Assembling a protein-protein interaction map of the SSU processome from existing datasets - PubMed (original) (raw)

Assembling a protein-protein interaction map of the SSU processome from existing datasets

Young H Lim et al. PLoS One. 2011.

Abstract

Background: The small subunit (SSU) processome is a large ribonucleoprotein complex involved in small ribosomal subunit assembly. It consists of the U3 snoRNA and ∼72 proteins. While most of its components have been identified, the protein-protein interactions (PPIs) among them remain largely unknown, and thus the assembly, architecture and function of the SSU processome remains unclear.

Methodology: We queried PPI databases for SSU processome proteins to quantify the degree to which the three genome-wide high-throughput yeast two-hybrid (HT-Y2H) studies, the genome-wide protein fragment complementation assay (PCA) and the literature-curated (LC) datasets cover the SSU processome interactome.

Conclusions: We find that coverage of the SSU processome PPI network is remarkably sparse. Two of the three HT-Y2H studies each account for four and six PPIs between only six of the 72 proteins, while the third study accounts for as little as one PPI and two proteins. The PCA dataset has the highest coverage among the genome-wide studies with 27 PPIs between 25 proteins. The LC dataset was the most extensive, accounting for 34 proteins and 38 PPIs, many of which were validated by independent methods, thereby further increasing their reliability. When the collected data were merged, we found that at least 70% of the predicted PPIs have yet to be determined and 26 proteins (36%) have no known partners. Since the SSU processome is conserved in all Eukaryotes, we also queried HT-Y2H datasets from six additional model organisms, but only four orthologues and three previously known interologous interactions were found. This provides a starting point for further work on SSU processome assembly, and spotlights the need for a more complete genome-wide Y2H analysis.

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Conflict of interest statement

Competing Interests: The authors have declared that no competing interests exist.

Figures

Figure 1

Figure 1. Interaction maps of the SSU processome proteins from existing HT-Y2H datasets.

Proteins are colored as described in the Materials and Methods; green nodes refer to proteins of the t-Utp/UtpA subcomplex, blue for UtpB, yellow for UtpC, gray for the U3 snoRNP proteins, brown for Bms1/Rcl1 and red for the Mpp10 subcomplex. Pink nodes refer to proteins that have yet to be assigned to a subcomplex. RNA helicases are depicted as diamonds. Multiple edges, or interactions, linking the proteins represent interactions identified in different studies or reciprocally identified as both bait and prey. Self-interactions are shown as looped edges. A) Results from the Uetz et al. dataset . B) Results from Ito et al. dataset . C) Results from the Hazbun et al. dataset . D) Results from the Yu et al. dataset .

Figure 2

Figure 2. Interaction map of the SSU processome proteins from the PCA dataset.

Nodes are colored as in Fig. 1.

Figure 3

Figure 3. Interaction map of the SSU processome proteins from the LC dataset.

Nodes are depicted as in Fig. 1.

Figure 4

Figure 4. The current, merged SSU processome interactome map from the three HT-Y2H, PCA, LC and interologue datasets.

Interologues identified in Drosophila (D) and C. elegans (C) are also shown, with red and blue edges, respectively. The PPI redundancy (same interactions identified by different studies, methods or reciprocally) was removed from the figure to highlight the interacting partners. Nodes are depicted as in Fig. 1. Standalone nodes depict proteins without interaction data from any of the compiled datasets.

Figure 5

Figure 5. Comparison of the overlap between the HT-Y2H, PCA and LC datasets for the PPIs of the SSU processome.

Numbers within the Venn diagram refer to the number of SSU processome proteins present and overlapping in the HT-Y2H, PCA and LC datasets.

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