Metabolomics- and proteomics-assisted genome annotation and analysis of the draft metabolic network of Chlamydomonas reinhardtii

Patrick May, Stefanie Wienkoop, Stefan Kempa, Björn Usadel, Niels Christian, Jens Rupprecht, Julia Weiss, Luis Recuenco-Munoz, Oliver Ebenhöh, Wolfram Weckwerth, Dirk Walther (Corresponding author)

    Publications: Contribution to journalArticlePeer Reviewed

    Abstract

    We present an integrated analysis of the molecular repertoire of Chlamydomonas reinhardtii under reference conditions. Bioinformatics annotation methods combined with GCxGC/MS-based metabolomics and LC/MS-based shotgun proteomics profiling technologies have been applied to characterize abundant proteins and metabolites, resulting in the detection of 1069 proteins and 159 metabolites. Of the measured proteins, 204 currently do not have EST sequence support; thus a significant portion of the proteomicsdetected proteins provide evidence for the validity of in silico gene models. Furthermore, the generated peptide data lend support to the validity of a number of proteins currently in the proposed model stage. By integrating genomic annotation information with experimentally identified metabolites and proteins, we constructed a draft metabolic network for Chlamydomonas. Computational metabolic modeling allowed an identification of missing enzymatic links. Some experimentally detected metabolites are not producible by the currently known and annotated enzyme set, thus suggesting entry points for further targeted gene discovery or biochemical pathway research. All data sets are made available as supplementary material as well as web-accessible databases and within the functional context via the Chlamydomonas-adapted MapMan annotation platform. Information of identified peptides is also available directly via the JGIChlamydomonas genomic resource database (http://genome.jgi-psf.org/Chlre3/Chlre3.home.html).
    Original languageEnglish
    Pages (from-to)157-166
    Number of pages10
    JournalGenetics: a periodical record of investigations bearing on heredity and variation
    Volume179
    Publication statusPublished - 2008

    Austrian Fields of Science 2012

    • 106002 Biochemistry
    • 305102 DNA analysis (Forensic medicine)
    • 106037 Proteomics

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