Screening of transgenic proteins expressed in transgenic food crops for the presence of short amino acid sequences identical to potential, IgE - binding linear epitopes of allergens

BMC Struct Biol. 2002 Dec 12:2:8. doi: 10.1186/1472-6807-2-8. Epub 2002 Dec 12.


Background: Transgenic proteins expressed by genetically modified food crops are evaluated for their potential allergenic properties prior to marketing, among others by identification of short identical amino acid sequences that occur both in the transgenic protein and allergenic proteins. A strategy is proposed, in which the positive outcomes of the sequence comparison with a minimal length of six amino acids are further screened for the presence of potential linear IgE-epitopes. This double track approach involves the use of literature data on IgE-epitopes and an antigenicity prediction algorithm.

Results: Thirty-three transgenic proteins have been screened for identities of at least six contiguous amino acids shared with allergenic proteins. Twenty-two transgenic proteins showed positive results of six- or seven-contiguous amino acids length. Only a limited number of identical stretches shared by transgenic proteins (papaya ringspot virus coat protein, acetolactate synthase GH50, and glyphosate oxidoreductase) and allergenic proteins could be identified as (part of) potential linear epitopes.

Conclusion: Many transgenic proteins have identical stretches of six or seven amino acids in common with allergenic proteins. Most identical stretches are likely to be false positives. As shown in this study, identical stretches can be further screened for relevance by comparison with linear IgE-binding epitopes described in literature. In the absence of literature data on epitopes, antigenicity prediction by computer aids to select potential antibody binding sites that will need verification of IgE binding by sera binding tests. Finally, the positive outcomes of this approach warrant further clinical testing for potential allergenicity.

Publication types

  • Evaluation Study
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Algorithms
  • Allergens / chemistry*
  • Allergens / genetics
  • Allergens / immunology
  • Amino Acid Sequence
  • Binding Sites, Antibody
  • Crops, Agricultural / genetics
  • Epitopes / chemistry*
  • Epitopes / immunology
  • Gene Expression
  • Immunoglobulin E / immunology*
  • Plants, Genetically Modified / immunology*
  • Plants, Genetically Modified / metabolism
  • Recombinant Proteins / chemistry
  • Recombinant Proteins / immunology
  • Recombinant Proteins / metabolism
  • Sequence Analysis, Protein / methods*
  • Sequence Homology, Amino Acid
  • Transgenes / immunology*


  • Allergens
  • Epitopes
  • Recombinant Proteins
  • Immunoglobulin E