highly expressed in guard cells. We showed that the PME34 mutation has a defect in the control of stomatal movement and greatly altered PME and polygalacturonase (EC 3.2.1.15) activity, resulting in a heat-sensitive phenotype. PME34 has a role in the regulation of transpiration through the control of the stomatal aperture due to its cell wall-modifying enzyme activity during the HS response. Hence, PME34 is required for regulating guard cell wall flexibility to mediate the heat response in Arabidopsis.

Combined Experimental and Computational Approaches Reveal Distinct pH Dependence of Pectin Methylesterase Inhibitors

The fine-tuning of the degree of methylesterification of cell wall pectin is a key to regulating cell elongation and ultimately the shape of the plant body. Pectin methylesterification is spatiotemporally controlled by pectin methylesterases (PMEs; 66 members in Arabidopsis [Arabidopsis thaliana]). The comparably large number of proteinaceous pectin methylesterase inhibitors (PMEIs; 76 members in Arabidopsis) questions the specificity of the PME-PMEI interaction and the functional role of such abundance. To understand the difference, or redundancy, between PMEIs, we used molecular dynamics (MD) simulations to predict the behavior of two PMEIs that are coexpressed and have distinct effects on plant development: AtPMEI4 and AtPMEI9. Simulations revealed the structural determinants of the pH dependence for the interaction of these inhibitors with AtPME3, a major PME expressed in roots. Key residues that are likely to play a role in the pH dependence were identified. The predictions obtained from MD simulations were confirmed in vitro, showing that AtPMEI9 is a stronger, less pH-independent inhibitor compared with AtPMEI4. Using pollen tubes as a developmental model, we showed that these biochemical differences have a biological significance. Application of purified proteins at pH ranges in which PMEI inhibition differed between AtPMEI4 and AtPMEI9 had distinct consequences on pollen tube elongation. Therefore, MD simulations have proven to be a powerful tool to predict functional diversity between PMEIs, allowing the discovery of a strategy that may be used by PMEIs to inhibit PMEs in different microenvironmental conditions and paving the way to identify the specific role of PMEI diversity in muro.

AtPME3, a ubiquitous cell wall pectin methylesterase of Arabidopsis thaliana, alters the metabolism of cruciferin seed storage proteins during post-germinative growth of seedlings

AtPME3 (At3g14310) is a ubiquitous cell wall pectin methylesterase. Atpme3-1 loss-of-function mutants exhibited distinct phenotypes from the wild type (WT), and were characterized by earlier germination and reduction of root hair production. These phenotypical traits were correlated with the accumulation of a 21.5-kDa protein in the different organs of 4-day-old Atpme3-1 seedlings grown in the dark, as well as in 6-week-old mutant plants. Microarray analysis showed significant down-regulation of the genes encoding several pectin-degrading enzymes and enzymes involved in lipid and protein metabolism in the hypocotyl of 4-day-old dark grown mutant seedlings. Accordingly, there was a decrease in proteolytic activity of the mutant as compared with the WT. Among the genes specifying seed storage proteins, two encoding CRUCIFERINS were up-regulated. Additional analysis by RT-qPCR showed an overexpression of four CRUCIFERIN genes in the mutant Atpme3-1, in which precursors of the α- and β-subunits of CRUCIFERIN accumulated. Together, these results provide evidence for a link between AtPME3, present in the cell wall, and CRUCIFERIN metabolism that occurs in vacuoles.

Linking hydrogen-mediated boron toxicity tolerance with improvement of root elongation, water status and reactive oxygen species balance: a case study for rice

BACKGROUND AND AIMS

Boron is essential for plant growth but hazardous when present in excess. As the antioxidant properties of hydrogen gas (H2) were recently described in plants, oxidative stress induced by excess boron was investigated along with other biological responses during rice (Oryza sativa) seed germination to study the beneficial role of H2 METHODS: Rice seeds were pretreated with exogenous H2 Using physiological, pharmacological and molecular approaches, the production of endogenous H2, growth status, reactive oxygen species (ROS) balance and relative gene expression in rice were measured under boron stress to investigate mechanisms of H2-mediated boron toxicity tolerance.

KEY RESULTS

In our test, boron-inhibited seed germination and seedling growth, and endogenous H2 production, were obviously blocked by exogenously applying H2 The re-establishment of ROS balance was confirmed by reduced lipid peroxidation and ROS accumulation. Meanwhile, activities of catalase (CAT) and peroxidase (POX) were increased. Suppression of pectin methylesterase (PME) activity and downregulation of PME transcripts by H2 were consistent with the alleviation of root growth inhibition caused by boron. Water status was improved as well. This result was confirmed by the upregulation of genes encoding specific aquaporins (AQPs), the maintenance of low osmotic potential and high content of soluble sugar. Increased transcription of representative AQP genes (PIP2;7 in particular) and BOR2 along with decreased BOR1 mRNA may contribute to lowering boron accumulation.

CONCLUSIONS

Hydrogen provides boron toxicity tolerance mainly by improving root elongation, water status and ROS balance.

Fitness costs of herbicide resistance across natural populations of the common morning glory, Ipomoea purpurea

Although fitness costs associated with plant defensive traits are widely expected, they are not universally detected, calling into question their generality. Here, we examine the potential for life-history trade-offs associated with herbicide resistance by examining seed germination, root growth, and above-ground growth across 43 naturally occurring populations of Ipomoea purpurea that vary in their resistance to RoundUp®, the most commonly used herbicide worldwide. We find evidence for life-history trade-offs associated with all three traits; highly resistant populations had lower germination, shorter roots, and smaller above-ground size. A visual exploration of the data indicated that the type of trade-off may differ among populations. Our results demonstrate that costs of adaptation may be present at stages other than simply the production of progeny in this agricultural weed. Additionally, the cumulative effect of costs at multiple life cycle stages can result in severe consequences to fitness when adapting to novel environments.

Tuning of pectin methylesterification: consequences for cell wall biomechanics and development

Recent publications have increased our knowledge of how pectin composition and the degree of homogalacturonan methylesterification impact the biochemical and biomechanical properties of plant cell walls, plant development, and plants' interactions with their abiotic and biotic environments. Experimental observations have shown that the relationships between the DM, the pattern of de-methylesterificaton, its effect on cell wall elasticity, other biomechanical parameters, and growth are not straightforward. Working towards a detailed understanding of these relationships at single cell resolution is one of the big tasks of pectin research. Pectins are highly complex polysaccharides abundant in plant primary cell walls. New analytical and microscopy techniques are revealing the composition and mechanical properties of the cell wall and increasing our knowledge on the topic. Progress in plant physiological research supports a link between cell wall pectin modifications and plant development and interactions with the environment. Homogalacturonan pectins, which are major components of the primary cell wall, have a potential for modifications such as methylesterification, as well as an ability to form cross-linked structures with divalent cations. This contributes to changing the mechanical properties of the cell wall. This review aims to give a comprehensive overview of the pectin component homogalacturonan, including its synthesis, modification, regulation and role in the plant cell wall.

Tuning of Pectin Methylesterification: PECTIN METHYLESTERASE INHIBITOR 7 MODULATES THE PROCESSIVE ACTIVITY OF CO-EXPRESSED PECTIN METHYLESTERASE 3 IN A pH-DEPENDENT MANNER

Pectin methylesterases (PMEs) catalyze the demethylesterification of homogalacturonan domains of pectin in plant cell walls and are regulated by endogenous pectin methylesterase inhibitors (PMEIs). In Arabidopsis dark-grown hypocotyls, one PME (AtPME3) and one PMEI (AtPMEI7) were identified as potential interacting proteins. Using RT-quantitative PCR analysis and gene promoter::GUS fusions, we first showed that AtPME3 and AtPMEI7 genes had overlapping patterns of expression in etiolated hypocotyls. The two proteins were identified in hypocotyl cell wall extracts by proteomics. To investigate the potential interaction between AtPME3 and AtPMEI7, both proteins were expressed in a heterologous system and purified by affinity chromatography. The activity of recombinant AtPME3 was characterized on homogalacturonans (HGs) with distinct degrees/patterns of methylesterification. AtPME3 showed the highest activity at pH 7.5 on HG substrates with a degree of methylesterification between 60 and 80% and a random distribution of methyl esters. On the best HG substrate, AtPME3 generates long non-methylesterified stretches and leaves short highly methylesterified zones, indicating that it acts as a processive enzyme. The recombinant AtPMEI7 and AtPME3 interaction reduces the level of demethylesterification of the HG substrate but does not inhibit the processivity of the enzyme. These data suggest that the AtPME3·AtPMEI7 complex is not covalently linked and could, depending on the pH, be alternately formed and dissociated. Docking analysis indicated that the inhibition of AtPME3 could occur via the interaction of AtPMEI7 with a PME ligand-binding cleft structure. All of these data indicate that AtPME3 and AtPMEI7 could be partners involved in the fine tuning of HG methylesterification during plant development.

Elevation of NO production increases Fe immobilization in the Fe-deficiency roots apoplast by decreasing pectin methylation of cell wall

Cell wall is the major component of root apoplast which is the main reservoir for iron in roots, while nitric oxide (NO) is involved in regulating the synthesis of cell wall. However, whether such regulation could influence the reutilization of iron stored in root apoplast remains unclear. In this study, we observed that iron deficiency elevated NO level in tomato (Solanum lycopersicum) roots. However, application of S-nitrosoglutathione, a NO donor, significantly enhanced iron retention in root apoplast of iron-deficient plants, accompanied with a decrease of iron level in xylem sap. Consequently, S-nitrosoglutathione treatment increased iron concentration in roots, but decreased it in shoots. The opposite was true for the NO scavenging treatment with 2-(4-carboxyphenyl)-4,4,5,5-tetramethylimidazoline-1-oxyl-3-oxide (cPTIO). Interestingly, S-nitrosoglutathione treatment increased pectin methylesterase activity and decreased degree of pectin methylation in root cell wall of both iron-deficient and iron-sufficient plants, which led to an increased iron retention in pectin fraction, thus increasing the binding capacity of iron to the extracted cell wall. Altogether, these results suggested that iron-deficiency-induced elevation of NO increases iron immobilization in root apoplast by decreasing pectin methylation in cell wall.

Transcriptional profiling by DDRT-PCR analysis reveals gene expression during seed development in Carya cathayensis Sarg

Hickory (Carya cathayensis Sarg.) seed has one of the highest oil content and is rich in polyunsaturated fatty acids (PUFAs), which kernel is helpful to human health, particularly to human brain function. A better elucidation of lipid accumulation mechanism would help to improve hickory production and seed quality. DDRT-PCR analysis was used to examine gene expression in hickory at thirteen time points during seed development process. A total of 67 unique genes involved in seed development were obtained, and those expression patterns were further confirmed by semi-quantitative RT-PCR and real time RT-PCR analysis. Of them, the genes with known functions were involved in signal transduction, amino acid metabolism, nuclear metabolism, fatty acid metabolism, protein metabolism, carbon metabolism, secondary metabolism, oxidation of fatty acids and stress response, suggesting that hickory underwent a complex metabolism process in seed development. Furthermore, 6 genes related to fatty acid synthesis were explored, and their functions in seed development process were further discussed. The data obtained here would provide the first clues for guiding further functional studies of fatty acid synthesis in hickory.

Re-analysis of protein data reveals the germination pathway and up accumulation mechanism of cell wall hydrolases during the radicle protrusion step of seed germination in Podophyllum hexandrum- a high altitude plant

Podophyllum hexandrum Royle is an important high-altitude plant of Himalayas with immense medicinal value. Earlier, it was reported that the cell wall hydrolases were up accumulated during radicle protrusion step of Podophyllum seed germination. In the present study, Podophyllum seed Germination protein interaction Network (PGN) was constructed by using the differentially accumulated protein (DAP) data set of Podophyllum during the radicle protrusion step of seed germination, with reference to Arabidopsis protein-protein interaction network (AtPIN). The developed PGN is comprised of a giant cluster with 1028 proteins having 10,519 interactions and a few small clusters with relevant gene ontological signatures. In this analysis, a germination pathway related cluster which is also central to the topology and information dynamics of PGN was obtained with a set of 60 key proteins. Among these, eight proteins which are known to be involved in signaling, metabolism, protein modification, cell wall modification, and cell cycle regulation processes were found commonly highlighted in both the proteomic and interactome analysis. The systems-level analysis of PGN identified the key proteins involved in radicle protrusion step of seed germination in Podophyllum.

Promotion of testa rupture during garden cress germination involves seed compartment-specific expression and activity of pectin methylesterases

Pectin methylesterase (PME) controls the methylesterification status of pectins and thereby determines the biophysical properties of plant cell walls, which are important for tissue growth and weakening processes. We demonstrate here that tissue-specific and spatiotemporal alterations in cell wall pectin methylesterification occur during the germination of garden cress (Lepidium sativum). These cell wall changes are associated with characteristic expression patterns of PME genes and resultant enzyme activities in the key seed compartments CAP (micropylar endosperm) and RAD (radicle plus lower hypocotyl). Transcriptome and quantitative real-time reverse transcription-polymerase chain reaction analysis as well as PME enzyme activity measurements of separated seed compartments, including CAP and RAD, revealed distinct phases during germination. These were associated with hormonal and compartment-specific regulation of PME group 1, PME group 2, and PME inhibitor transcript expression and total PME activity. The regulatory patterns indicated a role for PME activity in testa rupture (TR). Consistent with a role for cell wall pectin methylesterification in TR, treatment of seeds with PME resulted in enhanced testa permeability and promoted TR. Mathematical modeling of transcript expression changes in germinating garden cress and Arabidopsis (Arabidopsis thaliana) seeds suggested that group 2 PMEs make a major contribution to the overall PME activity rather than acting as PME inhibitors. It is concluded that regulated changes in the degree of pectin methylesterification through CAP- and RAD-specific PME and PME inhibitor expression play a crucial role during Brassicaceae seed germination.

BIIDXI, the At4g32460 DUF642 gene, is involved in pectin methyl esterase regulation during Arabidopsis thaliana seed germination and plant development

BACKGROUND

DUF642 proteins constitute a highly conserved family of proteins that are associated with the cell wall and are specific to spermatophytes. Transcriptome studies have suggested that members of this family are involved in seed development and germination processes. Previous in vitro studies have revealed that At4g32460- and At5g11420-encoded proteins interact with the catalytic domain of pectin methyl esterase 3 (AtPME3, which is encoded by At3g14310). PMEs play an important role in plant development, including seed germination. The aim of this study was to evaluate the function of the DUF642 gene At4g32460 during seed germination and plant development and to determine its relation to PME activity regulation.

RESULTS

Our results indicated that the DUF642 proteins encoded by At4g32460 and At5g11420 could be positive regulators of PME activity during several developmental processes. Transgenic lines overexpressing these proteins showed increased PME activity during seed germination, and improved seed germination performance. In plants expressing At4g32460 antisense RNA, PME activity was decreased in the leaves, and the siliques were very short and contained no seeds. This phenotype was also present in the SALK_142260 and SALK_054867 lines for At4g32460.

CONCLUSIONS

Our results suggested that the DUF642 family contributes to the complexity of the methylesterification process by participating in the fine regulation of pectin status during plant development.

Processive pectin methylesterases: the role of electrostatic potential, breathing motions and bond cleavage in the rectification of Brownian motions

Pectin methylesterases (PMEs) hydrolyze the methylester groups that are found on the homogalacturonan (HG) chains of pectic polysaccharides in the plant cell wall. Plant and bacterial PMEs are especially interesting as the resulting de-methylesterified (carboxylated) sugar residues are found to be arranged contiguously, indicating a so-called processive nature of these enzymes. Here we report the results of continuum electrostatics calculations performed along the molecular dynamics trajectory of a PME-HG-decasaccharide complex. In particular it was observed that, when the methylester groups of the decasaccharide were arranged in order to mimic the just-formed carboxylate product of de-methylesterification, a net unidirectional sliding of the model decasaccharide was subsequently observed along the enzyme’s binding groove. The changes that occurred in the electrostatic binding energy and protein dynamics during this translocation provide insights into the mechanism by which the enzyme rectifies Brownian motions to achieve processivity. The free energy that drives these molecular motors is thus demonstrated to be incorporated endogenously in the methylesterified groups of the HG chains and is not supplied exogenously.

How do pectin methylesterases and their inhibitors affect the spreading of tobamovirus?

After replication in the cytoplasm, viruses spread from the infected cell into the neighboring cells through plasmodesmata, membranous channels embedded by the cell wall. As obligate parasites, viruses have acquired the ability to utilize host factors that unwillingly cooperate for the viral infection process. For example, the viral movement proteins (MP) interacts with the host pectin methylesterase (PME) and both proteins cooperate to sustain the viral spread. However, how and where PMEs interact with MPs and how the PME/MP complexes favor the viral translocation is not well understood. Recently, we demonstrated that the overexpression of PME inhibitors (PMEIs) in tobacco and Arabidopsis plants limits the movement of Tobacco mosaic virus and Turnip vein clearing virus and reduces plant susceptibility to these viruses. Here we discuss how overexpression of PMEI may reduce tobamovirus spreading.

Substrate dynamics in enzyme action: rotations of monosaccharide subunits in the binding groove are essential for pectin methylesterase processivity

The dynamical behavior of biomacromolecules is a fundamental property regulating a large number of biological processes. Protein dynamics have been widely shown to play a role in enzyme catalysis; however, the interplay between substrate dynamics and enzymatic activity is less understood. We report insights into the role of dynamics of substrates in the enzymatic activity of PME from Erwinia chrysanthemi, a processive enzyme that catalyzes the hydrolysis of methylester groups from the galacturonic acid residues of homogalacturonan chains, the major component of pectin. Extensive molecular dynamics simulations of this PME in complex with decameric homogalacturonan chains possessing different degrees and patterns of methylesterification show how the carbohydrate substitution pattern governs the dynamics of the substrate in the enzyme's binding cleft, such that substrate dynamics represent a key prerequisite for the PME biological activity. The analyses reveal that correlated rotations around glycosidic bonds of monosaccharide subunits at and immediately adjacent to the active site are a necessary step to ensure substrate processing. Moreover, only substrates with the optimal methylesterification pattern attain the correct dynamical behavior to facilitate processive catalysis. This investigation is one of the few reported examples of a process where the dynamics of a substrate are vitally important.

Comparative transcriptome profiling of developing caryopses from two rice cultivars with differential dormancy

Pre-harvest sprouting (PHS) in rice causes poor grain quality and results in significant reductions in yield, leading to significant economic losses. In contrast, deep dormancy can lead to equally unwanted non-uniform germination. Therefore, a suitable level of dormancy is a critically important agronomic trait. In this study, an analysis of PHS in developing seeds of two Korean rice cultivars (vivipary), Gopum and Samgwang, revealed differences in dormancy in caryopses at 25 d after heading (DAH). To assess the transcriptomic characteristics associated with vivipary, we compared RNA profiles at early (3-6 DAH), middle (25 DAH), and late (40 DAH) developmental stages. Transcriptomic differentiation was most pronounced in caryopses at 25 DAH, the developmental stage at which differential dormancy was also the most prominent. A k-means clustering analysis of the two cultivars revealed groups of genes with similar or dissimilar expression profiles. Many of the genes that showed distinct differential expression profiles were those involved in seed maturation. Intriguingly, differential gene expression levels between the two cultivars were positively correlated with fold-changes in their expression during the early half of caryopsis development. This implies that the establishment of seed dormancy is strongly correlated with the altered transcriptomic patterns related to the progression of maturation. Our global RNA profiling suggests that caryopsis development in Gopum proceeds at a greater speed than in the Samgwang cultivar. Thus, a high degree of maturity and early dormancy release may be present in 25 DAH caryopses of Gopum, although we cannot exclude the possibility of genetic defects modifying dormancy. The comparative transcriptomic analysis of the two cultivars did not reveal noticeable differences in RNA profiles with respect to differences in abscisic acid (ABA) content or ABA sensitivity. Therefore, it is unlikely that ABA is directly involved in the differences in dormancy observed between the two cultivars.

Mining genes involved in the stratification of Paris polyphylla seeds using high-throughput embryo transcriptome sequencing

Background

Paris polyphylla var. yunnanensis is an important medicinal plant. Seed dormancy is one of the main factors restricting artificial cultivation. The molecular mechanisms of seed dormancy remain unclear, and little genomic or transcriptome data are available for this plant.

Results

In this study, massive parallel pyrosequencing on the Roche 454-GS FLX Titanium platform was used to generate a substantial sequence dataset for the P. polyphylla embryo. 369,496 high quality reads were obtained, ranging from 50 to 1146 bp, with a mean of 219 bp. These reads were assembled into 47,768 unigenes, which included 16,069 contigs and 31,699 singletons. Using BLASTX searches of public databases, 15,757 (32.3%) unique transcripts were identified. Gene Ontology and Cluster of Orthologous Groups of proteins annotations revealed that these transcripts were broadly representative of the P. polyphylla embryo transcriptome. The Kyoto Encyclopedia of Genes and Genomes assigned 5961 of the unique sequences to specific metabolic pathways. Relative expression levels analysis showed that eleven phytohormone-related genes and five other genes have different expression patterns in the embryo and endosperm in the seed stratification process.

Conclusions

Gene annotation and quantitative RT-PCR expression analysis identified 464 transcripts that may be involved in phytohormone catabolism and biosynthesis, hormone signal, seed dormancy, seed maturation, cell wall growth and circadian rhythms. In particular, the relative expression analysis of sixteen genes (CYP707A, NCED, GA20ox2, GA20ox3, ABI2, PP2C, ARP3, ARP7, IAAH, IAAS, BRRK, DRM, ELF1, ELF2, SFR6, and SUS) in embryo and endosperm and at two temperatures indicated that these related genes may be candidates for clarifying the molecular basis of seed dormancy in P. polyphlla var. yunnanensis.

Trichoderma inoculation ameliorates arsenic induced phytotoxic changes in gene expression and stem anatomy of chickpea (Cicer arietinum)

Arsenic, a carcinogenic metalloid severely affects plant growth in contaminated areas. Present study shows role of Trichoderma reesei NBRI 0716 (NBRI 0716) in ameliorating arsenic (As) stress on chickpea under greenhouse conditions. Arsenic stress adversely affected seed germination (25%), chlorophyll content (44%) and almost eliminated nodule formation that were significantly restored on NBRI 0716 inoculation. It also restored stem anomalies like reduced trichome turgidity and density, deformation in collenchymatous and sclerenchymatous cells induced by As stress. Semi-quantitative RT-PCR of stress responsive genes showed differential expression of genes involved in synthesis of cell wall degrading enzymes, dormancy termination and abiotic stress. Upregulation of drought responsive genes (DRE, EREBP, T6PS, MIPS, and PGIP), enhanced proline content and shrunken cortex cells in the presence of As suggests that it creates water deficiency in plants and these responses were modulated by NBRI 0716 which provides a protective role. NBRI0716 mediated production of As reductase enzyme in chickpea and thus contributed in As metabolism. The study suggests a multifarious role of NBRI0716 in mediating stress tolerance in chickpea towards As.

Demethylesterification of cell wall pectins in Arabidopsis plays a role in seed germination

The methylesterification status of cell wall homogalacturonans, mediated through the action of pectin methylesterases (PMEs), influences the biophysical properties of plant cell walls such as elasticity and porosity, important parameters for cell elongation and water uptake. The completion of seed germination requires cell wall extensibility changes in both the radicle itself and in the micropylar tissues surrounding the radicle. In wild-type seeds of Arabidopsis (Arabidopsis thaliana), PME activities peaked around the time of testa rupture but declined just before the completion of germination (endosperm weakening and rupture). We overexpressed an Arabidopsis PME inhibitor to investigate PME involvement in seed germination. Seeds of the resultant lines showed a denser methylesterification status of their cell wall homogalacturonans, but there were no changes in the neutral sugar and uronic acid composition of the cell walls. As compared with wild-type seeds, the PME activities of the overexpressing lines were greatly reduced throughout germination, and the low steady-state levels neither increased nor decreased. The most striking phenotype was a significantly faster rate of germination, which was not connected to altered testa rupture morphology but to alterations of the micropylar endosperm cells, evident by environmental scanning electron microscopy. The transgenic seeds also exhibited an apparent reduced sensitivity to abscisic acid with respect to its inhibitory effects on germination. We speculate that PME activity contributes to the temporal regulation of radicle emergence in endospermic seeds by altering the mechanical properties of the cell walls and thereby the balance between the two opposing forces of radicle elongation and mechanical resistance of the endosperm.

Distinct cell wall architectures in seed endosperms in representatives of the Brassicaceae and Solanaceae

In some species, a crucial role has been demonstrated for the seed endosperm during germination. The endosperm has been shown to integrate environmental cues with hormonal networks that underpin dormancy and seed germination, a process that involves the action of cell wall remodeling enzymes (CWREs). Here, we examine the cell wall architectures of the endosperms of two related Brassicaceae, Arabidopsis (Arabidopsis thaliana) and the close relative Lepidium (Lepidium sativum), and that of the Solanaceous species, tobacco (Nicotiana tabacum). The Brassicaceae species have a similar cell wall architecture that is rich in pectic homogalacturonan, arabinan, and xyloglucan. Distinctive features of the tobacco endosperm that are absent in the Brassicaceae representatives are major tissue asymmetries in cell wall structural components that reflect the future site of radicle emergence and abundant heteromannan. Cell wall architecture of the micropylar endosperm of tobacco seeds has structural components similar to those seen in Arabidopsis and Lepidium endosperms. In situ and biomechanical analyses were used to study changes in endosperms during seed germination and suggest a role for mannan degradation in tobacco. In the case of the Brassicaceae representatives, the structurally homogeneous cell walls of the endosperm can be acted on by spatially regulated CWRE expression. Genetic manipulations of cell wall components present in the Arabidopsis seed endosperm demonstrate the impact of cell wall architectural changes on germination kinetics.

Gene expression and enzymatic activity of pectin methylesterase during fruit development and ripening in Coffea arabica L

Coffee quality is directly related to the harvest and post harvest conditions. Non-uniform maturation of coffee fruits, combined with inadequate harvest, negatively affects the final quality of the product. Pectin methylesterase (PME) plays an important role in fruit softening due to the hydrolysis of methylester groups in cell wall pectins. In order to characterize the changes occurring during coffee fruit maturation, the enzymatic activity of PME was measured during different stages of fruit ripening. PME activity progressively increased from the beginning of the ripening process to the cherry fruit stage. In silico analysis of expressed sequence tags of the Brazilian Coffee Genome Project database identified 5 isoforms of PME. We isolated and cloned a cDNA homolog of PME for further characterization. CaPME4 transcription was analyzed in pericarp, perisperm, and endosperm tissues during fruit development and ripening as well as in other plant tissues. Northern blot analysis revealed increased transcription of CaPME4 in the pericarp 300 days after flowering. Low levels of CaPME4 mRNAs were observed in the endosperm 270 days after flowering. Expression of CaPME4 transcripts was strong in the branches and lower in root and flower tissues. We showed that CaPME4 acts specifically during the later stages of fruit ripening and possibly contributes to the softening of coffee fruit, thus playing a significant role in pectin degradation in the fruit pericarp.

A functional pectin methylesterase inhibitor protein (SolyPMEI) is expressed during tomato fruit ripening and interacts with PME-1

A pectin methylesterase inhibitor (SolyPMEI) from tomato has been identified and characterised by a functional genomics approach. SolyPMEI is a cell wall protein sharing high similarity with Actinidia deliciosa PMEI (AdPMEI), the best characterised inhibitor from kiwi. It typically affects the activity of plant pectin methylesterases (PMEs) and is inactive against a microbial PME. SolyPMEI transcripts were mainly expressed in flower, pollen and ripe fruit where the protein accumulated at breaker and turning stages of ripening. The expression of SolyPMEI correlated during ripening with that of PME-1, the major fruit specific PME isoform. The interaction of SolyPMEI with PME-1 was demonstrated in ripe fruit by gel filtration and by immunoaffinity chromatography. The analysis of the zonal distribution of PME activity and the co-localization of SolyPMEI with high esterified pectins suggest that SolyPMEI regulates the spatial patterning of distribution of esterified pectins in fruit.

Analysis of LuPME3, a pectin methylesterase from Linum usitatissimum, revealed a variability in PME proteolytic maturation

Pectin methylesterase (PME) catalyses the de-methylesterification of pectin in plant cell walls during cell elongation. (1) Pectins are mainly composed of α(1, 4)-D-galacturonosyl acid units that are synthesised in a methylesterified form in the Golgi apparatus to prevent any interaction with Ca2+ ions during their intracellular transport. (2) The highly methylesterified pectins are then secreted into the apoplasm (3) and subsequently de-methylesterified in muro by PMEs. This can either induce the formation of pectin gels through the Ca2+ crosslinking of neighbouring non-methylesterified chains or create substrates for pectin-degrading enzymes such as polygalacturonases and pectate lyases for the initiation of cell wall loosening. (4) PMEs belong to a large multigene family. Sixty-six PME-related genes are predicted in the Arabidopsis genome. (1) Among them, we have recently shown that AtPME3 (At3g14310), a major basic PME isoform in A. thaliana, is ubiquitously expressed in vascular tissues and play a role in adventitious rooting. (5) In flax (Linum usitatissimum), three genes encoding PMEs have been sequenced so far, including LuPME3, the orthologue of AtPME3. Analysis of the LuPME3 isoform brings new insights into the processing of these proteins.

Pectin Methylesterase genes influence solid wood properties of Eucalyptus pilularis

This association study of Eucalyptus pilularis populations provides empirical evidence for the role of Pectin Methylesterase (PME) in influencing solid wood characteristics of Eucalyptus. PME6 was primarily associated with the shrinkage and collapse of drying timber, which are phenotypic traits consistent with the role of pectin as a hydrophilic polysaccharide. PME7 was primarily associated with cellulose and pulp yield traits and had an inverse correlation with lignin content. Selection of specific alleles in these genes may be important for improving trees as sources of high-quality wood products. A heterozygote advantage was postulated for the PME7 loci and, in combination with haplotype blocks, may explain the absence of a homozygous class at all single-nucleotide polymorphisms investigated in this gene.

Challenges facing the forest industry in relation to seed dormancy and seed quality

Artificial regeneration of forests through planting requires high quantities of quality seeds for growing vigorous seedlings. These seedlings are raised in nurseries, where germination capacity (GC) and speed are the most important germination parameters. Germination performance is enhanced by prescribing species-specific dormancy-breaking treatments to individual seedlots in bare-root and container nurseries. For most conifer species in British Columbia, the dormancy-breaking treatments and germination conditions have been worked out, but fine-tuning and optimization could improve germination capacity and speed of germination. Implications of inter- and intra-species variations in germination behaviour and seed quality and their influence on the development of unintentional directional selection of specific genotypes are discussed. The potential of molecular and genomics approaches to understand the underlying biology of seed germination-related problems is also discussed.