Linked Life Data

17934214

Source:http://linkedlifedata.com/resource/pubmed/id/17934214

Statements in which the resource exists as a subject.
PredicateObject
rdf:type
lifeskim:mentions
pubmed:issue
2
pubmed:dateCreated
2008-2-7
pubmed:abstractText
Finding gene-specific peptides by mass spectrometry analysis to pinpoint gene loci responsible for particular protein products is a major challenge in proteomics especially in highly conserved gene families in higher eukaryotes. We used a combination of in silico approaches coupled to mass spectrometry analysis to advance the proteomics insight into Arabidopsis cytosolic ribosomal composition and its post-translational modifications. In silico digestion of all 409 ribosomal protein sequences in Arabidopsis defined the proportion of theoretical gene-specific peptides for each gene family and highlighted the need for low m/z cutoffs of MS ion selection for MS/MS to characterize low molecular weight, highly basic ribosomal proteins. We undertook an extensive MS/MS survey of the cytosolic ribosome using trypsin and, when required, chymotrypsin and pepsin. We then used custom software to extract and filter peptide match information from Mascot result files and implement high confidence criteria for calling gene-specific identifications based on the highest quality unambiguous spectra matching exclusively to certain in silico predicted gene- or gene family-specific peptides. This provided an in-depth analysis of the protein composition based on 1446 high quality MS/MS spectra matching to 795 peptide sequences from ribosomal proteins. These identified peptides from five gene families of ribosomal proteins not identified previously, providing experimental data on 79 of the 80 different types of ribosomal subunits. We provide strong evidence for gene-specific identification of 87 different ribosomal proteins from these 79 families. We also provide new information on 30 specific sites of co- and post-translational modification of ribosomal proteins in Arabidopsis by initiator methionine removal, N-terminal acetylation, N-terminal methylation, lysine N-methylation, and phosphorylation. These site-specific modification data provide a wealth of resources for further assessment of the role of ribosome modification in influencing translation in Arabidopsis.
pubmed:language
eng
pubmed:journal
pubmed:citationSubset
IM
pubmed:chemical
pubmed:status
MEDLINE
pubmed:month
Feb
pubmed:issn
1535-9484
pubmed:author
pubmed:issnType
Electronic
pubmed:volume
7
pubmed:owner
NLM
pubmed:authorsComplete
Y
pubmed:pagination
347-69
pubmed:meshHeading
pubmed-meshheading:17934214-Acetylation, pubmed-meshheading:17934214-Amino Acid Sequence, pubmed-meshheading:17934214-Arabidopsis, pubmed-meshheading:17934214-Arabidopsis Proteins, pubmed-meshheading:17934214-Computational Biology, pubmed-meshheading:17934214-Cytosol, pubmed-meshheading:17934214-Genes, Plant, pubmed-meshheading:17934214-Methylation, pubmed-meshheading:17934214-Mitochondrial Proteins, pubmed-meshheading:17934214-Molecular Sequence Data, pubmed-meshheading:17934214-Peptides, pubmed-meshheading:17934214-Phosphorylation, pubmed-meshheading:17934214-Protein Processing, Post-Translational, pubmed-meshheading:17934214-Protein Subunits, pubmed-meshheading:17934214-Proteome, pubmed-meshheading:17934214-Ribosomal Proteins, pubmed-meshheading:17934214-Ribosomes, pubmed-meshheading:17934214-Spectrometry, Mass, Electrospray Ionization
pubmed:year
2008
pubmed:articleTitle
Analysis of the Arabidopsis cytosolic ribosome proteome provides detailed insights into its components and their post-translational modification.
pubmed:affiliation
Australian Research Council (ARC) Centre of Excellence in Plant Energy Biology and School of Biomedical, Biomolecular and Chemical Sciences, The University of Western Australia, 35 Stirling Highway, M316, Crawley 6009, Western Australia, Australia.
pubmed:publicationType
Journal Article, Research Support, Non-U.S. Gov't