scholarly journals Nucleoside Analogue Mutagenesis of a Single-Stranded DNA Virus: Evolution and Resistance

2012 ◽  
Vol 86 (18) ◽  
pp. 9640-9646 ◽  
Author(s):  
Pilar Domingo-Calap ◽  
Marianoel Pereira-Gómez ◽  
Rafael Sanjuán
Keyword(s):  
Nucleoside Analogue ◽  
Rna Viruses ◽  
Spontaneous Mutation ◽  
Chemical Mutagenesis ◽  
Mutation Rates ◽  
Nucleotide Substitutions ◽  
Single Stranded Dna ◽  
Dna Viruses ◽  
Population Extinction ◽  
Nucleotide Mutation

It has been well established that chemical mutagenesis has adverse fitness effects in RNA viruses, often leading to population extinction. This is mainly a consequence of the high RNA virus spontaneous mutation rates, which situate them close to the extinction threshold. Single-stranded DNA viruses are the fastest-mutating DNA-based systems, with per-nucleotide mutation rates close to those of some RNA viruses, but chemical mutagenesis has been much less studied in this type of viruses. Here, we serially passaged bacteriophage ϕX174 in the presence of the nucleoside analogue 5-fluorouracil (5-FU). We found that 5-FU was unable to trigger population extinction for the range of concentrations tested, but it negatively affected viral adaptability. The phage evolved partial drug resistance, and parallel nucleotide substitutions appearing in independently evolved lines were identified as candidate resistance mutations. Using site-directed mutagenesis, two single-nucleotide substitutions in the lysis protein E (T572C and A781G) were shown to be selectively advantageous in the presence of 5-FU. In RNA viruses, base analogue resistance is often mediated by changes in the viral polymerase, but this mechanism is not possible for ϕX174 and other single-stranded DNA viruses because they do not encode their own polymerase. In addition to increasing mutation rates, 5-FU produces a wide variety of cytotoxic effects at the levels of replication, transcription, and translation. We found that substitutions T572C and A781G lost their ability to confer 5-FU resistance after cells were supplemented with deoxythymidine, suggesting that their mechanism of action is at the DNA level. We hypothesize that regulation of lysis time may allow the virus to optimize progeny size in cells showing defects in DNA synthesis.

scholarly journals Viral Mutation Rates

2010 ◽  
Vol 84 (19) ◽  
pp. 9733-9748 ◽  
Author(s):  
Rafael Sanjuán ◽  
Miguel R. Nebot ◽  
Nicola Chirico ◽  
Louis M. Mansky ◽  
Robert Belshaw
Keyword(s):  
Mutation Rate ◽  
Rna Viruses ◽  
Experimental Testing ◽  
Mutation Rates ◽  
Cell Infection ◽  
Nucleotide Substitutions ◽  
Data Set ◽  
Dna Viruses ◽  
Double Stranded Dna ◽  
Viral Mutation

ABSTRACT Accurate estimates of virus mutation rates are important to understand the evolution of the viruses and to combat them. However, methods of estimation are varied and often complex. Here, we critically review over 40 original studies and establish criteria to facilitate comparative analyses. The mutation rates of 23 viruses are presented as substitutions per nucleotide per cell infection (s/n/c) and corrected for selection bias where necessary, using a new statistical method. The resulting rates range from 10−8 to10−6 s/n/c for DNA viruses and from 10−6 to 10−4 s/n/c for RNA viruses. Similar to what has been shown previously for DNA viruses, there appears to be a negative correlation between mutation rate and genome size among RNA viruses, but this result requires further experimental testing. Contrary to some suggestions, the mutation rate of retroviruses is not lower than that of other RNA viruses. We also show that nucleotide substitutions are on average four times more common than insertions/deletions (indels). Finally, we provide estimates of the mutation rate per nucleotide per strand copying, which tends to be lower than that per cell infection because some viruses undergo several rounds of copying per cell, particularly double-stranded DNA viruses. A regularly updated virus mutation rate data set will be available at www.uv.es/rsanjuan/virmut .

scholarly journals Why genes overlap in viruses

2010 ◽  
Vol 277 (1701) ◽  
pp. 3809-3817 ◽  
Author(s):  
Nicola Chirico ◽  
Alberto Vianelli ◽  
Robert Belshaw
Keyword(s):  
Rna Viruses ◽  
Harmful Effect ◽  
Negative Relationship ◽  
Mutation Rates ◽  
Virus Species ◽  
Overlapping Genes ◽  
Genome Length ◽  
Dna Viruses ◽  
The Relationship ◽  
Gene Overlap

The genomes of most virus species have overlapping genes—two or more proteins coded for by the same nucleotide sequence. Several explanations have been proposed for the evolution of this phenomenon, and we test these by comparing the amount of gene overlap in all known virus species. We conclude that gene overlap is unlikely to have evolved as a way of compressing the genome in response to the harmful effect of mutation because RNA viruses, despite having generally higher mutation rates, have less gene overlap on average than DNA viruses of comparable genome length. However, we do find a negative relationship between overlap proportion and genome length among viruses with icosahedral capsids, but not among those with other capsid types that we consider easier to enlarge in size. Our interpretation is that a physical constraint on genome length by the capsid has led to gene overlap evolving as a mechanism for producing more proteins from the same genome length. We consider that these patterns cannot be explained by other factors, namely the possible roles of overlap in transcription regulation, generating more divergent proteins and the relationship between gene length and genome length.

scholarly journals Episodic diversifying selection and intragenomic interactions shape the evolution of DNA and RNA viruses

2019 ◽  
Author(s):  
Stéphane Aris-Brosou ◽  
Louis Parent ◽  
Neke Ibeh
Keyword(s):  
Rna Viruses ◽  
Viral Evolution ◽  
Amino Acid Level ◽  
Mutation Rates ◽  
Correlated Evolution ◽  
Dna Viruses ◽  
Diversifying Selection ◽  
Dna And Rna ◽  
Show Evidence ◽  
Key Aspects

AbstractViruses are known to have some of the highest and most diverse mutation rates found in any biological replicator, topped by single-stranded (ss) RNA viruses, while double-stranded (ds) DNA viruses have rates approaching those of bacteria. As mutation rates are tightly and negatively correlated with genome size, selection is a clear driver of viral evolution. However, the role of intragenomic interactions as drivers of viral evolution is less well documented. To understand how these two processes affect viral evolution, we systematically surveyed ssRNA, ssDNA, dsRNA, and dsDNA viruses, to find which virus type and which functions show evidence for episodic diversifying selection and correlated evolution. We show that while evidence for selection is mostly found in single stranded viruses, and correlated evolution is more prevalent in DNA viruses, the genes that are affected by both processes are involved in key aspects of their life cycle, favoring viral stability over proliferation. We further show that both evolutionary processes are intimately linked at the amino acid level, which suggests that selection alone does not explain the whole evolutionary —and epidemiological— potential of viruses.

scholarly journals Phylogenetic Evidence for the Rapid Evolution of Human B19 Erythrovirus

2006 ◽  
Vol 80 (7) ◽  
pp. 3666-3669 ◽  
Author(s):  
Laura A. Shackelton ◽  
Edward C. Holmes
Keyword(s):  
Host Cell ◽  
Evolutionary Dynamics ◽  
Rna Viruses ◽  
Rapid Evolution ◽  
Evolutionary Change ◽  
High Rate ◽  
Mutation Rates ◽  
Genome Replication ◽  
Nucleotide Substitutions ◽  
Viral Pathogen

ABSTRACT Human B19 erythrovirus is a ubiquitous viral pathogen, commonly infecting individuals before adulthood. As with all autonomous parvoviruses, its small single-stranded DNA genome is replicated with host cell machinery. While the mechanism of parvovirus genome replication has been studied in detail, the rate at which B19 virus evolves is unknown. By inferring the phylogenetic history and evolutionary dynamics of temporally sampled B19 sequences, we observed a surprisingly high rate of evolutionary change, at approximately 10−4 nucleotide substitutions per site per year. This rate is more typical of RNA viruses and suggests that high mutation rates are characteristic of the Parvoviridae.

scholarly journals Mutational fitness effects in RNA and single-stranded DNA viruses: common patterns revealed by site-directed mutagenesis studies

2010 ◽  
Vol 365 (1548) ◽  
pp. 1975-1982 ◽  
Author(s):  
Rafael Sanjuán
Keyword(s):  
Site Directed Mutagenesis ◽  
Directed Mutagenesis ◽  
Nucleotide Substitutions ◽  
Single Nucleotide ◽  
Single Stranded Dna ◽  
Dna Viruses ◽  
Fitness Effects ◽  
Lethal Mutations ◽  
Mean Fitness ◽  
The Mean

The fitness effects of mutations are central to evolution, yet have begun to be characterized in detail only recently. Site-directed mutagenesis is a powerful tool for achieving this goal, which is particularly suited for viruses because of their small genomes. Here, I discuss the evolutionary relevance of mutational fitness effects and critically review previous site-directed mutagenesis studies. The effects of single-nucleotide substitutions are standardized and compared for five RNA or single-stranded DNA viruses infecting bacteria, plants or animals. All viruses examined show very low tolerance to mutation when compared with cellular organisms. Moreover, for non-lethal mutations, the mean fitness reduction caused by single mutations is remarkably constant (0.10–0.13), whereas the fraction of lethals varies only modestly (0.20–0.41). Other summary statistics are provided. These generalizations about the distribution of mutational fitness effects can help us to better understand the evolution of RNA and single-stranded DNA viruses.

scholarly journals Molecular Nature of 11 Spontaneousde NovoMutations inDrosophila melanogaster

Genetics ◽  
2001 ◽  
Vol 157 (3) ◽  
pp. 1285-1292 ◽  
Author(s):  
Hsiao-Pei Yang ◽  
Ana Y Tanikawa ◽  
Alexey S Kondrashov
Keyword(s):  
De Novo ◽  
Homo Sapiens ◽  
Spontaneous Mutation ◽  
Loss Of Function ◽  
Nucleotide Substitutions ◽  
Eye Color ◽  
Coding Regions ◽  
Independent Events ◽  
Nucleotide Mutation ◽  
Molecular Nature

AbstractTo investigate the molecular nature and rate of spontaneous mutation in Drosophila melanogaster, we screened 887,000 individuals for de novo recessive loss-of-function mutations at eight loci that affect eye color. In total, 28 mutants were found in 16 independent events (13 singletons and three clusters). The molecular nature of the 13 events was analyzed. Coding exons of the locus were affected by insertions or deletions >100 nucleotides long (6 events), short frameshift insertions or deletions (4 events), and replacement nucleotide substitutions (1 event). In the case of 2 mutant alleles, coding regions were not affected. Because ∼70% of spontaneous de novo loss-of-function mutations in Homo sapiens are due to nucleotide substitutions within coding regions, insertions and deletions appear to play a much larger role in spontaneous mutation in D. melanogaster than in H. sapiens. If so, the per nucleotide mutation rate in D. melanogaster may be lower than in H. sapiens, even if their per locus mutation rates are similar.

scholarly journals The Rate and Character of Spontaneous Mutation in an RNA Virus

Genetics ◽  
2002 ◽  
Vol 162 (4) ◽  
pp. 1505-1511 ◽  
Author(s):  
José M Malpica ◽  
Aurora Fraile ◽  
Ignacio Moreno ◽  
Clara I Obies ◽  
John W Drake ◽  
...  
Keyword(s):  
Mutation Rate ◽  
Movement Protein ◽  
Rna Viruses ◽  
Rna Virus ◽  
Spontaneous Mutation ◽  
Mutation Rates ◽  
Lower Side ◽  
Mutation Process ◽  
Spontaneous Mutation Rate ◽  
Mutant Frequency

Abstract Estimates of spontaneous mutation rates for RNA viruses are few and uncertain, most notably due to their dependence on tiny mutation reporter sequences that may not well represent the whole genome. We report here an estimate of the spontaneous mutation rate of tobacco mosaic virus using an 804-base cognate mutational target, the viral MP gene that encodes the movement protein (MP). Selection against newly arising mutants was countered by providing MP function from a transgene. The estimated genomic mutation rate was on the lower side of the range previously estimated for lytic animal riboviruses. We also present the first unbiased riboviral mutational spectrum. The proportion of base substitutions is the same as that in a retrovirus but is lower than that in most DNA-based organisms. Although the MP mutant frequency was 0.02-0.05, 35% of the sequenced mutants contained two or more mutations. Therefore, the mutation process in populations of TMV and perhaps of riboviruses generally differs profoundly from that in populations of DNA-based microbes and may be strongly influenced by a subpopulation of mutator polymerases.

scholarly journals Viral RNA Mutations Are Region Specific and Increased by Ribavirin in a Full-Length Hepatitis C Virus Replication System

2002 ◽  
Vol 76 (17) ◽  
pp. 8505-8517 ◽  
Author(s):  
Ana Maria Contreras ◽  
Yoichi Hiasa ◽  
Wenping He ◽  
Adam Terella ◽  
Emmett V. Schmidt ◽  
...  
Keyword(s):  
Genetic Variation ◽  
Hepatitis C Virus ◽  
Hepatitis C ◽  
Rna Viruses ◽  
Full Length ◽  
Mutation Rates ◽  
Hcv Rna ◽  
Nucleotide Substitutions ◽  
Replication System ◽  
Error Catastrophe

ABSTRACT High rates of genetic variation ensure the survival of RNA viruses. Although this variation is thought to result from error-prone replication, RNA viruses must also maintain highly conserved genomic segments. A balance between conserved and variable viral elements is especially important in order for viruses to avoid “error catastrophe.” Ribavirin has been shown to induce error catastrophe in other RNA viruses. We therefore used a novel hepatitis C virus (HCV) replication system to determine relative mutation frequencies in variable and conserved regions of the HCV genome, and we further evaluated these frequencies in response to ribavirin. We sequenced the 5′ untranslated region (5′ UTR) and the core, E2 HVR-1, NS5A, and NS5B regions of replicating HCV RNA isolated from cells transfected with a T7 polymerase-driven full-length HCV cDNA plasmid containing a cis-acting hepatitis delta virus ribozyme to control 3′ cleavage. We found quasispecies in the E2 HVR-1 and NS5B regions of untreated replicating viral RNAs but not in conserved 5′ UTR, core, or NS5A regions, demonstrating that important cis elements regulate mutation rates within specific viral segments. Neither T7-driven replication nor sequencing artifacts produced these nucleotide substitutions in control experiments. Ribavirin broadly increased error generation, especially in otherwise invariant regions, indicating that it acts as an HCV RNA mutagen in vivo. Similar results were obtained in hepatocyte-derived cell lines. These results demonstrate the potential utility of our system for the study of intrinsic factors regulating genetic variation in HCV. Our results further suggest that ribavirin acts clinically by promoting nonviable HCV RNA mutation rates. Finally, the latter result suggests that our replication model may be useful for identifying agents capable of driving replicating virus into error catastrophe.

Rates of Spontaneous Mutation

Genetics ◽  
1998 ◽  
Vol 148 (4) ◽  
pp. 1667-1686 ◽  
Author(s):  
John W Drake ◽  
Brian Charlesworth ◽  
Deborah Charlesworth ◽  
James F Crow
Keyword(s):  
Cell Division ◽  
Base Pair ◽  
Rna Viruses ◽  
Spontaneous Mutation ◽  
Mutation Rates ◽  
Base Pairs ◽  
Evolutionary Forces ◽  
Sexual Generation ◽  
Higher Eukaryotes

Abstract Rates of spontaneous mutation per genome as measured in the laboratory are remarkably similar within broad groups of organisms but differ strikingly among groups. Mutation rates in RNA viruses, whose genomes contain ca. 104 bases, are roughly 1 per genome per replication for lytic viruses and roughly 0.1 per genome per replication for retroviruses and a retrotransposon. Mutation rates in microbes with DNA-based chromosomes are close to 1/300 per genome per replication; in this group, therefore, rates per base pair vary inversely and hugely as genome sizes vary from 6 × 103 to 4 × 107 bases or base pairs. Mutation rates in higher eukaryotes are roughly 0.1–100 per genome per sexual generation but are currently indistinguishable from 1/300 per cell division per effective genome (which excludes the fraction of the genome in which most mutations are neutral). It is now possible to specify some of the evolutionary forces that shape these diverse mutation rates.

The Mutation Rate and Cancer

Genetics ◽  
1998 ◽  
Vol 148 (4) ◽  
pp. 1483-1490 ◽  
Author(s):  
Aimee L Jackson ◽  
Lawrence A Loeb
Keyword(s):  
Mutation Rate ◽  
Somatic Mutations ◽  
Environmental Changes ◽  
Germ Line ◽  
Rna Viruses ◽  
Spontaneous Mutation ◽  
Mutation Rates ◽  
Major Question ◽  
Spontaneous Mutation Rate ◽  
The Stability

Abstract The stability of the human genome requires that mutations in the germ line be exceptionally rare events. While most mutations are neutral or have deleterious effects, a limited number of mutations are required for adaptation to environmental changes. Drake has provided evidence that DNA-based microbes have evolved a mechanism to yield a common spontaneous mutation rate of ~0.003 mutations per genome per replication (Drake 1991). In contrast, mutation rates of RNA viruses are much larger (Holland et al. 1982) and can approach the maximum tolerable deleterious mutation rate of one per genome (Eigen and Schuster 1977; Eigen 1993). Drake calculates that lytic RNA viruses display spontaneous mutation rates of approximately one per genome while most have mutation rates that are approximately 0.1 per genome (Drake 1993). This constancy of germline mutation rates among microbial species need not necessarily mean constancy of the somatic mutation rates. Furthermore, there need not be a constant rate for somatic mutations during development. In this review, we consider mutations in cancer, a pathology in which there appears to be an increase in the rate of somatic mutations throughout the genome. Moreover, within the eukaryotic genome, as in microbes, there are “hot-spots” that exhibit unusually high mutation frequencies. It seems conceivable to us that many tumors contain thousands of changes in DNA sequence. The major question is: how do these mutations arise, and how many are rate-limiting for tumor progression?

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