Evidence for replicative recombination in cauliflower mosaic virus

Dixon, Linda K.; Nyffenegger, T.; Delley, G.; Martı́nez-Izquierdo, José Antonio; Hohn, Th.

doi:10.1016/0042-6822(86)90310-7

Cited by 44 publications

(34 citation statements)

References 12 publications

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“…Three ORF I product caulimoviral sequences were used: CaMV, Cabb S isolate (Franck et al, 1980), CERV (Hull et aL, 1986) and FMV . Sequences of ORF I polypeptides of several other isolates of CaMV (Balazs et al, 1982;Gardner et al, 1981 ;Dixon et al, 1986;Hirochika et al, 1985) were not separately analysed since they differ only slightly from that of Cabb S. For comparison purposes, significance scores were determined as detailed below for published alignments that differed significantly from the present one. These included the alignment by Savithri & Murthy (1983) of AIMV (Barker et al, 1983), BMV (Ahlquist et aL, 1981) and CMV (Gould & Symons, 1982) sequences and that of Saito et al (1988) for TMV-like proteins.…”

Section: Methodsmentioning

confidence: 99%

Similarities Between Putative Transport Proteins of Plant Viruses

Melcher

1990

Journal of General Virology

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The nucleic acids of many plant viruses encode proteins with one or more of the following properties: an Mr of approximately 30000, localization in the cell wall of the infected plant and a demonstrated role in cell-tocell transport of infection. A progressive alignment strategy, aligning first those sequences known to be similar, and then aligning the resulting groups of sequences, was used to examine further the relatedness of the amino acid sequences of putative transport proteins of caulimoviruses, of proteins similar to the putative transport protein of alfalfa mosaic virus (AIMV) and of those similar to the tobacco mosaic virus (TMV) 30K protein. The strategy first identified regions in which multiple dipeptides of one group were similar to those of another group. The regions of similarity were brought into alignment by the conservative introduction of gaps. The positions of the introduction of gaps were adjusted to optimize similarity.Statistical significances of the resulting alignments, determined both by comparison with shuffled amino acid sequences and with the sequence alignment off-set by 1 to 15 residues in each direction, suggest that the amino acid sequences of the three groups of viruses are distantly related. Nevertheless, significant relationships between members of the caulimoviral group of sequences and members of each of the AIMV-like and TMV-like groups were found. These relationships and the analysis of the number of insertions/deletions between present sequences and a hypothetical common ancestor suggest that the sequences of the caulimoviral proteins are less diverged from the ancestor than either the AIMV-like or TMV-like proteins. The alignment identified common regions of predicted secondary structure and regions of similar hydropathy, regions possibly crucial for proper functioning of the proteins.

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Section: Methodsmentioning

confidence: 99%

Similarities Between Putative Transport Proteins of Plant Viruses

Melcher

1990

Journal of General Virology

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“…Junctions between parental sequences in recombinants obtained from the inoculation of plants with marked pairs of mutant DNAs (V. Vaden & U. Melcher, unpublished data), in isolates which appear to be chimeras of other isolates (Dixon et al, 1986;V. Vaden & U. Melcher, unpublished data), and in products of agroinfection with partially dimeric CaMV DNA (Grimsley et al, 1986) are consistent with their generation during reverse transcription.…”

Section: Introductionmentioning

confidence: 65%

“…Undetected exchanges may have occurred in other regions, particularly the large intergenic region. CaMV isolates CM4-184 (Dixon et al, 1986) and W (U. Melcher, unpublished data) are recombinants that arose without selective pressure apparently due to cross-isolate template switching between the ends of 35S RNAs during DNA minus strand synthesis by reverse transcription.…”

Section: Discussionmentioning

confidence: 99%

Competition between Isolates and Variants of Cauliflower Mosaic Virus in Infected Turnip Plants

Zhang¹,

Melcher²

1989

Journal of General Virology

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SUMMARYThe Cabb S isolate of cauliflower mosaic virus (CaMV) is the only isolate that can be recovered from turnip plants mixedly infected with Cabb S and an infectious variant of Cabb S. Analysis of the progeny resulting from mixed infections of turnip plants was done for a better understanding of this dominance. Cabb S DNA was the dominant DNA recovered from plants after a mixed infection with Cabb S and D/H or W isolates of CaMV, whereas UM130 (derived from Cabb S by the insertion of a short oligonucleotide in open reading frame III) coexisted in turnip plants with D/H, NY8153, CM4-184 and W isolates. To determine whether there are additional sequences responsible for the ability of Cabb S to dominate over UM130, coinoculation experiments were done using chimeric DNAs, obtained by in vivo recombination (IC141, IC143 and VR246) and by in vitro construction (W/CS and CS/W). Chimeras IC141, IC143 and VR246 coexisted in turnip plants with UM130. Chimera CS/W dominated over UM 130, whereas UM 130 dominated over W/CS. The location of Cabb S sequences in these chimeras suggests that more than one region is responsible for the competitive advantage of Cabb S DNA. A different modification of Cabb S DNA in open reading frame III also destroyed the ability of the DNA to dominate over the W isolate. In DNA from virions obtained after co-infection with U M 130 and CS/W, more molecules were recovered with U M 130-specific sequences at position 1364 than with those at position 2040. This and similar results with progeny from W/CS and UM130 co-infection suggest that genetic exchanges had occurred. However, exchanges were not detected in progeny from other mixed infections. Thus the dominance of the Cabb S isolate in mixed infections was due primarily to a better competitive ability of the Cabb S DNA. Plants inoculated first with UM130 and 2 to 8 days later with Cabb S contained only UM130 CaMV DNA, indicating that dominance was unable to overcome cross-protection.

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“…Several hot spots have been proposed as being involved in replicase-driven recombination in caulimoviruses, including the 5Ј end of the linear molecules and the transcription and reverse transcription initiation sites (10,17). Some of these regions of the CERV genome were often involved in CarSV-CERV junctions.…”

Section: Discussionmentioning

confidence: 99%

The DNA of a Plant Retroviroid-Like Element Is Fused to Different Sites in the Genome of a Plant Pararetrovirus and Shows Multiple Forms with Sequence Deletions

Vera

Daròs

Flores

et al. 2000

J Virol

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Carnation small viroid-like RNA (CarSV RNA) and its homologous DNA are the two forms of a unique plant retroviroid-like system. CarSV RNA is a 275-nucleotide noninfectious viroid-like RNA, present in certain carnation plants, which can adopt hammerhead structures in both polarity strands and self-cleave accordingly. CarSV DNA is organized as a series of head-to-tail multimers forming part of extrachromosomal elements in which CarSV DNA sequences are fused to sequences of carnation etched ring virus (CERV), a plant pararetrovirus. Analysis of more than 30 CarSV-CERV DNA junctions showed that distinct regions of the viral genome seem able to interact with CarSV DNA. All these junctions were short nucleotide stretches common to both CarSV and CERV DNAs. This suggests a polymerase-driven mechanism for their origin involving an enzyme with low processivity, most likely the viral reverse transcriptase. This view was further supported by the observation that most of CarSV sequences forming part of the junctions correspond either to strong secondary structure motifs in the conformation proposed for CarSV RNA or to its self-cleavage sites, which may have facilitated polymerase jumping. Accompanying the most-abundant CarSV RNA, a series of CarSV RNAs with sequence deletions were previously characterized. Here we have identified some of their corresponding DNA forms, together with other CarSV DNA forms with deletions not found in any CarSV RNA species identified so far. Some of these CarSV DNA forms have also been detected fused to CERV sequences. The existence of these shortened CarSV DNA versions may provide a continuous input of their corresponding transcripts and explain the persistence of CarSV RNAs with defective hammerhead structures for which an RNA-RNA model of amplification seems unlikely.Carnation small viroid-like RNA (CarSV RNA) and its homologous DNA, have been proposed as the two forms of a unique plant retroviroid-like system (5). CarSV RNA is a 275-nucleotide (nt) circular RNA present in certain carnation plants which can form hammerhead structures in both polarity strands and self-cleave in vitro as predicted by these ribozymes (16). Despite the structural similarities that CarSV RNA shares with viroid and viroid-like satellite RNAs (for reviews on these pathogens, see references 2, 9, 14, 15, and 31), two main differences separate them: CarSV RNA lacks an extracellular infectious phase, i.e., it cannot be transmitted horizontally from plant to plant, and also it exists as a homologous DNA counterpart (5; L. Palkovics, K. Salánki, A. Wittner, E. Tóth, and E. Balázs, 5th Int. Cong. Plant Mol. Biol., abstr. 1019, 1997). CarSV DNA accumulates at low levels in carnation since it is only detectable by PCR amplification, and examination of the patterns of PCR-amplified products indicates that CarSV DNA is organized as a series of head-to-tail multimers (5). The CarSV RNA-DNA element bears a close resemblance to two small linear RNAs from the newt (330 nt) and schistosomes (335 nt), which are also able to adopt ...

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Evidence for replicative recombination in cauliflower mosaic virus

Cited by 44 publications

References 12 publications

Similarities Between Putative Transport Proteins of Plant Viruses

Similarities Between Putative Transport Proteins of Plant Viruses

Competition between Isolates and Variants of Cauliflower Mosaic Virus in Infected Turnip Plants

The DNA of a Plant Retroviroid-Like Element Is Fused to Different Sites in the Genome of a Plant Pararetrovirus and Shows Multiple Forms with Sequence Deletions

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