Nucleic Acids Research

tRNA molecules active in higher plant mitochondria are encoded by: (i) `genuine' or `native' mitochondrial genes derived from the original endosymbiont genome; (ii) `chloroplast-like' genes present on chloroplast DNA regions which are thought to have been inserted in the mitochondrial genomes during their evolution; (iii) nuclear genes, in the case of imported tRNAs. In no case has redundancy of functional tRNAs of different genetic origin been observed (1).

In a previous compilation of higher plant mitochondrial tRNA genes (2) we reported 115 sequences in two different lists. The first contained complete gene sequences, the latter contained truncated or pseudo genes. In each list, the genes were further classified in the two classes `genuine' and `chloroplast-like'.

This compilation contains 158 sequences. The increase is due both to the availability of the complete Arabidopsis thaliana mitochondrial genome sequence (3) and also to the different approach used for sequence retrieval. While the first compilation was essentially based on analysis of the literature data, this compilation has been obtained by analysing nucleotide sequence databases with the FastA program (4). The program allows a reliable identification for any given sequence of the most similar sequences in the databases. tRNA genes reported in Tables 1 and 2 of the first compilation were used as query sequences. The analysis was performed directly at the European Bioinformatics Institute (EBI) World Wide Web server by means of the `Similarity Searches' service (http://www.ebi.ac.uk/services/services.html ). It was carried out against the whole EMBL Database in July 1997.

In this way several improvements have been obtained with respect to the previous compilation: (i) an increase in the number of sequences (eight more plants appear in the compilation); (ii) the cross-checking of the alignments among the genes; (iii) the identification of sequences containing tRNA genes not previously identified or searched for.

The sequence alignments for either the complete and truncated genes have been deposited as two separated lists (Lists 1 and 2) in the database `PLMItRNA' at the European Bioinformatics Institute (EBI) Data Library. Information on how to obtain the compilation can be requested by electronic mail at the netserv@ebi.ac.uk address, by sending the command `help PLMItRNA'. The compilation is also available via anonymous FTP from ftp.ebi.ac.uk in the directory pub/databases/PLMItRNA or from the EBI WWW server via the `EBI Databases' service (http://www.ebi.ac.uk/service ). A diskette version is also available from the authors.

DESCRIPTION OF THE COMPILATION AND DISCUSSION

Sequences of tRNA genes have been reported in the same way used in the previous collection (2): List 1 contains sequences of complete genes, List 2 contains sequences of truncated or pseudo genes. In each list the genes have been further classified as `genuine' or `chloroplast-like' and their sequences subdivided into the classical tRNA domains. Nucleotide positions have been numbered from 0 to 76. Positions of nucleotides which are not always present (0, 17, 17a, 20a, 20b, the nucleotides of the extra-loop, 47 and 74-76) are indicated by dashes. The genes are indicated by capital letters corresponding to the one letter code of the charged amino acid. Anticodons have been reported in small letters. Initials of the Latin name indicate the plant species: A.t., Arabidopsis thaliana (thale cress); B.v., Beta vulgaris (sugar beet); B.n., Brassica napus (rapeseed); B.o., Brassica oleracea (cauliflower); G.m., Glycine max (soybean); H.a., Helianthus annuus (sunflower); L.l., Lupinus luteus (lupine); L.e., Lycopersicon esculentum (tomato); O.b., Oenothera berteriana (primrose); P.h., Petunia hybrida (petunia); P.v., Phaseolus vulgaris (bean); P.s., Pisum sativum (pea); R.s., Raphanus sativus (horseradish); S.t., Solanum tuberosum (potato) for the dicotyledons, and L.m.. Lolium multiflorum (Italian ryegrass); Lo.e., Lophopyrum elongatum (tall wheatgrass); O.s., Oryza sativa (rice); S.b., Sorghum bicolor (sorghum); S.c., Secale cereale (rye); S.v., Sorghum vulgare (sorghum); T.a., Triticum aestivum (wheat); Z.m., Zea mays (maize) for the monocotyledons. La.l., Larix leptoeuropaea (larch) for the sole gymnosperm. The reference for each sequence is reported, when possible, as its DDBJ/EMBL/GenBank Database accession number.

Since in angiosperms a different distribution of genuine and chloroplast-like genes is observed between monocotyledonous and dicotyledonous plants, sequences belonging to dicotyledons are reported separately from those of monocotyledons. For each gene a `d' or `m' symbol indicates the first of the dicots or monocots respectively. A `g' indicates the sole gymnosperm in the case of the genuine trnH gene.

When redundancy of sequences is found, only the accession number of the longest sequence is reported, while shorter sequences are mentioned in brackets in the footnotes.

A + or - sign in List 1 indicates the result of transcription analysis when available.

Discrepancies between database sequences and literature data reported in the previous compilation are no longer reported.

In the course of this survey several points of interest for further studies and discussion on the organization of tRNA genes in higher plant mitochondria emerged.

The FastA analysis allowed the identification of complete or truncated tRNA genes which were not identified in the original sequences. These genes have been reported in Table 1 together with the accession numbers of the original sequences and the coordinates of their position. These results increase even more the number of the truncated genes, which appear to be particularly diffuse in higher plant mitochondrial genomes. They might be a consequence of the numerous rearrangements which occurred during the evolution of these complex genomes.

Table 1. tRNA genes not identified in the original sequences.

Complete genes
Genuine
trnF(gaa)	P.sativum	X14409: 124-196
Chloroplast-like
trnC(gca)	Z. mays	M74160: 2030-2100
trnH(gtg)	L.multiflorum	D28336: 421-495
trnV(gac)	H.annuus	X82386: 3226-3297a
Truncated genes
Genuine
trnI(cat)	A.thaliana	Y08502: 144 612-144 639
trnfM(cat)	A.thaliana	Y08501: 93 352-93 422a
trnfM(cat)	B.napus	S47089: 133-155
trnP(cgg)	A.thaliana	Y08502: 33 112-33 218
trnP(cgg)	B.napus	D13699: 3819-3924
trnP(cgg)	O.berteriana	X69555: 2576-2688
trnP(tgg)	P.sativum	X14409: 473-538
trnQ(ttg)	A.thaliana	Y08501: 184 527-184 575a
trnY(gta)	A.thaliana	Y08502: 62 130-62 210a
trnY(gta)	A.thaliana	Y08501: 191 953-192 025
trnY(gta)	A.thaliana	Y08501: 12 147-12 204
trnY(gta)	A.thaliana	Y08502: 133 650-133 731a
Chloroplast-like
trnM(cat)	B.napus	U10428: 1-42
trnR(acg)	Z.mays	M36716: 1773-1839
trnR(acg)	Z.mays	M12582: 2296-2364
trnR(acg)	Z.mays	X06667: 742-804

^aCoordinates allow the identification of the gene on the complementary strand.

Portions of an original genuine trnP-(cgg) gene have been revealed in the dicotyledonous A.thaliana, B.napus and O.berteriana (Table 1). This finding seems particularly interesting since tRNA-Pro(cgg) molecules or trnP-(cgg) genes have never been described in mitochondria of any eukaryotes. It is not possible from the data currently available to ascertain whether the presumable trnP-(cgg) genes might have coded for functional tRNA-Pro(cgg) molecules or for post-transcriptional edited tRNA-Pro(ugg) molecules. Editing in the anticodon sequence has never been described in plant mitochondria, but has been reported for marsupial mitochondria (5).

Several modifications in the anticodon sequence of the genuine pseudo trnF genes reported in List 2 have been described that would change the tRNA specificity. Anyway these sequences have not been reported as different genes owing to the few differences that they show with respect to the original trnF gene. On the contrary four trnY sequences can be detected in the A.thaliana mitochondial genome (cfr. the A.thaliana trnY genes in List 2 and related notes) which, even if they are thought to derive from an original trnF gene, show relevant modifications in the acceptor stem sequences.

The FastA analysis was carried out against the whole EMBL Database Library. It is worthwhile to note that not all the sequences reported in the compilation can be found in the EMBL `Organelle Library'. Some sequences obtained in the course of the development of sequencing projects for the A.thaliana genome correspond in fact to mitochondrial sequences. The A.thaliana genomic sequence B08367 is almost identical to a region of the A.thaliana mitochondrial sequence Y08502 (27 392-28 142). It contains two tRNA genes: the genuine trnE gene (coordinates 306-377) and a pseudo trnY gene (coordinates 193-267). One A.thaliana EST (Expressed Sequence Tag) sequence, Z17763, the function of which was not previously described, contains part of the genuine mitochondrial trnS(gct) gene and 270 nt of its 5[prime] flanking region. This gene is present in double copy in the A.thaliana mitochondrial genome (3) with the two copies of the gene sharing a 5[prime] flanking region of 22 nt. These data indicate that at least one copy of the trnS gene is transcribed.

REFERENCES

2. Veronico,P., Gallerani,R. and Ceci,L.R. (1996) Nucleic Acids Res., 24, 2199-2203. MEDLINE Abstract

3. Unseld,M., Marienfeld,J.R., Brandt,P. and Brennicke,A. (1997) Nature Genet., 15, 57-61. MEDLINE Abstract

4. Pearson,W.R. and Lipman,D.J. (1988) Proc. Natl. Acad. Sci. USA, 85, 2444-2448. MEDLINE Abstract

5. Morl,M., Dorner,M. and Paabo,S. (1995) Nucleic Acids Res., 23, 3380-3384. MEDLINE Abstract

*To whom correspondence should be addressed. Tel: +39 80 544 3311; Fax: +39 80 544 3317; Email: luigi.ceci@area.ba.cnr.it

CiteULike

Connotea

Del.icio.us

This Article Abstract Print PDF (27K) Alert me when this article is cited Alert me if a correction is posted Services Email this article to a friend Similar articles in this journal Similar articles in ISI Web of Science Similar articles in PubMed Alert me to new issues of the journal Add to My Personal Archive Download to citation manager Search for citing articles in: ISI Web of Science (1) Request Permissions Commercial Re-use Guidelines for Open Access NAR Content Google Scholar Articles by Sagliano, A. Articles by Ceci, L. R. Search for Related Content PubMed PubMed Citation Articles by Sagliano, A. Articles by Ceci, L. R. Social Bookmarking          What's this?