Mechanisms and Evolution of tRNA 5′-Editing in Mitochondria

  • Samantha Dodbele
  • Jane E. Jackman
  • Michael W. GrayEmail author
Part of the Nucleic Acids and Molecular Biology book series (NUCLEIC, volume 34)


In several protists and fungi, many of the tRNAs encoded by the mitochondrial genome are unusual in that they are predicted to have mismatches within the first three positions of the acceptor stem. However, examination of the sequences of the corresponding mature tRNAs has shown that these positions instead contain canonical Watson-Crick-type base pairs. This difference results from changes that are made at the transcript level, such that predicted mismatches are effectively corrected. The correction process, termed mitochondrial tRNA 5′-editing (mt-tRNA 5′-editing), involves removal in the 5′-to-3′ direction of several nucleotides, starting at the 5′-end of the acceptor stem and including those 5′ nucleotides at positions of mismatching, followed by sequential addition of nucleotides in the 3′-to-5′ direction to fill in the resulting gap, with nucleotides on the 3′ side of the stem serving to guide incorporation. While the nature of the nuclease(s) involved in removal of nucleotides during mt-tRNA 5′-editing is unknown, the addition function is carried out by a mitochondrion-targeted Thg1-like protein (TLP), a novel 3′-to-5′ nucleotidyltransferase (“reverse RNA polymerase”). Thg1 (tRNA-histidine guanylyltransferase), the founding member of the protein family to which TLPs also belong, catalyzes the addition of a single, non-templated G residue to the 5′-end of histidine tRNA, whereas TLPs involved in mt-tRNA 5′-editing robustly catalyze multiple rounds of templated addition of nucleotides to the 5′-end of appropriately truncated tRNA substrates. To date, mt-tRNA 5′-editing has been experimentally documented in several amoebozoan and fungal species and is predicted to occur in several other protist lineages. Consideration of phylogenetic distribution and biochemical characteristics suggests a constructive neutral evolution (CNE) scenario for the evolution of mt-tRNA 5′-editing, wherein mitochondrion-targeted TLPs independently emerge in discrete eukaryotic lineages, thereby allowing the fixation in the mitochondrial genome of tRNA mismatch mutations that would otherwise be purged by purifying selection.


  1. Abad MG, Rao BS, Jackman JE (2010) Template-dependent 3′–5′ nucleotide addition is a shared feature of tRNAHis guanylyltransferase enzymes from multiple domains of life. Proc Natl Acad Sci U S A 107:674–679CrossRefPubMedGoogle Scholar
  2. Abad MG, Long Y, Willcox A, Gott JM, Gray MW, Jackman JE (2011) A role for tRNAHis guanylyltransferase (Thg1)-like proteins from Dictyostelium discoideum in mitochondrial 5′-tRNA editing. RNA 17:613–623CrossRefPubMedPubMedCentralGoogle Scholar
  3. Abad MG, Long Y, Kinchen RD, Schindel ET, Gray MW, Jackman JE (2014) Mitochondrial tRNA 5′-editing in Dictyostelium discoideum and Polysphondylium pallidum. J Biol Chem 289:15155–15165CrossRefPubMedPubMedCentralGoogle Scholar
  4. 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 46:819–826CrossRefPubMedGoogle Scholar
  5. Betat H, Long Y, Jackman JE, Mörl M (2014) From end to end: tRNA editing at 5′- and 3′-terminal positions. Int J Mol Sci 15:23975–23998CrossRefPubMedPubMedCentralGoogle Scholar
  6. Bullerwell CE, Gray MW (2005) In vitro characterization of a tRNA editing activity in the mitochondria of Spizellomyces punctatus, a chytridiomycete fungus. J Biol Chem 280:2463–2470CrossRefPubMedGoogle Scholar
  7. Bullerwell CE, Forget L, Lang BF (2003) Evolution of monoblepharidalean fungi based on complete mitochondrial genome sequences. Nucleic Acids Res 31:1614–1623CrossRefPubMedPubMedCentralGoogle Scholar
  8. Burger G, Plante I, Lonergan KM, Gray MW (1995) The mitochondrial DNA of the amoeboid protozoon, Acanthamoeba castellanii: complete sequence, gene content and genome organization. J Mol Biol 245:522–537CrossRefPubMedGoogle Scholar
  9. Chen S-H, Habib G, Yang C-Y, Gu Z-W, Lee B, Weng S-a, Silberman CS-J, Deslypere J, Rosseneu M, Gotto A, Li W-H, Chan L (1987) Apolipoprotein B-48 is the product of a messenger RNA with an organ-specific in-frame stop codon. Science 238:363–366CrossRefPubMedGoogle Scholar
  10. Cooley L, Appel B, Söll D (1982) Post-transcriptional nucleotide addition is responsible for the formation of the 5′ terminus of histidine tRNA. Proc Natl Acad Sci U S A 79:6475–6479CrossRefPubMedPubMedCentralGoogle Scholar
  11. Corcoran JB, McCarthy S, Griffin B, Gaffney A, Bhreathnach U, Börgeson E, Hickey FB, Docherty NG, Higgins DF, Furlong F, Martin F, Godson C, Murphy M (2013) IHG-1 must be localised to mitochondria to decrease Smad7 expression and amplify TGF-β1-induced fibrotic responses. Biochim Biophys Acta 1833:1969–1978CrossRefPubMedGoogle Scholar
  12. Covello PS, Gray MW (1993) On the evolution of RNA editing. Trends Genet 9(8):265–268CrossRefPubMedGoogle Scholar
  13. Dewe JM, Whipple JM, Chernyakov I, Jaramillo LN, Phizicky EM (2012) The yeast rapid tRNA decay pathway competes with elongation factor 1A for substrate tRNAs and acts on tRNAs lacking one or more of several modifications. RNA 18:1886–1896CrossRefPubMedPubMedCentralGoogle Scholar
  14. Eichinger L, Pachebat JA, Glockner G, Rajandream MA, Sucgang R, Berriman M, Song J, Olsen R, Szafranski K, Xu Q, Tunggal B, Kummerfeld S, Madera M, Konfortov BA, Rivero F, Bankier AT, Lehmann R, Hamlin N, Davies R, Gaudet P, Fey P, Pilcher K, Chen G, Saunders D, Sodergren E, Davis P, Kerhornou A, Nie X, Hall N, Anjard C, Hemphill L, Bason N, Farbrother P, Desany B, Just E, Morio T, Rost R, Churcher C, Cooper J, Haydock S, van Driessche N, Cronin A, Goodhead I, Muzny D, Mourier T, Pain A, Lu M, Harper D, Lindsay R, Hauser H, James K, Quiles M, Madan Babu M, Saito T, Buchrieser C, Wardroper A, Felder M, Thangavelu M, Johnson D, Knights A, Loulseged H, Mungall K, Oliver K, Price C, Quail MA, Urushihara H, Hernandez J, Rabbinowitsch E, Steffen D, Sanders M, Ma J, Kohara Y, Sharp S, Simmonds M, Spiegler S, Tivey A, Sugano S, White B, Walker D, Woodward J, Winckler T, Tanaka Y, Shaulsky G, Schleicher M, Weinstock G, Rosenthal A, Cox EC, Chisholm RL, Gibbs R, Loomis WF, Platzer M, Kay RR, Williams J, Dear PH, Noegel AA, Barrell B, Kuspa A (2005) The genome of the social amoeba Dictyostelium discoideum. Nature 435:43–57CrossRefPubMedPubMedCentralGoogle Scholar
  15. Forget L, Ustinova J, Wang Z, Huss VAR, Lang BF (2002) Hyaloraphidium curvatum: a linear mitochondrial genome, tRNA editing, and an evolutionary link to lower fungi. Mol Biol Evol 19:310–319CrossRefPubMedGoogle Scholar
  16. Fu C-J, Sheikh S, Miao W, Andersson SGE, Baldauf SL (2014) Missing genes, multiple ORFs, and C-to-U type RNA editing in Acrasis kona (Heterolobosea, Excavata) mitochondrial DNA. Genome Biol Evol 6:2240–2257CrossRefPubMedPubMedCentralGoogle Scholar
  17. Giegé R, Sissler M, Florentz C (1998) Universal rules and idiosyncratic features in tRNA identity. Nucleic Acids Res 26:5017–5035CrossRefPubMedPubMedCentralGoogle Scholar
  18. Gott JM, Somerlot BH, Gray MW (2010) Two forms of RNA editing are required for tRNA maturation in Physarum mitochondria. RNA 16:482–488CrossRefPubMedPubMedCentralGoogle Scholar
  19. Gray MW (2001) Speculations on the origin and evolution of editing. In: Bass BL (ed) RNA editing, vol 34. Frontiers in molecular biology. Oxford University Press, Oxford, pp 160–184Google Scholar
  20. Gray MW (2003) Diversity and evolution of mitochondrial RNA editing systems. IUBMB Life 55:227–233CrossRefPubMedGoogle Scholar
  21. Gray MW (2012) Evolutionary origin of RNA editing. Biochemistry 51:5235–5242CrossRefPubMedGoogle Scholar
  22. Gray MW, Lukeš J, Archibald JM, Keeling PJ, Doolittle WF (2010) Irremediable complexity? Science 330:920–921CrossRefGoogle Scholar
  23. Gu W, Jackman JE, Lohan AJ, Gray MW, Phizicky EM (2003) tRNAHis maturation: an essential yeast protein catalyzes addition of a guanine nucleotide to the 5′ end of tRNAHis. Genes Dev 17:2889–2901CrossRefPubMedPubMedCentralGoogle Scholar
  24. Gu W, Hurto RL, Hopper AK, Grayhack EJ, Phizicky EM (2005) Depletion of Saccharomyces cerevisiae tRNAHis guanylyltransferase Thg1p leads to uncharged tRNAHis with additional m5C. Mol Cell Biol 25:8191–8201CrossRefPubMedPubMedCentralGoogle Scholar
  25. Heinemann IU, Randau L, Tomko RJJ, Söll D (2010) 3′-5′ tRNAHis guanylyltransferase in bacteria. FEBS Lett 584:3567–3572CrossRefPubMedPubMedCentralGoogle Scholar
  26. Herman EK, Greninger AL, Visvesvara GS, Marciano-Cabral F, Dacks JB, Chiu CY (2013) The mitochondrial genome and a 60-kb nuclear DNA segment from Naegleria fowleri, the causative agent of primary amoebic meningoencephalitis. J Eukaryot Microbiol 60:179–191CrossRefPubMedPubMedCentralGoogle Scholar
  27. Hickey FB, Corcoran JB, Docherty NG, Griffin B, Bhreathnach U, Furlong F, Martin F, Godson C, Murphy M (2011) IHG-1 promotes mitochondrial biogenesis by stabilizing PGC-1α. J Am Soc Nephrol 22:1475–1485CrossRefPubMedPubMedCentralGoogle Scholar
  28. Jackman JE, Phizicky EM (2006) tRNAHis guanylyltransferase adds G-1 to the 5′ end of tRNAHis by recognition of the anticodon, one of several features unexpectedly shared with tRNA synthetases. RNA 12:1007–1014CrossRefPubMedPubMedCentralGoogle Scholar
  29. Jackman JE, Gott JM, Gray MW (2012) Doing it in reverse: 3′-to-5′ polymerization by the Thg1 superfamily. RNA 18:886–899CrossRefPubMedPubMedCentralGoogle Scholar
  30. Jahn D, Pande S (1991) Histidine tRNA guanylyltransferase from Saccharomyces cerevisiae. II. Catalytic mechanism. J Biol Chem 266:22832–22836PubMedGoogle Scholar
  31. Kim S-H (1978) Three-dimensional structure of transfer RNA and its functional implications. Adv Enzymol Relat Areas Mol Biol 46:279–315PubMedGoogle Scholar
  32. Laforest MJ, Roewer I, Lang BF (1997) Mitochondrial tRNAs in the lower fungus Spizellomyces punctatus: tRNA editing and UAG ‘stop’ codons recognized as leucine. Nucleic Acids Res 25:626–632CrossRefPubMedPubMedCentralGoogle Scholar
  33. Laforest M-J, Bullerwell CE, Forget L, Lang BF (2004) Origin, evolution, and mechanism of 5′ tRNA editing in chytridiomycete fungi. RNA 10:1191–1199CrossRefPubMedPubMedCentralGoogle Scholar
  34. Ledee DR, Byers TJ (2009) Length and sequence heterogeneity in the mitochondrial internal transcribed spacer of Acanthamoeba spp. J Eukaryot Microbiol 56:257–262CrossRefPubMedGoogle Scholar
  35. Lohan A, Gray M (2007) Analysis of 5′- or 3′-terminal tRNA editing: mitochondrial 5′ tRNA editing in Acanthamoeba castellanii as the exemplar. Methods Enzymol 424:223–242CrossRefPubMedGoogle Scholar
  36. Lonergan KM, Gray MW (1993a) Editing of transfer RNAs in Acanthamoeba castellanii mitochondria. Science 259:812–816CrossRefPubMedGoogle Scholar
  37. Lonergan KM, Gray MW (1993b) Predicted editing of additional transfer RNAs in Acanthamoeba castellanii mitochondria. Nucleic Acids Res 21:4402CrossRefPubMedPubMedCentralGoogle Scholar
  38. Long Y, Jackman JE (2015) In vitro substrate specificities of 3′–5′ polymerases correlate with biological outcomes of tRNA 5′-editing reactions. FEBS Lett 589:2124–2130CrossRefPubMedPubMedCentralGoogle Scholar
  39. Long Y, Abad MG, Olson ED, Carrillo EY, Jackman JE (2016) Identification of distinct biological functions for four 3′-5′ RNA polymerases. Nucleic Acids Res 44:8395–8406CrossRefPubMedPubMedCentralGoogle Scholar
  40. Lukeš J, Archibald JM, Keeling PJ, Doolittle WF, Gray MW (2011) How a neutral evolutionary ratchet can build cellular complexity. IUBMB Life 63:528–537CrossRefPubMedGoogle Scholar
  41. Muller HJ (1964) The relation of recombination to mutational advance. Mutat Res 1:2–9CrossRefGoogle Scholar
  42. Murphy M, Docherty NG, Griffin B, Howlin J, McArdle E, McMahon R, Schmid H, Kretzler M, Droguett A, Mezzano S, Brady HR, Furlong F, Godson C, Martin F (2008) IHG-1 amplifies TGF-β1 signaling and is increased in renal fibrosis. J Am Soc Nephrol 19:1672–1680CrossRefPubMedPubMedCentralGoogle Scholar
  43. Murphy M, Hickey F, Godson C (2013) IHG-1 amplifies TGF-β1 signalling and mitochondrial biogenesis and is increased in diabetic kidney disease. Curr Opin Nephrol Hypertens 22:77–84CrossRefPubMedGoogle Scholar
  44. Ogawa S, Yoshino R, Angata K, Iwamoto M, Pi M, Kuroe K, Matsuo K, Morio T, Urushihara H, Yanagisawa K, Tanaka Y (2000) The mitochondrial DNA of Dictyostelium discoideum: complete sequence, gene content and genome organization. Mol Gen Genet 263:514–519PubMedGoogle Scholar
  45. Pombert J-F, Smirnov A, James ER, Janouškovec J, Gray MW, Keeling PJ (2013) The complete mitochondrial genome from an unidentified Phalansterium species. Protist Genom 1:25–32Google Scholar
  46. Powell LM, Wallis SC, Pease RJ, Edwards YH, Knott TJ, Scott J (1987) A novel form of tissue-specific RNA processing produces apolipoprotein-B48 in intestine. Cell 50:831–840CrossRefPubMedGoogle Scholar
  47. Preston MA, Phizicky EM (2010) The requirement for the highly conserved G−1 residue of Saccharomyces cerevisiae tRNAHis can be circumvented by overexpression of tRNAHis and its synthetase. RNA 16:1068–1077CrossRefPubMedPubMedCentralGoogle Scholar
  48. Price DH, Gray MW (1998) Editing of tRNA. In: Grosjean H, Benne R (eds) Modification and editing of RNA. ASM Press, Washington, pp 289–305CrossRefGoogle Scholar
  49. Price DH, Gray MW (1999a) Confirmation of predicted edits and demonstration of unpredicted edits in Acanthamoeba castellanii mitochondrial tRNAs. Curr Genet 35:23–29CrossRefPubMedGoogle Scholar
  50. Price DH, Gray MW (1999b) A novel nucleotide incorporation activity implicated in the editing of mitochondrial transfer RNAs in Acanthamoeba castellanii. RNA 5:302–317CrossRefPubMedPubMedCentralGoogle Scholar
  51. Rao BS, Maris EL, Jackman JE (2011) tRNA 5′-end repair activities of tRNAHis guanylyltransferase (Thg1)-like proteins from Bacteria and Archaea. Nucleic Acids Res 39:1833–1842CrossRefPubMedGoogle Scholar
  52. Rao BS, Mohammad F, Gray MW, Jackman JE (2013) Absence of a universal element for tRNAHis identity in Acanthamoeba castellanii. Nucleic Acids Res 41:1885–1894CrossRefPubMedGoogle Scholar
  53. Stoltzfus A (1999) On the possibility of constructive neutral evolution. J Mol Evol 49:169–181CrossRefPubMedGoogle Scholar
  54. Tanifuji G, Archibald JM, Hashimoto T (2016) Comparative genomics of mitochondria in chlorarachniophyte algae: endosymbiotic gene transfer and organellar genome dynamics. Sci Rep 6:21016CrossRefPubMedPubMedCentralGoogle Scholar
  55. Tanifuji G, Cenci U, Moog D, Dean S, Nakayama T, David V, Fiala I, Curtis BA, Sibbald SJ, Onodera NT, Colp M, Flegontov P, Johnson-MacKinnon J, McPhee M, Inagaki Y, Hashimoto T, Kelly S, Gull K, Lukeš J, Archibald JM (2017) Genome sequencing reveals metabolic and cellular interdependence in an amoeba-kinetoplastid symbiosis. Sci Rep 7:11688CrossRefPubMedPubMedCentralGoogle Scholar
  56. Whipple J, Lane E, Chernyakov I, D'Silva S, Phizicky E (2011) The yeast rapid tRNA decay pathway primarily monitors the structural integrity of the acceptor and T-stems of mature tRNA. Genes Dev 25:1173–1184CrossRefPubMedPubMedCentralGoogle Scholar
  57. Williams JB, Cooley L, Soll D (1990) Enzymatic addition of guanylate to histidine transfer RNA. Methods Enzymol 181:451–462CrossRefPubMedGoogle Scholar
  58. Yuan Y, Altman S (1995) Substrate recognition by human RNase P: identification of small, model substrates for the enzyme. EMBO J 14:159–168PubMedPubMedCentralCrossRefGoogle Scholar

Copyright information

© Springer International Publishing AG, part of Springer Nature 2018

Authors and Affiliations

  • Samantha Dodbele
    • 1
  • Jane E. Jackman
    • 1
  • Michael W. Gray
    • 2
    • 3
    Email author
  1. 1.Department of Chemistry and Biochemistry, The Ohio State Biochemistry ProgramCenter for RNA Biology, The Ohio State UniversityColumbusUSA
  2. 2.Department of Biochemistry and Molecular BiologyDalhousie UniversityHalifaxCanada
  3. 3.Center for Comparative Genomics and Evolutionary BioinformaticsDalhousie UniversityHalifaxCanada

Personalised recommendations