Turned on by genotoxic stress

Comment on: Travesa A, et al. EMBO J 2012; 31:1811-22.     

Long-term preservation of DNA in aqueous solutions in the presence of the chemical analogues of microbial autoregulators

he fact of long-term preservation of the physicochemical properties of DNA molecules in aqueous solutions in complexes with methylresorcinol, hexylresorcinol, and tyrosol, the chemical analogues of microbial autoregulators (d₁ factors) from the group of alkylhydroxybenzenes (AOB), was established. Compared to the control variants of storage of aqueous DNA solutions, the AOB influence consisted in the sum of correlating effects: the prevention of DNA degradation (according to spectrophotometric parameters) and the preservation of its viscous characteristics and electrophoretic mobility. The initial DNA properties were preserved to the greatest degree in the presence of hexylresorcinol, the compound with the longest alkyl radical. Possible mechanisms of the protective action of alkylhydroxybenzenes in relation to DNA are discussed, namely, the prevention of its hydrolysis due to isolation from the aqueous environment and maintaining DNA stability in the dormant forms of microorganisms.     

Synthesis, crystal structure, magnetic property and oxidative DNA cleavage activity of an octanuclear copper(II) complex showing water-perchlorate helical network

A new octanuclear copper(II) complex has been synthesized and structurally characterized by X-ray crystallography: [Cu(8)(HL)(4)(OH)(4)(H(2)O)(2)(ClO(4))(2)].(ClO(4))(2).2H(2)O (1) (H(3)L=2,6-bis(hydroxyethyliminoethyl)-4-methyl phenol). The complex is formed by the linkage of two terminal bimetallic cationic units and a tetranuclear mu(3)-hydroxo bridged dicubane core by a very short intramolecular hydrogen bond (O-H...O, 1.48(3)A and the angle 175 degrees). The coordination sphere of the terminal copper atoms is square pyramidal, the apical positions being occupied by water and a perchlorate ion. Complex 1 self-assembles to form a new type of water-perchlorate helical network [(H(2)O)(2)(ClO(4))](infinity) involving oxygen atoms of coordinated perchlorate ion and the two lattice water molecules through hydrogen-bonding interaction. The variable temperature-dependent susceptibility measurement (2-300K) of 1 reveals a strong antiferromagnetic coupling, J(1)=-220cm(-1) and J(2)=-98cm(-1) (J(1) and J(2) representing the exchange constant within [Cu(2+)](4) and [Cu(2+)](2) units, respectively). The complex binds to double-stranded supercoiled plasmid DNA giving a K(app) value of 1.2x10(7)M(-1) and displays efficient oxidative cleavage of supercoiled DNA in the presence of H(2)O(2) following a hydroxyl radical pathway.     

Influence of formamide on the thermal stability of DNA

The utility of formamide in the denaturation and renaturation of DNA has been examined. The melting temperature of duplex DNA is lowered by 0·6°C per per cent formamide. The depression of melting temperature is independent of the GC content. Formamide also increases the width of the thermal transition. Upto 30%, it does not affect the rate of DNA reassociation     

Studies on DNA binding to metal complexes of Sal<Subscript>2</Subscript>trien

The complexes [Fe(Sal2trien)]NO3 and Cu(Sal2trien) have been synthesized and their interaction with calf thymus DNA has been investigated for the first time using UV spectra, fluorescence spectra, thermal denaturation, and viscosity measurements. The experimental results show conformably that the mode of binding of the complex [Fe(Sal2trien)]NO3 to DNA is nonclassical electrostatic action, but the mode of binding of the complex Cu(Sal2trien) to DNA is classical intercalation.     

Intracellular sites of the synthesis of sweet potato mitochondrial F1ATPase subunits

Summary Five subunits (-, -, -, - and -subunits) of the six -and -subunits) in the F₁ portion (F₁ATPase) of sweet potato (Ipomoea batatas) mitochondrial adenosine triphosphatase were isolated by an electrophoretic method. The - and -subunits were not distinguishable immunologically but showed completely different tryptic peptide maps, indicating that they were different molecular species. In vitro protein synthesis with isolated sweet potato root mitochondria produced only the -subunit when analyzed with anti-sweet potato F₁ATPase antibody reacting with all the subunits except the -subunit. Sweet potato root poly(A)⁺RNA directed the synthesis of six polypeptides which were immunoprecipitated by the antibody: two of them immunologically related to the -subunit and the others to the - and -subunits. We conclude that the -subunit of the F₁ATPase is synthesized only in the mitochondria and the -, - and -subunits are in the cytoplasm.     

SiO2 nanoparticles induce global genomic hypomethylation in HaCaT cells

The increasing amount of nanotechnological products, found in our environment and those applicable in engineering, material sciences and medicine has stimulated a growing interest in examining their long-term impact on genetic and epigenetic processes. We examined here the epigenomic response to nm-SiO₂ particles in human HaCaT cells and methyltransferases (DNMTs) and DNA-binding domain proteins (MBDs) induced by nano-SiO₂ particles. Nm-SiO₂ treatment induced global hypoacetylation implying a global epigenomic response. The levels of DNMT1, DNMT3a and methyl-CpG binding protein 2 (MBD2) were also decreased in a dose dependent manner at mRNA and protein level. Epigenetic changes may have long-term effects on gene expression programming long after the initial signal has been removed, and if these changes remain undetected, it could lead to long-term untoward effects in biological systems. These studies suggest that nanoparticles could cause more subtle epigenetic changes which merit thorough examination of environmental nanoparticles and novel candidate nanomaterials for medical applications.     

Temperature dependence of UV radiation effects in Arctic and temperate isolates of three red macrophytes

The temperature dependence of UV effects was studied for Arctic and temperate isolates of the red macrophytes Palmaria palmata, Coccotylus truncatus and Phycodrys rubens. The effects of daily repeated artificial ultraviolet B and A radiation (UVBR: 280–320?nm, UVAR: 320–400?nm) treatments were examined for all isolates at 6, 12 and 18?°C by measuring growth, optimal quantum yield of PSII (F_v/F_m) and cyclobutane-pyrimidine dimer (CPD) accumulation. Furthermore, possible ecotypic differences in UV sensitivity between Arctic and temperate isolates were evaluated. Large species-specific differences in UV sensitivity were observed for all parameters: the lower subtidal species C. truncatus and P. rubens were highly sensitive to the UV treatments, whereas P. palmata, which predominantly occurs in the upper subtidal zone, was not affected by these treatments. Only minor differences were found between Arctic and temperate isolates, suggesting that no differences in UV sensitivity have evolved in these species. Relative growth rates were temperature-dependent, whereas species-specific UV effects on growth rates were relatively independent of temperature. In contrast, the species-specific decrease in F_v/F_m and its subsequent recovery were temperature-dependent in all species. UV effects on F_v/F_m were lower at 12 and 18?°C compared with 6?°C. In addition, UV effects on F_v/F_m decreased in the course of the experiment at all temperatures, indicating acclimation to the UV treatments. CPDs accumulated during the experiment in both isolates of P. rubens, whereas CPD concentrations remained low for the other two species. CPD accumulation appeared to be independent of temperature. The results suggest that summer temperatures occurring in temperate regions facilitate repair of UV-induced damage and acclimation to UV radiation in these algae compared with Arctic temperatures. Because the differences in UV effects on F_v/F_m, growth and CPD accumulation were relatively small over a broad range of temperatures, it was concluded that the influence of temperature on UV effects is small in these species.     

DNA isolation by a rapid method from human blood samples: Effects of MgCl2, EDTA,storage time,and temperature on DNA yield and quality

The isolation of DNA from whole blood by a modified rapid method (RM) was tested using various detergents and buffer conditions. Extraction of DNA with either NP-40 or Triton X-100 gave a high yield of undegraded DNA in less than an hour. The concentration of magnesium ion in the buffers was critical to obtaining intact, high molecular weight (HMW) DNA. Greater than 10 mM MgCl₂ led to degradation. Addition of EDTA to the buffer inhibits this degradation. Preparation of DNA from blood stored at room temperature or incubated at 37°C for 24 hr resulted in the same amount and quality of DNA as from samples frozen at −70°C. DNA from blood samples that had undergone more than four freeze-thaw cycles was found to be partially degraded. The modified RM can be applied to extract DNA from as little as 10 μl of blood (340 ng of DNA) and from dried blood samples. DNA samples remained intact and undegraded for longer times when DNA was dissolved in higher concentrations of EDTA. This work was supported by grants from the Indiana Department of Mental Health and PHS RO1 AG10297.     

Interaction Mode between Inclusion Complex of Vitamin K3 with γ- Cyclodextrin and Herring-Sperm DNA

Methods including spectroscopy, electronic chemistry and thermodynamics were used to study the inclusion effect between γ-cyclodextrin (CD) and vitamin K₃(K₃), as well as the interaction mode between herring-sperm DNA (hsDNA) and γ-CD-K₃ inclusion complex. The results from ultraviolet spectroscopic method indicated that VK₃ and γ-CD formed 1:1 inclusion complex, with the inclusion constant K_f = 1.02 × 10⁴ L/mol, which is based on Benesi–Hildebrand's viewpoint. The outcomes from the probe method and Scatchard methods suggested that the interaction mode between γ-CD-K₃ and DNA was a mixture mode, which included intercalation and electrostatic binding effects. The binding constants were K ^θ_25°C = 2.16 × 10⁴ L/mol, and K^θ_37°C = 1.06 × 10⁴ L/mol. The thermodynamic functions of the interaction between γ-CD-K₃ and DNA were Δ_rH_m^θ = ?2.74 × 10⁴ J/mol, Δ_rS_m^θ = 174.74 J·mol^?1K^?1, therefore, both Δ_rH_m^θ (enthalpy) and Δ_rS_m^θ (entropy) worked as driven forces in this action.     

Inorganic and organic UV filters: Their role and efficacy in sunscreens and suncare products

Minerals such as titanium dioxide, TiO₂, and zinc oxide, ZnO, are well known active semiconductor photocatalysts used extensively in heterogeneous photocatalysis to destroy environmental pollutants that are organic in nature. They are also extensively used in sunscreen lotions as active broadband sunscreens that screen both UVB (290-320 nm) and UVA (320-400 nm) sunlight radiation and as high SPF makers. When so photoactivated by UV light, however, these two particular metal oxides are known to generate highly oxidizing radicals (OH and ) and other reactive oxygen species (ROS) such as H₂O₂ and singlet oxygen, ¹O₂, which are known to be cytotoxic and/or genotoxic. Hydroxyl (OH) radicals photogenerated from photoactive TiO₂ specimens extracted from commercial sunscreen lotions [R. Dunford, A. Salinaro, L. Cai, N. Serpone, S. Horikoshi, H. Hidaka, J. Knowland, FEBS Lett. 418 (1997) 87] induce damage to DNA plasmids in vitro and to whole human skin cells in cultures. Accordingly, the titanium dioxide particle surface was modified to produce TiO₂ specimens of considerably reduced photoactivity. Deactivation of TiO₂ diminishes considerably, in some cases completely suppresses damage caused to DNA plasmids, to human cells, and to yeast cells compared to non-modified specimens exposed to UVB/UVA simulated solar radiation. The photostabilities of sunscreen organic active agents in neat polar and apolar solvents and in actual commercial formulations have been examined [N. Serpone, A. Salinaro, A.V. Emeline, S. Horikoshi, H. Hidaka, J. Zhao, Photochem. Photobiol. Sci. 1 (2002) 970]. With rare exceptions, the active ingredients undergo photochemical changes (in some cases form free radicals) and the sunscreen lotions lose considerable Sun protection efficacy only after a relatively short time when exposed to simulated sunlight UVB/UVA radiation, confirming the recent findings by Sayre et al. [R.M. Sayre, J.C. Dowdy, A.J. Gerwig, W.J. Shields, R.V. Lloyd, Photochem. Photobiol. 81 (2005) 452].     

Crystal structure and DNA-binding analysis of RecO from Deinococcus radiodurans

The RecFOR pathway has been shown to be essential for DNA repair through the process of homologous recombination in bacteria and, recently, to be important in the recovery of stalled replication forks following UV irradiation. RecO, along with RecR, RecF, RecQ and RecJ, is a principal actor in this fundamental DNA repair pathway. Here we present the three-dimensional structure of a member of the RecO family. The crystal structure of Deinococcus radiodurans RecO (drRecO) reveals possible binding sites for DNA and for the RecO-binding proteins within its three discrete structural regions: an N-terminal oligonucleotide/oligosaccharide-binding domain, a helical bundle and a zinc-finger motif. Furthermore, drRecO was found to form a stable complex with RecR and to bind both single- and double-stranded DNA. Mutational analysis confirmed the existence of multiple DNA-binding sites within the protein.     

Effects of polyploidy on photosynthesis

In polyploid plants the photosynthetic rate per cell is correlated with the amount of DNA per cell. The photosynthetic rate per unit leaf area is the product of the rate per cell times the number of photosynthetic cells per unit area. Therefore, the photosynthetic rate per unit leaf area will increase if there is a less than proportional increase in cell volume at higher ploidal levels, or if cell packing is altered to allow more cells per unit leaf area. In autopolyploids (Medicago sativa, C₃ species, and Pennisetum americanum, C₄ species) there is a doubling of photosynthesis per cell and of cell volume in the tetraploid compared to the diploid. However, there is a proportional decrease in number of cells per unit leaf area with this increase in ploidy such that the rate of photosynthesis per leaf area does not change. There is more diversity in the relationship between ploidal level (gene dosage) and photosynthetic rates per unit leaf area in allopolyploids. This is likely to reflect the effects of natural selection on leaf anatomy, and novel genetic interactions from contributed genomes which can occur with allopolyploidy. In allopolyploid wheat (C₃ species) a higher cell volume per unit DNA at the higher ploidal level is negatively correlated with photosynthesis rate per unit leaf area. Although photosynthesis per cell increases with ploidy, photosynthesis per leaf area decreases, being lowest in the allohexaploid, cultivated bread wheat (Triticum aestivum). Alternatively, doubling of photosynthetic rate per cell with doubling of DNA, with apparent natural selection for decreased cell volume per unit DNA, results in higher rates of photosynthesis per leaf area in octaploid compared to tetraploid Panicum virgatum (C₄) which may be a case of allopolyploidy. Similar responses probably occur in Festuca arundinacea. Therefore, in some systems anatomical factors affecting photosynthesis are also affected by ploidal level. It is important to evaluate that component as well as determining the effect on biochemical processes. Current information on polyploidy and photosynthesis in several species is discussed with respect to anatomy, biochemistry and bases for expressing photosynthetic rates.Abbreviations Chl chlorophyll - RuBPC ribulose-1,5-bisphosphate carboxylase     

Vanadium and 1, 25 (OH)2 vitamin D3 combination in inhibitions of 1,2, dimethylhydrazine-induced rat colon carcinogenesis

The current investigation demonstrates the antitumor effects of combined supplementations of vanadium (V) (4.27 µmol/L drinking water ad libitum) and1α, 25-dihydroxy vitamin D₃ (Vitamin D₃) (0.3 μg/100 μL propylene glycol per os twice a week) on 1, 2 dimethylhydrazine (DMH) (20 mg/kg body weight) induced rat colon carcinogenesis. There was a significant reduction in incidence (70%), multiplicity (P < 0.0001) and volume (P < 0.01) of colon tumors. HPLC-fluorescence assay detected the combinatorial actions of V and Vitamin D₃ against DMH-induced colonic O⁶-methylguanine DNA adducts formation (at four sequential time points; ANOVA, F = 13.56, P < 0.01). Simultaneous inhibition of DNA single strand breaks (P < 0.001) indicates the potency of the combination regimen in limiting the initiation event of colon carcinogenesis. Immunohistochemical analysis revealed that the effect of V and vitamin D₃ occurred through suppression of cell proliferation (BrdU-LI: P < 0.001) along with an induction of apoptosis (TUNEL-LI: P < 0.01). The immunoexpression of tumor suppressor p53 and downregulation of antiapoptotic protein BCl-2 in subsequent immunofluorescence assay further provide strong evidence for the combinatorial inhibitory actions of vanadium and vitamin D₃ against DMH-induced rat colon carcinogenesis.     

Inactivation of DNA polymerases by adenosine 2′,3′-riboepoxide 5′-triphosphate allows estimation of the primers affinity

Template-primer dependent inactivation of human DNA polymerase and Klenow fragment of E. coli DNA polymerase I by adenosine 2,3-riboepoxide 5-triphosphate was used for quantitative analysis of the K_d values for oligonucleotide primers of different length. The K_d values are smaller by a factor of 2.5 than the K_m values for the same primers determined in the reaction of DNA polymerization in the case of DNA polymerase . The K_d and K_m values are nearly the same for Klenow fragment. Such approach to the determination of K_m/K_d ratio can likely be used for detailed quantitative analysis of DNA polymerases.Abbreviations epATP adenosine 2,3-riboepoxide 5-triphosphate - KF Klenow fragment of E. coli DNA polymerase I - Pol I E. coli DNA polymerase I - Pol human placenta DNA polymerase      

Binding of Drosophila maternal Mamo protein to chromatin and specific DNA sequences

Alterations in chromatin structure dynamically occur during germline development in Drosophila and are essential for the production of functional gametes. We had previously reported that the maternal factor Mamo, which contains both a BTB/POZ domain and C₂H₂ zinc-finger domains and is enriched in primordial germ cells (PGCs), is required for the regulation of meiotic chromatin structure and the production of functional gametes. However, the molecular mechanisms by which Mamo regulates germline development remained unclear. To evaluate the molecular function of Mamo protein, we have investigated the binding of Mamo to chromatin and DNA sequences. Our data show that Mamo binds to chromatin and specific DNA sequences, particularly the polytene chromosomes of salivary gland cells. Overexpression of Mamo affected the organization of polytene chromosomes. Reduction in maternal Mamo levels impaired the formation of germline-specific chromatin structures in PGCs. Furthermore, we found that the zinc-finger domains of Mamo directly bind to specific DNA sequences. Our results suggest that Mamo plays a role in regulating chromatin structure in PGCs.     

Introduction: A Close Look at the Vacuolar ATPase

The vacuolar ATPases (V-type ATPases) are a family of ATP-dependent ion pumps and found in two principal locations, in endomembranes and in plasma membranes. This family of ATPases is responsible for acidification of intracellulare compartments and, in certain cases, ion transport across the plasma membrane of eucaryotic cells. V-ATPases are composed of two distinct domains: a catalytic V₁ sector, in which ATP hydrolysis takes place, and the membrane-embedded sector, V₀, which functions in ion conduction. In the past decade impressive progress has been made in elucidating the properties structure, function and moleculare biology. These knowledge sheds light also on the evolution of V-ATPases and their related families of A-(A₁A₀-ATPase) and F-type (F₁F₀-ATPases)ATPases.     

Verification of the Z-scheme in Chlamydomonas mutants with Photosystem I deficiency

In conflict with the Z-scheme of photosynthesis, it has recently been reported [Greenbaum et al. Nature (1995) 376: 438–441; Lee et al. Science (1996) 273: 364–367] that Photosystem II can drive ferredoxin reduction and photoautotrophic growth in some mutants of Chlamydomonas lacking detectable Photosystem I reaction centre, P700. Using the same mutants, B4 and F8, here we report that action spectra and parameters of flash yields of different photoreactions show the operation in ferredoxin-dependent H₂ photoproduction and CO₂ fixation of a fraction (at least 5% compared to wild- type) of the only Photosystem I complexes.     

Interaction of the Thermoplasma acidophilum A1A0-ATP synthase peripheral stalk with the catalytic domain

The peripheral stalk of the archaeal ATP synthase (A₁A₀)-ATP synthase is formed by the heterodimeric EH complex and is part of the stator domain, which counteracts the torque of rotational catalysis. Here we used nuclear magnetic resonance spectroscopy to probe the interaction of the C-terminal domain of the EH heterodimer (E_CT1H_CT) with the N-terminal 23 residues of the B subunit (B_NT). The data show a specific interaction of B_NT peptide with 26 residues of the E_CT1H_CT domain, thereby providing a molecular picture of how the peripheral stalk is anchored to the A₃B₃ catalytic domain in A₁A₀.

Structured summary

MINT-7260681: Hct (refseq:NP_393485), Ect1 (uniprotkb:Q9HM68) and Bnt (uniprotkb:Q9HM64) physically interact (MI:0915) by nuclear magnetic resonance (MI:0077)     

Diversity of nitrogen-fixing cyanobacteria under various ecosystems of Thailand: I. Morphology,physiology and genetic diversity

The diversity among 853 isolates of nitrogen-fixing cyanobacteria obtained from soil samples collected from different ecosystems including mountainous, forest and cultivated areas in the central, northern and northeastern regions of Thailand was examined. Most isolates showed slow growth rate and had filamentous, heterocystous cells. The percentage of heterocysts in the filaments of different isolates varied from 8.3 to 9.6. Only a few strains showed high nitrogen-fixing potential, while most of the strains exhibited low capacity for nitrogen fixation. Anabaena and Nostoc were the dominant genera among these isolates. One hundred and two isolates were randomly selected from this diverse collection to determine the extent of genetic diversity on the basis of DNA fingerprinting using the PCR method. Based on the PCR products obtained by using a combination of three primers, all strains could be distinguished from one another. When a subset of 45 isolates of Nostoc and a subset of 44 isolates of Anabaena were further analysed by PCR, a wide range of diversity was observed within each of these genera.