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Nucleic Acids Research Advance Access originally published online on December 14, 2006
Nucleic Acids Research 2007 35(1):325-339; doi:10.1093/nar/gkl1028
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Nucleic Acids Research, 2007, Vol. 35, No. 1 325-339
© 2006 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

Molecular Biology

Toxin–antitoxin regulation: bimodal interaction of YefM–YoeB with paired DNA palindromes exerts transcriptional autorepression

Barbara Kedzierska, Lu-Yun Lian1 and Finbarr Hayes*

Faculty of Life Sciences and Manchester Interdisciplinary Biocentre, The University of Manchester, 131 Princess Street Manchester M1 7DN, UK 1 School of Biological Sciences, University of Liverpool, Crown Street, Liverpool L69 7ZB, UK

*To whom correspondence should be addressed. Tel: +44 161 3068934; Fax: +44 161 3065201; Email: finbarr.hayes{at}manchester.ac.uk

Received October 6, 2006. Revised November 13, 2006. Accepted November 13, 2006.

Toxin–antitoxin (TA) complexes function in programmed cell death or stress response mechanisms in bacteria. The YefM–YoeB TA complex of Escherichia coli consists of YoeB toxin that is counteracted by YefM antitoxin. When liberated from the complex, YoeB acts as an endoribonuclease, preferentially cleaving 3' of purine nucleotides. Here we demonstrate that yefM-yoeB is transcriptionally autoregulated. YefM, a dimeric protein with extensive secondary structure revealed by circular dichroism (CD) and nuclear magnetic resonance (NMR) spectroscopy, is the primary repressor, whereas YoeB is a repression enhancer. The operator site 5' of yefM-yoeB comprises adjacent long and short palindromes with core 5'-TGTACA-3' motifs. YefM binds the long palindrome, followed sequentially by short palindrome recognition. In contrast, the repressor–corepressor complex recognizes both motifs more avidly, impyling that YefM within the complex has an enhanced DNA-binding affinity compared to free YefM. Operator interaction by YefM and YefM–YoeB is accompanied by structural transitions in the proteins. Paired 5'-TGTACA-3' motifs are common in yefM-yoeB regulatory regions in diverse genomes suggesting that interaction of YefM–YoeB with these motifs is a conserved mechanism of operon autoregulation. Artificial perturbation of transcriptional autorepression could elicit inappropriate YoeB toxin production and induction of bacterial cell suicide, a potentially novel antibacterial strategy.

Present address: Barbara Kedzierska, Department of Molecular Biology, University of Gdansk, Kladki 24, 80 822 Gdansk, Poland


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