Identification characterization structure and assembly of type III toxin antitoxin systems from Escherichia coli

Abstract

Bacteria adopt several defense strategies to enable their survival against the environmental threats they encounter from time to time. Toxin-antitoxin (TA) systems are being understood as a key bacterial defense mechanism against invading viruses, antibiotics, and other environmental stress. TA systems consist of a pair of genes, usually under a common promoter, that code for a toxin and its cognate antitoxin . The toxin is usually a protein, that arrests cellular growth during stress, whereas the antitoxin can be a protein or a non-coding RNA, that inhibits the toxin. The TA systems are classified into six different types based on the mechanism of inhibition of toxin by antitoxin. In type III TA systems, the toxin is an endoribonuclease (RNase) that cleaves cellular RNAs when free, whereas antitoxin is a non-coding RNA. The toxin also processes its own precursor antitoxin RNA into smaller repeats and subsequently assembles with them to form an inactive TA complex. During normal growth conditions, the antitoxin RNA inhibits the toxin protein by forming the RNA-protein TA complex. However, when the bacteria encounter stress such as phage infection, the active toxin gets released from the complex and prevents phage replication. Type III TA systems have been identified in several bacteria and classified into three different families - toxIN, cptIN, and tenpIN. However, type III systems have not been identified and well characterized in Escherichia coli. The identification and characterization of these systems in E. coli, which is the most commonly studied model organism with robust genetic manipulation tools available, would help in understanding them in detail for their functions and mechanism of action. In this thesis, by using protein sequence-based homology searches, we report the identification of ToxIN type III TA systems from several strains in E. coli...