ArticleGenetics2008
Metabolomics- and proteomics-assisted genome annotation and analysis of the draft metabolic network of Chlamydomonas reinhardtii.
Article in Genetics, 2008. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 48 papers.
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Who cites it
48 citing papers in PubMed.
- A Guide to Metabolic Network Modeling for Plant Biology.Plants (Basel, Switzerland) · 2025Review
- Unraveling metabolism underpinning biomass composition shift inFrontiers in plant science · 2025Article
- Review
- Multiplatform Metabolomics Characterization Reveals Novel Metabolites and Phospholipid Compositional Rules ofInternational journal of molecular sciences · 2023Article
- Is Genetic Engineering a Route to Enhance Microalgae-Mediated Bioremediation of Heavy Metal-Containing Effluents?Molecules (Basel, Switzerland) · 2022Review
- Proteomics unveil a central role for peroxisomes in butyrate assimilation of the heterotrophic Chlorophyte algaFrontiers in microbiology · 2022Article
- Review
- Efflux pumps and antimicrobial resistance: Paradoxical components in systems genomics.Progress in biophysics and molecular biology · 2019Review
- Omics Application of Bio-Hydrogen Production Through Green AlgaFrontiers in bioengineering and biotechnology · 2019Review
- Proteome evolution under non-substitutable resource limitation.Nature communications · 2018Article
- Analysis of bZIP Transcription Factor Family and Their Expressions under Salt Stress inInternational journal of molecular sciences · 2018Article
- Plant genome and transcriptome annotations: from misconceptions to simple solutions.Briefings in bioinformatics · 2018Article
- Recovery from N Deprivation Is a Transcriptionally and Functionally Distinct State inPlant physiology · 2018Article
- Advances in metabolic modeling of oleaginous microalgae.Biotechnology for biofuels · 2018Review
- Quantitative in vivo phosphoproteomics reveals reversible signaling processes during nitrogen starvation and recovery in the biofuel model organismBiotechnology for biofuels · 2017Article
- Knock-Down of the IFR1 Protein Perturbs the Homeostasis of Reactive Electrophile Species and Boosts Photosynthetic Hydrogen Production inFrontiers in plant science · 2017Article
- Proteomics and comparative genomics of Nitrososphaera viennensis reveal the core genome and adaptations of archaeal ammonia oxidizers.Proceedings of the National Academy of Sciences of the United States of America · 2016Article
- Pollen proteomics: from stress physiology to developmental priming.Plant reproduction · 2016Review
- FragariaCyc: A Metabolic Pathway Database for Woodland Strawberry Fragaria vesca.Frontiers in plant science · 2016Article
- Relevance of nutrient media composition for hydrogen production in Chlamydomonas.Photosynthesis research · 2015Review
Corrections and comments
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Authors and funding
11 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
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).
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