Substrate specificity of bacterial endoribonuclease toxins

Abstract

Bacterial endoribonuclease toxins belong to a protein family that inhibits bacterial growth by degrading mRNA or rRNA sequences. The toxin genes are organized in pairs with its cognate antitoxins in the chromosome and thus the activities of the toxins are antagonized by antitoxin proteins or RNAs during active translation. In response to a variety of cellular stresses, the endoribonuclease toxins appear to be released from antitoxin molecules via proteolytic cleavage of antitoxin proteins or preferential degradation of antitoxin RNAs and cleave a diverse range of mRNA or rRNA sequences in a sequence-specific or codon-specific manner, resulting in various biological phenomena such as antibiotic tolerance and persister cell formation. Given that substrate specificity of each endoribonuclease toxin is determined by its structure and the composition of active site residues, we summarize the biology, structure, and substrate specificity of the updated bacterial endoribonuclease toxins. [BMB Reports 2020; 53(12): 611-621].

Fig. 1

Bacterial endoribonuclease toxins in the toxin-antitoxin systems. The types of toxin-antitoxin systems are determined by how antitoxins antagonize the endoribonuclease toxins. In type I toxin-antitoxin systems, antitoxins are antisense RNAs and inhibit toxin translation by base-pairing. In type II toxin-antitoxin systems, antitoxins are proteins that directly bind to toxin and neutralize toxin’s endoribonuclease activity. Anti-toxin alone or toxin-antitoxin complex also binds to the promoter region and represses expression of the toxin-antitoxin operon. In type III toxin-antitoxin systems, antitoxins are small noncoding RNAs that are transcribed as longer transcripts and then processed by the cognate endoribonuclease toxin into 34-36 nt sRNAs. The processed sRNAs bind to the toxin protein and inhibit toxin’s endoribonuclease activity.

Fig. 2

Type II ribosome-dependent endoribonuclease toxins. Structures of type II ribosome-dependent endoribonuclease toxins. Amino acid sequences for the toxin protein structures were from Escherichia coli strain K-12 and Proteus vulgaris (for HigB). Amino acid residues involved in general base/acid are indicated in light blue and key residues required for mRNA cleavage are indicated in yellow. (A) RelE monomer (PDB ID: 3KIX). (B) YoeB monomer (PDB ID: 6N90). (C) YafQ monomer (PDB ID: 4Q2U). (D) HigB monomer (PDB ID: 5IFG). (E) YhaV monomer (PDB ID: 2KHE). For comparison, RNase Sa from Streptomyces aureofaciens (F) and RNase T1 from Aspergillus oryzae (G) were used. (F) RNase Sa mono-mer (PDB ID: 1NLI). (G) RNase T1 monomer (PBD ID: 1I0V).

Fig. 3

Type II ribosome-independent endoribonuclease toxins and type III endoribonuclease toxins. Structures of type II ribosome-independent endoribonuclease toxins (A-E) and type III endoribonuclease toxins (F-H). Amino acid sequences for the toxin protein structures were from Escherichia coli strain K-12 unless otherwise indicated. (A) MazF monomer (PDB ID: 1UB4). Hydrophilic residues required for interacting with a substrate are indicated in olive green. Pro-30 is required for determining substrate specificity (green) and Trp-14 is also involved in substrate specificity (blue). (B) ChpBK monomer (PDB ID: 1M1F). (C) PemK monomer (PDB ID: 1M1F) of Staphylococcus aureus. (D) HicA monomer (PDB ID: 4P78). Two residues required for HicA activity are indicated in green. (E) MqsR monomer (PDB ID: 3HI2). MqsR toxin is the only member of RelE superfamily that has a ribosome-independent endoribonuclease activity. Four key residues are indicated in green. (F) ToxN monomer of Pectobacterium atrosepticum (PDB ID: 2XD0). Six residues required for ToxN_Pa’s activity are indicated in blue. (G) ToxN monomer of Bacillus thuringiensis (PDB ID: 4ATO). Six key residues are also indicated in pink. (H) AbiQ monomer of Lactococcus lactis (PDB ID: 4GLK). Seven key residues are indicated in pale violet.