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MitoDrome


NAR Molecular Biology Database Collection entry number 226
D’Elia D.1, Catalano D.1, Licciulli F.1, Turi A.1, Tripoli G.2, Porcelli D.2, Saccone C.2,3 and Caggese C.2
1Istituto di Tecnologie Biomediche, Sezione di Bari, CNR, via Amendola 122/D, 70126 Bari, Italy;
22Dipartimento di Genetica e Anatomia Patologica, UniversitÀ di Bari, via Orabona, 4, 70126 Bari, Italy;
3Dipartimento di Biochimica e Biologia Molecolare, UniversitÀ di Bari, via E. Orabona 4, 70126 Bari, Italy

Database Description

MitoDrome is a database born with the aim of annotating D. melanogaster nuclear genes encoding mitochondrial proteins and contributing to the functional characterisation of these genes to support studies on human diseases related to mitochondrial dysfunctions. The D. melanogaster genomic data included in the last MitoDrome published version derived from a search of the Drosophila genomic, ESTs and cDNA sequences in the FlyBase database using as a probe the aminoacid sequences of the human mitochondrial proteins available in SWISSPROT database. On the basis of a computational comparative analysis, each D. melanogaster gene encoding a product sharing significant homology with a human mitochondrial protein was putatively classified as encoding a mitochondrion- targeted protein and annotated in the database.

Recent Developments

The recent availability of the complete genomic sequences of D. pseudoobscura and A. gambiae has prompted us to extend our analysis to the identification and characterization at the genomic level of the nuclear OXPHOS genes of these two dipteran species, using the sequences of the D. melanogaster genes involved in oxidative phosphorilation as probes for a search of their genomes. The orthologs of 78 putative OXPHOS nuclear genes present in each of the three Dipterans have been identified and annotated, taking into account conservation in amino acid sequence, intron/exon structure, intron length, and presence of duplications in the genome. In addition, a total of 47 putative paralogs of these genes in the three dipteran species investigated have also been identified and annotated. The need to add new data to MitoDrome together with the higher level of efficiency required to manage data and offer the database users the best in terms of usability and interoperability have imposed a complete restructuring of the database, resulting in an expanded MitoDrome Database Version retrievable at the address http://www2.ba.itb.cnr.it/mitodrome/.

This new database version collects the results of the comparative analyses carried out on D. melanogaster, D. pseudoobscura and A. gambiae OXPHOS nuclear genes together with an accurate manual annotation of their genomic sequences, transcripts (RNA), and polypeptide products.

The main changes introduced with respect to the last published version of MitoDrome concern the database structure, its web interface and, obviously, its content. Indeed, apart from structural changes, the new version includes (1) a more comprehensive set of Dipteran sequences, (2) a “Clusters” section where sets of putative orthologous and paralogous genes are grouped, (3) gene structure and protein sequences comparisons (4) data on P-insertion mutants of D. melanogaster OXPHOS nuclear genes. More details are provided in the on-line “Manual” accessible by the new MitoDrome Home page.

Our future plans include both the extension of the analysis to the nuclear OXPHOS genes of other organisms and the identification and annotation of the D. pseudoobscura and A. gambiae orthologs and paralogs of the other D. melanogaster genes collected in the previous version of MitoDrome. When this last goal is reached, the previous version of the MitoDrome database will be eliminated as obsolete, its data having been completely integrated in the new version.

Acknowledgements

This work has been supported by 'Ministero dell’Istruzione, dell’UniversitÀ e della Ricerca’ (MIUR), Italy, within the grants of PNR 2001-2003 (FIRB art.8) D.M. 199, Strategic Program: Post-genome, grant 31-063933 and Project n.2, Cluster C03 L. 488/929.

References

1. SARDIELLO M., LICIULLI F., CATALANO D., ATTIMONELLI M., and CAGGESE C. (2003) MitoDrome: a database of Drosophila melanogaster nuclear genes encoding proteins targeted to the mitochondrion Nucleic Acids Res. 31: 322-324


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