Local RNA flexibility perturbation of the IRES element induced by a novel ligand inhibits viral RNA translation

Lozano, Gloria; Trapote, Alejandro; Ramajo, Jorge; Elduque, Xavier; Grandas, Anna; Robles, Jordi; Pedroso, Enrique; Martínez‐Salas, Encarnación

doi:10.1080/15476286.2015.1025190

Cited by 29 publications

(26 citation statements)

References 66 publications

(95 reference statements)

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“…In turn, this characteristic provides useful therapeutic targets. Because IRES elements are essential for viral infection and harbor conserved RNA motifs, they constitute specific targets for antiviral compounds, as exemplified by a large variety of modified antisense oligonucleotides, siRNAs, morpholino oligomers, aptamers, and small molecules based on benzimidazole ( Aldaz-Carroll et al, 2002 ; Vagnozzi et al, 2007 ; Stone et al, 2008 ; Laxton et al, 2011 ; Fajardo et al, 2012 ; Boerneke et al, 2014 ; Sanchez-Luque et al, 2014 ; Lozano et al, 2015 ).…”

Section: Conserved Rna Motifs: a Therapeutic Target And A Hint To Prementioning

confidence: 99%

Insights into Structural and Mechanistic Features of Viral IRES Elements

et al. 2018

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Internal ribosome entry site (IRES) elements are cis-acting RNA regions that promote internal initiation of protein synthesis using cap-independent mechanisms. However, distinct types of IRES elements present in the genome of various RNA viruses perform the same function despite lacking conservation of sequence and secondary RNA structure. Likewise, IRES elements differ in host factor requirement to recruit the ribosomal subunits. In spite of this diversity, evolutionarily conserved motifs in each family of RNA viruses preserve sequences impacting on RNA structure and RNA–protein interactions important for IRES activity. Indeed, IRES elements adopting remarkable different structural organizations contain RNA structural motifs that play an essential role in recruiting ribosomes, initiation factors and/or RNA-binding proteins using different mechanisms. Therefore, given that a universal IRES motif remains elusive, it is critical to understand how diverse structural motifs deliver functions relevant for IRES activity. This will be useful for understanding the molecular mechanisms beyond cap-independent translation, as well as the evolutionary history of these regulatory elements. Moreover, it could improve the accuracy to predict IRES-like motifs hidden in genome sequences. This review summarizes recent advances on the diversity and biological relevance of RNA structural motifs for viral IRES elements.

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Section: Conserved Rna Motifs: a Therapeutic Target And A Hint To Prementioning

confidence: 99%

Insights into Structural and Mechanistic Features of Viral IRES Elements

et al. 2018

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“…In vitro transcription was performed for 1 h at 37 °C using T7 RNA polymerase, as described 62 . RNA was extracted with phenol-chloroform, ethanol precipitated and resuspended in TE.…”

Section: Methodsmentioning

confidence: 99%

Designing synthetic RNAs to determine the relevance of structural motifs in picornavirus IRES elements

Fernandez-Chamorro

Lozano

García-Martín

et al. 2016

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The function of Internal Ribosome Entry Site (IRES) elements is intimately linked to their RNA structure. Viral IRES elements are organized in modular domains consisting of one or more stem-loops that harbor conserved RNA motifs critical for internal initiation of translation. A conserved motif is the pyrimidine-tract located upstream of the functional initiation codon in type I and II picornavirus IRES. By computationally designing synthetic RNAs to fold into a structure that sequesters the polypyrimidine tract in a hairpin, we establish a correlation between predicted inaccessibility of the pyrimidine tract and IRES activity, as determined in both in vitro and in vivo systems. Our data supports the hypothesis that structural sequestration of the pyrimidine-tract within a stable hairpin inactivates IRES activity, since the stronger the stability of the hairpin the higher the inhibition of protein synthesis. Destabilization of the stem-loop immediately upstream of the pyrimidine-tract also decreases IRES activity. Our work introduces a hybrid computational/experimental method to determine the importance of structural motifs for biological function. Specifically, we show the feasibility of using the software RNAiFold to design synthetic RNAs with particular sequence and structural motifs that permit subsequent experimental determination of the importance of such motifs for biological function.

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“…In vitro transcription was performed for 1 h at 37°C using T7 RNA polymerase, as described in Lozano et al (2015) . RNA was extracted with phenol–chloroform, ethanol precipitated and then resuspended in TE.…”

Section: Methodsmentioning

confidence: 99%

RNAiFold2T: Constraint Programming design of thermo-IRES switches

et al. 2016

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Motivation: RNA thermometers (RNATs) are cis-regulatory elements that change secondary structure upon temperature shift. Often involved in the regulation of heat shock, cold shock and virulence genes, RNATs constitute an interesting potential resource in synthetic biology, where engineered RNATs could prove to be useful tools in biosensors and conditional gene regulation.Results: Solving the 2-temperature inverse folding problem is critical for RNAT engineering. Here we introduce RNAiFold2T, the first Constraint Programming (CP) and Large Neighborhood Search (LNS) algorithms to solve this problem. Benchmarking tests of RNAiFold2T against existent programs (adaptive walk and genetic algorithm) inverse folding show that our software generates two orders of magnitude more solutions, thus allowing ample exploration of the space of solutions. Subsequently, solutions can be prioritized by computing various measures, including probability of target structure in the ensemble, melting temperature, etc. Using this strategy, we rationally designed two thermosensor internal ribosome entry site (thermo-IRES) elements, whose normalized cap-independent translation efficiency is approximately 50% greater at 42 °C than 30 °C, when tested in reticulocyte lysates. Translation efficiency is lower than that of the wild-type IRES element, which on the other hand is fully resistant to temperature shift-up. This appears to be the first purely computational design of functional RNA thermoswitches, and certainly the first purely computational design of functional thermo-IRES elements.Availability: RNAiFold2T is publicly available as part of the new release RNAiFold3.0 at https://github.com/clotelab/RNAiFold and http://bioinformatics.bc.edu/clotelab/RNAiFold, which latter has a web server as well. The software is written in C ++ and uses OR-Tools CP search engine.Contact: clote@bc.eduSupplementary information: Supplementary data are available at Bioinformatics online.

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Local RNA flexibility perturbation of the IRES element induced by a novel ligand inhibits viral RNA translation

Cited by 29 publications

References 66 publications

Insights into Structural and Mechanistic Features of Viral IRES Elements

Insights into Structural and Mechanistic Features of Viral IRES Elements

Designing synthetic RNAs to determine the relevance of structural motifs in picornavirus IRES elements

RNAiFold2T: Constraint Programming design of thermo-IRES switches

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