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 AnthraxParatyphoid/enteric fever Cat scratch diseasePeptic ulcers and gastritis ChlamydiaPeriodontal disease CholeraPlague Dental cariesPneumonia Diarrhea (E. coli etc.)Salmonellosis DiphtheriaScarlet fever Epidemic typhusShigellosis (bacillary dysentery) Mediterranean feverSleeping sickness Gastroenteritis Strep throat GiardiaSyphilis GonorrheaToxic shock syndrome Legionnaires' disease Tuberculosis LeishmaniasisTularemia LeprosyTyphoid fever LeptospirosisUrethritis Listeriosis Urinary Tract Infections Lyme diseaseWhooping cough MalariaMeningitis Necrotizing fasciitisYeast infection Some hospital-acquired infections, animal/plant infections

4. 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? Prioritize for further biological study. - Previously studied biologically? - Can UBC microbiologists study it? - C. elegans homolog? Evolutionary significance. - Horizontal transfer? Date of transfer? Coevolution? Similar by chance? Modify screening method /algorithm Approach

5. Database: pathogen gene info (+ similar host/model host gene info) 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 Approach

6. 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 Interdisciplinary group

7. 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 Power of the Approach

8. Eukaryotic-like pathogen genes - YopH, a protein- tyrosine phosphatase, of Yersinia pestis - Enoyl-acyl carrier protein reductase (involved in lipid metabolism) of Chlamydia trachomatis 0.1 Aquifex aeolicus Haemophilus influenza Escherichia coli Anabaena Synechocystis Chlamydia trachomatis Petunia x hybrida Nicotiana tabacum Brassica napus Arabidopsis thaliana Oryza sativa 100 96 63 64 52 83 99

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 is 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. Fundamental research Interdisciplinary Major potential impact Lack of fit with alternative funding sources Peter Wall Major Thematic Grant

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