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.     

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.     

基于生物适应进化原理论证生物进化的动力

文章从现有主流生物进化理论存在的问题入手, 以生物适应进化原理为认识基础, 讨论生物进化的动力, 以求对生物进化机制有一个新的认识。在薛定谔“生命赖负熵生存”观点的指导下, 提出了“负熵流”包括能量流、物质流和信息流, 以及负熵流是生命生存和发育的动力的观点。作者在原有生物适应进化原理基础上, 修改完善并提出了“DNA、RNA和蛋白质在环境作用下的生物适应进化调控系统”理论, 并根据系统发育是个体发育的“积分”的观点, 推论得出生物与环境的负熵差引起的负熵流也是生命进化的动力, 对生物进化机制作出了新的理解。基于这样的生物进化机制的认识, 提出了“进化是一个子系统在其上一等级系统中, 将自身全部或部分信息遗传给下一代子系统, 并在其适应上一等级系统过程中, 产生一些新质, 终止一些旧质, 从而在其上一等级系统中得以延续的变化过程”的概念, 并探讨了一些与进化有关的其他争议问题。     

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.     

A brief summary of my ideas on evolution

A brief summary of my current ideas on evolution is presented. Three recent books that represent important synopses of evolution are considered in the discussion. Differences between plants and animals that have important implications for evolution in the two groups are discussed. Progress in understanding plant evolution requires synthetic studies integrating data from many different areas of research.     

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.     

Cultural evolution: implications for understanding the human language faculty and its evolution

Human language is unique among the communication systems of the natural world: it is socially learned and, as a consequence of its recursively compositional structure, offers open-ended communicative potential. The structure of this communication system can be explained as a consequence of the evolution of the human biological capacity for language or the cultural evolution of language itself. We argue, supported by a formal model, that an explanatory account that involves some role for cultural evolution has profound implications for our understanding of the biological evolution of the language faculty: under a number of reasonable scenarios, cultural evolution can shield the language faculty from selection, such that strongly constraining language-specific learning biases are unlikely to evolve. We therefore argue that language is best seen as a consequence of cultural evolution in populations with a weak and/or domain-general language faculty.     

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.     

Experimental elimination of parasites in nature leads to the evolution of increased resistance in hosts

A reduction in the strength of selection is expected to cause the evolution of reduced trait expression. Elimination of a parasite should thus cause the evolution of reduced resistance to that parasite. To test this prediction in nature, we studied the fourth- and eighth-generation descendants of guppies (Poecilia reticulata) introduced into four natural streams following experimental elimination of a common and deleterious parasite (Gyrodactylus spp.). After two generations of laboratory rearing to control for plasticity and maternal effects, we infected individual fish to assess their resistance to the parasite. Contrary to theoretical expectations, the introduced guppy populations had rapidly and repeatably evolved increased resistance to the now-absent parasite. This evolution was not owing to a resistance-tolerance trade-off, nor to differences in productivity among the sites. Instead, a leading candidate hypothesis is that the rapid life-history evolution typical in such introductions pleiotropically increases parasite resistance. Our study adds a new dimension to the growing evidence for contemporary evolution in the wild, and also points to the need for a re-consideration of simple expectations from host–parasite theory. In particular, our results highlight the need for increased consideration of multiple sources of selection and pleiotropy when studying evolution in natural contexts.     

鹿科麂属动物基因组演化研究进展

鹿科麂属(Muntiacus, Cervidae)在近两三百万年内经历了快速物种辐射, 但其物种间核型差异巨大. 5个现生种核型数据显示, 该类群染色体数目范围从小麂(Muntiacus reevesi)的46条到赤麂(M. muntjak vaginalis)的6条. 该类群的基因组在较短时间内发生了快速演化, 使其成为进化生物学研究的理想材料. 40多年来, 技术的革新使该领域的研究不断深入, 染色体重排的类型、推动重排的分子机制及物种间的核型演化历程逐渐被阐释. 而且, 研究中发现, 雄性黑麂(M. crinifrons)1p+4染色体的演化途径与哺乳动物Y染色体的演化历程相似, 可成为哺乳动物性染色体演化研究的珍贵模型. 有关麂属动物基因组演化依然有许多问题等待更加全面、深入的探讨. 本文总结了该领域研究进展, 并对未来研究热点进行了展望.     

The Importance of Understanding the Nature of Science for Accepting Evolution

Many students reject evolutionary theory, whether or not they adequately understand basic evolutionary concepts. We explore the hypothesis that accepting evolution is related to understanding the nature of science. In particular, students may be more likely to accept evolution if they understand that a scientific theory is provisional but reliable, that scientists employ diverse methods for testing scientific claims, and that relating data to theory can require inference and interpretation. In a study with university undergraduates, we find that accepting evolution is significantly correlated with understanding the nature of science, even when controlling for the effects of general interest in science and past science education. These results highlight the importance of understanding the nature of science for accepting evolution. We conclude with a discussion of key characteristics of science that challenge a simple portrayal of the scientific method and that we believe should be emphasized in classrooms.     

Microbial adaptive evolution

Bacterial species can adapt to significant changes in their environment by mutation followed by selection, a phenomenon known as “adaptive evolution.” With the development of bioinformatics and genetic engineering, research on adaptive evolution has progressed rapidly, as have applications of the process. In this review, we summarize various mechanisms of bacterial adaptive evolution, the technologies used for studying it, and successful applications of the method in research and industry. We particularly highlight the contributions of Dr. L. O. Ingram. Microbial adaptive evolution has significant impact on our society not only from its industrial applications, but also in the evolution, emergence, and control of various pathogens.     

Losing Sight of Regressive Evolution

When we teach evolution to our students, we tend to focus on “constructive” evolution, the processes which lead to the development of novel or modified structures. Most biology students are familiar with the subjects of finches’ beaks, giraffes’ necks, and hair in mammals. Of course, there is nothing inherently wrong with a constructivist approach to teaching evolution, but if it is our only focus, we may overlook the flip side of the coin. By the flip side of the coin, of course, we are referring to regressive evolution: the loss or degeneration of a trait. Regressive evolution does not often make its way into biology textbooks, but it is of great relevance nonetheless. In all likelihood, when a new trait evolves or an existing one is modified, something is sacrificed in return. In order to develop a flipper, a marine mammal must sacrifice individual digits. You may be familiar with one or more of the following familiar characters lost through regressive evolution: teeth in birds, scales in mammals, and tails in higher primates. For aficionados of cave biology like us, one of the most interesting examples of regressive evolution concerns cave fish: Why do cave fish lose their eyes?     

Human niche construction in interdisciplinary focus

Niche construction is an endogenous causal process in evolution, reciprocal to the causal process of natural selection. It works by adding ecological inheritance, comprising the inheritance of natural selection pressures previously modified by niche construction, to genetic inheritance in evolution. Human niche construction modifies selection pressures in environments in ways that affect both human evolution, and the evolution of other species. Human ecological inheritance is exceptionally potent because it includes the social transmission and inheritance of cultural knowledge, and material culture. Human genetic inheritance in combination with human cultural inheritance thus provides a basis for gene-culture coevolution, and multivariate dynamics in cultural evolution. Niche construction theory potentially integrates the biological and social aspects of the human sciences. We elaborate on these processes, and provide brief introductions to each of the papers published in this theme issue.     

比较基因组学在哺乳动物进化研究中的应用

哺乳动物经过长期进化,使其基因组在结构和功能上存在着明显的差异,构成了表型进化的基础。随着人类、部分哺乳动物基因组测序的完成,以比较基因组学为主要研究手段的哺乳动物进化研究应运而生,从而为在基因组水平上深入认识哺乳动物进化关系、揭示生命的起源和进化提供依据。对比较基因组学的主要研究方法进行了综述,进而探讨其在哺乳动物进化研究中的应用,并对哺乳动物比较基因组学的发展进行了展望。     

Mainstreaming Caenorhabditis elegans in experimental evolution

Experimental evolution provides a powerful manipulative tool for probing evolutionary process and mechanism. As this approach to hypothesis testing has taken purchase in biology, so too has the number of experimental systems that use it, each with its own unique strengths and weaknesses. The depth of biological knowledge about Caenorhabditis nematodes, combined with their laboratory tractability, positions them well for exploiting experimental evolution in animal systems to understand deep questions in evolution and ecology, as well as in molecular genetics and systems biology. To date, Caenorhabditis elegans and related species have proved themselves in experimental evolution studies of the process of mutation, host–pathogen coevolution, mating system evolution and life-history theory. Yet these organisms are not broadly recognized for their utility for evolution experiments and remain underexploited. Here, we outline this experimental evolution work undertaken so far in Caenorhabditis, detail simple methodological tricks that can be exploited and identify research areas that are ripe for future discovery.     

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.     

Science and the Concept of Evolution: From the Big Bang to the Origin and Evolution of Life

The common thread of evolution runs through all science disciplines, and the concept of evolution enables students to better understand the nature of the universe and our origins. “Science and the Concept of Evolution” is one of two interdisciplinary science Core courses taken by Dowling College undergraduates as part of their General Education requirements. The course examines basic principles and methods of science by following the concept of evolution from the big bang to the origin and evolution of life. Case studies of leading scientists illustrate how their ideas developed and contributed to the evolution of our understanding of the world. Evidences for physical, chemical, and biological evolution are explored, and students learn to view the evolution of matter and of ideas as a natural process of change over space and time.     

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.