Celiac disease T-cell epitopes from gamma-gliadins: immunoreactivity depends on the genome of origin, transcript frequency, and flanking protein variation
1 Plant Research International, Wageningen UR, P.O. Box 16, NL-6700 AA, Wageningen, The Netherlands
2 Wageningen UR Plant Breeding, Wageningen, The Netherlands
3 Leiden University Medical Centre, Leiden, The Netherlands
4 Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow, 119991, Russia
BMC Genomics 2012, 13:277 doi:10.1186/1471-2164-13-277Published: 22 June 2012
Additional file 1:
Ten full-length γ-gliadin sequences. Ten full length γ-gliadin nucleotide sequences obtained after the assemblage of 717 γ-gliadins transcripts at 98% homology. In brackets, the number of sequences in a contig.
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Additional file 2:
CD-epitopes of γ-gliadin transcripts of T. aestivum in their natural context. Alignments of the deduced aminoacid sequences of T.aestivum γ-gliadin transcript contigs (717 transcripts from the Genbank NCBI) spanning a part of the first repetitive domain and a part of the γ-gliadin sequence. CD T-cell epitopes are depicted in bold: γ-I (PQQSFPQQQ), γ-III (QQPQQPYPQ), γ-IV (SQPQQQFPQ), γ-VI (QQPFPQQPQ), γ-VIIa (PQPQQQFPQ), γ-VIIb (QQPQQPFPQ), Glia-γ2a (FPQQPQQPF), 26-mer FLQPQQPFPQQPQQPYPQQPQQPFPQ. Gli-A: T.aestivum γ-gliadin transcripts expressed from locus Gli-A1, Neighbor Joining topology group 6 (N = 140 transcripts) and 7 (N = 38 transcripts). Gli-B: T.aestivum γ-gliadin transcripts expressed from locus Gli-B1, Neighbor Joining topology group 3 (N = 41 transcripts), 5 (N = 125 transcripts) and 8 (N = 19 transcripts). Gli-D: T.aestivum γ-gliadin transcripts expressed from locus Gli-D1, Neighbor Joining topology group 9 (N = 293 transcripts) and 10 (N = 61 transcripts). Alignment gaps are indicated with dashes (−). Shorter sequences, not connected to domain I are marked with #. Glutamine residues that are a primary targets for the enzyme tissue transglutaminase are underlined (Q) in QxP target sites whereas moderate target sites are depicted in italics (Q) [13,14]. Variants of DQ2-γ-I are indicated. Cleavage sites: In black, trypsin; in grey with white letters, chymotrypsin-high specificity; in grey with black letters, chymotrypsin-low specificity; cleavage occurs at the right side (C-terminal direction) of the marked amino acid.
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Additional file 3:
In vitro T-cell stimulating capacity of natural variants of celiac disease epitope, DQ2-γ-I. Stimulation of a T-cell clone specific for CD epitope DQ2-γ-I, with natural occurring variants of DQ2-γ-I (9-mer epitope core PQQSFPQQQ and residues in the positions −1 to −4 and +1 to +4). Glutamine residues that are a primary targets for the enzyme tissue transglutaminase are underlined (Q) in QxP target sites whereas moderate target sites are depicted in italics (Q) [13,14]. SI = Stimulation Index = cpm of the stimulated culture/cpm unstimulated culture (with APC only); ++ = SI ≥ 50, + = 20 ≤ SI <50, ± =10 ≤ SI <20, - = SI <10. The stimulation is mediated by HLA-DQ2 carrying antigen presenting cells (APC). Peptide no. corresponds to the peptide numbering in Table 5.
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