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Structural Basis for the IgE-Binding Cross-Reacting Epitopic Peptides of Cup s 3, a PR-5 Thaumatin-like Protein Allergen from Common Cypress (Cupressus sempervirens) Pollen

Barre, Annick, Sénéchal, Hélène, Nguyen, Christophe, Granier, Claude, Poncet, Pascal, Rougé, Pierre·2023·Allergies
DOI 10.3390/allergies3010002
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Abstract

The present work was aimed at identifying the IgE-binding epitopic regions on the surface of the Cup s 3 allergen from the common cypress Cupressus sempervirens, that are possibly involved in the IgE-binding cross-reactivity reported between Cupressaceae species. Three main IgE-binding epitopic regions were mapped on the molecular surface of Cup s 3, the PR-5 thaumatin-like allergen of common cypress Cupressus sempervirens. They correspond to exposed areas containing either electropositive (R, K) or electronegative (D, E) residues. A coalescence occurs between epitopes #1 and #2, that creates an extended IgE-binding regions on the surface of the allergen. Epitope #3 contains a putative N-glycosylation site which is actually glycosylated and could therefore comprise a glycotope. However, most of the allergenic potency of Cup s 3 depends on non-glycosylated epitopic peptides. The corresponding regions of thaumatin-like allergens from other closely related Cupressaceae (Cryptomeria, Juniperus, Thuja) exhibit a very similar conformation that should account for the IgE-binding cross-reactivity observed among the Cupressaceae allergens.

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Figure 1 ( A ). Ribbon diagram of the Cup s 3 model showing the overall organization of the allergen in three distinct domains labeled I, II, and III, and the N - glycan chain (G) attached to residue Asn162 in domain II, represented in CPK colored cyan. ( B ). Molecular surface of Cup s 3 showing the electrostatic potentials patches. The electronegatively charged groove is outlined in yellow. ( C , D ). Mapping of the sequential IgE-binding epitopes 1 (colored pink), 2 (colored blue), and 3 (colored green) on the front face ( C ) and the back face ( D ) of the ribbon diagram of Cup s 3. ( E , F ). Mapping of the sequential IgE-binding epitopes 1 (colored pink), #2 (colored blue) and 3 (colored green) on the front face ( E ) and the back face ( F ) of the molecular surface of Cup s 3. Epitope 2 consists of two separate patches on the molecular surface of the TLP allergen. Note the coalescence of epitope 1 with both patches of epitope 2. Figure 1. ( A ). Ribbon diagram of the Cup s 3 model showing the overall organization of the allergen in three distinct domains labeled I, II, and III, and the N - glycan chain (G) attached to residue Asn162 in domain II, represented in CPK colored cyan. ( B ). Molecular surface of Cup s 3 showing the electrostatic potentials patches. The electronegatively charged groove is outlined in yellow. ( C , D ). Mapping of the sequential IgE-binding epitopes 1 (colored pink), 2 (colored blue), and 3 (colored green) on the front face ( C ) and the back face ( D ) of the ribbon diagram of Cup s 3. ( E , F ). Mapping of the sequential IgE-binding epitopes 1 (colored pink), #2 (colored blue) and 3 (colored green) on the front face ( E ) and the back face ( F ) of the molecular surface of Cup s 3. Epitope 2 consists of two separate patches on the molecular surface of the TLP allergen. Note the coalescence of epitope 1 with both patches of epitope 2.
Figure 1 ( A ). Ribbon diagram of the Cup s 3 model showing the overall organization of the allergen in three distinct domains labeled I, II, and III, and the N - glycan chain (G) attached to residue Asn162 in domain II, represented in CPK colored cyan. ( B ). Molecular surface of Cup s 3 showing the electrostatic potentials patches. The electronegatively charged groove is outlined in yellow. ( C , D ). Mapping of the sequential IgE-binding epitopes 1 (colored pink), 2 (colored blue), and 3 (colored green) on the front face ( C ) and the back face ( D ) of the ribbon diagram of Cup s 3. ( E , F ). Mapping of the sequential IgE-binding epitopes 1 (colored pink), #2 (colored blue) and 3 (colored green) on the front face ( E ) and the back face ( F ) of the molecular surface of Cup s 3. Epitope 2 consists of two separate patches on the molecular surface of the TLP allergen. Note the coalescence of epitope 1 with both patches of epitope 2. Figure 1. ( A ). Ribbon diagram of the Cup s 3 model showing the overall organization of the allergen in three distinct domains labeled I, II, and III, and the N - glycan chain (G) attached to residue Asn162 in domain II, represented in CPK colored cyan. ( B ). Molecular surface of Cup s 3 showing the electrostatic potentials patches. The electronegatively charged groove is outlined in yellow. ( C , D ). Mapping of the sequential IgE-binding epitopes 1 (colored pink), 2 (colored blue), and 3 (colored green) on the front face ( C ) and the back face ( D ) of the ribbon diagram of Cup s 3. ( E , F ). Mapping of the sequential IgE-binding epitopes 1 (colored pink), #2 (colored blue) and 3 (colored green) on the front face ( E ) and the back face ( F ) of the molecular surface of Cup s 3. Epitope 2 consists of two separate patches on the molecular surface of the TLP allergen. Note the coalescence of epitope 1 with both patches of epitope 2.CC-BY · From the PDF
Table 2. Multiple amino-acid sequence alignments of seven thaumatin-like proteins from Cupressaceae pollen. The sequence of Jun v 3 is incomplete in the NCBI databank. Grey boxes correspond to the absence of insertion which are only present in TLP-Cj and TLP-To. Cystein residues are in red and red dotted lines indicate the eight disulfide bridges. Table 2. Multiple amino-acid sequence alignments of seven thaumatin-like proteins from Cupressaceae pollen. The sequence of Jun v 3 is incomplete in the NCBI databank. Grey boxes correspond to the absence of insertion which are only present in TLP-Cj and TLP-To. Cystein residues are in red and red dotted lines indicate the eight disulfide bridges.
Table 2. Multiple amino-acid sequence alignments of seven thaumatin-like proteins from Cupressaceae pollen. The sequence of Jun v 3 is incomplete in the NCBI databank. Grey boxes correspond to the absence of insertion which are only present in TLP-Cj and TLP-To. Cystein residues are in red and red dotted lines indicate the eight disulfide bridges. Table 2. Multiple amino-acid sequence alignments of seven thaumatin-like proteins from Cupressaceae pollen. The sequence of Jun v 3 is incomplete in the NCBI databank. Grey boxes correspond to the absence of insertion which are only present in TLP-Cj and TLP-To. Cystein residues are in red and red dotted lines indicate the eight disulfide bridges.CC-BY · From the PDF
Figure 2 ( A ). Amino acid sequences of the 62 overlapping peptides used in the SPOT technique. Epitope 1 (pink background), 2 (purple background), and 3 (green background) are indicated. Cystein residues are in red. Peptide numbering in red. ( BA , BB ). Examples of SPOT results obtained with two different sera from cypress allergic patients used as a probe. ( BC ). Sequential IgE-binding epitopic stretches 1, 2, and 3 deduced from the stained spots are indicated in colored boxed white Figure 2. ( A ). Amino acid sequences of the 62 overlapping peptides used in the SPOT technique. Epitope 1 (pink background), 2 (purple background), and 3 (green background) are indicated. Cystein residues are in red. Peptide numbering in red. ( BA , BB ). Examples of SPOT results obtained with two different sera from cypress allergic patients used as a probe. ( BC ). Sequential IgE-binding epitopic stretches 1, 2, and 3 deduced from the stained spots are indicated in colored boxed white letters along the amino acid sequence of Cup s 3.
Figure 2 ( A ). Amino acid sequences of the 62 overlapping peptides used in the SPOT technique. Epitope 1 (pink background), 2 (purple background), and 3 (green background) are indicated. Cystein residues are in red. Peptide numbering in red. ( BA , BB ). Examples of SPOT results obtained with two different sera from cypress allergic patients used as a probe. ( BC ). Sequential IgE-binding epitopic stretches 1, 2, and 3 deduced from the stained spots are indicated in colored boxed white Figure 2. ( A ). Amino acid sequences of the 62 overlapping peptides used in the SPOT technique. Epitope 1 (pink background), 2 (purple background), and 3 (green background) are indicated. Cystein residues are in red. Peptide numbering in red. ( BA , BB ). Examples of SPOT results obtained with two different sera from cypress allergic patients used as a probe. ( BC ). Sequential IgE-binding epitopic stretches 1, 2, and 3 deduced from the stained spots are indicated in colored boxed white letters along the amino acid sequence of Cup s 3.CC-BY · From the PDF
Figure 3 ELISA inhibition of the interaction between cypress pollen e in the presence of 2 mM of synthetic peptides corresponding 9PGGGKRLDQ27), epitope 2 (peptide 2: 45RFWGRTGIT53), Figure 3. ELISA inhibition of the interaction between cypress pollen extract and IgE from CPAPs, in the presence of 2 mM of synthetic peptides corresponding to epitope 1 (peptide 1: 9PGGGKRLDQ27), epitope 2 (peptide 2: 45RFWGRTGIT53), epitope 3 (peptide 3: 161TNYSKIFKN169), and an equimolar mixture of the three peptides 1, 2, and 3 (peptides 1 + 2 + 3). All values are the mean ± s.d. of three separate measurements performed in the same experimental conditions.
Figure 3 ELISA inhibition of the interaction between cypress pollen e in the presence of 2 mM of synthetic peptides corresponding 9PGGGKRLDQ27), epitope 2 (peptide 2: 45RFWGRTGIT53), Figure 3. ELISA inhibition of the interaction between cypress pollen extract and IgE from CPAPs, in the presence of 2 mM of synthetic peptides corresponding to epitope 1 (peptide 1: 9PGGGKRLDQ27), epitope 2 (peptide 2: 45RFWGRTGIT53), epitope 3 (peptide 3: 161TNYSKIFKN169), and an equimolar mixture of the three peptides 1, 2, and 3 (peptides 1 + 2 + 3). All values are the mean ± s.d. of three separate measurements performed in the same experimental conditions.CC-BY · From the PDF
Image 5
CC-BY · From the PDF
Figure 5 Unrooted phylogenetic tree built up from the multiple alignment of thaumatin-like proteins of Actinidia deliciosa (Act d 2), Arabidopsis thaliana (Arab th), Atriplex numularia (Atri nu), Avena sativa (Aven sa), Benincasa hispida (Beni hi), Beta vulgaris (Beta vu), Brassica juncea (Bras ju), Brassica oleracea (Bras ol), Brassica rapa (Bras ra), Capsicum annuum (Cap a 1), Castanea sativa (Cas s TLP), Chenopodium quinoa (Che qu), Cicer arietinum (Cice ar), Cryptomeria japonica (TLP-Cj), Cupressus arizonica (TLP-Ca), Cupressus sempervirens (Cup s 3), Fragaria x ananassa (Frag an), Ficus awkeotsang (Ficu aw), Glycine max (Glyc ma), Helianthus annuus (Heli an), Hordeum vulgare (Hord vu), Juniperus ashei (Jun a 3), Juniperus rigida (TLP-Jr), Linum usitatissimum (Linu us), Lycopersicum esculentum (Lyco es), Malus domestica (Mal d 2), Musa acuminata (Mus a 4), Nicotiana glauca (Nico gl), Nicotiana tabacum (osmotin), Petunia hybrida (Petu hy), Prunus avium (Pru av 2), Prunus persica (Pru p 2), Pseudotsuga menziesii (Pseu me), Pyrus pyriformis (Pyr py 2), Sambucus nigra (Samb ni), Sequoia sempervirens (TLPSs), Solanum commersonii (Sola co), Solanum dulcamara (Sola du), Solanum nigrum (Sola ni), Solanum phyreja (Sola ph), Solanum tuberosum (Sola tu), Taxodium distichum (TLP-Txm), Thaumatococcus daniellii (thaumatin), Thuja occidentalis (TLP-To), Vitis riparia (Viti ri), Vitis vinifera (Vit v TLP), Zea mays (zeamatin). Thaumatin-like proteins belonging to the same plant family are boxed and the different family boxes are labeled and differently colored. Figure 5. Unrooted phylogenetic tree built up from the multiple alignment of thaumatin-like proteins of Actinidia deliciosa (Act d 2), Arabidopsis thaliana (Arab th), Atriplex numularia (Atri nu), Avena sativa (Aven sa), Benincasa hispida (Beni hi), Beta vulgaris (Beta vu), Brassica juncea (Bras ju), Brassica oleracea (Bras ol), Brassica rapa (Bras ra), Capsicum annuum (Cap a 1), Castanea sativa (Cas s TLP), Chenopodium quinoa (Che qu), Cicer arietinum (Cice ar), Cryptomeria japonica (TLP-Cj), Cupressus arizonica (TLP-Ca), Cupressus sempervirens (Cup s 3), Fragaria × ananassa (Frag an), Ficus awkeotsang (Ficu aw), Glycine max (Glyc ma), Helianthus annuus (Heli an), Hordeum vulgare (Hord vu), Juniperus ashei (Jun a 3), Juniperus rigida (TLP-Jr), Linum usitatissimum (Linu us), Lycopersicum esculentum (Lyco es), Malus domestica (Mal d 2), Musa acuminata (Mus a 4), Nicotiana glauca (Nico gl), Nicotiana tabacum (osmotin), Petunia hybrida (Petu hy), Prunus avium (Pru av 2), Prunus persica (Pru p 2), Pseudotsuga menziesii (Pseu me), Pyrus pyriformis (Pyr py 2), Sambucus nigra (Samb ni), Sequoia sempervirens (TLP-Ss), Solanum commersonii (Sola co), Solanum dulcamara (Sola du), Solanum nigrum (Sola ni), Solanum phyreja (Sola ph), Solanum tuberosum (Sola tu), Taxodium distichum (TLP-Txm), Thaumatococcus daniellii (thaumatin), Thuja occidentalis (TLP-To), Vitis riparia (Viti ri), Vitis vinifera (Vit v TLP), Zea mays (zeamatin). Thaumatinlike proteins belonging to the same plant family are boxed and the different family boxes are labeled and differently colored.
Figure 5 Unrooted phylogenetic tree built up from the multiple alignment of thaumatin-like proteins of Actinidia deliciosa (Act d 2), Arabidopsis thaliana (Arab th), Atriplex numularia (Atri nu), Avena sativa (Aven sa), Benincasa hispida (Beni hi), Beta vulgaris (Beta vu), Brassica juncea (Bras ju), Brassica oleracea (Bras ol), Brassica rapa (Bras ra), Capsicum annuum (Cap a 1), Castanea sativa (Cas s TLP), Chenopodium quinoa (Che qu), Cicer arietinum (Cice ar), Cryptomeria japonica (TLP-Cj), Cupressus arizonica (TLP-Ca), Cupressus sempervirens (Cup s 3), Fragaria x ananassa (Frag an), Ficus awkeotsang (Ficu aw), Glycine max (Glyc ma), Helianthus annuus (Heli an), Hordeum vulgare (Hord vu), Juniperus ashei (Jun a 3), Juniperus rigida (TLP-Jr), Linum usitatissimum (Linu us), Lycopersicum esculentum (Lyco es), Malus domestica (Mal d 2), Musa acuminata (Mus a 4), Nicotiana glauca (Nico gl), Nicotiana tabacum (osmotin), Petunia hybrida (Petu hy), Prunus avium (Pru av 2), Prunus persica (Pru p 2), Pseudotsuga menziesii (Pseu me), Pyrus pyriformis (Pyr py 2), Sambucus nigra (Samb ni), Sequoia sempervirens (TLPSs), Solanum commersonii (Sola co), Solanum dulcamara (Sola du), Solanum nigrum (Sola ni), Solanum phyreja (Sola ph), Solanum tuberosum (Sola tu), Taxodium distichum (TLP-Txm), Thaumatococcus daniellii (thaumatin), Thuja occidentalis (TLP-To), Vitis riparia (Viti ri), Vitis vinifera (Vit v TLP), Zea mays (zeamatin). Thaumatin-like proteins belonging to the same plant family are boxed and the different family boxes are labeled and differently colored. Figure 5. Unrooted phylogenetic tree built up from the multiple alignment of thaumatin-like proteins of Actinidia deliciosa (Act d 2), Arabidopsis thaliana (Arab th), Atriplex numularia (Atri nu), Avena sativa (Aven sa), Benincasa hispida (Beni hi), Beta vulgaris (Beta vu), Brassica juncea (Bras ju), Brassica oleracea (Bras ol), Brassica rapa (Bras ra), Capsicum annuum (Cap a 1), Castanea sativa (Cas s TLP), Chenopodium quinoa (Che qu), Cicer arietinum (Cice ar), Cryptomeria japonica (TLP-Cj), Cupressus arizonica (TLP-Ca), Cupressus sempervirens (Cup s 3), Fragaria × ananassa (Frag an), Ficus awkeotsang (Ficu aw), Glycine max (Glyc ma), Helianthus annuus (Heli an), Hordeum vulgare (Hord vu), Juniperus ashei (Jun a 3), Juniperus rigida (TLP-Jr), Linum usitatissimum (Linu us), Lycopersicum esculentum (Lyco es), Malus domestica (Mal d 2), Musa acuminata (Mus a 4), Nicotiana glauca (Nico gl), Nicotiana tabacum (osmotin), Petunia hybrida (Petu hy), Prunus avium (Pru av 2), Prunus persica (Pru p 2), Pseudotsuga menziesii (Pseu me), Pyrus pyriformis (Pyr py 2), Sambucus nigra (Samb ni), Sequoia sempervirens (TLP-Ss), Solanum commersonii (Sola co), Solanum dulcamara (Sola du), Solanum nigrum (Sola ni), Solanum phyreja (Sola ph), Solanum tuberosum (Sola tu), Taxodium distichum (TLP-Txm), Thaumatococcus daniellii (thaumatin), Thuja occidentalis (TLP-To), Vitis riparia (Viti ri), Vitis vinifera (Vit v TLP), Zea mays (zeamatin). Thaumatinlike proteins belonging to the same plant family are boxed and the different family boxes are labeled and differently colored.CC-BY · From the PDF

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Authors
Barre, A., Sénéchal, H., Nguyen, C., Granier, C., Poncet, P., & Rougé, P.
Affiliations
  • UMR 152 PharmaDev, Research and Development Institute, Paul Sabatier University, 35 Chemin des Maraîchers, CEDEX 09, 31062 Toulouse, France
  • Allergy & Environment Research Team, Biochemistry Department, Armand Trousseau Children Hospital, AP-HP, 26 Avenue Dr Arnold Netter, 75571 Paris, France
  • Institut des Biomolécules Max Mousseron CNRS, Faculté de Pharmacie, 15 Avenue Charles Flahault, BP 14491, CEDEX 5, 34093 Montpellier, France
  • Sys2Diag UMR 9005 CNRS/ALCEDIAG Complex System Modeling and Engineering for Diagnosis, Cap Delta/Parc Euromédecine, 1682 rue de la Valsière CS 61003, CEDEX 4, 34184 Montpellier, France
ORCID
Venue
Allergies
Publisher
MDPI AG
Published
2023-01-10
Volume
3
Issue
1
Pages
11-24
ISSN
2313-5786
DOI
10.3390/allergies3010002
Cited by
7
References
0
Language
en
Licence
creativecommons.org/licenses/by/4.0/ (vor)

About these checks

Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.

Statistics and arithmetic are recomputed, not judged.

Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.

What counts as a claim ›How we measure confidence ›How we check this ›

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