title: SO2426 is a positive regulator of siderophore expression in Shewanella oneidensis MR-1.
abstract: BACKGROUND
  The Shewanella oneidensis MR-1 genome encodes a predicted orphan DNA-binding response regulator, SO2426. Previous studies with a SO2426-deficient MR-1 strain suggested a putative functional role for SO2426 in the regulation of iron acquisition genes, in particular, the siderophore (hydroxamate) biosynthesis operon so3030-3031-3032. To further investigate the functional role of SO2426 in iron homeostasis, we employed computational strategies to identify putative gene targets of SO2426 regulation and biochemical approaches to validate the participation of SO2426 in the control of siderophore biosynthesis in S. oneidensis MR-1.
  
  
  RESULTS
  In silico prediction analyses revealed a single 14-bp consensus motif consisting of two tandem conserved pentamers (5'-CAAAA-3') in the upstream regulatory regions of 46 genes, which were shown previously to be significantly down-regulated in a so2426 deletion mutant. These genes included so3030 and so3032, members of an annotated siderophore biosynthetic operon in MR-1. Electrophoretic mobility shift assays demonstrated that the SO2426 protein binds to its motif in the operator region of so3030. A "short" form of SO2426, beginning with a methionine at position 11 (M11) of the originally annotated coding sequence for SO2426, was also functional in binding to its consensus motif, confirming previous 5' RACE results that suggested that amino acid M11 is the actual translation start codon for SO2426. Alignment of SO2426 orthologs from all sequenced Shewanella spp. showed a high degree of sequence conservation beginning at M11, in addition to conservation of a putative aspartyl phosphorylation residue and the helix-turn-helix (HTH) DNA-binding domain. Finally, the so2426 deletion mutant was unable to synthesize siderophores at wild-type rates upon exposure to the iron chelator 2,2'-dipyridyl.
  
  
  CONCLUSIONS
  Collectively, these data support the functional characterization of SO2426 as a positive regulator of siderophore-mediated iron acquisition and provide the first insight into a coordinate program of multiple regulatory schemes controlling iron homeostasis in S. oneidensis MR-1.
authors.affiliation: Department of Biological Sciences, Purdue University, West Lafayette, IN 47907, USA. khenne@anl.gov.
authors.forename: Kristene L
authors.initials: KL
authors.lastname: Henne
authors.forename: Xiu-Feng
authors.initials: XF
authors.lastname: Wan
authors.forename: Wei
authors.initials: W
authors.lastname: Wei
authors.forename: Dorothea K
authors.initials: DK
authors.lastname: Thompson
mesh_terms: D000595:Amino Acid Sequence; D001483:Base Sequence; D001665:Binding Sites; D053898:Biosynthetic Pathways / Q000235:genetics; D016000:Cluster Analysis; D019295:Computational Biology; D016384:Consensus Sequence; D004269:DNA, Bacterial / Q000378:metabolism; D024202:Electrophoretic Mobility Shift Assay; D017353:Gene Deletion; D015964:Gene Expression Regulation, Bacterial; D007501:Iron / Q000378:metabolism; D008969:Molecular Sequence Data; D010802:Phylogeny; D011401:Promoter Regions, Genetic; D011485:Protein Binding; D016415:Sequence Alignment; D020592:Shewanella / Q000235:genetics*; D017262:Siderophores / Q000096:biosynthesis*; D015534:Trans-Activators / Q000235:genetics / Q000378:metabolism*; D024363:Transcription Initiation Site
chemical_list: D004269:DNA, Bacterial; D017262:Siderophores; D015534:Trans-Activators; D007501:Iron