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NOPdb: Nucleolar Proteome Database.

Anthony Kar Lun Leung1, Laura Trinkle-Mulcahy, Yun Wah Lam

  • 1Division of Gene Regulation and Expression, Wellcome Trust Biocentre, School of Life Sciences, University of Dundee, Dundee DD1 5EH, UK. akleung@mit.edu

Nucleic Acids Research
|December 31, 2005
PubMed
Summary

The Nucleolar Proteome Database (NOPdb) archives over 700 human nucleolar proteins identified by mass spectrometry (MS). It provides insights into protein functions and interactions, aiding nucleolar research.

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Area of Science:

  • Proteomics
  • Molecular Biology
  • Bioinformatics

Background:

  • The nucleolus is a key nuclear organelle involved in ribosome biogenesis and other cellular processes.
  • Understanding the nucleolar proteome is crucial for deciphering its diverse functions.
  • Previous studies have identified nucleolar proteins, but a comprehensive, integrated database was lacking.

Purpose of the Study:

  • To create a comprehensive database of the human nucleolar proteome.
  • To annotate identified proteins with detailed information, including gene data, domain structures, and homology.
  • To provide quantitative data on protein level changes under specific conditions to infer protein interactions and functions.

Main Methods:

  • Purification of human nucleoli followed by extensive mass spectrometry (MS) analysis.

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  • Bioinformatic annotation of identified proteins, including gene information, protein domains, and cross-species homologues.
  • Quantitative proteomic analysis of approximately 500 nucleolar proteins under transcriptional inhibition at various timepoints.

    • Main Results:

    • The Nucleolar Proteome Database (NOPdb) was established, archiving data for over 700 human nucleolar proteins.
    • Detailed annotations include MS identification history, gene information, domain structures, and homologues.
    • Quantitative data revealed dynamic changes in protein abundance, offering clues to protein interactions and functions, particularly for novel proteins.

    Conclusions:

    • NOPdb serves as a valuable resource for researchers studying the nucleolus and its proteome.
    • The database facilitates the exploration of protein functions and interactions within the nucleolus.
    • Quantitative proteomic data aids in understanding nucleolar dynamics and the roles of uncharacterized proteins.