MitoDrome: a content manager system to manage and retrieve data on nuclear encoded mitochondrial proteins of D. melanogaster, D. pseudoobscura and A. gambiae

INTRODUCTION: Mitochondria are sub-cellular organelles whose activity is crucial for the energetic metabolism of most eukaryotic organisms. Indeed, free fatty acid metabolism, Krebs cycle reactions and oxidative phosphorylation (OXPHOS) take place at mitochondrial level and enzymes devoted to these biochemical pathways are differently distributed into the mitochondrial membranes and matrix compartment. Respiratory chain enzymes are organized into five large complexes (I-V) spanning the inner mitochondrial membrane. The majority of these proteins are nuclear encoded, synthesized in the cytosol and then targeted to mitochondria. The availability of the complete genome sequences of D. melanogaster, D. pseudoobscura and A. gambiae has allowed us to identify and characterize the nuclear OXPHOS genes of these three dipteran species using a comparative analysis approach starting from the “putative” human homologous proteins. To manage these data we have developed MitoDrome (1), a Content Manager System (CMS) based on a database and a Web interface containing: a submission tool accessible only to authors of database content and a public query and retrieval system tailored to the extraction of sequence data in a format suitable to perform analyses on protein and gene sequence regions (i.e. promoter region, 5’-3’ UTRs, introns, exons, etc.). MATERIALS AND METHODS: The database has been conceptually structured in a relational schema and implemented in the Database Management System MySQL. The Web interface has been developed in PHP and BioPerl running on an Apache HTTP Server. The database data content is manually submitted from a private section of the Web Interface. Each database entry consists of a nuclear gene encoding for a mitochondrial protein in a given species and reports information regarding: species name, gene name, functional product, putative sub-mitochondrial localization, Enzyme Classification (EC) code for enzyme, Gene Ontology (GO) classification, gene map and sequence of gene, gene transcript and protein. Links to other databases such as FlyBase (2), SwissProt (3), Ensembl (4) and GeneCards (5) are also provided. The query system of MitoDrome allows user to extract information on entry/cluster through a wizard interface and to save, locally, in different file format multiple/single entries features (ie: gene, exon, intron, transcript, UTRs, protein, ect.). RESULTS: D. melanogaster data are derived from the comparison between human mitochondrial proteins, available in SWISSPROT, and the D. melanogaster genome, ESTs and cDNA sequence data available in the FlyBase database. D. melanogaster genes sharing significant similarity with human mitochondrial proteins were classified as putative D. melanogaster mitochondrial genes and annotated in the database. The same analysis has been extended to D. pseudoobscura and A. gambiae using protein sequences of D. melanogaster as probe sequence. To date, the database contains, for each of the three Dipteran, 78 annotated nuclear genes, encoding mitochondrial proteins which are the putative counterparts of proteins of the human OXPHOS system. The gene annotation has been done by taking into account conservation in amino acid sequence, intron/exon structure, intron length, and presence of duplications in the genome. We have also identified 46 genes sharing significant sequence similarity with some of the genes annotated in the database. These 46 genes probably represent paralogs originated by events of transposition or recombination taking place during the evolution of the three species. However, no pairwise orthology could be assigned among Drosophila and Anopheles duplicated genes, indicating either rapid evolution or loss of paralogs. Putative orthologous and paralogous genes have been grouped in Cluster and for each gene comparative data analyses (gene structure and protein sequences comparison) are reported in the MitoDrome Cluster table. The database also contains a list of mutant insertion alleles of D. melanogaster genes which has mostly been compiled using information available from FlyBase and from the BDGP (Berkeley Drosophila Genome Project) P-Element Gene Disruption Project (6). MitoDrome can be queried and retrieved at the following address: http://www.ba.itb.cnr.it/MitoDrome/. 1. Sardiello M. et al. (2003) Nucleic Acids Res. 31,322-4 2. FlyBase Consortium (2003) Nucleic Acids Res. 31, 172-5 3. Bairoch, A. et al. (2000) Nucleic Acids Res 28, 45-48 4. Birney E. et al. (2004) Nucleic Acids Res. 32, 468-70 5. Safran M. et al. (2002) Bioinformatics 18,1542-3 6. Spradling A.C. et al. (1999) Genetics 153, 135-77