title: Analysis of expressed sequence tags from a single wheat cultivar facilitates interpretation of tandem mass spectrometry data and discrimination of gamma gliadin proteins that may play different functional roles in flour.
abstract: BACKGROUND
  The gamma gliadins are a complex group of proteins that together with other gluten proteins determine the functional properties of wheat flour. The proteins have unusually high levels of glutamine and proline and contain large regions of repetitive sequences. While most gamma gliadins are monomeric proteins containing eight conserved cysteine residues, some contain an additional cysteine residue that enables them to be linked with other gluten proteins into large polymers that are critical for flour quality. The ability to differentiate among the gamma gliadins is important for studies of wheat flour quality because proteins with similar sequences can have different effects on functional properties.
  
  
  RESULTS
  The complement of gamma gliadin genes expressed in the wheat cultivar Butte 86 was evaluated by analyzing publicly available expressed sequence tag (EST) data. Eleven contigs were assembled from 153 Butte 86 ESTs. Nine of the contigs encoded full-length proteins and four of the proteins contained nine cysteine residues. Only one of the encoded proteins was a perfect match with a sequence reported in NCBI. Contigs from four different publicly available EST assemblies encoded proteins that were perfect matches with some, but not all, of the Butte 86 gamma gliadins and the complement of identical proteins was different for each assembly. A specialized database that included the sequences of Butte 86 gamma gliadins was constructed for identification of flour proteins by tandem mass spectrometry (MS/MS). In a pilot experiment, proteins corresponding to six Butte 86 gamma gliadin contigs were distinguished by MS/MS, including one containing the extra cysteine residue. Two other proteins were identified as one of two closely related Butte 86 proteins but could not be distinguished unequivocally. Unique peptide tags specific for Butte 86 gamma gliadins are reported.
  
  
  CONCLUSIONS
  Inclusion of cultivar-specific gamma gliadin sequences in databases maximizes the number and quality of peptide identifications and increases sequence coverage of these gamma gliadins by MS/MS. This approach makes it possible to distinguish closely related proteins, to associate individual proteins with sequences of specific genes, and to evaluate proteomic data in a biological context to better address questions about wheat flour quality.
authors.affiliation: USDA-ARS Western Regional Research Center, U.S. Department of Agriculture-Agricultural Research Service, 800 Buchanan Street, Albany, CA 94710, USA. susan.altenbach@ars.usda.gov
authors.forename: Susan B
authors.initials: SB
authors.lastname: Altenbach
authors.forename: William H
authors.initials: WH
authors.lastname: Vensel
authors.forename: Frances M
authors.initials: FM
authors.lastname: Dupont
mesh_terms: D000595:Amino Acid Sequence; D020451:Contig Mapping; D018744:DNA, Plant / Q000235:genetics; D030562:Databases, Protein; D020224:Expressed Sequence Tags; D005433:Flour; D005903:Gliadin / Q000737:chemistry*; D008969:Molecular Sequence Data; D016415:Sequence Alignment; D020539:Sequence Analysis, Protein; D053719:Tandem Mass Spectrometry; D014908:Triticum / Q000737:chemistry / Q000235:genetics*
chemical_list: D018744:DNA, Plant; D005903:Gliadin