The complete nucleotide sequence of RNA 3 of citrus leaf rugose and citrus variegation ilarviruses

Prunus necrotic ringspot virus (PNRSV) occurs as numerous strains or isolates that vary widely in their pathogenic, biophysical and serological properties. Prior attempts to distinguish pathotypes based upon physical properties have not been successful ; our approach was to examine the molecular properties that may distinguish these isolates. The nucleic acid sequence was determined from 1n65 kbp RT-PCR products derived from RNA 3 of seven distinct isolates of PNRSV that differ sero-

Section: Introductionmentioning

confidence: 99%

Virulence and molecular polymorphism of Prunus necrotic ringspot virus isolates.

Hammond

Crosslin

1998

“…Evidence of viral recombination exists in the tobraviruses Angenent et al, 1990) and the equine encephalitis viruses (Hahn et al, 1988), where parts of the genome of one virus are found in the genome of a second virus. Clearly, from the comparisons in this paper and preceding papers on CiLRV (Ge & Scott, 1994;Scott & Ge, 1995), no evidence for CiLRV molecules being part of RBDV exists. Expectations of such evidence are, perhaps, simplistic and any relationship between ilarviruses and RBDV may be less defined and mimic to some degree the relationship between AMV and the ilarviruses.…”

Section: Short Communication 3235mentioning

confidence: 90%

“…A subgenomic RNA of 0-3 x 106 (RNA 4) is also encapsidated in the virions (Murphy et al, 1995). Sequence data indicate that the RNA 2, RNA 3 and RNA 4 of CiLRV are 2990, 2289 and 1009 nt in length, respectively (Ge & Scott, 1994;Scott & Ge, 1995). The data for RNA 3 and RNA 4, both in terms of length and organization, are in good agreement with the few published sequences available for ilarviruses and also agree with sequence data available for more extensively studied members of the Bromoviridae.…”

Section: S W Scott* and Xin Getmentioning

confidence: 99%

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The nucleotide sequence of citrus leaf rugose virus RNA 1

Scott

1995

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The nucleotide sequence of citrus leaf rugose virus (CiLRV) RNA 1 consists of 3404 nucleotides and contains one open reading frame (ORF) which encodes a putative translation product of 1051 amino acids with a calculated M r of 118 339. Both the nucleotide sequence of CiLRV RNA 1 and its translated polypeptide share similarities with those of the RNA 1 of alfalfa mosaic virus. However, the relationship is not as close as that which exists between the polymerase signatures of the two viruses, which are found on RNA 2. This is the first report of the full-length sequence for the RNA 1 of an ilarvirus and completes the first sequence for an entire ilarvirus genome. If it is typical of members of the genus then, as has long been speculated, the genomic organization of ilarviruses is identical to that of other genera in the family Bromoviridae.

“…The virus was grown in Chenopodium quinoa and purified according to van der Meer et al (1976). Details of the procedures used for cloning and sequencing have been described previously Scott & Ge, 1995). In essence, RNA was extracted from purified virions, polyadenylated, and cDNA was synthesized using oligo(dT)12_ls.…”

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confidence: 99%

The complete nucleotide sequence of the RNA 3 of lilac ring mottle ilarvirus

Scott

Ge²

1995

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The nucleotide sequence of lilac ring motile ilarvirus (LRMV) RNA 3 consists of 2287 nucleotides and contains two open reading frames (ORF). The first encodes a putative translation product of 285 amino acids (M r 31308) and the second encodes a putative translation product of 206 amino acids (M r 22 751). The 3' terminal nucleotides can be folded into a loop structure similar to models proposed for other ilarviruses, although the last four nucleotides are UCGC not AUGC. The absence of the terminal AUGC motif in both LRMV and two isolates of apple mosaic ilarvirus (ApMV) provides circumstantial evidence which confirms the importance of AUGC motifs upstream of the terminal AUGC in the protein binding function associated with these models. Although the 3' terminal structure of LRMV exhibits similarities to that of ApMV, comparison of the putative translation products of the two ORFs with similar products for other ilarviruses showed greatest identity with citrus leaf rugose (CiLRV) and citrus variegation (CW) ilarviruses both of which are members of subgroup 2 of this genus. Thus it is proposed that LRMV be reassigned to subgroup 2 rather than remaining in its current subgroup, 7, or being reassigned to subgroup 3 which contains ApMV.Lilac ring mottle virus (LRMV) was first described and characterized by van der Meer et al. (1976). It shares some of the properties of the members of the genus Ilarvirus, namely: four RNAs with M r values of 1.2, 1" 1, 0-9 and 0-4x 10 ~ and irregularly shaped isometric particles with some heterogeneity in size. The virus is strongly immunogenic but in serological tests did not exhibit any relationship with prunus necrotic ringspot (PNRSV), tobacco streak (TSV), elm mottle (EMV) and apple mosaic (ApMV) ilarviruses (van der Meer & Huttinga, 1979). Zuidema & Jaspars (1984) have proposed a model for the secondary structure of the 3' terminal regions of TSV and the closely related alfalfa mosaic virus (A1MV). In this model, hairpin (stem-loop) structures are stabilized by the presence of AUGC motifs with the terminal four nucleotides being AUGC. This secondary structure was proposed as being involved in the 'genome activation' common to both ilarviruses and A1MV in which the presence of either RNA 4 or the coat protein of the virus is required to initiate infection (van Vloten-Doting, 1975). In a subsequent report the 97 nucleotides at the 3' * Author for correspondence. Fax + 1 803 656 0274.I" Present address: Department of Biological Sciences, University of South Carolina, Columbia, SC 29208, USA.Sequence data from this article have been deposited with the EMBL/GenBauk databases under accession no. U17391. terminus of LRMV were described and shown to form a structure similar to that found in TSV and A1MV (Bol et al., 1985). However, the four nucleotides at the 3' terminus of LRMV were ACGC rather than AUGC.Two recent reports have examined extensively the secondary structure at the 3' terminus of A1MV and its involvement in protein binding. Houser-Scott et al. (1994) concluded that the ...