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Differential Control of Dntp Biosynthesis and Genome Integrity
www.nature.com/scientificreports OPEN Diferential control of dNTP biosynthesis and genome integrity maintenance by the dUTPase Received: 6 November 2015 Accepted: 12 June 2017 superfamily enzymes Published online: 20 July 2017 Rita Hirmondo1, Anna Lopata1, Eva Viola Suranyi1,2, Beata G. Vertessy1,2 & Judit Toth1 dUTPase superfamily enzymes generate dUMP, the obligate precursor for de novo dTTP biosynthesis, from either dUTP (monofunctional dUTPase, Dut) or dCTP (bifunctional dCTP deaminase/dUTPase, Dcd:dut). In addition, the elimination of dUTP by these enzymes prevents harmful uracil incorporation into DNA. These two benefcial outcomes have been thought to be related. Here we determined the relationship between dTTP biosynthesis (dTTP/dCTP balance) and the prevention of DNA uracilation in a mycobacterial model that encodes both the Dut and Dcd:dut enzymes, and has no other ways to produce dUMP. We show that, in dut mutant mycobacteria, the dTTP/dCTP balance remained unchanged, but the uracil content of DNA increased in parallel with the in vitro activity-loss of Dut accompanied with a considerable increase in the mutation rate. Conversely, dcd:dut inactivation resulted in perturbed dTTP/dCTP balance and two-fold increased mutation rate, but did not increase the uracil content of DNA. Thus, unexpectedly, the regulation of dNTP balance and the prevention of DNA uracilation are decoupled and separately brought about by the Dcd:dut and Dut enzymes, respectively. Available evidence suggests that the discovered functional separation is conserved in humans and other organisms. Proper control of the intracellular concentration of deoxyribonucleoside-5-triphosphates (dNTPs), the building blocks of DNA, is critically important for efcient and high-fdelity DNA replication and genomic stability1, 2. -
Technical Note: Colorimetric Protein Assays Assays for Determining Protein Concentration
Technical Note: Colorimetric Protein Assays Assays for Determining Protein Concentration Contents speed. No colorimetric assay is as simple and quick as direct UV measurements at 280 nm for Introduction ....................................................... 1 the determination of protein concentration. Assay Choice ..................................................... 1 However measurements at 280 nm rely on the Buffer Composition ........................................ 1 protein containing aromatic amino acids such as Sample Composition ...................................... 2 tyrosine (Y), phenylalanine (F), and, or tryptophan Standard Selection ......................................... 2 (W). Not all proteins contain these amino acids, Assays ................................................................ 2 and the relative proportions of theses amino acids Biuret, BCA, and Lowry Assays ..................... 3 differ between proteins. Furthermore, if nucleic Bradford Assay............................................... 3 acids are present in the sample, they would also Troubleshooting ............................................. 4 absorb light at 280 nm, further compromising FAQ’s .................................................................. 5 accuracy. Therefore, the sensitivity achieved Bibliography ...................................................... 5 without prior knowledge of the protein of interest’s Contact Us ......................................................... 6 absorbance maxima (λmax) and attenuation coefficient -
Origin Sites of Calcium Release and Calcium Oscillations in Frog Sympathetic Neurons
The Journal of Neuroscience, December, 15, 2000, 20(24):9059–9070 Origin Sites of Calcium Release and Calcium Oscillations in Frog Sympathetic Neurons Stefan I. McDonough, Zolta´ n Cseresnye´ s, and Martin F. Schneider Department of Biochemistry and Molecular Biology, University of Maryland Medical School, Baltimore, Maryland 21201 In many neurons, Ca 2ϩ signaling depends on efflux of Ca 2ϩ from levels within the cell body could increase or decrease indepen- intracellular stores into the cytoplasm via caffeine-sensitive ryan- dently of neighboring regions, suggesting independent action of odine receptors (RyRs) of the endoplasmic reticulum. We have spatially separate Ca 2ϩ stores. Confocal imaging of fluorescent used high-speed confocal microscopy to image depolarization- analogs of ryanodine and thapsigargin, and of MitoTracker, and caffeine-evoked increases in cytoplasmic Ca 2ϩ levels in showed potential structural correlates to the patterns of Ca 2ϩ individual cultured frog sympathetic neurons. Although caffeine- release and propagation. High densities of RyRs were found in a evoked Ca 2ϩ wave fronts propagated throughout the cell, in ring around the cell periphery, mitochondria in a broader ring just most cells the initial Ca 2ϩ release was from one or more discrete inside the RyRs, and sarco-endoplasmic reticulum Ca 2ϩ ATPase sites that were several micrometers wide and located at the cell pumps in hot spots at the cell edge. Discrete sites at the cell edge, even in Ca 2ϩ-free external solution. During cell-wide cy- edge primed to release Ca 2ϩ from intracellular stores might toplasmic [Ca 2ϩ] oscillations triggered by continual caffeine ap- preferentially convert Ca 2ϩ influx through a local area of plasma plication, the initial Ca 2ϩ release that began each Ca 2ϩ peak membrane into a cell-wide Ca 2ϩ increase. -
Thermostable and Long-Circulating Albumin-Conjugated Arthrobacter Globiformis Urate Oxidase
pharmaceutics Article Thermostable and Long-Circulating Albumin-Conjugated Arthrobacter globiformis Urate Oxidase Byungseop Yang and Inchan Kwon * School of Materials Science and Engineering, Gwangju Institute of Science and Technology (GIST), Gwangju 61005, Korea; [email protected] * Correspondence: [email protected]; Tel.: +82-62-715-2312 Abstract: Urate oxidase derived from Aspergillus flavus has been investigated as a treatment for tumor lysis syndrome, hyperuricemia, and gout. However, its long-term use is limited owing to potential immunogenicity, low thermostability, and short circulation time in vivo. Recently, urate oxidase isolated from Arthrobacter globiformis (AgUox) has been reported to be thermostable and less immunogenic than the Aspergillus-derived urate oxidase. Conjugation of human serum albumin (HSA) to therapeutic proteins has become a promising strategy to prolong circulation time in vivo. To develop a thermostable and long-circulating urate oxidase, we investigated the site-specific conjugation of HSA to AgUox based on site-specific incorporation of a clickable non-natural amino acid (frTet) and an inverse electron demand Diels–Alder reaction. We selected 14 sites for frTet incorporation using the ROSETTA design, a computational stability prediction program, among which AgUox containing frTet at position 196 (Ag12) exhibited enzymatic activity and thermostability comparable to those of wild-type AgUox. Furthermore, Ag12 exhibited a high HSA conjugation yield without compromising the enzymatic activity, generating well-defined HSA-conjugated AgUox (Ag12-HSA). In mice, the serum half-life of Ag12-HSA was approximately 29 h, which was roughly Citation: Yang, B.; Kwon, I. 17-fold longer than that of wild-type AgUox. Altogether, this novel formulated AgUox may hold Thermostable and Long-Circulating enhanced therapeutic efficacy for several diseases. -
UDP-N-Acetylglucosamine Transporter and UDP-Galactose Transporter
View metadata, citation and similar papers at core.ac.uk brought to you by CORE provided by Elsevier - Publisher Connector FEBS Letters 586 (2012) 4082–4087 journal homepage: www.FEBSLetters.org UDP-N-acetylglucosamine transporter and UDP-galactose transporter form heterologous complexes in the Golgi membrane ⇑ Dorota Maszczak-Seneczko a, Paulina Sosicka a, Michał Majkowski b, Teresa Olczak a, Mariusz Olczak a, a Laboratory of Biochemistry, Faculty of Biotechnology, University of Wroclaw, Wroclaw, Poland b Laboratory of Cytobiochemistry, Faculty of Biotechnology, University of Wroclaw, Wroclaw, Poland article info abstract Article history: UDP-galactose transporter (UGT; SLC35A2) and UDP-N-acetylglucosamine transporter (NGT; Received 6 August 2012 SLC35A3) are evolutionarily related. We hypothesize that their role in glycosylation may be coupled Revised 2 October 2012 through heterologous complex formation. Coimmunoprecipitation analysis and FLIM–FRET mea- Accepted 8 October 2012 surements performed on living cells showed that NGT and UGT form complexes when overexpressed Available online 23 October 2012 in MDCK-RCAr cells. We also postulate that the interaction of NGT and UGT may explain the dual Edited by Judit Ovádi localization of UGT2. For the first time we demonstrated in vivo homodimerization of the NGT nucle- otide sugar transporter. In conclusion, we suggest that NGT and UGT function in glycosylation is combined via their mutual interaction. Keywords: UDP-N-acetylglucosamine transporter UDP-galactose transporter Structured summary -
Step-By-Step Guide to Better Laboratory Management Practices
Step-by-Step Guide to Better Laboratory Management Practices Prepared by The Washington State Department of Ecology Hazardous Waste and Toxics Reduction Program Publication No. 97- 431 Revised January 2003 Printed on recycled paper For additional copies of this document, contact: Department of Ecology Publications Distribution Center PO Box 47600 Olympia, WA 98504-7600 (360) 407-7472 or 1 (800) 633-7585 or contact your regional office: Department of Ecology’s Regional Offices (425) 649-7000 (509) 575-2490 (509) 329-3400 (360) 407-6300 The Department of Ecology is an equal opportunity agency and does not discriminate on the basis of race, creed, color, disability, age, religion, national origin, sex, marital status, disabled veteran’s status, Vietnam Era veteran’s status or sexual orientation. If you have special accommodation needs, or require this document in an alternate format, contact the Hazardous Waste and Toxics Reduction Program at (360)407-6700 (voice) or 711 or (800) 833-6388 (TTY). Table of Contents Introduction ....................................................................................................................................iii Section 1 Laboratory Hazardous Waste Management ...........................................................1 Designating Dangerous Waste................................................................................................1 Counting Wastes .......................................................................................................................8 Treatment by Generator...........................................................................................................12 -
Disclosing the Essentiality of Ribose-5-Phosphate Isomerase B In
www.nature.com/scientificreports OPEN Disclosing the essentiality of ribose-5-phosphate isomerase B in Trypanosomatids Received: 04 January 2016 Joana Faria1,2, Inês Loureiro1,2, Nuno Santarém1,2, Pedro Cecílio1,2, Sandra Macedo-Ribeiro2,3, Accepted: 10 May 2016 Joana Tavares1,2,* & Anabela Cordeiro-da-Silva1,2,4,* Published: 27 May 2016 Ribose-5-phosphate isomerase (RPI) belongs to the non-oxidative branch of the pentose phosphate pathway, catalysing the inter-conversion of D-ribose-5-phosphate and D-ribulose-5-phosphate. Trypanosomatids encode a type B RPI, whereas humans have a structurally unrelated type A, making RPIB worthy of exploration as a potential drug target. Null mutant generation in Leishmania infantum was only possible when an episomal copy of RPIB gene was provided, and the latter was retained both in vitro and in vivo in the absence of drug pressure. This suggests the gene is essential for parasite survival. Importantly, the inability to remove the second allele of RPIB gene in sKO mutants complemented with an episomal copy of RPIB carrying a mutation that abolishes isomerase activity suggests the essentiality is due to its metabolic function. In vitro, sKO promastigotes exhibited no defect in growth, metacyclogenesis or macrophage infection, however, an impairment in intracellular amastigotes’ replication was observed. Additionally, mice infected with sKO mutants rescued by RPIB complementation had a reduced parasite burden in the liver. Likewise, Trypanosoma brucei is resistant to complete RPIB gene removal and mice infected with sKO mutants showed prolonged survival upon infection. Taken together our results genetically validate RPIB as a potential drug target in trypanosomatids. -
Comparative Analysis of High-Throughput Assays of Family-1 Plant Glycosyltransferases
International Journal of Molecular Sciences Article Comparative Analysis of High-Throughput Assays of Family-1 Plant Glycosyltransferases Kate McGraphery and Wilfried Schwab * Biotechnology of Natural Products, Technische Universität München, 85354 Freising, Germany; [email protected] * Correspondence: [email protected]; Tel.: +49-8161-712-912; Fax: +49-8161-712-950 Received: 27 January 2020; Accepted: 21 March 2020; Published: 23 March 2020 Abstract: The ability of glycosyltransferases (GTs) to reduce volatility, increase solubility, and thus alter the bioavailability of small molecules through glycosylation has attracted immense attention in pharmaceutical, nutraceutical, and cosmeceutical industries. The lack of GTs known and the scarcity of high-throughput (HTP) available methods, hinders the extrapolation of further novel applications. In this study, the applicability of new GT-assays suitable for HTP screening was tested and compared with regard to harmlessness, robustness, cost-effectiveness and reproducibility. The UDP-Glo GT-assay, Phosphate GT Activity assay, pH-sensitive GT-assay, and UDP2-TR-FRET assay were applied and tailored to plant UDP GTs (UGTs). Vitis vinifera (UGT72B27) GT was subjected to glycosylation reaction with various phenolics. Substrate screening and kinetic parameters were evaluated. The pH-sensitive assay and the UDP2-TR-FRET assay were incomparable and unsuitable for HTP plant GT-1 family UGT screening. Furthermore, the UDP-Glo GT-assay and the Phosphate GT Activity assay yielded closely similar and reproducible KM, vmax, and kcat values. Therefore, with the easy experimental set-up and rapid readout, the two assays are suitable for HTP screening and quantitative kinetic analysis of plant UGTs. This research sheds light on new and emerging HTP assays, which will allow for analysis of novel family-1 plant GTs and will uncover further applications. -
IER5 Is Involved in DNA Double-Strand Breaks Repair In
Int. J. Med. Sci. 2017, Vol. 14 1292 Ivyspring International Publisher International Journal of Medical Sciences 2017; 14(12): 1292-1300. doi: 10.7150/ijms.21510 Research Paper IER5 is involved in DNA Double-Strand Breaks Repair in Association with PAPR1 in Hela Cells Xin-Ping Yu1, Yu-Mei Wu1, Yang Liu1, Ming Tian1, Jian-Dong Wang1, Ku-Ke Ding2, Teng Ma3, Ping-Kun Zhou3 1. Department of Gynecologic Oncology, Beijing Obstetrics and Gynecology Hospital, Capital Medical University, Beijing, 100006, China; 2. National Institute for Radiological Protection, Chinese Center for Disease Control and Prevention, Beijing ,100088, China; 3. Department of Radiation Toxicology and Oncology, Beijing Key Laboratory for Radiobiology, Beijing Institute of Radiation Medicine, Beijing, 100850, China. Corresponding author: Yu-Mei Wu, Beijing Obstetrics and Gynecology Hospital, Capital Medical University, 17 Qi-he-lou St, Dongcheng District, Beijing 100006, China. E-mail: [email protected] © Ivyspring International Publisher. This is an open access article distributed under the terms of the Creative Commons Attribution (CC BY-NC) license (https://creativecommons.org/licenses/by-nc/4.0/). See http://ivyspring.com/terms for full terms and conditions. Received: 2017.06.17; Accepted: 2017.09.01; Published: 2017.09.30 Abstract The immediate early response gene 5 (IER5) is a radiation response gene induced in a dose-independent manner, and has been suggested to be a molecular biomarker for biodosimetry purposes upon radiation exposure. Here, we investigated the function of IER5 in DNA damage response and repair. We found that interference on IER5 expression significantly decreased the efficiency of repair of DNA double-strand breaks induced by ionizing radiations in Hela cells. -
Evaluation of Signaling Pathways Profiling in Human Dermal
toxins Article Evaluation of Signaling Pathways Profiling in Human Dermal Endothelial Cells Treated by Snake Venom Cysteine-Rich Secretory Proteins (svCRiSPs) from North American Snakes Using Reverse Phase Protein Array (RPPA) Montamas Suntravat 1,2,* , Oscar Sanchez 1, Armando Reyes 1, Abcde Cirilo 1, Jack S. Ocheltree 1, Jacob A. Galan 1,2, Emelyn Salazar 1 , Peter Davies 3 and Elda E. Sanchez 1,2 1 National Natural Toxins Research Center (NNTRC), Texas A&M University-Kingsville, MSC 224, 975 West Avenue B, Kingsville, TX 78363, USA; [email protected] (O.S.); [email protected] (A.R.); [email protected] (A.C.); [email protected] (J.S.O.); [email protected] (J.A.G.); [email protected] (E.S.); [email protected] (E.E.S.) 2 Department of Chemistry, Texas A&M University-Kingsville, MSC 161, Kingsville, TX 78363, USA 3 Institute of Biosciences and Technology, Texas A&M University, Houston, TX 77843, USA; [email protected] * Correspondence: [email protected] Abstract: Cysteine-Rich Secretory Proteins (CRiSPs) are typically found in many snake venoms; however, the role that these toxins play in the pathophysiology of snakebites is still unclear. Herein, we compared the effects of snake venom CRiSPs (svCRiSPs) from the most medically important Citation: Suntravat, M.; Sanchez, O.; species of North American snakes on endothelial cell permeability and vascular permeability. We Reyes, A.; Cirilo, A.; Ocheltree, J.S.; used reverse phase protein array (RPPA) to identify key signaling molecules on human dermal Galan, J.A.; Salazar, E.; Davies, P.; lymphatic (HDLECs) and blood (HDBECs) endothelial cells treated with svCRiSPs. -
Caffeine and Caffeic Acid Inhibit Growth and Modify Estrogen Receptor and Insulin-Like Growth Factor I Receptor Levels in Human Breast Cancer Ann H
Published OnlineFirst February 17, 2015; DOI: 10.1158/1078-0432.CCR-14-1748 Cancer Therapy: Clinical Clinical Cancer Research Caffeine and Caffeic Acid Inhibit Growth and Modify Estrogen Receptor and Insulin-like Growth Factor I Receptor Levels in Human Breast Cancer Ann H. Rosendahl1, Claire M. Perks2, Li Zeng2, Andrea Markkula1, Maria Simonsson1, Carsten Rose3, Christian Ingvar4, Jeff M.P. Holly2, and Helena Jernstrom€ 1 Abstract Purpose: Epidemiologic studies indicate that dietary factors, 0.018), compared with patients with low consumption (1 cup/ such as coffee, may influence breast cancer and modulate hor- day). Moderate to high consumption was associated with lower þ mone receptor status. The purpose of this translational study was risk for breast cancer events in tamoxifen-treated patients with ER to investigate how coffee may affect breast cancer growth in tumors (adjusted HR, 0.51; 95% confidence interval, 0.26–0.97). þ relation to estrogen receptor-a (ER) status. Caffeine and caffeic acid suppressed the growth of ER (P 0.01) À Experimental Design: The influence of coffee consumption on and ER (P 0.03) cells. Caffeine significantly reduced ER and þ patient and tumor characteristics and disease-free survival was cyclin D1 abundance in ER cells. Caffeine also reduced the assessed in a population-based cohort of 1,090 patients with insulin-like growth factor-I receptor (IGFIR) and pAkt levels in þ À invasive primary breast cancer in Sweden. Cellular and molecular both ER and ER cells. Together, these effects resulted in impaired effects by the coffee constituents caffeine and caffeic acid were cell-cycle progression and enhanced cell death. -
The Role of a Key Amino Acid Position in Species- Specific Proteinaceous Dutpase Inhibition
Article The Role of a Key Amino Acid Position in Species- Specific Proteinaceous dUTPase Inhibition András Benedek 1,2,*, Fanni Temesváry-Kis 1, Tamjidmaa Khatanbaatar 1, Ibolya Leveles 1,2, Éva Viola Surányi 1,2, Judit Eszter Szabó 1,2, Lívius Wunderlich 1 and Beáta G. Vértessy 1,2,* 1 Budapest University of Technology and Economics, Department of Applied Biotechnology and Food Science, H -1111 Budapest, Szent Gellért tér 4, Hungary; [email protected] (F.T-K.); [email protected] (T.K.); [email protected] (L.W.) 2 Research Centre for Natural Sciences, Hungarian Academy of Sciences, H-1117 Budapest, Magyar tudósok körútja 2, Hungary; [email protected] (I.L.); [email protected] (É.V.S.); [email protected] (J.E.S.) * Correspondence: [email protected] (A.B.); [email protected] (B.G.V.) Received: 14 May 2019; Accepted: 27 May 2019; Published: 6 June 2019 Abstract: Protein inhibitors of key DNA repair enzymes play an important role in deciphering physiological pathways responsible for genome integrity, and may also be exploited in biomedical research. The staphylococcal repressor StlSaPIbov1 protein was described to be an efficient inhibitor of dUTPase homologues showing a certain degree of species-specificity. In order to provide insight into the inhibition mechanism, in the present study we investigated the interaction of StlSaPIbov1 and Escherichia coli dUTPase. Although we observed a strong interaction of these proteins, unexpectedly the E. coli dUTPase was not inhibited. Seeking a structural explanation for this phenomenon, we identified a key amino acid position where specific mutations sensitized E.