Novel AlkB Dioxygenases—Alternative Models for In Silico and In Vivo Studies

Background: ALKBH proteins, the homologs of Escherichia coli AlkB dioxygenase, constitute a direct, single-protein repair system, protecting cellular DNA and RNA against the cytotoxic and mutagenic activity of alkylating agents, chemicals significantly contributing to tumor formation and used in cancer therapy. In silico analysis and in vivo studies have shown the existence of AlkB homologs in almost all organisms. Nine AlkB homologs (ALKBH1–8 and FTO) have been identified in humans. High ALKBH levels have been found to encourage tumor development, questioning the use of alkylating agents in chemotherapy. The aim of this work was to assign biological significance to multiple AlkB homologs by characterizing their activity in the repair of nucleic acids in prokaryotes and their subcellular localization in eukaryotes. Methodology and Findings: Bioinformatic analysis of protein sequence databases identified 1943 AlkB sequences with eight new AlkB subfamilies. Since Cyanobacteria and Arabidopsis thaliana contain multiple AlkB homologs, they were selected as model organisms for in vivo research. Using E. coli alkB2 mutant and plasmids expressing cyanobacterial AlkBs, we studied the repair of methyl methanesulfonate (MMS) and chloroacetaldehyde (CAA) induced lesions in ssDNA, ssRNA, and genomic DNA. On the basis of GFP fusions, we investigated the subcellular localization of ALKBHs in A. thaliana and established its mostly nucleo-cytoplasmic distribution. Some of the ALKBH proteins were found to change their localization upon MMS treatment. Conclusions: Our in vivo studies showed highly specific activity of cyanobacterial AlkB proteins towards lesions and nucleic acid type. Subcellular localization and translocation of ALKBHs in A. thaliana indicates a possible role for these proteins in the repair of alkyl lesions. We hypothesize that the multiplicity of ALKBHs is due to their involvement in the metabolism of nucleo-protein complexes; we find their repair by ALKBH proteins to be economical and effective alternative to degradation and de novo synthesis

Lethal and mutagenic properties of MMS-generated DNA lesions in Escherichia coli cells deficient in BER and AlkB-directed DNA repair.

Methylmethane sulphonate (MMS), an S(N)2-type alkylating agent, generates DNA methylated bases exhibiting cytotoxic and mutagenic properties. Such damaged bases can be removed by a system of base excision repair (BER) and by oxidative DNA demethylation catalysed by AlkB protein. Here, we have shown that the lack of the BER system and functional AlkB dioxygenase results in (i) increased sensitivity to MMS, (ii) elevated level of spontaneous and MMS-induced mutations (measured by argE3 --> Arg(+) reversion) and (iii) induction of the SOS response shown by visualization of filamentous growth of bacteria. In the xth nth nfo strain additionally mutated in alkB gene, all these effects were extreme and led to 'error catastrophe', resulting from the presence of unrepaired apurinic/apyrimidinic (AP) sites and 1-methyladenine (1meA)/3-methylcytosine (3meC) lesions caused by deficiency in, respectively, BER and AlkB dioxygenase. The decreased level of MMS-induced Arg(+) revertants in the strains deficient in polymerase V (PolV) (bearing the deletion of the umuDC operon), and the increased frequency of these revertants in bacteria overproducing PolV (harbouring the pRW134 plasmid) indicate the involvement of PolV in the error-prone repair of 1meA/3meC and AP sites. Comparison of the sensitivity to MMS and the induction of Arg(+) revertants in the double nfo alkB and xth alkB, and the quadruple xth nth nfo alkB mutants showed that the more AP sites there are in DNA, the stronger the effect of the lack of AlkB protein. Since the sum of MMS-induced Arg(+) revertants in xth, nfo and nth xth nfo and alkB mutants is smaller than the frequency of these revertants in the BER(-) alkB(-) strain, we consider two possibilities: (i) the presence of AP sites in DNA results in relaxation of its structure that facilitates methylation and (ii) additional AP sites are formed in the BER(-) alkB(-) mutants

Pseudomonas putida AlkA and AlkB Proteins Comprise Different Defense Systems for the Repair of Alkylation Damage to DNA – In Vivo, In Vitro, and In Silico Studies

Alkylating agents introduce cytotoxic and/or mutagenic lesions to DNA bases leading to induction of adaptive (Ada) response, a mechanism protecting cells against deleterious effects of environmental chemicals. In Escherichia coli, the Ada response involves expression of four genes: ada, alkA, alkB, and aidB. In Pseudomonas putida, the organization of Ada regulon is different, raising questions regarding regulation of Ada gene expression. The aim of the presented studies was to analyze the role of AlkA glycosylase and AlkB dioxygenase in protecting P. putida cells against damage to DNA caused by alkylating agents. The results of bioinformatic analysis, of survival and mutagenesis of methyl methanesulfonate (MMS) or N-methyl-N’-nitro-N-nitrosoguanidine (MNNG) treated P. putida mutants in ada, alkA and alkB genes as well as assay of promoter activity revealed diverse roles of Ada, AlkA and AlkB proteins in protecting cellular DNA against alkylating agents. We found AlkA protein crucial to abolish the cytotoxic but not the mutagenic effects of alkylans since: (i) the mutation in the alkA gene was the most deleterious for MMS/MNNG treated P. putida cells, (ii) the activity of the alkA promoter was Ada-dependent and the highest among the tested genes. P. putida AlkB (PpAlkB), characterized by optimal conditions for in vitro repair of specific substrates, complementation assay, and M13/MS2 survival test, allowed to establish conservation of enzymatic function of P. putida and E. coli AlkB protein. We found that the organization of P. putida Ada regulon differs from that of E. coli. AlkA protein induced within the Ada response is crucial for protecting P. putida against cytotoxicity, whereas Ada prevents the mutagenic action of alkylating agents. In contrast to E. coli AlkB (EcAlkB), PpAlkB remains beyond the Ada regulon and is expressed constitutively. It probably creates a backup system that protects P. putida strains defective in other DNA repair systems against alkylating agents of exo- and endogenous origin

Thrombus aspiration in ST elevation myocardial infarction: comparative efficacy in patients treated early and late after onset of symptoms

Background Restoration of myocardial perfusion is the goal of percutaneous coronary intervention (PCI) in patients with ST elevation myocardial infarction. A major predictor of no-reflow is the increasing time to treatment (TTT). Thrombus aspiration (TA) is reported to improve myocardial reperfusion as compared with standard PCI (SP). Objective To investigate the influence of TTT on TA efficacy. Design Pooled analysis of individual patients' data of three prospective randomised trials comparing TA and SP. Patients A total of 299 patients (150 in TA group and 149 in SP group) entered the study. The study population was divided into three subgroups according to the TTT: <= 3 h (short TTT subgroup), >3 h to <= 6 h (intermediate TTT subgroup), >6 h to <= 12 h (long TTT subgroup). Main outcome measures The goal of the study was the comparison of optimal myocardial reperfusion, defined as the combination of myocardial blush grade 2 or 3 at post-PCI angiography and ST resolution more than 70% at post-PCI ECG, between SP and TA according to TTT. Results In the SP group, increasing TTT was associated with a decreased rate of optimal reperfusion (27.4% vs 17.9% vs 10%, p for trend=0.06), whereas in the TA group the same trend was not seen (40.9% vs 33.8% vs 50%, p for trend=0.93). In a multivariate logistic regression model, a significant interaction (p=0.04) between time to treatment and thrombus aspiration was observed. Conclusions TA limits the adverse effects of TTT prolongation on myocardial reperfusion

Thrombus aspiration in ST elevation myocardial infarction: comparative efficacy in patients treated early and late after onset of symptoms

Background Restoration of myocardial perfusion is the goal of percutaneous coronary intervention (PCI) in patients with ST elevation myocardial infarction. A major predictor of no-reflow is the increasing time to treatment (TTT). Thrombus aspiration (TA) is reported to improve myocardial reperfusion as compared with standard PCI (SP). Objective To investigate the influence of TTT on TA efficacy. Design Pooled analysis of individual patients' data of three prospective randomised trials comparing TA and SP. Patients A total of 299 patients (150 in TA group and 149 in SP group) entered the study. The study population was divided into three subgroups according to the TTT: 3 h to 6 h to <= 12 h (long TTT subgroup). Main outcome measures The goal of the study was the comparison of optimal myocardial reperfusion, defined as the combination of myocardial blush grade 2 or 3 at post-PCI angiography and ST resolution more than 70% at post-PCI ECG, between SP and TA according to TTT. Results In the SP group, increasing TTT was associated with a decreased rate of optimal reperfusion (27.4% vs 17.9% vs 10%, p for trend=0.06), whereas in the TA group the same trend was not seen (40.9% vs 33.8% vs 50%, p for trend=0.93). In a multivariate logistic regression model, a significant interaction (p=0.04) between time to treatment and thrombus aspiration was observed. Conclusions TA limits the adverse effects of TTT prolongation on myocardial reperfusion

Thrombus aspiration in ST elevation myocardial infarction: comparative efficacy in patients treated early and late after onset of symptoms

Background Restoration of myocardial perfusion is the goal of percutaneous coronary intervention (PCI) in patients with ST elevation myocardial infarction. A major predictor of no-reflow is the increasing time to treatment (TTT). Thrombus aspiration (TA) is reported to improve myocardial reperfusion as compared with standard PCI (SP). Objective To investigate the influence of TTT on TA efficacy. Design Pooled analysis of individual patients' data of three prospective randomised trials comparing TA and SP. Patients A total of 299 patients (150 in TA group and 149 in SP group) entered the study. The study population was divided into three subgroups according to the TTT: &lt;= 3 h (short TTT subgroup), &gt;3 h to &lt;= 6 h (intermediate TTT subgroup), &gt;6 h to &lt;= 12 h (long TTT subgroup). Main outcome measures The goal of the study was the comparison of optimal myocardial reperfusion, defined as the combination of myocardial blush grade 2 or 3 at post-PCI angiography and ST resolution more than 70% at post-PCI ECG, between SP and TA according to TTT. Results In the SP group, increasing TTT was associated with a decreased rate of optimal reperfusion (27.4% vs 17.9% vs 10%, p for trend=0.06), whereas in the TA group the same trend was not seen (40.9% vs 33.8% vs 50%, p for trend=0.93). In a multivariate logistic regression model, a significant interaction (p=0.04) between time to treatment and thrombus aspiration was observed. Conclusions TA limits the adverse effects of TTT prolongation on myocardial reperfusion