脊髓灰质炎病毒的分子进化

本文根据脊髓灰质炎病毒3个型别参考毒株的基因组核苷酸序列和蛋白质氨基酸序列资料,首次试用Kimura的分子进化理论和计算方法,推算出脊髓灰质炎病毒型间的进化距离、分歧进化时间及病毒蛋白质氨基酸的替换率。结果表明:(1)型间毒株相互进化距离大致相等;(2)三个型病毒是由一个共同祖先病毒在距今约1—2千年以前几乎同时分歧进化而来;(3)型间毒株蛋白质氨基酸替换率也大致相等。     

真核基因中内含子是在蛋白异化过程中获得

本文对肌动蛋白家族中的内含子序列按同亚型和不同亚型在相同插入位置作了比较分析。结果得出：整个肌动蛋白的外显子序列是高度保守,由此推断整个肌动蛋白可能从共同祖先蛋白进化的。同亚型肌动蛋白的内含子序列的类似性随进化距离而变化,并且在短进化距离的物种间,在相同插入位置的内含子序列类似性都较高。不同亚型肌动蛋白的内含子序列的类似性都较低,即使是同一物种,如人,不同亚型肌动蛋白的内含子序列的类似性也远低于同亚型但进化距离较近的物种。由此可推断同亚型肌动蛋白的内含子序列可能从共同祖先进化,不同亚型肌动蛋白的内含子序列从不同祖先进化。综上结果可推出内含子可能是在蛋白异化过程中获得。     

促葡萄糖转运蛋白基因家族的分子进化研究

葡萄糖转运蛋白是一个在结构上相似功能上不同的多基因家族（ＧＬＵＴ１－ＧＬＵＴ５）。由于这一组蛋白和体内的葡萄糖利用有关,因此被认为是糖尿病胰岛素抵抗（抗性）的一个候选基因。本文比较了不同种生物这一基因家族的氨基酸和核苷酸顺序;推测了亲水性和疏水性分布;计算了蛋白质和核苷酸的进化距离,并在此基础上构建了分子进化树。研究表明：这一基因家族具有高度的同源性、极为相似的亲水性和疏水性分布以及结构的对称性。提示这一基因家族起源于一个共同的祖先并可能通过基因的重复而形成。这一进化机制可能有利于氨基酸结构的稳定及抵抗突变的作用。由于邻元法构建的进化树其分支长度存在差异,提示在这一基因家族的进化过程中,各分支上的进化速率并不相同。蛋白质进化距离和核苷酸进化距离所构建进化树的差异提示了在基因组中可能存在隐匿替换。两种方法构建的进化树都提示了ＧＬＵＴ１、３、４在结构和功能上要更为保守。     

动物肌动蛋白基因中内含子的来源及存在意义的探讨

对动物界演化过程中肌动蛋白家族内含子插入位置分布的演化规律作了分析,并对相同插入位置的内含子序列按同亚型和不同亚型作了比较。结果得出:从整个肌动蛋白家族的外显子序列高度保守性推断整个肌动蛋白家族可能是从共同的祖先蛋白进化而来的;从同亚型肌动蛋白内含子序列的类似性随进化距离而变化,但在短进化距离的物种间,类似性都较高,不同亚型肌动蛋白内含子序列的类似性都较低,即使是同一物种(如人),类似性也远低于同亚型但进化距离较近的物种,由此可推断,同亚型肌动蛋白的内含子序列可能从共同祖先进化,不同亚型肌动蛋白的内含子序列从不同祖先进化,综上推断可导出内含子可能是在蛋白异化过程中获得的:还发现内含子在肌动蛋白家族编码基因中位置的分布随进化方向不同而逐步形成两种截然不同的模式,由此提出了内含子的位置分布与动物演化方向之间可能具有某种必然联系,为内含子的存在提出了某种依据。     

分子绝对进化速率与物种分歧时间之间的定量关系

通过对美国国家生物技术信息中心数据库Gen Bank提供的一些蛋白质和核苷酸序列进行比对和分析,发现生物分子绝对进化速率k与进化时间或物种分歧时间t之间存在下列定量关系:lnk=-Ea/Rt+lnK0,式中Ea为位点突变活化能,k0为分子极限绝对进化速率,R为常数,并对其生物学意义进行了初步的探讨;数据分析还揭示出物种的分子极限绝对进化速率与进化时间或物种分歧时间之间也服从相似的定量公式,也就是说生物分子进化过程可能同时受到序列位点突变和控制物种分子极限绝对进化速率进化的两个"分子钟"作用,即存在"双重分子钟"现象。     

使用基因组数据进行贝叶斯物种分化时间估计

随着测序技术的发展,基因组数据呈井喷式增长.大量的基因组数据使得我们可以非常准确的估计出进化距离,即进化速率和物种分化时间的乘积.在很多情况下,我们想要了解的是物种分化的绝对时间.然而分子数据并没有分别提供进化速率和分化时间的信息,我们可以使用贝叶斯方法借助化石、先验等外部信息进行估计.近年来,进化模型和计算方法方面研究取得的进展使得我们可以在复杂模型下分析多基因数据.能够分析复杂模型的贝叶斯MCMC方法也成为了主流的物种分化时间估计方法.本文主要介绍贝叶斯物种分化时间估计的框架以及相关工作近年来的进展.     

点阵图法比较蛋白质序列的同源性

同一蛋白质家族的成员往往具有共同的祖先。但由于进化过程中突变、重组等分子事件的发生,它们之间的同源性常因分歧进化时间久远而不易发现。一个灵敏的揭示蛋白质序列同源性的方法显得十分必要。 点阵作图法是揭示蛋白质同源性的敏感而直观的方法。本实验室现行的序列分析软件(“Sequence”)采用单元积分法作点阵图(即以两氨     

酶祖先序列重建与定向进化

酶祖先序列重建是指通过计算机算法推导来自灭绝生物的祖先酶的氨基酸序列的技术。通常可分为6个步骤,依次为现代酶的核酸/氨基酸序列收集、多序列比对、系统发育树构建、祖先酶序列的计算机推测、基因克隆、酶学性质表征。该方法广泛应用于研究分子在行星时间尺度上对环境条件不断变化的适应性和进化机制。随着酶在生物催化领域中扮演越来越重要的角色,该方法逐渐成为研究酶序列、结构和功能关系的有力手段。同时,祖先酶大多具有温度稳定性、突变稳定性等特性,使其成为进一步定向进化的理想蛋白质支架。文中综述了酶祖先序列重建的计算机算法、应用和常用计算机软件,并结合最新研究进展,展望其在酶定向进化领域中的应用前景。     

中国野桑蚕性信息素合成激活肽(PBAN)基因的克隆及序列分析

根据家蚕(Bombyx mori)性信息素合成激活肽(pheromone biosynthesis activating neuropeptide,PBAN)基因DNA序列设计引物,扩增获得中国野桑蚕(Bombyx mandarina China)PBAN基因。分析表明,PBAN由33个氨基酸组成,在第14个氨基酸异亮氨酸和第15个氨基酸酪氨酸之间插入了698bp的内含子。根据PBAN及其基因cDNA、DNA序列分别构建分子进化树,结果显示3个水平比对结果构建的分子进化树有较好的一致性,推测PBAN基因可能适合于科、属之间的进化分析;并且PBAN基因内含子没有表现出特有的进化信息,推测PBAN基因内含子的进化与PBAN全长基因的进化在进化速率上并没有显著差别。相对于PBAN及α—SGNP、γ—SGNP,β—SGNP的进化速率相对较快,推测β—SGNP序列可能适合用于种间的进化分析。     

一种新的DNA序列进化距离及其应用

为了研究核苷酸变异,通过DNA序列的同源率,建立了DNA序列进化的动力学方程,进而得到了一种新的物种间进化距离dy(选择进化距离).由于核苷酸替代模型有很多,选用其中的4种模型,计算出其相应的选择进化距离dy,该进化距离包含了4种模型下的p距离、替代率为常数的距离d和替代率服从Г分布的Г距离dG.进一步根据动力学方程的特点,将模型转化为一元线性回归问题,用最小二乘法求得选择模型中的动力学参数b和各核苷酸位点每年的平均替代速率r.以16个物种的线粒体基因序列为例,说明这种新的进化距离并通过构建不同进化距离下的基因进化树来对各进化距离进行比较.结果表明:选择进化距离dy是一种有效的构建进化距离的方法.     

The use of amino acid sequence analysis in assessing evolution

The thirteen year history of assessing evolution by amino acid sequence analysis has made apparent the limitations imposed upon this system by the finite nature of the characters. This finiteness exists on several levels and ultimately expresses itself as parallelism, back mutation and the retention of primitive characters in the sequences of proteins from present day species and the putative ancestral protein chains. Sequence analysis shares these problems with other molecular approaches, but because it is concerned both with the nucleotide substitutions in the genome and with the functional roles of proteins, it has unique advantages. For example, the large fluctuation in the rate of fixation of mutations in a protein's evolution can be detected and used to point out the unreliability of any molecular clock for estimating divergence dates. Moreover, when consideration is given to studies which assign functional significance to specific amino acid sites in a protein, changes in function during the descent of a protein can be appreciated and their significance correlated with organismal evolution.     

A branch-and-bound algorithm for the inference of ancestral amino-acid sequences when the replacement rate varies among sites: Application to the evolution of five gene families

MOTIVATION: We developed an algorithm to reconstruct ancestral sequences, taking into account the rate variation among sites of the protein sequences. Our algorithm maximizes the joint probability of the ancestral sequences, assuming that the rate is gamma distributed among sites. Our algorithm probably finds the global maximum. The use of 'joint' reconstruction is motivated by studies that use the sequences at all the internal nodes in a phylogenetic tree, such as, for instance, the inference of patterns of amino-acid replacement, or tracing the biochemical changes that occurred during the evolution of a given protein family. RESULTS: We give an algorithm that guarantees finding the global maximum. The efficient search method makes our method applicable to datasets with large number sequences. We analyze ancestral sequences of five gene families, exploring the effect of the amount of among-site-rate-variation, and the degree of sequence divergence on the resulting ancestral states. AVAILABILITY AND SUPPLEMENTARY INFORMATION: http://evolu3.ism.ac.jp/~tal/ Contact: tal@ism.ac.jp     

Probabilistic reconstruction of ancestral protein sequences

Using a maximum-likelihood formalism, we have developed a method with which to reconstruct the sequences of ancestral proteins. Our approach allows the calculation of not only the most probable ancestral sequence but also of the probability of any amino acid at any given node in the evolutionary tree. Because we consider evolution on the amino acid level, we are better able to include effects of evolutionary pressure and take advantage of structural information about the protein through the use of mutation matrices that depend on secondary structure and surface accessibility. The computational complexity of this method scales linearly with the number of homologous proteins used to reconstruct the ancestral sequence.     

Determinants of rate variation in mammalian DNA sequence evolution

Attempts to analyze variation in the rates of molecular evolution among mammalian lineages have been hampered by paucity of data and by nonindependent comparisons. Using phylogenetically independent comparisons, we test three explanations for rate variation which predict correlations between rate variation and generation time, metabolic rate, and body size. Mitochondrial and nuclear genes, protein coding, rRNA, and nontranslated sequences from 61 mammal species representing 14 orders are used to compare the relative rates of sequence evolution. Correlation analyses performed on differences in genetic distance since common origin of each pair against differences in body mass, generation time, and metabolic rate reveal that substitution rate at fourfold degenerate sites in two out of three protein sequences is negatively correlated with generation time. In addition, there is a relationship between the rate of molecular evolution and body size for two nuclear-encoded sequences. No evidence is found for an effect of metabolic rate on rate of sequence evolution. Possible causes of variation in substitution rate between species are discussed.     

Assessing the accuracy of ancestral protein reconstruction methods

The phylogenetic inference of ancestral protein sequences is a powerful technique for the study of molecular evolution, but any conclusions drawn from such studies are only as good as the accuracy of the reconstruction method. Every inference method leads to errors in the ancestral protein sequence, resulting in potentially misleading estimates of the ancestral protein's properties. To assess the accuracy of ancestral protein reconstruction methods, we performed computational population evolution simulations featuring near-neutral evolution under purifying selection, speciation, and divergence using an off-lattice protein model where fitness depends on the ability to be stable in a specified target structure. We were thus able to compare the thermodynamic properties of the true ancestral sequences with the properties of “ancestral sequences” inferred by maximum parsimony, maximum likelihood, and Bayesian methods. Surprisingly, we found that methods such as maximum parsimony and maximum likelihood that reconstruct a “best guess” amino acid at each position overestimate thermostability, while a Bayesian method that sometimes chooses less-probable residues from the posterior probability distribution does not. Maximum likelihood and maximum parsimony apparently tend to eliminate variants at a position that are slightly detrimental to structural stability simply because such detrimental variants are less frequent. Other properties of ancestral proteins might be similarly overestimated. This suggests that ancestral reconstruction studies require greater care to come to credible conclusions regarding functional evolution. Inferred functional patterns that mimic reconstruction bias should be reevaluated.     

The Early Phases of Genetic Code Origin: Conjectures on the Evolution of Coded Catalysis

A review of the most significant contributions on the early phases of genetic code origin is presented. After stressing the importance of the key intermediary role played in protein synthesis, by peptidyl-tRNA, which is attributed with a primary function in ancestral catalysis, the general lines leading to the codification of the first amino acids in the genetic code are discussed. This is achieved by means of a model of protoribosome evolution which sees protoribosome as the central organiser of ancestral biosynthesis and the mediator of the encounter between compounds (metabolite-pre-tRNAs) and catalysts (peptidyl-pre-tRNAs). The encounter between peptidyl-pre-tRNA catalysts in protoribosome is favoured by metabolic pre-mRNAs and later resulted (given the high temperature at which this evolution is supposed to have taken place) in the evolution of mRNAs with codons of the type GNS. These mRNAs codified only for those amino acids that the coevolution theory of genetic code origin sees as the precursors of all other amino acids. Some aspects of the model here discussed might be rendered real by the transfer-messenger RNA molecule (tmRNA) which is here considered a molecular fossil of ancestral protein synthesis.     

A functional test of Neandertal and modern human mitochondrial targeting sequences

Targeting of nuclear-encoded proteins to different organelles, such as mitochondria, is a process that can result in the redeployment of proteins to new intracellular destinations during evolution. With the sequencing of the Neandertal genome, it has become possible to identify amino acid substitutions that occurred on the modern human lineage since its separation from the Neandertal lineage. Here we analyze the function of two substitutions in mitochondrial targeting sequences that occurred and rose to high frequency recently during recent human evolution. The ancestral and modern versions of the two targeting sequences do not differ in the efficiency with which they direct a protein to the mitochondria, an observation compatible with the neutral theory of molecular evolution.     

Post-genomic science: converting primary structure into physiological function

Exobiology, the study of the origin, evolution and distribution of life (including life on earth) within the context of cosmic evolution, is being given a remarkable boost by genome sequencing projects, which are now making the evolutionary histories of protein families routinely available. These histories comprise a multiple alignment for their protein sequences and the corresponding DNA sequences, an evolutionary tree showing the pedigree of these sequences, and reconstructed ancestral sequences for each node in the tree. In a post-genomic world having genomic sequences from an unlimited number of organisms, these histories will be used to connect structure, chemical reactivity, and physiological function to these families. This paper describes several “post-genomic” tools that exploit these evolutionary histories. They can be used to confirm or deny long distance homology between two protein families, identify proteins within a family that have new functions, and identify specific in vitro properties of the protein that are important for its physiological role. Evolution-based data structures for organizing large sequence databases are also described.