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 Chlamydomonasreinhardtii under reference conditions. Bioinformatics annotationmethods combined with GCxGC/MS-based metabolomics and LC/MS-basedshotgun proteomics profiling technologies have been applied to characterizeabundant proteins and metabolites, resulting in the detection of1069 proteins and 159 metabolites. Of the measured proteins, 204currently do not have EST sequence support; thus a significant portionof the proteomics-detected proteins provide evidence for the validityof in silico gene models. Furthermore, the generated peptide datalend support to the validity of a number of proteins currently inthe proposed model stage. By integrating genomic annotation informationwith experimentally identified metabolites and proteins, we constructeda draft metabolic network for Chlamydomonas. Computational metabolicmodeling allowed an identification of missing enzymatic links. Someexperimentally detected metabolites are not producible by the currentlyknown and annotated enzyme set, thus suggesting entry points forfurther targeted gene discovery or biochemical pathway research.All data sets are made available as supplementary material as wellas web-accessible databases and within the functional context viathe Chlamydomonas-adapted MapMan annotation platform. Informationof identified peptides is also available directly via the JGI-Chlamydomonasgenomic resource database.