Role of the 5′ leader sequence of alfalfa mosaic virus RNA 3 in replication and translation of the viral RNA

Vossen, E.A.G. van der; Neeleman, Lyda; Bol, John F.

doi:10.1093/nar/21.6.1361

Cited by 34 publications

(22 citation statements)

References 33 publications

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“…It has been found that addition of a poly(A) tail to the 3Ј ends of the AMV RNAs partially replaces the requirement for CP in the inoculum (13). Moreover, binding of CP to the 3Ј untranslated regions (UTRs) of RNAs 3 and 4 strongly enhanced translation of these RNAs (13; L. Neeleman, H. J. M. Linthorst, and J. F. Bol, submitted for publication).AMV RNAs are flanked by 5Ј and 3Ј UTRs that are highly structured and presumed to contain cis-acting elements involved in translation and replication (14,15,22,23,24,25,27,28). The 3Ј UTRs of the three RNAs consist of a common 3Ј-terminal sequence of 145 nucleotides (nt) preceded by 18 to 34 nt that are unique for each RNA.…”

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“…AMV RNAs are flanked by 5Ј and 3Ј UTRs that are highly structured and presumed to contain cis-acting elements involved in translation and replication (14,15,22,23,24,25,27,28). The 3Ј UTRs of the three RNAs consist of a common 3Ј-terminal sequence of 145 nucleotides (nt) preceded by 18 to 34 nt that are unique for each RNA.…”

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confidence: 99%

“…The 5Ј UTR of RNA 3 contains several 27-nt repeats that encompass ICR 2-like motifs (24). These motifs are homologous to box B elements, which are present in brome mosaic virus (BMV) RNAs and mediate recruitment of the BMV RNAs to viral replication complexes (3,19,20,24). The 5Ј UTRs of AMV RNAs 1 and 2 do not contain recognizable ICR 2-like motifs.…”

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“…Fig. 1A and B) is absent in the 5Ј UTR of RNA 3 (24). To analyze a possible role of this stem-loop in RNA replication, a mutation was introduced into RNA 1, disrupting base pairing in the upper half of the stem of the predicted hairpin ( Fig.…”

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The 5′ Untranslated Region of Alfalfa Mosaic Virus RNA 1 Is Involved in Negative-Strand RNA Synthesis

Vlot

Bol

2003

J Virol

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The three genomic RNAs of alfalfa mosaic virus each contain a unique 5 untranslated region (5 UTR). Replacement of the 5 UTR of RNA 1 by that of RNA 2 or 3 yielded infectious replicons. The sequence of a putative 5 stem-loop structure in RNA 1 was found to be required for negative-strand RNA synthesis. A similar putative 5 stem-loop structure is present in RNA 2 but not in RNA 3.Alfalfa mosaic virus (AMV) is a positive-strand tripartite RNA virus belonging to the family Bromoviridae (reviewed in reference 2). RNAs 1 and 2 encode the replicase proteins P1 and P2, respectively. P1 contains a methyltransferase-like domain in its N-terminal half, as well as a helicase-like domain in its C-terminal half (6,18). Residues in P1 that are highly conserved among alphaviral methyltransferase proteins or superfamily I helicases are required for AMV RNA replication (29,30). P2 is the viral RNA-dependent RNA polymerase (RdRp) protein (16). RNA 3 encodes the movement protein P3, as well as the coat protein, CP, which is translated from subgenomic RNA 4. The three genomic RNAs of AMV are not infectious unless either CP or CP-mRNA 4 is present in the inoculum (2). It has been found that addition of a poly(A) tail to the 3Ј ends of the AMV RNAs partially replaces the requirement for CP in the inoculum (13). Moreover, binding of CP to the 3Ј untranslated regions (UTRs) of RNAs 3 and 4 strongly enhanced translation of these RNAs (13; L. Neeleman, H. J. M. Linthorst, and J. F. Bol, submitted for publication).AMV RNAs are flanked by 5Ј and 3Ј UTRs that are highly structured and presumed to contain cis-acting elements involved in translation and replication (14,15,22,23,24,25,27,28). The 3Ј UTRs of the three RNAs consist of a common 3Ј-terminal sequence of 145 nucleotides (nt) preceded by 18 to 34 nt that are unique for each RNA. It has been shown that RNA 3 with its 3Ј UTR replaced with that of either RNA 1 or 2 is replicated in P12 plants at the level of wild-type (wt) RNA 3 (25). P12 plants express P1 and P2 from nuclear transgenes and support replication of RNA 3 and synthesis of RNA 4 (21). In AMV strain 425, the 5Ј UTRs of RNAs 1 and 2 consist of 100 and 54 nt, respectively, while the 5Ј UTR of RNA 3 consists of 345 nt that are predicted to fold into a complex structure (24). The 5Ј UTR of RNA 3 contains several 27-nt repeats that encompass ICR 2-like motifs (24). These motifs are homologous to box B elements, which are present in brome mosaic virus (BMV) RNAs and mediate recruitment of the BMV RNAs to viral replication complexes (3,19,20,24). The 5Ј UTRs of AMV RNAs 1 and 2 do not contain recognizable ICR 2-like motifs. However, the 5Ј-terminal 11 nt of RNAs 1 and 2 are identical, and the 5Ј UTRs of both RNAs contain a predicted 5Ј-terminal stem-loop structure consisting of a 12-bp stem and a 4-nt loop (M fold) ( Fig. 1A and B). Interestingly, replication of RNA 3 with its 5Ј UTR replaced with that of either RNA 1 or 2 was not supported in P12 plants (27).Replication of AMV RNA 1 carrying the 5 UTR of either RNA 2 or 3. In the ...

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The 5′ Untranslated Region of Alfalfa Mosaic Virus RNA 1 Is Involved in Negative-Strand RNA Synthesis

Vlot

Bol

2003

J Virol

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“…In AlMV, a tandem repeat at the 5h untranslated region of RNA 3 affected accumulation of P3 protein (Van der Vossen et al, 1993) and may be involved with ribosome binding (Pinck et al, 1981). In ononis yellow mosaic tymovirus, the repeat of the 5h untranslated region has been proposed to form a stem-loop structure to modulate initiation of translation of the overlapping tymoviral genes (Ding et al, 1989).…”

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Two novel subgenomic RNAs derived from RNA 3 of tomato aspermy cucumovirus.

Shi¹,

Ding²,

Symons³

1997

Journal of General Virology

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Two abundant subgenomic RNAs, designated RNA 3B and RNA 5, were found to be associated with the V strain of tomato aspermy cucumovirus (V-TAV). Sequence determination showed that the 3h-terminal 323 nucleotides (nt) of RNA 3B was identical to RNA 5, whereas its 5h-terminal 163 nt was a direct repeat (one nt difference) of the 5h-half of RNA 5, and that both RNAs are completely homologous to the 3h-terminal untranslated region of TAV RNA 3. TAV RNAs 3B and 5 were also detected in the infection of a pseudorecombinant virus con-

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Long Sequences in the 5′ Noncoding Region of Plum Pox Virus Are Not Necessary for Viral Infectivity but Contribute to Viral Competitiveness and Pathogenesis

1997

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The 5'-terminal 31 nucleotides of the 146-nucleotides-long 5' noncoding region of plum pox potyvirus (PPV) are highly conserved in all the members of the Potyvirus genus. To map the sequences of the 5' noncoding region that are necessary in vivo for infectivity, we have constructed a nested set of substitution and deletion mutants. While we were not able to infect Nicotiana clevelandii plants with full-length PPV transcripts bearing mutations in the 5'-terminal 35 nucleotides of the viral genome, the deletion of long sequences located between nucleotides 39 and 145 did not alter either the rate of infection or viral accumulation. Nevertheless, these mutants were not able to compete with the wild-type strain in coinoculation experiments. Plants infected with a PPV mutant that lacked nucleotides 127 to 145 showed a very mild symptomathology; the wild-type symptom severity was recovered after spontaneous second-site mutations.

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Role of the 5′ leader sequence of alfalfa mosaic virus RNA 3 in replication and translation of the viral RNA

Cited by 34 publications

References 33 publications

The 5′ Untranslated Region of Alfalfa Mosaic Virus RNA 1 Is Involved in Negative-Strand RNA Synthesis

The 5′ Untranslated Region of Alfalfa Mosaic Virus RNA 1 Is Involved in Negative-Strand RNA Synthesis

Two novel subgenomic RNAs derived from RNA 3 of tomato aspermy cucumovirus.

Long Sequences in the 5′ Noncoding Region of Plum Pox Virus Are Not Necessary for Viral Infectivity but Contribute to Viral Competitiveness and Pathogenesis

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