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Journal Article

An inventory of yeast proteins that are associated with nucleoli and ribosomal components

MPS-Authors

Staub,  Eike
Max Planck Society;

Mackowiak,  Sebastian
Max Planck Society;

http://pubman.mpdl.mpg.de/cone/persons/resource/persons50613

Vingron,  Martin
Gene regulation (Martin Vingron), Dept. of Computational Molecular Biology (Head: Martin Vingron), Max Planck Institute for Molecular Genetics, Max Planck Society;

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gb-2006-7-10-r98.pdf
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Citation

Staub, E., Mackowiak, S., & Vingron, M. (2006). An inventory of yeast proteins that are associated with nucleoli and ribosomal components. Genome Biology: Biology for the Post-Genomic Era, 7(10), R98-R98. doi:10.1186/gb-2006-7-10-r98.


Cite as: http://hdl.handle.net/11858/00-001M-0000-0010-8370-6
Abstract
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.