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The Nucleolar Proteome Database (NOPdb) archives data on more than 700 proteins that were identified by multiple mass spectrometry (MS) analyses from highly purified preparations of human nucleoli, the most prominent nuclear organelle. Each protein entry is annotated with information about its corresponding gene, its domain structures and relevant protein homologues across species, as well as documenting its MS identification history including all the peptides sequenced by tandem MS/MS. Moreover, data showing the quantitative changes in the relative levels of ~500 nucleolar proteins are compared at different timepoints upon transcriptional inhibition. Correlating changes in protein abundance at multiple timepoints, highlighted by visualization means in the NOPdb, provides clues regarding the potential interactions and relationships between nucleolar proteins and thereby suggests putative functions for factors within the 30% of the proteome which comprises novel/ uncharacterized proteins. The NOPdb (http://www.lamondlab.com/NOPdb) is searchable by either gene names, protein sequences, Gene Ontology terms or motifs, or by limiting the range for isoelectric points and/or molecular weights and links to other databases (e.g. LocusLink, OMIM and PubMed).
Recent develoments :
The database is currently also searchable by mRNA sequences or by short amino acid sequences. Moreover, we planned to include an online-documentation to help users to surf through the site and additional kinetic profiles for each protein, based on their responses to both different drug treatments and other metabolic and cell cycle variations.
The Human Frontier Science Program is acknowledged for a research grant entitled 'Functional organization of the cell nucleus investigated through proteomics and molecular dynamics’. We thank many colleagues working diligently to explore the dynamic nucleolar proteome in the ongoing collaboration between the laboratories of Angus I Lamond (University of Dundee) and Matthias Mann (University of Southern Denmark)
1. Andersen, J.S., Lyon, C.E., Fox, A.H., Leung, A.K., Lam, Y.W., Steen, H., Mann, M. and Lamond, A.I. (2002) Directed proteomic analysis of the human nucleolus. Curr Biol, 12, 1-11.
2.Leung, A.K., Andersen, J.S., Mann, M. and Lamond, A.I. (2003) Bioinformatic analysis of the nucleolus. Biochem J, 376, 553-569.
The NPD is a curated database that contains information on more than 1200 vertebrate proteins that are thought, or are known, to localise to the cell nucleus. Each entry is annotated with information on predicted protein size and isoelectric point, as well as any repeats, motifs or domains within the protein sequence. In addition, information on the sub-nuclear localisation of each protein is provided and the biological and molecular functions are described using Gene Ontology (GO) terms. The database is searchable by keyword, protein name, sub-nuclear compartment and protein domain/motif. Links to other databases are provided (e.g. Entrez, SWISS-PROT, OMIM, PubMed, PubMed Central). Thus, NPD provides a gateway through which the nuclear proteome may be explored. The database can be accessed at http://npd.hgu.mrc.ac.uk and is updated monthly.
We would like to acknowledge the help of MRC HGU computing services and Dr. Heidi Sutherland for comments and data entry during the development of NPD. We especially thank all colleagues who have contributed to the development and information content of NPD. The NPD was made possible by funding from the Medical Research Council (UK) and the James S. McDonnell Foundation. GD was supported by a fellowship from the Canadian Institutes of Health Research (CIHR) and WAB is a Centennial Fellow of the James S. McDonnell Foundation.
Bickmore, WA and HGE Sutherland (2002) Addressing protein localization within the nucleus EMBO J. 21(6):1248-1254.
Sutherland HG, Mumford GK, Newton K, Ford LV, Farrall R, Dellaire G, Caceres JF, Bickmore WA. (2001) Large-scale identification of mammalian proteins localized to nuclear sub-compartments. Hum Mol Genet. 10(18):1995-2011.
Tate P, Lee M, Tweedie S, Skarnes WC, Bickmore WA. (1998) Capturing novel mouse genes encoding chromosomal and other nuclear proteins. J Cell Sci. 111 (17):2575-85.
Images of plant organelles and protocols for plant organelle research12
The organelle genome database GOBASE is now on its thirteenth release [September 2005] and contains 410,000 mitochondrial sequences including ~2500 complete genomes, and 128,000 chloroplast sequences including 43 complete genomes. Most of these are derived from GenBank entries, with some few being locally generated. GOBASE organises and integrates diverse data related to organelles, including nucleotide and protein sequences, taxonomic data, RNA secondary structures, and genetic maps, all of which are collected and verified by expert curators. The GOBASE interface includes search pages for sequences, genes, introns, exons, proteins, genetic maps and taxonomic data
Recent develoments :
GOBASE has recently started including genome sequences of bacteria related to the ancestors of organelles; three genomes are currently included, of which one, that of Rickettsia prowazekii, has been fully reannotated, and the other two will be before the end of the year. Gene Ontology terms have been incorporated in the database. Deduced features based on incomplete annotations in GenBank have been added to the database. In cases where single genes in species are oversampled within GenBank, representative type examples are determined and only these examples are shown in the default interface configuration. Graphics illustrating the gene structure have been added for any gene more complicated than a single exon, and graphics representing the position of neighbouring genes have been added for all genes.
Support for GOBASE has been provided by operating grants from the Canadian Institutes of Health Research (CIHR), the Medical Research Council of Canada (MRC), and the Canadian Genome Analysis and Technology Program (CGAT), the Canadian Institute for Advanced Research (CIAR), Program in Evolutionary Biology, and by generous equipment grants from Sun Microsystems.
Introns in organelle genomes demonstrate wide variation in both features and behavior in Nature. Three classes of organelle introns are now recognized: 1) Group I, 2) Group II, and 3) Group III which are related to Group II introns. These introns have attracted considerable attention because of two remarkable properties: 1) the ability to self-splice, 2) the ability to function as mobile elements. These properties are being explored in order to understand gene evolution and as potential tools in genetic engineering and genomic analysis
Organelle DB is a Web-accessible database cataloging proteins localized to a known organelle, subcellular structures, or protein complex in organisms throughout the eukaryotic kingdom. As such, Organelle DB is a strong resource of data from the human proteome as well as from the major model organisms S. cerevisiae, A. thaliana, D. melanogaster, C. elegans, and M. musculus. In particular, Organelle DB is a central repository of yeast data, incorporating results and actual fluorescent images from ongoing large-scale studies of protein localization in Saccharomyces cerevisiae. Each protein in Organelle DB is presented with its sequence and, as available, a detailed description of its function; functions were extracted from relevant model organism databases, and links to these databases are provided within Organelle DB. To facilitate data interoperability, we have annotated all protein localizations using vocabulary from the Gene Ontology consortium.
Recent develoments :
Since its release in 2004, Organelle DB has grown by 20% to encompass over 30,000 proteins from 138 eukaryotic organisms. Organelle DB is a significant repository of biological images, housing 1500 micrographs of yeast cells carrying stained proteins. Furthermore, we have recently developed Organelle View, an extension of Organelle DB for the interactive visualization of organelles and subcellular structures in the budding yeast Saccharomyces cerevisiae. Organelle View offers a dimensional representation of a yeast cell; users can search Organelle View for proteins of interest, and the organelles housing these proteins will be highlighted in the cell image. Among other applications, Organelle View may serve as an educational aid engaging introductory biology students through a visually “fun” interface. Organelle View can be accessed from the Organelle DB home page or directly at http://organelleview.lsi.umich.edu.
Organelle DB is supported by grant no. DBI 0543017 from the National Science Foundation.
1. Wiwatwattana, N. and Kumar, A. (2005) Organelle DB: a cross-species database of protein localization and function. Nucleic Acids Res. 33: D598-D604.
Organelle genome resource at NCBI
Wolfsberg TG, Schafer S, Tatusov RL, Tatusov TA. Organelle genome resource at NCBI. Trends Biochem. Sci. 2001 Mar;26(3):199-203