Abstract
The gene encoding the XorII methyltransferase (M · XorII) was cloned from Xanthomonas oryzae pv. oryzae and characterized in Escherichia coli. The M · XorII activity was localized to a 3.1 kb BamHI-BstXI fragment, which contained two open reading frames (ORFs) of 1272 nucleotides (424 amino acids) and 408 nucleotides (136 amino acids). Ten polypeptide domains conserved in other M5 cytosine methyltransferases (MTases) were identified in the deduced amino acid sequence of the 1272 ORF. E. coli Mrr+ strains were transformed poorly by plasmids containing the XorII MTase gene, indicating the presence of at least one MCG in the recognition sequence for M · XorII (CGATCG). The 408 nucleotide ORF was 36% identical at the amino acid level to sequences of the E. coli dcm-vsr gene, which is required for very short patch repair. X. oryzae pv. oryzae genomic DNA that is resistant to digestion by Pvul and XorII hybridizes with a 7.0 kb fragment containing the XorII MTase gene and vsr homolog, whereas DNA from strains that lack M · XorII activity do not hybridize with the fragment.
Similar content being viewed by others
References
Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ (1990) Basic local alignment search tool. J Mol Biol 215:403–410
Ausubel FM, Brent R, Kingston RE, Moore DD, Seidman JG, Smith JA, Struhl K (1991) Current protocols in molecular biology. Wiley, New York
Bak AL, Christiansen C, Stenderup A (1970) Bacterial genome sizes determined by DNA renaturation studies. J Gen Microbiol 64:377–380
Buhk H-J, Behrens B, Tailor R, Wilke K, Prada JJ, Günthert U, Noyer-Weidner M, Jentsch S, Trautner TA (1984) Restriction and modification in Bacillus subtilis: nucleotide sequence, functional organization and product of the DNA methyltransferase gene of bacteriophage SPR. Gene 29:51–61
Caserta M, Zacharias W, Nwankwo D, Wilson GG, Wells RD (1987) Cloning, sequencing, in vivo promoter mapping, and expression in Escherichia coli of the gene for HhaI methyltransferase. J Biol Chem 262:4770–4777
Coulondre C, Miller JH, Farabaugh PJ, Gilbert W (1978) Molecular basis of substitution hotspots in Escherichia coli. Nature 274:775–780
De Feyter R, Kado CI, Gabriel DW (1990) Small, stable shuttle vectors for use in Xanthomonas. Gene 88:65–72
Endlich B, Linn S (1985) The DNA restriction endonuclease of Escherichia coli B. II: Further studies of the structure of DNA intermediates and products. J Biol Chem 260:5729–5738
Hennecke F, Kolmar H, Bründl K, Fritz H-J (1991) The vsr gene product of E. coli K-12 is a strand- and sequence-specific DNA mismatch endonuclease. Nature 353:776–778
Kessler C, Manta V (1990) Specificity of restriction endonuclease and DNA modification methyltransferases — a review. Gene 92:1–248
Kiss A, Pösfai G, Keller CC, Venetianer P, Roberts RJ (1985) Nucleotide sequence of the BsuRI restriction-modification system. Nucleic Acids Res 13:6403–6421
Klima-Sauskas S, Nelson JL, Roberts RJ (1991) The sequence specificity domain of cytosine-C5 MTases. Nucleic Acids Res 19:6183–6190
Krüger DH, Bickle TA (1983) Bacteriophage survival: multiple mechansims for avoiding deoxyribonucleic acid restriction systems of their hosts. Microbiol Rev 47:345–360
Kulakauskas S, Barsomian JM, Lubys A, Roberts RJ, Wilson GG (1993) Organization and sequence of the HpaII restriction-modification system and adjacent genes. Gene 142:9–15
Leach JE, White FF, Rhoads ML, Leung H (1990) A repetitive DNA sequence differentiates Xanthomonas campestris pv. oryzae from other pathovars of X. campestris. Mol Plant-Microbe Interact 3:238–246
Leach JE, Rhoads ML, Vera Cruz CM, White FF, Mew TW, Leung H (1992) Assessment of genetic diversity and population structure of Xanthomonas oryzae pv. oryzae with a repetitive DNA element. Appl Environ Microbiol 58:2188–2195
Lee F, Squires CL, Squires C, Yanofsky C (1976) Termination of transcription in vitro in the Escherichia coli tryptophan operon leader region. J Mol Biol 103:383–393
Levin BR (1986) Restriction-modification immunity and the maintenance of generic diversity in bacterial populations. In: Karlin S, Nevo E (eds) Evolutionary processes and theory. Academic Press, New York, pp 669–688
Li M, Schweiger HP (1993) Resolution of common DNA sequencing ambiguities of GC-rich DNA templates by terminal deoxynucleotidyl transferase without dGTP analogues. Focus 15:19–20
Lindahl T, Nyberg B (1974) Heat-induced deamination of cytosine residues in deoxyribonucleic acid. Biochemistry 13:3405–3410
Lunnen KD, Barsomian JM, Camp RR, Card CO, Chen S-Z, Croft R, Looney MC, Meda MM, Moran LS, Nwankwo DO, Slatko BE, Van Cott EM, Wilson GG (1988) Cloning type-II restriction and modification genes. Gene 74:25–32
McClelland M, Nelson M (1992) Effect of site-specific methylation on DNA modification methyltransferases and restriction endonucleases. Nucleic Acids Res 20:2145–2157
Mew TW (1987) Current status and future prospects of research on bacterial blight of rice. Annu Rev Phytopathol 25:359–382
Miller JH (1972) Experiments in molecular genetics. Cold Spring Harbor Laboratory, Cold Spring Harbor, New York
Morelle G (1989) A plasmid extraction procedure on a miniprep scale. Focus 11:7–8
Pósfai J, Bhagwat AS, Pósfai G, Roberts RJ (1989) Predictive motifs derived from cytosine methyltransferases. Nucleic Acids Res 17:2421–2435
Pribnow D (1979) Genetic control signals in DNA. In: Goldberger RF (ed) Biological regulation and development, vol 1. Gene expression. Plenum Press, New York, pp 219–277
Raleigh EA, Benner J, Bloom F, Braymer HD, DeCruz E, Dharmalingam K, Heitman J, Noyer-Weidner M, Piekarowicz A, Kretz PL, Short JM, Woodcock D (1991) Nomenclature relating to restriction of modified DNA in Escherichia coli. J Bacteriol 173:2707–2709
Sanger F, Nicklen S, Coulson AR (1977) DNA sequencing with chain- terminating inhibitors. Proc Natl Acad Sci USA 74:5463–5467
Simon R, Priefer U, Pühler A (1983) A broad host range mobilization system for in vitro genetic engineering: transposon mutagenesis in gram negative bacteria. Biotechnology 1:784–791
Smith MD, Longo M, Gerard GF, Chatterjee DK (1992a) Cloning and characterization of genes for the Pvul restriction and modification system. Nucleic Acids Res 20:5743–5747
Smith MW, Feng DF, Doolittle RF (1992b) Evolution by acquisition: the case for horizontal gene transfers. Trends Biochem Sci 17:489–493
Sohail A, Lieb M, Dar M, Bhagwat AS (1990) A gene required for very short patch repair in Escherichia coli is adjacent to the DNA cytosine MTase gene. J Bacteriol 172:4214–4221
Som S, Bhagwat AS, Friedman S (1987) Nucleotide sequence and expression of the gene encoding the EcoRII modification enzyme. Nucleic Acids Res 15:313–332
Stefan C, Xia Y, Van Etten JL (1991) Molecular cloning and characterization of the gene encoding the adenine methyltransferase M. CviRI from Chlorella virus XZ-6E. Nucleic Acids Res 19:307–311
Steitz JA (1979) Genetic signals and nucleotide sequences in messenger RNA. In: Goldberger RF (ed) Biological regulation and development, vol 1. Gene expression. Plenum Press, New York, pp 349–399
Sznyter LA, Slatko B, Moran L, O'Donnell HO, Brooks JE (1987) Nucleotide sequence of the DdeI restriction-modification system and characterization of the MTase protein. Nucleic Acids Res 15:8249–8266
Tsuchiya K, Mew TW, Wakimoto S (1982) Bacteriological and pathological characteristics of wild types and induced mutants of Xanthomonas campestris pv. oryzae. Phytopathology 72:43–46
Vera Cruz CM, Gossele F, Kersters K, Segers P, Van den Mooter M, Swings J, De Ley J (1984) Differentiation between Xanthomonas campestris pv. oryzae, Xanthomonas campestris pv. oryzicola and the bacterial ‘brown blotch’ pathogen on rice by numerical analysis of phenotypic features and protein gel electrophoregrams. J Gen Microbiol 130:2983–2999
Waite-Rees PA, Keating CJ, Moran LS, Slatko BE, Hornstra LJ, Benner JS (1991) Characterization and expression of the Escherichia coli Mrr restriction system. J Bacteriol 173:5207–5219
Walter J, Trautner TA, Noyer-Weidner M (1992) High plasticity of multispecific DNA methyltransferases in the region carrying DNA target-recognizing enzyme modules. EMBO J 11:4445–4450
Wang RYH, Shedlarski JG, Farber MB, Kuebbing D, Ehrlich M (1980) Two sequence specific endonucleases from Xanthomonas oryzae. Biochim Biophys Acta 606:371–385
Wilson GG (1988) Type II restriction-modification systems. Trends Genet 4:314–318
Yun CH (1991) Molecular characterization of a repetitive element of Xanthomonas oryzae pv. oryzae. PhD Thesis, Kansas State University, Manhattan
Author information
Authors and Affiliations
Additional information
Communicated by W. Arber
The sequence presented in this paper has been submitted to NCBI; the accession number is U06424
Rights and permissions
About this article
Cite this article
Choi, S.H., Leach, J.E. Identification of the XorII methyltransferase gene and a vsr homolog from Xanthomonas oryzae pv. oryzae . Molec. Gen. Genet. 244, 383–390 (1994). https://doi.org/10.1007/BF00286690
Received:
Accepted:
Issue Date:
DOI: https://doi.org/10.1007/BF00286690