Stability effects of mutations and protein evolvability

Tokuriki, Nobuhiko; Tawfik, Dan S.

doi:10.1016/j.sbi.2009.08.003

Cited by 693 publications

(720 citation statements)

References 63 publications

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“…If this is the case, we may expect to observe the same correlation between estimated evolutionary age and fitness for other reconstructed ancestral enzymes. However, the accuracy of inference is not only dependent on the distance from the leaves but also on protein-specific factors, such as branch lengths and the robustness of the protein fold to mutation (Tokiriki and Tawfik 2009). Even if inference accuracy is behind this trend, it still does not provide any insight into the molecular basis of the fitness effects.…”

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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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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“…6,7 In this viewpoint, enzymes preorganize a small subset of residues for efficient function by enforcing structurally strained conformations within the active site, and this is offset by favorable interactions distributed over the remaining majority of the protein structure. 3,4,[9][10][11][12] Computational studies have provided strong support for an additional but distinct foldability-function tradeoff hypothesis, which suggests that native state strain is only one manifestation of the burden imposed by the acquisition of function. In this viewpoint, the requirements of function enforce structural features that are unlikely to be optimal to nucleate protein folding (i.e., they will fold after barrier crossing and be denatured-like in the folding transition state) or are more likely to form intermediates before folding properly (requiring folding ''back-tracking'').…”

Section: Introductionmentioning

confidence: 99%

Experimental support for the foldability–function tradeoff hypothesis: Segregation of the folding nucleus and functional regions in fibroblast growth factor‐1

2012

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The acquisition of function is often associated with destabilizing mutations, giving rise to the stability-function tradeoff hypothesis. To test whether function is also accommodated at the expense of foldability, fibroblast growth factor-1 (FGF-1) was subjected to a comprehensive u-value analysis at each of the 11 turn regions. FGF-1, a b-trefoil fold, represents an excellent model system with which to evaluate the influence of function on foldability: because of its threefold symmetric structure, analysis of FGF-1 allows for direct comparisons between symmetryrelated regions of the protein that are associated with function to those that are not; thus, a structural basis for regions of foldability can potentially be identified. The resulting u-value distribution of FGF-1 is highly polarized, with the majority of positions described as either foldedlike or denatured-like in the folding transition state. Regions important for folding are shown to be asymmetrically distributed within the protein architecture; furthermore, regions associated with function (i.e., heparin-binding affinity and receptor-binding affinity) are localized to regions of the protein that fold after barrier crossing (late in the folding pathway). These results provide experimental support for the foldability-function tradeoff hypothesis in the evolution of FGF-1. Notably, the results identify the potential for folding redundancy in symmetric protein architecture with important implications for protein evolution and design.

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“…Although the majority of plants use the ancestral C 3 photosynthetic pathway, many flowering plants have evolved a derived pathway named C 4 photosynthesis. The latter concentrates CO 2 , and C 4 RubisCOs consequently have lower specificity for, and faster turnover of, CO 2 . The C 4 forms result from convergent evolution in multiple clades, with substitutions at a small number of sites under positive selection.…”

mentioning

confidence: 99%

“…The latter concentrates CO 2 , and C 4 RubisCOs consequently have lower specificity for, and faster turnover of, CO 2 . The C 4 forms result from convergent evolution in multiple clades, with substitutions at a small number of sites under positive selection. To understand the physical constraints on these evolutionary changes, we reconstructed in silico ancestral sequences and 3D structures of RubisCO from a large group of related C 3 and C 4 species.…”

mentioning

confidence: 99%

“…We show that RubisCO evolution has been constrained by stability-activity tradeoffs similar in character to those previously identified in laboratory-based experiments. The C 4 properties require a subset of several ancestral destabilizing mutations, which from their location in the structure are inferred to mainly be involved in enhancing conformational flexibility of the open-closed transition in the catalytic cycle. These mutations are near, but not in, the active site or at intersubunit interfaces.…”

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confidence: 99%

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Stability-activity tradeoffs constrain the adaptive evolution of RubisCO

Studer

Christin

Williams

et al. 2014

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

153

143

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A well-known case of evolutionary adaptation is that of ribulose-1,5-bisphosphate carboxylase (RubisCO), the enzyme responsible for fixation of CO 2 during photosynthesis. Although the majority of plants use the ancestral C 3 photosynthetic pathway, many flowering plants have evolved a derived pathway named C 4 photosynthesis. The latter concentrates CO 2 , and C 4 RubisCOs consequently have lower specificity for, and faster turnover of, CO 2 . The C 4 forms result from convergent evolution in multiple clades, with substitutions at a small number of sites under positive selection. To understand the physical constraints on these evolutionary changes, we reconstructed in silico ancestral sequences and 3D structures of RubisCO from a large group of related C 3 and C 4 species. We were able to precisely track their past evolutionary trajectories, identify mutations on each branch of the phylogeny, and evaluate their stability effect. We show that RubisCO evolution has been constrained by stability-activity tradeoffs similar in character to those previously identified in laboratory-based experiments. The C 4 properties require a subset of several ancestral destabilizing mutations, which from their location in the structure are inferred to mainly be involved in enhancing conformational flexibility of the open-closed transition in the catalytic cycle. These mutations are near, but not in, the active site or at intersubunit interfaces. The C 3 to C 4 transition is preceded by a sustained period in which stability of the enzyme is increased, creating the capacity to accept the functionally necessary destabilizing mutations, and is immediately followed by compensatory mutations that restore global stability.T he adaptive diversification of organisms often requires the evolution of novel enzymatic properties. The evolutionary shift from one enzymatic function to another involves crossing an energetic barrier in a fitness landscape (1). The number of mutations that confer advantageous function during such a shift is consequently limited. Some residues are critical for maintaining the stability of the protein fold, others are important for the catalytic activity itself. Due to the multiple roles of amino acids in proteins, the adaptation of one physical parameter of an enzyme is likely to affect other properties (2). As proteins usually form thermodynamically stable structures, their evolutionary trajectories are constrained to a narrow range of stability (3). Stability and activity are likely to be negatively correlated. Most possible amino acid changes in native proteins are destabilizing and, consequently, mutations that lead to a more favorable enzyme activity are likely to decrease the stability of the protein (2, 4). Compensatory mutations are then needed to restore global stability. These processes are referred to as stability-activity tradeoffs (5-7). Furthermore, proteins with higher stability confer greater evolvability, because there is more scope to accept destabilizing yet functionally beneficial changes (8). Wh...

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Stability effects of mutations and protein evolvability

Cited by 693 publications

References 63 publications

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

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

Experimental support for the foldability–function tradeoff hypothesis: Segregation of the folding nucleus and functional regions in fibroblast growth factor‐1

Stability-activity tradeoffs constrain the adaptive evolution of RubisCO

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