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The Regulation of Carbamoyl Phosphate Synthetase-Aspartate Transcarbamoylase-Dihydroorotase (Cad) by Phosphorylation and Protein-Protein Interactions
THE REGULATION OF CARBAMOYL PHOSPHATE SYNTHETASE-ASPARTATE TRANSCARBAMOYLASE-DIHYDROOROTASE (CAD) BY PHOSPHORYLATION AND PROTEIN-PROTEIN INTERACTIONS Eric M. Wauson A dissertation submitted to the faculty of the University of North Carolina at Chapel Hill in partial fulfillment of the requirements for the degree of Doctor of Philosophy in the Department of Pharmacology. Chapel Hill 2007 Approved by: Lee M. Graves, Ph.D. T. Kendall Harden, Ph.D. Gary L. Johnson, Ph.D. Aziz Sancar M.D., Ph.D. Beverly S. Mitchell, M.D. 2007 Eric M. Wauson ALL RIGHTS RESERVED ii ABSTRACT Eric M. Wauson: The Regulation of Carbamoyl Phosphate Synthetase-Aspartate Transcarbamoylase-Dihydroorotase (CAD) by Phosphorylation and Protein-Protein Interactions (Under the direction of Lee M. Graves, Ph.D.) Pyrimidines have many important roles in cellular physiology, as they are used in the formation of DNA, RNA, phospholipids, and pyrimidine sugars. The first rate- limiting step in the de novo pyrimidine synthesis pathway is catalyzed by the carbamoyl phosphate synthetase II (CPSase II) part of the multienzymatic complex Carbamoyl phosphate synthetase, Aspartate transcarbamoylase, Dihydroorotase (CAD). CAD gene induction is highly correlated to cell proliferation. Additionally, CAD is allosterically inhibited or activated by uridine triphosphate (UTP) or phosphoribosyl pyrophosphate (PRPP), respectively. The phosphorylation of CAD by PKA and ERK has been reported to modulate the response of CAD to allosteric modulators. While there has been much speculation on the identity of CAD phosphorylation sites, no definitive identification of in vivo CAD phosphorylation sites has been performed. Therefore, we sought to determine the specific CAD residues phosphorylated by ERK and PKA in intact cells. -
Proteomic Analysis of the Rad18 Interaction Network in DT40 – a Chicken B Cell Line
Proteomic analysis of the Rad18 interaction network in DT40 – a chicken B cell line Thesis submitted for the degree of Doctor of Natural Sciences at the Faculty of Biology, Ludwig-Maximilians-University Munich 15th January, 2009 Submitted by Sushmita Gowri Sreekumar Chennai, India Completed at the Helmholtz Zentrum München German Research Center for Environmental Health Institute of Clinical Molecular Biology and Tumor Genetics, Munich Examiners: PD Dr. Berit Jungnickel Prof. Heinrich Leonhardt Prof. Friederike Eckardt-Schupp Prof. Harry MacWilliams Date of Examination: 16th June 2009 To my Parents, Sister, Brother & Rajesh Table of Contents 1. SUMMARY ........................................................................................................................ 1 2. INTRODUCTION ............................................................................................................. 2 2.1. MECHANISMS OF DNA REPAIR ......................................................................................... 3 2.2. ADAPTIVE GENETIC ALTERATIONS – AN ADVANTAGE ....................................................... 5 2.3. THE PRIMARY IG DIVERSIFICATION DURING EARLY B CELL DEVELOPMENT ...................... 6 2.4. THE SECONDARY IG DIVERSIFICATION PROCESSES IN THE GERMINAL CENTER .................. 7 2.4.1. Processing of AID induced DNA lesions during adaptive immunity .................. 9 2.5. TARGETING OF SOMATIC HYPERMUTATION TO THE IG LOCI ............................................ 10 2.6. ROLE OF THE RAD6 PATHWAY IN IG DIVERSIFICATION -
Biosynthesis and Secretion of the Microbial Sulfated Peptide Raxx and Binding to the Rice XA21 Immune Receptor
Biosynthesis and secretion of the microbial sulfated peptide RaxX and binding to the rice XA21 immune receptor Dee Dee Luua,b,1, Anna Joea,b,c,1, Yan Chend, Katarzyna Paryse, Ofir Bahara,b,2, Rory Pruitta,b,3, Leanne Jade G. Chand, Christopher J. Petzoldd, Kelsey Longa,b, Clifford Adamchaka,b, Valley Stewartf, Youssef Belkhadire, and Pamela C. Ronalda,b,c,4 aDepartment of Plant Pathology, University of California, Davis, CA 95616; bThe Genome Center, University of California, Davis, CA 95616; cFeedstocks Division, Joint Bioenergy Institute, Emeryville, CA 94608; dTechnology Division, Joint Bioenergy Institute, Emeryville, CA 94608; eGregor Mendel Institute, Austrian Academy of Sciences, 1030 Vienna, Austria; and fDepartment of Microbiology & Molecular Genetics, University of California, Davis, CA 95616 Edited by Jonathan D. G. Jones, The Sainsbury Laboratory, Norwich, United Kingdom, and approved March 7, 2019 (received for review October 24, 2018) The rice immune receptor XA21 is activated by the sulfated micro- to Xoo strains lacking RaxX (7–10). Xoo strains lacking RaxX are bial peptide required for activation of XA21-mediated immunity X also compromised in virulence of rice plants lacking XA21 (10). (RaxX) produced by Xanthomonas oryzae pv. oryzae (Xoo). Muta- These results suggest a role for RaxX in bacterial virulence. tional studies and targeted proteomics revealed that the RaxX pre- Tyrosine sulfated RaxX16, a 16-residue synthetic peptide de- cursor peptide (proRaxX) is processed and secreted by the protease/ rived from residues 40–55 of the 60-residue RaxX precursor transporter RaxB, the function of which can be partially fulfilled by peptide (proRaxX), is the shortest characterized immunogenic a noncognate peptidase-containing transporter component B derivative of RaxX (10). -
A Database for Enzymes Involved in Novel Post-Translational Modifications Shradha Khater and Debasisa Mohanty*
Database, 2015, 1–12 doi: 10.1093/database/bav039 Original article Original article novPTMenzy: a database for enzymes involved in novel post-translational modifications Shradha Khater and Debasisa Mohanty* Bioinformatics Centre, National Institute of Immunology, Aruna Asaf Ali Marg, New Delhi 110067, India *Corresponding author: Tel: þ91 11 26703749; Fax: þ91 11 26742125; Email: [email protected] Citation details: Khater,S. and Mohanty,D. novPTMenzy: a database for enzymes involved in novel post-translational modifications. Database (2015) Vol. 2015: article ID bav039; doi:10.1093/database/bav039 Received 7 November 2014; Revised 30 March 2015; Accepted 1 April 2015 Abstract With the recent discoveries of novel post-translational modifications (PTMs) which play important roles in signaling and biosynthetic pathways, identification of such PTM cata- lyzing enzymes by genome mining has been an area of major interest. Unlike well-known PTMs like phosphorylation, glycosylation, SUMOylation, no bioinformatics resources are available for enzymes associated with novel and unusual PTMs. Therefore, we have developed the novPTMenzy database which catalogs information on the sequence, struc- ture, active site and genomic neighborhood of experimentally characterized enzymes involved in five novel PTMs, namely AMPylation, Eliminylation, Sulfation, Hydroxylation and Deamidation. Based on a comprehensive analysis of the sequence and structural features of these known PTM catalyzing enzymes, we have created Hidden Markov Model profiles for the identification of similar PTM catalyzing enzymatic domains in gen- omic sequences. We have also created predictive rules for grouping them into functional subfamilies and deciphering their mechanistic details by structure-based analysis of their active site pockets. These analytical modules have been made available as user friendly search interfaces of novPTMenzy database. -
1 Metabolic Dysfunction Is Restricted to the Sciatic Nerve in Experimental
Page 1 of 255 Diabetes Metabolic dysfunction is restricted to the sciatic nerve in experimental diabetic neuropathy Oliver J. Freeman1,2, Richard D. Unwin2,3, Andrew W. Dowsey2,3, Paul Begley2,3, Sumia Ali1, Katherine A. Hollywood2,3, Nitin Rustogi2,3, Rasmus S. Petersen1, Warwick B. Dunn2,3†, Garth J.S. Cooper2,3,4,5* & Natalie J. Gardiner1* 1 Faculty of Life Sciences, University of Manchester, UK 2 Centre for Advanced Discovery and Experimental Therapeutics (CADET), Central Manchester University Hospitals NHS Foundation Trust, Manchester Academic Health Sciences Centre, Manchester, UK 3 Centre for Endocrinology and Diabetes, Institute of Human Development, Faculty of Medical and Human Sciences, University of Manchester, UK 4 School of Biological Sciences, University of Auckland, New Zealand 5 Department of Pharmacology, Medical Sciences Division, University of Oxford, UK † Present address: School of Biosciences, University of Birmingham, UK *Joint corresponding authors: Natalie J. Gardiner and Garth J.S. Cooper Email: [email protected]; [email protected] Address: University of Manchester, AV Hill Building, Oxford Road, Manchester, M13 9PT, United Kingdom Telephone: +44 161 275 5768; +44 161 701 0240 Word count: 4,490 Number of tables: 1, Number of figures: 6 Running title: Metabolic dysfunction in diabetic neuropathy 1 Diabetes Publish Ahead of Print, published online October 15, 2015 Diabetes Page 2 of 255 Abstract High glucose levels in the peripheral nervous system (PNS) have been implicated in the pathogenesis of diabetic neuropathy (DN). However our understanding of the molecular mechanisms which cause the marked distal pathology is incomplete. Here we performed a comprehensive, system-wide analysis of the PNS of a rodent model of DN. -
Protein Identities in Evs Isolated from U87-MG GBM Cells As Determined by NG LC-MS/MS
Protein identities in EVs isolated from U87-MG GBM cells as determined by NG LC-MS/MS. No. Accession Description Σ Coverage Σ# Proteins Σ# Unique Peptides Σ# Peptides Σ# PSMs # AAs MW [kDa] calc. pI 1 A8MS94 Putative golgin subfamily A member 2-like protein 5 OS=Homo sapiens PE=5 SV=2 - [GG2L5_HUMAN] 100 1 1 7 88 110 12,03704523 5,681152344 2 P60660 Myosin light polypeptide 6 OS=Homo sapiens GN=MYL6 PE=1 SV=2 - [MYL6_HUMAN] 100 3 5 17 173 151 16,91913397 4,652832031 3 Q6ZYL4 General transcription factor IIH subunit 5 OS=Homo sapiens GN=GTF2H5 PE=1 SV=1 - [TF2H5_HUMAN] 98,59 1 1 4 13 71 8,048185945 4,652832031 4 P60709 Actin, cytoplasmic 1 OS=Homo sapiens GN=ACTB PE=1 SV=1 - [ACTB_HUMAN] 97,6 5 5 35 917 375 41,70973209 5,478027344 5 P13489 Ribonuclease inhibitor OS=Homo sapiens GN=RNH1 PE=1 SV=2 - [RINI_HUMAN] 96,75 1 12 37 173 461 49,94108966 4,817871094 6 P09382 Galectin-1 OS=Homo sapiens GN=LGALS1 PE=1 SV=2 - [LEG1_HUMAN] 96,3 1 7 14 283 135 14,70620005 5,503417969 7 P60174 Triosephosphate isomerase OS=Homo sapiens GN=TPI1 PE=1 SV=3 - [TPIS_HUMAN] 95,1 3 16 25 375 286 30,77169764 5,922363281 8 P04406 Glyceraldehyde-3-phosphate dehydrogenase OS=Homo sapiens GN=GAPDH PE=1 SV=3 - [G3P_HUMAN] 94,63 2 13 31 509 335 36,03039959 8,455566406 9 Q15185 Prostaglandin E synthase 3 OS=Homo sapiens GN=PTGES3 PE=1 SV=1 - [TEBP_HUMAN] 93,13 1 5 12 74 160 18,68541938 4,538574219 10 P09417 Dihydropteridine reductase OS=Homo sapiens GN=QDPR PE=1 SV=2 - [DHPR_HUMAN] 93,03 1 1 17 69 244 25,77302971 7,371582031 11 P01911 HLA class II histocompatibility antigen, -
UNIVERSITY of CALIFORNIA, IRVINE an Expanded Genetic Code
UNIVERSITY OF CALIFORNIA, IRVINE An expanded genetic code for the characterization and directed evolution of tyrosine-sulfated proteins DISSERTATION submitted in partial satisfaction of the requirements for the degree of DOCTOR OF PHILSOPHY in Biomedical Engineering by Xiang Li Dissertation Committee: Assistant Professor Chang C. Liu, Chair Associate Professor Wendy Liu Associate Professor Jennifer A. Prescher 2018 Portion of Chapter 2 © John Wiley and Sons Portion of Chapter 3 © Springer Portion of Chapter 4 © Royal Society of Chemistry All other materials © 2018 Xiang Li i Dedication To My parents Audrey Bai and Yong Li and My brother Joshua Li ii Table of Content LIST OF FIGURES ..................................................................................................................VI LIST OF TABLES ................................................................................................................. VIII CURRICULUM VITAE ...........................................................................................................IX ACKNOWLEDGEMENTS .................................................................................................... XII ABSTRACT .......................................................................................................................... XIII CHAPTER 1. INTRODUCTION ................................................................................................ 1 1.1. INTRODUCTION ................................................................................................................. -
Early Restoration of Parvalbumin Interneuron Activity Prevents Memory Loss and Network Hyperexcitability in a Mouse Model of Alzheimer’S Disease
Molecular Psychiatry (2020) 25:3380–3398 https://doi.org/10.1038/s41380-019-0483-4 ARTICLE Early restoration of parvalbumin interneuron activity prevents memory loss and network hyperexcitability in a mouse model of Alzheimer’s disease 1 2 3 4 4 2 Sara Hijazi ● Tim S. Heistek ● Philip Scheltens ● Ulf Neumann ● Derya R. Shimshek ● Huibert D. Mansvelder ● 1 1 August B. Smit ● Ronald E. van Kesteren Received: 6 June 2018 / Revised: 9 May 2019 / Accepted: 20 June 2019 / Published online: 20 August 2019 © The Author(s) 2019. This article is published with open access Abstract Neuronal network dysfunction is increasingly recognized as an early symptom in Alzheimer’s disease (AD) and may provide new entry points for diagnosis and intervention. Here, we show that amyloid-beta-induced hyperexcitability of hippocampal inhibitory parvalbumin (PV) interneurons importantly contributes to neuronal network dysfunction and memory impairment in APP/PS1 mice, a mouse model of increased amyloidosis. We demonstrate that hippocampal PV interneurons become hyperexcitable at ~16 weeks of age, when no changes are observed yet in the intrinsic properties of pyramidal cells. This 1234567890();,: 1234567890();,: hyperexcitable state of PV interneurons coincides with increased inhibitory transmission onto hippocampal pyramidal neurons and deficits in spatial learning and memory. We show that treatment aimed at preventing PV interneurons from becoming hyperexcitable is sufficient to restore PV interneuron properties to wild-type levels, reduce inhibitory input onto pyramidal cells, and rescue memory deficits in APP/PS1 mice. Importantly, we demonstrate that early intervention aimed at restoring PV interneuron activity has long-term beneficial effects on memory and hippocampal network activity, and reduces amyloid plaque deposition, a hallmark of AD pathology. -
Supplementary Materials
Supplementary Materials Figure S1. Bioinformatics evaluation of dystrophin isoform Dp427 and its central position in the molecular pathogenesis of X-linked muscular dystrophy. In order to generate a protein interaction map with known and predicted protein associations that include direct physical and indirect functional protein linkages, the bioinformatics STRING database [1,2] was used to analyse mass spectrometrically-identified proteins with a changed abundance in mdx-4cv skeletal muscles (Tables 1 and 2). S2 Figure S2. Focus of the bioinformatics evaluation of dystrophin isoform Dp427 and its central position in the molecular pathogenesis of X-linked muscular dystrophy. Shown is the middle part of the interaction map of altered muscle-associated proteins from mdx-4cv hind limb muscles, focusing on the central position of the dystrophin protein Dp427 (marked in yellow). In order to generate a protein interaction map with known and predicted protein associations that include direct physical and indirect functional protein linkages, the bioinformatics STRING database [1,2] was used to analyse mass spectrometrically-identified proteins with a changed abundance in mdx-4cv skeletal muscles (Tables 1 and 2). S3 Table S1. List of identified proteins that exhibit a significantly altered concentration in crude mdx-4cv hind limb muscle preparations as revealed by label-free LC-MS/MS analysis. This table contains the statistical q-values of the proteins listed in Tables 1 and 2. Accession Peptide Max Fold Highest Mean Description q Value Number -
Genitourinary Advanced Pca and Its Efficacy As a Therapeutic Agent Is Presently Being Studied in Clinical Trials
ANNUAL MEETING ABSTRACTS 133A because they were over age 80 and as such, the IHC results were likely due to acquired 599 Anterior Predominant Prostate Tumors: A Contemporary methylation of the MLH1 promoter. The remaining 4 patients with absent staining have Look at Zone of Origin been referred to Cancer Genetics for possible further work-up. The reimbursement rate HA Al-Ahmadie, SK Tickoo, A Gopalan, S Olgac, VE Reuter, SW Fine. Memorial Sloan and turn-around time for the IHC stains were similar to that for other IHC stains used Kettering Cancer Center, NY, NY. in clinical practice. Background: Aggressive PSA screening and prostate needle biopsy protocols have Conclusions: IHC stains for the MMR proteins are fast and relatively easy to institute in successfully detected low-volume posterior tumors, with a concurrent increase in routine evaluation of CRC, and we have not had difficulty interpreting the stains leading anterior-predominant prostate cancer (AT). Zone of origin, patterns of spread, and to additional testing. Furthermore, reimbursement was obtained at a level similar to extraprostatic extension of these tumors have not been well studied. other IHC stains used in clinical practice. The surgeons and oncologists welcomed the Design: We greatly expanded and refined our previous studies to include pathologic prognostic information. Further study is warranted to confirm these initial findings. features of 197 patients with largest tumors anterior to the urethra in whole-mounted radical prostatectomy specimens. 597 High Fidelity Image Cytometry in Neoplastic Lesions in Barrett’s Results: Of 197 AT, 97 (49.2%) were predominantly located in the peripheral zone Esophagus, Including Basal Crypt Dysplasia-Like Atypia with Surface (PZ-D), 70 (35.5%) in the transition zone (TZ-D), 16 (8.1%) were of indeterminate Maturation zone (IND), and 14 (7.1%) in both PZ and TZ (PZ+TZ). -
Parvalbumin Expression in Oligodendrocyte-Like CG4 Cells
www.nature.com/scientificreports There are amendments to this paper OPEN Parvalbumin expression in oligodendrocyte-like CG4 cells causes a reduction in mitochondrial Received: 11 February 2019 Accepted: 11 July 2019 volume, attenuation in reactive Published: xx xx xxxx oxygen species production and a decrease in cell processes’ length and branching Lucia Lichvarova, Walter Blum, Beat Schwaller & Viktoria Szabolcsi Forebrain glial cells - ependymal cells and astrocytes -acquire upon injury- a “reactive” phenotype associated with parvalbumin (PV) upregulation. Since free radicals, e.g. reactive oxygen species (ROS) play a role in the pathogenesis of multiple sclerosis, and that PV-upregulation in glial cells is inversely correlated with the level of oxidative stress, we hypothesized that PV-upregulation might also protect oligodendrocytes by decreasing ROS production. Lentiviral transduction techniques allowed for PV overexpression in CG4 oligodendrocyte progenitor cells (OPCs). Depending on the growth medium CG4 cells can be maintained in an OPC-like state, or induced to diferentiate into an oligodendrocyte (OLG)-like phenotype. While increased levels of PV had no efect on cell proliferation and invasiveness in vitro, PV decreased the mitochondria volume in CG4 cell bodies, as well as the mitochondrial density in CG4 processes in both OPC-like and OLG-like states. In line with the PV-induced global decrease in mitochondrial volume, elevated PV levels reduced transcript levels of mitochondrial transcription factors involved in mitochondria biogenesis. In diferentiated PV-overexpressing CG4 cells with a decreased mitochondrial volume, UV-induced ROS production was lower than in control CG4 cells hinting towards a possible role of PV in counteracting oxidative stress. -
Biological Macromolecular Crystal Growth
Biological Macromolecular Crystal Growth NASA ISS Research Academy and Pre-Application Meeting August 3-5, 2010 Yancy B. You ng ISS Payloads Office Marshall Space Flight Center Huntsville, AL [email protected] Introduction • Biological Macromolecular Crystal Growth (a.k.a., Protein Crystal Growth) research focuses on determining the three dimensional structure of bio- molecules − Viruses − Proteins − DNA − RNA • Structural determination provides basis for understanding function and can aid in: − Structure-guided design of pharmaceuticals, herbicides, insecticides − Further our understanding of life’s most fundamental processes (basic biological research) • Advances in diagnostic equipment and techniques have enhanced determination of new structures, but crystal production of sufficient quality for structural analysis continues to prove challenging to the scientific community 080310 Page No. 2 Why is Microgravity an Ideal Environment? • As crystals grow, solution around them becomes depleted of sample. On the groundthid this r ises caus ing tur bu len t convection. • Buoyancy driven convection and a) b) sedimentation are greatly reduced in the ISS microgravity environment resulting in: 1. Formation of stable depletion zone around the growing crystal: slow c) d) Schlieren photograph of a growth plume rising from a consistent addition of molecules to the lysozyme crystal (pH 4.0, 0.1M sodium acetate, 5% crystal lattice NaCl at 15°C.M.L. Pusey, J. Cryst. Growth, 122, 1-7, 1992) . 2. Reduction in secondary nucleation: fewer crystals competing for solute resulting in larger crystals 3. Suspension of growing crystals: do not settle to bottom of growth chamber (more uniform shape) Depletion zone around lysozyme crystal (ground based) Courtesy: Dr.