Mahmoud I. Shoulkamy

Repair and biochemical effects of DNA–protein crosslinks

Genomic DNA is associated with various structural, regulatory, and transaction proteins. The dynamic and reversible association between proteins and DNA ensures the accurate expression and propagation of genetic information. However, various endogenous, environmental, and chemotherapeutic agents induce DNA-protein crosslinks (DPCs), and hence covalently trap proteins on DNA. Since DPCs are extremely large compared to conventional DNA lesions, they probably impair many aspects of DNA transactions such as replication, transcription, and repair due to steric hindrance. Recent genetic and biochemical studies have shed light on the elaborate molecular mechanism by which cells repair or tolerate DPCs. This review summarizes the current knowledge regarding the repair and biochemical effects of the most ubiquitous form of DPCs, which are associated with no flanked DNA strand breaks. In bacteria small DPCs are eliminated by nucleotide excision repair (NER), whereas oversized DPCs are processed by RecBCD-dependent homologous recombination (HR). NER does not participate in the repair of DPCs in mammalian cells, since the upper size limit of DPCs amenable to mammalian NER is smaller than that of bacterial NER. Thus, DPCs are processed exclusively by HR. The reactivation of the stalled replication fork at DPCs by HR seems to involve fork breakage in mammalian cells but not in bacterial cells. In addition, recent proteomic studies have identified the numbers of proteins in DPCs induced by environmental and chemotherapeutic agents. However, it remains largely elusive how DPCs affect replication and transcription at the molecular level. Considering the extremely large nature of DPCs, it is possible that they impede the progression of replication and transcription machineries by mechanisms different from those for conventional DNA lesions. This might also be true for the DNA damage response and signaling mechanism.

Detection of DNA–protein crosslinks (DPCs) by novel direct fluorescence labeling methods: distinct stabilities of aldehyde and radiation-induced DPCs

Proteins are covalently trapped on DNA to form DNA–protein crosslinks (DPCs) when cells are exposed to DNA-damaging agents. DPCs interfere with many aspects of DNA transactions. The current DPC detection methods indirectly measure crosslinked proteins (CLPs) through DNA tethered to proteins. However, a major drawback of such methods is the non-linear relationship between the amounts of DNA and CLPs, which makes quantitative data interpretation difficult. Here we developed novel methods of DPC detection based on direct CLP measurement, whereby CLPs in DNA isolated from cells are labeled with fluorescein isothiocyanate (FITC) and quantified by fluorometry or western blotting using anti-FITC antibodies. Both formats successfully monitored the induction and elimination of DPCs in cultured cells exposed to aldehydes and mouse tumors exposed to ionizing radiation (carbon-ion beams). The fluorometric and western blotting formats require 30 and 0.3 μg of DNA, respectively. Analyses of the isolated genomic DPCs revealed that both aldehydes and ionizing radiation produce two types of DPC with distinct stabilities. The stable components of aldehyde-induced DPCs have half-lives of up to days. Interestingly, that of radiation-induced DPCs has an infinite half-life, suggesting that the stable DPC component exerts a profound effect on DNA transactions over many cell cycles.

Translocation and Stability of Replicative DNA Helicases upon Encountering DNA-Protein Cross-links

Background: DNA-protein cross-links (DPCs) are formed by DNA-damaging agents. Results: DPCs on the translocating strand but not on the nontranslocating strand block hexameric replicative helicases in a size-dependent manner. Stalled helicases dissociate from DNA with a half-life of 15–36 min. Conclusion: DPCs on the translocating and nontranslocating strands constitute helicase and polymerase blocks, respectively. Significance: Reversible and irreversible protein roadblocks may have distinct effects on replisomes. DNA-protein cross-links (DPCs) are formed when cells are exposed to various DNA-damaging agents. Because DPCs are extremely large, steric hindrance conferred by DPCs is likely to affect many aspects of DNA transactions. In DNA replication, DPCs are first encountered by the replicative helicase that moves at the head of the replisome. However, little is known about how replicative helicases respond to covalently immobilized protein roadblocks. In the present study we elucidated the effect of DPCs on the DNA unwinding reaction of hexameric replicative helicases in vitro using defined DPC substrates. DPCs on the translocating strand but not on the nontranslocating strand impeded the progression of the helicases including the phage T7 gene 4 protein, simian virus 40 large T antigen, Escherichia coli DnaB protein, and human minichromosome maintenance Mcm467 subcomplex. The impediment varied with the size of the cross-linked proteins, with a threshold size for clearance of 5.0–14.1 kDa. These results indicate that the central channel of the dynamically translocating hexameric ring helicases can accommodate only small proteins and that all of the helicases tested use the steric exclusion mechanism to unwind duplex DNA. These results further suggest that DPCs on the translocating and nontranslocating strands constitute helicase and polymerase blocks, respectively. The helicases stalled by DPC had limited stability and dissociated from DNA with a half-life of 15–36 min. The implications of the results are discussed in relation to the distinct stabilities of replisomes that encounter tight but reversible DNA-protein complexes and irreversible DPC roadblocks.

Aldehydes with high and low toxicities inactivate cells by damaging distinct cellular targets.

Aldehydes are genotoxic and cytotoxic molecules and have received considerable attention for their associations with the pathogenesis of various human diseases. In addition, exposure to anthropogenic aldehydes increases human health risks. The general mechanism of aldehyde toxicity involves adduct formation with biomolecules such as DNA and proteins. Although the genotoxic effects of aldehydes such as mutations and chromosomal aberrations are directly related to DNA damage, the role of DNA damage in the cytotoxic effects of aldehydes is poorly understood because concurrent protein damage by aldehydes has similar effects. In this study, we have analysed how saturated and α,β-unsaturated aldehydes exert cytotoxic effects through DNA and protein damage. Interestingly, DNA repair is essential for alleviating the cytotoxic effect of weakly toxic aldehydes such as saturated aldehydes but not highly toxic aldehydes such as long α,β-unsaturated aldehydes. Thus, highly toxic aldehydes inactivate cells exclusively by protein damage. Our data suggest that DNA interstrand crosslinks, but not DNA-protein crosslinks and DNA double-strand breaks, are the critical cytotoxic DNA damage induced by aldehydes. Further, we show that the depletion of intracellular glutathione and the oxidation of thioredoxin 1 partially account for the DNA damage-independent cytotoxicity of aldehydes. On the basis of these findings, we have proposed a mechanistic model of aldehyde cytotoxicity mediated by DNA and protein damage.

Radiation-induced DNA–protein cross-links: Mechanisms and biological significance ☆

Ionizing radiation produces various DNA lesions such as base damage, DNA single-strand breaks (SSBs), DNA double-strand breaks (DSBs), and DNA-protein cross-links (DPCs). Of these, the biological significance of DPCs remains elusive. In this article, we focus on radiation-induced DPCs and review the current understanding of their induction, properties, repair, and biological consequences. When cells are irradiated, the formation of base damage, SSBs, and DSBs are promoted in the presence of oxygen. Conversely, that of DPCs is promoted in the absence of oxygen, suggesting their importance in hypoxic cells, such as those present in tumors. DNA and protein radicals generated by hydroxyl radicals (i.e., indirect effect) are responsible for DPC formation. In addition, DPCs can also be formed from guanine radical cations generated by the direct effect. Actin, histones, and other proteins have been identified as cross-linked proteins. Also, covalent linkages between DNA and protein constituents such as thymine-lysine and guanine-lysine have been identified and their structures are proposed. In irradiated cells and tissues, DPCs are repaired in a biphasic manner, consisting of fast and slow components. The half-time for the fast component is 20min-2h and that for the slow component is 2-70h. Notably, radiation-induced DPCs are repaired more slowly than DSBs. Homologous recombination plays a pivotal role in the repair of radiation-induced DPCs as well as DSBs. Recently, a novel mechanism of DPC repair mediated by a DPC protease was reported, wherein the resulting DNA-peptide cross-links were bypassed by translesion synthesis. The replication and transcription of DPC-bearing reporter plasmids are inhibited in cells, suggesting that DPCs are potentially lethal lesions. However, whether DPCs are mutagenic and induce gross chromosomal alterations remains to be determined.

Induction of DNA-protein cross-links by ionizing radiation and their elimination from the genome.

Ionizing radiation produces various types of DNA lesions, such as base damage, single-strand breaks, double-strand breaks (DSBs), and DNA-protein cross-links (DPCs). Of these, DSBs are the most critical lesions underlying the lethal effects of ionizing radiation. With DPCs, proteins covalently trapped in DNA constitute strong roadblocks to replication and transcription machineries, and hence can be lethal to cells. The formation of DPCs by ionizing radiation is promoted in the absence of oxygen, whereas that of DSBs is retarded. Accordingly, the contribution of DPCs to the lethal events in irradiated cells may not be negligible for hypoxic cells, such as those present in tumors. However, the role of DPCs in the lethal effects of ionizing radiation remains largely equivocal. In the present study, normoxic and hypoxic mouse tumors were irradiated with X-rays [low linear energy transfer (LET) radiation] and carbon (C)-ion beams (high LET radiation), and the resulting induction of DPCs and DSBs and their removal from the genome were analyzed. X-rays and C-ion beams produced more DPCs in hypoxic tumors than in normoxic tumors. Interestingly, the yield of DPCs was slightly but statistically significantly greater (1.3- to 1.5-fold) for C-ion beams than for X-rays. Both X-rays and C-ion beams generated two types of DPC that differed according to their rate of removal from the genome. This was also the case for DSBs. The half-lives of the rapidly removed components of DPCs and DSBs were similar (<1 h), but those of the slowly removed components of DPCs and DSBs were markedly different (3.9-5 h for DSBs versus 63-70 h for DPCs). The long half-life and abundance of the slowly removed DPCs render them persistent in DNA, which may impede DNA transactions and confer deleterious effects on cells in conjunction with DSBs.

Depletion of RUVBL2 in Human Cells Confers Moderate Sensitivity to Anticancer Agents

Background: Many anticancer agents kill cancer cells by inducing lethal damage in DNA, but the capacity of DNA repair of cells reduce the therapeutic efficacy of anticancer agents. RuvB-like (RUVBL) 2 is part of large protein complexes such as TIP60 and INO80 that are involved in chromatin remodeling and DNA damage responses and repair. Relatively few studies have investigated the role of RUVBL2 in the survival of cells after exposure to anticancer agents. Methods: We depleted RUVBL2 in human MRC5-SV cells by small interfering (si) RNA and assessed the sensitivity of the cells to chemotherapeutic anticancer agents including cisplatin (cisPt), 2’-deoxy-5-azacytidine (azadC), and mitomycin C (MMC), and to physical DNA-damaging agents including X-rays. Results: The knockdown efficiency with 10 nM siRUVBL2 was 80% on day 3 post-transfection, and knockdown (>65%) persisted on day 6. The cell growth slowed significantly due to depletion of RUVBL2 when compared to mock- and control siRNA-treated cells, indicating that RUVBL2 is essential for the proliferation of cells. The RUVBL2-depleted cells were moderately sensitive to cisPt, azadC, and X-rays. The increase in the sensitivity to MMC was marginal. Conclusion: Depletion of RUVBL2 in cells confers moderate sensitivity to anticancer agents and X-rays, presumably through partial impairment of the homologous recombination repair of DNA double-strand break intermediates formed directly or indirectly by anticancer agents or X-rays. Further studies are necessary to clarify the exact role of RUVBL2 in this process.

Effect of Benomyl and Metalaxyl on reproduction of the plant parasite (Pythium Deliense) and the mycoparasite (P. Oligandrum)

Benomyl did not inhibit the growth of isolates of Pythium deliense and Pythium oligandrum but at concentrations of 10 ppm benomyl slightly inhibited the growth of P. oligandrum. Isolate of El-U002A of P. oligandrum was more sensitive to benomyl than the isolate El-U002B. Metalaxyl inhibited the growth of all pythia studied starting from 2 ppm and completed at 10 ppm. All concentrations (2, 5 and 10 ppm) of metalaxyl caused a decline in the mycelial dry weight but the degree of this decline was more pronounced at high concentrations of the fungicide for P. deliense while all concentrations of metalaxyl inhibited the growth of P. oligandrum. Benomyl did not effect the mycelial dry weight for all the pythia investigated. Zoospore production of P. deliense was generally high after 24 h incubation at 25°C. Water amended with 2, 5 and 10 ppm benomyl did not affect the two isolates tested. On the other hand, metalaxyl inhibited zoospore production of P. deliense at all concentrations studied especially the higher ones. Zoospore production of P. oligandrum appeared in the same manner as P. deliense but high concentrations of benomyl decreased zoospore production. Oospore production of P. deliense was not affected with 2, 5 and 10 ppm benomyl by the two isolates tested. On the other hand, metalaxyl inhibited oospore production of P. deliense at all concentrations studied especially the higher ones. Oospore production of P. oligandrum appeared in the same manner as P. deliense but high concentrations of benomyl decrease oospore production.