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

Kuhn, C. D. & Joshua-Tor, L. Eukaryotic Argonautes come into focus. Trends Biochem. Sci. 38, 263–271 (2013).

CAS  PubMed  Article  Google Scholar 

Pratt, A. J. & MacRae, I. J. The RNA-induced silencing complex: a versatile gene-silencing machine. J. Biol. Chem. 284, 17897–17901 (2009).

CAS  PubMed  PubMed Central  Article  Google Scholar 

Sheu-Gruttadauria, J. & MacRae, I. J. Structural foundations of RNA silencing by argonaute. J. Mol. Biol. 429, 2619–2639 (2017).

CAS  PubMed  PubMed Central  Article  Google Scholar 

Olina, A. V., Kulbachinskiy, A. V., Aravin, A. A. & Esyunina, D. M. Argonaute proteins and mechanisms of RNA interference in eukaryotes and prokaryotes. Biochemistry 83, 483–497 (2018).

CAS  PubMed  Google Scholar 

Hutvagner, G. & Simard, M. J. Argonaute proteins: key players in RNA silencing. Nat. Rev. Mol. Cell Biol. 9, 22–32 (2008).

CAS  PubMed  Article  Google Scholar 

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

CAS  PubMed  PubMed Central  Article  Google Scholar 

Kwak, P. B. & Tomari, Y. The N domain of Argonaute drives duplex unwinding during RISC assembly. Nat. Struct. Mol. Biol. 19, 145–151 (2012).

CAS  PubMed  Article  Google Scholar 

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

PubMed  PubMed Central  Article  Google Scholar 

Hegge, J. W., Swarts, D. C. & Van Der Oost, J. Prokaryotic argonaute proteins: novel genome-editing tools? Nat. Rev. Microbiol. 16, 5–11 (2018).

CAS  PubMed  Article  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).

PubMed  PubMed Central  Article  Google Scholar 

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

CAS  PubMed  PubMed Central  Article  Google Scholar 

Kuzmenko, A. et al. DNA targeting and interference by a bacterial Argonaute nuclease. Nature https://doi.org/10.1038/s41586-020-2605-1 (2020).

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

CAS  PubMed  PubMed Central  Article  Google Scholar 

Jolly, S. M. et al. Thermus thermophilus Argonaute functions in the completion of DNA replication. Cell 182, 1545–1559.e18 (2020).

CAS  PubMed  PubMed Central  Article  Google Scholar 

Olovnikov, I., Chan, K., Sachidanandam, R., Newman, D. K. & Aravin, A. A. Bacterial Argonaute samples the transcriptome to identify foreign DNA. Mol. Cell 51, 594–605 (2013).

CAS  PubMed  Article  Google Scholar 

Liu, Y. et al. A programmable omnipotent Argonaute nuclease from mesophilic bacteria Kurthia massiliensis. Nucleic Acids Res. https://doi.org/10.1093/nar/gkaa1278 (2021).

Kropocheva, E., Kuzmenko, A., Aravin, A. A., Esyunina, D. & Kulbachinskiy, A. A programmable pAgo nuclease with universal guide and target specificity from the mesophilic bacterium Kurthia massiliensis. Nucleic Acids Res. https://doi.org/10.1093/nar/gkab182 (2021).

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).

PubMed  PubMed Central  Article  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).

CAS  PubMed  Article  Google Scholar 

North, B. J. & Verdin, E. Sirtuins: Sir2-related NAD-dependent protein deacetylases. Genome Biol. 5, 224 (2004).

PubMed  PubMed Central  Article  Google Scholar 

Gallego-Jara, J. et al. Bacterial sirtuins overview: an open niche to explore. Front. Microbiol. 12, 744416 (2021).

PubMed  PubMed Central  Article  Google Scholar 

Wang, Y., Sheng, G., Juranek, S., Tuschl, T. & Patel, D. J. Structure of the guide-strand-containing argonaute silencing complex. Nature 456, 209–213 (2008).

CAS  PubMed  PubMed Central  Article  Google Scholar 

Frank, F., Sonenberg, N. & Nagar, B. Structural basis for 5′-nucleotide base-specific recognition of guide RNA by human AGO2. Nature 465, 818–822 (2010).

CAS  PubMed  Article  Google Scholar 

Ka, D., Oh, H., Park, E., Kim, J. H. & Bae, E. Structural and functional evidence of bacterial antiphage protection by Thoeris defense system via NAD+ degradation. Nat. Commun. 11, 2816 (2020).

CAS  PubMed  PubMed Central  Article  Google Scholar 

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

CAS  PubMed  Article  Google Scholar 

Dasgupta, S., Masukata, H. & Tomizawa, J. Multiple mechanisms for initiation of ColE1 DNA replication: DNA synthesis in the presence and absence of ribonuclease H. Cell 51, 1113–1122 (1987).

CAS  PubMed  Article  Google Scholar 

del Solar, G., Giraldo, R., Ruiz-Echevarria, M. J., Espinosa, M. & Diaz-Orejas, R. Replication and control of circular bacterial plasmids. Microbiol. Mol. Biol. Rev. 62, 434–464 (1998).

PubMed  PubMed Central  Article  Google Scholar 

Selzer, G., Som, T., Itoh, T. & Tomizawa, J. The origin of replication of plasmid p15A and comparative studies on the nucleotide sequences around the origin of related plasmids. Cell 32, 119–129 (1983).

CAS  PubMed  Article  Google Scholar 

Garb, J. et al. Multiple phage resistance systems inhibit infection via SIR2-dependent NAD+ depletion. Preprint at bioRxiv https://doi.org/10.1101/2021.12.14.472415 (2021).

Tal, N. et al. Cyclic CMP and cyclic UMP mediate bacterial immunity against phages. Cell 184, 5728–5739.e16 (2021).

CAS  PubMed  PubMed Central  Article  Google Scholar 

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

CAS  PubMed  Article  Google Scholar 

Zheng, L., Baumann, U. & Reymond, J. L. An efficient one-step site-directed and site-saturation mutagenesis protocol. Nucleic Acids Res. 32, e115 (2004).

PubMed  PubMed Central  Article  Google Scholar 

Ofir, G. et al. DISARM is a widespread bacterial defence system with broad anti-phage activities. Nat. Microbiol. 3, 90–98 (2018).

CAS  PubMed  Article  Google Scholar 

Doron, S. et al. Systematic discovery of antiphage defense systems in the microbial pangenome. Science 359, eaar4120 (2018).

PubMed  PubMed Central  Article  Google Scholar 

Mazzocco, A., Waddell, T. E., Lingohr, E. & Johnson, R. P. Enumeration of bacteriophages using the small drop plaque assay system. Methods Mol. Biol. https://doi.org/10.1007/978-1-60327-164-6_9 (2009).

Blanchet, C. E. et al. Versatile sample environments and automation for biological solution X-ray scattering experiments at the P12 beamline (PETRA III, DESY). J. Appl. Crystallogr. 48, 431–443 (2015).

CAS  PubMed  PubMed Central  Article  Google Scholar 

Franke, D., Petoukhov, M. V., Konarev, P. V. & Panjkovich, A. ATSAS 2.8: a comprehensive data analysis suite for small-angle scattering from macromolecular solutions. J. Appl. Crystallogr. https://doi.org/10.1107/S1600576717007786 (2017).

Konarev, P. V., Volkov, V. V., Sokolova, A. V., Koch, M. H. J. & Svergun, D. I. PRIMUS - a Windows-PC based system for small-angle scattering data analysis. J. Appl. Crystallogr. 36, 1277–1282 (2003).

CAS  Article  Google Scholar 

Svergun, D. I. Determination of the regularization parameter in indirect-transform methods using perceptual criteria. J. Appl. Crystallogr. 25, 495–503 (1992).

CAS  Article  Google Scholar 

Durand, D. et al. NADPH oxidase activator p67phox behaves in solution as a multidomain protein with semi-flexible linkers. J. Struct. Biol. 169, 45–53 (2010).

CAS  PubMed  Article  Google Scholar 

Svergun, D. I., Petoukhov, M. V. & Koch, M. H. J. Determination of domain structure of proteins from x-ray solution scattering. Biophys. J. 80, 2946–2953 (2001).

CAS  PubMed  PubMed Central  Article  Google Scholar 

Fischer, H., de Oliveira Neto, M., Napolitano, H. B., Polikarpov, I. & Craievich, A. F. Determination of the molecular weight of proteins in solution from a single small-angle X-ray scattering measurement on a relative scale. J. Appl. Crystallogr. 43, 101–109 (2010).

CAS  Article 

留言 (0)

沒有登入
gif