Nucleotide sequence of the putative recognition site for coat protein in the RN As of alfalfa mosaic virus and tobacco streak virus

Koper-Zwarthoff, Ellen C.; Bol, John F.

doi:10.1093/nar/8.15.3307

Cited by 78 publications

(38 citation statements)

References 17 publications

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“…( Koper-Zwarthoff & Bol, 1980). While not identical the three sequences formed structures with three loops and in all of them the AUGC motif appears to be conserved.…”

Section: Short Communicationmentioning

confidence: 97%

The nucleotide sequence of citrus leaf rugose ilarvirus RNA-2

Scott

1994

Journal of General Virology

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The nucleotide sequence of citrus leaf rugose ilarvirus (CiLRV) RNA-2 consists of 2990 nucleotides and contains one open reading frame (ORF) which encodes a deduced translation product of 832 amino acids with a calculated M~. of 95501 (95K). The 5' terminus of the RNA has a mTGppp cap. Both the nucleotide sequence of CiLRV RNA-2 and its translated polypeptide share homologies with the nucleotide sequence and translated polypeptide, respectively, of RNA-2 of alfalfa mosaic virus (AlMV). The homology occurs in the central region of both the nucleic acid sequence and the polypeptide. Homologies between either CiLRV or A1MV and other Bromoviridae (cucumber mosaic virus -CMV, brome mosaic virus -BMV and cowpea chlorotic mottle virus -CCMV) were far less. Alignment of the 104 amino acid region (polymerase signature) of the 95K protein against 10 other 'alpha-like' plant viral polymerase signatures showed that CiLRV and AlMV are more closely related to each other than to CMV, BMV or CCMV. This is the first report of the full-length sequence of RNA-2 of an ilarvirus.

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“…( Koper-Zwarthoff & Bol, 1980). While not identical the three sequences formed structures with three loops and in all of them the AUGC motif appears to be conserved.…”

Section: Short Communicationmentioning

confidence: 97%

The nucleotide sequence of citrus leaf rugose ilarvirus RNA-2

Scott

1994

Journal of General Virology

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“…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).…”

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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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“…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)(6)(7)(8).…”

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confidence: 99%

“…The 180-nucleotide 3´UTR secondary structure likely consists of six hairpins, most of which are separated by single-stranded tetranucleotide AUGC repeats (5)(6)(7)(8). These repeats are characteristic of AMV and ilarvirus RNA sequences and are important for CP binding (8)(9)(10)(11).…”

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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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Nucleotide sequence of the putative recognition site for coat protein in the RN As of alfalfa mosaic virus and tobacco streak virus

Cited by 78 publications

References 17 publications

The nucleotide sequence of citrus leaf rugose ilarvirus RNA-2

The nucleotide sequence of citrus leaf rugose ilarvirus RNA-2

Coat Protein Activation of Alfalfa Mosaic Virus Replication Is Concentration Dependent

Cofolding Organizes Alfalfa Mosaic Virus RNA and Coat Protein for Replication

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