Unraveling regulation and new components of human P-bodies through a protein interaction framework and experimental validation

Abstract

The cellular factors involved in mRNA degradation and translation repression can aggregate into cytoplasmic domains known as GW bodies or mRNA processing bodies (P-bodies). However, current understanding of P-bodies, especially the regulatory aspect, remains relatively fragmentary. To provide a framework for studying the mechanisms and regulation of P-body formation, maintenance, and disassembly, we compiled a list of P-body proteins found in various species and further grouped both reported and predicted human P-body proteins according to their functions. By analyzing protein-protein interactions of human P-body components, we found that many P-body proteins form complex interaction networks with each other and with other cellular proteins that are not recognized as P-body components. The observation suggests that these other cellular proteins may play important roles in regulating P-body dynamics and functions. We further used siRNA-mediated gene knockdown and immunofluorescence microscopy to demonstrate the validity of our in silico analyses. Our combined approach identifies new P-body components and suggests that protein ubiquitination and protein phosphorylation involving 14-3-3 proteins may play critical roles for post-translational modifications of P-body components in regulating P-body dynamics. Our analyses provide not only a global view of human P-body components and their physical interactions but also a wealth of hypotheses to help guide future research on the regulation and function of human P-bodies.

K63-Ubiquitylation and TRAF6 Pathways Regulate Mammalian P-Body Formation and mRNA Decapping

“…One candidate is RO52/TRIM21, which colocalizes with the deubiquitylating enzyme USP4 to P-bodies. Knockdown of both proteins reduces P-body numbers by unknown mechanisms (Zheng et al, 2011). Our results add another facet to the multifunctional TRAF6 protein that is known to integrate into a plethora of signaling complexes (Walsh et al, 2015).…”

Evidence Providing New Insights into TOB-Promoted Deadenylation and Supporting a Link between TOB's Deadenylation-Enhancing and Antiproliferative Activities

“…In contrast, a study reported that TOB1 is constitutively expressed in liver and its downregulation is required for normal liver regeneration (17). Furthermore, TOB2 and not TOB1 was found to colocalize with mRNA-processing bodies (13) that contain nontranslating mRNAs, as well as proteins involved in translational inhibition and mRNA degradation (3,12,15,30,44). It will be interesting to identify the different features of the TOB proteins that are responsible for these specific functions and to decipher the mechanisms controlling and/or coordinating the multiple actions of these two functionally important but redundant proteins.…”

Transforming Growth Factor β Regulates P-Body Formation through Induction of the mRNA Decay Factor Tristetraprolin

“…Several cellular factors involved in posttranscriptional regulation comprise P bodies (14); however, how such a factor(s) promotes controlled P-body assembly in response to TGF-␤ signaling is not known. Based on the ability of TTP to promote AREmediated decay and localize to P bodies (41, 42), we sought to determine if a causal link exists between TTP and TGF-␤-mediated P-body formation.…”

“…In many cases, ARE-mRNAs targeted for rapid decay require the components necessary for 5=-to-3= degradation and are localized to processing (P) bodies (11)(12)(13). These small cytoplasmic foci contain the components of the 5=-to-3= decay machinery along with other factors involved in microRNA (miRNA)-and small interfering RNA (siRNA)-mediated silencing, nonsense-mediated decay, and translational silencing (14). P-body assembly is a dynamic process that is tightly linked with the availability of free cytoplasmic mRNAs that drives the aggregation of mRNA-protein complexes in the cytoplasm into microscopically visible P bodies (15,16).…”