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Stress Granules and Processing Bodies in Translational Control Downloaded from http://cshperspectives.cshlp.org/ on September 29, 2021 - Published by Cold Spring Harbor Laboratory Press Stress Granules and Processing Bodies in Translational Control Pavel Ivanov,1,2,3 Nancy Kedersha,1,2 and Paul Anderson1,2 1Division of Rheumatology, Immunology and Allergy, Brigham and Women’s Hospital, Boston, Massachusetts 02115 2Department of Medicine, Harvard Medical School, Boston, Massachusetts 02115 3The Broad Institute of Harvard and M.I.T., Cambridge, Massachusetts 02142 Correspondence: [email protected] Stress granules (SGs) and processing bodies (PBs) are non-membrane-enclosed RNA granules that dynamically sequester translationally inactive messenger ribonucleoprotein particles (mRNPs) into compartments that are distinct from the surrounding cytoplasm. mRNP remod- eling, silencing, and/or storage involves the dynamic partitioning of closed-loop polyadeny- lated mRNPs into SGs, or the sequestration of deadenylated, linear mRNPs into PBs. SGs form when stress-activated pathways stall translation initiation but allow elongation and termina- tion to occur normally, resulting in a sudden excess of mRNPs that are spatially condensed into discrete foci by protein:protein, protein:RNA, and RNA:RNA interactions. In contrast, PBs can exist in the absence of stress, when specific factors promote mRNA deadenylation, condensation, and sequestration from the translational machinery. The formation and dis- solution of SGs and PBs reflect changes in messenger RNA (mRNA) metabolism and allow cells to modulate the proteome and/or mediate life or death decisions during changing environmental conditions. ight control of messenger RNA (mRNA) pro- non-membrane-enclosed subcellular compart- Tcessing, trafficking, degradation, and transla- ments, termed RNA granules, plays critical roles tion are important in regulating gene expression. in mRNA metabolism (Shin and Brangwynne These processes are controlled by specific RNA- 2017). Two of the best-studied RNA granules binding proteins (RBPs) that bind the mRNA are stress granules (SGs) and processing bodies within larger complexes called messenger ribo- (PBs), membraneless cytoplasmic foci formed by nucleoprotein particles (mRNPs) (Mitchell and the condensation of translationally inactivated Parker 2014). In eukaryotes, such mRNPs are mRNPs. Although the composition of seques- often localized to specific cellular compart- tered mRNAs and RBPs differs between SGs ments, both as a part of mRNA biogenesis under and PBs (Fig. 1), both RNA granules are linked optimal conditions, and as a part of response to translational control events that modulate the to changing conditions. Recent data suggest proteome and/or influence cell survival. The ac- that self-organization of mRNPs into various cumulation and condensation of untranslating Editors: Michael B. Mathews, Nahum Sonenberg, and John W.B. Hershey Additional Perspectives on Translation Mechanisms and Control available at www.cshperspectives.org Copyright © 2019 Cold Spring Harbor Laboratory Press; all rights reserved; doi: 10.1101/cshperspect.a032813 Cite this article as Cold Spring Harb Perspect Biol 2019;11:a032813 1 Downloaded from http://cshperspectives.cshlp.org/ on September 29, 2021 - Published by Cold Spring Harbor Laboratory Press P. Ivanov et al. elF4E 40S subunit CPEB RACK1 Smaug elF3 SG only Ago 1,2 elF4A/B DDX6/RCK elF4G FASTK DDX3 Edc3 PABP HuR UPF1/2 SG+PB Roquin Ataxin2 TIA-1/R Caprin1 TTP/BRF1 FMRP/FXR1 Rap55/Lsm14 G3BP1/2 UPF1/2 Pumillio PB XRN1 Staufen PMR1 TSN YB1 USP10 4E-T CAF DCP1a, DCP2 CCR4-Not1 Hedls/GE-1 GW182 Nesprin Figure 1. Selected stress granule (SG)- and processing body (PB)-associated proteins. Proteins (partial list) found exclusively in SGs (blue box), in both SGs and PB/GW-bodies (GWBs) (green box), or predominantly in PB/ GWBs (red box). Image obtained using arsenite-treated U2OS cells stained for eukaryotic initiation factor 3b (eIF3b) (blue), DCP1a (red), and eIF4E (green). mRNPs into these discrete cytoplasmic granules mRNAs. Colocalization of these factors in are governed by similar events that are intimate- discrete cytoplasmic granules was triggered by ly connected to various aspects of translational either heat-shock stress or sodium arsenite- control. induced oxidative stress (Kedersha et al. 1999). The term “stress granules” was first used to Unlike plant heat-shock granules, these mam- describe phase-dense cytoplasmic particles that malian mRNA-containing stress granules strictly appeared in mammalian cells subjected to heat required phosphorylation of eukaryotic transla- shock. These granules contained various heat- tion initiation factor 2α (eIF2α) (Kedersha et al. shock proteins (HSPs) (Collier and Schlesinger 1999), thus linking SGs to translational control. 1986; Collier et al. 1988), and similar particles PBs were first described as “XRN1 foci” be- were observed in heat-shocked tomato cells cause of the granular cytoplasmic localization (Nover et al. 1983, 1989). Although initial com- of the exoribonuclease XRN1 (Bashkirov et al. positional analysis revealed the presence of both 1997). Subsequent observations revealed that HSPs and mRNAs in tomato “heat SGs” (Nover other RNA decay-associated proteins were co- et al. 1983, 1989), later reports clarified that localized in these foci (Ingelfinger et al. 2002; these SGs did not actually contain RNA and van Dijk et al. 2002; Fenger-Gron et al. 2005; thus cannot be classified as RNA granules (We- Wilczynska et al. 2005; Yu et al. 2005; Eulalio ber et al. 2008). However, before this revised et al. 2007), leading to their designation as report, the term “stress granules” was also used to mRNA “processing bodies” (Sheth and Parker describe cytoplasmic foci containing the trans- 2006). Proteins associated with mRNA silenc- lational repressor T-cell intracellular antigen 1 ing, such as the argonautes and glycine-tryp- (TIA1), the translational enhancer poly(A)- tophan protein of 182 KDa (GW182)/trinucle- binding protein (PABPC1), and polyadenylated otide repeat containing 6A, were also found in 2 Cite this article as Cold Spring Harb Perspect Biol 2019;11:a032813 Downloaded from http://cshperspectives.cshlp.org/ on September 29, 2021 - Published by Cold Spring Harbor Laboratory Press Stress Granules and Processing Bodies in Translational Control organized puncta described as “GW-bodies” PBs are disassembled by 10–40 min of cyclohex- (GWBs), which were often coincident with PBs imide treatment (Andrei et al. 2005), suggesting (Eystathioy et al. 2003). For the purposes of this that their steady-state integrity requires ongoing review, we will include GWBs under the umbrella mRNP input. Conversely, puromycin-induced term PBs, but note that they are not identical premature termination of translating mRNAs (reviewed in Stoecklin and Kedersha 2013). promotes SG formation (Kedersha et al. 2000). Mitotic cells do not form SGs or PBs, at least in part because of arrested elongation that prevents STRESS GRANULES: COMPOSITION polysome disassembly (Sivan et al. 2007). The AND INITIATION effects of these drugs highlight the link between SGs consist of stalled preinitiation complexes SGs/PBs and translation, and distinguish them that include small (40S), but not large (60S), from other RNA granules (see online Movie 1). ribosomal subunits, translation initiation fac- SG disassembly occurs when cells adapt to tors eIF4F, eIF3, and PABP, and polyadenylated stress, or when stress is removed and normal mRNAs (reviewed in Anderson and Kedersha translational equilibrium is restored. Although 2009). Condensation of stalled preinitiation SG assembly requires translationally stalled PICs, complexes (PICs) into SGs is mediated by spe- formation of SGs themselves is not required for cific RBPs, some of which show sequence-spe- translational arrest in the cells; specific stresses cific binding to mRNAs, and others that interact or knockdown of specific SG-associated pro- with the translational machinery. These two teins and SG nucleators uncouple SG formation components, stalled PICs and SG-nucleating from translational arrest (Ohn et al. 2008; Ke- RBPs, together determine a threshold at which dersha et al. 2016). Thus, a separate step beyond SGs form or disperse. Some SG-associated RBPs translational arrest is required for SG formation. are shared with PBs, whereas other components For example, energy starvation induced by cold are limited to SGs or PBs only. In terms of shock stalls the translational cycle, induces eIF2α mRNA, SGs contain poly(A) mRNA, whereas phosphorylation, and triggers slow SG formation PBs contain largely deadenylated mRNA. Figure that takes hours rather than minutes, but these 1 shows the SG/PB distribution of some of the cold-shock SGs rapidly dissolve (5–10 min) best-characterized SG-specific proteins (blue), when cells are warmed up, although dephos- proteins common to both SGs and PBs (green), phorylation of eIF2α, polysome formation, and proteins specific to PBs (red). and restoration of full translation take several SGs and PBs are dynamic entities that are hours (Hofmann et al. 2012). In this case, SG in equilibrium with polysomes (Kedersha et al. dissolution seems to result from a “decondensa- 2000, 2005). SG-associated mRNPs and RBPs tion” of mRNPs rather than restored translation dynamically shuttle between SGs and poly- that depletes the untranslated pool of mRNPs. somes. Increasing the pool of translationally in- Inhibiting the energy-sensing 50AMP-activated activated mRNA promotes SG assembly, where- protein kinase
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