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Identification of SmtB/ArsR cis elements and proteins in archaea using the Prokaryotic InterGenic Exploration
Michael Bose1, David Slick, Mickey J Sarto
1Biological Sciences Department, University of Wisconsin-Parkside, Kenosha, WI 53141, USA.
Archaea (Vancouver, B.C.)
|August 1, 2006
Summary
Researchers identified SmtB/ArsR metal-responsive transcriptional regulators in prokaryotes. This study defines DNA binding signatures for these regulators, aiding in understanding their roles in metal detoxification and gene regulation across archaea and bacteria.
Area of Science:
- Microbiology
- Genomics
- Bioinformatics
Background:
- SmtB/ArsR metal-responsive transcriptional regulators are widely distributed in prokaryotes.
- Understanding their DNA binding specificities is crucial for deciphering gene regulation.
- Previous studies have not fully characterized the distribution and binding sites of this regulator family across diverse prokaryotes.
Purpose of the Study:
- To screen prokaryotic genome sequences for SmtB/ArsR DNA binding sites.
- To define sequence signatures for SmtB/ArsR binding activity.
- To investigate the presence and function of SmtB/ArsR regulators in archaea.
Main Methods:
- Position-dependent weight matrix approach for screening genome sequences.
- Analysis of intergenic sequences upstream of orthologous genes.
- Multiple sequence alignments of putative operator sites and winged helix-turn-helix motifs.
- Electrophoretic mobility shift assays (EMSA) for experimental validation.
Main Results:
- Sixty SmtB/ArsR operators linked to metal detoxification genes were predicted across 230 prokaryotic genomes.
- Nine archaeal species were found to possess SmtB/ArsR operators.
- Sequence signatures for SmtB/ArsR DNA binding were defined, and an archaeal SmtB/ArsR was experimentally confirmed.
- A web application, Prokaryotic InterGenic Exploration Database (PIGED), was developed.
Conclusions:
- The study provides a comprehensive prediction of SmtB/ArsR binding sites in prokaryotes, including archaea.
- Defined DNA binding signatures facilitate the identification and functional prediction of SmtB/ArsR regulators.
- The PIGED tool and identified signatures will aid in deciphering the roles of archaeal transcriptional regulators.
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