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Viruses
Special Issues
Functional and Structural Features of Viral RNA Elements
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Functional and Structural Features of Viral RNA Elements

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

Deadline for manuscript submissions: 31 May 2025 | Viewed by 9415

Special Issue Editor

Dr. Stefan Weger

E-Mail Website
Guest Editor
Charité University Medicine Berlin, Campus Benjamin Franklin, Clinic for Neurology with Experimental Neurology, Gene Therapy Group, 12203 Berlin, Germany
Interests: parvoviruses; interaction of viral regulatory proteins with host proteins; viral vectors; gene therapy
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

The outcome of viral infections including evasion from the immune system and pathogenicity can be regulated by multiple post-transcriptional mechanisms such as splicing, mRNA stability, mRNA export, translation initiation and mRNA modification or editing. The corresponding viral RNA sequences must therefore provide the structural and sequence determinants required for this process. Well-characterized examples are the internal ribosome entry site (IRES), for cap-independent protein translation first identified in Picornaviruses, or the RRE element required for the efficient export of HIV mRNAs. Such sequence elements may be involved in interactions with proteins or other RNA molecules or in intramolecular interactions between different parts of the regulatory sequence. They are often subject to evolutionary selection pressure to maximize functionality without expanding the viral genome size.

The current Special Issue addresses recent advances in unraveling the structural motifs contributing to the functionality of such viral cis-regulatory RNA sequences and the molecular mechanisms and host factors involved their mode of action. It further aims at a better understanding of the evolution of these regulatory elements for facilitating the prediction of sequences with similar functions in other viral genomes.

Dr. Stefan Weger
Guest Editor

Manuscript Submission Information

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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

  • RNA viruses
  • IRES elements
  • cap-independent protein synthesis
  • translation initiation
  • conserved RNA motifs

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Published Papers (4 papers)

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Research

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14 pages, 3020 KiB  
Article
PSPC1 Binds to HCV IRES and Prevents Ribosomal Protein S5 Binding, Inhibiting Viral RNA Translation
by Sachin Kumar Tripathi, Ashish Aneja, Teji Borgaonkar and Saumitra Das
Viruses 2024, 16(5), 738; https://doi.org/10.3390/v16050738 - 7 May 2024
Viewed by 1847
Abstract
Hepatitis C virus (HCV) infects the human liver, and its chronic infection is one of the major causes of Hepatocellular carcinoma. Translation of HCV RNA is mediated by an Internal Ribosome Entry Site (IRES) element located in the 5’UTR of viral RNA. Several [...] Read more.
Hepatitis C virus (HCV) infects the human liver, and its chronic infection is one of the major causes of Hepatocellular carcinoma. Translation of HCV RNA is mediated by an Internal Ribosome Entry Site (IRES) element located in the 5’UTR of viral RNA. Several RNA Binding proteins of the host interact with the HCV IRES and modulate its function. Here, we demonstrate that PSPC1 (Paraspeckle Component 1), an essential paraspeckle component, upon HCV infection is relocalized and interacts with HCV IRES to prevent viral RNA translation. Competition UV-crosslinking experiments showed that PSPC1 interacts explicitly with the SLIV region of the HCV IRES, which is known to play a vital role in ribosomal loading to the HCV IRES via interaction with Ribosomal protein S5 (RPS5). Partial silencing of PSPC1 increased viral RNA translation and, consequently, HCV replication, suggesting a negative regulation by PSPC1. Interestingly, the silencing of PSPC1 protein leads to an increased interaction of RPS5 at the SLIV region, leading to an overall increase in the viral RNA in polysomes. Overall, our results showed how the host counters viral infection by relocalizing nuclear protein to the cytoplasm as a survival strategy. Full article
(This article belongs to the Special Issue Functional and Structural Features of Viral RNA Elements)
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20 pages, 1429 KiB  
Article
The Mytilus chilensis Steamer-like Element-1 Retrotransposon Antisense mRNA Harbors an Internal Ribosome Entry Site That Is Modulated by hnRNPK
by Leandro Fernández-García, Constanza Ahumada-Marchant, Pablo Lobos-Ávila, Bastián Brauer, Fernando J. Bustos and Gloria Arriagada
Viruses 2024, 16(3), 403; https://doi.org/10.3390/v16030403 - 5 Mar 2024
Cited by 2 | Viewed by 2527
Abstract
LTR-retrotransposons are transposable elements characterized by the presence of long terminal repeats (LTRs) directly flanking an internal coding region. They share genome organization and replication strategies with retroviruses. Steamer-like Element-1 (MchSLE-1) is an LTR-retrotransposon identified in the genome of the Chilean [...] Read more.
LTR-retrotransposons are transposable elements characterized by the presence of long terminal repeats (LTRs) directly flanking an internal coding region. They share genome organization and replication strategies with retroviruses. Steamer-like Element-1 (MchSLE-1) is an LTR-retrotransposon identified in the genome of the Chilean blue mussel Mytilus chilensis. MchSLE-1 is transcribed; however, whether its RNA is also translated and the mechanism underlying such translation remain to be elucidated. Here, we characterize the MchSLE-1 translation mechanism. We found that the MchSLE-1 5′ and 3′LTRs command transcription of sense and antisense RNAs, respectively. Using luciferase reporters commanded by the untranslated regions (UTRs) of MchSLE-1, we found that in vitro 5′UTR sense is unable to initiate translation, whereas the antisense 5′UTR initiates translation even when the eIF4E-eIF4G interaction was disrupted, suggesting the presence of an internal ribosomal entry site (IRES). The antisense 5′UTR IRES activity was tested using bicistronic reporters. The antisense 5′UTR has IRES activity only when the mRNA is transcribed in the nucleus, suggesting that nuclear RNA-binding proteins are required to modulate its activity. Indeed, heterogeneous nuclear ribonucleoprotein K (hnRNPK) was identified as an IRES trans-acting factor (ITAF) of the MchSLE-1 IRES. To our knowledge, this is the first report describing an IRES in an antisense mRNA derived from a mussel LTR-retrotransposon. Full article
(This article belongs to the Special Issue Functional and Structural Features of Viral RNA Elements)
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Review

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22 pages, 1231 KiB  
Review
Viral RNA Interactome: The Ultimate Researcher’s Guide to RNA–Protein Interactions
by Wesley A. Hanson, Gabriel A. Romero Agosto and Silvi Rouskin
Viruses 2024, 16(11), 1702; https://doi.org/10.3390/v16111702 - 30 Oct 2024
Viewed by 2442
Abstract
RNA molecules in the cell are bound by a multitude of RNA-binding proteins (RBPs) with a variety of regulatory consequences. Often, interactions with these RNA-binding proteins are facilitated by the complex secondary and tertiary structures of RNA molecules. Viral RNAs especially are known [...] Read more.
RNA molecules in the cell are bound by a multitude of RNA-binding proteins (RBPs) with a variety of regulatory consequences. Often, interactions with these RNA-binding proteins are facilitated by the complex secondary and tertiary structures of RNA molecules. Viral RNAs especially are known to be heavily structured and interact with many RBPs, with roles including genome packaging, immune evasion, enhancing replication and transcription, and increasing translation efficiency. As such, the RNA–protein interactome represents a critical facet of the viral replication cycle. Characterization of these interactions is necessary for the development of novel therapeutics targeted at the disruption of essential replication cycle events. In this review, we aim to summarize the various roles of RNA structures in shaping the RNA–protein interactome, the regulatory roles of these interactions, as well as up-to-date methods developed for the characterization of the interactome and directions for novel, RNA-directed therapeutics. Full article
(This article belongs to the Special Issue Functional and Structural Features of Viral RNA Elements)
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Other

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10 pages, 2038 KiB  
Brief Report
A 44-Nucleotide Region in the Chikungunya Virus 3′ UTR Dictates Viral Fitness in Disparate Host Cells
by Stephanie E. Ander, Kathryn S. Carpentier, Wes Sanders, Cormac J. Lucas, Austin J. Jolly, Cydney N. Johnson, David W. Hawman, Mark T. Heise, Nathaniel J. Moorman and Thomas E. Morrison
Viruses 2024, 16(6), 861; https://doi.org/10.3390/v16060861 - 28 May 2024
Cited by 1 | Viewed by 1389
Abstract
We previously reported that deletion of a 44-nucleotide element in the 3′ untranslated region (UTR) of the Chikungunya virus (CHIKV) genome enhances the virulence of CHIKV infection in mice. Here, we find that while this 44-nucleotide deletion enhances CHIKV fitness in murine embryonic [...] Read more.
We previously reported that deletion of a 44-nucleotide element in the 3′ untranslated region (UTR) of the Chikungunya virus (CHIKV) genome enhances the virulence of CHIKV infection in mice. Here, we find that while this 44-nucleotide deletion enhances CHIKV fitness in murine embryonic fibroblasts in a manner independent of the type I interferon response, the same mutation decreases viral fitness in C6/36 mosquito cells. Further, the fitness advantage conferred by the UTR deletion in mammalian cells is maintained in vivo in a mouse model of CHIKV dissemination. Finally, SHAPE-MaP analysis of the CHIKV 3′ UTR revealed this 44-nucleotide element forms a distinctive two-stem-loop structure that is ablated in the mutant 3′ UTR without altering additional 3′ UTR RNA secondary structures. Full article
(This article belongs to the Special Issue Functional and Structural Features of Viral RNA Elements)
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