Evolution of restriction-modification systems with one restriction endonuclease and two DNA methyltransferases

Cover Page

Cite item

Full Text

Open Access Open Access
Restricted Access Access granted
Restricted Access Subscription Access

Abstract

Some restriction-modification systems contain two DNA methyltransferases. In the present work, we have classified such systems according to the families of catalytic domains present in restriction endonucleases and both DNA methyltransferases. The evolution of restriction-modification systems of one class was studied in detail. Systems in this class include an endonuclease with a NOV_C family domain and two DNA methyltransferases, both with DNA_methylase family domains. The phylogenetic tree of DNA methyltransferases from systems of this class consists of two clades of the same size. Two DNA methyltransferases of each restriction-modification system of the class belong to different clades. This indicates independent evolution of the two methyltransferases. We detected multiple cross-species horizontal transfers of systems as a whole, as well as cases of gene transfer between systems.

About the authors

A. S Fokina

Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University

Email: sas@belozersky.msu.ru
119234 Moscow, Russia

A. S Karyagina

N.F. Gamaleya National Research Center for Epidemiology and Microbiology, Ministry of Healthcare of the Russian Federation;Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow;All-Russia Research Institute of Agricultural Biotechnology

Email: sas@belozersky.msu.ru
123098 Moscow, Russia;119992 Moscow, Russia;127550 Moscow, Russia

I. S Rusinov

Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow

Email: sas@belozersky.msu.ru
119992 Moscow, Russia

D. M Moshensky

Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University;Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow

Email: sas@belozersky.msu.ru
119234 Moscow, Russia;119992 Moscow, Russia

S. A Spirin

Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow;National Research University Higher School of Economics;Federal Science Center System Research Institute of the Russian Academy of Sciences

Email: sas@belozersky.msu.ru
119992 Moscow, Russia;109028 Moscow, Russia;117218 Moscow, Russia

A. V Alexeevski

Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University;Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow;Federal Science Center System Research Institute of the Russian Academy of Sciences

Email: sas@belozersky.msu.ru
119234 Moscow, Russia;119992 Moscow, Russia;117218 Moscow, Russia

References

  1. Williams, R. J. (2003) Restriction endonucleases: Classification, properties, and applications, Mol. Biotechnol., 23, 225-244, doi: 10.1385/mb:23:3:225.
  2. Roberts, R. J. (2003) A nomenclature for restriction enzymes, DNA methyltransferases, homing endonucleases and their genes, Nucleic Acids Res., 31, 1805-1812, doi: 10.1093/nar/gkg274.
  3. Pingoud, A., Wilson, G. G., and Wende, W. (2014) Type II restriction endonucleases - a historical perspective and more, Nucleic Acids Res., 42, 7489-7527, doi: 10.1093/nar/gku447.
  4. Szybalski, W., Kim, S. C., Hasan, N., and Podhajska, A. J. (1991) Class-IIS restriction enzymes - a review, Gene, 100, 13-26, doi: 10.1016/0378-1119(91)90345-c.
  5. Madhusoodanan, U. K., and Rao, D. N. (2010) Diversity of DNA methyltransferases that recognize asymmetric target sequences, Crit. Rev. Biochem. Mol. Biol., 45, 125-145, doi: 10.3109/10409231003628007.
  6. Vasu, K., and Nagaraja, V. (2013) Diverse functions of restriction-modification systems in addition to cellular defense, Microbiol. Mol. Biol. Rev., 77, 53-72, doi: 10.1128/mmbr.00044-12.
  7. Furmanek-Blaszk, B., Boratynski, R., Zolcinska, N., and Sektas, M. (2009) M1.MboII and M2.MboII type IIS methyltransferases: Different specificities, the same target, Microbiology, 155, 1111-1121, doi: 10.1099/mic.0.025023-0.
  8. Kriukiene, E., Lubiene, J., Lagunavicius, A., and Lubys, A. (2005) MnlI - The member of H-N-H subtype of Type IIS restriction endonucleases, Biochim. Biophys. Acta, 1751, 194-204, doi: 10.1016/j.bbapap.2005.06.006.
  9. Sapranauskas, R., Sasnauskas, G., Lagunavicius, A., Vilkaitis, G., Lubys, A., and Siksnys, V. (2000) Novel subtype of type IIS restriction enzymes, J. Biol. Chem., 275, 30878-30885, doi: 10.1074/jbc.m003350200.
  10. Sugisaki, H., Kita, K., and Takanami, M. (1989) The FokI restriction-modification system, J. Biol. Chem., 264, 5757-5761, doi: 10.1016/s0021-9258(18)83614-6.
  11. Mistry, J., Chuguransky, S., Williams, L., Qureshi, M., Salazar, G. A., Sonnhammer, E. L. L., Tosatto, S. C. E., Paladin, L., Raj, S., Richardson, L. J., Finn, R. D., and Bateman, A. (2020) Pfam: The protein families database in 2021, Nucleic Acids Res., 49, D412-D419, doi: 10.1093/nar/gkaa913.
  12. Roberts, R. J., Vincze, T., Posfai, J., and Macelis, D. (2014) REBASE - a database for DNA restriction and modification: Enzymes, genes and genomes, Nucleic Acids Res., 43, D298-D299, doi: 10.1093/nar/gku1046.
  13. Lemoine, F., Correia, D., Lefort, V., Dopplt-Azeroual, O., Mareuil, F., Coen-Boulakia, S., and Gascuel, O. (2019) NGPhylogeny.fr: new generation phylogenetic services for non-specialists, Nucleic Acids Research, 47, W260-W265, doi: 10.1093/nar/gkz303.
  14. Letunic, I., and Bork, P. (2021) Interactive Tree Of Life (iTOL) v5: An online tool for phylogenetic tree display and annotation, Nucleic Acids Res., 49, W293-W296, doi: 10.1093/nar/gkab301.
  15. Li, W., and Godzik, A. (2006) Cd-hit: a fast program for clustering and comparing large sets of protein or nucleotide sequences, Bioinformatics, 22, 1658-1659, doi: 10.1093/bioinformatics/btl158.
  16. Steczkiewicz, K., Muszewska, A., Knizewski, L., Rychlewski, L., and Ginalski, K. (2012) Sequence, structure and functional diversity of PD-(D/E)XK phosphodiesterase superfamily, Nucleic Acids Res., 40, 7016-7045, doi: 10.1093/nar/gks382.
  17. Sukackaite, R., Grazulis, S., Bochtler, M., and Siksnys, V. (2008) The recognition domain of the BpuJI restriction endonuclease in complex with cognate DNA at 1.3-Å resolution, J. Mol. Biol., 378, 1084-1093, doi: 10.1016/j.jmb.2008.03.041.
  18. Sukackaite, R., Lagunavicius, A., Stankevicius, K., Urbanke, C., Venclovas, Č., and Siksnys, V. (2007) Restriction endonuclease BpuJI specific for the 5′-CCCGT sequence is related to the archaeal Holliday junction resolvase family, Nucleic Acids Res., 35, 2377-2389, doi: 10.1093/nar/gkm164.
  19. Degtyarev, S. K., Netesova, N. A., Chizhikov, V. E., and Abdurashitov, M. (1998) Cloning and characterization of the gene encoding M.FauI DNA methyltransferase, Biol. Chem., 379, 567-568.

Supplementary files

Supplementary Files
Action
1. JATS XML
Download

Copyright (c) 2023 Russian Academy of Sciences