黄病毒基因组3'非编码区的序列比较和二级结构分析揭示了多个假结。
Sequence comparison and secondary structure analysis of the 3' noncoding region of flavivirus genomes reveals multiple pseudoknots.
作者信息
Olsthoorn R C, Bol J F
机构信息
Institute of Molecular Plant Sciences, Gorlaeus Laboratories, Leiden University, The Netherlands.
出版信息
RNA. 2001 Oct;7(10):1370-7.
Abstract
Sequences of 191 flavivirus RNAs belonging to four sero-groups were used to predict the secondary structure of the 3' noncoding region (3' NCR) directly upstream of the conserved terminal hairpin. In mosquito-borne flavivirus RNAs (n = 164) a characteristic structure element was identified that includes a phylogenetically well-supported pseudoknot. This element is repeated in the dengue and Japanese encephalitis RNAs and centers around the conserved sequences CS2 and RCS2. In yellow fever virus RNAs that contain one CS2 motif, only one copy of this pseudoknotted structure was found. The conserved pseudoknotted element is absent from the 3' NCR of tick-borne virus RNAs, which altogether adopt a secondary structure that is very different from that of mosquito-borne virus RNAs. The strong conservation of the pseudoknot in mosquito-borne flavivirus RNAs implies a stronger relationship between these viruses than concluded from previous secondary structure analyses. The role of the (tandem) pseudoknots in flavivirus replication is discussed.
摘要
利用属于四个血清群的191种黄病毒RNA序列，预测保守末端发夹结构上游3'非编码区（3'NCR）的二级结构。在蚊媒黄病毒RNA（n = 164）中，鉴定出一个特征性结构元件，其中包括一个系统发育上得到有力支持的假结。该元件在登革热和日本脑炎RNA中重复出现，并以保守序列CS2和RCS2为中心。在含有一个CS2基序的黄热病毒RNA中，仅发现该假结结构的一个拷贝。蜱传病毒RNA的3'NCR中不存在保守的假结元件，其整体二级结构与蚊媒病毒RNA的二级结构非常不同。蚊媒黄病毒RNA中假结的高度保守意味着这些病毒之间的关系比之前二级结构分析得出的结论更为密切。文中讨论了（串联）假结在黄病毒复制中的作用。
相似文献
1
2
Essential role of cyclization sequences in flavivirus RNA replication.环化序列在黄病毒RNA复制中的重要作用。
J Virol. 2001 Jul;75(14):6719-28. doi: 10.1128/JVI.75.14.6719-6728.2001.
3
Complete genomic sequence of Powassan virus: evaluation of genetic elements in tick-borne versus mosquito-borne flaviviruses.波瓦桑病毒的完整基因组序列：蜱传与蚊传黄病毒遗传元件的评估
Virology. 1993 May;194(1):173-84. doi: 10.1006/viro.1993.1247.
4
Complete genome sequence, taxonomic assignment, and comparative analysis of the untranslated regions of the Modoc virus, a flavivirus with no known vector.莫多克病毒（一种无已知传播媒介的黄病毒）的全基因组序列、分类归属及非编码区的比较分析
Virology. 2002 Feb 1;293(1):125-40. doi: 10.1006/viro.2001.1241.
5
Evidence for the existence of a pseudoknot structure at the 3' terminus of the flavivirus genomic RNA.黄病毒基因组RNA 3'末端存在假结结构的证据。
Biochemistry. 1996 Apr 2;35(13):4222-30. doi: 10.1021/bi952398v.
6
The flavivirus 3'-noncoding region: extensive size heterogeneity independent of evolutionary relationships among strains of tick-borne encephalitis virus.黄病毒3'非编码区：蜱传脑炎病毒毒株间广泛的大小异质性，与进化关系无关。
Virology. 1995 Oct 20;213(1):169-78. doi: 10.1006/viro.1995.1557.
7
Genomics and evolution of Aedes-borne flaviviruses.蚊虫传播黄病毒的基因组学与进化。
J Gen Virol. 2010 Jan;91(Pt 1):87-94. doi: 10.1099/vir.0.014506-0. Epub 2009 Sep 9.
8
The majority of the nucleotides in the top loop of the genomic 3' terminal stem loop structure are cis-acting in a West Nile virus infectious clone.在西尼罗河病毒感染性克隆中，基因组3'末端茎环结构顶部环中的大多数核苷酸具有顺式作用。
Virology. 2005 Jan 20;331(2):238-46. doi: 10.1016/j.virol.2004.11.008.
9
Functional analysis of the tick-borne encephalitis virus cyclization elements indicates major differences between mosquito-borne and tick-borne flaviviruses.蜱传脑炎病毒环化元件的功能分析表明蚊传和蜱传黄病毒之间存在重大差异。
J Virol. 2006 Apr;80(8):4099-113. doi: 10.1128/JVI.80.8.4099-4113.2006.
10
Structure determination of the top-loop of the conserved 3'-terminal secondary structure in the genome of flaviviruses.黄病毒基因组中保守 3'末端二级结构的顶部环结构的测定。
Chembiochem. 2010 Jul 5;11(10):1404-12. doi: 10.1002/cbic.200900765.
引用本文的文献
1
A specific domain within the 3' untranslated region of Usutu virus confers resistance to the exonuclease ISG20.乌苏图病毒3'非翻译区的一个特定结构域赋予了对核酸外切酶ISG20的抗性。
Nat Commun. 2024 Oct 2;15(1):8528. doi: 10.1038/s41467-024-52870-w.
2
The Role of Noncoding RNA in the Transmission and Pathogenicity of Flaviviruses.非编码 RNA 在黄病毒传播和致病中的作用。
Viruses. 2024 Feb 2;16(2):242. doi: 10.3390/v16020242.
3
Subgenomic Flaviviral RNAs of Dengue Viruses.登革病毒的亚基因组 flaviviral RNA 。
Viruses. 2023 Nov 24;15(12):2306. doi: 10.3390/v15122306.
4
Interactions of host miRNAs in the flavivirus 3´UTR genome: From bioinformatics predictions to practical approaches.宿主 miRNA 在黄病毒 3´UTR 基因组中的相互作用：从生物信息学预测到实际方法。
Front Cell Infect Microbiol. 2022 Oct 13;12:976843. doi: 10.3389/fcimb.2022.976843. eCollection 2022.
5
Three-dimensional structure of a flavivirus dumbbell RNA reveals molecular details of an RNA regulator of replication.黄病毒哑铃状RNA的三维结构揭示了RNA复制调节因子的分子细节。
Nucleic Acids Res. 2021 Jul 9;49(12):7122-7138. doi: 10.1093/nar/gkab462.
6
Information Encoded by the Flavivirus Genomes beyond the Nucleotide Sequence.黄病毒基因组编码的信息超出了核苷酸序列。
Int J Mol Sci. 2021 Apr 3;22(7):3738. doi: 10.3390/ijms22073738.
7
Structures and Functions of the 3' Untranslated Regions of Positive-Sense Single-Stranded RNA Viruses Infecting Humans and Animals.感染人类和动物的正链单链 RNA 病毒的 3'非翻译区的结构和功能。
Front Cell Infect Microbiol. 2020 Aug 27;10:453. doi: 10.3389/fcimb.2020.00453. eCollection 2020.
8
A database of flavivirus RNA structures with a search algorithm for pseudoknots and triple base interactions.一个包含黄病毒 RNA 结构的数据库，带有搜索假结和三碱基相互作用的算法。
Bioinformatics. 2021 May 17;37(7):956-962. doi: 10.1093/bioinformatics/btaa759.
9
A Non-Replicative Role of the 3' Terminal Sequence of the Dengue Virus Genome in Membranous Replication Organelle Formation.登革病毒基因组 3' 末端序列在膜复制细胞器形成中的非复制作用。
Cell Rep. 2020 Jul 7;32(1):107859. doi: 10.1016/j.celrep.2020.107859.
10
RNA Structure Duplication in the Dengue Virus 3' UTR: Redundancy or Host Specificity?登革病毒 3'UTR 中的 RNA 结构复制：冗余还是宿主特异性？
mBio. 2019 Jan 8;10(1):e02506-18. doi: 10.1128/mBio.02506-18.
本文引用的文献
1
Essential role of cyclization sequences in flavivirus RNA replication.环化序列在黄病毒RNA复制中的重要作用。
J Virol. 2001 Jul;75(14):6719-28. doi: 10.1128/JVI.75.14.6719-6728.2001.
2
Genetic variation in the 3' non-coding region of dengue viruses.登革病毒3'非编码区的基因变异
Virology. 2001 Mar 1;281(1):75-87. doi: 10.1006/viro.2000.0748.
3
A novel in vitro replication system for Dengue virus. Initiation of RNA synthesis at the 3'-end of exogenous viral RNA templates requires 5'- and 3'-terminal complementary sequence motifs of the viral RNA.一种新型的登革病毒体外复制系统。在外源病毒RNA模板的3'端起始RNA合成需要病毒RNA的5'和3'末端互补序列基序。
J Biol Chem. 1999 Nov 19;274(47):33714-22. doi: 10.1074/jbc.274.47.33714.
4
RNA secondary structure prediction based on free energy and phylogenetic analysis.基于自由能和系统发育分析的RNA二级结构预测
J Mol Biol. 1999 Jun 18;289(4):935-47. doi: 10.1006/jmbi.1999.2801.
5
An approximation of loop free energy values of RNA H-pseudoknots.RNA H-假结的无环自由能值的近似值。
RNA. 1999 May;5(5):609-17. doi: 10.1017/s135583829998189x.
6
Translation elongation factor-1 alpha interacts with the 3' stem-loop region of West Nile virus genomic RNA.翻译延伸因子-1α与西尼罗河病毒基因组RNA的3'茎环区域相互作用。
J Virol. 1997 Sep;71(9):6433-44. doi: 10.1128/JVI.71.9.6433-6444.1997.
7
8
Secondary structure of the 3' untranslated region of flaviviruses: similarities and differences.黄病毒3'非翻译区的二级结构：异同点
Nucleic Acids Res. 1997 Mar 15;25(6):1194-202. doi: 10.1093/nar/25.6.1194.
9
Secondary structure model for the last two domains of single-stranded RNA phage Q beta.单链RNA噬菌体Qβ最后两个结构域的二级结构模型
J Mol Biol. 1995 Apr 14;247(5):903-17. doi: 10.1006/jmbi.1995.0189.
10
Contributions of the brome mosaic virus RNA-3 3'-nontranslated region to replication and translation.雀麦花叶病毒RNA - 3 3'非翻译区对复制和翻译的作用
J Virol. 1993 Jun;67(6):3295-303. doi: 10.1128/JVI.67.6.3295-3303.1993.
Zotero 插件