Constraining the metabolic genotype–phenotype relationship using a phylogeny of in silico methods
Reconstructed microbial metabolic networks facilitate a mechanistic description of the
genotype–phenotype relationship through the deployment of constraint-based …
genotype–phenotype relationship through the deployment of constraint-based …
An evolutionary perspective on the Crabtree effect
T Pfeiffer, A Morley - Frontiers in molecular biosciences, 2014 - frontiersin.org
The capability to ferment sugars into ethanol is a key metabolic trait of yeasts. Crabtree-
positive yeasts use fermentation even in the presence of oxygen, where they could, in …
positive yeasts use fermentation even in the presence of oxygen, where they could, in …
A protocol for generating a high-quality genome-scale metabolic reconstruction
Network reconstructions are a common denominator in systems biology. Bottom–up
metabolic network reconstructions have been developed over the last 10 years. These …
metabolic network reconstructions have been developed over the last 10 years. These …
Glycolytic strategy as a tradeoff between energy yield and protein cost
Contrary to the textbook portrayal of glycolysis as a single pathway conserved across all
domains of life, not all sugar-consuming organisms use the canonical Embden–Meyerhoff …
domains of life, not all sugar-consuming organisms use the canonical Embden–Meyerhoff …
Omic data from evolved E. coli are consistent with computed optimal growth from genome‐scale models
After hundreds of generations of adaptive evolution at exponential growth, Escherichia coli
grows as predicted using flux balance analysis (FBA) on genome‐scale metabolic models …
grows as predicted using flux balance analysis (FBA) on genome‐scale metabolic models …
Shifts in growth strategies reflect tradeoffs in cellular economics
The growth rate‐dependent regulation of cell size, ribosomal content, and metabolic
efficiency follows a common pattern in unicellular organisms: with increasing growth rates …
efficiency follows a common pattern in unicellular organisms: with increasing growth rates …
Upgrading liquor-making wastewater into medium chain fatty acid: insights into co-electron donors, key microflora, and energy harvest
Ethanol and lactate are considered suitable electron donors (EDs) for chain elongation (CE);
however, their respective shortcomings still limit the substrate conversion ratio and medium …
however, their respective shortcomings still limit the substrate conversion ratio and medium …
Pathway thermodynamics highlights kinetic obstacles in central metabolism
In metabolism research, thermodynamics is usually used to determine the directionality of a
reaction or the feasibility of a pathway. However, the relationship between thermodynamic …
reaction or the feasibility of a pathway. However, the relationship between thermodynamic …
Flux balance analysis of cyanobacterial metabolism: the metabolic network of Synechocystis sp. PCC 6803
H Knoop, M Gründel, Y Zilliges… - PLoS computational …, 2013 - journals.plos.org
Cyanobacteria are versatile unicellular phototrophic microorganisms that are highly
abundant in many environments. Owing to their capability to utilize solar energy and …
abundant in many environments. Owing to their capability to utilize solar energy and …
Network context and selection in the evolution to enzyme specificity
Enzymes are thought to have evolved highly specific catalytic activities from promiscuous
ancestral proteins. By analyzing a genome-scale model of Escherichia coli metabolism, we …
ancestral proteins. By analyzing a genome-scale model of Escherichia coli metabolism, we …