Nucleic Acids Research Advance Access originally published online on October 25, 2006
Nucleic Acids Research 2006 34(20):5915-5922; doi:10.1093/nar/gkl750
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Nucleic Acids Research, 2006, Vol. 34, No. 20 5915-5922
© 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.
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Competitive inhibition of natural antisense Sok-RNA interactions activates Hok-mediated cell killing in Escherichia coli
Department of Cell and Molecular Biology, Karolinska Institutet Berzelius väg 35, 171 77, Stockholm, Sweden 1 Département de Biologie Cellulaire Université de Genève Sciences III 30 Quai Ernest-Ansermet 1211 Genève 4, Switzerland 2 Department of Biochemistry and Molecular Biology, University of Southern Denmark DK-5230 Odense M, Denmark 3 Institute for Cell and Molecular Biosciences, Newcastle University Newcastle, NE2 4HH, UK
*To whom correspondence should be addressed. Tel: +46 8 5248 6385; Fax: +46 8 32 39 50; Email: liam.good{at}ki.se
Received August 11, 2006. Revised September 19, 2006. Accepted September 19, 2006.
Short regulatory RNAs are widespread in bacteria, and many function through antisense recognition of mRNA. Among the best studied antisense transcripts are RNA antitoxins that repress toxin mRNA translation. The hok/sok locus of plasmid R1 from Escherichia coli is an established model for RNA antitoxin action. Base-pairing between hok mRNA and Sok-antisense-RNA increases plasmid maintenance through post-segregational-killing of plasmid-free progeny cells. To test the model and the idea that sequestration of Sok-RNA activity could provide a novel antimicrobial strategy, we designed anti Sok peptide nucleic acid (PNA) oligomers that, according to the model, would act as competitive inhibitors of hok mRNA::Sok-RNA interactions. In hok/sok-carrying cells, anti Sok PNAs were more bactericidal than rifampicin. Also, anti Sok PNAs induced ghost cell morphology and an accumulation of mature hok mRNA, consistent with cell killing through synthesis of Hok protein. The results support the sense/antisense model for hok mRNA repression by Sok-RNA and demonstrate that antisense agents can be used to out-compete RNA::RNA interactions in bacteria. Finally, BLAST analyses of 
200 prokaryotic genomes revealed that many enteric bacteria have multiple hok/sok homologous and analogous RNA-regulated toxin–antitoxin loci. Therefore, it is possible to activate suicide in bacteria by targeting antitoxins.