Bacterial Immune Systems: to See the Virus and Die

Capa

Citar

Texto integral

Acesso aberto Acesso aberto
Acesso é fechado Acesso está concedido
Acesso é fechado Somente assinantes

Resumo

Bacterial immune systems can protect cells at different steps of viral infection, by preventing virus binding and genome injection, destroying viral nucleic acids, disrupting virus replication or assembly of viral particles. Recent studies have shown that along with systems that directly attack invader elements, there are many defense systems that induce the death of the infected cell, thus preventing the spread of viruses and plasmids in the population. The key event in the activation of various immune systems is the recognition of invader elements during infection. Two types of defense systems, CRISPR-Cas and Argonautte proteins, can directly recognize and cleave viral DNA or RNA using short complementary guide oligonucleotides. At the same time, recently discovered new groups of Argonautes can induce suicidal cell response and cause abortive infection. In this case, guided recognition of viral or plasmid targets leads to the activation of additional effector proteins that disrupt cellular metabolism, destroy the cell membrane, or cause nonspecific degradation of cellular and viral DNA. Such systems are important participants in the evolutionary race between viruses and bacteria and can serve as tools for genetic engineering and biotechnology.

Sobre autores

D. Gelfenbein

Institute of Gene Biology, Russian Academy of Sciences

Moscow, Russia

A. Kanevskaya

Institute of Gene Biology, Russian Academy of Sciences

Moscow, Russia

B. Godneeva

Institute of Gene Biology, Russian Academy of Sciences

Moscow, Russia

E. Kropocheva

Institute of Gene Biology, Russian Academy of Sciences

Moscow, Russia

L. Lisitskaya

Institute of Gene Biology, Russian Academy of Sciences

Moscow, Russia

V. Panteleev

Institute of Gene Biology, Russian Academy of Sciences

Moscow, Russia

A. Kulbachinskiy

Institute of Gene Biology, Russian Academy of Sciences

Email: avkulb@yandex.ru
Moscow, Russia

Bibliografia

  1. Nasir A., Romero-Severson E., Claverie J.M. Investigating the concept and origin of viruses // Trends Microbiol. 2020. V. 28. № 12. P. 959–967. https://doi.org/10.1016/j.tim.2020.08.003
  2. Georjon H., Bernheim A. The highly diverse antiphage defence systems of bacteria // Nat. Rev. Microbiol. 2023. V. 21. № 10. P. 686–700. https://doi.org/10.1038/s41579-023-00934-x
  3. Martinez M., Rizzuto I., Molina R. Knowing our enemy in the antimicrobial resistance era: Dissecting the molecular basis of bacterial defense systems // Int. J. Mol. Sci. 2024. V. 25. № 9. https://doi.org/10.3390/ijms25094929
  4. Isaev A.B., Musharova O.S., Severinov K.V. Microbial arsenal of antiviral defenses. Part II // Biochemistry (Moscow). 2021. V. 86. № 4. P. 449–470. https://doi.org/10.1134/S0006297921040064
  5. Isaev A.B., Musharova O.S., Severinov K.V. Microbial arsenal of antiviral defenses – part I//Biochemistry (Moscow). 2021. V. 86. № 3. P. 319–337. https://doi.org/10.1134/S0006297921030081
  6. Agapov A., Baker K.S., Bedekar P. et al. Multi-layered genome defences in bacteria // Curr. Opin Microbiol. 2024. V. 78. https://doi.org/10.1016/j.mib.2024.102436
  7. Bernheim A., Sorek R. The pan-immune system of bacteria: Antiviral defence as a community resource // Nat. Rev. Microbiol. 2020. V. 18. № 2. P. 113–119. https://doi.org/10.1038/s41579-019-0278-2
  8. Beavogui A., Lacroix A., Wiart N. et al. The defensome of complex bacterial communities // Nat. Commun. 2024. V. 15. № 1. P. 2146. https://doi.org/10.1038/s41467-024-46489-0
  9. Morehouse B.R. Phage defense origin of animal immunity // Curr. Opin Microbiol. 2023. V. 73. https://doi.org/10.1016/j.mib.2023.102295
  10. Bernheim A., Cury J., Poirier E.Z. The immune modules conserved across the tree of life: Towards a definition of ancestral immunity // PLoS Biol. 2024. V. 22. № 7. https://doi.org/10.1371/journal.pbio.3002717
  11. Van den Berg D.F., Costa A.R., Esser J.Q. et al. Bacterial homologs of innate eukaryotic antiviral defenses with anti-phage activity highlight shared evolutionary roots of viral defenses // Cell Host Microbe. 2024. V. 32. № 8. P. 1427–1443. https://doi.org/10.1016/j.chom.2024.07.007
  12. Gao L., Altae-Tran H., Bohning F. et al. Diverse enzymatic activities mediate antiviral immunity in prokaryotes // Science. 2020. V. 369. № 6507. P. 1077–1084. https://doi.org/10.1126/science.aba0372
  13. Millman A., Melamed S., Leavitt A. et al. An expanded arsenal of immune systems that protect bacteria from phages // Cell Host Microbe. 2022. V. 30. № 11. P. 1556–1569 e5. https://doi.org/10.1016/j.chom.2022.09.017
  14. Doron S., Melamed S., Ofir G. et al. Systematic discovery of antiphage defense systems in the microbial pangenome // Science. 2018. V. 359. № 6379. https://doi.org/10.1126/science.aar4120
  15. Baca C.F., Marraffini L.A. Nucleic acid recognition during prokaryotic immunity // Mol. Cell. 2025. V. 85. № 2. P. 309–322. https://doi.org/10.1016/j.molcel.2024.12.007
  16. Vassallo C.N., Doering C.R., Littlehale M.L. et al. A functional selection reveals previously undetected antiphage defence systems in the E. coli pangenome // Nat. Microbiol. 2022. V. 7. № 10. P. 1568–1579. https://doi.org/10.1038/s41564-022-01219-4
  17. Mayo-Munoz D., Pinilla-Redondo R., Birkholz N. et al. A host of armor: Prokaryotic immune strategies against mobile genetic elements // Cell Rep. 2023. V. 42. № 7. https://doi.org/10.1016/j.celrep.2023.112672
  18. Ledvina H.E., Whiteley A.T. Conservation and similarity of bacterial and eukaryotic innate immunity // Nat. Rev. Microbiol. 2024. V. 22. № 7. P. 420–434. https://doi.org/10.1038/s41579-024-01017-1
  19. Faure G., Saito M., Wilkinson M.E. et al. TIGR-Tas: A family of modular RNA-guided DNA-targeting systems in prokaryotes and their viruses // Science. 2025. https://doi.org/10.1126/science.adv9789
  20. Altae-Tran H., Kannan S., Suberski A.J. et al. Uncovering the functional diversity of rare CRISPRCas systems with deep terascale clustering // Science. 2023. V. 382. № 6673. https://doi.org/10.1126/science.adi1910
  21. Boyle T.A., Hatoum-Aslan A. Recurring and emerging themes in prokaryotic innate immunity // Curr. Opin Microbiol. 2023. V. 73. https://doi.org/10.1016/j.mib.2023.102324
  22. Rostol J.T., Marraffini L. (Ph)ighting phages: How bacteria resist their parasites // Cell Host Microbe. 2019. V. 25. № 2. P. 184–194. https://doi.org/10.1016/j.chom.2019.01.009
  23. Stokar-Avihail A., Fedorenko T., Hor J. et al. Discovery of phage determinants that confer sensitivity to bacterial immune systems // Cell. 2023. V. 186. № 9. P. 1863–1876 e16. https://doi.org/10.1016/j.cell.2023.02.029
  24. Kibby E.M., Conte A.N., Burroughs A.M. et al. Bacterial NLR-related proteins protect against phage // Cell. 2023. V. 186. № 11. P. 2410–2424 e18. https://doi.org/10.1016/j.cell.2023.04.015
  25. Gao L.A., Wilkinson M.E., Strecker J. et al. Prokaryotic innate immunity through pattern recognition of conserved viral proteins // Science. 2022. V. 377. № 6607. https://doi.org/10.1126/science.abm4096
  26. Burroughs A.M., Zhang D., Schaffer D.E. et al. Comparative genomic analyses reveal a vast, novel network of nucleotide-centric systems in biological conflicts, immunity and signaling // Nucl. Ac. Res. 2015. V. 43. № 22. P. 10633–10654. https://doi.org/10.1093/nar/gkv1267
  27. Ye Q., Lau R.K., Mathews I.T. et al. HORMA domain proteins and a trip13-like ATPase regulate bacterial cGAS-like enzymes to mediate bacteriophage immunity // Mol. Cell. 2020. V. 77. № 4. P. 709–722 e7. https://doi.org/10.1016/j.molcel.2019.12.009
  28. Pradhan B., Deep A., Konig J. et al. Loop-extrusionmediated plasmid DNA cleavage by the bacterial SMC Wadjet complex // Mol. Cell. 2025. V. 85. № 1. P. 107–116 e5. https://doi.org/10.1016/j.molcel.2024.11.002
  29. Roisné-Hamelin F., Liu H.W., Gruber S. Structure of a type II SMC Wadjet complex from Neobacillus vireti // bioRxiv. 2025. https://doi.org/10.1101/2025.03.10.642339.
  30. Gu Y., Li H., Deep A. et al. Bacterial Shedu immune nucleases share a common enzymatic core regulated by diverse sensor domains // Mol. Cell. 2025. V. 85. № 3. P. 523–536 e6. https://doi.org/10.1016/j.molcel.2024.12.004
  31. Loeff L., Walter A., Rosalen G.T. et al. DNA end sensing and cleavage by the Shedu anti-phage defense system // Cell. 2025. V. 188. № 3. P. 721–733 e17. https://doi.org/10.1016/j.cell.2024.11.030
  32. Hu H., Popp P.F., Hughes T.C.D. et al. Structure and mechanism of the Zorya anti-phage defence system // Nature. 2025. V. 639. № 8056. P. 1093–1101. https://doi.org/10.1038/s41586-024-08493-8
  33. Athukoralage J.S., White M.F. Cyclic nucleotide signaling in phage defense and counter-defense // Annu. Rev. Virol. 2022. V. 9. № 1. P. 451–468. https://doi.org/10.1146/annurev-virology-100120-010228
  34. Hobbs S.J., Kranzusch P.J. Nucleotide immune signaling in CBASS, Pycsar, Thoeris, and CRISPR antiphage defense // Annu. Rev. Microbiol. 2024. V. 78. № 1. P. 255–276. https://doi.org/10.1146/annurev-micro-041222-024843
  35. Rousset F., Sorek R. The evolutionary success of regulated cell death in bacterial immunity // Curr. Opin Microbiol. 2023. V. 74. https://doi.org/10.1016/j.mib.2023.102312
  36. Lopatina A., Tal N., Sorek R. Abortive Infection: Bacterial suicide as an antiviral immune strategy // Annu. Rev. Virol. 2020. V. 7. № 1. P. 371–384. https://doi.org/10.1146/annurev-virology-011620-040628
  37. Wang L., Zhang L. The arms race between bacteria CBASS and bacteriophages // Front. Immunol. 2023. V. 14. https://doi.org/10.3389/fimmu.2023.1224341
  38. Millman A., Bernheim A., Stokar-Avihail A. et al. Bacterial retrons function in anti-phage defense // Cell. 2020. V. 183. № 6. P. 1551–1561. e12. https://doi.org/10.1016/j.cell.2020.09.065
  39. Fineran P.C., Blower T.R., Foulds I.J. et al. The phage abortive infection system, ToxIN, functions as a protein-RNA toxin-antitoxin pair // Proc. Natl Acad. Sci. USA. 2009. V. 106. № 3. P. 894–899. https://doi.org/10.1073/pnas.0808832106
  40. LeRoux M., Laub M.T. Toxin-antitoxin systems as phage defense elements // Annu. Rev. Microbiol. 2022. V. 76. P. 21–43. https://doi.org/10.1146/annurev-micro-020722-013730
  41. Carabias A., Camara-Wilpert S., Mestre M.R. et al. Retron-Eco1 assembles NAD(+)-hydrolyzing filaments that provide immunity against bacteriophages // Mol. Cell. 2024. V. 84. № 11. P. 2185–2202. https://doi.org/10.1016/j.molcel.2024.05.001
  42. Hogrel G., Guild A., Graham S. et al. Cyclic nucleotideinduced helical structure activates a TIR immune effector // Nature. 2022. V. 608. № 7924. P. 808–812. https://doi.org/10.1038/s41586-022-05070-9
  43. Tamulaitiene G., Sabonis D., Sasnauskas G. et al. Activation of Thoeris antiviral system via SIR2 effector filament assembly // Nature. 2024. V. 627. № 8003. P. 431–436. https://doi.org/10.1038/s41586-024-07092-x
  44. Essuman K., Milbrandt J., Dangl J.L. et al. Shared TIR enzymatic functions regulate cell death and immunity across the tree of life // Science. 2022. V. 377. № 6605. https://doi.org/10.1126/science.abo0001
  45. Wang S., Kuang S., Song H. et al. The role of TIR domain-containing proteins in bacterial defense against phages // Nat. Commun. 2024. V. 15. № 1. P. 7384. https://doi.org/10.1038/s41467-024-51738-3
  46. Marmorstein R. Structure and chemistry of the Sir2 family of NAD+-dependent histone/protein deactylases // Biochem. Soc. Trans. 2004. V. 32. Pt 6. https://doi.org/10.1042/BST0320904
  47. Ofir G., Herbst E., Baroz M. et al. Antiviral activity of bacterial TIR domains via immune signalling molecules // Nature. 2021. V. 600. № 7887. P. 116–120. https://doi.org/10.1038/s41586-021-04098-7
  48. Shen Z., Lin Q., Yang X.Y. et al. Assembly-mediated activation of the SIR2-HerA supramolecular complex for anti-phage defense // Mol. Cell. 2023. V. 83. № 24. P. 4586–4599 e5. https://doi.org/10.1016/j.molcel.2023.11.007
  49. Tang D., Chen Y., Chen H. et al. Multiple enzymatic activities of a Sir2-HerA system cooperate for antiphage defense // Mol. Cell. 2023. V. 83. № 24. P. 4600–4613 e6. https://doi.org/10.1016/j.molcel.2023.11.010
  50. Garb J., Lopatina A., Bernheim A. et al. Multiple phage resistance systems inhibit infection via SIR2-dependent NAD(+) depletion // Nat. Microbiol. 2022. V. 7. № 11. P. 1849–1856. https://doi.org/10.1038/s41564-022-01207-8
  51. Li Y., Shen Z., Zhang M. et al. PtuA and PtuB assemble into an inf lammasome-like oligomer for anti-phage defense // Nat. Struct. Mol. Biol. 2024. V. 31. № 3. P. 413–423. https://doi.org/10.1038/s41594-023-01172-8
  52. Antine S.P., Johnson A.G., Mooney S.E. et al. Structural basis of Gabija anti-phage defence and viral immune evasion // Nature. 2024. V. 625. № 7994. P. 360–365. https://doi.org/10.1038/s41586-023-06855-2
  53. Li J., Cheng R., Wang Z. et al. Structures and activation mechanism of the Gabija anti-phage system // Nature. 2024. V. 629. № 8011. P. 467–473. https://doi.org/10.1038/s41586-024-07270-x
  54. Tuck O.T., Adler B.A., Armbruster E.G. et al. Genome integrity sensing by the broad-spectrum Hachiman antiphage defense complex // Cell. 2024. V. 187. № 24. P. 6914–6928. https://doi.org/10.1016/j.cell.2024.09.020
  55. Robins W.P., Meader B.T., Toska J. et al. DdmABCdependent death triggered by viral palindromic DNA sequences // Cell Rep. 2024. V. 43. № 7. https://doi.org/10.1016/j.celrep.2024.114450
  56. Patel D.J., Yu Y., Jia N. Bacterial origins of cyclic nucleotide-activated antiviral immune signaling // Mol. Cell. 2022. V. 82. № 24. P. 4591–4610. https://doi.org/10.1016/j.molcel.2022.11.006
  57. Burman N., Belukhina S., Depardieu F. et al. A virally encoded tRNA neutralizes the PARIS antiviral defence system // Nature. 2024. V. 634. № 8033. P. 424–431. https://doi.org/10.1038/s41586-024-07874-3
  58. Stella G., Marraffini L. Type III CRISPR-Cas: beyond the Cas10 effector complex // Trends Biochem. Sci. 2024. V. 49. № 1. P. 28–37. https://doi.org/10.1016/j.tibs.2023.10.006
  59. Duncan-Lowey B., Tal N., Johnson A.G. et al. CryoEM structure of the RADAR supramolecular antiphage defense complex // Cell. 2023. V. 186. № 5. P. 987–998 e15. https://doi.org/10.1016/j.cell.2023.01.012
  60. Gao Y., Luo X., Li P. et al. Molecular basis of RADAR anti-phage supramolecular assemblies // Cell. 2023. V. 186. № 5. P. 999–1012 e20. https://doi.org/10.1016/j.cell.2023.01.026
  61. Rousset F., Yirmiya E., Nesher S. et al. A conserved family of immune effectors cleaves cellular ATP upon viral infection // Cell. 2023. V. 186. № 17. P. 3619–3631 e13. https://doi.org/10.1016/j.cell.2023.07.020
  62. Hsueh B.Y., Severin G.B., Elg C.A. et al. Phage defence by deaminase-mediated depletion of deoxynucleotides in bacteria // Nat. Microbiol. 2022. V. 7. № 8. P. 1210–1220. https://doi.org/10.1038/s41564-022-01162-4
  63. Tal N., Millman A., Stokar-Avihail A. et al. Bacteria deplete deoxynucleotides to defend against bacteriophage infection // Nat. Microbiol. 2022. V. 7. № 8. P. 1200–1209. https://doi.org/10.1038/s41564-022-01158-0
  64. Duncan-Lowey B., Kranzusch P.J. CBASS phage defense and evolution of antiviral nucleotide signaling // Curr. Opin. Immunol. 2022. V. 74. P. 156–163. https://doi.org/10.1016/j.coi.2022.01.002
  65. Shi Y., Masic V., Mosaiab T. et al. Structural characterization of macro domain-containing Thoeris antiphage defense systems // Sci. Adv. 2024. V. 10. № 26. https://doi.org/10.1126/sciadv.adn3310
  66. Tal N., Morehouse B.R., Millman A. et al. Cyclic CMP and cyclic UMP mediate bacterial immunity against phages // Cell. 2021. V. 184. № 23. P. 5728–5739 e16. https://doi.org/10.1016/j.cell.2021.09.031
  67. Rousset F., Osterman I., Scherf T. et al. TIR signaling activates caspase-like immunity in bacteria // Science. 2025. V. 387. № 6733. P. 510–516. https://doi.org/10.1126/science.adu2262
  68. Johnson A.G., Mayer M.L., Schaefer S.L. et al. Structure and assembly of a bacterial gasdermin pore // Nature. 2024. V. 628. № 8008. P. 657–663. https://doi.org/10.1038/s41586-024-07216-3
  69. Johnson A.G., Wein T., Mayer M.L. et al. Bacterial gasdermins reveal an ancient mechanism of cell death // Science. 2022. V. 375. № 6577. P. 221–225. https://doi.org/10.1126/science.abj8432
  70. Steens J.A., Bravo J.P.K., Salazar C.R.P. et al. Type III-B CRISPR-Cas cascade of proteolytic cleavages // Science. 2024. V. 383. № 6682. P. 512–519. https://doi.org/10.1126/science.adk0378
  71. Ozcan A., Krajeski R., Ioannidi E. et al. Programmable RNA targeting with the single-protein CRISPR effector Cas7-11 // Nature. 2021. V. 597. № 7878. P. 720–725. https://doi.org/10.1038/s41586-021-03886-5
  72. Van Beljouw S.P.B., Haagsma A.C., Rodriguez-Molina A. et al. The gRAMP CRISPR-Cas effector is an RNA endonuclease complexed with a caspase-like peptidase // Science. 2021. V. 373. № 6561. P. 1349–1353. https://doi.org/10.1126/science.abk2718
  73. Hu C., van Beljouw S.P.B., Nam K.H. et al. Craspase is a CRISPR RNA-guided, RNA-activated protease // Science. 2022. V. 377. № 6612. P. 1278–1285. https://doi.org/10.1126/science.add5064
  74. Banh D.V., Roberts C.G., Morales-Amador A. et al. Bacterial cGAS senses a viral RNA to initiate immunity // Nature. 2023. V. 623. № 7989. P. 1001–1008. https://doi.org/10.1038/s41586-023-06743-9
  75. Lau R.K., Ye Q., Birkholz E.A. et al. Structure and mechanism of a cyclic trinucleotide-activated bacterial endonuclease mediating bacteriophage immunity // Mol. Cell. 2020. V. 77. № 4. P. 723–733. https://doi.org/10.1016/j.molcel.2019.12.010
  76. Severin G.B., Ramliden M.S., Hawver L.A. et al. Direct activation of a phospholipase by cyclic GMP-AMP in El Tor Vibrio cholerae // PNAS USA. 2018. V. 115. № 26. P. E6048–E6055. https://doi.org/10.1073/pnas.1801233115
  77. Lowey B., Whiteley A.T., Keszei A.F.A. et al. CBASS immunity uses CARF-related effectors to sense 3'- 5'- and 2'-5'-linked cyclic oligonucleotide signals and protect bacteria from phage infection // Cell. 2020. V. 182. № 1. P. 38–49. https://doi.org/10.1016/j.cell.2020.05.019
  78. Morehouse B.R., Govande A.A., Millman A. et al. STING cyclic dinucleotide sensing originated in bacteria // Nature. 2020. V. 586. № 7829. P. 429–433. https://doi.org/10.1038/s41586-020-2719-5
  79. Duncan-Lowey B., McNamara-Bordewick N.K., Tal N. et al. Effector-mediated membrane disruption controls cell death in CBASS antiphage defense // Mol. Cell. 2021. V. 81. № 24. P. 5039–5051 e5. https://doi.org/10.1016/j.molcel.2021.10.020
  80. Jenson J.M., Li T., Du F. et al. Ubiquitin-like conjugation by bacterial cGAS enhances anti-phage defence // Nature. 2023. V. 616. № 7956. P. 326–331. https://doi.org/10.1038/s41586-023-05862-7
  81. Yan Y., Xiao J., Huang F. et al. Phage defence system CBASS is regulated by a prokaryotic E2 enzyme that imitates the ubiquitin pathway // Nat. Microbiol. 2024. V. 9. № 6. P. 1566–1578. https://doi.org/10.1038/s41564-024-01684-z
  82. Kibby E.M., Robbins L.K., Deep A. et al. A bacterial NLR-related protein recognizes multiple unrelated phage triggers to sense infection // bioRxiv. 2024. https://doi.org/10.1101/2024.12.17.629029.
  83. Wang Y., Tian Y., Yang X. et al. Filamentation activates bacterial Avs5 antiviral protein // Nat. Commun. 2025. V. 16. № 1. P. 2408. https://doi.org/10.1038/s41467-025-57732-7
  84. Bobonis J., Mitosch K., Mateus A. et al. Bacterial retrons encode phage-defending tripartite toxinantitoxin systems // Nature. 2022. V. 609. № 7925. P. 144–150. https://doi.org/10.1038/s41586-022-05091-4
  85. Wang Y., Guan Z., Wang C. et al. Cryo-EM structures of Escherichia coli Ec86 retron complexes reveal architecture and defence mechanism // Nat. Microbiol. 2022. V. 7. № 9. P. 1480–1489. https://doi.org/10.1038/s41564-022-01197-7
  86. Wang Y., Wang C., Guan Z. et al. DNA methylation activates retron Ec86 filaments for antiphage defense // Cell Rep. 2024. V. 43. № 10. https://doi.org/10.1016/j.celrep.2024.114857
  87. Mestre M.R., Gonzalez-Delgado A., Gutierrez-Rus L.I. et al. Systematic prediction of genes functionally associated with bacterial retrons and classification of the encoded tripartite systems // Nucl. Ac. Res. 2020. V. 48. № 22. P. 12632–12647. https://doi.org/10.1093/nar/gkaa1149
  88. Bobadilla Ugarte P., Barendse P., Swarts D.C. Argonaute proteins confer immunity in all domains of life // Curr. Opin. Microbiol. 2023. V. 74. https://doi.org/10.1016/j.mib.2023.102313
  89. 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. 2014. V. 5. № 2. P. 141–181. https://doi.org/10.1002/wrna.1210
  90. Swarts D.C., Makarova K., Wang Y. et al. The evolutionary journey of Argonaute proteins // Nat. Struct. Mol. Biol. 2014. V. 21. № 9. P. 743–753. https://doi.org/10.1038/nsmb.2879
  91. Olina A.V., Kulbachinskiy A.V., Aravin A.A. et al. Argonaute proteins and mechanisms of RNA interference in eukaryotes and prokaryotes // Biochemistry (Moscow). 2018. V. 83. № 5. P. 483–497. https://doi.org/10.1134/S0006297918050024
  92. Lisitskaya L., Aravin A.A., Kulbachinskiy A. DNA interference and beyond: Structure and functions of prokaryotic Argonaute proteins // Nat. Commun. 2018. V. 9. № 1. P. 5165. https://doi.org/10.1038/s41467-018-07449-7
  93. Makarova K.S., Wolf Y.I., van der Oost J. et al. Prokaryotic homologs of Argonaute proteins are predicted to function as key components of a novel system of defense against mobile genetic elements // Biol. Direct. 2009. V. 4. https://doi.org/10.1186/1745-6150-4-29
  94. Ryazansky S., Kulbachinskiy A., Aravin A.A. The expanded universe of prokaryotic argonaute proteins // MBio. 2018. V. 9. № 6. https://doi.org/10.1128/mBio.01935-18
  95. Agapov A., Panteleev V., Kropocheva E. et al. Prokaryotic Argonaute nuclease cooperates with co-encoded RNase to acquire guide RNAs and target invader DNA // Nucl. Ac. Res. 2024. V. 52. P. 5895–5911. https://doi.org/10.1093/nar/gkae345
  96. Hegge J.W., Swarts D.C., Chandradoss S.D. et al. DNA-guided DNA cleavage at moderate temperatures by Clostridium butyricum Argonaute // Nucl. Ac. Res. 2019. V. 47. № 11. P. 5809–5821. https://doi.org/10.1093/nar/gkz306
  97. Kaya E., Doxzen K.W., Knoll K.R. et al. A bacterial Argonaute with noncanonical guide RNA specificity // PNAS USA. 2016. V. 113. № 15. P. 4057–4062. https://doi.org/10.1073/pnas.1524385113
  98. Kuzmenko A., Yudin D., Ryazansky S. et al. Programmable DNA cleavage by Ago nucleases from mesophilic bacteria Clostridium butyricum and Limnothrix rosea // Nucl. Ac. Res. 2019. V. 47. № 11. P. 5822–5836. https://doi.org/10.1093/nar/gkz379
  99. Kropocheva E., Kuzmenko A., Aravin A.A. et al. A programmable pAgo nuclease with universal guide and target specificity from the mesophilic bacterium Kurthia massiliensis // Nucl. Ac. Res. 2021. V. 49. № 7. P. 4054–4065. https://doi.org/10.1093/nar/gkab182
  100. Liu Y., Li W., Jiang X. et al. A programmable omnipotent Argonaute nuclease from mesophilic bacteria Kurthia massiliensis // Nucl. Ac. Res. 2021. V. 49. № 3. P. 1597–1608. https://doi.org/10.1093/nar/gkaa1278
  101. Lisitskaya L., Shin Y., Agapov A. et al. Programmable RNA targeting by bacterial Argonaute nucleases with unconventional guide binding and cleavage specificity // Nat. Commun. 2022. V. 13. № 1. P. 4624. https://doi.org/10.1038/s41467-022-32079-5
  102. Li W., Liu Y., He R. et al. A programmable pAgo nuclease with RNA target preference from the psychrotolerant bacterium Mucilaginibacter paludis // Nucl. Ac. Res. 2022. V. 50. № 9. P. 5226–5238. https://doi.org/10.1093/nar/gkac315
  103. Swarts D.C., Hegge J.W., Hinojo I. et al. Argonaute of the archaeon Pyrococcus furiosus is a DNA-guided nuclease that targets cognate DNA // Nucl. Ac. Res. 2015. V. 43. № 10. P. 5120–5129. https://doi.org/10.1093/nar/gkv415
  104. Swarts D.C., Jore M.M., Westra E.R. et al. DNAguided DNA interference by a prokaryotic Argonaute // Nature. 2014. V. 507. № 7491. P. 258–261. https://doi.org/10.1038/nature12971
  105. Zander A., Willkomm S., Ofer S. et al. Guideindependent DNA cleavage by archaeal Argonaute from Methanocaldococcus jannaschii // Nat. Microbiol. 2017. V. 2. https://doi.org/10.1038/nmicrobiol.2017.34
  106. Kropocheva E., Lisitskaya L., Agapov A. et al. Prokaryotic Argonaute proteins as a tool for biotechnology // Mol. Biol. 2022. V. 56. № 6. P. 854–873. https://doi.org/10.1134/S0026893322060103
  107. Enghiad B., Xue P., Singh N. et al. PlasmidMaker is a versatile, automated, and high throughput endto-end platform for plasmid construction // Nat. Commun. 2022. V. 13. № 1. P. 2697. https://doi.org/10.1038/s41467-022-30355-y
  108. Qin Y., Li Y., Hu Y. Emerging Argonaute-based nucleic acid biosensors // Trends Biotechnol. 2022. V. 40. № 8. P. 910–914. https://doi.org/10.1016/j.tibtech.2022.03.006
  109. Kuzmenko A., Oguienko A., Esyunina D. et al. DNA targeting and interference by a bacterial Argonaute nuclease // Nature. 2020. V. 587. № 7835. P. 632–637. https://doi.org/10.1038/s41586-020-2605-1
  110. Esyunina D., Okhtienko A., Olina A. et al. Specific targeting of plasmids with Argonaute enables genome editing // Nucl. Ac. Res. 2023. V. 51. № 8. P. 4086–4099. https://doi.org/10.1093/nar/gkad191
  111. Jolly S.M., Gainetdinov I., Jouravleva K. et al. Thermus thermophilus Argonaute functions in the completion of DNA replication // Cell. 2020. V. 182. № 6. P. 1545–1559 e18. https://doi.org/10.1016/j.cell.2020.07.036
  112. Olina A., Agapov A., Yudin D. et al. Bacterial Argonaute proteins aid cell division in the presence of tpoisomerase inhibitors in Escherichia coli // Microbiol. Spectr. 2023. V. 11. № 3. https://doi.org/10.1128/spectrum.04146-22
  113. Lisitskaya L., Kropocheva E., Agapov A. et al. Bacterial Argonaute nucleases reveal different modes of DNA targeting in vitro and in vivo // Nucl. Ac. Res. 2023. V. 51. № 10. P. 5106–5124. https://doi.org/10.1093/nar/gkad290
  114. Olovnikov I., Chan K., Sachidanandam R. et al. Bacterial argonaute samples the transcriptome to identify foreign DNA // Mol. Cell. 2013. V. 51. № 5. P. 594–605. https://doi.org/10.1016/j.molcel.2013.08.014
  115. Liu Y., Esyunina D., Olovnikov I. et al. Accommodation of helical imperfections in Rhodobacter sphaeroides Argonaute ternary complexes with guide RNA and target DNA // Cell Reports. 2018. V. 24. № 2. P. 453–462.
  116. Miyoshi T., Ito K., Murakami R. et al. Structural basis for the recognition of guide RNA and target DNA heteroduplex by Argonaute // Nat. Commun. 2016. V. 7. https://doi.org/10.1038/ncomms11846
  117. Song X., Lei S., Liu S. et al. Catalytically inactive long prokaryotic Argonaute systems employ distinct effectors to confer immunity via abortive infection // Nat. Commun. 2023. V. 14. № 1. P. 6970. https://doi.org/10.1038/s41467-023-42793-3
  118. Manakova E., Golovinas E., Poceviciute R. et al. The missing part: The Archaeoglobus fulgidus Argonaute forms a functional heterodimer with an N-L1-L2 domain protein // Nucl. Ac. Res. 2024. https://doi.org/10.1093/nar/gkad1241
  119. Zeng Z., Chen Y., Pinilla-Redondo R. et al. A short prokaryotic Argonaute activates membrane effector to confer antiviral defense // Cell Host Microbe. 2022. V. 30. № 7. P. 930–943 e6. https://doi.org/10.1016/j.chom.2022.04.015
  120. Loeff L., Adams D.W., Chanez C. et al. Molecular mechanism of plasmid elimination by the DdmDE defense system // Science. 2024. V. 385. № 6705. P. 188–194. https://doi.org/10.1126/science.adq0534
  121. Bravo J.P.K., Ramos D.A., Fregoso Ocampo R. et al. Plasmid targeting and destruction by the DdmDE bacterial defence system // Nature. 2024. V. 630. № 8018. P. 961–967. https://doi.org/10.1038/s41586-024-07515-9
  122. Yang X.Y., Shen Z., Wang C. et al. DdmDE eliminates plasmid invasion by DNA-guided DNA targeting // Cell. 2024. V. 187. № 19. P. 5253–5266 e16. https://doi.org/10.1016/j.cell.2024.07.028
  123. Koopal B., Mutte S.K., Swarts D.C. A long look at short prokaryotic Argonautes // Trends Cell Biol. 2023. V. 33. № 7. P. 605–618. https://doi.org/10.1016/j.tcb.2022.10.005
  124. Koopal B., Potocnik A., Mutte S.K. et al. Short prokaryotic Argonaute systems trigger cell death upon detection of invading DNA // Cell. 2022. V. 185. № 9. P. 1471–1486 e19. https://doi.org/10.1016/j.cell.2022.03.012
  125. Prostova M., Kanevskaya A., Panteleev V. et al. DNAtargeting short Argonautes complex with effector proteins for collateral nuclease activity and bacterial population immunity // Nat. Microbiol. 2024. V. 9. P. 1368–1381. https://doi.org/10.1038/s41564-024-01654-5
  126. Lu X., Xiao J., Wang L. et al. The nuclease-associated short prokaryotic Argonaute system nonspecifically degrades DNA upon activation by target recognition // Nucl. Ac. Res. 2024. V. 52. № 2. P. 844–855. https://doi.org/10.1093/nar/gkad1145
  127. Zaremba M., Dakineviciene D., Golovinas E. et al. Short prokaryotic Argonautes provide defence against incoming mobile genetic elements through NAD(+) depletion // Nat. Microbiol. 2022. V. 7. № 11. P. 1857–1869. https://doi.org/10.1038/s41564-022-01239-0
  128. Gao X., Shang K., Zhu K. et al. Nucleic-acid-triggered NADase activation of a short prokaryotic Argonaute // Nature. 2024. V. 625. № 7996. P. 822–831. https://doi.org/10.1038/s41586-023-06665-6
  129. Finocchio G., Koopal B., Potocnik A. et al. Target DNA-dependent activation mechanism of the prokaryotic immune system SPARTA // Nucl. Ac. Res. 2024. V. 52. P. 2012–2029. https://doi.org/10.1093/nar/gkad1248
  130. Shen Z., Yang X.Y., Xia S. et al. Oligomerizationmediated activation of a short prokaryotic Argonaute // Nature. 2023. V. 621. № 7977. P. 154–161. https://doi.org/10.1038/s41586-023-06456-z
  131. Cui N., Zhang J.T., Li Z. et al. Tetramerizationdependent activation of the Sir2-associated short prokaryotic Argonaute immune system // Nat. Commun. 2024. V. 15. № 1. P. 8610. https://doi.org/10.1038/s41467-024-52910-5
  132. Kim S.Y., Jung Y., Lim D. Argonaute system of Kordia jejudonensis is a heterodimeric nucleic acid-guided nuclease // Biochem. Biophys. Res. Commun. 2020. V. 525. № 3. P. 755–758. https://doi.org/10.1016/j.bbrc.2020.02.145
  133. Potocnik A., Swarts D.C. Short prokaryotic Argonaute system repurposed as a nucleic acid detection tool // Clin. Transl. Med. 2022. V. 12. № 9. https://doi.org/10.1002/ctm2.1059

Arquivos suplementares

Arquivos suplementares
Ação
1. JATS XML
Baixar

Declaração de direitos autorais © Russian Academy of Sciences, 2025

Согласие на обработку персональных данных с помощью сервиса «Яндекс.Метрика»

1. Я (далее – «Пользователь» или «Субъект персональных данных»), осуществляя использование сайта https://journals.rcsi.science/ (далее – «Сайт»), подтверждая свою полную дееспособность даю согласие на обработку персональных данных с использованием средств автоматизации Оператору - федеральному государственному бюджетному учреждению «Российский центр научной информации» (РЦНИ), далее – «Оператор», расположенному по адресу: 119991, г. Москва, Ленинский просп., д.32А, со следующими условиями.

2. Категории обрабатываемых данных: файлы «cookies» (куки-файлы). Файлы «cookie» – это небольшой текстовый файл, который веб-сервер может хранить в браузере Пользователя. Данные файлы веб-сервер загружает на устройство Пользователя при посещении им Сайта. При каждом следующем посещении Пользователем Сайта «cookie» файлы отправляются на Сайт Оператора. Данные файлы позволяют Сайту распознавать устройство Пользователя. Содержимое такого файла может как относиться, так и не относиться к персональным данным, в зависимости от того, содержит ли такой файл персональные данные или содержит обезличенные технические данные.

3. Цель обработки персональных данных: анализ пользовательской активности с помощью сервиса «Яндекс.Метрика».

4. Категории субъектов персональных данных: все Пользователи Сайта, которые дали согласие на обработку файлов «cookie».

5. Способы обработки: сбор, запись, систематизация, накопление, хранение, уточнение (обновление, изменение), извлечение, использование, передача (доступ, предоставление), блокирование, удаление, уничтожение персональных данных.

6. Срок обработки и хранения: до получения от Субъекта персональных данных требования о прекращении обработки/отзыва согласия.

7. Способ отзыва: заявление об отзыве в письменном виде путём его направления на адрес электронной почты Оператора: info@rcsi.science или путем письменного обращения по юридическому адресу: 119991, г. Москва, Ленинский просп., д.32А

8. Субъект персональных данных вправе запретить своему оборудованию прием этих данных или ограничить прием этих данных. При отказе от получения таких данных или при ограничении приема данных некоторые функции Сайта могут работать некорректно. Субъект персональных данных обязуется сам настроить свое оборудование таким способом, чтобы оно обеспечивало адекватный его желаниям режим работы и уровень защиты данных файлов «cookie», Оператор не предоставляет технологических и правовых консультаций на темы подобного характера.

9. Порядок уничтожения персональных данных при достижении цели их обработки или при наступлении иных законных оснований определяется Оператором в соответствии с законодательством Российской Федерации.

10. Я согласен/согласна квалифицировать в качестве своей простой электронной подписи под настоящим Согласием и под Политикой обработки персональных данных выполнение мною следующего действия на сайте: https://journals.rcsi.science/ нажатие мною на интерфейсе с текстом: «Сайт использует сервис «Яндекс.Метрика» (который использует файлы «cookie») на элемент с текстом «Принять и продолжить».