A class I chitinase from soybean seed coat

An Overview of Chitinase Zymography: Past and Present Methods and Protocols

Chitinases are a variety of different enzymes that facilitate the breakdown of chitin, a complex sugar molecule presents in the outer shells of arthropods and the cellular walls of fungi. Chitinase zymography is a powerful analytical technique to visualize and characterize chitinase activity in complex biological samples. In plants, chitinases contribute to defense mechanisms by degrading fungal cell walls and deterring pathogen invasion. They also influence plant growth and development by modulating interactions with soil microbes. This chapter provides different zymographic protocols for chitinase detection, including those using polyacrylamide gel electrophoresis (PAGE) with various chitin derivatives and staining methods. Calcofluor White M2R, is offering unique advantages for visualizing chitinase activity on native PAGE overlayed chitin amended gels. This overview highlights the importance of selecting appropriate substrates and assay conditions to achieve accurate and reliable results in chitinase zymography, thereby advancing the potential of chitinase-based technologies in industrial and environmental fields.

Physiological and metabolic analyses provide insight into soybean seed resistance to fusarium fujikuroi causing seed decay

Seed-borne pathogens cause diverse diseases at the growth, pre- and post-harvest stage of soybean resulting in a large reduction in yield and quality. The physiological and metabolic aspects of seeds are closely related to their defense against pathogens. Recently, Fusarium fujikuroi has been identified as the dominant seed-borne fungi of soybean seed decay, but little information on the responses of soybean seeds induced by F. fujikuroi is available. In this study, a time-course symptom development of seed decay was observed after F. fujikuroi inoculation through spore suspension soaking. The germination rate and the contents of soluble sugar and soluble protein were significantly altered over time. Both chitinase and β-1,3-glucanase as important fungal cell wall-degrading enzymes of soybean seeds were also rapidly and transiently activated upon the early infection of F. fujikuroi. Metabolic profile analysis showed that the metabolites in glycine, serine, and threonine metabolism and tryptophan metabolism were clearly induced by F. fujikuroi, but different metabolites were mostly enriched in isoflavone biosynthesis, flavone biosynthesis, and galactose pathways. Interestingly, glycitein and glycitin were dramatically upregulated while daidzein, genistein, genistin, and daidzin were largely downregulated. These results indicate a combination of physiological responses, cell wall-related defense, and the complicated metabolites of soybean seeds contributes to soybean seed resistance against F. fujikuroi, which are useful for soybean resistance breeding.

Organ-specific expression and epigenetic traits of genes encoding digestive enzymes in the lance-leaf sundew (Drosera adelae)

Over the last two decades, extensive studies have been performed at the molecular level to understand the evolution of carnivorous plants. As fruits, the repertoire of protein components in the digestive fluids of several carnivorous plants have gradually become clear. However, the quantitative aspects of these proteins and the expression mechanisms of the genes that encode them are still poorly understood. In this study, using the Australian sundew Drosera adelae, we identified and quantified the digestive fluid proteins. We examined the expression and methylation status of the genes corresponding to major hydrolytic enzymes in various organs; these included thaumatin-like protein, S-like RNase, cysteine protease, class I chitinase, β-1, 3-glucanase, and hevein-like protein. The genes encoding these proteins were exclusively expressed in the glandular tentacles. Furthermore, the promoters of the β-1, 3-glucanase and cysteine protease genes were demethylated only in the glandular tentacles, similar to the previously reported case of the S-like RNase gene da-I. This phenomenon correlated with high expression of the DNA demethylase DEMETER in the glandular tentacles, strongly suggesting that it performs glandular tentacle-specific demethylation of the genes. The current study strengthens and generalizes the relevance of epigenetics to trap organ-specific gene expression in D. adelae. We also suggest similarities between the trap organs of carnivorous plants and the roots of non-carnivorous plants.

Physiological and Proteomic Signatures Reveal Mechanisms of Superior Drought Resilience in Pearl Millet Compared to Wheat

Presently, pearl millet and wheat are belonging to highly important cereal crops. Pearl millet, however, is an under-utilized crop, despite its superior resilience to drought and heat stress in contrast to wheat. To investigate this in more detail, we performed comparative physiological screening and large scale proteomics of drought stress responses in drought-tolerant and susceptible genotypes of pearl millet and wheat. These chosen genotypes are widely used in breeding and farming practices. The physiological responses demonstrated large differences in the regulation of root morphology and photosynthetic machinery, revealing a stay-green phenotype in pearl millet. Subsequent tissue-specific proteome analysis of leaves, roots and seeds led to the identification of 12,558 proteins in pearl millet and wheat under well-watered and stress conditions. To allow for this comparative proteome analysis and to provide a platform for future functional proteomics studies we performed a systematic phylogenetic analysis of all orthologues in pearl millet, wheat, foxtail millet, sorghum, barley, brachypodium, rice, maize, Arabidopsis, and soybean. In summary, we define (i) a stay-green proteome signature in the drought-tolerant pearl millet phenotype and (ii) differential senescence proteome signatures in contrasting wheat phenotypes not capable of coping with similar drought stress. These different responses have a significant effect on yield and grain filling processes reflected by the harvest index. Proteome signatures related to root morphology and seed yield demonstrated the unexpected intra- and interspecies-specific biochemical plasticity for stress adaptation for both pearl millet and wheat genotypes. These quantitative reference data provide tissue- and phenotype-specific marker proteins of stress defense mechanisms which are not predictable from the genome sequence itself and have potential value for marker-assisted breeding beyond genome assisted breeding.

Proteome Responses to Individual Pathogens and Abiotic Conditions in Rice Seedlings

Rice plants under field conditions experience various biotic and abiotic stresses and are adapted to survive using a molecular cross-talk of genes and their protein products based on the severity of a given stress. Seedlings of cultivated variety ASD16 (resistant to fungal disease, blast; tolerant to abiotic stress, salinity) were subjected to salt, drought, high temperature and low temperature stress as well as infection by Rhizoctonia solani and Xanthomonas oryzae pv. oryzae (causing reemerging diseases such as sheath blight and leaf blight), respectively, the sheath blight and bacterial leaf blight pathogens. Leaf proteome was analyzed using two-dimensional electrophoresis and differentially expressed proteins were identified using mass spectrometry. In addition to many other differentially expressed proteins, acidic endochitinase was found to be upregulated during fungal infection and drought treatment, and a germin-like protein upregulated during fungal infection and high temperature stress. These two proteins were further validated at the gene expression level using reverse transcription-PCR in dual stress experiments. Pot culture plants were subjected to fungal infection followed by drought and drought followed by fungal infection to validate chitinase gene expression. Similarly, plants subjected to fungal infections followed by high temperature stress and vice versa were used to validate the expression of germin-like protein-coding gene. The results of the present study indicate that chitinase and germin-like protein are potential targets for further exploration to develop rice plants resistant or tolerant to biotic and abiotic stresses.

Physiological and Proteomic Signatures Reveal Mechanisms of Superior Drought Resilience in Pearl Millet Compared to Wheat

Presently, pearl millet and wheat are belonging to highly important cereal crops. Pearl millet, however, is an under-utilized crop, despite its superior resilience to drought and heat stress in contrast to wheat. To investigate this in more detail, we performed comparative physiological screening and large scale proteomics of drought stress responses in drought-tolerant and susceptible genotypes of pearl millet and wheat. These chosen genotypes are widely used in breeding and farming practices. The physiological responses demonstrated large differences in the regulation of root morphology and photosynthetic machinery, revealing a stay-green phenotype in pearl millet. Subsequent tissue-specific proteome analysis of leaves, roots and seeds led to the identification of 12,558 proteins in pearl millet and wheat under well-watered and stress conditions. To allow for this comparative proteome analysis and to provide a platform for future functional proteomics studies we performed a systematic phylogenetic analysis of all orthologues in pearl millet, wheat, foxtail millet, sorghum, barley, brachypodium, rice, maize, Arabidopsis, and soybean. In summary, we define (i) a stay-green proteome signature in the drought-tolerant pearl millet phenotype and (ii) differential senescence proteome signatures in contrasting wheat phenotypes not capable of coping with similar drought stress. These different responses have a significant effect on yield and grain filling processes reflected by the harvest index. Proteome signatures related to root morphology and seed yield demonstrated the unexpected intra- and interspecies-specific biochemical plasticity for stress adaptation for both pearl millet and wheat genotypes. These quantitative reference data provide tissue- and phenotype-specific marker proteins of stress defense mechanisms which are not predictable from the genome sequence itself and have potential value for marker-assisted breeding beyond genome assisted breeding.

A chitinase with antifungal activity from naked oat (Avena chinensis) seeds

A chitinase was purified from naked oat (Avena chinensis) seeds using simple chromatographic techniques. Its molecular weight and isoelectric point were determined as 35 kDa and 8.9, respectively. The purified chitinase exhibited specific activity of 3.6 U/mg and 15.6% yield using colloidal chitin as substrate. Partial amino acid sequence analysis and homology search indicated that it probably belonged to Class I plant chitinase, glycosyl hydrolase family 19. With chitin as substrate, the optimum pH and temperature of the chitinase were pH 7.0 and 40°C, respectively. The chitinase was remarkably stable from 30°C up to 50°C, but was inactivated at high temperatures above 85°C. Antifungal activity in vitro tests demonstrated this purified chitinase had potent, dose-dependent inhibitory activity against the fungi Panus conchatus and Trichoderma reesei. PRACTICAL APPLICATIONS: Chitinase has broad applications in many fields including the food industry and is recognized as one of the antifungal substances with potential use in plant disease resistance or biological control in agriculture. This study developed cost-effective purification methods for producing chitinase from naked oat (Avena chinensis) seeds, which may favor large-scale production of the enzyme. The remarkable stability of the chitinase at moderate temperatures (30°C-50°C), makes it a potentially useful enzyme in bioprocessing to produce chitooligosaccharides for various applications in the food, health, and agriculture sectors.

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.

Soybean seed coat chitinase as a defense protein against the stored product pest Callosobruchus maculatus

BACKGROUND

Chitinases (EC 3.2.1.14) are enzymes involved in the breaking of the β-1,4-glycosidic linkages of chitin. In insects, chitin is present mainly in the cuticle and in peritrophic membranes and peritrophic gel. Enzymes with the potential to damage peritrophic membranes and gel, such as chitinase, have been associated with plant defense systems. Identification and characterization of seed coat chitinase as a plant defense molecule may indicate a more effective target for manipulation strategies, which may lead to the prevention of consumption of embryonic tissues by larvae and consequently minimization of seed damage.

RESULTS

We studied the efficiency of soybean seed coat chitinase as a defense molecule against the insect Callosobruchus maculatus. The seed coat chitinase was isolated and identified by mass spectrometry, immunoreacted with an anti-chitinase antibody and shown to have activity against chitin azure and 4-methylumbelliferyl β-D-N,N',N''-triacetylchitotrioside. A chitinase fraction incorporated in artificial cotyledons at 0.1% reduced larval survival by approximately 77%, and at 0.5%, the reduction in larval mass was 60%. Fluorescein isothiocyanate (FITC)-labeled chitinase was detected in the guts and feces of larvae. At 25% in thick artificial seed coats, chitinase showed a high toxicity to larvae, with mortality of 90% and a reduction of larval mass of 87%.

CONCLUSION

Seed coat chitinase is an important seed defense molecule not only in the cotyledons but also in seed coats, acting as part of the array of defense mechanisms against Callosobruchus maculatus. © 2017 Society of Chemical Industry.

The dead seed coat functions as a long-term storage for active hydrolytic enzymes

Seed development culminates in programmed cell death (PCD) and hardening of organs enclosing the embryo (e.g., pericarp, seed coat) providing essentially a physical shield for protection during storage in the soil. We examined the proposal that dead organs enclosing embryos are unique entities that store and release upon hydration active proteins that might increase seed persistence in soil, germination and seedling establishment. Proteome analyses of dead seed coats of Brassicaceae species revealed hundreds of proteins being stored in the seed coat and released upon hydration, many are stress-associated proteins such as nucleases, proteases and chitinases. Functional analysis revealed that dead seed coats function as long-term storage for multiple active hydrolytic enzymes (e.g., nucleases) that can persist in active forms for decades. Substances released from the dead seed coat of the annual desert plant Anastatica hierochuntica displayed strong antimicrobial activity. Our data highlighted a previously unrecognized feature of dead organs enclosing embryos (e.g., seed coat) functioning not only as a physical shield for embryo protection but also as a long-term storage for active proteins and other substances that are released upon hydration to the “seedsphere” and could contribute to seed persistence in the soil, germination and seedling establishment.

Comparative Study of Lectin Domains in Model Species: New Insights into Evolutionary Dynamics

Lectins are present throughout the plant kingdom and are reported to be involved in diverse biological processes. In this study, we provide a comparative analysis of the lectin families from model species in a phylogenetic framework. The analysis focuses on the different plant lectin domains identified in five representative core angiosperm genomes (Arabidopsisthaliana, Glycine max, Cucumis sativus, Oryza sativa ssp. japonica and Oryza sativa ssp. indica). The genomes were screened for genes encoding lectin domains using a combination of Basic Local Alignment Search Tool (BLAST), hidden Markov models, and InterProScan analysis. Additionally, phylogenetic relationships were investigated by constructing maximum likelihood phylogenetic trees. The results demonstrate that the majority of the lectin families are present in each of the species under study. Domain organization analysis showed that most identified proteins are multi-domain proteins, owing to the modular rearrangement of protein domains during evolution. Most of these multi-domain proteins are widespread, while others display a lineage-specific distribution. Furthermore, the phylogenetic analyses reveal that some lectin families evolved to be similar to the phylogeny of the plant species, while others share a closer evolutionary history based on the corresponding protein domain architecture. Our results yield insights into the evolutionary relationships and functional divergence of plant lectins.

Molecular modelling, dynamics simulation and characterization of antifungal chitinase from Sechium edule

Chitinases are varied sized proteins which have the ability to degrade chitin and are present in a huge range of organisms like fungi, yeasts, arthropods, humans etc. and have been getting increased attention due to their biocontrol properties. In silico analysis sheds light on the extensive properties of this plant protein. In this paper, a particular antifungal protein Chitinase sourced from Sechium edule from East Khasi Hills, Meghalaya was characterized using an array of bioinformatics tools. The modelled protein showed conserved domains characteristic to glycosyl hydrolase, family 18 superfamily. Likewise, a part of the conserved domain area fits in with xylanase inhibitor Xip-1 and the class ΙΙΙ plant chitinases, for example, concanavalin B, hevamine, which have a GH18 area. The modelled wild type protein exhibited secondary characteristics comprising of 48.8% helix, 62.2% sheets and 13.8% turns, displaying an aliphatic index of 80.53 and instability index of 48.88 inferring upon the fact that the protein is relatively unstable without its appropriate environment. The paper functions as the first attempt to portray molecular dynamics simulation of Chitinase from Sechium edule reinforced by modelling and thorough characteristic analysis of the protein by employing parameters like Ramachandran Plot, Chou and Fasman Secondary Structure prediction, ProtParam etc. Further approaches like protein engineering and activity analysis suggested.

Soybean cyclophilin GmCYP1 interacts with an isoflavonoid regulator GmMYB176

Cyclophilins (CYPs) belong to the immunophilin superfamily with peptidyl-prolyl cis-trans isomerase (PPIase) activity. They catalyze the interconversion of the cis- and trans-rotamers of the peptidyl-prolyl amide bond of peptides. A yeast-two-hybrid screening using the isoflavonoid regulator GmMYB176 as bait identified GmCYP1 as one of the interacting proteins in soybean embryos. GmCYP1 localizes both in the nucleus and cytoplasm, and interacts in planta with GmMYB176, in the nucleus, and with SGF14l (a soybean 14-3-3 protein) in the nucleus and the cytoplasm. GmCYP1 contains a single cyclophilin-like domain and displays a high sequence identity with other plant CYPs that are known to have stress-specific function. Tissue-specific expression of GmCYP1 revealed higher expression in developing seeds compared to other vegetative tissues, suggesting their seed-specific role. Furthermore, GmCYP1 transcript level was reduced in response to stress. Since isoflavonoids are involved in plant stress resistance against biotic and abiotic factors, the interaction of GmCYP1 with the isoflavonoid regulators GmMYB176 and 14-3-3 protein suggests its role in defense in soybean.

Chitinase from Thermomyces lanuginosus SSBP and its biotechnological applications

Chitinases are ubiquitous class of extracellular enzymes, which have gained attention in the past few years due to their wide biotechnological applications. The effectiveness of conventional insecticides is increasingly compromised by the occurrence of resistance; thus, chitinase offers a potential alternative to the use of chemical fungicides. The thermostable enzymes from thermophilic microorganisms have numerous industrial, medical, environmental and biotechnological applications due to their high stability for temperature and pH. Thermomyces lanuginosus produced a large number of chitinases, of which chitinase I and II are successfully cloned and purified recently. Molecular dynamic simulations revealed that the stability of these enzymes are maintained even at higher temperature. In this review article we have focused on chitinases from different sources, mainly fungal chitinase of T. lanuginosus and its industrial application.

Structure-Function Relationship of a Novel PR-5 Protein with Antimicrobial Activity from Soy Hulls

An alkaline isoform of the PR-5 protein (designated GmOLPc) has been purified from soybean hulls and identified by MALDI-TOF/TOF-MS. GmOLPc effectively inhibited in vitro the growth of Phytophthora soja spore and Pseudomonas syringae pv glycinea. The antimicrobial activity of GmOLPc should be mainly ascribed to its high binding affinity with vesicles composed of DPPG, (1,3)-β-D-glucans, and weak endo-(1,3)-β-D-glucanase activity. From the 3D models, predicted by the homology modeling, GmOLPc contains an extended negatively charged cleft. The cleft was proved to be a prerequisite for endo-(1,3)-β-D-glucanase activity. Molecular docking revealed that the positioning of linear (1,3)-β-D-glucans in the cleft of GmOLPc allowed an interaction with Glu83 and Asp101 that were responsible for the hydrolytic cleavage of glucans. Interactions of GmOLPc with model membranes indicated that GmOLPc possesses good surface activity which could contribute to its antimicrobial activity, as proved by the behavior of perturbing the integrity of membranes through surface hydrophobic amino acid residues (Phe89 and Phe94).

Comparative investigation of seed coats of brown- versus yellow-colored soybean seeds using an integrated proteomics and metabolomics approach

Seed coat color is an important attribute determining consumption of soybean seeds. Soybean cultivar Mallikong (M) has yellow seed coat while its naturally mutated cultivar Mallikong mutant (MM), has brown colored seed coat. We used integrated proteomics and metabolomics approach to investigate the differences between seed coats of M and MM during different stages of seed development (4, 5, and 6 weeks after flowering). 2DE profiling of total seed coat proteins from three stages showed 178 differentially expressed spots between M and MM of which 172 were identified by MALDI-TOF/TOF. Of these, 62 were upregulated and 105 were downregulated in MM compared with M, while five spots were detected only in MM. Proteins involved in primary metabolism showed downregulation in MM suggesting energy in MM might be utilized for proanthocyanidin biosynthesis via secondary metabolic pathways that leads to the development of brown seed coat color. Besides, downregulation of two isoforms of isoflavone reductase indicated reduced isoflavones in seed coat of MM that was confirmed by quantitative estimation of total and individual isoflavones using HPLC. We propose that low isoflavones level in MM may offer a high substrate for proanthocyanidin production that results in the development of brown seed coat in MM.

Distribution and evolution of the lectin family in soybean (Glycine max)

Lectins are a diverse group of proteins that bind specific carbohydrates and are found throughout all kingdoms. In plants, lectins are involved in a range of important processes such as plant defense and stress signaling. Although the genome sequence of Glycine max (soybean) has been published, little is known about the abundance and expansion patterns of lectin genes in soybean. Using BLAST and hidden Markov models, a total of 359 putative lectin genes have been identified. Furthermore, these sequences could be classified in nine of the twelve plant lectin families identified today. Analysis of the domain organization demonstrated that most of the identified lectin genes encode chimerolectins, consisting of one or multiple lectin domains combined with other known protein domains. Both tandem and segmental duplication events have contributed to the expansion of the lectin gene family. These data provide a detailed understanding of the domain architecture and molecular evolution of the lectin gene family in soybean.

Polyphenol oxidase as a biochemical seed defense mechanism

Seed dormancy and resistance to decay are fundamental survival strategies, which allow a population of seeds to germinate over long periods of time. Seeds have physical, chemical, and biological defense mechanisms that protect their food reserves from decay-inducing organisms and herbivores. Here, we hypothesize that seeds also possess enzyme-based biochemical defenses, based on induction of the plant defense enzyme, polyphenol oxidase (PPO), when wild oat (Avena fatua L.) caryopses and seeds were challenged with seed-decaying Fusarium fungi. These studies suggest that dormant seeds are capable of mounting a defense response to pathogens. The pathogen-induced PPO activity from wild oat was attributed to a soluble isoform of the enzyme that appeared to result, at least in part, from proteolytic activation of a latent PPO isoform. PPO activity was also induced in wild oat hulls (lemma and palea), non-living tissues that cover and protect the caryopsis. These results are consistent with the hypothesis that seeds possess inducible enzyme-based biochemical defenses arrayed on the exterior of seeds and these defenses represent a fundamental mechanism of seed survival and longevity in the soil. Enzyme-based biochemical defenses may have broader implications since they may apply to other defense enzymes as well as to a diversity of plant species and ecosystems.

Characterization of an acidic chitinase from seeds of black soybean (Glycine max (L) Merr Tainan No. 3)

Using 4-methylumbelliferyl-β-D-N,N',N″-triacetylchitotrioside (4-MU-GlcNAc3) as a substrate, an acidic chitinase was purified from seeds of black soybean (Glycine max Tainan no. 3) by ammonium sulfate fractionation and three successive steps of column chromatography. The purified chitinase was a monomeric enzyme with molecular mass of 20.1 kDa and isoelectric point of 4.34. The enzyme catalyzed the hydrolysis of synthetic substrates p-nitrophenyl N-acetyl chitooligosaccharides with chain length from 3 to 5 (GlcNAcn, n = 3-5), and pNp-GlcNAc4 was the most degradable substrate. Using pNp-GlcNAc4 as a substrate, the optimal pH for the enzyme reaction was 4.0; kinetic parameters Km and kcat were 245 µM and 10.31 min-1, respectively. This enzyme also showed activity toward CM-chitin-RBV, a polymer form of chitin, and N-acetyl chitooligosaccharides, an oligomer form of chitin. The smallest oligomer substrate was an N-acetylglucosamine tetramer. These results suggested that this enzyme was an endo-splitting chitinase with short substrate cleavage activity and useful for biotechnological applications, in particular for the production of N-acetyl chitooligosaccharides.

DL-β-aminobutyric acid-induced resistance in soybean against Aphis glycines Matsumura (Hemiptera: Aphididae)

Priming can improve plant innate capability to deal with the stresses caused by both biotic and abiotic factors. In this study, the effect of DL-β-amino-n-butyric acid (BABA) against Aphis glycines Matsumura, the soybean aphid (SA) was evaluated. We found that 25 mM BABA as a root drench had minimal adverse impact on plant growth and also efficiently protected soybean from SA infestation. In both choice and non-choice tests, SA number was significantly decreased to a low level in soybean seedlings drenched with 25 mM BABA compared to the control counterparts. BABA treatment resulted in a significant increase in the activities of several defense enzymes, such as phenylalanine ammonia-lyase (PAL), peroxidase (POX), polyphenol oxidase (PPO), chitinase (CHI), and β-1, 3-glucanase (GLU) in soybean seedlings attacked by aphid. Meanwhile, the induction of 15 defense-related genes by aphid, such as AOS, CHS, MMP2, NPR1-1, NPR1-2, and PR genes, were significantly augmented in BABA-treated soybean seedlings. Our study suggest that BABA application is a promising way to enhance soybean resistance against SA.

The role of the testa during development and in establishment of dormancy of the legume seed

Timing of seed germination is one of the key steps in plant life cycles. It determines the beginning of plant growth in natural or agricultural ecosystems. In the wild, many seeds exhibit dormancy and will only germinate after exposure to certain environmental conditions. In contrast, crop seeds germinate as soon as they are imbibed usually at planting time. These domestication-triggered changes represent adaptations to cultivation and human harvesting. Germination is one of the common sets of traits recorded in different crops and termed the "domestication syndrome." Moreover, legume seed imbibition has a crucial role in cooking properties. Different seed dormancy classes exist among plant species. Physical dormancy (often called hardseededness), as found in legumes, involves the development of a water-impermeable seed coat, caused by the presence of phenolics- and suberin-impregnated layers of palisade cells. The dormancy release mechanism primarily involves seed responses to temperature changes in the habitat, resulting in testa permeability to water. The underlying genetic controls in legumes have not been identified yet. However, positive correlation was shown between phenolics content (e.g., pigmentation), the requirement for oxidation and the activity of catechol oxidase in relation to pea seed dormancy, while epicatechin levels showed a significant positive correlation with soybean hardseededness. myeloblastosis family of transcription factors, WD40 proteins and enzymes of the anthocyanin biosynthesis pathway were involved in seed testa color in soybean, pea and Medicago, but were not tested directly in relation to seed dormancy. These phenolic compounds play important roles in defense against pathogens, as well as affecting the nutritional quality of products, and because of their health benefits, they are of industrial and medicinal interest. In this review, we discuss the role of the testa in mediating legume seed germination, with a focus on structural and chemical aspects.

Co-expression of RCH10 and AGLU1 confers rice resistance to fungal sheath blight Rhizoctonia solani and blast Magnorpathe oryzae and reveals impact on seed germination

Rice sheath blight and blast caused by Rhizoctonia solani Kühn and Magnorpathe oryzae respectively, are the two most destructive fungal diseases in rice. With no genetic natural traits conferring resistance to sheath blight, transgenic manipulation provides an obvious approach. In this study, the rice basic chitinase gene (RCH10) and the alfalfa β-1,3-glucanase gene (AGLU1) were tandemly inserted into transformation vector pBI101 under the control of 35S promoter with its enhancer sequence to generate a double-defense gene expression cassette pZ100. The pZ100 cassette was transformed into rice (cv. Taipei 309) by Agrobacterium-mediated transformation. More than 160 independent transformants were obtained and confirmed by PCR. Northern analysis of inheritable progenies revealed similar levels of both RCH10 and AGLU1 transcripts in the same individuals. Disease resistance to both sheath blight and blast was challenged in open field inoculation. Immunogold detection revealed that RCH10 and AGLU1 proteins were initially located mainly in the chloroplasts and were delivered to the vacuole and cell wall upon infection, suggesting that these subcellular compartments act as the gathering and execution site for these anti-fungal proteins. We also observed that transgenic seeds display lower germination rate and seedling vigor, indicating that defense enhancement might be achieved at the expense of development.

Proteomic analysis of the testa from developing soybean seeds

Soybean (Glycine max (L.) Merr. cv Jack) seed development was separated into nine defined stages (S1 to S9). Testa (seed coats) were removed from developing seeds at stages S2, 4, 6, 8, and 9, and subjected to shotgun proteomic profiling. For each stage "total proteins" were isolated from 150 mg dry weight of seed coat using a phenol-based method, then reduced, alkylated, and digested with trypsin. The tryptic peptides were separated using a C18-reversed phase matrix, then analyzed using an LTQ Orbitrap Mass Spectrometer. Spectra were searched against the Phytozome G. max DB using the Sorcerer 2 IDA Sequest-based search algorithm. Identities were verified using Scaffold 3. A total of 306 (S2), 328 (S4), 273 (S6), 193 (S8), and 272 (S9) proteins were identified in three out of three biological replicates, and sorted into 11 functional groups: Primary Metabolism, Secondary Metabolism, Cellular Structure, Stress Responses, Nucleic Acid metabolism, Protein Synthesis, Protein Folding, Protein Targeting, Hormones and Signaling, Seed Storage Proteins, and Proteins of Unknown Function. In selected instances, individual seed coat proteins were quantified by spectral counting. The number of proteins involved in intermediary metabolism, flavonoid biosynthesis, protein folding and degradation are discussed as they relate to seed coat function.

BIOLOGICAL SIGNIFICANCE

Most previous analyses of seed coats have either targeted individual enzymes or used the results from high-throughput transcript profiling to infer biological function. Because there is seldom a linear correlation between transcript and protein levels, we have undertaken a shotgun proteomics-based description of soybean (G. max (L.) Merr. cv Jack) seed coats, as a function of development, in order to bridge this gap and to establish the baseline for a more comprehensive understanding of seed biology.

Eplt4 proteinaceous elicitor produced in Pichia pastoris has a protective effect against Cercosporidium sofinum infections of soybean leaves

A complementary DNA library was constructed from the mycelium of Trichoderma asperellum T4, and a highly expressed gene fragment named EplT4 was found. In order to find a more efficient and cost-effective way of obtaining EplT4, this study attempted to produce EplT4 using a Pichia pastoris expression system. The gene encoding EplT4, with an additional 6-His tag at the C-terminus, was cloned into the yeast vector pPIC9K and expressed in the P. pastoris strain GS115 to obtaining more protein for the further research. Transformants of P. pastoris were selected by PCR analysis, and the ability to secrete high levels of the EplT4 protein was determined. The optimal conditions for induction were assayed using the shake flask method and an enzyme-linked immunosorbent assay. The yield of purified EplT4 was approximately 20 mg/L by nickel affinity chromatography and gel-filtration chromatography. Western blot and matrix-assisted laser desorption/ionization time-of-flight mass spectrometer analysis revealed that the recombinant EplT4 was expressed in both its monomers and dimers. Soybean leaves treated with the EplT4 monomer demonstrated the induction of glucanase, chitinase III-A, cysteine proteinase inhibitor, and peroxidase genes. Early cellular events in plant defense response were also observed after incubation with EplT4. Soybean leaves protected by EplT4 against the pathogen Cercosporidium sofinum (Hara) indicated that EplT4 produced in P. pastoris was biologically active and would be potentially useful for improving food security.

Molecular and functional evolution of class I chitinases for plant carnivory in the caryophyllales

Proteins produced by the large and diverse chitinase gene family are involved in the hydrolyzation of glycosidic bonds in chitin, a polymer of N-acetylglucosamines. In flowering plants, class I chitinases are important pathogenesis-related proteins, functioning in the determent of herbivory and pathogen attack by acting on insect exoskeletons and fungal cell walls. Within the carnivorous plants, two subclasses of class I chitinases have been identified to play a role in the digestion of prey. Members of these two subclasses, depending on the presence or absence of a C-terminal extension, can be secreted from specialized digestive glands found within the morphologically diverse traps that develop from carnivorous plant leaves. The degree of homology among carnivorous plant class I chitinases and the method by which these enzymes have been adapted for the carnivorous habit has yet to be elucidated. This study focuses on understanding the evolution of carnivory and chitinase genes in one of the major groups of plants that has evolved the carnivorous habit: the Caryophyllales. We recover novel class I chitinase homologs from species of genera Ancistrocladus, Dionaea, Drosera, Nepenthes, and Triphyophyllum, while also confirming the presence of two subclasses of class I chitinases based upon sequence homology and phylogenetic affinity to class I chitinases available from sequenced angiosperm genomes. We further detect residues under positive selection and reveal substitutions specific to carnivorous plant class I chitinases. These substitutions may confer functional differences as indicated by protein structure homology modeling.

Chitinase III in pomegranate seeds (Punica granatum Linn.): a high-capacity calcium-binding protein in amyloplasts

Chitinases are a class of ubiquitous proteins that are widely distributed in plants. Defense is the major natural role for chitinases, primarily against fungal pathogens. Little is known regarding their non-defensive roles in seeds. In this study, a new class III chitinase from pomegranate seeds (pomegranate seed chitinase, PSC) was isolated and purified to homogeneity. The native state of PSC is a monomer with a molecular weight of approximately 30 kDa. This chitinase naturally binds calcium ions with high capacity and low affinity, suggesting that PSC is a calcium storage protein. Consistent with this idea, its amino acid sequence (inferred from cDNA) is rich in acidic amino acid residues, especially Asp, similar to reported calcium storage proteins. The presence of calcium considerably improves the stability of the protein but has little effect on its enzymatic activity. Transmission electron microscopy analyses indicate that, similar to phytoferritin, this enzyme is widely distributed in the stroma of amyloplasts of the embryonic cells, suggesting that amyloplasts in seeds could serve as an alternative plastid for calcium storage. Indeed, the transmission electron microscopy results showed that, within the embryonic cells, calcium ions are mainly distributed in the stroma of the amyloplasts, consistent with a role for PSC in calcium storage. Thus, the plant appears to have evolved a new plastid for calcium storage in seeds. During seed germination, the content of this enzyme decreases with time, suggesting that it is involved in the germination process.

Isolation of a new fungi and wound-induced chitinase class in corms of Crocus sativus

In plants, various chitinases have been identified and categorized into several groups based on the analysis of their sequences and domains. We have isolated SafchiA, a novel class of chitinase from saffron (Crocus sativus L.). The cDNA encoding SafchiA is mainly expressed in roots and corms, and its expression is induced by elicitor treatment, methyl jasmonate, wounding, and by the fungi Fusarium oxysporum, Beauveria and Phoma sp., suggesting a defence role of the protein. Furthermore, in vitro assays with the recombinant native protein showed chitinolytic, and antifungal activity. The deduced protein shares high similarity with chitinases belonging to family 19 of glycosyl-hydrolases, although some changes in the enzyme active site are present. To explore the properties of SafchiA we have expressed recombinant SafchiA in Escherichia coli and generated four different mutants affected in residues involved in the catalytic activity. One glutamic acid essential for family 19 chitinases activity is not present in C. sativus chitinase suggesting that only one acidic residue is necessary for the enzyme activity, in a similar manner as family 18 glycosyl-hydrolases.

Abundant class III acidic chitinase homologue in tamarind (Tamarindus indica) seed serves as the major storage protein

The phyla Leguminosae contains protease inhibitors, lectins, chitinases, and glycohydrolases as major defense proteins in their seeds. Electrophoretic analysis of the seed proteins of tamarind ( Tamarindus indica L.), an agri-waste material, indicated the unusual presence of two major proteins comparable to overexpression of recombinant proteins. These proteins were identified by amino-terminal analysis to be (1) Kunitz-type trypsin inhibitor and (2) class III endochitinase (34000 Da). These two proteins were purified to apparent homogeneity by a single-step chitin bead affinity chromatography and characterized. The Kunitz inhibitor was specific toward inhibiting trypsin with a stoichiometry of 1:1. The 33000 +/- 1000 Da protein, accounting for >50% of the total seed protein, is an acidic glycoprotein exhibiting a very low endotype hydrolytic activity toward chitin derivatives. SDS-PAGE followed by densitometry of tamarind seed germination indicates the disappearance of the chitinase with the concomitant appearance of a cysteine endopeptidase. On the basis of its abundance, accumulation without any pathogenesis-related stimulus, temporal regulation, amino acid composition, and very low enzyme activity, this 34000 Da protein designated "tamarinin" physiologically serves as the major storage protein.

Bacillus pumilusSG2 isolated from saline conditions produces and secretes two chitinases

AIMS

Isolation and characterization of chitinases from a halotolerant Bacillus pumilus.

METHODS AND RESULTS

Bacillus pumilus strain SG2 was isolated from saline conditions. It is able to produce chitinase activity at high salt concentration. SDS-PAGE analysis of the B. pumilus SG2 culture supernatant showed two major bands that were induced by chitin. The amino acid sequence of the two proteins, designated ChiS and ChiL, showed a high homology with the chitinase of B. subtilis CHU26, and chitinase A of B. licheniformis, respectively. N-terminal signal peptide of both proteins was also determined. The molecular weight and isoelectric point of the chitinases were determined to be 63 and 74 kDa, and 4.5 and 5.1, for ChiS and ChiL respectively. The genes encoding for both chitinases were isolated and their sequence determined. The regulation of the chitinase genes is under the control of the catabolite repression system.

CONCLUSIONS

Secreted chitinase genes and their flanking region on the genome of B. pumilus SG2 have been identified and sequenced.

SIGNIFICANCE AND IMPACT OF THE STUDY

This is the first report of a multiple chitinases-producing B. pumilus halotolerant strain. We have identified two chitinases by using a reverse genetics approach. The chitinases show resistance to salt.

GmEREBP1 is a transcription factor activating defense genes in soybean and Arabidopsis

Ethylene-responsive element-binding proteins (EREBPs) are plant-specific transcription factors, many of which have been linked to plant defense responses. Conserved EREBP domains bind to the GCC box, a promoter element found in pathogenesis-related (PR) genes. We previously identified an EREBP gene from soybean (GmEREBP1) whose transcript abundance decreased in soybean cyst-nematode-infected roots of a susceptible cultivar, whereas it increased in abundance in infected roots of a resistant cultivar. Here, we report further characterization of this gene. Transient expression analyses showed that GmEREBP1 is localized to the plant nucleus and functions as a transcriptional activator in soybean leaves. Transgenic soybean plants expressing GmEREBP1 activated the expression of the ethylene (ET)-responsive gene PR2 and the ET- and jasmonic acid (JA)-responsive gene PR3, and the salicylic acid (SA)-responsive gene PR1 but not the SA-responsive PR5. Similarly, transgenic Arabidopsis plants expressing GmEREBP1 showed elevated mRNA abundance of the ET-regulated gene PR3 and the ET- and JA-regulated defense-related gene PDF1.2 but not the ET-regulated GST2, and the SA-regulated gene PR1 but not the SA-regulated PR2 and PR5. Transgenic soybean and Arabidopsis plants inoculated with cyst nematodes did not display a significantly altered susceptibility to nematode infection. These results collectively show that GmEREBP1 functions as a transacting inducer of defense gene expression in both soybean and Arabidopsis and mediates the expression of both ET- and JA- and SA-regulated defense-related genes in these plant species.

A soybean seed protein with carboxylate-binding activity

The seed coat serves as a multifunctional organ with a role in protection and for the supply of nutrients to the embryo sac during development. The composition of the legume seed coat differs from other seed tissues in many ways including its protein composition. An abundant 24 kDa protein (SC24) has been purified and identified from soybean (Glycine max [L.] Merr) seed hulls. The corresponding cDNA and genomic DNA clones for SC24 were isolated and characterized, and expression patterns were determined. The deduced protein sequence of 219 amino acids included an N-terminal signal peptide. Transcripts encoding SC24 were present in the seed coat from 30 days after pollination (DAP) until maturity, but the protein was not detected until the final stages of seed maturation. In mature seeds, most of the SC24 protein was localized to the parenchyma and aleurone layers of the seed coat. The expression of SC24 was also induced in vegetative tissues by pathogen infection and by wounding. The SC24 protein bound to an affinity column containing an isophthalic acid ligand, and was eluted with 7 mM citrate. Polyclonal antibodies raised against recombinant SC24 cross-reacted with the seed coat peroxidase enzyme, suggesting that these two proteins may share an antigenic determinant. Overall, the results indicate that SC24 belongs to a novel class of plant defence proteins with carboxylate-binding activity.

Phaseococcin, an antifungal protein with antiproliferative and anti-HIV-1 reverse transcriptase activities from small scarlet runner beans

From the seeds of small scarlet runner beans (Phaseolus coccineus 'Minor'), an antifungal protein with an N-terminal sequence homologous to those of defensins was isolated. The antifungal protein bound to Affi-gel blue gel and Mono S but it did not bind to DEAE-cellulose. It was further purified by gel filtration on a Superdex peptide column. It exhibited a molecular mass of 5422 Da as determined by mass spectrometry. The protein, designated as phaseococcin, suppressed mycelial growth in a number of fungi including Botrytis cinerea, Coprinus comatus, Fusarium oxysporum, Mycosphaerella arachidicola, Physalospora piricola, and Rhizoctonia solani. It also inhibited proliferation in several Bacillus species and the leukemia cell lines HL60 and L1210 and curtailed the activity of HIV-1 reverse transcriptase. It did not affect proliferation of mouse splenocytes and neither did it inhibit protein synthesis in a cell-free rabbit reticulocyte lysate system.Key words: antifungal proteins, runner beans, antiproliferative.

Patterns of gene expression upon infection of soybean plants by Phytophthora sojae

To investigate patterns of gene expression in soybean (Glycine max) and Phytophthora sojae during an infection time course, we constructed a 4,896-gene microarray of host and pathogen cDNA transcripts. Analysis of rRNA from soybean and P. sojae was used to estimate the ratio of host and pathogen RNA present in mixed samples. Large changes in this ratio occurred between 12 and 24 h after infection, reflecting the rapid growth and proliferation of the pathogen within host tissues. From the microarray analysis, soybean genes that were identified as strongly upregulated during infection included those encoding enzymes of phytoalexin biosynthesis and defense and pathogenesis-related proteins. Expression of these genes generally peaked at 24 h after infection. Selected lipoxygenases and peroxidases were among the most strongly downregulated soybean genes during the course of infection. The number of pathogen genes expressed during infection reached a maximum at 24 h. The results show that it is possible to use a single microarray to simultaneously probe gene expression in two interacting organisms. The patterns of gene expression we observed in soybean and P. sojae support the hypothesis that the pathogen transits from biotrophy to necrotrophy between 12 and 24 h after infection.

Methyl jasmonate alters N partitioning, N reserves accumulation and induces gene expression of a 32-kDa vegetative storage protein that possesses chitinase activity in Medicago sativa taproots

This study presents the effects of methyl jasmonate (MeJA) on growth, N uptake, N partitioning, and N storage in taproots of non-nodulated alfalfa (cv. Lodi). When compared to untreated plants, addition of 100 micro M MeJA to the nutrient solution for 14 days reduced total growth and modified biomass partitioning between shoots and roots in favour of taproots and lateral roots. MeJA decreased N uptake (after 7 days) and increased N partitioning towards roots after 14 days. This preferential N partitioning to roots was accompanied by increased N storage in taproots as soluble proteins. Compared to total soluble proteins, VSP accumulation occurred earlier (7 days), and was greater (2-fold increase) in plants treated with 100 micro M MeJA. Steady-state transcript levels for two VSPs (32 and 57 kDa) also increased markedly (about 4-fold) in roots of plants treated with 100 micro M MeJA. This suggests that MeJA could act directly (transcriptional regulation) or indirectly (via the changes of N partitioning among alfalfa organs) on N storage as soluble proteins and in particular, VSPs. Because the deduced amino acid sequence of the 32 kDa VSP clone reveals high homology with Class III chitinases, we propose that the 32 kDa VSP may have a role in pathogen defense, in addition to its function as a storage protein.