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1.
Nature ; 582(7810): 60-66, 2020 06.
Artigo em Inglês | MEDLINE | ID: mdl-32494078

RESUMO

The nature of the first genetic polymer is the subject of major debate1. Although the 'RNA world' theory suggests that RNA was the first replicable information carrier of the prebiotic era-that is, prior to the dawn of life2,3-other evidence implies that life may have started with a heterogeneous nucleic acid genetic system that included both RNA and DNA4. Such a theory streamlines the eventual 'genetic takeover' of homogeneous DNA from RNA as the principal information-storage molecule, but requires a selective abiotic synthesis of both RNA and DNA building blocks in the same local primordial geochemical scenario. Here we demonstrate a high-yielding, completely stereo-, regio- and furanosyl-selective prebiotic synthesis of the purine deoxyribonucleosides: deoxyadenosine and deoxyinosine. Our synthesis uses key intermediates in the prebiotic synthesis of the canonical pyrimidine ribonucleosides (cytidine and uridine), and we show that, once generated, the pyrimidines persist throughout the synthesis of the purine deoxyribonucleosides, leading to a mixture of deoxyadenosine, deoxyinosine, cytidine and uridine. These results support the notion that purine deoxyribonucleosides and pyrimidine ribonucleosides may have coexisted before the emergence of life5.


Assuntos
DNA/química , Evolução Química , Origem da Vida , Nucleosídeos de Purina/síntese química , Nucleosídeos de Pirimidina/síntese química , RNA/química , Adenosina/análogos & derivados , Adenosina/química , Citidina/química , DNA/genética , Oxirredução/efeitos da radiação , Nucleosídeos de Purina/química , Nucleosídeos de Purina/genética , Nucleosídeos de Pirimidina/química , Nucleosídeos de Pirimidina/genética , RNA/genética , Uridina/química
2.
Sci Transl Med ; 12(541)2020 04 29.
Artigo em Inglês | MEDLINE | ID: mdl-32253226

RESUMO

Coronaviruses (CoVs) traffic frequently between species resulting in novel disease outbreaks, most recently exemplified by the newly emerged SARS-CoV-2, the causative agent of COVID-19. Here, we show that the ribonucleoside analog ß-d-N4-hydroxycytidine (NHC; EIDD-1931) has broad-spectrum antiviral activity against SARS-CoV-2, MERS-CoV, SARS-CoV, and related zoonotic group 2b or 2c bat-CoVs, as well as increased potency against a CoV bearing resistance mutations to the nucleoside analog inhibitor remdesivir. In mice infected with SARS-CoV or MERS-CoV, both prophylactic and therapeutic administration of EIDD-2801, an orally bioavailable NHC prodrug (ß-d-N4-hydroxycytidine-5'-isopropyl ester), improved pulmonary function and reduced virus titer and body weight loss. Decreased MERS-CoV yields in vitro and in vivo were associated with increased transition mutation frequency in viral, but not host cell RNA, supporting a mechanism of lethal mutagenesis in CoV. The potency of NHC/EIDD-2801 against multiple CoVs and oral bioavailability highlights its potential utility as an effective antiviral against SARS-CoV-2 and other future zoonotic CoVs.


Assuntos
Antivirais/administração & dosagem , Infecções por Coronavirus/tratamento farmacológico , Pneumonia Viral/tratamento farmacológico , Ribonucleosídeos/administração & dosagem , Replicação Viral/efeitos dos fármacos , Monofosfato de Adenosina/administração & dosagem , Monofosfato de Adenosina/análogos & derivados , Alanina/administração & dosagem , Alanina/análogos & derivados , Animais , Antibioticoprofilaxia , Betacoronavirus/fisiologia , Linhagem Celular , Infecções por Coronavirus/patologia , Citidina/administração & dosagem , Citidina/análogos & derivados , Modelos Animais de Doenças , Farmacorresistência Viral , Humanos , Pulmão/patologia , Camundongos , Camundongos Endogâmicos C57BL , Coronavírus da Síndrome Respiratória do Oriente Médio/fisiologia , Modelos Moleculares , Mutação/efeitos dos fármacos , Pandemias , Pneumonia Viral/patologia , Cultura Primária de Células , RNA Replicase/química , RNA Replicase/genética , RNA Viral , Distribuição Aleatória , Sistema Respiratório/citologia
3.
Anal Chim Acta ; 1098: 56-65, 2020 Feb 15.
Artigo em Inglês | MEDLINE | ID: mdl-31948587

RESUMO

RNA molecules carry diverse modifications that exert important influences in many cellular processes. In addition to the single modification occurring in either nucleobase or 2' hydroxyl of ribose in RNA, some dual modifications occur in both the nucleobase and 2' hydroxyl of ribose in RNA. 2'-O-methyl-5-methylcytidine (m5Cm), the dual modifications of cytidine, was first discovered from the tRNA of archaea. Recent studies identified that 2'-O-methyl-5-hydroxymethylcytidine (hm5Cm) and 2'-O-methyl-5-formylcytidine (f5Cm) were present in the anticodon of cytoplasmic tRNA of mammals. Similar to the series of single modification of cytidines of 5-methylcytosine (m5C), 5-hydroxymethylcytidine (hm5C), 5-formylcytidine (f5C), and 5-carboxylcytidine (ca5C) in nucleic acids, the dual modifications of m5Cm, hm5Cm, f5Cm and 2'-O-methyl-5-carboxylcytidine (ca5Cm) may also constitute the series of cytidine modifications in mammals. However, it is normally challenging to detect these modifications because of their low endogenous levels. Here, we established a method by chemical labeling-assisted liquid chromatography - electrospray ionization - tandem mass spectrometry (LC-ESI-MS/MS) analysis for the sensitive and simultaneous determination of all these four cytidine dual modifications, i.e., m5Cm, hm5Cm, f5Cm and ca5Cm. Three different labeling reagents (2-bromo-1-(3,4-dimeth oxyphenyl)-ethanone, BDMOPE; 2-bromo-1-(4-methoxyphenyl)-ethanone, BMOPE; 2-bromo-1-(4-diethylaminophenyl)-ethanone, BDEPE) were used for the chemical labeling. The results showed that the detection sensitivities of m5Cm, hm5Cm, f5Cm and ca5Cm increased up to 462 folds after chemical labeling. With the developed method, we achieved the simultaneous detection of m5Cm, hm5Cm and f5Cm in RNA of mammals. In addition, we found these cytidine dual modifications mainly exist in small RNA (<200 nt) and barely detected in other types of RNA. Moreover, we found that the levels of m5Cm in RNA of human lung carcinoma tissues significantly increased, while hm5Cm and f5Cm significantly decreased compared to tumor adjacent normal tissues. The significant changes of m5Cm, hm5Cm and f5Cm levels may serve as indicator for the detection and prognosis of lung cancer.


Assuntos
Citidina/análise , RNA/química , Animais , Cromatografia Líquida , Humanos , Espectrometria de Massas , Estrutura Molecular , Espectrometria de Massas em Tandem
5.
Cell Mol Life Sci ; 77(4): 719-733, 2020 Feb.
Artigo em Inglês | MEDLINE | ID: mdl-31302752

RESUMO

Cytidine base editors (CBEs) have been demonstrated to be useful for precisely inducing C:G-to-T:A base mutations in various organisms. In this study, we showed that the BE4-Gam system induced the targeted C-to-T base conversion in porcine blastocysts at an efficiency of 66.7-71.4% via the injection of a single sgRNA targeting a xeno-antigen-related gene and BE4-Gam mRNA. Furthermore, the efficiency of simultaneous three gene base conversion via the injection of three targeting sgRNAs and BE4-Gam mRNA into porcine parthenogenetic embryos was 18.1%. We also obtained beta-1,4-N-acetyl-galactosaminyl transferase 2, alpha-1,3-galactosyltransferase, and cytidine monophosphate-N-acetylneuraminic acid hydroxylase deficient pig by somatic cell nuclear transfer, which exhibited significantly decreased activity. In addition, a new CBE version (termed AncBE4max) was used to edit genes in blastocysts and porcine fibroblasts (PFFs) for the first time. While this new version demonstrated a three genes base-editing rate of 71.4% at the porcine GGTA1, B4galNT2, and CMAH loci, it increased the frequency of bystander edits, which ranged from 17.8 to 71.4%. In this study, we efficiently and precisely mutated bases in porcine blastocysts and PFFs using CBEs and successfully generated C-to-T and C-to-G mutations in pigs. These results suggest that CBEs provide a more simple and efficient method for improving economic traits, reducing the breeding cycle, and increasing disease tolerance in pigs, thus aiding in the development of human disease models.


Assuntos
Citidina/genética , Edição de Genes/métodos , Suínos/genética , Animais , Blastocisto/metabolismo , Sistemas CRISPR-Cas , Galactosiltransferases/genética , Vetores Genéticos/genética , Oxigenases de Função Mista/genética , Mutagênese , N-Acetilgalactosaminiltransferases/genética , RNA Guia/genética , Suínos/embriologia
6.
Oncogene ; 39(2): 414-427, 2020 01.
Artigo em Inglês | MEDLINE | ID: mdl-31477841

RESUMO

Drug resistance is a major problem limiting the efficacy of chemotherapy in cancer treatment, and the hypoxia-induced stabilization of HIF-1α plays a role in this process. HIF-1α overexpression has been observed in a variety of human cancers, including colorectal cancer (CRC). Therefore, targeting HIF-1α is a promising strategy for overcoming chemoresistance to enhance the efficacy of chemotherapies in CRC. Here, we show that DNMT inhibitors can induce HIF-1α degradation to overcome oxaliplatin resistance and enhance anti-CRC therapy. We found that a low-toxicity DNMT inhibitor, zebularine, could downregulate HIF-1α expression and overcome hypoxia-induced oxaliplatin resistance in HCT116 cells and showed efficacy in HCT116 xenograft models and AOM/DSS-induced CRC mouse models. Zebularine could induce the degradation of HIF-1α protein through hydroxylation. LC-MS analysis showed a decrease in succinate in various CRC cells under hypoxia and in colon tissues of AOM/DSS-induced CRC mice. The decrease was reversed by zebularine. Tumor angiogenesis was also reduced by zebularine. Furthermore, zebularine potentiated the anticancer effect of oxaliplatin in AOM/DSS-induced CRC models. This finding provides a new strategy in which an increase in HIF-1α hydroxylation could overcome oxaliplatin resistance to enhance anti-CRC therapy.


Assuntos
Antineoplásicos/farmacologia , Neoplasias Colorretais/patologia , Subunidade alfa do Fator 1 Induzível por Hipóxia/metabolismo , Terapia de Alvo Molecular , Oxaliplatina/farmacologia , Animais , Antineoplásicos/uso terapêutico , Neoplasias Colorretais/irrigação sanguínea , Neoplasias Colorretais/tratamento farmacológico , Neoplasias Colorretais/metabolismo , Citidina/análogos & derivados , Citidina/farmacologia , Regulação para Baixo/efeitos dos fármacos , Resistencia a Medicamentos Antineoplásicos/efeitos dos fármacos , Sinergismo Farmacológico , Feminino , Regulação Neoplásica da Expressão Gênica/efeitos dos fármacos , Células HCT116 , Humanos , Hidroxilação/efeitos dos fármacos , Camundongos , Neovascularização Patológica/tratamento farmacológico , Oxaliplatina/uso terapêutico , Estabilidade Proteica/efeitos dos fármacos , Proteólise/efeitos dos fármacos , Fator A de Crescimento do Endotélio Vascular/metabolismo , Ensaios Antitumorais Modelo de Xenoenxerto
7.
Endocrinology ; 161(1)2020 Jan 01.
Artigo em Inglês | MEDLINE | ID: mdl-31742329

RESUMO

Many neural sex differences are differences in the number of neurons of a particular phenotype. For example, male rodents have more calbindin-expressing neurons in the medial preoptic area (mPOA) and bed nucleus of the stria terminalis (BNST), and females have more neurons expressing estrogen receptor alpha (ERα) and kisspeptin in the ventromedial nucleus of the hypothalamus (VMH) and the anteroventral periventricular nucleus (AVPV), respectively. These sex differences depend on neonatal exposure to testosterone, but the underlying molecular mechanisms are unknown. DNA methylation is important for cell phenotype differentiation throughout the developing organism. We hypothesized that testosterone causes sex differences in neurochemical phenotype via changes in DNA methylation, and tested this by inhibiting DNA methylation neonatally in male and female mice, and in females given a masculinizing dose of testosterone. Neonatal testosterone treatment masculinized calbindin, ERα and kisspeptin cell number of females at weaning. Inhibiting DNA methylation with zebularine increased calbindin cell number only in control females, thus eliminating sex differences in calbindin in the mPOA and BNST. Zebularine also reduced the sex difference in ERα cell number in the VMH, in this case by increasing ERα neuron number in males and testosterone-treated females. In contrast, the neonatal inhibition of DNA methylation had no effect on kisspeptin cell number. We conclude that testosterone normally increases the number of calbindin cells and reduces ERα cells in males through orchestrated changes in DNA methylation, contributing to, or causing, the sex differences in both cell types.


Assuntos
Encéfalo/efeitos dos fármacos , Metilação de DNA/efeitos dos fármacos , Diferenciação Sexual/efeitos dos fármacos , Testosterona/farmacologia , Animais , Animais Recém-Nascidos , Encéfalo/citologia , Encéfalo/metabolismo , Química Encefálica/efeitos dos fármacos , Calbindinas/metabolismo , Citidina/administração & dosagem , Citidina/análogos & derivados , Citidina/farmacologia , Receptor alfa de Estrogênio/metabolismo , Feminino , Kisspeptinas/metabolismo , Masculino , Camundongos Endogâmicos C57BL , Neurônios/efeitos dos fármacos , Neurônios/metabolismo , Diferenciação Sexual/fisiologia , Fatores Sexuais , Testosterona/administração & dosagem
8.
Nucleic Acids Res ; 48(3): 1225-1238, 2020 02 20.
Artigo em Inglês | MEDLINE | ID: mdl-31807777

RESUMO

Tet3 regulates the dynamic balance between 5-methylcyotsine (5mC) and 5-hydroxymethylcytosine (5hmC) in DNA during brain development and homeostasis. However, it remains unclear how its functions are modulated in a context-dependent manner during neuronal differentiation. Here, we show that cyclin-dependent kinase 5 (cdk5) phosphorylates Tet3 at the highly conserved serine 1310 and 1379 residues within its catalytic domain, changing its in vitro dioxygenase activity. Interestingly, when stably expressed in Tet1, 2, 3 triple-knockout mouse embryonic stem cells (ESCs), wild-type Tet3 induces higher level of 5hmC and concomitant expression of genes associated with neurogenesis whereas phosphor-mutant (S1310A/S1379A) Tet3 causes elevated 5hmC and expression of genes that are linked to metabolic processes. Consistent with this observation, Tet3-knockout mouse ESCs rescued with wild-type Tet3 have higher level of 5hmC at the promoter of neuron-specific gene BRN2 when compared to cells that expressed phosphor-mutant Tet3. Wild-type and phosphor-mutant Tet3 also exhibit differential binding affinity to histone variant H2A.Z. The differential 5hmC enrichment and H2A.Z occupancy at BRN2 promoter is correlated with higher gene expression and more efficient neuronal differentiation of ESCs that expressed wild-type Tet3. Taken together, our results suggest that cdk5-mediated phosphorylation of Tet3 is required for robust activation of neuronal differentiation program.


Assuntos
Quinase 5 Dependente de Ciclina/genética , Citidina/análogos & derivados , Dioxigenases/genética , Neurogênese/genética , 5-Metilcitosina/análogos & derivados , 5-Metilcitosina/metabolismo , Animais , Diferenciação Celular/genética , Citidina/genética , Citidina/metabolismo , Metilação de DNA/genética , Proteínas de Ligação a DNA , Regulação da Expressão Gênica no Desenvolvimento/genética , Histonas/genética , Camundongos , Camundongos Knockout , Células-Tronco Embrionárias Murinas , Proteínas do Tecido Nervoso/genética , Neurônios/metabolismo , Fatores do Domínio POU/genética , Fosforilação , Regiões Promotoras Genéticas
9.
Spectrochim Acta A Mol Biomol Spectrosc ; 224: 117452, 2020 Jan 05.
Artigo em Inglês | MEDLINE | ID: mdl-31408792

RESUMO

Nucleoside drugs are known for their remarkable anticancer and antiviral properties. The development of nucleoside drugs has attracted much attention and generated a great deal of research interest. ß-L-cytidine and ß-D-cytidine are a pair of cytosine nucleoside enantiomers. In this work, the interactions between cytosine nucleoside enantiomers and human serum albumin were studied by ultraviolet-visible spectra, fluorescence spectrum and circular dichroism spectrum under simulated human physiological environment. The data of fluorescence spectra were corrected for the inner-filter effect to improve accuracy. Stern-Volmer quenching constants and binding constants in addition to thermodynamic parameters have been analyzed, which established that complexes formation have taken place via static quenching mechanism, and that hydrophobic force involved in these interactions. CD spectrum revealed that on addition of cytosine nucleoside enantiomers, the α-helix% of HSA increased slightly. What's more, molecular modeling method indicated that cytosine nucleoside enantiomers prefer binding at the IIIA site of HSA.


Assuntos
Citidina/química , Citidina/metabolismo , Albumina Sérica Humana/química , Albumina Sérica Humana/metabolismo , Humanos , Interações Hidrofóbicas e Hidrofílicas , Simulação de Acoplamento Molecular , Ligação Proteica , Espectrometria de Fluorescência , Estereoisomerismo
10.
Nat Commun ; 10(1): 5600, 2019 12 06.
Artigo em Inglês | MEDLINE | ID: mdl-31811240

RESUMO

RNAs contain post-transcriptional modifications, which fulfill a variety of functions in translation, secondary structure stabilization and cellular stress survival. Here, 2-methylthiocytidine (ms2C) is identified in tRNA of E. coli and P. aeruginosa using NAIL-MS (nucleic acid isotope labeling coupled mass spectrometry) in combination with genetic screening experiments. ms2C is only found in 2-thiocytidine (s2C) containing tRNAs, namely tRNAArgCCG, tRNAArgICG, tRNAArgUCU and tRNASerGCU at low abundances. ms2C is not formed by commonly known tRNA methyltransferases. Instead, we observe its formation in vitro and in vivo during exposure to methylating agents. More than half of the s2C containing tRNA can be methylated to carry ms2C. With a pulse-chase NAIL-MS experiment, the repair mechanism by AlkB dependent sulfur demethylation is demonstrated in vivo. Overall, we describe ms2C as a bacterial tRNA modification and damage product. Its repair by AlkB and other pathways is demonstrated in vivo by our powerful NAIL-MS approach.


Assuntos
Proteínas de Escherichia coli/metabolismo , Escherichia coli/metabolismo , Oxigenases de Função Mista/metabolismo , Processamento Pós-Transcricional do RNA , RNA Bacteriano/metabolismo , RNA de Transferência/metabolismo , Citidina/análogos & derivados , Citidina/metabolismo , Desmetilação , Escherichia coli/genética , Técnicas de Inativação de Genes , Marcação por Isótopo/métodos , Espectrometria de Massas/métodos , Metilação , Ácidos Nucleicos/metabolismo , Pseudomonas aeruginosa/metabolismo , tRNA Metiltransferases/metabolismo
11.
PLoS One ; 14(11): e0224565, 2019.
Artigo em Inglês | MEDLINE | ID: mdl-31725748

RESUMO

BACKGROUND: Muscle wasting in the critically ill is up to 2% per day and delays patient recovery and rehabilitation. It is linked to inflammation, organ failure and severity of illness. The aims of this study were to understand the relationship between muscle depth loss, and nutritional and inflammatory markers during prolonged critical illness. Secondly, to identify when during critical illness catabolism might decrease, such that targeted nutritional strategies may logically be initiated. METHODS: This study was conducted in adult intensive care units in two large teaching hospitals. Patients anticipated to be ventilated for >48 hours were included. Serum C-reactive protein (mg/L), urinary urea (mmol/24h), 3-methylhistidine (µmol/24h) and nitrogen balance (g/24h) were measured on days 1, 3, 7 and 14 of the study. Muscle depth (cm) on ultrasound were measured on the same days over the bicep (bicep and brachialis muscle), forearm (flexor compartment of muscle) and thigh (rectus femoris and vastus intermedius). RESULTS: Seventy-eight critically ill patients were included with mean age of 59 years (SD: 16) and median Intensive care unit (ICU) length of stay of 10 days (IQR: 6-16). Starting muscle depth, 8.5cm (SD: 3.2) to end muscle depth, 6.8cm (SD: 2.2) were on average significantly different over 14 days, with mean difference -1.67cm (95%CI: -2.3 to -1cm), p<0.0001. Protein breakdown and inflammation continued over 14 days of the study. CONCLUSION: Our patients demonstrated a continuous muscle depth loss and negative nitrogen balance over the 14 days of the study. Catabolism remained dominant throughout the study period. No obvious 'nutritional tipping point" to identify anabolism or recovery could be identified in our cohort. Our ICU patient cohort is one with a moderately prolonged stay. This group showed little consistency in data, reflecting the individuality of both disease and response. The data are consistent with a conclusion that a time based assumption of a tipping point does not exist. TRIAL REGISTRATION: International Standard Randomised Controlled Trial Number: ISRCTN79066838. Registration 25 July 2012.


Assuntos
Proteína C-Reativa/metabolismo , Citidina/análogos & derivados , Tempo de Internação , Músculo Esquelético , Atrofia Muscular , Ureia/urina , Adulto , Idoso , Estado Terminal , Citidina/urina , Feminino , Humanos , Masculino , Pessoa de Meia-Idade , Músculo Esquelético/metabolismo , Músculo Esquelético/fisiopatologia , Atrofia Muscular/sangue , Atrofia Muscular/fisiopatologia , Atrofia Muscular/urina
12.
Org Biomol Chem ; 17(43): 9435-9441, 2019 11 06.
Artigo em Inglês | MEDLINE | ID: mdl-31603457

RESUMO

To restrict pathogens, in a normal human cell, APOBEC3 enzymes mutate cytosine to uracil in foreign single-stranded DNAs. However, in cancer cells, APOBEC3B (one of seven APOBEC3 enzymes) has been identified as the primary source of genetic mutations. As such, APOBEC3B promotes evolution and progression of cancers and leads to development of drug resistance in multiple cancers. As APOBEC3B is a non-essential protein, its inhibition can be used to suppress emergence of drug resistance in existing anti-cancer therapies. Because of the vital role of APOBEC3 enzymes in innate immunity, selective inhibitors targeting only APOBEC3B are required. Here, we use the discriminative properties of wild-type APOBEC3A, APOBEC3B and APOBEC3G to deaminate different cytosines in the CCC-recognition motif in order to best place the cytidine analogue 2'-deoxyzebularine (dZ) in the CCC-motif. Using several APOBEC3 variants that mimic deamination patterns of wild-type enzymes, we demonstrate that selective inhibition of APOBEC3B in preference to other APOBEC3 constructs is feasible for the dZCC motif. This work is an important step towards development of in vivo tools to inhibit APOBEC3 enzymes in living cells by using short, chemically modified oligonucleotides.


Assuntos
Citidina Desaminase/antagonistas & inibidores , Citidina/análogos & derivados , DNA de Cadeia Simples/farmacologia , Inibidores Enzimáticos/farmacologia , Proteínas/antagonistas & inibidores , Linhagem Celular , Citidina/química , Citidina/farmacologia , Citidina Desaminase/metabolismo , DNA de Cadeia Simples/química , Inibidores Enzimáticos/síntese química , Inibidores Enzimáticos/química , Humanos , Estrutura Molecular , Proteínas/metabolismo
13.
Nucleic Acids Res ; 47(19): 10267-10281, 2019 11 04.
Artigo em Inglês | MEDLINE | ID: mdl-31665743

RESUMO

Post-transcriptional RNA modifications, the epitranscriptome, play important roles in modulating the functions of RNA species. Modifications of rRNA are key for ribosome production and function. Identification and characterization of enzymes involved in epitranscriptome shaping is instrumental for the elucidation of the functional roles of specific RNA modifications. Ten modified sites have been thus far identified in the mammalian mitochondrial rRNA. Enzymes responsible for two of these modifications have not been characterized. Here, we identify METTL15, show that it is the main N4-methylcytidine (m4C) methyltransferase in human cells and demonstrate that it is responsible for the methylation of position C839 in mitochondrial 12S rRNA. We show that the lack of METTL15 results in a reduction of the mitochondrial de novo protein synthesis and decreased steady-state levels of protein components of the oxidative phosphorylation system. Without functional METTL15, the assembly of the mitochondrial ribosome is decreased, with the late assembly components being unable to be incorporated efficiently into the small subunit. We speculate that m4C839 is involved in the stabilization of 12S rRNA folding, therefore facilitating the assembly of the mitochondrial small ribosomal subunits. Taken together our data show that METTL15 is a novel protein necessary for efficient translation in human mitochondria.


Assuntos
Metiltransferases/genética , Mitocôndrias/genética , Ribossomos Mitocondriais/química , RNA Ribossômico/genética , Citidina/genética , Humanos , Metilação , Mitocôndrias/química , Fosforilação Oxidativa , Biossíntese de Proteínas/genética , Dobramento de RNA/genética , Processamento Pós-Transcricional do RNA/genética , RNA Ribossômico/química
14.
Anal Bioanal Chem ; 411(27): 7221-7231, 2019 Nov.
Artigo em Inglês | MEDLINE | ID: mdl-31583449

RESUMO

DNA methylation is a typical epigenetic phenomenon. Numerous methods for detecting global DNA methylation levels have been developed, among which LC-MS/MS has emerged as an excellent method from the viewpoint of sensitivity, reproducibility, and cost. However, LC-MS/MS methods have limitations due to a lack of the stability and the standardization required for a laboratory assay. The present study aimed to establish a robust assay that guarantees highly accurate measurements of global DNA methylation levels. There are at least three facets of the developed method. The first is discovery of the solvent conditions to minimize sodium adducts. The second is improvement of separation of nucleosides by LC using the columns that had not been used in previous similar studies. The third is success in reduction of the uncertainty of the measurement results, which was achieved by the calibration using the ratio of mdC but not the absolute amount in the presence of internal standards. These facets represent the advantage over methods reported previously. Our developed method enables quantification of DNA methylation with a short time length (8 min) for one analysis as well as with the high reproducibility of measurements that is represented by the inter-day CV% being less than 5%. In addition, data obtained from measuring global DNA methylation levels in cultured cell lines, with or without pharmacological demethylation, support its use for biomedical research. This assay is expected to allow us to conduct initial screening of epigenetic alterations or aberration in a variety of cells.


Assuntos
Metilação de DNA , DNA/química , Espectrometria de Massas em Tandem/métodos , Linhagem Celular Tumoral , Cromatografia Líquida de Alta Pressão/economia , Cromatografia Líquida de Alta Pressão/métodos , Citidina/análogos & derivados , Citidina/análise , Citidina/genética , DNA/genética , Humanos , Espectrometria de Massas em Tandem/economia , Fatores de Tempo
15.
Anal Chim Acta ; 1081: 103-111, 2019 Nov 12.
Artigo em Inglês | MEDLINE | ID: mdl-31446947

RESUMO

Both DNA cytosine methylation (5-methyl-2'-deoxycytidine, m5dC) and RNA cytosine methylation (5-methylcytidine, m5rC) are important epigenetic marks that play regulatory roles in diverse biological processes. m5dC and m5rC can be further oxidized by the ten-eleven translocation (TET) proteins to form 5-hydroxymethyl-2'-deoxycytidine (hm5dC) and 5-hydroxymethylcytidine (hm5rC), respectively. 2'-O-methyl-5-hydroxymethylcytidine (hm5rCm) was recently also identified as a second oxidative metabolite of m5rC in RNA. Previous studies showed that the dysregulation of cytidine modifications in both DNA and RNA are closely related to a variety of human diseases. These cytidine modifications are generally excreted from cell into urine. If these cytidine modifications exhibit specific features related to certain diseases, determination of the cytidine modifications in urine could be utilized as non-invasive diagnostic of diseases. Here, we established a solid-phase extraction in combination with liquid chromatography-mass spectrometry (LC-MS/MS) analysis for simultaneous detection of these cytidine modifications in human urine samples. The developed method enabled the distinct detection of these cytidine modifications. We reported, for the first time, the presence of hm5rCm in human urine. Furthermore, we found that compared to the healthy controls, the contents of hm5dC, hm5rC, and hm5rCm showed significant increases in urine samples of cancer patients, including lymphoma patients, gastric cancer patients, and esophageal cancer patients. This study indicates that the urinary hydroxylmethylation modifications of hm5dC, hm5rC, and hm5rCm may serve as potential indicator of cancers.


Assuntos
Cromatografia Líquida/métodos , Citidina/análogos & derivados , Citidina/urina , Extração em Fase Sólida/métodos , Espectrometria de Massas em Tandem/métodos , Adulto , Idoso , Idoso de 80 Anos ou mais , DNA/química , Metilação de DNA , Feminino , Humanos , Masculino , Pessoa de Meia-Idade , RNA/química
16.
Nucleic Acids Res ; 47(14): 7676-7689, 2019 08 22.
Artigo em Inglês | MEDLINE | ID: mdl-31424549

RESUMO

The potent antiretroviral protein APOBEC3G (A3G) specifically targets and deaminates deoxycytidine nucleotides, generating deoxyuridine, in single stranded DNA (ssDNA) intermediates produced during HIV replication. A non-catalytic domain in A3G binds strongly to RNA, an interaction crucial for recruitment of A3G to the virion; yet, A3G displays no deamination activity for cytidines in viral RNA. Here, we report NMR and molecular dynamics (MD) simulation analysis for interactions between A3Gctd and multiple substrate or non-substrate DNA and RNA, in combination with deamination assays. NMR ssDNA-binding experiments revealed that the interaction with residues in helix1 and loop1 (T201-L220) distinguishes the binding mode of substrate ssDNA from non-substrate. Using 2'-deoxy-2'-fluorine substituted cytidines, we show that a 2'-endo sugar conformation of the target deoxycytidine is favored for substrate binding and deamination. Trajectories of the MD simulation indicate that a ribose 2'-hydroxyl group destabilizes the π-π stacking of the target cytosine and H257, resulting in dislocation of the target cytosine base from the catalytic position. Interestingly, APOBEC3A, which can deaminate ribocytidines, retains the ribocytidine in the catalytic position throughout the MD simulation. Our results indicate that A3Gctd catalytic selectivity against RNA is dictated by both the sugar conformation and 2'-hydroxyl group.


Assuntos
Desaminase APOBEC-3G/metabolismo , DNA de Cadeia Simples/metabolismo , DNA/metabolismo , Espectroscopia de Ressonância Magnética/métodos , Simulação de Dinâmica Molecular , RNA/metabolismo , Desaminase APOBEC-3G/química , Desaminase APOBEC-3G/genética , Biocatálise , Citidina/química , Citidina/metabolismo , DNA/química , DNA/genética , DNA de Cadeia Simples/química , DNA de Cadeia Simples/genética , Desaminação , HIV-1/genética , HIV-1/metabolismo , Humanos , Ligação Proteica , RNA/química , RNA/genética , RNA Viral/química , RNA Viral/genética , RNA Viral/metabolismo , Especificidade por Substrato , Vírion/genética , Vírion/metabolismo
17.
EBioMedicine ; 46: 317-329, 2019 Aug.
Artigo em Inglês | MEDLINE | ID: mdl-31303499

RESUMO

BACKGROUND: Most studies on regenerative medicine focus on cell-based therapies and transplantations. Small-molecule therapeutics, though proved effective in different medical conditions, have not been extensively investigated in regenerative research. It is known that healing potential decreases with development and developmental changes are driven by epigenetic mechanisms, which suggests epigenetic repression of regenerative capacity. METHODS: We applied zebularine, a nucleoside inhibitor of DNA methyltransferases, to stimulate the regenerative response in a model of ear pinna injury in mice. FINDINGS: We observed the regeneration of complex tissue that was manifested as improved ear hole repair in mice that received intraperitoneal injections of zebularine. Six weeks after injury, the mean hole area decreased by 83.2 ±â€¯9.4% in zebularine-treated and by 43.6 ±â€¯15.4% in control mice (p < 10-30). Combined delivery of zebularine and retinoic acid potentiated and accelerated this effect, resulting in complete ear hole closure within three weeks after injury. We found a decrease in DNA methylation and transcriptional activation of neurodevelopmental and pluripotency genes in the regenerating tissues. INTERPRETATION: This study is the first to demonstrate an effective induction of complex tissue regeneration in adult mammals using zebularine. We showed that the synergistic action of an epigenetic drug (zebularine) and a transcriptional activator (retinoic acid) could be effectively utilized to induce the regenerative response, thus delineating a novel pharmacological strategy for regeneration. The strategy was effective in the model of ear pinna regeneration in mice, but zebularine acts on different cell types, therefore, a similar approach can be tested in other tissues and organs.


Assuntos
Citidina/análogos & derivados , Epigênese Genética/efeitos dos fármacos , Cicatrização/efeitos dos fármacos , Cicatrização/genética , Animais , Biomarcadores , Proliferação de Células/efeitos dos fármacos , Ilhas de CpG , Citidina/farmacologia , Metilação de DNA/efeitos dos fármacos , Pavilhão Auricular/efeitos dos fármacos , Pavilhão Auricular/lesões , Queratinócitos/efeitos dos fármacos , Queratinócitos/metabolismo , Camundongos , Medicina Regenerativa , Tretinoína/farmacologia
18.
J Am Soc Mass Spectrom ; 30(9): 1758-1767, 2019 Sep.
Artigo em Inglês | MEDLINE | ID: mdl-31286444

RESUMO

Gas-phase conformations of the sodium-cationized forms of the 2'-deoxycytidine and cytidine mononucleotides, [pdCyd+Na]+ and [pCyd+Na]+, are examined by infrared multiple photon dissociation action spectroscopy. Complimentary electronic structure calculations at the B3LYP/6-311+G(2d,2p)//B3LYP/6-311+G(d,p) level of theory provide candidate conformations and their respective predicted IR spectra for comparison across the IR fingerprint and hydrogen-stretching regions. Comparisons of the predicted IR spectra and the measured infrared multiple photon dissociation action spectra provide insight into the impact of sodium cationization on intrinsic mononucleotide structure. Further, comparison of present results with those reported for the sodium-cationized cytidine nucleoside analogues elucidates the impact of the phosphate moiety on gas-phase structure. Across the neutral, protonated, and sodium-cationized cytidine mononucleotides, a preference for stabilization of the phosphate moiety and nucleobase orientation is observed, although the details of this stabilization differ with the state of cationization. Several low-energy conformations of [pdCyd+Na]+ and [pCyd+Na]+ involving several different orientations of the phosphate moiety and sugar puckering modes are observed experimentally.


Assuntos
Citidina/química , DNA/química , RNA/química , Sódio/química , Espectrofotometria Infravermelho/métodos , Cátions Monovalentes/química , Citidina Monofosfato/química , Desoxicitidina Monofosfato/química , Gases/química , Conformação de Ácido Nucleico
19.
Genes Dev ; 33(13-14): 739-740, 2019 07 01.
Artigo em Inglês | MEDLINE | ID: mdl-31262844

RESUMO

Box C/D small nucleolar RNAs (snoRNAs) and small Cajal body (CB) RNAs (scaRNAs) form ribonucleoprotein (RNP) complexes to mediate 2'-O-methylation of rRNAs and small nuclear RNAs (snRNAs), respectively. The site of methylation is determined by antisense elements in the box C/D RNAs that are complementary to sequences in target RNAs. However, numerous box C/D RNAs in mammalian cells lack antisense elements to rRNAs or snRNAs; thus, their targets remain unknown. In this issue of Genes & Development, Vitali and Kiss (pp. 741-746) demonstrate that "orphan" nucleolar box C/D snoRNA SNORD97 and CB box C/D scaRNA SCARNA97 contain antisense elements that target the wobble cytidine at position 34 of human elongator tRNAMet(CAT) for 2'-O-methylation (C34m). C34m is jointly mediated by SNORD97 and SCARNA97 despite their apparently different intranuclear locations. Furthermore, the investigators demonstrate that C34m prohibits site-specific cleavage of tRNAMet (CAT) into tRNA fragments (tRFs) by the stress-responsive endoribonuclease angiogenin, thereby uncovering a role for SNORD97 and SCARNA97 in the biogenesis of tRFs, which modulate a diverse set of cellular functions in human health and disease.


Assuntos
RNA de Transferência de Metionina , Ribonucleoproteínas , Animais , Corpos Enovelados , Citidina , Humanos , Metilação , RNA Nucleolar Pequeno
20.
Anticancer Res ; 39(7): 3609-3614, 2019 Jul.
Artigo em Inglês | MEDLINE | ID: mdl-31262886

RESUMO

BACKGROUND/AIM: The novel cytidine analog RX-3117, which is activated by uridine-cytidine kinase 2 (UCK2), shows encouraging activity in pancreatic and bladder cancer Phase IIa studies. In this study we highlight the potential role of UCK2 as a biomarker for selecting patients for RX-3117 treatment. PATIENTS AND METHODS: The online genomics analysis and visualization platform, R2, developed by the Oncogenomics department at the AMC (Amsterdam, The Netherlands) was used for in silico UCK2-mRNA correlation with overall survival of pancreatic cancer patients, while UCK2 protein expression was evaluated by immunohistochemistry on pancreatic tumor formalin-fixed-paraffin-embedded sections from independent pancreatic cancer patients. mRNA expression was also determined for SUIT-2, PANC-1 and PDAC-3. Lastly, the drug sensitivity to RX-3117 was investigated using the Sulforhodamine-B cytotoxicity assay. RESULTS: The in silico data showed that a high UCK2-mRNA expression was correlated with a shorter overall survival in pancreatic cancer patients. Moreover, UCK2 protein expression was high in 21/25 patients, showing a significantly shorter mean. Overall Survival (8.4 versus 34.3 months, p=0.045). Sensitivity to RX-3117 varied between 0.6 and 11 µM. CONCLUSION: Pancreatic cancer cells are sensitive to pharmacologically achievable RX-3117 concentrations and UCK2 might be exploited as a biomarker for patient treatment selection.


Assuntos
Adenocarcinoma/tratamento farmacológico , Antineoplásicos/farmacologia , Biomarcadores Tumorais/metabolismo , Citidina/análogos & derivados , Neoplasias Pancreáticas/tratamento farmacológico , Uridina Quinase/metabolismo , Adenocarcinoma/genética , Adenocarcinoma/metabolismo , Idoso , Biomarcadores Tumorais/genética , Linhagem Celular Tumoral , Citidina/farmacologia , Feminino , Humanos , Masculino , Neoplasias Pancreáticas/genética , Neoplasias Pancreáticas/metabolismo , RNA Mensageiro/metabolismo , Uridina Quinase/genética
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