Specific Repair Mechanisms Research Articles

O-211 The DNA double-strand break repair genes expression exhibits significant changes in the postnatal mouse testes from early to aged terms

Abstract Study question How does the DNA double-strand break (DSB) repair genes, Rad51, Rpa70, Ku80, and Xrcc4, expression change in the postnatal mouse testes from early to aged terms. Summary answer The Rad51, Rpa70, and Ku80 genes expression decreased in the postnatal mouse testes from early to aged terms. What is known already The DSB levels occurring in the spermatogenic cells during spermatogenesis increase during biological aging in men. DSBs can be repaired by specific repair mechanisms including homologous recombination (HR) or non-homologous end joining (NHEJ) pathways. While RAD51 and RPA70 are the main components of HR process, KU80 and XRCC4 play important roles in NHEJ pathway. As is known, gH2AX is a commonly used biomarker for determining the DSBs. Study design, size, duration The potential reasons of DSB levels in the spermatogenic cells during aging is not fully addressed yet. In this study, we aimed to analyze the expression of the Rad51, Rpa70, Ku80 and Xrcc4 genes at mRNA and protein levels in the postnatal mouse testes from early to aged terms. Participants/materials, setting, methods We comprised five groups based on the testicular histology, consisting of early (1- and 2-week-old), young (3- and 4-week-old), adult (5- and 6-week-old), late-adult (16-, 18- and 20-week-old), and aged (48-, 50- and 52-week-old). DSB repair genes expression at mRNA and protein levels were determined using qRT-PCR and immunohistochemistry techniques, respectively. The data were evaluated by using one-way ANOVA and Tukey post hoc test. P<0.05 was considered statistically significant. Main results and the role of chance The Rad51, Rpa70, Ku80, and Xrcc4 mRNA levels significantly decreased in the aged group when compared to the young, adult and late-adult groups (P<0.05). gH2AX was intensively localized in the nucleus of primary spermatocytes of postnatal testes, and its levels either in the total or seminiferous tubules or germinal epithelial cells involving primary spermatocytes, round spermatids, elongating spermatids, elongated spermatids, and Sertoli Cells were higher in the aged group than the remained groups (P<0.05). The DSB repair proteins were detected in the spermatogenic cells, in which pachytene spermatocytes showed stronger intensity. The levels of RAD51 and RP70 proteins implicating in HR pathway were lower in the seminiferous tubules of the aged group when compared to the adult and late-adult groups (P<0.05). Moreover, the total and seminiferous tubules analysis revealed that KU80 levels decreased in the aged group in comparison to the remaining groups except for early group, as observed for the spermatogonia, primary spermatocytes and round spermatids of the aged group (P<0.05). Although there were no significant differences found in the total and seminiferous tubule analysis for XRCC4 protein, its levels decreased in the round spermatids and elongating spermatids of the aged group compared to the adult and late-adult groups. Limitations, reasons for caution The limitation of this study is that we did not isolate spermatogenic cell types from aged mice to compare adult ones. Wider implications of the findings The increase of DSB in the spermatogenic cells of aged mice may derive from reduced levels of RAD51, RPA70 and KU80 proteins playing roles in DSB repair. Further researches are required to determine the molecular mechanisms resulting in decrease of these protein levels. Trial registration number not applicable

Mitochondrial tyrosyl-DNA phosphodiesterase 2 and its TDP2S short isoform.

Tyrosyl-DNA phosphodiesterase 2 (TDP2) repairs abortive topoisomerase II cleavage complexes. Here, we identify a novel short isoform of TDP2 (TDP2S) expressed from an alternative transcription start site. TDP2S contains a mitochondrial targeting sequence, contributing to its enrichment in the mitochondria and cytosol, while full-length TDP2 contains a nuclear localization signal and the ubiquitin-associated domain in the N-terminus. Our study reveals that both TDP2 isoforms are present and active in the mitochondria. Comparison of isogenic wild-type (WT) and TDP2 knockout (TDP2-/-/-) DT40 cells shows that TDP2-/-/- cells are hypersensitive to mitochondrial-targeted doxorubicin (mtDox), and that complementing TDP2-/-/- cells with human TDP2 restores resistance to mtDox. Furthermore, mtDox selectively depletes mitochondrial DNA in TDP2-/-/- cells. Using CRISPR-engineered human cells expressing only the TDP2S isoform, we show that TDP2S also protects human cells against mtDox. Finally, lack of TDP2 in the mitochondria reduces the mitochondria transcription levels in two different human cell lines. In addition to identifying a novel TDP2S isoform, our report demonstrates the presence and importance of both TDP2 isoforms in the mitochondria.

NAXE Mutations Disrupt the Cellular NAD(P)HX Repair System and Cause a Lethal Neurometabolic Disorder of Early Childhood

To safeguard the cell from the accumulation of potentially harmful metabolic intermediates, specific repair mechanisms have evolved. APOA1BP, now renamed NAXE, encodes an epimerase essential in the cellular metabolite repair for NADHX and NADPHX. The enzyme catalyzes the epimerization of NAD(P)HX, thereby avoiding the accumulation of toxic metabolites. The clinical importance of the NAD(P)HX repair system has been unknown. Exome sequencing revealed pathogenic biallelic mutations in NAXE in children from four families with (sub-) acute-onset ataxia, cerebellar edema, spinal myelopathy, and skin lesions. Lactate was elevated in cerebrospinal fluid of all affected individuals. Disease onset was during the second year of life and clinical signs as well as episodes of deterioration were triggered by febrile infections. Disease course was rapidly progressive, leading to coma, global brain atrophy, and finally to death in all affected individuals. NAXE levels were undetectable in fibroblasts from affected individuals of two families. In these fibroblasts we measured highly elevated concentrations of the toxic metabolite cyclic-NADHX, confirming a deficiency of the mitochondrial NAD(P)HX repair system. Finally, NAD or nicotinic acid (vitamin B3) supplementation might have therapeutic implications for this fatal disorder.

Cadmium versus copper toxicity: Insights from an integrated dissection of protein synthesis pathway in the digestive glands of mussel Mytilus galloprovincialis

The main purpose of this study was to investigate the impact of metal-mediated stress on the protein-synthesis pathway in mussels. To this end, mussels (Mytilus galloprovincialis) underwent a 15 days exposure to 100μg/L Cu2+ or Cd2+. Both metals, in particular Cd2+, accumulated in mussel digestive glands and generated a specific status of oxidative-stress. Exposure of mussels to each metal resulted in 40% decrease of the tRNA-aminoacylation efficiency, at the end of exposure. Cu2+ also caused a progressive loss in the capability of 40S-ribosomal subunits to form 48S pre-initiation complex, which reached 34% of the control at the end of exposure. Other steps of translation underwent less pronounced, but measurable damages. Mussels exposed to Cd2+ for 5 days presented a similar pattern of translational dysfunctions in digestive glands, but during the following days of exposure the ribosomal efficiency was gradually restored. Meanwhile, metallothionein levels significantly increased, suggesting that upon Cd2+-mediated stress the protein-synthesizing activity was reorganized both quantitatively and qualitatively. Conclusively, Cd2+ and Cu2+ affect translation at several levels. However, the pattern of translational responses differs, largely depending on the capability of each metal to affect cytotoxic pathways in the tissues, such as induction of antioxidant defense and specific repair mechanisms.

Dissection of DNA Damage Responses Using Multiconditional Genetic Interaction Maps

To protect the genome, cells have evolved a diverse set of pathways designed to sense, signal, and repair multiple types of DNA damage. To assess the degree of coordination and crosstalk among these pathways, we systematically mapped changes in the cell's genetic network across a panel of different DNA-damaging agents, resulting in ~1,800,000 differential measurements. Each agent was associated with a distinct interaction pattern, which, unlike single-mutant phenotypes or gene expression data, has high statistical power to pinpoint the specific repair mechanisms at work. The agent-specific networks revealed roles for the histone acetyltranferase Rtt109 in the mutagenic bypass of DNA lesions and the neddylation machinery in cell-cycle regulation and genome stability, while the network induced by multiple agents implicates Irc21, an uncharacterized protein, in checkpoint control and DNA repair. Our multiconditional genetic interaction map provides a unique resource that identifies agent-specific and general DNA damage response pathways.

Checkpoint mechanisms at the intersection between DNA damage and repair

In response to genomic insults cells trigger a signal transduction pathway, known as DNA damage checkpoint, whose role is to help the cell to cope with the damage by coordinating cell cycle progression, DNA replication and DNA repair mechanisms. Accumulating evidence suggests that activation of the first checkpoint kinase in the cascade is not due to the lesion itself, but it requires recognition and initial processing of the lesion by a specific repair mechanism. Repair enzymes likely convert a variety of physically and chemically different lesions to a unique common structure, a ssDNA region, which is the checkpoint triggering signal. Checkpoint kinases can modify the activity of repair mechanisms, allowing for efficient repair, on one side, and modulating the generation of the ssDNA signal, on the other. This strategy may be important to allow the most effective repair and a prompt recovery from the damage condition. Interestingly, at least in some cases, if the damage level is low enough the cell can deal with the lesions and it does not need to activate the checkpoint response. On the other hand if damage level is high or if the lesions are not rapidly repairable, checkpoint mechanisms become important for cell survival and preservation of genome integrity.

Elongating RNA Polymerase II Is Disassembled through Specific Degradation of Its Largest but Not Other Subunits in Response to DNA Damage in Vivo

Although previous biochemical studies have demonstrated global degradation of the largest subunit, Rpb1p, of RNA polymerase II in response to DNA damage, it is still not clear whether the initiating or elongating form of Rpb1p is targeted for degradation in vivo. Further, whether other components of RNA polymerase II are degraded in response to DNA damage remains unknown. Here, we show that the Rpb1p subunit of the elongating, but not initiating, form of RNA polymerase II is degraded at the active genes in response to 4-nitroquinoline-1-oxide-induced DNA damage in Saccharomyces cerevisiae. However, other subunits of RNA polymerase II are not degraded in response to DNA damage. Further, we show that Rpb1p is essential for RNA polymerase II assembly at the active gene, and thus, the degradation of Rpb1p following DNA damage disassembles elongating RNA polymerase II. Taken together, our data demonstrate that Rpb1p but not other subunits of elongating RNA polymerase II is specifically degraded in response to DNA damage, and such a degradation of Rpb1p is critical for the disassembly of elongating RNA polymerase II at the DNA lesion in vivo.

The Repair Enzyme Peptide Methionine-S-Sulfoxide Reductase Is Expressed in Human Epidermis and Upregulated by UVA Radiation

Recently, we reported that photoaging correlates well with the amount of oxidized protein accumulated in the upper dermis, while protein oxidation levels in the viable epidermis are very low. We hypothesized that this might be due to epidermal expression of the repair enzymes methionine sulfoxide reductases (MSRs). The expression of human methionine sulfoxide reductase A (MSRA) was investigated in HaCaT cells, primary human keratinocytes, and in human skin. High MSRA mRNA and protein levels as well as MSR activity were found in cultured human keratinocytes. MSRA was expressed in human epidermis, as shown by immunohistochemistry in healthy human skin. Repetitive in vivo exposure of human skin to solar-simulated light on 10 consecutive days (n=10 subjects) significantly increased epidermal MSRA expression. To further assess the functional relevance of the enzyme, its expression in response to UVB, UVA, and H(2)O(2) was investigated in HaCaT cells. While UVB lowered protein expression of MSRA, an upregulation was observed in response to low doses of UVA and H(2)O(2). In summary, MSRA represents the only enzyme so far identified in human skin that is capable of repairing oxidative protein damage. In addition to melanogenesis and DNA repair systems, a wavelength-specific activation of epidermal MSRA may be involved in epidermal photoprotection.

573. Enhanced Level of Gene Correction Mediated by Oligonucleotides Containing CpG Modification in the mdx Mouse Model for Duchenne Muscular Dystrophy

Single point mutations and large deletions of the dystrophin gene are responsible for Duchenne muscular dystrophy (DMD) a severe neuromuscular disorders characterized by complete absence of dystrophin expression in skeletal muscles. Gene editing mediated by single stranded oligonucleotides (ssODNs) represents an appealing option to treat the disease since it has the potential to treat both single point mutations as well as deletions that cause frame shift of the dystrophin mRNA. The major limitation of the technology has been so far the low level of genomic correction detected in muscle cells. We have focused on the development of new vectors capable to activate specific repair mechanisms and capable of directing the repair process specifically on the sequence of the genomic DNA targeted for correction. The methyl binding protein 4 (MBD4) takes an active role in the base excision repair mechanism and is highly expressed in muscles. In addition to containing a binding site for the methylcytosine, MBD4 contains also a specific glycosilase capable of recognizing a T to G transversion at CpG sites and direct the conversion of the thymine into methylcytosine. CpG modifications were introduced on the mutating base of the targeting oligonucleotide in the attempt to mimic a deamination of methylcytosine which results in the activation of MBD4. All the studies were conducted using the mdx mouse as a model for DMD. This strain contains a stop codon in exon 23 of the dystrophin gene that is responsible for the absence of dystrophin protein in skeletal muscles. As a target for the single base substitution we have chosen the splice boundary of exon 23 of the mouse dystrophin gene in order to induced exon skipping to bypass the nonsense mutation and induce expression of internally deleted but functional dystrophin proteins. We have designed ssODNs complimentary to the coding or the non-coding strand of the donor site of exon 23. CpG modifications were introduced at the targeted base. The ability of these modified ssODNs to increase gene repair was studied in muscle cells both in vitro and in vivo. The level of dystrophin protein expression was significantly increased by the use of ssODNs containing CpG modifications on the targeting base. Studies conducted on muscle cells in culture demonstrate up- regulation of MBD4 mRNA and the activation of the base excision repair mechanism through which MBD4 acts, demonstrating the specificity of the repair process recruited by the ssODNs. Correction of the dystrophin gene was shown to occur at the genomic level and was stable over prolonged periods of time. In muscle cells in culture, restoration of dystrophin expression was analyzed at the protein level by western blot and immunostaining analysis and at the mRNA level by RT-PCR. In vivo analysis also showed restoration of dystrophin in skeletal muscles of injected mice by immunostaining. These studies demonstrate that the efficacy of oligonucleotide- mediated gene correction can be increased by improving oligonucleotide design.

Hypothetical role of RNA damage avoidance in preventing human disease

Most of nucleic acids damaging agents are not only restricted to DNA but equally affect DNA and RNA molecules. Considering that RNA damage could be very toxic for the cell, a property used by some cancer treatments, it would not be unexpected to find out that several proteins may be involved in RNA damage avoidance mechanisms helping cells to counteract such cytotoxic effects. Up to now, only one specific repair mechanism allowing cells to deal with toxic effects of methylated RNA have been described. However, there are in the literature several data suggesting that this study may only be the tip of the iceberg and that cells might be able to counteract the deleterious effects of a large variety of RNA damage. In this review, we will discuss the different proteins that may be involved in the mechanism of RNA damage avoidance and their potential role in human diseases.

Aging in fungi: role of mitochondria in Podospora anserina

In experimental gerontology, there is a long tradition in the use of both unicellular and filamentous species of fungi. In the last three decades, biochemical, genetic and molecular approaches have proved very fruitful in elucidating different aspects of ageing. It was shown that various genes and molecular pathways are involved in life span control. The oxygenic energy metabolism plays a central role. During mitochondrial energy transduction, reactive oxygen species (ROS) are generated as by-products. These molecules are able to damage all cellular compounds leading to cellular dysfunctions. Within certain limits, however, cells are able to cope with ROS-related problems. First, ROS scavengers can be induced which are effective in lowering the molecular burden of ROS on cellular functions. Second, if damage occurs, specific repair mechanisms and the general turnover of affected molecules can maintain cellular functions. Finally, if damage of essential components is too severe, cells may induce specific pathways to compensate for the corresponding impairments. A coordinated interaction between different cellular compartments is involved in these processes. In this review I shall concentrate on the ageing in the filamentous ascomycete Podospora anserina. It is clear that both environmental as well as genetic traits are involved in the control of life span and that mitochondrial-nuclear interactions play a paramount role.

Influence of oxygen radical injury on DNA methylation.

One of the most prevalent products of oxygen radical injury in DNA is 8-hydroxyguanosine. Cells must be able to withstand damage by oxygen radicals and possess specific repair mechanisms that correct this oxidative lesion. However, when these defenses are oversaturated, such as under conditions of high oxidative stress, or when repair is inefficient, the miscoding potential of this lesion can result in mutations in the mammalian genome. In addition to causing genetic changes, active oxygen species can lead to epigenetic alterations in DNA methylation, without changing the DNA base sequence. Such changes in DNA methylation patterns can strongly affect the regulation of expression of many genes. Although DNA methylation patterns have been found to be altered during carcinogenesis, little is known about the mechanism(s) that produce this loss of epigenetic controls of gene expression in tumors. Replacement of guanine with the oxygen radical adduct 8-hydroxyguanine profoundly alters methylation of adjacent cytosines, suggesting a role for oxidative injury in the formation of aberrant DNA methylation patterns during carcinogenesis. In this paper, we review both the genetic and epigenetic mechanisms of oxidative DNA damage and its association with the carcinogenic process, with special emphasis on the influence of free radical injury on DNA methylation.

Enhanced gene expression of calcium regulatory proteins in stunned porcine myocardium

Increasing evidence points to a molecular disturbance of Ca2+ homeostasis in stunned myocardium. The aim of this study was therefore to investigate the expression of mRNAs for Ca2+ binding proteins related to the sarcoplasmic reticulum in a porcine model of myocardial stunning. In 22 anaesthetised pigs, stunning was achieved by one or two cycles of 10 min left anterior descending coronary artery occlusion and reperfusion. Hearts were excised at various timepoints of the protocol. Total RNA was extracted from stunned (experimental) as well as normally perfused (control) myocardium. Northern blot analysis using radioactive cDNA probes revealed that the Ca(2+)-ATPase mRNA levels increased 1.6-fold compared to the control value at 90 min of the second reperfusion. The steady state level of phospholamban mRNA rose 2.5-fold at 180 min of reperfusion. A 2.3-fold increase in calsequestrin mRNAs was observed after 90 min of the second reperfusion. The calmodulin and alpha, beta myosin heavy chain mRNA levels were unchanged. A glyceraldehyde-3-phosphate dehydrogenase cDNA probe served as a reference system. Nuclear run-on assays showed increased transcription for Ca(2+)-ATPase and calsequestrin at 90 min of reperfusion, supporting the view that increased mRNA levels seen with northern hybridisation were due to increased transcription of the respective gene. The results suggest specific repair mechanisms of stunned myocardium and point to the involvement of calcium regulatory proteins related to the sarcoplasmic reticulum in the pathogenesis of myocardial stunning.

Repair of ethylnitrosourea-induced DNA damage in the newborn rat. I. Alkali-labile lesions and in situ breaks

The extreme sensitivity of the developing rat brain to tumor induction by N-ethyl-N-nitrosourea (ENU) has been ascribed to the relatively inefficient repair of the presumed promutagenic lesion O6-ethylguanine from brain DNA. We have compared the brain of the newborn rat with liver, kidney and lung with respect to the repair of other types of DNA lesions that ENU induces, namely single strand breaks and alkali-labile lesions. The induction and repair or loss of these lesions has been analysed by alkaline sucrose gradient sedimentation using both mild as well as strong alkaline hydrolysis conditions. We found that ENU induces few lesions in the DNA of various organs that are detectable as breaks after mild alkaline hydrolysis. 24 h after ENU treatment such lesions are no longer detectable in brain DNA, while they are detectable in the DNA from other organs up to 10 days after ENU treatment. The number of ENU-induced lesions, detectable as breaks after strong alkaline hydrolysis, is far larger. These lesions were persistent in kidney DNA, disappeared slowly from liver DNA (t(1/2) = about 10 days), and more rapidly from brain and lung DNA (t(1/2) = 2-3 days). The latter result seems to be in contradiction with various reports that a large fraction of the ENU-induced alkali-labile lesions are stable in vivo. This difference between our results and those of others might be due to a difference between proliferating and non-proliferating cells. Whether the alkali-labile lesions are removed from brain and lung DNA by a specific repair mechanism or by other causes remains to be investigated.

Mechanism of the radioprotecting action of chemical compounds on Escherichia coli cells

The effect of radioprotection of indolylalkylamines (5-methoxytryptamine) and aminothiols (cysteamine) on E. coli cells is practically absent if the cells have genetic defects in the repair systems. This means that the explanation of radioprotection by scavenging of free radicals is invalid and that specific repair mechanisms may be involved. In order to explain the radioprotective mechanism it was suggested that the radioprotectors interact with the damaged sites in DNA so that they become partly screened from repairing endonucleases. Under these conditions the reduction of incision rate results in diminished enzymatic induction of lethal double-strand breaks in DNA, this being important only in wild type cells. To prove this hypothesis an experimental procedure was developed using bacterial cells carrying plasmids (ColE1). This procedure enabled to determine the in vivo rate of enzymatic incision of gamma-sites. It was found that the protectors did not change the total amount of gamma-damages in DNA but reduced the rate of enzymatic incision.