title: A two-dimensional electrophoresis proteomic reference map and systematic identification of 1367 proteins from a cell suspension culture of the model legume Medicago truncatula.
abstract: The proteome of a Medicago truncatula cell suspension culture was analyzed using two-dimensional electrophoresis and nanoscale HPLC coupled to a tandem Q-TOF mass spectrometer (QSTAR Pulsar i) to yield an extensive protein reference map. Coomassie Brilliant Blue R-250 was used to visualize more than 1661 proteins, which were excised, subjected to in-gel trypsin digestion, and analyzed using nanoscale HPLC/MS/MS. The resulting spectral data were queried against a custom legume protein database using the MASCOT search engine. A total of 1367 of the 1661 proteins were identified with high rigor, yielding an identification success rate of 83% and 907 unique protein accession numbers. Functional annotation of the M. truncatula suspension cell proteins revealed a complete tricarboxylic acid cycle, a nearly complete glycolytic pathway, a significant portion of the ubiquitin pathway with the associated proteolytic and regulatory complexes, and many enzymes involved in secondary metabolism such as flavonoid/isoflavonoid, chalcone, and lignin biosynthesis. Proteins were also identified from most other functional classes including primary metabolism, energy production, disease/defense, protein destination/storage, protein synthesis, transcription, cell growth/division, and signal transduction. This work represents the most extensive proteomic description of M. truncatula suspension cells to date and provides a reference map for future comparative proteomic and functional genomic studies of the response of these cells to biotic and abiotic stress.
authors.affiliation: Plant Biology Division, The Samuel Roberts Noble Foundation, Ardmore, Oklahoma 73402, USA.
authors.forename: Zhentian
authors.initials: Z
authors.lastname: Lei
authors.forename: Aaron M
authors.initials: AM
authors.lastname: Elmer
authors.forename: Bonnie S
authors.initials: BS
authors.lastname: Watson
authors.forename: Richard A
authors.initials: RA
authors.lastname: Dixon
authors.forename: Pedro J
authors.initials: PJ
authors.lastname: Mendes
authors.forename: Lloyd W
authors.initials: LW
authors.lastname: Sumner
mesh_terms: D000595:Amino Acid Sequence; D002478:Cells, Cultured; D015180:Electrophoresis, Gel, Two-Dimensional; D004734:Energy Metabolism; D005419:Flavonoids / Q000378:metabolism; D007527:Isoenzymes; D008031:Lignin / Q000378:metabolism; D013058:Mass Spectrometry; D046913:Medicago truncatula / Q000737:chemistry* / Q000166:cytology*; D008969:Molecular Sequence Data; D046912:Multiprotein Complexes; D010447:Peptide Hydrolases / Q000378:metabolism; D010940:Plant Proteins / Q000032:analysis* / Q000737:chemistry / Q000145:classification / Q000378:metabolism; D018517:Plant Roots / Q000378:metabolism; D021381:Protein Transport; D020543:Proteome / Q000032:analysis* / Q000737:chemistry / Q000378:metabolism; D040901:Proteomics; D016415:Sequence Alignment; D025801:Ubiquitin / Q000378:metabolism
chemical_list: D005419:Flavonoids; D007527:Isoenzymes; D046912:Multiprotein Complexes; D010940:Plant Proteins; D020543:Proteome; D025801:Ubiquitin; D008031:Lignin; D010447:Peptide Hydrolases