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Viruses
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Viral RNA Structural Biology
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Viral RNA Structural Biology

A special issue of Viruses (ISSN 1999-4915). This special issue belongs to the section "General Virology".

Deadline for manuscript submissions: closed (20 December 2021) | Viewed by 14745

Special Issue Editors

Dr. Stuart F.J. Le Grice

E-Mail Website
Guest Editor
Basic Research Laboratory National Cancer Institute, Frederick, MD 21702, USA
Interests: retrovirus replication; nucleoprotein complexes; antiviral strategies; regulatory RNAs; RNA therapeutics; chemical biology
Prof. Dr. Anne Simon

E-Mail Website
Guest Editor
Cell Biology and Molecular Genetics, University of Maryland, College Park, MD 20742, USA
Interests: plant viruses; plus-strand RNA virus replication/translation; RNA structure/function

Special Issue Information

Dear Colleagues,

Pathogenic RNA viruses are, without reservation, emerging as the most important group implicated in zoonotic transmission. This is perhaps best exemplified by SARS-CoV-2, the etiological agent of the current COVID-19 pandemic, which is presenting a major challenge to global disease control. Understanding their genome organization, replication strategies, and the host factors they usurp to accomplish this will likely provide a foundation for successful immunological and small molecule interventions. In order to achieve this, complementary, biochemical, and biophysical strategies in the form of high throughput, high resolution structural analyses are expected make important contributions. Constant improvements to techniques such as small angle X-ray scattering, X-ray crystallography, NMR spectroscopy, and cryo-electron microscopy are providing detailed information on individual regulatory domains, while chemoenzymatic probing (SHAPE-MaP) can now provide exciting glimpses of communication between elements of RNA genomes separated by several thousand nucleotides. It is also important to recognize the contribution of molecular modeling and molecular dynamics simulations, which are finding increased use as a complement biochemical and biophysical approaches in delineating the structure of regulatory RNAs. A final section of this Special Edition will address the structural features of single-stranded plant RNA viruses, the main agents of many serious diseases of agriculturally important crops.

Dr. Stuart F.J. Le Grice
Prof. Dr. Anne Simon
Guest Editors

Manuscript Submission Information

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Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Viruses is an international peer-reviewed open access monthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2600 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

  • retroviruses
  • hepadnaviruses
  • viral polymerases
  • RNA genome packaging
  • RNA structure
  • NMR spectroscopy
  • X-ray crystallography
  • molecular modelingcircular RNA
  • RNA vaccines

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Published Papers (4 papers)

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Research

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10 pages, 1685 KiB  
Communication
Trans-Activator Binding Site Context in RCNMV Modulates Subgenomic mRNA Transcription
by Jennifer S. H. Im, Laura R. Newburn, Gregory Kent and K. Andrew White
Viruses 2021, 13(11), 2252; https://doi.org/10.3390/v13112252 - 10 Nov 2021
Cited by 3 | Viewed by 2177
Abstract
Many positive-sense RNA viruses transcribe subgenomic (sg) mRNAs during infections that template the translation of a subset of viral proteins. Red clover necrotic mosaic virus (RCNMV) expresses its capsid protein through the transcription of a sg mRNA from RNA1 genome segment. This transcription [...] Read more.
Many positive-sense RNA viruses transcribe subgenomic (sg) mRNAs during infections that template the translation of a subset of viral proteins. Red clover necrotic mosaic virus (RCNMV) expresses its capsid protein through the transcription of a sg mRNA from RNA1 genome segment. This transcription event is activated by an RNA structure formed by base pairing between a trans-activator (TA) in RNA2 and a trans-activator binding site (TABS) in RNA1. In this study, the impact of the structural context of the TABS in RNA1 on the TA–TABS interaction and sg mRNA transcription was investigated using in vitro and in vivo approaches. The results (i) generated RNA secondary structure models for the TA and TABS, (ii) revealed that the TABS is partially base paired with proximal upstream sequences, which limits TA access, (iii) demonstrated that the aforementioned intra-RNA1 base pairing involving the TABS modulates the TA–TABS interaction in vitro and sg mRNA levels during infections, and (iv) revealed that the TABS in RNA1 can be modified to mediate sg mRNA transcription in a TA-independent manner. These findings advance our understanding of transcriptional regulation in RCNMV and provide novel insights into the origin of the TA–TABS interaction. Full article
(This article belongs to the Special Issue Viral RNA Structural Biology)
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29 pages, 8588 KiB  
Article
Structural Analysis and Whole Genome Mapping of a New Type of Plant Virus Subviral RNA: Umbravirus-Like Associated RNAs
by Jingyuan Liu, Elizabeth Carino, Sayanta Bera, Feng Gao, Jared P. May and Anne E. Simon
Viruses 2021, 13(4), 646; https://doi.org/10.3390/v13040646 - 9 Apr 2021
Cited by 29 | Viewed by 5174
Abstract
We report the biological and structural characterization of umbravirus-like associated RNAs (ulaRNAs), a new category of coat-protein dependent subviral RNA replicons that infect plants. These RNAs encode an RNA-dependent RNA polymerase (RdRp) following a −1 ribosomal frameshift event, are 2.7–4.6 kb in length, [...] Read more.
We report the biological and structural characterization of umbravirus-like associated RNAs (ulaRNAs), a new category of coat-protein dependent subviral RNA replicons that infect plants. These RNAs encode an RNA-dependent RNA polymerase (RdRp) following a −1 ribosomal frameshift event, are 2.7–4.6 kb in length, and are related to umbraviruses, unlike similar RNA replicons that are related to tombusviruses. Three classes of ulaRNAs are proposed, with citrus yellow vein associated virus (CYVaV) placed in Class 2. With the exception of CYVaV, Class 2 and Class 3 ulaRNAs encode an additional open reading frame (ORF) with movement protein-like motifs made possible by additional sequences just past the RdRp termination codon. The full-length secondary structure of CYVaV was determined using Selective 2’ Hydroxyl Acylation analyzed by Primer Extension (SHAPE) structure probing and phylogenic comparisons, which was used as a template for determining the putative structures of the other Class 2 ulaRNAs, revealing a number of distinctive structural features. The ribosome recoding sites of nearly all ulaRNAs, which differ significantly from those of umbraviruses, may exist in two conformations and are highly efficient. The 3′ regions of Class 2 and Class 3 ulaRNAs have structural elements similar to those of nearly all umbraviruses, and all Class 2 ulaRNAs have a unique, conserved 3′ cap-independent translation enhancer. CYVaV replicates independently in protoplasts, demonstrating that the reported sequence is full-length. Additionally, CYVaV contains a sequence in its 3′ UTR that confers protection to nonsense mediated decay (NMD), thus likely obviating the need for umbravirus ORF3, a known suppressor of NMD. This initial characterization lays down a road map for future investigations into these novel virus-like RNAs. Full article
(This article belongs to the Special Issue Viral RNA Structural Biology)
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Review

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17 pages, 1712 KiB  
Review
Evaluating RNA Structural Flexibility: Viruses Lead the Way
by Connor W. Fairman, Andrew M. L. Lever and Julia C. Kenyon
Viruses 2021, 13(11), 2130; https://doi.org/10.3390/v13112130 - 22 Oct 2021
Cited by 3 | Viewed by 2554
Abstract
Our understanding of RNA structure has lagged behind that of proteins and most other biological polymers, largely because of its ability to adopt multiple, and often very different, functional conformations within a single molecule. Flexibility and multifunctionality appear to be its hallmarks. Conventional [...] Read more.
Our understanding of RNA structure has lagged behind that of proteins and most other biological polymers, largely because of its ability to adopt multiple, and often very different, functional conformations within a single molecule. Flexibility and multifunctionality appear to be its hallmarks. Conventional biochemical and biophysical techniques all have limitations in solving RNA structure and to address this in recent years we have seen the emergence of a wide diversity of techniques applied to RNA structural analysis and an accompanying appreciation of its ubiquity and versatility. Viral RNA is a particularly productive area to study in that this economy of function within a single molecule admirably suits the minimalist lifestyle of viruses. Here, we review the major techniques that are being used to elucidate RNA conformational flexibility and exemplify how the structure and function are, as in all biology, tightly linked. Full article
(This article belongs to the Special Issue Viral RNA Structural Biology)
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21 pages, 4878 KiB  
Review
Chemical and Enzymatic Probing of Viral RNAs: From Infancy to Maturity and Beyond
by Orian Gilmer, Erwan Quignon, Anne-Caroline Jousset, Jean-Christophe Paillart, Roland Marquet and Valérie Vivet-Boudou
Viruses 2021, 13(10), 1894; https://doi.org/10.3390/v13101894 - 22 Sep 2021
Cited by 8 | Viewed by 3555
Abstract
RNA molecules are key players in a variety of biological events, and this is particularly true for viral RNAs. To better understand the replication of those pathogens and try to block them, special attention has been paid to the structure of their RNAs. [...] Read more.
RNA molecules are key players in a variety of biological events, and this is particularly true for viral RNAs. To better understand the replication of those pathogens and try to block them, special attention has been paid to the structure of their RNAs. Methods to probe RNA structures have been developed since the 1960s; even if they have evolved over the years, they are still in use today and provide useful information on the folding of RNA molecules, including viral RNAs. The aim of this review is to offer a historical perspective on the structural probing methods used to decipher RNA structures before the development of the selective 2′-hydroxyl acylation analyzed by primer extension (SHAPE) methodology and to show how they have influenced the current probing techniques. Actually, these technological breakthroughs, which involved advanced detection methods, were made possible thanks to the development of next-generation sequencing (NGS) but also to the previous works accumulated in the field of structural RNA biology. Finally, we will also discuss how high-throughput SHAPE (hSHAPE) paved the way for the development of sophisticated RNA structural techniques. Full article
(This article belongs to the Special Issue Viral RNA Structural Biology)
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