scholarly journals Substrate inhibition imposes fitness penalty at high protein stability

2018 ◽  
Author(s):  
Bharat V. Adkar ◽  
Sanchari Bhattacharyya ◽  
Amy I. Gilson ◽  
Wenli Zhang ◽  
Eugene I. Shakhnovich
Keyword(s):  
Adenylate Kinase ◽  
Narrow Range ◽  
Substrate Inhibition ◽  
Purifying Selection ◽  
Neutral Drift ◽  
E Coli ◽  
Physiological Conditions ◽  
Fitness Effects ◽  
Excess Substrate ◽  
Excess Stability

AbstractProteins are only moderately stable. It has long been debated whether this narrow range of stabilities is solely a result of neutral drift towards lower stability or purifying selection against excess stability is also at work — for which no experimental evidence was found so far. Here we show that mutations outside the active site in the essential E. coli enzyme adenylate kinase result in stability-dependent increase in substrate inhibition by AMP, thereby impairing overall enzyme activity at high stability. Such inhibition caused substantial fitness defects not only in the presence of excess substrate but also under physiological conditions. In the latter case, substrate inhibition caused differential accumulation of AMP in the stationary phase for the inhibition prone mutants. Further, we show that changes in flux through Adk could accurately describe the variation in fitness effects. Taken together, these data suggest that selection against substrate inhibition and hence excess stability may have resulted in a narrow range of optimal stability observed for modern proteins.

scholarly journals Substrate inhibition imposes fitness penalty at high protein stability

2019 ◽  
Vol 116 (23) ◽  
pp. 11265-11274 ◽  
Author(s):  
Bharat V. Adkar ◽  
Sanchari Bhattacharyya ◽  
Amy I. Gilson ◽  
Wenli Zhang ◽  
Eugene I. Shakhnovich
Keyword(s):  
Active Site ◽  
Adenylate Kinase ◽  
Narrow Range ◽  
Substrate Inhibition ◽  
Purifying Selection ◽  
Neutral Drift ◽  
Physiological Conditions ◽  
Fitness Effects ◽  
Excess Substrate ◽  
Excess Stability

Proteins are only moderately stable. It has long been debated whether this narrow range of stabilities is solely a result of neutral drift toward lower stability or purifying selection against excess stability—for which no experimental evidence was found so far—is also at work. Here, we show that mutations outside the active site in the essential Escherichia coli enzyme adenylate kinase (Adk) result in a stability-dependent increase in substrate inhibition by AMP, thereby impairing overall enzyme activity at high stability. Such inhibition caused substantial fitness defects not only in the presence of excess substrate but also under physiological conditions. In the latter case, substrate inhibition caused differential accumulation of AMP in the stationary phase for the inhibition-prone mutants. Furthermore, we show that changes in flux through Adk could accurately describe the variation in fitness effects. Taken together, these data suggest that selection against substrate inhibition and hence excess stability may be an important factor determining stability observed for modern-day Adk.

scholarly journals Optimization of lag phase shapes the evolution of a bacterial enzyme

2016 ◽  
Author(s):  
Bharat V. Adkar ◽  
Michael Manhart ◽  
Sanchari Bhattacharyya ◽  
Jian Tian ◽  
Michael Musharbash ◽  
...  
Keyword(s):  
Growth Rates ◽  
Adenylate Kinase ◽  
Fitness Landscape ◽  
Lag Phase ◽  
E Coli ◽  
Fitness Effects ◽  
Bacterial Enzyme ◽  
Lag Times ◽  
Essential Enzyme ◽  
Catalytic Capacity

AbstractMutations provide the variation that drives evolution, yet their effects on fitness remain poorly understood. Here we explore how mutations in the essential enzyme Adenylate Kinase (Adk) ofE. coliaffect multiple phases of population growth. We introduce a biophysical fitness landscape for these phases, showing how they depend on molecular and cellular properties of Adk. We find that Adk catalytic capacity in the cell (product of activity and abundance) is the major determinant of mutational fitness effects. We show that bacterial lag times are at a well-defined optimum with respect to Adk’s catalytic capacity, while exponential growth rates are only weakly affected by variation in Adk. Direct pairwise competitions between strains show how environmental conditions modulate the outcome of a competition where growth rates and lag times have a tradeoff, altogether shedding light on the multidimensional nature of fitness and its importance in the evolutionary optimization of enzymes.

Towards a mechanism of AMP-substrate inhibition in adenylate kinase fromEscherichia coli

FEBS Letters ◽  
1996 ◽  
Vol 397 (2-3) ◽  
pp. 273-276 ◽  
Author(s):  
Michael A. Sinev ◽  
Elena V. Sineva ◽  
Varda Ittah ◽  
Elisha Haas
Keyword(s):  
Adenylate Kinase ◽  
Substrate Inhibition ◽  
Fromescherichia Coli

scholarly journals Increased Survival of Antibiotic-Resistant Escherichia coli inside Macrophages

2012 ◽  
Vol 57 (1) ◽  
pp. 189-195 ◽  
Author(s):  
Migla Miskinyte ◽  
Isabel Gordo
Keyword(s):  
Escherichia Coli ◽  
Antibiotic Resistance ◽  
Bacterial Infections ◽  
Resistance Mutation ◽  
Fitness Cost ◽  
Resistance Mutations ◽  
Content Type ◽  
E Coli ◽  
Fitness Effects ◽  
K 12

ABSTRACTMutations causing antibiotic resistance usually incur a fitness cost in the absence of antibiotics. The magnitude of such costs is known to vary with the environment. Little is known about the fitness effects of antibiotic resistance mutations when bacteria confront the host's immune system. Here, we study the fitness effects of mutations in therpoB,rpsL, andgyrAgenes, which confer resistance to rifampin, streptomycin, and nalidixic acid, respectively. These antibiotics are frequently used in the treatment of bacterial infections. We measured two important fitness traits—growth rate and survival ability—of 12Escherichia coliK-12 strains, each carrying a single resistance mutation, in the presence of macrophages. Strikingly, we found that 67% of the mutants survived better than the susceptible bacteria in the intracellular niche of the phagocytic cells. In particular, allE. colistreptomycin-resistant mutants exhibited an intracellular advantage. On the other hand, 42% of the mutants incurred a high fitness cost when the bacteria were allowed to divide outside of macrophages. This study shows that single nonsynonymous changes affecting fundamental processes in the cell can contribute to prolonged survival ofE. coliin the context of an infection.

scholarly journals Genomewide Mutational Diversity in Escherichia coli Population Evolving in Prolonged Stationary Phase

mSphere ◽  
2017 ◽  
Vol 2 (3) ◽  
Author(s):  
Savita Chib ◽  
Farhan Ali ◽  
Aswin Sai Narain Seshasayee
Keyword(s):  
Escherichia Coli ◽  
Genetic Diversity ◽  
Stationary Phase ◽  
Phenotypic Diversity ◽  
Model System ◽  
Content Type ◽  
Neutral Drift ◽  
E Coli ◽  
Evolution By Natural Selection ◽  
Over Time

ABSTRACT Prolonged stationary phase in bacteria, contrary to its name, is highly dynamic, with extreme nutrient limitation as a predominant stress. Stationary-phase cultures adapt by rapidly selecting a mutation(s) that confers a growth advantage in stationary phase (GASP). The phenotypic diversity of starving E. coli populations has been studied in detail; however, only a few mutations that accumulate in prolonged stationary phase have been described. This study documented the spectrum of mutations appearing in Escherichia coli during 28 days of prolonged starvation. The genetic diversity of the population increases over time in stationary phase to an extent that cannot be explained by random, neutral drift. This suggests that prolonged stationary phase offers a great model system to study adaptive evolution by natural selection. Prolonged stationary phase is an approximation of natural environments presenting a range of stresses. Survival in prolonged stationary phase requires alternative metabolic pathways for survival. This study describes the repertoire of mutations accumulating in starving Escherichia coli populations in lysogeny broth. A wide range of mutations accumulates over the course of 1 month in stationary phase. Single nucleotide polymorphisms (SNPs) constitute 64% of all mutations. A majority of these mutations are nonsynonymous and are located at conserved loci. There is an increase in genetic diversity in the evolving populations over time. Computer simulations of evolution in stationary phase suggest that the maximum frequency of mutations observed in our experimental populations cannot be explained by neutral drift. Moreover, there is frequent genetic parallelism across populations, suggesting that these mutations are under positive selection. Finally, functional analysis of mutations suggests that regulatory mutations are frequent targets of selection. IMPORTANCE Prolonged stationary phase in bacteria, contrary to its name, is highly dynamic, with extreme nutrient limitation as a predominant stress. Stationary-phase cultures adapt by rapidly selecting a mutation(s) that confers a growth advantage in stationary phase (GASP). The phenotypic diversity of starving E. coli populations has been studied in detail; however, only a few mutations that accumulate in prolonged stationary phase have been described. This study documented the spectrum of mutations appearing in Escherichia coli during 28 days of prolonged starvation. The genetic diversity of the population increases over time in stationary phase to an extent that cannot be explained by random, neutral drift. This suggests that prolonged stationary phase offers a great model system to study adaptive evolution by natural selection.

scholarly journals E. Coli Adenylate Kinase Exhibits Inter-Domain Coupling

2019 ◽  
Vol 116 (3) ◽  
pp. 162a-163a
Author(s):  
Joseph E. Rehfus ◽  
Vincent J. Hilser
Keyword(s):  
Adenylate Kinase ◽  
E Coli ◽  
Domain Coupling

scholarly journals Excess substrate inhibition of soybean lipoxygenase-1 is mainly oxygen-dependent

FEBS Letters ◽  
1997 ◽  
Vol 408 (3) ◽  
pp. 324-326 ◽  
Author(s):  
Hugues Berry ◽  
Hélène Debat ◽  
Véronique Larreta-Garde
Keyword(s):  
Substrate Inhibition ◽  
Soybean Lipoxygenase ◽  
Excess Substrate

scholarly journals Escherichia coliLrp regulates one-third of the genome via direct, cooperative, and indirect routes

2018 ◽  
Author(s):  
Grace M. Kroner ◽  
Michael B. Wolfe ◽  
Peter L. Freddolino
Keyword(s):  
Escherichia Coli ◽  
Crucial Role ◽  
Regulatory Activity ◽  
Global Regulator ◽  
Full Spectrum ◽  
Global Trends ◽  
Cooperative Action ◽  
E Coli ◽  
Physiological Conditions ◽  
Regulatory Behavior

AbstractThe global regulator Lrp plays a crucial role in regulating metabolism, virulence and motility in response to environmental conditions. Lrp has previously been shown to activate or repress approximately 10% of genes inEscherichia coli. However, the full spectrum of targets, and how Lrp acts to regulate them, has stymied earlier study. We have combined matched ChIP-seq and RNA sequencing under nine physiological conditions to map the binding and regulatory activity of Lrp as it directs responses to nutrient abundance. In addition to identifying hundreds of novel Lrp targets, we observe two new global trends: first, that Lrp will often bind to promoters in a poised position under conditions when it has no regulatory activity, and second, that nutrient levels induce a global shift in the equilibrium between non-specific and sequence-specific DNA binding. The overall regulatory behavior of Lrp, which as we now show regulates 35% ofE. coligenes directly or indirectly under at least one condition, thus arises from the interaction between changes in Lrp binding specificity and cooperative action with other regulators.

scholarly journals Cell size regulation in bacteria

2014 ◽  
Author(s):  
Ariel Amir
Keyword(s):  
Cell Size ◽  
Narrow Range ◽  
Size Control ◽  
Exponential Dependence ◽  
Model Parameters ◽  
E Coli ◽  
Daughter Cells ◽  
Mother And Daughter ◽  
A Cell ◽  
Initiation Of Dna Replication

Various bacteria such as the canonical gram negative Escherichia coli or the well-studied gram positive Bacillus subtilis divide symmetrically after they approximately double their volume. Their size at division is not constant, but is typically distributed over a narrow range. Here, we propose an analytically tractable model for cell size control, and calculate the cell size and inter-division time distributions, and the correlations between these variables. We suggest ways of extracting the model parameters from experimental data, and show that existing data for E. coli supports partial size control, and a particular explanation: a cell attempts to add a constant volume from the time of initiation of DNA replication to the next initiation event. This hypothesis accounts for the experimentally observed correlations between mother and daughter cells as well as the exponential dependence of size on growth rate.

scholarly journals Evidence of evolutionary selection for co-translational folding

2017 ◽  
Author(s):  
William M. Jacobs ◽  
Eugene I. Shakhnovich
Keyword(s):  
Self Assembly ◽  
E Coli ◽  
Evolutionary Selection ◽  
Fitness Effects ◽  
Open Questions ◽  
Genome Wide ◽  
A Genome ◽  
Evolutionarily Conserved ◽  
Domain Boundaries ◽  
Selection For

Recent experiments and simulations have demonstrated that proteins can fold on the ribosome. However, the extent and generality of fitness effects resulting from co-translational folding remain open questions. Here we report a genome-wide analysis that uncovers evidence of evolutionary selection for co-translational folding. We describe a robust statistical approach to identify loci within genes that are both significantly enriched in slowly translated codons and evolutionarily conserved. Surprisingly, we find that domain boundaries can explain only a small fraction of these conserved loci. Instead, we propose that regions enriched in slowly translated codons are associated with co-translational folding intermediates, which may be smaller than a single domain. We show that the intermediates predicted by a native-centric model of co-translational folding account for the majority of these loci across more than 500 E. coli proteins. By making a direct connection to protein folding, this analysis provides strong evidence that many synonymous substitutions have been selected to optimize translation rates at specific locations within genes. More generally, our results indicate that kinetics, and not just thermodynamics, can significantly alter the efficiency of self-assembly in a biological context.

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