Thermodynamic analysis of conserved loop-stem interactions in P1-P2 frameshifting RNA pseudoknots from plant Luteoviridae
Thermodynamic analysis of conserved loop-stem interactions in P1-P2 frameshifting RNA pseudoknots from plant Luteoviridae
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DOI：
10.1021/bi025843c
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发表时间：
2002-08-27
期刊：
影响因子：
2.9
通讯作者：
Giedroc, DP
中科院分区：
文献类型：
--
作者：
Nixon, PL;Cornish, PV;Giedroc, DP
植物黄体病毒如甜菜西黄病毒（BWYV）、马铃薯卷叶病毒（PLRV）和豌豆生长花叶病毒（PEMV RNA 1; PEMV- 1）的RNA基因组包含一个短的mRNA假结基序，重叠于程序化-1 mRNA核糖体移框所需的P1和P2开放阅读框。在这些RNA系统中，结构、稳定性和功能之间的关系尚不清楚。利用m(5)-C-8取代的BWYV RNA确定了BWYV P1-P2假结在环L1的胞苷8上质子化（δ (N3H+) = 12.98 ppm），稳定了C+。（G-C）主槽底三重由Delta(DeltaG(37))（质子化）= 3.1 (+/-0.4)kcal mol（-1）。PLRV和PEMV-1 P1-P2假结的稳定性也强烈依赖于ph，尽管PEMV-1假结的结构背景不同，但Delta(DeltaG(37))（质子化）= 2.1 (+/-0.2)kcal mol（-1）。正如之前在BWYV伪结中发现的那样[Nixon and Giedroc (2000) J. Mol. Biol. 296,659]， PLRV和PEMV-1 rna都被大于或等于30 kcal Mol（-1）的δ tah稳定，超过二级结构预测，归因于环路l2 -茎S1小槽三重相互作用。与野生型BWYV RNA相比，含有单个2'-脱氧或A -> G取代的BWYV RNA破坏L2-S1氢键，在δ (DeltaG(37))（折叠）（pH = 7.0）范围从大约到1.8（+/-0.3）到大于或等于4.0 kcal mol（-1）之间强烈不稳定。这些发现表明，该假结家族的每个成员都采用紧密折叠的结构，最大限度地提高了L1-S2和L2-S1环茎相互作用的协同性和互补性，这在一定程度上抵消了短三碱基对假结茎S2较低的内在稳定性。
The RNA genomes of plant luteovirids beet western yellows virus (BWYV), potato leaf roll virus (PLRV), and pea enation mosaic virus (PEMV RNA 1; PEMV- 1) contain a short mRNA pseudoknotted motif overlapping the P1 and P2 open reading frames required for programmed -1 mRNA ribosomal frameshifting. The relationship between structure, stability, and function is poorly understood in these RNA systems. A m(5)-C-8-substituted BWYV RNA is employed to establish that the BWYV P1-P2 pseudoknot is protonated at cytidine 8 in loop L1 (delta(N3H+) = 12.98 ppm), which stabilizes a C+.(G-C) major groove base triple by Delta(DeltaG(37))(protonation) = 3.1 (+/-0.4) kcal mol(-1). The stabilities of both the PLRV and PEMV-1 P1-P2 pseudoknots are also strongly pH-dependent, with Delta(DeltaG(37))(protonation) = 2.1 (+/-0.2) kcal mol(-1) for the PEMV-1 pseudoknot despite a distinct structural context. As previously found for the BWYV pseudoknot [Nixon and Giedroc (2000) J. Mol. Biol. 296, 659], both the PLRV and PEMV-1 RNAs are stabilized by DeltaH greater than or equal to 30 kcal mol(-1) in excess of secondary structure predictions, attributed to loop L2-stem S1 minor groove triplex interactions. BWYV RNAs containing single 2'-deoxy or A --> G substitutions that disrupt L2-S1 hydrogen bonding are strongly destabilized with Delta(DeltaG(37))(folding) (pH = 7.0) ranging from approximate to1.8 (+/-0.3) to greater than or equal to4.0 kcal mol(-1), relative to the wild-type BWYV RNA. These findings suggest that each member of this family of pseudoknots adopts a tightly folded structure that maximizes the cooperativity and complementarity of L1-S2 and L2-S1 loop-stem interactions required in part to offset the low intrinsic stability of the short three base pair pseudoknot stem S2.