简并性还是多态性?——遗传密码子设定的进化特点的剖析(英文)

遗传密码子的设定表现出令人困惑的多态性特点 :不同氨基酸拥有的密码子的数目 ,除 5个外 ,从 1个到 6个都有 .这种特点显示出密码子无论在翻译行为还是进化轨迹上 ,都存在诸多的异质性 .因此 ,简并性一词的收敛含义 ,并不能表征这种多态性的进化内涵 .没有同义密码子的AUG(Met)和UGG (Trp)并无简并现象 .其余的密码子则可分为两大类 :一类是 ,4个同义密码子为 1组 ,具有相同的第 1、2位碱基 ,并遵循“3中读 2”的读出规则 .同组的 4个同义密码子 ,不过是来自同一个双字母原始密码子 (XYN)的孑遗物 ,从这个意义上讲 ,也不宜视为简并现象 ;另一类则主要是 ,2个同义密码子为一组 ,并遵循“3中读 3”读出规则 .它们是由编码 2个氨基酸的双义原始密码子 ,第 3位的未定碱基N进一步设定形成 .至于有 6个同义密码子的 ,特别令人困感不解的组别 ,实际上是 4 + 2个 ,这启示它们可能源于上述两大类 .遗传密码子多态性的起源 ,可能始于最初阶段 ,氨基酸同某类寡核苷酸的起始二联体的相互作用 ,而完成于所有的双义原始密码子的第 3位碱基的分化 .这种进化轨迹被传统的简并性一词所模糊 ,并导致鉴定各有关理论可信性的坚实依据和令不同观点取得共识的基础被掩盖起来 .这可能就是在遗传密码子起源领域里 ,长期存在着众     

析遗传密码子多态性之谜

建立了1个由16个“3读2”原始密码子组成的系统。它们分为“语义确切”的,和“双义的”,两大类。后者,通过不同的分化方式,进一步分化为语义确切的“3读3”现代密码子;前者则无需再分化,仍保留着“3读2”原始形态,成为孑遗密码子。首次解释了氨基酸具有不同数目密码子,以及线粒体内存在反常密码子的多态性现象,初步建立了密码子进化树,并提出了原始氨酰基－tRNA合成酶可能在密码子进一步分化中起关键作用的观点。     

tRNA序列的进化网络研究

根据tRNA序列的反密码子,把3420 条tRNA 序列分成了21组,其中包括20 组氨基酸及1 组Stop。通过tRNA序列的相似度构建了1 组整体网络和21 组子网络,并计算了它们在不同相似度下的平均度、平均聚类系数以及平均最短路径。通过分析、比较和讨论网络中的三个重要参数,进一步说明点突变是tRNA序列进化的重要机制,并反映了它们的进化近似符合中性理论,且在同一组氨基酸和Stop 内的tRNA序列在进化历史上的同源关系更密切;同时表明了tRNA 序列在进化过程中具有自相似性。     

遗传密码子研究进展

作为生命信息的基本遗传单位,基因组遗传密码的破译对于人们加深对生命本质的认识具有重要的理论价值和现实意义。目前,遗传密码子的研究重心已由遗传密码子的破译及反常密码子的发现转入到遗传密码子的起源与进化及扩张等研究。遗传密码子的起源与进化是当今基因组学研究的热点命题之一,相关的学说、假设层出不穷,但尚未取得实质性突破。另一方面,无义密码子的再定义及遗传密码的扩张等研究却极大的丰富和发展了遗传密码子的科学内涵,推动了生命科学研究的发展。文章综述了遗传密码子的多态性、起源与进化、无义密码子的再定义及遗传密码的扩张等方面的研究进展,并就其应用价值作了评述,期待为其在基因组学、医学等相关领域的应用研究提供参考。     

遗传密码子及其应用

作为生命信息的基本遗传单位,基因组遗传密码的破译对于人们加深对生命本质的认识具有重要的理论价值和现实意义.目前,遗传密码子的研究重心已由遗传密码子的破译及反常密码子的发现转入到遗传密码子的起源与进化及扩张等研究.遗传密码子的起源与进化是当今基因组学研究的热点命题之一,相关的学说、假设层出不穷,但尚未取得实质性突破.另一方面,无义密码子的再定义及遗传密码的扩张等研究却极大的丰富和发展了遗传密码子的科学内涵,推动了生命科学研究的发展.文章综述了遗传密码子的多态性、起源与进化、无义密码子的再定义及遗传密码的扩张等方面的研究进展,并就其应用价值作了评述,期待为其在基因组学、医学等相关领域的应用研究提供参考.     

tRNA上的反密码子到底怎样阅读

人教版必修2《遗传与进化》教材第66页在介绍tRNA的结构和功能时给出了下面一副插图: 显然这幅图是tRNA三叶草叶型的二级结构,此图在很多高校生化教材中很常见,且都是磷酸基团(-(P))位于左上端,羟基(-OH)位于右上端.图下端标有反密码子.那么代表反密码子的这3个碱基该怎么正确阅读呢?如果在此图中从左到右阅读,即P-3个连续碱基-OH,其实意味着反密码子是从tRNA的5 '端向3’端阅读的,即5’-3个连续碱基-3’.然而在教材同一页,接下来却出现了这样的文字叙述:"……如图所示(图4～6蛋白质合成示意图),反密码子为UAC的tRNA携带甲硫氨酸,通过与mRNA上的碱基AUG互补配对,进入位点1".     

同义密码子使用模式对多肽链共翻译折叠的影响研究进展

同义密码子使用模式作为核苷酸与氨基酸的纽带,其多样性介导了核糖体扫描速率,同时扩充了基因的遗传信息存储量。随着新型技术的应用,发现特异性密码子和密码子结合力可调节核糖体扫描速率并影响蛋白质构象。同义密码子使用模式通过多种方式在不同环节影响着核糖体扫描速率,同时还影响着自身mRNA的稳定性。本文简述了密码子使用模式如何在核糖体扫描翻译mRNA的过程中实现对多肽链翻译延伸的调控,为今后生物工程学领域如何优化蛋白高效表达提供可参考的思路与理念。     

微生物tRNA与密码子系统应用研究进展*

tRNA作为生命中心法则中翻译过程的重要参与分子,其种类、丰度都会对蛋白质的正常合成产生巨大影响。近年来通过对微生物tRNA的结构功能以及合成修饰过程的解析获得诸多启发,开展密码子扩展的研究,实现将非天然氨基酸引入特定位置从而获得新功能蛋白。同时,通过化学合成微生物基因组开展的密码子重编码工作将释放更多的密码子与tRNA用于更加广泛的密码子扩展研究。对微生物tRNA与密码子系统在合成生物学中的最新应用研究进展进行了综述,并讨论其未来的发展趋势。     

动物眼睛的起源与进化研究进展

动物眼睛的起源与进化过程是人类在探索自然奥秘过程中遇到的一个非常有趣且引人注目的研究热点,目前这方面的研究已取得了丰硕的成果。从眼睛出现的过程、眼睛进化所需的时间、眼睛的单起源论、眼睛的类型与进化、光感受器与眼睛进化的关系、光感受器和视蛋白的类型与进化这6个方面简要概述了动物眼睛起源与进化的主要研究进展。     

《理论古生物学文集》即将由中国科学院南京地质古生物研究所编辑出版

国内和国外学者撰写的有关古生物学若干理论问题的论文与译文,最近由中国科学院南京地质古生物研究所编辑,将在南京大学出版社正式出版。全书分成两个部分。第一部分系我国学者的论文,涉及用分支系统学的原理和方法研究中生代植物与二叠纪(竹蜓)类动物,用边域成种理论解释华南中生代假铰蚌类的起源、演化和散布,有关微进化和宏进化理论的含义并讨论腕足动物石燕族的起源与早期进化,以奥陶纪末期的集群绝灭为例研讨集群绝灭的基本原理,异时发育的概念及其在(竹蜓)类演化分析中的应用等。第二部分系外国学者著作的译文,大都是八十年代发表的新作,由从不同的角度探讨点断平衡论(Puuctuatcd Equalibrium)与种系渐进论(Phylctic Gradualism)、宏进化     

Codon usage bias: causative factors,quantification methods and genome‐wide patterns: with emphasis on insect genomes

Codon usage bias refers to the phenomenon where specific codons are used more often than other synonymous codons during translation of genes, the extent of which varies within and among species. Molecular evolutionary investigations suggest that codon bias is manifested as a result of balance between mutational and translational selection of such genes and that this phenomenon is widespread across species and may contribute to genome evolution in a significant manner. With the advent of whole‐genome sequencing of numerous species, both prokaryotes and eukaryotes, genome‐wide patterns of codon bias are emerging in different organisms. Various factors such as expression level, GC content, recombination rates, RNA stability, codon position, gene length and others (including environmental stress and population size) can influence codon usage bias within and among species. Moreover, there has been a continuous quest towards developing new concepts and tools to measure the extent of codon usage bias of genes. In this review, we outline the fundamental concepts of evolution of the genetic code, discuss various factors that may influence biased usage of synonymous codons and then outline different principles and methods of measurement of codon usage bias. Finally, we discuss selected studies performed using whole‐genome sequences of different insect species to show how codon bias patterns vary within and among genomes. We conclude with generalized remarks on specific emerging aspects of codon bias studies and highlight the recent explosion of genome‐sequencing efforts on arthropods (such as twelve Drosophila species, species of ants, honeybee, Nasonia and Anopheles mosquitoes as well as the recent launch of a genome‐sequencing project involving 5000 insects and other arthropods) that may help us to understand better the evolution of codon bias and its biological significance.     

The origins of larval forms: what the data indicate,and what they don't

What is a larva, if it is not what survives of an ancestor's adult, compressed into a transient pre‐reproductive phase, as suggested by Haeckel's largely disreputed model of evolution by recapitulation? A recently published article hypothesizes that larva and adult of holometabolous insects are developmental expressions of two different genomes coexisting in the same animal as a result of an ancient hybridization event between an onychophoran and a primitive insect with eventless post‐embryonic development. More likely, however, larvae originated from late embryonic or early post‐embryonic stages of ancestors with direct development. Evolutionary novelties would thus be intercalary rather than terminal, with respect to the ancestor's ontogenetic schedule. This scenario, supported by current research on holometabolous insects and marine invertebrates with complex life cycles, offers a serious alternative to the traditional scenario (‘what is early in ontogeny is also early in phylogeny’) underlying the current perception of the evolution of genetic regulatory networks.     

Looking for the Primordial Genetic Honeycomb

All life forms on Earth share the same biological program based on the DNA/RNA genomes and proteins. The genetic information, recorded in the nucleotide sequence of the DNA and RNA molecule, supplies the language of life which is transferred through the different generations, thus ensuring the perpetuation of genetic information on Earth. The presence of a genetic system is absolutely essential to life. Thus, the appearance in an ancestral era of a nucleic acid-like polymer able to undergo Darwinian evolution indicates the beginning of life on our planet. The building of primordial genetic molecules, whatever they were, required the presence of a protected environment, allowing the synthesis and concentration of precursors (nucleotides), their joining into larger molecules (polynucleotides), the protection of forming polymers against degradation (i.e. by cosmic and UV radiation), thus ensuring their persistence in a changing environment, and the expression of the “biological” potential of the molecule (its capacity to self-replicate and evolve). Determining how these steps occurred and how the primordial genetic molecules originated on Earth is a very difficult problem that still must be resolved. It has long been proposed that surface chemistry, i.e. on clay minerals, could have played a crucial role in the prebiotic formation of molecules basic to life. In the present work, we discuss results obtained in different fields that strengthen the hypothesis of a clay-surface-mediated origin of genetic material. Presented at: National Workshop on Astrobiology: Search for Life in the Solar System, Capri, Italy, 26 to 28 October, 2005.     

Origin of modern humans in East Asia: clues from the Y chromosome

East Asia is one of the most important regions for studying modern human origin and evolution. A lot of efforts have been made to detect the genetic diversity and to reconstruct the evolutionary history of East Asians, especially using Y chromosome genetic data, in recent years. The Y chromosome data supports the African origin of modern humans in East Asia and the later migration to East Asia through the southern tropic coastline route, and then the northward migration occurred, leading to peopling of the main continent. The genetic data of the Y chromosome reflects a clear prehistoric evolution and migration course of East Asians. As well, the Y chromosome data of East Asians provides clues to elucidate modern human origins and evolution in the neighboring regions, i.e. America, Oceania and the Pacific Islands.     

Origin of modern humans in East Asia: clues from the Y chromosome

East Asia is one of the most important regions for studying modern human origin and evolution. A lot of efforts have been made to detect the genetic diversity and to reconstruct the evolutionary history of East Asians, especially using Y chromosome genetic data, in recent years. The Y chromosome data supports the African origin of modern humans in East Asia and the later migration to East Asia through the southern tropic coastline route, and then the northward migration occurred, leading to peopling of the main continent. The genetic data of the Y chromosome reflects a clear prehistoric evolution and migration course of East Asians. As well, the Y chromosome data of East Asians provides clues to elucidate modern human origins and evolution in the neighboring regions, i.e. America, Oceania and the Pacific Islands.     

Natural history and experimental evolution of the genetic code

The standard genetic code is a set of rules that relates the 20 canonical amino acids in proteins to groups of three bases in the mRNA. It evolved from a more primitive form and the attempts to reconstruct its natural history are based on its present-day features. Genetic code engineering as a new research field was developed independently in a few laboratories during the last 15 years. The main intention is to re-program protein synthesis by expanding the coding capacities of the genetic code via re-assignment of specific codons to un-natural amino acids. This article focuses on the question as to which extent hypothetical scenarios that led to codon re-assignments during the evolution of the genetic code are relevant for its further evolution in the laboratory. Current attempts to engineer the genetic code are reviewed with reference to theoretical works on its natural history. Integration of the theoretical considerations into experimental concepts will bring us closer to designer cells with target-engineered genetic codes that should open not only tremendous possibilities for the biotechnology of the twenty-first century but will also provide a basis for the design of novel life forms.     

叶绿体基因组研究进展

作为植物细胞器的重要组成部分和光合作用的器官,叶绿体在生物进化的漫长历史中发挥了重要作用.伴随着生物技术的深入发展,人们发现叶绿体基因组结构和序列的信息在揭示物种起源、进化演变及其不同物种之间的亲缘关系等方面具有重要价值.与此同时,比核转化具有明显优势的叶绿体转化技术在遗传改良、生物制剂的生产等方面显示出巨大潜力,而叶绿体基因组结构和序列分析则是叶绿体转化的基石.基于叶绿体的这些重要作用,收集整理了有关的资料,从几个方面归纳了本领域最近的研究进展,希望能使读者对迅速发展的叶绿体基因组研究有更全面的了解,以及对叶绿体基因组在物种的进化、遗传、系统发育关系等方面的作用有更深刻的认识,同时也希望对叶绿体转化技术的研究和广泛应用产生积极作用.     

Codon usage in Homo sapiens: evidence for a coding pattern on the non-coding strand and evolutionary implications of dinucleotide discrimination

This study reports the analysis of codon usage in 35 complete Homo sapiens genes. Both codon frequency and inter-codon interference exhibit patterns of evolutionary interest. There is a significant positive correlation between the frequency with which a given codon is used and the frequency with which its complement is used. Since the frequency of appearance of the complementary codon on the coding strand is equal to the frequency of appearance of the original codon on the non-coding strand, in the same phase, the non-coding strand is found to resemble the coding strand in triplet composition. The same effect has been observed in Escherichia coli. This preference for the use of certain complementary triplets as codons suggests that the evolution of the use of the genetic code depended to some extent upon the double-stranded nature of the coding material. In addition, the effect of discrimination against the use of two dinucleotides, CpG and UpA, is observed in codon usage and also in adjacent codon interference. Codons beginning with G, or A, are unlikely to be preceded by codons ending in C, or U, respectively. Consideration of codon assignment in the genetic code together with the observed CpG infrequency suggests that the evolution of the code may have been influenced by conditions in which the use of CpG dinucleotides was unfavorable. The infrequent use of UpA dinucleotides can be explained as the result of frameshift mutation during gene evolution.     

Human lipoprotein lipase last exon is not translated,in contrast to lower vertebrates

We have sequenced the first fish (zebrafish,Brachydanio rerio) lipoprotein lipase (LPL) cDNA clone. Similarities were found in mammalian LPL cDNA, but the codon spanning the last two exons (which is thus split by the last intron) is AGA (Arg) as opposed to TGA in mammals. Exon 10 is thus partially translated. These results were confirmed with rainbow trout (Oncorhynchus mykiss). We also investigated whether mammal TGA coded for selenocystein (SeCys), the 21st amino acid, but found that this was not the case: TGA does not encode SeCys but is a stop codon. It thus appears that the sense codon AGA (fish) has been transformed into a stop codon TGA (human) during the course of evolution. It remains to be determined if the “loss” of the C-terminal end of mammalian LPL protein has conferred an advantage in terms of LPL activity or, on the contrary, a disadvantage (e.g., susceptibility to diabetes or atherosclerosis). Correspondence to: J. Etienne     

Viral adaption of staphylococcal phage: A genome-based analysis of the selective preference based on codon usage Bias

Given the high therapeutic value of the staphylococcal phage, the genome co-evolution of the phage and the host has gained great attention. Though the genome-wide AT richness in staphylococcal phages has been well-studied with nucleotide usage bias, here we proved that host factor, lifestyle and taxonomy are also important factors in understanding the phage nucleotide usages bias using information entropy formula. Such correlation is especially prominent when it comes to the synonymous codon usages of staphylococcal phages, despite the overall scattered codon usage pattern represented by principal component analysis. This strong relationship is explained by nucleotide skew which testified that the usage biases of nucleotide at different codon positions are acting on synonymous codons. Therefore, our study reveals a hidden relationship of genome evolution with host limitation and phagic phenotype, providing new insight into phage genome evolution at genetic level.