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

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 (

External organisation(s)
Max-Planck-Institut für Molekulare Pflanzenphysiologie, Universität Potsdam
Genetics: a periodical record of investigations bearing on heredity and variation
No. of pages
Publication date
Peer reviewed
Austrian Fields of Science 2012
106002 Biochemistry, 305102 DNA analysis (Forensic medicine), 106037 Proteomics
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