Complete Dissertation
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Strategies for Cryo-Electron Tomography of the Mycobacterial Cell Envelope and Its Pore Proteins and Functional Studies of Porin Mspa from Mycobacterium Smegmatis
Technische Universität München Max-Planck-Institut für Biochemie Abteilung für Molekulare Strukturbiologie Strategies for cryo-electron tomography of the mycobacterial cell envelope and its pore proteins and functional studies of porin MspA from Mycobacterium smegmatis Christian Werner Hoffmann Vollständiger Abdruck der von der Fakultät für Chemie der Technischen Universität München zur Erlangung des akademischen Grades eines Doktors der Naturwissenschaften genehmigten Dissertation. Vorsitzender: Univ. – Prof. Dr. J. Buchner Prüfer der Dissertation: 1. Hon. – Prof. Dr. W. Baumeister 2. Univ. – Prof. Dr. S. Weinkauf 3. Univ. – Prof. Dr. W. Liebl Die Dissertation wurde am 28.04.2010 bei der Technischen Universität München eingereicht und durch die Fakultät für Chemie am 14.07.2010 angenommen. TABLE OF CONTENTS A Table of contents A Table of contents .................................................................................................................... I B Abbreviations ........................................................................................................................ V C Zusammenfassung............................................................................................................ VIII D Summary ................................................................................................................................ X 1 Introduction ........................................................................................................................... 1 1.1 The genus Mycobacterium ............................................................................................. -
Expression and Regulation of the Porin Gene Mspa of Mycobacterium Smegmatis
Expression and regulation of the porin gene mspA of Mycobacterium smegmatis Den Naturwissenschaftlichen Fakultäten der Friedrich-Alexander-Universität Erlangen-Nürnberg zur Erlangung des Doktorgrades vorgelegt von Dietmar Hillmann aus Nürnberg Als Dissertation genehmigt von den Naturwissenschaftlichen Fakultäten der Universität Erlangen-Nürnberg Tag der mündlichen Prüfung: 15.12.2006 Vorsitzender der Promotionskommission: Prof. Dr. E. Bänsch Erstberichterstatter: Prof. Dr. M. Niederweis Zweitberichterstatter: Prof. Dr. A. Burkovski Index Index 1 Zusammenfassung / Summary 1 2 Introduction 2 2.1 The genus Mycobacterium 2 2.1.1 Taxonomy 2 2.1.2 The architecture of the mycobacterial cell wall 3 2.2 Porins: Structure and function in gram-negative bacteria 5 2.3 Mycobacterial porins 7 2.4 Porin regulation 10 2.5 Expression of mspA of M. smegmatis 12 2.6 Scope of the thesis 13 3 Results 14 3.1 Screening system to monitor mycobacterial promoter activity 14 3.2 Transcriptional mechanisms affecting mspA expression 18 3.2.1 Identification of the mspA promoter 18 3.2.2 A very long upstream DNA element is required for full activity of pmspA 22 3.2.3 Influence of translation initiation signals of pmspA on lacZ expression 24 3.2.4 Influence of a distal DNA element on pmspA activation 25 3.2.5 Alignment of the 5’ regions of mspA, mspB, mspC and mspD 27 3.3 Post-transcriptional mechanisms affecting mspA expression 28 3.3.1 Detection of an antisense RNA to the mspA transcript 28 3.3.2 Secondary structure of the 5’ UTR of mspA 31 3.4 pH dependent mspA expression -
Structure of the Mycobacterium Tuberculosis Ompatb Protein: a Model of an Oligomeric Channel in the Mycobacterial Cell Wall
proteins STRUCTURE O FUNCTION O BIOINFORMATICS Structure of the Mycobacterium tuberculosis OmpATb protein: A model of an oligomeric channel in the mycobacterial cell wall Yinshan Yang,1,2 Daniel Auguin,1,2,3 Ste´phane Delbecq,4 Emilie Dumas,1,2 Ge´rard Molle,1,2 Virginie Molle,5 Christian Roumestand,1,2* and Nathalie Saint1,2 1 Centre de Biochimie Structurale, CNRS UMR 5048, Universite´ Montpellier 1 et 2, F34090 Montpellier, France 2 INSERM U554 F34090 Montpellier, France 3 INRA, USC2030 ‘Arbres et Re´ponses aux Contraintes Hydrique et Environnementales’ (ARCHE), F-45067 Orle´ans Cedex 02, France 4 Dynamique des Interactions Membranaires Normales et Pathologiques, CNRS UMR 5235, Universite´ Montpellier 2, F34095 Montpellier Cedex 5, France 5 Institut de Biologie et de Chimie des Prote´ines, Universite´ de Lyon, CNRS UMR 5086, F69367 Lyon, France ABSTRACT INTRODUCTION The pore-forming outer membrane protein The etiological agent of tuberculosis (TB), Mycobacterium OmpATb from Mycobacterium tuberculosis is a viru- tuberculosis, causing nearly 2 million deaths per year, is presently lence factor required for acid resistance in host one of the most important infectious agents implicated in mortal- phagosomes. In this study, we determined the 3D ity worldwide. TB has emerged as a major public health threat structure of OmpATb by NMR in solution. We because of a significant increase in multiple-drug-resistant TB and found that OmpATb is composed of two independ- synergism between human immunodeficiency virus and M. tuber- ent domains separated by a proline-rich hinge culosis infection.1,2 One of the principle problems in TB therapy region. -
Microbial Musings – December 2020
EDITORIAL Thomas, Microbiology 2020;166:1107–1109 DOI 10.1099/mic.0.001019 OPEN ACCESS Microbial Musings – December 2020 Gavin H. Thomas* As we end this extraordinary year, the importance of micro- resistance (AMR)’ to our ‘Antimicrobials and AMR’ theme. biology continues to be demonstrated in our daily lives in Next month I will be announcing a significant number of new ways that we would never have predicted 12 months ago. This editors to handle submissions within our revised topic areas. month in the UK, the identification of a new variant of severe The first paper from this issue to highlight is one that would acute respiratory syndrome coronavirus 2 (SARS- CoV-2) fit nicely into the new Plant microbiology and soil health through the continuing work of the COVID-19 Genomics topic, as it is around the biology of two Bacillus species strains Consortium (@CovidGenomicsUK) led to an almost imme- that are currently used as biocontrol agents in China, and diate change in government policy, and while the manifesta- more specifically are used to protect oil seed rape crop from tions of the new variant are being uncovered, it is an example a pathogenic fungal infections. The work from Alex Mullins of evolution occurring in real time in front of the eyes of the (@AlexJMullins), collaborating with Eshwar Mahenthiral- general public. The development and delivery of multiple new ingam and Gordon Webster at the University of Cardiff, UK, vaccines against the virus are a true illustration that biology and colleagues at the Oil Crops Research Institute of Chinese has the potential to be the greatest technology of the 21st Academy of Agricultural Sciences, Wuhan, PR China, aimed century. -
Dr. Annika Guse [email protected]
Curriculum Vitae Annika Guse Dr. Annika Guse [email protected] Education & Training 2008 – 2012 Postdoctoral Fellow Stanford University, USA Biochemistry 2006 – 2007 Postdoctoral Fellow Technical University of Braunschweig, Germany Biotechnology 2002 – 2005 Ph.D. University of Vienna, Austria Molecular Biology graduated with distinction 1996 – 2001 B.Sc. / M.Sc. (Diplom) Technical University of Braunschweig, Germany Genetics, Cell Biology, Botany Research Experience 01/2013 – Emmy-Noether-Junior-Groupleader, University of Heidelberg, Centre for Organismal Studies (COS), Department of Molecular Evolution and Genomics, Germany Cellular basis of cnidarian symbiosis 09/2008 – 09/2012 Postdoctoral Fellow, Stanford University, Department of Biochemistry, USA Assembly mechanism of centromeres and kinetochores in higher eukaryotes Mentor: Prof. Dr. Aaron Straight 08/2006 – 08/2007 Postdoctoral Fellow, Technische Universität Braunschweig, Department of Biotechnolgy, Germany Functional knockdown of proteins at posttranslational levels with ER retained antibodies Mentor: Prof. Dr. Stefan Dübel 04/2002 – 06/2005 Ph.D., Research Institute of Molecular Pathology (IMP), Vienna, Austria AuroraB regulation of cytokinesis by phosphorylation of MKLP1 Supervisor: Prof. Dr. Michael Glotzer 2002 Research Assistant (2 months), John Innes Centre, Norwich, UK Molybdenum-cofactor-biosynthesis in E. coli Supervisor: Prof. Dr. Tracy Palmer 2001 Diploma Thesis, Technische Universität Braunschweig, Germany and John Innes Centre, Norwich, UK Thesis title: “The final step of molybdenum-cofactor-biosynthesis in E. coli: characterization of the MobA protein“ Supervisor Prof. Dr. Ralf-R. Mendel and Prof. Dr. Tracy Palmer 2000 Visiting student (5 months), John Innes Centre, Norwich, UK Supervisor: Prof. Dr. Tracy Palmer 1999 Visiting student (3 months), University of Cordoba, Spain Supervisor: Prof. Dr. -
The Tata Component of the Twin-Arginine Protein Transport System Forms Channel Complexes of Variable Diameter
The TatA component of the twin-arginine protein transport system forms channel complexes of variable diameter Ulrich Gohlke*†, Lee Pullan*‡, Christopher A. McDevitt§, Ida Porcelli§, Erik de Leeuw§, Tracy Palmer¶ʈ, Helen R. Saibil*, and Ben C. Berks§ *Institute of Structural Molecular Biology, School of Crystallography, Birkbeck College, Malet Street, London WC1E 7HX, United Kingdom; §Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, United Kingdom; ¶School of Biological Sciences, University of East Anglia, Norwich NR4 7TJ, United Kingdom; and ʈDepartment of Molecular Microbiology, John Innes Centre, Norwich NR4 7UH, United Kingdom Edited by William T. Wickner, Dartmouth Medical School, Hanover, NH, and approved June 8, 2005 (received for review April 29, 2005) The Tat system mediates Sec-independent transport of folded diameter (15, 17). TatBC has been shown to act as the receptor precursor proteins across the bacterial plasma membrane or the element of the translocation pathway (13, 16, 18), and TatC has chloroplast thylakoid membrane. Tat transport involves distinct been shown to contain the primary binding site for the signal high-molecular-weight TatA and TatBC complexes. Here we report peptide (18). The function of TatA is less clear. It is known that the 3D architecture of the TatA complex from Escherichia coli TatA is required subsequent to substrate recognition by the obtained by single-particle electron microscopy and random con- TatBC complex (16, 18, 19), and this has led to the suggestion ical tilt reconstruction. TatA forms ring-shaped structures of vari- that TatA constitutes the protein-conducting channel of the Tat able diameter in which the internal channels are large enough to system. -
BIOLOGY 639 SCIENCE ONLINE the Unexpected Brains Behind Blood Vessel Growth 641 THIS WEEK in SCIENCE 668 U.K
4 February 2005 Vol. 307 No. 5710 Pages 629–796 $10 07%.'+%#%+& 2416'+0(70%6+10 37#06+6#6+8' 51(69#4' #/2.+(+%#6+10 %'..$+1.1); %.10+0) /+%41#44#;5 #0#.;5+5 #0#.;5+5 2%4 51.76+105 Finish first with a superior species. 50% faster real-time results with FullVelocity™ QPCR Kits! Our FullVelocity™ master mixes use a novel enzyme species to deliver Superior Performance vs. Taq -Based Reagents FullVelocity™ Taq -Based real-time results faster than conventional reagents. With a simple change Reagent Kits Reagent Kits Enzyme species High-speed Thermus to the thermal profile on your existing real-time PCR system, the archaeal Fast time to results FullVelocity technology provides you high-speed amplification without Enzyme thermostability dUTP incorporation requiring any special equipment or re-optimization. SYBR® Green tolerance Price per reaction $$$ • Fast, economical • Efficient, specific and • Probe and SYBR® results sensitive Green chemistries Need More Information? Give Us A Call: Ask Us About These Great Products: Stratagene USA and Canada Stratagene Europe FullVelocity™ QPCR Master Mix* 600561 Order: (800) 424-5444 x3 Order: 00800-7000-7000 FullVelocity™ QRT-PCR Master Mix* 600562 Technical Services: (800) 894-1304 Technical Services: 00800-7400-7400 FullVelocity™ SYBR® Green QPCR Master Mix 600581 FullVelocity™ SYBR® Green QRT-PCR Master Mix 600582 Stratagene Japan K.K. *U.S. Patent Nos. 6,528,254, 6,548,250, and patents pending. Order: 03-5159-2060 Purchase of these products is accompanied by a license to use them in the Polymerase Chain Reaction (PCR) Technical Services: 03-5159-2070 process in conjunction with a thermal cycler whose use in the automated performance of the PCR process is YYYUVTCVCIGPGEQO covered by the up-front license fee, either by payment to Applied Biosystems or as purchased, i.e., an authorized thermal cycler. -
Extreme Genetic Diversity in the Type VII Secretion System of Listeria Monocytogenes Suggests a Role in Bacterial Antagonism
RESEARCH ARTICLE Bowran and Palmer, Microbiology DOI 10.1099/mic.0.001034 OPEN ACCESS Extreme genetic diversity in the type VII secretion system of Listeria monocytogenes suggests a role in bacterial antagonism Kieran Bowran and Tracy Palmer* Abstract The type VII protein secretion system (T7SS) has been characterized in members of the phyla Actinobacteria and Firmicutes. In mycobacteria the T7SS is intimately linked with pathogenesis and intracellular survival, while in Firmicutes there is mounting evi- dence that the system plays a key role in interbacterial competition. A conserved membrane- bound ATPase protein, termed EssC in Staphylococcus aureus, is a critical component of the T7SS and is the primary receptor for substrate proteins. Genetic diversity in the essC gene of S. aureus has previously been reported, resulting in four protein variants that are linked to specific subsets of substrates. Here we have analysed the genetic diversity of the T7SS-encoding genes and substrate proteins across Listeria mono- cytogenes genome sequences. We find that there are seven EssC variants across the species that differ in their C- terminal region; each variant is correlated with a distinct subset of genes for likely substrate and accessory proteins. EssC1 is most common and is exclusively linked with polymorphic toxins harbouring a YeeF domain, whereas EssC5, EssC6 and EssC7 variants all code for an LXG domain protein adjacent to essC. Some essC1 variant strains encode an additional, truncated essC at their T7 gene cluster. The truncated EssC, comprising only the C- terminal half of the protein, matches the sequence of either EssC2, EssC3 or EssC4. In each case the truncated gene directly precedes a cluster of substrate/accessory protein genes acquired from the corresponding strain. -
COMPARISON of FUNCTIONAL and STRUCTURAL PROPERTIES of an OUTER MEMBRANE PORIN BETWEEN Burkholderia Pseudomallei and Burkholderia
COMPARISON OF FUNCTIONAL AND STRUCTURAL PROPERTIES OF AN OUTER MEMBRANE PORIN BETWEEN Burkholderia pseudomallei AND Burkholderia thailandensis Miss Jaruwan Siritapetawee A Thesis Submitted in Partial Fulfillment of the Requirements for the Degree of Doctor of Philosophy in Biochemistry Suranaree University of Technology Academic Year 2004 ISBN 974-533-325-5 การเปรียบเทียบสมบัติเชิงหนาที่และเชิงโครงสรางของโปรตีนพอรินใน ผนังเซลลผิวนอกระหวางเชื้อ Burkholderia pseudomallei และ Burkholderia thailandensis นางสาวจารุวรรณ ศิริเทพทว ี วิทยานิพนธนี้เปนสวนหนึ่งของการศึกษาตามหลักสูตรปริญญาวิทยาศาสตรดุษฎีบัณฑิต สาขาวิชาชีวเคม ี มหาวิทยาลัยเทคโนโลยีสุรนาร ี ปการศึกษา 2547 ISBN 974-533-325-5 Acknowledgements I would like to express my sincere thank to my thesis advisor, Dr. Wipa Suginta for providing guidance, support, considerable and kind help. I am deeply grateful to my co-advisor, Dr. Richard, H. Ashley, Department of Biomedical Sciences, University of Edinburgh, UK, who gave me the useful guidance, valuable advice and provided the bacterium, Burkholderia thailandensis type strain ATCC700388. I would like to thank PD. Dr. Heino Prinz, Max Planck Institute for Molecular Physiology, Dortmund, Germany who helped with MALDI-TOF MS and ESI MS and peptide mass analysis, and Prof. Dieter Naumann, Robert-Koch Institute, Berlin, Germany with FTIR measurements. I also appreciate Miss Worada Samosornsuk, Faculty of Allied Health Science, Thammasat University, Thailand, for providing essential facilities for Burkholderia pseudomallei culture and drug susceptibility tests, and Dr. Chartchai Krittanai, Institute of Molecular Biology and Genetics, Mahidol University, Thailand, who kindly provided the CD spectropolarimeter for secondary structure determination. I would like to thank Shell studentship grant and Suranaree University of Technology grant for financial support throughout the project. Special thanks are extended to all friends, scientist and technician in the School of Biochemistry for their kind help and made me happy to work. -
BMC Bioinformatics Biomed Central
BMC Bioinformatics BioMed Central Software Open Access TMB-Hunt: An amino acid composition based method to screen proteomes for beta-barrel transmembrane proteins Andrew G Garrow, Alison Agnew and David R Westhead* Address: School of Biochemistry and Microbiology, University of Leeds, Leeds, LS2 9JT, UK Email: Andrew G Garrow - [email protected]; Alison Agnew - [email protected]; David R Westhead* - [email protected] * Corresponding author Published: 15 March 2005 Received: 01 November 2004 Accepted: 15 March 2005 BMC Bioinformatics 2005, 6:56 doi:10.1186/1471-2105-6-56 This article is available from: http://www.biomedcentral.com/1471-2105/6/56 © 2005 Garrow et al; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. Abstract Background: Beta-barrel transmembrane (bbtm) proteins are a functionally important and diverse group of proteins expressed in the outer membranes of bacteria (both gram negative and acid fast gram positive), mitochondria and chloroplasts. Despite recent publications describing reasonable levels of accuracy for discriminating between bbtm proteins and other proteins, screening of entire genomes remains troublesome as these molecules only constitute a small fraction of the sequences screened. Therefore, novel methods are still required capable of detecting new families of bbtm protein in diverse genomes. Results: We present TMB-Hunt, a program that uses a k-Nearest Neighbour (k-NN) algorithm to discriminate between bbtm and non-bbtm proteins on the basis of their amino acid composition. -
New Approaches and Concepts in Microbiology
New Approaches and Concepts in Microbiology EMBO | EMBL Symposium 10 – 13 July 2019 Heidelberg | Germany EMBL Advanced Training Centre ABSTRACT SUBMISSION DEADLINE 14 April 2019 SPEAKERS REGISTRATION DEADLINE David Bikard Mark Goulian Lalita Ramakrishnan Institut Pasteur, France University of University of Cambridge, 28 May 2019 Sebastian Bonhoeffer Pennsylvania, USA UK ETH Zürich, Switzerland Regine Hengge Uwe Sauer ORGANISERS Carmen Buchrieser Humboldt-Universität zu ETH Zürich, Switzerland Institut Pasteur, France Berlin, Germany Morten Otto Alexander Pascale Cossart Institut Pasteur, France Matt Cooper Kirsten Jung Sommer The University of Ludwig-Maximilians- Technical University of KC Huang Queensland, Australia Universität München, Denmark, Denmark Stanford University, USA Germany Ivan Dikic Natalie Strydanka Michael Laub University of Frankfurt, Dan Kahne University of British Massachusetts Institute of Technology, Germany Harvard University, USA Columbia, Canada USA Eran Elinav Roy Kishony Jan-Willem Veening Nassos Typas Weizmann Institute of Technion – Israel Institute University of Lausanne, EMBL Heidelberg, Germany Science, Israel of Technology, Israel Switzerland Tobias Erb Joseph Mougous Jörg Vogel Max Planck Institute for University of Washington, Helmholtz Institute for Terrestrial Microbiology, USA RNA-based Infection Germany Dianne Newman Research, Germany Kevin Foster California Institute of Matthew Waldor University of Oxford, UK Technology, USA Brigham and Women’s Hospital, USA Mariana Gomes de Tracy Palmer Pinho Newcastle University, UK Jade Wang Instituto de Tecnologia Eric Pamer University of Wisconsin- Química e Biológica, Memorial Sloan Kettering Madison, USA Portugal Cancer Center, USA Additional speakers will be selected from abstracts. #EESMicrobiology www.embo-embl-symposia.org CONTACT [email protected]. -
Actividad Formadora De Canales Transmembrana En La Superficie De Gordonia Jacobaea
Actividad formadora de canales transm embrana en la superficie de Gordonia jacobaea Mª Guadalupe Jiménez Galisteo ADVERTIMENT . La consulta d’aquesta tesi queda condicionada a l’acceptació de les següents condicions d'ús: La difusió d’aquesta tesi per mitjà del servei TDX ( www.tdx.cat ) i a través del Dipòsit Digital de la UB ( diposit.ub.edu ) ha estat autoritzada pels titulars dels drets de propietat intel·lectual únicament per a usos privats emmarcats en activitats d’investigació i docència. No s’autoritza la seva reproducció amb finalitats de lucre ni la seva difusió i posada a disposici ó des d’un lloc aliè al servei TDX ni al Dipòsit Digital de la UB . No s’autoritza la presentació del seu contingut en un a finestra o marc aliè a TDX o al Dipòsit Digital de la UB (framing). Aquesta reserva de drets afecta tant al resum de presentació de la tesi com als seus continguts. En la utilització o cita de parts de la tesi és obligat indicar el nom de la persona auto ra. ADVERTENCIA . La consulta de esta tesis queda condicionada a la aceptación de las siguientes condiciones de uso: La difusión de esta tesis por medio del servicio TDR ( www.tdx.cat ) y a través del Repositorio Digital de la UB ( diposit.ub.edu ) ha sido au torizada por los titulares de los derechos de propiedad intelectual únicamente para usos privados enmarcados en actividades de investigación y docencia. No se autoriza su reproducción con finalidades de lucro ni su difusión y puesta a disposición desde un sitio ajeno al servicio TDR o al Repositorio Digital de la UB .