-
Trends in Biochemical Sciences Oct 2023In bacteria, cCMP and cUMP have a key role in defense against infection with bacterial viruses. Bacteriophages encode phosphodiesterases (PDEs; 'nucleases'; Apyc1),...
In bacteria, cCMP and cUMP have a key role in defense against infection with bacterial viruses. Bacteriophages encode phosphodiesterases (PDEs; 'nucleases'; Apyc1), which cleave cCMP/cUMP, counteracting this defense. We propose that PDEs are of broader biological relevance, including cCMP/cUMP-cleaving PDEs of eukaryotic viruses, which may constitute new drug targets.
Topics: Humans; Phosphoric Diester Hydrolases; Cyclic CMP; Nucleotides, Cyclic; Virus Diseases
PubMed: 37365086
DOI: 10.1016/j.tibs.2023.05.013 -
Cells Jan 2022The etiology of dry mouth conditions is multi-faceted. Patients radiated after head and neck cancer (HNC) and those with primary Sjögren's syndrome (pSS) share many of...
The etiology of dry mouth conditions is multi-faceted. Patients radiated after head and neck cancer (HNC) and those with primary Sjögren's syndrome (pSS) share many of the same symptoms despite different causes. With the aim of better understanding the pathophysiology and biochemical processes behind dry mouth with different etiologies, we investigated the metabolic profile of 10 HNC patients, 9 pSS patients and 10 healthy controls using high-performance liquid chromatography-high resolution mass spectrometry (HPLC-MS) metabolomics. Principal component analysis (PCA) revealed different metabolic profiles when comparing all subjects included in the study. Both patient groups showed higher ratios of several pyrimidine nucleotides and nucleosides when compared to controls. This finding may indicate that purinergic signaling plays a role in dry mouth conditions. Moreover, significantly increased levels of DL-3-aminoisobutyric acid were found in HNC patients when compared to controls, and a similar tendency was observed in the pSS patients. Furthermore, a dysregulation in amino acid metabolism was observed in both patient groups. In conclusion, metabolomics analysis showed separate metabolic profiles for HNC and pSS patients as compared to controls that could be useful in diagnostics and for elucidating the different pathophysiologies. The demonstrated dysregulation of pyrimidine nucleotides and levels of metabolites derived from amino acids in the patient groups should be studied further.
Topics: Head and Neck Neoplasms; Humans; Metabolomics; Pyrimidine Nucleotides; Saliva; Sjogren's Syndrome; Xerostomia
PubMed: 35159133
DOI: 10.3390/cells11030323 -
Proceedings of the National Academy of... Apr 2018We have adapted the eXcision Repair-sequencing (XR-seq) method to generate single-nucleotide resolution dynamic repair maps of UV-induced cyclobutane pyrimidine dimers...
We have adapted the eXcision Repair-sequencing (XR-seq) method to generate single-nucleotide resolution dynamic repair maps of UV-induced cyclobutane pyrimidine dimers and (6-4) pyrimidine-pyrimidone photoproducts in the genome. We find that these photoproducts are removed from the genome primarily by incisions 13-18 nucleotides 5' and 6-7 nucleotides 3' to the UV damage that generate 21- to 27-nt-long excision products. Analyses of the excision repair kinetics both in single genes and at the genome-wide level reveal strong transcription-coupled repair of the transcribed strand at early time points followed by predominantly nontranscribed strand repair at later stages. We have also characterized the excision repair level as a function of the transcription level. The availability of high-resolution and dynamic repair maps should aid in future repair and mutagenesis studies in this model organism.
Topics: DNA Damage; DNA Repair; DNA, Fungal; Genome, Fungal; Pyrimidine Dimers; Saccharomyces cerevisiae; Transcription, Genetic; Ultraviolet Rays
PubMed: 29581276
DOI: 10.1073/pnas.1801687115 -
Biochemistry Feb 2020Viperin is a radical -adenosylmethionine (SAM) enzyme that inhibits viral replication by converting cytidine triphosphate (CTP) into 3'-deoxy-3',4'-didehydro-CTP and by...
Viperin is a radical -adenosylmethionine (SAM) enzyme that inhibits viral replication by converting cytidine triphosphate (CTP) into 3'-deoxy-3',4'-didehydro-CTP and by additional undefined mechanisms operating through its N- and C-terminal domains. Here, we describe crystal structures of viperin bound to a SAM analogue and CTP or uridine triphosphate (UTP) and report kinetic parameters for viperin-catalyzed reactions with CTP or UTP as substrates. Viperin orients the C4' hydrogen atom of CTP and UTP similarly for abstraction by a 5'-deoxyadenosyl radical, but the uracil moiety introduces unfavorable interactions that prevent tight binding of UTP. Consistently, is similar for CTP and UTP whereas the for UTP is much greater. The structures also show that nucleotide binding results in ordering of the C-terminal tail and reveal that this region contains a P-loop that binds the γ-phosphate of the bound nucleotide. Collectively, the results explain the selectivity for CTP and reveal a structural role for the C-terminal tail in binding CTP and UTP.
Topics: Animals; Crystallography, X-Ray; Cytidine Triphosphate; Kinetics; Mice; Models, Molecular; Molecular Structure; Mutation; Proteins; S-Adenosylhomocysteine; Substrate Specificity; Uridine Triphosphate
PubMed: 31917549
DOI: 10.1021/acs.biochem.9b00741 -
The Journal of Physical Chemistry... Jul 2023The repair of the cyclobutane pyrimidine dimer (CPD) lesion in DNA by photolyase is determined by its initial recognition, and the catalytic efficiency depends on a...
The repair of the cyclobutane pyrimidine dimer (CPD) lesion in DNA by photolyase is determined by its initial recognition, and the catalytic efficiency depends on a series of intermolecular electron-transfer (ET) processes. Here, we investigated the repair of a CPD structural isomer, replacing the deoxyribose with a pyranose sugar on the 5' site, and found a loss in binding efficiency and repair quantum yield. Using femtosecond spectroscopy, we characterized all elementary repair steps and observed a systemic slowdown of the four intermolecular ET reactions and the second bond splitting. Our observations and molecular dynamics simulations suggest that the sugar replacement disrupts the lesion binding configuration, weakening the electronic coupling between the cofactor and lesion and altering the stability of lesion intermediates. These findings highlight how the CPD photolyases have utilized the structural features of the CPD lesion and optimized its interactions with the cofactor and key active-site residues to maximize repair yields.
Topics: Deoxyribodipyrimidine Photo-Lyase; DNA Repair; Pyrimidine Dimers; DNA Damage; Sugars
PubMed: 37463310
DOI: 10.1021/acs.jpclett.3c01128 -
The Journal of Pharmacy and Pharmacology Dec 2014To provide an overview of a novel anti-hepatitis C agent, sofosbuvir. (Review)
Review
OBJECTIVE
To provide an overview of a novel anti-hepatitis C agent, sofosbuvir.
KEY FINDINGS
Sofosbuvir is a novel nucleotide analogue inhibitor of hepatitis C virus (HCV) NS5B polymerase that has recently been approved by the Federal Drug Administration for the treatment of HCV genotypes 1, 2, 3 or 4 in a variety of patients. The emergence of such a novel treatment provides benefit to previously untreated genotypes and patient populations, with little chance of promoting significant viral resistance. Excellent sustained virologic response rates 12 weeks after the end of treatment (SVR12) were seen in phase II and III clinical trials when sofosbuvir was used with ribavirin. Even more promising are the results from phase II and III clinical trials that evaluated sofosbuvir in combination with other oral direct acting antivirals (DAAs). Data with sofosbuvir in the hepatitis C virus (HCV)/HIV coinfected and in the pre- and post-transplantation populations are still emerging. The drug was very well tolerated in clinical studies, with the most common adverse events of headache, nausea and fatigue.
SUMMARY
Overall, sofosbuvir presents a new and effective treatment option for HCV-infected patients.
Topics: Antiviral Agents; Clinical Trials as Topic; Drug Therapy, Combination; Hepacivirus; Hepatitis C; Humans; Sofosbuvir; Treatment Outcome; Uridine Monophosphate; Viral Nonstructural Proteins
PubMed: 25175944
DOI: 10.1111/jphp.12294 -
Pyrimidine nucleotide synthesis in Pseudomonas nitroreducens and the regulatory role of pyrimidines.Microbiological Research Dec 2014Control of pyrimidine biosynthesis in the commercially important, hydrocarbon-utilizing bacterium Pseudomonas nitroreducens ATCC 33634 was investigated. When...
Control of pyrimidine biosynthesis in the commercially important, hydrocarbon-utilizing bacterium Pseudomonas nitroreducens ATCC 33634 was investigated. When glucose-grown wild-type cells were supplemented with uracil or orotic acid, the pyrimidine biosynthetic activities were depressed. Pyrimidine limitation of glucose-grown cells of an orotate phosphoribosyltransferase mutant caused aspartate transcarbamoylase and dihydroorotase activities to increase by about 4-fold while the other enzyme activities about doubled. In succinate-grown phosphoribosyltransferase mutant cells subjected to pyrimidine limitation, transcarbamoylase and dehydrogenase activities rose by about 5-fold while dihydroorotase activity more than tripled. In an OMP decarboxylase mutant, pyrimidine limitation of glucose-grown cells increased transcarbamoylase, dihydroorotase, dehydrogenase and phosphoribosyltransferase activities by 4-, 10-, 6- and 3.8-fold, respectively. Pyrimidine limitation of the succinate-grown decarboxylase mutant cells increased aspartate transcarbamoylase or dihydroorotase by more than 4-fold and the other activities by about 2-fold. Pyrimidine biosynthetic enzyme synthesis appeared to be regulated by pyrimidines with the regulation being influenced by the carbon source present. Aspartate transcarbamoylase activity in Ps. nitroreducens was regulated at the level of enzyme activity since the enzyme was strongly inhibited by UDP, pyrophosphate, ATP and ADP. Overall, the regulation of pyrimidine biosynthesis in Ps. nitroreducens can be used to differentiate it from other taxonomically related species of Pseudomonas.
Topics: Aspartate Carbamoyltransferase; Pseudomonas; Pyrimidine Nucleotides; Pyrimidines
PubMed: 24867376
DOI: 10.1016/j.micres.2014.04.003 -
Nucleic Acids Research Jul 2018A huge diversity of modified nucleobases is used as a tool for studying DNA and RNA. Due to practical reasons, the most suitable positions for modifications are C5 of...
A huge diversity of modified nucleobases is used as a tool for studying DNA and RNA. Due to practical reasons, the most suitable positions for modifications are C5 of pyrimidines and C7 of purines. Unfortunately, by using these two positions only, one cannot expand a repertoire of modified nucleotides to a maximum. Here, we demonstrate the synthesis and enzymatic incorporation of novel N4-acylated 2'-deoxycytidine nucleotides (dCAcyl). We find that a variety of family A and B DNA polymerases efficiently use dCAcylTPs as substrates. In addition to the formation of complementary CAcyl•G pair, a strong base-pairing between N4-acyl-cytosine and adenine takes place when Taq, Klenow fragment (exo-), Bsm and KOD XL DNA polymerases are used for the primer extension reactions. In contrast, a proofreading phi29 DNA polymerase successfully utilizes dCAcylTPs but is prone to form CAcyl•A base pair under the same conditions. Moreover, we show that terminal deoxynucleotidyl transferase is able to incorporate as many as several hundred N4-acylated-deoxycytidine nucleotides. These data reveal novel N4-acylated deoxycytidine nucleotides as beneficial substrates for the enzymatic synthesis of modified DNA, which can be further applied for specific labelling of DNA fragments, selection of aptamers or photoimmobilization.
Topics: DNA; DNA-Directed DNA Polymerase; Deoxycytosine Nucleotides
PubMed: 29846697
DOI: 10.1093/nar/gky435 -
Chemistry (Weinheim An Der Bergstrasse,... Aug 2016Research into antibacterial agents has recently gathered pace in light of the disturbing crisis of antimicrobial resistance. The development of modern tools offers the... (Review)
Review
Research into antibacterial agents has recently gathered pace in light of the disturbing crisis of antimicrobial resistance. The development of modern tools offers the opportunity of reviving the fallen era of antibacterial discovery through uncovering novel lead compounds that target vital bacterial cell components, such as lipid II. This paper provides a summary of the role of lipid II as well as an overview and insight into the structural features of macrocyclic peptides that inhibit this bacterial cell wall component. The recent discovery of teixobactin, a new class of lipid II inhibitor has generated substantial research interests. As such, the significant progress that has been achieved towards its development as a promising antibacterial agent is discussed.
Topics: Anti-Bacterial Agents; Bacteria; Cell Wall; Depsipeptides; Uridine Diphosphate N-Acetylmuramic Acid
PubMed: 27388768
DOI: 10.1002/chem.201601315 -
Science (New York, N.Y.) May 2015
Topics: Anti-HIV Agents; Chemistry, Organic; Drug Discovery; Hepatitis C; History, 20th Century; History, 21st Century; Sofosbuvir; Uridine Monophosphate
PubMed: 25953989
DOI: 10.1126/science.348.6235.622