scholarly journals A Six-Nucleotide Segment within the 3′ Untranslated Region of Hibiscus Chlorotic Ringspot Virus Plays an Essential Role in Translational Enhancement

2002 ◽  
Vol 76 (3) ◽  
pp. 1144-1153 ◽  
Author(s):  
Dora Chin-Yen Koh ◽  
D. X. Liu ◽  
Sek-Man Wong
Keyword(s):  
Gene Expression ◽  
Untranslated Region ◽  
Translational Regulation ◽  
Viral Gene Expression ◽  
Plant Viruses ◽  
Ringspot Virus ◽  
Viral Gene ◽  
Entry Site ◽  
Viral Mrnas ◽  
Translational Machinery

ABSTRACT RNA plant viruses use various translational regulatory mechanisms to control their gene expression. Translational enhancement of viral mRNAs that leads to higher levels of protein synthesis from specific genes may be essential for the virus to successfully compete for cellular translational machinery. The control elements have yet to be analyzed for members of the genus Carmovirus, a small group of plant viruses with positive-sense RNA genomes. In this study, we examined the 3′ untranslated region (UTR) of hibiscus chlorotic ringspot virus (HCRSV) genomic RNA (gRNA) and subgenomic RNA (sgRNA) for its role in the translational regulation of viral gene expression. The results showed that the 3′ UTR of HCRSV significantly enhanced the translation of several open reading frames on gRNA and sgRNA and a viral gene in a bicistronic construct with an inserted internal ribosome entry site. Through deletion and mutagenesis studies of both the bicistronic construct and full-length gRNA, we demonstrated that a six-nucleotide sequence, GGGCAG, that is complementary to the 3′ region of the 18S rRNA and a minimal length of 180 nucleotides are required for the enhancement of translation induced by the 3′ UTR.

scholarly journals Acetylation of cytidine residues boosts HIV-1 gene expression by increasing viral RNA stability

2020 ◽  
Author(s):  
Kevin Tsai ◽  
Ananda Ayyappan Jaguva Vasudevan ◽  
Cecilia Martinez Campos ◽  
Ann Emery ◽  
Ronald Swanstrom ◽  
...  
Keyword(s):  
Gene Expression ◽  
Rna Stability ◽  
Antiviral Drug ◽  
Viral Gene Expression ◽  
Mrna Translation ◽  
Viral Gene ◽  
Viral Mrnas ◽  
Cellular Target ◽  
Covalent Modifications ◽  
Hiv 1

AbstractCovalent modifications added to individual nucleotides on mRNAs, called epitranscriptomic modifications, have recently emerged as key regulators of both cellular and viral mRNA function1,2 and RNA methylation has now been shown to enhance the replication of human immunodeficiency virus 1 (HIV-1) and several other viruses3–11. Recently, acetylation of the N4 position of cytidine (ac4C) was reported to boost cellular mRNA function by increasing mRNA translation and stability12. We therefore hypothesized that ac4C and N-acetyltransferase 10 (NAT10), the cellular enzyme that adds ac4C to RNAs, might also have been subverted by HIV-1 to increase viral gene expression. We now confirm that HIV-1 transcripts are indeed modified by addition of ac4C at multiple discreet sites and demonstrate that silent mutagenesis of a subset of these ac4C addition sites inhibits HIV-1 gene expression in cis. Moreover, reduced expression of NAT10, and the concomitant decrease in the level of ac4C on viral RNAs, inhibits HIV-1 replication by reducing HIV-1 RNA stability. Interestingly Remodelin, a previously reported inhibitor of NAT10 function13,14, also inhibits HIV-1 replication without affecting cell viability, thus raising the possibility that the addition of ac4C to viral mRNAs might emerge as a novel cellular target for antiviral drug development.

scholarly journals Genome-Wide Analysis of Heterogeneous Nuclear Ribonucleoprotein (hnRNP) Binding to HIV-1 RNA Reveals a Key Role for hnRNP H1 in Alternative Viral mRNA Splicing

2019 ◽  
Vol 93 (21) ◽  
Author(s):  
Sebla B. Kutluay ◽  
Ann Emery ◽  
Srinivasa R. Penumutchu ◽  
Dana Townsend ◽  
Kasyap Tenneti ◽  
...  
Keyword(s):  
Gene Expression ◽  
Alternative Splicing ◽  
Viral Gene Expression ◽  
Viral Gene ◽  
Hnrnp A1 ◽  
Viral Mrnas ◽  
Temporal Regulation ◽  
Coding Potential ◽  
Hiv 1

ABSTRACT Alternative splicing of HIV-1 mRNAs increases viral coding potential and controls the levels and timing of gene expression. HIV-1 splicing is regulated in part by heterogeneous nuclear ribonucleoproteins (hnRNPs) and their viral target sequences, which typically repress splicing when studied outside their native viral context. Here, we determined the location and extent of hnRNP binding to HIV-1 mRNAs and their impact on splicing in a native viral context. Notably, hnRNP A1, hnRNP A2, and hnRNP B1 bound to many dispersed sites across viral mRNAs. Conversely, hnRNP H1 bound to a few discrete purine-rich sequences, a finding that was mirrored in vitro. hnRNP H1 depletion and mutation of a prominent viral RNA hnRNP H1 binding site decreased the use of splice acceptor A1, causing a deficit in Vif expression and replicative fitness. This quantitative framework for determining the regulatory inputs governing alternative HIV-1 splicing revealed an unexpected splicing enhancer role for hnRNP H1 through binding to its target element. IMPORTANCE Alternative splicing of HIV-1 mRNAs is an essential yet quite poorly understood step of virus replication that enhances the coding potential of the viral genome and allows the temporal regulation of viral gene expression. Although HIV-1 constitutes an important model system for general studies of the regulation of alternative splicing, the inputs that determine the efficiency with which splice sites are utilized remain poorly defined. Our studies provide an experimental framework to study an essential step of HIV-1 replication more comprehensively and in much greater detail than was previously possible and reveal novel cis-acting elements regulating HIV-1 splicing.

scholarly journals Widespread remodeling of the m6A RNA-modification landscape by a viral regulator of RNA processing and export

2021 ◽  
Vol 118 (30) ◽  
pp. e2104805118
Author(s):  
Kalanghad Puthankalam Srinivas ◽  
Daniel P. Depledge ◽  
Jonathan S. Abebe ◽  
Stephen A. Rice ◽  
Ian Mohr ◽  
...  
Keyword(s):  
Gene Expression ◽  
Messenger Rna ◽  
Rna Binding ◽  
Viral Gene Expression ◽  
Rna Modification ◽  
Viral Gene ◽  
Viral Mrnas ◽  
Simplex Virus ◽  
Processing Stability ◽  
Hsv 1

N6-methyladenosine (m6A) is the most abundant internal messenger RNA (mRNA) modification, contributing to the processing, stability, and function of methylated RNAs. Methylation occurs in the nucleus during pre-mRNA synthesis and requires a core methyltransferase complex consisting of METTL3, METTL14, and WTAP. During herpes simplex virus (HSV-1) infection, cellular gene expression is profoundly suppressed, allowing the virus to monopolize the host transcription and translation apparatus and antagonize antiviral responses. The extent to which HSV-1 uses or manipulates the m6A pathway is not known. Here, we show that, in primary fibroblasts, HSV-1 orchestrates a striking redistribution of the nuclear m6A machinery that progresses through the infection cycle. METTL3 and METTL14 are dispersed into the cytoplasm, whereas WTAP remains nuclear. Other regulatory subunits of the methyltransferase complex, along with the nuclear m6A-modified RNA binding protein YTHDC1 and nuclear demethylase ALKBH5, are similarly redistributed. These changes require ICP27, a viral regulator of host mRNA processing that mediates the nucleocytoplasmic export of viral late mRNAs. Viral gene expression is initially reduced by small interfering RNA (siRNA)-mediated inactivation of the m6A methyltransferase but becomes less impacted as the infection advances. Redistribution of the nuclear m6A machinery is accompanied by a wide-scale reduction in the installation of m6A and other RNA modifications on both host and viral mRNAs. These results reveal a far-reaching mechanism by which HSV-1 subverts host gene expression to favor viral replication.

scholarly journals Complex Effects of Deletions in the 5′ Untranslated Region of Primate Foamy Virus on Viral Gene Expression and RNA Packaging

2000 ◽  
Vol 74 (7) ◽  
pp. 3141-3148 ◽  
Author(s):  
Martin Heinkelein ◽  
Jana Thurow ◽  
Marco Dressler ◽  
Horst Imrich ◽  
Dieter Neumann-Haefelin ◽  
...  
Keyword(s):  
Gene Expression ◽  
Untranslated Region ◽  
Foamy Virus ◽  
Regulation Of Gene Expression ◽  
Viral Gene Expression ◽  
Retroviral Vectors ◽  
Particle Formation ◽  
Start Codon ◽  
Viral Gene ◽  
R Region

ABSTRACT Due to various advantageous features there is current interest in retroviral vectors derived from primate foamy viruses (PFVs). Two PFV cis-acting sequences have been mapped in the 5′ region of the RNA (pre-)genome and in the 3′ pol genomic region. In order to genetically separate PFV packaging constructs from vector constructs, we investigated the effect of deletions in the 5′ untranslated region (UTR) of PFV packaging constructs and vectors on gene expression and RNA incorporation into viral particles. Our results indicate that the 5′ UTR serves different previously unknown functions. First, the R region of the long terminal repeat was found to be required for PFV gag gene expression. This regulation of gene expression appeared to be mainly posttranscriptional. Second, constructs with sequence deletions between the R region and thegag gene start codon packaged as much viral mRNA into particles as the undeleted construct, and RNA from such a 5′-UTR-deleted packaging construct was copackaged into vector-virus particles, together with vector RNA which was preferentialy packaged. Finally, in the U5 region a sequence was identified that was required to allow cleavage of the Gag precursor protein by the polgene-encoded protease, suggesting a role of RNA in PFV particle formation. Taken together, the results indicate that complex interactions of the viral RNA, capsid, and polymerase proteins take place during PFV particle formation and that a clear separation of PFV vector and packaging construct sequences may be difficult to achieve.

scholarly journals New insights into internal ribosome entry site elements relevant for viral gene expression

2008 ◽  
Vol 89 (3) ◽  
pp. 611-626 ◽  
Author(s):  
Encarnación Martínez-Salas ◽  
Almudena Pacheco ◽  
Paula Serrano ◽  
Noemi Fernandez
Keyword(s):  
Gene Expression ◽  
Rna Binding ◽  
Viral Gene Expression ◽  
Rna Replication ◽  
Host Factors ◽  
Viral Gene ◽  
Entry Site ◽  
Internal Ribosome Entry ◽  
Positive Strand ◽  
Positive Strand Rna

A distinctive feature of positive-strand RNA viruses is the presence of high-order structural elements at the untranslated regions (UTR) of the genome that are essential for viral RNA replication. The RNA of all members of the family Picornaviridae initiate translation internally, via an internal ribosome entry site (IRES) element present in the 5′ UTR. IRES elements consist of cis-acting RNA structures that usually require specific RNA-binding proteins for translational machinery recruitment. This specialized mechanism of translation initiation is shared with other viral RNAs, e.g. from hepatitis C virus and pestivirus, and represents an alternative to the cap-dependent mechanism. In cells infected with many picornaviruses, proteolysis or changes in phosphorylation of key host factors induces shut off of cellular protein synthesis. This event occurs simultaneously with the synthesis of viral gene products since IRES activity is resistant to the modifications of the host factors. Viral gene expression and RNA replication in positive-strand viruses is further stimulated by viral RNA circularization, involving direct RNA–RNA contacts between the 5′ and 3′ ends as well as RNA-binding protein bridges. In this review, we discuss novel insights into the mechanisms that control picornavirus gene expression and compare them to those operating in other positive-strand RNA viruses.

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