Abstract
Aminoaql-tRNA synthetases catalyze the specific aminoacylation of tRNAs with their cognate amino acids, thus establishing the rules of the genetic code. The enzymes are universally distributed, and their sequences and structures reveal that the majority of them were established by the time of the divergence of archaeal and bacterial organisms, over 3000 millions years ago.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
Preview
Unable to display preview. Download preview PDF.
References
Schimmel PR, Soll D. Aminoacyl-tRNA synthetases: General features and recognition of transfer RNAs. Ann Rev Biochem 1979; 48:601–48.
Ribas de Pouplana L, Schimmel P. Operational RNA code for amino acids in relation to genetic code in evolution. J Biol Chem 2001; 276:6881–4.
Nagel GM, Doolittle RF. Evolution and relatedness in two aminoacyl-tRNA synthetase families. Proc Natl Acad Sci USA 1991; 88:8121–5.
Nagel GM, Doolittle RF. Phylogenetic analysis of the aminoacyl-tRNA synthetases. J Mol Evol 1995; 40:487–98.
Brown JR, Doolittle WF. Root of the universal tree of life based on ancient aminoacyl-tRNA synthetase gene duplications. Proc Natl Acad Sci USA 1995; 92:2441–5.
Giege R, Sissler M, Florentz C. Universal rules and idiosyncratic features in tRNA identity. Nuc Ac Res 1998; 26:5017–35.
Beuning PJ, Musier-Forsyth K. Transfer RNA recognition by aminoacyl-tRNA synthetases. Biopolymers 1999; 52:1–28.
Rich A. In: Kasha M, Pullman B, eds. Horizons in Biochemistry. New York: Academic Press, 1962:103–126.
Woese CR, Dugre DH, Kondo M et al. On the fundamental nature and evolution of the genetic code. CSH Symp Quant Biol 1966; 31:723–736.
Crick FH. The origin of the genetic code. J Mol Biol 1968; 38:367–79.
Orgel LE. Evolution of the genetic apparatus. J Mol Biol 1968; 38:381–93.
Wong JT. A co-evolution theory of the genetic code. Proc Natl Acad Sci USA 1975; 72:1909–12.
De Duve C. Blueprint for a cell: The nature and origin of life. Burlington, North Carolina: Neil Patterson, 1991.
Maizels N, Weiner AM. In: Gesteland RF, Atkins JF. The RNA world. New York: Cold Spring Harbor Laboratory Press, 1993.
Joyce GF, Orgel LE. In: Gesteland RF, Atkins JF. The RNA world. New York: Cold Spring Harbor Laboratory Press, 1993:1–26.
Szathmary E, Smith JM. The major evolutionary transitions. Nature 1995; 374:227–32.
Di Giulio, M. Reflections on the origin of the genetic code: A hypothesis. J Theor Biol 1998; 191:191–6.
Knight RD, Freeland SJ, Landweber LF. Selection, history and chemistry: the three faces of the genetic code. Trends Biochem Sci 1999; 24:241–7.
Szathmary E. The origin of the genetic code: amino acids as cofactors in an RNA world. Trends Genet 1999; 15:223–9.
Ellington AD, Szostak JW. In vitro selection of RNA molecules that bind specific ligands. Nature 1990; 346:818–22.
Guerrier-Takada C, Gardiner K, Marsh T et al. The RNA moiety of ribonuclease P is the catalytic subunit of the enzyme. Cell 1983; 35:849–57.
Illangasekare M, Sanchez G, Nickles T et al. Aminoacyl-RNA synthesis catalyzed by an RNA. Science 1995; 267:643–7.
Illangasekare M, Yarus M. A tiny RNA that catalyzes both aminoacyl-RNA and peptidyl-RNA synthesis. RNA 1999; 5:1482–9.
Jeffares DC, Poole AM, Penny D. Relics from the RNA world. J Molr Evol 1998; 46:18–36.
Saito H, Kourouklis D, Suga H. An in vitro evolved precursor tRNA with aminoacylation activity. EMBO J 2001; 20:1797–806.
Lee N, Suga H. A minihelix-loop RNA acts as a trans-aminoacylation catalyst. RNA 2001; 7:1043–51.
Saito H, Suga H. A ribozyme exclusively aminoacylates the 3-hydroxyl group of the tRNA terminal adenosine. J Am Chem Soc 2001; 123:7178–9.
Saito H, Watanabe K, Suga H. Concurrent molecular recognition of the amino acid and tRNA by a ribozyme. RNA 2001; 7:1867–78.
Noller HF. In: Gesteland RF, Atkins JF. The RNA world. New York: Cold Spring Harbor Laboratory Press, 1993:137–156.
Noller HF. tRNA-rRNA interactions and peptidyl transferase. FASEB J 1993; 7:87–9.
Cate JH, Yusupov MM, Yusupova GZ et al. X-ray crystal structures of 70S ribosome functional complexes. Science 1999; 285:2095–104.
Webster T, Tsai H, Kula M et al. Specific sequence homology and three-dimensional structure of an aminoacyl transfer RNA synthetase. Science 1984; 226:1315–7.
Hountondji C, Dessen P, Blanquet S. Sequence similarities among the family of aminoacyl-tRNA synthetases. Biochimie 1986; 68:1071–8.
Ludmerer SW, Schimmel P. Gene for yeast glutamine tRNA synthetase encodes a large amino-terminal extension and provides a strong confirmation of the signature sequence for a group of the aminoacyl-tRNA synthetases. J Biol Chem 1987; 262:10801–6.
Eriani G, Delarue M, Poch O et al. Partition of tRNA synthetases into two classes based on mutually exclusive sets of sequence motifs. Nature 1990; 347:203–6.
Cusack S, Berthet-Colominas C, Hartlein M et al. A second class of synthetase structure revealed by X-ray analysis of Escherichia coli seryl-tRNA synthetase at 2.5 A [see comments]. Nature 1990; 347:249–55.
Ibba M et al. A euryarchaeal lysyl-tRNA synthetase: resemblance to class I synthetases. Science 1997; 278:1119–22.
Schimmel P, Giege R, Moras D et al. An operational RNA code for amino acids and possible relationship to genetic code. Proc Natl Acad Sci USA 1993; 90:8763–8.
Schimmel P, Ribas de Pouplana L. Transfer RNA: From minihelix to genetic code. Cell 1995; 81:983–6.
Cusack S. Aminoacyl-tRNA synthetases. Cur Op Struct Biol 1997; 7:881–9.
Moras D. Structural and functional relationships between aminoacyl-tRNA synthetases. Trends Biochem Sci 1992; 17:159–64.
Carter CW Jr. Cognition, mechanism, and evolutionary relationships in aminoacyl-tRNA synthetases. Annu Rev Biochem 1993; 62:715–48.
Jasin M, Regan L, Schimmel P. Modular arrangement of functional domains along the sequence of an aminoacyl tRNA synthetase. Nature 1983; 306:441–7.
Shiba K, Schimmel P. Functional assembly of a randomly cleaved protein. Proc Natl Acad Sci USA 1992; 89:1880–4.
de Duve, C. Transfer RNAs: The second genetic code. Nature 1988; 333:117–118.
Schimmel P, Schmidt E. Making connections: RNA-dependent amino acid recognition. Trends Biochem Sci 1995; 20:1–2.
Lin L, Hale SP, Schimmel P. Aminoacylation error correction [letter]. Nature 1996; 384:33–4.
Nureki O et al. Enzyme structure with two catalytic sites for double-sieve selection of substrate [see comments]. Science 1998; 280:578–82.
Cusack S. Sequence, structure and evolutionary relationships between class 2 aminoacyl-tRNA synthetases: an update. Biochimie 1993; 75:1077–81.
Tsui WC, Fersht AR. Probing the principles of amino acid selection using the alanyl-tRNA synthetase from Escherichia coli. Nuc Ac Res 1981; 9:4627–37.
Beuning PJ, Musier-Forsyth K. Species-specific differences in amino acid editing by class II prolyl-tRNA synthetase. J Biol Chem 2001; 276:30779–85.
Beuning PJ, Musier-Forsyth K. Hydrolytic editing by a class II aminoacyl-tRNA synthetase. Proc Natl Acad Sci USA 2000; 97:8916–20.
Dock-Bregeon A et al. Transfer RNA-mediated editing in threonyl-tRNA synthetase. The class II solution to the double discrimination problem. Cell 2000; 103:877–84.
Sankaranarayanan R et al. The structure of threonyl-tRNA synthetase-tRNA(Thr) complex enlightens its repressor activity and reveals an essential zinc ion in the active site. Cell 1999; 97:371–81.
Beebe K, Ribas de Pouplana L, Schimmel P. Characterization of the editing activity of alanyl-tRNA synthetase. EMBO J; In press.
Sprinzl M, Cramer F. Site of aminoacylation of tRNAs from Escherichia coli with respect to the 2′-or 3′-hydroxyl group of the terminal adenosine. Proc Natl Acad Sci USA 1975; 72:3049–53.
Fraser TH, Rich A. Amino acids are not all initially attached to the same position on transfer RNA molecules. Proc Natl Acad Sci USA 1975; 72:3044–8.
Ribas de Pouplana L, Schimmel P. Two classes of tRNA synthetases suggested by sterically compatible dockings on tRNA acceptor stem. Cell 2001; 104.
Ribas de Pouplana L, Schimmel P. Aminoacyl-tRNA synthetases: potential markers of genetic code development. Trends BiochemSci 2001; 26:591–6.
Hashimoto T, Sanchez LB, Shirakura T et al. Secondary absence of mitochondria in Giardia lamblia and Trichomonas vaginalis revealed by valyl-tRNA synthetase phylogeny. Proc Natl Acad Sci USA 1998; 95:6860–5.
Chihade JW, Brown JR, Schimmel PR et al. Origin of mitochondria in relation to evolutionary history of eukaryotic alanyl-tRNA synthetase. Proc Natl Acad Sci USA 2000; 97:12153–7.
Bult CJ et al. Complete genome sequence of the methanogenic archaeon, Methanococcus jannaschii. Science 1996; 273:1058–73.
Ribas de Pouplana L, Turner RJ, Steer BA et al. Genetic code origins: tRNAs older than their synthetases? Proc Natl Acad Sci USA 1998; 95:11295–11300.
Brown JR, Doolittle WF. Gene descent, duplication, and horizontal transfer in the evolution of glutamyl-and glutaminyl-tRNA synthetases. J Mol Evol 1999; 49:485–95.
Lamour V et al. Evolution of the Glx-tRNA synthetase family: The glutaminyl enzyme as a case of horizontal gene transfer. Proc Natl Acad Sci USA 1994; 91:8670–4.
Becker HD et al. Thermus thermophilus contains an eubacterial and an archaebacterial aspartyl-tRNA synthetase. Biochemistry 2000; 39:3216–30.
Woese CR, Olsen GJ, Ibba M et al. Aminoacyl-tRNA synthetases, the genetic code, and the evolutionary process. Microbiol Mol Biol Rev 2000; 64:202–36.
Ibba M, Becker HD, Stathopoulos C et al. The adaptor hypothesis revisited. Trends Biochem Sci 2000; 25:311–6.
Stathopoulos C et al. One polypeptide with two aminoacyl-tRNA synthetase activities. Science 2000; 287:479–82.
Burke B, Lipman RS, Shiba K et al. Divergent adaptation of tRNA recognition by Methanococcus jannaschii prolyl-tRNA synthetase. J Biol Chem 2001; 276:20286–91.
Ribas de Pouplana L, Brown JR, Schimmel P. Structure-based phylogeny of class IIa tRNA synthetases in relation to an unusual biochemistry. J Mol Evol 2001; 53:261–8.
Fabrega C et al. An aminoacyl tRNA synthetase whose sequence fits into neither of the two known classes. Nature 2001; 411:110–4.
Ribas de Pouplana L, Frugier M, Quinn CL et al. Evidence that two present-day components needed for the genetic code appeared after nucleated cells separated from eubacteria. Proc Natl Acad Sci USA 1996; 93:166–70.
Brown JR, Robb FT, Weiss R et al. Evidence for the early divergence of tryptophanyl-and tyrosyl-tRNA synthetases. J Mol Evol 1997; 45:9–16.
Diaz-lazcoz Y et al. Evolution of genes, evolution of species: The case of aminoacyl-tRNA synthetases. Mol Biol Evol 1998; 15:1548–1561.
Wolf YI, Aravind L, Grishin NV et al. Evolution of aminoacyl-tRNA synthetases—analysis of unique domain architectures and phylogenetic trees reveals a complex history of horizontal gene transfer events. Genome Res 1999; 9:689–710.
Biou V, Yaremchuk A, Tukalo M et al. The 2.9 A crystal structure of T. thermophilus seryl-tRNA synthetase complexed with tRNA(Ser). Science 1994; 263:1404–10.
Fukai S et al. Structural basis for double-sieve discrimination of l-valine from l-isoleucine and l-threonine by the complex of tRNA(Val) and valyl-tRNA synthetase. Cell 2000; 103:793–803.
Bedouelle H. Recognition of tRNA(Tyr) by tyrosyl-tRNA synthetase. Biochimie 1990; 72:589–98.
Silvian LF, Wang J, Steitz TA. Insights into editing from an ile-tRNA synthetase structure with tRNAile and mupirocin. Science 1999; 285:1074–7.
Rould MA, Perona JJ, Soll D et al. Structure of E. coli glutaminyl-tRNA synthetase complexed with tRNA(Gln) and ATP at 2.8 A resolution [see comments]. Science 1989; 246:1135–42.
Ruff M et al. Class II aminoacyl transfer RNA synthetases: crystal structure of yeast aspartyl-tRNA synthetase complexed with tRNA(Asp). Science 1991; 252:1682–9.
Goldgur Y et al. The crystal structure of phenylalanyl-tRNA synthetase from thermus thermophilus complexed with cognate tRNAPhe. Structure 1997; 5:59–68.
Cusack S, Yaremchuk A, Tukalo M. The 2 A crystal structure of leucyl-tRNA synthetase and its complex with a leucyl-adenylate analogue. EMBO J 2000; 19:2351–61.
Baldwin AN, Berg P. Purification and properties of isoleucyl ribonucleic acid synthetase from Escherichia coli. J Biol Chem 1966; 241:831–8.
Eldred EW, Schimmel PR. Investigation of the transfer of amino acid from a transfer ribonucleic acid synthetase-aminoacyl adenylate complex to transfer ribonucleic acid. Biochemistry 1972; 11:17–23.
Fersht AR, Dingwall C. Evidence for the double-sieve editing mechanism in protein synthesis. Steric exclusion of isoleucine by valyl-tRNA synthetases. Biochemistry 1979; 18:2627–31.
Pelc SR, Welton MG. Stereochemical relationship between coding triplets and amino-acids. Nature 1966; 209:868–70.
Musier-Forsyth K, Schimmel P. Atomic determinants for aminoacylation of RNA minihelices and relationship to genetic code. Acc Chem Res 1999; 32:368–375.
Di Giulio M, Medugno M. Physicochemical optimization in the genetic code origin as the number of codified amino acids increases. J Mol Evol 1999; 49:1–10.
Ronneberg TA, Landweber LF, Freeland SJ. Testing a biosynthetic theory of the genetic code: Fact or artifact? Proc Natl Acad Sci USA 2000; 97:13690–5.
Di Giulio M. A blind empiricism against the coevolution theory of the origin of the genetic code. J Mol Evol 2001; 53:724–32.
Yarus M. An RNA-amino acid complex and the origin of the genetic code. New Biol 1991; 3:183–9.
Szathmary E. Coding coenzyme handles: a hypothesis for the origin of the genetic code. Proc Natl Acad Sci USA 1993; 90:9916–20.
Yarus M. RNA-ligand chemistry: A testable source for the genetic code. RNA 2000; 6:475–84.
Connell GJ, Illangesekare M, Yarus M. Three small ribooligonucleotides with specific arginine sites. Biochemistry 1993; 32:5497–502.
Zinnen S, Yarus M. An RNA pocket for the planar aromatic side chains of phenylalanine and tryptophane. Nuc Ac Symp Ser 1995; 33:148–51.
Tao J, Frankel AD. Arginine-binding RNAs resembling TAR identified by in vitro selection. Biochemistry 1996; 35:2229–38.
Majerfeld I, Yarus M. Isoleucine: RNA sites with associated coding sequences. RNA 1998; 4:471–8.
Yarus M. Amino acids as RNA ligands: A direct-RNA-template theory for the code’s origin. J Mol Evol 1998; 47:109–17.
Mannironi C, Scerch C, Fruscoloni P et al. Molecular recognition of amino acids by RNA aptamers: The evolution into an L-tyrosine binder of a dopamine-binding RNA motif. RNA 2000; 6:520–7.
Ellington AD, Khrapov M, Shaw CA. The scene of a frozen accident. RNA 2000; 6:485–98.
Rodin S, Ohno S, Rodin A. Transfer RNAs with complementary anticodons: could they reflect early evolution of discriminative genetic code adaptors? Proc Natl Acad Sci USA 1993; 90:4723–7.
Rodin S, Rodin A, Ohno S. The presence of codon-anticodon pairs in the acceptor stem of tRNAs. Proc Natl Acad Sci USA 1996; 93:4537–42.
Author information
Authors and Affiliations
Rights and permissions
Copyright information
© 2004 Eurekah.com and Kluwer Academic / Plenum Publishers
About this chapter
Cite this chapter
Ribas de Pouplana, L., Schimmel, P. (2004). Aminoacyl-tRNA Synthetases as Clues to Establishment of the Genetic Code. In: The Genetic Code and the Origin of Life. Springer, Boston, MA. https://doi.org/10.1007/0-387-26887-1_8
Download citation
DOI: https://doi.org/10.1007/0-387-26887-1_8
Publisher Name: Springer, Boston, MA
Print ISBN: 978-0-306-47843-7
Online ISBN: 978-0-387-26887-3
eBook Packages: Springer Book Archive