Anticodon-dependent conservation of bacterial tRNA gene sequences

RNA

Volumn 13, Issue 5, 2007, Pages 651-660

  Saks, Margaret E ^a   Conery, John S ^b  

^a NORTHWESTERN UNIVERSITY   (United States)

^b UNIVERSITY OF OREGON   (United States)

Author keywords

Anticodon; Bacteria; Evolution; Ribosome; Translation; tRNA; Wobble position

Indexed keywords

TRANSFER RNA;

ACYLATION; ANTICODON; ARTICLE; BACTERIAL GENE; BACTERIAL GENOME; GENE SEQUENCE; NONHUMAN; PRIORITY JOURNAL; PROTEIN SYNTHESIS; RIBOSOME; RNA TRANSLATION;

ANTICODON; BASE SEQUENCE; CONSERVED SEQUENCE; MODELS, GENETIC; RNA, BACTERIAL; RNA, TRANSFER;

BACTERIA (MICROORGANISMS);

EID: 34247376550     PISSN: 13558382     EISSN: 14699001     Source Type: Journal    
DOI: 10.1261/rna.345907     Document Type: Article

References (57)

1. Agris, P.F. 2004. Decoding the genome: A modified view. Nucleic Acids Res. 32: 223-238.
2. Ardell, D.H. and Andersson, S.G. 2006. TFAM detects co-evolution of tRNA identity rules with lateral transfer of histidyl-tRNA synthetase. Nucleic Acids Res. 34: 893-904.
3. Tyr. J. Mol. Biol. 231: 219-229.
4. Auffinger, P. and Westhof, E. 1999. Singly and bifurcated hydrogen-bonded base pairs in tRNA anticodon hairpins and ribozymes. J. Mol. Biol. 292: 467-483.
5. Baldauf, S.L., Palmer, J.D., and Doolittle, W.F. 1996. The root of the universal tree and the origin of eukaryotes based on elongation factor phylogeny. Proc. Natl. Acad. Sci. 93: 7749-7754.
6. Cedergren, R.J., LaRue, B., Sankoff, D., Lapalme, G., and Grosjean, H. 1980. Convergence and minimal mutation criteria for evaluating early events in tRNA evolution. Proc. Natl. Acad. Sci. 77: 2791-2795.
7. Claesson, C., Lustig, F., Boren, T., Simonsson, C., Barciszewska, M., and Lagerkvist, U. 1995. Glycine codon discrimination and the nucleotide in position 32 of the anticodon loop. J. Mol. Biol. 247: 191-196.
8. Cochella, L. and Green, R. 2005. An active role for tRNA in decoding beyond codon:anticodon pairing. Science 308: 1178-1180.
9. Dirheimer, G., Keith, G., Dumas, P., and Westhof, E. 1995. Primary, secondary, and tertiary structures of tRNAs. In tRNA: Structure, biosynthesis, and function (eds. D. Soll and U.L. RajBhandary), pp. 93-126. American Society for Microbiology, Washington, DC.
10. Fitch, W.M. and Upper, K. 1987. The phylogeny of tRNA sequences provides evidence for ambiguity reduction in the origin of the genetic code. Cold Spring Harb. Symp. Quant. Biol. 52: 759-767.
11. Giege, R., Sissler, M., and Florentz, C. 1998. Universal rules and idiosyncratic features in tRNA identity. Nucleic Acids Res. 26: 5017-5035.
12. Gutell, R.R., Weiser, B., Woese, C.R., and Noller, H.F. 1985. Comparative anatomy of 16-S-like ribosomal RNA. Prog. Nucleic Acid Res. Mol. Biol. 32: 155-216.
13. Hirsh, D. 1971. Tryptophan transfer RNA as the UGA suppressor. J. Mol. Biol. 58: 439-458.
14. Hoagland, M. 1996. Biochemistry or molecular biology? The discovery of "soluble RNA." Trends Biochem. Sci. 21: 77-80.
15. Keeling, P.J. and Inagaki, Y. 2004. A class of eukaryotic GTPase with a punctate distribution suggesting multiple functional replacements of translation elongation factor 1α. Proc. Natl. Acad. Sci. 101: 15380-15385.
16. Kleina, L.G., Masson, J.M., Normanly, J., Abelson, J., and Miller, J.H. 1990. Construction of Escherichia coli amber suppressor tRNA genes. II. Synthesis of additional tRNA genes and improvement of suppressor efficiency. J. Mol. Biol. 213: 705-717.
17. Thr2. FEBS Lett. 272: 55-57.
18. 2+-dependent interactions. RNA 10: 90-101.
19. 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.
20. LaRiviere, F.J., Wolfson, A.D., and Uhlenbeck, O.C. 2001. Uniform binding of aminoacyl-tRNAs to elongation factor Tu by thermodynamic compensation. Science 294: 165-168.
21. Lustig, F., Boren, T., Claesson, C., Simonsson, C., Barciszewska, M., and Lagerkvist, U. 1993. The nucleotide in position 32 of the tRNA anticodon loop determines ability of anticodon UCC to discriminate among glycine codons. Proc. Natl. Acad. Sci. 90: 3343-3347.
22. Marck, C. and Grosjean, H. 2002. tRNomics: Analysis of tRNA genes from 50 genomes of Eukarya, Archaea, and Bacteria reveals anticodon-sparing strategies and domain-specific features. RNA 8: 1189-1232.
23. Martinis, S.A. and Schimmel, P. 1995. Small RNA oligonucleotide substrates for specific aminoacylations. In tRNA: Structure, biosynthesis, and function (eds. D. Soll and U.L. RajBhandary), pp. 349-370. American Society for Microbiology, Washington, DC.
24. McClain, W.H. 1993. Rules that govern tRNA identity in protein synthesis. J. Mol. Biol. 234: 257-280.
25. McClain, W.H. and Foss, K. 1988. Changing the acceptor identity of a transfer RNA by altering nucleotides in a "variable pocket." Science 241: 1804-1807.
26. McClain, W.H. and Nicholas Jr., H.B. 1987. Differences between transfer RNA molecules. J. Mol. Biol. 194: 635-642.
27. Moazed, D. and Noller, H.F. 1989. Intermediate states in the movement of transfer RNA in the ribosome. Nature 342: 142-148.
28. Nissan, T.A. and Perona, J.J. 2000. Alternative designs for construction of the class II transfer RNA tertiary core. RNA 6: 1585-1596.
29. Nissan, T.A., Oliphant, B., and Perona, J.J. 1999. An engineered class I transfer RNA with a class II tertiary fold. RNA 5: 434-445.
30. Ogle, J.M., Brodersen, D.E., Clemons Jr., W.M., Tarry, M.J., Carter, A.P., and Ramakrishnan, V. 2001. Recognition of cognate transfer RNA by the 30S ribosomal subunit. Science 292: 897-902.
31. Olejniczak, M., Dale, T., Fahlman, R.P., and Uhlenbeck, O.C. 2005. Idiosyncratic tuning of tRNAs to achieve uniform ribosome binding. Nat. Struct. Mol. Biol. 12: 788-793.
32. Pallanck, L., Pak, M., and Schulman, L.H. 1995. tRNA discrimination in aminoacylation. In tRNA: Structure, biosynthesis, and function (eds. D. Soll and U.L. RajBhandary), pp. 371-394. American Society for Microbiology, Washington, DC.
33. RajBhandary, U.L. and Soll, D. 1995. Transfer RNA in its fourth decade. In tRNA: Structure, biosynthesis, and function (eds. D. Soll and U.L. RajBhandary), pp. 1-4. American Society for Microbiology, Washington, DC.
34. Rich, A. and RajBhandary, U.L. 1976. Transfer RNA: molecular structure, sequence, and properties. Annu. Rev. Biochem. 45: 805-860.
35. Saks, M.E., Sampson, J.R., and Abelson, J.N. 1994. The transfer RNA identity problem: A search for rules. Science 263: 191-197.
36. Saks, M.E., Sampson, J.R., and Abelson, J. 1998. Evolution of a transfer RNA gene through a point mutation in the anticodon. Science 279: 1665-1670.
37. Sanbonmatsu, K.Y., Joseph, S., and Tung, C.S. 2005. Simulating movement of tRNA into the ribosome during decoding. Proc. Natl. Acad. Sci. 102: 15854-15859.
38. Schultz, D.W. and Yarus, M. 1994. tRNA structure and ribosomal function. I. tRNA nucleotide 27-43 mutations enhance first position wobble. J. Mol. Biol. 235: 1381-1394.
39. 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.
40. Shimizu, M., Asahara, H., Tamura, K., Hasegawa, T., and Himeno, H. 1992. The role of anticodon bases and the discriminator nucleotide in the recognition of some E. coli tRNAs by their aminoacyl-tRNA synthetases. J. Mol. Evol. 35: 436-443.
41. Squires, C. and Carbon, J. 1971. Normal and mutant glycine transfer RNAs. Nat. New Biol. 233: 274-277.
42. 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.
43. Ile: Evidence of derivation from other tRNAs. Z. Naturforsch. C 42: 129-133.
44. Trp. Orig. Life Evol. Biosph. 18: 97-105.
45. Steinberg, S.V. and Kisselev, L.L. 1993. Mosaic tile model for tRNA-enzyme recognition. Nucleic Acids Res. 21: 1941-1947.
46. Steinberg, S., Leclerc, F., and Cedergren, R. 1997. Structural rules and conformational compensations in the tRNA L-form. J. Mol. Biol. 266: 269-282.
47. Tocchini-Valentini, G., Saks, M.E., and Abelson, J. 2000. tRNA leucine identity and recognition sets. J. Mol. Biol. 298: 779-793.
48. Leu in the post-transfer-editing conformation. Nat. Struct. Mol. Biol. 12: 923-930.
49. 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.
50. Valle, M., Zavialov, A., Li, W., Stagg, S.M., Sengupta, J., Nielsen, R.C., Nissen, P., Harvey, S.C., Ehrenberg, M., and Frank, J. 2003. Incorporation of aminoacyl-tRNA into the ribosome as seen by cryo-electron microscopy. Nat. Struct. Biol. 10: 899-906.
51. Westhof, E., Dumas, P., and Moras, D. 1985. Crystallographic refinement of yeast aspartic acid transfer RNA. J. Mol. Biol. 184: 119-145.
52. Yarus, M. 1982. Translational efficiency of transfer RNA's: Uses of an extended anticodon. Science 218: 646-652.
53. Yarus, M. and Smith, D. 1995. tRNA on the ribosome: A waggle theory. In tRNA: Structure, biosynthesis, and function (eds. D. Soll and U.L. RajBhandary), pp. 443-469. American Society for Microbiology, Washington, DC.
54. Yarus, M., Cline, S.W., Wier, P., Breeden, L., and Thompson, R.C. 1986. Actions of the anticodon arm in translation on the phenotypes of RNA mutants. J. Mol. Biol. 192: 235-255.
55. Yarus, M., Valle, M., and Frank, J. 2003. A twisted tRNA intermediate sets the threshold for decoding. RNA 9: 384-385.
56. 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.
57. Zamecnik, P. 2005. From protein synthesis to genetic insertion. Annu. Rev. Biochem. 74: 1-28.