Skip to main content

Emergence and Evolution

  • Chapter
  • First Online:
Book cover Aminoacyl-tRNA Synthetases in Biology and Medicine

Part of the book series: Topics in Current Chemistry ((TOPCURRCHEM,volume 344))

Abstract

The aminoacyl-tRNA synthetases (aaRSs) are essential components of the protein synthesis machinery responsible for defining the genetic code by pairing the correct amino acids to their cognate tRNAs. The aaRSs are an ancient enzyme family believed to have origins that may predate the last common ancestor and as such they provide insights into the evolution and development of the extant genetic code. Although the aaRSs have long been viewed as a highly conserved group of enzymes, findings within the last couple of decades have started to demonstrate how diverse and versatile these enzymes really are. Beyond their central role in translation, aaRSs and their numerous homologs have evolved a wide array of alternative functions both inside and outside translation. Current understanding of the emergence of the aaRSs, and their subsequent evolution into a functionally diverse enzyme family, are discussed in this chapter.

Graphical Abstract

This is a preview of subscription content, log in via an institution to check access.

Access this chapter

Chapter
USD 29.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD 299.00
Price excludes VAT (USA)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
Hardcover Book
USD 379.99
Price excludes VAT (USA)
  • Durable hardcover edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Institutional subscriptions

Notes

  1. 1.

    Specific aminoacyl-tRNA synthetases are denoted by their three-letter amino acid designation, e.g., LysRS for lysyl-tRNA synthetase. Lysine tRNA or tRNALys denote uncharged tRNA specific for lysine; lysyl-tRNA or Lys-tRNA denote tRNA aminoacylated with lysine.

References

  1. Illangasekare M, Yarus M (1999) A tiny RNA that catalyzes both aminoacyl-RNA and peptidyl-RNA synthesis. RNA 5(11):1482–1489

    CAS  Google Scholar 

  2. Lee N, Bessho Y, Wei K, Szostak JW, Suga H (2000) Ribozyme-catalyzed tRNA aminoacylation. Nat Struct Biol 7(1):28–33

    CAS  Google Scholar 

  3. Kumar RK, Yarus M (2001) RNA-catalyzed amino acid activation. Biochemistry 40(24):6998–7004

    CAS  Google Scholar 

  4. Francklyn C, Schimmel P (1989) Aminoacylation of RNA minihelices with alanine. Nature 337(6206):478–481

    CAS  Google Scholar 

  5. Musier-Forsyth K, Schimmel P (1994) Acceptor helix interactions in a class II tRNA synthetase: photoaffinity cross-linking of an RNA miniduplex substrate. Biochemistry 33(3):773–779

    CAS  Google Scholar 

  6. Schimmel P, Frugier M, Glasfeld E (1997) Peptides for RNA discrimination and for assembly of enzymes that act on RNA. Nucleic Acids Symp Ser (36):1

    Google Scholar 

  7. Ibba M, Curnow AW, Soll D (1997) Aminoacyl-tRNA synthesis: divergent routes to a common goal. Trends Biochem Sci 22(2):39–42

    CAS  Google Scholar 

  8. Ramaswamy K, Wei K, Suga H (2002) Minihelix-loop RNAs: minimal structures for aminoacylation catalysts. Nucleic Acids Res 30(10):2162–2171

    CAS  Google Scholar 

  9. Tamura K (2011) Ribosome evolution: emergence of peptide synthesis machinery. J Biosci 36(5):921–928

    CAS  Google Scholar 

  10. Xiao JF, Yu J (2007) A scenario on the stepwise evolution of the genetic code. Genomics Proteomics Bioinformatics 5(3–4):143–151

    CAS  Google Scholar 

  11. Woese CR, Olsen GJ, Ibba M, Soll D (2000) Aminoacyl-tRNA synthetases, the genetic code, and the evolutionary process. Microbiol Mol Biol Rev 64(1):202–236

    CAS  Google Scholar 

  12. Nagel GM, Doolittle RF (1995) Phylogenetic analysis of the aminoacyl-tRNA synthetases. J Mol Evol 40(5):487–498

    CAS  Google Scholar 

  13. Fournier GP, Andam CP, Alm EJ, Gogarten JP (2011) Molecular evolution of aminoacyl tRNA synthetase proteins in the early history of life. Orig Life Evol Biosph 41(6):621–632

    CAS  Google Scholar 

  14. Hohn MJ, Park HS, O'Donoghue P, Schnitzbauer M, Soll D (2006) Emergence of the universal genetic code imprinted in an RNA record. Proc Natl Acad Sci U S A 103(48):18095–18100

    CAS  Google Scholar 

  15. Eriani G, Delarue M, Poch O, Gangloff J, Moras D (1990) Partition of tRNA synthetases into two classes based on mutually exclusive sets of sequence motifs. Nature 347(6289):203–206

    CAS  Google Scholar 

  16. Cusack S (1995) Eleven down and nine to go. Nat Struct Biol 2(10):824–831

    CAS  Google Scholar 

  17. Arnez JG, Moras D (1997) Structural and functional considerations of the aminoacylation reaction. Trends Biochem Sci 22(6):211–216

    CAS  Google Scholar 

  18. Ribas de Pouplana L, Schimmel P (2001) Two classes of tRNA synthetases suggested by sterically compatible dockings on tRNA acceptor stem. Cell 104(2):191–193

    CAS  Google Scholar 

  19. Ibba M, Morgan S, Curnow AW, Pridmore DR, Vothknecht UC, Gardner W, Lin W, Woese CR, Soll D (1997) A euryarchaeal lysyl-tRNA synthetase: resemblance to class I synthetases. Science 278(5340):1119–1122

    CAS  Google Scholar 

  20. Terada T, Nureki O, Ishitani R, Ambrogelly A, Ibba M, Soll D, Yokoyama S (2002) Functional convergence of two lysyl-tRNA synthetases with unrelated topologies. Nat Struct Biol 9(4):257–262

    CAS  Google Scholar 

  21. First EA (2005) Catalysis of the tRNA aminoacylation reaction. In: Ibba M, Francklyn C, Cusack S (eds) The aminoacyl-tRNA synthetases. Landes Bioscience, Georgetown, pp 328–352

    Google Scholar 

  22. Bedouelle H (2005) Tyrosyl-tRNA synthetases. In: Ibba M, Francklyn C, Cusack S (eds) The aminoacyl-tRNA synthetases. Landes Bioscience, Georgetown

    Google Scholar 

  23. Sprinzl M, Cramer F (1975) 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 U S A 72(8):3049–3053

    CAS  Google Scholar 

  24. Fersht AR, Gangloff J, Dirheimer G (1978) Reaction pathway and rate-determining step in the aminoacylation of tRNAArg catalyzed by the arginyl-tRNA synthetase from yeast. Biochemistry 17(18):3740–3746

    CAS  Google Scholar 

  25. Zhang CM, Perona JJ, Ryu K, Francklyn C, Hou YM (2006) Distinct kinetic mechanisms of the two classes of aminoacyl-tRNA synthetases. J Mol Biol 361(2):300–311

    CAS  Google Scholar 

  26. Kaminska M, Shalak V, Mirande M (2001) The appended C-domain of human methionyl-tRNA synthetase has a tRNA-sequestering function. Biochemistry 40(47):14309–14316

    CAS  Google Scholar 

  27. O'Donoghue P, Luthey-Schulten Z (2003) On the evolution of structure in aminoacyl-tRNA synthetases. Microbiol Mol Biol Rev 67(4):550–573

    Google Scholar 

  28. Ibba M, Soll D (2001) The renaissance of aminoacyl-tRNA synthesis. EMBO Rep 2(5):382–387

    CAS  Google Scholar 

  29. Nureki O, Vassylyev DG, Tateno M, Shimada A, Nakama T, Fukai S, Konno M, Hendrickson TL, Schimmel P, Yokoyama S (1998) Enzyme structure with two catalytic sites for double-sieve selection of substrate. Science 280(5363):578–582

    CAS  Google Scholar 

  30. Chen JF, Guo NN, Li T, Wang ED, Wang YL (2000) CP1 domain in Escherichia coli leucyl-tRNA synthetase is crucial for its editing function. Biochemistry 39(22):6726–6731

    CAS  Google Scholar 

  31. Fukai S, Nureki O, Sekine S, Shimada A, Tao J, Vassylyev DG, Yokoyama S (2000) 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 103(5):793–803

    CAS  Google Scholar 

  32. Lincecum TL (2005) Leucyl-tRNA synthetases. In: Ibba M, Francklyn C, Cusack S (eds) The aminoacyl-tRNA synthetases. Landes Bioscience, Georgetown

    Google Scholar 

  33. Cusack S, Yaremchuk A, Tukalo M (2000) The 2 A crystal structure of leucyl-tRNA synthetase and its complex with a leucyl-adenylate analogue. EMBO J 19(10):2351–2361

    CAS  Google Scholar 

  34. Ravel JM, White MN, Shive W (1965) Activation of tyrosine analogs in relation to enzyme repression. Biochem Biophys Res Commun 20(3):352–359

    CAS  Google Scholar 

  35. Mitra SK, Mehler AH (1967) The arginyl transfer ribonucleic acid synthetase of Escherichia coli. J Biol Chem 242(23):5490–5494

    CAS  Google Scholar 

  36. Ibba M, Losey HC, Kawarabayasi Y, Kikuchi H, Bunjun S, Soll D (1999) Substrate recognition by class I lysyl-tRNA synthetases: a molecular basis for gene displacement. Proc Natl Acad Sci U S A 96(2):418–423

    CAS  Google Scholar 

  37. Lamour V, Quevillon S, Diriong S, N'Guyen VC, Lipinski M, Mirande M (1994) Evolution of the Glx-tRNA synthetase family: the glutaminyl enzyme as a case of horizontal gene transfer. Proc Natl Acad Sci U S A 91(18):8670–8674

    CAS  Google Scholar 

  38. Dubois DY (2005) Glutamyl-tRNA synthetases. In: Ibba M, Francklyn C, Cusack S (eds) The aminoacyl-tRNA synthetases. Landes Bioscience, Georgetown, pp 89–98

    Google Scholar 

  39. Ribas de Pouplana L, Frugier M, Quinn CL, Schimmel P (1996) 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 93(1):166–170

    CAS  Google Scholar 

  40. Andam CP, Williams D, Gogarten JP (2010) Biased gene transfer mimics patterns created through shared ancestry. Proc Natl Acad Sci U S A 107(23):10679–10684

    CAS  Google Scholar 

  41. Brown JR, Robb FT, Weiss R, Doolittle WF (1997) Evidence for the early divergence of tryptophanyl- and tyrosyl-tRNA synthetases. J Mol Evol 45(1):9–16

    CAS  Google Scholar 

  42. Frugier M, Moulinier L, Giege R (2000) A domain in the N-terminal extension of class IIb eukaryotic aminoacyl-tRNA synthetases is important for tRNA binding. EMBO J 19(10):2371–2380

    CAS  Google Scholar 

  43. Berthet-Colominas C, Seignovert L, Hartlein M, Grotli M, Cusack S, Leberman R (1998) The crystal structure of asparaginyl-tRNA synthetase from Thermus thermophilus and its complexes with ATP and asparaginyl-adenylate: the mechanism of discrimination between asparagine and aspartic acid. EMBO J 17(10):2947–2960

    CAS  Google Scholar 

  44. Commans S, Plateau P, Blanquet S, Dardel F (1995) Solution structure of the anticodon-binding domain of Escherichia coli lysyl-tRNA synthetase and studies of its interaction with tRNA(Lys). J Mol Biol 253(1):100–113

    CAS  Google Scholar 

  45. Delarue M, Moras D (1993) The aminoacyl-tRNA synthetase family: modules at work. Bioessays 15(10):675–687

    CAS  Google Scholar 

  46. Roy H, Ling J, Alfonzo J, Ibba M (2005) Loss of editing activity during the evolution of mitochondrial phenylalanyl-tRNA synthetase. J Biol Chem 280(46):38186–38192

    CAS  Google Scholar 

  47. Shiba K (2005) Glycyl-tRNA synthetases. In: Ibba C, Francklyn C, Cusack S (eds) The aminoacyl-tRNA synthetases. Landes Bioscience, Georgetown, pp 125–134

    Google Scholar 

  48. Newberry KJ, Hou YM, Perona JJ (2002) Structural origins of amino acid selection without editing by cysteinyl-tRNA synthetase. EMBO J 21(11):2778–2787

    CAS  Google Scholar 

  49. Silvian LF, Wang J, Steitz TA (1999) Insights into editing from an ile-tRNA synthetase structure with tRNAile and mupirocin. Science 285(5430):1074–1077

    CAS  Google Scholar 

  50. Nakama T, Nureki O, Yokoyama S (2001) Structural basis for the recognition of isoleucyl-adenylate and an antibiotic, mupirocin, by isoleucyl-tRNA synthetase. J Biol Chem 276(50):47387–47393

    CAS  Google Scholar 

  51. Tukalo M, Yaremchuk A, Fukunaga R, Yokoyama S, Cusack S (2005) The crystal structure of leucyl-tRNA synthetase complexed with tRNALeu in the post-transfer-editing conformation. Nat Struct Mol Biol 12(10):923–930

    CAS  Google Scholar 

  52. Rock FL, Mao W, Yaremchuk A, Tukalo M, Crepin T, Zhou H, Zhang YK, Hernandez V, Akama T, Baker SJ, Plattner JJ, Shapiro L, Martinis SA, Benkovic SJ, Cusack S, Alley MR (2007) An antifungal agent inhibits an aminoacyl-tRNA synthetase by trapping tRNA in the editing site. Science 316(5832):1759–1761

    CAS  Google Scholar 

  53. Lincecum TL Jr, Tukalo M, Yaremchuk A, Mursinna RS, Williams AM, Sproat BS, Van Den Eynde W, Link A, Van Calenbergh S, Grotli M, Martinis SA, Cusack S (2003) Structural and mechanistic basis of pre- and posttransfer editing by leucyl-tRNA synthetase. Mol Cell 11(4):951–963

    CAS  Google Scholar 

  54. Palencia A, Crepin T, Vu MT, Lincecum TL Jr, Martinis SA, Cusack S (2012) Structural dynamics of the aminoacylation and proofreading functional cycle of bacterial leucyl-tRNA synthetase. Nat Struct Mol Biol 19(7):677–684

    CAS  Google Scholar 

  55. Larson ET, Kim JE, Zucker FH, Kelley A, Mueller N, Napuli AJ, Verlinde CL, Fan E, Buckner FS, Van Voorhis WC, Merritt EA, Hol WG (2011) Structure of Leishmania major methionyl-tRNA synthetase in complex with intermediate products methionyladenylate and pyrophosphate. Biochimie 93(3):570–582

    CAS  Google Scholar 

  56. Nakanishi K, Ogiso Y, Nakama T, Fukai S, Nureki O (2005) Structural basis for anticodon recognition by methionyl-tRNA synthetase. Nat Struct Mol Biol 12(10):931–932

    CAS  Google Scholar 

  57. Shibata S, Gillespie JR, Ranade RM, Koh CY, Kim JE, Laydbak JU, Zucker FH, Hol WG, Verlinde CL, Buckner FS, Fan E (2012) Urea-based inhibitors of Trypanosoma brucei methionyl-tRNA synthetase: selectivity and in vivo characterization. J Med Chem 55(14):6342–6351

    CAS  Google Scholar 

  58. Crepin T, Schmitt E, Blanquet S, Mechulam Y (2004) Three-dimensional structure of methionyl-tRNA synthetase from Pyrococcus abyssi. Biochemistry 43(9):2635–2644

    CAS  Google Scholar 

  59. Ingvarsson H, Unge T (2010) Flexibility and communication within the structure of the Mycobacterium smegmatis methionyl-tRNA synthetase. FEBS J 277(19):3947–3962

    CAS  Google Scholar 

  60. Crepin T, Schmitt E, Mechulam Y, Sampson PB, Vaughan MD, Honek JF, Blanquet S (2003) Use of analogues of methionine and methionyl adenylate to sample conformational changes during catalysis in Escherichia coli methionyl-tRNA synthetase. J Mol Biol 332(1):59–72

    CAS  Google Scholar 

  61. Mechulam Y, Schmitt E, Maveyraud L, Zelwer C, Nureki O, Yokoyama S, Konno M, Blanquet S (1999) Crystal structure of Escherichia coli methionyl-tRNA synthetase highlights species-specific features. J Mol Biol 294(5):1287–1297

    CAS  Google Scholar 

  62. Fukai S, Nureki O, Sekine S, Shimada A, Vassylyev DG, Yokoyama S (2003) Mechanism of molecular interactions for tRNA(Val) recognition by valyl-tRNA synthetase. RNA 9(1):100–111

    CAS  Google Scholar 

  63. Delagoutte B, Moras D, Cavarelli J (2000) tRNA aminoacylation by arginyl-tRNA synthetase: induced conformations during substrates binding. EMBO J 19(21):5599–5610

    CAS  Google Scholar 

  64. Konno M, Sumida T, Uchikawa E, Mori Y, Yanagisawa T, Sekine S, Yokoyama S (2009) Modeling of tRNA-assisted mechanism of Arg activation based on a structure of Arg-tRNA synthetase, tRNA, and an ATP analog (ANP). FEBS J 276(17):4763–4779

    CAS  Google Scholar 

  65. Shimada A, Nureki O, Goto M, Takahashi S, Yokoyama S (2001) Structural and mutational studies of the recognition of the arginine tRNA-specific major identity element, A20, by arginyl-tRNA synthetase. Proc Natl Acad Sci U S A 98(24):13537–13542

    CAS  Google Scholar 

  66. Cavarelli J, Delagoutte B, Eriani G, Gangloff J, Moras D (1998) l-Arginine recognition by yeast arginyl-tRNA synthetase. EMBO J 17(18):5438–5448

    CAS  Google Scholar 

  67. Perona JJ, Swanson RN, Rould MA, Steitz TA, Soll D (1989) Structural basis for misaminoacylation by mutant E. coli glutaminyl-tRNA synthetase enzymes. Science 246(4934):1152–1154

    CAS  Google Scholar 

  68. Rould MA, Perona JJ, Soll D, Steitz TA (1989) Structure of E. coli glutaminyl-tRNA synthetase complexed with tRNA(Gln) and ATP at 2.8 A resolution. Science 246(4934):1135–1142

    CAS  Google Scholar 

  69. Deniziak M, Sauter C, Becker HD, Paulus CA, Giege R, Kern D (2007) Deinococcus glutaminyl-tRNA synthetase is a chimer between proteins from an ancient and the modern pathways of aminoacyl-tRNA formation. Nucleic Acids Res 35(5):1421–1431

    CAS  Google Scholar 

  70. Rath VL, Silvian LF, Beijer B, Sproat BS, Steitz TA (1998) How glutaminyl-tRNA synthetase selects glutamine. Structure 6(4):439–449

    CAS  Google Scholar 

  71. Bullock TL, Uter N, Nissan TA, Perona JJ (2003) Amino acid discrimination by a class I aminoacyl-tRNA synthetase specified by negative determinants. J Mol Biol 328(2):395–408

    CAS  Google Scholar 

  72. Rould MA, Perona JJ, Steitz TA (1991) Structural basis of anticodon loop recognition by glutaminyl-tRNA synthetase. Nature 352(6332):213–218

    CAS  Google Scholar 

  73. Sekine S, Nureki O, Dubois DY, Bernier S, Chenevert R, Lapointe J, Vassylyev DG, Yokoyama S (2003) ATP binding by glutamyl-tRNA synthetase is switched to the productive mode by tRNA binding. EMBO J 22(3):676–688

    CAS  Google Scholar 

  74. Sekine S, Shichiri M, Bernier S, Chenevert R, Lapointe J, Yokoyama S (2006) Structural bases of transfer RNA-dependent amino acid recognition and activation by glutamyl-tRNA synthetase. Structure 14(12):1791–1799

    CAS  Google Scholar 

  75. Nureki O, Vassylyev DG, Katayanagi K, Shimizu T, Sekine S, Kigawa T, Miyazawa T, Yokoyama S, Morikawa K (1995) Architectures of class-defining and specific domains of glutamyl-tRNA synthetase. Science 267(5206):1958–1965

    CAS  Google Scholar 

  76. Nureki O, O'Donoghue P, Watanabe N, Ohmori A, Oshikane H, Araiso Y, Sheppard K, Soll D, Ishitani R (2010) Structure of an archaeal non-discriminating glutamyl-tRNA synthetase: a missing link in the evolution of Gln-tRNAGln formation. Nucleic Acids Res 38(20):7286–7297

    CAS  Google Scholar 

  77. Schulze JO, Masoumi A, Nickel D, Jahn M, Jahn D, Schubert WD, Heinz DW (2006) Crystal structure of a non-discriminating glutamyl-tRNA synthetase. J Mol Biol 361(5):888–897

    CAS  Google Scholar 

  78. Ito T, Kiyasu N, Matsunaga R, Takahashi S, Yokoyama S (2010) Structure of nondiscriminating glutamyl-tRNA synthetase from Thermotoga maritima. Acta Crystallogr D Biol Crystallogr 66(Pt 7):813–820

    CAS  Google Scholar 

  79. Doublie S, Bricogne G, Gilmore C, Carter CW Jr (1995) Tryptophanyl-tRNA synthetase crystal structure reveals an unexpected homology to tyrosyl-tRNA synthetase. Structure 3(1):17–31

    CAS  Google Scholar 

  80. Retailleau P, Yin Y, Hu M, Roach J, Bricogne G, Vonrhein C, Roversi P, Blanc E, Sweet RM, Carter CW Jr (2001) High-resolution experimental phases for tryptophanyl-tRNA synthetase (TrpRS) complexed with tryptophanyl-5′AMP. Acta Crystallogr D Biol Crystallogr 57(Pt 11):1595–1608

    CAS  Google Scholar 

  81. Retailleau P, Huang X, Yin Y, Hu M, Weinreb V, Vachette P, Vonrhein C, Bricogne G, Roversi P, Ilyin V, Carter CW Jr (2003) Interconversion of ATP binding and conformational free energies by tryptophanyl-tRNA synthetase: structures of ATP bound to open and closed, pre-transition-state conformations. J Mol Biol 325(1):39–63

    CAS  Google Scholar 

  82. Retailleau P, Weinreb V, Hu M, Carter CW Jr (2007) Crystal structure of tryptophanyl-tRNA synthetase complexed with adenosine-5′ tetraphosphate: evidence for distributed use of catalytic binding energy in amino acid activation by class I aminoacyl-tRNA synthetases. J Mol Biol 369(1):108–128

    CAS  Google Scholar 

  83. Buddha MR, Crane BR (2005) Structure and activity of an aminoacyl-tRNA synthetase that charges tRNA with nitro-tryptophan. Nat Struct Mol Biol 12(3):274–275

    CAS  Google Scholar 

  84. Yang XL, Otero FJ, Ewalt KL, Liu J, Swairjo MA, Kohrer C, RajBhandary UL, Skene RJ, McRee DE, Schimmel P (2006) Two conformations of a crystalline human tRNA synthetase-tRNA complex: implications for protein synthesis. EMBO J 25(12):2919–2929

    CAS  Google Scholar 

  85. Arakaki TL, Carter M, Napuli AJ, Verlinde CL, Fan E, Zucker F, Buckner FS, Van Voorhis WC, Hol WG, Merritt EA (2010) The structure of tryptophanyl-tRNA synthetase from Giardia lamblia reveals divergence from eukaryotic homologs. J Struct Biol 171(2):238–243

    CAS  Google Scholar 

  86. Han GW, Yang XL, McMullan D, Chong YE, Krishna SS, Rife CL, Weekes D, Brittain SM, Abdubek P, Ambing E, Astakhova T, Axelrod HL, Carlton D, Caruthers J, Chiu HJ, Clayton T, Duan L, Feuerhelm J, Grant JC, Grzechnik SK, Jaroszewski L, Jin KK, Klock HE, Knuth MW, Kumar A, Marciano D, Miller MD, Morse AT, Nigoghossian E, Okach L, Paulsen J, Reyes R, van den Bedem H, White A, Wolf G, Xu Q, Hodgson KO, Wooley J, Deacon AM, Godzik A, Lesley SA, Elsliger MA, Schimmel P, Wilson IA (2010) Structure of a tryptophanyl-tRNA synthetase containing an iron-sulfur cluster. Acta Crystallogr Sect F Struct Biol Cryst Commun 66(Pt 10):1326–1334

    CAS  Google Scholar 

  87. Zhou M, Dong X, Shen N, Zhong C, Ding J (2010) Crystal structures of Saccharomyces cerevisiae tryptophanyl-tRNA synthetase: new insights into the mechanism of tryptophan activation and implications for anti-fungal drug design. Nucleic Acids Res 38(10):3399–3413

    CAS  Google Scholar 

  88. Merritt EA, Arakaki TL, Gillespie R, Napuli AJ, Kim JE, Buckner FS, Van Voorhis WC, Verlinde CL, Fan E, Zucker F, Hol WG (2011) Crystal structures of three protozoan homologs of tryptophanyl-tRNA synthetase. Mol Biochem Parasitol 177(1):20–28

    CAS  Google Scholar 

  89. Yaremchuk A, Kriklivyi I, Tukalo M, Cusack S (2002) Class I tyrosyl-tRNA synthetase has a class II mode of cognate tRNA recognition. EMBO J 21(14):3829–3840

    CAS  Google Scholar 

  90. Kobayashi T, Takimura T, Sekine R, Kelly VP, Kamata K, Sakamoto K, Nishimura S, Yokoyama S (2005) Structural snapshots of the KMSKS loop rearrangement for amino acid activation by bacterial tyrosyl-tRNA synthetase. J Mol Biol 346(1):105–117

    CAS  Google Scholar 

  91. Kuratani M, Sakai H, Takahashi M, Yanagisawa T, Kobayashi T, Murayama K, Chen L, Liu ZJ, Wang BC, Kuroishi C, Kuramitsu S, Terada T, Bessho Y, Shirouzu M, Sekine S, Yokoyama S (2006) Crystal structures of tyrosyl-tRNA synthetases from Archaea. J Mol Biol 355(3):395–408

    CAS  Google Scholar 

  92. Bonnefond L, Frugier M, Touze E, Lorber B, Florentz C, Giege R, Sauter C, Rudinger-Thirion J (2007) Crystal structure of human mitochondrial tyrosyl-tRNA synthetase reveals common and idiosyncratic features. Structure 15(11):1505–1516

    CAS  Google Scholar 

  93. Logan DT, Mazauric MH, Kern D, Moras D (1995) Crystal structure of glycyl-tRNA synthetase from Thermus thermophilus. EMBO J 14(17):4156–4167

    CAS  Google Scholar 

  94. Arnez JG, Dock-Bregeon AC, Moras D (1999) Glycyl-tRNA synthetase uses a negatively charged pit for specific recognition and activation of glycine. J Mol Biol 286(5):1449–1459

    CAS  Google Scholar 

  95. Cader MZ, Ren J, James PA, Bird LE, Talbot K, Stammers DK (2007) Crystal structure of human wildtype and S581L-mutant glycyl-tRNA synthetase, an enzyme underlying distal spinal muscular atrophy. FEBS Lett 581(16):2959–2964

    CAS  Google Scholar 

  96. Arnez JG, Harris DC, Mitschler A, Rees B, Francklyn CS, Moras D (1995) Crystal structure of histidyl-tRNA synthetase from Escherichia coli complexed with histidyl-adenylate. EMBO J 14(17):4143–4155

    CAS  Google Scholar 

  97. Arnez JG, Augustine JG, Moras D, Francklyn CS (1997) The first step of aminoacylation at the atomic level in histidyl-tRNA synthetase. Proc Natl Acad Sci U S A 94(14):7144–7149

    CAS  Google Scholar 

  98. Qiu X, Janson CA, Blackburn MN, Chhohan IK, Hibbs M, Abdel-Meguid SS (1999) Cooperative structural dynamics and a novel fidelity mechanism in histidyl-tRNA synthetases. Biochemistry 38(38):12296–12304

    CAS  Google Scholar 

  99. Aberg A, Yaremchuk A, Tukalo M, Rasmussen B, Cusack S (1997) Crystal structure analysis of the activation of histidine by Thermus thermophilus histidyl-tRNA synthetase. Biochemistry 36(11):3084–3094

    CAS  Google Scholar 

  100. Merritt EA, Arakaki TL, Gillespie JR, Larson ET, Kelley A, Mueller N, Napuli AJ, Kim J, Zhang L, Verlinde CL, Fan E, Zucker F, Buckner FS, van Voorhis WC, Hol WG (2010) Crystal structures of trypanosomal histidyl-tRNA synthetase illuminate differences between eukaryotic and prokaryotic homologs. J Mol Biol 397(2):481–494

    CAS  Google Scholar 

  101. Xu Z, Wei Z, Zhou JJ, Ye F, Lo WS, Wang F, Lau CF, Wu J, Nangle LA, Chiang KP, Yang XL, Zhang M, Schimmel P (2012) Internally deleted human tRNA synthetase suggests evolutionary pressure for repurposing. Structure 20(9):1470–1477

    CAS  Google Scholar 

  102. Yaremchuk A, Tukalo M, Grotli M, Cusack S (2001) A succession of substrate induced conformational changes ensures the amino acid specificity of Thermus thermophilus prolyl-tRNA synthetase: comparison with histidyl-tRNA synthetase. J Mol Biol 309(4):989–1002

    CAS  Google Scholar 

  103. Kamtekar S, Kennedy WD, Wang J, Stathopoulos C, Soll D, Steitz TA (2003) The structural basis of cysteine aminoacylation of tRNAPro by prolyl-tRNA synthetases. Proc Natl Acad Sci U S A 100(4):1673–1678

    CAS  Google Scholar 

  104. Larson ET, Kim JE, Napuli AJ, Verlinde CL, Fan E, Zucker FH, Van Voorhis WC, Buckner FS, Hol WG, Merritt EA (2012) Structure of the prolyl-tRNA synthetase from the eukaryotic pathogen Giardia lamblia. Acta Crystallogr D Biol Crystallogr 68(Pt 9):1194–1200

    CAS  Google Scholar 

  105. Crepin T, Yaremchuk A, Tukalo M, Cusack S (2006) Structures of two bacterial prolyl-tRNA synthetases with and without a cis-editing domain. Structure 14(10):1511–1525

    CAS  Google Scholar 

  106. Zhou H, Sun L, Yang XL, Schimmel P (2013) ATP-directed capture of bioactive herbal-based medicine on human tRNA synthetase. Nature 494:121–124

    CAS  Google Scholar 

  107. Fujinaga M, Berthet-Colominas C, Yaremchuk AD, Tukalo MA, Cusack S (1993) Refined crystal structure of the seryl-tRNA synthetase from Thermus thermophilus at 2.5 A resolution. J Mol Biol 234(1):222–233

    CAS  Google Scholar 

  108. Belrhali H, Yaremchuk A, Tukalo M, Larsen K, Berthet-Colominas C, Leberman R, Beijer B, Sproat B, Als-Nielsen J, Grubel G et al (1994) Crystal structures at 2.5 Angstrom resolution of seryl-tRNA synthetase complexed with two analogs of seryl adenylate. Science 263(5152):1432–1436

    CAS  Google Scholar 

  109. Chimnaronk S, Gravers Jeppesen M, Suzuki T, Nyborg J, Watanabe K (2005) Dual-mode recognition of noncanonical tRNAs(Ser) by seryl-tRNA synthetase in mammalian mitochondria. EMBO J 24(19):3369–3379

    CAS  Google Scholar 

  110. Itoh Y, Sekine S, Kuroishi C, Terada T, Shirouzu M, Kuramitsu S, Yokoyama S (2008) Crystallographic and mutational studies of seryl-tRNA synthetase from the archaeon Pyrococcus horikoshii. RNA Biol 5(3):169–177

    CAS  Google Scholar 

  111. Rocha R, Pereira PJ, Santos MA, Macedo-Ribeiro S (2011) Unveiling the structural basis for translational ambiguity tolerance in a human fungal pathogen. Proc Natl Acad Sci U S A 108(34):14091–14096

    CAS  Google Scholar 

  112. Sankaranarayanan R, Dock-Bregeon AC, Romby P, Caillet J, Springer M, Rees B, Ehresmann C, Ehresmann B, Moras D (1999) The structure of threonyl-tRNA synthetase-tRNA(Thr) complex enlightens its repressor activity and reveals an essential zinc ion in the active site. Cell 97(3):371–381

    CAS  Google Scholar 

  113. Torres-Larios A, Dock-Bregeon AC, Romby P, Rees B, Sankaranarayanan R, Caillet J, Springer M, Ehresmann C, Ehresmann B, Moras D (2002) Structural basis of translational control by Escherichia coli threonyl tRNA synthetase. Nat Struct Biol 9(5):343–347

    CAS  Google Scholar 

  114. Torres-Larios A, Sankaranarayanan R, Rees B, Dock-Bregeon AC, Moras D (2003) Conformational movements and cooperativity upon amino acid, ATP and tRNA binding in threonyl-tRNA synthetase. J Mol Biol 331(1):201–211

    CAS  Google Scholar 

  115. Ling J, Peterson KM, Simonovic I, Cho C, Soll D, Simonovic M (2012) Yeast mitochondrial threonyl-tRNA synthetase recognizes tRNA isoacceptors by distinct mechanisms and promotes CUN codon reassignment. Proc Natl Acad Sci U S A 109(9):3281–3286

    CAS  Google Scholar 

  116. Ling J, Peterson KM, Simonovic I, Soll D, Simonovic M (2012) The mechanism of pre-transfer editing in yeast mitochondrial threonyl-tRNA synthetase. J Biol Chem 287(34):28518–28525

    CAS  Google Scholar 

  117. Iwasaki W, Sekine S, Kuroishi C, Kuramitsu S, Shirouzu M, Yokoyama S (2006) Structural basis of the water-assisted asparagine recognition by asparaginyl-tRNA synthetase. J Mol Biol 360(2):329–342

    CAS  Google Scholar 

  118. Crepin T, Peterson F, Haertlein M, Jensen D, Wang C, Cusack S, Kron M (2011) A hybrid structural model of the complete Brugia malayi cytoplasmic asparaginyl-tRNA synthetase. J Mol Biol 405(4):1056–1069

    CAS  Google Scholar 

  119. Blaise M, Frechin M, Olieric V, Charron C, Sauter C, Lorber B, Roy H, Kern D (2011) Crystal structure of the archaeal asparagine synthetase: interrelation with aspartyl-tRNA and asparaginyl-tRNA synthetases. J Mol Biol 412(3):437–452

    CAS  Google Scholar 

  120. Ruff M, Krishnaswamy S, Boeglin M, Poterszman A, Mitschler A, Podjarny A, Rees B, Thierry JC, Moras D (1991) Class II aminoacyl transfer RNA synthetases: crystal structure of yeast aspartyl-tRNA synthetase complexed with tRNA(Asp). Science 252(5013):1682–1689

    CAS  Google Scholar 

  121. Schmitt E, Moulinier L, Fujiwara S, Imanaka T, Thierry JC, Moras D (1998) Crystal structure of aspartyl-tRNA synthetase from Pyrococcus kodakaraensis KOD: archaeon specificity and catalytic mechanism of adenylate formation. EMBO J 17(17):5227–5237

    CAS  Google Scholar 

  122. Poterszman A, Delarue M, Thierry JC, Moras D (1994) Synthesis and recognition of aspartyl-adenylate by Thermus thermophilus aspartyl-tRNA synthetase. J Mol Biol 244(2):158–167

    CAS  Google Scholar 

  123. Sauter C, Lorber B, Cavarelli J, Moras D, Giege R (2000) The free yeast aspartyl-tRNA synthetase differs from the tRNA(Asp)-complexed enzyme by structural changes in the catalytic site, hinge region, and anticodon-binding domain. J Mol Biol 299(5):1313–1324

    CAS  Google Scholar 

  124. Moulinier L, Eiler S, Eriani G, Gangloff J, Thierry JC, Gabriel K, McClain WH, Moras D (2001) The structure of an AspRS-tRNA(Asp) complex reveals a tRNA-dependent control mechanism. EMBO J 20(18):5290–5301

    CAS  Google Scholar 

  125. Rees B, Webster G, Delarue M, Boeglin M, Moras D (2000) Aspartyl tRNA-synthetase from Escherichia coli: flexibility and adaptability to the substrates. J Mol Biol 299(5):1157–1164

    CAS  Google Scholar 

  126. Merritt EA, Arakaki TL, Larson ET, Kelley A, Mueller N, Napuli AJ, Zhang L, Deditta G, Luft J, Verlinde CL, Fan E, Zucker F, Buckner FS, Van Voorhis WC, Hol WG (2010) Crystal structure of the aspartyl-tRNA synthetase from Entamoeba histolytica. Mol Biochem Parasitol 169(2):95–100

    CAS  Google Scholar 

  127. Neuenfeldt A, Lorber B, Ennifar E, Gaudry A, Sauter C, Sissler M, Florentz C (2013) Thermodynamic properties distinguish human mitochondrial aspartyl-tRNA synthetase from bacterial homolog with same 3D architecture. Nucleic Acids Res 41(4):2698–2708

    Google Scholar 

  128. Cusack S, Yaremchuk A, Tukalo M (1996) The crystal structures of T. thermophilus lysyl-tRNA synthetase complexed with E. coli tRNA(Lys) and a T. thermophilus tRNA(Lys) transcript: anticodon recognition and conformational changes upon binding of a lysyl-adenylate analogue. EMBO J 15(22):6321–6334

    CAS  Google Scholar 

  129. Onesti S, Desogus G, Brevet A, Chen J, Plateau P, Blanquet S, Brick P (2000) Structural studies of lysyl-tRNA synthetase: conformational changes induced by substrate binding. Biochemistry 39(42):12853–12861

    CAS  Google Scholar 

  130. Guo M, Ignatov M, Musier-Forsyth K, Schimmel P, Yang XL (2008) Crystal structure of tetrameric form of human lysyl-tRNA synthetase: implications for multisynthetase complex formation. Proc Natl Acad Sci U S A 105(7):2331–2336

    CAS  Google Scholar 

  131. Sakurama H, Takita T, Mikami B, Itoh T, Yasukawa K, Inouye K (2009) Two crystal structures of lysyl-tRNA synthetase from Bacillus stearothermophilus in complex with lysyladenylate-like compounds: insights into the irreversible formation of the enzyme-bound adenylate of L-lysine hydroxamate. J Biochem 145(5):555–563

    CAS  Google Scholar 

  132. Sokabe M, Ose T, Nakamura A, Tokunaga K, Nureki O, Yao M, Tanaka I (2009) The structure of alanyl-tRNA synthetase with editing domain. Proc Natl Acad Sci U S A 106(27):11028–11033

    CAS  Google Scholar 

  133. Naganuma M, Sekine S, Fukunaga R, Yokoyama S (2009) Unique protein architecture of alanyl-tRNA synthetase for aminoacylation, editing, and dimerization. Proc Natl Acad Sci U S A 106(21):8489–8494

    CAS  Google Scholar 

  134. Swairjo MA, Schimmel PR (2005) Breaking sieve for steric exclusion of a noncognate amino acid from active site of a tRNA synthetase. Proc Natl Acad Sci U S A 102(4):988–993

    CAS  Google Scholar 

  135. Guo M, Chong YE, Shapiro R, Beebe K, Yang XL, Schimmel P (2009) Paradox of mistranslation of serine for alanine caused by AlaRS recognition dilemma. Nature 462(7274):808–812

    CAS  Google Scholar 

  136. http://www.rcsb.org/pdb/explore/explore.do?structureId=3RF1 DOI:10.2210/pdb3rf1/pdb

  137. http://www.rcsb.org/pdb/explore/explore.do?structureId=1J5W DOI:10.2210/pdb1j5w/pdb

  138. Reshetnikova L, Moor N, Lavrik O, Vassylyev DG (1999) Crystal structures of phenylalanyl-tRNA synthetase complexed with phenylalanine and a phenylalanyl-adenylate analogue. J Mol Biol 287(3):555–568

    CAS  Google Scholar 

  139. Goldgur Y, Mosyak L, Reshetnikova L, Ankilova V, Lavrik O, Khodyreva S, Safro M (1997) The crystal structure of phenylalanyl-tRNA synthetase from thermus thermophilus complexed with cognate tRNAPhe. Structure 5(1):59–68

    CAS  Google Scholar 

  140. Moor N, Kotik-Kogan O, Tworowski D, Sukhanova M, Safro M (2006) The crystal structure of the ternary complex of phenylalanyl-tRNA synthetase with tRNAPhe and a phenylalanyl-adenylate analogue reveals a conformational switch of the CCA end. Biochemistry 45(35):10572–10583

    CAS  Google Scholar 

  141. Mermershtain I, Finarov I, Klipcan L, Kessler N, Rozenberg H, Safro MG (2011) Idiosyncrasy and identity in the prokaryotic Phe-system: crystal structure of E. coli phenylalanyl-tRNA synthetase complexed with phenylalanine and AMP. Protein Sci 20(1):160–167

    CAS  Google Scholar 

  142. Klipcan L, Moor N, Kessler N, Safro MG (2009) Eukaryotic cytosolic and mitochondrial phenylalanyl-tRNA synthetases catalyze the charging of tRNA with the meta-tyrosine. Proc Natl Acad Sci U S A 106(27):11045–11048

    CAS  Google Scholar 

  143. Klipcan L, Moor N, Finarov I, Kessler N, Sukhanova M, Safro MG (2012) Crystal structure of human mitochondrial PheRS complexed with tRNA(Phe) in the active "open" state. J Mol Biol 415(3):527–537

    CAS  Google Scholar 

  144. Kavran JM, Gundllapalli S, O'Donoghue P, Englert M, Soll D, Steitz TA (2007) Structure of pyrrolysyl-tRNA synthetase, an archaeal enzyme for genetic code innovation. Proc Natl Acad Sci U S A 104(27):11268–11273

    CAS  Google Scholar 

  145. Yanagisawa T, Ishii R, Fukunaga R, Kobayashi T, Sakamoto K, Yokoyama S (2008) Crystallographic studies on multiple conformational states of active-site loops in pyrrolysyl-tRNA synthetase. J Mol Biol 378(3):634–652

    CAS  Google Scholar 

  146. Nozawa K, O'Donoghue P, Gundllapalli S, Araiso Y, Ishitani R, Umehara T, Soll D, Nureki O (2009) Pyrrolysyl-tRNA synthetase-tRNA(Pyl) structure reveals the molecular basis of orthogonality. Nature 457(7233):1163–1167

    CAS  Google Scholar 

  147. Fukunaga R, Yokoyama S (2007) Structural insights into the first step of RNA-dependent cysteine biosynthesis in archaea. Nat Struct Mol Biol 14(4):272–279

    CAS  Google Scholar 

  148. Kamtekar S, Hohn MJ, Park HS, Schnitzbauer M, Sauerwald A, Soll D, Steitz TA (2007) Toward understanding phosphoseryl-tRNACys formation: the crystal structure of Methanococcus maripaludis phosphoseryl-tRNA synthetase. Proc Natl Acad Sci U S A 104(8):2620–2625

    CAS  Google Scholar 

  149. Bult CJ, White O, Olsen GJ, Zhou L, Fleischmann RD, Sutton GG, Blake JA, FitzGerald LM, Clayton RA, Gocayne JD, Kerlavage AR, Dougherty BA, Tomb JF, Adams MD, Reich CI, Overbeek R, Kirkness EF, Weinstock KG, Merrick JM, Glodek A, Scott JL, Geoghagen NS, Venter JC (1996) Complete genome sequence of the methanogenic archaeon, Methanococcus jannaschii. Science 273(5278):1058–1073

    CAS  Google Scholar 

  150. Smith DR, Doucette-Stamm LA, Deloughery C, Lee H, Dubois J, Aldredge T, Bashirzadeh R, Blakely D, Cook R, Gilbert K, Harrison D, Hoang L, Keagle P, Lumm W, Pothier B, Qiu D, Spadafora R, Vicaire R, Wang Y, Wierzbowski J, Gibson R, Jiwani N, Caruso A, Bush D, Reeve JN et al (1997) Complete genome sequence of Methanobacterium thermoautotrophicum deltaH: functional analysis and comparative genomics. J Bacteriol 179(22):7135–7155

    CAS  Google Scholar 

  151. Tumbula DL, Becker HD, Chang WZ, Soll D (2000) Domain-specific recruitment of amide amino acids for protein synthesis. Nature 407(6800):106–110

    CAS  Google Scholar 

  152. Gagnon Y, Lacoste L, Champagne N, Lapointe J (1996) Widespread use of the glu-tRNAGln transamidation pathway among bacteria. A member of the alpha purple bacteria lacks glutaminyl-trna synthetase. J Biol Chem 271(25):14856–14863

    CAS  Google Scholar 

  153. Curnow AW, Hong K, Yuan R, Kim S, Martins O, Winkler W, Henkin TM, Soll D (1997) Glu-tRNAGln amidotransferase: a novel heterotrimeric enzyme required for correct decoding of glutamine codons during translation. Proc Natl Acad Sci U S A 94(22):11819–11826

    CAS  Google Scholar 

  154. Bailly M, Blaise M, Lorber B, Becker HD, Kern D (2007) The transamidosome: a dynamic ribonucleoprotein particle dedicated to prokaryotic tRNA-dependent asparagine biosynthesis. Mol Cell 28(2):228–239

    CAS  Google Scholar 

  155. Rampias T, Sheppard K, Soll D (2010) The archaeal transamidosome for RNA-dependent glutamine biosynthesis. Nucleic Acids Res 38(17):5774–5783

    CAS  Google Scholar 

  156. Ito T, Yokoyama S (2010) Two enzymes bound to one transfer RNA assume alternative conformations for consecutive reactions. Nature 467(7315):612–616

    CAS  Google Scholar 

  157. Blaise M, Bailly M, Frechin M, Behrens MA, Fischer F, Oliveira CL, Becker HD, Pedersen JS, Thirup S, Kern D (2010) Crystal structure of a transfer-ribonucleoprotein particle that promotes asparagine formation. EMBO J 29(18):3118–3129

    CAS  Google Scholar 

  158. Bhaskaran H, Perona JJ (2011) Two-step aminoacylation of tRNA without channeling in Archaea. J Mol Biol 411(4):854–869

    CAS  Google Scholar 

  159. Sheppard K, Yuan J, Hohn MJ, Jester B, Devine KM, Soll D (2008) From one amino acid to another: tRNA-dependent amino acid biosynthesis. Nucleic Acids Res 36(6):1813–1825

    CAS  Google Scholar 

  160. Frechin M, Senger B, Braye M, Kern D, Martin RP, Becker HD (2009) Yeast mitochondrial Gln-tRNA(Gln) is generated by a GatFAB-mediated transamidation pathway involving Arc1p-controlled subcellular sorting of cytosolic GluRS. Genes Dev 23(9):1119–1130

    CAS  Google Scholar 

  161. Di Giulio M (1993) Origin of glutaminyl-tRNA synthetase: an example of palimpsest? J Mol Evol 37(1):5–10

    Google Scholar 

  162. Min B, Pelaschier JT, Graham DE, Tumbula-Hansen D, Soll D (2002) Transfer RNA-dependent amino acid biosynthesis: an essential route to asparagine formation. Proc Natl Acad Sci U S A 99(5):2678–2683

    CAS  Google Scholar 

  163. Becker HD, Kern D (1998) Thermus thermophilus: a link in evolution of the tRNA-dependent amino acid amidation pathways. Proc Natl Acad Sci U S A 95(22):12832–12837

    CAS  Google Scholar 

  164. Marcker K, Sanger F (1964) N-Formyl-methionyl-S-Rna. J Mol Biol 8:835–840

    CAS  Google Scholar 

  165. Lee CP, Seong BL, RajBhandary UL (1991) Structural and sequence elements important for recognition of Escherichia coli formylmethionine tRNA by methionyl-tRNA transformylase are clustered in the acceptor stem. J Biol Chem 266(27):18012–18017

    CAS  Google Scholar 

  166. Kolitz SE, Lorsch JR (2010) Eukaryotic initiator tRNA: finely tuned and ready for action. FEBS Lett 584(2):396–404

    CAS  Google Scholar 

  167. Tan TH, Bochud-Allemann N, Horn EK, Schneider A (2002) Eukaryotic-type elongator tRNAMet of Trypanosoma brucei becomes formylated after import into mitochondria. Proc Natl Acad Sci U S A 99(3):1152–1157

    CAS  Google Scholar 

  168. Tomsic J, Vitali LA, Daviter T, Savelsbergh A, Spurio R, Striebeck P, Wintermeyer W, Rodnina MV, Gualerzi CO (2000) Late events of translation initiation in bacteria: a kinetic analysis. EMBO J 19(9):2127–2136

    CAS  Google Scholar 

  169. Johansson L, Chen C, Thorell JO, Fredriksson A, Stone-Elander S, Gafvelin G, Arner ES (2004) Exploiting the 21st amino acid-purifying and labeling proteins by selenolate targeting. Nat Methods 1(1):61–66

    CAS  Google Scholar 

  170. Bock A (2005) Selenocysteine. In: Ibba M, Francklyn C, Cusack S (eds) The aminoacyl-tRNA synthetases. Landes Bioscience, Georgetown, pp 320–327

    Google Scholar 

  171. Yuan J, Palioura S, Salazar JC, Su D, O'Donoghue P, Hohn MJ, Cardoso AM, Whitman WB, Soll D (2006) RNA-dependent conversion of phosphoserine forms selenocysteine in eukaryotes and archaea. Proc Natl Acad Sci U S A 103(50):18923–18927

    CAS  Google Scholar 

  172. Commans S, Bock A (1999) Selenocysteine inserting tRNAs: an overview. FEMS Microbiol Rev 23(3):335–351

    CAS  Google Scholar 

  173. Baron C, Heider J, Bock A (1990) Mutagenesis of selC, the gene for the selenocysteine-inserting tRNA-species in E. coli: effects on in vivo function. Nucleic Acids Res 18(23):6761–6766

    CAS  Google Scholar 

  174. Palioura S, Sherrer RL, Steitz TA, Soll D, Simonovic M (2009) The human SepSecS-tRNASec complex reveals the mechanism of selenocysteine formation. Science 325(5938):321–325

    CAS  Google Scholar 

  175. Forchhammer K, Leinfelder W, Bock A (1989) Identification of a novel translation factor necessary for the incorporation of selenocysteine into protein. Nature 342(6248):453–456

    CAS  Google Scholar 

  176. Zinoni F, Heider J, Bock A (1990) Features of the formate dehydrogenase mRNA necessary for decoding of the UGA codon as selenocysteine. Proc Natl Acad Sci U S A 87(12):4660–4664

    CAS  Google Scholar 

  177. Berry MJ, Banu L, Chen YY, Mandel SJ, Kieffer JD, Harney JW, Larsen PR (1991) Recognition of UGA as a selenocysteine codon in type I deiodinase requires sequences in the 3′ untranslated region. Nature 353(6341):273–276

    CAS  Google Scholar 

  178. Allmang C, Wurth L, Krol A (2009) The selenium to selenoprotein pathway in eukaryotes: more molecular partners than anticipated. Biochim Biophys Acta 1790(11):1415–1423

    CAS  Google Scholar 

  179. Caban K, Copeland PR (2012) Selenocysteine insertion sequence (SECIS)-binding protein 2 alters conformational dynamics of residues involved in tRNA accommodation in 80 S ribosomes. J Biol Chem 287(13):10664–10673

    CAS  Google Scholar 

  180. Ambrogelly A, Palioura S, Soll D (2007) Natural expansion of the genetic code. Nat Chem Biol 3(1):29–35

    CAS  Google Scholar 

  181. Doolittle RF (1998) Microbial genomes opened up. Nature 392(6674):339–342

    CAS  Google Scholar 

  182. Stathopoulos C, Li T, Longman R, Vothknecht UC, Becker HD, Ibba M, Soll D (2000) One polypeptide with two aminoacyl-tRNA synthetase activities. Science 287(5452):479–482

    CAS  Google Scholar 

  183. Sauerwald A, Zhu W, Major TA, Roy H, Palioura S, Jahn D, Whitman WB, Yates JR 3rd, Ibba M, Soll D (2005) RNA-dependent cysteine biosynthesis in archaea. Science 307(5717):1969–1972

    CAS  Google Scholar 

  184. O'Donoghue P, Sethi A, Woese CR, Luthey-Schulten ZA (2005) The evolutionary history of Cys-tRNACys formation. Proc Natl Acad Sci U S A 102(52):19003–19008

    Google Scholar 

  185. Klotz MG, Arp DJ, Chain PS, El-Sheikh AF, Hauser LJ, Hommes NG, Larimer FW, Malfatti SA, Norton JM, Poret-Peterson AT, Vergez LM, Ward BB (2006) Complete genome sequence of the marine, chemolithoautotrophic, ammonia-oxidizing bacterium Nitrosococcus oceani ATCC 19707. Appl Environ Microbiol 72(9):6299–6315

    CAS  Google Scholar 

  186. Ivanova N, Sorokin A, Anderson I, Galleron N, Candelon B, Kapatral V, Bhattacharyya A, Reznik G, Mikhailova N, Lapidus A, Chu L, Mazur M, Goltsman E, Larsen N, D'Souza M, Walunas T, Grechkin Y, Pusch G, Haselkorn R, Fonstein M, Ehrlich SD, Overbeek R, Kyrpides N (2003) Genome sequence of Bacillus cereus and comparative analysis with Bacillus anthracis. Nature 423(6935):87–91

    CAS  Google Scholar 

  187. Ataide SF, Jester BC, Devine KM, Ibba M (2005) Stationary-phase expression and aminoacylation of a transfer-RNA-like small RNA. EMBO Rep 6(8):742–747

    CAS  Google Scholar 

  188. Deppenmeier U, Johann A, Hartsch T, Merkl R, Schmitz RA, Martinez-Arias R, Henne A, Wiezer A, Baumer S, Jacobi C, Bruggemann H, Lienard T, Christmann A, Bomeke M, Steckel S, Bhattacharyya A, Lykidis A, Overbeek R, Klenk HP, Gunsalus RP, Fritz HJ, Gottschalk G (2002) The genome of Methanosarcina mazei: evidence for lateral gene transfer between bacteria and archaea. J Mol Microbiol Biotechnol 4(4):453–461

    CAS  Google Scholar 

  189. Ambrogelly A, Korencic D, Ibba M (2002) Functional annotation of class I lysyl-tRNA synthetase phylogeny indicates a limited role for gene transfer. J Bacteriol 184(16):4594–4600

    CAS  Google Scholar 

  190. Soll D, Becker HD, Plateau P, Blanquet S, Ibba M (2000) Context-dependent anticodon recognition by class I lysyl-tRNA synthetases. Proc Natl Acad Sci U S A 97(26):14224–14228

    CAS  Google Scholar 

  191. Levengood JD, Roy H, Ishitani R, Soll D, Nureki O, Ibba M (2007) Anticodon recognition and discrimination by the alpha-helix cage domain of class I lysyl-tRNA synthetase. Biochemistry 46(39):11033–11038

    CAS  Google Scholar 

  192. Jester BC, Levengood JD, Roy H, Ibba M, Devine KM (2003) Nonorthologous replacement of lysyl-tRNA synthetase prevents addition of lysine analogues to the genetic code. Proc Natl Acad Sci U S A 100(24):14351–14356

    CAS  Google Scholar 

  193. Wang S, Praetorius-Ibba M, Ataide SF, Roy H, Ibba M (2006) Discrimination of cognate and noncognate substrates at the active site of class I lysyl-tRNA synthetase. Biochemistry 45(11):3646–3652

    CAS  Google Scholar 

  194. Ataide SF, Ibba M (2004) Discrimination of cognate and noncognate substrates at the active site of class II lysyl-tRNA synthetase. Biochemistry 43(37):11836–11841

    CAS  Google Scholar 

  195. Uy R, Wold F (1977) Posttranslational covalent modification of proteins. Science 198(4320):890–896

    CAS  Google Scholar 

  196. Hao B, Gong W, Ferguson TK, James CM, Krzycki JA, Chan MK (2002) A new UAG-encoded residue in the structure of a methanogen methyltransferase. Science 296(5572):1462–1466

    CAS  Google Scholar 

  197. Zhang Y, Gladyshev VN (2007) High content of proteins containing 21st and 22nd amino acids, selenocysteine and pyrrolysine, in a symbiotic deltaproteobacterium of gutless worm Olavius algarvensis. Nucleic Acids Res 35(15):4952–4963

    CAS  Google Scholar 

  198. Prat L, Heinemann IU, Aerni HR, Rinehart J, O'Donoghue P, Soll D (2012) Carbon source-dependent expansion of the genetic code in bacteria. Proc Natl Acad Sci U S A 109(51):21070–21075

    CAS  Google Scholar 

  199. Theobald-Dietrich A, Frugier M, Giege R, Rudinger-Thirion J (2004) Atypical archaeal tRNA pyrrolysine transcript behaves towards EF-Tu as a typical elongator tRNA. Nucleic Acids Res 32(3):1091–1096

    CAS  Google Scholar 

  200. Polycarpo C, Ambrogelly A, Ruan B, Tumbula-Hansen D, Ataide SF, Ishitani R, Yokoyama S, Nureki O, Ibba M, Soll D (2003) Activation of the pyrrolysine suppressor tRNA requires formation of a ternary complex with class I and class II lysyl-tRNA synthetases. Mol Cell 12(2):287–294

    CAS  Google Scholar 

  201. Blight SK, Larue RC, Mahapatra A, Longstaff DG, Chang E, Zhao G, Kang PT, Green-Church KB, Chan MK, Krzycki JA (2004) Direct charging of tRNA(CUA) with pyrrolysine in vitro and in vivo. Nature 431(7006):333–335

    CAS  Google Scholar 

  202. Polycarpo C, Ambrogelly A, Berube A, Winbush SM, McCloskey JA, Crain PF, Wood JL, Soll D (2004) An aminoacyl-tRNA synthetase that specifically activates pyrrolysine. Proc Natl Acad Sci U S A 101(34):12450–12454

    CAS  Google Scholar 

  203. Longstaff DG, Blight SK, Zhang L, Green-Church KB, Krzycki JA (2007) In vivo contextual requirements for UAG translation as pyrrolysine. Mol Microbiol 63(1):229–241

    CAS  Google Scholar 

  204. Jiang R, Krzycki JA (2012) PylSn and the homologous N-terminal domain of pyrrolysyl-tRNA synthetase bind the tRNA that is essential for the genetic encoding of pyrrolysine. J Biol Chem 287(39):32738–32746

    CAS  Google Scholar 

  205. Srinivasan G, James CM, Krzycki JA (2002) Pyrrolysine encoded by UAG in Archaea: charging of a UAG-decoding specialized tRNA. Science 296(5572):1459–1462

    CAS  Google Scholar 

  206. Herring S, Ambrogelly A, Gundllapalli S, O'Donoghue P, Polycarpo CR, Soll D (2007) The amino-terminal domain of pyrrolysyl-tRNA synthetase is dispensable in vitro but required for in vivo activity. FEBS Lett 581(17):3197–3203

    CAS  Google Scholar 

  207. Krzycki JA (2004) Function of genetically encoded pyrrolysine in corrinoid-dependent methylamine methyltransferases. Curr Opin Chem Biol 8(5):484–491

    CAS  Google Scholar 

  208. Fournier GP, Huang J, Gogarten JP (2009) Horizontal gene transfer from extinct and extant lineages: biological innovation and the coral of life. Philos Trans R Soc Lond B Biol Sci 364(1527):2229–2239

    CAS  Google Scholar 

  209. Gaston MA, Zhang L, Green-Church KB, Krzycki JA (2011) The complete biosynthesis of the genetically encoded amino acid pyrrolysine from lysine. Nature 471(7340):647–650

    CAS  Google Scholar 

  210. Hauenstein SI, Perona JJ (2008) Redundant synthesis of cysteinyl-tRNACys in Methanosarcina mazei. J Biol Chem 283(32):22007–22017

    CAS  Google Scholar 

  211. Crick FH (1958) On protein synthesis. Symp Soc Exp Biol 12:138–163

    CAS  Google Scholar 

  212. Crick FHC (1968) The origin of the genetic code. J Mol Biol 38(3):367–379

    CAS  Google Scholar 

  213. Jimenez-Sanchez A (1995) On the origin and evolution of the genetic code. J Mol Evol 41(6):712–716

    CAS  Google Scholar 

  214. Guo M, Schimmel P (2012) Structural analyses clarify the complex control of mistranslation by tRNA synthetases. Curr Opin Struct Biol 22(1):119–126

    CAS  Google Scholar 

  215. Loftfield RB, Vanderjagt D (1972) The frequency of errors in protein biosynthesis. Biochem J 128(5):1353–1356

    CAS  Google Scholar 

  216. Schimmel P, Giege R, Moras D, Yokoyama S (1993) An operational RNA code for amino acids and possible relationship to genetic code. Proc Natl Acad Sci U S A 90(19):8763–8768

    CAS  Google Scholar 

  217. Reynolds NM, Ling J, Roy H, Banerjee R, Repasky SE, Hamel P, Ibba M (2010) Cell-specific differences in the requirements for translation quality control. Proc Natl Acad Sci U S A 107(9):4063–4068

    CAS  Google Scholar 

  218. Li L, Boniecki MT, Jaffe JD, Imai BS, Yau PM, Luthey-Schulten ZA, Martinis SA (2011) Naturally occurring aminoacyl-tRNA synthetases editing-domain mutations that cause mistranslation in Mycoplasma parasites. Proc Natl Acad Sci U S A 108(23):9378–9383

    CAS  Google Scholar 

  219. Yadavalli SS, Ibba M (2013) Selection of tRNA charging quality control mechanisms that increase mistranslation of the genetic code. Nucleic Acids Res 41:1104–1112

    CAS  Google Scholar 

  220. Jakubowski H, Goldman E (1992) Editing of errors in selection of amino acids for protein synthesis. Microbiol Rev 56(3):412–429

    CAS  Google Scholar 

  221. Giege R, Sissler M, Florentz C (1998) Universal rules and idiosyncratic features in tRNA identity. Nucleic Acids Res 26(22):5017–5035

    CAS  Google Scholar 

  222. Tworowski D, Feldman AV, Safro MG (2005) Electrostatic potential of aminoacyl-tRNA synthetase navigates tRNA on its pathway to the binding site. J Mol Biol 350(5):866–882

    CAS  Google Scholar 

  223. Ebel JP, Giege R, Bonnet J, Kern D, Befort N, Bollack C, Fasiolo F, Gangloff J, Dirheimer G (1973) Factors determining the specificity of the tRNA aminoacylation reaction. Non-absolute specificity of tRNA-aminoacyl-tRNA synthetase recognition and particular importance of the maximal velocity. Biochimie 55(5):547–557

    CAS  Google Scholar 

  224. Guth EC, Francklyn CS (2007) Kinetic discrimination of tRNA identity by the conserved motif 2 loop of a class II aminoacyl-tRNA synthetase. Mol Cell 25(4):531–542

    CAS  Google Scholar 

  225. Ibba M, Sever S, Praetorius-Ibba M, Soll D (1999) Transfer RNA identity contributes to transition state stabilization during aminoacyl-tRNA synthesis. Nucleic Acids Res 27(18):3631–3637

    CAS  Google Scholar 

  226. Uter NT, Perona JJ (2004) Long-range intramolecular signaling in a tRNA synthetase complex revealed by pre-steady-state kinetics. Proc Natl Acad Sci U S A 101(40):14396–14401

    CAS  Google Scholar 

  227. Vasil'eva IA, Moor NA (2007) Interaction of aminoacyl-tRNA synthetases with tRNA: general principles and distinguishing characteristics of the high-molecular-weight substrate recognition. Biochemistry (Mosc) 72(3):247–263

    Google Scholar 

  228. Aphasizhev R, Senger B, Fasiolo F (1997) Importance of structural features for tRNA(Met) identity. RNA 3(5):489–497

    CAS  Google Scholar 

  229. Schimmel P, Ribas de Pouplana L (1995) Transfer RNA: from minihelix to genetic code. Cell 81(7):983–986

    CAS  Google Scholar 

  230. Wolstenholme DR, Macfarlane JL, Okimoto R, Clary DO, Wahleithner JA (1987) Bizarre tRNAs inferred from DNA sequences of mitochondrial genomes of nematode worms. Proc Natl Acad Sci U S A 84(5):1324–1328

    CAS  Google Scholar 

  231. Cavarelli J, Rees B, Ruff M, Thierry JC, Moras D (1993) Yeast tRNA(Asp) recognition by its cognate class II aminoacyl-tRNA synthetase. Nature 362(6416):181–184

    CAS  Google Scholar 

  232. Ibba M, Hong KW, Sherman JM, Sever S, Soll D (1996) Interactions between tRNA identity nucleotides and their recognition sites in glutaminyl-tRNA synthetase determine the cognate amino acid affinity of the enzyme. Proc Natl Acad Sci U S A 93(14):6953–6958

    CAS  Google Scholar 

  233. Hou YM, Schimmel P (1988) A simple structural feature is a major determinant of the identity of a transfer RNA. Nature 333(6169):140–145

    CAS  Google Scholar 

  234. Sugiura I, Nureki O, Ugaji-Yoshikawa Y, Kuwabara S, Shimada A, Tateno M, Lorber B, Giege R, Moras D, Yokoyama S, Konno M (2000) The 2.0 A crystal structure of Thermus thermophilus methionyl-tRNA synthetase reveals two RNA-binding modules. Structure 8(2):197–208

    CAS  Google Scholar 

  235. Ibba M, Kast P, Hennecke H (1994) Substrate specificity is determined by amino acid binding pocket size in Escherichia coli phenylalanyl-tRNA synthetase. Biochemistry 33(23):7107–7112

    CAS  Google Scholar 

  236. Sankaranarayanan R, Dock-Bregeon AC, Rees B, Bovee M, Caillet J, Romby P, Francklyn CS, Moras D (2000) Zinc ion mediated amino acid discrimination by threonyl-tRNA synthetase. Nat Struct Biol 7(6):461–465

    CAS  Google Scholar 

  237. Kleiman L, Jones CP, Musier-Forsyth K (2010) Formation of the tRNALys packaging complex in HIV-1. FEBS Lett 584(2):359–365

    CAS  Google Scholar 

  238. Jones CP, Saadatmand J, Kleiman L, Musier-Forsyth K (2013) Molecular mimicry of human tRNALys anti-codon domain by HIV-1 RNA genome facilitates tRNA primer annealing. RNA 19:219–229

    CAS  Google Scholar 

  239. Fu G, Xu T, Shi Y, Wei N, Yang XL (2012) tRNA-controlled nuclear import of a human tRNA synthetase. J Biol Chem 287(12):9330–9334

    CAS  Google Scholar 

  240. Azad AK, Stanford DR, Sarkar S, Hopper AK (2001) Role of nuclear pools of aminoacyl-tRNA synthetases in tRNA nuclear export. Mol Biol Cell 12(5):1381–1392

    CAS  Google Scholar 

  241. Yadavalli SS, Ibba M (2012) Quality control in aminoacyl-tRNA synthesis its role in translational fidelity. Adv Protein Chem Struct Biol 86:1–43

    CAS  Google Scholar 

  242. Schmidt E, Schimmel P (1994) Mutational isolation of a sieve for editing in a transfer RNA synthetase. Science 264(5156):265–267

    CAS  Google Scholar 

  243. Cvetesic N, Perona JJ, Gruic-Sovulj I (2012) Kinetic partitioning between synthetic and editing pathways in class I aminoacyl-tRNA synthetases occurs at both pre-transfer and post-transfer hydrolytic steps. J Biol Chem 287(30):25381–25394

    CAS  Google Scholar 

  244. Ling J, So BR, Yadavalli SS, Roy H, Shoji S, Fredrick K, Musier-Forsyth K, Ibba M (2009) Resampling and editing of mischarged tRNA prior to translation elongation. Mol Cell 33(5):654–660

    CAS  Google Scholar 

  245. Englisch S, Englisch U, von der Haar F, Cramer F (1986) The proofreading of hydroxy analogues of leucine and isoleucine by leucyl-tRNA synthetases from E. coli and yeast. Nucleic Acids Res 14(19):7529–7539

    CAS  Google Scholar 

  246. Dulic M, Cvetesic N, Perona JJ, Gruic-Sovulj I (2010) Partitioning of tRNA-dependent editing between pre- and post-transfer pathways in class I aminoacyl-tRNA synthetases. J Biol Chem 285(31):23799–23809

    CAS  Google Scholar 

  247. Nordin BE, Schimmel P (2003) Transiently misacylated tRNA is a primer for editing of misactivated adenylates by class I aminoacyl-tRNA synthetases. Biochemistry 42(44):12989–12997

    CAS  Google Scholar 

  248. Sarkar J, Martinis SA (2011) Amino-acid-dependent shift in tRNA synthetase editing mechanisms. J Am Chem Soc 133(46):18510–18513

    CAS  Google Scholar 

  249. Chen X, Ma JJ, Tan M, Yao P, Hu QH, Eriani G, Wang ED (2011) Modular pathways for editing non-cognate amino acids by human cytoplasmic leucyl-tRNA synthetase. Nucleic Acids Res 39(1):235–247

    CAS  Google Scholar 

  250. Sarkar J, Poruri K, Boniecki MT, McTavish KK, Martinis SA (2012) Yeast mitochondrial leucyl-tRNA synthetase CP1 domain has functionally diverged to accommodate RNA splicing at expense of hydrolytic editing. J Biol Chem 287(18):14772–14781

    CAS  Google Scholar 

  251. Fersht AR, Dingwall C (1979) An editing mechanism for the methionyl-tRNA synthetase in the selection of amino acids in protein synthesis. Biochemistry 18(7):1250–1256

    CAS  Google Scholar 

  252. Jakubowski H, Fersht AR (1981) Alternative pathways for editing non-cognate amino acids by aminoacyl-tRNA synthetases. Nucleic Acids Res 9(13):3105–3117

    CAS  Google Scholar 

  253. Kim HY, Ghosh G, Schulman LH, Brunie S, Jakubowski H (1993) The relationship between synthetic and editing functions of the active site of an aminoacyl-tRNA synthetase. Proc Natl Acad Sci U S A 90(24):11553–11557

    CAS  Google Scholar 

  254. Igloi GL, von der Haar F, Cramer F (1980) A novel enzymatic activity of phenylalanyl transfer ribonucleic acid synthetase from baker's yeast: zinc ion induced transfer ribonucleic acid independent hydrolysis of adenosine triphosphate. Biochemistry 19(8):1676–1680

    CAS  Google Scholar 

  255. Roy H, Ling J, Irnov M, Ibba M (2004) Post-transfer editing in vitro and in vivo by the beta subunit of phenylalanyl-tRNA synthetase. EMBO J 23(23):4639–4648

    CAS  Google Scholar 

  256. Sasaki HM, Sekine S, Sengoku T, Fukunaga R, Hattori M, Utsunomiya Y, Kuroishi C, Kuramitsu S, Shirouzu M, Yokoyama S (2006) Structural and mutational studies of the amino acid-editing domain from archaeal/eukaryal phenylalanyl-tRNA synthetase. Proc Natl Acad Sci U S A 103(40):14744–14749

    CAS  Google Scholar 

  257. Beebe K, Merriman E, Ribas De Pouplana L, Schimmel P (2004) A domain for editing by an archaebacterial tRNA synthetase. Proc Natl Acad Sci U S A 101(16):5958–5963

    CAS  Google Scholar 

  258. Korencic D, Ahel I, Schelert J, Sacher M, Ruan B, Stathopoulos C, Blum P, Ibba M, Soll D (2004) A freestanding proofreading domain is required for protein synthesis quality control in Archaea. Proc Natl Acad Sci U S A 101(28):10260–10265

    CAS  Google Scholar 

  259. Dock-Bregeon A, Sankaranarayanan R, Romby P, Caillet J, Springer M, Rees B, Francklyn CS, Ehresmann C, Moras D (2000) Transfer RNA-mediated editing in threonyl-tRNA synthetase. The class II solution to the double discrimination problem. Cell 103(6):877–884

    CAS  Google Scholar 

  260. Hussain T, Kruparani SP, Pal B, Dock-Bregeon AC, Dwivedi S, Shekar MR, Sureshbabu K, Sankaranarayanan R (2006) Post-transfer editing mechanism of a D-aminoacyl-tRNA deacylase-like domain in threonyl-tRNA synthetase from archaea. EMBO J 25(17):4152–4162

    CAS  Google Scholar 

  261. Wydau S, van der Rest G, Aubard C, Plateau P, Blanquet S (2009) Widespread distribution of cell defense against D-aminoacyl-tRNAs. J Biol Chem 284(21):14096–14104

    CAS  Google Scholar 

  262. Rigden DJ (2004) Archaea recruited D-Tyr-tRNATyr deacylase for editing in Thr-tRNA synthetase. RNA 10(12):1845–1851

    CAS  Google Scholar 

  263. Dwivedi S, Kruparani SP, Sankaranarayanan R (2005) A D-amino acid editing module coupled to the translational apparatus in archaea. Nat Struct Mol Biol 12(6):556–557

    CAS  Google Scholar 

  264. Calendar R, Berg P (1967) D-Tyrosyl RNA: formation, hydrolysis and utilization for protein synthesis. J Mol Biol 26(1):39–54

    CAS  Google Scholar 

  265. Ferri-Fioni ML, Fromant M, Bouin AP, Aubard C, Lazennec C, Plateau P, Blanquet S (2006) Identification in archaea of a novel D-Tyr-tRNATyr deacylase. J Biol Chem 281(37):27575–27585

    CAS  Google Scholar 

  266. Lee JW, Beebe K, Nangle LA, Jang J, Longo-Guess CM, Cook SA, Davisson MT, Sundberg JP, Schimmel P, Ackerman SL (2006) Editing-defective tRNA synthetase causes protein misfolding and neurodegeneration. Nature 443(7107):50–55

    CAS  Google Scholar 

  267. Ahel I, Korencic D, Ibba M, Soll D (2003) Trans-editing of mischarged tRNAs. Proc Natl Acad Sci U S A 100(26):15422–15427

    CAS  Google Scholar 

  268. Zhang H, Huang K, Li Z, Banerjei L, Fisher KE, Grishin NV, Eisenstein E, Herzberg O (2000) Crystal structure of YbaK protein from Haemophilus influenzae (HI1434) at 1.8 A resolution: functional implications. Proteins 40(1):86–97

    CAS  Google Scholar 

  269. An S, Musier-Forsyth K (2004) Trans-editing of Cys-tRNAPro by Haemophilus influenzae YbaK protein. J Biol Chem 279(41):42359–42362

    CAS  Google Scholar 

  270. Ruan B, Soll D (2005) The bacterial YbaK protein is a Cys-tRNAPro and Cys-tRNA Cys deacylase. J Biol Chem 280(27):25887–25891

    CAS  Google Scholar 

  271. Ruan LL, Zhou XL, Tan M, Wang ED (2013) Human cytoplasmic ProX edits mischarged tRNAPro with amino acid but not tRNA specificity. Biochem J 450:243–252

    CAS  Google Scholar 

  272. So BR, An S, Kumar S, Das M, Turner DA, Hadad CM, Musier-Forsyth K (2011) Substrate-mediated fidelity mechanism ensures accurate decoding of proline codons. J Biol Chem 286(36):31810–31820

    CAS  Google Scholar 

  273. Musier-Forsyth K, Stehlin C, Burke B, Liu H (1997) Understanding species-specific differences in substrate recognition by Escherichia coli and human prolyl-tRNA synthetases. Nucleic Acids Symp Ser 36:5–7

    CAS  Google Scholar 

  274. Bullard JM, Cai YC, Demeler B, Spremulli LL (1999) Expression and characterization of a human mitochondrial phenylalanyl-tRNA synthetase. J Mol Biol 288(4):567–577

    CAS  Google Scholar 

  275. Beuning PJ, Musier-Forsyth K (2001) Species-specific differences in amino acid editing by class II prolyl-tRNA synthetase. J Biol Chem 276(33):30779–30785

    CAS  Google Scholar 

  276. Lue SW, Kelley SO (2005) An aminoacyl-tRNA synthetase with a defunct editing site. Biochemistry 44(8):3010–3016

    CAS  Google Scholar 

  277. SternJohn J, Hati S, Siliciano PG, Musier-Forsyth K (2007) Restoring species-specific posttransfer editing activity to a synthetase with a defunct editing domain. Proc Natl Acad Sci U S A 104(7):2127–2132

    Google Scholar 

  278. Wong FC, Beuning PJ, Nagan M, Shiba K, Musier-Forsyth K (2002) Functional role of the prokaryotic proline-tRNA synthetase insertion domain in amino acid editing. Biochemistry 41(22):7108–7115

    CAS  Google Scholar 

  279. Wong FC, Beuning PJ, Silvers C, Musier-Forsyth K (2003) An isolated class II aminoacyl-tRNA synthetase insertion domain is functional in amino acid editing. J Biol Chem 278(52):52857–52864

    CAS  Google Scholar 

  280. Ling J, Reynolds N, Ibba M (2009) Aminoacyl-tRNA synthesis and translational quality control. Annu Rev Microbiol 63:61–78

    CAS  Google Scholar 

  281. Raina M, Elgamal S, Santangelo TJ, Ibba M (2012) Association of a multi-synthetase complex with translating ribosomes in the archaeon Thermococcus kodakarensis. FEBS Lett 586(16):2232–2238

    CAS  Google Scholar 

  282. Mirande M (2010) Processivity of translation in the eukaryote cell: role of aminoacyl-tRNA synthetases. FEBS Lett 584(2):443–447

    CAS  Google Scholar 

  283. Guo M, Yang XL, Schimmel P (2010) New functions of aminoacyl-tRNA synthetases beyond translation. Nat Rev Mol Cell Biol 11(9):668–674

    CAS  Google Scholar 

  284. Sajish M, Zhou Q, Kishi S, Valdez DM Jr, Kapoor M, Guo M, Lee S, Kim S, Yang XL, Schimmel P (2012) Trp-tRNA synthetase bridges DNA-PKcs to PARP-1 to link IFN-gamma and p53 signaling. Nat Chem Biol 8(6):547–554

    CAS  Google Scholar 

  285. Jia J, Arif A, Ray PS, Fox PL (2008) WHEP domains direct noncanonical function of glutamyl-prolyl tRNA synthetase in translational control of gene expression. Mol Cell 29(6):679–690

    CAS  Google Scholar 

  286. Smirnova EV, Lakunina VA, Tarassov I, Krasheninnikov IA, Kamenski PA (2012) Noncanonical functions of aminoacyl-tRNA synthetases. Biochemistry (Mosc) 77(1):15–25

    CAS  Google Scholar 

  287. Han JM, Jeong SJ, Park MC, Kim G, Kwon NH, Kim HK, Ha SH, Ryu SH, Kim S (2012) Leucyl-tRNA synthetase is an intracellular leucine sensor for the mTORC1-signaling pathway. Cell 149(2):410–424

    CAS  Google Scholar 

  288. Bonfils G, Jaquenoud M, Bontron S, Ostrowicz C, Ungermann C, De Virgilio C (2012) Leucyl-tRNA synthetase controls TORC1 via the EGO complex. Mol Cell 46(1):105–110

    CAS  Google Scholar 

  289. Putney SD, Schimmel P (1981) An aminoacyl tRNA synthetase binds to a specific DNA sequence and regulates its gene transcription. Nature 291(5817):632–635

    CAS  Google Scholar 

  290. Mayaux JF, Fayat G, Panvert M, Springer M, Grunberg-Manago M, Blanquet S (1985) Control of phenylalanyl-tRNA synthetase genetic expression. Site-directed mutagenesis of the pheS, T operon regulatory region in vitro. J Mol Biol 184(1):31–44

    CAS  Google Scholar 

  291. Putzer H, Laalami S, Brakhage AA, Condon C, Grunberg-Manago M (1995) Aminoacyl-tRNA synthetase gene regulation in Bacillus subtilis: induction, repression and growth-rate regulation. Mol Microbiol 16(4):709–718

    CAS  Google Scholar 

  292. Moine H, Romby P, Springer M, Grunberg-Manago M, Ebel JP, Ehresmann B, Ehresmann C (1990) Escherichia coli threonyl-tRNA synthetase and tRNA(Thr) modulate the binding of the ribosome to the translational initiation site of the thrS mRNA. J Mol Biol 216(2):299–310

    CAS  Google Scholar 

  293. Rho SB, Lincecum TL Jr, Martinis SA (2002) An inserted region of leucyl-tRNA synthetase plays a critical role in group I intron splicing. EMBO J 21(24):6874–6881

    CAS  Google Scholar 

  294. Myers CA, Kuhla B, Cusack S, Lambowitz AM (2002) tRNA-like recognition of group I introns by a tyrosyl-tRNA synthetase. Proc Natl Acad Sci U S A 99(5):2630–2635

    CAS  Google Scholar 

  295. Roy H, Ibba M (2008) RNA-dependent lipid remodeling by bacterial multiple peptide resistance factors. Proc Natl Acad Sci U S A 105(12):4667–4672

    CAS  Google Scholar 

  296. Maloney E, Stankowska D, Zhang J, Fol M, Cheng QJ, Lun S, Bishai WR, Rajagopalan M, Chatterjee D, Madiraju MV (2009) The two-domain LysX protein of Mycobacterium tuberculosis is required for production of lysinylated phosphatidylglycerol and resistance to cationic antimicrobial peptides. PLoS Pathog 5(7):e1000534

    Google Scholar 

  297. Ernst CM, Staubitz P, Mishra NN, Yang SJ, Hornig G, Kalbacher H, Bayer AS, Kraus D, Peschel A (2009) The bacterial defensin resistance protein MprF consists of separable domains for lipid lysinylation and antimicrobial peptide repulsion. PLoS Pathog 5(11):e1000660

    Google Scholar 

  298. Thomas CM, Hothersall J, Willis CL, Simpson TJ (2010) Resistance to and synthesis of the antibiotic mupirocin. Nat Rev Microbiol 8(4):281–289

    CAS  Google Scholar 

  299. Sauguet L, Moutiez M, Li Y, Belin P, Seguin J, Le Du MH, Thai R, Masson C, Fonvielle M, Pernodet JL, Charbonnier JB, Gondry M (2011) Cyclodipeptide synthases, a family of class-I aminoacyl-tRNA synthetase-like enzymes involved in non-ribosomal peptide synthesis. Nucleic Acids Res 39(10):4475–4489

    CAS  Google Scholar 

  300. Sareen D, Steffek M, Newton GL, Fahey RC (2002) ATP-dependent L-cysteine:1D-myo-inosityl 2-amino-2-deoxy-alpha-D-glucopyranoside ligase, mycothiol biosynthesis enzyme MshC, is related to class I cysteinyl-tRNA synthetases. Biochemistry 41(22):6885–6890

    CAS  Google Scholar 

  301. Mocibob M, Ivic N, Bilokapic S, Maier T, Luic M, Ban N, Weygand-Durasevic I (2010) Homologs of aminoacyl-tRNA synthetases acylate carrier proteins and provide a link between ribosomal and nonribosomal peptide synthesis. Proc Natl Acad Sci U S A 107(33):14585–14590

    CAS  Google Scholar 

  302. Salazar JC, Ahel I, Orellana O, Tumbula-Hansen D, Krieger R, Daniels L, Soll D (2003) Coevolution of an aminoacyl-tRNA synthetase with its tRNA substrates. Proc Natl Acad Sci U S A 100(24):13863–13868

    CAS  Google Scholar 

  303. Blaise M, Becker HD, Lapointe J, Cambillau C, Giege R, Kern D (2005) Glu-Q-tRNA(Asp) synthetase coded by the yadB gene, a new paralog of aminoacyl-tRNA synthetase that glutamylates tRNA(Asp) anticodon. Biochimie 87(9–10):847–861

    CAS  Google Scholar 

  304. Roy H, Zou SB, Bullwinkle TJ, Wolfe BS, Gilreath MS, Forsyth CJ, Navarre WW, Ibba M (2011) The tRNA synthetase paralog PoxA modifies elongation factor-P with (R)-beta-lysine. Nat Chem Biol 7(10):667–669

    CAS  Google Scholar 

  305. Sissler M, Delorme C, Bond J, Ehrlich SD, Renault P, Francklyn C (1999) An aminoacyl-tRNA synthetase paralog with a catalytic role in histidine biosynthesis. Proc Natl Acad Sci U S A 96(16):8985–8990

    CAS  Google Scholar 

  306. Dong J, Qiu H, Garcia-Barrio M, Anderson J, Hinnebusch AG (2000) Uncharged tRNA activates GCN2 by displacing the protein kinase moiety from a bipartite tRNA-binding domain. Mol Cell 6(2):269–279

    CAS  Google Scholar 

  307. Cedar H, Schwartz JH (1969) The asparagine synthetase of Escherichia coli. I. Biosynthetic role of the enzyme, purification, and characterization of the reaction products. J Biol Chem 244(15):4112–4121

    CAS  Google Scholar 

  308. Artymiuk PJ, Rice DW, Poirrette AR, Willet P (1994) A tale of two synthetases. Nat Struct Biol 1(11):758–760

    CAS  Google Scholar 

  309. Chapman-Smith A, Mulhern TD, Whelan F, Cronan JE Jr, Wallace JC (2001) The C-terminal domain of biotin protein ligase from E. coli is required for catalytic activity. Protein Sci 10(12):2608–2617

    CAS  Google Scholar 

  310. Safro M, Mosyak L (1995) Structural similarities in the noncatalytic domains of phenylalanyl-tRNA and biotin synthetases. Protein Sci 4(11):2429–2432

    CAS  Google Scholar 

  311. Buoncristiani MR, Howard PK, Otsuka AJ (1986) DNA-binding and enzymatic domains of the bifunctional biotin operon repressor (BirA) of Escherichia coli. Gene 44(2–3):255–261

    CAS  Google Scholar 

  312. Guitart T, Leon Bernardo T, Sagales J, Stratmann T, Bernues J, Ribas de Pouplana L (2010) New aminoacyl-tRNA synthetase-like protein in insecta with an essential mitochondrial function. J Biol Chem 285(49):38157–38166

    CAS  Google Scholar 

  313. Jaric J, Bilokapic S, Lesjak S, Crnkovic A, Ban N, Weygand-Durasevic I (2009) Identification of amino acids in the N-terminal domain of atypical methanogenic-type Seryl-tRNA synthetase critical for tRNA recognition. J Biol Chem 284(44):30643–30651

    CAS  Google Scholar 

  314. Holm L, Sander C (1995) DNA polymerase beta belongs to an ancient nucleotidyltransferase superfamily. Trends Biochem Sci 20(9):345–347

    CAS  Google Scholar 

  315. Carrodeguas JA, Theis K, Bogenhagen DF, Kisker C (2001) Crystal structure and deletion analysis show that the accessory subunit of mammalian DNA polymerase gamma, Pol gamma B, functions as a homodimer. Mol Cell 7(1):43–54

    CAS  Google Scholar 

  316. Hoagland MB (1955) An enzymic mechanism for amino acid activation in animal tissues. Biochim Biophys Acta 16(2):288–289

    CAS  Google Scholar 

  317. Davie EW, Koningsberger VV, Lipmann F (1956) The isolation of a tryptophan-activating enzyme from pancreas. Arch Biochem Biophys 65(1):21–38

    CAS  Google Scholar 

  318. Park SG, Schimmel P, Kim S (2008) Aminoacyl tRNA synthetases and their connections to disease. Proc Natl Acad Sci U S A 105(32):11043–11049

    CAS  Google Scholar 

  319. Kim S, You S, Hwang D (2011) Aminoacyl-tRNA synthetases and tumorigenesis: more than housekeeping. Nat Rev Cancer 11(10):708–718

    CAS  Google Scholar 

Download references

Author information

Authors and Affiliations

Authors

Corresponding author

Correspondence to Michael Ibba .

Editor information

Editors and Affiliations

Rights and permissions

Reprints and permissions

Copyright information

© 2013 Springer-Verlag Berlin Heidelberg

About this chapter

Cite this chapter

Bullwinkle, T.J., Ibba, M. (2013). Emergence and Evolution. In: Kim, S. (eds) Aminoacyl-tRNA Synthetases in Biology and Medicine. Topics in Current Chemistry, vol 344. Springer, Dordrecht. https://doi.org/10.1007/128_2013_423

Download citation

Publish with us

Policies and ethics