Intensive nuclear selection in tryptophan limited cultures of Escherichia coli B/r/l, trp

Summary The paradoxical constancy of the rate of mutation to resistance to bacteriophage T5 was observed long ago by Novick and Szilard. Mutation rates are independent of growth rate in tryptophan limited chemostat cultures, even though both average cell volume and DNA content increase with generation time. To examine nuclear selection in these multinucleate cells, cultures of E. coli B/r/l, trp were exposed briefly to acridine orange/visible light, and cells repackaged to uninucleate forms by shifting growth rates up to 0.5 divisions per hr. The kinetics of accumulation of mutant nuclei indicates that only a single master nucleus replicates in each cell, one of its progeny becomes the master nucleus during the following nuclear generation in the same cell, and both progeny become master nuclei if the cell divides. Autoradiographs showed that master nuclei are located at the ends of cells and that uninucleate cells are produced at each division, except possibly for a small fraction of aberrant divisions. This intensive selection during replication and inheritance of master nuclei provides an explanation for the constancy of cellular mutation rates, which is due to the constancy of the rate of DNA replication in these cultures and the (almost) complete selection for mutant nuclei in mutated cells.Work supported by the U. S. Atomic Energy Commission.     

The evolution of mutation rates: separating causes from consequences

Natural selection can adjust the rate of mutation in a population by acting on allelic variation affecting processes of DNA replication and repair. Because mutation is the ultimate source of the genetic variation required for adaptation, it can be appealing to suppose that the genomic mutation rate is adjusted to a level that best promotes adaptation. Most mutations with phenotypic effects are harmful, however, and thus there is relentless selection within populations for lower genomic mutation rates. Selection on beneficial mutations can counter this effect by favoring alleles that raise the mutation rate, but the effect of beneficial mutations on the genomic mutation rate is extremely sensitive to recombination and is unlikely to be important in sexual populations. In contrast, high genomic mutation rates can evolve in asexual populations under the influence of beneficial mutations, but this phenomenon is probably of limited adaptive significance and represents, at best, a temporary reprieve from the continual selection pressure to reduce mutation. The physiological cost of reducing mutation below the low level observed in most populations may be the most important factor in setting the genomic mutation rate in sexual and asexual systems, regardless of the benefits of mutation in producing new adaptive variation. Maintenance of mutation rates higher than the minimum set by this "cost of fidelity" is likely only under special circumstances.     

Avoiding Dangerous Missense: Thermophiles Display Especially Low Mutation Rates

Rates of spontaneous mutation have been estimated under optimal growth conditions for a variety of DNA-based microbes, including viruses, bacteria, and eukaryotes. When expressed as genomic mutation rates, most of the values were in the vicinity of 0.003–0.004 with a range of less than two-fold. Because the genome sizes varied by roughly 10⁴-fold, the mutation rates per average base pair varied inversely by a similar factor. Even though the commonality of the observed genomic rates remains unexplained, it implies that mutation rates in unstressed microbes reach values that can be finely tuned by evolution. An insight originating in the 1920s and maturing in the 1960s proposed that the genomic mutation rate would reflect a balance between the deleterious effect of the average mutation and the cost of further reducing the mutation rate. If this view is correct, then increasing the deleterious impact of the average mutation should be countered by reducing the genomic mutation rate. It is a common observation that many neutral or nearly neutral mutations become strongly deleterious at higher temperatures, in which case they are called temperature-sensitive mutations. Recently, the kinds and rates of spontaneous mutations were described for two microbial thermophiles, a bacterium and an archaeon. Using an updated method to extrapolate from mutation-reporter genes to whole genomes reveals that the rate of base substitutions is substantially lower in these two thermophiles than in mesophiles. This result provides the first experimental support for the concept of an evolved balance between the total genomic impact of mutations and the cost of further reducing the basal mutation rate.     

Conditional coalescent trees with two mutation rates and their application to genomic instability

Humans have invested several genes in DNA repair and fidelity replication. To account for the disparity between the rarity of mutations in normal cells and the large number of mutations present in cancer, an hypothesis is that cancer cells must exhibit a mutator phenotype (genomic instability) during tumor progression, with the initiation of abnormal mutation rates caused by the loss of mismatch repair. In this study we introduce a stochastic model of mutation in tumor cells with the aim of estimating the amount of genomic instability due to the alteration of DNA repair genes. Our approach took into account the difficulties generated by sampling within tumoral clones and the fact that these clones must be difficult to isolate. We provide corrections to two classical statistics to obtain unbiased estimators of the raised mutation rate, and we show that large statistical errors may be associated with such estimators. The power of these new statistics to reject genomic instability is assessed and proved to increase with the intensity of mutation rates. In addition, we show that genomic instability cannot be detected unless the raised mutation rates exceed the normal rates by a factor of at least 1000.     

The influence of hitchhiking and deleterious mutation upon asexual mutation rates

The question of how natural selection affects asexual mutation rates has been considered since the 1930s, yet our understanding continues to deepen. The distribution of mutation rates observed in natural bacteria remains unexplained. It is well known that environmental constancy can favor minimal mutation rates. In contrast, environmental fluctuation (e.g., at period T) can create indirect selective pressure for stronger mutators: genes modifying mutation rate may "hitchhike" to greater frequency along with environmentally favored mutations they produce. This article extends a well-known model of Leigh to consider fitness genes with multiple mutable sites (call the number of such sites alpha). The phenotypic effect of such a gene is enabled if all sites are in a certain state and disabled otherwise. The effects of multiple deleterious loci are also included (call the number of such loci gamma). The analysis calculates the indirect selective effects experienced by a gene inducing various mutation rates for given values of alpha, gamma, and T. Finite-population simulations validate these results and let us examine the interaction of drift with hitchhiking selection. We close by commenting on the importance of other factors, such as spatiotemporal variation, and on the origin of variation in mutation rates.     

On the mutation rate of herpes simplex virus type 1

All seven DNA-based microbes for which carefully established mutation rates and mutational spectra were previously available displayed a genomic mutation rate in the neighborhood of 0.003 per chromosome replication. The pathogenic mammalian DNA virus herpes simplex type 1 has an estimated genomic mutation rate compatible with that value.     

A genome-wide view of mutation rate co-variation using multivariate analyses

Background  

While the abundance of available sequenced genomes has led to many studies of regional heterogeneity in mutation rates, the co-variation among rates of different mutation types remains largely unexplored, hindering a deeper understanding of mutagenesis and genome dynamics. Here, utilizing primate and rodent genomic alignments, we apply two multivariate analysis techniques (principal components and canonical correlations) to investigate the structure of rate co-variation for four mutation types and simultaneously explore the associations with multiple genomic features at different genomic scales and phylogenetic distances.     

DNA turnover and the molecular clock

Summary Many detailed studies on the mechanisms by which different components of eukaryotic nuclear genomes have diverged reveal that the majority of sequences are seemingly not passively accumulating base substitutions in a clocklike manner solely determined by laws of diffusion at the population level. It appears that variation in the rates, units, biases, and gradients of several DNA turnover mechanisms are contributing to the course of DNA divergence. Turnover mechanisms have the potential to retard, maintain, or accelerate the rate of DNA differentiation between populations. Furthermore, examples are known of coding and noncoding DNA subject to the simultaneous operation of several turnover mechanisms leading to complex patterns of fine-scale restructuring and divergence, generally uninterpretable using selection and/or neutral drift arguments in isolation. Constancy in the rate of divergence, where observed over defined periods of time, could be a reflection of constancy in the rates and units of turnover. However, a consideration of the generally large disparity between rates of turnover and mutation reveals that DNA clocks, which would be independently driven by turnover in separate genomic components, would tend to be episodic. The utility of any given DNA sequence for measuring time and species relationships, like individual proteins, is proportional to the extent to which all contributing forces to the evolution of the sequence, internal and external, are understood.     

DNA and the theory of stabilizing selection

A comparison of structural-functional features of genomic DNAs allowed to estimate the role of internal and external factors in evolution of different groups of organisms. The basic difference between higher and lower organisms has been demonstrated. It is reflected in the difference of their reaction on to external factors in accordance with two adaptation types, the openness and autonomization. There is a correlation between structural-functional organization of genomic DNAs of higher and lower organisms and the above mentioned types of adaptation. DNA of lower organisms has been proposed to be characterized as "labile", and that of higher organisms, as "stable". The "DNA lability" means high mutation ability, which characterizes the existence of and evolution of lower organisms (genetic inconstancy of the lower organisms). On the contrary, "DNA stability" means the creation of stable genetic apparatus, reduction of variability in higher organisms (genetic constancy of higher organisms). This suggests the existence of the two principal ways of evolution.     

The fitness effects of spontaneous mutations in Caenorhabditis elegans

Abstract. Spontaneous mutation to mildly deleterious alleles has emerged as a potentially unifying component of a variety of observations in evolutionary genetics and molecular evolution. However, the biological significance of hypotheses based on mildly deleterious mutation depends critically on the rate at which new mutations arise and on their average effects. A long-term mutation-accumulation experiment with replicate lines of the nematode Caenorhabditis elegans maintained by single-progeny descent indicates that recurrent spontaneous mutation causes approximately 0.1% decline in fitness per generation, which is about an order of magnitude less than that suggested by previous studies with Drosophila . Two rather different approaches, Bateman-Mukai and maximum likelihood, suggest that this observation, along with the observed rate of increase in the variance of fitness among lines, is consistent with a genomic deleterious mutation rate for fitness of approximately 0.03 per generation and with an average homozygous effect of approximately 12%. The distribution of mutational effects for fitness appears to have a relatively low coefficient of variation, being no more extreme than expected for a negative exponential, and for one composite fitness measure (total progeny production) approaches constancy of effects. These results are derived from assays in a benign environment. At stressful temperatures, estimates of the genomic deleterious mutation rate (for genes expressed at such temperatures) is sixfold lower, whereas those for the average homozygous effect is approximately eightfold higher. Our results are reasonably compatible with existing estimates for flies, when one considers the differences between these species in the number of germ-line cell divisions per generation and the magnitude of transposable element activity.     

Genomic Background and Generation Time Influence Deleterious Mutation Rates in Daphnia

Understanding how genetic variation is generated and how selection shapes mutation rates over evolutionary time requires knowledge of the factors influencing mutation and its effects on quantitative traits. We explore the impact of two factors, genomic background and generation time, on deleterious mutation in Daphnia pulicaria, a cyclically parthenogenic aquatic microcrustacean, using parallel mutation-accumulation experiments. The deleterious mutational properties of life-history characters for individuals from two different populations, and for individuals maintained at two different generation times, were quantified and compared. Mutational properties varied between populations, especially for clutch size, suggesting that genomic background influences mutational properties for some characters. Generation time was found to have a greater effect on mutational properties, with higher per-generation deleterious mutation rates in lines with longer generation times. These results suggest that differences in genetic architecture among populations and species may be explained in part by demographic features that significantly influence generation time and therefore the rate of mutation.     

Experimental evolution and the dynamics of genomic mutation rate modifiers

Because genes that affect mutation rates are themselves subject to mutation, mutation rates can be influenced by natural selection and other evolutionary forces. The population genetics of mutation rate modifier alleles has been a subject of theoretical interest for many decades. Here, we review experimental contributions to our understanding of mutation rate modifier dynamics. Numerous evolution experiments have shown that mutator alleles (modifiers that elevate the genomic mutation rate) can readily rise to high frequencies via genetic hitchhiking in non-recombining microbial populations. Whereas these results certainly provide an explanatory framework for observations of sporadically high mutation rates in pathogenic microbes and in cancer lineages, it is nonetheless true that most natural populations have very low mutation rates. This raises the interesting question of how mutator hitchhiking is suppressed or its phenotypic effect reversed in natural populations. Very little experimental work has addressed this question; with this in mind, we identify some promising areas for future experimental investigation.     

Mutation rates, spectra and hotspots in mismatch repair-deficient Caenorhabditis elegans

Although it is clear that postreplicative DNA mismatch repair (MMR) plays a critical role in maintaining genomic stability in nearly all forms of life surveyed, much remains to be understood about the genome-wide impact of MMR on spontaneous mutation processes and the extent to which MMR-deficient mutation patterns vary among species. We analyzed spontaneous mutation processes across multiple genomic regions using two sets of mismatch repair-deficient (msh-2 and msh-6) Caenorhabditis elegans mutation-accumulation (MA) lines and compared our observations to mutation spectra in a set of wild-type (WT), repair-proficient C. elegans MA lines. Across most sequences surveyed in the MMR-deficient MA lines, mutation rates were approximately 100-fold higher than rates in the WT MA lines, although homopolymeric nucleotide-run (HP) loci composed of A:T base pairs mutated at an approximately 500-fold greater rate. In contrast to yeast and humans where mutation spectra vary substantially with respect to different specific MMR-deficient genotypes, mutation rates and patterns were overall highly similar between the msh-2 and msh-6 C. elegans MA lines. This, along with the apparent absence of a Saccharomyces cerevisiae MSH3 ortholog in the C. elegans genome, suggests that C. elegans MMR surveillance is carried out by a single Msh-2/Msh-6 heterodimer.     

Indirect mechanisms of genomic instability and the biological significance of mutations at tandem repeat loci

Radiation induction of genomic instability has two features: induction of untargeted mutation and delayed mutation. These phenomena have been studied mostly in tissue culture cells, but analyses have also been conducted in whole body systems. The study of response in whole body systems frequently applies repeat sequences as markers to detect mutations. These studies have generated conflicting findings. In addition, lack of knowledge of the mechanisms involved in repeat mutation confounds the interpretation of the biological significance of increased rates of repeat mutation. In this review, some of the existing controversies of genomic instability are discussed in relation to the mechanism of repeat mutation. Analyses of published and unpublished studies indicate a mechanistic similarity between radiation-induced genomic instability at repeat loci and dynamic mutations of triplet repeats. Because of their repetitive nature, repeat sequences frequently block progression of replication forks and are consequently resolved by slippage and/or recombination. Irradiation of cells induces S checkpoints and promotes slippage/recombination mediated repeat mutations. Thus, genomic instability at repeat loci might be viewed as a consequence of cellular attempts to restore the stability of replication in the face of the stalled replication fork; this process can occur both spontaneously as well as after exposure to radiation.     

Selection for robustness in mutagenized RNA viruses

Mutational robustness is defined as the constancy of a phenotype in the face of deleterious mutations. Whether robustness can be directly favored by natural selection remains controversial. Theory and in silico experiments predict that, at high mutation rates, slow-replicating genotypes can potentially outcompete faster counterparts if they benefit from a higher robustness. Here, we experimentally validate this hypothesis, dubbed the “survival of the flattest,” using two populations of the vesicular stomatitis RNA virus. Characterization of fitness distributions and genetic variability indicated that one population showed a higher replication rate, whereas the other was more robust to mutation. The faster replicator outgrew its robust counterpart in standard competition assays, but the outcome was reversed in the presence of chemical mutagens. These results show that selection can directly favor mutational robustness and reveal a novel viral resistance mechanism against treatment by lethal mutagenesis.     

The discovery of gene amplification in mammalian cells: to be in the right place at the right time

The constancy of the genome structure of an organism has been accepted dogma for a number of decades. The genetic variegation of maize as described by McClintock in the 1940s and subsequently shown to be mediated by transposable elements indicated a degree of genomic fluidity not appreciated previously. The discovery of gene amplification in somatic mammalian cells in 1977 has added a new component to the phenomenon of genomic fluidity, which has implications for various subdisciplines of biology.     

PERSPECTIVE: SPONTANEOUS DELETERIOUS MUTATION

Mildly deleterious mutation has been invoked as a leading explanation for a diverse array of observations in evolutionary genetics and molecular evolution and is thought to be a significant risk of extinction for small populations. However, much of the empirical evidence for the deleterious-mutation process derives from studies of Drosophila melanogaster, some of which have been called into question. We review a broad array of data that collectively support the hypothesis that deleterious mutations arise in flies at rate of about one per individual per generation, with the average mutation decreasing fitness by about only 2% in the heterozygous state. Empirical evidence from microbes, plants, and several other animal species provide further support for the idea that most mutations have only mildly deleterious effects on fitness, and several other species appear to have genomic mutation rates that are of the order of magnitude observed in Drosophila. However, there is mounting evidence that some organisms have genomic deleterious mutation rates that are substantially lower than one per individual per generation. These lower rates may be at least partially reconciled with the Drosophila data by taking into consideration the number of germline cell divisions per generation. To fully resolve the existing controversy over the properties of spontaneous mutations, a number of issues need to be clarified. These include the form of the distribution of mutational effects and the extent to which this is modified by the environmental and genetic background and the contribution of basic biological features such as generation length and genome size to interspecific differences in the genomic mutation rate. Once such information is available, it should be possible to make a refined statement about the long-term impact of mutation on the genetic integrity of human populations subject to relaxed selection resulting from modern medical procedures.     

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.