• We are sorry, but NCBI web applications do not support your browser and may not function properly. More information
Logo of rnaThe RNA SocietyeTOC AlertsSubscriptionsJournal HomeCSHL PressRNA
RNA. Oct 2002; 8(10): 1189–1232.
PMCID: PMC1370332

tRNomics: analysis of tRNA genes from 50 genomes of Eukarya, Archaea, and Bacteria reveals anticodon-sparing strategies and domain-specific features.

Abstract

From 50 genomes of the three domains of life (7 eukarya, 13 archaea, and 30 bacteria), we extracted, analyzed, and compared over 4,000 sequences corresponding to cytoplasmic, nonorganellar tRNAs. For each genome, the complete set of tRNAs required to read the 61 sense codons was identified, which permitted revelation of three major anticodon-sparing strategies. Other features and sequence peculiarities analyzed are the following: (1) fit to the standard cloverleaf structure, (2) characteristic consensus sequences for elongator and initiator tDNAs, (3) frequencies of bases at each sequence position, (4) type and frequencies of conserved 2D and 3D base pairs, (5) anticodon/tDNA usages and anticodon-sparing strategies, (6) identification of the tRNA-Ile with anticodon CAU reading AUA, (7) size of variable arm, (8) occurrence and location of introns, (9) occurrence of 3'-CCA and 5'-extra G encoded at the tDNA level, and (10) distribution of the tRNA genes in genomes and their mode of transcription. Among all tRNA isoacceptors, we found that initiator tDNA-iMet is the most conserved across the three domains, yet domain-specific signatures exist. Also, according to which tRNA feature is considered (5'-extra G encoded in tDNAs-His, AUA codon read by tRNA-Ile with anticodon CAU, presence of intron, absence of "two-out-of-three" reading mode and short V-arm in tDNA-Tyr) Archaea sequester either with Bacteria or Eukarya. No common features between Eukarya and Bacteria not shared with Archaea could be unveiled. Thus, from the tRNomic point of view, Archaea appears as an "intermediate domain" between Eukarya and Bacteria.

Full Text

The Full Text of this article is available as a PDF (15M).

Selected References

These references are in PubMed. This may not be the complete list of references from this article.
  • Steward FT, Garrod AE. Pyo-pericardium Cured by Drainage. Proc R Soc Med. 1908;1(CLIN):15–17. [PMC free article] [PubMed]
  • Schultz JC, Shahidi NT. Detection of tumor necrosis factor-alpha in bone marrow plasma and peripheral blood plasma from patients with aplastic anemia. Am J Hematol. 1994 Jan;45(1):32–38. [PubMed]
  • Adams MD, Celniker SE, Holt RA, Evans CA, Gocayne JD, Amanatides PG, Scherer SE, Li PW, Hoskins RA, Galle RF, et al. The genome sequence of Drosophila melanogaster. Science. 2000 Mar 24;287(5461):2185–2195. [PubMed]
  • Aebi M, Kirchner G, Chen JY, Vijayraghavan U, Jacobson A, Martin NC, Abelson J. 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. 1990 Sep 25;265(27):16216–16220. [PubMed]
  • Agris PF. Wobble position modified nucleosides evolved to select transfer RNA codon recognition: a modified-wobble hypothesis. Biochimie. 1991 Nov;73(11):1345–1349. [PubMed]
  • Andachi Y, Yamao F, Iwami M, Muto A, Osawa S. Occurrence of unmodified adenine and uracil at the first position of anticodon in threonine tRNAs in Mycoplasma capricolum. Proc Natl Acad Sci U S A. 1987 Nov;84(21):7398–7402. [PMC free article] [PubMed]
  • Andachi Y, Yamao F, Muto A, Osawa S. Codon recognition patterns as deduced from sequences of the complete set of transfer RNA species in Mycoplasma capricolum. Resemblance to mitochondria. J Mol Biol. 1989 Sep 5;209(1):37–54. [PubMed]
  • Andersson SG, Kurland CG. Genomic evolution drives the evolution of the translation system. Biochem Cell Biol. 1995 Nov-Dec;73(11-12):775–787. [PubMed]
  • Andersson SG, Zomorodipour A, Andersson JO, Sicheritz-Pontén T, Alsmark UC, Podowski RM, Näslund AK, Eriksson AS, Winkler HH, Kurland CG. The genome sequence of Rickettsia prowazekii and the origin of mitochondria. Nature. 1998 Nov 12;396(6707):133–140. [PubMed]
  • Arn EA, Abelson JN. The 2'-5' RNA ligase of Escherichia coli. Purification, cloning, and genomic disruption. J Biol Chem. 1996 Dec 6;271(49):31145–31153. [PubMed]
  • Aström SU, von Pawel-Rammingen U, Byström AS. The yeast initiator tRNAMet can act as an elongator tRNA(Met) in vivo. J Mol Biol. 1993 Sep 5;233(1):43–58. [PubMed]
  • Auffinger P, Westhof E. Singly and bifurcated hydrogen-bonded base-pairs in tRNA anticodon hairpins and ribozymes. J Mol Biol. 1999 Sep 24;292(3):467–483. [PubMed]
  • Auffinger P, Westhof E. An extended structural signature for the tRNA anticodon loop. RNA. 2001 Mar;7(3):334–341. [PMC free article] [PubMed]
  • Auxilien S, Crain PF, Trewyn RW, Grosjean H. Mechanism, specificity and general properties of the yeast enzyme catalysing the formation of inosine 34 in the anticodon of transfer RNA. J Mol Biol. 1996 Oct 4;262(4):437–458. [PubMed]
  • Barrell BG, Anderson S, Bankier AT, de Bruijn MH, Chen E, Coulson AR, Drouin J, Eperon IC, Nierlich DP, Roe BA, et al. Different pattern of codon recognition by mammalian mitochondrial tRNAs. Proc Natl Acad Sci U S A. 1980 Jun;77(6):3164–3166. [PMC free article] [PubMed]
  • Becker HF, Motorin Y, Sissler M, Florentz C, Grosjean H. Major identity determinants for enzymatic formation of ribothymidine and pseudouridine in the T psi-loop of yeast tRNAs. J Mol Biol. 1997 Dec 12;274(4):505–518. [PubMed]
  • Belfort M, Weiner A. Another bridge between kingdoms: tRNA splicing in archaea and eukaryotes. Cell. 1997 Jun 27;89(7):1003–1006. [PubMed]
  • Beuning Penny J, Nagan Maria C, Cramer Christopher J, Musier-Forsyth Karin, Gelpí Josep-Lluis, Bashford Donald. Efficient aminoacylation of the tRNA(Ala) acceptor stem: dependence on the 2:71 base pair. RNA. 2002 May;8(5):659–670. [PMC free article] [PubMed]
  • Blandin G, Durrens P, Tekaia F, Aigle M, Bolotin-Fukuhara M, Bon E, Casarégola S, de Montigny J, Gaillardin C, Lépingle A, et al. Genomic exploration of the hemiascomycetous yeasts: 4. The genome of Saccharomyces cerevisiae revisited. FEBS Lett. 2000 Dec 22;487(1):31–36. [PubMed]
  • Blattner FR, Plunkett G, 3rd, Bloch CA, Perna NT, Burland V, Riley M, Collado-Vides J, Glasner JD, Rode CK, Mayhew GF, et al. The complete genome sequence of Escherichia coli K-12. Science. 1997 Sep 5;277(5331):1453–1462. [PubMed]
  • Bolotin A, Wincker P, Mauger S, Jaillon O, Malarme K, Weissenbach J, Ehrlich SD, Sorokin A. The complete genome sequence of the lactic acid bacterium Lactococcus lactis ssp. lactis IL1403. Genome Res. 2001 May;11(5):731–753. [PMC free article] [PubMed]
  • Bonocora RP, Shub DA. A novel group I intron-encoded endonuclease specific for the anticodon region of tRNA(fMet) genes. Mol Microbiol. 2001 Mar;39(5):1299–1306. [PubMed]
  • Borén T, Elias P, Samuelsson T, Claesson C, Barciszewska M, Gehrke CW, Kuo KC, Lustig F. Undiscriminating codon reading with adenosine in the wobble position. J Mol Biol. 1993 Apr 5;230(3):739–749. [PubMed]
  • Bult CJ, White O, Olsen GJ, Zhou L, Fleischmann RD, Sutton GG, Blake JA, FitzGerald LM, Clayton RA, Gocayne JD, et al. Complete genome sequence of the methanogenic archaeon, Methanococcus jannaschii. Science. 1996 Aug 23;273(5278):1058–1073. [PubMed]
  • Burkard U, Willis I, Söll D. Processing of histidine transfer RNA precursors. Abnormal cleavage site for RNase P. J Biol Chem. 1988 Feb 15;263(5):2447–2451. [PubMed]
  • Burnol AF, Margottin F, Huet J, Almouzni G, Prioleau MN, Méchali M, Sentenac A. TFIIIC relieves repression of U6 snRNA transcription by chromatin. Nature. 1993 Apr 1;362(6419):475–477. [PubMed]
  • Cedergren R, Grosjean H, Larue B. Primordial reading of genetic information. Biosystems. 1986;19(4):259–266. [PubMed]
  • Cedergren RJ, Sankoff D, LaRue B, Grosjean H. The evolving tRNA molecule. CRC Crit Rev Biochem. 1981;11(1):35–104. [PubMed]
  • Cermakian N, McClain WH, Cedergren R. tRNA nucleotide 47: an evolutionary enigma. RNA. 1998 Aug;4(8):928–936. [PMC free article] [PubMed]
  • Chambaud I, Heilig R, Ferris S, Barbe V, Samson D, Galisson F, Moszer I, Dybvig K, Wróblewski H, Viari A, et al. The complete genome sequence of the murine respiratory pathogen Mycoplasma pulmonis. Nucleic Acids Res. 2001 May 15;29(10):2145–2153. [PMC free article] [PubMed]
  • Chihade JW, Hayashibara K, Shiba K, Schimmel P. Strong selective pressure to use G:U to mark an RNA acceptor stem for alanine. Biochemistry. 1998 Jun 23;37(25):9193–9202. [PubMed]
  • Cole ST, Brosch R, Parkhill J, Garnier T, Churcher C, Harris D, Gordon SV, Eiglmeier K, Gas S, Barry CE, 3rd, et al. Deciphering the biology of Mycobacterium tuberculosis from the complete genome sequence. Nature. 1998 Jun 11;393(6685):537–544. [PubMed]
  • Colot V, Rossignol JL. Eukaryotic DNA methylation as an evolutionary device. Bioessays. 1999 May;21(5):402–411. [PubMed]
  • Cornish-Bowden A. Nomenclature for incompletely specified bases in nucleic acid sequences: recommendations 1984. Nucleic Acids Res. 1985 May 10;13(9):3021–3030. [PMC free article] [PubMed]
  • Crick FH. Codon--anticodon pairing: the wobble hypothesis. J Mol Biol. 1966 Aug;19(2):548–555. [PubMed]
  • Crothers DM, Seno T, Söll G. Is there a discriminator site in transfer RNA? Proc Natl Acad Sci U S A. 1972 Oct;69(10):3063–3067. [PMC free article] [PubMed]
  • Curran JF. Decoding with the A:I wobble pair is inefficient. Nucleic Acids Res. 1995 Feb 25;23(4):683–688. [PMC free article] [PubMed]
  • Cusack S, Yaremchuk A, Tukalo M. The crystal structure of the ternary complex of T.thermophilus seryl-tRNA synthetase with tRNA(Ser) and a seryl-adenylate analogue reveals a conformational switch in the active site. EMBO J. 1996 Jun 3;15(11):2834–2842. [PMC free article] [PubMed]
  • Daniels CJ, Gupta R, Doolittle WF. Transcription and excision of a large intron in the tRNATrp gene of an archaebacterium, Halobacterium volcanii. J Biol Chem. 1985 Mar 10;260(5):3132–3134. [PubMed]
  • Deckert G, Warren PV, Gaasterland T, Young WG, Lenox AL, Graham DE, Overbeek R, Snead MA, Keller M, Aujay M, et al. The complete genome of the hyperthermophilic bacterium Aquifex aeolicus. Nature. 1998 Mar 26;392(6674):353–358. [PubMed]
  • Dennis PP, Omer A, Lowe T. A guided tour: small RNA function in Archaea. Mol Microbiol. 2001 May;40(3):509–519. [PubMed]
  • Deutscher MP. Ribonucleases, tRNA nucleotidyltransferase, and the 3' processing of tRNA. Prog Nucleic Acid Res Mol Biol. 1990;39:209–240. [PubMed]
  • Dieci Giorgio, Giuliodori Silvia, Catellani Manuela, Percudani Riccardo, Ottonello Simone. Intragenic promoter adaptation and facilitated RNA polymerase III recycling in the transcription of SCR1, the 7SL RNA gene of Saccharomyces cerevisiae. J Biol Chem. 2002 Mar 1;277(9):6903–6914. [PubMed]
  • Dong H, Nilsson L, Kurland CG. Co-variation of tRNA abundance and codon usage in Escherichia coli at different growth rates. J Mol Biol. 1996 Aug 2;260(5):649–663. [PubMed]
  • Donze D, Kamakaka RT. RNA polymerase III and RNA polymerase II promoter complexes are heterochromatin barriers in Saccharomyces cerevisiae. EMBO J. 2001 Feb 1;20(3):520–531. [PMC free article] [PubMed]
  • Dörner M, Altmann M, Päbo S, Mörl M. Evidence for import of a lysyl-tRNA into marsupial mitochondria. Mol Biol Cell. 2001 Sep;12(9):2688–2698. [PMC free article] [PubMed]
  • Clouet d'Orval B, Bortolin ML, Gaspin C, Bachellerie JP. Box C/D RNA guides for the ribose methylation of archaeal tRNAs. The tRNATrp intron guides the formation of two ribose-methylated nucleosides in the mature tRNATrp. Nucleic Acids Res. 2001 Nov 15;29(22):4518–4529. [PMC free article] [PubMed]
  • Duret L. tRNA gene number and codon usage in the C. elegans genome are co-adapted for optimal translation of highly expressed genes. Trends Genet. 2000 Jul;16(7):287–289. [PubMed]
  • Edgell DR, Belfort M, Shub DA. Barriers to intron promiscuity in bacteria. J Bacteriol. 2000 Oct;182(19):5281–5289. [PMC free article] [PubMed]
  • Edqvist J, Stråby KB, Grosjean H. Enzymatic formation of N2,N2-dimethylguanosine in eukaryotic tRNA: importance of the tRNA architecture. Biochimie. 1995;77(1-2):54–61. [PubMed]
  • el-Mabrouk N, Lisacek F. Very fast identification of RNA motifs in genomic DNA. Application to tRNA search in the yeast genome. J Mol Biol. 1996 Nov 22;264(1):46–55. [PubMed]
  • Fey J, Weil JH, Tomita K, Cosset A, Dietrich A, Small I, Maréchal-Drouard L. Editing of plant mitochondrial transfer RNAs. Acta Biochim Pol. 2001;48(2):383–389. [PubMed]
  • Fichant GA, Burks C. Identifying potential tRNA genes in genomic DNA sequences. J Mol Biol. 1991 Aug 5;220(3):659–671. [PubMed]
  • Filipowicz W. Imprinted expression of small nucleolar RNAs in brain: time for RNomics. Proc Natl Acad Sci U S A. 2000 Dec 19;97(26):14035–14037. [PMC free article] [PubMed]
  • Fitz-Gibbon Sorel T, Ladner Heidi, Kim Ung-Jin, Stetter Karl O, Simon Melvin I, Miller Jeffrey H. Genome sequence of the hyperthermophilic crenarchaeon Pyrobaculum aerophilum. Proc Natl Acad Sci U S A. 2002 Jan 22;99(2):984–989. [PMC free article] [PubMed]
  • Fleischmann RD, Adams MD, White O, Clayton RA, Kirkness EF, Kerlavage AR, Bult CJ, Tomb JF, Dougherty BA, Merrick JM, et al. Whole-genome random sequencing and assembly of Haemophilus influenzae Rd. Science. 1995 Jul 28;269(5223):496–512. [PubMed]
  • Fraser CM, Casjens S, Huang WM, Sutton GG, Clayton R, Lathigra R, White O, Ketchum KA, Dodson R, Hickey EK, et al. Genomic sequence of a Lyme disease spirochaete, Borrelia burgdorferi. Nature. 1997 Dec 11;390(6660):580–586. [PubMed]
  • Fraser CM, Gocayne JD, White O, Adams MD, Clayton RA, Fleischmann RD, Bult CJ, Kerlavage AR, Sutton G, Kelley JM, et al. The minimal gene complement of Mycoplasma genitalium. Science. 1995 Oct 20;270(5235):397–403. [PubMed]
  • Fraser CM, Norris SJ, Weinstock GM, White O, Sutton GG, Dodson R, Gwinn M, Hickey EK, Clayton R, Ketchum KA, et al. Complete genome sequence of Treponema pallidum, the syphilis spirochete. Science. 1998 Jul 17;281(5375):375–388. [PubMed]
  • Galibert F, Finan TM, Long SR, Puhler A, Abola P, Ampe F, Barloy-Hubler F, Barnett MJ, Becker A, Boistard P, et al. The composite genome of the legume symbiont Sinorhizobium meliloti. Science. 2001 Jul 27;293(5530):668–672. [PubMed]
  • Galli G, Hofstetter H, Birnstiel ML. Two conserved sequence blocks within eukaryotic tRNA genes are major promoter elements. Nature. 1981 Dec 17;294(5842):626–631. [PubMed]
  • Gaspin C, Cavaillé J, Erauso G, Bachellerie JP. Archaeal homologs of eukaryotic methylation guide small nucleolar RNAs: lessons from the Pyrococcus genomes. J Mol Biol. 2000 Apr 7;297(4):895–906. [PubMed]
  • Gautheret D, Damberger SH, Gutell RR. Identification of base-triples in RNA using comparative sequence analysis. J Mol Biol. 1995 Apr 21;248(1):27–43. [PubMed]
  • Gautheret D, Lambert A. Direct RNA motif definition and identification from multiple sequence alignments using secondary structure profiles. J Mol Biol. 2001 Nov 9;313(5):1003–1011. [PubMed]
  • Gerber AP, Keller W. RNA editing by base deamination: more enzymes, more targets, new mysteries. Trends Biochem Sci. 2001 Jun;26(6):376–384. [PubMed]
  • Glaser P, Frangeul L, Buchrieser C, Rusniok C, Amend A, Baquero F, Berche P, Bloecker H, Brandt P, Chakraborty T, et al. Comparative genomics of Listeria species. Science. 2001 Oct 26;294(5543):849–852. [PubMed]
  • Glass JI, Lefkowitz EJ, Glass JS, Heiner CR, Chen EY, Cassell GH. The complete sequence of the mucosal pathogen Ureaplasma urealyticum. Nature. 2000 Oct 12;407(6805):757–762. [PubMed]
  • Goodman HM, Olson MV, Hall BD. Nucleotide sequence of a mutant eukaryotic gene: the yeast tyrosine-inserting ochre suppressor SUP4-o. Proc Natl Acad Sci U S A. 1977 Dec;74(12):5453–5457. [PMC free article] [PubMed]
  • Gott JM, Emeson RB. Functions and mechanisms of RNA editing. Annu Rev Genet. 2000;34:499–531. [PubMed]
  • Grosjean H, Auxilien S, Constantinesco F, Simon C, Corda Y, Becker HF, Foiret D, Morin A, Jin YX, Fournier M, et al. Enzymatic conversion of adenosine to inosine and to N1-methylinosine in transfer RNAs: a review. Biochimie. 1996;78(6):488–501. [PubMed]
  • Grosjean H, Cedergren RJ, McKay W. Structure in tRNA data. Biochimie. 1982 Jun;64(6):387–397. [PubMed]
  • Grosjean H, Nicoghosian K, Haumont E, Söll D, Cedergren R. Nucleotide sequences of two serine tRNAs with a GGA anticodon: the structure-function relationships in the serine family of E. coli tRNAs. Nucleic Acids Res. 1985 Aug 12;13(15):5697–5706. [PMC free article] [PubMed]
  • Grosjean H, Szweykowska-Kulinska Z, Motorin Y, Fasiolo F, Simos G. Intron-dependent enzymatic formation of modified nucleosides in eukaryotic tRNAs: a review. Biochimie. 1997 May;79(5):293–302. [PubMed]
  • Gu X, Yu M, Ivanetich KM, Santi DV. Molecular recognition of tRNA by tRNA pseudouridine 55 synthase. Biochemistry. 1998 Jan 6;37(1):339–343. [PubMed]
  • Gu XR, Nicoghosian K, Cedergren RJ, Wong JT. Sequences of halobacterial tRNAs and the paucity of U in the first position of their anticodons. Nucleic Acids Res. 1983 Aug 25;11(16):5433–5442. [PMC free article] [PubMed]
  • Guillon JM, Meinnel T, Mechulam Y, Lazennec C, Blanquet S, Fayat G. Nucleotides of tRNA governing the specificity of Escherichia coli methionyl-tRNA(fMet) formyltransferase. J Mol Biol. 1992 Mar 20;224(2):359–367. [PubMed]
  • Guindy YS, Samuelsson T, Johansen TI. Unconventional codon reading by Mycoplasma mycoides tRNAs as revealed by partial sequence analysis. Biochem J. 1989 Mar 15;258(3):869–873. [PMC free article] [PubMed]
  • Guo Qing, Gong Qingguo, Tong Ka-Lok, Vestergaard Bente, Costa Annie, Desgres Jean, Wong Mansim, Grosjean Henri, Zhu Guang, Wong J Tze-Fei, et al. Recognition by tryptophanyl-tRNA synthetases of discriminator base on tRNATrp from three biological domains. J Biol Chem. 2002 Apr 19;277(16):14343–14349. [PubMed]
  • Hamada M, Huang Y, Lowe TM, Maraia RJ. Widespread use of TATA elements in the core promoters for RNA polymerases III, II, and I in fission yeast. Mol Cell Biol. 2001 Oct;21(20):6870–6881. [PMC free article] [PubMed]
  • Hani J, Feldmann H. tRNA genes and retroelements in the yeast genome. Nucleic Acids Res. 1998 Feb 1;26(3):689–696. [PMC free article] [PubMed]
  • Hao Bing, Gong Weimin, Ferguson Tsuneo K, James Carey M, Krzycki Joseph A, Chan Michael K. A new UAG-encoded residue in the structure of a methanogen methyltransferase. Science. 2002 May 24;296(5572):1462–1466. [PubMed]
  • Hardt WD, Schlegl J, Erdmann VA, Hartmann RK. Role of the D arm and the anticodon arm in tRNA recognition by eubacterial and eukaryotic RNase P enzymes. Biochemistry. 1993 Dec 7;32(48):13046–13053. [PubMed]
  • Heidelberg JF, Eisen JA, Nelson WC, Clayton RA, Gwinn ML, Dodson RJ, Haft DH, Hickey EK, Peterson JD, Umayam L, et al. DNA sequence of both chromosomes of the cholera pathogen Vibrio cholerae. Nature. 2000 Aug 3;406(6795):477–483. [PubMed]
  • Helm M, Brulé H, Friede D, Giegé R, Pütz D, Florentz C. Search for characteristic structural features of mammalian mitochondrial tRNAs. RNA. 2000 Oct;6(10):1356–1379. [PMC free article] [PubMed]
  • Himmelreich R, Hilbert H, Plagens H, Pirkl E, Li BC, Herrmann R. Complete sequence analysis of the genome of the bacterium Mycoplasma pneumoniae. Nucleic Acids Res. 1996 Nov 15;24(22):4420–4449. [PMC free article] [PubMed]
  • Hoang C, Ferré-D'Amaré AR. Cocrystal structure of a tRNA Psi55 pseudouridine synthase: nucleotide flipping by an RNA-modifying enzyme. Cell. 2001 Dec 28;107(7):929–939. [PubMed]
  • Holley RW. Structure of an alanine transfer ribonucleic acid. JAMA. 1965 Nov 22;194(8):868–871. [PubMed]
  • HOLLEY RW, EVERETT GA, MADISON JT, ZAMIR A. NUCLEOTIDE SEQUENCES IN THE YEAST ALANINE TRANSFER RIBONUCLEIC ACID. J Biol Chem. 1965 May;240:2122–2128. [PubMed]
  • Hou YM. Structural elements that contribute to an unusual tertiary interaction in a transfer RNA. Biochemistry. 1994 Apr 19;33(15):4677–4681. [PubMed]
  • Hou YM, Sterner T, Jansen M. Permutation of a pair of tertiary nucleotides in a transfer RNA. Biochemistry. 1995 Mar 7;34(9):2978–2984. [PubMed]
  • Houssier C, Grosjean H. Temperature jump relaxation studies on the interactions between transfer RNAs with complementary anticodons. The effect of modified bases adjacent to the anticodon triplet. J Biomol Struct Dyn. 1985 Oct;3(2):387–408. [PubMed]
  • Hubert N, Sturchler C, Westhof E, Carbon P, Krol A. The 9/4 secondary structure of eukaryotic selenocysteine tRNA: more pieces of evidence. RNA. 1998 Sep;4(9):1029–1033. [PMC free article] [PubMed]
  • Ikemura T. Codon usage and tRNA content in unicellular and multicellular organisms. Mol Biol Evol. 1985 Jan;2(1):13–34. [PubMed]
  • Inagaki Y, Kojima A, Bessho Y, Hori H, Ohama T, Osawa S. Translation of synonymous codons in family boxes by Mycoplasma capricolum tRNAs with unmodified uridine or adenosine at the first anticodon position. J Mol Biol. 1995 Aug 25;251(4):486–492. [PubMed]
  • Jahn D, Pande S. Histidine tRNA guanylyltransferase from Saccharomyces cerevisiae. II. Catalytic mechanism. J Biol Chem. 1991 Dec 5;266(34):22832–22836. [PubMed]
  • Jiang HQ, Motorin Y, Jin YX, Grosjean H. Pleiotropic effects of intron removal on base modification pattern of yeast tRNAPhe: an in vitro study. Nucleic Acids Res. 1997 Jul 15;25(14):2694–2701. [PMC free article] [PubMed]
  • Jukes TH, Osawa S. The genetic code in mitochondria and chloroplasts. Experientia. 1990 Dec 1;46(11-12):1117–1126. [PubMed]
  • Kagawa Y, Nojima H, Nukiwa N, Ishizuka M, Nakajima T, Yasuhara T, Tanaka T, Oshima T. High guanine plus cytosine content in the third letter of codons of an extreme thermophile. DNA sequence of the isopropylmalate dehydrogenase of Thermus thermophilus. J Biol Chem. 1984 Mar 10;259(5):2956–2960. [PubMed]
  • Kanaya S, Yamada Y, Kinouchi M, Kudo Y, Ikemura T. Codon usage and tRNA genes in eukaryotes: correlation of codon usage diversity with translation efficiency and with CG-dinucleotide usage as assessed by multivariate analysis. J Mol Evol. 2001 Oct-Nov;53(4-5):290–298. [PubMed]
  • Kanaya S, Yamada Y, Kudo Y, Ikemura T. Studies of codon usage and tRNA genes of 18 unicellular organisms and quantification of Bacillus subtilis tRNAs: gene expression level and species-specific diversity of codon usage based on multivariate analysis. Gene. 1999 Sep 30;238(1):143–155. [PubMed]
  • Kaneko T, Nakamura Y, Wolk CP, Kuritz T, Sasamoto S, Watanabe A, Iriguchi M, Ishikawa A, Kawashima K, Kimura T, et al. Complete genomic sequence of the filamentous nitrogen-fixing cyanobacterium Anabaena sp. strain PCC 7120. DNA Res. 2001 Oct 31;8(5):205–253. [PubMed]
  • Kaneko T, Sato S, Kotani H, Tanaka A, Asamizu E, Nakamura Y, Miyajima N, Hirosawa M, Sugiura M, Sasamoto S, et al. Sequence analysis of the genome of the unicellular cyanobacterium Synechocystis sp. strain PCC6803. II. Sequence determination of the entire genome and assignment of potential protein-coding regions. DNA Res. 1996 Jun 30;3(3):109–136. [PubMed]
  • Kano A, Andachi Y, Ohama T, Osawa S. Novel anticodon composition of transfer RNAs in Micrococcus luteus, a bacterium with a high genomic G + C content. Correlation with codon usage. J Mol Biol. 1991 Sep 20;221(2):387–401. [PubMed]
  • Kano A, Ohama T, Abe R, Osawa S. Unassigned or nonsense codons in Micrococcus luteus. J Mol Biol. 1993 Mar 5;230(1):51–56. [PubMed]
  • Katinka MD, Duprat S, Cornillot E, Méténier G, Thomarat F, Prensier G, Barbe V, Peyretaillade E, Brottier P, Wincker P, et al. Genome sequence and gene compaction of the eukaryote parasite Encephalitozoon cuniculi. Nature. 2001 Nov 22;414(6862):450–453. [PubMed]
  • Kawarabayasi Y, Hino Y, Horikawa H, Jin-no K, Takahashi M, Sekine M, Baba S, Ankai A, Kosugi H, Hosoyama A, et al. Complete genome sequence of an aerobic thermoacidophilic crenarchaeon, Sulfolobus tokodaii strain7. DNA Res. 2001 Aug 31;8(4):123–140. [PubMed]
  • Kawarabayasi Y, Hino Y, Horikawa H, Yamazaki S, Haikawa Y, Jin-no K, Takahashi M, Sekine M, Baba S, Ankai A, et al. Complete genome sequence of an aerobic hyper-thermophilic crenarchaeon, Aeropyrum pernix K1. DNA Res. 1999 Apr 30;6(2):83–152. [PubMed]
  • Kawarabayasi Y, Sawada M, Horikawa H, Haikawa Y, Hino Y, Yamamoto S, Sekine M, Baba S, Kosugi H, Hosoyama A, et al. Complete sequence and gene organization of the genome of a hyper-thermophilic archaebacterium, Pyrococcus horikoshii OT3. DNA Res. 1998 Apr 30;5(2):55–76. [PubMed]
  • Kenri T, Imamoto F, Kano Y. Construction and characterization of an Escherichia coli mutant deficient in the metY gene encoding tRNA(f2Met): either tRNA(f1Met) or tRNA(f2Met) is required for cell growth. Gene. 1992 May 1;114(1):109–114. [PubMed]
  • Kjems J, Leffers H, Olesen T, Garrett RA. A unique tRNA intron in the variable loop of the extreme thermophile Thermofilum pendens and its possible evolutionary implications. J Biol Chem. 1989 Oct 25;264(30):17834–17837. [PubMed]
  • Klenk HP, Clayton RA, Tomb JF, White O, Nelson KE, Ketchum KA, Dodson RJ, Gwinn M, Hickey EK, Peterson JD, et al. The complete genome sequence of the hyperthermophilic, sulphate-reducing archaeon Archaeoglobus fulgidus. Nature. 1997 Nov 27;390(6658):364–370. [PubMed]
  • Komine Y, Adachi T, Inokuchi H, Ozeki H. Genomic organization and physical mapping of the transfer RNA genes in Escherichia coli K12. J Mol Biol. 1990 Apr 20;212(4):579–598. [PubMed]
  • Koshlap KM, Guenther R, Sochacka E, Malkiewicz A, Agris PF. A distinctive RNA fold: the solution structure of an analogue of the yeast tRNAPhe T Psi C domain. Biochemistry. 1999 Jul 6;38(27):8647–8656. [PubMed]
  • Krupp G, Kahle D, Vogt T, Char S. Sequence changes in both flanking sequences of a pre-tRNA influence the cleavage specificity of RNase P. J Mol Biol. 1991 Feb 20;217(4):637–648. [PubMed]
  • Kunst F, Ogasawara N, Moszer I, Albertini AM, Alloni G, Azevedo V, Bertero MG, Bessières P, Bolotin A, Borchert S, et al. The complete genome sequence of the gram-positive bacterium Bacillus subtilis. Nature. 1997 Nov 20;390(6657):249–256. [PubMed]
  • Lander ES, Linton LM, Birren B, Nusbaum C, Zody MC, Baldwin J, Devon K, Dewar K, Doyle M, FitzHugh W, et al. Initial sequencing and analysis of the human genome. Nature. 2001 Feb 15;409(6822):860–921. [PubMed]
  • Larue B, Cedergren RJ, Sankoff D, Grosjean H. Evolution of methionine initiator and phenylalanine transfer RNAs. J Mol Evol. 1979 Dec;14(4):287–300. [PubMed]
  • Lee CP, Seong BL, RajBhandary UL. Structural and sequence elements important for recognition of Escherichia coli formylmethionine tRNA by methionyl-tRNA transformylase are clustered in the acceptor stem. J Biol Chem. 1991 Sep 25;266(27):18012–18017. [PubMed]
  • Leontis NB, Westhof E. Geometric nomenclature and classification of RNA base pairs. RNA. 2001 Apr;7(4):499–512. [PMC free article] [PubMed]
  • Levinger L, Bourne R, Kolla S, Cylin E, Russell K, Wang X, Mohan A. Matrices of paired substitutions show the effects of tRNA D/T loop sequence on Drosophila RNase P and 3'-tRNase processing. J Biol Chem. 1998 Jan 9;273(2):1015–1025. [PubMed]
  • Levitt M. Detailed molecular model for transfer ribonucleic acid. Nature. 1969 Nov 22;224(5221):759–763. [PubMed]
  • Li H, Trotta CR, Abelson J. Crystal structure and evolution of a transfer RNA splicing enzyme. Science. 1998 Apr 10;280(5361):279–284. [PubMed]
  • Lim VI, Curran JF. Analysis of codon:anticodon interactions within the ribosome provides new insights into codon reading and the genetic code structure. RNA. 2001 Jul;7(7):942–957. [PMC free article] [PubMed]
  • Limbach PA, Crain PF, McCloskey JA. Summary: the modified nucleosides of RNA. Nucleic Acids Res. 1994 Jun 25;22(12):2183–2196. [PMC free article] [PubMed]
  • Loria A, Pan T. Recognition of the T stem-loop of a pre-tRNA substrate by the ribozyme from Bacillus subtilis ribonuclease P. Biochemistry. 1997 May 27;36(21):6317–6325. [PubMed]
  • Lowe TM, Eddy SR. tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence. Nucleic Acids Res. 1997 Mar 1;25(5):955–964. [PMC free article] [PubMed]
  • Lykke-Andersen J, Aagaard C, Semionenkov M, Garrett RA. Archaeal introns: splicing, intercellular mobility and evolution. Trends Biochem Sci. 1997 Sep;22(9):326–331. [PubMed]
  • Major F, Gautheret D, Cedergren R. Reproducing the three-dimensional structure of a tRNA molecule from structural constraints. Proc Natl Acad Sci U S A. 1993 Oct 15;90(20):9408–9412. [PMC free article] [PubMed]
  • Mandal N, Mangroo D, Dalluge JJ, McCloskey JA, Rajbhandary UL. Role of the three consecutive G:C base pairs conserved in the anticodon stem of initiator tRNAs in initiation of protein synthesis in Escherichia coli. RNA. 1996 May;2(5):473–482. [PMC free article] [PubMed]
  • Matsugi J, Murao K, Ishikura H. Characterization of a B. subtilis minor isoleucine tRNA deduced from tDNA having a methionine anticodon CAT. J Biochem. 1996 Apr;119(4):811–816. [PubMed]
  • Mohan A, Whyte S, Wang X, Nashimoto M, Levinger L. The 3' end CCA of mature tRNA is an antideterminant for eukaryotic 3'-tRNase. RNA. 1999 Feb;5(2):245–256. [PMC free article] [PubMed]
  • Motorin Y, Grosjean H. Multisite-specific tRNA:m5C-methyltransferase (Trm4) in yeast Saccharomyces cerevisiae: identification of the gene and substrate specificity of the enzyme. RNA. 1999 Aug;5(8):1105–1118. [PMC free article] [PubMed]
  • Motorin Y, Keith G, Simon C, Foiret D, Simos G, Hurt E, Grosjean H. The yeast tRNA:pseudouridine synthase Pus1p displays a multisite substrate specificity. RNA. 1998 Jul;4(7):856–869. [PMC free article] [PubMed]
  • Mueller U, Schübel H, Sprinzl M, Heinemann U. Crystal structure of acceptor stem of tRNA(Ala) from Escherichia coli shows unique G.U wobble base pair at 1.16 A resolution. RNA. 1999 May;5(5):670–677. [PMC free article] [PubMed]
  • Munz P, Leupold U, Agris P, Kohli J. In vivo decoding rules in Schizosaccharomyces pombe are at variance with in vitro data. Nature. 1981 Nov 12;294(5837):187–188. [PubMed]
  • Muramatsu T, Nishikawa K, Nemoto F, Kuchino Y, Nishimura S, Miyazawa T, Yokoyama S. Codon and amino-acid specificities of a transfer RNA are both converted by a single post-transcriptional modification. Nature. 1988 Nov 10;336(6195):179–181. [PubMed]
  • Muramatsu T, Yokoyama S, Horie N, Matsuda A, Ueda T, Yamaizumi Z, Kuchino Y, Nishimura S, Miyazawa T. A novel lysine-substituted nucleoside in the first position of the anticodon of minor isoleucine tRNA from Escherichia coli. J Biol Chem. 1988 Jul 5;263(19):9261–9267. [PubMed]
  • Muto A, Osawa S. The guanine and cytosine content of genomic DNA and bacterial evolution. Proc Natl Acad Sci U S A. 1987 Jan;84(1):166–169. [PMC free article] [PubMed]
  • Nameki N. Identity elements of tRNA(Thr) towards Saccharomyces cerevisiae threonyl-tRNA synthetase. Nucleic Acids Res. 1995 Aug 11;23(15):2831–2836. [PMC free article] [PubMed]
  • Nelson KE, Clayton RA, Gill SR, Gwinn ML, Dodson RJ, Haft DH, Hickey EK, Peterson JD, Nelson WC, Ketchum KA, et al. Evidence for lateral gene transfer between Archaea and bacteria from genome sequence of Thermotoga maritima. Nature. 1999 May 27;399(6734):323–329. [PubMed]
  • Ng WV, Kennedy SP, Mahairas GG, Berquist B, Pan M, Shukla HD, Lasky SR, Baliga NS, Thorsson V, Sbrogna J, et al. Genome sequence of Halobacterium species NRC-1. Proc Natl Acad Sci U S A. 2000 Oct 24;97(22):12176–12181. [PMC free article] [PubMed]
  • Oba T, Andachi Y, Muto A, Osawa S. CGG: an unassigned or nonsense codon in Mycoplasma capricolum. Proc Natl Acad Sci U S A. 1991 Feb 1;88(3):921–925. [PMC free article] [PubMed]
  • Odell L, Huang V, Jakacka M, Pan T. Interaction of structural modules in substrate binding by the ribozyme from Bacillus subtilis RNase P. Nucleic Acids Res. 1998 Aug 15;26(16):3717–3723. [PMC free article] [PubMed]
  • Ohama T, Muto A, Osawa S. Role of GC-biased mutation pressure on synonymous codon choice in Micrococcus luteus, a bacterium with a high genomic GC-content. Nucleic Acids Res. 1990 Mar 25;18(6):1565–1569. [PMC free article] [PubMed]
  • Ohama T, Osawa S, Watanabe K, Jukes TH. Evolution of the mitochondrial genetic code. IV. AAA as an asparagine codon in some animal mitochondria. J Mol Evol. 1990 Apr;30(4):329–332. [PubMed]
  • Ohama T, Suzuki T, Mori M, Osawa S, Ueda T, Watanabe K, Nakase T. Non-universal decoding of the leucine codon CUG in several Candida species. Nucleic Acids Res. 1993 Aug 25;21(17):4039–4045. [PMC free article] [PubMed]
  • Omer Arina D, Ziesche Sonia, Ebhardt Holger, Dennis Patrick P. In vitro reconstitution and activity of a C/D box methylation guide ribonucleoprotein complex. Proc Natl Acad Sci U S A. 2002 Apr 16;99(8):5289–5294. [PMC free article] [PubMed]
  • Orellana O, Cooley L, Söll D. The additional guanylate at the 5' terminus of Escherichia coli tRNAHis is the result of unusual processing by RNase P. Mol Cell Biol. 1986 Feb;6(2):525–529. [PMC free article] [PubMed]
  • Osawa S, Collins D, Ohama T, Jukes TH, Watanabe K. Evolution of the mitochondrial genetic code. III. Reassignment of CUN codons from leucine to threonine during evolution of yeast mitochondria. J Mol Evol. 1990 Apr;30(4):322–328. [PubMed]
  • Osawa S, Jukes TH. Evolution of the genetic code as affected by anticodon content. Trends Genet. 1988 Jul;4(7):191–198. [PubMed]
  • Osawa S, Jukes TH, Muto A, Yamao F, Ohama T, Andachi Y. Role of directional mutation pressure in the evolution of the eubacterial genetic code. Cold Spring Harb Symp Quant Biol. 1987;52:777–789. [PubMed]
  • Osawa S, Jukes TH, Watanabe K, Muto A. Recent evidence for evolution of the genetic code. Microbiol Rev. 1992 Mar;56(1):229–264. [PMC free article] [PubMed]
  • Osawa S, Ohama T, Jukes TH, Watanabe K. Evolution of the mitochondrial genetic code. I. Origin of AGR serine and stop codons in metazoan mitochondria. J Mol Evol. 1989 Sep;29(3):202–207. [PubMed]
  • Palmer JR, Daniels CJ. In vivo definition of an archaeal promoter. J Bacteriol. 1995 Apr;177(7):1844–1849. [PMC free article] [PubMed]
  • Pande S, Jahn D, Söll D. Histidine tRNA guanylyltransferase from Saccharomyces cerevisiae. I. Purification and physical properties. J Biol Chem. 1991 Dec 5;266(34):22826–22831. [PubMed]
  • Pannucci JA, Haas ES, Hall TA, Harris JK, Brown JW. RNase P RNAs from some Archaea are catalytically active. Proc Natl Acad Sci U S A. 1999 Jul 6;96(14):7803–7808. [PMC free article] [PubMed]
  • Parkhill J, Wren BW, Mungall K, Ketley JM, Churcher C, Basham D, Chillingworth T, Davies RM, Feltwell T, Holroyd S, et al. The genome sequence of the food-borne pathogen Campylobacter jejuni reveals hypervariable sequences. Nature. 2000 Feb 10;403(6770):665–668. [PubMed]
  • Parkhill J, Wren BW, Thomson NR, Titball RW, Holden MT, Prentice MB, Sebaihia M, James KD, Churcher C, Mungall KL, et al. Genome sequence of Yersinia pestis, the causative agent of plague. Nature. 2001 Oct 4;413(6855):523–527. [PubMed]
  • Paule MR, White RJ. Survey and summary: transcription by RNA polymerases I and III. Nucleic Acids Res. 2000 Mar 15;28(6):1283–1298. [PMC free article] [PubMed]
  • Pavesi A, Conterio F, Bolchi A, Dieci G, Ottonello S. Identification of new eukaryotic tRNA genes in genomic DNA databases by a multistep weight matrix analysis of transcriptional control regions. Nucleic Acids Res. 1994 Apr 11;22(7):1247–1256. [PMC free article] [PubMed]
  • Percudani R. Restricted wobble rules for eukaryotic genomes. Trends Genet. 2001 Mar;17(3):133–135. [PubMed]
  • Percudani R, Pavesi A, Ottonello S. Transfer RNA gene redundancy and translational selection in Saccharomyces cerevisiae. J Mol Biol. 1997 May 2;268(2):322–330. [PubMed]
  • Perreau VM, Keith G, Holmes WM, Przykorska A, Santos MA, Tuite MF. The Candida albicans CUG-decoding ser-tRNA has an atypical anticodon stem-loop structure. J Mol Biol. 1999 Nov 12;293(5):1039–1053. [PubMed]
  • Pintard Lionel, Lecointe François, Bujnicki Janusz M, Bonnerot Claire, Grosjean Henri, Lapeyre Bruno. Trm7p catalyses the formation of two 2'-O-methylriboses in yeast tRNA anticodon loop. EMBO J. 2002 Apr 2;21(7):1811–1820. [PMC free article] [PubMed]
  • Price DH, Gray MW. Confirmation of predicted edits and demonstration of unpredicted edits in Acanthamoeba castellanii mitochondrial tRNAs. Curr Genet. 1999 Feb;35(1):23–29. [PubMed]
  • Quigley GJ, Rich A. Structural domains of transfer RNA molecules. Science. 1976 Nov 19;194(4267):796–806. [PubMed]
  • Reuven NB, Zhou Z, Deutscher MP. Functional overlap of tRNA nucleotidyltransferase, poly(A) polymerase I, and polynucleotide phosphorylase. J Biol Chem. 1997 Dec 26;272(52):33255–33259. [PubMed]
  • Rich A, RajBhandary UL. Transfer RNA: molecular structure, sequence, and properties. Annu Rev Biochem. 1976;45:805–860. [PubMed]
  • Robb FT, Maeder DL, Brown JR, DiRuggiero J, Stump MD, Yeh RK, Weiss RB, Dunn DM. Genomic sequence of hyperthermophile, Pyrococcus furiosus: implications for physiology and enzymology. Methods Enzymol. 2001;330:134–157. [PubMed]
  • Romby P, Carbon P, Westhof E, Ehresmann C, Ebel JP, Ehresmann B, Giegé R. Importance of conserved residues for the conformation of the T-loop in tRNAs. J Biomol Struct Dyn. 1987 Dec;5(3):669–687. [PubMed]
  • Rudinger J, Blechschmidt B, Ribeiro S, Sprinzl M. Minimalist aminoacylated RNAs as efficient substrates for elongation factor Tu. Biochemistry. 1994 May 17;33(19):5682–5688. [PubMed]
  • Rudinger J, Hillenbrandt R, Sprinzl M, Giegé R. Antideterminants present in minihelix(Sec) hinder its recognition by prokaryotic elongation factor Tu. EMBO J. 1996 Feb 1;15(3):650–657. [PMC free article] [PubMed]
  • Ruepp A, Graml W, Santos-Martinez ML, Koretke KK, Volker C, Mewes HW, Frishman D, Stocker S, Lupas AN, Baumeister W. The genome sequence of the thermoacidophilic scavenger Thermoplasma acidophilum. Nature. 2000 Sep 28;407(6803):508–513. [PubMed]
  • Salanoubat M, Genin S, Artiguenave F, Gouzy J, Mangenot S, Arlat M, Billault A, Brottier P, Camus JC, Cattolico L, et al. Genome sequence of the plant pathogen Ralstonia solanacearum. Nature. 2002 Jan 31;415(6871):497–502. [PubMed]
  • Santos MA, Perreau VM, Tuite MF. Transfer RNA structural change is a key element in the reassignment of the CUG codon in Candida albicans. EMBO J. 1996 Sep 16;15(18):5060–5068. [PMC free article] [PubMed]
  • Santos MA, Ueda T, Watanabe K, Tuite MF. The non-standard genetic code of Candida spp.: an evolving genetic code or a novel mechanism for adaptation? Mol Microbiol. 1997 Nov;26(3):423–431. [PubMed]
  • Schneider A, Maréchal-Drouard L. Mitochondrial tRNA import: are there distinct mechanisms? Trends Cell Biol. 2000 Dec;10(12):509–513. [PubMed]
  • Schultz DW, Yarus M. tRNA structure and ribosomal function. II. Interaction between anticodon helix and other tRNA mutations. J Mol Biol. 1994 Feb 4;235(5):1395–1405. [PubMed]
  • Schürer H, Schiffer S, Marchfelder A, Mörl M. This is the end: processing, editing and repair at the tRNA 3'-terminus. Biol Chem. 2001 Aug;382(8):1147–1156. [PubMed]
  • Seoighe C, Wolfe KH. Updated map of duplicated regions in the yeast genome. Gene. 1999 Sep 30;238(1):253–261. [PubMed]
  • Sharp PM, Li WH. The codon Adaptation Index--a measure of directional synonymous codon usage bias, and its potential applications. Nucleic Acids Res. 1987 Feb 11;15(3):1281–1295. [PMC free article] [PubMed]
  • She Q, Singh RK, Confalonieri F, Zivanovic Y, Allard G, Awayez MJ, Chan-Weiher CC, Clausen IG, Curtis BA, De Moors A, et al. The complete genome of the crenarchaeon Sulfolobus solfataricus P2. Proc Natl Acad Sci U S A. 2001 Jul 3;98(14):7835–7840. [PMC free article] [PubMed]
  • Shigenobu S, Watanabe H, Hattori M, Sakaki Y, Ishikawa H. Genome sequence of the endocellular bacterial symbiont of aphids Buchnera sp. APS. Nature. 2000 Sep 7;407(6800):81–86. [PubMed]
  • Simpson AJ, Reinach FC, Arruda P, Abreu FA, Acencio M, Alvarenga R, Alves LM, Araya JE, Baia GS, Baptista CS, et al. The genome sequence of the plant pathogen Xylella fastidiosa. The Xylella fastidiosa Consortium of the Organization for Nucleotide Sequencing and Analysis. Nature. 2000 Jul 13;406(6792):151–159. [PubMed]
  • Slesarev Alexei I, Mezhevaya Katja V, Makarova Kira S, Polushin Nikolai N, Shcherbinina Olga V, Shakhova Vera V, Belova Galina I, Aravind L, Natale Darren A, Rogozin Igor B, et al. The complete genome of hyperthermophile Methanopyrus kandleri AV19 and monophyly of archaeal methanogens. Proc Natl Acad Sci U S A. 2002 Apr 2;99(7):4644–4649. [PMC free article] [PubMed]
  • Smith D, Yarus M. Transfer RNA structure and coding specificity. II. A D-arm tertiary interaction that restricts coding range. J Mol Biol. 1989 Apr 5;206(3):503–511. [PubMed]
  • Smith DR, Doucette-Stamm LA, Deloughery C, Lee H, Dubois J, Aldredge T, Bashirzadeh R, Blakely D, Cook R, Gilbert K, et al. Complete genome sequence of Methanobacterium thermoautotrophicum deltaH: functional analysis and comparative genomics. J Bacteriol. 1997 Nov;179(22):7135–7155. [PMC free article] [PubMed]
  • Soma A, Uchiyama K, Sakamoto T, Maeda M, Himeno H. Unique recognition style of tRNA(Leu) by Haloferax volcanii leucyl-tRNA synthetase. J Mol Biol. 1999 Nov 12;293(5):1029–1038. [PubMed]
  • Souciet J, Aigle M, Artiguenave F, Blandin G, Bolotin-Fukuhara M, Bon E, Brottier P, Casaregola S, de Montigny J, Dujon B, et al. Genomic exploration of the hemiascomycetous yeasts: 1. A set of yeast species for molecular evolution studies. FEBS Lett. 2000 Dec 22;487(1):3–12. [PubMed]
  • Sprinzl M, Horn C, Brown M, Ioudovitch A, Steinberg S. Compilation of tRNA sequences and sequences of tRNA genes. Nucleic Acids Res. 1998 Jan 1;26(1):148–153. [PMC free article] [PubMed]
  • Srinivasan Gayathri, James Carey M, Krzycki Joseph A. Pyrrolysine encoded by UAG in Archaea: charging of a UAG-decoding specialized tRNA. Science. 2002 May 24;296(5572):1459–1462. [PubMed]
  • Steinberg S, Ioudovitch A. A role for the bulged nucleotide 47 in the facilitation of tertiary interactions in the tRNA structure. RNA. 1996 Jan;2(1):84–87. [PMC free article] [PubMed]
  • Stephens RS, Kalman S, Lammel C, Fan J, Marathe R, Aravind L, Mitchell W, Olinger L, Tatusov RL, Zhao Q, et al. Genome sequence of an obligate intracellular pathogen of humans: Chlamydia trachomatis. Science. 1998 Oct 23;282(5389):754–759. [PubMed]
  • Sterner T, Jansen M, Hou YM. Structural and functional accommodation of nucleotide variations at a conserved tRNA tertiary base pair. RNA. 1995 Oct;1(8):841–851. [PMC free article] [PubMed]
  • Stewart TS, Roberts RJ, Strominger JL. Novel species of tRNA. Nature. 1971 Mar 5;230(5288):36–38. [PubMed]
  • Stover CK, Pham XQ, Erwin AL, Mizoguchi SD, Warrener P, Hickey MJ, Brinkman FS, Hufnagle WO, Kowalik DJ, Lagrou M, et al. Complete genome sequence of Pseudomonas aeruginosa PAO1, an opportunistic pathogen. Nature. 2000 Aug 31;406(6799):959–964. [PubMed]
  • Sundararajan A, Michaud WA, Qian Q, Stahl G, Farabaugh PJ. Near-cognate peptidyl-tRNAs promote +1 programmed translational frameshifting in yeast. Mol Cell. 1999 Dec;4(6):1005–1015. [PubMed]
  • Suzuki T, Ueda T, Watanabe K. The 'polysemous' codon--a codon with multiple amino acid assignment caused by dual specificity of tRNA identity. EMBO J. 1997 Mar 3;16(5):1122–1134. [PMC free article] [PubMed]
  • Szweykowska-Kulinska Z, Senger B, Keith G, Fasiolo F, Grosjean H. Intron-dependent formation of pseudouridines in the anticodon of Saccharomyces cerevisiae minor tRNA(Ile). EMBO J. 1994 Oct 3;13(19):4636–4644. [PMC free article] [PubMed]
  • Takami H, Nakasone K, Takaki Y, Maeno G, Sasaki R, Masui N, Fuji F, Hirama C, Nakamura Y, Ogasawara N, et al. Complete genome sequence of the alkaliphilic bacterium Bacillus halodurans and genomic sequence comparison with Bacillus subtilis. Nucleic Acids Res. 2000 Nov 1;28(21):4317–4331. [PMC free article] [PubMed]
  • Tang Thean Hock, Rozhdestvensky Timofey S, d'Orval Béatrice Clouet, Bortolin Marie-Line, Huber Harald, Charpentier Bruno, Branlant Christiane, Bachellerie Jean-Pierre, Brosius Jürgen, Hüttenhofer Alexander. RNomics in Archaea reveals a further link between splicing of archaeal introns and rRNA processing. Nucleic Acids Res. 2002 Feb 15;30(4):921–930. [PMC free article] [PubMed]
  • Tettelin H, Saunders NJ, Heidelberg J, Jeffries AC, Nelson KE, Eisen JA, Ketchum KA, Hood DW, Peden JF, Dodson RJ, et al. Complete genome sequence of Neisseria meningitidis serogroup B strain MC58. Science. 2000 Mar 10;287(5459):1809–1815. [PubMed]
  • Tomb JF, White O, Kerlavage AR, Clayton RA, Sutton GG, Fleischmann RD, Ketchum KA, Klenk HP, Gill S, Dougherty BA, et al. The complete genome sequence of the gastric pathogen Helicobacter pylori. Nature. 1997 Aug 7;388(6642):539–547. [PubMed]
  • Tomita K, Weiner AM. Collaboration between CC- and A-adding enzymes to build and repair the 3'-terminal CCA of tRNA in Aquifex aeolicus. Science. 2001 Nov 9;294(5545):1334–1336. [PubMed]
  • Trotta CR, Miao F, Arn EA, Stevens SW, Ho CK, Rauhut R, Abelson JN. The yeast tRNA splicing endonuclease: a tetrameric enzyme with two active site subunits homologous to the archaeal tRNA endonucleases. Cell. 1997 Jun 13;89(6):849–858. [PubMed]
  • Tuohy TM, Li Z, Atkins JF, Deutscher MP. A functional mutant of tRNA(2Arg) with ten extra nucleotides in its TFC arm. J Mol Biol. 1994 Feb 4;235(5):1369–1376. [PubMed]
  • Ushida C, Muramatsu T, Mizushima H, Ueda T, Watanabe K, Stetter KO, Crain PF, McCloskey JA, Kuchino Y. Structural feature of the initiator tRNA gene from Pyrodictium occultum and the thermal stability of its gene product, tRNA(imet). Biochimie. 1996;78(10):847–855. [PubMed]
  • Valenzuela P, Venegas A, Weinberg F, Bishop R, Rutter WJ. Structure of yeast phenylalanine-tRNA genes: an intervening DNA segment within the region coding for the tRNA. Proc Natl Acad Sci U S A. 1978 Jan;75(1):190–194. [PMC free article] [PubMed]
  • Watanabe Yoh-ichi, Yokobori Shin-ichi, Inaba Toshiro, Yamagishi Akihiko, Oshima Tairo, Kawarabayasi Yutaka, Kikuchi Hisasi, Kita Kiyoshi. Introns in protein-coding genes in Archaea. FEBS Lett. 2002 Jan 2;510(1-2):27–30. [PubMed]
  • Weiss GB. Translational control of protein synthesis by tRNA unrelated to changes in tRNA concentration. J Mol Evol. 1973;2(2-3):199–204. [PubMed]
  • White O, Eisen JA, Heidelberg JF, Hickey EK, Peterson JD, Dodson RJ, Haft DH, Gwinn ML, Nelson WC, Richardson DL, et al. Genome sequence of the radioresistant bacterium Deinococcus radiodurans R1. Science. 1999 Nov 19;286(5444):1571–1577. [PMC free article] [PubMed]
  • Williams Kelly P. The tmRNA Website: invasion by an intron. Nucleic Acids Res. 2002 Jan 1;30(1):179–182. [PMC free article] [PubMed]
  • Woese CR, Kandler O, Wheelis ML. Towards a natural system of organisms: proposal for the domains Archaea, Bacteria, and Eucarya. Proc Natl Acad Sci U S A. 1990 Jun;87(12):4576–4579. [PMC free article] [PubMed]
  • Wood V, Gwilliam R, Rajandream M-A, Lyne M, Lyne R, Stewart A, Sgouros J, Peat N, Hayles J, Baker S, et al. The genome sequence of Schizosaccharomyces pombe. Nature. 2002 Feb 21;415(6874):871–880. [PubMed]
  • Yokobori S, Suzuki T, Watanabe K. Genetic code variations in mitochondria: tRNA as a major determinant of genetic code plasticity. J Mol Evol. 2001 Oct-Nov;53(4-5):314–326. [PubMed]
  • Yokogawa T, Suzuki T, Ueda T, Mori M, Ohama T, Kuchino Y, Yoshinari S, Motoki I, Nishikawa K, Osawa S, et al. Serine tRNA complementary to the nonuniversal serine codon CUG in Candida cylindracea: evolutionary implications. Proc Natl Acad Sci U S A. 1992 Aug 15;89(16):7408–7411. [PMC free article] [PubMed]

Articles from RNA are provided here courtesy of The RNA Society

Formats:

Related citations in PubMed

See reviews...See all...

Cited by other articles in PMC

See all...

Links

Recent Activity

Your browsing activity is empty.

Activity recording is turned off.

Turn recording back on

See more...