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Classification of Celiac disease epitopes of ω-gliadin through data mining and compared with Chinese spring genome sequence
Celiac disease (CD) is classified as an autoimmune disease of small intestine and occurred with people with the human leucocyte antigen (HLA) DQ2(8) cells. The gluten commonly called for the gliadins and glutenins from wheat and related proteins from barley and rye is significant cause of celiac disease. There are many sequences that recognized by T-cell according to species and different types of gliadins. In ω-gliadin, two sort of epitopes were figured out that consisting of some proline(P) and glutamine(Q) scattered in gliadin sequence.
All registered ω-gliadin sequences deposited in NCBI database were downloaded and collected. In order to classify groups depending on sequence difference, sequence similarity and their closeness were analyzed by phylogenetic trees using by MEGA (ver.6.06). Chinese spring genome sequence database offered by URGI (Unité de Recherche Génomique Info) is used for sequence assembly. Primers to validate presence of epitopes were designed by two different type from conserved and specific region. Primer pair from consensus region were designed in conserved domain of ω-gliadin sequences from public database by sequence alignment. And, sequence-specific primers of ω-gliadin were designed from the unique region of each ω-gliadin sequence comparing ω-gliadin sequences from NCBI database with draft sequence of Chinese spring in URGI.
The two known epitopes of ω-gliadin were located on same site, approximately from the 315th nucleotide to the 348th nucleotide in CDS. Candidate epitopes present in ω-gliadin were divided into three categories based on analysis of sequence similarity. This categorization shows similar pattern with groups that were previously reported by sequence motifs such as SRLL, AREL, ARQL and KELQ. However, sequence which has AREL motif and sequence ARQL motif were not distinguished obviously in ω-gliadin based on sequence alignment.
