Coat protein binds to the 3'-terminal part of RNA 4 of alfalfa mosaic virus

Houwing, Corrie J.; Jaspars, E.M.J.

doi:10.1021/bi00607a035

Cited by 76 publications

(51 citation statements)

References 33 publications

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“…4, B and C). A transition from a more flexible to a more constrained 3´ end upon CP binding agrees with a replication model suggesting that an RNA conformational change accompanies CP binding to the 3´ ends of the genomic RNAs (25). Circular dichroism analyses and polyacrylamide gel electrophoresis experiments also suggest that the AMV 3 UTR RNA becomes more compact in the presence of CP (11,17).…”

supporting

confidence: 78%

Cofolding Organizes Alfalfa Mosaic Virus RNA and Coat Protein for Replication

Guogas

Filman

Hogle

et al. 2004

Science

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Alfalfa mosaic virus genomic RNAs are infectious only when the viral coat protein binds to the RNA 3´ termini. The crystal structure of an alfalfa mosaic virus RNA-peptide complex reveals that conserved AUGC repeats and Pro-Thr-x-Arg-Ser-x-x-Tyr coat protein amino acids cofold upon interacting. Alternating AUGC residues have opposite orientation, and they base pair in different adjacent duplexes. Localized RNA backbone reversals stabilized by arginine-guanine interactions place the adenosines and guanines in reverse order in the duplex. The results suggest that a uniform, organized 3´ conformation, similar to that found on viral RNAs with transfer RNA-like ends, may be essential for replication.A general problem in positive-strand RNA virology is understanding how viral RNA replication is initiated by the RNA-dependent RNA polymerase (replicase) on the correct template and nucleotide in an infected cell. Alfalfa mosaic virus (AMV) and ilarviruses are unusual positive-sense viruses, the genomic RNAs of which are replicated only in the presence of the viral coat protein (CP) (1,2). These viruses are distinguished from many other members of the virus family Bromoviridae because they lack canonical features of the tRNA-like structure (TLS) common at the 3´ termini of the viral RNA genomes. The TLS is a necessary and sufficient feature for recruitment of the bromovirus replicase (3,4). CP-induced structural organization of the AMV RNA 3´ terminus may create a functional homolog of the tRNA tail and thereby permit recognition by the RNA-dependent RNA polymerase.CP binds specifically to the 3´ untranslated regions (3´UTRs) found on all four RNAs of the segmented AMV genome (5). The 180-nucleotide 3´UTR secondary structure likely consists of six hairpins, most of which are separated by single-stranded tetranucleotide AUGC repeats (5-8). These repeats are characteristic of AMV and ilarvirus RNA sequences and are important for CP binding (8-11). We previously identified a 39-nucleotide minimal high affinity AMV CP-binding site, consisting of the two terminal hairpins and their flanking AUGC nucleotides (nucleotides 843 to 881 in RNA4; i.e., AMV 843-881 ) (8,12,13) (fig. S1A). This fragment is competent to bind either full-length CP or a 26-amino acid peptide (CP26, fig. S1B) (13) representing the N-terminal RNA binding domain (14). The CP N terminus contains a ProThr-x-Arg-Ser-x-x-Tyr (PTxRSxxY) RNA binding domain conserved among AMV and ilarvirus CPs (14).

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supporting

confidence: 78%

Cofolding Organizes Alfalfa Mosaic Virus RNA and Coat Protein for Replication

Guogas

Filman

Hogle

et al. 2004

Science

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“…It was first proposed by Houwing and Jaspars that an RNA conformational change accompanies CP binding to the 3Ј ends of the genomic RNAs and thereby presents a recognition signal for replicase binding (20). Results from circular dichroism analyses and native polyacrylamide gel electrophoresis experiments support the idea that the 3Ј untranslated region (UTR) of AMV RNA3 and -4 undergoes a conformational change upon binding amino-terminal CP peptides (3).…”

Section: Alfalfa Mosaic Virus (Amv) and Ilarvirusmentioning

confidence: 94%

“…The viral CP is translated from a subgenomic RNA4, which is generated by the internal initiation of transcription from minus-strand RNA3. In vitro-transcribed RNA4 (CP mRNA) can substitute for CP in the activation of replication when inoculated with the genomic RNAs into tobacco protoplasts (46).It was first proposed by Houwing and Jaspars that an RNA conformational change accompanies CP binding to the 3Ј ends of the genomic RNAs and thereby presents a recognition signal for replicase binding (20). Results from circular dichroism analyses and native polyacrylamide gel electrophoresis experiments support the idea that the 3Ј untranslated region (UTR) of AMV RNA3 and -4 undergoes a conformational change upon binding amino-terminal CP peptides (3).…”

mentioning

confidence: 99%

Coat Protein Activation of Alfalfa Mosaic Virus Replication Is Concentration Dependent

Guogas

Laforest

Gehrke

2005

J Virol

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Alfalfa mosaic virus (AMV) and ilarvirusRNA-protein interactions play important roles in a variety of biological processes and are of particular importance in the life cycle of positive-strand RNA viruses, where the genomic RNA serves as the template for protein synthesis and replication. Alfalfa mosaic virus (AMV) and ilarviruses provide an interesting model system in which to study RNA-protein interactions because the viral coat protein (CP) has multiple roles in the viral life cycle, not all of which are completely understood. In addition to virion assembly (21, 44) the viral CP has roles in cell-to-cell movement (12, 43), infectivity (6, 23), and translation (28,29).Most bromoviruses have a tRNA-like structure (TLS) on the 3Ј end of the RNA genome. The TLS has been found to be important for recruiting the viral replicase (8, 13). Conversely, AMV and ilarviruses lack a canonical CCA 3Ј end common to the TLS and further require the presence of their own viral CP to initiate replication (6). It has been shown that CP binds specifically to the 3Ј untranslated region found on all three AMV genomic RNAs as well as the subgenomic RNA4 (5, 22, 24). Genomic RNA1 and -2 encode proteins with replicase functions (33). RNA3 is dicistronic, encoding the viral movement protein (MP) and CP. Only the upstream open reading frame, encoding the viral MP, is translated from genomic RNA3. The viral CP is translated from a subgenomic RNA4, which is generated by the internal initiation of transcription from minus-strand RNA3. In vitro-transcribed RNA4 (CP mRNA) can substitute for CP in the activation of replication when inoculated with the genomic RNAs into tobacco protoplasts (46).It was first proposed by Houwing and Jaspars that an RNA conformational change accompanies CP binding to the 3Ј ends of the genomic RNAs and thereby presents a recognition signal for replicase binding (20). Results from circular dichroism analyses and native polyacrylamide gel electrophoresis experiments support the idea that the 3Ј untranslated region (UTR) of AMV RNA3 and -4 undergoes a conformational change upon binding amino-terminal CP peptides (3). Further investigation of this RNA-protein interaction revealed a 26-aminoacid RNA binding motif in the N terminus of the CP that is sufficient to activate replication in mesophyll protoplasts (3,39). A minimal CP binding site was also identified at the terminal 39 nucleotides of the AMV 3Ј UTR (1, 17). While it is known that the genomic RNAs are not infectious in the absence of CP (6, 47), it is unclear how CP initiates infection or how it influences ongoing replication.Several models have been proposed to explain the genome activation phenomenon. The interaction of CP with the genomic RNA 3Ј UTR may serve to protect the RNAs from degradation (30); however, AMV genomic RNAs have been shown to be stable for several hours when inoculated into protoplasts in the absence of CP or polymerase (19). Olsthoorn et al. (31) described the conformational switch model, wherein the protein-free 3Ј UTR assumes a pseu...

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“…The observation that AlMV RNAs are able to withdraw CP subunits from virus particles in vitro indicated that the RNAs contain specific binding sites with a high affinity for CP (10). In subgenomic RNA 4, which is identical in sequence to the 3′-terminal sequence of 881 nucleotides (nt) of RNA 3, these high-affinity binding sites were predominantly localized in the 3′-terminal untranslated region (UTR) (11). The 3′-terminal 145 nt of RNAs 1, 2 and 3 show a sequence similarity of 80% and despite the nucleotide differences in these sequences, all termini can be folded into a similar secondary structure (12).…”

Section: Introductionmentioning

confidence: 99%

Structural Elements of the 3'-Terminal Coat Protein binding Site in Alfalfa Mosaic Virus RNAs

Reusken

Bol

1996

Nucleic Acids Research

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The 3′-termini of the three genomic RNAs of alfalfa mosaic virus (AlMV) and ilarviruses contain a number of AUGC-motifs separated by hairpin structures. Binding of coat protein (CP) to such elements in the RNAs is required to initiate infection of these viruses. Determinants for CP binding in the 3′-terminal 39 nucleotides (nt) of AlMV RNA 3 were analyzed by band-shift assays. From the 5′-to 3′-end this 39 nt sequence contains AUGC-motif 3, stem-loop structure 2 (STLP2), AUGC-motif 2, stem-loop structure 1 (STLP1) and AUGC-motif 1. A mutational analysis showed that all three AUGC-motifs were involved in CP binding. Mutation of the A-and U-residues of motifs 1 or 3 had no effect on CP binding but similar mutations in motif 2 abolished CP binding. A mutational analysis of the stem of STLP1 and STLP2 confirmed the importance of these hairpins for CP binding. Randomization of the sequence of the stems and loops of STLP1 and STLP2 had no effect on CP binding as long as the secondary structure was maintained. This indicates that the two hairpins are not involved in sequence-specific interactions with CP. They may function in a secondary structure-specific interaction with CP and/or in the assembly of the AUGC-motifs in a configuration required for CP binding.

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Coat protein binds to the 3'-terminal part of RNA 4 of alfalfa mosaic virus

Cited by 76 publications

References 33 publications

Cofolding Organizes Alfalfa Mosaic Virus RNA and Coat Protein for Replication

Cofolding Organizes Alfalfa Mosaic Virus RNA and Coat Protein for Replication

Coat Protein Activation of Alfalfa Mosaic Virus Replication Is Concentration Dependent

Structural Elements of the 3'-Terminal Coat Protein binding Site in Alfalfa Mosaic Virus RNAs

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