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).
Comments (0)