Potential new antibiotic sites in the ribosome revealed by deleterious mutations in RNA of the large ribosomal subunit

Journal of Biological Chemistry

Volumn 282, Issue 33, 2007, Pages 24329-24342

  Yassin, Aymen ^a,b   Mankin, Alexander S ^a  

^a UNIVERSITY OF ILLINOIS AT CHICAGO   (United States)

^b CAIRO UNIVERSITY   (Egypt)

Author keywords

[No Author keywords available]

Indexed keywords

BIOSYNTHESIS; GENETIC ENGINEERING; MUTAGENESIS; PROTEINS; RNA;

ANTIBIOTIC TARGETS; INTERSUBUNIT BRIDGE; RRNA ELEMENTS;

ANTIBIOTICS;

ANTIBIOTIC AGENT; RIBOSOME RNA;

ARTICLE; GENE MAPPING; GENE MUTATION; MUTAGENESIS; PHENOTYPE; PRIORITY JOURNAL; RIBOSOME SUBUNIT;

ANTI-BACTERIAL AGENTS; BINDING SITES; ESCHERICHIA COLI; MUTATION; RIBOSOMES; RNA, RIBOSOMAL; RNA, RIBOSOMAL, 23S;

EID: 34548236988     PISSN: 00219258     EISSN: 1083351X     Source Type: Journal    
DOI: 10.1074/jbc.M703106200     Document Type: Article

References (78)

1. Mushegian, A. R., and Koonin, E. V. (1996) Proc. Natl. Acad. Sci. U. S. A. 93, 10268-10273
2. Hutchison, C. A., Peterson, S. N., Gill, S. R., Cline, R. T., White, O., Fraser, C. M., Smith, H. O., and Venter, J. C. (1999) Science 286, 2165-2169
3. Schoolnik, G. K. (2002) Curr. Opin. Microbiol. 5, 20-26
4. Thomson, C. J., Power, E., Ruebsamen-Waigmann, H., and Labischinski, H. (2004) Curr. Opin. Microbiol. 7, 445-450
5. Poehlsgaard, J., and Douthwaite, S. (2005) Nat. Rev. Microbiol. 3, 870-881
6. Franceschi, F., and Duffy, E. M. (2006) Biochem. Pharmacol. 71, 1016-1025
7. Tenson, T., and Mankin, A. S. (2006) Mol. Microbiol. 59, 1664-1677
8. Schlunzen, F., Zarivach, R., Harms, J., Bashan, A., Tocilj, A., Albrecht, R., Yonath, A., and Franceschi, F. (2001) Nature 413, 814-821
9. Carter, A. P., Clemons, W. M., Brodersen, D. E., Morgan-Warren, R. J., Wimberly, B. T., and Ramakrishnan, V. (2000) Nature 407, 340-348
10. Tu, D., Blaha, G., Moore, P. B., and Steitz, T. A. (2005) Cell 121, 257-270
11. Moazed, D., and Noller, H. F. (1987) Nature 327, 389-394
12. Woodcock, J., Moazed, D., Cannon, M., Davies, J., and Noller, H. F. (1991) EMBO J. 10, 3099-3103
13. De Stasio, E. A., Moazed, D., Noller, H. F., and Dahlberg, A. E. (1989) EMBO J. 8, 1213-1216
14. Dinos, G., Wilson, D. N., Teraoka, Y., Szaflarski, W., Fucini, P., Kalpaxis, D., and Nierhaus, K. H. (2004) Mol. Cell 13, 113-124
15. Schluenzen, F., Takemoto, C., Wilson, D. N., Kaminishi, T., Harms, J. M., Hanawa-Suetsugu, K., Szaflarski, W., Kawazoe, M., Shirouzo, M., Nierhaus, K. H., Yokoyama, S., and Fucini, P. (2006) Nat. Struct. Mol. Biol. 13, 871-878
16. Schuwirth, B. S., Day, J. M., Hau, C. W., Janssen, G. R., Dahlberg, A. E., Cate, J. H., and Vila-Sanjurjo, A. (2006) Nat. Struct. Mol. Biol. 13, 879-886
17. Hansen, J. L., Moore, P. B., and Steitz, T. A. (2003) J. Mol. Biol. 330, 1061-1075
18. Yonath, A. (2005) Annu. Rev. Biochem. 74, 649-679
19. Thompson, J., Schmidt, F., and Cundliffe, E. (1982) J. Biol. Chem. 257, 7915-7917
20. Porse, B. T., Leviev, I., Mankin, A. S., and Garrett, R. A. (1998) J. Mol. Biol. 276, 391-404
21. Adrian, P. V., Mendrick, C., Loebenberg, D., McNicholas, P., Shaw, K. J., Klugman, K. P., Hare, R. S., and Black, T. A. (2000) Antimicrob. Agents Chemother. 44, 3101-3106
22. Belova, L., Tenson, T., Xiong, L., McNicholas, P. M., and Mankin, A. S. (2001) Proc. Natl. Acad. Sci. U. S. A. 98, 3726-3731
23. Treede, I., Jakobsen, L., Kirpekar, F., Vester, B., Weitnauer, G., Bechthold, A., and Douthwaite, S. (2003) Mol. Microbiol. 49, 309-318
24. Schroeder, S. J., Blaha, G., Tirado-Rives, J., Steitz, T. A., and Moore, P. B. (2007) J. Mol. Biol. 367, 1471-1479
25. Yassin, A., Fredrick, K., and Mankin, A. S. (2005) Proc. Natl. Acad. Sci. U. S. A. 102, 16620-16625
26. Laios, E., Waddington, M., Saraiya, A. A., Baker, K. A., O'Connor, E., Pamarathy, D., and Cunningham, P. R. (2004) Arch. Pathol. Lab. Med. 128, 1351-1359
27. Douthwaite, S., Powers, T., Lee, J. Y., and Noller, H. F. (1989) J. Mol. Biol. 209, 655-665
28. Powers, T., and Noller, H. F. (1991) EMBO J. 10, 2203-2214
29. Rottmann, N., Kleuvers, B., Atmadja, J., and Wagner, R. (1988) Eur. J. Biochem. 177, 81-90
30. Remaut, E., Stanssens, P., and Fiers, W. (1981) Gene (Amst.) 15, 81-93
31. Sergiev, P. V., Kiparisov, S. V., Burakovsky, D. E., Lesnyak, D. V., Leonov, A. A., Bogdanov, A. A., and Dontsova, O. A. (2005) J. Mol. Biol. 353, 116-123
32. Ron, E. Z., Kohler, R. E., and Davis, B. D. (1966) Science 153, 1119-1120
33. Fredrick, K., Dunny, G. M., and Noller, H. F. (2000) J. Mol. Biol. 298, 379-394
34. Sigmund, C. D., Ettayebi, M., Borden, A., and Morgan, E. A. (1988) Methods Enzymol. 164, 673-690
35. Moazed, D., and Noller, H. F. (1989) Cell 57, 585-597
36. Polacek, N., Patzke, S., Nierhaus, K. H., and Barta, A. (2000) Mol. Cell 6, 159-171
37. Powers, T., and Noller, H. F. (1990) Proc. Natl. Acad. Sci. U. S. A. 87, 1042-1046
38. Lieberman, K. R., and Dahlberg, A. E. (1994) J. Biol. Chem. 269, 16163-16169
39. Rodriguez-Correa, D., and Dahlberg, A. E. (2004) RNA 10, 28-33
40. Nierhaus, K. H. (1991) Biochimie (Paris) 73, 739-755
41. Chittum, H. S., and Champney, W. S. (1995) Curr. Microbiol. 30, 273-279
42. Yusupov, M. M., Yusupova, G. Z., Baucom, A., Lieberman, K., Earnest, T. N., Cate, J. H., and Noller, H. F. (2001) Science 292, 883-896
43. Gao, H., Sengupta, J., Valle, M., Korostelev, A., Eswar, N., Stagg, S. M., Van Roey, P., Agrawal, R. K., Harvey, S. C., Sali, A., Chapman, M. S., and Frank, J. (2003) Cell 113, 789-801
44. Komoda, T., Sato, N. S., Phelps, S. S., Namba, N., Joseph, S., and Suzuki, T. (2006) J. Biol. Chem. 281, 32303-32309
45. Liiv, A., and O'Connor, M. (2006) J. Biol. Chem. 281, 29850-29862
46. Gregory, S. T., Bayfield, M. A., O'Connor, M., Thompson, J., and Dahlberg, A. E. (2001) Cold Spring Harbor Symp. Quant. Biol. 66, 101-108
47. Murgola, E. J., Hijazi, K. A., Goringer, H. U., and Dahlberg, A. E. (1988) Proc. Natl. Acad. Sci. U. S. A. 85, 4162-4165
48. Chernyaeva, N. S., Murgola, E. J., and Mankin, A. S. (1999) J. Bacteriol. 181, 5257-5262
49. Wild, K., Halic, M., Sinning, I., and Beckmann, R. (2004) Nat. Struct. Mol. Biol. 11, 1049-1053
50. Deuerling, E., and Bukau, B. (2004) Crit. Rev. Biochem. Mol. Biol. 39, 261-277
51. Triman, K. L. (1999) Adv. Genet. 41, 157-195
52. Maeder, C., Conn, G. L., and Draper, D. E. (2006) Biochemistry 45, 6635-6643
53. Bogdanov, A. A., Dontsova, O. A., Dokudovskaya, S. S., and Lavrik, I. N. (1995) Biochem. Cell Biol. 73, 869-876
54. Sergiev, P., Dokudovskaya, S., Romanova, E., Topin, A., Bogdanov, A., Brimacombe, R., and Dontsova, O. (1998) Nucleic Acids Res. 26, 2519-2525
55. Khaitovich, P., and Mankin, A. S. (1999) J. Mol. Biol. 291, 1025-1034
56. Pace, B., Matthews, E. A., Johnson, K. D., Cantor, C. R., and Pace, N. R. (1982) Proc. Natl. Acad. Sci. U. S. A. 79, 36-40
57. Cannone, J. J., Subramanian, S., Schnare, M. N., Collett, J. R., D'Souza, L. M., Du, Y., Feng, B., Lin, N., Madabusi, L. V., Muller, K. M., Pande, N., Shang, Z., Yu, N., and Gutell, R. R. (2002) BMC Bioinformatics 3, 2
58. Macbeth, M. R., and Wool, I. G. (1999) J. Mol. Biol. 285, 965-975
59. Hobbie, S. N., Bruell, C., Kalapala, S., Akshay, S., Schmidt, S., Pfister, P., and Bottger, E. C. (2006) Biochimie (Paris) 88, 1033-1043
60. Sato, N. S., Hirabayashi, N., Agmon, I., Yonath, A., and Suzuki, T. (2006) Proc. Natl. Acad. Sci. U. S. A. 103, 15386-15391
61. Purohit, P., and Stern, S. (1994) Nature 370, 659-662
62. Fourmy, D., Recht, M. I., Blanchard, S. C., and Puglisi, J. D. (1996) Science 274, 1367-1371
63. Francois, B., Russell, R. J., Murray, J. B., Aboul-ela, F., Masquida, B., Vicens, Q., and Westhof, E. (2005) Nucleic Acids Res. 33, 5677-5690
64. Russell, R. J., Murray, J. B., Lentzen, G., Haddad, J., and Mobashery, S. (2003) J. Am. Chem. Soc. 125, 3410-3411
65. Zhou, Y., Gregor, V. E., Sun, Z., Ayida, B. K., Winters, G. C., Murphy, D., Simonsen, K. B., Vourloumis, D., Fish, S., Froelich, J. M., Wall, D., and Hermann, T. (2005) Antimicrob. Agents Chemother. 49, 4942-4949
66. Tor, Y. (2006) Biochimie (Paris) 88, 1045-1051
67. Endo, Y., and Wool, I. G. (1982) J. Biol. Chem. 257, 9054-9060
68. Moazed, D., Robertson, J. M., and Noller, H. F. (1988) Nature 334, 362-364
69. Chan, Y. L., Sitikov, A. S., and Wool, I. G. (2000) J. Mol. Biol. 298, 795-805
70. Nissen, P., Ippolito, J. A., Ban, N., Moore, P. B., and Steitz, T. A. (2001) Proc. Natl. Acad. Sci. U. S. A. 98, 4899-4903
71. Dohme, F., and Nierhaus, K. H. (1976) Proc. Natl. Acad. Sci. U. S. A. 73, 2221-2225
72. Zvereva, M. I., Shpanchenko, O. V., Dontsova, O. A., Nierhaus, K. H., and Bogdanov, A. A. (1998) FEBS Lett. 421, 249-251
73. Comartin, D. J., and Brown, E. D. (2006) Curr. Opin. Pharmacol. 6, 453-458
74. Schuwirth, B. S., Borovinskaya, M. A., Hau, C. W., Zhang, W., Vila-Sanjurjo, A., Holton, J. M., and Cate, J. H. (2005) Science 310, 827-834
75. Stelzl, U., Spahn, C. M., and Nierhaus, K. H. (2000) Proc. Natl. Acad. Sci. U. S. A. 97, 4597-4602
76. Gabashvili, I. S., Gregory, S. T., Valle, M., Grassucci, R., Worbs, M., Wahl, M. C., Dahlberg, A. E., and Frank, J. (2001) Mol. Cell 8, 181-188
77. Berisio, R., Schluenzen, F., Harms, J., Bashan, A., Auerbach, T., Baram, D., and Yonath, A. (2003) Nat. Struct. Biol. 10, 366-370
78. Mitra, K., Frank, J., and Driessen, A. (2006) Nat. Struct. Mol. Biol. 13, 957-964