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Conserved pathways within bacteria and yeast as revealed by global protein network alignment
Brian P Kelley1, Roded Sharan, Richard M Karp
1Whitehead Institute for Biomedical Research, 9 Cambridge Center, Cambridge, MA 02142, USA.
Summary
We developed a new method to compare protein networks from different species. This reveals conserved biological pathways and highlights pathway evolution in yeast.
Area of Science:
- Systems biology
- Computational biology
- Evolutionary biology
Background:
- Protein-protein interactions (PPIs) are fundamental to cellular processes.
- Comparing PPI networks across species can reveal conserved functions and evolutionary insights.
Purpose of the Study:
- To develop and apply a novel strategy for aligning PPI networks.
- To identify conserved pathways and complexes between distantly related species.
- To investigate pathway evolution and specialization in yeast.
Main Methods:
- Combined PPI network topology with protein sequence similarity for network alignment.
- Applied the strategy to compare Saccharomyces cerevisiae and Helicobacter pylori PPI networks.
Main Results:
- Identified a significant number of evolutionarily conserved pathways between yeast and bacteria.
- Observed evidence of pathway duplication and specialization within the yeast interactome.
- Discovered both known and novel conserved pathways, validated by cross-species presence.
Conclusions:
- The developed alignment strategy effectively identifies conserved biological pathways.
- Yeast and bacterial PPI networks share substantial evolutionary history.
- Pathway evolution, including duplication and specialization, is a key feature in yeast.