Variation in Phytopathogenic Viruses

Kunkel, L. O.

doi:10.1146/annurev.mi.01.100147.000505

Cited by 23 publications

(6 citation statements)

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“…Thus, there was the possibility of cloning a noninfectious RNA. In addition, the frequency of variants in a TMV population is extremely high (2,27), further increasing the possibility of generating cDNAs from other than wild-type starting material. For these reasons we produced multiple, independent cDNA clones of each region of the viral genome to increase the probability of generating a composite full-length construct corresponding to an infectious parental genotype.…”

Section: Discussionmentioning

confidence: 99%

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cDNA cloning of the complete genome of tobacco mosaic virus and production of infectious transcripts

Dawson

Beck

Knorr

et al. 1986

Proc. Natl. Acad. Sci. U.S.A.

228

133

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The entire genome of tobacco mosaic virus (TMV) was copied into a series of subgenomic cDNA clones. cDNA sequences of the 5' and 3' ends of TMV were cloned separately. A synthetic oligonucleotide primer was used to generate a Pst I site at the 5' terminus, whereas a different primer was used to generate an Nde I site at the 3' terminus.This strategy permitted removal of non-TMV sequences from doned cDNA inserts by treatment with exonuclease VII following restriction endonuclease cleavage. Pst I linkers were added to TMV 3' terminal cDNAs. Subgenomic cDNA fragments were ligated together into several independent fullgenomic constructions from which TMV cDNA sequences could be cleanly excised as a single fragment by Pst I digestion.Full-genomic TMV cDNA was ligated immediately downstream from the X phage promoter from pPM1 and transcribed in vitro with Escherichia coli RNA polymerase. RNA transcripts from three of four full-genomic cDNA constructions were infectious, even though they contained 6 non-TMV nucleotides at the 3' end. Transcripts from a construction with 6 extra nucleotides at the 5' end also were infectious. Progeny virus from plants infected with cDNA transcripts appeared identical to the parental vinrus. Restriction maps of independent cDNA clones of the same regions of the genome were identical to each other and as predicted from the reported nucleotide sequence of TMV. Also, sequences of the 200 nucleotides proximal to the 5' termini of four independent cDNA clones were identical to each other and to published sequences, suggesting that independent isolates of TMV may have remarkably similar sequences.Tobacco mosaic virus (TMV) is a virus with worldwide distribution that infects -200 plant species (1). Numerous strains of TMV cause serious losses in tobacco, tomato, and other crop plants. The virion is a rod-shaped particle 18 x 300 nm. The genome of TMV resides in a single strand of messenger-sense RNA encoding at least four proteins, two of which are translated from the same reading frame and two from processed mRNA fragments.Historically, TMV has contributed to the understanding of the genetics of RNA viruses, including the first studies on biological variability, mutability and protein sequence variation of viral genomes (2-4). TMV continues to offer numerous advantages as a genetic system. Variants of this virus express a large number of easily scored phenotypic characters useful in studying specific viral functions. Isolates of TMV that vary in symptomology, host range, elicitation of host defense mechanisms, cross-protection, encapsidation, cell-to-cell and long-distance movement within the host, and several functions of RNA replication have been described. TMV strains infecting tobacco and tomato have been most intensely investigated. Of these, two viral strains and a variant have been fully sequenced (5-7). However, in spite of our understanding of the general organization and replication of this virus, only a few viral functions have been assigned to specific sequences. The inabil...

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Section: Discussionmentioning

confidence: 99%

“…Historically, TMV has contributed to the understanding of the genetics of RNA viruses, including the first studies on biological variability, mutability and protein sequence variation of viral genomes (2)(3)(4). TMV continues to offer numerous advantages as a genetic system.…”

mentioning

confidence: 99%

cDNA cloning of the complete genome of tobacco mosaic virus and production of infectious transcripts

Dawson

Beck

Knorr

et al. 1986

Proc. Natl. Acad. Sci. U.S.A.

228

133

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“…This dates back to the 1920s and 1930s [46]. (For a discussion of the terms ''isolate'', ''strain'', ''mutant'' and ''variant'' see [33]).…”

Section: Analysis and Evidence For Genetic Variation Of Plant Virusesmentioning

confidence: 99%

Variation and evolution of plant virus populations

García‐Arenal

Fraile

Malpica

2003

International Microbiology

186

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Over the last 15 years, interest in plant virus evolution has re-emerged, as shown by the increasing number of papers published on this subject. In recent times, research in plant virus evolution has been viewed from a molecular, rather than populational, standpoint, and there is a need for work aimed at understanding the processes involved in plant virus evolution. However, accumulated data from analyses of experimental and natural populations of plant viruses are beginning to delineate some trends that often run contrary to accepted opinion: (1) high mutation rates are not necessarily adaptive, as a large fraction of the mutations are deleterious or lethal; (2) in spite of high potential for genetic variation, populations of plant viruses are not highly variable, and genetic stability is the rule rather than the exception; (3) the degree of constriction of genetic variation in virus-encoded proteins is similar to that in their eukaryotic hosts and vectors; and (4) in spite of huge census sizes of plant virus populations, selection is not the sole factor that shapes their evolution, and genetic drift may be important. Here, we review recent advances in understanding plant virus evolution, and describe the experimental and analytical methods most suited to this purpose.

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“…Considerable data now document the extensive genetic variability and potential for rapid evolution of RNA viruses (1)(2)(3)(4)(5)(6)(7)(8)(9)(10)(11)(12)(13)(14)(15)(16)(17)(18)(19). The molecular basis for this variation is extremely high mutation frequencies per average site in RNA virus genomes (ranging between 10-3 and 10-6 and usually of the order of 10' to .…”

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confidence: 99%

High frequency of single-base transitions and extreme frequency of precise multiple-base reversion mutations in poliovirus.

Torre

Giachetti

Semler

et al. 1992

Proc. Natl. Acad. Sci. U.S.A.

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We employed independent clones of a temperature-sensitive mutant of type 1 poliovirus, to quantitate the frequency of specific U -+ C transitions at nucleotide 5310, within the genomic region encoding polypeptide 3AB, which is involved in the initiation ofRNA replication.Only this U --C base substitution restores the wild-type phenotypic ability to form plaques at 39C; the other two base substitutions at this site are lethal. The observed frequency of this specific transition averaged 2 x i0S, and all revertant viruses forming plaques at39°C contained the expected cytidine at nucleotide 5310. Incredibly, only 3 of 10 revertants exhibited this one specific U --C transition whereas 7 of 10 exhibited this same transition plus four additional base substitutions that precisely reverted temperature-sensitive 3AB-310/4 to wildtype poliovirus sequence (these latter four mutations had been introduced into 3AB-310/4 as silent third base mutations to provide new restriction sites in infectious cDNAs). No other mutations were detected in this polypeptide 3AB domain in either the single-base or the precise 5-base revertants. No intermediates were seen; all revertants exhibited either the single U --C transition at nucleotide 5310 or the same transition plus four precise reversions to the wild-type sequence at sites 8, 11, 43, and 46 bases distant from nucleotide 5310. Similar results were obtained after transfection of cDNAderived transcripts. We discuss possible mechaniss for our data. These include (but may not be limited to) error-prone polymerase activity, sequential RNA recombination events joining independent mutations, or some unusual RNA editing process.Considerable data now document the extensive genetic variability and potential for rapid evolution of RNA viruses (1-19). The molecular basis for this variation is extremely high mutation frequencies per average site in RNA virus genomes (ranging between 10-3 and 10-6 and usually of the order of 10' to 10-5). Such high mutation frequencies dictate that even clones of RNA viruses are not homogeneous populations but consist of complex "mutant swarms" or "quasispecies" populations (20)(21)(22)(23)(24)(25)(26). By virtue of their extreme heterogeneity, quasispecies populations can adapt rapidly to new environments by selection of variants preexisting within the population. Some very low polymerase error values have been reported for poliovirus. Thus, Parvin et al. (27) have estimated a poliovirus mutation rate of <10-6 per site for viable neutral or quasineutral mutants of poliovirus.A similar low error frequency of 2.5 x 10-6 was estimated for the reversion of a poliovirus amber mutant (28). In contrast, frequencies of resistance to monoclonal antibody neutralization for poliovirus are in the range 10-3 to 10-5 base substitutions per site (29,30). In vitro measurements of poliovirus polymerase error frequencies (31) and the mutation frequency of poliovirus type 1 to a high degree of resistance to guanidine indicated specific single-site mutation frequencies...

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Variation in Phytopathogenic Viruses

Cited by 23 publications

References 0 publications

cDNA cloning of the complete genome of tobacco mosaic virus and production of infectious transcripts

cDNA cloning of the complete genome of tobacco mosaic virus and production of infectious transcripts

Variation and evolution of plant virus populations

High frequency of single-base transitions and extreme frequency of precise multiple-base reversion mutations in poliovirus.

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