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Nucleic Acids Research Pages 148-153  

Compilation of tRNA sequences and sequences of tRNA genes
Introduction
Results
   Presentation of sequences
   Numbering and alignment of the variable region
   Alignment of animal mitochondrial tRNAs
Acknowledgement
References

Compilation of tRNA sequences and sequences of tRNA genes

Compilation of tRNA sequences and sequences of tRNA genes

Mathias Sprinzl*, Carsten Horn, Melissa Brown, Anatoli Ioudovitch1, Sergey Steinberg1

Laboratorium für Biochemie, Universität Bayreuth, 95440 Bayreuth, Germany and 1Université de Montréal, Faculté de Médicine, Départment de Biochimie, C.P. 6128, Succursale Centre-Ville, Montréal, Québec H3C 3J7, Canada

Received September 16, 1997; Revised and Accepted October 6, 1997

ABSTRACT

Sequences of 3279 sequences of tRNA genes and tRNAs published up to December 1996 are included in the compilation. Alignment of the sequences, which is most compatible with the tRNA phylogeny and known three-dimensional structures of tRNA, is used. Sequences and references are available under http://www.uni-bayreuth.de/departments/biochemie/trna/

INTRODUCTION

The 1997 compilation contains 3279 sequences of tRNAs and tRNA genes. The last edition which appeared two years ago (1) was supplemented by 579 new sequences covering the literature up to December 1995. The sequences of tRNA mutants and of tRNAs originating from transformed or differentiated cells were not considered.

The tRNAs included in the compilation are listed in Table 1. Each tRNA or tRNA gene is specified by the (abbreviated) name of the organism from which it was isolated and a four digit code: the first three digits identify the organism, the last digit specifies the particular isoacceptor. The amino acid specificity of the tRNA is indicated by a one-letter amino acid code. The tRNAs coding for selenocysteine were annotated with the letter Z. Initiator tRNAs are annotated with the letter X.


The references are restricted to the first publication of the complete sequence unless additional information (e.g., base modification, corrections, etc.) was later obtained. In such cases additional references were added.

In order to facilitate a computer analysis an alignment is used which is most compatible with the tRNA phylogeny and known three-dimensional structures of tRNA. The corresponding numbering system is shown in Figure 1.


Figure 1 Numbering of nucleotides in tRNAs. Circles represent nucleotides which are always present; the ovals, nucleotides which are not present in each structure: these are nucleotides before the position 1 on the 5[prime]-end, before and after the two invariant GMP residues 18 and 19 in the D-loop, and the nucleotides in the variable loop. The nucleotide to be added at a given site is indicated by the number of the preceeding nucleotide followed by a colon and a letter in alphabetical order. The nucleotides in the variable stem have the prefix `e' and are located between position 45 and 46 obeying the base-pairing rules. The nucleotides in the 5[prime]-strand and the 3[prime]-strand are numbered by e11, e12, e13, ... and e21, e22, e23, ..., respectively; the second digit identifies the base-pair. In the case of a long variable region, the loop can be formed by up to 5 nt: e1, e2, e3, e4 and e5. Positions, in which invariant nucleotides usually occur are indicated by a thick line.


Table 1. List of tRNA sequences and sequences of tRNA genes included in the compilation

As was the case in the previous edition (1), this publication does not contain a sequence printout. Instead, the sequences, references and footnotes of tRNAs and tRNA genes listed in Table 1 are deposited in the European Bioinformatics Institute (EBI) Data Library. In addition, a World Wide Web page has been established and is available under http://www.uni-bayreuth.de/departments/biochemie/trna/ . The present publication should be quoted as a reference for the electronically accessible data.

Researchers who wish to perform an advanced search for tRNA sequences according to several criteria, e.g., anticodon, amino acid specificity, modified nucleoside, or wish to print the requested sequence in the form of Table 2 or cloverleaf format (Fig. 1) can obtain appropriate software on diskette. Please contact M. Sprinzl, Laboratorium für Biochemie, Universität Bayreuth, D-95440 Bayreuth, Germany, Fax: +49 921 552432, Email: Mathias.Sprinzl@uni-bayreuth.de.


Table 2. Format of tRNA sequences in the databank

RESULTS

Presentation of sequences

The sequences in the database are divided into three parts. The first two parts contain the sequences of the tRNA genes and tRNAs, respectively, which can be fitted into the canonical tRNA alignment. The third part lists tRNA and tRNA gene sequences, mainly of animal mitochondria, whose secondary structures differ from most tRNAs and could not be aligned according to Figure 1.

An example for sequence presentation in the database is given in Table 2. Each sequence in the compilation occupies two consecutive lines. The first line begins with the letter `D' or `R' and contains the six-position identification code of the sequence (`D' or `R' for DNA or RNA, respectively; a one-letter code for the amino acid, X for methionine-initiator, Z for selenocysteine; and the four-digit code specifying the organism and isoacceptor. After this, the sequence of the anticodon (in the case of tRNA sequences in its modified form) is given, followed by the name and the kingdom of organism (Table 1), and the sequence (99 standard positions). The second line begins with the sign `+' and contains the information about base-pairing (double helical regions only, tertiary interactions are not annotated). All other lines in the compilation begin with signs other than `D,' `R' or `+' (usually `*') and contain comments.

Nucleotides involved in Watson-Crick pairs are marked with `=', the GU pairs are indicated with the sign `*'. Nucleotides 26 and 44 are considered to form a base-pair included in the anticodon stem (Fig. 1).

The sequences in orginal publications denoted as `yeast' are assigned to Saccharomyces cerevisiae. The user should be aware, however, that some of these organisms have possibly been misclassified and that the original literature should be consulted.

This compilation uses a one-letter code for all nucleotides including modified ones. For standard nucleotides, adenosine, cytidine, guanosine, thymidine and uridine the usual abbreviations, A, C, G, T and U, respectively, are used. To designate modified nucleotides, the other ASCII signs are employed as defined in Table 3. Terminology and structure of the modified nucleosides occurring in tRNAs were used according to refs 2 and 3. Positions in particular sequence which are not filled (gaps in the generalised structure, Fig. 1) are indicated by a dash. All nucleotide insertions are denoted by underlining at the place of insertion.


Table 3. Modified nucleosides in tRNA and their abbreviations

Numbering and alignment of the variable region

The alignment of the variable region has been done in accordance with Steinberg and Kisselev (4). The extra arm is placed between nucleotides 45 and 46. It includes two double helical strands forming a stem and a loop. The annotations of the nucleotides in the extra arm positions begin with the letter `e' (extra) followed by a one- or two-digit number. We have reserved a space for 7 bp in the stem and 5 nt in the loop. The nucleotides in the loop are numbered from 1 to 5, whereas the nucleotides in the stem are numbered from 11 to 17 (5[prime]-branch) and from 27 to 21, in the reverse order, (3[prime]-branch), to indicate base-pair formation between nucleotides 11-21, 12-22, etc. (Fig. 1). In the tRNAs where the extra arm position 45 is empty but where the nucleotides 46-48 between the extra arm and T-domain are present, the positions will be filled in the order 48, 46, 47, i.e., tRNAs use position 48, 46 and 47 for the first, second and third nucleotide, respectively, depending on the length of the sequence in this region. A similar situation occurs in tRNAs without a long extra arm, where the most variable position 47 is deleted in many sequences.

Alignment of animal mitochondrial tRNAs

In properly aligned tRNA sequences, nucleotides occupying the same position in different tRNA sequences should play a comparable structural or functional role. Most animal mitochondrial tRNAs cannot be easily aligned with other tRNAs mainly because of the absence of information on their three-dimensional structure. Experimental data, however, point to the existence of tertiary interactions in these tRNAs. In this compilation, we use an alignment which accounts for these interactions as much as possible. Where we could do so, the animal mitochondrial tRNAs were included in Parts I and II. The alignment of animal mitochondrial tRNA is, however, not yet unambiguous.

Some animal mitochondrial tRNAs have completely unusual secondary structure and cannot be fitted in the tRNA alignment used here (Parts I and II). We treated these sequences separately including them into Part III. Here, each particular sequence has its own alignment. To this group belong the tRNAs from: (i) mitochondria of a parasitic worm lacking the T- or D-domain, (ii) mitochondria of mollusks, insects and echinoderm, with extended anticodon and T-stems and (iii) mammalian mitochondria, lacking the D-domain.

For some tRNA genes the secondary structure pattern cannot be clearly established. We have also included these sequences in Part III. It is possible that posttranscriptional modifications of these tRNAs will result in improvement of the secondary structure.

ACKNOWLEDGEMENT

This project was supported by Fonds der Chemischen Industrie, Deutsche Forschungsgemeinschaft, Project Sp 243/5-1.

REFERENCES

1. Sprinzl,M., Steegborn,S., Hübel,F. and Steinberg,S. (1996) Nucleic Acids Res., 24, 68-72. MEDLINE Abstract

2. Limbach,P.A., Crain,P.F. and McCloskey,J.A. (1994) Nucleic Acids Res., 22, 2183-2196. MEDLINE Abstract

3. Crain,P.F. and McCloskey,J.A. (1997) Nucleic Acids Res., 25, 126-127. [See also this issue Nucleic Acids Res. (1998) 26, 196-197.].

4. Steinberg,S.V. and Kisselev,L.L. (1992) Biochimie, 74, 337-351. MEDLINE Abstract

*To whom correspondence should be addressed. Tel: +49 921 552 420; Fax: +49 921 552 432; Email: mathias.sprinzl@uni-bayreuth.de

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Copyright© Oxford University Press, 1998.

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Depletion of Saccharomyces cerevisiae tRNAHis Guanylyltransferase Thg1p Leads to Uncharged tRNAHis with Additional m5C
Mol. Cell. Biol., September 15, 2005; 25(18): 8191 - 8201.
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Y. DING, C. Y. CHAN, and C. E. LAWRENCE
RNA secondary structure prediction by centroids in a Boltzmann weighted ensemble
RNA, August 1, 2005; 11(8): 1157 - 1166.
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M.-H. RENALIER, N. JOSEPH, C. GASPIN, P. THEBAULT, and A. MOUGIN
The Cm56 tRNA modification in archaea is catalyzed either by a specific 2'-O-methylase, or a C/D sRNP
RNA, July 1, 2005; 11(7): 1051 - 1063.
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R. KACHOURI, V. STRIBINSKIS, Y. ZHU, K. S. RAMOS, E. WESTHOF, and Y. LI
A surprisingly large RNase P RNA in Candida glabrata
RNA, July 1, 2005; 11(7): 1064 - 1072.
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 Cancer Res.Home page
T. Kato, Y. Daigo, S. Hayama, N. Ishikawa, T. Yamabuki, T. Ito, M. Miyamoto, S. Kondo, and Y. Nakamura
A Novel Human tRNA-Dihydrouridine Synthase Involved in Pulmonary Carcinogenesis
Cancer Res., July 1, 2005; 65(13): 5638 - 5646.
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 Nucleic Acids ResHome page
J. H. Havgaard, R. B. Lyngso, and J. Gorodkin
The FOLDALIGN web server for pairwise structural RNA alignment and mutual motif search
Nucleic Acids Res., July 1, 2005; 33(suppl_2): W650 - W653.
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 Nucleic Acids ResHome page
R. Hao, M.-W. Zhao, Z.-X. Hao, Y.-N. Yao, and E.-D. Wang
A T-stem slip in human mitochondrial tRNALeu(CUN) governs its charging capacity
Nucleic Acids Res., June 22, 2005; 33(11): 3606 - 3613.
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S. FRANCISCI, C. DE LUCA, R. OLIVA, V. MOREA, A. TRAMONTANO, and L. FRONTALI
Aminoacylation and conformational properties of yeast mitochondrial tRNA mutants with respiratory deficiency
RNA, June 1, 2005; 11(6): 914 - 927.
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S. K. Purushothaman, J. M. Bujnicki, H. Grosjean, and B. Lapeyre
Trm11p and Trm112p Are both Required for the Formation of 2-Methylguanosine at Position 10 in Yeast tRNA
Mol. Cell. Biol., June 1, 2005; 25(11): 4359 - 4370.
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 Nucleic Acids ResHome page
S. L. Hiley, T. Babak, and T. R. Hughes
Global analysis of yeast RNA processing identifies new targets of RNase III and uncovers a link between tRNA 5' end processing and tRNA splicing
Nucleic Acids Res., May 26, 2005; 33(9): 3048 - 3056.
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J. R. Patton, Y. Bykhovskaya, E. Mengesha, C. Bertolotto, and N. Fischel-Ghodsian
Mitochondrial Myopathy and Sideroblastic Anemia (MLASA): MISSENSE MUTATION IN THE PSEUDOURIDINE SYNTHASE 1 (PUS1) GENE IS ASSOCIATED WITH THE LOSS OF tRNA PSEUDOURIDYLATION
J. Biol. Chem., May 20, 2005; 280(20): 19823 - 19828.
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 BioinformaticsHome page
D. H. Mathews
Predicting a set of minimal free energy RNA secondary structures common to two sequences
Bioinformatics, May 15, 2005; 21(10): 2246 - 2253.
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P. CLOTE, F. FERRE, E. KRANAKIS, and D. KRIZANC
Structural RNA has lower folding energy than random RNA of the same dinucleotide frequency
RNA, May 1, 2005; 11(5): 578 - 591.
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R. LEIPUVIENE and G. R. BJORK
A reduced level of charged tRNAArgmnm5UCU triggers the wild-type peptidyl-tRNA to frameshift
RNA, May 1, 2005; 11(5): 796 - 807.
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A. ALEXANDROV, E. J. GRAYHACK, and E. M. PHIZICKY
tRNA m7G methyltransferase Trm8p/Trm82p: Evidence linking activity to a growth phenotype and implicating Trm82p in maintaining levels of active Trm8p
RNA, May 1, 2005; 11(5): 821 - 830.
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J. H. Havgaard, R. B. Lyngso, G. D. Stormo, and J. Gorodkin
Pairwise local structural alignment of RNA sequences with sequence similarity less than 40%
Bioinformatics, May 1, 2005; 21(9): 1815 - 1824.
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M. Kuratani, R. Ishii, Y. Bessho, R. Fukunaga, T. Sengoku, M. Shirouzu, S.-i. Sekine, and S. Yokoyama
Crystal Structure of tRNA Adenosine Deaminase (TadA) from Aquifex aeolicus
J. Biol. Chem., April 22, 2005; 280(16): 16002 - 16008.
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 Nucleic Acids ResHome page
E. Kikovska, M. Brannvall, J. Kufel, and L. A. Kirsebom
Substrate discrimination in RNase P RNA-mediated cleavage: importance of the structural environment of the RNase P cleavage site
Nucleic Acids Res., April 7, 2005; 33(6): 2012 - 2021.
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B. HUANG, M. J.O. JOHANSSON, and A. S. BYSTROM
An early step in wobble uridine tRNA modification requires the Elongator complex
RNA, April 1, 2005; 11(4): 424 - 436.
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M. Sakurai, T. Ohtsuki, and K. Watanabe
Modification at position 9 with 1-methyladenosine is crucial for structure and function of nematode mitochondrial tRNAs lacking the entire T-arm
Nucleic Acids Res., March 21, 2005; 33(5): 1653 - 1661.
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M. D. ROY, L. M. WITTENHAGEN, and S. O. KELLEY
Structural probing of a pathogenic tRNA dimer
RNA, March 1, 2005; 11(3): 254 - 260.
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A. T. Das, M. Vink, and B. Berkhout
Alternative tRNA Priming of Human Immunodeficiency Virus Type 1 Reverse Transcription Explains Sequence Variation in the Primer-Binding Site That Has Been Attributed to APOBEC3G Activity
J. Virol., March 1, 2005; 79(5): 3179 - 3181.
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S. L. Hiley, J. Jackman, T. Babak, M. Trochesset, Q. D. Morris, E. Phizicky, and T. R. Hughes
Detection and discovery of RNA modifications using microarrays
Nucleic Acids Res., January 7, 2005; 33(1): e2 - e2.
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B. Mallick, J. Chakrabarti, S. Sahoo, Z. Ghosh, and S. Das
Identity Elements of Archaeal tRNA.
DNA Res, January 1, 2005; 12(4): 235 - 246.
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K. C. Pang, S. Stephen, P. G. Engstrom, K. Tajul-Arifin, W. Chen, C. Wahlestedt, B. Lenhard, Y. Hayashizaki, and J. S. Mattick
RNAdb--a comprehensive mammalian noncoding RNA database
Nucleic Acids Res., January 1, 2005; 33(suppl_1): D125 - D130.
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M. Sprinzl and K. S. Vassilenko
Compilation of tRNA sequences and sequences of tRNA genes
Nucleic Acids Res., January 1, 2005; 33(suppl_1): D139 - D140.
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I. Behm-Ansmant, H. Grosjean, S. Massenet, Y. Motorin, and C. Branlant
Pseudouridylation at Position 32 of Mitochondrial and Cytoplasmic tRNAs Requires Two Distinct Enzymes in Saccharomyces cerevisiae
J. Biol. Chem., December 17, 2004; 279(51): 52998 - 53006.
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D. Korencic, C. Polycarpo, I. Weygand-Durasevic, and D. Soll
Differential Modes of Transfer RNASer Recognition in Methanosarcina barkeri
J. Biol. Chem., November 19, 2004; 279(47): 48780 - 48786.
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F. H. Wilson, A. Hariri, A. Farhi, H. Zhao, K. F. Petersen, H. R. Toka, C. Nelson-Williams, K. M. Raja, M. Kashgarian, G. I. Shulman, et al.
A Cluster of Metabolic Defects Caused by Mutation in a Mitochondrial tRNA
Science, November 12, 2004; 306(5699): 1190 - 1194.
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R. KNIGHT, A. BIRMINGHAM, and M. YARUS
BayesFold: Rational 2{degrees} folds that combine thermodynamic, covariation, and chemical data for aligned RNA sequences
RNA, September 1, 2004; 10(9): 1323 - 1336.
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J. Armengaud, J. Urbonavicius, B. Fernandez, G. Chaussinand, J. M. Bujnicki, and H. Grosjean
N2-Methylation of Guanosine at Position 10 in tRNA Is Catalyzed by a THUMP Domain-containing, S-Adenosylmethionine-dependent Methyltransferase, Conserved in Archaea and Eukaryota
J. Biol. Chem., August 27, 2004; 279(35): 37142 - 37152.
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L. Randau, S. Schauer, A. Ambrogelly, J. C. Salazar, J. Moser, S.-i. Sekine, S. Yokoyama, D. Soll, and D. Jahn
tRNA Recognition by Glutamyl-tRNA Reductase
J. Biol. Chem., August 13, 2004; 279(33): 34931 - 34937.
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D. H. MATHEWS
Using an RNA secondary structure partition function to determine confidence in base pairs predicted by free energy minimization
RNA, August 1, 2004; 10(8): 1178 - 1190.
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