genome sequencing and annotation

Genome sequencing and annotation

Comprehensive identification of virulence gene candidates by various means

Bioinformatic prioritization of virulence gene candidates and generation of hypotheses regarding functions of encoded factors

Experimental determination of functions of individual virulence factors

Integrate knowledge of factors for use in:

-eco-evo-systems biology study of pathogen

-comparative genomics

“Characterization bottleneck”

Pathogenomics research overview

Steps Limitations

(Conserved) hypotheticals and misannotationnext-gen sequencing problems with “mobilome”

Ongoing curation

Protein structure/function prediction

Bioinformatic and experimental screens

Andrews-Polymenis et al. 2009

Vivo

Sassetti and Rubin 2002

Wolfgang et al. 2003

Conservation of genome content and virulence determinants among clinical and environmental isolates of Pseudomonas aeruginosa

rpoS was downregulated in biofilm

Whiteley et al. 2001

Gene expression in Pseudomonas aeruginosa biofilms

Rediers et al. 2005

Valdivia and Falkow 1997

Fluorescence-based isolation of bacterial genes expressed within host cells

Valdivia and Falkow 1997

Chang et al. 2005

A high-throughput, near-saturating screen for type III effector genes from Pseudomonas syringae

Lindeberg et al. 2006

Collmer et al. 2002

Tobe et al. 2006

An extensive repertoire of type III secretion effectors in Escherichia coli O157

Mazurkiewicz et al. 2006

Signature-tagged mutagenesis

Mazurkiewicz et al. 2006

TraSH = Transposon site hybridization

Mazurkiewicz et al. 2006

Jacobs et al. 2003

Comprehensive transposon mutant library of Pseudomonas aeruginosa

Jacobs et al. 2003

Jacobs et al. 2003

Comprehensive transposon mutant library of Pseudomonas aeruginosa

Medini et al. 2008

Medini et al. 2008

Metzker 2010

Langridge et al. 2009

Langridge et al. 2009

Sorek and Cossart 2010

Sorek and Cossart 2010

Sorek and Cossart 2010

Chain et al. 2009

Chain et al. 2009

Howe et al. 2008