Skip Navigation

This Article
Right arrow Abstract Freely available
Right arrow Print PDF (706K) Freely available
Right arrow Supplementary Material
Right arrow Alert me when this article is cited
Right arrow Alert me if a correction is posted
Services
Right arrow Email this article to a friend
Right arrow Similar articles in this journal
Right arrow Similar articles in ISI Web of Science
Right arrow Similar articles in PubMed
Right arrow Alert me to new issues of the journal
Right arrow Add to My Personal Archive
Right arrow Download to citation manager
Right arrow Search for citing articles in:
ISI Web of Science (3)
Right arrowRequest Permissions
Right arrow Commercial Re-use Guidelines
for Open Access NAR Content
Google Scholar
Right arrow Articles by Rainaldi, G.
Right arrow Articles by Ceci, L. R.
Right arrow Search for Related Content
PubMed
Right arrow PubMed Citation
Right arrow Articles by Rainaldi, G.
Right arrow Articles by Ceci, L. R.
Social Bookmarking
Add to CiteULike   Add to Connotea   Add to Del.icio.us  
What's this?

Nucleic Acids Research, 2003, Vol. 31, No. 1 436-438
© 2003 Oxford University Press

PLMItRNA, a database on the heterogeneous genetic origin of mitochondrial tRNA genes and tRNAs in photosynthetic eukaryotes

Guglielmo Rainaldi, Mariateresa Volpicella, Flavio Licciulli1, Sabino Liuni1, Raffaele Gallerani and Luigi R. Ceci*,1

Dipartimento di Biochimica e Biologia Molecolare, Università di Bari, CNR, Via Amendola 165/A, 70126 Bari Italy 1 Centro di Studio sui Mitocondri e Metabolismo Energeticoc, CNR, Via Amendola 165/A, 70126 Bari Italy

*To whom correspondence should be addressed. Tel: +39 0805443311; Fax: +39 805443317; Email: luigi.ceci{at}area.ba.cnr.it

Received September 13, 2002; Accepted September 20, 2002

ABSTRACT

The updated version of PLMItRNA reports information and multialignments on 609 genes and 34 tRNA molecules active in the mitochondria of Viridiplantae (27 Embryophyta and 10 Chlorophyta), and photosynthetic algae (one Cryptophyta, four Rhodophyta and two Stramenopiles). Colour-code based tables reporting the different genetic origin of identified genes allow hyper-textual link to single entries. Promoter sequences identified for tRNA genes in the mitochondrial genomes of Angiospermae are also reported. The PLMItRNA database is accessible at http://bighost.area.ba.cnr.it/PLMItRNA/.

INTRODUCTION

PLMItRNA is a database dedicated to the distribution of tRNA genes and molecules in the mitochondria of photosynthetic eukaryotes (1). With the possible exceptions of Prototheca wickerhamii (2) and Nephroselmis olivacea (3), the genomes of these organelles do not code for a complete set of tRNAs. Missing tRNAs must therefore be imported from the cytoplasm. In the case of angiosperms, the presence of tRNA genes with different genetic origins (the original endosymbiont and chloroplast) can also be observed (4). The puzzling distribution of active tRNAs in the mitochondria of photosynthetic organisms is therefore the result of a selective process of recruitment of genes and molecules occurred during evolution.

Each entry in PLMItRNA reports information on the sequence and organism, useful to retrieve specific lists of entries by SRS at http://bighost.area.ba.cnr.it/srs6/.

Multialignments of sequences have been divided in four groups, corresponding to Viridiplantae (Chlorophyta/Embryophyta group) and to the three divisions of algae Cryptophyta, Rhodophyta and Stramenopiles. Within these four groups sequences are reported according to their classification in different classes as indicated in Table 1 for Viridiplantae and in a similar Table (see Table S3 in Supplementary Material) for Cryptophyta, Rhodophyta and Stramenopiles. These tables report a general view of all the complete tRNA genes and molecules identified in the mitochondrial genomes of photosynthetic eukaryotes. Coloured squares have hyper-textual link to single gene (or molecule) entry. Colour code refers to the different genetic origin of tRNA genes or molecules (see Table 1). Genes or molecules with chloroplast or nuclear origins are aligned separately.


View this table:
[in this window]
[in a new window]
  		Table 1. Gene coding for mitochondrial tRNS in Viridiplantae

 
PLMItRNA updating was carried out essentially as already described in the previous version (1).

More details on the organization of the database and how to retrieve list of specific entries can be found at the PLMItRNA home page: http://bighost.area.ba.cnr.it/PLMItRNA/.

PROMOTERS FOR tRNA GENES TRANSCRIPTION

In the current version of PLMItRNA a list of promoter sequences identified for tRNA genes in mitochondria of Angiosperms has been introduced, which could be useful for studies on the activation of foreign genes in the mitochondrial genomes. It is still a matter of investigation how the mitochondrial transcription machinery can recognize the chloroplast sequences to be transcribed. Transcription of cp-tRNA genes in mitochondrial genomes may be occurred owing to insertion downstream of pre-existing promoters, or thanks to evolutive rearrangements of their 5'-flanking regions which originated functional promoters. A consensus promoter sequence has been described for angiosperm mitochondrial genes which shows little differences between monocotyledons and dicotyledons (4,5). Promoter consensus is characterized by a highly conserved tetranucleotide motif, CRTA, that in monocots can diverge to TRTA, YYTA or RRTA. The tetranucleotide is part of a larger sequence, usually located at position from -7 to +2 with respect to the transcription start site. Apparently the same kind of promoters are used in the transcription of protein, ribosomal and tRNA genes (5). Table 2 reports promoter sequences described for tRNA genes in angiosperm mitochondria as experimentally determined or deduced by sequence comparison.


View this table:
[in this window]
[in a new window]
  		Table 2. Promoter sequences identified for tRNA genes in angiosperm mitochondrial genomes
 
SUPPLEMENTARY MATERIAL

Supplementary tables on the database are available at NAR Online.

REFERENCES

  1. Damiano,F., Gallerani,R., Liuni,S., Licciulli,F. and Ceci,L.R. (2001) PLMItRNA, a database for mitochondrial tRNA genes and tRNAs in photosynthetic eukaryotes. Nucleic Acids Res., 29, 167–168.[Abstract/Free Full Text]

  2. Wolff,G., Plante,I., Lang,B.F., Kuck,U. and Burger,G. (1994) Complete sequence of the mitochondrial DNA of the chlorophyte alga Prototheca wickerhamii. Gene content and genome organization. J. Mol. Biol., 237, 75–86.[CrossRef][Web of Science][Medline]

  3. Turmel,M., Lemieux,C., Burger,G., Lanz,F., Otis,C., Plante,I. and Gray,M.W. (1999) The complete mitochondrial DNA sequences of Nephroselmis olivacea and Pedinomonas minor: two radically different evolutionary patterns within green algae. Plant Cell, 11, 1717–1729.[Abstract/Free Full Text]

  4. Hoffmann,M., Kuhn,J., Daschner,K. and Binder,S. (2001) The RNA world of plant mitochondria. Prog. Nucleic Acid Res., 70, 119–154.[Web of Science][Medline]

  5. Fey,J. and Marechal-Drouard,L. (1999) Compilation and analysis of plant mitochondrial promoter sequences: an illustration of a divergent evolution between monocot and dicot mitochondria. Biochem. Biophys. Res. Comm., 256, 409–414.[CrossRef][Web of Science][Medline]

  6. Damiano,F., Ceci,L.R., Siculella,L. and Gallerani,R. (2002) Transcription of two sunflower (Helianthus annuus L.) mitochondrial tRNA genes having different genetic origins. Gene, 286, 25–32.[CrossRef][Web of Science][Medline]

  7. Binder,S. and Brennicke,A. (1993) A tRNA gene transcription initiation site is similar to mRNA and rRNA promoters in plant mitochondria. Nucleic Acids Res., 21, 5012–5019.[Abstract/Free Full Text]

  8. Coulthart,M.B., Spencer,D. and Gray,M.W. (1993) Comparative analysis of a recombining-repeat-sequence family in the mitochondrial genomes of wheat (Triticum aestivum L.) and rye (Secale cereale L.). Curr. Genet., 23, 255–265.[CrossRef][Web of Science][Medline]

  9. Nakazono,M., Tsutsumi,N., Sugiura,M. and Hirai,A. (1995) A small repeated sequence contains the transcription initiation sites for both trnfM and rrn26 in rice mitochondria. Plant Mol. Biol., 28, 343–346.[CrossRef][Web of Science][Medline]

  10. Kanno,A., Nakazono,M., HiraiA. and Kameya,T. (1997) A chloroplast derived trnH gene is expressed in the mitochondrial genome of gramineous plants. Plant Mol. Biol., 34, 353–356.[CrossRef][Web of Science][Medline]


Add to CiteULike CiteULike   Add to Connotea Connotea   Add to Del.icio.us Del.icio.us    What's this?


This article has been cited by other articles:


Home page
 Nucleic Acids ResHome page
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.
[Abstract] [Full Text] [PDF]

This Article
Right arrow Abstract Freely available
Right arrow Print PDF (706K) Freely available
Right arrow Supplementary Material
Right arrow Alert me when this article is cited
Right arrow Alert me if a correction is posted
Services
Right arrow Email this article to a friend
Right arrow Similar articles in this journal
Right arrow Similar articles in ISI Web of Science
Right arrow Similar articles in PubMed
Right arrow Alert me to new issues of the journal
Right arrow Add to My Personal Archive
Right arrow Download to citation manager
Right arrow Search for citing articles in:
ISI Web of Science (3)
Right arrowRequest Permissions
Right arrow Commercial Re-use Guidelines
for Open Access NAR Content
Google Scholar
Right arrow Articles by Rainaldi, G.
Right arrow Articles by Ceci, L. R.
Right arrow Search for Related Content
PubMed
Right arrow PubMed Citation
Right arrow Articles by Rainaldi, G.
Right arrow Articles by Ceci, L. R.
Social Bookmarking
Add to CiteULike   Add to Connotea   Add to Del.icio.us  
What's this?