Your browser doesn't support javascript.
loading
Show: 20 | 50 | 100
Results 1 - 20 de 12.454
Filter
1.
Int J Mol Sci ; 25(13)2024 Jul 06.
Article in English | MEDLINE | ID: mdl-39000550

ABSTRACT

The effect of the modulators of the mitochondrial ATP-dependent potassium channel (mitoKATP) on the structural and biochemical alterations in the substantia nigra and brain tissues was studied in a rat model of Parkinson's disease induced by rotenone. It was found that, in experimental parkinsonism accompanied by characteristic motor deficits, both neurons and the myelin sheath of nerve fibers in the substantia nigra were affected. Changes in energy and ion exchange in brain mitochondria were also revealed. The nucleoside uridine, which is a source for the synthesis of the mitoKATP channel opener uridine diphosphate, was able to dose-dependently decrease behavioral disorders and prevent the death of animals, which occurred for about 50% of animals in the model. Uridine prevented disturbances in redox, energy, and ion exchanges in brain mitochondria, and eliminated alterations in their structure and the myelin sheath in the substantia nigra. Cytochemical examination showed that uridine restored the indicators of oxidative phosphorylation and glycolysis in peripheral blood lymphocytes. The specific blocker of the mitoKATP channel, 5-hydroxydecanoate, eliminated the positive effects of uridine, suggesting that this channel is involved in neuroprotection. Taken together, these findings indicate the promise of using the natural metabolite uridine as a new drug to prevent and, possibly, stop the progression of Parkinson's disease.


Subject(s)
Mitochondria , Potassium Channels , Rotenone , Uridine , Animals , Uridine/pharmacology , Uridine/metabolism , Rats , Potassium Channels/metabolism , Mitochondria/metabolism , Mitochondria/drug effects , Male , Disease Models, Animal , Parkinson Disease/metabolism , Parkinson Disease/drug therapy , Parkinson Disease/etiology , Parkinson Disease/pathology , Substantia Nigra/metabolism , Substantia Nigra/drug effects , Substantia Nigra/pathology , Neuroprotective Agents/pharmacology , Oxidative Phosphorylation/drug effects , Rats, Wistar , Decanoic Acids/pharmacology , Hydroxy Acids/pharmacology
2.
Int J Mol Sci ; 25(13)2024 Jun 27.
Article in English | MEDLINE | ID: mdl-39000137

ABSTRACT

The URH1p enzyme from the yeast Saccharomyces cerevisiae has gained significant interest due to its role in nitrogenous base metabolism, particularly involving uracil and nicotinamide salvage. Indeed, URH1p was initially classified as a nucleoside hydrolase (NH) with a pronounced preference for uridine substrate but was later shown to also participate in a Preiss-Handler-dependent pathway for recycling of both endogenous and exogenous nicotinamide riboside (NR) towards NAD+ synthesis. Here, we present the detailed enzymatic and structural characterisation of the yeast URH1p enzyme, a member of the group I NH family of enzymes. We show that the URH1p has similar catalytic efficiencies for hydrolysis of NR and uridine, advocating a dual role of the enzyme in both NAD+ synthesis and nucleobase salvage. We demonstrate that URH1p has a monomeric structure that is unprecedented for members of the NH homology group I, showing that oligomerisation is not strictly required for the N-ribosidic activity in this family of enzymes. The size, thermal stability and activity of URH1p towards the synthetic substrate 5-fluoruridine, a riboside precursor of the antitumoral drug 5-fluorouracil, make the enzyme an attractive tool to be employed in gene-directed enzyme-prodrug activation therapy against solid tumours.


Subject(s)
Niacinamide , Saccharomyces cerevisiae Proteins , Saccharomyces cerevisiae , Niacinamide/analogs & derivatives , Niacinamide/metabolism , Niacinamide/chemistry , Saccharomyces cerevisiae/genetics , Saccharomyces cerevisiae/metabolism , Saccharomyces cerevisiae Proteins/metabolism , Saccharomyces cerevisiae Proteins/genetics , Saccharomyces cerevisiae Proteins/chemistry , Neoplasms/drug therapy , Neoplasms/genetics , Neoplasms/metabolism , Structure-Activity Relationship , Pyridinium Compounds/metabolism , Pyridinium Compounds/chemistry , N-Glycosyl Hydrolases/metabolism , N-Glycosyl Hydrolases/genetics , N-Glycosyl Hydrolases/chemistry , Uridine/metabolism , Uridine/analogs & derivatives , Uridine/chemistry , Substrate Specificity , Humans , Models, Molecular
3.
Chem Commun (Camb) ; 60(55): 7081-7084, 2024 Jul 04.
Article in English | MEDLINE | ID: mdl-38896044

ABSTRACT

In this report, we show that a very common modification (especially in tRNA), dihydrouridine, was efficiently produced by photoreduction of the canonical pyrimidine ribonucleoside, uridine in formamide. Formamide not only acts as a solvent in this reaction, but also as the reductant. The other three components of the canonical alphabet (C, A, G) remained intact under the same conditions, suggesting that dihydrouridine might have coexisted with all four canonical RNA nucleosides (C, U, A, G) at the dawn of life.


Subject(s)
Formamides , Oxidation-Reduction , Uridine , Uridine/chemistry , Uridine/analogs & derivatives , Uridine/chemical synthesis , Formamides/chemistry , Photochemical Processes
4.
Article in English | MEDLINE | ID: mdl-38905720

ABSTRACT

Decitabine is a DNA methyltransferase inhibitor used in the treatment of acute myeloid leukemia and myelodysplastic syndrome. The notion that ongoing trials are presently exploring the combined use of decitabine, with or without the cytidine deaminase inhibitor cedazuridine, and other antileukemic drugs necessitates a comprehensive understanding of pharmacokinetic properties and an evaluation of drug-drug interaction liabilities. We report here the development and validation of a sensitive UHPLC-MS/MS method for quantifying decitabine in mouse plasma, which should be useful for such studies. The method involved a one-step protein precipitation extraction, and chromatographic separation on an XBridge HILIC column using gradient elution. The method was found to be robust, accurate, precise, and sufficiently sensitive (lower limit of quantitation, 0.4 ng/mL) to determine decitabine concentrations in microvolumes of plasma from mice receiving the agent orally or intravenously in the presence or absence of cedazuridine.


Subject(s)
Decitabine , Tandem Mass Spectrometry , Animals , Tandem Mass Spectrometry/methods , Decitabine/pharmacokinetics , Decitabine/blood , Decitabine/administration & dosage , Mice , Chromatography, High Pressure Liquid/methods , Reproducibility of Results , Azacitidine/pharmacokinetics , Azacitidine/blood , Azacitidine/analogs & derivatives , Azacitidine/administration & dosage , Azacitidine/chemistry , Linear Models , Uridine/pharmacokinetics , Uridine/blood , Uridine/analogs & derivatives , Sensitivity and Specificity , Limit of Detection
5.
Biomolecules ; 14(6)2024 Jun 08.
Article in English | MEDLINE | ID: mdl-38927075

ABSTRACT

Atherosclerosis (AS) has become the leading cause of cardiovascular disease worldwide. Our previous study had observed that Nippostrongylus brasiliensis (Nb) infection or its derived products could inhibit AS development by inducing an anti-inflammatory response. We performed a metabolic analysis to screen Nb-derived metabolites with anti-inflammation activity and evaluated the AS-prevention effect. We observed that the metabolite uridine had higher expression levels in mice infected with the Nb and ES (excretory-secretory) products and could be selected as a key metabolite. ES and uridine interventions could reduce the pro-inflammatory responses and increase the anti-inflammatory responses in vitro and in vivo. The apolipoprotein E gene knockout (ApoE-/-) mice were fed with a high-fat diet for the AS modeling. Following the in vivo intervention, ES products or uridine significantly reduced serum and liver lipid levels, alleviated the formation of atherosclerosis, and reduced the pro-inflammatory responses in serum or plaques, while the anti-inflammatory responses showed opposite trends. After blocking with 5-HD (5-hydroxydecanoate sodium) in vitro, the mRNA levels of M2 markers were significantly reduced. When blocked with 5-HD in vivo, the degree of atherosclerosis was worsened, the pro-inflammatory responses were increased compared to the uridine group, while the anti-inflammatory responses decreased accordingly. Uridine, a key metabolite from Nippostrongylus brasiliensis, showed anti-inflammatory and anti-atherosclerotic effects in vitro and in vivo, which depend on the activation of the mitochondrial ATP-sensitive potassium channel.


Subject(s)
Anti-Inflammatory Agents , Atherosclerosis , Nippostrongylus , Uridine , Animals , Male , Mice , Anti-Inflammatory Agents/pharmacology , Apolipoproteins E/genetics , Apolipoproteins E/deficiency , Atherosclerosis/metabolism , Atherosclerosis/genetics , Disease Models, Animal , KATP Channels/metabolism , KATP Channels/genetics , Mice, Knockout , Mitochondria/metabolism , Mitochondria/drug effects , Uridine/pharmacology
6.
Methods Mol Biol ; 2726: 169-207, 2024.
Article in English | MEDLINE | ID: mdl-38780732

ABSTRACT

Nucleotide modifications are occurrent in all types of RNA and play an important role in RNA structure formation and stability. Modified bases not only possess the ability to shift the RNA structure ensemble towards desired functional confirmations. By changes in the base pairing partner preference, they may even enlarge or reduce the conformational space, i.e., the number and types of structures the RNA molecule can adopt. However, most methods to predict RNA secondary structure do not provide the means to include the effect of modifications on the result. With the help of a heavily modified transfer RNA (tRNA) molecule, this chapter demonstrates how to include the effect of different base modifications into secondary structure prediction using the ViennaRNA Package. The constructive approach demonstrated here allows for the calculation of minimum free energy structure and suboptimal structures at different levels of modified base support. In particular we, show how to incorporate the isomerization of uridine to pseudouridine ( Ψ ) and the reduction of uridine to dihydrouridine (D).


Subject(s)
Nucleic Acid Conformation , RNA , RNA/chemistry , RNA, Transfer/chemistry , RNA, Transfer/metabolism , Nucleotides/chemistry , Base Pairing , Computational Biology/methods , Thermodynamics , Software , Uridine/chemistry , Models, Molecular , Pseudouridine/chemistry
7.
J Agric Food Chem ; 72(20): 11405-11414, 2024 May 22.
Article in English | MEDLINE | ID: mdl-38717990

ABSTRACT

This study investigated the multiple herbicide resistance (MHR) mechanism of one Echinochloa crus-galli population that was resistant to florpyrauxifen-benzyl (FPB), cyhalofop-butyl (CHB), and penoxsulam (PEX). This population carried an Ala-122-Asn mutation in the acetolactate synthase (ALS) gene but no mutation in acetyl-CoA carboxylase (ACCase) and transport inhibitor response1 (TIR1) genes. The metabolism rate of PEX was 2-fold higher, and the production of florpyrauxifen-acid and cyhalofop-acid was lower in the resistant population. Malathion and 4-chloro-7-nitrobenzoxadiazole (NBD-Cl) could reverse the resistance, suggesting that cytochrome P450 (CYP450) and glutathione S-transferase (GST) contribute to the enhanced metabolism. According to RNA-seq and qRT-PCR validation, two CYP450 genes (CYP71C42 and CYP71D55), one GST gene (GSTT2), two glycosyltransferase genes (rhamnosyltransferase 1 and IAAGLU), and two ABC transporter genes (ABCG1 and ABCG25) were induced by CHB, FPB, and PEX in the resistant population. This study revealed that the target mutant and enhanced metabolism were involved in the MHR mechanism in E. crus-galli.


Subject(s)
Cytochrome P-450 Enzyme System , Echinochloa , Herbicide Resistance , Herbicides , Mutation , Plant Proteins , Herbicide Resistance/genetics , Herbicides/pharmacology , Herbicides/metabolism , Echinochloa/genetics , Echinochloa/drug effects , Echinochloa/metabolism , Echinochloa/growth & development , Plant Proteins/genetics , Plant Proteins/metabolism , Cytochrome P-450 Enzyme System/genetics , Cytochrome P-450 Enzyme System/metabolism , Acetyl-CoA Carboxylase/genetics , Acetyl-CoA Carboxylase/metabolism , Plant Weeds/drug effects , Plant Weeds/genetics , Plant Weeds/metabolism , Acetolactate Synthase/genetics , Acetolactate Synthase/metabolism , Butanes , Nitriles , Sulfonamides , Uridine/analogs & derivatives
8.
Biophys Chem ; 310: 107256, 2024 Jul.
Article in English | MEDLINE | ID: mdl-38728807

ABSTRACT

Understanding the mechanisms by which drugs interact with cell membranes is crucial for unraveling the underlying biochemical and biophysical processes that occur on the surface of these membranes. Our research focused on studying the interaction between an ester-type derivative of tristearoyl uridine and model cell membranes composed of lipid monolayers at the air-water interface. For that, we selected a specific lipid to simulate nontumorigenic cell membranes, namely 1,2-dihexadecanoyl-sn-glycero-3-phospho-l-serine. We noted significant changes in the surface pressure-area isotherms, with a noticeable shift towards larger areas, which was lower than expected for ideal mixtures, indicating monolayer condensation. Furthermore, the viscoelastic properties of the interfacial film demonstrated an increase in both the elastic and viscous parameters for the mixed film. We also observed structural alterations using vibrational spectroscopy, which revealed an increase in the all-trans to gauche conformers ratio. This confirmed the stiffening effect of the prodrug on the lipid monolayer. In summary, this study indicates that this lipophilic prodrug significantly impacts the lipid monolayer's thermodynamic, rheological, electrical, and molecular characteristics. This information is crucial for understanding how the drug interacts with specific sites on the cellular membrane. It also has implications for drug delivery, as the drug's passage into the cytosol may involve traversing the lipid bilayer.


Subject(s)
Cell Membrane , Prodrugs , Uridine , Prodrugs/chemistry , Prodrugs/pharmacology , Prodrugs/metabolism , Cell Membrane/chemistry , Cell Membrane/metabolism , Uridine/chemistry , Uridine/pharmacology , Phosphatidylserines/chemistry , Thermodynamics , Surface Properties , Viscosity , Elasticity
9.
Anal Chem ; 96(21): 8674-8681, 2024 May 28.
Article in English | MEDLINE | ID: mdl-38712815

ABSTRACT

Messenger RNA (mRNA) can be sequenced via indirect approaches such as Sanger sequencing and next generation sequencing (NGS), or direct approaches like bottom-up mass spectrometry (MS). Direct sequencing allows the confirmation of RNA modifications. However, the conventional bottom-up MS approach involves time-consuming in-solution digestions that require a large amount of sample, and can lead to the RNase contamination of the LC-MS system and column. Here, we describe a platform that enables online nucleotide mapping of mRNAs via the use of immobilized RNase cartridges and 2D-LC-MS instrumentation. The online approach was compared to conventional offline digestion protocols adapted from two published studies. For this purpose, five model mRNAs of varying lengths (996-4521 nucleotides) and chemistries (unmodified uridine vs 5-methoxyuridine (5moU)) were analyzed. The profiles and sequence coverages obtained after RNase T1 digestion were discussed. The online nucleotide mapping achieved comparable or slightly greater sequence coverage for the 5 mRNAs (5.8-51.5%) in comparison to offline approaches (3.7-50.4%). The sequence coverage was increased to 65.6-85.6 and 69.7-85.0% when accounting for the presence of nonunique digestion products generated by the RNase T1 and A, respectively. The online nucleotide mapping significantly reduced the digestion time (from 15 to <5 min), increased the signal intensity by more than 10-fold in comparison to offline approaches.


Subject(s)
RNA, Messenger , RNA, Messenger/analysis , RNA, Messenger/genetics , Nucleotide Mapping/methods , Mass Spectrometry , Chromatography, Liquid , Uridine/analogs & derivatives , Uridine/chemistry , Humans , Ribonuclease T1/metabolism
10.
Nat Commun ; 15(1): 4094, 2024 May 15.
Article in English | MEDLINE | ID: mdl-38750017

ABSTRACT

tRNA modifications affect ribosomal elongation speed and co-translational folding dynamics. The Elongator complex is responsible for introducing 5-carboxymethyl at wobble uridine bases (cm5U34) in eukaryotic tRNAs. However, the structure and function of human Elongator remain poorly understood. In this study, we present a series of cryo-EM structures of human ELP123 in complex with tRNA and cofactors at four different stages of the reaction. The structures at resolutions of up to 2.9 Å together with complementary functional analyses reveal the molecular mechanism of the modification reaction. Our results show that tRNA binding exposes a universally conserved uridine at position 33 (U33), which triggers acetyl-CoA hydrolysis. We identify a series of conserved residues that are crucial for the radical-based acetylation of U34 and profile the molecular effects of patient-derived mutations. Together, we provide the high-resolution view of human Elongator and reveal its detailed mechanism of action.


Subject(s)
Cryoelectron Microscopy , RNA, Transfer , Humans , RNA, Transfer/metabolism , RNA, Transfer/chemistry , RNA, Transfer/genetics , Uridine/chemistry , Uridine/metabolism , Mutation , Acetyl Coenzyme A/metabolism , Acetyl Coenzyme A/chemistry , Models, Molecular , Acetylation , Histone Acetyltransferases/metabolism , Histone Acetyltransferases/chemistry , Histone Acetyltransferases/genetics , Protein Binding
11.
J Med Virol ; 96(5): e29642, 2024 May.
Article in English | MEDLINE | ID: mdl-38708812

ABSTRACT

Molnupiravir, an oral direct-acting antiviral effective in vitro against SARS-CoV-2, has been largely employed during the COVID-19 pandemic, since December 2021. After marketing and widespread usage, a progressive increase in SARS-CoV-2 lineages characterized by a higher transition/transversion ratio, a characteristic signature of molnupiravir action, appeared in the Global Initiative on Sharing All Influenza Data (GISAID) and International Nucleotide Sequence Database Collaboration (INSDC) databases. Here, we assessed the drug effects by SARS-CoV-2 whole-genome sequencing on 38 molnupiravir-treated persistently positive COVID-19 outpatients tested before and after treatment. Seventeen tixagevimab/cilgavimab-treated outpatients served as controls. Mutational analyses confirmed that SARS-CoV-2 exhibits an increased transition/transversion ratio seven days after initiation of molnupiravir. Moreover we observed an increased G->A ratio compared to controls, which was not related to apolipoprotein B mRNAediting enzyme, catalytic polypeptide-like (APOBEC) activity. In addition, we demonstrated for the first time an increased diversity and complexity of the viral quasispecies.


Subject(s)
Antiviral Agents , COVID-19 Drug Treatment , Cytidine/analogs & derivatives , Genome, Viral , Hydroxylamines , SARS-CoV-2 , Humans , SARS-CoV-2/genetics , SARS-CoV-2/drug effects , Antiviral Agents/therapeutic use , Antiviral Agents/pharmacology , Hydroxylamines/pharmacology , Hydroxylamines/therapeutic use , Male , Female , Case-Control Studies , Middle Aged , Cytidine/therapeutic use , Cytidine/pharmacology , Aged , Adult , Whole Genome Sequencing , Genetic Variation , Uridine/pharmacology , COVID-19/virology , Mutation
12.
Eur Rev Med Pharmacol Sci ; 28(8): 3268-3274, 2024 Apr.
Article in English | MEDLINE | ID: mdl-38708485

ABSTRACT

BACKGROUND: We describe the first case of a pediatric patient with acute intermittent porphyria and severe chronic porphyric neuropathy treated with givosiran, a small-interfering RNA that drastically decreases delta-aminolevulinic acid production and reduces porphyric attacks' recurrence. CASE REPORT: A 12-year-old male patient with refractory acute intermittent porphyria and severe porphyric neuropathy was followed prospectively for 12 months after givosiran initiation (subcutaneous, 2.5 mg/kg monthly). Serial neurological, structural, and resting-state functional magnetic resonance imaging (MRI) evaluations were performed, including clinical scales and neurophysiological tests. Delta-aminolevulinic acid urinary levels dropped drastically during treatment. In parallel, all the administered neurological rating scales and neurophysiological assessments showed improvement in all domains. Moreover, an improvement in central motor conduction parameters and resting-state functional connectivity in the sensory-motor network was noticed. At the end of the follow-up, the patient could walk unaided after using a wheelchair for 5 years. CONCLUSIONS: A clear beneficial effect of givosiran was demonstrated in our patient with both clinical and peripheral nerve neurophysiologic outcome measures. Moreover, we first reported a potential role of givosiran in recovering central motor network impairment in acute intermittent porphyria (AIP), which was previously unknown. This study provides Class IV evidence that givosiran improves chronic porphyric neuropathy.


Subject(s)
Acetylgalactosamine/analogs & derivatives , Porphyria, Acute Intermittent , Humans , Male , Porphyria, Acute Intermittent/drug therapy , Child , Acetylgalactosamine/therapeutic use , Aminolevulinic Acid/analogs & derivatives , Aminolevulinic Acid/urine , Magnetic Resonance Imaging , Pyrrolidines/therapeutic use , Uridine/analogs & derivatives , Uridine/therapeutic use , Uridine/administration & dosage , Recovery of Function , Chronic Disease , Treatment Outcome
13.
mBio ; 15(6): e0042024, 2024 Jun 12.
Article in English | MEDLINE | ID: mdl-38700353

ABSTRACT

Chikungunya virus (CHIKV) is an enveloped, positive-sense RNA virus that has re-emerged to cause millions of human infections worldwide. In humans, acute CHIKV infection causes fever and severe muscle and joint pain. Chronic and debilitating arthritis and joint pain can persist for months to years. To date, there are no approved antivirals against CHIKV. Recently, the ribonucleoside analog 4'-fluorouridine (4'-FlU) was reported as a highly potent orally available inhibitor of SARS-CoV-2, respiratory syncytial virus, and influenza virus replication. In this study, we assessed 4'-FlU's potency and breadth of inhibition against a panel of alphaviruses including CHIKV, and found that it broadly suppressed alphavirus production in cell culture. 4'-FlU acted on the viral RNA replication step, and the first 4 hours post-infection were the critical time for its antiviral effect. In vitro replication assays identified nsP4 as the target of inhibition. In vivo, treatment with 4'-FlU reduced disease signs, inflammatory responses, and viral tissue burden in mouse models of CHIKV and Mayaro virus infection. Treatment initiated at 2 hours post-infection was most effective; however, treatment initiated as late as 24-48 hours post-infection produced measurable antiviral effects in the CHIKV mouse model. 4'-FlU showed effective oral delivery in our mouse model and resulted in the accumulation of both 4'-FlU and its bioactive triphosphate form in tissues relevant to arthritogenic alphavirus pathogenesis. Together, our data indicate that 4'-FlU inhibits CHIKV infection in vitro and in vivo and is a promising oral therapeutic candidate against CHIKV infection.IMPORTANCEAlphaviruses including chikungunya virus (CHIKV) are mosquito-borne positive-strand RNA viruses that can cause various diseases in humans. Although compounds that inhibit CHIKV and other alphaviruses have been identified in vitro, there are no licensed antivirals against CHIKV. Here, we investigated a ribonucleoside analog, 4'-fluorouridine (4'-FlU), and demonstrated that it inhibited infectious virus production by several alphaviruses in vitro and reduced virus burden in mouse models of CHIKV and Mayaro virus infection. Our studies also indicated that 4'-FlU treatment reduced CHIKV-induced footpad swelling and reduced the production of pro-inflammatory cytokines. Inhibition in the mouse model correlated with effective oral delivery of 4'-FlU and accumulation of both 4'-FlU and its bioactive form in relevant tissues. In summary, 4'-FlU exhibits potential as a novel anti-alphavirus agent targeting the replication of viral RNA.


Subject(s)
Alphavirus , Antiviral Agents , Chikungunya virus , Virus Replication , Virus Replication/drug effects , Animals , Antiviral Agents/pharmacology , Antiviral Agents/therapeutic use , Mice , Chikungunya virus/drug effects , Chikungunya virus/physiology , Alphavirus/drug effects , Alphavirus/physiology , Uridine/analogs & derivatives , Uridine/pharmacology , Humans , Chikungunya Fever/drug therapy , Chikungunya Fever/virology , Disease Models, Animal , Cell Line , Chlorocebus aethiops , Female , Vero Cells
14.
Plant J ; 119(2): 895-915, 2024 Jul.
Article in English | MEDLINE | ID: mdl-38753873

ABSTRACT

Plant mitochondrial and chloroplast transcripts are subject to numerous events of specific cytidine-to-uridine (C-to-U) RNA editing to correct genetic information. Key protein factors for this process are specific RNA-binding pentatricopeptide repeat (PPR) proteins, which are encoded in the nucleus and post-translationally imported into the two endosymbiotic organelles. Despite hundreds of C-to-U editing sites in the plant organelles, no comparable editing has been found for nucleo-cytosolic mRNAs raising the question why plant RNA editing is restricted to chloroplasts and mitochondria. Here, we addressed this issue in the model moss Physcomitrium patens, where all PPR-type RNA editing factors comprise specific RNA-binding and cytidine deamination functionalities in single proteins. To explore whether organelle-type RNA editing can principally also take place in the plant cytosol, we expressed PPR56, PPR65 and PPR78, three editing factors recently shown to also function in a bacterial setup, together with cytosolic co-transcribed native targets in Physcomitrium. While we obtained unsatisfying results upon their constitutive expression, we found strong cytosolic RNA editing under hormone-inducible expression. Moreover, RNA-Seq analyses revealed varying numbers of up to more than 900 off-targets in other cytosolic transcripts. We conclude that PPR-mediated C-to-U RNA editing is not per se incompatible with the plant cytosol but that its limited target specificity has restricted its occurrence to the much less complex transcriptomes of mitochondria and chloroplast in the course of evolution.


Subject(s)
Bryopsida , Chloroplasts , Cytosol , Mitochondria , RNA Editing , RNA, Plant , Chloroplasts/metabolism , Chloroplasts/genetics , Cytosol/metabolism , Bryopsida/genetics , Bryopsida/metabolism , Mitochondria/metabolism , Mitochondria/genetics , RNA, Plant/genetics , RNA, Plant/metabolism , Plant Proteins/genetics , Plant Proteins/metabolism , Cytidine/metabolism , Cytidine/genetics , RNA-Binding Proteins/metabolism , RNA-Binding Proteins/genetics , Gene Expression Regulation, Plant , Uridine/metabolism , Uridine/genetics
15.
Nucleic Acids Res ; 52(10): 5841-5851, 2024 Jun 10.
Article in English | MEDLINE | ID: mdl-38716877

ABSTRACT

Therapeutic fluoropyrimidines 5-fluorouracil (5-FU) and 5-fluorocytosine (5-FC) are in long use for treatment of human cancers and severe invasive fungal infections, respectively. 5-Fluorouridine triphosphate represents a bioactive metabolite of both drugs and is incorporated into target cells' RNA. Here we use the model fungus Saccharomyces cerevisiae to define fluorinated tRNA as a key mediator of 5-FU and 5-FC cytotoxicity when specific tRNA methylations are absent. tRNA methylation deficiency caused by loss of Trm4 and Trm8 was previously shown to trigger an RNA quality control mechanism resulting in partial destabilization of hypomodified tRNAValAAC. We demonstrate that, following incorporation into tRNA, fluoropyrimidines strongly enhance degradation of yeast tRNAValAAC lacking Trm4 and Trm8 dependent methylations. At elevated temperature, such effect occurs already in absence of Trm8 alone. Genetic approaches and quantification of tRNA modification levels reveal that enhanced fluoropyrimidine cytotoxicity results from additional, drug induced uridine modification loss and activation of tRNAValAAC decay involving the exonuclease Xrn1. These results suggest that inhibition of tRNA methylation may be exploited to boost therapeutic efficiency of 5-FU and 5-FC.


Subject(s)
Flucytosine , Fluorouracil , RNA, Transfer , Saccharomyces cerevisiae , Exoribonucleases/metabolism , Exoribonucleases/genetics , Flucytosine/pharmacology , Fluorouracil/pharmacology , Methylation , RNA Stability/drug effects , RNA, Transfer/metabolism , Saccharomyces cerevisiae/genetics , Saccharomyces cerevisiae/drug effects , Saccharomyces cerevisiae/metabolism , Saccharomyces cerevisiae Proteins/metabolism , Saccharomyces cerevisiae Proteins/genetics , tRNA Methyltransferases/metabolism , tRNA Methyltransferases/genetics , Uridine/metabolism
16.
Org Biomol Chem ; 22(22): 4568-4573, 2024 06 05.
Article in English | MEDLINE | ID: mdl-38771639

ABSTRACT

Wavelength-shifting molecular beacons were prepared from L-DNA. The clickable anchor for the two dyes, Cy3 and Cy5, was 2'-O-propargyl-L-uridine and was synthesized from L-ribose. Four clickable molecular beacons were prepared and double-modified with the azide dyes by a combination of click chemistry on a solid support for Cy3 during DNA synthesis and postsynthetic click chemistry for Cy5 in solution. Cy3 and Cy5 successfully formed a FRET pair in the beacons, and the closed form (red fluorescence) and the open form (green fluorescence) can be distinguished by the two-color fluorescence readout. Two molecular beacons were identified to show the greatest fluorescence contrast in temperature-dependent fluorescence measurements. The stability of the L-configured molecular beacons was demonstrated after several heating and cooling cycles as well as in the cell lysate. In comparison, D-configured molecular beacons showed a rapid decrease of fluorescence contrast in the cell lysate, which is caused by the opening of the beacons, probably due to degradation. This was confirmed in cell experiments using confocal microscopy. The L-configured molecular beacons are potential intracellular thermometers for future applications.


Subject(s)
Click Chemistry , DNA , Uridine , DNA/chemistry , Uridine/chemistry , Uridine/analogs & derivatives , Humans , Fluorescent Dyes/chemistry , Fluorescent Dyes/chemical synthesis , Fluorescence Resonance Energy Transfer , Carbocyanines/chemistry , Temperature
17.
Aging (Albany NY) ; 16(9): 7752-7773, 2024 05 01.
Article in English | MEDLINE | ID: mdl-38696320

ABSTRACT

Long non-coding RNAs (lncRNAs) are involved significantly in the development of human cancers. lncRNA HOTAIR has been reported to play an oncogenic role in many human cancers. Its specific regulatory role is still elusive. And it might have enormous potential to interpret the malignant progression of tumors in a broader perspective, that is, in pan-cancer. We comprehensively investigated the effect of HOTAIR expression on tumor prognosis across human malignancies by analyzing multiple cancer-related databases like The Cancer Genome Atlas (TCGA) and Tumor Immune Estimation Resource (TIMER). Bioinformatics data indicated that HOTAIR was overexpressed in most of these human malignancies and was significantly associated with the prognosis of patients with cancer, especially in colorectal cancer (CRC). Subsequently, this study further clarified the utility of HOTAIR that downregulation of its expression could result in reduced proliferation and invasion of CRC cells. Mechanistically, HOTAIR upregulated the metabolic enzymes UPP1 by recruiting histone methyltransferase EZH2, thereby increasing the tumor progression. Our results highlight the essential role of HOTAIR in pan-cancer and uridine bypass, suggesting that the HOTAIR/EZH2/UPP1 axis might be a novel target for overcoming CRC. We anticipate that the role of HOTAIR in metabolism could be important in the context of CRC and even exploited for therapeutic purposes.


Subject(s)
Cell Proliferation , Colorectal Neoplasms , Gene Expression Regulation, Neoplastic , RNA, Long Noncoding , Uridine , Humans , RNA, Long Noncoding/genetics , RNA, Long Noncoding/metabolism , Colorectal Neoplasms/genetics , Colorectal Neoplasms/metabolism , Uridine/metabolism , Cell Proliferation/genetics , Cell Line, Tumor , Enhancer of Zeste Homolog 2 Protein/genetics , Enhancer of Zeste Homolog 2 Protein/metabolism , Prognosis
18.
Mol Biol Rep ; 51(1): 502, 2024 Apr 10.
Article in English | MEDLINE | ID: mdl-38598020

ABSTRACT

BACKGROUND: Thyroid cancer, originating in the neck's thyroid gland, encompasses various types. Genetic mutations, particularly in BRAF and RET genes are crucial in its development. This study investigates the association between BRAF (rs113488022) and RET (rs77709286) polymorphisms and thyroid cancer risk in the Khyber Pakhtunkhwa (KP) population. METHODS: Blood samples from 100 thyroid cancer patients and 100 healthy controls were genotyped using ARMS-PCR followed by gel electrophoresis and statistical analysis. RESULTS: Analysis revealed a significant association between the minor allele T of BRAF (rs113488022) and thyroid cancer risk (P = 0.0001). Both genotypes of BRAF (rs113488022) showed significant associations with thyroid cancer risk (AT; P = 0.0012 and TT; P = 0.045). Conversely, the minor allele G of RET (rs77709286) exhibited a non-significant association with thyroid cancer risk (P = 0.2614), and neither genotype showed significant associations (CG; P = 0.317, GG; P = 0.651). Demographic and clinical parameters analysis using SPSS showed a non-significant association between BRAF and RET variants and age group (P = 0.878 and P = 0.536), gender (P = 0.587 and P = 0.21), tumor size (P = 0.796 and P = 0.765), or tumor localization (P = 0.689 and P = 0.727). CONCLUSION: In conclusion, this study emphasizes the significant association between BRAF polymorphism and thyroid cancer risk, while RET polymorphism showed a less pronounced impact. Further validation using larger and specific datasets is essential to establish conclusive results.


Subject(s)
Proto-Oncogene Proteins B-raf , Sulfones , Thyroid Neoplasms , Uridine/analogs & derivatives , Humans , Proto-Oncogene Proteins B-raf/genetics , Thyroid Neoplasms/epidemiology , Thyroid Neoplasms/genetics , Alleles , Proto-Oncogene Proteins c-ret/genetics
19.
Biomed Res Int ; 2024: 5924799, 2024.
Article in English | MEDLINE | ID: mdl-38590385

ABSTRACT

This study accessed the potential antimalarial activity of triterpene glycoside of H. atra through targeting orotidine 5-monophosphate decarboxylase protein (PfOMPDC) in P. falciparum by molecular docking. Nine triterpene glycosides from H. atra extract modeled the structure by the Corina web server and interacted with PfOMPDC protein by using Hex 8.0.0. The docking results were visualized and analyzed by Discovery Studio version 21.1.1. 17-Hydroxyfuscocineroside B showed the lowest binding energy in PfOMPDC interaction, which was -1,098.13 kJ/mol. Holothurin A3, echinoside A, and fuscocineroside C showed low binding energy. Nine triterpene glycosides of H. atra performed interaction with PfOMPDC protein at the same region. Holothurin A1 posed interaction with PfOMPDC protein by 8 hydrogen bonds, 3 hydrophobic interactions, and 8 unfavorable bonds. Several residues were detected in the same active sites of other triterpene glycosides. Residue TYR111 was identified in all triterpene glycoside complexes, except holothurin A3 and calcigeroside B. In summary, the triterpene glycoside of H. atra is potentially a drug candidate for malaria therapeutic agents. In vitro and in vivo studies were required for further investigation.


Subject(s)
Carboxy-Lyases , Cardiac Glycosides , Triterpenes , Uridine/analogs & derivatives , Molecular Docking Simulation , Glycosides/chemistry , Triterpenes/chemistry
SELECTION OF CITATIONS
SEARCH DETAIL