Article (Scientific journals)
Metabolomics- and proteomics-assisted genome annotation and analysis of the draft metabolic network of Chlamydomonas reinhardtii.
May, Patrick; Wienkoop, Stefanie; Kempa, Stefan et al.
2008In Genetics, 179 (1), p. 157-66
Peer reviewed
 

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Keywords :
Algal Proteins/genetics; Amino Acid Sequence; Animals; Chlamydomonas reinhardtii/genetics; Chromatography, Liquid; Computational Biology; Databases, Genetic; Expressed Sequence Tags; Internet; Mass Spectrometry; Metabolic Networks and Pathways/genetics; Models, Genetic; Molecular Sequence Data; Proteomics
Abstract :
[en] 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).
Disciplines :
UNKNOWN KEY #A01
Author, co-author :
May, Patrick   ;  Max-Planck-Institute for Molecular Plant Physiology > Bioinformatics
Wienkoop, Stefanie 
Kempa, Stefan 
Usadel, Bjorn 
Christian, Nils  ;  Max-Planck-Institute for Molecular Plant Physiology
Rupprecht, Jens
Weiss, Julia
Recuenco-Munoz, Luis
Ebenhoh, Oliver
Weckwerth, Wolfram
Walther, Dirk
 These authors have contributed equally to this work.
Language :
English
Title :
Metabolomics- and proteomics-assisted genome annotation and analysis of the draft metabolic network of Chlamydomonas reinhardtii.
Publication date :
2008
Journal title :
Genetics
ISSN :
0016-6731
Volume :
179
Issue :
1
Pages :
157-66
Peer reviewed :
Peer reviewed
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since 23 April 2013

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