Introduction {#Sec1}
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While the intracellular environment and embedded cellular machinery provide the needed vital force and necessary materials for viruses to replicate after infection, these host machineries are not available to these foreign invaders at ease. In fact, viruses have to counter the multiple layers of intracellular defense to replicate and establish their dominance for their propagation. RNA granules (Thomas *et al.*[@CR142]) are dynamic non-membrane subcellular structures (Ivanov *et al.*[@CR69]) containing translationally silenced messenger ribonucleoproteins (mRNPs), which play an important role in regulation of cellular homeostasis, RNA metabolism and gene expression at the posttranscriptional level (Anderson and Kedersha [@CR3]). Stress granules (SG) and processing bodies (PB) (Eulalio *et al.*[@CR36]) are two of RNA granules well characterized in yeast and mammalian cells (Poblete-Duran *et al.*[@CR119]) and are important components of the host cell antiviral defense.

SG are non-membranous, transiently assembled cytoplasmic aggregates of 48S mRNPs and associated proteins (Stohr *et al.*[@CR140]; Buchan and Parker [@CR14]), where stalled translation preinitiation complexes (PICs) repress the translation of nonessential mRNAs (Anderson *et al.*[@CR4]) and modulate cell signaling by sequestering key signal translation proteins (Kedersha *et al.*[@CR80]). Thus, SG are thought to be the aggregates of stable, translationally silent mRNAs (Kedersha and Anderson [@CR75]). A variety of environmental stresses, including viral infection, can trigger SG formation in eukaryotic cells (Anderson and Kedersha [@CR2]). In contrast, PB can exist in the absence of stress (Stoecklin and Kedersha [@CR139]), which are sites of active mRNA decay (Decker and Parker [@CR28]). SG initiate global translational arrest by storing mRNA (Anderson and Kedersha [@CR3]) for exchange with either polysomes for translation or PB for degradation (Kedersha *et al.*[@CR78]). RNA-binding proteins TIA-1 (Kedersha *et al.*[@CR76]; Gilks *et al.*[@CR49]), G3BP (Tourriere *et al.*[@CR144]; Matsuki *et al.*[@CR97]) and PABP (Ma *et al.*[@CR96]; Smith and Gray [@CR136]; Burgess *et al.*[@CR16]) are three fundamental components of SG during stress (Fig. [1](#Fig1){ref-type="fig"}). GW182 and de-capping/de-adenylating enzymes are specific components of PB (Kedersha *et al.*[@CR78]), where siRNA- or miRNA-guided mRNAs are processed and degraded (Liu *et al.*[@CR94]) (Fig. [1](#Fig1){ref-type="fig"}). Virus infection imposes stress on host cells (McInerney *et al.*[@CR101]) and thereby induces SG formation. SG can shut off the translation of bulk mRNAs (Poblete-Duran *et al.*[@CR119]) to regulate gene expression and compartmentalization of heterologous viral RNAs and proteins. At the same time, viruses must take strategies to confront these responses and maximize their own replication efficiency (White and Lloyd [@CR153]) by inhibition of SG formation and disruption of PB assembly via virally encoded factors.Fig. 1Mammalian RNA granules. HeLa cells immunostaining with anti-TIA-1 (left and middle, red) show stress granules (SG) during stress of NaAS~2~O~3~ (+arsenite, middle) and with anti-GW182 show processing bodies (PB) under physiological condition. Arrows indicate granules (SG or PB).

Viral Regulation of RNA Stress Granule Formation {#Sec2}
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SG Formation and Induction of SG by RNA Virus Infections {#Sec3}
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The process of SG formation can be artificially divided into the following steps (Fig. [2](#Fig2){ref-type="fig"}): (1) accumulation of stalled translation initiation complexes (Panas *et al.*[@CR116]) in response to various types of stress; (2) the RNA-binding proteins such as RAS-GTPase-activating protein SH3 domain-binding protein 1 (G3BP1) and T cell-restricted intracellular antigen 1 (TIA1) bind mRNAs and aggregate to nucleate SG formation. Self-aggregation of G3BP1 (Tourriere *et al.*[@CR144]) and the binding of TIA1 and TIAR (TIA-1-related protein) to polysome-free mRNAs, which exposes prion-like domains (Gilks et al. [@CR49]), trigger mRNP aggregation. The aggregation of proteins is dynamic, and can rapidly exchange between SG and cytosol (Kedersha *et al.*[@CR77], [@CR78]). (3) large SG aggregate from smaller foci via posttranslational modification and microtubule transport (McCormick and Khaperskyy [@CR99]). Many SG proteins undergo multiple post-translational modifications (Jayabalan *et al.*[@CR73]; Protter and Parker [@CR120]). For example, G3BP1 must be demethylated (Tsai *et al.*[@CR145]), dephosphorylated (Kedersha *et al.*[@CR81]) and poly(ADP)-ribosylated (Leung *et al.*[@CR87]) to promote SG nucleation. Accordingly, SG formation also requires ongoing transport of mRNPs along with an intact microtubule cytoskeleton (Ivanov *et al.*[@CR68]). Theoretically, viral interference with any of these important steps may modulate SG formation in cells. In fact, many viral factors can interfere with SG formation and/or function. Meanwhile, SG can entrap viral RNA in some cases (McCormick and Khaperskyy [@CR99]). Therefore, SG are thought to be antiviral (Rozelle *et al.*[@CR126]). Thus, to illustrate the relationship between SG and RNA viruses would be important for us to better understand the interactions of host and viruses.Fig. 2Viruses induce SG formation. Type I SG formation: RNAs derived from rotavirus, RSV and HCV activate PKR; High levels of glycoproteins produced from enveloped virus activate PERK; HCMV infection activates PERK; Sindbis virus genomic RNA activates GCN2. Type II SG formation: RVFV attenuates mTOR signaling to inhibite 4EBP phosphorylation. All above lead to the formation of stalled translation complexes to initiate the assembly of SG.

Up to the present, SG can be divided into two types according to their formation mode. Type I SG formation depends on phosphorylation of eukaryotic translation initiation factor-2α (eIF2α) by one of the eIF2 kinases---double-stranded RNA (dsRNA)-activated protein kinase or protein kinase R (PKR) (Srivastava *et al.*[@CR138]; Garcia *et al.*[@CR48]; Onomoto *et al.*[@CR115]), PKR-like ER kinase (PERK) (Harding *et al.*[@CR53], [@CR54]), general control non-derepressible protein 2 (GCN2) (Wek *et al.*[@CR151]; Deng *et al.*[@CR29]) or haeme-regulated inhibitor (HRI) (McEwen *et al.*[@CR100]), which are activated by distinct types of stress. Phosphorylated eIF2α stably binds to eIF2β, which prevents the recycle of eIF2 and regeneration of the eIF2-GTP-Met-tRNA~i~^Met^ ternary complex. Thus, eIF2α phosphorylation blocks recognition of the initiation codon and joining of the large ribosomal subunit, resulting in accumulation of stalled 48S mRNPs (Jackson *et al.*[@CR71]). Type II SG formation is independent of eIF2α phosphorylation, but requires eIF4F complex disruption such as inhibition of eIF4A RNA helicase (Bordeleau *et al.*[@CR12]; Dang *et al.*[@CR26]) or disruption of eIF4E activity (von der Haar *et al.*[@CR148]; Fournier *et al.*[@CR40]) for recognition and binding of RNA cap structure. The stress induced by nutrient, energy, oxygen or growth factor insufficiency inhibits mTOR complex 1 (mTORC1), whose activity is required for the dissociation of 4EBPs from eIF4E (Fujimura *et al.*[@CR43]) and enables eIF4E to form the eIF4F complex, and thus blocks assembly of pre-initiation complexes (Zoncu *et al.*[@CR165]).

Type I SG formation induced by viruses is the most and best-studied example (Table [1](#Tab1){ref-type="table"}, Fig. [3](#Fig3){ref-type="fig"}A). Various RNA products derived by viruses including long dsRNA (Rojas *et al.*[@CR125]), 5′-triphosphate RNA (5′-ppp-RNA) (Nallagatla *et al.*[@CR107]), dsRNA that is formed by the antiparallel mRNA transcripts of some DNA viruses (Willis *et al.*[@CR157]), and human immunodeficiency virus (HIV) transactivation-response region (TAR) RNA hairpins (Heinicke *et al.*[@CR56]), can be recognized by PKR. The activated PKR initiates SG assembly through eIF2α phosphorylation. For instance, the persistent phosphorylation of eIF2α (Montero *et al.*[@CR105]) during rotavirus infection is PKR-dependent as a consequence of the accumulation of viral dsRNA in the cytoplasm outside the viroplasms (virus-induced cytoplasmic inclusion bodies called viroplasms \[VMs\]) (Rojas *et al.*[@CR125]). Even though eIF2α is phosphorylated in rotavirus-infected cells, the formation of SG is prevented and viral proteins are efficiently translated, suggesting that the virus prevents the assembly of these structures presumably downstream of eIF2α phosphorylation to allow the translation of its mRNAs (Mazroui *et al.*[@CR98]). Very recently, Dhillon and Rao found that rotavirus induces formation and sequestration of remodeled SG and PB in the VMs which contain the majorities of their components but selective exclusion of a few proteins (G3BP1 and ZBP1 for SG, DDX6, EDC4 and Pan3 for PB), to promote virus replication (Dhillon and Rao [@CR30]). Oceguera *et al.* demonstrated that viral RNA of rotavirus could interact with several RNA binding proteins (RBPs) (Xrn1, Dcp1, Ago2, Hur) and interfere with their subcellular localization (Oceguera *et al.*[@CR113]). Lindquist *et al.* (Lindquist *et al.*[@CR91]) first determined that SG induction by respiratory syncytial virus (RSV) was mediated by PKR-dependent eIF2α phosphorylation. The RSV-mediated SG formation was significantly reduced in PKR-knockdown cells (Lindquist *et al.*[@CR90]). In addition, it has been shown that Hepatitis C virus (HCV) strongly activates PKR via the 5′-untranslated region (UTR) of its genome (Toroney *et al.*[@CR143]), thereby inducing SG. NS1-mutant Influenza virus A (IAV) (Khaperskyy *et al.*[@CR82]; Mok *et al.*[@CR104]; Ng *et al.*[@CR110]) and C protein-deficient Sendai virus (SeV) (Takeuchi *et al.*[@CR141]) lead to significant activation of PKR and eIF2α phosphorylation. Besides, PERK could be activated by high levels of glycoproteins produced from enveloped viruses (Chan and Egan [@CR19]), and general control non-derepressible-2 (GCN2) could be activated by Sindbis virus (SINV) genomic RNA (Berlanga *et al.*[@CR10]), both leading to phosphorylation of eIF2α. GCN2 prevents replication of SINV in the early stages of the viral replicative cycle by blocking the synthesis of NSPs from SINV RNA (Berlanga *et al.*[@CR10]; Frolova *et al.*[@CR42]; Gorchakov *et al.*[@CR50]).Table 1Regulation of SG by viruses.GenomeVirus familyVirusTypeMechanismReferencesdsDNA*Herpesviridae*HCMVInductionModifies the UPR and activates PERKIsler *et al*. ([@CR67])InhibitionpTRS1 and pIRS1 antagonize PKR to facilitate virus replicationZiehr *et al.* ([@CR164])KSHVInhibitionORF57 interacts with PKR and PACT to inhibit PKR activationSharma *et al*. ([@CR131])HSV-1Inhibitionvhs and Us11 protein play a key role in blocking the activation of PKRSciortino *et al*. ([@CR128])HSV-2Inhibitionvhs localizes to SG and its endoribonuclease activity is required to disrupt SG formationFinnen *et al*. ([@CR37], [@CR38], [@CR39])*Poxviridae*VVInhibitionSequesters crucial SG components within DNA factoriesKatsafanas and Moss ([@CR74]), Zaborowska *et al*. ([@CR163])InductionUntranslated mRNA accumulation in viral DNA factories induces RNA granules formationMeng and Xiang ([@CR102])dsRNA*Reoviridae*RotavirusInductionPhosphorylation of eIF2α is PKR-dependent as a consequence of the accumulation of viral dsRNAMontero *et al*. ([@CR105], Rojas *et al*. ([@CR125])ModulationInduces formation and sequestration in the VMs of remodeled SG and PBDhillon and Rao ([@CR30])(+)ssRNA*Picornaviridae*PVInhibitionViral 3C protease cleaves G3BPWhite *et al*. ([@CR154])FMDVInhibitionViral 3C protease cleaves G3BPYe *et al*. ([@CR160])Leader Protease Cleaves G3BP1 and G3BP2Visser *et al*. ([@CR147])TMEVInhibitionExpress the leader (L) protein to inhibit G3BP1 aggregationBorghese and Michiels ([@CR13])MengovirusInhibitionExpress the leader (L) protein to inhibit G3BP1 aggregationBorghese and Michiels ([@CR13])EV71Modulation2A protease inhibits typical SG formation but induces atypical SG formation by cleaving eIF4GIYang *et al*. ([@CR159])*Caliciviridae*FCVInhibitionNS6Pro cleaves G3BP1Humoud *et al*. ([@CR63])*Togaviridae*SINVInductionGenomic RNA activates GCN2Berlanga *et al*. ([@CR10])*Flaviviridae*WNVInhibition3′-end viral genome captures TIA-1/TIARLi *et al*. ([@CR88], Emara and Brinton ([@CR35])DENVInhibition3′-end viral genome captures TIA-1/TIARLi *et al*. ([@CR88]), Emara and Brinton ([@CR35]), Ward *et al*. ([@CR150])3′-UTR interacts with G3BP1, G3BP2, Caprin1 and USP10JEVInhibitionRecruits G3BP and USP10 to the perinuclear regionTu *et al*. ([@CR146])NS2A interact with PKR and prevent PKR dimerizationWard *et al*. ([@CR150])HCVInductionActivates PKR via the 5′- UTR of its genomeToroney *et al*. ([@CR143])InhibitionNS5A protein binds to the PKR dimerization domain to inhibit PKR activationToroney *et al*. ([@CR143])Modulate GADD34 and PP1 to de-phosphorylate eIF2αRuggieri *et al*. ([@CR127])HCV-JFH1ModulationRedistributes several SG components to the HCV replication complex (RC)Ariumi *et al*. ([@CR7], Garaigorta *et al*. ([@CR47], Pene *et al*. ([@CR118])ZIKVInhibitionInduces the redistribution of TIAR to the viral RNA replication sitesHou *et al*. ([@CR60])(−)ssRNA*Arenaviridae*JUNVInhibitionN and GPC impair the phosphorylation of eIF2αLinero *et al*. ([@CR92])*Bunyaviridae*RVFVInhibitionRVFV attenuates mTOR signaling to inhibite 4EBP phosphorylationHabjan *et al*. ([@CR52]), Ikegami *et al*. ([@CR64]), Hopkins *et al*. ([@CR59])*Coronaviridae*MERS-CoVInhibitionAccessory protein 4a bind viral dsRNA and prevent the viral dsRNA from PKR bindingRabouw *et al*. ([@CR121]), Nakagawa *et al*. ([@CR106])*Filoviridae*EBOVInhibitionVP35 bind viral dsRNA and prevent the viral dsRNA from PKR bindingNelson *et al*. ([@CR109], Le Sage *et al*. ([@CR86])ModulationSG proteins are selectively sequestered within virus inclusions and co-localize with viral RNA to form inclusion-bound granulesNelson *et al*. ([@CR109])*Rhabdoviridae*VSVModulationInduces formation of the SG-like structures that co-localize with viral replication proteins and RNADinh *et al*. ([@CR31])*Paramyxoviridae*MVInhibitionEncode a C protein to limit the accumulation of dsRNAOkonski and Samuel ([@CR114])SeVInhibitionEncode a C protein to limit the accumulation of dsRNATakeuchi *et al*. ([@CR141])Trailer RNA captures TIAR from SGIseni *et al*. ([@CR66])RSVInductionMediated by PKR-dependent eIF2α phosphorylation.Lindquist *et al*. ([@CR91])InhibitionSequestration of OGT in IBsFricke *et al*. ([@CR41])HPIV3InhibitionIBs shield viral RNAs from recognition by PKRHu *et al*. [@CR61])Fig. 3Viruses interfer with SG formation. **A** Viruses modulate eIF2α phosphorylation. IBs of HPIV3 shield viral RNAs from recognition by PKR; IAV NS1, MERS-CoV accessory protein 4a, EBOV VP35, SeV and MV C protein and KSHV ORF57 prevent viral dsRNA from binding by PKR; ORF57 interacts with PACT to prevent PKR activation; HCMV pTRS1 and pIRS1 and HSV-1 vhs and Us11 block PKR activation; HCV NS5A and JEV NS2A interact with PKR and prevent PKR dimerization; N and GPC of JUNV impair the phosphorylation of eIF2α; HCV modulates GADD34 and PP1 to de-phosphorylate eIF2α. **B** Viruses modulate SG formation downstream of eIF2α phosphorylation. 3C protease of PV, EMCV, FMDV and CVB3 cleaves G3BP at Q326; FCV NS6 protein cleaves G3BP at E405; 2A protease of EV71, PV and CVA cleaves eIF4G at G689; L protein of both TMEV and mengovirus inhibits G3BP1 aggregation; DENV 3′-UTR interacts with G3BP; SeV Trailer RNA captures TIAR from SG; WNV and Dengue virus (DENV) 3′-end genome captures TIA-1/TIAR; HSV-2 vhs localizes to SG and its endoribonuclease activity is required to disrupt SG formation; EBOV and RSV sequester SG proteins within viral inclusion bodies; VV sequesters crucial SG components within DNA factories.

Viruses also induce SG formation independent of eIF2α phosphorylation (Table [1](#Tab1){ref-type="table"}). The most typical example is from Rift Valley fever virus (RVFV) (Habjan *et al.*[@CR52]; Ikegami *et al.*[@CR64]) (Fig. [2](#Fig2){ref-type="fig"}). RVFV (Hopkins *et al.*[@CR59]) infection attenuates Akt/mTOR signaling and inhibits 4EBP phosphorylation and translation of 5′-TOP mRNAs, subsequently leading to an inhibition of global protein translation. 5′-TOP--containing mRNAs are indeed targeted to PB, where RVFV uses these cellular mRNAs for cap-snatching (Hopkins *et al.*[@CR59]). This can reflect that SG may interact with PB in a process that is thought to result in the exchange of mRNA cargos (Kedersha *et al.*[@CR79]). Whether any virus induces SG formation to cause translation inhibition due to the destruction of eIF4G or eIF4A is worth exploring in the future.

RNA Viruses Modulate SG Formation or Assembly {#Sec4}
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SG formation shuts off bulk host protein synthesis. However, all viruses depend on the host translation apparatus for their gene expression. Therefore, viruses, as intracellular parasites, have to modulate the stress response pathway and SG assembly to translate their proteins for virus replication. RNA viruses modulate stress response pathway at different levels of SG formation (Table [1](#Tab1){ref-type="table"}): One is to regulate eIF2α phosphorylation, and the other is to regulate the process of SG nucleation.

### RNA Viruses Modulate eIF2α Phosphorylation to Interfere with SG Formation {#Sec5}

In some cases, viral gene products can act as antagonists by targeting the virus-activated eIF2α kinases such as PKR or even by directly modulating the phosphorylation of eIF2α (Fig. [3](#Fig3){ref-type="fig"}A). IAV NS1 (Khaperskyy *et al.*[@CR82]; Ng *et al.*[@CR110]), Middle East respiratory syndrome coronavirus (MERS-CoV) accessory protein 4a (Rabouw *et al.*[@CR121]; Nakagawa *et al.*[@CR106]), and Ebola virus (EBOV) multifunctional protein VP35 (Nelson *et al.*[@CR109]; Le Sage *et al.*[@CR86]) bind viral dsRNA and prevent the viral dsRNA from PKR binding to inhibit SG formation. Inhibition of SG formation facilitates the translation of viral mRNAs, leading to efficient virus replication. HCV NS5A protein (Toroney *et al.*[@CR143]) binds to the PKR dimerization domain to inhibit PKR activation. Japanese encephalitis virus (JEV) NS2A protein (Tu *et al.*[@CR146]) might similarly interact with PKR and then prevent PKR dimer formation. SeV (Takeuchi *et al.*[@CR141]) and measles virus (MV) (Okonski and Samuel [@CR114]) encode a C protein to limit the accumulation of dsRNA to inhibit SG formation. It seems that a portion of RNA viruses encode RNA binding proteins to antagonize the activity of PKR. There are also other groups of RNA viruses which directly modulate the phosphorylation of eIF2α without PKR. Junín virus (JUNV) prevents SG assembly by impairing the phosphorylation of eIF2α through its nucleoprotein (N) and glycoprotein precursor (GPC) (Linero *et al.*[@CR92]). However, its mechanism remains to be elucidated, although it may be similar to HCV. Ruggieri and colleagues reported that HCV rapidly de-phosphorylated eIF2α through protein phosphatase 1 (PP1) and its regulatory subunit GADD34 (growth arrest and DNA-damage-inducible 34) (Kojima *et al.*[@CR84]; Clavarino *et al.*[@CR23]; Ruggieri *et al.*[@CR127]).

### RNA Viruses Cleave/Sequester/Redistribute Stress Granule-Nucleating Proteins to Interfere with SG Assembly {#Sec6}

Several RNA viruses have been shown to express viral effectors that can actively disrupt the accumulation of SG through cleavage of SG components (Fig. [3](#Fig3){ref-type="fig"}B). Poliovirus (PV) induces SG formation in early phase but induces SG disassembly at later stages via cleavage of G3BP by viral 3C, thus preventing SG formation (White *et al.*[@CR154]). Similar findings were also reported for encephalomyocarditis virus (EMCV) (Ng *et al.*[@CR110]), foot-and-mouth disease virus (FMDV) (Ye *et al.*[@CR160]; Visser *et al.*[@CR147]), coxsackievirus B3 (CBV3) (Fung *et al.*[@CR44]) and feline calicivirus (FCV) (Humoud *et al.*[@CR63]). FCV infection does not cause accumulation of SG, despite an increased phosphorylation of eIF2α (Humoud *et al.*[@CR63]). This is because FCV NS6Pro, a 3C-like proteinase, cleaves G3BP1 at a site different from the poliovirus 3C proteinase. Unlike FCV, murine norovirus (MNV) does not cleave G3BP1 and thus does not inhibit SG formation during virus infection (Humoud *et al.*[@CR63]). In general, picornaviruses inhibit SG formation by viral 2A/L or 3C cleaving the major components of SG. In recent study, Yang *et al*. found that the 2A protease of picornavirus (EV71, PV, CVA) inhibits typical SG formation, which is PKR and eIF2α phosphorylation-dependent, but induces atypical SG formation by cleaving eIF4GI to sequester cellular mRNA and release viral mRNA, thereby facilitating viral infection (Yang *et al.*[@CR159]). In other words, the 2A protease can transform the overall translation machinery favorable for productive viral infection by induction of atypical SG while blocking the typical SG in the presence of G3BP cleavage by viral 3C protease during viral infection (Yang *et al.*[@CR159]).

Redistribution or sequestering SG components to the viral replication sites is another strategy used by many viruses to impair SG assembly in infected cells (Fig. [3](#Fig3){ref-type="fig"}B). ZIKV infection induces the redistribution of TIAR to the viral RNA replication sites (Hou *et al.*[@CR60]); SeV Trailer RNA captures TIAR from SG (Iseni *et al.*[@CR66]); West Nile Virus (WNV) and Dengue virus (DENV) 3′-end viral genome captures TIA-1/TIAR (Li *et al.*[@CR88]; Emara and Brinton [@CR35]; Xia *et al.*[@CR158]); DENV 3′-UTR interacts with G3BP1, G3BP2, Caprin1 and USP10 (Ward *et al.*[@CR150]; Reineke *et al.*[@CR123]); JEV recruits G3BP and USP10 to the perinuclear region through the interaction of JEV core protein with Caprin-1, a SG-associated cellular factor (Ward *et al.*[@CR150]). Theiler murine encephalomyelitis virus (TMEV) and mengovirus, a strain of EMCV, express the leader (L) protein to inhibit G3BP1 aggregation (Borghese and Michiels [@CR13]). Sequestration or redistribution of SG components by viruses through protein--protein and protein-RNA interactions not only prevents SG assembly, but also facilitates viral genome replication. HCV-JFH1 infection redistributes several SG components, including G3BP1, ataxin-2 (ATX2), and poly(A)-binding protein 1 (PABP1), to the HCV replication complex (RC) (Ariumi *et al.*[@CR7]; Pene *et al.*[@CR118]), and co-opts G3BP1 to mediate efficient viral replication by interaction with NS5B and the 5′ end of the HCV minus-strand RNA (Ariumi *et al.*[@CR7]; Garaigorta *et al.*[@CR47]).

RNA Virus Inclusion Bodies (IBs) Emerging as a New Strategy Used by Viruses to Resist SG {#Sec7}
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Studies on Human parainfluenza virus type 3 (HPIV3) (Hu *et al.*[@CR61]), RSV (Rincheval *et al.*[@CR124]), EBOV (Hoenen *et al.*[@CR58]), Rabies virus (RABV) (Lahaye *et al.*[@CR85]) and Vesicular stomatitis virus (VSV) (Heinrich *et al.*[@CR57]) showed that inclusion bodies (IBs) of negative stranded RNA viruses are the sites of viral RNA synthesis. A recent study suggested an emerging role of IBs in HPIV3 replication by shielding newly synthesized viral RNA from the antiviral effect of SG (Hu *et al.*[@CR61]) (Fig. [3](#Fig3){ref-type="fig"}B). Sequestration of O-linked N-acetylglucosamine (OGN) transferase (OGT), an enzyme that catalyzes the posttranslational addition of OGN to protein targets, in RSV IBs was also proposed to regulate SG nucleation and suppression of SG formation (Fricke *et al.*[@CR41]) (Fig. [3](#Fig3){ref-type="fig"}B). Viral transcription and replication of RABV take place within Negri bodies (NBs), which are IB-like structures (Lahaye *et al.*[@CR85]). RABV-induced SG are normally located closely to NBs. Viral mRNAs rather than viral genomic RNA accumulate in the SG-like structures together with cellular mRNAs were found to be specially transported from NBs to SG-like structures (Nikolic *et al.*[@CR112]). VSV infection also induces formation of the SG-like structures that co-localize with viral replication proteins and RNA, which are different from canonical SG (Dinh *et al.*[@CR31]). SG proteins (eIF4G, eIF3, PABP) are selectively sequestered within Ebola virus inclusion bodies and co-localize with viral RNA to form inclusion body-bound granules, which are functionally and structurally different from canonical SG, probably leading to inhibit the antiviral role of SG (Nelson *et al.*[@CR109]) (Fig. [3](#Fig3){ref-type="fig"}B). Collectively, these findings provoke more investigations on the roles of viral IBs in viral replication and resisting cellular responses. Fig. 4Disruption of PB assembly by viruses. The mRNA translation can be stopped for various reasons including the binding of miRNA. The translating mRNA can be stripped of ribosomes and the initiation complex can be collaps when binding to miRNA-RISC complex. The mRNPs targeted by PB components undergo three outcomes: 1. Translational inhibition; 2. Pan2/3-mediated deadenylation; 3. RNA decay by other associated RNA decay factors (e.g., Xrn1, Dcp1a, DDX6, and Lsm). Several RNA and DNA viruses which inhibit PB assembly are shown.

DNA Viruses Regulate SG Formation {#Sec8}
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Unlike RNA viruses, the regulation of SG formation during infection with DNA viruses is poorly understood. It was reported that human cytomegalovirus (HCMV) infection modifies the unfolded protein response (UPR) and activates PERK (Fig. [2](#Fig2){ref-type="fig"}), but limiting the amount of phosphorylated eIF2α to maintain translation (Isler *et al.*[@CR67]). Kaposi's sarcoma-associated herpesvirus (KSHV) ORF57 (Sharma *et al.*[@CR131]) interacts with PKR and PKR-activating protein (PACT) (Patel *et al.*[@CR117]) to inhibit PKR binding dsRNA and prevent PACT-PKR interaction in the PKR pathway (Li *et al.*[@CR89]), respectively. HCMV pTRS1 and pIRS1 antagonize PKR to facilitate virus replication (Ziehr *et al.*[@CR164]). The HSV-1 vhs (Sciortino *et al.*[@CR128]) and Us11 protein (Cassady and Gross [@CR17]) play a key role in blocking the activation of PKR. Smiley and colleagues also demonstrated that infection with virion host shutoff protein (vhs)-defective herpes simplex virus 1 (HSV-1) triggers SG formation, and PKR is essential for SG formation in the absence of vhs (Dauber *et al.*[@CR27]) (Fig. [3](#Fig3){ref-type="fig"}A). Finnen *et al.* previously established that herpes simplex virus 2 (HSV-2) infection impacts stress granule accumulation in response to oxidative stress (Finnen *et al.*[@CR37]). They also demonstrated that disruption of SG is mediated by vhs (Finnen *et al.*[@CR38]), whose endoribonuclease activity is required to disrupt SG formation (Finnen *et al.*[@CR39]). HSV-2 vhs indeed have the ability to localize to SG (Finnen *et al.*[@CR39]) (Fig. [3](#Fig3){ref-type="fig"}B). This implies that removal of RNA from SG promotes its disassembly and that intact RNA is crucial for maintaining SG structure. It will be interesting to test the function of endoribonucleases in SG disassembly. Vaccinia virus (VV) sequesters crucial translation initiation factors, such as G3BP1, Caprin1, eIF4E, PABP and eIF4G (Katsafanas and Moss [@CR74]; Simpson-Holley *et al.*[@CR134]; Zaborowska *et al.*[@CR163]), within cytoplasmic viral DNA factories to utilize SG components for different purposes (Fig. [3](#Fig3){ref-type="fig"}B). A recent study (Meng and Xiang [@CR102]) suggested that the RNA granules are resulted from untranslated mRNA accumulation in viral DNA factories (Liu and Moss [@CR93]) and TIA-1 is probably not required for granule formation and anti-poxviruses. Instead, the granules formation is most likely driven by an array of RNA--protein interactions and requires no specific SG components (Sivan *et al.*[@CR135]; Meng and Xiang [@CR102]).

Viral Regulation of RNA Processing Body Assembly {#Sec9}
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Assembly of P-Bodies (PB) {#Sec10}
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PB were first reported in the scientific literature by Bashkirov *et al.* in [@CR8], and described as "small granules or discrete, prominent foci" or as the cytoplasmic location of the mouse exoribonuclease mXrn1p (Bashkirov *et al.*[@CR8]). Like SG, PB lack outer lipid membrane and now are recognized to be the sites where non-translating mRNAs accumulate for different fates including decay, storage, or returning to translation. A variety of enzymes involved in mRNA deadenylation (Ccr1, Caf1, Not1) (Sheth and Parker [@CR132]), decapping (Dcp1/2, Lsm1-7, Edc3proteins) (Ingelfinger *et al.*[@CR65]; Yu *et al.*[@CR162]), nonsense-mediated decay (NMD) proteins (SMG5-6-7, UPF1) (Ingelfinger *et al.*[@CR65]; Durand *et al.*[@CR33]), in addition to scaffolding proteins (Ge-1/Hedls) (Yu *et al.*[@CR162]) and translation control factors (CPEB, eIF4E-T) (Andrei *et al.*[@CR5]; Wilczynska *et al.*[@CR156]), are the components of PB and used as routine markers to distinguish these granules. Nonetheless, some components (APOBEC3G, BRF1, DDX3, FAST, TTP, Rap55) (McEwen *et al.*[@CR100]; Sen and Blau [@CR129]; Gallois-Montbrun *et al.*[@CR46]; Chen *et al.*[@CR21]) have also been shown to be shared by both SG and PB, suggesting a substantial linkage of these two structures and movement of mRNAs between both RNA granules. Interestingly, among these components, PB also include RNA-induced silencing complex (RISC) or miRNA associated argonaute (Ago) proteins (also shared with SG) and the GW182 protein which provides scaffolding activities for RISC to function, suggesting PB being the sites of miRNA mediated translation repression. The scaffolding activity of GW182 is critical for PB and knockdown of GW182 expression disrupts PB formation (Liu *et al.*[@CR94]). Notably, GW182 has been shown to bind to Ago2 which is critical for miRNA function and PB formation (Liu *et al.*[@CR94]). Recent evidence indicates that GW182 can recruit up to three molecules of Ago2 via its three GW motifs (glycine-tryptophan repeats) while each Ago protein has a single GW182-binding site (Elkayam *et al.*[@CR34]) (Fig. [4](#Fig4){ref-type="fig"}).

By applying fluorescence-activated particle sorting to purify PB in combination with mass spectrometry, Hubstenberger *et al*. identified 125 proteins that are significantly associated with PB (Hubstenberger *et al.*[@CR62]). By labeling several PB-localized proteins with a BirA (*E. coli* biotin ligase) enzyme in combination with mass spectrometry after streptavidin pulldown, Youn *et al*. identified 38 proteins in the PB (Youn *et al.*[@CR161]). ISGs (interferon stimulated genes) can also be found in PB during virus infection (Hebner *et al.*[@CR55]).

RNA Viruses and PB {#Sec11}
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In comparison to viral regulation of SG, interaction of virus and PB was not much explored. It is an assumption that RNA viruses must regulate RNA decay processes/machinery to prevent degradation of virus genomes and mRNAs. Recently, some progress has been made to understand the relationship between PB components and some viruses in the context of viral gene expression. The data in published literatures are summarized in (Table [2](#Tab2){ref-type="table"}). Mutation induced in the PB core components to affect the viral life cycles are well studied and tabulated in an earlier review (Beckham *et al.*[@CR9]). The report linking the assembly of yeast Ty3 retrotransposons virus---like particles with PB presented the first link between human retrovirus and PB (Checkley *et al.*[@CR20]). The later study revealed PB to be the site of anti-viral host factors APOBEC3G and APOBEC3F (A3G or A3F, apolipoprotein B mRNA-editing enzyme catalytic polypeptide 1-like) family of cytidine de-aminases, presumably representing a component of innate immunity against HIV (Wichroski *et al.*[@CR155]; Gallois-Montbrun *et al.*[@CR46]). In a different study, A3F was found to specifically interact with cellular signal recognition particle RNA (7SL RNA). Efficient packaging of 7SL RNA and A3F into HIV virons was mediated by the RNA-binding nucleocapsid domain of HIV-1 Gag (Wang *et al.*[@CR149]).Table 2Regulation of PB assembly by virusesGenomeVirus familyVirusP-bodies: accumulation/inhibitionMechanismReferencesdsDNA*Adenoviridae*AdenovirusInhibitionRedistribution of PB components by E4 11K including (Rck/p54/DDX6, Ago2, xrn1, Ge1, and Lsm-1)Greer *et al*. ([@CR51])*Herpesviridae*Kaposi's sarcoma herpes virus (KSHV)InhibitionDisruption of Ago2-GW182 interaction during lytic infection via ORF57Sharma N. *et al*. unpublishedHerpes simplex virus-1 (HSV-1)InhibitionVia ICP27Sharma N. *et al*. unpublishedCytomegalovirus (HCMV)AccumulationIncreased expression of Dcp1a, EDC4, Rck/p54/DDX6 and Rap55 proteinsSeto *et al*. [@CR130])dsRNA*Reoviridae*RotavirusInhibitionSponge for RNA binding proteins which can redistribute several components of PB including Ago2, GW182 and Dcp1Oceguera *et al*. [@CR113])Decreased expression of Pan3 and relocalization of Xrn1 and Dcp1Bhowmick *et al*. ([@CR11])(+)ssRNA*Flaviviridae*West Nile virus (WNV)InhibitionRedistribution of Lsm1, GW182, DDX6, DDX3 and Xrn1 to viral replication factories (RF)Chahar *et al*. [@CR18])Dengue virus (DENV)InhibitionN/AEmara and Brinton ([@CR35])Yellow fever virus (YFV)AccumulationsfRNA stalls Xrn1 and co-localizes at PBSilva *et al*. [@CR133])Hepatitis C virus (HCV)InhibitionRedistribution of DDX6, Lsm1, Xrn1, PATL1 and Ago2 to lipid dropletsAriumi *et al*. [@CR7])Dcp2 does not localize to viral factoriesAriumi *et al*. [@CR7])*Picornaviridae*Poliovirus (PV)InhibitionDegradation of Xrn1, Dcp1a and Pan3 but not of GW182, EDC3/EDC4Dougherty *et al*. ([@CR32])Viral Protease 2A blocks PB formationCoxsackievirus B3 (CVB3)InhibitionCleavage of Xrn1, Dcp1a and Pan3Dougherty *et al*. ([@CR32])*Dicistroviridae*Cricket paralysis virus (CrPV)InhibitionDisrupts only GW182/Dcp1 aggregate, but not Ago1/Ago2Khong and Jan [@CR83])*Togaviridae*Sindbis virus (SINV)InhibitionHuR-translocation out of the nucleusSokoloski *et al*. [@CR137])(−)ssRNA*Orthomyxoviridae*Influenza virus A (IAV)InhibitionInteraction of RAP55 and NSP1Mok *et al*. [@CR104])*Bunyaviridae*HantavirusAccumulationCap snatching occurs in PBMir *et al*. [@CR103])ssRNA-RT*Retroviridae*Human immunodeficiency virus type 1 (HIV-1)InhibitionHIV-1 mRNA interacts with DDX6, Ago 2 and APOBE3G and displaces from the PBNathans *et al*. [@CR108])Redistribution of PB components during the HIV-1 infectionAbrahamyan *et al*. [@CR1])Assembly intermediates (AIs) recruits DDX6 and ABCE1Reed *et al*. [@CR122])miR-29a-HIV-1 mRNA interactions enhance viral mRNA association with RISC and PBNathans *et al*. [@CR108])MOV10 overexpression inhibits HIV-1 replicationBurdick *et al*. [@CR15], Furtak *et al*. [@CR45])

The bona fide and unique dependence of viruses on PB came from the studies on plant brome mosaic virus (BMV) (Beckham *et al.*[@CR9]). This study suggested the accumulation of BMV mRNAs in PB was an important step in RNA replication complex assembly for BMV, and possibly for other positive-strand RNA viruses. Nonetheless, many RNA viruses initiate the process of transcription of viral RNA by the process of 'cap snatching' which involves the acquisition of capped 5′ oligonucleotides from cellular mRNAs. Interestingly, PB were shown to serve as a pool of primers in the case of Hantavirus while its nucleocapsid protein, which accumulates in PB, binds 5′ caps with high affinity (Mir *et al.*[@CR103]).

The base-pair complementarity between a miRNA and a target mRNA dictates the miRNA to specifically repress posttranscriptional expression of mRNAs. Subsequent events in this process involve relocation of RNA-induced silencing complexes (RISCs) together with several other RNA binding proteins to form PB. In this context, HIV-1 mRNA interacts with RISC proteins and disrupting PB structures enhances viral production and infectivity, suggesting a role of PB against viral infection (Nathans *et al.*[@CR108]). Specific miR-29a-HIV-1 mRNA interaction was found to enhance viral mRNA association with RISC and PB proteins and regulate HIV-1 production and infectivity. HIV Nef interacts with Ago2 via its glycine-tryptophan region and functions as a viral suppressor of RNAi (Aqil *et al.*[@CR6]). While overexpression of Mov10, a component of PB and an ATP-dependent 5′-3′ RNA helicase, inhibits HIV production (Burdick *et al.*[@CR15]; Furtak *et al.*[@CR45]), Mov10 and APOBEC3G localization to PB is not required for HIV virion incorporation and antiviral activity (Izumi *et al.*[@CR70]). It becomes clear that Mov10 inhibits virus infection by enhancing RIG-I-MAVS-Independent IFN Induction (Cuevas *et al.*[@CR25]) and stabilizing A3G from degradation (Chen *et al.*[@CR22]).

The anticipated evidence of viral disruption of PB also came from the study with poliovirus (PV), a plus-strand RNA virus showing that PB are disrupted during PV infection in cells by 4 h post infection (Dougherty *et al.*[@CR32]). This function is attributed to viral proteinase 3C which degrades several components of PB including Xrn1 and Dcp1a, but not affecting others such as GW182, Edc3 and Edc4. Rotaviruses disassemble PB by using viral RNA as a sponge for RNA binding proteins to redistribute several PB components, including Ago2, GW182 and Dcp1 PB (Oceguera *et al.*[@CR113]). In fact, rotavirus disrupts PB through multiple mechanisms. The viral NSP1 protein seems to degrade PB component Pan3, while relocalizing other two components (Xrn1 and Dcp1a) (Bhowmick *et al.*[@CR11]). Intriguingly, exclusion of SG and PB components from the viroplasm is important for rotavirus replication and progeny virus production (Dhillon and Rao [@CR30]).

DNA Viruses and PB {#Sec12}
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While RNA viruses have evolved to co-opt or modulate the assembly of PB, this effect is rather unclear during infection by DNA viruses. Since most of the DNA viruses replicate and assemble in the nucleus, therefore as proposed for RNA viruses, accumulation of viral RNAs in PB for assembly cannot be a strategy required by DNA viruses. However, the close relationship of PB with translational repression reasonably provides a foundation for PB being antiviral cellular components against DNA viruses. Thus it is assumed that those factories suppressing mRNA translation would inhibit protein production of DNA viruses. To fight back, the DNA viruses have to develope strategies to bypass this antagonism mediated by PB for their survival and productive infection (Table [2](#Tab2){ref-type="table"}).

Adenovirus E4 11 k, the product of E4 ORF3, accumulates viral late mRNA transcripts and at least five proteins of PB (Rck/p54/DDX6, Ago2, xrn1, Ge1, and Lsm-1) in the E4 11 k-induced cytoplasmic aggresomes. Redistribution of the PB components to the aggresomes, not to the PB, leads to inactivate or destroy these proteins. E4 11 k protein interacts with RNA helicase DDX6, one of the PB proteins, for its redistribution. Because PB are the sites for mRNA degradation, their alteration by E4 11 k suggests a role of E4 11 k in viral late mRNA accumulation (Greer *et al.*[@CR51]).

The role of PB in regulation of cytomegalovirus infection remains elusive. First, HCMV infection does not affect, but rather accumulates the formation of PB; second, PB formed during HCMV infection do not contain Ago2; third, HCMV prevents viral IE1 mRNA, a major IE gene product to encode a critical protein for viral gene expression and replication, from colocalization with PB (Seto *et al.*[@CR130]).

By generating a transgenic mice deficient of PB component LSm14A (or Rap55), recent studies showed that LSm14A plays a critical and specific role in the induction of antiviral cytokines (IFN-β, IFN-α, and IL-6) in dendritic cells (DCs). DNA viruses (HSV-1 and murine herpesvirus 68) and RNA virus VSV trigger this induction, but Sendai virus lacks such an effect (Anderson and Kedersha [@CR3]; Liu *et al.*[@CR95]). LSm14A deficiency specifically downregulates MITA/STING (stimulator of interferon genes) level in DCs by impairing its nuclear mRNA precursor processing. In contrast to its role in mRNA decay, this study revealed a role of LSm14 in nuclear mRNA precursor processing and cell-specific regulatory mechanism of antiviral immune responses (Liu *et al.*[@CR95]).

KSHV kaposin B, a latent protein linked with cancer progression, induces PB dispersion (Corcoran *et al.*[@CR24]). Kaposin B activates the stress-responsive kinase MK2 in endothelial cells (ECs) to selectively block the decay of AU-rich mRNAs (ARE-mRNAs) which encode pro-inflammatory cytokines and angiogenic factors and to reprogram ECs through post-transcriptional control of EC gene expression and secretion. KSHV ORF57 protein inhibits the formation of PB during lytic infection by disrupting the essential interaction of Ago2 with GW182 (unpublished data). These data provide the first evidence that a tumor virus RNA-binding protein ORF57 antagonizes the RNA regulatory pathway of host antiviral defenses during lytic infection.

Remarks and Perspectives {#Sec13}
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SG are highly dynamic structures (Jain *et al.*[@CR72]), which constantly exchange their components to regulate gene expression and are thought to be antiviral. SG composition appears to vary according to the inducing stimulus (Table [3](#Tab3){ref-type="table"}). It's clear that SG assembly/disassembly is a tightly regulated process which accompanies rearrangements of RNA and proteins (Wheeler *et al.*[@CR152]). Although significant advances have been made to understand how viruses regulate SG formation, our current knowledge is not suffucient to fully elucidate the machanism how SG are regulated in living cells. Further works are needed to address the following questions: First, is there any pathway to be a target for antiviral drug development? Second, do SG function as platforms that potentiate virus recognition? Third, is any unexplored pathway leading to SG formation which could be visualized by fluorescence in situ hybridization techniques---including single molecule RNA tracking methods in combination with super-resolution microscopy? Using viruses as a research tool will definitely teach us how the host fights virus infections and how the viruses get away from its host resistance.Table 3Viruses and SG components.GenomeVirus familyVirusSG componentsEffects on viral replication\*ReferencesProteinsRNAsdsDNA*Poxviridae*Vaccinia virusG3BP, Caprin-1, eIF4G, eIF4EViral but not host mRNASG stimulate viral translationKatsafanas and Moss [@CR74])(+)ssRNA*Picornaviridae*EV71Sam68, TIA-1, TIARCellular but not viral mRNAInduced aSG beneficial to viral translationYang *et al*. [@CR159])EV71-2A^C110S^eIF4G, G3BP, TIA-1Viral and cellular mRNAEV71-2A^C110S^ induced tSG inhibit viral translationYang *et al*. [@CR159])TMEV L^M60V^eIF3, TIA-1, PTB, G3BPNo viral RNA sequestered in SGN/ABorghese and Michiels [@CR13])(−)ssRNA*Rhabdoviridae*Rabies VirusG3BP1, TIA-1, PAPBViral and cellular mRNAEfficient for virus infectionNikolic *et al*. ([@CR112])VSVViral replication proteins and TIA-1, TIAR, PCBP2Viral RNANo effect on viral protein synthesis despite eIF2 phosphorylationDinh *et al*. [@CR31])*Paramyxoviridae*HPIV3TIA-1, G3BP, eIF4A, eIF4E, eIF4G+vRNA (the mRNA and the anti-genome RNA)Inhibition of SG formation facilitates HPIV3 replicationHu *et al*. [@CR61])RSVG3BP, HuR, eIF3η, TIA-1Genomic RNASG promote RSV replicationLindquist *et al*. ([@CR90])\**N*/*A* not available; aSG, atypical SG; tSG, typical SG.

PB affect viral infections in multiple ways. Thus, it is difficult to generalize a common viral strategy in a particular virus group to interact with the components of PB. The noticed evidence is that viruses in the same family may show extremely distant behavior when they come to interact with PB (Table [2](#Tab2){ref-type="table"}). More studies on virus interactions with PB will be required to characterize the PB to be proviral or antiviral in a context-dependent manner. Other key questions in the field for future studies are: (1) to understand the mechanisms that regulate PB formation in cells. Viral manipulation of PB may provide a better platform to understand this regulation; (2) to determine which viral RNA species preferentially travel through these RNA granules and which ones do not? (3) to identify the RNA elements dictating viral RNA to escape from SG and PB. Thus, discovery of virus regulations of PB assembly represents a new paradigm of virus-host interactions.

This work was supported by grants from the China Natural Science Foundation (81825015 and 31630086), the Natural Science Foundation of Hubei Province Innovation Group (2017CFA022), and Intramural Research Program of NCI/NIH (1ZIASC010357 to ZMZ).

Conflict of interest {#FPar1}
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The authors declare that they have no conflict of interest.

Animal and Human Rights Statement {#FPar2}
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This article does not contain any studies with human or animal subjects performed by any of the authors.
