title: The nuclear proteome of the green alga Chlamydomonas reinhardtii.
abstract: Nuclear proteins play a central role in regulating gene expression. Their identification is important for understanding how the nuclear repertoire changes over time under different conditions. Nuclear proteins are often underrepresented in proteomic studies due to the frequently low abundance of proteins involved in regulatory processes. So far, only few studies describing the nuclear proteome of plant species have been published. Recently, the genome sequence of the unicellular green alga Chlamydomonas reinhardtii has been obtained and annotated, allowing the development of further detailed studies for this organism. However, a detailed description of its nuclear proteome has not been reported so far. Here, we present an analysis of the nuclear proteome of the sequenced Chlamydomonas strain cc503. Using LC-MS/MS, we identified 672 proteins from nuclei isolates with a maximum 1% peptide spectrum false discovery rate. Besides well-known proteins (e.g. histones), transcription factors and other transcriptional regulators (e.g. tubby and HMG) were identified. The presence of protein motifs in nuclear proteins was investigated by computational tools, and specific over-represented protein motifs were identified. This study provides new insights into the complexity of the nuclear environment and reveals novel putative protein targets for further studies of nuclear mechanisms.
authors: GoFORSYS Research Unit for Systems Biology, Institute of Biochemistry and Biology, University of Potsdam, Potsdam-Golm, Germany.
authors: Flavia V
authors: FV
authors: Winck
authors: Diego M
authors: DM
authors: Riaño-Pachón
authors: Frederik
authors: F
authors: Sommer
authors: Jens
authors: J
authors: Rupprecht
authors: Bernd
authors: B
authors: Mueller-Roeber
mesh_terms: D020816:Amino Acid Motifs; D000595:Amino Acid Sequence; D002467:Cell Nucleus / Q000378:metabolism*; D016825:Chlamydomonas reinhardtii / Q000378:metabolism*; D008969:Molecular Sequence Data; D010446:Peptide Fragments / Q000737:chemistry; D010940:Plant Proteins / Q000737:chemistry / Q000378:metabolism*; D020543:Proteome / Q000737:chemistry / Q000378:metabolism*; D053719:Tandem Mass Spectrometry
chemical_list: D010446:Peptide Fragments; D010940:Plant Proteins; D020543:Proteome