一个新的生物界──古细菌界

一个新的生物界──古细菌界一类称为古细菌的有机体,与其他细菌（真细菌）一样不具有明确的细胞核,过去被一起归之于原核生物,以与有核的真核生物相区分。１９７７年,美国伊斯诺斯大学进化学家卡尔·伍斯发现,古细菌与真细菌和真核生物都颇有差别,在分类学上似可单...     

真核生物起源研究进展

作为重大进化谜题,真核生物起源的研究对于解码真核基因组、阐释真核细胞内部结构之间的关系有重要启示作用。在1977年美国微生物学家Carl Woese发现古细菌并提出三域生命之树之后,大量研究显示古细菌与真核生物在进化上存在着密切联系。21世纪以来,系统发育分析方法不断改进,泉古菌门(Crenarchaeota)、广古菌门(Euryarchaeota)之外与真核生物更加相似的新古细菌门类也相继被发现,这些证据更加支持将真核生物与古细菌合并为一域,形成二域生命之树。目前,通过宏基因组技术发现的Asgard古细菌是与真核生物进化距离最近的原核生物。然而,真核生物祖先的身份以及线粒体起源的时间等核心问题仍是学术界争论的焦点。本文结合近年来国内外研究成果,从生命之树的形态变化与真核生物演变的具体机制两个角度梳理了目前对真核生物起源的认知过程、现有水平和研究前景,以期为揭示真核生物起源进程的后续研究提供参考与指引。     

串联重复序列的物种差异及其生物功能

串联重复序列是指1-200个碱基左右的核心重复单位,以头尾相串联的方式重复多次所组成的重 复序列。它广泛存在于真核生物和一些原核生物的基因组中,并表现出种属、碱基组成等的特异性。在基因组 整体水平上,各种优势的重复序列类型不同。即使在同一重复序列类型内部,不同重复拷贝类别(如AT、AC 等)在基因组中的存在也表现出很大的差异。同时,这些重复序列类型和各重复拷贝类别在同一物种的不同染 色体间,以及基因的编码区和非编码区间也表现种属和碱基组成差异。这些差异显示了重复序列起源和进化的 复杂性,可能涉及到多种机制和因素,并与生物功能密切相关。另外,由于重复序列分析软件和统计标准还存 在算法、重复长度、完美性等问题,需要进一步探讨。此外,串联重复序列的自身进化关系、全基因组水平上 的进化地位、在基因组中的生物功能、重复序列数据库建立和应用研究等,将是今后研究的主要课题。     

真核生物转座子鉴定和分类计算方法

重复序列是真核生物基因组的重要组成成分,根据其序列特征及在基因组中的存在形式,可以进一步分为串联重复、片段重复和散在重复。其中,散在重复大多起源于转座子。根据转座介质的不同,转座子又可分为DNA和逆转录转座子。转座子的转座和扩增对基因的进化和基因组的稳定具有显著的影响;同时与其他类型的重复序列相比,转座子的结构和分类更为复杂多样,使得对转座子的鉴定和分类更为复杂和困难。鉴于此,文章简要概括了转座子的功能及分类,总结了真核生物转座子鉴定、分类和注释的3个步骤:(1)重复序列库的构建;(2)重复序列的校正和分类;(3)基因组注释。着重介绍了每一步骤所采用的不同计算方法,比较了不同方法的优缺点。只有把多种方法结合起来使用才能实现全基因组转座子的精确鉴定、分类和注释,这将为转座子的全基因组鉴定和分类提供借鉴意义。     

CRISPR在细菌分型和进化中的研究进展

规律成簇的间隔的短回文重复序列（CRISPR）是近年发现的一类存在于古细菌和细菌基因组内的结构,该结构可以使细菌获得对外源DNA如质粒和噬菌体的免疫,同时由于其结构的多态性,也可作为细菌分型和进化研究的位点。简要综述了CRSIPR系统的基本结构,及其在分型和进化应用方面的研究进展。     

简单重复DNA序列在哺乳动物mtDNA D-loop区的分布及进化特征

简单重复序列广泛分布于从原核到真核生物的基因组中, 其形成的分子机理目前尚不明确。对NCBI数据库中已有256种哺乳动物线粒体DNA (mtDNA) D-loop区进行序列比对分析, 根据其所含有的简单重复序列类型分为3组, 分别是53种哺乳动物含有六核苷酸重复序列; 104种哺乳动物含有非六核苷酸重复序列(＞6 bp); 99种哺乳动物不含有任何重复序列。通过碱基序列分析比对, 发现六核苷酸重复序列集中分布在CSB1-CSB2间隔区, 而非六核苷酸重复可以分布于终止区(TAS)、中央保守区(Central domain)以及CSB(Central sequence block)区。通过比较含有重复序列与不含重复序列的功能保守区发现, 简单重复序列的存在并不明确影响D-loop区内的中央保守区以及CSB1、CSB2、CSB3三个功能保守区的碱基序列保守性。在此基础上, 利用N-J法构建了256种哺乳动物的进化树, 分析了哺乳动物D-Loop区内重复序列在进化过程中的可能变化规律, 发现简单重复序列随着物种的进化地位的升高而呈现消失趋势。     

产甲烷细菌的极性脂质结构

古细菌的极性脂质是以植烷醇结构为特征的,它有别于真细菌和真核生物的正常脂质。构成产甲烷细菌极性脂质的基本骨架有四种:阿克醇、卡克醇、马克醇和海克醇。本文阐述了各种产甲烷细菌极性脂质成分的结构;从这些脂质成分的结构特点上看,或许极性脂质可作为系统分类和进化的标志。     

副溶血性弧菌群中规律成簇间隔短回文重复序列的比较分析

规律成簇间隔短回文重复序列(clustered regularly interspaced short palindromic repeats,CRISPR)是大多数细菌和古细菌在生存压力下进化出的一套抵抗噬菌体干扰的防御系统。本研究主要采用生物信息学的方法,对24株分离自人体且已完成全基因组测序的副溶血性弧菌内CRISPR结构进行了分析,结果发现:只有16株细菌包含1个及以上的CRISPR结构,共计29个CRISPR;仅11个具有真座位特征的CRISPR结构含有前导序列;CRISPR结构中的重复序列所形成的RNA二级结构具有一大一小共两环或一大二小共三环的特征;目前未找到与区间序列高度同源的外源遗传物质;仅含前导序列的CRISPR结构侧翼区才存在cas基因。副溶血性弧菌的CRISPR结构可能以水平基因转移的方式整合到细菌的染色体中,CRISPR结构不适合作为细菌分类的一项指标。     

WD-重复蛋白

 WD基元又称Trp-ASP或WD40,由40个左右的氨基酸残基组成,具有保守的GH和WD序列.WD基元存在于很多具有调控功能的蛋白质中,介导蛋白质之间的相互作用,在信号转导、蛋白运输、染色体修饰、转录或RNA加工等过程中具有重要作用.WD重复蛋白(WD-repeat protein)是含有多个保守的WD基元的蛋白质.近年发现,WD-repeat基因突变与人的几种疾病相关.本文对真核生物WD-重复蛋白的研究进展进行了综述,阐明了WD 重复蛋白的β-propeller结构特征及其作用机制,并对WD-重复蛋白的未来研究方向进行展望.     

斜纹夜蛾核多角体病毒DNA XbaI 4.0 kb片段锌指蛋白基因及重复序列分析

测定了斜纹夜蛾核多角体病毒 (Spodopteralituranucleopolyhedrovirus,SpltNPV)中山大学分离株基因组DNAXbaI4.0kb片段全序列 ,该片段包括一个锌指蛋白基因及三个区域的DNA重复序列 (SR1、SR2、SR3)。该锌指蛋白基因读码框为 2 196个核苷酸 ,编码 731个氨基酸的蛋白质 ,分子量为 83 .0 9kD ,该蛋白的等电点为 4.6 1。在其 5′非编码区内有一个杆状病毒早期启动子基序GAGT及一个TATA盒 ,在其终止密码的下游有 5个真核生物转录mRNA时poly(A)加尾信号AATAAA。在 2 2 3～ 2 41氨基酸残基之间有一个锌指蛋白基序 ,这一基序属于锌指蛋白基序中的C3HC4类 ,即环指 (Ringfinger)类基序。在 32 3～ 340氨基酸残基区域为一个核定位信号。该蛋白可能为一个高度折叠的蛋白质。在该片段中存在三个DNA重复序列区域 (SR1、SR2、SR3) ,其中SR1与SR3区域存在更大量的重复序列 ,SR1区域其中的一个重复序列长达 41bp ,SR1、SR3重复序列区域可能作为该病毒转录的增强子 ,或者作为DNA复制的起始点。     

Trend of amino acid composition of proteins of different taxa

Archaea, bacteria and eukaryotes represent the main kingdoms of life. Is there any trend for amino acid compositions of proteins found in full genomes of species of different kingdoms? What is the percentage of totally unstructured proteins in various proteomes? We obtained amino acid frequencies for different taxa using 195 known proteomes and all annotated sequences from the Swiss-Prot data base. Investigation of the two data bases (proteomes and Swiss-Prot) shows that the amino acid compositions of proteins differ substantially for different kingdoms of life, and this difference is larger between different proteomes than between different kingdoms of life. Our data demonstrate that there is a surprisingly small selection for the amino acid composition of proteins for higher organisms (eukaryotes) and their viruses in comparison with the "random" frequency following from a uniform usage of codons of the universal genetic code. On the contrary, lower organisms (bacteria and especially archaea) demonstrate an enhanced selection of amino acids. Moreover, according to our estimates, 12%, 3% and 2% of the proteins in eukaryotic, bacterial and archaean proteomes are totally disordered, and long (> 41 residues) disordered segments are found to occur in 16% of arhaean, 20% of eubacterial and 43% of eukaryotic proteins for 19 archaean, 159 bacterial and 17 eukaryotic proteomes, respectively. A correlation between amino acid compositions of proteins of various taxa, show that the highest correlation is observed between eukaryotes and their viruses (the correlation coefficient is 0.98), and bacteria and their viruses (the correlation coefficient is 0.96), while correlation between eukaryotes and archaea is 0.85 only.     

A census of protein repeats.

In this study, we analyzed all known protein sequences for repeating amino acid segments. Although duplicated sequence segments occur in 14 % of all proteins, eukaryotic proteins are three times more likely to have internal repeats than prokaryotic proteins. After clustering the repetitive sequence segments into families, we find repeats from eukaryotic proteins have little similarity with prokaryotic repeats, suggesting most repeats arose after the prokaryotic and eukaryotic lineages diverged. Consequently, protein classes with the highest incidence of repetitive sequences perform functions unique to eukaryotes. The frequency distribution of the repeating units shows only weak length dependence, implicating recombination rather than duplex melting or DNA hairpin formation as the limiting mechanism underlying repeat formation. The mechanism favors additional repeats once an initial duplication has been incorporated. Finally, we show that repetitive sequences are favored that contain small and relatively water-soluble residues. We propose that error-prone repeat expansion allows repetitive proteins to evolve more quickly than non-repeat-containing proteins.     

21 Ribosomal evidence suggests that archaea evolved after fungi

We are exploring the potential to trace species evolution with the ribosomal proteins (RibPs) present in bacterial, eukaryotic, and archaeal ribosomes and to compare the independent trees for consistency. The complete genomes of over 8400 bacteria, eukaryota, and archaea are presently in the SwissPro/TrEMBL (SPT) database. A search of SPT using a vector designed with ScanProsite formats (V1) finds and aligns 8405 sequences (5312 bacterial, 2905 eukaryotic, and 169 archaeal) that are homologous with bone fide bacterial S19 ribosomal proteins(S19s). When the 8405 sequences are perfectly aligned, 15 residues are conserved at 90% identity and 40 are conserved at 70% identity. We are not aware of any previous publication reporting sequence alignment of 8400 members of any single family including all bacteria, eukaryota and archaea, for which complete genomes have been published.A Pro and a Gly separated by 11 residues are 100% conserved in the 8405 S19s. In the position immediately before the fully conserved Gly, two residues (Asp and Asn) are present in 98.3% of the 8405 sequences. The Asp residue is found almost exclusively in 2190 gram-positive bacteria. The Asn residue is found in 3065 gram-negative bacteria, 123 Archaea, 1939 eukaryotes, and 64 specific species of gram-positive bacteria. There is biochemical evidence for the existence of distinct mitochondrial, chloroplast, and cytosolic ribosomes and reports that plants have all three forms and mammals only two. Reliable data concerning how individual ribosomal proteins differ in different types of ribosomes are meager. Examination of the eukaryotic S19s reveals the existence of three distinct types. Two of the distinctly different types are found in most fungi, three of the types are found in some viridiplante, and only one type is found in metazoa and archaea. We demonstrate the sequence homology between the mitochondrial form found in fungi and plants and the S19 proteins of alpha proteobacteria; between the chloroplast S19s and the S19s of cyanobacteria; and among the cytosolic S19s found only in fungi, metazoa, archaea, and in some viridiplantae. Our findings suggest that most archaeal species appeared after a gene duplication event in fungi that correlates with the origin of the cytosolic ribosome.     

PII signal transduction proteins: sensors of alpha-ketoglutarate that regulate nitrogen metabolism

PII proteins are small homotrimeric signal transduction proteins that regulate the activities of metabolic enzymes and permeases, and control the activities of signal transduction enzymes. The protein family shows high conservation, with examples in eukaryota (plants and eukaryotic algae), archaea, and bacteria. This distribution indicates that PII is one of the most ancient signalling proteins known.     

Genome-wide analysis of enzyme structure-function combination across three domains of life

To investigate diverse enzyme structure-function combination (SFC) types in different species, 34 different genome sequences were annotated using the protein catalytic domain database SCOPEC (http://www.enzome.com/enzome/), in which both the structure and function for each entry are known. Annotated enzymes with catalytic domains from the same SCOP superfamily are considered to have an identical structure. Annotated enzymes sharing the identical three-digit EC number are considered to have the same enzymatic function. Results reveal that the different SFC types for enzymes identified in archaea, bacteria and eukaryota are 137, 300 and 313, respectively. About 80% of the SFCs identified in archaea can be consistently found in bacteria and eukaryota species, whereas 28% and 35% combination types in bacteria and eukaryota respectively are unique to their corresponding groups. The number of functions per structure and the number of structures per function for the annotated sequences were measured in different species. Furthermore, a new concept was proposed to represent enzymatic structures as a functional similarity network. Thus, the current study will be helpful to enhance the global view on the evolution of enzymatic structure and function.     

Organism complexity anti-correlates with proteomic beta-aggregation propensity

We introduce a novel approach to estimate differences in the beta-aggregation potential of eukaryotic proteomes. The approach is based on a statistical analysis of the beta-aggregation propensity of polypeptide segments, which is calculated by an equation derived from first principles using the physicochemical properties of the natural amino acids. Our analysis reveals a significant decreasing trend of the overall beta-aggregation tendency with increasing organism complexity and longevity. A comparison with randomized proteomes shows that natural proteomes have a higher degree of polarization in both low and high beta-aggregation prone sequences. The former originates from the requirement of intrinsically disordered proteins, whereas the latter originates from the necessity of proteins with a stable folded structure.     

Occurrence of disordered patterns and homorepeats in eukaryotic and bacterial proteomes

Combining the motif discovery and disorder protein segment identification in PDB allows us to create the first and largest library of disordered patterns. At present the library includes 109 disordered patterns. Here we offer a comprehensive analysis of the occurrence of selected disordered patterns and 20 homorepeats of 6 residues long in 123 proteomes. 27 disordered patterns occur sparsely in all considered proteomes, but the patterns of low-complexity-homorepeats-appear more often in eukaryotic than in bacterial proteomes. A comparative analysis of the number of proteins containing homorepeats of 6 residues long and the disordered selected patterns in these proteomes has been performed. The matrices of correlation coefficients between numbers of proteins where at least once a homorepeat of six residues long for each of 20 types of amino acid residues and 109 disordered patterns from the library appears in 9 kingdoms of eukaryota and 5 phyla of bacteria have been calculated. As a rule, the correlation coefficients are higher inside the considered kingdom than between them. The largest fraction of homorepeats of 6 residues belongs to Amoebozoa proteomes (D. discoideum), 46%. Moreover, the longest uninterrupted repeats belong to S306 from D. discoideum (Amoebozoa). Homorepeats of some amino acids occur more frequently than others and the type of homorepeats varies across different proteomes, . For example, E6 appears most frequent for all considered proteomes for Chordata, Q6 for Arthropoda, S6 for Nematoda. The averaged occurrence of multiple long runs of 6 amino acids in a decreasing order for 97 eukaryotic proteomes is as follows: Q6, S6, A6, G6, N6, E6, P6, T6, D6, K6, L6, H6, R6, F6, V6, I6, Y6, C6, M6, W6, and for 26 bacterial proteomes it is A6, G6, P6, and the others occur seldom. This suggests that such short similar motifs are responsible for common functions for nonhomologous, unrelated proteins from different organisms.     

Identification of thermophilic species by the amino acid compositions deduced from their genomes

The global amino acid compositions as deduced from the complete genomic sequences of six thermophilic archaea, two thermophilic bacteria, 17 mesophilic bacteria and two eukaryotic species were analysed by hierarchical clustering and principal components analysis. Both methods showed an influence of several factors on amino acid composition. Although GC content has a dominant effect, thermophilic species can be identified by their global amino acid compositions alone. This study presents a careful statistical analysis of factors that affect amino acid composition and also yielded specific features of the average amino acid composition of thermophilic species. Moreover, we introduce the first example of a 'compositional tree' of species that takes into account not only homologous proteins, but also proteins unique to particular species. We expect this simple yet novel approach to be a useful additional tool for the study of phylogeny at the genome level.     

Frequent and widespread parallel evolution of protein sequences

Understanding the patterns and causes of protein sequence evolution is a major challenge in evolutionary biology. One of the critical unresolved issues is the relative contribution of selection and genetic drift to the fixation of amino acid sequence differences between species. Molecular homoplasy, the independent evolution of the same amino acids at orthologous sites in different taxa, is one potential signature of selection; however, relatively little is known about its prevalence in eukaryotic proteomes. To quantify the extent and type of homoplasy among evolving proteins, we used phylogenetic methodology to analyze 8 genome-scale data matrices from clades of different evolutionary depths that span the eukaryotic tree of life. We found that the frequency of homoplastic amino acid substitutions in eukaryotic proteins was more than 2-fold higher than expected under neutral models of protein evolution. The overwhelming majority of homoplastic substitutions were parallelisms that involved the most frequently exchanged amino acids with similar physicochemical properties and that could be reached by a single-mutational step. We conclude that the role of homoplasy in shaping the protein record is much larger than generally assumed, and we suggest that its high frequency can be explained by both weak positive selection for certain substitutions and purifying selection that constrains substitutions to a small number of functionally equivalent amino acids.