Modeling the evolution of genetic architecture: A continuum of alleles model with pairwise AxA epistasis

A continuum of alleles model with pair-wise AxA epistasis is proposed and its transmission genetic, and variational properties are analysed. The basic idea is that genes control the values of underlying variables, which affect the genotypic value of phenotypic characters proportional to a "scaling factor". Epistasis is the influence of one gene on the average effect of another gene. In this model, epistasis is introduced as a mutational effect of one gene on the scaling factors of another gene. In accordance with empirical results, the model assumes that the average direct effect of mutations is zero, as is the average epistatic effect. The model predicts that, on average, a mutation at one locus increases the expected mutational variance of mutations at another interacting locus. The increase in mutational variance is predicted to be equal to the variance of the pair-wise epistatic effects. This result is consistent with the observation that mutant phenotypes tend to be more variable than the wildtype phenotype. Another generic result of this model is that the frequency of canalizing mutations can at most be equal to the frequency of de-canalizing mutations. Furthermore, it is predicted that the mutational variance of a character increases at least linearly with the size of the character; hence this model is scale variant. In the case of two characters it is shown that the dimensionality of the locus-specific mutational effect distribution is invariant, i.e. the rank of the mutational covariance matrix M is invariant. While in additive models the mutational covariance matrix is always and entirely invariant, the invariance in the case of epistatic models is unexpected. Epistatic interactions can change the magnitude of the mutational (co)variances at a locus and can thus influence the structure of the mutational covariance matrix. However, in the present model the dimensionality of the mutational effect distribution remains the same. A consequence of this result is that, in this model, the genetic architecture of a set of characters is always evolvable i.e. no hard constraints can evolve.     

Mutational and phylogenetic analyses of the mycobacterial mbt gene cluster

The mycobactin siderophore system is present in many Mycobacterium species, including M. tuberculosis and other clinically relevant mycobacteria. This siderophore system is believed to be utilized by both pathogenic and nonpathogenic mycobacteria for iron acquisition in both in vivo and ex vivo iron-limiting environments, respectively. Several M. tuberculosis genes located in a so-called mbt gene cluster have been predicted to be required for the biosynthesis of the core scaffold of mycobactin based on sequence analysis. A systematic and controlled mutational analysis probing the hypothesized essential nature of each of these genes for mycobactin production has been lacking. The degree of conservation of mbt gene cluster orthologs remains to be investigated as well. In this study, we sought to conclusively establish whether each of nine mbt genes was required for mycobactin production and to examine the conservation of gene clusters orthologous to the M. tuberculosis mbt gene cluster in other bacteria. We report a systematic mutational analysis of the mbt gene cluster ortholog found in Mycobacterium smegmatis. This mutational analysis demonstrates that eight of the nine mbt genes investigated are essential for mycobactin production. Our genome mining and phylogenetic analyses reveal the presence of orthologous mbt gene clusters in several bacterial species. These gene clusters display significant organizational differences originating from an intricate evolutionary path that might have included horizontal gene transfers. Altogether, the findings reported herein advance our understanding of the genetic requirements for the biosynthesis of an important mycobacterial secondary metabolite with relevance to virulence.     

The p53 tumour suppressor gene: a model for molecular epidemiology of human cancer

The gene encoding the tumour suppressor protein p53 is one of the most commonly mutated genes in human cancers. Analysis of the mutational events that target the p53 gene has revealed evidence for both exogenous and endogenous mutational mechanisms. For example, the p53 mutational spectrum reveals evidence for a direct causal effect of ultraviolet radiation in skin cancer, of aflatoxin B1 in liver cancer and of tobacco smoke in lung cancer. This novel field, molecular epidemiology of human cancer risk, has added a new dimension to classical associative epidemiology by providing a direct link between human cancer and carcinogen exposure.     

Transcriptome‐wide effects of sexual selection on the fate of new mutations

Sexual selection on males is predicted to have widespread effects on genetic variation as a consequence of the pleiotropic allelic effects on sexual and nonsexual traits. We manipulated the opportunity for sexual selection on males during 27 generations of mutation accumulation in inbred lines of Drosophila serrata, and used a microarray platform to investigate the effect of sexual selection on the expression of 2689 genes. While gene expression signal was, on average, higher in the absence of sexual selection, this difference was small (0.1%). In contrast, sexual selection impacted substantially on the mutational variance in gene expression. Over all genes, mutational variance in gene expression was, on average, 42% higher when sexual selection operated than when it was absent. Our results indicate that sexual selection on males can generate widespread effects across the genome. An increase in mutational variance without a corresponding change in mean suggested that most expression traits were unlikely to be under direct sexual selection. Instead, the mutational variance in gene expression traits is consistent with divergence generated by widespread pleiotropic associations with traits affecting male mating success.     

Test of models for the sequence specificity of UV-induced mutations in mammalian cells

We have used mathematical modeling and statistical analysis to examine the correlation between UV-induced DNA damage and resulting base-substitution mutations in mammalian cells. The frequency and site specificity of UV-induced photoproducts in the supF gene of the pZ189 shuttle vector plasmid were compared with the frequency and site specificity of base-substitution mutations induced upon passage of the UV-irradiated vector in monkey cells. The hypothesis that the observed mutational spectrum is due to a preferential insertion of adenosine opposite UV photoproducts in the DNA template was found to best explain the mutational data. Models in which it was postulated that only (6-4) photoproducts, and not cyclobutane dimers, are mutagenic, or that the relative frequency of photoproduct formation does not influence mutation frequencies, fit the data much less well. This analysis demonstrates that molecular mechanisms of mutagenesis in mammalian cells can be deduced from mutational data obtained with a shuttle vector system.     

The presence of traces of iron and copper ions during gamma-irradiation does not result in clear mutational hot spots in the lacI gene.

Oxidative radicals, which are produced during ionizing irradiation of DNA in water, damage the DNA and may result in mutations, which are in general randomly distributed. Alternatively, the addition of transition metal ions, like iron or copper, to DNA in combination with H(2)O(2) and a reducing agent also results in the production of oxidative radicals. Due to binding of the transition metal ions to DNA, the production of these radicals is very local, and results in a mutational spectrum in which the mutations are not randomly distributed. If transition metal ions are complexed to the DNA during irradiation, and react with radiation-induced species such as hydrogen peroxide, site-specific formation of.OH radicals on these sites may occur, leading to the formation of mutational hot spots. This study examines the influence of the presence of traces of iron or copper ions during gamma-irradiation of plasmid DNA in water, on the possible formation of mutational hot spots in the lacI gene. Comparison of the mutational spectra, after irradiation in the presence or in the absence of transition metal ions, shows that there are indeed relatively more positions in the lacI gene where more than one mutation occurs, suggesting formation of mutational hot spots in the presence of transition metal ions. However, the appearance of these hot spots is rather weak. Although in all three mutational spectra G:C to A:T mutations are predominant, there are also some differences between the types of mutations in these spectra. These differences in mutational spectra might reflect the different preferences of iron and copper ions to bind specific sites in the DNA. Indeed, there appears to be a high association of mutations at CC or GG sites in the mutational spectrum in the presence of copper ions, confirming the observation that copper binds preferably at two adjacent guanines in the DNA. It can be concluded from this study that the presence of small amounts of transition metal ions during gamma-irradiation influences the types and distribution of gamma-radiation-induced mutations, although no major mutational hot spots can be observed.     

Molecular classification as prognostic factor and guide for treatment decision of pancreatic cancer

Clinico-pathological factors fail to consistently predict the outcome after pancreatic resection for pancreatic ductal adenocarcinoma (PDAC). PDACs show a high level of inter- and intra- tumor genetic heterogeneity. A molecular classification should help sort patients into less heterogeneous and more appropriate groups regarding the metastatic risk and the therapeutic response, with the consequences of better predicting evolution and better orienting the treatment. PDAC can be classified based on mutational subtypes and 18gene alterations. Whole-genome sequencing identified mutational signatures, mutational burden and hyper-mutated tumors with specific DNA repair defects. Their overlap/similarities allow the definition of molecular subtypes. DNA and RNA classifications can be used in prognosis assessment. They are useful in therapeutic choice for they allow the design of approaches that can predict the respective drug sensitivity of each molecular subtype. This review provides a comprehensive analysis of available molecular classifications in PDAC and how this can help guide clinical decisions.     

Interpretation of mutational spectra from different genes: analyses of PhIP-induced mutational specificity in the lacI and cII transgenes from colon of Big Blue rats

The cII assay provides an alternative choice to the lacI transgene for mutational studies involving Big Blue(R) transgenic mice and rats, or permits the evaluation of mutational responses in both genes. Here, we compare the mutational response of the cII gene from colon of Big Blue(R) F344 rats treated with a dietary mutagen and animal carcinogen, 2-amino-1-methyl-6-phenylimidazo[4,5-b]pyridine (PhIP), to those previously determined in the lacI transgene from colon of the same group of animals. A cursory inspection of PhIP-induced mutational spectra (MS) in cII and lacI suggests that the two transgenes respond differently to PhIP-induced mutation. However, a more thorough analysis of the MS in the two transgenes, including consideration of the number of mutational target sequences in each gene and nearest neighbor analyses of mutated nucleotides, indicates that PhIP-induced mutational specificity is similar in both genes. The evaluation of PhIP-induced mutational responses in these two transgenes serves as a model for intergenic mutational analyses.     

人类基因组突变热点区的简并度特异基因

突变热点区域是基因突变相对集中的区域,在生物的遗传和变异中有特殊的地位.针对特殊条件下发生突变形成的突变热点区域进行了相关研究.而人类基因组序列的测定和人类基因框架图的绘制,为在全基因组范围内进行突变热点研究提供了条件.分析了人类基因组中2 831个基因突变热点区域上简并度的性质,对突变热点区集中在高简并度区或者低简并度区的基因生物学功能进行了分析和分类.研究的焦点集中在某类功能的基因简并度特性一致的情况上.对搜集到的基因简并度特性利用聚类计算进行分析,找到了一些特殊的功能类,属于其中某类功能的基因能够通过聚类分析聚合到一起,从而说明简并度特性也是相近的,这为从基因的简并度特性预测表达物的功能提供了线索.     

Composition strand asymmetries in prokaryotic genomes: mutational bias and biased gene orientation

Most prokaryotic genomes display strand compositional asymmetries, but the reasons for these biases remain unclear. When the distribution of gene orientation is biased, as it often is, this may induce a bias in composition, as codon frequencies are not identical. We show here that this effect can be estimated and removed, and that the residual base skews are the highest at third base codon positions and lower at first and second positions. This strongly suggests that compositional asymmetries result from 1) a replication-related mutational bias that is filtered through selective pressure and/or from 2) an uneven distribution of gene orientation. In most cases, the mutational bias alters the codon usage and amino acid frequencies of the leading and the lagging strand. However, these features are not ubiquitous amongst prokaryotes, and the biological reasons for them remain to be found.     

Absence of PTEN/MMAC1 pseudogene in mice

The PTEN gene encodes a phosphatase that acts as a tumor-suppressor gene and is mutated in a variety of human cancers. Alterations of the PTEN gene in these tumor samples were identified using exon-by-exon analysis of the gene using single-stranded conformational polymorphism or direct sequencing of PTEN cDNA. However, in humans, mutational analysis of a PTEN cDNA template can produce false results because of a highly conserved PTEN processed pseudogene that shares more than 98% homology with the coding region of functional PTEN. PTEN-knockout mice develop tumors, suggesting that mouse tumor models are useful in vivo model systems to study PTEN function. Any mutational analysis of mouse PTEN cDNA may also produce false results if mice contain a highly conserved PTEN pseudogene. In this paper, we demonstrate the absence of any PTEN pseudogene in the mouse and discuss the significance of this observation for the mutational studies of the PTEN gene in mouse tumor models.     

A family of versatile centromeric vectors designed for use in the sectoring-shuffle mutagenesis assay in Saccharomyces cerevisiae

A simple assay called the sectoring shuffle was developed to monitor the mutational state of essential genes cloned into yeast centromeric plasmids. The essence of this assay is the creation of a conditional phenotype, colony color sectoring, for an essential gene in the absence of conditional thermosensitive or cold-sensitive alleles of that gene. This allows the quick determination of the mutational state of a cloned essential gene by observing its effect on the sectoring phenotype of the tester strain. During the course of this work we developed a family of 20 Escherichia coli-yeast shuttle vectors, pUN plasmids, containing ARS1 CEN4 and a variety of selectable markers as well as the SUP11 gene which can act as a color marker in the proper background. These vectors are compact and have been very useful for the sectoring-shuffle assay and for gene analysis in general. This paper describes these vectors, the sectoring shuffle and several applications of sectoring phenotypes.     

Relative contributions of structural designability and functional diversity in molecular evolution of duplicates

Analysis of increasingly saturated sequence databases have shown that gene family sizes are highly skewed with many families being small and few containing many, far-diverged homologs. Additionally, recently published results have identified a structural determinant of mutational plasticity: designability that correlates strongly with gene family size. In this paper, we explore the possible links between the two observations, exploring the possible effect of designability on duplication and divergence. We show that designability has an inverse of expected relationship with strength of selection. More designable domains that should have more mutational plasticity evolve slower. However, we also present evidence that recently duplicated genes have variable probability of locus fixation correlated with strength of selection. As expected, paralogs under stronger evolutionary pressure have a lower failure rate. Finally, we show that probability of pseudogene formation from gene duplication can be directly tied to designability and functional flexibility of the family. We present evidence that gene families with higher designability have diverged farther because of lower probability of pseudogenization. Additionally, mutational plasticity may play an integral role by influencing pseudogenization rate. Either way, we show that considering the failure rate of duplications is integral in understanding the determinants and dynamics of molecular evolution.     

Introduction, rescue and expression of plasmid genes in mammalian cells and Escherichia coli

A shuttle-vector system is described for the study of mutational specificity in mammalian cells. Using a plasmid (pGKTK) carrying the E. coli galactokinase gene (gk) and the herpes simplex virus thymidine kinase gene (tk), we demonstrate the introduction of a foreign gene into the chromosome of a mammalian cell (TK- mouse fibroblasts) and its efficient rescue back into E. coli. This system makes use of two genes, each of which can expressed in both E. coli and mammalian cells, thereby permitting one marker to be the mutational target and the other to maintain stable integration in the host. In addition, expression of both genes in bacteria makes it possible to deletion map mutants to facilitate their sequencing. In the case of a putative single-copy transformant (T8), about half of the rescued plasmids are identical in size and restriction pattern to the original plasmid. Each of these expressed the tk gene, indicating the fidelity of the rescue system.     

Spontaneous recurrent mutations and a complex rearrangement in the MECP2 gene in the light of current models of mutagenesis

Mutations in the methyl-CpG-binding protein 2 (MECP2) gene are associated with Rett syndrome (RTT). The MECP2 gene has some unique characteristics: (1) it is mainly affected by de novo mutations, due to recurrent independent mutational events in a defined "hot spot" regions or positions; (2) complex mutational events along a single allele are frequently found in this gene; (3) most mutations arise on paternal X chromosome. The recurrent point mutations involve mainly CpG dinucleotides, where C>T transitions are explained by methylation-mediated deamination. The complex mutational events might be explained by the genomic architecture of the region involving the MECP2 gene. The finding that most spontaneous mutations arise on paternal X-chromosome supports the higher contribution of replication-mediated mechanism of mutagenesis. We present 9 types of mutations in the MECP2 gene, detected in a group of 22 Bulgarian and 6 Romanian classical RTT patients. Thirteen patients were clarified on molecular level (46.4%). The point mutations in our sample account for 61.5%. One intraexonic deletion was detected in the present study (7.7%). One novel insertion c.321_322insGAAG, p.(Lys107_Leu108insGluAlafs2*) was found (7.7%). Large deletions and complex mutations account for 23%. A novel complex mutational event c.[584_624del41insTT; 638delTinsCA] was detected in a Romanian patient. We discuss different types of the MECP2 mutations detected in our sample in the light of the possible mechanisms of mutagenesis. Complex gene rearrangements involving a combination of deletions and insertions have always been most difficult to detect, to specify precisely and hence to explain in terms of their underlying mutational mechanisms.     

Mutation accumulation in populations of varying size: the distribution of mutational effects for fitness correlates in Caenorhabditis elegans

The consequences of mutation for population-genetic and evolutionary processes depend on the rate and, especially, the frequency distribution of mutational effects on fitness. We sought to approximate the form of the distribution of mutational effects by conducting divergence experiments in which lines of a DNA repair-deficient strain of Caenorhabditis elegans, msh-2, were maintained at a range of population sizes. Assays of these lines conducted in parallel with the ancestral control suggest that the mutational variance is dominated by contributions from highly detrimental mutations. This was evidenced by the ability of all but the smallest population-size treatments to maintain relatively high levels of mean fitness even under the 100-fold increase in mutational pressure caused by knocking out the msh-2 gene. However, we show that the mean fitness decline experienced by larger populations is actually greater than expected on the basis of our estimates of mutational parameters, which could be consistent with the existence of a common class of mutations with small individual effects. Further, comparison of the total mutation rate estimated from direct sequencing of DNA to that detected from phenotypic analyses implies the existence of a large class of evolutionarily relevant mutations with no measurable effect on laboratory fitness.     

A family of versatile centromeric vectors designed for use in the sectoring-shuffle mutagenesis assay in Saccharomyces cerevisiae

A simple assay called the sectoring shuffle was developed to monitor the mutational state of essential genes cloned into yeast centromeric plasmids. The essence of this assay is the creation of a conditional phenotype, colony color sectoring, for an essential gene in the absence of conditional thermosensitive or cold-sensitive alleles of that gene. This allows the quick determination of the mutational state of a cloned essential gene by observing its effect on the sectoring phenotype of the tester strain. During the course of this work we developed a family of 20 Escherichia coli-yeast shuttle vectors, pUN plasmids, containing ARS1 CEN4 and a variety of selectable markers as well as the SUP11 gene which can act as a color marker in the proper background. These vectors are compact and have been very useful for the sectoring-shuffle assay and for gene analysis in general. This paper decribes these vectors, the sectoring shuffle and several applications of sectoring phenotypes.     

Randomness of base substitution mutations induced in the lacI gene of Escherichia coli by ionizing radiation

The lacI system of Escherichia coli provides a method for monitoring mutational events at a large number of sites. Using this system, we have previously determined the mutational spectra for gamma-ray and beta-particle emissions resulting from the decay of tritium. Analysis of these mutational spectra reveals that base substitution mutations induced by ionizing radiation are distributed nearly randomly throughout the lacI gene and include all detectable substitution events. The distribution of ionizing radiation-induced mutagenesis is similar to the low frequency of occurrence mutational events induced by other SOS-dependent mutagens. The lack of an apparent nonrandom or high frequency of occurrence component seen with other SOS-dependent mutagens can be best explained as the result of the random interaction of ionizing radiation with the DNA bases leading to production of a variety of base substitutions.     

Bayesian analysis of mutational spectra

Studies that examine both the frequency of gene mutation and the pattern or spectrum of mutational changes can be used to identify chemical mutagens and to explore the molecular mechanisms of mutagenesis. In this article, we propose a Bayesian hierarchical modeling approach for the analysis of mutational spectra. We assume that the total number of independent mutations and the numbers of mutations falling into different response categories, defined by location within a gene and/or type of alteration, follow binomial and multinomial sampling distributions, respectively. We use prior distributions to summarize past information about the overall mutation frequency and the probabilities corresponding to the different mutational categories. These priors can be chosen on the basis of data from previous studies using an approach that accounts for heterogeneity among studies. Inferences about the overall mutation frequency, the proportions of mutations in each response category, and the category-specific mutation frequencies can be based on posterior distributions, which incorporate past and current data on the mutant frequency and on DNA sequence alterations. Methods are described for comparing groups and for assessing dose-related trends. We illustrate our approach using data from the literature.