- THIS ARTICLE
- Full Text
- Full Text (PDF)
- Data Supplement
- Alert me when this article is cited
- Alert me if a correction is posted
- SERVICES
- Similar articles in this journal
- Similar articles in PubMed
- Alert me to new issues of the journal
- Download to citation manager
- Reprints & Permissions
- CITING ARTICLES
- Citing Articles via HighWire
- Citing Articles via Google Scholar
- GOOGLE SCHOLAR
- Articles by May, P.
- Articles by Walther, D.
- Search for Related Content
- PUBMED
- PubMed Citation
- Articles by May, P.
- Articles by Walther, D.
Genetics, Vol. 179, 157-166, May 2008, Copyright © 2008
doi:10.1534/genetics.108.088336
Metabolomics- and Proteomics-Assisted Genome Annotation and Analysis of the Draft Metabolic Network of Chlamydomonas reinhardtii
Patrick May*,1,
Stefanie Wienkoop
,1,
Stefan Kempa,1,
Björn Usadel*,1,
Nils Christian,1,
Jens Rupprecht*,
Julia Weiss,
Luis Recuenco-Munoz,
Oliver Ebenhöh,1,
Wolfram Weckwerth,1 and
Dirk Walther*,1,2
* Max Planck Institute for Molecular Plant Physiology, 14424 Potsdam-Golm, Germany and GoFORSYS, Institute of Biochemistry and Biology, University of Potsdam, 14424 Potsdam-Golm, Germany 0331-5678
2 Corresponding author: Max Planck Institute for Molecular Plant Physiology, Am Mühlenberg 1, 14424 Potsdam, Germany.
E-mail: walther{at}mpimp-golm.mpg.de
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).
This article has been cited by other articles:
 |
|
 |
|
  O. Vallon and S. Dutcher Treasure Hunting in the Chlamydomonas Genome Genetics, May 1, 2008; 179(1): 3 - 6. [Full Text] [PDF]
|
|