title: Shewanella knowledgebase: integration of the experimental data and computational predictions suggests a biological role for transcription of intergenic regions.
abstract: Shewanellae are facultative gamma-proteobacteria whose remarkable respiratory versatility has resulted in interest in their utility for bioremediation of heavy metals and radionuclides and for energy generation in microbial fuel cells. Extensive experimental efforts over the last several years and the availability of 21 sequenced Shewanella genomes made it possible to collect and integrate a wealth of information on the genus into one public resource providing new avenues for making biological discoveries and for developing a system level understanding of the cellular processes. The Shewanella knowledgebase was established in 2005 to provide a framework for integrated genome-based studies on Shewanella ecophysiology. The present version of the knowledgebase provides access to a diverse set of experimental and genomic data along with tools for curation of genome annotations and visualization and integration of genomic data with experimental data. As a demonstration of the utility of this resource, we examined a single microarray data set from Shewanella oneidensis MR-1 for new insights into regulatory processes. The integrated analysis of the data predicted a new type of bacterial transcriptional regulation involving co-transcription of the intergenic region with the downstream gene and suggested a biological role for co-transcription that likely prevents the binding of a regulator of the upstream gene to the regulator binding site located in the intergenic region. Database URL: http://shewanella-knowledgebase.org:8080/Shewanella/ or http://spruce.ornl.gov:8080/Shewanella/
authors.affiliation: Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA. karpinetstv@ornl.gov
authors.forename: Tatiana V
authors.initials: TV
authors.lastname: Karpinets
authors.forename: Margaret F
authors.initials: MF
authors.lastname: Romine
authors.forename: Denise D
authors.initials: DD
authors.lastname: Schmoyer
authors.forename: Guruprasad H
authors.initials: GH
authors.lastname: Kora
authors.forename: Mustafa H
authors.initials: MH
authors.lastname: Syed
authors.forename: Michael R
authors.initials: MR
authors.lastname: Leuze
authors.forename: Margrethe H
authors.initials: MH
authors.lastname: Serres
authors.forename: Byung H
authors.initials: BH
authors.lastname: Park
authors.forename: Nagiza F
authors.initials: NF
authors.lastname: Samatova
authors.forename: Edward C
authors.initials: EC
authors.lastname: Uberbacher
mesh_terms: D001483:Base Sequence; D004269:DNA, Bacterial / Q000235:genetics*; D021901:DNA, Intergenic / Q000235:genetics*; D030541:Databases, Genetic; D017753:Ecosystem; D020868:Gene Silencing; D016680:Genome, Bacterial; D051188:Knowledge Bases; D008969:Molecular Sequence Data; D016415:Sequence Alignment; D020592:Shewanella / Q000235:genetics* / Q000502:physiology; D014158:Transcription, Genetic
chemical_list: D004269:DNA, Bacterial; D021901:DNA, Intergenic