Pathogenomics: Focusing studiesof bacterial pathogenicity through evolutionary analysis of genomes

Pathogenomics

Goal:

Identify previously unrecognized mechanisms of microbial pathogenicity using a unique combination of informatics, evolutionary biology, microbiology and genetics.

Explosion of data

23 of the 37 publicly available microbial genome sequences are for bacterial pathogens

Approximately 21,000 pathogen genes with no known function!

>95 bacterial pathogen genome projects in progress …

The need for new tools

Prioritize new genes for further laboratory study

Capitalize on the existing genomic data

Bacterial 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

Approach

Idea: Could we identify novel virulence factors by identifying pathogen genes more similar to host genes than you would expect based on phylogeny?

Prioritize for biological study. - Previously studied in the laboratory? - Can UBC microbiologists study it? - C. elegans homolog?

Search pathogen genes against databases. Identify those with eukaryotic similarity.

Evolutionary significance. - Horizontal transfer? Similar by chance?

Modify screening method /algorithm

Approach

Pathogens

Chlamydophila psittaci Respiratory disease, primarily in birdsMycoplasma mycoides Contagious bovine pleuropneumoniaMycoplasma hyopneumoniae Pneumonia in pigsPasteurella haemolytica Cattle shipping feverPasteurella multicoda Cattle septicemia, pig rhinitisRalstonia solanacearum Plant bacterial wiltXanthomonas citri Citrus cankerXylella fastidiosa Pierce’s Disease - grapevines

Bacterial wilt

World Research Community

ApproachPrioritized candidates

Study function of homolog in model host (C. elegans)

Study function of gene in bacterium.

Infection of mutant in model host

C. elegansDATABASE

Collaborations with others

• Fundamental research

• Interdisciplinary

• Major potential impact

• Lack of fit with alternative funding sources

Peter Wall Major Thematic Grant

Database front end

Haemophilus influenzae Rd-KW20 proteins most strongly matching eukaryotic proteins

PhyloBLAST – a tool for analysis Brinkman et al. Bioinformatics. Accepted

Eukaryote Bacteria Horizontal Transfer?

0.1Rat

Human

Escherichia coli

Caenorhabditis elegans

Pig roundworm

Methanococcus jannaschii

Methanobacterium thermoautotrophicum

Bacillus subtilis

Streptococcus pyogenes

Aquifex aeolicus

Acinetobacter calcoaceticus

Haemophilus influenzae

Chlorobium vibrioforme

E. coli Guanosine monophosphate reductase 81% similar to corresponding enzyme in humans and rats

Role in virulence not yet investigated.

Variance of the Mean %G+C for all Genes in a Genome: Correlation with bacteria’s clonal nature

nonclonal clonal

Variance of the Mean %G+C for all Genes in a Genome

Is this a measure of clonality of a bacterium?

Are intracellular bacteria more clonal because they are ecologically isolated from other bacteria?

Pathogenomics Project: Future Developments

• Identify eukaryotic motifs and domains in pathogen genes

• Identify further motifs associated with• Pathogenicity islands• Virulence determinants

• Functional tests for new predicted virulence factors

• Peter Wall Institute for Advanced Studies

• Pathogenomics group Ann M. Rose, Yossef Av-Gay, David L. Baillie, Fiona S. L.

Brinkman, Robert Brunham, Stefanie Butland, Rachel C. Fernandez, B. Brett Finlay, Hans Greberg, Robert E.W. Hancock, Steven J. Jones, Patrick Keeling, Audrey de Koning, Don G. Moerman, Sarah P. Otto, B. Francis Ouellette, Ivan Wan.

www.pathogenomics.bc.ca