MITOP, the mitochondrial proteome database: 2000 update

MITOP (http://www.mips.biochem.mpg.de/proj/medgen/mitop/) is a comprehensive database for genetic and functional information on both nuclear- and mitochondrial-encoded proteins and their genes. The five species files--Saccharomyces cerevisiae, Mus musculus, Caenorhabditis elegans, Neurospora crassa and Homo sapiens--include annotated data derived from a variety of online resources and the literature. A wide spectrum of search facilities is given in the overlapping sections 'Gene catalogues', 'Protein catalogues', 'Homologies', 'Pathways and metabolism' and 'Human disease catalogue' including extensive references and hyperlinks to other databases. Central features are the results of various homology searches, which should facilitate the investigations into interspecies relationships. Precomputed FASTA searches using all the MITOP yeast protein entries and a list of the best human EST hits with graphical cluster alignments related to the yeast reference sequence are presented. The orthologue tables with cross-listings to all the protein entries for each species in MITOP have been expanded by adding the genomes of Rickettsia prowazeckii and Escherichia coli. To find new mitochondrial proteins the complete yeast genome has been analyzed using the MITOPROT program which identifies mitochondrial targeting sequences. The 'Human disease catalogue' contains tables with a total of 110 human diseases related to mitochondrial protein abnormalities, sorted by clinical criteria and age of onset. MITOP should contribute to the systematic genetic characterization of the mitochondrial proteome in relation to human disease.     

MitoNuc: a database of nuclear genes coding for mitochondrial proteins. Update 2002

Mitochondria, besides their central role in energy metabolism, have recently been found to be involved in a number of basic processes of cell life and to contribute to the pathogenesis of many degenerative diseases. All functions of mitochondria depend on the interaction of nuclear and organelle genomes. Mitochondrial genomes have been extensively sequenced and analysed and data have been collected in several specialised databases. In order to collect information on nuclear coded mitochondrial proteins we developed MitoNuc, a database containing detailed information on sequenced nuclear genes coding for mitochondrial proteins in Metazoa. The MitoNuc database can be retrieved through SRS and is available via the web site http://bighost.area.ba.cnr.it/mitochondriome where other mitochondrial databases developed by our group, the complete list of the sequenced mitochondrial genomes, links to other mitochondrial sites and related information, are available. The MitoAln database, related to MitoNuc in the previous release, reporting the multiple alignments of the relevant homologous protein coding regions, is no longer supported in the present release. In order to keep the links among entries in MitoNuc from homologous proteins, a new field in the database has been defined: the cluster identifier, an alpha numeric code used to identify each cluster of homologous proteins. A comment field derived from the corresponding SWISS-PROT entry has been introduced; this reports clinical data related to dysfunction of the protein. The logic scheme of MitoNuc database has been implemented in the ORACLE DBMS. This will allow the end-users to retrieve data through a friendly interface that will be soon implemented.     

A database of six eukaryotic hypothetical genes and proteins

Assigning functions to proteins of unknown function is of considerable interest to the proteomic researchers as the genes encoding them are conserved over various species. Here, we describe HypoDB, a database of hypothetical genes and proteins in six eukaryotes. The database was collected and organized based on the number of entries in each chromosome with few annotations. Hypothetical protein database contains information related to gene and protein sequences, chromosome number and location, secondary and tertiary structure related data. AVAILABILITY: The database is available for free at http://www.trimslabs.com/database/hypodb/index.html.     

ProTherm, version 2.0: thermodynamic database for proteins and mutants

ProTherm 2.0 is the second release of the Thermo-dynamic Database for Proteins and Mutants that includes numerical data for several thermodynamic parameters, structural information, experimental methods and conditions, functional and literature information. The present release contains >5500 entries, an approximately 67% increase over the previous version. In addition, we have included information about reversibility of data, details about buffer and ion concentrations and the surrounding residues in space for all mutants. A WWW interface enables users to search data based on various conditions with different sorting options for outputs. Further, ProTherm has links with other structural and literature databases, and the mutation sites and surrounding residues are automatically mapped on the structures and can be directly viewed through 3DinSight developed in our laboratory. The ProTherm database is freely available through the WWW at http://www.rtc.riken.go.jp/protherm.html     

A mutation spectra database for bacterial and mammalian genes: 1998.

This database consists of over 24 000 mutations in 18 viral, bacterial, yeast or mammalian genes. The data are grouped as sets of DNA base sequence changes or spectra caused by a particular mutagen under defined conditions. The spectra are available on the World Wide Web at http://info.med.yale.edu/mutbase/ in two formats; in text format that can be browsed on-line or downloaded for use with a text editor and in dBASEIII format for use, after downloading, by relational database programs or by spreadsheets. Researchers are encouraged to submit DNA sequence changes to a suitable mutation database such as ours. A data entry program, MUTSIN, can be retrieved from this site. MUTSIN diagrams each mutation on the computer screen and alerts the user to any discrepancies.     

PLMItRNA, a database for higher plant mitochondrial tRNAs and tRNA genes.

The PLMItRNA database contains information and multialignments of tRNA genes and molecules detected in higher plant mitochondria. It has been developed from a previous compilation of higher plant mitochondrial tRNA genes [Sagliano,A., Volpicella,M., Gallerani,R. and Ceci,L.R. (1998) Nucleic Acids Res., 26, 154-155] and implemented with data and sequences of tRNA molecules retrieved from the literature. The current version of the database reports information on 171 genes and 16 tRNA molecules from 24 plants. PLMItRNA is accessible via WWW at http://bio-www.ba.cnr.it:8000/srs/     

RIBOi: a database for ribosome-interacting proteins

Antibiotics have been widely applied as effective agents for curing infectious diseases caused by pathogenic bacteria. However, the emergence of antibiotic resistance shows a growing threat to the effectiveness of clinical applications of antibiotics. To overcome this challenge, identifying new promising targets for drug development is now urgently needed. The inhibition of translation process is one of the most important mechanisms for many of the existing antibiotics. Meanwhile, ribosome is a universal translational machine in all living cells. It can link amino acids together through the guiding of mRNAs, functioning as the workplace of protein synthesis or translation. Targeting the regulation of ribosomal function and ribosome assembly is an attracting solution for identifying novel targets for antibiotic development. These targets are very critical for developing antibiotics with new mode of action, thus, holds the promise for tackling the ever-growing crisis of bacterial drug resistance.     

SECOST: sequence-conformation-structure database for amino acid residues in proteins.

The sequence-conformation-structure database for amino acid residues contains information on 114 828 individual residues derived from the spatial structures of 473 high-quality non-homologous proteins. The information in the database is obtained using a variety of different methods and can be used in various protein modeling applications.     

A mutation spectra database for bacterial and mammalian genes.

Each mutation spectrum in this database is a dataset of changes in DNA base sequence in mutations induced in a gene by a particular mutagen (including spontaneous processes) under defined conditions. There are 240 datasets with 24 500 mutants in nine bacterial genes, two phage genes, five mammalian genes and one yeast gene. The database is available on the Web at http://info.med.yale.edu/mutbase/ . The data tables can be viewed on the Web and downloaded in text form for local use. The data are also available in dBASE III, a format which can be utilized by essentially any desktop computer database program or spreadsheet, and makes feasible analyses of a large number of mutants. Researchers are invited to submit additional data. A data entry program, MUTSIN, diagrams each mutation on the computer screen as the data are entered and alerts the user to any discrepancies between the entry and the gene sequence.     

Genatlas database,genes and development defects

This article aims to illustrate the potentialities of the Genatlas database, taking, as an example, the developmental genes and their associated diseases in man. These genes belong to several categories intervening from the first stages of embryonic life. They operate at all steps of developmental cascades from extracellular signaling to activation of target genes. Quite a number of those genes have been identified in man, which are the orthologs of genes previously described in lower species. These genes are mapped and an increasing number are associated with developmental anomalies. These studies shed light on the mechanisms of congenital malformations. They disclose a large array of genetic and phenotypic heterogeneity and a high degree of complexity.     

YPD-A database for the proteins of Saccharomyces cerevisiae.

YPD is a database for the proteins of the budding yeast, Saccharomyces cerevisiae. YPD has two formats: (i) a spreadsheet which tabulates many of the physical and functional properties of yeast proteins, and (ii) the YPD Protein Reports which are formatted pages containing the protein properties, annotations gathered from the literature, and references with titles. YPD is available through the World-Wide Web, through an Email server, and by anonymous FTP. New releases of the YPD spreadsheet are produced every two to four months, and the on-line information is updated daily.     

O-GLYCBASE: a revised database of O-glycosylated proteins.

O-GLYCBASE is a comprehensive database of information on glycoproteins and their O-linked glycosylation sites. Entries are compiled and revised from the SWISS-PROT and PIR databases as well as directly from recently published reports. Nineteen percent of the entries extracted from the databases needed revision with respect to O-linked glycosylation. Entries include information about species, sequence, glycosylation site and glycan type, and are fully referenced. Sequence logos displaying the acceptor specificity for the GaINAc transferase are shown. A neural network method for prediction of mucin type O-glycosylation sites in mammalian glycoproteins exclusively from the primary sequence is made available by E-mail or WWW. The O-GLYCBASE database is also available electronically through our WWW server or by anonymous FTP.     

Engineering proteins, subcloning and hyperexpressing oxidoreductase genes.

A very efficient system for subcloning and studying protein sequences, combining previously established elements for hyperexpression, replication and screening, was used to hyperproduce and characterize seven different products. It expedited the cloning of genes, in a multipurpose recombinant DNA construct, for all the requirements to study and engineer proteins with a strain of Escherichia coli. Genes encoding six heme proteins and a flavoprotein have been subcloned and expressed to 13-30% of the total cell protein, greatly facilitating purification and analyses. Three of the heme proteins and the flavoprotein incorporated prosthetic groups in E. coli, and exhibited the expected activities. Four of the enzymes have been purified to homogeneity and two of these crystallized for X-ray diffraction analysis. A rapid mutagenesis protocol, based on polymerase chain reactions, was successfully applied to clone derivatives of one of these enzymes, cytochrome c peroxidase. Thus, this system fulfills all criteria for engineering proteins in an efficient and concerted manner.     

A database for the analysis of immunity genes in Drosophila: PADMA database

While microarray experiments generate voluminous data, discerning trends that support an existing or alternative paradigm is challenging. To synergize hypothesis building and testing, we designed the Pathogen Associated Drosophila MicroArray (PADMA) database for easy retrieval and comparison of microarray results from immunity-related experiments (www.padmadatabase.org). PADMA also allows biologists to upload their microarray-results and compare it with datasets housed within PADMA. We tested PADMA using a preliminary dataset from Ganaspis xanthopoda-infected fly larvae, and uncovered unexpected trends in gene expression, reshaping our hypothesis. Thus, the PADMA database will be a useful resource to fly researchers to evaluate, revise, and refine hypotheses.     

Columba: an integrated database of proteins,structures, and annotations

Background  

Structural and functional research often requires the computation of sets of protein structures based on certain properties of the proteins, such as sequence features, fold classification, or functional annotation. Compiling such sets using current web resources is tedious because the necessary data are spread over many different databases. To facilitate this task, we have created COLUMBA, an integrated database of annotations of protein structures.