scholarly journals Structures and Functions of Viral 5′ Non-Coding Genomic RNA Domain-I in Group-B Enterovirus Infections

Viruses ◽  
2020 ◽  
Vol 12 (9) ◽  
pp. 919 ◽  
Author(s):  
Marie Glenet ◽  
Laetitia Heng ◽  
Domitille Callon ◽  
Anne-Laure Lebreil ◽  
Paul-Antoine Gretteau ◽  
...  
Keyword(s):  
Viral Replication ◽  
Secondary Structures ◽  
Genomic Rna ◽  
Coding Region ◽  
Entry Site ◽  
Rna Domains ◽  
Group B ◽  
Human Infections ◽  
Domain I

Group-B enteroviruses (EV-B) are ubiquitous naked single-stranded positive RNA viral pathogens that are responsible for common acute or persistent human infections. Their genome is composed in the 5′ end by a non-coding region, which is crucial for the initiation of the viral replication and translation processes. RNA domain-I secondary structures can interact with viral or cellular proteins to form viral ribonucleoprotein (RNP) complexes regulating viral genomic replication, whereas RNA domains-II to -VII (internal ribosome entry site, IRES) are known to interact with cellular ribosomal subunits to initiate the viral translation process. Natural 5′ terminally deleted viral forms lacking some genomic RNA domain-I secondary structures have been described in EV-B induced murine or human infections. Recent in vitro studies have evidenced that the loss of some viral RNP complexes in the RNA domain-I can modulate the viral replication and infectivity levels in EV-B infections. Moreover, the disruption of secondary structures of RNA domain-I could impair viral RNA sensing by RIG-I (Retinoic acid inducible gene I) or MDA5 (melanoma differentiation-associated protein 5) receptors, a way to overcome antiviral innate immune response. Overall, natural 5′ terminally deleted viral genomes resulting in the loss of various structures in the RNA domain-I could be major key players of host–cell interactions driving the development of acute or persistent EV-B infections.

scholarly journals Structures and Functions of Viral 5’ Non-Coding Genomic RNA Domain-I in Enterovirus-B Infections

2020 ◽  
Author(s):  
Marie GLENET ◽  
Laetitia HENG ◽  
Domitille CALLON ◽  
Anne-Laure LEBREIL ◽  
Paul-Antoine GRETTEAU ◽  
...  
Keyword(s):  
Viral Replication ◽  
Secondary Structures ◽  
Genomic Rna ◽  
Coding Region ◽  
Viral Genomes ◽  
Rna Domains ◽  
Group B ◽  
Human Infections ◽  
Domain I

Group-B enteroviruses (EV-B) are ubiquitous naked single-stranded positive RNA viral pathogens that are responsible for common acute or persistent human infections. Their genome is composed in the 5'end by a non-coding region, which is crucial for the initiation of the viral replication and translation processes. RNA domain-I secondary structures can interact with viral or cellular proteins to form viral ribonucleoprotein (RNP) complexes regulating viral genomic replication, whereas RNA domains-II to -VII (IRES) are known to interact with cellular ribosomal subunits to initiate the viral translation process. Natural 5’ terminally deleted viral forms lacking some genomic RNA domain-I secondary structures have been described in EV-B induced murine or human infections. Recent in vitro studies have evidenced that the loss of some viral RNP complexes in the RNA domain-I can modulate the viral replication and infectivity levels in EV-B infections. Moreover, the disruption of secondary structures of RNA domain-I could impair viral RNA sensing by RIG-I or MDA5 receptors, a way to overcome antiviral innate immune response. Overall, natural 5′ terminally deleted viral genomes resulting in the loss of various structures in the RNA domain-I could be major key players of host-cell interactions driving the development of acute or persistent EV-B infections.

scholarly journals Translation Initiation at the CUU Codon Is Mediated by the Internal Ribosome Entry Site of an Insect Picorna-Like Virus In Vitro

1999 ◽  
Vol 73 (2) ◽  
pp. 1219-1226 ◽  
Author(s):  
Jun Sasaki ◽  
Nobuhiko Nakashima
Keyword(s):  
Capsid Protein ◽  
Translation Initiation ◽  
Internal Ribosome Entry Site ◽  
Protein Gene ◽  
Initiation Codon ◽  
Coding Region ◽  
Entry Site ◽  
Capsid Protein Gene ◽  
Internal Ribosome Entry

ABSTRACT AUG-unrelated translation initiation was found in an insect picorna-like virus, Plautia stali intestine virus (PSIV). The positive-strand RNA genome of the virus contains two nonoverlapping open reading frames (ORFs). The capsid protein gene is located in the 3′-proximal ORF and lacks an AUG initiation codon. We examined the translation mechanism and the initiation codon of the capsid protein gene by using various dicistronic and monocistronic RNAs in vitro. The capsid protein gene was translated cap independently in the presence of the upstream cistron, indicating that the gene is translated by internal ribosome entry. Deletion analysis showed that the internal ribosome entry site (IRES) consisted of approximately 250 bases and that its 3′ boundary extended slightly into the capsid-coding region. The initiation codon for the IRES-mediated translation was identified as the CUU codon, which is located just upstream of the 5′ terminus of the capsid-coding region by site-directed mutagenesis. In vitro translation assays of monocistronic RNAs lacking the 5′ part of the IRES showed that this CUU codon was not recognized by scanning ribosomes. This suggests that the PSIV IRES can effectively direct translation initiation without stable codon-anticodon pairing between the initiation codon and the initiator methionyl-tRNA.

scholarly journals Roles of the 5′ Untranslated Region of Nonprimate Hepacivirus in Translation Initiation and Viral Replication

2018 ◽  
Vol 92 (7) ◽  
Author(s):  
Tomohisa Tanaka ◽  
Teruhime Otoguro ◽  
Atsuya Yamashita ◽  
Hirotake Kasai ◽  
Takasuke Fukuhara ◽  
...  
Keyword(s):  
Viral Replication ◽  
Internal Ribosome Entry Site ◽  
Untranslated Region ◽  
Rna Stability ◽  
Specific Region ◽  
Entry Site ◽  
Subgenomic Replicon ◽  
Independent Manner ◽  
Internal Ribosome Entry ◽  
Domain I

ABSTRACTThe 5′ untranslated region (UTR) of hepatitis C virus (HCV), which is composed of four domains (I, II, III, and IV) and a pseudoknot, is essential for translation and viral replication. Equine nonprimate hepacivirus (EHcV) harbors a 5′ UTR consisting of a large 5′-terminal domain (I); three additional domains (I′, II, and III), which are homologous to domains I, II, and III, respectively, of HCV; and a pseudoknot, in the order listed. In this study, we investigated the roles of the EHcV 5′ UTR in translation and viral replication. The internal ribosome entry site (IRES) activity of the EHcV 5′ UTR was lower than that of the HCV 5′ UTR in several cell lines due to structural differences in domain III. Domains I and III of EHcV were functional in the HCV 5′ UTR in terms of IRES activity and the replication of the subgenomic replicon (SGR), although domain II was not exchangeable between EHcV and HCV for SGR replication. Furthermore, the region spanning domains I and I′ of EHcV (the 5′-proximal EHcV-specific region) improved RNA stability and provided the HCV SGR with microRNA 122 (miR-122)-independent replication capability, while EHcV domain I alone improved SGR replication and RNA stability irrespective of miR-122. These data suggest that the region spanning EHcV domains I and I′ improves RNA stability and viral replication regardless of miR-122 expression. The 5′-proximal EHcV-specific region may represent an inherent mechanism to facilitate viral replication in nonhepatic tissues.IMPORTANCEEHcV is the closest viral homolog to HCV among other hepaciviruses. HCV exhibits a narrow host range and liver-specific tropism, while epidemiological reports suggest that EHcV infects the liver and respiratory organs in horses, donkeys, and dogs. However, the mechanism explaining the differences in host or organ tropism between HCV and EHcV is unknown. In this study, our data suggest that the 5′ untranslated region (UTR) of EHcV is composed of an internal ribosome entry site (IRES) element that is functionally exchangeable with HCV IRES elements. Furthermore, the 5′-proximal EHcV-specific region enhances viral replication and RNA stability in a miR-122-independent manner. Our data suggest that the region upstream of domain II in the EHcV 5′ UTR contributes to the differences in tissue tropism observed between these hepaciviruses.

Lentiviral RNAs can use different mechanisms for translation initiation

2008 ◽  
Vol 36 (4) ◽  
pp. 690-693 ◽  
Author(s):  
Emiliano P. Ricci ◽  
Ricardo Soto Rifo ◽  
Cécile H. Herbreteau ◽  
Didier Decimo ◽  
Théophile Ohlmann
Keyword(s):  
Genomic Rna ◽  
Coding Region ◽  
Entry Site ◽  
Rna Motifs ◽  
Internal Ribosome Entry ◽  
Gag Polyprotein ◽  
Immunodeficiency Virus ◽  
Reticulocyte Lysate ◽  
Hiv 1 ◽  
Dependent Mechanism

The full-length genomic RNA of lentiviruses can be translated to produce proteins and incorporated as genomic RNA in the viral particle. Interestingly, both functions are driven by the genomic 5′-UTR (5′-untranslated region), which harbours structural RNA motifs for the replication cycle of the virus. Recent work has shown that this RNA architecture also functions as an IRES (internal ribosome entry site) in HIV-1 and -2, and in SIV (simian immunodeficiency virus). In addition, the IRES extends to the gag coding region for all these viruses and this leads to the synthesis of shorter isoforms of the Gag polyprotein from downstream initiation codons. In the present study, we have investigated how different members of the lentivirus family (namely HIV-1 and -2, and SIV) can initiate protein synthesis by distinct mechanisms. For this, we have used the competitive reticulocyte lysate that we have recently described. Our results show that HIV-1 is able to drive the synthesis of the Gag polyprotein both by a classical cap-dependent mechanism and an IRES, whereas HIV-2 and SIV appear to use exclusively an IRES mechanism.

scholarly journals Genomic-Scale Interaction Involving Complementary Sequences in the Hepatitis C Virus 5′UTR Domain IIa and the RNA-Dependent RNA Polymerase Coding Region Promotes Efficient Virus Replication

Viruses ◽  
2018 ◽  
Vol 11 (1) ◽  
pp. 17 ◽  
Author(s):  
Elodie Rance ◽  
Jerome Tanner ◽  
Caroline Alfieri
Keyword(s):  
Hepatitis C Virus ◽  
Hepatitis C ◽  
Virus Replication ◽  
Progeny Virus ◽  
Hcv Rna ◽  
Genomic Rna ◽  
Coding Region ◽  
Rna Dependent Rna Polymerase ◽  
High Affinity

The hepatitis C virus (HCV) genome contains structured elements thought to play important regulatory roles in viral RNA translation and replication processes. We used in vitro RNA binding assays to map interactions involving the HCV 5′UTR and distal sequences in NS5B to examine their impact on viral RNA replication. The data revealed that 5′UTR nucleotides (nt) 95–110 in the internal ribosome entry site (IRES) domain IIa and matching nt sequence 8528–8543 located in the RNA-dependent RNA polymerase coding region NS5B, form a high-affinity RNA-RNA complex in vitro. This duplex is composed of both wobble and Watson-Crick base-pairings, with the latter shown to be essential to the formation of the high-affinity duplex. HCV genomic RNA constructs containing mutations in domain IIa nt 95–110 or within the genomic RNA location comprising nt 8528–8543 displayed, on average, 5-fold less intracellular HCV RNA and 6-fold less infectious progeny virus. HCV genomic constructs containing complementary mutations for IRES domain IIa nt 95–110 and NS5B nt 8528–8543 restored intracellular HCV RNA and progeny virus titers to levels obtained for parental virus RNA. We conclude that this long-range duplex interaction between the IRES domain IIa and NS5B nt 8528–8543 is essential for optimal virus replication.

scholarly journals Singapore grouper iridovirus-encoded semaphorin homologue (SGIV-sema) contributes to viral replication, cytoskeleton reorganization and inhibition of cellular immune responses

2014 ◽  
Vol 95 (5) ◽  
pp. 1144-1155 ◽  
Author(s):  
Yang Yan ◽  
Huachun Cui ◽  
Chuanyu Guo ◽  
Jingguang Wei ◽  
Youhua Huang ◽  
...  
Keyword(s):  
Immune Responses ◽  
Viral Replication ◽  
Host Cells ◽  
Early Gene ◽  
Coding Region ◽  
Cytoskeletal Structure ◽  
Wide Range ◽  
Fish Cells ◽  
Cellular Immune

Semaphorins are a large, phylogenetically conserved family of proteins that are involved in a wide range of biological processes including axonal steering, organogenesis, neoplastic transformation, as well as immune responses. In this study, a novel semaphorin homologue gene belonging to the Singapore grouper iridovirus (SGIV), ORF155R (termed SGIV-sema), was cloned and characterized. The coding region of SGIV-sema is 1728 bp in length, encoding a predicted protein with 575 aa. SGIV-sema contains a ~370 aa N-terminal Sema domain, a conserved plexin-semaphorin-integrin (PSI) domain, and an immunoglobulin (Ig)-like domain near the C terminus. SGIV-sema is an early gene product during viral infection and predominantly distributed in the cytoplasm with a speckled and clubbed pattern of appearance. Functionally, SGIV-sema could promote viral replication during SGIV infection in vitro, with no effect on the proliferation of host cells. Intriguingly, ectopically expressed SGIV-sema could alter the cytoskeletal structure of fish cells, characterized by a circumferential ring of microtubules near the nucleus and a disrupted microfilament organization. Furthermore, SGIV-sema was able to attenuate the cellular immune response, as demonstrated by decreased expression of inflammation/immune-related genes such as IL-8, IL-15, TNF-α and mediator of IRF3 activation (MITA), in SGIV-sema-expressing cells before and after SGIV infection. Ultimately, our study identified a novel, functional SGIV gene that could regulate cytoskeletal structure, immune responses and facilitate viral replication.

scholarly journals Construction and In Vitro Properties of a Series of Attenuated Simian Immunodeficiency Viruses with All Accessory Genes Deleted

2001 ◽  
Vol 75 (9) ◽  
pp. 4056-4067 ◽  
Author(s):  
Yongjun Guan ◽  
James B. Whitney ◽  
Mervi Detorio ◽  
Mark A. Wainberg
Keyword(s):  
Rhesus Macaques ◽  
Wild Type Virus ◽  
Replication Capacity ◽  
Regulation System ◽  
Genomic Rna ◽  
Entry Site ◽  
Cmv Promoter ◽  
Accessory Genes

ABSTRACT We have generated simplified simian immunodeficiency virus (SIV) constructs lacking the nef, vpr,vpx, vif, tat, and revgenes (Δ6 viruses). To accomplish this, we began with an infectious molecular clone of SIV, i.e. SIVmac239, and replaced the deleted segments with three alternate elements: (i) a constitutive transport element (CTE) derived from simian retrovirus type 1 to replace the Rev/Rev-responsive element (RRE) posttranscriptional regulation system, (ii) a chimeric SIV long terminal repeat (LTR) containing a cytomegalovirus (CMV) promoter to augment transcription and virus production, and (iii) an internal ribosome entry site (IRES) upstream of the env gene to ensure expression of envelope proteins. This simplified construct (Δ6CCI) efficiently produced all viral structural proteins, and mature virions possessed morphology typical of wild-type virus. It was also observed that deletion of the six accessory genes dramatically affected both the specificity and efficiency of packaging of SIV genomic RNA into virions. However, the presence of both the CTE and the chimeric CMV promoter increased the specificity of viral genomic RNA packaging, while the presence of the IRES augmented packaging efficiency. The Δ6CCI virus was extremely attenuated in replication capacity yet retained infectiousness for CEMx174 and MT4 cells. We also generated constructs that retained either the rev gene or both the rev andvif genes and showed that these viruses, when complemented by the CMV promoter, i.e., Δ5-CMV and Δ4-CMV, were able to replicate in MT4 cells with moderate and high-level efficiency, respectively. Long-term culture of each of these constructs over 6 months revealed no potential for reversion. We hope to shortly evaluate these simplified constructs in rhesus macaques to determine their long-term safety as well as ability to induce protective immune responsiveness as proviral DNA vaccines.

scholarly journals Interaction of Cellular Proteins with the 5′ End of Norwalk Virus Genomic RNA

2000 ◽  
Vol 74 (18) ◽  
pp. 8558-8562 ◽  
Author(s):  
Ana Lorena Gutiérrez-Escolano ◽  
Zamirath Uribe Brito ◽  
Rosa M. del Angel ◽  
Xi Jiang
Keyword(s):  
Internal Ribosomal Entry Site ◽  
Cellular Proteins ◽  
Norwalk Virus ◽  
Genomic Rna ◽  
Entry Site ◽  
Mobility Shift ◽  
Stem Loop ◽  
Molecular Weights ◽  
Cell Extracts

ABSTRACT The lack of a susceptible cell line and an animal model for Norwalk virus (NV) infection has prompted the development of alternative strategies to generate in vitro RNAs that approximate the authentic viral genome. This approach has allowed the study of viral RNA replication and gene expression. In this study, using mobility shift and cross-linking assays, we detected several cellular proteins from HeLa and CaCo-2 cell extracts that bind to, and form stable complexes with, the first 110 nucleotides of the 5′ end of NV genomic RNA, a region previously predicted to form a double stem-loop structure. These proteins had molecular weights similar to those of the HeLa cellular proteins that bind to the internal ribosomal entry site of poliovirus RNA. HeLa proteins La, PCBP-2, and PTB, which are important for poliovirus translation, and hnRNP L, which is possibly implicated in hepatitis C virus translation, interact with NV RNA. These protein-RNA interactions are likely to play a role in NV translation and/or replication.

scholarly journals Identification of Cryptic Putative IRESs Initiating the Translation of Nonstructural Proteins Encoded by the HRV16 Genome

2021 ◽  
Author(s):  
Bingtian Shi ◽  
Qinqin Song ◽  
Xiaonuan Luo ◽  
Juan Song ◽  
Dong Xia ◽  
...  
Keyword(s):  
Fluorescent Protein ◽  
Ribosome Profiling ◽  
Raw Material ◽  
Alternative Mechanism ◽  
Nonstructural Proteins ◽  
Coding Region ◽  
Entry Site ◽  
Initiation Of Translation ◽  
Eukaryotic Mrnas

Abstract Cap-dependent initiation of translation is a canonical mechanism adopted by eukaryotic cells. Internal ribosome entry site (IRES)-dependent translation is a mechanism distinct from 5′ cap-dependent translation. IRES elements are located mainly in the 5′-untranslated regions (UTRs) of viral and eukaryotic mRNAs. In addition, IRESs are found in the coding regions of some viral and eukaryotic genomes and initiate the translation of some functional truncated isoforms. Here, via IRES-initiated expression of proteins, bicistronic vectors and ribosome profiling of the human rhinovirus 16 (HRV16), we found that the coding region of the nonstructural proteins P2 and P3 contained 5 putative IRES elements. These 5 putative IRESs were located within nucleotides 4286-4585, 5002-5126, 6245-6394, 6619-6718 and 6629-6778 and initiated green fluorescent protein (GFP) expression in vitro. This alternative mechanism might be effective and economical for eliminating the time and raw material required to synthesize the full-length polyprotein.

scholarly journals The different pathways of HIV genomic RNA translation

2010 ◽  
Vol 38 (6) ◽  
pp. 1548-1552 ◽  
Author(s):  
Nathalie Chamond ◽  
Nicolas Locker ◽  
Bruno Sargueil
Keyword(s):  
Rna Structure ◽  
Genomic Rna ◽  
Coding Region ◽  
Structural Determinants ◽  
Initiation Complex ◽  
Internal Ribosome Entry ◽  
Genomic Rnas ◽  
Initiation Factors ◽  
Rna Domains ◽  
And Function

Lentiviruses, the prototype of which is HIV-1, can initiate translation either by the classical cap-dependent mechanism or by internal recruitment of the ribosome through RNA domains called IRESs (internal ribosome entry sites). Depending on the virus considered, the mechanism of IRES-dependent translation differs widely. It can occur by direct binding of the 40S subunit to the mRNA, necessitating a subset or most of the canonical initiation factors and/or ITAF (IRES trans-acting factors). Nonetheless, a common feature of IRESs is that ribosomal recruitment relies, at least in part, on IRES structural determinants. Lentiviral genomic RNAs present an additional level of complexity, as, in addition to the 5′-UTR (untranslated region) IRES, the presence of a new type of IRES, embedded within Gag coding region was described recently. This IRES, conserved in all three lentiviruses examined, presents conserved structural motifs that are crucial for its activity, thus reinforcing the link between RNA structure and function. However, there are still important gaps in our understanding of the molecular mechanism underlying IRES-dependent translation initiation of HIV, including the determination of the initiation factors required, the dynamics of initiation complex assembly and the dynamics of the RNA structure during initiation complex formation. Finally, the ability of HIV genomic RNA to initiate translation through different pathways questions the possible mechanisms of regulation and their correlation to the viral paradigm, i.e. translation versus encapsidation of its genomic RNA.

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