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1.
J Mol Biol ; 436(16): 168672, 2024 Jun 20.
Artigo em Inglês | MEDLINE | ID: mdl-38908783

RESUMO

CTC1-STN1-TEN1 (CST) is a single-stranded DNA binding protein vital for telomere length maintenance with additional genome-wide roles in DNA replication and repair. While CST was previously shown to function in double-strand break repair and promote replication restart, it is currently unclear whether it has specialized roles in other DNA repair pathways. Proper and efficient repair of DNA is critical to protecting genome integrity. Telomeres and other G-rich regions are strongly predisposed to oxidative DNA damage in the form of 8-oxoguanines, which are typically repaired by the base-excision repair (BER) pathway. Moreover, recent studies suggest that CST functions in the repair of oxidative DNA lesions. Therefore, we tested whether CST interacts with and regulates BER protein activity. Here, we show that CST robustly stimulates proteins involved in BER, including OGG1, Pol ß, APE1, and LIGI, on both telomeric and non-telomeric DNA substrates. Biochemical reconstitution of the pathway indicates that CST stimulates BER. Finally, knockout of STN1 or CTC1 leads to increased levels of 8-oxoguanine, suggesting defective BER in the absence of CST. Combined, our results define an undiscovered function of CST in BER, where it acts as a stimulatory factor to promote efficient genome-wide oxidative repair.

2.
J Vis Exp ; (206)2024 Apr 26.
Artigo em Inglês | MEDLINE | ID: mdl-38738876

RESUMO

Functional characterization of proteins requires them to be expressed and purified in substantial amounts with high purity to perform biochemical assays. The Fast Protein Liquid Chromatography (FPLC) system allows high-resolution separation of complex protein mixtures. By adjusting various parameters in FPLC, such as selecting the appropriate purification matrix, regulating the protein sample's temperature, and managing the sample's flow rate onto the matrix and the elution rate, it is possible to ensure the protein's stability and functionality. In this protocol, we will demonstrate the versatility of the FPLC system to purify 6X-His-tagged flap endonuclease 1 (FEN1) protein, produced in bacterial cultures. To improve protein purification efficiency, we will focus on multiple considerations, including proper column packing and preparation, sample injection using a sample loop, flow rate of sample application to the column, and sample elution parameters. Finally, the chromatogram will be analyzed to identify fractions containing high yields of protein and considerations for proper recombinant protein long-term storage. Optimizing protein purification methods is crucial for improving the precision and reliability of protein analysis.


Assuntos
Cromatografia de Afinidade , Cromatografia de Afinidade/métodos , Endonucleases Flap/química , Endonucleases Flap/isolamento & purificação , Endonucleases Flap/metabolismo , Cromatografia Líquida/métodos , Histidina/química , Escherichia coli/genética , Escherichia coli/química , Escherichia coli/metabolismo , Oligopeptídeos/química , Oligopeptídeos/isolamento & purificação , Proteínas Recombinantes de Fusão/química , Proteínas Recombinantes de Fusão/isolamento & purificação , Proteínas Recombinantes de Fusão/genética , Proteínas Recombinantes de Fusão/metabolismo
3.
Nucleic Acids Res ; 51(22): 12185-12206, 2023 Dec 11.
Artigo em Inglês | MEDLINE | ID: mdl-37930834

RESUMO

The Msh2-Msh3 mismatch repair (MMR) complex in Saccharomyces cerevisiae recognizes and directs repair of insertion/deletion loops (IDLs) up to ∼17 nucleotides. Msh2-Msh3 also recognizes and binds distinct looped and branched DNA structures with varying affinities, thereby contributing to genome stability outside post-replicative MMR through homologous recombination, double-strand break repair (DSBR) and the DNA damage response. In contrast, Msh2-Msh3 promotes genome instability through trinucleotide repeat (TNR) expansions, presumably by binding structures that form from single-stranded (ss) TNR sequences. We previously demonstrated that Msh2-Msh3 binding to 5' ssDNA flap structures interfered with Rad27 (Fen1 in humans)-mediated Okazaki fragment maturation (OFM) in vitro. Here we demonstrate that elevated Msh2-Msh3 levels interfere with DNA replication and base excision repair in vivo. Elevated Msh2-Msh3 also induced a cell cycle arrest that was dependent on RAD9 and ELG1 and led to PCNA modification. These phenotypes also required Msh2-Msh3 ATPase activity and downstream MMR proteins, indicating an active mechanism that is not simply a result of Msh2-Msh3 DNA-binding activity. This study provides new mechanistic details regarding how excess Msh2-Msh3 can disrupt DNA replication and repair and highlights the role of Msh2-Msh3 protein abundance in Msh2-Msh3-mediated genomic instability.


Assuntos
Instabilidade Genômica , Proteínas de Saccharomyces cerevisiae , Humanos , DNA/genética , DNA/metabolismo , Reparo de Erro de Pareamento de DNA , Reparo do DNA , Proteínas de Ligação a DNA/metabolismo , Proteína 2 Homóloga a MutS/genética , Proteína 2 Homóloga a MutS/metabolismo , Proteína 3 Homóloga a MutS/genética , Proteína 3 Homóloga a MutS/metabolismo , Saccharomyces cerevisiae/genética , Saccharomyces cerevisiae/metabolismo , Proteínas de Saccharomyces cerevisiae/metabolismo
4.
Genes (Basel) ; 14(4)2023 03 23.
Artigo em Inglês | MEDLINE | ID: mdl-37107532

RESUMO

DNA polymerase delta is the primary polymerase that is involved in undamaged nuclear lagging strand DNA replication. Our mass-spectroscopic analysis has revealed that the human DNA polymerase δ is acetylated on subunits p125, p68, and p12. Using substrates that simulate Okazaki fragment intermediates, we studied alterations in the catalytic properties of acetylated polymerase and compared it to the unmodified form. The current data show that the acetylated form of human pol δ displays a higher polymerization activity compared to the unmodified form of the enzyme. Additionally, acetylation enhances the ability of the polymerase to resolve complex structures such as G-quadruplexes and other secondary structures that might be present on the template strand. More importantly, the ability of pol δ to displace a downstream DNA fragment is enhanced upon acetylation. Our current results suggest that acetylation has a profound effect on the activity of pol δ and supports the hypothesis that acetylation may promote higher-fidelity DNA replication.


Assuntos
DNA Polimerase III , Lisina , Humanos , DNA Polimerase III/genética , DNA Polimerase III/metabolismo , Lisina/genética , Acetilação , Replicação do DNA , DNA/genética , DNA/metabolismo
5.
Genes (Basel) ; 14(1)2022 12 29.
Artigo em Inglês | MEDLINE | ID: mdl-36672839

RESUMO

Flap endonuclease 1 (FEN1) is an essential enzyme that removes RNA primers and base lesions during DNA lagging strand maturation and long-patch base excision repair (BER). It plays a crucial role in maintaining genome stability and integrity. FEN1 is also implicated in RNA processing and biogenesis. A recent study from our group has shown that FEN1 is involved in trinucleotide repeat deletion by processing the RNA strand in R-loops through BER, further suggesting that the enzyme can modulate genome stability by facilitating the resolution of R-loops. However, it remains unknown how FEN1 can process RNA to resolve an R-loop. In this study, we examined the FEN1 cleavage activity on the RNA:DNA hybrid intermediates generated during DNA lagging strand processing and BER in R-loops. We found that both human and yeast FEN1 efficiently cleaved an RNA flap in the intermediates using its endonuclease activity. We further demonstrated that FEN1 was recruited to R-loops in normal human fibroblasts and senataxin-deficient (AOA2) fibroblasts, and its R-loop recruitment was significantly increased by oxidative DNA damage. We showed that FEN1 specifically employed its endonucleolytic cleavage activity to remove the RNA strand in an R-loop during BER. We found that FEN1 coordinated its DNA and RNA endonucleolytic cleavage activity with the 3'-5' exonuclease of APE1 to resolve the R-loop. Our results further suggest that FEN1 employed its unique tracking mechanism to endonucleolytically cleave the RNA strand in an R-loop by coordinating with other BER enzymes and cofactors during BER. Our study provides the first evidence that FEN1 endonucleolytic cleavage can result in the resolution of R-loops via the BER pathway, thereby maintaining genome integrity.


Assuntos
Endonucleases Flap , Estruturas R-Loop , Humanos , DNA/genética , DNA/metabolismo , Reparo do DNA/genética , Exonucleases/genética , Endonucleases Flap/genética , Endonucleases Flap/metabolismo , Instabilidade Genômica , RNA/genética
6.
Life Sci Alliance ; 4(9)2021 09.
Artigo em Inglês | MEDLINE | ID: mdl-34272328

RESUMO

Heterogeneous nuclear ribonucleoprotein E1 (hnRNP E1) is a tumor suppressor protein that binds site- and structure-specifically to RNA sequences to regulate mRNA stability, facilitate alternative splicing, and suppress protein translation on several metastasis-associated mRNAs. Here, we show that hnRNP E1 binds polycytosine-rich DNA tracts present throughout the genome, including those at promoters of several oncogenes and telomeres and monitors genome integrity. It binds DNA in a site- and structure-specific manner. hnRNP E1-knockdown cells displayed increased DNA damage signals including γ-H2AX at its binding sites and also showed increased mutations. UV and hydroxyurea treatment of hnRNP E1-knockdown cells exacerbated the basal DNA damage signals with increased cell cycle arrest, activation of checkpoint proteins, and monoubiquitination of proliferating cell nuclear antigen despite no changes in deubiquitinating enzymes. DNA damage caused by genotoxin treatment localized to hnRNP E1 binding sites. Our work suggests that hnRNP E1 facilitates functions of DNA integrity proteins at polycytosine tracts and monitors DNA integrity at these sites.


Assuntos
Sítios de Ligação , Proteínas de Ligação a DNA/metabolismo , DNA/metabolismo , Instabilidade Genômica , Poli C , Proteínas de Ligação a RNA/metabolismo , Animais , Sequência de Bases , DNA/química , DNA/genética , Dano ao DNA/efeitos dos fármacos , Dano ao DNA/efeitos da radiação , Humanos , Camundongos , Modelos Biológicos , Mutação , Taxa de Mutação , Conformação de Ácido Nucleico , Motivos de Nucleotídeos , Poli C/química , Ligação Proteica , Transdução de Sinais
7.
Curr Biol ; 31(6): 1141-1153.e7, 2021 03 22.
Artigo em Inglês | MEDLINE | ID: mdl-33400922

RESUMO

Stereocilia on auditory sensory cells are actin-based protrusions that mechanotransduce sound into an electrical signal. These stereocilia are arranged into a bundle with three rows of increasing length to form a staircase-like morphology that is required for hearing. Stereocilia in the shorter rows, but not the tallest row, are mechanotransducing because they have force-sensitive channels localized at their tips. The onset of mechanotransduction during mouse postnatal development refines stereocilia length and width. However, it is unclear how actin is differentially regulated between stereocilia in the tallest row of the bundle and the shorter, mechanotransducing rows. Here, we show actin turnover is increased at the tips of mechanotransducing stereocilia during bundle maturation. Correspondingly, from birth to postnatal day 6, these stereocilia had increasing amounts of available actin barbed ends, where monomers can be added or lost readily, as compared with the non-mechanotransducing stereocilia in the tallest row. The increase in available barbed ends depended on both mechanotransduction and MYO15 or EPS8, which are required for the normal specification and elongation of the tallest row of stereocilia. We also found that loss of the F-actin-severing proteins ADF and cofilin-1 decreased barbed end availability at stereocilia tips. These proteins enriched at mechanotransducing stereocilia tips, and their localization was perturbed by the loss of mechanotransduction, MYO15, or EPS8. Finally, stereocilia lengths and widths were dysregulated in Adf and Cfl1 mutants. Together, these data show that actin is remodeled, likely by a severing mechanism, in response to mechanotransduction.


Assuntos
Fatores de Despolimerização de Actina/metabolismo , Actinas/metabolismo , Mecanotransdução Celular , Estereocílios/metabolismo , Animais , Feminino , Audição , Masculino , Camundongos , Camundongos Endogâmicos C57BL
8.
Curr Genet ; 67(1): 85-92, 2021 Feb.
Artigo em Inglês | MEDLINE | ID: mdl-33079209

RESUMO

PIF1 family helicases are evolutionarily conserved among prokaryotes and eukaryotes. These enzymes function to support genome integrity by participating in multiple DNA transactions that can be broadly grouped into DNA replication, DNA repair, and telomere maintenance roles. However, the levels of PIF1 activity in cells must be carefully controlled, as Pif1 over-expression in Saccharomyces cerevisiae is toxic, and knockdown or over-expression of human PIF1 (hPIF1) supports cancer cell growth. This suggests that PIF1 family helicases must be subject to tight regulation in vivo to direct their activities to where and when they are needed, as well as to maintain those activities at proper homeostatic levels. Previous work shows that C-terminal phosphorylation of S. cerevisiae Pif1 regulates its telomere maintenance activity, and we recently identified that Pif1 is also regulated by lysine acetylation. The over-expression toxicity of Pif1 was exacerbated in cells lacking the Rpd3 lysine deacetylase, but mutation of the NuA4 lysine acetyltransferase subunit Esa1 ameliorated this toxicity. Using recombinant proteins, we found that acetylation stimulated the DNA binding affinity, ATPase activity, and DNA unwinding activities of Pif1. All three domains of the helicase were targets of acetylation in vitro, and multiple lines of evidence suggest that acetylation drives a conformational change in the N-terminal domain of Pif1 that impacts this stimulation. It is currently unclear what triggers lysine acetylation of Pif1 and how this modification impacts the many in vivo functions of the helicase, but future work promises to shed light on how this protein is tightly regulated within the cell.


Assuntos
DNA Helicases/genética , Instabilidade Genômica/genética , Histona Acetiltransferases/genética , Proteínas de Saccharomyces cerevisiae/genética , Acetilação , Reparo do DNA/genética , Replicação do DNA/genética , Regulação Fúngica da Expressão Gênica/genética , Histona Desacetilases/genética , Humanos , Neoplasias/genética , Neoplasias/metabolismo , Saccharomyces cerevisiae/genética , Telômero/genética , Homeostase do Telômero/genética
9.
J Biol Chem ; 295(46): 15482-15497, 2020 11 13.
Artigo em Inglês | MEDLINE | ID: mdl-32878983

RESUMO

In Saccharomyces cerevisiae, the Pif1 helicase functions in both nuclear and mitochondrial DNA replication and repair processes, preferentially unwinding RNA:DNA hybrids and resolving G-quadruplex structures. We sought to determine how the various activities of Pif1 are regulated in vivo Here, we report lysine acetylation of nuclear Pif1 and demonstrate that it influences both Pif1's cellular roles and core biochemical activities. Using Pif1 overexpression toxicity assays, we determined that the acetyltransferase NuA4 and deacetylase Rpd3 are primarily responsible for the dynamic acetylation of nuclear Pif1. MS analysis revealed that Pif1 was modified in several domains throughout the protein's sequence on the N terminus (Lys-118 and Lys-129), helicase domain (Lys-525, Lys-639, and Lys-725), and C terminus (Lys-800). Acetylation of Pif1 exacerbated its overexpression toxicity phenotype, which was alleviated upon deletion of its N terminus. Biochemical assays demonstrated that acetylation of Pif1 stimulated its helicase, ATPase, and DNA-binding activities, whereas maintaining its substrate preferences. Limited proteolysis assays indicate that acetylation of Pif1 induces a conformational change that may account for its altered enzymatic properties. We propose that acetylation is involved in regulating of Pif1 activities, influencing a multitude of DNA transactions vital to the maintenance of genome integrity.


Assuntos
Núcleo Celular/metabolismo , DNA Helicases/metabolismo , Lisina/metabolismo , Proteínas de Saccharomyces cerevisiae/metabolismo , Acetilação , DNA Helicases/química , DNA Helicases/genética , DNA Fúngico/metabolismo , Histona Acetiltransferases/química , Histona Acetiltransferases/metabolismo , Histona Desacetilases/metabolismo , Mutagênese Sítio-Dirigida , Domínios Proteicos , RNA Fúngico/metabolismo , Saccharomyces cerevisiae/metabolismo , Proteínas de Saccharomyces cerevisiae/química , Proteínas de Saccharomyces cerevisiae/genética , Especificidade por Substrato , Espectrometria de Massas em Tandem
10.
J Biol Chem ; 295(40): 13902-13913, 2020 10 02.
Artigo em Inglês | MEDLINE | ID: mdl-32763971

RESUMO

Trinucleotide repeat (TNR) expansion and deletion are responsible for over 40 neurodegenerative diseases and associated with cancer. TNRs can undergo somatic instability that is mediated by DNA damage and repair and gene transcription. Recent studies have pointed toward a role for R-loops in causing TNR expansion and deletion, and it has been shown that base excision repair (BER) can result in CAG repeat deletion from R-loops in yeast. However, it remains unknown how BER in R-loops can mediate TNR instability. In this study, using biochemical approaches, we examined BER enzymatic activities and their influence on TNR R-loops. We found that AP endonuclease 1 incised an abasic site on the nontemplate strand of a TNR R-loop, creating a double-flap intermediate containing an RNA:DNA hybrid that subsequently inhibited polymerase ß (pol ß) synthesis of TNRs. This stimulated flap endonuclease 1 (FEN1) cleavage of TNRs engaged in an R-loop. Moreover, we showed that FEN1 also efficiently cleaved the RNA strand, facilitating pol ß loop/hairpin bypass synthesis and the resolution of TNR R-loops through BER. Consequently, this resulted in fewer TNRs synthesized by pol ß than those removed by FEN1, thereby leading to repeat deletion. Our results indicate that TNR R-loops preferentially lead to repeat deletion during BER by disrupting the balance between the addition and removal of TNRs. Our discoveries open a new avenue for the treatment and prevention of repeat expansion diseases and cancer.


Assuntos
DNA Polimerase beta/química , Reparo do DNA , DNA Liase (Sítios Apurínicos ou Apirimidínicos)/química , Endonucleases Flap/química , Estruturas R-Loop , Repetições de Trinucleotídeos , Humanos
11.
Methods Mol Biol ; 2056: 25-68, 2020.
Artigo em Inglês | MEDLINE | ID: mdl-31586340

RESUMO

Trinucleotide repeat (TNR) tracts are inherently unstable during DNA replication, leading to repeat expansions and/or contractions. Expanded tracts are the cause of over 40 neurodegenerative and neuromuscular diseases. In this chapter, we focus on the (CAG)n and (CTG)n repeat sequences that, when expanded, lead to Huntington's disease (HD) and myotonic dystrophy type 1 (DM1), respectively, as well as a number of other neurodegenerative diseases. TNR tracts in most individuals are relatively small and stable in terms of length. However, TNR tracts become increasingly prone to expansion as tract length increases, eventually leading to very long tracts that disrupt coding (e.g. HD) or noncoding (e.g., DM1) regions of the genome. It is important to understand the early stages in TNR expansions, that is, the transition from small, stable lengths to susceptible threshold lengths. We describe PCR-based in vivo assays, using the model system Saccharomyces cerevisiae, to determine and characterize the dynamic behavior of TNR tracts in the stable and threshold ranges. We also describe a simple in vitro system to assess tract dynamics during 5' single-stranded DNA (ssDNA) flap processing and to assess the role of different DNA metabolism proteins in these dynamics. These assays can ultimately be used to determine factors that influence the early stages of TNR tract expansion.


Assuntos
DNA de Cadeia Simples/genética , Proteínas de Saccharomyces cerevisiae/genética , Saccharomyces cerevisiae/genética , Repetições de Trinucleotídeos , Replicação do DNA , Instabilidade Genômica , Humanos , Instabilidade de Microssatélites , Reação em Cadeia da Polimerase , Expansão das Repetições de Trinucleotídeos
12.
Methods Mol Biol ; 1983: 49-56, 2019.
Artigo em Inglês | MEDLINE | ID: mdl-31087292

RESUMO

Protein lysine acetylation is a reversible posttranslational modification that is catalyzed by a group of enzymes that are collectively referred to as lysine (K) acetyltransferases (KATs). These enzymes catalyze the transfer of the acetyl group from acetyl coenzyme A (Ac-CoA) to the ε-amino group of lysine amino acid. Protein lysine acetylation plays a critical role in the regulation of important cellular processes and it is therefore paramount that we understand the catalytic mechanisms of these enzymes. While there is a variety of methods that have been developed to analyze the enzymatic properties of KATs, majority of the proposed methods have considerable limitations. We describe here a reversed phase HPLC based method that monitors substrate consumption and product formation simultaneously. This method is highly reproducible and optimally suited for the determination of accurate kinetic parameters of KATs.


Assuntos
Cromatografia Líquida de Alta Pressão , Cromatografia de Fase Reversa , Lisina/química , Proteínas/química , Acetilcoenzima A/química , Acetilcoenzima A/metabolismo , Acetilação , Cromatografia Líquida de Alta Pressão/métodos , Cromatografia de Fase Reversa/métodos , Lisina/metabolismo , Lisina Acetiltransferases/química , Lisina Acetiltransferases/metabolismo , Proteínas/metabolismo
13.
Methods Mol Biol ; 1983: 207-224, 2019.
Artigo em Inglês | MEDLINE | ID: mdl-31087300

RESUMO

Cellular proteins are modified by lysine acetylation wherein an acetyltransferase transfers an acetyl group from acetyl co enzyme A onto the e-amino group of lysine residues. This modification is extremely dynamic and can be reversed by a deacetylase that removes the acetyl group. Addition of acetyl group to the lysine residue neutralizes its positive charge, thereby functioning as a molecular switch in regulating the enzymatic functions of the protein, its stability, and it cellular localization. Since this modification is extremely dynamic within the cell, biochemical studies characterizing changes in protein function are imperative to understand how this modification alters protein function in a specific cellular pathway. This unit describes in detail expression and purification of a recombinant nuclease and acetyltransferase, in vitro acetylation of the recombinant protein and biochemical assays to study the changes in enzymatic activity of the in vitro acetylated nuclease.


Assuntos
Endonucleases Flap/metabolismo , Lisina/metabolismo , Acetilação , DNA/metabolismo , Ensaios Enzimáticos/métodos , Endonucleases Flap/isolamento & purificação , Humanos , Processamento de Proteína Pós-Traducional , Proteínas Recombinantes/metabolismo , Fatores de Transcrição de p300-CBP/genética , Fatores de Transcrição de p300-CBP/isolamento & purificação , Fatores de Transcrição de p300-CBP/metabolismo
14.
J Virol ; 93(4)2019 02 15.
Artigo em Inglês | MEDLINE | ID: mdl-30518654

RESUMO

Simian virus 40 (SV40) exists as chromatin throughout its life cycle and undergoes typical epigenetic regulation mediated by changes in nucleosome location and associated histone modifications. In order to investigate the role of epigenetic regulation during the encapsidation of late-stage minichromosomes into virions, we mapped the locations of nucleosomes containing acetylated or methylated lysines in the histone tails of H3 and H4 present in the chromatin from 48-h-postinfection minichromosomes and disrupted virions. In minichromosomes obtained late in infection, nucleosomes were found carrying various histone modifications primarily in the regulatory region, with a major nucleosome located within the enhancer and other nucleosomes at the early and late transcriptional start sites. The nucleosome found in the enhancer would be expected to repress early transcription by blocking access to part of the SP1 binding sites and the left side of the enhancer in late-stage minichromosomes while also allowing late transcription. In chromatin from virions, the principal nucleosome located in the enhancer was shifted ∼70 bases in the late direction from what was found in minichromosomes, and the level of modified histones was increased throughout the genome. The shifting of the enhancer-associated nucleosome to the late side would effectively serve as a switch to relieve the repression of early transcription found in late minichromosomes while likely also repressing late transcription by blocking access to necessary regulatory sequences. This epigenetic switch appeared to occur during the final stage of virion formation.IMPORTANCE For a virus to complete infection, it must produce a new virus particle in which the genome is able to support a new infection. This is particularly important for viruses like simian virus 40 (SV40), which exist as chromatin throughout their life cycles, since chromatin structure plays a major role in the regulation of the life cycle. In order to determine the role of SV40 chromatin structure late in infection, we mapped the locations of nucleosomes and their histone tail modifications in SV40 minichromosomes and in the SV40 chromatin found in virions using chromatin immunoprecipitation-DNA sequencing (ChIP-Seq). We have identified a novel viral transcriptional control mechanism in which a nucleosome found in the regulatory region of the SV40 minichromosome is directed to slide during the formation of the virus particle, exposing transcription factor binding sites required for early transcription that were previously blocked by the presence of the nucleosome.


Assuntos
Nucleossomos/genética , Vírus 40 dos Símios/genética , Transcrição Gênica/genética , Acetilação , Animais , Sequência de Bases/genética , Sítios de Ligação , Linhagem Celular , Chlorocebus aethiops , Cromatina/metabolismo , Cromatina/virologia , Montagem e Desmontagem da Cromatina , DNA Viral/genética , Epigênese Genética/genética , Histonas/metabolismo , Nucleossomos/metabolismo , Processamento de Proteína Pós-Traducional , Vírus 40 dos Símios/metabolismo , Vírion/genética , Replicação Viral/genética
15.
Viruses ; 9(11)2017 11 17.
Artigo em Inglês | MEDLINE | ID: mdl-29149060

RESUMO

It is increasingly clear that DNA viruses exploit cellular epigenetic processes to control their life cycles during infection. This review will address epigenetic regulation in members of the polyomaviruses, adenoviruses, human papillomaviruses, hepatitis B, and herpes viruses. For each type of virus, what is known about the roles of DNA methylation, histone modifications, nucleosome positioning, and regulatory RNA in epigenetic regulation of the virus infection will be discussed. The mechanisms used by certain viruses to dysregulate the host cell through manipulation of epigenetic processes and the role of cellular cofactors such as BRD4 that are known to be involved in epigenetic regulation of host cell pathways will also be covered. Specifically, this review will focus on the role of epigenetic regulation in maintaining viral episomes through the generation of chromatin, temporally controlling transcription from viral genes during the course of an infection, regulating latency and the switch to a lytic infection, and global dysregulation of cellular function.


Assuntos
Vírus de DNA/genética , Epigênese Genética , Regulação Viral da Expressão Gênica , Fenômenos Fisiológicos Virais/genética , Vírus/genética , Metilação de DNA/genética , Vírus de DNA/fisiologia , Herpesvirus Humano 4/genética , Herpesvirus Humano 4/fisiologia , Código das Histonas/genética , Interações Hospedeiro-Patógeno/genética , Humanos , Nucleossomos/genética , Plasmídeos/genética , Processamento de Proteína Pós-Traducional , Latência Viral/genética
16.
Curr Protoc Microbiol ; 46: 14F.3.1-14F.3.26, 2017 08 11.
Artigo em Inglês | MEDLINE | ID: mdl-28800155

RESUMO

Simian virus 40 (SV40) is one of the best-characterized members of the polyomavirus family of small DNA tumor viruses. It has a small genome of 5243 bp and utilizes cellular proteins for its molecular biology, with the exception of the T-antigen protein, which is coded by the virus and is involved in regulating transcription and directing replication. Importantly, SV40 exists as chromatin in both the virus particle and intracellular minichromosomes. These facts, combined with high yields of virus and minichromosomes following infection and ease of manipulation, have made SV40 an extremely useful model to study all aspects of eukaryotic molecular biology. This unit describes procedures for working with SV40 and preparing SV40 chromatin from infected cells and virus particles, as well as procedures for using SV40 chromatin to study epigenetic regulation. © 2017 by John Wiley & Sons, Inc.


Assuntos
Epigenômica/métodos , Infecções por Polyomavirus/virologia , Vírus 40 dos Símios/genética , Infecções Tumorais por Vírus/virologia , Cultura de Vírus/métodos , Animais , Epigênese Genética , Humanos , Vírus 40 dos Símios/fisiologia
17.
Virology ; 503: 62-69, 2017 03.
Artigo em Inglês | MEDLINE | ID: mdl-28126638

RESUMO

The location of nucleosomes in SV40 virions and minichromosomes isolated during infection were determined by next generation sequencing (NGS). The patterns of reads within the regulatory region of chromatin from wild-type virions indicated that micrococcal nuclease-resistant nucleosomes were specifically positioned at nt 5223 and nt 363, while in minichromosomes isolated 48 h post-infection we observed nuclease-resistant nucleosomes at nt 5119 and nt 212. The nucleosomes at nt 5223 and nt 363 in virion chromatin would be expected to repress early and late transcription, respectively. In virions from the mutant cs1085, which does not repress early transcription, we found that these two nucleosomes were significantly reduced compared to wild-type virions confirming a repressive role for them. In chromatin from cells infected for only 30min with wild-type virus, we observed a significant reduction in the nucleosomes at nt 5223 and nt 363 indicating that the potential repression by these nucleosomes appeared to be relieved very early in infection.


Assuntos
Cromatina/genética , Regulação Viral da Expressão Gênica/genética , Nucleossomos/genética , Vírus 40 dos Símios/genética , Transcrição Gênica/genética , Animais , Sequência de Bases , Linhagem Celular , Chlorocebus aethiops , Sequenciamento de Nucleotídeos em Larga Escala , Regiões Promotoras Genéticas , Análise de Sequência de DNA
18.
Biochemistry ; 56(4): 647-656, 2017 01 31.
Artigo em Inglês | MEDLINE | ID: mdl-28098985

RESUMO

The process of base excision repair (BER) recognizes and repairs small lesions or inappropriate bases on DNA through either a short-patch or long-patch pathway. The enzymes involved in BER have been well-characterized on DNA substrates, and, somewhat surprisingly, many of these enzymes, including several DNA glycosylases, AP endonuclease (APE), FEN1 endonuclease, and DNA ligases, have been shown to have activity on DNA substrates within nucleosomes. DNA polymerase ß (Pol ß), however, exhibits drastically reduced or no activity on nucleosomal DNA. Interestingly, acetylation of Pol ß, by the acetyltransferase p300, inhibits its 5' dRP-lyase activity and presumably pushes repair of DNA substrates through the long-patch base excision repair (LP-BER) pathway. In addition to the major enzymes involved in BER, a chromatin architectural factor, HMGB1, was found to directly interact with and enhance the activity of APE1 and FEN1, and thus may aid in altering the structure of the nucleosome to be more accessible to BER factors. In this work, we investigated whether acetylation of Pol ß, either alone or in conjunction with HMGB1, facilitates its activity on nucleosome substrates. We find acetylated Pol ß exhibits enhanced strand displacement synthesis activity on DNA substrates, but, similar to the unmodified enzyme, has little or no activity on nucleosomes. Preincubation of DNA templates with HMGB1 has little or no stimulatory effect on Pol ß and even is inhibitory at higher concentrations. In contrast, preincubation of nucleosomes with HMGB1 rescues Pol ß gap-filling activity in nucleosomes, suggesting that this factor may help overcome the repressive effects of chromatin.


Assuntos
DNA Polimerase beta/química , Reparo do DNA , DNA/química , Proteína HMGB1/química , Nucleossomos/metabolismo , Acetilação , Animais , Galinhas , DNA/genética , DNA/metabolismo , DNA Polimerase beta/genética , DNA Polimerase beta/metabolismo , Expressão Gênica , Proteína HMGB1/genética , Proteína HMGB1/metabolismo , Histonas/química , Histonas/genética , Histonas/metabolismo , Humanos , Modelos Moleculares , Nucleossomos/ultraestrutura , Domínios e Motivos de Interação entre Proteínas , Estrutura Secundária de Proteína , Xenopus , Fatores de Transcrição de p300-CBP/química , Fatores de Transcrição de p300-CBP/genética , Fatores de Transcrição de p300-CBP/metabolismo
19.
Cell Cycle ; 15(11): 1506-17, 2016 06 02.
Artigo em Inglês | MEDLINE | ID: mdl-27104361

RESUMO

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.


Assuntos
Reparo de Erro de Pareamento de DNA , Reparo do DNA , Replicação do DNA , DNA/genética , Processamento de Proteína Pós-Traducional , Fatores de Transcrição de p300-CBP/genética , Acetilação , Sequência de Aminoácidos , Pareamento Incorreto de Bases , Sequência de Bases , DNA/metabolismo , Inibidores Enzimáticos/farmacologia , Genes Reporter , Proteínas de Fluorescência Verde/genética , Proteínas de Fluorescência Verde/metabolismo , Guanina/análogos & derivados , Guanina/metabolismo , Células HCT116 , Células HeLa , Humanos , Plasmídeos/química , Plasmídeos/metabolismo , Alinhamento de Sequência , Terpenos/farmacologia , Fatores de Transcrição de p300-CBP/metabolismo
20.
Viruses ; 7(3): 1409-28, 2015 Mar 23.
Artigo em Inglês | MEDLINE | ID: mdl-25807051

RESUMO

Adenovirus infections of immunocompromised pediatric hematopoietic stem cell transplant patients can develop into serious and often deadly multi-organ disease. There are no drugs approved for adenovirus infections. Cidofovir (an analog of 2-deoxycytidine monophosphate) is used at times but it can be nephrotoxic and its efficacy has not been proven in clinical trials. Brincidofovir, a promising lipid-linked derivative of cidofovir, is in clinical trials. Ganciclovir, an analog of 2-deoxyguanosine, has been employed occasionally but with unknown efficacy in the clinic. In this study, we evaluated valganciclovir against disseminated adenovirus type 5 (Ad5) infection in our permissive immunosuppressed Syrian hamster model. We administered valganciclovir prophylactically, beginning 12 h pre-infection or therapeutically starting at Day 1, 2, 3, or 4 post-infection. Valganciclovir significantly increased survival, reduced viral replication in the liver, and mitigated the pathology associated with Ad5 infection. In cultured cells, valganciclovir inhibited Ad5 DNA replication and blocked the transition from early to late stage of infection. Valganciclovir directly inhibited Ad5 DNA polymerase in vitro, which may explain, at least in part, its mechanism of action. Ganciclovir and valganciclovir are approved to treat infections by certain herpesviruses. Our results support the use of valganciclovir to treat disseminated adenovirus infections in immunosuppressed patients.


Assuntos
Infecções por Adenovirus Humanos/tratamento farmacológico , Infecções por Adenovirus Humanos/patologia , Adenovírus Humanos/efeitos dos fármacos , Antivirais/uso terapêutico , Ganciclovir/análogos & derivados , Hospedeiro Imunocomprometido , Replicação Viral/efeitos dos fármacos , Adenovírus Humanos/fisiologia , Animais , Antivirais/farmacologia , Linhagem Celular , DNA Polimerase Dirigida por DNA/metabolismo , Modelos Animais de Doenças , Células Epiteliais/virologia , Feminino , Ganciclovir/farmacologia , Ganciclovir/uso terapêutico , Humanos , Fígado/virologia , Masculino , Mesocricetus , Análise de Sobrevida , Resultado do Tratamento , Valganciclovir , Carga Viral
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