Received: 17 September 2018 Revised: 18 December 2018 Accepted: 28 December 2018 DOI: 10.1002/wrna.1524 ADVANCED REVIEW Stress-induced mRNP granules: Form and function of processing bodies and stress granules Anna R. Guzikowski1* | Yang S. Chen1* | Brian M. Zid2 1Division of Biological Sciences, University of California San Diego, La Jolla, California In response to stress, cells must quickly reprogram gene expression to adapt and 2Department of Chemistry and Biochemistry, survive. This is achieved in part by altering levels of mRNAs and their translation University of California San Diego, La Jolla, into proteins. Recently, the formation of two stress-induced messenger ribonucleo- California protein (mRNP) assemblies named stress granules and processing bodies has been Correspondence postulated to directly impact gene expression during stress. These assemblies Brian M. Zid, Department of Chemistry and Biochemistry, University of California San Diego, sequester and concentrate specific proteins and RNAs away from the larger cyto- La Jolla, CA. plasm during stress, thereby providing a layer of posttranscriptional gene regulation Email: [email protected] with the potential to directly impact mRNA levels, protein translation, and cell sur- Funding information vival. The function of these granules has generally been ascribed either by the pro- National Institutes of Health, Grant/Award Numbers: T32 EB009380, R35 GM128798 tein components concentrated into them or, more broadly, by global changes that occur during stress. Recent proteome- and transcriptome-wide studies have pro- vided a more complete view of stress-induced mRNP granule composition in var- ied cell types and stress conditions. However, direct measurements of the phenotypic and functional consequences of stress granule and processing body for- mation are lacking. This leaves our understanding of their roles during stress incomplete. Continued study into the function of these granules will be an impor- tant part in elucidating how cells respond to and survive stressful environmental changes. This article is categorized under: Translation > Translation Regulation RNA Interactions with Proteins and Other Molecules > RNA–Protein Complexes RNA Export and Localization > RNA Localization KEYWORDS P-body, phase separation, stress, stress granules, translation 1 | INTRODUCTION Cells are frequently exposed to fluctuating, potentially adverse environmental conditions. To survive adverse changes they must rapidly alter gene expression in order to maintain internal homeostasis. The cellular reprogramming that occurs in response to a disruptive or inimical external fluctuation is broadly termed as stress response. Cellular stress response typically includes slowing or ceasing growth that is concomitant with repression of overall translation, although certain genes important for survival and repair are highly induced. Concurrently, while overall translation is repressed, many posttranscriptional regu- latory proteins and mRNAs undergo a process called phase separation that results in the formation of concentrated, nonmem- branous cytoplasmic structures generally described as granules or foci. During stress, this phase separation process might segregate proteins and mRNAs in a way that is functionally important for the cell and that promotes survival. Therefore, these *Anna R. Guzikowski & Yang S. Chen contributed equally to this study. WIREs RNA. 2019;e1524. wires.wiley.com/rna © 2019 Wiley Periodicals, Inc. 1of17 https://doi.org/10.1002/wrna.1524 2of17 GUZIKOWSKI ET AL. structures are a subject of emergent interest. Although much progress has been made recently to identify the proteins and mRNAs that reside in these granules and the physical characteristics that underlie their formation, there is little known about the phenotypic or functional consequences of their formation during stress and therefore how significantly they contribute to stress response. There are many different types of cellular granules involved in a wide variety of biological processes such as nucleoli, paraspeckles, PML bodies, and Cajal bodies in the nucleus as well as the stress-induced processing bodies (PBs) and stress granules (SGs) in the cytoplasm. Here, we highlight the cytoplasmic PBs and SGs, two well-studied messenger ribonucleopro- tein (mRNP) granules that are present across eukaryotes during a variety of stressful conditions such as exposure to heat shock, oxidative stress, UV irradiation, osmotic stress, and nutrient starvation. The formation of these mRNP granules, which occurs on the scale of minutes after exposure to stress stimuli, is mediated by a physical process called liquid–liquid phase separation (LLPS; see Box 1 for more information). There are common biophysical characteristics and some shared compo- nents between SGs and PBs as well as granule-specific features. It should be noted that, while the aptly named SGs are broadly induced during stress, PBs are a bit more organismal-specific. Saccharomyces cerevisiae induces visible PBs primar- ily during stress response while, in mammalian cells, small, microscopically visible PBs are constitutive but they become much larger and more abundant during stress. It should also be noted that the majority of research into these stress-induced granules is performed with yeast and mammalian cell culture systems. Ultimately, we posit SGs and PBs should be considered as distinct yet closely related mRNP granules; their properties and role in posttranscriptional gene expression during stress response is the focus of this review and we will address them individually, as SGs or PBs, and together more generally, as stress-induced mRNP granules, when appropriate. Initial characterization of conditions that bring about stress-induced mRNP granules began in the late 1990s when researchers observed that impairment of translation initiation causes SG formation (Bashkirov, Scherthan, Solinger, Buer- stedde, & Heyer, 1997; Kedersha, Gupta, Li, Miller, & Anderson, 1999). A decrease in initiation is one hallmark of stress response; the canonical mechanism of eIF2α-phosphorylation can drive robust granule formation in some stress conditions (Kedersha et al., 1999). Importantly, however, the formation of SGs is not dependent on eIF2α-phosphorylation as the addi- tion of small molecules that block translation initiation through different mechanisms are sufficient to drive granule assembly (Dang et al., 2006; Mazroui et al., 2006; Mokas et al., 2009). Moreover, the genetic knockdown of specific translation initia- tion factor proteins (Mokas et al., 2009) or the overexpression of RNA-binding proteins (RBPs) that function to repress trans- lation (De Leeuw et al., 2007; Gilks, 2004; Kedersha et al., 2005; Mazroui et al., 2006; Wilczynska, 2005) also lead to mRNP granule formation. The observation that impaired translation drives SG and PB formation spurred further inquiry into their induction and the degree of interrelation between the two granules during stress response. Evidence emerged that SGs and PBs, each lacking membranes, are able to interact, potentially docking and swapping components (Buchan, Muhlrad, & Parker, 2008; Kedersha et al., 2005; Wilbertz et al., 2019). Nonetheless, it is known that these granules retain unique protein content and presumably RNA content, though the dynamics and degree of retention of RNAs with an individual granule is more poorly understood BOX 1 LIQUID–LIQUID PHASE SEPARATION The separation of components in a mixture is termed demixing. The demixing of liquids can take place if the energy of interaction between macromolecules is greater than the entropic energy reduction that arises from their homogeneous mixing. This process drives LLPS of a molecular mixture into two phases: a smaller volume of a concentrated, con- densed phase and a larger volume of a dilute, lower concentration phase. This can allow separation and compartmentali- zation of biomolecules into organelles without the presence of a membrane. As this is a thermodynamically favorable process, no external cellular energy (ATP) is necessary to maintain this separation within the cell. Biological LLPS is driven by collective weak interactions between multivalent substrates and intrinsically disordered proteins (IDPs). IDPs or intrinsically disordered regions (IDRs) are proteins or amino acids sequences that fail to form defined structures and instead assume multiple conformations. Many of these IDPs have low complexity domains where a small number of amino acid residues are overrepresented, especially many polar and charged amino acids including glutamine, proline, glutamic acid, lysine, arginine, glycine, and serine. Many proposed weak interactions help to overcome the entropic energy constraints of mixing that include electrostatic, cation–pi, and pi–pi interactions. While IDPs are important for phase separation, nucleic acids, especially RNA molecules, can also serve as multivalent substrates and drive demixing. In fact, RNA has been found sufficient to promote phase separation and alter the internal viscosity of membraneless compartments. GUZIKOWSKI ET AL. 3of17 than it is for proteins. Interestingly, one study found SG assembly was dependent on and promoted by the presence of pre- existing PBs in yeast cells, demonstrating the akin yet distinct nature of SGs and PBs (Buchan et al., 2008). On the other hand, a different study found that induction of PBs and SGs occurs via independent signaling pathways in yeast and reported no such dependency (Shah, Zhang, Ramachandran,