Structures and Functions of the 3′ Untranslated Regions of Positive-Sense Single-Stranded RNA Viruses Infecting Humans and Animals

Liu, Yuanzhi; Wang, Mingshu; Cheng, Anchun; Yang, Qiao; Wu, Ying; Jia, Renyong; Liu, Mafeng; Zhu, Dekang; Chen, Shun; Zhang, Shaqiu; Zhao, Xinxin; Huang, Juan; Mao, Sai; Ou, Xumin; Gao, Qun; Wang, Yin; Xu, Zhiwen; Chen, Zhengli; Zhu, Ling; Luo, Qihui; Liu, Yunya; Yu, Yanling; Zhang, Ling; Tian, Bin; Pan, Leichang; Chen, Xiaoyue

doi:10.3389/fcimb.2020.00453

Cited by 25 publications

(17 citation statements)

References 172 publications

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“…After ducklings are infected with DHAV-1, the main pathological changes are in the liver, and the extremely scattered infection also occurs in the kidneys [ 14 , 15 ]. Like other positive-sense single-stranded RNA viruses, its genome consists of a 5′ untranslated region (5′ UTR), an open reading frame (ORF), and a 3′ untranslated region (3′ UTR) [ 16 ]. The ORF is first translated into precursor polyprotein, which will be cleaved into structural protein and non-structural protein by viral protease 3C or 3CD.…”

Section: Introductionmentioning

confidence: 99%

Duck hepatitis A virus type 1 mediates cell cycle arrest in the S phase

Liu

Wang

et al. 2022

Virol J

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Background Duck hepatitis A virus type 1 (DHAV-1) is one of the most serious pathogens endangering the duck industry. However, there are few studies on the regulation of the cell cycle by DHAV-1. Methods In this study, flow cytometry was applied to analyze the effect of DHAV-1 infection on the cell cycle of duck embryo fibroblasts (DEFs). Subsequently, we analyzed the effects of cell cycle phases on DHAV-1 replication by real-time reverse transcriptase quantitative PCR (real-time RT-qPCR). Results Flow cytometry data analysis found that DEFs in the S phase increased by 25.85% and 54.21% at 24 h and 48 h after DHAV-1 infection, respectively. The levels of viral RNA detected by real-time RT-qPCR were higher in the DEFs with synchronization in the S phase or G0/G1 phase than in the control group. However, there was no difference in viral copy number between the G2/M phase arrest and control groups. In addition, non-structural protein 3D of DHAV-1 significantly increased cells in the S phase, indicating that 3D protein is one of the reasons for the cell cycle arrest in the S phase. Conclusions In summary, DHAV-1 infection induces the cell cycle arrest of DEFs in the S phase. Both S phase and G0/G1 phase synchronization facilitate the replication of DHAV-1, and 3D protein is one of the reasons for the S phase arrest.

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Section: Introductionmentioning

confidence: 99%

Duck hepatitis A virus type 1 mediates cell cycle arrest in the S phase

Liu

Wang

et al. 2022

Virol J

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“…In SvRSV isolates, these regions were more similar (98% nt sequence identity) than in LigLV and LigCSV (83–88% nt sequence identity). When the 3′-termini of the cileviruses CiLV-C, CiLV-C2, and PfGSV were included in the alignment, the presence of highly conserved nucleotide sequences in all these viruses became evident, likely denoting the putative functional role of these sequences as described in other viruses ( Dreher, 1999 ; Liu et al, 2020 ; Rasekhian et al, 2021 ). The implementation of the UTR-backed iterative BLASTN approach ( Zhang et al, 2022 ) using the 3′-terminus conserved nucleotide sequences of SvRSV, LigCSV, and LigLV, resulted in the recovery of contigs corresponding to the RNA1 and RNA2 segments already known, and new putative genomic segments were not identified.…”

Section: Resultsmentioning

confidence: 98%

A Novel Lineage of Cile-Like Viruses Discloses the Phylogenetic Continuum Across the Family Kitaviridae

et al. 2022

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An increasing number of plant species have been recognized or considered likely reservoirs of viruses transmitted by Brevipalpus mites. A tiny fraction of these viruses, primarily those causing severe economic burden to prominent crops, have been fully characterized. In this study, based on high-throughput sequencing, transmission electron microscopy analyses of virions in plant-infected tissues, viral transmission experiments, and the morphoanatomical identification of the involved Brevipalpus mites, we describe molecular and biological features of viruses representing three new tentative species of the family Kitaviridae. The genomes of Solanum violifolium ringspot virus (SvRSV, previously partially characterized), Ligustrum chlorotic spot virus (LigCSV), and Ligustrum leprosis virus (LigLV) have five open reading frames (ORFs) > 500 nts, two distributed in RNA1 and three in RNA2. RNA1 of these three viruses display the same genomic organization found in RNA1 of typical cileviruses, while their RNA2 are shorter, possessing only orthologs of genes p61, p32, and p24. LigCSV and LigLV are more closely related to each other than to SvRSV, but the identities between their genomic RNAs were lower than 70%. In gene-by-gene comparisons, ORFs from LigCSV and LigLV had the highest sequence identity values (nt sequences: 70–76% and deduced amino acid sequences: 74–83%). The next higher identity values were with ORFs from typical cileviruses, with values below 66%. Virions of LigLV (≈ 40 nm × 55 nm) and LigCSV (≈ 54 nm × 66 nm) appear almost spherical, contrasting with the bacilliform shape of SvRSV virions (≈ 47 nm × 101 nm). Mites collected from the virus-infected plants were identified as Brevipalpus papayensis, B. tucuman, and B. obovatus. Viruliferous B. papayensis mites successfully transmitted LigCSV to Arabidopsis thaliana. SvRSV, LigCSV, and LigLV seem to represent novel sub-lineages of kitaviruses that descent on parallel evolutionary branches from a common ancestor shared with the tentative cile-like virus hibiscus yellow blotch virus and typical cileviruses. Biological and molecular data, notably, the phylogenetic reconstruction based on the RdRp proteins in which strong support for monophyly of the family Kitaviridae is observed, mark an advance in the understanding of kitavirids.

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“…While the 5" UTR contains elements that regulate the efficiency and timing of translation initiation and viral replication, host factors binding to the 3" UTR can be critical to many aspects of the life cycle of a virus, including but not limited to RNA replication and stability. Host RBPs also mediate 5" UTR -3" UTR interactions, resulting in "circularization" of the viral genome 14,15 .…”

Section: Non-coding Regions In Viral Genomes Show Distinct Patterns Of Enrichmentmentioning

confidence: 99%

Investigating the human host - ssRNA virus interaction landscape using the SMEAGOL toolbox

A¹,

Ferrarini

Gruber

2021

Preprint

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Viruses are intracellular parasites that need their host cell to reproduce. Consequently, they have evolved numerous mechanisms to exploit the molecular machinery of their host cells, including the broad spectrum of host RNA-binding proteins (RBPs). However, the RBP interactome of viral genomes and the consequences of these interactions for infection are still to be mapped for most RNA viruses. To facilitate these efforts we have developed SMEAGOL, a fast and user-friendly toolbox to analyze the enrichment or depletion of RBP binding motifs across RNA sequences (https://github.com/gruber-sciencelab/SMEAGOL). To shed light on the interaction landscape of RNA viruses with human host cell RBPs at a large scale, we applied SMEAGOL to 197 single-stranded RNA (ssRNA) viral genome sequences. We find that the majority of ssRNA virus genomes are significantly enriched or depleted in binding motifs for human RBPs, suggesting selection pressure on these interactions. Our analysis provides an overview of potential virus - RBP interactions, covering the majority of ssRNA viral genomes fully sequenced to date, and represents a rich resource for studying host interactions vital to the virulence of ssRNA viruses. Our resource and the SMEAGOL toolbox will support future studies of virus / host interactions, ultimately feeding into better treatments.

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Structures and Functions of the 3′ Untranslated Regions of Positive-Sense Single-Stranded RNA Viruses Infecting Humans and Animals

Cited by 25 publications

References 172 publications

Duck hepatitis A virus type 1 mediates cell cycle arrest in the S phase

Duck hepatitis A virus type 1 mediates cell cycle arrest in the S phase

A Novel Lineage of Cile-Like Viruses Discloses the Phylogenetic Continuum Across the Family Kitaviridae

Investigating the human host - ssRNA virus interaction landscape using the SMEAGOL toolbox

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