Pyrrolo-C as a molecular probe for monitoring conformations of the tRNA 3′ end

RNA

Volumn 14, Issue 10, 2008, Pages 2245-2253

  Zhang, Chun Mei ^a   Liu, Cuiping ^a   Christian, Thomas ^a   Gamper, Howard ^a   Rozenski, Jef ^b   Pan, Dongli ^c   Randolph, John B ^d   Wickstrom, Eric ^a   Cooperman, Barry S ^c   Hou, Ya Ming ^a  

^a THOMAS JEFFERSON UNIVERSITY   (United States)

^b REGA INSTITUTE FOR MEDICAL RESEARCH   (Belgium)

^c UNIVERSITY OF PENNSYLVANIA   (United States)

^d Glen Research Corporation   (United States)

Author keywords

Aminoacylation; Pyrrolo cytosine ribonucleoside; Ribosome translocation; tRNACys, tRNA CCA adding enzyme, fluorescence

Indexed keywords

CYTOSINE DERIVATIVE; PROFLAVINE; PYRROLOCYTOSINE; TRANSFER RNA; UNCLASSIFIED DRUG;

AMINOACYLATION; ARTICLE; ENZYME SYNTHESIS; ESCHERICHIA COLI; KINETICS; MOLECULAR PROBE; PRIORITY JOURNAL; REVERSED PHASE HIGH PERFORMANCE LIQUID CHROMATOGRAPHY; RNA CONFORMATION; RNA SEQUENCE; RNA STRUCTURE; RNA TRANSPORT;

AMINOACYLATION; CYTOSINE; ESCHERICHIA COLI; FLUORESCENT DYES; NUCLEIC ACID CONFORMATION; PYRROLES; RIBOSOMES; RNA NUCLEOTIDYLTRANSFERASES; RNA PROBES; RNA, BACTERIAL; RNA, TRANSFER; RNA, TRANSFER, CYS;

ESCHERICHIA COLI;

EID: 52949129861     PISSN: 13558382     EISSN: 14699001     Source Type: Journal    
DOI: 10.1261/rna.1158508     Document Type: Article

References (46)

1. Berry, D., Jung, K., Wise, D., Sercel, A., Pearson, W., Mackie, H., Randolph, J., and Somers, R. 2004. Pyrrolo-dC and pyrrolo-C: Fluorescent analogs of cytidine and 2′-deoxycytidine for the study of oligonucleotides. Tetrahedron Lett. 45: 2457-2461.
2. Betteridge, T., Liu, H., Gamper, H., Kirillov, S., Cooperman, B.S., and Hou, Y.M. 2007. Fluorescent labeling of tRNAs for dynamics experiments. RNA 13: 1594-1601.
3. Cho, H.D., Oyelere, A.K., Strobel, S.A., and Weiner, A.M. 2003. Use of nucleotide analogs by class I and class II CCA-adding enzymes (tRNA nucleotidyltransferase): Deciphering the basis for nucleotide selection. RNA 9: 970-981.
4. Christian, T., Lipman, R.S., Evilia, C., and Hou, Y.M. 2000. Alternative design of a tRNA core for aminoacylation. J. Mol. Biol. 303: 503-514.
5. Dock-Bregeon, A.C., Rees, B., Torres-Larios, A., Bey, G., Caillet, J., and Moras, D. 2004. Achieving error-free translation: The mechanism of proofreading of threonyl-tRNA synthetase at atomic resolution. Mol. Cell 16: 375-386.
6. Dorner, S., Brunelle, J.L., Sharma, D., and Green, R. 2006. The hybrid state of tRNA binding is an authentic translation elongation intermediate. Nat. Struct. Mol. Biol. 13: 234-241.
7. Ermolenko, D.N., Spiegel, P.C., Majumdar, Z.K., Hickerson, R.P., Clegg, R.M., and Noller, H.F. 2007. The antibiotic viomycin traps the ribosome in an intermediate state of translocation. Nat. Struct. Mol. Biol. 14: 493-497.
8. Freist, W. 1989. Mechanisms of aminoacyl-tRNA synthetases: A critical consideration of recent results. Biochemistry 28: 6787-6795.
9. Hauenstein, S., Zhang, C.M., Hou, Y.M., and Perona, J.J. 2004. Shape-selective RNA recognition by cysteinyl-tRNA synthetase. Nat. Struct. Mol. Biol. 11: 1134-1141.
10. Hou, Y.M. 2000. Unusual synthesis by the Escherichia coli CCA-adding enzyme [in process citation]. RNA 6: 1031-1043.
11. Hou, Y.M., Gu, S.Q., Zhou, H., and Ingerman, L. 2005. Metal-ion-dependent catalysis and specificity of CCA-adding enzymes: A comparison of two classes. Biochemistry 44: 12849-12859.
12. Ibba, M., Francklyn, C., and Cusack, S. 2005. The aminoacyl-tRNA synthetases. Landes Bioscience, Georgetown, TX.
13. Kao, C., Zheng, M., and Rudisser, S. 1999. A simple and efficient method to reduce nontemplated nucleotide addition at the 3 terminus of RNAs transcribed by T7 RNA polymerase. RNA 5: 1268-1272.
14. Konevega, A.L., Fischer, N., Semenkov, Y.P., Stark, H., Wintermeyer, W., and Rodnina, M.V. 2007. Spontaneous reverse movement of mRNA-bound tRNA through the ribosome. Nat. Struct. Mol. Biol. 14: 318-324.
15. Korostelev, A., Trakhanov, S., Laurberg, M., and Noller, H.F. 2006. Crystal structure of a 70S ribosome-tRNA complex reveals functional interactions and rearrangements. Cell 126: 1065-1077.
16. Liu, C. and Martin, C.T. 2002. Promoter clearance by T7 RNA polymerase. Initial bubble collapse and transcript dissociation monitored by base analog fluorescence. J. Biol. Chem. 277: 2725-2731.
17. Moazed, D. and Noller, H.F. 1989a. Interaction of tRNA with 23S rRNA in the ribosomal A, P, and E sites. Cell 57: 585-597.
18. Moazed, D. and Noller, H.F. 1989b. Intermediate states in the movement of transfer RNA in the ribosome. Nature 342: 142-148.
19. Nissen, P., Hansen, J., Ban, N., Moore, P.B., and Steitz, T.A. 2000. The structural basis of ribosome activity in peptide bond synthesis [see comments]. Science 289: 920-930.
20. Ott, G., Faulhammer, H.G., and Sprinzl, M. 1989. Interaction of elongation factor Tu from Escherichia coli with aminoacyl-tRNA carrying a fluorescent reporter group on the 3′ terminus. Eur. J. Biochem. 184: 345-352.
21. Pan, D., Kirillov, S., Zhang, C.M., Hou, Y.M., and Cooperman, B.S. 2006. Rapid ribosomal translocation depends on the conserved 18-55 base pair in P-site transfer RNA. Nat. Struct. Mol. Biol. 13: 354-359.
22. Pan, D., Kirillov, S.V., and Cooperman, B.S. 2007. Kinetically competent intermediates in the translocation step of protein synthesis. Mol. Cell 25: 519-529.
23. Paulsen, H. and Wintermeyer, W. 1986. tRNA topography during translocation: Steady-state and kinetic fluorescence energy-transfer studies. Biochemistry 25: 2749-2756.
24. Phe. J. Mol. Biol. 151: 57-79.
25. Robertson, J.M., Paulsen, H., and Wintermeyer, W. 1986. Pre-steady-state kinetics of ribosomal translocation. J. Mol. Biol. 192: 351-360.
26. Rodnina, M.V., Fricke, R., and Wintermeyer, W. 1994. Transient conformational states of aminoacyl-tRNA during ribosome binding catalyzed by elongation factor Tu. Biochemistry 33: 12267-12275.
27. Rodnina, M.V., Savelsbergh, A., Katunin, V.I., and Wintermeyer, W. 1997. Hydrolysis of GTP by elongation factor G drives tRNA movement on the ribosome. Nature 385: 37-41.
28. Gln and ATP at 2.8 Å resolution [see comments]. Science 246: 1135-1142.
29. Asp. Science 252: 1682-1689.
30. Samaha, R.R., Green, R., and Noller, H.F. 1995. A base pair between tRNA and 23S rRNA in the peptidyl transferase centre of the ribosome [published erratum appears in Nature 1995 Nov 23;378(6555):419]. Nature 377: 309-314.
31. Sauerwald, A., Zhu, W., Major, T.A., Roy, H., Palioura, S., Jahn, D., Whitman, W.B., Yates 3rd., J.R., Ibba, M., and Soll, D. 2005. RNA-dependent cysteine biosynthesis in archaea. Science 307: 1969-1972.
32. Selmer, M., Dunham, C.M., Murphy IV., F.V., Weixlbaumer, A., Petry, S., Kelley, A.C., Weir, J.R., and Ramakrishnan, V. 2006. Structure of the 70S ribosome complexed with mRNA and tRNA. Science 313: 1935-1942.
33. Seth, M., Thurlow, D.L., and Hou, Y.M. 2002. Poly(C) synthesis by class I and class II CCA-adding enzymes. Biochemistry 41: 4521-4532.
34. Sherlin, L.D. and Perona, J.J. 2003. tRNA-dependent active site assembly in a Class I aminoacyl-tRNA synthetase. Structure 11: 591-603.
35. Silvian, L.F., Wang, J., and Steitz, T.A. 1999. Insights into editing from an ile-tRNA synthetase structure with tRNAile and mupirocin. Science 285: 1074-1077.
36. Stark, H., Rodnina, M.V., Wieden, H.J., Zemlin, F., Wintermeyer, W., and van Heel, M. 2002. Ribosome interactions of aminoacyl-tRNA and elongation factor Tu in the codon-recognition complex. Nat. Struct. Biol. 9: 849-854.
37. Tinsley, R.A. and Walter, N.G. 2006. Pyrrolo-C as a fluorescent probe for monitoring RNA secondary structure formation. RNA 12: 522-529.
38. Valle, M., Sengupta, J., Swami, N.K., Grassucci, R.A., Burkhardt, N., Nierhaus, K.H., Agrawal, R.K., and Frank, J. 2002. Cryo-EM reveals an active role for aminoacyl-tRNA in the accommodation process. EMBO J. 21: 3557-3567.
39. Wintermeyer, W. and Zachau, H.G. 1979. Fluorescent derivatives of yeast tRNAPhe. Eur. J. Biochem. 98: 465-475.
40. Yue, D., Maizels, N., and Weiner, A.M. 1996. CCA-adding enzymes and poly(A) polymerases are all members of the same nucleotidyltransferase superfamily: Characterization of the CCA-adding enzyme from the archaeal hyperthermophile Sulfolobus shibatae. RNA 2: 895-908.
41. Yusupov, M.M., Yusupova, G.Z., Baucom, A., Lieberman, K., Earnest, T.N., Cate, J.H., and Noller, H.F. 2001. Crystal structure of the ribosome at 5.5 Å resolution. Science 292: 883-896.
42. Yusupova, G., Jenner, L., Rees, B., Moras, D., and Yusupov, M. 2006. Structural basis for messenger RNA movement on the ribosome. Nature 444: 391-394.
43. Zhang, C.M. and Hou, Y.M. 2005. Domain-domain communication for tRNA aminoacylation: The importance of covalent connectivity. Biochemistry 44: 7240-7249.
44. Zhang, C.M., Christian, T., Newberry, K.J., Perona, J.J., and Hou, Y.M. 2003a. Zinc-mediated amino acid discrimination in cysteinyl-tRNA synthetase. J. Mol. Biol. 327: 911-917.
45. Cys. Nat. Struct. Mol. Biol. 15: 507-514.
46. Zhang, C.M., Perona, J.J., and Hou, Y.M. 2003b. Amino acid discrimination by a highly differentiated metal center of an aminoacyl-tRNA synthetase. Biochemistry 42: 10931-10937.