Genome Regions Involved in Multiple Regulatory Pathways Identified Using GSEL, A Genome-Wide Database of Regulatory Sequence Elements of Geobacter sulfurreducens

Organisms from the metal-reducing family Geobacteraceae participate in bioremediation of contaminated environments and in energy harvesting. We have developed a database and an accompanying online query system, GSEL, for Geobacter Sequence Elements (available from http://www.geobacter.org/research/gsel/). It compiles information on predicted transcription regulatory elements in the genome of G. sulfurreducens. These elements were derived from analyses that employed genome-wide transcription profiling, comparative genomics, and similarity searches. Clustering was employed to group overlapping sequence elements with similar genome locations. Subsequent scoring and sorting allowed us to identify individual sequence elements and regulatory clusters that were predicted by the highest number of independent microarray gene expression and sequence comparison data sets. These sequence elements and genome regions are likely to be involved in gene regulation under a variety of conditions or in multiple biological pathways.