Toxin-antitoxin systems (TAS), abundant in prokaryotic genomes, are small genetic elements that typically encode a stable toxin and its cognate labile antitoxin. TAS were first identified in plasmids as maintenance systems but chromosomal TAS are involved in diverse physiological functions in bacteria including stress responses, antibiotic tolerance, etc. The well-studied RelBE is a type II TA system that is ubiquitous in E. coli chromosomes but very uncommon in plasmids. Here we identified a RelE-like TA system with an apparent RHH (ribbon-helix-helix)-like antitoxin (here we named it RelBEI) that is unique in antibiotic-resistant IncI plasmids in E. coli. A search for TAS in available IncI plasmid sequences in GenBank by TA finder (http://202.120.12.133/TAfinder/index.php) revealed identical system in 72/125 IncI plasmids but only rarely in IncIγ plasmids. It is not reported in any other plasmid types to date. Sequencing and analysis of 17 E. coli strains with IncI1 plasmids from our own collection found that all of them lack chromosomal RelBE system but all have plasmid RelBEI. This RelBEI TAS is only distantly related to the E. coli chromosomal RelBE system and to other RelBE systems in the Enterobacteriaceae but appears to have similar functions. The RelEI toxin has growth inhibitory effects and an important role in formation of persister cell in E. coli. E. coli with RelEI expressed in trans produced ~1000 x more antibiotic tolerant persister cells than un-induced cells. Bacteria with RelBEI in natural IncI plasmid exhibit ~300 times more tolerant to antibiotic ciprofloxacin than that lack of RelBEI. The role of RelBEI in response to other stresses is currently being investigated. RelBEI act as a plasmid maintenance system in high and low copy number in different E. coli strains tested. This plasmid TA system offers more to the antibiotic resistance plasmid than maintenance and more to the bacterial cell than antibiotic resistance, and may be an important contributor to the success of IncI plasmids of this type.