Principles and Properties of Stress Granules

Stress granules: Guardians of cellular health and triggers of disease

Stress granules are membraneless organelles that serve as a protective cellular response to external stressors by sequestering non-translating messenger RNAs (mRNAs) and regulating protein synthesis. Stress granules formation mechanism is conserved across species, from yeast to mammals, and they play a critical role in minimizing cellular damage during stress. Composed of heterogeneous ribonucleoprotein complexes, stress granules are enriched not only in mRNAs but also in noncoding RNAs and various proteins, including translation initiation factors and RNA-binding proteins. Genetic mutations affecting stress granule assembly and disassembly can lead to abnormal stress granule accumulation, contributing to the progression of several diseases. Recent research indicates that stress granule dynamics are pivotal in determining their physiological and pathological functions, with acute stress granule formation offering protection and chronic stress granule accumulation being detrimental. This review focuses on the multifaceted roles of stress granules under diverse physiological conditions, such as regulation of mRNA transport, mRNA translation, apoptosis, germ cell development, phase separation processes that govern stress granule formation, and their emerging implications in pathophysiological scenarios, such as viral infections, cancer, neurodevelopmental disorders, neurodegeneration, and neuronal trauma.

Neuroimmune signaling mediates astrocytic nucleocytoplasmic disruptions and stress granule formation associated with TDP-43 pathology

Alterations in transactivating response region DNA-binding protein 43 (TDP-43) are prevalent in amyotrophic lateral sclerosis (ALS), frontotemporal dementia (FTD), and other neurological disorders. TDP-43 influences neuronal functions and might also affect glial cells. However, specific intracellular effects of TDP-43 alterations on glial cells and underlying mechanisms are not clear. We report that TDP-43 dysregulation in mouse and human cortical astrocytes causes nucleoporin mislocalization, nuclear envelope remodeling, and changes in nucleocytoplasmic protein transport. These effects are dependent on interleukin-1 (IL-1) receptor activity and nuclear factor kappa-light-chain-enhancer of activated B cells (NF-κB) signaling and are associated with the formation of cytoplasmic stress granules. Stimulation of IL-1 receptors and NF-κB signaling are necessary and sufficient to induce astrocytic stress granules and rapid nucleocytoplasmic changes, which are broadly alleviated by inhibition of the integrated stress response. These findings establish that TDP-43 alterations and neuroimmune factors can induce nucleocytoplasmic changes through NF-κB signaling, revealing mechanistic convergence of proteinopathy and neuroimmune pathways onto glial nucleocytoplasmic disruptions that may occur in diverse neurological conditions.

The Pseudoenzyme β-Amylase9 From Arabidopsis Activates α-Amylase3: A Possible Mechanism to Promote Stress-Induced Starch Degradation

Starch accumulation in plants provides carbon for nighttime use, for regrowth after periods of dormancy, and for times of stress. Both ɑ- and β-amylases (AMYs and BAMs, respectively) catalyze starch hydrolysis, but their functional roles are unclear. Moreover, the presence of catalytically inactive amylases that show starch excess phenotypes when deleted presents questions on how starch degradation is regulated. Plants lacking one of these catalytically inactive β-amylases, BAM9, have enhanced starch accumulation when combined with mutations in BAM1 and BAM3, the primary starch degrading BAMs in response to stress and at night, respectively. BAM9 has been reported to be transcriptionally induced by stress although the mechanism for BAM9 function is unclear. From yeast two-hybrid experiments, we identified the plastid-localized AMY3 as a potential interaction partner for BAM9. We found that BAM9 interacted with AMY3 in vitro and that BAM9 enhances AMY3 activity about three-fold. Modeling of the AMY3-BAM9 complex predicted a previously undescribed alpha-alpha hairpin in AMY3 that could serve as a potential interaction site. Additionally, AMY3 lacking the alpha-alpha hairpin is unaffected by BAM9. Structural analysis of AMY3 showed that it can form a homodimer in solution and that BAM9 appears to replace one of the AMY3 monomers to form a heterodimer. The presence of both BAM9 and AMY3 in many vascular plant lineages, along with model-based evidence that they heterodimerize, suggests that the interaction is conserved. Collectively these data suggest that BAM9 is a pseudoamylase that activates AMY3 in response to cellular stress, possibly facilitating stress recovery.

TGEV NSP1 enhances viral replication through antagonizing stress granule formation

Stress granules (SGs) are membrane-less organelles that form in response to adverse external stimuli. Upon viral invasion, SGs formation can serve as a cellular defence mechanism against infection. Transmissible gastroenteritis virus (TGEV), an α-coronavirus with a large positive-sense single-stranded RNA genome, causes diarrhoea, vomiting, dehydration, and even fatality in piglets. Previous studies have shown that coronaviruses employ various strategies to inhibit the SGs formation, thereby facilitating viral replication. However, the interplay between TGEV infection and the SGs formation remains unclear. In this study, we demonstrate that the SGs formation can enhance antiviral innate immunity mediated through the retinoic acid-inducible gene I (RIG-I) signaling pathway, thereby inhibiting TGEV replication. Nevertheless, TGEV counteracts the SGs formation by reducing the protein level of Ras-GTPase-activating protein SH3-domain-binding protein 1 (G3BP1) to promote its own replication. Among the TGEV-encoded proteins, non-structural protein 1 (NSP1) exhibits the strongest inhibitory effect on the SGs formation. In summary, our study systematically elucidated the relationship between TGEV and the SGs formation, providing insights into the mechanism of TGEV pathogenesis and a theoretical foundation for identifying novel anti-coronavirus targets.

DNA binding and mitotic phosphorylation protect polyglutamine proteins from assembly formation

Polyglutamine (polyQ) expansion is associated with pathogenic protein aggregation in neurodegenerative disorders. However, long polyQ tracts are also found in many transcription factors (TFs), such as FOXP2, a TF implicated in human speech. Here, we explore how FOXP2 and other glutamine-rich TFs avoid unscheduled assembly. Throughout interphase, DNA binding, irrespective of sequence specificity, has a solubilizing effect. During mitosis, multiple phosphorylation events promote FOXP2's eviction from chromatin and supplant the solubilizing function of DNA. Further, human-specific amino acid substitutions linked to the evolution of speech map to a mitotic phospho-patch, the "EVO patch," and reduce the propensity of the human FOXP2 to assemble. Fusing the pathogenic form of Huntingtin to either a DNA-binding domain, a phosphomimetic variant of this EVO patch, or a negatively charged peptide is sufficient to diminish assembly formation, suggesting that hijacking mechanisms governing solubility of glutamine-rich TFs may offer new strategies for treatment of polyQ expansion diseases.

Phase separation in mitochondrial fate and mitochondrial diseases

Mitochondria are central metabolic organelles that control cell fate and the development of mitochondrial diseases. Traditionally, phase separation directly regulates cell functions by driving RNA, proteins, or other molecules to concentrate into lipid droplets. Recent studies show that phase separation regulates cell functions and diseases through the regulation of subcellular organelles, particularly mitochondria. In fact, phase separation is involved in various mitochondrial activities including nucleoid assembly, autophagy, and mitochondria-related inflammation. Here, we outline the key mechanisms through which phase separation influences mitochondrial activities and the development of mitochondrial diseases. Insights into how phase separation regulates mitochondrial activities and diseases will help us develop interventions for related diseases.

SOD1, A Crucial Protein for Neural Biochemistry: Dysfunction and Risk of Amyotrophic Lateral Sclerosis

Neurons are very susceptible to oxidative stress. They are the major consumers of oxygen in the brain, which is used to provide energy through oxidative phosphorylation, the major source of reactive oxygen species (ROS). In addition, compared to other tissues, neurons have lower levels of catalase and glutathione and increased susceptibility to lipid peroxidation due to the elevated levels of unsaturated fatty acids. These characteristics increasingly emphasize the antioxidant enzyme Cu/Zn superoxide dismutase 1 (SOD1) to maintain neuronal redox homeostasis. In the last decade, SOD1 gained additional roles which are also important to the metabolism of neurons. SOD1 controls the production of ROS by the electron transport chain, activates the expression of genes involved in the protection against oxidative stress, and regulates the shift from oxidative to fermentative metabolism involved in astrocyte-neuron metabolic cooperation. Furthermore, impaired interaction between the phosphatase calcineurin and SOD1 seems to result in TDP-43 hyperphosphorylation, the main proteinopathy found in amyotrophic lateral sclerosis (ALS) patients. However, this enzyme is ubiquitously expressed, mutated, and damaged forms of SOD1 cause disease in motor neurons. In this review, we discuss the pivotal functions of SOD1 in neuronal biochemistry and their implications for ALS.

Large-scale purifications reveal yeast and human stress granule cores are heterogeneous particles with complex transcriptomes and proteomes

Stress granules are a conserved response of eukaryotic cells to environmental insults. These cytoplasmic ribonucleoprotein condensates have hitherto been primarily studied by microscopy, which showed previously that they comprise dense ∼200 nm cores embedded in a diffuse shell. We have developed large-scale purifications of budding yeast and mammalian (HEK293T cell) stress granule cores that do not rely on immunoprecipitation of candidate protein constituents. These unbiased preparations reveal that stress granule cores are discrete particles with variable size (average, 135 and 225 nm for yeast and human, respectively) and shape. Proteomics and transcriptomics demonstrate complex composition. The results of hybridization chain reaction fluorescence in situ hybridization (FISH) analyses in HEK293T cells are consistent with stress granule cores having heterogeneous composition, i.e., each stress granule core particle contains only a limited number of mRNA species. Biochemical purification now opens the way to mechanistic analysis of the heterogeneity and complexity of stress granules.

Phase separation of the oncogenic fusion protein EWS::FLI1 is modulated by its DNA-binding domain

Ewing sarcoma (EwS) is an aggressive cancer of bone and soft tissue that predominantly affects children and young adults. A chromosomal translocation joins the low-complexity domain (LCD) of the RNA-binding protein EWS (EWSLCD) with the DNA-binding domain of Friend leukemia integration 1 (FLI1DBD), creating EWS::FLI1, a potent fusion oncoprotein essential for EwS development and responsible for over 85% of EwS tumors. EWS::FLI1 forms biomolecular condensates in vivo and promotes tumorigenesis through mediation of aberrant transcriptional changes and by interfering with the normal functions of nucleic acid-binding proteins like EWS through a dominant-negative mechanism. In particular, the expression of EWS::FLI1 in EwS directly interferes with the biological functions of EWS leading to alternate splicing events and defects in DNA-damage repair pathways. Though the EWSLCD is capable of phase separation, here we report a direct interaction between FLI1DBD and EWSLCD that enhances condensate formation and alters the physical properties of the condensate. This effect was conserved for three related E-twenty-six transformation-specific (ETS) DNA-binding domains (DBDs) while DNA binding blocked the interaction with EWSLCD and inhibited EWS::FLI1 condensate formation. NMR spectroscopy and mutagenesis studies confirmed that ETS DBDs transiently interact with EWSLCD via the ETS DBDs "wings." Together these results revealed that ETS DBDs, particularly FLI1DBD, enhance EWSLCD condensate formation and rigidity, supporting a model in which electrostatic and structural interactions drive condensate dynamics with implications for EWS::FLI1-mediated transcriptional regulation in EwS.

Outer membrane tube formation by Francisella novicida involves extensive envelope modifications and is linked with type VI secretion and alterations to the host phagosomal membrane

Francisella tularensis is a gram-negative, intracellular pathogen that causes the zoonotic disease tularemia. Due to its ease of dissemination and high lethality, F. tularensis is classified as a tier 1 select agent with potential for misuse as a bioweapon. The mechanisms by which Francisella replicates intracellularly and interacts with the host during infection are not well understood. Francisella produces spherical outer membrane vesicles (OMVs) and novel tubular extensions of its cell surface that are also released extracellularly. These OMV and outer membrane tubes (OMTs) contain Francisella virulence factors and are produced in response to amino acid starvation and during infection of macrophages. To investigate how the OMTs are formed, we used cryogenic electron tomography to examine the model Francisella spp., Francisella novicida, during in vitro culture and within the macrophage phagosome. OMT formation involved progressive alterations of the bacterial envelope, resulting in extensions of both the inner and outer membranes. A dynamic cytoplasmic structure was present at the base of the OMT that extended into the tubes during elongation, together with cytoplasmic material. OMT produced within the macrophage phagosome was associated with changes to the phagosomal membrane, suggesting a role in phagosomal escape. Consistent with this, using confocal microscopy, we observed co-localization of the Francisella type VI secretion system with the OMT, both within bacteria and in released tubular vesicles. These findings reveal the cellular transformations that occur during membrane tubulation by Francisella and provide insights into the function of membrane-derived structures during host-pathogen interactions.

IMPORTANCE

Francisella tularensis is an intracellular bacterial pathogen that causes the zoonotic disease tularemia. Following uptake by host cells, the bacteria rapidly escape the phagosome and replicate intracellularly. In previous studies, we found that Francisella produces tubular extensions of its cell surface in response to specific cues and during macrophage infection. In the present study, we used cryogenic electron tomography to examine tube formation by the model Francisella sp., F. novicida. This analysis revealed that tube formation involves extensive bacterial envelope alterations and a dynamic cytoplasmic organelle. Furthermore, tubes produced by bacteria within infected macrophages were associated with the breakdown of the phagosomal membrane. In addition, we found that the Francisella type VI secretion system, which is essential for phagosomal escape, co-localized with the bacterial tubes. These findings reveal the cellular transformations that occur during membrane tubulation by Francisella and suggest a role for the tubes in phagosomal escape.

Dissecting the stress granule RNA world: dynamics, strategies, and data

Stress granules (SGs) are cytoplasmic ribonucleoprotein granules that commonly nucleate from the interaction of translationally stalled mRNAs and RNA-binding proteins. SGs are involved in the cellular adaptation to stress conditions participating in the regulation of gene expression and cell signaling. While dysregulation of SG dynamics has been increasingly implicated in human disease, a comprehensive understanding of SG composition, particularly of the RNA component, across various conditions remains elusive. Here, we review the physiological and pathological aspects of SGs, discuss current and future experimental strategies to identify SG components, and provide insights into the SG RNA world through the meta-analysis of 26 human SG transcriptome data sets.

Peptide Coacervates: Formation, Mechanism, and Biological Applications

Biomolecular coacervates, dynamic compartments formed via liquid-liquid phase separation (LLPS), are essential for orchestrating intracellular processes and have emerged as versatile tools in bioengineering. Peptides, with their modular amino acid sequences, exhibit unique potential in coacervate design due to their ability to undergo LLPS while offering precise control over molecular architecture and environmental responsiveness. Their simplicity, synthetic accessibility, and tunability make peptide-based coacervates particularly attractive for biomedical and materials applications. However, the formation and stability of these systems depend on a delicate balance of intrinsic factors (e.g., sequence charge, hydrophobicity, and chain length) and extrinsic conditions (e.g., pH, ionic strength, and temperature), necessitating a deeper understanding of their interplay. This review synthesizes recent advances in the molecular mechanisms driving peptide coacervation, emphasizing how sequence design and environmental cues govern phase behavior. We further highlight groundbreaking applications, from drug delivery platforms to protocell mimics, and discuss strategies to translate mechanistic insights into functional materials. By bridging fundamental principles with innovative applications, this work aims to accelerate the development of peptide coacervates as programmable, multifunctional systems, offering a roadmap for next-generation biochemical technologies.

Small-molecule dissolution of stress granules by redox modulation benefits ALS models

Neurodegenerative diseases, such as amyotrophic lateral sclerosis, are often associated with mutations in stress granule proteins. Aberrant stress granule condensate formation is associated with disease, making it a potential target for pharmacological intervention. Here, we identified lipoamide, a small molecule that specifically prevents cytoplasmic condensation of stress granule proteins. Thermal proteome profiling showed that lipoamide stabilizes intrinsically disordered domain-containing proteins, including SRSF1 and SFPQ, which are stress granule proteins necessary for lipoamide activity. SFPQ has redox-state-specific condensate dissolving behavior, which is modulated by the redox-active lipoamide dithiolane ring. In animals, lipoamide ameliorates aging-associated aggregation of a stress granule reporter protein, improves neuronal morphology and recovers motor defects caused by amyotrophic lateral sclerosis-associated FUS and TDP-43 mutants. Thus, lipoamide is a well-tolerated small-molecule modulator of stress granule condensation, and dissection of its molecular mechanism identified a cellular pathway for redox regulation of stress granule formation.

Subcellular level spatial transcriptomics with PHOTON

The subcellular localization of RNA is closely linked to its function. Many RNA species are partitioned into organelles and other subcellular compartments for storage, processing, translation, or degradation. Thus, capturing the subcellular spatial distribution of RNA would directly contribute to the understanding of RNA functions and regulation. Here, we present PHOTON, a method which combines high resolution imaging with high throughput sequencing to achieve spatial transcriptome profiling at subcellular resolution. We demonstrate PHOTON as a versatile tool to accurately capture the transcriptome of target cell types in situ at the tissue level such as granulosa cells in the ovary, as well as RNA content within subcellular compartments such as the nucleoli, the mitochondria, and the stress granules. Using PHOTON, we also reveal the functional role of m6A modifications on mRNA partitioning into stress granules. These results collectively demonstrate that PHOTON is a flexible and generalizable platform for understanding subcellular molecular dynamics through the transcriptomic lens.

A thermosensor FUST1 primes heat-induced stress granule formation via biomolecular condensation in Arabidopsis

The ability to sense cellular temperature and induce physiological changes is pivotal for plants to cope with warming climate. Biomolecular condensation is emerging as a thermo-sensing mechanism, but the underlying molecular basis remains elusive. Here we show that an intrinsically disordered protein FUST1 senses heat via its condensation in Arabidopsis thaliana. Heat-dependent condensation of FUST1 is primarily determined by its prion-like domain (PrLD). All-atom molecular dynamics simulation and experimental validation reveal that PrLD encodes a thermo-switch, experiencing lock-to-open conformational changes that control the intermolecular contacts. FUST1 interacts with integral stress granule (SG) components and localizes in the SGs. Importantly, FUST1 condensation is autonomous and precedes condensation of several known SG markers and is indispensable for SG assembly. Loss of FUST1 significantly delays SG assembly and impairs both basal and acquired heat tolerance. These findings illuminate the molecular basis for thermo-sensing by biomolecular condensation and shed light on the molecular mechanism of heat stress granule assembly.

Deciphering tuberculosis: lysosome-centric insights into pathogenesis and therapies

Tuberculosis is a widely spread disease caused by Mycobacterium tuberculosis (Mtb). The pathogenicity of the pathogen is closely associated with the immune defense mechanisms of the host cells. As key cellular degradation and metabolic centers, lysosomes critically regulate tuberculosis infection. When Mtb invades the host, it is taken up by macrophages and enters phagosomes. Subsequently, the phagosomes fuse with lysosomes and form phagolysosomes, which eliminate the pathogenic bacteria through the acidic environment and hydrolytic enzymes within lysosomes. However, Mtb can interfere with the normal functions of lysosomes through various strategies. It can secrete specific factors (such as ESAT-6, ppk-1, and AcpM) to inhibit the acidification of lysosomes, enzyme activity, and the fusion of phagosomes and lysosomes, thereby enabling Mtb proliferation within host cells. An in-depth exploration of the mechanism of the interaction between Mtb and lysosomes will both uncover bacterial immune evasion strategies and identify novel anti-tuberculosis therapeutic targets.

Temperature-Dependent Coarse-Grained Model for Simulations of Intrinsically Disordered Protein LCST and UCST Liquid-Liquid Phase Separations

Many intrinsically disordered proteins (IDPs) can undergo a liquid-liquid phase separation (LLPS) in water, depending on solution conditions (temperature, pH, and ionic strength). There are two types of LLPS that are controlled by temperature: those occurring above a lower critical solution temperature (LCST) and those occurring below an upper critical solution temperature (UCST). IDP coarse-grained (CG) models are particularly appropriate for investigating the physical and chemical factors that govern their LLPS and supramolecular organization. However, the development of CG models allowing simulations of both LCST and UCST behavior of temperature-sensitive IDPs is still in its infancy. In this context, we present here a novel temperature-dependent (TD) CG model for IDP simulations based on the MARTINI 3 force field. The model was developed by modifying the Lennard-Jones potentials between apolar or charged solute beads and water with a TD rescaling factor. It was parametrized to fit the TD potentials of mean force (PMF) between two apolar or two charged molecules computed using all-atom (AA) simulations. We show that the TD CG model is able to reproduce the experimentally known LLPS of both LCST and UCST low-complexity sequences and to estimate phase transition temperatures comparable to experimental measurements.

Stress granules: emerging players in neurodegenerative diseases

Stress granules (SGs) are membraneless organelles formed in the cellular cytoplasm under stressful conditions through liquid-liquid phase separation (LLPS). SG assembly can be both dependent and independent of the eIF2α pathway, whereas cellular protein quality control systems mediate SG disassembly. Chaperones and specific domains of RNA-binding proteins strongly contribute to the regulation SG dynamics. Chronic stress, arising in association with aging, may promote persistent SGs that are difficult to disassemble, thereby acting as a potential pathological nidus for protein aggregation in neurodegenerative diseases (NDDs). In this review, we discuss the dynamics of SGs and the factors involved with SG assembly and disassembly. We also highlight the relationship among LLPS, SGs, and the pathogenesis of different NDDs. More importantly, we summarize SG assembly-disassembly, which may be a double-edged sword in the pathophysiology of NDDs. This review aims to provide new insights into the biology and pathology of LLPS, SGs, and NDDs.

Aldolase-regulated G3BP1/2+ condensates control insulin mRNA storage in beta cells

Upregulation of insulin mRNA translation upon hyperglycemia in pancreatic islet β-cells involves several RNA-binding proteins. Here, we found that G3BP1, a stress granule marker downregulated in islets of subjects with type 2 diabetes, binds to insulin mRNA in glucose concentration-dependent manner. We show in mouse insulinoma MIN6-K8 cells exposed to fasting glucose levels that G3BP1 and its paralog G3BP2 colocalize to cytosolic condensates with eIF3b, phospho-AMPKαThr172 and Ins1/2 mRNA. Glucose stimulation dissolves G3BP1+/2+ condensates with cytosolic redistribution of their components. The aldolase inhibitor aldometanib prevents the glucose- and pyruvate-induced dissolution of G3BP1+/2+ condensates, increases phospho-AMPKαThr172 levels and reduces those of phospho-mTORSer2448. G3BP1 or G3BP2 depletion precludes condensate assembly. KO of G3BP1 decreases Ins1/2 mRNA abundance and translation as well as proinsulin levels, and impaires glucose-stimulated insulin secretion. Further, other insulin secretagogues such as exendin-4 and palmitate, but not high KCl, prompts the dissolution of G3BP1+/2+ condensates. G3BP1+/2+/Ins mRNA+ condensates are also found in primary mouse and human β-cells. Hence, G3BP1+/2+ condensates represent a conserved glycolysis/aldolase-regulated compartment for the physiological storage and protection of insulin mRNA in resting β-cells.

Phase Separation: Orchestrating Biological Adaptations to Environmental Fluctuations

Organisms have evolved various protective mechanisms to survive in complex and dynamic environments. Phase separation is a ubiquitous mechanism in plants, animals, and microorganisms. It facilitates the aggregation of biomolecules through weak interactions, forming membrane-less organelles that help organisms respond effectively to stress signals. These biomolecular condensates include DNA, RNA, and proteins. Proteins are categorized into scaffold and client proteins, whose coordinated actions ensure the compartmentalization of cellular signals, thereby regulating various biological processes. Studies indicate that, in response to stress, phase separation modulates gene expression, signal transduction, cytoskeleton dynamics, and protein homeostasis, ensuring the precise spatiotemporal control of cellular functions. These insights underscore the crucial role of phase separation in maintaining cellular integrity and adaptability.

Regulation of Protein Synthesis at the Translational Level: Novel Findings in Cardiovascular Biology

Translational regulation plays a pivotal role in cardiac gene expression, influencing protein synthesis in response to physiological and pathological stimuli. Although transcription regulates gene expression, translation ultimately determines protein levels, making it a crucial research focus. In cardiomyocytes, disruptions in this process contribute to various cardiac diseases, including hypertrophy, fibrosis, dilated cardiomyopathy, ischemic heart disease, and diabetic cardiomyopathy. Emerging evidence highlights the significance of translational regulation across multiple cardiac cell types, such as cardiomyocytes and fibroblasts, and its role in disease progression. During cardiac remodeling, transcriptomic changes are often modest, suggesting that post-transcriptional mechanisms, particularly translation, play a dominant role in cellular adaptation. This review discusses key methodologies for studying translational regulation and novel mechanisms of translational regulation related to different cardiac pathologies and highlights relevant therapeutic avenues for targeting these pathways.

Molecular Mechanisms of Protein Aggregation in ALS-FTD: Focus on TDP-43 and Cellular Protective Responses

Amyotrophic Lateral Sclerosis (ALS) and Frontotemporal Dementia (FTD) are two neurodegenerative disorders that share common genes and pathomechanisms and are referred to as the ALS-FTD spectrum. A hallmark of ALS-FTD pathology is the abnormal aggregation of proteins, including Cu/Zn superoxide dismutase (SOD1), transactive response DNA-binding protein 43 (TDP-43), fused in sarcoma/translocated in liposarcoma (FUS/TLS), and dipeptide repeat proteins resulting from C9orf72 hexanucleotide expansions. Genetic mutations linked to ALS-FTD disrupt protein stability, phase separation, and interaction networks, promoting misfolding and insolubility. This review explores the molecular mechanisms underlying protein aggregation in ALS-FTD, with a particular focus on TDP-43, as it represents the main aggregated species inside pathological inclusions and can also aggregate in its wild-type form. Moreover, this review describes the protective mechanisms activated by the cells to prevent protein aggregation, including molecular chaperones and post-translational modifications (PTMs). Understanding these regulatory pathways could offer new insights into targeted interventions aimed at mitigating cell toxicity and restoring cellular function.

Artificial Cells Capable of NO Generation with Light Controllable Membraneless Organelles for Melanoma Therapy

Membraneless organelles (MLOs) formed by liquid-liquid phase separation exhibit diverse important biofunctions in cells. The construction of artificial cells containing MLOs with enhanced complexity and functions is still challenging. Here a light-responsive protein, Cry2olig-IDRs, is designed and purified to form MLOs upon light (488 nm) irradiation. They are capable of rapidly recruiting positively charged inducible nitric oxide synthase (iNOS+) from surroundings to regulate its activity for NO production. NO-artificial cells are constructed by encapsulating Cry2olig-IDRs and iNOS+ into giant unilamellar vesicles, which are capable of rapid production of NO with high concentration due to the formation of MLOs upon light irradiation. NO-artificial cells are confirmed to possess the ability for melanoma tumor therapy in mice. These findings provide an efficient method for remotely regulating enzyme activity inside artificial cells, paving the path to build more sophisticated artificial cells for their biomedical applications.

Dysbiosis significantly elevates the probability of altered affective function in Alzheimer disease (AD)

Changes in the makeup of gut microbiota are linked to many neuropsychiatric diseases. Although the exact connection between gut dysbiosis and brain dysfunction is not yet fully understood, but recent data suggests that gut dysbiosis may contribute to the development of Alzheimer's disease (AD) by promoting neuroinflammation, insulin resistance, oxidative stress, and amyloid-beta (Aβ) aggregation. Gut dysbiosis in animal models is primarily characterized by an elevated ratio of Firmicutes/Bacteroidetes which may lead to the accumulation of amyloid precursor protein (APP) in the intestine, in the early stages of AD. Probiotics play a significant role in preventing against the symptoms of AD by restoring gut-brain homeostasis. This chapter provides an overview of the gut microbiota and its dysregulation in etiology of AD. Moreover, novel insights into alteration of the composition of gut microbiota as a preventive or therapeutic approach to AD are discussed.

Diverse influences on tau aggregation and implications for disease progression

Tau is an intrinsically disordered protein that accumulates in fibrillar aggregates in neurodegenerative diseases. The misfolding of tau can be understood as an equilibrium between different states and their propensity to form higher-order fibers, which is affected by several factors. First, modulation of the biochemical state of tau due to ionic conditions, post-translational modifications, cofactors, and interacting molecules or assemblies can affect the formation and structure of tau fibrils. Second, cellular processes impact tau aggregation through modulating stability, clearance, disaggregation, and transport. Third, through interactions with glial cells, the neuronal microenvironment can affect intraneuronal conditions with impacts on tau fibrilization and toxicity. Importantly, tau fibrils propagate through the brain via a "prion-like" manner, contributing to disease progression. This review highlights the biochemical and cellular pathways that modulate tau aggregation and discusses implications for pathobiology and tau-directed therapeutic approaches.

Chirality engineering-regulated liquid-liquid phase separation of stress granules and its role in chemo-sensitization and side effect mitigation

In recent years, the chiral biological effects of nanomedicines have garnered significant interest. Research has focused on understanding how material chirality affects cellular transcription and metabolism. Stress granules, which are membraneless organelles formed through liquid-liquid phase separation of G3BP1 proteins and related compartments, have been extensively studied and are closely associated with cellular damage repair and metabolism. The role and mechanism of chiral nanomaterials in modulating stress granules remain unclear. This study aimed to investigate the expression and structural characteristics of stress granules under the influence of chiral nanomaterials, both individually and in combination with chemotherapy. A library of chiral ligand-modified materials was constructed, and techniques such as immunofluorescence, live-cell imaging, fluorescence recovery after photobleaching assays, and proximity labeling combined with proteomics analysis were employed. These methods helped identify the protein corona adsorbed on the surface of the nanomaterials and explore their relationship with nanomaterial chirality. The findings suggest that the assembly of stress granules is influenced by chirality and can be regulated by chiral nanomaterials. Additionally, chemotherapy sensitivity in cancer cells was enhanced, and normal cells were protected by leveraging the chiral-dependent modulation of material assembly in stress granules. This study offers insights into the regulation of membraneless cellular structures based on chiral biological effects.

Decoding stress granules dynamics: Implications for neurodegenerative disease

Stress granules (SGs) are membrane-less cytoplasmic structures formed by cells in response to external stress, primarily composed of mRNA and proteins. The dynamic properties of their assembly, maintenance, and disassembly play crucial roles in cellular homeostasis. Recent studies have increasingly revealed that aberrations in SGs dynamics are closely related to the pathogenesis of various neurodegenerative diseases, including Alzheimer's disease, Parkinson's disease, and amyotrophic lateral sclerosis. This review summarizes the latest research progress on SGs dynamics in neurodegenerative diseases. It begins with an overview of the basic biological characteristics of SGs and their functions in neurons, followed by an in-depth exploration of the mechanisms and regulatory pathways of SGs dynamics. The review then summarizes potential therapeutic strategies targeting SGs dynamics abnormalities, particularly through small molecule drugs to modulate SGs formation and disassembly, aiming to delay or halt the progression of neurodegenerative diseases. The review also highlights the application prospects of these interventions in treating neurodegenerative diseases. Finally, the review introduces current techniques used to study SGs dynamics, discussing their advantages, limitations, and future development possibilities. This review aims to provide researchers with a comprehensive perspective to advance the understanding and clinical application of SGs dynamics in the field of neurodegenerative diseases.

O-GlcNAcylation reduces proteome solubility and regulates the formation of biomolecular condensates in human cells

O-GlcNAcylation plays critical roles in the regulation of protein functions and cellular activities, including protein interactions with other macromolecules. While the formation of biomolecular condensates (or biocondensates) regulated by O-GlcNAcylation in a few individual proteins has been reported, systematic investigation of O-GlcNAcylation on the regulation of biocondensate formation remains to be explored. Here we systematically study the roles of O-GlcNAcylation in regulating protein solubility and its impacts on RNA-protein condensates using mass spectrometry-based chemoproteomics. Unexpectedly, we observe a system-wide decrease in the solubility of proteins modified by O-GlcNAcylation, with glycoproteins involved in focal adhesion and actin binding exhibiting the most significant decrease. Furthermore, O-GlcNAcylation sites located in disordered regions and with fewer acidic and aromatic residues nearby are related to a greater drop in protein solubility. Additionally, we discover that a specific group of O-GlcNAcylation events promotes the dissociation of RNA-protein condensates under heat stress, while some enhance the formation of RNA-protein condensates during the recovery phase. Using site mutagenesis, inhibition of O-GlcNAc transferase, and fluorescence microscopy, we validate that O-GlcNAcylation regulates the formation of biocondensates for YTHDF3 and NUFIP2. This work advances our understanding of the functions of protein O-GlcNAcylation and its roles in the formation of biomolecular condensates.

Function in disorder: A review on the roles of the disordered dehydrin proteins in conferring stress tolerance

Water scarcity as a result of drought is considered to be among the most common forms of abiotic stress which directly hampers plant health. Such conditions often lead to various interlinked physiological conditions, including oxidative stress resulting from increased ROS levels that in turn, induce membranes dysfunction, leading to disruption in cellular ionic balance, and oxidation of macromolecules. Plants employ several mechanisms to counter these hostile conditions, which help them adapt to such unforgiving environments. Accumulation of specific types of proteins called dehydrins (DHNs) represents one such mechanism of adaptation. DHNs are ubiquitous in distribution and have been reported in different life forms; accumulating under a wide spectrum of stress. An important role of DHNs is to protect and maintain cell's macromolecular structure and function, thereby preserving membrane integrity, stabilizing proteins and nucleic acid, and conferring protection against oxidative stress. The present article explores different aspects of DHNs, including their structural compositions, architectures and conformational flexibility, and their role in combating a plethora of stress environments, with specific focus towards drought. Possible involvements of DHNs in intracellular biocondensates formation through phase separation and their role in stress sensing are also provided.

Deciphering the role of liquid-liquid phase separation in sarcoma: Implications for pathogenesis and treatment

Liquid-liquid phase separation (LLPS) is a significant reversible and dynamic process in organisms. Cells form droplets that are distinct from membrane-bound cell organelles by phase separation to keep biochemical processes in order. Nevertheless, the pathological state of LLPS contributes to the progression of a variety of tumor-related pathogenic issues. Sarcoma is one kind of highly malignant tumor characterized by aggressive metastatic potential and resistance to conventional therapeutic agents. Despite the significant clinical relevance, research on phase separation in sarcomas currently faces several major challenges. These include the limited availability of sarcoma samples, insufficient attention from the research community, and the complex genetic heterogeneity of sarcomas. Recently, emerging evidence have elaborated the specific effects and pathways of phase separation on different sarcoma subtypes, including the effect of sarcoma fusion proteins and other physicochemical factors on phase separation. This review aims to summarize the multiple roles of phase separation in sarcoma and novel molecular inhibitors that target phase separation. These insights will broaden the understanding of the mechanisms concerning sarcoma and offer new perspectives for future therapeutic strategies.

Targets and Gene Therapy of ALS (Part 1)

Amyotrophic lateral sclerosis (ALS) is a neurodegenerative disease characterized by the selective death of motor neurons, which causes muscle atrophy. Genetic forms of ALS are recorded only in 10% of cases. However, over the past decade, studies in genetics have substantially contributed to our understanding of the molecular mechanisms underlying ALS. The identification of key mutations such as SOD1, C9orf72, FUS, and TARDBP has led to the development of targeted therapy that is gradually being introduced into clinical trials, opening up a broad range of opportunities for correcting these mutations. In this review, we aimed to present an extensive overview of the currently known mechanisms of motor neuron degeneration associated with mutations in these genes and also the gene therapy methods for inhibiting the expression of their mutant proteins. Among these, antisense oligonucleotides, RNA interference (siRNA and miRNA), and gene-editing (CRISPR/Cas9) methods are of particular interest. Each has shown its efficacy in animal models when targeting mutant genes, whereas some of them have proven to be efficient in human clinical trials.

Revealing Stress Granule Compositional Heterogeneity through Antibody-Guided Proximity Labeling

Stress granules (SGs), transient nonmembranous cytoplasmic condensates that formed in response to cellular stresses, require precise characterization to unravel their cell-type and stress-specific protein compositions. This study introduced a G3BP1 antibody-guided proximity labeling (Ab-PL) method to explore the composition and diversity of SGs, overcoming the challenges of traditional enzyme-mediated proximity labeling techniques across various cell types, especially for the immune cells. Application of Ab-PL to HeLa and RAW264.7 cells under heat shock (HS), sodium arsenate (AS), and sodium chloride stress (SS) revealed two categories of SG proteins: "SG-core" and "SG-shell," characterized by their different abilities to undergo phase separation. The core proteins form the SG scaffold with strong self-segregation, while shell proteins are dynamically recruited based on the type of stress. Cell- and stress-specific SG proteins were also identified, highlighting compositional heterogeneity. Intriguingly, unique nuclear-cytoplasmic shuttling behaviors of SG components were observed under varying conditions, uncovering over 10 novel SG proteins, including REXO4, RBM28, and OGFR. This study provides a versatile tool for SG analysis across diverse cell types and offers insights into SG heterogeneity, which has potential implications for human diseases, paving the way for future studies on RNA metabolism, ribosome assembly, and immune regulation.

Gold-modified nanoporous silicon for photoelectrochemical regulation of intracellular condensates

Nano-enabled catalysis at the interface of metals and semiconductors has found numerous applications, but its role in mediating cellular responses is still largely unexplored. Here we explore the territory by examining the once elusive mechanism through which a nanoporous silicon-based photocatalyst facilitates the two-electron oxidation of water to generate hydrogen peroxide under physiological conditions. We achieve precise modulation of intracellular stress granule formation by the controlled photoelectrochemical production of hydrogen peroxide in the extracellular environment, thereby enhancing cellular resilience to significant oxidative stress. This photoelectrochemical strategy has been evaluated for its efficacy in treating myocardial ischaemia-reperfusion injury in an ex vivo rodent model. Our data suggest that a pretreatment regimen involving photoelectrochemical generation of hydrogen peroxide at mild concentrations mitigates myocardial ischaemia-reperfusion-induced functional decline and infarction. These findings suggest a viable wireless therapeutic intervention for managing ischaemic disease and highlight the biomedical potential of nanostructured semiconductor-based catalytic devices.

Pseudorabies virus IE180 protein hijacks G3BPs into the nucleus to inhibit stress granule formation

Pseudorabies virus (PRV) is a porcine alphaherpesvirus that can infect different animal species and cause pruritus and lethal encephalitis. Stress granules (SGs) are membrane-free cytoplasmic structures formed by liquid-liquid phase separation of G3BP proteins during cell translation inhibition, which generally plays an antiviral role in various viral infections. In this study, we found that infection with different PRV strains inhibits the formation of SGs in host cells. We found that IE180, the only immediate early protein of PRV, has a distinct inhibitory effect on SG formation and colocalizes with SG-nucleating G3BP proteins (G3BP1/2) in the nucleus during PRV infection. Co-immunoprecipitation assays demonstrated an interaction between IE180 and G3BP1/G3BP2, and this interaction appears to depend on the Herpesvirus ICP4-like protein N-terminal (ICP4L-N) domain of IE180 and both NTF2L and RBD domains of G3BP1. Since G3BPs mainly function in the cytoplasm to induce SG formation, we constructed several IE180 protein truncations lacking a nuclear localization sequence to alter the subcellular localization of IE180 to the cytoplasm. Mutant IE180 protein was mainly expressed in the cytoplasm and still suppressed SG formation induced by arsenite or poly(I:C), but its ability to inhibit SG formation was weakened. Importantly, knockout of G3BPs facilitated PRV replication in H1299 cells, while exogenous expression of G3BPs and formation of SGs in wild-type H1299 cells suppressed PRV replication. In summary, our study indicates that PRV IE180 suppresses SG formation and hijacks G3BPs into the nucleus to benefit virus replication.IMPORTANCEHerpesviruses, including pseudorabies virus (PRV), have evolved different strategies to compromise host immune responses. Stress granules (SGs) are one of the targets that viruses can overcome in order to increase replication. The related herpes simplex virus 1 (HSV-1) inhibits SG formation to promote virus replication, but the underlying mechanisms remain unknown. In this study, we confirmed that infection with different PRV strains inhibits SG formation. Interestingly, we found that the PRV immediate early protein IE180 interacts with G3BP proteins and hijacks these proteins into the nucleus to prevent SG formation. In line with the antiviral effect of SGs on PRV replication, exogenous expression of G3BPs and formation of SGs in G3BP1/2 knockout H1299 cells significantly compromised PRV replication. The reported mechanism appears to be also utilized by HSV-1 to prevent SG formation. Therefore, our study elucidates a novel mechanism by which alphaherpesviruses inhibit SG formation, which provides a new perspective to inquire into the immune escape of PRV and other alphaherpesviruses.

Connecting the Dots: Stress Granule and Cardiovascular Diseases

Stress granules (SGs) are membrane-less cytoplasmic assemblies composed of mRNAs and RNA-binding proteins (RBPs) that transiently form to cope with various cellular stressors by halting mRNA translation and, consequently, protein synthesis. SG formation plays a crucial role in regulating multiple cellular processes, including cellular senescence, inflammatory responses, and adaptation to oxidative stress under both physiological and pathological conditions. Dysregulation of SG assembly and disassembly has been implicated in the pathogenesis of various diseases, including cardiovascular diseases (CVDs), cancer, viral and bacterial infections, and degenerative diseases. In this review, we survey the key aspects of SGs biogenesis and biological functions, with a particular focus on their causal involvement in CVDs. Furthermore, we summarized several SG-modulating compounds and discussed the therapeutic potential of small molecules targeting SG-related diseases in clinical settings.

Integrator loss leads to dsRNA formation that triggers the integrated stress response

Integrator (INT) is a metazoan-specific complex that targets promoter-proximally paused RNA polymerase II (RNAPII) for termination, preventing immature RNAPII from entering gene bodies and functionally attenuating transcription of stress-responsive genes. Mutations in INT subunits are associated with many human diseases, including cancer, ciliopathies, and neurodevelopmental disorders, but how reduced INT activity contributes to disease is unknown. Here, we demonstrate that the loss of INT-mediated termination in human cells triggers the integrated stress response (ISR). INT depletion causes upregulation of short genes such as the ISR transcription factor activating transcription factor 3 (ATF3). Further, immature RNAPII that escapes into genes upon INT depletion is prone to premature termination, generating incomplete pre-mRNAs with retained introns. Retroelements within retained introns form double-stranded RNA (dsRNA) that is recognized by protein kinase R (PKR), which drives ATF4 activation and prolonged ISR. Critically, patient cells with INT mutations exhibit dsRNA accumulation and ISR activation, thereby implicating chronic ISR in diseases caused by INT deficiency.

RNF144A-VRK2-G3BP1 axis regulates stress granule assembly

Under the cellular stress, stress granules (SGs) help survival and proliferation of the cell. Unfortunately, the same SGs help unwanted cancer cells under stressful environment, including anti-cancer chemotherapy treatment. While SGs elevate the cancer cell's resistance to chemotherapy, the mechanism behind the formation of SGs in cancer cell under chemotherapy treatment is still to be revealed. Here, we identified that the level of VRK2 and the phosphorylation of its novel substrate, G3BP1, are reduced when the cellular stress was increased by sodium arsenite (SA) or cisplatin treatment. We also demonstrated that the level of RNF144A is increased in response to the stress and further downregulates VRK2 through proteasomal degradation in various types of cancer cells. Furthermore, inhibition of SG formation by the overexpression of VRK2 sensitized the cells to the stress and chemotherapy. Together, our study establishes an RNF144A-VRK2-G3BP1 axis that regulates SG formation and suggest its potential usage in anti-cancer therapy.

Backbone-mediated weakening of pairwise interactions enables percolation in peptide-based mimics of protein condensates

Biomolecular condensates formed by intrinsically disordered proteins (IDPs) are semidilute solutions. These can be approximated as solutions of blob-sized segments, which are peptide-sized motifs. We leveraged the blob picture and molecular dynamics simulations to quantify differences between inter-residue interactions in model compound and peptide-based mimics of dense versus dilute phases. The all-atom molecular dynamics simulations use a polarizable forcefield. In model compound solutions, the interactions between aromatic residues are stronger than interactions between cationic and aromatic residues. This holds in dilute and dense phases. Cooperativity within dense phases enhances pairwise interactions leading to finite-sized nanoscale clusters. The results for peptide-based condensates paint a different picture. Backbone amides add valence to the associating molecules. While this enhances pairwise inter-residue interactions in dilute phases, it weakens pair interactions in dense phases, doing so in a concentration-dependent manner. Weakening of pair interactions enables fluidization characterized by short-range order and long-range disorder. The higher valence afforded by the peptide backbone generates system-spanning networks. As a result, dense phases of peptides are best described as percolated network fluids. Overall, our results show how peptide backbones enhance pairwise interactions in dilute phases while weakening these interactions to enable percolation within dense phases.

Cooperative role of PACT and ADAR1 in preventing aberrant PKR activation by self-derived double-stranded RNA

Double-stranded RNAs (dsRNAs) produced during viral infections are recognized by the innate immune sensor protein kinase R (PKR), triggering a host translation shutoff that inhibits viral replication and propagation. Given the harmful effects of uncontrolled PKR activation, cells must tightly regulate PKR to ensure that its activation occurs only in response to viral infections, not endogenous dsRNAs. Here, we use CRISPR-Translate, a FACS-based genome-wide CRISPR-Cas9 knockout screening method that exploits translation levels as a readout and identifies PACT as a key inhibitor of PKR during viral infection. We find that PACT-deficient cells hyperactivate PKR in response to different RNA viruses, raising the question of why cells need to limit PKR activity. Our results demonstrate that PACT cooperates with ADAR1 to suppress PKR activation from self-dsRNAs in uninfected cells. The simultaneous deletion of PACT and ADAR1 results in synthetic lethality, which can be fully rescued in PKR-deficient cells. We propose that both PACT and ADAR1 act as essential barriers against PKR, creating a threshold of tolerable levels to endogenous dsRNA in cells without activating PKR-mediated translation shutdown and cell death.

Perillaldehyde Improves Parkinson-Like Deficits by Targeting G3BP Mediated Stress Granule Assembly in Preclinical Models

Stress granules (SGs) fulfill a pivotal role in host defense mechanisms, by sequestering both mRNA and protein via the process of liquid-liquid phase separation (LLPS). In this study, we showed that perillaldehyde (PAE), a natural occurring compound, bound directly to the core protein of SGs, Ras GTPase-activating protein-binding protein 1/2 (G3BP1/2), thereby inducing the assembly of SGs through the LLPS of G3BP/RNA complexes in vitro. Moreover, in Parkinson's disease (PD) models using Caenorhabditis elegans (C. elegans) and mice, PAE administration prompted SG formation, enhanced eIF2α phosphorylation, shielded dopaminergic neurons from toxic insults, mitigated α-synuclein (α-syn) aggregation, and improved PD-like motor disorders. In addition, these findings revealed that the interaction between G3BP1 and histone deacetylase 6 (HDAC6) inhibited the functions of cytoplasmic HDAC6 and reduced α-syn aggregation in cells and worms. Notably, the inhibition of SG assembly via gtbp-1 and tiar-1 RNAi effectively counteracted the beneficial effects of PAE in C. elegans. Collectively, these results imply that PAE may exert neuroprotective effects by targeting G3BP-mediated SG formation, thereby safeguarding dopaminergic neurons from toxic damage.

µMap proximity labeling in living cells reveals stress granule disassembly mechanisms

Phase-separated condensates are membrane-less intracellular structures comprising dynamic protein interactions that organize essential biological processes. Understanding the composition and dynamics of these organelles advances our knowledge of cellular behaviors and disease pathologies related to granule dysregulation. In this study, we apply microenvironment mapping with a HaloTag-based platform (HaloMap) to characterize intracellular stress granule dynamics in living cells. After validating the robustness and sensitivity of this approach, we then profile the stress granule proteome throughout the formation and disassembly and under pharmacological perturbation. These experiments reveal several ubiquitin-related modulators, including the HECT (homologous to E6AP C terminus) E3 ligases ITCH and NEDD4L, as well as the ubiquitin receptor toll-interacting protein TOLLIP, as key mediators of granule disassembly. In addition, we identify an autophagy-related pathway that promotes granule clearance. Collectively, this work establishes a general photoproximity labeling approach for unraveling intracellular protein interactomes and uncovers previously unexplored regulatory mechanisms of stress granule dynamics.

TIA1-Mediated Stress Granules Promote the Neuroinflammation and Demyelination in Experimental Autoimmune Encephalomyelitis through Upregulating IL-31RA Signaling

The dysfunction of stress granules (SGs) plays a crucial role in the pathogenesis of various neurological disorders, with T cell intracellular antigen 1 (TIA1) being a key component of SGs. However, the role and mechanism of TIA1-mediated SGs in experimental autoimmune encephalomyelitis (EAE) remain unclear. In this study, upregulation of TIA1, its translocation from the nucleus to the cytoplasm, and co-localization with G3BP1 (a marker of SGs) are observed in the spinal cord neurons of EAE mice. Deletion of TIA1 in the CNS alleviates neuroinflammation, suppresses demyelination and axonal damage, and reduces neuronal loss in EAE mice. Furthermore, alleviation of autophagy dysfunction and reduction of chronic persistent SGs are observed in Tia1Nestin-CKO EAE mice. Mechanistically, IL-31RA levels are decreased in Tia1Nestin-CKO EAE mice, which inhibit the downstream PI3K/AKT signaling pathway associated with IL-31RA, thereby enhancing autophagy and suppressing the NF-κB signaling pathway, further alleviating EAE symptoms. Knockdown of TIA1 in primary neurons and N2a cells treated with sodium arsenite also reduces the formation of SGs. These findings reveal an unrecognized role of TIA1-mediated SGs in promoting neuroinflammation and demyelination, offering novel therapeutic targets for MS.

Exploring the Cytoplasmic Retention of CRISPR-Cas9 in Eukaryotic Cells: The Role of Nuclear Localization Signals and Ribosomal Interactions

Cas9 must be localized to the nucleus to access the genome of mammalian cells. For most proteins, adding a single nuclear localization signal (NLS) is sufficient to promote nuclear entry. However, Cas9 nuclear entry appears to be inefficient as multiple NLSs are typically added to Cas9. Here, we found that three different Cas9 variants interact with the ribosome in HEK293T cells, and that this interaction is RNA mediated. Following immunoprecipitation-mass spectrometry of cytoplasmic-localized Cas9-0NLS and nuclear-localized Cas9-4NLS constructs, we identified novel Cas9 interactors in postmitotic neurons, including KEAP1 and additional ribosomal subunits, the latter were enriched in Cas9-0NLS samples. Collectively, our results suggest that Cas9 is sequestered in the cytoplasm of mammalian cells, in part, via interaction with the ribosome. Increasing the number of NLSs on Cas9 and/or increasing the amount of cytoplasmic guide RNA has the potential to outcompete ribosomal RNA binding and promote efficient nuclear localization of CRISPR-Cas9 variants.

The potential mechanism maintaining transactive response DNA binding protein 43 kDa in the mouse stroke model

The disruption of transactive response DNA binding protein 43 kDa (TDP-43) shuttling leads to the depletion of nuclear localization and the cytoplasmic accumulation of TDP-43. We aimed to evaluate the mechanism underlying the behavior of TDP-43 in ischemic stroke. Adult male C57BL/6 J mice were subjected to 30 or 60 min of transient middle cerebral artery occlusion (tMCAO), and examined at 1, 6, and 24 h post reperfusion. Immunostaining was used to evaluate the expression of TDP-43, G3BP1, HDAC6, and RAD23B. The total and cytoplasmic number of TDP-43-positive cells increased compared with sham operation group and peaked at 6 h post reperfusion after tMCAO. The elevated expression of G3BP1 protein peaked at 6 h after reperfusion and decreased at 24 h after reperfusion in ischemic mice brains. We also observed an increase of expression level of HDAC6 and the number of RAD23B-positive cells increased after tMCAO. RAD23B was colocalized with TDP-43 24 h after tMCAO. We proposed that the formation of stress granules might be involved in the mislocalization of TDP-43, based on an evaluation of G3BP1 and HDAC6. Subsequently, RAD23B, may also contribute to the downstream degradation of mislocalized TDP-43 in mice tMCAO model.

The roles of intrinsically disordered proteins in neurodegeneration

Neurodegenerative diseases such as Amyotrophic Lateral Sclerosis, Alzheimer's disease, Parkinson's disease, and Huntington's disease share a common pathological hallmark: the accumulation of misfolded proteins, particularly involving intrinsically disordered proteins (IDPs) like TDP-43, FUS, Tau, α-synuclein, and Huntingtin. These proteins undergo pathological aggregation, forming toxic inclusions that disrupt cellular function. The dysregulation of proteostasis mechanisms, including the ubiquitin-proteasome system (UPS), ubiquitin-independent proteasome system (UIPS), autophagy, and molecular chaperones, exacerbates these proteinopathies by failing to clear misfolded proteins effectively. Emerging therapeutic strategies aim to restore proteostasis through proteasome activators, autophagy enhancers, and chaperone-based interventions to prevent the toxic accumulation of IDPs. Additionally, understanding liquid-liquid phase separation (LLPS) and its role in stress granule dynamics offers novel insights into how aberrant phase transitions contribute to neurodegeneration. By targeting the molecular pathways involved in IDP aggregation and proteostasis regulation, and better understanding the specificity of each component, research in this area will pave the way for innovative therapeutic approaches to combat these neurodegenerative diseases. This review discusses the molecular mechanisms underpinning IDP pathology, highlights recent advancements in drug discovery, and explores the potential of targeting proteostasis machinery to develop effective therapies.

On subcellular distribution of the zinc finger 469 protein (ZNF469) and observed discrepancy in the localization of endogenous and overexpressed ZNF469

The zinc finger 469 gene (ZNF469) is a single-exon gene predicted to encode a protein of 3953 amino acids. Despite pathogenic ZNF469 variants being associated with Brittle Cornea Syndrome (BCS), relatively little is known about ZNF469 beyond its participation in regulating the expression of genes encoding extracellular matrix proteins. In this study, we examined the expression and intracellular localization of ZNF469 in different cell lines. The level of ZNF469 mRNA varied from low levels in HEK293 cells to high levels in HeLa cells and primary fibroblasts. Antibodies against ZNF469 reacted among others with a protein of approximately 400 kDa in immunoblot analysis, which was mainly present in the insoluble fraction of the cytoplasm. Immunofluorescence analysis of interphase cells showed small cytoplasmic puncta and weak nuclear staining. In dividing HeLa cells, the antibodies recognized foci that also stained for proteasomes. In transfected cells, ZNF469 was observed mainly in foci resembling nuclear speckles in interphase and at the midbody during mitosis. The nuclear foci showed overlapping staining with proteasomes. In live cell imaging, liquid-like properties of the nuclear foci were recorded as they changed shape and position and occasionally fused with each other. During stress granule formation, cytoplasmic foci showed overlapping staining with G3BP1. Finally, in silico analysis revealed large intrinsically disordered regions with multiple low complexity domains in ZNF469. Our data indicate that ZNF469 forms aggregates possibly as biomolecular condensates when overexpressed. However, care must be taken when analyzing the intracellular distribution of ZNF469 due to the discrepancy in the localization of endogenous ZNF469 and overexpressed ZNF469 in transfected cells.

Multiplexed dynamic control of temperature to probe and observe mammalian cells

Temperature is an important biological stimulus, yet there is a lack of approaches to modulate the temperature of biological samples in a dynamic and high-throughput manner. The thermoPlate is a device for programmable control of temperature in a 96-well plate, compatible with cell culture and microscopy. The thermoPlate maintains feedback control of temperature independently in each well, with minutes-scale heating and cooling through ΔT = 15-20°C. We first used the thermoPlate to characterize the rapid temperature-dependent phase separation of a synthetic elastin-like polypeptide (ELP53). We then examined stress granule (SG) formation in response to dynamic heat stress, revealing adaptation of SGs to persistent heat and formation of a memory of stress that prevented SG formation in response to subsequent heat shocks. The capabilities and open-source nature of the thermoPlate will empower the study and engineering of a wide range of thermoresponsive phenomena. A record of this paper's transparent peer review process is included in the Supplemental information.

Live-cell imaging of circular and long noncoding RNAs associated with FUS pathological aggregates by Pepper fluorescent RNA

Lately, important advancements in visualizing RNAs in fixed and live cells have been achieved. Although mRNA imaging techniques are well-established, the development of effective methods for studying noncoding RNAs (ncRNAs) in living cells is still challenging but necessary, as they show a variety of functions and intracellular localizations, including participation in highly dynamic processes like phase transition, which is still poorly studied in vivo. Addressing this issue, we tagged two exemplary ncRNAs with the fluorescent RNA (fRNA) Pepper. Specifically, we showed that circ-HDGFRP3 interacts with p-bodies and is recruited in pathological FUS aggregates in a dynamic fashion, and we super-resolved its distribution in such condensates via structured illumination microscopy. Moreover, we tracked the long noncoding RNA (lncRNA) nHOTAIRM1, a motor neuron-specific constituent of stress granules, monitoring its behavior throughout the oxidative-stress response in physiological and pathological conditions. Overall, as fRNA development progresses, our work demonstrates an effective use of Pepper for monitoring complex processes, such as phase transition, in living cells through the visualization of circular RNAs (circRNAs) and lncRNAs with super-resolution power.

The formation of chaperone-rich GET bodies depends on the tetratricopeptide repeat region of Sgt2 and is reversed by NADH

The guided-entry of tail-anchored proteins (GET) pathway is a post-translational targeting route to the endoplasmic reticulum (ER). Upon glucose withdrawal, the soluble GET proteins re-localize to dynamic cytosolic foci, here termed GET bodies. Our data reveal that the pre-targeting complex components, Sgt2 and the Get4-Get5 heterodimer, and the Get3 ATPase play important roles in the assembly of these structures in Saccharomyces cerevisiae. More specifically, the TPR region of Sgt2 is required as a GET body scaffold. Systematic compositional analyses of GET bodies reveal their chaperone-rich nature and the presence of numerous proteins involved in metabolic processes. Temporal analyses of GET body assembly demonstrate the sequential recruitment of different chaperones, and we discover the requirement of Sis1 and Sti1 for maintaining the dynamic properties of these structures. In vivo, NADH derived from the oxidation of ethanol to acetaldehyde can induce GET body disassembly in a reaction depending on the alcohol dehydrogenase Adh2 and in vitro, addition of NADH resolves GET bodies. This suggests a mechanistic basis for their formation and disassembly in response to the metabolic shift caused by glucose withdrawal and re-addition.

Coarse-Grained Model of Disordered RNA for Simulations of Biomolecular Condensates

Protein-RNA condensates are involved in a range of cellular activities. Coarse-grained molecular models of intrinsically disordered proteins have been developed to shed light on and predict single-chain properties and phase separation. An RNA model compatible with such models for disordered proteins would enable the study of complex biomolecular mixtures involving RNA. Here, we present a sequence-independent coarse-grained, two-beads-per-nucleotide model of disordered, flexible RNA based on a hydropathy scale. We parametrize the model, which we term CALVADOS-RNA, using a combination of bottom-up and top-down approaches to reproduce local RNA geometry and intramolecular interactions based on atomistic simulations and in vitro experiments. The model semiquantitatively captures several aspects of RNA-RNA and RNA-protein interactions. We examined RNA-RNA interactions by comparing calculated and experimental virial coefficients and nonspecific RNA-protein interaction by studying the reentrant phase behavior of protein-RNA mixtures. We demonstrate the utility of the model by simulating the formation of mixed condensates consisting of the disordered region of MED1 and RNA chains and the selective partitioning of disordered regions from transcription factors into these and compare the results to experiments. Despite the simplicity of our model, we show that it captures several key aspects of protein-RNA interactions and may therefore be used as a baseline model to study several aspects of the biophysics and biology of protein-RNA condensates.