A competence-regulated toxin-antitoxin system inHaemophilus influenzae

Abstract

ABSTRACTNatural competence allows bacteria to respond to environmental and nutritional cues by taking up free DNA from their surroundings, thus gaining both nutrients and genetic information. In the Gram-negative bacteriumHaemophilus influenzae, the genes needed for DNA uptake are induced by the CRP andSxytranscription factors in response to lack of preferred carbon sources and nucleotide precursors. Here we show that one of these genes,HI0659, encodes the antitoxin of a competence-regulated toxin-antitoxin operon (‘toxTA’), likely acquired by horizontal gene transfer from aStreptococcusspecies. Deletion of the putative toxin(HI0660)restores uptake to the antitoxin mutant. The fulltoxTAoperon was present in only 17 of the 181 strains we examined; complete deletion was seen in 22 strains and deletions removing parts of the toxin gene in 142 others. In addition to the expected Sxy-and CRP-dependent-competence promoter,HI0659/660transcript analysis using RNA-seq identified an internal antitoxin-repressed promoter whose transcription starts withintoxTand will yield nonfunctional protein. We propose that the most likely effect of unopposed toxin expression is non-specific cleavage of mRNAs and arrest or death of competent cells in the culture. Although the high frequency oftoxTandtoxTAdeletions suggests that this competence-regulated toxin-antitoxin system may be mildly deleterious, it could also facilitate downregulation of protein synthesis and recycling of nucleotides under starvation conditions. Although our analyses were focused on the effects oftoxTA, the RNA-seq dataset will be a useful resource for further investigations into competence regulation.ABBREVIATED SUMMARYThe competence regulon ofHaemophilus influenzaeincludes an unprecedented toxin/antitoxin gene pair. When not opposed by antitoxin, the toxin completely prevents DNA uptake but causes only very minor decreases in cell growth and competence gene expression. The TA gene pair was acquired by horizontal gene transfer, and the toxin gene has undergone repeated deletions in other strains.