The layered structure of human mitochondrial DNA nucleoids

Journal of Biological Chemistry

Volumn 283, Issue 6, 2008, Pages 3665-3675

  Bogenhagen, Daniel F ^a   Rousseau, Denis ^b   Burke, Stephanie ^a  

^a STONY BROOK UNIVERSITY   (United States)

^b CEA GRENOBLE   (France)

Author keywords

[No Author keywords available]

Indexed keywords

CHROMATOGRAPHIC ANALYSIS; DNA; GENES; MITOCHONDRIA; NUCLEIC ACIDS; ORGANIC ACIDS;

CENTRAL CORES; COMPLEX ASSEMBLIES; DNA STRUCTURES; IMMUNOAFFINITY CHROMATOGRAPHIES; IN CELLS; IN-VIVO; LAYERED STRUCTURES; METABOLIC PROTEINS; MITOCHONDRIAL DNAS; MITOCHONDRIAL DNAS (MTDNA); MITOCHONDRIAL MATRIXES; NUCLEOIDS; TERMINAL DOMAINS;

PROTEINS;

CELL PROTEIN; CHAPERONE; FORMALDEHYDE; MEMBRANE PROTEIN; MITOCHONDRIAL DNA; MITOCHONDRIAL PROTEIN; NUCLEOID PROTEIN; PROTEIN ATAD3; PROTEINASE; UNCLASSIFIED DRUG; CROSS LINKING REAGENT; DNA;

ARTICLE; CROSS LINKING; DNA REPLICATION; DNA STRUCTURE; DNA TRANSCRIPTION; HUMAN; HUMAN CELL; IMMUNOBLOTTING; IMMUNOFLUORESCENCE; NUCLEOTIDE SEQUENCE; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN DNA BINDING; PROTEIN FUNCTION; UNINDEXED SEQUENCE; BIOLOGICAL MODEL; CELL NUCLEUS; CHEMISTRY; CHROMATOGRAPHY; CYTOPLASM; FLUORESCENCE MICROSCOPY; HELA CELL; METABOLISM; METHODOLOGY; MITOCHONDRION; POLYACRYLAMIDE GEL ELECTROPHORESIS; PROTEIN TERTIARY STRUCTURE;

CELL NUCLEUS; CHROMATOGRAPHY; CROSS-LINKING REAGENTS; CYTOPLASM; DNA; DNA, MITOCHONDRIAL; ELECTROPHORESIS, POLYACRYLAMIDE GEL; HELA CELLS; HUMANS; MICROSCOPY, FLUORESCENCE; MITOCHONDRIA; MITOCHONDRIAL PROTEINS; MODELS, BIOLOGICAL; PROTEIN STRUCTURE, TERTIARY;

EID: 41249098355     PISSN: 00219258     EISSN: 1083351X     Source Type: Journal    
DOI: 10.1074/jbc.M708444200     Document Type: Article

References (73)

1. Chen, X. J., and Butow, R. A. (2005) Nat. Rev. Genet. 6, 815-825
2. Malka, F., Lombes, A., and Rojo, M. (2006) Biochim. Biophys. Acta 1763, 463-472
3. Kucej, M., and Butow, R. A. (2007) Trends Cell Biol. 17, 586-592
4. Laipis, P., Walle, M. V. D., and Hauswirth, W. (1988) Proc. Natl. Acad. Sci. U. S. A. 85, 8107-8110
5. Marchington, D., Macaulay, V., Hartshorne, G., Barlow, D., and Poulton, J. (1998) Am. J. Hum. Gen. 63, 769-775
6. Cao, L., Shitara, H., Horii, T., Nagao, Y., Imai, H., Abe, K., Hara, T., Hayashi, J.-I., and Yonekawa, H. (2007) Nat. Genet. 39, 386-390
7. Chen, H., Chomyn, A., and Chan, D. C. (2005) J. Biol. Chem. 280, 26185-26192
8. Chen, H., McCaffery, J. M., and Chan, D. C. (2007) Cell 130, 548-562
9. Iborra, F., Kimura, H., and Cook, P. (2004) BMC Biol. 2, 9
10. Woldringh, C. L. (2002) Mol. Microbiol. 45, 17-29
11. Nass, M. (1969) Science 165, 25-35
12. Albring, M., Griffith, J., and Attardi, G. (1977) Proc. Natl. Acad. Sci. U. S. A. 74, 1348-1352
13. Kaufman, B. A., Durisic, N., Mativetsky, J. M., Costantino, S., Hancock, M. A., Grutter, P., and Shoubridge, E. A. (2007) Mol. Biol. Cell 18, 3225-3236
14. Alam, T. I., Kanki, T., Muta, T., Ukaji, K., Abe, Y., Nakayama, H., Takio, K., Hamasaki, N., and Kang, D. (2003) Nucleic Acids Res. 31, 1640-1645
15. Wiesner, R. J., Zsurka, G., and Kunz, W. S. (2006) Free Radical Res. 40, 1284-1294
16. Cotney, J., Wang, Z., and Shadel, G. S. (2007) Nucleic Acids Res. 35, 4042-4054
17. Shen, E. L., and Bogenhagen, D. F. (2001) Nucleic Acids Res. 29, 2822-2828
18. Wang, Y., and Bogenhagen, D. F. (2006) J. Biol. Chem. 281, 25791-25802
19. Kaufman, B., Newman, S., Hallberg, R., Slaughter, C., Perlman, P., and Butow, R. (2000) Proc. Natl. Acad. Sci. U. S. A. 97, 7772-7777
20. Orlando, V. (2000) Trends Biochem. Sci. 25, 99-104
21. He, J., Mao, C.-C., Reyes, A., Sembongi, H., Di Re, M., Granycome, C., Clippingdale, A. B., Fearnley, I. M., Harbour, M., Robinson, A. J., Reichelt, S., Spelbrink, J. N., Walker, J. E., and Holt, I. J. (2007) J. Cell Biol. 176, 141-146
22. Bogenhagen, D. F., Wang, Y., Shen, E. L., and Kobayashi, R. (2003) Mol. Cell Proteomics 2, 1205-1216
23. Morrissey, J. (1981) Anal. Biochem. 117, 307-310
24. Attardi, G., and Schatz, G. (1988) Annu. Rev. Cell Biol. 4, 289-333
25. Lu, B., Yadav, S., Shah, P. G., Liu, T., Tian, B., Pukszta, S., Villaluna, N., Kutejova, E., Newlon, C. S., Herzog, J. H., and Suzuki, C. K. (2007) J. Biol. Chem. 282, 17363-17374
26. Cheng, X., Kanki, T., Fukuoh, A., Ohgaki, K., Takeya, R., Aoki, Y., Hamasaki, N., and Kang, D. (2005) J. Biochem. (Tokyo) 138, 673-678
27. Liu, L., Rodriguez-Belmonte, E. M., Mazloum, N., Xie, B., and Lee, M. Y. W. T. (2003) J. Biol. Chem. 278, 10041-10047
28. Xie, B., Li, H., Wang, Q., Xie, S., Rahmeh, A., Dai, W., and Lee, M. Y. W. T. (2005) J. Biol. Chem. 280, 22375-22384
29. Arakaki, N., Nishihama, T., Kohda, A., Owaki, H., Kuramoto, Y., Abe, R., Kita, T., Suenaga, M., Himeda, T., Kuwajima, M., Shibata, H., and Higuti, T. (2006) Biochim. Biophys. Acta 1760, 1364-1372
30. Da Cruz, S., Xenarios, I., Langridge, J., Vilbois, F., Parone, P. A., and Martinou, J.-C. (2003) J. Biol. Chem. 278, 41566-41571
31. Schaffrik, M., Mack, B., Matthias, C., Rauch, J., and Gires, O. (2006) Cell Mol. Life Sci. 63, 2162-2174
32. Lee, D. G., and Bell, S. P. (2000) Curr. Biol. 12, 280-285
33. Neuwald, A. F. (2005) Nucleic Acids Res. 33, 3614-3628
34. Park, C. B., Asin-Cayuela, J., Camara, Y., Shi, Y., Pellegrini, M., Gaspari, M., Wibom, R., Hultenby, K., Erdjument-Bromage, H., Tempst, P., Falkenberg, M., Gustafsson, C. M., and Larsson, N.-G. (2007) Cell 130, 273-285
35. Perez-Jannotti, R. M., Klein, S. M., and Bogenhagen, D. F. (2001) J. Biol. Chem. 276, 48978-48987
36. Lakshmipathy, U., and Campbell, C. (1999) Mol. Cell Biol. 19, 3869-3876
37. Cerritelli, S. M., Frolova, E. G., Feng, C., Grinberg, A., Love, P. E., and Crouch, R. J. (2003) Mol. Cell 11, 807-815
38. Schwerzmann, K., Cruz-Orive, L., Eggman, R., Sanger, A., and Weibel, E. (1986) J. Cell Biol. 102, 97-103
39. Tzagoloff, A. (1982) Mitochondria, p. 211, Plenum Publishing Corp., New York
40. Solomon, M. J., and Varshavsky, A. (1985) Proc. Natl. Acad. Sci. U. S. A. 82, 6470-6474
41. Kurdistani, S. K., and Grunstein, M. (2003) Methods 31, 90-95
42. Wells, J., and Farnham, P. J. (2002) Methods 26, 48-56
43. Crompton, M. (1999) Biochem. J. 341, 233-249
44. Fu, G. K., and Markovitz, D. M. (1998) Biochemistry 37, 1905-1909
45. Liu, T., Lu, B., Lee, I., Ondrovicova, G., Kutejova, E., and Suzuki, C. K. (2004) J. Biol. Chem. 279, 13902-13910
46. Adams, D. J., Beveridge, D. J., van der Weyden, L., Mangs, H., Leedman, P. J., and Morris, B. J. (2003) J. Biol. Chem. 278, 44894-44903
47. Chen, X. J., Wang, X., Kaufman, B. A., and Butow, R. A. (2005) Science 307, 714-717
48. Chen, X. J., Wang, X., and Butow, R. A. (2007) Proc. Natl. Acad. Sci. U. S. A. 104, 13738-13743
49. Zelenaya-Troitskaya, O., Perlman, P. S., and Butow, R. A. (1995) EMBO J. 14, 3268-3276
50. Bateman, J. M., Iacovino, M., Perlman, P. S., and Butow, R. A. (2002) J. Biol. Chem. 277, 47946-47953
51. Davis, A., and Clayton, D. (1996) J. Cell Biol. 135, 883-893
52. Magnusson, J., Orth, M., Lestienne, P., and Taanman, J.-W. (2003) Exp. Cell Res. 289, 133-142
53. Bogenhagen, D., and Clayton, D. (1977) Cell 11, 719-727
54. Gelfand, R., and Attardi, G. (1981) Mol. Cell Biol. 1, 497-511
55. Cantatore, P., Flagella, Z., Fracasso, F., Lezza, A. M. S., Gadaleta, M. N., and de Montalvo, A. (1987) FEBS Lett. 213, 144-148
56. Partikian, A., Olveczky, B., Swaminathan, R., Li, Y., and Verkman, A. S. (1998) J. Cell Biol. 140, 821-829
57. Wang, Z., Cotney, J., and Shadel, G. S. (2007) J. Biol. Chem. 282, 12610-12618
58. Mootha, V. K., Lepage, P., Miller, K., Bunkenborg, J., Reich, M., Hjerrild, M., Delmonte, T., Villeneuve, A., Sladek, R., Xu, F., Mitchell, G. A., Morin, C., Mann, M., Hudson, T. J., Robinson, B., Rioux, J. D., and Lander, E. S. (2003) Proc. Natl. Acad. Sci. U. S. A. 100, 605-610
59. Xu, F., Morin, C., Mitchell, G., Ackerley, C., and Robinson, B. H. (2004) Biochem. J. 382, 331-336
60. Mili, S., and Pinol-Roma, S. (2003) Mol. Cell Biol. 23, 4972-4982
61. Holt, I. J., He, J., Mao, C.-C., Kirk-up, J. D. B., Martinsson, P., Sembongi, H., Reyes, A., and Spelbrink, J. N. (2007) Mitochondrion 7, 311-321
62. Capaldi, R. A., Aggeler, R., Gilkerson, R., Hanson, G., Knowles, M., Marcus, A., Margineantu, D., Marusich, M., Murray, J., Oglesbee, D., Remington, S. J., and Rossignol, R. (2002) Biochim. Biophys. Acta 1555, 192-195
63. Liu, M., and Spremulli, L. (2000) J. Biol. Chem. 275, 29400-29406
64. Hatefi, Y. (1985) Annu. Rev. Biochem. 54, 1015-1069
65. Lynch, A. S., and Wang, J. C. (1993) J. Bacteriol. 175, 1645-1655
66. Bryan, A. C., Rodeheffer, M. S., Wearn, C. M., and Shadel, G. S. (2002) Genetics 160, 75-82
67. Falkenberg, M., Gaspari, M., Rantanen, A., Trifunovic, A., Larsson, N.-G., and Gustafsson, C. M. (2002) Nat. Genet. 31, 289-294
68. McCulloch, V., Seidel-Rogol, B. L., and Shadel, G. S. (2002) Mol. Cell Biol. 22, 1116-1125
69. Fernandez-Silva, P., Martinez-Azorin, F., Micol, V., and Attardi, G. (1997) EMBO J. 16, 1066-1079
70. Garrido, N., Griparic, L., Jokitalo, E., Wartiovaara, J., van der Bliek, A. M., and Spelbrink, J. N. (2003) Mol. Biol. Cell 14, 1583-1596
71. Valgardsdottir, R., Brede, G., Eide, L. G., Frengen, E., and Prydz, H. (2001) J. Biol. Chem. 276, 32056-32063
72. Zhang, H., Barcelo, J. M., Lee, B., Kohlhagen, G., Zimonjic, D. B., Popescu, N. C., and Pommier, Y. (2001) Proc. Natl. Acad. Sci. U. S. A. 98, 10608-10613
73. Whitford, T. A. (1993) Isolation and cDNA Cloning of a Xenopus Mitochondrial Serine Hydroxymethyltransferase Which Binds to ssDNA. Ph.D. thesis, State University of New York at Stony Brook