Effects of Short-term Spontaneous Mutation Accumulation for Life History Traits in Grape Phylloxera, Daktulosphaira vitifoliae

Mutation is the source of all genetic variation, but rate of input and effects of new mutations for phenotypic traits related to fitness and the role they play in the maintenance of genetic variation are still subject to controversy. These parameters are important in models of the evolution of sex and recombination, the persistence of asexual populations, and the extinction of small populations. Most estimates have come from a few model organisms. Here, mutation accumulation experiments were conducted with three clones of grape phylloxera, Daktulosphaira vitifoliae Fitch, a gall forming herbivore and pest of grapes, to estimate the rate of input and effects of spontaneous mutation on life history traits. This is perhaps the first such experiment using a non-model organism of economic importance. Significant heritable genetic variation accrued in one of three sets of lines for one of four traits measured, and deleterious effects of mutation were found for two of four traits in two of the three sets of lines. Estimates of the parameters by the Bateman–Mukai (BM) method were within the range found in previous studies but at the lower end for genomic mutation rate, U 0.023 and mutational variance, V _M 0.0003, the upper end for average heterozygous effect, , of –0.11, and on the order of previous estimates for mutational heritability, h _M 0.007. Under a model of equal effects of mutations, maximum likelihood (ML) estimates of U were slightly higher, and of lower, than the BM estimates. Support limits were too large to provide much confidence in the ML estimates, however, and models of mutational effects assuming a gamma distribution of effects under different values of the shape parameter, , could not be distinguished though likelihoods tended to be lower at lower values of (more leptokurtic). Rapid accumulation of deleterious mutations suggest that for many pest species, adaptive response under agricultural conditions may depend more on the standing variation derived from introductions than new mutation.     

Fitness Is Strongly Influenced by Rare Mutations of Large Effect in a Microbial Mutation Accumulation Experiment

Our understanding of the evolutionary consequences of mutation relies heavily on estimates of the rate and fitness effect of spontaneous mutations generated by mutation accumulation (MA) experiments. We performed a classic MA experiment in which frequent sampling of MA lines was combined with whole genome resequencing to develop a high-resolution picture of the effect of spontaneous mutations in a hypermutator (ΔmutS) strain of the bacterium Pseudomonas aeruginosa. After ∼644 generations of mutation accumulation, MA lines had accumulated an average of 118 mutations, and we found that average fitness across all lines decayed linearly over time. Detailed analyses of the dynamics of fitness change in individual lines revealed that a large fraction of the total decay in fitness (42.3%) was attributable to the fixation of rare, highly deleterious mutations (comprising only 0.5% of fixed mutations). Furthermore, we found that at least 0.64% of mutations were beneficial and probably fixed due to positive selection. The majority of mutations that fixed (82.4%) were base substitutions and we failed to find any signatures of selection on nonsynonymous or intergenic mutations. Short indels made up a much smaller fraction of the mutations that were fixed (17.4%), but we found evidence of strong selection against indels that caused frameshift mutations in coding regions. These results help to quantify the amount of natural selection present in microbial MA experiments and demonstrate that changes in fitness are strongly influenced by rare mutations of large effect.     

Factors Affecting the Sexual Reproduction of a Dermatophyte, Arthroderma benhamiae, in Synthetic Media

Sexual reproduction of many dermatophytes is easily induced in complex media such as soil plus keratin. In Arthroderma benhamiae this process could be initiated also in synthetic agar media. A number of carbon sources (glucose, fructose, galactose, mannose, maltose, lactose, sorbose, sucrose) had about the same stimulatory effect on reproduction, while xylose was inhibitory. Organic sulphur was not crucial for the process in contrast to the nitrogen supply. The nitrogen sources could be divided into four groups; I. very stimulatory (arginine, citrulline, isoleucine, leucine, ornithine, phenylalanine, proline, valine, glutathione); II. stimulatory (alanine, asparagine, lysine, serine); III. slightly stimulatory (aspartic acid, cysteine, glutamic acid, glycine, histidine, urea, NH₄Cl, NH₄-tartrate); IV. inhibitory (hydroxyproline, methionine, threonine, tryptophan). Synergistic effects were shown between some amino acids. Generally a combination between 5 g/l glucose and 300–400 mg/l nitrogen induced the largest number of cleistothecia, regardless of the nitrogen source used. The level varied between the sources, however. A C/N ratio of about 10 was optimal while a value above 20 gave no cleistothecia. The optimal temperature for the process was 30°C. Sexual reproduction occurred between pH 4.4 and 8.0 (final values). However, at a final pH above 7.2 the number of ascospores/cleistothecium was reduced.     

HorkaD, a Chromosome Instability-Causing Mutation in Drosophila, Is a Dominant-Negative Allele of lodestar

Correct segregation of chromosomes is particularly challenging during the rapid nuclear divisions of early embryogenesis. This process is disrupted by Horka^D, a dominant-negative mutation in Drosophila melanogaster that causes female sterility due to chromosome tangling and nondisjunction during oogenesis and early embryogenesis. Horka^D also renders chromosomes unstable during spermatogenesis, which leads to the formation of diplo//haplo mosaics, including the gynandromorphs. Complete loss of gene function brings about maternal-effect lethality: embryos of the females without the Horka^D-identified gene perish due to disrupted centrosome function, defective spindle assembly, formation of chromatin bridges, and abnormal chromosome segregation during the cleavage divisions. These defects are indicators of mitotic catastrophe and suggest that the gene product acts during the meiotic and the cleavage divisions, an idea that is supported by the observation that germ-line chimeras exhibit excessive germ-line and cleavage function. The gene affected by the Horka^D mutation is lodestar, a member of the helicase-related genes. The Horka^D mutation results in replacement of Ala777 with Thr, which we suggest causes chromosome instability by increasing the affinity of Lodestar for chromatin.     

Monooxygenases Play Only a Minor Role in Resistance to Synthetic Pyrethroids in the Cattle Tick, Boophilus Microplus

We investigated the role of monooxygenases in resistance to synthetic pyrethroids (SPs) in the cattle tick, Boophilus microplus. We found that monooxygenases play only a minor role in resistance to SPs in both resistant and susceptible strains of B. microplus. We blocked the monooxygenases with piperonyl butoxide (PBO) and simultaneously applied the SPs, flumethrin and cypermethrin to larval B. microplus. PBO increased the effect of flumethrin (synergism ratios 2.7–8.9) more than it increased the effect of cypermethrin (synergism ratios 1.9–3.1). Of the four strains tested, Parkhurst, which is resistant to SPs, was the least affected by the addition of PBO (synergism ratios after cypermethrin was applied 1.9; after flumethrin 2.7) whereas N.R.F.S., the strain susceptible to SPs, was the most affected by synergism between PBO and SPs (synergism ratio after cypermethrin was applied 3.1; after flumethrin 8.9). We hypothesize that B. microplus lacks monooxygenases capable of conferring resistance to SPs because it and its recent ancestors were blood-feeders rather than herbivores.     

Externalization of Phosphatidylserine May Not Be an Early Signal of Apoptosis in Neuronal Cells, but Only the Phosphatidylserine-Displaying Apoptotic Cells Are Phagocytosed by Microglia

Abstract: Earlier reports on nonneural cells have shown that the normally inner plasma membrane lipid, phosphatidylserine (PS), flip-flops out during the early stages of apoptosis, whereas DNA laddering and plasma membrane permeabilization occur during the late stages. In this study, the applicability of these parameters to CNS-derived neuronal cells was tested using hippocampal HN2-5, cells that undergo apoptosis under anoxia. Because such insults on unsynchronized cells, e.g., undifferentiated HN2-5 cells, result in both early and late apoptotic cells, we mechanically separated these cells into three fractions containing (a) cells that had completely detached during anoxia, (b) cells that remained weakly attached to the tissue culture dish and, once detached by trituration in serum-containing medium, did not reattach, and (c) cells that reattached in 2–3 h. Fractions a and b contained cells that showed pronounced DNA laddering, whereas cells in fraction c did not show any DNA laddering. Double staining with fluorescein isothiocyanate-annexin V (which binds to PS) and propidium iodide (which stains the DNA in cells with a permeable cell membrane) revealed that all cells in fraction a had a permeable cell membrane (propidium iodide-positive) and PS molecules in the outer leaflet of the plasma membrane (fluorescein isothiocyanate-annexin V-positive). By contrast, fractions b and c contained cells with no externalized PS molecules. Cells in fractions a–c also showed, respectively, 50-, 21-, and 5.5-fold higher caspase-3 (CPP32) activity than that in healthy control cells. All these results show that fraction a contained late apoptotic cells, which also had the highest CPP32 activity; cells in fraction b were at an intermediate stage, when DNA laddering had already occurred; and fraction c contained very early apoptotic cells, in which no DNA laddering had yet occurred. Therefore, in the neuronal HN2-5 cells, externalization of PS occurs only during the final stages of apoptosis when the cells have completely lost their adhesion properties. Further experiments showed that ameboid microglial cells isolated from neonatal mouse brain phagocytosed only the cells in fraction a. These results show that in CNS-derived HN2-5 cells, (a) PS externalization is a late apoptotic event and is concomitant with a complete loss of surface adhesion of the apoptotic cells and (b) PS externalization is crucial for microglial recognition and phagocytosis of the apoptotic HN2-5 cells. Thus, PS externalization could be causally linked to the final detachment of apoptotic neuronal cells, which in turn prepares them for rapid phagocytosis by microglia.     

A Novel p53 Mutant Found in Iatrogenic Urothelial Cancers Is Dysfunctional and Can Be Rescued by a Second-site Global Suppressor Mutation

Exposure to herbal remedies containing the carcinogen aristolochic acid (AA) has been widespread in some regions of the world. Rare A→T TP53 mutations were recently discovered in AA-associated urothelial cancers. The near absence of these mutations among all other sequenced human tumors suggests that they could be biologically silent. There are no cell banks with established lines derived from human tumors with which to explore the influence of the novel mutants on p53 function and cellular behavior. To investigate their impact, we generated isogenic mutant clones by integrase-mediated cassette exchange at the p53 locus of platform (null) murine embryonic fibroblasts and kidney epithelial cells. Common tumor mutants (R248W, R273C) were compared with the AA-associated mutants N131Y, R249W, and Q104L. Assays of cell proliferation, migration, growth in soft agar, apoptosis, senescence, and gene expression revealed contrasting outcomes on cellular behavior following introduction of N131Y or Q104L. The N131Y mutant demonstrated a phenotype akin to common tumor mutants, whereas Q104L clone behavior resembled that of cells with wild-type p53. Wild-type p53 responses were restored in double-mutant cells harboring N131Y and N239Y, a second-site rescue mutation, suggesting that pharmaceutical reactivation of p53 function in tumors expressing N131Y could have therapeutic benefit. N131Y is likely to contribute directly to tumor phenotype and is a promising candidate biomarker of AA exposure and disease. Rare mutations thus do not necessarily point to sites where amino acid exchanges are phenotypically neutral. Encounter with mutagenic insults targeting cryptic sites can reveal specific signature hotspots.     

Contemporary Gene Flow is a Major Force Shaping the Aspergillus fumigatus Population in Auckland,New Zealand

Mycopathologia - Aspergillus fumigatus is a globally distributed opportunistic fungal pathogen capable of causing highly lethal invasive aspergillosis in immunocompromised individuals. Recent...     

Twinkle, the Mitochondrial Replicative DNA Helicase, Is Widespread in the Eukaryotic Radiation and May Also Be the Mitochondrial DNA Primase in Most Eukaryotes

Recently, the human protein responsible for replicative mtDNA helicase activity was identified and designated Twinkle. Twinkle has been implicated in autosomal dominant progressive external ophthalmoplegia (adPEO), a mitochondrial disorder characterized by mtDNA deletions. The Twinkle protein appears to have evolved from an ancestor shared with the bifunctional primase-helicase found in the T-odd bacteriophages. However, the question has been raised as to whether human Twinkle possesses primase activity, due to amino acid sequence divergence and absence of a zinc-finger motif thought to play an integral role in DNA binding. To date, a primase protein participating in mtDNA replication has not been identified in any eukaryote. Here we investigate the wider phylogenetic distribution of Twinkle by surveying and analyzing data from ongoing EST and genome sequencing projects. We identify Twinkle homologues in representatives from five of six major eukaryotic assemblages (“supergroups”) and present the sequence of the complete Twinkle gene from two members of Amoebozoa, a supergroup of amoeboid protists at the base of the opisthokont (fungal/metazoan) radiation. Notably, we identify conserved primase motifs including the zinc finger in all Twinkle sequences outside of Metazoa. Accordingly, we propose that Twinkle likely serves as the primase as well as the helicase for mtDNA replication in most eukaryotes whose genome encodes it, with the exception of Metazoa. [Reviewing Editior: Dr. Rüdiger Cerff]     

A Nematode Calreticulin,Rs-CRT,Is a Key Effector in Reproduction and Pathogenicity of Radopholus similis

Radopholus similis is a migratory plant-parasitic nematode that causes severe damage to many agricultural and horticultural crops. Calreticulin (CRT) is a Ca²⁺-binding multifunctional protein that plays key roles in the parasitism, immune evasion, reproduction and pathogenesis of many animal parasites and plant nematodes. Therefore, CRT is a promising target for controlling R. similis. In this study, we obtained the full-length sequence of the CRT gene from R. similis (Rs-crt), which is 1,527-bp long and includes a 1,206-bp ORF that encodes 401 amino acids. Rs-CRT and Mi-CRT from Meloidogyne incognita showed the highest similarity and were grouped on the same branch of the phylogenetic tree. Rs-crt is a multi-copy gene that is expressed in the oesophageal glands and gonads of females, the gonads of males, the intestines of juveniles and the eggs of R. similis. The highest Rs-crt expression was detected in females, followed by juveniles, eggs and males. The reproductive capability and pathogenicity of R. similis were significantly reduced after treatment with Rs-crt dsRNA for 36 h. Using plant-mediated RNAi, we confirmed that Rs-crt expression was significantly inhibited in the nematodes, and resistance to R. similis was significantly improved in transgenic tomato plants. Plant-mediated RNAi-induced silencing of Rs-crt could be effectively transmitted to the F2 generation of R. similis; however, the silencing effect of Rs-crt induced by in vitro RNAi was no longer detectable in F1 and F2 nematodes. Thus, Rs-crt is essential for the reproduction and pathogenicity of R. similis.     

Woot, an Active Gypsy-Class Retrotransposon in the Flour Beetle, Tribolium Castaneum, Is Associated with a Recent Mutation

A recently isolated, lethal mutation of the homeotic Abdominal gene of the red flour beetle Tribolium castaneum is associated with an insertion of a novel retrotransposon into an intron. Sequence analysis indicates that this retrotransposon, named Woot, is a member of the gypsy family of mobile elements. Most strains of T. castaneum appear to harbor ~25-35 copies of Woot per genome. Woot is composed of long terminal repeats of unprecedented length (3.6 kb each), flanking an internal coding region 5.0 kb in length. For most copies of Woot, the internal region includes two open reading frames (ORFs) that correspond to the gag and pol genes of previously described retrotransposons and retroviruses. The copy of Woot inserted into Abdominal bears an apparent single frameshift mutation that separates the normal second ORF into two. Woot does not appear to generate infectious virions by the criterion that no envelop gene is discernible. The association of Woot with a recent mutation suggests that this retroelement is currently transpositionally active in at least some strains.     

The Mouse MC13 Mutant Is a Novel ENU Mutation in Collagen Type II,Alpha 1

Phenotype-driven mutagenesis experiments are a powerful approach to identifying novel alleles in a variety of contexts. The traditional disadvantage of this approach has been the subsequent task of identifying the affected locus in the mutants of interest. Recent advances in bioinformatics and sequencing have reduced the burden of cloning these ENU mutants. Here we report our experience with an ENU mutagenesis experiment and the rapid identification of a mutation in a previously known gene. A combination of mapping the mutation with a high-density SNP panel and a candidate gene approach has identified a mutation in collagen type II, alpha I (Col2a1). Col2a1 has previously been studied in the mouse and our mutant phenotype closely resembles mutations made in the Col2a1 locus.     

Multiple Metabolic Alterations Exist in Mutant PI3K Cancers,but Only Glucose Is Essential as a Nutrient Source

Targeting tumour metabolism is becoming a major new area of pharmaceutical endeavour. Consequently, a systematic search to define whether there are specific energy source dependencies in tumours, and how these might be dictated by upstream driving genetic mutations, is required. The PI3K-AKT-mTOR signalling pathway has a seminal role in regulating diverse cellular processes including cell proliferation and survival, but has also been associated with metabolic dysregulation. In this study, we sought to define how mutations within PI3KCA may affect the metabolic dependency of a cancer cell, using precisely engineered isogenic cell lines. Studies revealed gene expression signatures in PIK3CA mutant cells indicative of a consistent up-regulation of glycolysis. Interestingly, the genes up- and down-regulated varied between isogenic models suggesting that the primary node of regulation is not the same between models. Additional gene expression changes were also observed, suggesting that metabolic pathways other than glycolysis, such as glutaminolysis, were also affected. Nutrient dependency studies revealed that growth of PIK3CA mutant cells is highly dependent on glucose, whereas glutamine dependency is independent of PIK3CA status. In addition, the glucose dependency exhibited by PIK3CA mutant cells could not be overridden by supplementation with other nutrients. This specific dependence on glucose for growth was further illustrated by studies evaluating the effects of targeted disruption of the glycolytic pathway using siRNA and was also found to be present across a wider panel of cancer cell lines harbouring endogenous PIK3CA mutations. In conclusion, we have found that PIK3CA mutations lead to a shift towards a highly glycolytic phenotype, and that despite suggestions that cancer cells are adept at utilising alternative nutrient sources, PIK3CA mutant cells are not able to compensate for glucose withdrawal. Understanding the metabolic dependencies of PIK3CA mutant cancers will provide critical information for the design of effective therapies and tumour visualisation strategies.     

MG160, a Membrane Protein of the Golgi Apparatus Which Is Homologous to a Fibroblast Growth Factor Receptor and to a Ligand for E-selectin, Is Found Only in the Golgi Apparatus and Appears Early in Chicken Embryo Development

While over 20 intrinsic proteins of the Golgi apparatus have been identified and sequenced, there is no information on their developmental history, i.e., whether all Golgi proteins are expressed simultaneously or whether there is a hierarchical or stage-specific order of their expression during embryonic development. In this study we have examined the emergence and distribution of MG160 during the development of chicken embryos. MG160 is a conserved membrane sialoglycoprotein of the Golgi apparatus of most cells displaying over 90% amino acid sequence identities with two apparently unrelated molecules, namely CFR, a chicken fibroblast growth factor receptor, and ESL-1, a ligand for E-selectin (Gonatas et al., J. Biol. Chem. 1989, 264, 646-653; Burrus and Olwin, J. Biol. Chem. 1989, 264, 18647-18653; Burrus et al., Mol. Cell Biol. 1992, 12, 5600-5609; Gonatas et al., J. Cell Sci. 108, 457-467; Steegmaier et al., Nature 1995, 373, 615-620). This study was carried out by in situ hybridization, using a 56-mer antisense probe for the chicken homologue of MG160 which differs only by four bases from the corresponding segment of the rat cDNA and by immunocytochemistry and Western blotting using a polyclonal antiserum against MG160. The protein was ubiquitously and exclusively localized in the Golgi apparatus and appeared early in development within the ectoblast and primitive endoblast prior to the formation of the primitive streak. At 2 to 3 days, MG160 was particularly prominent in the notochord, neural tube, somites, and cartilage cells. In organs with central lumens, such as the neural tube, the Golgi apparatus, visualized by immunostaining for MG160, was elongated and it was located at the apical pole of cells. In 6-day-old embryos, the ongoing physiologic degeneration of the notochord was accompanied by fragmentation of the immunostained Golgi apparatus and decreased labeling of the mRNA for MG160. In order to gain information on possible interactions between MG160 and basic fibroblast growth factor (bFGF), the localization of both molecules was studied by immunocytochemistry in 3-day-old chicken embryos. While MG160 was ubiquitous in the Golgi apparatus of all cells and tissues, endogenous bFGF was not detected while exogenous bFGF bound only to basement membranes. These results indicate that MG160 is a primordial protein of the Golgi apparatus and are consistent with the hypothesis that the binding of MG160 to fibroblast growth factors and E-selectin is not related to the still unknown principal function of MG160 in the Golgi apparatus.     

Mutation of a Gene Encoding a Putative Glycoprotease Leads to Reduced Salt Tolerance, Altered Pigmentation, and Cyanophycin Accumulation in the Cyanobacterium Synechocystis sp. Strain PCC 6803

The salt-sensitive mutant 549 of the cyanobacterium Synechocystis sp. strain PCC 6803 was genetically and physiologically characterized. The mutated site and corresponding wild-type site were cloned and partially sequenced. The genetic analysis revealed that during the mutation about 1.8 kb was deleted from the chromosome of mutant 549. This deletion affected four open reading frames: a gcp gene homolog, the psaFJ genes, and an unknown gene. After construction of mutants with single mutations, only the gcp mutant showed a reduction in salt tolerance comparable to that of the initial mutant, indicating that the deletion of this gene was responsible for the salt sensitivity and that the other genes were of minor importance. Besides the reduced salt tolerance, a remarkable change in pigmentation was observed that became more pronounced in salt-stressed cells. The phycobilipigment content decreased, and that of carotenoids increased. Investigations of changes in the ultrastructure revealed an increase in the amount of characteristic inclusion bodies containing the high-molecular-weight nitrogen storage polymer cyanophycin (polyaspartate and arginine). The salt-induced accumulation of cyanophycin was confirmed by chemical estimations. The putative glycoprotease encoded by the gcp gene might be responsible for the degradation of cyanophycin in Synechocystis. Mutation of this gene leads to nitrogen starvation of the cells, accompanied by characteristic changes in pigmentation, ultrastructure, and salt tolerance level.