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

Authors

  • Maureen Hummel,

    1. Molecular Plant Physiology, Utrecht University, Utrecht, The Netherlands
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    • Present address: Maureen Hummel, Center for Plant Cell Biology, Department of Botany and Plant Sciences, University of California, Riverside, CA 92521-0124, USA

  • Jan H. G. Cordewener,

    1. BU Bioscience, Plant Research International, Wageningen, The Netherlands
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  • Joost C. M. de Groot,

    1. BU Bioscience, Plant Research International, Wageningen, The Netherlands
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    • Deceased 11.11.2010.

  • Sjef Smeekens,

    1. Molecular Plant Physiology, Utrecht University, Utrecht, The Netherlands
    2. Centre for BioSystems Genomics, Wageningen, The Netherlands
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  • Antoine H. P. America,

    1. BU Bioscience, Plant Research International, Wageningen, The Netherlands
    2. Centre for BioSystems Genomics, Wageningen, The Netherlands
    3. Netherlands Proteomics Centre, Utrecht, The Netherlands
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  • Johannes Hanson

    Corresponding author
    1. Centre for BioSystems Genomics, Wageningen, The Netherlands
    2. Umeå Plant Science Center, Department of Plant Physiology, Umeå University, Umeå, Sweden
    • Molecular Plant Physiology, Utrecht University, Utrecht, The Netherlands
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Correspondence: Dr. Johannes Hanson, Molecular Plant Physiology, Utrecht University, Padualaan 8, 3584 CH, Utrecht, The Netherlands

Fax: +31-30-253-3655

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.

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