Catalytically inactive long prokaryotic Argonaute systems employ distinct effectors to confer immunity via abortive infection

Abstract

Argonaute proteins (Agos) bind short nucleic acids as guides and are directed by them to recognize target complementary nucleic acids. Diverse prokaryotic Agos (pAgos) play potential functions in microbial defense. The functions and mechanisms of a group of full-length yet catalytically inactive pAgos, long-B pAgos, remain unclear. Here, we show that most long-B pAgos are functionally connected with distinct associated proteins, including nucleases, Sir2-domain-containing proteins and trans-membrane proteins, respectively. The long-B pAgo-nuclease system (BPAN) is activated by guide RNA-directed target DNA recognition and performs collateral DNA degradation in vitro. In vivo, the system mediates genomic DNA degradation after sensing invading plasmid, which kills the infected cells and results in the depletion of the invader from the cell population. Together, the BPAN system provides immunoprotection via abortive infection. Our data also suggest that the defense strategy is employed by other long-B pAgos equipped with distinct associated proteins.

An antiplasmid system drives antibiotic resistance gene integration in carbapenemase-producing Escherichia coli lineages

“…However, unique to ApsB-like proteins is the conservation of a MID-like domain of long pAgos, which we showed to be essential for its activity. This suggests that ApsB is involved in a guide-dependent recognition of the target, ApsA bringing the nuclease activity, similarly to what has recently been described for a group of catalytically inactive long true pAgos 38 . While these Argonaute systems confer immunity also via abortive infection 38 , we do not have evidence that ApsAB kills plasmid invaded cells.…”

“…This suggests that ApsB is involved in a guide-dependent recognition of the target, ApsA bringing the nuclease activity, similarly to what has recently been described for a group of catalytically inactive long true pAgos 38 . While these Argonaute systems confer immunity also via abortive infection 38 , we do not have evidence that ApsAB kills plasmid invaded cells. Despite the absence of similarity between DdmE and ApsB, both DdmDE and ApsAB share an antiplasmid activity, like a second E. coli system, only 28/25% similar to ST38 ApsAB (Fig.…”

Prokaryotic Argonaute nuclease cooperates with co-encoded RNase to acquire guide RNAs and target invader DNA

“…The first published study of the in vivo specificity of a full-length RNA-guided pAgo, catalytically inactive RsAgo from the long-B clade encoded by Rhodobacter sphaeroides , showed that it binds guide RNAs that are produced from the whole transcriptome independently of the co-encoded nuclease ( 29 ). Other long-B pAgos and short pAgos are also loaded with guide RNAs in bacterial cells but their biogenesis pathways have not been studied ( 27 , 28 , 40 , 41 ).…”

The nuclease-associated short prokaryotic Argonaute system nonspecifically degrades DNA upon activation by target recognition

“…Unlike long-A pAgos, long-B pAgos utilize RNA guides to bind DNA targets, but they cannot cleave the targets due to the absence of the catalytic DEDX tetrad ( 12 ). A recent study showed that long-B pAgos, in conjunction with their associated effector proteins including nuclease, SIR2-domain-containing proteins and transmembrane proteins, play a role in host defense by inducing abortive infection ( 13 ). While our knowledge of the functions of long pAgos is continually advancing, research on short pAgos is still in its early stages.…”