DNA-targeting short Argonautes complex with effector proteins for collateral nuclease activity and bacterial population immunity

Joshua-Tor, L. The Argonautes. Cold Spring Harb. Symp. Quant. Biol. 71, 67–72 (2006).

Article  CAS  PubMed  Google Scholar 

Lisitskaya, L., Aravin, A. A. & Kulbachinskiy, A. DNA interference and beyond: structure and functions of prokaryotic Argonaute proteins. Nat. Commun. 9, 5165 (2018).

Article  PubMed  PubMed Central  Google Scholar 

Swarts, D. C. et al. The evolutionary journey of Argonaute proteins. Nat. Struct. Mol. Biol. 21, 743–753 (2014).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Makarova, K. S., Wolf, Y. I., van der Oost, J. & Koonin, E. V. Prokaryotic homologs of Argonaute proteins are predicted to function as key components of a novel system of defense against mobile genetic elements. Biol. Direct 4, 29 (2009).

Article  PubMed  PubMed Central  Google Scholar 

Ryazansky, S., Kulbachinskiy, A. & Aravin, A. A. The expanded universe of prokaryotic Argonaute proteins. mBio 9, e01935–18 (2018).

Article  PubMed  PubMed Central  Google Scholar 

Wein, T. & Sorek, R. Bacterial origins of human cell-autonomous innate immune mechanisms. Nat. Rev. Immunol. 22, 629–638 (2022).

Article  CAS  PubMed  Google Scholar 

Burroughs, A. M., Ando, Y. & Aravind, L. New perspectives on the diversification of the RNA interference system: insights from comparative genomics and small RNA sequencing. Wiley Interdiscip. Rev. RNA 5, 141–181 (2014).

Article  CAS  PubMed  Google Scholar 

Bobadilla Ugarte, P., Barendse, P. & Swarts, D. C. Argonaute proteins confer immunity in all domains of life. Curr. Opin. Microbiol. 74, 102313 (2023).

Article  CAS  PubMed  Google Scholar 

Sheng, G. et al. Structure-based cleavage mechanism of Thermus thermophilus Argonaute DNA guide strand-mediated DNA target cleavage. Proc. Natl Acad. Sci. USA 111, 652–657 (2014).

Article  CAS  PubMed  Google Scholar 

Swarts, D. C. et al. Argonaute of the archaeon Pyrococcus furiosus is a DNA-guided nuclease that targets cognate DNA. Nucleic Acids Res. 43, 5120–5129 (2015).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Swarts, D. C. et al. DNA-guided DNA interference by a prokaryotic Argonaute. Nature 507, 258–261 (2014).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Zander, A. et al. Guide-independent DNA cleavage by archaeal Argonaute from Methanocaldococcus jannaschii. Nat. Microbiol. 2, 17034 (2017).

Article  CAS  PubMed  Google Scholar 

Hegge, J. W. et al. DNA-guided DNA cleavage at moderate temperatures by Clostridium butyricum Argonaute. Nucleic Acids Res. 47, 5809–5821 (2019).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Kaya, E. et al. A bacterial Argonaute with noncanonical guide RNA specificity. Proc. Natl Acad. Sci. USA 113, 4057–4062 (2016).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Kuzmenko, A., Yudin, D., Ryazansky, S., Kulbachinskiy, A. & Aravin, A. A. Programmable DNA cleavage by Ago nucleases from mesophilic bacteria Clostridium butyricum and Limnothrix rosea. Nucleic Acids Res. 47, 5822–5836 (2019).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Willkomm, S., Makarova, K. & Grohmann, D. DNA silencing by prokaryotic Argonaute proteins adds a new layer of defence against invading nucleic acids. FEMS Microbiol. Rev. 42, 376–387 (2018).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Koopal, B., Mutte, S. K. & Swarts, D. C. A long look at short prokaryotic Argonautes. Trends Cell Biol. 33, 605–618 (2023).

Article  CAS  PubMed  Google Scholar 

Koopal, B. et al. Short prokaryotic Argonaute systems trigger cell death upon detection of invading DNA. Cell 185, 1471–1486 e1419 (2022).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Kim, S. Y., Jung, Y. & Lim, D. Argonaute system of Kordia jejudonensis is a heterodimeric nucleic acid-guided nuclease. Biochem. Biophys. Res. Commun. 525, 755–758 (2020).

Article  CAS  PubMed  Google Scholar 

Zaremba, M. et al. Short prokaryotic Argonautes provide defence against incoming mobile genetic elements through NAD(+) depletion. Nat. Microbiol. 7, 1857–1869 (2022).

Article  CAS  PubMed  Google Scholar 

Wang, X. et al. Structural insights into mechanisms of Argonaute protein-associated NADase activation in bacterial immunity. Cell Res. 33, 699–711 (2023).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Garb, J. et al. Multiple phage resistance systems inhibit infection via SIR2-dependent NAD(+) depletion. Nat. Microbiol. 7, 1849–1856 (2022).

Article  CAS  PubMed  Google Scholar 

Ofir, G. et al. Antiviral activity of bacterial TIR domains via immune signalling molecules. Nature 600, 116–120 (2021).

Article  CAS  PubMed  Google Scholar 

Essuman, K., Milbrandt, J., Dangl, J. L. & Nishimura, M. T. Shared TIR enzymatic functions regulate cell death and immunity across the tree of life. Science 377, eabo0001 (2022).

Article  CAS  PubMed  Google Scholar 

Nishino, T., Komori, K., Tsuchiya, D., Ishino, Y. & Morikawa, K. Crystal structure of the archaeal holliday junction resolvase Hjc and implications for DNA recognition. Structure 9, 197–204 (2001).

Article  CAS  PubMed  Google Scholar 

Middleton, C. L., Parker, J. L., Richard, D. J., White, M. F. & Bond, C. S. Substrate recognition and catalysis by the Holliday junction resolving enzyme Hje. Nucleic Acids Res. 32, 5442–5451 (2004).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Finocchio, G. et al. Target DNA-dependent activation mechanism of the prokaryotic immune system SPARTA. Nucleic Acids Res. 52, 2012–2029 (2024).

Article  PubMed  PubMed Central  Google Scholar 

Shen, Z. et al. Oligomerization-mediated activation of a short prokaryotic Argonaute. Nature 621, 154–161 (2023).

Article  CAS  PubMed  Google Scholar 

Guo, L. et al. Auto-inhibition and activation of a short Argonaute-associated TIR–APAZ defense system. Nat. Chem. Biol. https://doi.org/10.1038/s41589-023-01478-0 (2023).

Steczkiewicz, K., Muszewska, A., Knizewski, L., Rychlewski, L. & Ginalski, K. Sequence, structure and functional diversity of PD-(D/E)XK phosphodiesterase superfamily. Nucleic Acids Res. 40, 7016–7045 (2012).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Buisson, M. et al. A bridge crosses the active-site canyon of the Epstein–Barr virus nuclease with DNase and RNase activities. J. Mol. Biol. 391, 717–728 (2009).

Article  CAS  PubMed  Google Scholar 

Meeske, A. J., Nakandakari-Higa, S. & Marraffini, L. A. Cas13-induced cellular dormancy prevents the rise of CRISPR-resistant bacteriophage. Nature 570, 241–245 (2019).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Rostol, J. T. et al. The Card1 nuclease provides defence during type III CRISPR immunity. Nature 590, 624–629 (2021).

Article  PubMed  PubMed Central  Google Scholar 

Rostol, J. T. & Marraffini, L. A. Non-specific degradation of transcripts promotes plasmid clearance during type III-A CRISPR–Cas immunity. Nat. Microbiol. 4, 656–662 (2019).

Article  PubMed  PubMed Central  Google Scholar 

Gootenberg, J. S. et al. Nucleic acid detection with CRISPR–Cas13a/C2c2. Science 356, 438–442 (2017).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Gainetdinov, I. et al. Relaxed targeting rules help PIWI proteins silence transposons. Nature 619, 394–402 (2023).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Lopatina, A., Tal, N. & Sorek, R. Abortive infection: bacterial suicide as an antiviral immune strategy. Annu. Rev. Virol. 7, 371–384 (2020).

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