A putative mobile genetic element carrying a novel type IIF restriction-modification system (PluTI)

Nucleic Acids Research

Volumn 38, Issue 9, 2010, Pages 3019-3030

  Khan, Feroz ^a,b   Furuta, Yoshikazu ^a,b   Kawai, Mikihiko ^a,c   Kaminska, Katarzyna H ^d   Ishikawa, Ken ^a,b   Bujnicki, Janusz M ^a,d,e   Kobayashi, Ichizo ^a,b  

^a Graduate School of Frontier Sciences   (Japan)

^b UNIVERSITY OF TOKYO   (Japan)

^c NATIONAL INSTITUTE FOR BASIC BIOLOGY   (Japan)

^d INTERNATIONAL INSTITUTE OF MOLECULAR AND CELL BIOLOGY   (Poland)

^e ADAM MICKIEWICZ UNIVERSITY   (Poland)

Author keywords

[No Author keywords available]

Indexed keywords

PROTEIN R.PLUTI; RESTRICTION ENDONUCLEASE; UNCLASSIFIED DRUG; DNA METHYLTRANSFERASE; TYPE II SITE SPECIFIC DEOXYRIBONUCLEASE;

AMINO ACID SEQUENCE; ARTICLE; BACTERIAL GENETICS; CELL FREE SYSTEM; CONTROLLED STUDY; ENZYME ACTIVITY; ENZYME ANALYSIS; ENZYME DEGRADATION; ENZYME MODIFICATION; ESCHERICHIA COLI; GENE INSERTION SEQUENCE; GENOME ANALYSIS; GENOME SIZE; IN VITRO STUDY; IN VIVO STUDY; MOLECULAR RECOGNITION; NONHUMAN; NUCLEOTIDE SEQUENCE; OPEN READING FRAME; PHOTORHABDUS LUMINESCENS; PRIORITY JOURNAL; PROTEIN EXPRESSION; SEQUENCE HOMOLOGY; BACTERIAL GENOME; CHEMISTRY; DNA CLEAVAGE; ENZYMOLOGY; GENETICS; INTERSPERSED REPEAT; KINETICS; METABOLISM; MOLECULAR GENETICS; NUCLEOTIDE REPEAT; PHOTORHABDUS;

BACTERIA (MICROORGANISMS); ESCHERICHIA COLI; PHOTORHABDUS LUMINESCENS;

AMINO ACID SEQUENCE; DEOXYRIBONUCLEASES, TYPE II SITE-SPECIFIC; DNA CLEAVAGE; DNA MODIFICATION METHYLASES; GENOME, BACTERIAL; INTERSPERSED REPETITIVE SEQUENCES; KINETICS; MOLECULAR SEQUENCE DATA; PHOTORHABDUS; REPETITIVE SEQUENCES, NUCLEIC ACID; SEQUENCE HOMOLOGY, AMINO ACID;

EID: 77953268817     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkp1221     Document Type: Article

References (56)

1. Roberts, R.J., Vincze, T., Posfai, J. and Macelis, D. (2009) REBASE-a database for DNA restriction and modification: enzymes, genes and genomes. Nucleic Acids Res., 38, D234-D236.
2. Kobayashi, I. (2004) Restriction-modification systems as minimal forms of life. In Pingoud, A. (ed.), Restriction Endonucleases. Springer, Berlin, pp. 19-62.
3. van Zyl, L.J., Deane, S.M., Louw, L.A. and Rawlings, D.E. (2008) Presence of a family of plasmids (29 to 65 kilobases) with a 26-kilobase common region in different strains of the sulfur-oxidizing bacterium Acidithiobacillus caldus. Appl. Environ. Microbiol., 74, 4300-4308.
4. Stiens, M., Becker, A., Bekel, T., Godde, V., Goesmann, A., Niehaus, K., Schneiker-Bekel, S., Selbitschka, W., Weidner, S., Schluter, A. et al. (2008) Comparative genomic hybridisation and ultrafast pyrosequencing revealed remarkable differences between the Sinorhizobium meliloti genomes of the model strain Rm1021 and the field isolate SM11. J. Biotechnol., 136, 31-37.
5. Furuta, Y., Abe, K. and Kobayashi, I. (2010) Genome comparison and context analysis reveals putative mobile forms of restriction-modification systems and related rearrangements. Nucleic Acids Res., doi:10.1093/nar/gkp1226.
6. Nobusato, A., Uchiyama, I., Ohashi, S. and Kobayashi, I. (2000) Insertion with long target duplication: a mechanism for gene mobility suggested from comparison of two related bacterial genomes. Gene, 259, 99-108.
7. Kobayashi, I. (2001) Behavior of restriction-modification systems as selfish mobile elements and their impact on genome evolution. Nucleic Acids Res., 29, 3742-3756.
8. Naito, T., Kusano, K. and Kobayashi, I. (1995) Selfish behavior of restriction-modification systems. Science, 267, 897-899.
9. Orlowski, J. and Bujnicki, J.M. (2008) Structural and evolutionary classification of Type II restriction enzymes based on theoretical and experimental analyses. Nucleic Acids Res., 36, 3552-3569.
10. Roberts, R.J., Belfort, M., Bestor, T., Bhagwat, A.S., Bickle, T.A., Bitinaite, J., Blumenthal, R.M., Degtyarev, S.K., Dryden, D.T.F., Dybvig, K. et al. (2003) A nomenclature for restriction enzymes, DNA methyltransferases, homing endonucleases and their genes. Nucleic Acids Res., 31, 1805-1812.
11. Pingoud, A., Fuxreiter, M., Pingoud, V. and Wende, W. (2005) Type II restriction endonucleases: structure and mechanism. Cell Mol. Life Sci., 62, 685-707.
12. Asakura, Y. and Kobayashi, I. (2009) From damaged genome to cell surface: transcriptome changes during bacterial cell death triggered by loss of a restriction-modification gene complex. Nucleic Acids Res., 37, 3021-3031.
13. Mucke, M., Kruger, D.H. and Reuter, M. (2003) Diversity of type II restriction endonucleases that require two DNA recognition sites. Nucleic Acids Res., 31, 6079-6084.
14. Deibert, M., Grazulis, S., Sasnauskas, G., Siksnys, V. and Huber, R. (2000) Structure of the tetrameric restriction endonuclease NgoMIV in complex with cleaved DNA. Nat. Struct. Biol., 7, 792-799.
15. Bozic, D., Grazulis, S., Siksnys, V. and Huber, R. (1996) Crystal structure of Citrobacter freundii restriction endonuclease Cfr10I at 2.15 A resolution. J. Mol. Biol., 255, 176-186.
16. Grazulis, S., Deibert, M., Rimseliene, R., Skirgaila, R., Sasnauskas, G., Lagunavicius, A., Repin, V., Urbanke, C., Huber, R. and Siksnys, V. (2002) Crystal structure of the Bse634I restriction endonuclease: comparison of two enzymes recognizing the same DNA sequence. Nucleic Acids Res., 30, 876-885.
17. Siksnys, V., Skirgaila, R., Sasnauskas, G., Urbanke, C., Cherny, D., Grazulis, S. and Huber, R. (1999) The Cfr10I restriction enzyme is functional as a tetramer. J. Mol. Biol., 291, 1105-1118.
18. Wentzell, L.M. and Halford, S.E. (1998) DNA looping by the Sfi I restriction endonuclease. J. Mol. Biol., 281, 433-444.
19. Embleton, M.L., Siksnys, V. and Halford, S.E. (2001) DNA cleavage reactions by type II restriction enzymes that require two copies of their recognition sites. J. Mol. Biol., 311, 503-514.
20. Gowers, D.M., Bellamy, S.R. and Halford, S.E. (2004) One recognition sequence, seven restriction enzymes, five reaction mechanisms. Nucleic Acids Res., 32, 3469-3479.
21. Sokolowska, M., Czapinska, H. and Bochtler, M. (2009) Crystal structure of the ββα-Me type II restriction endonuclease Hpy99I with target DNA. Nucleic Acids Res., 37, 3799-3810.
22. Ishikawa, K., Watanabe, M., Kuroita, T., Uchiyama, I., Bujnicki, J.M., Kawakami, B., Tanokura, M. and 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, e112.
23. Chinen, A., Uchiyama, I. and Kobayashi, I. (2000) Comparison between Pyrococcus horikoshii and Pyrococcus abyssi genome sequences reveals linkage of restriction-modification genes with large genome polymorphisms. Gene, 259, 109-121.
24. Miyazono, K., Watanabe, M., Kosinski, J., Ishikawa, K., Kamo, M., Sawasaki, T., Nagata, K., Bujnicki, J.M., Endo, Y., Tanokura, M. et al. (2007) Novel protein fold discovered in the PabI family of restriction enzymes. Nucleic Acids Res., 35, 1908-1918.
25. Yanisch-Perron, C., Vieira, J. and Messing, J. (1985) Improved M13 phage cloning vectors and host strains: nucleotide sequences of the M13mp18 and pUC19 vectors. Gene, 33, 103-119.
26. Duchaud, E., Rusniok, C., Frangeul, L., Buchrieser, C., Givaudan, A., Taourit, S., Bocs, S., Boursaux-Eude, C., Chandler, M., Charles, J.F. et al. (2003) The genome sequence of the entomopathogenic bacterium Photorhabdus luminescens. Nat. Biotechnol., 21, 1307-1313.
27. Guzman, L.M., Belin, D., Carson, M.J. and Beckwith, J. (1995) Tight regulation, modulation, and high-level expression by vectors containing the arabinose PBAD promoter. J. Bacteriol., 177, 4121-4130.
28. Sawasaki, T., Ogasawara, T., Morishita, R. and Endo, Y. (2002) A cell-free protein synthesis system for high-throughput proteomics. Proc. Natl Acad. Sci. USA, 99, 14652-14657.
29. Altschul, S.F., Madden, T.L., Schaffer, A.A., Zhang, J., Zhang, Z., Miller, W. and Lipman, D.J. (1997) Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res., 25, 3389-3402.
30. Soding, J. (2005) Protein homology detection by HMM-HMM comparison. Bioinformatics, 21, 951-960.
31. Kurowski, M.A. and Bujnicki, J.M. (2003) GeneSilico protein structure prediction meta-server. Nucleic Acids Res., 31, 3305-3307.
32. Komori, K., Fujita, N., Ichiyanagi, K., Shinagawa, H., Morikawa, K. and Ishino, Y. (1999) PI-PfuI and PI-PfuII, intein-coded homing endonucleases from Pyrococcus furiosus. I. Purification and identification of the homing-type endonuclease activities. Nucleic Acids Res., 27, 4167-4174.
33. Williamson, V.M. and Kaya, H.K. (2003) Sequence of a symbiont. Nat. Biotechnol., 21, 1294-1295.
34. Kanehisa, M. and Goto, S. (2000) KEGG: kyoto encyclopedia of genes and genomes. Nucleic Acids Res., 28, 27-30.
35. Yu, W., Mierau, I., Mars, A., Johnson, E., Dunny, G. and McKay, L.L. (1995) Novel insertion sequence-like element IS982 in lactococci. Plasmid, 33, 218-225.
36. Gingeras, T.R., MIlazzo, J.P. and Roberts, R.J. (1978) A computer assisted method for the determination of restriction enzyme recognifion sites. Nucleic Acids Res., 5, 4105-4127.
37. Taylor, J.D. and Halford, S.E. (1992) The activity of the EcoRV restriction endonuclease is influenced by flanking DNA sequences both inside and outside the DNA-protein complex. Biochemistry, 31, 90-97.
38. Wentzell, L.M., Nobbs, T.J. and Halford, S.E. (1995) The SfiI restriction endonuclease makes a four-strand DNA break at two copies of its recognition sequence. J. Mol. Biol., 248, 581-595.
39. Gormley, N.A., Hillberg, A.L. and Halford, S.E. (2002) The type IIs restriction endonuclease BspMI is a tetramer that acts concertedly at two copies of an asymmetric DNA sequence. J. Biol. Chem., 277, 4034-4041.
40. Oller, A.R., Vanden Broek, W., Conrad, M. and Topal, M.D. (1991) Ability of DNA and spermidine to affect the activity of restriction endonucleases from several bacterial species. Biochemistry, 30, 2543-2549.
41. Zebala, J.A., Choi, J. and Barany, F. (1992) Characterization of steady state, single-turnover, and binding kinetics of the TaqI restriction endonuclease. J. Biol. Chem., 267, 8097-8105.
42. Kaminska, K.H., Kawai, M., Boniecki, M., Kobayashi, I. and Bujnicki, J.M. (2008) Type II restriction endonuclease R.Hpy188I belongs to the GIY-YIG nuclease superfamily, but exhibits an unusual active site. BMC Struct. Biol., 8, 48.
43. Saravanan, M., Bujnicki, J.M., Cymerman, I.A., Rao, D.N. and Nagaraja, V. (2004) Type II restriction endonuclease R.KpnI is a member of the HNH nuclease superfamily. Nucleic Acids Res., 32, 6129-6135.
44. Bujnicki, J.M. and Rychlewski, L. (2001) Grouping together highly diverged PD-(D/E)XK nucleases and identification of novel superfamily members using structure-guided alignment of sequence profiles. J. Mol. Microbiol. Biotechnol., 3, 69-72.
45. Sapranauskas, R., Sasnauskas, G., Lagunavicius, A., Vilkaitis, G., Lubys, A. and Siksnys, V. (2000) Novel subtype of type IIs restriction enzymes. BfiI endonuclease exhibits similarities to the EDTA-resistant nuclease Nuc of Salmonella typhimurium. J. Biol. Chem., 275, 30878-30885.
46. Hwang, S., Gou, Z. and Kuznetsov, I.B. (2007) DP-Bind: a web server for sequence-based prediction of DNA-binding residues in DNA-binding proteins. Bioinformatics, 23, 634-636.
47. Wang, L. and Brown, S.J. (2006) BindN: a web-based tool for efficient prediction of DNA and RNA binding sites in amino acid sequences. Nucleic Acids Res., 34, W243-W248.
48. Marchler-Bauer, A., Anderson, J.B., Chitsaz, F., Derbyshire, M.K., DeWeese-Scott, C., Fong, J.H., Geer, L.Y., Geer, R.C., Gonzales, N.R., Gwadz, M. et al. (2009) CDD: specific functional annotation with the Conserved Domain Database. Nucleic Acids Res., 37, D205-D210.
49. Koonin, E.V. and Gorbalenya, A.E. (1992) The superfamily of UvrA-related ATPases includes three more subunits of putative ATP-dependent nucleases. Protein Seq. Data Anal., 5, 43-45.
50. Myung, H. and Calendar, R. (1995) The old exonuclease of bacteriophage P2. J. Bacteriol., 177, 497-501.
51. Heffron, F., McCarthy, B.J., Ohtsubo, H. and Ohtsubo, E. (1979) DNA sequence analysis of the transposon Tn3: three genes and three sites involved in transposition of Tn3. Cell, 18, 1153-1163.
52. Radnedge, L., Davis, M.A., Youngren, B. and Austin, S.J. (1997) Plasmid maintenance functions of the large virulence plasmid of Shigella flexneri. J. Bacteriol., 179, 3670-3675.
53. Zhang, Y., Zhang, J., Hoeflich, K.P., Ikura, M., Qing, G. and Inouye, M. (2003) MazF cleaves cellular mRNAs specifically at ACA to block protein synthesis in Escherichia coli. Mol. Cell, 12, 913-923.
54. Bujnicki, J.M. (2003) Crystallographic and bioinformatic studies on restriction endonucleases: inference of evolutionary relationships in the "midnight zone" of homology. Curr. Protein Pept. Sci., 4, 327-337.
55. Kosinski, J., Feder, M. and Bujnicki, J.M. (2005) The PD-(D/E)XK superfamily revisited: identification of new members among proteins involved in DNA metabolism and functional predictions for domains of (hitherto) unknown function. BMC Bioinformatics, 6, 172.
56. Pei, J. and Grishin, N.V. (2007) PROMALS: towards accurate multiple sequence alignments of distantly related proteins. Bioinformatics, 23, 802-808.