The Genomic 3′ UTR of Flaviviruses Is a Translation Initiation Enhancer

Abstract

Viruses rely on the cellular machinery of host cells to synthesize their proteins, and have developed different mechanisms enabling them to compete with cellular mRNAs for access to it. The genus Flavivirus is a large group of positive, single-stranded RNA viruses that includes several important human pathogens, such as West Nile, Dengue and Zika virus. The genome of flaviviruses bears a type 1 cap structure at its 5′ end, needed for the main translation initiation mechanism. Several members of the genus also use a cap-independent translation mechanism. The present work provides evidence that the WNV 5′ end also promotes a cap-independent translation initiation mechanism in mammalian and insect cells, reinforcing the hypothesis that this might be a general strategy of flaviviruses. In agreement with previous reports, we show that this mechanism depends on the presence of the viral genomic 3′ UTR. The results also show that the 3′ UTR of the WNV genome enhances translation of the cap-dependent mechanism. Interestingly, WNV 3′ UTR can be replaced by the 3′ UTR of other flaviviruses and the translation enhancing effect is maintained, suggesting a molecular mechanism that does not involve direct RNA-RNA interactions to be at work. In addition, the deletion of specific structural elements of the WNV 3′ UTR leads to increased cap-dependent and cap-independent translation. These findings suggest the 3′ UTR to be involved in a fine-tuned translation regulation mechanism.

Interactions of host miRNAs in the flavivirus 3´UTR genome: From bioinformatics predictions to practical approaches

“…The 3’UTR of flaviviruses replaced the poly(A) tail present in other viral and cellular mRNAs ( Holden and Harris, 2004 ). It is important for viral translation and replication ( Koraka et al., 2009 ; Wei et al., 2009 ; Berzal-Herranz et al., 2022 ) and is also associated with virulence ( Koraka et al., 2009 ; Thaisonthi et al., 2013 ). This region is the target of several cellular proteins, such as translation elongation factor 1α (EF-1α); polypyrimidine tract binding protein (PTB); autoantigen La; p100; RNA binding motif protein, X-linked (RBMX); and insulin like growth factor 2 mRNA-binding protein 1 (IF2B1) ( De Nova-Ocampo et al., 2002 ; García-Montalvo et al., 2004 ; Lei et al., 2011 ).…”

“…These SL structures are conserved among flaviviruses and are responsible for the inhibition of the activity of Xrn-1 nuclease, an important process for the generation of sfRNAs, which participate in the antiviral evasion mechanisms in both mammals and mosquitoes ( Funk et al., 2010 ; Villordo et al., 2015 ; Göertz et al., 2016 ; Chen et al., 2018 ; Bellone et al., 2020 ), including viral adaptation, fitness, virulence, and tissue tropism ( Funk et al., 2010 ; Liu et al., 2018 ; Finol and Ooi, 2019 ; Sparks et al., 2020 ). In WNV, the SL-III has an inhibitory effect on translation since its deletion increase viral translation efficiency ( Berzal-Herranz et al., 2022 ). In ZIKV, the SLI element has a putative binding site for the Msi protein, and the interaction of this protein with the viral genome has been proposed to inhibit viral translation and to promote the accumulation of the viral genome that is degraded by the Xrn-1 nuclease to generate more sfRNAs ( Schneider and Wolfinger, 2019 ).…”

“…In ZIKV, there is a putative binding site for the Msi protein ( Schneider and Wolfinger, 2019 ). DB1 and its pseudoknot in WNV ( Berzal-Herranz et al., 2022 ) and DB2 in duck Tembusu virus (DTMUV) ( Wang et al., 2020 ) are particularly important in viral translation. In JEV, mutations in DB1 promote viral replication in BHK-21 cells but reduce the neuroinvasiveness and neuropathogenicity of the virus ( Xing et al., 2021 ).…”

Inter- and Intramolecular RNA–RNA Interactions Modulate the Regulation of Translation Mediated by the 3′ UTR in West Nile Virus

“…Evidence exists that specific RNA elements in the 3′ UTR help regulate essential viral processes, including translation, replication and infectivity [ 5 , 6 , 7 ], as well as the transitions between them. During early infection, the viral genome is used as mRNA to initiate viral protein synthesis at the capped 5′ UTR.…”

“…During early infection, the viral genome is used as mRNA to initiate viral protein synthesis at the capped 5′ UTR. The efficiency of translation depends on structural elements located in the 3′ UTR [ 7 , 8 , 9 ], although the molecular mechanism underlying this remains unknown. Among others, these elements include SL-III, the so-called 5′ dumbbell (5′DB) and the CS1 sequence.…”