Jacques Laval

Chemical biology of nitric oxide: Regulation and protective and toxic mechanisms

Publisher Summary This chapter discusses the important aspects of the solution chemistry of nitrogen oxide (NO) and reactive nitrogen oxide species (RNOS), biochemical targets of NO and intermediates in the autoxidation (NO X ), and the effect of NO in the presence of other toxic molecules, such as reactive oxygen species (ROS). There are two types of nitric-oxide synthase: constitutive (cNOS) and inducible (iNOS). Since cNOS generates low levels of NO, direct effects rather than indirect effects of NO would be particularly relevant. In case of iNOS, considerably higher concentrations of NO are formed for longer periods of time; therefore, both direct and indirect effects could be relevant. This chapter discusses, from a chemical perspective, those processes that are involved in the interactions with key cellular components as well as detoxification and control of NO in vivo . Defining the chemical, biochemical, and cellular pathways of NO quantitatively can provide insights into the role that NO plays in the etiology of various diseases that in turn can provide a basis for the development of new therapeutic agents. The chemical biology of NO will provide the understanding as to how NO can be regulatory, toxic, and protective in biological systems.

Formamidopyrimidine-DNA glycosylase of Escherichia coli: cloning and sequencing of the fpg structural gene and overproduction of the protein

An Escherichia coli genomic library composed of large DNA fragments (10‐15 kb) was constructed using the plasmid pBR322 as vector. From it 700 clones were individually screened for increased excision of the ring‐opened form of N7‐methylguanine (2‐6‐diamino‐4‐hydroxy‐5N‐methyl‐formamidopyrimidine) or Fapy. One clone overproduced the Fapy‐DNA glycosylase activity by a factor of 10‐fold as compared with the wild‐type strain. The Fapy‐DNA glycosylase overproducer character was associated with a 15‐kb recombinant plasmid (pFPG10). After subcloning a 1.4‐kb fragment which contained the Fapy‐DNA glycosylase gene (fpg+) was inserted in the plasmids pUC18 and pUC19 yielding pFPG50 and pFPG60 respectively. The cells harbouring pFPG60 displayed a 50‐ to 100‐fold increase in glycosylase activity and overexpressed a 31‐kd protein. From these cells the Fapy‐DNA glycosylase was purified to apparent physical homogeneity as evidenced by a single protein band at 31 kd on SDS‐polyacrylamide gels. The amino acid composition of the protein and the amino acid sequence deduced from the nucleotide sequence demonstrate that the cloned fragment contains the structural gene coding for the Fapy‐DNA glycosylase. The nucleotide sequence of the fpg gene is composed of 809 base pairs and codes for a protein of 269 amino acids with a calculated mol. wt of 30.2 kd.

Clustered DNA Damages Induced by X Rays in Human Cells

Abstract Sutherland, B. M., Bennett, P. V., Sutherland, J. C. and Laval, J. Clustered DNA Damages Induced by X Rays in Human Cells. Radiat. Res. 157, 611–616 (2002). Although DNA DSBs are known to be important in producing the damaging effects of ionizing radiation in cells, bistranded clustered DNA damages—two or more oxidized bases, abasic sites or strand breaks on opposing DNA strands within a few helical turns—are postulated to be difficult to repair and thus to be critical radiation-induced lesions. Gamma rays can induce clustered damages in DNA in solution, and high-energy iron ions produce DSBs and oxidized pyrimidine clusters in human cells, but it was not known whether sparsely ionizing radiation can produce clustered damages in mammalian cells. We show here that X rays induce abasic clusters, oxidized pyrimidine clusters, and oxidized purine clusters in DNA in human cells. Non-DSB clustered damages comprise about 70% of the complex lesions produced in cells. The relative levels of specific cluster classes depend on the environment of the DNA.

Enzymology of the repair of free radicals-induced DNA damage.

A number of intrinsic and extrinsic mutagens induce structural damage in cellular DNA. These DNA damages are cytotoxic, miscoding or both and are believed to be at the origin of cell lethality, tissue degeneration, ageing and cancer. In order to counteract immediately the deleterious effects of such lesions, leading to genomic instability, cells have evolved a number of DNA repair mechanisms including the direct reversal of the lesion, sanitation of the dNTPs pools, mismatch repair and several DNA excision pathways including the base excision repair (BER) nucleotide excision repair (NER) and the nucleotide incision repair (NIR). These repair pathways are universally present in living cells and extremely well conserved. This review is focused on the repair of lesions induced by free radicals and ionising radiation. The BER pathway removes most of these DNA lesions, although recently it was shown that other pathways would also be efficient in the removal of oxidised bases. In the BER pathway the process is initiated by a DNA glycosylase excising the modified and mismatched base by hydrolysis of the glycosidic bond between the base and the deoxyribose of the DNA, generating a free base and an abasic site (AP-site) which in turn is repaired since it is cytotoxic and mutagenic.

Human cDNA expressing a functional DNA glycosylase excising 3-methyladenine and 7-methylguanine

A cDNA expression library from a human cell line was introduced into an E. coli strain deficient in the repair of 3-meAde bases in DNA. E. coli strains deficient in the repair of 3-meAde are unusually sensitive to DNA methylating agents. A plasmid pANPG10 (Alkyl-N-Purine-DNA Glycosylase) was rescued from the library based on its ability to reduce the sensitivity of the mutant strain to methylmethane sulfonate. Crude extracts of the E. coli mutant strain hosting the plasmid pANPG10 release both 3-meAde and 7-meGua from DNA. The longest open reading frame in the sequence codes for a polypeptide of 230 amino acids of molecular weight 25.5 kD, with a pI of 9.1. The derived amino acid sequence of the human 3-meAde-DNA glycosylase has 85% sequence identity with the 3-meAde-DNA glycosylase from rat hepatoma cells.

Two rotameric forms of open ring 7-methylguanine are present in alkylated polynucleotides.

High performance liquid chromatography analysis of imidazole open ring 7-methylguanine, 2-6 diamino-4-hydroxy-5N-methyl-formamidopyrimidine (rom7G), showed two well-separated peaks (fI and fII) of the same magnitude. Rechromatography of each isolated component indicated that they are slowly interconverted to give a 1:1 mixture. NMR analysis demonstrated that the two species observed on reversed phase HPLC are rotational isomers. Thermodynamic measurements strongly suggested that the equilibrium can be assigned to rotation around the N-methyl formamido bond. The two species, fI and fII, separated by HPLC were identified as rotamers E and Z, respectively. The structures of fI and fII were also determined. A polynucleotide containing rom7G was obtained by alkaline treatment of poly (dGC) containing 7-methylguanine. In order to study its structure within the polynucleotide, rom7G was enzymatically excized by E.coli rom7G-DNA glycosylase. The analysis of the products released by the enzyme showed a 1:4 mixture of the two rotamers favoring the Z form (fII).

Specific Binding of a Designed Pyrrolidine Abasic Site Analog to Multiple DNA Glycosylases

In the base excision DNA repair pathway, DNA glycosylases recognize damaged bases in DNA and catalyze their excision through hydrolysis of the N-glycosidic bond. Attempts to understand the structural basis for DNA damage recognition by DNA glycosylases have been hampered by the short-lived association of these enzymes with their DNA substrates. To overcome this problem, we have employed an approach involving the design and synthesis of inhibitors that form stable complexes with DNA glycosylases, which can then be studied biochemically and structurally. We have previously reported that double-stranded DNA containing a pyrrolidine abasic site analog (PYR) forms an extremely stable complex with the DNA glycosylase AlkA and potently inhibits the reaction catalyzed by the enzyme (Schärer, O. D., Ortholand, J.-Y., Ganesan, A., Ezaz-Nikpay, K., and Verdine, G. L. (1995) J. Am. Chem. Soc.117, 6623–6624). Here we investigate the interaction of this inhibitor with a variety of additional DNA glycosylases. With the exception of uracil DNA glycosylase all the glycosylases tested bind specifically to PYR-containing oligonucleotides. By comparing the interaction of DNA glycosylases with PYR and the structurally related tetrahydrofuran abasic site analog, we assess the importance of the positively charged ammonium group of the pyrrolidine in binding to the active site of these enzymes. Such a general inhibitor of DNA glycosyases provides a valuable tool to study stable complexes of these enzymes bound to substrate-like molecules.

Imidazole open ring 7-methylguanine : An inhibitor of DNA synthesis

Guanine methylated at the N7 position (me7G) is susceptible to cleavage of the imidazole ring yielding: 2,6-diamino-4-hydroxy-5N-methyl-formamidopyrimidine (rom7G). DNA synthesis catalysed by E.coli DNA polymerase I, using as templates poly(dGC) containing either me7G or rom7G, show that rom7G blocks DNA chain elongation. It implies a potential killing effect. Furthermore rom7G does not induce mispairing with either dAMP or dTMP. me7G does not affect DNA synthesis. The results suggest that, beside AP-sites, rom7G is a potential killing lesion in cells treated by alkylating agents.

A discussion of mechanisms of NO genotoxicty: Implication of inhibition of DNA repair proteins

The involvement of NO in genotoxicity and carcinogenic mechanisms may be varied. On one hand NO can form RNOS which can modify DNA. Most of these experiments were done under very high concentrations of NO and RNOS and may have little or nothing to do with in vivo mechanisms. However, NO can affect DNA specific repair systems even in whole cells at lower NO and RNOS concentrations which might enhance the damage of another agent. Though NO might alter DNA directly, the most likely involvement of its genotoxic action is through the increase in sensitivity to other mutagenic agents. From this discussion, it appears that the primary source of RNOS is from iNOS. Thus genotoxicity either by direct chemical alteration of DNA or interference with the repair system would be from an iNOS source.

Gene-specific nuclear and mitochondrial repair of formamidopyrimidine DNA glycosylase-sensitive sites in Chinese hamster ovary cells

This study examines the capacity of a mammalian cell to repair, at the gene level, DNA base lesions generated by photoactivation of acridine orange. Chinese hamster ovary fibroblasts were exposed to acridine orange and visible light, and gene-specific DNA repair was measured in the dihydrofolate reductase (DHFR) gene and in the mitochondrial genome. DNA lesions were recognized by Escherichia coli formamidepyrimidine-DNA glycosylase (FPG) which removes predominantly 8-oxodG and the corresponding formamidopyrimidine ring opened bases, and subsequently cleaves the DNA at the resulting apurinic site. FPG-recognized DNA lesions increased linearly with increasing photo-activation of AO, while cell survival was not affected by light alone and was negligibly affected by preincubation with AO in the dark. The frequency of induction of FPG-sensitive DNA damage by photoactivation of AO was similar in the transcribed and non-transcribed nuclear DNA as well as in the mitochondrial DNA. FPG-sensitive sites in the DHFR gene were repaired quickly, with 84% of adducts repaired within 4 h. The lesion frequency, kinetics and percent of repair of non-transcribed genomic DNA did not differ significantly from repair in the active DHFR gene up to 1 h postexposure. At late time points, transcribed DNA was repaired faster than the non-transcribed DNA. Mitochondrial DNA was efficiently repaired, at a rate similar to that in the active nuclear DNA.