( eported in PNAS was made possible with ...)Examination of internal 'wiring' of yeast, worm, and fly reveals conserved circuits

eported in PNAS was made possible with yet another type of database called the Database of Interacting Proteins. That repository contains the results of tens of thousands of laboratory measurements of physical interactions of proteins in more than 100 species. Ideker and his colleagues developed a computerized tool called PathBLAST to search through the Database of Interacting Proteins for protein interactions that are conserved in the three most thoroughly studied species: yeast, worm, and fly,.

The research team completed a rigorous statistical comparative analysis of a total of 14,145 yeast (Saccharomyces cerevisiae), worm (Caenorhabditis elegans), and fly (Drosophila melanogaster) proteins with 38,965 known interactions. Their PathBLAST tool generated a list of similar proteins in the three species that were involved in similar interactions: there were 183 protein clusters and 240 communication pathways conserved in all three. The finding suggests that only 0.5 percent of the protein clusters and communication pathways are conserved in the three species, but Ideker estimated that as many as 80 percent of the actual protein interactions have yet to be discovered.

"We are currently limited by the information and technology we have to date, so when we open up the hood of these three organisms we actually have selective and poor vision," said Ideker. "Nevertheless, when we found protein interactions and communication pathways conserved across all three species we were more confident that we are seeing something real."

Biologists have known for many years that in even distantly related species, nature doesn't reinvent the wheel. Similar proteins involved in essential cellular functions are often similar across species. "This new result indicates that the way in which the most functionally important proteins are assembled into machinery from one species to another is also, to a certain degree, conserved," said Ideker. "The circuitry is not exac
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Source:University of California - San Diego

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