Evolution: constantly avoiding mutation.

The genomic mutation rate of the archaeon Sulfolobus acidocaldarius, which inhabits a harsh and potentially mutagenic environment, surprisingly agrees well with the previously observed constancy of genomic mutation rates in microbes. The evolutionary explanation for this constancy of genomic mutation rates remains obscure.     

Evolution of mutation rates in bacteria

Evolutionary success of bacteria relies on the constant fine-tuning of their mutation rates, which optimizes their adaptability to constantly changing environmental conditions. When adaptation is limited by the mutation supply rate, under some conditions, natural selection favours increased mutation rates by acting on allelic variation of the genetic systems that control fidelity of DNA replication and repair. Mutator alleles are carried to high frequency through hitchhiking with the adaptive mutations they generate. However, when fitness gain no longer counterbalances the fitness loss due to continuous generation of deleterious mutations, natural selection favours reduction of mutation rates. Selection and counter-selection of high mutation rates depends on many factors: the number of mutations required for adaptation, the strength of mutator alleles, bacterial population size, competition with other strains, migration, and spatial and temporal environmental heterogeneity. Such modulations of mutation rates may also play a role in the evolution of antibiotic resistance.     

Evolution: bacterial mutation in stationary phase

A recent study indicates that the genomic mutation rate of the gut bacterium Escherichia coli is substantially higher in nongrowing than growing cultures. These findings are important in the light of the ongoing controversy over the generality and robustness of stationary phase mutagenesis and its evolutionary implications.     

Evolution of variation in presence and absence of genes in bacterial pathways

ABSTRACT: BACKGROUND: Bacterial genomes exhibit a remarkable degree of variation in the presence and absence of genes, which probably extends to the level of individual pathways. This variation may be a consequence of the significant evolutionary role played by horizontal gene transfer, but might also be explained by the loss of genes through mutation. A challenge is to understand why there would be variation in gene presence within pathways if they confer a benefit only when complete. RESULTS: Here, we develop a mathematical model to study how variation in pathway content is produced by horizontal transfer, gene loss and partial exposure of a population to a novel environment. CONCLUSIONS: We discuss the possibility that variation in gene presence acts as cryptic genetic variation on which selection acts when the appropriate environment occurs. We find that a high level of variation in gene presence can be readily explained by decay of the pathway through mutation when there is no longer exposure to the selective environment, or when selection becomes too weak to maintain the genes. In the context of pathway variation the role of horizontal gene transfer is probably the initial introduction of a complete novel pathway rather than in building up the variation in a genome without the pathway.     

A mutation of Escherichia coli SecA protein that partially compensates for the absence of SecB.

The Escherichia coli SecB protein is a cytosolic chaperone protein that is required for rapid export of a subset of exported proteins. To aid in elucidation of the activities of SecB that contribute to rapid export kinetics, mutations that partially suppressed the export defect caused by the absence of SecB were selected. One of these mutations improves protein export in the absence of SecB and is the result of a duplication of SecA coding sequences, leading to the synthesis of a large, in-frame fusion protein. Unexpectedly, this mutation conferred a second phenotype. The secA mutation exacerbated the defective protein export caused by point mutations in the signal sequence of pre-maltose-binding protein. One explanation for these results is that the mutant SecA protein has sustained a duplication of its binding site(s) for exported protein precursors so that the mutant SecA is altered in its interaction with precursor molecules.     

Evolution of evolvability via adaptation of mutation rates

We examine a simple form of the evolution of evolvability-the evolution of mutation rates-in a simple model system. The system is composed of many agents moving, reproducing, and dying in a two-dimensional resource-limited world. We first examine various macroscopic quantities (three types of genetic diversity, a measure of population fitness, and a measure of evolutionary activity) as a function of fixed mutation rates. The results suggest that (i) mutation rate is a control parameter that governs a transition between two qualitatively different phases of evolution, an ordered phase characterized by punctuated equilibria of diversity, and a disordered phase of characterized by noisy fluctuations around an equilibrium diversity, and (ii) the ability of evolution to create adaptive structure is maximized when the mutation rate is just below the transition between these two phases of evolution. We hypothesize that this transition occurs when the demands for evolutionary memory and evolutionary novelty are typically balanced. We next allow the mutation rate itself to evolve, and we observe that evolving mutation rates adapt to values at this transition. Furthermore, the mutation rates adapt up (or down) as the evolutionary demands for novelty (or memory) increase, thus supporting the balance hypothesis.     

The A391E mutation enhances FGFR3 activation in the absence of ligand

The A391E mutation in the transmembrane domain of fibroblast growth factor receptor 3 leads to aberrant development of the cranium. It has been hypothesized that the mutant glutamic acid stabilizes the dimeric receptor due to hydrogen bonding and enhances its ligand-independent activation. We previously tested this hypothesis in lipid bilayers and showed that the mutation stabilizes the isolated transmembrane domain dimer by -1.3°kcal/mol. Here we further test the hypothesis, by investigating the effect of the A391E mutation on the activation of full-length fibroblast growth factor receptor 3 in human embryonic kidney 293T cells in the absence of ligand. We find that the mutation enhances the ligand-independent activation propensity of the receptor by -1.7°kcal/mol. This value is consistent with the observed strength of hydrogen bonds in membranes, and supports the above hypothesis.     

Evolution of robustness to noise and mutation in gene expression dynamics

Phenotype of biological systems needs to be robust against mutation in order to sustain themselves between generations. On the other hand, phenotype of an individual also needs to be robust against fluctuations of both internal and external origins that are encountered during growth and development. Is there a relationship between these two types of robustness, one during a single generation and the other during evolution? Could stochasticity in gene expression have any relevance to the evolution of these types of robustness? Robustness can be defined by the sharpness of the distribution of phenotype; the variance of phenotype distribution due to genetic variation gives a measure of 'genetic robustness', while that of isogenic individuals gives a measure of 'developmental robustness'. Through simulations of a simple stochastic gene expression network that undergoes mutation and selection, we show that in order for the network to acquire both types of robustness, the phenotypic variance induced by mutations must be smaller than that observed in an isogenic population. As the latter originates from noise in gene expression, this signifies that the genetic robustness evolves only when the noise strength in gene expression is larger than some threshold. In such a case, the two variances decrease throughout the evolutionary time course, indicating increase in robustness. The results reveal how noise that cells encounter during growth and development shapes networks' robustness to stochasticity in gene expression, which in turn shapes networks' robustness to mutation. The necessary condition for evolution of robustness, as well as the relationship between genetic and developmental robustness, is derived quantitatively through the variance of phenotypic fluctuations, which are directly measurable experimentally.     

Evolution of a polymorphic regulatory element in interferon-gamma through transposition and mutation

Mammalian transposable elements have intrinsic regulatory elements that can activate neighboring genes, and it is speculated that they can also carry extrinsic transactivating DNA sequences to new genomic locations. We have identified a polymorphic segment of the human interferon-gamma promoter region where two adjacent binding sites for NF-kappaB and NFAT originated from the insertion of an Alu element approximately 22-34 MYA. Both binding sites lie outside the Alu consensus sequence but within the boundaries of the insertion, suggesting that this segment of DNA was comobilized when the Alu element moved from another part of the genome. Sequence comparisons and examination of DNA-protein interactions across nine different primate species indicate that the inserted sequence contained the intact NFAT binding site, whereas the ability to bind NF-kappaB evolved through a series of mutations after the insertion. These observations are consistent with the notion that retropseudogenes can comobilize intact regulatory sequences to new locations and thereby influence the evolution of gene regulatory networks; however, the extent to which such events have shaped the evolution of gene regulation remains unknown.     

Morphogenesis in the absence of integrins: mutation of both Drosophila beta subunits prevents midgut migration

Two integrin beta subunits are encoded in the Drosophila genome. The betaPS subunit is widely expressed and heterodimers containing this subunit are required for many developmental processes. The second betasubunit, betanu, is a divergent integrin expressed primarily in the midgut endoderm. To elucidate its function, we generated null mutations in the gene encoding betanu. We find that betanu is not required for viability or fertility, and overall the mutant flies are normal in appearance. However, we could observe betanu function in the absence of betaPS. Consistent with its expression, removal of betanu only enhanced the phenotype of betaPS in the developing midgut. In embryos lacking the zygotic contribution of betaPS, loss of betanu resulted in enhanced separation between the midgut and the surrounding visceral mesoderm. In the absence of both maternal and zygotic betaPS, a delay in midgut migration was observed, but removing betanu as well blocked migration completely. These results demonstrate that the second beta subunit can partially compensate for loss of betaPS integrins, and that integrins are essential for migration of the primordial midgut cells. The two beta subunits mediate midgut migration by distinct mechanisms: one that requires talin and one that does not. Other examples of developmental cell migration, such as that of the primordial germ cells, occurred normally in the absence of integrins. Having generated the tools to eliminate integrin function completely, we confirm that Drosophila integrins do not control proliferation as they do in mammals, and have identified alphaPS3 as a heterodimeric partner for betanu.     

Evolution of sex: role of deleterious mutation and mobile elements

Prevalence of sexual reproduction is still enigma. The main character of sex is alleles mixing that could be advantageous either in unstable environment (in this case sex provides high temp of evolution) or in unstable genotype (in this case sex provides purge of genome from deleterious mutations). As long as not all species inhabit highly changeable environments, variation of genotypes is more important factor. As the majority of new mutations is deleterious, effective mechanism of genome purging is needed. Maintenance of "purging mechanism" may be a single role of sex. Two promising mutational hypotheses--clade selection (Muller's ratchet and Nunney's hypothesis) and mutational deterministic hypothesis of Kondrashov claim that more effective elimination of slightly-deleterious mutations provides main advantage to sexual population in comparison with asexual. Despite prima facie similarity, these hypotheses differ in mechanisms, work at different temporal scales and have different consequences. Kondrashov's hypothesis reveals short-term advantage of sexual reproduction, and thus, based on the individual selection. Clade selection displays long-term advantage of sexual reproduction that could be realized only by group selection. The role of mobile elements in evolution of sexual reproduction is also discussed. Firstly, mobile elements ("sexual molecular parasites") can complicate the problem: having been domesticated in asexual genomes and remaining active in sexual genomes they lead to higher mutational rate in sexual organisms and so violate assumption critical for both mutational hypotheses of "other things being equal". Secondly, mobile elements could be leader factor of origin of sex (hypothesis proposed by Hickey). Because theory of group selection could explain maintenance of sex, but not its origin, mobile elements could induce the origin of sex but were not able to maintain it, so the next scenario of evolution of sex is proposed: mobile elements induced origin of sex, which was established later by group selection because provided long term benefit (Muller's ratchet and Nunney's hypothesis). So, on all stages of evolution, sex was not advantageous for the organism per se.     

Ultraviolet-induced framshift mutagenesis in Salmonella typhimurium: absence of an effect of mutation frequency decline

Enhanced yields of UV-induced back mutants to prototrophy are observed when irradiated cells of the Salmonella typhimurium frameshift strain LT2 hisC3076 (R46) are plated on defined medium containing broth (2.5%, v/v) rather than a trace (0.02 μg/ml) of the required nutrient (histidine). This broth effect is not abolished, and is in fact augmented, in an excision-deficient derivative of hisC3076 (R46) carrying the uvr-302 mutation. Since similar broth effects on UV-induced base-pair substitution mutagenesis have usually been attributed to inhibition of mutation frequency decline (MFD), and since MFD is in turn thought to reflect the activity of an intact excision-repair system, we sought to determine whether or not UV-induced premutational lesions leadinf to the production of frameshifts are susceptible to MFD. Results with the doubly auxotrophic strain LT2 hisC3076 leuA150 (pKM101) showed that in a population of cells actually undergoing MFD (as judged by a rapid loss of UV-induced reversions of the base-pair substitution marker leuA150), no concomitant loss of UV-induced reversions of the frameshift hisC3076 marker could be detected.