Use of Highly Conserved Motifs in Plant Virus RNA Polymerases as the Tags for Specific Detection of Carmovirus-Related RNA-Dependent RNA Polymerase Genes

Morozov, S. Yu.; Ryabov, Eugene V.; Leiser, Robert-Matthias; Завриев, С. К.

doi:10.1006/viro.1995.1084

Cited by 20 publications

(13 citation statements)

References 0 publications

Supporting

Mentioning

Contrasting

Unclassified

Order By: Relevance

“…Two small ORFs, located in the central part of the viral genome, encode polypeptides of 7 (p7) and 12 (p12) kDa, respectively, which are presumably involved in virus movement, and the 3Ј-proximal ORF encodes a 37-kDa capsid protein (CP). This genome organization was deduced from a Spanish isolate, and no additional sequences from other isolates have been reported so far, with the exception of those corresponding to the CP gene and flanking sequences of a Dutch isolate and a small portion (408 nt) of the RdRp gene of a Russian isolate (5,39). Moreover, in contrast with other viral groups for which extensive analysis of sequence variation has been done (see reference 22 and references therein), studies on the genetic heterogeneity of carmoviruses are very scarce, precluding an estimation of the genome stability in this viral genus.…”

mentioning

confidence: 99%

Insights into the Selective Pressures Restricting Pelargonium Flower Break Virus Genome Variability: Evidence for Host Adaptation

Rico

Ivars

Elena

et al. 2006

J Virol

View full text Add to dashboard Cite

The molecular diversity of Pelargonium flower break virus (PFBV) was assessed using a collection of isolates from different geographical origins, hosts, and collecting times. The genomic region examined was 1,828 nucleotides (nt) long and comprised the coding sequences for the movement (p7 and p12) and the coat (CP) proteins, as well as flanking segments including the entire 3 untranslated region (3 UTR). Some constraints limiting viral heterogeneity could be inferred from sequence analyses, such as the conservation of the amino acid sequences of p7 and of the shell domain of the CP, the maintenance of a leucine zipper motif in p12, and the preservation of a particular folding in the 3 UTR. A remarkable covariation, involving five specific amino acid sites, was found in the CP of isolates largely propagated in the local lesion host Chenopodium quinoa and in the progeny of a PFBV variant subjected to serial passages in this host. Concomitant with this covariation, up to 30 nucleotide substitutions in a 1,428-nt region of the viral RNA could be attributable to C. quinoa-specific adaptation, representing one of the most outstanding cases of host-driven genome variation for a plant virus. Globally, the results indicate that the selective pressures exerted by the host play a critical role in shaping PFBV populations and that these populations are likely being selected for at both protein and RNA levels.It is commonly believed that the high mutation rates characteristic of RNA viruses, together with their short replication times and large populations, favor their rapid adaptation to changing situations (12, 13). Despite the high potential for genetic variation of these pathogens, a considerable number of studies on the diversity of plant virus populations have found a remarkable genetic stability (reviewed in reference 21). This stability is usually considered to be the result of selective pressures inherently imposed by genome replication and expression strategies and by virus-vector and virus-host interactions. In addition, random genetic drift due to bottlenecks associated with transmission or colonization events may also limit the eventual accumulation of variation (21,23,47). Investigating the factors affecting the diversity levels of viral populations can undoubtedly provide significant clues for the development of efficient and stable control strategies for viral pathogens (22,27,49).Pelargonium flower break virus (PFBV) is one of the most prevalent viruses infecting geraniums (Pelargonium spp.) throughout the world (1, 3, 6, 19, 41, 52). Its most conspicuous symptoms are white flower streaking, chlorotic spotting of leaves, and growth reduction causing significant losses in crop production. PFBV is mainly transmitted by vegetative propagation and mechanical inoculation, although transmissions by irrigation systems and by the western flower thrips Frankiniella occidentalis may also occur (30).PFBV is a member of the genus Carmovirus (family Tombusviridae) and, like all the species in the group, produces icosahe...

show abstract

mentioning

confidence: 99%

Insights into the Selective Pressures Restricting Pelargonium Flower Break Virus Genome Variability: Evidence for Host Adaptation

Rico

Ivars

Elena

et al. 2006

J Virol

View full text Add to dashboard Cite

show abstract

“…The sequences used lie over regions that are conserved within the carmoviruses [Morozov et al, 1995], The following primers were used: LI, 5'-CGTATACTGGCTCCTCTGC-3; Ul, 5-CACAGT-TGTTACCTTGCC-3 ; U2, 5-CGCTGGACAAGAT-CTGGG-3 ; U3, 5-CCCTGTCCGGAAAAGGGG-3 . The primers were designed to amplify 343, 510 and 832 bp fragments from PFBV-RNA-dependent RNA polymerase (RdRp) gene, respectively, T'he primer pairs L2 with the sequences 5'-CCCAGATTTCAGGCCCGC-3' and U2, flanking a 1543 base portion of the RdRp gene were also used.…”

Section: Rna Extractionmentioning

confidence: 99%

Use of the Reverse Transcription‐Polymerase Chain Reaction for the Detection of Pelargonium Flower Break Carmovirus

Franck

Loebenstein

Gera

1997

Journal of Phytopathology

View full text Add to dashboard Cite

A polymerase chain reaction (PCR)-based assay was used to detect pelargonium fiower break carmovirus (PFBV) in total RNA extractions made from infected Pelargonium plants. Extracts were reverse transcribed (RT) and the resultant cDNA was amplified by PCR, using oligonucleotide primers specific for 343, 510 and 832 base pair fragments of the RNA-dependent RNA polymerase gene of PFBV.The specificity and sensitivity of RT-PCR were compared with the enzyme-linked immunosorbent assay (ELISA) for the detection of PFBV in Pelargonium tissues. The virus could be detected efficiently in high dilutions of sap from infected plants and at low concentrations of purified virus. Although BLISA is a powerful tool for virus detection, RT-PCR was over 1000 times more sensitive in detecting PFBV in leaf extracts of infected Pelargonium than was ELISA. The limit of detecting PFBV RNA by RT-PCR was 200 fg, compared with 200 pg of virus by ELISA.

show abstract

“…The capsid protein (CP) was estimated to be~37-40 kDa on SDS-PAGE and western blot analysis, and the double-stranded (ds)RNA profile consisted of three major bands about 4.2, 1.9, and 1.5 kb. Using primers specific to the carmovirus RNA-dependent RNA polymerase (RdRP) [4], a small RT-PCR product was amplified from the viral genome and sequenced. Homology searches in BLAST programs [5] suggested that the virus could indeed be a new carmovirus.…”

Section: Introductionmentioning

confidence: 99%

Complete nucleotide sequence of Nootka lupine vein-clearing virus

et al. 2007

View full text Add to dashboard Cite

The complete genome sequence of Nootka lupine vein-clearing virus (NLVCV) was determined to be 4,172 nucleotides in length containing four open reading frames (ORFs) with a similar genetic organization of virus species in the genus Carmovirus, family Tombusviridae. The order and gene product size, starting from the 5'-proximal ORF consisted of: (1) polymerase/replicase gene, ORF1 (p27) and ORF1RT (readthrough) (p87), (2) movement proteins ORF2 (p7) and ORF3 (p9), and, (3) the 3'-proximal coat protein ORF4, (p37). The genomic 5'- and 3'-proximal termini contained a short (59 nt) and a relatively longer 405 nt untranslated region, respectively. The longer replicase gene product contained the GDD motif common to RNA-dependent RNA polymerases. Phylogenetically, NLVCV formed a subgroup with the following four carmoviruses when separately comparing the amino acids of the coat protein or replicase protein: Angelonia flower break virus (AnFBV), Carnation mottle virus (CarMV), Pelargonium flower break virus (PFBV), and Saguaro cactus virus (SgCV). Whole genome nucleotide analysis (percent identities) among the carmoviruses with NLVCV suggested a similar pattern. The species demarcation criteria in the genus Carmovirus for the amino acid sequence identity of the polymerase (<52%) and coat (<41%) protein genes restricted NLVCV as a distinct species, and instead, placed it as a tentative strain of CarMV, PFBV, or SgCV when both the polymerase and CP were used as the determining factors. In contrast, the species criteria that included different host ranges with no overlap and lack of serology relatedness between NLVCV and the carmoviruses, suggested that NLVCV was a distinct species. The relatively low cutoff percentages allowed for the polymerase and CP genes to dictate the inclusion/exclusion of a distinct carmovirus species should be reevaluated. Therefore, at this time we have concluded that NLVCV should be classified as a tentative new species in the genus Carmovirus, family Tombusviridae.

show abstract

Use of Highly Conserved Motifs in Plant Virus RNA Polymerases as the Tags for Specific Detection of Carmovirus-Related RNA-Dependent RNA Polymerase Genes

Cited by 20 publications

References 0 publications

Insights into the Selective Pressures Restricting Pelargonium Flower Break Virus Genome Variability: Evidence for Host Adaptation

Insights into the Selective Pressures Restricting Pelargonium Flower Break Virus Genome Variability: Evidence for Host Adaptation

Use of the Reverse Transcription‐Polymerase Chain Reaction for the Detection of Pelargonium Flower Break Carmovirus

Complete nucleotide sequence of Nootka lupine vein-clearing virus

Contact Info

Product

Resources

About