Login | Register

Biophysical and biochemical characterization of human tRNA nucleotidyltransferase variants


Biophysical and biochemical characterization of human tRNA nucleotidyltransferase variants

Chung, Michael (2019) Biophysical and biochemical characterization of human tRNA nucleotidyltransferase variants. Masters thesis, Concordia University.

[thumbnail of Chung_MSc_F2019.pdf]
Text (application/pdf)
Chung_MSc_F2019.pdf - Accepted Version
Available under License Spectrum Terms of Access.


The enzyme ATP(CTP):tRNA nucleotidyltransferase (tRNA-NT) is required for tRNA maturation and repair. This enzyme adds to tRNAs the universally conserved 3’-cytidine-cytidine-adenosine (CCA) sequence required for aminoacylation. Given the essential role of this enzyme in protein synthesis, human disease phenotypes have been linked to mutations in the gene encoding this protein (Aksentijevich et al. 2014; Chakraborty et al. 2014; Sasarman et al. 2015; DeLuca et al. 2016; Hull et al. 2016; Wedatilake et al. 2016; Frans et al. 2017; Lougaris et al. 2018; Giannelou et al. 2018; Bader-Meunier et al. 2018; Gorodetsky et al. 2018; Kumaki et al. 2019; Abdulhadi et al. 2019). The variant proteins characterized to date have shown reduced thermostability relative to the native enzyme (Leibovitch et al. 2018, 2019), suggesting that reduced stability of tRNA-NT may lead to the phenotypes observed.

Here, we looked at additional variant proteins to see if these disease-linked variants also show reduced thermostability. The variant proteins characterized here were E43Δ which had a glutamate residue deleted near the N-terminus of the protein, R99W which contained an arginine-to-tryptophan substitution near the active site of the enzyme, and A[8] with a frame shift that truncated the protein by nine amino acids and altered the new C-terminal eight amino acids.

Interestingly, biophysical and biochemical characterization of these variants showed no major decrease in thermostability relative to the native enzyme. However, all three variants showed a reduced ability to incorporate AMP into a specific tRNA template in vitro. This suggests that, in addition to reduced thermostability, effects in AMP incorporation may also be linked to a disease phenotype. Interestingly, the E43Δ, R99W and A[8] variants all affected different aspects of AMP incorporation, reflecting their different locations in the protein and suggesting that AMP incorporation may be mediated by different domains and substructures spanning the entire enzyme and not confined simply to the active site.

Divisions:Concordia University > Faculty of Arts and Science > Biology
Item Type:Thesis (Masters)
Authors:Chung, Michael
Institution:Concordia University
Degree Name:M. Sc.
Date:22 July 2019
Thesis Supervisor(s):Joyce, Paul
Keywords:tRNA nucleotidyltransferase, TRNT1, CCA, tRNA maturation, protein translation, enzyme, human, SIFD
ID Code:985646
Deposited By: Michael Chung
Deposited On:05 Feb 2020 02:26
Last Modified:05 Feb 2020 02:26


Aebi M, Kirchner G, Chen J-Y, Vijayraghavan U, Jacobson A, Martin NC, Abelson J. 1990. Isolation of a temperature-sensitive mutant with an altered tRNA nucleotidyltransferase and cloning of the gene encoding tRNA nucleotidyltransferase in the yeast Saccharomyces cerevisiae. J Biol Chem. 265(27):16216–16220.

Aksentijevich I, Zhou Q, Giannelou A, Sediva A, Stone D, Rosenzweig S, Edwan J, Pelletier M, Monique S, Šrámková L, et al. 2014. TRNT1 missense mutations define an autoinflammatory disease characterized by recurrent fever, severe anemia, and B-cell immunodeficiency. Pediatr Rheumatol. 12(Suppl 1):O21.

Aravind L, Koonin EV. 1998. The HD domain defines a new superfamily of metal-dependent phosphohydrolases. Trends Biochem Sci. 23(12):469–472.

Aravind L, Koonin EV. 1999. DNA polymerase β-like nucleotidyltransferase superfamily: Identification of three new families, classification and evolutionary history. Nucleic Acids Res. 27(7):1609–1618.

Arts G-J, Kuersten S, Romby P, Ehresmann B, Mattaj IW. 1998. The role of exportin-t in selective nuclear export of mature tRNAs. EMBO J. 17(24):7430–7441.

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(5):985–994.

Aurora R, Rose GD. 1998. Helix capping. Protein Sci. 7(1):21–38.

Ausubel M, Brent R, Kingston RE, Moore DD, Seidman JG, Smith JA, Struhl K, editors. 1989. Current protocols in molecular biology. 1st ed. Media, PA, USA: John Wiley & Sons.

Bader-Meunier B, Rieux-Laucat F, Touzot F, Frémond M-L, André-Schmutz I, Fraitag S, Bodemer C. 2018. Inherited immunodeficiency: A new association with early-onset childhood panniculitis. Pediatrics. 141(Supplement 5):S496–S500.

Betat H, Mede T, Tretbar S, Steiner L, Stadler PF, Mörl M, Prohaska SJ. 2015. The ancestor of modern Holozoa acquired the CCA-adding enzyme from Alphaproteobacteria by horizontal gene transfer. Nucleic Acids Res. 43(14):6739–6746.

Betat H, Mörl M. 2015. The CCA-adding enzyme: A central scrutinizer in tRNA quality control. BioEssays. 37(9):975–982.

Betat H, Rammelt C, Martin G, Mörl M. 2004. Exchange of regions between bacterial poly(A) polymerase and the CCA-adding enzyme generates altered specificities. Mol Cell. 15(3):389–398.

Betat H, Rammelt C, Mörl M. 2010. tRNA nucleotidyltransferases: Ancient catalysts with an unusual mechanism of polymerization. Cell Mol Life Sci. 67(9):1447–1463.

Bio-Rad protein assay. 2018a. [accessed 2018 Dec 9]. https://www.bio-rad.com/webroot/web/pdf/lsr/literature/LIT33.pdf.

Bradford MM. 1976. A rapid and sensitive method for the quantitation of microgram quantities of protein utilizing the principle of protein-dye binding. Anal Biochem. 72:248–254.

Chakraborty PK, Schmitz-Abe K, Kennedy EK, Mamady H, Naas T, Durie D, Campagna DR, Lau A, Sendamarai AK, Wiseman DH, et al. 2014. Mutations in TRNT1 cause congenital sideroblastic anemia with immunodeficiency, fevers, and developmental delay (SIFD). Blood. 124(18):2867–2871.

Chan CW, Chetnani B, Mondragón A. 2013. Structure and function of the T-loop structural motif in noncoding RNAs. Wiley Interdiscip Rev RNA. 4(5):507–522.

Cho HD, Oyelere AK, Strobel SA, Weiner AM. 2003. Use of nucleotide analogs by class I and class II CCA-adding enzymes (tRNA nucleotidyltransferase): Deciphering the basis for nucleotide selection. RNA. 9(8):970–981.

Cho HD, Verlinde CLMJ, 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. 104(1):54–59.

DeLuca AP, Whitmore SS, Barnes J, Sharma TP, Westfall TA, Scott CA, Weed MC, Wiley JS, Wiley LA, Johnston RM, et al. 2016. Hypomorphic mutations in TRNT1 cause retinitis pigmentosa with erythrocytic microcytosis. Hum Mol Genet. 25(1):44–56.

Deutscher MP. 1983. tRNA nucleotidyltransferase and the -C-C-A terminus of transfer RNA. In: Jacob ST, editor. Enzymes of nucleic acid synthesis and modification. Vol. 2. 1st ed. Boca Raton, Florida, USA: CRC Press. (CRC series in the biochemistry and molecular biology of the cell nucleus). p. 159.

Deutscher MP. 1990. Transfer RNA nucleotidyltransferase. Methods Enzymol. 181:434–439.

Engelman DM, Steitz TA, Goldman A. 1986. Identifying nonpolar transbilayer helices in amino acid sequences of membrane proteins. Annu Rev Biophys Biophys Chem. 15:321–353.

Ernst FGM, Rickert C, Bluschke A, Betat H, Steinhoff H-J, Mörl M. 2015. Domain movements during CCA-addition: A new function for motif C in the catalytic core of the human tRNA nucleotidyltransferases. RNA Biol. 12(4):435–446.

Frans G, Moens L, Schaballie H, Wuyts G, Liston A, Poesen K, Janssens A, Rice GI, Crow YJ, Meyts I, et al. 2017. Homozygous N-terminal missense mutation in TRNT1 leads to progressive B-cell immunodeficiency in adulthood. J Allergy Clin Immunol. 139(1):360-363.e6.

Giaever G, Chu AM, Ni L, Connelly C, Riles L, Véronneau S, Dow S, Lucau-Danila A, Anderson K, André B, et al. 2002. Functional profiling of the Saccharomyces cerevisiae genome. Nature. 418:387–391.

Giannelou A, Wang H, Zhou Q, Park YH, Abu-Asab MS, Ylaya K, Stone DL, Sediva A, Sleiman R, Sramkova L, et al. 2018. Aberrant tRNA processing causes an autoinflammatory syndrome responsive to TNF inhibitors. Ann Rheum Dis. 77(4):612–619.

Giegé R, Jühling F, Pütz J, Stadler P, Sauter C, Florentz C. 2012. Structure of transfer RNAs: Similarity and variability. Wiley Interdiscip Rev RNA. 3(1):37–61.

Goring ME, Leibovitch M, Gea-Mallorqui E, Karls S, Richard F, Hanic-Joyce PJ, Joyce PBM. 2013. The ability of an arginine to tryptophan substitution in Saccharomyces cerevisiae tRNA nucleotidyltransferase to alleviate a temperature-sensitive phenotype suggests a role for motif C in active site organization. Biochim Biophys Acta BBA - Proteins Proteomics. 1834(10):2097–2106.

Gorodetsky C, Morel CF, Tein I. 2018. Expanding the phenotype of TRNT1 mutations to include Leigh syndrome. Can J Neurol Sci. Suppl. 2(S51):P.133.

Green CJ, Stewart GC, Hollis MA, Vold BS, Bott KF. 1985. Nucleotide sequence of the Bacillus subtilis ribosomal RNA operon, rrnB. Gene. 37(1–3):261–266.

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

Hendrickson TL. 2001. Recognizing the D-loop of transfer RNAs. Proc Natl Acad Sci. 98(24):13473–13475.

Hoffmeier A, Betat H, Bluschke A, Günther R, Junghanns S, Hofmann H-J, Mörl M. 2010. Unusual evolution of a catalytic core element in CCA-adding enzymes. Nucleic Acids Res. 38(13):4436–4447.

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

Hull S, Malik ANJ, Arno G, Mackay DS, Plagnol V, Michaelides M, Mansour S, Albanese A, Brown KT, Holder GE, et al. 2016. Expanding the phenotype of TRNT1-related immunodeficiency to include childhood cataract and inner retinal dysfunction. JAMA Ophthalmol. 134(9):1049.

Jakubowski H. 2012. Quality control in tRNA charging. Wiley Interdiscip Rev RNA. 3(3):295–310.

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(Database):D159–D162.

Just A, Butter F, Trenkmann M, Heitkam T, Morl M, Betat H. 2008. A comparative analysis of two conserved motifs in bacterial poly(A) polymerase and CCA-adding enzyme. Nucleic Acids Res. 36(16):5212–5220.

Kelly SM, Jess TJ, Price NC. 2005. How to study proteins by circular dichroism. Biochim Biophys Acta BBA - Proteins Proteomics. 1751(2):119–139.

Kim DE, Chivian D, Baker D. 2004. Protein structure prediction and analysis using the Robetta server. Nucleic Acids Res. 32(Web Server):W526–W531.

Kim DF, Green R. 1999. Base-pairing between 23S rRNA and tRNA in the ribosomal A site. Mol Cell. 4(5):859–864.

Kim S, Liu C, Halkidis K, Gamper HB, Hou Y-M. 2009. Distinct kinetic determinants for the stepwise CCA addition to tRNA. RNA. 15(10):1827–1836.

Kim SH, Quigley GJ, Suddath FL, McPherson A, Sneden D, Kim JJ, Weinzierl J, Rich A. 1973. Three-dimensional structure of yeast phenylalanine transfer RNA: Folding of the polynucleotide chain. Science. 179(4070):285–288.

de Korte D, Haverkort WA, van Gennip AH, Roos D. 1985. Nucleotide profiles of normal human blood cells determined by high-performance liquid chromatography. Anal Biochem. 147(1):197–209.

Kuhn C-D, Wilusz JE, Zheng Y, Beal PA, Joshua-Tor L. 2015. On-enzyme refolding permits small RNA and tRNA surveillance by the CCA-adding enzyme. Cell. 160(4):644–658.

Kumaki E, Tanaka K, Imai K, Aoki-Nogami Y, Ishiguro A, Okada S, Kanegane H, Ishikawa F, Morio T. 2019. Atypical SIFD with novel TRNT1 mutations: A case study on the pathogenesis of B-cell deficiency. Int J Hematol. [accessed 2019 Feb 17].

Kutay U, Lipowsky G, Izaurralde E, Bischoff FR, Schwarzmaier P, Hartmann E, Görlich D. 1998. Identification of a tRNA-specific nuclear export receptor. Mol Cell. 1(3):359–369.

Leatherbarrow RJ. 2009. GraFit. Horley, U.K.: Erithacus Software Ltd.

Leibovitch M. 2016. Exploring the interplay of structure, stability, activity and localization in tRNA nucleotidyltransferase function. [Montreal, Quebec, Canada]: Concordia University.

Leibovitch M, Bublak D, Hanic-Joyce PJ, Tillmann B, Flinner N, Amsel D, Scharf K-D, Mirus O, Joyce PBM, Schleiff E. 2013. The folding capacity of the mature domain of the dual-targeted plant tRNA nucleotidyltransferase influences organelle selection. Biochem J. 453(3):401–412.

Leibovitch M, Hanic-Joyce PJ, Joyce PBM. 2018. In vitro studies of disease-linked variants of human tRNA nucleotidyltransferase reveal decreased thermal stability and altered catalytic activity. Biochim Biophys Acta BBA - Proteins Proteomics. 1866(4):527–540.

Leibovitch M, Reid NE, Victoria J, Hanic-Joyce PJ, Joyce PBM. 2019. Analysis of the pathogenic I326T variant of human tRNA nucleotidyltransferase reveals reduced catalytic activity and thermal stability in vitro linked to a conformational change. Biochim Biophys Acta BBA - Proteins Proteomics. 1867(6):616–626.

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(6):815–824.

Lipowsky G, Bischoff FR, Izaurralde E, Kutay U, Schäfer S, Gross HJ, Beier H, Görlich D. 1999. Coordination of tRNA nuclear export with processing of tRNA. RNA. 5(4):539–549.

Liu JC-H, Liu M, Horowitz J. 1998. Recognition of the universally conserved 3′-CCA end of tRNA by elongation factor EF-Tu. RNA. 4(6):639–646.

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(5):762–772.

Lougaris V, Chou J, Baronio M, Gazzurelli L, Lorenzini T, Soresina A, Moratto D, Badolato R, Seleman M, Bellettato M, et al. 2018. Novel biallelic TRNT1 mutations resulting in sideroblastic anemia, combined B and T cell defects, hypogammaglobulinemia, recurrent infections, hypertrophic cardiomyopathy and developmental delay. Clin Immunol. 188:20–22.

Makhatadze GI. 2005. Thermodynamics of α‐helix formation. Adv Protein Chem. 72:199–226.

Martin G, Keller W. 2007. RNA-specific ribonucleotidyl transferases. RNA. 13(11):1834–1849.

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

Mucocutaneous features of congenital sideroblastic anemia associated with B cell immunodeficiency, periodic fevers, and developmental delay (SIFD). 2019. [accessed 2019 Mar 14]. http://rgdoi.net/10.13140/RG.2.2.17007.69286.

Neuenfeldt A, Just A, Betat H, Morl M. 2008. Evolution of tRNA nucleotidyltransferases: A small deletion generated CC-adding enzymes. Proc Natl Acad Sci. 105(23):7953–7958.

Nissen P, Hansen J, Ban N, Moore PB, Steitz TA. 2000. The structural basis of ribosome activity in peptide bond synthesis. Science. 289:920–930.

Oh B-K, Pace NR. 1994. Interaction of the 3′-end of tRNA with ribonuclease P RNA. Nucleic Acids Res. 22(20):4087–4094.

Pagani R, Tabucchi A, Carlucci F, Leoncini R, Consolmagno E, Molinelli M, Valerio P. 1991. Some aspects of purine nucleotide metabolism in human lymphocytes before and after infection with HIV-1 virus: Nucleotide content. Adv Exp Med Biol. 309B:43–46.

Pearson WR, Lipman DJ. 1988. Improved tools for biological sequence comparison. Proc Natl Acad Sci. 85(8):2444–2448.

Phizicky EM, Hopper AK. 2010. tRNA biology charges to the front. Genes Dev. 24(17):1832–1860.

Popenda M, Szachniuk M, Antczak M, Purzycka KJ, Lukasiak P, Bartol N, Blazewicz J, Adamiak RW. 2012. Automated 3D structure composition for large RNAs. Nucleic Acids Res. 40(14):e112–e112.

QuikChange II site-directed mutagenesis kit. 2015. [accessed 2018 Nov 29]. https://www.agilent.com/cs/library/usermanuals/public/200523.pdf.

Rahman MS. 2017. Biophysical and biochemical characterization of yeast tRNA nucleotidyltransferase variants. [Montreal, Quebec, Canada]: Concordia University.

Rasband WS. 2018. ImageJ. Bethesda, Maryland, USA: National Institutes of Health.

Remmert M, Biegert A, Hauser A, Söding J. 2012. HHblits: Lightning-fast iterative protein sequence searching by HMM-HMM alignment. Nat Methods. 9(2):173–175.

Rosset R, Monier R. 1963. On the instability of transfer-RNA terminal nucleotide sequence in yeast. Biochem Biophys Res Commun. 10(2):195–199.

Rubin GM. 1973. The nucleotide sequence of Saccharomyces cerevisiae 5.8 S ribosomal ribonucleic acid. J Biol Chem. 248(11):3860–3875.

Sambrook J, Maniatis T, Fritsch EF. 1989. Molecular cloning. 2nd ed. Cold Spring Harbor Laboratory Press.

Sarin PS, Zamecnik PC. 1964. On the stability of aminoacyl-s-RNA to nucleophilic catalysis. Biochim Biophys Acta. 91(4):653–655.

Sasarman F, Thiffault I, Weraarpachai W, Salomon S, Maftei C, Gauthier J, Ellazam B, Webb N, Antonicka H, Janer A, et al. 2015. The 3′ addition of CCA to mitochondrial tRNASer(AGY) is specifically impaired in patients with mutations in the tRNA nucleotidyl transferase TRNT1. Hum Mol Genet. 24(10):2841–2847.

Shan X, Russell TA, Paul SM, Kushner DB, Joyce PBM. 2008. Characterization of a temperature-sensitive mutation that impairs the function of yeast tRNA nucleotidyltransferase. Yeast. 25(3):219–233.

Sharma TP, Wiley LA, Whitmore SS, Anfinson KR, Cranston CM, Oppedal DJ, Daggett HT, Mullins RF, Tucker BA, Stone EM. 2017. Patient-specific induced pluripotent stem cells to evaluate the pathophysiology of TRNT1-associated retinitis pigmentosa. Stem Cell Res. 21:58–70.

Shi P-Y, Maizels N, Weiner AM. 1998. CCA addition by tRNA nucleotidyltransferase: Polymerization without translocation? EMBO J. 17(11):3197–3206.

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(11):2372–2378.

Simpson RJ, Adams PD, Golemis EA. 2009. Basic methods in protein purification and analysis. 1st ed. Cold Spring Harbor Laboratory Press.

Soukup GA, Breaker RR. 1999. Relationship between internucleotide linkage geometry and the stability of RNA. RNA. 5(10):1308–1325.

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.

Steitz T, Smerdon S, Jager J, Joyce C. 1994. A unified polymerase mechanism for nonhomologous DNA and RNA polymerases. Science. 266:2022–2025.

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

Taher AT, Viprakasit V, Musallam KM, Cappellini MD. 2013. Treating iron overload in patients with non-transfusion-dependent thalassemia. Am J Hematol. 88(5):409–415.

Tamura K, Hasegawa T. 1997. Role of the CCA end of tRNA and its vicinity in aminoacylation. Nucleic Acids Symp Ser. 37:133–134.

The PyMOL molecular graphics system. 2018b. Schrödinger.

Thompson JE, Venegas FD, Raines RT. 1994. Energetics of catalysis by ribonucleases: Fate of the 2’,3’-cyclic phosphodiester intermediate. Biochemistry. 33(23):7408–7414.

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.

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.

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

Torrance JD, Whittaker D. 1979. Distribution of erythrocyte nucleotides in pyrimidine 5′‐nucleotidase deficiency. Br J Haematol. 43(3):423–434.

Tretbar S, Neuenfeldt A, Betat H, Morl M. 2011. An inhibitory C-terminal region dictates the specificity of A-adding enzymes. Proc Natl Acad Sci. 108(52):21040–21045.

Wangsa-Wirawan ND. 2003. Retinal oxygen: Fundamental and clinical aspects. Arch Ophthalmol. 121:547–557.

Wedatilake Y, Niazi R, Fassone E, Powell CA, Pearce S, Plagnol V, Saldanha JW, Kleta R, Chong WK, Footitt E, et al. 2016. TRNT1 deficiency: Clinical, biochemical and molecular genetic features. Orphanet J Rare Dis. 11(90).

Weiner AM. 2004. tRNA maturation: RNA polymerization without a nucleic acid template. Curr Biol. 14(20):R883–R885.

Weinger JS, Parnell KM, Dorner S, Green R, Strobel SA. 2004. Substrate-assisted catalysis of peptide bond formation by the ribosome. Nat Struct Mol Biol. 11(11):1101–1106.

Wellner K, Betat H, Mörl M. 2018. A tRNA’s fate is decided at its 3′ end: Collaborative actions of CCA-adding enzyme and RNases involved in tRNA processing and degradation. Biochim Biophys Acta BBA - Gene Regul Mech. 1861(4):433–441.

Wende S, Bonin S, Gotze O, Betat H, Morl M. 2015. The identity of the discriminator base has an impact on CCA addition. Nucleic Acids Res. 43(11):5617–5629.

Werner A, Siems W, Schmidt H, Rapoport I, Gerber G, Toguzov RT, Tikhonov YV, Pimenov AM. 1987. Determination of nucleotides, nucleosides and nucleobases in cells of different complexity by reversed-phase and ion-pair high-performance liquid chromatography. J Chromatogr B Biomed Sci App. 421:257–265.

Wilusz JE, Whipple JM, Phizicky EM, Sharp PA. 2011. tRNAs marked with CCACCA are targeted for degradation. Science. 334(6057):817–821.

Wiseman DH, May A, Jolles S, Connor P, Powell C, Heeney MM, Giardina PJ, Klaassen RJ, Chakraborty P, Geraghty MT, et al. 2013. A novel syndrome of congenital sideroblastic anemia, B-cell immunodeficiency, periodic fevers, and developmental delay (SIFD). Blood. 122(1):112–123.

Wong C, Sridhara S, Bardwell JCA, Jakob U. 2000. Heating greatly speeds Coomassie Blue staining and destaining. BioTechniques. 28(3):426, 428, 430, 432.

Wu X-Q, Gross HJ. 1993. The long extra arms of human tRNA(Ser)Sec and tRNASer function as major identity elements for serylation in an orientation-dependent, but not sequence-specific manner. Nucleic Acids Res. 21(24):5589–5594.

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. 12(5):1165–1172.

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

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(35):36819–36827.

Yamashita S, Takeshita D, Tomita K. 2014. Translocation and rotation of tRNA during template-independent RNA polymerization by tRNA nucleotidyltransferase. Structure. 22(2):315–325.

Yamashita S, Tomita K. 2016. Mechanism of 3′-matured tRNA discrimination from 3′-immature tRNA by class-II CCA-adding enzyme. Structure. 24(6):918–925.

Yan Y, Zhang D, Zhou P, Li B, Huang S-Y. 2017. HDOCK: A web server for protein–protein and protein–DNA/RNA docking based on a hybrid strategy. Nucleic Acids Res. 45(W1):W365–W373.

Yang N. 2008. ATP: CTP nucleotidyltransferase: Interaction with tRNA and functional roles of conserved arginine residues, the C-terminus, the tRNA T-loop, and metal ions. [Worcester, Massachusetts, USA]: Clark University.

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.

Yue D, Weiner AM, Maizels N. 1998. The CCA-adding enzyme has a single active site. J Biol Chem. 273(45):29693–29700.

Yumada Y, Ohki M, Ishikura H. 1983. The nucleotide sequence of Bacillus subtilis tRNA genes. Nucleic Acids Res. 11(10):3037–3045.

Zhu L, 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(32):14875–14877.

Zhu L, Deutscher MP. 1987. tRNA nucleotidyltransferase is not essential for Escherichia coli viability. EMBO J. 6(8):2473–2477.
All items in Spectrum are protected by copyright, with all rights reserved. The use of items is governed by Spectrum's terms of access.

Repository Staff Only: item control page

Downloads per month over past year

Research related to the current document (at the CORE website)
- Research related to the current document (at the CORE website)
Back to top Back to top