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Bioinformatics Advance Access originally published online on August 8, 2006
Bioinformatics 2006 22(21):2581-2584; doi:10.1093/bioinformatics/btl418
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© 2006 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commerical 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.

The HicAB cassette, a putative novel, RNA-targeting toxin-antitoxin system in archaea and bacteria

Kira S. Makarova 1, Nick V. Grishin 2 and Eugene V. Koonin 1,*

1 National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health Bethesda, MD 20894, USA
2 Howard Hughes Medical Institute and Department of Biochemistry, University of Texas Southwestern Medical Center at Dallas 5323 Harry Hines Boulevard, Dallas, TX 75390-9050, USA

*To whom correspondence should be addressed.

Toxin-antitoxin systems (TAS) are abundant, diverse, horizontally mobile gene modules that encode powerful resistance mechanisms in prokaryotes. We use the comparative-genomic approach to predict a new TAS that consists of a two-gene cassette encoding uncharacterized HicA and HicB proteins. Numerous bacterial and archaeal genomes encode from one to eight HicAB modules which appear to be highly prone to horizontal gene transfer. The HicB protein (COG1598/COG4226) has a partially degraded RNAse H fold, whereas HicA (COG1724) contains a double-stranded RNA-binding domain. The stable combination of these two domains suggests a link to RNA metabolism, possibly, via an RNA interference-type mechanism. In most HicB proteins, the RNAse H-like domain is fused to a DNA-binding domain, either of the ribbon-helix-helix or of the helix-turn-helix class; in other TAS, proteins containing these DNA-binding domains function as antitoxins. Thus, the HicAB module is predicted to be a novel TAS whose mechanism involves RNA-binding and, possibly, cleavage.

Contact: koonin{at}ncbi.nlm.nih.gov

Supplementary information: Supplementary data are available at Bioinformatics online.

Received on July 18, 2006; accepted on July 26, 2006

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