DOCSLIB.ORG

Insect Transmitted Plant Pathogenic Mollicutes, Spiroplasma Kunkelii and Aster Yellows Witches' Broom Phytoplasma: from Structural Genomics to Functional Genomics

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
Insect Transmitted Plant Pathogenic Mollicutes, Spiroplasma Kunkelii and Aster Yellows Witches' Broom Phytoplasma: from Structural Genomics to Functional Genomics INSECT TRANSMITTED PLANT PATHOGENIC MOLLICUTES, SPIROPLASMA KUNKELII AND ASTER YELLOWS WITCHES' BROOM PHYTOPLASMA: FROM STRUCTURAL GENOMICS TO FUNCTIONAL GENOMICS DISSERTATION Presented in Partial Fulfillment of the Requirements for the Degree Doctor of Philosophy in the Graduate School of The Ohio State University By Xiaodong Bai, M.S. * * * * * The Ohio State University 2004 Dissertation Committee: Dr. Saskia A. Hogenhout, Adviser Approved by Dr. David L. Denlinger Dr. David M. Francis Adviser Dr. Parwinder S. Grewal Department of Entomology ABSTRACT The mollicutes, Spiroplasma kunkelii and aster yellows witches' broom (AY-WB) phytoplasma, are insect-transmitted plant pathogens. These mollicutes invade and replicate in cells of various insect organs and tissues, and inhabit and replicate in plant phloem tissues. They cause severe symptoms to many plant species worldwide, including economically important crops and ornamental plants. Their fastidious nature and lack of genetic tools have hampered the research on these plant pathogenic mollicutes. I employed various approaches, including genome sequencing, comparative genomics, functional genomics, and conventional molecular techniques, to study the biology and pathogenicity mechanisms of S. kunkelii and AY-WB phytoplasma. The partial genome of S. kunkelii and the complete genome of AY-WB phytoplasma were sequenced. Genome annotation revealed the presence of multiple spiroplasma phage DNA sequences in S. kunkelii and many repetitive elements in both genomes, suggestive of frequent recombination events. The genome sequence data provide genetic basis for the study of the biology and pathogenicity mechanisms of these organisms. Whereas spiroplasmas and phytoplasmas are distantly related to each other, they share the plant and insect habitats. Therefore, they may share genes involved in insect ii transmission and plant pathogenicity that are missing from the animal and human pathogenic mycoplasmas. To test this hypothesis, comparative genome analysis among mollicutes was conducted, and resulted in the identification of four genes that are present in the genomes of all plant-pathogenic mollicutes sequenced so far, but missing from the mycoplasmas. Another gene within both genomes might have been derived by horizontal gene transfer between spiroplasmas and phytoplasmas. The observation of spiroplasma surface appendages prompted the search of genes involved in fimbriae or pili formation. Four traE gene homologs were identified as membrane-bound ATPases in S. kunkelii M2 strain. Two homologs were localized in S. kunkelii chromosome and two in plasmids. The presence of these homologs varied among S. kunkelii strains of different geographical locations. The expression of the genes was detected in culture medium and during infection of insects and plants. Adjacent sequences of traE homologs suggest the involvement of TraE in spiroplasma conjugation and subsequent recombination, and adhesion. The secreted proteins of AY-WB phytoplasma are likely to directly interact with host cell components. Hence, the AY-WB phytoplasma genome sequence was mined for potentially secreted proteins that were further characterized by high-throughput functional assays such as virus-based expression in Nicotiana benthamiana (tobacco) and Lycopersicon esculentum (tomato). The in planta assay resulted in the identification of 17 candidate effector proteins. The detailed functional characterization was focused on two phytoplasma proteins (A11 and A30) that have a nuclear localization signal (NLS), and therefore, may be imported into plant nuclei in an importin α-dependent manner. Plant iii localization study with the yellow fluorescent protein fusions of these two proteins revealed their localization in the plant nuclei and confirmed their dependence on plant importin α for nuclear transport. Transcripts corresponding to the phytoplasma proteins were detected in AY-WB phytoplasma-infected insects and plants by RT-PCR. Microarrays demonstrated that phytoplasma A11 protein affected the expression profiles of 53 tomato genes, including several transcription factors, indicating that phytoplasma A11 protein directly or indirectly interacts with these proteins. These data are supportive of the hypothesis that A11 is a bona fide effector protein involved in plant pathogenicity. In summary, the research described in this dissertation resulted in the identification of several mollicute genes that are potentially involved in insect transmission and plant pathogenicity. It demonstrated that the genome sequencing, comparative genomics, and functional genomics approaches allow efficient identification and characterization of such genes in bacterial genomes. The importance of the research lies in the application of high throughput bioinformatics, genomics and molecular approaches in the study of agriculturally important organisms for which little information, and molecular and diagnosis/detection tools are available. The described research and approaches might be useful for other pathogenic mollicutes that are recalcitrant to in vitro manipulation, detection and characterization, including the economically important mycoplasmas that impact human health and livestock industries. iv Dedicated to my parents, my brother and those I love v ACKNOWLEDGMENTS I wish to thank my adviser, Dr. Saskia A. Hogenhout, for her intellectual support and encouragement that made the whole research and this dissertation possible, and for her continuous support of my career development. I thank my Student Advisory Committee members, Dr. David L. Denlinger, Dr. David M. Francis, and Dr. Parwinder S. Grewal, for their advice and support of my graduate study. I thank Dr. Sophien Kamoun for his brilliant ideas and continuous support of my research and for the stimulating discussions. I am grateful to those who helped me with various experiments and techniques during my research, especially Mr. Ian Holford for computer programming, Dr. El- Desouky Ammar and Dr. Tea Meulia for electron and confocal microscopy, Dr. Michael M. Goodin for protein localization in plants, Dr. David M. Francis and Ms. Jorunn Bos for microarray data analysis, Mr. Valdir Ribeiro Correa, Ms. Diane M. Hartzler, Ms. Angela D. Strock, Ms. Miaoying Tian and Ms. Diane M. Kinney for help with the PVX assays, Dr. Thirumala Kanneganti for assistance with virus-induced gene silencing experiments, Mr. Edgar Huitema, Mr. Mark W. Jones, and Dr. Margaret Redinbaugh for isotope usage, Ms. Kristen J. Willie, Ms. Janet McCormick, and Dr. Juliette Hanson for mouse antibody production. vi This research is supported by The Ohio State University – Ohio Agricultural Research and Development Center (OARDC) Research Enhancement Competitive Grant Program, Ohio Plant Biotechnology Consortium (OPBC) and the AY-WB phytoplasma genome-sequencing project is supported by the United States Department of Agriculture / National Science Foundation (USDA/NSF) Microbial Genome Sequencing Program. vii VITA Oct. 15, 1974................................................ Born - Daqing, P. R. China 1992-1996.................................................... B.S. Department of Biological Science and Technology, Zhejiang University, Hangzhou, P. R. China 1996-1999.................................................... M.S. Institute of Zoology, Chinese Academy of Sciences, Beijing, P. R. China 1999-2000.................................................... Researcher, Qingdao Yongsheng Guangyuan Corporation, Qingdao, P. R. China 2000-present ................................................ Graduate Research Associate, Department of Entomology, The Ohio State University, OH, USA HONORS AND AWARDS • Department Fellowship, Department of Entomology, The Ohio State University – Agricultural Research and Development Center (OARDC), OH, U.S.A. 2003- 2004 • OARDC Director’s Fellowship, The Ohio State University, OH, U.S.A. 2000- 2003 • Research Grant from OARDC Research Enhancement Competitive Grant Program, The Ohio State University, OH, U.S.A. 2003-2004 • American Phytopathological Society Foundation The Raymond G. Grogan Travel Award, Milwaukee, MI, U.S.A. 2002 • Chinese Academy of Sciences Di’Ao scholarship, Beijing, P.R. China. 1999 viii PUBLICATIONS Research publications 1. Xiaodong Bai, Tatiana Fazzolari, and Saskia A. Hogenhout. 2004. Identification and Characterization of Spiroplasma kunkelii traE genes. Gene 336(1), 81-91. 2. Xiaodong Bai, Jianhua Zhang, Ian R. Holford, and Saskia A. Hogenhout. 2004. Comparative genomics identifies genes shared by distantly related insect-transmitted plant pathogenic mollicutes. FEMS Microbiology Letters 235, 249-258. 3. Wencai Yang, Xiaodong Bai, Eileen Kabelka, Christina Eaton, Sophien Kamoun, Esther van der Knaap, and David Francis. 2004. Discovery of single nucleotide polymorphisms in Lycopersicon esculentum and mapping of fruit color QTL in elite populations. Molecular Breeding 14, 21-34. 4. El-Desouky Ammar, Dave Fulton, Xiaodong Bai, Tea Meulia and Saskia A. Hogenhout. 2003. An attachment tip and fimbriae-like structures in plant- and insect- pathogenic spiroplasmas of the class Mollicutes. Archives of Microbiology 181(2), 97- 105. 5. Xiaodong Bai and Saskia A. Hogenhout. 2002. A genome sequence survey of the mollicute corn stunt spiroplasma Spiroplasma kunkelii. FEMS Microbiology Letters 210(1), 7-17. 6. Qiang Liu, Yan Ye, Xiaodong Bai, and Cui Ding. 2001. Genetic localization of the synergistic factor of Pseudaletia separata granulosis virus. Acta Entomologica Sinia 44(2), 148-154.
Load more

Recommended publications
  • The Role of Earthworm Gut-Associated Microorganisms in the Fate of Prions in Soil
    THE ROLE OF EARTHWORM GUT-ASSOCIATED MICROORGANISMS IN THE FATE OF PRIONS IN SOIL Von der Fakultät für Lebenswissenschaften der Technischen Universität Carolo-Wilhelmina zu Braunschweig zur Erlangung des Grades eines Doktors der Naturwissenschaften (Dr. rer. nat.) genehmigte D i s s e r t a t i o n von Taras Jur’evič Nechitaylo aus Krasnodar, Russland 2 Acknowledgement I would like to thank Prof. Dr. Kenneth N. Timmis for his guidance in the work and help. I thank Peter N. Golyshin for patience and strong support on this way. Many thanks to my other colleagues, which also taught me and made the life in the lab and studies easy: Manuel Ferrer, Alex Neef, Angelika Arnscheidt, Olga Golyshina, Tanja Chernikova, Christoph Gertler, Agnes Waliczek, Britta Scheithauer, Julia Sabirova, Oleg Kotsurbenko, and other wonderful labmates. I am also grateful to Michail Yakimov and Vitor Martins dos Santos for useful discussions and suggestions. I am very obliged to my family: my parents and my brother, my parents on low and of course to my wife, which made all of their best to support me. 3 Summary.....................................................………………………………………………... 5 1. Introduction...........................................................................................................……... 7 Prion diseases: early hypotheses...………...………………..........…......…......……….. 7 The basics of the prion concept………………………………………………….……... 8 Putative prion dissemination pathways………………………………………….……... 10 Earthworms: a putative factor of the dissemination of TSE infectivity in soil?.………. 11 Objectives of the study…………………………………………………………………. 16 2. Materials and Methods.............................…......................................................……….. 17 2.1 Sampling and general experimental design..................................................………. 17 2.2 Fluorescence in situ Hybridization (FISH)………..……………………….………. 18 2.2.1 FISH with soil, intestine, and casts samples…………………………….……... 18 Isolation of cells from environmental samples…………………………….……….
    [Show full text]
  • Investigating Prevalence and Geographical Distribution of Mycoplasma Sp. in the Gut of Atlantic Salmon (Salmo Salar L.)
    Master’s Thesis 2020 60 ECTS Faculty of Chemistry, Biotechnology and Food Science Investigating prevalence and geographical distribution of Mycoplasma sp. in the gut of Atlantic Salmon (Salmo salar L.) Mari Raudstein MSc Biotechnology ACKNOWLEDGEMENTS This master project was performed at the Faculty of Chemistry, Biotechnology and Food Science, at the Norwegian University of Life Sciences (NMBU), with Professor Knut Rudi as primary supervisor and associate professor Lars-Gustav Snipen as secondary supervisor. To begin with, I want to express my gratitude to my supervisor Knut Rudi for giving me the opportunity to include fish, one of my main interests, in my thesis. Professor Rudi has helped me execute this project to my best ability by giving me new ideas and solutions to problems that would occur, as well as answering any questions I would have. Further, my secondary supervisor associate professor Snipen has helped me in acquiring and interpreting shotgun data for this thesis. A big thank you to both of you. I would also like to thank laboratory engineer Inga Leena Angell for all the guidance in the laboratory, and for her patience when answering questions. Also, thank you to Ida Ormaasen, Morten Nilsen, and the rest of the Microbial Diversity group at NMBU for always being positive, friendly, and helpful – it has been a pleasure working at the MiDiv lab the past year! I am very grateful to the salmon farmers providing me with the material necessary to study salmon gut microbiota. Without the generosity of Lerøy Sjøtroll in Bømlo, Lerøy Aurora in Skjervøy and Mowi in Chile, I would not be able to do this work.
    [Show full text]
  • Fitness Costs of Chlorantraniliprole Resistance Related to the Senpf Overexpression in the Spodoptera Exigua (Lepidoptera: Noctuidae)
    International Journal of Molecular Sciences Article Fitness Costs of Chlorantraniliprole Resistance Related to the SeNPF Overexpression in the Spodoptera exigua (Lepidoptera: Noctuidae) Changwei Gong † , Xinge Yao †, Qunfang Yang, Xuegui Wang *, Yuming Zhang, Yumeng Wang and Litao Shen Biorational Pesticide Research Laboratory, Agricultural College, Sichuan Agricultural University, Chengdu 611130, China; [email protected] (C.G.); [email protected] (X.Y.); [email protected] (Q.Y.); [email protected] (Y.Z.); [email protected] (Y.W.); [email protected] (L.S.) * Correspondence: [email protected]; Tel.: +86-28-8629-0977 † Changwei Gong and Xinge Yao contributed equally to this work. Abstract: Spodoptera exigua, a multifeeding insect pest, has developed a high level of resistance to chlorantraniliprole, which is a benzoylurea insecticide that targets the ryanodine receptors (RyRs). Herein, the resistant strain (SE-Sel) and sensitive strain (SE-Sus) were obtained by bidirectional screening for six generations. The potential oviposited eggs and oviposition rate of the SE-Sel strain were dramatically lower than those of the SE-Sus strain; on the contrary, the weights of prepupae and preadult were significantly increased. As a post-mating response, the higher number of non- oviposited eggs in the SE-Sel strain was caused by a lower mating rate. In addition, the expression levels of vitellogenin (SeVg) and its receptor (SeVgR) in the SE-Sel strain were consistently lower than those in the SE-Sus strain. An RyRI4743M mutation, contributing to the resistance to chlorantraniliprole, Citation: Gong, C.; Yao, X.; Yang, Q.; was located in the S3 transmembrane segments and might have affected the release of calcium ions; Wang, X.; Zhang, Y.; Wang, Y.; Shen, L.
    [Show full text]
  • Species Determination – What's in My Sample?
    Species determination – what’s in my sample? What is my sample? • When might you not know what your sample is? • One species • You have a malaria sample but don’t know which species • Misidentification or no identification from culture/MALDI-TOF • Metagenomic samples • Contamination Taxonomic Classifiers • Compare sequence reads against a database and determine the species • BLAST works for a single sequence, too slow for a whole run • Classifiers use database indexing and k-mer searching • Similar accuracy to BLAST but much much faster Wood and Salzberg Genome Biology 2014, 15:R46 Page 3 of 12 http://genomebiology.com/2014/15/3/R46 Kraken taxonomic classifier Figure 1 The Kraken sequence classification algorithm. To classify a sequence, each k-mer in the sequence is mapped to the lowest common ancestor (LCA) of the genomes that contain that k-mer in a database. The taxa associated with the sequence’s k-mers, as well as the taxa’s ancestors, form a pruned subtree of the general taxonomy tree, which is used for classification. In the classification tree, each node has a 15 weight equal to the number of k-mersWood in the and sequence Salzberg associatedGenome with the Biology node’s taxon. 2014 Each root-to-leaf:R46 (RTL) path in the classification tree is scored by adding all weights in the path, and the maximal RTL path in the classification tree is the classification path (nodes highlighted in yellow). The leaf of this classification path (the orange, leftmost leaf in the classification tree) is the classification used for the query sequence.
    [Show full text]
  • 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.
    [Show full text]
  • 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.
    [Show full text]
  • 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).
    [Show full text]
  • Acholeplasma Florum, a New Species Isolated from Plants? R
    INTERNATIONALJOURNAL OF SYSTEMATICBACTERIOLOGY, Jan. 1984, p. 11-15 Vol. 34, No. 1 0020-7713/84/010011-05$02.OO/O Copyright 0 1984, International Union of Microbiological Societies Acholeplasma florum, a New Species Isolated from Plants? R. E. McCOY,l* H. G. BASHAM,' J. G. TULLY,* D. L. ROSE,2 P. CARLE,3 AND J. M. BOVE3 University of Florida Agricultural Research and Education Center, Fort Lauderdale, Florida 33314'; Laboratory of Molecular Microbiology, National Institute of Allergy and Infectious Diseases, Frederick, Maryland 21 70i2;and lnstitut National de la Recherche Agronomique, Pont de la Maye 33140, France3 Three acholeplasmas isolated from floral surfaces of healthy plants in Florida were found to be similar in their biochemical and serological properties. These organisms did not require serum or cholesterol for growth, although addition of some supplementary fatty acids (as represented by Tween 80) was necessary for growth to occur in serum-free medium. The three strains possessed biochemical properties typical of the Acholeplasmataceae and were distinguished from the nine previously recognized Acholeplasma species by serological and deoxyribopucleic acid-deoxyribonucleic acid hybridization techniques. The genome molec- ular weight of the three Acholeplasma strains was lo9, and the guanine-plus-cytosine content of the deoxyribonucleic acid was 27 to 28 mol%. On the basis of these results and other morphological, biological, and serological properties, we propose that these organisms represent a new species, Acholeplasmaflorurn. Strain L1 (= ATCC 33453) is the type strain. Plant surfaces, particularly flowers, have recently been Media and cultivation procedures. Isolates were routinely proven to be fertile sites for isolation of members of the grown in MC broth or in the serum fraction medium de- Mycoplasrnatales (5, 11-13, 26).
    [Show full text]
  • 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.
    [Show full text]
  • Genomic Islands in Mycoplasmas
    G C A T T A C G G C A T genes Review Genomic Islands in Mycoplasmas Christine Citti * , Eric Baranowski * , Emilie Dordet-Frisoni, Marion Faucher and Laurent-Xavier Nouvel Interactions Hôtes-Agents Pathogènes (IHAP), Université de Toulouse, INRAE, ENVT, 31300 Toulouse, France; [email protected] (E.D.-F.); [email protected] (M.F.); [email protected] (L.-X.N.) * Correspondence: [email protected] (C.C.); [email protected] (E.B.) Received: 30 June 2020; Accepted: 20 July 2020; Published: 22 July 2020 Abstract: Bacteria of the Mycoplasma genus are characterized by the lack of a cell-wall, the use of UGA as tryptophan codon instead of a universal stop, and their simplified metabolic pathways. Most of these features are due to the small-size and limited-content of their genomes (580–1840 Kbp; 482–2050 CDS). Yet, the Mycoplasma genus encompasses over 200 species living in close contact with a wide range of animal hosts and man. These include pathogens, pathobionts, or commensals that have retained the full capacity to synthesize DNA, RNA, and all proteins required to sustain a parasitic life-style, with most being able to grow under laboratory conditions without host cells. Over the last 10 years, comparative genome analyses of multiple species and strains unveiled some of the dynamics of mycoplasma genomes. This review summarizes our current knowledge of genomic islands (GIs) found in mycoplasmas, with a focus on pathogenicity islands, integrative and conjugative elements (ICEs), and prophages. Here, we discuss how GIs contribute to the dynamics of mycoplasma genomes and how they participate in the evolution of these minimal organisms.
    [Show full text]
  • Molecular Detection of Urogenital Mollicutes in Patients with Invasive Malignant Prostate Tumor Osama Mohammed Saed Abdul-Wahab1, Mishari H
    Abdul-Wahab et al. Infectious Agents and Cancer (2021) 16:6 https://doi.org/10.1186/s13027-021-00344-9 RESEARCH ARTICLE Open Access Molecular detection of urogenital mollicutes in patients with invasive malignant prostate tumor Osama Mohammed Saed Abdul-Wahab1, Mishari H. Al-Shyarba2, Boutheina Ben Abdelmoumen Mardassi3, Nessrine Sassi3, Majed Saad Shaya Al Fayi4, Hassan Otifi5, Abdullah Hassan Al Murea6, Béhija Mlik3 and Elhem Yacoub3* Abstract Background: The etiology of prostate cancer (PCa) is multiple and complex. Among the causes recently cited are chronic infections engendered by microorganisms that often go unnoticed. A typical illustration of such a case is infection due to mollicutes bacteria. Generally known by their lurking nature, urogenital mollicutes are the most incriminated in PCa. This study was thus carried out in an attempt to establish the presence of these mollicutes by PCR in biopsies of confirmed PCa patients and to evaluate their prevalence. Methods: A total of 105 Formalin-Fixed Paraffin-Embedded prostate tissues collected from 50 patients suffering from PCa and 55 with benign prostate hyperplasia were subjected to PCR amplification targeting species-specific genes of 5 urogenital mollicutes species, Mycoplasma genitalium, M. hominis, M. fermentans, Ureaplasma parvum, and U. urealyticum. PCR products were then sequenced to confirm species identification. Results significance was statistically assessed using Chi-square and Odds ratio tests. Results: PCR amplification showed no positive results for M. genitalium, M. hominis, and M. fermentans in all tested patients. Strikingly, Ureaplasma spp. were detected among 30% (15/50) of PCa patients. Nucleotide sequencing further confirmed the identified ureaplasma species, which were distributed as follows: 7 individuals with only U.
    [Show full text]
  • The Phylogenetic Composition and Structure of Soil Microbial Communities Shifts in Response to Elevated Carbon Dioxide
    View metadata, citation and similar papers at core.ac.uk brought to you by CORE provided by University of Minnesota Digital Conservancy The ISME Journal (2012) 6, 259–272 & 2012 International Society for Microbial Ecology All rights reserved 1751-7362/12 www.nature.com/ismej ORIGINAL ARTICLE The phylogenetic composition and structure of soil microbial communities shifts in response to elevated carbon dioxide Zhili He1, Yvette Piceno2, Ye Deng1, Meiying Xu1,3, Zhenmei Lu1,4, Todd DeSantis2, Gary Andersen2, Sarah E Hobbie5, Peter B Reich6 and Jizhong Zhou1,2 1Institute for Environmental Genomics, Department of Botany and Microbiology, University of Oklahoma, Norman, OK, USA; 2Ecology Department, Earth Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA; 3Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Guangdong Institute of Microbiology, Guangzhou, China; 4College of Life Sciences, Zhejiang University, Hangzhou, China; 5Department of Ecology, Evolution, and Behavior, St Paul, MN, USA and 6Department of Forest Resources, University of Minnesota, St Paul, MN, USA One of the major factors associated with global change is the ever-increasing concentration of atmospheric CO2. Although the stimulating effects of elevated CO2 (eCO2) on plant growth and primary productivity have been established, its impacts on the diversity and function of soil microbial communities are poorly understood. In this study, phylogenetic microarrays (PhyloChip) were used to comprehensively survey the richness, composition and structure of soil microbial communities in a grassland experiment subjected to two CO2 conditions (ambient, 368 p.p.m., versus elevated, 560 p.p.m.) for 10 years. The richness based on the detected number of operational taxonomic units (OTUs) significantly decreased under eCO2.
    [Show full text]