Konings D A, Nash M A, Maizel J V, Arlinghaus R B
Laboratory of Mathematical Biology, National Cancer Institute, Frederick, Maryland 21702.
J Virol. 1992 Feb;66(2):632-40. doi: 10.1128/JVI.66.2.632-640.1992.
We searched for the presence of common RNA structural motifs in mammalian type C retroviruses related to murine leukemia viruses and the closely related avian spleen necrosis virus. A novel motif consisting of a pair of hairpins, called hairpin pair motif, was detected in the 5' untranslated regions of the genomes of these retroviruses. A combination of computational analyses that included the assessment of phylogenetic sequence conservation by multiple alignment, the search for regions with unusual RNA folding properties, and the analysis of RNA secondary structure by suboptimal free-energy calculations highlighted the significance of this hairpin pair motif. The hairpin pair motif encompasses 70 to 80 nucleotides between the splice donor site and the gag translational initiation codon of these viruses. The motif is composed of two adjacent hairpins both with a perfectly conserved GACG tetraloop. We propose that the novel GACG-hairpin pair motif described here constitutes an essential component of the regulatory machinery in these type C retroviruses.
我们在与鼠白血病病毒及密切相关的禽脾坏死病毒相关的哺乳动物C型逆转录病毒中寻找常见的RNA结构基序。在这些逆转录病毒基因组的5'非翻译区检测到一种由一对发夹组成的新型基序，称为发夹对基序。一系列计算分析，包括通过多序列比对评估系统发育序列保守性、寻找具有异常RNA折叠特性的区域以及通过次优自由能计算分析RNA二级结构，突出了这种发夹对基序的重要性。发夹对基序在这些病毒的剪接供体位点和gag翻译起始密码子之间包含70至80个核苷酸。该基序由两个相邻的发夹组成，两者都具有完全保守的GACG四环。我们提出，这里描述的新型GACG - 发夹对基序构成了这些C型逆转录病毒调控机制的重要组成部分。
