Cis-active RNA elements (CREs) and picornavirus RNA replication

Steil, Benjamin P.; Barton, David J.

doi:10.1016/j.virusres.2008.07.027

Cited by 102 publications

(101 citation statements)

References 132 publications

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“…These elements include L and 2A proteins, which exist in a large variety of molecular forms in picornaviruses (1,20,40), or CRE, whose location in the genome varies tremendously among picornaviruses (9,18,19,50,73,80,81), or other elements located in the 5= and 3= noncoding regions (71,78). For a number of picornaviruses, the viability of interspecies chimera carrying a noncognate version of either L (58) and 2A protein (47) or CRE (73) and IRES (48,78) was demonstrated experimentally.…”

Section: Resultsmentioning

confidence: 99%

Toward Genetics-Based Virus Taxonomy: Comparative Analysis of a Genetics-Based Classification and the Taxonomy of Picornaviruses

Lauber

Gorbalenya

2012

J Virol

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bVirus taxonomy has received little attention from the research community despite its broad relevance. In an accompanying paper (C. Lauber and A. E. Gorbalenya, J. Virol. 86:3890 -3904, 2012), we have introduced a quantitative approach to hierarchically classify viruses of a family using pairwise evolutionary distances (PEDs) as a measure of genetic divergence. When applied to the six most conserved proteins of the Picornaviridae, it clustered 1,234 genome sequences in groups at three hierarchical levels (to which we refer as the "GENETIC classification"). In this study, we compare the GENETIC classification with the expert-based picornavirus taxonomy and outline differences in the underlying frameworks regarding the relation of virus groups and genetic diversity that represent, respectively, the structure and content of a classification. To facilitate the analysis, we introduce two novel diagrams. The first connects the genetic diversity of taxa to both the PED distribution and the phylogeny of picornaviruses. The second depicts a classification and the accommodated genetic diversity in a standardized manner. Generally, we found striking agreement between the two classifications on species and genus taxa. A few disagreements concern the species Human rhinovirus A and Human rhinovirus C and the genus Aphthovirus, which were split in the GENETIC classification. Furthermore, we propose a new supergenus level and universal, level-specific PED thresholds, not reached yet by many taxa. Since the species threshold is approached mostly by taxa with large sampling sizes and those infecting multiple hosts, it may represent an upper limit on divergence, beyond which homologous recombination in the six most conserved genes between two picornaviruses might not give viable progeny. R esearch in virology relies on virus taxonomy for providing a unified intellectual and practical framework for analysis, generalization, and knowledge dissemination. Despite its broad relevance, taxonomy has received relatively little attention from the research community. Virus taxonomy is developed under the direction of the Committee on Taxonomy of Viruses (ICTV) and recognizes five hierarchically arranged ranks: order, family, subfamily, genus, and species (in ascending order of intervirus similarity), with order and subfamily levels being used less commonly. Virus species are of principal importance (60), and for their demarcation the so-called polythetic species concept (3, 74) is applied. Accordingly, viruses are recognized as single species if they share a broad range of characteristics while constituting a replicating lineage that occupies a particular ecological niche (36, 75). These characteristics, so-called demarcation criteria, are devised for each genus separately and are revised periodically (16,35). To ensure that each virus is classified, they are allowed to vary greatly between and even within families, with no single unifying property being sought after (for a review, see reference 76). Consequently, virus species are operatio...

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Section: Resultsmentioning

confidence: 99%

Toward Genetics-Based Virus Taxonomy: Comparative Analysis of a Genetics-Based Classification and the Taxonomy of Picornaviruses

Lauber

Gorbalenya

2012

J Virol

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“…Picornavirus L-proteins are associated with virulence and pathology, as they affect host and virus RNA translation and protease activity (Glaser et al, 2001;Guarné et al, 1998;Hinton et al, 2002). Not identified, although expected to be present, was a viral genome-linked protein (VPg), a highly heterogeneous class of small proteins bound covalently to the 59 terminus of most RNA viruses (including iflaviruses) and involved in RNA stability, genome replication, translation and movement (Hébrard et al, 2009;Ng et al, 2008;Steil & Barton, 2009). These processes also involve the 59-and 39-UTRs, as well as numerous host factors (Belsham, 2009).…”

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confidence: 99%

Genetic characterization of slow bee paralysis virus of the honeybee (Apis mellifera L.)

Miranda

Dainat

Locke

et al. 2010

Journal of General Virology

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Complete genome sequences were determined for two distinct strains of slow bee paralysis virus (SBPV) of honeybees (Apis mellifera). The SBPV genome is approximately 9.5 kb long and contains a single ORF flanked by 59-and 39-UTRs and a naturally polyadenylated 39 tail, with a genome organization typical of members of the family Iflaviridae. The two strains, labelled 'Rothamsted' and 'Harpenden', are 83 % identical at the nucleotide level (94 % identical at the amino acid level), although this variation is distributed unevenly over the genome. The two strains were found to co-exist at different proportions in two independently propagated SBPV preparations. The natural prevalence of SBPV for 847 colonies in 162 apiaries across five European countries was ,2 %, with positive samples found only in England and Switzerland, in colonies with variable degrees of Varroa infestation.Slow bee paralysis virus (SBPV) is one of several honeybee (Apis mellifera) viruses linked to high mortality of colonies infested with the ectoparasitic mite Varroa destructor (Carreck et al., 2010;Martin et al., 1998). SBPV was discovered fortuitously in England in 1974, during propagation experiments involving bee virus X. It induces paralysis of the anterior two pairs of legs about 10 days after injection into the abdomen of adult bees (Bailey & Woods, 1974), with high virus accumulation in the head, the hypopharyngeal, mandibular and salivary glands, the fat body, crop and forelegs, but less in the hindlegs, midgut, rectum and thorax (Denholm, 1999). Like most honeybee viruses, SBPV persists naturally as a covert infection, most likely through oral transmission (Bailey & Ball, 1991). However, SBPV can be transmitted readily among adult bees and to pupae by Varroa mites (Santillán-Galicia et al., 2010), with lethal consequences at the individual bee and colony levels (Carreck et al., 2010). Overt SBPV infection can also be induced in adult bees (but not in pupae) by injection with inert fluids, especially the The GenBank/EMBL/DDBJ accession numbers for the complete genome sequences of SBPV strains Rothamsted and Harpenden are EU035616 and GU938761, respectively.A supplementary table showing primers and performance indicators of several universal and strain-specific RT-qPCR assays is available with the online version of this paper.

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“…In some cases, these structured RNAs fold into specific, stable three-dimensional structures that interact with components of the host cell, with other parts of the viral genome, or with virally encoded proteins. These interactions manipulate the host cell's machinery or control viral processes, influencing steps as diverse as translation, replication, encapsulation, localization, and others (e.g., Dreher 2009;Filbin and Kieft 2009;Giedroc and Cornish 2009;Steil and Barton 2009;Zoll et al 2009). It is clear that structured RNA sequences can be a critical component of the replication strategy of these viruses.…”

Section: Introductionmentioning

confidence: 99%

“…The virus' RNA genome utilizes several different regions of structured RNA to drive important events during infection. This includes an internal ribosome entry site (IRES) and a cloverleaf structure that are both found in the 59 UTR (Pelletier and Sonenberg 1988;Barton et al 2001), and the cis-acting replication element (CRE) in the protein coding region (Paul et al 2000;Goodfellow et al 2003;Steil and Barton 2009). Recently, another viral RNA sequence of novel function was discovered in the poliovirus genome, in the open reading frame (ORF) that encodes for the viral 3C protease (3C Pro ) (Fig.…”

Section: Introductionmentioning

confidence: 99%

Structural architecture of an RNA that competitively inhibits RNase L

Keel¹,

Jha²,

Kieft³

2011

RNA

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Activation of RNase L endonuclease activity is part of the mammalian innate immune response to viral infection. The poliovirus RNA genome contains a sequence in its protein-coding region that can act as a competitive inhibitor of RNase L. Mutation, sequence, and functional analysis of this competitive inhibitor RNA (ciRNA) revealed that its activity depends on specific sequences, showed that a loop-loop hairpin interaction forms in the ciRNA, and suggested the presence of a loop E motif. These features lead to the hypothesis that the ciRNA's function is conferred in part by a specific three-dimensional folded RNA architecture. By using a combination of biophysical, mutational, and functional studies, we have mapped features of the threedimensional architecture of the ciRNA in its unbound form. We show that the loop-loop interaction forms in the free ciRNA and affects the overall structure, perhaps forming long-range tertiary interactions with the loop E motif. Local tight RNA-RNA backbone packing occurs in parts of the structure, but the fold appears to be less stable than many other tightly packed RNAs. This feature may allow the ciRNA to accommodate the translocation of ribosomes and polymerase across this multifunctional region of the viral RNA but also to function as an RNase L inhibitor.

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Cis-active RNA elements (CREs) and picornavirus RNA replication

Cited by 102 publications

References 132 publications

Toward Genetics-Based Virus Taxonomy: Comparative Analysis of a Genetics-Based Classification and the Taxonomy of Picornaviruses

Toward Genetics-Based Virus Taxonomy: Comparative Analysis of a Genetics-Based Classification and the Taxonomy of Picornaviruses

Genetic characterization of slow bee paralysis virus of the honeybee (Apis mellifera L.)

Structural architecture of an RNA that competitively inhibits RNase L

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