The bacterial spore: from molecules to systems

412 Pages·2016·21.287 MB·English

by  Driks, Adam, Eichenberger, Patrick

THE Bacterial Spore
FROM MOLECULES TO SYSTEMS
The study of bacterial spores ranges from biosecurity to ecology

The fi rst articles describing the sporulation process were published by Robert Koch and Ferdinand
Cohn in the late 19th century. Although most of the work accomplished in the past 50 years has T THE
focused on the model organism Bacillus subtilis, more recent work has signifi cantly expanded the H
scope of sporulation research to integrate medically relevant spore pathogens, such as Bacillus E
anthracis and Clostridium diffi cile, as well as investigations of the ecology of spore-forming species. Bacterial
This new direction is supported by an explosion of novel techniques that can also be applied to B
nonmodel organisms, such as next-generation sequencing, metagenomics, and transcriptomics.
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The Bacterial Spore provides a comprehensive series of reviews of the major topics in spore biology
c
that represent intensive, cutting-edge spore research. Editors Adam Driks and Patrick Eichenberger
t
have assembled chapters written by a team of diverse and multidisciplinary experts in biodefense
e
and microbial forensics to produce an overview of topics of spore research—such as spore molecular
biology, bioremediation, systems biology, issues in biodefense, and the challenge of food safety— r Spore
that is accessible to any reader regardless of expertise. The Bacterial Spore also encompasses the i
a
diversity of spore research, which will appeal to those seeking to broaden their knowledge. FROM
l
The Bacterial Spore is a reference for a wide range of readers, including geneticists, cell biologists,
physiologists, structural and evolutionary biologists, applied scientists, advanced undergraduate S MOLECULES
and graduate students, and nonresearchers such as national security professionals.
p
TO SYSTEMS
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“ The Bacterial Spore: From Molecules to Systems is an ambitious effort at consolidating this body
r
of research in a way that highlights the biological diversity of bacterial spore formers, their industrial
e
and medical applications, and fundamental mechanistic insights gained from their study in a way
that is accessible to both the novice and expert microbiologist.”
—KUMARAN S. RAMAMURTHI, Ph.D., Investigator, National Cancer Institute, National Institutes of Health
ADAM DRIKS is a Professor in the Department of Microbiology and Immunology in the D
Stritch School of Medicine at Loyola University Chicago. He received his Ph.D. from R
I
Brandeis University, in the laboratory of Dr. David DeRosier, where he analyzed the K
S
composition and assembly of bacterial fl agella. He performed postdoctoral research
•
in the laboratory of Dr. Richard Losick at Harvard University, where he initiated his
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work on assembly and composition of the Bacillus spore coat. I
C
H
PATRICK EICHENBERGER is an Associate Professor of Biology in the Center for Genomics E
N
and Systems Biology at New York University. He obtained his Ph.D. from the University
B
of Geneva, where he studied molecular mechanisms of transcriptional activation in E
R
the laboratory of Dr. Hans Geiselmann. He started his work on spore formation in the
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laboratory of Dr. Richard Losick at Harvard University. He established his own laboratory E
R
in 2004 at New York University, where he studies global gene transcription networks
and mechanisms of spore coat assembly in Bacillus subtilis and related bacteria.
ADAM DRIKS • PATRICK EICHENBERGER
BacterialSporeFULL.indd 1 3/31/16 4:03 PM
THE
Bacterial
Spore
FROM
MOLECULES
TO SYSTEMS

THE
Bacterial
Spore
FROM
MOLECULES
TO SYSTEMS
EDITED BY
ADAM DRIKS
Stritch School of Medicine, Loyola University Chicago, Maywood, IL
PATRICK EICHENBERGER
Center for Genomics & Systems Biology, New York University, New York, NY
Washington, DC
Copyright 2016 © by ASM Press. ASM Press is a registered trademark of the American
Society for Microbiology. All rights reserved. No part of this publication may be reproduced
or transmitted in whole or in part or reutilized in any form or by any means, electronic
or mechanical, including photocopying and recording, or by any information storage and
retrieval system, without permission in writing from the publisher.
Disclaimer: To the best of the publisher’s knowledge, this publication provides information
concerning the subject matter covered that is accurate as of the date of publication. The
publisher is not providing legal, medical, or other professional services. Any reference
herein to any specific commercial products, procedures, or services by trade name, trademark,
manufacturer, or otherwise does not constitute or imply endorsement, recommendation,
or favored status by the American Society for Microbiology (ASM). The views and opinions
of the author(s) expressed in this publication do not necessarily state or reflect those of
ASM, and they shall not be used to advertise or endorse any product.
Library of Congress Cataloging-in-Publication Data
Names: Driks, Adam, editor. | Eichenberger, Patrick (Professor of biology), editor.
Title: The bacterial spore : from molecules to systems / edited by Adam Driks and
Patrick Eichenberger.
Description: Washington, DC : ASM Press, [2016] | ?2016 | Includes bibliographical
references and index.
Identifiers: LCCN 2016012264 (print) | LCCN 2016014762 (ebook) | ISBN
9781555816759 (print : alk. paper) | ISBN 9781555819323 ()
Subjects: LCSH: Bacterial spores. | Sporeforming bacteria.
Classification: LCC QR79 .B328 2016 (print) | LCC QR79 (ebook) | DDC 579--dc23 LC
record available at http://lccn.loc.gov/2016012264
Printed in the United States of America
10 9 8 7 6 5 4 3 2 1
Address editorial correspondence to: ASM Press, 1752 N St., N.W., Washington,
DC 20036-2904, USA.
Send orders to: ASM Press, P.O. Box 605, Herndon, VA 20172, USA.
Phone: [phone]. Fax: [phone].
E-mail: [email protected]
Online: http://estore.asm.org
Contents
Contributors vii
Preface xi
I. generaL overvIew of the bacillaceae
anD CLostrIDIa
1. Genome Diversity of Spore-Forming Firmicutes 3
Michael Y. Galperin
2. Evolution in the Bacillaceae 21
Patricia Fajardo-Cavazos, Heather Maughan, and Wayne L. Nicholson
3. Ecology of Bacillaceae 59
Ines Mandic-Mulec, Polonca Stefanic, and Jan Dirk van Elsas
4. Sporulation in Bacteria: Beyond the Standard Model 87
Elizabeth A. Hutchison, David A. Miller, and Esther R. Angert
II. the bacillaceae: bacillUS SUbTiliS
5. Chance and Necessity in Bacillus subtilis Development 105
Nicolas Mirouze and David Dubnau
6. Bacillus subtilis Systems Biology: Applications of -Omics
Techniques to the Study of Endospore Formation 129
Ashley R. Bate, Richard Bonneau, and Patrick Eichenberger
v
vi Contents
7. Protein Targeting during Bacillus subtilis Sporulation 145
Jonathan Dworkin
8. Spore Peptidoglycan 157
David L. Popham and Casey B. Bernhards
9. The Spore Coat 179
Adam Driks and Patrick Eichenberger
1 0. Spore Resistance Properties 201
Peter Setlow
1 1. Spore Germination 217
Anne Moir and Gareth Cooper
III. the bacillaceae: bacillUS anThraciS
12. The Phylogeny of Bacillus cereus sensu lato 239
Richard T. Okinaka and Paul Keim
1 3. The Bacillus anthracis Exosporium: What’s the Big
“Hairy” Deal? 253
Joel A. Bozue, Susan Welkos, and Christopher K. Cote
1 4. Animal Models for the Pathogenesis, Treatment, and Prevention
of Infection by Bacillus anthracis 269
Susan Welkos, Joel A. Bozue, Nancy Twenhafel,
and Christopher K. Cote
Iv. the CLostrIDIa
15. Physiology and Sporulation in Clostridium 315
Peter Du¨rre
1 6. Clostridium perfringens Sporulation and Sporulation-Associated
Toxin Production 331
Jihong Li, Daniel Paredes-Sabja, Mahfuzur R. Sarker,
and Bruce A. McClane
v. PraCtICaL teChnoLogIes
17. Spore Surface Display 351
Rachele Isticato and Ezio Ricca
1 8. The Role of Bacterial Spores in Metal Cycling and Their Potential
Application in Metal Contaminant Bioremediation 367
Cristina N. Butterfield, Sung-Woo Lee, and Bradley M. Tebo
I ndex 387
Contributors
Esther R. Angert
Department of Microbiology, Cornell University, Wing Hall, Ithaca, NY 14853
Ashley R. Bate
Center for Genomics and Systems Biology, Department of Biology, New York
University, New York, NY 10003
Casey B. Bernhards
U.S. Army Edgewood Chemical Biological Center, 5183 Blackhawk Rd., E3835,
Aberdeen Proving Ground, MD 21010
Richard Bonneau
Center for Genomics and Systems Biology, Department of Biology, New York
University, New York, NY 10003
Joel A. Bozue
U.S. Army Medical Research Institute of Infectious Diseases, Division of
Bacteriology, 1425 Porter Street, Fort Detrick, MD 21702
Cristina N. Butterfield
Division of Environmental and Biomolecular Systems, Institute of Environmental
Health, Oregon Health & Science University, 3181 S. W. Sam Jackson Park Rd.,
Portland, OR 97239
Gareth Cooper
Krebs Institute, Department of Molecular Biology & Biotechnology, University
of Sheffield, Sheffield S10 2TN, United Kingdom
Christopher K. Cote
U.S. Army Medical Research Institute of Infectious Diseases, Division of
Bacteriology, 1425 Porter Street, Fort Detrick, MD 21702
vii
viii Contributors
Adam Driks
Department of Microbiology and Immunology, Stritch School of Medicine,
Loyola University Chicago, Maywood, IL 60153
David Dubnau
Public Health Research Center of New Jersey Medical School, 225 Warren Street,
Newark, NJ 07103
Peter Dürre
Institut für Mikrobiologie und Biotechnologie, Universität Ulm, 89069 Ulm,
Germany
Jonathan Dworkin
Department of Microbiology & Immunology, College of Physicians and
Surgeons, Columbia University, New York, NY 10032
Patrick Eichenberger
Center for Genomics and Systems Biology, Department of Biology, New York
University, New York, NY 10003
Patricia Fajardo-Cavazos
Department of Microbiology & Cell Science, University of Florida, Space Life
Sciences Laboratory, 505 Odyssey Way, Rm. 201, Exploration Park at Kennedy
Space Center, Merritt Island, FL 32953
Michael Y. Galperin
National Center for Biotechnology Information, National Library of Medicine,
National Institutes of Health, Bethesda, MD 20894
Elizabeth A. Hutchison
Department of Biology, SUNY Geneseo, 1 College Circle, Geneseo, NY 14454
Rachele Isticato
Department of Biology, Federico II University of Naples, Naples, 80126 Italy
Paul Keim
Center for Microbial Genetics and Genomics, Northern Arizona University,
1298 S. Knoles Drive, Northern Arizona University, Flagstaff, AZ 86011-4073
Sung-Woo Lee
Division of Environmental and Biomolecular Systems, Institute of Environmental
Health, Oregon Health & Science University, 3181 S. W. Sam Jackson Park Rd.,
Portland, OR 97239
Jihong Li
Department of Microbiology and Molecular Genetics, University of Pittsburgh
School of Medicine, Pittsburgh, PA 15219
Ines Mandic-Mulec
University of Ljubljana, Biotechnical Faculty, Department of Food Science and
Technology, Vecna pot 111, 1000 Ljubljana, SIovenia
Heather Maughan
Ronin Institute (Headquartered in Montclair, NJ), Mildmay, ON Canada N0G 2J0
Contributors ix
Bruce A. McClane
Department of Microbiology and Molecular Genetics, University of Pittsburgh
School of Medicine, Pittsburgh, PA 15219
David A. Miller
Department of Microbiology, Medical Instill Development, 201 Housatonic Ave.,
New Milford, CT 06776
Nicolas Mirouze
UMR1319 Micalis, Bat. Biotechnologie (440), I.N.R.A., Domaine de Vilvert,
78352 Jouy-en-Josas Cedex, FR
Anne Moir
Krebs Institute, Department of Molecular Biology & Biotechnology, University
of Sheffield, Sheffield S10 2TN, United Kingdom
Wayne L. Nicholson
Department of Microbiology & Cell Science, University of Florida, Space Life
Sciences Laboratory, 505 Odyssey Way, Rm. 201, Exploration Park at Kennedy
Space Center, Merritt Island, FL 32953
Richard T. Okinaka
Center for Microbial Genetics and Genomics, Northern Arizona University,
1298 S. Knoles Drive, Northern Arizona University, Flagstaff,
AZ 86011-4073
Daniel Paredes-Sabja
Departamento de Ciencias Biológicas, Universidad Andrés Bello, Santiago,
920-8640, Chile
David L. Popham
Department of Biological Sciences, Life Sciences I – MC0910, 970 Washington
St. SW, Virginia Tech, Blacksburg, VA 24061
Ezio Ricca
Department of Biology, Federico II University of Naples, Naples, 80126 Italy
Mahfuzur R. Sarker
Department of Biomedical Sciences, College of Veterinary Medicine,
Department of Microbiology, College of Science, Oregon State University,
Corvallis, OR 15219
Peter Setlow
Department of Molecular, Microbial and Structural Biology, University of
Connecticut Health Center, Farmington, CT 06030-3305
Polonca Stefanic
University of Ljubljana, Biotechnical Faculty, Department of Food Science and
Technology, Vecna pot 111, 1000 Ljubljana, SIovenia
Bradley M. Tebo
Division of Environmental and Biomolecular Systems, Institute of Environmental
Health, Oregon Health & Science University, 3181 S. W. Sam Jackson Park Rd.,
Portland, OR 97239