title: Application of label-free shotgun nUPLC-MS(E) and 2-DE approaches in the study of Botrytis cinerea mycelium.
abstract: The phytopathogenic fungus Botrytis cinerea infects more than different 200 plant species and causes substantial losses in numerous crops. The B05.10 and T4 wild-type strain genomes have been recently sequenced, becoming a model system for necrotrophic pathogens, as well as opening up new alternatives in functional genomics, such as proteomics. We analyzed B. cinerea mycelium from these two wild-type strains, introducing label-free shotgun nUPLC-MS(E) methodology to complement the 2-DE-MS-based approach. We assessed the label-free nUPLC-MS(E) methodology for protein identification and quantification using five mycelium protein dilutions. A total of 225 and 170 protein species were identified by nUPLC-MS(E) in the B05.10 and T4 strains, respectively. Moreover, 129 protein species were quantified in both strains. Significant differences in protein abundance were found in 15 more abundant and 16 less abundant protein species in the B05.10 strain compared to the T4 strain. Twenty-nine qualitative and 15 significant quantitative differences were found using 2-DE. The label-free nUPLC-MS(E) was a reliable, reproducible and sensitive method for protein identification and quantification to study the B. cinerea mycelial proteome. Results obtained by gel-based and gel-free complementary approaches allow a deeper characterization of this fungus, as well as the identification of potential virulence factors.
authors.affiliation: Agroforestry and Plant Biochemistry and Proteomics Research Group, Department of Biochemistry and Molecular Biology, University of Córdoba, Agrifood Campus of International Excellence, ceiA3, 14071-Córdoba, Spain.
authors.forename: Raquel
authors.initials: R
authors.lastname: Gonzalez-Fernandez
authors.forename: Kerman
authors.initials: K
authors.lastname: Aloria
authors.forename: Jesus M
authors.initials: JM
authors.lastname: Arizmendi
authors.forename: Jesus V
authors.initials: JV
authors.lastname: Jorrin-Novo
mesh_terms: D000595:Amino Acid Sequence; D020171:Botrytis / Q000737:chemistry*; D015180:Electrophoresis, Gel, Two-Dimensional; D005656:Fungal Proteins / Q000302:isolation & purification*; D013058:Mass Spectrometry / Q000379:methods; D008969:Molecular Sequence Data; D025282:Mycelium / Q000737:chemistry*; D010446:Peptide Fragments / Q000302:isolation & purification*; D059748:Proteolysis; D040901:Proteomics; D015203:Reproducibility of Results; D012680:Sensitivity and Specificity; D014357:Trypsin / Q000737:chemistry
chemical_list: D005656:Fungal Proteins; D010446:Peptide Fragments; D014357:Trypsin