对3000多个序列的比较分析揭示了真核生物小亚基核糖体RNA的V4区域存在两个假结。
Comparative analysis of more than 3000 sequences reveals the existence of two pseudoknots in area V4 of eukaryotic small subunit ribosomal RNA.
作者信息
Wuyts J, De Rijk P, Van de Peer Y, Pison G, Rousseeuw P, De Wachter R
机构信息
Departement Biochemie, Universiteit Antwerpen (UIA), Universiteitsplein 1, B 2610 Antwerpen, Belgium.
出版信息
Nucleic Acids Res. 2000 Dec 1;28(23):4698-708. doi: 10.1093/nar/28.23.4698.
Abstract
The secondary structure of V4, the largest variable area of eukaryotic small subunit ribosomal RNA, was re-examined by comparative analysis of 3253 nucleotide sequences distributed over the animal, plant and fungal kingdoms and a diverse set of protist taxa. An extensive search for compensating base pair substitutions and for base covariation revealed that in most eukaryotes the secondary structure of the area consists of 11 helices and includes two pseudoknots. In one of the pseudoknots, exchange of base pairs between the two stems seems to occur, and covariation analysis points to the presence of a base triple. The area also contains three potential insertion points where additional hairpins or branched structures are present in a number of taxa scattered throughout the eukaryotic domain.
摘要
真核生物小亚基核糖体RNA最大可变区V4的二级结构，通过对分布于动物、植物和真菌界以及各种原生生物类群的3253个核苷酸序列进行比较分析，得以重新审视。广泛搜索补偿性碱基对替换和碱基共变现象发现，在大多数真核生物中，该区域的二级结构由11个螺旋组成，包括两个假结。在其中一个假结中，两个茎之间似乎发生了碱基对交换，共变分析表明存在一个碱基三联体。该区域还包含三个潜在的插入点，在真核生物域中分散的许多类群中存在额外的发夹或分支结构。
相似文献
1
Comparative analysis of more than 3000 sequences reveals the existence of two pseudoknots in area V4 of eukaryotic small subunit ribosomal RNA.对3000多个序列的比较分析揭示了真核生物小亚基核糖体RNA的V4区域存在两个假结。
Nucleic Acids Res. 2000 Dec 1;28(23):4698-708. doi: 10.1093/nar/28.23.4698.
2
A proposal for the secondary structure of a variable area of eukaryotic small ribosomal subunit RNA involving the existence of a pseudoknot.关于真核生物小核糖体亚基RNA可变区二级结构的一项提议，该结构涉及假结的存在。
Nucleic Acids Res. 1990 Oct 11;18(19):5695-704. doi: 10.1093/nar/18.19.5695.
3
An overview of the secondary structure of the V4 region of eukaryotic small-subunit ribosomal RNA.真核生物小亚基核糖体RNA V4区域二级结构概述
Nucleic Acids Res. 1991 Jan 25;19(2):227-35. doi: 10.1093/nar/19.2.227.
4
Sequence and secondary structure of the mitochondrial small-subunit rRNA V4, V6, and V9 domains reveal highly species-specific variations within the genus Agrocybe.线粒体小亚基rRNA V4、V6和V9结构域的序列及二级结构揭示了田头菇属内高度的物种特异性变异。
Appl Environ Microbiol. 1998 Nov;64(11):4149-60. doi: 10.1128/AEM.64.11.4149-4160.1998.
5
The origin and evolution of variable-region helices in V4 and V7 of the small-subunit ribosomal RNA of branchiopod crustaceans.鳃足纲甲壳动物小亚基核糖体RNA的V4和V7可变区螺旋的起源与进化
Mol Biol Evol. 1998 Nov;15(11):1430-46. doi: 10.1093/oxfordjournals.molbev.a025871.
6
Database on the structure of small ribosomal subunit RNA.小核糖体亚基RNA结构数据库。
Nucleic Acids Res. 1996 Jan 1;24(1):86-91. doi: 10.1093/nar/24.1.86.
7
Nucleotide sequence of a crustacean 18S ribosomal RNA gene and secondary structure of eukaryotic small subunit ribosomal RNAs.一种甲壳类动物18S核糖体RNA基因的核苷酸序列及真核生物小亚基核糖体RNA的二级结构
Nucleic Acids Res. 1984 Dec 11;12(23):8749-68. doi: 10.1093/nar/12.23.8749.
8
Secondary structure and molecular evolution of the mitochondrial small subunit ribosomal RNA in Agaricales (Euagarics clade, Homobasidiomycota).伞菌目（真担子菌亚纲，伞菌纲）线粒体小亚基核糖体RNA的二级结构与分子进化
J Mol Evol. 2003 Oct;57(4):383-96. doi: 10.1007/s00239-003-2487-5.
9
Evolution of large subunit rRNA structure. The 3' terminal domain contains elements of secondary structure specific to major phylogenetic groups.大亚基核糖体RNA结构的演化。3'末端结构域包含主要系统发育类群特有的二级结构元件。
Biochimie. 1989 Jun;71(6):701-9. doi: 10.1016/0300-9084(89)90086-2.
10
A comparison of the crystal structures of eukaryotic and bacterial SSU ribosomal RNAs reveals common structural features in the hypervariable regions.真核生物和细菌的小亚基核糖体 RNA 的晶体结构比较显示了超变区的共同结构特征。
PLoS One. 2012;7(5):e38203. doi: 10.1371/journal.pone.0038203. Epub 2012 May 31.
引用本文的文献
1
A Genus Comparison in the Topological Analysis of RNA Structures.RNA结构拓扑分析中的属比较
Acta Biotheor. 2025 Aug 1;73(3):11. doi: 10.1007/s10441-025-09500-9.
2
18S rRNA variability maps reveal three highly divergent, conserved motifs within Rotifera.18S rRNA 变异性图谱揭示轮虫内三个高度分化、保守的基序。
BMC Ecol Evol. 2021 Jun 10;21(1):118. doi: 10.1186/s12862-021-01845-2.
3
Comparison of Deep-Sea Picoeukaryotic Composition Estimated from the V4 and V9 Regions of 18S rRNA Gene with a Focus on the Hadal Zone of the Mariana Trench.深海小型真核生物组成的 V4 和 V9 区 18S rRNA 基因估计比较——以马里亚纳海沟深渊区为重点。
Microb Ecol. 2022 Jan;83(1):34-47. doi: 10.1007/s00248-021-01747-2. Epub 2021 Apr 3.
4
Taxonomy on three novel species of Sphaeromyxa Thélohan 1892 (Myxozoa, Bivalvulida, Sphaeromyxidae) with insight into the evolution of the genus.三种新型 Sphaeromyxa Thélohan 1892（Myxozoa，Bivalvulida，Sphaeromyxidae）物种的分类学研究，深入探讨了该属的进化。
Parasitol Res. 2020 May;119(5):1493-1503. doi: 10.1007/s00436-020-06656-w. Epub 2020 Mar 17.
5
Insight into picophytoplankton diversity of the subarctic White Sea-The first recording of Pedinophyceae in environmental DNA.深入了解亚北极白海的微微型浮游植物多样性——环境 DNA 中首次记录的 Pedinophyceae。
Microbiologyopen. 2019 Oct;8(10):e892. doi: 10.1002/mbo3.892. Epub 2019 Jun 11.
6
An algebraic language for RNA pseudoknots comparison.用于 RNA 假结比较的代数语言。
BMC Bioinformatics. 2019 Apr 18;20(Suppl 4):161. doi: 10.1186/s12859-019-2689-5.
7
Protists Within Corals: The Hidden Diversity.珊瑚体内的原生生物：隐藏的多样性
Front Microbiol. 2018 Aug 31;9:2043. doi: 10.3389/fmicb.2018.02043. eCollection 2018.
8
Rhizarian 'Novel Clade 10' Revealed as Abundant and Diverse Planktonic and Terrestrial Flagellates, including Aquavolon n. gen.根足虫类“新分支10”被揭示为丰富多样的浮游和陆生鞭毛虫，包括新属Aquavolon。
J Eukaryot Microbiol. 2018 Nov;65(6):828-842. doi: 10.1111/jeu.12524. Epub 2018 May 14.
9
Cryptic infection of a broad taxonomic and geographic diversity of tadpoles by Perkinsea protists.珀金藻原生生物对广泛分类和地理分布多样的蝌蚪的隐匿感染。
Proc Natl Acad Sci U S A. 2015 Aug 25;112(34):E4743-51. doi: 10.1073/pnas.1500163112. Epub 2015 Aug 10.
10
Evaluating the Species Boundaries of Green Microalgae (Coccomyxa, Trebouxiophyceae, Chlorophyta) Using Integrative Taxonomy and DNA Barcoding with Further Implications for the Species Identification in Environmental Samples.利用综合分类学和DNA条形码评估绿色微藻（绿球藻属， trebouxiophyceae纲，绿藻门）的物种界限，并对环境样本中的物种鉴定具有进一步意义。
PLoS One. 2015 Jun 16;10(6):e0127838. doi: 10.1371/journal.pone.0127838. eCollection 2015.
本文引用的文献
1
Evolution of Hypervariable Regions, V4 and V7, of Insect 18S rRNA and Their Phylogenetic Implications.昆虫18S rRNA高变区V4和V7的进化及其系统发育意义
Zoolog Sci. 2000 Jan 1;17(1):111-21. doi: 10.2108/zsj.17.111.
2
The origin and evolution of variable-region helices in V4 and V7 of the small-subunit ribosomal RNA of branchiopod crustaceans.鳃足纲甲壳动物小亚基核糖体RNA的V4和V7可变区螺旋的起源与进化
Mol Biol Evol. 1998 Nov;15(11):1430-46. doi: 10.1093/oxfordjournals.molbev.a025871.
3
PseudoBase: a database with RNA pseudoknots.伪结数据库（PseudoBase）：一个包含RNA伪结的数据库。
Nucleic Acids Res. 2000 Jan 1;28(1):201-4. doi: 10.1093/nar/28.1.201.
4
The European large subunit ribosomal RNA database.欧洲大亚基核糖体RNA数据库。
Nucleic Acids Res. 2000 Jan 1;28(1):177-8. doi: 10.1093/nar/28.1.177.
5
The European small subunit ribosomal RNA database.欧洲小亚基核糖体RNA数据库。
Nucleic Acids Res. 2000 Jan 1;28(1):175-6. doi: 10.1093/nar/28.1.175.
6
X-ray crystal structures of 70S ribosome functional complexes.70S核糖体功能复合物的X射线晶体结构。
Science. 1999 Sep 24;285(5436):2095-104. doi: 10.1126/science.285.5436.2095.
7
Placement of protein and RNA structures into a 5 A-resolution map of the 50S ribosomal subunit.将蛋白质和RNA结构置于50S核糖体亚基的5埃分辨率图谱中。
Nature. 1999 Aug 26;400(6747):841-7. doi: 10.1038/23641.
8
Structure of a bacterial 30S ribosomal subunit at 5.5 A resolution.细菌30S核糖体亚基在5.5埃分辨率下的结构。
Nature. 1999 Aug 26;400(6747):833-40. doi: 10.1038/23631.
9
Construction of a variability map for eukaryotic large subunit ribosomal RNA.真核生物大亚基核糖体RNA变异图谱的构建。
Nucleic Acids Res. 1999 Jul 15;27(14):2825-31. doi: 10.1093/nar/27.14.2825.
10
Expanded sequence dependence of thermodynamic parameters improves prediction of RNA secondary structure.热力学参数对序列依赖性的扩展改进了RNA二级结构的预测。
J Mol Biol. 1999 May 21;288(5):911-40. doi: 10.1006/jmbi.1999.2700.
Zotero 插件