Showing papers on "Nuclear DNA published in 2013"
TL;DR: African swine fever virus (ASFV) is a large icosahedral DNA virus which replicates predominantly in the cytoplasm of infected cells and a similar mechanism of replication to Poxviruses has been proposed for ASFV.
405 citations
TL;DR: A second primase in human cells, PrimPol, is described, which has the ability to start DNA chains with deoxynucleotides unlike regular primases, which use exclusively ribonucleotide, which is a DNA polymerase tailored to bypass the most common oxidative lesions in DNA.
303 citations
TL;DR: It is demonstrated here that mitochondrial localization of telomerase specifically prevents nuclear DNA damage by decreasing levels of mitochondrial ROS, suggesting that this decrease of oxidative stress might be a possible cause for high stress resistance of cancer cells and could be especially important for cancer stem cells.
Abstract: Most cancer cells express high levels of telomerase and proliferate indefinitely. In addition to its telomere maintenance function, telomerase also has a pro-survival function resulting in an increased resistance against DNA damage and decreased apoptosis induction. However, the molecular mechanisms for this protective function remain elusive and it is unclear whether it is connected to telomere maintenance or is rather a non-telomeric function of the telomerase protein, TERT. It was shown recently that the protein subunit of telomerase can shuttle from the nucleus to the mitochondria upon oxidative stress where it protects mitochondrial function and decreases intracellular oxidative stress. Here we show that endogenous telomerase (TERT protein) shuttles from the nucleus into mitochondria upon oxidative stress in cancer cells and analyzed the nuclear exclusion patterns of endogenous telomerase after treatment with hydrogen peroxide in different cell lines. Cell populations excluded TERT from the nucleus upon oxidative stress in a heterogeneous fashion. We found a significant correlation between nuclear localization of telomerase and high DNA damage, while cells which excluded telomerase from the nucleus displayed no or very low DNA damage. We modeled nuclear and mitochondrial telomerase using organelle specific localization vectors and confirmed that mitochondrial localization of telomerase protects the nucleus from inflicted DNA damage and apoptosis while, in contrast, nuclear localization of telomerase correlated with higher amounts of DNA damage and apoptosis. It is known that nuclear DNA damage can be caused by mitochondrially generated reactive oxygen species (ROS). We demonstrate here that mitochondrial localization of telomerase specifically prevents nuclear DNA damage by decreasing levels of mitochondrial ROS. We suggest that this decrease of oxidative stress might be a possible cause for high stress resistance of cancer cells and could be especially important for cancer stem cells.
151 citations
TL;DR: Several APOBEC3 family members have access to the nuclear compartment and can impede the cell cycle, most likely through DNA deamination and the ensuing DNA damage response.
Abstract: Humans have seven APOBEC3 DNA cytosine deaminases. The activity of these enzymes allows them to restrict a variety of retroviruses and retrotransposons, but may also cause pro-mutagenic genomic uracil lesions. During interphase the APOBEC3 proteins have different subcellular localizations: cell-wide, cytoplasmic or nuclear. This implies that only a subset of APOBEC3s have contact with nuclear DNA. However, during mitosis, the nuclear envelope breaks down and cytoplasmic proteins may enter what was formerly a privileged zone. To address the hypothesis that all APOBEC3 proteins have access to genomic DNA, we analyzed the localization of the APOBEC3 proteins during mitosis. We show that APOBEC3A, APOBEC3C and APOBEC3H are excluded from condensed chromosomes, but become cell-wide during telophase. However, APOBEC3B, APOBEC3D, APOBEC3F and APOBEC3G are excluded from chromatin throughout mitosis. After mitosis, APOBEC3B becomes nuclear, and APOBEC3D, APOBEC3F and APOBEC3G become cytoplasmic. Both structural motifs as well as size may be factors in regulating chromatin exclusion. Deaminase activity was not dependent on cell cycle phase. We also analyzed APOBEC3-induced cell cycle perturbations as a measure of each enzyme’s capacity to inflict genomic DNA damage. AID, APOBEC3A and APOBEC3B altered the cell cycle profile, and, unexpectedly, APOBEC3D also caused changes. We conclude that several APOBEC3 family members have access to the nuclear compartment and can impede the cell cycle, most likely through DNA deamination and the ensuing DNA damage response. Such genomic damage may contribute to carcinogenesis, as demonstrated by AID in B cell cancers and, recently, APOBEC3B in breast cancers.
130 citations
TL;DR: It is postulate that poor efficacy of DNA repair is impaired above average for a particular age when combined with the enhanced sensitivity of retinal pigment epithelium cells to environmental stress factors, contributes to the pathogenesis of AMD.
Abstract: Aging and oxidative stress seem to be the most important factors in the pathogenesis of age-related macular degeneration (AMD), a condition affecting many elderly people in the developed world. However, aging is associated with the accumulation of oxidative damage in many biomolecules, including DNA. Furthermore, mitochondria may be especially important in this process because the reactive oxygen species produced in their electron transport chain can damage cellular components. Therefore, the cellular response to DNA damage, expressed mainly through DNA repair, may play an important role in AMD etiology. In several studies the increase in mitochondrial DNA (mtDNA) damage and mutations, and the decrease in the efficacy of DNA repair have been correlated with the occurrence and the stage of AMD. It has also been shown that mitochondrial DNA accumulates more DNA lesions than nuclear DNA in AMD. However, the DNA damage response in mitochondria is executed by nucleus-encoded proteins, and thus mutagenesis in nuclear DNA (nDNA) may affect the ability to respond to mutagenesis in its mitochondrial counterpart. We reported that lymphocytes from AMD patients displayed a higher amount of total endogenous basal and oxidative DNA damage, exhibited a higher sensitivity to hydrogen peroxide and UV radiation, and repaired the lesions induced by these factors less effectively than did cells from control individuals. We postulate that poor efficacy of DNA repair (i.e., is impaired above average for a particular age) when combined with the enhanced sensitivity of retinal pigment epithelium cells to environmental stress factors, contributes to the pathogenesis of AMD. Collectively, these data suggest that the cellular response to both mitochondrial and nuclear DNA damage may play an important role in AMD pathogenesis.
82 citations
TL;DR: This work presents a hypothetical model for the possible redox chemistry that underlies the binding of the meiosis-specific protein Spo11 to DNA and hypothesizes that repair of oxidative damage on nuclear DNA could be a major driving force in the evolution of meiosis.
Abstract: The maintenance of sexual reproduction in eukaryotes is still a major enigma in evolutionary biology. Meiosis represents the only common feature of sex in all eukaryotic kingdoms, and thus, we regard it a key issue for discussing its function. Almost all asexuality modes maintain meiosis either in a modified form or as an alternative pathway, and facultatively apomictic plants increase frequencies of sexuality relative to apomixis after abiotic stress. On the physiological level, abiotic stress causes oxidative stress. We hypothesize that repair of oxidative damage on nuclear DNA could be a major driving force in the evolution of meiosis. We present a hypothetical model for the possible redox chemistry that underlies the binding of the meiosis-specific protein Spo11 to DNA. During prophase of meiosis I, oxidized sites at the DNA molecule are being targeted by the catalytic tyrosine moieties of Spo11 protein, which acts like an antioxidant reducing the oxidized target. The oxidized tyrosine residues, tyrosyl radicals, attack the phosphodiester bonds of the DNA backbone causing DNA double strand breaks that can be repaired by various mechanisms. Polyploidy in apomictic plants could mitigate oxidative DNA damage and decrease Spo11 activation. Our hypothesis may contribute to explaining various enigmatic phenomena: first, DSB formation outnumbers crossovers and, thus, effective recombination events by far because the target of meiosis may be the removal of oxidative lesions; second, it offers an argument for why expression of sexuality is responsive to stress in many eukaryotes; and third, repair of oxidative DNA damage turns meiosis into an essential characteristic of eukaryotic reproduction.
75 citations
TL;DR: The identification of causative molecular defects in nuclear or mitochondrial genome leads to the definite diagnosis of mitochondrial myopathy, which is characterized by early fatigue and/or fixed muscle weakness.
73 citations
TL;DR: Experimental evidence is presented to show that single-stranded breaks occur in nuclear DNA during ageing of rye embryos in the dry state, which can be attributed to DNA repair before the onset of semi-conservative DNA replication.
Abstract: Experimental evidence is presented to show that single-stranded breaks occur in nuclear DNA during ageing of rye embryos in the dry state. Total DNA is retained and on imbibition unscheduled DNA synthesis occurs which can be attributed to DNA repair before the onset of semi-conservative DNA replication.
61 citations
TL;DR: Processes such as triacylglycerol metabolism, energy production, protein folding, response to unfolded proteins, and cellular detoxification were found to be altered in these cells.
Abstract: Purpose
Sperm DNA fragmentation has been suggested as a marker for infertility diagnosis and prognosis Hence, understanding its impact on male physiology and post-genomic pathways would be clinically important We performed the proteomics and functional enrichment analyses of viable spermatozoa from ejaculates with low and high sperm DNA fragmentation to identify protein expression and pathways altered in association with sperm DNA fragmentation
57 citations
TL;DR: The term ‘mitoepigenetics’ is proposed to be proposed to include all four above-noted types of interactions between mitochondria and epigenetics, and a more restricted usage of the term’s use for molecular events dealing solely with the intra-mitochondrial epigenetics and the modifications of mitochondrial genome is suggested.
Abstract: Mitochondria, intracellular organelles with their own genome, have been shown capable of interacting with epigenetic mechanisms in at least four different ways. First, epigenetic mechanisms that regulate the expression of nuclear genome influence mitochondria by modulating the expression of nuclear-encoded mitochondrial genes. Second, a cell-specific mitochondrial DNA content (copy number) and mitochondrial activity determine the methylation pattern of nuclear genes. Third, mitochondrial DNA variants influence the nuclear gene expression patterns and the nuclear DNA (ncDNA) methylation levels. Fourth and most recent line of evidence indicates that mitochondrial DNA similar to ncDNA also is subject to epigenetic modifications, particularly by the 5-methylcytosine and 5-hydroxymethylcytosine marks. The latter interaction of mitochondria with epigenetics has been termed 'mitochondrial epigenetics'. Here we summarize recent developments in this particular area of epigenetic research. Furthermore, we propose the term 'mitoepigenetics' to include all four above-noted types of interactions between mitochondria and epigenetics, and we suggest a more restricted usage of the term 'mitochondrial epigenetics' for molecular events dealing solely with the intra-mitochondrial epigenetics and the modifications of mitochondrial genome.
50 citations
TL;DR: Far from the hypothesis that mtDNA variation is neutral, this work shows that mitochondrial polymorphism can have a strong impact on fitness components and hence on the evolutionary fate of the yeast populations, while respiratory environments may increase the probability to fix Sc-mtDNA.
Abstract: In eukaryotes, mitochondrial DNA (mtDNA) has high rate of nucleotide substitution leading to different mitochondrial haplotypes called mitotypes. However, the impact of mitochondrial genetic variant on phenotypic variation has been poorly considered in microorganisms because mtDNA encodes very few genes compared to nuclear DNA, and also because mitochondrial inheritance is not uniparental. Here we propose original material to unravel mitotype impact on phenotype: we produced interspecific hybrids between S. cerevisiae and S. uvarum species, using fully homozygous diploid parental strains. For two different interspecific crosses involving different parental strains, we recovered 10 independent hybrids per cross, and allowed mtDNA fixation after around 80 generations. We developed PCR-based markers for the rapid discrimination of S. cerevisiae and S. uvarum mitochondrial DNA. For both crosses, we were able to isolate fully isogenic hybrids at the nuclear level, yet possessing either S. cerevisiae mtDNA (Sc-mtDNA) or S. uvarum mtDNA (Su-mtDNA). Under fermentative conditions, the mitotype has no phenotypic impact on fermentation kinetics and products, which was expected since mtDNA are not necessary for fermentative metabolism. Alternatively, under respiratory conditions, hybrids with Sc-mtDNA have higher population growth performance, associated with higher respiratory rate. Indeed, far from the hypothesis that mtDNA variation is neutral, our work shows that mitochondrial polymorphism can have a strong impact on fitness components and hence on the evolutionary fate of the yeast populations. We hypothesize that under fermentative conditions, hybrids may fix stochastically one or the other mt-DNA, while respiratory environments may increase the probability to fix Sc-mtDNA.
TL;DR: A multimarker phylogeographical survey is conducted to explore the evolutionary independence of these mitochondrial DNA lineages of the crested newt T. karelinii sensu lato and includes representatives of the other species to guide the interpretation of the results.
TL;DR: The clinician should be aware of the pediatric presentation of mitochondrial disease and have an understanding of the myriad of nuclear genes responsible for these disorders, which can be best understood by utilizing a classification system of location and function within the mitochondria.
01 Jan 2013
TL;DR: Current knowledge on the DNA/chromatin composition, origin, and mitotic and meiotic drive mechanisms of B chromosomes are surveyed and effects and transcripts associated with Bs are discussed.
Abstract: B chromosomes are dispensable and often selfish elements of the genome which follow their own evolutionary pathway. B chromosomes are a major source of intraspecific variation in nuclear DNA amounts in numerous species and the distribution of Bs among different groups of angiosperms is not random. B chromosome inheritance is irregular and non-Mendelian, and therefore polymorphisms exist with respect to the number of Bs within populations or even within different cell lines of an individual carrying Bs. Drive mechanisms play a major role in the equilibrium of B frequency in populations. The most widely accepted view is that Bs are derived from the A chromosome complement. Some evidence also suggests that Bs can be spontaneously generated in response to the new genomic conditions after interspecific hybridization. The molecular processes that gave rise to Bs during evolution remain unclear. Here, we survey current knowledge on the DNA/chromatin composition, origin, and mitotic and meiotic drive mechanisms of B chromosomes and discuss effects and transcripts associated with Bs.
TL;DR: It is demonstrated that H. pylori infection of gastric adenocarcinoma cells causes mtDNA mutations and a decrease of mtDNA content, and the results demonstrate that multiple DNA repair activities are involved in protecting mtDNA during infection.
TL;DR: DNA transfer from chloroplasts and mitochondria to the nucleus is ongoing in eukaryotes but the mechanisms involved are poorly understood, and mitochondrial DNAs tended to insert more frequently into regions of open chromatin revealed by human DNase-seq and Formaldehyde-Assisted Isolation of Regulatory Elements-seq databases.
Abstract: DNA transfer from chloroplasts and mitochondria to the nucleus is ongoing in eukaryotes but the mechanisms involved are poorly understood. Mitochondrial DNA was observed to integrate into the nuclear genome through DNA double-strand break repair in Nicotiana tabacum. Here, 14 nuclear insertions of chloroplast DNA (nupts) that are unique to Oryza sativa subsp. indica were identified. Comparisons with the preinsertion nuclear loci identified in the related subspecies, O. sativa subsp. japonica, which lacked these nupts, indicated that chloroplast DNA had integrated by nonhomologous end joining. Analyzing public DNase-seq data revealed that nupts were significantly more frequent in open chromatin regions of the nucleus. This preference was tested further in the chimpanzee genome by comparing nuclear loci containing integrants of mitochondrial DNA (numts) with their corresponding numt-lacking preinsertion sites in the human genome. Mitochondrial DNAs also tended to insert more frequently into regions of open chromatin revealed by human DNase-seq and Formaldehyde-Assisted Isolation of Regulatory Elements-seq databases.
TL;DR: An important role of nursery populations in increasing genetic recombination within the species and the existence of extensive phenomena of migration of isolates that have been likely spread worldwide with infected plant material are suggested.
Abstract: Mammella, M. A., Martin, F. N., Cacciola, S. O., Coffey, M. D., Faedda, R., and Schena, L. 2013. Analyses of the population structure in a global collection of Phytophthora nicotianae isolates inferred from mitochondrial and nuclear DNA sequences. Phytopathology 103:610-622. Genetic variation within the heterothallic cosmopolitan plant pathogen Phytophthora nicotianae was determined in 96 isolates from a wide range of hosts and geographic locations by characterizing four mitochondrial (10% of the genome) and three nuclear loci. In all, 52 single-nucleotide polymorphisms (SNPs) (an average of 1 every 58 bp) and 313 sites with gaps representing 5,450 bases enabled the identification of 50 different multilocus mitochondrial haplotypes. Similarly, 24 SNPs (an average of 1 every 69 bp), with heterozygosity observed at each locus, were observed in three nuclear regions (hyp, scp, and β-tub) differentiating 40 multilocus nuclear genotypes. Both mitochondrial and nuclear markers revealed a high level of dispersal of isolates and an inconsistent geographic structuring of populations. However, a specific association was observed for host of origin and genetic grouping with both nuclear and mitochondrial sequences. In particular, the majority of citrus isolates from Italy, California, Florida, Syria, Albania, and the Philippines clustered in the same mitochondrial group and shared at least one nuclear allele. A similar association was also observed for isolates recovered from Nicotiana and Solanum spp. The present study suggests an important role of nursery populations in increasing genetic recombination within the species and the existence of extensive phenomena of migration of isolates that have been likely spread worldwide with infected plant material.
TL;DR: The results indicate that defects in the repair/tolerance of oxidatively generated DNA lesions are not sufficient to explain these severe clinical features of certain XP patients, and provides further evidence that XPA and XPC proteins have specific roles in cell protection and repair/Tolerance of ROS-induced DNA damage.
TL;DR: It is concluded that the generation of defective, apoptotic human spermatozoa is associated with disorders of spermatogenesis that lead to a global hypermethylation of their nuclear DNA.
Abstract: Summary
The methylation status of human spermatozoa has been examined in relation to the isopycnic density of these cells and their tendency to spontaneously default to an apoptotic state. DNA methylation was evaluated using three independent procedures: high-pressure liquid chromatography, flow cytometry and immunocytochemistry. All three techniques revealed that poor-quality spermatozoa recovered from the low-density region of Percoll gradients were characterised by a global hypermethylation of their DNA. Hypermethylation was visualised with an anti-5-methylcytosine antibody as punctate areas of cross-reactivity randomly distributed throughout the chromatin. Immunocytochemical evidence was also obtained suggesting that the sperm mitochondrial genome exists in a heavily methylated state, as a possible buffer against unscheduled transcription. Defective human spermatozoa were also shown to exhibit a tendency to default to an apoptotic state characterised by an increase in annexin V binding. The measurement of annexin V binding levels in individual sperm populations was found to be highly correlated with sperm vitality (P < 0.001) and the methylation status of their DNA (P < 0.001). We conclude that the generation of defective, apoptotic human spermatozoa is associated with disorders of spermatogenesis that lead to a global hypermethylation of their nuclear DNA.
TL;DR: Many native breeds of horses as well as ponies were assessed for their genetic diversity and ancestry on the basis of studies on mitochondrial DNA to address the questions of evolution along with breed development and conservation.
Abstract: It is imperative to assess the maternal lineage in order to achieve a broad picture of evolution, phylogenetic and genetic biodiversity within and among different breeds of livestock. In recent past, there has been a considerable advancement in sequencing of complete mammalian mtDNA molecules and their analysis. Most of the studies have focused on the mitochondrial D-loop region, the most variable part of mtDNA due to increased substitution rate than in the rest of the mtDNA genome which serves as a better genetic marker to assess the diversity. Mitochondrial DNA (mtDNA) possesses several favorable characteristics, including large quantity in the cell, small genome size, haploid, maternal inheritance with extremely low probability of paternal leakage, higher mutation rate than nuclear DNA, and amenable to change mainly through mutation rather than recombination. All these features make mtDNA a useful and one of the most frequently used markers in molecular systematic and has been widely employed to address questions of genetic diversity, population structure and population evolution of animals including equines. Many native breeds of horses as well as ponies were assessed for their genetic diversity and ancestry on the basis of studies on mitochondrial DNA to address the questions of evolution along with breed development and conservation.
TL;DR: Overall the findings indicate a high degree of nuclear genetic differentiation between the two lineages of L. rubellus, implying reproductive isolation at the two study sites and therefore the potential existence of cryptic species.
Abstract: Mitochondrial DNA analysis has revealed two distinct phylogenetic lineages within the ecotoxological sentinel earthworm model Lumbricus rubellus Hoffmeister, 1843. The existence of these lineages could complicate ecotoxicological studies that use the species as a sentinel for soil contamination testing, as they may respond differently to contamination; however, as mitochondrial haplotypes are not always expected to segregate in the same way as chromosomal DNA in natural populations, we further investigated this issue by using nuclear DNA markers (microsatellites) to measure genetic diversity, differentiation, and gene flow in sympatric populations of the two L. rubellus lineages at two sites in South Wales. Our results show that sympatric populations of the two lineages are more genetically differentiated than geographically distant populations of the same lineage, and Bayesian clustering analysis revealed no evidence of gene flow between the lineages at either site. Additionally, DNA sequencing of these microsatellite loci uncovered substantial differentiation between lineages at homologous flanking regions. Overall our findings indicate a high degree of nuclear genetic differentiation between the two lineages of L. rubellus, implying reproductive isolation at the two study sites and therefore the potential existence of cryptic species. The existence of two cryptic taxa has major implications for the application of L. rubellus as an ecotoxicological sentinel. It may therefore be necessary to consider the lineages as separate taxa during future ecotoxicological studies.
TL;DR: Higher CSF DNA levels on presentation, rather than plasma DNA levels, are associated with worse outcomes in patients with acute spontaneous aneurysmal SAH, and more prospective multicenter investigations are needed to confirm the predictive value of CSF and plasmaDNA levels on outcome.
Abstract: Object Increased plasma nuclear and mitochondrial DNA levels have been reported in critically ill patients, and extracellular DNA may originate from damaged tissues having undergone necrosis. This study tested the hypothesis that nuclear and mitochondrial DNA levels in CSF and plasma are substantially increased in patients with acute spontaneous aneurysmal subarachnoid hemorrhage (SAH) and decrease thereafter, such that nuclear and mitochondrial DNA levels may be predictive of treatment outcomes. Methods Serial nuclear and mitochondrial DNA levels in CSF and plasma from 21 adult patients with spontaneous aneurysmal SAH and 39 healthy volunteers who received myelography examinations during the study period were evaluated. Results Data showed that circulating plasma nuclear DNA concentrations and both nuclear and mitochondrial DNA levels in CSF significantly increased in patients with aneurysmal SAH on admission compared with the volunteers. In patients with poor outcome, the CSF nuclear and mitochondrial D...
TL;DR: The hypothesis that shifts in breeding systems and genome size are correlated, as polyploidy is suggested to be a possible mechanism for the evolution of monoecy in liverworts and could therefore be associated with larger genome sizes is tested.
TL;DR: Results indicate that AGT protein monoepoxides produce cytotoxic and mutagenic DPC lesions within chromosomal DNA, and suggest that covalent D PC lesions contribute to the cytot toxic and Mutagenic effects of bis-electrophiles.
Abstract: Although cytotoxic alkylating agents possessing two electrophilic reactive groups are thought to act by cross-linking cellular biomolecules, their exact mechanisms of action have not been established. In cells, these compounds form a mixture of DNA lesions, including nucleobase monoadducts, interstrand and intrastrand cross-links, and DNA-protein cross-links (DPCs). Interstrand DNA-DNA cross-links block replication and transcription by preventing DNA strand separation, contributing to toxicity and mutagenesis. In contrast, potential contributions of drug-induced DPCs are poorly understood. To gain insight into the biological consequences of DPC formation, we generated DNA-reactive protein reagents and examined their toxicity and mutagenesis in mammalian cells. Recombinant human O(6)-alkylguanine DNA alkyltransferase (AGT) protein or its variants (C145A and K125L) were treated with 1,2,3,4-diepoxybutane to yield proteins containing 2-hydroxy-3,4-epoxybutyl groups on cysteine residues. Gel shift and mass spectrometry experiments confirmed that epoxide-functionalized AGT proteins formed covalent DPC but no other types of nucleobase damage when incubated with duplex DNA. Introduction of purified AGT monoepoxides into mammalian cells via electroporation generated AGT-DNA cross-links and induced cell death and mutations at the hypoxanthine-guanine phosphoribosyltransferase gene. Smaller numbers of DPC lesions and reduced levels of cell death were observed when using protein monoepoxides generated from an AGT variant that fails to accumulate in the cell nucleus (K125L), suggesting that nuclear DNA damage is required for toxicity. Taken together, these results indicate that AGT protein monoepoxides produce cytotoxic and mutagenic DPC lesions within chromosomal DNA. More generally, these data suggest that covalent DPC lesions contribute to the cytotoxic and mutagenic effects of bis-electrophiles.
TL;DR: Evidence is presented supporting the idea that the nucleolus, and the rDNA contained therein, play more roles in the biology of the cell than simply ribosome biogenesis, and that rapid alterations in nucleolar structure in response to changing conditions manifest themselves in altered genomic structures that have functional consequences.
Abstract: The nucleolus is a prominent nuclear structure that is the site of ribosomal RNA (rRNA) transcription, and hence ribosome biogenesis. Cellular demand for ribo-somes, and hence rRNA, is tightly linked to cell growth and the rRNA makes up the majority of all the RNA within a cell. To fulfill the cellular demand for rRNA, the ribo somal RNA (rDNA) genes are amplified to high copy number and transcribed at very high rates. As such, understanding the rDNA has profound consequences for our compre-hension of genome and transcriptional organization in cells. In this review, we address the question of whether the nucleolus is a raft adrift the sea of nuclear DNA, or actively contributes to genome organization. We present evidence supporting the idea that the nucleolus, and the rDNA contained therein, play more roles in the biology of the cell than simply ribosome biogenesis. We propose that the nucleolus and the rDNA are central factors in the spa-tial organization of the genome, and that rapid alterations in nucleolar structure in response to changing conditions manifest themselves in altered genomic structures that have functional consequences. Finally, we discuss some predictions that result from the nucleolus having a central role in nuclear organization. Keywords: genome architecture; nucleolus; rDNA.
TL;DR: Bacterial wilt resistant somatic hybrids obtained via protoplast fusion between potato and eggplant and three types of nuclear genomes were identified in the hybrids through GISH and SSR analysis may explain partially the inheritance behavior of the hybrids which is informative for potato improvement.
Abstract: Bacterial wilt resistant somatic hybrids were obtained via protoplast fusion between potato and eggplant and three types of nuclear genomes were identified in the hybrids through GISH and SSR analysis.
Cultivated potato (Solanum tuberosum L.) lacks resistance to bacterial wilt caused by Ralstonia solanacearum. Interspecific symmetric protoplast fusion was conducted to transfer bacterial wilt resistance from eggplant (S. melongena, 2n = 2x = 24) into dihaploid potato (2n = 2x = 24). In total, 34 somatic hybrids were obtained, and of these, 11 rooted and were tested for genome components and resistance to race 1 of R. solanacearum. The hybrids exhibited multiple ploidy levels and contained the dominant nuclear genome from the potato parent. Three types of nuclear genomes were identified in the hybrids through genomic in situ hybridization (GISH) and simple sequence repeat (SSR) analysis, including (1) the potato type of the tetraploids in which eggplant chromosomes could not be detected by GISH but their nuclear DNA was confirmed by SSR, (2) the biased type of the hexaploids in which the chromosome dosage was 2 potato:1 eggplant, and (3) the chromosome translocation type of the mixoploids and aneuploids that was characterized by various rates of translocations of nonhomologous chromosomes. Cytoplasmic genome analysis revealed that mitochondrial DNA of both parents coexisted and/or recombined in most of the hybrids. However, only potato chloroplast DNA was retained in the hybrids speculating a compatibility between cpDNA and nuclear genome of the cell. The pathogen inoculation assay suggested a successful transfer of bacterial wilt resistance from eggplant to the hybrids that provides potential resistance for potato breeding against bacterial wilt. The genome components characterized in present research may explain partially the inheritance behavior of the hybrids which is informative for potato improvement.
TL;DR: It is proposed that NF-κB’s most notable function after DNA damage in primary cells is related to the release of cytokines, thereby contributing to sterile inflammation.
Abstract: Activation of NF-κB (nuclear factor of kappa light chain gene enhancer in B cells) in response to DNA damage is considered to contribute to repair of genetic lesions, increased cell survival and cytokine release. The molecular mechanisms orchestrating this cytoplasmic event involve core components of the nuclear DNA damage response machinery, including ATM-kinase (ataxia telangiectasia mutated kinase) and PARP-1 (poly (ADP-ribose) polymerase 1). The physiological consequences of defective NF-κB activation in this context, however, remain poorly investigated. Here we report on the role of the ‘p53-induced protein with a death domain’, PIDD, which appears rate limiting in this process, as is PARP-1. Despite impaired NF-κB activation, DNA damage did not increase cell death or reduce clonal survival of various cell types lacking PIDD, such as mouse embryonic fibroblasts or stem and progenitor cells of the hematopoietic system. Furthermore, lymphomagenesis induced by γ-irradiation (IR) was unaffected by deficiency for PIDD or PARP-1, indicating that loss of DNA damage-triggered NF-κB signalling does not affect IR-driven tumorigenesis. However, loss of either gene compromised cytokine release after acute IR injury. Hence, we propose that NF-κB’s most notable function after DNA damage in primary cells is related to the release of cytokines, thereby contributing to sterile inflammation.
01 Oct 2013
TL;DR: This study demonstrates the specific delivery of a platinum drug to mitochondria and investigates the effects of directing this agent outside the nucleus.
Abstract: An analog of the anticancer drug cisplatin (mtPt) was delivered to mitochondria of human cells using a peptide specifically targeting this organelle. mtPt induces apoptosis without damaging nuclear DNA, indicating that mtDNA damage is sufficient to mediate the activity of a platinum-based chemotherapeutic. This study demonstrates the specific delivery of a platinum drug to mitochondria and investigates the effects of directing this agent outside the nucleus.
TL;DR: It seems that the loss of nuclear DNA diversity in R. brelichi does not represent the most prominent conservation threat for the long-term survival of the species, and conservation efforts should therefore focus more on immediate threats such as development of tourism and habitat destruction.
Abstract: To evaluate the conservation status of a species or population it is necessary to gain insight into its ecological requirements, reproduction, genetic population structure, and overall genetic diversity. In our study we examined the genetic diversity of Rhinopithecus brelichi by analyzing microsatellite data and compared them with already existing data derived from mitochondrial DNA, which revealed that R. brelichi exhibits the lowest mitochondrial diversity of all so far studied Rhinopithecus species. In contrast, the genetic diversity of nuclear DNA is high and comparable to other Rhinopithecus species, i.e. the examined microsatellite loci are similarly highly polymorphic as in other species of the genus. An explanation for these differences in mitochondrial and nuclear genetic diversity could be a male biased dispersal. Females most likely stay within their natal band and males migrate between bands, thus mitochondrial DNA will not be exchanged between bands but nuclear DNA via males. A Bayesian Skyline Plot based on mitochondrial DNA sequences shows a strong decrease of the female effective population size (Nef) starting about 3,500 to 4,000 years ago, which concurs with the increasing human population in the area and respective expansion of agriculture. Given that we found no indication for a loss of nuclear DNA diversity in R. brelichi it seems that this factor does not represent the most prominent conservation threat for the long-term survival of the species. Conservation efforts should therefore focus more on immediate threats such as development of tourism and habitat destruction.
TL;DR: M measurement of the size of stomata and caryopsis allowed prediction of ploidy levels in the field and laboratory and confirmed the occurrence of diploid and tetraploid M. sinensis plants as well as a putative triploids M. × giganteus native to Korea.
Abstract: Because of its high biomass productivity and nutrient-use efficiency, Miscanthus spp. have emerged as promising bioenergy crops. Polyploidism in Miscanthus species is important because it allows non-native countries to cultivate sterile types, such as triploid M. × giganteus, in order to prevent ecosystem disturbance. Although M. sacchariflorus and M. sinensis are considered to be native to Korea, China, and Japan, accurate information describing the ploidy levels of these species has not yet been well established. To evaluate rough ploidy levels, 215 accessions of Miscanthus species were estimated by relative fluorescence intensities of DAPI-stained nuclei. After evaluation of rough ploidy levels, 20 plants were randomly selected by species and ploidy levels, and ploidy levels were examined by counting chromosomes, estimating propidium iodide-stained DNA content with flow cytometry, and measuring sizes of stomata and caryopsis. Among the 20 plants examined, 3 were diploid and 6 were tetraploid M. sacchariflorus (4.56 ± 0.01 and 8.90 ± 0.14 pg/2C nuclear DNA content, respectively), while 6 were diploid and 3 were triploid M. sinensis (5.40 ± 0.18 and 8.29 ± 0.33 pg/2C nuclear DNA content, respectively). One plant was a putative triploid M. × giganteus having 7.31 pg/2C nuclear DNA content, which was similar to an M. × giganteus plant from Illinois, USA having 7.23 pg/2C nuclear DNA content. We confirmed the occurrence of diploid and tetraploid M. sacchariflorus and M. sinensis plants as well as a putative triploid M. × giganteus native to Korea. Thus, measurement of the size of stomata and caryopsis allowed prediction of ploidy levels in the field and laboratory.