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          Institute: MPI für molekulare Genetik     Collection: Department of Computational Molecular Biology     Display Documents



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ID: 311439.0, MPI für molekulare Genetik / Department of Computational Molecular Biology
An inventory of yeast proteins that are associated with nucleoli and ribosomal components
Authors:Staub, Eike; Mackowiak, Sebastian; Vingron, Martin
Language:English
Date of Publication (YYYY-MM-DD):2006-10-26
Title of Journal:Genome Biology : Biology for the Post-Genomic Era
Volume:7
Issue / Number:10
Start Page:R98
End Page:R98
Copyright:© 2006 Staub et al.; licensee BioMed Central Ltd.
This is an open access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
Review Status:not specified
Audience:Experts Only
Abstract / Description:Background:
Although baker's yeast is a primary model organism for research on eukaryotic ribosome assembly and nucleoli, the list of its proteins that are functionally associated with nucleoli or ribosomes is still incomplete. We trained a naïve Bayesian classifier to predict novel proteins that are associated with yeast nucleoli or ribosomes based on parts lists of nucleoli in model organisms and large-scale protein interaction data sets. Phylogenetic profiling and gene expression analysis were carried out to shed light on evolutionary and regulatory aspects of nucleoli and ribosome assembly.
Results:
We predict that, in addition to 439 known proteins, a further 62 yeast proteins are associated with components of the nucleolus or the ribosome. The complete set comprises a large core of archaeal-type proteins, several bacterial-type proteins, but mostly eukaryote-specific inventions. Expression of nucleolar and ribosomal genes tends to be strongly co-regulated compared to other yeast genes.
Conclusion:
The number of proteins associated with nucleolar or ribosomal components in yeast is at least 14% higher than known before. The nucleolus probably evolved from an archaeal-type ribosome maturation machinery by recruitment of several bacterial-type and mostly eukaryote-specific factors. Not only expression of ribosomal protein genes, but also expression of genes encoding the 90S processosome, are strongly co-regulated and both regulatory programs are distinct from each other.
Comment of the Author/Creator:The electronic version of this article is the complete one and can be found online at: http://genomebiology.com/2006/7/10/R98
External Publication Status:published
Document Type:Article
Version Comment:Automatic journal name synchronization
Communicated by:Martin Vingron
Affiliations:MPI für molekulare Genetik
Identifiers:ISSN:1465-6906
DOI:10.1186/gb-2006-7-10-r98
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