tRNA Biogenesis and Processing

Part of the Nucleic Acids and Molecular Biology book series (NUCLEIC, volume 28)


tRNAs are essential in all domains of life; this becomes especially important in trypanosomatids, where for all purposes the same set of tRNAs are utilized for cytoplasmic and mitochondrial protein synthesis. What makes the system special is that although tRNA biogenesis starts in the nucleus, the resulting products will satisfy translational requirements in two very different compartments. The balance between intracellular tRNA transport and post-transcriptional modifications may modulate tRNA function in gene expression. This chapter will summarize what is currently known about various processes that a tRNA must undergo in a trypanosomatid cell to become fully functional. Whenever possible, we will highlight both commonalities and differences with other systems, while emphasizing open questions that may lead to new and surprising discoveries in this group of evolutionarily divergent organisms.


Editing Mitochondria Modification Processing tRNA transport Trypanosomes 


  1. Alexandrov A, Chernyakov I, Gu W, Hiley SL, Hughes TR, Grayhack EJ, Phizicky EM (2006) Rapid tRNA decay can result from lack of nonessential modifications. Mol Cell 21:87–96PubMedCrossRefGoogle Scholar
  2. Alfonzo JD, Soll D (2009) Mitochondrial tRNA import–the challenge to understand has just begun. Biol Chem 390:717–722PubMedCrossRefGoogle Scholar
  3. Alfonzo JD, Blanc V, Estevez AM, Rubio MA, Simpson L (1999) C to U editing of the anticodon of imported mitochondrial tRNA(Trp) allows decoding of the UGA stop codon in Leishmania tarentolae. EMBO J 18:7056–7062PubMedCrossRefGoogle Scholar
  4. Anderson J, Phan L, Cuesta R, Carlson BA, Pak M, Asano K, Bjork GR, Tamame M, Hinnebusch AG (1998) The essential Gcd10p-Gcd14p nuclear complex is required for 1-methyladenosine modification and maturation of initiator methionyl-tRNA. Genes Dev 12:3650–3662PubMedCrossRefGoogle Scholar
  5. Arhin GK, Shen S, Irmer H, Ullu E, Tschudi C (2004) Role of a 300-kilodalton nuclear complex in the maturation of Trypanosoma brucei initiator methionyl-tRNA. Eukaryot Cell 3:893–899PubMedCrossRefGoogle Scholar
  6. Arhin GK, Shen S, Perez IF, Tschudi C, Ullu E (2005) Downregulation of the essential Trypanosoma brucei La protein affects accumulation of elongator methionyl-tRNA. Mol Biochem Parasitol 144:104–108PubMedCrossRefGoogle Scholar
  7. Arts GJ, Kuersten S, Romby P, Ehresmann B, Mattaj IW (1998) The role of exportin-t in selective nuclear export of mature tRNAs. EMBO J 17:7430–7441PubMedCrossRefGoogle Scholar
  8. Baird NJ, Fang XW, Srividya N, Pan T, Sosnick TR (2007) Folding of a universal ribozyme: the ribonuclease P RNA. Q Rev Biophys 40:113–161PubMedCrossRefGoogle Scholar
  9. Benne R, Van den Burg J, Brakenhoff JP, Sloof P, Van Boom JH, Tromp MC (1986) Major transcript of the frameshifted coxII gene from trypanosome mitochondria contains four nucleotides that are not encoded in the DNA. Cell 46:819–826PubMedCrossRefGoogle Scholar
  10. Bhattacharyya SN, Mukherjee S, Adhya S (2000) Mutations in a tRNA import signal define distinct receptors at the two membranes of Leishmania mitochondria. Mol Cell Biol 20:7410–7417PubMedCrossRefGoogle Scholar
  11. Bouzaidi-Tiali N, Aeby E, Charriere F, Pusnik M, Schneider A (2007) Elongation factor 1a mediates the specificity of mitochondrial tRNA import in T. brucei. EMBO J 26:4302–4312PubMedCrossRefGoogle Scholar
  12. Bruske EI, Sendfeld F, Schneider A (2009) Thiolated tRNAs of Trypanosoma brucei are imported into mitochondria and dethiolated after import. J Biol Chem 284:36491–36499PubMedCrossRefGoogle Scholar
  13. Carrara G, Calandra P, Fruscoloni P, Tocchini-Valentini GP (1995) Two helices plus a linker: a small model substrate for eukaryotic RNase P. Proc Natl Acad Sci U S A 92:2627–2631PubMedCrossRefGoogle Scholar
  14. Charriere F, Helgadottir S, Horn EK, Soll D, Schneider A (2006) Dual targeting of a single tRNA(Trp) requires two different tryptophanyl-tRNA synthetases in Trypanosoma brucei. Proc Natl Acad Sci U S A 103:6847–6852PubMedCrossRefGoogle Scholar
  15. Cook AG, Fukuhara N, Jinek M, Conti E (2009) Structures of the tRNA export factor in the nuclear and cytosolic states. Nature 461:60–65PubMedCrossRefGoogle Scholar
  16. Crain PF, Alfonzo JD, Rozenski J, Kapushoc ST, McCloskey JA, Simpson L (2002) Modification of the universally unmodified uridine-33 in a mitochondria-imported edited tRNA and the role of the anticodon arm structure on editing efficiency. RNA 8:752–761PubMedCrossRefGoogle Scholar
  17. De Robertis EM, Olson MV (1979) Transcription and processing of cloned yeast tyrosine tRNA genes microinjected into frog oocytes. Nature 278:137–143PubMedCrossRefGoogle Scholar
  18. Dorner M, Altmann M, Paabo S, Morl M (2001) Evidence for import of a lysyl-tRNA into marsupial mitochondria. Mol Biol Cell 12:2688–2698PubMedGoogle Scholar
  19. Engelke DR, Hopper AK (2006) Modified view of tRNA: stability amid sequence diversity. Mol Cell 21:144–145PubMedCrossRefGoogle Scholar
  20. Esakova O, Krasilnikov AS (2010) Of proteins and RNA: the RNase P/MRP family. RNA 16:1725–1747PubMedCrossRefGoogle Scholar
  21. Esseiva AC, Naguleswaran A, Hemphill A, Schneider A (2004) Mitochondrial tRNA import in Toxoplasma gondii. J Biol Chem 279:42363–42368PubMedCrossRefGoogle Scholar
  22. Foldynova-Trantirkova S, Paris Z, Sturm NR, Campbell DA, Lukes J (2005) The Trypanosoma brucei La protein is a candidate poly(U) shield that impacts spliced leader RNA maturation and tRNA intron removal. Int J Parasitol 35:359–366PubMedCrossRefGoogle Scholar
  23. Frank DN, Pace NR (1998) Ribonuclease P: unity and diversity in a tRNA processing ribozyme. Annu Rev Biochem 67:153–180PubMedCrossRefGoogle Scholar
  24. Gaston KW, Rubio MA, Spears JL, Pastar I, Papavasiliou FN, Alfonzo JD (2007) C to U editing at position 32 of the anticodon loop precedes tRNA 5′ leader removal in trypanosomatids. Nucleic Acids Res 35:6740–6749PubMedCrossRefGoogle Scholar
  25. Gerber AP, Keller W (1999) An adenosine deaminase that generates inosine at the wobble position of tRNAs. Science 286:1146–1149PubMedCrossRefGoogle Scholar
  26. Goswami S, Dhar G, Mukherjee S, Mahata B, Chatterjee S, Home P, Adhya S (2006) A bifunctional tRNA import receptor from Leishmania mitochondria. Proc Natl Acad Sci U S A 103:8354–8359PubMedCrossRefGoogle Scholar
  27. Gray MW (2003) Diversity and evolution of mitochondrial RNA editing systems. IUBMB Life 55:227–233PubMedCrossRefGoogle Scholar
  28. Greer CL, Soll D, Willis I (1987) Substrate recognition and identification of splice sites by the tRNA-splicing endonuclease and ligase from Saccharomyces cerevisiae. Mol Cell Biol 7:76–84PubMedGoogle Scholar
  29. Guerrier-Takada C, Gardiner K, Marsh T, Pace N, Altman S (1983) The RNA moiety of ribonuclease P is the catalytic subunit of the enzyme. Cell 35:849–857PubMedCrossRefGoogle Scholar
  30. Hancock K, Hajduk SL (1990) The mitochondrial tRNAs of Trypanosoma brucei are nuclear encoded. J Biol Chem 265:19208–19215PubMedGoogle Scholar
  31. Holzmann J, Frank P, Loffler E, Bennett KL, Gerner C, Rossmanith W (2008) RNase P without RNA: identification and functional reconstitution of the human mitochondrial tRNA processing enzyme. Cell 135:462–474PubMedCrossRefGoogle Scholar
  32. Hopper AK, Pai DA, Engelke DR (2010) Cellular dynamics of tRNAs and their genes. FEBS Lett 584:310–317PubMedCrossRefGoogle Scholar
  33. Hsieh J, Fierke CA (2009) Conformational change in the Bacillus subtilis RNase P holoenzyme–pre-tRNA complex enhances substrate affinity and limits cleavage rate. RNA 15:1565–1577PubMedCrossRefGoogle Scholar
  34. Johnson PF, Abelson J (1983) The yeast tRNATyr gene intron is essential for correct modification of its tRNA product. Nature 302:681–687PubMedCrossRefGoogle Scholar
  35. Juhling F, Morl M, Hartmann RK, Sprinzl M, Stadler PF, Putz J (2009) tRNAdb 2009: compilation of tRNA sequences and tRNA genes. Nucleic Acids Res 37:159–162CrossRefGoogle Scholar
  36. Kaneko T, Suzuki T, Kapushoc ST, Rubio MA, Ghazvini J, Watanabe K, Simpson L (2003) Wobble modification differences and subcellular localization of tRNAs in Leishmania tarentolae: implication for tRNA sorting mechanism. EMBO J 22:657–667PubMedCrossRefGoogle Scholar
  37. Kapushoc ST, Alfonzo JD, Simpson L (2002) Differential localization of nuclear-encoded tRNAs between the cytosol and mitochondrion in Leishmania tarentolae. RNA 8:57–68PubMedCrossRefGoogle Scholar
  38. Kazantsev AV, Krivenko AA, Pace NR (2009) Mapping metal-binding sites in the catalytic domain of bacterial RNase P RNA. RNA 15:266–276PubMedCrossRefGoogle Scholar
  39. Leidel S, Pedrioli PG, Bucher T, Brost R, Costanzo M, Schmidt A, Aebersold R, Boone C, Hofmann K, Peter M (2009) Ubiquitin-related modifier Urm1 acts as a sulphur carrier in thiolation of eukaryotic transfer RNA. Nature 458:228–232PubMedCrossRefGoogle Scholar
  40. Levinger L, Greene V, Birk A, Bourne R, Kolla S, Whyte S (1995) RNase P and 3′-tRNase processing matrices in the analysis of Drosophila transfer RNA D/T loop tertiary contacts. Nucleic Acids Symp Ser 33:82–84PubMedGoogle Scholar
  41. Levinger L, Morl M, Florentz C (2004) Mitochondrial tRNA 3′ end metabolism and human disease. Nucleic Acids Res 32:5430–5441PubMedCrossRefGoogle Scholar
  42. Lill R, Muhlenhoff U (2006) Iron-sulfur protein biogenesis in eukaryotes: components and mechanisms. Annu Rev Cell Dev Biol 22:457–486PubMedCrossRefGoogle Scholar
  43. Lima BD, Simpson L (1996) Sequence-dependent in vivo importation of tRNAs into the mitochondrion of Leishmania tarentolae. RNA 2:429–440PubMedGoogle Scholar
  44. Lipowsky G, Bischoff FR, Izaurralde E, Kutay U, Schafer S, Gross HJ, Beier H, Gorlich D (1999) Coordination of tRNA nuclear export with processing of tRNA. RNA 5:539–549PubMedCrossRefGoogle Scholar
  45. Lithgow T, Schneider A (2010) Evolution of macromolecular import pathways in mitochondria, hydrogenosomes and mitosomes. Philos Trans R Soc Lond B Biol Sci 365:799–817PubMedCrossRefGoogle Scholar
  46. Lye LF, Chen DH, Suyama Y (1993) Selective import of nuclear-encoded tRNAs into mitochondria of the protozoan Leishmania tarentolae. Mol Biochem Parasitol 58:233–245PubMedCrossRefGoogle Scholar
  47. Mahapatra S, Ghosh T, Adhya S (1994) Import of small RNAs into Leishmania mitochondria in vitro. Nucleic Acids Res 22:3381–3386PubMedCrossRefGoogle Scholar
  48. Mahapatra S, Ghosh S, Bera SK, Ghosh T, Das A, Adhya S (1998) The D arm of tRNATyr is necessary and sufficient for import into Leishmania mitochondria in vitro. Nucleic Acids Res 26:2037–2041PubMedCrossRefGoogle Scholar
  49. Marechal-Drouard L, Weil JH, Guillemaut P (1988) Import of several tRNAs from the cytoplasm into the mitochondria in bean Phaseolus vulgaris. Nucleic Acids Res 16:4777–4788PubMedCrossRefGoogle Scholar
  50. Martin RP, Schneller JM, Stahl AJ, Dirheimer G (1979) Import of nuclear deoxyribonucleic acid coded lysine-accepting transfer ribonucleic acid (anticodon C–U–U) into yeast mitochondria. Biochemistry 18:4600–4605PubMedCrossRefGoogle Scholar
  51. Mayer M, Schiffer S, Marchfelder A (2000) tRNA 3′ processing in plants: nuclear and mitochondrial activities differ. Biochemistry 39:2096–2105PubMedCrossRefGoogle Scholar
  52. Melton DA, De Robertis EM, Cortese R (1980) Order and intracellular location of the events involved in the maturation of a spliced tRNA. Nature 284:143–148PubMedCrossRefGoogle Scholar
  53. Mottram JC, Bell SD, Nelson RG, Barry JD (1991) tRNAs of Trypanosoma brucei. Unusual gene organization and mitochondrial importation. J Biol Chem 266:18313–18317PubMedGoogle Scholar
  54. Mukherjee S, Basu S, Home P, Dhar G, Adhya S (2007) Necessary and sufficient factors for the import of transfer RNA into the kinetoplast mitochondrion. EMBO Rep 8:589–595PubMedCrossRefGoogle Scholar
  55. Nashimoto M, Tamura M, Kaspar RL (1999) Selection of cleavage site by mammalian tRNA 3′ processing endoribonuclease. J Mol Biol 287:727–740PubMedCrossRefGoogle Scholar
  56. Navaratnam N, Morrison JR, Bhattacharya S, Patel D, Funahashi T, Giannoni F, Teng BB, Davidson NO, Scott J (1993) The p27 catalytic subunit of the apolipoprotein B mRNA editing enzyme is a cytidine deaminase. J Biol Chem 268:20709–20712PubMedGoogle Scholar
  57. Paris Z, Rubio MA, Lukes J, Alfonzo JD (2009) Mitochondrial tRNA import in Trypanosoma brucei is independent of thiolation and the Rieske protein. RNA 15:1398–1406PubMedCrossRefGoogle Scholar
  58. Phizicky EM, Alfonzo JD (2009) Do all modifications benefit all tRNAs? FEBS Lett 584:265–271CrossRefGoogle Scholar
  59. Pusnik M, Charriere F, Maser P, Waller RF, Dagley MJ, Lithgow T, Schneider A (2009) The single mitochondrial porin of Trypanosoma brucei is the main metabolite transporter in the outer mitochondrial membrane. Mol Biol Evol 26:671–680PubMedCrossRefGoogle Scholar
  60. Randau L, Stanley BJ, Kohlway A, Mechta S, Xiong Y, Soll D (2009) A cytidine deaminase edits C to U in transfer RNAs in Archaea. Science 324:657–659PubMedCrossRefGoogle Scholar
  61. Rinehart J, Krett B, Rubio MA, Alfonzo JD, Soll D (2005) Saccharomyces cerevisiae imports the cytosolic pathway for Gln-tRNA synthesis into the mitochondrion. Genes Dev 19:583–592PubMedCrossRefGoogle Scholar
  62. Rubio MA, Liu X, Yuzawa H, Alfonzo JD, Simpson L (2000) Selective importation of RNA into isolated mitochondria from Leishmania tarentolae. RNA 6:988–1003PubMedCrossRefGoogle Scholar
  63. Rubio MA, Ragone FL, Gaston KW, Ibba M, Alfonzo JD (2006) C to U editing stimulates A to I editing in the anticodon loop of a cytoplasmic threonyl tRNA in Trypanosoma brucei. J Biol Chem 281:115–120PubMedCrossRefGoogle Scholar
  64. Rubio MA, Pastar I, Gaston KW, Ragone FL, Janzen CJ, Cross GA, Papavasiliou FN, Alfonzo JD (2007) An adenosine-to-inosine tRNA-editing enzyme that can perform C-to-U deamination of DNA. Proc Natl Acad Sci U S A 104:7821–7826PubMedCrossRefGoogle Scholar
  65. Rubio MA, Rinehart JJ, Krett B, Duvezin-Caubet S, Reichert AS, Soll D, Alfonzo JD (2008) Mammalian mitochondria have the innate ability to import tRNAs by a mechanism distinct from protein import. Proc Natl Acad Sci U S A 105:9186–9191PubMedCrossRefGoogle Scholar
  66. Rusconi CP, Cech TR (1996) The anticodon is the signal sequence for mitochondrial import of glutamine tRNA in Tetrahymena. Genes Dev 10:2870–2880PubMedCrossRefGoogle Scholar
  67. Salavati R, Panigrahi AK, Stuart KD (2001) Mitochondrial ribonuclease P activity of Trypanosoma brucei. Mol Biochem Parasitol 115:109–117PubMedCrossRefGoogle Scholar
  68. Salinas T, Duchene AM, Delage L, Nilsson S, Glaser E, Zaepfel M, Marechal-Drouard L (2006) The voltage-dependent anion channel, a major component of the tRNA import machinery in plant mitochondria. Proc Natl Acad Sci U S A 103:18362–18367PubMedCrossRefGoogle Scholar
  69. Salinas T, Duchene AM, Marechal-Drouard L (2008) Recent advances in tRNA mitochondrial import. Trends Biochem Sci 33:320–329PubMedCrossRefGoogle Scholar
  70. Schiffer S, Helm M, Theobald-Dietrich A, Giege R, Marchfelder A (2001) The plant tRNA 3′ processing enzyme has a broad substrate spectrum. Biochemistry 40:8264–8272PubMedCrossRefGoogle Scholar
  71. Sherrer RL, Yermovsky-Kammerer AE, Hajduk SL (2003) A sequence motif within trypanosome precursor tRNAs influences abundance and mitochondrial localization. Mol Cell Biol 23:9061–9072PubMedCrossRefGoogle Scholar
  72. Shi X, Chen DH, Suyama Y (1994) A nuclear tRNA gene cluster in the protozoan Leishmania tarentolae and differential distribution of nuclear-encoded tRNAs between the cytosol and mitochondria. Mol Biochem Parasitol 65:23–37PubMedCrossRefGoogle Scholar
  73. Simpson AM, Suyama Y, Dewes H, Campbell DA, Simpson L (1989) Kinetoplastid mitochondria contain functional tRNAs which are encoded in nuclear DNA and also contain small minicircle and maxicircle transcripts of unknown function. Nucleic Acids Res 17:5427–5445PubMedCrossRefGoogle Scholar
  74. Sprinzl M, Vassilenko KS (2005) Compilation of tRNA sequences and sequences of tRNA genes. Nucleic Acids Res 33(Database Issue):D139–D140PubMedCrossRefGoogle Scholar
  75. Stange N, Gross HJ, Beier H (1988) Wheat germ splicing endonuclease is highly specific for plant pre-tRNAs. EMBO J 7:3823–3828PubMedGoogle Scholar
  76. Suyama Y (1967) The origins of mitochondrial ribonucleic acids in Tetrahymena pyriformis. Biochemistry 6:2829–2839PubMedCrossRefGoogle Scholar
  77. Suyama Y, Wong S, Campbell DA (1998) Regulated tRNA import in Leishmania mitochondria. Biochim Biophys Acta 1396:138–142PubMedCrossRefGoogle Scholar
  78. Takaku H, Minagawa A, Takagi M, Nashimoto M (2004) A novel 4-base-recognizing RNA cutter that can remove the single 3′ terminal nucleotides from RNA molecules. Nucleic Acids Res 32:91CrossRefGoogle Scholar
  79. Tan TH, Pach R, Crausaz A, Ivens A, Schneider A (2002) tRNAs in Trypanosoma brucei: genomic organization, expression, and mitochondrial import. Mol Cell Biol 22:3707–3717PubMedCrossRefGoogle Scholar
  80. Vogel A, Schilling O, Spath B, Marchfelder A (2005) The tRNase Z family of proteins: physiological functions, substrate specificity and structural properties. Biol Chem 386:1253–1264PubMedGoogle Scholar
  81. Wohlgamuth-Benedum JM, Rubio MA, Paris Z, Long S, Poliak P, Lukes J, Alfonzo JD (2009) Thiolation controls cytoplasmic tRNA stability and acts as a negative determinant for tRNA editing in mitochondria. J Biol Chem 284:23947–23953PubMedCrossRefGoogle Scholar
  82. Wolin SL, Cedervall T (2002) The La protein. Annu Rev Biochem 71:375–403PubMedCrossRefGoogle Scholar
  83. Xiao S, Scott F, Fierke CA, Engelke DR (2002) Eukaryotic ribonuclease P: a plurality of ribonucleoprotein enzymes. Annu Rev Biochem 71:165–189PubMedCrossRefGoogle Scholar
  84. Xiong Y, Steitz TA (2006) A story with a good ending: tRNA 3′-end maturation by CCA-adding enzymes. Curr Opin Struct Biol 16:12–17PubMedCrossRefGoogle Scholar
  85. Yoo CJ, Wolin SL (1997) The yeast La protein is required for the 3′ endonucleolytic cleavage that matures tRNA precursors. Cell 89:393–402PubMedCrossRefGoogle Scholar
  86. Yuan Y, Altman S (1995) Substrate recognition by human RNase P: identification of small, model substrates for the enzyme. EMBO J 14:159–168PubMedGoogle Scholar

Copyright information

© Springer-Verlag GmbH Berlin Heidelberg 2012

Authors and Affiliations

  1. 1.Department of Microbiology, The Ohio State Center for RNA BiologyThe Ohio State UniversityColumbusUSA
  2. 2.Ohio State Biochemistry ProgramThe Ohio State UniversityColumbusUSA

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