Why are proteins so robust to site mutations?

There have been repeated observations that proteins are surprisingly robust to site mutations, enduring significant numbers of substitutions with little change in structure, stability, or function. These results are almost paradoxical in light of what is known about random heteropolymers and the sensitivity of their properties to seemingly trivial mutations. To address this discrepancy, the preservation of biological protein properties in the presence of mutation has been interpreted as indicating the independence of selective pressure on such properties. Such results also lead to the prediction that de novo protein design should be relatively easy, in contrast to what is observed. Here, we use a computational model with lattice proteins to demonstrate how this robustness can result from population dynamics during the evolutionary process. As a result, sequence plasticity may be a characteristic of evolutionarily derived proteins and not necessarily a property of designed proteins. This suggests that this robustness must be re-interpreted in evolutionary terms, and has consequences for our understanding of both in vivo and in vitro protein evolution.     

Why are proteins marginally stable?

Most globular proteins are marginally stable regardless of size or activity. The most common interpretation is that proteins must be marginally stable in order to function, and so marginal stability represents the results of positive selection. We consider the issue of marginal stability directly using model proteins and the dynamical aspects of protein evolution in populations. We find that the marginal stability of proteins is an inherent property of proteins due to the high dimensionality of the sequence space, without regard to protein function. In this way, marginal stability can result from neutral, non-adaptive evolution. By allowing evolving protein sub-populations with different stability requirements for functionality to complete, we find that marginally stable populations of proteins tend to dominate. Our results show that functionalities consistent with marginal stability have a strong evolutionary advantage, and might arise because of the natural tendency of proteins towards marginal stability.     

Adaptive evolution in ecological communities

Understanding how natural selection drives evolution is a key challenge in evolutionary biology. Most studies of adaptation focus on how a single environmental factor, such as increased temperature, affects evolution within a single species. The biological relevance of these experiments is limited because nature is infinitely more complex. Most species are embedded within communities containing many species that interact with one another and the physical environment. To understand the evolutionary significance of such ecological complexity, experiments must test the evolutionary impact of interactions among multiple species during adaptation. Here we highlight an experiment that manipulates species composition and tracks evolutionary responses within each species, while testing for the mechanisms by which species interact and adapt to their environment. We also discuss limitations of previous studies of adaptive evolution and emphasize how an experimental evolution approach can circumvent such shortcomings. Understanding how community composition acts as a selective force will improve our ability to predict how species adapt to natural and human-induced environmental change.     

Predators modify the evolutionary response of prey to temperature change

As climate regimes shift in many ecosystems worldwide, evolution may be a critical process allowing persistence in rapidly changing environments. Organisms regularly interact with other species, yet whether climate-mediated evolution can occur in the context of species interactions is not well understood. We tested whether a species interaction could modify evolutionary responses to temperature. We demonstrate that predation pressure by Dipteran larvae (Chaoborus americanus) modified the evolutionary response of a freshwater crustacean (Daphnia pulex) to its thermal environment over approximately seven generations in laboratory conditions. Daphnia kept at 21°C evolved higher population growth rates than those kept at 18°C, but only in those populations that were also reared with predators. Furthermore, predator-mediated selection resulted in the evolution of elevated Daphnia thermal plasticity. This laboratory natural selection experiment demonstrates that biotic interactions can modify evolutionary adaptation to temperature. Understanding the interplay between multiple selective forces can improve predictions of ecological and evolutionary responses of organisms to rapid environmental change.     

Origins of globular structure in proteins

Since natural proteins are the products of a long evolutionary process, the structural properties of present-day proteins should depend not only on physico-chemical constraints, but also on evolutionary constraints. Here we propose a model for protein evolution, in which membranes play a key role as a scaffold for supporting the gradual evolution from flexible polypeptides to well-folded proteins. We suggest that the folding process of present-day globular proteins is a relic of this putative evolutionary process. To test the hypothesis that membranes once acted as a cradle for the folding of globular proteins, extensive research on membrane proteins and the interactions of globular proteins with membranes will be required.     

REVIEW: Optimality models in the age of experimental evolution and genomics

Optimality models have been used to predict evolution of many properties of organisms. They typically neglect genetic details, whether by necessity or design. This omission is a common source of criticism, and although this limitation of optimality is widely acknowledged, it has mostly been defended rather than evaluated for its impact. Experimental adaptation of model organisms provides a new arena for testing optimality models and for simultaneously integrating genetics. First, an experimental context with a well‐researched organism allows dissection of the evolutionary process to identify causes of model failure – whether the model is wrong about genetics or selection. Second, optimality models provide a meaningful context for the process and mechanics of evolution, and thus may be used to elicit realistic genetic bases of adaptation – an especially useful augmentation to well‐researched genetic systems. A few studies of microbes have begun to pioneer this new direction. Incompatibility between the assumed and actual genetics has been demonstrated to be the cause of model failure in some cases. More interestingly, evolution at the phenotypic level has sometimes matched prediction even though the adaptive mutations defy mechanisms established by decades of classic genetic studies. Integration of experimental evolutionary tests with genetics heralds a new wave for optimality models and their extensions that does not merely emphasize the forces driving evolution.     

The foldability landscape of model proteins

Molecular evolution may be considered as a walk in a multidimensional fitness landscape, where the fitness at each point is associated with features such as the function, stability, and survivability of these molecules. We present a simple model for the evolution of protein sequences on a landscape with a precisely defined fitness function. We use simple lattice models to represent protein structures, with the ability of a protein sequence to fold into the structure with lowest energy, quantified as the foldability, representing the fitness of the sequence. The foldability of the sequence is characterized based on the spin glass model of protein folding. We consider evolution as a walk in this foldability landscape and study the nature of the landscape and the resulting dynamics. Selective pressure is explicitly included in this model in the form of a minimum foldability requirement. We find that different native structures are not evenly distributed in interaction space, with similar structures and structures with similar optimal foldabilities clustered together. Evolving proteins marginally fulfill the selective criteria of foldability. As the selective pressure is increased, evolutionary trajectories become increasingly confined to “neutral networks,” where the sequence and the interactions can be significantly changed while a constant structure is maintained. © 1997 John Wiley & Sons, Inc. Biopoly 42: 427–438, 1997     

中国榕小蜂触角感受器形态特征及进化适应性分析

【目的】榕树与传粉榕小蜂体系是协同进化、专性传粉的经典系统,每种榕树上一般还生活有种类丰富、数目众多的非传粉榕小蜂。在选择压力下,榕小蜂为在榕果内生存产生了明显的适应性形态。触角感受器是昆虫通讯系统的单元,其形态是反映生态和进化适应性的最佳特征之一。本文旨在对中国部分传粉和非传粉榕小蜂的触角感受器的形态多样性和进化适应性进行系统研究。【方法】对来源于海南和云南15种榕树上24种榕小蜂54个型的触角感受器形态进行了扫描电镜观察,基于现有的分子系统发育树,对传粉榕小蜂触角感受器的形态特征进行了性状演化分析,并对榕小蜂的形态特征进行了进化适应性分析。【结果】榕小蜂触角感受器普遍存在雌雄二型现象。雌蜂触角感受器种类有毛状、锥状、板状、刺状、钟形、腔锥状和栓锥状等,数目丰富,并且进果产卵的传粉雌蜂和果外产卵的非传粉雌蜂之间、进果产卵的传粉雌蜂和进果产卵的非传粉雌蜂之间在形态上存在差异。传粉雄蜂和不具有雄性多型现象的非传粉雄蜂触角感受器极为退化,具有雄性多型的非传粉雄蜂触角感受器形态在种内不具有显著差异。性状演化分析表明进化路径相当复杂,可能存在多次独立进化过程。触角感受器的形态类型与其进化适应性相关。【结论】榕小蜂触角感受器类型多样,形态变化丰富,并为适应榕果内的生存而产生了进化适应性特点。雌蜂和雄蜂在榕果内受到了完全不同的选择压力,行使不同的生态功能,从而产生了不同的适应性形态。不同的适应性形态可能与雌蜂不同的产卵行为、雄蜂不同的交配策略具有一定联系。该文是首次对中国榕小蜂触角感受器形态进行系统研究的报道,有助于更好地理解榕小蜂的形态特征、进化路线、行为策略和生态关系。     

Mutation matrices and physical-chemical properties: Correlations and implications

To investigate how the properties of individual amino acids result in proteins with particular structures and functions, we have examined the correlations between previously derived structure-dependent mutation rates and changes in various physical-chemical properties of the amino acids such as volume, charge, α-helical and β-sheet propensity, and hydrophobicity. In most cases we found the ΔG of transfer from octanol to water to be the best model for evolutionary constraints, in contrast to the much weaker correlation with the ΔG of transfer from cyclohexane to water, a property found to be highly correlated to changes in stability in site-directed mutagenesis studies. This suggests that natural evolution may follow different rules than those suggested by results obtained in the laboratory. A high degree of conservation of a surface residue's relative hydrophobicity was also observed, a fact that cannot be explained by constraints on protein stability but that may reflect the consequences of the reverse-hydrophobic effect. Local propensity, especially α-helical propensity, is rather poorly conserved during evolution, indicating that non-local interactions dominate protein structure formation. We found that changes in volume were important in specific cases, most significantly in transitions among the hydrophobic residues in buried locations. To demonstrate how these techniques could be used to understand particular protein families, we derived and analyzed mutation matrices for the hypervariable and framework regions of antibody light chain V regions. We found a surprisingly high conservation of hydrophobicity in the hypervariable region, possibly indicating an important role for hydrophobicity in antigen recognition. Proteins 27:336–344, 1997. © 1997 Wiley-Liss, Inc.     

Thermal Adaptation of Viruses and Bacteria

A previously established multiscale population genetics model posits that fitness can be inferred from the physical properties of proteins under the physiological assumption that a loss of stability by any protein confers the lethal phenotype to an organism. Here, we develop this model further by positing that replication rate (fitness) of a bacterial or viral strain directly depends on the copy number of folded proteins, which determine its replication rate. Using this model, and both numerical and analytical approaches, we studied the adaptation process of bacteria and viruses at varied environmental temperatures. We found that a broad distribution of protein stabilities observed in the model and in experiment is the key determinant of thermal response for viruses and bacteria. Our results explain most of the earlier experimental observations: the striking asymmetry of thermal response curves; the absence of evolutionary tradeoff, which was expected but not found in experiments; correlation between denaturation temperature for several protein families and the optimal growth temperature of their carrier organisms; and proximity of bacterial or viral optimal growth temperatures to their evolutionary temperatures. Our theory quantitatively and with high accuracy described thermal response curves for 35 bacterial species using, for each species, only two adjustable parameters—the number of rate-determining genes and the energy barrier for metabolic reactions.     

Evolution of model proteins on a foldability landscape

We model the evolution of simple lattice proteins as a random walk in a fitness landscape, where the fitness represents the ability of the protein to fold. At higher selective pressure, the evolutionary trajectories are confined to neutral networks where the native structure is conserved and the dynamics are non self-averaging and nonexponential. The optimizability of the corresponding native structure has a strong effect on the size of these neutral networks and thus on the nature of the evolutionary process. Proteins 29:461–466, 1997. © 1997 Wiley-Liss, Inc.     

The interaction of sexually and naturally selected traits in the adaptive radiations of cichlid fishes

The question of how genetic variation translates into organismal diversity has puzzled biologists for decades. Despite recent advances in evolutionary and developmental genetics, the mechanisms that underlie adaptation, diversification and evolutionary innovation remain largely unknown. The exceptionally diverse species flocks of cichlid fishes are textbook examples of adaptive radiation and explosive speciation and emerge as powerful model systems to study the genetic basis of animal diversification. East Africa's hundreds of endemic cichlid species are akin to a natural mutagenesis screen and differ greatly not only in ecologically relevant (hence naturally selected) characters such as mouth morphology and body shape, but also in sexually selected traits such as coloration. One of the most fascinating aspects of cichlid evolution is the frequent occurrence of evolutionary parallelisms, which has led to the question whether selection alone is sufficient to produce these parallel morphologies, or whether a developmental or genetic bias has influenced the direction of diversification. Here, I review fitness-relevant traits that could be responsible for the cichlids' evolutionary success and assess whether these were shaped by sexual or natural selection. I then focus on the interaction and the relative importance of sexual vs. natural selection in cichlid evolution. Finally, I discuss what is currently known about the genes underlying the morphogenesis of adaptively relevant traits and highlight the importance of the forthcoming cichlid genomes in the quest of the genetic basis of diversification in this group.     

Conservation and coevolution in the scale-free human gene coexpression network

The role of natural selection in biology is well appreciated. Recently, however, a critical role for physical principles of network self-organization in biological systems has been revealed. Here, we employ a systems level view of genome-scale sequence and expression data to examine the interplay between these two sources of order, natural selection and physical self-organization, in the evolution of human gene regulation. The topology of a human gene coexpression network, derived from tissue-specific expression profiles, shows scale-free properties that imply evolutionary self-organization via preferential node attachment. Genes with numerous coexpressed partners (the hubs of the coexpression network) evolve more slowly on average than genes with fewer coexpressed partners, and genes that are coexpressed show similar rates of evolution. Thus, the strength of selective constraints on gene sequences is affected by the topology of the gene coexpression network. This connection is strong for the coding regions and 3' untranslated regions (UTRs), but the 5' UTRs appear to evolve under a different regime. Surprisingly, we found no connection between the rate of gene sequence divergence and the extent of gene expression profile divergence between human and mouse. This suggests that distinct modes of natural selection might govern sequence versus expression divergence, and we propose a model, based on rapid, adaptation-driven divergence and convergent evolution of gene expression patterns, for how natural selection could influence gene expression divergence.     

Protein structure and function at low temperatures

Proteins represent the major components in the living cell that provide the whole repertoire of constituents of cellular organization and metabolism. In the process of evolution, adaptation to extreme conditions mainly referred to temperature, pH and low water activity. With respect to life at low temperatures, effects on protein structure, protein stability and protein folding need consideration. The sequences and topologies of proteins from psychrophilic, mesophilic and thermophilic organisms are found to be highly homologous. Commonly, adaptive changes refer to multiple alterations of the amino acid sequence, which presently cannot be correlated with specific changes of structure and stability; so far it has not been possible to attribute specific increments in the free energy of stabilization to well-defined amino-acid exchanges in an unambiguous way. The stability of proteins is limited at high and low temperatures. Their expression and self-organization may be accomplished under conditions strongly deviating from optimum growth conditions. Molecular adaptation to extremes of temperature seems to be accompanied by a flattening of the temperature profile of the free energy of stabilization. In principle, the free energy of stabilization of proteins is small compared to the total molecular energy. As a consequence, molecular adaptation to extremes of physical conditions only requires marginal alterations of the intermolecular interactions and packing density. Careful statistical and structural analyses indicate that altering the number of ion pairs and hydrophobic interactions allows the flexibility of proteins to be adjusted so that full catalytic function is maintained at varying temperatures.     

Limits to adaptation in asexual populations

In asexual populations, the rate of adaptation is basically limited by the frequency and properties of spontaneous beneficial mutations. Hence, knowledge of these mutational properties and how they are affected by particular evolutionary conditions is a precondition for understanding the process of adaptation. Here, we address how the rate of adaptation of asexual populations is limited by its population size and mutation rate, as well as by two factors affecting the fraction of mutations that confer a benefit, i.e. the initial adaptedness of the population and the variability of the environment. These factors both influence which mutations are likely to occur, as well as the probability that they will ultimately contribute to adaptation. We attempt to separate the consequences of these basic population features in terms of their effect on the rate of adaptation by using results from evolution experiments with microorganisms.     

Using thermodynamics to obtain geochemical information from genomes

Thermodynamic characterization of the relative stabilities of chemical compounds is a pillar of conceptual models in various fields of geosciences. Analogous models applied to genomes can yield new information about the relationship between genomes and their geochemical environments. In this perspective article, we present a chemical and thermodynamic analysis of prokaryotic lineages that have been the target of previous phylogenomic studies of evolutionary adaptation to varying redox conditions. The thermodynamic model development begins by quantifying the effects of hydrogen activity (aH₂) and temperature on the relative stabilities of organic compounds with different carbon oxidation state. When applied to proteins instead of metabolites, the same techniques can be used to identify combinations of aH₂ and temperature at which reference proteomes for Class I or Class II methanogens are relatively stable. The calculated aH₂ values are compatible with reported measurements for habitats of methanogens ranging from highly reducing submarine hydrothermal systems to less reducing environments including methanogenic sediments. In contrast to the transition between the two classes of methanogenic archaea, that between basal and terrestrial groups of Thaumarchaeota (denoting the origin of ammonia-oxidizing archaea) occurs at a less-reducing redox boundary. These examples reveal the consequences of energy minimization driving evolution and show how geochemical calculations involving biomolecules can be used to quantify and better understand the coevolution of the geosphere and biosphere.     

Convergent selection pressures drive the evolution of rhodopsin kinetics at high altitudes via nonparallel mechanisms

Convergent evolution in response to similar selective pressures is a well‐known phenomenon in evolutionary biology. Less well understood is how selection drives convergence in protein function, and the underlying mechanisms by which this can be achieved. Here, we investigate functional convergence in the visual system of two distantly related lineages of high‐altitude adapted Andean and Himalayan catfishes. Statistical analyses revealed in the two high‐altitude lineages, a parallel acceleration of evolutionary rates in rhodopsin, the dim‐light visual pigment. However, the elevated rates were found to be accompanied by substitutions at different sites in the protein. Experiments substituting Andean‐ or Himalayan‐specific residues significantly accelerated the kinetic rates of rhodopsin, destabilizing the ligand‐bound forms. As found in cold‐adapted enzymes, this phenotype likely compensates for a cold‐induced decrease in kinetic rates, properties of rhodopsin mediating rod sensitivity and visual performance. Our study suggests that molecular convergence in protein function can be driven by parallel shifts in evolutionary rates but via nonparallel molecular mechanisms. Signatures of natural selection may therefore be a powerful guide for identifying complex instances of functional convergence across a wider range of protein systems.     

NEW MODEL SYSTEMS FOR EXPERIMENTAL EVOLUTION

Microbial experimental evolution uses a few well‐characterized model systems to answer fundamental questions about how evolution works. This special section highlights novel model systems for experimental evolution, with a focus on marine model systems that can be used to understand evolutionary responses to global change in the oceans.     

How enzymes adapt: lessons from directed evolution

Enzymes that are adapted to widely different temperature niches are being used to investigate the molecular basis of protein stability and enzyme function. However, natural evolution is complex: random noise, historical accidents and ignorance of the selection pressures at work during adaptation all cloud comparative studies. Here, we review how adaptation in the laboratory by directed evolution can complement studies of natural enzymes in the effort to understand stability and function. Laboratory evolution experiments can attempt to mimic natural evolution and identify different adaptive mechanisms. However, laboratory evolution might make its biggest contribution in explorations of nonnatural functions, by allowing us to distinguish the properties nutured by evolution from those dictated by the laws of physical chemistry.     

Mutational reversions during adaptive protein evolution

Adaptation is often regarded as the sequential fixation of individually, intrinsically beneficial mutations. Contrary to this expectation, we find a surprisingly large number of evolutionary trajectories on which natural selection first favors a mutation, then favors its removal, and later still favors its ultimate restoration during the course of antibiotic resistance evolution. The existence of reversion trajectories implies that natural selection may not follow the most parsimonious path separating two alleles, even during adaptation. Altogether, this discovery highlights the unusual and potentially circuitous routes natural selection can follow during adaptation.