The Experts below are selected from a list of 1968 Experts worldwide ranked by ideXlab platform

Erling Seeberg - One of the best experts on this subject based on the ideXlab platform.

  • alkb mediated oxidative demethylation reverses DNA damage in escherichia coli
    Nature, 2002
    Co-Authors: Pal O Falnes, Rune F Johansen, Erling Seeberg
    Abstract:

    The bacterial AlkB protein is known to be involved in cellular recovery from alkylation damage; however, the function of this protein remains unknown. AlkB homologues have been identified in several organisms, including humans, and a recent sequence alignment study has suggested that these proteins may belong to a superfamily of 2-oxoglutarate-dependent and iron-dependent oxygenases (2OG-Fe(ii)-oxygenases)1. Here we show that AlkB from Escherichia coli is indeed a 2-oxoglutarate-dependent and iron-dependent DNA repair enzyme that releases replication blocks in Alkylated DNA by a mechanism involving oxidative demethylation of 1-methyladenine residues. This mechanism represents a new pathway for DNA repair and the third type of DNA damage reversal mechanism so far discovered.

  • excision of 3 methylguanine from Alkylated DNA by 3 methyladenine DNA glycosylase i of escherichia coli
    Nucleic Acids Research, 1993
    Co-Authors: Svein Bjelland, Magnar Bjoras, Erling Seeberg
    Abstract:

    Escherichia coli has two DNA glycosylases for repair of DNA damage caused by simple alkylating agents. The inducible AlkA DNA glycosylase (3-methyladenine [m3A] DNA glycosylase II) removes several different Alkylated bases including m3A and 3-methylguanine (m3G) from DNA, whereas the constitutively expressed Tag enzyme (m3A DNA glycosylase I) has appeared to be specific for excision of m3A. In this communication we have reexamined the substrate specificity of Tag by using synthetic DNA rich in GC base pairs to facilitate detection of any possible methyl-G removal. In such DNA Alkylated with [3H]dimethyl sulphate, we found that m3G was excised from double-stranded DNA by both glycosylases, although more efficiently by AlkA than by Tag. This was further confirmed using both N-[3H]methyl-N-nitrosourea- and [3H]dimethyl sulphate-treated native DNA, from which Tag excised m3G with an efficiency that was about 70 times lower than for AlkA. These results can explain the previous observation that high levels of Tag expression will suppress the alkylation sensitivity of alkA mutant cells, further implying that m3G is formed in quantity sufficient to represent an important cytotoxic lesion if left unrepaired in cells exposed to alkylating agents.

Carsten Krebs - One of the best experts on this subject based on the ideXlab platform.

  • mechanism of taurine α ketoglutarate dioxygenase taud from escherichia coli
    European Journal of Inorganic Chemistry, 2005
    Co-Authors: Martin J Bollinger, John C Price, Lee M Hoffart, Eric W Barr, Carsten Krebs
    Abstract:

    The iron(II)- and α-ketoglutarate-dependent dioxygenases comprise enzymes that catalyze a variety of important reactions in biology, including steps in the biosynthesis of collagen and antibiotics, the degradation of xenobiotics, the repair of Alkylated DNA, and the sensing of oxygen and response to hypoxia. In these reactions, the reductive activation of oxygen is coupled to hydroxylation of the substrate and decarboxylation of the co-substrate, α-ketoglutarate. It is believed that a single, conserved mechanistic pathway for formation of a high-valent iron intermediate that attacks the substrate is operant in all members of this family. Application

  • the first direct characterization of a high valent iron intermediate in the reaction of an α ketoglutarate dependent dioxygenase a high spin fe iv complex in taurine α ketoglutarate dioxygenase taud from escherichia coli
    Biochemistry, 2003
    Co-Authors: John C Price, Martin J Bollinger, Eric W Barr, Bhramara Tirupati, Carsten Krebs
    Abstract:

    The Fe(II)- and α-ketoglutarate(αKG)-dependent dioxygenases have roles in synthesis of collagen and sensing of oxygen in mammals, in acquisition of nutrients and synthesis of antibiotics in microbes, and in repair of Alkylated DNA in both. A consensus mechanism for these enzymes, involving (i) addition of O2 to a five-coordinate, (His)2(Asp)-facially coordinated Fe(II) center to which αKG is also bound via its C-1 carboxylate and ketone oxygen; (ii) attack of the uncoordinated oxygen of the bound O2 on the ketone carbonyl of αKG to form a bicyclic Fe(IV)-peroxyhemiketal complex; (iii) decarboxylation of this complex concomitantly with formation of an oxo-ferryl (Fe(IV)O2-) intermediate; and (iv) hydroxylation of the substrate by the Fe(IV)O2- complex via a substrate radical intermediate, has repeatedly been proposed, but none of the postulated intermediates occurring after addition of O2 has ever been detected. In this work, an oxidized Fe intermediate in the reaction of one of these enzymes, taurine/α-ke...

Leona D. Samson - One of the best experts on this subject based on the ideXlab platform.

  • inflammation necrosis and the kinase rip3 are key mediators of aag dependent alkylation induced retinal degeneration
    Science Signaling, 2019
    Co-Authors: Mariacarmela Allocca, Joshua J Corrigan, Aprotim Mazumder, Kimberly R Fake, Leona D. Samson
    Abstract:

    DNA-alkylating agents are commonly used to kill cancer cells, but the base excision repair (BER) pathway they trigger can also produce toxic intermediates that cause tissue damage, such as retinal degeneration (RD). Apoptosis, a process of programmed cell death, is assumed to be the main mechanism of this alkylation-induced photoreceptor (PR) cell death in RD. Here, we studied the involvement of necroptosis (another programmed cell death process) and inflammation in alkylation-induced RD. Male mice exposed to a methylating agent exhibited a reduced number of PR cell rows, active gliosis, and cytokine induction and macrophage infiltration in the retina. Dying PRs exhibited a necrotic morphology, increased 8-hydroxyguanosine abundance (an oxidative damage marker), and overexpression of the necroptosis-associated genes Rip1 and Rip3 The activity of PARP1, which mediates BER, cell death, and inflammation, was increased in PR cells and associated with the release of proinflammatory chemokine HMGB1 from PR nuclei. Mice lacking the anti-inflammatory cytokine IL-10 exhibited more severe RD, whereas deficiency of RIP3 (also known as RIPK3) conferred partial protection. Female mice were partially protected from alkylation-induced RD, showing reduced necroptosis and inflammation compared to males. PRs in mice lacking the BER-initiating DNA glycosylase AAG did not exhibit alkylation-induced necroptosis or inflammation. Our findings show that AAG-initiated BER at Alkylated DNA bases induces sex-dependent RD primarily by triggering necroptosis and activating an inflammatory response that amplifies the original damage and, furthermore, reveal new potential targets to prevent this side effect of chemotherapy.

  • cloning and characterization of a mouse 3 methyladenine 7 methl guanine methylguanine DNA glycosylase cDNA whose gene maps to chromosme 11
    Carcinogenesis, 1993
    Co-Authors: Bevin P. Engelward, Michael S. Boosalis, Zuoming Deng, Beiru J Chen, Michael J Siciliano, Leona D. Samson
    Abstract:

    : In Escherichia coli, the repair of 3-methyladenine (3MeA) DNA lesions by DNA glycosylases prevents alkylation induced cell death. We described previously the isolation of a human 3MeA DNA glycosylase (AAG) cDNA that maps to chromosome 16 and hybridizes to specific genomic DNA fragments from a number of mammals, including mouse. As a first step in the generation of a 3MeA DNA glycosylase deficient mouse by homologous replacement in embryonic stem cells, we have cloned the mouse 3MeA DNA glycosylase cDNA. The cloned 1095 base pair cDNA contains a complete 333 amino acid open reading frame that predicts a 36.5 kDa protein and hybridizes to a 1.5 kb mRNA transcript. Mouse 3MeA DNA glycosylase (Aag) transcript levels vary by up to 21 fold among tissues, being highest in the testes and lowest in the heart. The Aag cDNA encodes a glycosylase able to release 3MeA, 7-methylguanine (7MeG) and 3-methylguanine (3MeG) from Alkylated DNA. The expression of Aag in E. coli provides substantial resistance against killing by methylating agents, but, unlike its E. coli counterparts, the Aag glycosylase fails to protect against killing by ethylating and propylating agents. A 232 amino acid stretch of the predicted mouse protein shares extensive amino acid identity with rat (93%) and human (83%) 3MeA DNA glycosylases and we observe that all three mammalian glycosylases have a bipartite nuclear localization signal. The Aag gene maps to mouse chromosome 11, suggesting a segment of conserved synteny between mouse chromosome 11 and human chromosome 16, which bears the human 3MeA DNA glycosylase gene. Cloning the mouse 3MeA DNA glycosylase cDNA is a step toward understanding the role of this DNA repair enzyme in mammals.

  • cloning and characterization of a 3 methyladenine DNA glycosylase cDNA from human cells whose gene maps to chromosome 16
    Proceedings of the National Academy of Sciences of the United States of America, 1991
    Co-Authors: Leona D. Samson, Michael S. Boosalis, Bruce Derfler, Katherine M Call
    Abstract:

    We described previously the isolation of a Saccharomyces cerevisiae 3-methyladenine (3-MeAde) DNA glycosylase repair gene (MAG) by its expression in glycosylase-deficient Escherichia coli alkA tag mutant cells and its ability to rescue these cells from the toxic effects of alkylating agents. Here we extend this cross-species functional complementation approach to the isolation of a full-length human 3-MeAde DNA glycosylase cDNA that rescues alkA tag E. coli from killing by methyl methanesulfonate, and we have mapped the gene to human chromosome 16. The cloned cDNA, expressed from the pBR322 beta-lactamase promoter, contains an 894-base-pair open reading frame encoding a 32,894-Da protein able to release 3-MeAde, but not 7-methylguanine, from Alkylated DNA. Surprisingly, the predicted human protein does not share significant amino acid sequence homology with the bacterial AlkA and Tag glycosylases or the yeast MAG glycosylase, but it does share extensive amino acid sequence homology with a rat 3-MeAde DNA glycosylase and significant DNA sequence homology with genes from several mammalian species. The cloning of a human 3-MeAde DNA glycosylase cDNA represents a key step in generating 3-MeAde repair-deficient cells and the determination of the in vivo role of this DNA repair enzyme in protecting against the toxic and carcinogenic effects of alkylating agents.

Elzbieta Grzesiuk - One of the best experts on this subject based on the ideXlab platform.

  • inducible repair of Alkylated DNA in microorganisms
    Mutation Research-reviews in Mutation Research, 2015
    Co-Authors: Damian Mielecki, Michal Wrzesinski, Elzbieta Grzesiuk
    Abstract:

    Alkylating agents, which are widespread in the environment, also occur endogenously as primary and secondary metabolites. Such compounds have intrinsically extremely cytotoxic and frequently mutagenic effects, to which organisms have developed resistance by evolving multiple repair mechanisms to protect cellular DNA. One such defense against alkylation lesions is an inducible Adaptive (Ada) response. In Escherichia coli, the Ada response enhances cell resistance by the biosynthesis of four proteins: Ada, AlkA, AlkB, and AidB. The glycosidic bonds of the most cytotoxic lesion, N3-methyladenine (3meA), together with N3-methylguanine (3meG), O(2)-methylthymine (O(2)-meT), and O(2)-methylcytosine (O(2)-meC), are cleaved by AlkA DNA glycosylase. Lesions such as N1-methyladenine (1meA) and N3-methylcytosine (3meC) are removed from DNA and RNA by AlkB dioxygenase. Cytotoxic and mutagenic O(6)-methylguanine (O(6)meG) is repaired by Ada DNA methyltransferase, which transfers the methyl group onto its own cysteine residue from the methylated oxygen. We review (i) the individual Ada proteins Ada, AlkA, AlkB, AidB, and COG3826, with emphasis on the ubiquitous and versatile AlkB and its prokaryotic and eukaryotic homologs; (ii) the organization of the Ada regulon in several bacterial species; (iii) the mechanisms underlying activation of Ada transcription. In vivo and in silico analysis of various microorganisms shows the widespread existence and versatile organization of Ada regulon genes, including not only ada, alkA, alkB, and aidB but also COG3826, alkD, and other genes whose roles in repair of Alkylated DNA remain to be elucidated. This review explores the comparative organization of Ada response and protein functions among bacterial species beyond the classical E. coli model.

  • ada response a strategy for repair of Alkylated DNA in bacteria
    Fems Microbiology Letters, 2014
    Co-Authors: Damian Mielecki, Elzbieta Grzesiuk
    Abstract:

    Alkylating agents are widespread in the environment and also occur endogenously. They can be cytotoxic or mutagenic to the cells introducing Alkylated bases to DNA or RNA. All organisms have evolved multiple DNA repair mechanisms to counteract the effects of DNA alkylation: the most cytotoxic lesion, N3-methyladenine (3meA), is excised by AlkA glycosylase initiating base excision repair (BER); toxic N1-methyladenine (1meA) and N3-methylcytosine (3meC), induced in DNA and RNA, are removed by AlkB dioxygenase; and mutagenic and cytotoxic O6-methylguanine (O6meG) is repaired by Ada methyltransferase. In Escherichia coli, Ada response involves the expression of four genes, ada, alkA, alkB, and aidB, encoding respective proteins Ada, AlkA, AlkB, and AidB. The Ada response is conserved among many bacterial species; however, it can be organized differently, with diverse substrate specificity of the particular proteins. Here, an overview of the organization of the Ada regulon and function of individual proteins is presented. We put special effort into the characterization of AlkB dioxygenases, their substrate specificity, and function in the repair of alkylation lesions in DNA/RNA.

  • Bacterial DNA repair genes and their eukaryotic homologues: 3. AlkB dioxygenase and Ada methyltransferase in the direct repair of Alkylated DNA.
    Polskie Towarzystwo Biochemiczne (Polish Biochemical Society), 2007
    Co-Authors: Jadwiga Nieminuszczy, Elzbieta Grzesiuk
    Abstract:

    Environmental and endogenous alkylating agents generate cytotoxic and mutagenic lesions in DNA. Exposure of prokaryotic cells to sublethal doses of DNA alkylating agents induces so called adaptive response (Ada response) involving the expression of a set of genes which allows the cells to tolerate the toxic and mutagenic action of such agents. The Ada response includes the expression of four genes: ada, alkA, alkB, and aidB. The product of ada gene, Ada protein, is an activator of transcription of all four genes. DNA bases damaged by alkylation are removed by distinct strategies. The most toxic lesion 3meA is removed by specific DNA glycosylase initiating base excising repair. The toxic and mutagenic O6meG is repaired directly by methyltransferases. 1meA and 3meC are corrected by AlkB DNA dioxygenase. The mechanisms of action of E. coli AlkB dioxygenase and its human homologs ABH2 and ABH3 are described in more details.

Martin J Bollinger - One of the best experts on this subject based on the ideXlab platform.

  • mechanism of taurine α ketoglutarate dioxygenase taud from escherichia coli
    European Journal of Inorganic Chemistry, 2005
    Co-Authors: Martin J Bollinger, John C Price, Lee M Hoffart, Eric W Barr, Carsten Krebs
    Abstract:

    The iron(II)- and α-ketoglutarate-dependent dioxygenases comprise enzymes that catalyze a variety of important reactions in biology, including steps in the biosynthesis of collagen and antibiotics, the degradation of xenobiotics, the repair of Alkylated DNA, and the sensing of oxygen and response to hypoxia. In these reactions, the reductive activation of oxygen is coupled to hydroxylation of the substrate and decarboxylation of the co-substrate, α-ketoglutarate. It is believed that a single, conserved mechanistic pathway for formation of a high-valent iron intermediate that attacks the substrate is operant in all members of this family. Application

  • the first direct characterization of a high valent iron intermediate in the reaction of an α ketoglutarate dependent dioxygenase a high spin fe iv complex in taurine α ketoglutarate dioxygenase taud from escherichia coli
    Biochemistry, 2003
    Co-Authors: John C Price, Martin J Bollinger, Eric W Barr, Bhramara Tirupati, Carsten Krebs
    Abstract:

    The Fe(II)- and α-ketoglutarate(αKG)-dependent dioxygenases have roles in synthesis of collagen and sensing of oxygen in mammals, in acquisition of nutrients and synthesis of antibiotics in microbes, and in repair of Alkylated DNA in both. A consensus mechanism for these enzymes, involving (i) addition of O2 to a five-coordinate, (His)2(Asp)-facially coordinated Fe(II) center to which αKG is also bound via its C-1 carboxylate and ketone oxygen; (ii) attack of the uncoordinated oxygen of the bound O2 on the ketone carbonyl of αKG to form a bicyclic Fe(IV)-peroxyhemiketal complex; (iii) decarboxylation of this complex concomitantly with formation of an oxo-ferryl (Fe(IV)O2-) intermediate; and (iv) hydroxylation of the substrate by the Fe(IV)O2- complex via a substrate radical intermediate, has repeatedly been proposed, but none of the postulated intermediates occurring after addition of O2 has ever been detected. In this work, an oxidized Fe intermediate in the reaction of one of these enzymes, taurine/α-ke...