Direct activation of a bacterial innate immune system by a viral capsid protein

Abstract

Bacteria have evolved diverse immunity mechanisms to protect themselves against the constant onslaught of bacteriophages1–3. Similar to how eukaryotic innate immune systems sense foreign invaders through pathogen-associated molecular patterns4 (PAMPs), many bacterial immune systems that respond to bacteriophage infection require phage-specific triggers to be activated. However, the identities of such triggers and the sensing mechanisms remain largely unknown. Here we identify and investigate the anti-phage function of CapRelSJ46, a fused toxin–antitoxin system that protects Escherichia coli against diverse phages. Using genetic, biochemical and structural analyses, we demonstrate that the C-terminal domain of CapRelSJ46 regulates the toxic N-terminal region, serving as both antitoxin and phage infection sensor. Following infection by certain phages, newly synthesized major capsid protein binds directly to the C-terminal domain of CapRelSJ46 to relieve autoinhibition, enabling the toxin domain to pyrophosphorylate tRNAs, which blocks translation to restrict viral infection. Collectively, our results reveal the molecular mechanism by which a bacterial immune system directly senses a conserved, essential component of phages, suggesting a PAMP-like sensing model for toxin–antitoxin-mediated innate immunity in bacteria. We provide evidence that CapRels and their phage-encoded triggers are engaged in a ‘Red Queen conflict’5, revealing a new front in the intense coevolutionary battle between phages and bacteria. Given that capsid proteins of some eukaryotic viruses are known to stimulate innate immune signalling in mammalian hosts6–10, our results reveal a deeply conserved facet of immunity.

Activation of programmed cell death and counter-defense functions of phage accessory genes

“…In particular, assaying AGs individually in many wild bacterial strains can directly identify thus-far elusive triggers of defense systems. Abortive defense systems are generally thought to detect conserved phage factors (nucleic acids, capsid, terminase, portal, or a general effect such as host transcriptional arrest) [54][55][56] , but our results show that poorly conserved phage genes can also trigger suicide mechanisms in the host and its prophages.…”

Selection of ade novogene that can promote survival ofE. coliby modulating protein homeostasis pathways

“…Short proteins with a similar antitoxin function to RamF might be found in phages. A growing body of work suggests that TA systems, including mazEF system 77 , provide anti-phage defense to bacterial cells via an abortive infection mechanism [78][79][80][81] . Upon cellular entry of phage, toxins are liberated from their antitoxins, often leading to cell death, which prevents phage replication and spread through a population of cells.…”

The structure of DarB in complex with Rel NTD reveals nonribosomal activation of Rel stringent factors

“…For structure determination, as described in ( 49 ), we used the coordinates of Rel Tt NTD as search model for the HD and SYNTH domains (PDB ID 6S2T) ( 17 ) and PDB ID 6YJ8 for DarB. The Molecular replacement (MR) solution from Phaser was used in combination with Rosetta as implemented in the MR-Rosetta ( 50 ) suit from the Phenix package ( 51 ).…”

“…Hydrogen-deuterium exchange mass spectrometry HDX-MS experiments were performed on an HDX platform composed of a Synapt G2-Si mass spectrometer (Waters Corporation) connected to a nanoACQUITY ultraperformance liquid chromatography (UPLC) system, as described in (49). Samples of Rel Bs NTD , DarB, and the Rel Bs NTD :DarB complex were prepared at a concentration of 20 to 50 μM.…”