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2015 ; 5
(3
): 1441-66
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Comprehensive Protein Interactome Analysis of a Key RNA Helicase: Detection of
Novel Stress Granule Proteins
#MMPMID26184334
Bish R
; Cuevas-Polo N
; Cheng Z
; Hambardzumyan D
; Munschauer M
; Landthaler M
; Vogel C
Biomolecules
2015[Jul]; 5
(3
): 1441-66
PMID26184334
show ga
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
TIF1?, 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.
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