Binding of HIV-1 TAR mRNA to a peptide nucleic acid oligomer and its conjugates with metal-ion-binding multidentate ligands

A peptide nucleic acid (PNA) oligomer and a series of PNA conjugates featuring covalently attached pendant 1,4,7,10-tetraazacyclododecane (cyclen) or bis((pyridin-2-yl)methyl)amine (DPA) moieties have been synthesized that are complementary to regions of the HIV-1 TAR messenger RNA stem-loop. Thermal denaturation studies, in conjunction win with native gel shift assays, suggest that the PNAs “invade” TAR to produce a mixture of two 1:1 PNA–TAR adducts, tentatively assigned as an “open-duplex” structure, in which the TAR stem-loop dissociates and the PNA hybridizes with its RNA complement via Watson–Crick base-pairing, and a triplex-type structure, in which the initially displaced RNA segment is bound to the PNA:RNA duplex through Hoogsteen base-pairing. Thermal denaturation experiments with the TAR sequence and single-stranded RNA and DNA oligonucleotides, both in the presence and in the absence of Zn²⁺ ions, show that the introduction of cyclen or DPA ligand arms into the PNA oligomer leads to a small but reproducible increase in the T _m values. This is attributed to hydrogen-bonding and/or electrostatic interactions between protonated forms of cyclen/DPA and the cognate RNA or DNA oligonucleotide targets. Contrary to expectations, the addition of Zn²⁺ ions did not further enhance duplex formation through binding of Zn(II)–cyclen or Zn(II)–DPA moieties to the complementary RNA or DNA. Native gel shift assays further confirmed the stability increase of the metal-free cyclen- and DPA-modified PNA hybrids as compared with a control PNA sequence. Electronic supplementary material  The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

Polyribosomes and messenger RNA from RAT liver mitochondria

Summary Rat liver mitochondrial polyribosomes were isolated free from cytoplasmic ribonucleoprotein contaminations in a number of criteria (sedimentation and buoyant density patterns, ribosomal RNA composition). Heterogeneous poly A containing RNA from mitochondrial polysomes was purified by two-stage cellulose chromatography. This RNA was in vitro labelled with¹²⁵I up to specific activity ~10⁶–10⁷ cts.min^–1.µg ^–1 and used for hybridization experiments with separate complementary strands of mitochondrial DNA and nuclear DNA fragments. The proportions of mitochondrial poly A containing RNA that is complementary to heavy and light strands of mtDNA were respectively 31.5% and 8.3%. Besides, a significant RNA fraction was complementary to unique sequences of nuclear DNA (2–3 copies per haploid genome). The hybrids that were formed possessed a high T_m indicative of a perfect base pairing. A dual intracellular origin of mitochondrial messenger RNA is discussed.     

Increase of plasma membrane oxidoreductase activity is not correlated with the production of extracellular Superoxide radicals in human Namalwa cells

Summary We have considered the regulatory interrelationship of the plasma membrane oxidoreductase (PMOR) system and the mitochondrial respiratory capacity of human Namalwa (lymphoblastoid) cells. To this end, we made use of mitchondrially respiratory competent (⁺) cells and ⁰ cells, which lack mitochondrial DNA (mtDNA) and consequently mitochondrial respiratory activity. NADH-fer-ricyanide reductase activity of the PMOR system is increased 3-fold in ⁰ Namalwa cells compared to ⁺ cells. It is also shown for the first time that addition of coenzyme Q₁₀ and coenzyme Q₁₀-ana-logues, which can rescue ⁰ Namalwa cells in the absence of pyravate, gives rise to a further 2–3-fold increase in plasma membrane NADH-ferricyanide reductase activity. These systems were examined to determine if there exists a correlation between the regulation of the PMOR system and extracellular Superoxide radical formation as measured with the fluorescence probe L-012. No correlation was found between NADH-ferricyanide reductase activity and extracellular Superoxide radical production. PMOR function in cellular proliferation appears therefore not to involve extracellular Superoxide radical production.Abbreviations CoQ₁₀ coenzyme Q₁₀ - EtBr ethidium bromide - HCO-60 polyoxyethylated hydrogenated castor oil - HEPES 4-(2-hydroxyethyl)-1-piperazineethanesulfonic acid - mtDNA mitochondrial DNA - L-012 8-amino-5-chloro-7-phenylpyrido(3,4-d)pyridazine-1,4(2H,3H)dione - SOD Superoxide dismutase     

Yeast mutants resistant to ethidium bromide

Summary Yeast mutants resistant to ethidium bromide have been isolated among sensitive grande cells (⁺) for their ability to grow on glycerol in the presence of the dye. Mutant cells are also resistant to acriflavin and do not yield petites (^-) when grown on galactose with the mutagen. Genetic analysis reveals that resistance to ethidium bromide is controlled by a cytoplasmic factor, carried by, or linked to, the determinant (mitochondrial DNA). The expression of resistance to ethidium bromide seems to be related to the presence in the cell of a product of mitochondrial protein synthesis. It is concluded that some mitochondrial DNA sequence is involved in the resistance to ethidium bromide of yeast mitochondria.     

Superoxide anion production by the mitochondrial respiratory chain of hepatocytes of rats with experimental toxic hepatitis

The progression of toxic hepatitis is accompanied by the activation of oxidative processes in the liver associated with an enhancement of the mitochondrial respiratory chain activity and superoxide anion production (О₂^˙-). The purpose of this study was to examine our previously formulated assumption concerning the predominant contribution of the complex I to О₂^˙- production increase by the mitochondrial respiratory chain of hepatocytes in toxic hepatitis (Shiryaeva et al. Tsitologiia, 49, 125–132 2007). Toxic hepatitis was induced by a combined application of ССl₄ and ethanol. Respiratory chain function analysis was executed with submitochondrial particles (SP) in the presence of specific inhibitors. It was shown that the rate of О₂^˙- production by SP of animals with toxic hepatitis, when NADH was delivered, was 2.5-fold higher as compared with the control. The rates of О₂^˙- production by SP of rats with toxic hepatitis in the presence of NADH or NADH + rotenone were similar. The О₂^˙- production rate by control SP in the presence of NADH + rotenone corresponded to the О₂^˙- production rate by toxic hepatitis SP when only NADH was delivered. When NADH + myxothiazol were delivered to the incubation system, О₂^˙- production by toxic hepatitis SP was 72% higher than for the control. Conversely, in the presence of antimycin A, the production of О₂^˙- by toxic hepatitis SP was lower compared to the control. Collectively, the presented data indicate that the О₂^˙- production rate was enhanced by the complex I of the hepatocyte mitochondrial respiratory chain in experimental toxic hepatitis. Complex III contribution to the production of О₂^˙- was insignificant. We assume that the increase in О₂^˙- production by the respiratory chain may be considered not only as the mechanism of pathology progression, but also as a compensatory mechanism preserving the electron transport function of the mitochondrial respiratory chain when complex I functioning is blocked in part.     

Caldinitratiruptor microaerophilus, gen. nov., sp. nov. isolated from a French hot spring (Chaudes-Aigues, Massif Central): a novel cultivated facultative microaerophilic anaerobic thermophile pertaining to the Symbiobacterium branch within the Firmicutes

A novel facultative microaerophilic nitrate-reducing bacterium designated CA62N^T was isolated from a thermal spring in France. Cells were non-motile rods (2–3 × 0.2 μm) and showed low cytoplasmic density when observed under a phase-contrast microscope. Strain CA62N^T grew at temperatures between 50 and 75°C (optimum 65°C) and at a pH between 6.3 and 7.9 (optimum 7.0). NaCl was not required for growth but was tolerated up to 10 gl⁻¹. Sulfate, thiosulfate, elemental sulfur, sulfite, and nitrite were not used as electron acceptors. Nitrate was reduced to nitrite. Strain CA62N^T used lactate, pyruvate, glucose, mannose, fructose, and casamino acids and some amino acids as electron donors only in the presence of nitrate as electron acceptor. None of these substrates was fermented. The main end-products of glucose oxidation were acetate, CO₂, and traces of H₂. The G + C content of the genomic DNA was 70.3 mol% (HPLC techniques). Phylogenetic analysis of the small-subunit (SSU) ribosomal RNA (rRNA) gene sequence indicated that strain CA62N^T was affiliated to the Symbiobacterium branch within the Firmicutes and had Symbiobacterium thermophilum and “S. toebii” as its closest phylogenetic relatives. On the basis of phylogenetical and physiological characteristics, strain CA62N^T is proposed to be the type strain for the novel species in the novel genus, Caldinitratiruptor microaerophilus gen. nov., sp. nov. (DSM 22660, JCM 16183).     

Fine structure of the 21S ribosomal RNA region on yeast mitochondrial DNA

Summary The omega locus controls the polarity of recombination and transmission of genetic markers in the 21S ribosomal RNA region in yeast mtDNA. Polarity is observed in crosses between omega⁺ and omega^- strains. These two strains differ by the presence of an intervening sequence in the 21S ribosomal RNA gene of omega⁺ strains. Mutations of the omega^- allele, omega neutral (omegaⁿ), can eliminate the polarity effect. We have made DNA:RNA hybrids containing ribosomal RNA from an omegaⁿ strain and mtDNA from Saccharomyces carlsbergensis (identical to omega^- in the nucleotide sequence of the omega region). These hybrids contain no mismatch at the omega region detectable by digestion with S₁ nuclease. We conclude that omegaⁿ differs from omega^- only in a point mutation or analogous small alteration and that the omegaⁿ mutation can result either m a C^r phenotype (omegaⁿC^r) or in the phenotypic suppression of pre-existing C^r mutations (omegaⁿC^s). All results can be explained by a model which postulates interaction in the ribosome between the C^r and omegaⁿ regions of the ribosomal RNA and interference of the omegaⁿ mutation with splicing of the precursor ribosomal RNA in omega⁺ strains. The mechanism of omega-directed polarity is discussed.Abbreviations rRNA ribosomal RNA - bp base pair(s) - kb kilo base pair(s)     

The mechano-gated K<Subscript>2P</Subscript> channel TREK-1

The versatility of neuronal electrical activity is largely conditioned by the expression of different structural and functional classes of K⁺ channels. More than 80 genes encoding the main K⁺ channel alpha subunits have been identified in the human genome. Alternative splicing, heteromultimeric assembly, post-translational modification and interaction with auxiliary regulatory subunits further increase the molecular and functional diversity of K⁺ channels. Mammalian two-pore domain K⁺ channels (K_2P) make up one class of K⁺ channels along with the inward rectifiers and the voltage- and/or calcium-dependent K⁺ channels. Each K_2P channel subunit is made up of four transmembrane segments and two pore-forming (P) domains, which are arranged in tandem and function as either homo- or heterodimeric channels. This novel structural arrangement is associated with unusual gating properties including “background” or “leak” K⁺ channel activity, in which the channels show constitutive activity at rest. In this review article, we will focus on the lipid-sensitive mechano-gated K_2P channel TREK-1 and will emphasize on the polymodal function of this “unconventional” K⁺ channel. EBSA Satellite meeting: Ion channels, Leeds, July 2007.     

Local repeat sequence organization of an intergenic spacer in the chloroplast genome ofChlamydomonas reinhardtii leads to DNA expansion and sequence scrambling: A complex mode of “copychoice replication”?

Parent-specific, randomly amplified polymorphic DNA (RAPD) markers were obtained from total genomic DNA ofChlamydomonas reinhardtii. Such parent-specific RAPD bands (genomic fingerprints) segregated uniparentally (through mt⁺) in a cross between a pair of polymorphic interfertile strains ofChlamydomonas (C. reinhardtii andC. minnesotti), suggesting that they originated from the chloroplast genome. Southern analysis mapped the RAPD-markers to the chloroplast genome. One of the RAPD-markers, “P2” (1.6 kb) was cloned, sequenced and was fine mapped to the 3 kb region encompassing 3′ end of 23S, full 5S and intergenic region between 5S and psbA. This region seems divergent enough between the two parents, such that a specific PCR designed for a parental specific chloroplast sequence within this region, amplified a marker in that parent only and not in the other, indicating the utility of RAPD-scan for locating the genomic regions of sequence divergence. Remarkably, the RAPD-product, “P2” seems to have originated from a PCR-amplification of a much smaller (about 600 bp), but highly repeat-rich (direct and inverted) domain of the 3 kb region in a manner that yielded no linear sequence alignment with its own template sequence. The amplification yielded the same uniquely “sequence-scrambled” product, whether the template used for PCR was total cellular DNA, chloroplast DNA or a plasmid clone DNA corresponding to that region. The PCR product, a "unique" new sequence, had lost the repetitive organization of the template genome where it had originated from and perhaps represented a “complex path” of copy-choice replication.     

Seizure-like afterdischarges simulated in a model neuron

To explore non-synaptic mechanisms in paroxysmal discharges, we used a computer model of a simplified hippocampal pyramidal cell, surrounded by interstitial space and a “glial-endothelial” buffer system. Ion channels for Na⁺, K⁺, Ca²⁺ and Cl⁻ _, ion antiport 3Na/Ca, and “active” ion pumps were represented in the neuron membrane. The glia had “leak” conductances and an ion pump. Fluxes, concentration changes and cell swelling were computed. The neuron was stimulated by injecting current. Afterdischarge (AD) followed stimulation if depolarization due to rising interstitial K⁺ concentration ([K⁺]_o) activated persistent Na⁺ current (I _Na,P). AD was either simple or self-regenerating; either regular (tonic) or burst-type (clonic); and always self-limiting. Self-regenerating AD required sufficient I _Na,P to ensure re-excitation. Burst firing depended on activation of dendritic Ca²⁺ currents and Ca-dependent K⁺ current. Varying glial buffer function influenced [K⁺]_o accumulation and afterdischarge duration. Variations in Na⁺ and K⁺ currents influenced the threshold and the duration of AD. The data show that high [K⁺]_o and intrinsic membrane currents can produce the feedback of self-regenerating afterdischarges without synaptic input. The simulated discharge resembles neuron behavior during paroxysmal firing in living brain tissue. Action Editor: David Terman     

Temperature-sensitive respiratory-deficient mitochondrial mutations: Isolation and genetic mapping

Summary In order to find new genetic loci and functions on the yeast mitochondrial DNA, especially mutations affecting the mitochondrial protein synthesis apparatus, temperature sensitive mutants have been isolated after MnCl₂ mutagenesis and mitochondrial and nuclear mutants classified according to their pattern of recombination with three rho^- tester strains.Eighteen cold- and heat-sensitive respiratory deficient mitochondrial mutants have been isolated and localized on the mitochondrial genome by deletion mapping using 113 rho^- strains. Eight of them appear to represent new loci, among which some are probably mutations of the tRNA and rRNA genes.     

A resonance Raman band assignable to the O–O stretching mode in the resting oxidized state of bovine heart cytochrome <Emphasis Type="Italic">c</Emphasis> oxidase

In the resting oxidized state (the fully oxidized “as-isolated” state) of cytochrome c oxidase (CcO) preparation, a resonance Raman band is observed at 755 cm^-1 upon 647.1 nm excitation in resonance with an absorption band at 655 nm. Addition of cyanide eliminates the Raman band concomitant with loss of the absorption band at 655 nm. These results strongly suggest that the Raman band at 755 cm^-1 originates from the O−O stretching mode of the bridging peroxide (Fe−O^-−O^-−Cu) in the O₂ reduction site of the fully oxidized “as-isolated” CcO. Although the peroxide bridged structure has been proposed on the basis of X-ray crystallography and reductive titration experiments, the present vibrational spectroscopic analyses reveal conclusively the chemical nature of the bridging ligand at the O₂ reduction site of the fully oxidized “as-isolated” bovine heart CcO.     

Petite deletion map of the mitochondrial oxi3 region in Saccharomyces cerevisiae.

Summary Fifty eight mitochondrial mutants (p ⁺ mit^- mutants), all deficient in cytochrome oxidase activity and previously assigned to the genetic region oxi3 on the mitochondrial DNA, were mapped by the method of petite deletion mapping.This procedure resulted in the identification of at least twenty one different classes of oxi3 mutants, which could be arranged in a linear order.Moreover, it provided a set of twenty three p ^- petite mutants, each containing a differentially deleted mit DNA segment included in the oxi3 region. The two sets of mutants, p ⁺ oxi3 ^- and p ^- oxi3 ⁺, will be of interest for a further genetic and physical analysis of this mitochondrial DNA segment which spans over about ten thousand base pairs and controls the subunit I of cytochrome oxidase.     

The immunologic aspects in advanced ovarian cancer patients treated with paclitaxel and carboplatin chemotherapy

Till now, little is known about the effects of chemotherapy on the immunity of cancer patients and the ideal timing (“window” period) for immunotherapy combined with chemotherapy. In this study, we addressed the immunogenicity of apoptotic ovarian cancer cells induced by paclitaxel and carboplatin, the immunologic aspects in ovarian cancer patients under chemotherapy, and the CTL response when CD8⁺ T cells were stimulated with tumor antigen in the “window” period. The immunogenicity of apoptotic ovarian cancer cells was detected first. Then, blood samples from each ovarian cancer patient were obtained before (S₀) and at days 5–7 (S₁), days 12–14 (S₂) and days 25–28 (S₃) after chemotherapy. The proportions of immunocyte subsets and the function of NK cells were studied. We found that apoptotic ovarian cancer cells elicited a powerful CTL response with antitumor activity in vitro. The proportions of CD3⁺ T cells, CD4⁺ T cells and the ratio of CD4⁺ to CD8⁺ cells did not change significantly on S₁, S₂ and S₃, compared to S₀, whereas the percentage of Treg cells decreased remarkably on S₂. The proportions of Th1, Tc1, CD45RO memory T, NKT cells and the ratio of Tc1 to Tc2 cells increased significantly on S₂. IFN-γ secreting CD8⁺ T cells also increased remarkably on S₂, especially when CD8⁺ T cells were stimulated with autologous tumor antigen. From our point of view, chemotherapy induces temporary immune reconstitution and augments anti-tumor immune response. It is probable that the “window” period of days 12–14 after chemotherapy provides the best opportunity for immunotherapy.     

Complete mitochondrial genome of <Emphasis Type="Italic">Otis tarda</Emphasis> (Gruiformes: Otididae) and phylogeny of Gruiformes inferred from mitochondrial DNA sequences

The complete nucleotide sequence of mitochondrial genome of the Great bustard (Otis tarda) was determined by using polymerase chain reaction (PCR) method. The genome is 16,849 bp in size, containing 13 protein-coding, 2 ribosomal and 22 transfer RNA genes. Sequences of the tRNA genes can be folded into canonical cloverleaf secondary structure except for tRNA-Cys and tRNA-Ser (AGY), which lose “DHU” arm. Sequence analysis showed that the O. tarda mitochondrial control region (mtCR) contained many elements in common with other avian mtCRs. A microsatellite repeat was found in the 3′-peripheral domain of the O. tarda mtCR. Based on the mitochondrial DNA sequences of 12S rRNA, 16S rRNA and tRNA-Val, a phylogenetic study of Gruiformes was performed. The result showed that Otididae was a sister group to “core Gruiformes” and Charadriiformes with strong support (97% posterior probability values) in Bayesian analysis. The taxonomic status of Rhynochetidae, Mesitornithidae, Pedionomidae and Turnicidae that traditionally belonged to Gruiformes was also discussed in this paper.     

“Chelatable iron pool”: inositol 1,2,3-trisphosphate fulfils the conditions required to be a safe cellular iron ligand

Mammalian cells contain a pool of iron that is not strongly bound to proteins, which can be detected with fluorescent chelating probes. The cellular ligands of this biologically important “chelatable”, “labile” or “transit” iron are not known. Proposed ligands are problematic, because they are saturated by magnesium under cellular conditions and/or because they are not “safe”, i.e. they allow iron to catalyse hydroxyl radical formation. Among small cellular molecules, certain inositol phosphates (InsPs) excel at complexing Fe³⁺ in such a “safe” manner in vitro. However, we previously calculated that the most abundant InsP, inositol hexakisphosphate, cannot interact with Fe³⁺ in the presence of cellular concentrations of Mg²⁺. In this work, we study the metal complexation behaviour of inositol 1,2,3-trisphosphate [Ins(1,2,3)P ₃], a cellular constituent of unknown function and the simplest InsP to display high-affinity, “safe”, iron complexation. We report thermodynamic constants for the interaction of Ins(1,2,3)P ₃ with Na⁺, K⁺, Mg²⁺, Ca²⁺, Cu²⁺, Fe²⁺ and Fe³⁺. Our calculations indicate that Ins(1,2,3)P ₃ can be expected to complex all available Fe³⁺ in a quantitative, 1:1 reaction, both in cytosol/nucleus and in acidic compartments, in which an important labile iron subpool is thought to exist. In addition, we calculate that the fluorescent iron probe calcein would strip Fe³⁺ from Ins(1,2,3)P ₃ under cellular conditions, and hence labile iron detected using this probe may include iron bound to Ins(1,2,3)P ₃. Therefore Ins(1,2,3)P ₃ is the first viable proposal for a transit iron ligand. Electronic supplementary material  The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

Characterization of a novel small RNA encoded by Dictyostelium discoideum mitochondrial DNA

In this study, we analyzed a mitochondrial small (ms) RNA in Dictyostelium discoideum, which is 129 nucleotides long and has a GC content of only 22.5%. In the mitochondrial DNA, a single-copy gene (msr) for the ms RNA was located downstream of the gene for large-subunit rRNA. The location of msr was similar to that of the 5S rRNA gene in prokaryotes and chloroplasts, but clearly different from that in mitochondria of plants, liverwort and the chlorophycean alga Prototheca wikerhamii, in which small-subunit rRNA and 5S rRNA genes are closely linked. The primary sequence of ms RNA showed low homology with mitochondrial 5S rRNA from plants, liverwort and the chlorophycean alga, but the proposed secondary structure of ms RNA was similar to that of cytoplasmic 5S rRNA. In addition, ms RNA showed a highly conserved GAAC sequence in the same loop as in common 5S rRNA. However, ms RNA was detected mainly in the mitochondrial 25 000 × g supernatant fraction which was devoid of ribosomes. It is possible that ms RNA is an evolutionary derivative of mitochondrial 5S rRNA. Received: 17 May 1997 / Accepted: 26 August 1997     

Mitochondrial resistance to miconazole in Saccharomyces cerevisiae

Summary One mutant of mitochondrial origin resistant to miconazole has been isolated and characterized in S. cerevisiae. The mutation is linked to the locus oli1, the structural gene for subunit 9 of ATPase on mitochondrial DNA. Miconazole inhibited the mitochondrial ATPase of the wild type while the enzyme of the resistant mutant was insensitive to this effect. Levels of ATP decreased to one-third of the control in the wild type in the presence of miconazole, while they were unaffected in the mutant.Abbreviations MNNG N-methyl-N-nitrosoguanidine - Mic^s/Mic^r phenotypic sensitivity/resistance to miconazole - M ₁ ^R mitochondrial locus conferring miconazole resistance - rho⁺/rho^- grand/cytoplasmic petite - rho^o cytoplasmic petite deleted of all mitochondrial DNA - w⁺ mitochondrial locus conferring polarity of recombination     

Production of asymmetric somatic hybrid plants between Cichorium intybus L. and Helianthus annuus L.

In order to obtain male-sterile asymmetric somatic hybrids between chicory (Cichorium intybus L.) and a sunflower (Helianthus annuus L.) male-sterile cytoplasmic line, mesophyll chicory protoplasts inactivated with iodoacetic acid and hypocotyl sunflower protoplasts irradiated with γ-rays have been fused, using PEG and applying two different procedures. Thirty three plants were regenerated from putative hybrid calli. A cytological analysis of their root-tip cells indicated that most of them had 18 chromosomes, the same number as chicory. Through Southern hybridisation on total DNA using the maize mitochondrial specific gene probes Cox I, Cox II and Cob, three plants were identified as cytoplasmic asymmetric hybrids, as shown by hybridisation bands specific for both chicory and sunflower. One of the regenerated plants produced a novel pattern of hybridisation that was not detected in either parent. When hybridisation of total DNA was carried out with an atpA mitochondrial gene probe the same three cybrids presented both the fertile chicory fragment and the male-sterile sunflower fragment. Finally, Southern hybridisation with an ORF 522 probe, which in sunflower is co-transcribed with the atpA gene, confirmed the hybrid nature of the three plants. The morphology of the cybrids resembled the parental chicory phenotype, and at anthesis their anthers produced fewer pollen grains which could not germinate either ”in vitro” or ”in situ.” Cybrid plants grown in the field produced seeds when free-pollination occurred. Received: 26 April 2000 / Accepted: 28 August 2000