The Central Enzyme of N-Linked Protein Glycosylation
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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. -
Supplementary Information
Supplementary information (a) (b) Figure S1. Resistant (a) and sensitive (b) gene scores plotted against subsystems involved in cell regulation. The small circles represent the individual hits and the large circles represent the mean of each subsystem. Each individual score signifies the mean of 12 trials – three biological and four technical. The p-value was calculated as a two-tailed t-test and significance was determined using the Benjamini-Hochberg procedure; false discovery rate was selected to be 0.1. Plots constructed using Pathway Tools, Omics Dashboard. Figure S2. Connectivity map displaying the predicted functional associations between the silver-resistant gene hits; disconnected gene hits not shown. The thicknesses of the lines indicate the degree of confidence prediction for the given interaction, based on fusion, co-occurrence, experimental and co-expression data. Figure produced using STRING (version 10.5) and a medium confidence score (approximate probability) of 0.4. Figure S3. Connectivity map displaying the predicted functional associations between the silver-sensitive gene hits; disconnected gene hits not shown. The thicknesses of the lines indicate the degree of confidence prediction for the given interaction, based on fusion, co-occurrence, experimental and co-expression data. Figure produced using STRING (version 10.5) and a medium confidence score (approximate probability) of 0.4. Figure S4. Metabolic overview of the pathways in Escherichia coli. The pathways involved in silver-resistance are coloured according to respective normalized score. Each individual score represents the mean of 12 trials – three biological and four technical. Amino acid – upward pointing triangle, carbohydrate – square, proteins – diamond, purines – vertical ellipse, cofactor – downward pointing triangle, tRNA – tee, and other – circle. -
Tannous A, Pisoni GB, Hebert DN, Molinari M. N-Linked Sugar
Seminars in Cell & Developmental Biology 41 (2015) 79–89 Contents lists available at ScienceDirect Seminars in Cell & Developmental Biology j ournal homepage: www.elsevier.com/locate/semcdb Review N-linked sugar-regulated protein folding and quality control in the ER a,1 b,1 a,∗ b,c,d,∗∗ Abla Tannous , Giorgia Brambilla Pisoni , Daniel N. Hebert , Maurizio Molinari a Department of Biochemistry and Molecular Biology, Program in Molecular and Cellular Biology, University of Massachusetts, Amherst, MA 01003, USA b Università della Svizzera italiana, CH-6900 Lugano, Switzerland c Institute for Research in Biomedicine, Protein Folding and Quality Control, CH-6500 Bellinzona, Switzerland d Ecole Polytechnique Fédérale de Lausanne, School of Life Sciences, CH-1015 Lausanne, Switzerland a r t a b i s c l e i n f o t r a c t Article history: Asparagine-linked glycans (N-glycans) are displayed on the majority of proteins synthesized in the endo- Available online 19 December 2014 plasmic reticulum (ER). Removal of the outermost glucose residue recruits the lectin chaperone malectin possibly involved in a first triage of defective polypeptides. Removal of a second glucose promotes engage- Keywords: ment of folding and quality control machineries built around the ER lectin chaperones calnexin (CNX) Endoplasmic reticulum and calreticulin (CRT) and including oxidoreductases and peptidyl–prolyl isomerases. Deprivation of the N-glycosylation last glucose residue dictates the release of N-glycosylated polypeptides from the lectin chaperones. Cor- Protein folding and quality control rectly folded proteins are authorized to leave the ER. Non-native polypeptides are recognized by the ER Calnexin Calreticulin quality control key player UDP-glucose glycoprotein glucosyltransferase 1 (UGT1), re-glucosylated and re-addressed to the CNX/CRT chaperone binding cycle to provide additional opportunity for the protein to UDP-glucose glycoprotein glucosyltransferase 1 fold in the ER. -
Release of Glycosyltransferase and Glycosidase Activities from Normal and Transformed Cell Lines1
[CANCER RESEARCH 41, 2611-2615, July 1981J 0008-5472/81 /0041-OOOOS02.00 Release of Glycosyltransferase and Glycosidase Activities from Normal and Transformed Cell Lines1 Wayne D. Klohs,2 Ralph Mastrangelo, and Milton M. Weiser Division of Gastroenterology and Nutrition, Department of Medicine, State University of New York at Buffalo, Buffalo, New York 14215 ABSTRACT Indeed, a cancer-associated isoenzyme of serum galactosyl transferase has been reported in humans and animals with The release of galactosyltransferase, sialyltransferase, and certain malignant cancers (24, 26). Bernacki and Kim (2) and several glycosidase activities into the growth media from sev Weiser and Podolsky (34) have suggested that such increases eral normal and transformed cell lines was examined. Six of in serum glycosyltransferase levels may be the consequence the seven cell lines released galactosyltransferase into their of both an increased production and release from the tumor culture media. Only the human leukemia CCRF-CEM cells cells, perhaps through cell surface shedding of the enzymes, failed to release demonstrable galactosyltransferase activity. but the validity of this supposition has yet to be demonstrated. Release of galactosyltransferase activity into the media closely It is also not clear whether the elevated levels of circulating paralleled the growth curves for all but the BHKpy cells. These glycosyltransferases perform any molecular or physiological cells continued to release peak levels of galactosyltransferase function relative to the malignant -
Nucleotide Sugars in Chemistry and Biology
molecules Review Nucleotide Sugars in Chemistry and Biology Satu Mikkola Department of Chemistry, University of Turku, 20014 Turku, Finland; satu.mikkola@utu.fi Academic Editor: David R. W. Hodgson Received: 15 November 2020; Accepted: 4 December 2020; Published: 6 December 2020 Abstract: Nucleotide sugars have essential roles in every living creature. They are the building blocks of the biosynthesis of carbohydrates and their conjugates. They are involved in processes that are targets for drug development, and their analogs are potential inhibitors of these processes. Drug development requires efficient methods for the synthesis of oligosaccharides and nucleotide sugar building blocks as well as of modified structures as potential inhibitors. It requires also understanding the details of biological and chemical processes as well as the reactivity and reactions under different conditions. This article addresses all these issues by giving a broad overview on nucleotide sugars in biological and chemical reactions. As the background for the topic, glycosylation reactions in mammalian and bacterial cells are briefly discussed. In the following sections, structures and biosynthetic routes for nucleotide sugars, as well as the mechanisms of action of nucleotide sugar-utilizing enzymes, are discussed. Chemical topics include the reactivity and chemical synthesis methods. Finally, the enzymatic in vitro synthesis of nucleotide sugars and the utilization of enzyme cascades in the synthesis of nucleotide sugars and oligosaccharides are briefly discussed. Keywords: nucleotide sugar; glycosylation; glycoconjugate; mechanism; reactivity; synthesis; chemoenzymatic synthesis 1. Introduction Nucleotide sugars consist of a monosaccharide and a nucleoside mono- or diphosphate moiety. The term often refers specifically to structures where the nucleotide is attached to the anomeric carbon of the sugar component. -
Structure of the Mammalian Oligosaccharyl-Transferase Complex
ARTICLE Received 26 Sep 2013 | Accepted 6 Dec 2013 | Published 10 Jan 2014 DOI: 10.1038/ncomms4072 Structure of the mammalian oligosaccharyl- transferase complex in the native ER protein translocon Stefan Pfeffer1,*, Johanna Dudek2,*, Marko Gogala3, Stefan Schorr2, Johannes Linxweiler2, Sven Lang2, Thomas Becker3, Roland Beckmann3, Richard Zimmermann2 & Friedrich Fo¨rster1 In mammalian cells, proteins are typically translocated across the endoplasmic reticulum (ER) membrane in a co-translational mode by the ER protein translocon, comprising the protein- conducting channel Sec61 and additional complexes involved in nascent chain processing and translocation. As an integral component of the translocon, the oligosaccharyl-transferase complex (OST) catalyses co-translational N-glycosylation, one of the most common protein modifications in eukaryotic cells. Here we use cryoelectron tomography, cryoelectron microscopy single-particle analysis and small interfering RNA-mediated gene silencing to determine the overall structure, oligomeric state and position of OST in the native ER protein translocon of mammalian cells in unprecedented detail. The observed positioning of OST in close proximity to Sec61 provides a basis for understanding how protein translocation into the ER and glycosylation of nascent proteins are structurally coupled. The overall spatial orga- nization of the native translocon, as determined here, serves as a reliable framework for further hypothesis-driven studies. 1 Department of Molecular Structural Biology, Max-Planck Institute of Biochemistry, Am Klopferspitz 18, D-82152 Martinsried, Germany. 2 Department of Medical Biochemistry and Molecular Biology, Saarland University, D-66421 Homburg, Germany. 3 Gene Center and Center for integrated Protein Science Munich, Department of Biochemistry, University of Munich, D-81377 Munich, Germany. -
An Assay Method for Glycogen Debranching Enzyme Using New Fluorogenic Substrates and Its Application to Detection of the Enzyme in Mouse Brain
J. Biochem. 123, 932-936 (1998) An Assay Method for Glycogen Debranching Enzyme Using New Fluorogenic Substrates and Its Application to Detection of the Enzyme in Mouse Brain Kaoru Omichi1 and Sumihiro Hase Department of Chemistry, Graduate School of Science, Osaka University, Toyonaka, Osaka 560-0043 Received for publication, December 11, 1997 An assay method for glycogen debranching enzyme involving fluorogenic dextrins as substrates was developed. Two dextrins were prepared from 6-0-ƒ¿-D-glucosyl-ƒ¿-cyclo dextrin and glucose by taking advantage of the action of Bacillus macerans cyclodextrin glucanotransferase, and converted by pyridylamination to fluorogenic derivatives. Struc tural analysis of the fluorogenic dextrins by FAB-MS, partial acid hydrolysis, and gluco amylase digestion revealed that they were Glcƒ¿l-4(Glcƒ¿l-6)Glcƒ¿l-4Glcƒ¿l-4Glcƒ¿l-4Glc- PA (FD6) and Glcƒ¿l-4Glcƒ¿l-4(Glcƒ¿l-6)Glcƒ¿l-4Glcƒ¿l-4Glcƒ¿l-4Glc-PA (FD7). Using the glycogen debranching enzyme from rabbit muscle, FD6 and FD7 were, respectively, hydrolyzed to PA-maltopentaose and PA-maltohexaose, in addition to glucose, showing that these two fluorogenic dextrins are suitable substrates for assaying the glycogen debranching enzyme. An assay method involving the separation and quantification by HPLC of the characteristic fluorogenic products was successfully applied to determination of the distribution of the enzyme activity in mouse cerebrum. Key words: assay methods, fluorogenic substrate, glycogen debranching enzyme, HPLC. Glycogen debranching enzyme is known to be involved in enzymes such as a-amylase [EC 3.2.1.1] and ƒ¿-gluco- the degradation of glycogen into glucose-1-phosphate and sidase [EC 3.2.1.20]. -
Carboxy Terminally Truncated Forms of Ribophorin I Are Degraded in Pre-Golgi Compartments by a Calcium-Dependent Process Yung Shyeng Tsao, N
View metadata, citation and similar papers at core.ac.uk brought to you by CORE provided by PubMed Central Carboxy Terminally Truncated Forms of Ribophorin I Are Degraded in Pre-Golgi Compartments by a Calcium-dependent Process Yung Shyeng Tsao, N. Erwin Ivessa, Milton Adesnik, David D. Sabatini, and Gert Kreibich Department of Cell Biology, New York University School ofMedicine, New York 10016 Abstract. Two COOH terminally truncated variants of when added immediately after labeling, ionophores ribophorin I (RI), a type I transmembrane glycoprotein that inhibit vesicular flow out of the ER, such as car- of 583 amino acids that is segregated to the rough bonyl cyanide m-chlorophenylhydrazone (CCCP) and portions of the ER and is associated with the protein- monensin, suppressed the second phase of degradation translocating apparatus of this organelle, were expressed of 81332 . On the other hand, when CCCP was added in permanent HeLa cell transformants . Both variants, after the second phase of degradation of 81332 was ini- one membrane anchored but lacking part of the cyto- tiated, the degradation was unaffected. Moreover, in plasmic domain (RI,67) and the other consisting of the cells treated with brefeldin A the degradation of 81332 luminal 332 N112-terminal amino acids (RI332), were became monophasic, and took place with a half-life retained intracellularly but, in contrast to the endoge- intermediate between those of the two normal phases. nous long lived, full length ribophorin I (tv2 = 25 h), These results point to the existence of two subcellular were rapidly degraded (ti/2 < 50 min) by a nonlyso- compartments where abnormal ER proteins can be de- somal mechanism. -
Generate Metabolic Map Poster
Authors: Pallavi Subhraveti Peter D Karp Ingrid Keseler An online version of this diagram is available at BioCyc.org. Biosynthetic pathways are positioned in the left of the cytoplasm, degradative pathways on the right, and reactions not assigned to any pathway are in the far right of the cytoplasm. Transporters and membrane proteins are shown on the membrane. Anamika Kothari Periplasmic (where appropriate) and extracellular reactions and proteins may also be shown. Pathways are colored according to their cellular function. Gcf_000980815Cyc: Corynebacterium camporealensis DSM 44610 Cellular Overview Connections between pathways are omitted for legibility. Ron Caspi phosphate phosphate (S)-lactate phosphate ammonium predicted ABC RS04760 RS02955 RS06425 RS10630 transporter of phosphate phosphate (S)-lactate phosphate ammonium phosphate Amine and Tetrapyrrole Biosynthesis Amino Acid Degradation glutaminyl-tRNA gln Aminoacyl-tRNA Charging Polyamine a ring-opened 7- a DNA containing (1S,2R)-1- a [ThiI sulfur- biosynthesis via transamidation Biosynthesis an apo [peptidyl- all-trans- an L-asparaginyl- an L-cysteinyl- Polyprenyl Biosynthesis siroheme biosynthesis TCA cycle TCA cycle IV (2-oxoglutarate decarboxylase) L-valine degradation I L-asparagine methylguanine coenzyme A an apurinic/ ser C-(indol-3- carrier protein]- cys a [glutamine- L-isoleucine degradation I L-leucine degradation I L-threonine carrier protein] ATP retinyl palmitate [tRNA Asn ] [tRNA Cys ] dGDP spermidine degradation I in DNA apyrimidinic site yl)glycerol L-cysteine synthetase]- -
(12) Patent Application Publication (10) Pub. No.: US 2016/0244489 A1 MASIGNAN Et Al
US 20160244489A1 (19) United States (12) Patent Application Publication (10) Pub. No.: US 2016/0244489 A1 MASIGNAN et al. (43) Pub. Date: Aug. 25, 2016 (54) PROTEINS AND NUCLEICACIDS FROM application No. 1 1/884,812, filed on Mar. 26, 2008, MENINGITIS/SEPSIS-ASSOCATED now Pat. No. 8,758,764, filed as application No. PCT/ ESCHERICHA COL US2006/005913 on Feb. 17, 2006. (71) Applicants: GlaxoSmithKline Biologicals SA, (60) Provisional application No. 60/712,720, filed on Aug. Rixensart (BE); J. Craig Venter 29, 2005, provisional application No. 60/654,632, Institute, Inc., Rockville, MD (US) filed on Feb. 18, 2005. (72) Inventors: Vega MASIGNANI, Siena (IT): Danilo Gomes MORIEL, Monteriggioni (IT): Publication Classification Francesco BERLANDA SCORZA, Trento (IT): Nathalie NORAIS, Siena (51) Int. Cl. (IT): Maria Rita FONTANA, Siena C07K I4/245 (2006.01) (IT); Mariagrazia PIZZA, Siena (IT): A6139/08 (2006.01) Laura SERINO, Monticiano (IT): C07K 6/2 (2006.01) Herve TETTELIN, Gaithersburg, MD (52) U.S. Cl. (US) CPC ........... C07K 14/245 (2013.01); C07K 16/1232 (73) Assignees: GlaxoSmithKline Biologicals SA, (2013.01); A61 K39/0258 (2013.01); A61 K Rixensart (BE); J. Craig Venter 2039/523 (2013.01) Institute, Inc., Rockville, MD (US) (21) Appl. No.: 15/150,204 (57) ABSTRACT (22) Filed: May 9, 2016 Disclosed herein are various open reading frames from a Related U.S. Application Data strain of E. coli responsible for neonatal meningitis (MNEC), (62) Division of application No. 14/293,967, filed on Jun. 2, and a Subset of these that is of particular interest for preparing 2014, now Pat. -
Classification: Biological Sciences, Biochemistry Title: Selective Protein
bioRxiv preprint doi: https://doi.org/10.1101/828921; this version posted November 2, 2019. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission. Classification: Biological Sciences, Biochemistry Title: Selective protein O-GlcNAcylation in cells by a proximity-directed O-GlcNAc transferase Authors: Daniel H. Ramirez,1 Chanat Aonbangkhen,1 Hung-Yi Wu,1 Jeffrey A. Naftaly,1,^ Stephanie Tang,1 Timothy R. O’Meara,1 Christina M. Woo1,* Author affiliation: 1 Department of Chemistry and Chemical Biology, Harvard University, 12 Oxford St, Cambridge, MA 02138, USA ^ Current address: Laboratory of Stem Cell Biology and Molecular Embryology, The Rockefeller University, New York, NY 10065, USA Corresponding Author: Christina M. Woo Department of Chemistry and Chemical Biology Harvard University 12 Oxford St Cambridge, MA 02138, USA 617-495-3858 [email protected] Keywords: O-GlcNAc, O-GlcNAc transferase, nanobody, glycoproteomics, protein engineering bioRxiv preprint doi: https://doi.org/10.1101/828921; this version posted November 2, 2019. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission. Abstract O-Linked N-acetylglucosamine (O-GlcNAc) is a monosaccharide that plays an essential role in cellular signaling throughout the nucleocytoplasmic proteome of eukaryotic cells. Yet, the study of post-translational modifications like O-GlcNAc has been limited by the lack of strategies to induce O-GlcNAcylation on a target protein in cells. Here, we report a generalizable genetic strategy to induce O-GlcNAc to specific target proteins in cells using a nanobody as a proximity- directing agent fused to O-GlcNAc transferase (OGT). -
Targeting Multiple Pro-Apoptotic Signaling Pathways with Curcumin in Prostate Cancer Cells
RESEARCH ARTICLE Targeting multiple pro-apoptotic signaling pathways with curcumin in prostate cancer cells Mariela Rivera1, Yanilda Ramos1, Madeline RodrõÂguez-ValentõÂn1, Sheila Lo pez-Acevedo1, Luis A. Cubano1, Jin Zou2, Qiang Zhang3, Guangdi Wang3, Nawal M. Boukli1* 1 Department of Microbiology and Immunology, Biomedical Proteomics Facility, Universidad Central del Caribe School of Medicine, BayamoÂn, Puerto Rico, United States of America, 2 Center for Cancer Research and Therapeutic Development, Clark Atlanta University, Atlanta, Georgia, United States of America, a1111111111 3 Department of Chemistry, RCMI Cancer Research Center, Xavier University of Louisiana, New Orleans, a1111111111 Louisiana, United States of America a1111111111 a1111111111 * [email protected] a1111111111 Abstract Curcumin, an extract from the turmeric rhizome (Curcuma longa), is known to exhibit anti- OPEN ACCESS inflammatory, antioxidant, chemopreventive and antitumoral activities against aggressive Citation: Rivera M, Ramos Y, RodrõÂguez-ValentõÂn and recurrent cancers. Accumulative data indicate that curcumin may induce cancer cell M, LoÂpez-Acevedo S, Cubano LA, Zou J, et al. death. However, the detailed mechanism underlying its pro-apoptotic and anti-cancer (2017) Targeting multiple pro-apoptotic signaling pathways with curcumin in prostate cancer cells. effects remains to be elucidated. In the present study, we examined the signaling pathways PLoS ONE 12(6): e0179587. https://doi.org/ triggered by curcumin, specifically, the exact molecular mechanisms of curcumin-induced 10.1371/journal.pone.0179587 apoptosis in highly metastatic human prostate cancer cells. The effect of curcumin was eval- Editor: Aamir Ahmad, University of South Alabama uated using for the first time in prostate cancer, a gel-free shotgun quantitative proteomic Mitchell Cancer Institute, UNITED STATES analysis coupled with Tandem Mass Tag isobaric labeling-based-signaling networks.