ArticleArchaea (Vancouver, B.C.)2014
Towards a computational model of a methane producing archaeum.
Article in Archaea (Vancouver, B.C.), 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 9 papers.
What it found
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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.
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Who cites it
9 citing papers in PubMed, 18 citations in OpenAlex.
- Physiological and transcriptomic response to methyl-coenzyme M reductase limitation inApplied and environmental microbiology · 2024Article
- Limited Mechanistic Link Between the Monod Equation and Methanogen Growth: a Perspective from Metabolic Modeling.Microbiology spectrum · 2022Article
- 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
- Perspective: On the importance of hydrodynamic interactions in the subcellular dynamics of macromolecules.The Journal of chemical physics · 2016Article
- Spatially-resolved metabolic cooperativity within dense bacterial colonies.BMC systems biology · 2015Article
- Achievements and challenges in structural bioinformatics and computational biophysics.Bioinformatics (Oxford, England) · 2015Article
- Single-Molecule Pull-Down FRET to Dissect the Mechanisms of Biomolecular Machines.Methods in enzymology · 2015Article
Corrections and comments
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Authors and funding
8 authors at 1 institution in 1 country.
Funding
Abstract
Progress towards a complete model of the methanogenic archaeum Methanosarcina acetivorans is reported. We characterized size distribution of the cells using differential interference contrast microscopy, finding them to be ellipsoidal with mean length and width of 2.9 μ m and 2.3 μ m, respectively, when grown on methanol and 30% smaller when grown on acetate. We used the single molecule pull down (SiMPull) technique to measure average copy number of the Mcr complex and ribosomes. A kinetic model for the methanogenesis pathways based on biochemical studies and recent metabolic reconstructions for several related methanogens is presented. In this model, 26 reactions in the methanogenesis pathways are coupled to a cell mass production reaction that updates enzyme concentrations. RNA expression data (RNA-seq) measured for cell cultures grown on acetate and methanol is used to estimate relative protein production per mole of ATP consumed. The model captures the experimentally observed methane production rates for cells growing on methanol and is most sensitive to the number of methyl-coenzyme-M reductase (Mcr) and methyl-tetrahydromethanopterin:coenzyme-M methyltransferase (Mtr) proteins. A draft transcriptional regulation network based on known interactions is proposed which we intend to integrate with the kinetic model to allow dynamic regulation.
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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.