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At least 343 records · Page 19Linked to original sources
PubMed2000

DNA sequence analysis of the complete mitochondrial genome of the green alga Scenedesmus obliquus: evidence for UAG being a leucine and UCA being a non-sense codon.

The complete DNA sequence of the mitochondrial genome of the chlorophyceen alga Scenedesmus obliquus was determined. The circular genome of 42781bp contains a basic set of 13 mitochondrial genes, which are conserved among plant or algal chondriomes. In addition, two scrambled rRNA and 27 tRNA genes are present, together with four intronic sequences (group I and II) and five open reading frames (ORFs), which show no significant homology to other ORFs from organellar genomes. The comparison with deduced amino acid sequences from 13 conserved mitochondrial genes gives rise to the conclusion that two deviations from the standard genetic code must be present in S. obliquus mitochondria: (i) UAG codes for leucine as was already found in some other algal mitochondria; (ii) UCA is a stop codon, which seems unique for mitochondrial genomes. This was supported by our finding that a tRNA-Leu gene possesses a UCA anticodon and by a missing tRNA-serine, able to decode the UCA codon. Consistent with these data is the absence of any UCA codon from conserved mitochondrial ORFs. This codon occurs only close to the end of all ORFs, while UAA or UGA codons are found at some distance from any conserved ORF. Codon changes by RNA editing can be excluded, since RT-PCR analysis does not reveal any evidence for post-transcriptional RNA modifications of the primary transcript.

Algal Proteins↗
PubMed2005

Cisplatin is a DNA-damaging antitumour compound triggering multifactorial biochemical responses in cancer cells: importance of apoptotic pathways.

cis-diamminedichloroplatinum(II) (cisplatin) is among the most active antitumour agent used in human chemotherapy. The purpose of this review is to give an insight in several molecular mechanisms that mediate the sensitivity of cancer cells to this drug and to show how recent progress in our knowledge on some critical molecular events should lay the foundations of a more rational approach to anticancer drug design. Cisplatin is primarily considered as a DNA-damaging anticancer drug, mainly forming different types of bifunctional adducts in its reaction with cellular DNA. We will address the question of cellular activity disruption that cisplatin could cause through binding to more sensitive region of the genome such as telomeres. Cellular mechanisms of resistance to cisplatin are multifactorial and contribute to severe limitation in the use of this drug in clinics. They include molecular events modulating the amount of drug-DNA interaction, such as a reduction in cisplatin accumulation inside cancer cells or inactivation of cisplatin by thiol-containing species. Other important mechanisms acting downstream to the initial reaction of cisplatin with DNA, include an increase in adducts repair and a decrease in induction of apoptosis. Recently accumulating evidence suggest a role of the long patch DNA mismatch repair system in sensing cisplatin-damaged DNA and in triggering cell death through a c-Abl- and p73-dependent cascade; two other important pathways have been unravelled that are the mitogen-activated protein kinase cascade and the tumor suppressor p53. Several of these mechanisms underlying cisplatin resistance have been exploited to design new platinum derivatives. This issue will be covered in the present review.

Animals↗
PubMed2001

[Studies of the resistance of the recombinant alphavirus RNAs containing dengue-2 PrM gene to virus infection].

The amplified PrM gene of dengue-2 virus was cloned into the downstream SP6 promoter-pSFV vector and the recombinant plasmid (pSF.rM2) DNA which contained sense- or antisense-PrM gene, was selected. pSF.rM2 DNA and helper DNA linearized by the enzyme SpeI digestion were both transcribed in vitro into recombinant RNAs which contained the capping analog on the 5'-end and contaansfected into BHK cells by electroportation. The the transfected host cells were challenged with dengue-2 virus and the resistant efficiency of recombinant virus RNAs containing sense- or antisense-PrM gene to virus infection were observed, respectively. The recombinant plasmids (pSFV-PrM) containing sense- or antisense-PrM gene were selected with determination of the nucleotide sequence. The recombinant virus particles were obtained with recombinant RNA and helper RNA co-transfected into BHK cells. Host cells transfected with antisense-PrM RNA derived complete resistance to dengue-2 virus replication and the efficiency was higher than that of the recombinant virus RNA containing sense-PrM gene.

Alphavirus↗
PubMed2006

Chromatin remodeling and repair of DNA double-strand breaks.

Eukaryotic cells have developed conserved mechanisms to efficiently sense and repair DNA damage that results from constant chromosomal lesions. DNA repair has to proceed in the context of chromatin, and both histone-modifiers and ATP-dependent chromatin remodelers have been implicated in this process. Here, we review the current understanding and new hypotheses on how different chromatin-modifying activities function in DNA repair in yeast and metazoan cells.

Adenosine Triphosphate↗
PubMed2003

Biological chemistry of reactive oxygen and nitrogen and radiation-induced signal transduction mechanisms.

In the past few years, nuclear DNA damage-sensing mechanisms activated by ionizing radiation have been identified, including ATM/ATR and the DNA-dependent protein kinase. Less is known about sensing mechanisms for cytoplasmic ionization events and how these events influence nuclear processes. Several studies have demonstrated the importance of cytoplasmic signaling pathways in cytoprotection and mutagenesis. For cytoplasmic signaling, radiation-stimulated reactive oxygen species (ROS) and reactive nitrogen species (RNS) are essential activators of these pathways. This review summarizes recent studies on the chemistry of radiation-induced ROS/RNS generation and emphasizes interactions between ROS and RNS and the relative roles of cellular ROS/RNS generators as amplifiers of the initial ionization events. Cellular mechanisms for regulating ROS/RNS levels are discussed. The mechanisms by which cells sense ROS/RNS are examined in terms of how ROS/RNS modify protein structure and function, for example, interactions with metal-thiol clusters, protein tyrosine nitration, protein cysteine oxidation, S-thiolation and S-nitrosylation. We propose that radiation-induced ROS are the initiators and that nitric oxide (NO*) or derivatives are the effectors activating these signal transduction pathways. In responding to cellular ionization events, the cell converts an oxidative signal to a nitrosative one because ROS are too reactive and unspecific in their reactions for regulatory purposes and the cell is equipped to precisely modulate NO* levels.

Nitrates↗
PubMed2001

p53 protein at the hub of cellular DNA damage response pathways through sequence-specific and non-sequence-specific DNA binding.

Our environment contains physical, chemical and pathological agents that challenge the integrity of our DNA. In addition to DNA repair, higher multicellular organisms have evolved multiple pathways of response to damage including programmed cell death-apoptosis. The p53 protein appears to sense multiple types of DNA damage and coordinate with multiple options for cellular response. The p53 protein activities depend upon its DNA binding. Specific p53 protein post-translational modifications are required for efficient sequence-specific binding and transcriptional activities. Non-sequence-specific DNA binding may involve a wide spectrum of p53 proteins and predominate as DNA damage is more severe or p53 protein is more highly induced. p53 protein is not strictly required for DNA damage sensing and repair. Rather, p53 protein may govern an apoptosis checkpoint through competition with DNA repair proteins for non-sequence-specific binding to exposed single-stranded regions in the DNA duplex. This model provides a framework for testing mechanisms of p53-mediated apoptosis dependent upon the p53 protein modification state, the level of p53 protein accumulation, the level of DNA damage and the capacity of the damaged cell to repair.

Animals↗
PubMed2005

DNA repair proteins affect the lifecycle of herpes simplex virus 1.

We report that herpes simplex virus 1 (HSV-1) infection can activate and exploit a cellular DNA damage response that aids viral replication in nonneuronal cells. Early in HSV-1 infection, several members of the cellular DNA damage-sensing machinery are activated and accumulate at sites of viral DNA replication. When this cellular response is abrogated, formation of HSV-1 replication centers is retarded, and viral production is compromised. In neurons, HSV-1 replication centers fail to mature, and the DNA damage response is not initiated. These data suggest that the failure of neurons to mount a DNA damage response to HSV-1 may contribute to the establishment of latency.

Animals↗
PubMed2006

DNA binding by an imidazole-sensing CooA variant is dependent on the heme redox state.

CooA is a transcription factor from Rhodospirillum rubrum that is regulated by the binding of the small molecule effector, CO, to a heme moiety in the protein. The heme in CooA is axially ligated by two endogenous donors in the Fe(III) and Fe(II) states of the protein, and CO binding to the Fe(II) state results in replacement of the distal ligand. Reduction of the heme in the absence of CO results in a ligand switch on the proximal side, in which a cysteine thiolate in the Fe(III) state is replaced by a histidine in the Fe(II) state. Recently, a variant, termed RW CooA, was designed to respond to a new effector; Fe(II) RW CooA shows high specificity and induced DNA-binding activity in the presence of imidazole. Spectroscopic characterization of the imidazole adducts of RW CooA revealed that, unlike CO, imidazole binds to both Fe(III) RW CooA and Fe(II) RW CooA. The spectral characteristics are consistent with normal function of the redox-mediated ligand switch; Fe(III)-imidazole RW CooA bears a thiolate ligand and Fe(II)-imidazole RW CooA bears a neutral donor ligand. Since the effector binds to both redox states, RW CooA was used to probe the role of the redox-mediated ligand switch in the CooA activation mechanism. Functional studies of Fe(III)-imidazole and Fe(II)-imidazole ligated RW CooA demonstrate that only the Fe(II)-imidazole form is active for DNA binding. Thus, the ligand switch is essential for the activating conformational change and may prevent aberrant activation of CooA by other neutral diatomic molecules.

Bacterial Proteins↗
PubMed2003

Electron microscopy and 3D reconstructions reveal that human ATM kinase uses an arm-like domain to clamp around double-stranded DNA.

The human tumor suppressor gene ataxia telangiectasia mutated (ATM) encodes a 3056 amino-acid protein kinase that regulates cell cycle checkpoints. ATM is defective in the neurodegenerative and cancer predisposition syndrome ataxia-telangiectasia. ATM protein kinase is activated by DNA damage and responds by phosphorylating downstream effectors involved in cell cycle arrest and DNA repair, such as p53, MDM2, CHEK2, BRCA1 and H2AX. ATM is probably a component of, or in close proximity to, the double-stranded DNA break-sensing machinery. We have observed purified human ATM protein, ATM-DNA and ATM-DNA-avidin bound complexes by single-particle electron microscopy and obtained three-dimensional reconstructions which show that ATM is composed of two main domains comprising a head and an arm. DNA binding to ATM induces a large conformational movement of the arm-like domain. Taken together, these three structures suggest that ATM is capable of interacting with DNA, using its arm to clamp around the double helix.

Ataxia Telangiectasia Mutated Proteins↗
PubMed2006

Inhibition of tRNA₃(Lys)-primed reverse transcription by human APOBEC3G during human immunodeficiency virus type 1 replication.

Cells are categorized as being permissive or nonpermissive according to their ability to produce infectious human immunodeficiency virus type 1 (HIV-1) lacking the viral protein Vif. Nonpermissive cells express the human cytidine deaminase APOBEC3G (hA3G), and Vif has been shown to bind to APOBEC3G and facilitate its degradation. Vif-negative HIV-1 virions produced in nonpermissive cells incorporate hA3G and have a severely reduced ability to produce viral DNA in newly infected cells. While it has been proposed that the reduction in DNA production is due to hA3G-facilitated deamination of cytidine, followed by DNA degradation, we provide evidence here that a decrease in the synthesis of the DNA by reverse transcriptase may account for a significant part of this reduction. During the infection of cells with Vif-negative HIV-1 produced from 293T cells transiently expressing hA3G, much of the inhibition of early (> or =50% reduction) and late (> or =95% reduction) viral DNA production, and of viral infectivity (> or =95% reduction), can occur independently of DNA deamination. The inhibition of the production of early minus-sense strong stop DNA is also correlated with a similar inability of tRNA(3)(Lys) to prime reverse transcription. A similar reduction in tRNA(3)(Lys) priming and viral infectivity is also seen in the naturally nonpermissive cell H9, albeit at significantly lower levels of hA3G expression.

APOBEC-3G Deaminase↗
PubMed2006

DNase II and the Chk2 DNA damage pathway form a genetic barrier blocking replication of horizontally transferred DNA.

We have previously shown that DNA from dying tumor cells may be transferred to living cells via the uptake of apoptotic bodies and may contribute to tumor progression. DNA encoding H-ras(V12) and c-myc oncogenes may be transferred to the nucleus of the phagocyte but will only integrate and propagate in p53- and p21-deficient mouse embryonic fibroblasts, whereas normal cells are resistant to transformation. Here, we show that this protective mechanism (activation of p53 and p21 after uptake of apoptotic bodies) is dependent on DNA fragmentation, where inhibition of the caspase-activated DNase in the apoptotic cells, in conjunction with genetic ablation of lysosomal DNase II in the phagocytes, completely blocks p53 activation and consequently allows DNA replication of transferred DNA. We, therefore, suggest that there is a causal relationship between DNA degradation during apoptosis and p53 activation. In addition, we could further show that Chk2-/- cells were capable of replicating the hyg(R) gene taken up from engulfed apoptotic cells, suggesting involvement of the DNA damage response. These data show that the phagocytosing cell is sensing the degraded DNA within the apoptotic cell, hence preventing these genes from being replicated, probably through activation of the DNA damage response. We, therefore, hypothesize that DNase II together with the Chk2, p53, and p21 pathway form a genetic barrier blocking the replication of potentially harmful DNA introduced via apoptotic bodies, thereby preventing transformation and malignant development.

Animals↗
PubMed2004

[Effect of eukaryotic expression plasmid DNA methyltransferase gene on methylation status and transcription level of DNA mismatch repair genes in human colon cancer cell line].

OBJECTIVE: To analyze the effect of eukaryotic plasmids containing sense or antisense DNA methyltransferase (Dnmt1) genes on the methylation status and transcription level of DNA mismatch repair (MMR) genes and microsatellite instability (MSI) in human colon cancer cell line. METHODS: Human colorectal cells of the SW1116 line were cultured. Recombinant plasmids containing sense Dnmt1 (HMT) or antisense Dnmt1 (THM) gene, pCMV-HMT and pCMV-THM, were constructed. Then pCMV-HMT, pCMV-THM, and pcMV blank plasmid were transfected into SW1116 cells respectively by using lipofectAMINE. The expression of Dnmt1 protein was examined by Western blotting. The transcription levels of hMLH1 and hMSH2 genes were detected by using real-time (RT-PCR). The status of methylation in promoters of hMLH1 and hMSH2 genes were examined with methylation specific PCR (MSP). The MSI of DNA in SW1116 cells was evaluated by silver-stained polyacrylamide gel electrophoresis. RESULTS: Both the expressions of the hMLH1 and hMSH2 gene mRNAs were remarkably decreased in the SW1116-HMT cells in comparison with those in the untransfected cells. The expression of hMSH2 gene mRNA in the SW1116-THM cells was remarkably increased in comparison with that in the untransfected cells. No significant difference in the expressions of the hMLH1 and hMSH2 gene mRNAs was found between the SW1116 cells transfected with blank pCMV and the untransfected SW1116 cells. MSP showed that the methylation level in the regions of hMLH1 and hMSH2 promoters was remarkably increased in the SW1116 cells transfected with sense Dnmtl plasmid. However, in the SW1116 cells the hMSH2 promoter region was changed from partially-methylated into de-methylated, and the hMLH1 promoter region remained non-methylated. MST test showed that extra bands indicating MSI were seen only in the D2S123 groups. CONCLUSION: Dnmt1 regulates the expression and methylation status of MMR genes and affects MSI in human colon cancer cell line SW1116.

Adaptor Proteins, Signal Transducing↗
PubMed1993

Transcriptional analysis of the virion-sense genes of the geminivirus beet curly top virus.

The genome of the geminivirus beet curly top virus (BCTV) consists of a single circular DNA containing overlapping open reading frames (ORFs) located on both the virion-sense and complementary-sense DNA strands. To investigate the expression of these ORFs, RNA extracted from infected Nicotiana benthamiana and Beta vulgaris has been examined for the presence of viral transcripts. An abundant 1.1-kb virion-sense polyadenylated RNA and four complementary-sense polyadenylated RNAs of 1.7, 1.5, 1.3, and 0.7 kb have been identified by northern blot hybridization, confirming the bidirectional transcription strategy implied by the arrangement of ORFs. We previously demonstrated that two overlapping virion-sense ORFs are involved in coat protein synthesis (ORF V1) and viral single-stranded DNA accumulation (ORF V2). Mutants of a third virion-sense ORF (ORF V3), located upstream and overlapping ORFs V1 and V2, retain the ability to replicate efficiently in N. benthamiana leaf discs but produce an asymptomatic infection in N. benthamiana and B. vulgaris at low frequency, associated with reduced levels of viral DNA compared to wild-type infection. Our data support the recent suggestion that ORF V3 participates in virus movement. The 1.1 kb virion-sense RNA comprises a population of overlapping transcripts with 5' termini suitably positioned for the expression of ORFs V1, V2, and V3. The overlapping arrangement of the transcripts and juxtaposition of putative regulatory elements could provide a means for the temporal control of virion-sense gene expression.

Amino Acid Sequence↗
PubMed1999

5,10,15,20-Tetrakis(4-N-methylpyridyl)porphyrinato-palladium(II ) as a differentiation probe for sensing binding modes with B-DNA duplexes: electronic MCD and CD spectra.

We report our detailed electronic MCD, CD, and optical spectroscopic measurements and analysis of the porphyrin Soret (B(o)) region of four-coordinate 5,10,15,20-tetrakis(4-N-methylpyridyl)porphyrinatopalladium( II), PdP(4), and its bound states with B-DNA duplexes poly(A-T)2, poly(G-C)2, and calf thymus DNA (CT DNA). For system PdP(4)/poly(A-T)2 it was possible to conclude that the porphyrin is bound edge-on in the major groove, specifically at the 5'AT3' site. For this orientation the porphyrin's electric dipole transition moments (edtm), mu(x) (most perturbed direction) and mu(y) (least perturbed direction), have tilt angles alpha approximately 90 degrees and approximately 45 degrees , respectively, relative to the helix axis. It was further concluded from the small shifts of B(o) optical and MCD band intensities and wavelengths and from the net MCD (+) A-term sign retention upon binding that the porphyrin's frontier ppi MOs (1a(1u) 3a(2u) 4eg) are only weakly perturbed by the heterocyclic bases of poly(A-T)2, and therefore that the LUMO (4eg) splitting is less than the |1a(1u)-3a(2u| energy separation, deltaHOMO, that is, deltaLUMO < deltaHOMO for the bound state in PdP(4)/poly(A-T)2. For intercalation systems PdP(4)/ poly(G-C)2 and /CT DNA, with PdP(4) centered in the intercalation "pocket" and having two of its 4-N-methylpyridyls extending into each of the major and minor grooves, the edtms mu(x) and mu(y) were determined to be oriented perpendicular (gamma approximately 0 degrees) and parallel (gamma approximately 90 degrees) to the hydrogen bonds of the base pairs, respectively. Intercalation is characterized by a much stronger binding interaction, viz., the B(o) optical band and net MCD extrema wavelength shifts are relatively large, and the net MCD (+) A-term of PdP(4) is substantially quenched as it becomes the (-) pseudo-A-term of intercalated PdP(4)/poly(G-C)2. This A-term sign reversal informs that the porphyrin MOs are so strongly perturbed by the GC base pairs that deltaLUMO > deltaHOMO, which gives rise to a (-) pseudo-A-term. Also, the findings demonstrate (1) the potential of PdP(4) as a sensitive, discriminating analytical probe of DNA sequences and (2) the diagnostic capability of the composite of five spectra [net MCD, CD, and optical of free and bound PdP(4)] in differentiating the site and sequence selectivity and preferred binding mode of this porphyrin.

Binding Sites↗
PubMed1999

Sensing of ionizing radiation-induced DNA damage by ATM through interaction with histone deacetylase.

The ATM gene is mutated in individuals with ataxia telangiectasia, a human genetic disease characterized by extreme sensitivity to radiation. The ATM protein acts as a sensor of radiation-induced cellular damage and contributes to cell cycle regulation, signal transduction, and DNA repair; however, the mechanisms underlying these functions of ATM remain largely unknown. Binding and immunoprecipitation assays have now shown that ATM interacts with the histone deacetylase HDAC1 both in vitro and in vivo, and that the extent of this association is increased after exposure of MRC5CV1 human fibroblasts to ionizing radiation. Histone deacetylase activity was also detected in immunoprecipitates prepared from these cells with antibodies to ATM, and this activity was blocked by the histone deacetylase inhibitor trichostatin A. These results suggest a previously unanticipated role for ATM in the modification of chromatin components in response to ionizing radiation.

Ataxia Telangiectasia Mutated Proteins↗
PubMed2001

Overexpression of parathyroid hormone-related protein enhances apoptosis in the rat intestinal cell line, IEC-6.

We used the rat intestinal cell line, IEC-6, to study potential effects of overexpression of PTH-related protein (PTHrP) on apoptosis. A clonal line of PTHrP-overexpressing cells was established by stably transfecting parental cells with PTHrP complementary DNA in a sense orientation (sense). A similarly transfected line stably, transfected with empty vector, served as control (vector). Immunoreactive PTHrP, measured in culture medium, showed that sense cells secreted approximately 30 times as much PTHrP as did vector control cells. Apoptosis induced by serum withdrawal was evaluated by several methods. DNA laddering was demonstrable in sense-transfected cells as early as 12 h after serum withdrawal but not until later time points in vector-transfected control cells. Flow cytometric analysis of propidium iodide-stained cells showed a greater increase in the sub-G1 (apoptotic) population in sense cells, compared with vector. Fluorescent microscopy with Hoechst 33258 dye showed increased nuclear fragmentation and condensation in sense cells. Studies of apoptotic gene expression by ribonuclease protection assay, and protein by Western blot analysis, showed an enhanced ratio of Bax to Bcl-x(L) in sense cells. Mutation of the PTHrP nuclear localization amino acid sequence negated the ability of PTHrP to enhance apoptosis.

Animals↗