Skip to main content
NCBI home page
The EMBO Journal logoLink to The EMBO Journal
. 1998 Jan 2;17(1):297–305. doi: 10.1093/emboj/17.1.297

Genetic code in evolution: switching species-specific aminoacylation with a peptide transplant.

K Wakasugi 1, C L Quinn 1, N Tao 1, P Schimmel 1
PMCID: PMC1170380  PMID: 9427763

Abstract

The genetic code is established in aminoacylation reactions whereby amino acids are joined to tRNAs bearing the anticodons of the genetic code. Paradoxically, while the code is universal there are many examples of species-specific aminoacylations, where a tRNA from one taxonomic domain cannot be acylated by a synthetase from another. Here we consider an example where a human, but not a bacterial, tRNA synthetase charges its cognate eukaryotic tRNA and where the bacterial, but not the human, enzyme charges the cognate bacterial tRNA. While the bacterial enzyme has less than 10% sequence identity with the human enzyme, transplantation of a 39 amino acid peptide from the human into the bacterial enzyme enabled the latter to charge its eukaryotic tRNA counterpart in vitro and in vivo. Conversely, substitution of the corresponding peptide of the bacterial enzyme for that of the human enabled the human enzyme to charge bacterial tRNA. This peptide element discriminates a base pair difference in the respective tRNA acceptor stems. Thus, functionally important co-adaptations of a synthetase to its tRNA act as small modular units that can be moved across taxonomic domains and thereby preserve the universality of the code.

Full Text

The Full Text of this article is available as a PDF (480.0 KB).

Selected References

These references are in PubMed. This may not be the complete list of references from this article.

  1. Auld D. S., Schimmel P. Switching recognition of two tRNA synthetases with an amino acid swap in a designed peptide. Science. 1995 Mar 31;267(5206):1994–1996. doi: 10.1126/science.7701322. [DOI] [PubMed] [Google Scholar]
  2. Auld D. S., Schmimmel P. Single sequence of a helix-loop peptide confers functional anticodon recognition on two tRNA synthetases. EMBO J. 1996 Mar 1;15(5):1142–1148. [PMC free article] [PubMed] [Google Scholar]
  3. Barker D. G., Bruton C. J., Winter G. The tyrosyl-tRNA synthetase from Escherichia coli. Complete nucleotide sequence of the structural gene. FEBS Lett. 1982 Dec 27;150(2):419–423. doi: 10.1016/0014-5793(82)80781-3. [DOI] [PubMed] [Google Scholar]
  4. Bedouelle H., Guez-Ivanier V., Nageotte R. Discrimination between transfer-RNAs by tyrosyl-tRNA synthetase. Biochimie. 1993;75(12):1099–1108. doi: 10.1016/0300-9084(93)90009-h. [DOI] [PubMed] [Google Scholar]
  5. Bedouelle H. Recognition of tRNA(Tyr) by tyrosyl-tRNA synthetase. Biochimie. 1990 Aug;72(8):589–598. doi: 10.1016/0300-9084(90)90122-w. [DOI] [PubMed] [Google Scholar]
  6. Bedouelle H., Winter G. A model of synthetase/transfer RNA interaction as deduced by protein engineering. 1986 Mar 27-Apr 2Nature. 320(6060):371–373. doi: 10.1038/320371a0. [DOI] [PubMed] [Google Scholar]
  7. Berben G., Dumont J., Gilliquet V., Bolle P. A., Hilger F. The YDp plasmids: a uniform set of vectors bearing versatile gene disruption cassettes for Saccharomyces cerevisiae. Yeast. 1991 Jul;7(5):475–477. doi: 10.1002/yea.320070506. [DOI] [PubMed] [Google Scholar]
  8. Boeke J. D., LaCroute F., Fink G. R. A positive selection for mutants lacking orotidine-5'-phosphate decarboxylase activity in yeast: 5-fluoro-orotic acid resistance. Mol Gen Genet. 1984;197(2):345–346. doi: 10.1007/BF00330984. [DOI] [PubMed] [Google Scholar]
  9. Brick P., Bhat T. N., Blow D. M. Structure of tyrosyl-tRNA synthetase refined at 2.3 A resolution. Interaction of the enzyme with the tyrosyl adenylate intermediate. J Mol Biol. 1989 Jul 5;208(1):83–98. doi: 10.1016/0022-2836(89)90090-9. [DOI] [PubMed] [Google Scholar]
  10. Burbaum J. J., Schimmel P. Structural relationships and the classification of aminoacyl-tRNA synthetases. J Biol Chem. 1991 Sep 15;266(26):16965–16968. [PubMed] [Google Scholar]
  11. Carter C. W., Jr Cognition, mechanism, and evolutionary relationships in aminoacyl-tRNA synthetases. Annu Rev Biochem. 1993;62:715–748. doi: 10.1146/annurev.bi.62.070193.003435. [DOI] [PubMed] [Google Scholar]
  12. Chow C. M., RajBhandary U. L. Saccharomyces cerevisiae cytoplasmic tyrosyl-tRNA synthetase gene. Isolation by complementation of a mutant Escherichia coli suppressor tRNA defective in aminoacylation and sequence analysis. J Biol Chem. 1993 Jun 15;268(17):12855–12863. [PubMed] [Google Scholar]
  13. Cusack S., Härtlein M., Leberman R. Sequence, structural and evolutionary relationships between class 2 aminoacyl-tRNA synthetases. Nucleic Acids Res. 1991 Jul 11;19(13):3489–3498. doi: 10.1093/nar/19.13.3489. [DOI] [PMC free article] [PubMed] [Google Scholar]
  14. Doublié S., Bricogne G., Gilmore C., Carter C. W., Jr Tryptophanyl-tRNA synthetase crystal structure reveals an unexpected homology to tyrosyl-tRNA synthetase. Structure. 1995 Jan 15;3(1):17–31. doi: 10.1016/s0969-2126(01)00132-0. [DOI] [PubMed] [Google Scholar]
  15. Eriani G., Delarue M., Poch O., Gangloff J., Moras D. Partition of tRNA synthetases into two classes based on mutually exclusive sets of sequence motifs. Nature. 1990 Sep 13;347(6289):203–206. doi: 10.1038/347203a0. [DOI] [PubMed] [Google Scholar]
  16. Fersht A. R., Shindler J. S., Tsui W. C. Probing the limits of protein-amino acid side chain recognition with the aminoacyl-tRNA synthetases. Discrimination against phenylalanine by tyrosyl-tRNA synthetases. Biochemistry. 1980 Nov 25;19(24):5520–5524. doi: 10.1021/bi00565a009. [DOI] [PubMed] [Google Scholar]
  17. Frolova L. Y., Grigorieva A. Y., Sudomoina M. A., Kisselev L. L. The human gene encoding tryptophanyl-tRNA synthetase: interferon-response elements and exon-intron organization. Gene. 1993 Jun 30;128(2):237–245. doi: 10.1016/0378-1119(93)90568-n. [DOI] [PubMed] [Google Scholar]
  18. Frugier M., Florentz C., Giegé R. Efficient aminoacylation of resected RNA helices by class II aspartyl-tRNA synthetase dependent on a single nucleotide. EMBO J. 1994 May 1;13(9):2218–2226. doi: 10.1002/j.1460-2075.1994.tb06499.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  19. Garret M., Pajot B., Trézéguet V., Labouesse J., Merle M., Gandar J. C., Benedetto J. P., Sallafranque M. L., Alterio J., Gueguen M. A mammalian tryptophanyl-tRNA synthetase shows little homology to prokaryotic synthetases but near identity with mammalian peptide chain release factor. Biochemistry. 1991 Aug 6;30(31):7809–7817. doi: 10.1021/bi00245a021. [DOI] [PubMed] [Google Scholar]
  20. Giegé R., Puglisi J. D., Florentz C. tRNA structure and aminoacylation efficiency. Prog Nucleic Acid Res Mol Biol. 1993;45:129–206. doi: 10.1016/s0079-6603(08)60869-7. [DOI] [PubMed] [Google Scholar]
  21. Gietz R. D., Sugino A. New yeast-Escherichia coli shuttle vectors constructed with in vitro mutagenized yeast genes lacking six-base pair restriction sites. Gene. 1988 Dec 30;74(2):527–534. doi: 10.1016/0378-1119(88)90185-0. [DOI] [PubMed] [Google Scholar]
  22. Hale S. P., Auld D. S., Schmidt E., Schimmel P. Discrete determinants in transfer RNA for editing and aminoacylation. Science. 1997 May 23;276(5316):1250–1252. doi: 10.1126/science.276.5316.1250. [DOI] [PubMed] [Google Scholar]
  23. Hamann C. S., Hou Y. M. Enzymatic aminoacylation of tRNA acceptor stem helices with cysteine is dependent on a single nucleotide. Biochemistry. 1995 May 16;34(19):6527–6532. doi: 10.1021/bi00019a034. [DOI] [PubMed] [Google Scholar]
  24. Hipps D., Shiba K., Henderson B., Schimmel P. Operational RNA code for amino acids: species-specific aminoacylation of minihelices switched by a single nucleotide. Proc Natl Acad Sci U S A. 1995 Jun 6;92(12):5550–5552. doi: 10.1073/pnas.92.12.5550. [DOI] [PMC free article] [PubMed] [Google Scholar]
  25. Hountondji C., Dessen P., Blanquet S. Sequence similarities among the family of aminoacyl-tRNA synthetases. Biochimie. 1986 Sep;68(9):1071–1078. doi: 10.1016/s0300-9084(86)80181-x. [DOI] [PubMed] [Google Scholar]
  26. Kleeman T. A., Wei D., Simpson K. L., First E. A. Human tyrosyl-tRNA synthetase shares amino acid sequence homology with a putative cytokine. J Biol Chem. 1997 May 30;272(22):14420–14425. doi: 10.1074/jbc.272.22.14420. [DOI] [PubMed] [Google Scholar]
  27. Labouze E., Bedouelle H. Structural and kinetic bases for the recognition of tRNATyr by tyrosyl-tRNA synthetase. J Mol Biol. 1989 Feb 20;205(4):729–735. doi: 10.1016/0022-2836(89)90317-3. [DOI] [PubMed] [Google Scholar]
  28. Landès C., Perona J. J., Brunie S., Rould M. A., Zelwer C., Steitz T. A., Risler J. L. A structure-based multiple sequence alignment of all class I aminoacyl-tRNA synthetases. Biochimie. 1995;77(3):194–203. doi: 10.1016/0300-9084(96)88125-9. [DOI] [PubMed] [Google Scholar]
  29. Lee C. P., Dyson M. R., Mandal N., Varshney U., Bahramian B., RajBhandary U. L. Striking effects of coupling mutations in the acceptor stem on recognition of tRNAs by Escherichia coli Met-tRNA synthetase and Met-tRNA transformylase. Proc Natl Acad Sci U S A. 1992 Oct 1;89(19):9262–9266. doi: 10.1073/pnas.89.19.9262. [DOI] [PMC free article] [PubMed] [Google Scholar]
  30. Lee C. P., RajBhandary U. L. Mutants of Escherichia coli initiator tRNA that suppress amber codons in Saccharomyces cerevisiae and are aminoacylated with tyrosine by yeast extracts. Proc Natl Acad Sci U S A. 1991 Dec 15;88(24):11378–11382. doi: 10.1073/pnas.88.24.11378. [DOI] [PMC free article] [PubMed] [Google Scholar]
  31. Lin L., Hale S. P., Schimmel P. Aminoacylation error correction. Nature. 1996 Nov 7;384(6604):33–34. doi: 10.1038/384033b0. [DOI] [PubMed] [Google Scholar]
  32. Moras D. Structural and functional relationships between aminoacyl-tRNA synthetases. Trends Biochem Sci. 1992 Apr;17(4):159–164. doi: 10.1016/0968-0004(92)90326-5. [DOI] [PubMed] [Google Scholar]
  33. Musier-Forsyth K., Scaringe S., Usman N., Schimmel P. Enzymatic aminoacylation of single-stranded RNA with an RNA cofactor. Proc Natl Acad Sci U S A. 1991 Jan 1;88(1):209–213. doi: 10.1073/pnas.88.1.209. [DOI] [PMC free article] [PubMed] [Google Scholar]
  34. Nagel G. M., Doolittle R. F. Evolution and relatedness in two aminoacyl-tRNA synthetase families. Proc Natl Acad Sci U S A. 1991 Sep 15;88(18):8121–8125. doi: 10.1073/pnas.88.18.8121. [DOI] [PMC free article] [PubMed] [Google Scholar]
  35. Nair S., Ribas de Pouplana L., Houman F., Avruch A., Shen X., Schimmel P. Species-specific tRNA recognition in relation to tRNA synthetase contact residues. J Mol Biol. 1997 May 30;269(1):1–9. doi: 10.1006/jmbi.1997.1025. [DOI] [PubMed] [Google Scholar]
  36. Quinn C. L., Tao N., Schimmel P. Species-specific microhelix aminoacylation by a eukaryotic pathogen tRNA synthetase dependent on a single base pair. Biochemistry. 1995 Oct 3;34(39):12489–12495. doi: 10.1021/bi00039a001. [DOI] [PubMed] [Google Scholar]
  37. Ribas de Pouplana L., Frugier M., Quinn C. L., Schimmel P. Evidence that two present-day components needed for the genetic code appeared after nucleated cells separated from eubacteria. Proc Natl Acad Sci U S A. 1996 Jan 9;93(1):166–170. doi: 10.1073/pnas.93.1.166. [DOI] [PMC free article] [PubMed] [Google Scholar]
  38. Rould M. A., Perona J. J., Söll D., Steitz T. A. Structure of E. coli glutaminyl-tRNA synthetase complexed with tRNA(Gln) and ATP at 2.8 A resolution. Science. 1989 Dec 1;246(4934):1135–1142. doi: 10.1126/science.2479982. [DOI] [PubMed] [Google Scholar]
  39. Saks M. E., Sampson J. R., Abelson J. N. The transfer RNA identity problem: a search for rules. Science. 1994 Jan 14;263(5144):191–197. doi: 10.1126/science.7506844. [DOI] [PubMed] [Google Scholar]
  40. Sampson J. R., DiRenzo A. B., Behlen L. S., Uhlenbeck O. C. Nucleotides in yeast tRNAPhe required for the specific recognition by its cognate synthetase. Science. 1989 Mar 10;243(4896):1363–1366. doi: 10.1126/science.2646717. [DOI] [PubMed] [Google Scholar]
  41. Schimmel P. Aminoacyl tRNA synthetases: general scheme of structure-function relationships in the polypeptides and recognition of transfer RNAs. Annu Rev Biochem. 1987;56:125–158. doi: 10.1146/annurev.bi.56.070187.001013. [DOI] [PubMed] [Google Scholar]
  42. Schimmel P. An operational RNA code for amino acids and variations in critical nucleotide sequences in evolution. J Mol Evol. 1995 May;40(5):531–536. doi: 10.1007/BF00166621. [DOI] [PubMed] [Google Scholar]
  43. Schimmel P., Giegé R., Moras D., Yokoyama S. An operational RNA code for amino acids and possible relationship to genetic code. Proc Natl Acad Sci U S A. 1993 Oct 1;90(19):8763–8768. doi: 10.1073/pnas.90.19.8763. [DOI] [PMC free article] [PubMed] [Google Scholar]
  44. Schimmel P., Ribas de Pouplana L. Transfer RNA: from minihelix to genetic code. Cell. 1995 Jun 30;81(7):983–986. doi: 10.1016/s0092-8674(05)80002-9. [DOI] [PubMed] [Google Scholar]
  45. Schimmel P., Shepard A., Shiba K. Intron locations and functional deletions in relation to the design and evolution of a subgroup of class I tRNA synthetases. Protein Sci. 1992 Oct;1(10):1387–1391. doi: 10.1002/pro.5560011018. [DOI] [PMC free article] [PubMed] [Google Scholar]
  46. Schulman L. H., Pelka H. Anticodon switching changes the identity of methionine and valine transfer RNAs. Science. 1988 Nov 4;242(4879):765–768. doi: 10.1126/science.3055296. [DOI] [PubMed] [Google Scholar]
  47. Schulman L. H. Recognition of tRNAs by aminoacyl-tRNA synthetases. Prog Nucleic Acid Res Mol Biol. 1991;41:23–87. [PubMed] [Google Scholar]
  48. Senger B., Despons L., Walter P., Fasiolo F. The anticodon triplet is not sufficient to confer methionine acceptance to a transfer RNA. Proc Natl Acad Sci U S A. 1992 Nov 15;89(22):10768–10771. doi: 10.1073/pnas.89.22.10768. [DOI] [PMC free article] [PubMed] [Google Scholar]
  49. Shiba K., Schimmel P., Motegi H., Noda T. Human glycyl-tRNA synthetase. Wide divergence of primary structure from bacterial counterpart and species-specific aminoacylation. J Biol Chem. 1994 Nov 25;269(47):30049–30055. [PubMed] [Google Scholar]
  50. Shiba K., Suzuki N., Shigesada K., Namba Y., Schimmel P., Noda T. Human cytoplasmic isoleucyl-tRNA synthetase: selective divergence of the anticodon-binding domain and acquisition of a new structural unit. Proc Natl Acad Sci U S A. 1994 Aug 2;91(16):7435–7439. doi: 10.1073/pnas.91.16.7435. [DOI] [PMC free article] [PubMed] [Google Scholar]
  51. Starzyk R. M., Webster T. A., Schimmel P. Evidence for dispensable sequences inserted into a nucleotide fold. Science. 1987 Sep 25;237(4822):1614–1618. doi: 10.1126/science.3306924. [DOI] [PubMed] [Google Scholar]
  52. Steinberg S., Misch A., Sprinzl M. Compilation of tRNA sequences and sequences of tRNA genes. Nucleic Acids Res. 1993 Jul 1;21(13):3011–3015. doi: 10.1093/nar/21.13.3011. [DOI] [PMC free article] [PubMed] [Google Scholar]
  53. Vidal-Cros A., Bedouelle H. Role of residue Glu152 in the discrimination between transfer RNAs by tyrosyl-tRNA synthetase from Bacillus stearothermophilus. J Mol Biol. 1992 Feb 5;223(3):801–810. doi: 10.1016/0022-2836(92)90991-r. [DOI] [PubMed] [Google Scholar]
  54. Winter G., Koch G. L., Hartley B. S., Barker D. G. The amino acid sequence of the tyrosyl-tRNA synthetase from Bacillus stearothermophilus. Eur J Biochem. 1983 May 2;132(2):383–387. doi: 10.1111/j.1432-1033.1983.tb07374.x. [DOI] [PubMed] [Google Scholar]

Articles from The EMBO Journal are provided here courtesy of Nature Publishing Group

RESOURCES