Email updates

Keep up to date with the latest news and content from Genome Biology and BioMed Central.

Open Access Research

Conservation of the binding site for the arginine repressor in all bacterial lineages

Kira S Makarova13, Andrey A Mironov2 and Mikhail S Gelfand2*

Author Affiliations

1 Department of Pathology, Uniformed Services University of the Health Sciences, Bethesda, MD 20814, USA and National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA

2 State Scientific Center GosNIIGenetika, Moscow 113545, Russia

3 Institute of Cytology and Genetics, Russian Academy of Sciences, Novosibirsk 630090, Russia

For all author emails, please log on.

Genome Biology 2001, 2:research0013-research0013.8  doi:10.1186/gb-2001-2-4-research0013

Published: 22 March 2001

Abstract

Background

The arginine repressor ArgR/AhrC is a transcription factor universally conserved in bacterial genomes. Its recognition signal (the ARG box), a weak palindrome, is also conserved between genomes, despite a very low degree of similarity between individual sites within a genome. Thus, the arginine repressor is different from two other universal transcription factors - HrcA, whose recognition signal is very strongly conserved both within and between genomes, and LexA/DinR, whose signal is strongly conserved within, but not between, genomes. The arginine regulon is well studied in Escherichia coli and to some extent in Bacillus subtilis and some other genomes. Here, we apply the comparative genomic approach to the prediction of the ArgR-binding sites in all completely sequenced bacterial genomes.

Results

Orthologs of ArgR/AhrC were identified in the complete genomes of E. coli, Haemophilus influenzae, Vibrio choleras, B. subtilis, Mycobacterium tuberculosis, Thermotoga maritima, Chlamydia pneumoniae and Deinococcus radiodurans. Candidate arginine repressor binding sites were identified upstream of arginine transport and metabolism genes.

Conclusions

We found that the ArgR/AhrC recognition signal is conserved in all genomes that contain genes encoding orthologous transcription factors of this family. All genomes studied except M. tuberculosis contain ABC transport cassettes (related to the Art system of E. coli) belonging to the candidate arginine regulons.