This document discusses proteomic strategies for discovering bacterial virulence factors. It notes that studying virulence factors is key to understanding pathogenesis and finding new targets for drugs and vaccines. While past approaches used genomics and transcriptomics, proteomics directly compares the proteins expressed under different conditions. This can identify proteins not predicted by other methods and provide insights into post-translational modifications and protein localization during infection. The proteomic approach generally follows a protocol of sequencing and characterizing proteins expressed during pathogenesis and comparing them to controls.

1. Proteomic strategies for discovery
of bacterial virulence factors
Lily Fernandez
Biotechnology Lab II
April 27, 2010

2. Importance
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Studying virulence factors is key in understanding pathogenesis.
Finding new virulence factors leads to the discovery of novel
drug targets and development of vaccines.
Virulence factors in bacteria:
 Membrane proteins
 Polysaccharide capsules
 Secretory proteins (toxins)
 Outer membrane components (LPS)
 “Others” (biofilm, 2-component systems)
See Virulence factors of pathogenic bacteria

3. 
Wikipedia - Schematic diagram of virulence factors of Helicobacter pylori, with English annotation
http://commons.wikimedia.org/wiki/File:H_pylori_virulence_factors_en.png

4. Some approaches
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A long, long time ago… biochemical and genetic analysis.
Genomics: sequencing and annotation reveal candidate
virulence genes.
Comparative genomics: DNA microarrays monitor thousands
of genes simultaneously, comparing genes in host or pathogen.
Comparative transcriptomics: compares transcriptional profiles
of model strain to pathogenic strain.
http://www.advanomics.com/transcriptomicsrna.html

5. Some problems with these approaches…
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Genomes require better annotation.
Microarrays have problems with standardization and high
background noise.
Relating genomic, transcriptomic and proteomic data is
challenging.
Not a full picture of what goes on.

6. Proteomic approach
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Similar to previous approaches, but compares proteins
differentially expressed under different conditions.
Can identify proteins that are not predicted by genomics
or transcriptomics.
Can tell us:
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What proteins are expressed in a virulent strain that are not
expressed in an avirulent strain
Where proteins are located at different time points
Presence of any post-translational modifications

7. Animation – general protocol
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Guide to sequencing and identifying proteins

8. Summary
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Identifying virulence factors in bacteria is important in
developing novel drugs and vaccines.
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Since virulence factors are mostly proteins, this type of
research follows a general protocol for sequencing and
characterizing proteins – the focus is on proteins
expressed during pathogenesis.
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The proteins characterized by 2-D electrophoresis and
mass spectrometry are compared to controls.

9. http://thepersonalgenome.com/2008/01/fromtrickle-down-genomics-to-the-virtuous-circle/
"To really understand biological processes, we need
to understand how proteins function in and around
cells since they are the functioning units.”
Hanno Steen, PhD, director of the Proteomics Center
at the Children's Hospital Boston