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. 1992 Oct 11;20(19):5047–5052. doi: 10.1093/nar/20.19.5047

Identification of the CTAG-recognizing restriction-modification systems MthZI and MthFI from Methanobacterium thermoformicicum and characterization of the plasmid-encoded mthZIM gene.

J Nölling 1, W M de Vos 1
PMCID: PMC334282  PMID: 1408820

Abstract

Two CTAG-recognizing restriction and modification (R/M) systems, designated MthZI and MthFI, were identified in the thermophilic archaeon Methanobacterium thermoformicicum strains Z-245 and FTF, respectively. Further analysis revealed that the methyltransferase (MTase) genes are plasmid-located in both strains. The plasmid pFZ1-encoded mthZIM gene of strain Z-245 was further characterized by subcloning and expression studies in Escherichia coli followed by nucleotide sequence analysis. The mthZIM gene is 1065 bp in size and may code for a protein of 355 amino acids (M(r) 42,476 Da). The deduced amino acid sequence of the M.MthZI enzyme shares substantial similarity with four distinct regions from several m4C- and m6A-MTases, and contains the TSPPY motif that is so far only found in m4C-MTases. Partially overlapping with the mthZIM gene and in reverse orientation, an additional ORF was identified with a size of 606 bp potentially coding for a protein of 202 amino acids (M(r) 23.710 Da). This ORF is suggested to encode the corresponding endonuclease R.MthZI.

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Selected References

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  1. Boyer H. W., Roulland-Dussoix D. A complementation analysis of the restriction and modification of DNA in Escherichia coli. J Mol Biol. 1969 May 14;41(3):459–472. doi: 10.1016/0022-2836(69)90288-5. [DOI] [PubMed] [Google Scholar]
  2. Brooks J. E., Nathan P. D., Landry D., Sznyter L. A., Waite-Rees P., Ives C. L., Moran L. S., Slatko B. E., Benner J. S. Characterization of the cloned BamHI restriction modification system: its nucleotide sequence, properties of the methylase, and expression in heterologous hosts. Nucleic Acids Res. 1991 Feb 25;19(4):841–850. doi: 10.1093/nar/19.4.841. [DOI] [PMC free article] [PubMed] [Google Scholar]
  3. Brown J. W., Daniels C. J., Reeve J. N. Gene structure, organization, and expression in archaebacteria. Crit Rev Microbiol. 1989;16(4):287–338. doi: 10.3109/10408418909105479. [DOI] [PubMed] [Google Scholar]
  4. Chandrasegaran S., Lunnen K. D., Smith H. O., Wilson G. G. Cloning and sequencing the HinfI restriction and modification genes. Gene. 1988 Oct 30;70(2):387–392. doi: 10.1016/0378-1119(88)90210-7. [DOI] [PubMed] [Google Scholar]
  5. Chatterjee D. K., Hammond A. W., Blakesley R. W., Adams S. M., Gerard G. F. Genetic organization of the KpnI restriction--modification system. Nucleic Acids Res. 1991 Dec 11;19(23):6505–6509. doi: 10.1093/nar/19.23.6505. [DOI] [PMC free article] [PubMed] [Google Scholar]
  6. Connaughton J. F., Kaloss W. D., Vanek P. G., Nardone G. A., Chirikjian J. G. The complete sequence of the Bacillus amyloliquefaciens proviral H2, BamHI methylase gene. Nucleic Acids Res. 1990 Jul 11;18(13):4002–4002. doi: 10.1093/nar/18.13.4002. [DOI] [PMC free article] [PubMed] [Google Scholar]
  7. Devereux J., Haeberli P., Smithies O. A comprehensive set of sequence analysis programs for the VAX. Nucleic Acids Res. 1984 Jan 11;12(1 Pt 1):387–395. doi: 10.1093/nar/12.1part1.387. [DOI] [PMC free article] [PubMed] [Google Scholar]
  8. Hausner W., Frey G., Thomm M. Control regions of an archaeal gene. A TATA box and an initiator element promote cell-free transcription of the tRNA(Val) gene of Methanococcus vannielii. J Mol Biol. 1991 Dec 5;222(3):495–508. doi: 10.1016/0022-2836(91)90492-o. [DOI] [PubMed] [Google Scholar]
  9. Heidmann S., Seifert W., Kessler C., Domdey H. Cloning, characterization and heterologous expression of the SmaI restriction-modification system. Nucleic Acids Res. 1989 Dec 11;17(23):9783–9796. doi: 10.1093/nar/17.23.9783. [DOI] [PMC free article] [PubMed] [Google Scholar]
  10. Kapfer W., Walter J., Trautner T. A. Cloning, characterization and evolution of the BsuFI restriction endonuclease gene of Bacillus subtilis and purification of the enzyme. Nucleic Acids Res. 1991 Dec 11;19(23):6457–6463. doi: 10.1093/nar/19.23.6457. [DOI] [PMC free article] [PubMed] [Google Scholar]
  11. Kaszubska W., Aiken C., O'Connor C. D., Gumport R. I. Purification, cloning and sequence analysis of RsrI DNA methyltransferase: lack of homology between two enzymes, RsrI and EcoRI, that methylate the same nucleotide in identical recognition sequences. Nucleic Acids Res. 1989 Dec 25;17(24):10403–10425. doi: 10.1093/nar/17.24.10403. [DOI] [PMC free article] [PubMed] [Google Scholar]
  12. Klimasauskas S., Timinskas A., Menkevicius S., Butkienè D., Butkus V., Janulaitis A. Sequence motifs characteristic of DNA[cytosine-N4]methyltransferases: similarity to adenine and cytosine-C5 DNA-methylases. Nucleic Acids Res. 1989 Dec 11;17(23):9823–9832. doi: 10.1093/nar/17.23.9823. [DOI] [PMC free article] [PubMed] [Google Scholar]
  13. Krüger D. H., Bickle T. A. Bacteriophage survival: multiple mechanisms for avoiding the deoxyribonucleic acid restriction systems of their hosts. Microbiol Rev. 1983 Sep;47(3):345–360. doi: 10.1128/mr.47.3.345-360.1983. [DOI] [PMC free article] [PubMed] [Google Scholar]
  14. Lauster R. Evolution of type II DNA methyltransferases. A gene duplication model. J Mol Biol. 1989 Mar 20;206(2):313–321. doi: 10.1016/0022-2836(89)90481-6. [DOI] [PubMed] [Google Scholar]
  15. Lauster R., Kriebardis A., Guschlbauer W. The GATATC-modification enzyme EcoRV is closely related to the GATC-recognizing methyltransferases DpnII and dam from E. coli and phage T4. FEBS Lett. 1987 Aug 10;220(1):167–176. doi: 10.1016/0014-5793(87)80897-9. [DOI] [PubMed] [Google Scholar]
  16. McClelland M., Nelson M. Effect of site-specific methylation on DNA modification methyltransferases and restriction endonucleases. Nucleic Acids Res. 1992 May 11;20 (Suppl):2145–2157. doi: 10.1093/nar/20.suppl.2145. [DOI] [PMC free article] [PubMed] [Google Scholar]
  17. Musgrave D. R., Sandman K. M., Reeve J. N. DNA binding by the archaeal histone HMf results in positive supercoiling. Proc Natl Acad Sci U S A. 1991 Dec 1;88(23):10397–10401. doi: 10.1073/pnas.88.23.10397. [DOI] [PMC free article] [PubMed] [Google Scholar]
  18. Nölling J., de Vos W. M. Characterization of the archaeal, plasmid-encoded type II restriction-modification system MthTI from Methanobacterium thermoformicicum THF: homology to the bacterial NgoPII system from Neisseria gonorrhoeae. J Bacteriol. 1992 Sep;174(17):5719–5726. doi: 10.1128/jb.174.17.5719-5726.1992. [DOI] [PMC free article] [PubMed] [Google Scholar]
  19. Pósfai J., Bhagwat A. S., Pósfai G., Roberts R. J. Predictive motifs derived from cytosine methyltransferases. Nucleic Acids Res. 1989 Apr 11;17(7):2421–2435. doi: 10.1093/nar/17.7.2421. [DOI] [PMC free article] [PubMed] [Google Scholar]
  20. Reiter W. D., Hüdepohl U., Zillig W. Mutational analysis of an archaebacterial promoter: essential role of a TATA box for transcription efficiency and start-site selection in vitro. Proc Natl Acad Sci U S A. 1990 Dec;87(24):9509–9513. doi: 10.1073/pnas.87.24.9509. [DOI] [PMC free article] [PubMed] [Google Scholar]
  21. Sanger F., Nicklen S., Coulson A. R. DNA sequencing with chain-terminating inhibitors. Proc Natl Acad Sci U S A. 1977 Dec;74(12):5463–5467. doi: 10.1073/pnas.74.12.5463. [DOI] [PMC free article] [PubMed] [Google Scholar]
  22. Schmid K., Thomm M., Laminet A., Laue F. G., Kessler C., Stetter K. O., Schmitt R. Three new restriction endonucleases MaeI, MaeII and MaeIII from Methanococcus aeolicus. Nucleic Acids Res. 1984 Mar 26;12(6):2619–2628. doi: 10.1093/nar/12.6.2619. [DOI] [PMC free article] [PubMed] [Google Scholar]
  23. Stephenson F. H., Ballard B. T., Boyer H. W., Rosenberg J. M., Greene P. J. Comparison of the nucleotide and amino acid sequences of the RsrI and EcoRI restriction endonucleases. Gene. 1989 Dec 21;85(1):1–13. doi: 10.1016/0378-1119(89)90458-7. [DOI] [PubMed] [Google Scholar]
  24. Tao T., Walter J., Brennan K. J., Cotterman M. M., Blumenthal R. M. Sequence, internal homology and high-level expression of the gene for a DNA-(cytosine N4)-methyltransferase, M.Pvu II. Nucleic Acids Res. 1989 Jun 12;17(11):4161–4175. doi: 10.1093/nar/17.11.4161. [DOI] [PMC free article] [PubMed] [Google Scholar]
  25. Van Cott E. M., Wilson G. G. Cloning the FnuDI, NaeI, NcoI and XbaI restriction-modification systems. Gene. 1988 Dec 25;74(1):55–59. doi: 10.1016/0378-1119(88)90251-x. [DOI] [PubMed] [Google Scholar]
  26. Wilson G. G., Murray N. E. Restriction and modification systems. Annu Rev Genet. 1991;25:585–627. doi: 10.1146/annurev.ge.25.120191.003101. [DOI] [PubMed] [Google Scholar]
  27. Wilson G. G. Organization of restriction-modification systems. Nucleic Acids Res. 1991 May 25;19(10):2539–2566. doi: 10.1093/nar/19.10.2539. [DOI] [PMC free article] [PubMed] [Google Scholar]
  28. Woese C. R., Kandler O., Wheelis M. L. Towards a natural system of organisms: proposal for the domains Archaea, Bacteria, and Eucarya. Proc Natl Acad Sci U S A. 1990 Jun;87(12):4576–4579. doi: 10.1073/pnas.87.12.4576. [DOI] [PMC free article] [PubMed] [Google Scholar]
  29. Yanisch-Perron C., Vieira J., Messing J. Improved M13 phage cloning vectors and host strains: nucleotide sequences of the M13mp18 and pUC19 vectors. Gene. 1985;33(1):103–119. doi: 10.1016/0378-1119(85)90120-9. [DOI] [PubMed] [Google Scholar]
  30. Zillig W. Comparative biochemistry of Archaea and Bacteria. Curr Opin Genet Dev. 1991 Dec;1(4):544–551. doi: 10.1016/s0959-437x(05)80206-0. [DOI] [PubMed] [Google Scholar]

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