Evolutionary analysis of genomes and gene networks from taxonomic and phenotypic perspective
Speaker: Natalia Maltsev
Mathematics and Computer Science division, Argonne National Laboratory,
Computation Institute, the University of Chicago
Evolutionary analysis of diverse sets of organisms is essential for understanding mechanisms of their adaptation to environments. Common ancestry of eukaryotes, prokaryotes and archaeobacteria leads to similarity of many molecular functions. However, differences in organisms’ structural complexity, physiology, and lifestyle result in divergent evolution and emergence of variants of molecular function, metabolic organization, and phenotypic features. Recent progress in genomics, bioinformatics and physiological studies now allows for systematic exploration of adaptive mechanisms that led to diversification of biological systems. Such adaptive changes usually are not limited to one component of the system, on the contrary, in the process of adaptation, organisms undergo co-adaptive changes, such as the complementary changes of protein sequences to accommodate changes in an enzyme’s active site or co-evolution of properties of different steps in metabolic pathways.
We have developed computational systems (e.g. PUMA2 [PUMA]), GNARE [GNARE] tools (e.g. Chisel [Chisel]) and databases (e.g. Sentra [Sentra]) that allow comparative and evolutionary analysis of genomes, metabolic networks and signal transduction systems in the framework of phenotypic and taxonomic information. Such organism-centric view allows exploring genomic data from a systems-level perspective. It facilitates tracing the evolutionary steps that underlie the emergence of the entire biochemical pathways, rather than individual gene products, and to document an evolutionary progression of organisms that house these pathways. It also allows identifying evolutionary patterns of organization characteristic of particular taxonomic groups and phenotypes.
The talk will describe the approach and its application to analysis of microbial genomes and metagenomes.
References:
[PUMA] Maltsev N, Glass E, Sulakhe D, Rodriguez A, Syed MH, Bompada T, Zhang Y, D’Souza M. PUMA2 – grid-based high-throughput analysis of genomes and metabolic pathways. Nucleic Acids Res. 2006 Jan 1;34(Database issue) :D369-372.
[GNARE] D. Sulakhe, M. D’Souza, M. Syed, A. Rodriguez, Y. Zhang, E. Glass, M. Romine, N. Maltsev. GNARE Â A Grid-based Server for the Analysis of User Submitted Genomes. Accepted for publication in Nucleic Acids Res. 2007 (special issue). NAR-00335-Web-B-2007.R1
[Sentra] M. D’Souza, E. Glass, M. Syed, Yi Zhang, M. Galperin, N. Maltsev. Sentra – a database of Prokaryotic Signal Transduction. Nucleic Acids Res. 2007 Jan;35 (Database issue):D271-3. Epub 2006 Nov 29.
[Chisel]Chisel – http://compbio.mcs.anl.gov/CHISEL