Abstract
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.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
References
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 21:87–96
Alfonzo JD, Soll D (2009) Mitochondrial tRNA import–the challenge to understand has just begun. Biol Chem 390:717–722
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 18:7056–7062
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 12:3650–3662
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 3:893–899
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 144:104–108
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 17:7430–7441
Baird NJ, Fang XW, Srividya N, Pan T, Sosnick TR (2007) Folding of a universal ribozyme: the ribonuclease P RNA. Q Rev Biophys 40:113–161
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 46:819–826
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 20:7410–7417
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 26:4302–4312
Bruske EI, Sendfeld F, Schneider A (2009) Thiolated tRNAs of Trypanosoma brucei are imported into mitochondria and dethiolated after import. J Biol Chem 284:36491–36499
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 92:2627–2631
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 103:6847–6852
Cook AG, Fukuhara N, Jinek M, Conti E (2009) Structures of the tRNA export factor in the nuclear and cytosolic states. Nature 461:60–65
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 8:752–761
De Robertis EM, Olson MV (1979) Transcription and processing of cloned yeast tyrosine tRNA genes microinjected into frog oocytes. Nature 278:137–143
Dorner M, Altmann M, Paabo S, Morl M (2001) Evidence for import of a lysyl-tRNA into marsupial mitochondria. Mol Biol Cell 12:2688–2698
Engelke DR, Hopper AK (2006) Modified view of tRNA: stability amid sequence diversity. Mol Cell 21:144–145
Esakova O, Krasilnikov AS (2010) Of proteins and RNA: the RNase P/MRP family. RNA 16:1725–1747
Esseiva AC, Naguleswaran A, Hemphill A, Schneider A (2004) Mitochondrial tRNA import in Toxoplasma gondii. J Biol Chem 279:42363–42368
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 35:359–366
Frank DN, Pace NR (1998) Ribonuclease P: unity and diversity in a tRNA processing ribozyme. Annu Rev Biochem 67:153–180
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 35:6740–6749
Gerber AP, Keller W (1999) An adenosine deaminase that generates inosine at the wobble position of tRNAs. Science 286:1146–1149
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 103:8354–8359
Gray MW (2003) Diversity and evolution of mitochondrial RNA editing systems. IUBMB Life 55:227–233
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 7:76–84
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 35:849–857
Hancock K, Hajduk SL (1990) The mitochondrial tRNAs of Trypanosoma brucei are nuclear encoded. J Biol Chem 265:19208–19215
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 135:462–474
Hopper AK, Pai DA, Engelke DR (2010) Cellular dynamics of tRNAs and their genes. FEBS Lett 584:310–317
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 15:1565–1577
Johnson PF, Abelson J (1983) The yeast tRNATyr gene intron is essential for correct modification of its tRNA product. Nature 302:681–687
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 37:159–162
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 22:657–667
Kapushoc ST, Alfonzo JD, Simpson L (2002) Differential localization of nuclear-encoded tRNAs between the cytosol and mitochondrion in Leishmania tarentolae. RNA 8:57–68
Kazantsev AV, Krivenko AA, Pace NR (2009) Mapping metal-binding sites in the catalytic domain of bacterial RNase P RNA. RNA 15:266–276
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 458:228–232
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 33:82–84
Levinger L, Morl M, Florentz C (2004) Mitochondrial tRNA 3′ end metabolism and human disease. Nucleic Acids Res 32:5430–5441
Lill R, Muhlenhoff U (2006) Iron-sulfur protein biogenesis in eukaryotes: components and mechanisms. Annu Rev Cell Dev Biol 22:457–486
Lima BD, Simpson L (1996) Sequence-dependent in vivo importation of tRNAs into the mitochondrion of Leishmania tarentolae. RNA 2:429–440
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 5:539–549
Lithgow T, Schneider A (2010) Evolution of macromolecular import pathways in mitochondria, hydrogenosomes and mitosomes. Philos Trans R Soc Lond B Biol Sci 365:799–817
Lye LF, Chen DH, Suyama Y (1993) Selective import of nuclear-encoded tRNAs into mitochondria of the protozoan Leishmania tarentolae. Mol Biochem Parasitol 58:233–245
Mahapatra S, Ghosh T, Adhya S (1994) Import of small RNAs into Leishmania mitochondria in vitro. Nucleic Acids Res 22:3381–3386
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 26:2037–2041
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 16:4777–4788
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 18:4600–4605
Mayer M, Schiffer S, Marchfelder A (2000) tRNA 3′ processing in plants: nuclear and mitochondrial activities differ. Biochemistry 39:2096–2105
Melton DA, De Robertis EM, Cortese R (1980) Order and intracellular location of the events involved in the maturation of a spliced tRNA. Nature 284:143–148
Mottram JC, Bell SD, Nelson RG, Barry JD (1991) tRNAs of Trypanosoma brucei. Unusual gene organization and mitochondrial importation. J Biol Chem 266:18313–18317
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 8:589–595
Nashimoto M, Tamura M, Kaspar RL (1999) Selection of cleavage site by mammalian tRNA 3′ processing endoribonuclease. J Mol Biol 287:727–740
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 268:20709–20712
Paris Z, Rubio MA, Lukes J, Alfonzo JD (2009) Mitochondrial tRNA import in Trypanosoma brucei is independent of thiolation and the Rieske protein. RNA 15:1398–1406
Phizicky EM, Alfonzo JD (2009) Do all modifications benefit all tRNAs? FEBS Lett 584:265–271
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 26:671–680
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 324:657–659
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 19:583–592
Rubio MA, Liu X, Yuzawa H, Alfonzo JD, Simpson L (2000) Selective importation of RNA into isolated mitochondria from Leishmania tarentolae. RNA 6:988–1003
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 281:115–120
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 104:7821–7826
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 105:9186–9191
Rusconi CP, Cech TR (1996) The anticodon is the signal sequence for mitochondrial import of glutamine tRNA in Tetrahymena. Genes Dev 10:2870–2880
Salavati R, Panigrahi AK, Stuart KD (2001) Mitochondrial ribonuclease P activity of Trypanosoma brucei. Mol Biochem Parasitol 115:109–117
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 103:18362–18367
Salinas T, Duchene AM, Marechal-Drouard L (2008) Recent advances in tRNA mitochondrial import. Trends Biochem Sci 33:320–329
Schiffer S, Helm M, Theobald-Dietrich A, Giege R, Marchfelder A (2001) The plant tRNA 3′ processing enzyme has a broad substrate spectrum. Biochemistry 40:8264–8272
Sherrer RL, Yermovsky-Kammerer AE, Hajduk SL (2003) A sequence motif within trypanosome precursor tRNAs influences abundance and mitochondrial localization. Mol Cell Biol 23:9061–9072
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 65:23–37
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 17:5427–5445
Sprinzl M, Vassilenko KS (2005) Compilation of tRNA sequences and sequences of tRNA genes. Nucleic Acids Res 33(Database Issue):D139–D140
Stange N, Gross HJ, Beier H (1988) Wheat germ splicing endonuclease is highly specific for plant pre-tRNAs. EMBO J 7:3823–3828
Suyama Y (1967) The origins of mitochondrial ribonucleic acids in Tetrahymena pyriformis. Biochemistry 6:2829–2839
Suyama Y, Wong S, Campbell DA (1998) Regulated tRNA import in Leishmania mitochondria. Biochim Biophys Acta 1396:138–142
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 32:91
Tan TH, Pach R, Crausaz A, Ivens A, Schneider A (2002) tRNAs in Trypanosoma brucei: genomic organization, expression, and mitochondrial import. Mol Cell Biol 22:3707–3717
Vogel A, Schilling O, Spath B, Marchfelder A (2005) The tRNase Z family of proteins: physiological functions, substrate specificity and structural properties. Biol Chem 386:1253–1264
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 284:23947–23953
Wolin SL, Cedervall T (2002) The La protein. Annu Rev Biochem 71:375–403
Xiao S, Scott F, Fierke CA, Engelke DR (2002) Eukaryotic ribonuclease P: a plurality of ribonucleoprotein enzymes. Annu Rev Biochem 71:165–189
Xiong Y, Steitz TA (2006) A story with a good ending: tRNA 3′-end maturation by CCA-adding enzymes. Curr Opin Struct Biol 16:12–17
Yoo CJ, Wolin SL (1997) The yeast La protein is required for the 3′ endonucleolytic cleavage that matures tRNA precursors. Cell 89:393–402
Yuan Y, Altman S (1995) Substrate recognition by human RNase P: identification of small, model substrates for the enzyme. EMBO J 14:159–168
Author information
Authors and Affiliations
Corresponding author
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2012 Springer-Verlag GmbH Berlin Heidelberg
About this chapter
Cite this chapter
Spears, J.L., Rubio, M.A.T., Sample, P.J., Alfonzo, J.D. (2012). tRNA Biogenesis and Processing. In: Bindereif, A. (eds) RNA Metabolism in Trypanosomes. Nucleic Acids and Molecular Biology, vol 28. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-642-28687-2_5
Download citation
DOI: https://doi.org/10.1007/978-3-642-28687-2_5
Published:
Publisher Name: Springer, Berlin, Heidelberg
Print ISBN: 978-3-642-28686-5
Online ISBN: 978-3-642-28687-2
eBook Packages: Biomedical and Life SciencesBiomedical and Life Sciences (R0)