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tRNA nucleotidyltransferases: ancient catalysts with an unusual mechanism of polymerization

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Abstract

RNA polymerases are important enzymes involved in the realization of the genetic information encoded in the genome. Thereby, DNA sequences are used as templates to synthesize all types of RNA. Besides these classical polymerases, there exists another group of RNA polymerizing enzymes that do not depend on nucleic acid templates. Among those, tRNA nucleotidyltransferases show remarkable and unique features. These enzymes add the nucleotide triplet C–C–A to the 3′-end of tRNAs at an astonishing fidelity and are described as “CCA-adding enzymes”. During this incorporation of exactly three nucleotides, the enzymes have to switch from CTP to ATP specificity. How these tasks are fulfilled by rather simple and small enzymes without the help of a nucleic acid template is a fascinating research area. Surprising results of biochemical and structural studies allow scientists to understand at least some of the mechanistic principles of the unique polymerization mode of these highly unusual enzymes.

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References

  1. Aravind L, Koonin EV (1999) DNA polymerase beta-like nucleotidyltransferase superfamily: identification of three new families, classification and evolutionary history. Nucleic Acids Res 27:1609–1618

    Article  PubMed  CAS  Google Scholar 

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

    Article  PubMed  CAS  Google Scholar 

  3. Kwak JE, Wickens M (2007) A family of poly(U) polymerases. RNA 13:860–867

    Article  PubMed  CAS  Google Scholar 

  4. Ito J, Braithwaite DK (1991) Compilation and alignment of DNA polymerase sequences. Nucleic Acids Res 19:4045–4057

    Article  PubMed  CAS  Google Scholar 

  5. Yue D, Maizels N, Weiner AM (1996) CCA-adding enzymes and poly(A) polymerases are all members of the same nucleotidyltransferase superfamily: characterization of the CCA-adding enzyme from the archaeal hyperthermophile Sulfolobus shibatae. RNA 2:895–908

    PubMed  CAS  Google Scholar 

  6. Martin G, Keller W (2007) RNA-specific ribonucleotidyl transferases. RNA 13:1834–1849

    Article  PubMed  CAS  Google Scholar 

  7. Cabaniols JP, Fazilleau N, Casrouge A, Kourilsky P, Kanellopoulos JM (2001) Most alpha/beta T cell receptor diversity is due to terminal deoxynucleotidyl transferase. J Exp Med 194:1385–1390

    Article  PubMed  CAS  Google Scholar 

  8. Li Z, Pandit S, Deutscher MP (1998) Polyadenylation of stable RNA precursors in vivo. Proc Natl Acad Sci USA 95:12158–12162

    Article  PubMed  CAS  Google Scholar 

  9. Aphasizhev R (2005) RNA uridylyltransferases. Cell Mol Life Sci 62:2194–2203

    Article  PubMed  CAS  Google Scholar 

  10. Trippe R, Guschina E, Hossbach M, Urlaub H, Luhrmann R, Benecke BJ (2006) Identification, cloning, and functional analysis of the human U6 snRNA-specific terminal uridylyl transferase. RNA 12:1494–1504

    Article  PubMed  CAS  Google Scholar 

  11. Hartmann RK, Gossringer M, Späth B, Fischer S, Marchfelder A (2009) The making of tRNAs and more—RNase P and tRNase Z. Prog Mol Biol Transl Sci 85:319–368

    Article  PubMed  CAS  Google Scholar 

  12. Mörl M, Marchfelder A (2001) The final cut. The importance of tRNA 3′-processing. EMBO Rep 2:17–20

    Article  PubMed  Google Scholar 

  13. Schürer H, Schiffer S, Marchfelder A, Mörl M (2001) This is the end: processing, editing and repair at the tRNA 3′-terminus. Biol Chem 382:1147–1156

    Article  PubMed  Google Scholar 

  14. Wegrzyn G, Wegrzyn A (2008) Is tRNA only a translation factor or also a regulator of other processes? J Appl Genet 49:115–122

    PubMed  Google Scholar 

  15. Sprinzl M, Cramer F (1979) The -C-C-A end of tRNA and its role in protein biosynthesis. Prog Nucleic Acid Res Mol Biol 22:1–69

    Article  PubMed  CAS  Google Scholar 

  16. Green R, Noller HF (1997) Ribosomes and translation. Annu Rev Biochem 66:679–716

    Article  PubMed  CAS  Google Scholar 

  17. Simonovic M, Steitz TA (2008) Peptidyl-CCA deacylation on the ribosome promoted by induced fit and the O3′-hydroxyl group of A76 of the unacylated A-site tRNA. RNA 14:2372–2378

    Article  PubMed  CAS  Google Scholar 

  18. Marck C, Grosjean H (2002) tRNomics: analysis of tRNA genes from 50 genomes of Eukarya, Archaea, and Bacteria reveals anticodon-sparing strategies and domain-specific features. RNA 8:1189–1232

    Article  PubMed  CAS  Google Scholar 

  19. Deutscher MP, Lin JJ, Evans JA (1977) Transfer RNA metabolism in Escherichia coli cells deficient in tRNA nucleotidyltransferase. J Mol Biol 117:1081–1094

    Article  PubMed  CAS  Google Scholar 

  20. Lizano E, Scheibe M, Rammelt C, Betat H, Mörl M (2008) A comparative analysis of CCA-adding enzymes from human and E. coli: differences in CCA addition and tRNA 3′-end repair. Biochimie 90:762–772

    Article  PubMed  CAS  Google Scholar 

  21. Zhu L, Deutscher MP (1987) tRNA nucleotidyltransferase is not essential for Escherichia coli viability. EMBO J 6:2473–2477

    PubMed  CAS  Google Scholar 

  22. Clark JM (1988) Novel non-templated nucleotide addition reactions catalyzed by procaryotic and eucaryotic DNA polymerases. Nucleic Acids Res 16:9677–9686

    Article  PubMed  CAS  Google Scholar 

  23. Milligan JF, Groebe DR, Witherell GW, Uhlenbeck OC (1987) Oligoribonucleotide synthesis using T7 RNA polymerase and synthetic DNA templates. Nucleic Acids Res 15:8783–8798

    Article  PubMed  CAS  Google Scholar 

  24. Deutscher MP (1982) tRNA nucleotidyltransferase. In: Boyer PD (ed) The enzymes. Academic Press, New York, pp 183–215

    Google Scholar 

  25. Masiakowski P, Deutscher MP (1980) Dissection of the active site of rabbit liver tRNA nucleotidyltransferase. Specificity and properties of subsites for donor nucleotide triphosphates. J Biol Chem 255:11240–11246

    PubMed  CAS  Google Scholar 

  26. Masiakowski P, Deutscher MP (1980) Dissection of the active site of rabbit liver tRNA nucleotidyltransferase. Specificity and properties of the tRNA and acceptor subsites determined with model acceptor substrates. J Biol Chem 255:11233–11239

    PubMed  CAS  Google Scholar 

  27. Vörtler S, Mörl M (2010) tRNA-nucleotidyltransferases: highly unusual RNA polymerases with vital functions. FEBS Lett 584(2):297–302

    Google Scholar 

  28. Xiong Y, Li F, Wang J, Weiner AM, Steitz TA (2003) Crystal structures of an archaeal class I CCA-adding enzyme and its nucleotide complexes. Mol Cell Biochem 12:1165–1172

    Google Scholar 

  29. Okabe M, Tomita K, Ishitani R, Ishii R, Takeuchi N, Arisaka F, Nureki O, Yokoyama S (2003) Divergent evolutions of trinucleotide polymerization revealed by an archaeal CCA-adding enzyme structure. EMBO J 22:5918–5927

    Google Scholar 

  30. Shi PY, Maizels N, Weiner AM (1998) CCA addition by tRNA nucleotidyltransferase: polymerization without translocation? EMBO J 17:3197–3206

    Article  PubMed  CAS  Google Scholar 

  31. Cho HD, Sood VD, Baker D, Weiner AM (2008) On the role of a conserved, potentially helix-breaking residue in the tRNA-binding alpha-helix of archaeal CCA-adding enzymes. RNA 14(7):1284–1289

    Article  PubMed  CAS  Google Scholar 

  32. Tomita K, Fukai S, Ishitani R, Ueda T, Takeuchi N, Vassylyev DG, Nureki O (2004) Structural basis for template-independent RNA polymerization. Nature 430:700–704

    Article  PubMed  CAS  Google Scholar 

  33. Xiong Y, Steitz TA (2004) Mechanism of transfer RNA maturation by CCA-adding enzyme without using an oligonucleotide template. Nature 430:640–645

    Article  PubMed  CAS  Google Scholar 

  34. 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

    Article  PubMed  CAS  Google Scholar 

  35. Cho HD, Chen Y, Varani G, Weiner AM (2006) A model for C74 addition by CCA-adding enzymes: C74 addition, like C75 and A76 addition, does not involve tRNA translocation. J Biol Chem 281:9801–9811

    Article  PubMed  CAS  Google Scholar 

  36. Cho HD, Verlinde CL, Weiner AM (2005) Archaeal CCA-adding enzymes: central role of a highly conserved beta-turn motif in RNA polymerization without translocation. J Biol Chem 280:9555–9566

    Article  PubMed  CAS  Google Scholar 

  37. Toh Y, Numata T, Watanabe K, Takeshita D, Nureki O, Tomita K (2008) Molecular basis for maintenance of fidelity during the CCA-adding reaction by a CCA-adding enzyme. EMBO J 27:1944–1952

    Article  PubMed  CAS  Google Scholar 

  38. Tomita K, Ishitani R, Fukai S, Nureki O (2006) Complete crystallographic analysis of the dynamics of CCA sequence addition. Nature 443:956–960

    Article  PubMed  CAS  Google Scholar 

  39. Yue D, Weiner AM, Maizels N (1998) The CCA-adding enzyme has a single active site. J Biol Chem 273:29693–29700

    Article  PubMed  CAS  Google Scholar 

  40. Steitz TA (1998) A mechanism for all polymerases. Nature 391:231–232

    Article  PubMed  CAS  Google Scholar 

  41. Steitz TA, Smerdon SJ, Jager J, Joyce CM (1994) A unified polymerase mechanism for nonhomologous DNA and RNA polymerases. Science 266:2022–2025

    Article  PubMed  CAS  Google Scholar 

  42. Martin G, Doublie S, Keller W (2007) Determinants of substrate specificity in RNA-dependent nucleotidyl transferases. Biochim Biophys Acta 1779(4):206–216

    PubMed  Google Scholar 

  43. Schimmel P, Yang XL (2004) Two classes give lessons about CCA. Nat Struct Mol Biol 11:807–808

    Article  PubMed  CAS  Google Scholar 

  44. Augustin MA, Reichert AS, Betat H, Huber R, Mörl M, Steegborn C (2003) Crystal structure of the human CCA-adding enzyme: insights into template-independent polymerization. J Mol Biol 328:985–994

    Article  PubMed  CAS  Google Scholar 

  45. Li F, Xiong Y, Wang J, Cho HD, Tomita K, Weiner AM, Steitz TA (2002) Crystal structures of the Bacillus stearothermophilus CCA-adding enzyme and its complexes with ATP or CTP. Cell 111:815–824

    Article  PubMed  CAS  Google Scholar 

  46. Toh Y, Takeshita D, Numata T, Fukai S, Nureki O, Tomita K (2009) Mechanism for the definition of elongation and termination by the class II CCA-adding enzyme. EMBO J 28(21):3353–3365

    Article  PubMed  CAS  Google Scholar 

  47. Martin G, Keller W (2004) Sequence motifs that distinguish ATP(CTP):tRNA nucleotidyl transferases from eubacterial poly(A) polymerases. RNA 10:899–906

    Article  PubMed  CAS  Google Scholar 

  48. Li Z, Sun Y, Thurlow DL (1997) RNA minihelices as model substrates for ATP/CTP:tRNA nucleotidyltransferase. Biochem J 327:847–851

    PubMed  CAS  Google Scholar 

  49. Shi PY, Weiner AM, Maizels N (1998) A top-half tDNA minihelix is a good substrate for the eubacterial CCA-adding enzyme. RNA 4:276–284

    PubMed  CAS  Google Scholar 

  50. Betat H, Rammelt C, Martin G, Mörl M (2004) Exchange of regions between bacterial poly(A) polymerase and CCA adding enzyme generates altered specificities. Mol Cell 15:389–398

    Article  PubMed  CAS  Google Scholar 

  51. Cho HD, Verlinde CL, Weiner AM (2007) Reengineering CCA-adding enzymes to function as (U, G)- or dCdCdA-adding enzymes or poly(C, A) and poly(U, G) polymerases. Proc Natl Acad Sci USA 104:54–59

    Article  PubMed  CAS  Google Scholar 

  52. Neuenfeldt A, Just A, Betat H, Mörl M (2008) Evolution of tRNA nucleotidyltransferases: a small deletion generated CC-adding enzymes. Proc Natl Acad Sci USA 105:7953–7958

    Article  PubMed  CAS  Google Scholar 

  53. Kim S, Liu C, Halkidis K, Gamper HB, Hou YM (2009) Distinct kinetic determinants for the stepwise CCA addition to tRNA. RNA 15:1827–1836

    Article  PubMed  CAS  Google Scholar 

  54. Just A, Butter F, Trenkmann M, Heitkam T, Mörl M, Betat H (2008) A comparative analysis of two conserved motifs in bacterial poly(A) polymerase and CCA-adding enzyme. Nucleic Acids Res 36:5212–5220

    Article  PubMed  CAS  Google Scholar 

  55. McGann RG, Deutscher MP (1980) Purification and characterization of a mutant tRNA nucleotidyltransferase. Eur J Biochem 106:321–328

    Article  PubMed  CAS  Google Scholar 

  56. Zhu LQ, Cudny H, Deutscher MP (1986) A mutation in Escherichia coli tRNA nucleotidyltransferase that affects only AMP incorporation is in a sequence often associated with nucleotide-binding proteins. J Biol Chem 261:14875–14877

    PubMed  CAS  Google Scholar 

  57. Hegg LA, Kou M, Thurlow DL (1990) Recognition of the tRNA-like structure in tobacco mosaic viral RNA by ATP/CTP:tRNA nucleotidyltransferases from Escherichia coli and Saccharomyces cerevisiae. J Biol Chem 265:17441–17445

    PubMed  CAS  Google Scholar 

  58. Cho HD, Tomita K, Suzuki T, Weiner AM (2002) U2 small nuclear RNA is a substrate for the CCA-adding enzyme (tRNA nucleotidyltransferase). J Biol Chem 277:3447–3455

    Article  PubMed  CAS  Google Scholar 

  59. Williams MA, Johzuka Y, Mulligan RM (2000) Addition of non-genomically encoded nucleotides to the 3′-terminus of maize mitochondrial mRNAs: truncated rps12 mRNAs frequently terminate with CCA. Nucleic Acids Res 28:4444–4451

    Article  PubMed  CAS  Google Scholar 

  60. Jin Y, Bian T (2004) Nontemplated nucleotide addition prior to polyadenylation: a comparison of Arabidopsis cDNA and genomic sequences. RNA 10:1695–1697

    Article  PubMed  CAS  Google Scholar 

  61. Zandueta-Criado A, Bock R (2004) Surprising features of plastid ndhD transcripts: addition of non-encoded nucleotides and polysome association of mRNAs with an unedited start codon. Nucleic Acids Res 32:542–550

    Article  PubMed  CAS  Google Scholar 

  62. Franze de Fernandez MT, Hayward WS, August JT (1972) Bacterial proteins required for replication of phage Q ribonucleic acid. Purification and properties of host factor I, a ribonucleic acid-binding protein. J Biol Chem 247:824–831

    PubMed  CAS  Google Scholar 

  63. Scheibe M, Bonin S, Hajnsdorf E, Betat H, Mörl M (2007) Hfq stimulates the activity of the CCA-adding enzyme. BMC Mol Biol 8:92

    Article  PubMed  CAS  Google Scholar 

  64. Lee T, Feig AL (2008) The RNA binding protein Hfq interacts specifically with tRNAs. RNA 14:514–523

    Article  PubMed  CAS  Google Scholar 

  65. Kufel J, Allmang C, Verdone L, Beggs JD, Tollervey D (2002) Lsm proteins are required for normal processing of pre-tRNAs and their efficient association with La-homologous protein Lhp1p. Mol Cell Biol 22:5248–5256

    Article  PubMed  CAS  Google Scholar 

  66. Hajnsdorf E, Regnier P (2000) Host factor Hfq of Escherichia coli stimulates elongation of poly(A) tails by poly(A) polymerase I. Proc Natl Acad Sci USA 97:1501–1505

    Article  PubMed  CAS  Google Scholar 

  67. Mohanty BK, Maples VF, Kushner SR (2004) The Sm-like protein Hfq regulates polyadenylation dependent mRNA decay in Escherichia coli. Mol Microbiol 54:905–920

    Article  PubMed  CAS  Google Scholar 

  68. Aravind L, Koonin EV (1998) The HD domain defines a new superfamily of metal-dependent phosphohydrolases. Trends Biochem Sci 23:469–472

    Article  PubMed  CAS  Google Scholar 

  69. Yakunin AF, Proudfoot M, Kuznetsova E, Savchenko A, Brown G, Arrowsmith CH, Edwards AM (2004) The HD domain of the Escherichia coli tRNA nucleotidyltransferase has 2′,3′-cyclic phosphodiesterase, 2′-nucleotidase, and phosphatase activities. J Biol Chem 279:36819–36827

    Article  PubMed  CAS  Google Scholar 

  70. Soukup GA, Breaker RR (1999) Relationship between internucleotide linkage geometry and the stability of RNA. RNA 5:1308–1325

    Article  PubMed  CAS  Google Scholar 

  71. Thompson JE, Venegas FD, Raines RT (1994) Energetics of catalysis by ribonucleases: fate of the 2′,3′-cyclic phosphodiester intermediate. Biochemistry 33:7408–7414

    Article  PubMed  CAS  Google Scholar 

  72. Bralley P, Chang SA, Jones GH (2005) A phylogeny of bacterial RNA nucleotidyltransferases: Bacillus halodurans contains two tRNA nucleotidyltransferases. J Bacteriol 187:5927–5936

    Article  PubMed  CAS  Google Scholar 

  73. Bralley P, Cozad M, Jones GH (2009) Geobacter sulfurreducens contains separate C- and A-adding tRNA nucleotidyltransferases and a poly(A) polymerase. J Bacteriol 191:109–114

    Article  PubMed  CAS  Google Scholar 

  74. Tomita K, Weiner AM (2001) Collaboration between CC- and A-adding enzymes to build and repair the 3′-terminal CCA of tRNA in Aquifex aeolicus. Science 294:1334–1336

    Article  PubMed  CAS  Google Scholar 

  75. Tomita K, Weiner AM (2002) Closely related CC- and A-adding enzymes collaborate to construct and repair the 3′-terminal CCA of tRNA in Synechocystis sp. and Deinococcus radiodurans. J Biol Chem 277:48192–48198

    Article  PubMed  CAS  Google Scholar 

  76. Lizano E, Schuster J, Müller M, Kelso J, Mörl M (2007) A splice variant of the human CCA-adding enzyme with modified activity. J Mol Biol 366:1258–1265

    Article  PubMed  CAS  Google Scholar 

  77. Carpousis AJ (2007) The RNA degradosome of Escherichia coli: an mRNA-degrading machine assembled on RNase E. Annu Rev Microbiol 61:71–87

    Article  PubMed  CAS  Google Scholar 

  78. O’Hara EB, Chekanova JA, Ingle CA, Kushner ZR, Peters E, Kushner SR (1995) Polyadenylylation helps regulate mRNA decay in Escherichia coli. Proc Natl Acad Sci USA 92:1807–1811

    Article  PubMed  Google Scholar 

  79. Symmons MF, Williams MG, Luisi BF, Jones GH, Carpousis AJ (2002) Running rings around RNA: a superfamily of phosphate-dependent RNases. Trends Biochem Sci 27:11–18

    Article  PubMed  CAS  Google Scholar 

  80. Raynal LC, Krisch HM, Carpousis AJ (1998) The Bacillus subtilis nucleotidyltransferase is a tRNA CCA-adding enzyme. J Bacteriol 180:6276–6282

    PubMed  CAS  Google Scholar 

  81. Sohlberg B, Huang J, Cohen SN (2003) The Streptomyces coelicolor polynucleotide phosphorylase homologue, and not the putative poly(A) polymerase, can polyadenylate RNA. J Bacteriol 185:7273–7278

    Article  PubMed  CAS  Google Scholar 

  82. Lisitsky I, Klaff P, Schuster G (1996) Addition of destabilizing poly (A)-rich sequences to endonuclease cleavage sites during the degradation of chloroplast mRNA. Proc Natl Acad Sci USA 93:13398–13403

    Article  PubMed  CAS  Google Scholar 

  83. Yehudai-Resheff S, Schuster G (2000) Characterization of the E. coli poly(A) polymerase: nucleotide specificity, RNA-binding affinities and RNA structure dependence. Nucleic Acids Res 28:1139–1144

    Article  PubMed  CAS  Google Scholar 

  84. Patthy L (1991) Modular exchange principles in proteins. Curr Opin Struct Biol 1:351–361

    Article  CAS  Google Scholar 

  85. Patthy L (1996) Exon shuffling and other ways of module exchange. Matrix Biol 15:301–310 discussion 311–312

    Article  PubMed  CAS  Google Scholar 

  86. Riley M, Labedan B (1997) Protein evolution viewed through Escherichia coli protein sequences: introducing the notion of a structural segment of homology, the module. J Mol Biol 268:857–868

    Article  PubMed  CAS  Google Scholar 

  87. Maizels N, Weiner AM (1994) Phylogeny from function: evidence from the molecular fossil record that tRNA originated in replication, not translation. Proc Natl Acad Sci USA 91:6729–6734

    Article  PubMed  CAS  Google Scholar 

  88. Maizels N, Weiner AM (1999) The genomic tag hypothesis: what molecular fossils tell us about the evolution of tRNA. In: Gesteland RF, Cech TR, Atkins JF (eds) The RNA world. Cold Spring Harbour Laboratory Press, Cold Spring Harbour, pp 79–111

    Google Scholar 

  89. Weiner AM, Maizels N (1999) The genomic tag hypothesis: modern viruses as molecular fossils of ancient strategies for genomic replication, and clues regarding the origin of protein synthesis. Biol Bull 196:327–328 discussion 329–330

    Article  PubMed  CAS  Google Scholar 

  90. Bard J, Zhelkovsky AM, Helmling S, Earnest TN, Moore CL, Bohm A (2000) Structure of yeast poly(A) polymerase alone and in complex with 3′-dATP. Science 289:1346–1349

    Article  PubMed  CAS  Google Scholar 

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  1. Institute for Biochemistry, University of Leipzig, Brüderstr. 34, 04103, Leipzig, Germany

    Heike Betat & Mario Mörl

  2. Institute for Biochemistry, Martin Luther University Halle-Wittenberg, Kurt-Mothes-Str. 3, 06120, Halle, Germany

    Christiane Rammelt

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  1. Heike Betat
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Betat, H., Rammelt, C. & Mörl, M. tRNA nucleotidyltransferases: ancient catalysts with an unusual mechanism of polymerization. Cell. Mol. Life Sci. 67, 1447–1463 (2010). https://doi.org/10.1007/s00018-010-0271-4

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