Protein Quality Control Acts on Folding Intermediates to Shape the Effects of Mutations on Organismal Fitness

Bershtein, Shimon; Mu, Wanmeng; Serohijos, Adrian W.R.; Zhou, Jingwen; Shakhnovich, Eugene I.

doi:10.1016/j.molcel.2012.11.004

Cited by 154 publications

(217 citation statements)

References 58 publications

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“…However, flux dynamics theory (14,15) predicts, and experiments demonstrate, that fitness and IC 50 for TMP can be accurately predicted when the combined effect of mutations that simultaneously change the abundance, activity, and TMP binding affinity of mutant DHFR are taken into account. Further, using the earlier established relationship (13) between DHFR abundance (cellular property) and population of the molten globule state (molecular property of DHFR), we show that the fitness landscape of DHFR mutations can be derived from the molecular properties of DHFR alone. This multiscale analysis provides an example of a predictive quantitative biophysical fitness landscape for an essential enzyme.…”

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confidence: 72%

“…The rare occurrence of off-target adaptive mutations makes DHFR an attractive model to study the fitness landscape of antibiotic resistance. In a recent study (2) strains carrying various combinations of TMP resistance-conferring mutations in folA were incorporated onto the Escherichia coli chromosome (12,13) and their fitness (growth rate) was determined, providing the fitness landscape for the chosen set of variants. The analysis in ref.…”

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confidence: 99%

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Biophysical principles predict fitness landscapes of drug resistance

Rodrigues

Bershtein

et al. 2016

Proc. Natl. Acad. Sci. U.S.A.

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Fitness landscapes of drug resistance constitute powerful tools to elucidate mutational pathways of antibiotic escape. Here, we developed a predictive biophysics-based fitness landscape of trimethoprim (TMP) resistance for Escherichia coli dihydrofolate reductase (DHFR). We investigated the activity, binding, folding stability, and intracellular abundance for a complete set of combinatorial DHFR mutants made out of three key resistance mutations and extended this analysis to DHFR originated from Chlamydia muridarum and Listeria grayi. We found that the acquisition of TMP resistance via decreased drug affinity is limited by a trade-off in catalytic efficiency. Protein stability is concurrently affected by the resistant mutants, which precludes a precise description of fitness from a single molecular trait. Application of the kinetic flux theory provided an accurate model to predict resistance phenotypes (IC50) quantitatively from a unique combination of the in vitro protein molecular properties. Further, we found that a controlled modulation of the GroEL/ES chaperonins and Lon protease levels affects the intracellular steady-state concentration of DHFR in a mutation-specific manner, whereas IC50 is changed proportionally, as indeed predicted by the model. This unveils a molecular rationale for the pleiotropic role of the protein quality control machinery on the evolution of antibiotic resistance, which, as we illustrate here, may drastically confound the evolutionary outcome. These results provide a comprehensive quantitative genotype–phenotype map for the essential enzyme that serves as an important target of antibiotic and anticancer therapies.

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confidence: 72%

mentioning

confidence: 99%

Biophysical principles predict fitness landscapes of drug resistance

Rodrigues

Bershtein

et al. 2016

Proc. Natl. Acad. Sci. U.S.A.

Self Cite

153

265

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“…However, there are a number of experiments which could be used to test our hypothesis regarding the uncoupling of LeuB from the rest of the leucine biosynthesis pathway. A recent study by Bershtein et al (2013) suggests that overexpression of the chaperone complex GroEL/ES or deletion of the Lon protease can rescue the slow growth of E. coli strains carrying destabilised mutant proteins by affecting the balance between protein production, folding and degradation. Although our ancestral LeuBs are not destabilised in comparison with BCVX, this could be an interesting experiment to perform.…”

Section: Discussionmentioning

confidence: 99%

Reconstructed Ancestral Enzymes Impose a Fitness Cost upon Modern Bacteria Despite Exhibiting Favourable Biochemical Properties

et al. 2015

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Ancestral sequence reconstruction has been widely used to study historical enzyme evolution, both from biochemical and cellular perspectives. Two properties of reconstructed ancestral proteins/enzymes are commonly reported-high thermostability and high catalytic activity-compared with their contemporaries. Increased protein stability is associated with lower aggregation rates, higher soluble protein abundance and a greater capacity to evolve, and therefore, these proteins could be considered ''superior'' to their contemporary counterparts. In this study, we investigate the relationship between the favourable in vitro biochemical properties of reconstructed ancestral enzymes and the organismal fitness they confer in vivo. We have previously reconstructed several ancestors of the enzyme LeuB, which is essential for leucine biosynthesis. Our initial fitness experiments revealed that overexpression of ANC4, a reconstructed LeuB that exhibits high stability and activity, was only able to partially rescue the growth of a DleuB strain, and that a strain complemented with this enzyme was outcompeted by strains carrying one of its descendants. When we expanded our study to include five reconstructed LeuBs and one contemporary, we found that neither in vitro protein stability nor the catalytic rate was correlated with fitness. Instead, fitness showed a strong, negative correlation with estimated evolutionary age (based on phylogenetic relationships). Our findings suggest that, for reconstructed ancestral enzymes, superior in vitro properties do not translate into organismal fitness in vivo. The molecular basis of the relationship between fitness and the inferred age of ancestral LeuB enzymes is unknown, but may be related to the reconstruction process. We also hypothesise that the ancestral enzymes may be incompatible with the other, contemporary enzymes of the metabolic network.

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“…The relationship between GroEL over-production and the fixation of deleterious mutations, however unknown, has been shown to be complex. Some evidence pinpoints the function of GroEL in concert with other protein quality control mechanisms, such as the protease Lon, in the folding of proteins at intermediate states of folding, thereby maintaining an equilibrium of folded and active proteins in the cell [56]. Overexpression of groE has been also shown to rescue the fitness of cells bearing a variety of slow-growing, or even deleterious, DHFR mutants and restore their growth to wild type levels [56].…”

Section: Groel Provides Robustness To Mutations and Facilitates The Ementioning

confidence: 99%

“…Some evidence pinpoints the function of GroEL in concert with other protein quality control mechanisms, such as the protease Lon, in the folding of proteins at intermediate states of folding, thereby maintaining an equilibrium of folded and active proteins in the cell [56]. Overexpression of groE has been also shown to rescue the fitness of cells bearing a variety of slow-growing, or even deleterious, DHFR mutants and restore their growth to wild type levels [56]. A prediction derived from these studies is that protein clients requiring GroEL for folding should be candidates for accelerated evolution more readily so than proteins those do not require GroEL.…”

Section: Groel Provides Robustness To Mutations and Facilitates The Ementioning

confidence: 99%

Survival and innovation: The role of mutational robustness in evolution

Fares

2015

Biochimie

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a b s t r a c tBiological systems are resistant to perturbations caused by the environment and by the intrinsic noise of the system. Robustness to mutations is a particular aspect of robustness in which the phenotype is resistant to genotypic variation. Mutational robustness has been linked to the ability of the system to generate heritable genetic variation (a property known as evolvability). It is known that greater robustness leads to increased evolvability. Therefore, mechanisms that increase mutational robustness fuel evolvability. Two such mechanisms, molecular chaperones and gene duplication, have been credited with enormous importance in generating functional diversity through the increase of system's robustness to mutational insults. However, the way in which such mechanisms regulate robustness remains largely uncharacterized. In this review, I provide evidence in support of the role of molecular chaperones and gene duplication in innovation. Specifically, I present evidence that these mechanisms regulate robustness allowing unstable systems to survive long periods of time, and thus they provide opportunity for other mutations to compensate the destabilizing effects of functionally innovative mutations. The findings reported in this study set new questions with regards to the synergy between robustness mechanisms and how this synergy can alter the adaptive landscape of proteins. The ideas proposed in this article set the ground for future research in the understanding of the role of robustness in evolution.

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Protein Quality Control Acts on Folding Intermediates to Shape the Effects of Mutations on Organismal Fitness

Cited by 154 publications

References 58 publications

Biophysical principles predict fitness landscapes of drug resistance

Biophysical principles predict fitness landscapes of drug resistance

Reconstructed Ancestral Enzymes Impose a Fitness Cost upon Modern Bacteria Despite Exhibiting Favourable Biochemical Properties

Survival and innovation: The role of mutational robustness in evolution

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