Dr. Gustavo Caetano-Anolles, associate professor of bioinformatics, UIUC Department of Crop Science, will speak on the evolution of the protein world.

Title: "Charting the living world: Structural phylogenomics"

Presentation slides: [PDF]

Abstract: The recent genomic revolution has resulted in massive acquisition of nucleic acid sequences, with over 180 completely sequenced genomes yielding about a million protein sequences. This effort outpaces structural genomics with its 24,000 structural entries. However, a small repertoire of protein architectures (known as protein folds) can be mapped onto about half of amino acid residues encoded in genome sequences. Consequently, the world of protein molecules, though uncharted, appears finite and its study feasible at global levels.

We recently designed a general framework capable of reconstructing evolutionary history directly from the structure of macromolecules. The framework enables global bottom-up or top-bottom approaches of genomic analysis and is supported by three fundamental premises: (1) that molecular structure is far more conserved than sequence and carries considerable phylogenetic signal, (2) that successfully implemented biological designs tend to be reused over and over again in nature, and (3) that there is a universal tendency towards molecular order. Bottom-up strategies unify phylogenetic analysis with structural biology using a Hennigian cladistic approach based on shared and derived features descriptive of common descent. Conversely, top-bottom strategies reveal global diversification using information embedded in entire genomic and proteomic complements. This enabled the charting of the protein world. In order to study protein diversity and evolution at a global scale, we counted the number of genes that could be assigned to particular protein architectures in genomes and used these measures of genomic demography to map the world of proteins and track architectural and organismal history at the proteome level.

Rooted phylogenies of proteomes and fold architectures were used to classify proteins, define structural transformations, determine general evolutionary trends in proteins structure, and study the evolution of metabolic and signaling networks. Phylogenetic tracings revealed patterns unique to multicellularity and inter-cellular signaling that could benefit the study of plant-microbial interactions.