Short prokaryotic Argonautes provide defence against incoming mobile genetic elements through NAD+ depletion

Zaremba, Mindaugas; Dakineviciene, Donata; Golovinas, Edvardas; Zagorskaitė, Evelina; Stankunas, Edvinas; Lopatina, Anna; Sorek, Rotem; Manakova, E.; Rukšėnaitė, Audronė; Šilanskas, Arūnas; Ašmontas, Simonas; Grybauskas, Algirdas; Tylenyte, Ugne; Jurgelaitis, Edvinas; Grigaitis, Rokas; Timinskas, Kęstutis; Venclovas, C̆eslovas; Šikšnys, Virginijus

doi:10.1038/s41564-022-01239-0

Cited by 66 publications

(94 citation statements)

References 65 publications

(82 reference statements)

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“…3 B). We found that under these conditions AfAgo-gRNA complex shows an even stronger preference for DNA targets over RNA targets, similarly to related long-B and short pAgos 15 , 16 , 36 (Table 1 ). Experiments with pre-formed RNA/RNA, RNA/DNA and DNA/DNA duplexes (Table 1 , Supplementary Fig.…”

Section: Resultsmentioning

confidence: 60%

“…The majority (~ 60%) of identified pAgos are ‘short’, as they encode just MID and PIWI domains, the latter being catalytically inactive due to active site mutations. The mechanism, guide/target preferences and function of short pAgos is an emerging topic in the Argonaute field, as evidenced by recent characterization of SPARTA and GsSir2/Ago antiviral systems 15 , 16 , 30 .…”

Section: Introductionmentioning

confidence: 99%

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Structural basis for sequence-specific recognition of guide and target strands by the Archaeoglobus fulgidus Argonaute protein

Manakova

Golovinas

Pocevičiūtė

et al. 2023

Sci Rep

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Argonaute (Ago) proteins are found in all three domains of life. The best-characterized group is eukaryotic Argonautes (eAgos). Being the structural core of RNA interference machinery, they use guide RNA molecules for RNA targeting. Prokaryotic Argonautes (pAgos) are more diverse, both in terms of structure (there are eAgo-like ‘long’ and truncated ‘short’ pAgos) and mechanism, as many pAgos are specific for DNA, not RNA guide and/or target strands. Some long pAgos act as antiviral defence systems. Their defensive role was recently demonstrated for short pAgo-encoding systems SPARTA and GsSir2/Ago, but the function and action mechanisms of all other short pAgos remain unknown. In this work, we focus on the guide and target strand preferences of AfAgo, a truncated long-B Argonaute protein encoded by an archaeon Archaeoglobus fulgidus. We demonstrate that AfAgo associates with small RNA molecules carrying 5′-terminal AUU nucleotides in vivo, and characterize its affinity to various RNA and DNA guide/target strands in vitro. We also present X-ray structures of AfAgo bound to oligoduplex DNAs that provide atomic details for base-specific AfAgo interactions with both guide and target strands. Our findings broaden the range of currently known Argonaute-nucleic acid recognition mechanisms.

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Section: Resultsmentioning

confidence: 60%

Section: Introductionmentioning

confidence: 99%

Structural basis for sequence-specific recognition of guide and target strands by the Archaeoglobus fulgidus Argonaute protein

Manakova

Golovinas

Pocevičiūtė

et al. 2023

Sci Rep

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“…In this study, we describe a new immune strategy mediated by a family of enzymatic effectors that degrade (d)ATP in response to viral infection. This discovery expands the repertoire of immune domains known to target essential metabolites to limit viral replication, including the TIR 4,23,24,38,57 , SIR2 8,40,41 and SEFIR 37 domains that degrade NAD + , and dCTP deaminases 12 , dGTPases 12 and SAMHD1 58 that degrade deoxynucleotides. The central role of ATP makes it an ideal target for degradation in order to simultaneously inhibit multiple cellular processes that are essential for viral propagation.…”

Section: Discussionmentioning

confidence: 97%

“…The presence of the PNP domain in the N-termini of multiple Avs proteins strongly suggests that it functions as the cell-targeting effector domain in these proteins. We also found the PNP domain in short prokaryotic argonaute (pAgo) systems, which sense phage infection via a pAgo protein and induce cell death via an associated effector protein [38][39][40][41] . Effector proteins of short pAgo systems are diverse, and include protein domains that disrupt membrane integrity or cleave cellular NAD + 38-41 .…”

Section: A Specialized Immune Nucleosidase Domain Functions In Multip...mentioning

confidence: 97%

A conserved family of immune effectors cleaves cellular ATP upon viral infection

Rousset

Yirmiya

Nesher

et al. 2023

Preprint

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During viral infection, cells can deploy immune strategies that deprive viruses of molecules essential for their replication. In this study, we report a family of immune effectors in bacteria which, in response to phage infection, degrade cellular ATP and 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 CBASS, prokaryotic argonautes and NLR-like proteins, and we show that degradation of (d)ATP during infection halts phage propagation and aborts infection. By analyzing homologs of the immune ATP nucleosidase domain, we discover and characterize Detocs, a new family of bacterial defense systems with a two-component phosphotransfer signaling architecture. The immune ATP nucleosidase domain is also encoded within a diverse set of eukaryotic proteins that have immune-like architectures, and we show biochemically that these 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.

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“…Global bacterial transcription and translation activity, metabolism, and availability of cellular components can impact the efficiency of phage infection, even in nearly identical host strains 8 . While some phage defense systems have been shown to manipulate bacterial physiology to favor host population survival (such as a group of Sir2-domaincontaining systems that respond to phage infection by degrading cellular NAD+, a necessary coenzyme in central carbon metabolism [9][10][11] ), the impact of bacterial host physiology on phage infection is largely not mechanistically understood. This knowledge gap is compounded by the dynamic interplay between cell state and environment, which is fairly static in a laboratory setting but varies dramatically in a bacterium's natural environment.…”

Section: Introductionmentioning

confidence: 99%

Adaptation to bile and anaerobicity limitsVibrio choleraephage adsorption

Netter

Seed

2023

Preprint

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Bacteriophages (viruses of bacteria) play a pivotal role in shaping both the evolution and dynamics of bacterial populations. Bacteria employ arsenals of genetically encoded phage defense systems, but can alternatively achieve protection by changing the availability of cellular resources that phages rely on for propagation. These physiological changes are often adaptive responses to unique environmental signals. The facultative pathogen Vibrio cholerae adapts to both aquatic and intestinal environments with niche-specific physiological changes that ensure its evolutionary success in such disparate settings. In both niches, V. cholerae is susceptible to predation by lytic phages like ICP1. However, both phages and susceptible bacterial hosts coexist in nature, indicating that environmental cues may modulate V. cholerae cell state to protect against phage infection. This work explores one such modification in response to the intestine-specific signals of bile and anaerobicity. We found that V. cholerae grown in these conditions reduces O1-antigen decoration on its outer membrane lipopolysaccharide. Because the O1-antigen is an essential moiety for ICP1 phage infection, we investigated the effect of partial O1-antigen depletion as a mechanism of phage defense and observed that O1-depletion limits phage adsorption. We identified mechanistic contributions to O1-depletion, including the essentiality of a weak acid tolerance system for O1 production at low pH, and alterations in transcriptional profiles indicating limitations in resources for O1-biosynthesis. This analysis illustrates a complex interplay between signals relevant to the intestinal environment and bacterial physiology that provide V. cholerae with protection from phage predation.

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Short prokaryotic Argonautes provide defence against incoming mobile genetic elements through NAD+ depletion

Cited by 66 publications

References 65 publications

Structural basis for sequence-specific recognition of guide and target strands by the Archaeoglobus fulgidus Argonaute protein

Structural basis for sequence-specific recognition of guide and target strands by the Archaeoglobus fulgidus Argonaute protein

A conserved family of immune effectors cleaves cellular ATP upon viral infection

Adaptation to bile and anaerobicity limitsVibrio choleraephage adsorption

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