Halophiles: Genetics and Genomes PDF
Preview Halophiles: Genetics and Genomes
Halophiles Genetics and Genomes Edited by R. Thane Papke and Aharon Oren Caister Academic Press Halophiles Genetics and Genomes Edited by R. Thane Papke Department of Molecular and Cell Biology University of Connecticut Storrs, CT USA and Aharon Oren Department of Plant and Environmental Sciences The Hebrew University of Jerusalem Jerusalem Israel Caister Academic Press Copyright © 2014 Caister Academic Press Norfolk, UK www.caister.com British Library Cataloguing-in-Publication Data A catalogue record for this book is available from the British Library ISBN: 978-1-908230-42-3 (hardback) ISBN: 978-1-908230-65-2 (ebook) Description or mention of instrumentation, software, or other products in this book does not imply endorsement by the author or publisher. The author and publisher do not assume responsibility for the validity of any products or procedures mentioned or described in this book or for the consequences of their use. All rights reserved. No part of this publication may be reproduced, stored in a retrieval system, or transmitted, in any form or by any means, electronic, mechanical, photocopying, recording or otherwise, without the prior permission of the publisher. No claim to original U.S. Government works. Cover design adapted from photos taken by Scott Chimileski, Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT, USA. Contents Contributors v Preface ix 1 Ecology and Evolution of Haloquadratum walsbyi Through the Lens of Genomics and Metagenomics 1 Lejla Pašić and Francisco Rodríguez-Valera 2 Salinibacter ruber: The Never Ending Microdiversity? 37 Arantxa Peña, María Gomariz, Marianna Lucio, Pedro González- Torres, Jaime Huertas-Cepa, Manuel Martínez-García, Fernando Santos, Phillippe Schmitt-Kopplin, Toni Gabaldón, Ramon Rosselló-Móra and Josefa Antón 3 Horizontal Gene Transfer in Halobacteria 57 Matthew S. Fullmer, J. Peter Gogarten and R. Thane Papke 4 Comparative Genomics of Haloarchaeal Viruses 77 Elina Roine 5 Microbial Adaptation to Saline Environments: Lessons from the Genomes of Natranaerobius thermophilus and Halobacillus halophilus 107 Noha M. Mesbah, Inga Hänelt, Baisuo Zhao and Volker Müller 6 Staying in Shape: The Haloarchaeal Cell Wall 129 Jerry Eichler, Adi Arbiv, Chen Cohen-Rosenzweig, Lina Kaminski, Lina Kandiba, Zvia Konrad and Shai Naparstek 7 Cell Cycle and Polyploidy in Haloarchaea 145 Karolin Zerulla, Anke Baumann and Jörg Soppa iv | Contents 8 Cell Regulation by Proteolytic Systems and Protein Conjugation 167 Julie Maupin-Furlow Index 195 Contributors Josefa Antón Jerry Eichler Department of Physiology, Genetics and Department of Life Sciences Microbiology Ben Gurion University University of Alicante Beersheva Alicante Israel Spain [email protected] [email protected] Matthew S. Fullmer Adi Arbiv Department of Molecular and Cell Biology Department of Life Sciences University of Connecticut Ben Gurion University Storrs, CT Beersheva USA Israel [email protected] [email protected] Toni Gabaldón Anke Baumann Pompeu Fabra University (UPF); and Institute for Molecular Biosciences Bioinformatics and Genomics Programme Goethe University Frankfurt am Main Centre for Genomic Regulation (CRG) Frankfurt am Main Barcelona Germany Spain [email protected] [email protected] Chen Cohen-Rosenzweig J. Peter Gogarten Department of Life Sciences Department of Molecular and Cell Biology Ben Gurion University University of Connecticut Beersheva Storrs, CT Israel USA [email protected] [email protected] vi | Contributors María Gomariz Lina Kandiba Evolutionary Genomics Group Department of Life Sciences Department of Physiology, Genetics and Ben Gurion University Microbiology; and Beersheva Department of Materials Israel Optics and Electronics [email protected] University Miguel Hernández Elche Zvia Konrad Alicante Department of Life Sciences Spain Ben Gurion University [email protected] Beersheva Israel Pedro González-Torres [email protected] Department of Physiology, Genetics and Microbiology Marianna Lucio University of Alicante Research Unit Analytical BioGeoChemistry Alicante Helmholtz Zentrum Munich, German Spain Research Center for Environmental Health [email protected] Neuherberg Germany Inga Hänelt [email protected] Department of Molecular Microbiology and Bioenergetics Manuel Martínez-García Goethe University Frankfurt am Main Department of Physiology, Genetics and Frankfurt am Main Microbiology Germany University of Alicante [email protected] Alicante Spain Jaime Huertas-Cepa [email protected] Pompeu Fabra University (UPF); and Bioinformatics and Genomics Programme Julie Maupin-Furlow Centre for Genomic Regulation (CRG) Department of Microbiology and Cell Science Barcelona University of Florida Spain Gainesville, FL [email protected] USA [email protected] Lina Kaminski Department of Life Sciences Noha M. Mesbah Ben Gurion University Department of Biochemistry Beersheva Faculty of Pharmacy Israel Suez Canal University [email protected] Ismailia Egypt [email protected] Contributors | vii Volker Müller Arantxa Peña Department of Molecular Microbiology and Department of Physiology, Genetics and Bioenergetics Microbiology Goethe University Frankfurt am Main University of Alicante Frankfurt am Main Alicante; and Germany Department of Biology-Microbiology University of Balearic Islands [email protected] Palma de Mallorca Balearic Islands Shai Naparstek Spain Department of Life Sciences Ben Gurion University [email protected] Beersheva Israel Francisco Rodríguez-Valera Evolutionary Genomics Group [email protected] División de Microbiología Universidad Miguel Hernández Aharon Oren San Juan de Alicante Department of Plant and Environmental Spain Sciences The Institute of Life Sciences [email protected] The Hebrew University of Jerusalem Jerusalem Elina Roine Israel Department of Biosciences University of Helsinki [email protected] Helsinki Finland R. Thane Papke Department of Molecular and Cell Biology [email protected] University of Connecticut Storrs, CT Ramon Rosselló-Móra USA Marine Microbiology Group Department of Ecology and Marine Resources [email protected] Institut Mediterrani d’Estudis Avançast IMEDEA (CSIC-UIB) Lejla Pašić Esporles Department of Biology Balearic Islands Biotechnical Faculty Spain University of Ljubljana Ljubljana [email protected] Slovenia Fernando Santos [email protected] Department of Physiology, Genetics and Microbiology University of Alicante Alicante Spain [email protected] viii | Contributors Phillippe Schmitt-Kopplin Karolin Zerulla Research Unit Analytical BioGeoChemistry Institute for Molecular Biosciences Helmholtz Zentrum Munich, German Goethe University Frankfurt am Main Research Center for Environmental Health Frankfurt am Main Neuherberg; and Germany Analytical Food Chemistry Department [email protected] Technische Universität München Freising-Weihenstephan Baisuo Zhao Germany Graduate School Chinese [email protected]\ Academy of Agricultural Sciences Beijing Jörg Soppa China Institute for Molecular Biosciences [email protected] Goethe University Frankfurt am Main Frankfurt am Main Germany [email protected] Preface Admittedly, it is trying to study microorganisms whose growth media fills the labora- tory with steam, or the centrifuge heads with salt, or which grow so slowly that weeks, instead of hours, may be required for experiments and whose genetics are unknown or almost impossible to study. These words were written by the late Donn Kushner (1927–2001) in his introduction to his book Microbial Life in Extreme Environments (Kushner, 1978a). Although much progress has been made in the 35 years that have passed since, the message is still perfectly true. Some of the most intriguing halophiles such as the flat square archaeon Haloquadratum walsbyi are still very difficult to grow and at best grow very slowly. Genetic systems have been developed only for a limited number of extremely halophilic Archaea, and a few moderately halophilic Bacteria. But thanks to the development of genetic systems for organisms such as Halobacte- rium salinarum, Haloferax volcanii (Euryarchaeota) and Halobacillus halophilus (Firmicutes) we now have a fair number of model organisms in which the molecular biology of diverse groups of halophilic microorganisms can be studied. Modern molecular techniques of genomics and culture-independent methods of metagenomics have also contributed much towards our understanding of the functioning of a wide range of halophilic microorganisms and their viruses. This book contains eight essays covering different aspects of the genetics and the genom- ics of halophiles, with special emphasis on those topics in which significant progress has been made in recent years. Organisms featured are extreme as well as moderate halophiles, types that grow at neutral as well as alkaline pH, species that prefer moderate as well as high temperatures for growth. The first chapters mainly deal with genomic and culture-independent metagenomic approaches to understanding the diversity and evolution of halophiles in their natural environment. Cultures of Haloquadratum walsbyi are now available, but they are difficult to handle. However, very much has been learned about their properties by culture-inde- pendent approaches, as shown in Chapter 1 by Lejla Pašić and Francisco Rodríguez-Valera. Salinibacter ruber is an extremely halophilic member of the Bacteria resembling in many properties the halophilic Archaea. It was discovered little over a decade ago, and also here genomic and metagenomic approaches have greatly increased our understanding of its biology (Chapter 2 by Aranxa Peña and co-workers). In Chapter 3, Matthew Fullmer and his colleagues document the frequency and wide-spread nature of horizontal gene transfer (HGT) among the haloarchaea in their natural environment, and provide conjecture on
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