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

GSEL Version 2, an Online Genome-Wide Query System of Operon Organization and Regulatory Sequence Elements of Geobacter sulfurreducens

“…For details, see Yan et al (2006). b While v. 1 of GSEL included duplicate entries of sequence elements with ScanACE with scores > m i , (Krushkal et al, 2008;Yan et al, 2007), this redundancy has been removed from GSEL database v. 2.…”

“…QU ET AL. Jara et al, 2003;Ueki and Lovley, 2007;Yan et al, 2006 Transcriptional terminators (Krushkal et al, 2008), this redundancy has been removed from GSEL database v. 2.…”

“…To address the need for an integrated resource for regulation of gene expression in Geobacter, we developed an online database and an accompanying online query system, GSEL (for Geobacter Sequence Elements), compiling available information about predicted regulatory sequence elements and operon organization in the genome of G. sulfurreducens (Qu et al, 2009). As reported earlier (Krushkal et al, 2008), version 1 of the GSEL database and query system was developed using text and html formats, Unix Shell scripts, and JavaScript. It contained information about promoter elements and transcription factor binding sites predicted upstream of operons with significant changes in expression under different perturbation conditions (Krushkal et al, 2007(Krushkal et al, , 2009Mahadevan et al, 2008;Yan et al, 2006), genome sites similar to known regulatory sequences from Escherichia coli (Yan et al, 2007), an extensively studied member of g-Proteobacteria, and previously published (Rodionov et al, 2004) conserved sequence sites that were identified using genome analysis of closely related members of d-Proteobacteria.…”

“…Although the online Geobacter server provides a broad informational resource for studies of Geobacteraceae, GSEL v. 2 is a database with a specific focus on operon organization and regulatory sequence elements in G. sulfurreducens, the most extensively studied model representative of Geobacteraceae. GSEL v. 2 is an expanded, updated, and curated resource that has undergone significant development since the release of version 1 (Krushkal et al, 2008). It incorporates a new online graphical browser, and includes updated operon predictions and new information on predicted and experimentally validated genome regulatory sites, which have been manually curated in GSEL v. 2.…”

“…Each sequence element corresponds to a short oligonucleotide fragment with a specific location in the genome of G. sulfurreducens that is suggested to have a regulatory role based on either experimental data or in silico predictions. Version 1 of GSEL contained 10 categories of sequence elements (Krushkal et al, 2008). Among new sequence elements added to GSEL v. 2 have been predictions of RpoN-regulated promoters, suggested to be regulated using the alternative sigma factor s 54 (Leang et al, 2009), sequence sites predicted for the enhancer binding protein PilR (Barbe et al, unpublished), and ribosome-binding sites (Y. Qu and J.…”