title: Defining the boundaries and characterizing the landscape of functional genome expression in vascular tissues of Populus using shotgun proteomics.
abstract: Current state-of-the-art experimental and computational proteomic approaches were integrated to obtain a comprehensive protein profile of Populus vascular tissue. This featured: (1) a large sample set consisting of two genotypes grown under normal and tension stress conditions, (2) bioinformatics clustering to effectively handle gene duplication, and (3) an informatics approach to track and identify single amino acid polymorphisms (SAAPs). By applying a clustering algorithm to the Populus database, the number of protein entries decreased from 64,689 proteins to a total of 43,069 protein groups, thereby reducing 7505 identified proteins to a total of 4226 protein groups, in which 2016 were singletons. This reduction implies that ∼50% of the measured proteins shared extensive sequence homology. Using conservative search criteria, we were able to identify 1354 peptides containing a SAAP and 201 peptides that become tryptic due to a K or R substitution. These newly identified peptides correspond to 502 proteins, including 97 previously unidentified proteins. In total, the integration of deep proteome measurements on an extensive sample set with protein clustering and peptide sequence variants provided an exceptional level of proteome characterization for Populus, allowing us to spatially resolve the vascular tissue proteome.
authors: Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, United States.
authors: Paul
authors: P
authors: Abraham
authors: Rachel
authors: R
authors: Adams
authors: Richard J
authors: RJ
authors: Giannone
authors: Udaya
authors: U
authors: Kalluri
authors: Priya
authors: P
authors: Ranjan
authors: Brian
authors: B
authors: Erickson
authors: Manesh
authors: M
authors: Shah
authors: Gerald A
authors: GA
authors: Tuskan
authors: Robert L
authors: RL
authors: Hettich
mesh_terms: D000595:Amino Acid Sequence; D002473:Cell Wall / Q000378:metabolism; D019295:Computational Biology; D015870:Gene Expression; D018506:Gene Expression Regulation, Plant; D018745:Genome, Plant; D008969:Molecular Sequence Data; D010446:Peptide Fragments / Q000737:chemistry; D010449:Peptide Mapping; D010940:Plant Proteins / Q000737:chemistry / Q000235:genetics* / Q000378:metabolism; D058526:Plant Vascular Bundle / Q000235:genetics* / Q000378:metabolism; D020641:Polymorphism, Single Nucleotide; D032107:Populus / Q000235:genetics* / Q000378:metabolism; D059748:Proteolysis; D020543:Proteome / Q000737:chemistry / Q000235:genetics* / Q000378:metabolism; D040901:Proteomics; D017422:Sequence Analysis, DNA; D013312:Stress, Physiological; D053719:Tandem Mass Spectrometry
chemical_list: D010446:Peptide Fragments; D010940:Plant Proteins; D020543:Proteome