Molecular Archaeology of Flaviviridae Untranslated Regions: Duplicated RNA Structures in the Replication Enhancer of Flaviviruses and Pestiviruses Emerged via Convergent Evolution

Gritsun, Dmitri J.; Jones, Ian M.; Gould, Ernest A.; Грицун, Т.С.

doi:10.1371/journal.pone.0092056

Cited by 41 publications

(54 citation statements)

References 61 publications

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“…1A) and correlates well with a previously proposed structure (Gritsun et al, 2014). The TBEV 3′NCR consists of two distinct regions: the 5′-end, named the “variable” region that varies in length and sequence among various tick-borne flaviviruses and within their strains, and the 3′-terminal “core” region (∼340 nts at the extreme 3′ end), which contains several elements essential for viral replication (Gritsun et al, 1997; Wallner et al, 1995).…”

Section: Results and Disscussionsupporting

confidence: 88%

MicroRNA-based control of tick-borne flavivirus neuropathogenesis: Challenges and perspectives

et al. 2016

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In recent years, microRNA-targeting has become an effective strategy for selective control of tissue-tropism and pathogenicity of both DNA and RNA viruses. Previously, we reported the successful application of this strategy to control the neurovirulent phenotype of a model chimeric tick-borne encephalitis/dengue type 4 virus (TBEV/DEN4), containing the structural protein genes of a highly virulent TBEV in the genetic backbone of non-neuroinvasive DEN4 virus. In the present study, we investigated the suitability of this approach for the attenuation of the more neurovirulent chimeric virus (TBEV/LGTV), which is based on the genetic backbone of the naturally attenuated member of the TBEV serocomplex, a Langat virus (LGTV). Unlike the TBEV/DEN4, the TBEV/LGTV virus retained the ability of its parental viruses to spread from the peripheral site of inoculation to the CNS. We evaluated ten potential sites in the 3′NCR of the TBEV/LGTV genome for placement of microRNA (miRNA) targets and found that the TBEV/LGTV genome is more restrictive for such genetic manipulations compared to TBEV/DEN4. In addition, unlike TBEV/DEN4 virus, the introduction of multiple miRNA targets into either the 3′NCR or ORF of the TBEV/LGTV genome had only a modest effect on virus attenuation in the developing CNS of highly permissive newborn mice. However, simultaneous miRNA-targeting in the ORF and 3′NCR had synergistic effect on control and silencing of virus replication in the brain and completely abolished the virus neurotropism. Furthermore, neuroinvasiveness of miRNA-targeted TBEV/LGTV viruses in very sensitive immunodeficient SCID mice was significantly limited. Immunocompetent animals immunized with such viruses were completely protected against challenge with the neurovirulent LGTV parent. These findings support the rationale of the miRNA-targeting approach to develop live attenuated virus vaccines against various neurotropic viruses.

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Section: Results and Disscussionsupporting

confidence: 88%

MicroRNA-based control of tick-borne flavivirus neuropathogenesis: Challenges and perspectives

et al. 2016

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“…R-Coffee (Moretti et al ., 2008) was utilized to generate multiple alignments between available 3’ UTR regions of flaviviruses for identification of conserved repeat regions and location of homologous secondary structure RNA elements in concert with direct comparison to structural elements and sequences identified from previous studies (Gritsun & Gould, 2006a; b; c; Markoff, 2003). Mfold web server was utilized to predict secondary structure formation with the maximum distance between paired bases set to 80 as previously described by Gritsun et al 2014 (Gritsun et al ., 2014; Zuker, 2003). …”

Section: Methodsmentioning

confidence: 99%

Characterization of a novel insect-specific flavivirus from Brazil: potential for inhibition of infection of arthropod cells with medically important flaviviruses

Kenney

Solberg

Langevin

et al. 2014

Journal of General Virology

126

132

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In the past decade there has been an upsurge in the number of newly described insect-specific flaviviruses isolated pan-globally. We recently described the isolation of a novel flavivirus (tentatively designated “Nhumirim virus”; NHUV) (Pauvolid-Correa et al., in review) that represents an example of a unique subset of apparently insect-specific viruses that phylogenetically affiliate with dual-host mosquito-borne flaviviruses despite appearing to be limited to replication in mosquito cells. We characterized the in vitro growth potential, 3’ untranslated region (UTR) sequence homology with alternative flaviviruses, and evaluated the virus’s capacity to suppress replication of representative Culex spp. vectored pathogenic flaviviruses in mosquito cells. Only mosquito cell lines were found to support NHUV replication, further reinforcing the insect-specific phenotype of this virus. Analysis of the sequence and predicted RNA secondary structures of the 3’ UTR indicate NHUV to be most similar to viruses within the yellow fever serogroup, Japanese encephalitis serogroup, and viruses in the tick-borne flavivirus clade. NHUV was found to share the fewest conserved sequence elements when compared to traditional insect-specific flaviviruses. This suggests that, despite being apparently insect-specific, this virus likely diverged from an ancestral mosquito-borne flavivirus. Co-infection experiments indicated that prior or concurrent infection of mosquito cells with NHUV resulted in significant reduction in viral production of West Nile virus (WNV), St. Louis encephalitis virus (SLEV) and Japanese encephalitis virus. The inhibitory effect was most effective against WNV and SLEV with over a million-fold and 10,000-fold reduction in peak titers, respectively.

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“…1). Sequence alignments suggest the flavivirus 3′ NCR evolved by multiple duplications of an ancient RNA motif homologous to a long repeat sequence identified in tick-borne flaviviruses and that the short direct repeat sequences remaining in the 3′ NCRs of current mosquito-borne flaviviruses are evolutionary remnants of this ancient long repeat sequence (Olsthoorn and Bol 2001, Gritsun and Gould 2007, Gritsun, Jones et al 2014). The number of remnant repeat sequences in the 3′ NCR varies in different flavivirus genomes.…”

Section: Additional Conserved 3′ Ncr Sequencesmentioning

confidence: 99%

“…One or two conserved “dumbbell-like” (DB) or “Y-shaped” secondary structures are located in the 3′ NCR upstream of the CYC sequence (Gritsun, Jones et al 2014). Mosquito-borne flaviviruses have two copies, a 5′ DB and a 3′ DB (Fig.…”

Section: Additional Conserved Rna Structures In the 3′ Ncrmentioning

confidence: 99%

“…The numbers and types of RNA structures and conserved sequences in the variable region 5′ of the dumbbell structures vary among different subgroups of flaviviruses (Olsthoorn and Bol 2001, Gritsun and Gould 2007, Gritsun, Jones et al 2014, Selisko, Wang et al 2014). In WNV genomes, four additional conserved SLs (SL-I, SL-II, SL-III, and SL-IV) are located 5′ of the dumbbell structures (Fig.…”

Section: Additional Conserved Rna Structures In the 3′ Ncrmentioning

confidence: 99%

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Functions of the 3′ and 5′ genome RNA regions of members of the genus Flavivirus

Brinton

Basu

2015

Virus Research

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The positive sense genomes of members of the genus Flavivirus in the family Flaviviridae are ~11 kb nts in length and have a 5′ type I cap but no 3′ poly A. The 5′ and 3′ terminal regions contain short conserved sequences that are proposed to be repeated remnants of an ancient sequence. However, the functions of most of these conserved sequences have not yet been determined. The terminal regions of the genome also contain multiple conserved RNA structures. Functional data for many of these structures has been obtained. Three sets of complementary 3′ and 5′ terminal region sequences, some of which are located in conserved RNA structures, interact to form a panhandle structure that is required for initiation of minus strand RNA synthesis with the 5′ terminal structure functioning as the promoter. How the switch from the terminal RNA structure base pairing to the long distance RNA-RNA interaction is triggered and regulated is not well understood but evidence suggests involvement of a cell protein binding to three sites on the 3′ terminal RNA structures and a cis-acting metastable 3′ RNA element in the 3′ terminal structure. Cell proteins may also be involved in facilitating exponential replication of nascent genomic RNA within replication vesicles at later times of infection cycle. Other conserved RNA structures and/or sequences in the 5′ and 3′ terminal regions have been proposed to regulate genome translation. Additional functions of the 5′ and 3′ terminal sequences have also been reported.

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Molecular Archaeology of Flaviviridae Untranslated Regions: Duplicated RNA Structures in the Replication Enhancer of Flaviviruses and Pestiviruses Emerged via Convergent Evolution

Cited by 41 publications

References 61 publications

MicroRNA-based control of tick-borne flavivirus neuropathogenesis: Challenges and perspectives

MicroRNA-based control of tick-borne flavivirus neuropathogenesis: Challenges and perspectives

Characterization of a novel insect-specific flavivirus from Brazil: potential for inhibition of infection of arthropod cells with medically important flaviviruses

Functions of the 3′ and 5′ genome RNA regions of members of the genus Flavivirus

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