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Zhang H, Zhang T, Wan X, Chen C, Wang S, Qin D, Li L, Yu L, Wu X. LSM14B coordinates protein component expression in the P-body and controls oocyte maturation. J Genet Genomics 2024; 51:48-60. [PMID: 37481122 DOI: 10.1016/j.jgg.2023.07.006] [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: 03/23/2023] [Revised: 07/13/2023] [Accepted: 07/14/2023] [Indexed: 07/24/2023]
Abstract
The generation of mature and healthy oocytes is the most critical event in the entire female reproductive process, and the mechanisms regulating this process remain to be studied. Here, we demonstrate that Smith-like (LSM) family member 14B (LSM14B) regulates oocyte maturation, and the loss of LSM14B in mouse ovaries leads to abnormal oocyte MII arrest and female infertility. Next, we find the aberrant transcriptional activation, indicated by abnormal non-surrounded nucleolus and surrounded nucleolus oocyte proportions, and abnormal chromosome assembly and segregation in Lsm14b-deficient mouse oocytes. The global transcriptome analysis suggests that many transcripts involved in cytoplasmic processing body (P-body) function are altered in Lsm14b-deficient mouse oocytes. Deletion of Lsm14b results in the expression and/or localization changes of P-body components (such as LSM14A, DCP1A, and 4E-T). Notably, DDX6, a key component of the P-body, is downregulated and accumulates in the nuclei in Lsm14b-deficient mouse oocytes. Taken together, our data suggest that LSM14B links mouse oocyte maturation to female fertility through the regulation of the P-body.
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Affiliation(s)
- Huiru Zhang
- State Key Laboratory of Reproductive Medicine and Offspring Health, Nanjing Medical University, Nanjing, Jiangsu 210029, China
| | - Tao Zhang
- State Key Laboratory of Reproductive Medicine and Offspring Health, Nanjing Medical University, Nanjing, Jiangsu 210029, China
| | - Xiang Wan
- State Key Laboratory of Reproductive Medicine and Offspring Health, Nanjing Medical University, Nanjing, Jiangsu 210029, China
| | - Chang Chen
- State Key Laboratory of Reproductive Medicine and Offspring Health, Nanjing Medical University, Nanjing, Jiangsu 210029, China
| | - Shu Wang
- State Key Laboratory of Reproductive Medicine and Offspring Health, Nanjing Medical University, Nanjing, Jiangsu 210029, China
| | - Dongdong Qin
- State Key Laboratory of Reproductive Medicine and Offspring Health, Nanjing Medical University, Nanjing, Jiangsu 210029, China
| | - Lufan Li
- State Key Laboratory of Reproductive Medicine and Offspring Health, Nanjing Medical University, Nanjing, Jiangsu 210029, China
| | - Luping Yu
- Center for Reproductive Medicine and Obstetrics and Gynecology, Nanjing Drum Tower Hospital, Nanjing University Medical School, Nanjing, Jiangsu 210029, China.
| | - Xin Wu
- State Key Laboratory of Reproductive Medicine and Offspring Health, Nanjing Medical University, Nanjing, Jiangsu 210029, China.
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52
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Gorsheneva NA, Sopova JV, Azarov VV, Grizel AV, Rubel AA. Biomolecular Condensates: Structure, Functions, Methods of Research. BIOCHEMISTRY. BIOKHIMIIA 2024; 89:S205-S223. [PMID: 38621751 DOI: 10.1134/s0006297924140116] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/29/2023] [Revised: 10/12/2023] [Accepted: 10/16/2023] [Indexed: 04/17/2024]
Abstract
The term "biomolecular condensates" is used to describe membraneless compartments in eukaryotic cells, accumulating proteins and nucleic acids. Biomolecular condensates are formed as a result of liquid-liquid phase separation (LLPS). Often, they demonstrate properties of liquid-like droplets or gel-like aggregates; however, some of them may appear to have a more complex structure and high-order organization. Membraneless microcompartments are involved in diverse processes both in cytoplasm and in nucleus, among them ribosome biogenesis, regulation of gene expression, cell signaling, and stress response. Condensates properties and structure could be highly dynamic and are affected by various internal and external factors, e.g., concentration and interactions of components, solution temperature, pH, osmolarity, etc. In this review, we discuss variety of biomolecular condensates and their functions in live cells, describe their structure variants, highlight domain and primary sequence organization of the constituent proteins and nucleic acids. Finally, we describe current advances in methods that characterize structure, properties, morphology, and dynamics of biomolecular condensates in vitro and in vivo.
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Affiliation(s)
| | - Julia V Sopova
- St. Petersburg State University, St. Petersburg, 199034, Russia.
| | | | - Anastasia V Grizel
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA 30332, USA.
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53
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Ryan L, Rubinsztein DC. The autophagy of stress granules. FEBS Lett 2024; 598:59-72. [PMID: 38101818 DOI: 10.1002/1873-3468.14787] [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: 09/21/2023] [Revised: 10/20/2023] [Accepted: 11/10/2023] [Indexed: 12/17/2023]
Abstract
Our understanding of stress granule (SG) biology has deepened considerably in recent years, and with this, increased understanding of links has been made between SGs and numerous neurodegenerative diseases. One of the proposed mechanisms by which SGs and any associated protein aggregates may become pathological is based upon defects in their autophagic clearance, and so the precise processes governing the degradation of SGs are important to understand. Mutations and disease-associated variants implicated in amyotrophic lateral sclerosis, Huntington's disease, Parkinson's disease and frontotemporal lobar dementia compromise autophagy, whilst autophagy-inhibiting drugs or knockdown of essential autophagy proteins result in the persistence of SGs. In this review, we will consider the current knowledge regarding the autophagy of SG.
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Affiliation(s)
- Laura Ryan
- Department of Medical Genetics, Cambridge Institute for Medical Research (CIMR), University of Cambridge, UK
- UK Dementia Research Institute, Cambridge Institute for Medical Research (CIMR), University of Cambridge, UK
| | - David C Rubinsztein
- Department of Medical Genetics, Cambridge Institute for Medical Research (CIMR), University of Cambridge, UK
- UK Dementia Research Institute, Cambridge Institute for Medical Research (CIMR), University of Cambridge, UK
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54
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Wadhwa N, Kapoor S, Kapoor M. Arabidopsis T-DNA mutants affected in TRDMT1/DNMT2 show differential protein synthesis and compromised stress tolerance. FEBS J 2024; 291:92-113. [PMID: 37584564 DOI: 10.1111/febs.16935] [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: 01/21/2023] [Revised: 07/18/2023] [Accepted: 08/14/2023] [Indexed: 08/17/2023]
Abstract
TRDMT1/DNMT2 belongs to the conserved family of nucleic acid methyltransferases. Unlike the animal systems, studies on TRDMT1/DNMT2 in land plants have been limited. We show that TRDMT1/DNMT2 is strongly conserved in the green lineage. Studies in mosses have previously shown that TRDMT1/DNMT2 plays a crucial role in modulating molecular networks involved in stress perception and signalling and in transcription/stability of specific tRNAs under stress. To gain deeper insight into its biological roles in a flowering plant, we examined more closely the previously reported Arabidopsis SALK_136635C line deficient in TRDMT1/DNMT2 function [Goll MG et al. (2006) Science 311, 395-398]. RNAs derived from Arabidopsis Dnmt2-deficient plants lacked m5 C38 in tRNAAsp . In this study, by transient expression assays we show that Arabidopsis TRDMT1/DNMT2 is distributed in the nucleus, cytoplasm and RNA-processing bodies, suggesting a role for TRDMT1/DNMT2 in RNA metabolic processes possibly by shuttling between cellular compartments. Bright-field and high-resolution SEM and qPCR analysis reveal roles of TRDMT1/DNMT2 in proper growth and developmental progression. Quantitative proteome analysis by LC-MS/MS coupled with qPCR shows AtTRDMT1/AtDNMT2 function to be crucial for protein synthesis and cellular homeostasis via housekeeping roles and proteins with poly-Asp stretches and RNA pol II activity on selected genes are affected in attrdmt1/atdnmt2. This shift in metabolic pathways primes the mutant plants to become increasingly sensitive to oxidative and osmotic stress. Taken together, our study sheds light on the mechanistic role of TRDMT1/DNMT2 in a flowering plant.
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Affiliation(s)
- Nikita Wadhwa
- University School of Biotechnology, Guru Gobind Singh Indraprastha University, New Delhi, India
| | - Sanjay Kapoor
- University School of Biotechnology, Guru Gobind Singh Indraprastha University, New Delhi, India
- Interdisciplinary Centre for Plant Genomics and Department of Plant Molecular Biology, University of Delhi South Campus, New Delhi, India
| | - Meenu Kapoor
- University School of Biotechnology, Guru Gobind Singh Indraprastha University, New Delhi, India
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55
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Makiyama T, Obama T, Watanabe Y, Chatani M, Azetsu Y, Kawaguchi K, Imanaka T, Itabe H. Behavior of intracellular lipid droplets during cell division in HuH7 hepatoma cells. Exp Cell Res 2023; 433:113855. [PMID: 37995922 DOI: 10.1016/j.yexcr.2023.113855] [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: 06/23/2023] [Revised: 11/16/2023] [Accepted: 11/16/2023] [Indexed: 11/25/2023]
Abstract
Intracellular lipid droplets (LDs) are ubiquitous organelles found in many cell types. During mitosis, membranous organelles, including mitochondria, are divided into small pieces and transferred to daughter cells; however, the process of LD transfer to daughter cells is not fully elucidated. Herein, we investigated the behavior of LDs during mitosis in HuH7 human hepatoma cells. While fragments of the Golgi apparatus were scattered in the cytosol during mitosis, intracellular LDs retained their size and spherical morphology as they translocated to the two daughter cells. LDs were initially distributed throughout the cell during prophase but positioned outside the spindle in metaphase, aligning at the far sides of the centrioles. A similar distribution of LDs during mitosis was observed in another hepatocarcinoma HepG2 cells. When the spindle was disrupted by nocodazole treatment or never in mitosis gene A-related kinase 2A knockdown, LDs were localized in the area outside the chromosomes, suggesting that spindle formation is not necessary for LD localization at metaphase. The amount of major LD protein perilipin 2 reduced while LDs were enriched in perilipin 3 during mitosis, indicating the potential alteration of LD protein composition. Conclusively, the behavior of LDs during mitosis is distinct from that of other organelles in hepatocytes.
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Affiliation(s)
- Tomohiko Makiyama
- Department of Biological Chemistry, Showa University Graduate School of Pharmacy, 1-5-8 Hatanodai, Shinagawa, Tokyo, 142-8555, Japan.
| | - Takashi Obama
- Department of Biological Chemistry, Showa University Graduate School of Pharmacy, 1-5-8 Hatanodai, Shinagawa, Tokyo, 142-8555, Japan
| | - Yuichi Watanabe
- Department of Biological Chemistry, Showa University Graduate School of Pharmacy, 1-5-8 Hatanodai, Shinagawa, Tokyo, 142-8555, Japan
| | - Masahiro Chatani
- Department of Pharmacology, Showa University School of Dentistry, 1-5-8 Hatanodai, Shinagawa, Tokyo, 142-8555, Japan; Pharmacological Research Center, Showa University, 1-5-8 Hatanodai, Shinagawa, Tokyo, 142-8555, Japan
| | - Yuki Azetsu
- Department of Pharmacology, Showa University School of Dentistry, 1-5-8 Hatanodai, Shinagawa, Tokyo, 142-8555, Japan; Pharmacological Research Center, Showa University, 1-5-8 Hatanodai, Shinagawa, Tokyo, 142-8555, Japan
| | - Kosuke Kawaguchi
- Graduate School of Medicine and Pharmaceutical Sciences, University of Toyama, 2630 Sugitani, Toyama, 930-0194, Japan
| | - Tsuneo Imanaka
- Graduate School of Medicine and Pharmaceutical Sciences, University of Toyama, 2630 Sugitani, Toyama, 930-0194, Japan; Faculty of Pharmaceutical Sciences, Hiroshima International University, 5-1-1 Hirokoshinkai, Kure City, Hiroshima, 737-0112, Japan
| | - Hiroyuki Itabe
- Department of Biological Chemistry, Showa University Graduate School of Pharmacy, 1-5-8 Hatanodai, Shinagawa, Tokyo, 142-8555, Japan
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56
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Ramšak M, Ramirez DA, Hough LE, Shirts MR, Vidmar S, Eleršič Filipič K, Anderluh G, Jerala R. Programmable de novo designed coiled coil-mediated phase separation in mammalian cells. Nat Commun 2023; 14:7973. [PMID: 38042897 PMCID: PMC10693550 DOI: 10.1038/s41467-023-43742-w] [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: 06/29/2023] [Accepted: 11/17/2023] [Indexed: 12/04/2023] Open
Abstract
Membraneless liquid compartments based on phase-separating biopolymers have been observed in diverse cell types and attributed to weak multivalent interactions predominantly based on intrinsically disordered domains. The design of liquid-liquid phase separated (LLPS) condensates based on de novo designed tunable modules that interact in a well-understood, controllable manner could improve our understanding of this phenomenon and enable the introduction of new features. Here we report the construction of CC-LLPS in mammalian cells, based on designed coiled-coil (CC) dimer-forming modules, where the stability of CC pairs, their number, linkers, and sequential arrangement govern the transition between diffuse, liquid and immobile condensates and are corroborated by coarse-grained molecular simulations. Through modular design, we achieve multiple coexisting condensates, chemical regulation of LLPS, condensate fusion, formation from either one or two polypeptide components or LLPS regulation by a third polypeptide chain. These findings provide further insights into the principles underlying LLPS formation and a design platform for controlling biological processes.
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Affiliation(s)
- Maruša Ramšak
- Department of Synthetic Biology and Immunology, National Institute of Chemistry, Ljubljana, Slovenia
- Interdisciplinary doctoral study of biomedicine, Medical Faculty, University of Ljubljana, Ljubljana, Slovenia
| | - Dominique A Ramirez
- Department of Biochemistry, University of Colorado Boulder, Boulder, CO, USA
| | - Loren E Hough
- Department of Physics and BioFrontiers Institute, University of Colorado Boulder, Boulder, CO, USA
| | - Michael R Shirts
- Department of Chemical and Biological Engineering, University of Colorado Boulder, Boulder, CO, USA
| | - Sara Vidmar
- Department of Synthetic Biology and Immunology, National Institute of Chemistry, Ljubljana, Slovenia
- Interdisciplinary doctoral study of biomedicine, Medical Faculty, University of Ljubljana, Ljubljana, Slovenia
| | - Kristina Eleršič Filipič
- Department of Molecular Biology and Nanobiotechnology, National Institute of Chemistry, Ljubljana, Slovenia
| | - Gregor Anderluh
- Department of Molecular Biology and Nanobiotechnology, National Institute of Chemistry, Ljubljana, Slovenia
| | - Roman Jerala
- Department of Synthetic Biology and Immunology, National Institute of Chemistry, Ljubljana, Slovenia.
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57
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Yu L, Kong N, Lin Y, Qiu P, Xu Q, Zhang Y, Zhen X, Yan G, Sun H, Mei J, Cao G. NUSAP1 regulates mouse oocyte meiotic maturation. J Cell Biochem 2023; 124:1931-1947. [PMID: 37992207 DOI: 10.1002/jcb.30498] [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: 08/07/2023] [Revised: 10/25/2023] [Accepted: 11/01/2023] [Indexed: 11/24/2023]
Abstract
The correct assembly of the spindle apparatus directly regulates the precise separation of chromosomes in mouse oocytes, which is crucial for obtaining high-quality oocytes capable of successful fertilization. The localization, assembly, migration, and disassembly of the spindle are regulated by a series of spindle-associated proteins, which exhibit unique expression level variations and specific localization in oocytes. Proteomic analysis revealed that among many representative spindle-associated proteins, the expression level of nucleolar and spindle-associated protein 1 (NUSAP1) significantly increased after meiotic resumption, with a magnitude of change higher than that of other proteins. However, the role of NUSAP1 during oocyte meiosis maturation has not been reported. Here, we report that NUSAP1 is distributed within the cell nucleus during the germinal vesicle (GV) oocytes with non-surrounded nucleolus stage and is not enriched in the nucleus during the GV-surrounded nucleolus stage. Interestingly, NUSAP1 forms distinct granular aggregates near the spindle poles during the prophase of the first meiotic division (Pro-MI), metaphase I, and anaphase I/telophase I stages. Nusap1 depletion leads to chromosome misalignment, increased aneuploidy, and abnormal spindle assembly, particularly a decrease in spindle pole width. Correspondingly, RNA-seq analysis revealed significant suppression of the "establishment of spindle orientation" signaling pathway. Additionally, the attenuation of F-actin in NUSAP1-deficient oocytes may affect the asymmetric division process. Gene ontology analysis of NUSAP1 interactomes, identified through mass spectrometry here, revealed significant enrichment for RNA binding. As an RNA-binding protein, NUSAP1 is likely involved in the regulation of messenger RNA homeostasis by influencing the dynamics of processing (P)-body components. Overall, our results demonstrate the critical importance of precise regulation of NUSAP1 expression levels and protein localization for maintaining mouse oocyte meiosis.
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Affiliation(s)
- Lina Yu
- Center for Reproductive Medicine and Obstetrics and Gynecology, Nanjing Drum Tower Hospital Clinical College of Nanjing Medical University, Nanjing, China
- State Key Laboratory of Reproductive Medicine and Offspring Health, Nanjing Medical University, Nanjing, China
| | - Na Kong
- Center for Reproductive Medicine and Obstetrics and Gynecology, Nanjing Drum Tower Hospital Clinical College of Nanjing Medical University, Nanjing, China
- Center for Molecular Reproductive Medicine, Nanjing University, Nanjing, China
| | - Yuling Lin
- State Key Laboratory of Reproductive Medicine and Offspring Health, Nanjing Medical University, Nanjing, China
| | - Panpan Qiu
- Center for Molecular Reproductive Medicine, Nanjing University, Nanjing, China
| | - Qian Xu
- Center for Reproductive Medicine and Obstetrics and Gynecology, Nanjing Drum Tower Hospital, Affiliated Hospital of Medical School, Nanjing University, Nanjing, China
| | - Yang Zhang
- Center for Molecular Reproductive Medicine, Nanjing University, Nanjing, China
| | - Xin Zhen
- Center for Molecular Reproductive Medicine, Nanjing University, Nanjing, China
| | - Guijun Yan
- Center for Molecular Reproductive Medicine, Nanjing University, Nanjing, China
| | - Haixiang Sun
- State Key Laboratory of Reproductive Medicine and Offspring Health, Nanjing Medical University, Nanjing, China
| | - Jie Mei
- Center for Reproductive Medicine and Obstetrics and Gynecology, Nanjing Drum Tower Hospital Clinical College of Nanjing Medical University, Nanjing, China
- Center for Molecular Reproductive Medicine, Nanjing University, Nanjing, China
| | - Guangyi Cao
- Center for Reproductive Medicine and Obstetrics and Gynecology, Nanjing Drum Tower Hospital Clinical College of Nanjing Medical University, Nanjing, China
- Center for Molecular Reproductive Medicine, Nanjing University, Nanjing, China
- Guangdong Provincial Key Laboratory of Reproductive Medicine, Guangzhou, China
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58
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Gao G, Sumrall ES, Pitchiaya S, Bitzer M, Alberti S, Walter NG. Biomolecular condensates in kidney physiology and disease. Nat Rev Nephrol 2023; 19:756-770. [PMID: 37752323 DOI: 10.1038/s41581-023-00767-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/27/2023] [Indexed: 09/28/2023]
Abstract
The regulation and preservation of distinct intracellular and extracellular solute microenvironments is crucial for the maintenance of cellular homeostasis. In mammals, the kidneys control bodily salt and water homeostasis. Specifically, the urine-concentrating mechanism within the renal medulla causes fluctuations in extracellular osmolarity, which enables cells of the kidney to either conserve or eliminate water and electrolytes, depending on the balance between intake and loss. However, relatively little is known about the subcellular and molecular changes caused by such osmotic stresses. Advances have shown that many cells, including those of the kidney, rapidly (within seconds) and reversibly (within minutes) assemble membraneless, nano-to-microscale subcellular assemblies termed biomolecular condensates via the biophysical process of hyperosmotic phase separation (HOPS). Mechanistically, osmotic cell compression mediates changes in intracellular hydration, concentration and molecular crowding, rendering HOPS one of many related phase-separation phenomena. Osmotic stress causes numerous homo-multimeric proteins to condense, thereby affecting gene expression and cell survival. HOPS rapidly regulates specific cellular biochemical processes before appropriate protective or corrective action by broader stress response mechanisms can be initiated. Here, we broadly survey emerging evidence for, and the impact of, biomolecular condensates in nephrology, where initial concentration buffering by HOPS and its subsequent cellular escalation mechanisms are expected to have important implications for kidney physiology and disease.
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Affiliation(s)
- Guoming Gao
- Biophysics Graduate Program, University of Michigan, Ann Arbor, MI, USA
- Department of Chemistry and Center for RNA Biomedicine, University of Michigan, Ann Arbor, MI, USA
| | - Emily S Sumrall
- Biophysics Graduate Program, University of Michigan, Ann Arbor, MI, USA
- Department of Chemistry and Center for RNA Biomedicine, University of Michigan, Ann Arbor, MI, USA
| | | | - Markus Bitzer
- Department of Medicine, University of Michigan, Ann Arbor, MI, USA
| | - Simon Alberti
- Technische Universität Dresden, Biotechnology Center (BIOTEC) and Center for Molecular and Cellular Engineering (CMCB), Dresden, Germany
| | - Nils G Walter
- Department of Chemistry and Center for RNA Biomedicine, University of Michigan, Ann Arbor, MI, USA.
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59
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Hatfield D, Rodriguez W, Mehrmann T, Muller M. The antiviral protein Shiftless blocks p-body formation during KSHV infection. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.11.16.567185. [PMID: 38014318 PMCID: PMC10680731 DOI: 10.1101/2023.11.16.567185] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/29/2023]
Abstract
P-bodies (PB) are non-membranous foci involved in determining mRNA fate by affecting translation and mRNA decay. In this study, we identify the anti-viral factor SHFL as a potent disassembly factor of PB. We show that PBs remain sparse in the presence of SHFL even in the context of oxidative stress, a major trigger for PB induction. Mutational approaches revealed that SHFL RNA binding activity is not required for its PB disassembly function. However, we have identified a new region of SHFL which bridges two distant domains as responsible for PB disassembly. Furthermore, we show that SHFL ability to disrupt PB formation is directly linked to its anti-viral activity during KSHV infection. While WT SHFL efficiently restricts KSHV lytic cycle, PB disruption defective mutants no longer lead to reactivation defects. SHFL-mediated PB disassembly also leads to increased expression of key anti-viral cytokines, further expanding SHFL dependent anti-viral state. Taken together, our observations suggest a role of SHFL in PB disassembly, which could have important anti-viral consequences during infection.
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60
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Malsick LE, Wilusz J. Dynamic "Cap"-abilities of P-bodies and the XRN1-EDC4 axis. EMBO J 2023; 42:e115310. [PMID: 37750488 PMCID: PMC10620757 DOI: 10.15252/embj.2023115310] [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: 08/15/2023] [Revised: 08/28/2023] [Accepted: 08/30/2023] [Indexed: 09/27/2023] Open
Abstract
RNA turnover regulates the quality and quantity of cellular gene expression through a coordinated cavalcade of enzymes, factors, and phase transitions. In this issue, Brothers et al reveal the importance of balanced communication between the Xrn1 exonuclease and the EDC4 decapping factor to coordinate P-body dynamics and maintain cellular fitness.
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Affiliation(s)
- Lauren E Malsick
- Department of Microbiology, Immunology, and PathologyColorado State UniversityFort CollinsCOUSA
| | - Jeffrey Wilusz
- Department of Microbiology, Immunology, and PathologyColorado State UniversityFort CollinsCOUSA
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61
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Brothers WR, Ali F, Kajjo S, Fabian MR. The EDC4-XRN1 interaction controls P-body dynamics to link mRNA decapping with decay. EMBO J 2023; 42:e113933. [PMID: 37621215 PMCID: PMC10620763 DOI: 10.15252/embj.2023113933] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2023] [Revised: 07/19/2023] [Accepted: 07/22/2023] [Indexed: 08/26/2023] Open
Abstract
Deadenylation-dependent mRNA decapping and decay is the major cytoplasmic mRNA turnover pathway in eukaryotes. Many mRNA decapping and decay factors are associated with each other via protein-protein interaction motifs. For example, the decapping enzyme DCP2 and the 5'-3' exonuclease XRN1 interact with the enhancer of mRNA-decapping protein 4 (EDC4), a large scaffold that has been reported to stimulate mRNA decapping. mRNA decapping and decay factors are also found in processing bodies (P-bodies), evolutionarily conserved ribonucleoprotein granules that are often enriched with mRNAs targeted for decay, yet paradoxically are not required for mRNA decay to occur. Here, we show that disrupting the EDC4-XRN1 interaction or altering their stoichiometry inhibits mRNA decapping, with microRNA-targeted mRNAs being stabilized in a translationally repressed state. Importantly, we demonstrate that this concomitantly leads to larger P-bodies that are responsible for preventing mRNA decapping. Finally, we demonstrate that P-bodies support cell viability and prevent stress granule formation when XRN1 is limiting. Taken together, these data demonstrate that the interaction between XRN1 and EDC4 regulates P-body dynamics to properly coordinate mRNA decapping with 5'-3' decay in human cells.
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Affiliation(s)
- William R Brothers
- Lady Davis Institute for Medical ResearchJewish General HospitalMontrealQCCanada
| | - Farah Ali
- Lady Davis Institute for Medical ResearchJewish General HospitalMontrealQCCanada
| | - Sam Kajjo
- Lady Davis Institute for Medical ResearchJewish General HospitalMontrealQCCanada
| | - Marc R Fabian
- Lady Davis Institute for Medical ResearchJewish General HospitalMontrealQCCanada
- Department of BiochemistryMcGill UniversityMontrealQCCanada
- Department of OncologyMcGill UniversityMontrealQCCanada
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62
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Krempl C, Lazzaretti D, Sprangers R. A structural biology view on the enzymes involved in eukaryotic mRNA turnover. Biol Chem 2023; 404:1101-1121. [PMID: 37709756 DOI: 10.1515/hsz-2023-0182] [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: 04/13/2023] [Accepted: 08/24/2023] [Indexed: 09/16/2023]
Abstract
The cellular environment contains numerous ribonucleases that are dedicated to process mRNA transcripts that have been targeted for degradation. Here, we review the three dimensional structures of the ribonuclease complexes (Pan2-Pan3, Ccr4-Not, Xrn1, exosome) and the mRNA decapping enzymes (Dcp2, DcpS) that are involved in mRNA turnover. Structures of major parts of these proteins have been experimentally determined. These enzymes and factors do not act in isolation, but are embedded in interaction networks which regulate enzyme activity and ensure that the appropriate substrates are recruited. The structural details of the higher order complexes that form can, in part, be accurately deduced from known structural data of sub-complexes. Interestingly, many of the ribonuclease and decapping enzymes have been observed in structurally different conformations. Together with experimental data, this highlights that structural changes are often important for enzyme function. We conclude that the known structural data of mRNA decay factors provide important functional insights, but that static structural data needs to be complemented with information regarding protein motions to complete the picture of how transcripts are turned over. In addition, we highlight multiple aspects that influence mRNA turnover rates, but that have not been structurally characterized so far.
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Affiliation(s)
- Christina Krempl
- Institute of Biophysics and Physical Biochemistry, Regensburg Center for Biochemistry, University of Regensburg, D-93053 Regensburg, Germany
| | - Daniela Lazzaretti
- Institute of Biophysics and Physical Biochemistry, Regensburg Center for Biochemistry, University of Regensburg, D-93053 Regensburg, Germany
| | - Remco Sprangers
- Institute of Biophysics and Physical Biochemistry, Regensburg Center for Biochemistry, University of Regensburg, D-93053 Regensburg, Germany
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63
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Németh-Szatmári O, Nagy-Mikó B, Györkei Á, Varga D, Kovács BBH, Igaz N, Bognár B, Rázga Z, Nagy G, Zsindely N, Bodai L, Papp B, Erdélyi M, Kiricsi M, Blastyák A, Collart MA, Boros IM, Villányi Z. Phase-separated ribosome-nascent chain complexes in genotoxic stress response. RNA (NEW YORK, N.Y.) 2023; 29:1557-1574. [PMID: 37460154 PMCID: PMC10578487 DOI: 10.1261/rna.079755.123] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/21/2023] [Accepted: 06/26/2023] [Indexed: 09/20/2023]
Abstract
Assemblysomes are EDTA- and RNase-resistant ribonucleoprotein (RNP) complexes of paused ribosomes with protruding nascent polypeptide chains. They have been described in yeast and human cells for the proteasome subunit Rpt1, and the disordered amino-terminal part of the nascent chain was found to be indispensable for the accumulation of the Rpt1-RNP into assemblysomes. Motivated by this, to find other assemblysome-associated RNPs we used bioinformatics to rank subunits of Saccharomyces cerevisiae protein complexes according to their amino-terminal disorder propensity. The results revealed that gene products involved in DNA repair are enriched among the top candidates. The Sgs1 DNA helicase was chosen for experimental validation. We found that indeed nascent chains of Sgs1 form EDTA-resistant RNP condensates, assemblysomes by definition. Moreover, upon exposure to UV, SGS1 mRNA shifted from assemblysomes to polysomes, suggesting that external stimuli are regulators of assemblysome dynamics. We extended our studies to human cell lines. The BLM helicase, ortholog of yeast Sgs1, was identified upon sequencing assemblysome-associated RNAs from the MCF7 human breast cancer cell line, and mRNAs encoding DNA repair proteins were overall enriched. Using the radiation-resistant A549 cell line, we observed by transmission electron microscopy that 1,6-hexanediol, an agent known to disrupt phase-separated condensates, depletes ring ribosome structures compatible with assemblysomes from the cytoplasm of cells and makes the cells more sensitive to X-ray treatment. Taken together, these findings suggest that assemblysomes may be a component of the DNA damage response from yeast to human.
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Affiliation(s)
- Orsolya Németh-Szatmári
- Department of Biochemistry and Molecular Biology, University of Szeged, 6726 Szeged, Hungary
| | - Bence Nagy-Mikó
- Department of Biochemistry and Molecular Biology, University of Szeged, 6726 Szeged, Hungary
| | - Ádám Györkei
- Institute of Biochemistry, Biological Research Centre, 6726 Szeged, Hungary
- Section for Physiology and Cell Biology, Department of Biosciences, University of Oslo, 0316 Oslo, Norway
| | - Dániel Varga
- Department of Optics and Quantum Electronics, University of Szeged, 6720 Szeged, Hungary
| | - Bálint Barna H Kovács
- Department of Optics and Quantum Electronics, University of Szeged, 6720 Szeged, Hungary
| | - Nóra Igaz
- Department of Biochemistry and Molecular Biology, University of Szeged, 6726 Szeged, Hungary
| | - Bence Bognár
- Department of Biochemistry and Molecular Biology, University of Szeged, 6726 Szeged, Hungary
| | - Zsolt Rázga
- Department of Pathology, Faculty of Medicine, University of Szeged, 6720 Szeged, Hungary
| | - Gábor Nagy
- Department of Biochemistry and Molecular Biology, University of Szeged, 6726 Szeged, Hungary
| | - Nóra Zsindely
- Department of Biochemistry and Molecular Biology, University of Szeged, 6726 Szeged, Hungary
| | - László Bodai
- Department of Biochemistry and Molecular Biology, University of Szeged, 6726 Szeged, Hungary
| | - Balázs Papp
- Institute of Biochemistry, Biological Research Centre, 6726 Szeged, Hungary
| | - Miklós Erdélyi
- Department of Optics and Quantum Electronics, University of Szeged, 6720 Szeged, Hungary
| | - Mónika Kiricsi
- Department of Biochemistry and Molecular Biology, University of Szeged, 6726 Szeged, Hungary
| | - András Blastyák
- Institute of Genetics, Biological Research Centre, 6726 Szeged, Hungary
| | - Martine A Collart
- Department of Microbiology and Molecular Medicine, Institute of Genetics and Genomics Geneva, Faculty of Medicine, University of Geneva, 1211 Geneva 4, Switzerland
| | - Imre M Boros
- Department of Biochemistry and Molecular Biology, University of Szeged, 6726 Szeged, Hungary
| | - Zoltán Villányi
- Department of Biochemistry and Molecular Biology, University of Szeged, 6726 Szeged, Hungary
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64
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Kumar G, Hazra JP, Sinha S. Disordered regions endow structural flexibility to shell proteins and function towards shell-enzyme interactions in 1,2-propanediol utilization microcompartment. J Biomol Struct Dyn 2023; 41:8891-8901. [PMID: 36318590 DOI: 10.1080/07391102.2022.2138552] [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: 07/12/2022] [Accepted: 10/16/2022] [Indexed: 11/07/2022]
Abstract
Intrinsically disordered regions in proteins have been functionally linked to the protein-protein interactions and genesis of several membraneless organelles. Depending on their residual makeup, hydrophobicity or charge distribution they may remain in extended form or may assume certain conformations upon biding to a partner protein or peptide. The present work investigates the distribution and potential roles of disordered regions in the integral proteins of 1,2-propanediol utilization microcompartments. We use bioinformatics tools to identify the probable disordered regions in the shell proteins and enzyme of the 1,2-propanediol utilization microcompartment. Using a combination of computational modelling and biochemical techniques we elucidate the role of disordered terminal regions of a major shell protein and enzyme. Our findings throw light on the importance of disordered regions in the self-assembly, providing flexibility to shell protein and mediating its interaction with a native enzyme.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Gaurav Kumar
- Chemical Biology Unit, Institute of Nano Science and Technology, Mohali, India
| | - Jagadish Prasad Hazra
- Department of Chemical Sciences, Indian Institute of Science Education and Research, Mohali, India
| | - Sharmistha Sinha
- Chemical Biology Unit, Institute of Nano Science and Technology, Mohali, India
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65
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Kershaw CJ, Nelson MG, Castelli LM, Jennings MD, Lui J, Talavera D, Grant CM, Pavitt GD, Hubbard SJ, Ashe MP. Translation factor and RNA binding protein mRNA interactomes support broader RNA regulons for posttranscriptional control. J Biol Chem 2023; 299:105195. [PMID: 37633333 PMCID: PMC10562868 DOI: 10.1016/j.jbc.2023.105195] [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: 07/07/2023] [Revised: 08/18/2023] [Accepted: 08/20/2023] [Indexed: 08/28/2023] Open
Abstract
The regulation of translation provides a rapid and direct mechanism to modulate the cellular proteome. In eukaryotes, an established model for the recruitment of ribosomes to mRNA depends upon a set of conserved translation initiation factors. Nevertheless, how cells orchestrate and define the selection of individual mRNAs for translation, as opposed to other potential cytosolic fates, is poorly understood. We have previously found significant variation in the interaction between individual mRNAs and an array of translation initiation factors. Indeed, mRNAs can be separated into different classes based upon these interactions to provide a framework for understanding different modes of translation initiation. Here, we extend this approach to include new mRNA interaction profiles for additional proteins involved in shaping the cytoplasmic fate of mRNAs. This work defines a set of seven mRNA clusters, based on their interaction profiles with 12 factors involved in translation and/or RNA binding. The mRNA clusters share both physical and functional characteristics to provide a rationale for the interaction profiles. Moreover, a comparison with mRNA interaction profiles from a host of RNA binding proteins suggests that there are defined patterns in the interactions of functionally related mRNAs. Therefore, this work defines global cytoplasmic mRNA binding modules that likely coordinate the synthesis of functionally related proteins.
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Affiliation(s)
- Christopher J Kershaw
- Division of Molecular and Cellular Function, School of Biological Sciences, The University of Manchester, Manchester, UK
| | - Michael G Nelson
- Division of Molecular and Cellular Function, School of Biological Sciences, The University of Manchester, Manchester, UK
| | - Lydia M Castelli
- Division of Molecular and Cellular Function, School of Biological Sciences, The University of Manchester, Manchester, UK
| | - Martin D Jennings
- Division of Molecular and Cellular Function, School of Biological Sciences, The University of Manchester, Manchester, UK
| | - Jennifer Lui
- Division of Molecular and Cellular Function, School of Biological Sciences, The University of Manchester, Manchester, UK
| | - David Talavera
- Division of Cardiovascular Sciences, School of Medical Sciences, The University of Manchester, Manchester, UK
| | - Chris M Grant
- Division of Molecular and Cellular Function, School of Biological Sciences, The University of Manchester, Manchester, UK
| | - Graham D Pavitt
- Division of Molecular and Cellular Function, School of Biological Sciences, The University of Manchester, Manchester, UK.
| | - Simon J Hubbard
- Division of Molecular and Cellular Function, School of Biological Sciences, The University of Manchester, Manchester, UK.
| | - Mark P Ashe
- Division of Molecular and Cellular Function, School of Biological Sciences, The University of Manchester, Manchester, UK.
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66
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Zuberek J, Warzecha M, Dobrowolski M, Modrak-Wojcik A. An intramolecular disulphide bond in human 4E-T affects its binding to eIF4E1a protein. EUROPEAN BIOPHYSICS JOURNAL : EBJ 2023; 52:497-510. [PMID: 37798395 PMCID: PMC10618305 DOI: 10.1007/s00249-023-01684-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Revised: 09/14/2023] [Accepted: 09/16/2023] [Indexed: 10/07/2023]
Abstract
The cap at the 5'terminus of mRNA is a key determinant of gene expression in eukaryotic cells, which among others is required for cap dependent translation and protects mRNA from degradation. These properties of cap are mediated by several proteins. One of them is 4E-Transporter (4E-T), which plays an important role in translational repression, mRNA decay and P-bodies formation. 4E-T is also one of several proteins that interact with eukaryotic initiation factor 4E (eIF4E), a cap binding protein which is a key component of the translation initiation machinery. The molecular mechanisms underlying the interactions of these two proteins are crucial for mRNA processing. Studying the interactions between human eIF4E1a and the N-terminal fragment of 4E-T that possesses unstructured 4E-binding motifs under non-reducing conditions, we observed that 4E-T preferentially forms an intramolecular disulphide bond. This "disulphide loop" reduces affinity of 4E-T for eIF4E1a by about 300-fold. Considering that only human 4E-T possesses two cysteines located between the 4E binding motifs, we proposed that the disulphide bond may act as a switch to regulate interactions between the two proteins.
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Affiliation(s)
- Joanna Zuberek
- Division of Biophysics, Institute of Experimental Physics, Faculty of Physics, University of Warsaw, Warsaw, Poland.
| | - Marek Warzecha
- Division of Biophysics, Institute of Experimental Physics, Faculty of Physics, University of Warsaw, Warsaw, Poland
| | - Mateusz Dobrowolski
- Division of Biophysics, Institute of Experimental Physics, Faculty of Physics, University of Warsaw, Warsaw, Poland
| | - Anna Modrak-Wojcik
- Division of Biophysics, Institute of Experimental Physics, Faculty of Physics, University of Warsaw, Warsaw, Poland
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67
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Liu Z, Cao H, Fan Y, Wang Y, Wang J. Strong Inhibition of Ice Growth by Biomimetic Crowding Coacervates. Angew Chem Int Ed Engl 2023; 62:e202311047. [PMID: 37534606 DOI: 10.1002/anie.202311047] [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: 08/01/2023] [Revised: 08/02/2023] [Accepted: 08/03/2023] [Indexed: 08/04/2023]
Abstract
The freezing of biological fluids is intensively studied but remains elusive as it is affected not only by the various components but also by the crowding nature of the biological fluids. Herein, we constructed spherical crowders, fibrous crowders, and coacervates by various components ranging from surfactants to polymers and proteins, to mimic three typical crowders in biological fluids, i.e., globular proteins, fibrous networks, and condensates of biomolecules. It is elucidated that the three crowders exhibit low, moderate, and strong ice growth inhibition activity, respectively, resulting from their different abilities in slowing down water dynamics. Intriguingly, the coacervate consisting of molecules without obvious ice growth inhibition activity strongly inhibits ice growth, which is firstly employed as a highly-potent cryoprotectant. This work provides new insights into the survival of freezing-tolerant organisms and opens an avenue for the design of ice-controlling materials.
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Affiliation(s)
- Zhang Liu
- Technical Institute of Physics and Chemistry, Chinese Academy of Sciences, Beijing, 100190, P. R. China
| | - Huimei Cao
- Beijing National Laboratory for Molecular Sciences, Institute of Chemistry, Chinese Academy of Sciences, Beijing, 100190, P. R. China
- School of Chemical Sciences, University of Chinese Academy of Sciences, Beijing, 100190, P. R. China
| | - Yaxun Fan
- Beijing National Laboratory for Molecular Sciences, Institute of Chemistry, Chinese Academy of Sciences, Beijing, 100190, P. R. China
| | - Yilin Wang
- Beijing National Laboratory for Molecular Sciences, Institute of Chemistry, Chinese Academy of Sciences, Beijing, 100190, P. R. China
- School of Chemical Sciences, University of Chinese Academy of Sciences, Beijing, 100190, P. R. China
| | - Jianjun Wang
- Technical Institute of Physics and Chemistry, Chinese Academy of Sciences, Beijing, 100190, P. R. China
- School of Chemical Sciences, University of Chinese Academy of Sciences, Beijing, 100190, P. R. China
- School of Future Technology, University of Chinese Academy of Sciences, Beijing, 100190, P. R. China
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68
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Field S, Jang GJ, Dean C, Strader LC, Rhee SY. Plants use molecular mechanisms mediated by biomolecular condensates to integrate environmental cues with development. THE PLANT CELL 2023; 35:3173-3186. [PMID: 36879427 PMCID: PMC10473230 DOI: 10.1093/plcell/koad062] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/10/2022] [Revised: 02/01/2023] [Accepted: 02/09/2023] [Indexed: 06/18/2023]
Abstract
This review highlights recent literature on biomolecular condensates in plant development and discusses challenges for fully dissecting their functional roles. Plant developmental biology has been inundated with descriptive examples of biomolecular condensate formation, but it is only recently that mechanistic understanding has been forthcoming. Here, we discuss recent examples of potential roles biomolecular condensates play at different stages of the plant life cycle. We group these examples based on putative molecular functions, including sequestering interacting components, enhancing dwell time, and interacting with cytoplasmic biophysical properties in response to environmental change. We explore how these mechanisms could modulate plant development in response to environmental inputs and discuss challenges and opportunities for further research into deciphering molecular mechanisms to better understand the diverse roles that biomolecular condensates exert on life.
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Affiliation(s)
- Sterling Field
- Department of Plant Biology, Carnegie Institution for Science, Stanford, CA 94305, USA
| | - Geng-Jen Jang
- Department of Cell and Developmental Biology, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK
| | - Caroline Dean
- Department of Cell and Developmental Biology, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK
| | - Lucia C Strader
- Department of Biology, Duke University, Durham, NC 27708, USA
| | - Seung Y Rhee
- Department of Plant Biology, Carnegie Institution for Science, Stanford, CA 94305, USA
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69
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Cantley J, Eizirik DL, Latres E, Dayan CM. Islet cells in human type 1 diabetes: from recent advances to novel therapies - a symposium-based roadmap for future research. J Endocrinol 2023; 259:e230082. [PMID: 37493471 PMCID: PMC10502961 DOI: 10.1530/joe-23-0082] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/21/2023] [Accepted: 07/25/2023] [Indexed: 07/27/2023]
Abstract
There is a growing understanding that the early phases of type 1 diabetes (T1D) are characterised by a deleterious dialogue between the pancreatic beta cells and the immune system. This, combined with the urgent need to better translate this growing knowledge into novel therapies, provided the background for the JDRF-DiabetesUK-INNODIA-nPOD symposium entitled 'Islet cells in human T1D: from recent advances to novel therapies', which took place in Stockholm, Sweden, in September 2022. We provide in this article an overview of the main themes addressed in the symposium, pointing to both promising conclusions and key unmet needs that remain to be addressed in order to achieve better approaches to prevent or reverse T1D.
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Affiliation(s)
- J Cantley
- School of Medicine, University of Dundee, Dundee, United Kingdom of Great Britain and Northern Ireland
| | - D L Eizirik
- ULB Center for Diabetes Research, Université Libre de Bruxelles Faculté de Médecine, Bruxelles, Belgium
| | - E Latres
- JDRF International, New York, NY, USA
| | - C M Dayan
- Cardiff University School of Medicine, Cardiff, United Kingdom of Great Britain and Northern Ireland
| | - the JDRF-DiabetesUK-INNODIA-nPOD Stockholm Symposium 2022
- School of Medicine, University of Dundee, Dundee, United Kingdom of Great Britain and Northern Ireland
- ULB Center for Diabetes Research, Université Libre de Bruxelles Faculté de Médecine, Bruxelles, Belgium
- JDRF International, New York, NY, USA
- Cardiff University School of Medicine, Cardiff, United Kingdom of Great Britain and Northern Ireland
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70
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Wang W, Wang C, Wang Y, Ma J, Wang T, Tao Z, Liu P, Li S, Hu Y, Gu A, Wang H, Qiu C, Li P. The P-body component DECAPPING5 and the floral repressor SISTER OF FCA regulate FLOWERING LOCUS C transcription in Arabidopsis. THE PLANT CELL 2023; 35:3303-3324. [PMID: 37220754 PMCID: PMC10473201 DOI: 10.1093/plcell/koad151] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/16/2022] [Revised: 03/28/2023] [Accepted: 04/30/2023] [Indexed: 05/25/2023]
Abstract
Flowering is the transition from vegetative to reproductive growth and is critical for plant adaptation and reproduction. FLOWERING LOCUS C (FLC) plays a central role in flowering time control, and dissecting its regulation mechanism provides essential information for crop improvement. Here, we report that DECAPPING5 (DCP5), a component of processing bodies (P-bodies), regulates FLC transcription and flowering time in Arabidopsis (Arabidopsis thaliana). DCP5 and its interacting partner SISTER OF FCA (SSF) undergo liquid-liquid phase separation (LLPS) that is mediated by their prion-like domains (PrDs). Enhancing or attenuating the LLPS of both proteins using transgenic methods greatly affects their ability to regulate FLC and flowering time. DCP5 regulates FLC transcription by modulating RNA polymerase II enrichment at the FLC locus. DCP5 requires SSF for FLC regulation, and loss of SSF or its PrD disrupts DCP5 function. Our results reveal that DCP5 interacts with SSF, and the nuclear DCP5-SSF complex regulates FLC expression at the transcriptional level.
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Affiliation(s)
- Wanyi Wang
- The National Engineering Lab of Crop Stress Resistance Breeding, School of Life Sciences, Anhui Agricultural University, Hefei 230036, China
| | - Chuanhong Wang
- The National Engineering Lab of Crop Stress Resistance Breeding, School of Life Sciences, Anhui Agricultural University, Hefei 230036, China
| | - Yunhe Wang
- The National Engineering Lab of Crop Stress Resistance Breeding, School of Life Sciences, Anhui Agricultural University, Hefei 230036, China
| | - Jing Ma
- The National Engineering Lab of Crop Stress Resistance Breeding, School of Life Sciences, Anhui Agricultural University, Hefei 230036, China
| | - Tengyue Wang
- The National Engineering Lab of Crop Stress Resistance Breeding, School of Life Sciences, Anhui Agricultural University, Hefei 230036, China
| | - Zhen Tao
- The National Engineering Lab of Crop Stress Resistance Breeding, School of Life Sciences, Anhui Agricultural University, Hefei 230036, China
| | - Peipei Liu
- The National Engineering Lab of Crop Stress Resistance Breeding, School of Life Sciences, Anhui Agricultural University, Hefei 230036, China
| | - Shuai Li
- The National Engineering Lab of Crop Stress Resistance Breeding, School of Life Sciences, Anhui Agricultural University, Hefei 230036, China
| | - Yuanyuan Hu
- The National Engineering Lab of Crop Stress Resistance Breeding, School of Life Sciences, Anhui Agricultural University, Hefei 230036, China
| | - Aiju Gu
- The National Engineering Lab of Crop Stress Resistance Breeding, School of Life Sciences, Anhui Agricultural University, Hefei 230036, China
| | - Hui Wang
- The National Engineering Lab of Crop Stress Resistance Breeding, School of Life Sciences, Anhui Agricultural University, Hefei 230036, China
| | - Chunhong Qiu
- The National Engineering Lab of Crop Stress Resistance Breeding, School of Life Sciences, Anhui Agricultural University, Hefei 230036, China
| | - Peijin Li
- The National Engineering Lab of Crop Stress Resistance Breeding, School of Life Sciences, Anhui Agricultural University, Hefei 230036, China
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71
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Solis-Miranda J, Chodasiewicz M, Skirycz A, Fernie AR, Moschou PN, Bozhkov PV, Gutierrez-Beltran E. Stress-related biomolecular condensates in plants. THE PLANT CELL 2023; 35:3187-3204. [PMID: 37162152 PMCID: PMC10473214 DOI: 10.1093/plcell/koad127] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/08/2022] [Revised: 04/07/2023] [Accepted: 04/27/2023] [Indexed: 05/11/2023]
Abstract
Biomolecular condensates are membraneless organelle-like structures that can concentrate molecules and often form through liquid-liquid phase separation. Biomolecular condensate assembly is tightly regulated by developmental and environmental cues. Although research on biomolecular condensates has intensified in the past 10 years, our current understanding of the molecular mechanisms and components underlying their formation remains in its infancy, especially in plants. However, recent studies have shown that the formation of biomolecular condensates may be central to plant acclimation to stress conditions. Here, we describe the mechanism, regulation, and properties of stress-related condensates in plants, focusing on stress granules and processing bodies, 2 of the most well-characterized biomolecular condensates. In this regard, we showcase the proteomes of stress granules and processing bodies in an attempt to suggest methods for elucidating the composition and function of biomolecular condensates. Finally, we discuss how biomolecular condensates modulate stress responses and how they might be used as targets for biotechnological efforts to improve stress tolerance.
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Affiliation(s)
- Jorge Solis-Miranda
- Institutode Bioquimica Vegetal y Fotosintesis, Consejo Superior de Investigaciones Cientificas (CSIC)-Universidad de Sevilla, 41092 Sevilla, Spain
| | - Monika Chodasiewicz
- Biological and Environmental Science and Engineering Division, Center for Desert Agriculture, King Abdullah University of Science and Technology, Thuwal 23955-6900, Saudi Arabia
| | | | - Alisdair R Fernie
- Max-Planck-Institute of Molecular Plant Physiology, 14476 Potsdam-Golm, Germany
| | - Panagiotis N Moschou
- Department of Plant Biology, Uppsala BioCenter, Swedish University of Agricultural Sciences and Linnean Center for Plant Biology, 75007 Uppsala, Sweden
- Department of Biology, University of Crete, Heraklion 71409, Greece
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology-Hellas, Heraklion 70013, Greece
| | - Peter V Bozhkov
- Department of Molecular Sciences, Uppsala BioCenter, Swedish University of Agricultural Sciences and Linnean Center for Plant Biology, 75007 Uppsala, Sweden
| | - Emilio Gutierrez-Beltran
- Institutode Bioquimica Vegetal y Fotosintesis, Consejo Superior de Investigaciones Cientificas (CSIC)-Universidad de Sevilla, 41092 Sevilla, Spain
- Departamento de Bioquimica Vegetal y Biologia Molecular, Facultad de Biologia, Universidad de Sevilla, 41012 Sevilla, Spain
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72
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Seyhan AA. Circulating microRNAs as Potential Biomarkers in Pancreatic Cancer-Advances and Challenges. Int J Mol Sci 2023; 24:13340. [PMID: 37686149 PMCID: PMC10488102 DOI: 10.3390/ijms241713340] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2023] [Revised: 08/21/2023] [Accepted: 08/25/2023] [Indexed: 09/10/2023] Open
Abstract
There is an urgent unmet need for robust and reliable biomarkers for early diagnosis, prognosis, and prediction of response to specific treatments of many aggressive and deadly cancers, such as pancreatic cancer, and liquid biopsy-based miRNA profiling has the potential for this. MiRNAs are a subset of non-coding RNAs that regulate the expression of a multitude of genes post-transcriptionally and thus are potential diagnostic, prognostic, and predictive biomarkers and have also emerged as potential therapeutics. Because miRNAs are involved in the post-transcriptional regulation of their target mRNAs via repressing gene expression, defects in miRNA biogenesis pathway and miRNA expression perturb the expression of a multitude of oncogenic or tumor-suppressive genes that are involved in the pathogenesis of various cancers. As such, numerous miRNAs have been identified to be downregulated or upregulated in many cancers, functioning as either oncomes or oncosuppressor miRs. Moreover, dysregulation of miRNA biogenesis pathways can also change miRNA expression and function in cancer. Profiling of dysregulated miRNAs in pancreatic cancer has been shown to correlate with disease diagnosis, indicate optimal treatment options and predict response to a specific therapy. Specific miRNA signatures can track the stages of pancreatic cancer and hold potential as diagnostic, prognostic, and predictive markers, as well as therapeutics such as miRNA mimics and miRNA inhibitors (antagomirs). Furthermore, identified specific miRNAs and genes they regulate in pancreatic cancer along with downstream pathways can be used as potential therapeutic targets. However, a limited understanding and validation of the specific roles of miRNAs, lack of tissue specificity, methodological, technical, or analytical reproducibility, harmonization of miRNA isolation and quantification methods, the use of standard operating procedures, and the availability of automated and standardized assays to improve reproducibility between independent studies limit bench-to-bedside translation of the miRNA biomarkers for clinical applications. Here I review recent findings on miRNAs in pancreatic cancer pathogenesis and their potential as diagnostic, prognostic, and predictive markers.
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Affiliation(s)
- Attila A. Seyhan
- Laboratory of Translational Oncology and Experimental Cancer Therapeutics, Warren Alpert Medical School, Brown University, Providence, RI 02912, USA;
- Department of Pathology and Laboratory Medicine, Warren Alpert Medical School, Brown University, Providence, RI 02912, USA
- Joint Program in Cancer Biology, Lifespan Health System and Brown University, Providence, RI 02912, USA
- Legorreta Cancer Center, Brown University, Providence, RI 02912, USA
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73
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Wilby EL, Weil TT. Relating the Biogenesis and Function of P Bodies in Drosophila to Human Disease. Genes (Basel) 2023; 14:1675. [PMID: 37761815 PMCID: PMC10530015 DOI: 10.3390/genes14091675] [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: 07/31/2023] [Revised: 08/17/2023] [Accepted: 08/18/2023] [Indexed: 09/29/2023] Open
Abstract
Drosophila has been a premier model organism for over a century and many discoveries in flies have furthered our understanding of human disease. Flies have been successfully applied to many aspects of health-based research spanning from behavioural addiction, to dysplasia, to RNA dysregulation and protein misfolding. Recently, Drosophila tissues have been used to study biomolecular condensates and their role in multicellular systems. Identified in a wide range of plant and animal species, biomolecular condensates are dynamic, non-membrane-bound sub-compartments that have been observed and characterised in the cytoplasm and nuclei of many cell types. Condensate biology has exciting research prospects because of their diverse roles within cells, links to disease, and potential for therapeutics. In this review, we will discuss processing bodies (P bodies), a conserved biomolecular condensate, with a particular interest in how Drosophila can be applied to advance our understanding of condensate biogenesis and their role in disease.
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Affiliation(s)
| | - Timothy T. Weil
- Department of Zoology, University of Cambridge, Downing Street, Cambridge CB2 3EJ, UK;
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Piroska L, Fenyi A, Thomas S, Plamont MA, Redeker V, Melki R, Gueroui Z. α-Synuclein liquid condensates fuel fibrillar α-synuclein growth. SCIENCE ADVANCES 2023; 9:eadg5663. [PMID: 37585526 PMCID: PMC10431715 DOI: 10.1126/sciadv.adg5663] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/06/2023] [Accepted: 07/13/2023] [Indexed: 08/18/2023]
Abstract
α-Synuclein (α-Syn) aggregation into fibrils with prion-like features is intimately associated with Lewy pathology and various synucleinopathies. Emerging studies suggest that α-Syn could form liquid condensates through phase separation. The role of these condensates in aggregation and disease remains elusive and the interplay between α-Syn fibrils and α-Syn condensates remains unexplored, possibly due to difficulties in triggering the formation of α-Syn condensates in cells. To address this gap, we developed an assay allowing the controlled assembly/disassembly of α-Syn condensates in cells and studied them upon exposure to preformed α-Syn fibrillar polymorphs. Fibrils triggered the evolution of liquid α-Syn condensates into solid-like structures displaying growing needle-like extensions and exhibiting pathological amyloid hallmarks. No such changes were elicited on α-Syn that did not undergo phase separation. We, therefore, propose a model where α-Syn within condensates fuels exogenous fibrillar seeds growth, thus speeding up the prion-like propagation of pathogenic aggregates.
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Affiliation(s)
- Leonard Piroska
- PASTEUR, Department of Chemistry, École Normale Supérieure, PSL University, Sorbonne Université, CNRS, 75005 Paris, France
| | - Alexis Fenyi
- Institut Francois Jacob (MIRCen), CEA, CNRS, Fontenay-aux-Roses, France
| | - Scott Thomas
- PASTEUR, Department of Chemistry, École Normale Supérieure, PSL University, Sorbonne Université, CNRS, 75005 Paris, France
| | - Marie-Aude Plamont
- PASTEUR, Department of Chemistry, École Normale Supérieure, PSL University, Sorbonne Université, CNRS, 75005 Paris, France
| | - Virginie Redeker
- Institut Francois Jacob (MIRCen), CEA, CNRS, Fontenay-aux-Roses, France
| | - Ronald Melki
- Institut Francois Jacob (MIRCen), CEA, CNRS, Fontenay-aux-Roses, France
| | - Zoher Gueroui
- PASTEUR, Department of Chemistry, École Normale Supérieure, PSL University, Sorbonne Université, CNRS, 75005 Paris, France
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75
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Pan J, Qiu Q, Kumar D, Xu J, Tong X, Shen Z, Zhu M, Hu X, Gong C. Interaction between Bombyx mori Cytoplasmic Polyhedrosis Virus NSP8 and BmAgo2 Inhibits RNA Interference and Enhances Virus Proliferation. Microbiol Spectr 2023; 11:e0493822. [PMID: 37341621 PMCID: PMC10434170 DOI: 10.1128/spectrum.04938-22] [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: 12/01/2022] [Accepted: 05/28/2023] [Indexed: 06/22/2023] Open
Abstract
Some insect viruses encode suppressors of RNA interference (RNAi) to counteract the antiviral RNAi pathway. However, it is unknown whether Bombyx mori cytoplasmic polyhedrosis virus (BmCPV) encodes an RNAi suppressor. In this study, the presence of viral small interfering RNA (vsiRNA) in BmN cells infected with BmCPV was confirmed by small RNA sequencing. The Dual-Luciferase reporter test demonstrated that BmCPV infection may prevent firefly luciferase (Luc) gene silencing caused by particular short RNA. It was also established that the inhibition relied on the nonstructural protein NSP8, which suggests that NSP8 was a possible RNAi suppressor. In cultured BmN cells, the expressions of viral structural protein 1 (vp1) and NSP9 were triggered by overexpression of nsp8, suggesting that BmCPV proliferation was enhanced by NSP8. A pulldown assay was conducted with BmCPV genomic double-stranded RNA (dsRNA) labeled with biotin. The mass spectral detection of NSP8 in the pulldown complex suggests that NSP8 is capable of direct binding to BmCPV genomic dsRNA. The colocalization of NSP8 and B. mori Argonaute 2 (BmAgo2) was detected by an immunofluorescence assay, leading to the hypothesis that NSP8 interacts with BmAgo2. Coimmunoprecipitation further supported the present investigation. Moreover, vasa intronic protein, a component of RNA-induced silencing complex (RISC), could be detected in the coprecipitation complex of NSP8 by mass spectrum analysis. NSP8 and the mRNA decapping protein (Dcp2) were also discovered to colocalize to processing bodies (P bodies) for RNAi-mediated gene silencing in Saccharomyces cerevisiae. These findings revealed that by interacting with BmAgo2 and suppressing RNAi, NSP8 promoted BmCPV growth. IMPORTANCE It has been reported that the RNAi pathway is inhibited by binding RNAi suppressors encoded by some insect-specific viruses belonging to Dicistroviridae, Nodaviridae, or Birnaviridae to dsRNAs to protect dsRNAs from being cut by Dicer-2. However, it is unknown whether BmCPV, belonging to Spinareoviridae, encodes an RNAi suppressor. In this study, we found that nonstructural protein NSP8 encoded by BmCPV inhibits small interfering RNA (siRNA)-induced RNAi and that NSP8, as an RNAi suppressor, can bind to viral dsRNAs and interact with BmAgo2. Moreover, vasa intronic protein, a component of RISC, was found to interact with NSP8. Heterologously expressed NSP8 and Dcp2 were colocalized to P bodies in yeast. These results indicated that NSP8 promoted BmCPV proliferation by binding itself to BmCPV genomic dsRNAs and interacting with BmAgo2 through suppression of siRNA-induced RNAi. Our findings deepen our understanding of the game between BmCPV and silkworm in regulating viral infection.
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Affiliation(s)
- Jun Pan
- School of Biology and Basic Medical Sciences, Soochow University, Suzhou, Jiangsu, China
| | - Qunnan Qiu
- School of Biology and Basic Medical Sciences, Soochow University, Suzhou, Jiangsu, China
| | - Dhiraj Kumar
- School of Biology and Basic Medical Sciences, Soochow University, Suzhou, Jiangsu, China
- Department of Zoology, Hansraj College, University of Delhi, Delhi, India
| | - Jian Xu
- School of Biology and Basic Medical Sciences, Soochow University, Suzhou, Jiangsu, China
| | - Xinyu Tong
- School of Biology and Basic Medical Sciences, Soochow University, Suzhou, Jiangsu, China
| | - Zeen Shen
- School of Biology and Basic Medical Sciences, Soochow University, Suzhou, Jiangsu, China
| | - Min Zhu
- School of Biology and Basic Medical Sciences, Soochow University, Suzhou, Jiangsu, China
| | - Xiaolong Hu
- School of Biology and Basic Medical Sciences, Soochow University, Suzhou, Jiangsu, China
- Agricultural Biotechnology Research Institute, Agricultural Biotechnology and Ecological Research Institute, Soochow University, Suzhou, China
| | - Chengliang Gong
- School of Biology and Basic Medical Sciences, Soochow University, Suzhou, Jiangsu, China
- Agricultural Biotechnology Research Institute, Agricultural Biotechnology and Ecological Research Institute, Soochow University, Suzhou, China
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76
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Daskalaki I, Markaki M, Gkikas I, Tavernarakis N. Local coordination of mRNA storage and degradation near mitochondria modulates C. elegans ageing. EMBO J 2023; 42:e112446. [PMID: 37427543 PMCID: PMC10425844 DOI: 10.15252/embj.2022112446] [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: 08/23/2022] [Revised: 06/10/2023] [Accepted: 06/17/2023] [Indexed: 07/11/2023] Open
Abstract
Mitochondria are central regulators of healthspan and lifespan, yet the intricate choreography of multiple, tightly controlled steps regulating mitochondrial biogenesis remains poorly understood. Here, we uncover a pivotal role for specific elements of the 5'-3' mRNA degradation pathway in the regulation of mitochondrial abundance and function. We find that the mRNA degradation and the poly-A tail deadenylase CCR4-NOT complexes form distinct foci in somatic Caenorhabditis elegans cells that physically and functionally associate with mitochondria. Components of these two multi-subunit complexes bind transcripts of nuclear-encoded mitochondria-targeted proteins to regulate mitochondrial biogenesis during ageing in an opposite manner. In addition, we show that balanced degradation and storage of mitochondria-targeted protein mRNAs are critical for mitochondrial homeostasis, stress resistance and longevity. Our findings reveal a multifaceted role of mRNA metabolism in mitochondrial biogenesis and show that fine-tuning of mRNA turnover and local translation control mitochondrial abundance and promote longevity in response to stress and during ageing.
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Affiliation(s)
- Ioanna Daskalaki
- Institute of Molecular Biology and BiotechnologyFoundation for Research and Technology‐HellasHeraklionGreece
- Department of Biology, School of Sciences and EngineeringUniversity of CreteHeraklionGreece
| | - Maria Markaki
- Institute of Molecular Biology and BiotechnologyFoundation for Research and Technology‐HellasHeraklionGreece
| | - Ilias Gkikas
- Institute of Molecular Biology and BiotechnologyFoundation for Research and Technology‐HellasHeraklionGreece
| | - Nektarios Tavernarakis
- Institute of Molecular Biology and BiotechnologyFoundation for Research and Technology‐HellasHeraklionGreece
- Division of Basic Sciences, School of MedicineUniversity of CreteHeraklionGreece
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77
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Shan LY, Tian Y, Liu WX, Fan HT, Li FG, Liu WJ, Li A, Shen W, Sun QY, Liu YB, Zhou Y, Zhang T. LSM14B controls oocyte mRNA storage and stability to ensure female fertility. Cell Mol Life Sci 2023; 80:247. [PMID: 37578641 PMCID: PMC10425512 DOI: 10.1007/s00018-023-04898-2] [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: 05/15/2023] [Revised: 07/07/2023] [Accepted: 07/24/2023] [Indexed: 08/15/2023]
Abstract
Controlled mRNA storage and stability is essential for oocyte meiosis and early embryonic development. However, how to regulate mRNA storage and stability in mammalian oogenesis remains elusive. Here we showed that LSM14B, a component of membraneless compartments including P-body-like granules and mitochondria-associated ribonucleoprotein domain (MARDO) in germ cell, is indispensable for female fertility. To reveal loss of LSM14B disrupted primordial follicle assembly and caused mRNA reduction in non-growing oocytes, which was concomitant with the impaired assembly of P-body-like granules. 10× Genomics single-cell RNA-sequencing and immunostaining were performed. Meanwhile, we conducted RNA-seq analysis of GV-stage oocytes and found that Lsm14b deficiency not only impaired the maternal mRNA accumulation but also disrupted the translation in fully grown oocytes, which was closely associated with dissolution of MARDO components. Moreover, Lsm14b-deficient oocytes reassembled a pronucleus containing decondensed chromatin after extrusion of the first polar body, through compromising the activation of maturation promoting factor, while the defects were restored via WEE1/2 inhibitor. Together, our findings reveal that Lsm14b plays a pivotal role in mammalian oogenesis by specifically controlling of oocyte mRNA storage and stability.
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Affiliation(s)
- Li-Ying Shan
- State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock (R2BGL), College of Life Sciences, Inner Mongolia University, Hohhot, 010070, China
| | - Yu Tian
- State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock (R2BGL), College of Life Sciences, Inner Mongolia University, Hohhot, 010070, China
| | - Wen-Xiang Liu
- State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock (R2BGL), College of Life Sciences, Inner Mongolia University, Hohhot, 010070, China
| | - Hai-Tao Fan
- State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock (R2BGL), College of Life Sciences, Inner Mongolia University, Hohhot, 010070, China
| | - Feng-Guo Li
- State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock (R2BGL), College of Life Sciences, Inner Mongolia University, Hohhot, 010070, China
| | - Wen-Juan Liu
- State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock (R2BGL), College of Life Sciences, Inner Mongolia University, Hohhot, 010070, China
| | - Ang Li
- State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock (R2BGL), College of Life Sciences, Inner Mongolia University, Hohhot, 010070, China
- Fertility Preservation Lab, Guangdong-Hong Kong Metabolism & Reproduction Joint Laboratory, Reproductive Medicine Center, Guangdong Second Provincial General Hospital, Guangzhou, 510317, China
| | - Wei Shen
- College of Life Sciences, Institute of Reproductive Sciences, Qingdao Agricultural University, Qingdao, 266109, China
| | - Qing-Yuan Sun
- Fertility Preservation Lab, Guangdong-Hong Kong Metabolism & Reproduction Joint Laboratory, Reproductive Medicine Center, Guangdong Second Provincial General Hospital, Guangzhou, 510317, China
| | - Yong-Bin Liu
- State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock (R2BGL), College of Life Sciences, Inner Mongolia University, Hohhot, 010070, China.
| | - Yang Zhou
- State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock (R2BGL), College of Life Sciences, Inner Mongolia University, Hohhot, 010070, China.
| | - Teng Zhang
- State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock (R2BGL), College of Life Sciences, Inner Mongolia University, Hohhot, 010070, China.
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78
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George J, Stegmann M, Monaghan J, Bailey-Serres J, Zipfel C. Arabidopsis translation initiation factor binding protein CBE1 negatively regulates accumulation of the NADPH oxidase respiratory burst oxidase homolog D. J Biol Chem 2023; 299:105018. [PMID: 37423301 PMCID: PMC10432800 DOI: 10.1016/j.jbc.2023.105018] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2022] [Revised: 06/08/2023] [Accepted: 06/10/2023] [Indexed: 07/11/2023] Open
Abstract
Cell surface pattern recognition receptors sense invading pathogens by binding microbial or endogenous elicitors to activate plant immunity. These responses are under tight control to avoid excessive or untimely activation of cellular responses, which may otherwise be detrimental to host cells. How this fine-tuning is accomplished is an area of active study. We previously described a suppressor screen that identified Arabidopsis thaliana mutants with regained immune signaling in the immunodeficient genetic background bak1-5, which we named modifier of bak1-5 (mob) mutants. Here, we report that bak1-5 mob7 mutant restores elicitor-induced signaling. Using a combination of map-based cloning and whole-genome resequencing, we identified MOB7 as conserved binding of eIF4E1 (CBE1), a plant-specific protein that interacts with the highly conserved eukaryotic translation initiation factor eIF4E1. Our data demonstrate that CBE1 regulates the accumulation of respiratory burst oxidase homolog D, the NADPH oxidase responsible for elicitor-induced apoplastic reactive oxygen species production. Furthermore, several mRNA decapping and translation initiation factors colocalize with CBE1 and similarly regulate immune signaling. This study thus identifies a novel regulator of immune signaling and provides new insights into reactive oxygen species regulation, potentially through translational control, during plant stress responses.
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Affiliation(s)
- Jeoffrey George
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich, United Kingdom; Institute of Plant and Microbial Biology and Zürich-Basel Plant Science Center, University of Zürich, Zürich, Switzerland
| | - Martin Stegmann
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich, United Kingdom
| | - Jacqueline Monaghan
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich, United Kingdom
| | - Julia Bailey-Serres
- Department of Botany and Plant Sciences, Center for Plant Cell Biology, University of California, Riverside, Riverside, California, USA
| | - Cyril Zipfel
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich, United Kingdom; Institute of Plant and Microbial Biology and Zürich-Basel Plant Science Center, University of Zürich, Zürich, Switzerland.
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79
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Pietilä MK, Bachmann JJ, Ravantti J, Pelkmans L, Fraefel C. Cellular state landscape and herpes simplex virus type 1 infection progression are connected. Nat Commun 2023; 14:4515. [PMID: 37500668 PMCID: PMC10374626 DOI: 10.1038/s41467-023-40148-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2022] [Accepted: 07/14/2023] [Indexed: 07/29/2023] Open
Abstract
Prediction, prevention and treatment of virus infections require understanding of cell-to-cell variability that leads to heterogenous disease outcomes, but the source of this heterogeneity has yet to be clarified. To study the multimodal response of single human cells to herpes simplex virus type 1 (HSV-1) infection, we mapped high-dimensional viral and cellular state spaces throughout the infection using multiplexed imaging and quantitative single-cell measurements of viral and cellular mRNAs and proteins. Here we show that the high-dimensional cellular state scape can predict heterogenous infections, and cells move through the cellular state landscape according to infection progression. Spatial information reveals that infection changes the cellular state of both infected cells and of their neighbors. The multiplexed imaging of HSV-1-induced cellular modifications links infection progression to changes in signaling responses, transcriptional activity, and processing bodies. Our data show that multiplexed quantification of responses at the single-cell level, across thousands of cells helps predict infections and identify new targets for antivirals.
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Affiliation(s)
- Maija K Pietilä
- Institute of Virology, University of Zurich, Zurich, Switzerland.
| | - Jana J Bachmann
- Institute of Virology, University of Zurich, Zurich, Switzerland
| | - Janne Ravantti
- Molecular and Integrative Biosciences Research Programme, University of Helsinki, Helsinki, Finland
| | - Lucas Pelkmans
- Department of Molecular Life Sciences, University of Zurich, Zurich, Switzerland
| | - Cornel Fraefel
- Institute of Virology, University of Zurich, Zurich, Switzerland.
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80
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Abstract
Biomolecular condensates are reversible compartments that form through a process called phase separation. Post-translational modifications like ADP-ribosylation can nucleate the formation of these condensates by accelerating the self-association of proteins. Poly(ADP-ribose) (PAR) chains are remarkably transient modifications with turnover rates on the order of minutes, yet they can be required for the formation of granules in response to oxidative stress, DNA damage, and other stimuli. Moreover, accumulation of PAR is linked with adverse phase transitions in neurodegenerative diseases, including Alzheimer's disease, Parkinson's disease, and amyotrophic lateral sclerosis. In this review, we provide a primer on how PAR is synthesized and regulated, the diverse structures and chemistries of ADP-ribosylation modifications, and protein-PAR interactions. We review substantial progress in recent efforts to determine the molecular mechanism of PAR-mediated phase separation, and we further delineate how inhibitors of PAR polymerases may be effective treatments for neurodegenerative pathologies. Finally, we highlight the need for rigorous biochemical interrogation of ADP-ribosylation in vivo and in vitro to clarify the exact pathway from PARylation to condensate formation.
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Affiliation(s)
- Kevin Rhine
- Program in Cell, Molecular, Developmental Biology, and Biophysics, Johns Hopkins University, Baltimore, Maryland 21218, United States
- Department of Biology, Johns Hopkins University, Baltimore, Maryland 21218, United States
| | - Hana M Odeh
- Department of Biochemistry and Biophysics, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania 19104, United States
| | - James Shorter
- Department of Biochemistry and Biophysics, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania 19104, United States
| | - Sua Myong
- Program in Cell, Molecular, Developmental Biology, and Biophysics, Johns Hopkins University, Baltimore, Maryland 21218, United States
- Department of Biophysics, Johns Hopkins University, Baltimore, Maryland 21218, United States
- Physics Frontier Center (Center for the Physics of Living Cells), University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
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81
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Chukrallah LG, Potgieter S, Chueh L, Snyder EM. Two RNA binding proteins, ADAD2 and RNF17, interact to form a heterogeneous population of novel meiotic germ cell granules with developmentally dependent organelle association. PLoS Genet 2023; 19:e1010519. [PMID: 37428816 PMCID: PMC10359003 DOI: 10.1371/journal.pgen.1010519] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2022] [Revised: 07/20/2023] [Accepted: 06/17/2023] [Indexed: 07/12/2023] Open
Abstract
Mammalian male germ cell differentiation relies on complex RNA biogenesis events, many of which occur in non-membrane bound organelles termed RNA germ cell granules that are rich in RNA binding proteins (RBPs). Though known to be required for male germ cell differentiation, we understand little of the relationships between the numerous granule subtypes. ADAD2, a testis specific RBP, is required for normal male fertility and forms a poorly characterized granule in meiotic germ cells. This work aimed to understand the role of ADAD2 granules in male germ cell differentiation by clearly defining their molecular composition and relationship to other granules. Biochemical analyses identified RNF17, a testis specific RBP that forms meiotic male germ cell granules, as an ADAD2-interacting protein. Phenotypic analysis of Adad2 and Rnf17 mutants identified a rare post-meiotic chromatin defect, suggesting shared biological roles. ADAD2 and RNF17 were found to be dependent on one another for granularization and together form a previously unstudied set of germ cell granules. Based on co-localization studies with well-characterized granule RBPs and organelle-specific markers, a subset of the ADAD2-RNF17 granules are found to be associated with the intermitochondrial cement and piRNA biogenesis. In contrast, a second, morphologically distinct population of ADAD2-RNF17 granules co-localized with the translation regulators NANOS1 and PUM1, along with the molecular chaperone PDI. These large granules form a unique funnel-shaped structure that displays distinct protein subdomains and is tightly associated with the endoplasmic reticulum. Developmental studies suggest the different granule populations represent different phases of a granule maturation process. Lastly, a double Adad2-Rnf17 mutant model suggests the interaction between ADAD2 and RNF17, as opposed to loss of either, is the likely driver of the Adad2 and Rnf17 mutant phenotypes. These findings shed light on the relationship between germ cell granule pools and define new genetic approaches to their study.
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Affiliation(s)
- Lauren G. Chukrallah
- Department of Animal Science, Rutgers, The State University of New Jersey, New Brunswick, New Jersey, United States of America
| | - Sarah Potgieter
- Department of Animal Science, Rutgers, The State University of New Jersey, New Brunswick, New Jersey, United States of America
| | - Lisa Chueh
- Department of Animal Science, Rutgers, The State University of New Jersey, New Brunswick, New Jersey, United States of America
| | - Elizabeth M. Snyder
- Department of Animal Science, Rutgers, The State University of New Jersey, New Brunswick, New Jersey, United States of America
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82
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Liu P, Chen Y, Zhang Z, Yuan Z, Sun JG, Xia S, Cao X, Chen J, Zhang CJ, Chen Y, Zhan H, Jin Y, Bao X, Gu Y, Zhang M, Xu Y. Noncanonical contribution of microglial transcription factor NR4A1 to post-stroke recovery through TNF mRNA destabilization. PLoS Biol 2023; 21:e3002199. [PMID: 37486903 PMCID: PMC10365314 DOI: 10.1371/journal.pbio.3002199] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2022] [Accepted: 06/14/2023] [Indexed: 07/26/2023] Open
Abstract
Microglia-mediated neuroinflammation is involved in various neurological diseases, including ischemic stroke, but the endogenous mechanisms preventing unstrained inflammation is still unclear. The anti-inflammatory role of transcription factor nuclear receptor subfamily 4 group A member 1 (NR4A1) in macrophages and microglia has previously been identified. However, the endogenous mechanisms that how NR4A1 restricts unstrained inflammation remain elusive. Here, we observed that NR4A1 is up-regulated in the cytoplasm of activated microglia and localizes to processing bodies (P-bodies). In addition, we found that cytoplasmic NR4A1 functions as an RNA-binding protein (RBP) that directly binds and destabilizes Tnf mRNA in an N6-methyladenosine (m6A)-dependent manner. Remarkably, conditional microglial deletion of Nr4a1 elevates Tnf expression and worsens outcomes in a mouse model of ischemic stroke, in which case NR4A1 expression is significantly induced in the cytoplasm of microglia. Thus, our study illustrates a novel mechanism that NR4A1 posttranscriptionally regulates Tnf expression in microglia and determines stroke outcomes.
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Affiliation(s)
- Pinyi Liu
- Department of Neurology, Nanjing Drum Tower Hospital, Affiliated Hospital of Medical School and the State Key Laboratory of Pharmaceutical Biotechnology, Nanjing University, Nanjing, China
| | - Yan Chen
- Department of Neurology, Nanjing Drum Tower Hospital, Affiliated Hospital of Medical School and the State Key Laboratory of Pharmaceutical Biotechnology, Nanjing University, Nanjing, China
| | - Zhi Zhang
- Department of Neurology, Nanjing Drum Tower Hospital, Affiliated Hospital of Medical School and the State Key Laboratory of Pharmaceutical Biotechnology, Nanjing University, Nanjing, China
| | - Zengqiang Yuan
- The Brain Science Center, Beijing Institute of Basic Medical Sciences, Beijing, China
- Center of Alzheimer's Disease, Beijing Institute for Brain Disorders, Beijing, China
| | - Jian-Guang Sun
- The Brain Science Center, Beijing Institute of Basic Medical Sciences, Beijing, China
- Center of Alzheimer's Disease, Beijing Institute for Brain Disorders, Beijing, China
| | - Shengnan Xia
- Department of Neurology, Nanjing Drum Tower Hospital, Affiliated Hospital of Medical School and the State Key Laboratory of Pharmaceutical Biotechnology, Nanjing University, Nanjing, China
| | - Xiang Cao
- Department of Neurology, Nanjing Drum Tower Hospital, Affiliated Hospital of Medical School and the State Key Laboratory of Pharmaceutical Biotechnology, Nanjing University, Nanjing, China
| | - Jian Chen
- Department of Neurology, Nanjing Drum Tower Hospital, Affiliated Hospital of Medical School and the State Key Laboratory of Pharmaceutical Biotechnology, Nanjing University, Nanjing, China
| | - Cun-Jin Zhang
- Department of Neurology, Nanjing Drum Tower Hospital, Affiliated Hospital of Medical School and the State Key Laboratory of Pharmaceutical Biotechnology, Nanjing University, Nanjing, China
| | - Yanting Chen
- Department of Neurology, Nanjing Drum Tower Hospital, Affiliated Hospital of Medical School and the State Key Laboratory of Pharmaceutical Biotechnology, Nanjing University, Nanjing, China
| | - Hui Zhan
- Department of Neurology, Nanjing Drum Tower Hospital, Affiliated Hospital of Medical School and the State Key Laboratory of Pharmaceutical Biotechnology, Nanjing University, Nanjing, China
| | - Yuexinzi Jin
- Department of Neurology, Nanjing Drum Tower Hospital, Affiliated Hospital of Medical School and the State Key Laboratory of Pharmaceutical Biotechnology, Nanjing University, Nanjing, China
| | - Xinyu Bao
- Department of Neurology, Nanjing Drum Tower Hospital, Affiliated Hospital of Medical School and the State Key Laboratory of Pharmaceutical Biotechnology, Nanjing University, Nanjing, China
| | - Yue Gu
- Department of Neurology, Nanjing Drum Tower Hospital, Affiliated Hospital of Medical School and the State Key Laboratory of Pharmaceutical Biotechnology, Nanjing University, Nanjing, China
| | - Meijuan Zhang
- Department of Neurology, Nanjing Drum Tower Hospital, Affiliated Hospital of Medical School and the State Key Laboratory of Pharmaceutical Biotechnology, Nanjing University, Nanjing, China
| | - Yun Xu
- Department of Neurology, Nanjing Drum Tower Hospital, Affiliated Hospital of Medical School and the State Key Laboratory of Pharmaceutical Biotechnology, Nanjing University, Nanjing, China
- Jiangsu Province Stroke Center for Diagnosis and Therapy, Nanjing, China
- Nanjing Neurology Clinic Medical Center, Nanjing, China
- Institute of Brain Sciences, Nanjing University, Nanjing, China
- Jiangsu Key Laboratory for Molecular Medicine, Medical School of Nanjing University, Nanjing, China
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83
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Vock IW, Simon MD. bakR: uncovering differential RNA synthesis and degradation kinetics transcriptome-wide with Bayesian hierarchical modeling. RNA (NEW YORK, N.Y.) 2023; 29:958-976. [PMID: 37028916 DOI: 10.1261/rna.079451.122] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/16/2022] [Accepted: 03/14/2023] [Indexed: 06/18/2023]
Abstract
Differential expression analysis of RNA sequencing (RNA-seq) data can identify changes in cellular RNA levels, but provides limited information about the kinetic mechanisms underlying such changes. Nucleotide recoding RNA-seq methods (NR-seq; e.g., TimeLapse-seq, SLAM-seq, etc.) address this shortcoming and are widely used approaches to identify changes in RNA synthesis and degradation kinetics. While advanced statistical models implemented in user-friendly software (e.g., DESeq2) have ensured the statistical rigor of differential expression analyses, no such tools that facilitate differential kinetic analysis with NR-seq exist. Here, we report the development of Bayesian analysis of the kinetics of RNA (bakR; https:// github.com/simonlabcode/bakR), an R package to address this need. bakR relies on Bayesian hierarchical modeling of NR-seq data to increase statistical power by sharing information across transcripts. Analyses of simulated data confirmed that bakR implementations of the hierarchical model outperform attempts to analyze differential kinetics with existing models. bakR also uncovers biological signals in real NR-seq data sets and provides improved analyses of existing data sets. This work establishes bakR as an important tool for identifying differential RNA synthesis and degradation kinetics.
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Affiliation(s)
- Isaac W Vock
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06536, USA
- Institute of Biomolecular Design and Discovery, Yale University, West Haven, Connecticut 06477, USA
| | - Matthew D Simon
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06536, USA
- Institute of Biomolecular Design and Discovery, Yale University, West Haven, Connecticut 06477, USA
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84
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Silva JL, Foguel D, Ferreira VF, Vieira TCRG, Marques MA, Ferretti GDS, Outeiro TF, Cordeiro Y, de Oliveira GAP. Targeting Biomolecular Condensation and Protein Aggregation against Cancer. Chem Rev 2023. [PMID: 37379327 DOI: 10.1021/acs.chemrev.3c00131] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/30/2023]
Abstract
Biomolecular condensates, membrane-less entities arising from liquid-liquid phase separation, hold dichotomous roles in health and disease. Alongside their physiological functions, these condensates can transition to a solid phase, producing amyloid-like structures implicated in degenerative diseases and cancer. This review thoroughly examines the dual nature of biomolecular condensates, spotlighting their role in cancer, particularly concerning the p53 tumor suppressor. Given that over half of the malignant tumors possess mutations in the TP53 gene, this topic carries profound implications for future cancer treatment strategies. Notably, p53 not only misfolds but also forms biomolecular condensates and aggregates analogous to other protein-based amyloids, thus significantly influencing cancer progression through loss-of-function, negative dominance, and gain-of-function pathways. The exact molecular mechanisms underpinning the gain-of-function in mutant p53 remain elusive. However, cofactors like nucleic acids and glycosaminoglycans are known to be critical players in this intersection between diseases. Importantly, we reveal that molecules capable of inhibiting mutant p53 aggregation can curtail tumor proliferation and migration. Hence, targeting phase transitions to solid-like amorphous and amyloid-like states of mutant p53 offers a promising direction for innovative cancer diagnostics and therapeutics.
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Affiliation(s)
- Jerson L Silva
- Institute of Medical Biochemistry Leopoldo de Meis, National Institute of Science and Technology for Structural Biology and Bioimaging, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro, RJ 21941-902, Brazil
| | - Debora Foguel
- Institute of Medical Biochemistry Leopoldo de Meis, National Institute of Science and Technology for Structural Biology and Bioimaging, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro, RJ 21941-902, Brazil
| | - Vitor F Ferreira
- Faculty of Pharmacy, Fluminense Federal University (UFF), Rio de Janeiro, RJ 21941-902, Brazil
| | - Tuane C R G Vieira
- Institute of Medical Biochemistry Leopoldo de Meis, National Institute of Science and Technology for Structural Biology and Bioimaging, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro, RJ 21941-902, Brazil
| | - Mayra A Marques
- Institute of Medical Biochemistry Leopoldo de Meis, National Institute of Science and Technology for Structural Biology and Bioimaging, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro, RJ 21941-902, Brazil
| | - Giulia D S Ferretti
- Institute of Medical Biochemistry Leopoldo de Meis, National Institute of Science and Technology for Structural Biology and Bioimaging, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro, RJ 21941-902, Brazil
| | - Tiago F Outeiro
- Department of Experimental Neurodegeneration, Center for Biostructural Imaging of Neurodegeneration, University Medical Center, 37075 Göttingen, Germany
- Max Planck Institute for Multidisciplinary Sciences, 37075 Göttingen, Germany
- Translational and Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Framlington Place, Newcastle Upon Tyne NE2 4HH, U.K
- Scientific employee with an honorary contract at Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE), 37075 Göttingen, Germany
| | - Yraima Cordeiro
- Faculty of Pharmacy, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro, RJ 21941-902, Brazil
| | - Guilherme A P de Oliveira
- Institute of Medical Biochemistry Leopoldo de Meis, National Institute of Science and Technology for Structural Biology and Bioimaging, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro, RJ 21941-902, Brazil
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85
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Shivam S, Ertl R, Sexl V, El-Matbouli M, Kumar G. Differentially expressed transcripts of Tetracapsuloides bryosalmonae (Cnidaria) between carrier and dead-end hosts involved in key biological processes: novel insights from a coupled approach of FACS and RNA sequencing. Vet Res 2023; 54:51. [PMID: 37365650 PMCID: PMC10291810 DOI: 10.1186/s13567-023-01185-7] [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: 01/23/2023] [Accepted: 05/29/2023] [Indexed: 06/28/2023] Open
Abstract
Tetracapsuloides bryosalmonae is a malacosporean endoparasite that infects a wide range of salmonids and causes proliferative kidney disease (PKD). Brown trout serves as a carrier host whereas rainbow trout represents a dead-end host. We thus asked if the parasite adapts to the different hosts by changing molecular mechanisms. We used fluorescent activated cell sorting (FACS) to isolate parasites from the kidney of brown trout and rainbow trout following experimental infection with T. bryosalmonae. The sorted parasite cells were then subjected to RNA sequencing. By this approach, we identified 1120 parasite transcripts that were expressed differentially in parasites derived from brown trout and rainbow trout. We found elevated levels of transcripts related to cytoskeleton organisation, cell polarity, peptidyl-serine phosphorylation in parasites sorted from brown trout. In contrast, transcripts related to translation, ribonucleoprotein complex biogenesis and subunit organisation, non-membrane bounded organelle assembly, regulation of protein catabolic process and protein refolding were upregulated in rainbow trout-derived parasites. These findings show distinct molecular adaptations of parasites, which may underlie their distinct outcomes in the two hosts. Moreover, the identification of these differentially expressed transcripts may enable the identification of novel drug targets that may be exploited as treatment against T. bryosalmonae. We here also describe for the first time how FACS based isolation of T. bryosalmonae cells from infected kidney of fish fosters research and allows to define differentially expressed parasite transcripts in carrier and dead-end fish hosts.
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Affiliation(s)
- Saloni Shivam
- Division of Fish Health, University of Veterinary Medicine Vienna, Vienna, Austria
- Karwar Regional Station of Indian Council of Agricultural Research, Central Marine Fisheries Research Institute, Karwar, Karnataka, India
| | - Reinhard Ertl
- VetCore Facility for Research, University of Veterinary Medicine Vienna, Vienna, Austria
| | - Veronika Sexl
- Institute of Pharmacology and Toxicology, University of Veterinary Medicine Vienna, Vienna, Austria
| | - Mansour El-Matbouli
- Division of Fish Health, University of Veterinary Medicine Vienna, Vienna, Austria
- School of Biotechnology, Badr University in Cairo, Badr City, Cairo, Egypt
| | - Gokhlesh Kumar
- Division of Fish Health, University of Veterinary Medicine Vienna, Vienna, Austria.
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86
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Moon S, Namkoong S. Ribonucleoprotein Granules: Between Stress and Transposable Elements. Biomolecules 2023; 13:1027. [PMID: 37509063 PMCID: PMC10377603 DOI: 10.3390/biom13071027] [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: 05/23/2023] [Revised: 06/19/2023] [Accepted: 06/21/2023] [Indexed: 07/30/2023] Open
Abstract
Transposable elements (TEs) are DNA sequences that can transpose and replicate within the genome, leading to genetic changes that affect various aspects of host biology. Evolutionarily, hosts have also developed molecular mechanisms to suppress TEs at the transcriptional and post-transcriptional levels. Recent studies suggest that stress-induced formation of ribonucleoprotein (RNP) granules, including stress granule (SG) and processing body (P-body), can play a role in the sequestration of TEs to prevent transposition, suggesting an additional layer of the regulatory mechanism for TEs. RNP granules have been shown to contain factors involved in RNA regulation, including mRNA decay enzymes, RNA-binding proteins, and noncoding RNAs, which could potentially contribute to the regulation of TEs. Therefore, understanding the interplay between TEs and RNP granules is crucial for elucidating the mechanisms for maintaining genomic stability and controlling gene expression. In this review, we provide a brief overview of the current knowledge regarding the interplay between TEs and RNP granules, proposing RNP granules as a novel layer of the regulatory mechanism for TEs during stress.
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Affiliation(s)
- Sungjin Moon
- Department of Biological Sciences, Kangwon National University, Chuncheon 24341, Republic of Korea
| | - Sim Namkoong
- Department of Biochemistry, Kangwon National University, Chuncheon 24341, Republic of Korea
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87
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Rangachari V. Biomolecular condensates - extant relics or evolving microcompartments? Commun Biol 2023; 6:656. [PMID: 37344557 PMCID: PMC10284869 DOI: 10.1038/s42003-023-04963-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2023] [Accepted: 05/22/2023] [Indexed: 06/23/2023] Open
Abstract
Unprecedented discoveries during the past decade have unearthed the ubiquitous presence of biomolecular condensates (BCs) in diverse organisms and their involvement in a plethora of biological functions. A predominant number of BCs involve coacervation of RNA and proteins that demix from homogenous solutions by a process of phase separation well described by liquid-liquid phase separation (LLPS), which results in a phase with higher concentration and density from the bulk solution. BCs provide a simple and effective means to achieve reversible spatiotemporal control of cellular processes and adaptation to environmental stimuli in an energy-independent manner. The journey into the past of this phenomenon provides clues to the evolutionary origins of life itself. Here I assemble some current and historic discoveries on LLPS to contemplate whether BCs are extant biological hubs or evolving microcompartments. I conclude that BCs in biology could be extant as a phenomenon but are co-evolving as functionally and compositionally complex microcompartments in cells alongside the membrane-bound organelles.
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Affiliation(s)
- Vijayaraghavan Rangachari
- Department of Chemistry and Biochemistry, School of Mathematics and Natural Sciences and Center for Molecular and Cellular Biosciences, University of Southern Mississippi, Hattiesburg, MS, 39402, USA.
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88
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Hassel KR, Brito-Estrada O, Makarewich CA. Microproteins: Overlooked regulators of physiology and disease. iScience 2023; 26:106781. [PMID: 37213226 PMCID: PMC10199267 DOI: 10.1016/j.isci.2023.106781] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/23/2023] Open
Abstract
Ongoing efforts to generate a complete and accurate annotation of the genome have revealed a significant blind spot for small proteins (<100 amino acids) originating from short open reading frames (sORFs). The recent discovery of numerous sORF-encoded proteins, termed microproteins, that play diverse roles in critical cellular processes has ignited the field of microprotein biology. Large-scale efforts are currently underway to identify sORF-encoded microproteins in diverse cell-types and tissues and specialized methods and tools have been developed to aid in their discovery, validation, and functional characterization. Microproteins that have been identified thus far play important roles in fundamental processes including ion transport, oxidative phosphorylation, and stress signaling. In this review, we discuss the optimized tools available for microprotein discovery and validation, summarize the biological functions of numerous microproteins, outline the promise for developing microproteins as therapeutic targets, and look forward to the future of the field of microprotein biology.
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Affiliation(s)
- Keira R. Hassel
- The Heart Institute, Division of Molecular Cardiovascular Biology, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH 45229, USA
- University of Cincinnati College of Medicine, Cincinnati, OH 45229, USA
| | - Omar Brito-Estrada
- The Heart Institute, Division of Molecular Cardiovascular Biology, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH 45229, USA
- University of Cincinnati College of Medicine, Cincinnati, OH 45229, USA
| | - Catherine A. Makarewich
- The Heart Institute, Division of Molecular Cardiovascular Biology, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH 45229, USA
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH 45229, USA
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89
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Szelągowski A, Kozakiewicz M. A Glance at Biogenesis and Functionality of MicroRNAs and Their Role in the Neuropathogenesis of Parkinson's Disease. OXIDATIVE MEDICINE AND CELLULAR LONGEVITY 2023; 2023:7759053. [PMID: 37333462 PMCID: PMC10270766 DOI: 10.1155/2023/7759053] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Revised: 05/11/2023] [Accepted: 05/20/2023] [Indexed: 06/20/2023]
Abstract
MicroRNAs (miRNAs) are short, noncoding RNA transcripts. Mammalian miRNA coding sequences are located in introns and exons of genes encoding various proteins. As the central nervous system is the largest source of miRNA transcripts in living organisms, miRNA molecules are an integral part of the regulation of epigenetic activity in physiological and pathological processes. Their activity depends on many proteins that act as processors, transporters, and chaperones. Many variants of Parkinson's disease have been directly linked to specific gene mutations which in pathological conditions are cumulated resulting in the progression of neurogenerative changes. These mutations can often coexist with specific miRNA dysregulation. Dysregulation of different extracellular miRNAs has been confirmed in many studies on the PD patients. It seems reasonable to conduct further research on the role of miRNAs in the pathogenesis of Parkinson's disease and their potential use in future therapies and diagnosis of the disease. This review presents the current state of knowledge about the biogenesis and functionality of miRNAs in the human genome and their role in the neuropathogenesis of Parkinson's disease (PD)-one of the most common neurodegenerative disorders. The article also describes the process of miRNA formation which can occur in two ways-the canonical and noncanonical one. However, the main focus was on miRNA's use in in vitro and in vivo studies in the context of pathophysiology, diagnosis, and treatment of PD. Some issues, especially those regarding the usefulness of miRNAs in PD's diagnostics and especially its treatment, require further research. More standardization efforts and clinical trials on miRNAs are needed.
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Affiliation(s)
- Adam Szelągowski
- Nicolaus Copernicus University in Toruń Ludwik Rydygier Collegium Medicum in Bydgoszcz, Faculty of Health Sciences, Department of Geriatrics, Bydgoszcz, Poland
| | - Mariusz Kozakiewicz
- Nicolaus Copernicus University in Toruń Ludwik Rydygier Collegium Medicum in Bydgoszcz, Faculty of Health Sciences, Department of Geriatrics, Bydgoszcz, Poland
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90
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Ma Q, Huang F, Guo W, Feng K, Huang T, Cai Y. Identification of Phase-Separation-Protein-Related Function Based on Gene Ontology by Using Machine Learning Methods. Life (Basel) 2023; 13:1306. [PMID: 37374089 DOI: 10.3390/life13061306] [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: 03/23/2023] [Revised: 05/06/2023] [Accepted: 05/30/2023] [Indexed: 06/29/2023] Open
Abstract
Phase-separation proteins (PSPs) are a class of proteins that play a role in the process of liquid-liquid phase separation, which is a mechanism that mediates the formation of membranelle compartments in cells. Identifying phase separation proteins and their associated function could provide insights into cellular biology and the development of diseases, such as neurodegenerative diseases and cancer. Here, PSPs and non-PSPs that have been experimentally validated in earlier studies were gathered as positive and negative samples. Each protein's corresponding Gene Ontology (GO) terms were extracted and used to create a 24,907-dimensional binary vector. The purpose was to extract essential GO terms that can describe essential functions of PSPs and build efficient classifiers to identify PSPs with these GO terms at the same time. To this end, the incremental feature selection computational framework and an integrated feature analysis scheme, containing categorical boosting, least absolute shrinkage and selection operator, light gradient-boosting machine, extreme gradient boosting, and permutation feature importance, were used to build efficient classifiers and identify GO terms with classification-related importance. A set of random forest (RF) classifiers with F1 scores over 0.960 were established to distinguish PSPs from non-PSPs. A number of GO terms that are crucial for distinguishing between PSPs and non-PSPs were found, including GO:0003723, which is related to a biological process involving RNA binding; GO:0016020, which is related to membrane formation; and GO:0045202, which is related to the function of synapses. This study offered recommendations for future research aimed at determining the functional roles of PSPs in cellular processes by developing efficient RF classifiers and identifying the representative GO terms related to PSPs.
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Affiliation(s)
- Qinglan Ma
- School of Life Sciences, Shanghai University, Shanghai 200444, China
| | - FeiMing Huang
- School of Life Sciences, Shanghai University, Shanghai 200444, China
| | - Wei Guo
- Key Laboratory of Stem Cell Biology, Shanghai Jiao Tong University School of Medicine (SJTUSM) & Shanghai Institutes for Biological Sciences (SIBS), Chinese Academy of Sciences (CAS), Shanghai 200030, China
| | - KaiYan Feng
- Department of Computer Science, Guangdong AIB Polytechnic College, Guangzhou 510507, China
| | - Tao Huang
- Bio-Med Big Data Center, CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China
- CAS Key Laboratory of Tissue Microenvironment and Tumor, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Yudong Cai
- School of Life Sciences, Shanghai University, Shanghai 200444, China
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91
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Ciancone AM, Seo KW, Chen M, Borne AL, Libby AH, Bai DL, Kleiner RE, Hsu KL. Global Discovery of Covalent Modulators of Ribonucleoprotein Granules. J Am Chem Soc 2023; 145:11056-11066. [PMID: 37159397 PMCID: PMC10392812 DOI: 10.1021/jacs.3c00165] [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] [Indexed: 05/11/2023]
Abstract
Stress granules (SGs) and processing-bodies (PBs, P-bodies) are ubiquitous and widely studied ribonucleoprotein (RNP) granules involved in cellular stress response, viral infection, and the tumor microenvironment. While proteomic and transcriptomic investigations of SGs and PBs have provided insights into molecular composition, chemical tools to probe and modulate RNP granules remain lacking. Herein, we combine an immunofluorescence (IF)-based phenotypic screen with chemoproteomics to identify sulfonyl-triazoles (SuTEx) capable of preventing or inducing SG and PB formation through liganding of tyrosine (Tyr) and lysine (Lys) sites in stressed cells. Liganded sites were enriched for RNA-binding and protein-protein interaction (PPI) domains, including several sites found in RNP granule-forming proteins. Among these, we functionally validate G3BP1 Y40, located in the NTF2 dimerization domain, as a ligandable site that can disrupt arsenite-induced SG formation in cells. In summary, we present a chemical strategy for the systematic discovery of condensate-modulating covalent small molecules.
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Affiliation(s)
- Anthony M. Ciancone
- Department of Chemistry, University of Virginia, Charlottesville, Virginia 22904, United States
| | - Kyung W. Seo
- Department of Chemistry, Princeton University, Princeton, NJ 08544, USA
| | - Miaomiao Chen
- Department of Chemistry, University of Virginia, Charlottesville, Virginia 22904, United States
| | - Adam L. Borne
- Department of Pharmacology, University of Virginia School of Medicine, Charlottesville, Virginia 22908, United States
| | - Adam H. Libby
- Department of Chemistry, University of Virginia, Charlottesville, Virginia 22904, United States
- University of Virginia Cancer Center, University of Virginia, Charlottesville, VA 22903, USA
| | - Dina L. Bai
- Department of Chemistry, University of Virginia, Charlottesville, Virginia 22904, United States
| | - Ralph E. Kleiner
- Department of Chemistry, Princeton University, Princeton, NJ 08544, USA
| | - Ku-Lung Hsu
- Department of Chemistry, University of Virginia, Charlottesville, Virginia 22904, United States
- Department of Pharmacology, University of Virginia School of Medicine, Charlottesville, Virginia 22908, United States
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, Virginia 22908, United States
- University of Virginia Cancer Center, University of Virginia, Charlottesville, VA 22903, USA
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92
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Bortoletto AS, Parchem RJ. KRAS Hijacks the miRNA Regulatory Pathway in Cancer. Cancer Res 2023; 83:1563-1572. [PMID: 36946612 PMCID: PMC10183808 DOI: 10.1158/0008-5472.can-23-0296] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2023] [Revised: 03/01/2023] [Accepted: 03/20/2023] [Indexed: 03/23/2023]
Abstract
Extensive studies have focused on the misregulation of individual miRNAs in cancer. More recently, mutations in the miRNA biogenesis and processing machinery have been implicated in several malignancies. Such mutations can lead to global miRNA misregulation, which may promote many of the well-known hallmarks of cancer. Interestingly, recent evidence also suggests that oncogenic Kristen rat sarcoma viral oncogene homolog (KRAS) mutations act in part by modulating the activity of members of the miRNA regulatory pathway. Here, we highlight the vital role mutations in the miRNA core machinery play in promoting malignant transformation. Furthermore, we discuss how mutant KRAS can simultaneously impact multiple steps of miRNA processing and function to promote tumorigenesis. Although the ability of KRAS to hijack the miRNA regulatory pathway adds a layer of complexity to its oncogenic nature, it also provides a potential therapeutic avenue that has yet to be exploited in the clinic. Moreover, concurrent targeting of mutant KRAS and members of the miRNA core machinery represents a potential strategy for treating cancer.
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Affiliation(s)
- Angelina S. Bortoletto
- Center for Cell and Gene Therapy, Stem Cell and Regenerative Medicine Center, Department of Molecular and Cellular Biology, Department of Neuroscience, Translational Biology and Molecular Medicine Program, Medical Scientist Training Program, Baylor College of Medicine, Houston, Texas
| | - Ronald J. Parchem
- Center for Cell and Gene Therapy, Stem Cell and Regenerative Medicine Center, Department of Molecular and Cellular Biology, Department of Neuroscience, Translational Biology and Molecular Medicine Program, Medical Scientist Training Program, Baylor College of Medicine, Houston, Texas
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93
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Blake LA, Liu Y, Inoue T, Wu B. A Rapid Inducible RNA Decay system reveals fast mRNA decay in P-bodies. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.04.26.538452. [PMID: 37162943 PMCID: PMC10168379 DOI: 10.1101/2023.04.26.538452] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
RNA decay plays a crucial role in regulating mRNA abundance and gene expression. Modulation of RNA degradation is imperative to investigate an RNA's function. However, information regarding where and how RNA decay occurs remains scarce, partially because existing technologies fail to initiate RNA decay with the spatiotemporal precision or transcript specificity required to capture this stochastic and transient process. Here, we devised a general method that employs inducible tethering of regulatory protein factors to target RNAs and modulate their metabolism. Specifically, we established a Rapid Inducible Decay of RNA (RIDR) technology to degrade target mRNA within minutes. The fast and synchronous induction enabled direct visualization of mRNA decay dynamics in cells with spatiotemporal precision previously unattainable. When applying RIDR to endogenous ACTB mRNA, we observed rapid formation and disappearance of RNA granules, which coincided with pre-existing processing bodies (P-bodies). We measured the time-resolved RNA distribution in P-bodies and cytoplasm after induction, and compared different models of P-body function. We determined that mRNAs rapidly decayed in P-bodies upon induction. Additionally, we validated the functional role of P-bodies by knocking down specific a P-body constituent protein and RNA degradation enzyme. This study determined compartmentalized RNA decay kinetics for the first time. Together, RIDR provides a valuable and generalizable tool to study the spatial and temporal RNA metabolism in cells.
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94
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Sikorski V, Selberg S, Lalowski M, Karelson M, Kankuri E. The structure and function of YTHDF epitranscriptomic m 6A readers. Trends Pharmacol Sci 2023; 44:335-353. [PMID: 37069041 DOI: 10.1016/j.tips.2023.03.004] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2022] [Revised: 03/12/2023] [Accepted: 03/13/2023] [Indexed: 04/19/2023]
Abstract
Specific RNA sequences modified by a methylated adenosine, N6-methyladenosine (m6A), contribute to the post-transcriptional regulation of gene expression. The quantity of m6A in RNA is orchestrated by enzymes that write and erase it, while its effects are mediated by proteins that bind to read this modification. Dysfunction of this post-transcriptional regulatory process has been linked to human disease. Although the initial focus has been on pharmacological targeting of the writer and eraser enzymes, interest in the reader proteins has been challenged by a lack of clear understanding of their functional roles and molecular mechanisms of action. Readers of m6A-modified RNA (m6A-RNA) - the YTH (YT521-B homology) domain-containing protein family paralogs 1-3 (YTHDF1-3, referred to here as DF1-DF3) - are emerging as therapeutic targets as their links to pathological processes such as cancer and inflammation and their roles in regulating m6A-RNA fate become clear. We provide an updated understanding of the modes of action of DF1-DF3 and review their structures to unlock insights into drug design approaches for DF paralog-selective inhibition.
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Affiliation(s)
- Vilbert Sikorski
- Faculty of Medicine, Department of Pharmacology, University of Helsinki, Finland
| | - Simona Selberg
- Institute of Chemistry, University of Tartu, Tartu, Estonia
| | - Maciej Lalowski
- Helsinki Institute of Life Science (HiLIFE), Meilahti Clinical Proteomics Core Facility, Department of Biochemistry and Developmental Biology, Faculty of Medicine, University of Helsinki, Helsinki, Finland; Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, Poznan, Poland
| | - Mati Karelson
- Institute of Chemistry, University of Tartu, Tartu, Estonia
| | - Esko Kankuri
- Faculty of Medicine, Department of Pharmacology, University of Helsinki, Finland.
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95
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Shil S, Tsuruta M, Kawauchi K, Miyoshi D. Biomolecular Liquid-Liquid Phase Separation for Biotechnology. BIOTECH 2023; 12:26. [PMID: 37092470 PMCID: PMC10123627 DOI: 10.3390/biotech12020026] [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: 03/09/2023] [Revised: 03/28/2023] [Accepted: 03/30/2023] [Indexed: 04/05/2023] Open
Abstract
The liquid-liquid phase separation (LLPS) of biomolecules induces condensed assemblies called liquid droplets or membrane-less organelles. In contrast to organelles with lipid membrane barriers, the liquid droplets induced by LLPS do not have distinct barriers (lipid bilayer). Biomolecular LLPS in cells has attracted considerable attention in broad research fields from cellular biology to soft matter physics. The physical and chemical properties of LLPS exert a variety of functions in living cells: activating and deactivating biomolecules involving enzymes; controlling the localization, condensation, and concentration of biomolecules; the filtration and purification of biomolecules; and sensing environmental factors for fast, adaptive, and reversible responses. The versatility of LLPS plays an essential role in various biological processes, such as controlling the central dogma and the onset mechanism of pathological diseases. Moreover, biomolecular LLPS could be critical for developing new biotechnologies such as the condensation, purification, and activation of a series of biomolecules. In this review article, we introduce some fundamental aspects and recent progress of biomolecular LLPS in living cells and test tubes. Then, we discuss applications of biomolecular LLPS toward biotechnologies.
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Affiliation(s)
| | | | | | - Daisuke Miyoshi
- Faculty of Frontiers of Innovative Research in Science and Technology (FIRST), Konan University, 7-1-20 Minatojima-minamimachi, Chuo-ku, Kobe 650-0047, Hyogo, Japan
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96
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Ran XB, Ding LW, Sun QY, Yang H, Said JW, Zhentang L, Madan V, Dakle P, Xiao JF, Loh X, Li Y, Xu L, Xiang XQ, Wang LZ, Goh BC, Lin DC, Chng WJ, Tan SY, Jha S, Koeffler HP. Targeting RNA Exonuclease XRN1 Potentiates Efficacy of Cancer Immunotherapy. Cancer Res 2023; 83:922-938. [PMID: 36638333 DOI: 10.1158/0008-5472.can-21-3052] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2021] [Revised: 06/29/2022] [Accepted: 01/11/2023] [Indexed: 01/15/2023]
Abstract
Despite the remarkable clinical responses achieved with immune checkpoint blockade therapy, the response rate is relatively low and only a subset of patients can benefit from the treatment. Aberrant RNA accumulation can mediate IFN signaling and stimulate an immune response, suggesting that targeting RNA decay machinery might sensitize tumor cells to immunotherapy. With this in mind, we identified an RNA exoribonuclease, XRN1, as a potential therapeutic target to suppress RNA decay and stimulate antitumor immunity. Silencing of XRN1 suppressed tumor growth in syngeneic immunocompetent mice and potentiated immunotherapy efficacy, while silencing of XRN1 alone did not affect tumor growth in immunodeficient mice. Mechanistically, XRN1 depletion activated IFN signaling and the viral defense pathway; both pathways play determinant roles in regulating immune evasion. Aberrant RNA-sensing signaling proteins (RIG-I/MAVS) mediated the expression of IFN genes, as depletion of each of them blunted the elevation of antiviral/IFN signaling in XRN1-silenced cells. Analysis of pan-cancer CRISPR-screening data indicated that IFN signaling triggered by XRN1 silencing is a common phenomenon, suggesting that the effect of XRN1 silencing may be extended to multiple types of cancers. Overall, XRN1 depletion triggers aberrant RNA-mediated IFN signaling, highlighting the importance of the aberrant RNA-sensing pathway in regulating immune responses. These findings provide the molecular rationale for developing XRN1 inhibitors and exploring their potential clinical application in combination with cancer immunotherapy. SIGNIFICANCE Targeting XRN1 activates an intracellular innate immune response mediated by RNA-sensing signaling and potentiates cancer immunotherapy efficacy, suggesting inhibition of RNA decay machinery as a novel strategy for cancer treatment.
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Affiliation(s)
- Xue-Bin Ran
- Department of Pathology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Ling-Wen Ding
- Department of Pathology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
| | - Qiao-Yang Sun
- Department of Hematology, Singapore General Hospital, Singapore, Singapore
| | - Henry Yang
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
| | - Jonathan W Said
- Santa Monica-University of California, Los Angeles Medical Center, California, Los Angeles
| | - Lao Zhentang
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
- Department of Hematology, Singapore General Hospital, Singapore, Singapore
| | - Vikas Madan
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
| | - Pushkar Dakle
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
| | - Jin-Fen Xiao
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
- Division of Hematology/Oncology, Cedars-Sinai Medical Center, UCLA School of Medicine, California, Los Angeles
| | - Xinyi Loh
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
| | - Ying Li
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
| | - Liang Xu
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
- College of life Science, Zhejiang University, Hangzhou, China
| | - Xiao-Qiang Xiang
- Department of Clinical Pharmacy and Pharmacy Administration, School of Pharmacy, Fudan University, Shanghai, China
| | - Ling-Zhi Wang
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
| | - Boon Cher Goh
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
| | - De-Chen Lin
- Division of Hematology/Oncology, Cedars-Sinai Medical Center, UCLA School of Medicine, California, Los Angeles
| | - Wee Joo Chng
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
| | - Soo-Yong Tan
- Department of Pathology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Sudhakar Jha
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
- NUS Center for Cancer Research, Yong Loo Lin School of Medicine, National University, Singapore, Singapore
- Department of Physiological Sciences, College of Veterinary Medicine, Oklahoma State University, Stillwater, Oklahoma
| | - H Phillip Koeffler
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
- Division of Hematology/Oncology, Cedars-Sinai Medical Center, UCLA School of Medicine, California, Los Angeles
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97
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Ramirez PW, Pantoja C, Beliakova-Bethell N. An Evaluation on the Role of Non-Coding RNA in HIV Transcription and Latency: A Review. HIV AIDS (Auckl) 2023; 15:115-134. [PMID: 36942082 PMCID: PMC10024501 DOI: 10.2147/hiv.s383347] [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: 12/21/2022] [Accepted: 02/24/2023] [Indexed: 03/16/2023] Open
Abstract
The existence of latent cellular reservoirs is recognized as the major barrier to an HIV cure. Reactivating and eliminating "shock and kill" or permanently silencing "block and lock" the latent HIV reservoir, as well as gene editing, remain promising approaches, but so far have proven to be only partially successful. Moreover, using latency reversing agents or "block and lock" drugs pose additional considerations, including the ability to cause cellular toxicity, a potential lack of specificity for HIV, or low potency when each agent is used alone. RNA molecules, such as microRNAs (miRNAs) and long non-coding RNAs (lncRNAs) are becoming increasingly recognized as important regulators of gene expression. RNA-based approaches for combatting HIV latency represent a promising strategy since both miRNAs and lncRNAs are more cell-type and tissue specific than protein coding genes. Thus, a higher specificity of targeting the latent HIV reservoir with less overall cellular toxicity can likely be achieved. In this review, we summarize current knowledge about HIV gene expression regulation by miRNAs and lncRNAs encoded in the human genome, as well as regulatory molecules encoded in the HIV genome. We discuss both the transcriptional and post-transcriptional regulation of HIV gene expression to align with the current definition of latency, and describe RNA molecules that either promote HIV latency or have anti-latency properties. Finally, we provide perspectives on using each class of RNAs as potential targets for combatting HIV latency, and describe the complexity of the interactions between different RNA molecules, their protein targets, and HIV.
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Affiliation(s)
- Peter W Ramirez
- Department of Biological Sciences, California State University, Long Beach, CA, USA
| | - Christina Pantoja
- Department of Biological Sciences, California State University, Long Beach, CA, USA
| | - Nadejda Beliakova-Bethell
- VA San Diego Healthcare System and Veterans Medical Research Foundation, San Diego, CA, USA
- Department of Medicine, University of California, San Diego, CA, USA
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98
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Che X, Wu J, Liu H, Su J, Chen X. Cellular liquid-liquid phase separation: Concept, functions, regulations, and detections. J Cell Physiol 2023; 238:847-865. [PMID: 36870067 DOI: 10.1002/jcp.30980] [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: 06/06/2022] [Revised: 10/05/2022] [Accepted: 02/08/2023] [Indexed: 03/06/2023]
Abstract
Liquid-liquid phase separation is a multicomponent system separated into phases with different compositions and structures. It has been identified and explored in organisms after being introduced from the thermodynamic field. Condensate, the product of phase separation, exists in different scales of cellular structures, such as nucleolus, stress granules, and other organelles in nuclei or cytoplasm. And also play critical roles in different cellular behaviors. Here, we review the concept, thermodynamical and biochemical principles of phase separation. We summarized the main functions including the adjustment of biochemical reaction rates, the regulation of macromolecule folding state, subcellular structural support, the mediation of subcellular location, and intimately linked to different kinds of diseases, such as cancer and neurodegeneration. Advanced detection methods to investigate phase separation are collected and analyzed. We conclude with the discussion of anxiety of phase separation, and thought about how progress can be made to develop precise detection methods and disclose the potential application of condensates.
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Affiliation(s)
- Xuanlin Che
- Department of Dermatology, Xiangya Hospital, Central South University, Changsha, Hunan, China.,Hunan Key Laboratory of Skin Cancer and Psoriasis, Xiangya Hospital, Changsha, Hunan, China.,Hunan Engineering Research Center of Skin Health and Disease, Xiangya Hospital, Changsha, Hunan, China.,Xiangya Clinical Research Center for Cancer Immunotherapy, Central South University, Changsha, Hunan, China
| | - Jiajun Wu
- Department of Orthopaedics, Xiangya Hospital, Central South University, Changsha, China
| | - Hua Liu
- Department of Orthopaedics, Xiangya Hospital, Central South University, Changsha, China
| | - Juan Su
- Department of Dermatology, Xiangya Hospital, Central South University, Changsha, Hunan, China.,Hunan Key Laboratory of Skin Cancer and Psoriasis, Xiangya Hospital, Changsha, Hunan, China.,Hunan Engineering Research Center of Skin Health and Disease, Xiangya Hospital, Changsha, Hunan, China.,Xiangya Clinical Research Center for Cancer Immunotherapy, Central South University, Changsha, Hunan, China
| | - Xiang Chen
- Department of Dermatology, Xiangya Hospital, Central South University, Changsha, Hunan, China.,Hunan Key Laboratory of Skin Cancer and Psoriasis, Xiangya Hospital, Changsha, Hunan, China.,Hunan Engineering Research Center of Skin Health and Disease, Xiangya Hospital, Changsha, Hunan, China.,Xiangya Clinical Research Center for Cancer Immunotherapy, Central South University, Changsha, Hunan, China
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99
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Shiny transcriptional junk: lncRNA-derived peptides in cancers and immune responses. Life Sci 2023; 316:121434. [PMID: 36706831 DOI: 10.1016/j.lfs.2023.121434] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2022] [Revised: 01/11/2023] [Accepted: 01/19/2023] [Indexed: 01/27/2023]
Abstract
By interacting with DNA, RNA, and proteins, long noncoding RNAs (lncRNAs) have been linked to several pathological states. LncRNA-derived peptides, as a novel modality of action of lncRNAs, have recently become a research hotspot. An increasing body of evidence has demonstrated the important role of these peptides in carcinogenesis and cancer progression and immune response. This review first describes lncRNA-derived peptides, the regulators that control their translation, and the roles of these peptides in multiple biological processes and disease states including cancers. In the following section, we comprehensively analyzed the significant role lncRNA-derived peptide played in the immune response. This review provides fresh perspectives on the biological role of lncRNAs and their relationship with diseases, particularly with cancers and the immune response, providing a theoretical basis for these lncRNA-derived peptides as therapeutic and diagnostic targets in cancers and inflammatory diseases.
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100
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Staruszkiewicz M, Pituch-Noworolska A, Skoczen S. Uncommon types of autoantibodies - Detection and clinical associations. Autoimmun Rev 2023; 22:103263. [PMID: 36563770 DOI: 10.1016/j.autrev.2022.103263] [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: 11/18/2022] [Accepted: 12/18/2022] [Indexed: 12/24/2022]
Abstract
Immunofluorescence is a basic method for detection of autoantibodies in serum. It is used as screening for people with symptoms suggesting autoimmune process and disease. Antinuclear antibodies (ANA) assay detecting antibodies against nuclear proteins used commonly for diagnosis of systemic autoimmune disease, although antibodies against cytoplasmic components and mitotic structures are usable in clinic. The majority of ANA nuclear patterns have been comprehensively studied with increasing data. However, the cytoplasmic and mitotic patterns are underestimated and still require further assessment. In this review the clinical associations and significance of uncommon types of autoantibodies are presented and discussed.
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Affiliation(s)
| | | | - Szymon Skoczen
- Department of Paediatric Oncology and Haematology, Jagiellonian University, Medical College, Krakow, Poland; Department of Oncology and Haematology, University Children's Hospital, Krakow, Poland.
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