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Laboratory evolution reveals a two-dimensional rate-yield tradeoff in microbial metabolism
- Source :
- Cheng, C, O'Brien, E J, McCloskey, D, Utrilla, J, Olson, C, LaCroix, R A, Sandberg, T E, Feist, A M, Palsson, B O & King, Z A 2019, ' Laboratory evolution reveals a two-dimensional rate-yield tradeoff in microbial metabolism ', PLOS Computational Biology, vol. 15, no. 6, e1007066 . https://doi.org/10.1371/journal.pcbi.1007066, PLoS Computational Biology, Vol 15, Iss 6, p e1007066 (2019), PLoS Computational Biology
- Publication Year :
- 2018
- Publisher :
- Cold Spring Harbor Laboratory, 2018.
-
Abstract
- Growth rate and yield are fundamental features of microbial growth. However, we lack a mechanistic and quantitative understanding of the rate-yield relationship. Studies pairing computational predictions with experiments have shown the importance of maintenance energy and proteome allocation in explaining rate-yield tradeoffs and overflow metabolism. Recently, adaptive evolution experiments of Escherichia coli reveal a phenotypic diversity beyond what has been explained using simple models of growth rate versus yield. Here, we identify a two-dimensional rate-yield tradeoff in adapted E. coli strains where the dimensions are (A) a tradeoff between growth rate and yield and (B) a tradeoff between substrate (glucose) uptake rate and growth yield. We employ a multi-scale modeling approach, combining a previously reported coarse-grained small-scale proteome allocation model with a fine-grained genome-scale model of metabolism and gene expression (ME-model), to develop a quantitative description of the full rate-yield relationship for E. coli K-12 MG1655. The multi-scale analysis resolves the complexity of ME-model which hindered its practical use in proteome complexity analysis, and provides a mechanistic explanation of the two-dimensional tradeoff. Further, the analysis identifies modifications to the P/O ratio and the flux allocation between glycolysis and pentose phosphate pathway (PPP) as potential mechanisms that enable the tradeoff between glucose uptake rate and growth yield. Thus, the rate-yield tradeoffs that govern microbial adaptation to new environments are more complex than previously reported, and they can be understood in mechanistic detail using a multi-scale modeling approach.<br />Author summary This study reconciles multiple existing microbial rate-yield tradeoff theories with experimental data. There is great interest in developing quantitative descriptions of the relationship between growth rate and growth yield [1]. However, some reported experiments [2–4] in the literature do not agree with existing theories [5–7]. Specifically, overflow metabolism in E. coli can either be coupled [5, 8] or decoupled [2–4] from growth rate. We found that adaptive laboratory evolution (ALE) experiments of E. coli reveal a two-dimensional rate-yield tradeoff in adapted strains where the dimensions are (i) a tradeoff between growth rate and growth yield, previously reported by [5], and (ii) a tradeoff between substrate uptake rate and growth yield. The appearance of this two-dimensional tradeoff during adaptation suggests that microorganisms adapting to new environments are subject to a more complex set of rate-yield tradeoffs than previously reported [5, 6]. In this study, the two-dimensional rate-yield tradeoff is quantitatively explained through our multi-scale modeling approach, combining a previously reported small-scale proteome allocation model [5] with a genome-scale model of metabolism and gene-expression (ME-model) [9]. The modeling approach is also instrumental to future studies.
- Subjects :
- 0301 basic medicine
Proteome
Proteomes
Physiology
Enzyme Metabolism
Microbial metabolism
Biochemistry
0302 clinical medicine
Glucose Metabolism
Medicine and Health Sciences
Growth rate
Biology (General)
Enzyme Chemistry
Overflow metabolism
Mathematics
Ecology
Systems Biology
Physics
Enzymes
Computational Theory and Mathematics
Modeling and Simulation
Physical Sciences
Carbohydrate Metabolism
Metabolic Pathways
Protons
Biological system
Research Article
Evolutionary Processes
QH301-705.5
Systems biology
Excretion
Models, Biological
Evolution, Molecular
03 medical and health sciences
Cellular and Molecular Neuroscience
Bacterial Proteins
Evolutionary Adaptation
Genetics
Escherichia coli
Molecular Biology
Ecology, Evolution, Behavior and Systematics
Nuclear Physics
Nucleons
Evolutionary Biology
Biology and Life Sciences
Proteins
Metabolic pathway
030104 developmental biology
Metabolism
Yield (chemistry)
Enzymology
Adaptation
Physiological Processes
Flux (metabolism)
030217 neurology & neurosurgery
Genome, Bacterial
Adaptive evolution
Subjects
Details
- Language :
- English
- Database :
- OpenAIRE
- Journal :
- Cheng, C, O'Brien, E J, McCloskey, D, Utrilla, J, Olson, C, LaCroix, R A, Sandberg, T E, Feist, A M, Palsson, B O & King, Z A 2019, ' Laboratory evolution reveals a two-dimensional rate-yield tradeoff in microbial metabolism ', PLOS Computational Biology, vol. 15, no. 6, e1007066 . https://doi.org/10.1371/journal.pcbi.1007066, PLoS Computational Biology, Vol 15, Iss 6, p e1007066 (2019), PLoS Computational Biology
- Accession number :
- edsair.doi.dedup.....288cae23c69f8a48f1d5dffac804608f
- Full Text :
- https://doi.org/10.1101/414912