Manel Ben M’hadheb-Gharbi

Role of GNRA Motif Mutations within Stem-Loop V of Internal Ribosome Entry Segment in Coxsackievirus B3 Molecular Attenuation

The lengthy 5′ nontranslated region of coxsackievirus B3 (CVB3) forms a highly ordered secondary structure containing an internal ribosome entry segment (IRES), which plays an important role in controlling viral translation and pathogenesis. The stem-loop V (SL-V) of this IRES contains a large lateral bulge loop which encompasses two conserved GNRA motifs. In this study, we analyzed the effects of point mutations within the GNRA motifs of the CVB3 IRES. We characterized in vitro virus production and translation efficiency and we tested in vivo virulence of two CVB3 mutants produced by site-directed mutagenesis. The GNAA1 and GNAA2 RNAs displayed decreased translation initiation efficiency when translated in rabbit reticulocyte lysates. This translation defect was correlated with reduced yields of infectious virus particles in HeLa cells in comparison with the wild type.When inoculated orally into Swiss mice, both mutant viruses were avirulent and caused neither inflammation nor necrosis in hearts. These results highlight the important role of the GNRA motifs within the SL-V of the IRES of CVB3, in directing translation initiation.

Prolonged viral RNA detection in the central nervous system of one-week-old Swiss albino mice following coxsackievirus B4 and echovirus 9 infection.

Objectives: Type B coxsackieviruses (CV-B), together with echoviruses (E), are among the most common pathogens encountered in aseptic meningitis and meningoencephalitis. They frequently infect the central nervous system (CNS). The mechanisms of virus spreading in the CNS are poorly understood. In the present study, we investigated CV-B4 and E-9 spreading and neurotropism within intraperitoneally inoculated one-week-old Swiss albino mice. Methods: Seminested RT-PCR and virus isolation were used to assay viral distribution. Results: Viral RNA was present in various organs: brain, spinal cord, spleen and heart at various times post-infection (p.i.); ranging from 1 day p.i. up to 30, 60 and 90 days p.i, respectively, for CV-B4-JVB-, E-9 Barty- and CV-B4-E2-infected mice. Organs became negative for virus isolation after 5 days p.i., except for brain and heart from CV-B4 E2-infected mice, which remained positive for up to 10 and 15 days p.i., respectively. Negative viral RNA strand was detected mainly in brain and spinal cord of infected mice until 30 and 60 days p.i. Conclusion: This is the first report on the persistence of CV-B4 and E-9 in the CNS of intraperitoneally inoculated mice.

Cellular Proteins Act as Bridge Between 5′ and 3′ Ends of the Coxsackievirus B3 Mediating Genome Circularization During RNA Translation

The positive single-stranded RNA genome of the Coxsackievirus B3 (CVB3) contains a 5′ untranslated region (UTR) which hosts the internal ribosome entry site (IRES) element that governs cap-independent translation initiation and a polyadenylated 3′ UTR which is required for stimulating the IRES activity. Viral RNA genomes could circularize to regulate initiation of translation and RNA synthesis at 5′ and 3′ ends. Interactions could either take place by direct RNA–RNA contacts, through cellular protein bridges mediating RNA circularization or both. Accordingly, we aimed to assess the nature of molecular interactions between these two regions and to evaluate cellular factors required for mRNA 3′ end-mediated stimulation of CVB3 IRES-driven translation. By gel shift assays, we have showed that combining, in vitro, 5′ and 3′ UTR fragments had no discernible effect on the structures of RNAs, arguing against the presence of specific canonical RNA–RNA cyclization sequences between these two regions. Competitive UV crosslinking assays using BHK-21 cell extract showed common cellular proteins eIF3b, PTB, and La binding to both 5′- and 3′ end RNAs. PCBP 1–2 and PABP were shown to bind, respectively, to 5′ and 3′ UTR probes. Taking together, these data suggest that CVB3 5′–3′ end bridging occurs through 5′ UTR–protein–protein–3′ UTR interactions and not through RNA–RNA direct contact. The dual involvement of the 3′ and 5′ UTRs in controlling viral translation and RNA synthesis highlights the relevance of these regions in the infectious virus life cycle, making them suitable candidates for targeted CVB3 antiviral therapy.

Impaired binding of standard initiation factors eIF3b, eIF4G and eIF4B to domain V of the live-attenuated coxsackievirus B3 Sabin3-like IRES - alternatives for 5′UTR-related cardiovirulence mechanisms

AbstractInternal ribosome entry site (IRES) elements fold into highly organized conserved secondary and probably tertiary structures that guide the ribosome to an internal site of the RNA at the IRES 3′end. The composition of the cellular proteome is under the control of multiple processes, one of the most important being translation initiation. In each poliovirus Sabin vaccine strain, a single point mutation in the IRES secondary-structure domain V is a major determinant of neurovirulence and translation attenuation. Here we are extrapolating poliovirus findings to a genomic related virus named coxsackievirus B3 CVB3); a causative agent of viral myocarditis. We have previously reported that Sabin3-like mutation (U473 → C) introduced in the domain V sequence of the CVB3 IRES led to a defective mutant with a serious reduction in translation efficiency and ribosomal initiation complex assembly, besides an impaired RNA-protein binding pattern. With the aim to identify proteins interacting with both CVB3 wild-type and Sabin3-like domain V RNAs and to assess the effect of the Sabin3-like mutation on these potential interactions, we have used a proteomic approach. This procedure allowed the identification of three RNA-binding proteins interacting with the domain V: eIF4G (p220), eIF3b (p116) and eIF4B (p80). Moreover, we report that this single-nucleotide exchange impairs the interaction pattern and the binding affinity of these standard translation initiation factors within the IRES domain V of the mutant strain. Taken together, these data indicate how this decisive Sabin3-like mutation mediates viral translation attenuation; playing a key role in the understanding of the cardiovirulence attenuation within this construct. Hence, these data provide further evidence for the crucial role of RNA structure for the IRES activity, and reinforce the idea of a distribution of function between the different IRES structural domains.Virtual slideThe virtual slide(s) for this article can be found here: http://www.diagnosticpathology.diagnomx.eu/vs/6160165131045880.

Role of RNA Structure Motifs in IRES-Dependent Translation Initiation of the Coxsackievirus B3: New Insights for Developing Live-Attenuated Strains for Vaccines and Gene Therapy

Internal ribosome entry site (IRES) elements are highly structured RNA sequences that function to recruit ribosomes for the initiation of translation. In contrast to the canonical cap-binding, the mechanism of IRES-mediated translation initiation is still poorly understood. Translation initiation of the coxsackievirus B3 (CVB3), a causative agent of viral myocarditis, has been shown to be mediated by a highly ordered structure of the 5′ untranslated region (5′UTR), which harbors an IRES. Taking into account that efficient initiation of mRNA translation depends on temporally and spatially orchestrated sequence of RNA–protein and RNA–RNA interactions, and that, at present, little is known about these interactions, we aimed to describe recent advances in our understanding of molecular structures and biochemical functions of the translation initiation process. Thus, this review will explore the IRES elements as important RNA structures and the significance of these structures in providing an alternative mechanism of translation initiation of the CVB3 RNA. Since translation initiation is the first intracellular step during the CVB3 infection cycle, the IRES region provides an ideal target for antiviral therapies. Interestingly, the 5′ and 3′UTRs represent promising candidates for the study of CVB3 cardiovirulence and provide new insights for developing live-attenuated vaccines.

Nucleic acid-based biotechnologies for food-borne pathogen detection using routine time-intensive culture-based methods and fast molecular diagnostics

Diseases caused by food-borne pathogens constitute a major burden to consumers, food business operators, and national governments. Bacterial and viral pathogens are the major biotic factors influencing food safety. A vast array of culture dependent analytical methods and protocols have been developed. Recently, nucleic acid-based methods have begun to replace or complement culture-based methods for routine use in food control laboratories. Basic advantages provided by nucleic acid-based technologies are faster speed and more information, such as sub-species identification, antibiotic resistance, and food microbiology. In particular, PCR and alternative methods have been developed to a stage that provides good speed, sensitivity, specificity, and reproducibility with minimized risk of carryover contamination. This review briefly summarizes currently available and developing molecular technologies that may be candidates for involvement in microbiological molecular diagnostic methods in the next decade.

Inoculation of the attenuated Coxsackievirus B3 Sabin3-like strain induces a protection against virulent CVB3 Nancy and CVB4 E2 strains in Swiss mice by both oral and intraperitoneal routes

We have previously addressed the question of whether the attenuating mutations of domain V of the Poliovirus IRES were specific for a given genomic context or whether they could be extrapolated to a genomic related virus, the Coxsackievirus B3 (CVB3). Accordingly, we have described that Sabin3-like mutation (U473→C) introduced in the CVB3 genome led to a defective mutant with a serious reduction in translation efficiency. In this study, we assessed the protection provided by the Sabin3-like mutant against CVB3 infection. For this purpose, we analyzed, in vivo, the Sabin3-like phenotype in Swiss mice inoculated with CVB3 and CVB4 E2 prototype strains either by oral or intraperitoneal (i.p) routes and explored the capacity of this mutant to act as a vaccine vector after the challenge. The Sabin3-like RNA was detected by semi-nested PCR in different organs: heart, pancreas and intestine at 10 days post-inoculation with both oral and i.p routes. Additionally, we did not observe any histological alterations in heart and intestine tissues. RNA was detected in the different organs of all mice immunized with the Sabin3-like strain and challenged with either CVB3 or CVB4 E2 by oral route at 7 days post-challenge. In contrast, no histological alteration of heart or pancreas tissues was observed after challenge with both wild-strains. Interestingly, the detection of viral RNA in heart, pancreas and intestine of mice immunized by i.p route was negative at 7 days post-challenge with CVB3 and CVB4 E2, and mice were protected from myocarditis and pancreatitis.