Identification of multiple rate-limiting steps during the human mitochondrial transcription cycle in vitro

Journal of Biological Chemistry

Volumn 285, Issue 21, 2010, Pages 16387-16402

  Lodeiro, Maria F ^a   Uchida, Akira U ^a   Arnold, Jamie J ^a   Reynolds, Shelley L ^a   Moustafa, Ibrahim M ^a   Cameron, Craig E ^a  

^a PENNSYLVANIA STATE UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BIOCHEMICAL PATHWAY; COMPLEX FORMATIONS; CONCENTRATION OF; DINUCLEOTIDES; DNA OLIGONUCLEOTIDES; ELONGATION COMPLEX; HUMAN MITOCHONDRIA; IN-VITRO; MITOCHONDRIAL TRANSCRIPTION; MULTISUBUNIT; PHOSPHODIESTER BONDS; PROTEIN COMPONENTS; RATE-LIMITING STEPS; RNA POLYMERASE; TRANSCRIPTION INITIATION;

COMPLEXATION; ESCHERICHIA COLI; FUNCTIONAL POLYMERS; MACHINERY; OLIGONUCLEOTIDES; REACTION KINETICS; RNA; TRANSCRIPTION FACTORS;

TRANSCRIPTION;

DINUCLEOTIDE; DNA; OLIGONUCLEOTIDE; RECOMBINANT PROTEIN; RNA POLYMERASE; TRANSCRIPTION FACTOR;

ARTICLE; COMPLEX FORMATION; ESCHERICHIA COLI; GENETIC TRANSCRIPTION; HUMAN; IN VITRO STUDY; MITOCHONDRION; NONHUMAN; NUCLEOTIDE SEQUENCE; PLASMID; POLYACRYLAMIDE GEL ELECTROPHORESIS; PRIORITY JOURNAL; PROMOTER REGION; PROTEIN FUNCTION; PROTEIN INTERACTION; PROTEIN STRUCTURE; TRANSCRIPTION INITIATION; TRANSCRIPTION REGULATION;

CELL-FREE SYSTEM; DNA, MITOCHONDRIAL; DNA-BINDING PROTEINS; DNA-DIRECTED RNA POLYMERASES; ESCHERICHIA COLI; HUMANS; METHYLTRANSFERASES; MITOCHONDRIAL PROTEINS; MULTIPROTEIN COMPLEXES; PROMOTER REGIONS, GENETIC; RECOMBINANT PROTEINS; TRANSCRIPTION FACTORS; TRANSCRIPTION, GENETIC;

ESCHERICHIA COLI;

EID: 77952329046     PISSN: 00219258     EISSN: 1083351X     Source Type: Journal    
DOI: 10.1074/jbc.M109.092676     Document Type: Article

References (77)

1. Wallace, D. C. (2005) Annu. Rev. Genet. 39, 359-407
2. Wallace, D. C. (2008) Genetics 179, 727-735
3. Wallace, D. C. (2007) Annu. Rev. Biochem. 76, 781-821
4. Shadel, G. S. (2004) Trends Genet. 20, 513-519
5. DiMauro, S., and Schon, E. A. (2008) Annu. Rev. Neurosci. 31, 91-123
6. Schon, E. A., and DiMauro, S. (2007) Novartis Found Symp. 287, 214-233
7. Chan, S. S., and Copeland, W. C. (2009) Biochim. Biophys. Acta 1787, 312-319
8. Copeland, W. C. (2008) Annu. Rev. Med. 59, 131-146
9. Larsson, N. G., and Clayton, D. A. (1995) Annu. Rev. Genet. 29, 151-178
10. Clayton, D. A. (2000) Hum. Reprod. 15, Suppl. 2, 11-17
11. Bonawitz, N. D., Clayton, D. A., and Shadel, G. S. (2006) Mol. Cell 24, 813-825
12. Falkenberg, M., Larsson, N. G., and Gustafsson, C. M. (2007) Annu. Rev. Biochem. 76, 679-699
13. Martin, M., Cho, J., Cesare, A. J., Griffith, J. D., and Attardi, G. (2005) Cell 123, 1227-1240
14. Pham, X. H., Farge, G., Shi, Y., Gaspari, M., Gustafsson, C. M., and Falkenberg, M. (2006) J. Biol. Chem. 281, 24647-24652
15. Rodeheffer, M. S., Boone, B. E., Bryan, A. C., and Shadel, G. S. (2001) J. Biol. Chem. 276, 8616-8622
16. Parisi, M. A., and Clayton, D. A. (1991) Science 252, 965-969
17. Thomas, J. O., and Travers, A. A. (2001) Trends Biochem. Sci. 26, 167-174
18. Fisher, R. P., Parisi, M. A., and Clayton, D. A. (1989) Genes Dev. 3, 2202-2217
19. Larsson, N. G., Oldfors, A., Holme, E., and Clayton, D. A. (1994) Biochem. Biophys. Res. Commun. 200, 1374-1381
20. Ekstrand, M. I., Falkenberg, M., Rantanen, A., Park, C. B., Gaspari, M., Hultenby, K., Rustin, P., Gustafsson, C. M., and Larsson, N. G. (2004) Hum. Mol. Genet. 13, 935-944
21. Falkenberg, M., Gaspari, M., Rantanen, A., Trifunovic, A., Larsson, N. G., and Gustafsson, C. M. (2002) Nat. Genet. 31, 289-294
22. McCulloch, V., Seidel-Rogol, B. L., and Shadel, G. S. (2002) Mol. Cell. Biol. 22, 1116-1125
23. Adán, C., Matsushima, Y., Hernández-Sierra, R., Marco-Ferreres, R., Fernández-Moreno, M. A., González-Vioque, E., Calleja, M., Aragón, J. J., Kaguni, L. S., and Garesse, R. (2008) J. Biol. Chem. 283, 12333-12342
24. Matsushima, Y., Adán, C., Garesse, R., and Kaguni, L. S. (2005) J. Biol. Chem. 280, 16815-16820
25. Matsushima, Y., Garesse, R., and Kaguni, L. S. (2004) J. Biol. Chem. 279, 26900-26905
26. Metodiev, M. D., Lesko, N., Park, C. B., Cámara, Y., Shi, Y., Wibom, R., Hultenby, K., Gustafsson, C. M., and Larsson, N. G. (2009) Cell Metab. 9, 386-397
27. Sologub, M., Litonin, D., Anikin, M., Mustaev, A., and Temiakov, D. (2009) Cell 139, 934-944
28. Fisher, R. P., and Clayton, D. A. (1985) J. Biol. Chem. 260, 11330-11338
29. McCulloch, V., and Shadel, G. S. (2003) Mol. Cell. Biol. 23, 5816-5824
30. Dairaghi, D. J., Shadel, G. S., and Clayton, D. A. (1995) J. Mol. Biol. 249, 11-28
31. Fernández-Silva, P., Enriquez, J. A., and Montoya, J. (2003) Exp. Physiol. 88, 41-56
32. Gaspari, M., Falkenberg, M., Larsson, N. G., and Gustafsson, C. M. (2004) EMBO J. 23, 4606-4614
33. Gangelhoff, T. A., Mungalachetty, P. S., Nix, J. C., and Churchill, M. E. (2009) Nucleic Acids Res. 37, 3153-3164
34. Arnold, J. J., and Cameron, C. E. (1999) J. Biol. Chem. 274, 2706-2716
35. Arnold, J. J., Ghosh, S. K., Bevilacqua, P. C., and Cameron, C. E. (1999) BioTechniques 27, 450-456
36. Fisher, R. P., and Clayton, D. A. (1988) Mol. Cell. Biol. 8, 3496-3509
37. Wang, Z., Cotney, J., and Shadel, G. S. (2007) J. Biol. Chem. 282, 12610-12618
38. Fisher, R. P., Topper, J. N., and Clayton, D. A. (1987) Cell 50, 247-258
39. Chang, D. D., Fisher, R. P., and Clayton, D. A. (1987) Biochim. Biophys. Acta 909, 85-91
40. Martin, C. T., and Coleman, J. E. (1989) Biochemistry 28, 2760-2762
41. Gaines, G., Rossi, C., and Attardi, G. (1987) J. Biol. Chem. 262, 1907-1915
42. Amiott, E. A., and Jaehning, J. A. (2006) J. Biol. Chem. 281, 34982-34988
43. Amiott, E. A., and Jaehning, J. A. (2006) Mol. Cell 22, 329-338
44. Martin, C. T., and Coleman, J. E. (1987) Biochemistry 26, 2690-2696
45. Diaz, G. A., Raskin, C. A., and McAllister, W. T. (1993) J. Mol. Biol. 229, 805-811
46. Bandwar, R. P., Jia, Y., Stano, N. M., and Patel, S. S. (2002) Biochemistry 41, 3586-3595
47. Nayak, D., Guo, Q., and Sousa, R. (2009) J. Biol. Chem. 284, 13641-13647
48. Tang, G. Q., Paratkar, S., and Patel, S. S. (2009) J. Biol. Chem. 284, 5514-5522
49. Daube, S. S., and von Hippel, P. H. (1992) Science 258, 1320-1324
50. Milligan, J. F., Groebe, D. R., Witherell, G. W., and Uhlenbeck, O. C. (1987) Nucleic Acids Res. 15, 8783-8798
51. Martin, C. T., Muller, D. K., and Coleman, J. E. (1988) Biochemistry 27, 3966-3974
52. Tintut, Y., Wang, J. T., and Gralla, J. D. (1995) J. Biol. Chem. 270, 24392-24398
53. Gong, P., and Martin, C. T. (2006) J. Biol. Chem. 281, 23533-23544
54. Gnatt, A. L., Cramer, P., Fu, J., Bushnell, D. A., and Kornberg, R. D. (2001) Science 292, 1876-1882
55. Macdonald, L. E., Zhou, Y., and McAllister, W. T. (1993) J. Mol. Biol. 232, 1030-1047
56. Hsu, L. M., Vo, N. V., Kane, C. M., and Chamberlin, M. J. (2003) Biochemistry 42, 3777-3786
57. Goldman, S. R., Ebright, R. H., and Nickels, B. E. (2009) Science 324, 927-928
58. Kuzmine, I., Gottlieb, P. A., and Martin, C. T. (2003) J. Biol. Chem. 278, 2819-2823
59. Villemain, J., Guajardo, R., and Sousa, R. (1997) J. Mol. Biol. 273, 958-977
60. Jia, Y., Kumar, A., and Patel, S. S. (1996) J. Biol. Chem. 271, 30451-30458
61. Bandwar, R. P., and Patel, S. S. (2002) J. Mol. Biol. 324, 63-72
62. Davis, C. A., Capp, M. W., Record, M. T., Jr., and Saecker, R. M. (2005) Proc. Natl. Acad. Sci. U.S.A. 102, 285-290
63. Place, C., Oddos, J., Buc, H., McAllister, W. T., and Buckle, M. (1999) Biochemistry 38, 4948-4957
64. Holstege, F. C., and Timmers, H. T. (1997) Methods 12, 203-211
65. Price, D. H. (2008) Mol. Cell 30, 7-10
66. Seila, A. C., Core, L. J., Lis, J. T., and Sharp, P. A. (2009) Cell Cycle 8, 2557-2564
67. Gilmour, D. S. (2009) Chromosoma 118, 1-10
68. Kireeva, M. L., and Kashlev, M. (2009) Proc. Natl. Acad. Sci. U.S.A. 106, 8900-8905
69. Asin-Cayuela, J., and Gustafsson, C. M. (2007) Trends Biochem. Sci. 32, 111-117
70. Rutherford, S. T., Villers, C. L., Lee, J. H., Ross, W., and Gourse, R. L. (2009) Genes Dev. 23, 236-248
71. Wade, J. T., and Struhl, K. (2008) Curr. Opin. Genet. Dev. 18, 130-136
72. Fuda, N. J., Ardehali, M. B., and Lis, J. T. (2009) Nature 461, 186-192
73. Uptain, S. M., Kane, C. M., and Chamberlin, M. J. (1997) Annu. Rev. Biochem. 66, 117-172
74. Landick, R. (2006) Biochem. Soc. Trans. 34, 1062-1066
75. Nudler, E. (2009) Annu. Rev. Biochem. 78, 335-361
76. Murakami, K. S., and Darst, S. A. (2003) Curr. Opin. Struct. Biol. 13, 31-39
77. Kapanidis, A. N., Margeat, E., Ho, S. O., Kortkhonjia, E., Weiss, S., and Ebright, R. H. (2006) Science 314, 1144-1147