Assembling a protein-protein interaction map of the SSU processome from existing datasets
Young H Lim1, J Michael Charette, Susan J Baserga
1Department of Molecular Biophysics and Biochemistry, Yale University School of Medicine, New Haven, Connecticut, United States of America.
Plos One
|March 23, 2011
Summary
Protein-protein interactions within the small subunit (SSU) processome are largely unknown. Current data reveal sparse coverage of the SSU processome interactome, highlighting the need for further research into its assembly and function.
Area of Science:
- Molecular Biology
- Cell Biology
- Biochemistry
Background:
- The small subunit (SSU) processome is crucial for ribosome biogenesis, comprising the U3 snoRNA and approximately 72 proteins.
- While SSU processome components are known, their protein-protein interactions (PPIs) and subsequent assembly, architecture, and function remain poorly understood.
Purpose of the Study:
- To assess the coverage of the SSU processome protein-protein interaction (PPI) network using existing high-throughput datasets.
- To identify gaps in knowledge regarding SSU processome protein interactions and guide future research.
Main Methods:
- Queried protein-protein interaction (PPI) databases for SSU processome proteins.
- Analyzed data from three genome-wide high-throughput yeast two-hybrid (HT-Y2H) studies, a genome-wide protein fragment complementation assay (PCA), and literature-curated (LC) datasets.
- Examined HT-Y2H datasets from six additional model organisms for conserved interactions.
Main Results:
- Coverage of the SSU processome PPI network is sparse across all analyzed datasets.
- The protein fragment complementation assay (PCA) dataset showed the highest coverage among genome-wide studies (27 PPIs, 25 proteins).
- Literature-curated (LC) data provided the most extensive interactome information (34 proteins, 38 PPIs), with many validated interactions.
- Over 70% of predicted PPIs remain undetermined, and 36% of proteins have no known interaction partners.
- Analysis of other model organisms yielded limited orthologous interactions.
Conclusions:
- Existing high-throughput methods provide incomplete coverage of the SSU processome interactome.
- A significant portion of SSU processome proteins lack identified interaction partners, hindering understanding of complex assembly and function.
- Further comprehensive genome-wide analyses, particularly yeast two-hybrid studies, are essential to elucidate the complete SSU processome interactome and its role in eukaryotic biology.
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