scholarly journals SARS-CoV-2 Nucleocapsid protein attenuates stress granule formation and alters gene expression via direct interaction with host mRNAs

Author(s):  
Syed Nabeel-Shah ◽  
Hyunmin Lee ◽  
Nujhat Ahmed ◽  
Edyta Marcon ◽  
Shaghayegh Farhangmehr ◽  
...  

AbstractThe COVID-19 pandemic has caused over one million deaths thus far. There is an urgent need for the development of specific viral therapeutics and a vaccine. SARS-CoV-2 nucleocapsid (N) protein is highly expressed upon infection and is essential for viral replication, making it a promising target for both antiviral drug and vaccine development. Here, starting from a functional proteomics workflow, we initially catalogued the protein-protein interactions of 21 SARS-CoV-2 proteins in HEK293 cells, finding that the stress granule resident proteins G3BP1 and G3BP2 copurify with N with high specificity. We demonstrate that N protein expression in human cells sequesters G3BP1 and G3BP2 through its physical interaction with these proteins, attenuating stress granule (SG) formation. The ectopic expression of G3BP1 in N-expressing cells was sufficient to reverse this phenotype. Since N is an RNA-binding protein, we performed iCLIP-sequencing experiments in cells, with or without exposure to oxidative stress, to identify the host RNAs targeted by N. Our results indicate that SARS-CoV-2 N protein binds directly to thousands of mRNAs under both conditions. Like the G3BPs stress granule proteins, N was found to predominantly bind its target mRNAs in their 3’UTRs. RNA sequencing experiments indicated that expression of N results in wide-spread gene expression changes in both unstressed and oxidatively stressed cells. We suggest that N regulates host gene expression by both attenuating stress granules and binding directly to target mRNAs.

2010 ◽  
Vol 15 (5) ◽  
pp. 1210-1224 ◽  
Author(s):  
Parvaneh Nikpour ◽  
Modjtaba Emadi Baygi ◽  
Christine Steinhoff ◽  
Christiane Hader ◽  
Anna C. Luca ◽  
...  

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Shan Lu ◽  
Qiaozhen Ye ◽  
Digvijay Singh ◽  
Yong Cao ◽  
Jolene K. Diedrich ◽  
...  

AbstractThe multifunctional nucleocapsid (N) protein in SARS-CoV-2 binds the ~30 kb viral RNA genome to aid its packaging into the 80–90 nm membrane-enveloped virion. The N protein is composed of N-terminal RNA-binding and C-terminal dimerization domains that are flanked by three intrinsically disordered regions. Here we demonstrate that the N protein’s central disordered domain drives phase separation with RNA, and that phosphorylation of an adjacent serine/arginine rich region modulates the physical properties of the resulting condensates. In cells, N forms condensates that recruit the stress granule protein G3BP1, highlighting a potential role for N in G3BP1 sequestration and stress granule inhibition. The SARS-CoV-2 membrane (M) protein independently induces N protein phase separation, and three-component mixtures of N + M + RNA form condensates with mutually exclusive compartments containing N + M or N + RNA, including annular structures in which the M protein coats the outside of an N + RNA condensate. These findings support a model in which phase separation of the SARS-CoV-2 N protein contributes both to suppression of the G3BP1-dependent host immune response and to packaging genomic RNA during virion assembly.


Biology ◽  
2021 ◽  
Vol 10 (5) ◽  
pp. 361
Author(s):  
Myeongwoo Jung ◽  
Eun-Kyung Lee

HuD (also known as ELAVL4) is an RNA–binding protein belonging to the human antigen (Hu) family that regulates stability, translation, splicing, and adenylation of target mRNAs. Unlike ubiquitously distributed HuR, HuD is only expressed in certain types of tissues, mainly in neuronal systems. Numerous studies have shown that HuD plays essential roles in neuronal development, differentiation, neurogenesis, dendritic maturation, neural plasticity, and synaptic transmission by regulating the metabolism of target mRNAs. However, growing evidence suggests that HuD also functions as a pivotal regulator of gene expression in non–neuronal systems and its malfunction is implicated in disease pathogenesis. Comprehensive knowledge of HuD expression, abundance, molecular targets, and regulatory mechanisms will broaden our understanding of its role as a versatile regulator of gene expression, thus enabling novel treatments for diseases with aberrant HuD expression. This review focuses on recent advances investigating the emerging role of HuD, its molecular mechanisms of target gene regulation, and its disease relevance in both neuronal and non–neuronal systems.


2019 ◽  
Vol 39 (10) ◽  
pp. 2014-2027 ◽  
Author(s):  
Allison B. Herman ◽  
Milessa Silva Afonso ◽  
Sheri E. Kelemen ◽  
Mitali Ray ◽  
Christine N. Vrakas ◽  
...  

Objective: Stress granules (SGs) are dynamic cytoplasmic aggregates containing mRNA, RNA-binding proteins, and translation factors that form in response to cellular stress. SGs have been shown to contribute to the pathogenesis of several human diseases, but their role in vascular diseases is unknown. This study shows that SGs accumulate in vascular smooth muscle cells (VSMCs) and macrophages during atherosclerosis. Approach and Results: Immunohistochemical analysis of atherosclerotic plaques from LDLR − /− mice revealed an increase in the stress granule-specific markers Ras-G3BP1 (GTPase-activating protein SH3 domain-binding protein) and PABP (poly-A-binding protein) in intimal macrophages and smooth muscle cells that correlated with disease progression. In vitro, PABP+ and G3BP1+ SGs were rapidly induced in VSMC and bone marrow–derived macrophages in response to atherosclerotic stimuli, including oxidized low-density lipoprotein and mediators of mitochondrial or oxidative stress. We observed an increase in eIF2α (eukaryotic translation initiation factor 2-alpha) phosphorylation, a requisite for stress granule formation, in cells exposed to these stimuli. Interestingly, SG formation, PABP expression, and eIF2α phosphorylation in VSMCs is reversed by treatment with the anti-inflammatory cytokine interleukin-19. Microtubule inhibitors reduced stress granule accumulation in VSMC, suggesting cytoskeletal regulation of stress granule formation. SG formation in VSMCs was also observed in other vascular disease pathologies, including vascular restenosis. Reduction of SG component G3BP1 by siRNA significantly altered expression profiles of inflammatory, apoptotic, and proliferative genes. Conclusions: These results indicate that SG formation is a common feature of the vascular response to injury and disease, and that modification of inflammation reduces stress granule formation in VSMC.


2020 ◽  
Vol 21 (18) ◽  
pp. 6598
Author(s):  
Carlos Pascual-Caro ◽  
Yolanda Orantos-Aguilera ◽  
Irene Sanchez-Lopez ◽  
Jaime de Juan-Sanz ◽  
Jan B. Parys ◽  
...  

STIM1 is an endoplasmic reticulum (ER) protein that modulates the activity of a number of Ca2+ transport systems. By direct physical interaction with ORAI1, a plasma membrane Ca2+ channel, STIM1 activates the ICRAC current, whereas the binding with the voltage-operated Ca2+ channel CaV1.2 inhibits the current through this latter channel. In this way, STIM1 is a key regulator of Ca2+ signaling in excitable and non-excitable cells, and altered STIM1 levels have been reported to underlie several pathologies, including immunodeficiency, neurodegenerative diseases, and cancer. In both sporadic and familial Alzheimer’s disease, a decrease of STIM1 protein levels accounts for the alteration of Ca2+ handling that compromises neuronal cell viability. Using SH-SY5Y cells edited by CRISPR/Cas9 to knockout STIM1 gene expression, this work evaluated the molecular mechanisms underlying the cell death triggered by the deficiency of STIM1, demonstrating that STIM1 is a positive regulator of ITPR3 gene expression. ITPR3 (or IP3R3) is a Ca2+ channel enriched at ER-mitochondria contact sites where it provides Ca2+ for transport into the mitochondria. Thus, STIM1 deficiency leads to a strong reduction of ITPR3 transcript and ITPR3 protein levels, a consequent decrease of the mitochondria free Ca2+ concentration ([Ca2+]mit), reduction of mitochondrial oxygen consumption rate, and decrease in ATP synthesis rate. All these values were normalized by ectopic expression of ITPR3 in STIM1-KO cells, providing strong evidence for a new mode of regulation of [Ca2+]mit mediated by the STIM1-ITPR3 axis.


Blood ◽  
2008 ◽  
Vol 112 (11) ◽  
pp. 2863-2863
Author(s):  
Amanda Chen ◽  
Mahmoud Yazdani-Abyaneh ◽  
W. Beau Mitchell

Abstract Platelet alpha granules, which contain both membrane-bound and secreted proteins, are formed in the megakaryocyte and then delivered along proplatelet elaborations to the newly forming platelets. A critical but poorly understood process is the post-translational processing, sorting and delivery of proteins to alpha granules prior to their delivery to the proplatelet. Defects in the processing and trafficking of platelet proteins can result in reduced platelet formation. In addition, platelet alpha granules may be differentially packaged with pro- or anti-angiogenic proteins, suggesting that protein sorting events that occur before alpha granule formation may significantly impact platelet end-point function. Thus, research at the intersection of protein trafficking and thrombopoiesis may lead to clearer understanding of the mechanisms of proplatelet formation, the mechanisms of disease in inherited platelet disorders, and the mechanisms of platelet function in inflammation, tumor metastasis and angiogenesis. We have used the platelet integrin aIIbb3 as a model protein to investigate the mechanisms of these processes. In this study we identified proteins that interacted with aIIb in either HEK293 cells or stem cell derived megakaryocytes. The purpose of expanding the “interactome” of aIIb is to identify novel protein-protein interactions that are important for protein delivery to the megakaryocyte surface, and thus could be important for alpha granule and proplatelet formation. We used two methods of capturing interacting proteins: 1) a two-cell pull-down assay using Histidine-tagged aIIb and b3 as bait for umbilical cord blood derived megakaryocyte lysate, followed by nickel bead extraction, 2) a crosslinking assay in which photoreactive, crosslinking amino acids are incorporated into growing megakaryocytes, then crosslinked by exposure to UV light. To enrich the population of aIIb residing in the ER and Golgi, a mutant aIIb subunit containing a R858G mutation, which prevents cleavage of pro-aIIb to mature aIIb resulting in intracellular retention, was used as bait in some assays. The captured proteins from both methods were separated by SDS-PAGE and analyzed by mass spectroscopy. Two or more unique peptides were identified for 93 proteins, and 33 proteins were identified in two or more separate experiments. Of these proteins, 45 were potential protein-trafficking proteins, known to interact with aIIb, or of unknown function. Further analysis of one of these proteins, DNAJC10, suggested that it plays a role in aIIbb3 biogenesis and trafficking. DNAJC10 is an HSP40 type protein with a BiP binding domain and a second domain containing two disulfide isomerase motifs. It has been shown to be induced during ER stress, and may assist in delivering misfolded ER proteins to the proteasome for degradation. Immunoprecipitation of aIIb and b3 followed by immunoblot with anti-DNAJC10 mAb revealed protein bands corresponding to the molecular mass of DNAJC10, indicating direct or indirect physical interaction of aIIb and b3 with DNAJC10. siRNA mediated knockdown of DNAJC10 increased aIIbb3 surface expression on human megakaryocytes by 12%. Together these findings indicate that DNAJC10 interacts with aIIbb3 and may play a role in regulating aIIbb3 surface expression. This study offers new insights into the control of aIIbb3 surface expression and further studies may reveal new targets for anti- or pro-integrin therapies.


Author(s):  
Asa Mcgray ◽  
Timothy Gingerich ◽  
James Petrik ◽  
Jonathan Lamarre

AbstractThrombospondin-1 (TSP-1) is a matricellular protein that participates in numerous normal and pathological tissue processes and is rapidly modulated by different stimuli. The presence of 8 highly-conserved AU rich elements (AREs) within the 3′-untranslated region (3′UTR) of the TSP-1 mRNA suggests that post-transcriptional regulation is likely to represent one mechanism by which TSP-1 gene expression is regulated. We investigated the roles of these AREs, and proteins which bind to them, in the control of TSP-1 mRNA stability. The endogenous TSP-1 mRNA half-life is approximately 2.0 hours in HEK293 cells. Luciferase reporter mRNAs containing the TSP-1 3′UTR show a similar rate of decay, suggesting that the 3′UTR influences the decay rate. Site-directed mutagenesis of individual and adjacent AREs prolonged reporter mRNA halflife to between 2.2 and 4.4 hours. Mutation of all AREs increased mRNA half life to 8.8 hours, suggesting that all AREs have some effect, but that specific AREs may have key roles in stability regulation. A labeled RNA oligonucleotide derived from the most influential ARE was utilized to purify TSP-1 AREbinding proteins. The AU-binding protein AUF1 was shown to associate with this motif. These studies reveal that AREs in the 3′UTR control TSP-1 mRNA stability and that the RNA binding protein AUF1 participates in this control. These studies suggest that ARE-dependent control of TSP-1 mRNA stability may represent an important component in the control of TSP-1 gene expression.


2019 ◽  
Author(s):  
Yu Sun ◽  
Aziz Eshov ◽  
Junjie U. Guo

ABSTRACTExpansion of an intronic (GGGGCC)n repeat region within the C9orf72 gene is a major cause of familial amyotrophic lateral sclerosis and frontotemporal dementia (c9ALS/FTD). A pathological hallmark in c9ALS/FTD is the accumulation of misprocessed RNAs, which are often targets of RNA surveillance pathways in normal cells. Here we show that nonsense-mediated decay (NMD) and other RNA decay mechanisms involving upstream frameshift 1 (UPF1), collectively referred to as UPF1-mediated RNA decay (UMD), are broadly inhibited in c9ALS/FTD brains. These effects are recapitulated in cultured cells by the ectopic expression of arginine-rich dipeptide repeats (DPRs), poly(GR) and poly(PR). Despite these two DPRs causing the recruitment of UPF1 to stress granules, stress granule formation is neither sufficient nor necessary for UMD inhibition. Our results suggest that UMD inhibition may accelerate the accumulation of deleterious RNAs and polypeptides in c9ALS/FTD.


2021 ◽  
Author(s):  
Kevin M. Creamer ◽  
Eric C. Larsen ◽  
Jeanne B. Lawrence

Repetitive sequences including transposable elements (TEs) and transposon-derived fragments account for nearly half of the human genome. While transposition-competent TEs must be repressed to maintain genomic stability, mutated and fragmented TEs comprising the bulk of repetitive sequences can also contribute to regulation of host gene expression and broader genome organization. Here we analyzed published ChIP-seq data sets to identify proteins broadly enriched on TEs in the human genome. We show two of the proteins identified, C2H2 zinc finger-containing proteins ZNF146 (also known as OZF) and ZNF507, are targeted to distinct sites within LINE-1 ORF2 at thousands of locations in the genome. ZNF146 binding sites are found at old and young LINE-1 elements. In contrast, ZNF507 preferentially binds at young LINE-1 sequences correlated to sequence changes in LINE-1 elements at ZNF507s binding site. To gain further insight into ZNF146 and ZNF507 function, we disrupt their expression in HEK293 cells using CRISPR/Cas9 and perform RNA sequencing, finding modest gene expression changes in cells where ZNF507 has been disrupted. We further identify a physical interaction between ZNF507 and PRMT5, suggesting ZNF507 may target arginine methylation activity to LINE-1 sequences.


2020 ◽  
Author(s):  
Amanjot Singh ◽  
Joern Huelsmeier ◽  
Arvind Reddy Kandi ◽  
Sai Shruti Pothapragada ◽  
Jens Hillebrand ◽  
...  

ABSTRACTAtaxin-2 is a conserved translational control protein associated with spinocerebellar ataxia type II (SCA2) and amyotrophic lateral sclerosis (ALS) as well as an important target for ALS therapeutics under development. Despite its clinical and biological significance, Ataxin-2’s activities, mechanisms and functions are not well understood. While Drosophila Ataxin-2 (Atx2) mediates mRNP condensation via a C-terminal intrinsically disordered domain (cIDR), how Ataxin-2 IDRs work with structured (Lsm, Lsm-AD and PAM2) domains to enable positive and negative regulation of target mRNAs remains unclear. Using TRIBE (Targets of RNA-Binding Proteins Identified by Editing) technology, we identified and analysed Atx-2 target mRNAs in the Drosophila brain. We show that Atx2 preferentially interacts with AU-rich elements (AREs) in 3’UTRs and plays a broad role in stabilization of identified target mRNAs. Strikingly, Atx2 interaction with its targets is dependent on the cIDR domain required for neuronal-granule formation. In contrast, Atx2 lacking its Lsm domain not only interacts more efficiently with the target mRNA identified, but also forms larger RNP granules. Providing an extensive dataset of Atx2-interacting brain mRNAs, our results demonstrate that Atx2: (a) interacts with target mRNAs within RNP granules; (b) modulates the turnover of these target mRNAs; (c) has an additional essential role outside of mRNP granules; and (d) contains distinct protein domains that drive or oppose RNP-granule assembly. These findings increase understanding of neuronal translational control mechanisms and inform Ataxin-2-based interventions in development for SCA2 and ALS.


Sign in / Sign up

Export Citation Format

Share Document