Identification and classification of bacterial Type III toxin-antitoxin systems encoded in chromosomal and plasmid genomes

Tim R. Blower, Francesca L. Short, Feng Rao, Kenji Mizuguchi, Xue Y. Pei, Peter C. Fineran, Ben F. Luisi, George P. C. Salmond

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Abstract

Toxin-antitoxin systems are widespread in bacteria and archaea. They perform diverse functional roles, including the generation of persistence, maintenance of genetic loci and resistance to bacteriophages through abortive infection. Toxin-antitoxin systems have been divided into three types, depending on the nature of the interacting macromolecules. The recently discovered Type III toxin-antitoxin systems encode protein toxins that are inhibited by pseudoknots of antitoxic RNA, encoded by short tandem repeats upstream of the toxin gene. Recent studies have identified the range of Type I and Type II systems within current sequence databases. Here, structure-based homology searches were combined with iterative protein sequence comparisons to obtain a current picture of the prevalence of Type III systems. Three independent Type III families were identified, according to toxin sequence similarity. The three families were found to be far more abundant and widespread than previously known, with examples throughout the Firmicutes, Fusobacteria and Proteobacteria. Functional assays confirmed that representatives from all three families act as toxin-antitoxin loci within Escherichia coli and at least two of the families confer resistance to bacteriophages. This study shows that active Type III toxin-antitoxin systems are far more diverse than previously known, and suggests that more remain to be identified.

Original languageEnglish
Pages (from-to)6158-6173
Number of pages16
JournalNucleic Acids Research
Volume40
Issue number13
Early online date19 Mar 2012
DOIs
Publication statusPublished - Jul 2012
Externally publishedYes

Bibliographical note

Copyright the Author(s) 2012. Version archived for private and non-commercial use with the permission of the author/s and according to publisher conditions. For further rights please contact the publisher.

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