Open access peer-reviewed chapter

Comparative Analysis of Molecular Allergy Features of Seed Proteins from Soybean (Glycine max) and Other Legumes Extensively Used for Food

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Andrea Roman-Mateo, Esther Rodriguez-de Haro, Jose M. Berral-Hens, Sonia Morales-Santana and Jose C. Jimenez-Lopez

Submitted: 24 June 2022 Reviewed: 08 August 2022 Published: 06 October 2022

DOI: 10.5772/intechopen.106971

From the Edited Volume

Seed Biology Updates

Edited by Jose C. Jimenez-Lopez

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Abstract

Food allergies due to eating habits, pollution, and other factors are a growing problem in Western nations as well as developing countries. Symptoms of food allergies include changes in the respiratory and digestive systems. Legumes are a potential solution to the enormous demands for healthy, nutritive, and sustainable food. However, legumes also contain families of proteins that can cause food allergies. Some of these legumes include peanut, pea, chickpea, soy, and lupine. It has been shown that processing can alter the allergenicity of legumes since thermic and enzymatic resistance can affect these properties. Cross-reactivity (CR) is an allergy feature of some allergen proteins when the immune system recognizes part of the common share sequences (epitopes) in these allergic proteins. The research about molecular allergy includes comparisons of immunoglobulin E (IgE) and T-cell epitopes, assessment of three-dimensional structure and comparison of secondary structure elements, post-transduction modifications analysis by bioinformatic approach, and post-transduction modifications affecting epitopes properties may facilitate molecular tools to predict protein allergic behavior establishing prevention measurements that could promote the use of legumes and other seeds. This chapter provides an overview of the structural features of the main allergen proteins from legumes and their allergenic potential.

Keywords

  • food allergy
  • cross allergenicity
  • legumes
  • allergen proteins
  • soy
  • lupine

1. Introduction

Legumes are dicotyledon plants in the order Fabales and the family Fabacea. They produce fruit contained in pods and filled with seeds. In this chapter, we discuss three species of legumes in the genus Lupinus (Lupinus albus, L. angustiflora, and Lupinus luteus) and the most common allergenic species of the family Papilionaceae, including soja Glycine max; Arachis hypogaea, A. duraensis, and A. ipaensis; lentil (Lens culinaris); pea (Pisum sativum); and chickpea (Cicer arietinum).

A food allergy is an immune system reaction that occurs after eating certain types of food. Symptoms are variable and can be caused even by small amounts of allergenic proteins, leading to hives, swollen airways, and digestive problems. Food allergies are a growing concern worldwide. This increase is suspected to be related with industrial production, pollution, additives, and consumption of trash food [1]. There are reports of children of East Asian or African ethnicity in Western nations having an increased risk of developing food allergies compared with Caucasian children. This suggests that adopting Westernized food habits could increase food allergies in African or Asian countries [2, 3].

The research about healthy, low-cost alternative products that can meet the enormous demands of a growing population involve legumes [4]. Legume crops represent a sustainability solution, serving as a fundamental source of high-quality alternative protein, reducing the emission of greenhouse gases, allowing the sequestration of carbon in soils, saving the CO2 print thanks to the nitrogen fertilizer, it free high-quality organic matter that facilitate water retention and perform the soil nutrients circulation among others uses [5]. Despite their advantages, legumes contain proteins that can potentially cause food allergies. Several allergens from different legumes have been identified and characterized as proteins with potential allergic effects. These include lentil, pea, chickpea, soy, peanut, and lupine [6].

Clinically, the absence of sensibilization phase is a reliable indicator of the tolerance to an allergen. In this context, the presence of sensitization to a specific allergen protein has to be proven [7] both, the specific reactivity to a particular allergen protein and the cross-reactivity to other related allergens. The most frequent cross-reactivity process described clinically is that between lupin and peanut [8].

In Spain, consumption of legumes is common because they are an important part of the Mediterranean diet. It is estimated that consumption of legumes in Spain is 4.8 kg per year, with a greater percentage of children eating them as compared to adults. Legume consumption in Spain is greater in girls than in boys [9]. One study in Spain showed that food allergies were detected in 20.8% of children and 14% of adults. In the overall Spanish population, legumes were responsible of the 14.3% of the food allergies [10]. Another study of Spain’s pediatric population found that 10% of children suffered from food allergies caused by lentil and 6.7% of children suffered from food allergies caused by peanuts. Lentil was found to be the most allergenic, causing 78% of reactions, followed by chickpea (72%) and peanut (33%) [9].

In Europe, legumes are the fifth-leading cause of food allergies [11]. A meta-analysis of studies conducted in Europe between January 2000 and September 2012 found that the percentage of the population with symptoms of food allergies plus specific immunoglobulin E (IgE) positivity activation to at least one food allergen was 3%–4.6% in children and 2.2%–2.66% in adults [12]. The same study concluded that the frequency of food allergy is greatest in northwestern European countries compared to southern European countries, which had the lowest prevalence. Some factors related to food allergies include environmental, genetic, and epigenetic factors that could suggest differences between global populations [13].

The general prevalence of food allergies is not clearly defined due to the lack of reliable data and the highly variable allergy patterns in different parts of the world. A selection of mixed developed country data (Allergy, Asthma & Immunology Research 2018) found that some allergies, like those to peanut, demonstrate heritability in Caucasian populations; skin immune responses shows differences between Asians and Caucasians. These types of studies have not yet been conducted in non-White populations, however, there exists some interest data showing that Black South African children present a significantly lower prevalence of peanut allergy compared to children of mixed-race origin (Black and Caucasian) by unknown factors [13].

One interesting fact about cross-reactivity is that it could be caused by proteins that come from species that are taxonomically distant. Examples of these antigens are panallergens, which are proteins conserved by evolution due to their important defense, structural, and storage functions [7]. If a person has an allergy to cow milk proteins, they are also probably allergic to goat milk proteins [14]. In the case of legumes, cross-reactivity to more than one legume is often found in children [9].

Overall, allergic features of allergen proteins could be attenuated by thermic proteolytic denaturalization due to the modification of the quaternary protein structure where superficial epitopes of these proteins’ antigenic regions can still develop some allergenicity reactions. Despite this, there are studies that also show resistance to thermic, chemical, and proteolytic denaturalization, with is a common characteristic in legumes [15]. Some examples of resistance to denaturalization include allergen proteins like Cupins, very stable storage proteins that include legumins (11 S) and vicilins (7 S), both containing two common β-barrel structures in their globular domain. These appear to be a relevant stable structural motif, confirming resistance to denaturation and proteolysis [16]. Lipid transfer proteins (LTPs) have resistance to pepsin and to chemical digestion [17]; PR-proteins have thermostable structure [10] allowing them staying unalterable at physiological temperature. This stability plays an important role in allowing allergen active protein fragments to pass to the gastrointestinal tract, causing a food allergy.

There is a large public database of allergenic legume proteins with several isoforms. The commonly shared partial epitopes and their conservation in the same family of proteins in different species could be helpful in designing possible strategies to prevent cross-reactivity.

The aim of this work is to carry out an exhaustive molecular and structural analysis of the most common allergenic legume proteins through bioinformatic approaches.

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2. Materials and methods

2.1 Search of legume proteins sequences

We used the Allergome and UniProt databases to search for allergenic legume proteins for this study. The proteins chosen are characterized by having complete sequences and being in mature form. The search was carried out on the available species of lentil, pea, chickpea, soybean, and lupine (Table 1A-E).

SpeciesProtein nameProtein typeUniProtKB
A.
Soy allergen sequences
Glycine maxGly m 5ProfilinC6T9L1 (C6T9L1_SOYBN)
Gly m 5.0301ProfilinP25974 (GLCB1_SOYBN
Gly m 82 s albuminC6SYA7 (C6SYA7_SOYBN)
Gly m 8.01012 s albuminP19594 (2SS_SOYBN)
B.
Selected sequences of Lupinus
Lupinus albusLup a 17 s vicilinQ53HY0 (CONB1_LUPAL)
Lup a alpha conglutin11 s conglutinQ53I54 (Q53I54_LUPAL)
Lup a delta conglutin2 s albuminQ333K7 (Q333K7_LUPAL)
Lup a gamma conglutinAspartic proteaseQ9FEX1 (CONG2_LUPAL)
Lup a 4PR-proteinO24010 (O24010_LUPAL)
Lupinus angustifoliusLup an 17 s vicilinB0YJF8 (B0YJF8_LUPAN)
Lup an 3LTPA0A1J7GK90 (A0A1J7GK90_LUPAN)
Lup an 3.0101LTPA0A4P1RWD8 (A0A4P1RWD8_LUPAN)
Lup an alpha conglutin11 s globulinF5B8V6 (CONA1_LUPAN)
Lup an delta conglutin2 s albuminF5B8W8 (COND1_LUPAN)
Lup an gamma conglutinAspartic proteaseQ42369 (CONG1_LUPAN)
Lupinus luteusLup l 4PR- proteinP52778 (L18A_LUPLU)
C.
Selected sequences of Pea
Pisum sativumPis s 27 s vicilinP13915 (CVCA_PEA)
Pis s 3LTPA0A158V755 (NLTP2_PEA)
Pis s 6PR-proteinP13239 (DRR1_PEA)
Pis s agglutininAgglutininB5A8N6 (B5A8N6_PEA)
Pis s albuminAlbuminP08688 (ALB2_PEA)
D.
Selected sequences of Chickpea
Cicer arietinumCic a 17 s vicilinQ304D4 (Q304D4_CICAR)
Cic a 3LTPO23758 (NLTP_CICAR)
Cic a 4PR-proteinQ39450 (Q39450_CICAR)
Cic a 611 s globulinQ9SMJ4 (LEG_CICAR)
E.
Selected sequences of Peanut
Arachis hypogaeaAra h 17 s vicilinB3IXL2 (B3IXL2_ARAHY)
Ara h 1.01017 s vicilinP43238 (ALL12_ARAHY)
Ara h 2.01012 s albuminQ6PSU2–2 (CONG7_ARAHY)
Ara h 2.02012 s albuminQ6PSU2–3 (CONG7_ARAHY)
Ara h 311 s globulinA1DZF0 (A1DZF0_ARAHY)
Ara h 3.020111 s globulinQ9SQH7 (Q9SQH7_ARAHY)
Ara h agglutininAgglutininP02872 (LECG_ARAHY)
Ara h 5ProfilinD3K177 (D3K177_ARAHY)
Ara h 5.0101ProfilinQ9SQI9 (PROF_ARAHY)
Ara h 62 s albuminA1DZE9 (A1DZE9_ARAHY)
Ara h 6.01012S albuminQ647G9 (CONG_ARAHY)
Ara h 7.01012 s albuminQ9SQH1 (Q9SQH1_ARAHY9
Ara h 7.02012 s albuminB4XID4 (B4XID4_ARAHY)
Ara h 7.03012 s albuminQ647G8 (Q647G8_ARAHY)
Ara h 8PR- 10 proteinB1PYZ4 (B1PYZ4_ARAHY)
Ara h 8.0101PR-10 proteinQ6VT83 (Q6VT83_ARAHY)
Ara h 8.0201PR- 10 proteinB0YIU5 (B0YIU5_ARAHY)
Ara h 9.01019 k-LPTB6CEX8 (B6CEX8_ARAHY)
Ara h 10.010116kD proteinQ647G5 (OL101_ARAHY)
Ara h 11.010114KD oleosinQ45W87 (OL111_ARAHY)
Ara h 11.010214kD oleosinQ45W86 (OL112_ARAHY)
Ara h 13.0102DefensineC0HJZ1 (DEF3_ARAHY)
Ara h 14.010117.5kD oleosinQ9AXI1 (OL141_ARAHY)
Ara h 14.010217kD oleosinQ9AXI0 (OL142_ARAHY)
Ara h 14.010317kD oleosinQ6J1J8 (OL143_ARAHY)
Ara h 15.010117kD oleosinQ647G3 (OLE15_ARAHY)
Ara h 167 k LPTA0A445DA28 (A0A445DA28_ARAHY)
Ara h 1711 k LTPA0A445AL51 (A0A445AL51_ARAHY)
Arachis duranensisAra d 22 s albuminA5Z1Q8 (A5Z1Q8_ARADU)
Ara d 62 s albuminA5Z1Q5 (A5Z1Q5_ARADU)
Arachis ipaensisAra i 22 s albuminA5Z1Q9 (A5Z1Q9_ARAIP)
Ara i 62 s albuminA5Z1Q6 (A5Z1Q6_ARAIP)
F.
Selected sequences of Lentil
Lens culinarisLen c 3LTPA0AT28 (NLTP1_LENCU)
Len c 3.0101LTPA0AT29 (NLTP2_LENCU)
Len c agglutininAgglutininP02870 (LEC_LENCU)

Table 1.

Summary of the sequences used in successive studies.

Table includes the species name, the common name of the allergen, the type of protein according to its biological nature/function, and the UniProt entry name (UniProtKB). All sequences were used for alignment, T-cell epitope search, and IgE analysis. Sequences from all lupin and soybean species were used for the post-translational modification search tasks (A and B). For secondary and tertiary structure assessment, only the sequences of interest were used: G. max (Gly m 5, Gly m 5.0301, Gly m 8, and Gly m 8.0101); L. albus (Lup a 1 and Lup a alpha conglutin); Lupinus angustifolius (Lup an alpha e); P. sativum (Pis s albumin); C. arietinum (Cic a 6); and A. hypogaea (Ara h 5.0101).

2.2 Alignment of sequences

The complete and mature sequences of lentil (Len c 3, Len c 3.0101, and Len c aglutinin), chickpea (Cic a 1, Cic a 3, Cic a 4, Cic a 6), pea (Pis s 2 (7 s vicilin), Pis s 3 (LTP), Pis s 3.0101(LTP), Pis s 6 (PR-protein, Pis S aglutin, Pis s albumin)), lupine (Lup a 1, Lup a alpha conglutin, Lup a delta conglutin, Lup a gamma conglutin, Lup a 4, Lup an 1, Lup an 1.0101, Lup an 3, Lup an 3.0101, Lup an alpha conglutin, Lup an delta conglutin, Lup an gamma conglutin, Lup l 4), and peanut (Ara d 2, Ara d 6, Ara h 1, Ara h 1.0101, Ara h 2, Ara h 2.0101, Ara h 2.0201, Ara h 2.0202, Ara h 3, Ara h 3.0201, Ara h agglutin, Ara h 5, Ara h 5.0101, Ara h 6, Ara h 6.0101, Ara h 7.0101, Ara h 7.0102, Ara h 7.0301, Ara h 8, Ara h 8.0101, Ara h 8.0201, Ara h 9.0101, Ara h 10.0101, Ara h 11.0101, Ara h 11.0102, Ara h 13.0102, Ara h 14.0101, Ara h 14.0102, Ara h 14.0103, Ara h 15.0101, Ara h 16, Ara h 17) were aligned by pairs against soybean allergens (Gly m 5, Gly m 5.0301, Gly m 8, Gly m 8.0101) extracting the identity percentage and comparing the possible differences in the amino acid nature of the protein sequences (positive charge, negative charge, and polarity) of the allergens listed above.

2.3 Functional domain analysis

We used the program Pfam v34.0 (http://pfam.xfam.org/) to identify the possible domains present in the isoforms of legume proteins.

2.4 Post-translational modification site prediction

We used the MusiteDeep deep learning framework (https://github.com/duolinwang/MusiteDeep_web) to search for the presence of possible post-translational modifications and identify how they affect the potential allergenicity of the study proteins [18]. The prediction models used are phosphorylation (Y, S, T); N-linked glycosylation (N); O-linked glycosylation (S, T); ubiquitination; N6-acetyllysine (K); Methylarginine (R); Methyllysine (K); Hydroxyproline (P) and Hydroxylysine (K) with a threshold value of 0.8.

S-nitrosylations and T-nitrations were also studied via the iSNO-AAPair tool (Y. Xu et al., 2013), which was used to predict cysteine S-nitrosylation sites (http://app.aporc.org/iSNO-AAPair) with a threshold value greater than 0.8. The GPS-YNO2 tool (Liu et al., 2011) was used to predict tyrosine nitration sites (http://yno2.biocuckoo.org).

2.5 Secondary structure assessment

Secondary structure was assessed using PSIPRED (http://bioinf.cs.ucl.ac.uk/psipred/). Sequence alignment was performed with CLUSTALW (https://www.genome.jp/tools-bin/clustalw), which was visualized with the BioEdit program, and in which the consensus secondary structure was annotated.

2.6 Modeling of three-dimensional structure

The three-dimensional structures of olive ALDH proteins were modeled using the Phyre2 web program (http://www.sbg.bio.ic.ac.uk/phyre2), which is based on Markov algorithms to generate alignments of the problem protein sequences with proteins with experimentally obtained protein crystallographic models (PDB).

2.7 Identification of IgE-binding epitopes

We used the AlgPred server (www.imtech.res.in/raghava/algpred/submission.html), which creates arrays using sequences from known allergens, to identify IgE-binding epitopes and to determine potential allergenicity of proteins based on of their amino acid and dipeptide composition.

2.8 Identification of T cell binding epitopes

We used the ProPred program (Singh et al., 2011) (http://webs.iiitd.edu.in/raghava/propred/) to analyze the protein sequences of legumes in the study. The analysis was performed with a 2% threshold for the most common human HLA-DR alleles among the Caucasian population: [DRB1*0101 (DR1), DRB1*0301 (DR3), DRB1*0401 (DR4), DRB1*0701 (DR7), DRB1*0801 (DR8), DRB1*1101 (DR5), and DRB1*1501 (DR2)].

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3. Results and discussion

3.1 Sequences obtained from the Allergome database

We used the Allergome database to retrieve the available sequences of complete proteins of legumes, following the link to UniProt. The legumes included in this study are lentil, lupin, pea, chickpea, and peanut. Only two major allergens (Gly m 5 and Gly m 8) with their available isoforms were extracted from soybean and used as reference to carry out the alignments and further analyses.

The reference proteins, soybean major allergens Gly m 5 and Gly m 8 with their isoforms, correspond to profilin, 7 s globulins, and albumin 2 s protein families. The allergen Gly m 8 is considered to have the highest sensitivity [19], specificity, and reproducibility [20] to clinical reaction to soybean in atopic patients. The combination of Gly m 5 and Gly m 8 was suggested as one of the best ways to perform the estimation of the sensitization level and to improve the diagnosis of soybean allergy in children [21]. Thus, in the case of high similarity between the sequences of these soy allergens and the allergens of the other legumes included in this study, the diagnosis of possible cross-reactions between them could be facilitated.

3.2 Alignment of allergen protein sequences

Sequence alignments were performed to compare the common and differential features between allergen proteins and legumes. Overall, and according to the CODEX Alimentarius Commission in 2003, only proteins with a percentage of identity greater than 50% by local alignment (BLAST) are at risk of allergy or cross-reactivity [22]. Therefore, results obtained from protein–protein alignment beforehand do not show values high enough to make a prediction of possible cross-reactivity between soybean proteins and the rest of the legumes (Table 2).

Glycine maxArachis duranensisLens culinaris
Protein nameAra d 2Ara d 6Len c 3Len c 3.0101Len c agglutinin
A.
Percentages of Amino Acid Sequence Identity by Alignment of Peanut and Lentil Species against Reference Soybean Sequences
Gly m 5842860675239515711.803
Gly m 5.0301900959094556581711.349
Gly m 832.73829.94994210.4659375
Gly m 8.010133.33329.94994298849278
Glycine maxLupinus angustifolius
Protein nameLup an 1Lup an 10,101Lup an 3Lup an 30,101Lup an alpha conglutinLup an delta conglutinLup an gamma conglutin
B.
Percentages of Amino Acid Sequence Identity by Alignment of Lupin Species against Reference Soybean Sequences
Gly m 524.46339.7395843417.304844415.028
Gly m 5.030124.46339.7394.31417.304844414.657
Gly m 88114620911.56111.243661635.625298
Gly m 8.01017877620912.06911.765661636.255066
Glycine maxCicer arietinumArachis ipaensis
Protein nameCic a 1Cic a 3Cic a 4Cic a 6Ara i 2Ara i 6
C.
Percentages of Amino Acid Sequence Identity by Alignment of Chickpea and Peanut Species against Reference Soybean Sequences
Gly m 536.7596378813.58787536292
Gly m 5.030137.5756378755688.856136
Gly m 8714310.5265021758531.46129.94
Gly m 8.0101651310.5265021758531.46130.539
Glycine maxLupinus albus
Protein nameLup a 1Lup a 4Lup a alpha conglutinLup a delta conglutinLup a gamma conglutinLup l 4
D.
Percentages of Amino Acid Sequence Identity by Alignment of Lupin Species against Reference Soybean Sequences
Gly m 548.4176.2516.637803613.6456798
Gly m 5.030148.7176.2516.637825914.0987456
Gly m 8515110.698650135.625442513.115
Gly m 8.01015009106.1836.25443513.115
Glycine maxPisum sativum
Protein namePis s 2Pis s 3Pis s 3.0101Pis s 6Pis S agglutinPis s albumin
E.
Percentages of Amino Acid Sequence Identity by Alignment of Pea Species against Reference Soybean Sequences
Gly m 541.63854675882679893626798
Gly m 5.030141.63851455369679811.42910.444
Gly m 8575911.76510.58813.40211.2738.98
Gly m 8.01015.4111.17610.58813.40210.2049388
Glycine maxArachis hypogaea
Protein nameAra h 1Ara h 1.0101Ara h 2Ara h 2.0101Ara h 2.0201Ara h 2.0202Ara h 3Ara h 3.0201
F.
Percentages of Amino Acid Sequence Identity by Alignment of Peanut Species against Reference Soybean Sequences
Gly m 536.58535.726875388118874903115.41214.685
Gly m 5.030136.74835.8858.8590099292923415.76214.86
Gly m 85769830731.46132.73834.81833.1335.416015
Gly m 8.01017329766831.46133.33331.81833.7354.575636
Glycine maxArachis hypogaea
Protein nameAra h agglutininAra h 5Ara h 5.0101Ara h 6Ara h 6.0101Ara h 7.0101Ara h 7.0102Ara h 7.0301
G.
Percentages of Amino Acid Sequence Identity by Alignment of Peanut Species against Reference Soybean Sequences
Gly m 513.8166349613666066292798270626292
Gly m 5.030113.71749045.3369516136829668349131
Gly m 8857110.734601528.14429.9423.49730.33722,286
Gly m 8.0101857110.674909128.14430.53923.49730.89922.857
Glycine maxArachis hypogaea
Protein nameAra h 8Ara h 8.0101Ara h 8.0201Ara h 9.0101Ara h 10.0101Ara h 11.0101Ara h 11.0102Ara h 13.0102
H.
Percentages of Amino Acid Sequence Identity by Alignment of Peanut Species aAgainst Reference Soybean Sequences
Gly m 5618177616.9235967761698272073139
Gly m 5.0301693575396.923.826828698272073139
Gly m 811.42910.23311.6410.40564786.146.149877
Gly m 8.010111.79211.6411.6410.40568836.146.149259
Glycine maxArachis hypogaea
Protein nameAra h 14.0101Ara h 14.0102Ara h 14.0103Ara h 15.0101Ara h 16Ara h 17
I.
Percentages of Amino Acid Sequence Identity by Alignment of Peanut Species against Reference Soybean Sequences
Gly m 5874478488296722146983905
Gly m 5.0301874478488296722146984121
Gly m 85785585957855.611.11111.243
Gly m 8.01015372585957855.611.3111.243

Table 2.

Percentages of amino acid sequence identity by alignment of different legume species against reference soybean sequences.

Degree of identity resulting from the alignment of amino acid sequences. These have been obtained by alignment between soybean proteins, used as reference, against different legume species (lentil, chickpea, pea, lupine, and peanut) including major allergens and isoforms.

The highest percentage of identity was the result of the alignment between the Gly m 5 proteins and the Gly m 5.0301 isoform (Table 3) with the Lup a 1 protein with values of 48.41% and 48.72%, respectively (Table 2D). However, these percentages do not exceed the minimum alignment percentage recommended as guidance. Despite this, there are reported cases of cross-reactivity between other proteins with which there is a percentage lower than the standard minimum value considered for cross-reactivity and lower than that which occurs between these proteins, as in the case of Gly m 8 and Ara h 2 [23], with an identity percentage of 31.46% (Table 2F).

Alignment Frequency Calculations
Average of the difference of the frequencies between the different isoforms of soybean proteins with the alignment of the different proteins of legume species.
Gly m 5/Gly m 5.03010,599 (over all)values > 3%5587 (Cic a 6)
3646 (Pis s albumin)
Gly m 8/Gly m 8.01010,468 (over all)values > 3%3076 (Ara h 5.0101)
Max identity values obtained by sequences alignment
Greater value48,717 (over all)
Gly m 5.0301 vs. Lup a 1

Table 3.

Summary of the largest (greater than 3%) and smallest differences as a result of legume–soy protein alignment.

The multiple alignment analysis between Gly m 5 and the isoform Gly m 5.0301 with the Lup a 1 protein obtained a percentage of common identity of 35.80% with 207 identical positions (Image 1).

These data show that the percentage of identity of allergens must be kept in mind to compare allergens and to predict potential allergenicity and cross-reactivity, since not only do sequential epitopes have to be taken into account for that purpose, but also 3D and specific structural conformations of particular allergen proteins must be considered.

Using the information obtained by alignment, some of the proteins in the comparative analysis with soybean could be of interest at the molecular allergy level, such as Lup a delta conglutin and Lup an delta conglutin with percentages of identity with Gly m 8 and Gly m 8.0101 ranging from 35 to 36%. It also presents notable alignment percentage differences with Gly m 5 and Gly m 5.0301 (Table 2B,D), with approximately 8% being the most notable difference in identity with respect to the other conglutins. Another candidate protein for analysis is Lup a delta conglutin with percentages of identity of 35.63% and 36.25% compared to Gly 8 and its isoform Gly m 8.0101, respectively (Table 2D) and Lup an delta conglutin of 35.62% and 36.25%, respectively (Table 2B). The identity ratios are lower than the minimum value considered to establish cross-reactivity with soybean. However, with such similar percentages among conglutin sequences it is worthy to conduct a deeper analysis. Multiple alignment shows a high rate of conservation between lupin proteins from the different species of L. albus and Lupinus angustifolia. Comparison of gamma conglutin protein sequences of both species, soybean obtained a low identity percentage of 13–15% compared to Gly m 5 and 4–5% compared to Gly m 8 (Table 2B,D). Alignment between both conglutins showed an identity of 84.21%, with 128 identical positions and 12 similar positions (Figure 1), with an identity value high enough to consider cross-reactivity among them. Indeed, these sequences showed high conservation rate among lupin proteins from different species such as L. albus and L. angustifolia. The three-dimensional structure of these conglutins will be further analyzed in later sections (Figure 2).

Figure 1.

2D structure of allergen proteins. Multiple alignment of the major Lup a gamma conglutin (Lupinus albus) against Lup an gamma conglutin (Lupinus angustifoluis) with the secondary sequence represented in yellow by coil zones and in red by helix zones. In addition to the percentage of joint identity, number of identical amino acid positions and number of amino acid have similar physicochemical nature.

Figure 2.

Three-dimensional structural analysis of seed allergen proteins. Figures of first row corresponding to the 3D structures of the Lup a gamma conglutin protein; second row represent different views of Lup an gamma conglutin; and third raw are the figures of the consensus sequence with depicted match regions in pink color over the consensus figure (last row). Red color highlights the alpha-helix and yellow color the beta-strand.

Considering the identity percentages previously indicated, the Ara h 2 identity percentage of 31% at Gly m 8 with demonstrated cross-reactivity and the 48% identity of Lup a 1 with soybean, we found more cases of proteins with intermediate values. Such is the case of Pis s 2 with Gly m 5 and its isoform with an identity of 41.638% (Table 2E) and Cic a 1 with 36.76% and 37.58% identity with Gly m 5 and its isoform, respectively (Table 2C). On the other hand, the characterization of demonstrated cross-reactivity between soybean and peanut, as is the case of Ara h 1 with Gly m 5 and its isoform Gly m 5.0301, showed a 36.59% and 36.75% identity, respectively [24]. The rest of the alignments show percentages less than the described data of identity range and may be discarded from the depth in their CR study (Table 2).

Interestingly, the percentage of alignment identity between soybean isoforms was low, with values less than 1%, specifically, in the alignment of soybean major allergen Gly m 5 and its isoform Gly m 5.0301. The sequences of these two allergens were compared to the rest of the legume proteins considered in this study. We obtained a different percentage of identity of 0.6%, as well as 0.47% when compared Gly m 8 with Gly m 8.0101 (Table 3). The largest differences were found between soybean isoforms and legumes; Gly m 5/Gly m 5.0301 was 5.60% against chickpea protein Cic a 6 (Table 2C); 3.65% against pea Pis s albumin (Table 2E) protein; and Gly m 8 /Gly m 8.0101 3.07% against peanut (A. hypogaea) protein Ara h 5.0101 (Table 2G). Table 3 summarizes this data.

The existence of differences between isoforms of other legume species of the same allergen protein family could open the way for new studies finding significant differences in multiple cross-reactivity candidacy. For example, such as the case of Lup an 1 and Lup an 1. 0101 with identity differences exceeding 13% in alignment with Gly m 5, and ranging between 24.46% and 39.74%, respectively (Table 2B). These differences make Lup an 1 an unsuitable candidate for cross-reactivity, whereas its isoform Lup an 1.0101 could be a candidate for cross-reactivity with soybean.

3.3 Post-translational modification analysis

Post-translational modifications affecting the allergen protein sequences have been defined and involved in processes like alcohol or tiol addition (glycosidations), methyl groups (methylations), phosphates (phosphorylations), carboxyl groups (carboxylations), nitro groups (T-nitrations), or nitroxil groups (S- nitrosylations).

These types of modifications may induce rearrangements in structure, which could indirectly affect lineal and/or conformational epitopes’ influence pm molecular allergy, limiting or favoring immunological recognition as well as generating antigenic diversity [25]. It is interesting to analyze location of where these modifications may occur and the type of modification together with the influence of these modifications in the 2D structural elements.

Phosphorylation is considered a factor of change of molecular pH dynamics [26], generating important alterations in the biophysics of the protein [27]. It has been observed sites of phosphorylation in most of the proteins examined: Gly 5, Gly 8 and their isoforms; Lup a 1, Lup a alpha and delta conglutins (L. albus); Lup an 1 and its isoform Lup an 1.0101, Lup an alpha, Lup an delta and Lup an gamma (L. angustifolius). In the sequences of Lup l 4 (L. luteus) and Cic a 6 (C. arietinum) are also abundant modifications as glycosidations which potential importance in the allergenicity behavior of these proteins. In this regard, it has been demonstrated in some cases the increasing immunogenicity [28] for Gly 5 and Gly 8; Lup a 1, Lup a 4, Lup a alpha, delta, and gamma conglutins; Lup an 1 and it isoform Lup an 1.0101, Lup an alpha and gamma conglutins; Lup l 4 and Cic a 6 (Table 4).

AllergenPost-translational modifications
PhosphorylationGlycosylationPyrrolidone carboxylic acidMethylationNitrationNitrosylation
A.
Post-translational modifications predicted over soybean: Glycine max (Gly m)
Gly m 5232; 234; 235351158;172
Gly m 5.0301232; 234; 235351158; 172
Gly m 8155; 15612014
Gly m 8.0101155; 1561202514
B.
Post-translational Modifications Predicted Over Lupinus: Lupinus albus (Lup a), L. angustifolius (Lup an), and L. luteus (Lup l)
Lup a 171; 79; 104444269;316
Lup a 413; 82157; 269; 316
Lup a alpha conglutin34740329102199; 448; 49736; 334
Lup a delta conglutin75;7673; 10827
Lup a gama conglutin13328261
Lup an 180;82;85152; 434126; 158340
Lup an 1.010180;82;85; 469; 488434; 519126; 158340; 488
Lup an 32313; 27
Lup an 3.010110428; 112
Lup an alpha conglutin247; 259; 341397; 439249784; 442; 49131
Lup an delta conglutin76; 77; 80;8342
Lup an gamma conglutin357130259350; 391; 440
Lup l 411278; 82100; 156
C.
Post-translational Modifications Predicted Over Chickpea: Cicer arietinum (Cic a) and Peanut: Arachis hypogaea (Ara h)
Cic a 6139; 195; 207; 225; 2711; 22044364; 107
Ara h 5.01016; 125115

Table 4.

Post-translational modifications predicted over legumes.

Specific amino acids affected by each type of post-translational modification on the different legume proteins: phosphorylation, glycosylation, carboxylation (pyrrolidone carboxylic acid), methylation, nitrosylation, and nitration sites. The (−) symbol means no results.

Methylations are quite less abundant modifications. It is observed that their deficiency generates serious alterations in the functioning of proteins, thus having important implications on their three-dimensional structuring as carboxylation [29]. Only two methylation sites were found: one on Lup a alpha conglutin and one on Lup an alpha conglutin (Table 4B). Carboxylations were found on the Gly m 8.0101 isoform; Lup a alpha, delta, and gamma conglutins; Lup an 1 and its isoform Lup an 1.0101; and Lup an 3 and Lup an alpha conglutin (Table 4A,B).

Nitrosylation and nitrations generate strong covalent bonds in the protein structure [30, 31]. Nitrations were found on Lup a 1, Lup a 4, and Lup a alpha conglutin; Lup a gamma conglutin, Lup an 1, and Lup an 1.0101; Lup an 3.0101, Lup an alpha and gamma conglutin; Lup l 4; Cic a 6 and Ara h 5.0101. Nitrosylations in comparison were less abundant, found in Lup a alpha conglutin; Lup an 3 and its isoform Lup an 3.0101, and Lup an alpha, delta, and gamma conglutins (Table 4).

Post-translational modifications on T-cell epitopes have been found in Gly m 5.0301 isoform, a glycosidation at position 351, and a nitration at 172; Lup a alpha conglutin presents three methylation sites at positions 199, 448, and 497; Lup a delta conglutin contains a glycosidation site at position 76; a nitrosylation site at position 13 was found in Lup an 3, while in its isoform a nitration at position 104 and a nitrosylation at position 112 are highlighted; Lup an delta conglutin presents a candidate phosphorylation site at position 76 and Cic a 6 a nitrosylation at 107. In other cases, IgE epitopes are affected, with the only case of Lup a alpha conglutin with a methylation site at position 102. Table 5 presents a summary of this data.

Allergen namePost-translational Modifications
PhosphorylationGlycosylationMethylationNitrationNitrosylation
A.
T-cell epitopes from allergens affected by post-translational modifications
Gly m 5.0301FVVNATSNL(351)YLQGFDHNI(172)
Lup a alpha conglutinFGPLRRCN (199)
YVLNGSAWF (448)
YVAFKTNDI (497)
Lup a delta conglutinLVAALVLVV (76)
Lup an 3VLICMVVVS(13)
Lup an 3.0101YKISTSTNC (104)YKISTSTNC(112)
Lup an delta conglutinLVVHTSASR (76)
Cic a 6FGMVFPGCV(107)
B.
IgE epitopes from allergens affected by post-translational modifications
Lup a alpha conglutinIETWNPNNQEFECAG (102)

Table 5.

T-cell and IgE epitopes from allergens affected by post-translational modifications.

This table summarizes the T-cell and IgE epitopes directly affected by the main post-translational modifications indicating the amino acid number affected.

The direct implications of these post-translational modifications may be directly linked to the effects on the variation of the structure of these regions, generating differential epitopes recognition and consequently the allergen response.

Analyzing the location and type of modifications could help to elucidate the relationship of protein structure epitope distribution to the allergen potential of the protein, however, it will not be confirmed whether the different modifications would accentuate or lessen the allergenic impact until a clinical review of the process is carried out. The possibility of inducing post-translational modifications on plant proteins as a therapeutic tool is being examined [27].

3.4 Secondary structure analysis

The combined analysis of secondary structure with multiple alignments allows a direct sequence–structure–functional comparation between different allergen proteins. An interesting analysis has been made to identify the areas of allergens with shared mutual domains as part of structural domains with important implications for cross-reactivity potential.

The Gly m 5, Gly m 5.0301, and Lup a 1 secondary structure comparison showed that in sequences of these proteins (Table 2A), the percentage of identity with Lup a 1 was the highest compared to the rest of the alignments performed (Table 3). However, the percentage was not potentially enough to induce cross-reactivity. Comparative analysis between the secondary structure predictions of these proteins shows strong similarities in the distribution of α-helix and β-strand over middle regions of the proteins (amino acids 20–430) (Figure 3), giving an additional perspective of the possible regions with potential cross-reactivity in addition to the information provided by the alignments.

Figure 3.

2D structure of allergen proteins. Multiple alignment of the major allergen Gly m 5, its isoform Gly m 5.0301 from (Glycine max) and Lup a 1 (Lupinus albus) together with the secondary sequence is represented in yellow by coiled-coil zones and in red by helix zones. In addition to the percentage of joint identity, number of identical amino acid positions and number of amino acid have similar physicochemical nature.

The three allergen proteins include Cupin superfamily domains with a wide variety of representative enzymes, but notably contains the non-enzymatic seed storage proteins [32]. Functional domains that could be candidates to potentially undergo post-translational modifications for Lup a 1 are one of the two barrel domains with antiparallel b-sheets. The first one is a Cupin_1.1 (Table 6A), a candidate for glycosidation (Table 4B). Similarly, in the case of Gly m 5 and its isoform Gly m 5.0301, in both proteins where also present these modifications in their globular domain (antiparallel β-barrels) (Table 6A), which is a candidate to undergo glycosylation (Table 4A). In three cases, modifications by glycosidation of one of their functional domains is a shared functional and allergenic feature.

ProteinFunctional domainAlignment amino acid range
A.
Functional Domains Predicted Over Gly m 5, Gly m 5.0301 and Lup a 1
Lup a 1Cupin_1.1332–486
Cupin_1137–227
Gly m 5Cupin_1240–389
Cupin_286–144
Gly m 5.0301Cupin_1240–393
Cupin_286–144
B.
Functional Domains Predicted Over Lup a gamma conglutin and Lup an gamma conglutin
Lup a gamma conglutinXylanase inhibitor C-terminal271–428
Xylanase inhibitor N-terminal66–240
Lup an gamma conglutinXylanase inhibitor C-terminal269–429
Xylanase inhibitor N-terminal63–237

Table 6.

Functional domains predicted over legumes allergens.

This table summarizes the protein domains of the different proteins in their different types, specifying the range of amino acids that occupy in alignment.

Lup a gamma conglutin and Lup an gamma conglutin were analyzed. Although they belong to different species of lupin, they showed few differences in alignment and their comparison with soybean proteins of reference (Table 2B,D). The identity percentage among them is greater than 50%. These allergen proteins could be considered to exhibit CR, due to sequence identity but also to similarities of their secondary structure (Figure 1).

Regarding the predictions of post-translational modifications of these proteins relevant to 2D structural domains, it was found that Lup a gamma conglutin can be modified by a potential glycosidation (Table 4B). This modification is located in the region of the protein domain xylanase inhibitor C-terminal (Table 6B). Lup an gamma conglutin has two possible domains affected by post-translational modifications: a phosphorylation and two nitrosylations (Table 4B) that affect the region comprised in the C-terminal xylanase inhibitor domain (Table 6B) and two nitrosylations (Table 4B) over the same domain. It also presents a glycosidation (Table 4B) in the xylanase inhibitor N-terminal domain (Table 6B).

3.5 Three-dimensional structure analysis

Analysis of three-dimensional structure of proteins (Figure 4) provides insight into their sequence conformation and epitope arrangement. It also helps to determine the consequences of possible structural changes occurring between protein isoforms with minimal or large number of changes (Table 2) in their sequences [33].

Figure 4.

3D structural analysis of seed allergen proteins. Three-dimensional structures of the Gly m 5.0301 proteins are described, followed by Gly m 5.0301 and the change points between the two proteins marked in soft pink color in consensus figure (last row). Red denotes the alpha-helix and yellow denotes the beta-strand. T-epitope location is marked by a blue circle.

Post-translational modifications over protein domains also may generate changes in their three-dimensional structure, affecting exposure epitopes and increasing or decreasing their allergenic potential.

Some candidates to examine the three-dimensional structure are Gly m 5, Gly m 5.0101, and Lup a 1 that share common barrel domains with alternating folds between the α-helix and β-strand. These domains are in a special conformation, forming a solenoid in which the β-strand is arranged on the inside of the toroid and the α-helix is arranged on the outside in the same domain (Figures 2 and 5).

Figure 5.

3D structural analysis of seed allergen proteins. Three-dimensional structures of the Gly m 5 proteins followed by Lup a 1 and representative changes between these two proteins marked in pink in the consensus figure (last row). Red denotes the alpha-helix and yellow denotes the beta-strand.

The three-dimensional structure of the proteins Gly m 5, Gly m 5.0301 (Glycine max), and Lup a 1 (L. albus) showed a structure with large number of similarities, which is also reflected in the previous analysis of their secondary structure (Figure 3), with two barrel domains common in all of them.

The structural differences observed in the consensus structure between the three structures indicate that in Gly m 5.0301, an element of the 2D structure corresponding to a β-strand structural connection is not present in the isoform Gly m 5. Neither is it present in Lup a 1, which is a specific and important structural feature that can make a specific conformational epitope (Figures 4 and 5). This structural change does not contain any epitope sequence. However, the change found is located between the Cupin-1 domain of Gly m 5 and its isoform, whereas this change in Lup a 1 is located in the Cupin_1.1 domain (Table 6A).

Tridimensional structure comparison between Lup a gamma conglutin and Lup an gamma conglutin result on two principal differences observed between both conglutins, which is an α-helix in the gamma conglutin of L. albus that is not present in L. angustifolius (Figure 2). Regarding post-translational modification sites, in this loop there are no predicted modifications in this region encompassing the N-terminal xylanase inhibitor domain (Table 6B).

The 3D analysis was useful to determine other cases of interest previously mentioned, such as Pis s 2 and Cic a 1 in comparison with Gly m 5 and its isoform that showed considerable identity ratios (Table 2C,E). Lup an 1 and Lup an 1.0101 showed large differences between their identity, and even more differences were found when compared to Gly m 5, which is somehow reflected in their 3D structures.

3.6 Identification and analysis of T-cell binding epitopes

An epitope is the portion of a macromolecule that is recognized by the immune system, specifically the sequence to which antibodies, B-cell receptors or T-cell receptors, can bind to initiate an immune response. Analysis of the epitopes shared for specific allergen proteins could be relevant to identify potential cross-reactivity. Presence of common T-cell epitopes among different legume species may support cross-reactivity processes; the greater the probability of occurrence, the larger the number of common epitopes.

The data obtained from the analysis of T-cell epitopes allows us to know which epitopes are shared among allergen proteins in the different legume species and to examine possible cases of cross-reactivity. Thus, in the case of soybean G. max, epitopes common to peanut, A. hypogaea species and chickpea C. airietinum species are described in Table 7A. It is remarkable that the soybean protein isoform Gly m 5.0301 has an epitope in common with Ara h 9.0101, while the major allergen Gly m 5 does not contain this epitope (Table 7A). This feature may be related to the cross-reactivity between specific sequences and these legume cultivars containing these specific proteins.

Allergen nameT-cell epitopes
LRSSNSFQTLRSRNPIYS
A.
Range of amino acids occupied by T-cell epitopes joint over soy
Gly m 5288–296
Gly m 5.030136–44242–250
Ara h 9.010121–29
Cic a 1250–258
Allergen nameT-cell epitopes
LVLVLGIVFMMACNGLTIYVLHKIEEIFVLSSSQNSLVAALVLVVLVVHTSASR
B part 1
Range of amino acids occupied by T-cell epitopes joint over lupin, peanut, and chickpea
Lup a 111–19
Lup a 466–75
Lup a alpha conglutin
Lup a delta conglutin67–7573–81
Lup a gamma conglutin16–2463–71
Lup an delta conglutin62–7069–77
Lup an gamma conglutin13–2177% (FVSSSSQD) 69–77
Ara d 613–20
Ara h 8.010277% (YVLHKIDAI)
66–74
Cic a 488% (YVLHKIEAI)
123–132
Allergen nameT-cell epitopes
FQRLNALEPLRCAGVALSIRVLERFDQFGPLRRCNVVLNGRATITIIVRNIKGKN
B part 2
Lup a 1133–138177–190
Lup a 4
Lup a alpha conglutin83–91112–120192–200279–287
Lup an 180% (IRVLERFNQ)204–212248–259
Lup an 1.010180% (IRVLERFNQ)204–213248–260
Lup an alpha conglutin86–94115–123286–294
Lup an delta conglutin191–198
Ara h 180% (IRVLQRFDQ) 204–212
Ara h 1.010180% (IRVLQRFDQ) 193–201
Allergen nameT-cell epitopes
IVRVSREQIIRVNKHMVRRVRRPHWRISDEN
B part 3
Lup a 1302–310
Lup a alpha conglutin355–363
Lup a gamma conglutin318–326412–420
Lup an 177% (IVRVSKKQI)373–381
Lup an 1.010177% (IVRVSKKQI) 373–381
Lup an 3.0101360–367
Lup an delta conglutin88% (IRVNKHL) 324–33288% (WRISSEN) 421–429
Allergen nameT-cell epitopes
FPILGWLGLFVIPAGYPIFVPYYNVNAYVLNGSAWFYVAFKTNDIYKFLVPPPQ
B part 4
Lup a 1433–442
Lup a 4
Lup a alpha conglutin411–418432–444445–452493–501542–550
Lup an 3.010188.88% (FPILRWLGL) 413–421434–442447–455495–503544–552
Ara h 377% (FVPHYNTNA) 404–412
Ara h 3.020177% (FVPHYNTNA) 454–465
Allergen nameT-cell epitope
FLLAAHAS
C.
Range of amino acids occupied by T-cell epitopes joint over peanut
Ara d 213–20
Ara h 213–21
Ara h 2.010113–21
Ara h 2.020113–21
Ara h 2.020213–21

Table 7.

Range of amino acids occupied by T-cell epitopes joint over legumes.

This table lists the T -cell epitopes shared on at least two occasions by different species, describing the range of amino acids in which they are located and the percentage of identity with the epitope in the case in which identity is not exact.

On the other hand, the different lupin species show that up to 18 T-cell epitopes are found commonly shared between L. albus and L. angustifolius (Table 7B part 1, 2, 3 and 4). Shared epitopes are also observed between L. albus and A. hypogaea (four epitopes) (Table 7B part 1, 2 and 4); A. duranensis (one epitope), C. arietinum (same number of epitopes) (Table 7 part 1). Comparison with L. angustifolius showed three epitopes commonly shared with A. hypogaea (Table 7B parts 2, 3 and 4), and one epitope with C. arietinum and L. culinaris (Table 7B part 3).

Among these allergen proteins, there are also epitopes shared more than one time among more than two species. The same epitope is shared among the allergenic proteins: Lup a 4 with Ara h 8.0101 and Cic a 4 (Table 7B part 1); Lup an alpha conglutin, Lup an 3.0101, Ara h 3, and Ara h 3.0201 (Table 7B part 4). the most shared epitope was between Lup an 3, Lup an 3.0101, Ara h 9.0101, Ara h 17, Cic a 3, Len c 3, and Len c 3.0101 (Table 7B part 3).

Prediction of secondary and tertiary structures allowed us to determine the spatial location of epitopes in proteins and to assess whether they may be affected in their spatial arrangement by post-translational modifications in protein domains over interest proteins.

Gly m 5, Gly m 5.0301, and Lup a 1 analysis also showed that T-epitope regions founded over these proteins integrate part of the functional barrel domains of these proteins. In the case of Gly m 5, a single T-epitope (Table 6A) is located in the region of the structural domain between β-strands (Figure 5). This region is located into Gly m 5-barrel domain (Cupin_1) (Table 6A) in the amino acidic region located close to the site of glycosidation (Table 5A). This structural epitope is of special interest by its specificity, location, and potential specific allergenicity induced by this protein.

The T-cell epitopes analyzed on L. gamma conglutins resulted in the presence of two epitopes on the C-terminal xylanase and one on the N-terminal xylanase domain of L. albus (Table 6B, Table 7B part 1and 2) and one over N-terminal xylanase domain of L. angustifolius (Table 6B and 7 part 1). These are not directly or proximally affected by post-translational modifications, but they do affect the domains in which they are located.

Therefore, epitopic regions matched between L. albus and L. angustifolius conglutin, which are the most abundant compared to other epitopes (Table 7B). This supports the idea of conservation of protein structures and evidences the data found by simple comparative alignment.

3.7 Identification and analysis of IgE-binding epitopes

The IgE antibodies are produced by immune B cells, which in turn are stimulated by T cells responsible for recognizing the epitope in a sensitization step. To trigger the allergen inflammatory process, IgE antibodies stimulate the release of histamines. Thus, the recognition of these sequences allows for predicting the recognition capacity of IgE antibodies and whether they will potentially trigger the allergenic response (Figure 6).

Figure 6.

Summary of the epitope recognision process.

The analysis of the allergenic nature of the protein based on amino acid and dipeptide analysis composition has been used for the assessment of the above proteins. It is noticeable that the 30cases with clinically confirmed allergenic epitopes are predicted by their sequence to have an allergenic nature, as is the case of Gly m 8 (Table 8B), Ara h 13.0102, and Ara h 15.0101 (Table 8: D). Other potential allergens are Lup a 4 (Table 8A), Lup an 3 and Lup an 3.0101 (Table 8A) and Lup an delta conglutin; Pis s 3, Pis s 3.0101, Pis s 6, Pis s agglutin and Pis s albumin (Table 8B); Ara h 5, Ara h 5.0101 (Table 8C), Ara h 8, Ara h 8.0101, Ara h 8.0102 (Table 8D); as both: 43 Lup l 4 (Table 8A); Ara h 17 (Table 8D) and Cic a 3 (Table 8C).

Lupinus angustifoliusLupinus albus
Allergen nameBased on amino acid compositionBased on dipeptide compositionAllergen nameBased on amin oacid compositionBased on dipeptide composition
A.
Prediction of Lupinus allergenic character
Lup an 1Potential allergenPotential allergenLup a 1
Lup an 1.0101Lup a 4Potential allergenPotential allergen
Lup an 3Potential allergenPotential allergenLup a alpha conglutin
Lup an 3.0101Potential allergenPotential allergenLup a delta conglutinPotential allergenPotential allergen
Lup an alpha conglutinLup a gama conglutin
Lup an delta conglutinPotential allergenPotential allergenLupinus luteus
Lup an gamma conglutinLup l 4AllergenPotential allergen
Pisum sativumGlycine max
Allergen nameBased on amino acid compositionBased on dipeptide compositionAllergen nameBased on amino acid compositionBased on dipeptide composition
B.
Prediction of pea and soy allergenic character
Pis s 2Potential allergenAllergenGly m 5AllergenAllergen
Pis s 3Potential allergenPotential allergenGly m 5.0301AllergenAllergen
Pis s 3.0101Potential allergenPotential allergenGly m8AllergenAllergen
Pis s 6Potential allergenPotential allergenGly m 8.0101AllergenNo allergen
Pis s aglutinPotential allergenPotential allergen
Pis s albuminPotential allergenPotential allergen
Cicer arietinumArachis hypogaea
Allergen nameBased on amino acid compositionBased on dipeptide compositionAllergen nameBased on amino acid compositionBased on dipeptide composition
C.
Prediction of chickpea and peanut allergenic character
Cic a 1Ara h 1AllergenAllergen
Cic a 3Potential allergenAllergenAra h 1.0101AllergenAllergen
Cic a 4Potential allergenPotential allergenAra h 2
Cic a 6Ara h 2.0101
Arachis duranensisAra h 2.0201
Ara d 2Ara h 2.0202
Ara d 6Ara h 3
Arachis ipaensisAra h 3.0201
Ara i 2.0101Ara h 5Potential allergenPotential allergen
Ara i 6.0101Ara h 5.0101Potential allergenPotential allergen
Arachis hypogaeaA. hypogaea
Allergen nameBased on amino acid compositionBased on dipeptide compositionAllergen nameBased on amino acid compositionBased on dipeptide composition
D.
Prediction of peanut allergenic character
Ara h 6Ara h 11.0101
Ara h 6.0101Ara h 11.0102
Ara h 7.0101AllergenAra h 13.0102AllergenAllergen
Ara h 7.0201Ara h 14.0101
Ara h 7.0301Ara h 14.0102
Ara h 8Potential allergenPotential allergenAra h 14.0103
Ara h 8.0101Potential allergenPotential allergenAra h 15.0101AllergenAllergen
Ara h 8.0102Potential allergenPotential allergenAra h 16Allergen
Ara h 9.0101AllergenAllergenAra h 17Potential allergenAllergen
Ara h 10.0101Ara h aglutinPotential allergen

Table 8.

Allergenic legume character prediction.

The table summarizes the predictions about the allergenic potential of proteins based on the amino acid and peptide composition. The signal (−) means that the protein has clinically proven epitopes.

Other proteins assessed as ambiguous or non-allergenic even though they present bibliographic and clinical antecedents of being allergenic include Lup a gamma conglutin [34] and Lup an gamma conglutin [35] (Table 8A); Ara h 10.0101 [36], Ara h 11.0101, and Ara h 11.0102 [37]; and Ara i 2.0101 and Ara i 6.0101 [38] (Table 8C).

Gly m 5, Gly m 5.0301, and Lup a 1 have shown that the IgE epitopes found on these proteins are part of the functional barrel domains of these proteins. In Lup a 1 protein, two epitopes are located in the Cupin_1.1 domain, which is not affected by post-translational modifications; soybean proteins Gly m 5 contain an IgE-epitope inside the Cupin_1 domain, moreover Gly m 5.0301 also contains the same epitope in the same region and in different positions having no modifications. However, Gly m 5.0301 does contain epitopes directly affected by glycosidation, within the structural Cupin_1 domain, an epitope at position 351 (Table 5A,6A and 9A).

Allergen nameIgE epitopes
HRIFLADKDNNFGKLFEVKSYLQEFSRNTELHLLGFGINKDLAFPGSGERRYTARLKEG
A.
IgE epitopes shared between different legume species: Glycine max (Gly m), Lupinus albus /Lup a), Arachis hypogaea (Ara h), and Cicer arietinum (Cic a)
Gly m 570% 415-QRNFLAGEKD70% 297- NNFGKFFEIT70% 217-SYLQGFSHNI
Gly m 5.030170% 418-QRNFLAGEKD70% 300-NNFGKFFEIT70% 220-SYLQGFSHNI
Lup a 170% 286-SYFSGFSRNT80% 483-NLRLLGFGIN70% 517-KELTFPGSAE80% 456-RRYSARLSEG
Lup an 1.010180% NLRLLGFGIN70% KELTFPGSIE
Ara h 1100% HRIFLADKD90% NNFGRLFEVK90%SYQGFSRNT100% ELHLLGFGIN100% KDLAFPGSGE100%RRYTARLKEG
Ara h 1.0101100%HRIFLADKD100% NNFGKLFEVK100%SYLQEFSRNT100% ELHLLGFGIN100%KDLAFPGSGE100%RRYTARLKEG
Cic a 180% DLFLLGFGIN70%KEVAFPGSAE
Allergen nameIgE epitopes
GNIFSGFTPEFLEQAIETWNPNNQEFECAGDRRCQSQLERHASARQQWELKIQRDEDSKRELRNL
B.
IgE epitopes shared between different legume species: Lupinus albus (Lup a), Lupinus angustifolius (Lup an), Arachis duranensis (Ara d), Arachis hypogaea (Ara h), and Cicer arietinum (Cic a)
Lup a alpha conglutin66.67% GNVLSGFDDEFLEEA73.34% IETWNPKNDELRCAG
Lup an alpha conglutin66.67% GNVLSGFNDEFLEEA73.34% IETWNPKNDQLRCAG
Ara d 2100% DRRCQSQLER100%HASARQQWEL100%KIQRDEDS100% KRELRNL
Ara d 685.71% KRELMNL
Ara h 2100% DRRCQSQLER100% HASARQQWEL100% KIQRDEDS100% KRELRNL
Ara h 2.010170% DRRCQSQLER100% HASARQQWEL100% KIQRDEDS100% KRELRNL
Ara h 2.0201100% DRRCQSQLER100% HASARQQWEL100% KIQRDEDS100% KRELRNL
Ara h 2.0202100% DRRCQSQLER100% HASARQQWEL100% KIQRDEDS100% KRELRNL
Ara h 386.67% GNIFSGFTSEFLAQA100% IETWNPNNQEFECAG
Ara h 3.0201100% GNIFSGFTPEFLEQA100% IETWNPNNQEFECAG
Ara h 7.020185.71% ERELRNL
Cic a 673.33% GNIFSGFKRDFLEDA73.33% IETWNPSNKQFACAG
Allergen nameIgE epitopes
LQGRQQLRPCEQHLMQQRCDLDVEQWELQGDRRDPYSPRDPYSPSQDPYSPS
C.
IgE epitopes shared between different legume species: Arachis duranensis (Ara d) and Arachis hypogaea (Ara h)
Ara d 2100% LQGRQQ100% LRPCEQHLMQ100% QRCDLDVE100% QWELQGDR100% RDPYSP83.33% RDPYSP100% SQDPYSPS
Ara d 680% LKPCEQHIMQ87.5% QRCDLDVS
Ara h 2100% LQGRQQ100% LRPCEQHLMQ87.5% QRCDLEVE100% QWELQGDR100% RDPYSP83.3% QDPYSP100% SQDPYSPS
Ara h 2.0101100% LQGRQQ100% LRPCEQHLMQ87.5% QRCDLEVE100% QWELQGDR100% RDPYSP83.3% QDPYSP100% SQDPYSPS
Ara h 2.0201100% LQGRQQ100% LRPCEQHLMQ87.5% QRCDLEVE100% QWELQGDR100% RDPYSP83.3% QDPYSP100% SQDPYSPS
Ara h 2.0202100% LQGRQQ100% LRPCEQHLMQ87.5% QRCDLEVE100% QWELQGDR100% RDPYSP83.3% QDPYSP100% SQDPYSPS
Ara h 6.010187.5% QRCDLDVS
Ara h 7.020170% LRPCEEHIRQ
Ara h 7.030170% LRPCEEHIRQ
D.
IgE epitopes shared between different legume species: Arachis duranensis (Ara d) and A. hypogaea (Ara h)
Ara d 2100% LQGRQQ100% LRPCEQHLMQ100% QRCDLDVE100% QWELQGDR100% RDPYSP83.33% RDPYSP100% SQDPYSPS
Ara d 680% LKPCEQHIMQ87.5% QRCDLDVS
Ara h 2100% LQGRQQ100% LRPCEQHLMQ87.5% QRCDLEVE100% QWELQGDR100% RDPYSP83.3% QDPYSP100% SQDPYSPS
Ara h 2.0101100% LQGRQQ100% LRPCEQHLMQ87.5% QRCDLEVE100% QWELQGDR100% RDPYSP83.3% QDPYSP100% SQDPYSPS
Ara h 2.0201100% LQGRQQ100% LRPCEQHLMQ87.5% QRCDLEVE100% QWELQGDR100% RDPYSP83.3% QDPYSP100% SQDPYSPS
Ara h 2.0202100% LQGRQQ100% LRPCEQHLMQ87.5% QRCDLEVE100% QWELQGDR100% RDPYSP83.3% QDPYSP100% SQDPYSPS
Ara h 6.010187.5% QRCDLDVS
Ara h 7.020170% LRPCEEHIRQ
Ara h 7.030170% LRPCEEHIRQ

Table 9.

IgE epitopes shared between different legume species.

This table summarizes the IgE epitopes clinically confirmed in different species, and the accuracy percentage of these epitopes found according to the protein sequence.

The clinically proven epitopes found in the sequence analysis allowed us to observe how many and to what extent IgE epitopes are shared between proteins of different species and to assess potential cross-reactivity. According to the results, some of the candidate species and proteins for cross-reactivity with soybean (G. max) are the peanut (A. hypogaea) with three IgE epitopes commonly shared; lupin (L. albus) with one epitope in common (Table 9A). These findings are supported by bibliographic reports [38]. It is also found that L. albus shares four epitopes with A. hypogea and L. angustifolius (Table 9A), and other two with A. hypogea. Looking at other cases, it is observed that in close species such as peanut, species such as A. duranensis and A. hypogea shared ten common epitopes (Table 9B,C), similarly to Lupinus finding four epitopes in common (Table 9A,B).

In addition, shared T-cell epitopes have been found among species that do not include soybean such as L. albus and L. angustifolia (Table 9: AB), but not found in L. luteus; A. hypogaea (Table 9A-D), and A. duranensis (Table 9B-D); C. arietinum (Table 9A,B); and P. sativum (Table 9A). These epitopes have been identified as relevant epitopes in previous studies on sensitizations between allergens of different species with similar structure and sequence leading to the development of allergic cross-reactions [38, 39].

An interesting fact is that different isoforms of the same protein may or may not present the same IgE epitope and, in the case of having it, it does not necessarily have the same degree of similarity. Establishing a relationship with the information obtained in the alignments, we can conclude that the small differences observed in the sequence between isoforms of the same protein can be key to conformation and epitopes presence (Table 10).

Allergen nameIgE epitopes
DITNPINLREKESHFVSARPEQEERGQRRWVTVRGGLRILSPDRK
IgE epitopes shared only by same legume species: Arachis hypogaea (Ara h)
Ara h 190% DITNPINLRD90% RESHFVSARP90% EQEERGQRR
Ara h 1.0101100%DITNPINLRE100%KESHFVSARP100%EQEERGQRRW
Ara h 393,345%VTCRGGLRILSPDRK
Ara h 3.020186.67% VTVRGGLRILSPDRK

Table 10.

IgE epitopes shared only by same legume species.

This table summarizes the IgE epitopes clinically confirmed in different species, and the accuracy percentage of these epitopes found according to the protein sequence.

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4. Conclusions

This chapter presented a study of functional and allergenic features of legume seed proteins.

Analysis of allergenic legume proteins legume as well as all available isoforms allowed for extracting shared epitopes that can be linked to cross-reactivity processes among the eight studied species (G. max, A. hypogaea, L. albus, L. angustifolius, A. duranensis, C. arietinum, P. sativum, and L. culinaris). Shared epitopes were not found with soybean or with the rest of the legume allergens examined from A. duranensis.

Small differences in the amino acid sequences (less than 1%) of the same allergen isoforms implied important changes in epitopic conformation and sequences of T-cell and IgE recognizable epitopes. Small differences in amino sequences of isoforms from the same inferred changes over 2D and 3D structure conformation that may affect functional protein domains. Post-translational modifications allowed identification of possible phosphorylation, glycosylation, carboxylation, methylation, nitrosylation, and nitration sites in protein functional domains, near or directly located in different type of epitopes with potential influence in allergenic response.

Primary sequence alignments together with three-dimensional protein modeling allowed to study the conservation of proteins as conglutin gamma proteins among different Lupinus. species, assessing also their potential allergenicity.

The changes described close to the sequence or related to spatial distribution of the epitopes may involve potential alterations on protein allergenicity.

Obtaining reliable clinical data on legume allergies in developing countries could be helpful in clarifying whether the increase in food allergies is actually due to poor dietary habits and increasing industrialization processes.

Further studies on the characterization of more allergenic proteins, including isoforms of major allergens already described, not only sequential but also three-dimensional conformational epitopes, can be a great advancement for the prevention of cross-reactivity and the improvement of knowledge of allergies produced by legumes, which in turn could promote the introduction of this food as a substitute for other foods of lower nutritional quality and with greater environmental impact.

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Acknowledgments

This study has been partially funded by The Spanish Ministry of Economy, Industry and Competitiveness through the grants Ref.: RYC-2014-2016,536 (Ramon y Cajal Research Program) to JCJ-L; and Ministry of Health and Families, Andalusian government. Funding for I + D + i in biomedical research and health sciences in Andalusia, grant Ref.: PI-0450-2019.

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Conflicts of interest

The authors have declared that no competing interests exist.

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Abbreviations

LTPLipid Transfer Protein
3Dthree-dimensional
PRproteins Pathogenesis-related proteins

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Written By

Andrea Roman-Mateo, Esther Rodriguez-de Haro, Jose M. Berral-Hens, Sonia Morales-Santana and Jose C. Jimenez-Lopez

Submitted: 24 June 2022 Reviewed: 08 August 2022 Published: 06 October 2022