Abstract
The temperate B.subtilis phages phi 3T and rho 11s code, in addition to the multispecific DNA (cytosine-C5) methyltransferases (C5-MTases) M.phi 3TI and M.rho 11sI, which were previously characterized, for the identical monospecific C5-MTases M.phi 3TII and M.rho 11sII. These enzymes modify the C to TCGA sites, a novel target specificity among C5-MTases. The primary sequence of M.phi 3TII (326 amino acids) shows all conserved motifs typical of the building plan of C5-MTases. The degree of relatedness between M.phi 3TII and all other mono- or multispecific C5-MTases ranges from 30-40% amino acid identity. Particularly M.phi 3TII does not show pronounced similarity to M.phi 3TI indicating that both MTase genes were not generated from one another but were acquired independently by the phage. The amino terminal part of the M.phi 3TII (preceding the variable region 'V'), which predominantly constitutes the catalytic domain of the enzyme, exhibits pronounced sequence similarity to the amino termini of a family of A-N6-MTases, which--like M.Taql--recognize the general sequence TNNA. This suggests that recently described similarities in the general three dimensional organization of C5- and A-N6-MTases imply divergent evolution of these enzymes originating from a common molecular ancestor.
Full text
PDF






Images in this article
Selected References
These references are in PubMed. This may not be the complete list of references from this article.
- Barany F., Danzitz M., Zebala J., Mayer A. Cloning and sequencing of genes encoding the TthHB8I restriction and modification enzymes: comparison with the isoschizomeric TaqI enzymes. Gene. 1992 Mar 1;112(1):3–12. doi: 10.1016/0378-1119(92)90296-2. [DOI] [PubMed] [Google Scholar]
- 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]
- Chai S., Bravo A., Lüder G., Nedlin A., Trautner T. A., Alonso J. C. Molecular analysis of the Bacillus subtilis bacteriophage SPP1 region encompassing genes 1 to 6. The products of gene 1 and gene 2 are required for pac cleavage. J Mol Biol. 1992 Mar 5;224(1):87–102. doi: 10.1016/0022-2836(92)90578-8. [DOI] [PubMed] [Google Scholar]
- Chen L., MacMillan A. M., Chang W., Ezaz-Nikpay K., Lane W. S., Verdine G. L. Direct identification of the active-site nucleophile in a DNA (cytosine-5)-methyltransferase. Biochemistry. 1991 Nov 19;30(46):11018–11025. doi: 10.1021/bi00110a002. [DOI] [PubMed] [Google Scholar]
- Cheng X., Kumar S., Posfai J., Pflugrath J. W., Roberts R. J. Crystal structure of the HhaI DNA methyltransferase complexed with S-adenosyl-L-methionine. Cell. 1993 Jul 30;74(2):299–307. doi: 10.1016/0092-8674(93)90421-l. [DOI] [PubMed] [Google Scholar]
- 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]
- 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]
- Fürste J. P., Pansegrau W., Frank R., Blöcker H., Scholz P., Bagdasarian M., Lanka E. Molecular cloning of the plasmid RP4 primase region in a multi-host-range tacP expression vector. Gene. 1986;48(1):119–131. doi: 10.1016/0378-1119(86)90358-6. [DOI] [PubMed] [Google Scholar]
- Guha S. Determination of DNA sequences containing methylcytosine in Bacillus subtilis Marburg. J Bacteriol. 1985 Aug;163(2):573–579. doi: 10.1128/jb.163.2.573-579.1985. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Ito H., Sadaoka A., Kotani H., Hiraoka N., Nakamura T. Cloning, nucleotide sequence, and expression of the HincII restriction-modification system. Nucleic Acids Res. 1990 Jul 11;18(13):3903–3911. doi: 10.1093/nar/18.13.3903. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Janulaitis A., Vaisvila R., Timinskas A., Klimasauskas S., Butkus V. Cloning and sequence analysis of the genes coding for Eco57I type IV restriction-modification enzymes. Nucleic Acids Res. 1992 Nov 25;20(22):6051–6056. doi: 10.1093/nar/20.22.6051. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Karreman C., de Waard A. Agmenellum quadruplicatum M.AquI, a novel modification methylase. J Bacteriol. 1990 Jan;172(1):266–272. doi: 10.1128/jb.172.1.266-272.1990. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Klimasauskas S., Kumar S., Roberts R. J., Cheng X. HhaI methyltransferase flips its target base out of the DNA helix. Cell. 1994 Jan 28;76(2):357–369. doi: 10.1016/0092-8674(94)90342-5. [DOI] [PubMed] [Google Scholar]
- 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]
- Kumar S., Cheng X., Klimasauskas S., Mi S., Posfai J., Roberts R. J., Wilson G. G. The DNA (cytosine-5) methyltransferases. Nucleic Acids Res. 1994 Jan 11;22(1):1–10. doi: 10.1093/nar/22.1.1. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Lange C., Noyer-Weidner M., Trautner T. A., Weiner M., Zahler S. A. M.H2I, a multispecific 5C-DNA methyltransferase encoded by Bacillus amyloliquefaciens phage H2. Gene. 1991 Apr;100:213–218. doi: 10.1016/0378-1119(91)90369-m. [DOI] [PubMed] [Google Scholar]
- Lauster R., Trautner T. A., Noyer-Weidner M. Cytosine-specific type II DNA methyltransferases. A conserved enzyme core with variable target-recognizing domains. J Mol Biol. 1989 Mar 20;206(2):305–312. doi: 10.1016/0022-2836(89)90480-4. [DOI] [PubMed] [Google Scholar]
- Maxam A. M., Gilbert W. A new method for sequencing DNA. Proc Natl Acad Sci U S A. 1977 Feb;74(2):560–564. doi: 10.1073/pnas.74.2.560. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 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]
- Narva K. E., Wendell D. L., Skrdla M. P., Van Etten J. L. Molecular cloning and characterization of the gene encoding the DNA methyltransferase, M.CviBIII, from Chlorella virus NC-1A. Nucleic Acids Res. 1987 Dec 10;15(23):9807–9823. doi: 10.1093/nar/15.23.9807. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 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]
- Pósfai G., Kim S. C., Szilák L., Kovács A., Venetianer P. Complementation by detached parts of GGCC-specific DNA methyltransferases. Nucleic Acids Res. 1991 Sep 25;19(18):4843–4847. doi: 10.1093/nar/19.18.4843. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 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]
- 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]
- Smith H. O., Annau T. M., Chandrasegaran S. Finding sequence motifs in groups of functionally related proteins. Proc Natl Acad Sci U S A. 1990 Jan;87(2):826–830. doi: 10.1073/pnas.87.2.826. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 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]
- 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]
- Stefan C., Xia Y. N., Van Etten J. L. Molecular cloning and characterization of the gene encoding the adenine methyltransferase M.CviRI from Chlorella virus XZ-6E. Nucleic Acids Res. 1991 Jan 25;19(2):307–311. doi: 10.1093/nar/19.2.307. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Theriault G., Roy P. H., Howard K. A., Benner J. S., Brooks J. E., Waters A. F., Gingeras T. R. Nucleotide sequence of the PaeR7 restriction/modification system and partial characterization of its protein products. Nucleic Acids Res. 1985 Dec 9;13(23):8441–8461. doi: 10.1093/nar/13.23.8441. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 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]
- Uozumi T., Hoshino T., Miwa K., Horinouchi S., Beppu T., Arima K. Restriction and modification in Bacillus species: genetic transformation of bacteria with DNA from different species, part I. Mol Gen Genet. 1977 Mar 28;152(1):65–69. doi: 10.1007/BF00264941. [DOI] [PubMed] [Google Scholar]
- Walder R. Y., Walder J. A., Donelson J. E. The organization and complete nucleotide sequence of the PstI restriction-modification system. J Biol Chem. 1984 Jun 25;259(12):8015–8026. [PubMed] [Google Scholar]
- Woodcock D. M., Crowther P. J., Doherty J., Jefferson S., DeCruz E., Noyer-Weidner M., Smith S. S., Michael M. Z., Graham M. W. Quantitative evaluation of Escherichia coli host strains for tolerance to cytosine methylation in plasmid and phage recombinants. Nucleic Acids Res. 1989 May 11;17(9):3469–3478. doi: 10.1093/nar/17.9.3469. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 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]
- Xu G. L., Kapfer W., Walter J., Trautner T. A. BsuBI--an isospecific restriction and modification system of PstI: characterization of the BsuBI genes and enzymes. Nucleic Acids Res. 1992 Dec 25;20(24):6517–6523. doi: 10.1093/nar/20.24.6517. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 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]
- Yasbin R. E., Fields P. I., Andersen B. J. Properties of Bacillus subtilis 168 derivatives freed of their natural prophages. Gene. 1980 Dec;12(1-2):155–159. doi: 10.1016/0378-1119(80)90026-8. [DOI] [PubMed] [Google Scholar]


