Molecular Biology and Pathogenicity of Molecular Biology and Pathogenicity of Mycoplasmas

Edited by

Shmuel Razin The Hebrew University-Hadassah Medical School Jerusalem, Israel and

Richard Herrmann University 0/ Heidelberg Heidelberg, Germany

Springer Science+Business Media, LLC ISBN 978-1-4757-8232-5 ISBN 978-0-306-47606-8 (eBook) DOI 10.1007/978-0-306-47606-8

©2002 Springer Science+Business Media New York Originally published by Kluwer Academic I Plenum Publishers, New York in 2002. Softcover reprint ofthe hardcover 1st edition 2002 http://www.wkap.nll W 9 8 765 4 3 2 1 A C.I.P. record for this book is available from the Library of Congress All rights reserved No part of this book may be reproduced, stored in a retrleval system, or transmitted in any form or by any means, electronic, mechanical, photocopying, microfilming, recording, or otherwise, without written permission from the Publisher, with the exception of any material supplied specifically for the purpose of being entered and executed on a computer system, for exclusive use by the purchaser of the work. Foreword: From the Enigmatic Pleuropneumonia-like Organisms to the Paradigmatic

Over a century ago, Edmond Nocard and Pierre Roux were engaged in the study ofinfectious bovine pleuropneumonia. The etiological agents were filterab1e, 1ike the recently discovered viruses but could be cu1tured in sterile growth media simi1ar to bacteria1 culture.I When related taxa were discovered, they were designated p1europneumonia-like organisms (PPLO). The driving force for the first half of the century or more of PPLO research was the interest in a number of anima1 diseases associated with these organismsand the possibility oftheir involvement in human diseases. In 1960, Volume 79 Article 10 ofthe Annals ofthe New York Academy of Sciences' presented the proceedings of a previous year's meeting entitled, "Biology ofthe Pleuropneumonia-like Organisms." Among the authors were several of the pioneers in the description of these still incompletely characterized microbes. The papers in this volume reveal great uncertainty about the relation of the PPLO to bacteria, newly discovered bacterial L forms, viruses, and other infectious agents such as the rickettsia. Of course, 1959 was less than a century after the founding of microbiology by Koch and Pasteur. Most of the papers in the Academy volume focus on pathogenicity with particular reference to animal diseases of importance to agriculture. A few papers began to probe the biochemical characterization ofthese organisms. In the late 1950s, efforts were underway, from the perspective of biophysics, to seek the lower limit of life, the smallest, autonomous, self­ replicating organisms. This began as a search for microbial oddities and seemed to lead relentlessly toward the pleuropneumonia-like organisms, which might therefore have a special role to play in molecular biology . This second domain of interest in the PPLO resulted in the "Conference on the Molecular Biology of the Pleuropneumonia-like Organisms" held June 14-16, 1962, at the Vniversity of Connecticut. The site ofthe meeting v vi Foreword was the result of the efforts of Robert Cleverdon. The rapidly developing discipline of molecular biology and the rapidly expanding knowledge of the PPLO were brought together at this meeting. In addition to the PPLO· specialists, the conference invited Julius Marmur to compare PPLO DNA to DNA of other organisms; David Garfinkel, who was one of the first to develop computer models of ; Cyrus Levinthal to talk about coding; and Henry Quastler to discuss information theory constraints on very small cells. The conference was an announcement ofthe role ofPPLO in the fundamental understanding ofmolecular biology. Looking back 40-some years to the Connecticut meeting, it was a rather bold enterprise. The meeting was international and inter-disciplinary and began aseries of important collaborations with influences resonating down to the present. If I may be allowed a personal remark, it was where I first met Shmuel Razin, .who has been a leading figure in the emerging mycoplasma research and a good friend. This present volume is in some ways the fulfillment of the promise of that early meeting. It is an example of the collaborative work of scientists in building an understanding of fundamental aspects ofbiology. In the three years between the 1959 New York Academy meeting and the University of Connecticut meeting, the problem of establishing the structural nature of PPLO cellularity had been approached in many ways. The first Academy meeting had left uncertainty about whether we were dealing with normal cells, syncitia, or some other form ofbiological organization, perhaps a novel method of structure. In retrospect the uncertainties resulted from small size and absence of a rigid cell wall. From a physiological point of view, we regarded a cell as an aqueous core surrounded by a membrane with limited conductivity for polar molecules and ions, but this required proof. This type of problem could be studied by a biophysical method going back to J. Clerk Maxwell in 1873.3 It involved dielectric dispersion measurements on a packed suspension of cells between two platinum plates. We solicited the collaboration of Herman Schwan of the University of Pennsylvania, who was a specialist in dielectric dispersion studies. This led to the experimental conclusion" that the organization was indeed cellular with membranes having a capacitance of 1.3 pfarad/cm., which is anormal value for other living cells. These results allowed us to speak more definitely of the smallest living cells. In subsequent years, S. Razin and others have carried out detailed characterization of the membrane that gave rise to the electrical properties. Although the dielectric work is seldom cited, the dielectric dispersion studies were to me of enormous significance. They established the nature of the mycoplasma. Robert Cleverdon and I in 1959 had posited another feature of the organism, the small amount of DNA per cell or minimum .' Our experimental value was misleadingly small, which I believe was due to errors in our method of determining cell number. In 1962 Mark Tourtellotte and I explored the question, "What are the Foreword VB

smallest dimensions compatible with life?,,6 We were driven by the assumption that mycoplasma were primitive organisms. Another mea culpa: Carl Woese, Jack Maniloff, and L. B. Zablen later showed from molecular taxonomie arguments that, rather than being primitive, mycoplasma are the ultimate parasites and saprophytes.' I would now argue that primitive organisms must be autotrophs, and mycoplasma are the ultimate heterotrophs. Nonetheless, I believe that the taxon is of importance in the basic study ofallliving cells. In May 1966, a second meeting of the New York Academy of Seiences brought together a considerably larger group to discuss "Biology of the Mycoplasma''." The impressive volume is 824 pages. In the opening remarks, Leonard Hayflick notes, "Since the first conference dedicated to them seven years ago, taxonomie dignity has been obtained by replacing the name PPLO with proper Linnean terminology." The major subject of the 1966 volume is microbiology and characterization of mycoplasma. Much of what we now call molecular biology was in the seetion called physiology and pathogenicity. It divided according to the host taxon. In any case, from our point of view, the fundamentals ofthe material discussed in this volume had been laid down. The 1966 publication also included areport on Hans Bode's work on unambiguously determining the genome size and configuration of mycoplasma DNA. 9 This was an important normalizing ofthis taxon among the prokaryotes. In the absence ofmethods for determining the sequence of DNA nucleotides, other methods were then undertaken, such as lohn Ryan's analysis of t-RNA and r-RNA coding regions.!" This ultimately led to the studies on gene organization ofMycoplasma capricolum by Akira Muto and his coworkers and by Shmuel Razin and bis coworkers. In the 60s and 70s, mycoplasma also turned out to be a taxon of choice for certain basic membrane studies for two reasons. First, the small size resulted in a high surface-to-volume ratio and a large fraction of the cell's mass as membrane. Secondly, the absence of a cell wall facilitated the preparation ofmembrane. In addition, varying the fatty acid composition of the growth medium permitted considerable control in the membrane fatty acid composition. As a result, aseries of physical chemical studies of bilayer-phase transitions was carried out on purified membrane and whole cells.",12 It is doubtful that these fundamental membrane experiments could have been done with any other taxon . In asense, all ofthis was serendipity. Cells that were being studied for other reasons turned out to be ideal for basic biophysical characterizations of cellularity and fundamentals of membrane structure and function. The science that is the subject ofthis volume has covered about a century from the discovery of the etiological agent ofbovine pleuropneumonia to the sequencing ofthe genome ofMycoplasma genitalium and other species. It is rooted in the bacteriology ofPasteur and Koch, expands in the biochemistry Vlll Foreword ofWatson and Crick, matures into present day genomics and looks ahead to proteomics and physiomics. Starting as a sideshow of early microbiology, mycoplasma have become central to modem computational and theoretical biology and the understanding of infectious disease. To look ahead, I'm confident that the first decade of the 21st century will lead to a complete computer model of mycoplasma cell function. As the biology of the 21sI century unfolds, I suspect that the minimal cell concept as embodied in the mycoplasma will continue to be central to the understanding of life. The publishers and editors have chosen an appropriate moment in time for this volume.

HAROLD J. MOROWITZ Robinson Professor, Krasnow Institute for Advanced Studies, George Mason University, Fairfax, Virginia 22030, USA

I Nocard, E., E. R. Roux, Mm. Borrel, Salimbeni & Dujardin-Beaumetz. 1989. Le microbe de la peripneumonie. Ann. Inst. Pasteur 12: 240. 2 Biology of the Pleuropneumonia-like Organisms. Volume 79, Art. 10, Pages 305-758 . Annals ofthe New York Academy of Sciences, 1960. 3 MaxwelI, J. c., A Treatise ofElectricity and Magnetism, 1973, Oxford University Press. 4 Schwan, H. P. and Morowitz, J. H. Electrical Properties of the Membranes of Pleuropneumonia-Iike Organisms, A5969 , 1962, Biophysical Journal 2, 295-407. 5 Morowitz, H. J. and Cleverdon, R. C., An Extreme Examp1e ofthe Coding Problem , 1959, Avian PPLO 5969. Biochim. Biophys. Acta 34, 578-579. 6 Morowitz, H. J. and Tourtellotte, M. E., The SmalIest Living CelIs, 1962, Scientific American 206, 117-126. 7 Woese, C. R., J. Maniloff and L. B. Zablen , 1980, Phylogenetic Analy sis of the Mycoplasmas. Proc. Nat. Acad. Sei., USA, 77, 494-498 . 8 Biology ofthe Mycoplasma, 1967, Vo1ume 143, Art 1, Pages 1-824, Annals ofthe New York Academy ofSciences. 9 Bode, H. R. and Morowitz, H. 1., 1967, Size and Structure ofthe Mycoplasma hominis H39 Chromosome,J. Mol. Bioi., 23,191-199. 10 Ryan, 1. L. and Morowitz, H. 1., 1969, Partial Purification of Native r-RNA and t-RNA Cistrons from Mycoplasma SP. (Kid), Proc. Nat Acad. Sei. 73, 1282-1289 . 11 Stein, 1. M., TourtelIotte, M. E., Reinhert , 1. C., McElhaney, R. N. and Rader, R. L., 1969, Calorimetric Evidence of Liquid-Crystalline State of Lipids in Biomembrane. Proc. Nat. Acad. Sei. USA, 63,104-109 . 12 Melchior, D. L., Morowitz, H. J., Sturtevant, 1. M. and Tsong, T Y., 1970, Phase Transitions in Membrane Lipids. Biochim . Biophys. Acta. 219, 114-122. Preface

The mycoplasmas (c1ass Mollicutes) represent a wide spectrum of phylogenetically related parasitic bacteria. They have already served in the past as models for basic research but in many cases these studies were hindered by the lack of efficient methods for genetic transformation and by the fastidious growth of many mollicute species. The newly developed or improved methods of molecular biology and bioinformatics helped to overcome these problems to some extent. High through-put DNA sequencing, handling of large data sets, the peR technology with the possibility to mutate DNA with relative ease and express mycoplasmal genes in foreign hosts have contributed to the success of many research projects summarized in the present book . The recent sequencing of the entire of , M pneumoniae, M pulmonis and Ureaplasma urealyticum has marked a turning point in the molecular genetic analysis of these organisms. Studying gene expression with complete cells at the level of transcription (transcriptome analysis) and at the level of translation (proteome analysis) and relating the products to genes or ORFs defined by total genome sequences promises to provide us with the definition of the total protein complement of a cell. The Mollicutes group inc1udes the smallest known self-replicating organisms carrying the smallest number of genes. There is no wonder, therefore, that mycoplasmas have a special appeal to those interested in the definition ofthe minimal set ofgenes essential for life considering this as an important step on the way ofreaching the goal of defining in molecular terms the entire machinery of a self­ replicating cell,

ix x Preface

The application of mo1ecu1ar markers has also pushed forward our understanding of the phylogeny of Mollicutes, p1acing their taxonomy on a sound mo1ecu1ar basis. The use of mo1ecular markers and comparative genomics in taxonomy has extended the scope of mycoplasmology by enabling the classification of uncultivable mycoplasmas, such as the plant pathogenic phytoplasmas, and the recent inclusion in Mollicutes of the Eperythrozoon and Haemobartonella species, classified previously as rickettsia. Considerable advances were also made towards better understanding of mycoplasma pathogenesis. Most impressive are the findings concerning the interaction of mycoplasmas with the immune system, macrophage activation, cytokine induction, mycoplasma ceIl components acting as -superantigens, and autoimmune manifestations. Evasion of the host immune system by antigenic variation of mycoplasmal surface components is another subject that has gained much attention recently, as weIl as the molecular definition of mycoplasmal adhesins. The recent demonstration of the ability of mycoplasmas to enter host cells, cause fusogenic, apoptotic and oncogenic effects, as weIl as the possible association of mycoplasmas with activation of arthritis, and several other human diseases of unknown aetiology had their share in intensifying research on mycoplasma pathogenesis, bringing more researchers into the circle of those interested in this group of organisms. The last multi-authored treatise on mycoplasmas: "Mycoplasmas: Molecular Biology and Pathogenesis" (J. Maniloff, R.N. McElhaney, L.R. Finch, and J.B. Baseman, eds.) was published in 1992. Large parts of tbis book are now out of date. Several reviews covering different aspects of mycoplasmology have been published during the last decade. Clearly, these reviews could not fill the gap created by the lack ofa comprehensive, up-to­ date multi-authored treatise including the new advances in the molecular aspects of mycoplasma research. The need for such a book has been feIt for quite a wbile, not on1y by mycoplasmologists, but also by molecular biologists and the many researchers newly attracted to the study of Mollicutes as excellent models in genomics and proteomics. Some comments as to the nomenclature used in the book: While the trivial terms "mycoplasmas" or "mollicutes" are used interchangeably to denote any species included in Mollicutes, the names ureaplasmas, entomoplasmas, mesoplasmas, spiroplasmas, acholeplasmas, asteroleplasmas, and anaeroplasmas are routinely used for members of the corresponding genera, and the term phytoplasmas is reserved for the uncultivable plant mycoplasmas. Preface xi

Considering the relatively large number of chapters and contributors, keeping to the deadline set by the publisher is an achievement by itself. Obviously, this could not be accomplished without the cooperation of the many contributors. We express our gratitude and appreciation for their friendly collaboration in this endeavor. We thank also the Senior Publishing Editor (Biosciences) Joanna Lawrence, for her prompt and most efficient help in facilitating the fast publication of this book.

Shmuel Razin Richard Herrmann Contents

MYCOPLASMA DIVERSITY AND CELL BIOLOGY

1. Taxonomy ofMollicutes Karl-Erik Johansson and Bertil Pettersson

2. Phylogeny and Evolution 31 Jaek Maniloff

3. Myeoplasmas ofHumans 45 Alain Blanehard and Cecile M. Bebear

4. Myeoplasmas ofAnimals 73 Joaehim Frey

5. Myeoplasmas ofPlants and Inseets 91 Erieh Seemüller, Monique Gamier, and Bemd Schneider

6. Cell Division 117 Makoto Miyata

7. The Cell Membrane and Transport 131 Äke Wieslander and Maria Rosen

8. Central Carbohydrate Pathways: Metabolie Flexibility and the Extra Role of Some "Housekeeping" Enzymes 163 J.Dennis Pollack

xiii xiv Contents

9. Database Systems for the Analysis ofBiochemical Pathways 201 Isabel Rojas-Mujica and Erich Bornberg-Bauer

MOLECULAR GENETICS

10. Mycoplasmas and the Minimal Genome Concept 221 C1ydeA. Hutchison III and Michael G. Montague

11. Comparative Genome Analysis ofthe Mollicutes 255 Thomas Dandekar, Berend Sne1, Steffen Schmidt, Warren Lathe, Mikita Suyama, Martijn Huynen, and Peer Bork

12. Transcriptome and Proteome Analysis ofMollicutes 279 n January Weiner 3 \ Carl-U1richZimmermann, Barbara Ueberle, and Richard Herrmann

13. DNA Replication, Repair and Stress Response 303 Nianxiang Zou and Kevin Dybvig

14. Transcription and Translation 323 Akira Muto and Chisato Ushida

15. Extrachromosomal Elements and Gene Transfer 347 Joel Renaudin

16. Restriction-Modification Systems and Chromosomal Rearrangements in Mycoplasmas 371 Ramakrishnan Sitaraman and Kevin Dybvig

PATHOGENESIS

17. Invasion ofMycoplasmas into and Fusion with Host Cells 391 Shlomo Rottem

18. Apoptotic, Antiapoptotic, Clastogenic and Oncogenic Effects 403 Shyh-Ching Lo

19. Genetic Mechanisms ofSurface Variation 417 David Yogev, Glenn F. Browning and Kim S. Wise

20. Immunomodulation by Mycoplasmas: Artifacts, Facts and Active Molecules 445 Peter F. Muhlradt Contents xv

21. Myc oplasma arthritidis Pathogenicity: Membranes, MAM and MAVI 473 Leigh R. Washbum and Barry C. Cole

22. Cytadherence and the Cytoskeleton 491 Mitchell F. Balish and Duncan C. Krause

23. Disease Manifestations and Epidemiology 519 Enno Jacobs

24. Diagnosis ofMycoplasmal Infections 531 Shmuel Razin

25. Antimycoplasmal Agents 545 Cecile M. Bebear and Christiane Bebear

Index 567