An SOS-Regulated Type 2 Toxin-Antitoxin System

Abstract

The Escherichia coli chromosome encodes seven demonstrated type 2 toxin-antitoxin (TA) systems: cassettes of two or three cotranscribed genes, one encoding a stable toxin protein that can cause cell stasis or death, another encoding a labile antitoxin protein, and sometimes a third regulatory protein. We demonstrate that the yafNO genes constitute an additional chromosomal type 2 TA system that is upregulated during the SOS DNA damage response. The yafNOP genes are part of the dinB operon, of which dinB underlies stress-induced mutagenesis mechanisms. yafN was identified as a putative antitoxin by homology to known antitoxins, implicating yafO (and/or yafP) as a putative toxin. Using phage-mediated cotransduction assays for linkage disruption, we show first that yafN is an essential gene and second that it is essential only when yafO is present. Third, yafP is not a necessary part of either the toxin or the antitoxin. Fourth, although DinB is required, the yafNOP genes are not required for stress-induced mutagenesis in the Escherichia coli Lac assay. These results imply that yafN encodes an antitoxin that protects cells against a yafO-encoded toxin and show a protein-based TA system upregulated by the SOS response.Toxin-antitoxin (TA) systems are modules in bacterial genomes that can cause growth arrest and/or programmed cell death in cells harboring them (1,18,19,54). Type 1 TA systems consist of an RNA antitoxin and a protein toxin, in which the RNA antitoxin inhibits translation of the toxin mRNA. Type 2 TA systems typically consist of two genes in an operon, transcriptionally and translationally coupled, in which, usually, the upstream gene encodes a labile antitoxin protein and the downstream gene encodes a stable toxin protein (Fig. 1A). Continuous transcription of the operon, and thus continuous transcription of the antitoxin, ensures protection from the effects of the toxin. Interruption in transcription of the operon tips the balance in favor of the toxin because antitoxin is no longer made and is rapidly degraded.TA systems were originally identified on plasmids as "plasmid-addiction modules" (34) that maintain the plasmid in the host cell. Failure of cells to inherit the plasmid results in rapid loss of the labile antitoxin, unmasking of the stable preexisting toxin, and death of the cell in a process known as postsegregational killing (13, 38).More recently, TA systems have been discovered in the Escherichia coli chromosome, raising the question of their function there (1, 19). Proposed functions for chromosomal TA systems include roles in nutritional stress response (8), protection from phages (27), formation of "persister" cells that resist antibiotics (32), selfish genetic elements (38, 54), and antiaddiction modules that allow bacteria to resist plasmid addiction (54). Several type 2 chromosomal TA systems have been demonstrated in E. coli, including relBE, mazEF, and hipAB (1,3,19,20,39,45,50). Of these, relBE and mazEF exert their toxic effects during controlled responses such as during amino ...

Development of a Tunable Wide-Range Gene Induction System Useful for the Study of Streptococcal Toxin-Antitoxin Systems

“…However, based upon the current knowledge of HicAB in E. coli and S. mutans, there are several qualities of HicAB that are inconsistent with the general perception of chromosomal TA modules as inhibitors of cell growth. (i) Often it is not possible to generate single mutations within antitoxin genes unless the antitoxin is ectopically expressed (38,39). In E. coli, H. ducreyi, and S. mutans, hicB mutants are readily obtained and viable.…”

DNA Damage Responses in Prokaryotes: Regulating Gene Expression, Modulating Growth Patterns, and Manipulating Replication Forks

“…Several toxin genes are induced during an SOS response, although the physiological impacts of most are yet to be deciphered (see Kawano et al 2007;Magnuson 2007;Unoson and Wagner 2008;Yamaguchi et al 2011;Gerdes and Maisonneuve 2012). An interesting example involves the E. coli yafN and yafO genes, which are downstream of dinB, and like dinB, up-regulated during an SOS response (Singletary et al 2009). Although not proven, the investigators suggest that the toxin YafO delays reentry into the cell cycle following an SOS response, acting as a checkpoint to allow maximal repair of the damage.…”

Stability of the GraA Antitoxin Depends on Growth Phase, ATP Level, and Global Regulator MexT

“…For instance, the HipAB system is able to boost the (p)ppGpp-mediated stringent response and activation of the Lon protease, which degrades several antitoxins in Escherichia coli (14)(15)(16)(17). Furthermore, MqsRA can modulate the RpoS-controlled stress response (18), and YafNO is upregulated during the DNA damage-induced SOS response (14,19). Nevertheless, the real importance of genomic TA systems has remained ambiguous, as the deletion of a single system usually has no apparent effect on bacterial fitness (20,21).…”