ArticlePLoS computational biology2019
Predicting proteome allocation, overflow metabolism, and metal requirements in a model acetogen.
Article in PLoS computational biology, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 25 papers.
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Who cites it
25 citing papers in PubMed, 59 citations in OpenAlex.
- Model of metabolism and gene expression predicts proteome allocation in Pseudomonas putida.NPJ systems biology and applications · 2025Article
- Integration of proteomic data with genome-scale metabolic models: A methodological overview.Protein science : a publication of the Protein Society · 2024Review
- Overflow metabolism at the thermodynamic limit of life: How carboxydotrophic acetogens mitigate carbon monoxide toxicity.Microbial biotechnology · 2023Article
- Enzyme-constrained metabolic model andComputational and structural biotechnology journal · 2023Article
- Predicting stress response and improved protein overproduction in Bacillus subtilis.NPJ systems biology and applications · 2022Article
- Characterizing the Interplay of Rubisco and Nitrogenase Enzymes in Anaerobic-Photoheterotrophically Grown Rhodopseudomonas palustris CGA009 through a Genome-Scale Metabolic and Expression Model.Microbiology spectrum · 2022Article
- Genome-scale metabolic modeling in antimicrobial pharmacology.Engineering microbiology · 2022Review
- Construction of Multiscale Genome-Scale Metabolic Models: Frameworks and Challenges.Biomolecules · 2022Review
- Engineering Acetogenic Bacteria for Efficient One-Carbon Utilization.Frontiers in microbiology · 2022Review
- Biosynthesis Based on One-Carbon Mixotrophy.Advances in biochemical engineering/biotechnology · 2022Article
- Systems Biology on Acetogenic Bacteria for Utilizing C1 Feedstocks.Advances in biochemical engineering/biotechnology · 2022Article
- Review
- Review
- Genome-Scale Reconstruction of Microbial Dynamic Phenotype: Successes and Challenges.Microorganisms · 2021Review
- Yeast optimizes metal utilization based on metabolic network and enzyme kinetics.Proceedings of the National Academy of Sciences of the United States of America · 2021Article
- Article
- The Expanding Computational Toolbox for Engineering Microbial Phenotypes at the Genome Scale.Microorganisms · 2020Review
- Reconstructing organisms in silico: genome-scale models and their emerging applications.Nature reviews. Microbiology · 2020Review
- Modeling of nitrogen fixation and polymer production in the heterotrophic diazotrophMetabolic engineering communications · 2020Article
- Synthetic Biology on Acetogenic Bacteria for Highly Efficient Conversion of C1 Gases to Biochemicals.International journal of molecular sciences · 2020Review
Corrections and comments
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Authors and funding
9 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The unique capability of acetogens to ferment a broad range of substrates renders them ideal candidates for the biotechnological production of commodity chemicals. In particular the ability to grow with H2:CO2 or syngas (a mixture of H2/CO/CO2) makes these microorganisms ideal chassis for sustainable bioproduction. However, advanced design strategies for acetogens are currently hampered by incomplete knowledge about their physiology and our inability to accurately predict phenotypes. Here we describe the reconstruction of a novel genome-scale model of metabolism and macromolecular synthesis (ME-model) to gain new insights into the biology of the model acetogen Clostridium ljungdahlii. The model represents the first ME-model of a Gram-positive bacterium and captures all major central metabolic, amino acid, nucleotide, lipid, major cofactors, and vitamin synthesis pathways as well as pathways to synthesis RNA and protein molecules necessary to catalyze these reactions, thus significantly broadens the scope and predictability. Use of the model revealed how protein allocation and media composition influence metabolic pathways and energy conservation in acetogens and accurately predicted secretion of multiple fermentation products. Predicting overflow metabolism is of particular interest since it enables new design strategies, e.g. the formation of glycerol, a novel product for C. ljungdahlii, thus broadening the metabolic capability for this model microbe. Furthermore, prediction and experimental validation of changing secretion rates based on different metal availability opens the window into fermentation optimization and provides new knowledge about the proteome utilization and carbon flux in acetogens.
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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.