Bold Indicates Differences in Gene Content
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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. -
Bacteria Belonging to Pseudomonas Typographi Sp. Nov. from the Bark Beetle Ips Typographus Have Genomic Potential to Aid in the Host Ecology
insects Article Bacteria Belonging to Pseudomonas typographi sp. nov. from the Bark Beetle Ips typographus Have Genomic Potential to Aid in the Host Ecology Ezequiel Peral-Aranega 1,2 , Zaki Saati-Santamaría 1,2 , Miroslav Kolaˇrik 3,4, Raúl Rivas 1,2,5 and Paula García-Fraile 1,2,4,5,* 1 Microbiology and Genetics Department, University of Salamanca, 37007 Salamanca, Spain; [email protected] (E.P.-A.); [email protected] (Z.S.-S.); [email protected] (R.R.) 2 Spanish-Portuguese Institute for Agricultural Research (CIALE), 37185 Salamanca, Spain 3 Department of Botany, Faculty of Science, Charles University, Benátská 2, 128 01 Prague, Czech Republic; [email protected] 4 Laboratory of Fungal Genetics and Metabolism, Institute of Microbiology of the Academy of Sciences of the Czech Republic, 142 20 Prague, Czech Republic 5 Associated Research Unit of Plant-Microorganism Interaction, University of Salamanca-IRNASA-CSIC, 37008 Salamanca, Spain * Correspondence: [email protected] Received: 4 July 2020; Accepted: 1 September 2020; Published: 3 September 2020 Simple Summary: European Bark Beetle (Ips typographus) is a pest that affects dead and weakened spruce trees. Under certain environmental conditions, it has massive outbreaks, resulting in attacks of healthy trees, becoming a forest pest. It has been proposed that the bark beetle’s microbiome plays a key role in the insect’s ecology, providing nutrients, inhibiting pathogens, and degrading tree defense compounds, among other probable traits. During a study of bacterial associates from I. typographus, we isolated three strains identified as Pseudomonas from different beetle life stages. In this work, we aimed to reveal the taxonomic status of these bacterial strains and to sequence and annotate their genomes to mine possible traits related to a role within the bark beetle holobiont. -
Copyright by Jeremy Daniel O'connell 2012
Copyright by Jeremy Daniel O’Connell 2012 The Dissertation Committee for Jeremy Daniel O’Connell Certifies that this is the approved version of the following dissertation: Systemic Protein Aggregation in Stress and Aging Restructures Cytoplasmic Architecture Committee: Edward Marcotte, Supervisor Dean Appling Andrew Ellington Makkuni Jayaram Scott Stevens Systemic Protein Aggregation in Stress and Aging Restructures Cytoplasmic Architecture by Jeremy Daniel O’Connell, B.S. Dissertation Presented to the Faculty of the Graduate School of The University of Texas at Austin in Partial Fulfillment of the Requirements for the Degree of Doctor of Philosophy The University of Texas at Austin September 2012 Dedication Cytisus laburnum, simul vincet omnem To my dad and mom who encouraged and enabled my education with countless sacrifices, I promised this graduation would be the one we would attend, and I am truly sorry I was not swift enough to make that possible. Acknowledgements Foremost, I thank my advisor Edward Marcotte, for not just a second lease on a life in science but one in an amazing lab environment. His intellectual rigor, enduring patience, amazing work ethic, and enthusiasm for discovery were an inspiration. I thank my collaborators in this project: Gwen Stovall, Alice Zhao, Gabe Wu, and Mark Tsechansky for their comradery and support on this great adventure. I thank the talented undergraduates: Maguerite West-Driga, Ariel Royall, and Tyler McDonald who stuck with me. Each of you will soon be a better scientist than I ever will, and I hope you enjoyed and learned from our research together nearly as much as I did. -
Compression of Large Sets of Sequence Data Reveals Fine Diversification of Functional Profiles in Multigene Families of Proteins
Technical note Compression of Large Sets of Sequence Data Reveals Fine Diversification of Functional Profiles in Multigene Families of Proteins: A Study for Peptidyl-Prolyl cis/trans Isomerases (PPIase) Andrzej Galat Retired from: Service d’Ingénierie Moléculaire des Protéines (SIMOPRO), CEA-Université Paris-Saclay, France; [email protected]; Tel.: +33-0164465072 Received: 21 December 2018; Accepted: 21 January 2019; Published: 11 February 2019 Abstract: In this technical note, we describe analyses of more than 15,000 sequences of FK506- binding proteins (FKBP) and cyclophilins, also known as peptidyl-prolyl cis/trans isomerases (PPIases). We have developed a novel way of displaying relative changes of amino acid (AA)- residues at a given sequence position by using heat-maps. This type of representation allows simultaneous estimation of conservation level in a given sequence position in the entire group of functionally-related paralogues (multigene family of proteins). We have also proposed that at least two FKBPs, namely FKBP36, encoded by the Fkbp6 gene and FKBP51, encoded by the Fkbp5 gene, can form dimers bound via a disulfide bridge in the nucleus. This type of dimer may have some crucial function in the regulation of some nuclear complexes at different stages of the cell cycle. Keywords: FKBP; cyclophilin; PPIase; heat-map; immunophilin 1 Introduction About 30 years ago, an exciting adventure began in finding some correlations between pharmacological activities of macrocyclic hydrophobic drugs, namely the cyclic peptide cyclosporine A (CsA), and two macrolides, namely FK506 and rapamycin, which have profound and clinically useful immunosuppressive effects, especially in organ transplantations and in combating some immune disorders. -
The Genome of Nanoarchaeum Equitans: Insights Into Early Archaeal Evolution and Derived Parasitism
The genome of Nanoarchaeum equitans: Insights into early archaeal evolution and derived parasitism Elizabeth Waters†‡, Michael J. Hohn§, Ivan Ahel¶, David E. Graham††, Mark D. Adams‡‡, Mary Barnstead‡‡, Karen Y. Beeson‡‡, Lisa Bibbs†, Randall Bolanos‡‡, Martin Keller†, Keith Kretz†, Xiaoying Lin‡‡, Eric Mathur†, Jingwei Ni‡‡, Mircea Podar†, Toby Richardson†, Granger G. Sutton‡‡, Melvin Simon†, Dieter So¨ ll¶§§¶¶, Karl O. Stetter†§¶¶, Jay M. Short†, and Michiel Noordewier†¶¶ †Diversa Corporation, 4955 Directors Place, San Diego, CA 92121; ‡Department of Biology, San Diego State University, 5500 Campanile Drive, San Diego, CA 92182; §Lehrstuhl fu¨r Mikrobiologie und Archaeenzentrum, Universita¨t Regensburg, Universita¨tsstrasse 31, D-93053 Regensburg, Germany; ‡‡Celera Genomics Rockville, 45 West Gude Drive, Rockville, MD 20850; Departments of ¶Molecular Biophysics and Biochemistry and §§Chemistry, Yale University, New Haven, CT 06520-8114; and ʈDepartment of Biochemistry, Virginia Polytechnic Institute and State University, Blacksburg, VA 24061 Communicated by Carl R. Woese, University of Illinois at Urbana–Champaign, Urbana, IL, August 21, 2003 (received for review July 22, 2003) The hyperthermophile Nanoarchaeum equitans is an obligate sym- (6–8). Genomic DNA was either digested with restriction en- biont growing in coculture with the crenarchaeon Ignicoccus. zymes or sheared to provide clonable fragments. Two plasmid Ribosomal protein and rRNA-based phylogenies place its branching libraries were made by subcloning randomly sheared fragments point early in the archaeal lineage, representing the new archaeal of this DNA into a high-copy number vector (Ϸ2.8 kbp library) kingdom Nanoarchaeota. The N. equitans genome (490,885 base or low-copy number vector (Ϸ6.3 kbp library). DNA sequence pairs) encodes the machinery for information processing and was obtained from both ends of plasmid inserts to create repair, but lacks genes for lipid, cofactor, amino acid, or nucleotide ‘‘mate-pairs,’’ pairs of reads from single clones that should be biosyntheses. -
Stereoselective Synthesis of a 4- -Glucoside of Valienamine and Its X
www.nature.com/scientificreports OPEN Stereoselective synthesis of a 4‑⍺‑glucoside of valienamine and its X‑ray structure in complex with Streptomyces coelicolor GlgE1‑V279S Anshupriya Si1,4, Thilina D. Jayasinghe2,4, Radhika Thanvi1, Sunayana Kapil3, Donald R. Ronning2* & Steven J. Sucheck1* Glycoside hydrolases (GH) are a large family of hydrolytic enzymes found in all domains of life. As such, they control a plethora of normal and pathogenic biological functions. Thus, understanding selective inhibition of GH enzymes at the atomic level can lead to the identifcation of new classes of therapeutics. In these studies, we identifed a 4‑⍺‑glucoside of valienamine (8) as an inhibitor of Streptomyces coelicolor (Sco) GlgE1‑V279S which belongs to the GH13 Carbohydrate Active EnZyme family. The results obtained from the dose–response experiments show that 8 at a concentration of 1000 µM reduced the enzyme activity of Sco GlgE1‑V279S by 65%. The synthetic route to 8 and a closely related 4‑⍺‑glucoside of validamine (7) was achieved starting from readily available D‑maltose. A key step in the synthesis was a chelation‑controlled addition of vinylmagnesium bromide to a maltose‑derived enone intermediate. X‑ray structures of both 7 and 8 in complex with Sco GlgE1‑ V279S were solved to resolutions of 1.75 and 1.83 Å, respectively. Structural analysis revealed the valienamine derivative 8 binds the enzyme in an E2 conformation for the cyclohexene fragment. Also, the cyclohexene fragment shows a new hydrogen‑bonding contact from the pseudo‑diaxial C(3)–OH to the catalytic nucleophile Asp 394 at the enzyme active site. -
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. -
Small Regulatory Rnas Controlling Complex Phenotypes in Vibrio Cholerae
Small regulatory RNAs controlling complex phenotypes in Vibrio cholerae Dissertation Zur Erlangung des Doktorgrades der Naturwissenschaften (Dr. rer. nat.) der Fakultät für Biologie der Ludwig-Maximilians-Universität München vorgelegt von Roman Herzog aus Augsburg München, Juli 2020 Diese Dissertation wurde angefertigt unter der Leitung von Prof. Dr. Kai Papenfort im Bereich von Department Biologie I an der Ludwig-Maximilians-Universität München Gutachter: 1. Prof. Dr. Kai Papenfort 2. Prof. Dr. Heinrich Jung Datum der Abgabe: 21.07.2020 Tag der mündlichen Prüfung: 15.12.2020 II Eidesstattliche Erklärung Ich versichere hiermit an Eides statt, dass die vorgelegte Dissertation von mir selbstständig und ohne unerlaubte Hilfe angefertigt wurde. Des Weiteren erkläre ich, dass ich nicht anderweitig ohne Erfolg versucht habe, eine Dissertation einzureichen oder mich der Doktorprüfung zu unterziehen. Die folgende Dissertation liegt weder ganz, noch in wesentlichen Teilen einer anderen Prüfungskommission vor. Roman Herzog, München, den 20. Juli 2020 Statutory Declaration I declare that I have authored this thesis independently, that I have not used other than the declared sources/resources. As well I declare, that I have not submitted a dissertation without success and not passed the oral exam. The present dissertation (neither the entire dissertation nor parts) has not been presented to another examination board. Roman Herzog, Munich, 20 July 2020 III Contents Eidesstattliche Erklärung ........................................................................................................III -
Characterization of Nudix Hydrolases: a Utilitarian
CHARACTERIZATION OF NUDIX HYDROLASES: A UTILITARIAN SUPERFAMILY OF ENZYMES By Andres Hernandez de la Peña A dissertation submitted to the Johns Hopkins University in conformity with the requirements for the degree of Doctor of Philosophy Baltimore, Maryland August, 2015 Abstract The present work details the structural and enzymatic characterization of Nudix hydrolases from three different organisms – Bdellovibrio bacteriovorus, Mycobacterium tuberculosis, and Tetrahymena thermophila. Each of these Nudix enzymes presents unique questions about their physiological function within their organism which are answered with a combination of structural biology, genetic manipulation, enzyme kinetics, and a wide range of protein assays. We demonstrate that RenU, from M. tuberculosis, is part of Redox Homeostasis Control System (RHOCS), which senses and regulates NADH concentrations. This control systems involves two other proteins, the serine/threonine protein kinase G (pknG) and the L13 ribosomal subunits, without which the bacterium fails to evade lysosomal delivery and falls prey to the oxidative arsenal of the macrophage host. Bd-NDPSase, a Nudix enzyme encoded by the B. bacteriovorus gene BD3179, localizes to the periplasmic space of the bacterium and hydrolyses at least four nucleoside diphosphate sugars in vitro. Through atomic-resolution models from X-ray diffraction, we identified a motif that differentiates this hydrolase from the similar, but more substrate specific, ADP- ribose hydrolase from E. coli. Lastly, we show that Nud1p from T. thermophila is a member of the Ezl1p complex, the histone methyltransferase Polycomb Group homologue of this protozoan. With the use of in vitro enzymatic assays we show, in addition, that Nu1dp hydrolyses CoA preferentially over acetyl-CoA and other nucleoside derivatives. -
Synthesis and Application of Light-Switchable Arylazopyrazole Rapamycin Analogs
Organic & Biomolecular Chemistry Synthesis and Application of Light-Switchable Arylazopyrazole Rapamycin Analogs Journal: Organic & Biomolecular Chemistry Manuscript ID OB-COM-08-2019-001719.R1 Article Type: Communication Date Submitted by the 25-Aug-2019 Author: Complete List of Authors: Courtney, Taylor; University of Pittsburgh, Chemistry Horst, Trevor; University of Pittsburgh, Chemistry Hankinson, Chasity; University of Pittsburgh, Chemistry Deiters, Alexander; University of Pittsburgh, Chemistry Page 1 of 11 Organic & Biomolecular Chemistry Synthesis and Application of Light-Switchable Arylazopyrazole Rapamycin Analogs Taylor M. Courtney, Trevor J. Horst, Chasity P. Hankinson, and Alexander Deiters* Department of Chemistry, University of Pittsburgh, Pittsburgh, PA 15260, United States [email protected] Abstract: Rapamycin-induced dimerization of FKBP and FRB has been utilized as a tool for co-localizing two proteins of interest in numerous applications. Due to the tight binding interaction of rapamycin with FKBP and FRB, the ternary complex formation is essentially irreversible. Since biological processes occur in a highly dynamic fashion with cycles of protein association and dissociation to generate a cellular response, it is useful to have chemical tools that function in a similar manner. We have developed arylazopyrazole-modified rapamycin analogs which undergo a configurational change upon light exposure and we observed enhanced ternary complex formation for the cis-isomer over the trans-isomer for one of the analogs. Introduction: Chemical inducers of dimerization (CIDs) are prominent tools used by chemical biologists to place biological processes under conditional control.1-4 The most commonly utilized CID is rapamycin, a natural product that binds to FK506 binding protein (FKBP) with a 0.2 nM Kd. -
Roles of Amino Acids in the <Italic>Escherichia Coli</Italic
Article pubs.acs.org/biochemistry Roles of Amino Acids in the Escherichia coli Octaprenyl Diphosphate Synthase Active Site Probed by Structure-Guided Site-Directed Mutagenesis † ∥ † ‡ § † ‡ Keng-Ming Chang, Shih-Hsun Chen, Chih-Jung Kuo, , Chi-Kang Chang, Rey-Ting Guo, , ∥ † ‡ § Jinn-Moon Yang, and Po-Huang Liang*, , , † Institute of Biochemical Sciences, National Taiwan University, Taipei 106, Taiwan ‡ Taiwan International Graduate Program, Academia Sinica, Taipei 115, Taiwan § Institute of Biological Chemistry, Academia Sinica, Taipei 115, Taiwan ∥ Department of Biological Science and Technology, National Chiao Tung University, Hsin-Chu 300, Taiwan *S Supporting Information ABSTRACT: Octaprenyl diphosphate synthase (OPPS) catalyzes consecutive condensation reactions of farnesyl diphosphate (FPP) with five molecules of isopentenyl diphosphates (IPP) to generate C40 octaprenyl diphosphate, which constitutes the side chain of ubiquinone or menaquinone. To understand the roles of active site amino acids in substrate binding and catalysis, we conducted site- directed mutagenesis studies with Escherichia coli OPPS. In conclusion, D85 is the most important residue in the first DDXXD motif for both FPP and IPP binding through an H-bond network involving R93 and R94, respectively, whereas R94, K45, R48, and H77 are responsible for IPP binding by providing H-bonds and ionic interactions. K170 and T171 may stabilize the farnesyl carbocation intermediate to facilitate the reaction, whereas R93 and K225 may stabilize the catalytic base (MgPPi) for HR proton abstraction after IPP condensation. K225 and K235 in a flexible loop may interact with FPP when the enzyme becomes a closed conformation, which is therefore crucial for catalysis. Q208 is near the hydrophobic part of IPP and is important for IPP binding and catalysis. -
Abstracts from the 10Th World Congress for Microcirculation
DOI:10.1111/micc.12246 Abstracts Abstracts from the 10th World Congress for Microcirculation September 25th – 27th, 2015 Kyoto, Japan PLENARY LECTURES vascular neutrophils that constantly patrol the lung and can detect and phagocytose bacteria attached to endothelium suggesting some communication inter-cellular communica- PL1 tion. Clearly much anti-microbial activity occurs in the Imaging the microcirculation in infections vasculature prior to dissemination of bacteria into tissues. P Kubes University of Calgary, Calgary, Canada PL2 Using spinning disk microscopy has allowed us to track pathogens and immune cells in the microcirculation. Mapping oxygen in the brain of awake resting Observing the liver microvasculature revealed numerous mice immune speed bumps that slowed, delayed and even S Charpak prevented bacteria from disseminating to other organs. For Laboratory of Neurophysiology and New Microscopies, Inserm U1128, example, when Borrelia burgdorferi enters the vasculature Paris Descartes University, Paris, France they are immediately caught by the liver vascular macro- The brain is extremely sensitive to hypoxia. Yet, the phage, the Kupffer cells and are engulfed and antigens are physiological values of oxygen concentration in the brain presented on CD1d to resident vascular immune cells remain elusive because high resolution measurements have including invariant Natural Killer T cells (iNKT cells). These only been performed during anesthesia, which affects two iNKT cells receive messages and rapidly make gamma main parameters modulating tissue oxygenation, i.e. interferon to help with immunity. Absence of these events neuronal activity and cerebral blood flow. Using the recent leads to massive dissemination of borrelia especially to joints. finding that measurements of capillary erythrocyte-associ- In the joints the iNKT cells live closely apposed but outside ated transients i.e.