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Viral Condensates and Virus Interference with Host Membraneless Organelles

A special issue of International Journal of Molecular Sciences (ISSN 1422-0067). This special issue belongs to the section "Molecular Immunology".

Deadline for manuscript submissions: closed (30 June 2023) | Viewed by 10316

Special Issue Editors


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Guest Editor
Equipe Biologie Moléculaire des Pneumovirus, Unité de virologie et Immunologie Moléculaires, INRAE - Domaine de Vilvert, 78352 Jouy-en-Josas, France
Interests: respiratory syncytial virus; protein-protein interactions; viral factories; nucleoprotein; phosphoprotein

Special Issue Information

Dear Colleagues,

Intrinsically disordered proteins (IDPs) or regions (IDRs) are ubiquitous functional proteins/regions devoid of stable secondary and tertiary structure. Compelling experimental evidence gathered during the last decade points to a critical role for IDPs/IDRs, either alone or in conjunction with nucleic acids, in promoting liquid–liquid phase separation (LLPS). LLPS is a physicochemical process whereby an initially homogenous solution turns into two distinct phases—a “dense” phase that contains the major portion of the dissolved macromolecules, and a “light” phase containing the solvent. LLPS is not merely an in vitro process. Rather, it also occurs in the cellular context, where it drives the formation of so-called membrane-less organelles (MLOs) (e.g., nucleoli, nuclear speckles, Cajal bodies, processing bodies, stress granules, aggresomes, centrosomes, etc). MLOs are supramolecular assemblies possessing regulatory, structural, and enzymatic functions. They are responsible for the spatial and temporal organization of the cell and play a crucial role in a number of physiological processes. Liquid biocondensates resulting from LLPS can also undergo “maturation”, developing into gelled and/or solid-like forms that can eventually nucleate amyloid-like fibrils. Protein aggregation into amyloid fibrils is the archetype of aberrant biomolecular self-assembly processes associated with uncurable neurodegenerative diseases. Likewise, phase transitions from liquid to solid are mostly associated with pathological states.

The phenomenon of LLPS is also exploited by viruses. Viruses take advantage of LLPS for their replication either by interfering with (dis)assembly and regulation of host MLOs or by eliciting the formation of viral factories, i.e., condensates made of their own proteins either alone or in association with nucleic acids. Such viral inclusions are sites where viral replication and assembly take place and where specific viral and cellular proteins, along with nucleic acids, concentrate. They serve as platforms for optimized viral replication and/or assembly via selective uptake or exclusion of specific cellular components and shielding from the host immune defense. So far, the majority of studies have focused on LLPS in relation with replication compartments, and few studies have described interference with host functions. Likewise, only a few studies have focused on the functional impact of phase transitions towards gelled and/or fibrillar states of viral condensates. Examples of fibrils made of viral proteins have just begun to be reported, and the possible implications for pathogenesis are just starting to be discussed.

This Special Issue aims at filling this gap by collecting contributions that cover different aspects of viral condensate formation with an emphasis on new promising antiviral approaches that target these processes.

Dr. Sonia Longhi
Dr. Marie Galloux
Guest Editors

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Published Papers (5 papers)

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Editorial

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3 pages, 467 KiB  
Editorial
Unraveling Liquid–Liquid Phase Separation (LLPS) in Viral Infections to Understand and Treat Viral Diseases
by Marie Galloux and Sonia Longhi
Int. J. Mol. Sci. 2024, 25(13), 6981; https://doi.org/10.3390/ijms25136981 - 26 Jun 2024
Viewed by 1205
Abstract
In the field of virology, liquid–liquid phase separation (LLPS) has emerged as a pivotal mechanism enabling the compartmentalization required for specific steps of the viral replication cycle [...] Full article
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Research

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20 pages, 5872 KiB  
Article
Challenges in Imaging Analyses of Biomolecular Condensates in Cells Infected with Influenza A Virus
by Temitope Akhigbe Etibor, Aidan O’Riain, Marta Alenquer, Christian Diwo, Sílvia Vale-Costa and Maria João Amorim
Int. J. Mol. Sci. 2023, 24(20), 15253; https://doi.org/10.3390/ijms242015253 - 17 Oct 2023
Viewed by 1737
Abstract
Biomolecular condensates are crucial compartments within cells, relying on their material properties for function. They form and persist through weak, transient interactions, often undetectable by classical biochemical approaches. Hence, microscopy-based techniques have been the most reliable methods to detail the molecular mechanisms controlling [...] Read more.
Biomolecular condensates are crucial compartments within cells, relying on their material properties for function. They form and persist through weak, transient interactions, often undetectable by classical biochemical approaches. Hence, microscopy-based techniques have been the most reliable methods to detail the molecular mechanisms controlling their formation, material properties, and alterations, including dissolution or phase transitions due to cellular manipulation and disease, and to search for novel therapeutic strategies targeting biomolecular condensates. However, technical challenges in microscopy-based analysis persist. This paper discusses imaging, data acquisition, and analytical methodologies’ advantages, challenges, and limitations in determining biophysical parameters explaining biomolecular condensate formation, dissolution, and phase transitions. In addition, we mention how machine learning is increasingly important for efficient image analysis, teaching programs what a condensate should resemble, aiding in the correlation and interpretation of information from diverse data sources. Influenza A virus forms liquid viral inclusions in the infected cell cytosol that serve as model biomolecular condensates for this study. Our previous work showcased the possibility of hardening these liquid inclusions, potentially leading to novel antiviral strategies. This was established using a framework involving live cell imaging to measure dynamics, internal rearrangement capacity, coalescence, and relaxation time. Additionally, we integrated thermodynamic characteristics by analysing fixed images through Z-projections. The aforementioned paper laid the foundation for this subsequent technical paper, which explores how different modalities in data acquisition and processing impact the robustness of results to detect bona fide phase transitions by measuring thermodynamic traits in fixed cells. Using solely this approach would greatly simplify screening pipelines. For this, we tested how single focal plane images, Z-projections, or volumetric analyses of images stained with antibodies or live tagged proteins altered the quantification of thermodynamic measurements. Customizing methodologies for different biomolecular condensates through advanced bioimaging significantly contributes to biological research and potential therapeutic advancements. Full article
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18 pages, 8108 KiB  
Article
Hardening of Respiratory Syncytial Virus Inclusion Bodies by Cyclopamine Proceeds through Perturbation of the Interactions of the M2-1 Protein with RNA and the P Protein
by Cédric Diot, Charles-Adrien Richard, Jennifer Risso-Ballester, Davy Martin, Jenna Fix, Jean-François Eléouët, Christina Sizun, Marie-Anne Rameix-Welti and Marie Galloux
Int. J. Mol. Sci. 2023, 24(18), 13862; https://doi.org/10.3390/ijms241813862 - 8 Sep 2023
Cited by 7 | Viewed by 1676
Abstract
Respiratory syncytial virus (RSV) RNA synthesis takes place in cytoplasmic viral factories also called inclusion bodies (IBs), which are membrane-less organelles concentrating the viral RNA polymerase complex. The assembly of IBs is driven by liquid-liquid phase separation promoted by interactions between the viral [...] Read more.
Respiratory syncytial virus (RSV) RNA synthesis takes place in cytoplasmic viral factories also called inclusion bodies (IBs), which are membrane-less organelles concentrating the viral RNA polymerase complex. The assembly of IBs is driven by liquid-liquid phase separation promoted by interactions between the viral nucleoprotein N and the phosphoprotein P. We recently demonstrated that cyclopamine (CPM) inhibits RSV multiplication by disorganizing and hardening IBs. Although a single mutation in the viral transcription factor M2-1 induced resistance to CPM, the mechanism of action of CPM still remains to be characterized. Here, using FRAP experiments on reconstituted pseudo-IBs both in cellula and in vitro, we first demonstrated that CPM activity depends on the presence of M2-1 together with N and P. We showed that CPM impairs the competition between P and RNA binding to M2-1. As mutations on both P and M2-1 induced resistance against CPM activity, we suggest that CPM may affect the dynamics of the M2-1-P interaction, thereby affecting the relative mobility of the proteins contained in RSV IBs. Overall, our results reveal that stabilizing viral protein-protein interactions is an attractive new antiviral approach. They pave the way for the rational chemical optimization of new specific anti-RSV molecules. Full article
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12 pages, 2305 KiB  
Article
Nyamanini Virus Nucleoprotein and Phosphoprotein Organize Viral Inclusion Bodies That Associate with Host Biomolecular Condensates in the Nucleus
by Yuya Hirai and Masayuki Horie
Int. J. Mol. Sci. 2023, 24(7), 6550; https://doi.org/10.3390/ijms24076550 - 31 Mar 2023
Viewed by 2166
Abstract
Many mononegaviruses form inclusion bodies (IBs) in infected cells. However, little is known about nuclear IBs formed by mononegaviruses, since only a few lineages of animal-derived mononegaviruses replicate in the nucleus. In this study, we characterized the IBs formed by Nyamanini virus (NYMV), [...] Read more.
Many mononegaviruses form inclusion bodies (IBs) in infected cells. However, little is known about nuclear IBs formed by mononegaviruses, since only a few lineages of animal-derived mononegaviruses replicate in the nucleus. In this study, we characterized the IBs formed by Nyamanini virus (NYMV), a unique tick-borne mononegavirus undergoing replication in the nucleus. We discovered that NYMV forms IBs, consisting of condensates and puncta of various sizes and morphologies, in the host nucleus. Likewise, we found that the expressions of NYMV nucleoprotein (N) and phosphoprotein (P) alone induce the formation of condensates and puncta in the nucleus, respectively, even though their morphologies are somewhat different from the IBs observed in the actual NYMV-infected cells. In addition, IB-like structures can be reconstructed by co-expressions of NYMV N and P, and localization analyses using a series of truncated mutants of P revealed that the C-terminal 27 amino acid residues of P are important for recruiting P to the condensates formed by N. Furthermore, we found that nuclear speckles, cellular biomolecular condensates, are reorganized and recruited to the IB-like structures formed by the co-expressions of N and P, as well as IBs formed in NYMV-infected cells. These features are unique among mononegaviruses, and our study has contributed to elucidating the replication mechanisms of nuclear-replicating mononegaviruses and the virus–host interactions. Full article
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Review

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14 pages, 2378 KiB  
Review
The Formation and Function of Birnaviridae Virus Factories
by Andrew J. Brodrick and Andrew J. Broadbent
Int. J. Mol. Sci. 2023, 24(10), 8471; https://doi.org/10.3390/ijms24108471 - 9 May 2023
Cited by 1 | Viewed by 2699
Abstract
The use of infectious bursal disease virus (IBDV) reverse genetics to engineer tagged reporter viruses has revealed that the virus factories (VFs) of the Birnaviridae family are biomolecular condensates that show properties consistent with liquid–liquid phase separation (LLPS). Although the VFs are not [...] Read more.
The use of infectious bursal disease virus (IBDV) reverse genetics to engineer tagged reporter viruses has revealed that the virus factories (VFs) of the Birnaviridae family are biomolecular condensates that show properties consistent with liquid–liquid phase separation (LLPS). Although the VFs are not bound by membranes, it is currently thought that viral protein 3 (VP3) initially nucleates the formation of the VF on the cytoplasmic leaflet of early endosomal membranes, and likely drives LLPS. In addition to VP3, IBDV VFs contain VP1 (the viral polymerase) and the dsRNA genome, and they are the sites of de novo viral RNA synthesis. Cellular proteins are also recruited to the VFs, which are likely to provide an optimal environment for viral replication; the VFs grow due to the synthesis of the viral components, the recruitment of other proteins, and the coalescence of multiple VFs in the cytoplasm. Here, we review what is currently known about the formation, properties, composition, and processes of these structures. Many open questions remain regarding the biophysical nature of the VFs, as well as the roles they play in replication, translation, virion assembly, viral genome partitioning, and in modulating cellular processes. Full article
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