Functional Identification of a Hydroxyproline-O-galactosyltransferase Specific for Arabinogalactan Protein Biosynthesis in Arabidopsis

Although plants contain substantial amounts of arabinogalactan proteins (AGPs), the enzymes responsible for AGP glycosylation are largely unknown. Bioinformatics indicated that AGP galactosyltransferases (GALTs) are members of the carbohydrate-active enzyme glycosyltransferase (GT) 31 family (CAZy GT31) involved in N- and O-glycosylation. Six Arabidopsis GT31 members were expressed in Pichia pastoris and tested for enzyme activity. The At4g21060 gene (named AtGALT2) was found to encode activity for adding galactose (Gal) to hydroxyproline (Hyp) in AGP protein backbones. AtGALT2 specifically catalyzed incorporation of [¹⁴C]Gal from UDP-[¹⁴C]Gal to Hyp of model substrate acceptors having AGP peptide sequences, consisting of non-contiguous Hyp residues, such as (Ala-Hyp) repetitive units exemplified by chemically synthesized (AO)₇ and anhydrous hydrogen fluoride-deglycosylated d(AO)₅₁. Microsomal preparations from Pichia cells expressing AtGALT2 incorporated [¹⁴C]Gal to (AO)₇, and the resulting product co-eluted with (AO)₇ by reverse-phase HPLC. Acid hydrolysis of the [¹⁴C]Gal-(AO)₇ product released ¹⁴C-radiolabel as Gal only. Base hydrolysis of the [¹⁴C]Gal-(AO)₇ product released a ¹⁴C-radiolabeled fragment that co-eluted with a Hyp-Gal standard after high performance anion-exchange chromatography fractionation. AtGALT2 is specific for AGPs because substrates lacking AGP peptide sequences did not act as acceptors. Moreover, AtGALT2 uses only UDP-Gal as the substrate donor and requires Mg²⁺ or Mn²⁺ for high activity. Additional support that AtGALT2 encodes an AGP GALT was provided by two allelic AtGALT2 knock-out mutants, which demonstrated lower GALT activities and reductions in β-Yariv-precipitated AGPs compared with wild type plants. Confocal microscopic analysis of fluorescently tagged AtGALT2 in tobacco epidermal cells indicated that AtGALT2 is probably localized in the endomembrane system consistent with its function.     

Probing the microenvironmental of benzo[a]pyrene diol epoxide-DNA adducts by triplet excited state quenching methods

Triplet flash photolysis techniques, coupled with quenching of the triplets by molecular oxygen, are utilized as probes of the microenvironment of polycyclic aromatic molecules bound covalently and non-covalently to DNA. The triplet-oxygen quenching properties of the following adducts in aqueous solutions at 25±1°C were investigated: covalent adducts derived from the reaction of (±)-7β,8α-dihydroxy-9α,10α-epoxy -7,8,9,10-tetrahydrobenzo[a]pyrene (BaPDE) and of (±)-9,10-epoxy-7,8,9,10-tetrahydrobenzo[a]pyrene (BaPE) with DNA, and non-covalent intercalation complexes of acridine orange (AO) and DNA. In all cases the quenching follows the Stern-Volmer quenching law with a quenching constant of K_O2^T≈10⁹ M^?1·s^?1 for the covalent BaPDE-DNA and BaPE-DNA complexes in aqueous solution. This value of K_O2^T is characteristic of free molecules (not bound to DNA) and indicates that the pyrene chromophore is totally accessible to oxygen, and is thus not located at an intercalation-type of binding site in these covalent adducts. In contrast, the AO-DNA complexes are characterized by values of K_O2^T≈10⁸ M^?1·s^?1 indicating that the intercalated AO molecules are about ten times less accessible to molecular oxygen than free AO molecules. The K_O2^T values for the covalent BaPDE-DNA and BaPE-DNA adducts decrease when the DNA concentration is increased in the 1·10^?4?3·10^?3 M range (expressed in nucleotide concentration). This effect is attributed to intermolecular DNA-DNA interactions in which segments of adjacent DNA molecules tend to cover the pyrene chromophores on other strands, thus decreasing their accessibility to oxygen. In contrast the values of K_O2^T for the non-covalent AO-DNA intercalation complexes are independent of DNA concentration, as expected for interior binding sites.     

Aldehyde oxidase generates deoxyribonucleic acid single strand nicks in vitro

SUMMARY

We purified aldehyde oxidase (AO) from rabbit livers and found that AO produced deoxyribonucleic acid (DNA) single strand nicks in vitro. Acetaldehyde, benzaldehyde, and certain purine bases were effective substrates for AO catalyzed DNA strand nicking. DNA strand nicking did not occur with the reducing substrates nicotinamide-adenine dinucleotide or dithionite that produce superoxide anion (O_2′^?). Inclusion of electron transport inhibitors, potassium cyanide, ferricyanide or menadione, prevented AO catalyzed nicking. AO induced DNA strand nicking was dependent upon hydrogen peroxide (H₂O₂) formation and most likely generation of hydroxyl radical (HO'). The present observations may be pertinent to the recently proposed involvement of AO in inherited juvenile familial amyotrophic lateral sclerosis (JFALS) and other oxygen radical mediated diseases.     

Interaction between tryptophan‐Sm(III) complex and DNA with the use of a acridine orange dye fluorophor probe

The interaction of the Trp–Sm(III) complex with herring sperm DNA (hs‐DNA) was investigated with the use of acridine orange (AO) dye as a spectral probe for UV‐vis spectrophotometry and fluorescence spectroscopy. The results showed that the both the Trp–Sm(III) complex and the AO molecule could intercalate into the double helix of the DNA. The Sm(III)–(Trp)₃ complex was stabilized by intercalation into the DNA with binding constants: K^?_25°C = 7.14 × 10⁵ L·mol^?1 and K^?_37°C = 5.28 × 10⁴ L·mol^?1, and it could displace the AO dye from the AO–DNA complex in a competitive reaction. Computation of the thermodynamic functions demonstrates that Δ_rH_m^? is the primary driving power of the interaction between the Sm(III)(Trp)₃ complex and the DNA. The results from Scatchard and viscometry methods suggested that the interaction mode between the Sm(III)(Trp)₃ complex and the hs‐DNA is groove binding and weak intercalation binding. Copyright © 2015 John Wiley & Sons, Ltd.     

Spectroscopic studies on the interaction mechanisms of safranin T with herring sperm DNA using acridine orange as a fluorescence probe

Under the condition of physiological pH environment (pH = 7.40), the interactions of safranin T (ST) with herring sperm DNA were studied by means of spectral methods using acridine orange (AO) as a fluorescence probe. The spectroscopic characteristics of DNA–AO in the case of ST (along with the increase of concentration) were observed in an aqueous medium. The binding constants for ST stranded DNA and competitive bindings of ST interacting with DNA–AO systems were examined by fluorescence spectra, and the binding mechanism of ST with DNA was researched via viscosity measurements. All the testimony manifested that bonding modes between ST and DNA were evidenced to be intercalative binding and electrostatic binding, and the combining constant of ST with DNA was obtained. The binding of ST to DNA was driven by entropy and enthalpy through the calculated thermodynamic parameters (Δ_rH_m^?, Δ_rS_m and Δ_rG_m^?). Copyright © 2014 John Wiley & Sons, Ltd.     

Intracellular events during infection by Haemophilus influenzae phage and transfection by its DNA

Intracellular events following infection of competent Haemophilus influenzae by HPlcl phage, or transfection by DNA from the phage, were examined. Physical separation of a large fraction of the intracellular phage DNA from the bulk of the host DNA was achieved by lysis of infected or transfected cells with digitonin, followed by low-speed centrifugation. The small amount of bacterial DNA remaining with the phage DNA in the supernatants could be distinguished from phage DNA by its ability to yield transformants. After infection by whole phage, three forms of intracellular phage DNA were observable by sedimentation velocity analysis: form III, the slowest-sedimenting one; form II, which sedimented 1.1 times faster than III, and form I, which sedimented 1.6 times faster than III. It was shown by electron microscopy, velocity sedimentation in alkali, and equilibrium sedimentation with ethidium bromide, that forms I, II and III are twisted circles, open circles, and linear duplexes, respectively.After the entry of phage DNA into wild-type cells in transfection, the DNA is degraded at early times, but later some of the fragments are reassembled, resulting in molecules that sediment faster than the monomer length of phage DNA. Some of the fast-sedimenting molecules are presumably concatemers and are generated by recombination. In strain rec₁^? the fast-sedimenting molecules do not appear and degradation of phage DNA is even more pronounced than in wild-type cells. In strain rec₂^? there is little degradation of phage DNA, and the proportion of fast-sedimenting molecules is much smaller than in wild-type cells. Since rec₁^? and rec₂^? are transfected with much lower efficiency than wild type, our hypothesis is that both fragmentation and generation of fast-sedimenting phage DNA by recombination are required for more efficient transfection.     

Anaerobic Degradation of Uric Acid by Gut Bacteria of Termites

A study was done of anaerobic degradation of uric acid (UA) by representative strains of uricolytic bacteria isolated from guts of Reticulitermes flavipes termites. Streptococcus strain UAD-1 degraded UA incompletely, secreting a fluorescent compound into the medium, unless formate (or a formicogenic compound) was present as a cosubstrate. Formate functioned as a reductant, and its oxidation to CO₂ by formate dehydrogenase provided 2H⁺ + 2e⁻ needed to drive uricolysis to completion. Uricolysis by Streptococcus UAD-1 thus corresponded to the following equation: 1UA + 1formate → 4CO₂ + 1acetate + 4NH₃. Urea did not appear to be an intermediate in CO₂ and NH₃ formation during uricolysis by strain UAD-1. Formate dehydrogenase and uricolytic activities of strain UAD-1 were inducible by growth of cells on UA. Bacteroides termitidis strain UAD-50 degraded UA as follows: 1UA → 3.5 CO₂ + 0.75acetate + 4NH₃. Exogenous formate was neither required for nor stimulatory to uricolysis by strain UAD-50. Studies of UA catabolism by Citrobacter strains were limited, because only small amounts of UA were metabolized by cells in liquid medium. Uricolytic activity of such bacteria in situ could be important to the carbon, nitrogen, and energy economy of R. flavipes.     

The effect of photosensitizing dyes on the 3H-thymidine incorporation of cells grown in vitro

The photodynamic inactivation of ³H-thymidine incorporation in mouse embryo (ME) and mouse L cells by acridine orange (AO), methylene blue (MB) or neutral red (NR) has been studied by estimating the number of nuclei capable of incorporating ³H-thymidine during a 24 h period following light exposure. In the dark NR and AO reduced the number of ME-nuclei incorporating ³H-thymidine but MB caused an increase in non-scheduled DNA synthesis. The dark effect on L cells was less but the photoinactivation of thymidine uptake was proportionally greater in these cells. Polyoma virus was shown to be capable of growing in cells whose thymidine uptake was reduced or completely stopped by photoinactivation with NR. However, if the NR damage was very great, or when AO was used to photosensitize cells, the synthesis of viral DNA was interfered with.     

Different instability of nuclear DNA at acid hydrolysis in cancerous and noncancerous cells as revealed by fluorescent staining with acridine orange

Summary Ehrlich cancer cells and inflammatory cells in mouse ascitic fluid were hydrolyzed and stained with acridine orange (AO). The AO hydrolysis curves for G₁/G₂+M phase cancer cells and inflammatory cells were differentially determined using flow cytometry by monitoring the metachromatic red-shifted fluorescence of the fluorochrome bound to the single-stranded DNA produced by acid hydrolysis. By computer fitting of the Bateman function to the hydrolysis curves, the kinetic parameters k ₁ (rate constant for the degradation of the produced single-stranded DNA), and y ₀ (theoretical value of the single-stranded DNA present initially) were determined. It was found that the k ₂ value, which reflects the degree of DNA instability, was much higher for cancer cells in both the G₁ and G₂+M phases than for inflammatory cells. This finding led us to develop a method for the differential AO staining of cancer cells and non-cancerous cells utilizing the different degree of DNA instability at acid hydrolysis. AO staining after hydrolysis with 2N HCl at 30°C for 8.5 min was found to be the optimal method. In the 60 cases of human malignant epithelial and nonepithelial tumors tested, all of the malignant tumor cells emitted metachromatic red fluorescence, while all of the nonmalignant tumor cells (5 cases of benign tumor) and normal cells emitted orthochromatic green fluorescence when observed with a violet excitation light under a fluorescence microscope. This new technique can be a useful tool for the screening of malignancy in exfoliative cytology and also for basic cancer research.In honour of Prof. P. van Duijn     

Uptake of bacterial DNA by Chlamydomonas reinhardi

Escherichia coli [³H]DNA supplied to vegetative cultures of wild-type (mt+) and CW15 (mt+; mutant lacking the cell wall) Chlamydomonas reinhardi could bind to the cell wall of the wild-type and to the cell membrane of CW15 mutant cells. The extent of this binding decreased with time and was to a large degree (over 90%) DNA-ase-sensitive. Nevertheless, about 0.01% of the bacterial DNA remained irreversibly associated with the cells when they reached stationary phase. The irreversible binding of the donor bacterial DNA to Chlamydomonas cells could be increased by treatment of the cultures with polycations such as DEAE-dextran, poly-L-lysine and poly-L-ornithine. Although the CW15 cells rapidly degraded bacterial DNA in the culture medium wild-type cells showed only a small effect on the molecular weight of the donor DNA.The acid-insoluble radioactivity irreversibly bound to WT (+) cells consisted mainly of oligonucleotides with a small proportion present as less depolymerized donor DNA. No radioactivity, however, was found to be associated with the recipient high molecular weight Chlamydomonas DNA.No labeled donor DNA could be recognized in the cells given bacterial [³H]DNA in early stationary phase. Instead, radioactivity found in Chlamydomonas DNA corresponded to reutilization of [³H]thymine derivatives released as a result of [³H] DNA degradation. No evidence for the integration of detectable amounts of donor DNA sequences into the host cell DNA was obtained.     

Phosphorus-32, a Clinically Available Drug,Inhibits Cancer Growth by Inducing DNA Double-Strand Breakage

Radioisotopes that emit electrons (beta particles), such as radioiodine, can effectively kill target cells, including cancer cells. Aqueous ³²P[PO₄] is a pure beta-emitter that has been used for several decades to treat non-malignant human myeloproliferative diseases. ³²P[PO₄] was directly compared to a more powerful pure beta-emitter, the clinically important ⁹⁰Y isotope. In vitro, ³²P[PO₄] was more effective at killing cells than was the more powerful isotope ⁹⁰Y (P ≤ 0.001) and also caused substantially more double-stranded DNA breaks than did ⁹⁰Y. In vivo, a single low-dose intravenous dose of aqueous elemental ³²P significantly inhibited tumor growth in the syngeneic murine cancer model (P ≤ 0.001). This effect is exerted by direct incorporation into nascent DNA chains, resulting in double-stranded breakage, a unique mechanism not duplicatable by other, more powerful electron-emitting radioisotopes. ³²P[PO₄] should be considered for human clinical trials as a potential novel anti-cancer drug.     

Depicting the binding of furazolidone/furacilin with DNA by multiple spectroscopies,voltammetric as well as molecular docking

The interaction between DNA and furazolidone/furacillin was investigated using various analytical techniques including spectroscopy and electroanalysis and molecular modelling. With the aid of acridine orange (AO), the fluorescence lifetimes of DNA–AO, DNA–furazolidone/furacillin–AO remained almost the same, which proved that the ground state complex was formed due to furazolidone/furacillin binding with DNA. Circular dichroism spectra and Fourier transform infrared spectroscopy showed that the second structure of DNA changed. Viscosity experiments presented that relative viscosity of DNA was increased with the increasing concentrations of furazolidone and almost unchanged for furacilin. In addition, the results of melting temperature (T_m), ionic strength, site competition experiments, cyclic voltammetry, and molecular docking all proved the intercalation binding mode for furazolidone and groove binding mode for furacilin. The binding constants (K_a) obtained from Wolfe–Shimmer equation were calculated as 3.66 × 10⁴ L mol^?1 and 3.95 × 10⁴ L mol^?1 for furazolidone–DNA and furacilin–DNA, respectively.     

Nanovariant RNAs: nucleotide sequence and interaction with bacteriophage Qbeta replicase

Gene 2 amber mutants of bacteriophage T4 grown on su^? hosts produce whole particles of which less than 0.5% are infective on su⁺ hosts. Although the DNA of such particles is full-sized and un-nicked, it is degraded to acid-soluble fragments after infection of exo V⁺ hosts. This breakdown does not occur on exo V^? deficient hosts, and such hosts are fully permissive for gene 2-defective particles. We have now determined that giant-headed, gene 2-defective particles containing several genome lengths of DNA per head are fully infective on exo V⁺ hosts even though part of the parental DNA is degraded to acid-soluble fragments early after infection. Restriction of gene 2-defective particles must therefore be due to exonucleolytic degradation of the incoming DNA. If the parental DNA is of sufficient length to enable a complete genome to survive this degradation before production of anti-exoV, such particles are now infective.     

Biodegradation of para-nitrophenol by Citricoccus nitrophenolicus strain PNP1T at high pH

A gram-positive bacterium Citricoccus nitrophenolicus (strain PNP1^T, DSM 23311^T, CCUG 59571^T) isolated from a waste water treatment plant was capable of effectively degrading p-nitrophenol (pNP) as a source of carbon, nitrogen and energy for growth. Degradation of pNP required oxygen and resulted in the stoichiometric release of nitrite. Strain PNP1^T also degraded 4-chlorophenol, phenol and salicylate. pNP was degraded at pH values between 6.8 and 10.0 and at temperatures between 15–32 °C. pNP at concentrations up to 150 mg L^?1 were degraded during growth in media at pH ≤ 10, whereas 200 mg L^?1 was completely inhibitory to growth. When incubated in an NH₄Cl-free medium (pH 10) containing both pNP and acetate, pNP is degraded with concomitant release of nitrite which was subsequently assimilated during acetate degradation. Intact cells of strain PNP1^T suspended in NaHCO₃/Na₂CO₃ buffer were able to continuously degrade 200 mg L^?1 pNP over a 40 day period at pH 10.     

TherecA-dependent spontaneous degradation of proximal F merogenotes inEscherichia coli

Proximal F’ elements of KLF-1 type are relatively stable inEscherichia coli rec A recipients. In such merodiploids the transferability of F’-DNA and the plasmid determined fertility functions are expressed. When introduced into the wild typerecA ⁺ cells the F′-DNA is degraded and several classes of DNA molecules of molar mass about 66 Mg/mol and lower exist in the cell in 1–2 copies, per bacterial chromosome. As was detected by complementation analysis, the chromosomal genes determining the host specificity for DNA (hsd) originally located on the F’ element seem to be salvaged during the process of DNA degradation probably by recombination with the bacterial chromosome.     

Relationship between excision repair and the cytotoxic and mutagenic effect of the ‘anti’ 7,8-diol-9,10-epoxide of benzo[a]pyrene in human cells

The cytotoxic and mutagenic effect of (±)-7β,8α-dihydroxy-9α,10α-epoxy-7,8,9,10-tetrahydrobenzo[a]pyrene (anti BPDE) in normally excision diploid human cells treated just prior to onset of S was compared with that of cells allowed ～ 16 h for excision repair before onset of S and with that observed in excision-deficient serodema pigmentosum (SP12BE) cells. The cells were synchronized by release from density inhibition of cell replication. DNA synthesis began ～ 22 h after the cells were plated at lower density (i.e., 1.4 × 10⁴ cells/cm²). The frequency of thioguanine-resistant mutants induced in normal cells treated just prior to onset of S was ～ 12- to 16-fold higher than that observed in cells treated in early G₁ or treated in G₀ (confluence) and then plated at lower density. The frequency approximated that expected for XP12BE cells from extrapolation of data obtained at lower doses. The frequency of mutants measured in normal cells treated in exponential growth was also much higher than that in the cells treated in early G₁ or in G₀, No such difference could be seen in XP12BE cells treated in exponential growth or in G₀. In contrast to the mutagenicity data in the normal cells, there was no significant difference in the slope of the survival curve of normal cells treated at various times prior to S phase at low densities. However, normal cells treated even at the onset of S exhibited survival equal to XP12BE cells give a 4- to 5-fold lower dose. The data support the hypothesis that DNA synthesis is the cellular event which converts unexcised DNA lesions into mutations. However, they indicate that S is not the event primarily responsible for translating DNA damage into cell death. Accompanying studies on the rate of excision of anti BPDE adducts from the normal cells during the period priot to S support the conclusions.