The Intraleader AUG Nucleotide Sequence Context is Important for Equine Arteritis Virus Replication

RNA virus genomes contain cis-acting sequences and structural elements involved in virus replication. Both full-length and subgenomic negative-strand RNA synthesis are initiated at the 3′ terminus of the positive-strand genomic RNA of Equine arteritis virus (EAV). To investigate the molecular mechanism of EAV RNA synthesis, the RNA secondary structure of the 3′-proximal region of the genome was analysed by chemical and enzymic probing. Based on the RNA secondary structure model derived from this analysis, several deletions were engineered in a full-length cDNA copy of the viral genome. Two RNA domains were identified that are essential for virus replication and most likely play a key role in viral RNA synthesis. The first domain, located directly upstream of the 3′ untranslated region (UTR) (nt 12610–12654 of the genome), is mainly single-stranded but contains one small stem–loop structure. The second domain is located within the 3′ UTR (nt 12661–12690) and folds into a prominent stem–loop structure with a large loop region. The location of this stem–loop structure near the 3′ terminus of the genome suggests that it may act as a recognition signal during the initiation of minus-strand RNA synthesis.

Download Full-text

Identification of the RNA Pseudoknot within the 3′ End of the Porcine Reproductive and Respiratory Syndrome Virus Genome as a Pathogen-Associated Molecular Pattern To Activate Antiviral Signaling via RIG-I and Toll-Like Receptor 3

Journal of Virology ◽

10.1128/jvi.00097-18 ◽

2018 ◽

Vol 92 (12) ◽

Cited By ~ 9

Author(s):

Sha Xie ◽

Xin-xin Chen ◽

Songlin Qiao ◽

Rui Li ◽

Yangang Sun ◽

...

Keyword(s):

Pattern Recognition ◽

Virus Replication ◽

Rna Synthesis ◽

Antiviral Response ◽

Innate Immune ◽

Equine Arteritis Virus ◽

Respiratory Syndrome Virus ◽

Type I ◽

Toll Like Receptor ◽

Simian Hemorrhagic Fever Virus

ABSTRACTOnce infected by viruses, cells can detect pathogen-associated molecular patterns (PAMPs) on viral nucleic acid by host pattern recognition receptors (PRRs) to initiate the antiviral response. Porcine reproductive and respiratory syndrome virus (PRRSV) is the causative agent of porcine reproductive and respiratory syndrome (PRRS), characterized by reproductive failure in sows and respiratory diseases in pigs of different ages. To date, the sensing mechanism of PRRSV has not been elucidated. Here, we reported that the pseudoknot region residing in the 3′ untranslated regions (UTR) of the PRRSV genome, which has been proposed to regulate RNA synthesis and virus replication, was sensed as nonself by retinoic acid-inducible gene I (RIG-I) and Toll-like receptor 3 (TLR3) and strongly induced type I interferons (IFNs) and interferon-stimulated genes (ISGs) in porcine alveolar macrophages (PAMs). The interaction between the two stem-loops inside the pseudoknot structure was sufficient for IFN induction, since disruption of the pseudoknot interaction powerfully dampened the IFN induction. Furthermore, transfection of the 3′ UTR pseudoknot transcripts in PAMs inhibited PRRSV replicationin vitro. Importantly, the predicted similar structures of other arterivirus members, including equine arteritis virus (EAV), lactate dehydrogenase-elevating virus (LDV), and simian hemorrhagic fever virus (SHFV), also displayed strong IFN induction activities. Together, in this work we identified an innate recognition mechanism by which the PRRSV 3′ UTR pseudoknot region served as PAMPs of arteriviruses and activated innate immune signaling to produce IFNs that inhibit virus replication. All of these results provide novel insights into innate immune recognition during virus infection.IMPORTANCEPRRS is the most common viral disease in the pork industry. It is caused by PRRSV, a positive single-stranded RNA virus, whose infection often leads to persistent infection. To date, it is not yet clear how PRRSV is recognized by the host and what is the exact mechanism of IFN induction. Here, we investigated the nature of PAMPs on PRRSV and the associated PRRs. We found that the 3′ UTR pseudoknot region of PRRSV, which has been proposed to regulate viral RNA synthesis, could act as PAMPs recognized by RIG-I and TLR3 to induce type I IFN production to suppress PRRSV infection. This report is the first detailed description of pattern recognition for PRRSV, which is important in understanding the antiviral response of arteriviruses, especially PRRSV, and extends our knowledge on virus recognition.

Download Full-text

The Topology of Bulges in the Long Stem of the Flavivirus 3′ Stem-Loop Is a Major Determinant of RNA Replication Competence

Journal of Virology ◽

10.1128/jvi.79.4.2309-2324.2005 ◽

2005 ◽

Vol 79 (4) ◽

pp. 2309-2324 ◽

Cited By ~ 60

Author(s):

Li Yu ◽

Lewis Markoff

Keyword(s):

Secondary Structure ◽

Nucleotide Sequence ◽

Virus Replication ◽

Mammalian Cells ◽

Nucleotide Sequences ◽

Genome Replication ◽

Stem Loop ◽

Mosquito Cells ◽

Virus Serotype ◽

Long Stem

ABSTRACT All flavivirus genomes contain a 3′terminal stem-loop secondary structure (3′SL) formed by the most downstream ∼100 nucleotides (nt) of the viral RNA. The 3′SL is required for virus replication and has been shown to bind both virus-coded and cellular proteins. Results of the present study using an infectious DNA for WN virus strain 956 initially demonstrated that the dengue virus serotype 2 (DEN2) 3′SL nucleotide sequence could not substitute for that of the WN 3′SL to support WN genome replication. To determine what WN virus-specific 3′SL nucleotide sequences were required for WN virus replication, WN virus 3′SL nucleotide sequences were selectively deleted and replaced by analogous segments of the DEN2 3′SL nucleotide sequence such that the overall 3′SL secondary structure was not disrupted. Top and bottom portions of the WN virus 3′SL were defined according to previous studies (J. L. Blackwell and M. A. Brinton, J. Virol. 71:6433-6444, 1997; L. Zeng, L., B. Falgout, and L. Markoff, J. Virol. 72:7510-7522, 1998). A bulge in the top portion of the long stem of the WN 3′SL was essential for replication of mutant WN RNAs, and replication-defective RNAs failed to produce negative strands in transfected cells. Introduction of a second bulge into the bottom portion of the long stem of the wild-type WN 3′SL markedly enhanced the replication competence of WN virus in mosquito cells but had no effect on replication in mammalian cells. This second bulge was identified as a host cell-specific enhancer of flavivirus replication. Results suggested that bulges and their topological location within the long stem of the 3′SL are primary determinants of replication competence for flavivirus genomes.

Download Full-text

An autophagy-independent role for LC3 in equine arteritis virus replication

Autophagy ◽

10.4161/auto.22743 ◽

2013 ◽

Vol 9 (2) ◽

pp. 164-174 ◽

Cited By ~ 39

Author(s):

Iryna Monastyrska ◽

Mustafa Ulasli ◽

Peter J.M. Rottier ◽

Jun-Lin Guan ◽

Fulvio Reggiori ◽

...

Keyword(s):

Virus Replication ◽

Equine Arteritis Virus

Download Full-text

indelPost: harmonizing ambiguities in simple and complex indel alignments

Bioinformatics ◽

10.1093/bioinformatics/btab601 ◽

2021 ◽

Author(s):

Kohei Hagiwara ◽

Michael N Edmonson ◽

David A Wheeler ◽

Jinghui Zhang

Keyword(s):

Nucleotide Sequence ◽

Supplementary Information ◽

Supplementary Data ◽

Flanking Sequence ◽

Sequence Context ◽

Accurate Analysis ◽

Mapping Algorithms ◽

Insertions And Deletions ◽

Improved Performance ◽

Ambiguous Data

Abstract Summary Small insertions and deletions (indels) in nucleotide sequence may be represented differently between mapping algorithms and variant callers, or in the flanking sequence context. Representational ambiguity is especially profound for complex indels, complicating comparisons between multiple mappings and call sets. Complex indels may additionally suffer from incomplete allele representation, potentially leading to critical misannotation of variant effect. We present indelPost, a Python library that harmonizes these ambiguities for simple and complex indels via realignment and read-based phasing. We demonstrate that indelPost enables accurate analysis of ambiguous data and can derive the correct complex indel alleles from the simple indel predictions provided by standard small variant detectors, with improved performance over a specialized tool for complex indel analysis. Availability indelPost is freely available at: https://github.com/stjude/indelPost. Supplementary information Supplementary data are available at Bioinformatics online.

Download Full-text