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Molecular Biology and Evolution Dec 2023The de novo synthesis of deoxythymidine triphosphate uses several pathways: gram-negative bacteria use deoxycytidine triphosphate deaminase to convert deoxycytidine...
Functional Prokaryotic-Like Deoxycytidine Triphosphate Deaminases and Thymidylate Synthase in Eukaryotic Social Amoebae: Vertical, Endosymbiotic, or Horizontal Gene Transfer?
The de novo synthesis of deoxythymidine triphosphate uses several pathways: gram-negative bacteria use deoxycytidine triphosphate deaminase to convert deoxycytidine triphosphate into deoxyuridine triphosphate, whereas eukaryotes and gram-positive bacteria instead use deoxycytidine monophosphate deaminase to transform deoxycytidine monophosphate to deoxyuridine monophosphate. It is then unusual that in addition to deoxycytidine monophosphate deaminases, the eukaryote Dictyostelium discoideum has 2 deoxycytidine triphosphate deaminases (Dcd1Dicty and Dcd2Dicty). Expression of either DcdDicty can fully rescue the slow growth of an Escherichia coli dcd knockout. Both DcdDicty mitigate the hydroxyurea sensitivity of a Schizosaccharomyces pombe deoxycytidine monophosphate deaminase knockout. Phylogenies show that Dcd1Dicty homologs may have entered the common ancestor of the eukaryotic groups of Amoebozoa, Obazoa, Metamonada, and Discoba through an ancient horizontal gene transfer from a prokaryote or an ancient endosymbiotic gene transfer from a mitochondrion, followed by horizontal gene transfer from Amoebozoa to several other unrelated groups of eukaryotes. In contrast, the Dcd2Dicty homologs were a separate horizontal gene transfer from a prokaryote or a virus into either Amoebozoa or Rhizaria, followed by a horizontal gene transfer between them. ThyXDicty, the D. discoideum thymidylate synthase, another enzyme of the deoxythymidine triphosphate biosynthesis pathway, was suggested previously to be acquired from the ancestral mitochondria or by horizontal gene transfer from alpha-proteobacteria. ThyXDicty can fully rescue the E. coli thymidylate synthase knockout, and we establish that it was obtained by the common ancestor of social amoebae not from mitochondria but from a bacterium. We propose horizontal gene transfer and endosymbiotic gene transfer contributed to the enzyme diversity of the deoxythymidine triphosphate synthesis pathway in most social amoebae, many Amoebozoa, and other eukaryotes.
Topics: DCMP Deaminase; Gene Transfer, Horizontal; Escherichia coli; Amoeba; Thymidylate Synthase; Dictyostelium; Deoxycytidine Monophosphate
PubMed: 38064674
DOI: 10.1093/molbev/msad268 -
Biological Psychiatry Feb 2024The gut microbiome has been implicated in the pathogenesis of mental disorders where the gut-brain axis acts as a bidirectional communication network.
BACKGROUND
The gut microbiome has been implicated in the pathogenesis of mental disorders where the gut-brain axis acts as a bidirectional communication network.
METHODS
Herein, we investigated the compositional and functional differences of gut microbiome between patients with first-episode psychosis (FEP) (n = 26) and healthy control participants (n = 22) using whole-genome shotgun sequencing. In addition, we assessed the oral microbiome in patients with FEP (n = 13) and listed their taxonomic diversity.
RESULTS
Our findings suggest that there is a dysbiosis of gut microbiota in patients with FEP. Relative abundance of Bifidobacterium adolescentis, Prevotella copri, and Turicibacter sanguinis was markedly increased (linear discriminant analysis scores [log] > 1, and Mann-Whitney U test; false discovery rate-adjusted p values < .05) in the FEP group compared with the healthy control participants. Pathway analysis indicated that several metabolic pathways, particularly deoxyribonucleotide biosynthesis, branched-chain amino acid biosynthesis, tricarboxylic acid cycle, and fatty acid elongation and biosynthesis, were dysregulated in the FEP group compared with the healthy control group. In addition, this preliminary study was able to identify specific gut microbes (at baseline) that were predictive of weight gain in the FEP group at a 1-year follow-up. Bacteroides dorei, Bifidobacterium adolescentis, Turicibacter sanguinis, Roseburia spp., and Ruminococcus lactaris were positively associated (eXtreme gradient boosting, XGBoost regression model, Shapley additive explanations, R = 0.82) with weight gain.
CONCLUSIONS
Our findings may suggest the involvement of gut microbiota in the pathogenesis of psychosis. The benefit of modulation of the gut microbiome in the treatment of psychotic disorders should be explored further.
Topics: Humans; Firmicutes; Microbiota; Psychotic Disorders; Weight Gain
PubMed: 38061464
DOI: 10.1016/j.biopsych.2023.10.024 -
Advances in Gerontology = Uspekhi... 2023In recent years, more and more attention of researchers has been paid to the study of dilated cardiomyopathy (DCMP). The prevalence of this disease in older age groups...
In recent years, more and more attention of researchers has been paid to the study of dilated cardiomyopathy (DCMP). The prevalence of this disease in older age groups is higher than previously thought, and the course of the disease is associated with a worse prognosis and treatment difficulties. Researchers are considering various signaling molecules whose expression changes are associated with myocardial damage and the development of DCMP; evaluation of changes in the expression of melatonin and its receptors in DCMP requires further study. The aim of the study was to study the age-related features of the expression of melatonin and its receptors (MT1, MT2) in the myocardium and their changes depending on the presence of dilated cardiomyopathy. Immunocytochemical and immunohistochemical methods were used to evaluate the expression of melatonin and its MT1, MT2 receptors in myocardial autopsy material and cardiomyocyte cultures of people of different ages with and without cardiovascular pathology. The study revealed age-associated changes in the form of a decrease in the expression of melatonin and its MT1 and MT2 receptors in the myocardium. In individuals with DCMP of all age groups, a more significant decrease in expression was noted: melatonin by 1,6-1,7 times in old age and 3,2 times in old age; MT1 by 1,8 and 2 times, respectively; MT2 by 1,4 and 4 times, respectively. The relationship between the decrease in the expression of melatonin and its receptors in myocardial tissues with age and the presence of DCMP was revealed. The data obtained allow us to clarify age-dependent changes in melatonin and its receptors, as well as to assume their important role in the development of DCMP, which requires further study.
Topics: Humans; Aged; Melatonin; Cardiomyopathy, Dilated; Deoxycytidine Monophosphate; Receptor, Melatonin, MT1; Myocardium; Receptor, Melatonin, MT2
PubMed: 38010187
DOI: No ID Found -
Journal of Pharmaceutical Sciences Feb 2024The emergence of thrombopoietin mimetic peptides presents a promising therapeutic strategy for addressing thrombocytopenia. This particular study aimed to establish a...
The emergence of thrombopoietin mimetic peptides presents a promising therapeutic strategy for addressing thrombocytopenia. This particular study aimed to establish a direct, expeditious, and efficient method for modifying and purifying a novel thrombopoietin mimetic peptide. Precursor proteins were subjected to modification utilizing three distinct fatty acids: CHON, CHON, and CHON. Liquid chromatography analyses demonstrated that CHON yielded the most effective modification results. Mass spectrometry findings validated the correspondence between the theoretical and actual molecular weights of each sample. In vivo experiments conducted on normal mice showcased that the CHON modification group exhibited the highest platelet count, peaking at an impressive 5047 × 10/L. This count was approximately twice that of the peak platelet count observed in the dTMP group and four times higher than the control group. Pharmacokinetic investigations revealed that the CHON modification group displayed the lengthiest half-life among beagles, persisting for 128.5 h. This duration was approximately 28.5 times longer than that of the unmodified dTMP group. These findings underscore the effectiveness of the established CHON modification and purification method in preserving the biological activity of the thrombopoietin mimetic peptide. The novel thrombopoietin mimetic peptide showcased notable attributes of simplicity and cost-effectiveness, while also exhibiting a significant platelet-promoting effect and an extended half-life. Consequently, this novel peptide holds substantial significance for advancing the treatment of thrombocytopenia.
Topics: Animals; Dogs; Mice; Peptides; Platelet Count; Thrombocytopenia; Thymidine Monophosphate
PubMed: 38006944
DOI: 10.1016/j.xphs.2023.11.020 -
Inorganic Chemistry Dec 2023Ribonucleotide reductase (RNR) catalyzes the reduction of ribonucleotides to deoxyribonucleotides in all organisms. There is an ∼35 Å long-range electron-hole...
Ribonucleotide reductase (RNR) catalyzes the reduction of ribonucleotides to deoxyribonucleotides in all organisms. There is an ∼35 Å long-range electron-hole transfer pathway during the catalytic process of class Ia RNR, which can be described as Tyrβ ↔ [Trpβ]? ↔ Tyrβ ↔ Tyrα ↔ Tyrα ↔ Cysα. The formation of the Y radical initiates this long-range radical transfer process. However, the generation mechanism of Y is not yet clear due to confusion over the intermediate X structures. Based on the two reported X structures, we examined the possible mechanisms of Y generation by density functional theory (DFT) calculations. Our examinations revealed that the generation of the Y radical from the two different core structures of X was via a similar two-step reaction, with the first step of proton transfer for the formation of the proton receptor of Y and the second step of a proton-coupled long-range electron transfer reaction with the proton transfer from the Y hydroxyl group to the terminal hydroxide ligand of Fe and simultaneously electron transfer from the side chain of Y to Fe. These findings provide an insight into the formation mechanism of Y catalyzed by the double-iron center of the β subunit of class Ia RNR.
Topics: Ribonucleotide Reductases; Protons; Electron Transport; Iron; Catalysis; Tyrosine
PubMed: 37987809
DOI: 10.1021/acs.inorgchem.3c02505 -
Biochemical Pharmacology Dec 2023Ribonucleotide reductase (RR) is a rate-limiting enzyme that facilitates DNA replication and repair by reducing nucleotide diphosphates (NDPs) to deoxyribonucleotide...
Ribonucleotide reductase (RR) is a rate-limiting enzyme that facilitates DNA replication and repair by reducing nucleotide diphosphates (NDPs) to deoxyribonucleotide diphosphates (dNDPs) and is thereby crucial for cell proliferation and cancer development. The E2F family of transcription factors includes key regulators of gene expression involved in cell cycle control. In this study, E2F8 expression was significantly increased in most cancer tissues of lung adenocarcinoma (LUAD) patients and was correlated with the expression of RRM2 through database and clinical samples analysis. The protein expression of E2F8 and RRM2 were positively correlated with tumor-node-metastasis (TNM) pathological stage, and high expression of E2F8 and RRM2 predicted a low 5-year overall survival rate in LUAD patients. Overexpression and knockdown experiments showed that E2F8 was essential for LUAD cell proliferation, DNA synthesis, and cell cycle progression, which were RRM2-dependent. Reporter gene, ChIP-qPCR, and DNA pulldown-Western blot assays indicated that E2F8 activated the transcription of the RRM2 gene by directly binding with the RRM2 promoter in LUAD cells. Previous studies indicated that inhibition of WEE1 kinase can suppress the phosphorylation of CDK1/2 and promote the degradation of RRM2. We further showed here that the combination of E2F8 knockdown with MK-1775, an inhibitor of WEE1 being evaluated in clinical trials, synergistically suppressed proliferation and promoted apoptosis of LUAD cells in vitro and in vivo. Thus, this study reveals a novel role of E2F8 as a proto-oncogenic transcription activator by activating RRM2 expression in LUAD, and targeting both the transcription and degradation mechanisms of RRM2 could produce a synergistic inhibitory effect for LUAD treatment in addition to conventional inhibition of RR enzyme activity.
Topics: Humans; Adenocarcinoma of Lung; Cell Cycle Proteins; Cell Line, Tumor; Cell Proliferation; DNA; DNA Replication; Gene Expression Regulation, Neoplastic; Lung Neoplasms; Protein-Tyrosine Kinases; Repressor Proteins
PubMed: 37863324
DOI: 10.1016/j.bcp.2023.115854 -
Journal of Bacteriology Oct 2023Ribonucleotides frequently contaminate DNA and, if not removed, cause genomic instability. Consequently, all organisms are equipped with RNase H enzymes to remove...
Ribonucleotides frequently contaminate DNA and, if not removed, cause genomic instability. Consequently, all organisms are equipped with RNase H enzymes to remove RNA-DNA hybrids (RDHs). lacking RNase HI () and RNase HII () enzymes, the ∆ ∆ double mutant, accumulates RDHs in its DNA. These RDHs can convert into RNA-containing DNA lesions (R-lesions) of unclear nature that compromise genomic stability. The ∆ double mutant has severe phenotypes, like growth inhibition, replication stress, sensitivity to ultraviolet radiation, SOS induction, increased chromosomal fragmentation, and defects in nucleoid organization. In this study, we found that RNase HI deficiency also alters wild-type levels of DNA supercoiling. Despite these severe chromosomal complications, ∆ double mutant survives, suggesting that dedicated pathways operate to avoid or repair R-lesions. To identify these pathways, we systematically searched for mutants synthetic lethal (colethal) with the defect using an unbiased color screen and a candidate gene approach. We identified both novel and previously reported -colethal and -coinhibited mutants, characterized them, and sorted them into avoidance or repair pathways. These mutants operate in various parts of nucleic acid metabolism, including replication fork progression, R-loop prevention and removal, nucleoid organization, tRNA modification, recombinational repair, and chromosome-dimer resolution, demonstrating the pleiotropic nature of RNase H deficiency. IMPORTANCE Ribonucleotides (rNs) are structurally very similar to deoxyribonucleotides. Consequently, rN contamination of DNA is common and pervasive across all domains of life. Failure to remove rNs from DNA has severe consequences, and all organisms are equipped with RNase H enzymes to remove RNA-DNA hybrids. RNase H deficiency leads to complications in bacteria, yeast, and mouse, and diseases like progressive external ophthalmoplegia (mitochondrial defects in RNASEH1) and Aicardi-Goutières syndrome (defects in RNASEH2) in humans. mutant, deficient in RNases H, has severe chromosomal complications. Despite substantial problems, nearly half of the mutant population survives. We have identified novel and previously confirmed pathways in various parts of nucleic acid metabolism that ensure survival with RNase H deficiency.
Topics: Humans; Animals; Mice; Escherichia coli; Ultraviolet Rays; DNA; Genomic Instability; Ribonuclease H; RNA; Ribonucleotides
PubMed: 37819120
DOI: 10.1128/jb.00280-23 -
Nucleic Acids Research Nov 2023The cellular imbalance between high concentrations of ribonucleotides (NTPs) and low concentrations of deoxyribonucleotides (dNTPs), is challenging for DNA polymerases...
The cellular imbalance between high concentrations of ribonucleotides (NTPs) and low concentrations of deoxyribonucleotides (dNTPs), is challenging for DNA polymerases when building DNA from dNTPs. It is currently believed that DNA polymerases discriminate against NTPs through a steric gate model involving a clash between a tyrosine and the 2'-hydroxyl of the ribonucleotide in the polymerase active site in B-family DNA polymerases. With the help of crystal structures of a B-family polymerase with a UTP or CTP in the active site, molecular dynamics simulations, biochemical assays and yeast genetics, we have identified a mechanism by which the finger domain of the polymerase sense NTPs in the polymerase active site. In contrast to the previously proposed polar filter, our experiments suggest that the amino acid residue in the finger domain senses ribonucleotides by steric hindrance. Furthermore, our results demonstrate that the steric gate in the palm domain and the sensor in the finger domain are both important when discriminating NTPs. Structural comparisons reveal that the sensor residue is conserved among B-family polymerases and we hypothesize that a sensor in the finger domain should be considered in all types of DNA polymerases.
Topics: Catalytic Domain; Crystallography, X-Ray; Deoxyribonucleotides; DNA; DNA Polymerase II; Ribonucleotides; Saccharomyces cerevisiae
PubMed: 37819038
DOI: 10.1093/nar/gkad817 -
Cellular and Molecular Biology... Sep 2023This research examined the effects of varying amounts of fibrinogen (the fibrin precursor) and HA-MA on mechanical strength, BMSC proliferation, and chondrogenesis...
Bone marrow concentration in combination with hyaluronan and fibrin for the treatment of primary and non-primary in orthopaedic cases of osteochondral defects of the ankle.
This research examined the effects of varying amounts of fibrinogen (the fibrin precursor) and HA-MA on mechanical strength, BMSC proliferation, and chondrogenesis potential in vitro. In order to start a culture, fibrinogen, aprotinin, doxycycline, and HA-MA were well mixed in 200 L of AMEM containing 1% (w/v) photoinitiator. In order to produce a fibrin gel, thrombin was used at 1, 3,5, and 7 days after implantation, live/dead staining and a metabolic-activity test were used to examine the viability and proliferation of BMSCs inside fibrin/HA-MA. The cell lysis solution from the Real Time ready Cell Lysis Kit was added to each gel. Both primer and probe mixes, as well as DNA polymerase, deoxyribonucleotide triphosphates, an activator, and an enhancer, were mixed before the lysis process began to asses mRNA expression. The mechanical strength of fibrin hydrogels was shown to be proportional to the quantity of HA-MA utilised in the reinforcement. Quantitative polymerase chain reaction demonstrated a reduction in the expression of collagen type 1 alpha 1 mRNA in BMSCs after they were treated in a fibrin/HA-MA hydrogel. Using fibrin/HA-MA hydrogel as a delivery technique for bone marrow stem cells may induce BMSC differentiation into chondrocytes and perhaps aid in articular cartilage repair for OA therapy (BMSCs). We concluded that the utilisation of bone marrow concentration in conjunction with a combination of fibrin and Hyaluronan treatment is safe for patients suffering from OCD of the ankle and is well tolerated by these patients as both a primary treatment and a non-primary treatment option.
Topics: Humans; Hyaluronic Acid; Ankle; Bone Marrow; Fibrin; Orthopedics; Hydrogels; RNA, Messenger; Fibrinogen; Chondrogenesis; Bone Marrow Cells
PubMed: 37807338
DOI: 10.14715/cmb/2023.69.9.4 -
Cellular and Molecular Biology... Sep 2023Even though colon cancer ranks among the leading causes of cancer mortality, early detection dramatically increases survival rates. Many studies have been conducted to...
Even though colon cancer ranks among the leading causes of cancer mortality, early detection dramatically increases survival rates. Many studies have been conducted to determine whether altered metabolite levels may serve as a potential biomarker of cancer that affects key metabolic pathways. The goal of the study was to detect metabolic biomarkers in patients with colon cancer using liquid chromatography-mass spectrometry (LC-MS). This study consisted of 30 patients with colon cancer. An analysis of the metabolomes of cancer samples and para-carcinoma tissues was conducted. We identified a series of important metabolic changes in colon cancer by analyzing metabolites in cancerous tissues compared to their normal counterparts. They are mainly involved in the pentose phosphate pathway, the TCA cycle, glycolysis, galactose metabolism, and butanoate metabolism. As well, we observed dysregulation of AMP, dTMP, fructose, and D-glucose in colon cancer. Additionally, the AUCs for AMP, dTMP, fructose, and D-glucose were greater than 0.7 for the diagnosis of colon cancer. In conclusion, AMP, dTMP, fructose, and D-glucose showed excellent diagnostic performance and could serve as novel disease biomarkers for colon cancer diagnosis.
Topics: Humans; Tandem Mass Spectrometry; Carbon; Chromatography, High Pressure Liquid; Thymidine Monophosphate; Biomarkers; Carcinoma; Colonic Neoplasms; Glucose; Fructose; Metabolomics
PubMed: 37807318
DOI: 10.14715/cmb/2023.69.9.25