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Bioinformatics Advance Access published online on August 8, 2006
Bioinformatics, doi:10.1093/bioinformatics/btl418
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Published by Oxford University Press 2006
Received July 18, 2006
Accepted July 26, 2006

Discovery note

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 Blvd, Dallas, TX 75390-9050, USA

* To whom correspondence should be addressed.
Eugene V. Koonin, E-mail: koonin{at}ncbi.nlm.nih.gov


  Abstract

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 RNAseH-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.

Associate Editor: Nikolaus Rajewsky
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