Next Article in Journal
Is Cell Death Primary or Secondary in the Pathophysiology of Idiopathic Parkinson’s Disease?
Next Article in Special Issue
The 3' to 5' Exoribonuclease DIS3: From Structure and Mechanisms to Biological Functions and Role in Human Disease
Previous Article in Journal
Activation of Proinflammatory Responses in Cells of the Airway Mucosa by Particulate Matter: Oxidant- and Non-Oxidant-Mediated Triggering Mechanisms
Previous Article in Special Issue
Knockout of RNA Binding Protein MSI2 Impairs Follicle Development in the Mouse Ovary: Characterization of MSI1 and MSI2 during Folliculogenesis
 
 
Article

Comprehensive Protein Interactome Analysis of a Key RNA Helicase: Detection of Novel Stress Granule Proteins

1
Center for Genomics and Systems Biology, Department of Biology, New York University, 12 Waverly Place, New York, NY 10003, USA
2
The Cleveland Clinic, Department of Neurosciences, Lerner Research Institute, 9500 Euclid Avenue, Cleveland, OH 44195, USA
3
RNA Biology and Post-Transcriptional Regulation, Max-Delbrück-Center for Molecular Medicine, Berlin-Buch, Robert-Rössle-Str. 10, Berlin 13092, Germany
*
Author to whom correspondence should be addressed.
These authors contributed equally to this work.
Academic Editor: André P. Gerber
Biomolecules 2015, 5(3), 1441-1466; https://doi.org/10.3390/biom5031441
Received: 10 May 2015 / Accepted: 15 June 2015 / Published: 15 July 2015
(This article belongs to the Special Issue RNA-Binding Proteins—Structure, Function, Networks and Disease)
DDX6 (p54/RCK) is a human RNA helicase with central roles in mRNA decay and translation repression. To help our understanding of how DDX6 performs these multiple functions, we conducted the first unbiased, large-scale study to map the DDX6-centric protein-protein interactome using immunoprecipitation and mass spectrometry. Using DDX6 as bait, we identify a high-confidence and high-quality set of protein interaction partners which are enriched for functions in RNA metabolism and ribosomal proteins. The screen is highly specific, maximizing the number of true positives, as demonstrated by the validation of 81% (47/58) of the RNA-independent interactors through known functions and interactions. Importantly, we minimize the number of indirect interaction partners through use of a nuclease-based digestion to eliminate RNA. We describe eleven new interactors, including proteins involved in splicing which is an as-yet unknown role for DDX6. We validated and characterized in more detail the interaction of DDX6 with Nuclear fragile X mental retardation-interacting protein 2 (NUFIP2) and with two previously uncharacterized proteins, FAM195A and FAM195B (here referred to as granulin-1 and granulin-2, or GRAN1 and GRAN2). We show that NUFIP2, GRAN1, and GRAN2 are not P-body components, but re-localize to stress granules upon exposure to stress, suggesting a function in translation repression in the cellular stress response. Using a complementary analysis that resolved DDX6’s multiple complex memberships, we further validated these interaction partners and the presence of splicing factors. As DDX6 also interacts with the E3 SUMO ligase TIF1β, we tested for and observed a significant enrichment of sumoylation amongst DDX6’s interaction partners. Our results represent the most comprehensive screen for direct interaction partners of a key regulator of RNA life cycle and localization, highlighting new stress granule components and possible DDX6 functions—many of which are likely conserved across eukaryotes. View Full-Text
Keywords: DDX6; post-transcriptional regulation; protein interactions; SUMOylation; NUFIP2; FAM195A; FAM195B; stress granules; P bodies; mRNA degradation DDX6; post-transcriptional regulation; protein interactions; SUMOylation; NUFIP2; FAM195A; FAM195B; stress granules; P bodies; mRNA degradation
Show Figures

Graphical abstract

MDPI and ACS Style

Bish, R.; Cuevas-Polo, N.; Cheng, Z.; Hambardzumyan, D.; Munschauer, M.; Landthaler, M.; Vogel, C. Comprehensive Protein Interactome Analysis of a Key RNA Helicase: Detection of Novel Stress Granule Proteins. Biomolecules 2015, 5, 1441-1466. https://doi.org/10.3390/biom5031441

AMA Style

Bish R, Cuevas-Polo N, Cheng Z, Hambardzumyan D, Munschauer M, Landthaler M, Vogel C. Comprehensive Protein Interactome Analysis of a Key RNA Helicase: Detection of Novel Stress Granule Proteins. Biomolecules. 2015; 5(3):1441-1466. https://doi.org/10.3390/biom5031441

Chicago/Turabian Style

Bish, Rebecca, Nerea Cuevas-Polo, Zhe Cheng, Dolores Hambardzumyan, Mathias Munschauer, Markus Landthaler, and Christine Vogel. 2015. "Comprehensive Protein Interactome Analysis of a Key RNA Helicase: Detection of Novel Stress Granule Proteins" Biomolecules 5, no. 3: 1441-1466. https://doi.org/10.3390/biom5031441

Find Other Styles

Article Access Map by Country/Region

1
Only visits after 24 November 2015 are recorded.
Back to TopTop