The dependence of HNO2 mutagenesis in phage T4 on ligase and the lack of dependence of 2AP mutagenesis on repair functions

Summary A temperature sensitive ligase allele of phage T4 reduced or eliminated HNO₂ induced reversion of am mutants. Since at the temperatures used, the ligase mutant is defective in the repair of some types of lethal lesions (i.e., UV, MMS and EMS induced lesions) these results indicate that HNO₂ mutagenesis may occur through a ligase dependent repair pathway. In contrast, 2AP induced mutation was not inhibited by mutants defective in the gene 30 ligase or in genes 32, 39, 41, 44, 45, 46, 47, 49, 52, 56, 58–61 and v. This indicates that 2AP mutagenesis probably does not depend on a repair pathway in phage T4.     

An enzyme kinetics study of the pH dependence of chloride activation of oxygen evolution in photosystem II

Oxygen evolution by photosystem II (PSII) involves activation by Cl^? ion, which is regulated by extrinsic subunits PsbQ and PsbP. In this study, the kinetics of chloride activation of oxygen evolution was studied in preparations of PSII depleted of the PsbQ and PsbP subunits (NaCl-washed and Na₂SO₄/pH 7.5-treated) over a pH range from 5.3 to 8.0. At low pH, activation by chloride was followed by inhibition at chloride concentrations >100 mM, whereas at high pH activation continued as the chloride concentration increased above 100 mM. Both activation and inhibition were more pronounced at lower pH, indicating that Cl^? binding depended on protonation events in each case. The simplest kinetic model that could account for the complete data set included binding of Cl^? at two sites, one for activation and one for inhibition, and four protonation steps. The intrinsic (pH-independent) dissociation constant for Cl^? activation, K _S, was found to be 0.9 ± 0.2 mM for both preparations, and three of the four pK _as were determined, with the fourth falling below the pH range studied. The intrinsic inhibition constant, K _I, was found to be 64 ± 2 and 103 ± 7 mM for the NaCl-washed and Na₂SO₄/pH7.5-treated preparations, respectively, and is considered in terms of the conditions likely to be present in the thylakoid lumen. This enzyme kinetics analysis provides a more complete characterization of chloride and pH dependence of O₂ evolution activity than has been previously presented.     

Deletion mutagenesis during polymerase chain reaction: dependence on DNA polymerase

Polymerase chain reaction (PCR) was performed with two polymerases. Thermus aquaticus DNA polymerase (Taq), and modified T7 DNA polymerase (Sequenase). Both polymerases were used to amplify the same portion of the human 18S rRNA gene. We report a PCR artifact, namely a deletion of 54 bp, when Taq polymerase was used to amplify a portion of the human 18S rRNA gene. PCR performed with Sequenase did not produce this artifact. The deletion eliminated a potentially stable hairpin loop. Our data are consistent with the following model for generation of the deletion: (i) the formation of an intrastrand hairpin, and (ii) polymerization across the base of the hairpin, thus deleting the nucleotide sequence in the hairpin. Furthermore, we show that the deletion occurs mainly during synthesis of the (-)DNA strand. Our observations suggest that similar artifacts may occur in other sequences containing stable secondary structures.     

Effects of oxygen radical scavengers and antioxidants on phagocyte-induced mutagenesis

Phagocytic leukocytes from normal humans can produce mutations in bacteria. To define further the role of oxygen radicals in this mutagenic process, we performed experiments in which scavengers or antioxidants were added to the incubation of phagocytes and bacteria. We found that 1) superoxide dismutase, catalase, mannitol, and benzoate were all capable of inhibiting mutation, 2) sulfhydryl compounds and vitamin E were also inhibitory, and 3) the presence of vitamin C in the incubations increased the mutation frequency. These data suggest an important role for hydroxyl radicals in mediating phagocyte-induced mutations.     

gamma-Ray mutagenesis in bacteriophage T4 is not enhanced by oxygen.

As in the induction of r mutants in bacteriophage T4 by gamma-rays, the radiation-induced reversion of T4 amber mutants to wild-type was found to depend on the product of the DNA-repair gene x of the phage. Neither the efficiency of induction of r mutants nor the efficiency of reversion of ambers was enhanced by the presence of oxygen during irradiation. T4 differed in this respect from phage T7, for which no indication has been found that gamma-ray mutagenesis results from error-prone repair of DNA damage. Notwithstanding the substantial contribution of misrepair to mutation induction in T4, the efficiency of induction per base-pair observed for irradiation under oxygen was lower than that found previously for T7.     

Biphasic oxygen kinetics of cellular respiration and linear oxygen dependence of antimycin A inhibited oxygen consumption

Oxygen kinetics in fibroblasts was biphasic. This was quantitatively explained by a major mitochondrial hyperbolic component in the low-oxygen range and a linear increase of rotenone-and antimycin A-inhibited oxygen consumption in the high-oxygen range. This suggests an increased production of reactive oxygen species and oxidative stress at elevated, air-level oxygen concentrations. The high oxygen affinity of mitochondrial respiration provides the basis for the maintenance of a high aerobic scope at physiological low-oxygen levels, whereas further pronounced depression of oxygen pressure induces energetic stress under hypoxia.     

Effects of chromium(VI) and chromium(III) on energy charge and oxygen consumption in rat thymocytes

The cytotoxic effects of chromium compounds in two oxidation states have been studied in rat thymocytes. endogenous nucleotide levels and oxygen consumption were examined as relevant parameters of the physiological state of the cell. Incubation of rat thymocytes with Cr(VI) produced a marked unbalance of endogenous purine nucleotide pool and a parallel decrease in oxygen consumption. A close correlation between the reduction of oxygen consumption and ATP level in rat thymocytes treated with increasing concentrations of Cr(VI) has been found. In rat thymocytes permeabilized with digitonin and in isolated rat liver mitochondria both Cr(VI) and Cr(III) showed, at different range of concentrations, a marked inhibition of maximal oxygen consumption rate (uncoupled respiration). The effects observed were depending on chromium oxidation state and on different mitochondrial sites of substrate oxidation.     

Characteristics of mutagenesis by glyoxal in Salmonella typhimurium: contribution of singlet oxygen

The characteristics of mutagenesis by glyoxal in Salmonella tester strains TA100 and TA104, and particularly a possible role of active oxygen species, were investigated. Glyoxal was converted into a non-mutagenic chemical with glutathione (GSH) by glyoxalase I, and the mutagenic activity was enhanced by the depletion of intracellular GSH. Glyoxal caused the reduction of nitro blue tetrazolium, which was suppressed by the addition of 2,5-diphenylfuran, superoxide dismutase (SOD) and catalase (CAT), scavengers of singlet oxygen (1O2), superoxide radical (O2-) and hydrogen peroxide (H2O2), respectively. However, only the 1O2 scavenger almost completely suppressed the mutagenic activity of glyoxal. Mutagenicity assays using strains pretreated with N,N-diethyldithiocarbamate of a SOD inhibitor and strains with low levels of SOD and CAT indicated that the mutagenesis by glyoxal was independent of intracellular levels of SOD and CAT, though glyoxal itself repressed them. Therefore, all the results suggest that 1O2 formed from glyoxal is related to its mutagenesis, but that neither O2- nor H2O2 is intracellularly predominantly related to it. The action of glyoxal against SOD and CAT, and the formation of glyoxal adducts with amino acids as their components are also discussed.     

An electron paramagnetic resonance investigation of the oxygen dependence of the arterial-venous gradient of nitrosyl hemoglobin in blood circulation

Whether there is a nitrosyl hemoglobin (HbNO) gradient between the venous and the arterial parts of the circulatory system is a very controversial issue in nitric oxide research. We have carefully evaluated the measurement of HbNO concentration in blood using EPR generated in vivo by the NO donor DEANO under various oxygen tensions. We found that the absolute concentrations of HbNO in venous and arterial blood were the same within experimental error, independent of hemoglobin saturation; only the ratios of 5-coordinate and 6-coordinate HbNO differed. The HbNO concentration increased when the oxygen concentration breathed by the rats decreased in a manner that was linear in hemoglobin saturation. These results do not support the existence of an arterial-venous gradient of HbNO under our experimental conditions.     

An SOS-regulated operon involved in damage-inducible mutagenesis in Caulobacter crescentus

DNA polymerases of the Y-family, such as Escherichia coli UmuC and DinB, are specialized enzymes induced by the SOS response, which bypass lesions allowing the continuation of DNA replication. umuDC orthologs are absent in Caulobacter crescentus and other bacteria, raising the question about the existence of SOS mutagenesis in these organisms. Here, we report that the C.crescentus dinB ortholog is not involved in damage-induced mutagenesis. However, an operon composed of two hypothetical genes and dnaE2, encoding a second copy of the catalytic subunit of Pol III, is damage inducible in a recA-dependent manner, and is responsible for most ultraviolet (UV) and mitomycin C-induced mutations in C.crescentus. The results demonstrate that the three genes are required for the error-prone processing of DNA lesions. The two hypothetical genes were named imuA and imuB, after inducible mutagenesis. ImuB is similar to proteins of the Y-family of polymerases, and possibly cooperates with DnaE2 in lesion bypass. The mutations arising as a consequence of the activity of the imuAB dnaE2 operon are rather unusual for UV irradiation, including G:C to C:G transversions.     

An N-ethyl-N-nitrosourea mutagenesis screen for epigenetic mutations in the mouse

The mammalian epigenetic phenomena of X inactivation and genomic imprinting are incompletely understood. X inactivation equalizes X-linked expression between males and females by silencing genes on one X chromosome during female embryogenesis. Genomic imprinting functionally distinguishes the parental genomes, resulting in parent-specific monoallelic expression of particular genes. N-ethyl-N-nitrosourea (ENU) mutagenesis was used in the mouse to screen for mutations in novel factors involved in X inactivation. Previously, we reported mutant pedigrees identified through this screen that segregate aberrant X-inactivation phenotypes and we mapped the mutation in one pedigree to chromosome 15. We now have mapped two additional mutations to the distal chromosome 5 and the proximal chromosome 10 in a second pedigree and show that each of the mutations is sufficient to induce the mutant phenotype. We further show that the roles of these factors are specific to embryonic X inactivation as neither genomic imprinting of multiple genes nor imprinted X inactivation is perturbed. Finally, we used mice bearing selected X-linked alleles that regulate X chromosome choice to demonstrate that the phenotypes of all three mutations are consistent with models in which the mutations have affected molecules involved specifically in the choice or the initiation of X inactivation.     

An efficient one-step site-directed and site-saturation mutagenesis protocol

We have developed a new primer design method based on the QuickChange™ site-directed mutagenesis protocol, which significantly improves the PCR amplification efficiency. This design method minimizes primer dimerization and ensures the priority of primer-template annealing over primer self-pairing during the PCR. Several different multiple mutations (up to 7 bases) were successfully performed with this partial overlapping primer design in a variety of vectors ranging from 4 to 12 kb in length. In comparison, all attempts failed when using complete-overlapping primer pairs as recommended in the standard QuickChange™ protocol. Our protocol was further extended to site-saturation mutagenesis by introducing randomized codons. Our data indicated no specific sequence selection during library construction, with the randomized positions resulting in average occurrence of each base in each position. This method should be useful to facilitate the preparation of high-quality site saturation libraries.     

An approach to analyzing UV mutagenesis in E. coli

UV mutagenesis of single-strand DNA phage can be divided into three types: induced untargeted; induced targeted; and uninduced targeted. We report the development of new tools to determine the number of processes which contribute to these types of mutagenesis. An E. coli tRNA gene, glyU, has been cloned using M13 derivatives mp8 and mp9 as vectors. The nucleotide sequence of glyU and its flanking regions is presented. In this paper, phage glyU anticodon mutants are detected by their ability to suppress GAA and GAT missense mutations in trpA. We used phage carrying GAG and CTC at the anticodon position and found results consistent with the hypothesis that two processes act to produce the transition to GAA suppression: an uninduced regionally targeted process; and an induced locally targeted process with some untargeted activity. The transversion frequency to GAT suppression on the other hand responded as if only an uninduced locally targeted process was involved. Thus, we hypothesize that the new tools have discriminated three different processes of mutagenesis and we discuss further work designed to test this hypothesis.     

Speciation of chromium in chromium yeast

High-performance liquid chromatography was used to separate Cr(III) and Cr(VI) in samples with detection by inductively coupled plasma mass spectrometry(ICP-MS). The separation was achieved on a weak anion exchange column. The mobile phase was pH 7.0 ammonium nitrate solution. The redox reaction between Cr(III) and Cr(VI) was avoided during separation and determination. This separation method could be used to separate the samples with large concentration differences between Cr(III) and Cr(VI). The alkaline digestion was used to extract chromium in solid sample, which had no effect on the retention time and the peak area of the Cr(VI). However, the conversion of Cr(VI) from Cr(III) was observed during alkaline digestion, which displayed positive relation with the ratio of Cr(III) and Cr(VI) in samples. Both Cr(III) and Cr(VI) contents of chromium yeasts cultured in media with different chromium additions were determined. The spike recoveries of Cr(VI) for chromium yeasts were in the range of 95–108 %.     

Parameter dependence of myoglobin-facilitated transport of oxygen in the presence of membranes

Some physicochemical entities involved in the facilitated transport of oxygen along a transport path z1 less than or equal to z less than or equal to zn with membranes impermeable to myoglobin at zi, i = 1,...,n, were identified in an earlier paper [Math. Biosci. 95:209 (1989)]. These entities are the partition between the oxygen and oxymyoglobin flows, the flow transfers taking place near a membrane, and the membrane resistance. Expressions for these entities were obtained that explicitly involve the parameters of the system. In this paper, for the case of prescribed boundary oxygen concentrations x1 and xn, these expressions are incorporated into (i) an explicit representation for the facilitated transport value in terms of the difference, E(x1)-E(xn), between the boundary oxymyoglobin equilibrium values and the sum, gamma, of the membrane resistances, and (ii) a representation for the distribution of the membrane oxygen concentrations xi at zi, i = 2,...,n-1. This makes it possible to analyze the manner in which the facilitated transport depends on the parameters. For a physiological range of parameter values, the facilitated transport was found to increase as either the oxygen-myoglobin association rate constant k', the dissociation rate constant k, the oxygen diffusion coefficient, or the oxymyoglobin diffusion coefficient increases. Thus, the facilitated transport does not depend directly on ratios of chemical and diffusion coefficients. Although the increase in the oxygen diffusion coefficient does not per se affect the chemical conductance, it diminishes the membrane resistance through an interface feature, with a resulting increase in the facilitated transport. For a larger range of values of k' and k, the dependences of the facilitated transport on k' and on k are both biphasic and are similar in shape. However, the mechanisms involved are different: The associated changes in E(x1)-E(xn) and in gamma that result from the increase in k' are opposite to those that result from an increase in k. The use of (i) and (ii) permits, also, discrimination between the different roles of the physicochemical entities involved in a given facilitated transport change. In some cases (e.g., the decreasing phase of the facilitated transport as k' increases), this change depends in an essential manner on a secondary modification of the profile xi, i = 1,...,n, along the transport path.     

An insertional mutagenesis approach to Dictyostelium cell death

Programmed cell death (PCD) in Dictyostelium shows a pattern of ordered degeneration similar to that observed in higher eukaryotes but somewhat different from the most studied form of PCD, i.e. apoptosis. To contribute to a genetic definition of this process, Dictyostelium HMX44A cells have been subjected to insertional mutagenesis, followed by selection based on several rounds of differentiation/regrowth to recover only cells resistant to death. We describe here the approach used, a partial characterization of the first mutant thus obtained called C5 showing some dissociation of cell death signs, and, in this case where plasmid rescue was not possible, as a first step towards identification of the gene at play recovery of genomic flanking sequences via genomic recircularization and PCR. This work demonstrates the feasibility of an insertional mutagenesis approach to obtain death-resistant mutants in Dictyostelium.