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|
|Date of Publication (YYYY-MM-DD):||2006-10-26|
|Title of Journal:||Genome Biology : Biology for the Post-Genomic Era|
|Issue / Number:||10|
|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|
|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.
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.
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|
|Version Comment:||Automatic journal name synchronization|
|Communicated by:||Martin Vingron|
|Affiliations:||MPI für molekulare Genetik|