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John W Drake - One of the best experts on this subject based on the ideXlab platform.
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rates of Spontaneous Mutation insights gained over the last half century
2016Co-Authors: John W DrakeAbstract:Nikolai Timofeeff-Ressovsky understood well the need for both explicit theory and quantitation in biology. His adventures with Karl Zimmer and Max Delbruck and the somewhat romantic portrayal of those ideas by Erwin Schrodinger contributed notably to the development of population genetics and led to the modern theory of Mutation. A central mystery in Timofeeff’s time was the size and composition of the gene, which he probed by the methods of radiation mutagenesis. A subsequent central mystery has been whether order may somehow underlie the apparent chaos of Mutation rates . Although the first hints of order appeared in the late 1960s, the robustness of certain formulations of Mutation rates did not become apparent until the 1990s. It is now clear that each of four major groups of organisms has its own characteristic rate of Spontaneous Mutation. The riboviruses hover at the edge of Mutational meltdown, the retroelements live a few-fold less dangerously, the DNA-based microbes maintain a very small genomic rate (except in special circumstances), and the higher eukaryotes seem to have adopted a rate only a few-fold higher than the DNA-based microbes (with remarkable consequences over the course of a sexual generation). The evolutionary forces driving these characteristic rates are poorly understood.
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the three faces of riboviral Spontaneous Mutation spectrum mode of genome replication and Mutation rate
PLOS Genetics, 2012Co-Authors: Libertad Garciavillada, John W DrakeAbstract:Riboviruses (RNA viruses without DNA replication intermediates) are the most abundant pathogens infecting animals and plants. Only a few riboviral infections can be controlled with antiviral drugs, mainly because of the rapid appearance of resistance Mutations. Little reliable information is available concerning i) kinds and relative frequencies of Mutations (the Mutational spectrum), ii) mode of genome replication and Mutation accumulation, and iii) rates of Spontaneous Mutation. To illuminate these issues, we developed a model in vivo system based on phage Qs infecting its natural host, Escherichia coli. The Qs RT gene encoding the Read-Through protein was used as a Mutation reporter. To reduce uncertainties in Mutation frequencies due to selection, the experimental Qs populations were established after a single cycle of infection and selection against RT − mutants during phage growth was ameliorated by plasmid-based RT complementation in trans. The dynamics of Qs genome replication were confirmed to reflect the linear process of iterative copying (the stamping-machine mode). A total of 32 RT mutants were detected among 7,517 Qs isolates. Sequencing analysis of 45 RT Mutations revealed a spectrum dominated by 39 transitions, plus 4 transversions and 2 indels. A clear template•primer mismatch bias was observed: A•C>C•A>U•G>G•U> transversion mismatches. The average Mutation rate per base replication was ≈9.1×10−6 for base substitutions and ≈2.3×10−7 for indels. The estimated Mutation rate per genome replication, μg, was ≈0.04 (or, per phage generation, ≈0.08), although secondary RT Mutations arose during the growth of some RT mutants at a rate about 7-fold higher, signaling the possible impact of transitory bouts of hyperMutation. These results are contrasted with those previously reported for other riboviruses to depict the current state of the art in riboviral mutagenesis.
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the rate and character of Spontaneous Mutation in an rna virus
Genetics, 2002Co-Authors: Jose M Malpica, John W Drake, Aurora Fraile, Ignacio M Moreno, Clara I Obies, Fernando GarciaarenalAbstract: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.
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the distribution of rates of Spontaneous Mutation over viruses prokaryotes and eukaryotes
Annals of the New York Academy of Sciences, 1999Co-Authors: John W DrakeAbstract:Although Mutation has chaotic aspects, Spontaneous Mutation rates assume certain characteristic values when expressed per genome per genome duplication. The rate among lytic RNA viruses is roughly 1, while the rate among retroelements is roughly 0.2. The rate among viral and cellular microbes with DNA chromosomes is close to 0.0034. Mutation rates among higher eukaryotes, estimated from specific-locus studies, vary greatly. Most of this variation can be suppressed if the rates are expressed per cell division instead of per sexual generation, and if the genome size is taken to be only a little larger than the sum of the protein-encoding sequences; then, the Mutation rate is roughly 0.01. The reasons for different characteristic Mutation rates among different organism groups remain mysterious and pose a substantial challenge to students of evolution.
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rates of Spontaneous Mutation
Genetics, 1998Co-Authors: John W Drake, Brian Charlesworth, Deborah Charlesworth, James F CrowAbstract: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. 10(4) 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 x 10(3) to 4 x 10(7) 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.
Fernando Garciaarenal - One of the best experts on this subject based on the ideXlab platform.
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the rate and character of Spontaneous Mutation in an rna virus
Genetics, 2002Co-Authors: Jose M Malpica, John W Drake, Aurora Fraile, Ignacio M Moreno, Clara I Obies, Fernando GarciaarenalAbstract: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.
Patricia L. Foster - One of the best experts on this subject based on the ideXlab platform.
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determinants of Spontaneous Mutation in the bacterium escherichia coli as revealed by whole genome sequencing
Proceedings of the National Academy of Sciences of the United States of America, 2015Co-Authors: Patricia L. Foster, Ellen Popodi, Jesse P Townes, Haixu TangAbstract:A complete understanding of evolutionary processes requires that factors determining Spontaneous Mutation rates and spectra be identified and characterized. Using Mutation accumulation followed by whole-genome sequencing, we found that the Mutation rates of three widely diverged commensal Escherichia coli strains differ only by about 50%, suggesting that a rate of 1–2 × 10−3 Mutations per generation per genome is common for this bacterium. Four major forces are postulated to contribute to Spontaneous Mutations: intrinsic DNA polymerase errors, endogenously induced DNA damage, DNA damage caused by exogenous agents, and the activities of error-prone polymerases. To determine the relative importance of these factors, we studied 11 strains, each defective for a major DNA repair pathway. The striking result was that only loss of the ability to prevent or repair oxidative DNA damage significantly impacted Mutation rates or spectra. These results suggest that, with the exception of oxidative damage, endogenously induced DNA damage does not perturb the overall accuracy of DNA replication in normally growing cells and that repair pathways may exist primarily to defend against exogenously induced DNA damage. The thousands of Mutations caused by oxidative damage recovered across the entire genome revealed strong local-sequence biases of these Mutations. Specifically, we found that the identity of the 3′ base can affect the mutability of a purine by oxidative damage by as much as eightfold.
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Measuring Spontaneous Mutation Rates
Methods for General and Molecular Microbiology Third Edition, 2007Co-Authors: Patricia L. FosterAbstract:Spontaneous Mutations are Mutations that occur in the absence of exogenous causes. Of particular interest are the Spontaneous Mutation rates of organisms that live in environments so extreme that the coding properties of their DNA should be destroyed. This chapter provides a guide to methods used for calculating Mutation rates in the hope that it will be useful to scientists and students who wish to use Mutation rates in their research. In addition, the Luria-Delbruck distribution applies to other cases in which a rare initiating event is amplified in a population. There are two basic methods to determine Mutation rates: mutant accumulation and fluctuation analysis. All methods to estimate Spontaneous Mutation rates are based on theoretical models of Mutational processes and cell growth. Of the less complicated methods, the Lea-Coulson method of the median and the Jones median estimator are reliable if Mutation rates are low to moderate; if Mutation rates are very low (m = 1), only the p0 method is applicable. Drake's formula is based on the same assumption as the Luria-Delbruck method of the mean, i.e., that Mutations occur only during the deterministic period of mutant accumulation. All the methods for calculating Mutation rates from fluctuation tests are discussed and are dependent for their applicability on the model of expansion of mutant clones originally described by Luria and Delbruck and extended by Lea and Coulson.
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methods for determining Spontaneous Mutation rates
Methods in Enzymology, 2006Co-Authors: Patricia L. FosterAbstract:Abstract Spontaneous Mutations arise as a result of cellular processes that act upon or damage DNA. Accurate determination of Spontaneous Mutation rates can contribute to our understanding of these processes and the enzymatic pathways that deal with them. The methods that are used to calculate Mutation rates are based on the model for the expansion of mutant clones originally described by Luria and Delbruck (1943) and extended by Lea and Coulson (1949). The accurate determination of Mutation rates depends on understanding the strengths and limitations of these methods and how to optimize a fluctuation assay for a given method. This chapter describes the proper design of a fluctuation assay, several of the methods used to calculate Mutation rates, and ways to evaluate the results statistically.
T Skopek - One of the best experts on this subject based on the ideXlab platform.
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Extent of CpG methylation is not proportional to the in vivo Spontaneous Mutation frequency at transgenic loci in Big Blue rodents.
Mutation Research, 2001Co-Authors: J J Monroe, M G Manjanatha, T SkopekAbstract:Abstract The lacI transgene used in the Big Blue™ (BB) mouse and rat Mutation assays typically displays Spontaneous Mutation frequencies in the 5×10 −5 range. Recently, the bone marrow and bladder of the Big Blue™ rat were reported to have, by an order of magnitude, the lowest Spontaneous Mutation frequencies ever observed for lacI in a transgenic animal, approaching the value for endogenous targets such as hprt (∼10 −6 ). Since Spontaneous Mutations in transgenes have been attributed in part to deamination of 5-methylcytosine in CpG sequences, we have investigated the methylation status of the lacI transgene in bone marrow of BB rats and compared it to that present in other tissues including liver, spleen, and breast. The first 400 bases of the lacI gene were investigated using bisulfite genomic sequencing since this region contains the majority of both Spontaneous and induced Mutations. Surprisingly, all the CpG cytosines in the lacI sequence were fully methylated in all the tissues examined from both 2- and 14-week-old rats. Thus, there is no correlation between 5-methylcytosine content at CpG sites in lacI and the frequency of Spontaneous Mutation at this marker. We also investigated the methylation status of another widely used transgenic Mutation target, the cII gene. The CpG sites in cII in BB rats were fully methylated while those in BB mice were partially methylated (each site approximately 50% methylated). Since Spontaneous Mutation frequency at cII is comparable in rat and mouse, the methylation status of CpG sequences in this gene also does not correlate with Spontaneous frequency. We conclude that other mechanisms besides Spontaneous deamination of 5-methylcytosine at CpG sites are driving Spontaneous Mutation at BB transgenic loci.
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Effect of target gene CpG content on Spontaneous Mutation in299 transgenic mice.
Mutation research, 1998Co-Authors: T Skopek, D Marino, K Kort, J Miller, M Trumbauer, S Gopal, H ChenAbstract:Transgenic Mutation assays utilizing bacterial target genes display a high frequency of Spontaneous Mutation at CpG sequences. This is believed to result from the fact that: (1) the prokaryotic genes currently being used as transgenic Mutation targets have a high CpG content and (2) these sequences are methylated by mammalian cells to produce 5-methylcytosine (5MC), a known promutagenic base. To study the effect of CpG content on the frequency and type of Spontaneous Mutation, we have synthesized an analogue of the bacterial lacI target gene (mrkII) that contains a reduced number of CpG sequences. This gene was inserted into a lambda vector and used to construct transgenic mice that undergo vector rescue from genomic DNA upon in vitro packaging. Results on Spontaneous Mutation frequency and spectrum have been collected and compared to those observed at the lacI gene in Big Blue transgenic mice. Spontaneous Mutations at the mrkII gene occurred at a frequency in the mid-10-5 range and were predominantly base pair substitutions, similar to results seen in Big Blue. However, mrkII Mutations were distributed toward the carboxyl end of the gene instead of the bias toward the amino terminus seen in lacI. Unexpectedly, 23% of the Spontaneous mrkII Mutations were GC-->AT transitions at CpG sequences (compared to 32% in lacI), despite the reduction in CpG number from 95 in lacI to only 13 in mrkII. Nine of the CpG bases undergoing transition Mutations in mrkII have not been recorded previously as Spontaneous sites in Big Blue. Therefore, substantial reduction of the number of CpG sequences in the lacI transgene did not significantly reduce the rate of Spontaneous Mutation or alter the contribution of CpG-related events. This suggests that other factors are also operating to establish frequency and composition of Spontaneous Mutations in transgenic targets.
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Effect of target gene CpG content on Spontaneous Mutation in transgenic mice
Mutation Research, 1998Co-Authors: T Skopek, K Kort, M Trumbauer, S Gopal, Deborah R. Marino, Judith E. Miller, Howard Y. ChenAbstract:Abstract Transgenic Mutation assays utilizing bacterial target genes display a high frequency of Spontaneous Mutation at CpG sequences. This is believed to result from the fact that: (1) the prokaryotic genes currently being used as transgenic Mutation targets have a high CpG content and (2) these sequences are methylated by mammalian cells to produce 5-methylcytosine (5MC), a known promutagenic base. To study the effect of CpG content on the frequency and type of Spontaneous Mutation, we have synthesized an analogue of the bacterial lacI target gene ( mrkII ) that contains a reduced number of CpG sequences. This gene was inserted into a lambda vector and used to construct trangenic mice that undergo vector rescue from genomic DNA upon in vitro packaging. Results on Spontaneous Mutation frequency and spectrum have been collected and compared to those observed at the lacI gene in Big Blue™ transgenic mice. Spontaneous Mutations at the mrkII gene occurred at a frequency in the mid-10 −5 range and were predominantly base pair substitutions, similar to results seen in Big Blue™. However, mrkII Mutations were distributed toward the carboxyl end of the gene instead of the bias toward the amino terminus seen in lacI . Unexpectedly, 23% of the Spontaneous mrkII Mutations were GC → AT transitions at CpG sequences (compared to 32% in lacI ), despite the reduction in CpG number from 95 in lacI to only 13 in mrkII . Nine of the CpG bases undergoing transition Mutations in mrkII have not been recorded previously as Spontaneous sites in Big Blue™. Therefore, substantial reduction of the number of CpG sequences in the lacI transgene did not significantly reduce the rate of Spontaneous Mutation or alter the contribution of CpG-related events. This suggests that other factors are also operating to establish frequency and composition of Spontaneous Mutations in transgenic targets.
Jose M Malpica - One of the best experts on this subject based on the ideXlab platform.
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the rate and character of Spontaneous Mutation in an rna virus
Genetics, 2002Co-Authors: Jose M Malpica, John W Drake, Aurora Fraile, Ignacio M Moreno, Clara I Obies, Fernando GarciaarenalAbstract: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.
