Co-crystal structure of a T-box riboswitch stem I domain in complex with its cognate tRNA.
Co-crystal structure of a T-box riboswitch stem I domain in complex with its cognate tRNA.
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作者：
在革兰氏阳性菌中，T-box核开关调节氨酰基-tRNA合成酶（ARSs）和其他蛋白质的表达，以响应不同营养状态下tRNA氨基酰化水平的波动。t -box位于它们所调节的mrna的5 ' -非翻译区（utr），并包含两个保守结构域。茎I含有与同源tRNA的反密码子碱基配对的特异三核苷酸。3 ' to Stem I是antiterminator结构域，该结构域与tRNA受体端碱基配对，并评估其氨基酰化状态。尽管具有高度的系统发育保守性，并且在病原体中广泛存在，但这种核糖开关识别tRNA的结构基础仍然不明确。在这里，我们证明了~100个核苷酸的T-box Stem I是特异性的、高亲和力（Kd ~150 nM） tRNA结合所必需的和充分的，并报道了其与同源tRNA复合物的结构，分辨率为3.2 Å。除反密码子外，Stem I还识别tRNA的整体结构，这是由核糖体等大型核糖核蛋白（RNPs）或ars等蛋白质完成的，但对于紧凑的mRNA结构域是前所未有的。c形的茎I支撑l形的tRNA形成一个扩展的（1604 Å2）分子间界面。除了特异物-反密码子相互作用外，Stem I顶端附近的两个互指t环以类似于RNase P的J11/12-J12/11基序和核糖体e位点的L1柄的方式堆叠在tRNA肘部上。由于这些rnp和t -box是不相关的，这种识别通用tRNA特征的策略可能是趋同进化的。利用tRNA固有的灵活性及其保守的转录后修饰，Stem I和tRNA相互诱导的契合导致了高度的形状互补性，这除了提供特异性和亲和力外，还在全球范围内组织T-box来协调tRNA依赖的转录调控。
In Gram-positive bacteria, T-box riboswitches regulate expression of aminoacyl-tRNA synthetases (ARSs) and other proteins in response to fluctuating tRNA aminoacylation levels under various nutritional states. T-boxes reside in the 5’-untranslated regions (UTRs) of the mRNAs they regulate, and comprise two conserved domains. Stem I harbors the specifier trinucleotide that base-pairs with the anticodon of cognate tRNA. 3’ to Stem I is the antiterminator domain, which base-pairs with the tRNA acceptor end and evaluates its aminoacylation state. Despite high phylogenetic conservation and widespread occurrence in pathogens, the structural basis of tRNA recognition by this riboswitch remains ill-defined. Here, we demonstrate that the ~100-nucleotide T-box Stem I is necessary and sufficient for specific, high-affinity (Kd ~150 nM) tRNA binding, and report its structure in complex with cognate tRNA at 3.2 Å resolution. Stem I recognizes the overall architecture of tRNA in addition to its anticodon, something accomplished by large ribonucleoproteins (RNPs) like the ribosome or proteins such as ARSs, but unprecedented for a compact mRNA domain. The C-shaped Stem I cradles the L-shaped tRNA forming an extended (1604 Å2) intermolecular interface. In addition to the specifier-anticodon interaction, two interdigitated T-loops near the apex of Stem I stack on the tRNA elbow in a manner analogous to those of the J11/12-J12/11 motif of RNase P and the L1 stalk of the ribosomal E-site. Since these RNPs and T-boxes are unrelated, this strategy to recognize an universal tRNA feature likely evolved convergently. Mutually induced fit of Stem I and the tRNA exploiting the intrinsic flexibility of tRNA and its conserved post-transcriptional modifications results in high shape complementarity, which in addition to providing specificity and affinity, globally organizes the T-box to orchestrate tRNA-dependent transcription regulation.
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DOI：
10.1107/s0907444905036693
发表时间：
2006-01-01
影响因子：
2.2
作者：
Evans, P
通讯作者：
Evans, P
影响因子：
14.9
作者：
Dalluge, JJ;Hashizume, T;Davis, DR
通讯作者：
Davis, DR
DOI：
10.1126/science.1202692
发表时间：
2011-05-20
期刊：
Science (New York, N.Y.)
影响因子：
--
作者：
Dunkle JA;Wang L;Feldman MB;Pulk A;Chen VB;Kapral GJ;Noeske J;Richardson JS;Blanchard SC;Cate JH
通讯作者：
Cate JH
DOI：
10.1073/pnas.1222214110
发表时间：
2013-04-30
影响因子：
11.1
作者：
Grigg, Jason C.;Chen, Yujie;Ke, Ailong
通讯作者：
Ke, Ailong
影响因子：
64.5
作者：
GRUNDY, FJ;HENKIN, TM
通讯作者：
HENKIN, TM