The decay of the chromosomally encoded ccd0157 toxin-antitoxin system in the Escherichia coli species

Abstract

The origin and the evolution of toxin-antitoxin (TA) systems remain to be uncovered. TA systems are abundant in bacterial chromosomes and are thought to be part of the flexible genome that originates from horizontal gene transfer. To gain insight into TA system evolution, we analyzed the distribution of the chromosomally encoded ccd0157 system in 395 natural isolates of Escherichia coli. It was discovered in the E. coli O157:H7 strain in which it constitutes a genomic islet between two core genes ( folA and apaH). Our study revealed that the folA-apaH intergenic region is plastic and subject to insertion of foreign DNA. It could be composed (i) of a repetitive extragenic palindromic (REP) sequence, (ii) of the ccd0157 system or subtle variants of it, (iii) of a large DNA piece that contained a ccdA0157 antitoxin remnant in association with ORFs of unknown function, or (iv) of a variant of it containing an insertion sequence in the ccdA0157 remnant. Sequence analysis and functional tests of the ccd0157 variants revealed that 69% of the variants were composed of an active toxin and antitoxin, 29% were composed of an active antitoxin and an inactive toxin, and in 2% of the cases both ORFs were inactive. Molecular evolution analysis showed that ccdB0157 is under neutral evolution, suggesting that this system is devoid of any biological role in the E. coli species. Copyright © 2009 by the Genetics Society of America.