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RNA Structure and Function

A special issue of International Journal of Molecular Sciences (ISSN 1422-0067). This special issue belongs to the section "Molecular Biophysics".

Deadline for manuscript submissions: closed (15 December 2022) | Viewed by 8437

Special Issue Editor

Research Group Bioinformatics and Computational Biology, Währinger Straße 29, 1090 Wien, Room 5.31, Universitat Wien, Vienna, Austria
Interests: RNA structure prediction; non-coding RNA; co-trancriptional folding; RNA viruses

Special Issue Information

Dear Colleagues,

Research conducted over the last 25 years has revealed a varied picture of the importance of RNA in mediating biological processes in all kingdoms of life. With the understanding that RNA is more than an information intermediate and the insight that non-coding RNAs are key players in regulation and metabolism came the quest for elucidating the interplay of RNA structure and function. RNAs interact with other RNAs or proteins, rendering them attractive research targets. Likewise, the availability of novel experimental and theoretical developments, such as high-throughput structure probing or single-cell technologies has leveraged the expansion of the field.

In the Special Issue ‘RNA Structure and Function’ we would like to bring together experimental and theoretical studies in all aspects of RNA biology that help to address the interplay and interaction of structured/unstructured RNAs and their biological function.

Original articles and reviews are welcome.

Dr. Michael T. Wolfinger
Guest Editor

Keywords

RNA structure

RNA function

RNA biology

RNA structure prediction

non-coding RNA

co-trancriptional folding

Published Papers (4 papers)

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Research

13 pages, 2837 KiB  
Article
Molecular Characteristics of Subgenomic RNAs and the Cap-Dependent Translational Advantage Relative to Corresponding Genomic RNAs of Tomato spotted wilt virus
by Chen Yang, Chengming Yu, Zhenjia Zhang, Deya Wang and Xuefeng Yuan
Int. J. Mol. Sci. 2022, 23(23), 15074; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms232315074 - 01 Dec 2022
Viewed by 1279
Abstract
Tomato spotted wilt virus (TSWV) causes severe viral diseases on many economically important plants of Solanaceae. During the infection process of TSWV, a series of 3′-truncated subgenomic RNAs (sgRNAs) relative to corresponding genomic RNAs were synthesized, which were responsible for the expression of [...] Read more.
Tomato spotted wilt virus (TSWV) causes severe viral diseases on many economically important plants of Solanaceae. During the infection process of TSWV, a series of 3′-truncated subgenomic RNAs (sgRNAs) relative to corresponding genomic RNAs were synthesized, which were responsible for the expression of some viral proteins. However, corresponding genomic RNAs (gRNAs) seem to possess the basic elements for expression of these viral proteins. In this study, molecular characteristics of sgRNAs superior to genomic RNAs in viral protein expression were identified. The 3′ ends of sgRNAs do not cover the entire intergenic region (IGR) of TSWV genomic RNAs and contain the remarkable A-rich characteristics. In addition, the 3′ terminal nucleotides of sgRNAs are conserved among different TSWV isolates. Based on the eIF4E recruitment assay and subsequent northern blot, it is suggested that the TSWV sgRNA, but not gRNA, is capped in vivo; this is why sgRNA is competent for protein expression relative to gRNA. In addition, the 5′ and 3′ untranslated region (UTR) of sgRNA-Ns can synergistically enhance cap-dependent translation. This study further enriched the understanding of sgRNAs of ambisense RNA viruses. Full article
(This article belongs to the Special Issue RNA Structure and Function)
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17 pages, 33374 KiB  
Article
The CAR–mRNA Interaction Surface Is a Zipper Extension of the Ribosome A Site
by Carol Dalgarno, Kristen Scopino, Mitsu Raval, Clara Nachmanoff, Eric D. Sakkas, Daniel Krizanc, Kelly M. Thayer and Michael P. Weir
Int. J. Mol. Sci. 2022, 23(3), 1417; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms23031417 - 26 Jan 2022
Viewed by 2441
Abstract
The ribosome CAR interaction surface behaves as an extension of the decoding center A site and has H-bond interactions with the +1 codon, which is next in line to enter the A site. Through molecular dynamic simulations, we investigated the codon sequence specificity [...] Read more.
The ribosome CAR interaction surface behaves as an extension of the decoding center A site and has H-bond interactions with the +1 codon, which is next in line to enter the A site. Through molecular dynamic simulations, we investigated the codon sequence specificity of this CAR–mRNA interaction and discovered a strong preference for GCN codons, suggesting that there may be a sequence-dependent layer of translational regulation dependent on the CAR interaction surface. Dissection of the CAR–mRNA interaction through nucleotide substitution experiments showed that the first nucleotide of the +1 codon dominates over the second nucleotide position, consistent with an energetically favorable zipper-like activity that emanates from the A site through the CAR–mRNA interface. Moreover, the CAR/+1 codon interaction is affected by the identity of nucleotide 3 of +1 GCN codons, which influences the stacking of G and C. Clustering analysis suggests that the A-site decoding center adopts different neighborhood substates that depend on the identity of the +1 codon. Full article
(This article belongs to the Special Issue RNA Structure and Function)
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15 pages, 1894 KiB  
Article
Genome Features of a New Double-Stranded RNA Helper Virus (LBCbarr) from Wine Torulaspora delbrueckii Killer Strains
by Manuel Ramírez, Rocío Velázquez, Antonio López-Piñeiro and Alberto Martínez
Int. J. Mol. Sci. 2021, 22(24), 13492; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms222413492 - 16 Dec 2021
Cited by 6 | Viewed by 2040
Abstract
The killer phenotype of Torulaspora delbrueckii (Td) and Saccharomyces cerevisiae (Sc) is encoded in the genome of medium-size dsRNA viruses (V-M). Killer strains also contain a helper large size (4.6 kb) dsRNA virus (V-LA) which is required for maintenance and replication of V-M. [...] Read more.
The killer phenotype of Torulaspora delbrueckii (Td) and Saccharomyces cerevisiae (Sc) is encoded in the genome of medium-size dsRNA viruses (V-M). Killer strains also contain a helper large size (4.6 kb) dsRNA virus (V-LA) which is required for maintenance and replication of V-M. Another large-size (4.6 kb) dsRNA virus (V-LBC), without known helper activity to date, may join V-LA and V-M in the same yeast. T. delbrueckii Kbarr1 killer strain contains the killer virus Mbarr1 in addition to two L viruses, TdV-LAbarr1 and TdV-LBCbarr1. In contrast, the T. delbrueckii Kbarr2 killer strain contains two M killer viruses (Mbarr1 and M1) and a LBC virus (TdV-LBCbarr2), which has helper capability to maintain both M viruses. The genomes of TdV-LBCbarr1 and TdV-LBCbarr2 were characterized by high-throughput sequencing (HTS). Both RNA genomes share sequence identity and similar organization with their ScV-LBC counterparts. They contain all conserved motifs required for translation, packaging, and replication of viral RNA. Their Gag-Pol amino-acid sequences also contain the features required for cap-snatching and RNA polymerase activity. However, some of these motifs and features are similar to those of LA viruses, which may explain that at least TdV-LBCbarr2 has a helper ability to maintain M killer viruses. Newly sequenced ScV-LBC genomes contained the same motifs and features previously found in LBC viruses, with the same genome location and secondary structure. Sequence comparison showed that LBC viruses belong to two clusters related to each species of yeast. No evidence for associated co-evolution of specific LBC with specific M virus was found. The presence of the same M1 virus in S. cerevisiae and T. delbrueckii raises the possibility of cross-species transmission of M viruses. Full article
(This article belongs to the Special Issue RNA Structure and Function)
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15 pages, 3132 KiB  
Article
CriTER-A: A Novel Temperature-Dependent Noncoding RNA Switch in the Telomeric Transcriptome of Chironomus riparius
by Cristina Romero-López, Alfredo Berzal-Herranz, José Luis Martínez-Guitarte and Mercedes de la Fuente
Int. J. Mol. Sci. 2021, 22(19), 10310; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms221910310 - 24 Sep 2021
Cited by 1 | Viewed by 1333
Abstract
The telomeric transcriptome of Chironomus riparius has been involved in thermal stress response. One of the telomeric transcripts, the so-called CriTER-A variant, is highly overexpressed upon heat shock. On the other hand, its homologous variant CriTER-B, which is the most frequently encoded noncoding [...] Read more.
The telomeric transcriptome of Chironomus riparius has been involved in thermal stress response. One of the telomeric transcripts, the so-called CriTER-A variant, is highly overexpressed upon heat shock. On the other hand, its homologous variant CriTER-B, which is the most frequently encoded noncoding RNA in the telomeres of C. riparius, is only slightly affected by thermal stress. Interestingly, both transcripts show high sequence homology, but less is known about their folding and how this could influence their differential behaviour. Our study suggests that CriTER-A folds as two different conformers, whose relative proportion is influenced by temperature conditions. Meanwhile, the CriTER-B variant shows only one dominant conformer. Thus, a temperature-dependent conformational equilibrium can be established for CriTER-A, suggesting a putative functional role of the telomeric transcriptome in relation to thermal stress that could rely on the structure–function relationship of the CriTER-A transcripts. Full article
(This article belongs to the Special Issue RNA Structure and Function)
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