Conference: Genomes 2008 (11 th April) - S7

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I joined the session when Fiona Brinkman was saying that hyperthermophilic bacterias have higher number of cytoplasmic protein. Later came Alexei Savchenko who was speaking that pathogens manipulate the host signalling for their benefit (e.g. uibiquitination). He also mentioned that Toronto centre has target of getting 60 high quality pdb structure per year and also look at these for catalytic activity using enzymatic assay. For more on this session, I took the nice notes from Swati which are pasted below:

The tubercle bacilli: Molecular determinants of pathogenicity and attenuation.

• Comparison between virulent strains and strains that have lost their ability to cause disease.
• RD1 was absent in M. Bovis BCG and microti but present in virulent strains.
• RD1 codes for ESAT-6 and ESX-1.
• Biologically relevant model of ESAT-6 and its protein partner CFP-10 was generated. ESAT-6 and CFP-10 was involved in the host-pathogen interation.
• Finally it was found that PhoP/PhoR was involved in the regulation of ESAT-6 secretion.

Generating protein interaction map for pathogens using yeast two hybrid.
Russel L. Finley, Wayne State University, Detroit, USA

- Organism- Campylobacter jejuni

• Two-hybrid system used to generate a protein interaction map.
• The map includes thousand of interaction and covers 80% of C. jejuni proteins.
• This approach is used to find the protein functions, pathway structure and potential new drug target for C. jejuni.

Insights into the evolution of pathogens using improved bioinformatics approaches.
Fiona Brinkman, Simon Fraser University, Canada

- Computational methods for the predication of protein subcellular localization, predication of genomic island and identification of orthologous.

• Used VFDB (most robust curated database)

- Signature tagged mutagenesis data

- Analysed 100 pathogens and nonpathogens.

- Increase in Genome size = Increase in networks

• Genomic Island plays an important role in evolution.

- Certain offensive virulence factor associated with

Genomewide structural and biochemical annotation of uncharacterized proteins from pathogenic bacteria.
Alexei Savchenko, University of Toronto, Canada

- Selected uncharacterized proteins from pathogenic bacteria.

• How the protein purification was done?
• Used X-ray to determine protein structure.
• Designed enzymatic assays to screen purified proteins for enzymatic activity.
• Biochemical characterization of protein was determined by the application of secondary screens with natural substrate.

- The main focus of this study was to annotate effectors proteins from Shigella flexneri cause shigellosis in humans.

clipped from http://www.pasteur.fr/infosci/conf/sb/genomes_2008/program.html Session 7: Computational, Structural Genomics and Systems Biology Chair: BennoSCHWIKOWSKI, Institut Pasteur, Paris, France Russel L Finley Jr, Wayne State University, Detroit, USA Generating protein interaction maps for pathogens using yeast two-hybrid Jörg Stelling, ETH Zürich, Switzerland Systems analysis of signal transduction pathways Fiona Brinkman, Simon Fraser University, Burnaby, Canada Insights into the evolution of pathogens using improved bioinformatics approaches Alexei Savchenko, University of Toronto, Toronto, Canada Genomewide structural and biochemical annotation of uncharacterised proteins from pathogenic bacteria