Rapid growth inhibitory activity of a YafQ-family endonuclease toxin of the Helicobacter pylori tfs4 integrative and conjugative element

Kwadwo Boampong,Stephanie L Smith,Robin M Delahay

doi:10.1038/s41598-020-72063-x

Abstract

Prokaryotic and archaeal chromosomes encode a diversity of toxin–antitoxin (TA) systems that contribute to a variety of stress-induced cellular processes in addition to stability and maintenance of mobile elements. Here, we find DinJ-YafQ family TA systems to be broadly distributed amongst diverse phyla, consistent with other ParE/RelE superfamily TAs, but more unusually occurring as a multiplicity of species-specific subtypes. In the gastric pathogen Helicobacter pylori we identify six distinct subtypes, of which three are predominantly associated with the mobilome, including the disease-associated integrative and conjugative element (ICE), tfs4. Whereas, the ICE-encoded proteins have characteristic features of DinJ-YafQ family Type II TA systems in general, the toxin component is distinguished by a broad metal-ion-dependent endonuclease activity with specificity for both RNA and DNA. We show that the remarkably rapid growth inhibitory activity of the ICE toxin is a correlate of a C-terminal lysine doublet which likely augments catalytic activity by increasing the positive electrostatic potential in the vicinity of the conserved active site. Our collective results reveal a structural feature of an ICE TA toxin that influences substrate catalysis and toxin function which may be relevant to specific TA-mediated responses in diverse genera of bacteria.

Highlights

Toxin–antitoxin systems are virtually ubiquitous amongst bacteria and archaea and commonly encoded on plasmids and bacteriophages from which they can be disseminated, acquired and stably integrated into host chromosomes[1,2,3,4]
In H. pylori, we identify the variable presence of six distinct subtypes which includes HP0892-HP0893, HP0894-HP0895 in addition to three TAs encoded by either plasmids or the tfs[4] integrative and conjugative element (ICE)
Up to five Type II TA systems have been identified in H. pylori[29] of which two, HP0892–HP0893 and HP0894–HP0895 are members of the DinJYafQ family[24,25]

Summary

Introduction

Toxin–antitoxin systems are virtually ubiquitous amongst bacteria and archaea and commonly encoded on plasmids and bacteriophages from which they can be disseminated, acquired and stably integrated into host chromosomes[1,2,3,4] They were first revealed to play a role in plasmid m aintenance[2], chromosomallyencoded TA systems in particular are recognised to have numerous important physiological roles which promote bacterial survival, including formation of a persister state, inhibition of bacteriophage, regulation of stress responses, biofilm formation and p athogenesis[5,6,7,8,9,10,11]. Type II toxins tend to be endoribonucleases (RNases) which inhibit translation by related, but distinct mechanisms These involve ribosome-dependent[18,19,20] or independent cleavage of mRNA21 or the inhibition of ribosome-associated factors[22], exceptionally, ParDE family toxins inhibit replication by interference with DNA gyrase function[16]. Four different Type II TA systems have been described so far in H. pylori, HP0892-HP0893, HP0894-HP0895, HP0315-HP0316 and HP0968-HP0967, the latter two comprising toxins of the virulence-associated protein family, V apD28,29

Methods

Results

Conclusion