Stress granules formed during different RNA virus infections show remarkable plasticity and substantial virus-specific differences in their formation and composition

Reto M. Lang, Silvio Steiner, Jenna Kelly, Anne-Christine Uldry, Pratik Dave, Sophie Braga-Lagache, Jeffrey Chao, Manfred Heller, Volker Thiel

Posted on: 3 November 2025 , updated on: 5 November 2025

Preprint posted on 14 August 2025

Naah, MHV plays stress granules like a pro: show up late, strip out the translation machinery, keep your RNA away, and let these 'empty shells' persist while you replicate freely.

Selected by Mohammed JALLOH

Categories: cell biology, immunology, microbiology, molecular biology

Why I picked this preprint

As a virologist and stress granules biologist, I chose to highlight this preprint because it fundamentally challenges our understanding of how stress granules work in antiviral defense. Using sophisticated proximity labeling proteomics and live-cell imaging, the authors reveal that stress granules are far more plastic and virus-specific than previously appreciated. The striking finding that MHV efficiently excludes its RNA from stress granules while SFV accumulates its RNA within them suggests these structures play different roles depending on the infecting virus. This work has important implications for understanding host-pathogen interactions and may explain why some viruses tolerate stress granule formation while others actively suppress it.

Background

Stress granules (SGs) are cytoplasmic condensates that form during cellular stress, containing translationally stalled mRNAs and associated proteins (1-3). SGs serve as antiviral signaling platforms by sequestering viral RNA and translation machinery (5,6,27). However, many viruses manipulate SGs differently: some prevent their formation or disassemble them, while others tolerate or even exploit them (8,9). Whether SGs formed during different viral infections share common features or exhibit virus-specific characteristics remains unclear.

Main goal

The authors of this preprint sought to comprehensively characterize and compare the proteome, formation kinetics, and composition of stress granules induced by two distinct RNA viruses: mouse hepatitis virus (MHV, a coronavirus) and Semliki Forest virus (SFV, an alphavirus), using oxidative stress-induced stress granules as a canonical reference.

Key Findings

Stress granule formation timing differs dramatically between MHV and SFV infections

The authors found fundamentally different timing kinetics between the two viruses (preprint-Fig4A-B). MHV induced rapid SG formation at 3 hours post-infection, reaching maximum numbers at 4-5 hpi, followed by complete dissolution by 8 hpi. These early granules showed robust activation of the integrated stress response and phosphorylation of eIF2α (preprint-Fig4C-D), indicating virus-induced oxidative stress. In contrast, SFV showed minimal stress response activation with substantially lower phosphorylation levels (preprint-Fig 4B-C). Despite these differences, cycloheximide inhibited SG formation from both viruses, confirming they are in equilibrium with polysomes like canonical stress granules.

Virus-induced stress granules are depleted of translation initiation factors

Proximity labeling combined with quantitative mass spectrometry revealed profound differences in the protein composition of virus-induced granules (preprint-Fig 5). Key translation initiation factors such as G3BP1, G3BP2, TIAL, and CAPRIN1 were present alongside ribosomal proteins. However, critical initiation factors like eIF3 and eIF4 showed reduced enrichment (preprint-Fig 6A, 7A). Direct comparison between MHV and SFV showed that SFV-enriched proteins were strongly associated with “organized” and “translation initiation” categories (preprint-Fig 6D), while MHV-enriched proteins associated with mRNP and nucleolar categories. This suggests entirely different relationships with stress granules—SFV’s RNA is sequestered in these structures, while MHV uses a different mechanism.

SG-localized viral RNA shows distinct patterns between viruses

Single molecule RNA fluorescence in situ hybridization (smRNA-FISH) revealed a fundamental difference in viral RNA localization relative to SGs (preprint-Fig 8). MHV genomic RNA was detected by probes targeting the nsp3-coding sequence and frequently localized to specific puncta outside of stress granules. In contrast, SFV RNA accumulated normally in MHV-induced granules but showed low colocalization with G3BP1 foci in SFV infections. Viral RNAs like ATF4 accumulated normally in MHV-induced granules (preprint-S13 Fig), demonstrating that these structures can selectively recruit host mRNAs. This indicates the viruses have fundamentally different strategies for managing RNA in stress granules.

Conclusions

This study reveals remarkable plasticity in stress granule formation and composition that is largely dependent on the infecting virus (summarized in Figure 9). The findings challenge the concept of a universal “antiviral stress granule” and support different functional roles for these structures during viral infections.

SFV induces canonical stress granules early in infection that accumulate viral RNA and translation factors, potentially limiting viral gene expression by sequestering these essential components. To counter this antiviral effect, the virus actively dissolves stress granules as infection progresses.

In contrast, MHV prevents stress granule formation early in infection and only tolerates atypical granules during late infection. These late-stage structures contain the major stress granule markers G3BP1, TIA1, and UBAP2L but show reduced abundance of canonical stress granule proteins and efficiently exclude viral RNA. This altered composition allows MHV to tolerate these condensates without compromising viral replication during the late stages of infection.

Outstanding Questions

smRNA-FISH spatial resolution limitations: The high abundance of viral RNA, particularly for MHV, presents technical challenges for resolving individual RNA molecules at most timepoints, relying instead on intensity correlations. More sophisticated expansion microscopy or super-resolution imaging might reveal whether some MHV RNA truly localizes to stress granule edges or whether the exclusion is absolute.

Timing of stress granule “peak” may not be directly comparable: The authors compare stress granule numbers at different absolute timepoints for MHV (8 hpi) vs. SFV (5 hpi) based on when granule numbers peak. However, these timepoints represent different stages of infection relative to the viral lifecycle, making direct proteomic comparisons potentially confounded by infection stage rather than purely stress granule composition differences.

References

Kedersha N, Gupta M, Li W, Miller I, Anderson P (1999). RNA-binding proteins TIA-1 and TIAR link the phosphorylation of eIF-2α to the assembly of mammalian stress granules. J Cell Biol 147(7):1431–41.
Kedersha N, Stoecklin G, Ayodele M, Yacono P, Lykke-Andersen J, Fitzler MJ, et al. (2005). Stress granules and processing bodies are dynamically linked sites of mRNP remodeling. Journal of Cell Biology 169(6):871–84.
Guillén-Boixet J, Kopach A, Holehouse AS, Wittmann S, Jahnel M, Schlüßler R, et al. (2020). RNA-Induced Conformational Switching and Clustering of G3BP Drive Stress Granule Assembly by Condensation. Cell 181(2):346-361.e17.
Cirillo L, Cieren A, Barbieri S, Khong A, Schwager F, Parker R, et al. (2020). UBAP2L Forms Distinct Cores that Act in Nucleating Stress Granules Upstream of G3BP1. Current Biology 30(4):698-707.e6.
Onomoto K, Jogi M, Yoo JS, Narita R, Morimoto S, Takemura A, et al. (2012). Critical Role of an Antiviral Stress Granule Containing RIG-I and PKR in Viral Detection and Innate Immunity. PLoS One 7(8):e43031.
Manivannan P, Siddiqui MA, Malathi K (2020). RNase L Amplifies Interferon Signaling by Inducing Protein Kinase R-Mediated Antiviral Stress Granules. J Virol 94(13):1–21.
Chathuranga WAG, Nikapitiya C, Kim JH, Chathuranga K, Weerawardhana A, Dodantenna N, et al. (2023). Gadd45β is critical for regulation of type I interferon signaling by facilitating G3BP-mediated stress granule formation. Cell Rep 42(11):113358.
Katoh H, Okamoto T, Fukuhara T, Kambara H, Morita E, Mori Y, et al. (2013). Japanese Encephalitis Virus Core Protein Inhibits Stress Granule Formation through an Interaction with Caprin-1 and Facilitates Viral Propagation. J Virol 87(1):489–502.
Panas MD, Varjak M, Lulla A, Eng KE, Merits A, Hedestam GBK, et al. (2012). Sequestration of G3BP coupled with efficient translation inhibits stress granules in Semliki Forest virus infection. Mol Biol Cell 23(24):4701–12.
Burke JM, Ratnayake OC, Watkins JM, Perera R, Parker R (2024). G3BP1-dependent condensation of translationally inactive viral RNAs antagonizes infection. Sci Adv 10(5):eadl0531.
Beauclair G, Streicher F, Chazal M, Bruni D, Lesage S, Gracias S, et al. (2020). Retinoic Acid Inducible Gene I and Protein Kinase R, but Not Stress Granules, Mediate the Proinflammatory Response to Yellow Fever Virus. J Virol 94(22):e00403-20.
Markmiller S, Soltanieh S, Server KL, Mak R, Jin W, Fang MY, et al. (2018). Context-Dependent and Disease-Specific Diversity in Protein Interactions within Stress Granules. Cell 172(3):590-604.e13.
Youn JY, Dunham WH, Hong SJ, Knight JDR, Bashkurov M, Chen GI, et al. (2018). High-Density Proximity Mapping Reveals the Subcellular Organization of mRNA-Associated Granules and Bodies. Mol Cell 69(3):517-532.e11.
Reineke LC, Kedersha N, Langereis MA, van Kuppeveld FJM, Lloyd RE (2015). Stress granules regulate double-stranded RNA-dependent protein kinase activation through a complex containing G3BP1 and Caprin1. mBio 6(2):1–12.

doi: https://doi.org/10.1242/prelights.41979

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