Chromosomal toxin–antitoxin loci can diminish large‐scale genome reductions in the absence of selection

Abstract

SummarySuperintegrons (SIs) are chromosomal genetic elements containing assemblies of genes, each flanked by a recombination sequence (attC site) targeted by the integron integrase. SIs may contain hundreds of attC sites and intrinsic instability is anticipated; yet SIs are remarkably stable. This implies that either selective pressure maintains the genes or mechanisms exist which favour their persistence in the absence of selection. Toxin/antitoxin (TA) systems encode a stable toxin and a specific, unstable antitoxin. Once activated, the continued synthesis of the unstable antitoxin is necessary for cell survival. A bioinformatic search of accessible microbial genomes for SIs and TA systems revealed that large SIs harboured TA gene cassettes while smaller SIs did not. We demonstrated the function of TA loci in different genomic contexts where large-scale deletions can occur; in SIs and in a 165 kb dispensable region of the Escherichia coli genome. When devoid of TA loci, large-scale genome loss was evident in both environments. The inclusion of two TA loci, relBE1 and parDE1, which we identified in the Vibrio vulnificus SI rendered these environments refractory to gene loss. Thus, chromosomal TA loci can stabilize massive SI arrays and limit the extensive gene loss that is a hallmark of reductive evolution.

Noncanonical SMC protein in Mycobacterium smegmatis restricts maintenance of Mycobacterium fortuitum plasmids

“…However, it is still under debate whether these modules are acquired to gain fitness under stress conditions (57) or to protect the cell from toxic effects after the curing of plasmids harboring addiction modules (58). As a corollary to the mechanism used by F plasmid to ensure its presence in all of the progenies of the host, the chromosomal toxin-antitoxin (TA) modules guard against the deletion of important genomic loci (59). Noticeably, eptABCD operon is flanked by two of the three TA modules present in M. smegmatis to prevent loss of the operon (60).…”

Diverse Functions of Restriction-Modification Systems in Addition to Cellular Defense

“…A similar role in the stabilization of genomic islands was proposed for T-A systems. It was observed that chromosomally encoded T-A systems stabilized neighboring regions of the genome (104). It is rather enigmatic that some genomes have an abundance of R-M components.…”

The evolutionary dynamics of integrons in changing environments

“…For example, the chromosomal integrons in different Vibrio species are much larger (some carry 4200 cassettes) and more diverse. Many carry toxin-antitoxin systems (for example, Rowe-Magnus et al, 2003;Szekeres et al, 2007;reviewed in Cambray et al, 2010), some carry their own promoters or have 41 open reading frame, and ORFans are prevalent. Interestingly, however, in cases where the function can be inferred it appears that the gene products produced from the cassettes are often involved in interactions with the environment that may be subject to rapid change (for example, functions associated with host interactions and virulence, interaction with phages and biofilm formation).…”