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. 1988 Aug;7(8):2601–2609. doi: 10.1002/j.1460-2075.1988.tb03110.x

Sequential order of target-recognizing domains in multispecific DNA-methyltransferases.

K Wilke 1, E Rauhut 1, M Noyer-Weidner 1, R Lauster 1, B Pawlek 1, B Behrens 1, T A Trautner 1
PMCID: PMC457134  PMID: 3142766

Abstract

In the multispecific DNA(cytosine-5)-methyltransferases (Mtases) of Bacillus subtilis phages SPR and phi 3T the domains responsible for recognition of DNA methylation targets CCA/TGG, CCGG, GGCC (SPR) and GCNGC, GGCC (phi 3T) represent contiguous sequences of approximately 50 amino acids each. These domains are tandemly arranged and do not overlap. They are part of a 'variable' segment within the enzymes which is flanked by 'conserved' amino acids, which are very similar amongst bacterial monospecific and the multispecific Mtases studied here. These results follow from a mutational analysis of the SPR and phi 3T Mtase genes. They further support our concept of a modular enzyme organization, according to which variability of type II Mtases with respect to target recognition is achieved by a combination of the same enzyme core with a variety of target-recognizing domains.

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Selected References

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  1. Balganesh T. S., Reiners L., Lauster R., Noyer-Weidner M., Wilke K., Trautner T. A. Construction and use of chimeric SPR/phi 3T DNA methyltransferases in the definition of sequence recognizing enzyme regions. EMBO J. 1987 Nov;6(11):3543–3549. doi: 10.1002/j.1460-2075.1987.tb02681.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2. Behrens B., Noyer-Weidner M., Pawlek B., Lauster R., Balganesh T. S., Trautner T. A. Organization of multispecific DNA methyltransferases encoded by temperate Bacillus subtilis phages. EMBO J. 1987 Apr;6(4):1137–1142. doi: 10.1002/j.1460-2075.1987.tb04869.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  3. Berg J. M. Potential metal-binding domains in nucleic acid binding proteins. Science. 1986 Apr 25;232(4749):485–487. doi: 10.1126/science.2421409. [DOI] [PubMed] [Google Scholar]
  4. Birnboim H. C., Doly J. A rapid alkaline extraction procedure for screening recombinant plasmid DNA. Nucleic Acids Res. 1979 Nov 24;7(6):1513–1523. doi: 10.1093/nar/7.6.1513. [DOI] [PMC free article] [PubMed] [Google Scholar]
  5. Bolivar F., Rodriguez R. L., Greene P. J., Betlach M. C., Heyneker H. L., Boyer H. W., Crosa J. H., Falkow S. Construction and characterization of new cloning vehicles. II. A multipurpose cloning system. Gene. 1977;2(2):95–113. [PubMed] [Google Scholar]
  6. 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]
  7. Brosius J., Cate R. L., Perlmutter A. P. Precise location of two promoters for the beta-lactamase gene of pBR322. S1 mapping of ribonucleic acid isolated from Escherichia coli or synthesized in vitro. J Biol Chem. 1982 Aug 10;257(15):9205–9210. [PubMed] [Google Scholar]
  8. Buhk H. J., Behrens B., Tailor R., Wilke K., Prada J. J., Günthert U., Noyer-Weidner M., Jentsch S., Trautner T. A. Restriction and modification in Bacillus subtilis: nucleotide sequence, functional organization and product of the DNA methyltransferase gene of bacteriophage SPR. Gene. 1984 Jul-Aug;29(1-2):51–61. doi: 10.1016/0378-1119(84)90165-3. [DOI] [PubMed] [Google Scholar]
  9. Caserta M., Zacharias W., Nwankwo D., Wilson G. G., Wells R. D. Cloning, sequencing, in vivo promoter mapping, and expression in Escherichia coli of the gene for the HhaI methyltransferase. J Biol Chem. 1987 Apr 5;262(10):4770–4777. [PubMed] [Google Scholar]
  10. Chang S., Cohen S. N. High frequency transformation of Bacillus subtilis protoplasts by plasmid DNA. Mol Gen Genet. 1979 Jan 5;168(1):111–115. doi: 10.1007/BF00267940. [DOI] [PubMed] [Google Scholar]
  11. Demple B., Sedgwick B., Robins P., Totty N., Waterfield M. D., Lindahl T. Active site and complete sequence of the suicidal methyltransferase that counters alkylation mutagenesis. Proc Natl Acad Sci U S A. 1985 May;82(9):2688–2692. doi: 10.1073/pnas.82.9.2688. [DOI] [PMC free article] [PubMed] [Google Scholar]
  12. Dev I. K., Yates B. B., Leong J., Dallas W. S. Functional role of cysteine-146 in Escherichia coli thymidylate synthase. Proc Natl Acad Sci U S A. 1988 Mar;85(5):1472–1476. doi: 10.1073/pnas.85.5.1472. [DOI] [PMC free article] [PubMed] [Google Scholar]
  13. Günthert U., Lauster R., Reiners L. Multispecific DNA methyltransferases from Bacillus subtilis phages. Properties of wild-type and various mutant enzymes with altered DNA affinity. Eur J Biochem. 1986 Sep 15;159(3):485–492. doi: 10.1111/j.1432-1033.1986.tb09912.x. [DOI] [PubMed] [Google Scholar]
  14. Günthert U., Reiners L., Lauster R. Cloning and expression of Bacillus subtilis phage DNA methyltransferase genes in Escherichia coli and B. subtilis. Gene. 1986;41(2-3):261–270. doi: 10.1016/0378-1119(86)90106-x. [DOI] [PubMed] [Google Scholar]
  15. Hardy L. W., Finer-Moore J. S., Montfort W. R., Jones M. O., Santi D. V., Stroud R. M. Atomic structure of thymidylate synthase: target for rational drug design. Science. 1987 Jan 23;235(4787):448–455. doi: 10.1126/science.3099389. [DOI] [PubMed] [Google Scholar]
  16. Humphreys G. O., Willshaw G. A., Smith H. R., Anderson E. S. Mutagenesis of plasmid DNA with hydroxylamine: isolation of mutants of multi-copy plasmids. Mol Gen Genet. 1976 Apr 23;145(1):101–108. doi: 10.1007/BF00331564. [DOI] [PubMed] [Google Scholar]
  17. Katz L., Kingsbury D. T., Helinski D. R. Stimulation by cyclic adenosine monophosphate of plasmid deoxyribonucleic acid replication and catabolite repression of the plasmid deoxyribonucleic acid-protein relaxation complex. J Bacteriol. 1973 May;114(2):577–591. doi: 10.1128/jb.114.2.577-591.1973. [DOI] [PMC free article] [PubMed] [Google Scholar]
  18. Kiss A., Posfai G., Keller C. C., Venetianer P., Roberts R. J. Nucleotide sequence of the BsuRI restriction-modification system. Nucleic Acids Res. 1985 Sep 25;13(18):6403–6421. doi: 10.1093/nar/13.18.6403. [DOI] [PMC free article] [PubMed] [Google Scholar]
  19. Kramer W., Drutsa V., Jansen H. W., Kramer B., Pflugfelder M., Fritz H. J. The gapped duplex DNA approach to oligonucleotide-directed mutation construction. Nucleic Acids Res. 1984 Dec 21;12(24):9441–9456. doi: 10.1093/nar/12.24.9441. [DOI] [PMC free article] [PubMed] [Google Scholar]
  20. Kwoh T. J., Zipser D., Wigler M. Mutational analysis of the cloned chicken thymidine kinase gene. J Mol Appl Genet. 1983;2(2):191–200. [PubMed] [Google Scholar]
  21. 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]
  22. Lobel L. I., Goff S. P. Construction of mutants of Moloney murine leukemia virus by suppressor-linker insertional mutagenesis: positions of viable insertion mutations. Proc Natl Acad Sci U S A. 1984 Jul;81(13):4149–4153. doi: 10.1073/pnas.81.13.4149. [DOI] [PMC free article] [PubMed] [Google Scholar]
  23. McClarin J. A., Frederick C. A., Wang B. C., Greene P., Boyer H. W., Grable J., Rosenberg J. M. Structure of the DNA-Eco RI endonuclease recognition complex at 3 A resolution. Science. 1986 Dec 19;234(4783):1526–1541. doi: 10.1126/science.3024321. [DOI] [PubMed] [Google Scholar]
  24. Messing J., Crea R., Seeburg P. H. A system for shotgun DNA sequencing. Nucleic Acids Res. 1981 Jan 24;9(2):309–321. doi: 10.1093/nar/9.2.309. [DOI] [PMC free article] [PubMed] [Google Scholar]
  25. Messing J., Vieira J. A new pair of M13 vectors for selecting either DNA strand of double-digest restriction fragments. Gene. 1982 Oct;19(3):269–276. doi: 10.1016/0378-1119(82)90016-6. [DOI] [PubMed] [Google Scholar]
  26. Noyer-Weidner M., Diaz R., Reiners L. Cytosine-specific DNA modification interferes with plasmid establishment in Escherichia coli K12: involvement of rglB. Mol Gen Genet. 1986 Dec;205(3):469–475. doi: 10.1007/BF00338084. [DOI] [PubMed] [Google Scholar]
  27. Noyer-Weidner M., Jentsch S., Kupsch J., Bergbauer M., Trautner T. A. DNA methyltransferase genes of Bacillus subtilis phages: structural relatedness and gene expression. Gene. 1985;35(1-2):143–150. doi: 10.1016/0378-1119(85)90166-0. [DOI] [PubMed] [Google Scholar]
  28. Noyer-Weidner M., Jentsch S., Pawlek B., Günthert U., Trautner T. A. Restriction and modification in Bacillus subtilis: DNA methylation potential of the related bacteriophages Z, SPR, SP beta, phi 3T, and rho 11. J Virol. 1983 May;46(2):446–453. doi: 10.1128/jvi.46.2.446-453.1983. [DOI] [PMC free article] [PubMed] [Google Scholar]
  29. Noyer-Weidner M., Pawlek B., Jentsch S., Günthert U., Trautner T. A. Restriction and modification in Bacillus subtilis: gene coding for a BsuR-specific modification methyltransferase in the temperate bacteriophage phi 3T. J Virol. 1981 Jun;38(3):1077–1080. doi: 10.1128/jvi.38.3.1077-1080.1981. [DOI] [PMC free article] [PubMed] [Google Scholar]
  30. Noyer-Weidner M., Reiners-Schramm L. Highly efficient positive selection of recombinant plasmids using a novel rglB-based Escherichia coli K-12 vector system. Gene. 1988 Jun 30;66(2):269–278. doi: 10.1016/0378-1119(88)90363-0. [DOI] [PubMed] [Google Scholar]
  31. Pabo C. O., Sauer R. T. Protein-DNA recognition. Annu Rev Biochem. 1984;53:293–321. doi: 10.1146/annurev.bi.53.070184.001453. [DOI] [PubMed] [Google Scholar]
  32. Prentki P., Krisch H. M. In vitro insertional mutagenesis with a selectable DNA fragment. Gene. 1984 Sep;29(3):303–313. doi: 10.1016/0378-1119(84)90059-3. [DOI] [PubMed] [Google Scholar]
  33. Pósfai G., Baldauf F., Erdei S., Pósfai J., Venetianer P., Kiss A. Structure of the gene coding for the sequence-specific DNA-methyltransferase of the B. subtilis phage SPR. Nucleic Acids Res. 1984 Dec 11;12(23):9039–9049. doi: 10.1093/nar/12.23.9039. [DOI] [PMC free article] [PubMed] [Google Scholar]
  34. Pósfai G., Kiss A., Erdei S., Pósfai J., Venetianer P. Structure of the Bacillus sphaericus R modification methylase gene. J Mol Biol. 1983 Nov 5;170(3):597–610. doi: 10.1016/s0022-2836(83)80123-5. [DOI] [PubMed] [Google Scholar]
  35. 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]
  36. Sedgwick B., Robins P., Totty N., Lindahl T. Functional domains and methyl acceptor sites of the Escherichia coli ada protein. J Biol Chem. 1988 Mar 25;263(9):4430–4433. [PubMed] [Google Scholar]
  37. Soberon X., Covarrubias L., Bolivar F. Construction and characterization of new cloning vehicles. IV. Deletion derivatives of pBR322 and pBR325. Gene. 1980 May;9(3-4):287–305. doi: 10.1016/0378-1119(90)90328-o. [DOI] [PubMed] [Google Scholar]
  38. Som S., Bhagwat A. S., Friedman S. Nucleotide sequence and expression of the gene encoding the EcoRII modification enzyme. Nucleic Acids Res. 1987 Jan 12;15(1):313–332. doi: 10.1093/nar/15.1.313. [DOI] [PMC free article] [PubMed] [Google Scholar]
  39. Sznyter L. A., Slatko B., Moran L., O'Donnell K. H., Brooks J. E. Nucleotide sequence of the DdeI restriction-modification system and characterization of the methylase protein. Nucleic Acids Res. 1987 Oct 26;15(20):8249–8266. doi: 10.1093/nar/15.20.8249. [DOI] [PMC free article] [PubMed] [Google Scholar]
  40. Tran-Betcke A., Behrens B., Noyer-Weidner M., Trautner T. A. DNA methyltransferase genes of Bacillus subtilis phages: comparison of their nucleotide sequences. Gene. 1986;42(1):89–96. doi: 10.1016/0378-1119(86)90153-8. [DOI] [PubMed] [Google Scholar]
  41. Trautner T. A., Pawlek B., Günthert U., Canosi U., Jentsch S., Freund M. Restriction and modification in Bacillus subtilis: identification of a gene in the temperate phage SP beta coding for a BsuR specific modification methyltransferase. Mol Gen Genet. 1980;180(2):361–367. doi: 10.1007/BF00425849. [DOI] [PubMed] [Google Scholar]
  42. Vieira J., Messing J. The pUC plasmids, an M13mp7-derived system for insertion mutagenesis and sequencing with synthetic universal primers. Gene. 1982 Oct;19(3):259–268. doi: 10.1016/0378-1119(82)90015-4. [DOI] [PubMed] [Google Scholar]
  43. Viret J. F., Alonso J. C. A new mutator strain of Bacillus subtilis. Mol Gen Genet. 1987 Jun;208(1-2):353–356. doi: 10.1007/BF00330465. [DOI] [PubMed] [Google Scholar]
  44. Williams D. M., Duvall E. J., Lovett P. S. Cloning restriction fragments that promote expression of a gene in Bacillus subtilis. J Bacteriol. 1981 Jun;146(3):1162–1165. doi: 10.1128/jb.146.3.1162-1165.1981. [DOI] [PMC free article] [PubMed] [Google Scholar]
  45. Wu J. C., Santi D. V. Kinetic and catalytic mechanism of HhaI methyltransferase. J Biol Chem. 1987 Apr 5;262(10):4778–4786. [PubMed] [Google Scholar]
  46. 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]
  47. Zahler S. A., Korman R. Z., Rosenthal R., Hemphill H. E. Bacillus subtilis bacteriophage SPbeta: localization of the prophage attachment site, and specialized transduction. J Bacteriol. 1977 Jan;129(1):556–558. doi: 10.1128/jb.129.1.556-558.1977. [DOI] [PMC free article] [PubMed] [Google Scholar]
  48. Zoller M. J., Smith M. Oligonucleotide-directed mutagenesis of DNA fragments cloned into M13 vectors. Methods Enzymol. 1983;100:468–500. doi: 10.1016/0076-6879(83)00074-9. [DOI] [PubMed] [Google Scholar]

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