Bacterial Genomes and Infectious Diseases
Bacterial Genomes and Infectious Diseases
Edited by
Voon L. Chan, P h D
Department of Medical Genetics and Microbiology University of Toronto, Toronto, Ontario, Canada
Philip M. Sherman, MD, FRCPC
Department of Paediatrics
Department of Laboratory Medicine and Pathobiology Hospital for Sick Children
University of Toronto, Toronto, Ontario, Canada
Billy Bourke, MD, FRCPI
Children's Research Center, Our Lady's Hospital for Sick Children, School of Medicine and Medical Science,
Conway Institute for Biomolecular and Biomedical Research,
University College, Dublin, Ireland
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Library of Congress Cataloging in Publication Data
Bacterial genomes and infectious diseases / edited by Voon L. Chan, Philip M. Sherman, Billy Bourke.
p. cm.
Includes bibliographical references and index.
ISBN 1-58829-496-X (alk. paper)
1. Bacterial genomes. 2. Communicable diseases--Pathogenesis. I.
Chan, Voon L. II. Sherman, Philip M. III. Bourke, Billy.
QH434.B334 2006 616.9'201--dc22
2005034347
v
Preface
The first bacterial genome, Haemophilus influenzae, was completely sequenced, annotated, and published in 1995. Today, more than 200 prokaryotic (archaeal and bacterial) genomes have been completed and over 500 prokaryotic genomes are in vari- ous stages of completion. Seventeen eukaryotic genomes plus four eukaryotic chromo- somes have been completed. The concept of achieving better understanding of an organism through knowledge of the complete genomic sequence was first demonstrated in 1978 when the first bacteriophage genome, )X174, was sequenced. Complete genomic sequences of prokaryotes have led to a better understanding of the biology and evolution of the microbes, and, for pathogens, facilitated identification of new vaccine candidates, putative virulence genes, targets for antibiotics, new strategy for rapid diagnosis, and investigation of bacteria–host interactions and disease mecha- nisms.
Recent increased interest in microbial pathogens and infectious diseases is largely attributed to the re-emergence of infectious diseases like tuberculosis, emergence of new infectious diseases like AIDS and severe acute respiratory syndrome, the problem of an increasing rate of emergence of antibiotic-resistant variants of pathogens, and the fear of bioterrorism. Microbes are highly diverse and abundant in the biosphere. Less than 1% of these morphologically identified microbes can be cultured in vitro using standard techniques and conditions. With such abundance of microbes in nature, we can expect to see new variants and new species evolve and a small number will emerge as pathogens to humans.
In the first section of Bacterial Genomes and Infectious Diseases, some major gen- eral findings about bacterial genomes and their impact on strategy and approach for investigating mechanisms of pathogenesis of infectious diseases are discussed. Later chapters focus on the value and power of genomics, proteomics, glycomics, and bioinformatics as applied to selected specific bacterial pathogens.
Bacterial Genomes and Infectious Diseases is designed to provide valuable reading for senior microbiology, pathobiology and genetics undergraduate and graduate stu- dents, medical students, clinician scientists, infectious diseases clinicians, and medical microbiologists.
Voon L. Chan,
PhDPhilip M. Sherman,
MD,
FRCPCBilly Bourke,
MD,
FRCPIvii
Contents
Preface ...v Contributors ...ix Introduction ... xi
1 Microbial Genomes
Voon Loong Chan ... 1
2 Evolution and Origin of Virulence IsolatesVoon Loong Chan, Philip M. Sherman, and Billy Bourke ... 21
3 Genomic Approach to Understanding InfectiousDisease Mechanisms
Voon Loong Chan, Philip M. Sherman, and Billy Bourke ... 31
4 Knockout and Disease Models in Toll-LikeReceptor-Mediated Immunity
Huey-Lan Huang and Wen-Chen Yeh ... 41
5 Campylobacter: From Glycome to PathogenesisJohn Kelly, Jean-Robert Brisson, N. Martin Young,
Harold C. Jarrell, and Christine M. Szymanski ... 63
6 Genomics of Helicobacter SpeciesZhongming Ge and David B. Schauer ... 91
7 The Organization of Leptospira at a Genomic LevelDieter M. Bulach, Torsten Seemann, Richard L. Zuerner,
and Ben Adler ... 109
8 Listeria monocytogenesKeith Ireton ... 125
9 Mycobacterial GenomesDavid C. Alexander and Jun Liu ... 151
10 MycoplasmaYuko Sasaki ... 175
11 Genome Comparisons of Diverse Staphylococcus aureus StrainsMartin J. McGavin ... 191
12 Type III Secretion Systems in Yersinia pestisandYersinia pseudotuberculosis
James B. Bliska, Michelle B. Ryndak,
and Jens P. Grabenstein ... 213
13 Genomics and the Evolution of Pathogenic Vibrio choleraeWilliam S. Jermyn, Yvonne A. O’Shea,
Anne Marie Quirke, and E. Fidelma Boyd ... 227
viii Contents
14 Future Directions of Infectious Disease ResearchPhilip M. Sherman, Billy Bourke, and Voon Loong Chan ... 255
Index ... 265ix
Contributors
B
ENA
DLER• Australian Bacterial Pathogenesis Program and Australian Research Council Centre of Excellence in Structural and Functional Microbial Genomics, Department of Microbiology, Monash University Clayton, Victoria, Australia D
AVIDC. A
LEXANDER• Montreal General Hospital Research Institute, McGill
University Health Center, Montreal, Quebec, Canada
J
AMESB. B
LISKA• Department of Molecular Genetics and Microbiology, Center
for Infectious Diseases, State University of New York at Stony Brook, Stony Brook, NY E. F
IDELMAB
OYD• Department of Microbiology, University College Cork, National
University of Ireland, Cork, Ireland
B
ILLYB
OURKE•Children's Research Center, Our Lady's Hospital for Sick Children, School of Medicine and Medical Science, Conway Institute for Biomolecular and Biomedical Research, University College Dublin, Ireland
J
EAN-R
OBERTB
RISSON• Institute for Biological Sciences, National Research Council, Ottawa, Ontario, Canada
D
IETERB
ULACH• Australian Bacterial Pathogenesis Program, Department of Microbiology, Monash University Clayton, Victoria, Australia
V
OONL. (R
ICKY) C
HAN• Department of Medical Genetics and Microbiology, University of Toronto, Toronto, Ontario, Canada
Z
HONGMINGG
E• Division of Comparative Medicine, Massachusetts Institute of Technology, Cambridge, MA
J
ENSP. G
RABENSTEIN• School of Medicine, New York University, New York, NY H
UEY-L
ANH
UANG• The Campbell Family Institute for Breast Cancer Research,
Ontario Cancer Institute, University Health Network and Department of Medical Biophysics, University of Toronto, Ontario, Canada
K
EITHI
RETON• Department of Molecular Biology and Microbiology, University of Central Florida, Orlando, FL
H
AROLDC. J
ARRELL• Institute for Biological Sciences, National Research Council, Ottawa, Ontario, Canada
J
OHNK
ELLY• Institute for Biological Sciences, National Research Council, Ottawa, Ontario, Canada
J
UNL
IU• Department of Medical Genetics and Microbiology, University of Toronto, Toronto, Ontario, Canada
M
ARTINJ. M
CG
AVIN• Division of Microbiology, Sunnybrook and Women's College Health Science Centre, Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada
Y
VONNEA. O’S
HEA• Department of Microbiology, University College Cork, National University of Ireland, Cork, Ireland
A
NNEM
ARIEQ
UIRKE• Department of Microbiology, University College Cork,
National University of Ireland, Cork, Ireland
x Contributors M
ICHELLEB. R
YNDAK• TB Center, Public Health Research Institute, Newark, NJ Y
UKOS
ASAKI• Department of Bacterial Pathogenesis and Infection Control,
National Institute of Infectious Diseases, Musashimurayama, Tokyo, Japan D
AVIDB. S
CHAUER• Division of Comparative Medicine and Biological Engineering
Division, Massachusetts Institute of Technology, Cambridge, MA T
ORSTENS
EEMANN• Victorian Bioinformatics Consortium, Clayton School
of Information Technology, Monash University, Clayton, Victoria, Australia P
HILIPM. S
HERMAN• Department of Paediatrics, Department of Laboratory
Medicine and Pathobiology, Hospital for Sick Children, University of Toronto, Toronto, Canada
C
HRISTINEM. S
ZYMANSKI• Institute for Biological Sciences, National Research Council, Ottawa, Ontario, Canada
W
EN-C
HENY
EH• The Cambell Family Institiute for Breast Cancer Research, Ontario Cancer Institute, University Health Network and Department of Medical Biophysics, University of Toronto, Toronto, Canada
N. M
ARTINY
OUNG• Institute for Biological Sciences, National Research Council, Ottawa, Ontario, Canada
J
ERMYNS. W
ILLIAM• Department of Microbiology, University College Cork, National University of Ireland, Cork, Ireland
R
ICHARDL. Z
UERNER• Bacterial Diseases of Livestock Research Unit, National
Animal Disease Center, USDA, Agricultural Research Service, Ames, IA
Introduction
Billy Bourke
1. Genomic Data as a Cornerstone for Biomedical Science
A fundamental starting point for effective research in any scientific field is to first submit the constituents of that particular domain of science to a process of categoriza- tion, taxonomy, and systematics. Linnaeus, a compulsive cataloger, spent a lifetime classifying living species and Tycho Brahe laboriously mapped the position of the plan- ets and stars of the heavens for 20 yr of his life (1). These enormous tasks embodied years of painstaking and repetitive observation and calculation. Although predicated on deeply unglamorous, day-to-day work, the resulting body of data formed the basis of all further scientific inquiry and discovery in the fields of botany and astronomy, thereafter.
The late 20th century will be remembered as a time of major discovery in many scientific fields. Undoubtedly, for the biological sciences, the major achievement of recent years has been the advent of genomics. Technology-driven, laborious, and, some might say, scientifically unexciting, genomic sequencing is reminiscent of the work of Linnaeus and Brahe. However, in also laying down a fundamental scientific corner- stone in biological sciences, the evolution of genomic sequencing represents an achievement equivalent to those established centuries ago by these great scientists.
2. The Birth of Bacterial Genome Sequencing
In the nonscientific community, the proposal to sequence complete genomes is usu- ally linked with the “flag ship” Human Genome Project (2). However, the genomes of other organisms, in particular those of bacteria, in many respects form the vanguard of genome sequencing science. The first ever genome sequenced was that of the bacte- riophage )X174, the 5500 base chromosome that was decoded by Sanger and his col- leagues in 1978 (3). Around this time, interest arose in attempting to sequence the whole genome of Escherichia coli K-12, culminating in a more formal proposal from Fred Blattner in 1983 (4). However, efforts to complete the E. coli sequence became embroiled in controversy (5). Based on early predictions, Blattner and colleagues set a goal of sequencing 1 Mb per year. However, after nearly 4 yr of sequencing, only 1.4 Mb was completed (6). Projections for the E. coli sequencing project were undoubt- edly overly optimistic and the whole process proved significantly more time consum- ing than expected. Blattner first had to finish the process of breaking the whole E. coli genome into 400 overlapping O clones, then break each clone into random subclones before sequencing each clone and ordering them according to overlapping sequences (6).
Although the E. coli genome sequence project started with a healthy advantage com- pared with other bacterial sequencing efforts, in the early 1990s a dark horse appeared
xi
on the genomic horizon. By using rapid, fluorescence-based sequencing technology, a random (“shotgun”) sequencing strategy, advanced computerization of data collection and processing, novel software for generating contigs, and efficient long polymerase chain reaction cloning to reduce the time needed to fill gaps in the sequence, The Insti- tute of Genome Research (TIGR) successfully sequenced the whole Haemophilus in- fluenza genome in about 1 yr (7). The genome of Mycoplasma genitalium, the smallest genome known for a self-replicating organism (580 kb) (also from the TIGR group) followed soon after in the same year (8). Using the novel dye-terminator fluorescence sequencing technology, Blattner and his colleagues went on to complete and publish the entire E. coli K12 genome sequence 2 yr later (9).
The impact of this new technology and the interest in genome sequencing as a fun- damental tool for understanding basic biological process, especially infectious diseases and their treatment, has led to an explosion in the numbers of organisms being sequenced. At the time of this writing, 179 prokaryotic genomes have been sequenced and approx 500 bacterial genomes are in the process of being sequenced. The rapid evolution of sequencing technology has been truly staggering and the accompanying costs have dropped substantially. The M. genitalium sequence was calculated to cost approx $0.30 per basepair. However, by 2002, random sequencing of genomes cover- ing more than 99% of the whole sequence could be completed within a few days, at a cost of only $0.04 per basepair. Completion of a shotgun sequenced bacterial genome by closure of gaps and annotation can usually be accomplished within a few months and the cost of a completely annotated genome is less than $0.10 per basepair (10).
Therefore, with a cost of less than $100,000 for a small- to medium-sized organism, even the genomes of bacteria of lesser commercial interest can be sequenced. Such accessibility to whole genome sequencing, even for research groups without major financial resourcing, has led to a “democratization” of scientific exploration in micro- biology worldwide (11).
3. Pathogens and the Postgenomics Era
Although the generation and analysis of extensive volumes of sequence data is a major accomplishment, it is not an end in itself. Clearly, the motivation for sequencing genomes comes for a desire to understand the biology of living organisms. A major stimulus for research across all fields of biology is to understand and combat human diseases. It is not surprising then that many of the first organisms to be sequenced were important human pathogens. Indeed, given the small size and the paucity of intragenic DNA, the potential for the genome sequences of bacterial pathogens to yield biologi- cally useful information of direct relevance to human disease outstrips that of the Human Genome Project, at least in the short to medium term.
The deluge of data generated by genome sequencing projects has forced a quantum leap in the application of computer science and bioinformatics to help analyze effi- ciently the information generated. This evolution of “biology in silico” is not the only interdisciplinary scientific alliance forged in the post genomic era. Microarray technol- ogy, proteomics, immunoinformatics, structural biology, and combinatorial chemistry, all of which are predicated on a knowledge of genome sequence, have opened the door to high-throughput technologies, increasing by orders of magnitude the efficiency with
xii Bourke
which novel virulence genes, potential drug targets, and vaccine strategies can be iden- tified (12–14).
Bacterial Genomes and Infectious Diseases focuses on how bacterial genomics has contributed to some of the major strides taken in understanding the basic biology of a variety of important human pathogens. Knowledge of the genetic content of individual pathogens has pointed toward novel virulence factors, provided unprecedented insights into pathogen evolution, uncovered key epidemiological relationships between differ- ent strains of the same organism, and helped forge important new links with other scientific disciplines for the exploration of infectious pathogenesis.
Bacterial genomics is at the cutting edge of a movement evolving in modern scien- tific research toward the integration of scientific subspecialities. The following chap- ters detail some of the initial fruits of this reductionist approach to understanding bacterial pathogens. Although much further information about individual organisms will come from analysis of existing data, the future challenge for microbiology and infectious disease in the postgenomic era lies in the integration of present knowledge with other areas of scientific research with a view to developing a better understanding of the biology of living organisms and the manner in which pathogens inflict disease.
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