Wang Yue, Wills Norma M, Du Zhihua, Rangan Anupama, Atkins John F, Gesteland Raymond F, Hoffman David W
Department of Chemistry and Biochemistry, Institute for Cell and Molecular Biology, University of Texas at Austin, 78712, USA.
RNA. 2002 Aug;8(8):981-96. doi: 10.1017/s1355838202024044.
Mutational and NMR methods were used to investigate features of sequence, structure, and dynamics that are associated with the ability of a pseudoknot to stimulate a -1 frameshift. In vitro frameshift assays were performed on retroviral gag-pro frameshift-stimulating pseudoknots and their derivatives, a pseudoknot from the gene 32 mRNA of bacteriophage T2 that is not naturally associated with frameshifting, and hybrids of these pseudoknots. Results show that the gag-pro pseudoknot from human endogenous retrovirus-K10 (HERV) stimulates a -1 frameshift with an efficiency similar to that of the closely related retrovirus MMTV. The bacteriophage T2 mRNA pseudoknot was found to be a poor stimulator of frameshifting, supporting a hypothesis that the retroviral pseudoknots have distinctive properties that make them efficient frameshift stimulators. A hybrid, designed by combining features of the bacteriophage and retroviral pseudoknots, was found to stimulate frameshifting while retaining significant structural similarity to the nonframeshifting bacteriophage pseudoknot. Mutational analyses of the retroviral and hybrid pseudoknots were used to evaluate the effects of an unpaired (wedged) adenosine at the junction of the pseudoknot stems, changing the base pairs near the junction of the two stems, and changing the identity of the loop 2 nucleotide nearest the junction of the stems. Pseudoknots both with and without the wedged adenosine can stimulate frameshifting, though the identities of the nucleotides near the stem1/stem2 junction do influence efficiency. NMR data showed that the bacteriophage and hybrid pseudoknots are similar in their local structure at the junction of the stems, indicating that pseudoknots that are similar in this structural feature can differ radically in their ability to stimulate frameshifting. NMR methods were used to compare the internal motions of the bacteriophage T2 pseudoknot and representative frameshifting pseudoknots. The stems of the investigated pseudoknots are similarly well ordered on the time scales to which nitrogen-15 relaxation data are sensitive; however, solvent exchange rates for protons at the junction of the two stems of the nonframeshifting bacteriophage pseudoknot are significantly slower than the analogous protons in the representative frameshifting pseudoknots.
采用突变和核磁共振方法研究与假结刺激 -1 移码能力相关的序列、结构和动力学特征。对逆转录病毒gag-pro移码刺激假结及其衍生物、噬菌体T2基因32 mRNA中一个与移码自然无关的假结以及这些假结的杂交体进行了体外移码试验。结果表明,人类内源性逆转录病毒-K10(HERV)的gag-pro假结刺激 -1 移码的效率与密切相关的逆转录病毒MMTV相似。发现噬菌体T2 mRNA假结是移码的弱刺激物,支持了逆转录病毒假结具有使其成为高效移码刺激物的独特性质这一假说。通过结合噬菌体和逆转录病毒假结的特征设计的杂交体,被发现能刺激移码,同时与非移码噬菌体假结保持显著的结构相似性。对逆转录病毒和杂交假结进行突变分析,以评估假结茎连接处未配对(楔入)腺苷的影响、改变两个茎连接处附近的碱基对以及改变最靠近茎连接处的环2核苷酸的身份。有和没有楔入腺苷的假结都能刺激移码,尽管茎1/茎2连接处附近核苷酸的身份确实会影响效率。核磁共振数据表明,噬菌体和杂交假结在茎连接处的局部结构相似,这表明在这一结构特征上相似的假结在刺激移码的能力上可能有很大差异。利用核磁共振方法比较了噬菌体T2假结和代表性移码假结的内部运动。所研究假结的茎在氮-15弛豫数据敏感的时间尺度上同样排列有序;然而,非移码噬菌体假结两个茎连接处质子的溶剂交换速率明显慢于代表性移码假结中的类似质子。