Functional modules in prokaryotic genomes

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Genome and metagenomics projects continue to flood databases with genes whose products have unknown functions. Computational methods are essential to provide clues about the functions of such gene products because the genetic databases grow at a much faster rate than those of experimental functional characterizations. The main aims of this research program are (a) to detect functional modules, groups of genes whose products work together, and (b) to contribute to the understanding of their evolution. To do so, I will develop and refine computational methods to predict functional relationships of gene products. Detected groups and networks of functional interactions should complement currently known modules as well as reveal new ones. Examples of functional modules in Prokaryotes (Bacteria and Archaea) include: operons, stretches of genes transcribed together; regulons, genes whose expression is coordinated by the same regulatory protein; stimulons, genes responding to a particular signal or stimulus; and pathogenicity islands, groups of genes whose products confer pathogenic characteristics. Because the specific members of a functional module within each genome vary, another aim is to identify the main players or core genes within each module, and the peripheral players, which might be responsible for particular adaptations. Another result will be the classification of the modules, and their genes, into groups ranging from most functionally committed, those that keep a function throughout evolution, to very plastic, those whose functions widely diverge. This work will exploit the rich source of information coming from the various microbial genome projects, from metagenomics (environmental and community genomics), as well as from knowledge accumulated through the history of molecular biology.