Plant & Animal Genomes XIII Conference Plant & Animal Genomes XIII ConferenceJanuary 15-19, 2005
Town & Country Convention Center
San Diego, CA
Song Yang , Russ Doolittle , Philip E Bourne
It is truly remarkable that all of Nature is comprised of a very limited set of parts in the form of protein domain folds - taken here to mean independent and stable folding units. While the exact number remains a point of some conjecture, no one disputes that it is a small number in the 1000’s. Since some folds are promiscuous, taking part in a variety of functions and some are selective, perhaps having a sole function, until we know all biological functions from all organisms we can not be assured of knowing all folds. Nevertheless, at this time we can assign, with reasonable reliability, the number and distribution of domain folds to all fully sequenced genomes (over 150 from the three major kingdoms), achieving 30-60% coverage depending on the complexity of the genome.
This presentation will argue that, based on these assignments, a useful contribution can be made to the field of molecular evolution. This statement is based on two underlying principles: 1. structure can provide information on distant evolutionary relationships not seem by current methods of sequence analysis; 2. since Nature is comprised of a very limited parts list of protein domain folds, for a species to loose or gain a fold is a major distinguishing event.
Using these two principles we will describe our recent efforts in structure-based phylogenetic analysis, including one interpretation of the tree of life.