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Cui Q, Liu Z, Bai G. Friend or foe: The role of stress granule in neurodegenerative disease. Neuron 2024; 112:2464-2485. [PMID: 38744273 DOI: 10.1016/j.neuron.2024.04.025] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2023] [Revised: 03/12/2024] [Accepted: 04/19/2024] [Indexed: 05/16/2024]
Abstract
Stress granules (SGs) are dynamic membraneless organelles that form in response to cellular stress. SGs are predominantly composed of RNA and RNA-binding proteins that assemble through liquid-liquid phase separation. Although the formation of SGs is considered a transient and protective response to cellular stress, their dysregulation or persistence may contribute to various neurodegenerative diseases. This review aims to provide a comprehensive overview of SG physiology and pathology. It covers the formation, composition, regulation, and functions of SGs, along with their crosstalk with other membrane-bound and membraneless organelles. Furthermore, this review discusses the dual roles of SGs as both friends and foes in neurodegenerative diseases and explores potential therapeutic approaches targeting SGs. The challenges and future perspectives in this field are also highlighted. A more profound comprehension of the intricate relationship between SGs and neurodegenerative diseases could inspire the development of innovative therapeutic interventions against these devastating diseases.
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Affiliation(s)
- Qinqin Cui
- Department of Neurology of Second Affiliated Hospital and School of Brain Science and Brain Medicine, Zhejiang University School of Medicine, Hangzhou 310058, China; Nanhu Brain-Computer Interface Institute, Hangzhou 311100, China.
| | - Zongyu Liu
- Department of Neurology of Second Affiliated Hospital and School of Brain Science and Brain Medicine, Zhejiang University School of Medicine, Hangzhou 310058, China
| | - Ge Bai
- Department of Neurology of Second Affiliated Hospital and School of Brain Science and Brain Medicine, Zhejiang University School of Medicine, Hangzhou 310058, China; Nanhu Brain-Computer Interface Institute, Hangzhou 311100, China; Liangzhu Laboratory, MOE Frontier Science Center for Brain Science and Brain-Machine Integration, State Key Laboratory of Brain-Machine Intelligence, Zhejiang University, Hangzhou 311121, China; NHC and CAMS Key Laboratory of Medical Neurobiology, Zhejiang University, Hangzhou 310058, China; Institute of Fundamental and Transdisciplinary Research, Zhejiang University, Hangzhou 310058, China.
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2
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Li Y, Xu C, Qian X, Wang G, Han C, Hua H, Dong M, Chen J, Yu H, Zhang R, Feng X, Yang Z, Pan Y. Myeloid PTEN loss affects the therapeutic response by promoting stress granule assembly and impairing phagocytosis by macrophages in breast cancer. Cell Death Discov 2024; 10:344. [PMID: 39080255 PMCID: PMC11289284 DOI: 10.1038/s41420-024-02094-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2024] [Revised: 06/25/2024] [Accepted: 07/08/2024] [Indexed: 08/02/2024] Open
Abstract
Breast cancer (BRCA) has become the most common type of cancer in women. Improving the therapeutic response remains a challenge. Phosphatase and tensin homologue deleted on chromosome 10 (PTEN) is a classic tumour suppressor with emerging new functions discovered in recent years, and myeloid PTEN loss has been reported to impair antitumour immunity. In this study, we revealed a novel mechanism by which myeloid PTEN potentially affects antitumour immunity in BRCA. We detected accelerated stress granule (SG) assembly under oxidative stress in PTEN-deficient bone marrow-derived macrophages (BMDMs) through the EGR1-promoted upregulation of TIAL1 transcription. PI3K/AKT/mTOR (PAM) pathway activation also promoted SG formation. ATP consumption during SG assembly in BMDMs impaired the phagocytic ability of 4T1 cells, potentially contributing to the disruption of antitumour immunity. In a BRCA neoadjuvant cohort, we observed a poorer response in myeloid PTENlow patients with G3BP1 aggregating as SGs in CD68+ cells, a finding that was consistent with the observation in our study that PTEN-deficient macrophages tended to more readily assemble SGs with impaired phagocytosis. Our results revealed the unconventional impact of SGs on BMDMs and might provide new perspectives on drug resistance and therapeutic strategies for the treatment of BRCA patients.
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Affiliation(s)
- Yan Li
- Department of Clinical Oncology, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, 230001, China
- Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, 230001, China
| | - Chao Xu
- Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, 230001, China
| | - Xiaojun Qian
- Department of Clinical Oncology, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, 230001, China
- Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, 230001, China
| | - Gang Wang
- Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, 230001, China
| | - Chaoqiang Han
- Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, 230001, China
| | - Hui Hua
- Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, 230001, China
| | - Menghao Dong
- Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, 230001, China
| | - Jian Chen
- Department of Clinical Oncology, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, 230001, China
- Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, 230001, China
| | - Haiyang Yu
- Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, 230001, China
| | - Rutong Zhang
- Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, 230001, China
| | - Xiaoxi Feng
- Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, 230001, China
| | - Zhenye Yang
- Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, 230001, China.
| | - Yueyin Pan
- Department of Clinical Oncology, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, 230001, China.
- Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, 230001, China.
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3
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Lindamood HL, Liu TM, Read TA, Vitriol EA. Using ALS to understand profilin 1's diverse roles in cellular physiology. Cytoskeleton (Hoboken) 2024. [PMID: 39056295 DOI: 10.1002/cm.21896] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2024] [Revised: 07/03/2024] [Accepted: 07/10/2024] [Indexed: 07/28/2024]
Abstract
Profilin is an actin monomer-binding protein whose role in actin polymerization has been studied for nearly 50 years. While its principal biochemical features are now well understood, many questions remain about how profilin controls diverse processes within the cell. Dysregulation of profilin has been implicated in a broad range of human diseases, including neurodegeneration, inflammatory disorders, cardiac disease, and cancer. For example, mutations in the profilin 1 gene (PFN1) can cause amyotrophic lateral sclerosis (ALS), although the precise mechanisms that drive neurodegeneration remain unclear. While initial work suggested proteostasis and actin cytoskeleton defects as the main pathological pathways, multiple novel functions for PFN1 have since been discovered that may also contribute to ALS, including the regulation of nucleocytoplasmic transport, stress granules, mitochondria, and microtubules. Here, we will review these newly discovered roles for PFN1, speculate on their contribution to ALS, and discuss how defects in actin can contribute to these processes. By understanding profilin 1's involvement in ALS pathogenesis, we hope to gain insight into this functionally complex protein with significant influence over cellular physiology.
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Affiliation(s)
- Halli L Lindamood
- Department of Neuroscience and Regenerative Medicine, Medical College of Georgia at Augusta University, Augusta, Georgia, USA
| | - Tatiana M Liu
- Department of Neuroscience and Regenerative Medicine, Medical College of Georgia at Augusta University, Augusta, Georgia, USA
| | - Tracy-Ann Read
- Department of Neuroscience and Regenerative Medicine, Medical College of Georgia at Augusta University, Augusta, Georgia, USA
| | - Eric A Vitriol
- Department of Neuroscience and Regenerative Medicine, Medical College of Georgia at Augusta University, Augusta, Georgia, USA
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4
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Milano SN, Bayer LV, Ko JJ, Casella CE, Bratu DP. The role of ER exit sites in maintaining P-body organization and transmitting ER stress response during Drosophila melanogaster oogenesis. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.07.03.601952. [PMID: 39005311 PMCID: PMC11245038 DOI: 10.1101/2024.07.03.601952] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/16/2024]
Abstract
Processing bodies (P-bodies) are cytoplasmic membrane-less organelles which host multiple mRNA processing events. While the fundamental principles of P-body organization are beginning to be elucidated in vitro, a nuanced understanding of how their assembly is regulated in vivo remains elusive. Here, we investigate the potential link between ER exit sites and P-bodies in Drosophila melanogaster egg chambers. Employing a combination of live and super-resolution imaging, we found that P-bodies associated with ER exit sites are larger and less mobile than cytoplasmic P-bodies, indicating that they constitute a distinct class of P-bodies which are more mature than their cytoplasmic counterparts. Moreover, we demonstrate that altering the composition of ER exit sites has differential effects on core P-body proteins (Me31B, Cup, and Trailer Hitch) suggesting a potential role for ER exit sites in P-body organization. We further show that in the absence of ER exit sites, P-body integrity is compromised and the stability and translational repression efficiency of the maternal mRNA, oskar, are reduced. Finally, we show that ER stress is communicated to P-bodies via ER exit sites, highlighting the pivotal role of ER exit sites as a bridge between membrane-bound and membrane-less organelles in ER stress response. Together, our data unveils the significance of ER exit sites not only in governing P-body organization, but also in facilitating inter-organellar communication during stress, potentially bearing implications for a variety of disease pathologies.
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Affiliation(s)
- Samantha N. Milano
- Department of Biological Sciences, Hunter College, City University of New York, NY, 10065 USA
- Program in Molecular, Cellular, and Developmental Biology, The Graduate Center, City University of New York, NY, 10016 USA
| | - Livia V. Bayer
- Department of Biological Sciences, Hunter College, City University of New York, NY, 10065 USA
| | - Julie J. Ko
- Department of Biological Sciences, Hunter College, City University of New York, NY, 10065 USA
| | - Caroline E. Casella
- Department of Biological Sciences, Hunter College, City University of New York, NY, 10065 USA
| | - Diana P. Bratu
- Department of Biological Sciences, Hunter College, City University of New York, NY, 10065 USA
- Program in Molecular, Cellular, and Developmental Biology, The Graduate Center, City University of New York, NY, 10016 USA
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5
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Buchan JR. Stress granule and P-body clearance: Seeking coherence in acts of disappearance. Semin Cell Dev Biol 2024; 159-160:10-26. [PMID: 38278052 PMCID: PMC10939798 DOI: 10.1016/j.semcdb.2024.01.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2024] [Accepted: 01/07/2024] [Indexed: 01/28/2024]
Abstract
Stress granules and P-bodies are conserved cytoplasmic biomolecular condensates whose assembly and composition are well documented, but whose clearance mechanisms remain controversial or poorly described. Such understanding could provide new insight into how cells regulate biomolecular condensate formation and function, and identify therapeutic strategies in disease states where aberrant persistence of stress granules in particular is implicated. Here, I review and compare the contributions of chaperones, the cytoskeleton, post-translational modifications, RNA helicases, granulophagy and the proteasome to stress granule and P-body clearance. Additionally, I highlight the potentially vital role of RNA regulation, cellular energy, and changes in the interaction networks of stress granules and P-bodies as means of eliciting clearance. Finally, I discuss evidence for interplay of distinct clearance mechanisms, suggest future experimental directions, and suggest a simple working model of stress granule clearance.
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Affiliation(s)
- J Ross Buchan
- Department of Molecular and Cellular Biology, University of Arizona, Tucson 85716, United States.
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6
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Ueda T, Takeuchi T, Fujikake N, Suzuki M, Minakawa EN, Ueyama M, Fujino Y, Kimura N, Nagano S, Yokoseki A, Onodera O, Mochizuki H, Mizuno T, Wada K, Nagai Y. Dysregulation of stress granule dynamics by DCTN1 deficiency exacerbates TDP-43 pathology in Drosophila models of ALS/FTD. Acta Neuropathol Commun 2024; 12:20. [PMID: 38311779 PMCID: PMC10840176 DOI: 10.1186/s40478-024-01729-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2023] [Accepted: 01/11/2024] [Indexed: 02/06/2024] Open
Abstract
The abnormal aggregation of TDP-43 into cytoplasmic inclusions in affected neurons is a major pathological hallmark of amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD). Although TDP-43 is aberrantly accumulated in the neurons of most patients with sporadic ALS/FTD and other TDP-43 proteinopathies, how TDP-43 forms cytoplasmic aggregates remains unknown. In this study, we show that a deficiency in DCTN1, a subunit of the microtubule-associated motor protein complex dynactin, perturbs the dynamics of stress granules and drives the formation of TDP-43 cytoplasmic aggregation in cultured cells, leading to the exacerbation of TDP-43 pathology and neurodegeneration in vivo. We demonstrated using a Drosophila model of ALS/FTD that genetic knockdown of DCTN1 accelerates the formation of ubiquitin-positive cytoplasmic inclusions of TDP-43. Knockdown of components of other microtubule-associated motor protein complexes, including dynein and kinesin, also increased the formation of TDP-43 inclusions, indicating that intracellular transport along microtubules plays a key role in TDP-43 pathology. Notably, DCTN1 knockdown delayed the disassembly of stress granules in stressed cells, leading to an increase in the formation of pathological cytoplasmic inclusions of TDP-43. Our results indicate that a deficiency in DCTN1, as well as disruption of intracellular transport along microtubules, is a modifier that drives the formation of TDP-43 pathology through the dysregulation of stress granule dynamics.
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Affiliation(s)
- Tetsuhiro Ueda
- Department of Neurology, Faculty of Medicine, Kindai University, 377-2 Ohnohigashi, Osakasayama, Osaka, 589-8511, Japan
- Department of Neurotherapeutics, Osaka University Graduate School of Medicine, Osaka, 565-0871, Japan
- Department of Neurology, Kyoto Prefectural University of Medicine, Kyoto, 602-0841, Japan
| | - Toshihide Takeuchi
- Life Science Research Institute, Kindai University, 377-2 Ohnohigashi, Osakasayama, Osaka, 589-8511, Japan.
- Department of Neurotherapeutics, Osaka University Graduate School of Medicine, Osaka, 565-0871, Japan.
| | - Nobuhiro Fujikake
- Department of Degenerative Neurological Diseases, National Institute of Neuroscience, National Center of Neurology and Psychiatry, Tokyo, 187-8502, Japan
| | - Mari Suzuki
- Department of Neurotherapeutics, Osaka University Graduate School of Medicine, Osaka, 565-0871, Japan
- Department of Degenerative Neurological Diseases, National Institute of Neuroscience, National Center of Neurology and Psychiatry, Tokyo, 187-8502, Japan
| | - Eiko N Minakawa
- Department of Neurophysiology, National Institute of Neuroscience, National Center of Neurology and Psychiatry, Tokyo, 187-8502, Japan
| | - Morio Ueyama
- Department of Neurology, Faculty of Medicine, Kindai University, 377-2 Ohnohigashi, Osakasayama, Osaka, 589-8511, Japan
- Department of Neurotherapeutics, Osaka University Graduate School of Medicine, Osaka, 565-0871, Japan
- Department of Degenerative Neurological Diseases, National Institute of Neuroscience, National Center of Neurology and Psychiatry, Tokyo, 187-8502, Japan
| | - Yuzo Fujino
- Department of Neurology, Faculty of Medicine, Kindai University, 377-2 Ohnohigashi, Osakasayama, Osaka, 589-8511, Japan
- Department of Neurology, Kyoto Prefectural University of Medicine, Kyoto, 602-0841, Japan
| | - Nobuyuki Kimura
- Department of Veterinary Associated Science, Faculty of Veterinary Medicine, Okayama University of Science, Ehime, 794-8555, Japan
| | - Seiichi Nagano
- Department of Neurotherapeutics, Osaka University Graduate School of Medicine, Osaka, 565-0871, Japan
- Department of Neurology, Osaka University Graduate School of Medicine, Osaka, 565-0871, Japan
| | - Akio Yokoseki
- Department of Neurology, Brain Research Institute, Niigata University, Niigata, 951-8585, Japan
| | - Osamu Onodera
- Department of Neurology, Brain Research Institute, Niigata University, Niigata, 951-8585, Japan
| | - Hideki Mochizuki
- Department of Neurology, Osaka University Graduate School of Medicine, Osaka, 565-0871, Japan
| | - Toshiki Mizuno
- Department of Neurology, Kyoto Prefectural University of Medicine, Kyoto, 602-0841, Japan
| | - Keiji Wada
- Department of Degenerative Neurological Diseases, National Institute of Neuroscience, National Center of Neurology and Psychiatry, Tokyo, 187-8502, Japan
| | - Yoshitaka Nagai
- Department of Neurology, Faculty of Medicine, Kindai University, 377-2 Ohnohigashi, Osakasayama, Osaka, 589-8511, Japan.
- Life Science Research Institute, Kindai University, 377-2 Ohnohigashi, Osakasayama, Osaka, 589-8511, Japan.
- Department of Neurotherapeutics, Osaka University Graduate School of Medicine, Osaka, 565-0871, Japan.
- Department of Neurology, Osaka University Graduate School of Medicine, Osaka, 565-0871, Japan.
- Department of Degenerative Neurological Diseases, National Institute of Neuroscience, National Center of Neurology and Psychiatry, Tokyo, 187-8502, Japan.
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7
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Hu S, Zhang Y, Yi Q, Yang C, Liu Y, Bai Y. Time-resolved proteomic profiling reveals compositional and functional transitions across the stress granule life cycle. Nat Commun 2023; 14:7782. [PMID: 38012130 PMCID: PMC10682001 DOI: 10.1038/s41467-023-43470-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2022] [Accepted: 11/09/2023] [Indexed: 11/29/2023] Open
Abstract
Stress granules (SGs) are dynamic, membrane-less organelles. With their formation and disassembly processes characterized, it remains elusive how compositional transitions are coordinated during prolonged stress to meet changing functional needs. Here, using time-resolved proteomic profiling of the acute to prolonged heat-shock SG life cycle, we identify dynamic SG proteins, further segregated into early and late proteins. Comparison of different groups of SG proteins suggests that their biochemical properties help coordinate SG compositional and functional transitions. In particular, early proteins, with high phase-separation-propensity, drive the rapid formation of the initial SG platform, while late proteins are subsequently recruited as discrete modules to further functionalize SGs. This model, supported by immunoblotting and immunofluorescence imaging, provides a conceptual framework for the compositional transitions throughout the acute to prolonged SG life cycle. Additionally, an early SG constituent, non-muscle myosin II, is shown to promote SG formation by increasing SG fusion, underscoring the strength of this dataset in revealing the complexity of SG regulation.
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Affiliation(s)
- Shuyao Hu
- School of Life Science and Technology, ShanghaiTech University, 201210, Shanghai, China.
| | - Yufeng Zhang
- School of Life Science and Technology, ShanghaiTech University, 201210, Shanghai, China
| | - Qianqian Yi
- School of Life Science and Technology, ShanghaiTech University, 201210, Shanghai, China
| | - Cuiwei Yang
- School of Life Science and Technology, ShanghaiTech University, 201210, Shanghai, China
| | - Yanfen Liu
- School of Life Science and Technology, ShanghaiTech University, 201210, Shanghai, China.
| | - Yun Bai
- School of Life Science and Technology, ShanghaiTech University, 201210, Shanghai, China.
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8
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Cochard A, Safieddine A, Combe P, Benassy M, Weil D, Gueroui Z. Condensate functionalization with microtubule motors directs their nucleation in space and allows manipulating RNA localization. EMBO J 2023; 42:e114106. [PMID: 37724036 PMCID: PMC10577640 DOI: 10.15252/embj.2023114106] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2023] [Revised: 08/24/2023] [Accepted: 08/28/2023] [Indexed: 09/20/2023] Open
Abstract
The localization of RNAs in cells is critical for many cellular processes. Whereas motor-driven transport of ribonucleoprotein (RNP) condensates plays a prominent role in RNA localization in cells, their study remains limited by the scarcity of available tools allowing to manipulate condensates in a spatial manner. To fill this gap, we reconstitute in cellula a minimal RNP transport system based on bioengineered condensates, which were functionalized with kinesins and dynein-like motors, allowing for their positioning at either the cell periphery or centrosomes. This targeting mostly occurs through the active transport of the condensate scaffolds, which leads to localized nucleation of phase-separated condensates. Then, programming the condensates to recruit specific mRNAs is able to shift the localization of these mRNAs toward the cell periphery or the centrosomes. Our method opens novel perspectives for examining the role of RNA localization as a driver of cellular functions.
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Affiliation(s)
- Audrey Cochard
- Department of Chemistry, École Normale SupérieurePSL University, Sorbonne Université, CNRSParisFrance
- Sorbonne Université, CNRS, Institut de Biologie Paris‐Seine (IBPS), Laboratoire de Biologie du DéveloppementParisFrance
| | - Adham Safieddine
- Sorbonne Université, CNRS, Institut de Biologie Paris‐Seine (IBPS), Laboratoire de Biologie du DéveloppementParisFrance
| | - Pauline Combe
- Department of Chemistry, École Normale SupérieurePSL University, Sorbonne Université, CNRSParisFrance
| | - Marie‐Noëlle Benassy
- Sorbonne Université, CNRS, Institut de Biologie Paris‐Seine (IBPS), Laboratoire de Biologie du DéveloppementParisFrance
| | - Dominique Weil
- Sorbonne Université, CNRS, Institut de Biologie Paris‐Seine (IBPS), Laboratoire de Biologie du DéveloppementParisFrance
| | - Zoher Gueroui
- Department of Chemistry, École Normale SupérieurePSL University, Sorbonne Université, CNRSParisFrance
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9
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Boccaccio GL, Thomas MG, García CC. Membraneless Organelles and Condensates Orchestrate Innate Immunity Against Viruses. J Mol Biol 2023; 435:167976. [PMID: 36702393 DOI: 10.1016/j.jmb.2023.167976] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2022] [Revised: 01/10/2023] [Accepted: 01/17/2023] [Indexed: 01/24/2023]
Abstract
The cellular defense against viruses involves the assembly of oligomers, granules and membraneless organelles (MLOs) that govern the activation of several arms of the innate immune response. Upon interaction with specific pathogen-derived ligands, a number of pattern recognition receptors (PRRs) undergo phase-separation thus triggering downstream signaling pathways. Among other relevant condensates, inflammasomes, apoptosis-associated speck-like protein containing a caspase-recruitment domain (ASC) specks, cyclic GMP-AMP synthase (cGAS) foci, protein kinase R (PKR) clusters, ribonuclease L-induced bodies (RLBs), stress granules (SGs), processing bodies (PBs) and promyelocytic leukemia protein nuclear bodies (PML NBs) play different roles in the immune response. In turn, viruses have evolved diverse strategies to evade the host defense. Viral DNA or RNA, as well as viral proteases or proteins carrying intrinsically disordered regions may interfere with condensate formation and function in multiple ways. In this review we discuss current and hypothetical mechanisms of viral escape that involve the disassembly, repurposing, or inactivation of membraneless condensates that govern innate immunity. We summarize emerging interconnections between these diverse condensates that ultimately determine the cellular outcome.
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Affiliation(s)
- Graciela Lidia Boccaccio
- Laboratorio de Biología Celular del ARN, Instituto Leloir (FIL) and Instituto de Investigaciones Bioquímicas de Buenos Aires (IIBBA) - Consejo Nacional de Investigaciones Científicas y Tecnológicas (CONICET), Buenos Aires, Argentina; Departamento de Fisiología y Biología Molecular y Celular (FBMyC), Facultad de Ciencias Exactas y Naturales (FCEN), Universidad de Buenos Aires, Buenos Aires, Argentina.
| | - María Gabriela Thomas
- Laboratorio de Biología Celular del ARN, Instituto Leloir (FIL) and Instituto de Investigaciones Bioquímicas de Buenos Aires (IIBBA) - Consejo Nacional de Investigaciones Científicas y Tecnológicas (CONICET), Buenos Aires, Argentina. https://www.twitter.com/_gabithomas
| | - Cybele Carina García
- Departamento de Química Biológica (QB), Facultad de Ciencias Exactas y Naturales (FCEN), and IQUIBICEN, Consejo Nacional de Investigaciones Científicas y Tecnológicas (CONICET) and Universidad de Buenos Aires, Buenos Aires, Argentina
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10
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Stachelek K, Harutyunyan N, Lee S, Beck A, Kim J, Xu L, Berry JL, Nagiel A, Reynolds CP, Murphree AL, Lee TC, Aparicio JG, Cobrinik D. Non-synonymous, synonymous, and non-coding nucleotide variants contribute to recurrently altered biological processes during retinoblastoma progression. Genes Chromosomes Cancer 2023; 62:275-289. [PMID: 36550020 PMCID: PMC10006380 DOI: 10.1002/gcc.23120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2022] [Revised: 12/15/2022] [Accepted: 12/20/2022] [Indexed: 12/24/2022] Open
Abstract
Retinoblastomas form in response to biallelic RB1 mutations or MYCN amplification and progress to more aggressive and therapy-resistant phenotypes through accumulation of secondary genomic changes. Progression-related changes include recurrent somatic copy number alterations and typically non-recurrent nucleotide variants, including synonymous and non-coding variants, whose significance has been unclear. To determine if nucleotide variants recurrently affect specific biological processes, we identified altered genes and over-represented variant gene ontologies in 168 exome or whole-genome-sequenced retinoblastomas and 12 tumor-matched cell lines. In addition to RB1 mutations, MYCN amplification, and established retinoblastoma somatic copy number alterations, the analyses revealed enrichment of variant genes related to diverse biological processes including histone monoubiquitination, mRNA processing (P) body assembly, and mitotic sister chromatid segregation and cytokinesis. Importantly, non-coding and synonymous variants increased the enrichment significance of each over-represented biological process term. To assess the effects of such mutations, we examined the consequences of a 3' UTR variant of PCGF3 (a BCOR-binding component of Polycomb repressive complex I), dual 3' UTR variants of CDC14B (a regulator of sister chromatid segregation), and a synonymous variant of DYNC1H1 (a regulator of P-body assembly). One PCGF3 and one of two CDC14B 3' UTR variants impaired gene expression whereas a base-edited DYNC1H1 synonymous variant altered protease sensitivity and stability. Retinoblastoma cell lines retained only ~50% of variants detected in tumors and enriched for new variants affecting p53 signaling. These findings reveal potentially important differences in retinoblastoma cell lines and tumors and implicate synonymous and non-coding variants, along with non-synonymous variants, in retinoblastoma oncogenesis.
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Affiliation(s)
- Kevin Stachelek
- The Vision Center and Saban Research Institute, Children’s Hospital Los Angeles, Los Angeles, CA
- Cancer Biology and Genomics Program, Keck School of Medicine, University of Southern California, Los Angeles, CA
| | - Narine Harutyunyan
- The Vision Center and Saban Research Institute, Children’s Hospital Los Angeles, Los Angeles, CA
| | - Susan Lee
- The Vision Center and Saban Research Institute, Children’s Hospital Los Angeles, Los Angeles, CA
| | - Assaf Beck
- The Vision Center and Saban Research Institute, Children’s Hospital Los Angeles, Los Angeles, CA
| | - Jonathan Kim
- The Vision Center and Saban Research Institute, Children’s Hospital Los Angeles, Los Angeles, CA
- Department of Ophthalmology and Roski Eye Institute, Keck School of Medicine, University of Southern California, Los Angeles, CA
| | - Liya Xu
- The Vision Center and Saban Research Institute, Children’s Hospital Los Angeles, Los Angeles, CA
- Department of Ophthalmology and Roski Eye Institute, Keck School of Medicine, University of Southern California, Los Angeles, CA
| | - Jesse L. Berry
- The Vision Center and Saban Research Institute, Children’s Hospital Los Angeles, Los Angeles, CA
- Department of Ophthalmology and Roski Eye Institute, Keck School of Medicine, University of Southern California, Los Angeles, CA
- Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA
| | - Aaron Nagiel
- The Vision Center and Saban Research Institute, Children’s Hospital Los Angeles, Los Angeles, CA
- Department of Ophthalmology and Roski Eye Institute, Keck School of Medicine, University of Southern California, Los Angeles, CA
| | - C. Patrick Reynolds
- Department of Pediatrics and Cancer Center, Texas Tech University Health Sciences Center, School of Medicine, Lubbock, TX
| | - A. Linn Murphree
- The Vision Center and Saban Research Institute, Children’s Hospital Los Angeles, Los Angeles, CA
- Department of Ophthalmology and Roski Eye Institute, Keck School of Medicine, University of Southern California, Los Angeles, CA
| | - Thomas C. Lee
- The Vision Center and Saban Research Institute, Children’s Hospital Los Angeles, Los Angeles, CA
- Department of Ophthalmology and Roski Eye Institute, Keck School of Medicine, University of Southern California, Los Angeles, CA
| | - Jennifer G. Aparicio
- The Vision Center and Saban Research Institute, Children’s Hospital Los Angeles, Los Angeles, CA
| | - David Cobrinik
- The Vision Center and Saban Research Institute, Children’s Hospital Los Angeles, Los Angeles, CA
- Department of Ophthalmology and Roski Eye Institute, Keck School of Medicine, University of Southern California, Los Angeles, CA
- Department of Biochemistry & Molecular Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA
- Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA
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11
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Fujikawa D, Nakamura T, Yoshioka D, Li Z, Moriizumi H, Taguchi M, Tokai-Nishizumi N, Kozuka-Hata H, Oyama M, Takekawa M. Stress granule formation inhibits stress-induced apoptosis by selectively sequestering executioner caspases. Curr Biol 2023; 33:1967-1981.e8. [PMID: 37119817 DOI: 10.1016/j.cub.2023.04.012] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2021] [Revised: 02/23/2023] [Accepted: 04/06/2023] [Indexed: 05/01/2023]
Abstract
Cytoplasmic stress granules (SGs) are phase-separated membrane-less organelles that form in response to various stress stimuli. SGs are mainly composed of non-canonical stalled 48S preinitiation complexes. In addition, many other proteins also accumulate into SGs, but the list is still incomplete. SG assembly suppresses apoptosis and promotes cell survival under stress. Furthermore, hyperformation of SGs is frequently observed in various human cancers and accelerates tumor development and progression by reducing stress-induced damage of cancer cells. Therefore, they are of clinical importance. However, the precise mechanism underlying SG-mediated inhibition of apoptosis remains ill-defined. Here, using a proximity-labeling proteomic approach, we comprehensively analyzed SG-resident proteins and identified the executioner caspases, caspase-3 and -7, as SG components. We demonstrate that accumulation of caspase-3/7 into SGs is mediated by evolutionarily conserved amino acid residues within their large catalytic domains and inhibits caspase activities and consequent apoptosis induced by various stresses. Expression of an SG-localization-deficient caspase-3 mutant in cells largely counteracted the anti-apoptotic effect of SGs, whereas enforced relocalization of the caspase-3 mutant to SGs restored it. Thus, SG-mediated sequestration of executioner caspases is a mechanism underlying the broad cytoprotective function of SGs. Furthermore, using a mouse xenograft tumor model, we show that this mechanism prevents cancer cells from apoptosis in tumor tissues, thereby promoting cancer progression. Our results reveal the functional crosstalk between SG-mediated cell survival and caspase-mediated cell death signaling pathways and delineate a molecular mechanism that dictates cell-fate decisions under stress and promotes tumorigenesis.
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Affiliation(s)
- Daichi Fujikawa
- Division of Cell Signaling and Molecular Medicine, Institute of Medical Science, The University of Tokyo, 4-6-1, Shirokanedai, Minato-ku, Tokyo 108-8639, Japan; Department of Biological Sciences, Graduate School of Science, The University of Tokyo, 7-3-1, Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Takanori Nakamura
- Division of Cell Signaling and Molecular Medicine, Institute of Medical Science, The University of Tokyo, 4-6-1, Shirokanedai, Minato-ku, Tokyo 108-8639, Japan
| | - Daisuke Yoshioka
- Division of Cell Signaling and Molecular Medicine, Institute of Medical Science, The University of Tokyo, 4-6-1, Shirokanedai, Minato-ku, Tokyo 108-8639, Japan; Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, 5-1-5, Kashiwanoha, Kashiwa 277-8562, Chiba, Japan
| | - Zizheng Li
- Division of Cell Signaling and Molecular Medicine, Institute of Medical Science, The University of Tokyo, 4-6-1, Shirokanedai, Minato-ku, Tokyo 108-8639, Japan; Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, 5-1-5, Kashiwanoha, Kashiwa 277-8562, Chiba, Japan
| | - Hisashi Moriizumi
- Division of Cell Signaling and Molecular Medicine, Institute of Medical Science, The University of Tokyo, 4-6-1, Shirokanedai, Minato-ku, Tokyo 108-8639, Japan; Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, 5-1-5, Kashiwanoha, Kashiwa 277-8562, Chiba, Japan
| | - Mari Taguchi
- Division of Cell Signaling and Molecular Medicine, Institute of Medical Science, The University of Tokyo, 4-6-1, Shirokanedai, Minato-ku, Tokyo 108-8639, Japan; Department of Biological Sciences, Graduate School of Science, The University of Tokyo, 7-3-1, Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Noriko Tokai-Nishizumi
- Division of Cell Signaling and Molecular Medicine, Institute of Medical Science, The University of Tokyo, 4-6-1, Shirokanedai, Minato-ku, Tokyo 108-8639, Japan
| | - Hiroko Kozuka-Hata
- Medical Proteomics Laboratory, Institute of Medical Science, The University of Tokyo, 4-6-1, Shirokanedai, Minato-ku, Tokyo 108-8639, Japan
| | - Masaaki Oyama
- Medical Proteomics Laboratory, Institute of Medical Science, The University of Tokyo, 4-6-1, Shirokanedai, Minato-ku, Tokyo 108-8639, Japan
| | - Mutsuhiro Takekawa
- Division of Cell Signaling and Molecular Medicine, Institute of Medical Science, The University of Tokyo, 4-6-1, Shirokanedai, Minato-ku, Tokyo 108-8639, Japan; Department of Biological Sciences, Graduate School of Science, The University of Tokyo, 7-3-1, Hongo, Bunkyo-ku, Tokyo 113-0033, Japan; Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, 5-1-5, Kashiwanoha, Kashiwa 277-8562, Chiba, Japan; Medical Proteomics Laboratory, Institute of Medical Science, The University of Tokyo, 4-6-1, Shirokanedai, Minato-ku, Tokyo 108-8639, Japan.
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12
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Knowles AA, Campbell SG, Cross NA, Stafford P. Dysregulation of Stress-Induced Translational Control by Porphyromonas gingivalis in Host Cells. Microorganisms 2023; 11:microorganisms11030606. [PMID: 36985180 PMCID: PMC10057856 DOI: 10.3390/microorganisms11030606] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Revised: 02/15/2023] [Accepted: 02/21/2023] [Indexed: 03/04/2023] Open
Abstract
Porphyromonas gingivalis contributes to the chronic oral disease periodontitis, triggering the activation of host inflammatory responses, inducing cellular stresses such as oxidation. During stress, host cells can activate the Integrated Stress Response (ISR), a pathway which determines cellular fate, by either downregulating protein synthesis and initiating a stress–response gene expression program, or by initiating programmed cell death. Recent studies have implicated the ISR within both host antimicrobial defenses and the pathomechanism of certain microbes. In this study, using a combination of immunofluorescence confocal microscopy and immunoblotting, the molecular mechanisms by which P. gingivalis infection alters translation attenuation during oxidative stress-induced activation of the ISR in oral epithelial cells were investigated. P. gingivalis infection alone did not result in ISR activation. In contrast, infection coupled with stress caused differential stress granule formation and composition. Infection heightened stress-induced translational repression independently of core ISR mediators. Heightened translational repression during stress was observed with both P. gingivalis–conditioned media and outer membrane vesicles, implicating a secretory factor in this exacerbated translational repression. The effects of gingipain inhibitors and gingipain-deficient P. gingivalis mutants confirmed these pathogen-specific proteases as the effector of exacerbated translational repression. Gingipains are known to degrade the mammalian target of rapamycin (mTOR) and the findings of this study implicate the gingipain-mTOR axis as the effector of host translational dysregulation during stress.
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13
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Nabariya DK, Heinz A, Derksen S, Krauß S. Intracellular and intercellular transport of RNA organelles in CXG repeat disorders: The strength of weak ties. Front Mol Biosci 2022; 9:1000932. [PMID: 36589236 PMCID: PMC9800848 DOI: 10.3389/fmolb.2022.1000932] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2022] [Accepted: 12/06/2022] [Indexed: 12/23/2022] Open
Abstract
RNA is a vital biomolecule, the function of which is tightly spatiotemporally regulated. RNA organelles are biological structures that either membrane-less or surrounded by membrane. They are produced by the all the cells and indulge in vital cellular mechanisms. They include the intracellular RNA granules and the extracellular exosomes. RNA granules play an essential role in intracellular regulation of RNA localization, stability and translation. Aberrant regulation of RNA is connected to disease development. For example, in microsatellite diseases such as CXG repeat expansion disorders, the mutant CXG repeat RNA's localization and function are affected. RNA is not only transported intracellularly but can also be transported between cells via exosomes. The loading of the exosomes is regulated by RNA-protein complexes, and recent studies show that cytosolic RNA granules and exosomes share common content. Intracellular RNA granules and exosome loading may therefore be related. Exosomes can also transfer pathogenic molecules of CXG diseases from cell to cell, thereby driving disease progression. Both intracellular RNA granules and extracellular RNA vesicles may serve as a source for diagnostic and treatment strategies. In therapeutic approaches, pharmaceutical agents may be loaded into exosomes which then transport them to the desired cells/tissues. This is a promising target specific treatment strategy with few side effects. With respect to diagnostics, disease-specific content of exosomes, e.g., RNA-signatures, can serve as attractive biomarker of central nervous system diseases detecting early physiological disturbances, even before symptoms of neurodegeneration appear and irreparable damage to the nervous system occurs. In this review, we summarize the known function of cytoplasmic RNA granules and extracellular vesicles, as well as their role and dysfunction in CXG repeat expansion disorders. We also provide a summary of established protocols for the isolation and characterization of both cytoplasmic and extracellular RNA organelles.
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Affiliation(s)
| | | | | | - Sybille Krauß
- Human Biology/Neurobiology, Institute of Biology, Faculty IV, School of Science and Technology, University of Siegen, Siegen, Germany
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14
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Actin dynamics in protein homeostasis. Biosci Rep 2022; 42:231720. [PMID: 36043949 PMCID: PMC9469105 DOI: 10.1042/bsr20210848] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2022] [Revised: 08/22/2022] [Accepted: 08/31/2022] [Indexed: 11/17/2022] Open
Abstract
Cell homeostasis is maintained in all organisms by the constant adjustment of cell constituents and organisation to account for environmental context. Fine-tuning of the optimal balance of proteins for the conditions, or protein homeostasis, is critical to maintaining cell homeostasis. Actin, a major constituent of the cytoskeleton, forms many different structures which are acutely sensitive to the cell environment. Furthermore, actin structures interact with and are critically important for the function and regulation of multiple factors involved with mRNA and protein production and degradation, and protein regulation. Altogether, actin is a key, if often overlooked, regulator of protein homeostasis across eukaryotes. In this review, we highlight these roles and how they are altered following cell stress, from mRNA transcription to protein degradation.
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15
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van Leeuwen W, VanInsberghe M, Battich N, Salmén F, van Oudenaarden A, Rabouille C. Identification of the stress granule transcriptome via RNA-editing in single cells and in vivo. CELL REPORTS METHODS 2022; 2:100235. [PMID: 35784648 PMCID: PMC9243631 DOI: 10.1016/j.crmeth.2022.100235] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/07/2021] [Revised: 01/24/2022] [Accepted: 05/20/2022] [Indexed: 11/09/2022]
Abstract
Stress granules are phase-separated assemblies formed around RNAs. So far, the techniques available to identify these RNAs are not suitable for single cells and small tissues displaying cell heterogeneity. Here, we used TRIBE (target of RNA-binding proteins identified by editing) to profile stress granule RNAs. We used an RNA-binding protein (FMR1) fused to the catalytic domain of an RNA-editing enzyme (ADAR), which coalesces into stress granules upon oxidative stress. RNAs colocalized with this fusion are edited, producing mutations that are detectable by VASA sequencing. Using single-molecule FISH, we validated that this purification-free method can reliably identify stress granule RNAs in bulk and single S2 cells and in Drosophila neurons. Similar to mammalian cells, we find that stress granule mRNAs encode ATP binding, cell cycle, and transcription factors. This method opens the possibility to identify stress granule RNAs and other RNA-based assemblies in other single cells and tissues.
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Affiliation(s)
| | | | - Nico Battich
- Hubrecht Institute of the KNAW & UMC Utrecht, Utrecht, the Netherlands
| | - Fredrik Salmén
- Hubrecht Institute of the KNAW & UMC Utrecht, Utrecht, the Netherlands
| | | | - Catherine Rabouille
- Hubrecht Institute of the KNAW & UMC Utrecht, Utrecht, the Netherlands
- Section Cell Biology, Center for Molecular Medicine, University Medical Center Utrecht, Utrecht, the Netherlands
- Department of Biomedical Sciences in Cells and Systems, UMC Groningen, Groningen, the Netherlands
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16
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Zhou C. The Molecular and Functional Interaction Between Membrane-Bound Organelles and Membrane-Less Condensates. Front Cell Dev Biol 2022; 10:896305. [PMID: 35547815 PMCID: PMC9081682 DOI: 10.3389/fcell.2022.896305] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2022] [Accepted: 04/07/2022] [Indexed: 12/15/2022] Open
Abstract
A major recent advance in cell biology is the mechanistic and kinetic understanding of biogenesis of many membrane-less condensates. As membrane-less condensates and membrane-bound organelles are two major approaches used by the eukaryotic cells to organize cellular contents, it is not surprising that these membrane-less condensates interact with the membrane-bound organelles and are dynamically regulated by the cellular signaling, metabolic states, and proteostasis network. In this review, I will discuss recent progress in the biogenesis of membrane-less condensates and their connections with well-studied membrane-bound organelles. Future work will reveal the molecular and functional connectome among different condensates and membrane-bound organelles.
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Affiliation(s)
- Chuankai Zhou
- Buck Institute for Research on Aging, Novato, CA, United States.,Leonard Davis School of Gerontology, University of Southern California, Los Angeles, CA, United States
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17
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Shah SH, Schiapparelli LM, Ma Y, Yokota S, Atkins M, Xia X, Cameron EG, Huang T, Saturday S, Sun CB, Knasel C, Blackshaw S, Yates Iii JR, Cline HT, Goldberg JL. Quantitative transportomics identifies Kif5a as a major regulator of neurodegeneration. eLife 2022; 11:68148. [PMID: 35259089 PMCID: PMC8947766 DOI: 10.7554/elife.68148] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2021] [Accepted: 03/07/2022] [Indexed: 11/29/2022] Open
Abstract
Many neurons in the adult central nervous system, including retinal ganglion cells (RGCs), degenerate and die after injury. Early axon protein and organelle trafficking failure is a key component in many neurodegenerative disorders yet changes to axoplasmic transport in disease models have not been quantified. We analyzed early changes in the protein ‘transportome’ from RGC somas to their axons after optic nerve injury and identified transport failure of an anterograde motor protein Kif5a early in RGC degeneration. We demonstrated that manipulating Kif5a expression affects anterograde mitochondrial trafficking in RGCs and characterized axon transport in Kif5a knockout mice to identify proteins whose axon localization was Kif5a-dependent. Finally, we found that knockout of Kif5a in RGCs resulted in progressive RGC degeneration in the absence of injury. Together with expression data localizing Kif5a to human RGCs, these data identify Kif5a transport failure as a cause of RGC neurodegeneration and point to a mechanism for future therapeutics.
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Affiliation(s)
- Sahil H Shah
- Byers Eye Institute and Spencer Center for Vision Research, Stanford University, Palo Alto, United States
| | | | - Yuanhui Ma
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, United States
| | - Satoshi Yokota
- Byers Eye Institute and Spencer Center for Vision Research, Stanford University, Palo Alto, United States
| | - Melissa Atkins
- Byers Eye Institute and Spencer Center for Vision Research, Stanford University, Palo Alto, United States
| | - Xin Xia
- Byers Eye Institute and Spencer Center for Vision Research, Stanford University, Palo Alto, United States
| | - Evan G Cameron
- Byers Eye Institute and Spencer Center for Vision Research, Stanford University, Palo Alto, United States
| | - Thanh Huang
- Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, United States
| | - Sarah Saturday
- Neuroscience Department, The Scripps Research Institute, La Jolla, United States
| | - Catalin B Sun
- Byers Eye Institute and Spencer Center for Vision Research, Stanford University, Palo Alto, United States
| | - Cara Knasel
- Byers Eye Institute and Spencer Center for Vision Research, Stanford University, Palo Alto, United States
| | - Seth Blackshaw
- Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, United States
| | - John R Yates Iii
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, United States
| | - Hollis T Cline
- Neuroscience Department, The Scripps Research Institute, La Jolla, United States
| | - Jeffrey L Goldberg
- Byers Eye Institute and Spencer Center for Vision Research, Stanford University, Palo Alto, United States
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18
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Sidibé H, Vande Velde C. Collective Learnings of Studies of Stress Granule Assembly and Composition. METHODS IN MOLECULAR BIOLOGY (CLIFTON, N.J.) 2022; 2428:199-228. [PMID: 35171482 DOI: 10.1007/978-1-0716-1975-9_13] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Stress granules have gained considerable exposure and interest in recent years. These micron-sized entities, composed of RNA and protein, form following a stress exposure and have been linked to several pathologies. Understanding stress granule function is paramount but has been arduous due to the membraneless nature of these organelles. Several new methodologies have recently been developed to catalogue the protein and RNA composition of stress granules. Collectively, this work has provided important insights to potential stress granule functions as well as molecular mechanisms for their assembly and disassembly. This chapter reviews the latest advancements in the understanding of stress granule dynamics and discusses the various protocols developed to study their composition.
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Affiliation(s)
- Hadjara Sidibé
- Department of Neurosciences, Université de Montréal and CHUM Research Center, Montreal, QC, Canada
| | - Christine Vande Velde
- Department of Neurosciences, Université de Montréal and CHUM Research Center, Montreal, QC, Canada.
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19
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Böddeker TJ, Rosowski KA, Berchtold D, Emmanouilidis L, Han Y, Allain FHT, Style RW, Pelkmans L, Dufresne ER. Non-specific adhesive forces between filaments and membraneless organelles. NATURE PHYSICS 2022; 18:571-578. [PMID: 35582428 PMCID: PMC9106579 DOI: 10.1038/s41567-022-01537-8] [Citation(s) in RCA: 37] [Impact Index Per Article: 18.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/22/2021] [Accepted: 02/04/2022] [Indexed: 05/07/2023]
Abstract
Many membraneless organelles are liquid-like domains that form inside the active, viscoelastic environment of living cells through phase separation. To investigate the potential coupling of phase separation with the cytoskeleton, we quantify the structural correlations of membraneless organelles (stress granules) and cytoskeletal filaments (microtubules) in a human-derived epithelial cell line. We find that microtubule networks are substantially denser in the vicinity of stress granules. When microtubules are depolymerized, the sub-units localize near the surface of the stress granules. We interpret these data using a thermodynamic model of partitioning of particles to the surface and bulk of the droplets. In this framework, our data are consistent with a weak (≲k B T) affinity of the microtubule sub-units for stress granule interfaces. As microtubules polymerize, their interfacial affinity increases, providing sufficient adhesion to deform droplets and/or the network. Our work suggests that proteins and other objects in the cell have a non-specific affinity for droplet interfaces that increases with the contact area and becomes most apparent when they have no preference for the interior of a droplet over the rest of the cytoplasm. We validate this basic physical phenomenon in vitro through the interaction of a simple protein-RNA condensate with microtubules.
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Affiliation(s)
| | | | - Doris Berchtold
- Department of Molecular Life Sciences, University of Zurich, Zurich, Switzerland
| | | | - Yaning Han
- Institute of Biochemistry, ETH Zurich, Zurich, Switzerland
| | | | | | - Lucas Pelkmans
- Department of Molecular Life Sciences, University of Zurich, Zurich, Switzerland
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20
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Regulation of spatially restricted gene expression: linking RNA localization and phase separation. Biochem Soc Trans 2021; 49:2591-2600. [PMID: 34821361 DOI: 10.1042/bst20210320] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2021] [Revised: 11/08/2021] [Accepted: 11/09/2021] [Indexed: 11/17/2022]
Abstract
Subcellular restriction of gene expression is crucial to the functioning of a wide variety of cell types. The cellular machinery driving spatially restricted gene expression has been studied for many years, but recent advances have highlighted novel mechanisms by which cells can generate subcellular microenvironments with specialized gene expression profiles. Particularly intriguing are recent findings that phase separation plays a role in certain RNA localization pathways. The burgeoning field of phase separation has revolutionized how we view cellular compartmentalization, revealing that, in addition to membrane-bound organelles, phase-separated cytoplasmic microenvironments - termed biomolecular condensates - are compositionally and functionally distinct from the surrounding cytoplasm, without the need for a lipid membrane. The coupling of phase separation and RNA localization allows for precise subcellular targeting, robust translational repression and dynamic recruitment of accessory proteins. Despite the growing interest in the intersection between RNA localization and phase separation, it remains to be seen how exactly components of the localization machinery, particularly motor proteins, are able to associate with these biomolecular condensates. Further studies of the formation, function, and transport of biomolecular condensates promise to provide a new mechanistic understanding of how cells restrict gene expression at a subcellular level.
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21
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Hyperosmotic Stress Induces a Specific Pattern for Stress Granule Formation in Human-Induced Pluripotent Stem Cells. Stem Cells Int 2021; 2021:8274936. [PMID: 34697543 PMCID: PMC8538399 DOI: 10.1155/2021/8274936] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2021] [Revised: 09/13/2021] [Accepted: 09/16/2021] [Indexed: 11/18/2022] Open
Abstract
Stress granules (SGs) are assemblies of selective messenger RNAs (mRNAs), translation factors, and RNA-binding proteins in small untranslated messenger ribonucleoprotein (mRNP) complexes in the cytoplasm. Evidence indicates that different types of cells have shown different mechanisms to respond to stress and the formation of SGs. In the present work, we investigated how human-induced pluripotent stem cells (hiPSCs/IMR90-1) overcome hyperosmotic stress compared to a cell line that does not harbor pluripotent characteristics (SH-SY5Y cell line). Gradient concentrations of NaCl showed a different pattern of SG formation between hiPSCs/IMR90-1 and the nonpluripotent cell line SH-SY5Y. Other pluripotent stem cell lines (hiPSCs/CRTD5 and hESCs/H9 (human embryonic stem cell line)) as well as nonpluripotent cell lines (BHK-21 and MCF-7) were used to confirm this phenomenon. Moreover, the formation of hyperosmotic SGs in hiPSCs/IMR90-1 was independent of eIF2α phosphorylation and was associated with low apoptosis levels. In addition, a comprehensive proteomics analysis was performed to identify proteins involved in regulating this specific pattern of hyperosmotic SG formation in hiPSCs/IMR90-1. We found possible implications of microtubule organization on the response to hyperosmotic stress in hiPSCs/IMR90-1. We have also unveiled a reduced expression of tubulin that may protect cells against hyperosmolarity stress while inhibiting SG formation without affecting stem cell self-renewal and pluripotency. Our observations may provide a possible cellular mechanism to better understand SG dynamics in pluripotent stem cells.
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22
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Chatterjee D, Chakrabarti O. Role of stress granules in modulating senescence and promoting cancer progression: Special emphasis on glioma. Int J Cancer 2021; 150:551-561. [PMID: 34460104 DOI: 10.1002/ijc.33787] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2021] [Revised: 07/22/2021] [Accepted: 08/24/2021] [Indexed: 12/12/2022]
Abstract
Stress granules (SGs) contain mRNAs and proteins stalled in translation during stress; these are increasingly being implicated in diseases, including neurological disorders and cancer. The dysregulated assembly, persistence, disassembly and clearance of SGs contribute to the process of senescence. Senescence has long been a mysterious player in cellular physiology and associated diseases. The systemic process of aging has been pivotal in the development of various neurological disorders like age-related neuropathy, Alzheimer's disease and Parkinson's disease. Glioma is a cancer of neurological origin with a very poor prognosis and high rate of recurrence, SGs have only recently been implicated in its pathogenesis. Senescence has long been established to play an antitumorigenic role, however, relatively less studied is its protumorigenic importance. Here, we have evaluated the existing literature to assess the crosstalk of the two biological phenomena of senescence and SG formation in the context of tumorigenesis. In this review, we have attempted to analyze the contribution of senescence in regulating diverse cellular processes, like, senescence associated secretory phenotype (SASP), microtubular reorganization, telomeric alteration, autophagic clearance and how intricately these phenomena are tied with the formation of SGs. Finally, we propose that interplay between senescence, its contributing factors and the genesis of SGs can drive tumorigenicity of gliomas, which can potentially be utilized for therapeutic intervention.
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Affiliation(s)
- Debmita Chatterjee
- Biophysics & Structural Genomics Division, Saha Institute of Nuclear Physics, Kolkata, India
| | - Oishee Chakrabarti
- Biophysics & Structural Genomics Division, Saha Institute of Nuclear Physics, Kolkata, India.,Homi Bhabha National Institute, Mumbai, Maharashtra, India
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23
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Wang L, Yang W, Li B, Yuan S, Wang F. Response to stress in biological disorders: Implications of stress granule assembly and function. Cell Prolif 2021; 54:e13086. [PMID: 34170048 PMCID: PMC8349659 DOI: 10.1111/cpr.13086] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2021] [Revised: 06/06/2021] [Accepted: 06/07/2021] [Indexed: 12/17/2022] Open
Abstract
It is indispensable for cells to adapt and respond to environmental stresses, in order for organisms to survive. Stress granules (SGs) are condensed membrane‐less organelles dynamically formed in the cytoplasm of eukaryotes cells to cope with diverse intracellular or extracellular stress factors, with features of liquid‐liquid phase separation. They are composed of multiple constituents, including translationally stalled mRNAs, translation initiation factors, RNA‐binding proteins and also non‐RNA‐binding proteins. SG formation is triggered by stress stimuli, viral infection and signal transduction, while aberrant assembly of SGs may contribute to tissue degenerative diseases. Recently, a growing body of evidence has emerged on SG response mechanisms for cells facing high temperatures, oxidative stress and osmotic stress. In this review, we aim to summarize factors affecting SGs assembly, present the impact of SGs on germ cell development and other biological processes. We particularly emphasize the significance of recently reported RNA modifications in SG stress responses. In parallel, we also review all current perspectives on the roles of SGs in male germ cells, with a particular focus on the dynamics of SG assembly.
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Affiliation(s)
- Lingjuan Wang
- Institute Reproductive Health, Tongji Medical College, Huazhong University of Science and Technology, Hubei, China
| | - Weina Yang
- Institute Reproductive Health, Tongji Medical College, Huazhong University of Science and Technology, Hubei, China
| | - Bin Li
- Tianjin Medical University General Hospital, Tianjin, China.,State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China
| | - Shuiqiao Yuan
- Institute Reproductive Health, Tongji Medical College, Huazhong University of Science and Technology, Hubei, China
| | - Fengli Wang
- Institute Reproductive Health, Tongji Medical College, Huazhong University of Science and Technology, Hubei, China
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24
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Asadi MR, Sadat Moslehian M, Sabaie H, Jalaiei A, Ghafouri-Fard S, Taheri M, Rezazadeh M. Stress Granules and Neurodegenerative Disorders: A Scoping Review. Front Aging Neurosci 2021; 13:650740. [PMID: 34248597 PMCID: PMC8261063 DOI: 10.3389/fnagi.2021.650740] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2021] [Accepted: 05/17/2021] [Indexed: 12/13/2022] Open
Abstract
Cytoplasmic ribonucleoproteins called stress granules (SGs) are considered as one of the main cellular solutions against stress. Their temporary presence ends with stress relief. Any factor such as chronic stress or mutations in the structure of the components of SGs that lead to their permanent presence can affect their interactions with pathological aggregations and increase the degenerative effects. SGs involved in RNA mechanisms are important factors in the pathophysiology of neurodegenerative disorders such as amyotrophic lateral sclerosis (ALS), frontotemporal degeneration (FTD), and Alzheimer's diseases (AD). Although many studies have been performed in the field of SGs and neurodegenerative disorders, so far, no systematic studies have been executed in this field. The purpose of this study is to provide a comprehensive perspective of all studies about the role of SGs in the pathogenesis of neurodegenerative disorders with a focus on the protein ingredients of these granules. This scoping review is based on a six-stage methodology structure and the PRISMA guideline. A systematic search of seven databases for qualified articles was conducted until December 2020. Publications were screened independently by two reviewers and quantitative and qualitative analysis was performed on the extracted data. Bioinformatics analysis was used to plot the network and predict interprotein interactions. In addition, GO analysis was performed. A total of 48 articles were identified that comply the inclusion criteria. Most studies on neurodegenerative diseases have been conducted on ALS, AD, and FTD using human post mortem tissues. Human derived cell line studies have been used only in ALS. A total 29 genes of protein components of SGs have been studied, the most important of which are TDP-43, TIA-1, PABP-1. Bioinformatics studies have predicted 15 proteins to interact with the protein components of SGs, which may be the constituents of SGs. Understanding the interactions between SGs and pathological aggregations in neurodegenerative diseases can provide new targets for treatment of these disorders.
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Affiliation(s)
- Mohammad Reza Asadi
- Molecular Medicine Research Center, Tabriz University of Medical Sciences, Tabriz, Iran.,Department of Medical Genetics, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Marziyeh Sadat Moslehian
- Department of Medical Genetics, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Hani Sabaie
- Department of Medical Genetics, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Abbas Jalaiei
- Department of Medical Genetics, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Soudeh Ghafouri-Fard
- Department of Medical Genetics, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Mohammad Taheri
- Skull Base Research Center, Loghman Hakim Hospital, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Maryam Rezazadeh
- Molecular Medicine Research Center, Tabriz University of Medical Sciences, Tabriz, Iran.,Department of Medical Genetics, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran
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25
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Knowles A, Campbell S, Cross N, Stafford P. Bacterial Manipulation of the Integrated Stress Response: A New Perspective on Infection. Front Microbiol 2021; 12:645161. [PMID: 33967983 PMCID: PMC8100032 DOI: 10.3389/fmicb.2021.645161] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Accepted: 02/16/2021] [Indexed: 11/13/2022] Open
Abstract
Host immune activation forms a vital line of defence against bacterial pathogenicity. However, just as hosts have evolved immune responses, bacteria have developed means to escape, hijack and subvert these responses to promote survival. In recent years, a highly conserved group of signalling cascades within the host, collectively termed the integrated stress response (ISR), have become increasingly implicated in immune activation during bacterial infection. Activation of the ISR leads to a complex web of cellular reprogramming, which ultimately results in the paradoxical outcomes of either cellular homeostasis or cell death. Therefore, any pathogen with means to manipulate this pathway could induce a range of cellular outcomes and benefit from favourable conditions for long-term survival and replication. This review aims to outline what is currently known about bacterial manipulation of the ISR and present key hypotheses highlighting areas for future research.
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Affiliation(s)
- Alex Knowles
- Biomolecular Sciences Research Centre, Department of Biosciences and Chemistry, Faculty of Health and Wellbeing, Sheffield Hallam University, Sheffield, United Kingdom
| | - Susan Campbell
- Biomolecular Sciences Research Centre, Department of Biosciences and Chemistry, Faculty of Health and Wellbeing, Sheffield Hallam University, Sheffield, United Kingdom
| | - Neil Cross
- Biomolecular Sciences Research Centre, Department of Biosciences and Chemistry, Faculty of Health and Wellbeing, Sheffield Hallam University, Sheffield, United Kingdom
| | - Prachi Stafford
- Biomolecular Sciences Research Centre, Department of Biosciences and Chemistry, Faculty of Health and Wellbeing, Sheffield Hallam University, Sheffield, United Kingdom
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26
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Choi MR, Jin YB, Kim HN, Chai YG, Im CN, Lee SR, Kim DJ. Gene expression in the striatum of cynomolgus monkeys after chronic administration of cocaine and heroin. Basic Clin Pharmacol Toxicol 2021; 128:686-698. [PMID: 33404192 DOI: 10.1111/bcpt.13554] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2020] [Revised: 12/26/2020] [Accepted: 01/01/2021] [Indexed: 01/16/2023]
Abstract
Cocaine and heroin cause impairment of neural plasticity in the brain including striatum. This study aimed to identify genes differentially expressed in the striatum of cynomolgus monkeys in response to cocaine and heroin. After chronic administration of cocaine and heroin in the monkeys, we performed large-scale transcriptome profiling in the striatum using RNA-Seq technology and analysed functional annotation. We found that 547 and 1238 transcripts were more than 1.5-fold up- or down-regulated in cocaine- and heroin-treated groups, respectively, compared to the control group, and 3432 transcripts exhibited differential expression between cocaine- and heroin-treated groups. Functional annotation analysis indicated that genes associated with nervous system development (NAGLU, MOBP and TTL7) and stress granule disassembly (KIF5B and KLC1) were differentially expressed in the cocaine-treated group compared to the control group, whereas gene associated with neuron apoptotic process (ERBB3) was differentially expressed in the heroin-treated group. In addition, IPA network analysis indicated that genes (TRAF6 and TRAF3IP2) associated with inflammation were increased by the chronic administration of cocaine and heroin. These results provide insight into the correlated molecular mechanisms as well as the upregulation and down-regulation of genes in the striatum after chronic exposure to cocaine and heroin.
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Affiliation(s)
- Mi Ran Choi
- Department of Psychiatry, Seoul St. Mary's Hospital, The Catholic University of Korea College of Medicine, Seoul, Republic of Korea
| | - Yeung-Bae Jin
- Department of Laboratory Animal Medicine, College of Veterinary Medicine, Gyeongsang National University, Jinju, Republic of Korea
| | - Han-Na Kim
- National Primate Research Center (NPRC), Korea Research Institute of Bioscience and Biotechnology (KRIBB), Cheongju, Republic of Korea
| | - Young Gyu Chai
- Department of Molecular and Life Sciences, Hanyang University, Ansan, Republic of Korea
| | - Chang-Nim Im
- Department of Psychiatry, Seoul St. Mary's Hospital, The Catholic University of Korea College of Medicine, Seoul, Republic of Korea
| | - Sang-Rae Lee
- National Primate Research Center (NPRC), Korea Research Institute of Bioscience and Biotechnology (KRIBB), Cheongju, Republic of Korea.,Department of Functional Genomics, University of Science and Technology, Daejeon, Republic of Korea
| | - Dai-Jin Kim
- Department of Psychiatry, Seoul St. Mary's Hospital, The Catholic University of Korea College of Medicine, Seoul, Republic of Korea
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27
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Koppers M, Özkan N, Farías GG. Complex Interactions Between Membrane-Bound Organelles, Biomolecular Condensates and the Cytoskeleton. Front Cell Dev Biol 2020; 8:618733. [PMID: 33409284 PMCID: PMC7779554 DOI: 10.3389/fcell.2020.618733] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2020] [Accepted: 12/03/2020] [Indexed: 12/13/2022] Open
Abstract
Membrane-bound and membraneless organelles/biomolecular condensates ensure compartmentalization into functionally distinct units enabling proper organization of cellular processes. Membrane-bound organelles form dynamic contacts with each other to enable the exchange of molecules and to regulate organelle division and positioning in coordination with the cytoskeleton. Crosstalk between the cytoskeleton and dynamic membrane-bound organelles has more recently also been found to regulate cytoskeletal organization. Interestingly, recent work has revealed that, in addition, the cytoskeleton and membrane-bound organelles interact with cytoplasmic biomolecular condensates. The extent and relevance of these complex interactions are just beginning to emerge but may be important for cytoskeletal organization and organelle transport and remodeling. In this review, we highlight these emerging functions and emphasize the complex interplay of the cytoskeleton with these organelles. The crosstalk between membrane-bound organelles, biomolecular condensates and the cytoskeleton in highly polarized cells such as neurons could play essential roles in neuronal development, function and maintenance.
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Affiliation(s)
| | | | - Ginny G. Farías
- Cell Biology, Neurobiology and Biophysics, Department of Biology, Faculty of Science, Utrecht University, Utrecht, Netherlands
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28
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Wang F, Li J, Fan S, Jin Z, Huang C. Targeting stress granules: A novel therapeutic strategy for human diseases. Pharmacol Res 2020; 161:105143. [PMID: 32814168 PMCID: PMC7428673 DOI: 10.1016/j.phrs.2020.105143] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/23/2020] [Revised: 08/07/2020] [Accepted: 08/10/2020] [Indexed: 12/16/2022]
Abstract
Stress granules (SGs) are assemblies of mRNA and proteins that form from mRNAs stalled in translation initiation in response to stress. Chronic stress might even induce formation of cytotoxic pathological SGs. SGs participate in various biological functions including response to apoptosis, inflammation, immune modulation, and signalling pathways; moreover, SGs are involved in pathogenesis of neurodegenerative diseases, viral infection, aging, cancers and many other diseases. Emerging evidence has shown that small molecules can affect SG dynamics, including assembly, disassembly, maintenance and clearance. Thus, targeting SGs is a potential therapeutic strategy for the treatment of human diseases and the promotion of health. The established methods for detecting SGs provided ready tools for large-scale screening of agents that alter the dynamics of SGs. Here, we describe the effects of small molecules on SG assembly, disassembly, and their roles in the disease. Moreover, we provide perspective for the possible application of small molecules targeting SGs in the treatment of human diseases.
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Affiliation(s)
- Fei Wang
- School of Pharmacy, Shanghai University of Traditional Chinese Medicine, 1200 Cailun Road, Shanghai, 201203, China
| | - Juan Li
- College of Chemistry and Life Sciences, Zhejiang Normal University, 688 Yingbin Road, Jinhua, Zhejiang, 321004, China
| | - Shengjie Fan
- School of Pharmacy, Shanghai University of Traditional Chinese Medicine, 1200 Cailun Road, Shanghai, 201203, China
| | - Zhigang Jin
- College of Chemistry and Life Sciences, Zhejiang Normal University, 688 Yingbin Road, Jinhua, Zhejiang, 321004, China.
| | - Cheng Huang
- School of Pharmacy, Shanghai University of Traditional Chinese Medicine, 1200 Cailun Road, Shanghai, 201203, China.
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29
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Hofmann S, Kedersha N, Anderson P, Ivanov P. Molecular mechanisms of stress granule assembly and disassembly. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2020; 1868:118876. [PMID: 33007331 DOI: 10.1016/j.bbamcr.2020.118876] [Citation(s) in RCA: 162] [Impact Index Per Article: 40.5] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 07/20/2020] [Revised: 09/18/2020] [Accepted: 09/19/2020] [Indexed: 12/11/2022]
Abstract
Stress granules (SGs) are membrane-less ribonucleoprotein (RNP)-based cellular compartments that form in the cytoplasm of a cell upon exposure to various environmental stressors. SGs contain a large set of proteins, as well as mRNAs that have been stalled in translation as a result of stress-induced polysome disassembly. Despite the fact that SGs have been extensively studied for many years, their function is still not clear. They presumably help the cell to cope with the encountered stress, and facilitate the recovery process after stress removal upon which SGs disassemble. Aberrant formation of SGs and impaired SG disassembly majorly contribute to various pathological phenomena in cancer, viral infections, and neurodegeneration. The assembly of SGs is largely driven by liquid-liquid phase separation (LLPS), however, the molecular mechanisms behind that are not fully understood. Recent studies have proposed a novel mechanism for SG formation that involves the interplay of a large interaction network of mRNAs and proteins. Here, we review this novel concept of SG assembly, and discuss the current insights into SG disassembly.
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Affiliation(s)
- Sarah Hofmann
- Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Nancy Kedersha
- Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Paul Anderson
- Brigham and Women's Hospital, Harvard Medical School, Harvard Initiative for RNA Medicine, Boston, MA 02115, USA
| | - Pavel Ivanov
- Brigham and Women's Hospital, Harvard Medical School, Harvard Initiative for RNA Medicine, Boston, MA 02115, USA.
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30
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Cao X, Jin X, Liu B. The involvement of stress granules in aging and aging-associated diseases. Aging Cell 2020; 19:e13136. [PMID: 32170904 PMCID: PMC7189987 DOI: 10.1111/acel.13136] [Citation(s) in RCA: 52] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2019] [Revised: 02/14/2020] [Accepted: 02/20/2020] [Indexed: 12/12/2022] Open
Abstract
Stress granules (SGs) are nonmembrane assemblies formed in cells in response to stress conditions. SGs mainly contain untranslated mRNA and a variety of proteins. RNAs and scaffold proteins with intrinsically disordered regions or RNA-binding domains are essential for the assembly of SGs, and multivalent macromolecular interactions among these components are thought to be the driving forces for SG assembly. The SG assembly process includes regulation through post-translational modification and involvement of the cytoskeletal system. During aging, many intracellular bioprocesses become disrupted by factors such as cellular environmental changes, mitochondrial dysfunction, and decline in the protein quality control system. Such changes could lead to the formation of aberrant SGs, as well as alterations in their maintenance, disassembly, and clearance. These aberrant SGs might in turn promote aging and aging-associated diseases. In this paper, we first review the latest progress on the molecular mechanisms underlying SG assembly and SG functioning under stress conditions. Then, we provide a detailed discussion of the relevance of SGs to aging and aging-associated diseases.
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Affiliation(s)
- Xiuling Cao
- State Key Laboratory of Subtropical Silviculture School of Forestry and Biotechnology Zhejiang A&F University Hangzhou China
| | - Xuejiao Jin
- State Key Laboratory of Subtropical Silviculture School of Forestry and Biotechnology Zhejiang A&F University Hangzhou China
| | - Beidong Liu
- State Key Laboratory of Subtropical Silviculture School of Forestry and Biotechnology Zhejiang A&F University Hangzhou China
- Department of Chemistry and Molecular Biology University of Gothenburg Goteborg Sweden
- Center for Large‐scale Cell‐based Screening Faculty of Science University of Gothenburg Goteborg Sweden
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31
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Franchini DM, Lanvin O, Tosolini M, Patras de Campaigno E, Cammas A, Péricart S, Scarlata CM, Lebras M, Rossi C, Ligat L, Pont F, Arimondo PB, Laurent C, Ayyoub M, Despas F, Lapeyre-Mestre M, Millevoi S, Fournié JJ. Microtubule-Driven Stress Granule Dynamics Regulate Inhibitory Immune Checkpoint Expression in T Cells. Cell Rep 2020; 26:94-107.e7. [PMID: 30605689 DOI: 10.1016/j.celrep.2018.12.014] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2018] [Revised: 11/02/2018] [Accepted: 12/03/2018] [Indexed: 12/31/2022] Open
Abstract
Despite the clinical success of blocking inhibitory immune checkpoint receptors such as programmed cell death-1 (PD-1) in cancer, the mechanisms controlling the expression of these receptors have not been fully elucidated. Here, we identify a post-transcriptional mechanism regulating PD-1 expression in T cells. Upon activation, the PDCD1 mRNA and ribonucleoprotein complexes coalesce into stress granules that require microtubules and the kinesin 1 molecular motor to proceed to translation. Hence, PD-1 expression is highly sensitive to microtubule or stress granule inhibitors targeting this pathway. Evidence from healthy donors and cancer patients reveals a common regulation for the translation of CTLA4, LAG3, TIM3, TIGIT, and BTLA but not of the stimulatory co-receptors OX40, GITR, and 4-1BB mRNAs. In patients, disproportionality analysis of immune-related adverse events for currently used microtubule drugs unveils a significantly higher risk of autoimmunity. Our findings reveal a fundamental mechanism of immunoregulation with great importance in cancer immunotherapy.
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Affiliation(s)
- Don-Marc Franchini
- Cancer Research Centre of Toulouse, INSERM UMR 1037, 31037 Toulouse, France; Université Toulouse III Paul Sabatier, 31330 Toulouse, France; ERL 5294, CNRS, 31037 Toulouse, France; Institut Universitaire du Cancer de Toulouse-Oncopole, 31100 Toulouse, France; Laboratoire d'Excellence "TOUCAN," Toulouse, France; Programme Hospitalo-Universitaire en Cancérologie CAPTOR, 31059 Toulouse, France; Institut Carnot Lymphome CALYM, 69495 Pierre-Benite, France.
| | - Olivia Lanvin
- Cancer Research Centre of Toulouse, INSERM UMR 1037, 31037 Toulouse, France; Université Toulouse III Paul Sabatier, 31330 Toulouse, France; ERL 5294, CNRS, 31037 Toulouse, France; Institut Universitaire du Cancer de Toulouse-Oncopole, 31100 Toulouse, France; Laboratoire d'Excellence "TOUCAN," Toulouse, France; Programme Hospitalo-Universitaire en Cancérologie CAPTOR, 31059 Toulouse, France; Institut Carnot Lymphome CALYM, 69495 Pierre-Benite, France
| | - Marie Tosolini
- Cancer Research Centre of Toulouse, INSERM UMR 1037, 31037 Toulouse, France; Université Toulouse III Paul Sabatier, 31330 Toulouse, France; ERL 5294, CNRS, 31037 Toulouse, France; Institut Universitaire du Cancer de Toulouse-Oncopole, 31100 Toulouse, France; Laboratoire d'Excellence "TOUCAN," Toulouse, France; Programme Hospitalo-Universitaire en Cancérologie CAPTOR, 31059 Toulouse, France; Institut Carnot Lymphome CALYM, 69495 Pierre-Benite, France
| | - Emilie Patras de Campaigno
- Medical and Clinical Pharmacology Unit, CHU Toulouse University Hospital, 31000 Toulouse, France; Medical and Pharmacoepidemiology Research Unit, INSERM 1027, 31000 Toulouse, France; Centre d'Investigations Cliniques, CIC 1436, Toulouse University Hospital, 31000 Toulouse, France
| | - Anne Cammas
- Cancer Research Centre of Toulouse, INSERM UMR 1037, 31037 Toulouse, France; Université Toulouse III Paul Sabatier, 31330 Toulouse, France; Laboratoire d'Excellence "TOUCAN," Toulouse, France
| | - Sarah Péricart
- Cancer Research Centre of Toulouse, INSERM UMR 1037, 31037 Toulouse, France; Université Toulouse III Paul Sabatier, 31330 Toulouse, France; ERL 5294, CNRS, 31037 Toulouse, France; Institut Universitaire du Cancer de Toulouse-Oncopole, 31100 Toulouse, France; Laboratoire d'Excellence "TOUCAN," Toulouse, France; Programme Hospitalo-Universitaire en Cancérologie CAPTOR, 31059 Toulouse, France; Institut Carnot Lymphome CALYM, 69495 Pierre-Benite, France
| | - Clara-Maria Scarlata
- Cancer Research Centre of Toulouse, INSERM UMR 1037, 31037 Toulouse, France; Université Toulouse III Paul Sabatier, 31330 Toulouse, France; Institut Universitaire du Cancer de Toulouse-Oncopole, 31100 Toulouse, France
| | - Morgane Lebras
- Cancer Research Centre of Toulouse, INSERM UMR 1037, 31037 Toulouse, France; Université Toulouse III Paul Sabatier, 31330 Toulouse, France; Laboratoire d'Excellence "TOUCAN," Toulouse, France
| | - Cédric Rossi
- Cancer Research Centre of Toulouse, INSERM UMR 1037, 31037 Toulouse, France; Université Toulouse III Paul Sabatier, 31330 Toulouse, France; ERL 5294, CNRS, 31037 Toulouse, France; Institut Universitaire du Cancer de Toulouse-Oncopole, 31100 Toulouse, France; Laboratoire d'Excellence "TOUCAN," Toulouse, France; Programme Hospitalo-Universitaire en Cancérologie CAPTOR, 31059 Toulouse, France; Institut Carnot Lymphome CALYM, 69495 Pierre-Benite, France
| | - Laetitia Ligat
- Cancer Research Centre of Toulouse, INSERM UMR 1037, 31037 Toulouse, France; Université Toulouse III Paul Sabatier, 31330 Toulouse, France
| | - Fréderic Pont
- Cancer Research Centre of Toulouse, INSERM UMR 1037, 31037 Toulouse, France; Université Toulouse III Paul Sabatier, 31330 Toulouse, France
| | - Paola B Arimondo
- Programme Hospitalo-Universitaire en Cancérologie CAPTOR, 31059 Toulouse, France; Epigenetic Targeting of Cancer, FRE3600 CNRS, 31035 Toulouse, France
| | - Camille Laurent
- Cancer Research Centre of Toulouse, INSERM UMR 1037, 31037 Toulouse, France; Université Toulouse III Paul Sabatier, 31330 Toulouse, France; ERL 5294, CNRS, 31037 Toulouse, France; Institut Universitaire du Cancer de Toulouse-Oncopole, 31100 Toulouse, France; Laboratoire d'Excellence "TOUCAN," Toulouse, France; Programme Hospitalo-Universitaire en Cancérologie CAPTOR, 31059 Toulouse, France; Institut Carnot Lymphome CALYM, 69495 Pierre-Benite, France
| | - Maha Ayyoub
- Cancer Research Centre of Toulouse, INSERM UMR 1037, 31037 Toulouse, France; Université Toulouse III Paul Sabatier, 31330 Toulouse, France; Institut Universitaire du Cancer de Toulouse-Oncopole, 31100 Toulouse, France
| | - Fabien Despas
- Medical and Clinical Pharmacology Unit, CHU Toulouse University Hospital, 31000 Toulouse, France; Medical and Pharmacoepidemiology Research Unit, INSERM 1027, 31000 Toulouse, France; Centre d'Investigations Cliniques, CIC 1436, Toulouse University Hospital, 31000 Toulouse, France
| | - Maryse Lapeyre-Mestre
- Medical and Clinical Pharmacology Unit, CHU Toulouse University Hospital, 31000 Toulouse, France; Medical and Pharmacoepidemiology Research Unit, INSERM 1027, 31000 Toulouse, France; Centre d'Investigations Cliniques, CIC 1436, Toulouse University Hospital, 31000 Toulouse, France
| | - Stefania Millevoi
- Cancer Research Centre of Toulouse, INSERM UMR 1037, 31037 Toulouse, France; Université Toulouse III Paul Sabatier, 31330 Toulouse, France; Laboratoire d'Excellence "TOUCAN," Toulouse, France.
| | - Jean-Jacques Fournié
- Cancer Research Centre of Toulouse, INSERM UMR 1037, 31037 Toulouse, France; Université Toulouse III Paul Sabatier, 31330 Toulouse, France; ERL 5294, CNRS, 31037 Toulouse, France; Institut Universitaire du Cancer de Toulouse-Oncopole, 31100 Toulouse, France; Laboratoire d'Excellence "TOUCAN," Toulouse, France; Programme Hospitalo-Universitaire en Cancérologie CAPTOR, 31059 Toulouse, France; Institut Carnot Lymphome CALYM, 69495 Pierre-Benite, France.
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Venkei ZG, Choi CP, Feng S, Chen C, Jacobsen SE, Kim JK, Yamashita YM. A kinesin Klp10A mediates cell cycle-dependent shuttling of Piwi between nucleus and nuage. PLoS Genet 2020; 16:e1008648. [PMID: 32168327 PMCID: PMC7094869 DOI: 10.1371/journal.pgen.1008648] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2019] [Revised: 03/25/2020] [Accepted: 02/03/2020] [Indexed: 12/26/2022] Open
Abstract
The piRNA pathway protects germline genomes from selfish genetic elements (e.g. transposons) through their transcript cleavage in the cytoplasm and/or their transcriptional silencing in the nucleus. Here, we describe a mechanism by which the nuclear and cytoplasmic arms of the piRNA pathway are linked. We find that during mitosis of Drosophila spermatogonia, nuclear Piwi interacts with nuage, the compartment that mediates the cytoplasmic arm of the piRNA pathway. At the end of mitosis, Piwi leaves nuage to return to the nucleus. Dissociation of Piwi from nuage occurs at the depolymerizing microtubules of the central spindle, mediated by a microtubule-depolymerizing kinesin, Klp10A. Depletion of klp10A delays the return of Piwi to the nucleus and affects piRNA production, suggesting the role of nuclear-cytoplasmic communication in piRNA biogenesis. We propose that cell cycle-dependent communication between the nuclear and cytoplasmic arms of the piRNA pathway may play a previously unappreciated role in piRNA regulation. The piRNA pathway that defends germline from selfish elements operates in two subpathways, one mediated by Piwi in Drosophila to silence transcription of targets in the nucleus and the other mediated by Aub and Ago3 to cleave transcripts of targets in the cytoplasm. How these two subpathways might coordinate with each other, particularly at the cell biological level, remains elusive. This study shows that Piwi interacts with Aub/Ago3 specifically in mitosis in nuage, the organelle that serves as the platform for piRNA cytoplasmic subpathway. Piwi returns to the nucleus at the end of mitosis, and our study suggests that dissociation of Piwi from nuage is facilitated by microtubule depolymerization by a kinesin Klp10A at the central spindle. We propose that cell-cycle-dependent interaction of two piRNA subpathways may play an important role in piRNA production.
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Affiliation(s)
- Zsolt G. Venkei
- Life Sciences Institute, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Charlotte P. Choi
- Department of Biology, Johns Hopkins University, Baltimore, Maryland, United States of America
| | - Suhua Feng
- Department of Molecular, Cell and Developmental Biology, University of California, Los Angeles, California, United States of America
- Eli and Edyth Broad Center of Regenerative Medicine and Stem Cell Research, University of California, Los Angeles, California, United States of America
| | - Cuie Chen
- Life Sciences Institute, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Steven E. Jacobsen
- Department of Molecular, Cell and Developmental Biology, University of California, Los Angeles, California, United States of America
- Eli and Edyth Broad Center of Regenerative Medicine and Stem Cell Research, University of California, Los Angeles, California, United States of America
- Howard Hughes Medical Institute, University of California, Los Angeles, California, United States of America
| | - John K. Kim
- Department of Biology, Johns Hopkins University, Baltimore, Maryland, United States of America
| | - Yukiko M. Yamashita
- Life Sciences Institute, University of Michigan, Ann Arbor, Michigan, United States of America
- Department of Cell and Developmental Biology, University of Michigan, Ann Arbor, Michigan, United States of America
- Howard Hughes Medical Institute, University of Michigan Ann Arbor, Michigan, United States of America
- * E-mail:
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33
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Abo-Rady M, Kalmbach N, Pal A, Schludi C, Janosch A, Richter T, Freitag P, Bickle M, Kahlert AK, Petri S, Stefanov S, Glass H, Staege S, Just W, Bhatnagar R, Edbauer D, Hermann A, Wegner F, Sterneckert JL. Knocking out C9ORF72 Exacerbates Axonal Trafficking Defects Associated with Hexanucleotide Repeat Expansion and Reduces Levels of Heat Shock Proteins. Stem Cell Reports 2020; 14:390-405. [PMID: 32084385 PMCID: PMC7066330 DOI: 10.1016/j.stemcr.2020.01.010] [Citation(s) in RCA: 44] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2019] [Revised: 01/18/2020] [Accepted: 01/21/2020] [Indexed: 12/13/2022] Open
Abstract
In amyotrophic lateral sclerosis (ALS) motor neurons (MNs) undergo dying-back, where the distal axon degenerates before the soma. The hexanucleotide repeat expansion (HRE) in C9ORF72 is the most common genetic cause of ALS, but the mechanism of pathogenesis is largely unknown with both gain- and loss-of-function mechanisms being proposed. To better understand C9ORF72-ALS pathogenesis, we generated isogenic induced pluripotent stem cells. MNs with HRE in C9ORF72 showed decreased axonal trafficking compared with gene corrected MNs. However, knocking out C9ORF72 did not recapitulate these changes in MNs from healthy controls, suggesting a gain-of-function mechanism. In contrast, knocking out C9ORF72 in MNs with HRE exacerbated axonal trafficking defects and increased apoptosis as well as decreased levels of HSP70 and HSP40, and inhibition of HSPs exacerbated ALS phenotypes in MNs with HRE. Therefore, we propose that the HRE in C9ORF72 induces ALS pathogenesis via a combination of gain- and loss-of-function mechanisms.
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Affiliation(s)
- Masin Abo-Rady
- Technische Universität Dresden, Center for Regenerative Therapies TU Dresden (CRTD), 01307 Dresden, Germany
| | - Norman Kalmbach
- Department of Neurology, Hannover Medical School, 30625 Hannover, Germany
| | - Arun Pal
- Department of Neurology, Technische Universität Dresden, 01307 Dresden, Germany
| | - Carina Schludi
- German Center for Neurodegenerative Diseases (DZNE) and Munich Cluster for System Neurology (SyNergy), 81377 Munich, Germany
| | - Antje Janosch
- Max Planck Institute of Molecular Cell Biology and Genetics, 01307 Dresden, Germany
| | - Tanja Richter
- Institute of Human Genetics, University of Ulm, 89081 Ulm, Germany
| | - Petra Freitag
- Institut für Klinische Genetik, Medizinische Fakultät Carl Gustav Carus, Technische Universität Dresden, 01307 Dresden, Germany
| | - Marc Bickle
- Max Planck Institute of Molecular Cell Biology and Genetics, 01307 Dresden, Germany
| | - Anne-Karin Kahlert
- Institut für Klinische Genetik, Medizinische Fakultät Carl Gustav Carus, Technische Universität Dresden, 01307 Dresden, Germany
| | - Susanne Petri
- Department of Neurology, Hannover Medical School, 30625 Hannover, Germany
| | - Stefan Stefanov
- Technische Universität Dresden, Center for Regenerative Therapies TU Dresden (CRTD), 01307 Dresden, Germany
| | - Hannes Glass
- Department of Neurology, Technische Universität Dresden, 01307 Dresden, Germany; Translational Neurodegeneration Section "Albrecht-Kossel", Department of Neurology and Center for Transdisciplinary Neurosciences Rostock (CTNR), University Medical Center Rostock, University of Rostock, 18147 Rostock, Germany
| | - Selma Staege
- Department of Neurology, Hannover Medical School, 30625 Hannover, Germany
| | - Walter Just
- Institute of Human Genetics, University of Ulm, 89081 Ulm, Germany
| | | | - Dieter Edbauer
- German Center for Neurodegenerative Diseases (DZNE) and Munich Cluster for System Neurology (SyNergy), 81377 Munich, Germany
| | - Andreas Hermann
- Technische Universität Dresden, Center for Regenerative Therapies TU Dresden (CRTD), 01307 Dresden, Germany; Department of Neurology, Technische Universität Dresden, 01307 Dresden, Germany; Translational Neurodegeneration Section "Albrecht-Kossel", Department of Neurology and Center for Transdisciplinary Neurosciences Rostock (CTNR), University Medical Center Rostock, University of Rostock, 18147 Rostock, Germany; German Center for Neurodegenerative Diseases (DZNE) Rostock/Greifswald, 18147 Rostock, Germany
| | - Florian Wegner
- Department of Neurology, Hannover Medical School, 30625 Hannover, Germany.
| | - Jared L Sterneckert
- Technische Universität Dresden, Center for Regenerative Therapies TU Dresden (CRTD), 01307 Dresden, Germany.
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Spannl S, Tereshchenko M, Mastromarco GJ, Ihn SJ, Lee HO. Biomolecular condensates in neurodegeneration and cancer. Traffic 2019; 20:890-911. [PMID: 31606941 DOI: 10.1111/tra.12704] [Citation(s) in RCA: 58] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2019] [Revised: 10/03/2019] [Accepted: 10/06/2019] [Indexed: 12/14/2022]
Abstract
The intracellular environment is partitioned into functionally distinct compartments containing specific sets of molecules and reactions. Biomolecular condensates, also referred to as membrane-less organelles, are diverse and abundant cellular compartments that lack membranous enclosures. Molecules assemble into condensates by phase separation; multivalent weak interactions drive molecules to separate from their surroundings and concentrate in discrete locations. Biomolecular condensates exist in all eukaryotes and in some prokaryotes, and participate in various essential house-keeping, stress-response and cell type-specific processes. An increasing number of recent studies link abnormal condensate formation, composition and material properties to a number of disease states. In this review, we discuss current knowledge and models describing the regulation of condensates and how they become dysregulated in neurodegeneration and cancer. Further research on the regulation of biomolecular phase separation will help us to better understand their role in cell physiology and disease.
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Affiliation(s)
- Stephanie Spannl
- Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada
| | - Maria Tereshchenko
- Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada
| | | | - Sean J Ihn
- Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada
| | - Hyun O Lee
- Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada
- Canada Research Chairs Program, University of Toronto, Toronto, Ontario, Canada
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35
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Schmidt JM, de Manuel M, Marques-Bonet T, Castellano S, Andrés AM. The impact of genetic adaptation on chimpanzee subspecies differentiation. PLoS Genet 2019; 15:e1008485. [PMID: 31765391 PMCID: PMC6901233 DOI: 10.1371/journal.pgen.1008485] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2019] [Revised: 12/09/2019] [Accepted: 10/17/2019] [Indexed: 12/25/2022] Open
Abstract
Chimpanzees, humans' closest relatives, are in danger of extinction. Aside from direct human impacts such as hunting and habitat destruction, a key threat is transmissible disease. As humans continue to encroach upon their habitats, which shrink in size and grow in density, the risk of inter-population and cross-species viral transmission increases, a point dramatically made in the reverse with the global HIV/AIDS pandemic. Inhabiting central Africa, the four subspecies of chimpanzees differ in demographic history and geographical range, and are likely differentially adapted to their particular local environments. To quantitatively explore genetic adaptation, we investigated the genic enrichment for SNPs highly differentiated between chimpanzee subspecies. Previous analyses of such patterns in human populations exhibited limited evidence of adaptation. In contrast, chimpanzees show evidence of recent positive selection, with differences among subspecies. Specifically, we observe strong evidence of recent selection in eastern chimpanzees, with highly differentiated SNPs being uniquely enriched in genic sites in a way that is expected under recent adaptation but not under neutral evolution or background selection. These sites are enriched for genes involved in immune responses to pathogens, and for genes inferred to differentiate the immune response to infection by simian immunodeficiency virus (SIV) in natural vs. non-natural host species. Conversely, central chimpanzees exhibit an enrichment of signatures of positive selection only at cytokine receptors, due to selective sweeps in CCR3, CCR9 and CXCR6 -paralogs of CCR5 and CXCR4, the two major receptors utilized by HIV to enter human cells. Thus, our results suggest that positive selection has contributed to the genetic and phenotypic differentiation of chimpanzee subspecies, and that viruses likely play a predominate role in this differentiation, with SIV being a likely selective agent. Interestingly, our results suggest that SIV has elicited distinctive adaptive responses in these two chimpanzee subspecies.
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MESH Headings
- Adaptation, Physiological/genetics
- Adaptation, Physiological/immunology
- Animals
- Demography
- Genetic Drift
- Genetic Speciation
- HIV/genetics
- HIV/immunology
- HIV/pathogenicity
- Humans
- Immunity, Innate/genetics
- Pan troglodytes/genetics
- Pan troglodytes/immunology
- Pan troglodytes/virology
- Polymorphism, Single Nucleotide/genetics
- Receptors, CCR/genetics
- Receptors, CCR3/genetics
- Receptors, CCR5/genetics
- Receptors, CXCR4/genetics
- Receptors, CXCR6/immunology
- Selection, Genetic/genetics
- Simian Immunodeficiency Virus/genetics
- Simian Immunodeficiency Virus/immunology
- Simian Immunodeficiency Virus/pathogenicity
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Affiliation(s)
- Joshua M. Schmidt
- UCL Genetics Institute, Department of Genetics, Evolution and Environment, University College London, London, United Kingdom
- Max Planck Institute for Evolutionary Anthropology, Department of Evolutionary Genetics, Leipzig, Germany
- * E-mail: (JMS); (AMA)
| | - Marc de Manuel
- Institut de Biologia Evolutiva (Consejo Superior de Investigaciones Científicas–Universitat Pompeu Fabra), Barcelona, Spain
| | - Tomas Marques-Bonet
- Institut de Biologia Evolutiva (Consejo Superior de Investigaciones Científicas–Universitat Pompeu Fabra), Barcelona, Spain
- National Centre for Genomic Analysis–Centre for Genomic Regulation, Barcelona Institute of Science and Technology, Barcelona, Spain
- Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain
| | - Sergi Castellano
- Max Planck Institute for Evolutionary Anthropology, Department of Evolutionary Genetics, Leipzig, Germany
- Genetics and Genomic Medicine Programme, Great Ormond Street Institute of Child Health, University College London (UCL), London, United Kingdom
- UCL Genomics, London, United Kingdom
| | - Aida M. Andrés
- UCL Genetics Institute, Department of Genetics, Evolution and Environment, University College London, London, United Kingdom
- Max Planck Institute for Evolutionary Anthropology, Department of Evolutionary Genetics, Leipzig, Germany
- * E-mail: (JMS); (AMA)
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Guarino AM, Mauro GD, Ruggiero G, Geyer N, Delicato A, Foulkes NS, Vallone D, Calabrò V. YB-1 recruitment to stress granules in zebrafish cells reveals a differential adaptive response to stress. Sci Rep 2019; 9:9059. [PMID: 31227764 PMCID: PMC6588705 DOI: 10.1038/s41598-019-45468-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2018] [Accepted: 06/04/2019] [Indexed: 01/14/2023] Open
Abstract
The survival of cells exposed to adverse environmental conditions entails various alterations in cellular function including major changes in the transcriptome as well as a radical reprogramming of protein translation. While in mammals this process has been extensively studied, stress responses in non-mammalian vertebrates remain poorly understood. One of the key cellular responses to many different types of stressors is the transient generation of structures called stress granules (SGs). These represent cytoplasmic foci where untranslated mRNAs are sorted or processed for re-initiation, degradation, or packaging into mRNPs. Here, using the evolutionarily conserved Y-box binding protein 1 (YB-1) and G3BP1 as markers, we have studied the formation of stress granules in zebrafish (D. rerio) in response to different environmental stressors. We show that following heat shock, zebrafish cells, like mammalian cells, form stress granules which contain both YB-1 and G3BP1 proteins. Moreover, zfYB-1 knockdown compromises cell viability, as well as recruitment of G3BP1 into SGs, under heat shock conditions highlighting the essential role played by YB-1 in SG assembly and cell survival. However, zebrafish PAC2 cells do not assemble YB-1-positive stress granules upon oxidative stress induced by arsenite, copper or hydrogen peroxide treatment. This contrasts with the situation in human cells where SG formation is robustly induced by exposure to oxidative stressors. Thus, our findings point to fundamental differences in the mechanisms whereby mammalian and zebrafish cells respond to oxidative stress.
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Affiliation(s)
- Andrea Maria Guarino
- University of Naples Federico II, Department of Biology, Monte Sant'Angelo Campus, Via Cinthia 4, Naples, 80126, Italy
| | - Giuseppe Di Mauro
- Institute of Toxicology and Genetics, Karlsruhe Institute of Technology, Hermann-von-Helmholtz-Platz 1, 76344, Eggenstein-Leopoldshafen, Germany.,University of Ferrara, Department of Life Sciences and Biotechnology, Via Borsari 46, 44121, Ferrara, Italy
| | - Gennaro Ruggiero
- Institute of Toxicology and Genetics, Karlsruhe Institute of Technology, Hermann-von-Helmholtz-Platz 1, 76344, Eggenstein-Leopoldshafen, Germany
| | - Nathalie Geyer
- Institute of Toxicology and Genetics, Karlsruhe Institute of Technology, Hermann-von-Helmholtz-Platz 1, 76344, Eggenstein-Leopoldshafen, Germany
| | - Antonella Delicato
- University of Naples Federico II, Department of Biology, Monte Sant'Angelo Campus, Via Cinthia 4, Naples, 80126, Italy
| | - Nicholas S Foulkes
- Institute of Toxicology and Genetics, Karlsruhe Institute of Technology, Hermann-von-Helmholtz-Platz 1, 76344, Eggenstein-Leopoldshafen, Germany
| | - Daniela Vallone
- Institute of Toxicology and Genetics, Karlsruhe Institute of Technology, Hermann-von-Helmholtz-Platz 1, 76344, Eggenstein-Leopoldshafen, Germany.
| | - Viola Calabrò
- University of Naples Federico II, Department of Biology, Monte Sant'Angelo Campus, Via Cinthia 4, Naples, 80126, Italy.
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Dental pulp cell-derived powerful inducer of TNF-α comprises PKR containing stress granule rich microvesicles. Sci Rep 2019; 9:3825. [PMID: 30846715 PMCID: PMC6405945 DOI: 10.1038/s41598-019-40046-2] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2018] [Accepted: 01/24/2019] [Indexed: 11/16/2022] Open
Abstract
It is well known that dental pulp tissue can evoke some of the most severe acute inflammation observed in the human body. We found that dental pulp cells secrete a factor that induces tumor necrosis factor-α production from macrophages, and designated this factor, dental pulp cell-derived powerful inducer of TNF-α (DPIT). DPIT was induced in dental pulp cells and transported to recipient cells via microvesicles. Treatment of dental pulp cells with a PKR inhibitor markedly suppressed DPIT activity, and weak interferon signals were constitutively activated inside the cells. In recipient macrophages, stimulation with DPIT-containing supernatants from pulp cells resulted in activation of both nuclear factor-κB and MAP kinases like JNK and p38. Proteomics analyses revealed that many stress granule-related proteins were present in supernatants from dental pulp cells as well as microvesicle marker proteins like GAPDH, β-actin, HSPA8, HSPB1, HSPE1, and HSPD1. Furthermore, giant molecule AHNAK and PKR were detected in microvesicles derived from dental pulp cells, and gene silencing of AHNAK in dental pulp cells led to reduced DPIT activity. Thus, it appeared that the core protein of DPIT was PKR, and that PKR was maintained in an active state in stress granule aggregates with AHNAK and transported via microvesicles. The activity of DPIT for TNF-α induction was far superior to that of gram-negative bacterial endotoxin. Therefore, we, report for the first time, that active PKR is transported via microvesicles as stress granule aggregates and induces powerful inflammatory signals in macrophages.
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38
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Falahati H, Haji-Akbari A. Thermodynamically driven assemblies and liquid-liquid phase separations in biology. SOFT MATTER 2019; 15:1135-1154. [PMID: 30672955 DOI: 10.1039/c8sm02285b] [Citation(s) in RCA: 58] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
The sustenance of life depends on the high degree of organization that prevails through different levels of living organisms, from subcellular structures such as biomolecular complexes and organelles to tissues and organs. The physical origin of such organization is not fully understood, and even though it is clear that cells and organisms cannot maintain their integrity without consuming energy, there is growing evidence that individual assembly processes can be thermodynamically driven and occur spontaneously due to changes in thermodynamic variables such as intermolecular interactions and concentration. Understanding the phase separation in vivo requires a multidisciplinary approach, integrating the theory and physics of phase separation with experimental and computational techniques. This paper aims at providing a brief overview of the physics of phase separation and its biological implications, with a particular focus on the assembly of membraneless organelles. We discuss the underlying physical principles of phase separation from its thermodynamics to its kinetics. We also overview the wide range of methods utilized for experimental verification and characterization of phase separation of membraneless organelles, as well as the utility of molecular simulations rooted in thermodynamics and statistical physics in understanding the governing principles of thermodynamically driven biological self-assembly processes.
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Affiliation(s)
- Hanieh Falahati
- Department of Neuroscience, Yale School of Medicine, New Haven, CT 06510, USA.
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39
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Garcia-Moreno M, Järvelin AI, Castello A. Unconventional RNA-binding proteins step into the virus-host battlefront. WILEY INTERDISCIPLINARY REVIEWS-RNA 2018; 9:e1498. [PMID: 30091184 PMCID: PMC7169762 DOI: 10.1002/wrna.1498] [Citation(s) in RCA: 49] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/12/2018] [Revised: 06/01/2018] [Accepted: 06/05/2018] [Indexed: 12/15/2022]
Abstract
The crucial participation of cellular RNA‐binding proteins (RBPs) in virtually all steps of virus infection has been known for decades. However, most of the studies characterizing this phenomenon have focused on well‐established RBPs harboring classical RNA‐binding domains (RBDs). Recent proteome‐wide approaches have greatly expanded the census of RBPs, discovering hundreds of proteins that interact with RNA through unconventional RBDs. These domains include protein–protein interaction platforms, enzymatic cores, and intrinsically disordered regions. Here, we compared the experimentally determined census of RBPs to gene ontology terms and literature, finding that 472 proteins have previous links with viruses. We discuss what these proteins are and what their roles in infection might be. We also review some of the pioneering examples of unorthodox RBPs whose RNA‐binding activity has been shown to be critical for virus infection. Finally, we highlight the potential of these proteins for host‐based therapies against viruses. This article is categorized under:
RNA Interactions with Proteins and Other Molecules > Protein–RNA Interactions: Functional Implications RNA in Disease and Development > RNA in Disease RNA Interactions with Proteins and Other Molecules > RNA–Protein Complexes
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Affiliation(s)
| | - Aino I Järvelin
- Department of Biochemistry, University of Oxford, Oxford, UK
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40
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Wang W, Chen S, Das S, Losert W, Parent CA. Adenylyl cyclase A mRNA localized at the back of cells is actively translated in live chemotaxing Dictyostelium. J Cell Sci 2018; 131:jcs.216176. [PMID: 29618632 DOI: 10.1242/jcs.216176] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2018] [Accepted: 03/26/2018] [Indexed: 11/20/2022] Open
Abstract
Dictyostelium discoideum cells transport adenylyl cyclase A (ACA)-containing vesicles to the back of polarized cells to relay exogenous cAMP signals during chemotaxis. Fluorescence in situ hybridization (FISH) experiments showed that ACA mRNA is also asymmetrically distributed at the back of polarized cells. By using the MS2 bacteriophage system, we now visualize the distribution of ACA mRNA in live chemotaxing cells. We found that the ACA mRNA localization is not dependent on the translation of the protein product and requires multiple cis-acting elements within the ACA-coding sequence. We show that ACA mRNA is associated with actively translating ribosomes and is transported along microtubules towards the back of cells. By monitoring the recovery of ACA-YFP after photobleaching, we observed that local translation of ACA-YFP occurs at the back of cells. These data represent a novel functional role for localized translation in the relay of chemotactic signals during chemotaxis.
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Affiliation(s)
- Weiye Wang
- Laboratory of Cellular and Molecular Biology, Center for Cancer Research, NCI, NIH, Bethesda, MD 20892, USA
| | - Song Chen
- Laboratory of Cellular and Molecular Biology, Center for Cancer Research, NCI, NIH, Bethesda, MD 20892, USA.,Department of Pharmacology, Michigan Medicine, Ann Arbor, MI 48109, USA.,Institute for Physical Science and Technology, University of Maryland, College Park, MD 20742, USA
| | - Satarupa Das
- Laboratory of Cellular and Molecular Biology, Center for Cancer Research, NCI, NIH, Bethesda, MD 20892, USA.,Institute for Physical Science and Technology, University of Maryland, College Park, MD 20742, USA
| | - Wolfgang Losert
- Institute for Physical Science and Technology, University of Maryland, College Park, MD 20742, USA
| | - Carole A Parent
- Laboratory of Cellular and Molecular Biology, Center for Cancer Research, NCI, NIH, Bethesda, MD 20892, USA .,Department of Pharmacology, Michigan Medicine, Ann Arbor, MI 48109, USA.,Institute for Physical Science and Technology, University of Maryland, College Park, MD 20742, USA
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41
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Perez-Pepe M, Fernández-Alvarez AJ, Boccaccio GL. Life and Work of Stress Granules and Processing Bodies: New Insights into Their Formation and Function. Biochemistry 2018; 57:2488-2498. [PMID: 29595960 DOI: 10.1021/acs.biochem.8b00025] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
The dynamic formation of stress granules (SGs), processing bodies (PBs), and related RNA organelles regulates diverse cellular processes, including the coordination of functionally connected messengers, the translational regulation at the synapse, and the control of viruses and retrotransposons. Recent studies have shown that pyruvate kinase and other enzymes localize in SGs and PBs, where they become protected from stress insults. These observations may have implications for enzyme regulation and metabolic control exerted by RNA-based organelles. The formation of these cellular bodies is governed by liquid-liquid phase separation (LLPS) processes, and it needs to be strictly controlled to prevent pathogenic aggregation. The intracellular concentration of key metabolites, such as ATP and sterol derivatives, may influence protein solubility, thus affecting the dynamics of liquid organelles. LLPS in vitro depends on the thermal diffusion of macromolecules, which is limited inside cells, where the condensation and dissolution of membrane-less organelles are helped by energy-driven processes. The active transport by the retrograde motor dynein helps SG assembly, whereas the anterograde motor kinesin mediates SG dissolution; a tug of war between these two molecular motors allows transient SG formation. There is evidence that the efficiency of dynein-mediated transport increases with the number of motor molecules associated with the cargo. The dynein-dependent transport may be influenced by cargo size as larger cargos can load a larger number of motors. We propose a model based on this emergent property of dynein motors, which would be collectively stronger during SG condensation and weaker during SG breakdown, thus allowing kinesin-mediated dispersion.
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Affiliation(s)
- Marcelo Perez-Pepe
- Instituto Leloir and Instituto de Investigaciones Bioquı́micas de Buenos Aires (IIBBA)-CONICET , Buenos Aires , Argentina
| | - Ana J Fernández-Alvarez
- Instituto Leloir and Instituto de Investigaciones Bioquı́micas de Buenos Aires (IIBBA)-CONICET , Buenos Aires , Argentina
| | - Graciela L Boccaccio
- Instituto Leloir and Instituto de Investigaciones Bioquı́micas de Buenos Aires (IIBBA)-CONICET , Buenos Aires , Argentina
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42
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Chudinova EM, Nadezhdina ES. Interactions between the Translation Machinery and Microtubules. BIOCHEMISTRY (MOSCOW) 2018; 83:S176-S189. [PMID: 29544439 DOI: 10.1134/s0006297918140146] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Microtubules are components of eukaryotic cytoskeleton that are involved in the transport of various components from the nucleus to the cell periphery and back. They also act as a platform for assembly of complex molecular ensembles. Ribonucleoprotein (RNP) complexes, such as ribosomes and mRNPs, are transported over significant distances (e.g. to neuronal processes) along microtubules. The association of RNPs with microtubules and their transport along these structures are essential for compartmentalization of protein biosynthesis in cells. Microtubules greatly facilitate assembly of stress RNP granules formed by accumulation of translation machinery components during cell stress response. Microtubules are necessary for the cytoplasm-to-nucleus transport of proteins, including ribosomal proteins. At the same time, ribosomal proteins and RNA-binding proteins can influence cell mobility and cytoplasm organization by regulating microtubule dynamics. The molecular mechanisms underlying the association between the translation machinery components and microtubules have not been studied systematically; the results of such studies are mostly fragmentary. In this review, we attempt to fill this gap by summarizing and discussing the data on protein and RNA components of the translation machinery that directly interact with microtubules or microtubule motor proteins.
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Affiliation(s)
- E M Chudinova
- Institute of Protein Research, Russian Academy of Sciences, Pushchino, Moscow Region, 142290, Russia.
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43
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Berry J, Brangwynne CP, Haataja M. Physical principles of intracellular organization via active and passive phase transitions. REPORTS ON PROGRESS IN PHYSICS. PHYSICAL SOCIETY (GREAT BRITAIN) 2018; 81:046601. [PMID: 29313527 DOI: 10.1088/1361-6633/aaa61e] [Citation(s) in RCA: 244] [Impact Index Per Article: 40.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Exciting recent developments suggest that phase transitions represent an important and ubiquitous mechanism underlying intracellular organization. We describe key experimental findings in this area of study, as well as the application of classical theoretical approaches for quantitatively understanding these data. We also discuss the way in which equilibrium thermodynamic driving forces may interface with the fundamentally out-of-equilibrium nature of living cells. In particular, time and/or space-dependent concentration profiles may modulate the phase behavior of biomolecules in living cells. We suggest future directions for both theoretical and experimental work that will shed light on the way in which biological activity modulates the assembly, properties, and function of viscoelastic states of living matter.
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Affiliation(s)
- Joel Berry
- Department of Mechanical and Aerospace Engineering, Princeton University, Princeton, NJ 08544, United States of America. Department of Materials Science and Engineering, University of Pennsylvania, Philadelphia, PA 19104, United States of America
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44
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Kang JS, Hwang YS, Kim LK, Lee S, Lee WB, Kim-Ha J, Kim YJ. OASL1 Traps Viral RNAs in Stress Granules to Promote Antiviral Responses. Mol Cells 2018; 41:214-223. [PMID: 29463066 PMCID: PMC5881095 DOI: 10.14348/molcells.2018.2293] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2017] [Revised: 12/11/2017] [Accepted: 12/17/2017] [Indexed: 12/24/2022] Open
Abstract
Oligoadenylate synthetase (OAS) protein family is the major interferon (IFN)-stimulated genes responsible for the activation of RNase L pathway upon viral infection. OAS-like (OASL) is also required for inhibition of viral growth in human cells, but the loss of one of its mouse homolog, OASL1, causes a severe defect in termination of type I interferon production. To further investigate the antiviral activity of OASL1, we examined its subcellular localization and regulatory roles in IFN production in the early and late stages of viral infection. We found OASL1, but not OASL2, formed stress granules trapping viral RNAs and promoted efficient RLR signaling in early stages of infection. Stress granule formation was dependent on RNA binding activity of OASL1. But in the late stages of infection, OASL1 interacted with IRF7 transcripts to inhibit translation resulting in down regulation of IFN production. These results implicate that OASL1 plays context dependent functions in the antiviral response for the clearance and resolution of viral infections.
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Affiliation(s)
- Ji-Seon Kang
- Department of Biochemistry, College of Life Science and Biotechnology, Yonsei University, Seoul 03722,
Korea
- Severance Biomedical Science Institute and BK21 PLUS project to Medical Sciences, Gangnam Severance Hospital, Yonsei University College of Medicine, Seoul 06230,
Korea
| | - Yune-Sahng Hwang
- Department for Integrated OMICs for Biomedical Science, Yonsei University, Seoul 03722,
Korea
| | - Lark Kyun Kim
- Severance Biomedical Science Institute and BK21 PLUS project to Medical Sciences, Gangnam Severance Hospital, Yonsei University College of Medicine, Seoul 06230,
Korea
| | - Sujung Lee
- Department of Integrative Bioscience and Biotechnology, College of Life Sciences, Sejong University, Seoul 05006,
Korea
| | - Wook-Bin Lee
- Department of Biochemistry, College of Life Science and Biotechnology, Yonsei University, Seoul 03722,
Korea
- Korea Institute of Science and Technology (KIST) Gangneung Institute of Natural Products, Gangneung 25451,
Korea
| | - Jeongsil Kim-Ha
- Department of Integrative Bioscience and Biotechnology, College of Life Sciences, Sejong University, Seoul 05006,
Korea
| | - Young-Joon Kim
- Department of Biochemistry, College of Life Science and Biotechnology, Yonsei University, Seoul 03722,
Korea
- Department for Integrated OMICs for Biomedical Science, Yonsei University, Seoul 03722,
Korea
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45
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Fernández-Carrillo C, Pérez-Vilaró G, Díez J, Pérez-Del-Pulgar S. Hepatitis C virus plays with fire and yet avoids getting burned. A review for clinicians on processing bodies and stress granules. Liver Int 2018; 38:388-398. [PMID: 28782251 DOI: 10.1111/liv.13541] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/14/2016] [Accepted: 08/02/2017] [Indexed: 02/13/2023]
Abstract
Over the last few years, many reports have defined several types of RNA cell granules composed of proteins and messenger RNA (mRNA) that regulate gene expression on a post-transcriptional level. Processing bodies (P-bodies) and stress granules (SGs) are among the best-known RNA granules, only detectable when they accumulate into very dynamic cytosolic foci. Recently, a tight association has been found between positive-stranded RNA viruses, including hepatitis C virus (HCV), and these granules. The present article offers a comprehensive review on the complex and paradoxical relationship between HCV, P-bodies and SGs from a translational perspective. Despite the fact that components of P-bodies and SGs have assiduously controlled mRNA expression, either by sequestration or degradation, for thousands of years, HCV has learned how to dangerously exploit certain of them for its own benefit in an endless biological war. Thus, HCV has gained the ability to hack ancient host machineries inherited from prokaryotic times. While P-bodies and SGs are crucial to the HCV cycle, in the interferon-free era we still lack detailed knowledge of the mechanisms involved, processes that may underlie the long-term complications of HCV infection.
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Affiliation(s)
| | - Gemma Pérez-Vilaró
- Department of Experimental and Health Sciences, Molecular Virology, Universitat Pompeu Fabra, Barcelona, Spain
| | - Juana Díez
- Department of Experimental and Health Sciences, Molecular Virology, Universitat Pompeu Fabra, Barcelona, Spain
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46
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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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47
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Tang SJ. Potential Role of Phase Separation of Repetitive DNA in Chromosomal Organization. Genes (Basel) 2017; 8:genes8100279. [PMID: 29057826 PMCID: PMC5664129 DOI: 10.3390/genes8100279] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2017] [Revised: 10/07/2017] [Accepted: 10/13/2017] [Indexed: 01/19/2023] Open
Abstract
The basic principles of chromosomal organization in eukaryotic cells remain elusive. Current mainstream research efforts largely concentrate on searching for critical packaging proteins involved in organizing chromosomes. I have taken a different perspective, by considering the role of genomic information in chromatins. In particular, I put forward the concept that repetitive DNA elements are key chromosomal packaging modules, and their intrinsic property of homology-based interaction can drive chromatin folding. Many repetitive DNA families have high copy numbers and clustered distribution patterns in the linear genomes. These features may facilitate the interactions among members in the same repeat families. In this paper, the potential liquid–liquid phase transition of repetitive DNAs that is induced by their extensive interaction in chromosomes will be considered. I propose that the interaction among repetitive DNAs may lead to phase separation of interacting repetitive DNAs from bulk chromatins. Phase separation of repetitive DNA may provide a physical mechanism that drives rapid massive changes of chromosomal conformation.
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Affiliation(s)
- Shao-Jun Tang
- Department of Neuroscience and Cell Biology, University of Texas Medical Branch, Galveston, TX 77555, USA.
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48
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Shao J, Gao F, Zhang B, Zhao M, Zhou Y, He J, Ren L, Yao Z, Yang J, Su C, Gao X. Aggregation of SND1 in Stress Granules is Associated with the Microtubule Cytoskeleton During Heat Shock Stimulus. Anat Rec (Hoboken) 2017; 300:2192-2199. [PMID: 28758359 PMCID: PMC5697672 DOI: 10.1002/ar.23642] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2017] [Revised: 05/19/2017] [Accepted: 05/30/2017] [Indexed: 12/19/2022]
Abstract
Stress granules (SGs) are dynamic dense structures in the cytoplasm that form in response to a variety of environmental stress stimuli. Staphylococcal nuclease and Tudor domain containing 1 (SND1) is a type of RNA‐binding protein and has been identified as a transcriptional co‐activator. Our previous studies have shown that SND1 is a component of the stress granule, which forms under stress conditions. Here, we observed that SND1 granules were often surrounded by ɑ‐tubulin‐microtubules in 45°C‐treated HeLa cells at 15 min or colocalized with microtubules at 30 or 45 min. Furthermore, Nocodazole‐mediated microtubule depolymerization could significantly affect the efficient recruitment of SND1 proteins to the SGs during heat shock stress. In addition, the 45°C heat shock mediated the enhancement of eIF2α phosphorylation, which was not affected by treatment with Nocodazole, an agent that disrupts the cytoskeleton. The intact microtubule cytoskeletal tracks are important for the efficient assembly of SND1 granules under heat shock stress and may facilitate SND1 shuttling between cytoplasmic RNA foci. Anat Rec, 300:2192–2199, 2017. © 2017 The Authors The Anatomical Record published by Wiley Periodicals, Inc. on behalf of American Association of Anatomists.
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Affiliation(s)
- Jie Shao
- Department of Clinical Laboratory, Tianjin Medical University Cancer Institute & Hospital, Tianjin, 300060, People's Republic of China
| | - Fei Gao
- Department of Pediatric Cardiology, Tianjin Children's Hospital, Tianjin, 300070, People's Republic of China
| | - Bingbing Zhang
- Department of Clinical Laboratory, Tianjin Medical University Cancer Institute & Hospital, Tianjin, 300060, People's Republic of China
| | - Meng Zhao
- Department of Clinical Laboratory, Tianjin Medical University Cancer Institute & Hospital, Tianjin, 300060, People's Republic of China
| | - Yunli Zhou
- Department of Clinical Laboratory, Tianjin Medical University Cancer Institute & Hospital, Tianjin, 300060, People's Republic of China
| | - Jinyan He
- Department of Immunology, Basic Medical College, Tianjin Medical University, Tianjin, 300070, People's Republic of China.,Key Laboratory of Educational Ministry of China, Tianjin, 300070, People's Republic of China.,Department of Physiology, Basic Medical College, Tianjin Medical University, Tianjin, 300070, People's Republic of China
| | - Li Ren
- Department of Clinical Laboratory, Tianjin Medical University Cancer Institute & Hospital, Tianjin, 300060, People's Republic of China
| | - Zhi Yao
- Department of Immunology, Basic Medical College, Tianjin Medical University, Tianjin, 300070, People's Republic of China.,Key Laboratory of Educational Ministry of China, Tianjin, 300070, People's Republic of China.,Laboratory of Molecular Immunology, Research Center of Basic Medical Science, Tianjin Medical University, Tianjin, 300070, People's Republic of China
| | - Jie Yang
- Department of Immunology, Basic Medical College, Tianjin Medical University, Tianjin, 300070, People's Republic of China.,Key Laboratory of Educational Ministry of China, Tianjin, 300070, People's Republic of China.,Laboratory of Molecular Immunology, Research Center of Basic Medical Science, Tianjin Medical University, Tianjin, 300070, People's Republic of China
| | - Chao Su
- Department of Immunology, Basic Medical College, Tianjin Medical University, Tianjin, 300070, People's Republic of China.,Key Laboratory of Educational Ministry of China, Tianjin, 300070, People's Republic of China.,Laboratory of Molecular Immunology, Research Center of Basic Medical Science, Tianjin Medical University, Tianjin, 300070, People's Republic of China
| | - Xingjie Gao
- Department of Immunology, Basic Medical College, Tianjin Medical University, Tianjin, 300070, People's Republic of China.,Key Laboratory of Educational Ministry of China, Tianjin, 300070, People's Republic of China.,Laboratory of Molecular Immunology, Research Center of Basic Medical Science, Tianjin Medical University, Tianjin, 300070, People's Republic of China
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49
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Abstract
Efficient viral gene expression is threatened by cellular stress response programmes that rapidly reprioritize the translation machinery in response to varied environmental assaults, including virus infection. This results in inhibition of bulk synthesis of housekeeping proteins and causes the aggregation of messenger ribonucleoprotein complexes into cytoplasmic foci that are known as stress granules, which can entrap viral mRNAs. There is accumulating evidence for the antiviral nature of stress granules, which is supported by the discovery of many viral factors that interfere with stress granule formation and/or function. This Review focuses on recent advances in our understanding of the role of translation inhibition and stress granules in antiviral immune responses.
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50
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Panas MD, Ivanov P, Anderson P. Mechanistic insights into mammalian stress granule dynamics. J Cell Biol 2017; 215:313-323. [PMID: 27821493 PMCID: PMC5100297 DOI: 10.1083/jcb.201609081] [Citation(s) in RCA: 260] [Impact Index Per Article: 37.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2016] [Revised: 10/19/2016] [Accepted: 10/20/2016] [Indexed: 12/11/2022] Open
Abstract
The accumulation of stalled translation preinitiation complexes (PICs) mediates the condensation of stress granules (SGs). Interactions between prion-related domains and intrinsically disordered protein regions found in SG-nucleating proteins promote the condensation of ribonucleoproteins into SGs. We propose that PIC components, especially 40S ribosomes and mRNA, recruit nucleators that trigger SG condensation. With resolution of stress, translation reinitiation reverses this process and SGs disassemble. By cooperatively modulating the assembly and disassembly of SGs, ribonucleoprotein condensation can influence the survival and recovery of cells exposed to unfavorable environmental conditions.
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Affiliation(s)
- Marc D Panas
- Division of Rheumatology, Immunology, and Allergy, Harvard Medical School and Brigham and Women's Hospital, Boston, MA 02115
| | - Pavel Ivanov
- Division of Rheumatology, Immunology, and Allergy, Harvard Medical School and Brigham and Women's Hospital, Boston, MA 02115
| | - Paul Anderson
- Division of Rheumatology, Immunology, and Allergy, Harvard Medical School and Brigham and Women's Hospital, Boston, MA 02115
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