During viral infection, cells can deploy immune strategies that deprive viruses of molecules essential for their replication. Here, we report a family of immune effectors in bacteria that, upon phage infection, degrade cellular adenosine triphosphate (ATP) and deoxyadenosine triphosphate (dATP) by cleaving the N-glycosidic bond between the adenine and sugar moieties. These ATP nucleosidase effectors are widely distributed within multiple bacterial defense systems, including cyclic oligonucleotide-based antiviral signaling systems (CBASS), prokaryotic argonautes, and nucleotide-binding leucine-rich repeat (NLR)-like proteins, and we show that ATP and dATP degradation during infection halts phage propagation. By analyzing homologs of the immune ATP nucleosidase domain, we discover and characterize Detocs, a family of bacterial defense systems with a two-component phosphotransfer-signaling architecture. The immune ATP nucleosidase domain is also encoded within diverse eukaryotic proteins with immune-like architectures, and we show biochemically that eukaryotic homologs preserve the ATP nucleosidase activity. Our findings suggest that ATP and dATP degradation is a cell-autonomous innate immune strategy conserved across the tree of life.
Sensor:Unknown
Activator:Unknown
Effector:Nucleotide modifying
PFAM:PF01048, PF18742
relevantAbstracts:
-doi:10.1016/j.cell.2023.07.020
contributors:
-François Rousset
-Nathalie Bechon
relevantAbstracts:
-doi:10.1016/j.cell.2023.07.020
---
# Detocs
## Description
Detocs (**De**fensive **T**w**o**-**C**omponent **S**ystem) is a family of 3-gene defense systems that mediate anti-phage activity by abortive infection.
Detocs (**De**fensive **T**w**o**-**C**omponent **S**ystem) is a family of 3-gene defense systems. Upon phage recognition, Detocs degrades ATP, which can lead to premature phage lysis or abortive infection depending on the infecting phage, in a way that is currently not fully understood. Detocs shares homology with the bacterial two-component system, a well known bacterial gene regulation system composed of an environment sensor and a cytosolic response regulator mediating gene expression.
## Molecular mechanism
Detocs shares homology with two-component signal transduction systems. Two-component systems are ubiquitous in prokaryotes and comprise a sensor kinase that typically senses an environmental signal through its N-terminal domain, triggering autophosphorylation of a conserved histidine residue near the C-terminal kinase domain. The phosphate group is then transferred to a conserved aspartate on the N-terminal receiver domain of the second protein, called the “response regulator”. Phosphorylation of the receiver domain activates the C-terminal domain of the response regulator, usually a DNA-binding domain that regulates the expression of target genes. In Detocs, the N-terminal sensor domain on the histidine kinase (DtcA) is intracellular and comprises tetratricopeptide repeats that are believed to sense phage infection; the C-terminal domain of the response regulator (DtcC) is replaced a PNP domain that was shown to specifically cleave ATP molecules into adenine and ribose-5’-triphosphate, both in vitro and during phage infection. Detocs activity leads to a drastic reduction in ATP and dATP levels during infection and to an accumulation of adenine. In parallel, ADP, AMP, dADP and dAMP levels are also reduced, likely in an indirect manner. Detocs induces growth arrest of T5-infected cells, but not of SECphi27-infected cells, suggesting that the outcome of infection following ATP degradation is phage-specific.
Detocs is a family of 3-gene systems that resembles bacterial twocomponent systems. Twocomponent systems are common prokaryotic gene regulation modules made of two component, a sensor kinase and response regulator. The sensor typically senses an environmental signal through its N-terminal domain, leading to the autophosphorylation of a conserved histidine in its kinase C-terminal domain. This phosphate group is then transfered to the N-terminal receiver domain of the response regulator, which activates the response regulator's C-terminal domain, usually a DNA binding domain involved in gene regulation. This allows bacteria to modify gene expression based on environemental cues.
While the genetic architecture of Detocs is similar to that of regulatory two-component systems, Detocs also encodes another protein, DtcB, with a standalone receiver domain that is not linked to any effector domain. A point mutation in the receiving aspartate of DtcB is toxic, while overexpression of DtcB impairs the defense capacity of Detocs. Therefore, DtcB likely serves as a “buffer” protein that absorbs phosphate signals that result from inadvertent leaky activation of DtcA in the absence of phage infection, thus preventing autoimmunity.
Detocs DtcA ressembles an intracellular sensor kinase. Its N-terminal end comprises tetratricopeptide repeats that are usually involved in protein/protein interactions and are believed to be responsible for sensing phage infection, while its C-terminal end possesses a kinase domain. Detocs DtcC, resembles a response regulator. It has an N-terminal receiver domain, and its C-terminal is variable depending on systems and it always contains a predicted effector domain (PNP, nuclease, transmembrane, hydrolase...). Unlike two-component system, Detocs encodes an additional third protein, DtcB, with a standalone receiver domain that is not linked to any effector domain. A point mutation in the receiving aspartate of DtcB is toxic, while overexpression of DtcB impairs the defense capacity of Detocs. Therefore, DtcB likely serves as a “buffer” protein that absorbs phosphate signals that result from inadvertent leaky activation of DtcA in the absence of phage infection, thus preventing autoimmunity.
While 80% of Detocs operons encode PNP effectors, in a minority of these operons the PNP is replaced by other domains known to function as cell-killing effectors in bacterial defense systems, including endonuclease and transmembrane-spanning domains. A Detocs operon with a transmembrane α/β hydrolase effector from Enterobacter cloacae JD6301 was able to efficiently protect E. coli against diverse phages (Rousset et al., 2023).
The best described Detocs system uses a PNP effector, which was shown to specifically cleave ATP molecules into adenine and ribose-5’-triphosphate, both in vitro and during phage infection. Detocs activity leads to a drastic reduction in ATP and dATP levels during infection and to an accumulation of adenine. In parallel, ADP, AMP, dADP and dAMP levels are also reduced, likely in an indirect manner. Detocs induces growth arrest of T5-infected cells, but not of SECphi27-infected cells, suggesting that the outcome of infection following ATP degradation is phage-specific. The exact way in which this leads to defense against phages is not yet clear, but is believed to be a form of abortive infection. While PNP effectors represent 80% of Detocs operons, other cell-killing effectors can be found in a minority of Detocs systems. A Detocs operon with a transmembrane α/β hydrolase effector from *Enterobacter cloacae* JD6301 was able to efficiently protect *E. coli* against diverse phages :ref{doi=10.1016/j.cell.2023.07.020}.
