Metabolomics- and proteomics-assisted genome annotation and analysis of the draft metabolic network of Chlamydomonas reinhardtii.
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 proteomics-detected 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 JGI-Chlamydomonas genomic resource database (http://genome.jgi-psf.org/Chlre3/Chlre3.home.html).
May
Patrick
P
GoFORSYS, Institute of Biochemistry and Biology, University of Potsdam, 14424 Potsdam-Golm, Germany 0331-5678.
Wienkoop
Stefanie
S
Kempa
Stefan
S
Usadel
Björn
B
Christian
Nils
N
Rupprecht
Jens
J
Weiss
Julia
J
Recuenco-Munoz
Luis
L
Ebenhöh
Oliver
O
Weckwerth
Wolfram
W
Walther
Dirk
D
D020418:Algal Proteins / Q000235:genetics*; D000595:Amino Acid Sequence; D000818:Animals; D016825:Chlamydomonas reinhardtii / Q000235:genetics*; D002853:Chromatography, Liquid; D019295:Computational Biology; D030541:Databases, Genetic; D020224:Expressed Sequence Tags; D020407:Internet; D013058:Mass Spectrometry; D053858:Metabolic Networks and Pathways / Q000235:genetics*; D008957:Models, Genetic; D008969:Molecular Sequence Data; D040901:Proteomics
D020418:Algal Proteins