P-Bodies: Composition, Properties, and Functions

Abstract

Processing bodies (P-bodies) are cytoplasmic ribonucleoprotein (RNP) granules primarily composed of translationally repressed mRNAs and proteins related to mRNA decay, suggesting roles in post-transcriptional regulation. P-bodies are conserved in eukaryotic cells and exhibit properties of liquid droplets. However, the function of P-bodies in translational repression and/or mRNA decay remains contentious. Here we review recent advances in our understanding of the molecular composition of P-bodies, the interactions and processes that regulate P-body liquid-liquid phase separation (LLPS), and the cellular localization of mRNA decay machinery, in the context of how these discoveries refine models of P-body function.

Figure 1

Recently identified P-body proteins. (A) Proposed interactions between inhibitory microprotein NBDY and the mRNA decapping complex. (B) m⁶A-dependent mRNA localization to P-bodies and mRNA degradation mediated by YTHDF2.

Figure 2

Factors that drive P-Body assembly and liquid–liquid phase separation (LLPS). (A) Interactions between P-body proteins. Components critical to P-body assembly are colored in blue, which include P-body proteins required for the maintenance of pre-existing P-bodies and factors that affect the induction of new P-bodies by arsenite or vinblastine treatment, cold shock, or glucose depletion. Components colored in pink directly interact with RNA.⁻ Solid black lines indicated direct protein–protein interactions, and red lines indicate mutual exclusiveness. Dotted black lines suggest indirect or putative interactions. Only interactions with at least two sources of evidence derived from BioGRID are included (except for PatL1, whose interaction with many P-body components is not well covered in the database^,). (B) Intermolecular interactions that promote LLPS. Upper box: simultaneous protein–protein interactions between intrinsically disordered regions (IDRs) and dimerization of P-body components. Lower box: association between positively charged IDRs of P-body components such as Edc3 with RNA transcripts promotes phase separation, possibly through electrostatic and cation−π interactions.