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At least 19 recordsLinked to original sources
PubMed1978

Role of uracil-DNA glycosylase in the repair of deaminated cytosine residues of DNA in Escherichia coli.

Uracil-DNA glycosylase, which acts specifically on uracil-containing DNA, was purified 250-fold from an extract of Escherichia coli 1100. The enzyme releases free uracil from DNA, producing alkali-labile apyrimidinic sites in the DNA. The enzyme is active on both native and heat-denatured DNA of phage PBS1, which contains uracil in place of thymine. piX174 DNA which had been treated with bisulfite and then at alkaline pH was susceptible to the action of uracil-DNA glycosylase. Since DNA treated with bisulfite alone was less susceptible to the enzyme, it is likely that the enzyme recognizes deaminated cytosine, namely uracil, but not bisulfite adducts of uracil and cytosine in the treated DNA. DNA treated with nitrite or hydroxylamine was not attacked by the enzyme. Enzyme activity acting on bisulfite-treated DNA was absent from an extract of E. coli mutant BD10 (ung). The mutant exhibited higher sensitivity to bisulfite than did the wild-type strain and was unable to reactivate phage T1 pre-exposed to bisulfite and weak alkali.

Binding Sites↗
PubMed1977

Kinetics of deamination of cytosine nucleosides with etherified sugar hydroxyls.

The kinetics of deamination of derivatives of the therapeutically important 1-beta-D-arabinofuranosylcytosine with etherified (methylated) sugar hydroxyls has provided additional direct evidence for involvement of the 2'-hydroxyl in intramolecular catalysed deamination. In the case of 1-beta-D-lyxofuranosylcytosine, the kinetics of deamination of its 2'-O-methyl and 3'-O-methyl derivatives pointed to similar involvement of the "up" 2'-OH in intramolecular catalysed deamination. Participation by the 3'-OH, which is also in the "up" position, was excluded. A qualitative correlation was shown to exist between the electron density distributions on C(4) and C(6) of the cytosine rings in cytosine, 1-methylcytosine and cytidine, and their relative susceptibilities to deamination.

Cytidine↗
PubMed1977

Tetrahydrouridine: Physiologic disposition and effect upon deamination of cytosine arabinoside in man.

[14C]-tetrahydrouridine (THU), a strong inhibitor of cytidine (CR) deaminase, was, after iv administration, rapidly and quantitatively cleared from the blood with a plasma half-life of about 1 hour. The main pathway of excretion was through the kidneys: most of a dose of 50 mg/kg was excreted within 12 hours and excretion was essentially complete within 48 hours. Oral administration of the same dose revealed absorption of about 10% from the gastrointestinal tract. THU at 10, 25, and 50 mg/kg given 15 minutes before [3H]-cytosine arabinoside (ara-C) at a dose of 0.003 mg/kg produced about a two fold increase in ara-C blood levels at all times measured from 5 minutes to 4 hours, with only slight increases in the half-life of ara-C. A dose-related effect of THU upon the deamination of ara-C was obvious only during the time from 15 minutes to 1 hour after the injection of 3H-ara-C. The inhibitory effect of THU upon CR deaminase was also reflected in a considerably increased ratio of ara-C/uracil arabinoside in the urine.

Administration, Oral↗
PubMed2025

Defining the genome-wide mutagenic impact of APOBEC3 enzymes.

Somatic mutations drive cancer initiation and tumor evolution. Therefore, the etiology of mutagenesis in cancer is important to preventative and treatment strategies. Somatic mutagenesis in cancer is a multifactorial process and includes both endogenous and exogenous sources of mutations. One recently recognized source of mutagenesis in cancer is the innate immune APOBEC3 family of enzymes, which catalyze cytosine deamination to restrict viral infection but can aberrantly act on the cellular genome, resulting in mutations. Single base substitution (SBS) signatures, or mutational patterns, identified in cancer genomes have demonstrated widespread mutagenesis caused by APOBEC3 enzymes throughout human tumors. To comprehensively define the consequences of APOBEC3 mutagenesis, we developed an experimental pipeline for prospective analysis of genome-wide mutations caused by APOBEC3 activity. This pipeline can be adapted to analyze additional sources of mutagenesis across a spectrum of cells.

Humans↗
PubMed2026

Selective Inhibition of DNA Polymerase Proofreading: A Metabolic-Fidelity Mechanism Explains Agent Orange-Associated Myelodysplasia.

We performed a focused review to better understand the pathogenesis of Agent Orange (AO)-associated myelodysplastic syndrome (MDS). We first examined the mechanisms underlying conventional (de novo) MDS, a clonal hematopoietic neoplasm that typically develops in later life, and integrated these findings with our recent analysis of obesity-associated carcinogenesis. Accordingly, we propose that genomic instability in de novo MDS results from selective inhibition of the DNA polymerase proofreading exonuclease. In obesity-associated carcinogenesis, impaired AMP-activated protein kinase (AMPK) activity disrupts mitochondrial ATP production, increasing intracellular AMP concentrations. Elevated AMP selectively inhibits the proofreading exonuclease while preserving polymerase activity, allowing replication errors to escape correction and become fixed as somatic mutations. Molecular studies demonstrate that AO-associated MDS exhibits essentially the same mutational profile as de novo disease despite arising after 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD) exposure in young, otherwise healthy military personnel. Because TCDD is highly lipophilic, it accumulates in adipose tissue and is released slowly over decades, producing sustained mitochondrial dysfunction, reduced ATP synthesis, and chronic elevation of intracellular AMP. We propose that this metabolic disturbance converges on the same endpoint-selective inhibition of the proofreading exonuclease-thereby promoting mutagenesis and clonal evolution. Recent studies further strengthen the central role of proofreading by demonstrating that many mutations, including many found in MDS, previously attributed to spontaneous cytosine deamination, instead arise from DNA polymerase misincorporation of thymidine opposite cytosine, particularly at CpG dinucleotides, emphasizing the critical importance of fully active proofreading in preventing such misincorporations from accumulating as mutations in the genome of the cell.

AMP↗
PubMed2026

The shape of fitness functions and the distribution of mutational effect sizes jointly limit adaptation by regulatory mutations.

Mutations in gene regulatory regions have been shown to play a role in rapid adaptation, but the factors determining their contribution are largely unknown. Here, using the metabolic enzyme cytosine deaminase of budding yeast, we examine whether adaptation to 5-fluorocytosine, which requires reduced cytosine deamination and can readily arise from amino acid substitutions, may be reached by single promoter mutations. We generated all single-nucleotide substitutions and indels in the FCY1 promoter and assayed the resulting mutants in presence of 5-fluorocytosine. This revealed that no promoter mutation is sufficient for adaptation to occur. We next investigated how this inaccessibility of adaptation arises by combining large-scale expression measurements with the experimental characterization of the corresponding expression-fitness function. These experiments showed that the shape of this function precludes single promoter mutations from being adaptive. Although 24% of mutations significantly affect expression, the fitness curve is flat around wild-type level. As such, adaptation can only emerge from a severe reduction of expression, which cannot occur from a single mutation in the promoter. Our results show that the contribution of regulatory mutations to rapid adaptation depends not only on the distribution of mutational effect sizes on expression level but also on the shape of the function linking fitness to expression levels.

Promoter Regions, Genetic↗
PubMed2026

FALCON2: compression-based metagenomic classification of ancient viruses.

MOTIVATION: Ancient DNA (aDNA) sequences present unique challenges for taxonomic classification due to extreme fragmentation (reads 20-100 bp), end-biased cytosine deamination, and high contamination rates. Conventional metagenomic classifiers based on exact k-mer matching or alignment lose discriminative power on such short and damaged reads, limiting the analysis of paleogenomic samples. RESULTS: We present FALCON2, a compression-based metagenomic classifier that leverages position-aware finite-context models to maintain high accuracy on degraded viral ancient viruses. FALCON2 consolidates the capabilities of its predecessor, FALCON-meta, into a unified executable with enhanced features including model persistence, direct processing of compressed inputs, multiple file handling, and optional pre-filtering methodologies for contaminated samples. Under controlled benchmarking with database, taxonomy, and thread parity on simulated viral datasets, FALCON2 achieved an Area Under the Curve of Receiver Operating Characteristic (AUC-ROC) of 0.999, an Area Under Precision-Recall Curve (AUPRC) of 0.968, and an F1-score of 0.918, substantially outperforming Centrifuge (AUPRC = 0.625), Kraken2 (AUPRC = 0.184), and CLARK-S (AUPRC = 0.013) on pooled micro-averaged metrics. FALCON2's advantage is most pronounced on ultra-short reads (20-40 bp), where exact k-mers become sparse. FALCON2 pre-filtering at threshold 0.7 improved precision by 10 percentage points with negligible recall loss. FALCON2 runs on systems with 4-8 GB RAM for typical analyses. AVAILABILITY AND IMPLEMENTATION: FALCON2 is freely available at https://github.com/cobilab/FALCON2 under GPL v3 license. Benchmarking data and scripts are archived at DOI: https://doi.org/10.5281/zenodo.17291214.

Metagenomics↗
PubMed1975

N-Glycosidase activity in extracts of Bacillus subtilis and its inhibition after infection with bacteriophage PBS2.

We have detected in crude extracts of Bacillus subtilis an N-glycosidase activity which catalyzes the release of free uracil from DNA of the subtilis phage PBS2 labeled with [3H]uridine. This DNA contains deoxyuridine instead of thymidine. The enzyme is active in the presence of 1.0 mM EDTA and under these conditions Escherichia coli or T7 DNA labeled with [3H]thymidine is not degraded to labeled acid-soluble products. The activity resembles an N-glycosidase from E. coli which releases free uracil from DNA containing deaminated cytosine residues. Both enzymes in crude extracts are active in the presence of EDTA, do not require dialyzable co-factors, and have the same pH optimum. They differ in that the enzyme from E. coli is more sensitive to heat, sulfhydryl reagents, and salt. The enzyme from B. subtilis is inactive on DNA containing 5-bromouracil or hydroxymethyluracil. Extracts of PBS2-infected B. subtilis lose the N-glycosidase activity within 4 min after infection and contain a factor that inhibits the N-glycosidase activity within 4 min after infection and contain a factor that inhibits the N-glycosidase activity in extracts of uninfected cells in vitro.

Bacillus subtilis↗
PubMed1975

Isolation and purification of blasticidin S deaminase from Aspergillus terreus.

An enzyme catalyzing the deamination of the cytosine moiety of blasticidin S was extracted from a fungal strain that belongs to Aspergillus terreus. The enzyme was purified with ammonium sulfate fractionation, Sephadex G-100 column and DEAE cellulose column chromatography, followed by preparative polyacrylamide gel electrophoresis. Blasticidin S deaminase could be separated easily from co-existing cytidine deaminase by DEAE column chromatography or gel electrophoresis, and preliminary study on the substrate specificity showed that this enzyme acts on blasticidin S derivatives, such as cytomycin and acetylblasticidin S, but not on cytosine, cytidine, purine bases or their nucleosides. Blasticidin S deaminase could be induced by the addition of blasticidin S to the culture, and sulfhydryl compounds, such as mercaptoethanol, were effective in protecting the enzyme from inactivation. The homogeneity of the enzyme was examined by both sedimentation analysis and polyacrylamide gel electrophoresis. The molecular weight and isoelectric point were found to be around 30,000 and 4.35, respectively. Some other properties were also examined.

Aminohydrolases↗
PubMedDate not supplied

Inhibition of deamination of 14C-cytosine arabinoside (NSC-63878): a useful biologic assay for tetrahydrouridine (NSC-112907).

Inhibition of the deamination of 14C-cytosine arabinoside by two lots of tetrahydrouridine was studied in monkey serum. The average inhibition of deaminase activity was 78% for tetrahydrouridine lot AJ39 (1.0 muM) when the concentration of cytosine arabinoside ranged from 44.2 to 170.7 muM; under the same conditions tetrahydrouridine lot AJ22 inhibited deamination by an average of 68%. Apparent Ki values were 0.26 muM for AJ39 and 0.43 muM for AJ22. The assay may be used to check the relative biologic activity of various lots of tetrahydrouridine.

Animals↗
PubMed2024

An in vitro cytidine deaminase assay to monitor APOBEC activity on DNA.

APOBEC enzymes promote the deamination of cytosine (C) to uracil (U) in DNA to defend cells against viruses but also serve as a predominant source of mutations in cancer genomes. This protocol describes an assay to monitor APOBEC deaminase activity in vitro on a synthetic DNA oligonucleotide. The method described here focuses specifically on APOBEC3B to illustrate the different steps of the assay. However, the protocol can be applied to monitor the DNA deaminase activity of any other member of the APOBEC family, such as APOBEC3A. This assay involves preparing APOBEC3B-expressing cell extract or purifying APOBEC3B by immunoprecipitation, followed by incubation with a single-stranded DNA containing a TpC motif. The deaminated cytosine is then removed by recombinant Uracil DNA Glycosylase present in the reaction to form an abasic site. The abasic site creates a weakness in the DNA's backbone, causing the DNA to be cleaved under high temperatures and alkaline conditions. Denaturing gel electrophoresis is used to separate cleaved DNA from full-length DNA, enabling the quantification of the percentage of deamination induced by APOBEC3B. This protocol can be used to determine the presence of APOBEC and the regulation of APOBEC activity in specific cell lines, to study substrate preference targeted by different members of the APOBEC family and different APOBEC mutants, or to determine the efficiency and specificity of inhibitor compounds against APOBEC enzymes.

Cytidine Deaminase↗
PubMed1979

Alterations in metabolism of cytidine components in rat liver after oral administration of butylated hydroxytoluene (in vivo study).

The administration of the antioxidant, butylated hydroxytoluene (BHT) to rats decreased the utilization of [2-14C]orotic acid for the synthesis of cytidine nucleotides in the acid-soluble extract and RNA of the liver. The specific activity of the uridine components was slightly decreased. The depression of the specific activity of the cytidine components depended on the dose of the drug. Simultaneously preformed [U-14C]cytidine in experimental rats was to a higher degree transported to the liver and incorporated into RNA cytosine; its deamination was markedly suppressed. Both phenomena depend on the BHT dose. The concentration of both the uridine and the cytidine components of the acid-soluble extract remained unaffected by the administration of BHT. The utilization of [2-14C]orotic acid for the synthesis of DNA cytosine was depressed after the administration of BHT; by contrast, the specific activity of DNA thymine was higher. The incorporation of [1-14C]palmitic acid into microsomal phospholipids was not substantially influenced over the dose range 25--500 mg BHT/kg. The specific activity of neutral lipids in microsomes increased.

Animals↗
PubMed1976

Mechanism of the mutagenic action of hydroxylamine. X. Certain specificities in the mutagenesis of N-hydroxy and N-methoxy analogs of cytosine and adenine derivatives.

In contrast with N4-methoxycytidine, N6-methoxyadenosine and the corresponding 2'-deoxynucleosides, N4-hydroxycytidine readily penetrates cells of Escherichia coli. Apparently this explains the non-mutagenicity of the N-methoxy compounds when added to an E. coli suspension, and the potent mutagenic effects of the N4-hydroxy analogs under the same conditions. 1-Deazaadenosine and N9- and N1-hydroxyalkyl-substituted adenines and cytosines, inhibitors of adenosine and cytidinedeaminases, are also incapable of crossing the E. coli cell wall.

Adenine↗
PubMed1977

Partial purification and characterization of a uracil DNA N-glycosidase from Bacillus subtilis.

A uracil specific DNA N-glycosidase activity has been partially purified from crude extracts of Bacillus subtilis. The enzyme has a molecular weight of approximately 24 000 with no subunit structure. It has no requirement for any known cofactors but is inhibited in the presence of Co2+, Fe2+, or Zn2+. The enzyme is specific for uracil in single- and double-stranded deoxyribonucleopolymers and does not release free uracil from RNA or from poly(rU):poly(dA). In addition, neither Udr, dUMP, nor dUTP is recognized as substrate. The enzyme will attack small poly(dU) oligomers but the minimum size recognized as substrate is (pU)4. This enzyme may have a role in the repair (by base excision) or uracil in DNA arising either by incorporation during DNA synthesis or by deamination of cytosine in DNA.

Bacillus subtilis↗
PubMed1977

Repair of nitrous acid damage to DNA in Escherichia coli.

A number of mutant strains of Escherichia coli have been examined for their sensitivity to nitrous acid and in some instances to methylmethanesulfonate. All ung- mutants tested are abnormally sensitive to nitrous acid. Since the ung mutation is phenotypically expressed as a defect in uracil DNA glycosidase, this observation supports the contention that treatment of cells with nitrous acid causes deamination of cytosine to uracil. In addition the observed sentitivity indicates that the ung gene is involved in the repair of uracil in DNA. Studies with other mutants suggest that both exonuclease III and DNA polymerase I of E. coli are involved in the repair of nitrous acid damage in vivo.

Cell Survival↗