title: Genome-wide expression profiling in Geobacter sulfurreducens: identification of Fur and RpoS transcription regulatory sites in a relGsu mutant.
abstract: Rel(Gsu) is the single Geobacter sulfurreducens homolog of RelA and SpoT proteins found in many organisms. These proteins are involved in the regulation of levels of guanosine 3', 5' bispyrophosphate, ppGpp, a molecule that signals slow growth and stress response under nutrient limitation in bacteria. We used information obtained from genome-wide expression profiling of the rel(Gsu) deletion mutant to identify putative regulatory sites involved in transcription networks modulated by Rel(Gsu) or ppGpp. Differential gene expression in the rel(Gsu) deletion mutant, as compared to the wild type, was available from two growth conditions, steady state chemostat cultures and stationary phase batch cultures. Hierarchical clustering analysis of these two datasets identified several groups of operons that are likely co-regulated. Using a search for conserved motifs in the upstream regions of these co-regulated operons, we identified sequences similar to Fur- and RpoS-regulated sites. These findings suggest that Fur- and RpoS-dependent gene expression in G. sulfurreducens is affected by Rel(Gsu)-mediated signaling.
authors.affiliation: Department of Preventive Medicine, University of Tennessee Health Science Center, 66 N. Pauline, Memphis, TN 38163, USA. jkrushka@utmem.edu
authors.forename: Julia
authors.initials: J
authors.lastname: Krushkal
authors.forename: Bin
authors.initials: B
authors.lastname: Yan
authors.forename: Laurie N
authors.initials: LN
authors.lastname: DiDonato
authors.forename: Marko
authors.initials: M
authors.lastname: Puljic
authors.forename: Kelly P
authors.initials: KP
authors.lastname: Nevin
authors.forename: Trevor L
authors.initials: TL
authors.lastname: Woodard
authors.forename: Ronald M
authors.initials: RM
authors.lastname: Adkins
authors.forename: Barbara A
authors.initials: BA
authors.lastname: Methé
authors.forename: Derek R
authors.initials: DR
authors.lastname: Lovley
mesh_terms: D001426:Bacterial Proteins / Q000378:metabolism*; D001483:Base Sequence; D017353:Gene Deletion; D020869:Gene Expression Profiling; D015964:Gene Expression Regulation, Bacterial; D005798:Genes, Bacterial; D016680:Genome, Bacterial; D045302:Geobacter / Q000235:genetics*; D008025:Ligases / Q000235:genetics / Q000502:physiology*; D009154:Mutation; D009876:Operon / Q000235:genetics; D011401:Promoter Regions, Genetic; D012045:Regulatory Sequences, Nucleic Acid; D012097:Repressor Proteins / Q000378:metabolism*; D012808:Sigma Factor / Q000378:metabolism*; D014158:Transcription, Genetic
chemical_list: D001426:Bacterial Proteins; D012097:Repressor Proteins; D012808:Sigma Factor; C068477:ferric uptake regulating proteins, bacterial; C069567:sigma factor KatF protein, Bacteria; D008025:Ligases; C028812:guanosine 3',5'-polyphosphate synthetases