Transgenic insertion of the cyanobacterial membrane protein ictB increases grain yield in Zea mays through increased photosynthesis and carbohydrate production.

The C4 crop maize (Zea mays) is the most widely grown cereal crop worldwide and is an essential feedstock for food and bioenergy. Improving maize yield is important to achieve food security and agricultural sustainability in the 21st century. One potential means to improve crop productivity is to enhance photosynthesis. ictB, a membrane protein that is highly conserved across cyanobacteria, has been shown to improve photosynthesis, and often biomass, when introduced into diverse C3 plant species. Here, ictB from Synechococcus sp. strain PCC 7942 was inserted into maize using Agrobacterium-mediated transformation. In three controlled-environment experiments, ictB insertion increased leaf starch and sucrose content by up to 25% relative to controls. Experimental field trials in four growing seasons, spanning the Midwestern United States (Summers 2018 & 2019) and Argentina (Winter 2018 & 2019), showed an average of 3.49% grain yield improvement, by as much as 5.4% in a given season and up to 9.4% at certain trial locations. A subset of field trial locations was used to test for modification of ear traits and ФPSII, a proxy for photosynthesis. Results suggested that yield gain in transgenics could be associated with increased ФPSII, and the production of longer, thinner ears with more kernels. ictB localized primarily to the microsome fraction of leaf bundle-sheath cells, but not to chloroplasts. Extramembrane domains of ictB interacted in vitro with proteins involved in photosynthesis and carbohydrate metabolism. To our knowledge, this is the first published evidence of ictB insertion into a species using C4 photosynthesis and the largest-scale demonstration of grain yield enhancement from ictB insertion in planta. Results show that ictB is a valuable yield gene in the economically important crop maize, and are an important proof of concept that transgenic manipulation of photosynthesis can be used to create economically viable crop improvement traits.

Characteristics and safety assessment of intractable proteins in genetically modified crops.

Genetically modified (GM) crops may contain newly expressed proteins that are described as "intractable". Safety assessment of these proteins may require some adaptations to the current assessment procedures. Intractable proteins are defined here as those proteins with properties that make it extremely difficult or impossible with current methods to express in heterologous systems; isolate, purify, or concentrate; quantify (due to low levels); demonstrate biological activity; or prove equivalency with plant proteins. Five classes of intractable proteins are discussed here: (1) membrane proteins, (2) signaling proteins, (3) transcription factors, (4) N-glycosylated proteins, and (5) resistance proteins (R-proteins, plant pathogen recognition proteins that activate innate immune responses). While the basic tiered weight-of-evidence approach for assessing the safety of GM crops proposed by the International Life Sciences Institute (ILSI) in 2008 is applicable to intractable proteins, new or modified methods may be required. For example, the first two steps in Tier I (hazard identification) analysis, gathering of applicable history of safe use (HOSU) information and bioinformatics analysis, do not require protein isolation. The extremely low level of expression of most intractable proteins should be taken into account while assessing safety of the intractable protein in GM crops. If Tier II (hazard characterization) analyses requiring animal feeding are judged to be necessary, alternatives to feeding high doses of pure protein may be needed. These alternatives are discussed here.

Quantitation of soybean allergens using tandem mass spectrometry.

Soybean (Glycine max) seed contain some proteins that are allergenic to humans and animals. However, the concentration of these allergens and their expression variability among germplasms is presently unknown. To address this problem, 10 allergens were quantified from 20 nongenetically modified commercial soybean varieties using parallel, label-free mass spectrometry approaches. Relative quantitation was performed by spectral counting and absolute quantitation was performed using multiple reaction monitoring (MRM) with synthetic, isotope-labeled peptides as internal standards. During relative quantitation analysis, 10 target allergens were identified, and five of these allergens showed expression levels higher than technical variation observed for bovine serum albumin (BSA) internal standard (∼11%), suggesting expression differences among the varieties. To confirm this observation, absolute quantitation of these allergens from each variety was performed using MRM. Eight of the 10 allergens were quantified for their concentration in seed and ranged from approximately 0.5 to 5.7 µg/mg of soy protein. MRM analysis reduced technical variance of BSA internal standards to approximately 7%, and confirmed differential expression for four allergens across the 20 varieties. This is the first quantitative assessment of all major soybean allergens. The results show the total quantity of allergens measured among the 20 soy varieties was mostly similar.

Characterization and crystal structure of lysine insensitive Corynebacterium glutamicum dihydrodipicolinate synthase (cDHDPS) protein.

The lysine insensitive Corynebacterium glutamicum dihydrodipicolinate synthase enzyme (cDHDPS) was recently successfully introduced into maize plants to enhance the level of lysine in the grain. To better understand lysine insensitivity of the cDHDPS, we expressed, purified, kinetically characterized the protein, and solved its X-ray crystal structure. The cDHDPS enzyme has a fold and overall structure that is highly similar to other DHDPS proteins. A noteworthy feature of the active site is the evidence that the catalytic lysine residue forms a Schiff base adduct with pyruvate. Analyses of the cDHDPS structure in the vicinity of the putative binding site for S-lysine revealed that the allosteric binding site in the Escherichia coli DHDPS protein does not exist in cDHDPS due to three non-conservative amino acids substitutions, and this is likely why cDHDPS is not feedback inhibited by lysine.

Analytical criteria for performance characteristics of IgE binding methods for evaluating safety of biotech food products.

There is detailed guidance on how to perform bioinformatic analyses and enzymatic degradation studies for genetically modified crops under consideration for approval by regulatory agencies; however, there is no consensus in the scientific community on the details of how to perform IgE serum studies. IgE serum studies are an important safety component to acceptance of genetically modified crops when the introduced protein is novel, the introduced protein is similar to known allergens, or the crop is allergenic. In this manuscript, we describe the characteristics of the reagents, validation of assay performance, and data analysis necessary to optimize the information obtained from serum testing of novel proteins and genetically modified (GM) crops and to make results more accurate and comparable between different investigations.

Application of current allergy assessment guidelines to next-generation biotechnology-derived crops.

In any single day, our immune systems are exposed to thousands of different proteins from the environment and the food we eat. In a portion of the human population, some of those proteins will stimulate the immune systems to synthesize immunoglobulin E in an allergenic response. The discrepancy between the vast numbers of proteins we encounter and the limited number of proteins that actually become allergens have led scientists on a quest to discover what unique features exist that make proteins destined to be allergens. The information gained from these studies has led to an allergy assessment strategy that characterizes the potential allergenicity of biotechnology products prior to their commercialization. This testing strategy appears to be effective as shown by the fact that there have been no clinically documented food allergic reactions to any of the biotechnology proteins introduced into food crops, to date. The next generation of biotechnology products will most likely contain more complex traits, including nutritionally enhanced food crops, and the question arises as to whether the current allergy assessment strategy will be sufficient to protect the health of the consuming public. In this paper, we discuss general allergen characteristics in order to better understand how proteins become allergens, summarize the current allergy assessment process, evaluate the different aspects of this process for their adequacy in determining the allergenic potential of engineered functional foods, and, finally, we assess the possibility of new technologies having a positive impact on the allergy assessment of nutritionally enhanced crops.

Comparison of conventional FASTA identity searches with the 80 amino acid sliding window FASTA search for the elucidation of potential identities to known allergens.

Food and Agriculture Organization/World Health Organization (FAO/WHO) recommended that IgE cross-reactivity between a transgenic protein and allergen be considered when there is >or= 35% identity over a sliding "window" of 80 amino acids. Our objective was to evaluate the false positive and negative rates observed using the FAO/WHO versus conventional FASTA analyses. Data used as queries against allergen databases and analyzed to assess false positive rates included: 1,102 hypothetical corn ORFs; 907 randomly selected proteins; 89 randomly selected corn proteins; and 97 corn seed proteins. To evaluate false negative rates of both methods: Bet v 1a along with several crossreacting fruit/vegetable allergens and a bean alpha-amylase inhibitor were used as queries. Both methods were also evaluated for their ability to detect a putative nonallergenic test protein containing a sequence derived from Ara h 1. FASTA versions 3.3t0 and 3.4t25 were utilized. Data indicate a conventional FASTA analysis produced fewer false positives and equivalent false negative rates. Conventional FASTA versus sliding window derived E scores were generally more significant. Results suggest a conventional FASTA search provides more relevant identity to the query protein and better reflects the functional similarities between proteins. It is recommended that the conventional FASTA analysis be conducted to compare identities of proteins to allergens.

Serum testing of genetically modified soybeans with special emphasis on potential allergenicity of the heterologous protein CP4 EPSPS.

Roundup Ready soy contains the CP4-enolpyruvylshikimate-3-phosphate synthase (CP4 EPSPS) protein. Serum IgE from two distinct populations of soy-allergic patients were recruited to determine their IgE-binding specificity. One population consisted of 10 adult patients from Europe, whose primary diagnosis was soy food allergy with some also having mite allergy. In addition, 6 primarily mite-allergic, 6 food-allergic (celery, carrot, milk, shrimp, walnut, and apple), and 5 non-allergic patients were tested. Another population consisted of 13 children from Korea, whose primary diagnosis was atopic dermatitis and secondarily soy and egg sensitization. In addition, 11 non-allergic patients were tested. Each patient population was extensively characterized with respect to clinical symptoms, specific IgE (CAP) scores, and total IgE. Immunoblots and ELISA assays were developed using serum IgE from these patients and soy extracts, CP4 EPSPS, rice extract, ovalbumin, rubisco, purified major peanut allergen Ara h 2, the putative soy allergen Gly m Bd 30k and mite allergen Der f 2 proteins as the intended targets. Immunoblot results indicated that soy-allergic patients bound soy extracts but did not specifically bind rubisco or CP4 EPSPS. ELISA results were in general agreement with the immunoblot results except that rubisco bound significant quantities of serum IgE from some patients. These results indicate that the CP4 EPSPS protein does not bind significant quantities of IgE from two geographically distinct sensitive populations and there is no evidence for an increased allergenic potential of this biotech protein.

Human subjects without peanut allergy demonstrate T cell-dependent, TH2-biased, peanut-specific cytokine and chemokine responses independent of TH1 expression.

BACKGROUND: Peanut allergy is a major cause of anaphylaxis. Regulation of immune responses to peanut allergen, particularly why sensitization does not usually progress to allergic reactions, is not well investigated. Most studies focus exclusively on serologic responses and individuals with peanut allergy. OBJECTIVE: We sought to determine the existence, prevalence, and nature of peanut-specific, T cell-dependent cytokine and chemokine responses of adults who eat peanut without having symptoms. METHODS: We developed systems to examine specific immunity in peanut-tolerant individuals who had (1) negative histories and negative peanut skin test responses, (2) negative histories and positive peanut skin test responses, and (3) clinically apparent peanut allergy. After primary culture of PBMCs restimulated with whole peanut extract, we quantified responses characteristic of TH1 (IFN-gamma and CXCL10) and TH2-like immunity (IL-5, IL-13, CCL17, and CCL22) using ultrasensitive ELISAs. Antigen-presenting cell costimulatory requirements (CD4, HLA-DR, CD80/86, and cytotoxic T lymphocyte-associated antigen 4 [CTLA4] Ig) were determined. RESULTS: T cell-dependent, peanut-specific IL-5, IL-13, and CCL22 were common in peanut-tolerant individuals, regardless of whether they had positive or negative skin test responses. These were blocked by anti-CD4 and were dependent on CD28/CD86 costimulation. None of the 70 individuals studied had demonstrable IFN-gamma or CXCL10 responses to peanut. All demonstrated TH1 and TH2 responses to the ubiquitous recall antigen streptokinase. CONCLUSIONS: Qualitatively similar and quantitatively increasing peanut-specific TH2 responses in the consistent absence of putatively protective TH1 immunity were found in both peanut-tolerant individuals and those with peanut allergy. CLINICAL IMPLICATIONS: The continuum of responses between individuals with negative and individuals with positive skin test results, rather than TH1 versus TH2 bias, might be important in peanut allergy.

Evaluation of available IgE-binding epitope data and its utility in bioinformatics.

This paper reviews the role played by IgE-binding epitopes in eliciting clinical symptoms, the types of IgE-binding epitopes in allergenic proteins, the methods used to identify IgE-binding epitopes, and the availability of IgE-binding epitopes in allergenic sources. Finally, bioinformatics methods to assess protein allergenicity using knowledge of IgE-binding epitopes are discussed.

Animal models of food allergy: opportunities and barriers.

The potential for animal models to mimic the human disease process makes them an attractive tool for determining disease mechanisms, predicting disease triggers, and testing treatment regimens. With this in mind, animal models of food allergy have been receiving increasing attention as research tools to answer some of the difficult questions regarding food-allergy disease. Most of the food-allergy animal models developed to date have been designed to test reagents for immunotherapeutic treatment of allergic disease and to predict the potential human allergenicity of proteins. Current animal models under development are rodent, swine, and dog. The variables affecting development of such models include allergen concentration, allergen matrix or food source, allergen route of exposure, duration, animal age, adjuvant use, and dose range of allergens. Each model presents opportunities for and barriers to a fuller understanding of the allergic response. The conditions inherent to each model and the intended purpose of the study should therefore be considered prior to its use.

The value of short amino acid sequence matches for prediction of protein allergenicity.

Typically, genetically engineered crops contain traits encoded by one or a few newly expressed proteins. The allergenicity assessment of newly expressed proteins is an important component in the safety evaluation of genetically engineered plants. One aspect of this assessment involves sequence searches that compare the amino acid sequence of the protein to all known allergens. Analyses are performed to determine the potential for immunologically based cross-reactivity where IgE directed against a known allergen could bind to the protein and elicit a clinical reaction in sensitized individuals. Bioinformatic searches are designed to detect global sequence similarity and short contiguous amino acid sequence identity. It has been suggested that potential allergen cross-reactivity may be predicted by identifying matches as short as six to eight contiguous amino acids between the protein of interest and a known allergen. A series of analyses were performed, and match probabilities were calculated for different size peptides to determine if there was a scientifically justified search window size that identified allergen sequence characteristics. Four probability modeling methods were tested: (1) a mock protein and a mock allergen database, (2) a mock protein and genuine allergen database, (3) a genuine allergen and genuine protein database, and (4) a genuine allergen and genuine protein database combined with a correction for repeating peptides. These analyses indicated that searches for short amino acid sequence matches of eight amino acids or fewer to identify proteins as potential cross-reactive allergens is a product of chance and adds little value to allergy assessments for newly expressed proteins.

Allergenic characteristics of a modified peanut allergen.

Attempts to treat peanut allergy using traditional methods of allergen desensitization are accompanied by a high risk of anaphylaxis. The aim of this study was to determine if modifications to the IgE-binding epitopes of a major peanut allergen would result in a safer immunotherapeutic agent for the treatment of peanut-allergic patients. IgE-binding epitopes on the Ara h 2 allergen were modified, and modified Ara h 2 (mAra h 2) protein was produced. Wild-type (wAra h 2) and mAra h 2 proteins were analyzed for their ability to interact with T-cells, their ability to bind IgE, and their ability to release mediators from a passively sensitized RBL-2H3 cell line. Multiple T-cell epitopes were identified on the major peanut allergen, Ara h 2. Ara h 2 amino acid regions 11-35, 86-125, and 121-155 contained the majority of peptides that interact with T-cells from most patients. The wAra h 2 and mAra h 2 proteins stimulated proliferation of T-cells from peanut-allergic patients to similar levels. In contrast, the mAra h 2 protein exhibited greatly reduced IgE-binding capacity compared to the wild-type allergen. In addition, the modified allergen released significantly lower amounts of beta-hexosaminidase, a marker for IgE-mediated RBL-2H3 degranulation, compared to the wild-type allergen.

Comparative potency of Ara h 1 and Ara h 2 in immunochemical and functional assays of allergenicity.

To assess the relative potency of the major peanut allergens, Ara h 1 and Ara h 2, we examined the relative ability of purified proteins to bind IgE on immunoblots, to cross-link allergen specific IgE in an in vitro assay of degranulation based on RBL SX-38 cells, and to bind IgE in the ImmunoCap assay. Sera from 12 highly sensitive, peanut allergic patients were studied in all assays. IgE immunoblots with crude peanut extracts showed binding of IgE to multiple bands including the 63 kDa and 17-19 kDa bands that contain Ara h 1 and Ara h 2, respectively. In the functional assay, Ara h 2 was more potent than Ara h 1 in 11 of 12 sera tested with a median potency that was 52.5-fold more than Ara h 1 (P < 0.005). Contrary to findings with the functional assay, IgE immunoblots with purified Ara h 1 and Ara h 2 showed substantially lighter binding of IgE to Ara h 2 compared with Ara h 1 (P = 0.02). The ImmunoCap assay gave intermediate results with slightly more IgE binding to Ara h 2 than to Ara h 1 (P = 0.005). In conclusion, Ara h 2 is a very potent allergen and is much more potent than Ara h 1 for most sera using an in vitro assay of IgE cross-linking and cell activation. This finding is different from what was predicted based on immunoblots or with the ImmunoCap assay.

What makes a food protein an allergen?

Food allergens are almost always proteins, but not all food proteins are allergens. This one statement sums up the purpose of this article, defining the difference between an innocuous food protein and a food allergen. The simplest answer is that a food allergen has the ability to first elicit an IgE response, and then, on subsequent exposures, to elicit a clinical response to the same or similar protein. However, this simplistic answer avoids the more complex issues of defining the biochemical characteristics that allow a food protein to survive the extremes of food processing, escape the digestive enzymes of the human gastrointestinal tract, and interact with the immune system. More than 700 allergen sequences have been identified from food and nonfood sources. However, despite increasing knowledge of the structure and amino acid sequences of the identified allergens, only a few biochemical characteristics can be associated with food allergens. Food allergen characteristics, including abundance of the protein in the food; multiple, linear IgE binding epitopes; resistance of the protein to digestion and processing; and allergen structure are discussed, and the possible reasons they predispose some food proteins to become allergens are suggested.

New approaches for treatment of peanut allergy: chances for a cure.

Food allergy is a major cause of life-threatening hypersensitive reactions. Food-induced anaphylaxis is the most common reason for a person to present to the emergency department for treatment of the anaphylactic reaction. Avoiding the allergenic food is the only currently available method for sensitized patients to prevent further reactions. Strict avoidance of specific foods is accepted treatment of food-induced allergic reactions but is often an unrealistic therapeutic strategy for the treatment and prevention of food-induced hypersensivity reactions for the many reasons. Desirable therapeutic strategies for the treatment and prevention of the food allergies must be safe, relatively inexpensive, and easily administered. Recent advances in the understanding of the immunological mechanisms underlying allergic disease and better characterization of food allergens have greatly expanded the potential therapeutic option for future use. Several different forms of immunodulatory therapies are currently under investigation: peptide immunotherapy, mutated protein immunotherapy, allergen DNA immunization, vaccination with immunostimulatory DNA sequences, and anti-immunoglobulin E-therapy.

Monitoring peanut allergen in food products by measuring Ara h 1.

BACKGROUND: Peanut allergy is an important health problem in the United States, affecting approximately 0.6% of children. Inadvertent exposure to peanut is a risk factor for life-threatening food-induced anaphylaxis. OBJECTIVE: The purpose of this investigation was to develop an immunoassay for a major peanut allergen, Ara h 1, to detect peanut allergen in foods so that the risk of inadvertent exposure can be reduced. METHODS: A specific 2-site monoclonal antibody-based ELISA was developed to measure Ara h 1 in foods. The sensitivity of the assay was 30 ng/mL. Ara h 1 was measured in foods (n = 83) with or without peanut and in experiments to optimize allergen yield and to determine peanut contamination in spiked foods. RESULTS: Ara h 1 levels in food products ranged from less than 0.1 microg/g to 500 microg/g. Ara h 1 measured in ng/mL was transformed to microg/g for food products. Peanut butter contained the highest amounts of Ara h 1. Peanut extracts contained from 0.5 to 15 mg Ara h 1/g of peanut depending on the extraction conditions. Optimal extraction of Ara h 1 was obtained by using phosphate buffer with 1 mol/L NaCl and Tween at 60 degrees C. Ara h 1 was not always detected in presence of chocolate under the extraction conditions tested. Spiking experiments showed that the assay could detect approximately 0.1% Ara h 1 contamination of food with ground peanut. There was an excellent correlation between Ara h 1 levels and peanut content measured by using a commercial polyclonal antibody-based ELISA (r = 93, n = 31, P <.001). CONCLUSION: A new sensitive and specific monoclonal antibody-based ELISA was used to monitor Ara h 1 content in food products. This assay should be useful for monitoring peanut contamination in the food manufacturing and processing industry and in developing thresholds for sensitization or allergic reaction in persons with peanut allergy.

Protein structure plays a critical role in peanut allergen stability and may determine immunodominant IgE-binding epitopes.

Hypersensitivity to peanuts is a reaction mediated by IgE Abs in response to several peanut protein allergens. Among these allergenic proteins, Ara h 2 is one of the most commonly recognized allergens. Ara h 2 is a 17-kDa protein that has eight cysteine residues that could form up to four disulfide bonds. Circular dichroism studies showed substantial changes in the secondary and tertiary structures of the reduced Ara h 2 as compared with the native protein. Upon treatment with trypsin, chymotrypsin, or pepsin, a number of relatively large fragments are produced that are resistant to further enzymatic digestion. These resistant Ara h 2 peptide fragments contain intact IgE-binding epitopes and several potential enzyme cut sites that are protected from the enzymes by the compact structure of the protein. The enzyme-treated allergen remains essentially intact despite the action of proteases until the fragments are dissociated when the disulfide linkages are reduced. Amino acid sequence analysis of the resistant protein fragments indicates that they contain most of the immunodominant IgE-binding epitopes. These results provide a link between allergen structure and the immunodominant IgE-binding epitopes within a population of food-allergic individuals.

Modification of peanut allergen Ara h 3: effects on IgE binding and T cell stimulation.

BACKGROUND: Peanut allergy is a major health concern due to the increased prevalence, potential severity, and chronicity of the reaction. The cDNA encoding a third peanut allergen, Ara h 3, has been previously cloned and characterized. Mutational analysis of the Ara h 3 IgE-binding epitopes with synthetic peptides revealed that single amino acid changes at critical residues could diminish IgE binding. METHODS: Specific oligonucleotides were used in polymerase chain reactions to modify the cDNA encoding Ara h 3 at critical IgE binding sites. Four point mutations were introduced into the Ara h 3 cDNA at codons encoding critical amino acids in epitopes 1, 2, 3 and 4. Recombinant modified proteins were used in SDS-PAGE/Western IgE immunoblot, SDS-PAGE/Western IgE immunoblot inhibition and T cell proliferation assays to determine the effects of these changes on in vitro clinical indicators of peanut hypersensitivity. RESULTS: Higher amounts of modified Ara h 3 were required to compete with the wild-type allergen for peanut-specific serum IgE. Immunoblot analysis with individual serum IgE from Ara-h-3-allergic patients showed that IgE binding to the modified protein decreased approximately 35-85% in comparison to IgE binding to wild-type Ara h 3. Also, the modified Ara h 3 retained the ability to stimulate T cell activation in PBMCs donated by Ara-h-3-allergic patients. CONCLUSIONS: The engineered hypoallergenic Ara h 3 variant displays two characteristics essential for recombinant allergen immunotherapy; it has a reduced binding capacity for serum IgE from peanut-hypersensitive patients and it can stimulate T-cell proliferation and activation.