Optimality and evolutionary tuning of the expression level of a protein

@article{Dekel2005OptimalityAE,
  title={Optimality and evolutionary tuning of the expression level of a protein},
  author={Erez Dekel and Uri Alon},
  journal={Nature},
  year={2005},
  volume={436},
  pages={588-592}
}
Different proteins have different expression levels. It is unclear to what extent these expression levels are optimized to their environment. Evolutionary theories suggest that protein expression levels maximize fitness, but the fitness as a function of protein level has seldom been directly measured. To address this, we studied the lac system of Escherichia coli, which allows the cell to use the sugar lactose for growth. We experimentally measured the growth burden due to production and… 
Nonlinear Fitness Landscape of a Molecular Pathway
TLDR
It is argued that fitness nonlinearities, expression barriers, and gene–environment interactions are generic features of fitness landscapes for metabolic pathways, and their implications for the evolution of regulation are discussed.
Expression Level, Evolutionary Rate, and the Cost of Expression
TLDR
Although the model is based on selection for protein function, it is consistent with findings that a protein's rate of evolution is at most weakly correlated with its importance for fitness as measured by gene knockout experiments.
Optimality and evolution of transcriptionally regulated gene expression
TLDR
The decoupling of regulatory and metabolic functions of the Escherichia coli lac system is shown to evolve within several hundreds of generations to optima that are predicted by these costs and benefits.
Evolutionary pressures on microbial metabolic strategies in the chemostat
TLDR
A theoretical framework is provided that relates a kinetic, mechanistic view on metabolism with cellular physiology and evolutionary dynamics in the chemostat and shows that the optimal enzyme levels are the result of a trade-off between the cost of their production and the benefit of their catalytic function.
Escherichia coli robustly expresses ATP synthase at growth rate maximizing concentrations
TLDR
This work indicates that bacteria can achieve robust optimal protein expression for immediate growth- rate, and focuses on the ATP-producing enzyme F1F0 H+-ATPase, which is an abundant enzyme and ubiquitously expressed across conditions.
Optimality and sub-optimality in a bacterial growth law
TLDR
It is found that the growth law is optimal in many conditions, including a range of perturbations to lactose uptake, but provides sub-optimal growth on several other carbon sources.
Constitutive versus Responsive Gene Expression Strategies for Growth in Changing Environments
TLDR
The fitness of a constitutive and a responsive expression strategy in time-varying environments is studied, and constitutive expression can provide higher fitness than responsive expression even when regulatory machinery comes at no cost.
Cost-Benefit Tradeoffs in Engineered lac Operons
TLDR
Quantitative fitness measurements in 27 redesigned operons are reported that suggested that protein production is not the primary origin of fitness costs and instead it is discovered that the lac permease activity, which relates linearly to cost, is the major physiological burden to the cell.
Gene Architectures that Minimize Cost of Gene Expression.
Modeling the cost and benefit of proteome regulation in a growing bacterial cell.
TLDR
There is a window of environments or a 'niche' in which the unregulated cell has a higher fitness than the regulated cell, and outside this niche there is a large space of constant and time varying environments in which regulation is an advantage and which would therefore favour the evolution of regulation.
...
1
2
3
4
5
...

References

SHOWING 1-10 OF 38 REFERENCES
Metabolic flux and fitness.
TLDR
The results determine the adaptive topography of these gene products relative to growth in limiting lactose and enable predictions concerning the selective effects of genetic variants found in natural populations to be predicted.
Parallel changes in gene expression after 20,000 generations of evolution in Escherichia coli
TLDR
DNA expression arrays are used to examine whether gene-expression profiles in two populations evolved in parallel, which would indicate adaptation, and to gain insight into the mechanisms underlying their adaptation.
The protein burden of lac operon products.
  • A. L. Koch
  • Biology
    Journal of molecular evolution
  • 1983
TLDR
While one would expect under carbon and energy limitation in the chemostat the protein burden to be larger than under unlimited conditions, it is so small that even the refined technique used here could not measure it accurately.
Escherichia coli K-12 undergoes adaptive evolution to achieve in silico predicted optimal growth
TLDR
When placed under growth selection pressure, the growth rate of E. coli on glycerol reproducibly evolved from a sub-optimal value to the optimal growth rate predicted from a whole-cell in silico model, opening the possibility of using adaptive evolution of entire metabolic networks to realize metabolic states that have been determined a priori based on insilico analysis.
Dynamics and bistability in a reduced model of the lac operon.
TLDR
A previously published model which accounts for the dynamics of mRNA, lactose, allolactose, permease and beta-galactosidase involvement is simplified and it was shown that it may indeed display bistability, depending on the extracellular lactose concentration and growth rate.
Effects of carriage and expression of the Tn10 tetracycline-resistance operon on the fitness of Escherichia coli K12.
TLDR
Tight gene regulation has eliminated antagonistic pleiotropic effects of the resistance gene on fitness, so that possession of an inducible Tn10-encoded tetracycline-resistance operon imposes essentially no burden in the absence of antibiotic.
Computation, prediction, and experimental tests of fitness for bacteriophage T7 mutants with permuted genomes.
TLDR
A simulation based on experimental data from bacteriophage T7 that computes the developmental cycle of the wild-type phage and also of mutants that have an altered genome order was created and the fitness of more than 10 mutants was used to compute.
Analysis of optimality in natural and perturbed metabolic networks
TLDR
The method of minimization of metabolic adjustment (MOMA), whereby the hypothesis that knockout metabolic fluxes undergo a minimal redistribution with respect to the flux configuration of the wild type is tested, is tested and found to be useful in understanding the evolutionary optimization of metabolism.
The organization of metabolic reaction networks. III. Application for diauxic growth on glucose and lactose.
TLDR
A mathematical model to describe carbon catabolite repression in Escherichia coli is developed and in part validated and all experiments could be sufficiently described with a single set of parameters.
...
1
2
3
4
...