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Center for Nonlinear Studies |
Reconstructing the molecular and biochemical make up of ancient lineages has remained a technical and conceptual challenge. This in part owes to the fact that the “gold standard” approaches towardsresolving deep phylogeny such as comparative genomics and gene phylogenies do not work very well for the most ancient molecules and arelimited in their ability to recover deep historical events. Fortunately, we are on the cusp of a structural revolution – structural data arestarting to increase exponentially, as genome data did in the last decade. With ~100,000 structures available in the Protein Data Bank, we can now dissect the very early evolutionary history by looking at the deeper structural relationships that are often invisible to sequence-based comparisons and specifically determine how structure and function coevolve. Here, I discuss the application of structural phylogenomics in uncovering the evolutionary history of viral andprokaryotic proteomes. A systematic analysis of the conservation and utilization of protein fold structures in cells and viruses traced the path from the earliest protein folds to the development of the complex protein machinery used in modern cells. The exercise also identified unique viral protein folds that could become potential targets for drug industry. I will also discuss some of my recent work on developing bioinformatics resources to detect horizontally-derived genes in prokaryotes and its application to the NIH Human Microbiome Project.
(1) http://advances.sciencemag.org/content/1/8/e1500527
(2) https://blogs.scientificamerican.com/artful-amoeba/uneven-distribution-of-viruses-suggests-surprising-evolutionary-power/
(3) https://academic.oup.com/nar/article-lookup/doi/10.1093/nar/gkv1245
Host: David Métivier