Stimulation of deoxyribonucleic acid excision repair in human fibroblasts pretreated with sodium butyrate

Potential Clinical Applications of the Postbiotic Butyrate in Human Skin Diseases

Human skin is the largest organ and the most external interface between the environment and the body. Vast communities of viruses, bacteria, archaea, fungi, and mites, collectively named the skin microbiome (SM), cover the skin surface and connected structures. Skin-resident microorganisms contribute to the establishment of cutaneous homeostasis and can modulate host inflammatory responses. Imbalances in the SM structure and function (dysbiosis) are associated with several skin conditions. Therefore, novel target for the skincare field could be represented by strategies, which restore or preserve the SM natural/individual balance. Several of the beneficial effects exerted by the SM are aroused by the microbial metabolite butyrate. Since butyrate exerts a pivotal role in preserving skin health, it could be used as a postbiotic strategy for preventing or treating skin diseases. Herein, we describe and share perspectives of the potential clinical applications of therapeutic strategies using the postbiotic butyrate against human skin diseases.

Potential anti-genotoxic effect of sodium butyrate to modulate induction of DNA damage by tamoxifen citrate in rat bone marrow cells

Sodium butyrate (SB) is one of the histone deacetylase inhibitors (HDACi's) that is recently evidenced to have a prooxidant activity and an ability to reduce hydrogen peroxide-induced DNA damage. Since the majority of estrogen receptor positive breast cancer patients are treated with tamoxifen citrate (TC), which exerts well established oxidative and genotoxic effects, thus the basic objective of this study is to determine whether SB could ameliorate or curate tamoxifen citrate-induced oxidative DNA damage and genotoxic effect in vivo through up-regulation of some antioxidant enzymes. The individual and combined effects of SB and TC have been examined on rat bone marrow cells, using Micronucleus assays (MN), Comet assay, DNA fragmentation, expression of some antioxidant genes using Real time-PCR and finally, oxidative stress analysis. SB significantly increased the mitotic activity (P < 0.05), while TC induced marked micronuclei and oxidative DNA damage, in the SB post-treatment group, the combination of SB (300 mg/kg) and TC (40 mg/kg) was able to decrease the induction of MN and oxidative DNA damage through up-regulation of Cat, Sod and Gpx1 genes significantly at (P < 0.05) more efficiently than that in the SB pre-treatment one. Therefore, we postulate that SB can be used therapeutically in combination with TC treatment to modulate TC genotoxic effect by reducing its oxidative stress, and thus being an appropriate agonist agent to combine with TC than each compound alone.

Acetylation regulates DNA repair mechanisms in human cells

The p300-mediated acetylation of enzymes involved in DNA repair and replication has been previously shown to stimulate or inhibit their activities in reconstituted systems. To explore the role of acetylation on DNA repair in cells we constructed plasmid substrates carrying inactivating damages in the EGFP reporter gene, which should be repaired in cells through DNA mismatch repair (MMR) or base excision repair (BER) mechanisms. We analyzed efficiency of repair within these plasmid substrates in cells exposed to deacetylase and acetyltransferase inhibitors, and also in cells deficient in p300 acetyltransferase. Our results indicate that protein acetylation improves DNA mismatch repair in MMR-proficient HeLa cells and also in MMR-deficient HCT116 cells. Moreover, results suggest that stimulated repair of mismatches in MMR-deficient HCT116 cells is done though a strand-displacement synthesis mechanism described previously for Okazaki fragments maturation and also for the EXOI-independent pathway of MMR. Loss of p300 reduced repair of mismatches in MMR-deficient cells, but did not have evident effects on BER mechanisms, including the long patch BER pathway. Hypoacetylation of the cells in the presence of acetyltransferase inhibitor, garcinol generally reduced efficiency of BER of 8-oxoG damage, indicating that some steps in the pathway are stimulated by acetylation.

Overview for the histone codes for DNA repair

DNA damage occurs continuously as a result of various factors-intracellular metabolism, replication, and exposure to genotoxic agents, such as ionizing radiation and chemotherapy. If left unrepaired, this damage could result in changes or mutations within the cell genomic material. There are a number of different pathways that the cell can utilize to repair these DNA breaks. However, it is of utmost interest to know how the DNA damage is signaled to the various DNA pathways. As DNA damage occurs within the chromatin, we postulate that modifications of histones are important for signaling the position of DNA damage, recruiting the DNA repair proteins to the site of damage, and creating an open structure such that the repair proteins can access the site of damage. We discuss the modifications that occur on the histones and the manner in which they relate to the type of damage that has occurred as well as the DNA repair pathways that are activated.

Acetylation regulates WRN catalytic activities and affects base excision DNA repair

Background

The Werner protein (WRN), defective in the premature aging disorder Werner syndrome, participates in a number of DNA metabolic processes, and we have been interested in the possible regulation of its function in DNA repair by post-translational modifications. Acetylation mediated by histone acetyltransferases is of key interest because of its potential importance in aging, DNA repair and transcription.

Methodology/Principal Findings

Here, we have investigated the p300 acetylation mediated changes on the function of WRN in base excision DNA repair (BER). We show that acetylation of WRN increases in cells treated with methyl methanesulfonate (MMS), suggesting that acetylation of WRN may play a role in response to DNA damage. This hypothesis is consistent with our findings that acetylation of WRN stimulates its catalytic activities in vitro and in vivo, and that acetylated WRN enhances pol β-mediated strand displacement DNA synthesis more than unacetylated WRN. Furthermore, we show that cellular exposure to the histone deacetylase inhibitor sodium butyrate stimulates long patch BER in wild type cells but not in WRN depleted cells, suggesting that acetylated WRN participates significantly in this process.

Conclusion/Significance

Collectively, these results provide the first evidence for a specific role of p300 mediated WRN acetylation in regulating its function during BER.

An epigenetic code for DNA damage repair pathways?

Exposure of living cells to intracellular or external mutagens results in DNA damage. Accumulation of DNA damage can lead to serious consequences because of the deleterious mutation rate resulting in genomic instability, cellular senescence, and cell death. To counteract genotoxic stress, cells have developed several strategies to detect defects in DNA structure. The eukaryotic genomic DNA is packaged through histone and nonhistone proteins into a highly condensed structure termed chromatin. Therefore the cellular enzymatic machineries responsible for DNA replication, recombination, and repair must circumvent this natural barrier in order to gain access to the DNA. Several studies have demonstrated that histone/chromatin modifications such as acetylation, methylation, and phosphorylation play crucial roles in DNA repair processes. This review will summarize the recent data that suggest a regulatory role of the epigenetic code in DNA repair processes. We will mainly focus on different covalent reversible modifications of histones as an initial step in early response to DNA damage and subsequent DNA repair. Special focus on a potential epigenetic histone code for these processes will be given in the last section. We also discuss new technologies and strategies to elucidate the putative epigenetic code for each of the DNA repair processes discussed.

UV irradiation stimulates histone acetylation and chromatin remodeling at a repressed yeast locus

Chromatin immunoprecipitation with anti-acetyl histone H3 (K9 and K14) and anti-acetyl histone H4 (K5, K8, K12, and K16) antibodies shows that Lys-9 and/or Lys-14 of histone H3, but not the relevant sites of histone H4 in nucleosomes at the repressed MFA2 promoter, are hyperacetylated after UV irradiation. This level of histone hyperacetylation diminishes gradually as repair proceeds. Accompanying this, chromatin in the promoter becomes more accessible to restriction enzymes after UV irradiation and returns to the pre-UV state gradually. UV-related histone hyperacetylation and chromatin remodeling in the MFA2 promoter depend on Gcn5p and partially on Swi2p, respectively. Deletion of GCN5, but not of SWI2, impairs repair of DNA damage in the MFA2 promoter. The post-UV histone modifications and chromatin remodeling at the repressed MFA2 promoter do not activate MFA2 transcriptionally, nor do they require damage recognition by Rad4p or Rad14p. Furthermore, we show that UV irradiation triggers genome-wide histone hyperacetylation at both histone H3 and H4. These experiments indicate that chromatin at a yeast repressed locus undergoes active change after UV radiation treatment and that failure to achieve histone H3 hyperacetylation impairs the repair of DNA damage.

Modulation of DNA damage and DNA repair in chromatin

DNA is packaged in the highly compact and dynamic structure of chromatin in eukaryotic cells. It is generally accepted that DNA processing events in the nucleus, such as transcription, replication, recombination, and repair, are restricted by this packaging. For some processes (e.g., transcription), the chromatin fiber is "preset" in a more open structure to allow access of proteins to specific regions of DNA within this structural hierarchy. These regions contain modified nucleosomes that accommodate a less compact state of chromatin and allow access to specific regions of DNA. DNA repair proteins, however, must access DNA lesions in all structural domains of chromatin after sudden insult to the genome. Damaged DNA must be recognized, removed, and replaced by repair enzymes at all levels of chromatin packaging. Therefore, the modulation of DNA damage and its repair in chromatin is crucial to our understanding of the fate of potential mutagenic and carcinogenic lesions in DNA. In this review, we discuss the modulation of DNA damage and DNA repair by chromatin structure, and the modulation of chromatin structure by these events.

Strand breaks are repaired efficiently in human ribosomal genes

We examined repair of DNA strand breaks induced by the anti-cancer drug bleomycin in both Pol I and Pol II transcribed genes in permeabilized human fibroblasts. The majority of these breaks (>80%) are single strand breaks (SSBs) thought to be repaired by base excision repair enzymes. Repair was examined in each strand of a 7. 2-kilobase fragment, completely within the Pol I transcribed region of ribosomal DNA (rDNA) and an 8.3-kilobase fragment completely within the Pol II transcribed region of the dihydrofolate reductase (DHFR) gene. Bleomycin dose-response studies revealed no bias for SSBs in either strand of the rDNA fragment. Furthermore, repair of SSBs is rapid (approximately 80% resealed in 60 min) in both the transcribed and nontranscribed strands of rDNA. Rapid repair of SSBs is also observed in both strands of the DHFR gene (approximately 60% resealed in 60 min). In contrast, little (or no) repair of UV photodimers occurs in either strand of human rDNA, regardless of whether cells are confluent or actively growing. Thus, DNA lesions in human ribosomal genes may be more accessible to base excision repair enzymes than those involved in nucleotide excision repair.

Modulatory effect of sodium butyrate on AluI-induced chromosomal aberrations in CHO cells

Exponentially growing CHO cells exposed to millimolar concentrations of sodium butyrate (SB) for 24 h were treated with AluI using two methods of cell poration, i.e., electroporation and streptolysin O (SLO). Under both conditions, SB was found to induce a 2-4-fold increase in AluI-induced chromosomal aberrations. When cells in monolayer were treated with AluI/SLO, lower concentrations of SB (2.5 mM) and AluI (1-4 U/ml) were required to produce a similar effect as that observed for electroporated cells, demonstrating the differential sensitivity of the two methods. Furthermore, in AluI/SLO-treated cells, a higher percentage of cells was found to show increased frequencies of aberrations per cell, compared to AluI/electroporated cells. The mechanism by which SB modulates the cell response to AluI treatment might involve changes in chromatin configuration thereby increasing the accessibility of AluI to different parts of chromatin.

Purification of DNA fragments containing excision-repair patches from human cells using streptavidin-biotin

We have developed a method for purifying DNA fragments containing excision-repair patches which involves incorporation of biotinated deoxyuridine monophosphate into repair patches followed by isolation of biotin-containing DNA fragments using streptavidin and either isopycnic density gradient centrifugation or gel electrophoresis. Normal human fibroblasts were damaged with UV radiation, rendered permeable and allowed to perform repair synthesis in the presence of ATP, dATP, dGTP, [3H]dCTP and biotinated deoxyuridine triphosphate. The DNA was purified, sonicated to a number-average molecular weight of 150 bp, then incubated with streptavidin, a protein with a high affinity for biotin and with a density of 1.3 g/ml in cesium trifluoroacetate compared to 1.6 g/ml for DNA. Isopycnic centrifugation in cesium trifluoroacetate resulted in the separation of the streptavidin-DNA complex with little or no dissociation. The streptavidin-DNA complex was also separated from free DNA by electrophoresis in 2% agarose. This method is applicable to any type DNA damage repaired by the excision repair pathways in which thymine is present in the repair patches, including damage from chemical carcinogens and ionizing radiation.

Histone hyperacetylation can induce unfolding of the nucleosome core particle

A direct correlation exists between the level of histone H4 hyperacetylation induced by sodium butyrate and the extent to which nucleosomes lose their compact shape and become elongated (62.0% of the particles have a length/width ratio over 1.6; overall mean in the length/width ratio = 1.83 +/- 0.48) when bound to electron microscope specimen grids at low ionic strength (1mM EDTA, 10mM Tris, pH 8.0). A marked proportion of elongated core particles is also observed in the naturally occurring hyperacetylated chicken testis chromatin undergoing spermatogenesis when analyzed at low ionic strength (36.8% of the particles have a length/width ratio over 1.6). Core particles of elongated shape (length/width ratio over 1.6) generated under low ionic strength conditions are absent in the hypoacetylated chicken erythrocyte chromatin and represent only 2.3% of the untreated Hela S3 cell core particles containing a low proportion of hyperacetylated histones. The marked differences between control and hyperacetylated core particles are absent if the particles are bound to the carbon support film in the presence of 0.2 M NaCl, 6mM MgCl2 and 10mM Tris pH 8.0, conditions known to stabilize nucleosomes. A survey of the published work on histone hyperacetylation together with the present results indicate that histone hyperacetylation does not produce any marked disruption of the core particle 'per se', but that it decreases intranucleosomal stabilizing forces as judged by the lowered stability of the hyperacetylated core particle under conditions of shearing stress such as cationic competition by the carbon support film of the EM grid for DNA binding.

In situ enzymology of DNA replication and ultraviolet-induced DNA repair synthesis in permeable human cells

Using permeable diploid human fibroblasts, we have studied the deoxyribonucleoside triphosphate concentration dependences of ultraviolet- (UV-) induced DNA repair synthesis and semiconservative DNA replication. In both cell types (AG1518 and IMR-90) examined, the apparent Km values for dCTP, dGTP, and dTTP for DNA replication were between 1.2 and 2.9 microM. For UV-induced DNA repair synthesis, the apparent Km values were substantially lower, ranging from 0.11 to 0.44 microM for AG1518 cells and from 0.06 to 0.24 microM for IMR-90 cells. Control experiments established that these values were not significantly influenced by nucleotide degradation during the permeable cell incubations or by the presence of residual endogenous nucleotides within the permeable cells. Recent data implicate DNA polymerase delta in UV-induced repair synthesis and suggest that DNA polymerases alpha and delta are both involved in semiconservative replication. We measured Km values for dGTP and dTTP for polymerases alpha and delta, for comparison with the values for replication and repair synthesis. Km values for polymerase alpha were 2.0 microM for dGTP and 5.0 microM for dTTP. For polymerase delta, the Km values were 2.0 microM for dGTP and 3.5 microM for dTTP. The deoxyribonucleotide Km values for DNA polymerase delta are much greater than the Km values for UV-induced repair synthesis, suggesting that when polymerase delta functions in DNA repair, its characteristics are altered substantially either by association with accessory proteins or by direct posttranslational modification. In contrast, the deoxyribonucleotide binding characteristics of the DNA replication machinery differ little from those of the isolated DNA polymerases.(ABSTRACT TRUNCATED AT 250 WORDS)

Analysis of butylphenyl-guanine, butylphenyl-deoxyguanosine, and butylphenyl-deoxyguanosine triphosphate inhibition of DNA replication and ultraviolet-induced DNA repair synthesis using permeable human fibroblasts

The purine base and nucleoside analogues N2-(p-n-butylphenyl)-guanine (BuPh-Gua) and N2-(p-n-butylphenyl)-2'-deoxyguanosine (BuPh-dGuo) are strong inhibitors of isolated mammalian DNA polymerase alpha, but are less potent that expected as inhibitors of DNA replication in intact cultured cells [G. E. Wright, L. W. Dudycz, Z. Kazimierczuk, N. C. Brown and N. N. Khan, J. med. Chem. 30, 109 (1987)]. The mechanistic basis for these observations was explored using permeable human fibroblasts. DNA replication in the permeable cells was inhibited only slightly by BuPh-Gua and BuPh-dGuo at 100 microM, the highest concentration which could be attained. Similar results were obtained for ultraviolet-induced DNA repair synthesis, a process which is though to involve the same DNA polymerase as replication. More detailed studies were performed using the corresponding nucleotide analogue, N2-(p-n-butylphenyl)-2'-deoxyguanosine-5'-triphosphate (BuPh-dGTP), which is much more water-soluble than the base and nucleoside. The apparent Ki values for BuPh-dGTP inhibition of both replication and ultraviolet-induced repair synthesis in permeable cells were approximately 3 microM. These values are several hundred-fold greater than the apparent Ki for BuPh-dGTP inhibition of isolated human DNA polymerase alpha, which is approximately 10 nM. We conclude that BuPh-Gua and BuPh-dGuo are poor inhibitors of DNA replication in intact cells not because of permeability barriers, but because, unlike polymerase alpha, cellular DNA synthesis is relatively insensitive to this group of inhibitors. These results suggest that polymerase alpha may not be a good general model for predicting the potency of base, deoxyribonucleoside and deoxyribonucleotide analogues as inhibitors of mammalian cellular DNA replication. The fact that the permeable cell systems accurately reflect the relative insensitivity to butylphenyl-guanine derivatives of mammalian DNA replication suggests that permeable cells may be useful tools in future studies of base and nucleoside analogues.

Stimulation of DNA repair synthesis of rat thymocytes by novobiocin and nalidixic acid in vitro without detectable DNA damage

Scheduled (SDS) and unscheduled (UDS) DNA synthesis as well as nucleoid sedimentation was investigated in vitro under the influence of novobiocin (NB) and nalidixic acid (NA) using intact thymic (T-cells) and splenic (S-cells) rat cells and cells which were exposed to X-rays, UV irradiation, methyl methanesulfonate (MMS), and DNA polymerase inhibitors. At concentrations of greater than or equal to 56.25 (S-cells) and greater than or equal to 225 micrograms/ml (T-cells), respectively, NB inhibited SDS in a dose-dependent manner. Within a concentration range of greater than or equal to 225-900 micrograms NB/ml, UDS of S-cells decreased to values far below the tracer ([3H-methyl]-thymidine) incorporation of control cells, whereas UDS of T-cells increased by at least 200%. Within a concentration range of 450-1800 micrograms/ml, NA enhanced SDS and UDS by about 30% in S-cells and by 100% in T-cells. The stimulating activity of NB and/or NA could be eliminated specifically by the DNA polymerase beta inhibitor 2',3'-dideoxythymidine. Enhanced nucleoid sedimentation was observed at NB concentrations greater than or equal to 750 micrograms/ml; S-cells revealed a higher sedimentation rate than T-cells. It is suggested that NB (and NA) influence DNA topology in a rather cell specific manner, stimulating UDS of T-cells by a DNA polymerase beta - dependent repair-like mechanism.

DNA replication and UV-induced DNA repair synthesis in human fibroblasts are much less sensitive than DNA polymerase alpha to inhibition by butylphenyl-deoxyguanosine triphosphate

In mammalian cells, both semiconservative DNA replication and the DNA repair patch synthesis induced by high doses of ultraviolet radiation are known to be inhibited by aphidicolin, indicating the involvement in these processes of one or both of the aphidicolin-sensitive DNA polymerases, alpha and/or delta. In this paper, N2-(p-n-butylphenyl)-2'-deoxyguanosine-5'-triphosphate, a strong inhibitor of polymerase alpha and a weak inhibitor of polymerase delta, is used to further characterize the DNA polymerase(s) involved in these two forms of nuclear DNA synthesis. In permeable human fibroblasts, DNA replication and ultraviolet-induced DNA repair synthesis are more resistant to the inhibitor than DNA polymerase alpha by factors of approximately 500 and 3000, respectively. These findings are most consistent with the involvement of DNA polymerase delta in these processes.