Dynamic protein composition of Arabidopsis thaliana cytosolic ribosomes in response to sucrose feeding as revealed by label free MSE proteomics

M. Hummel, J.H.G.C. Cordewener, J.C.M. de Groot, S. Smeekens, A.H.P. America, J. Hanson

    Research output: Contribution to journalArticleAcademicpeer-review

    47 Citations (Scopus)

    Abstract

    Cytosolic ribosomes are among the largest multisubunit cellular complexes. Arabidopsis thaliana ribosomes consist of 79 different ribosomal proteins (r-proteins) that each are encoded by two to six (paralogous) genes. It is unknown whether the paralogs are incorporated into the ribosome and whether the relative incorporation of r-protein paralogs varies in response to environmental cues. Immunopurified ribosomes were isolated from A. thaliana rosette leaves fed with sucrose. Trypsin digested samples were analyzed by qTOF-LC-MS using both MSE and classical MS/MS. Peptide features obtained by using these two methods were identified using MASCOT and Proteinlynx Global Server searching the theoretical sequences of A. thaliana proteins. The A. thaliana genome encodes 237 r-proteins and 69% of these were identified with proteotypic peptides for most of the identified proteins. These r-proteins were identified with average protein sequence coverage of 32% observed by MSE. Interestingly, the analysis shows that the abundance of r-protein paralogs in the ribosome changes in response to sucrose feeding. This is particularly evident for paralogous RPS3aA, RPS5A, RPL8B, and RACK1 proteins. These results show that protein synthesis in the A. thaliana cytosol involves a heterogeneous ribosomal population. The implications of these findings in the regulation of translation are discussed.
    Original languageEnglish
    Pages (from-to)1024-1038
    JournalProteomics
    Volume12
    Issue number7
    DOIs
    Publication statusPublished - 2012

    Keywords

    • messenger-rna translation
    • mass-spectrometric analysis
    • data-independent analysis
    • leaf adaxial identity
    • gene-expression
    • extraribosomal functions
    • 80s ribosome
    • eukaryotic ribosome
    • oxygen deprivation
    • subunit

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