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Cloning and characterization of the TneDI restriction–modification system of Thermotoga neapolitana

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Abstract

A putative Type II restriction–modification system of Thermotoga neapolitana, TneDI, was cloned into Escherichia coli XL1-Blue MRF′ and characterized. Gene CTN_0339 specifies the endonuclease R.TneDI, while CTN_0340 encodes the cognate DNA methyltransferase M.TneDI. Both enzymes were purified simply by heating the cell lysates of E. coli followed by centrifugation. The enzymes were active over a broad range of temperatures, from 42°C to at least 77°C, with the highest activities observed at 77°C. R.TneDI cleaved at the center of the recognition sequence (CG↓CG) and generated blunt-end cuts. Overexpression of R.TneDI in BL21(DE3) was confirmed by both SDS-PAGE and Western blotting.

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References

  • Adamczyk-Poplawska M, Lower M, Piekarowicz A (2009) Characterization of the NgoAXP: phase-variable type III restriction–modification system in Neisseria gonorrhoeae. FEMS Microbiol Lett 300(1):25–35

    Article  PubMed  CAS  Google Scholar 

  • Altschul SF, Madden TL, Schaffer AA, Zhang J, Zhang Z, Miller W, Lipman DJ (1997) Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 25(17):3389–3402

    Article  PubMed  CAS  Google Scholar 

  • Belkin S, Wirsen CO, Jannasch HW (1986) A new sulfur-reducing, extremely thermophilic eubacterium from a submarine thermal vent. Appl Environ Microbiol 51(6):1180–1185

    PubMed  CAS  Google Scholar 

  • Clark JM (1988) Novel non-templated nucleotide addition reactions catalyzed by procaryotic and eucaryotic DNA polymerases. Nucleic Acids Res 16(20):9677–9686

    Article  PubMed  CAS  Google Scholar 

  • Ehrlich M, Gama-Sosa MA, Carreira LH, Ljungdahl LG, Kuo KC, Gehrke CW (1985) DNA methylation in thermophilic bacteria: N4-methylcytosine, 5-methylcytosine, and N6-methyladenine. Nucleic Acids Res 13(4):1399–1412

    Article  PubMed  CAS  Google Scholar 

  • Gaido ML, Strobl JS (1987) Methylation sensitivity of the restriction enzymes FnuDII and AccII. Arch Microbiol 146(4):338–340

    Article  PubMed  CAS  Google Scholar 

  • Gaido ML, Prostko CR, Strobl JS (1988) Isolation and characterization of BsuE methyltransferase, a CGCG specific DNA methyltransferase from Bacillus subtilis. J Biol Chem 263(10):4832–4836

    PubMed  CAS  Google Scholar 

  • Gong W, O’Gara M, Blumenthal RM, Cheng X (1997) Structure of pvuII DNA-(cytosine N4) methyltransferase, an example of domain permutation and protein fold assignment. Nucleic Acids Res 25(14):2702–2715

    Article  PubMed  CAS  Google Scholar 

  • Hjorleifsdottir S, Petursdottir SK, Korpela J, Torsti AM, Mattila P, Kristjansson JK (1996) Screening for restriction endonucleases in aerobic, thermophilic eubacteria. Biotechnol Tech 10(1):13–18

    Article  CAS  Google Scholar 

  • Howard KA, Card C, Benner JS, Callahan HL, Maunus R, Silber K, Wilson G, Brooks JE (1986) Cloning the DdeI restriction–modification system using a two-step method. Nucleic Acids Res 14(20):7939–7951

    Article  PubMed  CAS  Google Scholar 

  • Ishikawa K, Watanabe M, Kuroita T, Uchiyama I, Bujnicki JM, Kawakami B, Tanokura M, Kobayashi I (2005) Discovery of a novel restriction endonuclease by genome comparison and application of a wheat-germ-based cell-free translation assay: PabI (5’-GTA/C) from the hyperthermophilic archaeon Pyrococcus abyssi. Nucleic Acids Res 33(13):e112

    Article  PubMed  Google Scholar 

  • Lui AC, McBride BC, Vovis GF, Smith M (1979) Site specific endonuclease from Fusobacterium nucleatum. Nucleic Acids Res 6(1):1–15

    Article  PubMed  CAS  Google Scholar 

  • Malone T, Blumenthal RM, Cheng X (1995) Structure-guided analysis reveals nine sequence motifs conserved among DNA amino-methyltransferases, and suggests a catalytic mechanism for these enzymes. J Mol Biol 253(4):618–632

    Article  PubMed  CAS  Google Scholar 

  • Matveyev AV, Young KT, Meng A, Elhai J (2001) DNA methyltransferases of the cyanobacterium Anabaena PCC 7120. Nucleic Acids Res 29(7):1491–1506

    Article  PubMed  CAS  Google Scholar 

  • Miyake M, Kotani H, Asada Y (1992) Isolation and identification of restriction endonuclease, SelI from a cyanobacterium, Synechococcus elongatus. Nucleic Acids Res 20(10):2605

    Article  PubMed  CAS  Google Scholar 

  • Morana A, Stiuso P, Colonna G, Lamberti M, Carteni M, De Rosa M (2002) Stabilization of S-adenosyl-l-methionine promoted by trehalose. Biochim Biophys Acta 1573(2):105–108

    PubMed  CAS  Google Scholar 

  • Pingoud A, Fuxreiter M, Pingoud V, Wende W (2005) Type II restriction endonucleases: structure and mechanism. Cell Mol Life Sci 62(6):685–707

    Article  PubMed  CAS  Google Scholar 

  • Roberts RJ, Belfort M, Bestor T, Bhagwat AS, Bickle TA, Bitinaite J, Blumenthal RM, Degtyarev S, Dryden DT, Dybvig K, Firman K, Gromova ES, Gumport RI, Halford SE, Hattman S, Heitman J, Hornby DP, Janulaitis A, Jeltsch A, Josephsen J, Kiss A, Klaenhammer TR, Kobayashi I, Kong H, Kruger DH, Lacks S, Marinus MG, Miyahara M, Morgan RD, Murray NE, Nagaraja V, Piekarowicz A, Pingoud A, Raleigh E, Rao DN, Reich N, Repin VE, Selker EU, Shaw PC, Stein DC, Stoddard BL, Szybalski W, Trautner TA, Van Etten JL, Vitor JM, Wilson GG, Xu SY (2003) A nomenclature for restriction enzymes, DNA methyltransferases, homing endonucleases and their genes. Nucleic Acids Res 31(7):1805–1812

    Article  PubMed  CAS  Google Scholar 

  • Roberts RJ, Vincze T, Posfai J, Macelis D (2010) REBASE—a database for DNA restriction and modification: enzymes, genes and genomes. Nucleic Acids Res 38(Database issue):D234–D236

    Article  PubMed  CAS  Google Scholar 

  • Schroder C, Selig M, Schonheit P (1994) Glucose fermentation to acetate, CO2 and H2 in the anaerobic hyperthermophilic eubacterium Thermotoga Maritima: involvement of the Embden–Meyerhof pathway. Arch Microbiol 161(6):460–470

    CAS  Google Scholar 

  • Sears A, Peakman LJ, Wilson GG, Szczelkun MD (2005) Characterization of the Type III restriction endonuclease PstII from Providencia stuartii. Nucleic Acids Res 33(15):4775–4787

    Article  PubMed  CAS  Google Scholar 

  • Slatko BE, Benner JS, Jager-Quinton T, Moran LS, Simcox TG, Van Cott EM, Wilson GG (1987) Cloning, sequencing and expression of the TaqI restriction–modification system. Nucleic Acids Res 15(23):9781–9796

    Article  PubMed  CAS  Google Scholar 

  • Stier I, Kiss A (2010) The type II restriction endonuclease MvaI has dual specificity. Nucleic Acids Res 38(22):8231–8238

    Article  PubMed  CAS  Google Scholar 

  • Strobl JS, Thompson EB (1984) Methylation of either cytosine in the recognition sequence CGCG inhibits ThaI cleavage of DNA. Nucleic Acids Res 12(21):8073–8083

    Article  PubMed  CAS  Google Scholar 

  • Studier FW, Rosenberg AH, Dunn JJ, Dubendorff JW (1990) Use of T7 RNA polymerase to direct expression of cloned genes. Meth Enzymol 185:60–89

    Article  PubMed  CAS  Google Scholar 

  • Thomm M, Frey G, Bolton BJ, Laue F, Kessler C, Stetter KO (1988) MvnI: a restriction enzyme in the archaebacterium Methanococcus vannielii. FEMS Microbiol Lett 52(3):229–233

    Article  CAS  Google Scholar 

  • Thompson JD, Higgins DG, Gibson TJ (1994) CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res 22(22):4673–4680

    Article  PubMed  CAS  Google Scholar 

  • Van Ooteghem SA, Beer SK, Yue PC (2002) Hydrogen production by the thermophilic bacterium Thermotoga neapolitana. Appl Biochem Biotechnol 98:177–189

    Article  PubMed  Google Scholar 

  • Venetianer P, Orosz A (1988) BepI restriction endonuclease, a new isoschisomer of FnuDII. Nucleic Acids Res 16(1):350

    Article  PubMed  CAS  Google Scholar 

  • Whitehead PR, Brown NL (1985) A simple and rapid method for screening bacteria for type II restriction endonucleases: enzymes in Aphanothece halophytica. Arch Microbiol 141(1):70–74

    Article  PubMed  CAS  Google Scholar 

  • Wilson GG, Murray NE (1991) Restriction and modification systems. Annu Rev Genet 25:585–627

    Article  PubMed  CAS  Google Scholar 

Download references

Acknowledgments

We are grateful to Dr. Robert M. Blumenthal at the University of Toledo College of Medicine for insightful discussions and critical reading of the manuscript. This work was supported by the BGSU internal funds to ZX.

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Correspondence to Zhaohui Xu.

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Communicated by L. Huang.

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Xu, Z., Han, D., Cao, J. et al. Cloning and characterization of the TneDI restriction–modification system of Thermotoga neapolitana . Extremophiles 15, 665 (2011). https://doi.org/10.1007/s00792-011-0397-9

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