GATC methylation by Dam methylase in archaea: Its roles and possible transcription regulation by an FFRP

Proceedings of the Japan Academy Series B: Physical and Biological Sciences

Volumn 81, Issue 7, 2005, Pages 278-290

  Koike, Hideaki ^a   Yokoyama, Katsushi ^a,b   Kawashima, Tsuyoshi ^a,b   Yamasaki, Tomoko ^a   Makino, Shin Ichi ^a,c   Clowney, Lester ^a,b   Suzuki, Masashi ^a  

^a NATIONAL INSTITUTE OF ADVANCED INDUSTRIAL SCIENCE AND TECHNOLOGY AIST   (Japan)

^b JAPAN SCIENCE AND TECHNOLOGY AGENCY   (Japan)

^c EHIME UNIVERSITY   (Japan)

Author keywords

DNA melting; DNA Methylation; DNA replication; Thermophiles; Transcription regulation

Indexed keywords

ARCHAEA; ESCHERICHIA COLI; PYROCOCCUS; PYROCOCCUS SP.;

EID: 33644589531     PISSN: 03862208     EISSN: None     Source Type: Journal    
DOI: 10.2183/pjab.81.278     Document Type: Article

References (77)

1. Dunn, D. B., and Smith, J. D. (1958) Biochem. J. 68, 627-636.
2. Marinus, M. G., and Morris, N. R. (1973) J. Bacteriol. 114, 1143-1150.
3. Marinus, M. G. (1987) Ann. Rev. Genet. 21, 113-131.
4. Messer, W., and Noyer-Weidner, M. (1988) Cell 54, 735-737.
5. Claverys, J. P., and Lacks, S. A. (1986) Microbiol. Rev. 50, 133-165.
6. Barras, F., and Marinus, M. G. (1989) Trends Genet. 5, 139-143.
7. Modrich, P. (1989) J. Biol. Chem. 264, 6597-6600.
8. Palmer, B. R., and Marinus, M. G. (1994) Gene 143, 1-12.
9. Crooke, E. (1995) Cell 82, 877-880.
10. Modrich, P., and Lahue, R. (1996) Ann. Rev. Biochem. 65, 101-133.
11. Messer, W., Bellekes, U., and Lother, H. (1985) EMBO J. 4, 1327-1332.
12. Smith, D. W., Garland, A. M., Herman, G., Enns, R. E., Baker, T. A., and Zyskind, J. W. (1985) EMBO J. 4, 1319-1326.
13. Barbeyron, T., Kean, K., and Forterre, P. (1984) J. Bacteriol. 160, 586-590.
14. Lodwick, D., Ross, H. N. M., Harris, J. E., Almond, J. W., and Grant, W. D. (1986) J. Gen. Microbiol. 132, 3055-3059.
15. Baranyi, U., Klein, R., Lubitz, W., Krüger, D. H., and Witte, A. (2000) Mol. Microbiol. 35, 1168-1179.
16. Kawashima, T., Yamamoto, Y., Aramaki, H., Nunoshiba, T., Kawamoto, T., Watanabe, K., Yamazaki, M., Kanehori, K., Amano, N., Ohya, Y. et al. (1999) Proc. Jpn. Acad. Ser. B 75, 213-218.
17. Kawashima, T., Amano, N., Koike, H., Makino, S., Higuchi, S., Kawashima-Ohya, Y., Watanabe, K., Yamazaki, M., Kanehori, K,. Kawamoto, T. et al. (2000) Proc. Natl. Acad. Sci. USA 97, 14257-14262.
18. Ruepp, A., Graml, W., Santos-Martinez, M.-L., Koretke, K. K., Volker, C., Mewes, H. W., Frishman, D., Stocker, S., Lupas, A. N., and Baumeister, W. (2000) Nature 407, 508-513.
19. Fazakerley, G. V., Téoule, R., Guy, A., Fritzsche, H., and Guschlbauer, W. (1985) Biochemistry 24, 4540-4548.
20. Engel, J. D., and Von Hippel, P. H. (1974) Biochemistry 13, 4143-4158.
21. Engel, J. D., and Von Hippel, P. H. (1978) J. Biol. Chem. 253, 927-934.
22. Yamasaki, T., Yamasaki, K., and Suzuki, M. (1998) Proc. Jpn. Acad. Ser. B 74, 210-215.
23. Gómez-Eichelmann, M. C. (1979) J. Bacteriol. 140, 574-579.
24. Kawarabayasi, Y., Sawada, M., Horikawa, H., Haikawa, Y., Hino, Y., Yamamoto, S., Sekine, M., Baba, S., Kosugi, H., Hosoyama, A. et al. (1998) DNA Res. 5, 55-76.
25. Maeder, D. L., Weiss, R. B., Dunn, D. M., Cherry, J. L., Gonzalez, J. M., DiRuggeiero, J., and Robb, F. T. (1999) Genetics 152, 1299-1305.
26. She, Q., Singh, R. K., Confalonieri, F., Zivanovic, Y., Allard, G., Awayez, M. J., Chan-Weiher, C. C.-Y., Clausen, I. G., Curtis, B. A., Moors, A. D. et al. (2001) Proc. Natl. Acad. Sci. USA 98, 7835-7840.
27. Ng, W. V., Kennedy, S. P., Mahairas, G. G., Berquist, B., Pan, M., Shukla, H. D., Lasky, S. R., Baliga, N. S., Thorsson, V., Sbrogna, J. et al. (2000) Proc. Natl. Acad. Sci. USA 97, 12176-12181.
28. Malone, T., Blumenthal, R. M., and Cheng, X. (1995) J. Mol. Biol. 253, 618-632.
29. Yanisch-Perron, C., Vieira, J., and Messing, J. (1985) Gene 33, 103-119.
30. Roberts, R. J., Vincze, T., Posfai, J., and Macelis, D. (2003) Nucl. Acids Res. 31, 418-420.
31. Bult, C. J., White, O., Olsen, G. J., Zhou, L., Fleischmann, R. D., Sutton, G. G., Blake, J. A., FitzGerald, L. M., Clayton, R. A., Gocayne, J. D. et al. (1996) Science 273, 1058-1073.
32. Smith, D. R., Doucette-Stamm, L. A., Deloughery, C., Lee, H.-M., Dubois, J., Aldredge, T., Bashirzadeh, R., Blakely, D., Cook, R., Gilbert, K. et al. (1997) J. Bacteriol. 179, 7135-7155.
33. Klenk, H.-P., Clayton, R. A., Tomb, J.-F., White, O., Nelson, K. E., Ketchum, K., Dodson, R. J., Gwinn, M., Hickey, E. K., Peterson, J. D. et al. (1997) Nature 390, 364-370.
34. Kawarabayasi, Y., Hino, Y., Horikawa, H., Yamazaki, S., Haikawa, Y., Jin-no, K., Takahashi, M., Sekine, M., Baba, S., Ankai, A. et al. (1999) DNA Res. 6, 83-101.
35. Kawarabayasi, Y., Hino, Y., Horikawa, H., Jin-no, K., Takahashi, M., Sekine, M., Baba, S., Ankai, A., Kosugi, H., Hosoyama, A. et al. (2001) DNA Res. 8, 123-140.
36. Cohen, G. N., Barbe, V., Flament, D., Galperin, M., Heilig, R., Lecompte, O., Poch, O., Prieur, D., Querellou, J., Ripp, R. et al. (2003) Mol. Microbiol. 47, 1495-1512.
37. Mount, D. W. (2001) Bioinformatics: Sequence and Genome Analysis. Cold Spring Harbor Laboratory Press, New York.
38. Durban, R., Eddy, S., Krogh, A., and Mitchison, G. (1998) Biological sequence analysis. Cambridge University Press, Cambridge.
39. Fütterer, O., Angelov, A., Liesegang, H., Gottschalk, G., Schleper, C., Shepers, B., Dock, C., Antraniklian, G., and Liebl, W. (2004) Proc. Natl. Acad. Sci. USA 101, 9091-9096.
40. Hendrickson, E. L., Kaul, R., Zhou, Y., Bovee, D., Chapman, P., Chung, J., Conway de Macario, E., Dodsworth, J. A., Gillett, W., Graham, D. E. et al. (2004) J. Bacteriol. 186, 6965-6969.
41. Koike, H., Ishijima, S. A., Clowney, L., and Suzuki, M. (2004) Proc. Natl. Acad. Sci. USA 101, 2840-2845.
42. Suzuki, M. (2003) Proc. Jpn. Acad., Ser. B 79, 274-289.
43. Koike, H., Sakuma, M., Mikami, A., Amamo, N., and Suzuki, M. (2003) Proc. Jpn. Acad., Ser. B 79, 63-69.
44. Suzuki, M., Amano, N., and Koike, H. (2003) Proc. Jpn. Acad., Ser. B 79, 92-98.
45. Suzuki, M., and Koike, H. (2003) Proc. Jpn. Acad., Ser. B 79, 114-119.
46. Suzuki, M. (2003) Proc. Jpn. Acad., Ser. B 79, 213-222.
47. Suzuki, M., Koike, H., and Aramaki, H. (2003) Proc. Jpn. Acad., Ser. B 79, 242-247.
48. Ishijima, S. A., Clowney, L., Koike, H., and Suzuki, M. (2003) Proc. Jpn. Acad., Ser. B 79, 299-304.
49. Ishijima, S. A., Clowney, L., Koike, H., and Suzuki, M. (2004) Proc. Jpn. Acad., Ser. B 80, 22-27.
50. Ishijima, S. A., Clowney, L., Koike, H., and Suzuki, M. (2004) Proc. Jpn. Acad., Ser. B 80, 107-113.
51. Clowney, L., Ishijima, S. A., and Suzuki, M. (2004) Proc. Jpn. Acad., Ser. B 80, 148-155.
52. Ishijima, S. A., Clowney, L., and Suzuki, M. (2004) Proc. Jpn. Acad., Ser. B 80, 183-188.
53. Ishijima, S. A., Clowney, L., and Suzuki, M. (2004) Proc. Jpn. Acad., Ser. B 80, 236-243.
54. Ishijima, S. A., Clowney, L., and Suzuki, M. (2004) Proc. Jpn. Acad., Ser. B 80, 459-468.
55. Sakuma, M., Koike, H., and Suzuki, M. (2005) Proc. Jpn. Acad., Ser. B 81, 26-32.
56. Yokoyama, K., Ebihara, S., Kikuchi, T., and Suzuki, M. (2005) Proc. Jpn. Acad., Ser. B 81, 64-75.
57. Sakuma, M., Nakamura, M., Koike, H., and Suzuki, M. (2005) Proc. Jpn. Acad., Ser. B 81, 111-117.
58. Yokoyama, K., and Suzuki, M. (2005) Proc. Jpn. Acad., Ser. B 81, 64-75.
59. Kawashima, T., Yokoyama, K., Higuchi, S., and Suzuki, M. (2005) Proc. Jpn. Acad., Ser. B 81, 204-219.
60. Yokoyama, K., Ishijima, S. A., Clowney, L., Koike, H., Aramaki, H., Tanaka, C., Makino, K., and Suzuki, M. (2005) FEMS Microbiol. Review (in press).
61. Kudo, N., Allen, M. D., Koike, H., Katsuya, Y., and Suzuki, M. (2001) Acta Cryst. D57, 469-471.
62. Gui, Y., Wang, Q., Stormo, G. D., and Calvo, J. M. (1995) J. Bacteriol. 177, 4872-4880.
63. Ouhammouch, M., and Geiduschek, E. P. (2001) EMBO J. 20, 146-156.
64. Suzuki, M. (1993) EMBO J. 12, 3221-3226.
65. Suzuki, M. (1994) Structure 2, 317-326.
66. Suzuki, M., and Yagi, N. (1994) Proc. Natl. Acad. Sci. USA 91, 12357-12361.
67. Pearson, W. R., and Lipman, D. L. (1988) Proc. Natl. Acad. Sci. USA 85, 2444-2448.
68. Koike, H., Amano, N., Tateno, M., Ohfuku, Y., Suckow, J. M., and Suzuki, M. (1999) Proc. Jpn. Acad., Ser. B 75, 37-42.
69. Becker, R. A., Chambers, J. M., and Wilks, A. R. (1988) The New S Language. Chapman & Hall, London.
70. Higgins, D. G., Bleasby, A. J., and Fuchs, R. (1992) Comput. Appl. Biosci. 8, 189-191.
71. Ramakrishnan, V., and Adams, M. W. W. (1995) in Thermophiles (eds. Robb, F. T., and Place, A. R.) Cold Spring Harbor Laboratory Press, New York, USA., pp. 95-96.
72. Saiki, R. K., Gelfand, D. H., Stoffel, S., Scharf, S. J., Higuchi, R., Horn, G. T., Mullis, K. B., and Erlich, H. A. (1988) Science 239, 487-491.
73. Fukui, T., Atomi, H., Kanai, T., Matsumi, R., Fujiwara, S., and Imanaka, T. (2005) Genome Res. 15, 352-363.
74. Deppenmeier, U., Johann, A., Hartsch, T., Merkl, R., Schmitz, R. A., Martinez-Arias, R., Henne, A., Wiezer, A., Baumer, S., Jacobi, C. et al. (2002) J. Mol. Microb. Biotechnol. 4, 453-461.
75. Slesarev, A. I., Mezhevaya, K. V., Makarova, K. S., Polushin, N. N., Shcherbinina, O. V., Shakhova, V. V., Belova, G. I., Aravind, L., Natale, D. A., Rogozin, I. B. et al. (2002) Proc. Natl. Acad. Sci. USA 99, 4644-4649.
76. Baliga, N. S., Bonneau, R., Facciotti, M. T., Pan, M., Glusman, G., Deutsch, E. W., Shannon, P., Chiu, Y., Weng, R. S., Gan, R. R. et al. (2004) Genome Res. 14, 2221-2234.
77. Waters, E., Hohn, M. J., Ahel, I., Graham, D. E., Adams, M. D., Barnstead, M., Beeson, K. Y., Bibbs, L., Bolanos, R., Keller, M. et al. (2003) Proc. Natl. Acad. Sci. USA 100, 12984-12988.