ArticleScientific reports2018
Ribosome-dependent conformational flexibility changes and RNA dynamics of IRES domains revealed by differential SHAPE.
Article in Scientific reports, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 20 papers.
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Who cites it
20 citing papers in PubMed, 25 citations in OpenAlex.
- Article
- The mechanism of ribosomal recruitment during translation initiation on the Type 2 encephalomyocarditis virus IRES.The EMBO journal · 2026Article
- Impact of Gemin5 in protein synthesis: phosphoresidues of the dimerization domain regulate ribosome binding.RNA biology · 2025Article
- Ins and outs of IRES elements: function and significance.Biochemical Society transactions · 2025Review
- Review
- Selectively expressed RNA molecules as a versatile tool for functionalized cell targeting.Nature communications · 2025Article
- Modeling the structure and DAP5-binding site of the FGF-9 5'-UTR RNA utilized in cap-independent translation.RNA (New York, N.Y.) · 2024Article
- Oligomerization regulates the interaction of Gemin5 with members of the SMN complex and the translation machinery.Cell death discovery · 2024Article
- Article
- Structural basis for Gemin5 decamer-mediated mRNA binding.Nature communications · 2022Article
- Gemin5-dependent RNA association with polysomes enables selective translation of ribosomal and histone mRNAs.Cellular and molecular life sciences : CMLS · 2022Article
- Functional and structural deficiencies of Gemin5 variants associated with neurological disorders.Life science alliance · 2022Article
- Picornavirus translation strategies.FEBS open bio · 2022Review
- Eukaryotic initiation factor 4F promotes a reorientation of eukaryotic initiation factor 3 binding on the 5' and the 3' UTRs of barley yellow dwarf virus mRNA.Nucleic acids research · 2022Article
- RNA-protein coevolution study of Gemin5 uncovers the role of the PXSS motif of RBS1 domain for RNA binding.RNA biology · 2020Article
- Emerging Roles of Gemin5: From snRNPs Assembly to Translation Control.International journal of molecular sciences · 2020Review
- Structural basis for the dimerization of Gemin5 and its role in protein recruitment and translation control.Nucleic acids research · 2020Article
- Rab1b and ARF5 are novel RNA-binding proteins involved in FMDV IRES-driven RNA localization.Life science alliance · 2019Article
- Deconstructing internal ribosome entry site elements: an update of structural motifs and functional divergences.Open biology · 2018Review
- The landscape of the non-canonical RNA-binding site of Gemin5 unveils a feedback loop counteracting the negative effect on translation.Nucleic acids research · 2018Article
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Authors and funding
3 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
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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