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Hildebrandt MR, Wang Y, Li L, Yasmin L, Glubrecht DD, Godbout R. Cytoplasmic aggregation of DDX1 in developing embryos: Early embryonic lethality associated with Ddx1 knockout. Dev Biol 2019; 455:420-433. [DOI: 10.1016/j.ydbio.2019.07.014] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2019] [Revised: 07/04/2019] [Accepted: 07/19/2019] [Indexed: 01/12/2023]
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102
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Eum H, Shin Y, Song Y, Kim Y, Kang SW. ATP-driven reactions are required for the assembly of large stress granules. Biochem Biophys Res Commun 2019; 521:238-244. [PMID: 31630798 DOI: 10.1016/j.bbrc.2019.10.116] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2019] [Accepted: 10/13/2019] [Indexed: 12/13/2022]
Abstract
Stress granules (SGs) are functional messenger ribonucleoprotein aggregates, and their assembly is an important cellular process required for remodeling the signaling network to cope with extensive environmental stresses. SG formation is a stepwise process that involves the formation of a stable core followed by a less stable outer shell, and this process is often hampered by faulty regulation of protein phosphorylation. It remains unclear, however, which kinase activity is essential for SG formation. Here, we screened small molecule library of kinase inhibitors using a well-validated fluorogenic SG probe. Our screen, time-lapse microscopy, and biochemical analyses identified an ATP-mimetic SG inhibitor that selectively interferes with the fusion and growth, rather than the initial assembly, of SG core structures into the large assemblies. Thus, SGs utilize ATP-dependent chemical reactions to achieve their functional architectures.
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Affiliation(s)
- Hongsik Eum
- Department of Biomedical Sciences, University of Ulsan College of Medicine, Seoul, Republic of Korea; Asan Medical Institute of Convergence Science and Technology, Asan Medical Center, Seoul, Republic of Korea
| | - Yejin Shin
- Department of Biomedical Sciences, University of Ulsan College of Medicine, Seoul, Republic of Korea; Asan Medical Institute of Convergence Science and Technology, Asan Medical Center, Seoul, Republic of Korea
| | - Youngsup Song
- Department of Biomedical Sciences, University of Ulsan College of Medicine, Seoul, Republic of Korea; Asan Medical Institute of Convergence Science and Technology, Asan Medical Center, Seoul, Republic of Korea
| | - Yongsub Kim
- Department of Biomedical Sciences, University of Ulsan College of Medicine, Seoul, Republic of Korea; Asan Medical Institute of Convergence Science and Technology, Asan Medical Center, Seoul, Republic of Korea
| | - Sang-Wook Kang
- Department of Biomedical Sciences, University of Ulsan College of Medicine, Seoul, Republic of Korea; Asan Medical Institute of Convergence Science and Technology, Asan Medical Center, Seoul, Republic of Korea.
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103
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Youn JY, Dyakov BJ, Zhang J, Knight JD, Vernon RM, Forman-Kay JD, Gingras AC. Properties of Stress Granule and P-Body Proteomes. Mol Cell 2019; 76:286-294. [DOI: 10.1016/j.molcel.2019.09.014] [Citation(s) in RCA: 159] [Impact Index Per Article: 31.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2019] [Revised: 09/06/2019] [Accepted: 09/09/2019] [Indexed: 01/01/2023]
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104
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Abstract
RNA localization mechanisms have been intensively studied and include localized protection of mRNA from degradation, diffusion-coupled local entrapment of mRNA, and directed transport of mRNAs along the cytoskeleton. While it is well understood how cells utilize these three mechanisms to organize mRNAs within the cytoplasm, a newly appreciated mechanism of RNA localization has emerged in recent years in which mRNAs phase-separate and form liquid-like droplets. mRNAs both contribute to condensation of proteins into liquid-like structures and are themselves regulated by being incorporated into membraneless organelles. This ability to condense into droplets is in many instances contributing to previously appreciated mRNA localization phenomena. Here we review how phase separation enables mRNAs to selectively and efficiently colocalize and be coregulated, allowing control of gene expression in time and space.
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Affiliation(s)
- Erin M Langdon
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA;
| | - Amy S Gladfelter
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA; .,Marine Biological Laboratory, Woods Hole, Massachusetts 02543, USA
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105
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Pravata VM, Muha V, Gundogdu M, Ferenbach AT, Kakade PS, Vandadi V, Wilmes AC, Borodkin VS, Joss S, Stavridis MP, van Aalten DMF. Catalytic deficiency of O-GlcNAc transferase leads to X-linked intellectual disability. Proc Natl Acad Sci U S A 2019; 116:14961-14970. [PMID: 31296563 PMCID: PMC6660750 DOI: 10.1073/pnas.1900065116] [Citation(s) in RCA: 47] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
O-GlcNAc transferase (OGT) is an X-linked gene product that is essential for normal development of the vertebrate embryo. It catalyses the O-GlcNAc posttranslational modification of nucleocytoplasmic proteins and proteolytic maturation of the transcriptional coregulator Host cell factor 1 (HCF1). Recent studies have suggested that conservative missense mutations distal to the OGT catalytic domain lead to X-linked intellectual disability in boys, but it is not clear if this is through changes in the O-GlcNAc proteome, loss of protein-protein interactions, or misprocessing of HCF1. Here, we report an OGT catalytic domain missense mutation in monozygotic female twins (c. X:70779215 T > A, p. N567K) with intellectual disability that allows dissection of these effects. The patients show limited IQ with developmental delay and skewed X-inactivation. Molecular analyses revealed decreased OGT stability and disruption of the substrate binding site, resulting in loss of catalytic activity. Editing this mutation into the Drosophila genome results in global changes in the O-GlcNAc proteome, while in mouse embryonic stem cells it leads to loss of O-GlcNAcase and delayed differentiation down the neuronal lineage. These data imply that catalytic deficiency of OGT could contribute to X-linked intellectual disability.
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Affiliation(s)
- Veronica M Pravata
- Division of Gene Regulation and Expression, School of Life Sciences, University of Dundee, DD1 5EH Dundee, United Kingdom
| | - Villo Muha
- Division of Gene Regulation and Expression, School of Life Sciences, University of Dundee, DD1 5EH Dundee, United Kingdom
| | - Mehmet Gundogdu
- Division of Gene Regulation and Expression, School of Life Sciences, University of Dundee, DD1 5EH Dundee, United Kingdom
| | - Andrew T Ferenbach
- Division of Gene Regulation and Expression, School of Life Sciences, University of Dundee, DD1 5EH Dundee, United Kingdom
| | - Poonam S Kakade
- Division of Cell and Developmental Biology, School of Life Sciences, University of Dundee, DD1 5EH Dundee, United Kingdom
| | - Vasudha Vandadi
- Division of Gene Regulation and Expression, School of Life Sciences, University of Dundee, DD1 5EH Dundee, United Kingdom
| | - Ariane C Wilmes
- Division of Gene Regulation and Expression, School of Life Sciences, University of Dundee, DD1 5EH Dundee, United Kingdom
| | - Vladimir S Borodkin
- Division of Gene Regulation and Expression, School of Life Sciences, University of Dundee, DD1 5EH Dundee, United Kingdom
| | - Shelagh Joss
- West of Scotland Genetic Service, Queen Elizabeth University Hospital, G51 4TF Glasgow, United Kingdom
| | - Marios P Stavridis
- Division of Cell and Developmental Biology, School of Life Sciences, University of Dundee, DD1 5EH Dundee, United Kingdom
| | - Daan M F van Aalten
- Division of Gene Regulation and Expression, School of Life Sciences, University of Dundee, DD1 5EH Dundee, United Kingdom;
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106
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UBAP2L arginine methylation by PRMT1 modulates stress granule assembly. Cell Death Differ 2019; 27:227-241. [PMID: 31114027 PMCID: PMC7205891 DOI: 10.1038/s41418-019-0350-5] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2018] [Revised: 04/28/2019] [Accepted: 05/03/2019] [Indexed: 02/06/2023] Open
Abstract
Stress granules (SGs) are discrete assemblies of stalled messenger ribonucleoprotein complexes (mRNPs) that form when eukaryotic cells encounter environmental stress. RNA-binding proteins (RBPs) mediate their condensation by recruiting populations of mRNPs. However, the cellular and molecular mechanisms underlying the role of ubiquitin-associated protein 2-like (UBAP2L) in the regulation of SG dynamics remain elusive. Here, we show that UBAP2L is required for both SG assembly and disassembly. UBAP2L overexpression nucleated SGs under stress-null conditions. The UBAP2L Arg–Gly–Gly (RGG) motif was required for SG competence, and mediated the recruitment of SG components, including mRNPs, RBPs, and ribosomal subunits. The domain of unknown function (DUF) of UBAP2L-mediated interaction with ras GTPase-activating protein-binding protein (G3BP)1/2, and its deletion caused the cytoplasmic–nuclear transport of UBAP2L and G3BP1/2, thereby compromising SG formation. The protein arginine methyltransferase PRMT1 asymmetrically dimethylated UBAP2L by targeting the RGG motif. Increased arginine methylation blocked, whereas its decrease enhanced UBAP2L interactions with SG components, ablating and promoting SG assembly, respectively. These results provide new insights into the mechanisms by which UBAP2L regulates SG dynamics and RNA metabolism.
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107
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Grimaldi G, Catara G, Palazzo L, Corteggio A, Valente C, Corda D. PARPs and PAR as novel pharmacological targets for the treatment of stress granule-associated disorders. Biochem Pharmacol 2019; 167:64-75. [PMID: 31102582 DOI: 10.1016/j.bcp.2019.05.019] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2019] [Accepted: 05/13/2019] [Indexed: 12/13/2022]
Abstract
Among the post-translational modifications, ADP-ribosylation has been for long time the least integrated in the scheme of the structural protein modifications affecting physiological functions. In spite of the original findings on bacterial-dependent ADP-ribosylation catalysed by toxins such as cholera and pertussis toxin, only with the discovery of the poly-ADP-ribosyl polymerase (PARP) family the field has finally expanded and the role of ADP-ribosylation has been recognised in both physiological and pathological processes, including cancer, infectious and neurodegenerative diseases. This is now a rapidly expanding field of investigation, centred on the role of the different PARPs and their substrates in various diseases, and on the potential of PARP inhibitors as novel pharmacological tools to be employed in relevant pathological context. In this review we analyse the role that members of the PARP family and poly-ADP-ribose (PAR; the product of PARP1 and PARP5a activity) play in the processes following the exposure of cells to different stresses. The cell response that arises following conditions such as heat, osmotic, oxidative stresses or viral infection relies on the formation of stress granules, which are transient cytoplasmic membrane-less structures, that include untranslated mRNA, specific proteins and PAR, this last one serving as the "collector" of all components (that bind to it in a non-covalent manner). The resulting phenotypes are cells in which translation, intracellular transport or pro-apoptotic pathways are reversibly inhibited, for the time the given stress holds. Interestingly, the formation of defective stress granules has been detected in diverse pathological conditions including neurological disorders and cancer. Analysing the molecular details of stress granule formation under these conditions offers a novel view on the pathogenesis of these diseases and, as a consequence, the possibility of identifying novel drug targets for their treatment.
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Affiliation(s)
- Giovanna Grimaldi
- Institute of Protein Biochemistry, National Research Council of Italy, Via Pietro Castellino 111, Naples 80131, Italy.
| | - Giuliana Catara
- Institute of Protein Biochemistry, National Research Council of Italy, Via Pietro Castellino 111, Naples 80131, Italy
| | - Luca Palazzo
- Institute of Protein Biochemistry, National Research Council of Italy, Via Pietro Castellino 111, Naples 80131, Italy
| | - Annunziata Corteggio
- Institute of Protein Biochemistry, National Research Council of Italy, Via Pietro Castellino 111, Naples 80131, Italy
| | - Carmen Valente
- Institute of Protein Biochemistry, National Research Council of Italy, Via Pietro Castellino 111, Naples 80131, Italy
| | - Daniela Corda
- Institute of Protein Biochemistry, National Research Council of Italy, Via Pietro Castellino 111, Naples 80131, Italy.
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108
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109
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Freeman BT, Sokolowski M, Roy-Engel AM, Smither ME, Belancio VP. Identification of charged amino acids required for nuclear localization of human L1 ORF1 protein. Mob DNA 2019; 10:20. [PMID: 31080522 PMCID: PMC6501352 DOI: 10.1186/s13100-019-0159-2] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2018] [Accepted: 04/10/2019] [Indexed: 01/10/2023] Open
Abstract
Background Long Interspersed Element 1 (LINE-1) is a retrotransposon that is present in 500,000 copies in the human genome. Along with Alu and SVA elements, these three retrotransposons account for more than a third of the human genome sequence. These mobile elements are able to copy themselves within the genome via an RNA intermediate, a process that can promote genome instability. LINE-1 encodes two proteins, ORF1p and ORF2p. Association of ORF1p, ORF2p and a full-length L1 mRNA in a ribonucleoprotein (RNP) particle, L1 RNP, is required for L1 retrotransposition. Previous studies have suggested that fusion of a tag to L1 proteins can interfere with L1 retrotransposition. Results Using antibodies detecting untagged human ORF1p, western blot analysis and manipulation of ORF1 sequence and length, we have identified a set of charged amino acids in the C-terminal region of ORF1p that are important in determining its subcellular localization. Mutation of 7 non-identical lysine residues is sufficient to make the resulting ORF1p to be predominantly cytoplasmic, demonstrating intrinsic redundancy of this requirement. These residues are also necessary for ORF1p to retain its association with KPNA2 nuclear pore protein. We demonstrate that this interaction is significantly reduced by RNase treatment. Using co-IP, we have also determined that human ORF1p associates with all members of the KPNA subfamily. Conclusions The prediction of NLS sequences suggested that specific sequences within ORF1p could be responsible for its subcellular localization by interacting with nuclear binding proteins. We have found that multiple charged amino acids in the C-terminus of ORF1p are involved in ORF1 subcellular localization and interaction with KPNA2 nuclear pore protein. Our data demonstrate that different amino acids can be mutated to have the same phenotypic effect on ORF1p subcellular localization, demonstrating that the net number of charged residues or protein structure, rather than their specific location, is important for the ORF1p nuclear localization. We also identified that human ORF1p interacts with all members of the KPNA family of proteins and that multiple KPNA family genes are expressed in human cell lines. Electronic supplementary material The online version of this article (10.1186/s13100-019-0159-2) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- B T Freeman
- 1Department of Structural and Cellular Biology, Tulane University School of Medicine, Tulane Cancer Center, Tulane Center for Aging, New Orleans, LA 70112 USA
| | - M Sokolowski
- 1Department of Structural and Cellular Biology, Tulane University School of Medicine, Tulane Cancer Center, Tulane Center for Aging, New Orleans, LA 70112 USA
| | - A M Roy-Engel
- 2Department of Epidemiology, School of Public Health and Tropical Medicine, Tulane Cancer Center, Tulane University, New Orleans, Louisiana 70112 USA
| | - M E Smither
- 1Department of Structural and Cellular Biology, Tulane University School of Medicine, Tulane Cancer Center, Tulane Center for Aging, New Orleans, LA 70112 USA
| | - V P Belancio
- 1Department of Structural and Cellular Biology, Tulane University School of Medicine, Tulane Cancer Center, Tulane Center for Aging, New Orleans, LA 70112 USA
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110
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Mazloomian A, Araki S, Ohori M, El-Naggar AM, Yap D, Bashashati A, Nakao S, Sorensen PH, Nakanishi A, Shah S, Aparicio S. Pharmacological systems analysis defines EIF4A3 functions in cell-cycle and RNA stress granule formation. Commun Biol 2019; 2:165. [PMID: 31069274 PMCID: PMC6499833 DOI: 10.1038/s42003-019-0391-9] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2018] [Accepted: 03/11/2019] [Indexed: 12/13/2022] Open
Abstract
The RNA helicase EIF4A3 regulates the exon junction complex and nonsense-mediated mRNA decay functions in RNA transcript processing. However, a transcriptome-wide network definition of these functions has been lacking, in part due to the lack of suitable pharmacological inhibitors. Here we employ short-duration graded EIF4A3 inhibition using small molecule allosteric inhibitors to define the transcriptome-wide dependencies of EIF4A3. We thus define conserved cellular functions, such as cell cycle control, that are EIF4A3 dependent. We show that EIF4A3-dependent splicing reactions have a distinct genome-wide pattern of associated RNA-binding protein motifs. We also uncover an unanticipated role of EIF4A3 in the biology of RNA stress granules, which sequester and silence the translation of most mRNAs under stress conditions and are implicated in cell survival and tumour progression. We show that stress granule induction and maintenance is suppressed on the inhibition of EIF4A3, in part through EIF4A3-associated regulation of G3BP1 and TIA1 scaffold protein expression.
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Affiliation(s)
- Alborz Mazloomian
- Department of Molecular Oncology, BC Cancer, part of the Provincial Health Services Authority, 675 West 10th Avenue, Vancouver, BC V5Z 1L3 Canada
- Department of Pathology and Laboratory Medicine, G227-2211 Wesbrook Mall, University of British Columbia, Vancouver, BC V6T 2B5 Canada
| | - Shinsuke Araki
- Research Department, Takeda Pharmaceutical Company Limited, 26-1, Muraoka-Higashi 2-chome, Fujisawa, Kanagawa 251-8555 Japan
| | - Momoko Ohori
- Research Department, Takeda Pharmaceutical Company Limited, 26-1, Muraoka-Higashi 2-chome, Fujisawa, Kanagawa 251-8555 Japan
| | - Amal M. El-Naggar
- Department of Molecular Oncology, BC Cancer, part of the Provincial Health Services Authority, 675 West 10th Avenue, Vancouver, BC V5Z 1L3 Canada
- Department of Pathology and Laboratory Medicine, G227-2211 Wesbrook Mall, University of British Columbia, Vancouver, BC V6T 2B5 Canada
- Department of Pathology, Faculty of Medicine, Menoufia University, Menoufia Governorate, Egypt
| | - Damian Yap
- Department of Molecular Oncology, BC Cancer, part of the Provincial Health Services Authority, 675 West 10th Avenue, Vancouver, BC V5Z 1L3 Canada
- Department of Pathology and Laboratory Medicine, G227-2211 Wesbrook Mall, University of British Columbia, Vancouver, BC V6T 2B5 Canada
| | - Ali Bashashati
- Department of Molecular Oncology, BC Cancer, part of the Provincial Health Services Authority, 675 West 10th Avenue, Vancouver, BC V5Z 1L3 Canada
- Department of Pathology and Laboratory Medicine, G227-2211 Wesbrook Mall, University of British Columbia, Vancouver, BC V6T 2B5 Canada
| | - Shoichi Nakao
- Research Department, Takeda Pharmaceutical Company Limited, 26-1, Muraoka-Higashi 2-chome, Fujisawa, Kanagawa 251-8555 Japan
| | - Poul H. Sorensen
- Department of Molecular Oncology, BC Cancer, part of the Provincial Health Services Authority, 675 West 10th Avenue, Vancouver, BC V5Z 1L3 Canada
- Department of Pathology and Laboratory Medicine, G227-2211 Wesbrook Mall, University of British Columbia, Vancouver, BC V6T 2B5 Canada
| | - Atsushi Nakanishi
- Research Department, Takeda Pharmaceutical Company Limited, 26-1, Muraoka-Higashi 2-chome, Fujisawa, Kanagawa 251-8555 Japan
| | - Sohrab Shah
- Department of Molecular Oncology, BC Cancer, part of the Provincial Health Services Authority, 675 West 10th Avenue, Vancouver, BC V5Z 1L3 Canada
- Department of Pathology and Laboratory Medicine, G227-2211 Wesbrook Mall, University of British Columbia, Vancouver, BC V6T 2B5 Canada
- Department of Epidemiology & Biostatistics, Memorial Sloan Kettering Cancer Center, 417 E68th St, New York, NY 10065 USA
| | - Samuel Aparicio
- Department of Molecular Oncology, BC Cancer, part of the Provincial Health Services Authority, 675 West 10th Avenue, Vancouver, BC V5Z 1L3 Canada
- Department of Pathology and Laboratory Medicine, G227-2211 Wesbrook Mall, University of British Columbia, Vancouver, BC V6T 2B5 Canada
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111
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Guzikowski AR, Chen YS, Zid BM. Stress-induced mRNP granules: Form and function of processing bodies and stress granules. WILEY INTERDISCIPLINARY REVIEWS. RNA 2019; 10:e1524. [PMID: 30793528 PMCID: PMC6500494 DOI: 10.1002/wrna.1524] [Citation(s) in RCA: 90] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/17/2018] [Revised: 12/18/2018] [Accepted: 12/28/2018] [Indexed: 12/12/2022]
Abstract
In response to stress, cells must quickly reprogram gene expression to adapt and survive. This is achieved in part by altering levels of mRNAs and their translation into proteins. Recently, the formation of two stress-induced messenger ribonucleoprotein (mRNP) assemblies named stress granules and processing bodies has been postulated to directly impact gene expression during stress. These assemblies sequester and concentrate specific proteins and RNAs away from the larger cytoplasm during stress, thereby providing a layer of posttranscriptional gene regulation with the potential to directly impact mRNA levels, protein translation, and cell survival. The function of these granules has generally been ascribed either by the protein components concentrated into them or, more broadly, by global changes that occur during stress. Recent proteome- and transcriptome-wide studies have provided a more complete view of stress-induced mRNP granule composition in varied cell types and stress conditions. However, direct measurements of the phenotypic and functional consequences of stress granule and processing body formation are lacking. This leaves our understanding of their roles during stress incomplete. Continued study into the function of these granules will be an important part in elucidating how cells respond to and survive stressful environmental changes. This article is categorized under: Translation > Translation Regulation RNA Interactions with Proteins and Other Molecules > RNA-Protein Complexes RNA Export and Localization > RNA Localization.
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Affiliation(s)
- Anna R. Guzikowski
- Division of Biological Sciences, University of California San Diego, La Jolla, CA, United States of America
| | - Yang S. Chen
- Division of Biological Sciences, University of California San Diego, La Jolla, CA, United States of America
| | - Brian M. Zid
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, CA, United States of America
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112
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Ivanov P, Kedersha N, Anderson P. Stress Granules and Processing Bodies in Translational Control. Cold Spring Harb Perspect Biol 2019; 11:cshperspect.a032813. [PMID: 30082464 DOI: 10.1101/cshperspect.a032813] [Citation(s) in RCA: 280] [Impact Index Per Article: 56.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Stress granules (SGs) and processing bodies (PBs) are non-membrane-enclosed RNA granules that dynamically sequester translationally inactive messenger ribonucleoprotein particles (mRNPs) into compartments that are distinct from the surrounding cytoplasm. mRNP remodeling, silencing, and/or storage involves the dynamic partitioning of closed-loop polyadenylated mRNPs into SGs, or the sequestration of deadenylated, linear mRNPs into PBs. SGs form when stress-activated pathways stall translation initiation but allow elongation and termination to occur normally, resulting in a sudden excess of mRNPs that are spatially condensed into discrete foci by protein:protein, protein:RNA, and RNA:RNA interactions. In contrast, PBs can exist in the absence of stress, when specific factors promote mRNA deadenylation, condensation, and sequestration from the translational machinery. The formation and dissolution of SGs and PBs reflect changes in messenger RNA (mRNA) metabolism and allow cells to modulate the proteome and/or mediate life or death decisions during changing environmental conditions.
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Affiliation(s)
- Pavel Ivanov
- Division of Rheumatology, Immunology and Allergy, Brigham and Women's Hospital, Boston, Massachusetts 02115.,Department of Medicine, Harvard Medical School, Boston, Massachusetts 02115.,The Broad Institute of Harvard and M.I.T., Cambridge, Massachusetts 02142
| | - Nancy Kedersha
- Division of Rheumatology, Immunology and Allergy, Brigham and Women's Hospital, Boston, Massachusetts 02115.,Department of Medicine, Harvard Medical School, Boston, Massachusetts 02115
| | - Paul Anderson
- Division of Rheumatology, Immunology and Allergy, Brigham and Women's Hospital, Boston, Massachusetts 02115.,Department of Medicine, Harvard Medical School, Boston, Massachusetts 02115
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113
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Markmiller S, Fulzele A, Higgins R, Leonard M, Yeo GW, Bennett EJ. Active Protein Neddylation or Ubiquitylation Is Dispensable for Stress Granule Dynamics. Cell Rep 2019; 27:1356-1363.e3. [PMID: 31042464 PMCID: PMC6508666 DOI: 10.1016/j.celrep.2019.04.015] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2018] [Revised: 02/26/2019] [Accepted: 04/02/2019] [Indexed: 12/17/2022] Open
Abstract
Stress granule (SG) formation is frequently accompanied by ubiquitin proteasome system (UPS) impairment and ubiquitylated protein accumulation. SGs, ubiquitin, and UPS components co-localize, but the relationship between the ubiquitin pathway and SGs has not been systematically characterized. We utilize pharmacological inhibition of either the ubiquitin- or NEDD8-activating enzyme (UAE or NAE) to probe whether active ubiquitylation or neddylation modulate SG dynamics. We show that UAE inhibition results in rapid loss of global protein ubiquitylation using ubiquitin-specific proteomics. Critically, inhibiting neither UAE nor NAE significantly affected SG formation or disassembly, indicating that active protein ubiquitylation or neddylation is dispensable for SG dynamics. Using antibodies with varying preference for free ubiquitin or polyubiquitin and fluorescently tagged ubiquitin variants in combination with UAE inhibition, we show that SGs co-localize primarily with unconjugated ubiquitin rather than polyubiquitylated proteins. These findings clarify the role of ubiquitin in SG biology and suggest that free ubiquitin may alter SG protein interactions.
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Affiliation(s)
- Sebastian Markmiller
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA 92093, USA; Stem Cell Program, University of California, San Diego, La Jolla, CA 92093, USA; Institute for Genomic Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Amit Fulzele
- Cell and Developmental Biology, Division of Biological Sciences, University of California, San Diego, La Jolla, CA 92093, USA
| | - Reneé Higgins
- Cell and Developmental Biology, Division of Biological Sciences, University of California, San Diego, La Jolla, CA 92093, USA
| | - Marilyn Leonard
- Cell and Developmental Biology, Division of Biological Sciences, University of California, San Diego, La Jolla, CA 92093, USA
| | - Gene W Yeo
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA 92093, USA; Stem Cell Program, University of California, San Diego, La Jolla, CA 92093, USA; Institute for Genomic Medicine, University of California, San Diego, La Jolla, CA 92093, USA.
| | - Eric J Bennett
- Cell and Developmental Biology, Division of Biological Sciences, University of California, San Diego, La Jolla, CA 92093, USA.
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Farley MM, Watkins TA. Intrinsic Neuronal Stress Response Pathways in Injury and Disease. ANNUAL REVIEW OF PATHOLOGY-MECHANISMS OF DISEASE 2019; 13:93-116. [PMID: 29414247 DOI: 10.1146/annurev-pathol-012414-040354] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
From injury to disease to aging, neurons, like all cells, may face various insults that can impact their function and survival. Although the consequences are substantially dictated by the type, context, and severity of insult, distressed neurons are far from passive. Activation of cellular stress responses aids in the preservation or restoration of nervous system function. However, stress responses themselves can further advance neuropathology and contribute significantly to neuronal dysfunction and neurodegeneration. Here we explore the recent advances in defining the cellular stress responses within neurodegenerative diseases and neuronal injury, and we emphasize axonal injury as a well-characterized model of neuronal insult. We highlight key findings and unanswered questions about neuronal stress response pathways, from the initial detection of cellular insults through the underlying mechanisms of the responses to their ultimate impact on the fates of distressed neurons.
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Affiliation(s)
- Madeline M Farley
- Department of Neurosurgery, Baylor College of Medicine, Houston, Texas 77030;
| | - Trent A Watkins
- Department of Neurosurgery, Baylor College of Medicine, Houston, Texas 77030;
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115
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Rayman JB, Karl KA, Kandel ER. TIA-1 Self-Multimerization, Phase Separation, and Recruitment into Stress Granules Are Dynamically Regulated by Zn 2. Cell Rep 2019; 22:59-71. [PMID: 29298433 DOI: 10.1016/j.celrep.2017.12.036] [Citation(s) in RCA: 63] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2017] [Revised: 11/08/2017] [Accepted: 12/11/2017] [Indexed: 01/09/2023] Open
Abstract
Stress granules are non-membranous structures that transiently form in the cytoplasm during cellular stress, where they promote translational repression of non-essential RNAs and modulate cell signaling by sequestering key signal transduction proteins. These and other functions of stress granules facilitate an adaptive cellular response to environmental adversity. A key component of stress granules is the prion-related RNA-binding protein, T cell intracellular antigen-1 (TIA-1). Here, we report that recombinant TIA-1 undergoes rapid multimerization and phase separation in the presence of divalent zinc, which can be reversed by the zinc chelator, TPEN. Similarly, the formation and maintenance of TIA-1-positive stress granules in arsenite-treated cells are inhibited by TPEN. In addition, Zn2+ is released in cells treated with arsenite, before stress granule formation. These findings suggest that Zn2+ is a physiological ligand of TIA-1, acting as a stress-inducible second messenger to promote multimerization of TIA-1 and subsequent localization into stress granules.
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Affiliation(s)
- Joseph B Rayman
- Department of Neuroscience, College of Physicians and Surgeons of Columbia University, New York, NY 10032, USA; Zuckerman Mind Brain Behavior Institute, Columbia University, New York, NY 10032, USA
| | - Kevin A Karl
- Department of Neuroscience, College of Physicians and Surgeons of Columbia University, New York, NY 10032, USA; Howard Hughes Medical Institute at Columbia University, New York, NY 10032, USA; Zuckerman Mind Brain Behavior Institute, Columbia University, New York, NY 10032, USA
| | - Eric R Kandel
- Department of Neuroscience, College of Physicians and Surgeons of Columbia University, New York, NY 10032, USA; Department of Psychiatry, College of Physicians and Surgeons of Columbia University, New York, NY 10032, USA; Howard Hughes Medical Institute at Columbia University, New York, NY 10032, USA; Zuckerman Mind Brain Behavior Institute, Columbia University, New York, NY 10032, USA; Kavli Institute for Brain Science, Columbia University, New York, NY 10032, USA.
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116
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Verdile V, De Paola E, Paronetto MP. Aberrant Phase Transitions: Side Effects and Novel Therapeutic Strategies in Human Disease. Front Genet 2019; 10:173. [PMID: 30967892 PMCID: PMC6440380 DOI: 10.3389/fgene.2019.00173] [Citation(s) in RCA: 45] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2018] [Accepted: 02/18/2019] [Indexed: 12/12/2022] Open
Abstract
Phase separation is a physiological process occurring spontaneously when single-phase molecular complexes separate in two phases, a concentrated phase and a more diluted one. Eukaryotic cells employ phase transition strategies to promote the formation of intracellular territories not delimited by membranes with increased local RNA concentration, such as nucleolus, paraspeckles, P granules, Cajal bodies, P-bodies, and stress granules. These organelles contain both proteins and coding and non-coding RNAs and play important roles in different steps of the regulation of gene expression and in cellular signaling. Recently, it has been shown that most human RNA-binding proteins (RBPs) contain at least one low-complexity domain, called prion-like domain (PrLD), because proteins harboring them display aggregation properties like prion proteins. PrLDs support RBP function and contribute to liquid–liquid phase transitions that drive ribonucleoprotein granule assembly, but also render RBPs prone to misfolding by promoting the formation of pathological aggregates that lead to toxicity in specific cell types. Protein–protein and protein-RNA interactions within the separated phase can enhance the transition of RBPs into solid aberrant aggregates, thus causing diseases. In this review, we highlight the role of phase transition in human disease such as amyotrophic lateral sclerosis (ALS), frontotemporal dementia (FTD), and in cancer. Moreover, we discuss novel therapeutic strategies focused to control phase transitions by preventing the conversion into aberrant aggregates. In this regard, the stimulation of chaperone machinery to disassemble membrane-less organelles, the induction of pathways that could inhibit aberrant phase separation, and the development of antisense oligonucleotides (ASOs) to knockdown RNAs could be evaluated as novel therapeutic strategies for the treatment of those human diseases characterized by aberrant phase transition aggregates.
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Affiliation(s)
- Veronica Verdile
- University of Rome "Foro Italico", Rome, Italy.,Laboratory of Cellular and Molecular Neurobiology, Fondazione Santa Lucia, Rome, Italy
| | - Elisa De Paola
- University of Rome "Foro Italico", Rome, Italy.,Laboratory of Cellular and Molecular Neurobiology, Fondazione Santa Lucia, Rome, Italy
| | - Maria Paola Paronetto
- University of Rome "Foro Italico", Rome, Italy.,Laboratory of Cellular and Molecular Neurobiology, Fondazione Santa Lucia, Rome, Italy
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117
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Abstract
In the early 1980s, while using purified glycosyltransferases to probe glycan structures on surfaces of living cells in the murine immune system, we discovered a novel form of serine/threonine protein glycosylation (O-linked β-GlcNAc; O-GlcNAc) that occurs on thousands of proteins within the nucleus, cytoplasm, and mitochondria. Prior to this discovery, it was dogma that protein glycosylation was restricted to the luminal compartments of the secretory pathway and on extracellular domains of membrane and secretory proteins. Work in the last 3 decades from several laboratories has shown that O-GlcNAc cycling serves as a nutrient sensor to regulate signaling, transcription, mitochondrial activity, and cytoskeletal functions. O-GlcNAc also has extensive cross-talk with phosphorylation, not only at the same or proximal sites on polypeptides, but also by regulating each other's enzymes that catalyze cycling of the modifications. O-GlcNAc is generally not elongated or modified. It cycles on and off polypeptides in a time scale similar to phosphorylation, and both the enzyme that adds O-GlcNAc, the O-GlcNAc transferase (OGT), and the enzyme that removes O-GlcNAc, O-GlcNAcase (OGA), are highly conserved from C. elegans to humans. Both O-GlcNAc cycling enzymes are essential in mammals and plants. Due to O-GlcNAc's fundamental roles as a nutrient and stress sensor, it plays an important role in the etiologies of chronic diseases of aging, including diabetes, cancer, and neurodegenerative disease. This review will present an overview of our current understanding of O-GlcNAc's regulation, functions, and roles in chronic diseases of aging.
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Affiliation(s)
- Gerald W Hart
- From the Complex Carbohydrate Research Center and Biochemistry and Molecular Biology Department, University of Georgia, Athens, Georgia 30602
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118
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Abstract
Eukaryotic cells contain a large number of RNA-protein assemblies, generically referred to as ribonucleoprotein (RNP) granules. Such RNP granules include stress granules and P-bodies in the cytosol and the nucleolus, Cajal bodies, and paraspeckles in the nucleus. A variety of imaging approaches have been used to reveal different components, structural features, and dynamics of RNP granules. In this review, we discuss imaging approaches that have been used to study stress granules and the insights gained from these experiments. A general theme is that these approaches can be transferred to other RNP granules to examine similar aspects of their composition, ultrastructure, dynamics and control.
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Affiliation(s)
- Briana Van Treeck
- Department of Chemistry and Biochemistry, University of Colorado, Boulder, Colorado 80303
| | - Roy Parker
- Department of Chemistry and Biochemistry, University of Colorado, Boulder, Colorado 80303
- Howard Hughes Medical Institute, Boulder, Colorado 80303
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119
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Markmiller S, Soltanieh S, Server KL, Mak R, Jin W, Fang MY, Luo EC, Krach F, Yang D, Sen A, Fulzele A, Wozniak JM, Gonzalez DJ, Kankel MW, Gao FB, Bennett EJ, Lécuyer E, Yeo GW. Context-Dependent and Disease-Specific Diversity in Protein Interactions within Stress Granules. Cell 2019; 172:590-604.e13. [PMID: 29373831 DOI: 10.1016/j.cell.2017.12.032] [Citation(s) in RCA: 554] [Impact Index Per Article: 110.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2017] [Revised: 10/04/2017] [Accepted: 12/19/2017] [Indexed: 12/14/2022]
Abstract
Stress granules (SGs) are transient ribonucleoprotein (RNP) aggregates that form during cellular stress and are increasingly implicated in human neurodegeneration. To study the proteome and compositional diversity of SGs in different cell types and in the context of neurodegeneration-linked mutations, we used ascorbate peroxidase (APEX) proximity labeling, mass spectrometry, and immunofluorescence to identify ∼150 previously unknown human SG components. A highly integrated, pre-existing SG protein interaction network in unstressed cells facilitates rapid coalescence into larger SGs. Approximately 20% of SG diversity is stress or cell-type dependent, with neuronal SGs displaying a particularly complex repertoire of proteins enriched in chaperones and autophagy factors. Strengthening the link between SGs and neurodegeneration, we demonstrate aberrant dynamics, composition, and subcellular distribution of SGs in cells from amyotrophic lateral sclerosis (ALS) patients. Using three Drosophila ALS/FTD models, we identify SG-associated modifiers of neurotoxicity in vivo. Altogether, our results highlight SG proteins as central to understanding and ultimately targeting neurodegeneration.
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Affiliation(s)
- Sebastian Markmiller
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA 92093, USA; Stem Cell Program, University of California, San Diego, La Jolla, CA 92093, USA; Institute for Genomic Medicine, University of California, San Diego, La Jolla, CA 92039, USA
| | - Sahar Soltanieh
- Institut de Recherches Cliniques de Montréal, Montréal, QC H2W 1R7, Canada
| | - Kari L Server
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA 92093, USA; Stem Cell Program, University of California, San Diego, La Jolla, CA 92093, USA; Institute for Genomic Medicine, University of California, San Diego, La Jolla, CA 92039, USA
| | - Raymond Mak
- Division of Biological Sciences, University of California, San Diego, La Jolla, CA 92093, USA
| | - Wenhao Jin
- Department of Physiology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117593, Singapore
| | - Mark Y Fang
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA 92093, USA; Stem Cell Program, University of California, San Diego, La Jolla, CA 92093, USA; Institute for Genomic Medicine, University of California, San Diego, La Jolla, CA 92039, USA
| | - En-Ching Luo
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA 92093, USA; Stem Cell Program, University of California, San Diego, La Jolla, CA 92093, USA; Institute for Genomic Medicine, University of California, San Diego, La Jolla, CA 92039, USA
| | - Florian Krach
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA 92093, USA; Stem Cell Program, University of California, San Diego, La Jolla, CA 92093, USA; Institute for Genomic Medicine, University of California, San Diego, La Jolla, CA 92039, USA
| | - Dejun Yang
- Department of Neurology, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Anindya Sen
- Neuromuscular & Movement Disorders, Biogen, Cambridge, MA 02142, USA
| | - Amit Fulzele
- Division of Biological Sciences, University of California, San Diego, La Jolla, CA 92093, USA
| | - Jacob M Wozniak
- Department of Pharmacology, University of California, San Diego, La Jolla, CA 92093, USA; Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA 92093, USA
| | - David J Gonzalez
- Department of Pharmacology, University of California, San Diego, La Jolla, CA 92093, USA; Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA 92093, USA
| | - Mark W Kankel
- Neuromuscular & Movement Disorders, Biogen, Cambridge, MA 02142, USA
| | - Fen-Biao Gao
- Department of Neurology, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Eric J Bennett
- Division of Biological Sciences, University of California, San Diego, La Jolla, CA 92093, USA
| | - Eric Lécuyer
- Institut de Recherches Cliniques de Montréal, Montréal, QC H2W 1R7, Canada; Département de Biochimie et Médecine Moléculaire, Université de Montréal, Montréal, QC H3C 3J7, Canada; Division of Experimental Medicine, McGill University, Montréal, QC H3A 1A3, Canada
| | - Gene W Yeo
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA 92093, USA; Stem Cell Program, University of California, San Diego, La Jolla, CA 92093, USA; Institute for Genomic Medicine, University of California, San Diego, La Jolla, CA 92039, USA; Department of Physiology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117593, Singapore; Molecular Engineering Laboratory, A(∗)STAR, Singapore 138673, Singapore.
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120
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Abstract
Stress granules are nonmembranous organelles that function as a stress-adaptation mechanism. We have recently shown that stress granules are mobilized by mutant KRAS pancreatic cancer cells under stress to enhance tumor fitness and survival. In this chapter, we outline a method for inducing, detecting, and quantifying stress granules in pancreatic cancer cells in vitro and in vivo. This method can be utilized to better understand the mechanisms driving stress granule formation and their role in pancreatic tumorigenesis.
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Affiliation(s)
- Edward Sim
- Department of Cancer Biology, Thomas Jefferson University, Philadelphia, PA, USA
| | - Elena Irollo
- Department of Cancer Biology, Thomas Jefferson University, Philadelphia, PA, USA
| | - Elda Grabocka
- Department of Cancer Biology, Thomas Jefferson University, Philadelphia, PA, USA.
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121
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Hofweber M, Dormann D. Friend or foe-Post-translational modifications as regulators of phase separation and RNP granule dynamics. J Biol Chem 2018; 294:7137-7150. [PMID: 30587571 DOI: 10.1074/jbc.tm118.001189] [Citation(s) in RCA: 235] [Impact Index Per Article: 39.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Ribonucleoprotein (RNP) granules are membrane-less organelles consisting of RNA-binding proteins (RBPs) and RNA. RNA granules form through liquid-liquid phase separation (LLPS), whereby weak promiscuous interactions among RBPs and/or RNAs create a dense network of interacting macromolecules and drive the phase separation. Post-translational modifications (PTMs) of RBPs have emerged as important regulators of LLPS and RNP granule dynamics, as they can directly weaken or enhance the multivalent interactions between phase-separating macromolecules or can recruit or exclude certain macromolecules into or from condensates. Here, we review recent insights into how PTMs regulate phase separation and RNP granule dynamics, in particular arginine (Arg)-methylation and phosphorylation. We discuss how these PTMs regulate the phase behavior of prototypical RBPs and how, as "friend or foe," they might influence the assembly, disassembly, or material properties of cellular RNP granules, such as stress granules or amyloid-like condensates. We particularly highlight how PTMs control the phase separation and aggregation behavior of disease-linked RBPs. We also review how disruptions of PTMs might be involved in aberrant phase transitions and the formation of amyloid-like protein aggregates as observed in neurodegenerative diseases.
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Affiliation(s)
- Mario Hofweber
- From the BioMedical Center, Cell Biology, Ludwig-Maximilians-University Munich, Grosshaderner Strasse 9, 82152 Planegg-Martinsried.,the Graduate School of Systemic Neurosciences, Ludwig-Maximilians-University Munich, Grosshaderner Strasse 2, 82152 Planegg-Martinsried, and
| | - Dorothee Dormann
- From the BioMedical Center, Cell Biology, Ludwig-Maximilians-University Munich, Grosshaderner Strasse 9, 82152 Planegg-Martinsried, .,the Graduate School of Systemic Neurosciences, Ludwig-Maximilians-University Munich, Grosshaderner Strasse 2, 82152 Planegg-Martinsried, and.,the Munich Cluster for Systems Neurology (SyNergy), Feodor-Lynen-Strasse 17, 81377 Munich, Germany
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122
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Acetylation of intrinsically disordered regions regulates phase separation. Nat Chem Biol 2018; 15:51-61. [PMID: 30531905 DOI: 10.1038/s41589-018-0180-7] [Citation(s) in RCA: 164] [Impact Index Per Article: 27.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2017] [Accepted: 10/26/2018] [Indexed: 12/29/2022]
Abstract
Liquid-liquid phase separation (LLPS) of proteins containing intrinsically disordered regions (IDRs) has been proposed as a mechanism underlying the formation of membrane-less organelles. Tight regulation of IDR behavior is essential to ensure that LLPS only takes place when necessary. Here, we report that IDR acetylation/deacetylation regulates LLPS and assembly of stress granules (SGs), membrane-less organelles forming in response to stress. Acetylome analysis revealed that the RNA helicase DDX3X, an important component of SGs, is a novel substrate of the deacetylase HDAC6. The N-terminal IDR of DDX3X (IDR1) can undergo LLPS in vitro, and its acetylation at multiple lysine residues impairs the formation of liquid droplets. We also demonstrated that enhanced LLPS propensity through deacetylation of DDX3X-IDR1 by HDAC6 is necessary for SG maturation, but not initiation. Our analysis provides a mechanistic framework to understand how acetylation and deacetylation of IDRs regulate LLPS spatiotemporally, and impact membrane-less organelle formation in vivo.
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123
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Rotavirus Induces Formation of Remodeled Stress Granules and P Bodies and Their Sequestration in Viroplasms To Promote Progeny Virus Production. J Virol 2018; 92:JVI.01363-18. [PMID: 30258011 DOI: 10.1128/jvi.01363-18] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2018] [Accepted: 09/20/2018] [Indexed: 02/06/2023] Open
Abstract
Rotavirus replicates in unique virus-induced cytoplasmic inclusion bodies called viroplasms (VMs), the composition and structure of which have yet to be understood. Based on the analysis of a few proteins, earlier studies reported that rotavirus infection inhibits stress granule (SG) formation and disrupts P bodies (PBs). However, the recent demonstration that rotavirus infection induces cytoplasmic relocalization and colocalization with VMs of several nuclear hnRNPs and AU-rich element-binding proteins (ARE-BPs), which are known components of SGs and PBs, suggested the possibility of rotavirus-induced remodeling of SGs and PBs, prompting us to analyze a large number of the SG and PB components to understand the status of SGs and PBs in rotavirus-infected cells. Here we demonstrate that rotavirus infection induces molecular triage by selective exclusion of a few proteins of SGs (G3BP1 and ZBP1) and PBs (DDX6, EDC4, and Pan3) and sequestration of the remodeled/atypical cellular organelles, containing the majority of their components, in the VM. The punctate SG and PB structures are seen at about 4 h postinfection (hpi), coinciding with the appearance of small VMs, many of which fuse to form mature large VMs with progression of infection. By use of small interfering RNA (siRNA)-mediated knockdown and/or ectopic overexpression, the majority of the SG and PB components, except for ADAR1, were observed to inhibit viral protein expression and virus growth. In conclusion, this study demonstrates that VMs are highly complex supramolecular structures and that rotavirus employs a novel strategy of sequestration in the VM and harnessing of the remodeled cellular RNA recycling bins to promote its growth.IMPORTANCE Rotavirus is known to replicate in specialized virus-induced cytoplasmic inclusion bodies called viroplasms (VMs), but the composition and structure of VMs are not yet understood. Here we demonstrate that rotavirus interferes with normal SG and PB assembly but promotes formation of atypical SG-PB structures by selective exclusion of a few components and employs a novel strategy of sequestration of the remodeled SG-PB granules in the VMs to promote virus growth by modulating their negative influence on virus infection. Rotavirus VMs appear to be complex supramolecular structures formed by the union of the triad of viral replication complexes and remodeled SGs and PBs, as well as other host factors, and designed to promote productive virus infection. These observations have implications for the planning of future research with the aim of understanding the structure of the VM, the mechanism of morphogenesis of the virus, and the detailed roles of host proteins in rotavirus biology.
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124
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Ubiquilin 2 modulates ALS/FTD-linked FUS-RNA complex dynamics and stress granule formation. Proc Natl Acad Sci U S A 2018; 115:E11485-E11494. [PMID: 30442662 DOI: 10.1073/pnas.1811997115] [Citation(s) in RCA: 82] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
The ubiquitin-like protein ubiquilin 2 (UBQLN2) has been genetically and pathologically linked to the neurodegenerative diseases amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD), but its normal cellular functions are not well understood. In a search for UBQLN2-interacting proteins, we found an enrichment of stress granule (SG) components, including ALS/FTD-linked heterogeneous ribonucleoprotein fused in sarcoma (FUS). Through the use of an optimized SG detection method, we observed UBQLN2 and its interactors at SGs. A low complexity, Sti1-like repeat region in UBQLN2 was sufficient for its localization to SGs. Functionally, UBQLN2 negatively regulated SG formation. UBQLN2 increased the dynamics of FUS-RNA interaction and promoted the fluidity of FUS-RNA complexes at a single-molecule level. This solubilizing effect corresponded to a dispersal of FUS liquid droplets in vitro and a suppression of FUS SG formation in cells. ALS-linked mutations in UBQLN2 reduced its association with FUS and impaired its function in regulating FUS-RNA complex dynamics and SG formation. These results reveal a previously unrecognized role for UBQLN2 in regulating the early stages of liquid-liquid phase separation by directly modulating the fluidity of protein-RNA complexes and the dynamics of SG formation.
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125
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Lou Q, Hu Y, Ma Y, Dong Z. RNA interference may suppress stress granule formation by preventing argonaute 2 recruitment. Am J Physiol Cell Physiol 2018; 316:C81-C91. [PMID: 30404558 DOI: 10.1152/ajpcell.00251.2018] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
RNA-induced silencing complex (RISC) is formed during RNA interference (RNAi), whereas stress granules (SG) are assembled in response to cellular stress. Here, we demonstrate an interesting connection between RISC and SG that may involve argonaute 2 (Ago2), a core component of RISC. We analyzed SG induction by arsenite, the commonly used SG inducer. SG formation was suppressed in heat shock transcription factor 1 (Hsf1) or hypoxia-inducible factor-1α (Hif1α) shRNA-transfected cells but not in Hsf1 or Hif1α-knockout cells, suggesting that RNAi per se (rather than gene deficiency) may account for the suppressive effect on SG. In support, the suppressive effect of RNAi on SG formation was reversed by the RISC-loading inhibitor aurintricarboxylic acid. In non-RNAi cells, arsenite induced the accumulation of Ago2 in SGs as shown by its colocalization and coimmunoprecipitation with SG proteins, but Ago2 was not recruited to SG in the cells with RNAi. Consistently, arsenite induced the dissociation of Ago2 from RISC proteins in non-RNAi cells but not in RNAi cells. CRISPR-Cas9-medicated ablation of Ago2 attenuated SG formation during arsenite treatment, suggesting a critical role of Ago2 in SG assembly. Together, these results indicate that RISC and SG may compete for some key components, such as Ago2. In response to cellular stress, Ago2 is recruited for SG assembly; however, during RNAi, Ago2 is held in RISC, becoming unavailable for SG formation.
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Affiliation(s)
- Qiang Lou
- Joint National Laboratory for Antibody Drug Engineering, Henan University School of Basic Medical Sciences , Kaifeng, Henan , China.,Department of Cellular Biology and Anatomy, Medical College of Georgia at Augusta University and Charlie Norwood VA Medical Center , Augusta, Georgia
| | - Yanzhong Hu
- Joint National Laboratory for Antibody Drug Engineering, Henan University School of Basic Medical Sciences , Kaifeng, Henan , China
| | - Yanfang Ma
- Joint National Laboratory for Antibody Drug Engineering, Henan University School of Basic Medical Sciences , Kaifeng, Henan , China
| | - Zheng Dong
- Joint National Laboratory for Antibody Drug Engineering, Henan University School of Basic Medical Sciences , Kaifeng, Henan , China.,Department of Cellular Biology and Anatomy, Medical College of Georgia at Augusta University and Charlie Norwood VA Medical Center , Augusta, Georgia
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126
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Ditlev JA, Case LB, Rosen MK. Who's In and Who's Out-Compositional Control of Biomolecular Condensates. J Mol Biol 2018; 430:4666-4684. [PMID: 30099028 PMCID: PMC6204295 DOI: 10.1016/j.jmb.2018.08.003] [Citation(s) in RCA: 221] [Impact Index Per Article: 36.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2018] [Revised: 08/01/2018] [Accepted: 08/05/2018] [Indexed: 02/06/2023]
Abstract
Biomolecular condensates are two- and three-dimensional compartments in eukaryotic cells that concentrate specific collections of molecules without an encapsulating membrane. Many condensates behave as dynamic liquids and appear to form through liquid-liquid phase separation driven by weak, multivalent interactions between macromolecules. In this review, we discuss current models and data regarding the control of condensate composition, and we describe our current understanding of the composition of representative condensates including PML nuclear bodies, P-bodies, stress granules, the nucleolus, and two-dimensional membrane localized LAT and nephrin clusters. Specific interactions, such as interactions between modular binding domains, weaker interactions between intrinsically disorder regions and nucleic acid base pairing, and nonspecific interactions, such as electrostatic interactions and hydrophobic interactions, influence condensate composition. Understanding how specific condensate composition is determined is essential to understanding condensates as biochemical entities and ultimately discerning their cellular and organismic functions.
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Affiliation(s)
- Jonathon A Ditlev
- Department of Biophysics and Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA.
| | - Lindsay B Case
- Department of Biophysics and Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA.
| | - Michael K Rosen
- Department of Biophysics and Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA.
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127
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ADP-ribosyl-binding and hydrolase activities of the alphavirus nsP3 macrodomain are critical for initiation of virus replication. Proc Natl Acad Sci U S A 2018; 115:E10457-E10466. [PMID: 30322911 DOI: 10.1073/pnas.1812130115] [Citation(s) in RCA: 96] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Alphaviruses are plus-strand RNA viruses that cause encephalitis, rash, and arthritis. The nonstructural protein (nsP) precursor polyprotein is translated from genomic RNA and processed into four nsPs. nsP3 has a highly conserved macrodomain (MD) that binds ADP-ribose (ADPr), which can be conjugated to protein as a posttranslational modification involving transfer of ADPr from NAD+ by poly ADPr polymerases (PARPs). The nsP3MD also removes ADPr from mono ADP-ribosylated (MARylated) substrates. To determine which aspects of alphavirus replication require nsP3MD ADPr-binding and/or hydrolysis function, we studied NSC34 neuronal cells infected with chikungunya virus (CHIKV). Infection induced ADP-ribosylation of cellular proteins without increasing PARP expression, and inhibition of MARylation decreased virus replication. CHIKV with a G32S mutation that reduced ADPr-binding and hydrolase activities was less efficient than WT CHIKV in establishing infection and in producing nsPs, dsRNA, viral RNA, and infectious virus. CHIKV with a Y114A mutation that increased ADPr binding but reduced hydrolase activity, established infection like WT CHIKV, rapidly induced nsP translation, and shut off host protein synthesis with reduced amplification of dsRNA. To assess replicase function independent of virus infection, a transreplicase system was used. Mutant nsP3MDs D10A, G32E, and G112E with no binding or hydrolase activity had no replicase activity, G32S had little, and Y114A was intermediate to WT. Therefore, ADP ribosylation of proteins and nsP3MD ADPr binding are necessary for initiation of alphavirus replication, while hydrolase activity facilitates amplification of replication complexes. These observations are consistent with observed nsP3MD conservation and limited tolerance for mutation.
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128
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Reineke LC, Neilson JR. Differences between acute and chronic stress granules, and how these differences may impact function in human disease. Biochem Pharmacol 2018; 162:123-131. [PMID: 30326201 PMCID: PMC6421087 DOI: 10.1016/j.bcp.2018.10.009] [Citation(s) in RCA: 49] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2018] [Accepted: 10/10/2018] [Indexed: 12/12/2022]
Abstract
Stress granules are macromolecular aggregates of mRNA and proteins assembling in response to stresses that promote the repression of protein synthesis. Most of the work characterizing stress granules has been done under acute stress conditions or during viral infection. Comparatively less work has been done to understand stress granule assembly during chronic stress, specifically regarding the composition and function of stress granules in this alternative context. Here, we describe key aspects of stress granule biology under acute stress, and how these stress granule hallmarks differ in the context of chronic stress conditions. We will provide perspective for future work aimed at further uncovering the form and function of both acute and chronic stress granules and discuss aspects of stress granule biology that have the potential to be exploited in human disease.
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Affiliation(s)
- Lucas C Reineke
- Department of Molecular Physiology and Biophysics, Houston, TX, USA; Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX, USA.
| | - Joel R Neilson
- Department of Molecular Physiology and Biophysics, Houston, TX, USA; Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX, USA
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129
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O-GlcNAc modification of eIF4GI acts as a translational switch in heat shock response. Nat Chem Biol 2018; 14:909-916. [PMID: 30127386 DOI: 10.1038/s41589-018-0120-6] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2017] [Accepted: 07/10/2018] [Indexed: 11/09/2022]
Abstract
Heat shock response (HSR) is an ancient signaling pathway leading to thermoprotection of nearly all living organisms. Emerging evidence suggests that intracellular O-linked β-N-acetylglucosamine (O-GlcNAc) serves as a molecular 'thermometer' by reporting ambient temperature fluctuations. Whether and how O-GlcNAc modification regulates HSR remains unclear. Here we report that, upon heat shock stress, the key translation initiation factor eIF4GI undergoes dynamic O-GlcNAcylation at the N-terminal region. Without O-GlcNAc modification, the preferential translation of stress mRNAs is impaired. Unexpectedly, stress mRNAs are entrapped within stress granules (SGs) that are no longer dissolved during stress recovery. Mechanistically, we show that stress-induced eIF4GI O-GlcNAcylation repels poly(A)-binding protein 1 and promotes SG disassembly, thereby licensing stress mRNAs for selective translation. Using various eIF4GI mutants created by CRISPR/Cas9, we demonstrate that eIF4GI acts as a translational switch via reversible O-GlcNAcylation. Our study reveals a central mechanism linking heat stress sensing, protein remodeling, SG dynamics and translational reprogramming.
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130
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Zhou Y, Bai Y, Liu H, Jiang X, Tong T, Fang L, Wang D, Ke Q, Liang J, Xiao S. Tellurium/Bovine Serum Albumin Nanocomposites Inducing the Formation of Stress Granules in a Protein Kinase R-Dependent Manner. ACS APPLIED MATERIALS & INTERFACES 2018; 10:25241-25251. [PMID: 29993233 DOI: 10.1021/acsami.8b09402] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
The effect of nanoparticles (NPs) on cellular stress responses is important to the understanding of nanotoxicities and developing safe therapies. Although the relationship between NPs and cellular stress responses has been preliminarily investigated, stress responses to NPs remain unclear. Here, tellurium/bovine serum albumin (Te/BSA) nanocomposites were prepared using sodium tellurite, BSA, and glutathione as precursors. The as-prepared Te/BSA nanocomposites, with particle size similar to that of many viruses, are found to induce the formation of stress granules (SGs), a kind of cytoplasmic RNA granule formed under various stresses. The SGs in Te/BSA nanocomposite-treated cells are composed of T-cell internal antigen 1 (TIA1), TIA1-related protein, and eukaryotic initiation factor 3η. Using chemical inhibitors and small interfering RNA-mediated silencing, protein kinase R (PKR) is identified as the α-subunit of eukaryotic initiation factor 2 (eIF2α)-kinase activated upon Te/BSA nanocomposite incubation, which is also the dominant kinase responsible for eIF2α activation under virus infection. Mechanistically, PKR is activated in a heparin-dependent manner. This study reveals a biological effect of Te/BSA nanocomposites on stress responses, providing a preliminary basis for further research on viruslike particles and the application of NPs in biology.
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Anders M, Chelysheva I, Goebel I, Trenkner T, Zhou J, Mao Y, Verzini S, Qian SB, Ignatova Z. Dynamic m 6A methylation facilitates mRNA triaging to stress granules. Life Sci Alliance 2018; 1:e201800113. [PMID: 30456371 PMCID: PMC6238392 DOI: 10.26508/lsa.201800113] [Citation(s) in RCA: 117] [Impact Index Per Article: 19.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2018] [Revised: 06/25/2018] [Accepted: 06/26/2018] [Indexed: 12/21/2022] Open
Abstract
Reversible post-transcriptional modifications on messenger RNA emerge as prevalent phenomena in RNA metabolism. The most abundant among them is N6-methyladenosine (m6A) which is pivotal for RNA metabolism and function; its role in stress response remains elusive. We have discovered that in response to oxidative stress, transcripts are additionally m6A modified in their 5' vicinity. Distinct from that of the translationally active mRNAs, this methylation pattern provides a selective mechanism for triaging mRNAs from the translatable pool to stress-induced stress granules. These stress-induced newly methylated sites are selectively recognized by the YTH domain family 3 (YTHDF3) "reader" protein, thereby revealing a new role for YTHDF3 in shaping the selectivity of stress response. Our findings describe a previously unappreciated function for RNA m6A modification in oxidative-stress response and expand the breadth of physiological roles of m6A.
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Affiliation(s)
- Maximilian Anders
- Institute for Biochemistry and Molecular Biology, Department of Chemistry, University of Hamburg, Hamburg, Germany
| | - Irina Chelysheva
- Institute for Biochemistry and Molecular Biology, Department of Chemistry, University of Hamburg, Hamburg, Germany
| | - Ingrid Goebel
- Institute for Biochemistry and Molecular Biology, Department of Chemistry, University of Hamburg, Hamburg, Germany
| | - Timo Trenkner
- Institute for Biochemistry and Molecular Biology, Department of Chemistry, University of Hamburg, Hamburg, Germany
| | - Jun Zhou
- Division of Nutritional Science, Cornell University, Ithaca, NY, USA
| | - Yuanhui Mao
- Division of Nutritional Science, Cornell University, Ithaca, NY, USA
| | - Silvia Verzini
- Institute for Biochemistry and Molecular Biology, Department of Chemistry, University of Hamburg, Hamburg, Germany
| | - Shu-Bing Qian
- Division of Nutritional Science, Cornell University, Ithaca, NY, USA
| | - Zoya Ignatova
- Institute for Biochemistry and Molecular Biology, Department of Chemistry, University of Hamburg, Hamburg, Germany
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132
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Duan F, Wu H, Jia D, Wu W, Ren S, Wang L, Song S, Guo X, Liu F, Ruan Y, Gu J. O-GlcNAcylation of RACK1 promotes hepatocellular carcinogenesis. J Hepatol 2018; 68:1191-1202. [PMID: 29454068 DOI: 10.1016/j.jhep.2018.02.003] [Citation(s) in RCA: 74] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/25/2017] [Revised: 01/30/2018] [Accepted: 02/03/2018] [Indexed: 12/20/2022]
Abstract
BACKGROUND & AIMS Aberrant oncogenic mRNA translation and protein O-linked β-N-acetylglucosaminylation (O-GlcNAcylation) are general features during tumorigenesis. Nevertheless, whether and how these two pathways are interlinked remain unknown. Our previous study indicated that ribosomal receptor for activated C-kinase 1 (RACK1) promoted chemoresistance and growth in hepatocellular carcinoma (HCC). The aim of this study is to examine the role of RACK1 O-GlcNAcylation in oncogene translation and HCC carcinogenesis. METHODS The site(s) of RACK1 for O-GlcNAcylation was mapped by mass spectrometry analysis. HCC cell lines were employed to examine the effects of RACK1 O-GlcNAcylation on the translation of oncogenic factors and behaviors of tumor cells in vitro. Transgenic knock-in mice were used to detect the role of RACK1 O-GlcNAcylation in modulating HCC tumorigenesis in vivo. The correlation of RACK1 O-GlcNAcylation with tumor progression and relapse were analyzed in clinical HCC samples. RESULTS We found that ribosomal RACK1 was highly modified by O-GlcNAc at Ser122. O-GlcNAcylation of RACK1 enhanced its protein stability, ribosome binding and interaction with PKCβII (PRKCB), leading to increased eukaryotic translation initiation factor 4E phosphorylation and translation of potent oncogenes in HCC cells. Genetic ablation of RACK1 O-GlcNAcylation at Ser122 dramatically suppressed tumorigenesis, angiogenesis, and metastasis in vitro and in diethylnitrosamine (DEN)-induced HCC mouse model. Increased RACK1 O-GlcNAcylation was also observed in HCC patient samples and correlated with tumor development and recurrence after chemotherapy. CONCLUSIONS These findings demonstrate that RACK1 acts as key mediator linking O-GlcNAc metabolism to cap-dependent translation during HCC tumorigenesis. Targeting RACK1 O-GlcNAcylation provides promising options for HCC treatment. LAY SUMMARY O-GlcNAcylation of ribosomal receptor for activated C-kinase 1 at the amino acid serine122 promotes its stability, ribosome localization and interaction with the protein kinase, PKCβII, thus driving the translation of oncogenes and tumorigenesis of hepatocellular carcinoma. Increased O-GlcNAcylation of ribosomal receptor for activated C-kinase 1 is positively correlated with tumor growth, metastasis and recurrence in patients with hepatocellular carcinoma.
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Affiliation(s)
- Fangfang Duan
- Key Laboratory of Glycoconjugate Research Ministry of Health, School of Basic Medical Sciences, Fudan University, Shanghai 200032, China; Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Fudan University, Shanghai 200032, China
| | - Hao Wu
- Key Laboratory of Glycoconjugate Research Ministry of Health, School of Basic Medical Sciences, Fudan University, Shanghai 200032, China; Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Fudan University, Shanghai 200032, China
| | - Dongwei Jia
- Key Laboratory of Glycoconjugate Research Ministry of Health, School of Basic Medical Sciences, Fudan University, Shanghai 200032, China; Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Fudan University, Shanghai 200032, China
| | - Weicheng Wu
- Key Laboratory of Glycoconjugate Research Ministry of Health, School of Basic Medical Sciences, Fudan University, Shanghai 200032, China; Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Fudan University, Shanghai 200032, China
| | - Shifang Ren
- Key Laboratory of Glycoconjugate Research Ministry of Health, School of Basic Medical Sciences, Fudan University, Shanghai 200032, China; Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Fudan University, Shanghai 200032, China
| | - Lan Wang
- Key Laboratory of Glycoconjugate Research Ministry of Health, School of Basic Medical Sciences, Fudan University, Shanghai 200032, China; Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Fudan University, Shanghai 200032, China
| | - Shushu Song
- Key Laboratory of Glycoconjugate Research Ministry of Health, School of Basic Medical Sciences, Fudan University, Shanghai 200032, China; Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Fudan University, Shanghai 200032, China
| | - Xinying Guo
- Key Laboratory of Glycoconjugate Research Ministry of Health, School of Basic Medical Sciences, Fudan University, Shanghai 200032, China; Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Fudan University, Shanghai 200032, China
| | - Fenglin Liu
- Department of General Surgery, Zhongshan Hospital, Fudan University, Shanghai 200032, China.
| | - Yuanyuan Ruan
- Key Laboratory of Glycoconjugate Research Ministry of Health, School of Basic Medical Sciences, Fudan University, Shanghai 200032, China; Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Fudan University, Shanghai 200032, China.
| | - Jianxin Gu
- Key Laboratory of Glycoconjugate Research Ministry of Health, School of Basic Medical Sciences, Fudan University, Shanghai 200032, China; Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Fudan University, Shanghai 200032, China; Institutes of Biomedical Sciences, Fudan University, Shanghai 200032, China
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Yu P, Hu L, Xie J, Chen S, Huang L, Xu Z, Liu X, Zhou Q, Yuan P, Yan X, Jin J, Shen Y, Zhu W, Fu L, Chen Q, Yu J, Hu J, Cao Q, Wan R, Hong K. O-GlcNAcylation of cardiac Nav1.5 contributes to the development of arrhythmias in diabetic hearts. Int J Cardiol 2018; 260:74-81. [PMID: 29530619 DOI: 10.1016/j.ijcard.2018.02.099] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/16/2017] [Revised: 02/20/2018] [Accepted: 02/23/2018] [Indexed: 12/22/2022]
Abstract
BACKGROUND Cardiovascular complications are major causes of mortality and morbidity in diabetic patients. The mechanisms underlying the progression of diabetic heart (DH) to ventricular arrhythmias are unclear. O-linked GlcNAcylation (O-GlcNAc) is a reversible post-translational modification for the regulation of diverse cellular processes. The purpose of this study was to assess whether the cardiac voltage-gated sodium channel (Nav1.5) is subjected to O-linked GlcNAcylation (O-GlcNAc), which plays an essential role in DH-induced arrhythmias. METHODS AND RESULTS In this study, Sprague-Dawley rats (male, 200-230 g) were treated with a single high-dose of streptozotocin (STZ, 80 mg/kg) to generate a rat model of diabetes. STZ-induced 3-month diabetic rats displayed increased susceptibility to ventricular arrhythmias. The elevated O-GlcNAc modification was correlated with decreases in both total and cytoplasmic Nav1.5 expression in vivo and in vitro. In addition, both co-immunoprecipitation and immunostaining assays demonstrated that hyperglycemia could increase the O-GlcNAc-modified Nav1.5 levels and decrease the interaction between Nav1.5 and Nav1.5-binding proteins Nedd4-2/SAP-97. Furthermore, patch-clamp measurements in HEK-293 T cells showed that Nav1.5 current densities decreased by 30% after high-glucose treatment, and the sodium currents increased via O-GlcNAc inhibition. CONCLUSION Our data suggested that hyperglycemia increased the O-GlcNAc modification of Nav1.5 expression and decreased the interaction between Nav1.5 and Nedd4-2/SAP-97, which led to the abnormal expression and distribution of Nav1.5, loss of function of the sodium channel, and prolongation of the PR/QT interval. Excessive O-GlcNAc modification of Nav1.5 is a novel signaling event, which may be an underlying contributing factor for the development of the arrhythmogenesis in DH.
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Affiliation(s)
- Peng Yu
- Department of Cardiovascular Medicine, the Second Affiliated Hospital of Nanchang University, Nanchang, Jiangxi, 330006, China; Jiangxi Key Laboratory of Molecular Medicine, Nanchang, Jiangxi 330006, China
| | - Lili Hu
- Department of Cardiovascular Medicine, the Second Affiliated Hospital of Nanchang University, Nanchang, Jiangxi, 330006, China; Department of Nephrology, the Second Affiliated Hospital of Nanchang University, Nanchang, Jiangxi 330006, China
| | - Jinyan Xie
- Jiangxi Key Laboratory of Molecular Medicine, Nanchang, Jiangxi 330006, China
| | - Sisi Chen
- Department of General Surgery, the Second Affiliated Hospital of Nanchang University, Nanchang, Jiangxi 330006, China
| | - Lin Huang
- Department of Cardiovascular Medicine, the Second Affiliated Hospital of Nanchang University, Nanchang, Jiangxi, 330006, China; Jiangxi Key Laboratory of Molecular Medicine, Nanchang, Jiangxi 330006, China
| | - Zixuan Xu
- Department of Cardiovascular Medicine, the Second Affiliated Hospital of Nanchang University, Nanchang, Jiangxi, 330006, China; Jiangxi Key Laboratory of Molecular Medicine, Nanchang, Jiangxi 330006, China
| | - Xiao Liu
- Department of Cardiovascular Medicine, the Second Affiliated Hospital of Nanchang University, Nanchang, Jiangxi, 330006, China; Jiangxi Key Laboratory of Molecular Medicine, Nanchang, Jiangxi 330006, China
| | - Qiongqiong Zhou
- Department of Cardiovascular Medicine, the Second Affiliated Hospital of Nanchang University, Nanchang, Jiangxi, 330006, China; Jiangxi Key Laboratory of Molecular Medicine, Nanchang, Jiangxi 330006, China
| | - Ping Yuan
- Department of Cardiovascular Medicine, the Second Affiliated Hospital of Nanchang University, Nanchang, Jiangxi, 330006, China; Jiangxi Key Laboratory of Molecular Medicine, Nanchang, Jiangxi 330006, China
| | - Xia Yan
- Jiangxi Key Laboratory of Molecular Medicine, Nanchang, Jiangxi 330006, China
| | - Jiejin Jin
- Jiangxi Key Laboratory of Molecular Medicine, Nanchang, Jiangxi 330006, China
| | - Yang Shen
- Jiangxi Key Laboratory of Molecular Medicine, Nanchang, Jiangxi 330006, China
| | - Wengen Zhu
- Department of Cardiovascular Medicine, the Second Affiliated Hospital of Nanchang University, Nanchang, Jiangxi, 330006, China; Jiangxi Key Laboratory of Molecular Medicine, Nanchang, Jiangxi 330006, China
| | - Linghua Fu
- Department of Cardiovascular Medicine, the Second Affiliated Hospital of Nanchang University, Nanchang, Jiangxi, 330006, China; Jiangxi Key Laboratory of Molecular Medicine, Nanchang, Jiangxi 330006, China
| | - Qi Chen
- Department of Cardiovascular Medicine, the Second Affiliated Hospital of Nanchang University, Nanchang, Jiangxi, 330006, China
| | - Jianhua Yu
- Department of Cardiovascular Medicine, the Second Affiliated Hospital of Nanchang University, Nanchang, Jiangxi, 330006, China
| | - Jianxin Hu
- Department of Cardiovascular Medicine, the Second Affiliated Hospital of Nanchang University, Nanchang, Jiangxi, 330006, China
| | - Qing Cao
- Jiangxi Key Laboratory of Molecular Medicine, Nanchang, Jiangxi 330006, China
| | - Rong Wan
- Department of Cardiovascular Medicine, the Second Affiliated Hospital of Nanchang University, Nanchang, Jiangxi, 330006, China; Jiangxi Key Laboratory of Molecular Medicine, Nanchang, Jiangxi 330006, China.
| | - Kui Hong
- Department of Cardiovascular Medicine, the Second Affiliated Hospital of Nanchang University, Nanchang, Jiangxi, 330006, China; Jiangxi Key Laboratory of Molecular Medicine, Nanchang, Jiangxi 330006, China.
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Constable S, Lim JM, Vaidyanathan K, Wells L. O-GlcNAc transferase regulates transcriptional activity of human Oct4. Glycobiology 2018; 27:927-937. [PMID: 28922739 DOI: 10.1093/glycob/cwx055] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2017] [Accepted: 06/10/2017] [Indexed: 01/06/2023] Open
Abstract
O-linked β-N-acetylglucosamine (O-GlcNAc) is a single sugar modification found on many different classes of nuclear and cytoplasmic proteins. Addition of this modification, by the enzyme O-linked N-acetylglucosamine transferase (OGT), is dynamic and inducible. One major class of proteins modified by O-GlcNAc is transcription factors. O-GlcNAc regulates transcription factor properties through a variety of different mechanisms including localization, stability and transcriptional activation. Maintenance of embryonic stem (ES) cell pluripotency requires tight regulation of several key transcription factors, many of which are modified by O-GlcNAc. Octamer-binding protein 4 (Oct4) is one of the key transcription factors required for pluripotency of ES cells and more recently, the generation of induced pluripotent stem (iPS) cells. The action of Oct4 is modulated by the addition of several post-translational modifications, including O-GlcNAc. Previous studies in mice found a single site of O-GlcNAc addition responsible for transcriptional regulation. This study was designed to determine if this mechanism is conserved in humans. We mapped 10 novel sites of O-GlcNAc attachment on human Oct4, and confirmed a role for OGT in transcriptional activation of Oct4 at a site distinct from that found in mouse that allows distinction between different Oct4 target promoters. Additionally, we uncovered a potential new role for OGT that does not include its catalytic function. These results confirm that human Oct4 activity is being regulated by OGT by a mechanism that is distinct from mouse Oct4.
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Affiliation(s)
- Sandii Constable
- Complex Carbohydrate Research Center and Department of Biochemistry and Molecular Biology, The University of Georgia, 315 Riverbend Road, Athens, GA 30602, USA
| | - Jae-Min Lim
- Complex Carbohydrate Research Center and Department of Biochemistry and Molecular Biology, The University of Georgia, 315 Riverbend Road, Athens, GA 30602, USA.,Department of Chemistry, Changwon National University, Changwon, Gyeongnam 641-773, South Korea
| | - Krithika Vaidyanathan
- Complex Carbohydrate Research Center and Department of Biochemistry and Molecular Biology, The University of Georgia, 315 Riverbend Road, Athens, GA 30602, USA
| | - Lance Wells
- Complex Carbohydrate Research Center and Department of Biochemistry and Molecular Biology, The University of Georgia, 315 Riverbend Road, Athens, GA 30602, USA
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135
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Alberti S, Carra S. Quality Control of Membraneless Organelles. J Mol Biol 2018; 430:4711-4729. [PMID: 29758260 DOI: 10.1016/j.jmb.2018.05.013] [Citation(s) in RCA: 62] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2018] [Revised: 05/04/2018] [Accepted: 05/04/2018] [Indexed: 02/06/2023]
Abstract
The formation of membraneless organelles (MLOs) by phase separation has emerged as a new way of organizing the cytoplasm and nucleoplasm of cells. Examples of MLOs forming via phase separation are nucleoli in the nucleus and stress granules in the cytoplasm. The main components of these MLOs are macromolecules such as RNAs and proteins. In order to assemble by phase separation, these proteins and RNAs have to undergo many cooperative interactions. These cooperative interactions are supported by specific molecular features within phase-separating proteins, such as multivalency and the presence of disordered domains that promote weak and transient interactions. However, these features also predispose phase-separating proteins to aberrant behavior. Indeed, evidence is emerging for a strong link between phase-separating proteins, MLOs, and age-related diseases. In this review, we discuss recent progress in understanding the formation, properties, and functions of MLOs. We pay special attention to the emerging link between MLOs and age-related diseases, and we explain how changes in the composition and physical properties of MLOs promote their conversion into an aberrant state. Furthermore, we discuss the key role of the protein quality control machinery in regulating the properties and functions of MLOs and thus in preventing age-related diseases.
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Affiliation(s)
- Simon Alberti
- Max Planck Institute of Molecular Cell Biology and Genetics, 01307 Dresden, Germany.
| | - Serena Carra
- Department of Biomedical, Metabolic and Neural Science, University of Modena and Reggio Emilia, Center for Neuroscience and Neurotechnology, 41125 Modena, Italy.
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136
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Fay MM, Anderson PJ. The Role of RNA in Biological Phase Separations. J Mol Biol 2018; 430:4685-4701. [PMID: 29753780 DOI: 10.1016/j.jmb.2018.05.003] [Citation(s) in RCA: 71] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2018] [Revised: 05/02/2018] [Accepted: 05/03/2018] [Indexed: 12/13/2022]
Abstract
Phase transitions that alter the physical state of ribonucleoprotein particles contribute to the spacial and temporal organization of the densely packed intracellular environment. This allows cells to organize biologically coupled processes as well as respond to environmental stimuli. RNA plays a key role in phase separation events that modulate various aspects of RNA metabolism. Here, we review the role that RNA plays in ribonucleoprotein phase separations.
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Affiliation(s)
- Marta M Fay
- Division of Rheumatology, Immunology and Allergy, Brigham and Women's Hospital, Boston, MA 02115, USA; Department of Medicine, Harvard Medical School, Boston, MA 02115, USA
| | - Paul J Anderson
- Division of Rheumatology, Immunology and Allergy, Brigham and Women's Hospital, Boston, MA 02115, USA; Department of Medicine, Harvard Medical School, Boston, MA 02115, USA.
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137
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Abstract
To survive, organisms must orchestrate competing biochemical and regulatory processes in time and space. Recent work has suggested that the underlying chemical properties of some biomolecules allow them to self-organize and that life may have exploited this property to organize biochemistry in space and time. Such phase separation is ubiquitous, particularly among the many regulatory proteins that harbor prion-like intrinsically disordered domains. And yet, despite evident regulation by post-translational modification and myriad other stimuli, the biological significance of many phase-separated compartments remains uncertain. Many potential functions have been proposed, but far fewer have been demonstrated. A burgeoning subfield at the intersection of cell biology and polymer physics has defined the biophysical underpinnings that govern the genesis and stability of these particles. The picture is complex: many assemblies are composed of multiple proteins that each have the capacity to phase separate. Here, we briefly discuss this foundational work and survey recent efforts combining targeted biochemical perturbations and quantitative modeling to specifically address the diverse roles that phase separation processes may play in biology.
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Affiliation(s)
- Alan K. Itakura
- Department of Biology, Stanford University, 269 Campus Drive, Stanford, CA 94305
| | - Raymond A. Futia
- Department of Biology, Stanford University, 269 Campus Drive, Stanford, CA 94305
| | - Daniel F. Jarosz
- Department of Chemical and Systems Biology, Stanford University, 269 Campus Drive, Stanford, CA 94305
- Department of Developmental Biology, Stanford University, 269 Campus Drive, Stanford, CA 94305
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138
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Repici M, Hassanjani M, Maddison DC, Garção P, Cimini S, Patel B, Szegö ÉM, Straatman KR, Lilley KS, Borsello T, Outeiro TF, Panman L, Giorgini F. The Parkinson's Disease-Linked Protein DJ-1 Associates with Cytoplasmic mRNP Granules During Stress and Neurodegeneration. Mol Neurobiol 2018; 56:61-77. [PMID: 29675578 PMCID: PMC6334738 DOI: 10.1007/s12035-018-1084-y] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2018] [Accepted: 04/11/2018] [Indexed: 12/22/2022]
Abstract
Mutations in the gene encoding DJ-1 are associated with autosomal recessive forms of Parkinson’s disease (PD). DJ-1 plays a role in protection from oxidative stress, but how it functions as an “upstream” oxidative stress sensor and whether this relates to PD is still unclear. Intriguingly, DJ-1 may act as an RNA binding protein associating with specific mRNA transcripts in the human brain. Moreover, we previously reported that the yeast DJ-1 homolog Hsp31 localizes to stress granules (SGs) after glucose starvation, suggesting a role for DJ-1 in RNA dynamics. Here, we report that DJ-1 interacts with several SG components in mammalian cells and localizes to SGs, as well as P-bodies, upon induction of either osmotic or oxidative stress. By purifying the mRNA associated with DJ-1 in mammalian cells, we detected several transcripts and found that subpopulations of these localize to SGs after stress, suggesting that DJ-1 may target specific mRNAs to mRNP granules. Notably, we find that DJ-1 associates with SGs arising from N-methyl-d-aspartate (NMDA) excitotoxicity in primary neurons and parkinsonism-inducing toxins in dopaminergic cell cultures. Thus, our results indicate that DJ-1 is associated with cytoplasmic RNA granules arising during stress and neurodegeneration, providing a possible link between DJ-1 and RNA dynamics which may be relevant for PD pathogenesis.
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Affiliation(s)
- Mariaelena Repici
- Department of Genetics and Genome Biology, University of Leicester, Leicester, LE1 7RH, UK
| | - Mahdieh Hassanjani
- Department of Genetics and Genome Biology, University of Leicester, Leicester, LE1 7RH, UK
| | - Daniel C Maddison
- Department of Genetics and Genome Biology, University of Leicester, Leicester, LE1 7RH, UK
| | | | - Sara Cimini
- Neuroscience Department, IRCCS-Istituto Di Ricerche Farmacologiche "Mario Negri", Milan, Italy
| | - Bhavini Patel
- Department of Genetics and Genome Biology, University of Leicester, Leicester, LE1 7RH, UK
| | - Éva M Szegö
- Department of Experimental Neurodegeneration, Center for Nanoscale Microscopy and Molecular Physiology of the Brain (CNMPB), Center for Biostructural Imaging of Neurodegeneration (BIN), University Medical Center Göttingen, Waldweg 33, 37073, Göttingen, Germany
| | - Kornelis R Straatman
- Centre for Core Biotechnology Services, University of Leicester, Leicester, LE1 7RH, UK
| | - Kathryn S Lilley
- Cambridge Centre for Proteomics, Department of Biochemistry, University of Cambridge, Cambridge, UK
| | - Tiziana Borsello
- Neuroscience Department, IRCCS-Istituto Di Ricerche Farmacologiche "Mario Negri", Milan, Italy.,Department of Pharmacological and Biomolecular Sciences, Università degli Studi di Milano, Milan, Italy
| | - Tiago F Outeiro
- Department of Experimental Neurodegeneration, Center for Nanoscale Microscopy and Molecular Physiology of the Brain (CNMPB), Center for Biostructural Imaging of Neurodegeneration (BIN), University Medical Center Göttingen, Waldweg 33, 37073, Göttingen, Germany.,Max Planck Institute for Experimental Medicine, Göttingen, Germany.,Institute of Neuroscience, The Medical School, Newcastle University, Framlington Place, Newcastle Upon Tyne, NE2 4HH, UK
| | - Lia Panman
- MRC Toxicology Unit, Leicester, LE1 9HN, UK
| | - Flaviano Giorgini
- Department of Genetics and Genome Biology, University of Leicester, Leicester, LE1 7RH, UK.
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139
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Xie X, Matsumoto S, Endo A, Fukushima T, Kawahara H, Saeki Y, Komada M. Deubiquitylases USP5 and USP13 are recruited to and regulate heat-induced stress granules through their deubiquitylating activities. J Cell Sci 2018; 131:jcs.210856. [PMID: 29567855 DOI: 10.1242/jcs.210856] [Citation(s) in RCA: 46] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2017] [Accepted: 03/16/2018] [Indexed: 12/21/2022] Open
Abstract
Stress granules are transient cytoplasmic foci induced by various stresses that contain translation-stalled mRNAs and RNA-binding proteins. They are proposed to modulate mRNA translation and stress responses. Here, we show that the deubiquitylases USP5 and USP13 are recruited to heat-induced stress granules. Heat-induced stress granules also contained K48- and K63-linked ubiquitin chains. Depletion of USP5 or USP13 resulted in elevated ubiquitin chain levels and accelerated assembly of heat-induced stress granules, suggesting that these enzymes regulate the stability of the stress granules through their ubiquitin isopeptidase activity. Moreover, disassembly of heat-induced stress granules after returning the cells to normal temperatures was markedly repressed by individual depletion of USP5 or USP13. Finally, overexpression of a ubiquitin mutant lacking the C-terminal diglycine motif caused the accumulation of unanchored ubiquitin chains and the repression of the disassembly of heat-induced stress granules. As unanchored ubiquitin chains are preferred substrates for USP5, we suggest that USP5 regulates the assembly and disassembly of heat-induced stress granules by mediating the hydrolysis of unanchored ubiquitin chains while USP13 regulates stress granules through deubiquitylating protein-conjugated ubiquitin chains.This article has an associated First Person interview with the first author of the paper.
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Affiliation(s)
- Xuan Xie
- Cell Biology Center, Institute of Innovative Research, Tokyo Institute of Technology, Yokohama 226-8501, Japan.,Department of Biological Sciences, Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, Yokohama 226-8501, Japan
| | - Shunsuke Matsumoto
- Department of Biological Sciences, Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, Yokohama 226-8501, Japan
| | - Akinori Endo
- Cell Biology Center, Institute of Innovative Research, Tokyo Institute of Technology, Yokohama 226-8501, Japan
| | - Toshiaki Fukushima
- Cell Biology Center, Institute of Innovative Research, Tokyo Institute of Technology, Yokohama 226-8501, Japan .,Department of Life Science and Technology, School of Life Science and Technology, Tokyo Institute of Technology, Yokohama 226-8501, Japan
| | - Hiroyuki Kawahara
- Department of Biological Sciences, Tokyo Metropolitan University, Tokyo 192-0397, Japan
| | - Yasushi Saeki
- Laboratory of Protein Metabolism, Tokyo Metropolitan Institute of Medical Science, Tokyo 156-8506, Japan
| | - Masayuki Komada
- Cell Biology Center, Institute of Innovative Research, Tokyo Institute of Technology, Yokohama 226-8501, Japan .,Department of Life Science and Technology, School of Life Science and Technology, Tokyo Institute of Technology, Yokohama 226-8501, Japan
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140
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Abstract
Under stress, certain eukaryotic proteins and RNA assemble to form membraneless organelles known as stress granules. The most well-studied stress granule components are RNA-binding proteins that undergo liquid-liquid phase separation (LLPS) into protein-rich droplets mediated by intrinsically disordered low-complexity domains (LCDs). Here we show that stress granules include proteasomal shuttle factor UBQLN2, an LCD-containing protein structurally and functionally distinct from RNA-binding proteins. In vitro, UBQLN2 exhibits LLPS at physiological conditions. Deletion studies correlate oligomerization with UBQLN2's ability to phase-separate and form stress-induced cytoplasmic puncta in cells. Using nuclear magnetic resonance (NMR) spectroscopy, we mapped weak, multivalent interactions that promote UBQLN2 oligomerization and LLPS. Ubiquitin or polyubiquitin binding, obligatory for UBQLN2's biological functions, eliminates UBQLN2 LLPS, thus serving as a switch between droplet and disperse phases. We postulate that UBQLN2 LLPS enables its recruitment to stress granules, where its interactions with ubiquitinated substrates reverse LLPS to enable shuttling of clients out of stress granules.
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141
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Yang X, Hu Z, Fan S, Zhang Q, Zhong Y, Guo D, Qin Y, Chen M. Picornavirus 2A protease regulates stress granule formation to facilitate viral translation. PLoS Pathog 2018; 14:e1006901. [PMID: 29415027 PMCID: PMC5819834 DOI: 10.1371/journal.ppat.1006901] [Citation(s) in RCA: 59] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2017] [Revised: 02/20/2018] [Accepted: 01/23/2018] [Indexed: 12/30/2022] Open
Abstract
Stress granules (SGs) contain stalled messenger ribonucleoprotein complexes and are related to the regulation of mRNA translation. Picornavirus infection can interfere with the formation of SGs. However, the detailed molecular mechanisms and functions of picornavirus-mediated regulation of SG formation are not clear. Here, we found that the 2A protease of a picornavirus, EV71, induced atypical stress granule (aSG), but not typical stress granule (tSG), formation via cleavage of eIF4GI. Furthermore, 2A was required and sufficient to inhibit tSGs induced by EV71 infection, sodium arsenite, or heat shock. Infection of 2A protease activity-inactivated recombinant EV71 (EV71-2AC110S) failed to induce aSG formation and only induced tSG formation, which is PKR and eIF2α phosphorylation-dependent. By using a Renilla luciferase mRNA reporter system and RNA fluorescence in situ hybridization assay, we found that EV71-induced aSGs were beneficial to viral translation through sequestering only cellular mRNAs, but not viral mRNAs. In addition, we found that the 2A protease of other picornaviruses such as poliovirus and coxsackievirus also induced aSG formation and blocked tSG formation. Taken together, our results demonstrate that, on one hand, EV71 infection induces tSG formation via the PKR-eIF2α pathway, and on the other hand, 2A, but not 3C, blocks tSG formation. Instead, 2A induces aSG formation by cleaving eIF4GI to sequester cellular mRNA but release viral mRNA, thereby facilitating viral translation. When cellular translation initiation is stalled, translation initiation complexes aggregate in cytoplasm. We call these aggregations stress granules (SGs), and they can be marked by components such as TIA-1. SGs are always considered to be antiviral structures during viral infection, but viruses also regulate SG formation to facilitate their survival. Here, we show that the 2A protease of EV71 induced TIA-1 foci formation, and we analyzed these TIA-1 foci and found that they were different from typical stress granules (tSGs); thus, we named them atypical stress granules (aSGs). 2A alone could block tSG formation, and we found that protease activity of 2A was required for aSG induction and tSG blockage, but functioned in different ways. When the protease activity of 2A in EV71 was blocked (EV71-2AC110S), the tSGs but not aSGs appeared in infected cells. These tSGs contained cellular and viral mRNAs and translation initiation factors to inhibit viral translation, but aSGs contained only cellular mRNAs to promote viral translation. We propose a model revealing that EV71 escapes cellular antiviral response by manipulating SG formation: 2A transforms the overall translation shutdown system to a selective virally beneficial system by switching from tSGs to aSGs.
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Affiliation(s)
- Xiaodan Yang
- State Key Laboratory of Virology and Modern Virology Research Center, College of Life Sciences, Wuhan University, LuoJia Hill, Wuhan, China
| | - Zhulong Hu
- State Key Laboratory of Virology and Modern Virology Research Center, College of Life Sciences, Wuhan University, LuoJia Hill, Wuhan, China
| | - Shanshan Fan
- State Key Laboratory of Virology and Modern Virology Research Center, College of Life Sciences, Wuhan University, LuoJia Hill, Wuhan, China
| | - Qiang Zhang
- State Key Laboratory of Virology and Modern Virology Research Center, College of Life Sciences, Wuhan University, LuoJia Hill, Wuhan, China
| | - Yi Zhong
- State Key Laboratory of Virology and Modern Virology Research Center, College of Life Sciences, Wuhan University, LuoJia Hill, Wuhan, China
| | - Dong Guo
- State Key Laboratory of Virology and Modern Virology Research Center, College of Life Sciences, Wuhan University, LuoJia Hill, Wuhan, China
| | - Yali Qin
- State Key Laboratory of Virology and Modern Virology Research Center, College of Life Sciences, Wuhan University, LuoJia Hill, Wuhan, China
| | - Mingzhou Chen
- State Key Laboratory of Virology and Modern Virology Research Center, College of Life Sciences, Wuhan University, LuoJia Hill, Wuhan, China
- * E-mail:
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142
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Rehage N, Davydova E, Conrad C, Behrens G, Maiser A, Stehklein JE, Brenner S, Klein J, Jeridi A, Hoffmann A, Lee E, Dianzani U, Willemsen R, Feederle R, Reiche K, Hackermüller J, Leonhardt H, Sharma S, Niessing D, Heissmeyer V. Binding of NUFIP2 to Roquin promotes recognition and regulation of ICOS mRNA. Nat Commun 2018; 9:299. [PMID: 29352114 PMCID: PMC5775257 DOI: 10.1038/s41467-017-02582-1] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2017] [Accepted: 12/12/2017] [Indexed: 12/02/2022] Open
Abstract
The ubiquitously expressed RNA-binding proteins Roquin-1 and Roquin-2 are essential for appropriate immune cell function and postnatal survival of mice. Roquin proteins repress target mRNAs by recognizing secondary structures in their 3'-UTRs and by inducing mRNA decay. However, it is unknown if other cellular proteins contribute to target control. To identify cofactors of Roquin, we used RNA interference to screen ~1500 genes involved in RNA-binding or mRNA degradation, and identified NUFIP2 as a cofactor of Roquin-induced mRNA decay. NUFIP2 binds directly and with high affinity to Roquin, which stabilizes NUFIP2 in cells. Post-transcriptional repression of human ICOS by endogenous Roquin proteins requires two neighboring non-canonical stem-loops in the ICOS 3'-UTR. This unconventional cis-element as well as another tandem loop known to confer Roquin-mediated regulation of the Ox40 3'-UTR, are bound cooperatively by Roquin and NUFIP2. NUFIP2 therefore emerges as a cofactor that contributes to mRNA target recognition by Roquin.
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Affiliation(s)
- Nina Rehage
- Institute for Immunology at the Biomedical Center, Ludwig-Maximilians-Universität München, Grosshaderner Strasse 9, 82152, Planegg-Martinsried, Germany
- Research Unit Molecular Immune Regulation, Helmholtz Zentrum München, Marchioninistrasse 25, 81377, München, Germany
| | - Elena Davydova
- Group Intracellular Transport and RNA Biology, Institute of Structural Biology, Helmholtz Zentrum München, Ingolstädter Landstrasse 1, 85764, Neuherberg, Germany
| | - Christine Conrad
- Institute for Immunology at the Biomedical Center, Ludwig-Maximilians-Universität München, Grosshaderner Strasse 9, 82152, Planegg-Martinsried, Germany
| | - Gesine Behrens
- Institute for Immunology at the Biomedical Center, Ludwig-Maximilians-Universität München, Grosshaderner Strasse 9, 82152, Planegg-Martinsried, Germany
| | - Andreas Maiser
- Center for Integrated Protein Science at the Department of Biology, Ludwig-Maximilians-Universität München, Grosshaderner Strasse 2, 82152, Planegg-Martinsried, Germany
| | - Jenny E Stehklein
- Research Unit Molecular Immune Regulation, Helmholtz Zentrum München, Marchioninistrasse 25, 81377, München, Germany
| | - Sven Brenner
- Research Unit Molecular Immune Regulation, Helmholtz Zentrum München, Marchioninistrasse 25, 81377, München, Germany
| | - Juliane Klein
- Institute for Immunology at the Biomedical Center, Ludwig-Maximilians-Universität München, Grosshaderner Strasse 9, 82152, Planegg-Martinsried, Germany
| | - Aicha Jeridi
- Research Unit Molecular Immune Regulation, Helmholtz Zentrum München, Marchioninistrasse 25, 81377, München, Germany
| | - Anne Hoffmann
- Young Investigators Group Bioinformatics and Transcriptomics, Department Molecular Systems Biology, Helmholtz Centre for Environmental Research - UFZ, Permoserstraße 15, 04318, Leipzig, Germany
- Bioinformatics Group, Department of Computer Science; and Interdisciplinary Center of Bioinformatics, Leipzig University, Härtelstraße 16-18, 04107, Leipzig, Germany
| | - Eunhae Lee
- Division of Cell Biology, La Jolla Institute for Allergy and Immunology, 9420 Athena Circle, La Jolla, CA, 92037, USA
- The Functional Genomics Center, La Jolla Institute for Allergy and Immunology, 9420 Athena Circle, La Jolla, CA, 92037, USA
| | - Umberto Dianzani
- Department of Health Sciences, Universita' del Piemonte Orientale, via Solaroli 17, 28100, Novara, Italy
| | - Rob Willemsen
- CBG Department of Clinical Genetics, Erasmus MC, Wytemaweg 80, 3015 CN, Rotterdam, Netherlands
| | - Regina Feederle
- Monoclonal Antibody Core Facility and Research Group, Institute for Diabetes and Obesity, Helmholtz Zentrum München, Marchioninistrasse 25, 81377, München, Germany
| | - Kristin Reiche
- Bioinformatic Unit, Department of Diagnostics, Fraunhofer Institute for Cell Therapy and Immunology- IZI, 04103, Leipzig, Germany
| | - Jörg Hackermüller
- Young Investigators Group Bioinformatics and Transcriptomics, Department Molecular Systems Biology, Helmholtz Centre for Environmental Research - UFZ, Permoserstraße 15, 04318, Leipzig, Germany
| | - Heinrich Leonhardt
- Center for Integrated Protein Science at the Department of Biology, Ludwig-Maximilians-Universität München, Grosshaderner Strasse 2, 82152, Planegg-Martinsried, Germany
| | - Sonia Sharma
- Division of Cell Biology, La Jolla Institute for Allergy and Immunology, 9420 Athena Circle, La Jolla, CA, 92037, USA.
- The Functional Genomics Center, La Jolla Institute for Allergy and Immunology, 9420 Athena Circle, La Jolla, CA, 92037, USA.
| | - Dierk Niessing
- Group Intracellular Transport and RNA Biology, Institute of Structural Biology, Helmholtz Zentrum München, Ingolstädter Landstrasse 1, 85764, Neuherberg, Germany.
- Department of Cell Biology at the Biomedical Center, Ludwig-Maximilians-Universität München, Grosshaderner Strasse 9, 82152, Planegg-Martinsried, Germany.
- Institute of Pharmaceutical Biotechnology, Ulm University, James Franck Ring N27, 89081, Ulm, Germany.
| | - Vigo Heissmeyer
- Institute for Immunology at the Biomedical Center, Ludwig-Maximilians-Universität München, Grosshaderner Strasse 9, 82152, Planegg-Martinsried, Germany.
- Research Unit Molecular Immune Regulation, Helmholtz Zentrum München, Marchioninistrasse 25, 81377, München, Germany.
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143
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Fernandes N, Eshleman N, Buchan JR. Stress Granules and ALS: A Case of Causation or Correlation? ADVANCES IN NEUROBIOLOGY 2018; 20:173-212. [PMID: 29916020 DOI: 10.1007/978-3-319-89689-2_7] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Amyotrophic Lateral Sclerosis (ALS) is a fatal neurodegenerative disease characterized by cytoplasmic protein aggregates within motor neurons. These aggregates are linked to ALS pathogenesis. Recent evidence has suggested that stress granules may aid the formation of ALS protein aggregates. Here, we summarize current understanding of stress granules, focusing on assembly and clearance. We also assess the evidence linking alterations in stress granule formation and dynamics to ALS protein aggregates and disease pathology.
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Affiliation(s)
- Nikita Fernandes
- Department of Molecular and Cellular Biology, University of Arizona, Tucson, AZ, USA
| | - Nichole Eshleman
- Department of Molecular and Cellular Biology, University of Arizona, Tucson, AZ, USA
| | - J Ross Buchan
- Department of Molecular and Cellular Biology, University of Arizona, Tucson, AZ, USA.
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144
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Abstract
Ribonucleic acid (RNA) homeostasis is dynamically modulated in response to changing physiological conditions. Tight regulation of RNA abundance through both transcription and degradation determines the amount, timing, and location of protein translation. This balance is of particular importance in neurons, which are among the most metabolically active and morphologically complex cells in the body. As a result, any disruptions in RNA degradation can have dramatic consequences for neuronal health. In this chapter, we will first discuss mechanisms of RNA stabilization and decay. We will then explore how the disruption of these pathways can lead to neurodegenerative disease.
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145
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You X, Qin H, Ye M. Recent advances in methods for the analysis of protein o-glycosylation at proteome level. J Sep Sci 2017; 41:248-261. [PMID: 28988430 DOI: 10.1002/jssc.201700834] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2017] [Revised: 09/15/2017] [Accepted: 09/16/2017] [Indexed: 12/12/2022]
Abstract
O-Glycosylation, which refers to the glycosylation of the hydroxyl group of side chains of Serine/Threonine/Tyrosine residues, is one of the most common post-translational modifications. Compared with N-linked glycosylation, O-glycosylation is less explored because of its complex structure and relatively low abundance. Recently, O-glycosylation has drawn more and more attention for its various functions in many sophisticated biological processes. To obtain a deep understanding of O-glycosylation, many efforts have been devoted to develop effective strategies to analyze the two most abundant types of O-glycosylation, i.e. O-N-acetylgalactosamine and O-N-acetylglucosamine glycosylation. In this review, we summarize the proteomics workflows to analyze these two types of O-glycosylation. For the large-scale analysis of mucin-type glycosylation, the glycan simplification strategies including the ''SimpleCell'' technology were introduced. A variety of enrichment methods including lectin affinity chromatography, hydrophilic interaction chromatography, hydrazide chemistry, and chemoenzymatic method were introduced for the proteomics analysis of O-N-acetylgalactosamine and O-N-acetylglucosamine glycosylation.
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Affiliation(s)
- Xin You
- CAS Key Laboratory of Separation Science for Analytical Chemistry, National Chromatographic R&A Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Hongqiang Qin
- CAS Key Laboratory of Separation Science for Analytical Chemistry, National Chromatographic R&A Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Mingliang Ye
- CAS Key Laboratory of Separation Science for Analytical Chemistry, National Chromatographic R&A Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, China.,University of Chinese Academy of Sciences, Beijing, China
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146
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Tsai WC, Reineke LC, Jain A, Jung SY, Lloyd RE. Histone arginine demethylase JMJD6 is linked to stress granule assembly through demethylation of the stress granule-nucleating protein G3BP1. J Biol Chem 2017; 292:18886-18896. [PMID: 28972166 DOI: 10.1074/jbc.m117.800706] [Citation(s) in RCA: 49] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2017] [Revised: 09/22/2017] [Indexed: 12/19/2022] Open
Abstract
Stress granules (SG) are membrane-less organelles that are condensates of stalled translation initiation complexes and mRNAs. SG formation is a cytoprotective response to environmental stress and results from protein interactions involving regions of low amino acid complexity and poorly defined post-translational modifications of SG components. Many RNA-binding proteins are methylated, and we previously demonstrated that the potent SG-nucleating protein G3BP1 is methylated by protein arginine methyltransferase 1 and 5 (PRMT1 and PRMT5). G3BP1 methylation represses SG formation and is reversible. Here we functionally link JMJD6 (Jumonji C domain-containing protein 6) to G3BP1 demethylation. Our findings reveal that JMJD6 is a novel SG component that interacts with G3BP1 complexes, and its expression reduces G3BP1 monomethylation and asymmetric dimethylation at three Arg residues. Knockdown of JMJD6 repressed SG formation and G3BP1 demethylation, but SG formation and G3BP1 demethylation were rescued with catalytically active but not mutant JMJD6. These results suggest that JMJD6 functions directly or indirectly as an arginine demethylase of G3BP1 that promotes SG formation.
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Affiliation(s)
- Wei-Chih Tsai
- From the Departments of Molecular Virology and Microbiology
| | - Lucas C Reineke
- From the Departments of Molecular Virology and Microbiology.,Molecular Physiology and Biophysics, and
| | - Antrix Jain
- Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, Texas 77030
| | - Sung Yun Jung
- Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, Texas 77030
| | - Richard E Lloyd
- From the Departments of Molecular Virology and Microbiology,
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147
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Respiratory Syncytial Virus: Infection, Detection, and New Options for Prevention and Treatment. Clin Microbiol Rev 2017; 30:277-319. [PMID: 27903593 DOI: 10.1128/cmr.00010-16] [Citation(s) in RCA: 342] [Impact Index Per Article: 48.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Respiratory syncytial virus (RSV) infection is a significant cause of hospitalization of children in North America and one of the leading causes of death of infants less than 1 year of age worldwide, second only to malaria. Despite its global impact on human health, there are relatively few therapeutic options available to prevent or treat RSV infection. Paradoxically, there is a very large volume of information that is constantly being refined on RSV replication, the mechanisms of RSV-induced pathology, and community transmission. Compounding the burden of acute RSV infections is the exacerbation of preexisting chronic airway diseases and the chronic sequelae of RSV infection. A mechanistic link is even starting to emerge between asthma and those who suffer severe RSV infection early in childhood. In this article, we discuss developments in the understanding of RSV replication, pathogenesis, diagnostics, and therapeutics. We attempt to reconcile the large body of information on RSV and why after many clinical trials there is still no efficacious RSV vaccine and few therapeutics.
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148
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Sheinberger J, Shav-Tal Y. mRNPs meet stress granules. FEBS Lett 2017; 591:2534-2542. [DOI: 10.1002/1873-3468.12765] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2017] [Revised: 07/19/2017] [Accepted: 07/21/2017] [Indexed: 12/14/2022]
Affiliation(s)
- Jonathan Sheinberger
- The Mina & Everard Goodman Faculty of Life Sciences; Institute of Nanotechnology; Bar-Ilan University; Ramat Gan Israel
| | - Yaron Shav-Tal
- The Mina & Everard Goodman Faculty of Life Sciences; Institute of Nanotechnology; Bar-Ilan University; Ramat Gan Israel
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149
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Quantitative time-resolved chemoproteomics reveals that stable O-GlcNAc regulates box C/D snoRNP biogenesis. Proc Natl Acad Sci U S A 2017; 114:E6749-E6758. [PMID: 28760965 DOI: 10.1073/pnas.1702688114] [Citation(s) in RCA: 60] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
O-linked GlcNAcylation (O-GlcNAcylation), a ubiquitous posttranslational modification on intracellular proteins, is dynamically regulated in cells. To analyze the turnover dynamics of O-GlcNAcylated proteins, we developed a quantitative time-resolved O-linked GlcNAc proteomics (qTOP) strategy based on metabolic pulse-chase labeling with an O-GlcNAc chemical reporter and stable isotope labeling with amino acids in cell culture (SILAC). Applying qTOP, we quantified the turnover rates of 533 O-GlcNAcylated proteins in NIH 3T3 cells and discovered that about 14% exhibited minimal removal of O-GlcNAc or degradation of protein backbones. The stability of those hyperstable O-GlcNAcylated proteins was more sensitive to O-GlcNAcylation inhibition compared with the more dynamic populations. Among the hyperstable population were three core proteins of box C/D small nucleolar ribonucleoprotein complexes (snoRNPs): fibrillarin (FBL), nucleolar protein 5A (NOP56), and nucleolar protein 5 (NOP58). We showed that O-GlcNAcylation stabilized these proteins and was essential for snoRNP assembly. Blocking O-GlcNAcylation on FBL altered the 2'-O-methylation of rRNAs and impaired cancer cell proliferation and tumor formation in vivo.
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150
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Stress-induced O-GlcNAcylation: an adaptive process of injured cells. Biochem Soc Trans 2017; 45:237-249. [PMID: 28202678 DOI: 10.1042/bst20160153] [Citation(s) in RCA: 90] [Impact Index Per Article: 12.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2016] [Revised: 11/30/2016] [Accepted: 12/14/2016] [Indexed: 02/07/2023]
Abstract
In the 30 years, since the discovery of nucleocytoplasmic glycosylation, O-GlcNAc has been implicated in regulating cellular processes as diverse as protein folding, localization, degradation, activity, post-translational modifications, and interactions. The cell co-ordinates these molecular events, on thousands of cellular proteins, in concert with environmental and physiological cues to fine-tune epigenetics, transcription, translation, signal transduction, cell cycle, and metabolism. The cellular stress response is no exception: diverse forms of injury result in dynamic changes to the O-GlcNAc subproteome that promote survival. In this review, we discuss the biosynthesis of O-GlcNAc, the mechanisms by which O-GlcNAc promotes cytoprotection, and the clinical significance of these data.
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