Identification of SmtB-ArsR cis elements and proteins in archaea using the Prokaryotic InterGenic Exploration Database PIGEDReport as inadecuate




Identification of SmtB-ArsR cis elements and proteins in archaea using the Prokaryotic InterGenic Exploration Database PIGED - Download this document for free, or read online. Document in PDF available to download.

Archaea - Volume 2 2006, Issue 1, Pages 39-49

Research Article

Biological Sciences Department, University of Wisconsin-Parkside, Kenosha, WI 53141, USA

Department of Chemistry, DePauw University, Greencastle, IN 46135, USA

Received 21 September 2005; Accepted 5 January 2006

Copyright © 2006 Hindawi Publishing Corporation. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

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.





Author: Michael Bose, David Slick, Mickey J. Sarto, Patrick Murphy, David Roberts, Jacqueline Roberts, and Robert D. Barber

Source: https://www.hindawi.com/



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