RNA二级结构在微生物系统发育分析上的应用*

RNA二级结构用于微生物分类和系统发育分析在近年来逐渐受到注意并发展起来。文章就此方面的发展做了简要综述,其中对在系统发育分析上的应用部分作了较重点介绍。     

纤毛虫分子系统发育学的研究进展

在回顾纤毛虫分子系统发育学产生发展历史的基础上,介绍了随着20年中RFLP、RAPD和DNA序列分析等分子生物学技术作为该学科的主要研究方法在种群遗传多样性与进化、种上阶元系统发育学两方面取得的研究成果和近期研究进展,最后在探讨纤毛虫分子系统发育学存在的一些问题和解决方法的同时,预测了纤毛虫分子系统发育学今后将极大地推动真核生物的起源与进化,内共生等重要生物进化问题的研究。     

系统发育研究中直同源预测方法的选择策略

测序技术的不断发展和价格的日益降低使得系统发育组学更深层次的研究成为可能。在系统发育组学分析中,至关重要的步骤是直同源预测,这是因为进行系统发育重建的先决条件是进行比对的基因是直同源的。这里我们简单地回顾了直同源的定义和直同源预测的不同方法,与此同时,我们还给出了一些选择更合适的直同源预测方法的建议。     

散白蚁属Reticulitermes分子系统发育与生物地理学研究进展

散白蚁属Reticulitermes隶属于等翅目鼻白蚁科Rhinotermitidae,是一类危害严重的重要社会性昆虫。文章回顾了近年来国内外散白蚁属系统发育和生物地理学研究进展,主要比较了传统方法和分子方法对散白蚁属系统发育的研究,包括对鼻白蚁科的进化关系研究,散白蚁属的分子系统发育现状,分子技术发展过程的总结。对散白蚁属的地理分布与其进化关系研究进行了阐述。线粒体、核基因标记和微卫星系统发育分析可以用于推测具有重要经济价值的散白蚁种类如北美散白蚁等的入侵路线和可能的入侵机制。文章最后展望了新兴测序技术、线粒体全基因组、转录组和宏基因组分析等可以用于散白蚁属系统发育分析。     

常用系统发育树构建算法和软件鸟瞰

系统发育树又称进化树、生命树等,在达尔文的"进化论"一书中首次出现,之后系统发育树的重构被广大生物学家所接受。该文阐述了构建系统发育树的基本流程,对目前用于构建系统发育树的四类算法(距离法、最大简约法、最大似然法和贝叶斯法)进行了详细地分析和比较,并介绍了一些常用系统发育树构建和分析软件(PHYLIP、MEGA、MrBayes)的特点。     

植物内生固氮菌系统发育进化新进展

在植物内生固氮菌系统发育进化关系研究中,常用的方法有形态学与蛋白质水平法、数值分类和自动化鉴定法、化学分类法、分子遗传学方法等。本文简要介绍了常用方法的关键技术,并归纳了它们的优缺点。生物学的研究进入基因组时代后,随着高通量DNA测序技术在微生物学领域应用的迅速发展,全基因组测序被应用到微生物系统发育进化研究中,然而目前并未发现对已测全基因组序列的植物内生固氮菌进行系统总结。本文在对已测序植物内生固氮菌进行归纳的基础上,又详细研究了基于基因组数据的几种具有代表性的新方法(ANI分析法、最大唯一匹配指数法、核心基因组分析、组分矢量法、基因流动性分析),并结合目前系统发育进化研究常用方法,对植物内生固氮菌系统发育进化研究趋势进行总结和展望,旨在使植物内生固氮菌的系统发育进化关系研究在精确度、可靠性等方面有所突破。     

基因树冲突与系统发育基因组学研究

随着越来越多的基因序列被运用于系统发育重建中,随之产生的基因树冲突已成为分子系统发育研究中日益突出的问题.因此,在分子系统发育研究中,应正确理解基因树和物种树之间的差异,充分注意和分析基因树冲突的原因,正确解释分子系统发育的结果.本文通过一些典型实例分析了在多基因系统发育研究中引发基因树冲突的三类主要原因:随机误差、系统误差和生物学因素.在此基础上,对近年来兴起的系统发育基因组学进行了介绍,并以稻属Oryza研究为例,阐述了系统发育基因组学方法在解决基因树冲突以及系统发育研究中的优势和应用价值,并进一步探讨了解决基因树冲突的策略和方法,以期为分子系统发育研究提供一些肩示和帮助.     

系统发育分析中的最大简约法及其优化

随着生物技术的不断发展和系统发育学的深入研究, 在重构系统发育树时, 研究人员往往要面对更多的挑战和困难, 比如： (1)需要分析的样本数（物种数或个体数）不断增加; (2)需要分析的数据量迅速扩大。尤其在基因组测序技术的推动下, 基于分子信息的系统发育重建需要极大的计算量, 因此数学方法、 计算机技术以及其他辅助工具对于系统发育重建的效率和精确度起着至关重要的作用。最大简约法（maximum parsimony）是一种重要的系统发育重建方法, 提高其计算效率对系统发育学研究具有重要意义, 针对该算法的优化改进需要生物学家和计算机专家的共同努力。本文通过详细地阐述最大简约法的计算流程, 分析其参数选择对计算效率的影响, 帮助更多的计算机使用者, 在并不了解系统发育学基础的情况下, 更方便地针对实际的系统发育算法问题给出更好、 更快、 更精准的解决方案; 同时为系统发育研究工作者, 较为清晰地解释最大简约法的构树思想和计算逻辑, 推动针对最大简约法的不断改进与优化。     

哺乳动物系统发育基因组学研究进展

哺乳动物是一类最进化并在地球上占主导地位的动物类群,重建其系统发育关系一直是分子系统学的研究热点。随着越来越多物种全基因组测序的完成,在基因组水平上探讨该类动物的系统发育关系与进化成为研究的热点。本文从全基因组序列,稀有基因组变异及染色体涂染等几个方面简要介绍了当前系统发育基因组学在现生哺乳动物分子系统学中的应用,综合已有的研究归纳整理了胎盘亚纲的总目及目间的系统发育关系,给出了胎盘动物19 个目的系统发育树。本文还分析了哺乳动物系统发育基因组学目前所面临的主要问题及未来的发展前景。     

等位基因杂合子现象及其在系统发育学分析中的研究概述

系统发育研究已是澄清所有进化历史问题的必由之路。选择合适的分子标记以及最大限度地挖掘和利用其所包含的系统发育信息是构建可靠的系统发育树的关键。等位基因杂合子(Intra-individual allele heterozygotes, IIAHs)是核基因内含子作为系统发育研究中的分子标记时常常出现的现象。如何挖掘并利用其中所包含的系统发育信息成为近年来系统发育学的研究热点。文章从此现象的产生、杂合子的分离以及现有的研究方法3个方面详尽概述, 阐述了IIAHs及其在系统发育分析中的最新研究进展。     

Molecular phylogenetic analysis places Percolomonas cosmopolitus within Heterolobosea: evolutionary implications

Percolomonas cosmopolitus is a common free-living flagellate of uncertain phylogenetic position that was placed within the Heterolobosea on the basis of ultrastructure studies. To test the relationship between Percolomonas and Heterolobosea, we analysed the primary structure of the actin and small-subunit ribosomal RNA (SSU rRNA) genes of P. cosmopolitus as well as the predicted secondary structure of the SSU rRNA. Percolomonas shares common secondary structure patterns of the SSU rRNA with heterolobosean taxa, which, together with the results of actin gene analysis, confirms that it is closely related to Heterolobosea. Phylogenetic reconstructions based on the sequences of the SSU rRNA gene suggest Percolomonas belongs to the family Vahlkampfiidae. The first Bayesian analysis of a large taxon sampling of heterolobosean SSU rRNA genes clarifies the phylogenetic relationships within this group.     

虎纹蛙及其它几种蛙科动物线粒体16S rRNA的空间结构分析

测定了虎纹蛙16S rRNA基因全序列,并从GeneBank上下载了5种蛙科动物同源序列,利用CLUSTAL与MEGA3.1软件比较了种间的序列差异,用RNAdraw软件推测分析二级结构的空间构象,并根据空间结构对这6种蛙科动物的分类地位进行讨论分析。结果表明：虎纹蛙与黑斑蛙的二级结构最为相似,与泽蛙结构大体一致,而与黑斑蛙同属的金线蛙则表现出较大的差异;凹耳蛙与上述几种差别较大;福建大头娃与这几种蛙科动物差距最为明显。空间结构分析与序列比较结果存在一定的差异。     

Secondary structure probing of the human RNase MRP RNA reveals the potential for MRP RNA subsets

RNase MRP is a ribonucleoprotein endoribonuclease involved in eukaryotic pre-rRNA processing. The enzyme possesses an RNA subunit, structurally related to that of RNase P RNA, that is thought to be catalytic. RNase MRP RNA sequences from Saccharomycetaceae species are structurally well defined through detailed phylogenetic and structural analysis. In contrast, higher eukaryote MRP RNA structure models are based on comparative sequence analysis of only five sequences and limited probing data. Detailed structural analysis of the Homo sapiens MRP RNA, entailing enzymatic and chemical probing, is reported. The data are consistent with the phylogenetic secondary structure model and demonstrate unequivocally that higher eukaryote MRP RNA structure differs significantly from that reported for Saccharomycetaceae species. Neither model can account for all of the known MRP RNAs and we thus propose the evolution of at least two subsets of RNase MRP secondary structure, differing predominantly in the predicted specificity domain.     

番石榴实蝇和瓜实蝇的线粒体L-rRNA基因测序及双翅目昆虫L-rRNA基因的结构特征与系统发育关系分析

RNA二级结构比一级结构包含更多的信息, 在物种系统发育分析中更能反应真实情况。因而, 本研究对番石榴实蝇Bactrocera correcta和瓜实蝇B. cucurbitae的L-rRNA全基因进行了测序, 构建了双翅目L-rRNA基因二级结构的模式图, 并分析了其结构特征, 而后基于H45~H47茎环结构参数和结构序列及L-rRNA结构序列对双翅目13科的系统发育关系进行了初步分析。结果表明： 双翅目昆虫具有保守的L-rRNA二级结构; 不同结构区碱基组成和分布不均匀, Ⅳ区和Ⅴ区的完全保守碱基含量最高, GC含量最高, 绝大部分科Ⅵ区的AT斜率均小于0; 科内特有碱基和科间少数保守碱基大部分为G或C。瘿蚊科与双翅目其他科具有较远的系统发育关系, 而丽蝇科、 寄蝇科和食蚜蝇科有相近的系统发育关系; 虻科与网翅虻科同在一个小分支; 蠓科与蚊科同在一个大的系统发育分支。利用单方面参数不易得到理想的进化结果, 准确系统发育分析需要结合多方面的参数。     

Long range RNA-RNA interactions in the 30 S ribosomal subunit of E. coli.

We have attempted to identify long-range interactions in the tertiary structure of RNA in the E. coli 30 S ribosome. Native subunits were cleaved with ribonuclease and separated into nucleoprotein fragments which were deproteinized and fractionated into multi-oligonucleotide complexes under conditions intended to preserve RNA-RNA interactions. The final products were denatured by urea and heat and their constituent oligonucleotides resolved and sequenced. Many complexes contained complementary sequences known to be bound together in the RNA secondary structure, attesting to the validity of the technique. Other co-migrating oligonucleotides, not joined in the secondary structure, contained mutually complementary sequences in locations that allow base-pairing interaction without disrupting pre-existing secondary structure. In seven instances the complementary relationship was found to have been preserved during phylogenetic diversification.     

Molecular phylogeny of protists: origin and evolution of the Dinoflagellates

Abstract

Molecular sequence data have become prominent tools for phylogenetic relationship inference, particularly useful in the analysis of highly diverse taxonomic orders. Ribosomal RNA sequences provide markers that can be used in the study of phylogeny, because their function and structure have been conserved to a large extent throughout the evolutionary history of organisms. These sequences are inferred from cloned or enzymatically amplified gene sequences, or determined by direct RNA sequencing. The first step of the phylogenetic interpretation of nucleic acid sequence variations implies proper alignment of corresponding sequences from various organisms. Best alignment based on similarity criteria is greatly reinforced, in the case of ribosomal RNAs, by secondary structure homologies. Distance matrix methods to infer evolutionary trees are based on the assumption that the phylogenetic distance between each pair of organisms is proportional to the number of nucleotide substitution events. Computed tree inference methods usually take into consideration the possibility of unequal mutation rates among lineages. Divergence times can be estimated on the tree, provided that at least one lineage has been dated by fossil records. We have utilized this approach based on ribosomal RNA sequence comparison to investigate the phylogenetic relationship between dinoflagellated and other eukaryote protists, and to refine controverse phylogenies of the class Dinophycae.     

Mutant prohead RNAs in the in vitro packaging of bacteriophage phi 29 DNA-gp3.

The 174-base prohead RNA encoded by bacteriophage phi 29 of Bacillus subtilis, essential for packaging of the DNA-gp3 (DNA-gene product 3) complex, was expressed efficiently from the cloned gene. Computer programs for RNA structure analysis were used to fold hypothetical RNA mutants and thus to target mutagenesis of the RNA for studies of structure and function. Five mutants of the RNA were then produced by oligonucleotide-directed mutagenesis that were altered in the primary sequence at selected sites; two of these mutants were predicted to be altered in secondary structure from a model established previously by a phylogenetic analysis. The binding of the 32P end-labeled mutant RNAs to RNA-free proheads was comparable with that of the wild-type RNA. However, the capability of the mutant RNAs to reconstitute RNA-free proheads for DNA-gp3 packaging in the defined in vitro system and for assembly of phage in RNA-free extracts was variable, depending upon the alteration. Changes of highly conserved bases that retained the predicted secondary structure of the RNA model were tolerated to a much greater extent than changes predicted to alter the RNA secondary structure.     

Secondary structure model for the ITS-2 precursor rRNA of strongyloid nematodes of equids: implications for phylogenetic inference

In order to maximise the positional homology in the primary sequence alignment of the second internal transcribed spacer for 30 species of equine strongyloid nematodes, the secondary structures of the precursor ribosomal RNA were predicted using an approach combining an energy minimisation method and comparative sequence analysis. The results indicated that a common secondary structure model of the second internal transcribed spacer of these nematodes was maintained, despite significant interspecific differences (2–56%) in primary sequences. The secondary structure model was then used to refine the primary second internal transcribed spacer sequence alignment. The “manual” and “structure” alignments were both subjected to phylogenetic analysis using three different tree-building methods to compare the effect of using different sequence alignments on phylogenetic inference. The topologies of the phylogenetic trees inferred from the manual second internal transcribed spacer alignment were usually different to those derived from the structure second internal transcribed spacer alignment. The results suggested that the positional homology in the second internal transcribed spacer primary sequence alignment was maximised when the secondary structure model was taken into consideration.     

RNA的二级结构在动物分子系统学研究中的应用

作为一类重要的信息和功能分子,RNA在分子系统学研究中有着特殊的重要作用。RNA除了其一级结构以外,其二级结构亦可用于同源性比较。由于高级结构与功能的关系更为密切,比较的结果可以揭示一些在一级结构比较中难以发现的现象。