The Importance of RNA-binding Proteins and RNA in the Antiviral State

A special issue of Microorganisms (ISSN 2076-2607). This special issue belongs to the section "Molecular Microbiology and Immunology".

Deadline for manuscript submissions: closed (31 December 2021) | Viewed by 11587

Special Issue Editor


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Guest Editor
Sir Michael Stoker Building, Garscube Campus, MRC University of Glasgow Centre for Virus Research, 464 Bearsden Road, Glasgow G61 1QH, UK
Interests: RNA binding proteins; RNA Virus; protein-RNA interactions; virus-host interactions; antivirals; interferon
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Special Issue Information

Dear Colleagues,

Viruses are intracellular parasites that require the host cell to replicate and spread. Viral RNAs and replication intermediates present unusual signatures that are recognised by specialised RNA-binding proteins (RBPs). These signatures include tri-phosphate 5’ ends, undermethylated cap, sequence biases (e.g. CpG-rich regions) and double stranded RNA. Interaction of antiviral RBPs with RNA trigger important alterations in the host cell, including the suppression of protein synthesis and the activation of the antiviral transcriptional programme. Moreover, cellular RNA can also exert, together with cellular RBPs, antiviral effects. These RNA molecules include micro (mi)RNA, piwi-interacting RNA (piRNA) and, more recently, long non-coding (lnc)RNAs. On the other hand, viruses encode proteins and RNAs that can antagonise these cellular antiviral mechanisms, leading to a competition between cellular and viral mechanisms to define the fate of viral infection.

In the last years, important efforts have been undertaken to improve our understanding on these critical antiviral host-virus interactions. Therefore, this issue focuses on this rapidly evolving field, considering research articles, methods and reviews to consolidate and expand our knowledge on these important host-virus interactions. The three main focus of the issue are:

  • RBPs as critical weapons in the antiviral arsenal of the host cell. This section will expand our knowledge of the roles of cellular RBPs as sensors and effectors of the innate immunity system;
  • Viral RBPs that interfere with the antiviral response. This section will focus on the viral RBPs that interfere with host gene expression, or prevent the detection of the viral RNA by antiviral sensors, to impair the capacity of the cell to respond to virus infection.
  • Cellular RNA as regulators of the antiviral response.

Dr. Alfredo Castello
Guest Editor

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Published Papers (3 papers)

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Research

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17 pages, 8299 KiB  
Article
Amino Acid Residues Involved in Inhibition of Host Gene Expression by Influenza A/Brevig Mission/1/1918 PA-X
by Kevin Chiem, Luis Martinez-Sobrido, Aitor Nogales and Marta L. DeDiego
Microorganisms 2021, 9(5), 1109; https://0-doi-org.brum.beds.ac.uk/10.3390/microorganisms9051109 - 20 May 2021
Cited by 4 | Viewed by 2576
Abstract
The influenza A virus (IAV) PA-X protein is a virulence factor that selectively degrades host mRNAs leading to protein shutoff. This function modulates host inflammation, antiviral responses, cell apoptosis, and pathogenesis. In this work we describe a novel approach based on the use [...] Read more.
The influenza A virus (IAV) PA-X protein is a virulence factor that selectively degrades host mRNAs leading to protein shutoff. This function modulates host inflammation, antiviral responses, cell apoptosis, and pathogenesis. In this work we describe a novel approach based on the use of bacteria and plasmid encoding of the PA-X gene under the control of the bacteriophage T7 promoter to identify amino acid residues important for A/Brevig Mission/1/1918 H1N1 PA-X’s shutoff activity. Using this system, we have identified PA-X mutants encoding single or double amino acid changes, which diminish its host shutoff activity, as well as its ability to counteract interferon responses upon viral infection. This novel bacteria-based approach could be used for the identification of viral proteins that inhibit host gene expression as well as the amino acid residues responsible for inhibition of host gene expression. Full article
(This article belongs to the Special Issue The Importance of RNA-binding Proteins and RNA in the Antiviral State)
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Review

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22 pages, 995 KiB  
Review
Mutational Landscape and Interaction of SARS-CoV-2 with Host Cellular Components
by Mansi Srivastava, Dwight Hall, Okiemute Beatrice Omoru, Hunter Mathias Gill, Sarah Smith and Sarath Chandra Janga
Microorganisms 2021, 9(9), 1794; https://0-doi-org.brum.beds.ac.uk/10.3390/microorganisms9091794 - 24 Aug 2021
Cited by 9 | Viewed by 3301
Abstract
The emergence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and its rapid evolution has led to a global health crisis. Increasing mutations across the SARS-CoV-2 genome have severely impacted the development of effective therapeutics and vaccines to combat the virus. However, the [...] Read more.
The emergence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and its rapid evolution has led to a global health crisis. Increasing mutations across the SARS-CoV-2 genome have severely impacted the development of effective therapeutics and vaccines to combat the virus. However, the new SARS-CoV-2 variants and their evolutionary characteristics are not fully understood. Host cellular components such as the ACE2 receptor, RNA-binding proteins (RBPs), microRNAs, small nuclear RNA (snRNA), 18s rRNA, and the 7SL RNA component of the signal recognition particle (SRP) interact with various structural and non-structural proteins of the SARS-CoV-2. Several of these viral proteins are currently being examined for designing antiviral therapeutics. In this review, we discuss current advances in our understanding of various host cellular components targeted by the virus during SARS-CoV-2 infection. We also summarize the mutations across the SARS-CoV-2 genome that directs the evolution of new viral strains. Considering coronaviruses are rapidly evolving in humans, this enables them to escape therapeutic therapies and vaccine-induced immunity. In order to understand the virus’s evolution, it is essential to study its mutational patterns and their impact on host cellular machinery. Finally, we present a comprehensive survey of currently available databases and tools to study viral–host interactions that stand as crucial resources for developing novel therapeutic strategies for combating SARS-CoV-2 infection. Full article
(This article belongs to the Special Issue The Importance of RNA-binding Proteins and RNA in the Antiviral State)
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17 pages, 2941 KiB  
Review
RNA Helicase DDX3: A Double-Edged Sword for Viral Replication and Immune Signaling
by Tomás Hernández-Díaz, Fernando Valiente-Echeverría and Ricardo Soto-Rifo
Microorganisms 2021, 9(6), 1206; https://0-doi-org.brum.beds.ac.uk/10.3390/microorganisms9061206 - 03 Jun 2021
Cited by 20 | Viewed by 5042
Abstract
DDX3 is a cellular ATP-dependent RNA helicase involved in different aspects of RNA metabolism ranging from transcription to translation and therefore, DDX3 participates in the regulation of key cellular processes including cell cycle progression, apoptosis, cancer and the antiviral immune response leading to [...] Read more.
DDX3 is a cellular ATP-dependent RNA helicase involved in different aspects of RNA metabolism ranging from transcription to translation and therefore, DDX3 participates in the regulation of key cellular processes including cell cycle progression, apoptosis, cancer and the antiviral immune response leading to type-I interferon production. DDX3 has also been described as an essential cellular factor for the replication of different viruses, including important human threats such HIV-1 or HCV, and different small molecules targeting DDX3 activity have been developed. Indeed, increasing evidence suggests that DDX3 can be considered not only a promising but also a viable target for anticancer and antiviral treatments. In this review, we summarize distinct functional aspects of DDX3 focusing on its participation as a double-edged sword in the host immune response and in the replication cycle of different viruses. Full article
(This article belongs to the Special Issue The Importance of RNA-binding Proteins and RNA in the Antiviral State)
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