title: Identification of SmtB/ArsR cis elements and proteins in archaea using the Prokaryotic InterGenic Exploration Database (PIGED).
abstract: Microbial genome sequencing projects have revealed an apparently wide distribution of SmtB/ArsR metal-responsive transcriptional regulators among prokaryotes. Using a position-dependent weight matrix approach, prokaryotic genome sequences were screened for SmtB/ArsR DNA binding sites using data derived from intergenic sequences upstream of orthologous genes encoding these regulators. Sixty SmtB/ArsR operators linked to metal detoxification genes, including nine among various archaeal species, are predicted among 230 annotated and draft prokaryotic genome sequences. Independent multiple sequence alignments of putative operator sites and corresponding winged helix-turn-helix motifs define sequence signatures for the DNA binding activity of this SmtB/ArsR subfamily. Prediction of an archaeal SmtB/ArsR based upon these signature sequences is confirmed using purified Methanosarcina acetivorans C2A protein and electrophoretic mobility shift assays. Tools used in this study have been incorporated into a web application, the Prokaryotic InterGenic Exploration Database (PIGED; http://bioinformatics.uwp.edu/~PIGED/home.htm), facilitating comparable studies. Use of this tool and establishment of orthology based on DNA binding signatures holds promise for deciphering potential cellular roles of various archaeal winged helix-turn-helix transcriptional regulators.
authors.affiliation: Biological Sciences Department, University of Wisconsin-Parkside, Kenosha, WI 53141, USA.
authors.forename: Michael
authors.initials: M
authors.lastname: Bose
authors.forename: David
authors.initials: D
authors.lastname: Slick
authors.forename: Mickey J
authors.initials: MJ
authors.lastname: Sarto
authors.forename: Patrick
authors.initials: P
authors.lastname: Murphy
authors.forename: David
authors.initials: D
authors.lastname: Roberts
authors.forename: Jacqueline
authors.initials: J
authors.lastname: Roberts
authors.forename: Robert D
authors.initials: RD
authors.lastname: Barber
mesh_terms: D001105:Archaea / Q000235:genetics*; D001426:Bacterial Proteins / Q000032:analysis / Q000235:genetics*; D001665:Binding Sites; D019641:DNA, Archaeal / Q000378:metabolism; D004268:DNA-Binding Proteins / Q000032:analysis / Q000235:genetics*; D019992:Databases as Topic; D019766:Genes, Archaeal; D010802:Phylogeny; D011387:Prokaryotic Cells / Q000378:metabolism; D012097:Repressor Proteins / Q000032:analysis / Q000235:genetics*; D015534:Trans-Activators / Q000032:analysis / Q000235:genetics*; D051540:Winged-Helix Transcription Factors / Q000502:physiology
chemical_list: D001426:Bacterial Proteins; D019641:DNA, Archaeal; D004268:DNA-Binding Proteins; D012097:Repressor Proteins; D015534:Trans-Activators; D051540:Winged-Helix Transcription Factors