Prospects for the Mechanism of Spiroplasma Swimming
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Spiroplasma Arp Sequences: Relationships
SPIROPLASMA ARP SEQUENCES: RELATIONSHIPS WITH EXTRACHROMOSOMAL ELEMENTS By BHARAT DILIP JOSHI Bachelor of Science University of Pune, India 1995 Master of Science University of Pune, India 1997 Submitted to the Faculty of the Graduate College of the Oklahoma State University in partial fulfillment of the requirements for the Degree of DOCTOR OF PHILOSOPHY July, 2006 SPIROPLASMA ARP SEQUENCES: RELATIONSHIPS WITH EXTRACHROMOSOMAL ELEMENTS Dissertation Approved: Dr. Ulrich K. Melcher Dissertation Adviser Dr. Andrew J. Mort Dr. Robert L. Matts Dr. Richard C. Essenberg ________________________________________________ Dr. Jacqueline Fletcher Dr. A. Gordon Emslie Dean of the Graduate College ii TABLE OF CONTENTS Chapter Page I. LITERATURE REVIEW ............................................................................... 1 Background ........................................................................................... 1 Economic Importance............................................................................ 1 Classification ......................................................................................... 2 Transmission in Nature ......................................................................... 3 Molecular Mollicute-host Interactions .................................................. 4 Molecular Spiroplasma-host Interactions ............................................. 4 Mollicute Extrachromosomal DNAs .................................................... 7 Objectives of the Present Study ........................................................... -
Spiroplasma Infection Among Ixodid Ticks Exhibits Species Dependence and Suggests a Vertical Pattern of Transmission
microorganisms Article Spiroplasma Infection among Ixodid Ticks Exhibits Species Dependence and Suggests a Vertical Pattern of Transmission Shohei Ogata 1, Wessam Mohamed Ahmed Mohamed 1 , Kodai Kusakisako 1,2, May June Thu 1,†, Yongjin Qiu 3 , Mohamed Abdallah Mohamed Moustafa 1,4 , Keita Matsuno 5,6 , Ken Katakura 1, Nariaki Nonaka 1 and Ryo Nakao 1,* 1 Laboratory of Parasitology, Department of Disease Control, Faculty of Veterinary Medicine, Graduate School of Infectious Diseases, Hokkaido University, N 18 W 9, Kita-ku, Sapporo 060-0818, Japan; [email protected] (S.O.); [email protected] (W.M.A.M.); [email protected] (K.K.); [email protected] (M.J.T.); [email protected] (M.A.M.M.); [email protected] (K.K.); [email protected] (N.N.) 2 Laboratory of Veterinary Parasitology, School of Veterinary Medicine, Kitasato University, Towada, Aomori 034-8628, Japan 3 Hokudai Center for Zoonosis Control in Zambia, School of Veterinary Medicine, The University of Zambia, P.O. Box 32379, Lusaka 10101, Zambia; [email protected] 4 Department of Animal Medicine, Faculty of Veterinary Medicine, South Valley University, Qena 83523, Egypt 5 Unit of Risk Analysis and Management, Research Center for Zoonosis Control, Hokkaido University, N 20 W 10, Kita-ku, Sapporo 001-0020, Japan; [email protected] 6 International Collaboration Unit, Research Center for Zoonosis Control, Hokkaido University, N 20 W 10, Kita-ku, Sapporo 001-0020, Japan Citation: Ogata, S.; Mohamed, * Correspondence: [email protected]; Tel.: +81-11-706-5196 W.M.A.; Kusakisako, K.; Thu, M.J.; † Present address: Food Control Section, Department of Food and Drug Administration, Ministry of Health and Sports, Zabu Thiri, Nay Pyi Taw 15011, Myanmar. -
Extremozymes of the Hot and Salty Halothermothrix Orenii
Extremozymes of the Hot and Salty Halothermothrix orenii Author Kori, Lokesh D Published 2012 Thesis Type Thesis (PhD Doctorate) School School of Biomolecular and Physical Sciences DOI https://doi.org/10.25904/1912/2191 Copyright Statement The author owns the copyright in this thesis, unless stated otherwise. Downloaded from http://hdl.handle.net/10072/366220 Griffith Research Online https://research-repository.griffith.edu.au Extremozymes of the hot and salty Halothermothrix orenii LOKESH D. KORI (M.Sc. Biotechnology) School of Biomolecular and Physical Sciences Science, Environment, Engineering and Technology Griffith University, Australia Submitted in fulfillment of the requirements of the degree of Doctor of Philosophy December 2011 STATEMENT OF ORIGINALITY STATEMENT OF ORIGINALITY This work has not previously been submitted for a degree or diploma in any university. To the best of my knowledge and belief, the thesis contains no material previously published or written by another person except where due reference is made in the thesis itself. LOKESH DULICHAND KORI II ACKNOWLEDGEMENTS ACKNOWLEDGEMENTS I owe my deepest gratitude to my supervisor Prof. Bharat Patel, for offering me an opportunity for being his postgraduate. His boundless knowledge motivates me for keep going and enjoy the essence of science. Without his guidance, great patience and advice, I could not finish my PhD program successfully. I take this opportunity to give my heartiest thanks to Assoc. Prof. Andreas Hofmann, (Structural Chemistry, Eskitis Institute for Cell & Molecular Therapies, Griffith University) for his support and encouragement for crystallographic work. I am grateful to him for teaching me about the protein structures, in silico analysis and their hidden chemistry. -
Bacterial Communities of the Upper Respiratory Tract of Turkeys
www.nature.com/scientificreports OPEN Bacterial communities of the upper respiratory tract of turkeys Olimpia Kursa1*, Grzegorz Tomczyk1, Anna Sawicka‑Durkalec1, Aleksandra Giza2 & Magdalena Słomiany‑Szwarc2 The respiratory tracts of turkeys play important roles in the overall health and performance of the birds. Understanding the bacterial communities present in the respiratory tracts of turkeys can be helpful to better understand the interactions between commensal or symbiotic microorganisms and other pathogenic bacteria or viral infections. The aim of this study was the characterization of the bacterial communities of upper respiratory tracks in commercial turkeys using NGS sequencing by the amplifcation of 16S rRNA gene with primers designed for hypervariable regions V3 and V4 (MiSeq, Illumina). From 10 phyla identifed in upper respiratory tract in turkeys, the most dominated phyla were Firmicutes and Proteobacteria. Diferences in composition of bacterial diversity were found at the family and genus level. At the genus level, the turkey sequences present in respiratory tract represent 144 established bacteria. Several respiratory pathogens that contribute to the development of infections in the respiratory system of birds were identifed, including the presence of Ornithobacterium and Mycoplasma OTUs. These results obtained in this study supply information about bacterial composition and diversity of the turkey upper respiratory tract. Knowledge about bacteria present in the respiratory tract and the roles they can play in infections can be useful in controlling, diagnosing and treating commercial turkey focks. Next-generation sequencing has resulted in a marked increase in culture-independent studies characterizing the microbiome of humans and animals1–6. Much of these works have been focused on the gut microbiome of humans and other production animals 7–11. -
Movements of Mycoplasma Mobile Gliding Machinery Detected by High
bioRxiv preprint doi: https://doi.org/10.1101/2021.01.28.428740; this version posted January 29, 2021. 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 4.0 International license. 1 mBio (Research Article) 2 3 Movements of Mycoplasma mobile gliding machinery detected by 4 high-speed atomic force microscopy 5 Kohei Kobayashia*, Noriyuki Koderab*, Taishi Kasaia, Yuhei O Taharaa,c, Takuma 6 Toyonagaa, Masaki Mizutania, Ikuko Fujiwaraa, Toshio Andob, Makoto Miyataa,c,# 7 8 aGraduate School of Science, Osaka City University, 3-3-138 Sugimoto, 9 Sumiyoshi-ku, Osaka 558-8585, Japan. 10 bNano Life Science Institute (WPI-NanoLSI), Kanazawa University, Kakuma-chou, 11 Kanazawa, Ishikawa 920-1192, Japan. 12 cThe OCU Advanced Research Institute for Natural Science and Technology 13 (OCARINA), Osaka City University, 3-3-138 Sugimoto, Sumiyoshi-ku, Osaka 14 558-8585, Japan. 15 16 Address correspondence to Makoto Miyata, [email protected] 17 *These authors contributed equally to this work. 18 Present address: Taishi Kasai: Department of Life Science, Rikkyo University, 19 3-34-1 Nishiikebukuro, Toshima-ku, Tokyo 171-8501, Japan. 1 bioRxiv preprint doi: https://doi.org/10.1101/2021.01.28.428740; this version posted January 29, 2021. 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 4.0 International license. -
Global Metagenomic Survey Reveals a New Bacterial Candidate Phylum in Geothermal Springs
ARTICLE Received 13 Aug 2015 | Accepted 7 Dec 2015 | Published 27 Jan 2016 DOI: 10.1038/ncomms10476 OPEN Global metagenomic survey reveals a new bacterial candidate phylum in geothermal springs Emiley A. Eloe-Fadrosh1, David Paez-Espino1, Jessica Jarett1, Peter F. Dunfield2, Brian P. Hedlund3, Anne E. Dekas4, Stephen E. Grasby5, Allyson L. Brady6, Hailiang Dong7, Brandon R. Briggs8, Wen-Jun Li9, Danielle Goudeau1, Rex Malmstrom1, Amrita Pati1, Jennifer Pett-Ridge4, Edward M. Rubin1,10, Tanja Woyke1, Nikos C. Kyrpides1 & Natalia N. Ivanova1 Analysis of the increasing wealth of metagenomic data collected from diverse environments can lead to the discovery of novel branches on the tree of life. Here we analyse 5.2 Tb of metagenomic data collected globally to discover a novel bacterial phylum (‘Candidatus Kryptonia’) found exclusively in high-temperature pH-neutral geothermal springs. This lineage had remained hidden as a taxonomic ‘blind spot’ because of mismatches in the primers commonly used for ribosomal gene surveys. Genome reconstruction from metagenomic data combined with single-cell genomics results in several high-quality genomes representing four genera from the new phylum. Metabolic reconstruction indicates a heterotrophic lifestyle with conspicuous nutritional deficiencies, suggesting the need for metabolic complementarity with other microbes. Co-occurrence patterns identifies a number of putative partners, including an uncultured Armatimonadetes lineage. The discovery of Kryptonia within previously studied geothermal springs underscores the importance of globally sampled metagenomic data in detection of microbial novelty, and highlights the extraordinary diversity of microbial life still awaiting discovery. 1 Department of Energy Joint Genome Institute, Walnut Creek, California 94598, USA. 2 Department of Biological Sciences, University of Calgary, Calgary, Alberta T2N 1N4, Canada. -
The Mysterious Orphans of Mycoplasmataceae
The mysterious orphans of Mycoplasmataceae Tatiana V. Tatarinova1,2*, Inna Lysnyansky3, Yuri V. Nikolsky4,5,6, and Alexander Bolshoy7* 1 Children’s Hospital Los Angeles, Keck School of Medicine, University of Southern California, Los Angeles, 90027, California, USA 2 Spatial Science Institute, University of Southern California, Los Angeles, 90089, California, USA 3 Mycoplasma Unit, Division of Avian and Aquatic Diseases, Kimron Veterinary Institute, POB 12, Beit Dagan, 50250, Israel 4 School of Systems Biology, George Mason University, 10900 University Blvd, MSN 5B3, Manassas, VA 20110, USA 5 Biomedical Cluster, Skolkovo Foundation, 4 Lugovaya str., Skolkovo Innovation Centre, Mozhajskij region, Moscow, 143026, Russian Federation 6 Vavilov Institute of General Genetics, Moscow, Russian Federation 7 Department of Evolutionary and Environmental Biology and Institute of Evolution, University of Haifa, Israel 1,2 [email protected] 3 [email protected] 4-6 [email protected] 7 [email protected] 1 Abstract Background: The length of a protein sequence is largely determined by its function, i.e. each functional group is associated with an optimal size. However, comparative genomics revealed that proteins’ length may be affected by additional factors. In 2002 it was shown that in bacterium Escherichia coli and the archaeon Archaeoglobus fulgidus, protein sequences with no homologs are, on average, shorter than those with homologs [1]. Most experts now agree that the length distributions are distinctly different between protein sequences with and without homologs in bacterial and archaeal genomes. In this study, we examine this postulate by a comprehensive analysis of all annotated prokaryotic genomes and focusing on certain exceptions. -
MIB–MIP Is a Mycoplasma System That Captures and Cleaves Immunoglobulin G
MIB–MIP is a mycoplasma system that captures and cleaves immunoglobulin G Yonathan Arfia,b,1, Laetitia Minderc,d, Carmelo Di Primoe,f,g, Aline Le Royh,i,j, Christine Ebelh,i,j, Laurent Coquetk, Stephane Claveroll, Sanjay Vasheem, Joerg Joresn,o, Alain Blancharda,b, and Pascal Sirand-Pugneta,b aINRA (Institut National de la Recherche Agronomique), UMR 1332 Biologie du Fruit et Pathologie, F-33882 Villenave d’Ornon, France; bUniversity of Bordeaux, UMR 1332 Biologie du Fruit et Pathologie, F-33882 Villenave d’Ornon, France; cInstitut Européen de Chimie et Biologie, UMS 3033, University of Bordeaux, 33607 Pessac, France; dInstitut Bergonié, SIRIC BRIO, 33076 Bordeaux, France; eINSERM U1212, ARN Regulation Naturelle et Artificielle, 33607 Pessac, France; fCNRS UMR 5320, ARN Regulation Naturelle et Artificielle, 33607 Pessac, France; gInstitut Européen de Chimie et Biologie, University of Bordeaux, 33607 Pessac, France; hInstitut de Biologie Structurale, University of Grenoble Alpes, F-38044 Grenoble, France; iCNRS, Institut de Biologie Structurale, F-38044 Grenoble, France; jCEA, Institut de Biologie Structurale, F-38044 Grenoble, France; kCNRS UMR 6270, Plateforme PISSARO, Institute for Research and Innovation in Biomedicine - Normandie Rouen, Normandie Université, F-76821 Mont-Saint-Aignan, France; lProteome Platform, Functional Genomic Center of Bordeaux, University of Bordeaux, F-33076 Bordeaux Cedex, France; mJ. Craig Venter Institute, Rockville, MD 20850; nInternational Livestock Research Institute, 00100 Nairobi, Kenya; and oInstitute of Veterinary Bacteriology, University of Bern, CH-3001 Bern, Switzerland Edited by Roy Curtiss III, University of Florida, Gainesville, FL, and approved March 30, 2016 (received for review January 12, 2016) Mycoplasmas are “minimal” bacteria able to infect humans, wildlife, introduced into naive herds (8). -
Role of Protein Phosphorylation in Mycoplasma Pneumoniae
Pathogenicity of a minimal organism: Role of protein phosphorylation in Mycoplasma pneumoniae Dissertation zur Erlangung des mathematisch-naturwissenschaftlichen Doktorgrades „Doctor rerum naturalium“ der Georg-August-Universität Göttingen vorgelegt von Sebastian Schmidl aus Bad Hersfeld Göttingen 2010 Mitglieder des Betreuungsausschusses: Referent: Prof. Dr. Jörg Stülke Koreferent: PD Dr. Michael Hoppert Tag der mündlichen Prüfung: 02.11.2010 “Everything should be made as simple as possible, but not simpler.” (Albert Einstein) Danksagung Zunächst möchte ich mich bei Prof. Dr. Jörg Stülke für die Ermöglichung dieser Doktorarbeit bedanken. Nicht zuletzt durch seine freundliche und engagierte Betreuung hat mir die Zeit viel Freude bereitet. Des Weiteren hat er mir alle Freiheiten zur Verwirklichung meiner eigenen Ideen gelassen, was ich sehr zu schätzen weiß. Für die Übernahme des Korreferates danke ich PD Dr. Michael Hoppert sowie Prof. Dr. Heinz Neumann, PD Dr. Boris Görke, PD Dr. Rolf Daniel und Prof. Dr. Botho Bowien für das Mitwirken im Thesis-Komitee. Der Studienstiftung des deutschen Volkes gilt ein besonderer Dank für die finanzielle Unterstützung dieser Arbeit, durch die es mir unter anderem auch möglich war, an Tagungen in fernen Ländern teilzunehmen. Prof. Dr. Michael Hecker und der Gruppe von Dr. Dörte Becher (Universität Greifswald) danke ich für die freundliche Zusammenarbeit bei der Durchführung von zahlreichen Proteomics-Experimenten. Ein ganz besonderer Dank geht dabei an Katrin Gronau, die mich in die Feinheiten der 2D-Gelelektrophorese eingeführt hat. Außerdem möchte ich mich bei Andreas Otto für die zahlreichen Proteinidentifikationen in den letzten Monaten bedanken. Nicht zu vergessen ist auch meine zweite Außenstelle an der Universität in Barcelona. Dr. Maria Lluch-Senar und Dr. -
Metazoan Ribosome Inactivating Protein Encoding Genes Acquired by Horizontal Gene Transfer Received: 30 September 2016 Walter J
www.nature.com/scientificreports OPEN Metazoan Ribosome Inactivating Protein encoding genes acquired by Horizontal Gene Transfer Received: 30 September 2016 Walter J. Lapadula1, Paula L. Marcet2, María L. Mascotti1, M. Virginia Sanchez-Puerta3 & Accepted: 5 April 2017 Maximiliano Juri Ayub1 Published: xx xx xxxx Ribosome inactivating proteins (RIPs) are RNA N-glycosidases that depurinate a specific adenine residue in the conserved sarcin/ricin loop of 28S rRNA. These enzymes are widely distributed among plants and their presence has also been confirmed in several bacterial species. Recently, we reported for the first timein silico evidence of RIP encoding genes in metazoans, in two closely related species of insects: Aedes aegypti and Culex quinquefasciatus. Here, we have experimentally confirmed the presence of these genes in mosquitoes and attempted to unveil their evolutionary history. A detailed study was conducted, including evaluation of taxonomic distribution, phylogenetic inferences and microsynteny analyses, indicating that mosquito RIP genes derived from a single Horizontal Gene Transfer (HGT) event, probably from a cyanobacterial donor species. Moreover, evolutionary analyses show that, after the HGT event, these genes evolved under purifying selection, strongly suggesting they play functional roles in these organisms. Ribosome inactivating proteins (RIPs, EC 3.2.2.22) irreversibly modify ribosomes through the depurination of an adenine residue in the conserved alpha-sarcin/ricin loop of 28S rRNA1–4. This modification prevents the binding of elongation factor 2 to the ribosome, arresting protein synthesis5, 6. The occurrence of RIP genes has been exper- imentally confirmed in a wide range of plant taxa, as well as in several species of Gram positive and Gram negative bacteria7–9. -
Complete Genomes of Two Dipteran-Associated Spiroplasmas Provided Insights Into the Origin, Dynamics, and Impacts of Viral Invasion in Spiroplasma
GBE Complete Genomes of Two Dipteran-Associated Spiroplasmas Provided Insights into the Origin, Dynamics, and Impacts of Viral Invasion in Spiroplasma Chuan Ku1,Wen-SuiLo1,2,3, Ling-Ling Chen1, and Chih-Horng Kuo1,2,4,* 1Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan 2Molecular and Biological Agricultural Sciences Program, Taiwan International Graduate Program, National Chung Hsing University and Academia Sinica, Taipei, Taiwan 3Graduate Institute of Biotechnology, National Chung Hsing University, Taichung, Taiwan 4Biotechnology Center, National Chung Hsing University, Taichung, Taiwan *Corresponding author: E-mail: [email protected]. Accepted: May 21, 2013 Data deposition: The genome sequences reported in this study have been deposited at DDBJ/EMBL/GenBank under the accessions CP005077 and CP005078. Abstract Spiroplasma is a genus of wall-less, low-GC, Gram-positive bacteria with helical morphology. As commensals or pathogens of plants, insects, ticks, or crustaceans, they are closely related with mycoplasmas and form a monophyletic group (Spiroplasma– Entomoplasmataceae–Mycoides) with Mycoplasma mycoides and its relatives. In this study, we report the complete genome sequences of Spiroplasma chrysopicola and S. syrphidicola from the Chrysopicola clade. These species form the sister group to the Citri clade, which includes several well-known pathogenic spiroplasmas. Surprisingly, these two newly available genomes from the Chrysopicola clade contain no plectroviral genes, which were found to be highly repetitive in the previously sequenced genomes from the Citri clade. Based on the genome alignment and patterns of GC-skew, these two Chrysopicola genomes appear to be relatively stable, rather than being highly rearranged as those from the Citri clade. -
Bacterial Vector-Borne Plant Diseases: Unanswered Questions and Future Directions
Bacterial Vector-Borne Plant Diseases: Unanswered Questions and Future Directions Weijie Huang, Paola Reyes-Caldas, Marina Mann, Shirin Seifbarghi, Alexandra Kahn, Rodrigo P.P. Almeida, Laure Béven, Michelle Heck, Saskia Hogenhout, Gitta Coaker To cite this version: Weijie Huang, Paola Reyes-Caldas, Marina Mann, Shirin Seifbarghi, Alexandra Kahn, et al.. Bacterial Vector-Borne Plant Diseases: Unanswered Questions and Future Directions. Molecular Plant, Cell Press/Oxford UP, 2020, 13 (10), pp.1379-1393. 10.1016/j.molp.2020.08.010. hal-03035576 HAL Id: hal-03035576 https://hal.inrae.fr/hal-03035576 Submitted on 2 Dec 2020 HAL is a multi-disciplinary open access L’archive ouverte pluridisciplinaire HAL, est archive for the deposit and dissemination of sci- destinée au dépôt et à la diffusion de documents entific research documents, whether they are pub- scientifiques de niveau recherche, publiés ou non, lished or not. The documents may come from émanant des établissements d’enseignement et de teaching and research institutions in France or recherche français ou étrangers, des laboratoires abroad, or from public or private research centers. publics ou privés. Distributed under a Creative Commons Attribution - NonCommercial - NoDerivatives| 4.0 International License Molecular Plant ll Perspective Bacterial Vector-Borne Plant Diseases: Unanswered Questions and Future Directions Weijie Huang1,9, Paola Reyes-Caldas2,9, Marina Mann3,9, Shirin Seifbarghi2,9, Alexandra Kahn4,9, Rodrigo P.P. Almeida4, Laure Be´ ven5, Michelle Heck3,6,7, Saskia A. Hogenhout1,8 and Gitta Coaker2,* 1Department of Crop Genetics, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK 2Department of Plant Pathology, University of California, Davis, CA, 95616, USA 3Department of Plant Pathology and Plant-Microbe Biology, Cornell University, Ithaca, NY 14853, USA 4Department of Environmental Science, Policy and Management, University of California, Berkeley, CA 94720, USA 5UMR 1332 Biologie du Fruit et Pathologie, Univ.