Genetic engineering for high methionine grain legumes

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.

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.

The Level of Methionine Residues in Storage Proteins Is the Main Limiting Factor of Protein-Bound-Methionine Accumulation in Arabidopsis Seeds

The low level of methionine, an essential sulfur-containing amino acid, limits the nutritional quality of seeds. Two main factors can control the level of protein-bound methionine: the level of free methionine that limits protein accumulation and the methionine residues inside the storage proteins. To reveal the main limiting factor, we generated transgenic Arabidopsis thaliana seed-specific plants expressing the methionine-rich sunflower seed storage (SSA) protein (A1/A2). The contents of protein-bound methionine in the water-soluble protein fraction that includes the SSA in A1/A2 were 5.3- and 10.5-fold, respectively, compared to control, an empty vector (EV). This suggests that free methionine can support this accumulation. To elucidate if the level of free methionine could be increased further in the protein-bound methionine, these lines were crossed with previously characterized plants having higher levels of free methionine in seeds (called SSE). The progenies of the crosses (A1S, A2S) exhibited the highest level of protein-bound methionine, but this level did not differ significantly from A2, suggesting that all the methionine residues of A2 were filled with methionine. It also suggests that the content of methionine residues in the storage proteins is the main limiting factor. The results also proposed that the storage proteins can change their content in response to high levels of free methionine or SSA. This was assumed since the water-soluble protein fraction was highest in A1S/A2S as well as in SSE compared to EV and A1/A2. By using these seeds, we also aimed at gaining more knowledge about the link between high free methionine and the levels of metabolites that usually accumulate during abiotic stresses. This putative connection was derived from a previous analysis of SSE. The results of metabolic profiling showed that the levels of 29 and 20 out of the 56 metabolites were significantly higher in SSE and A1, respectively, that had higher level of free methionine, compared A1S/A2S, which had lower free methionine levels. This suggests a strong link between high free methionine and the accumulation of stress-associated metabolites.

Revisiting the attempts to fortify methionine content in plant seeds

The sulfur-containing amino acid methionine belongs to the group of essential amino acids, meaning that humans and animals must consume it in their diets. However, plant seeds have low levels of methionine, limiting their nutritional potential. For this reason, efforts have been made over the years to increase methionine levels in seeds. Here, we summarize these efforts and focus particularly on those utilizing diverse genetic and molecular tools. Four main approaches are described: (i) expression of methionine-rich storage proteins in a seed-specific manner to incorporate more soluble methionine into the protein fraction; (ii) reduction of methionine-poor storage proteins inside the seeds to reinforce the accumulation of methionine-rich proteins; (iii) silencing methionine catabolic enzymes; and (iv) up-regulation of key biosynthetic enzymes participating in methionine synthesis. We focus on the biosynthetic genes that operate de novo in seeds and that belong to the sulfur assimilation and aspartate family pathways, as well as genes from the methionine-specific pathway. We also include those enzymes that operate in non-seed tissues that contribute to the accumulation of methionine in seeds, such as S-methylmethionine enzymes. Finally, we discuss the biotechnological potential of these manipulations to increase methionine content in plant seeds and their effect on seed germination.

Plant sulfur and Big Data

Sulfur is an essential mineral nutrient for plants, therefore, the pathways of its uptake and assimilation have been extensively studied. Great progress has been made in elucidation of the individual genes and enzymes and their regulation. Sulfur assimilation has been intensively investigated by -omics technologies and has been target of several genome wide genetic approaches. This brought a significant step in our understanding of the regulation of the pathway and its integration in cellular metabolism. However, the large amount of information derived from other experiments not directly targeting sulfur has also brought new and exciting insights into processes affecting sulfur homeostasis. In this review we will integrate the findings of the targeted experiments with those that brought unintentional progress in sulfur research, and will discuss how to synthesize the large amount of information available in various repositories into a meaningful dissection of the regulation of a specific metabolic pathway. We then speculate how this might be used to further advance knowledge on control of sulfur metabolism and what are the main questions to be answered.

Making metabolism accessible and meaningful: is the definition of a central metabolic dogma within reach?

Intermediary metabolism, a dominant research area before the emergence of molecular biology, is attracting renewed interest for fundamental and applied reasons as documented here. Nonetheless, the field may appear to be a thicket precluding entry to all but the most determined. Here we present a metabolic overview that makes this important and fascinating area accessible to a broad range of the molecular biological and biotechnological communities that are being attracted to biological problems crying out for metabolic solutions. This is accomplished by identifying seven key concepts, a so-called metabolic central dogma, that provide a core understanding analogous to the "Central Dogma of Molecular Biology" which focused upon maintenance and flow of genetic information.

Computational approaches for the classification of seed storage proteins

Seed storage proteins comprise a major part of the protein content of the seed and have an important role on the quality of the seed. These storage proteins are important because they determine the total protein content and have an effect on the nutritional quality and functional properties for food processing. Transgenic plants are being used to develop improved lines for incorporation into plant breeding programs and the nutrient composition of seeds is a major target of molecular breeding programs. Hence, classification of these proteins is crucial for the development of superior varieties with improved nutritional quality. In this study we have applied machine learning algorithms for classification of seed storage proteins. We have presented an algorithm based on nearest neighbor approach for classification of seed storage proteins and compared its performance with decision tree J48, multilayer perceptron neural (MLP) network and support vector machine (SVM) libSVM. The model based on our algorithm has been able to give higher classification accuracy in comparison to the other methods.

Transgenic soybean plants overexpressing O-acetylserine sulfhydrylase accumulate enhanced levels of cysteine and Bowman-Birk protease inhibitor in seeds

Soybeans provide an excellent source of protein in animal feed. Soybean protein quality can be enhanced by increasing the concentration of sulfur-containing amino acids. Previous attempts to increase the concentration of sulfur-containing amino acids through the expression of heterologous proteins have met with limited success. Here, we report a successful strategy to increase the cysteine content of soybean seed through the overexpression of a key sulfur assimilatory enzyme. We have generated several transgenic soybean plants that overexpress a cytosolic isoform of O-acetylserine sulfhydrylase (OASS). These transgenic soybean plants exhibit a four- to tenfold increase in OASS activity when compared with non-transformed wild-type. The OASS activity in the transgenic soybeans was significantly higher at all the stages of seed development. Unlike the non-transformed soybean plants, there was no marked decrease in the OASS activity even at later stages of seed development. Overexpression of cytosolic OASS resulted in a 58-74% increase in protein-bound cysteine levels compared with non-transformed wild-type soybean seeds. A 22-32% increase in the free cysteine levels was also observed in transgenic soybeans overexpressing OASS. Furthermore, these transgenic soybean plants showed a marked increase in the accumulation of Bowman-Birk protease inhibitor, a cysteine-rich protein. The overall increase in soybean total cysteine content (both free and protein-bound) satisfies the recommended levels required for the optimal growth of monogastric animals.

Ber e 1 protein: the versatile major allergen from Brazil nut seeds

Due mainly to its extremely high content of sulphur amino acids, Ber e 1 protein, the major allergen from Brazil nut, has attracted much scientific and press attention. Ber e 1 was the main target protein in early biotechnology transgenic work, in early processing studies of plant storage proteins, in plant vacuolar targeting studies and as the main protein in early nutritional supplementation experiments. Ber e 1 was also one of the first food allergens to be unintentionally transferred from one plant to another and was involved in the first reported case of systemic allergic reaction caused by a food allergen transferred in semen. In this review, many of the Ber e 1 unique biotechnological and structural functions are discussed with a particular emphasis on its use as model protein for studies of intrinsic allergenicity of food proteins.

Biofortification of soybean meal: immunological properties of the 27 kDa γ-zein

Legumes, including soybeans ( Glycine max ), are deficient in sulfur-containing amino acids, which are required for the optimal growth of monogastric animals. This deficiency can be overcome by expressing heterologous proteins rich in sulfur-containing amino acids in soybean seeds. A maize 27 kDa γ-zein, a cysteine-rich protein, has been successfully expressed in several crops including soybean, barley, and alfalfa with the intent to biofortify these crops for animal feed. Previous work has shown that the maize 27 kDa zein can withstand digestion by pepsin and elicit an immunogenic response in young pigs. By use of sera from patients who tested positive by ImmunoCAP assay for elevated IgE to maize proteins, specific IgE binding to the 27 kDa γ-zein is demonstrated. Bioinformatic analysis using the full-length and 80 amino acid sliding window FASTA searches identified significant sequence homology of the 27 kDa γ-zein with several known allergens. Immunoblot analysis using human serum that cross-reacts with maize seed proteins also revealed specific IgE-binding to the 27 kDa γ-zein in soybean seed protein extracts containing the 27 kDa zein. This study demonstrates for the first time the allergenicity potential of the 27 kDa γ-zein and the potential that this protein has to limit livestock performance when used in soybeans that serve as a biofortified feed supplement.

Recent progress in deciphering the biosynthesis of aspartate-derived amino acids in plants

Plants are either directly or indirectly the source of most of the essential amino acids in animal diets. Four of these essential amino acids-methionine, threonine, isoleucine, and lysine-are all produced from aspartate via a well studied biosynthesis pathway. Given the nutritional interest in essential amino acids, the aspartate-derived amino acid pathway has been the subject of extensive research. Additionally, several pathway enzymes serve as targets for economically important herbicides, and some of the downstream products are biosynthetic precursors for other essential plant metabolites such as ethylene and S-adenosylmethionine. Recent and ongoing research on the aspartate-derived family of amino acids has identified new enzyme activities, regulatory mechanisms, and in vivo metabolic functions. Together, these discoveries will open up new possibilities for plant metabolic engineering.

Aspartate-Derived Amino Acid Biosynthesis in Arabidopsis thaliana

The aspartate-derived amino acid pathway in plants leads to the biosynthesis of lysine, methionine, threonine, and isoleucine. These four amino acids are essential in the diets of humans and other animals, but are present in growth-limiting quantities in some of the world's major food crops. Genetic and biochemical approaches have been used for the functional analysis of almost all Arabidopsis thaliana enzymes involved in aspartate-derived amino acid biosynthesis. The branch-point enzymes aspartate kinase, dihydrodipicolinate synthase, homoserine dehydrogenase, cystathionine gamma synthase, threonine synthase, and threonine deaminase contain well-studied sites for allosteric regulation by pathway products and other plant metabolites. In contrast, relatively little is known about the transcriptional regulation of amino acid biosynthesis and the mechanisms that are used to balance aspartate-derived amino acid biosynthesis with other plant metabolic needs. The aspartate-derived amino acid pathway provides excellent examples of basic research conducted with A. thaliana that has been used to improve the nutritional quality of crop plants, in particular to increase the accumulation of lysine in maize and methionine in potatoes.

Reserve accumulation in legume seeds

The accumulation of seed reserves is the result of distinct processes occurring in parallel in the main seed compartments of either maternal (seed coats) or zygotic (embryo, endosperm) origin. With the development of legume genomic resources, recent advances have been made toward understanding the metabolic control of seed filling and the regulatory network underlying reserve accumulation. Genetic variability for seed composition has been studied along with the environmental factors influencing reserve accumulation. Nutrient availability and sink strength were both found to be limiting for reserve accumulation. Genes and/or QTL controlling seed protein content and sulfur-amino acid levels have been identified. These new findings will support our attempts to engineer legume seed composition for added end user value.

Structure and stability of 2S albumin-type peanut allergens: implications for the severity of peanut allergic reactions

Resistance to proteolytic enzymes and heat is thought to be a prerequisite property of food allergens. Allergens from peanut (Arachis hypogaea) are the most frequent cause of fatal food allergic reactions. The allergenic 2S albumin Ara h 2 and the homologous minor allergen Ara h 6 were studied at the molecular level with regard to allergenic potency of native and protease-treated allergen. A high-resolution solution structure of the protease-resistant core of Ara h 6 was determined by NMR spectroscopy, and homology modelling was applied to generate an Ara h 2 structure. Ara h 2 appeared to be the more potent allergen, even though the two peanut allergens share substantial cross-reactivity. Both allergens contain cores that are highly resistant to proteolytic digestion and to temperatures of up to 100 degrees C. Even though IgE antibody-binding capacity was reduced by protease treatment, the mediator release from a functional equivalent of a mast cell or basophil, the humanized RBL (rat basophilic leukaemia) cell, demonstrated that this reduction in IgE antibody-binding capacity does not necessarily translate into reduced allergenic potency. Native Ara h 2 and Ara h 6 have virtually identical allergenic potency as compared with the allergens that were treated with digestive enzymes. The folds of the allergenic cores are virtually identical with each other and with the fold of the corresponding regions in the undigested proteins. The extreme immunological stability of the core structures of Ara h 2 and Ara h 6 provides an explanation for the persistence of the allergenic potency even after food processing.

Quantitative trait loci controlling sulfur containing amino acids, methionine and cysteine, in soybean seeds

Soybean [Glycine max (L.) Merr.] is the single largest source of protein in animal feed. However, a major limitation of soy proteins is their deficiency in sulfur-containing amino acids, methionine (Met) and cysteine (Cys). The objective of this study was to identify quantitative trait loci (QTL) associated with Met and Cys concentration in soybean seed. To achieve this objective, 101 F(6)-derived recombinant inbred lines (RIL) from a population developed from a cross of N87-984-16 x TN93-99 were used. Ground soybean seed samples were analyzed for Met and Cys concentration using a near infrared spectroscopy instrument. Data were analyzed using SAS software and QTL Cartographer. RIL differed (P<0.01) in Met and Cys concentrations, with a range of 5.1-7.3 (g kg(-1) seed dry weight) for Cys and 4.4-8.8 (g kg(-1) seed dry weight) for Met. Heritability estimates on an entry mean basis were 0.14 and 0.57 for Cys and Met, respectively. A total of 94 polymorphic simple sequence repeat molecular genetic markers were screened in the RIL. Single factor ANOVA was used to identify candidate QTL, which were confirmed by composite interval mapping using QTL Cartographer. Four QTL linked to molecular markers Satt235, Satt252, Satt427 and Satt436 distributed on three molecular linkage groups (MLG) D1a, F and G were associated with Cys and three QTL linked to molecular markers Satt252, Satt564 and Satt590 distributed on MLG F, G and M were associated with Met concentration in soybean seed. QTL associated with Met and Cys in soybean seed will provide important information to breeders targeting improvements in the nutritional quality of soybean.

Isolation by improved thermal asymmetric interlaced PCR and characterization of a seed-specific 2S albumin gene and its promoter from grape (Vitis vinifera L.)

A seed-specific 2S albumin gene and its promoter region of grape (Vitis vinifera L.) were isolated using an improved thermal asymmetric interlaced PCR that allowed efficient amplification of target sequence of up to 3 kbp in length directly from genomic DNA. The 2S albumin VvAlb1 (for V. vinifera 2S albumin 1) gene from different grape cultivars encompasses a coding region of 504-540 nucleotides corresponding to a deduced amino acid sequence of 167-179 residues. This deduced protein contains up to 30% glutamine residues and eight cysteine residues arranged in a pattern highly conserved among 2S albumins for disulfide bond formation. DNA sequence alignment revealed that the same VvAlb1 gene among different grape cultivars varied greatly, including an insertion of up to 36 bp near the 3' end of the gene sequence isolated from 'Thompson Seedless'. DNA sequence analysis indicated that several conserved seed-specific regulatory motifs were clustered within a 0.6-kbp region 5' upstream of the transcription start site. To further test promoter activity, the sequence of this region was used to drive a bifunctional EGFP/NPTII fusion gene in Agrobacterium-mediated transformation of grape somatic embryos and leaf discs of grape and tobacco (Nicotiana tabacum L.). A high level of GFP expression, comparable with that derived from an enhanced double CsVMV promoter, was observed in the cotyledonary but not hypocotyl and vegetative tissues of grape and tobacco. These results suggest that the VvAlb1 gene promoter isolated is capable of conferring seed-specific gene expression.

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.

Metabolic engineering of amino acids and storage proteins in plants

Amino acid pathways are important targets for plant metabolic engineering. Since plants represent the major global food supply, large efforts are devoted to increasing the content of "essential" amino acids, which are absolutely required in human foods and animal feeds. Engineering of amino acids is also undertaken to improve plant growth and stress tolerance. Many of the pathways of amino acid metabolism in plants have been elucidated, and genes encoding most of the enzymes are now available. The expression of recombinant genes in transgenic plants, coupled with genetic and biochemical approaches, has contributed significantly to the understanding of regulatory networks of the metabolism of amino acids and their incorporation into proteins. This knowledge is now being extensively applied to metabolic engineering of crops, and this is reflected by a large patent literature. The problems of engineering plant amino acid metabolism, and ways to solve them, are discussed using the essential amino acids lysine and methionine as examples.

Identification of sunflower seed IgE-binding proteins

BACKGROUND

Sunflower seed can cause severe anaphylactic reactions in some susceptible individuals. It is conceivable that the 2S sunflower seed protein is an allergen based on its high degree of homology (34%) with the allergenic mature 2S albumin protein of the Brazil nut. The first step in determining the allergenicity of sunflower seed proteins is to identify IgE-binding proteins.

METHODS

Sera from sunflower seed-sensitive individuals were evaluated by radioallergosorbent test (RAST), isoelectric focusing (IEF) and sodium dodecyl sulfate-polyacrylamide gel electrophoresis immunoblotting with sunflower seed proteins.

RESULTS

Positive RAST scores (>2) were observed in 3 individuals and immunoblotting demonstrated IgE-binding to 2-7 distinct proteins ranging in size from 10 to 50 kD. Two out of 3 sera recognized two proteins between 16 and 17 kD. The lower molecular weight protein (16 kD) approximates to the prepo region of the precursor methionine-rich 2S albumin protein found in sunflower seed (SFA-8/SSA). IEF followed by immunoblotting demonstrated several IgE-binding proteins, including two proteins with isoelectric points of 5.97 and 5.3, respectively, which are consistent with the mature and immature forms of the SFA-8/SSA region.

CONCLUSIONS

Sunflower seed contains several IgE-binding proteins, including regions of the high-methionine 2S albumin SFA-8/SSA.