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1.
Transl Psychiatry ; 14(1): 207, 2024 May 24.
Artículo en Inglés | MEDLINE | ID: mdl-38789433

RESUMEN

Previous evidence suggests elevated levels of oxidatively-induced DNA damage, particularly 8-hydroxy-2'-deoxyguanosine (8-OH-dG), and abnormalities in the repair of 8-OH-dG by the base excision repair (BER) in bipolar disorder (BD). However, the genetic disposition of these abnormalities remains unknown. In this study, we aimed to investigate the levels of oxidatively-induced DNA damage and BER mechanisms in individuals with BD and their siblings, as compared to healthy controls (HCs). 46 individuals with BD, 41 siblings of individuals with BD, and 51 HCs were included in the study. Liquid chromatography-tandem mass spectrometry was employed to evaluate the levels of 8-OH-dG in urine, which were then normalized based on urine creatinine levels. The real-time-polymerase chain reaction was used to measure the expression levels of 8-oxoguanine DNA glycosylase 1 (OGG1), apurinic/apyrimidinic endonuclease 1 (APE1), poly ADP-ribose polymerase 1 (PARP1), and DNA polymerase beta (POLß). The levels of 8-OH-dG were found to be elevated in both individuals with BD and their siblings when compared to the HCs. The OGG1 and APE1 expressions were downregulated, while POLß expressions were upregulated in both the patient and sibling groups compared to the HCs. Age, smoking status, and the number of depressive episodes had an impact on APE1 expression levels in the patient group while body mass index, smoking status, and past psychiatric history had an impact on 8-OH-dG levels in siblings. Both individuals with BD and unaffected siblings presented similar abnormalities regarding oxidatively-induced DNA damage and BER, suggesting a link between abnormalities in DNA damage/BER mechanisms and familial susceptibility to BD. Our findings suggest that targeting the oxidatively-induced DNA damage and BER pathway could offer promising therapeutic strategies for reducing the risk of age-related diseases and comorbidities in individuals with a genetic predisposition to BD.


Asunto(s)
8-Hidroxi-2'-Desoxicoguanosina , Trastorno Bipolar , Daño del ADN , ADN Glicosilasas , Reparación del ADN , Estrés Oxidativo , Hermanos , Humanos , Trastorno Bipolar/genética , Trastorno Bipolar/metabolismo , Femenino , Masculino , Adulto , ADN Glicosilasas/genética , Estrés Oxidativo/genética , Persona de Mediana Edad , ADN Polimerasa beta/genética , ADN Polimerasa beta/metabolismo , ADN-(Sitio Apurínico o Apirimidínico) Liasa/genética , Estudios de Casos y Controles , Adulto Joven , Desoxiguanosina/análogos & derivados , Desoxiguanosina/orina , Reparación por Escisión
2.
Biomolecules ; 14(5)2024 May 02.
Artículo en Inglés | MEDLINE | ID: mdl-38785954

RESUMEN

In the cell, DNA polymerase ß (Polß) is involved in many processes aimed at maintaining genome stability and is considered the main repair DNA polymerase participating in base excision repair (BER). Polß can fill DNA gaps formed by other DNA repair enzymes. Single-nucleotide polymorphisms (SNPs) in the POLB gene can affect the enzymatic properties of the resulting protein, owing to possible amino acid substitutions. For many SNP-associated Polß variants, an association with cancer, owing to changes in polymerase activity and fidelity, has been shown. In this work, kinetic analyses and molecular dynamics simulations were used to examine the activity of naturally occurring polymorphic variants G274R, G290C, and R333W. Previously, the amino acid substitutions at these positions have been found in various types of tumors, implying a specific role of Gly-274, Gly-290, and Arg-333 in Polß functioning. All three polymorphic variants had reduced polymerase activity. Two substitutions-G274R and R333W-led to the almost complete disappearance of gap-filling and primer elongation activities, a decrease in the deoxynucleotide triphosphate-binding ability, and a lower polymerization constant, due to alterations of local contacts near the replaced amino acid residues. Thus, variants G274R, G290C, and R333W may be implicated in an elevated level of unrepaired DNA damage.


Asunto(s)
Sustitución de Aminoácidos , ADN Polimerasa beta , Simulación de Dinámica Molecular , Polimorfismo de Nucleótido Simple , ADN Polimerasa beta/metabolismo , ADN Polimerasa beta/genética , ADN Polimerasa beta/química , Humanos , Cinética , Reparación del ADN/genética , Nucleótidos/metabolismo , Nucleótidos/genética
3.
Biochemistry ; 63(11): 1412-1422, 2024 Jun 04.
Artículo en Inglés | MEDLINE | ID: mdl-38780930

RESUMEN

The catalytic function of DNA polymerase ß (pol ß) fulfills the gap-filling requirement of the base excision DNA repair pathway by incorporating a single nucleotide into a gapped DNA substrate resulting from the removal of damaged DNA bases. Most importantly, pol ß can select the correct nucleotide from a pool of similarly structured nucleotides to incorporate into DNA in order to prevent the accumulation of mutations in the genome. Pol ß is likely to employ various mechanisms for substrate selection. Here, we use dCTP analogues that have been modified at the ß,γ-bridging group of the triphosphate moiety to monitor the effect of leaving group basicity of the incoming nucleotide on precatalytic conformational changes, which are important for catalysis and selectivity. It has been previously shown that there is a linear free energy relationship between leaving group pKa and the chemical transition state. Our results indicate that there is a similar relationship with the rate of a precatalytic conformational change, specifically, the closing of the fingers subdomain of pol ß. In addition, by utilizing analogue ß,γ-CHX stereoisomers, we identified that the orientation of the ß,γ-bridging group relative to R183 is important for the rate of fingers closing, which directly influences chemistry.


Asunto(s)
ADN Polimerasa beta , Conformación Proteica , ADN Polimerasa beta/química , ADN Polimerasa beta/metabolismo , ADN Polimerasa beta/genética , Humanos , Nucleótidos de Desoxicitosina/metabolismo , Nucleótidos de Desoxicitosina/química , Especificidad por Sustrato , Modelos Moleculares , Cinética , ADN/metabolismo , ADN/química , Reparación del ADN
4.
Environ Mol Mutagen ; 65 Suppl 1: 57-71, 2024 Apr.
Artículo en Inglés | MEDLINE | ID: mdl-38619421

RESUMEN

Gene knock-out (KO) mouse models for DNA polymerase beta (Polß) revealed that loss of Polß leads to neonatal lethality, highlighting the critical organismic role for this DNA polymerase. While biochemical analysis and gene KO cell lines have confirmed its biochemical role in base excision repair and in TET-mediated demethylation, more long-lived mouse models continue to be developed to further define its organismic role. The Polb-KO mouse was the first of the Cre-mediated tissue-specific KO mouse models. This technology was exploited to investigate roles for Polß in V(D)J recombination (variable-diversity-joining rearrangement), DNA demethylation, gene complementation, SPO11-induced DNA double-strand break repair, germ cell genome stability, as well as neuronal differentiation, susceptibility to genotoxin-induced DNA damage, and cancer onset. The revolution in knock-in (KI) mouse models was made possible by CRISPR/cas9-mediated gene editing directly in C57BL/6 zygotes. This technology has helped identify phenotypes associated with germline or somatic mutants of Polß. Such KI mouse models have helped uncover the importance of key Polß active site residues or specific Polß enzyme activities, such as the PolbY265C mouse that develops lupus symptoms. More recently, we have used this KI technology to mutate the Polb gene with two codon changes, yielding the PolbL301R/V303R mouse. In this KI mouse model, the expressed Polß protein cannot bind to its obligate heterodimer partner, Xrcc1. Although the expressed mutant Polß protein is proteolytically unstable and defective in recruitment to sites of DNA damage, the homozygous PolbL301R/V303R mouse is viable and fertile, yet small in stature. We expect that this and additional targeted mouse models under development are poised to reveal new biological and organismic roles for Polß.


Asunto(s)
ADN Polimerasa beta , Ratones , Animales , ADN Polimerasa beta/genética , ADN Polimerasa beta/metabolismo , Ratones Endogámicos C57BL , Reparación del ADN , Daño del ADN , Línea Celular , Ratones Noqueados
5.
Int J Mol Sci ; 25(8)2024 Apr 10.
Artículo en Inglés | MEDLINE | ID: mdl-38673769

RESUMEN

Base excision repair (BER), which involves the sequential activity of DNA glycosylases, apurinic/apyrimidinic endonucleases, DNA polymerases, and DNA ligases, is one of the enzymatic systems that preserve the integrity of the genome. Normal BER is effective, but due to single-nucleotide polymorphisms (SNPs), the enzymes themselves-whose main function is to identify and eliminate damaged bases-can undergo amino acid changes. One of the enzymes in BER is DNA polymerase ß (Polß), whose function is to fill gaps in DNA. SNPs can significantly affect the catalytic activity of an enzyme by causing an amino acid substitution. In this work, pre-steady-state kinetic analyses and molecular dynamics simulations were used to examine the activity of naturally occurring variants of Polß that have the substitutions L19P and G66R in the dRP-lyase domain. Despite the substantial distance between the dRP-lyase domain and the nucleotidyltransferase active site, it was found that the capacity to form a complex with DNA and with an incoming dNTP is significantly altered by these substitutions. Therefore, the lower activity of the tested polymorphic variants may be associated with a greater number of unrepaired DNA lesions.


Asunto(s)
Sustitución de Aminoácidos , ADN Polimerasa beta , Simulación de Dinámica Molecular , Polimorfismo de Nucleótido Simple , ADN Polimerasa beta/química , ADN Polimerasa beta/genética , ADN Polimerasa beta/metabolismo , Humanos , Reparación del ADN , Cinética , Dominio Catalítico , ADN/metabolismo , ADN/genética , ADN/química , Dominios Proteicos
6.
Nucleic Acids Res ; 52(7): 3810-3822, 2024 Apr 24.
Artículo en Inglés | MEDLINE | ID: mdl-38366780

RESUMEN

Base excision repair (BER) involves the tightly coordinated function of DNA polymerase ß (polß) and DNA ligase I (LIG1) at the downstream steps. Our previous studies emphasize that defective substrate-product channeling, from gap filling by polß to nick sealing by LIG1, can lead to interruptions in repair pathway coordination. Yet, the molecular determinants that dictate accurate BER remains largely unknown. Here, we demonstrate that a lack of gap filling by polß leads to faulty repair events and the formation of deleterious DNA intermediates. We dissect how ribonucleotide challenge and cancer-associated mutations could adversely impact the ability of polß to efficiently fill the one nucleotide gap repair intermediate which subsequently results in gap ligation by LIG1, leading to the formation of single-nucleotide deletion products. Moreover, we demonstrate that LIG1 is not capable of discriminating against nick DNA containing a 3'-ribonucleotide, regardless of base-pairing potential or damage. Finally, AP-Endonuclease 1 (APE1) shows distinct substrate specificity for the exonuclease removal of 3'-mismatched bases and ribonucleotides from nick repair intermediate. Overall, our results reveal that unfilled gaps result in impaired coordination between polß and LIG1, defining a possible type of mutagenic event at the downstream steps where APE1 could provide a proofreading role to maintain BER efficiency.


Asunto(s)
ADN Ligasa (ATP) , ADN Polimerasa beta , Reparación del ADN , ADN Polimerasa beta/metabolismo , ADN Polimerasa beta/genética , ADN Ligasa (ATP)/metabolismo , ADN Ligasa (ATP)/genética , Humanos , ADN-(Sitio Apurínico o Apirimidínico) Liasa/metabolismo , ADN-(Sitio Apurínico o Apirimidínico) Liasa/genética , ADN/metabolismo , ADN/genética , Daño del ADN , ADN Ligasas/metabolismo , ADN Ligasas/genética , Reparación por Escisión
7.
Cell Death Dis ; 15(1): 78, 2024 01 20.
Artículo en Inglés | MEDLINE | ID: mdl-38245510

RESUMEN

The circadian-controlled DNA repair exhibits a strong diurnal rhythm. Disruption in circadian clock and DNA repair is closely linked with hepatocellular carcinoma (HCC) progression, but the mechanism remains unknown. Here, we show that polymerase beta (POLB), a critical enzyme in the DNA base excision repair pathway, is rhythmically expressed at the translational level in mouse livers. Hepatic POLB dysfunction dampens clock homeostasis, whereas retards HCC progression, by mediating the methylation of the 4th CpG island on the 5'UTR of clock gene Per1. Clinically, POLB is overexpressed in human HCC samples and positively associated with poor prognosis. Furthermore, the hepatic rhythmicity of POLB protein expression is orchestrated by Calreticulin (CALR). Our findings provide important insights into the molecular mechanism underlying the synergy between clock and food signals on the POLB-driven BER system and reveal new clock-dependent carcinogenetic effects of POLB. Therefore, chronobiological modulation of POLB may help to promote precise interventions for HCC.


Asunto(s)
Carcinoma Hepatocelular , Relojes Circadianos , ADN Polimerasa beta , Neoplasias Hepáticas , Animales , Humanos , Ratones , Carcinoma Hepatocelular/genética , Carcinoma Hepatocelular/metabolismo , Relojes Circadianos/genética , Ritmo Circadiano/genética , Desmetilación , ADN Polimerasa beta/genética , ADN Polimerasa beta/metabolismo , Epigénesis Genética , Neoplasias Hepáticas/genética , Neoplasias Hepáticas/metabolismo , Proteínas Circadianas Period/genética
8.
Biochimie ; 219: 84-95, 2024 Apr.
Artículo en Inglés | MEDLINE | ID: mdl-37573020

RESUMEN

Mammalian Base Excision Repair (BER) DNA ligases I and IIIα (LigI, LigIIIα) are major determinants of DNA repair fidelity, alongside with DNA polymerases. Here we compared activities of human LigI and LigIIIα on specific and nonspecific substrates representing intermediates of distinct BER sub-pathways. The enzymes differently discriminate mismatches in the nicked DNA, depending on their identity and position, but are both more selective against the 3'-end non-complementarity. LigIIIα is less active than LigI in premature ligation of one-nucleotide gapped DNA and more efficiently discriminates misinsertion products of DNA polymerase ß-catalyzed gap filling, that reinforces a leading role of LigIIIα in the accuracy of short-patch BER. LigI and LigIIIα reseal the intermediate of long-patch BER containing an incised synthetic AP site (F) with different efficiencies, depending on the DNA sequence context, 3'-end mismatch presence and coupling of the ligation reaction with DNA repair synthesis. Processing of this intermediate in the absence of flap endonuclease 1 generates non-canonical DNAs with bulged F site, which are very inefficiently repaired by AP endonuclease 1 and represent potential mutagenic repair products. The extent of conversion of the 5'-adenylated intermediates of specific and nonspecific substrates is revealed to depend on the DNA sequence context; a higher sensitivity of LigI to the sequence is in line with the enzyme structural feature of DNA binding. LigIIIα exceeds LigI in generation of potential abortive ligation products, justifying importance of XRCC1-mediated coordination of LigIIIα and aprataxin activities for the efficient DNA repair.


Asunto(s)
ADN Polimerasa beta , Reparación del ADN , Animales , Humanos , ADN/genética , ADN/metabolismo , ADN Polimerasa beta/genética , ADN Polimerasa beta/metabolismo , ADN Polimerasa Dirigida por ADN/metabolismo , ADN Ligasas/genética , ADN Ligasas/metabolismo , Reparación por Escisión , Mamíferos/metabolismo , Proteína 1 de Reparación por Escisión del Grupo de Complementación Cruzada de las Lesiones por Rayos X/genética , Proteína 1 de Reparación por Escisión del Grupo de Complementación Cruzada de las Lesiones por Rayos X/metabolismo
9.
Cell Biochem Biophys ; 81(4): 765-776, 2023 Dec.
Artículo en Inglés | MEDLINE | ID: mdl-37695502

RESUMEN

Free fatty acids (FFAs) hepatic accumulation and the resulting oxidative stress contribute to several chronic liver diseases including nonalcoholic steatohepatitis. However, the underlying pathological mechanisms remain unclear. In this study, we propose a novel mechanism whereby the toxicity of FFAs detrimentally affects DNA repair activity. Specifically, we have discovered that oleic acid (OA), a prominent dietary free fatty acid, inhibits the activity of DNA polymerase ß (Pol ß), a crucial enzyme involved in base excision repair (BER), by actively competing with 2'-deoxycytidine-5'-triphosphate. Consequently, OA hinders the efficiency of BER, leading to the accumulation of DNA damage in hepatocytes overloaded with FFAs. Additionally, the excessive presence of both OA and palmitic acid (PA) lead to mitochondrial dysfunction in hepatocytes. These findings suggest that the accumulation of FFAs hampers Pol ß activity and contributes to mitochondrial dysfunction, shedding light on potential pathogenic mechanisms underlying FFAs-related diseases.


Asunto(s)
ADN Polimerasa beta , Ácido Oléico , Ácido Oléico/farmacología , ADN Polimerasa beta/genética , ADN Polimerasa beta/metabolismo , Reparación del ADN , Hepatocitos/metabolismo , Ácidos Grasos/metabolismo , Mitocondrias/metabolismo
10.
Nucleic Acids Res ; 51(13): 7036-7052, 2023 07 21.
Artículo en Inglés | MEDLINE | ID: mdl-37260088

RESUMEN

In order to cope with the risk of stress-induced mutagenesis, cells in all kingdoms of life employ Y-family DNA polymerases to resolve resulting DNA lesions and thus maintaining the integrity of the genome. In Escherichia coli, the DNA polymerase IV, or DinB, plays this crucial role in coping with these type of mutations via the so-called translesion DNA synthesis. Despite the availability of several high-resolution crystal structures, important aspects of the functional repertoire of DinB remain elusive. In this study, we use advanced solution NMR spectroscopy methods in combination with biophysical characterization to elucidate the crucial role of the Thumb domain within DinB's functional cycle. We find that the inherent dynamics of this domain guide the recognition of double-stranded (ds) DNA buried within the interior of the DinB domain arrangement and trigger allosteric signals through the DinB protein. Subsequently, we characterized the RNA polymerase interaction with DinB, revealing an extended outside surface of DinB and thus not mutually excluding the DNA interaction. Altogether the obtained results lead to a refined model of the functional repertoire of DinB within the translesion DNA synthesis pathway.


Asunto(s)
ADN Polimerasa beta , Proteínas de Escherichia coli , ADN Polimerasa beta/genética , Proteínas de Escherichia coli/metabolismo , Escherichia coli/metabolismo , ADN/genética , ADN/metabolismo , Mutación
11.
Cells ; 12(9)2023 05 02.
Artículo en Inglés | MEDLINE | ID: mdl-37174699

RESUMEN

To maintain the integrity of the genome, there is a set of enzymatic systems, one of which is base excision repair (BER), which includes sequential action of DNA glycosylases, apurinic/apyrimidinic endonucleases, DNA polymerases, and DNA ligases. Normally, BER works efficiently, but the enzymes themselves (whose primary function is the recognition and removal of damaged bases) are subject to amino acid substitutions owing to natural single-nucleotide polymorphisms (SNPs). One of the enzymes in BER is DNA polymerase ß (Polß), whose function is to fill gaps in DNA with complementary dNMPs. It is known that many SNPs can cause an amino acid substitution in this enzyme and a significant decrease in the enzymatic activity. In this study, the activity of four natural variants of Polß, containing substitution E154A, G189D, M236T, or R254I in the transferase domain, was analyzed using molecular dynamics simulations and pre-steady-state kinetic analyses. It was shown that all tested substitutions lead to a significant reduction in the ability to form a complex with DNA and with incoming dNTP. The G189D substitution also diminished Polß catalytic activity. Thus, a decrease in the activity of studied mutant forms may be associated with an increased risk of damage to the genome.


Asunto(s)
ADN Polimerasa beta , Transferasas , Humanos , Sustitución de Aminoácidos , ADN/metabolismo , ADN Polimerasa beta/genética , ADN Polimerasa beta/metabolismo , Reparación del ADN/genética , ADN-(Sitio Apurínico o Apirimidínico) Liasa/metabolismo , Transferasas/genética , Transferasas/metabolismo
12.
Nucleic Acids Res ; 51(11): 5547-5564, 2023 06 23.
Artículo en Inglés | MEDLINE | ID: mdl-37070185

RESUMEN

Saccharomyces cerevisiae DNA polymerase IV (Pol4) like its homolog, human DNA polymerase lambda (Polλ), is involved in Non-Homologous End-Joining and Microhomology-Mediated Repair. Using genetic analysis, we identified an additional role of Pol4 also in homology-directed DNA repair, specifically in Rad52-dependent/Rad51-independent direct-repeat recombination. Our results reveal that the requirement for Pol4 in repeat recombination was suppressed by the absence of Rad51, suggesting that Pol4 counteracts the Rad51 inhibition of Rad52-mediated repeat recombination events. Using purified proteins and model substrates, we reconstituted in vitro reactions emulating DNA synthesis during direct-repeat recombination and show that Rad51 directly inhibits Polδ DNA synthesis. Interestingly, although Pol4 was not capable of performing extensive DNA synthesis by itself, it aided Polδ in overcoming the DNA synthesis inhibition by Rad51. In addition, Pol4 dependency and stimulation of Polδ DNA synthesis in the presence of Rad51 occurred in reactions containing Rad52 and RPA where DNA strand-annealing was necessary. Mechanistically, yeast Pol4 displaces Rad51 from ssDNA independent of DNA synthesis. Together our in vitro and in vivo data suggest that Rad51 suppresses Rad52-dependent/Rad51-independent direct-repeat recombination by binding to the primer-template and that Rad51 removal by Pol4 is critical for strand-annealing dependent DNA synthesis.


Asunto(s)
ADN Polimerasa beta , Recombinasa Rad51 , Proteína Recombinante y Reparadora de ADN Rad52 , Proteínas de Saccharomyces cerevisiae , Saccharomyces cerevisiae , Humanos , ADN/metabolismo , ADN Polimerasa beta/genética , ADN Polimerasa III/genética , ADN Polimerasa III/metabolismo , Reparación del ADN , Recombinasa Rad51/genética , Recombinasa Rad51/metabolismo , Proteína Recombinante y Reparadora de ADN Rad52/genética , Proteína Recombinante y Reparadora de ADN Rad52/metabolismo , Reparación del ADN por Recombinación , Saccharomyces cerevisiae/genética , Saccharomyces cerevisiae/metabolismo , Proteínas de Saccharomyces cerevisiae/genética , Proteínas de Saccharomyces cerevisiae/metabolismo
13.
J Biol Chem ; 299(5): 104636, 2023 05.
Artículo en Inglés | MEDLINE | ID: mdl-36963489

RESUMEN

Base excision repair (BER) is carried out by a series of proteins that function in a step-by-step process to identify, remove, and replace DNA damage. During BER, the DNA transitions through various intermediate states as it is processed by each DNA repair enzyme. Left unrepaired, these BER intermediates can transition into double-stranded DNA breaks and promote genome instability. Previous studies have proposed a short-lived complex consisting of the BER intermediate, the incoming enzyme, and the outgoing enzyme at each step of the BER pathway to protect the BER intermediate. The transfer of BER intermediates between enzymes, known as BER coordination or substrate channeling, remains poorly understood. Here, we utilize single-molecule total internal reflection fluorescence microscopy to investigate the mechanism of BER coordination between apurinic/apyrimidinic endonuclease 1 (APE1) and DNA polymerase ß (Pol ß). When preformed complexes of APE1 and the incised abasic site product (APE1 product and Pol ß substrate) were subsequently bound by Pol ß, the Pol ß enzyme dissociated shortly after binding in most of the observations. In the events where Pol ß binding was followed by APE1 dissociation during substrate channeling, Pol ß remained bound for a longer period of time to allow disassociation of APE1. Our results indicate that transfer of the BER intermediate from APE1 to Pol ß during BER is dependent on the dissociation kinetics of APE1 and the duration of the ternary complex on the incised abasic site.


Asunto(s)
ADN Polimerasa beta , Reparación del ADN , Daño del ADN , ADN Polimerasa beta/genética , ADN Polimerasa beta/metabolismo , Reparación del ADN/fisiología , Enzimas Reparadoras del ADN/genética , Enzimas Reparadoras del ADN/metabolismo , ADN-(Sitio Apurínico o Apirimidínico) Liasa/genética , ADN-(Sitio Apurínico o Apirimidínico) Liasa/metabolismo , Imagen Individual de Molécula , Microscopía Fluorescente , Humanos
14.
Cells ; 11(22)2022 11 21.
Artículo en Inglés | MEDLINE | ID: mdl-36429121

RESUMEN

DNA polymerase ß plays a fundamental role in the life cycle of Trypanosoma cruzi since it participates in the kinetoplast DNA repair and replication. This enzyme can be found in two forms in cell extracts of T. cruzi epimastigotes form. The H form is a phosphorylated form of DNA polymerase ß, while the L form is not phosphorylated. The protein kinases which are able to in vivo phosphorylate DNA polymerase ß have not been identified yet. In this work, we purified the H form of this DNA polymerase and identified the phosphorylation sites. DNA polymerase ß is in vivo phosphorylated at several amino acid residues including Tyr35, Thr123, Thr137 and Ser286. Thr123 is phosphorylated by casein kinase 2 and Thr137 and Ser286 are phosphorylated by protein kinase C-like enzymes. Protein kinase C encoding genes were identified in T. cruzi, and those genes were cloned, expressed in bacteria and the recombinant protein was purified. It was found that T. cruzi possesses three different protein kinase C-like enzymes named TcPKC1, TcPKC2, and TcPKC3. Both TcPKC1 and TcPKC2 were able to in vitro phosphorylate recombinant DNA polymerase ß, and in addition, TcPKC1 gets auto phosphorylated. Those proteins contain several regulatory domains at the N-terminus, which are predicted to bind phosphoinositols, and TcPKC1 contains a lipocalin domain at the C-terminus that might be able to bind free fatty acids. Tyr35 is phosphorylated by an unidentified protein kinase and considering that the T. cruzi genome does not contain Tyr kinase encoding genes, it is probable that Tyr35 could be phosphorylated by a dual protein kinase. Wee1 is a eukaryotic dual protein kinase involved in cell cycle regulation. We identified a Wee1 homolog in T. cruzi and the recombinant kinase was assayed using DNA polymerase ß as a substrate. T. cruzi Wee1 was able to in vitro phosphorylate recombinant DNA polymerase ß, although we were not able to demonstrate specific phosphorylation on Tyr35. Those results indicate that there exists a cell signaling pathway involving PKC-like kinases in T. cruzi.


Asunto(s)
Enfermedad de Chagas , ADN Polimerasa beta , Trypanosoma cruzi , Humanos , ADN Polimerasa beta/genética , ADN Polimerasa beta/metabolismo , Quinasa de la Caseína II/metabolismo , Proteína Quinasa C/metabolismo
16.
Nat Commun ; 13(1): 3193, 2022 06 09.
Artículo en Inglés | MEDLINE | ID: mdl-35680862

RESUMEN

Efficient and accurate DNA synthesis is enabled by DNA polymerase fidelity checkpoints that promote insertion of the right instead of wrong nucleotide. Erroneous X-family polymerase (pol) λ nucleotide insertion leads to genomic instability in double strand break and base-excision repair. Here, time-lapse crystallography captures intermediate catalytic states of pol λ undergoing right and wrong natural nucleotide insertion. The revealed nucleotide sensing mechanism responds to base pair geometry through active site deformation to regulate global polymerase-substrate complex alignment in support of distinct optimal (right) or suboptimal (wrong) reaction pathways. An induced fit during wrong but not right insertion, and associated metal, substrate, side chain and pyrophosphate reaction dynamics modulated nucleotide insertion. A third active site metal hastened right but not wrong insertion and was not essential for DNA synthesis. The previously hidden fidelity checkpoints uncovered reveal fundamental strategies of polymerase DNA repair synthesis in genomic instability.


Asunto(s)
ADN Polimerasa beta , Nucleótidos , ADN/metabolismo , ADN Polimerasa beta/genética , ADN Polimerasa beta/metabolismo , Inestabilidad Genómica , Humanos , Cinética , Modelos Moleculares , Nucleótidos/metabolismo
17.
Int J Mol Sci ; 23(4)2022 Feb 21.
Artículo en Inglés | MEDLINE | ID: mdl-35216513

RESUMEN

DNA polymerase ß (Polß) is considered the main repair DNA polymerase involved in the base excision repair (BER) pathway, which plays an important part in the repair of damaged DNA bases usually resulting from alkylation or oxidation. In general, BER involves consecutive actions of DNA glycosylases, AP endonucleases, DNA polymerases, and DNA ligases. It is known that protein-protein interactions of Polß with enzymes from the BER pathway increase the efficiency of damaged base repair in DNA. However natural single-nucleotide polymorphisms can lead to a substitution of functionally significant amino acid residues and therefore affect the catalytic activity of the enzyme and the accuracy of Polß action. Up-to-date databases contain information about more than 8000 SNPs in the gene of Polß. This review summarizes data on the in silico prediction of the effects of Polß SNPs on DNA repair efficacy; available data on cancers associated with SNPs of Polß; and experimentally tested variants of Polß. Analysis of the literature indicates that amino acid substitutions could be important for the maintenance of the native structure of Polß and contacts with DNA; others affect the catalytic activity of the enzyme or play a part in the precise and correct attachment of the required nucleotide triphosphate. Moreover, the amino acid substitutions in Polß can disturb interactions with enzymes involved in BER, while the enzymatic activity of the polymorphic variant may not differ significantly from that of the wild-type enzyme. Therefore, investigation regarding the effect of Polß natural variants occurring in the human population on enzymatic activity and protein-protein interactions is an urgent scientific task.


Asunto(s)
ADN Polimerasa beta/genética , Reparación del ADN/genética , ADN/genética , Animales , Daño del ADN/genética , Humanos , Polimorfismo Genético
18.
J Chemother ; 34(6): 391-400, 2022 Oct.
Artículo en Inglés | MEDLINE | ID: mdl-34870566

RESUMEN

The therapeutic efficacy of TMZ, a common used drug for chemotherapy, is limited by the resistance from colorectal cancer cells. Base excision repair (BER) pathway has been identified as one of the reasons for drug resistance. By blocking Polß-dependent BER (Base Excision Repair) pathway, the efficacy of TMZ treatment can be improved greatly. Several Polß inhibitors that have been identified could not become approved drugs due to lack of potency or specificity. To find therapeutic candidates with exquisite specificity and high affinity to Polß, phage display technology was used in the current research. We screened out a candidate Polß inhibitor, 10 D, that can inhibit the activity of Polßand SP-BER (Short-Patch Base excision Repair) pathway. Co-treatment with 10 D enhanced the sensitivity of colorectal cancer (CRC) cells to TMZ both in vitro and in vivo. Our data suggested that the novel Polß inhibitor we identified can improve TMZ efficacy and optimize CRC chemotherapy.


Asunto(s)
Bacteriófagos , Neoplasias Colorrectales , ADN Polimerasa beta , Bacteriófagos/metabolismo , Neoplasias Colorrectales/tratamiento farmacológico , Neoplasias Colorrectales/patología , ADN Polimerasa beta/genética , ADN Polimerasa beta/metabolismo , Reparación del ADN , Humanos , Biblioteca de Péptidos , Temozolomida/farmacología , Temozolomida/uso terapéutico
19.
Crit Rev Oncog ; 27(2): 17-33, 2022.
Artículo en Inglés | MEDLINE | ID: mdl-36734870

RESUMEN

DNA polymerase beta (Pol ß) is a 39 kD vertebrate polymerase that lacks proofreading ability, yet still maintains a moderate fidelity of DNA synthesis. Pol ß is a key enzyme that functions in the base excision repair and non-homologous end joining pathways of DNA repair. Mechanisms of fidelity for Pol ß are still being elucidated but are likely to involve dynamic conformational motions of the enzyme upon its binding to DNA and deoxynucleoside triphosphates. Recent studies have linked germline and somatic variants of Pol ß with cancer and autoimmunity. These variants induce genomic instability by a number of mechanisms, including error-prone DNA synthesis and accumulation of single nucleotide gaps that lead to replication stress. Here, we review the structure and function of Pol ß, and we provide insights into how structural changes in Pol ß variants may contribute to genomic instability, mutagenesis, disease, cancer development, and impacts on treatment outcomes.


Asunto(s)
ADN Polimerasa beta , Neoplasias , Humanos , ADN Polimerasa beta/genética , ADN Polimerasa beta/química , ADN Polimerasa beta/metabolismo , Replicación del ADN/genética , ADN/genética , Reparación del ADN/genética , Inestabilidad Genómica , Neoplasias/genética
20.
Front Immunol ; 13: 1039009, 2022.
Artículo en Inglés | MEDLINE | ID: mdl-36624848

RESUMEN

Base excision repair (BER) has evolved to maintain the genomic integrity of DNA following endogenous and exogenous agent induced DNA base damage. In contrast, aberrant BER induces genomic instability, promotes malignant transformation and can even trigger cancer development. Previously, we have shown that deoxyribo-5'-phosphate (dRP) lyase deficient DNA polymerase beta (POLB) causes replication associated genomic instability and sensitivity to both endogenous and exogenous DNA damaging agents. Specifically, it has been established that this loss of dRP lyase function promotes inflammation associated gastric cancer. However, the way that aberrant POLB impacts the immune signaling and inflammatory responses is still unknown. Here we show that a dRP lyase deficient variant of POLB (Leu22Pro, or L22P) increases mitotic dysfunction associated genomic instability, which eventually leads to a cytosolic DNA mediated inflammatory response. Furthermore, poly(ADP-ribose) polymerase 1 inhibition exacerbates chromosomal instability and enhances the cytosolic DNA mediated inflammatory response. Our results suggest that POLB plays a significant role in modulating inflammatory signaling, and they provide a mechanistic basis for future potential cancer immunotherapies.


Asunto(s)
ADN Polimerasa beta , Humanos , ADN Polimerasa beta/genética , ADN Polimerasa beta/metabolismo , Reparación del ADN , ADN/genética , Replicación del ADN , Inestabilidad Genómica
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