Библиография

1. 1. Mushegian A.R. Are there 10 virus particles on earth, or more, or fewer? // J. Bacteriol. 2020. V. 202. № 9. https://doi.org/10.1128/jb.00052-20
2. 2. Tesson F., Hervé A., Mordret E. et al. Systematic and quantitative view of the antiviral arsenal of prokaryotes // Nat. Communications. 2022. V. 13. № 1. P. 2561. https://doi.org/10.1038/s41467-022-29864-w
3. 3. Loenen W.A.M., Dryden D.T.F., Raleigh E.A., Wilson G.G. Type I restriction enzymes and their relatives // Nucl. Ac. Res. 2014. V. 42. № 1. P. 20–44. https://doi.org/10.1093/nar/gkt1046
4. 4. Murray N.E. Type I restriction systems: Sophisticated molecular machines // Microbiol. Reviews. 2000. V. 64. P. 412–434. https://doi.org/10.1128/MMBR.64.2.412-434.2000
5. 5. Dryden D.T.F., Cooper L.P., Murray N.E. Purification and characterization of the methyltransferase from the Type I restriction and modification system of Escherichia coli K12* // J. Biol. Chemistry. 1993. V. 268. P. 13228–13236. https://doi.org/10.1074/jbc.268.19.13228
6. 6. Makovets S., Doronina V.A., Murray N.E. Regulation of endonuclease activity by proteolysis prevents breakage of unmodified bacterial chromosomes by Type I restriction enzymes // PNAS USA. 1999. V. 96. № 17. https://doi.org/10.1073/pnas.96.17.9684
7. 7. Rosenberg J.M., McClarin J.A., Frederick C.A. Structure and recognition mechanism of EcoRI endonuclease // Trends in Biochem. Sci. 1987. V. 12. P. 395–398. https://doi.org/10.1016/0968-0004 (87)90223-X
8. 8. Piatt S.C., Loparo J.J., Price A.C. The role of noncognate sites in the 1D search mechanism of EcoRI // Biophys. J. 2019. V. 116. № 12. P. 2367–2377. https://doi.org/10.1016/j.bpj.2019.04.033
9. 9. Kruger D.H., Reuter M., Hansen S., Schroeder C. Influence of phage T3 and T7 gene functions on a Type III (EcoPI) DNA restriction-modification system in vivo // Mol. & General Genetics. 1982. V. 185. № 3. P. 457–461. https://doi.org/10.1007/BF00331306
10. 10. Goldfarb T., Sherro H., Weinstock E. et al. BREX is a novel phage resistance system widespread in microbial genomes // EMBO J. 2015. V. 34. № 2. P. 169–183. https://doi.org/10.15252/embj.201490297
11. 11. Gordeeva J., Morozova N., Sterro N. et al. BREX system of Escherichia coli distinguishes self from non-self by methylation of a specific DNA site // Nucl. Ac. Res. 2019. V. 47. № 1. P. 253–265. https://doi.org/10.1093/nar/gkz1178
12. 12. Makarova K.S., Wolf Y.L., Iranzo J. et al. Evolutionary classification of CRISPR-Cas systems: A burst of Class 2 and derived variants // Nat. Reviews Microbiol. 2020. V. 18. № 2. P. 67–83. https://doi.org/10.1038/s41579-019-0299-x
13. 13. Sternberg S.H., Richter H., Charpentier E., Qinnon U. Adaptation in CRISPR-Cas systems // Mol. Cell. 2016. V. 61. № 6. P. 797–808. https://doi.org/10.1016/j.molcel.2016.01.034
14. 14. Mojica F.J.M., Diez-Villaseñor C., García-Martánez J., Soria E. Intervening sequences of regularly spaced prokaryotic repeats derive from foreign genetic elements // J. Mol. Evol. 2005. V. 60. № 2. P. 174–182. https://doi.org/10.1007/s00239-004-0046-3
15. 15. Zavilgelsky G.B., Rastorguev S.M. DNA mimicry by proteins as an effective mechanism for regulation of activity of DNA-dependent enzymes // Biochemistry (Moscow). 2007. V. 72. № 9. P. 913–919. https://doi.org/10.1134/S0006297907090016
16. 16. Belogurov A.A., Delver E.P., Rodzevich O.V. IncN plasmid pKM101 and Incl1 plasmid Collb-P9 encode homologous antirestriction proteins in their leading regions // J. Bacteriology. 1992. V. 174. № 15. P. 5079–5085. https://doi.org/10.1128/JB.174.15.5079-5085.1992
17. 17. McMahon S.A., Roberts G.A., Johnson K.A. et al. Extensive DNA mimicry by the ArdA anti-restriction protein and its role in the spread of antibiotic resistance // Nucl. Ac. Res. 2009. V. 37. № 15. P. 4887–4897. https://doi.org/10.1093/nar/gkp507
18. 18. Rastorguev S.M., Zavilgelsky G.B. Role of “antirestriction” motif in functional activity of antirestriction protein ArdA pKM101 (IncN) // Russ. J. Genetics. 2003. V. 39. № 2. P. 286–292. https://doi.org/10.1023/A:1022994216828
19. 19. Walkinshaw M.D., Taylor P., Sturrock S.S. et al. Structure of Ocr from bacteriophage T7, a protein that mimics B-form DNA // Mol. Cell. 2002. V. 9. № 1. P. 187–194. https://doi.org/10.1016/S1097-2765 (02)00439-1
20. 20. Dunn J.J., Elzinga M., Mark K.K., Studier F.W. Amino acid sequence of the gene 0.3 protein of bacteriophage T7 and nucleotide sequence of its mRNA // J. Biol. Chemistry. 1981. V. 256. № 5. P. 2579–2585. https://doi.org/10.1074/jbc.256.5.2579
21. 21. Moffatt B.A., Studier F.W. Entry of bacteriophage T7 DNA into the cell and escape from host restriction // J. Bacteriology. 1988. V. 170. № 5. P. 2095–2105. https://doi.org/10.1128/JB.170.5.2095-2105.1988
22. 22. Gladysheva-Azgari M.V., Sharko F.S., Evieeva M.A. et al. ArdA genes from pKM101 and from B. bifidum chromosome have a different range of regulated genes // Heliyon. 2023. V. 9. № 12. https://doi.org/10.1016/j.heliyon.2023.e22986
23. 23. Serfiotis-Mitsa D., Herbert A.P., Roberts G.A. et al. The structure of the KlcA and ArdB proteins reveals a novel fold and antirestriction activity against type I DNA restriction systems in vivo but not in vitro // Nucl. Ac. Res. 2009. V. 38. № 5. P. 1723–1737. https://doi.org/10.1093/nar/gkp1178
24. 24. Goryanin I.I., Kudryavtseva A.A., Balabanov V.P. et al. Antirestriction activities of KlcA (rp4) and ArdB (r64) proteins // FEMS Microbiol. Letters. 2018. V. 365. № 23. https://doi.org/10.1093/femsle/fny254
25. 25. Oke M., Carter L.G., Johnson K.A. et al. Supplementary material the scottish structural proteomics facility: Targets, methods and outputs supporting material the scottish structural proteomics facility, targets, methods and outputs. https://doi.org/10.1038/sdata.2015.44
26. 26. Kudryavtseva A.A., Livinyuk V.Yu., Didina V.S. et al. The importance of C-terminal aspartic acid residue (D141) to the antirestriction activity of the ArdB (R64) protein // Mol. Biol. 2017. V. 51. № 5. P. 724–727. https://doi.org/10.1134/S002689331705008X
27. 27. Kudryavtseva A.A., Okhrimenko I.S., Didina V.S. et al. Antirestriction protein ArdB (R64) interacts with DNA // Biochemistry (Moscow). 2020. V. 85. № 3. P. 318–325. https://doi.org/10.1134/S0006297920030055
28. 28. Balabanov V.P., Kudryavtseva A.A., Melkina O.E. et al. ArdB Protective Activity for Unmodified Lambda Phage Against EcoRI Restriction Decreases in UV-treated Escherichia coli. V. 76. N.Y.: Springer, LLC, 2019. https://doi.org/10.1007/978-3-030-16357-8_7
29. 29. Mol C.D., Arval A.S., Sanderson R.J. et al. Crystal structure of human uracil-DNA glycosylase in complex with a protein inhibitor: Protein mimicry of DNA // Cell. 1995. V. 82. № 5. P. 701–708. https://doi.org/10.1016/0092-8674 (95)90476-X
30. 30. Ramirez B.E., Bax A., Yoshin O.N., Camerini-Otero R.D. Solution structure of Dini provides insight into its mode of RecA inactivation // Protein Science. 2000. V. 9. № 11. P. 2161–2169. https://doi.org/10.1110/ps.9.11.2161
31. 31. Parsons L.M., Liu F., Orban J. HU-α binds to the putative double-stranded DNA mimic hi1450 from Haemophilus influenzae // Protein Science. 2009. V. 14. № 6. P. 1684–1687. https://doi.org/10.1002/pro.122
32. 32. Kudryavtseva A.A., Vlasov A.V., Zinovev E.V. et al. ArdA protein specificity against type I restriction-modification systems // Mol. Biol. 2024. V. 58. № 3. P. 527–533. https://doi.org/10.1134/S0026897324030064
33. 33. Utkina A.A., Kudryavtseva A.A., Melkina O.E. et al. A new family of small ArdA proteins reveals an antirestriction activity // BioRxiv. 2025. https://doi.org/10.1101/2025.01.01.522123
34. 34. Zavilgelsky G.B. Antirestriction // Mol. Biol. 2000. V. 34. № 5. P. 724–732. https://doi.org/10.1023/A:1004774316694
35. 35. Kudryavtseva A.A., Csefalvay E., Gnuchikh E.Y. et al. Broadness and specificity: ArdB, ArdA, and Ocr against various restriction-modification systems // Front. in Microbiology. 2023. V. 14. https://doi.org/10.3389/fmicb.2023.1125374
36. 36. Wimmer F., Englert F., Wandera K.G. et al. Interrogating two extensively self-targeting type I CRISPR-cas systems in Xanthomonas albilineans reveals distinct anti-CRISPR proteins that block dna degradation // Nucl. Ac. Res. 2023. V. 52. № 2. P. 769–783. https://doi.org/10.1093/nar/gkac1211
37. 37. Bubnov D.M., Yuzbashev T.V., Khozov A.A. et al. Robust counterselection and advanced λ red recombinering enable markerless chromosomal integration of large heterologous constructs // Nucl. Ac. Res. 2022. V. 50. № 15. P. 8947–8960. https://doi.org/10.1093/nar/gkab1054