Transfer RNA Recognition and Aminoacylation by Synthetases

Abstract

Fidelity of transfer ribonucleic acid (tRNA) charging by amino acids ensures correct translation of the genetic code into proteins. Charging is catalysed by a set of enzymes known as aminoacyl‐tRNA synthetases. Owing to the degeneracy of the genetic code, some of the different tRNAs have the same amino acid attached to them. Specificity of charging obeys universal rules and is ensured by positive elements, the identity determinants unique to each tRNA and responsible for its recognition by the cognate synthetase, and negative elements, the antideterminants that prevent false recognitions. To fulfil the aminoacylation specificity and prevent noncognate aminoacyl‐tRNA delivery to the ribosome, some synthetases also mediate proofreading reactions that increase fidelity of the tRNA charging. In such reactions, misactivated amino acids or mischarged tRNAs are checked in specific sites and noncognate products are hydrolysed. However, mischarging is beneficial under certain stress circumstances or when catalysed by nondiscriminatory synthetases, and represents a driving force in evolution.

Key Concepts:

  • Translational expression of the genetic code refers to aminoacyl‐tRNA‐ and ribosome‐dependent decoding of genes into proteins, a process highly dependent on fidelity of tRNA aminoacylation by synthetases.

  • The rules that account for the aminoacylation identity of tRNAs are referred to as the second genetic code.

  • The RNA operational code is encoded in the acceptor stem of tRNA and is crucial for recognition by aminoacyl‐tRNA synthetases and specific aminoacylation.

  • Allostery in tRNA‐synthetase systems concerns long‐range transfer of chemical information (up to 75 Å) to the synthetase catalytic site (through the body of tRNA and/or synthetase) triggered by contacts of tRNA identity determinants with the synthetase.

  • Engineering the identity of tRNA‐synthetase systems allows reprogramming the genetic code.

Keywords: allostery; aminoacyl‐tRNA synthetase; genetic code; identity antideterminant; identity determinants; protein synthesis; RNA recognition; translation; tRNA; tRNA post‐transcriptional modification

Figure 1.

Cloverleaf folding of tRNA with location of known identity determinants and its three‐dimensional L‐shaped organisation. The standard cloverleaf structure of cytosolic tRNAs and conventional numbering system are used. Constant nucleotides (nts) are explicitly indicated (T and Ψ are modified residues: ribothymidine and pseudouridine). Note the presence within the variable region (nts 44 to 48) of the long extra arm of tRNALeu, tRNASer and tRNATyr. The • symbol indicates Watson–Crick base pairings, including G•U pairs; dotted green lines indicate other pairings, mostly between constant and/or semi‐constant residues important for tRNA L‐shaped architecture. The inset represents the L‐shaped structure of tRNA and highlights its different domains. Location of identity elements in the tRNA molecule is shown with a distinction between identities of tRNAs recognised by class I and class II synthetases. Characterised individual modified residues that act as identity determinants in tRNA anticodon loops are shown in the inset (k2C, lysidine; s2U, 2‐thiouridine; mnm5s2U, 5‐methylaminomethyl‐2‐thiouridine; Q, queuosine; I, inosine; Ψ, pseudouridine; m1G, 1‐methylguanosine; t6A, N6‐threonylcarbamoyladenosine; yW, wybutosine).

Figure 2.

Synthetase class‐dependent binding modes of tRNA and ATP molecules as revealed in GlnRS:tRNAGln:ATP and AspRS:tRNAAsp:ATP complexes. The upper part of the figure shows the different binding approaches of the catalytic domain of the aaRS molecules relative to the acceptor arm of tRNA. The structures of monomeric E. coli GlnRS and dimeric S. cerevisiae AspRS (only one monomer represented) are chosen as class‐representative aaRSs and are displayed so that to emphasise the two binding modes of tRNA via the minor or major groove side of its amino acid acceptor helix. The lower part of the figure shows the conformation of tRNA and ATP in the complexes. Binding of tRNA implies that CCA folds back in class I complexes and remains in regular helical conformation in class II complexes. The class‐specific architecture of the aaRS catalytic domain implies further that ATP exhibits an extended conformation in class I aaRSs (reminiscent of that found in other enzymes containing a Rossmann fold) and a bent conformation in class II aaRSs (with the γ‐phosphate folded back over the adenine base). The tRNA and ATP conformations are those found in the GlnRS–tRNAGln–ATP (left side) and AspRS–tRNAAsp–ATP (right side) complexes. Notice that tRNA binding on GlnRS and AspRS implies an unfolding of the anticodon loops with the unstacking of the anticodon bases favouring specific contacts with amino acids from the anticodon‐binding domains.

close

References

Ador L, Camasses A, Erbs P et al. (1999) Active site mapping of yeast aspartyl‐tRNA synthetase by in vivo selection of enzyme mutations lethal for cell growth. Journal of Molecular Biology 288: 231–242.

Aldinger CA, Leisinger AK and Igloi GL (2012) The influence of identity elements on the aminoacylation of tRNAArg by plant and E. coli arginyl‐tRNA synthetases. FEBS Journal 279: 3622–3638.

Alexander RW, Eargle J and Luthey‐Schulten Z (2010) Experimental and computational determination of tRNA dynamics. FEBS Letters 584: 376–386.

Ambrogelly A, Frugier M, Ibba M, Söll D and Giegé R (2005a) Transfer RNA recognition by class I lysyl‐tRNA synthetase from the Lyme disease pathogen Borrelia burgdorferi. FEBS Letters 579: 2629–2634.

Ambrogelly A, Kamtekar S, Stathopoulos C, Kennedy D and Söll D (2005b) Asymmetric behavior of archaeal prolyl‐tRNA synthetase. FEBS Letters 579: 6017–6022.

Ardell DH (2010) Computational analysis of tRNA identity. FEBS Letters 584: 325–333.

Auld DS and Schimmel P (1995) Switching recognition of two tRNA synthetases with an amino acid swap in a designed peptide. Science 267: 1994–1996.

Bezerra AR, Simoes J, Lee W et al. (2013) Reversion of a fungal genetic code alteration links proteome instability with genomic and phenotypic diversification. Proceedings of the National Academy of Sciences of the USA 110: 11079–11084.

Blaise M, Bailly M, Fréchin M et al. (2010) Crystal structure of a transfer‐ribonucleoprotein particle that promotes asparagine formation. EMBO Journal 29: 3118–3129.

Bonnefond L, Frugier M, Giegé R and Rudinger‐Thirion J (2005) Human mitochondrial TyrRS disobeys the tyrosine idenity rules. RNA 11: 558–562.

Bullock TL, Uter N, Nissan TA and Perona JJ (2003) Amino acid discrimination by a class I aminoacyl‐tRNA synthetase specified by negative determinants. Journal of Molecular Biology 328: 395–408.

Chimnaronk S, Gravers Jeppesen M, Suzuki T, Nyborg J and Watanabe K (2005) Dual‐mode recognition of noncanonical tRNAsSer by seryl‐tRNA synthetase in mammalian mitochondria. EMBO Journal 24: 3369–3379.

Cusack S, Berthet‐Colominas C, Härtlein M, Nassar N and Leberman R (1990) A second class of synthetase structure revealed by X‐ray analysis of Escherichia coli seryl‐tRNA synthetase at 2.5 Å. Nature 347: 249–255.

Dreher TW, Tsai CH and Skuzeski JM (1996) Aminoacylation identity switch of turnip yellow mosaic virus RNA from valine to methionine results in an infectious virus. Proceedings of the National Academy of Sciences of the USA 93: 12212–12216.

Ebel J‐P, Giegé R, Bonnet J et al. (1973) Factors determining the specificity of the tRNA aminoacylation reaction. Biochimie 55: 547–557.

Eriani G, Delarue M, Poch O, Gangloff J and Moras D (1990) Partition of tRNA synthetases into two classes based on mutually exclusive sets of sequence motifs. Nature 347: 203–206.

Fechter P, Rudinger‐Thirion J, Florentz C and Giegé R (2001) Novel features in the tRNA‐like world of plant viral RNAs. Cellular and Molecular Life Sciences 58: 1547–1561.

Fender A, Gaudry A, Jühling F, Sissler M and Florentz C (2012) Adaptation of aminoacylation identity rules to mammalian mitochondria. Biochimie 94: 1090–1097.

Fersht AR, Ashford JS, Bruton CJ et al. (1975) Active site titration and aminoacyl adenylate binding stoichiometry of aminoacyl‐tRNA synthetases. Biochemistry 14: 1–4.

Francin M and Mirande M (2006) Identity elements for specific aminoacylation of a tRNA by mammalian lysyl‐tRNA synthetase bearing a nonspecific tRNA‐interacting factor. Biochemistry 45: 10153–10160.

Frugier M, Florentz C, Schimmel P and Giegé R (1993) Triple aminoacylation specificity of a chimerized transfer RNA. Biochemistry 32: 14053–14061.

Giegé R (2006) The early history of tRNA recognition by aminoacyl‐tRNA synthetases. Journal of Biosciences 31: 477–488.

Giegé R, Jühling F, Pütz J et al. (2012) Structure of transfer RNAs: Similarity and variability. Wiley Interdisciplinary Reviews: RNA 3: 37–61.

Giegé R and Lapointe J (2009) Transfer RNA aminoacylation and modified nucleosides. In: Grosjean H (ed.) DNA and RNA Modification Enzymes: Structure, Mechanism, Function and Evolution, pp. 475–492. Georgetown, TX: Landes Bioscience.

Giegé R, Puglisi JD and Florentz C (1993) tRNA structure and aminoacylation efficiency. Progress in Nucleic Acid Research and Molecular Biology 45: 129–206.

Giegé R, Sissler M and Florentz C (1998) Universal rules and idiosyncratic features in tRNA identity. Nucleic Acids Research 26: 5017–5035.

Giegé R and Springer M (2012) Aminoacyl‐tRNA synthetases in the bacterial world. In: Curtiss III R, Kaper JB, Squires CL, Karp PD, Neidhardt FC and Slauch JM (eds) EcoSal –Escherichia coli and Salmonella: Cellular and Molecular Biology, new edn. Washington, DC: ASM Press. http://www.ecosal.org

Hou Y‐M and Schimmel P (1988) A simple structural feature is a major determinant of the identity of a transfer RNA. Nature 333: 140–145.

Ibba M, Francklyn C and Cusack S (eds) (2005) The Aminoacyl‐tRNA Synthetases. Georgetown, TX: Landes Bioscience.

Ito T and Yokoyama S (2010) Two enzymes bound to one tRNA assume alternative conformations for consecutive reactions. Nature 467: 612–616.

Kumazawa Y, Himeno H, Miura K‐I and Watanabe K (1991) Unilateral aminoacylation specificity between bovine mitochondria and eubacteria. Journal of Biochemistry (Tokyo) 109: 421–427.

Laowanapiban P, Kapustina M, Vonrhein C et al. (2009) Independent saturation of three TrpRS subsites generates a partially assembled state similar to those observed in molecular simulations. Proceedings of the National Academy of Sciences of the USA 106: 1790–1795.

Lee JW, Beebe K, Nangle LA et al. (2006) Editing‐defective tRNA synthetase causes protein misfolding and neurodegeneration. Nature 443: 50–55.

Li L, Boniecki MT, Jaffe JD et al. (2011) Naturally occurring aminoacyl‐tRNA synthetases editing‐domain mutations that cause mistranslation in Mycoplasma parasites. Proceedings of the National Academy of Sciences of the USA 108: 9378–9383.

Mallick B, Chakrabarti J, Sahoo S, Ghosh Z and Das S (2005) Identity elements of archaeal tRNA. DNA Research 12: 235–246.

Martinis SA and Schimmel P (1995) Small RNA oligonucleotide substrates for specific aminoacylations. In: Söll D and RajBhandary UL (eds) tRNA: Structure, Biosynthesis, and Function, pp. 349–370. Washington, DC: American Society for Microbiology Press.

Mascarenhas AP, An S, Rosen AE, Martinis SA and Musier‐Forsyth K (2009) Fidelity mechanisms of aminoacyl‐tRNA synthetases. In: Köhrer C and RajBhandary UL (eds) Protein Engineering, vol. 22, pp. 155–203. Berlin: Springer.

McClain WH (1993) Rules that govern tRNA identity in protein synthesis. Journal of Molecular Biology 234: 257–280.

McClain WH and Foss K (1988) Changing the identity of a tRNA by introducing a G‐U wobble pair near the 3′ acceptor end. Science 240: 793–796.

Muramatsu T, Nishikawa K, Nemoto F et al. (1988) Codon and amino‐acid specificities of a transfer RNA are both converted by a single post‐transcriptional modification. Nature 336: 179–181.

Musier‐Forsyth K and Schimmel P (1999) Atomic determinants for aminoacylation of RNA minihelices and relationship to genetic code. Accounts of Chemical Research 32: 368–375.

Neuenfeldt A, Lorber B, Ennifar E et al. (2013) Thermodynamic properties distinguish human mitochondrial aspartyl‐tRNA synthetase from bacterial homolog with same 3D architecture. Nucleic Acids Research 41: 2698–2708.

Normanly J and Abelson J (1989) tRNA identity. Annual Review of Biochemistry 58: 1029–1049.

Ohta A, Yamagishi Y and Suga H (2008) Synthesis of biopolymers using genetic code reprogramming. Current Opinion Chemical Biology 12: 159–167.

Pan T (2013) Adaptive translation as a mechanism of stress response and adaptation. Annual Review of Genetics 47: 121–137.

Perona JJ and Hou Y‐M (2007) Indirect readout of tRNA for aminoacylation. Biochemistry 46: 10419–10432.

Perret V, Garcia A, Grosjean H et al. (1990) Relaxation of transfer RNA specificity by removal of modified nucleotides. Nature 344: 787–789.

Pütz J, Puglisi JD, Florentz C and Giegé R (1991) Identity elements for specific aminoacylation of yeast tRNAAsp by cognate aspartyl‐tRNA synthetase. Science 252: 1696–1699.

Pütz J, Puglisi JD, Florentz C and Giegé R (1993) Additive, cooperative and anti‐cooperative effects between identity nucleotides of a tRNA. EMBO Journal 12: 2949–2957.

Rodriguez‐Hernandez A and Perona JJ (2011) Heat maps for intramolecular communication in an RNP enzyme encoding glutamine. Structure 19: 386–396.

Rosen AE and Musier‐Forsyth K (2004) Recognition of G−1:C73 atomic groups by Escherichia coli histidyl‐tRNA synthetase. Journal of the American Chemical Society 126: 64–65.

Rould MA, Perona JJ, Söll D and Steitz TA (1989) Structure of E. coli glutaminyl‐tRNA synthetase complexed with tRNAGln and ATP at 2.8 Å resolution. Science 246: 1135–1142.

Ruff M, Krishnaswamy S, Boeglin M et al. (1991) Class II aminoacyl transfer RNA synthetases: crystal structure of yeast aspartyl‐tRNA synthetase complexed with tRNAAsp. Science 252: 1682–1689.

Saks ME, Sampson JR and Abelson JN (1994) The transfer RNA identity problem: a search for rules. Science 263: 191–197.

Sauerwald A, Zhu W, Major TA et al. (2005) RNA‐dependent cysteine biosynthesis in archaea. Science 307: 1969–1972.

Schimmel P, Giegé R, Moras D and Yokoyama S (1993) An operational RNA code for amino acids and possible relationship to genetic code. Proceedings of the National Academy of Sciences of the USA 90: 8763–8768.

Schmitt E, Meinnel T, Panvert M, Mechulam Y and Blanquet S (1993) Two acidic residues of Escherichia coli methionyl‐tRNA synthetase act as negative discriminants towards the binding of non‐cognate tRNA anticodons. Journal of Molecular Biology 233: 615–628.

Tinkle‐Peterson E and Uhlenbeck OC (1992) Determination of recognition nucleotides for Escherichia coli phenylalanyl‐tRNA synthetase. Biochemistry 31: 10380–10389.

Tocchini‐Valentini G, Saks M and Abelson J (2000) tRNA leucine identity and recognition sets. Journal of Molecular Biology 298: 779–793.

Tsuchiya W and Hasegawa T (2009) Molecular recognition of tryptophan tRNA by tryptophanyl‐tRNA synthetase from Aeropyrum pernix K1. Journal of Biochemistry (Tokyo) 145: 635–641.

Young TS and Schultz PG (2010) Beyond the canonical 20 amino acids: expanding the genetic lexicon. Journal of Biological Chemistry 285: 11039–11044.

Yuan J, O'Donoghue P, Ambrogelly A et al. (2010) Distinct genetic code expansion strategies for selenocysteine and pyrrolysine are reflected in different aminoacyl‐tRNA formation systems. FEBS Letters 584: 342–349.

Further Reading

Alexander RW and Schimmel P (2001) Domain‐domain communication in aminoacyl‐tRNA synthetases. Progress in Nucleic Acid Research and Molecular Biology 69: 317–349.

Beuning PJ and Musier‐Forsyth K (1999) Transfer RNA recognition by aminoacyl‐tRNA synthetases. Biopolymers 52: 1–28.

Dreher T (2010) Viral tRNA‐like structures. Wiley Interdisciplinary Reviews: RNA 1: 402–414.

Francklyn CS, First EA, Perona JJ and Hou Y‐M (2008) Methods for kinetic and thermodynamic analysis of aminoacyl‐tRNA synthetases. Methods 44: 100–118.

Francklyn CS and Minajigi A (2010) tRNA as an active chemical scaffold for diverse chemical transformations. FEBS Letters 584: 366–375.

Grosjean H (ed.) (2009) DNA and RNA Modification Enzymes: Comparative Structure, Mechanism, Functions, Cellular Interactions and Evolution. Austin, TX: Landes Bioscience.

Köhrer C and RajBhandary UL (eds) (2009) Protein Engineering. Berlin: Springer‐Verlag.

Mans MW, Pleij CWA and Bosch L (1991) tRNA‐like structures. Structure, function and evolutionary significance. European Journal of Biochemistry 201: 303–324.

Watanabe K (2010) Unique features of animal mitochondrial translation systems – The non‐universal genetic code, unusual features of the translational apparatus and their relevance to human mitochondrial diseases. Proceedings of the Japan Academy Series B, Physical and Biological Sciences 86: 11–39.

Contact Editor close
Submit a note to the editor about this article by filling in the form below.

* Required Field

How to Cite close
Giegé, Richard, and Eriani, Gilbert(Sep 2014) Transfer RNA Recognition and Aminoacylation by Synthetases. In: eLS. John Wiley & Sons Ltd, Chichester. http://www.els.net [doi: 10.1002/9780470015902.a0000531.pub3]