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An abstract of a study related to the bioinformatic analysis of gene regulation in Geobacter sulfurreducens, which was conducted by Julia Krushkal and colleagues, is presented.

An abstract of the article "Bioinformatic analysis of gene regulation in the metal-reducing bacterial family Geobacteraceae," by Julia Krushkal, Ronald M. Adkins, and Jeanette Peeples is presented.

AbstractGeobacter sulfurreducensis a model organism within the delta-Proteobacterial family Geobacteraceae,members of which can participate in environmental bioremediation of metal and organic waste contaminants and in production of bioenergy. In this report, we describe a new, significantly expanded and updated, version 2 of the GSEL (GeobacterSequence Elements) database (http://geobacter.org/research/gsel2/and http://geobacter.org/refs/gsel2/) and its accompanying online query system, which compiles information on operon organization and regulatory sequence elements in the genome of G. sulfurreducens. It incorporates a new online graphical browser, provides novel search capabilities, and includes updated operon predictions along with new information on predicted and experimentally validated genome regulatory sites. The GSEL database and online search system provides a unique and comprehensive tool cataloging information about gene regulation in G. sulfurreducens, aiding in investigation of mechanisms that regulate its ability to generate electric power, bioremediate environmental waste, and adapt to environmental changes. [ABSTRACT FROM AUTHOR]

ABSTRACTGeobacteraceaeare a family of metal reducing bacteria with important applications in bioremediation and electricity generation. G. sulfurreducensis a representative of Geobacteraceaethat has been extensively studied with the goal of extending the understanding of this family of organisms for optimizing their practical applications. Here, we have analyzed gene expression data from 10 experiments involving environmental and genetic perturbations and have identified putative transcription factor binding sites (TFBS) involved in regulating key aspects of metabolism. Specifically, we considered data from both a subset of 10 microarray experiments (7 of 10) and all 10 experiments. The expression data from these two sets were independently clustered, and the upstream regions of genes and operons from the clusters in both sets were used to identify TFBS using the AlignACE program. This analysis resulted in the identification of motifs upstream of several genes involved in central metabolism, sulfate assimilation, and energy metabolism, as well as genes potentially encoding acetate permease. Further, similar TFBS were identified from the analysis of both sets, suggesting that these TFBS are significant in the regulation of metabolism in G. sulfurreducens. In addition, we have utilized microarray data to derive condition specific constraints on the capacity of key enzymes in central metabolism. We have incorporated these constraints into the metabolic model of G. sulfurreducensand simulated Fe(II)-limited growth. The resulting prediction was consistent with data, suggesting that regulatory constraints are important for simulating growth phenotypes in nonoptimal environments. [ABSTRACT FROM AUTHOR]