Amyotrophic lateral sclerosis-linked FUS/TLS alters stress granule assembly and dynamics

BACKGROUND: Amyotrophic lateral sclerosis (ALS)-linked fused in sarcoma/translocated in liposarcoma (FUS/TLS or FUS) is concentrated within cytoplasmic stress granules under conditions of induced stress. Since only the mutants, but not the endogenous wild-type FUS, are associated with stress granules under most of the stress conditions reported to date, the relationship between FUS and stress granules represents a mutant-specific phenotype and thus may be of significance in mutant-induced pathogenesis. While the association of mutant-FUS with stress granules is well established, the effect of the mutant protein on stress granules has not been examined. Here we investigated the effect of mutant-FUS on stress granule formation and dynamics under conditions of oxidative stress. RESULTS: We found that expression of mutant-FUS delays the assembly of stress granules. However, once stress granules containing mutant-FUS are formed, they are more dynamic, larger and more abundant compared to stress granules lacking FUS. Once stress is removed, stress granules disassemble more rapidly in cells expressing mutant-FUS. These effects directly correlate with the degree of mutant-FUS cytoplasmic localization, which is induced by mutations in the nuclear localization signal of the protein. We also determine that the RGG domains within FUS play a key role in its association to stress granules. While there has been speculation that arginine methylation within these RGG domains modulates the incorporation of FUS into stress granules, our results demonstrate that this post-translational modification is not involved. CONCLUSIONS: Our results indicate that mutant-FUS alters the dynamic properties of stress granules, which is consistent with a gain-of-toxic mechanism for mutant-FUS in stress granule assembly and cellular stress response

Drug-induced stress granule formation protects sensory hair cells in mouse cochlear explants during ototoxicity

Stress granules regulate RNA translation during cellular stress, a mechanism that is generally presumed to be protective, since stress granule dysregulation caused by mutation or ageing is associated with neurodegenerative disease. Here, we investigate whether pharmacological manipulation of the stress granule pathway in the auditory organ, the cochlea, affects the survival of sensory hair cells during aminoglycoside ototoxicity, a common cause of acquired hearing loss. We show that hydroxamate (-)-9, a silvestrol analogue that inhibits eIF4A, induces stress granule formation in both an auditory cell line and ex-vivo cochlear cultures and that it prevents ototoxin-induced hair-cell death. In contrast, preventing stress granule formation using the small molecule inhibitor ISRIB increases hair-cell death. Furthermore, we provide the first evidence of stress granule formation in mammalian hair cells in-vivo triggered by aminoglycoside treatment. Our results demonstrate that pharmacological induction of stress granules enhances cell survival in native-tissue, in a clinically-relevant context. This establishes stress granules as a viable therapeutic target not only for hearing loss but also other neurodegenerative diseases.EI:595 - Action on Hearing Loss; 091092/Z/09/Z - Wellcome Trust (Wellcome); MR/N004329/1 - RCUK | Medical Research Council (MRC)Published versio

The Stress Granule Transcriptome Reveals Principles of mRNA Accumulation in Stress Granules

Stress granules are mRNA-protein assemblies formed from nontranslating mRNAs. Stress granules are important in the stress response and may contribute to some degenerative diseases. Here, we describe the stress granule transcriptome of yeast and mammalian cells through RNA-sequencing (RNA-seq) analysis of purified stress granule cores and single-molecule fluorescence in situ hybridization (smFISH) validation. While essentially every mRNA, and some noncoding RNAs (ncRNAs), can be targeted to stress granules, the targeting efficiency varies from \u3c1% to \u3e95%. mRNA accumulation in stress granules correlates with longer coding and UTR regions and poor translatability. Quantifying the RNA-seq analysis by smFISH reveals that only 10% of bulk mRNA molecules accumulate in mammalian stress granules and that only 185 genes have more than 50% of their mRNA molecules in stress granules. These results suggest that stress granules may not represent a specific biological program of messenger ribonucleoprotein (mRNP) assembly, but instead form by condensation of nontranslating mRNPs in proportion to their length and lack of association with ribosomes. Transcriptome analysis coupled with single-molecule FISH validation of stress granule cores provides new insight into the mRNAs and ncRNAs that accumulate in stress granules. Ten percent of bulk mRNA molecules accumulate in stress granules, and targeting efficiency correlates with poorer translation efficiency and longer coding and UTR length

Analyzing plant stress granules in response to plant viruses

Plant viruses have the ability to redirect host machineries and processes to establish a productive infection. Virus-host interactions lead to the reprogramming of the plant cell cycle and transcriptional controls, inhibition of cell death pathways, interference with cell signaling and protein turnover, and suppression defense pathways. Stress granules (SGs) are structures within cells that regulate gene expression during stress response, e.g. viral infection. In mammalian cells assembly of SGs is dependent on the Ras-GAP SH3-domain–binding protein (G3BP). The C-terminal domain of the viral nonstructural protein 3 (nsP3) of Semliki Forest virus (SFV) forms a complex with mammalian G3BP and sequesters it into viral RNA replication complexes in a manner that inhibits the formation of SGs. The binding domain of nsP3 to HsG3BP was mapped to two tandem ‘FGDF’ repeat motifs close to the C-terminus of the viral proteins. It was speculated that plant viruses employ a similar strategy to inhibit SG function.Universidad de Málaga. Campus de Excelencia Internacional Andalucía Tech. Vicerrectorado de Investigación y Programa de doctorado "Biotecnología Avanzada

Atomic structures of TDP-43 LCD segments and insights into reversible or pathogenic aggregation.

The normally soluble TAR DNA-binding protein 43 (TDP-43) is found aggregated both in reversible stress granules and in irreversible pathogenic amyloid. In TDP-43, the low-complexity domain (LCD) is believed to be involved in both types of aggregation. To uncover the structural origins of these two modes of β-sheet-rich aggregation, we have determined ten structures of segments of the LCD of human TDP-43. Six of these segments form steric zippers characteristic of the spines of pathogenic amyloid fibrils; four others form LARKS, the labile amyloid-like interactions characteristic of protein hydrogels and proteins found in membraneless organelles, including stress granules. Supporting a hypothetical pathway from reversible to irreversible amyloid aggregation, we found that familial ALS variants of TDP-43 convert LARKS to irreversible aggregates. Our structures suggest how TDP-43 adopts both reversible and irreversible β-sheet aggregates and the role of mutation in the possible transition of reversible to irreversible pathogenic aggregation

Similarities of stress granules and cytosolic prions

Eukaryotic cells contain several organelles that lack a delimiting membrane. These membrane-less organelles take over important functions within the cell and influence biological reactions by condensing nucleic acids and proteins into dense droplets. Upon environmental stress, one kind of membrane-less organelle, termed stress granules, assembles to sequester non-essential mRNA transcripts while translation is stalled. Together with RNA-binding proteins, mRNA transcripts form a network by multiple weak interactions within stress granules. Many RNA-binding proteins thereby facilitate the assembly of stress granules by their low-complexity or prion-like domains, which were identified based on their structural similarities with yeast prion domains. Several RNA-binding proteins that are part of stress granules were found aggregated in degenerative disorders. Therefore, stress granules have been proposed to contribute to the disease process by acting as nucleation sites for protein aggregates, which might evolve into pathological protein inclusions over time. In this study, we compared similarities and differences between stress granules and cytosolic prion aggregates. Specifically, we tested the hypothesis if recruitment of a protein with a prion-like domain to stress granules induces its conversion into a protein aggregate with self-perpetuating properties. To this end, we made use of the yeast prion domain NM of Sup35, expressed in mammalian cells, that can form cytosolic prions upon exposure to recombinant NM fibrils. Here we show that the interactome of NM prions significantly overlaps with that of stress granules. The presence of neither soluble nor aggregated NM altered the dynamics of stress granules, but stress granule disassembly was slightly impaired. Importantly, prolonged presence of stress granules did not induce NM aggregation, but rather led to cell death. Interestingly, chemicals that induce stress granules drastically increased NM aggregate formation upon concomitant induction with recombinant NM fibrils. However, stress granules per se were not required for the increased induction rate, as concomitant exposure to drugs or siRNA that interfere with stress granule formation did not lower the NM aggregate induction rates. We propose a model where stress that triggers a stress granule response results in a cellular environment that allows more effective protein aggregate induction by exogenous seeds. One possible explanation for this is that the cellular quality control mechanism is overloaded under stress and thus cannot combat the additional aggregate induction by an exogenous seed. Therefore, the role of stress granules in the pathogenesis of neurodegenerative disorders might be different than so far anticipated. Still, triggers that cause stress granule formation enhance protein aggregation in the presence of exogenous seeds, thereby likely contributing to disease progression

STRESS GRANULES MODULATE SYK TO CAUSE MICROGLIAL DYSFUNCTION IN ALZHEIMER’S DISEASE

Microglial cells in the brains of Alzheimer’s patients are recruited to amyloid beta (Aβ) plaques and exhibit an activated phenotype, but are defective for plaque removal by phagocytosis. To explore the molecular basis for these phenomena, I hypothesized that defects in the functions of the protein-tyrosine kinase SYK, which is important both for macrophage activation and phagocytosis, might underlie much of this pathology. Recent evidence from our lab indicates that SYK can associate with stress granules, ribonucleoprotein particles that form in stressed cells and contain inactive translation initiation complexes. I found that microglial cell lines and primary mouse brain microglia, when stressed by exposure to sodium arsenite or Aβ(1-42) peptides or fibrils, form extensive stress granules to which the tyrosine kinase, SYK, is recruited. SYK enhances the formation of stress granules as evidenced by the inhibition of stress granule formation by small molecule inhibitors, knockdown of SYK expression by shRNA and SYK haploinsufficiency in mouse microglial cells. SYK is active within the resulting stress granules where it catalyzes the phosphorylation of stress granule-associated proteins on tyrosine. SYK-dependent stress granul

Proteins that contain a functional Z-DNA-binding domain localize to cytoplasmic stress granules

Long double-stranded RNA may undergo hyper-editing by adenosine deaminases that act on RNA (ADARs), where up to 50% of adenosine residues may be converted to inosine. However, although numerous RNAs may undergo hyper-editing, the role for inosine-containing hyper-edited double-stranded RNA in cells is poorly understood. Nevertheless, editing plays a critical role in mammalian cells, as highlighted by the analysis of ADAR-null mutants. In particular, the long form of ADAR1 (ADAR1(p150)) is essential for viability. Moreover, a number of studies have implicated ADAR1(p150) in various stress pathways. We have previously shown that ADAR1(p150) localized to cytoplasmic stress granules in HeLa cells following either oxidative or interferon-induced stress. Here, we show that the Z-DNA-binding domain (Zα(ADAR1)) exclusively found in ADAR1(p150) is required for its localization to stress granules. Moreover, we show that fusion of Zα(ADAR1) to either green fluorescent protein (GFP) or polypyrimidine binding protein 4 (PTB4) also results in their localization to stress granules. We additionally show that the Zα domain from other Z-DNA-binding proteins (ZBP1, E3L) is likewise sufficient for localization to stress granules. Finally, we show that Z-RNA or Z-DNA binding is important for stress granule localization. We have thus identified a novel role for Z-DNA-binding domains in mammalian cells

Protein Methylation and Stress Granules: Posttranslational Remodeler or Innocent Bystander?

Stress granules contain a large number of post-translationally modified proteins, and studies have shown that these modifications serve as recruitment tags for specific proteins and even control the assembly and disassembly of the granules themselves. Work originating from our laboratory has focused on the role protein methylation plays in stress granule composition and function. We have demonstrated that both asymmetrically and symmetrically dimethylated proteins are core constituents of stress granules, and we have endeavored to understand when and how this occurs. Here we seek to integrate this data into a framework consisting of the currently known post-translational modifications affecting stress granules to produce a model of stress granule dynamics that, in turn, may serve as a benchmark for understanding and predicting how post-translational modifications regulate other granule types

Background-deflection Brillouin microscopy reveals altered biomechanics of intracellular stress granules by ALS protein FUS

Altered cellular biomechanics have been implicated as key photogenic triggers in age-related diseases. An aberrant liquid-to-solid phase transition, observed in in vitro reconstituted droplets of FUS protein, has been recently proposed as a possible pathogenic mechanism for amyotrophic lateral sclerosis (ALS). Whether such transition occurs in cell environments is currently unknown as a consequence of the limited measuring capability of the existing techniques, which are invasive or lack of subcellular resolution. Here we developed a non-contact and label-free imaging method, named background-deflection Brillouin microscopy, to investigate the three-dimensional intracellular biomechanics at a sub-micron resolution. Our method exploits diffraction to achieve an unprecedented 10,000-fold enhancement in the spectral contrast of single-stage spectrometers, enabling, to the best of our knowledge, the first direct biomechanical analysis on intracellular stress granules containing ALS mutant FUS protein in fixed cells. Our findings provide fundamental insights on the critical aggregation step underlying the neurodegenerative ALS disease