Quantitative proteomics identifies proteins that resist translational repression and become dysregulated in ALS-FUS

Baron, Desiree M.; Matheny, Tyler; Lin, Ying‐Li; Leszyk, John D.; Kenna, Kevin P.; Gall, Katherine V.; Santos, David P.; Tischbein, Maeve; Funes, Salome; Hayward, Lawrence J.; Kiskinis, Evangelos; Landers, John E.; Parker, Roy; Shaffer, Scott A.; Bosco, Daryl A.

doi:10.1093/hmg/ddz048

Cited by 18 publications

(19 citation statements)

References 90 publications

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“…As a first step to explore the effects of oxidative stress on global translation, we analysed new protein synthesis in response to arsenite treatment in PC-3 prostate cancer (PCA) cells, using Click-chemistry based azidohomoalanine (AHA) labelling as described ( 36 ). As expected based on the literature ( 41 ), arsenite treatment significantly reduced global protein synthesis (Figure 1A ). To probe selective mRNA translation under oxidative stress, we catalogued transcripts associated with PSs under arsenite treatment (2 h at 200 uM).…”

Section: Resultssupporting

confidence: 90%

“…We also compared our PSseq data with a recent proteomic study highlighting proteins that evade stress-induced translational repression in arsenite-treated cells, as identified by quantitative bio-orthogonal noncanonical amino acid tagging (BONCAT) and stable isotope labeling by amino acids in culture (SILAC) ( 41 ). That study revealed hundreds of proteins that remain actively synthesized during stress-induced translational repression in arsenite treated human neuroblastoma cell lines.…”

Section: Resultsmentioning

confidence: 99%

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G3BP1-linked mRNA partitioning supports selective protein synthesis in response to oxidative stress

Somasekharan¹,

Zhang²,

Saxena³

et al. 2020

Nucleic Acids Research

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Abstract Cells limit energy-consuming mRNA translation during stress to maintain metabolic homeostasis. Sequestration of mRNAs by RNA binding proteins (RBPs) into RNA granules reduces their translation, but it remains unclear whether RBPs also function in partitioning of specific transcripts to polysomes (PSs) to guide selective translation and stress adaptation in cancer. To study transcript partitioning under cell stress, we catalogued mRNAs enriched in prostate carcinoma PC-3 cell PSs, as defined by polysome fractionation and RNA sequencing (RNAseq), and compared them to mRNAs complexed with the known SG-nucleator protein, G3BP1, as defined by spatially-restricted enzymatic tagging and RNAseq. By comparing these compartments before and after short-term arsenite-induced oxidative stress, we identified three major categories of transcripts, namely those that were G3BP1-associated and PS-depleted, G3BP1-dissociated and PS-enriched, and G3BP1-associated but also PS-enriched. Oxidative stress profoundly altered the partitioning of transcripts between these compartments. Under arsenite stress, G3BP1-associated and PS-depleted transcripts correlated with reduced expression of encoded mitochondrial proteins, PS-enriched transcripts that disassociated from G3BP1 encoded cell cycle and cytoprotective proteins whose expression increased, while transcripts that were both G3BP1-associated and PS-enriched encoded proteins involved in diverse stress response pathways. Therefore, G3BP1 guides transcript partitioning to reprogram mRNA translation and support stress adaptation.

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Section: Resultssupporting

confidence: 90%

Section: Resultsmentioning

confidence: 99%

G3BP1-linked mRNA partitioning supports selective protein synthesis in response to oxidative stress

Somasekharan¹,

Zhang²,

Saxena³

et al. 2020

Nucleic Acids Research

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“…Expression of FUS R495X in neuronal cells is reported to cause the dispersion of the protein COPBI-the coatomer beta subunit of the coat protein complex I involved in retrograde vesicular trafficking from Golgi and ER [61]. Intriguingly, expression of nsP3 WT, but not the G32E mutant, restored the dispersed pattern of COPBI in FUS R495X-transfected neuronal SH-SY5Y cells to the compact, juxtanuclear pattern observed in untransfected cells (Fig.…”

Section: Adp-ribosylhydrolase Activity Of Nsp3 Suppresses the Formatimentioning

confidence: 83%

Alphavirus nsP3 ADP-ribosylhydrolase Activity Disrupts Stress Granule Formation

Jayabalan

Griffin

Leung

2019

Preprint

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Formation of stress granules (SGs), cytoplasmic condensates of stalled translation initiation complexes, is regulated by post-translational protein modification. Alphaviruses interfere with SG formation in response to inhibition of host protein synthesis through the activities of nonstructural protein 3 (nsP3). nsP3 has a conserved N-terminal macrodomain that binds and can remove ADP-ribose from ADPribosylated proteins and a C-terminal hypervariable domain that binds essential SG component G3BP1.We showed that the hydrolase activity of chikungunya virus nsP3 macrodomain removed ADPribosylation of G3BP1 and suppressed SG formation. ADP-ribosylhydrolase-deficient nsP3 mutants allowed stress-induced cytoplasmic condensation of translation initiation factors. nsP3 also disassembled SG-like aggregates enriched with translation initiation factors that are induced by the expression of FUS mutant R495X linked to amyotrophic lateral sclerosis. Therefore, our data indicate that regulation of ADP-ribosylation controls the localization of translation initiation factors during virus infection and other pathological conditions. All rights reserved. No reuse allowed without permission. INTRODUCTIONNon-membranous structures are prevalent in cells and critical for cellular functions, including RNA metabolism, embryonic cell fate specification, and neuronal activities [1][2][3]. Although the components of these non-membranous structures are often dynamically exchanged with the surrounding milieu, the compositions of these cellular structures remain distinct [4]. It is, however, unclear how individual components are selectively retained in these non-membranous structures.Stress granules (SGs), one of the best characterized dynamic non-membranous structures, are RNAprotein assemblies formed in response to a variety of environmental cues [3]. In most cases, these environmental cues activate stress-responsive protein kinases that phosphorylate the eukaryotic initiation factor 2 alpha (eIF2α), resulting in the stalling of translation initiation [3]. The sudden influx of untranslated mRNAs is proposed to seed the formation of SGs, where the polynucleotide promotes local concentration of proteins through non-covalent binding [5]. These RNA-binding proteins are highly enriched with low-complexity regions, and emergent data indicate that the nonspecific, weak interactions between these regions are responsible for the condensation of proteins to form higherorder structures, such as microscopically visible SGs [6][7][8]. Depending on the type of stress, the composition of SGs could vary [9], but certain common components, such as Ras GTP-activating protein-binding proteins G3BP1/2, are essential for SG formation [10,11]. Dysregulation of SG assembly/disassembly and mutations in the low-complexity region of specific SG proteins are implicated in the pathogenesis of diseases such as viral infection, cancer and neurodegeneration [1,[12][13][14]. Therefore, understanding the regulatory mechanisms of SG assembly is critical for designing novel th...

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“…The prolonged sequestration of important RBPs and mRNAs needed for cell survival combined with translational impairment might also be a mechanism of cell death [84]. A recent study in neuronal cells demonstrated that in response to stress there was a significant correlation between the proteins being actively translated and those transcripts depleted from SGs, including proteins associated with neurodegenerative diseases [85]. Further, it was found that mutant RBPs within SGs can further alter neuronal gene expression [85].…”

Section: Rna-binding Proteins and Stress Granules In Neurodegenerativmentioning

confidence: 99%

“…A recent study in neuronal cells demonstrated that in response to stress there was a significant correlation between the proteins being actively translated and those transcripts depleted from SGs, including proteins associated with neurodegenerative diseases [85]. Further, it was found that mutant RBPs within SGs can further alter neuronal gene expression [85]. Significant advances in identifying the components and structure of SGs was reviewed by Youn et al [86].…”

Section: Rna-binding Proteins and Stress Granules In Neurodegenerativmentioning

confidence: 99%

The Potential Contribution of Dysfunctional RNA-Binding Proteins to the Pathogenesis of Neurodegeneration in Multiple Sclerosis and Relevant Models

Libner

Salapa

Levin

2020

IJMS

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Neurodegeneration in multiple sclerosis (MS) is believed to underlie disease progression and permanent disability. Many mechanisms of neurodegeneration in MS have been proposed, such as mitochondrial dysfunction, oxidative stress, neuroinflammation, and RNA-binding protein dysfunction. The purpose of this review is to highlight mechanisms of neurodegeneration in MS and its models, with a focus on RNA-binding protein dysfunction. Studying RNA-binding protein dysfunction addresses a gap in our understanding of the pathogenesis of MS, which will allow for novel therapies to be generated to attenuate neurodegeneration before irreversible central nervous system damage occurs.

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Quantitative proteomics identifies proteins that resist translational repression and become dysregulated in ALS-FUS

Cited by 18 publications

References 90 publications

G3BP1-linked mRNA partitioning supports selective protein synthesis in response to oxidative stress

G3BP1-linked mRNA partitioning supports selective protein synthesis in response to oxidative stress

Alphavirus nsP3 ADP-ribosylhydrolase Activity Disrupts Stress Granule Formation

The Potential Contribution of Dysfunctional RNA-Binding Proteins to the Pathogenesis of Neurodegeneration in Multiple Sclerosis and Relevant Models

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