DOCSLIB.ORG

Information to Users

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text

Load more

INFORMATION TO USERS This manuscript has been reproduced from the microfilm master. UMI films the text directly from the original or copy submitted. Thus, some thesis and dissertation copies are in typewriter face, while others may be from any type of computer printer. The quality of this reproduction is dependent upon the quality of the copy submitted. Broken or indistinct print, colored or poor quality illustrations and photographs, print bleedthrough, substandard margins, and improper alignment can adversely affect reproduction. In the unlikely event that the author did not send UMI a complete manuscript and there are missing pages, these will be noted. Also, if unauthorized copyright material had to be removed, a note will indicate the deletion. Oversize materials (e.g., maps, drawings, charts) are reproduced by sectioning the original, beginning at the upper left-hand comer and continuing from left to right in equal sections with small overlaps. Each original is also photographed in one exposure and is included in reduced form at the back of the book. Photographs included in the original manuscript have been reproduced xerographically in this copy. Higher quality 6” x 9” black and white photographic prints are available for any photographs or illustrations appearing in this copy for an additional charge. Contact UMI directly to order. UMI A Bell & Howell Information Company 300 North Zeeb Road, Ann Arbor MI 48106-1346 USA 313/761-4700 800/521-0600 CHARACTERIZATION OF THE PSEUDOMONAS AERUGINOSA PILT GENE WHICH IS REQUIRED FOR TWITCHING MOTILITY AND PILUS FUNCTION DISSERTATION Presented in Partial Fulfillment of the Requirements for the Degree Doctor of Philosophy in the Graduate School of The Ohio State University By Patricia Lynn Antalis, B. S. * * * * * The Ohio State University 1996 Dissertation Committee: Approved by Kathleen E. Kendrick, Adviser Aldis Darzins Neil R. Baker Adviser Charles J. Daniels Department of Microbiology UMI Number: 9630843 UMI Microform 9630843 Copyright 1996, by UMI Company. All rights reserved. This microform edition is protected against unauthorized copying under Title 17, United States Code. UMI 300 North Zeeb Road Ann Arbor, MI 48103 DEDICATION To my husband, and best friend, George ACKNOWLEDGMENTS I would like to express my appreciation to each of my committee members for their guidance, especially my advisers Dr. Aldis Darzins and Dr. Kathleen Kendrick. Thanks also go to Lynn O'Donnell and Mary Russell for their camaraderie, advice and wit. I am indebted to family for their continual support, especially my sister and brother-in-law for their generosity and humor during this last year. I am most grateful to my husband for his patience and for his reminding me of what is truly important. VITA November 12,1966 ......................Bom - Wheeling, West Virginia 1989............................................. B. S. in Biology, The Ohio State University, Columbus, Ohio 1987 ............................................... Research Assistant, Department of Zoology, The Ohio State University 1987 -1989...................................Research Assistant, Department of Entomology, The Ohio State University 1989 - present...............................Graduate Teaching Associate, Department of Microbiology, The Ohio State University FIELDS OF STUDY Major Field: Microbiology Studies in Bacterial Gene Regulation Dr. K. E. Kendrick and Dr. A. Darzins, Advisers TABLE OF CONTENTS DEDICATION.................................................................. ACKNOWLEDGMENTS................................................. VITA................................................................................ TABLE OF CONTENTS................................................. LIST OF FIGURES........................................................... LIST OF TABLES............................................................ LIST OF ABBREVIATIONS............................................ CHAPTER I: Introduction ........................................... Role of Pseudomonas aeruginosa pili in adherence Structure of P. aeruginosa pilin............................. P. aeruginosa pilus biogenesis .............................. Occurrence of type IV pili in other bacteria .......... Pilus retraction ..................................................... Twitching motility Goals of this project................................................................................. 39 CHAPTER II: Materials and Methods........................................................... 40 Media and culture conditions .................................................................. 40 Bacterial strains, plasmids, and bacteriophages......................................41 Phage sensitivity and twitching motility assays................................... 46 Electron microscopy techniques ....................................................... 47 Mapping of the HOD1 phage-resistance m utation................................. 48 LDgo studies ................................................................................................ 48 Standard DNA isolation and manipulation techniques ........................... 49 Transfer of plasmid DNA intoPseudomonas ......................................... 52 Generation of nested deletions for DNA sequence analysis .................... 54 DNA hybridization methods .................................................................... 55 Standard methods for protein analysis..................................................... 58 Overexpression ofpilT in E.coli and Pseudomonas using T7 promoter-based systems.............................................................60 RNA isolation and manipulation ............................................................. 61 PCR conditions for generation of SI nuclease probes ..............................66 Enzyme assays ......................................................................................... 67 Generation of random mutations in p ilT.................................................. 69 CHAPTER III: pilT is Required for Phage Sensitivity and Twitching Motility in P. aeruginosa P A O l................................................. 71 Introduction ............................................................................................ 71 vi R esults ........................................................................................................73 Isolation of phage-resistant mutants of PAOl defective in pilus biogenesis ................................................................73 Complementation of the hyperpiliated m utants......................76 Conjugations! mapping of the HOD1 phage-resistance locus ..................................................................................... 80 Overexpression ofpilT in E.coli and Pseudomonas using T7 promoter-based system s ...............................................82 Nucleotide sequence of the pilT open reading frame............... 90 Disruption of pilT in PA O l......................................................... 90 Characterization of the mutated pilT allele from HOD1 95 Generation of pilT mutants by using random mutagenesis . 99 Virulence of HOD1 in a mouse infection model ...................... 104 Discussion ............................................................................................... 107 CHAPTER IV: Construction and Analysis of pilU and pilT pilU Mutants in P. aeruginosa P A O l ........................................................... 130 Introduction ................................................................................................130 R esults ..................................................................................................... 132 Introduction of pilU into the pilT mutant HOD1 ................ 132 Construction and complementation analysis of a pilU mutant ........................................................................ 133 Construction and complementation analysis of a pUTpilU double m u ta n t ................................................... 140 Discussion................................................................................................ 145 CHAPTER V: Expression ofpilT is Differentially Regulated at the Transcriptional Level...............................................................147 Introduction ................................................................................................147 Results .......................................................................................................149 Northern analysis of the pilT transcript................................. 149 pilT expression does not require the alternative sigma factor RpoN.............................................................152 Identification of promoter activity in thepilT pilU intergenic region................................................................ 152 Identification of the region required for pilT promoter activity............................................................................... 155 Quantitative analysis of pilT expression on solid and liquid m edia ................................................................ 162 Mapping of the transcription start sites ofpilT and analysis of transcript populations.....................................168 Identification of potential regulatoiy regions upstream ofp ilT................................................................................. 182 Discussion ................................................................................................
Recommended publications
  • RANDY SCHEKMAN Department of Molecular and Cell Biology, Howard Hughes Medical Institute, University of California, Berkeley, USA

    RANDY SCHEKMAN Department of Molecular and Cell Biology, Howard Hughes Medical Institute, University of California, Berkeley, USA

    GENES AND PROTEINS THAT CONTROL THE SECRETORY PATHWAY Nobel Lecture, 7 December 2013 by RANDY SCHEKMAN Department of Molecular and Cell Biology, Howard Hughes Medical Institute, University of California, Berkeley, USA. Introduction George Palade shared the 1974 Nobel Prize with Albert Claude and Christian de Duve for their pioneering work in the characterization of organelles interrelated by the process of secretion in mammalian cells and tissues. These three scholars established the modern field of cell biology and the tools of cell fractionation and thin section transmission electron microscopy. It was Palade’s genius in particular that revealed the organization of the secretory pathway. He discovered the ribosome and showed that it was poised on the surface of the endoplasmic reticulum (ER) where it engaged in the vectorial translocation of newly synthesized secretory polypeptides (1). And in a most elegant and technically challenging investigation, his group employed radioactive amino acids in a pulse-chase regimen to show by autoradiograpic exposure of thin sections on a photographic emulsion that secretory proteins progress in sequence from the ER through the Golgi apparatus into secretory granules, which then discharge their cargo by membrane fusion at the cell surface (1). He documented the role of vesicles as carriers of cargo between compartments and he formulated the hypothesis that membranes template their own production rather than form by a process of de novo biogenesis (1). As a university student I was ignorant of the important developments in cell biology; however, I learned of Palade’s work during my first year of graduate school in the Stanford biochemistry department.
  • Interplay Between Ompa and Rpon Regulates Flagellar Synthesis in Stenotrophomonas Maltophilia

    Interplay Between Ompa and Rpon Regulates Flagellar Synthesis in Stenotrophomonas Maltophilia

    microorganisms Article Interplay between OmpA and RpoN Regulates Flagellar Synthesis in Stenotrophomonas maltophilia Chun-Hsing Liao 1,2,†, Chia-Lun Chang 3,†, Hsin-Hui Huang 3, Yi-Tsung Lin 2,4, Li-Hua Li 5,6 and Tsuey-Ching Yang 3,* 1 Division of Infectious Disease, Far Eastern Memorial Hospital, New Taipei City 220, Taiwan; [email protected] 2 Department of Medicine, National Yang Ming Chiao Tung University, Taipei 112, Taiwan; [email protected] 3 Department of Biotechnology and Laboratory Science in Medicine, National Yang Ming Chiao Tung University, Taipei 112, Taiwan; [email protected] (C.-L.C.); [email protected] (H.-H.H.) 4 Division of Infectious Diseases, Department of Medicine, Taipei Veterans General Hospital, Taipei 112, Taiwan 5 Department of Pathology and Laboratory Medicine, Taipei Veterans General Hosiptal, Taipei 112, Taiwan; [email protected] 6 Ph.D. Program in Medical Biotechnology, Taipei Medical University, Taipei 110, Taiwan * Correspondence: [email protected] † Liao, C.-H. and Chang, C.-L. contributed equally to this work. Abstract: OmpA, which encodes outer membrane protein A (OmpA), is the most abundant transcript in Stenotrophomonas maltophilia based on transcriptome analyses. The functions of OmpA, including adhesion, biofilm formation, drug resistance, and immune response targets, have been reported in some microorganisms, but few functions are known in S. maltophilia. This study aimed to elucidate the relationship between OmpA and swimming motility in S. maltophilia. KJDOmpA, an ompA mutant, Citation: Liao, C.-H.; Chang, C.-L.; displayed compromised swimming and failure of conjugation-mediated plasmid transportation. The Huang, H.-H.; Lin, Y.-T.; Li, L.-H.; hierarchical organization of flagella synthesis genes in S.
  • (12) Patent Application Publication (10) Pub. No.: US 2004/0058321 A1 Brunkow Et Al

    (12) Patent Application Publication (10) Pub. No.: US 2004/0058321 A1 Brunkow Et Al

    US 200400.58321A1 (19) United States (12) Patent Application Publication (10) Pub. No.: US 2004/0058321 A1 BrunkOW et al. (43) Pub. Date: Mar. 25, 2004 (54) COMPOSITIONS AND METHODS FOR Related U.S. Application Data INCREASING BONE MINERALIZATION (63) Continuation of application No. 09/449,218, filed on (75) Inventors: Mary E. Brunkow, Seattle, WA (US); Nov. 24, 1999, now Pat. No. 6,395,511. David J. Galas, Claremont, CA (US); Brian Kovacevich, Renton, WA (US); (60) Provisional application No. 60/110,283, filed on Nov. John T. Mulligan, Seattle, WA (US); 27, 1998. Bryan Paeper, Seattle, WA (US); Jeffrey Van Ness, Claremont, CA (US); Publication Classification David G. Winkler, Seattle, WA (US) (51) Int. Cl. ............................ C12O 1/68; CO7H 21/04; Correspondence Address: A61K 39/395; C12P 21/02; SEED INTELLECTUAL PROPERTY LAW C12N 5/06; CO7K 16/22 GROUP PLLC (52) U.S. Cl. ......................... 435/6; 435/69.1; 435/320.1; 701 FIFTHAVE 435/325; 530/388.25; 424/145.1; SUTE 6300 536/23.5 SEATTLE, WA 98104-7092 (US) (57) ABSTRACT (73) Assignee: Darwin Discovery Ltd., Slough (GB) A novel class or family of TGF-B binding proteins is (21) Appl. No.: 10/095,248 disclosed. Also disclosed are assays for Selecting molecules for increasing bone mineralization and methods for utilizing (22) Filed: Mar. 7, 2002 Such molecules. Patent Application Publication Mar. 25, 2004 Sheet 1 of 6 US 2004/0058321 A1 Common Cysteine Backbone 1. 50 human-gremlin.pro human-Cerberus pro MHLLLFOLLY LLPLGKTTRH ODGRONOSSL SPYLLPRNOR ELPTGNHEEA human-dan pro re-asawwara reserwrwarrara's swarara-as-a-Wiswe sawsWawswaas awaawawa-a-a-ay human-beer pro 51 100 human-gremlin.pro MSRTAYTVGALLLLLGTLLPA AEGKKKGSOG human-CerberuS.
  • Chapter 3. the Beginnings of Genomic Biology – Molecular

    Chapter 3. the Beginnings of Genomic Biology – Molecular

    Chapter 3. The Beginnings of Genomic Biology – Molecular Genetics Contents 3. The beginnings of Genomic Biology – molecular genetics 3.1. DNA is the Genetic Material 3.6.5. Translation initiation, elongation, and termnation 3.2. Watson & Crick – The structure of DNA 3.6.6. Protein Sorting in Eukaryotes 3.3. Chromosome structure 3.7. Regulation of Eukaryotic Gene Expression 3.3.1. Prokaryotic chromosome structure 3.7.1. Transcriptional Control 3.3.2. Eukaryotic chromosome structure 3.7.2. Pre-mRNA Processing Control 3.3.3. Heterochromatin & Euchromatin 3.4. DNA Replication 3.7.3. mRNA Transport from the Nucleus 3.4.1. DNA replication is semiconservative 3.7.4. Translational Control 3.4.2. DNA polymerases 3.7.5. Protein Processing Control 3.4.3. Initiation of replication 3.7.6. Degradation of mRNA Control 3.4.4. DNA replication is semidiscontinuous 3.7.7. Protein Degradation Control 3.4.5. DNA replication in Eukaryotes. 3.8. Signaling and Signal Transduction 3.4.6. Replicating ends of chromosomes 3.8.1. Types of Cellular Signals 3.5. Transcription 3.8.2. Signal Recognition – Sensing the Environment 3.5.1. Cellular RNAs are transcribed from DNA 3.8.3. Signal transduction – Responding to the Environment 3.5.2. RNA polymerases catalyze transcription 3.5.3. Transcription in Prokaryotes 3.5.4. Transcription in Prokaryotes - Polycistronic mRNAs are produced from operons 3.5.5. Beyond Operons – Modification of expression in Prokaryotes 3.5.6. Transcriptions in Eukaryotes 3.5.7. Processing primary transcripts into mature mRNA 3.6. Translation 3.6.1.
  • Interplay of Virulence, Antibiotic Resistance and Epidemiology in Escherichia Coli Clinical Isolates

    Interplay of Virulence, Antibiotic Resistance and Epidemiology in Escherichia Coli Clinical Isolates

    Interplay of virulence, antibiotic resistance and epidemiology in Escherichia coli clinical isolates Elisabet Guiral Vilalta Aquesta tesi doctoral està subjecta a la llicència Reconeixement- NoComercial – SenseObraDerivada 4.0. Espanya de Creative Commons. Esta tesis doctoral está sujeta a la licencia Reconocimiento - NoComercial – SinObraDerivada 4.0. España de Creative Commons. This doctoral thesis is licensed under the Creative Commons Attribution-NonCommercial- NoDerivs 4.0. Spain License. Facultat de Medicina Departament de Fonaments Clínics Programa de Doctorat de Medicina i Recerca Translacional “Interplay of virulence, antibiotic resistance and epidemiology in Escherichia coli clinical isolates” Doctoranda: Elisabet Guiral Vilalta Departament de Fonaments Clínics Institut de Salut Global de Barcelona‐ Universitat de Barcelona‐ Hospital Clínic de Barcelona Directors de tesi: Dr. Jordi Vila Estapé i Dra. Sara M. Soto González Departament de Fonaments Clínics Institut de Salut Global de Barcelona‐ Universitat de Barcelona‐ Hospital Clínic de Barcelona Barcelona, Setembre 2018 El Dr. JORDI VILA ESTAPÉ, Catedràtic del Departament de Fonaments Clínics de la Facultat de Medicina de la Universitat de Barcelona, Cap del Servei de Microbiologia de l’Hospital Clínic de Barcelona i Research Professor i Director de la Iniciativa de Resistències Antimicrobianes de l’Institut de Salut Global de Barcelona (ISGlobal) i la Dra. SARA M. SOTO GONZÁLEZ, Professora Associada del Departament de Fonaments Clínics de la Universitat de Barcelona i Associate Research Professor d’ ISGlobal, CERTIFIQUEN: Que el treball de recerca titulat “Interplay of virulence, antibiotic resistance and epidemiology in Escherichia coli clinical isolates”, presentat per ELISABET GUIRAL VILALTA, ha estat realitzat al Laboratori de Microbiologia de l’ISGlobal, dins les dependències de l’Hospital Clínic de Barcelona, sota la seva direcció i compleix tots els requisits necessaris per la seva tramitació i posterior defensa davant del Tribunal corresponent.
  • Fidelity of Human Immunodeficiency Viruses Type 1 and Type 2 Reverse Transcriptases in DNA Synthesis Reactions Using DNA and RNA Templates

    Fidelity of Human Immunodeficiency Viruses Type 1 and Type 2 Reverse Transcriptases in DNA Synthesis Reactions Using DNA and RNA Templates

    UNIVERSIDAD AUTÓNOMA DE MADRID Programa de Doctorado en Biociencias Moleculares Fidelity of Human Immunodeficiency Viruses Type 1 and Type 2 Reverse Transcriptases in DNA Synthesis Reactions using DNA and RNA Templates Alba Sebastián Martín Madrid, noviembre, 2018 Universidad Autónoma de Madrid Facultad de Ciencias Departamento de Biología Molecular Programa de doctorado en Biociencias Moleculares Fidelity of Human Immunodeficiency Viruses Type 1 and Type 2 Reverse Transcriptases in DNA Synthesis Reactions using DNA and RNA Templates Memoria presentada por Alba Sebastián Martín, graduada en Biología, para optar al título de doctora en Biociencias Moleculares por la Universidad Autónoma de Madrid Director de la Tesis: Dr. Luis Menéndez Arias Este trabajo ha sido realizado en el Centro de Biología Molecular ‘Severo Ochoa’ (UAM-CSIC), con el apoyo de una beca de Formación de Profesorado Universitario, financiada por el Ministerio de Educación, Cultura y Deporte (FPU13/00693). Abbreviations 3TC 2’ 3’-dideoxy-3’-thiacytidine AIDS Acquired immunodeficiency syndrome AMV Avian myeloblastosis virus APOBEC Apolipoprotein B mRNA editing enzyme ATP Adenosine 5’ triphosphate AZT 3’-azido-2’, 3’-dideoxythymidine (zidovudine) AZT-MP 3´-azido-2´, 3´-dideoxythymidine monophosphate AZTppppA 3´azido-3´-deoxythymidine-(5´)-tetraphospho-(5´)-adenosine bp Base pair BSA Bovine serum albumin CA Capsid protein cDNA Complementary DNA Cir-Seq Circular sequencing CypA Cyclophilin A dATP 2’-deoxyadenoside 5’-triphosphate dCTP 2’-deoxycytidine 5’-triphosphate ddC
  • Mechanism to Control the Cell Lysis and the Cell Survival Strategy in Stationary Phase Under Heat Stress Rashed Noor*

    Mechanism to Control the Cell Lysis and the Cell Survival Strategy in Stationary Phase Under Heat Stress Rashed Noor*

    Noor SpringerPlus (2015) 4:599 DOI 10.1186/s40064-015-1415-7 REVIEW Open Access Mechanism to control the cell lysis and the cell survival strategy in stationary phase under heat stress Rashed Noor* Abstract An array of stress signals triggering the bacterial cellular stress response is well known in Escherichia coli and other bacteria. Heat stress is usually sensed through the misfolded outer membrane porin (OMP) precursors in the peri- plasm, resulting in the activation of σE (encoded by rpoE), which binds to RNA polymerase to start the transcription of genes required for responding against the heat stress signal. At the elevated temperatures, σE also serves as the transcription factor for σH (the main heat shock sigma factor, encoded by rpoH), which is involved in the expression of several genes whose products deal with the cytoplasmic unfolded proteins. Besides, oxidative stress in form of the reactive oxygen species (ROS) that accumulate due to heat stress, has been found to give rise to viable but non- culturable (VBNC) cells at the early stationary phase, which is in turn lysed by the σE-dependent process. Such lysis of the defective cells may generate nutrients for the remaining population to survive with the capacity of formation of colony forming units (CFUs). σH is also known to regulate the transcription of the major heat shock proteins (HSPs) required for heat shock response (HSR) resulting in cellular survival. Present review concentrated on the cellular sur- vival against heat stress employing the harmonized impact of σE and σH regulons and the HSPs as well as their inter connectivity towards the maintenance of cellular survival.
  • Table of Contents

    Table of Contents

    Copyright by William Paul Robins 2008 The Dissertation Committee for William Paul Robins certifies that this is the approved version of the following dissertation ANTITERMINATION IS OPERATIVE IN BACTERIOPHAGE T7 AND IS LARGELY DEPENDENT ON ONE PROMOTER Committee: ____________________________________ Ian J. Molineux , Supervisor ____________________________________ Whitney Yin ____________________________________ Tanya Paull ____________________________________ Richard Meyer ____________________________________ Charles Earhart ANTITERMINATION IS OPERATIVE IN BACTERIOPHAGE T7 AND IS LARGELY DEPENDENT ON ONE PROMOTER by William Paul Robins, 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 August 2008 DEDICATION This Dissertation is dedicated to the memory of my grandfather, Paul Rogers. His profound love of nature influenced my desire to study Science. ACKNOWLEDGEMENTS I would like to thank my supervisor Ian Molineux for his support and encouragement. His rigorous, thorough, and enthusiastic approach to science has been a valuable experience. I expect his mentoring will be a very positive influence on my future endeavors. I am also grateful to Pricilla Kemp for additional help and assistance in my work. I would also like to acknowledge Dhruti Savalia for investigating and analyzing my promoter mutations using abortive transcription assays and primer extension experiments. Her biochemical approach on T7 gene 2 was a very useful complement to the phage genetics in our lab. Finally, I need to thank my family; especially my wife Hannah Robins, my son Jefferson Pinkus and my parents Sam Robins and Gail Levansellar. v ANTITERMINATION IS OPERATIVE IN BACTERIOPHAGE T7 AND IS LARGELY DEPENDENT ON ONE PROMOTER William Paul Robins, Ph.D.
  • (Λ) Rex Phenotype

    (Λ) Rex Phenotype

    Isolation and Characterization of Host mutations that Supress the Bacteriophage Lambda (λ) Rex Phenotype by Hibah Alattas A thesis presented to the University of Waterloo in fulfillment of the thesis requirement for the degree of Master of Science in Pharmacy Waterloo, Ontario, Canada, 2015 ©Hibah Alattas 2015 Author’s Declaration I hereby declare that I am the sole author of this thesis. This is a true copy of the thesis, including any required final revisions, as accepted by my examiners. I understand that my thesis may be made electronically available to the public. ii Abstract The Bacteriophage lambda (λ) T4rII exclusion (Rex) phenotype is defined as the inability of T4rII mutant bacteriophage to form plaques on a lawn of E. coli lysogenized by bacteriophage λ. More than six decades have passed following the discovery of Rex by Seymour Benzer in 1955, yet the mechanism behind this elusive exclusion system remains a mystery. The Rex system is encoded by two genes of λ (rexA, and rexB), the expression of which, is primarily regulated by the repressor gene cI from the PM promoter. The onset of the Rex phenotype, somehow triggered by T4rII infection of a Rex+ lysogen, results in rapid membrane depolarization and a harsh cellular environment that in many ways resembles the stationary phase in metabolism and morphology. In addition, the disruption of the RexA:RexB balance, particularly the over expression of rexA to rexB, can lead to same manifestations without infection, indicating that stoichiometry of RexA:RexB is important. Despite some cell killing, infected lysogens can to some extent recover from Rex activation.
  • Escherichia Coli

    Escherichia Coli

    Escherichia coli “E. coli” redirects here. For the protozoan commensal, 1 Biology and biochemistry see Entamoeba coli. This article is about Escherichia coli as a species. For E. coli in medicine, see Pathogenic Escherichia coli. For E. coli in molecular biology, see Escherichia coli (molecular biology). Escherichia coli (/ˌɛʃᵻˈrɪkiə ˈkoʊlaɪ/;[1] also known as E. coli) is a Gram-negative, facultatively anaerobic, rod- shaped bacterium of the genus Escherichia that is com- monly found in the lower intestine of warm-blooded or- ganisms (endotherms).[2] Most E. coli strains are harm- less, but some serotypes can cause serious food poisoning in their hosts, and are occasionally responsible for product recalls due to food contamination.[3][4] The harmless strains are part of the normal flora of the gut, and can [5] benefit their hosts by producing vitamin K2, and pre- venting colonization of the intestine with pathogenic bac- teria.[6][7] E. coli is expelled into the environment within Model of successive binary fission in E. coli fecal matter. The bacterium grows massively in fresh fe- cal matter under aerobic conditions for 3 days, but its numbers decline slowly afterwards.[8] E. coli and other facultative anaerobes constitute about 0.1% of gut flora,[9] and fecal–oral transmission is the major route through which pathogenic strains of the bac- terium cause disease. Cells are able to survive outside the body for a limited amount of time, which makes them potential indicator organisms to test environmental sam- ples for fecal contamination.[10][11] A growing body of re- search, though, has examined environmentally persistent E.
  • The Whole Set of the Constitutive Promoters Recognized by Four Minor Sigma Subunits of Escherichia Coli RNA Polymerase

    The Whole Set of the Constitutive Promoters Recognized by Four Minor Sigma Subunits of Escherichia Coli RNA Polymerase

    RESEARCH ARTICLE The whole set of the constitutive promoters recognized by four minor sigma subunits of Escherichia coli RNA polymerase Tomohiro Shimada1,2¤, Kan Tanaka2, Akira Ishihama1* 1 Research Center for Micro-Nano Technology, Hosei University, Koganei, Tokyo, Japan, 2 Laboratory for Chemistry and Life Science, Institute of Innovative Research, Tokyo Institute of Technology, Nagatsuda, Yokohama, Japan a1111111111 ¤ Current address: School of Agriculture, Meiji University, Kawasaki, Kanagawa, Japan a1111111111 * [email protected] a1111111111 a1111111111 a1111111111 Abstract The promoter selectivity of Escherichia coli RNA polymerase (RNAP) is determined by the sigma subunit. The model prokaryote Escherichia coli K-12 contains seven species of the OPEN ACCESS sigma subunit, each recognizing a specific set of promoters. For identification of the ªconsti- Citation: Shimada T, Tanaka K, Ishihama A (2017) tutive promotersº that are recognized by each RNAP holoenzyme alone in the absence of The whole set of the constitutive promoters other supporting factors, we have performed the genomic SELEX screening in vitro for their recognized by four minor sigma subunits of binding sites along the E. coli K-12 W3110 genome using each of the reconstituted RNAP Escherichia coli RNA polymerase. PLoS ONE 12(6): holoenzymes and a collection of genome DNA segments of E. coli K-12. The whole set of e0179181. https://doi.org/10.1371/journal. pone.0179181 constitutive promoters for each RNAP holoenzyme was then estimated based on the loca- tion of RNAP-binding sites. The first successful screening of the constitutive promoters was Editor: Dipankar Chatterji, Indian Institute of 70 Science, INDIA achieved for RpoD (σ ), the principal sigma for transcription of growth-related genes.
  • Stationary Phase in Gramnegative Bacteria

    Stationary Phase in Gramnegative Bacteria

    REVIEW ARTICLE Stationary phase in gram-negative bacteria Juana Marıa´ Navarro Llorens1, Antonio Tormo1 & Esteban Martınez-Garc´ ıa´ 2 1Departamento de Bioquımica´ y Biologıa´ Molecular I, Universidad Complutense de Madrid, Madrid, Spain; and 2Departamento de Biotecnologıa´ Microbiana, Centro Nacional de Biotecnologıa,´ CSIC, Madrid, Spain Correspondence: Esteban Martınez´ Garcıa,´ Abstract Departamento de Biotecnologıa´ Microbiana, Centro Nacional de Biotecnologıa,´ CSIC, Conditions that sustain constant bacterial growth are seldom found in nature. C/Darwin, 3, 28049 Madrid, Spain. Tel.: Oligotrophic environments and competition among microorganisms force bacter- 134 91 585 4573; fax: 134 91 585 4506; ia to be able to adapt quickly to rough and changing situations. A particular e-mail: [email protected] lifestyle composed of continuous cycles of growth and starvation is commonly referred to as feast and famine. Bacteria have developed many different mechan- Received 17 March 2009; revised 18 January isms to survive in nutrient-depleted and harsh environments, varying from 2010; accepted 25 January 2010. producing a more resistant vegetative cell to complex developmental programmes. Final version published online 8 March 2010. As a consequence of prolonged starvation, certain bacterial species enter a dynamic nonproliferative state in which continuous cycles of growth and death occur until DOI:10.1111/j.1574-6976.2010.00213.x ‘better times’ come (restoration of favourable growth conditions). In the labora- Editor: Ramon Dıaz´ Orejas tory, microbiologists approach famine situations using batch culture conditions. The entrance to the stationary phase is a very regulated process governed by the Keywords alternative sigma factor RpoS. Induction of RpoS changes the gene expression stationary phase; starvation; rpoS; growth pattern, aiming to produce a more resistant cell.