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PubMedDate not supplied

Mutation rate: some biological and biochemical considerations.

This article discusses ideas about the ways in which the high fidelity of DNA replication is achieved: base selection, exonucleolytic editing, and postreplicative proofreading. I also review possible mechanisms for the enhanced mutation rate associated with SOS induction. The concept of environmental control of mutation rate and other modes of genetic variation is also considered from the point of view that SOS induction is an example of "genetic revolution".

Base Composition↗
PubMed2004

Higher mutation rate helps to rescue genes from the elimination by selection.

Directional mutation pressure associated with replication processes is the main cause of the asymmetry between the leading and lagging DNA strands in bacterial genomes. On the other hand, the asymmetry between sense and antisense strands of protein coding sequences is a result of both mutation and selection pressures. Thus, there are two different ways of superposition of the sense strand, on the leading or lagging strand. Besides many other implications of these two possible situations, one seems to be very important - because of the asymmetric replication-associated mutation pressure, the mutation rate of genes depends on their location. Using Monte Carlo methods, we have simulated, under experimentally determined directional mutation pressure, the divergence rate and the elimination rate of genes depending on their location in respect to the leading/lagging DNA strands in the asymmetric prokaryotic genome. We have found that the best survival strategy for the majority of genes is to sometimes switch between DNA strands. Paradoxically, this strategy results in higher substitution rates but remains in agreement with observations in bacterial genomes that such inversions are very frequent and divergence rate between homologs lying on different DNA strands is very high.

Amino Acid Substitution↗
PubMed1994

Fluctuation tests: how reliable are the estimates of mutation rates?

Fifty one years ago, Luria and Delbrück published in Genetics a paper that was to become a classic. In it they proved, beyond all reasonable doubt, that bacteria were mutating to phage resistance long before they could have encountered any bacteriophage. Luria and Delbrück also showed how the same experimental data could be used to estimate bacterial mutation rates. Since that time and in many different contexts the methods that they introduced have been used to estimate mutation rates. However, little seems to be known about the errors to be expected in such estimates. In what follows I examine how much uncertainty in the estimates is to be expected merely on the basis of the stochastic variability inherent in the sampling process. On the basis of this examination I question a few traditional ideas and conclude with some practical suggestions. The results were obtained by stimulation. It is my hope that they may inspire others to provide a rigorous theoretical basis for such calculations.

Bacteria↗
PubMed1988

Estimation of mutation rates based on the analysis of polypeptide constituents of cultured human lymphoblastoid cells.

A subclone of a human diploid lymphoblastoid cell line, TK-6, with consistently high cloning efficiency has been used to estimate the rates of somatic mutations on the basis of protein variation detected by two-dimensional polyacrylamide gel electrophoresis. A panel of 267 polypeptide spots per gel was screened, representing the products of approximately 263 unselected loci. The rate of human somatic mutation in vitro was estimated by measuring the proportion of protein variants among cell clones isolated at various times during continuous exponential growth of a TK-6 cell population. Three mutants of spontaneous origin were observed, giving an estimated spontaneous rate of 6 x 10(-8) electrophoretic mutations per allele per cell generation (i.e., 1.2 x 10(-7) per locus per cell generation). Following treatment of cells with N-ethyl-N-nitrosourea, a total of 74 confirmed variants at 54 loci were identified among 1143 clones analyzed (approximately 601,000 allele tests). The induced variants include 65 electromorphs which exhibit altered isoelectric charge and/or apparent molecular weight and nine nullimorphs for each of which a gene product was not detected at its usual location on the gel. The induced frequency for these 65 structural gene mutants is 1.1 x 10(-4) per allele. An excess of structural gene mutations at ten known polymorphic loci and repeat mutations at these and other loci suggest nonrandomness of mutation in human somatic cells. Nullimorphs occurring at three heterozygous loci in TK-6 cells may be caused by genetic processes other than structural gene mutation.

Cell Line↗
PubMed2004

Abundance, distribution, and mutation rates of homopolymeric nucleotide runs in the genome of Caenorhabditis elegans.

Homopolymeric nucleotide runs, also called mononucleotide microsatellites, are a ubiquitous, dominant, and mutagenic feature of eukaryotic genomes. A clear understanding of the forces that shape patterns of homopolymer evolution, however, is lacking. We provide a focused investigation of the abundance, chromosomal distribution, and mutation spectra of the four strand-specific homopolymer types (A, T, G, C) >or=8 bp in the genome of Caenorhabditis elegans. A and T homopolymers vastly outnumber G and C HPs, and the run-length distributions of A and T homopolymers differ significantly from G and C homopolymers. A scanning window analysis of homopolymer chromosomal distribution reveals distinct clusters of homopolymer density in autosome arms that are regions of high recombination in C. elegans. Dramatic biases are detected among closely spaced homopolymers; for instance, we observe 994 A homopolymers immediately followed by a T homopolymer (5' to 3') and only 8 instances of T homopolymers directly followed by an A homopolymer. Empirical homopolymer mutation assays in a set of C. elegans mutation-accumulation lines reveal an approximately 20-fold higher mutation rate for G and C homopolymers compared to A and T homopolymers. Nuclear A and T homopolymers are also found to mutate approximately 100-fold more slowly than mitochondrial A and T homopolymers. This integrative approach yields a total nuclear genome-wide homopolymer mutation rate estimate of approximately 1.6 mutations per genome per generation.

Animals↗
PubMed1981

The frequency of private electrophoretic variants and indirect estimates of mutation rate in scheduled tribes from South India.

Data on private electrophoretic variants for 18 Scheduled Tribe populations from south India have been utilized to estimate mutation rate by two indirect procedures. The values of mu for the total pooled data are 0.150 x 10(-6) and 0.264 x 10(-6)/locus per generation by the methods of Kimura and Ohta30 and Nei44 respectively. Three different groups of these tribes yield the unweighted average values of mu as 0.193 x 10(-6) and 0.410 x 10(-6)/locus per generation by the two methods given above. The estimates on individual populations, however, show a wide variability, even if only the non-zero results are considered. The unweighted average of these individual tribe estimates is an order of magnitude higher than the estimates obtained for the total populations of all the 18 tribes. The problems involved in estimating mutation rate from protein data using indirect methods in tribal populations of India are considerable because of their levels of detribalization and acculturation. The validity of the low values of mu in these tribes, in comparison with the much higher estimates for the populations from the other parts of the world, is discussed.

Electrophoresis↗
PubMed2005

High mutation rates, bottlenecks, and robustness of RNA viral quasispecies.

Population bottlenecks are stochastic events that strongly condition the structure and evolution of natural populations. Their effects are readily observable in highly heterogeneous populations, such as RNA viruses, since bottlenecks cause a fast accumulation of mutations. Considering that most mutations are deleterious, it was predicted that the frequent application of bottlenecks would yield a population unable to replicate. However, in vitro as well as in vivo systems evolving through bottlenecks present a remarkable resistance to extinction. This observation reveals the robustness of RNA viruses and points to the existence of internal mechanisms which must confer a high degree of adaptability to fast mutating populations. In this contribution, we review experimental observations regarding the survival of RNA viruses, both in laboratory experiments and in natural populations. By means of a simple theoretical model of evolution which incorporates strong reductions of the population size, we explore the relationship between the number of replication rounds that a single founder particle undergoes before the next bottleneck is applied, and the mutation rate in a particular environment. Our numerical results reveal that the mutation rate has evolved in a concerted way with the degree of optimization achieved by the population originated from the founder particle. We hypothesize that this mechanism generates a mutation-selection equilibrium in natural populations that maximizes adaptability while maintaining their structure.

Base Sequence↗
PubMed2004

Mutation rate and predicted phenotypic target sizes in ethylnitrosourea-treated mice.

Chemical mutagenesis of the mouse is ongoing in several centers around the world, with varying estimates of mutation rate and number of sites mutable to phenotype. To address these questions, we sequenced approximately 9.6 Mb of DNA from G1 progeny of ethylnitrosourea-treated mice in a large, broad-spectrum screen. We identified 10 mutations at eight unique sites, including six nonsynonymous coding substitutions. This calibrates the nucleotide mutation rate for two mutagenesis centers, implies significance criteria for positional cloning efforts, and provides working estimates of effective genetic target sizes for selected phenotypes.

Alkylating Agents↗
PubMed1986

Estimation of the male to female ratio of mutation rates from the segregation of X-chromosomal DNA haplotypes in Duchenne muscular dystrophy families.

A novel procedure is presented to estimate the ratio of male to female mutation rates for Duchenne muscular dystrophy (DMD). X-specific restriction fragment length polymorphisms are used to establish DNA haplotypes in three-generation DMD families. From the proportion of DMD patients who have inherited their maternal grandfather's X chromosome, the ratio of mutation rates can be calculated. In contrast to classical methods, the proposed procedure is not restricted to sporadic or familiar cases nor is any information on the carrier status of female relatives required.

DNA↗
PubMed1989

Mutation rates in hybrids between sibling species of Drosophila.

It has recently been suggested that sterility or inviability in species hybrids might result from the movement of transposable elements. Because such movement is often detectable by an increased mutation rate, I studied the effect of interspecific hybridization in the Drosophila melanogaster group on the mutation rate of X-linked visibles. This rate did not differ between hybrids and intraspecific controls. This was also true for the germ-line excision rate of a transposable element, although the rate of somatic excision was two to sixfold higher in hybrids than in pure species. Combined with previous work, these results do not support a role for transposable elements in speciation.

Animals↗
PubMed2002

Estimation of mutation rate at human glycophorin A locus in hematopoietic stem cell progenitors.

Surveys of human mutant cells exhibit a few individuals with relatively high "outlying" values, which might be explained by rare mutations occurring during development. To estimate how commonly this occurs, mutant red cell frequencies at the glycophorin A locus in 135 neonates and 109 children and adolescents from three research centers are compared with simulations in which mutations arise from successive cycles of binary fission. The simulations predict the data most accurately when the mutation rate in stem cell precursors is about 2-4 x 10(-7) per division cycle, which is similar to previous estimates from adult stem cell divisions. If these mutation rates are accurate, and the number of stem cell divisions during adult life is as low as previously estimated, it is predicted that up to one-sixth of mutant stem cells over a lifetime arose in early life. However, these mutant stem cells would be difficult to detect in surveys because their distribution within the general population is so skewed.

Adolescent↗
PubMed1994

Familial adenomatous polyposis (FAP): frequency, penetrance, and mutation rate.

The nationwide Danish polyposis register includes all known Danish cases of familial adenomatous polyposis (FAP) and their relatives. By identifying all FAP patients born between 1920 and 1949, we found the frequency of the disease to be 1 in 13,528. By comparing the number of affected and nonaffected offspring born to affected parents during the same period we found the penetrance of the disease for inherited cases to be close to 100% at the age of 40 years. The mutation rate found by the direct method was 9 mutations per million gametes per generation and the proportion of new mutants was estimated to 25%. Fitness for patients between 15 and 29 years was found close to one, while for patients older than 30 the fitness was reduced, but increasing during the three decades (from 0.44 to 0.71) probably because treatment became more widespread and efficient. As we have used the overall fitness in the period, 0.87, to estimate the mutation rate by the indirect method, we found a lower value than by the direct method, namely 5 mutations per million gametes per generation.

Adenomatous Polyposis Coli↗
PubMed2005

High mutation rate in dopa-responsive dystonia: detection with comprehensive GCHI screening.

Mutations in GTP cyclohydrolase I (GCHI) are found in 50 to 60% of cases with dopa-responsive dystonia (DRD). Heterozygous GCHI exon deletions, undetectable by sequencing, have recently been described in three DRD families. We tested 23 individuals with DRD for the different mutation types by conventional and quantitative PCR analyses and found mutations, including two large exon deletions, in 87%. The authors attribute this high mutation rate to rigorous inclusion criteria and comprehensive mutational analysis.

Adolescent↗
PubMed1989

Mutation rate estimates are not compatible with autosomal dominant inheritance of the dysplastic nevus "syndrome".

Dysplastic nevi represent precursor lesions harboring an increased risk of evolving into melanoma. Their association with familial melanoma is usually considered a monogenic syndrome with autosomal dominant transmission. To test this concept we estimated the mutation rates. When derived directly from the sporadic occurrence of the trait, the mutation rate is exceedingly high (0.9%-2.5%), whereas, as estimated with the aid of Haldane's formula it would be 0.007% to 0.02%. Accordingly, newly arising mutation would outnumber eliminated mutations by 100:1. Even if only 80% of all old mutations are passed onto the next generation, this ratio of 100:1 would rapidly change. After only a few generations, 10% of the world population should be affected with the dysplastic nevus "syndrome". The apparent lack of a genetic equilibrium between newly arising and eliminated mutations is not compatible with autosomal dominant inheritance of the dysplastic nevus "syndrome."

Chromosome Aberrations↗
PubMed1985

Homozygosity in a population of variable size and mutation rate.

A formula is obtained for the probability that two genes at a single locus, sampled at random from a population at time t, are of particular types. The model assumed is a diffusion approximation to a neutral Wright-Fisher model in which mutation is not necessarily symmetric and the population size is a function of time. It is shown that for symmetric mutation in a population undergoing a step-function type bottleneck, homozygosity increases with decreasing population size. A formula is given for the distribution of the number of segregating sites occurring in two randomly sampled sequences of completely linked sites, with general mutation at a site and identical mutation structure between sites. We give similar results for a population of fixed size but for which the mutation rate is a function of time, and not necessarily symmetric. We confirm the intuitively clear effect that increasing the mutation rate decreases homozygosity.

Alleles↗
PubMed1995

Increased mutation rate at the hprt locus accompanies microsatellite instability in colon cancer.

Hereditary Non-Polyposis Colon Cancer (HNPCC) tumors and some sporadic colon cancers acquire somatic changes in the length of microsatellite sequences. We hypothesized that this 'replication error' (RER) phenotype in these cancers reflects a more general defect which should result in hypermutability of expressed genes. To test this hypothesis mutations of hprt were studied in RER and non-RER tumor cell lines. Increased mutation rates of greater than 100-fold were found in RER compared to non-RER lines. Heterogeneity within the RER group suggests the likely existence of different classes of RER tumors. One non-RER cell line demonstrated a greater than 10-fold increase in mutation rate, suggesting that a novel mutator phenotype may exist in some non-RER tumors.

Cell Division↗
PubMedDate not supplied

Estimation of mutation rates induced by large doses of gamma, proton and neutron irradiation of the X-chromosome of the nematode Panagrellus redivivus.

The radiation-resistant free-living nematode Panagrellus redivivus was used to study mutation rates in oocytes, following gamma, proton and neutron irradiation in the dose range 45-225 grays. gamma-Radiation produced approximately 0.001 lethal X-chromosomes per gray over the range tested. Proton or neutron irradiation produced approximately 0.003 lethal X-chromosomes per gray at lower doses, with the mutation rate dropping to 0.001 lethal X-chromosome per gray at the higher doses. These results suggest a dose-dependent mutation-repair system. Cell lethality was also examined. gamma-Radiation produced the greatest amount of cell lethality at all doses, while neutron irradiation had no cell lethal effect at any of the doses examined.

Animals↗