ArticleBMC systems biology2011
Metabolic reconstruction of the archaeon methanogen Methanosarcina Acetivorans.
Article in BMC systems biology, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 31 papers.
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Who cites it
31 citing papers in PubMed, 53 citations in OpenAlex.
- Synthetic Biology of Plants and Microbes for Agriculture, Environment, and Future Applications.Chemical reviews · 2026Review
- IGM: Integrated Gene-expression Modeling for multi-condition flux-preserving genome-scale metabolic models.PloS one · 2026Article
- An integrated systems biology approach reveals differences in formate metabolism in the genusiScience · 2023Article
- Model Organisms To Study Methanogenesis, a Uniquely Archaeal Metabolism.Journal of bacteriology · 2023Review
- Optimizing Strategies for Bio-Based Ethanol Production Using Genome-Scale Metabolic Modeling of the Hyperthermophilic Archaeon, Pyrococcus furiosus.Applied and environmental microbiology · 2023Article
- Methyl-Based Methanogenesis: an Ecological and Genomic Review.Microbiology and molecular biology reviews : MMBR · 2023Review
- A Genome-Scale Metabolic Model ofMetabolites · 2022Article
- Review
- GPRuler: Metabolic gene-protein-reaction rules automatic reconstruction.PLoS computational biology · 2021Article
- Reconstructing organisms in silico: genome-scale models and their emerging applications.Nature reviews. Microbiology · 2020Review
- Review
- A Membrane-Bound Cytochrome EnablesmBio · 2019Article
- Current status and applications of genome-scale metabolic models.Genome biology · 2019Review
- Kinetic modeling of Stickland reactions-coupled methanogenesis for a methanogenic culture.AMB Express · 2019Article
- Review
- Genome-Scale Metabolic Modeling of Archaea Lends Insight into Diversity of Metabolic Function.Archaea (Vancouver, B.C.) · 2017Review
- Genome-wide gene expression and RNA half-life measurements allow predictions of regulation and metabolic behavior in Methanosarcina acetivorans.BMC genomics · 2016Article
- Control of fluxes in metabolic networks.Genome research · 2016Article
- Metabolic processes of Methanococcus maripaludis and potential applications.Microbial cell factories · 2016Review
- Assessing methanotrophy and carbon fixation for biofuel production by Methanosarcina acetivorans.Microbial cell factories · 2016Article
Corrections and comments
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Authors and funding
3 authors at 2 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundMethanogens are ancient organisms that are key players in the carbon cycle accounting for about one billion tones of biological methane produced annually. Methanosarcina acetivorans, with a genome size of ~5.7 mb, is the largest sequenced archaeon methanogen and unique amongst the methanogens in its biochemical characteristics. By following a systematic workflow we reconstruct a genome-scale metabolic model for M. acetivorans. This process relies on previously developed computational tools developed in our group to correct growth prediction inconsistencies with in vivo data sets and rectify topological inconsistencies in the model.
resultsThe generated model iVS941 accounts for 941 genes, 705 reactions and 708 metabolites. The model achieves 93.3% prediction agreement with in vivo growth data across different substrates and multiple gene deletions. The model also correctly recapitulates metabolic pathway usage patterns of M. acetivorans such as the indispensability of flux through methanogenesis for growth on acetate and methanol and the unique biochemical characteristics under growth on carbon monoxide.
conclusionsBased on the size of the genome-scale metabolic reconstruction and extent of validated predictions this model represents the most comprehensive up-to-date effort to catalogue methanogenic metabolism. The reconstructed model is available in spreadsheet and SBML formats to enable dissemination.
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