Proteomic Characterization of a Lunasin-Enriched Soybean Extract Potentially Useful in the Treatment of Helicobacter pylori Infection

Helicobacter pylori infection affects over 50% of the world's population and leads to chronic inflammation and gastric disorders, being the main pathogen correlated to gastric cancer development. Increasing antibiotic resistance levels are a major global concern and alternative treatments are needed. Soybean peptides and other compounds might be an alternative in the treatment to avoid, eradicate and/or control symptoms of H. pylori infection. This study aimed to characterize a lunasin-enriched soybean extract (LSE) using proteomics tools and to evaluate its antioxidant, anti-inflammatory and antibacterial properties against H. pylori infection. By LC-MS/MS analysis, 124 proteins were identified, with 2S albumin (lunasin and large-chain subunits) being the fourth most abundant protein (8.9%). Lunasin consists of 44 amino acid residues and an intramolecular disulfide bond. LSE at a low dose (0.0625 mg/mL) reduced ROS production in both H. pylori-infected and non-infected AGS gastric cells. This led to a significant reduction of 6.71% in the levels of pro-inflammatory interleukin (IL)-8. LSE also showed antibacterial activity against H. pylori, which can be attributed to other soybean proteins and phenolic compounds. Our findings suggest that LSE might be a promising alternative in the management of H. pylori infection and its associated symptoms.

Elemental sulfur concentration can be used as a rapid, reliable, and cost-effective predictor of sulfur amino acid content of soybean seeds

In this study, we have examined the feasibility of using elemental sulfur content of soybean seeds as a proxy for the overall sulfur amino acid content of soybean seeds. Earlier, we have identified by high throughput ionomic phenotyping several high and low sulfur containing soybean lines from the USDA Soybean Germplasm Collection. Here, we measured the cysteine and methionine content of select soybean lines by high-performance liquid chromatography. Our results demonstrate that those soybean lines which had high elemental sulfur content also had a higher cysteine and methionine content when compared to soybean lines with low elemental sulfur. SDS-PAGE and immunoblot analysis revealed that the accumulation of Bowman Birk protease inhibitor and lunasin in soybean seeds may only be marginally correlated with the elemental sulfur levels. However, we found a positive correlation between the levels of trypsin and chymotrypsin inhibitor activities and elemental sulfur and sulfur amino acid content of the seeds. Thus, elemental sulfur content and/or protease inhibitor activity measurement can be utilized as a rapid and cost-effective method to predict the overall sulfur amino acid content of soybean seeds. Our findings will benefit breeders in their endeavors to develop soybean cultivars with enhanced sulfur amino acid content.

Genetic mapping and functional genomics of soybean seed protein

Soybean is an utterly important crop for high-quality meal protein and vegetative oil. Soybean seed protein content has become a key factor in nutrients for livestock feed as well as human dietary consumption. Genetic improvement of soybean seed protein is highly desired to meet the demands of rapidly growing world population. Molecular mapping and genomic analysis in soybean have identified many quantitative trait loci (QTL) underlying seed protein content control. Exploring the mechanisms of seed storage protein regulation will be helpful to achieve the improvement of protein content. However, the practice of breeding higher protein soybean is challenging because soybean seed protein is negatively correlated with seed oil content and yield. To overcome the limitation of such inverse relationship, deeper insights into the property and genetic control of seed protein are required. Recent advances of soybean genomics have strongly enhanced the understandings for molecular mechanisms of soybean with better seed quality. Here, we review the research progress in the genetic characteristics of soybean storage protein, and up-to-date advances of molecular mappings and genomics of soybean protein. The key factors underlying the mechanisms of the negative correlation between protein and oil in soybean seeds are elaborated. We also briefly discuss the future prospects of breaking the bottleneck of the negative correlation to develop high protein soybean without penalty of oil and yield.

Supplementary Information

The online version contains supplementary material available at 10.1007/s11032-023-01373-5.

A fast and cost-effective procedure for reliable measurement of trypsin inhibitor activity in soy and soy products

Rapid and accurate measurement of trypsin inhibitor is critical for soy processors to assess the quality of soy meal. Currently, trypsin inhibitor activity is measured using the American Oil Chemists' Society (AOCS) and the American Association of Cereal Chemists International (AACCI) approved method. We have modified and improved the AACCI/AOCS approved method resulting in the elimination of several time-consuming steps and drastically reducing the assay volume. By employing our simplified procedure, we have measured trypsin inhibitor activity of several soy and soy products. A side-by side comparison of our simplified procedure with AOCS approved method revealed strikingly similar results indicating that several time-consuming and tedious steps associated with AACCI/AOCS approved methods can be eliminated without sacrificing the accuracy of the assay. Moreover, we demonstrate that our assay can also be carried out in 96-well microplates which will enable high-throughput screening of large number of soy meal samples.

Amino acids induce high seed-specific expression driven by a soybean (Glycine max) glycinin seed storage protein promoter

We characterize GFP expression driven by a soybean glycinin promoter in transgenic soybean. We demonstrate specific amino acid-mediated induction of this promoter in developing soybean seeds in vitro. In plants, gene expression is primarily regulated by promoter regions which are located upstream of gene coding sequences. Promoters allow transcription in certain tissues and respond to environmental stimuli as well as other inductive phenomena. In soybean, seed storage proteins (SSPs) accumulate during seed development and account for most of the monetary and nutritional value of this crop. To better study the regulatory functions of a SSP promoter, we developed a cotyledon culture system where media and media addenda were evaluated for their effects on cotyledon development and promoter activity. Stably transformed soybean events containing a glycinin SSP promoter regulating the green fluorescent protein (GFP) were generated. Promoter activity, as visualized by GFP expression, was only observed in developing in planta seeds and in vitro-cultured isolated embryos and cotyledons from developing seeds when specific media addenda were included. Asparagine, proline, and especially glutamine induced glycinin promoter activity in cultured cotyledons from developing seeds. Other amino acids did not induce the glycinin promoter. Here, we report, for the first time, induction of a reintroduced glycinin SSP promoter by specific amino acids in cotyledon tissues during seed development.

Confocal Fluorescence Microscopy Investigation for the Existence of Subdomains within Protein Storage Vacuoles in Soybean Cotyledons

In legumes, the seed storage proteins accumulate within specialized organelles called protein storage vacuoles (PSVs). In several plant species, PSVs are differentiated into subdomains that accumulate different kinds of proteins. Even though the existence of subdomains is common in cereals and legumes, it has not been reported in soybean PSVs. The two most abundant seed proteins of soybean, 7S and 11S globulins, have different temporal accumulation patterns and exhibit considerable solubility differences that could result in differential accretion of these proteins within the PSVs. Here, we employed confocal fluorescent microscopy to examine the presence or absence of subdomains within the soybean PSVs. Eosin-stained sections of FAA-fixed paraffin embedded soybean seeds, when viewed by confocal fluorescence microscopy, revealed the presence of intricate subdomains within the PSVs. However, fluorescence immunolabeling studies demonstrated that the 7S and 11S globulins were evenly distributed within the PSVs and failed to corroborate the existence of subdomains within the PSVs. Similarly, confocal scanning microscopy examination of free-hand, vibratome and cryostat sections also failed to demonstrate the existence of subdomains within PSVs. The subdomains, which were prominently seen in PSVs of FAA-fixed soybean seeds, were not observed when the seeds were fixed either in glutaraldehyde/paraformaldehyde or glutaraldehyde. Our studies demonstrate that the apparent subdomains observed in FAA-fixed seeds may be a fixation artifact.

Human-Soybean Allergies: Elucidation of the Seed Proteome and Comprehensive Protein-Protein Interaction Prediction

The soybean crop, Glycine max (L.) Merr., is consumed by humans, Homo sapiens, worldwide. While the respective bodies of literature and -omics data for each of these organisms are extensive, comparatively few studies investigate the molecular biological processes occurring between the two. We are interested in elucidating the network of protein-protein interactions (PPIs) involved in human-soybean allergies. To this end, we leverage state-of-the-art sequence-based PPI predictors amenable to predicting the enormous comprehensive interactome between human and soybean. A network-based analytical approach is proposed, leveraging similar interaction profiles to identify candidate allergens and proteins involved in the allergy response. Interestingly, the predicted interactome can be explored from two complementary perspectives: which soybean proteins are predicted to interact with specific human proteins and which human proteins are predicted to interact with specific soybean proteins. A total of eight proteins (six specific to the human proteome and two to the soy proteome) have been identified and supported by the literature to be involved in human health, specifically related to immunological and neurological pathways. This study, beyond generating the most comprehensive human-soybean interactome to date, elucidated a soybean seed interactome and identified several proteins putatively consequential to human health.

Development of soybean experimental lines with enhanced protein and sulfur amino acid content

Soybean is the preferred protein source for both poultry and swine feed. However, this preferred status is being challenged due to competition from alternative feed ingredients. To overcome this, it becomes necessary for breeders to develop soybean cultivars that contain higher protein and better nutritional composition. In this study, we have developed experimental soybean lines that not only contain significantly higher amounts of protein but also improved sulfur amino acid content. This objective was achieved by crossing a O-acetylserine sulfhydrylase (OASS) overexpressing transgenic soybean line with elevated levels of sulfur amino acid content (CS) with a high protein Korean soybean cultivar (Lee 5). Introgression of high protein and overexpression of OASS was monitored in the experimental lines at each successive generation (F2-F6) by measuring protein content and OASS activity. The average protein content of transgenic CS and Lee 5 seeds were 34.8 % and 44.7 %, while in the experimental soybean lines the protein content ranged from 41.3 %-47.7 %, respectively. HPLC and inductively coupled plasma-mass spectrometry analyses revealed that all the experimental lines developed in this study contained significantly higher amounts of sulfur containing amino acids and elemental sulfur in the seeds. The sulfur amino acid (cysteine + methionine) content of the experimental lines ranged from 1.1 % to 1.26 % while the parents Lee 5 and CS had 0.79 % and 1.1 %, respectively. SDS-PAGE and western blot analysis demonstrated that the accumulation of Bowman-Birk protease inhibitor and lunasin, two sulfur amino acid rich peptides, were elevated in experimental soybean lines. High-resolution 2D-gel electrophoresis and Delta2D gel analysis validated that an overall increase in the different subunits of 7S β-conglycinin and 11S glycinin were mainly responsible for the observed increase in the total amount of protein in experimental lines.

Rheological and Solubility Properties of Soy Protein Isolate

Soy protein isolate (SPI) powders often have poor water solubility, particularly at pH values close to neutral, which is an attribute that is an issue for its incorporation into complex nutritional systems. Therefore, the objective of this study was to improve SPI solubility while maintaining low viscosity. Thus, the intention was to examine the solubility and rheological properties of a commercial SPI powder at pH values of 2.0, 6.9, and 9.0, and determine if heat treatment at acidic or alkaline conditions might positively influence protein solubility, once re-adjusted back to pH 6.9. Adjusting the pH of SPI dispersions from pH 6.9 to 2.0 or 9.0 led to an increase in protein solubility with a concomitant increase in viscosity at 20 °C. Meanwhile, heat treatment at 90 °C significantly improved the solubility at all pH values and resulted in a decrease in viscosity in samples heated at pH 9.0. All SPI dispersions measured under low-amplitude rheological conditions showed elastic-like behaviour (i.e., G′ > G″), indicating a weak “gel-like” structure at frequencies less than 10 Hz. In summary, the physical properties of SPI can be manipulated through heat treatment under acidic or alkaline conditions when the protein subunits are dissociated, before re-adjusting to pH 6.9.

Gastrointestinal Digestion of Food Proteins under the Effects of Released Bioactive Peptides on Digestive Health

The gastrointestinal tract represents a specialized interface between the organism and the external environment. Because of its direct contact with lumen substances, the modulation of digestive functions by dietary substances is supported by a growing body of evidence. Food-derived bioactive peptides have demonstrated a plethora of activities in the organism with increasing interest toward their impact over the digestive system and related physiological effects. This review updates the biological effects of food proteins, specifically milk and soybean proteins, associated to gastrointestinal health and highlights the study of digestion products and released peptides, the identification of the active form/s, and the evaluation of the mechanisms of action underlying their relationship with the digestive cells and receptors. The approach toward the modifications that food proteins and peptides undergo during gastrointestinal digestion and their bioavailability is a crucial step for current investigations on the field. The recent literature on the regulation of digestive functions by peptides has been mostly considered in terms of their influence on gastrointestinal motility and signaling, oxidative damage and inflammation, and malignant cellular proliferation. A final section regarding the actual challenges and future perspectives in this scientific topic is critically discussed.

Overexpression of ATP sulfurylase improves the sulfur amino acid content, enhances the accumulation of Bowman-Birk protease inhibitor and suppresses the accumulation of the β-subunit of β-conglycinin in soybean seeds

ATP sulfurylase, an enzyme which catalyzes the conversion of sulfate to adenosine 5'-phosphosulfate (APS), plays a significant role in controlling sulfur metabolism in plants. In this study, we have expressed soybean plastid ATP sulfurylase isoform 1 in transgenic soybean without its transit peptide under the control of the 35S CaMV promoter. Subcellular fractionation and immunoblot analysis revealed that ATP sulfurylase isoform 1 was predominantly expressed in the cell cytoplasm. Compared with that of untransformed plants, the ATP sulfurylase activity was about 2.5-fold higher in developing seeds. High-resolution 2-D gel electrophoresis and immunoblot analyses revealed that transgenic soybean seeds overexpressing ATP sulfurylase accumulated very low levels of the β-subunit of β-conglycinin. In contrast, the accumulation of the cysteine-rich Bowman-Birk protease inhibitor was several fold higher in transgenic soybean plants when compared to the non-transgenic wild-type seeds. The overall protein content of the transgenic seeds was lowered by about 3% when compared to the wild-type seeds. Metabolite profiling by LC-MS and GC-MS quantified 124 seed metabolites out of which 84 were present in higher amounts and 40 were present in lower amounts in ATP sulfurylase overexpressing seeds compared to the wild-type seeds. Sulfate, cysteine, and some sulfur-containing secondary metabolites accumulated in higher amounts in ATP sulfurylase transgenic seeds. Additionally, ATP sulfurylase overexpressing seeds contained significantly higher amounts of phospholipids, lysophospholipids, diacylglycerols, sterols, and sulfolipids. Importantly, over expression of ATP sulfurylase resulted in 37-52% and 15-19% increases in the protein-bound cysteine and methionine content of transgenic seeds, respectively. Our results demonstrate that manipulating the expression levels of key sulfur assimilatory enzymes could be exploited to improve the nutritive value of soybean seeds.

Soybean Mutants Lacking Abundant Seed Storage Proteins Are Impaired in Mobilization of Storage Reserves and Germination

Spontaneous and radiation-induced mutants of soybean, despite loss of abundant seed proteins, have been reported to grow and reproduce normally without any apparent physiological abnormalities. Here, we report the development and characterization of a soybean line (BSH-2) that lacks several abundant seed storage proteins. One-dimensional and high-resolution two-dimensional gel electrophoresis revealed the absence of the α' and α subunits of β-conglycinin and G1, G2, G4, and G5 glycinin in the newly developed mutant line (BSH-2). Like our earlier developed soybean mutant line (BSH-3), the seeds of BSH-2 also accumulated high levels of free amino acids as compared with wild-type DN47 seeds. An examination of the germination rates revealed that both BSH-2 and BSH-3 had significantly lower germination rates compared with the parent line DN47. Two-dimensional gel electrophoresis analysis demonstrated that these mutants had slower rates of mobilization of seed storage proteins. The delayed mobilization of storage proteins in BSH-2 and BSH-3 seeds was also correlated with a delayed induction of proteolytic activity in the mutants when compared to DN47. Similarly, qRT-PCR analysis revealed distinct expression pattern of genes involved in proteolytic pathway in the mutants when compared to DN47. Transmission electron microscopy observation of soybean seeds at two germination stages revealed striking differences in the breakdown of protein storage vacuoles and lipid bodies in the mutants. Our study demonstrates that BSH-2 and BSH-3 are compromised in mobilization of storage reserves and the absence of abundant storage proteins may affect the seed germination efficiency and post-germinative seedling establishment.

Recent update on methodologies for extraction and analysis of soybean seed proteins

Soybean is one of the best sources of plant protein. Development of improved soybean cultivars through classical breeding and new biotech approaches is important to meet the growing global demand for soybeans. There is a critical need to investigate changes in protein content and profiles to ensure the safety and nutritional quality of new soybean varieties and their food products. A proteomics study begins with an optimal combination of extraction, separation and detection approaches. This review attempts to provide a summary of current updates in the methodologies used for extraction, separation and detection of protein from soybean, the basic foundations for good proteomic research. This information can be effectively used to investigate modifications in protein content and profiles in new varieties of soybeans and other crops. © 2018 Society of Chemical Industry.

Review: The promise and limits for enhancing sulfur-containing amino acid content of soybean seed

Soybeans are an excellent source of protein in monogastric diets and rations with ∼75% of soybeans produced worldwide used primarily for animal feed. Even though soybeans are protein-rich and have a well-balanced amino acid profile, the nutritive quality of this important crop could be further improved by elevating the concentrations of certain amino acids. The levels of the sulfur-containing amino acids cysteine and methionine in soybean seed proteins are inadequate for optimal growth and development of monogastric animals, which necessitates dietary supplementation. Subsequently, concerted efforts have been made to increase the concentrations of cysteine and methionine in soybean seeds by both classical breeding and genetic engineering; however, these efforts have met with only limited success. In this review, we discuss the strengths and weakness of different approaches in elevating the sulfur amino acid content of soybeans. Manipulation of enzymes involved in the sulfur assimilatory pathway appears to be a viable avenue for improving sulfur amino acid content. This approach requires a through biochemical characterization of sulfur assimilatory enzymes in soybean seeds. We highlight recent studies targeting key sulfur assimilatory enzymes and the manipulation of sulfur metabolism in transgenic soybeans to improve the nutritive value of soybean proteins.

Development and Characterization of a Soybean Experimental Line Lacking the α' Subunit of β-Conglycinin and G1, G2, and G4 Glycinin

A soybean experimental line (BSH-3) devoid of a subset of seed storage proteins was developed by crossing a mutant donor line "HS99B" with a Chinese cultivar "Dongnong47" (DN47). One-dimensional and high-resolution 2-D gel electrophoresis revealed the absence of G1 (A1aB2), G2 (A2B1a), and G4 (A5A4B3) glycinin and the α' subunit of β-conglycinin in BSH-3 seeds. Despite the lack of these abundant seed proteins, BSH-3 seeds still accumulated 38% protein. BSH-3 seeds also accumulated high levels of free amino acids as compared with DN47 seeds, particularly arginine, and the amount of several essential amino acids were significantly elevated in BSH-3 seeds. Elevated accumulation of α and β-subunit of β-conglycinin, G5 glycinin, Kunitz trypsin inhibitor, and Bowman-Birk protease inhibitor indicates seed proteome rebalancing in BSH-3 seeds. Immunoblot analysis using sera from soybean allergic patients demonstrated the complete lack of a major allergen (α' subunit of β-conglycinin) in BSH-3 seeds. However, elevated levels of other allergens were found in BSH-3 seeds due to proteome rebalancing. Transmission electron microscopy observation of mature seeds of BSH-3 revealed striking differences in the appearance of the protein storage vacuoles when compared with DN47.

Molecular mapping and genomics of soybean seed protein: a review and perspective for the future

KEY MESSAGE

Genetic improvement of soybean protein meal is a complex process because of negative correlation with oil, yield, and temperature. This review describes the progress in mapping and genomics, identifies knowledge gaps, and highlights the need of integrated approaches. Meal protein derived from soybean [Glycine max (L) Merr.] seed is the primary source of protein in poultry and livestock feed. Protein is a key factor that determines the nutritional and economical value of soybean. Genetic improvement of soybean seed protein content is highly desirable, and major quantitative trait loci (QTL) for soybean protein have been detected and repeatedly mapped on chromosomes (Chr.) 20 (LG-I), and 15 (LG-E). However, practical breeding progress is challenging because of seed protein content's negative genetic correlation with seed yield, other seed components such as oil and sucrose, and interaction with environmental effects such as temperature during seed development. In this review, we discuss rate-limiting factors related to soybean protein content and nutritional quality, and potential control factors regulating seed storage protein. In addition, we describe advances in next-generation sequencing technologies for precise detection of natural variants and their integration with conventional and high-throughput genotyping technologies. A syntenic analysis of QTL on Chr. 15 and 20 was performed. Finally, we discuss comprehensive approaches for integrating protein and amino acid QTL, genome-wide association studies, whole-genome resequencing, and transcriptome data to accelerate identification of genomic hot spots for allele introgression and soybean meal protein improvement.

Whole-Genome Resequencing Identifies the Molecular Genetic Cause for the Absence of a Gy5 Glycinin Protein in Soybean PI 603408

During ongoing proteomic analysis of the soybean (Glycine max (L.) Merr) germplasm collection, PI 603408 was identified as a landrace whose seeds lack accumulation of one of the major seed storage glycinin protein subunits. Whole genomic resequencing was used to identify a two-base deletion affecting glycinin 5 The newly discovered deletion was confirmed to be causative through immunological, genetic, and proteomic analysis, and no significant differences in total seed protein content were found to be due to the glycinin 5 loss-of-function mutation per se In addition to focused studies on this one specific glycinin subunit-encoding gene, a total of 1,858,185 nucleotide variants were identified, of which 39,344 were predicted to affect protein coding regions. In order to semiautomate analysis of a large number of soybean gene variants, a new SIFT 4G (Sorting Intolerant From Tolerated 4 Genomes) database was designed to predict the impact of nonsynonymous single nucleotide soybean gene variants, potentially enabling more rapid analysis of soybean resequencing data in the future.

Proteomic Analysis of Pigeonpea (Cajanus cajan) Seeds Reveals the Accumulation of Numerous Stress-Related Proteins

Pigeonpea is one of the major sources of dietary protein for more than a billion people living in South Asia. This hardy legume is often grown in low-input and risk-prone marginal environments. Considerable research effort has been devoted by a global research consortium to develop genomic resources for the improvement of this legume crop. These efforts have resulted in the elucidation of the complete genome sequence of pigeonpea. Despite these developments, little is known about the seed proteome of this important crop. Here, we report the proteome of pigeonpea seed. To enable the isolation of maximum number of seed proteins, including those that are present in very low amounts, three different protein fractions were obtained by employing different extraction media. High-resolution two-dimensional (2-D) electrophoresis followed by MALDI-TOF-TOF-MS/MS analysis of these protein fractions resulted in the identification of 373 pigeonpea seed proteins. Consistent with the reported high degree of synteny between the pigeonpea and soybean genomes, a large number of pigeonpea seed proteins exhibited significant amino acid homology with soybean seed proteins. Our proteomic analysis identified a large number of stress-related proteins, presumably due to its adaptation to drought-prone environments. The availability of a pigeonpea seed proteome reference map should shed light on the roles of these identified proteins in various biological processes and facilitate the improvement of seed composition.

Cryopreservation of bull semen: Evolution from egg yolk based to soybean based extenders

Since the inception of bovine semen cryopreservation, egg yolk and milk based extenders have been used to protect sperm from the detrimental effects of cooling and freezing. In recent years, demand for alternatives to conventional commercial extenders has arisen as the risk of introducing exotic diseases through transporting egg yolk based products has been recognized. Egg yolk can also interfere with sperm evaluation and the presence of particulate material in the extender may reduce fertility. Soybeans contain lecithin, a phospholipid fraction that can substitute for high molecular weight lipoprotein and phospholipids from egg yolk and prevent or ameliorate damage to the sperm plasma membrane that occurs during extension, cooling, and cryopreservation. Soy lecithin based extenders have been evaluated for processing and freezing bovine semen, although extender from soybean milk has not been studied as extensively. Commercially available soy lecithin based extenders are used increasingly but remain under scrutiny and are not universally accepted. With these observations in mind, this review is intended to examine effects of conventional cryopreservation procedures, methods of assessment, and potential for developing soybean extract as an acceptable alternative to traditional egg yolk and milk based extenders for bull sperm cryopreservation.

Chromosome doubling to overcome the chrysanthemum cross barrier based on insight from transcriptomic and proteomic analyses

Background

Cross breeding is the most commonly used method in chrysanthemum (Chrysanthemum morifolium) breeding; however, cross barriers always exist in these combinations. Many studies have shown that paternal chromosome doubling can often overcome hybridization barriers during cross breeding, although the underlying mechanism has seldom been investigated.

Results

In this study, we performed two crosses: C. morifolium (pollen receptor) × diploid C. nankingense (pollen donor) and C. morifolium × tetraploid C. nankingense. Seeds were obtained only from the latter cross. RNA-Seq and isobaric tags for relative and absolute quantitation (iTRAQ) were used to investigate differentially expressed genes and proteins during key embryo development stages in the latter cross. A previously performed cross, C. morifolium × diploid C. nankingense, was compared to our results and revealed that transcription factors (i.e., the agamous-like MADS-box protein AGL80 and the leucine-rich repeat receptor protein kinase EXS), hormone-responsive genes (auxin-binding protein 1), genes and proteins related to metabolism (ATP-citrate synthase, citrate synthase and malate dehydrogenase) and other genes reported to contribute to embryo development (i.e., LEA, elongation factor and tubulin) had higher expression levels in the C. morifolium × tetraploid C. nankingense cross. In contrast, genes related to senescence and cell death were down-regulated in the C. morifolium × tetraploid C. nankingense cross.

Conclusions

The data resources helped elucidate the gene and protein expression profiles and identify functional genes during different development stages. When the chromosomes from the male parent are doubled, the genes contributing to normal embryo developmentare more abundant. However, genes with negative functions were suppressed, suggesting that chromosome doubling may epigenetically inhibit the expression of these genes and allow the embryo to develop normally.

Electronic supplementary material

The online version of this article (doi:10.1186/s12864-016-2939-0) contains supplementary material, which is available to authorized users.

An effective and simple procedure to isolate abundant quantities of biologically active chemopreventive Lunasin Protease Inhibitor Concentrate (LPIC) from soybean

Lunasin is a 5-kDa soybean bioactive peptide with demonstrated anti-cancer and anti-inflammatory properties. Recently, purification methods have been developed to obtain gram quantities of lunasin. However, these methods are cumbersome, time consuming and cost-prohibitive. To overcome these constrains we have developed a novel method which involves extraction of soybean flour with 30% ethanol followed by preferential precipitation of lunasin and protease inhibitors by calcium. The calcium precipitated protein fraction, which we termed as Lunasin Protease Inhibitor Concentrate (LPIC), contains three abundant proteins with molecular weights of 21, 14 and 5 kDa. This simple procedure yields 3.2g of LPIC from 100g of soybean flour and the entire isolation procedure can be completed in less than 2h. Treatment of THP-1 human monocyte cell lines with LPIC resulted in suppression of lipopolysaccharide-stimulated cytokine expression, demonstrating that the LPIC isolated by our simple procedure is biologically active.

Effects of proteome rebalancing and sulfur nutrition on the accumulation of methionine rich δ-zein in transgenic soybeans

Expression of heterologous methionine-rich proteins to increase the overall sulfur amino acid content of soybean seeds has been only marginally successful, presumably due to low accumulation of transgenes in soybeans or due to gene silencing. Proteome rebalancing of seed proteins has been shown to promote the accumulation of foreign proteins. In this study, we have utilized RNAi technology to suppress the expression of the β-conglycinin, the abundant 7S seed storage proteins of soybean. Western blot and 2D-gel analysis revealed that β-conglycinin knockdown line (SAM) failed to accumulate the α', α, and β-subunits of β-conglycinin. The proteome rebalanced SAM retained the overall protein and oil content similar to that of wild-type soybean. We also generated transgenic soybean lines expressing methionine-rich 11 kDa δ-zein under the control of either the glycinin or β-conglycinin promoter. The introgression of the 11 kDa δ-zein into β-conglycinin knockdown line did not enhance the accumulation of the 11 kDa δ-zein. However, when the same plants were grown in sulfur-rich medium, we observed 3- to 16-fold increased accumulation of the 11 kDa δ-zein. Transmission electron microscopy observation revealed that seeds grown in sulfur-rich medium contained numerous endoplasmic reticulum derived protein bodies. Our findings suggest that sulfur availability, not proteome rebalancing, is needed for high-level accumulation of heterologous methionine-rich proteins in soybean seeds.

Imbibition of soybean seeds in warm water results in the release of copious amounts of Bowman-Birk protease inhibitor, a putative anticarcinogenic agent

Protease inhibitors play a protective role against pathogenic microorganisms and herbivorous insects. The two predominant protease inhibitors of soybean seeds are the Kunitz trypsin inhibitor (KTI) and Bowman-Birk protease inhibitor (BBI). In this study, we report that soybean seeds incubated in warm water release large amounts of proteins into the surrounding media. Two-dimensional gel electrophoresis analysis of the seed exudates resulted in the separation of 93 distinct protein spots out of which 90 spots were identified by LC-MS/MS. The basic 7S globulin and the BBI are the two predominant proteins found in the soybean seed exudates. In addition to 7S and 11S seed storage proteins, others known to protect the seeds against pathogens and pests including KTI, peroxidase, α-galactosidase, and endo-1.3-β-glucanase were also identified in the seed exudates. Soybean seed exudate obtained by incubating the seeds in warm water was also able to inhibit the growth of human breast cancer cell line MCF-7. Since soybean seeds release large amounts of enzymatically active BBI when immersed in warm water, our procedure could be exploited as a simplified alternative method for the preparation of BBI concentrate which is being used as a cancer chemoprotective agent.

Proteomic analysis of soybean defense response induced by cotton worm (prodenia litura, fabricius) feeding

BACKGROUND

Cotton worm is one of the main insects of soybean in southern China. Plants may acquire defense mechanisms that confer protection from predation by herbivores. Induced responses can lead to increased resistance against herbivores in many species. This study focuses on searching changed proteins in soybean defense response induced by cotton worm feeding.

RESULTS

Ten protein spots that are changed in abundance in response to cotton worm feeding were identified by Two-dimensional gel electrophoresis (2-DE). A total of 11 unique proteins from these spots were identified by MALDI-TOF MS. The mRNA and protein relative expression levels of most changed proteins were up-regulated. These proteins were mainly involved in physiological processes, including active oxygen removal, defense signal transduction, and metabolism regulation.

CONCLUSION

This is the first proteomic analysis of the soybean defense response induced by cotton worm. The differentially expressed proteins could work together to play a major role in the induced defense response. PAL and SAMS were up-regulated at both the protein and mRNA levels. These genes can be strongest candidates for further functional research.

Gene duplication and an accelerated evolutionary rate in 11S globulin genes are associated with higher protein synthesis in dicots as compared to monocots

BACKGROUND

Seed storage proteins are a major source of dietary protein, and the content of such proteins determines both the quantity and quality of crop yield. Significantly, examination of the protein content in the seeds of crop plants shows a distinct difference between monocots and dicots. Thus, it is expected that there are different evolutionary patterns in the genes underlying protein synthesis in the seeds of these two groups of plants.

RESULTS

Gene duplication, evolutionary rate and positive selection of a major gene family of seed storage proteins (the 11S globulin genes), were compared in dicots and monocots. The results, obtained from five species in each group, show more gene duplications, a higher evolutionary rate and positive selections of this gene family in dicots, which are rich in 11S globulins, but not in the monocots.

CONCLUSION

Our findings provide evidence to support the suggestion that gene duplication and an accelerated evolutionary rate may be associated with higher protein synthesis in dicots as compared to monocots.

Molecular evolution of glycinin and β-conglycinin gene families in soybean (Glycine max L. Merr.)

There are two main classes of multi-subunit seed storage proteins, glycinin (11S) and β-conglycinin (7S), which account for approximately 70% of the total protein in a typical soybean seed. The subunits of these two protein classes are encoded by a number of genes. The genomic organization of these genes follows a complex evolutionary history. This research was designed to describe the origin and maintenance of genes in each of these gene families by analyzing the synteny, phylogenies, selection pressure and duplications of the genes in each gene family. The ancestral glycinin gene initially experienced a tandem duplication event; then, the genome underwent two subsequent rounds of whole-genome duplication, thereby resulting in duplication of the glycinin genes, and finally a tandem duplication likely gave rise to the Gy1 and Gy2 genes. The β-conglycinin genes primarily originated through the more recent whole-genome duplication and several tandem duplications. Purifying selection has had a key role in the maintenance of genes in both gene families. In addition, positive selection in the glycinin genes and a large deletion in a β-conglycinin exon contribute to the diversity of the duplicate genes. In summary, our results suggest that the duplicated genes in both gene families prefer to retain similar function throughout evolution and therefore may contribute to phenotypic robustness.

Proteomic analysis of high protein soybean (Glycine max) accessions demonstrates the contribution of novel glycinin subunits

Limited biochemical information is available on soybean accessions that have seed protein content greater than 45% of the seed dry weight. SDS-PAGE analysis of seed proteins from nine soybean accessions revealed significantly higher amount of seed storage proteins in these accessions when compared with that of soybean cultivar Williams 82. High-resolution two-dimensional gel electrophoretic analysis of seed proteins revealed significant differences among several seed storage protein components in these accessions. A total of 51 protein spots were identified using peptide mass fingerprinting (MALDI-TOF MS). The contribution of these proteins to the overall protein content of the accessions was quantified using Delta2D image analysis software. Results showed that among the majority of the nine accessions, the largest difference in higher protein quantity was within the seed 11S storage globulins. The high protein trait from PI407788A was successfully transferred to an experimental line, LG99-469, demonstrating that this trait was transferable and robust.

A rapid and simple procedure for the depletion of abundant storage proteins from legume seeds to advance proteome analysis: a case study using Glycine max

2-D analysis of plant proteomes containing thousands of proteins has limited dynamic resolution because only abundant proteins can be detected. Proteomic assessment of the non-abundant proteins within seeds is difficult when 60-80% is storage proteins. Resolution can be improved through sample fractionation using separation techniques based upon different physiological or biochemical principles. We have developed a fast and simple fractionation technique using 10 mM Ca(2+) to precipitate soybean (Glycine max) seed storage globulins, glycinin and beta-conglycinin. This method removes 87+/-4% of the highly abundant seed proteins from the extract, allowing for 541 previously inconspicuous proteins present in soybean seed to be more detectable (volume increase of >or=50%) using fluorescent detection. Of those 541 enhanced spots, 197 increased more than 2.5-fold when visualized with Coomassie. The majority of those spots were isolated and identified using peptide mass fingerprinting. Fractionation also provided detection of 63 new phosphorylated protein spots and enhanced the visibility of 15 phosphorylated protein spots, using 2-D electrophoretic separation and an in-gel phosphoprotein stain. Application of this methodology toward other legumes, such as peanut, bean, pea, alfalfa and others, also containing high amounts of storage proteins, was examined, and is reported here.

Identification of several gy4 nulls from the USDA soybean germplasm collection provides new genetic resources for the development of high-quality tofu cultivars

Tofu, a cheese-like food made by curdling soy milk, is a major dietary staple of Asian countries. Consumption of tofu and other soy products is steadily increasing in North America due to its well-known health benefits. Soybean A(5), A(4), and B(3) peptide null lines 'Enrei' and 'Raiden' are commonly utilized in breeding programs to develop high-quality tofu cultivars. To expand the genetic diversity it is desirable to identify and utilize other A(5), A(4), and B(3) null genotypes in the development of improved tofu cultivars that are adapted to North American conditions. In this study were screened diverse soybean accessions from the USDA Soybean Germplasm Collection to identify Gy4 mutants, the locus that controls A(5), A(4), and B(3) peptide production. Analysis of total seed proteins from 485 soybean lines by SDS-PAGE enabled the identification of 38 accessions that lacked the A(5), A(4), and B(3) peptides. These accessions showed marked differences in seed size and seed coat color and represented different maturity groups ranging from 0 to IX. To ascertain the molecular basis for the lack of A(5), A(4), and B(3) peptides in the newly identified Gy4 mutants, the nucleotide sequence of a portion of the Gy4 gene was determined from eight soybean accessions representing different maturity groups. These eight Gy4 mutants revealed a single point mutation that changed the translation initiation codon ATG to ATA, resulting in the A(5), A(4), and B(3) null phenotype. The newly identified Gy4 mutants from this study will enable plant breeders to expand the genetic diversity of North American food-quality soybeans and also aid in the development of hypoallergenic soybeans.

Preparative procedures markedly influence the appearance and structural integrity of protein storage vacuoles in soybean seeds

In legumes, vacuoles serve as the final depository for storage proteins. The protein storage vacuoles (PSVs) of soybean contain electron-transparent globoid regions in which phytic acid ( myo-inositol-1,2,3,4,5,6-hexakisphosphate) is sequestered. This paper reports the effect of preparative procedures on the appearance and ultrastructural integrity of PSVs in soybeans. Electron microscopy examination of both developing and mature soybean seeds that were postfixed with osmium tetroxide revealed PSVs that had a homogeneous appearance with very few globoid crystals dispersed in them. Numerous electron-dense lipid bodies were readily seen in these cells. Omission of osmium tetroxide strikingly altered the appearance of PSVs and aided the visualization of the location of the globoids in the PSVs. In contrast to the osmicated tissue, lipid bodies appeared as electron-transparent spheres. The choice of dehydration reagent or staining procedure had little influence on the appearance of the PSVs. The results of this study demonstrate the profound effect of osmium tetroxide on the appearance and structural integrity of PSVs in soybean.

Identification, characterization, epitope mapping, and three-dimensional modeling of the alpha-subunit of beta-conglycinin of soybean, a potential allergen for young pigs

Soybean meal (SBM), the major byproduct of soybean oil extraction, is the main protein source for swine diets globally. In the United States, 8.6 million metric tons of SBM was used in swine rations in 2004. The pathological effect and immunological response of SBM feeding have been demonstrated in swine. In this study, we have utilized plasma collected from piglet feed with SBM in immunoblot analysis to detect proteins that elicited antigenic responses. We have identified soybean beta-conglycinin alpha-subunit as being a potential allergen for young piglets. Characterization of this protein indicated that deglycosylation and pepsin digestion did not eliminate immunoreactivity of this protein. Epitope mapping utilizing planar cellulose supports technology (SPOT) showed that three peptides spanning amino acids S185-R231 were critical for the allergenicity. A computer-generated three-dimensional structure model of the alpha-subunit of beta-conglycinin indicated that the antigenic epitopes were located on the surface of the protein. Information from this study may assist in the construction of recombinant nonallergenic soybean protein useable for both immunotherapy and the potential production of hypoallergenic soybean plants.

Identification of glycinin and beta-conglycinin subunits that contribute to the increased protein content of high-protein soybean lines

Seed protein concentration of commercial soybean cultivars calculated on a dry weight basis ranges from approximately 37 to 42% depending on genotype and location. A concerted research effort is ongoing to further increase protein concentration. Several soybean plant introductions (PI) are known to contain greater than 50% protein. These PIs are exploited by breeders to incorporate the high-protein trait into commercial North American cultivars. Currently, limited information is available on the biochemical and genetic mechanisms that regulate high-proteins. In this study, we have carried out proteomic and molecular analysis of seed proteins of LG00-13260 and its parental high-protein lines PI 427138 and BARC-6. Sodium dodecyl sulfate polyacrylamide gel electrophoresis analysis revealed that the high-protein lines accumulated increased amounts of beta-conglycinin and glycinins, when compared with Williams 82. High-resolution two-dimensional electrophoresis utilizing pH 4-7 and pH 6-11 ampholytes enabled improved resolution of soybean seed proteins. A total of 38 protein spots, representing the different subunits of beta-conglycinin and glycinin, were identified by matrix-assisted laser desorption ionization time-of-flight mass spectrometry. High-protein was correlated with an increase in the accumulation of most of the subunits representing beta-conglycinin and glycinin. Comparisons of the amino acid profiles of high-protein soybean lines revealed that the concentration of sulfur amino acids, a reflection of protein quality, was not influenced by the protein concentration. Southern blot analysis showed the presence of genotypic variation at the DNA level between PI 427138 and BARC-6 for the genes encoding group1 glycinin, beta-conglycinin, Bowman-Birk inhibitor (BBI), and the Kunitz trypsin inhibitor (KTI). LG00-13260 inherited the allelic variants of the parental line PI 427138 for glycinin, beta-conglycinin, and KTI, while BBI was inherited from the parental line BARC-6. The results of our study indicate that high-seed protein concentration is attributed to greater accumulation of specific components of beta-conglycinin and glycinin subunits presumably mediated by preferential expression of these genes during seed development.

Nitrogen lowers the sulfur amino acid content of soybean (Glycine max [L.] Merr.) by regulating the accumulation of Bowman-Birk protease inhibitor

Soybeans in general contain 35-40% protein. Efforts are underway to increase further this protein content, thus enhancing their nutritive value. Even though higher protein is a desirable characteristic, whether such an increase will be accompanied by enhanced protein quality is not known. Soybean protein quality could be significantly improved by increasing the concentration of the sulfur-containing amino acids, cysteine and methionine. To ascertain if a correlation existed between protein quantity and quality, a comparison of the amino acids of soybeans differing in protein content was made. Soybeans with higher protein content had a significantly lower percentage of sulfur amino acids, while those with lower protein exhibited a higher content of cysteine and methionine. Nitrogen application elevated the protein content but lowered that of the sulfur amino acids. Transmission electron microscopy examination of thin sections of low protein soybean seeds revealed several protein storage vacuoles that were partially filled with storage proteins. Fluorescence two-dimensional difference gel electrophoresis of soybean seed proteins revealed that nitrogen application favored the accumulation of the beta-subunit of beta-conglycinin while decreasing the accumulation of Bowman-Birk protease inhibitor (BBI), a protein rich in cysteine. Sodium dodecyl sulfate-polyacrylamide gel electrophoresis of 60% 2-propanol-extracted proteins showed a drastic reduction in the accumulation of BBI with increasing protein content. Northern blot analysis indicated that nitrogen had a negative influence on the expression of the BBI gene. Our results indicate that the negative correlation between total protein and sulfur amino acid content is mostly mediated by the differential accumulation of BBI.

Expression of an 11 kDa methionine-rich delta-zein in transgenic soybean results in the formation of two types of novel protein bodies in transitional cells situated between the vascular tissue and storage parenchyma cells

Soybean (Glycine max (L.) Merr.) is an important protein source in human diets and animal feeds. The sulphur content of soybean seed proteins, however, is not optimal for ration formulations. Thus, increasing the methionine and cysteine content of soybean seed proteins would enhance the nutritional quality of this widely utilized legume. We have earlier reported the isolation of an 11 kDa delta-zein protein rich in methionine from the endosperm of the maize (Zea mays L.) inbred line W23a1 [Kim, W.-S. and Krishnan, H.B. (2003) Allelic variation and differential expression of methionine-rich-delta-zeins in maize inbred lines B73 and W23a1. Planta, 217, 66-74]. Using Agrobacterium-mediated transformation, a construct consisting of the coding region of the cloned delta-zein gene under regulation of the beta-conglycinin alpha'-promoter was introduced into the soybean genome. The 11 kDa delta-zein gene was expressed in the seeds of transgenic soybeans, although low-level expression was also detected in the leaves. In situ hybridization indicated that the 11 kDa delta-zein mRNA was expressed predominantly in transitional cells located between the vascular tissue and storage parenchyma cells. Immunohistochemistry of developing transgenic soybeans revealed that the accumulation of the 11 kDa delta-zein occurred primarily in these transitional cells. Expression of the 11 kDa delta-zein gene in transgenic soybean resulted in the formation of two endoplasmic reticulum-derived protein bodies that were designated as either spherical or complex. Immunocytochemical localization demonstrated that both the spherical and complex protein bodies accumulated the 11 kDa delta-zein. Although expression of the 11 kDa delta-zein gene elevated the methionine content of the alcohol-soluble protein fraction 1.5-1.7-fold above that of the non-transgenic line, the overall methionine content of seed flour was not increased. Our results suggest that the confined expression of the 11 kDa delta-zein gene in transitional cells could be limiting the increase in methionine content in transgenic soybean seeds.

Allelic variation and differential expression of methionine-rich delta-zeins in maize inbred lines B73 and W23a1

The sulfur-amino-acid-rich delta-zeins of maize ( Zea mays L.) are represented by 18-kDa and 10-kDa proteins. We have cloned a novel 11-kDa methionine-rich delta-zein from developing endosperm of the inbred line W23a1. The nucleotide sequence of this new delta-zein is identical to the published 10-kDa delta-zein, except for an insertion of 18 nucleotides between +316 and +333 bp from the translation start site. Antibodies raised against the recombinant 18-kDa delta-zein recognized both the 18-kDa and 10-kDa delta-zein from total seed protein extracts of different maize inbred lines. Western blot analysis revealed differences in the levels of the delta-zeins in different inbred lines and some of the inbred lines lacked either the 10-kDa or the 18-kDa delta-zeins. Northern blot analysis revealed temporal differences in the RNA transcript levels of the 11-kDa and 18-kDa delta-zeins between B73 and W23a1. Such differences were not evident on Western blot analysis where similar protein accumulation profiles were seen for both lines. Immunostaining of paraffin sections of developing maize endosperm with the 18-kDa delta-zein antibodies revealed specific labeling of protein bodies found in the first few starchy layers from the aleurone layer. Electron-microscopic observation of thin-sections of B73 and W23a1 endosperm cells confirmed the presence of recently discovered novel, vacuole-like structures in these inbred lines. Immunogold labeling studies revealed that the delta-zeins were localized in the endoplasmic-reticulum-derived protein bodies and showed no preferential gold particle labeling over either the light or electron-dense material found in these protein bodies.