Control of bacterial immune signaling by a WYL domain transcription factor

Abstract

Bacteria use diverse immune systems to defend themselves from ubiquitous viruses termed bacteriophages (phages). Many anti-phage systems function by abortive infection to kill a phage-infected cell, raising the question of how they are regulated to avoid cell killing outside the context of infection. Here, we identify a transcription factor associated with the widespread CBASS bacterial immune system, that we term CapW. CapW forms a homodimer and binds a palindromic DNA sequence in the CBASS promoter region. Two crystal structures of CapW suggest that the protein switches from an unliganded, DNA binding-competent state to a ligand-bound state unable to bind DNA. We show that CapW strongly represses CBASS gene expression in uninfected cells, and that phage infection causes increased CBASS expression in a CapW-dependent manner. Unexpectedly, this CapW-dependent increase in CBASS expression is not required for robust anti-phage activity, suggesting that CapW may mediate CBASS activation and cell death in response to a signal other than phage infection. Our results parallel concurrent reports on the structure and activity of BrxR, a transcription factor associated with the BREX anti-phage system, suggesting that CapW and BrxR are members of a family of universal defense signaling proteins.

Bacterial cGAS senses a viral RNA to initiate immunity

“…Next, we investigated how Ssc-CBASS is activated by Φ80ɑ-vir. We first considered the possibility of transcriptional activation of the operon during infection, as was reported for the type III CBASS of Escherichia coli upec-117 28 . RT-qPCR, however, failed to detect an increase in the transcription of the Ssc-CBASS genes upon infection (Fig.…”

Structure and activity of a bacterial defense‐associated 3′‐5′ exonuclease

“…[16][17][18] We recently showed that E. coli upec-117 CBASS protects bacteria against infection by phage λ, and that the system's predicted MTA/SAH-family nucleosidase Cap17 is required for immunity, while Cap18 is dispensable for immunity. 10 These data show that Cap18 is not the primary effector of the E. coli upec-117 CBASS system, suggesting an accessory role for the protein. Our structure of Cap18 shows that this protein lacks a recognized second messenger binding domain, suggesting that its activity is unlikely to be modulated by second messengers produced by its cognate CD-NTase.…”

“…CBASS effector proteins, including the CapV phospholipase and the NucC and Cap4 dsDNA endonucleases, are activated by the cyclic di‐ or trinucleotide second messenger produced by their cognate CD‐NTase 16–18 . We recently showed that E. coli upec‐117 CBASS protects bacteria against infection by phage λ, and that the system's predicted MTA/SAH‐family nucleosidase Cap17 is required for immunity, while Cap18 is dispensable for immunity 10 . These data show that Cap18 is not the primary effector of the E. coli upec‐117 CBASS system, suggesting an accessory role for the protein.…”

“…19 This proposed role is also consistent with our prior finding that in the E. coli upec-117 CBASS system, deletion of the cap18 gene does not affect the system's ability to protect against infection by phage λ. 10 Further work will be required to determine the functional relationship between Cap18 and the transcriptional regulation of CBASS.…”

“…6,10 We manually inspected each of these systems, and found that in many cases, the noted exonuclease is encoded in a separate, neighboring operon (Tables S1 and S2). In those cases where Cap18 is encoded within the CBASS operon, we noticed that over 50% of those operons also encode transcriptional regulators of the CapW 10…”