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PubMed2001

Costs and benefits of high mutation rates: adaptive evolution of bacteria in the mouse gut.

We have shown that bacterial mutation rates change during the experimental colonization of the mouse gut. A high mutation rate was initially beneficial because it allowed faster adaptation, but this benefit disappeared once adaptation was achieved. Mutator bacteria accumulated mutations that, although neutral in the mouse gut, are often deleterious in secondary environments. Consistently, the competitiveness of mutator bacteria is reduced during transmission to and re-colonization of similar hosts. The short-term advantages and long-term disadvantages of mutator bacteria could account for their frequency in nature.

Adaptation, Physiological↗

PubMed1987

Mutation at the APRT locus in Friend erythroleukaemia cells. 1. Mutation rates and properties of mutants.

Spontaneous mutation at the adenine phosphoribosyl transferase (APRT) locus in clone 707 of the Friend cell line was examined. The frequency of cells resistant to 2,6-diaminopurine (DAP) was found to be 2.6 X 10(-5) with a mutation rate of 1.81 X 10(-6) cell-1 generation-1. APRT activities in 9 DAP-resistant clones were found to vary between 0 and 27% the level observed in wild-type cells. It is suggested that clone 707 cells are heterozygous or functionally hemizygous at the APRT locus.

Adenine Phosphoribosyltransferase↗

PubMed2005

Deleterious genomic mutation rate for viability in Drosophila melanogaster using concomitant sibling controls.

New deleterious mutations may reduce health and fitness and are involved in the evolution and maintenance of numerous biological processes. Hence, it is important to estimate the deleterious genomic mutation rate (U) in representative higher organisms. However, these estimated rates vary widely, mainly because of inadequate experimental controls. Here we describe an experimental design (the Binscy assay) with concomitant sibling controls and estimate U for viability in Drosophila melanogaster to be 0.31. This estimate, like most published studies, focuses on viability mutations and the overall deleterious genomic mutation rate would therefore be higher.

Animals↗

PubMed2004

A subgroup of microsatellite stable colorectal cancers has elevated mutation rates and different responses to alkylating and oxidising agents.

An early step in the carcinogenesis of hereditary non-polyposis colorectal cancer (HNPCC) and some sporadic colorectal cancers (CRCs) is the acquisition of a 'mutator phenotype' resulting from defects in DNA mismatch repair (MMR) genes, which normally maintain genomic stability. This mutator phenotype causes an approximately 100-1000-fold increase in base substitutions and small insertion/deletion mutations thereby driving carcinogenesis. It also causes genome-wide microsatellite instability (MSI) due to the inability to repair mutations within these small, hard to replicate, repetitive DNA elements. In contrast, less is known about the role of mutator phenotypes in microsatellite stable (MSS) CRC. In this report, we have measured the mutation rates in 11 MSS CRC cell lines to obtain an estimate of the prevalence of mutator phenotypes in MSS carcinogenesis. Of the 11 cell lines, three of them (27%) possess spontaneous hypoxanthine phosphoribosyltransferase mutation rates approximately 10-100-fold above background. When challenged with alkylating and oxidising agents, the degree of survival and apoptotic responses are different, indicating that these cell lines may represent more than one mutator phenotype. These data demonstrate that a significant portion of MSS CRC cell lines has increased mutation rates and that this may play a role in MSS CRC carcinogenesis.

Alkylating Agents↗

PubMed2025

Estimation of demography and mutation rates from one million haploid genomes.

As genetic sequencing costs have plummeted, datasets with sizes previously unthinkable have begun to appear. Such datasets present opportunities to learn about evolutionary history, particularly via rare alleles that record the very recent past. However, beyond the computational challenges inherent in the analysis of many large-scale datasets, large population-genetic datasets present theoretical problems. In particular, the majority of population-genetic tools require the assumption that each mutant allele in the sample is the result of a single mutation (the "infinite-sites" assumption), which is violated in large samples. Here, we present DR EVIL, a method for estimating mutation rates and recent demographic history from very large samples. DR EVIL avoids the infinite-sites assumption by using a diffusion approximation to a branching-process model with recurrent mutation. This approach results in tractable likelihoods that are accurate for rare alleles. We show that DR EVIL performs well in simulations and apply it to rare-variant data from one million haploid samples. We identify mutation-rate heterogeneity even after accounting for trinucleotide context and methylation status. We also predict that at modern sample sizes, the alleles at most polymorphic sites with high mutation rates represent the descendants of multiple mutation events.

Haploidy↗

PubMedDate not supplied

Estimation of mutation rates from the number of rare alleles in a sample.

To estimate the mutation rate from rare electrophoretic variants, a revised estimating equation is derived that takes into account the sampling distribution of the observed number of rare alleles in a sample drawn from the population. A check of the approximations used here suggests that the derived estimating equation is superior to the currently available one that is based on the expected number of rare alleles in the population. The new method is illustrated with a collation of electrophoretic data from literature. It is shown that the assumptions made in the theoretical treatment do not affect the estimate, per se, when the observed number of rare alleles is chosen as a statistic for estimating the mutation rates.

Alleles↗

PubMed1999

Recovery of mutations of different sizes from a population sample of DNA sequences under variable mutation rates across sites.

Mutations may be classified according to their positions of occurrence in the genealogy of the sampled DNA sequences from a population. A mutation is said to be of size i if it has i descendants in the sample. Such classifications for mutations may yield detailed insights into the evolutionary history and properties of the population. Statistical methods based on such classification have been developed and shown to be efficient and powerful. However, the utility of these statistical methods critically depends on reliable and robust recovery of mutations of different sizes. We investigated the distributional changes of mutations of different sizes due to genealogy reconstruction using the unweighted pair-group method with arithmetic mean (UPGMA) and the performance of maximum-parsimony method in inferring mutations of different sizes on a given topology. Genealogy reconstruction by UPGMA was found to change the distribution of mutations of different sizes on constructed topologies. Multiple hits at some nucleotide sites made it difficult to infer mutations of different sizes with the maximum-parsimony method, even when the true topology was designated. These results suggest that while the newly developed statistical methods employing information on mutations of different sites are powerful, they also impose significant new challenges for developing methods to accurately recover mutations of different sizes from population DNA sequence data.

Algorithms↗

PubMed1972

A study of spontaneous mutation rates at ten loci detectable by starch gel electrophoresis in Drosophila melanogaster.

Spontaneous mutation rates at ten allozyme loci on chromosomes II and III of Drosophila melanogaster were studied. Over the three and a half years study, one alpha-GPD mutation and two different IDH mutations were obtained. The alpha-GPD mutation was inherited in the Mendelian fashion, as expected. The two IDH mutations were peculiar in that the band of new types appeared only in females. In males, only the original bands were stained, and the positions where mutant alleles' bands should be present were blank. Both IDH mutant homozygotes appeared as null allele homozygotes, while in females clear-cut single bands were present.-The rates of spontaneous mutation varied greatly. Eight loci studied (MDH, ADH, EST-6, APH, EST-C, ODH, XDH, AO) did not give any germ-line mutation. The average germ-line mutation rate over all ten loci was estimated at 4.5 x 10(-6). This rate is considerably smaller than that for sex-linked recessive visible mutations (Muller, Valencia and Valencia 1950), but it is somewhat less than autosomal recessive visible mutations (Glass and Ritterhoff 1956).

Alcohol Oxidoreductases↗

PubMed1990

Is the initial event in carcinogenesis an enhancement of the mutation rate?

The age-specific incidence rates of adult cancer indicate that the carcinogenic process is a power function of elapsed time. If the malignant clone arises by a series of mutations, and each mutation is regarded as an independent event with a small instantaneous probability of occurrence, then the slope of the age-specific incidence gives an indication of the number of genes involved. In most cases, the epidemiological data exhibit an age-specific incidence the slope of which is between a fourth and a seventh power of age. Assuming that the mutations involved are deletions and must occur in otherwise viable and proliferative cells, the mutation rate required to generate enough mutant cells to fit the cancer incidence data must be remarkably high in the pre-malignant cell population. The initiation process may thus be an event that results in a raised mutation rate in the affected cell and its progeny. It is proposed that the process of induction involves one or more mutations that induce a metabolic lesion that has the effect of increasing the subsequent mutation rate in the affected clone. A possible mechanism involving free radical generation is suggested and some of the biological implications of the proposal examined.

Adult↗

PubMed1996

The mutation rate and cancer.

The selection of advantageous mutations underlies tumorigenesis. The growth of a tumor is therefore a form of evolution at the somatic level, in which the population is comprised of individual cells within the tumor. Models of tumorigenesis have considered the relative importance of mutation and selection. We show that selection is more important than an increased mutation rate in the growth of a tumor. Some cancers may acquire a "mutator phenotype," probably leading to faster growth, but mutator phenotypes are not necessary for carcinogenesis.

Biological Evolution↗

PubMed1998

Mutation rate: a simple concept has become complex.

The factors that cause new mutations or affect the rate at which they occur have important implications for many areas of genetics. But recent work on phenomena such as premeiotic mutations, which yield a cluster of identical new mutants at the some time, led us to realize that researchers are using the term "mutation rate" in different, and sometimes contradictory, ways. One premeiotic genetic change may ultimately yield several new mutant offspring, but should this be considered one new mutation or many? The way the data are handled in analyses can have a significant effect on the results. How, then, does one handle clusters in the estimation of mutation rates? We explore this question and propose that geneticists begin to distinguish clearly between three different phenomena that to this point have been given the same name: the initial prerepair "genetic damage rate," the postrepair "mutational event rate," and the observed "mutation rate" as it is expressed in the proportion of new mutant offspring. We believe that all new mutant offspring should be counted when estimating mutation rate, irrespective of when in the developmental cycle it is believed that the initial mutational event occurred.

Animals↗

PubMed2004

Dual reporter system to dissect cis- and trans-effects influencing the mutation rate in a hypermutating cell line.

Activation induced cytidine deaminase (AID) plays a key role in the induction of somatic hypermutation and class switching in the immunoglobulin genes of B-lymphocytes. AID expression by itself is sufficient to induce a GC-basepair biased mutator phenotype in lymphoid and non-lymphoid cell lines. Nevertheless a network of cis-regulatory elements and additional trans-factor proteins seems to govern the molecular mechanism of somatic hypermutation. To address the nature of mutation rate changes observed in the hypermutating pre-B cell line 18-81, we extended our previously described green fluorescent protein (GFP) reversion-system. Introducing an additional mutation reporter transgene enables us to discriminate between cis- and trans-factor caused alterations in the mutator phenotype. We show here that in cell line 18-81 the mutation rate declines upon prolonged periods of cell culture. The gradual loss of the mutator phenotype in cell line 18-81 is due to the downregulation of endogenous AID expression and can be reconstituted by overexpression of human AID protein. A correlation between AID mRNA levels and mutation rates is evident and even small changes in AID expression levels cause a significant effect on the mutability of the reporter transgenes.

Animals↗

PubMed1997

Sex differences in mutation rate in higher primates estimated from AMG intron sequences.

To study sex differences in mutation rate in primates, we sequenced the third introns of the AMGX and AMGY genes from humans, orangutans, and squirrel monkeys and estimated that the male-to-female ratio of mutation rate is alpha = 5.14 with the 95% confidence interval (2.42, 16.6). Combining this data set and the data sets from ZFX/ZFY and SMCX/SMCY introns, we obtained an estimate of alpha = 5.06 with the 95% confidence interval reduced to (3.24, 8.79). The alpha value is significantly higher in higher primates than in rodents.

Animals↗

PubMed2004

Host-parasite coevolution and optimal mutation rates for semiconservative quasispecies.

In this paper, we extend a model of host-parasite coevolution to incorporate the semiconservative nature of DNA replication for both the host and the parasite. We find that the optimal mutation rate for the semiconservative and conservative hosts converge for realistic genome lengths, thus maintaining the admirable agreement between theory and experiment found previously for the conservative model and justifying the conservative approximation in some cases. We demonstrate that, while the optimal mutation rate for a conservative and semiconservative parasite interacting with a given immune system is similar to that of a conservative parasite, the properties away from this optimum differ significantly. We suspect that this difference, coupled with the requirement that a parasite optimize survival in a range of viable hosts, may help explain why semiconservative viruses are known to have significantly lower mutation rates than their conservative counterparts.

Adaptation, Physiological↗

PubMed1995

Association of increased spontaneous mutation rates with high levels of transcription in yeast.

Complex processes such as transcription, replication, repair, and recombination require changes in chromatin structure and the interactions of numerous trans-acting factors with DNA sequences, raising the possibility that these processes may be interrelated. Here the effect of transcription on the rate of spontaneous mutation in the yeast Saccharomyces cerevisiae was examined. With the use of a lys2 frameshift allele under the control of a highly inducible promoter, the rate of spontaneous reversion was shown to increase when the mutant gene was highly transcribed. Thus, transcriptionally active DNA and enhanced spontaneous mutation rates are associated in yeast.

Alleles↗

PubMed2001

Polychlorinated biphenyl contamination and minisatellite DNA mutation rates of tree swallows.

The evidence that exposure to polychlorinated biphenyls (PCBs) leads to mutations is equivocal and controversial. Using multilocus DNA fingerprinting, we compared the mutation rate of tree swallows (Tachycineta bicolor) nesting at sites with high and low levels of contamination with PCBs. The upper Hudson River, USA, is highly contaminated with PCBs as a result of releases from two capacitor manufacturing plants in Hudson Falls and Fort Edward, New York, USA. Tree swallows nesting nearby have some of the highest known concentrations of PCBs in their tissues of any contemporary bird population (up to 114,000 ng PCB/g tissue). We found no difference in mutation rates between sites in New York with high PCB contamination and reference sites in Wisconsin, USA, and Ontario and Alberta, Canada, with known or presumably low levels of contamination. Thus, the mechanism behind altered reproductive behavior of tree swallows along the upper Hudson River is most likely physiological impairment, such as endocrine disruption, rather than mutation.

Animals↗

PubMed1978

Estimation of expected number of rare alleles of a locus and calculation of mutation rate.

An approach is described for the estimation of the number of rare variants in the population from the number in a sample drawn at random from the population. This quantity is used to derive an estimate of the mutation rate. The data required are the number of rare variants in the sample and the distribution of offspring within a population of well-defined size with little or no immigration. Application of this approach to data on 28 loci assayed in the Yanamamo, a tribe of South American Indians, yields an average mutation rate of 0.1 approximately 0.2 x 10(-5). Determination of this figure is subject to several assumptions concerning the nature of the rare variants and the structure of the population. Violation of these assumptions will generally result in the underestimate of the true mutation rate.

Journal Article↗

PubMed1994

A model for the correlation of mutation rate with GC content and the origin of GC-rich isochores.

Based on the biochemical kinetics of DNA replication and mutagenesis, including misincorporation and correction, a model has been developed for studying the relationships among the mutation rate (u), the G+C content of the sequence (f), and the G+C proportion in the nucleotide precursor pool (N). Also a measure for the next-nucleotide effect, called the maximum capacity of the next-nucleotide effect (MC), has been proposed. Under the normal physiological conditions of mammalian germ cells, our results indicate: (1) the equilibrium G+C content in a sequence is approximately equal to the G+C proportion in the nucleotide precursor pool, i.e., f approximately N, which is independent of the next-nucleotide effect; (2) an inverted-V-shaped distribution of mutation rates with respect to G+C contents is predicted, when the next-nucleotide effect is week, i.e., MC approximately 1; (3) the distribution becomes flatter (i.e., inverted-U-shaped) as MC increases, but the peak at 50% GC is still observed when MC < 2; and (4) the peak disappears when MC > 2.8, that is, when the next-nucleotide effect becomes strong. Our results suggest that changes in the relative concentrations of nucleotide precursors can cause variations among genes both in mutation rate and in G+C content and that compositional isochores (DNA segments with a homogeneous G+C content) can arise in a genome due to differences in replication times of DNA segments.

Base Composition↗