Genome Mapping and Genomics in Animal-Associated Microbes

252 Pages·2009·7.592 MB·English

by  Nammalwar Sriranganathan, Mohamed N. Seleem (auth.), Vishvanath Nene, Chittaranjan Kole (eds.)

Genome Mapping and Genomics in
Animal-Associated Microbes
Vishvanath Nene, Chittaranjan Kole
(Editors)
Genome Mapping
and Genomics in
Animal-Associated
Microbes
123
VISHVANATH NENE CHITTARANJAN KOLE
Institute for Genome Sciences and Department of Genetics & Biochemistry
Department of Microbiology & Clemson University, 111 Jordan Hall
Immunology Clemson, SC 29634
University of Maryland School of Medicine USA
Baltimore, MD 21021
USA e-mail: [email protected]
e-mail: [email protected]
ISBN 978-3-540-74040-7 e-ISBN 978-3-540-74042-1
DOI 10.1007/978-3-540-74042-1
Library of Congress Control Number: 2008932285
© Springer-Verlag Berlin Heidelberg 2009
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Preface
The ability to cost-effectively and rapidly sequence genomes, advances in com-
putational biology and development of high-throughput technologies that facili-
tate dissection of the ever-expanding list of “omics” has revolutionized research
approaches within the biological sciences. For example, the concept of reverse
vaccinology has brought antigen identification into the genomics era, and bioin-
formatics tools can now be used to select and prioritize a list of candidate vaccine
antigens from predicted pathogen proteomes for further testing. In addition,
the ability to infer metabolic capacity based on pathogen genome sequences has
resulted in the identification of several targets for chemogenomics, a discipline
that may lead to the generation of novel chemotherapeutics. These two tangible
outputs, candidate vaccine antigens and drug targets, have energized efforts in
developing improved methods of pathogen control. In addition, development of
genome-wide molecular diagnostic tools provides an opportunity to study patho-
gen genotypes and population dynamics, and should allow those all-important
correlates with phenotype to be made. Thus, genomics technologies are now being
used to develop a holistic approach to study the genetics of host and pathogen
populations and their molecular responses to each other at a level of detail not
previously possible. Application of genomics technologies to study the process of
infection, disease, vaccination, and interventions leading to immunity is likely to
result in building databases, which will help realize the holy grail of developing
rational approaches for pathogen and disease control.
The scope for a book on genome mapping and genomics of animal-associated
microbes is too huge. We decided to exclude viruses and nonpathogenic microbial
associations and chose livestock as the target animals. We concentrated on select-
ing bacterial or protozoan pathogens of global and developing country signifi-
cance. We also picked pathogens whose genome sequence has been available for a
few years so that the impact of genomics in driving research would be more appar-
ent to the reader. Of the six pathogens chosen, most affect ruminants, and three are
vector-transmitted, increasing the complexity of their “animal” associations but
providing another target for potential intervention.
We are grateful to the senior authors and co-authors of the chapters presented
in this volume, as they have done a marvelous job in summarizing complex
topics. They have provided excellent overviews of their pet pathogens as well
as comparative aspects with related pathogens. Remarkable progress has been
made in studying the organisms reported on here and the next few years promise
exciting scientific breakthroughs in both basic and applied pathogen biology.
Baltimore, MD Vishvanath Nene
Clemson, SC Chittaranjan Kole
June 2008
Contents
Contributors . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .XIII
Abbreviations . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . XVII
1 Brucella
Nammalwar Sriranganathan, Mohamed N. Seleem, Steven C. Olsen,
Luis E. Samartino, Adrian M. Whatmore, Betsy Bricker, David O’Callaghan,
Shirley M. Halling, Oswald R. Crasta, Rebecca A. Wattam, Anjan Purkayastha,
Bruno W. Sobral, Eric E. Snyder, Kelley Williams, Gong-Xi Yu, Thomas A. Ficht,
C. Marty Roop II, Paul deFigueiredo, Stephen M. Boyle, Oliver He, and
Rene M. Tsolis . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1
1.1.1 Discovery of the Brucellae . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1
1.1.2 Species Discovery . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1
1.1.3 Zoonoses . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2
1.1.4 Eradication Program . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3
1.1.5 Vaccination . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3
1.1.6 Molecular Study and Diagnoses . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4
1.2 Economic and Zoonotic Implications of Brucella . . . . . . . . . . . . . . . . . . . . . . 4
1.2.1 Distribution of Brucella spp. Worldwide . . . . . . . . . . . . . . . . . . . . . . . 4
1.2.2 Zoonotic Characteristics of Brucella spp. . . . . . . . . . . . . . . . . . . . . . . 5
1.2.3 Ecomonic Losses to Producers and Costs for Human
Clinical Care . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5
1.2.4 Control Programs and Associated Economic Costs . . . . . . . . . . . . . . 6
1.2.5 Conclusions . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7
1.3 Brucella Taxonomy . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7
1.3.1 Morphology/Life Cycle . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7
1.3.2 Phylogenetic Position of the Genus . . . . . . . . . . . . . . . . . . . . . . . . . . . 7
1.3.3 Brucella Taxonomy . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9
1.4 Molecular Epidemiology and Population Dynamics of Brucella . . . . . . . . . 10
1.4.1 Tools for Molecular Epidemiology . . . . . . . . . . . . . . . . . . . . . . . . . . . 10
1.4.2 Population Dynamics and How They Can Impact
Molecular Epidemiology . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 11
1.4.3 Conclusions . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 13
1.5 Physical and Genetic Map of Genomes . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 13
1.5.1 Bacterial Genomes and Their Analyses . . . . . . . . . . . . . . . . . . . . . . . 13
1.5.2 Global Organization–Physical Maps . . . . . . . . . . . . . . . . . . . . . . . . . . 13
1.5.3 The Brucella Genome is Highly Conserved . . . . . . . . . . . . . . . . . . . . 14
1.5.4 The Brucella Genome and α-Proteobacteria Evolution . . . . . . . . . . 14
1.5.5 Multiple Genomes and Genome Rearrangements . . . . . . . . . . . . . . 14
1.5.6 Mobile Genetic Elements, Repeat Elements
and Genomic Rearrangements . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 15
1.5.7 Genomic Polymorphisms: Transposons, Phage
and Plasmid Associated Sequences . . . . . . . . . . . . . . . . . . . . . . . . . . . 16
1.5.8 Genetic Maps: Synteny . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 16
VIII Contents
1.6 Genome Sequencing and Bioinformatics Resources . . . . . . . . . . . . . . . . . . . 16
1.6.1 Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 16
1.6.2 Genome Sequencing . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 17
1.6.3 High-Throughput Sequencing Technologies . . . . . . . . . . . . . . . . . . . 17
1.6.4 Brucella Genome Sequences . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 18
1.6.5 Bioinformatics Resources . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 20
1.6.6 Biological Data Curation in the Age of High-Throughput
Technologies . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 21
1.6.7 Bioinformatics Resources for Brucella . . . . . . . . . . . . . . . . . . . . . . . . 21
1.6.8 The Brucella Bioinformatics Portal . . . . . . . . . . . . . . . . . . . . . . . . . . . 21
1.6.9 The Pathogen Portal . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 23
1.6.10 The PathoSystems Resource Integration Center . . . . . . . . . . . . . . . . 24
1.6.11 Summary . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 26
1.7 Comparative Genomics of Brucella . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 26
1.7.1 Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 26
1.7.2 Comparative Analysis of Brucella and Related Species . . . . . . . . . . 27
1.7.3 Comparative Genomic Analysis of Brucella . . . . . . . . . . . . . . . . . . . 29
1.7.4 Summary . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 35
1.8 Functional Genomics . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 35
1.8.1 Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 35
1.8.2 Genomics: Global Approaches . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 36
1.8.3 Rational Approaches . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 38
1.8.4 Transcriptomics . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 40
1.8.5 Bacterial Microarrays . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 40
1.8.6 Host Cell Microarrays . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 41
1.8.7 Proteomics . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 41
1.8.8 Higher Order (Protein–Protein) Interactions . . . . . . . . . . . . . . . . . . 42
1.8.9 Conclusions . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 42
1.9 Genome Mapping and Microarray Contributions
to Understanding Brucella Pathobiology and Host Responses
to Brucella Infections . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 43
1.9.1 Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 43
1.9.2 Biology of a Brucella Infection . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 43
1.9.3 Genome Mapping for Understanding Brucella Pathobiology . . . . . 44
1.9.4 Genome Mapping for Understanding Host Response Against
Brucella Infections . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 47
1.10 Future Directions and Prospects . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 51
References . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 52
2 Mycobacterium avium subspecies paratuberculosis
Ling-Ling Li, Sushmita Singh, John Bannantine, Sagarika Kanjilal,
and Vivek Kapur . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 65
2.1 Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 65
2.1.1 The Pathogen and the Disease It Causes . . . . . . . . . . . . . . . . . . . . . . 65
2.1.2 Morphology, Taxonomic Position, Life-Cycle,
and Host-Range of Map . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 67
2.2 The Genome Sequence of Map . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 68
2.2.1 Characteristics of the Map K-10 Genome . . . . . . . . . . . . . . . . . . . . . 68
2.2.2 Repetitive DNA in Map . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 68
2.2.3 Protein Encoding Genes . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 69
2.2.4 Unique Regions and Unique Genes . . . . . . . . . . . . . . . . . . . . . . . . . . . 69
Contents IX
2.2.5 Mycobactin Synthesis . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 70
2.2.6 Insights into Virulence and Pathogenicity Gleaned
from the Map Genome . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 70
2.2.7 Distinguishing Characteristics of the Map Genome . . . . . . . . . . . . 70
2.2.8 Genomics-Based Insights into Map Metabolism . . . . . . . . . . . . . . . 71
2.3 Population Studies of Map . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 72
2.3.1 Multi-Locus Enzyme Electrophoresis (MLEE) . . . . . . . . . . . . . . . . . 73
2.3.2 DNA-Based Tools . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 73
2.3.3 Multi-Locus Short Sequence Repeats (MLSSR) . . . . . . . . . . . . . . . . . 75
2.3.4 Variable Number of Tandem Repeats (VNTR) . . . . . . . . . . . . . . . . . 77
2.4 Concluding Comments . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 78
References . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 79
3 Anaplasma
Kelly A. Brayton, Michael J. Dark, and Guy H. Palmer . . . . . . . . . . . . . . . . . . . . . . . 85
3.1 Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 85
3.2 History . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 85
3.3 Impact on Animal Health . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 87
3.4 Taxonomy . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 87
3.5 Strains . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 91
3.5.1 Genotype . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 91
3.5.2 Strain Diversity . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 91
3.6 Population Studies . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 93
3.7 Genome Sequence and Resources . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 94
3.7.1 Genome Architecture and General Features . . . . . . . . . . . . . . . . . . . 94
3.7.2 Metabolism . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 96
3.7.3 Cell Wall Biogenesis . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 98
3.7.4 Transporters . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 99
3.7.5 Paralogous Gene Families . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 102
3.8 Comparative Genomics . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 105
3.9 Future Scope . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 108
References . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 110
4 Ehrlichia
Basil A. Allsopp and Jere W. McBride . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 117
4.1 Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 117
4.1.1 History of Ehrlichia . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 117
4.1.2 Taxonomic Position . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 117
4.1.3 Ultrastructure . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 118
4.1.4 Life Cycle . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 119
4.1.5 Entry and Development in Host Cells . . . . . . . . . . . . . . . . . . . . . . . 120
4.1.6 Epidemiology . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 120
4.1.7 Diseases . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 121
4.1.8 Economic Importance . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 122
4.1.9 Ehrlichia as Zoonotic Pathogens . . . . . . . . . . . . . . . . . . . . . . . . . . . . 123
4.2 Genomics. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 123
4.2.1 Genetic Variability of Ehrlichia . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 124
4.2.2 Genome Sequencing . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 128
4.2.3 Genomic Insights into the Biology of Ehrlichia . . . . . . . . . . . . . . . 140
4.2.4 Molecular Diagnostics . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 148
X Contents
4.2.5 Vaccine Development . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 150
4.2.6 Comparative Genomics of Ehrlichia Species . . . . . . . . . . . . . . . . . . 152
4.3 Future Scope . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 155
References . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 156
5 Cryptosporidium
Guan Zhu, Shinichiro Enomoto, Jason M. Fritzler, Mitchell S. Abrahamsen,
and Thomas J. Templeton . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 165
5.1 Cryptosporidium and Cryptosporidiosis . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .165
5.1.1 Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 165
5.1.2 Taxonomic Position . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 166
5.1.3 Life Cycle . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 167
5.1.4 Cryptosporidium Genotypes . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 170
5.1.5 Treatment . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 170
5.2 Genome Sequencing, Mapping, and Resources . . . . . . . . . . . . . . . . . . . . . . . 172
5.2.1 History of Genome Sequencing Projects . . . . . . . . . . . . . . . . . . . . . 172
5.2.2 General Features of Cryptosporidium Genomes . . . . . . . . . . . . . . . 172
5.2.3 Comparison Between C. parvum and C. hominis Genomes . . . . . 174
5.2.4 Genome Databases and Resources . . . . . . . . . . . . . . . . . . . . . . . . . . 176
5.2.5 Genome Maps . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 177
5.3 Cryptosporidium Biology: Insights from the Complete Genome . . . . . . . . 178
5.3.1 Streamlined Metabolism . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 178
5.3.2 Expanded Families of Transporters . . . . . . . . . . . . . . . . . . . . . . . . . 179
5.3.3 Lineage-Specific Expansion of Proteases . . . . . . . . . . . . . . . . . . . . . 180
5.3.4 Cryptosporidium-Specific Amplified Gene Families . . . . . . . . . . . . 180
5.3.5 The Surface Protein Repertoire of Cryptosporidium . . . . . . . . . . . 180
5.3.6 Mucin-Like Proteins. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 181
5.3.7 The TRAP Family of Motility and Invasion Proteins . . . . . . . . . . . 181
5.3.8 The LCCL Domain Family . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 182
5.3.9 The Oocyst Wall Proteins . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 182
5.3.10 The Role of Lateral Gene Transfer in the Origin
of Apicomplexan Extracellular Proteins . . . . . . . . . . . . . . . . . . . . . . 182
5.4 Parasite Targets for New Therapeutics . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 184
References . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 185
6 Theileria
Richard P. Bishop, David O. Odongo, David J. Mann, Terry W. Pearson,
Chihiro Sugimoto, Lee R. Haines, Elizabeth Glass, Kirsty Jensen, Ulrike Seitzer,
Jabbar S. Ahmed, Simon P. Graham, and Etienne P. de Villiers . . . . . . . . . . . . . . . 191
6.1 Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 191
6.1.1 The Genus Theileria . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 191
6.1.2 Economic Importance of Theileria . . . . . . . . . . . . . . . . . . . . . . . . . . 192
6.1.3 Theileria Taxonomy . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 192
6.1.4 Epidemiology and Pathology of Theileria Infections . . . . . . . . . . . 193
6.1.5 Theileria Life Cycle and Cell Biology . . . . . . . . . . . . . . . . . . . . . . . . 194
6.2 Physical Mapping of the T. parva Genome . . . . . . . . . . . . . . . . . . . . . . . . . . 196
6.3 The Theileria parva and T. annulata Genome Sequences . . . . . . . . . . . . . . 196
6.3.1 Telomere-Associated Sequences . . . . . . . . . . . . . . . . . . . . . . . . . . . . 198
6.3.2 Comparative Genomics of T. parva and T. annulata . . . . . . . . . . . 200
6.3.3 Current Status of the Theileria orientalis Genome
Sequencing Project . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 201
Contents XI
6.4 Population Genetics and Molecular Epidemiology
of T. parva and T. annulata . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 202
6.5 Genetic Recombination in T. parva. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 203
6.6 The Transcriptome of Theileria parva Schizonts as Revealed
Using MPSS . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 205
6.6.1 Transcription of the Multicopy Tpr and Tar Loci . . . . . . . . . . . . . . 206
6.7 A Snapshot of the T. parva Proteome . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 206
6.8 Transcriptional Analyses of Host–Pathogen Interactions
of T. annulata Infections in Bovine Macrophages . . . . . . . . . . . . . . . . . . . 209
6.9 Application of Genomics to Understand the Biology
of Theileria–Mammalian Host Cell Interaction . . . . . . . . . . . . . . . . . . . . . 211
6.9.1 Insights into the Interaction of Theileria with Bovine
Leukocytes Derived from Analysis of the Virtual Proteomes
of T. parva and T. annulata. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 211
6.9.2 Analysis of the T. parva Predicted Proteome in Relation
to Cell Cycle Regulation and Modulation of Mammalian
Host Cell Function . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 213
6.9.3 Predicted Cyclin-Dependent Kinases in the T. parva Genome . . . 213
6.9.4 Predicted Cyclins in the T. parva Genome . . . . . . . . . . . . . . . . . . . . 213
6.9.5 Sequence Homologues of Additional Parasite-Encoded
Cell Cycle Regulators . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 219
6.9.6 Potential Modulators of the Host Cell Identified
in the Theileria Genomes . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 219
6.10 Application of Genomics to the Development and Deployment
of Vaccines for the Control of Theileria . . . . . . . . . . . . . . . . . . . . . . . . . . . . 221
6.10.1 Molecular Tools to Support Live Vaccination Against
East Coast Fever . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 221
6.10.2 Live Attenuated Cell Culture Vaccines for the Control
of T. annulata . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 221
6.10.3 Application of Genomics to Development of Subunit
Vaccines for Control of ECF . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 222
6.11 Initial Investigation of Theileria Interaction with Ixodid Tick
V ectors Using Expressed Sequence Tags Derived from
R. appendiculatus and A. variegatum Tick Salivary Gland
Transcripts . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 224
6.12 Opportunities for Future Research . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 224
References . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 225
Index . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 233
Contributors
Mitchell S. Abrahamsen Kelly A. Brayton
Department of Veterinary Programs in Genomics
and Biomedical Science and Vector-borne Diseases
College of Veterinary Medicine Department of Veterinary
University of Minnesota Microbiology and Pathology
St. Paul, MN 55108, USA Washington State University
[email protected] Pullman
WA 99164-7040, USA
Jabbar S. Ahmed [email protected]
Division of Veterinary Infection
Biology and Immunology
Parkallee 22, Research Center Borstel Betsy Bricker
23845 Borstel, Germany National Animal Disease Center
[email protected] ARS, USDA, 2300 Dayton Road
Ames, IA 50010, USA
Basil A. Allsopp
[email protected]
Department of Veterinary
Tropical Diseases
Faculty of Veterinary Science
Oswald R. Crasta
University of Pretoria
Cyberinfrastructure Group
Private Bag X04
Virginia Bioinformatics Institute
Onderstepoort 0110, South Africa
Virginia Polytechnic
[email protected]
and State University
Blacksburg VA 24061, USA
John Bannantine
[email protected]
National Animal Disease Center
USDA-ARS, Ames
IA 50010-0000, USA
Michael J. Dark
[email protected]
Programs in Genomics
and Vector-borne Diseases
Richard Bishop
Department of Veterinary
The International Livestock
Microbiology and Pathology
Research Institute (ILRI)
Washington State University
P.O. Box 30709
Pullman
Nairobi 00100, Kenya
WA 99164-7040, USA
[email protected]
[email protected]
Stephen M. Boyle
Center for Molecular Medicine
and Infectious Diseases Paul deFigueiredo
Virginia-Maryland Regional College Plant Pathology
of Veterinary Medicine Texas A&M University
Virginia Tech, Blacksburg College Station
VA 24061-0342, USA TX 77843, USA
[email protected] pjdefi [email protected]