title: Proteome distribution between nucleoplasm and nucleolus and its relation to ribosome biogenesis in Arabidopsis thaliana.
abstract: Ribosome biogenesis is an essential process initiated in the nucleolus. In eukaryotes, multiple ribosome biogenesis factors (RBFs) can be found in the nucleolus, the nucleus and in the cytoplasm. They act in processing, folding and modification of the pre-ribosomal (r)RNAs, incorporation of ribosomal proteins (RPs), export of pre-ribosomal particles to the cytoplasm, and quality control mechanisms. Ribosome biogenesis is best established for Saccharomyces cerevisiae. Plant ortholog assignment to yeast RBFs revealed the absence of about 30% of the yeast RBFs in plants. In turn, few plant specific proteins have been identified by biochemical experiments to act in plant ribosome biogenesis. Nevertheless, a complete inventory of plant RBFs has not been established yet. We analyzed the proteome of the nucleus and nucleolus of Arabidopsis thaliana and the post-translational modifications of these proteins. We identified 1602 proteins in the nucleolar and 2544 proteins in the nuclear fraction with an overlap of 1429 proteins. For a randomly selected set of proteins identified by the proteomic approach we confirmed the localization inferred from the proteomics data by the localization of GFP fusion proteins. We assigned the identified proteins to various complexes and functions and found about 519 plant proteins that have a potential to act as a RBFs, but which have not been experimentally characterized yet. Last, we compared the distribution of RBFs and RPs in the various fractions with the distribution established for yeast.
authors.affiliation: a Institute for Molecular Biosciences.
authors.forename: Denise
authors.initials: D
authors.lastname: Palm
authors.affiliation: a Institute for Molecular Biosciences.|b Cluster of Excellence Macromolecular Complexes.
authors.forename: Stefan
authors.initials: S
authors.lastname: Simm
authors.affiliation: d Department of Otorhinolaryngology , Head and Neck Surgery.
authors.forename: Katrin
authors.initials: K
authors.lastname: Darm
authors.affiliation: a Institute for Molecular Biosciences.
authors.forename: Benjamin L
authors.initials: BL
authors.lastname: Weis
authors.affiliation: a Institute for Molecular Biosciences.
authors.forename: Maike
authors.initials: M
authors.lastname: Ruprecht
authors.affiliation: a Institute for Molecular Biosciences.|b Cluster of Excellence Macromolecular Complexes.|c Buchman Institute for Molecular Life Sciences, Goethe University Frankfurt , Max von Laue Str. Nine, Frankfurt , Germany.
authors.forename: Enrico
authors.initials: E
authors.lastname: Schleiff
authors.affiliation: d Department of Otorhinolaryngology , Head and Neck Surgery.|e Interfaculty Institute of Genetics and Functional Genomics, University Medicine Greifswald , Ferdinand-Sauerbruch-Straße DZ7 J.05.06, Greifswald , Germany.
authors.forename: Christian
authors.initials: C
authors.lastname: Scharf
mesh_terms: D000107:Acetylation; D017360:Arabidopsis / Q000378:metabolism*; D002466:Cell Nucleolus / Q000378:metabolism*; D002478:Cells, Cultured; D010766:Phosphorylation; D010940:Plant Proteins / Q000378:metabolism*; D020543:Proteome; D012270:Ribosomes / Q000378:metabolism*
chemical_list: D010940:Plant Proteins; D020543:Proteome
keywords: Arabidopsis thaliana; nucleolus; nucleus; orthology; proteomics; rRNA processing; ribosome biogenesis