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PubMed2004

Chromosomal instability at common fragile sites in Seckel syndrome.

Seckel syndrome (SCKL) is a rare, genetically heterogeneous disorder, with dysmorphic facial appearance, growth retardation, microcephaly, mental retardation, variable chromosomal instability, and hematological disorders. To date, three loci have been linked to this syndrome, and recently, the gene encoding ataxia-telangiectasia and Rad3-related protein (ATR) was identified as the gene mutated at the SCKL1 locus. The ATR mutation affects splicing efficiency, resulting in low levels of ATR in affected individuals. Elsewhere, we reported increased instability at common chromosomal fragile sites in cells lacking the replication checkpoint gene ATR. Here, we tested whether cells from patients carrying the SCKL1 mutation would show increased chromosome breakage following replication stress. We found that, compared with controls, there is greater chromosomal instability, particularly at fragile sites, in SCKL1-affected patient cells after treatment with aphidicolin, an inhibitor of DNA polymerase alpha and other polymerases. The difference in chromosomal instability between control and patient cells increases at higher levels of aphidicolin treatment, suggesting that the low level of ATR present in these patients is not sufficient to respond appropriately to replication stress. This is the first human genetic syndrome associated with increased chromosome instability at fragile sites following replication stress, and these findings may be related to the phenotypic findings in patients with SCKL1.

Abnormalities, Multiple↗

PubMedDate not supplied

Re-adaptation of the esophageal mucosa of rats to protracted stress.

BACKGROUND: Previous studies showed that the DNA synthesis (DS) in the esophagus of rats significantly increased at 4 weeks of stress, but decreased to normal values at 8 weeks. The possibility that this DS adaptation (DSA) could be maintained beyond 8 weeks was explored. MATERIALS AND METHODS: Sixty-five rats were investigated: 60 were transported to the stress laboratory (30 were water-plunged and 30 were controls) for 8 weeks. After 8 weeks, groups of stressed and control animals (n = 5) were allowed to rest one, two, three and four weeks, ending with single water-plunging or sham-handling. All animals (including 5 untreated) received i.p. injection of 3H-thymidine before sacrifice. The ratio radioactive DNA/total DNA reflected the DS of the esophagus. The isotope mainly labeled mucosal cells. RESULTS: DS significantly increased at 10 and 11 weeks (p < 0.05), but decreased below 8 week values at 12 weeks. CONCLUSION: DSA values at 8 stress weeks did not prevail since DS substantially increased in stressed rats at 10 and 11 weeks. At 12 weeks, DS re-adaptation (DSRA) occurred. Importantly, it took 8 weeks to achieve DSA, but only 4 weeks to accomplish DSRA. Control animals also showed DS fluctuations, but to a lower degree. The model described may prove of value in studies aimed to abate the disparate fluctuations of DNA synthesis in the esophageal mucosa during the various phases of protracted stress.

Acute Disease↗

PubMed2006

Mitochondrial abnormalities and oxidative imbalance in Alzheimer disease.

A number of mitochondrial and metabolic abnormalities were identified in the hippocampal neurons of Alzheimer disease compared to age-matched controls. Hippocampal neurons are the most vulnerable to disease-associated pathology (i.e., cell death and proteinaceous lesions) and contain numerous markers of oxidative stress. Interestingly we found that the levels of mitochondrial DNA and cytochrome oxidase-1 in these neurons are markedly increased compared with those of age-matched control brains, even though the number of mitochondria per neuron is decreased. We hypothesize that the increased levels of mitochondrial DNA and cytochrome oxidase-1 may reflect an attempt by oxidatively-challenged neurons to replicate mitochondria, albeit unsuccessfully, as a response to the energetic/oxidative stress. Indeed, in this context, numerous signs of mitosis are observed in pyramidal neurons. Mitotic signals that promote cell cycle re-entry might be expected to also signal the synthesis of new mitochondria. Alternatively, these abnormalities may indicate altered turnover of mitochondrial components as a result of reduced degradation of mitochondrial byproducts or altered mitochondrial transport that redistributes mitochondrial DNA and cytochrome oxidase-1 to the cell body.

Alzheimer Disease↗

PubMed2006

Production of reactive oxygen species in response to replication stress and inappropriate mitosis in fission yeast.

Previous studies have indicated that replication stress can trigger apoptosis-like cell death, accompanied (where tested) by production of reactive oxygen species (ROS), in mammalian cells and budding yeast (Saccharomyces cerevisiae). In mammalian cells, inappropriate entry into mitosis also leads to cell death. Here, we report similar responses in fission yeast (Schizosaccharomyces pombe). We used ROS- and death-specific fluorescent stains to measure the effects of mutations in replication initiation and checkpoint genes in fission yeast on the frequencies of ROS production and cell death. We found that certain mutant alleles of each of the four tested replication initiation genes caused elevated ROS and cell death. Where tested, these effects were not enhanced by checkpoint-gene mutations. Instead, when cells competent for replication but defective in both the replication and damage checkpoints were treated with hydroxyurea, which slows replication fork movement, the frequencies of ROS production and cell death were greatly increased. This was a consequence of elevated CDK activity, which permitted inappropriate entry into mitosis. Thus, studies in fission yeast are likely to prove helpful in understanding the pathways that lead from replication stress and inappropriate mitosis to cell death in mammalian cells.

Cell Cycle Proteins↗

PubMed1998

Nuclear domain 10, the site of DNA virus transcription and replication.

Within the highly organized nuclear structure, specific nuclear domains (ND10) are defined by accumulations of proteins that can be interferon-upregulated, implicating ND10 as sites of a nuclear defense mechanism. Compatible with such a mechanism is the deposition of herpesvirus, adenovirus, and papovavirus genomes at the periphery of ND10. However, these DNA viruses begin their transcription at ND10 and consequently initiate replication at these sites, suggesting that viruses have evolved ways to circumvent this potential cellular defense and exploit it. Other ND10-associated proteins belong to ubiquitin-related pathways. These findings, together with the accumulation of various overexpressed cellular and viral proteins, suggest that ND10 function as nuclear dumps or as nuclear depots. Consistent with the recruitment or deposition of various proteins and viral genomes adjacent to ND10, ND10 themselves may only be protein accumulations at specific but as yet undefined nuclear deposition sites. The concept of specific nuclear deposition sites may explain the juxtaposition of various nuclear bodies and allows testable predictions about a potential supramolecular regulatory mechanism whereby proteins are selectively segregated or released by global changes induced in nuclear functions such as viral infections, stress, or hormonal induction.

Animals↗

PubMed2004

Epstein-Barr virus lytic replication elicits ATM checkpoint signal transduction while providing an S-phase-like cellular environment.

When exposed to genotoxic stress, eukaryotic cells demonstrate a DNA damage response with delay or arrest of cell-cycle progression, providing time for DNA repair. Induction of the Epstein-Barr virus (EBV) lytic program elicited a cellular DNA damage response, with activation of the ataxia telangiectasia-mutated (ATM) signal transduction pathway. Activation of the ATM-Rad3-related (ATR) replication checkpoint pathway, in contrast, was minimal. The DNA damage sensor Mre11-Rad50-Nbs1 (MRN) complex and phosphorylated ATM were recruited and retained in viral replication compartments, recognizing newly synthesized viral DNAs as abnormal DNA structures. Phosphorylated p53 also became concentrated in replication compartments and physically interacted with viral BZLF1 protein. Despite the activation of ATM checkpoint signaling, p53-downstream signaling was blocked, with rather high S-phase CDK activity associated with progression of lytic infection. Therefore, although host cells activate ATM checkpoint signaling with response to the lytic viral DNA synthesis, the virus can skillfully evade this host checkpoint security system and actively promote an S-phase-like environment advantageous for viral lytic replication.

Ataxia Telangiectasia Mutated Proteins↗

PubMed1996

Computation of DNA structural variability--a new predictor of DNA regulatory regions.

MOTIVATION: Local separation of the two strands of the DNA duplex is an essential step in important biological activities, including the initiation of transcription and replication. This conformational transition occurs in response to imposed stresses, which are stringently regulated in vivo. RESULTS: This paper describes two computational methods to analyse this phenomenon: an approximate statistical mechanical method and a Monte Carlo sampling technique. Analysis of genomic DNA sequences shows that sites of predicted duplex destabilization are closely associated with regions regulating transcription, with the most destabilized sites coinciding with 3' gene termini. Experimental results supporting this conclusion are described. The incorporation of this technique into computational searches for regulatory regions is discussed. AVAILABILITY: Because the programs implementing these calculations are complex to use and not completely developed, they have not been released yet. However, the author will analyze any DNA sequences upon request. Sequences may be submitted electronically to benham/msvax.mssm.edu.

DNA↗

PubMed2004

Oxidative stress in NRTI-induced toxicity: evidence from clinical experience and experiments in vitro and in vivo.

This article reviews the relationship of oxidative stress with nucleoside reverse transcriptase inhibitor (NRTI)-induced toxicity and suggests how oxi-dative stress may participate in NRTI-mediated toxicity. NRTIs are pro-drugs that require intracellular phosphorylation to their 5' triphosphates by cellular kinases to inhibit viral and mitochondrial DNA (mtDNA) replication. NRTIs in highly active antiretroviral therapy have decreased morbidity and mortality, but side effects can be limiting after prolonged use. These side effects may be linked through mitochondrial dysfunction arising from altered mtDNA replication and oxidative stress via destruction of elements of mtDNA replication, decreased oxidative phosphorylation, and cellular function. Although oxidative stress is associated with NRTI therapy, there is still debate about whether it plays a direct role in NRTI-induced toxicity. The impact of oxidative stress on cardiovascular disease is likely to increase because patients with HIV infection are living longer as a result of effective antiretroviral therapy.

Animals↗

PubMed1991

On the origins of genetic variants.

Two contrasting mechanisms responsible for the creation of genetic variants are described: one is the manifestation of the limited accuracy of the cellular machinery for DNA replication, the other results from the ability of cells to repair damaged DNA. Replication-dependent variants and those caused by episodical DNA damage enhance the probability that a small fraction of a cell population may survive a sudden (physical or biological) change of environmental conditions. Replication-independent variants arise during persistent but not immediately lethal stress (e.g. starvation) of a non-dividing population. The variants observed under these conditions are of selective advantage because they are able to cope with the particular stress situation. The molecular basis of their creation is a matter of intensive debate.

Biological Evolution↗

PubMed1976

Chloroplast Growth and Replication in Germinating Spinach Cotyledons following Massive gamma-Irradiation of the Seed.

Spinach seeds (Spinacia oleracea L.) given massive doses of gamma-irradiation (500 krad) germinate and form a seedling with two green cotyledons and a radicle, but develop no further. Irradiated cotyledons show no increase in cell number or total DNA over a 7-day period in the light, while in control cotyledons there is a small increase in cell number and large increases in total DNA and chloroplast number. The chloroplasts of irradiated cotyledons are delayed in their division, become greatly enlarged and contain large amounts of starch. The whole population of chloroplasts subsequently undergoes a wave of division. The daughter chloroplasts show normal thylakoid development, but have some abnormal structural features caused by the radiation stress. Information on the effect of X-irradiation, ultraviolet irradiation, and 5-fluorodeoxyuridine on chloroplast replication and on chloroplast and nuclear DNA synthesis was obtained from cultured spinach leaf discs. It appears that chloroplast replication is more resistant to ionizing radiation than cell division and can proceed in the absence of nuclear DNA synthesis and greatly reduced chloroplast DNA synthesis.

Journal Article↗

PubMed1984

Mathematical principles of cell division.

The report given here is an attempt of the mathematical formulations to solve a problem concerning cell division and the control of mass and volume of the nucleus and cytoplasm. The study of the interaction forces on the nucleus and the vibrational frequencies during cell division are analyzed in detail. Lastly, the vibrations of a cell and the coalescence of the vacuoles inside a living plant cell are discussed theoretically.

Animals↗

PubMed2005

UVA-induced oxidative damage and cytotoxicity depend on the mode of exposure.

The reciprocity rule (Bunsen-Roscoe law) states that a photochemical reaction is directly proportional to the total energy dose, irrespective of the dose distribution. In photomedicine the validity of this law is usually taken for granted, although the influence of radiation intensity and dose distribution are largely unknown. We have examined in a tissue culture model the effects of fractionated versus single dose exposure to UV from a metal halide source on survival, DNA synthesis, glutathione, and oxidative membrane damage. Exposure to fractionated UVA was followed by an increased rate of cell death compared to single dose exposure, when intervals between fractions where short (10-120 min). Longer intervals had the opposite effect. Corresponding results were obtained for DNA synthesis (BrdU incorporation). The increased cytotoxicity of dose fractionation with short intervals could not be abrogated by non-enzymatic antioxidants (astaxanthin, ascorbic acid, alpha-tocopherol). Fractionated irradiation with short intervals led to higher degree of depletion of glutathione (GSH) and to enhanced formation of thiobarbituric acid reactive substances (TBARS) in comparison to an identical single dose. Long intervals between fractions induced opposite effects. Taken together, these data indicate that immediately after UVA exposure cells are more sensitive to a further oxidative attack making repeated exposure with short intervals more cytotoxic than continuous single dose UVA. This might have implications also for responses to UVA in vivo and further studies will have to extend these findings to the situation in healthy and diseased human skin.

Antioxidants↗

PubMed2002

Redox regulation of adenovirus-induced AP-1 activation by overexpression of manganese-containing superoxide dismutase.

Adenovirus gene therapy is a promising tool in the clinical treatment of many genetic and acquired diseases. However, it has also caused pathogenic effects in organs such as the liver. The redox-sensitive transcription factors AP-1 and NF-kappaB have been implicated in these effects. To study the mechanisms of adenovirus-mediated AP-1 and NF-kappaB activation and the possible involvement of oxidative stress in adenovirus transduction, rats were injected with either replication-defective recombinant adenovirus with DNA containing the cytomegalovirus promoter region only (AdCMV), adenovirus containing human manganese-containing superoxide dismutase (MnSOD) cDNA (AdMnSOD), or vehicle. Compared to vehicle and AdCMV transduction, MnSOD gene transfer yielded a fivefold increase in liver MnSOD activity 7 days postinjection. Gel shift assay showed that AdCMV transduction induced DNA binding activity for AP-1 but not NF-kappaB. MnSOD overexpression abolished this activation. Western blotting analysis of c-Fos and c-Jun suggested that up-regulation of c-fos and c-jun gene expression does not directly contribute to the induction of AP-1 activation. Glutathione/glutathione disulfide ratios were decreased by adenovirus transduction and restored by MnSOD overexpression. The AP-1 binding activity that was induced by AdCMV was decreased by immunoprecipitation of Ref-1 protein. Ref-1 involvement was confirmed by restoration of AP-1 binding activity after the immunoprecipitated Ref-1 protein had been added back. AP-1 DNA binding activity was also elevated in control and AdMnSOD-injected rats after addition of the immunoprecipitated Ref-1 protein. These data indicate that cellular transduction by recombinant adenovirus stimulates AP-1 DNA binding activity. Furthermore, our results suggest that MnSOD overexpression decreases AP-1 DNA binding activity by regulating intracellular redox status, with the possible involvement of Ref-1 in this redox-sensitive pathway.

Adenoviridae↗

PubMed2005

A network of multi-tasking proteins at the DNA replication fork preserves genome stability.

To elucidate the network that maintains high fidelity genome replication, we have introduced two conditional mutant alleles of DNA2, an essential DNA replication gene, into each of the approximately 4,700 viable yeast deletion mutants and determined the fitness of the double mutants. Fifty-six DNA2-interacting genes were identified. Clustering analysis of genomic synthetic lethality profiles of each of 43 of the DNA2-interacting genes defines a network (consisting of 322 genes and 876 interactions) whose topology provides clues as to how replication proteins coordinate regulation and repair to protect genome integrity. The results also shed new light on the functions of the query gene DNA2, which, despite many years of study, remain controversial, especially its proposed role in Okazaki fragment processing and the nature of its in vivo substrates. Because of the multifunctional nature of virtually all proteins at the replication fork, the meaning of any single genetic interaction is inherently ambiguous. The multiplexing nature of the current studies, however, combined with follow-up supporting experiments, reveals most if not all of the unique pathways requiring Dna2p. These include not only Okazaki fragment processing and DNA repair but also chromatin dynamics.

Adenosine Triphosphatases↗

PubMed2026

Identification of a plastid-targeted RecQ-like helicase in the red alga Cyanidioschyzon merolae.

Plastids retain their own genomic DNA (plastid DNA, ptDNA) which must be faithfully maintained for proper organelle function. However, the molecular mechanisms responsible for ptDNA maintenance remain poorly understood, particularly in red algae. Here, we identified a plastid-targeted RecQ-like helicase (ptRECQ) in the unicellular red alga Cyanidioschyzon merolae. Biochemical assays demonstrated that ptRECQ possesses ATP-dependent helicase activity and preferentially unwinds splayed DNA substrates that mimic replication fork structures. ptrecQ mutant cells were hypersensitive to nalidixic acid, a ptDNA gyrase inhibitor that induces replication stress, indicating a role for ptRECQ in plastid genome maintenance under replication stress. Phylogenetic analyses showed that ptRECQ is broadly conserved in red algae, absent from green algae and land plants, and phylogenetically distinct from cyanobacterial RecQ proteins. These results suggest that red algae employ a ptDNA maintenance system that differs from that of the green lineage.

Rhodophyta↗

PubMed2006

Polo-like kinase-1 controls proteasome-dependent degradation of Claspin during checkpoint recovery.

DNA-damage checkpoints maintain genomic integrity by mediating a cell-cycle delay in response to genotoxic stress or stalled replication forks. In response to damage, the checkpoint kinase ATR phosphorylates and activates its effector kinase Chk1 in a process that critically depends on Claspin . However, it is not known how exactly this kinase cascade is silenced. Here we demonstrate that the abundance of Claspin is regulated through proteasomal degradation. In response to DNA damage, Claspin is transiently stabilized, and its expression depends on Chk1 kinase activity. In addition, we show that Claspin is degraded upon mitotic entry, a process that depends on the beta-TrCP-SCF ubiquitin ligase and Polo-like kinase-1 (Plk1). We demonstrate that Claspin interacts with both beta-TrCP and Plk1 and that inactivation of these components or the beta-TrCP recognition motif in Claspin prevents its mitotic degradation. Interestingly, expression of a nondegradable Claspin mutant inhibits recovery from a DNA-damage-induced checkpoint arrest. Thus, we conclude that Claspin levels are tightly regulated, both during unperturbed cell cycles and after DNA damage. Moreover, our data demonstrate that the degradation of Claspin at the onset of mitosis is an essential step for the recovery of a cell from a DNA-damage-induced cell-cycle arrest.

Adaptor Proteins, Signal Transducing↗

PubMed1986

In vivo levels of diadenosine tetraphosphate and adenosine tetraphospho-guanosine in Physarum polycephalum during the cell cycle and oxidative stress.

Cellular levels of diadenosine tetraphosphate (Ap4A) and adenosine tetraphospho-guanosine (Ap4G) were specifically measured during the cell cycle of Physarum polycephalum by a high-pressure liquid chromatographic method. Ap4A was also measured indirectly by a coupled phosphodiesterase-luciferase assay. No cell cycle-specific changes in either Ap4A or Ap4G were detected in experiments involving different methods of assay, different strains of P. polycephalum, or different methods of fixation of macroplasmodia. Our results on Ap4A are in contrast with those reported previously (C. Weinmann-Dorsch, G. Pierron, R. Wick, H. Sauer, and F. Grummt, Exp. Cell Res. 155:171-177, 1984). Weinmann-Dorsch et al. reported an 8- to 30-fold increase in Ap4A in early S phase in P. polycephalum, as measured by the phosphodiesterase-luciferase assay. We also measured levels of Ap4A, Ap4G, and ATP in macroplasmodia treated with 0.1 mM dinitrophenol. Ap4A and Ap4G transiently increased three- to sevenfold after 1 h and then decreased concomitantly with an 80% decrease in the level of ATP after 2 h in the presence of dinitrophenol. These results do not support the hypothesis that Ap4A is a positive pleiotypic activator that modulates DNA replication, but they are consistent with the hypothesis proposed for procaryotes that Ap4A and Ap4G are signal nucleotides or alarmones of oxidative stress (B.R. Bochner, P.C. Lee, S.W. Wilson, C.W. Cutler, and B.N. Ames, Cell 37:225-232, 1984).

Adenine Nucleotides↗

PubMed2005

Regulation of replicative senescence by NADP+ -dependent isocitrate dehydrogenase.

The free radical hypothesis of aging postulates that senescence is due to an accumulation of cellular oxidative damage, caused largely by reactive oxygen species that are produced as by-products of normal metabolic processes. Recently, we demonstrated that the control of cytosolic and mitochondrial redox balance and the cellular defense against oxidative damage is one of the primary functions of cytosolic (IDPc) and mitochondrial NADP+ -dependent isocitrate dehydrogenase (IDPm) by supplying NADPH for antioxidant systems. In this paper, we demonstrate that modulation of IDPc or IDPm activity in IMR-90 cells regulates cellular redox status and replicative senescence. When we examined the regulatory role of IDPc and IDPm against the aging process with IMR-90 cells transfected with cDNA for IDPc or IDPm in sense and antisense orientations, a clear inverse relationship was observed between the amount of IDPc or IDPm expressed in target cells and their susceptibility to senescence, which was reflected by changes in replicative potential, cell cycle, senescence-associated beta-galactosidase activity, expression of p21 and p53, and morphology of cells. Furthermore, lipid peroxidation, oxidative DNA damage, and intracellular peroxide generation were higher and cellular redox status shifted to a prooxidant condition in the cell lines expressing the lower level of IDPc or IDPm. The results suggest that IDPc and IDPm play an important regulatory role in cellular defense against oxidative stress and in the senescence of IMR-90 cells.

Aging↗