I Monovalent Cation Effects on Histidine Kinase Chea Activity By
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METACYC ID Description A0AR23 GO:0004842 (Ubiquitin-Protein Ligase
Electronic Supplementary Material (ESI) for Integrative Biology This journal is © The Royal Society of Chemistry 2012 Heat Stress Responsive Zostera marina Genes, Southern Population (α=0. -
Phosphatidylinositol-3-Kinase in Tomato (Solanum Lycopersicum. L) Fruit and Its Role in Ethylene Signal Transduction and Senescence
Phosphatidylinositol-3-Kinase in Tomato (Solanum lycopersicum. L) Fruit and Its Role in Ethylene Signal Transduction and Senescence by Mohd Sabri Pak Dek A Thesis presented to The University of Guelph In partial fulfilment of requirements for the degree of Doctor of Philosophy in Plant Agriculture Guelph, Ontario, Canada © Mohd Sabri Pak Dek,June, 2015 ABSTRACT PHOSPHATIDYLINOSITOL-3-KINASE IN TOMATO (SOLANUM LYCOPERSICUM. L) FRUIT AND ITS ROLE IN ETHYLENE SIGNAL TRANSDUCTION AND SENESCENCE Mohd Sabri Pak Dek Co-Advisors: University of Guelph, 2015 Professor G. Paliyath Professor J. Subramanian The ripening process is initiated by ethylene through a signal transduction cascade leads to the expression of ripening-related genes and catabolism of membrane, cell wall, and storage components. One of the minor components in membrane phospholipids is phosphatidylinositol (PI). Phosphatidylinositol-3-kinase (PIK) is an enzyme that phosphorylates PI at the 3-OH position of inositol head group to produce phosphatidylinositol 3-phosphate (PI3P). Phosphorylation of PI may be an early event in the ethylene signal transduction pathway that generates negatively charged domains on the plasma membrane. PI3P domains may potentially serve as a docking site for phospholipase D (PLD) after ethylene stimulation. It is hypothesized that ethylene stimulation may activate PI3K resulting in enhanced level of phosphorylated phosphatidylinositol. However, the properties and function of PI3K is not well understood in plants. In the present study, the effect of PI3K inhibition during tomato fruit ripening was evaluated. This study demonstrated that PI3K activity is required for normal ripening process of the fruit. Inhibition of PI3K activity using wortmannin significantly reduced tomato ripening process. -
Molecular Mechanisms Involved Involved in the Interaction Effects of HCV and Ethanol on Liver Cirrhosis
Virginia Commonwealth University VCU Scholars Compass Theses and Dissertations Graduate School 2010 Molecular Mechanisms Involved Involved in the Interaction Effects of HCV and Ethanol on Liver Cirrhosis Ryan Fassnacht Virginia Commonwealth University Follow this and additional works at: https://scholarscompass.vcu.edu/etd Part of the Physiology Commons © The Author Downloaded from https://scholarscompass.vcu.edu/etd/2246 This Thesis is brought to you for free and open access by the Graduate School at VCU Scholars Compass. It has been accepted for inclusion in Theses and Dissertations by an authorized administrator of VCU Scholars Compass. For more information, please contact [email protected]. Ryan C. Fassnacht 2010 All Rights Reserved Molecular Mechanisms Involved in the Interaction Effects of HCV and Ethanol on Liver Cirrhosis A thesis submitted in partial fulfillment of the requirements for the degree of Master of Science at Virginia Commonwealth University. by Ryan Christopher Fassnacht, B.S. Hampden Sydney University, 2005 M.S. Virginia Commonwealth University, 2010 Director: Valeria Mas, Ph.D., Associate Professor of Surgery and Pathology Division of Transplant Department of Surgery Virginia Commonwealth University Richmond, Virginia July 9, 2010 Acknowledgement The Author wishes to thank his family and close friends for their support. He would also like to thank the members of the molecular transplant team for their help and advice. This project would not have been possible with out the help of Dr. Valeria Mas and her endearing -
Structure-Function Analysis of the Catalytic Domain of the Histidine Kinase Chea
Loyola University Chicago Loyola eCommons Dissertations Theses and Dissertations 1997 Structure-Function Analysis of the Catalytic Domain of the Histidine Kinase Chea Dolph David Ellefson Loyola University Chicago Follow this and additional works at: https://ecommons.luc.edu/luc_diss Part of the Microbiology Commons Recommended Citation Ellefson, Dolph David, "Structure-Function Analysis of the Catalytic Domain of the Histidine Kinase Chea" (1997). Dissertations. 3425. https://ecommons.luc.edu/luc_diss/3425 This Dissertation is brought to you for free and open access by the Theses and Dissertations at Loyola eCommons. It has been accepted for inclusion in Dissertations by an authorized administrator of Loyola eCommons. For more information, please contact [email protected]. This work is licensed under a Creative Commons Attribution-Noncommercial-No Derivative Works 3.0 License. Copyright © 1997 Dolph David Ellefson LOYOLA UNIVERSITY MEDICAL CENTER LIBRARY LOYOLA UNIVERSITY OF CHICAGO STRUCTURE-FUNCTION ANALYSIS OF THE CATALYTIC DOMAIN OF THE HISTIDINE KINASE CHEA A DISSERTATION SUBMITTED TO THE FACULTY OF THE GRADUATE SCHOOL IN CANDIDACY FOR THE DEGREE OF DOCTOR OF PHILOSOPHY DEPARTMENT OF MICROBIOLOGY AND IMMUNOLOGY BY DOLPH DAVID ELLEFSON CHICAGO, ILLINOIS MAY, 1997 Copyright by Dolph David Ellefson, 1997 All Rights Reserved ii ACKNOWLEDGEMENTS I would like to thank my director, Dr. Alan J. Wolfe, for his support, advice, and encouragment during the many years in his laboratory. In his laboratory, I was given a rare opportunity to explore a new arena of science and interact with a field of gifted researchers who I would not known otherwise. I would also like to thank the members of my committee, Ors. -
A Thesis Entitled Phor, Phop and Mshc
A Thesis entitled PhoR, PhoP and MshC: Three essential proteins of Mycobacterium tuberculosis by Erica Loney Submitted to the Graduate Faculty as partial fulfillment of the requirements for the Master of Science Degree in Chemistry __________________________________ Dr. Donald R. Ronning, Committee Chair __________________________________ Dr. John J. Bellizzi, Committee Member __________________________________ Dr. Ronald Viola, Committee Member __________________________________ Dr. Patricia R. Komuniecki, Dean College of Graduate Studies The University of Toledo May 2014 Copyright 2014, Erica Loney This document is copyrighted material. Under copyright law, no parts of this document may be produced without the expressed permission of the author. An Abstract of PhoR, PhoP and MshC: Three essential proteins of Mycobacterium tuberculosis by Erica Loney Submitted to the Graduate Faculty as partial fulfillment of the requirements for the Master of Science Degree in Chemistry The University of Toledo May 2014 The tuberculosis (TB) pandemic is responsible for 1.6 million deaths annually, most of which occur in developing nations. TB is treatable, though patient non- compliance, co-infection with HIV, and the long, 6-9 month treatment regimen have resulted in the emergence of drug-resistant TB. For these reasons, the development of novel anti-tuberculin drugs is essential. Three proteins – PhoR, PhoP, and MshC – of Mycobacterium tuberculosis (M.tb), the causative agent of TB, are the focus of this thesis. The PhoPR two-component system is a phosphorelay system responsible for the virulence of M.tb. The histidine kinase PhoR responds to a yet-unknown environmental stimulus and autophosphorylates a conserved histidine. The phosphate is transferred to an aspartate of the response regulator PhoP, which then forms a head-to-head homodimer and initiates the transcription of 114 virulence genes. -
Polymerase Ribozyme with Promoter Recognition
In vitro Evolution of a Processive Clamping RNA Polymerase Ribozyme with Promoter Recognition by Razvan Cojocaru BSc, Simon Fraser University, 2014 Thesis Submitted in Partial Fulfillment of the Requirements for the Degree of Doctor of Philosophy in the Department of Molecular Biology and Biochemistry Faculty of Science © Razvan Cojocaru 2021 SIMON FRASER UNIVERSITY Summer 2021 Copyright in this work is held by the author. Please ensure that any reproduction or re-use is done in accordance with the relevant national copyright legislation. Declaration of Committee Name: Razvan Cojocaru Degree: Doctor of Philosophy Title: In vitro Evolution of a Processive Clamping RNA Polymerase Ribozyme with Promoter Recognition Committee: Chair: Lisa Craig Professor, Molecular Biology and Biochemistry Peter Unrau Supervisor Professor, Molecular Biology and Biochemistry Dipankar Sen Committee Member Professor, Molecular Biology and Biochemistry Michel Leroux Committee Member Professor, Molecular Biology and Biochemistry Mani Larijani Internal Examiner Associate Professor, Molecular Biology and Biochemistry Gerald Joyce External Examiner Professor, Jack H. Skirball Center for Chemical Biology and Proteomics Salk Institute for Biological Studies Date Defended/Approved: August 12, 2021 ii Abstract The RNA World hypothesis proposes that the early evolution of life began with RNAs that can serve both as carriers of genetic information and as catalysts. Later in evolution, these functions were gradually replaced by DNA and enzymatic proteins in cellular biology. I start by reviewing the naturally occurring catalytic RNAs, ribozymes, as they play many important roles in biology today. These ribozymes are central to protein synthesis and the regulation of gene expression, creating a landscape that strongly supports an early RNA World. -
Yeast Genome Gazetteer P35-65
gazetteer Metabolism 35 tRNA modification mitochondrial transport amino-acid metabolism other tRNA-transcription activities vesicular transport (Golgi network, etc.) nitrogen and sulphur metabolism mRNA synthesis peroxisomal transport nucleotide metabolism mRNA processing (splicing) vacuolar transport phosphate metabolism mRNA processing (5’-end, 3’-end processing extracellular transport carbohydrate metabolism and mRNA degradation) cellular import lipid, fatty-acid and sterol metabolism other mRNA-transcription activities other intracellular-transport activities biosynthesis of vitamins, cofactors and RNA transport prosthetic groups other transcription activities Cellular organization and biogenesis 54 ionic homeostasis organization and biogenesis of cell wall and Protein synthesis 48 plasma membrane Energy 40 ribosomal proteins organization and biogenesis of glycolysis translation (initiation,elongation and cytoskeleton gluconeogenesis termination) organization and biogenesis of endoplasmic pentose-phosphate pathway translational control reticulum and Golgi tricarboxylic-acid pathway tRNA synthetases organization and biogenesis of chromosome respiration other protein-synthesis activities structure fermentation mitochondrial organization and biogenesis metabolism of energy reserves (glycogen Protein destination 49 peroxisomal organization and biogenesis and trehalose) protein folding and stabilization endosomal organization and biogenesis other energy-generation activities protein targeting, sorting and translocation vacuolar and lysosomal -
Expression, Purification and Characterisation of Full-Length
B doi:10.1016/S0022-2836(02)00424-2 available online at http://www.idealibrary.com on w J. Mol. Biol. (2002) 320, 201–213 Expression, Purification and Characterisation of Full-length Histidine Protein Kinase RegB from Rhodobacter sphaeroides Christopher A. Potter1, Alison Ward1, Cedric Laguri2 Michael P. Williamson2, Peter J.F. Henderson1 and Mary K. Phillips-Jones1* 1Division of Microbiology The global redox switch between aerobic and anaerobic growth in School of Biochemistry and Rhodobacter sphaeroides is controlled by the RegA/RegB two-component Molecular Biology, University system, in which RegB is the integral membrane histidine protein kinase, of Leeds, Leeds LS2 9JT, UK and RegA is the cytosolic response regulator. Despite the global regulatory importance of this system and its many homologues, there have been no 2Department of Molecular reported examples to date of heterologous expression of full-length RegB Biology and Biotechnology or any histidine protein kinases. Here, we report the amplified expression University of Sheffield of full-length functional His-tagged RegB in Escherichia coli, its purifi- Sheffield S10 2TN, UK cation, and characterisation of its properties. Both the membrane-bound and purified solubilised RegB protein demonstrate autophosphorylation activity, and the purified protein autophosphorylates at the same rate under both aerobic and anaerobic conditions confirming that an additional regulator is required to control/inhibit autophosphorylation. The intact protein has similar activity to previously characterised soluble forms, but is dephosphorylated more rapidly than the soluble form (half- life ca 30 minutes) demonstrating that the transmembrane segment present in the full-length RegB may be an important regulator of RegB activity. -
Structure-Function Studies of Enzymes from Ribose Metabolism
Comprehensive Summaries of Uppsala Dissertations from the Faculty of Science and Technology 939 Structure-Function Studies of Enzymes from Ribose Metabolism BY C. EVALENA ANDERSSON ACTA UNIVERSITATIS UPSALIENSIS UPPSALA 2004 !"" #$"" % & % % ' ( ) * + &( , +( !""( - . - % + / % 0 ( , ( 1#1( ( ( 2-3 1. 45 ." 2 * & & * % * &( , % . * % % ( ) % / ( 0 6 / % ,)' & % % & ( )* % 6 % 6 * ( 0 6 * * % ( - % & 7 % & % & && ( ' && ,)' % /( 2 8 * ,)' & ,'.'' ( ) * % / % * 6 & & / 6 ( 0 . . . ( - * & * % %% & ( 9 * 6 / %% % ( -: % & * . & . , /( , & % * /( ) % / % & % ( ! 6 . . & / 6 % " # $ % # %& '()# %$# # *+',-. # ; ( + , !"" 2--3 ".!#!< 2-3 1. 45 ." $ $$$ .#111 = $>> (6(> ? @ $ $$$ .#111A List of Papers This thesis is based on the following papers, which are referred to in the text by their Roman numerals: I Andersson, C. E. & Mowbray, S. L. (2002). Activation of ribokinase by monovalent cations. J. Mol. Biol. 315, 409-19 II Zhang, R., Andersson, C. E., Savchenko, -
200703 Supplemental Magnani Et Al Clean Version
Supplemental Data Sleeping Beauty-engineered CAR T cells achieve anti-leukemic activity without severe toxicities Chiara F. Magnani, Giuseppe Gaipa, Federico Lussana, Daniela Belotti, Giuseppe Gritti, Sara Napolitano, Giada Matera, Benedetta Cabiati, Chiara Buracchi, Gianmaria Borleri, Grazia Fazio, Silvia Zaninelli, Sarah Tettamanti, Stefania Cesana, Valentina Colombo, Michele Quaroni, Giovanni Cazzaniga, Attilio Rovelli, Ettore Biagi, Stefania Galimberti, Andrea Calabria, Fabrizio Benedicenti, Eugenio Montini, Silvia Ferrari, Martino Introna, Adriana Balduzzi, Maria Grazia Valsecchi, Giuseppe Dastoli, Alessandro Rambaldi, Andrea Biondi Table of Contents: Supplemental Methods ...................................................................................................... 2 Supplemental Figure 1. .................................................................................................... 13 Supplemental Figure 2. .................................................................................................... 14 Supplemental Figure 3. .................................................................................................... 15 Supplemental Figure 4. .................................................................................................... 16 Supplemental Figure 5. .................................................................................................... 17 Supplemental Figure 6. .................................................................................................... 18 Supplemental -
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. -
Enzymatic and Structural Characterization of the Naegleria Fowleri Glucokinase 1 2 Jillian E. Milanes1, Jimmy Suryadi1, Jan
bioRxiv preprint doi: https://doi.org/10.1101/469072; this version posted November 14, 2018. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC-ND 4.0 International license. 1 Enzymatic and structural characterization of the Naegleria fowleri glucokinase 2 3 Jillian E. Milanes1, Jimmy Suryadi1, Jan Abendroth2, Wesley C. Van Voorhis3, Kayleigh F. 4 Barrett3, David M. Dranow2, Isabelle Q. Phan4, Stephen L. Patrick1, Soren D. Rozema5, 5 Muhammad M. Khalifa5, Jennifer E. Golden5, and James C. Morris1# 6 7 8 1Eukaryotic Pathogens Innovation Center 9 Department of Genetics and Biochemistry 10 Clemson University 11 Clemson, SC 29634 12 13 2CrystalCore 14 Beryllium Discovery 15 Bainbridge Island, WA 98110 16 17 3Center for Emerging and Re-emerging Infectious Diseases 18 Division of Allergy and Infectious Diseases, Department of Medicine 19 University of Washington 20 Seattle, WA 98109 21 22 4Seattle Structural Genomics Center for Infectious Disease 23 Center for Global Infection Disease Research 24 Seattle Children’s Research Institute 25 Seattle, WA 98109 26 27 5School of Pharmacy 28 Pharmaceutical Sciences Division 29 University of Wisconsin-Madison 30 Madison, WI 53705 31 32 33 Running title: Crystal structure of the glucokinase from the human pathogen N. fowleri 34 35 #Address correspondence to: James C. Morris, PhD, 249 LSB, 190 Collings Street, 36 Clemson SC 29634. FAX: (864) 656-0393; Email: [email protected] 1 bioRxiv preprint doi: https://doi.org/10.1101/469072; this version posted November 14, 2018.