# Structure, Biology, and Therapeutic Application of Toxin-Antitoxin Systems in Pathogenic Bacteria
## 2 Functions of Six Different Types of Bacterial TA Systems
### Type II  
Type II TA systems are the most widely distributed and the best characterized among prokaryotes and archaea. Such a system is commonly composed of toxin and antitoxin proteins that are expressed independently in the same operon but form a stable complex under normal growth condition, which renders the toxin post-translationally inactive [7; 12; 90; 91; 92]. In most cases, the TA complex or the antitoxin alone can bind to the corresponding TA operon and repress its transcription. A binding stoichiometry between toxin and antitoxin dictates the transcription level of TA operons in the cell, which can be explained by the mechanism of \"conditional cooperativity\". Antitoxins commonly form dimeric proteins, each monomer is usually composed of the \(N\)-terminal domain required for dimerization and DNA binding and the C-terminal domain for toxin binding [93]. The catalytic site ofthe toxin is sterically blocked by the \(C\)-terminal region of the antitoxin. This domain is intrinsically disordered in a free state but typically undergoes coupled folding with toxin binding. Due to the flexibility of antitoxins, their entire structures have not been determined. On the basis of structural and functional features of the toxin, bacterial type II TA modules can be roughly categorized into eight superfamilies: RelBE, MazEF, VapBC, CedAB, ParDE, HigAB, HipBA, and Phd-Doc. Among them, the RelE, MazF, and HigB toxins are known as sequence-specific endo-ribonucleases that impede the global translations of cellular mRNAs [52; 56; 57; 94; 95; 96; 97; 98; 99; 100]. The archaeal RelBE and _E. coli_ MazEF families have been extensively studied. The RelE toxin is a ribosome-dependent ribonuclease that binds to the A-site of the ribosome and then cleaves nascent mRNA [57]. The RelB antitoxin wraps around the toxin, forming a large complex structure that inhibits the entrance of the toxin into the ribosomal A-site [101; 102]. The MazEF systems were first identified as the ParDE and PemIK systems on plasmids R1 and R100, respectively, which are responsible for plasmid stability [103; 104]. They are the first plasmid addiction systems to be identified, and the homologues were discovered on bacterial chromosomes. The MazF toxin cleaves mRNA specifically at ACA sequences [52], and its toxicity is abolished by binding to the MazE antitoxin. Recent data have shown that _E. coli_ MazF specifically cleaves at an ACA triplet in 16S rRNA of 30S ribosomal subunit, leading to a loss of nucleotides in helix 45 and the anti-Shine-Dalgarno (aSD) sequence [53]. The modified ribosome with the rRNA truncation facilitates the selective translation of leaderless mRNAs produced by MazF. Two MazF toxins from _M. tuberculosis_ target 23S or 16S rRNA at specific sites [105; 106]; MazF-mt6 and MazF-mt3 cleave 23S rRNA at the evolutionarily conserved sequence UUCCU in the ribosomal A site [105; 106], and MazF-mt3 also cleaves within the aSD sequence of 16S rRNA. MazF-mt9 from _M. tuberculosis_ cleaves at a single site within the D-loop of tRNA\({}^{\text{Pro14}}\) or the anticodon stem-loop (ASL) of tRNA\({}^{\text{Lys43}}\)[107]. This high selectivity is conferred by recognition of sequence and structural determinants of tRNA. The CedAB operon on the F plasmid is the oldest known TA module that couples plasmid replication to cell division, which was later described as a plasmid addiction system. The CedAB complex functions as a repressor of its operon [108], but the transcription is in a dynamic equilibrium because the CedA antitoxin is continuously degraded by the Lon protease [109]. The ternary complex of CedB with the covalent gyrase-DNA complex leads to an inhibition of DNA transcription and to the accumulation of breaks in the chromosomal DNA [110]. CedB also exerts its function by forming a binary complex with gyrase alone [111; 112]. The inhibition of DNA gyrase mediates the SOS response and eventually causes cell death. The toxin-target complex can be dissociated by the CedA antitoxin in a rejuvenation process [112].