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Internal Initiation of Translation of Bovine Viral Diarrhea Virus RNA

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Internal Initiation of Translation of Bovine Viral Diarrhea Virus RNA Virology 258, 249–256 (1999) Article ID viro.1999.9741, available online at http://www.idealibrary.com on View metadata, citation and similar papers at core.ac.uk brought to you by CORE provided by Elsevier - Publisher Connector Internal Initiation of Translation of Bovine Viral Diarrhea Virus RNA Tatyana V. Pestova*,† and Christopher U. T. Hellen*,1 *Department of Microbiology and Immunology, Morse Institute for Molecular Genetics, State University of New York Health Science Center at Brooklyn, 450 Clarkson Avenue, Box 44, Brooklyn, New York 11203; and †A. N. Belozersky Institute of Physico-Chemical Biology, Moscow State University, 119899 Moscow, Russia Received October 9, 1998; returned to author for revision December 9, 1998; accepted April 5, 1999 Initiation of translation on the bovine viral diarrhea virus (BVDV) internal ribosomal entry site (IRES) was reconstituted in vitro from purified translation components to the stage of 48S ribosomal initiation complex formation. Ribosomal binding and positioning on this mRNA to form a 48S complex did not require the initiation factors eIF4A, eIF4B, or eIF4F, and translation of this mRNA was resistant to inhibition by a trans-dominant eIF4A mutant that inhibited cap-mediated initiation of translation. The BVDV IRES contains elements that are bound independently by ribosomal 40S subunits and by eukaryotic initiation factor (eIF) 3, as well as determinants that mediate direct attachment of 43S ribosomal complexes to the initiation codon. © 1999 Academic Press Key Words: bovine viral diarrhea virus; IRES; pestivirus; RNA–protein interaction; translation. INTRODUCTION of domain II, near nucleotide 75, and the 39 border of this IRES is downstream of the initiation codon (Chon Bovine viral diarrhea virus (BVDV) is the prototype of et al., 1998). The activity of the BVDV IRES is severely the genus Pestivirus of the Flaviviridae family. The impaired by mutations that affect the integrity of sub- other currently accepted members of this genus are domains between these borders (Poole et al., 1995; classical swine fever virus (CSFV) and border disease Chon et al., 1998). virus of sheep. The positive-sense RNA genomes of The first step in initiation of translation of all eukary- pestiviruses contain one long open reading frame otic mRNAs is formation of a 43S preinitiation complex flanked by 59 and 39 nontranslated regions (NTRs) (Collett et al., 1988; Meyers et al., 1989; Becher et al., that comprises a 40S subunit, initiator tRNA, GTP, and 1998). The 59 NTRs of BVDV, CSFV, and of the related eukaryotic initiation factors (eIFs) 2 and 3 (Merrick, 9 hepatitis C virus (HCV) promote translation of the viral 1992). Attachment of this complex to the 5 end of polyprotein by cap-independent internal ribosomal en- capped mRNAs requires eIF4A, eIF4B, and eIF4F and follows binding of the eIF4E subunit of eIF4F to the 59 try (Tsukiyama-Kohara et al., 1992; Poole et al., 1995; 7 Rijnbrand et al., 1997). IRES-mediated initiation of terminal m G cap (Merrick, 1992; Pestova et al.,1998a). translation was first identified in picornaviruses, such Attachment of the 43S complex to an internal position as encephalomyocarditis virus (EMCV), which now on the EMCV IRES also requires eIF4A, eIF4B, and the epitomizes the group of IRES elements that have been eIF4G subunit of eIF4F (Pestova et al., 1996a,b). At- characterized most extensively (Hellen and Wimmer, tachment does not require eIF4E; instead, eIF4G binds 1995; Jackson and Kaminski, 1995). Pestivirus IRES specifically to this IRES upstream of the initiation elements have been characterized less well. The codon and is thought to recruit eIF4A, eIF4B, and a CSFV IRES comprises most of the 59 NTR, which con- 43S complex to form the 48S complex at the initiation sists of major structural domains I, II, and III, and a codon (Pestova et al., 1996b; Kolupaeva et al., 1998). pseudoknot upstream of the initiation codon that is By contrast, the mechanism of initiation on HCV and essential for IRES activity (Wang et al., 1995; Lemon CSFV IRES elements differs significantly from all and Honda, 1997; Rijnbrand et al., 1997; Pestova et al., known modes of eukaryotic translation initiation. It is 1998b). The CSFV IRES is ;100 nt shorter than the exceptionally simple: 43S complexes bind directly to EMCV IRES and has an unrelated sequence and struc- CSFV and HCV IRES elements independently of eIFs ture. The 59 border of the BVDV IRES is at the 59 end 4A, 4B, and 4F (Pestova et al., 1998b). These two IRES elements contain determinants in domain III that me- diate interaction with eIF3 (Buratti et al., 1998; Pestova 1 To whom correspondence and reprint requests should be ad- et al., 1998b; Sizova et al., 1998). In addition, they dressed. Fax (718) 270-2656. contain multiple, poorly defined determinants whose 0042-6822/99 $30.00 249 Copyright © 1999 by Academic Press All rights of reproduction in any form reserved. 250 PESTOVA AND HELLEN coordinated action promotes direct factor-indepen- of prominent toeprints at UGA403–405 was absolutely de- Met dent binding to 40S subunits such that the initiation pendent on the presence of both Met-tRNAi (Fig. 2A, codon is positioned precisely at or in the immediate lane 5) and eIF2 (data not shown). We conclude that vicinity of the ribosomal P site (Pestova et al., 1998b). these toeprints are caused by assembly of a 48S initia- This activity is perturbed by mutations throughout the tion complex at the BVDV initiation codon. Their position HCV IRES (Wang et al., 1994, 1995; Lemon and Honda, relative to the BVDV initiation codon is identical to that of 1997; Hellen and Pestova, 1999; Pestova et al., 1998b); toeprints caused by 48S complexes assembled at the significantly, the IRES is the most conserved part of CSFV initiation codon that are competent to complete the the HCV genome (Simmonds, 1995). remaining stages in translation initiation up to and in- The BVDV 59 NTR differs from the CSFV and HCV 59 cluding formation of the first peptide bond (Pestova et al., ; NTRs at 35 and at over 50% of nucleotides, respectively 1998b). Prominent new toeprints at G388 and particularly (Hellen and Pestova, 1999). Much smaller sequence dif- at UGA403–405 (indicative of 48S complex formation on the Met ferences between the IRES elements of poliovirus strains BVDV IRES) appeared when eIF3 and Met-tRNAi were or of EMCV variants are sufficient to cause significant added to assembly reactions that already contained changes in factor requirements for initiation (Svitkin et BVDV mRNA, 40S subunits, GMP-PNP, and eIF2 (Fig. 2A, al., 1988; Kaminski and Jackson, 1998). We report here lanes 4 and 5). The observation that new toeprints were that we have dissected the initiation process on the detected at the leading edge of the 40S subunit and at BVDV IRES using an in vitro approach in order to com- the initiation codon at this stage in initiation suggests pare it with initiation on related IRES elements and to that codon–anticodon basepairing is accompanied by a gain further insights into the nature of the RNA determi- small conformational change in the BVDV mRNA at and nants that mediate the different functions in initiation of downstream of the initiation codon. HCV-like IRESes. Neither the presence nor the intensity of the toeprints at G388 and UGA403–405 was affected by eIF4A, eIF4B, and RESULTS eIF4F together (compare Figs. 2B, lanes 3 and 4, and 2A, 43S complexes binds directly at the initiation codon lanes 3 and 4). We conclude that 48S complex formation of the BVDV IRES on the BVDV IRES is absolutely dependent on eIF2 and does not require or involve eIF4A, eIF4B, or eIF4F. Ribo- To dissect internal ribosomal entry on the BVDV IRES, somal 48S complexes formed on the BVDV IRES in the we reconstituted this process in vitro to the stage of 48S absence of eIF4A, eIF4B, and eIF4F were competent to ribosomal initiation complex formation using purified complete all remaining stages in initiation, up to and translation components (40S ribosomal subunits, initia- including formation of the first peptide bond. Assembly of tion factors, aminoacylated initiator tRNA and mRNA). active 80S ribosomal complexes was mediated by a Ribosomal complexes were analyzed by toeprinting ribosomal salt wash fraction (the 02.–0.8 M KCl phospho- (primer extension inhibition), which involves cDNA syn- cellulose elution fraction derived from the 50–70% A.S. thesis by reverse transcriptase on a template RNA to cut) that did not contain eIF4A, eIF4B, or eIF4F (data not which a ribosome or protein is bound. cDNA synthesis is shown). Additional data that support the conclusion that arrested either directly by the bound ribonucleoprotein eIF4A, eIF4B, and eIF4F are not required for BVDV IRES- (RNP) complex, yielding a toeprint at its leading edge, or mediated initiation are described below. indirectly, by stabilization of adjacent helices. The result- ing toeprints are located on a sequencing gel, so that the Specific binding of eIF3 and 40S ribosomal subunits position of bound proteins or complexes can be located to the BVDV IRES precisely. The BVDV IRES is highly structured (Fig. 1) and as a We correlated each of the toeprints caused by 48S result, RT arrest occurs at several sites on naked BVDV initiation complexes with binding of a specific translation RNA. These sites include A320,G327, and U352 (Fig. 2A, lane component to the BVDV IRES by systematically omitting 1). Ribosomal complexes were assembled from 40S sub- components and then toeprinting complexes formed in Met units, eIF2, eIF3, GMP-PNP, and Met-tRNAi on BVDV nt their absence. Ribosomal 40S subunits alone arrested 9 29–1109 mRNA transcripts. GMP-PNP is a nonhydrolyz- primer extension at U362 at the 3 border of the able GTP analog that causes 48S complexes to accumu- pseudoknot, weakly at G381 and G388, as well as at late.
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