ArticleJournal of bacteriology2012
Genome-scale metabolic reconstruction and hypothesis testing in the methanogenic archaeon Methanosarcina acetivorans C2A.
Article in Journal of bacteriology, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 42 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
42 citing papers in PubMed, 85 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
- A constraint-based framework for exploring the impact of multireaction dependencies on metabolic functions.NPJ systems biology and applications · 2025Article
- Microbial and chemical predictors of methane release from a stratified thermokarst permafrost hotspot.Frontiers in microbiology · 2025Article
- An integrated systems biology approach reveals differences in formate metabolism in the genusiScience · 2023Article
- The effective deficiency of biochemical networks.Scientific reports · 2023Article
- Model Organisms To Study Methanogenesis, a Uniquely Archaeal Metabolism.Journal of bacteriology · 2023Review
- A Protocol for the Automatic Construction of Highly Curated Genome-Scale Models of Human Metabolism.Bioengineering (Basel, Switzerland) · 2023Article
- Methyl-Based Methanogenesis: an Ecological and Genomic Review.Microbiology and molecular biology reviews : MMBR · 2023Review
- The hidden simplicity of metabolic networks is revealed by multireaction dependencies.Science advances · 2022Article
- A Genome-Scale Metabolic Model ofMetabolites · 2022Article
- Review
- A structural property for reduction of biochemical networks.Scientific reports · 2021Article
- An alternative resource allocation strategy in the chemolithoautotrophic archaeonProceedings of the National Academy of Sciences of the United States of America · 2021Article
- Reconstructing organisms in silico: genome-scale models and their emerging applications.Nature reviews. Microbiology · 2020Review
- Review
- Comparative analysis of differential proteome-wide protein-protein interaction network ofBiochemistry and biophysics reports · 2019Article
- Energy Conservation and Hydrogenase Function in Methanogenic Archaea, in Particular the GenusMicrobiology and molecular biology reviews : MMBR · 2019Review
- A Membrane-Bound Cytochrome EnablesmBio · 2019Article
- Current status and applications of genome-scale metabolic models.Genome biology · 2019Review
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
4 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Methanosarcina acetivorans strain C2A is a marine methanogenic archaeon notable for its substrate utilization, genetic tractability, and novel energy conservation mechanisms. To help probe the phenotypic implications of this organism's unique metabolism, we have constructed and manually curated a genome-scale metabolic model of M. acetivorans, iMB745, which accounts for 745 of the 4,540 predicted protein-coding genes (16%) in the M. acetivorans genome. The reconstruction effort has identified key knowledge gaps and differences in peripheral and central metabolism between methanogenic species. Using flux balance analysis, the model quantitatively predicts wild-type phenotypes and is 96% accurate in knockout lethality predictions compared to currently available experimental data. The model was used to probe the mechanisms and energetics of by-product formation and growth on carbon monoxide, as well as the nature of the reaction catalyzed by the soluble heterodisulfide reductase HdrABC in M. acetivorans. The genome-scale model provides quantitative and qualitative hypotheses that can be used to help iteratively guide additional experiments to further the state of knowledge about methanogenesis.
Indexed as
Identifiers
What OpenQuestion holds
Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.