Identification of SmtB/ArsR cis elements and proteins in archaea using the Prokaryotic InterGenic Exploration Database (PIGED).
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.
Bose
Michael
M
Biological Sciences Department, University of Wisconsin-Parkside, Kenosha, WI 53141, USA.
Slick
David
D
Sarto
Mickey J
MJ
Murphy
Patrick
P
Roberts
David
D
Roberts
Jacqueline
J
Barber
Robert D
RD
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
D001426:Bacterial Proteins; D019641:DNA, Archaeal; D004268:DNA-Binding Proteins; D012097:Repressor Proteins; D015534:Trans-Activators; D051540:Winged-Helix Transcription Factors