title: Bioinformatic analysis of the nucleolus.
abstract: The nucleolus is a plurifunctional, nuclear organelle, which is responsible for ribosome biogenesis and many other functions in eukaryotes, including RNA processing, viral replication and tumour suppression. Our knowledge of the human nucleolar proteome has been expanded dramatically by the two recent MS studies on isolated nucleoli from HeLa cells [Andersen, Lyon, Fox, Leung, Lam, Steen, Mann and Lamond (2002) Curr. Biol. 12, 1-11; Scherl, Coute, Deon, Calle, Kindbeiter, Sanchez, Greco, Hochstrasser and Diaz (2002) Mol. Biol. Cell 13, 4100-4109]. Nearly 400 proteins were identified within the nucleolar proteome so far in humans. Approx. 12% of the identified proteins were previously shown to be nucleolar in human cells and, as expected, nearly all of the known housekeeping proteins required for ribosome biogenesis were identified in these analyses. Surprisingly, approx. 30% represented either novel or uncharacterized proteins. This review focuses on how to apply the derived knowledge of this newly recognized nucleolar proteome, such as their amino acid/peptide composition and their homologies across species, to explore the function and dynamics of the nucleolus, and suggests ways to identify, in silico, possible functions of the novel/uncharacterized proteins and potential interaction networks within the human nucleolus, or between the nucleolus and other nuclear organelles, by drawing resources from the public domain.
authors.affiliation: Division of Gene Regulation and Expression, School of Life Sciences, Wellcome Trust Biocentre, University of Dundee, Scotland, UK. a.k.l.leung@dundee.ac.uk
authors.forename: Anthony K L
authors.initials: AK
authors.lastname: Leung
authors.forename: Jens S
authors.initials: JS
authors.lastname: Andersen
authors.forename: Matthias
authors.initials: M
authors.lastname: Mann
authors.forename: Angus I
authors.initials: AI
authors.lastname: Lamond
mesh_terms: D020816:Amino Acid Motifs; D000595:Amino Acid Sequence; D000596:Amino Acids / Q000032:analysis; D002466:Cell Nucleolus / Q000737:chemistry* / Q000502:physiology / Q000648:ultrastructure; D019295:Computational Biology; D006801:Humans; D008969:Molecular Sequence Data; D009687:Nuclear Proteins / Q000032:analysis / Q000737:chemistry* / Q000502:physiology; D020543:Proteome / Q000032:analysis
chemical_list: D000596:Amino Acids; D009687:Nuclear Proteins; D020543:Proteome