The Experts below are selected from a list of 14013 Experts worldwide ranked by ideXlab platform
Youri I Pavlov - One of the best experts on this subject based on the ideXlab platform.
-
disruption of transcriptional coactivator sub1 leads to genome wide re distribution of clustered mutations induced by apobec in active yeast genes
PLOS Genetics, 2015Co-Authors: Artem G Lada, Igor B. Rogozin, Sergei Kliver, Alok Dhar, Dmitrii E Polev, Alexey Masharsky, Youri I PavlovAbstract:Mutations in genomes of species are frequently distributed non-randomly, resulting in mutation clusters, including recently discovered kataegis in tumors. DNA editing deaminases play the prominent role in the etiology of these mutations. To gain insight into the enigmatic mechanisms of localized hypermutagenesis that lead to cluster formation, we analyzed the mutational single nucleotide variations (SNV) data obtained by whole-genome sequencing of drug-resistant mutants induced in yeast diploids by AID/APOBEC deaminase and Base Analog 6-HAP. Deaminase from sea lamprey, PmCDA1, induced robust clusters, while 6-HAP induced a few weak ones. We found that PmCDA1, AID, and APOBEC1 deaminases preferentially mutate the beginning of the actively transcribed genes. Inactivation of transcription initiation factor Sub1 strongly reduced deaminase-induced can1 mutation frequency, but, surprisingly, did not decrease the total SNV load in genomes. However, the SNVs in the genomes of the sub1 clones were re-distributed, and the effect of mutation clustering in the regions of transcription initiation was even more pronounced. At the same time, the mutation density in the protein-coding regions was reduced, resulting in the decrease of phenotypically detected mutants. We propose that the induction of clustered mutations by deaminases involves: a) the exposure of ssDNA strands during transcription and loss of protection of ssDNA due to the depletion of ssDNA-binding proteins, such as Sub1, and b) attainment of conditions favorable for APOBEC action in subpopulation of cells, leading to enzymatic deamination within the currently expressed genes. This model is applicable to both the initial and the later stages of oncogenic transformation and explains variations in the distribution of mutations and kataegis events in different tumor cells.
-
itpa inosine triphosphate pyrophosphatase from surveillance of nucleotide pools to human disease and pharmacogenetics
Mutation Research-reviews in Mutation Research, 2013Co-Authors: Peter D Simone, Youri I Pavlov, Gloria E. O. BorgstahlAbstract:Abstract Cellular nucleotide pools are often contaminated by Base Analog nucleotides which interfere with a plethora of biological reactions, from DNA and RNA synthesis to cellular signaling. An evolutionarily conserved inosine triphosphate pyrophosphatase (ITPA) removes the non-canonical purine (d)NTPs inosine triphosphate and xanthosine triphosphate by hydrolyzing them into their monophosphate form and pyrophosphate. Mutations in the ITPA orthologs in model organisms lead to genetic instability and, in mice, to severe developmental anomalies. In humans there is genetic polymorphism in ITPA. One allele leads to a proline to threonine substitution at amino acid 32 and causes varying degrees of ITPA deficiency in tissues and plays a role in patients’ response to drugs. Structural analysis of this mutant protein reveals that the protein is destabilized by the formation of a cavity in its hydrophobic core. The Pro32Thr allele is thought to cause the observed dominant negative effect because the resulting active enzyme monomer targets both homo- and heterodimers to degradation.
-
genome wide mutation avalanches induced in diploid yeast cells by a Base Analog or an apobec deaminase
PLOS Genetics, 2013Co-Authors: Artem G Lada, Igor B. Rogozin, Alok Dhar, Vladimir N Noskov, Elena I Stepchenkova, Irina S R Waisertreiger, James D Eudy, Robert Boissy, Masayuki Hirano, Youri I PavlovAbstract:Genetic information should be accurately transmitted from cell to cell; conversely, the adaptation in evolution and disease is fueled by mutations. In the case of cancer development, multiple genetic changes happen in somatic diploid cells. Most classic studies of the molecular mechanisms of mutagenesis have been performed in haploids. We demonstrate that the parameters of the mutation process are different in diploid cell populations. The genomes of drug-resistant mutants induced in yeast diploids by Base Analog 6-hydroxylaminopurine (HAP) or AID/APOBEC cytosine deaminase PmCDA1 from lamprey carried a stunning load of thousands of unselected mutations. Haploid mutants contained almost an order of magnitude fewer mutations. To explain this, we propose that the distribution of induced mutation rates in the cell population is uneven. The mutants in diploids with coincidental mutations in the two copies of the reporter gene arise from a fraction of cells that are transiently hypersensitive to the mutagenic action of a given mutagen. The progeny of such cells were never recovered in haploids due to the lethality caused by the inactivation of single-copy essential genes in cells with too many induced mutations. In diploid cells, the progeny of hypersensitive cells survived, but their genomes were saturated by heterozygous mutations. The reason for the hypermutability of cells could be transient faults of the mutation prevention pathways, like sanitization of nucleotide pools for HAP or an elevated expression of the PmCDA1 gene or the temporary inability of the destruction of the deaminase. The hypothesis on spikes of mutability may explain the sudden acquisition of multiple mutational changes during evolution and carcinogenesis.
-
hypersensitivity of escherichia coli δ uvrb bio mutants to 6 hydroxylaminopurine and other Base Analogs is due to a defect in molybdenum cofactor biosynthesis
Journal of Bacteriology, 2000Co-Authors: Stanislav G Kozmin, Youri I Pavlov, Ronnie L Dunn, Roel M SchaaperAbstract:The biological effects of many mutagenic agents are due to DNA Base modifications, both in the DNA and the DNA precursor pool. A group of mutagens containing a preformed modified Base, often referred to as Base Analogs (14), have received increasing attention recently. For example, 8-oxoguanine, in the form of 8-oxo-dGTP or 8-oxo-GTP, is a spontaneously arising guanine oxidation product that contributes substantially to the infidelity of DNA replication (13, 35, 37) or transcription (58). Specialized systems protecting the cell against 8-oxoguanine have been found in organisms from bacteria to humans (for reviews, see references 13 and 37), including the MutT enzyme, which is capable of hydrolyzing 8-oxo-dGTP, an activity referred to as pool sanitizing (2, 35). Other examples of mutagenic precursor pool contaminants are 5-hydroxy-dCTP (12) and 2-hydroxy-dATP (15), both oxidative stress products. The human MutT homolog hMTH1 has strong activity towards 2-hydroxy-dATP, suggesting that it, in addition to 8-oxo-GTP, could be an important threat if not actively removed (15). In addition, Base Analogs can be useful tools for probing the mechanisms of mutation avoidance during DNA replication, including Base-Base discrimination by DNA polymerases (51, 54). An important group of Base Analogs are the N-hydroxy derivatives of adenine and cytidine (see reference 27 for a review). For example, 6-hydroxylaminopurine (N-6-hydroxyadenine) (HAP) and 2-amino-6-hydroxylaminopurine (AHAP) are very powerful mutagens in phage, bacteria, yeast, and eukaryotic cells (42, 43), and they have been termed universal mutagens (42). These adenine derivatives are active when provided as Bases or, in some organisms, nucleosides, as they are apparently converted efficiently into the corresponding deoxynucleoside triphosphates (dNTPs), which are then incorporated into DNA by DNA polymerase. Because of the ambiguous Base pairing properties of these dNTPs, their incorporation is highly mutagenic. We have previously performed studies on the genetic requirements of HAP mutagenesis in the bacterium Escherichia coli for the purpose of understanding at which levels cells may try to prevent mutagenesis by this and related agents (43). We found little or no protection by the exonucleolytic proofreading (dnaQ gene) or the postreplicative mismatch repair system (encoded by the mutHLS genes), two systems that play important roles in preventing mutations resulting from the mispairings of normal Bases (50). This lack of discrimination is likely one of the reasons for the strong mutagenic potential of HAP. However, a strain carrying a deletion of the chromosomal uvrB-bio region had hypersensitivity to HAP for both mutagenesis and toxicity, implying the existence of a protective system. The deletion also conferred sensitivity to AHAP (43) and other Analogs (31). Sensitivity of a uvrB-bio deletion strain for AHAP and related compounds has also been found in Salmonella enterica serovar Typhimurium (23–25). However, hypersensitivity is not conferred by the uvrB5 point mutation (43) or two different uvrA deficiencies (23, 24, 43). This argues against the uvrABC excision repair system being responsible for protection against HAP and related compounds. We concluded that certain genes in the uvrB-bio region, other than uvrB, were responsible for the observed sensitivity. In the present report, we investigate the nature of the gene or genes within this region of the E. coli chromosome that are responsible for this enhanced Base Analog sensitivity. The results point to an important role of the molybdenum cofactor, presumably through the action of a molybdenum cofactor-containing enzyme activity.
-
multiple antimutagenesis mechanisms affect mutagenic activity and specificity of the Base Analog 6 n hydroxylaminopurine in bacteria and yeast
Mutation Research, 1998Co-Authors: Stanislav G Kozmin, Igor B. Rogozin, Polina V Shcherbakova, Roel M Schaaper, V N Kulikov, Vladimir N Noskov, Maria L Guetsova, Vladimir V Alenin, Kira S Makarova, Youri I PavlovAbstract:Abstract Base Analog 6- N -hydroxylaminopurine is a potent mutagen in variety of prokaryotic and eukaroytic organisms. In the review, we discuss recent results of the studies of HAP mutagenic activity, genetic control and specificity in bacteria and yeast with the emphasis to the mechanisms protecting living cells from mutagenic and toxic effects of this Base Analog.
Roel M Schaaper - One of the best experts on this subject based on the ideXlab platform.
-
tusa yhhp and iscs are required for molybdenum cofactor dependent Base Analog detoxification
MicrobiologyOpen, 2013Co-Authors: Stanislav G Kozmin, Elena I Stepchenkova, Roel M SchaaperAbstract:Lack of molybdenum cofactor (Moco) in Escherichia coli leads to hypersensitivity to the mutagenic and toxic effects of N-hydroxylated Base Analogs, such as 6-N-hydroxylaminopurine (HAP). This phenotype is due to the loss of two Moco-dependent activities, YcbX and YiiM, that are capable of reducing HAP to adenine. Here, we describe two novel HAP-sensitive mutants containing a defect in iscS or tusA (yhhP) gene. IscS is a major L-cysteine desulfurase involved in iron–sulfur cluster synthesis, thiamine synthesis, and tRNA thiomodification. TusA is a small sulfur-carrier protein that interacts with IscS. We show that both IscS and TusA operate within the Moco-dependent pathway. Like other Moco-deficient strains, tusA and iscS mutants are HAP sensitive and resistant to chlorate under anaerobic conditions. The Base-Analog sensitivity of iscS or tusA strains could be suppressed by supplying exogenous L-cysteine or sulfide or by an increase in endogenous sulfur donors (cysB constitutive mutant). The data suggest that iscS and tusA mutants have a defect in the mobilization of sulfur required for active YcbX/YiiM proteins as well as nitrate reductase, presumably due to lack of functional Moco. Overall, our data imply a novel and indispensable role of the IscS/TusA complex in the activity of several molybdoenzymes.
-
role for cysj flavin reductase in molybdenum cofactor dependent resistance of escherichia coli to 6 n hydroxylaminopurine
Journal of Bacteriology, 2010Co-Authors: Stanislav G Kozmin, Jian Wang, Roel M SchaaperAbstract:We have previously described a novel Escherichia coli detoxification system for the removal of toxic and mutagenic N-hydroxylated nucleoBases and related compounds that requires the molybdenum cofactor. Two subpathways (ycbX and yiiM) were identified, each employing a novel molybdo activity capable of inactivating N-hydroxylated compounds by reduction to the corresponding amine. In the present study, we identify the cysJ gene product as one additional component of this system. While the CysJ protein has been identified as the NADPH:flavin oxidoreductase component of the CysJI sulfite reductase complex (CysJ8I4), we show that the role of CysJ in Base Analog detoxification is unique and independent of CysI and sulfite reductase. We further show that CysJ functions as a specific partner of the YcbX molybdoenzyme. We postulate that the function of CysJ in this pathway is to provide, via its NADPH:flavin reductase activity, the reducing equivalents needed for the detoxification reaction at the YcbX molybdocenter. In support of the proposed interaction of the CysJ and YcbX proteins, we show that an apparent CysJ-YcbX “hybrid” protein from two Vibrio species is capable of compensating for a double cysJ ycbX defect in E. coli.
-
molybdenum cofactor dependent resistance to n hydroxylated Base Analogs in escherichia coli is independent of moba function
Mutation Research, 2007Co-Authors: Stanislav G Kozmin, Roel M SchaaperAbstract:Lack of molybdenum cofactor (MoCo) in Escherichia coli and related microorganisms was found to cause hypersensitivity to certain N-hydroxylated Base Analogs, such as HAP (6-N-hydroxylaminopurine). This observation has lead to a previous proposal that E. coli contains a molybdoenzyme capable of detoxifying such N-hydroxylated Analogs. Here, we show that, unexpectedly, deletion of all known or putative molybdoenzymes in E. coli failed to reveal any Base-Analog sensitivity, suggesting that a novel type of MoCo-dependent activity is involved. Further, we establish that protection against the Analogs does not require the common molybdopterin guanine-dinucleotide (MGD) form of the cofactor, but instead the guanosine monophosphate (GMP)-free version of MoCo (MPT) is sufficient.
-
hypersensitivity of escherichia coli δ uvrb bio mutants to 6 hydroxylaminopurine and other Base Analogs is due to a defect in molybdenum cofactor biosynthesis
Journal of Bacteriology, 2000Co-Authors: Stanislav G Kozmin, Youri I Pavlov, Ronnie L Dunn, Roel M SchaaperAbstract:The biological effects of many mutagenic agents are due to DNA Base modifications, both in the DNA and the DNA precursor pool. A group of mutagens containing a preformed modified Base, often referred to as Base Analogs (14), have received increasing attention recently. For example, 8-oxoguanine, in the form of 8-oxo-dGTP or 8-oxo-GTP, is a spontaneously arising guanine oxidation product that contributes substantially to the infidelity of DNA replication (13, 35, 37) or transcription (58). Specialized systems protecting the cell against 8-oxoguanine have been found in organisms from bacteria to humans (for reviews, see references 13 and 37), including the MutT enzyme, which is capable of hydrolyzing 8-oxo-dGTP, an activity referred to as pool sanitizing (2, 35). Other examples of mutagenic precursor pool contaminants are 5-hydroxy-dCTP (12) and 2-hydroxy-dATP (15), both oxidative stress products. The human MutT homolog hMTH1 has strong activity towards 2-hydroxy-dATP, suggesting that it, in addition to 8-oxo-GTP, could be an important threat if not actively removed (15). In addition, Base Analogs can be useful tools for probing the mechanisms of mutation avoidance during DNA replication, including Base-Base discrimination by DNA polymerases (51, 54). An important group of Base Analogs are the N-hydroxy derivatives of adenine and cytidine (see reference 27 for a review). For example, 6-hydroxylaminopurine (N-6-hydroxyadenine) (HAP) and 2-amino-6-hydroxylaminopurine (AHAP) are very powerful mutagens in phage, bacteria, yeast, and eukaryotic cells (42, 43), and they have been termed universal mutagens (42). These adenine derivatives are active when provided as Bases or, in some organisms, nucleosides, as they are apparently converted efficiently into the corresponding deoxynucleoside triphosphates (dNTPs), which are then incorporated into DNA by DNA polymerase. Because of the ambiguous Base pairing properties of these dNTPs, their incorporation is highly mutagenic. We have previously performed studies on the genetic requirements of HAP mutagenesis in the bacterium Escherichia coli for the purpose of understanding at which levels cells may try to prevent mutagenesis by this and related agents (43). We found little or no protection by the exonucleolytic proofreading (dnaQ gene) or the postreplicative mismatch repair system (encoded by the mutHLS genes), two systems that play important roles in preventing mutations resulting from the mispairings of normal Bases (50). This lack of discrimination is likely one of the reasons for the strong mutagenic potential of HAP. However, a strain carrying a deletion of the chromosomal uvrB-bio region had hypersensitivity to HAP for both mutagenesis and toxicity, implying the existence of a protective system. The deletion also conferred sensitivity to AHAP (43) and other Analogs (31). Sensitivity of a uvrB-bio deletion strain for AHAP and related compounds has also been found in Salmonella enterica serovar Typhimurium (23–25). However, hypersensitivity is not conferred by the uvrB5 point mutation (43) or two different uvrA deficiencies (23, 24, 43). This argues against the uvrABC excision repair system being responsible for protection against HAP and related compounds. We concluded that certain genes in the uvrB-bio region, other than uvrB, were responsible for the observed sensitivity. In the present report, we investigate the nature of the gene or genes within this region of the E. coli chromosome that are responsible for this enhanced Base Analog sensitivity. The results point to an important role of the molybdenum cofactor, presumably through the action of a molybdenum cofactor-containing enzyme activity.
-
multiple antimutagenesis mechanisms affect mutagenic activity and specificity of the Base Analog 6 n hydroxylaminopurine in bacteria and yeast
Mutation Research, 1998Co-Authors: Stanislav G Kozmin, Igor B. Rogozin, Polina V Shcherbakova, Roel M Schaaper, V N Kulikov, Vladimir N Noskov, Maria L Guetsova, Vladimir V Alenin, Kira S Makarova, Youri I PavlovAbstract:Abstract Base Analog 6- N -hydroxylaminopurine is a potent mutagen in variety of prokaryotic and eukaroytic organisms. In the review, we discuss recent results of the studies of HAP mutagenic activity, genetic control and specificity in bacteria and yeast with the emphasis to the mechanisms protecting living cells from mutagenic and toxic effects of this Base Analog.
Stanislav G Kozmin - One of the best experts on this subject based on the ideXlab platform.
-
tusa yhhp and iscs are required for molybdenum cofactor dependent Base Analog detoxification
MicrobiologyOpen, 2013Co-Authors: Stanislav G Kozmin, Elena I Stepchenkova, Roel M SchaaperAbstract:Lack of molybdenum cofactor (Moco) in Escherichia coli leads to hypersensitivity to the mutagenic and toxic effects of N-hydroxylated Base Analogs, such as 6-N-hydroxylaminopurine (HAP). This phenotype is due to the loss of two Moco-dependent activities, YcbX and YiiM, that are capable of reducing HAP to adenine. Here, we describe two novel HAP-sensitive mutants containing a defect in iscS or tusA (yhhP) gene. IscS is a major L-cysteine desulfurase involved in iron–sulfur cluster synthesis, thiamine synthesis, and tRNA thiomodification. TusA is a small sulfur-carrier protein that interacts with IscS. We show that both IscS and TusA operate within the Moco-dependent pathway. Like other Moco-deficient strains, tusA and iscS mutants are HAP sensitive and resistant to chlorate under anaerobic conditions. The Base-Analog sensitivity of iscS or tusA strains could be suppressed by supplying exogenous L-cysteine or sulfide or by an increase in endogenous sulfur donors (cysB constitutive mutant). The data suggest that iscS and tusA mutants have a defect in the mobilization of sulfur required for active YcbX/YiiM proteins as well as nitrate reductase, presumably due to lack of functional Moco. Overall, our data imply a novel and indispensable role of the IscS/TusA complex in the activity of several molybdoenzymes.
-
role for cysj flavin reductase in molybdenum cofactor dependent resistance of escherichia coli to 6 n hydroxylaminopurine
Journal of Bacteriology, 2010Co-Authors: Stanislav G Kozmin, Jian Wang, Roel M SchaaperAbstract:We have previously described a novel Escherichia coli detoxification system for the removal of toxic and mutagenic N-hydroxylated nucleoBases and related compounds that requires the molybdenum cofactor. Two subpathways (ycbX and yiiM) were identified, each employing a novel molybdo activity capable of inactivating N-hydroxylated compounds by reduction to the corresponding amine. In the present study, we identify the cysJ gene product as one additional component of this system. While the CysJ protein has been identified as the NADPH:flavin oxidoreductase component of the CysJI sulfite reductase complex (CysJ8I4), we show that the role of CysJ in Base Analog detoxification is unique and independent of CysI and sulfite reductase. We further show that CysJ functions as a specific partner of the YcbX molybdoenzyme. We postulate that the function of CysJ in this pathway is to provide, via its NADPH:flavin reductase activity, the reducing equivalents needed for the detoxification reaction at the YcbX molybdocenter. In support of the proposed interaction of the CysJ and YcbX proteins, we show that an apparent CysJ-YcbX “hybrid” protein from two Vibrio species is capable of compensating for a double cysJ ycbX defect in E. coli.
-
molybdenum cofactor dependent resistance to n hydroxylated Base Analogs in escherichia coli is independent of moba function
Mutation Research, 2007Co-Authors: Stanislav G Kozmin, Roel M SchaaperAbstract:Lack of molybdenum cofactor (MoCo) in Escherichia coli and related microorganisms was found to cause hypersensitivity to certain N-hydroxylated Base Analogs, such as HAP (6-N-hydroxylaminopurine). This observation has lead to a previous proposal that E. coli contains a molybdoenzyme capable of detoxifying such N-hydroxylated Analogs. Here, we show that, unexpectedly, deletion of all known or putative molybdoenzymes in E. coli failed to reveal any Base-Analog sensitivity, suggesting that a novel type of MoCo-dependent activity is involved. Further, we establish that protection against the Analogs does not require the common molybdopterin guanine-dinucleotide (MGD) form of the cofactor, but instead the guanosine monophosphate (GMP)-free version of MoCo (MPT) is sufficient.
-
hypersensitivity of escherichia coli δ uvrb bio mutants to 6 hydroxylaminopurine and other Base Analogs is due to a defect in molybdenum cofactor biosynthesis
Journal of Bacteriology, 2000Co-Authors: Stanislav G Kozmin, Youri I Pavlov, Ronnie L Dunn, Roel M SchaaperAbstract:The biological effects of many mutagenic agents are due to DNA Base modifications, both in the DNA and the DNA precursor pool. A group of mutagens containing a preformed modified Base, often referred to as Base Analogs (14), have received increasing attention recently. For example, 8-oxoguanine, in the form of 8-oxo-dGTP or 8-oxo-GTP, is a spontaneously arising guanine oxidation product that contributes substantially to the infidelity of DNA replication (13, 35, 37) or transcription (58). Specialized systems protecting the cell against 8-oxoguanine have been found in organisms from bacteria to humans (for reviews, see references 13 and 37), including the MutT enzyme, which is capable of hydrolyzing 8-oxo-dGTP, an activity referred to as pool sanitizing (2, 35). Other examples of mutagenic precursor pool contaminants are 5-hydroxy-dCTP (12) and 2-hydroxy-dATP (15), both oxidative stress products. The human MutT homolog hMTH1 has strong activity towards 2-hydroxy-dATP, suggesting that it, in addition to 8-oxo-GTP, could be an important threat if not actively removed (15). In addition, Base Analogs can be useful tools for probing the mechanisms of mutation avoidance during DNA replication, including Base-Base discrimination by DNA polymerases (51, 54). An important group of Base Analogs are the N-hydroxy derivatives of adenine and cytidine (see reference 27 for a review). For example, 6-hydroxylaminopurine (N-6-hydroxyadenine) (HAP) and 2-amino-6-hydroxylaminopurine (AHAP) are very powerful mutagens in phage, bacteria, yeast, and eukaryotic cells (42, 43), and they have been termed universal mutagens (42). These adenine derivatives are active when provided as Bases or, in some organisms, nucleosides, as they are apparently converted efficiently into the corresponding deoxynucleoside triphosphates (dNTPs), which are then incorporated into DNA by DNA polymerase. Because of the ambiguous Base pairing properties of these dNTPs, their incorporation is highly mutagenic. We have previously performed studies on the genetic requirements of HAP mutagenesis in the bacterium Escherichia coli for the purpose of understanding at which levels cells may try to prevent mutagenesis by this and related agents (43). We found little or no protection by the exonucleolytic proofreading (dnaQ gene) or the postreplicative mismatch repair system (encoded by the mutHLS genes), two systems that play important roles in preventing mutations resulting from the mispairings of normal Bases (50). This lack of discrimination is likely one of the reasons for the strong mutagenic potential of HAP. However, a strain carrying a deletion of the chromosomal uvrB-bio region had hypersensitivity to HAP for both mutagenesis and toxicity, implying the existence of a protective system. The deletion also conferred sensitivity to AHAP (43) and other Analogs (31). Sensitivity of a uvrB-bio deletion strain for AHAP and related compounds has also been found in Salmonella enterica serovar Typhimurium (23–25). However, hypersensitivity is not conferred by the uvrB5 point mutation (43) or two different uvrA deficiencies (23, 24, 43). This argues against the uvrABC excision repair system being responsible for protection against HAP and related compounds. We concluded that certain genes in the uvrB-bio region, other than uvrB, were responsible for the observed sensitivity. In the present report, we investigate the nature of the gene or genes within this region of the E. coli chromosome that are responsible for this enhanced Base Analog sensitivity. The results point to an important role of the molybdenum cofactor, presumably through the action of a molybdenum cofactor-containing enzyme activity.
-
multiple antimutagenesis mechanisms affect mutagenic activity and specificity of the Base Analog 6 n hydroxylaminopurine in bacteria and yeast
Mutation Research, 1998Co-Authors: Stanislav G Kozmin, Igor B. Rogozin, Polina V Shcherbakova, Roel M Schaaper, V N Kulikov, Vladimir N Noskov, Maria L Guetsova, Vladimir V Alenin, Kira S Makarova, Youri I PavlovAbstract:Abstract Base Analog 6- N -hydroxylaminopurine is a potent mutagen in variety of prokaryotic and eukaroytic organisms. In the review, we discuss recent results of the studies of HAP mutagenic activity, genetic control and specificity in bacteria and yeast with the emphasis to the mechanisms protecting living cells from mutagenic and toxic effects of this Base Analog.
Gloria E. O. Borgstahl - One of the best experts on this subject based on the ideXlab platform.
-
itpa inosine triphosphate pyrophosphatase from surveillance of nucleotide pools to human disease and pharmacogenetics
Mutation Research-reviews in Mutation Research, 2013Co-Authors: Peter D Simone, Youri I Pavlov, Gloria E. O. BorgstahlAbstract:Abstract Cellular nucleotide pools are often contaminated by Base Analog nucleotides which interfere with a plethora of biological reactions, from DNA and RNA synthesis to cellular signaling. An evolutionarily conserved inosine triphosphate pyrophosphatase (ITPA) removes the non-canonical purine (d)NTPs inosine triphosphate and xanthosine triphosphate by hydrolyzing them into their monophosphate form and pyrophosphate. Mutations in the ITPA orthologs in model organisms lead to genetic instability and, in mice, to severe developmental anomalies. In humans there is genetic polymorphism in ITPA. One allele leads to a proline to threonine substitution at amino acid 32 and causes varying degrees of ITPA deficiency in tissues and plays a role in patients’ response to drugs. Structural analysis of this mutant protein reveals that the protein is destabilized by the formation of a cavity in its hydrophobic core. The Pro32Thr allele is thought to cause the observed dominant negative effect because the resulting active enzyme monomer targets both homo- and heterodimers to degradation.
Myron F Goodman - One of the best experts on this subject based on the ideXlab platform.
-
Base Analog and neighboring Base effects on substrate specificity of recombinant human g t mismatch specific thymine dna glycosylase
Biochemistry, 1996Co-Authors: Paola Gallinari, Myron F Goodman, Linda B Bloom, Josef Jiricny, Rufus S DayAbstract:We studied the substrate specificity of the human G:T mismatch-specific thymine glycosylase that initiates the repair of G:T and G:U Base mismatches to G:C Base pairs. Such mismatches arise when 5-methylcytosine or cytosine deaminate spontaneously (and hydrolytically) in DNA. Substrates were 45-bp DNA heteroduplexes that bore single G:T, m6G:T, 2,6-diaminopurine:T, 2-amino-6-(methylamino)-purine:T, 2-aminopurine:T, and G:m4T mispairs. The Bases 5' to the poorly matched G were altered in selected G:T substrates to yield mispairs in four different contexts, ApG, CpG, GpG, and TpG. The recombinant thymine glycosylase was incubated with the 45-bp DNA substrates, each labeled at the 5'-terminus of the strand containing the mismatched T. The DNAs were then treated with 0.1 N NaOH to catalyze phosphodiester bond breakage at the newly-generated AP sites, and the products were analyzed on DNA sequencing gels. As indicated by the amounts of the 20-nt incision product, the removal of the thymine Base by the enzyme increased linearly between 0 and 40 min at which time the generation of product from all substrates ceased, probably because of enzyme inactivation. The rate of incision was greatest (0.7 fmol/min) with DNA containing the G:T mispair followed by the DNA containing the m6G:T mispair (0.38 fmol/min) and the DNA with the 2-amino-6-(methylamino)purine:T mispair (0.15 fmol/ min); the extent of reaction was 90%, 40%, and 20% respectively. By contrast to previous findings with cell-free extracts, DNA substrates containing 2,6-diaminopurine:T, 2-aminopurine:T, and G:m4T mispairs were not incised (< 2%). The amount of incision of the 45-bp DNA substrates containing G:T mispairs in the CpG context was 3-12-fold greater than in the TpG, GpG, and ApG contexts.
-
Base Analog and neighboring Base effects on substrate specificity of recombinant human g t mismatch specific thymine dna glycosylase
Biochemistry, 1996Co-Authors: Paola Gallinari, Myron F Goodman, Linda B Bloom, Yaozhong Xu, Josef JiricnyAbstract:We studied the substrate specificity of the human G:T mismatch-specific thymine glycosylase that initiates the repair of G:T and G:U Base mismatches to G:C Base pairs. Such mismatches arise when 5-methylcytosine or cytosine deaminate spontaneously (and hydrolytically) in DNA. Substrates were 45-bp DNA heteroduplexes that bore single G:T, m6G:T, 2,6-diaminopurine:T, 2-amino-6-(methylamino)purine:T, 2-aminopurine:T, and G:m4T mispairs. The Bases 5‘ to the poorly matched G were altered in selected G:T substrates to yield mispairs in four different contexts, ApG, CpG, GpG, and TpG. The recombinant thymine glycosylase was incubated with the 45-bp DNA substrates, each labeled at the 5‘-terminus of the strand containing the mismatched T. The DNAs were then treated with 0.1 N NaOH to catalyze phosphodiester bond breakage at the newly-generated AP sites, and the products were analyzed on DNA sequencing gels. As indicated by the amounts of the 20-nt incision product, the removal of the thymine Base by the enzyme in...
-
spectroscopic and calorimetric characterizations of dna duplexes containing 2 aminopurine
Biochemistry, 1996Co-Authors: Ramon Eritja, Myron F Goodman, Kenneth J BreslauerAbstract:The Base Analog 2-aminopurine (AP) strongly promotes A·T to G·C and G·C to A·T transitions in bacteria and bacteriophage. During DNA replication, the primary mutagenic event involves formation of a heteroduplex with an AP·C site at a much higher frequency than formation of the corresponding heteroduplex with an A·C site. It is not known if AP-induced mutagenesis correlates with differences in the thermodynamic properties of an AP·C versus an A·C site, or whether interactions involving DNA polymerases are controlling. To address this specific question, and more generally to characterize AP-containing duplexes, we have used a combination of spectroscopic and calorimetric techniques to determine the thermodynamic properties of six 11-mer duplexes. The sequences of these duplexes are identical except for the identity of the variable central Base pair which can be either A·T, A·C, AP·T, AP·C, AP·A, or AP·G, and which we use to designate each duplex. Analyses and interpretation of the optically and calorimetric...
-
nmr study of the conformation of the 2 aminopurine cytosine mismatch in dna
Biochemistry, 1996Co-Authors: Patricia Fagan, Myron F Goodman, Ramon Eritja, Carme Fabrega, David E WemmerAbstract:DNA polymerase makes errors by misincorporating natural DNA Bases and Base Analogs. Because of the wide variety of possible mismatches and the varying efficiency with which they are repaired, structural studies are necessary to understand in detail how these mispairs differ and can be distinguished from standard Watson-Crick Base pairs. 2-Aminopurine (AP) is a highly mutagenic Base Analog. The objective of this study was to determine the geometry of the AP{center_dot}C mispair in DNA at neutral pH. Although several studies have focused on the AP{center_dot} mispair in DNA, there is not as of yet consensus on its structure. At least four models have been proposed for this mispair. Through the use of NMR spectroscopy with selective {sup 15}N-labeling of exocyclic amino nitrogens on Bases of interest, we are able to resolve ambiguities in previous studies. We find here that, in two different DNA sequences, the AP{center_dot}C mispair at neutral and high pH is in a wobble geometry. The structure and stability of this Base mispair is dependent upon the local Base sequence. 48 refs., 4 figs., 1 tab.
