Development of a new application of the comet assay to assess levels of O6-methylguanine in genomic DNA (CoMeth)

O⁶-methylguanine (O⁶meG) is one of the most premutagenic, precarcinogenic, and precytotoxic DNA lesions formed by alkylating agents. Repair of this DNA damage is achieved by the protein MGMT, which transfers the alkyl groups from the O⁶ position of guanine to a cysteine residue in its active center. Because O⁶meG repair by MGMT is a stoichiometric reaction that irreversibly inactivates MGMT, which is subsequently degraded, the repair capacity of O⁶meG lesions is dependent on existing active MGMT molecules. In the absence of active MGMT, O⁶meG is not repaired, and during replication, O⁶meG:T mispairs are formed. The MMR system recognizes these mispairs and introduces a gap into the strand. If O⁶meG remains in one of the template strands the futile MMR repair process will be repeated, generating more strand breaks (SBs). The toxicity of O⁶meG is, therefore, dependent on MMR and DNA SB induction of cell death. MGMT, on the other hand, protects against O⁶meG toxicity by removing the methyl residue from the guanine. Although removal of O⁶meG makes MGMT an important anticarcinogenic mechanism of DNA repair, its activity significantly decreases the efficacy of cancer chemotherapeutic drugs that aim at achieving cell death through the action of the MMR system on unrepaired O⁶meG lesions. Here, we report on a modification of the comet assay (CoMeth) that allows the qualitative assessment of O⁶meG lesions after their conversion to strand breaks in proliferating MMR-proficient cells after MGMT inhibition. This functional assay allows the testing of compounds with effects on O⁶meG levels, as well as on MGMT or MMR activity, in a proliferating cell system. The expression of MGMT and MMR genes is often altered by promoter methylation, and new epigenetically active compounds are being designed to increase chemotherapeutic efficacy. The CoMeth assay allows the testing of compounds with effects on O⁶meG, MGMT, or MMR activity. This proliferating cell system complements other methodologies that look at effects on these parameters individually through analytical chemistry or in vitro assays with recombinant proteins.     

A novel DNA damage recognition protein in Schizosaccharomyces pombe

Toxic and mutagenic O⁶-alkylguanine adducts in DNA are repaired by O⁶-alkylguanine-DNA alkyltransferases (MGMT) by transfer of the alkyl group to a cysteine residue in the active site. Comparisons in silico of prokaryotes and lower eukaryotes reveal the presence of a group of proteins [alkyltransferase-like (ATL) proteins] showing amino acid sequence similarity to MGMT, but where the cysteine at the putative active site is replaced by tryptophan. To examine whether ATL proteins play a role in the biological effects of alkylating agents, we inactivated the gene, referred to as atl1⁺, in Schizosaccharomyces pombe, an organism that does not possess a functional MGMT homologue. The mutants are substantially more susceptible to the toxic effects of the methylating agents, N-methyl-N-nitrosourea, N-methyl-N′nitro-N-nitrosoguanidine and methyl methanesulfonate and longer chain alkylating agents including N-ethyl-N-nitrosourea, ethyl methanesulfonate, N-propyl-N-nitrosourea and N-butyl-N-nitrosourea. Purified Atl1 protein does not transfer methyl groups from O⁶-methylguanine in [³H]-methylated DNA but reversibly inhibits methyl transfer by human MGMT. Atl1 binds to short single-stranded oligonucleotides containing O⁶-methyl, -benzyl, -4-bromothenyl or -hydroxyethyl-guanine but does not remove the alkyl group or base and does not cleave the oligonucleotide in the region of the lesion. This suggests that Atl1 acts by binding to O⁶-alkylguanine lesions and signalling them for processing by other DNA repair pathways. This is the first report describing an activity that protects S.pombe against the toxic effects of O⁶-alkylguanine adducts and the biological function of a family of proteins that is widely found in prokaryotes and lower eukaryotes.     

甲基鸟嘌呤甲基转移酶表达调节在肿瘤发生和治疗中的作用

甲基鸟嘌呤甲基转移酶（O⁶-methylguanine-DNA methyltransferase,MGMT）是从细菌到哺乳类机体中存在的一种独特的DNA修复蛋白,其作用是在DNA损伤的修复过程,催化DNA分子鸟嘌呤O⁶位上的烷基从鸟嘌呤碱基转移至MGMT蛋白的半胱氨酸残基上,而使DNA分子鸟嘌呤复原.因此,机体中MGMT适当的表达有利于修复由烷化剂诱导而形成的O⁶烷基鸟嘌呤DNA加合物.MGMT蛋白的含量和活性不但在基因水平受到各种因素的调控,并且与某些药物的直接作用有关.调节MGMT在细胞内的活性,对于防御肿瘤的发生及某些肿瘤的治疗过程中克服肿瘤耐药性和克服骨髓毒性具有重要的意义.     

The O6-methylguanine-DNA methyltransferase from the hyperthermophilic archaeon Pyrococcus sp. KOD1: a thermostable repair enzyme

The enzyme O⁶-methylguanine-DNA methyltransferase (MGMT) is the most common form of cellular defense against the biological effects of O⁶-methylguanine (O⁶-MeG) in DNA. Based on PCR amplification using primers derived from conserved amino acid sequences of MGMTs from 11 species, we isolated the DNA region coding for MGMT from the hyperthermophilic archaeon Pyrococcus sp. KOD1. The MGMT gene from KOD1 (mgtk) comprises 522 nucleotides, encoding 174 amino acid residues; its product shows considerable similarity to the corresponding mammalian, yeast and bacterial enzymes, especially around putative methyl acceptor sites. Phylogenetic analysis of MGMTs showed that archaeal MGMTs were grouped with their bacterial counterparts. The location of the MGMT gene on the KOD1 chromosome was also determined. The cloned KOD1 MGMT gene was overexpressed using the T7 RNA polymerase expression system, and the recombinant protein was purified by ammonium sulfate fractionation, heat treatment, ion-exchange chromatography and gel filtration chromatography. The purified recombinant protein was assayed for its enzyme activity by monitoring transfer of [³H]methyl groups from the substrate DNA to the MGMT protein; the activity was found to be stable at 90°?C for at least 30?min. When the mgtk gene was placed under the control of the lac promoter and expressed in the methyltransferase-deficient Escherichia coli strain KT233 (Δada, Δogt) cells, a MGMT was produced. The enzyme was functional in vivo and complemented the mutant phenotype, making the cells resistant to the cytotoxic properties of the alkylating agent N-methyl-N′-nitro-N-nitrosoguanidine.     

Inhibition of O6-methylguanine-DNA methyltransferase by an alkyltransferase-like protein from Escherichia coli

The alkyltransferase-like (ATL) proteins contain primary sequence motifs resembling those found in DNA repair O⁶-alkylguanine-DNA alkyltransferase proteins. However, in the putative active site of ATL proteins, a tryptophan (W⁸³) residue replaces the cysteine at the known active site of alkyltransferases. The Escherichia coli atl gene was expressed as a fusion protein and purified. Neither ATL nor C⁸³ or A⁸³ mutants transferred [³H] from [³H]-methylated DNA to themselves, and the levels of O⁶-methyl guanine (O⁶-meG) in substrate DNA were not affected by ATL. However, ATL inhibited the transfer of methyl groups to human alkyltransferase (MGMT). Inhibition was reduced by prolonged incubation in the presence of MGMT, again suggesting that O⁶-meG in the substrate is not changed by ATL. Gel-shift assays show that ATL binds to short single- or double-stranded oligonucleotides containing O⁶-meG, but not to oligonucleotides containing 8-oxoguanine, ethenoadenine, 5-hydroxycytosine or O⁴-methylthymine. There was no evidence of demethylation of O⁶-meG or of glycosylase or endonuclease activity. Overexpression of ATL in E.coli increased, or did not affect, the toxicity of N-methyl-N′-nitro-N-nitrosoguanidine in an alklyltransferase-proficient and -deficient strain, respectively. These results suggest that ATL may act as a damage sensor that flags O⁶-meG and possibly other O⁶-alkylation lesions for processing by other repair pathways.     

Cross talk between the nuclease and helicase activities of Dna2: role of an essential iron-sulfur cluster domain

Dna2 nuclease/helicase is a multitasking protein involved in DNA replication and recombinational repair, and it is important for preservation of genomic stability. Yeast Dna2 protein contains a conserved putative Fe-S (iron-sulfur) cluster signature motif spanning the nuclease active site. We show that this motif is indeed an Fe-S cluster domain. Mutation of cysteines involved in metal coordination greatly reduces not just the nuclease activity but also the ATPase activity of Dna2, suggesting that the nuclease and helicase activities are coupled. The affinity for DNA is not significantly reduced, but binding mode in the C to A mutants is altered. Remarkably, a point mutation (P504S), proximal to the Fe-S cluster domain, which renders cells temperature sensitive, closely mimics the global defects of the Fe-S cluster mutation itself. This points to an important role of this conserved proline residue in stabilizing the Fe-S cluster. The C to A mutants are deficient in DNA replication and repair in vivo, and, strikingly, the degree to which they are defective correlates directly with degree of loss of enzymatic activity. Taken together with previous results showing that mutations in the ATP domain affect nuclease function, our results provide a new mechanistic paradigm for coupling between nuclease and helicase modules fused in the same polypeptide.     

The O6-methylguanine-DNA methyltransferase from the hyperthermophilic archaeon Pyrococcus sp. KOD1: a thermostable repair enzyme

The enzyme O⁶-methylguanine-DNA methyltransferase (MGMT) is the most common form of cellular defense against the biological effects of O⁶-methylguanine (O⁶-MeG) in DNA. Based on PCR amplification using primers derived from conserved amino acid sequences of MGMTs from 11 species, we isolated the DNA region coding for MGMT from the hyperthermophilic archaeon Pyrococcus sp. KOD1. The MGMT gene from KOD1 (mgtk) comprises 522 nucleotides, encoding 174 amino acid residues; its product shows considerable similarity to the corresponding mammalian, yeast and bacterial enzymes, especially around putative methyl acceptor sites. Phylogenetic analysis of MGMTs showed that archaeal MGMTs were grouped with their bacterial counterparts. The location of the MGMT gene on the KOD1 chromosome was also determined. The cloned KOD1 MGMT gene was overexpressed using the T7 RNA polymerase expression system, and the recombinant protein was purified by ammonium sulfate fractionation, heat treatment, ion-exchange chromatography and gel filtration chromatography. The purified recombinant protein was assayed for its enzyme activity by monitoring transfer of [³H]methyl groups from the substrate DNA to the MGMT protein; the activity was found to be stable at 90° C for at least 30 min. When the mgtk gene was placed under the control of the lac promoter and expressed in the methyltransferase-deficient Escherichia coli strain KT233 (Δada, Δogt) cells, a MGMT was produced. The enzyme was functional in vivo and complemented the mutant phenotype, making the cells resistant to the cytotoxic properties of the alkylating agent N-methyl-N′-nitro-N-nitrosoguanidine. Received: 2 October 1997 / Accepted: 28 November 1997     

The effect of substitution of Phe181 and Phe182 with Ala on activity,substrate specificity and stabilization of substrate at the active site of Bacillus thermocatenulatus lipase

Steric hindrance leads to limitation in the access of substrate into the enzyme active site. In order to decrease steric hindrance, two conserved residues, Phe¹⁸¹ and Phe¹⁸², in the lid domain of Bacillus thermocatenulatus lipase were substituted with alanine by using site-directed mutagenesis. As a result, three mutant lipases were produced. Circular dichroism (CD) spectroscopy showed that the secondary structure of all lipases is similar to one another. F181A mutation increased the distance between phe¹⁸¹ and catalytic ser¹¹⁴, which is buried in the active site by 3.24 Å. It can be suggested that such an increase in distance may lead to a decrease in steric hindrance. F181A mutation increased overall lipase activity by up to 2.6-fold (4670 U mg⁻¹) toward C8 substrate. It also resulted in optimal lipase activity at 65 °C rather than 55 °C. F182A mutation increased the distance between phe¹⁸² and catalytic ser¹¹⁴ by 1.54 Å but failed to induce any significant effect on lipase activity. However, F181A–F182A mutation significantly decreased the activity due to decreased van der Waals interactions between the phenyl group of phenylalanines and the acyl chain of triacylglycerol. These results indicate that presence of one of the two residues, Phe¹⁸¹ or Phe¹⁸², is important for stabilizing triacylglycerols in active site.     

Does the environment around the H-cluster allow coordination of the pendant amine to the catalytic iron center in [FeFe] hydrogenases? Answers from theory

[FeFe] hydrogenases are H₂-evolving enzymes that feature a diiron cluster in their active site (the [2Fe]_H cluster). One of the iron atoms has a vacant coordination site that directly interacts with H₂, thus favoring its splitting in cooperation with the secondary amine group of a neighboring, flexible azadithiolate ligand. The vacant site is also the primary target of the inhibitor O₂. The [2Fe]_H cluster can span various redox states. The active-ready form (H_ox) attains the Fe^IIFe^I state. States more oxidized than H_ox were shown to be inactive and/or resistant to O₂. In this work, we used density functional theory to evaluate whether azadithiolate-to-iron coordination is involved in oxidative inhibition and protection against O₂, a hypothesis supported by recent results on biomimetic compounds. Our study shows that Fe–N(azadithiolate) bond formation is favored for an Fe^IIFe^II active-site model which disregards explicit treatment of the surrounding protein matrix, in line with the case of the corresponding Fe^IIFe^II synthetic system. However, the study of density functional theory models with explicit inclusion of the amino acid environment around the [2Fe]_H cluster indicates that the protein matrix prevents the formation of such a bond. Our results suggest that mechanisms other than the binding of the azadithiolate nitrogen protect the active site from oxygen in the so-called H _ox ^inact state.     

Effects of Some Growth Factors and Cytokines on the Expression of the Repair Enzyme MGMT and Protein MARP in Human Cells In Vitro

The inducible repair enzyme O⁶-methylguanine-DNA methyltransferase (MGMT) eliminates O⁶-methylguanine adducts in DNA and protects the cells from damaging effects of alkylating agents. We have found that anti-MGMT antibodies recognize both the MGMT protein with a mol. weight?~?24 kDa and a protein with a mol. weight?~?48 kDa, which was named MARP (anti-methyltransferase antibody recognizable protein). A number of growth factors and cytokines were shown to regulate the expression of MGMT and MARP proteins. The ranges of concentrations of several growth factors and cytokines that caused increasing or decreasing protein amounts in human cell cultures were determined. The results of special biological experiments have allowed us to assume a possible role of MARP in the repair of alkyl adducts in human cells.     

Reversible sequestration of active site cysteines in a 2Fe-2S-bridged dimer provides a mechanism for glutaredoxin 2 regulation in human mitochondria

Human mitochondrial glutaredoxin 2 (GLRX2), which controls intracellular redox balance and apoptosis, exists in a dynamic equilibrium of enzymatically active monomers and quiescent dimers. Crystal structures of both monomeric and dimeric forms of human GLRX2 reveal a distinct glutathione binding mode and show a 2Fe-2S-bridged dimer. The iron-sulfur cluster is coordinated through the N-terminal active site cysteine, Cys-37, and reduced glutathione. The structures indicate that the enzyme can be inhibited by a high GSH/GSSG ratio either by forming a 2Fe-2S-bridged dimer that locks away the N-terminal active site cysteine or by binding non-covalently and blocking the active site as seen in the monomer. The properties that permit GLRX2, and not other glutaredoxins, to form an iron-sulfur-containing dimer are likely due to the proline-to-serine substitution in the active site motif, allowing the main chain more flexibility in this area and providing polar interaction with the stabilizing glutathione. This appears to be a novel use of an iron-sulfur cluster in which binding of the cluster inactivates the protein by sequestering active site residues and where loss of the cluster through changes in subcellular redox status creates a catalytically active protein. Under oxidizing conditions, the dimers would readily separate into iron-free active monomers, providing a structural explanation for glutaredoxin activation under oxidative stress.     

A PDI-catalyzed thiol–disulfide switch regulates the production of hydrogen peroxide by human Ero1

Oxidative folding in the endoplasmic reticulum (ER) involves ER oxidoreductin 1 (Ero1)-mediated disulfide formation in protein disulfide isomerase (PDI). In this process, Ero1 consumes oxygen (O₂) and releases hydrogen peroxide (H₂O₂), but none of the published Ero1 crystal structures reveal any potential pathway for entry and exit of these reactants. We report that additional mutation of the Cys²⁰⁸–Cys²⁴¹ disulfide in hyperactive Ero1α (Ero1α-C104A/C131A) potentiates H₂O₂ production, ER oxidation, and cell toxicity. This disulfide clamps two helices that seal the flavin cofactor where O₂ is reduced to H₂O₂. Through its carboxyterminal active site, PDI unlocks this seal by forming a Cys²⁰⁸/Cys²⁴¹-dependent mixed-disulfide complex with Ero1α. The H₂O₂-detoxifying glutathione peroxidase 8 also binds to the Cys²⁰⁸/Cys²⁴¹ loop region. Supported by O₂ diffusion simulations, these data describe the first enzymatically controlled O₂ access into a flavoprotein active site, provide molecular-level understanding of Ero1α regulation and H₂O₂ production/detoxification, and establish the deleterious consequences of constitutive Ero1 activity.     

Reduction of protein disulfide isomerase results in open conformations and stimulates dynamic exchange between structural ensembles

Human protein disulfide isomerase (PDI) is an essential redox-regulated enzyme required for oxidative protein folding. It comprises four thioredoxin domains, two catalytically active (a, a’) and two inactive (b, b’), organized to form a flexible abb’a’ U-shape. Snapshots of unbound oxidized and reduced PDI have been obtained by X-ray crystallography. Yet, how PDI’s structure changes in response to the redox environment and inhibitor binding remains controversial. Here, we used multiparameter confocal single-molecule FRET to track the movements of the two catalytic domains with high temporal resolution. We found that at equilibrium, PDI visits three structurally distinct conformational ensembles, two “open” (O₁ and O₂) and one “closed” (C). We show that the redox environment dictates the time spent in each ensemble and the rate at which they exchange. While oxidized PDI samples O₁, O₂, and C more evenly and in a slower fashion, reduced PDI predominantly populates O₁ and O₂ and exchanges between them more rapidly, on the submillisecond timescale. These findings were not expected based on crystallographic data. Using mutational analyses, we further demonstrate that the R300-W396 cation-π interaction and active site cysteines dictate, in unexpected ways, how the catalytic domains relocate. Finally, we show that irreversible inhibitors targeting the active sites of reduced PDI did not abolish these protein dynamics but rather shifted the equilibrium toward the closed ensemble. This work introduces a new structural framework that challenges current views of PDI dynamics, helps rationalize its multifaceted role in biology, and should be considered when designing PDI-targeted therapeutics.     

SITE SPECIFIC INCORPORATION OF 6-AZAURIDINE INTO THE GENOMIC HDV RIBOZYME ACTIVE SITE

The HDV ribozyme is proposed to catalyze its self cleavage reaction by a proton transfer mechanism wherein the N3 of its C75 acts as a general acid. The C75 to U mutation, which raises the N3 pK_a from about 4 to almost 10, abolishes all enzymatic activity. To test if a U analogue with a neutral pK_a can restore ribozyme function we incorporated 6-azauridine (n⁶U), a uridine analogue with histidine-like N3 pK_a, into the genomic HDV ribozyme active site by 2′-O-ACE oligoribonucleotide protection chemistry. The resulting ribozymes were analyzed for their ability to undergo the HDV ribozyme cis-cleavage reaction. Incorporation of n⁶U at nucleotide position 75 did not restore ribozyme function compared to the U75 mutant. This suggests that the HDV ribozyme reaction mechanism involves more than positioning of a neutral nucleobase at the active site and implies that the exocyclic amino group of C75 participates in establishing the proper active site fold.     

The nitrosated bile acid DNA lesion O6-carboxymethylguanine is a substrate for the human DNA repair protein O6-methylguanine-DNA methyltransferase

The consumption of red meat is a risk factor in human colorectal cancer (CRC). One hypothesis is that red meat facilitates the nitrosation of bile acid conjugates and amino acids, which rapidly convert to DNA-damaging carcinogens. Indeed, the toxic and mutagenic DNA adduct O⁶-carboxymethylguanine (O⁶-CMG) is frequently present in human DNA, increases in abundance in people with high levels of dietary red meat and may therefore be a causative factor in CRC. Previous reports suggested that O⁶-CMG is not a substrate for the human version of the DNA damage reversal protein O⁶-methylguanine-DNA methyltransferase (MGMT), which protects against the genotoxic effects of other O⁶-alkylguanine lesions by removing alkyl groups from the O⁶-position. We now show that synthetic oligodeoxyribonucleotides containing the known MGMT substrate O⁶-methylguanine (O⁶-MeG) or O⁶-CMG effectively inactivate MGMT in vitro (IC₅₀ 0.93 and 1.8 nM, respectively). Inactivation involves the removal of the O⁶-alkyl group and its transfer to the active-site cysteine residue of MGMT. O⁶-CMG is therefore an MGMT substrate, and hence MGMT is likely to be a protective factor in CRC under conditions where O⁶-CMG is a potential causative agent.     

Frataxin Directly Stimulates Mitochondrial Cysteine Desulfurase by Exposing Substrate-binding Sites,and a Mutant Fe-S Cluster Scaffold Protein with Frataxin-bypassing Ability Acts Similarly

For iron-sulfur (Fe-S) cluster synthesis in mitochondria, the sulfur is derived from the amino acid cysteine by the cysteine desulfurase activity of Nfs1. The enzyme binds the substrate cysteine in the pyridoxal phosphate-containing site, and a persulfide is formed on the active site cysteine in a manner depending on the accessory protein Isd11. The persulfide is then transferred to the scaffold Isu, where it combines with iron to form the Fe-S cluster intermediate. Frataxin is implicated in the process, although it is unclear where and how, and deficiency causes Friedreich ataxia. Using purified proteins and isolated mitochondria, we show here that the yeast frataxin homolog (Yfh1) directly and specifically stimulates cysteine binding to Nfs1 by exposing substrate-binding sites. This novel function of frataxin does not require iron, Isu1, or Isd11. Once bound to Nfs1, the substrate cysteine is the source of the Nfs1 persulfide, but this step is independent of frataxin and strictly dependent on Isd11. Recently, a point mutation in Isu1 was found to bypass many frataxin functions. The data presented here show that the Isu1 suppressor mimics the frataxin effects on Nfs1, explaining the bypassing activity. We propose a regulatory mechanism for the Nfs1 persulfide-forming activity. Specifically, at least two separate conformational changes must occur in the enzyme for optimum activity as follows: one is mediated by frataxin interaction that exposes the “buried” substrate-binding sites, and the other is mediated by Isd11 interaction that brings the bound substrate cysteine and the active site cysteine in proximity for persulfide formation.