Ribosome-dependent conformational flexibility changes and RNA dynamics of IRES domains revealed by differential SHAPE

被引:16
|
作者
Lozano, Gloria [1 ]
Francisco-Velilla, Rosario [1 ]
Martinez-Salas, Encarnacion [1 ]
机构
[1] Univ Autonoma Madrid, CSIC, Ctr Biol Mol Severo Ochoa, Nicolas Cabrera 1, E-28049 Madrid, Spain
来源
SCIENTIFIC REPORTS | 2018年 / 8卷
关键词
TRANSLATION INITIATION; C2'-ENDO NUCLEOTIDES; HCV IRES; VIRUS; ACCURATE; VISUALIZATION; RECRUITMENT; SECONDARY; MECHANISM; RELEVANCE;
D O I
10.1038/s41598-018-23845-x
中图分类号
O [数理科学和化学]; P [天文学、地球科学]; Q [生物科学]; N [自然科学总论];
学科分类号
07 ; 0710 ; 09 ;
摘要
Internal ribosome entry site (IRES) elements are RNA regions that recruit the translation machinery internally. Here we investigated the conformational changes and RNA dynamics of a picornavirus IRES upon incubation with distinct ribosomal fractions. Differential SHAPE analysis of the free RNA showed that nucleotides reaching the final conformation on long timescales were placed at domains 4 and 5, while candidates for long-range interactions were located in domain 3. Salt-washed ribosomes induced a fast RNA local flexibility modification of domains 2 and 3, while ribosome-associated factors changed domains 4 and 5. Consistent with this, modeling of the three-dimensional RNA structure indicated that incubation of the IRES with native ribosomes induced a local rearrangement of the apical region of domain 3, and a reorientation of domains 4 and 5. Furthermore, specific motifs within domains 2 and 3 showed a decreased flexibility upon incubation with ribosomal subunits in vitro, and presence of the IRES enhanced mRNA association to the ribosomal subunits in whole cell lysates. The finding that RNA modules can provide direct IRES-ribosome interaction suggests that linking these motifs to additional sequences able to recruit trans-acting factors could be useful to design synthetic IRESs with novel activities.
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页数:13
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