Pathogenomics

1
Pathogenomics
Goal Identify previously unrecognized mechanisms
of microbial pathogenicity using a unique
combination of informatics, evolutionary biology,
microbiology and genetics.
2
Pathogenicity
Processes of microbial pathogenicity at the
molecular level are still minimally
understood Pathogen proteins identified that
manipulate host cells by interacting with, or
mimicking, host proteins. Idea Could we
identify novel virulence factors by identifying
pathogen genes more similar to host genes than
you would expect based on phylogeny?
3
Pathogens
Anthrax Paratyphoid/enteric fever Cat scratch
disease Peptic ulcers and gastritis Chlamydia Per
iodontal disease Cholera Plague Dental
caries Pneumonia Diarrhea (E. coli
etc.) Salmonellosis Diphtheria Scarlet
fever Epidemic typhus Shigellosis (bacillary
dysentery) Mediterranean fever Sleeping
sickness Gastroenteritis Strep
throat Giardia Syphilis Gonorrhea Toxic shock
syndrome Legionnaires' disease Tuberculosis
Leishmaniasis Tularemia Leprosy Typhoid
fever Leptospirosis Urethritis Listeriosis
Urinary Tract Infections Lyme disease Whooping
cough Malaria Meningitis Necrotizing
fasciitis Yeast infection Some hospital-acquired
infections, animal/plant infections
4
Approach
Screen for candidate genes. Search pathogen genes
against sequence databases. Identify those with
notable similarity to eukaryotic genes.

• Rank candidates.
• how much like host protein?
• info available about protein?

Modify screening method /algorithm
Evolutionary significance. - Horizontal
transfer? Date of transfer? Coevolution? Similar
by chance?

• Prioritize for further biological study.
• - Previously studied biologically?
• Can UBC microbiologists study it?
• C. elegans homolog?

5
Approach
Prioritized candidates

• If C. elegans homolog
• Target gene for knockout.
• Analysis of knockout (expression chip, pathogen
  infection)
• GFP fusion analysis

If pathogen studied by UBC microbiologists -
Obtain knockout - Analysis of knockout
(expression chip, pathogenicity in C. elegans or
other model - Subcellular localization
If pathogen is not a focus of UBC group Contact
other groups (possible collaboration)
C. elegans gene info continually exchanged with
microbiologists
Pathogen gene info continually exchanged with
eukaryotic geneticists
Database pathogen gene info ( similar
host/model host gene info)
6
Interdisciplinary group

• Informatics/Bioinformatics
• Genome Sequence Centre, BC
• Centre for Molecular Medicine and Therapeutics

• Evolutionary Theory
• Dept of Zoology
• Dept of Botany
• Canadian Institute for Advanced Research

• Pathogen Functions
• Dept. Microbiology
• Biotechnology Laboratory
• Dept. Medicine
• BC Centre for Disease Control

• Host Functions
• Dept. Medical Genetics
• C. elegans Reverse Genetics Facility
• Dept. Biological Sciences SFU

7
Power of the Approach

• Interdisciplinary team unique ideas and
  collaborations
• Expression-independent method
• Automated approach continually updated
• Better understanding pathogen gene and similar
  host gene
• Insight into horizontal gene transfer events and
  the evolution of pathogen-host interactions.
• Public database
• other researchers may capitalize on
  the findings
• promote further collaboration

8
Eukaryotic-like pathogen genes
Aquifex aeolicus
96
- YopH, a protein-tyrosine phosphatase, of
Yersinia pestis - Enoyl-acyl carrier protein
reductase (involved in lipid metabolism) of
Chlamydia trachomatis
Haemophilus influenza
100
Escherichia coli
Anabaena
100
Synechocystis
100
Chlamydia trachomatis
63
Petunia x hybrida
64
Nicotiana tabacum
83
Brassica napus
99
Arabidopsis thaliana
0.1
52
Oryza sativa
9
Database front end for Pathogens
10
Candidate proteins are ranked
11
Customized blast result shows pair-wise
distance and species information
12
Customize the tree-building parameters
13
View the constructed tree. Organism information i
s shown
14
Also see prokaryotic-like proteins
within Eukaryotic genomes
15
Important if transfer is between a prokaryote
and an eukaryotic parasite
16
Bacterium Eukaryote Horizontal Transfer
Trichomonas vaginalis Sialidase is 92-95 similar
to Sialidase of Pasteurellaceae
bacteria. Sialidase is a virulence factor used
by some bacteria to parasitize the mucous
membranes of animals.
17
Peter Wall Major Thematic Grant

• Fundamental research
• Interdisciplinary
• Major potential impact
• Lack of fit with alternative funding sources

18
Acknowledgements

• Pathogenomics group
• Ann M. Rose, Steven J. Jones, Yossef Av-Gay,
  David L. Baillie, Fiona S. L. Brinkman, Robert
  Brunham, Stefanie Butland, Rachel C. Fernandez,
  B. Brett Finlay, Robert E.W. Hancock, Christy
  Haywood-Farmer, Hans Greberg, Patrick Keeling,
  Audrey de Koning, Don G. Moerman, Sarah P. Otto,
  B. Francis Ouellette, Iain E. P. Taylor, Ivan
  Wan.
• Peter Wall Foundation