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Castillo PE, Jung H, Klann E, Riccio A. Presynaptic Protein Synthesis in Brain Function and Disease. J Neurosci 2023; 43:7483-7488. [PMID: 37940588 PMCID: PMC10634577 DOI: 10.1523/jneurosci.1454-23.2023] [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: 08/01/2023] [Revised: 08/10/2023] [Accepted: 08/15/2023] [Indexed: 11/10/2023] Open
Abstract
Local protein synthesis in mature brain axons regulates the structure and function of presynaptic boutons by adjusting the presynaptic proteome to local demands. This crucial mechanism underlies experience-dependent modifications of brain circuits, and its dysregulation may contribute to brain disorders, such as autism and intellectual disability. Here, we discuss recent advancements in the axonal transcriptome, axonal RNA localization and translation, and the role of presynaptic local translation in synaptic plasticity and memory.
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Affiliation(s)
- Pablo E Castillo
- Dominick P. Purpura Department of Neuroscience, Albert Einstein College of Medicine, Bronx, New York 10461
- Department of Psychiatry and Behavioral Sciences, Albert Einstein College of Medicine, Bronx, New York 10461
| | - Hosung Jung
- Department of Anatomy, Graduate School of Medical Science, Brain Korea 21 Project, Yonsei University College of Medicine, Seoul, 03722, Republic of Korea
| | - Eric Klann
- Center for Neural Science, New York University, New York, New York 10003
- New York University Neuroscience Institute, New York University Grossman School of Medicine, New York, New York 10016
| | - Antonella Riccio
- UCL Laboratory for Molecular Cell Biology University College London, London, WC1E 6BT, United Kingdom
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52
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Child JR, Hofler AC, Chen Q, Yang BH, Kristofich J, Zheng T, Hannigan MM, Elles AL, Reid DW, Nicchitta CV. Examining SRP pathway function in mRNA localization to the endoplasmic reticulum. RNA (NEW YORK, N.Y.) 2023; 29:1703-1724. [PMID: 37643813 PMCID: PMC10578483 DOI: 10.1261/rna.079643.123] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/25/2023] [Accepted: 07/17/2023] [Indexed: 08/31/2023]
Abstract
Signal recognition particle (SRP) pathway function in protein translocation across the endoplasmic reticulum (ER) is well established; its role in RNA localization to the ER remains, however, unclear. In current models, mRNAs undergo translation- and SRP-dependent trafficking to the ER, with ER localization mediated via interactions between SRP-bound translating ribosomes and the ER-resident SRP receptor (SR), a heterodimeric complex comprising SRA, the SRP-binding subunit, and SRB, an integral membrane ER protein. To study SRP pathway function in RNA localization, SR knockout (KO) mammalian cell lines were generated and the consequences of SR KO on steady-state and dynamic mRNA localization examined. CRISPR/Cas9-mediated SRPRB KO resulted in profound destabilization of SRA. Pairing siRNA silencing of SRPRA in SRPRB KO cells yielded viable SR KO cells. Steady-state mRNA compositions and ER-localization patterns in parental and SR KO cells were determined by cell fractionation and deep sequencing. Notably, steady-state cytosol and ER mRNA compositions and partitioning patterns were largely unaltered by loss of SR expression. To examine SRP pathway function in RNA localization dynamics, the subcellular trafficking itineraries of newly exported mRNAs were determined by 4-thiouridine (4SU) pulse-labeling/4SU-seq/cell fractionation. Newly exported mRNAs were distinguished by high ER enrichment, with ER localization being SR-independent. Intriguingly, under conditions of translation initiation inhibition, the ER was the default localization site for all newly exported mRNAs. These data demonstrate that mRNA localization to the ER can be uncoupled from the SRP pathway function and reopen questions regarding the mechanism of RNA localization to the ER.
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Affiliation(s)
- Jessica R Child
- Department of Cell Biology, Duke University School of Medicine, Durham, North Carolina 27710, USA
| | - Alex C Hofler
- Department of Biochemistry, Duke University School of Medicine, Durham, North Carolina 27710, USA
| | - Qiang Chen
- Department of Cell Biology, Duke University School of Medicine, Durham, North Carolina 27710, USA
| | - Brenda H Yang
- Department of Cell Biology, Duke University School of Medicine, Durham, North Carolina 27710, USA
| | - JohnCarlo Kristofich
- Department of Cell Biology, Duke University School of Medicine, Durham, North Carolina 27710, USA
| | - Tianli Zheng
- Department of Cell Biology, Duke University School of Medicine, Durham, North Carolina 27710, USA
| | - Molly M Hannigan
- Department of Cell Biology, Duke University School of Medicine, Durham, North Carolina 27710, USA
| | - Andrew L Elles
- Department of Cell Biology, Duke University School of Medicine, Durham, North Carolina 27710, USA
| | - David W Reid
- Department of Cell Biology, Duke University School of Medicine, Durham, North Carolina 27710, USA
| | - Christopher V Nicchitta
- Department of Cell Biology, Duke University School of Medicine, Durham, North Carolina 27710, USA
- Department of Biochemistry, Duke University School of Medicine, Durham, North Carolina 27710, USA
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53
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Meydan S, Guydosh NR. Is there a localized role for translational quality control? RNA (NEW YORK, N.Y.) 2023; 29:1623-1643. [PMID: 37582617 PMCID: PMC10578494 DOI: 10.1261/rna.079683.123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/19/2023] [Accepted: 07/26/2023] [Indexed: 08/17/2023]
Abstract
It is known that mRNAs and the machinery that translates them are not uniformly distributed throughout the cytoplasm. As a result, the expression of some genes is localized to particular parts of the cell and this makes it possible to carry out important activities, such as growth and signaling, in three-dimensional space. However, the functions of localized gene expression are not fully understood, and the underlying mechanisms that enable localized expression have not been determined in many cases. One consideration that could help in addressing these challenges is the role of quality control (QC) mechanisms that monitor translating ribosomes. On a global level, QC pathways are critical for detecting aberrant translation events, such as a ribosome that stalls while translating, and responding by activating stress pathways and resolving problematic ribosomes and mRNAs at the molecular level. However, it is unclear how these pathways, even when uniformly active throughout the cell, affect local translation. Importantly, some QC pathways have themselves been reported to be enriched in the proximity of particular organelles, but the extent of such localized activity remains largely unknown. Here, we describe the major QC pathways and review studies that have begun to explore their roles in localized translation. Given the limited data in this area, we also pose broad questions about the possibilities and limitations for how QC pathways could facilitate localized gene expression in the cell with the goal of offering ideas for future experimentation.
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Affiliation(s)
- Sezen Meydan
- National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892, USA
- National Institute of General Medical Sciences, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Nicholas R Guydosh
- National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892, USA
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54
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Otis JP, Mowry KL. Hitting the mark: Localization of mRNA and biomolecular condensates in health and disease. WILEY INTERDISCIPLINARY REVIEWS. RNA 2023; 14:e1807. [PMID: 37393916 PMCID: PMC10758526 DOI: 10.1002/wrna.1807] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Revised: 05/29/2023] [Accepted: 06/06/2023] [Indexed: 07/04/2023]
Abstract
Subcellular mRNA localization is critical to a multitude of biological processes such as development of cellular polarity, embryogenesis, tissue differentiation, protein complex formation, cell migration, and rapid responses to environmental stimuli and synaptic depolarization. Our understanding of the mechanisms of mRNA localization must now be revised to include formation and trafficking of biomolecular condensates, as several biomolecular condensates that transport and localize mRNA have recently been discovered. Disruptions in mRNA localization can have catastrophic effects on developmental processes and biomolecular condensate biology and have been shown to contribute to diverse diseases. A fundamental understanding of mRNA localization is essential to understanding how aberrations in this biology contribute the etiology of numerous cancers though support of cancer cell migration and biomolecular condensate dysregulation, as well as many neurodegenerative diseases, through misregulation of mRNA localization and biomolecular condensate biology. This article is categorized under: RNA Export and Localization > RNA Localization RNA in Disease and Development > RNA in Disease RNA in Disease and Development > RNA in Development.
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Affiliation(s)
- Jessica P. Otis
- Department of Molecular Biology, Cell Biology, and Biochemistry, Brown University, Providence, RI, United States, 02912
| | - Kimberly L. Mowry
- Department of Molecular Biology, Cell Biology, and Biochemistry, Brown University, Providence, RI, United States, 02912
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55
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Harris MT, Marr MT. The intrinsically disordered region of eIF5B stimulates IRES usage and nucleates biological granule formation. Cell Rep 2023; 42:113283. [PMID: 37862172 PMCID: PMC10680144 DOI: 10.1016/j.celrep.2023.113283] [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: 08/27/2022] [Revised: 03/22/2023] [Accepted: 09/29/2023] [Indexed: 10/22/2023] Open
Abstract
Cells activate stress response pathways to survive adverse conditions. Such responses involve the inhibition of global cap-dependent translation. This inhibition is a block that essential transcripts must escape via alternative methods of translation initiation, e.g., an internal ribosome entry site (IRES). IRESs have distinct structures and generally require a limited repertoire of translation factors. Cellular IRESs have been identified in many critical cellular stress response transcripts. We previously identified cellular IRESs in the murine insulin receptor (Insr) and insulin-like growth factor 1 receptor (Igf1r) transcripts and demonstrated their resistance to eukaryotic initiation factor 4F (eIF4F) inhibition. Here, we find that eIF5B preferentially promotes Insr, Igf1r, and hepatitis C virus IRES activity through a non-canonical mechanism that requires its highly charged and disordered N terminus. We find that the N-terminal region of eIF5B can drive cytoplasmic granule formation. This eIF5B granule is triggered by cellular stress and is sufficient to specifically promote IRES activity.
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Affiliation(s)
- Meghan T Harris
- Department of Biology and Rosenstiel Basic Medical Sciences Research Center, Brandeis University, Waltham, MA 02453, USA
| | - Michael T Marr
- Department of Biology and Rosenstiel Basic Medical Sciences Research Center, Brandeis University, Waltham, MA 02453, USA.
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56
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Rusiecka OM, Molica F, Nielsen MS, Tollance A, Morel S, Frieden M, Chanson M, Boengler K, Kwak BR. Mitochondrial pannexin1 controls cardiac sensitivity to ischaemia/reperfusion injury. Cardiovasc Res 2023; 119:2342-2354. [PMID: 37556386 PMCID: PMC10597630 DOI: 10.1093/cvr/cvad120] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Revised: 04/27/2023] [Accepted: 05/18/2023] [Indexed: 08/11/2023] Open
Abstract
AIMS No effective therapy is available in clinics to protect the heart from ischaemia/reperfusion (I/R) injury. Endothelial cells are activated after I/R, which may drive the inflammatory response by releasing ATP through pannexin1 (Panx1) channels. Here, we investigated the role of Panx1 in cardiac I/R. METHODS AND RESULTS Panx1 was found in cardiac endothelial cells, neutrophils, and cardiomyocytes. After in vivo I/R, serum Troponin-I, and infarct size were less pronounced in Panx1-/- mice, but leukocyte infiltration in the infarct area was similar between Panx1-/- and wild-type mice. Serum Troponin-I and infarct size were not different between mice with neutrophil-specific deletion of Panx1 and Panx1fl/fl mice, suggesting that cardioprotection by Panx1 deletion rather involved cardiomyocytes than the inflammatory response. Physiological cardiac function in wild-type and Panx1-/- hearts was similar. The time to onset of contracture and time to maximal contracture were delayed in Panx1-/- hearts, suggesting reduced sensitivity of these hearts to ischaemic injury. Moreover, Panx1-/- hearts showed better recovery of left ventricle developed pressure, cardiac contractility, and relaxation after I/R. Ischaemic preconditioning failed to confer further protection in Panx1-/- hearts. Panx1 was found in subsarcolemmal mitochondria (SSM). SSM in WT or Panx1-/- hearts showed no differences in morphology. The function of the mitochondrial permeability transition pore and production of reactive oxygen species in SSM was not affected, but mitochondrial respiration was reduced in Panx1-/- SSM. Finally, Panx1-/- cardiomyocytes had a decreased mitochondrial membrane potential and an increased mitochondrial ATP content. CONCLUSION Panx1-/- mice display decreased sensitivity to cardiac I/R injury, resulting in smaller infarcts and improved recovery of left ventricular function. This cardioprotective effect of Panx1 deletion seems to involve cardiac mitochondria rather than a reduced inflammatory response. Thus, Panx1 may represent a new target for controlling cardiac reperfusion damage.
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Affiliation(s)
- Olga M Rusiecka
- Department of Pathology and Immunology, Faculty of Medicine, University of Geneva, Rue Michel-Servet 1, CH-1211 Geneva, Switzerland
| | - Filippo Molica
- Department of Pathology and Immunology, Faculty of Medicine, University of Geneva, Rue Michel-Servet 1, CH-1211 Geneva, Switzerland
| | - Morten S Nielsen
- Department of Biomedical Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Axel Tollance
- Department of Cell Physiology and Metabolism, Faculty of Medicine, University of Geneva, Geneva, Switzerland
| | - Sandrine Morel
- Department of Pathology and Immunology, Faculty of Medicine, University of Geneva, Rue Michel-Servet 1, CH-1211 Geneva, Switzerland
| | - Maud Frieden
- Department of Cell Physiology and Metabolism, Faculty of Medicine, University of Geneva, Geneva, Switzerland
| | - Marc Chanson
- Department of Cell Physiology and Metabolism, Faculty of Medicine, University of Geneva, Geneva, Switzerland
| | - Kerstin Boengler
- Institute of Physiology, Justus-Liebig University, Giessen, Germany
| | - Brenda R Kwak
- Department of Pathology and Immunology, Faculty of Medicine, University of Geneva, Rue Michel-Servet 1, CH-1211 Geneva, Switzerland
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57
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Geng Q, Keya JJ, Hotta T, Verhey KJ. KIF1C, an RNA transporting kinesin-3, undergoes liquid-liquid phase separation through its C-terminal disordered domain. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.10.23.563538. [PMID: 37961614 PMCID: PMC10634753 DOI: 10.1101/2023.10.23.563538] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2023]
Abstract
The spatial distribution of mRNA is critical for local control of protein production. Recent studies have identified the kinesin-3 family member KIF1C as an RNA transporter. However, it is not clear how KIF1C interacts with RNA molecules. Here, we show that KIF1C's C-terminal tail domain is an intrinsically disordered region (IDR) containing a prion-like domain (PLD) that is unique compared to the C-terminal tails of other kinesin family members. In cells, KIF1C constructs undergo reversible formation of dynamic puncta that display physical properties of liquid condensates and incorporate RNA molecules in a sequence-selective manner. The IDR is necessary and sufficient for driving liquid-liquid phase separation (LLPS) but the condensate properties can be modulated by adjacent coiled-coil segments. The purified KIF1C IDR domain undergoes LLPS in vitro at near-endogenous nM concentrations in a salt-dependent manner. Deletion of the IDR abolished the ability of KIF1C to undergo LLPS and disrupted the distribution of mRNA cargoes to the cell periphery. Our work thus uncovers an intrinsic correlation between the LLPS activity of KIF1C and its role as an RNA transporter. In addition, as the first kinesin motor reported to undergo LLPS, our work reveals a previously uncharacterized mode of motor-cargo interaction that extends our understanding of the behavior of cytoskeletal motor proteins.
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Affiliation(s)
- Qi Geng
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI, USA
| | - Jakia Jannat Keya
- Department of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Takashi Hotta
- Department of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Kristen J Verhey
- Department of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, MI, USA
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58
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McKenna ED, Sarbanes SL, Cummings SW, Roll-Mecak A. The Tubulin Code, from Molecules to Health and Disease. Annu Rev Cell Dev Biol 2023; 39:331-361. [PMID: 37843925 DOI: 10.1146/annurev-cellbio-030123-032748] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2023]
Abstract
Microtubules are essential dynamic polymers composed of α/β-tubulin heterodimers. They support intracellular trafficking, cell division, cellular motility, and other essential cellular processes. In many species, both α-tubulin and β-tubulin are encoded by multiple genes with distinct expression profiles and functionality. Microtubules are further diversified through abundant posttranslational modifications, which are added and removed by a suite of enzymes to form complex, stereotyped cellular arrays. The genetic and chemical diversity of tubulin constitute a tubulin code that regulates intrinsic microtubule properties and is read by cellular effectors, such as molecular motors and microtubule-associated proteins, to provide spatial and temporal specificity to microtubules in cells. In this review, we synthesize the rapidly expanding tubulin code literature and highlight limitations and opportunities for the field. As complex microtubule arrays underlie essential physiological processes, a better understanding of how cells employ the tubulin code has important implications for human disease ranging from cancer to neurological disorders.
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Affiliation(s)
- Elizabeth D McKenna
- Cell Biology and Biophysics Unit, Porter Neuroscience Research Center, National Institute of Neurological Disorders and Stroke, Bethesda, Maryland, USA;
| | - Stephanie L Sarbanes
- Cell Biology and Biophysics Unit, Porter Neuroscience Research Center, National Institute of Neurological Disorders and Stroke, Bethesda, Maryland, USA;
| | - Steven W Cummings
- Cell Biology and Biophysics Unit, Porter Neuroscience Research Center, National Institute of Neurological Disorders and Stroke, Bethesda, Maryland, USA;
| | - Antonina Roll-Mecak
- Cell Biology and Biophysics Unit, Porter Neuroscience Research Center, National Institute of Neurological Disorders and Stroke, Bethesda, Maryland, USA;
- Biochemistry and Biophysics Center, National Heart, Lung, and Blood Institute, Bethesda, Maryland, USA
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59
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Gu J, Zhou X, Sutherland L, Kato M, Jaczynska K, Rizo J, McKnight SL. Oxidative regulation of TDP-43 self-association by a β-to-α conformational switch. Proc Natl Acad Sci U S A 2023; 120:e2311416120. [PMID: 37782781 PMCID: PMC10576115 DOI: 10.1073/pnas.2311416120] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2023] [Accepted: 09/04/2023] [Indexed: 10/04/2023] Open
Abstract
An evolutionarily conserved region of the TDP-43 low-complexity domain (LCD) twenty residues in length can adopt either an α-helical or β-strand conformation. When in the latter conformation, TDP-43 self-associates via the formation of a labile, cross-β structure. Self-association can be monitored via the formation of phase-separated protein droplets. Exposure of droplets to hydrogen peroxide leads to oxidation of conserved methionine residues distributed throughout the LCD. Oxidation disassembles the cross-β structure, thus eliminating both self-association and phase separation. Here, we demonstrate that this process reciprocally enables formation of α-helical structure in precisely the same region formerly functioning to facilitate β-strand-mediated self-association. We further observe that the α-helical conformation allows interaction with a lipid-like detergent and that exposure to lipids enhances the β-to-α conformational switch. We hypothesize that regulation of this oxidative switch will prove to be important to the control of localized translation within vertebrate cells. The experimental observations reported herein were heavily reliant on studies of 1,6-hexanediol, a chemical agent that selectively dissolves labile structures formed via the self-association of protein domains of low sequence complexity. This aliphatic alcohol is shown to exert its dissociative activity primarily via hydrogen-bonding interactions with carbonyl oxygen atoms of the polypeptide backbone. Such observations underscore the central importance of backbone-mediated protein:protein interactions that facilitate the self-association and phase separation of LCDs.
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Affiliation(s)
- Jinge Gu
- Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, TX75235
| | - Xiaoming Zhou
- Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, TX75235
| | - Lillian Sutherland
- Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, TX75235
| | - Masato Kato
- Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, TX75235
- Institute for Quantum Life Science, National Institutes for Quantum Science and Technology, Inage-ku, Chiba263-8555, Japan
| | - Klaudia Jaczynska
- Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, TX75235
| | - Josep Rizo
- Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, TX75235
| | - Steven L. McKnight
- Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, TX75235
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Barber KR, Vizcarra VS, Zilch A, Majuta L, Diezel CC, Culver OP, Hughes BW, Taniguchi M, Streicher JM, Vanderah TW, Riegel AC. The Role of Ryanodine Receptor 2 in Drug-Associated Learning. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.10.03.560743. [PMID: 37873212 PMCID: PMC10592901 DOI: 10.1101/2023.10.03.560743] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/25/2023]
Abstract
Type-2 ryanodine receptor (RyR2) ion channels facilitate the release of Ca 2+ from stores and serve an important function in neuroplasticity. The role for RyR2 in hippocampal-dependent learning and memory is well established and chronic hyperphosphorylation of RyR2 (RyR2P) is associated with pathological calcium leakage and cognitive disorders, including Alzheimer's disease. By comparison, little is known about the role of RyR2 in the ventral medial prefrontal cortex (vmPFC) circuitry important for working memory, decision making, and reward seeking. Here, we evaluated the basal expression and localization of RyR2 and RyR2P in the vmPFC. Next, we employed an operant model of sucrose, cocaine, or morphine self-administration (SA) followed by a (reward-free) recall test, to reengage vmPFC neurons and reactivate reward-seeking and re-evaluated the expression and localization of RyR2 and RyR2P in vmPFC. Under basal conditions, RyR2 was expressed in pyramidal cells but not regularly detected in PV/SST interneurons. On the contrary, RyR2P was rarely observed in PFC somata and was restricted to a different subcompartment of the same neuron - the apical dendrites of layer-5 pyramidal cells. Chronic SA of drug (cocaine or morphine) and nondrug (sucrose) rewards produced comparable increases in RyR2 protein expression. However, recalling either drug reward impaired the usual localization of RyR2P in dendrites and markedly increased its expression in somata immunoreactive for Fos, a marker of highly activated neurons. These effects could not be explained by chronic stress or drug withdrawal and instead appeared to require a recall experience associated with prior drug SA. In addition to showing the differential distribution of RyR2/RyR2P and affirming the general role of vmPFC in reward learning, this study provides information on the propensity of addictive drugs to redistribute RyR2P ion channels in a neuronal population engaged in drug-seeking. Hence, focusing on the early impact of addictive drugs on RyR2 function may serve as a promising approach to finding a treatment for substance use disorders.
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61
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Schindler K, Jung GI, Londoño-Vásquez D, Park S, Skop A, Balboula A. An oocyte meiotic midbody cap is required for developmental competence in mice. RESEARCH SQUARE 2023:rs.3.rs-3399188. [PMID: 37886573 PMCID: PMC10602078 DOI: 10.21203/rs.3.rs-3399188/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/28/2023]
Abstract
Embryo development depends upon maternally derived materials. Mammalian oocytes undergo extreme asymmetric cytokinesis events, producing one large egg and two small polar bodies (PB). During cytokinesis in somatic cells, the midbody (MB) and subsequent assembly of the midbody remnant (MBR), a signaling organelle containing RNAs, transcription factors and translation machinery, is thought to influence cellular function or fate. The role of the MB and MBR in gametes, in particular, oocytes, remains unclear. Here, we examined the formation and function of meiotic MBs (mMB) and mMB remnants (mMBRs) using mouse oocytes and demonstrate that mMBs have a specialized meiotic mMB cap structure that is orientated toward PBs. We show that that mMBs are translationally active, and that mMB caps are required to retain nascent proteins in eggs. We propose that this specialized mMB cap maintains genetic factors in eggs allowing for full developmental competency.
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62
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Alecki C, Rizwan J, Le P, Jacob-Tomas S, Xu S, Minotti S, Wu T, Durham H, Yeo GW, Vera M. Localized synthesis of molecular chaperones sustains neuronal proteostasis. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.10.03.560761. [PMID: 37873158 PMCID: PMC10592939 DOI: 10.1101/2023.10.03.560761] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/25/2023]
Abstract
Neurons are challenged to maintain proteostasis in neuronal projections, particularly with the physiological stress at synapses to support intercellular communication underlying important functions such as memory and movement control. Proteostasis is maintained through regulated protein synthesis and degradation and chaperone-assisted protein folding. Using high-resolution fluorescent microscopy, we discovered that neurons localize a subset of chaperone mRNAs to their dendrites, particularly more proximal regions, and increase this asymmetric localization following proteotoxic stress through microtubule-based transport from the soma. The most abundant chaperone mRNA in dendrites encodes the constitutive heat shock protein 70, HSPA8. Proteotoxic stress in cultured neurons, induced by inhibiting proteasome activity or inducing oxidative stress, enhanced transport of Hspa8 mRNAs to dendrites and the percentage of mRNAs engaged in translation on mono and polyribosomes. Knocking down the ALS-related protein Fused in Sarcoma (FUS) and a dominant mutation in the heterogenous nuclear ribonucleoprotein A2/B1 (HNRNPA2B1) impaired stress-mediated localization of Hspa8 mRNA to dendrites in cultured murine motor neurons and human iPSC-derived neurons, respectively, revealing the importance of these RNA-binding proteins in maintaining proteostasis. These results reveal the increased dendritic localization and translation of the constitutive HSP70 Hspa8 mRNA as a crucial neuronal stress response to uphold proteostasis and prevent neurodegeneration.
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Affiliation(s)
- Celia Alecki
- Department of Biochemistry, McGill University, Montreal, Quebec H3G 1Y6, Canada
| | - Javeria Rizwan
- Department of Biochemistry, McGill University, Montreal, Quebec H3G 1Y6, Canada
| | - Phuong Le
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Suleima Jacob-Tomas
- Department of Biochemistry, McGill University, Montreal, Quebec H3G 1Y6, Canada
| | - Stella Xu
- Department of Biochemistry, McGill University, Montreal, Quebec H3G 1Y6, Canada
| | - Sandra Minotti
- Department of Neurology and Neurosurgery and Montreal Neurological Institute, McGill University, Montreal, Quebec H3A 2B4, Canada
| | - Tad Wu
- Department of Biochemistry, McGill University, Montreal, Quebec H3G 1Y6, Canada
| | - Heather Durham
- Department of Neurology and Neurosurgery and Montreal Neurological Institute, McGill University, Montreal, Quebec H3A 2B4, Canada
| | - Gene W Yeo
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Maria Vera
- Department of Biochemistry, McGill University, Montreal, Quebec H3G 1Y6, Canada
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Cheng AP, Kwon S, Adeshara T, Göhre V, Feldbrügge M, Weiberg A. Extracellular RNAs released by plant-associated fungi: from fundamental mechanisms to biotechnological applications. Appl Microbiol Biotechnol 2023; 107:5935-5945. [PMID: 37572124 PMCID: PMC10485130 DOI: 10.1007/s00253-023-12718-7] [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: 05/31/2023] [Revised: 07/15/2023] [Accepted: 07/19/2023] [Indexed: 08/14/2023]
Abstract
Extracellular RNAs are an emerging research topic in fungal-plant interactions. Fungal plant pathogens and symbionts release small RNAs that enter host cells to manipulate plant physiology and immunity. This communication via extracellular RNAs between fungi and plants is bidirectional. On the one hand, plants release RNAs encapsulated inside extracellular vesicles as a defense response as well as for intercellular and inter-organismal communication. On the other hand, recent reports suggest that also full-length mRNAs are transported within fungal EVs into plants, and these fungal mRNAs might get translated inside host cells. In this review article, we summarize the current views and fundamental concepts of extracellular RNAs released by plant-associated fungi, and we discuss new strategies to apply extracellular RNAs in crop protection against fungal pathogens. KEY POINTS: • Extracellular RNAs are an emerging topic in plant-fungal communication. • Fungi utilize RNAs to manipulate host plants for colonization. • Extracellular RNAs can be engineered to protect plants against fungal pathogens.
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Affiliation(s)
- An-Po Cheng
- Faculty of Biology, Ludwig-Maximilians Universität München (LMU), 82152, Martinsried, Germany
| | - Seomun Kwon
- Institute for Microbiology, Heinrich Heine Universität Düsseldorf, 40225, Düsseldorf, Germany
| | - Trusha Adeshara
- Institute for Microbiology, Heinrich Heine Universität Düsseldorf, 40225, Düsseldorf, Germany
| | - Vera Göhre
- Institute for Microbiology, Heinrich Heine Universität Düsseldorf, 40225, Düsseldorf, Germany
| | - Michael Feldbrügge
- Institute for Microbiology, Heinrich Heine Universität Düsseldorf, 40225, Düsseldorf, Germany
| | - Arne Weiberg
- Faculty of Biology, Ludwig-Maximilians Universität München (LMU), 82152, Martinsried, Germany.
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64
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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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65
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Wang J, Horlacher M, Cheng L, Winther O. RNA trafficking and subcellular localization-a review of mechanisms, experimental and predictive methodologies. Brief Bioinform 2023; 24:bbad249. [PMID: 37466130 PMCID: PMC10516376 DOI: 10.1093/bib/bbad249] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2023] [Revised: 05/30/2023] [Accepted: 06/16/2023] [Indexed: 07/20/2023] Open
Abstract
RNA localization is essential for regulating spatial translation, where RNAs are trafficked to their target locations via various biological mechanisms. In this review, we discuss RNA localization in the context of molecular mechanisms, experimental techniques and machine learning-based prediction tools. Three main types of molecular mechanisms that control the localization of RNA to distinct cellular compartments are reviewed, including directed transport, protection from mRNA degradation, as well as diffusion and local entrapment. Advances in experimental methods, both image and sequence based, provide substantial data resources, which allow for the design of powerful machine learning models to predict RNA localizations. We review the publicly available predictive tools to serve as a guide for users and inspire developers to build more effective prediction models. Finally, we provide an overview of multimodal learning, which may provide a new avenue for the prediction of RNA localization.
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Affiliation(s)
- Jun Wang
- Bioinformatics Centre, Department of Biology, University of Copenhagen, København Ø 2100, Denmark
| | - Marc Horlacher
- Computational Health Center, Helmholtz Center, Munich, Germany
| | - Lixin Cheng
- Shenzhen People’s Hospital, First Affiliated Hospital of Southern University of Science and Technology, Second Clinical Medicine College of Jinan University, Shenzhen 518020, China
| | - Ole Winther
- Bioinformatics Centre, Department of Biology, University of Copenhagen, København Ø 2100, Denmark
- Center for Genomic Medicine, Rigshospitalet (Copenhagen University Hospital), Copenhagen 2100, Denmark
- Section for Cognitive Systems, Department of Applied Mathematics and Computer Science, Technical University of Denmark, Kongens Lyngby 2800, Denmark
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66
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Martin-Geary AC, Blakes AJM, Dawes R, Findlay SD, Lord J, Walker S, Talbot-Martin J, Wieder N, D’Souza EN, Fernandes M, Hilton S, Lahiri N, Campbell C, Jenkinson S, DeGoede CGEL, Anderson ER, Burge CB, Sanders SJ, Ellingford J, Baralle D, Banka S, Whiffin N. Systematic identification of disease-causing promoter and untranslated region variants in 8,040 undiagnosed individuals with rare disease. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2023:2023.09.12.23295416. [PMID: 37745552 PMCID: PMC10516070 DOI: 10.1101/2023.09.12.23295416] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/26/2023]
Abstract
Background Both promoters and untranslated regions (UTRs) have critical regulatory roles, yet variants in these regions are largely excluded from clinical genetic testing due to difficulty in interpreting pathogenicity. The extent to which these regions may harbour diagnoses for individuals with rare disease is currently unknown. Methods We present a framework for the identification and annotation of potentially deleterious proximal promoter and UTR variants in known dominant disease genes. We use this framework to annotate de novo variants (DNVs) in 8,040 undiagnosed individuals in the Genomics England 100,000 genomes project, which were subject to strict region-based filtering, clinical review, and validation studies where possible. In addition, we performed region and variant annotation-based burden testing in 7,862 unrelated probands against matched unaffected controls. Results We prioritised eleven DNVs and identified an additional variant overlapping one of the eleven. Ten of these twelve variants (82%) are in genes that are a strong match to the individual's phenotype and six had not previously been identified. Through burden testing, we did not observe a significant enrichment of potentially deleterious promoter and/or UTR variants in individuals with rare disease collectively across any of our region or variant annotations. Conclusions Overall, we demonstrate the value of screening promoters and UTRs to uncover additional diagnoses for previously undiagnosed individuals with rare disease and provide a framework for doing so without dramatically increasing interpretation burden.
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Affiliation(s)
- Alexandra C Martin-Geary
- Big Data Institute, University of Oxford, UK
- Wellcome Centre for Human Genetics, University of Oxford, UK
| | - Alexander J M Blakes
- Manchester Centre for Genomic Medicine, Division of Evolution and Genomic Sciences, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK
| | - Ruebena Dawes
- Big Data Institute, University of Oxford, UK
- Wellcome Centre for Human Genetics, University of Oxford, UK
| | - Scott D Findlay
- Department of Biology, Massachusetts Institute of Technology, Cambridge, USA
| | | | | | | | - Nechama Wieder
- Big Data Institute, University of Oxford, UK
- Wellcome Centre for Human Genetics, University of Oxford, UK
| | - Elston N D’Souza
- Big Data Institute, University of Oxford, UK
- Wellcome Centre for Human Genetics, University of Oxford, UK
| | - Maria Fernandes
- Big Data Institute, University of Oxford, UK
- Wellcome Centre for Human Genetics, University of Oxford, UK
| | - Sarah Hilton
- Manchester Centre for Genomic Medicine, Manchester University NHS Foundation Trust, Health Innovation Manchester, Manchester M13 9WL, UK
| | - Nayana Lahiri
- St George’s, University of London & St George’s University Hospitals NHS Foundation Trust, Institute of Molecular and Clinical Sciences, London, SW17 0QT, UK
| | - Christopher Campbell
- Manchester Centre for Genomic Medicine, Manchester University NHS Foundation Trust, Health Innovation Manchester, Manchester M13 9WL, UK
| | - Sarah Jenkinson
- Manchester Centre for Genomic Medicine, Manchester University NHS Foundation Trust, Health Innovation Manchester, Manchester M13 9WL, UK
| | - Christian G E L DeGoede
- Department of Paediatric Neurology, Clinical research Facility, Lancashire Teaching Hospitals NHS Trust
- Manchester Metropolitan University
| | - Emily R Anderson
- Liverpool Centre for Genomic Medicine, Liverpool Women’s Hospital, Liverpool, UK
| | | | - Stephan J Sanders
- Institute of Developmental and Regenerative Medicine, Department of Paediatrics, University of Oxford, Oxford, OX3 7TY, UK
- Department of Psychiatry and Behavioral Sciences, UCSF Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA 94158, USA
- New York Genome Center, New York, NY, USA
| | - Jamie Ellingford
- Manchester Centre for Genomic Medicine, Division of Evolution and Genomic Sciences, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK
- Manchester Centre for Genomic Medicine, Manchester University NHS Foundation Trust, Health Innovation Manchester, Manchester M13 9WL, UK
| | - Diana Baralle
- School of Human Development and Health, Faculty of Medicine, University of Southampton, Southampton, United Kingdom
| | - Siddharth Banka
- Manchester Centre for Genomic Medicine, Manchester University NHS Foundation Trust, Health Innovation Manchester, Manchester M13 9WL, UK
| | - Nicola Whiffin
- Big Data Institute, University of Oxford, UK
- Wellcome Centre for Human Genetics, University of Oxford, UK
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
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67
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Tijaro-Bulla S, Nyandwi SP, Cui H. Physiological and engineered tRNA aminoacylation. WILEY INTERDISCIPLINARY REVIEWS. RNA 2023; 14:e1789. [PMID: 37042417 DOI: 10.1002/wrna.1789] [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: 12/23/2022] [Revised: 03/11/2023] [Accepted: 03/21/2023] [Indexed: 04/13/2023]
Abstract
Aminoacyl-tRNA synthetases form the protein family that controls the interpretation of the genetic code, with tRNA aminoacylation being the key chemical step during which an amino acid is assigned to a corresponding sequence of nucleic acids. In consequence, aminoacyl-tRNA synthetases have been studied in their physiological context, in disease states, and as tools for synthetic biology to enable the expansion of the genetic code. Here, we review the fundamentals of aminoacyl-tRNA synthetase biology and classification, with a focus on mammalian cytoplasmic enzymes. We compile evidence that the localization of aminoacyl-tRNA synthetases can be critical in health and disease. In addition, we discuss evidence from synthetic biology which made use of the importance of subcellular localization for efficient manipulation of the protein synthesis machinery. This article is categorized under: RNA Processing Translation > Translation Regulation RNA Processing > tRNA Processing RNA Export and Localization > RNA Localization.
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Affiliation(s)
| | | | - Haissi Cui
- Department of Chemistry, University of Toronto, Toronto, Ontario, Canada
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68
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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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69
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Munro J, Gillen SL, Mitchell L, Laing S, Karim SA, Rink CJ, Waldron JA, Bushell M. Optimisation of Sample Preparation from Primary Mouse Tissue to Maintain RNA Integrity for Methods Examining Translational Control. Cancers (Basel) 2023; 15:3985. [PMID: 37568801 PMCID: PMC10417042 DOI: 10.3390/cancers15153985] [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: 06/09/2023] [Revised: 07/26/2023] [Accepted: 07/31/2023] [Indexed: 08/13/2023] Open
Abstract
The protein output of different mRNAs can vary by two orders of magnitude; therefore, it is critical to understand the processes that control gene expression operating at the level of translation. Translatome-wide techniques, such as polysome profiling and ribosome profiling, are key methods for determining the translation rates occurring on specific mRNAs. These techniques are now widely used in cell lines; however, they are underutilised in tissues and cancer models. Ribonuclease (RNase) expression is often found to be higher in complex primary tissues in comparison to cell lines. Methods used to preserve RNA during lysis often use denaturing conditions, which need to be avoided when maintaining the interaction and position of the ribosome with the mRNA is required. Here, we detail the cell lysis conditions that produce high-quality RNA from several different tissues covering a range of endogenous RNase expression levels. We highlight the importance of RNA integrity for accurate determination of the global translation status of the cell as determined by polysome gradients and discuss key aspects to optimise for accurate assessment of the translatome from primary mouse tissue.
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Affiliation(s)
- June Munro
- Cancer Research UK Beatson Institute, Garscube Estate, Switchback Road, Bearsden, Glasgow G61 1BD, UK
| | - Sarah L. Gillen
- Cancer Research UK Beatson Institute, Garscube Estate, Switchback Road, Bearsden, Glasgow G61 1BD, UK
| | - Louise Mitchell
- Cancer Research UK Beatson Institute, Garscube Estate, Switchback Road, Bearsden, Glasgow G61 1BD, UK
| | - Sarah Laing
- School of Cancer Sciences, University of Glasgow, Garscube Estate, Switchback Road, Bearsden, Glasgow G61 1QH, UK
| | - Saadia A. Karim
- Cancer Research UK Beatson Institute, Garscube Estate, Switchback Road, Bearsden, Glasgow G61 1BD, UK
| | - Curtis J. Rink
- Cancer Research UK Beatson Institute, Garscube Estate, Switchback Road, Bearsden, Glasgow G61 1BD, UK
- School of Cancer Sciences, University of Glasgow, Garscube Estate, Switchback Road, Bearsden, Glasgow G61 1QH, UK
| | - Joseph A. Waldron
- Cancer Research UK Beatson Institute, Garscube Estate, Switchback Road, Bearsden, Glasgow G61 1BD, UK
| | - Martin Bushell
- Cancer Research UK Beatson Institute, Garscube Estate, Switchback Road, Bearsden, Glasgow G61 1BD, UK
- School of Cancer Sciences, University of Glasgow, Garscube Estate, Switchback Road, Bearsden, Glasgow G61 1QH, UK
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70
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Gasparski AN, Moissoglu K, Pallikkuth S, Meydan S, Guydosh NR, Mili S. mRNA location and translation rate determine protein targeting to dual destinations. Mol Cell 2023; 83:2726-2738.e9. [PMID: 37506697 PMCID: PMC10530421 DOI: 10.1016/j.molcel.2023.06.036] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Revised: 04/25/2023] [Accepted: 06/30/2023] [Indexed: 07/30/2023]
Abstract
Numerous proteins are targeted to two or multiple subcellular destinations where they exert distinct functional consequences. The balance between such differential targeting is thought to be determined post-translationally, relying on protein sorting mechanisms. Here, we show that mRNA location and translation rate can also determine protein targeting by modulating protein binding to specific interacting partners. Peripheral localization of the NET1 mRNA and fast translation lead to higher cytosolic retention of the NET1 protein by promoting its binding to the membrane-associated scaffold protein CASK. By contrast, perinuclear mRNA location and/or slower translation rate favor nuclear targeting by promoting binding to importins. This mRNA location-dependent mechanism is modulated by physiological stimuli and profoundly impacts NET1 function in cell motility. These results reveal that the location of protein synthesis and the rate of translation elongation act in coordination as a "partner-selection" mechanism that robustly influences protein distribution and function.
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Affiliation(s)
- Alexander N Gasparski
- Laboratory of Cellular and Molecular Biology, National Cancer Institute, NIH, Bethesda, MD 20892, USA
| | - Konstadinos Moissoglu
- Laboratory of Cellular and Molecular Biology, National Cancer Institute, NIH, Bethesda, MD 20892, USA
| | - Sandeep Pallikkuth
- Laboratory of Cellular and Molecular Biology, National Cancer Institute, NIH, Bethesda, MD 20892, USA
| | - Sezen Meydan
- Laboratory of Biochemistry and Genetics, National Institute of Diabetes and Digestive and Kidney Diseases, NIH, Bethesda, MD 20892, USA; National Institute of General Medical Sciences, NIH, Bethesda, MD 20892, USA
| | - Nicholas R Guydosh
- Laboratory of Biochemistry and Genetics, National Institute of Diabetes and Digestive and Kidney Diseases, NIH, Bethesda, MD 20892, USA
| | - Stavroula Mili
- Laboratory of Cellular and Molecular Biology, National Cancer Institute, NIH, Bethesda, MD 20892, USA.
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71
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Eichler CE, Li H, Grunberg ME, Gavis ER. Localization of oskar mRNA by agglomeration in ribonucleoprotein granules. PLoS Genet 2023; 19:e1010877. [PMID: 37624861 PMCID: PMC10484445 DOI: 10.1371/journal.pgen.1010877] [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: 03/23/2023] [Revised: 09/07/2023] [Accepted: 07/19/2023] [Indexed: 08/27/2023] Open
Abstract
Localization of oskar mRNA to the posterior of the Drosophila oocyte is essential for abdominal patterning and germline development. oskar localization is a multi-step process involving temporally and mechanistically distinct transport modes. Numerous cis-acting elements and trans-acting factors have been identified that mediate earlier motor-dependent transport steps leading to an initial accumulation of oskar at the posterior. Little is known, however, about the requirements for the later localization phase, which depends on cytoplasmic flows and results in the accumulation of large oskar ribonucleoprotein granules, called founder granules, by the end of oogenesis. Using super-resolution microscopy, we show that founder granules are agglomerates of smaller oskar transport particles. In contrast to the earlier kinesin-dependent oskar transport, late-phase localization depends on the sequence as well as on the structure of the spliced oskar localization element (SOLE), but not on the adjacent exon junction complex deposition. Late-phase localization also requires the oskar 3' untranslated region (3' UTR), which targets oskar to founder granules. Together, our results show that 3' UTR-mediated targeting together with SOLE-dependent agglomeration leads to accumulation of oskar in large founder granules at the posterior of the oocyte during late stages of oogenesis. In light of previous work showing that oskar transport particles are solid-like condensates, our findings indicate that founder granules form by a process distinct from that of well-characterized ribonucleoprotein granules like germ granules, P bodies, and stress granules. Additionally, they illustrate how an individual mRNA can be adapted to exploit different localization mechanisms depending on the cellular context.
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Affiliation(s)
- Catherine E. Eichler
- Department of Molecular Biology, Princeton University, Princeton, New Jersey, United States of America
| | - Hui Li
- Department of Molecular Biology, Princeton University, Princeton, New Jersey, United States of America
| | - Michelle E. Grunberg
- Department of Molecular Biology, Princeton University, Princeton, New Jersey, United States of America
| | - Elizabeth R. Gavis
- Department of Molecular Biology, Princeton University, Princeton, New Jersey, United States of America
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72
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Abruzzi KC, Ratner C, Rosbash M. Comparison of TRIBE and STAMP for identifying targets of RNA binding proteins in human and Drosophila cells. RNA (NEW YORK, N.Y.) 2023; 29:1230-1242. [PMID: 37169395 PMCID: PMC10351885 DOI: 10.1261/rna.079608.123] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/28/2023] [Accepted: 04/28/2023] [Indexed: 05/13/2023]
Abstract
RNA binding proteins (RBPs) perform a myriad of functions and are implicated in numerous neurological diseases. To identify the targets of RBPs in small numbers of cells, we developed TRIBE, in which the catalytic domain of the RNA editing enzyme ADAR (ADARcd) is fused to an RBP. When the RBP binds to an mRNA, ADAR catalyzes A to G modifications in the target mRNA that can be easily identified in standard RNA sequencing. In STAMP, the concept is the same except the ADARcd is replaced by the RNA editing enzyme APOBEC. Here we compared TRIBE and STAMP side-by-side in human and Drosophila cells. The goal is to learn the pros and cons of each method so that researchers can choose the method best suited to their RBP and system. In human cells, TRIBE and STAMP were performed using the RBP TDP-43. Although they both identified TDP-43 target mRNAs, combining the two methods more successfully identified high-confidence targets. In Drosophila cells, RBP-APOBEC fusions generated only low numbers of editing sites, comparable to the level of control editing. This was true for two different RBPs, Hrp48 and Thor (Drosophila EIF4E-BP), indicating that STAMP does not work well in Drosophila.
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Affiliation(s)
- Katharine C Abruzzi
- Howard Hughes Medical Institute, Brandeis University, Waltham, Massachusetts 02454, USA
| | - Corrie Ratner
- Howard Hughes Medical Institute, Brandeis University, Waltham, Massachusetts 02454, USA
| | - Michael Rosbash
- Howard Hughes Medical Institute, Brandeis University, Waltham, Massachusetts 02454, USA
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73
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Das S, Lituma PJ, Castillo PE, Singer RH. Maintenance of a short-lived protein required for long-term memory involves cycles of transcription and local translation. Neuron 2023; 111:2051-2064.e6. [PMID: 37100055 PMCID: PMC10330212 DOI: 10.1016/j.neuron.2023.04.005] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2022] [Revised: 01/03/2023] [Accepted: 04/03/2023] [Indexed: 04/28/2023]
Abstract
Activity-dependent expression of immediate early genes (IEGs) is critical for long-term synaptic remodeling and memory. It remains unknown how IEGs are maintained for memory despite rapid transcript and protein turnover. To address this conundrum, we monitored Arc, an IEG essential for memory consolidation. Using a knockin mouse where endogenous Arc alleles were fluorescently tagged, we performed real-time imaging of Arc mRNA dynamics in individual neurons in cultures and brain tissue. Unexpectedly, a single burst stimulation was sufficient to induce cycles of transcriptional reactivation in the same neuron. Subsequent transcription cycles required translation, whereby new Arc proteins engaged in autoregulatory positive feedback to reinduce transcription. The ensuing Arc mRNAs preferentially localized at sites marked by previous Arc protein, assembling a "hotspot" of translation, and consolidating "hubs" of dendritic Arc. These cycles of transcription-translation coupling sustain protein expression and provide a mechanism by which a short-lived event may support long-term memory.
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Affiliation(s)
- Sulagna Das
- Department of Cell Biology, Albert Einstein College of Medicine, Bronx, New York, NY 10461, USA; Program in RNA Biology, Albert Einstein College of Medicine, Bronx, New York, NY 10461, USA.
| | - Pablo J Lituma
- Dominick P. Purpura Department of Neuroscience, Albert Einstein College of Medicine, Bronx, New York, NY 10461, USA
| | - Pablo E Castillo
- Dominick P. Purpura Department of Neuroscience, Albert Einstein College of Medicine, Bronx, New York, NY 10461, USA; Department of Psychiatry and Behavioral Sciences, Albert Einstein College of Medicine, Bronx, New York, NY 10461, USA
| | - Robert H Singer
- Department of Cell Biology, Albert Einstein College of Medicine, Bronx, New York, NY 10461, USA; Program in RNA Biology, Albert Einstein College of Medicine, Bronx, New York, NY 10461, USA; Dominick P. Purpura Department of Neuroscience, Albert Einstein College of Medicine, Bronx, New York, NY 10461, USA.
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74
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Busselez J, Uzbekov RE, Franco B, Pancione M. New insights into the centrosome-associated spliceosome components as regulators of ciliogenesis and tissue identity. WILEY INTERDISCIPLINARY REVIEWS. RNA 2023; 14:e1776. [PMID: 36717357 DOI: 10.1002/wrna.1776] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/06/2022] [Revised: 12/20/2022] [Accepted: 12/27/2022] [Indexed: 02/01/2023]
Abstract
Biomolecular condensates are membrane-less assemblies of proteins and nucleic acids. Centrosomes are biomolecular condensates that play a crucial role in nuclear division, cytoskeletal remodeling, and cilia formation in animal cells. Spatial omics technology is providing new insights into the dynamic exchange of spliceosome components between the nucleus and the centrosome/cilium. Intriguingly, centrosomes are emerging as cytoplasmic sites for information storage, enriched with RNA molecules and RNA-processing proteins. Furthermore, growing evidence supports the view that nuclear spliceosome components assembled at the centrosome function as potential coordinators of splicing subprograms, pluripotency, and cell differentiation. In this article, we first discuss the current understanding of the centrosome/cilium complex, which controls both stem cell differentiation and pluripotency. We next explore the molecular mechanisms that govern splicing factor assembly and disassembly around the centrosome and examine how RNA processing pathways contribute to ciliogenesis. Finally, we discuss numerous unresolved compelling questions regarding the centrosome-associated spliceosome components and transcript variants within the cytoplasm as sources of RNA-based secondary messages in the regulation of cell identity and cell fate determination. This article is categorized under: RNA-Based Catalysis > RNA Catalysis in Splicing and Translation RNA Interactions with Proteins and Other Molecules > RNA-Protein Complexes RNA Processing > Splicing Regulation/Alternative Splicing RNA Processing > RNA Processing.
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Affiliation(s)
- Johan Busselez
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Illkirch-Graffenstaden, France
| | - Rustem E Uzbekov
- Faculté de Médecine, Université de Tours, Tours, France
- Faculty of Bioengineering and Bioinformatics, Moscow State University, Moscow, Russia
| | - Brunella Franco
- Telethon Institute of Genetics and Medicine (TIGEM), Naples, Italy
- Department of Translational Medicine, Medical Genetics, University of Naples "Federico II", Naples, Italy
- Scuola Superiore Meridionale (SSM, School of Advanced Studies), Genomics and Experimental Medicine program, University of Naples Federico II, Naples, Italy
| | - Massimo Pancione
- Department of Sciences and Technologies, University of Sannio, Benevento, Italy
- Department of Biochemistry and Molecular Biology, Faculty of Pharmacy, Complutense University Madrid, Madrid, Spain
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75
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Zhao L, Fonseca A, Meschichi A, Sicard A, Rosa S. Whole-mount smFISH allows combining RNA and protein quantification at cellular and subcellular resolution. NATURE PLANTS 2023; 9:1094-1102. [PMID: 37322128 PMCID: PMC10356603 DOI: 10.1038/s41477-023-01442-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Accepted: 05/12/2023] [Indexed: 06/17/2023]
Abstract
Multicellular organisms result from complex developmental processes largely orchestrated through the quantitative spatiotemporal regulation of gene expression. Yet, obtaining absolute counts of messenger RNAs at a three-dimensional resolution remains challenging, especially in plants, owing to high levels of tissue autofluorescence that prevent the detection of diffraction-limited fluorescent spots. In situ hybridization methods based on amplification cycles have recently emerged, but they are laborious and often lead to quantification biases. In this article, we present a simple method based on single-molecule RNA fluorescence in situ hybridization to visualize and count the number of mRNA molecules in several intact plant tissues. In addition, with the use of fluorescent protein reporters, our method also enables simultaneous detection of mRNA and protein quantity, as well as subcellular distribution, in single cells. With this method, research in plants can now fully explore the benefits of the quantitative analysis of transcription and protein levels at cellular and subcellular resolution in plant tissues.
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Affiliation(s)
- Lihua Zhao
- Department of Plant Biology, Swedish University of Agricultural Sciences (SLU), Uppsala, Sweden
| | - Alejandro Fonseca
- Department of Plant Biology, Swedish University of Agricultural Sciences (SLU), Uppsala, Sweden
| | - Anis Meschichi
- Department of Plant Biology, Swedish University of Agricultural Sciences (SLU), Uppsala, Sweden
| | - Adrien Sicard
- Department of Plant Biology, Swedish University of Agricultural Sciences (SLU), Uppsala, Sweden.
| | - Stefanie Rosa
- Department of Plant Biology, Swedish University of Agricultural Sciences (SLU), Uppsala, Sweden.
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76
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Zeng H, Huang J, Ren J, Wang CK, Tang Z, Zhou H, Zhou Y, Shi H, Aditham A, Sui X, Chen H, Lo JA, Wang X. Spatially resolved single-cell translatomics at molecular resolution. Science 2023; 380:eadd3067. [PMID: 37384709 PMCID: PMC11146668 DOI: 10.1126/science.add3067] [Citation(s) in RCA: 34] [Impact Index Per Article: 34.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2022] [Accepted: 05/07/2023] [Indexed: 07/01/2023]
Abstract
The precise control of messenger RNA (mRNA) translation is a crucial step in posttranscriptional gene regulation of cellular physiology. However, it remains a challenge to systematically study mRNA translation at the transcriptomic scale with spatial and single-cell resolution. Here, we report the development of ribosome-bound mRNA mapping (RIBOmap), a highly multiplexed three-dimensional in situ profiling method to detect cellular translatome. RIBOmap profiling of 981 genes in HeLa cells revealed cell cycle-dependent translational control and colocalized translation of functional gene modules. We mapped 5413 genes in mouse brain tissues, yielding spatially resolved single-cell translatomic profiles for 119,173 cells and revealing cell type-specific and brain region-specific translational regulation, including translation remodeling during oligodendrocyte maturation. Our method detected widespread patterns of localized translation in neuronal and glial cells in intact brain tissue networks.
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Affiliation(s)
- Hu Zeng
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Jiahao Huang
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Jingyi Ren
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | | | - Zefang Tang
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Haowen Zhou
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Yiming Zhou
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Hailing Shi
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Abhishek Aditham
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Xin Sui
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Hongyu Chen
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Jennifer A. Lo
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Xiao Wang
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
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77
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Zhang YP, Wang ZG, Tian YF, Jiang LH, Zhao L, Kong DM, Li X, Pang DW, Liu SL. In Situ Self-Assembly of Fluorogenic RNA Nanozipper Enables Real-Time Imaging of Single Viral mRNA Translation. Angew Chem Int Ed Engl 2023; 62:e202217230. [PMID: 37082873 DOI: 10.1002/anie.202217230] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2022] [Revised: 04/19/2023] [Accepted: 04/20/2023] [Indexed: 04/22/2023]
Abstract
Real-time visualization of individual viral mRNA translation activities in live cells is essential to obtain critical details of viral mRNA dynamics and to detect its transient responses to environmental stress. Fluorogenic RNA aptamers are powerful tools for real-time imaging of mRNA in live cells, but monitoring the translation activity of individual mRNAs remains a challenge due to their intrinsic photophysical properties. Here, we develop a genetically encoded turn-on 3,5-difluoro-4-hydroxybenzylidene imidazolinone (DFHBI)-binding RNA nanozipper with superior brightness and high photostability by in situ self-assembly of multiple nanozippers along single mRNAs. The nanozipper enables real-time imaging of the mobility and dynamic translation of individual viral mRNAs in live cells, providing information on the spatial dynamics and translational elongation rate of viral mRNAs.
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Affiliation(s)
- Yu-Peng Zhang
- State Key Laboratory of Medicinal Chemical Biology, Tianjin Key Laboratory of Biosensing and Molecular Recognition, Research Center for Analytical Sciences, College of Chemistry, and School of Medicine, Nankai University, Tianjin, 300071, P. R. China
| | - Zhi-Gang Wang
- State Key Laboratory of Medicinal Chemical Biology, Tianjin Key Laboratory of Biosensing and Molecular Recognition, Research Center for Analytical Sciences, College of Chemistry, and School of Medicine, Nankai University, Tianjin, 300071, P. R. China
| | - Yi-Fan Tian
- State Key Laboratory of Medicinal Chemical Biology, Tianjin Key Laboratory of Biosensing and Molecular Recognition, Research Center for Analytical Sciences, College of Chemistry, and School of Medicine, Nankai University, Tianjin, 300071, P. R. China
| | - Lin-Han Jiang
- State Key Laboratory of Medicinal Chemical Biology, Tianjin Key Laboratory of Biosensing and Molecular Recognition, Research Center for Analytical Sciences, College of Chemistry, and School of Medicine, Nankai University, Tianjin, 300071, P. R. China
| | - Liang Zhao
- State Key Laboratory of Medicinal Chemical Biology, Tianjin Key Laboratory of Biosensing and Molecular Recognition, Research Center for Analytical Sciences, College of Chemistry, and School of Medicine, Nankai University, Tianjin, 300071, P. R. China
| | - De-Ming Kong
- State Key Laboratory of Medicinal Chemical Biology, Tianjin Key Laboratory of Biosensing and Molecular Recognition, Research Center for Analytical Sciences, College of Chemistry, and School of Medicine, Nankai University, Tianjin, 300071, P. R. China
| | - Xing Li
- Beijing Institutes of Life Science, Chinese Academy of Science, Beijing, 100101, China
| | - Dai-Wen Pang
- State Key Laboratory of Medicinal Chemical Biology, Tianjin Key Laboratory of Biosensing and Molecular Recognition, Research Center for Analytical Sciences, College of Chemistry, and School of Medicine, Nankai University, Tianjin, 300071, P. R. China
- Haihe Laboratory of Sustainable Chemical Transformations, Tianjin, 300192, China
| | - Shu-Lin Liu
- State Key Laboratory of Medicinal Chemical Biology, Tianjin Key Laboratory of Biosensing and Molecular Recognition, Research Center for Analytical Sciences, College of Chemistry, and School of Medicine, Nankai University, Tianjin, 300071, P. R. China
- Engineering Research Center of Nano Geomaterials of Ministry of Education, Faculty of Materials Science and Chemistry, China University of Geosciences, Wuhan, 430074, P. R. China
- Haihe Laboratory of Sustainable Chemical Transformations, Tianjin, 300192, China
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78
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Lamolle G, Simón D, Iriarte A, Musto H. Main Factors Shaping Amino Acid Usage Across Evolution. J Mol Evol 2023:10.1007/s00239-023-10120-5. [PMID: 37264211 DOI: 10.1007/s00239-023-10120-5] [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: 03/22/2023] [Accepted: 05/17/2023] [Indexed: 06/03/2023]
Abstract
The standard genetic code determines that in most species, including viruses, there are 20 amino acids that are coded by 61 codons, while the other three codons are stop triplets. Considering the whole proteome each species features its own amino acid frequencies, given the slow rate of change, closely related species display similar GC content and amino acids usage. In contrast, distantly related species display different amino acid frequencies. Furthermore, within certain multicellular species, as mammals, intragenomic differences in the usage of amino acids are evident. In this communication, we shall summarize some of the most prominent and well-established factors that determine the differences found in the amino acid usage, both across evolution and intragenomically.
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Affiliation(s)
- Guillermo Lamolle
- Laboratorio de Genómica Evolutiva, Facultad de Ciencias, Universidad de La República, Montevideo, Uruguay
| | - Diego Simón
- Laboratorio de Genómica Evolutiva, Facultad de Ciencias, Universidad de La República, Montevideo, Uruguay
- Laboratorio de Virología Molecular, Centro de Investigaciones Nucleares, Facultad de Ciencias, Universidad de La República, Montevideo, Uruguay
- Laboratorio de Evolución Experimental de Virus, Institut Pasteur de Montevideo, Montevideo, Uruguay
| | - Andrés Iriarte
- Laboratorio de Genómica Evolutiva, Facultad de Ciencias, Universidad de La República, Montevideo, Uruguay
- Laboratorio de Biología Computacional, Departamento de Desarrollo Biotecnológico, Instituto de Higiene, Facultad de Medicina, Universidad de La República, Montevideo, Uruguay
| | - Héctor Musto
- Laboratorio de Genómica Evolutiva, Facultad de Ciencias, Universidad de La República, Montevideo, Uruguay.
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79
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Farajzadeh N, Shahbabian K, Bouaziz Y, Querido E, Chartrand P. Phosphorylation controls the oligomeric state of She2 and mRNA localization in yeast. RNA (NEW YORK, N.Y.) 2023; 29:745-755. [PMID: 36921931 PMCID: PMC10187671 DOI: 10.1261/rna.079555.122] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Accepted: 02/24/2023] [Indexed: 05/18/2023]
Abstract
Messenger RNA (mRNA) localization is an important mechanism controlling local protein synthesis. In budding yeast, asymmetric localization of transcripts such as ASH1 mRNA to the bud tip depends on the She2 RNA-binding protein. She2 assembles as a tetramer to bind RNA, but the regulation of this process as part of the mRNA locasome is still unclear. Here, we performed a phosphoproteomic analysis of She2 in vivo and identified new phosphosites, several of which are located at the dimerization or tetramerization interfaces of She2. Remarkably, phosphomimetic mutations at these residues disrupt the capacity of She2 to promote Ash1 asymmetric accumulation. A detailed analysis of one of these residues, T109, shows that a T109D mutation inhibits She2 oligomerization and its interaction with She3 and the importin-α Srp1. She2 proteins harboring the T109D mutation also display reduced expression. More importantly, this phosphomimetic mutation strongly impairs the capacity of She2 to bind RNA and disrupts ASH1 mRNA localization. These results demonstrate that the control of She2 oligomerization by phosphorylation constitutes an important regulatory step in the mRNA localization pathway.
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Affiliation(s)
- Nastaran Farajzadeh
- Department of Biochemistry and Molecular Medicine, Université de Montréal, Montréal, Quebec H3C 3J7, Canada
| | - Karen Shahbabian
- Department of Biochemistry and Molecular Medicine, Université de Montréal, Montréal, Quebec H3C 3J7, Canada
| | - Yani Bouaziz
- Department of Biochemistry and Molecular Medicine, Université de Montréal, Montréal, Quebec H3C 3J7, Canada
| | - Emmanuelle Querido
- Department of Biochemistry and Molecular Medicine, Université de Montréal, Montréal, Quebec H3C 3J7, Canada
| | - Pascal Chartrand
- Department of Biochemistry and Molecular Medicine, Université de Montréal, Montréal, Quebec H3C 3J7, Canada
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80
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Schuhmacher JS, Tom Dieck S, Christoforidis S, Landerer C, Davila Gallesio J, Hersemann L, Seifert S, Schäfer R, Giner A, Toth-Petroczy A, Kalaidzidis Y, Bohnsack KE, Bohnsack MT, Schuman EM, Zerial M. The Rab5 effector FERRY links early endosomes with mRNA localization. Mol Cell 2023; 83:1839-1855.e13. [PMID: 37267905 DOI: 10.1016/j.molcel.2023.05.012] [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: 07/22/2022] [Revised: 12/06/2022] [Accepted: 05/08/2023] [Indexed: 06/04/2023]
Abstract
Localized translation is vital to polarized cells and requires precise and robust distribution of different mRNAs and ribosomes across the cell. However, the underlying molecular mechanisms are poorly understood and important players are lacking. Here, we discovered a Rab5 effector, the five-subunit endosomal Rab5 and RNA/ribosome intermediary (FERRY) complex, that recruits mRNAs and ribosomes to early endosomes through direct mRNA-interaction. FERRY displays preferential binding to certain groups of transcripts, including mRNAs encoding mitochondrial proteins. Deletion of FERRY subunits reduces the endosomal localization of transcripts in cells and has a significant impact on mRNA levels. Clinical studies show that genetic disruption of FERRY causes severe brain damage. We found that, in neurons, FERRY co-localizes with mRNA on early endosomes, and mRNA loaded FERRY-positive endosomes are in close proximity of mitochondria. FERRY thus transforms endosomes into mRNA carriers and plays a key role in regulating mRNA distribution and transport.
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Affiliation(s)
- Jan S Schuhmacher
- Max Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauerstrasse 108, 01307 Dresden, Germany
| | - Susanne Tom Dieck
- Max Planck Institute for Brain Research, Max-von-Laue-Str. 4, 60438 Frankfurt am Main, Germany
| | - Savvas Christoforidis
- Biomedical Research Institute, Foundation for Research and Technology, 45110 Ioannina, Greece; Laboratory of Biological Chemistry, Department of Medicine, School of Health Sciences, University of Ioannina, 45110 Ioannina, Greece
| | - Cedric Landerer
- Max Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauerstrasse 108, 01307 Dresden, Germany; Center for Systems Biology Dresden, Pfotenhauerstrasse 108, 01307 Dresden, Germany
| | - Jimena Davila Gallesio
- Department of Molecular Biology, University Medical Center Göttingen, Humboldtallee 23, 37073 Göttingen, Germany
| | - Lena Hersemann
- Max Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauerstrasse 108, 01307 Dresden, Germany
| | - Sarah Seifert
- Max Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauerstrasse 108, 01307 Dresden, Germany
| | - Ramona Schäfer
- Max Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauerstrasse 108, 01307 Dresden, Germany
| | - Angelika Giner
- Max Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauerstrasse 108, 01307 Dresden, Germany
| | - Agnes Toth-Petroczy
- Max Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauerstrasse 108, 01307 Dresden, Germany; Center for Systems Biology Dresden, Pfotenhauerstrasse 108, 01307 Dresden, Germany
| | - Yannis Kalaidzidis
- Max Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauerstrasse 108, 01307 Dresden, Germany
| | - Katherine E Bohnsack
- Department of Molecular Biology, University Medical Center Göttingen, Humboldtallee 23, 37073 Göttingen, Germany
| | - Markus T Bohnsack
- Department of Molecular Biology, University Medical Center Göttingen, Humboldtallee 23, 37073 Göttingen, Germany; Göttingen Centre for Molecular Biosciences, University of Göttingen, Justus-von-Liebig-Weg 11, 37077 Göttingen, Germany; Max Planck Institute for Multidisciplinary Sciences, Am Fassberg 11, 37077 Göttingen, Germany
| | - Erin M Schuman
- Max Planck Institute for Brain Research, Max-von-Laue-Str. 4, 60438 Frankfurt am Main, Germany
| | - Marino Zerial
- Max Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauerstrasse 108, 01307 Dresden, Germany; Center for Systems Biology Dresden, Pfotenhauerstrasse 108, 01307 Dresden, Germany.
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81
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Quentin D, Schuhmacher JS, Klink BU, Lauer J, Shaikh TR, Huis In 't Veld PJ, Welp LM, Urlaub H, Zerial M, Raunser S. Structural basis of mRNA binding by the human FERRY Rab5 effector complex. Mol Cell 2023; 83:1856-1871.e9. [PMID: 37267906 DOI: 10.1016/j.molcel.2023.05.009] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2022] [Revised: 12/05/2022] [Accepted: 05/05/2023] [Indexed: 06/04/2023]
Abstract
The pentameric FERRY Rab5 effector complex is a molecular link between mRNA and early endosomes in mRNA intracellular distribution. Here, we determine the cryo-EM structure of human FERRY. It reveals a unique clamp-like architecture that bears no resemblance to any known structure of Rab effectors. A combination of functional and mutational studies reveals that while the Fy-2 C-terminal coiled-coil acts as binding region for Fy-1/3 and Rab5, both coiled-coils and Fy-5 concur to bind mRNA. Mutations causing truncations of Fy-2 in patients with neurological disorders impair Rab5 binding or FERRY complex assembly. Thus, Fy-2 serves as a binding hub connecting all five complex subunits and mediating the binding to mRNA and early endosomes via Rab5. Our study provides mechanistic insights into long-distance mRNA transport and demonstrates that the particular architecture of FERRY is closely linked to a previously undescribed mode of RNA binding, involving coiled-coil domains.
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Affiliation(s)
- Dennis Quentin
- Department of Structural Biochemistry, Max Planck Institute of Molecular Physiology, 44227 Dortmund, Germany
| | - Jan S Schuhmacher
- Max Planck Institute of Molecular Cell Biology and Genetics, 01307 Dresden, Germany
| | - Björn U Klink
- Department of Structural Biochemistry, Max Planck Institute of Molecular Physiology, 44227 Dortmund, Germany; Center for Soft Nanoscience and Institute of Molecular Physics and Biophysics, 48149 Münster, Germany
| | - Jeni Lauer
- Max Planck Institute of Molecular Cell Biology and Genetics, 01307 Dresden, Germany
| | - Tanvir R Shaikh
- Department of Structural Biochemistry, Max Planck Institute of Molecular Physiology, 44227 Dortmund, Germany
| | - Pim J Huis In 't Veld
- Department of Mechanistic Cell Biology, Max Planck Institute of Molecular Physiology, 44227 Dortmund, Germany
| | - Luisa M Welp
- Max Planck Institute for Multidisciplinary Sciences, 37077 Göttingen, Germany
| | - Henning Urlaub
- Max Planck Institute for Multidisciplinary Sciences, 37077 Göttingen, Germany; Institute of Clinical Chemistry, University Medical Center Göttingen, 37075 Göttingen, Germany
| | - Marino Zerial
- Max Planck Institute of Molecular Cell Biology and Genetics, 01307 Dresden, Germany.
| | - Stefan Raunser
- Department of Structural Biochemistry, Max Planck Institute of Molecular Physiology, 44227 Dortmund, Germany.
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82
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Raymond WS, Ghaffari S, Aguilera LU, Ron E, Morisaki T, Fox ZR, May MP, Stasevich TJ, Munsky B. Using mechanistic models and machine learning to design single-color multiplexed nascent chain tracking experiments. Front Cell Dev Biol 2023; 11:1151318. [PMID: 37325568 PMCID: PMC10267835 DOI: 10.3389/fcell.2023.1151318] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2023] [Accepted: 05/09/2023] [Indexed: 06/17/2023] Open
Abstract
mRNA translation is the ubiquitous cellular process of reading messenger-RNA strands into functional proteins. Over the past decade, large strides in microscopy techniques have allowed observation of mRNA translation at a single-molecule resolution for self-consistent time-series measurements in live cells. Dubbed Nascent chain tracking (NCT), these methods have explored many temporal dynamics in mRNA translation uncaptured by other experimental methods such as ribosomal profiling, smFISH, pSILAC, BONCAT, or FUNCAT-PLA. However, NCT is currently restricted to the observation of one or two mRNA species at a time due to limits in the number of resolvable fluorescent tags. In this work, we propose a hybrid computational pipeline, where detailed mechanistic simulations produce realistic NCT videos, and machine learning is used to assess potential experimental designs for their ability to resolve multiple mRNA species using a single fluorescent color for all species. Our simulation results show that with careful application this hybrid design strategy could in principle be used to extend the number of mRNA species that could be watched simultaneously within the same cell. We present a simulated example NCT experiment with seven different mRNA species within the same simulated cell and use our ML labeling to identify these spots with 90% accuracy using only two distinct fluorescent tags. We conclude that the proposed extension to the NCT color palette should allow experimentalists to access a plethora of new experimental design possibilities, especially for cell Signaling applications requiring simultaneous study of multiple mRNAs.
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Affiliation(s)
- William S Raymond
- School of Biomedical Engineering, Colorado State University, Fort Collins, CO, United States
| | - Sadaf Ghaffari
- Department of Computer Science, Colorado State University, Fort Collins, CO, United States
| | - Luis U Aguilera
- Department of Chemical and Biological Engineering, Colorado State University, Fort Collins, CO, United States
| | - Eric Ron
- School of Biomedical Engineering, Colorado State University, Fort Collins, CO, United States
| | - Tatsuya Morisaki
- Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, CO, United States
| | - Zachary R Fox
- School of Biomedical Engineering, Colorado State University, Fort Collins, CO, United States
- Computational Sciences and Engineering Division, Oak Ridge National Laboratory, Oak Ridge, TN, United States
| | - Michael P May
- School of Biomedical Engineering, Colorado State University, Fort Collins, CO, United States
| | - Timothy J Stasevich
- Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, CO, United States
- World Research Hub Initiative and Cell Biology Unit, Institute of Innovative Research, Tokyo Institute of Technology, Yokohama, Japan
| | - Brian Munsky
- School of Biomedical Engineering, Colorado State University, Fort Collins, CO, United States
- Department of Chemical and Biological Engineering, Colorado State University, Fort Collins, CO, United States
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83
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Piao W, Li C, Sun P, Yang M, Ding Y, Song W, Jia Y, Yu L, Lu Y, Jin H. Identification of RNA-Binding Protein Targets with HyperTRIBE in Saccharomyces cerevisiae. Int J Mol Sci 2023; 24:ijms24109033. [PMID: 37240377 DOI: 10.3390/ijms24109033] [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: 04/19/2023] [Revised: 05/17/2023] [Accepted: 05/18/2023] [Indexed: 05/28/2023] Open
Abstract
As a master regulator in cells, RNA-binding protein (RBP) plays critical roles in organismal development, metabolism and various diseases. It regulates gene expression at various levels mostly by specific recognition of target RNA. The traditional CLIP-seq method to detect transcriptome-wide RNA targets of RBP is less efficient in yeast due to the low UV transmissivity of their cell walls. Here, we established an efficient HyperTRIBE (Targets of RNA-binding proteins Identified By Editing) in yeast, by fusing an RBP to the hyper-active catalytic domain of human RNA editing enzyme ADAR2 and expressing the fusion protein in yeast cells. The target transcripts of RBP were marked with new RNA editing events and identified by high-throughput sequencing. We successfully applied HyperTRIBE to identifying the RNA targets of two yeast RBPs, KHD1 and BFR1. The antibody-free HyperTRIBE has competitive advantages including a low background, high sensitivity and reproducibility, as well as a simple library preparation procedure, providing a reliable strategy for RBP target identification in Saccharomyces cerevisiae.
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Affiliation(s)
- Weilan Piao
- Key Laboratory of Molecular Medicine and Biotherapy, School of Life Science, Beijing Institute of Technology, No. 5 South Zhongguancun Street, Beijing 100081, China
| | - Chong Li
- Key Laboratory of Molecular Medicine and Biotherapy, School of Life Science, Beijing Institute of Technology, No. 5 South Zhongguancun Street, Beijing 100081, China
| | - Pengkun Sun
- Key Laboratory of Molecular Medicine and Biotherapy, School of Life Science, Beijing Institute of Technology, No. 5 South Zhongguancun Street, Beijing 100081, China
| | - Miaomiao Yang
- Key Laboratory of Molecular Medicine and Biotherapy, School of Life Science, Beijing Institute of Technology, No. 5 South Zhongguancun Street, Beijing 100081, China
| | - Yansong Ding
- Key Laboratory of Molecular Medicine and Biotherapy, School of Life Science, Beijing Institute of Technology, No. 5 South Zhongguancun Street, Beijing 100081, China
| | - Wei Song
- Key Laboratory of Molecular Medicine and Biotherapy, School of Life Science, Beijing Institute of Technology, No. 5 South Zhongguancun Street, Beijing 100081, China
| | - Yunxiao Jia
- Key Laboratory of Molecular Medicine and Biotherapy, School of Life Science, Beijing Institute of Technology, No. 5 South Zhongguancun Street, Beijing 100081, China
| | - Liqun Yu
- Key Laboratory of Molecular Medicine and Biotherapy, School of Life Science, Beijing Institute of Technology, No. 5 South Zhongguancun Street, Beijing 100081, China
| | - Yanming Lu
- Key Laboratory of Molecular Medicine and Biotherapy, School of Life Science, Beijing Institute of Technology, No. 5 South Zhongguancun Street, Beijing 100081, China
| | - Hua Jin
- Key Laboratory of Molecular Medicine and Biotherapy, School of Life Science, Beijing Institute of Technology, No. 5 South Zhongguancun Street, Beijing 100081, China
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84
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Arnould B, Quillin AL, Heemstra JM. Tracking the Message: Applying Single Molecule Localization Microscopy to Cellular RNA Imaging. Chembiochem 2023; 24:e202300049. [PMID: 36857087 PMCID: PMC10192057 DOI: 10.1002/cbic.202300049] [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: 01/20/2023] [Revised: 02/28/2023] [Accepted: 03/01/2023] [Indexed: 03/02/2023]
Abstract
RNA function is increasingly appreciated to be more complex than merely communicating between DNA sequence and protein structure. RNA localization has emerged as a key contributor to the intricate roles RNA plays in the cell, and the link between dysregulated spatiotemporal localization and disease warrants an exploration beyond sequence and structure. However, the tools needed to visualize RNA with precise resolution are lacking in comparison to methods available for studying proteins. In the past decade, many techniques have been developed for imaging RNA, and in parallel super resolution and single-molecule techniques have enabled imaging of single molecules in cells. Of these methods, single molecule localization microscopy (SMLM) has shown significant promise for probing RNA localization. In this review, we highlight current approaches that allow super resolution imaging of specific RNA transcripts and summarize challenges and future opportunities for developing innovative RNA labeling methods that leverage the power of SMLM.
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Affiliation(s)
- Benoît Arnould
- Department of Chemistry, Washington University in St. Louis, St. Louis, MO 63130, USA
| | - Alexandria L Quillin
- Department of Chemistry, Washington University in St. Louis, St. Louis, MO 63130, USA
| | - Jennifer M Heemstra
- Department of Chemistry, Washington University in St. Louis, St. Louis, MO 63130, USA
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85
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Becker JT, Auerbach AA, Harris RS. APEX3 - an optimized tool for rapid and unbiased proximity labeling. J Mol Biol 2023; 435:168145. [PMID: 37182813 DOI: 10.1016/j.jmb.2023.168145] [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: 02/15/2023] [Revised: 05/03/2023] [Accepted: 05/09/2023] [Indexed: 05/16/2023]
Abstract
Macromolecular interactions regulate all aspects of biology. The identification of interacting partners and complexes is important for understanding cellular processes, host-pathogen conflicts, and organismal development. Multiple methods exist to label and enrich interacting proteins in living cells. Notably, the soybean ascorbate peroxidase, APEX2, rapidly biotinylates adjacent biomolecules in the presence of biotin-phenol and hydrogen peroxide. However, during initial experiments with this system, we found that APEX2 exhibits a cytoplasmic-biased localization and is sensitive to the nuclear export inhibitor leptomycin B (LMB). This led us to identify a putative nuclear export signal (NES) at the carboxy-terminus of APEX2 (NESAPEX2), structurally adjacent to the conserved heme binding site. This putative NES is functional as evidenced by cytoplasmic localization and LMB sensitivity of a mCherry-NESAPEX2 chimeric construct. Single amino acid substitutions of multiple hydrophobic residues within NESAPEX2 eliminate cytoplasm-biased localization of both mCherry-NESAPEX2 as well as full-length APEX2. However, all but one of these NES substitutions also compromises peroxide-dependent labeling. This unique separation-of-function mutant, APEX2-L242A, is termed APEX3. Localization and functionality of APEX3 are confirmed by fusion to the nucleocytoplasmic shuttling transcriptional factor, RELA. APEX3 is therefore an optimized tool for unbiased proximity labeling of cellular proteins and interacting factors.
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Affiliation(s)
- Jordan T Becker
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota Twin Cities, Minneapolis, MN, USA 55455; Department of Microbiology and Immunology, University of Minnesota Twin Cities, Minneapolis, MN, USA 55455; Institute for Molecular Virology, University of Minnesota Twin Cities, Minneapolis, MN, USA 55455.
| | - Ashley A Auerbach
- Department of Biochemistry and Structural Biology, University of Texas Health San Antonio, San Antonio, TX, USA 78229
| | - Reuben S Harris
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota Twin Cities, Minneapolis, MN, USA 55455; Department of Biochemistry and Structural Biology, University of Texas Health San Antonio, San Antonio, TX, USA 78229; Howard Hughes Medical Institute, University of Texas Health San Antonio, San Antonio, TX, USA 78229.
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86
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Kołosowska KA, Schratt G, Winterer J. microRNA-dependent regulation of gene expression in GABAergic interneurons. Front Cell Neurosci 2023; 17:1188574. [PMID: 37213213 PMCID: PMC10196030 DOI: 10.3389/fncel.2023.1188574] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2023] [Accepted: 04/20/2023] [Indexed: 05/23/2023] Open
Abstract
Information processing within neuronal circuits relies on their proper development and a balanced interplay between principal and local inhibitory interneurons within those circuits. Gamma-aminobutyric acid (GABA)ergic inhibitory interneurons are a remarkably heterogeneous population, comprising subclasses based on their morphological, electrophysiological, and molecular features, with differential connectivity and activity patterns. microRNA (miRNA)-dependent post-transcriptional control of gene expression represents an important regulatory mechanism for neuronal development and plasticity. miRNAs are a large group of small non-coding RNAs (21-24 nucleotides) acting as negative regulators of mRNA translation and stability. However, while miRNA-dependent gene regulation in principal neurons has been described heretofore in several studies, an understanding of the role of miRNAs in inhibitory interneurons is only beginning to emerge. Recent research demonstrated that miRNAs are differentially expressed in interneuron subclasses, are vitally important for migration, maturation, and survival of interneurons during embryonic development and are crucial for cognitive function and memory formation. In this review, we discuss recent progress in understanding miRNA-dependent regulation of gene expression in interneuron development and function. We aim to shed light onto mechanisms by which miRNAs in GABAergic interneurons contribute to sculpting neuronal circuits, and how their dysregulation may underlie the emergence of numerous neurodevelopmental and neuropsychiatric disorders.
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Affiliation(s)
| | - Gerhard Schratt
- Lab of Systems Neuroscience, Department of Health Science and Technology, Institute for Neuroscience, Swiss Federal Institute of Technology ETH, Zurich, Switzerland
| | - Jochen Winterer
- Lab of Systems Neuroscience, Department of Health Science and Technology, Institute for Neuroscience, Swiss Federal Institute of Technology ETH, Zurich, Switzerland
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87
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Jiang L, Cai H, Zhou W, Li Z, Zhang L, Bi H. RNA-Targeting Carbon Dots for Live-Cell Imaging of Granule Dynamics. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2023; 35:e2210776. [PMID: 36645339 DOI: 10.1002/adma.202210776] [Citation(s) in RCA: 30] [Impact Index Per Article: 30.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/20/2022] [Revised: 01/02/2023] [Indexed: 05/26/2023]
Abstract
It is significant to monitor the different RNA granules dynamics and phase separation process inside cells under various stresses, for example, oxidative stress. The current small-molecule RNA probes work well only in fixed cells and usually encounter problems such as insufficient stability and biocompatibility, and thus a specific RNA-targeting fluorescent nanoprobe that can be used in the living cells is urgently desired. Here, the de novo design and microwave-assisted synthesis of a novel RNA-targeting, red-emissive carbon dots (named as M-CDs) are reported by choosing neutral red and levofloxacin as precursors. The as-synthesized M-CDs is water-soluble with a high fluorescence quantum yield of 22.83% and can selectively bind to RNA resulting in an enhanced red fluorescence. More interestingly, such an RNA-targeting, red-emissive M-CDs can be fast internalized into cells within 5 s and thus used for real-time imaging the dynamic process of intracellular stress granules under oxidative stress, revealing some characteristics of granules that have not been identified by previously reported RNA and protein biomarkers. This research paves a new pathway for visualizing bulk RNA dynamics and studying phase-separation behaviors in living cells by rational design of the fluorescent carbon dots in terms of structure and functionality.
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Affiliation(s)
- Lei Jiang
- School of Chemistry and Chemical Engineering, Anhui University, 111 Jiulong Road, Hefei, 230601, P. R. China
| | - Hao Cai
- School of Materials Science and Engineering, Anhui University, 111 Jiulong Road, Hefei, 23060, P. R. China
| | - Wanwan Zhou
- Ministry of Education Key Laboratory for Membrane-less Organelles & Cellular Dynamics, Hefei National Laboratory for Physical Sciences at the Microscale, Division of Life Sciences and Medicine, University of Science and Technology of China, Huangshan Road, Hefei, Anhui, 230027, P. R. China
| | - Zijian Li
- School of Materials Science and Engineering, Anhui University, 111 Jiulong Road, Hefei, 23060, P. R. China
| | - Liang Zhang
- Ministry of Education Key Laboratory for Membrane-less Organelles & Cellular Dynamics, Hefei National Laboratory for Physical Sciences at the Microscale, Division of Life Sciences and Medicine, University of Science and Technology of China, Huangshan Road, Hefei, Anhui, 230027, P. R. China
| | - Hong Bi
- School of Materials Science and Engineering, Anhui University, 111 Jiulong Road, Hefei, 23060, P. R. China
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88
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Abstract
RNA granules are mesoscale assemblies that form in the absence of limiting membranes. RNA granules contain factors for RNA biogenesis and turnover and are often assumed to represent specialized compartments for RNA biochemistry. Recent evidence suggests that RNA granules assemble by phase separation of subsoluble ribonucleoprotein (RNP) complexes that partially demix from the cytoplasm or nucleoplasm. We explore the possibility that some RNA granules are nonessential condensation by-products that arise when RNP complexes exceed their solubility limit as a consequence of cellular activity, stress, or aging. We describe the use of evolutionary and mutational analyses and single-molecule techniques to distinguish functional RNA granules from "incidental condensates."
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Affiliation(s)
- Andrea Putnam
- Howard Hughes Medical Institute, Department of Molecular Biology and Genetics, Johns Hopkins University, Baltimore, Maryland 21205, USA
| | - Laura Thomas
- Howard Hughes Medical Institute, Department of Molecular Biology and Genetics, Johns Hopkins University, Baltimore, Maryland 21205, USA
| | - Geraldine Seydoux
- Howard Hughes Medical Institute, Department of Molecular Biology and Genetics, Johns Hopkins University, Baltimore, Maryland 21205, USA
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89
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Atmakuru PS, Dhawan J. The cilium-centrosome axis in coupling cell cycle exit and cell fate. J Cell Sci 2023; 136:308872. [PMID: 37144419 DOI: 10.1242/jcs.260454] [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] [Indexed: 05/06/2023] Open
Abstract
The centrosome is an evolutionarily conserved, ancient organelle whose role in cell division was first described over a century ago. The structure and function of the centrosome as a microtubule-organizing center, and of its extracellular extension - the primary cilium - as a sensory antenna, have since been extensively studied, but the role of the cilium-centrosome axis in cell fate is still emerging. In this Opinion piece, we view cellular quiescence and tissue homeostasis from the vantage point of the cilium-centrosome axis. We focus on a less explored role in the choice between distinct forms of mitotic arrest - reversible quiescence and terminal differentiation, which play distinct roles in tissue homeostasis. We outline evidence implicating the centrosome-basal body switch in stem cell function, including how the cilium-centrosome complex regulates reversible versus irreversible arrest in adult skeletal muscle progenitors. We then highlight exciting new findings in other quiescent cell types that suggest signal-dependent coupling of nuclear and cytoplasmic events to the centrosome-basal body switch. Finally, we propose a framework for involvement of this axis in mitotically inactive cells and identify future avenues for understanding how the cilium-centrosome axis impacts central decisions in tissue homeostasis.
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Affiliation(s)
- Priti S Atmakuru
- CSIR Centre for Cellular and Molecular Biology, Hyderabad 500 007, India
| | - Jyotsna Dhawan
- CSIR Centre for Cellular and Molecular Biology, Hyderabad 500 007, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
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90
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de Morree A, Rando TA. Regulation of adult stem cell quiescence and its functions in the maintenance of tissue integrity. Nat Rev Mol Cell Biol 2023; 24:334-354. [PMID: 36922629 PMCID: PMC10725182 DOI: 10.1038/s41580-022-00568-6] [Citation(s) in RCA: 38] [Impact Index Per Article: 38.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/29/2022] [Indexed: 03/18/2023]
Abstract
Adult stem cells are important for mammalian tissues, where they act as a cell reserve that supports normal tissue turnover and can mount a regenerative response following acute injuries. Quiescent stem cells are well established in certain tissues, such as skeletal muscle, brain, and bone marrow. The quiescent state is actively controlled and is essential for long-term maintenance of stem cell pools. In this Review, we discuss the importance of maintaining a functional pool of quiescent adult stem cells, including haematopoietic stem cells, skeletal muscle stem cells, neural stem cells, hair follicle stem cells, and mesenchymal stem cells such as fibro-adipogenic progenitors, to ensure tissue maintenance and repair. We discuss the molecular mechanisms that regulate the entry into, maintenance of, and exit from the quiescent state in mice. Recent studies revealed that quiescent stem cells have a discordance between RNA and protein levels, indicating the importance of post-transcriptional mechanisms, such as alternative polyadenylation, alternative splicing, and translation repression, in the control of stem cell quiescence. Understanding how these mechanisms guide stem cell function during homeostasis and regeneration has important implications for regenerative medicine.
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Affiliation(s)
- Antoine de Morree
- Department of Neurology and Neurological Science, Stanford University School of Medicine, Stanford, CA, USA.
- Paul F. Glenn Center for the Biology of Aging, Stanford University School of Medicine, Stanford, CA, USA.
- Department of Biomedicine, Aarhus University, Aarhus, Denmark.
| | - Thomas A Rando
- Department of Neurology and Neurological Science, Stanford University School of Medicine, Stanford, CA, USA.
- Paul F. Glenn Center for the Biology of Aging, Stanford University School of Medicine, Stanford, CA, USA.
- Center for Tissue Regeneration, Repair, and Restoration, Veterans Affairs Palo Alto Health Care System, Palo Alto, CA, USA.
- Broad Stem Cell Research Center, University of California, Los Angeles, Los Angeles, CA, USA.
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91
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Liu W, Pan Y, Yang L, Xie Y, Chen X, Chang J, Hao W, Zhu L, Wan B. Developmental toxicity of TCBPA on the nervous and cardiovascular systems of zebrafish (Danio rerio): A combination of transcriptomic and metabolomics. J Environ Sci (China) 2023; 127:197-209. [PMID: 36522053 DOI: 10.1016/j.jes.2022.04.022] [Citation(s) in RCA: 18] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Revised: 04/19/2022] [Accepted: 04/19/2022] [Indexed: 06/17/2023]
Abstract
Tetrachlorobisphenol A (TCBPA), a widely used halogenated flame retardant, is frequently detected in environmental compartments and human samples. However, unknown developmental toxicity and mechanisms limit the entire understanding of its effects. In this study, zebrafish (Danio rerio) embryos were exposed to various concentrations of TCBPA while a combination of transcriptomics, behavioral and biochemical analyzes as well as metabolomics were applied to decipher its toxic effects and the potential mechanisms. We found that TCBPA could interfere with nervous and cardiovascular development through focal adhesion and extracellular matrix-receptor (ECM-receptor) interaction pathways through transcriptomic analysis. Behavioral and biochemical analysis results indicated abnormal swimming behavior of zebrafish larvae. Morphological observations revealed that TCBPA could cause the loss of head blood vessels. Metabolomic analysis showed that arginine-related metabolic pathways were one of the main pathways leading to TCBPA developmental toxicity. Our study demonstrated that by using omics, TCBPA was shown to have neurological and cardiovascular developmental toxicity and the underlying mechanisms were uncovered and major pathways identified.
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Affiliation(s)
- Wentao Liu
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yifan Pan
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Lu Yang
- Agricultural Information Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Yun Xie
- Institute of Food Safety, Chinese Academy of Inspection and Quarantine, Beijing 100176, China
| | - Xuanyue Chen
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jing Chang
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Weiyu Hao
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Lifei Zhu
- Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China
| | - Bin Wan
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; University of Chinese Academy of Sciences, Beijing 100049, China.
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92
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Yu Y, Wang S, Xu C, Xiang L, Huang W, Zhang X, Tian B, Mao C, Li T, Wang S. The β-1,3-Glucanase Degrades Callose at Plasmodesmata to Facilitate the Transport of the Ribonucleoprotein Complex in Pyrus betulaefolia. Int J Mol Sci 2023; 24:ijms24098051. [PMID: 37175758 PMCID: PMC10179145 DOI: 10.3390/ijms24098051] [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: 03/16/2023] [Revised: 04/13/2023] [Accepted: 04/18/2023] [Indexed: 05/15/2023] Open
Abstract
Grafting is widely used to improve the stress tolerance and the fruit yield of horticultural crops. Ribonucleoprotein complexes formed by mRNAs and proteins play critical roles in the communication between scions and stocks of grafted plants. In Pyrus betulaefolia, ankyrin was identified previously to promote the long-distance movement of the ribonucleoprotein complex(PbWoxT1-PbPTB3) by facilitating callose degradation at plasmodesmata. However, the mechanism of the ankyrin-mediated callose degradation remains elusive. In this study, we discovered a β-1,3-glucanase (EC 3.2.1.39, PbPDBG) using ankyrin as a bait from plasmodesmata by co-immunoprecipitation and mass spectrometry. Ankyrin was required for the plasmodesmata-localization of PbPDBG. The grafting and bombardment experiments indicated that overexpressing PbPDBG resulted in decreased callose content at plasmodesmata, and thereby promoting the long-distance transport of the ribonucleoprotein complex. Altogether, our findings revealed that PbPDBG was the key factor in ankyrin-mediated callose degradation at plasmodesmata.
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Affiliation(s)
- Yunfei Yu
- Laboratory of Fruit Cell and Molecular Breeding, China Agricultural University, Beijing 100193, China
| | - Shengyuan Wang
- Laboratory of Fruit Cell and Molecular Breeding, China Agricultural University, Beijing 100193, China
| | - Chaoran Xu
- Laboratory of Fruit Cell and Molecular Breeding, China Agricultural University, Beijing 100193, China
| | - Ling Xiang
- Laboratory of Fruit Cell and Molecular Breeding, China Agricultural University, Beijing 100193, China
| | - Wenting Huang
- Laboratory of Fruit Cell and Molecular Breeding, China Agricultural University, Beijing 100193, China
| | - Xiao Zhang
- Laboratory of Fruit Cell and Molecular Breeding, China Agricultural University, Beijing 100193, China
| | - Baihui Tian
- Laboratory of Fruit Cell and Molecular Breeding, China Agricultural University, Beijing 100193, China
| | - Chong Mao
- Laboratory of Fruit Cell and Molecular Breeding, China Agricultural University, Beijing 100193, China
| | - Tianzhong Li
- Laboratory of Fruit Cell and Molecular Breeding, China Agricultural University, Beijing 100193, China
| | - Shengnan Wang
- Laboratory of Fruit Cell and Molecular Breeding, China Agricultural University, Beijing 100193, China
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93
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Gasparski AN, Moissoglu K, Pallikkuth S, Meydan S, Guydosh NR, Mili S. mRNA Location and Translation Rate Determine Protein Targeting to Dual Destinations. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.04.24.538105. [PMID: 37163129 PMCID: PMC10168211 DOI: 10.1101/2023.04.24.538105] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
Numerous proteins are targeted to two or multiple subcellular destinations where they exert distinct functional consequences. The balance between such differential targeting is thought to be determined post-translationally, relying on protein sorting mechanisms. Here, we show that protein targeting can additionally be determined by mRNA location and translation rate, through modulating protein binding to specific interacting partners. Peripheral localization of the NET1 mRNA and fast translation lead to higher cytosolic retention of the NET1 protein, through promoting its binding to the membrane-associated scaffold protein CASK. By contrast, perinuclear mRNA location and/or slower translation rate favor nuclear targeting, through promoting binding to importins. This mRNA location-dependent mechanism is modulated by physiological stimuli and profoundly impacts NET1 function in cell motility. These results reveal that the location of protein synthesis and the rate of translation elongation act in coordination as a 'partner-selection' mechanism that robustly influences protein distribution and function.
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Affiliation(s)
- Alexander N Gasparski
- Laboratory of Cellular and Molecular Biology, National Cancer Institute, NIH, Bethesda, 20892, MD, USA
| | - Konstadinos Moissoglu
- Laboratory of Cellular and Molecular Biology, National Cancer Institute, NIH, Bethesda, 20892, MD, USA
| | - Sandeep Pallikkuth
- Laboratory of Cellular and Molecular Biology, National Cancer Institute, NIH, Bethesda, 20892, MD, USA
| | - Sezen Meydan
- Laboratory of Biochemistry and Genetics, National Institute of Diabetes and Digestive and Kidney Diseases, NIH, Bethesda, 20892, MD, USA
- National Institute of General Medical Sciences, NIH, Bethesda, 20892, MD, USA
| | - Nicholas R Guydosh
- Laboratory of Biochemistry and Genetics, National Institute of Diabetes and Digestive and Kidney Diseases, NIH, Bethesda, 20892, MD, USA
| | - Stavroula Mili
- Laboratory of Cellular and Molecular Biology, National Cancer Institute, NIH, Bethesda, 20892, MD, USA
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94
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Chen M, Yan R, Luo J, Ning J, Zhou R, Ding L. The Role of PGC-1α-Mediated Mitochondrial Biogenesis in Neurons. Neurochem Res 2023:10.1007/s11064-023-03934-8. [PMID: 37097395 DOI: 10.1007/s11064-023-03934-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2022] [Revised: 03/28/2023] [Accepted: 03/31/2023] [Indexed: 04/26/2023]
Abstract
Neurons are highly dependent on mitochondrial ATP production and Ca2+ buffering. Neurons have unique compartmentalized anatomy and energy requirements, and each compartment requires continuously renewed mitochondria to maintain neuronal survival and activity. Peroxisome proliferator-activated receptor-gamma coactivator-1α (PGC-1α) is a key factor in the regulation of mitochondrial biogenesis. It is widely accepted that mitochondria are synthesized in the cell body and transported via axons to the distal end. However, axonal mitochondrial biogenesis is necessary to maintain axonal bioenergy supply and mitochondrial density due to limitations in mitochondrial axonal transport rate and mitochondrial protein lifespan. In addition, impaired mitochondrial biogenesis leading to inadequate energy supply and neuronal damage has been observed in neurological disorders. In this review, we focus on the sites where mitochondrial biogenesis occurs in neurons and the mechanisms by which it maintains axonal mitochondrial density. Finally, we summarize several neurological disorders in which mitochondrial biogenesis is affected.
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Affiliation(s)
- Mengjie Chen
- Beijing Hospital of Traditional Chinese Medicine, Capital Medical University, Beijing, 100010, China
| | - Ruyu Yan
- Beijing Hospital of Traditional Chinese Medicine, Capital Medical University, Beijing, 100010, China
| | - Jiansheng Luo
- Beijing Hospital of Traditional Chinese Medicine, Capital Medical University, Beijing, 100010, China
| | - Jiaqi Ning
- Beijing Hospital of Traditional Chinese Medicine, Capital Medical University, Beijing, 100010, China
| | - Ruiling Zhou
- Beijing Hospital of Traditional Chinese Medicine, Capital Medical University, Beijing, 100010, China
| | - Lingling Ding
- Beijing Hospital of Traditional Chinese Medicine, Capital Medical University, Beijing, 100010, China.
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95
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Birnbaum R, Biswas J, Singer RH, Sharp DJ. mRNA Localization and Local Translation of the Microtubule Severing Enzyme, Fidgetin-Like 2, in Polarization, Migration and Outgrowth. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.04.17.537087. [PMID: 37131812 PMCID: PMC10153175 DOI: 10.1101/2023.04.17.537087] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Cell motility requires strict spatiotemporal control of protein expression. During cell migration, mRNA localization and local translation in subcellular areas like the leading edge and protrusions are particularly advantageous for regulating the reorganization of the cytoskeleton. Fidgetin-Like 2 (FL2), a microtubule severing enzyme (MSE) that restricts migration and outgrowth, localizes to the leading edge of protrusions where it severs dynamic microtubules. FL2 is primarily expressed during development but in adulthood, is spatially upregulated at the leading edge minutes after injury. Here, we show mRNA localization and local translation in protrusions of polarized cells are responsible for FL2 leading edge expression after injury. The data suggests that the RNA binding protein IMP1 is involved in the translational regulation and stabilization of FL2 mRNA, in competition with the miRNA let-7. These data exemplify the role of local translation in microtubule network reorganization during migration and elucidate an unexplored MSE protein localization mechanism.
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Affiliation(s)
- Rayna Birnbaum
- Dominick P. Purpura Department of Neuroscience, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Jeetayu Biswas
- Present address: Department of Medicine, Weill Cornell Medicine, New York Presbyterian Hospital, New York, NY 10021, USA
- Department of Cell Biology, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Robert H. Singer
- Dominick P. Purpura Department of Neuroscience, Albert Einstein College of Medicine, Bronx, NY 10461, USA
- Department of Cell Biology, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - David J. Sharp
- Dominick P. Purpura Department of Neuroscience, Albert Einstein College of Medicine, Bronx, NY 10461, USA
- Department of Molecular Pharmacology, Albert Einstein College of Medicine, Bronx, NY 10461, USA
- Microcures, Inc., Research and Development, Bronx, NY, 10461, USA
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96
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Duncan S, Johansson HE, Ding Y. Reference genes for quantitative Arabidopsis single molecule RNA fluorescence in situ hybridization. JOURNAL OF EXPERIMENTAL BOTANY 2023; 74:2405-2415. [PMID: 36579724 PMCID: PMC10082928 DOI: 10.1093/jxb/erac521] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/22/2022] [Accepted: 12/28/2022] [Indexed: 06/06/2023]
Abstract
Subcellular mRNA quantities and spatial distributions are fundamental for driving gene regulatory programmes. Single molecule RNA fluorescence in situ hybridization (smFISH) uses fluorescent probes to label individual mRNA molecules, thereby facilitating both localization and quantitative studies. Validated reference mRNAs function as positive controls and are required for calibration. Here we present selection criteria for the first set of Arabidopsis smFISH reference genes. Following sequence and transcript data assessments, four mRNA probe sets were selected for imaging. Transcript counts per cell, correlations with cell size, and corrected fluorescence intensities were all calculated for comparison. In addition to validating reference probe sets, we present sample preparation steps that can retain green fluorescent protein fluorescence, thereby providing a method for simultaneous RNA and protein detection. In summary, our reference gene analyses, modified protocol, and simplified quantification method together provide a firm foundation for future quantitative single molecule RNA studies in Arabidopsis root apical meristem cells.
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Affiliation(s)
- Susan Duncan
- John Innes Centre, Norwich Research Park, Norwich, UK
| | - Hans E Johansson
- LGC Biosearch Technologies, 2199 S. McDowell Blvd, Petaluma, CA 94954, USA
| | - Yiliang Ding
- John Innes Centre, Norwich Research Park, Norwich, UK
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97
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Gould R, Brady S. Identifying mRNAs Residing in Myelinating Oligodendrocyte Processes as a Basis for Understanding Internode Autonomy. Life (Basel) 2023; 13:945. [PMID: 37109474 PMCID: PMC10142070 DOI: 10.3390/life13040945] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2023] [Revised: 03/28/2023] [Accepted: 03/31/2023] [Indexed: 04/07/2023] Open
Abstract
In elaborating and maintaining myelin sheaths on multiple axons/segments, oligodendrocytes distribute translation of some proteins, including myelin basic protein (MBP), to sites of myelin sheath assembly, or MSAS. As mRNAs located at these sites are selectively trapped in myelin vesicles during tissue homogenization, we performed a screen to identify some of these mRNAs. To confirm locations, we used real-time quantitative polymerase chain reaction (RT-qPCR), to measure mRNA levels in myelin (M) and 'non-myelin' pellet (P) fractions, and found that five (LPAR1, TRP53INP2, TRAK2, TPPP, and SH3GL3) of thirteen mRNAs were highly enriched in myelin (M/P), suggesting residences in MSAS. Because expression by other cell-types will increase p-values, some MSAS mRNAs might be missed. To identify non-oligodendrocyte expression, we turned to several on-line resources. Although neurons express TRP53INP2, TRAK2 and TPPP mRNAs, these expressions did not invalidate recognitions as MSAS mRNAs. However, neuronal expression likely prevented recognition of KIF1A and MAPK8IP1 mRNAs as MSAS residents and ependymal cell expression likely prevented APOD mRNA assignment to MSAS. Complementary in situ hybridization (ISH) is recommended to confirm residences of mRNAs in MSAS. As both proteins and lipids are synthesized in MSAS, understanding myelination should not only include efforts to identify proteins synthesized in MSAS, but also the lipids.
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Affiliation(s)
- Robert Gould
- Whitman Research Center, Marine Biology Laboratory, Woods Hole, MA 02543, USA
| | - Scott Brady
- Departments of Anatomy and Cell Biology, University of Illinois at Chicago, Chicago, IL 60612, USA;
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98
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Nam J, Gwon Y. Neuronal biomolecular condensates and their implications in neurodegenerative diseases. Front Aging Neurosci 2023; 15:1145420. [PMID: 37065458 PMCID: PMC10102667 DOI: 10.3389/fnagi.2023.1145420] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2023] [Accepted: 03/01/2023] [Indexed: 04/03/2023] Open
Abstract
Biomolecular condensates are subcellular organizations where functionally related proteins and nucleic acids are assembled through liquid-liquid phase separation, allowing them to develop on a larger scale without a membrane. However, biomolecular condensates are highly vulnerable to disruptions from genetic risks and various factors inside and outside the cell and are strongly implicated in the pathogenesis of many neurodegenerative diseases. In addition to the classical view of the nucleation-polymerization process that triggers the protein aggregation from the misfolded seed, the pathologic transition of biomolecular condensates can also promote the aggregation of proteins found in the deposits of neurodegenerative diseases. Furthermore, it has been suggested that several protein or protein-RNA complexes located in the synapse and along the neuronal process are neuron-specific condensates displaying liquid-like properties. As their compositional and functional modifications play a crucial role in the context of neurodegeneration, further research is needed to fully understand the role of neuronal biomolecular condensates. In this article, we will discuss recent findings that explore the pivotal role of biomolecular condensates in the development of neuronal defects and neurodegeneration.
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Affiliation(s)
| | - Youngdae Gwon
- Department of Molecular Cell Biology, Sungkyunkwan University School of Medicine, Suwon, Republic of Korea
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99
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Piol D, Robberechts T, Da Cruz S. Lost in local translation: TDP-43 and FUS in axonal/neuromuscular junction maintenance and dysregulation in amyotrophic lateral sclerosis. Neuron 2023; 111:1355-1380. [PMID: 36963381 DOI: 10.1016/j.neuron.2023.02.028] [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: 10/19/2022] [Revised: 12/21/2022] [Accepted: 02/16/2023] [Indexed: 03/26/2023]
Abstract
Key early features of amyotrophic lateral sclerosis (ALS) are denervation of neuromuscular junctions and axonal degeneration. Motor neuron homeostasis relies on local translation through controlled regulation of axonal mRNA localization, transport, and stability. Yet the composition of the local transcriptome, translatome (mRNAs locally translated), and proteome during health and disease remains largely unexplored. This review covers recent discoveries on axonal translation as a critical mechanism for neuronal maintenance/survival. We focus on two RNA binding proteins, transactive response DNA binding protein-43 (TDP-43) and fused in sarcoma (FUS), whose mutations cause ALS and frontotemporal dementia (FTD). Emerging evidence points to their essential role in the maintenance of axons and synapses, including mRNA localization, transport, and local translation, and whose dysfunction may contribute to ALS. Finally, we describe recent advances in omics-based approaches mapping compartment-specific local RNA and protein compositions, which will be invaluable to elucidate fundamental local processes and identify key targets for therapy development.
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Affiliation(s)
- Diana Piol
- VIB-KU Leuven Center for Brain and Disease Research, Department of Neurosciences, KU Leuven, Leuven Brain Institute, Leuven, Belgium
| | - Tessa Robberechts
- VIB-KU Leuven Center for Brain and Disease Research, Department of Neurosciences, KU Leuven, Leuven Brain Institute, Leuven, Belgium
| | - Sandrine Da Cruz
- VIB-KU Leuven Center for Brain and Disease Research, Department of Neurosciences, KU Leuven, Leuven Brain Institute, Leuven, Belgium.
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100
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Xu X, Wang X, Liao YP, Luo L, Xia T, Nel AE. Use of a Liver-Targeting Immune-Tolerogenic mRNA Lipid Nanoparticle Platform to Treat Peanut-Induced Anaphylaxis by Single- and Multiple-Epitope Nucleotide Sequence Delivery. ACS NANO 2023; 17:4942-4957. [PMID: 36853930 PMCID: PMC10019335 DOI: 10.1021/acsnano.2c12420] [Citation(s) in RCA: 30] [Impact Index Per Article: 30.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Accepted: 02/17/2023] [Indexed: 05/22/2023]
Abstract
While oral desensitization is capable of alleviating peanut allergen anaphylaxis, long-term immune tolerance is the sought-after goal. We developed a liver-targeting lipid nanoparticle (LNP) platform to deliver mRNA-encoded peanut allergen epitopes to liver sinusoidal endothelial cells (LSECs), which function as robust tolerogenic antigen-presenting cells that induce FoxP3+ regulatory T-cells (Tregs). The mRNA strand was constructed by including nucleotide sequences encoding for nonallergenic MHC-II binding T-cell epitopes, identified in the dominant peanut allergen, Ara h2. These epitopes were inserted in the mRNA strand downstream of an MHC-II targeting sequence, further endowed in vitro with 5' and 3' capping sequences, a PolyA tail, and uridine substitution. Codon-optimized mRNA was used for microfluidics synthesis of LNPs with an ionizable cationic lipid, also decorated with a lipid-anchored mannose ligand for LSEC targeting. Biodistribution to the liver was confirmed by in vivo imaging, while ELISpot assays demonstrated an increase in IL-10-producing Tregs in the spleen. Prophylactic administration of tandem-repeat or a combination of encapsulated Ara h2 epitopes induced robust tolerogenic effects in C3H/HeJ mice, sensitized to and subsequently challenged with crude peanut allergen extract. In addition to alleviating physical manifestations of anaphylaxis, there was suppression of Th2-mediated cytokine production, IgE synthesis, and mast cell release, accompanied by increased IL-10 and TGF-β production in the peritoneum. Similar efficacy was demonstrated during LNP administration postsensitization. While nondecorated particles had lesser but significant effects, PolyA/LNP-Man lacked protective effects. These results demonstrate an exciting application of mRNA/LNP for treatment of food allergen anaphylaxis, with the promise to be widely applicable to the allergy field.
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Affiliation(s)
- Xiao Xu
- Division
of NanoMedicine, Department of Medicine, University of California, Los Angeles, California 90095, United States
| | - Xiang Wang
- Division
of NanoMedicine, Department of Medicine, University of California, Los Angeles, California 90095, United States
- Center
of Environmental Implications of Nanotechnology (UC CEIN), University of California, Los Angeles, California 90095, United States
- California
NanoSystems Institute, University of California, Los Angeles, California 90095, United States
| | - Yu-Pei Liao
- Division
of NanoMedicine, Department of Medicine, University of California, Los Angeles, California 90095, United States
| | - Lijia Luo
- Division
of NanoMedicine, Department of Medicine, University of California, Los Angeles, California 90095, United States
| | - Tian Xia
- Division
of NanoMedicine, Department of Medicine, University of California, Los Angeles, California 90095, United States
- Center
of Environmental Implications of Nanotechnology (UC CEIN), University of California, Los Angeles, California 90095, United States
- California
NanoSystems Institute, University of California, Los Angeles, California 90095, United States
| | - Andre E. Nel
- Division
of NanoMedicine, Department of Medicine, University of California, Los Angeles, California 90095, United States
- Center
of Environmental Implications of Nanotechnology (UC CEIN), University of California, Los Angeles, California 90095, United States
- California
NanoSystems Institute, University of California, Los Angeles, California 90095, United States
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