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Comparative and evolutionary analysis of major peanut allergen gene families.

Ratnaparkhe MB, Lee TH, Tan X, Wang X, Li J, Kim C, Rainville LK, Lemke C, Compton RO, Robertson J, Gallo M, Bertioli DJ, Paterson AH - Genome Biol Evol (2014)

Bottom Line: These regions were also compared with orthologs in many additional dicot plant species to help clarify the timing of evolutionary events.Our analysis indicates differences in conserved motifs in allergen proteins and in the promoter regions of the allergen-encoding genes.Phylogenetic analysis and genomic organization studies provide new insights into the evolution of the major peanut allergen-encoding genes.

View Article: PubMed Central - PubMed

Affiliation: Plant Genome Mapping Laboratory, University of Georgia Directorate of Soybean Research, Indian Council of Agriculture Research (ICAR), Indore, (M.P.), India.

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Related in: MedlinePlus

Multiple sequence alignment of Arah3 and Arah2 sequences from peanut. (a) Amino acid sequences of sixteen Arah3 and two 11S proteins were aligned to find conserved epitopes. Epitopes 1 and 2 are conserved among the 16 Arah3 sequences however absent from two 11S storage protein genes (44O16.04 and 259D10.22). Epitope 3 is shared by all the Arah3 and two 11S storage proteins with minor differences in amino acid residues. Epitope 4 is not conserved and is deleted in several Arah3 genes. Genebank accession numbers of Arah3 homologs are: Gly1: AAG01363.1, Ahy1: AAU21490.1, Ahy2: AAU21491.1, Ahy-4: AAW56067.1, Arah3_iso: ACH91862.1, Arah3/arah4: AAM46958.1, arachin_6: ABL14270.1, Iso-ara: ABI17154.1, Arah3: ADQ53859.1, Glycinin: AAC63045.1. (b) Multiple sequence alignment of Arah2 and Arah6 sequences from peanut. Amino acid sequences of 16 allergen proteins related to Arah2 and Arah6 were also aligned to identify the conserved epitopes. Epitope 10 is shared by both Arah2 and Arah6, whereas epitopes (1–9) are conserved only in Arah2. Genebank accessions numbers: Cong_ARAHY: AAU21495.1, Conglutin: AAW56068.1, Conglutin2: AF366561.1, Conglutin8: ABL14269.1, Arah6: AAD56337.1, Arah6_2: gi159163254, Arah6_3: AAW34231.1, Conglutin_d: ABQ96212.1, Arah2isoform: AAM78596.1, 2Sprotein1: GI:57669905, Conglutin_d2: ABW36075.1, Ara: AY848699.1, Conglutin d3: ABW36069.1. Epitopes, conserved motifs, and amino acids are highlighted.
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evu189-F10: Multiple sequence alignment of Arah3 and Arah2 sequences from peanut. (a) Amino acid sequences of sixteen Arah3 and two 11S proteins were aligned to find conserved epitopes. Epitopes 1 and 2 are conserved among the 16 Arah3 sequences however absent from two 11S storage protein genes (44O16.04 and 259D10.22). Epitope 3 is shared by all the Arah3 and two 11S storage proteins with minor differences in amino acid residues. Epitope 4 is not conserved and is deleted in several Arah3 genes. Genebank accession numbers of Arah3 homologs are: Gly1: AAG01363.1, Ahy1: AAU21490.1, Ahy2: AAU21491.1, Ahy-4: AAW56067.1, Arah3_iso: ACH91862.1, Arah3/arah4: AAM46958.1, arachin_6: ABL14270.1, Iso-ara: ABI17154.1, Arah3: ADQ53859.1, Glycinin: AAC63045.1. (b) Multiple sequence alignment of Arah2 and Arah6 sequences from peanut. Amino acid sequences of 16 allergen proteins related to Arah2 and Arah6 were also aligned to identify the conserved epitopes. Epitope 10 is shared by both Arah2 and Arah6, whereas epitopes (1–9) are conserved only in Arah2. Genebank accessions numbers: Cong_ARAHY: AAU21495.1, Conglutin: AAW56068.1, Conglutin2: AF366561.1, Conglutin8: ABL14269.1, Arah6: AAD56337.1, Arah6_2: gi159163254, Arah6_3: AAW34231.1, Conglutin_d: ABQ96212.1, Arah2isoform: AAM78596.1, 2Sprotein1: GI:57669905, Conglutin_d2: ABW36075.1, Ara: AY848699.1, Conglutin d3: ABW36069.1. Epitopes, conserved motifs, and amino acids are highlighted.

Mentions: Amino acid sequences of all sixteen Arah3 and two 11S proteins were aligned to find conserved epitopes (fig. 10a). A previous study using a recombinant Arah3 discovered four IgE epitopes containing critical amino acid residues. The number of patients sera recognizing epitope 3 is significantly larger than the number recognizing epitopes 1, 2, and 4 (Rabjohn et al. 1999). We found that epitopes 1 and 2 are conserved among the 16 Arah3 sequences but absent from two 11S storage protein genes (44O16.07 and 259D10.22). Epitope 3 is shared by all the Arah3 and two 11S storage proteins with minor differences in amino acid residues. Epitope 4 is not conserved and is deleted in several Arah3. According to the identified epitope 4, it is composed of 15 amino acid residues (DEDEYEYDEEDRRRG), recognized by serum IgE from 38% of peanut patients tested and the amino acid residues, particularly the sixth residue, glutamic acid (E), are critical for IgE-binding of epitope 4. Deletions and amino acid variations were also observed in signal peptides, flexible loops and flexible regions of Arah3 and related protein sequences. Mutation analysis of the epitopes reveals that single or critical amino acid changes within these peptides can lead to a reduction or loss of IgE-binding ability, and consequently can affect the allergen’s immunogenicity (Rabjohn et al. 1999). Arah3 and related proteins belong to the 11S globulin storage protein family that is characterized by three common features. The first one is that they contain an acidic and basic chain separated by a conserved Asn–Gly (N–G) peptide bond. Second, the formation of intra and interdisulfide bonds is observed due to four conserved cysteine residue. Third, an Asn–Gln (N–Q) peptide bond is present that serves as a potential proteolytic cleavage site (fig. 10a). Sixteen allergen proteins related to Arah2 and Arah6 were also aligned to identify the conserved epitopes. Epitope 10 is shared by both Arah2 and Arah6, whereas epitopes 1–9 are conserved only in Arah2 (fig. 10b).Fig. 10.—


Comparative and evolutionary analysis of major peanut allergen gene families.

Ratnaparkhe MB, Lee TH, Tan X, Wang X, Li J, Kim C, Rainville LK, Lemke C, Compton RO, Robertson J, Gallo M, Bertioli DJ, Paterson AH - Genome Biol Evol (2014)

Multiple sequence alignment of Arah3 and Arah2 sequences from peanut. (a) Amino acid sequences of sixteen Arah3 and two 11S proteins were aligned to find conserved epitopes. Epitopes 1 and 2 are conserved among the 16 Arah3 sequences however absent from two 11S storage protein genes (44O16.04 and 259D10.22). Epitope 3 is shared by all the Arah3 and two 11S storage proteins with minor differences in amino acid residues. Epitope 4 is not conserved and is deleted in several Arah3 genes. Genebank accession numbers of Arah3 homologs are: Gly1: AAG01363.1, Ahy1: AAU21490.1, Ahy2: AAU21491.1, Ahy-4: AAW56067.1, Arah3_iso: ACH91862.1, Arah3/arah4: AAM46958.1, arachin_6: ABL14270.1, Iso-ara: ABI17154.1, Arah3: ADQ53859.1, Glycinin: AAC63045.1. (b) Multiple sequence alignment of Arah2 and Arah6 sequences from peanut. Amino acid sequences of 16 allergen proteins related to Arah2 and Arah6 were also aligned to identify the conserved epitopes. Epitope 10 is shared by both Arah2 and Arah6, whereas epitopes (1–9) are conserved only in Arah2. Genebank accessions numbers: Cong_ARAHY: AAU21495.1, Conglutin: AAW56068.1, Conglutin2: AF366561.1, Conglutin8: ABL14269.1, Arah6: AAD56337.1, Arah6_2: gi159163254, Arah6_3: AAW34231.1, Conglutin_d: ABQ96212.1, Arah2isoform: AAM78596.1, 2Sprotein1: GI:57669905, Conglutin_d2: ABW36075.1, Ara: AY848699.1, Conglutin d3: ABW36069.1. Epitopes, conserved motifs, and amino acids are highlighted.
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evu189-F10: Multiple sequence alignment of Arah3 and Arah2 sequences from peanut. (a) Amino acid sequences of sixteen Arah3 and two 11S proteins were aligned to find conserved epitopes. Epitopes 1 and 2 are conserved among the 16 Arah3 sequences however absent from two 11S storage protein genes (44O16.04 and 259D10.22). Epitope 3 is shared by all the Arah3 and two 11S storage proteins with minor differences in amino acid residues. Epitope 4 is not conserved and is deleted in several Arah3 genes. Genebank accession numbers of Arah3 homologs are: Gly1: AAG01363.1, Ahy1: AAU21490.1, Ahy2: AAU21491.1, Ahy-4: AAW56067.1, Arah3_iso: ACH91862.1, Arah3/arah4: AAM46958.1, arachin_6: ABL14270.1, Iso-ara: ABI17154.1, Arah3: ADQ53859.1, Glycinin: AAC63045.1. (b) Multiple sequence alignment of Arah2 and Arah6 sequences from peanut. Amino acid sequences of 16 allergen proteins related to Arah2 and Arah6 were also aligned to identify the conserved epitopes. Epitope 10 is shared by both Arah2 and Arah6, whereas epitopes (1–9) are conserved only in Arah2. Genebank accessions numbers: Cong_ARAHY: AAU21495.1, Conglutin: AAW56068.1, Conglutin2: AF366561.1, Conglutin8: ABL14269.1, Arah6: AAD56337.1, Arah6_2: gi159163254, Arah6_3: AAW34231.1, Conglutin_d: ABQ96212.1, Arah2isoform: AAM78596.1, 2Sprotein1: GI:57669905, Conglutin_d2: ABW36075.1, Ara: AY848699.1, Conglutin d3: ABW36069.1. Epitopes, conserved motifs, and amino acids are highlighted.
Mentions: Amino acid sequences of all sixteen Arah3 and two 11S proteins were aligned to find conserved epitopes (fig. 10a). A previous study using a recombinant Arah3 discovered four IgE epitopes containing critical amino acid residues. The number of patients sera recognizing epitope 3 is significantly larger than the number recognizing epitopes 1, 2, and 4 (Rabjohn et al. 1999). We found that epitopes 1 and 2 are conserved among the 16 Arah3 sequences but absent from two 11S storage protein genes (44O16.07 and 259D10.22). Epitope 3 is shared by all the Arah3 and two 11S storage proteins with minor differences in amino acid residues. Epitope 4 is not conserved and is deleted in several Arah3. According to the identified epitope 4, it is composed of 15 amino acid residues (DEDEYEYDEEDRRRG), recognized by serum IgE from 38% of peanut patients tested and the amino acid residues, particularly the sixth residue, glutamic acid (E), are critical for IgE-binding of epitope 4. Deletions and amino acid variations were also observed in signal peptides, flexible loops and flexible regions of Arah3 and related protein sequences. Mutation analysis of the epitopes reveals that single or critical amino acid changes within these peptides can lead to a reduction or loss of IgE-binding ability, and consequently can affect the allergen’s immunogenicity (Rabjohn et al. 1999). Arah3 and related proteins belong to the 11S globulin storage protein family that is characterized by three common features. The first one is that they contain an acidic and basic chain separated by a conserved Asn–Gly (N–G) peptide bond. Second, the formation of intra and interdisulfide bonds is observed due to four conserved cysteine residue. Third, an Asn–Gln (N–Q) peptide bond is present that serves as a potential proteolytic cleavage site (fig. 10a). Sixteen allergen proteins related to Arah2 and Arah6 were also aligned to identify the conserved epitopes. Epitope 10 is shared by both Arah2 and Arah6, whereas epitopes 1–9 are conserved only in Arah2 (fig. 10b).Fig. 10.—

Bottom Line: These regions were also compared with orthologs in many additional dicot plant species to help clarify the timing of evolutionary events.Our analysis indicates differences in conserved motifs in allergen proteins and in the promoter regions of the allergen-encoding genes.Phylogenetic analysis and genomic organization studies provide new insights into the evolution of the major peanut allergen-encoding genes.

View Article: PubMed Central - PubMed

Affiliation: Plant Genome Mapping Laboratory, University of Georgia Directorate of Soybean Research, Indian Council of Agriculture Research (ICAR), Indore, (M.P.), India.

Show MeSH
Related in: MedlinePlus