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PubMed2000

Implication of the G2 checkpoint in the maintenance of genome integrity.

Checkpoints are surveillance mechanisms that block cell cycle transitions, for instance in response to DNA damage. We summarise here recent progress in the molecular characterisation of the G2 checkpoint which controls the entry into mitosis, and review new evidence which implicates deregulated expression of checkpoint proteins and proteins involved in DNA damage repair in cancer development. There now exists good evidence that individuals who have inherited mutations in genes involved in G2 checkpoint and DNA damage repair are predisposed to the development of various types of cancer, their cells having a strong tendency to accumulate additional mutations. However, the occurrence of mutations of most of these genes in sporadic tumors has yet to be analysed more accurately.

Animals↗
PubMed2005

Mitochondrial DNA mutations, apoptosis, and the misfolded protein response.

Studies of transgenic mice with accelerated accumulation of mtDNA mutations specifically in the heart lead us to propose that apoptotic signaling and cell death is central to the pathogenesis of mtDNA mutations in aging. It is the cellular response to that apoptotic signaling and the organ?s compensatory response to a loss of cells that specify the phenotype of an accumulation of mtDNA mutations. In the heart, cardiomyocytes induce a vigorous anti-apoptotic, pro-survival response to counteract mitochondrial apoptotic signaling. The heart up-regulates contractility of remaining myocytes in order to maintain cardiac output. We hypothesize that mutant mitochondrial proteins originate apoptotic signaling by interacting with proteins already in place in the mitochondrial outer membrane that regulate apoptosis, for example the pro-apoptotic protein Bak. Since it is unlikely that all mutant mitochondrial proteins have the necessary structure and localization within the inner membrane to activate Bak appropriately, only a small fraction of an age-associated burden of mtDNA mutations may be pathogenic. In this model, reactive oxygen species generated by mitochondrial respiration drive the formation of mtDNA mutations, but are not the primary mechanism for their pathogenicity.

Animals↗
PubMed1999

Lack of significant differences in association rates and affinities of antibodies from short-term and long-term responses to hen egg lysozyme.

The affinities (Ka) and association rate constants (kon) of 23 mouse (BALB/c) anti-lysozyme mAbs obtained after short and prolonged immunizations have been measured by plasmon resonance techniques. The affinities for the 23 Abs, measured using their Fab, range from Ka = 1.1 x 10(7) to 1.4 x 10(10) M-1. There is no significant correlation between time or dose of immunization and affinity or association rates, indicating no time- or dose-dependent maturation of the response within the doses and times that were explored. IgMs are produced early and late in the response, with intrinsic affinities <10(5) M-1. Two independently derived mAbs, D44.1 (short term) and F10.6.6 (from a longer term response), result from identical or nearly identical somatic recombination events of germline gene segments. F10.6.6 has more mutations and a higher affinity constant (Ka = 1.4 x 10(10) M-1) than D44.1 (Ka = 1.1 x 10(7) M-1). Although higher affinities may result from an accumulation of mutations, they do not correlate with the length and dose of immunogenic challenge.

Animals↗
PubMed1980

Analysis of rpsD mutations in Escherichia coli. IV. Accumulation of minor forms of protein S7(K) in ribosomes of rpsD mutant strains due to translational read-through.

A certain proportion of protein S7 exists in an altered form in E. coli rpsD (S4) mutants. Depending on the type of S4 mutation involved, two different forms of the altered S7 can be distinguished. The unusual form is longer than normal S7 by about 500 daltons due to extra material at the carboxyl end of the protein. It is suggested that a mutationally altered S4 might lower the efficiency of termination during translation of the messenger for S7. This results in an increased frequency of translational read-through, which gives the observed longer forms of S7. Data are interpreted to mean that one class of S4 mutants might suppress UGA and UAG whereas another class only suppresses UGA.

Amino Acids↗
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↗
PubMed2000

Asynchronous accumulation of lettuce infectious yellows virus RNAs 1 and 2 and identification of an RNA 1 trans enhancer of RNA 2 accumulation.

Time course and mutational analyses were used to examine the accumulation in protoplasts of progeny RNAs of the bipartite Crinivirus, Lettuce infectious yellow virus (LIYV; family Closteroviridae). Hybridization analyses showed that simultaneous inoculation of LIYV RNAs 1 and 2 resulted in asynchronous accumulation of progeny LIYV RNAs. LIYV RNA 1 progeny genomic and subgenomic RNAs could be detected in protoplasts as early as 12 h postinoculation (p.i.) and accumulated to high levels by 24 h p.i. The LIYV RNA 1 open reading frame 2 (ORF 2) subgenomic RNA was the most abundant of all LIYV RNAs detected. In contrast, RNA 2 progeny were not readily detected until ca. 36 h p.i. Mutational analyses showed that in-frame stop codons introduced into five of seven RNA 2 ORFs did not affect accumulation of progeny LIYV RNA 1 or RNA 2, confirming that RNA 2 does not encode proteins necessary for LIYV RNA replication. Mutational analyses also supported that LIYV RNA 1 encodes proteins necessary for replication of LIYV RNAs 1 and 2. A mutation introduced into the LIYV RNA 1 region encoding the overlapping ORF 1B and ORF 2 was lethal. However, mutations introduced into only LIYV RNA 1 ORF 2 resulted in accumulation of progeny RNA 1 near or equal to wild-type RNA 1. In contrast, the RNA 1 ORF 2 mutants did not efficiently support the trans accumulation of LIYV RNA 2. Three distinct RNA 1 ORF 2 mutants were analyzed and all exhibited a similar phenotype for progeny LIYV RNA accumulation. These data suggest that the LIYV RNA 1 ORF 2 encodes a trans enhancer for RNA 2 accumulation.

Base Sequence↗
PubMed2001

Mutation frequency and type during ageing in mouse seminiferous tubules.

Mutations arise in the germline by errors of replication, recombination and repair, and the movement of transposable elements. Transgenic mice bearing reporter genes such as lacZ have proven useful for measurements of spontaneous and induced mutation frequencies, as well as studies of the effects of ageing. In this study, testicular DNA from lacZ transgenic mice was examined for age-related effects on mutation frequency and type. The recovered transgene was tested for simple substitutions and rearrangements including transposition of endogenous mobile elements. There was no evidence for either an age-related accumulation of mutations, or for the insertion of retrotransposons into the lacZ reporter gene in the testis. We conclude that the frequency of retrotransposition of several mouse mobile elements into the lacZ reporter gene is less than 3.73x10(-8). This is significantly less than the known frequency of approximately 7% of all spontaneous mutations in the mouse being due to retrotransposition of these elements.

Aging↗
PubMed2024

Genetic linkage disequilibrium of deleterious mutations in threatened mammals.

The impact of negative selection against deleterious mutations in endangered species remains underexplored. Recent studies have measured mutation load by comparing the accumulation of deleterious mutations, however, this method is most effective when comparing within and between populations of phylogenetically closely related species. Here, we introduced new statistics, LDcor, and its standardized form nLDcor, which allows us to detect and compare global linkage disequilibrium of deleterious mutations across species using unphased genotypes. These statistics measure averaged pairwise standardized covariance and standardize mutation differences based on the standard deviation of alleles to reflect selection intensity. We then examined selection strength in the genomes of seven mammals. Tigers exhibited an over-dispersion of deleterious mutations, while gorillas, giant pandas, and golden snub-nosed monkeys displayed negative linkage disequilibrium. Furthermore, the distribution of deleterious mutations in threatened mammals did not reveal consistent trends. Our results indicate that these newly developed statistics could help us understand the genetic burden of threatened species.

Animals↗
PubMed2004

Light exposure stimulates formation of A2E oxiranes in a mouse model of Stargardt's macular degeneration.

Recessive Stargardt's macular degeneration is a blinding disease of children caused by mutations in the ABCA4 (ABCR) gene. Mice with a knockout mutation in abcr accumulate toxic lipofuscin pigments in ocular tissues, similar to affected humans. The major fluorophore of lipofuscin is the bis-retinoid, N-retinylidene-N-retinylethanolamine (A2E). In the current study, we sought to define the effect of increasing light on A2E accumulation. We crossed the abcr(-/-) mutation onto an albino background. The retinoid profiles in albino mice indicated higher retinal illuminance than in pigmented mice exposed to similar ambient light. Unexpectedly, A2E levels were not higher in the albino mice. Also, A2E levels in abcr(-/-) mice reared under cyclic light at 30, 120, or 1,700 lux were similar. Thus, increased retinal illuminance was not correlated with higher A2E. A2E has been shown to undergo light-dependent oxidation to yield a series of A2E epoxides or oxiranes. These oxiranes react with DNA in vitro, suggesting a potential mechanism for A2E cytotoxicity. We analyzed ocular tissues from abcr(-/-) mice for A2E oxiranes by mass spectrometry. Unlike A2E, the oxiranes were more abundant in albino vs. pigmented abcr(-/-) mice, and in abcr(-/-) mice exposed to increasing ambient light. These observations suggest that both the biosynthesis of A2E and its conversion to oxiranes are accelerated by light. Finally, we showed that the formation of A2E oxiranes is strongly suppressed by treating the abcr(-/-) mice with Accutane (isotretinoin), an inhibitor of rhodopsin regeneration.

ATP-Binding Cassette Transporters↗
PubMed1999

The rate of spontaneous mutation for life-history traits in Caenorhabditis elegans.

Spontaneous mutations were accumulated in 100 replicate lines of Caenorhabditis elegans over a period of approximately 50 generations. Periodic assays of these lines and comparison to a frozen control suggest that the deleterious mutation rate for typical life-history characters in this species is at least 0.05 per diploid genome per generation, with the average mutational effect on the order of 14% or less in the homozygous state and the average mutational heritability approximately 0.0034. While the average mutation rate per character and the average mutational heritability for this species are somewhat lower than previous estimates for Drosophila, these differences can be reconciled to a large extent when the biological differences between these species are taken into consideration.

Animals↗
PubMed2005

Evolutionary traction: the cost of adaptation and the evolution of sex.

The advantage of sexual reproduction remains a puzzle for evolutionary biologists. Everything else being equal, asexual populations are expected to have twice the number of offspring produced by similar sexual populations. Yet, asexual species are uncommon among higher eukaryotes. In models assuming small populations, high mutation rates, or frequent environmental changes, sexual reproduction seems to have at least a two-fold advantage over asexuality. But the advantage of sex for large populations, low mutation rates, and rare or mild environmental changes remains a conundrum. Here we show that without recombination, rare advantageous mutations can result in increased accumulation of deleterious mutations ('evolutionary traction'), which explains the long-term advantage of sex under a wide parameter range.

Adaptation, Biological↗
PubMed2006

Analysis of loss of heterozygosity for tumor-suppressor genes can accurately classify and predict the clinical behavior of mucinous tumors arising from the appendix.

BACKGROUND: Pseudomyxoma peritonei is a rare heterogenous clinical syndrome with a variable clinical course. On the basis of the hypothesis that cumulative mutational damage can predict biological aggressiveness, we evaluated the utility of integrated histopathology and molecular analysis for patients with pseudomyxoma peritonei syndrome. METHODS: Tissue specimens from 23 mucinous appendiceal tumors were analyzed. DNA samples from multiple sites were analyzed for loss of heterozygosity by using a panel of 15 allelic loss microsatellite markers and K-ras-2 point mutational damage. The fractional mutational rate (FMR), determined as the number of mutated markers divided by the total number of informative markers, was calculated by using the six most informative markers and the K-ras-2 gene. Kappa statistics were calculated to test the association between FMR and the histopathologic classification. RESULTS: Our study included 6 female and 17 male patients with a mean age of 53.6 years and a mean survival of 43.9 months. We found an association between tumor loss of heterozygosity markers and histopathologic classification (P < .05). In addition, there was also an association between the FMR and pathological classification as well as between the FMR and survival (P < .05). An FMR less than .25 indicated low-grade disease, an FMR of .25 to .50 indicated intermediate grade, and an FMR greater than .5 indicated a high-grade tumor. CONCLUSIONS: Mutational profiling of accumulated allelic loss and point mutational damage correlated strongly with histopathologic definitions of pseudomyxoma peritonei disease and helped to predict the prognosis of these patients. FMR, along with histopathology, offers a comprehensive classification of these rare tumors.

Adenocarcinoma, Mucinous↗
PubMed1992

DNA polymerase beta mutations in human colorectal cancer.

Increasing numbers of alterations have been found in protooncogenes (e.g., ras, myc), as well as tumor suppressor genes (e.g., p53, Rb) in various types of tumors. The multiple mutations cannot be explained by the spontaneous mutation rate. It has been suggested that mutator phenotypes leading to the accumulation of these mutations may be required in the early stages of tumorigenesis. To test this hypothesis, the entire coding region of DNA polymerase beta, a repair enzyme, mRNA from colorectal tumors, and corresponding normal mucosa were amplified by polymerase chain reaction, cloned, and sequenced. Mutations in the catalytic domain of DNA polymerase beta were detected in colorectal tumor specimens compared to the normal colorectal mucosa, placenta, and blood samples. Since these mutations changed the structure of polymerase beta, it is expected that the efficiency of the DNA repair system would be impaired and thus may account for the high mutation rate observed in colorectal carcinomas.

Base Sequence↗
PubMed1995

Comparison of P53 protein overexpression with P53 mutation in bladder cancer: clinical and biologic aspects.

BACKGROUND: Alterations of the tumor suppressor gene p53 are known to occur in bladder cancer. Although p53 overexpression is associated with mutation of the p53 gene, a substantial discrepancy between molecular genetic alteration in p53 and overexpression of the protein has been found. EXPERIMENTAL DESIGN: Tumor specimens of 39 bladder cancer patients were immunohistochemically analyzed for p53 overexpression, and the results were compared with the presence of a mutation as assessed by single strand conformation polymorphism (SSCP) and direct sequencing. Both clinical and biologic aspects were studied. RESULTS: A significant correlation between p53 overexpression and poor survival in the whole group studied was found (p < 0.01). No association between p53 overexpression and decreased survival was found for invasive tumors in contrast with other studies. Differences in treatment of the patients and different Ab and scoring systems used might explain these differences. In our study, the Kaplar-Meier curves showed the same result for p53 overexpression and p53 mutation when the whole group and the invasive tumors were studied. However, in the group of superficial tumors, which was unfortunately too small for statistical analysis, we found p53 overexpression in three tumors, and no p53 mutations were found. A good concordance between p53 mutation and p53 overexpression was found (p < 0.02). However, two out of eight tumors with an SSCP-proven p53 mutation showed no p53 immunoreactivity, probably as a result of loss of the nuclear localization signal. Twenty three percent (7/31) of the tumors showed p53 overexpression without any sign of a mutation. CONCLUSIONS: Our results indicate that, despite good concordance between p53 mutation and p53 overexpression, there is no direct casual relationship between mutation and protein accumulation. Apparently, other events than mutation can trigger p53 stability.

Adult↗
PubMed1996

Histone-like protein HU and bacterial DNA topology: suppression of an HU deficiency by gyrase mutations.

The abundant bacterial protein called HU has the ability to wrap and bend DNA in vitro, and thus it has long been thought to play a role in DNA supercoiling. In the absence of HU, Escherichia coli formed tiny colonies on agar, rapidly accumulated suppressor mutations, and was hypersensitive to novobiocin. Three types of evidence implicated gyrase in the suppression of an HU deficiency. First, spontaneous suppressors that restored normal growth and reduced sensitivity to novobiocin mapped in gyrB, one of the genes encoding DNA gyrase. Second, a pair of known gyrB mutations (gyrB-203 Ts gyrB-221 NovR) allowed normal growth at permissive (30 degrees C) but not at intermediate (37 degrees C) conditions. Third, introduction of a gyrB-expressing plasmid restored normal colony size. DNA supercoiling comparisons showed that chromosomal supercoiling decreased in the absence of HU and increased toward wild-type levels in the presence of a spontaneous gyrB suppressor. Taken together, these data establish that HU has a physiological role in chromosomal DNA topology, probably by facilitating the action of gyrase.

Alleles↗
PubMed2004

Control region mutations and the 'common deletion' are frequent in the mitochondrial DNA of patients with esophageal squamous cell carcinoma.

BACKGROUND: North central China has some of the highest rates of esophageal squamous cell carcinoma in the world with cumulative mortality surpassing 20%. Mitochondrial DNA (mtDNA) accumulates more mutations than nuclear DNA and because of its high abundance has been proposed as a early detection device for subjects with cancer at various sites. We wished to examine the prevalence of mtDNA mutation and polymorphism in subjects from this high risk area of China. METHODS: We used DNA samples isolated from tumors, adjacent normal esophageal tissue, and blood from 21 esophageal squamous cell carcinoma cases and DNA isolated from blood from 23 healthy persons. We completely sequenced the control region (D-Loop) from each of these samples and used a PCR assay to assess the presence of the 4977 bp common deletion. RESULTS: Direct DNA sequencing revealed that 7/21 (33%, 95% CI = 17-55%) tumor samples had mutations in the control region, with clustering evident in the hyper-variable segment 1 (HSV1) and the homopolymeric stretch surrounding position 309. The number of mutations per subject ranged from 1 to 16 and there were a number of instances of heteroplasmy. We detected the 4977 bp 'common deletion' in 92% of the tumor and adjacent normal esophageal tissue samples examined, whereas no evidence of the common deletion was found in corresponding peripheral blood samples. CONCLUSIONS: Control region mutations were insufficiently common to warrant attempts to develop mtDNA mutation screening as a clinical test for ESCC. The common deletion was highly prevalent in the esophageal tissue of cancer cases but absent from peripheral blood. The potential utility of the common deletion in an early detection system will be pursued in further studies.

Carcinoma, Squamous Cell↗
PubMed1997

Lethal mutations and genomic instability.

The delayed expression of cell death in progeny of irradiated survivors was christened 'lethal mutations' by Tikvah Alper in 1984. The effect occurs when clones, or populations of cells grown up from irradiated progenitor cells, are replated and reassessed for cloning efficiency or population doubling time. The effect has been shown to be associated with the low dose shoulder region of the survival curve and is due to events occurring in the first two hours post irradiation, i.e. the 'fast repair' period. In this review the lethal mutation data accumulated over the past ten years is discussed in relation to our modern understanding of cellular and molecular events in radiation carcinogenesis and genomic instability research. It is suggested that lethal mutations are associated with a general epigenetic or field effect occurring in all irradiated cells, which makes them more prone to mutations, some of which are lethal. The implications of this for our current approach to risk estimates and therapeutic dose calculation, need to be addressed.

Animals↗