蛋白质定向进化的研究进展

在工业生物催化过程和生物细胞工厂构建方面,蛋白质定向进化被广泛地应用于酶的分子改造.蛋白质定向进化不仅可以针对某一目的蛋白进行改造,还可以改善代谢途径、优化代谢网络、获得期望表型细胞.为了获得更高效的突变效率,快捷、高通量的筛选方法,提高蛋白质定向进化的效果,研究者不断开发蛋白质体内、体外进化方法,取得了新的进展和应用.本文介绍了最近发展的蛋白质定向进化技术的原理、方法及特点,总结了突变文库的筛选方法和蛋白质定向进化的最新应用,最后讨论了蛋白质定向进化存在的挑战和未来发展方向.     

Strong links between genomic and anatomical diversity in both mammalian olfactory chemosensory systems

Mammalian olfaction comprises two chemosensory systems: the odorant-detecting main olfactory system (MOS) and the pheromone-detecting vomeronasal system (VNS). Mammals are diverse in their anatomical and genomic emphases on olfactory chemosensation, including the loss or reduction of these systems in some orders. Despite qualitative evidence linking the genomic evolution of the olfactory systems to specific functions and phenotypes, little work has quantitatively tested whether the genomic aspects of the mammalian olfactory chemosensory systems are correlated to anatomical diversity. We show that the genomic and anatomical variation in these systems is tightly linked in both the VNS and the MOS, though the signature of selection is different in each system. Specifically, the MOS appears to vary based on absolute organ and gene family size while the VNS appears to vary according to the relative proportion of functional genes and relative anatomical size and complexity. Furthermore, there is little evidence that these two systems are evolving in a linked fashion. The relationships between genomic and anatomical diversity strongly support a role for natural selection in shaping both the anatomical and genomic evolution of the olfactory chemosensory systems in mammals.     

Systems for in vivo hypermutation: a quest for scale and depth in directed evolution

Traditional approaches to the directed evolution of genes of interest (GOIs) place constraints on the scale of experimentation and depth of evolutionary search reasonably achieved. Engineered genetic systems that dramatically elevate the mutation of target GOIs in vivo relieve these constraints by enabling continuous evolution, affording new strategies in the exploration of sequence space and fitness landscapes for GOIs. We describe various in vivo hypermutation systems for continuous evolution, discuss how different architectures for in vivo hypermutation facilitate evolutionary search scale and depth in their application to problems in protein evolution and engineering, and outline future opportunities for the field.     

Reversal of evolutionary downsizing caused by selective harvest of large fish

Evolutionary responses to the long-term exploitation of individuals from a population may include reduced growth rate, age at maturation, body size and productivity. Theoretical models suggest that these genetic changes may be slow or impossible to reverse but rigorous empirical evidence is lacking. Here, we provide the first empirical demonstration of a genetically based reversal of fishing-induced evolution. We subjected six populations of silverside fish (Menidia menidia) to three forms of size-selective fishing for five generations, thereby generating twofold differences among populations in mean weight and yield (biomass) at harvest. This was followed by an additional five generations during which size-selective harvest was halted. We found that evolutionary changes were reversible. Populations evolving smaller body size when subjected to size-selective fishing displayed a slow but significant increase in size when fishing ceased. Neither phenotypic variance in size nor juvenile survival was reduced by the initial period of selective fishing, suggesting that sufficient genetic variation remained to allow recovery. By linear extrapolation, we predict full recovery in about 12 generations, although the rate of recovery may taper off near convergence. The recovery rate in any given wild population will also depend on other agents of selection determined by the specifics of life history and environment. By contrast, populations that in the first five generations evolved larger size and yield showed little evidence of reversal. These results show that populations have an intrinsic capacity to recover genetically from harmful evolutionary changes caused by fishing, even without extrinsic factors that reverse the selection gradient. However, harvested species typically have generation times of 3–7 years, so recovery may take decades. Hence, the need to account for evolution in managing fisheries remains.     

Molecular Evolutionary Dynamics of Energy Limited Microorganisms

Microorganisms have the unique ability to survive extended periods of time in environments with extremely low levels of exploitable energy. To determine the extent that energy limitation affects microbial evolution, we examined the molecular evolutionary dynamics of a phylogenetically diverse set of taxa over the course of 1,000 days. We found that periodic exposure to energy limitation affected the rate of molecular evolution, the accumulation of genetic diversity, and the rate of extinction. We then determined the degree that energy limitation affected the spectrum of mutations as well as the direction of evolution at the gene level. Our results suggest that the initial depletion of energy altered the direction and rate of molecular evolution within each taxon, though after the initial depletion the rate and direction did not substantially change. However, this consistent pattern became diminished when comparisons were performed across phylogenetically distant taxa, suggesting that although the dynamics of molecular evolution under energy limitation are highly generalizable across the microbial tree of life, the targets of adaptation are specific to a given taxon.     

发育重演律与生物进化

发育重演律是生物个体发育的一般规律,该规律认为生物个体的发育是类囊胚不断形成和演化的过程,并认为生物进化亦是类囊胚不断形成和演化的过程.因类囊胚层级不断增加而导致的生物体结构复杂程度提高的演化为纵向进化,而不能提高生物体复杂程度的演化为横向演化,生物的纵向进化具有周期性.生物种系进化与个体发育之间具有严格的对应关系,一个物种经历的纵向进化的周期数与该物种所属个体完成发育所经历的细胞分化的周期数相等.     

Genome architecture drives protein evolution in ciliates

Studies of microbial eukaryotes have been pivotal in the discovery of biological phenomena, including RNA editing, self-splicing RNA, and telomere addition. Here we extend this list by demonstrating that genome architecture, namely the extensive processing of somatic (macronuclear) genomes in some ciliate lineages, is associated with elevated rates of protein evolution. Using newly developed likelihood-based procedures for studying molecular evolution, we investigate 6 genes to compare 1) ciliate protein evolution to that of 3 other clades of eukaryotes (plants, animals, and fungi) and 2) protein evolution in ciliates with extensively processed macronuclear genomes to that of other ciliate lineages. In 5 of the 6 genes, ciliates are estimated to have a higher ratio of nonsynonymous/synonymous substitution rates, consistent with an increase in the rate of protein diversification in ciliates relative to other eukaryotes. Even more striking, there is a significant effect of genome architecture within ciliates as the most divergent proteins are consistently found in those lineages with the most highly processed macronuclear genomes. We propose a model whereby genome architecture-specifically chromosomal processing, amitosis within macronuclei, and epigenetics-allows ciliates to explore protein space in a novel manner. Further, we predict that examination of diverse eukaryotes will reveal additional evidence of the impact of genome architecture on molecular evolution.     

Higher rates of sex evolve under K‐selection

The geographical distribution of sexual and related asexual species has been suggested to correlate with habitat stability; sexual species tend to be in stable habitats (K‐selection), whereas related asexual taxa tend to be in unstable habitats (r‐selection). We test whether this broad‐scale pattern can be re‐created at a microevolutionary scale by experimentally evolving populations of facultatively sexual rotifers under different ecological conditions. Consistent with the pattern in nature, we find that the rate of sex evolves to lower levels in the r‐selected than in K‐selection environments. We consider several different explanations for these results.     

Feedback selection and the evolution of modifiers

The problem of modifier evolution was examined with regard to the idea that modifier evolution can be considered as a result of selection for adaptation speed in populations far from equilibrium. This kind of selection was called feedback selection in order to emphasize the difference to theories which consider modifier evolution near the equilibrium. The basic principles of this kind of selection are derived for asexual populations and the problem of dominance is discussed in the light of this concept. In general the results support the view, that the genetic properties of a character are selected along with the character itself.This work was supported by the Austrian Fonds zur Förderung der Wissenschaftlichen Forschung (Proj. Nr. 3502).     

Modelling contemporary evolution in stickleback

During the past decade, two lines of research have advanced our understanding of micro‐evolution. On the one hand, a number of studies have generated evidence for strong selection on phenotypes ( Kingsolver et al. 2001 ) and the contemporary (sometimes deemed ‘rapid’) evolution of phenotypic traits ( Hendry & Kinnison 1999 ). On the other hand, other studies have sought to identify the genes that underlie ecologically important traits ( Ungerer et al. 2008 ). Over the next decade, micro‐evolutionists might expect considerable progress from the study of contemporary evolution at both the phenotypic and genetic level simultaneously. In this issue of Molecular Ecology, Le Rouzic et al. (2011) present a teaser for this approach. They examined contemporary evolution of an adaptive trait with a well‐studied genetic basis, the number of lateral plates, in threespine stickleback (Gasterosteus aculeatus L.). A time series of 20 years of change for this trait after introduction into a pond in Norway was compared with a similar time series of 12 years following the invasion of a lake in Alaska. Using a modelling approach, the authors then teased apart selection acting upon the phenotype and selection acting on a major effect gene. In both time series, selection was strong and consistent. The models suggested that selection could act directly on the phenotype, or through the gene’s pleiotropic effects.     

Evidence for male-driven evolution in Drosophila

In several vertebrate taxa studied to date, mutation rates arehigher in males than females (male-driven evolution). The male-to-femalemutation rate () can be estimated by contrasting DNA divergencedata at X-linked, Y-linked, and autosomal loci. Previous studiesin Drosophila, comparing X-linked and autosomal divergence,have found no evidence for male-driven evolution in this genus.Here, I compare levels of nucleotide divergence between homologousX- and Y-linked loci in Drosophila miranda. Using divergenceat both synonymous sites and at short introns, I estimate tobe approximately 2. This study thus provides the first evidencefor male-biased mutation rates outside vertebrates, supportingthe view that DNA sequence evolution is male driven in a widevariety of taxa.     

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 current status of REH theory

Summary The recent evaluation by Fitch (1980) of REH theory for macromolecular divergence is a severely erroneous and distorted analysis of our work over the past decade. We reply to those distortions here. At present, there is no factual basis for believing Fitch's assessment that corrections which move evolutionary estimates of total mutations fixed closer to the true distance must do so at the expense of an increased variance sufficient to compromise the value of the improvement. By direct calculation the variance in the estimates of total mutations fixed given by REH theory is comparable to that of other models now in the literature for the case in which genetic events are equiprobable. A general argument is given that suggests that, as we consider more and more carefully the selective, functional, and structural constraints on the evolution of genes and proteins, this variance may be expected to decrease toward a lower bound.     

The ecology of social transitions in human evolution

We know that there are fundamental differences between humans and living apes, and also between living humans and their extinct relatives. It is also probably the case that the most significant and divergent of these differences relate to our social behaviour and its underlying cognition, as much as to fundamental differences in physiology, biochemistry or anatomy. In this paper, we first attempt to demarcate what are the principal differences between human and other societies in terms of social structure, organization and relationships, so that we can identify what derived features require explanation. We then consider the evidence of the archaeological and fossil record, to determine the most probable context in time and taxonomy, of these evolutionary trends. Finally, we attempt to link five major transitional points in hominin evolution to the selective context in which they occurred, and to use the principles of behavioural ecology to understand their ecological basis. Critical changes in human social organization relate to the development of a larger scale of fission and fusion; the development of a greater degree of nested substructures within the human community; and the development of intercommunity networks. The underlying model that we develop is that the evolution of ‘human society’ is underpinned by ecological factors, but these are influenced as much by technological and behavioural innovations as external environmental change.     

Domains within the mammalian ornithine decarboxylase messenger RNA have evolved independently and episodically

Summary Ornithine decarboxylase (ODC) is the first enzyme in the polyamine biosynthetic pathway. We have studied the evolutionary history of the mammalian ODC mRNA, focusing on the rate of accumulation of sequence divergence within specific subregions of the molecule. The phylogenetic relationships among the mRNAs from several mammalian species, including two mouse species, rat, hamster, and human, were determined based upon the numbers of synonymous substitutions in pair-wise comparisons of mRNA coding regions. The separation times for the mRNAs were very similar to those for the corresponding species, suggesting that ODC is encoded by orthologous genes in the different species. Analysis of divergence patterns in four subregions, or domains, of the mRNA (the 5untranslated region, the coding region, and two domains of the 3-untranslated region) showed that the domains have evolved in a noncoordinate fashion. Furthermore, evolution of each subregion has been episodic, with periods of both rapid and slow sequence divergence. We suggest that the episodic pattern of ODC mRNA evolution may indicate the existence of selection pressures that were exerted in a time- and domain-specific manner during mammalian speciation.     

The evolution and evolutionary consequences of marginal thermostability in proteins

When we seek to explain the characteristics of living systems in their evolutionary context, we are often interested in understanding how and why certain properties arose through evolution, and how these properties then affected the continuing evolutionary process. This endeavor has been assisted by the use of simple computational models that have properties characteristic of natural living systems but allow simulations over evolutionary timescales with full transparency. We examine a model of the evolution of a gene under selective pressure to code for a protein that exists in a prespecified folded state at a given growth temperature. We observe the emergence of proteins with modest stabilities far below those possible with the model, with a denaturation temperature tracking the simulation temperature, despite the absence of selective pressure for such marginal stability. This demonstrates that neither observations of marginally stable proteins, nor even instances where increased stability interferes with function, provide evidence that marginal stability is an adaptation. Instead the marginal stability is the result of a balance between predominantly destabilizing mutations and selection that shifts depending on effective population size. Even if marginal stability is not an adaptation, the natural tendency of proteins toward marginal stability, and the range of stabilities that occur during evolution, may have significant effect on the evolutionary process.     

The probability of parallel evolution

Abstract How often will natural selection drive parallel evolution at the DNA sequence level? More precisely, what is the probability that selection will cause two populations that live in identical environments to substitute the same beneficial mutation? Here I show that, under fairly general conditions, the answer is simple: if a wild‐type sequence can mutate to n different beneficial mutations, replicate populations will on average fix the same mutation with probability P= 2/(n + 1). This probability, which is derived using extreme value theory, is independent of most biological details, including the length of the gene in question and the precise distribution of fitness effects among alleles. I conclude that the probability of parallel evolution under natural selection is nearly twice as large as that under neutrality.     

Calculating independent contrasts for the comparative study of substitution rates

Phylogenetic comparative methods have been used to study patterns of correlated evolution between biological traits of all kinds, and are increasingly used to identify predictors of the rate of DNA substitution. Substitution rate differs from most traits studied in that it cannot be observed directly, but must be inferred from substitutions accrued over a long period of time. Studying a mathematical model of trait and rate evolution, we show that the special nature of substitution rates can lead to a severe loss of power for standard comparative methods. We further show how strategies designed to maximise power, by increasing the number of data points, can have the opposite effect when substitution rate is involved. We then propose two modifications of the standard methods that can mitigate these problems. First, we show how pre-existing tests for homogeneity of variance can be used to identify and exclude those data from which changes in substitution rate cannot be reliably inferred. Second, we show that power can be increased by comparing substitution rate with the time average of the predictor trait along the history of the lineage, and introduce a maximum likelihood estimator of this quantity.