The 5′-Untranslated Region of Picornaviral Genomes

Agol, Vadim I.

doi:10.1016/s0065-3527(08)60278-x

Cited by 102 publications

(60 citation statements)

References 324 publications

(292 reference statements)

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“…The extended nature of the RNA helices has been confirmed by electron microscopy studies, which show that the hepatitis C virus IRES does not form a globular structure (5,35). In contrast, the tertiary folds proposed to date for the PV IRES are theoretical (1,22). Although it is anticipated that data from electron microscopy studies will soon be available for this IRES (5), the resolution of such analyses precludes a comprehension of higher-order structure at the nucleotide level.…”

Section: Discussionmentioning

confidence: 99%

Poliovirus Internal Ribosome Entry Segment Structure Alterations That Specifically Affect Function in Neuronal Cells: Molecular Genetic Analysis

Malnou

Pöyry

Jackson

et al. 2002

J Virol

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Translation of poliovirus RNA is driven by an internal ribosome entry segment (IRES) present in the 5 noncoding region of the genomic RNA. This IRES is structured into several domains, including domain V, which contains a large lateral bulge-loop whose predicted secondary structure is unclear. The primary sequence of this bulge-loop is strongly conserved within enteroviruses and rhinoviruses: it encompasses two GNAA motifs which could participate in intrabulge base pairing or (in one case) could be presented as a GNRA tetraloop. We have begun to address the question of the significance of the sequence conservation observed among enterovirus reference strains and field isolates by using a comprehensive site-directed mutagenesis program targeted to these two GNAA motifs. Mutants were analyzed functionally in terms of (i) viability and growth kinetics in both HeLa and neuronal cell lines, (ii) structural analyses by biochemical probing of the RNA, and (iii) translation initiation efficiencies in vitro in rabbit reticulocyte lysates supplemented with HeLa or neuronal cell extracts. Phenotypic analyses showed that only viruses with both GNAA motifs destroyed were significantly affected in their growth capacities, which correlated with in vitro translation defects. The phenotypic defects were strongly exacerbated in neuronal cells, where a temperature-sensitive phenotype could be revealed at between 37 and 39.5°C. Biochemical probing of mutated domain V, compared to the wild type, demonstrated that such mutations lead to significant structural perturbations. Interestingly, revertant viruses possessed compensatory mutations which were distant from the primary mutations in terms of sequence and secondary structure, suggesting that intradomain tertiary interactions could exist within domain V of the IRES.Poliovirus (PV) is often considered the prototype of the Enterovirus genus of the Picornaviridae family. As such, its genome is a single-stranded RNA molecule of positive polarity. It is now well established that the long 5Ј untranslated region (5Ј-UTR; 742 nucleotides [nt] for PV type 1 Mahoney strain [PV1(M)]) plays different important roles in the PV life cycle. The first hundred nucleotides form a cloverleaf structure involved in RNA replication (3), acting at the initiation of negative-strand RNA synthesis (4). Similarly, on negativestrand replication intermediates, the complement of the 5Ј-UTR is involved in the synthesis of positive-strand viral RNA (32). Furthermore, the 5Ј-UTR contains an internal ribosome entry segment (IRES) which promotes translation initiation by a cap-and 5Ј-end-independent mechanism, following direct entry of the 40S ribosomal subunit at the 3Ј end of the IRES (for a review, see reference 6). The PV IRES is approximately 450 nt long and has a predicted secondary structure comprised of five complex stem-loops (Fig. 1A), one of which has been reported to be dispensable for efficient translation at least ex vivo (9). The original predicted secondary structure of the PV 5Ј-UTR was initially b...

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Section: Discussionmentioning

confidence: 99%

Poliovirus Internal Ribosome Entry Segment Structure Alterations That Specifically Affect Function in Neuronal Cells: Molecular Genetic Analysis

Malnou

Pöyry

Jackson

et al. 2002

J Virol

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“…However, available evidence suggests that the internal initiation of HAV and HCV translation, like that of EMCV, involves the binding of the 40S ribosome subunit to the viral RNA at a position close to the initiator AUG codon, rather than at an upstream site with subsequent 3Ј scanning to the AUG codon as occurs with the poliovirus IRES (1,11,12,29,35,36). Thus, it is likely that PTB facilitates the initial interaction of the 40S subunit with these viral RNAs, rather than its subsequent 3Ј movement along the RNA (50).…”

Section: Discussionmentioning

confidence: 99%

Transient Expression of Cellular Polypyrimidine-Tract Binding Protein Stimulates Cap-Independent Translation Directed by Both Picornaviral and Flaviviral Internal Ribosome Entry Sites In Vivo

Gosert

Chang

Rijnbrand

et al. 2000

Molecular and Cellular Biology

123

105

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The regulation of cap-independent translation directed by the internal ribosome entry sites (IRESs) present in some viral and cellular RNAs is poorly understood. Polypyrimidine-tract binding protein (PTB) binds specifically to several viral IRESs. IRES-directed translation may be reduced in cell-free systems that are depleted of PTB and restored by reconstitution of lysates with recombinant PTB. However, there are no data concerning the effects of PTB on IRES-directed translation in vivo. We transfected cells with plasmids expressing dicistronic transcripts in which the upstream cistron encoded PTB or PTB deletion mutants (including a null mutant lacking amino acid residues 87 to 531). The downstream cistron encoded a reporter protein (chloramphenicol acetyltransferase [CAT]) under translational control of the poliovirus IRES which was placed within the intercistronic space. In transfected BS-C-1 cells, transcripts expressing wild-type PTB produced 12-fold more reporter protein than similar transcripts encoding the PTB null mutant. There was a 2.4-fold difference in CAT produced from these transcripts in HeLa cells, which contain a greater natural abundance of PTB. PTB similarly stimulated CAT production from transcripts containing the IRES of hepatitis A virus or hepatitis C virus in BS-C-1 cells and Huh-7 cells (37-to 44-fold increase and 5 to 5.3-fold increase, respectively). Since PTB had no quantitative or qualitative effect on transcription from these plasmids, we conclude that PTB stimulates translation of representative picornaviral and flaviviral RNAs in vivo. This is likely to reflect the stabilization of higher ordered RNA structures within the IRES and was not observed with PTB mutants lacking RNA recognition motifs located in the C-terminal third of the molecule.The cap-independent initiation of translation on the plussense genomic RNAs of picornaviruses and some flaviviruses requires binding of the small ribosome subunit to the RNA at a site located hundreds of nucleotides downstream of its 5Ј terminus (34,54,75). This interaction is controlled by highly structured, cis-acting RNA elements located within the 5Ј nontranslated region (5ЈNTR), the internal ribosome entry site (IRES). IRES elements were first identified within viral RNAs but have been increasingly recognized within the lengthy 5ЈNTRs of cellular mRNAs encoding certain critical mammalian growth factors, including fibroblast growth factor 2 (76), human insulin-like growth factor II (74), and platelet-derived growth factor B (4), as well as eukaryotic translation initiation factor 4G (eIF4G) (19). In directing the internal initiation of translation, these viral and cellular IRES elements function in concert with both canonical and possibly noncanonical transacting cellular translation initiation factors. Factors influencing the efficiency of internal ribosome entry directed by IRESs are likely to play important roles in determining the cellular tropisms of some viruses or the posttranscriptional regulation of proteins translated under the...

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“…The first AUG codon is probably the initiation codon for the PYFV polyprotein because (i) this AUG has an A residue in position -3 which is unlikely to be skipped by a scanning ribosomal 40S subunit (Kozak, 1987), (ii) the base composition from nts 1 to 278 (34-2% U, 24.8% C, 13.3% G and 27.7% A) has a high U + A and low G residue content consistent with leader sequences in RNA of other plant viruses (Gallie et al, 1987) and if the 5' untranslated region (UTR) is extended to nt 590 the G content rises to 20.0 %; and (iii) an oligopyrimidine tract precedes the first AUG codon. Oligopyrimidine tracts also precede the initiation codons of tomato black ring virus (TBRV) RNA 1 (Greif et al, 1988) and cowpea mosaic virus (CPMV) B RNA (Lomonossoff & Shanks, 1983), and are important in translation initiation of picornavirus RNA (reviewed by Agol, 1991). Collett et al, 1988) and yellow fever flavivirus (YFV; Rice et al, 1985).…”

Section: Orfs In Pyfvmentioning

confidence: 99%

The nucleotide sequence of parsnip yellow fleck virus: a plant picorna-like virus

Turnbull-Ross¹,

Reavy²,

Mayo³

et al. 1992

Journal of General Virology

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The complete sequence of 9871 nucleotides (nts) of parsnip yellow fleck virus (PYFV; isolate P-121) was determined from cDNA clones and by direct sequencing of viral RNA. The RNA contains a large open reading frame between nts 279 and 9362 which encodes a polyprotein of 3027 amino acids with a calculated Mr of 336212 (336K). A PYFV polyclonal antiserum reacted with the proteins expressed from phage carrying cDNA clones from the 5' half of the PYFV genome. Comparison of the polyprotein sequence of PYFV with other viral polyprotein sequences reveals similarities to the putative NTP-binding and RNA polymerase domains of cowpea mosaic comovirus, tomato black ring nepovirus and several animal picornaviruses. The 3' untranslated region of PYFV RNA is 509 nts long and does not have a poly(A) tail. The Y-terminal 121 nts may form a stem-loop structure which resembles that formed in the genomic RNA of mosquito-borne flaviviruses.

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The 5′-Untranslated Region of Picornaviral Genomes

Cited by 102 publications

References 324 publications

Poliovirus Internal Ribosome Entry Segment Structure Alterations That Specifically Affect Function in Neuronal Cells: Molecular Genetic Analysis

Poliovirus Internal Ribosome Entry Segment Structure Alterations That Specifically Affect Function in Neuronal Cells: Molecular Genetic Analysis

Transient Expression of Cellular Polypyrimidine-Tract Binding Protein Stimulates Cap-Independent Translation Directed by Both Picornaviral and Flaviviral Internal Ribosome Entry Sites In Vivo

The nucleotide sequence of parsnip yellow fleck virus: a plant picorna-like virus

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