Special Issue "Viral RNA Structural Biology"

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

Deadline for manuscript submissions: 15 July 2021.

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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Keywords

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

Published Papers (1 paper)

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Research

Article
Structural Analysis and Whole Genome Mapping of a New Type of Plant Virus Subviral RNA: Umbravirus-Like Associated RNAs
Viruses 2021, 13(4), 646; https://doi.org/10.3390/v13040646 - 09 Apr 2021
Cited by 1 | Viewed by 440
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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