1
|
Chen S, Collart MA. Membrane-associated mRNAs: A Post-transcriptional Pathway for Fine-turning Gene Expression. J Mol Biol 2024; 436:168579. [PMID: 38648968 DOI: 10.1016/j.jmb.2024.168579] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2023] [Revised: 04/14/2024] [Accepted: 04/16/2024] [Indexed: 04/25/2024]
Abstract
Gene expression is a fundamental and highly regulated process involving a series of tightly coordinated steps, including transcription, post-transcriptional processing, translation, and post-translational modifications. A growing number of studies have revealed an additional layer of complexity in gene expression through the phenomenon of mRNA subcellular localization. mRNAs can be organized into membraneless subcellular structures within both the cytoplasm and the nucleus, but they can also targeted to membranes. In this review, we will summarize in particular our knowledge on localization of mRNAs to organelles, focusing on important regulators and available techniques for studying organellar localization, and significance of this localization in the broader context of gene expression regulation.
Collapse
Affiliation(s)
- Siyu Chen
- Department of Microbiology and Molecular Medicine, Faculty of Medicine, University of Geneva, Institute of Genetics and Genomics of Geneva, Geneva, Switzerland.
| | - Martine A Collart
- Department of Microbiology and Molecular Medicine, Faculty of Medicine, University of Geneva, Institute of Genetics and Genomics of Geneva, Geneva, Switzerland.
| |
Collapse
|
2
|
Zaninello M, Schlegel T, Nolte H, Pirzada M, Savino E, Barth E, Klein I, Wüstenberg H, Uddin T, Wolff L, Wirth B, Lehmann HC, Cioni JM, Langer T, Rugarli EI. CLUH maintains functional mitochondria and translation in motoneuronal axons and prevents peripheral neuropathy. SCIENCE ADVANCES 2024; 10:eadn2050. [PMID: 38809982 PMCID: PMC11135423 DOI: 10.1126/sciadv.adn2050] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/02/2023] [Accepted: 04/24/2024] [Indexed: 05/31/2024]
Abstract
Transporting and translating mRNAs in axons is crucial for neuronal viability. Local synthesis of nuclear-encoded mitochondrial proteins protects long-lived axonal mitochondria from damage; however, the regulatory factors involved are largely unknown. We show that CLUH, which binds mRNAs encoding mitochondrial proteins, prevents peripheral neuropathy and motor deficits in the mouse. CLUH is enriched in the growth cone of developing spinal motoneurons and is required for their growth. The lack of CLUH affects the abundance of target mRNAs and the corresponding mitochondrial proteins more prominently in axons, leading to ATP deficits in the growth cone. CLUH interacts with ribosomal subunits, translation initiation, and ribosome recycling components and preserves axonal translation. Overexpression of the ribosome recycling factor ABCE1 rescues the mRNA and translation defects, as well as the growth cone size, in CLUH-deficient motoneurons. Thus, we demonstrate a role for CLUH in mitochondrial quality control and translational regulation in axons, which is essential for their development and long-term integrity and function.
Collapse
Affiliation(s)
- Marta Zaninello
- Institute for Genetics, University of Cologne, Cologne 50931, Germany
- Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), Cologne 50931, Germany
| | - Tim Schlegel
- Institute for Genetics, University of Cologne, Cologne 50931, Germany
- Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), Cologne 50931, Germany
| | - Hendrik Nolte
- Max Planck Institute for Biology of Ageing, Cologne 50931, Germany
| | - Mujeeb Pirzada
- Institute for Genetics, University of Cologne, Cologne 50931, Germany
- Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), Cologne 50931, Germany
| | - Elisa Savino
- Division of Neuroscience, IRCCS San Raffaele Scientific Institute, Milan 20132, Italy
| | - Esther Barth
- Institute for Genetics, University of Cologne, Cologne 50931, Germany
- Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), Cologne 50931, Germany
| | - Ines Klein
- Department of Neurology, University of Cologne, Cologne 50931, Germany
| | - Hauke Wüstenberg
- Department of Neurology, University of Cologne, Cologne 50931, Germany
| | - Tesmin Uddin
- Institute for Genetics, University of Cologne, Cologne 50931, Germany
- Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), Cologne 50931, Germany
| | - Lisa Wolff
- Institute of Human Genetics, University of Cologne, Cologne 50931, Germany
| | - Brunhilde Wirth
- Institute for Genetics, University of Cologne, Cologne 50931, Germany
- Institute of Human Genetics, University of Cologne, Cologne 50931, Germany
- Center for Molecular Medicine (CMMC), University of Cologne, Cologne 50931, Germany
- Center for Rare Diseases Cologne (CESEK), University Hospital of Cologne, Cologne 50937, Germany
| | - Helmar C. Lehmann
- Department of Neurology, University of Cologne, Cologne 50931, Germany
| | - Jean-Michel Cioni
- Division of Neuroscience, IRCCS San Raffaele Scientific Institute, Milan 20132, Italy
| | - Thomas Langer
- Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), Cologne 50931, Germany
- Max Planck Institute for Biology of Ageing, Cologne 50931, Germany
| | - Elena I. Rugarli
- Institute for Genetics, University of Cologne, Cologne 50931, Germany
- Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), Cologne 50931, Germany
- Center for Molecular Medicine (CMMC), University of Cologne, Cologne 50931, Germany
| |
Collapse
|
3
|
Koppers M, Özkan N, Nguyen HH, Jurriens D, McCaughey J, Nguyen DTM, Li CH, Stucchi R, Altelaar M, MacGillavry HD, Kapitein LC, Hoogenraad CC, Farías GG. Axonal endoplasmic reticulum tubules control local translation via P180/RRBP1-mediated ribosome interactions. Dev Cell 2024:S1534-5807(24)00322-8. [PMID: 38815583 DOI: 10.1016/j.devcel.2024.05.005] [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: 10/12/2022] [Revised: 01/31/2024] [Accepted: 05/09/2024] [Indexed: 06/01/2024]
Abstract
Local mRNA translation in axons is critical for the spatiotemporal regulation of the axonal proteome. A wide variety of mRNAs are localized and translated in axons; however, how protein synthesis is regulated at specific subcellular sites in axons remains unclear. Here, we establish that the axonal endoplasmic reticulum (ER) supports axonal translation in developing rat hippocampal cultured neurons. Axonal ER tubule disruption impairs local translation and ribosome distribution. Using nanoscale resolution imaging, we find that ribosomes make frequent contacts with axonal ER tubules in a translation-dependent manner and are influenced by specific extrinsic cues. We identify P180/RRBP1 as an axonally distributed ribosome receptor that regulates local translation and binds to mRNAs enriched for axonal membrane proteins. Importantly, the impairment of axonal ER-ribosome interactions causes defects in axon morphology. Our results establish a role for the axonal ER in dynamically localizing mRNA translation, which is important for proper neuron development.
Collapse
Affiliation(s)
- Max Koppers
- Cell Biology, Neurobiology and Biophysics, Department of Biology, Faculty of Science, Utrecht University, 3584 CH Utrecht, the Netherlands.
| | - Nazmiye Özkan
- Cell Biology, Neurobiology and Biophysics, Department of Biology, Faculty of Science, Utrecht University, 3584 CH Utrecht, the Netherlands
| | - Ha H Nguyen
- Cell Biology, Neurobiology and Biophysics, Department of Biology, Faculty of Science, Utrecht University, 3584 CH Utrecht, the Netherlands
| | - Daphne Jurriens
- Cell Biology, Neurobiology and Biophysics, Department of Biology, Faculty of Science, Utrecht University, 3584 CH Utrecht, the Netherlands
| | - Janine McCaughey
- Cell Biology, Neurobiology and Biophysics, Department of Biology, Faculty of Science, Utrecht University, 3584 CH Utrecht, the Netherlands
| | - Dan T M Nguyen
- Cell Biology, Neurobiology and Biophysics, Department of Biology, Faculty of Science, Utrecht University, 3584 CH Utrecht, the Netherlands
| | - Chun Hei Li
- Cell Biology, Neurobiology and Biophysics, Department of Biology, Faculty of Science, Utrecht University, 3584 CH Utrecht, the Netherlands
| | - Riccardo Stucchi
- Cell Biology, Neurobiology and Biophysics, Department of Biology, Faculty of Science, Utrecht University, 3584 CH Utrecht, the Netherlands; Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, 3584 CH Utrecht, the Netherlands
| | - Maarten Altelaar
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, 3584 CH Utrecht, the Netherlands
| | - Harold D MacGillavry
- Cell Biology, Neurobiology and Biophysics, Department of Biology, Faculty of Science, Utrecht University, 3584 CH Utrecht, the Netherlands
| | - Lukas C Kapitein
- Cell Biology, Neurobiology and Biophysics, Department of Biology, Faculty of Science, Utrecht University, 3584 CH Utrecht, the Netherlands
| | - Casper C Hoogenraad
- Cell Biology, Neurobiology and Biophysics, Department of Biology, Faculty of Science, Utrecht University, 3584 CH Utrecht, the Netherlands; Department of Neuroscience, Genentech, Inc., South San Francisco, CA 94080, USA
| | - Ginny G Farías
- Cell Biology, Neurobiology and Biophysics, Department of Biology, Faculty of Science, Utrecht University, 3584 CH Utrecht, the Netherlands.
| |
Collapse
|
4
|
Blake LA, De La Cruz A, Wu B. Imaging spatiotemporal translation regulation in vivo. Semin Cell Dev Biol 2024; 154:155-164. [PMID: 36963991 PMCID: PMC10514244 DOI: 10.1016/j.semcdb.2023.03.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2022] [Revised: 03/08/2023] [Accepted: 03/15/2023] [Indexed: 03/26/2023]
Abstract
Translation is regulated spatiotemporally to direct protein synthesis when and where it is needed. RNA localization and local translation have been observed in various subcellular compartments, allowing cells to rapidly and finely adjust their proteome post-transcriptionally. Local translation on membrane-bound organelles is important to efficiently synthesize proteins targeted to the organelles. Protein-RNA phase condensates restrict RNA spatially in membraneless organelles and play essential roles in translation regulation and RNA metabolism. In addition, the temporal translation kinetics not only determine the amount of protein produced, but also serve as an important checkpoint for the quality of ribosomes, mRNAs, and nascent proteins. Translation imaging provides a unique capability to study these fundamental processes in the native environment. Recent breakthroughs in imaging enabled real-time visualization of translation of single mRNAs, making it possible to determine the spatial distribution and key biochemical parameters of in vivo translation dynamics. Here we reviewed the recent advances in translation imaging methods and their applications to study spatiotemporal translation regulation in vivo.
Collapse
Affiliation(s)
- Lauren A Blake
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; The Center for Cell Dynamics, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Ana De La Cruz
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; The Center for Cell Dynamics, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Bin Wu
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; The Solomon H Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; The Center for Cell Dynamics, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA.
| |
Collapse
|
5
|
Horste EL, Fansler MM, Cai T, Chen X, Mitschka S, Zhen G, Lee FCY, Ule J, Mayr C. Subcytoplasmic location of translation controls protein output. Mol Cell 2023; 83:4509-4523.e11. [PMID: 38134885 PMCID: PMC11146010 DOI: 10.1016/j.molcel.2023.11.025] [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: 01/30/2023] [Revised: 08/15/2023] [Accepted: 11/21/2023] [Indexed: 12/24/2023]
Abstract
The cytoplasm is highly compartmentalized, but the extent and consequences of subcytoplasmic mRNA localization in non-polarized cells are largely unknown. We determined mRNA enrichment in TIS granules (TGs) and the rough endoplasmic reticulum (ER) through particle sorting and isolated cytosolic mRNAs by digitonin extraction. When focusing on genes that encode non-membrane proteins, we observed that 52% have transcripts enriched in specific compartments. Compartment enrichment correlates with a combinatorial code based on mRNA length, exon length, and 3' UTR-bound RNA-binding proteins. Compartment-biased mRNAs differ in the functional classes of their encoded proteins: TG-enriched mRNAs encode low-abundance proteins with strong enrichment of transcription factors, whereas ER-enriched mRNAs encode large and highly expressed proteins. Compartment localization is an important determinant of mRNA and protein abundance, which is supported by reporter experiments showing that redirecting cytosolic mRNAs to the ER increases their protein expression. In summary, the cytoplasm is functionally compartmentalized by local translation environments.
Collapse
Affiliation(s)
- Ellen L Horste
- Gerstner Sloan Kettering Graduate School of Biomedical Sciences, New York, NY 10065, USA; Cancer Biology and Genetics Program, Sloan Kettering Institute, New York, NY 10065, USA
| | - Mervin M Fansler
- Cancer Biology and Genetics Program, Sloan Kettering Institute, New York, NY 10065, USA; Tri-Institutional Training Program in Computational Biology and Medicine, Weill-Cornell Graduate College, New York, NY 10021, USA
| | - Ting Cai
- Cancer Biology and Genetics Program, Sloan Kettering Institute, New York, NY 10065, USA
| | - Xiuzhen Chen
- Cancer Biology and Genetics Program, Sloan Kettering Institute, New York, NY 10065, USA
| | - Sibylle Mitschka
- Cancer Biology and Genetics Program, Sloan Kettering Institute, New York, NY 10065, USA
| | - Gang Zhen
- Cancer Biology and Genetics Program, Sloan Kettering Institute, New York, NY 10065, USA
| | - Flora C Y Lee
- UK Dementia Research Institute, King's College London, London SE5 9NU, UK; The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Jernej Ule
- UK Dementia Research Institute, King's College London, London SE5 9NU, UK; The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Christine Mayr
- Gerstner Sloan Kettering Graduate School of Biomedical Sciences, New York, NY 10065, USA; Cancer Biology and Genetics Program, Sloan Kettering Institute, New York, NY 10065, USA; Tri-Institutional Training Program in Computational Biology and Medicine, Weill-Cornell Graduate College, New York, NY 10021, USA.
| |
Collapse
|
6
|
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.
Collapse
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
| |
Collapse
|
7
|
Jung M, Zimmermann R. Quantitative Mass Spectrometry Characterizes Client Spectra of Components for Targeting of Membrane Proteins to and Their Insertion into the Membrane of the Human ER. Int J Mol Sci 2023; 24:14166. [PMID: 37762469 PMCID: PMC10532041 DOI: 10.3390/ijms241814166] [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: 08/09/2023] [Revised: 09/07/2023] [Accepted: 09/12/2023] [Indexed: 09/29/2023] Open
Abstract
To elucidate the redundancy in the components for the targeting of membrane proteins to the endoplasmic reticulum (ER) and/or their insertion into the ER membrane under physiological conditions, we previously analyzed different human cells by label-free quantitative mass spectrometry. The HeLa and HEK293 cells had been depleted of a certain component by siRNA or CRISPR/Cas9 treatment or were deficient patient fibroblasts and compared to the respective control cells by differential protein abundance analysis. In addition to clients of the SRP and Sec61 complex, we identified membrane protein clients of components of the TRC/GET, SND, and PEX3 pathways for ER targeting, and Sec62, Sec63, TRAM1, and TRAP as putative auxiliary components of the Sec61 complex. Here, a comprehensive evaluation of these previously described differential protein abundance analyses, as well as similar analyses on the Sec61-co-operating EMC and the characteristics of the topogenic sequences of the various membrane protein clients, i.e., the client spectra of the components, are reported. As expected, the analysis characterized membrane protein precursors with cleavable amino-terminal signal peptides or amino-terminal transmembrane helices as predominant clients of SRP, as well as the Sec61 complex, while precursors with more central or even carboxy-terminal ones were found to dominate the client spectra of the SND and TRC/GET pathways for membrane targeting. For membrane protein insertion, the auxiliary Sec61 channel components indeed share the client spectra of the Sec61 complex to a large extent. However, we also detected some unexpected differences, particularly related to EMC, TRAP, and TRAM1. The possible mechanistic implications for membrane protein biogenesis at the human ER are discussed and can be expected to eventually advance our understanding of the mechanisms that are involved in the so-called Sec61-channelopathies, resulting from deficient ER protein import.
Collapse
Affiliation(s)
| | - Richard Zimmermann
- Medical Biochemistry and Molecular Biology, Saarland University, 66421 Homburg, Germany;
| |
Collapse
|
8
|
Kejiou NS, Ilan L, Aigner S, Luo E, Tonn T, Ozadam H, Lee M, Cole G, Rabano I, Rajakulendran N, Yee BA, Najafabadi H, Moraes T, Angers S, Yeo G, Cenik C, Palazzo A. Pyruvate Kinase M (PKM) binds ribosomes in a poly-ADP ribosylation dependent manner to induce translational stalling. Nucleic Acids Res 2023; 51:6461-6478. [PMID: 37224531 PMCID: PMC10325899 DOI: 10.1093/nar/gkad440] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2022] [Revised: 05/01/2023] [Accepted: 05/10/2023] [Indexed: 05/26/2023] Open
Abstract
In light of the numerous studies identifying post-transcriptional regulators on the surface of the endoplasmic reticulum (ER), we asked whether there are factors that regulate compartment specific mRNA translation in human cells. Using a proteomic survey of spatially regulated polysome interacting proteins, we identified the glycolytic enzyme Pyruvate Kinase M (PKM) as a cytosolic (i.e. ER-excluded) polysome interactor and investigated how it influences mRNA translation. We discovered that the PKM-polysome interaction is directly regulated by ADP levels-providing a link between carbohydrate metabolism and mRNA translation. By performing enhanced crosslinking immunoprecipitation-sequencing (eCLIP-seq), we found that PKM crosslinks to mRNA sequences that are immediately downstream of regions that encode lysine- and glutamate-enriched tracts. Using ribosome footprint protection sequencing, we found that PKM binding to ribosomes causes translational stalling near lysine and glutamate encoding sequences. Lastly, we observed that PKM recruitment to polysomes is dependent on poly-ADP ribosylation activity (PARylation)-and may depend on co-translational PARylation of lysine and glutamate residues of nascent polypeptide chains. Overall, our study uncovers a novel role for PKM in post-transcriptional gene regulation, linking cellular metabolism and mRNA translation.
Collapse
Affiliation(s)
- Nevraj S Kejiou
- Department of Biochemistry, University of Toronto, Toronto, ON, Canada
| | - Lena Ilan
- Department of Biochemistry, University of Toronto, Toronto, ON, Canada
| | - Stefan Aigner
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA
| | - Enching Luo
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA
| | - Tori Tonn
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX, USA
| | - Hakan Ozadam
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX, USA
| | - Muyoung Lee
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX, USA
| | - Gregory B Cole
- Department of Biochemistry, University of Toronto, Toronto, ON, Canada
| | - Ines Rabano
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA
| | | | - Brian A Yee
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA
| | - Hamed S Najafabadi
- Department of Human Genetics, McGill University, Montreal, QC, Canada
- McGill University and Genome Quebec Innovation Centre, Montreal, QC, Canada
| | - Trevor F Moraes
- Department of Biochemistry, University of Toronto, Toronto, ON, Canada
| | - Stephane Angers
- Department of Biochemistry, University of Toronto, Toronto, ON, Canada
- Leslie Dan Faculty of Pharmacy, University of Toronto, Toronto, ON, Canada
| | - Gene W Yeo
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA
| | - Can Cenik
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX, USA
| | | |
Collapse
|
9
|
Nguyen T, Mills JC, Cho CJ. The coordinated management of ribosome and translation during injury and regeneration. Front Cell Dev Biol 2023; 11:1186638. [PMID: 37427381 PMCID: PMC10325863 DOI: 10.3389/fcell.2023.1186638] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2023] [Accepted: 06/06/2023] [Indexed: 07/11/2023] Open
Abstract
Diverse acute and chronic injuries induce damage responses in the gastrointestinal (GI) system, and numerous cell types in the gastrointestinal tract demonstrate remarkable resilience, adaptability, and regenerative capacity in response to stress. Metaplasias, such as columnar and secretory cell metaplasia, are well-known adaptations that these cells make, the majority of which are epidemiologically associated with an elevated cancer risk. On a number of fronts, it is now being investigated how cells respond to injury at the tissue level, where diverse cell types that differ in proliferation capacity and differentiation state cooperate and compete with one another to participate in regeneration. In addition, the cascades or series of molecular responses that cells show are just beginning to be understood. Notably, the ribosome, a ribonucleoprotein complex that is essential for translation on the endoplasmic reticulum (ER) and in the cytoplasm, is recognized as the central organelle during this process. The highly regulated management of ribosomes as key translational machinery, and their platform, rough endoplasmic reticulum, are not only essential for maintaining differentiated cell identity, but also for achieving successful cell regeneration after injury. This review will cover in depth how ribosomes, the endoplasmic reticulum, and translation are regulated and managed in response to injury (e.g., paligenosis), as well as why this is essential for the proper adaptation of a cell to stress. For this, we will first discuss how multiple gastrointestinal organs respond to stress through metaplasia. Next, we will cover how ribosomes are generated, maintained, and degraded, in addition to the factors that govern translation. Finally, we will investigate how ribosomes and translation machinery are dynamically regulated in response to injury. Our increased understanding of this overlooked cell fate decision mechanism will facilitate the discovery of novel therapeutic targets for gastrointestinal tract tumors, focusing on ribosomes and translation machinery.
Collapse
Affiliation(s)
- Thanh Nguyen
- Department of Medicine, Baylor College of Medicine, Houston, TX, United States
| | - Jason C. Mills
- Department of Medicine, Baylor College of Medicine, Houston, TX, United States
- Department of Pathology and Immunology, Baylor College of Medicine, Houston, TX, United States
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX, United States
| | - Charles J. Cho
- Department of Medicine, Baylor College of Medicine, Houston, TX, United States
| |
Collapse
|
10
|
Gao Y, Zhu Y, Sun Q, Chen D. Argonaute-dependent ribosome-associated protein quality control. Trends Cell Biol 2023; 33:260-272. [PMID: 35981909 DOI: 10.1016/j.tcb.2022.07.007] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2022] [Revised: 07/19/2022] [Accepted: 07/25/2022] [Indexed: 11/17/2022]
Abstract
Ribosome-associated protein quality control (RQC) is a protein surveillance mechanism that eliminates defective nascent polypeptides. The E3 ubiquitin ligase, Ltn1, is a key regulator of RQC that targets substrates for ubiquitination. Argonaute proteins (AGOs) are central players in miRNA-mediated gene silencing and have recently been shown to also regulate RQC by facilitating Ltn1. Therefore, AGOs directly coordinate post-transcriptional gene silencing and RQC, ensuring efficient gene silencing. We summarize the principles of RQC and the functions of AGOs in miRNA-mediated gene silencing, and discuss how AGOs associate with the endoplasmic reticulum (ER) to assist Ltn1 in controlling RQC. We highlight that RQC not only eliminates defective nascent polypeptides but also removes unwanted protein products when AGOs participate.
Collapse
Affiliation(s)
- Yajie Gao
- Institute of Biomedical Research, Yunnan University, Kunming 650500, China
| | - Yuanxiang Zhu
- Institute of Biomedical Research, Yunnan University, Kunming 650500, China
| | - Qinmiao Sun
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; Institute of Stem Cells and Regeneration, Chinese Academy of Sciences, Beijing 100101, China.
| | - Dahua Chen
- Institute of Biomedical Research, Yunnan University, Kunming 650500, China.
| |
Collapse
|
11
|
Dave P, Roth G, Griesbach E, Mateju D, Hochstoeger T, Chao JA. Single-molecule imaging reveals translation-dependent destabilization of mRNAs. Mol Cell 2023; 83:589-606.e6. [PMID: 36731471 PMCID: PMC9957601 DOI: 10.1016/j.molcel.2023.01.013] [Citation(s) in RCA: 15] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Revised: 11/07/2022] [Accepted: 01/06/2023] [Indexed: 02/04/2023]
Abstract
The relationship between mRNA translation and decay is incompletely understood, with conflicting reports suggesting that translation can either promote decay or stabilize mRNAs. The effect of translation on mRNA decay has mainly been studied using ensemble measurements and global transcription and translation inhibitors, which can have pleiotropic effects. We developed a single-molecule imaging approach to control the translation of a specific transcript that enabled simultaneous measurement of translation and mRNA decay. Our results demonstrate that mRNA translation reduces mRNA stability, and mathematical modeling suggests that this process is dependent on ribosome flux. Furthermore, our results indicate that miRNAs mediate efficient degradation of both translating and non-translating target mRNAs and reveal a predominant role for mRNA degradation in miRNA-mediated regulation. Simultaneous observation of translation and decay of single mRNAs provides a framework to directly study how these processes are interconnected in cells.
Collapse
Affiliation(s)
- Pratik Dave
- Friedrich Miescher Institute for Biomedical Research, 4058 Basel, Switzerland
| | - Gregory Roth
- Friedrich Miescher Institute for Biomedical Research, 4058 Basel, Switzerland
| | - Esther Griesbach
- Friedrich Miescher Institute for Biomedical Research, 4058 Basel, Switzerland
| | - Daniel Mateju
- Friedrich Miescher Institute for Biomedical Research, 4058 Basel, Switzerland
| | - Tobias Hochstoeger
- Friedrich Miescher Institute for Biomedical Research, 4058 Basel, Switzerland; University of Basel, 4003 Basel, Switzerland
| | - Jeffrey A Chao
- Friedrich Miescher Institute for Biomedical Research, 4058 Basel, Switzerland.
| |
Collapse
|
12
|
Hwang H, Yun S, Arcanjo RB, Divyanshi, Chen S, Mei W, Nowak RA, Kwon T, Yang J. Regulation of RNA localization during oocyte maturation by dynamic RNA-ER association and remodeling of the ER. Cell Rep 2022; 41:111802. [PMID: 36516762 PMCID: PMC9811979 DOI: 10.1016/j.celrep.2022.111802] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2022] [Revised: 08/30/2022] [Accepted: 11/17/2022] [Indexed: 12/14/2022] Open
Abstract
Asymmetric localization of mRNAs is crucial for cell polarity and cell fate determination. By performing fractionation RNA-seq, we report here that a large number of maternal RNAs are associated with the ER in Xenopus oocytes but are released into the cytosol after oocyte maturation. We provide evidence that the majority of ER-associated RNA-binding proteins (RBPs) remain associated with the ER after oocyte maturation. However, all ER-associated RBPs analyzed exhibit reduced binding to some of their target RNAs after oocyte maturation. Our results further show that the ER is remodeled massively during oocyte maturation, leading to the formation of a widespread tubular ER network in the animal hemisphere that is required for the asymmetric localization of mRNAs in mature eggs. Thus, our findings demonstrate that dynamic regulation of RNA-ER association and remodeling of the ER are important for the asymmetric localization of RNAs during development.
Collapse
Affiliation(s)
- Hyojeong Hwang
- Department of Comparative Biosciences, University of Illinois at Urbana-Champaign, Urbana, IL 61802, USA
| | - Seongmin Yun
- Department of Biomedical Engineering, Ulsan National Institute of Science and Technology (UNIST), Ulsan 44919, Republic of Korea
| | - Rachel Braz Arcanjo
- Department of Animal Sciences, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Divyanshi
- Department of Cell and Developmental Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61802, USA
| | - Sijie Chen
- Department of Comparative Biosciences, University of Illinois at Urbana-Champaign, Urbana, IL 61802, USA
| | - Wenyan Mei
- Department of Comparative Biosciences, University of Illinois at Urbana-Champaign, Urbana, IL 61802, USA
| | - Romana A. Nowak
- Department of Animal Sciences, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Taejoon Kwon
- Department of Biomedical Engineering, Ulsan National Institute of Science and Technology (UNIST), Ulsan 44919, Republic of Korea,Correspondence: (T.K.), (J.Y.)
| | - Jing Yang
- Department of Comparative Biosciences, University of Illinois at Urbana-Champaign, Urbana, IL 61802, USA,Department of Cell and Developmental Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61802, USA,Lead contact,Correspondence: (T.K.), (J.Y.)
| |
Collapse
|
13
|
Khairnar RC, Parihar N, Prabhavalkar KS, Bhatt LK. Emerging targets signaling for inflammation in Parkinson's disease drug discovery. Metab Brain Dis 2022; 37:2143-2161. [PMID: 35536461 DOI: 10.1007/s11011-022-00999-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/17/2022] [Accepted: 04/29/2022] [Indexed: 10/18/2022]
Abstract
Parkinson's disease (PD) patients not only show motor features such as bradykinesia, tremor, and rigidity but also non-motor features such as anxiety, depression, psychosis, memory loss, attention deficits, fatigue, sexual dysfunction, gastrointestinal issues, and pain. Many pharmacological treatments are available for PD patients; however, these treatments are partially or transiently effective since they only decrease the symptoms. As these therapies are unable to restore dopaminergic neurons and stop the development of Parkinson's disease, therefore, the need for an effective therapeutic approach is required. The current review summarizes novel targets for PD, that can be utilized to identify disease-modifying treatments.
Collapse
Affiliation(s)
- Rhema Chandan Khairnar
- Department of Pharmacology, SVKM's Dr. Bhanuben Nanavati College of Pharmacy, Vile Parle (West), Mumbai, 400056, India
| | - Niraj Parihar
- Department of Pharmacology, SVKM's Dr. Bhanuben Nanavati College of Pharmacy, Vile Parle (West), Mumbai, 400056, India
| | - Kedar S Prabhavalkar
- Department of Pharmacology, SVKM's Dr. Bhanuben Nanavati College of Pharmacy, Vile Parle (West), Mumbai, 400056, India
| | - Lokesh Kumar Bhatt
- Department of Pharmacology, SVKM's Dr. Bhanuben Nanavati College of Pharmacy, Vile Parle (West), Mumbai, 400056, India.
| |
Collapse
|
14
|
Chen J, Li S, Huang Z, Cao C, Wang A, He Q. METTL3 suppresses anlotinib sensitivity by regulating m 6A modification of FGFR3 in oral squamous cell carcinoma. Cancer Cell Int 2022; 22:295. [PMID: 36167542 PMCID: PMC9516809 DOI: 10.1186/s12935-022-02715-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2022] [Accepted: 09/09/2022] [Indexed: 12/01/2022] Open
Abstract
Background N6-methyladenosine (m6A) is an abundant nucleotide modification in mRNA, but there were few studies on its role in cancer drug sensitivity and resistance. Anlotinib has been proved to have effective antitumor effects in oral squamous cell carcinoma (OSCC) in our previous study. Here, we sought to investigate the treatment target of anlotinib and the function and mechanisms of m6A modification in regulating anlotinib effect in OSCC. Methods Anlotinib treatment in a dose-dependent manner, western blotting, qRT-PCR and cell lost-of-function assays were used to study the treatment target of anlotinib in OSCC. RNA m6A dot blot assays, the m6A MeRIP-seq and MeRIP-qPCR, RNA and protein stability assays were used to explore the m6A modification of the treatment target of anlotinib. Cell lost-of-function assays after METTL3 depletion were conducted to investigate the effect of m6A modification level on the therapeutic effect of anlotinib in OSCC. Patient-derived tumor xenograft (PDX) models and immunohistochemistry staining were performed to study the relationship of METTL3 and antitumor sensitivity of anlotinib in vivo. Results Anlotinib targeted FGFR3 in the treatment of OSCC and inhibited tumor cell proliferation and promoted apoptosis by inactivating the FGFR3/AKT/mTOR signaling pathway. METTL3 was identified to target and modify FGFR3 m6A methylation and then decrease the stability of mRNA. METTL3 expression level was related to the anlotinib sensitivity in OSCC cells in vitro and METTL3 knockdown promoted anlotinib sensitivity of OSCC cells by inhibiting the FGFR3 expression. PDX models samples furthermore showed that METTL3 and FGFR3 levels were tightly correlated with the anlotinib efficacy in OSCC. Conclusions In summary, our work revealed that FGFR3 was served as the treatment target of anlotinib and METTL3-mediated FGFR3 m6A modification played a critical function in the anlotinib sensitivity in OSCC. Supplementary Information The online version contains supplementary material available at 10.1186/s12935-022-02715-7.
Collapse
Affiliation(s)
- Jie Chen
- Department of Oral and Maxillofacial Surgery, The First Affiliated Hospital, Sun Yat-Sen University, Guangzhou, 510080, China.,Hospital of Stomatology, Guangdong Provincial Key Laboratory of Stomatology, Guanghua School of Stomatology, Sun Yat-Sen University, Guangzhou, 510055, China
| | - Shuai Li
- Department of Oral and Maxillofacial Surgery, The First Affiliated Hospital, Sun Yat-Sen University, Guangzhou, 510080, China.,Department of Oral and Maxillofacial Surgery, College of Stomatology, Guangxi Medical University, Nanning, China
| | - Zhexun Huang
- Center of Oral Implantology, Stomatological Hospital, Southern Medical University, Guangzhou, 510280, China
| | - Congyuan Cao
- Department of Oral and Maxillofacial Surgery, The First Affiliated Hospital, Sun Yat-Sen University, Guangzhou, 510080, China
| | - Anxun Wang
- Department of Oral and Maxillofacial Surgery, The First Affiliated Hospital, Sun Yat-Sen University, Guangzhou, 510080, China.
| | - Qianting He
- Department of Oral and Maxillofacial Surgery, The First Affiliated Hospital, Sun Yat-Sen University, Guangzhou, 510080, China.
| |
Collapse
|
15
|
Lang S, Nguyen D, Bhadra P, Jung M, Helms V, Zimmermann R. Signal Peptide Features Determining the Substrate Specificities of Targeting and Translocation Components in Human ER Protein Import. Front Physiol 2022; 13:833540. [PMID: 35899032 PMCID: PMC9309488 DOI: 10.3389/fphys.2022.833540] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2021] [Accepted: 05/17/2022] [Indexed: 12/11/2022] Open
Abstract
In human cells, approximately 30% of all polypeptides enter the secretory pathway at the level of the endoplasmic reticulum (ER). This process involves cleavable amino-terminal signal peptides (SPs) or more or less amino-terminal transmembrane helices (TMHs), which serve as targeting determinants, at the level of the precursor polypeptides and a multitude of cytosolic and ER proteins, which facilitate their ER import. Alone or in combination SPs and TMHs guarantee the initial ER targeting as well as the subsequent membrane integration or translocation. Cytosolic SRP and SR, its receptor in the ER membrane, mediate cotranslational targeting of most nascent precursor polypeptide chains to the polypeptide-conducting Sec61 complex in the ER membrane. Alternatively, fully-synthesized precursor polypeptides and certain nascent precursor polypeptides are targeted to the ER membrane by either the PEX-, SND-, or TRC-pathway. Although these targeting pathways may have overlapping functions, the question arises how relevant this is under cellular conditions and which features of SPs and precursor polypeptides determine preference for a certain pathway. Irrespective of their targeting pathway(s), most precursor polypeptides are integrated into or translocated across the ER membrane via the Sec61 channel. For some precursor polypeptides specific Sec61 interaction partners have to support the gating of the channel to the open state, again raising the question why and when this is the case. Recent progress shed light on the client spectrum and specificities of some auxiliary components, including Sec62/Sec63, TRAM1 protein, and TRAP. To address the question which precursors use a certain pathway or component in intact human cells, i.e., under conditions of fast translation rates and molecular crowding, in the presence of competing precursors, different targeting organelles, and relevant stoichiometries of the involved components, siRNA-mediated depletion of single targeting or transport components in HeLa cells was combined with label-free quantitative proteomics and differential protein abundance analysis. Here, we present a summary of the experimental approach as well as the resulting differential protein abundance analyses and discuss their mechanistic implications in light of the available structural data.
Collapse
Affiliation(s)
- Sven Lang
- Medical Biochemistry and Molecular Biology, Saarland University, Homburg, Germany
- *Correspondence: Sven Lang, ; Richard Zimmermann,
| | - Duy Nguyen
- Center for Bioinformatics, Saarland University, Saarbrücken, Germany
| | - Pratiti Bhadra
- Center for Bioinformatics, Saarland University, Saarbrücken, Germany
| | - Martin Jung
- Medical Biochemistry and Molecular Biology, Saarland University, Homburg, Germany
| | - Volkhard Helms
- Center for Bioinformatics, Saarland University, Saarbrücken, Germany
| | - Richard Zimmermann
- Medical Biochemistry and Molecular Biology, Saarland University, Homburg, Germany
- *Correspondence: Sven Lang, ; Richard Zimmermann,
| |
Collapse
|
16
|
Gómez-Puerta S, Ferrero R, Hochstoeger T, Zubiri I, Chao J, Aragón T, Voigt F. Live imaging of the co-translational recruitment of XBP1 mRNA to the ER and its processing by diffuse, non-polarized IRE1α. eLife 2022; 11:e75580. [PMID: 35730412 PMCID: PMC9217131 DOI: 10.7554/elife.75580] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2021] [Accepted: 06/01/2022] [Indexed: 11/13/2022] Open
Abstract
Endoplasmic reticulum (ER) to nucleus homeostatic signaling, known as the unfolded protein response (UPR), relies on the non-canonical splicing of XBP1 mRNA. The molecular switch that initiates splicing is the oligomerization of the ER stress sensor and UPR endonuclease IRE1α (inositol-requiring enzyme 1 alpha). While IRE1α can form large clusters that have been proposed to function as XBP1 processing centers on the ER, the actual oligomeric state of active IRE1α complexes as well as the targeting mechanism that recruits XBP1 to IRE1α oligomers remains unknown. Here, we have developed a single-molecule imaging approach to monitor the recruitment of individual XBP1 transcripts to the ER surface. Using this methodology, we confirmed that stable ER association of unspliced XBP1 mRNA is established through HR2 (hydrophobic region 2)-dependent targeting and relies on active translation. In addition, we show that IRE1α-catalyzed splicing mobilizes XBP1 mRNA from the ER membrane in response to ER stress. Surprisingly, we find that XBP1 transcripts are not recruited into large IRE1α clusters, which are only observed upon overexpression of fluorescently tagged IRE1α during ER stress. Our findings support a model where ribosome-engaged, immobilized XBP1 mRNA is processed by small IRE1α assemblies that could be dynamically recruited for processing of mRNA transcripts on the ER.
Collapse
Affiliation(s)
- Silvia Gómez-Puerta
- Department of Gene Therapy and Regulation of Gene Expression, Center for Applied Medical Research (CIMA), University of NavarraPamplonaSpain
| | - Roberto Ferrero
- Department of Gene Therapy and Regulation of Gene Expression, Center for Applied Medical Research (CIMA), University of NavarraPamplonaSpain
| | - Tobias Hochstoeger
- Friedrich Miescher Institute for Biomedical ResearchBaselSwitzerland
- University of BaselBaselSwitzerland
| | - Ivan Zubiri
- Department of Gene Therapy and Regulation of Gene Expression, Center for Applied Medical Research (CIMA), University of NavarraPamplonaSpain
| | - Jeffrey Chao
- Friedrich Miescher Institute for Biomedical ResearchBaselSwitzerland
| | - Tomás Aragón
- Department of Gene Therapy and Regulation of Gene Expression, Center for Applied Medical Research (CIMA), University of NavarraPamplonaSpain
| | - Franka Voigt
- Friedrich Miescher Institute for Biomedical ResearchBaselSwitzerland
| |
Collapse
|
17
|
Arata Y, Shiga I, Ikeda Y, Jurica P, Kimura H, Kiyono K, Sako Y. Insulin signaling shapes fractal scaling of C. elegans behavior. Sci Rep 2022; 12:10481. [PMID: 35729173 PMCID: PMC9213454 DOI: 10.1038/s41598-022-13022-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2022] [Accepted: 05/03/2022] [Indexed: 11/08/2022] Open
Abstract
Fractal scaling in animal behavioral activity, where similar temporal patterns appear repeatedly over a series of magnifications among time scales, governs the complex behavior of various animal species and, in humans, can be altered by neurodegenerative diseases and aging. However, the mechanism underlying fractal scaling remains unknown. Here, we cultured C. elegans in a microfluidic device for 3 days and analyzed temporal patterns of C. elegans activity by fractal analyses. The residence-time distribution of C. elegans behaviors shared a common feature with those of human and mice. Specifically, the residence-time power-law distribution of the active state changed to an exponential-like decline at a longer time scale, whereas the inactive state followed a power-law distribution. An exponential-like decline appeared with nutrient supply in wild-type animals, whereas this decline disappeared in insulin-signaling-defective daf-2 and daf-16 mutants. The absolute value of the power-law exponent of the inactive state distribution increased with nutrient supply in wild-type animals, whereas the value decreased in daf-2 and daf-16 mutants. We conclude that insulin signaling differentially affects mechanisms that determine the residence time in active and inactive states in C. elegans behavior. In humans, diabetes mellitus, which is caused by defects in insulin signaling, is associated with mood disorders that affect daily behavioral activities. We hypothesize that comorbid behavioral defects in patients with diabetes may be attributed to altered fractal scaling of human behavior.
Collapse
Affiliation(s)
- Yukinobu Arata
- Cellular Informatics Laboratory, Cluster for Pioneering Research (CPR), RIKEN, 2-1 Hirosawa, Wako, Saitama, 351-0198, Japan.
| | - Itsuki Shiga
- Graduate School of Engineering Science, Osaka University, 1-3 Machikaneyama-cho, Toyonaka, Osaka, 560-8531, Japan
| | - Yusaku Ikeda
- Cellular Informatics Laboratory, Cluster for Pioneering Research (CPR), RIKEN, 2-1 Hirosawa, Wako, Saitama, 351-0198, Japan
- Department of Mechanical Engineering, School of Engineering, Tokai University, 4-1-1 Kitakaname, Hiratsuka, Kanagawa, 259-1292, Japan
| | - Peter Jurica
- Cellular Informatics Laboratory, Cluster for Pioneering Research (CPR), RIKEN, 2-1 Hirosawa, Wako, Saitama, 351-0198, Japan
| | - Hiroshi Kimura
- Department of Mechanical Engineering, School of Engineering, Tokai University, 4-1-1 Kitakaname, Hiratsuka, Kanagawa, 259-1292, Japan
| | - Ken Kiyono
- Graduate School of Engineering Science, Osaka University, 1-3 Machikaneyama-cho, Toyonaka, Osaka, 560-8531, Japan
| | - Yasushi Sako
- Cellular Informatics Laboratory, Cluster for Pioneering Research (CPR), RIKEN, 2-1 Hirosawa, Wako, Saitama, 351-0198, Japan
| |
Collapse
|
18
|
Guo Y, Lee RE. Long-term imaging of individual mRNA molecules in living cells. CELL REPORTS METHODS 2022; 2:100226. [PMID: 35784652 PMCID: PMC9243547 DOI: 10.1016/j.crmeth.2022.100226] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/14/2021] [Revised: 03/10/2022] [Accepted: 05/04/2022] [Indexed: 12/04/2022]
Abstract
Single-cell imaging of individual mRNAs has revealed core mechanisms of the central dogma. However, most approaches require cell fixation or have limited sensitivity for live-cell applications. Here, we describe SunRISER (SunTag-based reporter for imaging signal-enriched mRNA), a computationally and experimentally optimized approach for unambiguous detection of single mRNA molecules in living cells. When viewed by epifluorescence microscopy, SunRISER-labeled mRNAs show strong signal to background and resistance to photobleaching, which together enable long-term mRNA imaging studies. SunRISER variants, using 8× and 10× stem-loop arrays, demonstrate effective mRNA detection while significantly reducing alterations to target mRNA sequences. We characterize SunRISER to observe mRNA inheritance during mitosis and find that stressors enhance diversity among post-mitotic sister cells. Taken together, SunRISER enables a glimpse into living cells to observe aspects of the central dogma and the role of mRNAs in rare and dynamical trafficking events.
Collapse
Affiliation(s)
- Yue Guo
- Department of Computational and Systems Biology, School of Medicine, University of Pittsburgh, Pittsburgh, PA 15213, USA
- Department of Physics and Astronomy, University of Pittsburgh, Pittsburgh, PA 15260, USA
| | - Robin E.C. Lee
- Department of Computational and Systems Biology, School of Medicine, University of Pittsburgh, Pittsburgh, PA 15213, USA
- Center for Systems Immunology, School of Medicine, University of Pittsburgh, Pittsburgh, PA 15213, USA
| |
Collapse
|
19
|
Cialek CA, Galindo G, Morisaki T, Zhao N, Montgomery TA, Stasevich TJ. Imaging translational control by Argonaute with single-molecule resolution in live cells. Nat Commun 2022; 13:3345. [PMID: 35688806 PMCID: PMC9187665 DOI: 10.1038/s41467-022-30976-3] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2021] [Accepted: 05/24/2022] [Indexed: 11/29/2022] Open
Abstract
A major challenge to our understanding of translational control has been deconvolving the individual impact specific regulatory factors have on the complex dynamics of mRNA translation. MicroRNAs (miRNAs), for example, guide Argonaute and associated proteins to target mRNAs, where they direct gene silencing in multiple ways that are not well understood. To better deconvolve these dynamics, we have developed technology to directly visualize and quantify the impact of human Argonaute2 (Ago2) on the translation and subcellular localization of individual reporter mRNAs in living cells. We show that our combined translation and Ago2 tethering sensor reflects endogenous miRNA-mediated gene silencing. Using the sensor, we find that Ago2 association leads to progressive silencing of translation at individual mRNA. Silencing was occasionally interrupted by brief bursts of translational activity and took 3–4 times longer than a single round of translation, consistent with a gradual increase in the inhibition of translation initiation. At later time points, Ago2-tethered mRNAs cluster and coalesce with P-bodies, where a translationally silent state is maintained. These results provide a framework for exploring miRNA-mediated gene regulation in live cells at the single-molecule level. Furthermore, our tethering-based, single-molecule reporter system will likely have wide-ranging application in studying RNA-protein interactions. Guided by miRNA, Argonaute proteins silence mRNA in multiple ways that are not well understood. Here, the authors develop live-cell biosensors to image the impact tethered regulatory factors, such as Argonaute, have on single-mRNA translation dynamics.
Collapse
Affiliation(s)
- Charlotte A Cialek
- Department of Biochemistry & Molecular Biology, Colorado State University, Fort Collins, CO, 80523, USA
| | - Gabriel Galindo
- Department of Biochemistry & Molecular Biology, Colorado State University, Fort Collins, CO, 80523, USA
| | - Tatsuya Morisaki
- Department of Biochemistry & Molecular Biology, Colorado State University, Fort Collins, CO, 80523, USA
| | - Ning Zhao
- Department of Biochemistry & Molecular Biology, Colorado State University, Fort Collins, CO, 80523, USA
| | - Taiowa A Montgomery
- Department of Biology, Colorado State University, Fort Collins, CO, 80523, USA.
| | - Timothy J Stasevich
- Department of Biochemistry & Molecular Biology, Colorado State University, Fort Collins, CO, 80523, USA. .,Cell Biology Center and World Research Hub Initiative, Tokyo Institute of Technology, Yokohama, Japan.
| |
Collapse
|
20
|
Zinnall U, Milek M, Minia I, Vieira-Vieira CH, Müller S, Mastrobuoni G, Hazapis OG, Del Giudice S, Schwefel D, Bley N, Voigt F, Chao JA, Kempa S, Hüttelmaier S, Selbach M, Landthaler M. HDLBP binds ER-targeted mRNAs by multivalent interactions to promote protein synthesis of transmembrane and secreted proteins. Nat Commun 2022; 13:2727. [PMID: 35585045 PMCID: PMC9117268 DOI: 10.1038/s41467-022-30322-7] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2021] [Accepted: 04/13/2022] [Indexed: 01/09/2023] Open
Abstract
The biological role of RNA-binding proteins in the secretory pathway is not well established. Here, we describe that human HDLBP/Vigilin directly interacts with more than 80% of ER-localized mRNAs. PAR-CLIP analysis reveals that these transcripts represent high affinity HDLBP substrates and are specifically bound in their coding sequences (CDS), in contrast to CDS/3’UTR-bound cytosolic mRNAs. HDLBP crosslinks strongly to long CU-rich motifs, which frequently reside in CDS of ER-localized mRNAs and result in high affinity multivalent interactions. In addition to HDLBP-ncRNA interactome, quantification of HDLBP-proximal proteome confirms association with components of the translational apparatus and the signal recognition particle. Absence of HDLBP results in decreased translation efficiency of HDLBP target mRNAs, impaired protein synthesis and secretion in model cell lines, as well as decreased tumor growth in a lung cancer mouse model. These results highlight a general function for HDLBP in the translation of ER-localized mRNAs and its relevance for tumor progression. RNA binding protein HDLBP (or Vigilin) localizes in the endoplasmic reticulum (ER) membrane. Here the authors show that HDLBP contributes to translation of ER-targeted mRNAs.
Collapse
Affiliation(s)
- Ulrike Zinnall
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin Institute for Medical Systems Biology, Berlin, Germany
| | - Miha Milek
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin Institute for Medical Systems Biology, Berlin, Germany. .,National Institute of Chemistry, Ljubljana, Slovenia. .,Core Unit Bioinformatics, Berlin Institute of Health at Charité, Berlin, Germany.
| | - Igor Minia
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin Institute for Medical Systems Biology, Berlin, Germany
| | - Carlos H Vieira-Vieira
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin Institute for Medical Systems Biology, Berlin, Germany
| | - Simon Müller
- Institute of Molecular Medicine, Medical Faculty, Martin Luther University, Halle, Germany
| | - Guido Mastrobuoni
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin Institute for Medical Systems Biology, Berlin, Germany
| | - Orsalia-Georgia Hazapis
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin Institute for Medical Systems Biology, Berlin, Germany
| | - Simone Del Giudice
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin Institute for Medical Systems Biology, Berlin, Germany
| | - David Schwefel
- Charite-Universitätsmedizin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Institute of Medical Physics and Biophysics, Berlin, Germany
| | - Nadine Bley
- Institute of Molecular Medicine, Medical Faculty, Martin Luther University, Halle, Germany
| | - Franka Voigt
- Friedrich Miescher Institute for Biomedical Research, 4058, Basel, Switzerland
| | - Jeffrey A Chao
- Friedrich Miescher Institute for Biomedical Research, 4058, Basel, Switzerland
| | - Stefan Kempa
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin Institute for Medical Systems Biology, Berlin, Germany
| | - Stefan Hüttelmaier
- Institute of Molecular Medicine, Medical Faculty, Martin Luther University, Halle, Germany
| | - Matthias Selbach
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin Institute for Medical Systems Biology, Berlin, Germany.,Charite-Universitätsmedizin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Institute of Medical Physics and Biophysics, Berlin, Germany
| | - Markus Landthaler
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin Institute for Medical Systems Biology, Berlin, Germany. .,IRI Life Sciences, Institute of Biology, Humboldt-Universität zu Berlin, Berlin, Germany.
| |
Collapse
|
21
|
Chen X, Mayr C. A working model for condensate RNA-binding proteins as matchmakers for protein complex assembly. RNA (NEW YORK, N.Y.) 2022; 28:76-87. [PMID: 34706978 PMCID: PMC8675283 DOI: 10.1261/rna.078995.121] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
Abstract
Most cellular processes are carried out by protein complexes, but it is still largely unknown how the subunits of lowly expressed complexes find each other in the crowded cellular environment. Here, we will describe a working model where RNA-binding proteins in cytoplasmic condensates act as matchmakers between their bound proteins (called protein targets) and newly translated proteins of their RNA targets to promote their assembly into complexes. Different RNA-binding proteins act as scaffolds for various cytoplasmic condensates with several of them supporting translation. mRNAs and proteins are recruited into the cytoplasmic condensates through binding to specific domains in the RNA-binding proteins. Scaffold RNA-binding proteins have a high valency. In our model, they use homotypic interactions to assemble condensates and they use heterotypic interactions to recruit protein targets into the condensates. We propose that unoccupied binding sites in the scaffold RNA-binding proteins transiently retain recruited and newly translated proteins in the condensates, thus promoting their assembly into complexes. Taken together, we propose that lowly expressed subunits of protein complexes combine information in their mRNAs and proteins to colocalize in the cytoplasm. The efficiency of protein complex assembly is increased by transient entrapment accomplished by multivalent RNA-binding proteins within cytoplasmic condensates.
Collapse
Affiliation(s)
- Xiuzhen Chen
- Cancer Biology and Genetics Program, Memorial Sloan Kettering Cancer Center, New York, New York 10065, USA
| | - Christine Mayr
- Cancer Biology and Genetics Program, Memorial Sloan Kettering Cancer Center, New York, New York 10065, USA
| |
Collapse
|
22
|
Gasparski AN, Mason DE, Moissoglu K, Mili S. Regulation and outcomes of localized RNA translation. WILEY INTERDISCIPLINARY REVIEWS. RNA 2022; 13:e1721. [PMID: 35166036 PMCID: PMC9787767 DOI: 10.1002/wrna.1721] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/19/2021] [Revised: 01/18/2022] [Accepted: 01/22/2022] [Indexed: 12/31/2022]
Abstract
Spatial segregation of mRNAs in the cytoplasm of cells is a well-known biological phenomenon that is widely observed in diverse species spanning different kingdoms of life. In mammalian cells, localization of mRNAs has been documented and studied quite extensively in highly polarized cells, most notably in neurons, where localized mRNAs function to direct protein production at sites that are quite distant from the soma. Recent studies have strikingly revealed that a large proportion of the cellular transcriptome exhibits polarized distributions even in cells that lack an obvious need for long-range transport, such as fibroblasts or epithelial cells. This review focuses on emerging concepts regarding the functional outcomes of mRNA targeting in the cytoplasm of such cells. We also discuss regulatory mechanisms controlling these events, with an emphasis on the role of cell mechanics and the organization of the cytoskeleton. This article is categorized under: Translation > Regulation RNA Export and Localization > RNA Localization.
Collapse
Affiliation(s)
- Alexander N. Gasparski
- Laboratory of Cellular and Molecular Biology, Center for Cancer ResearchNational Cancer Institute, NIHBethesdaMarylandUSA
| | - Devon E. Mason
- Laboratory of Cellular and Molecular Biology, Center for Cancer ResearchNational Cancer Institute, NIHBethesdaMarylandUSA
| | - Konstadinos Moissoglu
- Laboratory of Cellular and Molecular Biology, Center for Cancer ResearchNational Cancer Institute, NIHBethesdaMarylandUSA
| | - Stavroula Mili
- Laboratory of Cellular and Molecular Biology, Center for Cancer ResearchNational Cancer Institute, NIHBethesdaMarylandUSA
| |
Collapse
|
23
|
Svitkin YV, Gingras AC, Sonenberg N. Membrane-dependent relief of translation elongation arrest on pseudouridine- and N1-methyl-pseudouridine-modified mRNAs. Nucleic Acids Res 2021; 50:7202-7215. [PMID: 34933339 PMCID: PMC9303281 DOI: 10.1093/nar/gkab1241] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2021] [Revised: 11/12/2021] [Accepted: 12/03/2021] [Indexed: 11/13/2022] Open
Abstract
Expression of therapeutically important proteins has benefited dramatically from the advent of chemically modified mRNAs that feature decreased lability and immunogenicity. This had a momentous effect on the rapid development of COVID-19 mRNA vaccines. Incorporation of the naturally occurring pseudouridine (Ψ) or N1-methyl-pseudouridine (N1mΨ) into in vitro transcribed mRNAs prevents the activation of unwanted immune responses by blocking eIF2α phosphorylation, which inhibits translation. Here, we report that Ψs in luciferase (Luc) mRNA exacerbate translation pausing in nuclease-untreated rabbit reticulocyte lysate (uRRL) and promote the formation of high-order-ribosome structures. The major deceleration of elongation occurs at the Ψ-rich nucleotides 1294-1326 of Ψ-Luc mRNA and results in premature termination of translation. The impairment of translation is mainly due to the shortage of membranous components. Supplementing uRRL with canine microsomal membranes (CMMs) relaxes the impediments to ribosome movement, resolves collided ribosomes, and greatly enhances full-size luciferase production. CMMs also strongly stimulated an extremely inefficient translation of N1mΨ-Luc mRNA in uRRL. Evidence is presented that translational pausing can promote membrane recruitment of polysomes with nascent polypeptides that lack a signal sequence. Our results highlight an underappreciated role of membrane binding to polysomes in the prevention of ribosome collision and premature release of nascent polypeptides.
Collapse
Affiliation(s)
- Yuri V Svitkin
- Department of Biochemistry, McGill University, Montréal, Québec H3A 1A3, Canada.,Rosalind and Morris Goodman Cancer Institute, Montréal, Québec H3A 1A3, Canada
| | - Anne-Claude Gingras
- Lunenfeld-Tanenbaum Research Institute, Sinai Health System, and Department of Molecular Genetics, University of Toronto, Toronto, Ontario, M5G 1×5, Canada
| | - Nahum Sonenberg
- Department of Biochemistry, McGill University, Montréal, Québec H3A 1A3, Canada.,Rosalind and Morris Goodman Cancer Institute, Montréal, Québec H3A 1A3, Canada
| |
Collapse
|
24
|
Child JR, Chen Q, Reid DW, Jagannathan S, Nicchitta CV. Recruitment of endoplasmic reticulum-targeted and cytosolic mRNAs into membrane-associated stress granules. RNA (NEW YORK, N.Y.) 2021; 27:1241-1256. [PMID: 34244458 PMCID: PMC8456999 DOI: 10.1261/rna.078858.121] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/08/2021] [Accepted: 07/03/2021] [Indexed: 06/13/2023]
Abstract
Stress granules (SGs) are membraneless organelles composed of mRNAs and RNA binding proteins which undergo assembly in response to stress-induced inactivation of translation initiation. In general, SG recruitment is limited to a subpopulation of a given mRNA species and RNA-seq analyses of purified SGs revealed that signal sequence-encoding (i.e., endoplasmic reticulum [ER]-targeted) transcripts are significantly underrepresented, consistent with prior reports that ER localization can protect mRNAs from SG recruitment. Using translational profiling, cell fractionation, and single molecule mRNA imaging, we examined SG biogenesis following activation of the unfolded protein response (UPR) by 1,4-dithiothreitol (DTT) and report that gene-specific subsets of cytosolic and ER-targeted mRNAs can be recruited into SGs. Furthermore, we demonstrate that SGs form in close proximity to or directly associated with the ER membrane. ER-associated SG assembly was also observed during arsenite stress, suggesting broad roles for the ER in SG biogenesis. Recruitment of a given mRNA into SGs required stress-induced translational repression, though translational inhibition was not solely predictive of an mRNA's propensity for SG recruitment. SG formation was prevented by the transcriptional inhibitors actinomycin D or triptolide, suggesting a functional link between gene transcriptional state and SG biogenesis. Collectively these data demonstrate that ER-targeted and cytosolic mRNAs can be recruited into ER-associated SGs and this recruitment is sensitive to transcriptional inhibition. We propose that newly transcribed mRNAs exported under conditions of suppressed translation initiation are primary SG substrates, with the ER serving as the central subcellular site of SG formation.
Collapse
Affiliation(s)
- Jessica R Child
- Department of Cell Biology, 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
| | - David W Reid
- Department of Cell Biology, Duke University School of Medicine, Durham, North Carolina 27710, USA
| | - Sujatha Jagannathan
- Department of Biochemistry and Molecular Genetics, University of Colorado, Anschutz Medical Campus, Denver, Colorado 80045, USA
- RNA Bioscience Initiative, University of Colorado, Anschutz Medical Campus, Denver, Colorado 80045, USA
| | - Christopher V Nicchitta
- Department of Cell Biology, Duke University School of Medicine, Durham, North Carolina 27710, USA
| |
Collapse
|
25
|
Vinter DJ, Hoppe C, Minchington TG, Sutcliffe C, Ashe HL. Dynamics of hunchback translation in real-time and at single-mRNA resolution in the Drosophila embryo. Development 2021; 148:dev196121. [PMID: 33722899 PMCID: PMC8077512 DOI: 10.1242/dev.196121] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2020] [Accepted: 03/10/2021] [Indexed: 12/15/2022]
Abstract
The Hunchback (Hb) transcription factor is crucial for anterior-posterior patterning of the Drosophila embryo. The maternal hb mRNA acts as a paradigm for translational regulation due to its repression in the posterior of the embryo. However, little is known about the translatability of zygotically transcribed hb mRNAs. Here, we adapt the SunTag system, developed for imaging translation at single-mRNA resolution in tissue culture cells, to the Drosophila embryo to study the translation dynamics of zygotic hb mRNAs. Using single-molecule imaging in fixed and live embryos, we provide evidence for translational repression of zygotic SunTag-hb mRNAs. Whereas the proportion of SunTag-hb mRNAs translated is initially uniform, translation declines from the anterior over time until it becomes restricted to a posterior band in the expression domain. We discuss how regulated hb mRNA translation may help establish the sharp Hb expression boundary, which is a model for precision and noise during developmental patterning. Overall, our data show how use of the SunTag method on fixed and live embryos is a powerful combination for elucidating spatiotemporal regulation of mRNA translation in Drosophila.
Collapse
Affiliation(s)
| | | | | | | | - Hilary L. Ashe
- Faculty of Biology, Medicine and Health, University of Manchester, Manchester M13 9PT, UK
| |
Collapse
|
26
|
Basyuk E, Rage F, Bertrand E. RNA transport from transcription to localized translation: a single molecule perspective. RNA Biol 2021; 18:1221-1237. [PMID: 33111627 PMCID: PMC8354613 DOI: 10.1080/15476286.2020.1842631] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2020] [Revised: 10/21/2020] [Accepted: 10/22/2020] [Indexed: 12/21/2022] Open
Abstract
Transport of mRNAs is an important step of gene expression, which brings the genetic message from the DNA in the nucleus to a precise cytoplasmic location in a regulated fashion. Perturbation of this process can lead to pathologies such as developmental and neurological disorders. In this review, we discuss recent advances in the field of mRNA transport made using single molecule fluorescent imaging approaches. We present an overview of these approaches in fixed and live cells and their input in understanding the key steps of mRNA journey: transport across the nucleoplasm, export through the nuclear pores and delivery to its final cytoplasmic location. This review puts a particular emphasis on the coupling of mRNA transport with translation, such as localization-dependent translational regulation and translation-dependent mRNA localization. We also highlight the recently discovered translation factories, and how cellular and viral RNAs can hijack membrane transport systems to travel in the cytoplasm.
Collapse
Affiliation(s)
- Eugenia Basyuk
- Institut de Génétique Humaine, CNRS-UMR9002, Univ Montpellier, Montpellier, France
- Present address: Laboratoire de Microbiologie Fondamentale et Pathogénicité, CNRS-UMR 5234, Université de Bordeaux, Bordeaux, France
| | - Florence Rage
- Institut de Génétique Moléculaire de Montpellier, CNRS-UMR5535, Univ Montpellier, Montpellier, France
| | - Edouard Bertrand
- Institut de Génétique Humaine, CNRS-UMR9002, Univ Montpellier, Montpellier, France
- Institut de Génétique Moléculaire de Montpellier, CNRS-UMR5535, Univ Montpellier, Montpellier, France
- Equipe Labélisée Ligue Nationale Contre Le Cancer, Montpellier, France
| |
Collapse
|
27
|
Pinheiro H, Pimentel MR, Sequeira C, Oliveira LM, Pezzarossa A, Roman W, Gomes ER. mRNA distribution in skeletal muscle is associated with mRNA size. J Cell Sci 2021; 134:jcs256388. [PMID: 34297126 PMCID: PMC7611476 DOI: 10.1242/jcs.256388] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2020] [Accepted: 06/18/2021] [Indexed: 12/30/2022] Open
Abstract
Skeletal muscle myofibers are large and elongated cells with multiple and evenly distributed nuclei. Nuclear distribution suggests that each nucleus influences a specific compartment within the myofiber and implies a functional role for nuclear positioning. Compartmentalization of specific mRNAs and proteins has been reported at the neuromuscular and myotendinous junctions, but mRNA distribution in non-specialized regions of the myofibers remains largely unexplored. We report that the bulk of mRNAs are enriched around the nucleus of origin and that this perinuclear accumulation depends on recently transcribed mRNAs. Surprisingly, mRNAs encoding large proteins - giant mRNAs - are spread throughout the cell and do not exhibit perinuclear accumulation. Furthermore, by expressing exogenous transcripts with different sizes we found that size contributes to mRNA spreading independently of mRNA sequence. Both these mRNA distribution patterns depend on microtubules and are independent of nuclear dispersion, mRNA expression level and stability, and the characteristics of the encoded protein. Thus, we propose that mRNA distribution in non-specialized regions of skeletal muscle is size selective to ensure cellular compartmentalization and simultaneous long-range distribution of giant mRNAs.
Collapse
Affiliation(s)
- Helena Pinheiro
- Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa. Avenida Professor Egas Moniz, 1649-028 Lisboa, Portugal
| | - Mafalda Ramos Pimentel
- Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa. Avenida Professor Egas Moniz, 1649-028 Lisboa, Portugal
| | - Catarina Sequeira
- Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa. Avenida Professor Egas Moniz, 1649-028 Lisboa, Portugal
| | - Luís Manuel Oliveira
- Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa. Avenida Professor Egas Moniz, 1649-028 Lisboa, Portugal
| | - Anna Pezzarossa
- Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa. Avenida Professor Egas Moniz, 1649-028 Lisboa, Portugal
| | - William Roman
- Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa. Avenida Professor Egas Moniz, 1649-028 Lisboa, Portugal
- Experimental and Health Sciences (DCEXS), Universitat Pompeu Fabra (UPF), 08002 Barcelona, Spain
| | - Edgar R. Gomes
- Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa. Avenida Professor Egas Moniz, 1649-028 Lisboa, Portugal
- Instituto de Histologia e Biologia do Desenvolvimento, Faculdade de Medicina, Universidade de Lisboa, Avenida Professor Egas Moniz, 1649-028 Lisboa, Portugal
| |
Collapse
|
28
|
Das S, Vera M, Gandin V, Singer RH, Tutucci E. Intracellular mRNA transport and localized translation. Nat Rev Mol Cell Biol 2021; 22:483-504. [PMID: 33837370 PMCID: PMC9346928 DOI: 10.1038/s41580-021-00356-8] [Citation(s) in RCA: 126] [Impact Index Per Article: 42.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/25/2021] [Indexed: 02/08/2023]
Abstract
Fine-tuning cellular physiology in response to intracellular and environmental cues requires precise temporal and spatial control of gene expression. High-resolution imaging technologies to detect mRNAs and their translation state have revealed that all living organisms localize mRNAs in subcellular compartments and create translation hotspots, enabling cells to tune gene expression locally. Therefore, mRNA localization is a conserved and integral part of gene expression regulation from prokaryotic to eukaryotic cells. In this Review, we discuss the mechanisms of mRNA transport and local mRNA translation across the kingdoms of life and at organellar, subcellular and multicellular resolution. We also discuss the properties of messenger ribonucleoprotein and higher order RNA granules and how they may influence mRNA transport and local protein synthesis. Finally, we summarize the technological developments that allow us to study mRNA localization and local translation through the simultaneous detection of mRNAs and proteins in single cells, mRNA and nascent protein single-molecule imaging, and bulk RNA and protein detection methods.
Collapse
Affiliation(s)
- Sulagna Das
- Department of Anatomy and Structural Biology, Albert Einstein College of Medicine, New York, NY, USA.,Gruss-Lipper Biophotonics Center, Albert Einstein College of Medicine, New York, NY, USA
| | - Maria Vera
- Department of Biochemistry, McGill University, Montreal, Quebec, Canada
| | | | - Robert H. Singer
- Department of Anatomy and Structural Biology, Albert Einstein College of Medicine, New York, NY, USA.,Gruss-Lipper Biophotonics Center, Albert Einstein College of Medicine, New York, NY, USA.,Janelia Research Campus of the HHMI, Ashburn, VA, USA.,;
| | - Evelina Tutucci
- Systems Biology Lab, Amsterdam Institute of Molecular and Life Sciences (AIMMS), Vrije Universiteit Amsterdam, Amsterdam, The Netherlands.,;
| |
Collapse
|
29
|
Vedula P, Kurosaka S, MacTaggart B, Ni Q, Papoian G, Jiang Y, Dong DW, Kashina A. Different translation dynamics of β- and γ-actin regulates cell migration. eLife 2021; 10:68712. [PMID: 34165080 PMCID: PMC8328520 DOI: 10.7554/elife.68712] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2021] [Accepted: 06/19/2021] [Indexed: 12/13/2022] Open
Abstract
β- and γ-cytoplasmic actins are ubiquitously expressed in every cell type and are nearly identical at the amino acid level but play vastly different roles in vivo. Their essential roles in embryogenesis and mesenchymal cell migration critically depend on the nucleotide sequences of their genes, rather than their amino acid sequences; however, it is unclear which gene elements underlie this effect. Here we address the specific role of the coding sequence in β- and γ-cytoplasmic actins’ intracellular functions, using stable polyclonal populations of immortalized mouse embryonic fibroblasts with exogenously expressed actin isoforms and their ‘codon-switched’ variants. When targeted to the cell periphery using β-actin 3′UTR; β-actin and γ-actin have differential effects on cell migration. These effects directly depend on the coding sequence. Single-molecule measurements of actin isoform translation, combined with fluorescence recovery after photobleaching, demonstrate a pronounced difference in β- and γ-actins’ translation elongation rates in cells, leading to changes in their dynamics at focal adhesions, impairments in actin bundle formation, and reduced cell anchoring to the substrate during migration. Our results demonstrate that coding sequence-mediated differences in actin translation play a key role in cell migration. Most mammalian cells make both β- and γ-actin, two proteins which shape the cell’s internal skeleton and its ability to migrate. The molecules share over 99% of their sequence, yet they play distinct roles. In fact, deleting the β-actin gene in mice causes death in the womb, while the animals can survive with comparatively milder issues without their γ-actin gene. How two similar proteins can have such different biological roles is a long-standing mystery. A closer look could hold some clues: β- and γ-actin may contain the same blocks (or amino acids), but the genetic sequences that encode these proteins differ by about 13%. This is because different units of genetic information – known as synonymous codons – can encode the same amino acid. These ‘silent substitutions’ have no effect on the sequence of the proteins, yet a cell reads synonymous codons (and therefore produces proteins) at different speeds. To find out the impact of silent substitutions, Vedula et al. swapped the codons for the two proteins, forcing mouse cells to produce β-actin using γ-actin codons, and vice versa. Cells with non-manipulated γ-actin and those with β-actin made using γ-actin codons could move much faster than cells with β-actin. This suggested that silent substitutions were indeed affecting the role of the protein. Vedula et al. found that cells read γ-codons – and therefore made γ-actin – much more slowly than β-codons: this also affected how quickly the protein could be dispatched where it was needed in the cell. Slower production meant that bundles of γ-actin were shorter, which allowed cells to move faster by providing a weaker anchoring system. Overall, this work provides new links between silent substitutions and protein behavior, a relatively new research area which is likely to shed light on other protein families.
Collapse
Affiliation(s)
- Pavan Vedula
- Department of Biomedical Sciences, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, United States
| | - Satoshi Kurosaka
- Institute of Advanced Technology, Kindai University, Kainan, Wakayama, Japan
| | - Brittany MacTaggart
- Department of Biomedical Sciences, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, United States
| | - Qin Ni
- Department of Chemical and Biomolecular Engineering, University of Maryland, College Park, United States
| | - Garegin Papoian
- Department of Chemistry, University of Maryland, College Park, United States
| | - Yi Jiang
- Department of Mathematics and Statistics, Georgia State University, Atlanta, United States
| | - Dawei W Dong
- Department of Biomedical Sciences, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, United States.,Institute for Biomedical Informatics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, United States
| | - Anna Kashina
- Department of Biomedical Sciences, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, United States
| |
Collapse
|
30
|
Klein MC, Lerner M, Nguyen D, Pfeffer S, Dudek J, Förster F, Helms V, Lang S, Zimmermann R. TRAM1 protein may support ER protein import by modulating the phospholipid bilayer near the lateral gate of the Sec61-channel. Channels (Austin) 2021; 14:28-44. [PMID: 32013668 PMCID: PMC7039644 DOI: 10.1080/19336950.2020.1724759] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
In mammalian cells, one-third of all polypeptides is transported into or through the ER-membrane via the Sec61-channel. While the Sec61-complex facilitates the transport of all polypeptides with amino-terminal signal peptides (SP) or SP-equivalent transmembrane helices (TMH), the translocating chain-associated membrane protein (now termed TRAM1) was proposed to support transport of a subset of precursors. To identify possible determinants of TRAM1 substrate specificity, we systematically identified TRAM1-dependent precursors by analyzing cellular protein abundance changes upon TRAM1 depletion in HeLa cells using quantitative label-free proteomics. In contrast to previous analysis after TRAP depletion, SP and TMH analysis of TRAM1 clients did not reveal any distinguishing features that could explain its putative substrate specificity. To further address the TRAM1 mechanism, live-cell calcium imaging was carried out after TRAM1 depletion in HeLa cells. In additional contrast to previous analysis after TRAP depletion, TRAM1 depletion did not affect calcium leakage from the ER. Thus, TRAM1 does not appear to act as SP- or TMH-receptor on the ER-membrane’s cytosolic face and does not appear to affect the open probability of the Sec61-channel. It may rather play a supportive role in protein transport, such as making the phospholipid bilayer conducive for accepting SP and TMH in the vicinity of the lateral gate of the Sec61-channel. Abbreviations: ER, endoplasmic reticulum; OST, oligosaccharyltransferase; RAMP, ribosome-associated membrane protein; SP, signal peptide; SR, SRP-receptor; SRP, signal recognition particle; TMH, signal peptide-equivalent transmembrane helix; TRAM, translocating chain-associated membrane protein; TRAP, translocon-associated protein.
Collapse
Affiliation(s)
| | - Monika Lerner
- Medical Biochemistry and Molecular Biology, Saarland University, Homburg, Germany
| | - Duy Nguyen
- Center for Bioinformatics, Saarland University, Saarbrücken, Germany
| | | | - Johanna Dudek
- Medical Biochemistry and Molecular Biology, Saarland University, Homburg, Germany
| | - Friedrich Förster
- Bijvoet Center for Biomolecular Research, Utrecht University, Utrecht, The Netherlands
| | - Volkhard Helms
- Center for Bioinformatics, Saarland University, Saarbrücken, Germany
| | - Sven Lang
- Medical Biochemistry and Molecular Biology, Saarland University, Homburg, Germany
| | - Richard Zimmermann
- Medical Biochemistry and Molecular Biology, Saarland University, Homburg, Germany
| |
Collapse
|
31
|
Bhadra P, Schorr S, Lerner M, Nguyen D, Dudek J, Förster F, Helms V, Lang S, Zimmermann R. Quantitative Proteomics and Differential Protein Abundance Analysis after Depletion of Putative mRNA Receptors in the ER Membrane of Human Cells Identifies Novel Aspects of mRNA Targeting to the ER. Molecules 2021; 26:3591. [PMID: 34208277 PMCID: PMC8230838 DOI: 10.3390/molecules26123591] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2021] [Revised: 06/07/2021] [Accepted: 06/09/2021] [Indexed: 11/28/2022] Open
Abstract
In human cells, one-third of all polypeptides enter the secretory pathway at the endoplasmic reticulum (ER). The specificity and efficiency of this process are guaranteed by targeting of mRNAs and/or polypeptides to the ER membrane. Cytosolic SRP and its receptor in the ER membrane facilitate the cotranslational targeting of most ribosome-nascent precursor polypeptide chain (RNC) complexes together with the respective mRNAs to the Sec61 complex in the ER membrane. Alternatively, fully synthesized precursor polypeptides are targeted to the ER membrane post-translationally by either the TRC, SND, or PEX19/3 pathway. Furthermore, there is targeting of mRNAs to the ER membrane, which does not involve SRP but involves mRNA- or RNC-binding proteins on the ER surface, such as RRBP1 or KTN1. Traditionally, the targeting reactions were studied in cell-free or cellular assays, which focus on a single precursor polypeptide and allow the conclusion of whether a certain precursor can use a certain pathway. Recently, cellular approaches such as proximity-based ribosome profiling or quantitative proteomics were employed to address the question of which precursors use certain pathways under physiological conditions. Here, we combined siRNA-mediated depletion of putative mRNA receptors in HeLa cells with label-free quantitative proteomics and differential protein abundance analysis to characterize RRBP1- or KTN1-involving precursors and to identify possible genetic interactions between the various targeting pathways. Furthermore, we discuss the possible implications on the so-called TIGER domains and critically discuss the pros and cons of this experimental approach.
Collapse
Affiliation(s)
- Pratiti Bhadra
- Center for Bioinformatics, Saarland Informatics Campus, Saarland University, 66041 Saarbrücken, Germany; (P.B.); (D.N.); (V.H.)
| | - Stefan Schorr
- Medical Biochemistry and Molecular Biology, Saarland University, 66421 Homburg, Germany; (S.S.); (M.L.); (J.D.); (S.L.)
| | - Monika Lerner
- Medical Biochemistry and Molecular Biology, Saarland University, 66421 Homburg, Germany; (S.S.); (M.L.); (J.D.); (S.L.)
| | - Duy Nguyen
- Center for Bioinformatics, Saarland Informatics Campus, Saarland University, 66041 Saarbrücken, Germany; (P.B.); (D.N.); (V.H.)
| | - Johanna Dudek
- Medical Biochemistry and Molecular Biology, Saarland University, 66421 Homburg, Germany; (S.S.); (M.L.); (J.D.); (S.L.)
| | - Friedrich Förster
- Bijvoet Center for Biomolecular Research, Utrecht University, 3584 CH Utrecht, The Netherlands;
| | - Volkhard Helms
- Center for Bioinformatics, Saarland Informatics Campus, Saarland University, 66041 Saarbrücken, Germany; (P.B.); (D.N.); (V.H.)
| | - Sven Lang
- Medical Biochemistry and Molecular Biology, Saarland University, 66421 Homburg, Germany; (S.S.); (M.L.); (J.D.); (S.L.)
| | - Richard Zimmermann
- Medical Biochemistry and Molecular Biology, Saarland University, 66421 Homburg, Germany; (S.S.); (M.L.); (J.D.); (S.L.)
| |
Collapse
|
32
|
Lashkevich KA, Dmitriev SE. mRNA Targeting, Transport and Local Translation in Eukaryotic Cells: From the Classical View to a Diversity of New Concepts. Mol Biol 2021; 55:507-537. [PMID: 34092811 PMCID: PMC8164833 DOI: 10.1134/s0026893321030080] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2021] [Revised: 02/26/2021] [Accepted: 03/12/2021] [Indexed: 12/28/2022]
Abstract
Spatial organization of protein biosynthesis in the eukaryotic cell has been studied for more than fifty years, thus many facts have already been included in textbooks. According to the classical view, mRNA transcripts encoding secreted and transmembrane proteins are translated by ribosomes associated with endoplasmic reticulum membranes, while soluble cytoplasmic proteins are synthesized on free polysomes. However, in the last few years, new data has emerged, revealing selective translation of mRNA on mitochondria and plastids, in proximity to peroxisomes and endosomes, in various granules and at the cytoskeleton (actin network, vimentin intermediate filaments, microtubules and centrosomes). There are also long-standing debates about the possibility of protein synthesis in the nucleus. Localized translation can be determined by targeting signals in the synthesized protein, nucleotide sequences in the mRNA itself, or both. With RNA-binding proteins, many transcripts can be assembled into specific RNA condensates and form RNP particles, which may be transported by molecular motors to the sites of active translation, form granules and provoke liquid-liquid phase separation in the cytoplasm, both under normal conditions and during cell stress. The translation of some mRNAs occurs in specialized "translation factories," assemblysomes, transperons and other structures necessary for the correct folding of proteins, interaction with functional partners and formation of oligomeric complexes. Intracellular localization of mRNA has a significant impact on the efficiency of its translation and presumably determines its response to cellular stress. Compartmentalization of mRNAs and the translation machinery also plays an important role in viral infections. Many viruses provoke the formation of specific intracellular structures, virus factories, for the production of their proteins. Here we review the current concepts of the molecular mechanisms of transport, selective localization and local translation of cellular and viral mRNAs, their effects on protein targeting and topogenesis, and on the regulation of protein biosynthesis in different compartments of the eukaryotic cell. Special attention is paid to new systems biology approaches, providing new cues to the study of localized translation.
Collapse
Affiliation(s)
- Kseniya A Lashkevich
- Belozersky Institute of Physico-Chemical Biology, Moscow State University, 119234 Moscow, Russia.,Faculty of Bioengineering and Bioinformatics, Moscow State University, 119234 Moscow, Russia
| | - Sergey E Dmitriev
- Belozersky Institute of Physico-Chemical Biology, Moscow State University, 119234 Moscow, Russia.,Faculty of Bioengineering and Bioinformatics, Moscow State University, 119234 Moscow, Russia.,Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia
| |
Collapse
|
33
|
Wei J, Li DK, Hu X, Cheng C, Zhang Y. Galectin-1-RNA interaction map reveals potential regulatory roles in angiogenesis. FEBS Lett 2021; 595:623-636. [PMID: 33483966 DOI: 10.1002/1873-3468.14047] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2020] [Revised: 12/29/2020] [Accepted: 12/30/2020] [Indexed: 12/17/2022]
Abstract
Hyperactive angiogenesis contributes to the immunosuppressive microenvironment important for immunotherapy. Galectin-1, encoded by LGALS1, can trigger the vascular signaling programs and mediate the anti-angiogenic treatment response. However, the mechanism through which galectin-1 regulates angiogenesis is poorly understood. It has been suggested that galectin-1 may associate with mRNAs in cells. This study applied the iRIP-seq methodology to study the potential role of galectin-1 as an RNA-binding protein. We found that galectin-1 interacts with a large number of mRNAs, with a preference for binding near stop codons and a preference for UGCA/UGGA and GAGCAG as binding motifs. Galectin-1 binds to the mRNAs of angiogenesis-associated genes including VEGFA, EGR1, and LAMA5, suggesting that galectin-1 may regulate angiogenesis via its mRNA-binding activity. We further show that shLGALS1 inhibits capillary tube formation in an in vitro angiogenesis assay and alters the expression levels of several galectin-1-bound angiogenesis-associated mRNAs. These results uncover a previously unrecognized mRNA-binding activity of galectin-1.
Collapse
Affiliation(s)
- Jiajun Wei
- Department of Neurology, Renmin Hospital of Wuhan University, China
| | - Daniel K Li
- Department of Biology and Biotechnology, School of Chemistry, Chemical Engineering and Life Sciences, Wuhan University of Technology, China
| | - Xinyu Hu
- Department of Biotechnology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China
| | - Chao Cheng
- ABLife BioBigData Institute, Wuhan, China
| | - Yi Zhang
- ABLife BioBigData Institute, Wuhan, China
| |
Collapse
|
34
|
Lee ES, Wolf EJ, Ihn SSJ, Smith HW, Emili A, Palazzo AF. TPR is required for the efficient nuclear export of mRNAs and lncRNAs from short and intron-poor genes. Nucleic Acids Res 2021; 48:11645-11663. [PMID: 33091126 PMCID: PMC7672458 DOI: 10.1093/nar/gkaa919] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2019] [Revised: 09/21/2020] [Accepted: 10/02/2020] [Indexed: 12/14/2022] Open
Abstract
While splicing has been shown to enhance nuclear export, it has remained unclear whether mRNAs generated from intronless genes use specific machinery to promote their export. Here, we investigate the role of the major nuclear pore basket protein, TPR, in regulating mRNA and lncRNA nuclear export in human cells. By sequencing mRNA from the nucleus and cytosol of control and TPR-depleted cells, we provide evidence that TPR is required for the efficient nuclear export of mRNAs and lncRNAs that are generated from short transcripts that tend to have few introns, and we validate this with reporter constructs. Moreover, in TPR-depleted cells reporter mRNAs generated from short transcripts accumulate in nuclear speckles and are bound to Nxf1. These observations suggest that TPR acts downstream of Nxf1 recruitment and may allow mRNAs to leave nuclear speckles and properly dock with the nuclear pore. In summary, our study provides one of the first examples of a factor that is specifically required for the nuclear export of intronless and intron-poor mRNAs and lncRNAs.
Collapse
Affiliation(s)
- Eliza S Lee
- University of Toronto, Department of Biochemistry, Canada
| | - Eric J Wolf
- University of Toronto, Department of Molecular Genetics, Canada
| | - Sean S J Ihn
- University of Toronto, Department of Biochemistry, Canada
| | | | - Andrew Emili
- University of Toronto, Department of Molecular Genetics, Canada.,Boston University School of Medicine, Department of Biochemistry, Boston, MA, USA
| | | |
Collapse
|
35
|
Xu H, Wang J, Liang Y, Fu Y, Li S, Huang J, Xu H, Zou W, Chen B. TriTag: an integrative tool to correlate chromatin dynamics and gene expression in living cells. Nucleic Acids Res 2021; 48:e127. [PMID: 33104788 PMCID: PMC7736787 DOI: 10.1093/nar/gkaa906] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2020] [Revised: 08/29/2020] [Accepted: 10/21/2020] [Indexed: 02/07/2023] Open
Abstract
A wealth of single-cell imaging studies have contributed novel insights into chromatin organization and gene regulation. However, a comprehensive understanding of spatiotemporal gene regulation requires developing tools to combine multiple monitoring systems in a single study. Here, we report a versatile tag, termed TriTag, which integrates the functional capabilities of CRISPR-Tag (DNA labeling), MS2 aptamer (RNA imaging) and fluorescent protein (protein tracking). Using this tag, we correlate changes in chromatin dynamics with the progression of endogenous gene expression, by recording both transcriptional bursting and protein production. This strategy allows precise measurements of gene expression at single-allele resolution across the cell cycle or in response to stress. TriTag enables capturing an integrated picture of gene expression, thus providing a powerful tool to study transcriptional heterogeneity and regulation.
Collapse
Affiliation(s)
- Haiyue Xu
- Department of Cell Biology, and Bone Marrow Transplantation Center of the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310058, China
| | - Junyan Wang
- Department of Cell Biology, and Bone Marrow Transplantation Center of the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310058, China
| | - Ying Liang
- Department of Cell Biology, and Bone Marrow Transplantation Center of the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310058, China
| | - Yujuan Fu
- Department of Cell Biology, and Bone Marrow Transplantation Center of the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310058, China
| | - Sihui Li
- Department of Cell Biology, and Bone Marrow Transplantation Center of the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310058, China
| | - Jinghan Huang
- School of Physics and Astronomy, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Heng Xu
- School of Physics and Astronomy, Shanghai Jiao Tong University, Shanghai 200240, China.,Institute of Natural Sciences, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Wei Zou
- The Fourth Affiliated Hospital, Zhejiang University School of Medicine, Yiwu 322000, China.,Insititute of Translational Medicine, Zhejiang University, Hangzhou 310003, China
| | - Baohui Chen
- Department of Cell Biology, and Bone Marrow Transplantation Center of the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310058, China.,Institute of Hematology, Zhejiang University & Zhejiang Engineering Laboratory for Stem Cell and Immunotherapy, Hangzhou 310058, China.,Zhejiang Laboratory for Systems & Precision Medicine, Zhejiang University Medical Center, Hangzhou 311121, China.,Zhejiang Provincial Key Laboratory of Genetic & Developmental Disorders, Hangzhou 310058, China
| |
Collapse
|
36
|
Mateju D, Eichenberger B, Voigt F, Eglinger J, Roth G, Chao JA. Single-Molecule Imaging Reveals Translation of mRNAs Localized to Stress Granules. Cell 2020; 183:1801-1812.e13. [PMID: 33308477 DOI: 10.1016/j.cell.2020.11.010] [Citation(s) in RCA: 153] [Impact Index Per Article: 38.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2020] [Revised: 09/14/2020] [Accepted: 11/05/2020] [Indexed: 12/22/2022]
Abstract
Cellular stress leads to reprogramming of mRNA translation and formation of stress granules (SGs), membraneless organelles consisting of mRNA and RNA-binding proteins. Although the function of SGs remains largely unknown, it is widely assumed they contain exclusively non-translating mRNA. Here, we re-examine this hypothesis using single-molecule imaging of mRNA translation in living cells. Although we observe non-translating mRNAs are preferentially recruited to SGs, we find unequivocal evidence that mRNAs localized to SGs can undergo translation. Our data indicate that SG-associated translation is not rare, and the entire translation cycle (initiation, elongation, and termination) can occur on SG-localized transcripts. Furthermore, translating mRNAs can be observed transitioning between the cytosol and SGs without changing their translational status. Together, these results demonstrate that mRNA localization to SGs is compatible with translation and argue against a direct role for SGs in inhibition of protein synthesis.
Collapse
Affiliation(s)
- Daniel Mateju
- Friedrich Miescher Institute for Biomedical Research, 4058 Basel, Switzerland
| | - Bastian Eichenberger
- Friedrich Miescher Institute for Biomedical Research, 4058 Basel, Switzerland; University of Basel, 4003 Basel, Switzerland
| | - Franka Voigt
- Friedrich Miescher Institute for Biomedical Research, 4058 Basel, Switzerland
| | - Jan Eglinger
- Friedrich Miescher Institute for Biomedical Research, 4058 Basel, Switzerland
| | - Gregory Roth
- Friedrich Miescher Institute for Biomedical Research, 4058 Basel, Switzerland
| | - Jeffrey A Chao
- Friedrich Miescher Institute for Biomedical Research, 4058 Basel, Switzerland.
| |
Collapse
|
37
|
Braselmann E, Rathbun C, Richards EM, Palmer AE. Illuminating RNA Biology: Tools for Imaging RNA in Live Mammalian Cells. Cell Chem Biol 2020; 27:891-903. [PMID: 32640188 PMCID: PMC7595133 DOI: 10.1016/j.chembiol.2020.06.010] [Citation(s) in RCA: 53] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2020] [Revised: 05/30/2020] [Accepted: 06/15/2020] [Indexed: 01/06/2023]
Abstract
The central dogma teaches us that DNA makes RNA, which in turn makes proteins, the main building blocks of the cell. But this over simplified linear transmission of information overlooks the vast majority of the genome produces RNAs that do not encode proteins and the myriad ways that RNA regulates cellular functions. Historically, one of the challenges in illuminating RNA biology has been the lack of tools for visualizing RNA in live cells. But clever approaches for exploiting RNA binding proteins, in vitro RNA evolution, and chemical biology have resulted in significant advances in RNA visualization tools in recent years. This review provides an overview of current tools for tagging RNA with fluorescent probes and tracking their dynamics, localization andfunction in live mammalian cells.
Collapse
Affiliation(s)
- Esther Braselmann
- Department of Biochemistry, BioFrontiers Institute, University of Colorado Boulder, 3415 Colorado Avenue, Boulder, CO 80309, USA
| | - Colin Rathbun
- Department of Biochemistry, BioFrontiers Institute, University of Colorado Boulder, 3415 Colorado Avenue, Boulder, CO 80309, USA
| | - Erin M Richards
- Department of Biochemistry, BioFrontiers Institute, University of Colorado Boulder, 3415 Colorado Avenue, Boulder, CO 80309, USA
| | - Amy E Palmer
- Department of Biochemistry, BioFrontiers Institute, University of Colorado Boulder, 3415 Colorado Avenue, Boulder, CO 80309, USA.
| |
Collapse
|
38
|
A Dual Protein-mRNA Localization Screen Reveals Compartmentalized Translation and Widespread Co-translational RNA Targeting. Dev Cell 2020; 54:773-791.e5. [PMID: 32783880 DOI: 10.1016/j.devcel.2020.07.010] [Citation(s) in RCA: 63] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2018] [Revised: 06/01/2020] [Accepted: 07/14/2020] [Indexed: 12/21/2022]
Abstract
Local translation allows spatial control of gene expression. Here, we performed a dual protein-mRNA localization screen, using smFISH on 523 human cell lines expressing GFP-tagged genes. 32 mRNAs displayed specific cytoplasmic localizations with local translation at unexpected locations, including cytoplasmic protrusions, cell edges, endosomes, Golgi, the nuclear envelope, and centrosomes, the latter being cell-cycle-dependent. Automated classification of mRNA localization patterns revealed a high degree of intercellular heterogeneity. Surprisingly, mRNA localization frequently required ongoing translation, indicating widespread co-translational RNA targeting. Interestingly, while P-body accumulation was frequent (15 mRNAs), four mRNAs accumulated in foci that were distinct structures. These foci lacked the mature protein, but nascent polypeptide imaging showed that they were specialized translation factories. For β-catenin, foci formation was regulated by Wnt, relied on APC-dependent polysome aggregation, and led to nascent protein degradation. Thus, translation factories uniquely regulate nascent protein metabolism and create a fine granular compartmentalization of translation.
Collapse
|
39
|
Hannigan MM, Hoffman AM, Thompson JW, Zheng T, Nicchitta CV. Quantitative Proteomics Links the LRRC59 Interactome to mRNA Translation on the ER Membrane. Mol Cell Proteomics 2020; 19:1826-1849. [PMID: 32788342 DOI: 10.1074/mcp.ra120.002228] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2020] [Revised: 08/04/2020] [Indexed: 12/22/2022] Open
Abstract
Protein synthesis on the endoplasmic reticulum (ER) requires the dynamic coordination of numerous cellular components. Together, resident ER membrane proteins, cytoplasmic translation factors, and both integral membrane and cytosolic RNA-binding proteins operate in concert with membrane-associated ribosomes to facilitate ER-localized translation. Little is known, however, regarding the spatial organization of ER-localized translation. This question is of growing significance as it is now known that ER-bound ribosomes contribute to secretory, integral membrane, and cytosolic protein synthesis alike. To explore this question, we utilized quantitative proximity proteomics to identify neighboring protein networks for the candidate ribosome interactors SEC61β (subunit of the protein translocase), RPN1 (oligosaccharyltransferase subunit), SEC62 (translocation integral membrane protein), and LRRC59 (ribosome binding integral membrane protein). Biotin labeling time course studies of the four BioID reporters revealed distinct labeling patterns that intensified but only modestly diversified as a function of labeling time, suggesting that the ER membrane is organized into discrete protein interaction domains. Whereas SEC61β and RPN1 reporters identified translocon-associated networks, SEC62 and LRRC59 reporters revealed divergent protein interactomes. Notably, the SEC62 interactome is enriched in redox-linked proteins and ER luminal chaperones, with the latter likely representing proximity to an ER luminal chaperone reflux pathway. In contrast, the LRRC59 interactome is highly enriched in SRP pathway components, translation factors, and ER-localized RNA-binding proteins, uncovering a functional link between LRRC59 and mRNA translation regulation. Importantly, analysis of the LRRC59 interactome by native immunoprecipitation identified similar protein and functional enrichments. Moreover, [35S]-methionine incorporation assays revealed that siRNA silencing of LRRC59 expression reduced steady state translation levels on the ER by ca. 50%, and also impacted steady state translation levels in the cytosol compartment. Collectively, these data reveal a functional domain organization for the ER and identify a key role for LRRC59 in the organization and regulation of local translation.
Collapse
Affiliation(s)
- Molly M Hannigan
- Department of Cell Biology, Duke University School of Medicine, Durham, North Carolina, USA
| | - Alyson M Hoffman
- Department of Biochemistry, Duke University School of Medicine, Durham, North Carolina, USA
| | - J Will Thompson
- Department of Pharmacology and Cancer Biology, Duke University School of Medicine, Durham, North Carolina, USA; Department of Duke Proteomics and Metabolomics Shared Resource, Duke University School of Medicine, Durham, North Carolina, USA
| | - Tianli Zheng
- Department of Cell Biology, Duke University School of Medicine, Durham, North Carolina, USA
| | - Christopher V Nicchitta
- Department of Cell Biology, Duke University School of Medicine, Durham, North Carolina, USA; Department of Biochemistry, Duke University School of Medicine, Durham, North Carolina, USA.
| |
Collapse
|
40
|
Wang WX, Prajapati P, Nelson PT, Springer JE. The Mitochondria-Associated ER Membranes Are Novel Subcellular Locations Enriched for Inflammatory-Responsive MicroRNAs. Mol Neurobiol 2020; 57:2996-3013. [PMID: 32451872 PMCID: PMC7320068 DOI: 10.1007/s12035-020-01937-y] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2020] [Accepted: 05/13/2020] [Indexed: 12/22/2022]
Abstract
The mitochondria-associated endoplasmic reticulum (ER) membranes (MAMs) are specific ER domains that contact the mitochondria and function to facilitate communication between ER and mitochondria. Disruption of contact between the mitochondria and ER is associated with a variety of pathophysiological conditions including neurodegenerative diseases. Considering the many cellular functions of MAMs, we hypothesized that MAMs play an important role in regulating microRNA (miRNA) activity linked to its unique location between mitochondria and ER. Here we present new findings from human and rat brains indicating that the MAMs are subcellular sites enriched for specific miRNAs. We employed subcellular fractionation and TaqMan® RT-qPCR miRNA analysis to quantify miRNA levels in subcellular fractions isolated from male rat brains and six human brain samples. We found that MAMs contain a substantial number of miRNAs and the profile differs significantly from that of cytosolic, mitochondria, or ER. Interestingly, MAMs are particularly enriched in inflammatory-responsive miRNAs, including miR-146a, miR-142-3p, and miR-142-5p in both human and rat brains; miR-223 MAM enrichment was observed only in human brain samples. Further, mitochondrial uncoupling or traumatic brain injury in male rats resulted in the alteration of inflammatory miRNA enrichment in the isolated subcellular fractions. These observations demonstrate that miRNAs are distributed differentially in organelles and may re-distribute between organelles and the cytosol in response to cellular stress and metabolic demands.
Collapse
Affiliation(s)
- Wang-Xia Wang
- Sanders-Brown Center on Aging, University of Kentucky, 800 S. Limestone, Lexington, KY, 40536, USA.
- Spinal Cord and Brain Injury Research Center, University of Kentucky, Lexington, KY, 40536, USA.
- Pathology & Laboratory Medicine, University of Kentucky, Lexington, KY, 40536, USA.
| | - Paresh Prajapati
- Spinal Cord and Brain Injury Research Center, University of Kentucky, Lexington, KY, 40536, USA
- Neuroscience, University of Kentucky, Lexington, KY, 40536, USA
| | - Peter T Nelson
- Sanders-Brown Center on Aging, University of Kentucky, 800 S. Limestone, Lexington, KY, 40536, USA
- Pathology & Laboratory Medicine, University of Kentucky, Lexington, KY, 40536, USA
| | - Joe E Springer
- Spinal Cord and Brain Injury Research Center, University of Kentucky, Lexington, KY, 40536, USA
- Neuroscience, University of Kentucky, Lexington, KY, 40536, USA
| |
Collapse
|
41
|
Li D, Wang J. Ribosome heterogeneity in stem cells and development. J Cell Biol 2020; 219:e202001108. [PMID: 32330234 PMCID: PMC7265316 DOI: 10.1083/jcb.202001108] [Citation(s) in RCA: 45] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2020] [Revised: 04/03/2020] [Accepted: 04/06/2020] [Indexed: 02/08/2023] Open
Abstract
Translation control is critical to regulate protein expression. By directly adjusting protein levels, cells can quickly respond to dynamic transitions during stem cell differentiation and embryonic development. Ribosomes are multisubunit cellular assemblies that mediate translation. Previously seen as invariant machines with the same composition of components in all conditions, recent studies indicate that ribosomes are heterogeneous and that different ribosome types can preferentially translate specific subsets of mRNAs. Such heterogeneity and specialized translation functions are very important in stem cells and development, as they allow cells to quickly respond to stimuli through direct changes of protein abundance. In this review, we discuss ribosome heterogeneity that arises from multiple features of rRNAs, including rRNA variants and rRNA modifications, and ribosomal proteins, including their stoichiometry, compositions, paralogues, and posttranslational modifications. We also discuss alterations of ribosome-associated proteins (RAPs), with a particular focus on their consequent specialized translational control in stem cells and development.
Collapse
Affiliation(s)
- Dan Li
- Department of Cell, Developmental and Regenerative Biology, The Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai, New York, NY
- The Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, New York, NY
| | - Jianlong Wang
- Department of Cell, Developmental and Regenerative Biology, The Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai, New York, NY
- The Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, New York, NY
- Department of Medicine, Columbia Center for Human Development, Columbia University Irving Medical Center, New York, NY
| |
Collapse
|
42
|
Cialek CA, Koch AL, Galindo G, Stasevich TJ. Lighting up single-mRNA translation dynamics in living cells. Curr Opin Genet Dev 2020; 61:75-82. [PMID: 32408104 PMCID: PMC7508770 DOI: 10.1016/j.gde.2020.04.003] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2020] [Revised: 03/12/2020] [Accepted: 04/08/2020] [Indexed: 12/11/2022]
Abstract
Over the past five years, technological advances have made it possible to image the translation of single mRNA in the natural context of living cells. With these advances, researchers are beginning to shed light on when, where, and to what degree mRNA are translated with single-molecule precision. These works provide insight into the heterogeneity of translation amongst single transcripts, behavior that is averaged out in complementary bulk assays. In this review, we discuss the rapidly maturing field of live-cell, single-mRNA imaging of translation, beginning with a brief overview of recent technological advances. The remainder of the review focuses on the new biological insights gained from these technologies. We conclude with a discussion of the future of this technology.
Collapse
Affiliation(s)
- Charlotte A Cialek
- Department of Biochemistry & Molecular Biology, Colorado State University, Fort Collins, Colorado 80523, USA
| | - Amanda L Koch
- Department of Biochemistry & Molecular Biology, Colorado State University, Fort Collins, Colorado 80523, USA
| | - Gabriel Galindo
- Department of Biochemistry & Molecular Biology, Colorado State University, Fort Collins, Colorado 80523, USA
| | - Timothy J Stasevich
- Department of Biochemistry & Molecular Biology, Colorado State University, Fort Collins, Colorado 80523, USA; World Research Hub Initiative, Institute of Innovative Research, Tokyo Institute of Technology, Yokohama 2268503, Japan.
| |
Collapse
|
43
|
Translation Efficiency and Degradation of ER-Associated mRNAs Modulated by ER-Anchored poly(A)-Specific Ribonuclease (PARN). Cells 2020; 9:cells9010162. [PMID: 31936572 PMCID: PMC7017053 DOI: 10.3390/cells9010162] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2019] [Revised: 01/05/2020] [Accepted: 01/07/2020] [Indexed: 12/21/2022] Open
Abstract
Translation is spatiotemporally regulated and endoplasmic reticulum (ER)-associated mRNAs are generally in efficient translation. It is unclear whether the ER-associated mRNAs are deadenylated or degraded on the ER surface in situ or in the cytosol. Here, we showed that ER possessed active deadenylases, particularly the poly(A)-specific ribonuclease (PARN), in common cell lines and mouse tissues. Consistently, purified recombinant PARN exhibited a strong ability to insert into the Langmuir monolayer and liposome. ER-anchored PARN was found to be able to reshape the poly(A) length profile of the ER-associated RNAs by suppressing long poly(A) tails without significantly influencing the cytosolic RNAs. The shortening of long poly(A) tails did not affect global translation efficiency, which suggests that the non-specific action of PARN towards long poly(A) tails was beyond the scope of translation regulation on the ER surface. Transcriptome sequencing analysis indicated that the ER-anchored PARN trigged the degradation of a small subset of ER-enriched transcripts. The ER-anchored PARN modulated the translation of its targets by redistributing ribosomes to heavy polysomes, which suggests that PARN might play a role in dynamic ribosome reallocation. During DNA damage response, MK2 phosphorylated PARN-Ser557 to modulate PARN translocation from the ER to cytosol. The ER-anchored PARN modulated DNA damage response and thereby cell viability by promoting the decay of ER-associated MDM2 transcripts with low ribosome occupancy. These findings revealed that highly regulated communication between mRNA degradation rate and translation efficiency is present on the ER surface in situ and PARN might contribute to this communication by modulating the dynamic ribosome reallocation between transcripts with low and high ribosome occupancies.
Collapse
|
44
|
Leung PKK, Lo KKW. Modulation of emission and singlet oxygen photosensitisation in live cells utilising bioorthogonal phosphorogenic probes and protein tag technology. Chem Commun (Camb) 2020; 56:6074-6077. [DOI: 10.1039/d0cc02056g] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
We developed a strategy to exploit the bioorthogonal reactivity and phosphorogenic property of iridium(iii) polypyridine nitrone complexes and SNAP-tag protein for the modulation of emission and single oxygen photosensitisation in live cells.
Collapse
Affiliation(s)
| | - Kenneth Kam-Wing Lo
- Department of Chemistry
- City University of Hong Kong
- Kowloon
- P. R. China
- State Key Laboratory of Terahertz and Millimeter Waves
| |
Collapse
|
45
|
Abstract
In eukaryotes, most mRNAs that encode secretory or membrane-bound proteins are translated by ribosomes associated with the surface of the endoplasmic reticulum (ER). Other such mRNAs are tethered to the ER by mRNA receptors. However, there has been much debate as to whether all mRNAs, regardless of their encoded polypeptide, are anchored to the ER at some low level. Here we describe a protocol to visualize ER-associated mRNAs in tissue culture cells by single-molecule fluorescence in situ hybridization (smFISH). Using this protocol, we have established that a subset of all mRNAs, regardless of whether they encode secretory or cytosolic proteins, are ER associated in a ribosome-dependent manner.
Collapse
Affiliation(s)
- Jingze J Wu
- Department of Biochemistry, University of Toronto, Toronto, ON, Canada
| | | |
Collapse
|
46
|
Kim SH, Vieira M, Shim JY, Choi H, Park HY. Recent progress in single-molecule studies of mRNA localization in vivo. RNA Biol 2019; 16:1108-1118. [PMID: 30336727 PMCID: PMC6693552 DOI: 10.1080/15476286.2018.1536592] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2018] [Revised: 08/28/2018] [Accepted: 10/08/2018] [Indexed: 12/26/2022] Open
Abstract
From biogenesis to degradation, mRNA goes through diverse types of regulation and interaction with other biomolecules. Uneven distribution of mRNA transcripts and the diverse isoforms and modifications of mRNA make us wonder how cells manage the complexity and keep the functional integrity for the normal development of cells and organisms. Single-molecule microscopy tools have expanded the scope of RNA research with unprecedented spatiotemporal resolution. In this review, we highlight the recent progress in the methods for labeling mRNA targets and analyzing the quantitative information from fluorescence images of single mRNA molecules. In particular, the MS2 system and its various applications are the main focus of this article. We also review how recent studies have addressed biological questions related to the significance of mRNA localization in vivo. Efforts to visualize the dynamics of single mRNA molecules in live cells will push forward our knowledge on the nature of heterogeneity in RNA sequence, structure, and distribution as well as their molecular function and coordinated interaction with RNA binding proteins.
Collapse
Affiliation(s)
- Songhee H. Kim
- Department of Physics and Astronomy, Seoul National University, Seoul, Korea
- Institute of Molecular Biology and Genetics, Seoul National University, Seoul, Korea
| | - Melissa Vieira
- Interdisciplinary Program in Neuroscience, Seoul National University, Seoul, Korea
| | - Jae Youn Shim
- Department of Physics and Astronomy, Seoul National University, Seoul, Korea
| | - Hongyoung Choi
- Department of Physics and Astronomy, Seoul National University, Seoul, Korea
| | - Hye Yoon Park
- Department of Physics and Astronomy, Seoul National University, Seoul, Korea
- Institute of Molecular Biology and Genetics, Seoul National University, Seoul, Korea
- Interdisciplinary Program in Neuroscience, Seoul National University, Seoul, Korea
- Institute of Applied Physics, Seoul National University, Seoul, Korea
| |
Collapse
|
47
|
Zhao N, Kamijo K, Fox PD, Oda H, Morisaki T, Sato Y, Kimura H, Stasevich TJ. A genetically encoded probe for imaging nascent and mature HA-tagged proteins in vivo. Nat Commun 2019; 10:2947. [PMID: 31270320 PMCID: PMC6610143 DOI: 10.1038/s41467-019-10846-1] [Citation(s) in RCA: 53] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2018] [Accepted: 05/29/2019] [Indexed: 01/07/2023] Open
Abstract
To expand the toolbox of imaging in living cells, we have engineered a single-chain variable fragment binding the linear HA epitope with high affinity and specificity in vivo. The resulting probe, called the HA frankenbody, can light up in multiple colors HA-tagged nuclear, cytoplasmic, membrane, and mitochondrial proteins in diverse cell types. The HA frankenbody also enables state-of-the-art single-molecule experiments in living cells, which we demonstrate by tracking single HA-tagged histones in U2OS cells and single mRNA translation dynamics in both U2OS cells and neurons. Together with the SunTag, we also track two mRNA species simultaneously to demonstrate comparative single-molecule studies of translation can now be done with genetically encoded tools alone. Finally, we use the HA frankenbody to precisely quantify the expression of HA-tagged proteins in developing zebrafish embryos. The versatility of the HA frankenbody makes it a powerful tool for imaging protein dynamics in vivo.
Collapse
Affiliation(s)
- Ning Zhao
- Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, CO, 80523, USA
| | - Kouta Kamijo
- Graduate School of Life Science and Technology, Tokyo Institute of Technology, Yokohama, 226-8503, Japan
| | - Philip D Fox
- Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, CO, 80523, USA
| | - Haruka Oda
- Cell Biology Center, Institute of Innovative Research, Tokyo Institute of Technology, Yokohama, 226-8503, Japan
| | - Tatsuya Morisaki
- Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, CO, 80523, USA
| | - Yuko Sato
- Graduate School of Life Science and Technology, Tokyo Institute of Technology, Yokohama, 226-8503, Japan
- Cell Biology Center, Institute of Innovative Research, Tokyo Institute of Technology, Yokohama, 226-8503, Japan
| | - Hiroshi Kimura
- Graduate School of Life Science and Technology, Tokyo Institute of Technology, Yokohama, 226-8503, Japan
- Cell Biology Center, Institute of Innovative Research, Tokyo Institute of Technology, Yokohama, 226-8503, Japan
- World Research Hub Initiative, Institute of Innovative Research, Tokyo Institute of Technology, Yokohama, 226-8503, Japan
| | - Timothy J Stasevich
- Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, CO, 80523, USA.
- World Research Hub Initiative, Institute of Innovative Research, Tokyo Institute of Technology, Yokohama, 226-8503, Japan.
| |
Collapse
|
48
|
Lyon K, Aguilera LU, Morisaki T, Munsky B, Stasevich TJ. Live-Cell Single RNA Imaging Reveals Bursts of Translational Frameshifting. Mol Cell 2019; 75:172-183.e9. [PMID: 31178355 DOI: 10.1016/j.molcel.2019.05.002] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2018] [Revised: 03/14/2019] [Accepted: 04/30/2019] [Indexed: 11/25/2022]
Abstract
Ribosomal frameshifting during the translation of RNA is implicated in human disease and viral infection. While previous work has uncovered many details about single RNA frameshifting kinetics in vitro, little is known about how single RNA frameshift in living systems. To confront this problem, we have developed technology to quantify live-cell single RNA translation dynamics in frameshifted open reading frames. Applying this technology to RNA encoding the HIV-1 frameshift sequence reveals a small subset (∼8%) of the translating pool robustly frameshift. Frameshifting RNA are translated at similar rates as non-frameshifting RNA (∼3 aa/s) and can continuously frameshift for more than four rounds of translation. Fits to a bursty model of frameshifting constrain frameshifting kinetic rates and demonstrate how ribosomal traffic jams contribute to the persistence of the frameshifting state. These data provide insight into retroviral frameshifting and could lead to alternative strategies to perturb the process in living cells.
Collapse
Affiliation(s)
- Kenneth Lyon
- Department of Biochemistry and Molecular Biology, Institute of Genome Architecture and Function, Colorado State University, Fort Collins, CO 80523, USA
| | - Luis U Aguilera
- Department of Chemical and Biological Engineering and School of Biomedical Engineering, Colorado State University, Fort Collins, CO 80523, USA
| | - Tatsuya Morisaki
- Department of Biochemistry and Molecular Biology, Institute of Genome Architecture and Function, Colorado State University, Fort Collins, CO 80523, USA
| | - Brian Munsky
- Department of Chemical and Biological Engineering and School of Biomedical Engineering, Colorado State University, Fort Collins, CO 80523, USA.
| | - Timothy J Stasevich
- Department of Biochemistry and Molecular Biology, Institute of Genome Architecture and Function, Colorado State University, Fort Collins, CO 80523, USA; World Research Hub Initiative, Institute of Innovative Research, Tokyo Institute of Technology, Yokohama, Kanagawa 226-8503, Japan.
| |
Collapse
|
49
|
Hoffman AM, Chen Q, Zheng T, Nicchitta CV. Heterogeneous translational landscape of the endoplasmic reticulum revealed by ribosome proximity labeling and transcriptome analysis. J Biol Chem 2019; 294:8942-8958. [PMID: 31004035 DOI: 10.1074/jbc.ra119.007996] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2019] [Revised: 03/27/2019] [Indexed: 12/21/2022] Open
Abstract
The endoplasmic reticulum (ER) is a nexus for mRNA localization and translation, and recent studies have demonstrated that ER-bound ribosomes also play a transcriptome-wide role in regulating proteome composition. The Sec61 translocon (SEC61) serves as the receptor for ribosomes that translate secretory/integral membrane protein-encoding mRNAs, but whether SEC61 also serves as a translation site for cytosolic protein-encoding mRNAs remains unknown. Here, using a BioID proximity-labeling approach in HEK293T Flp-In cell lines, we examined interactions between ER-resident proteins and ribosomes in vivo Using in vitro analyses, we further focused on bona fide ribosome interactors (i.e. SEC61) and ER proteins (ribophorin I, leucine-rich repeat-containing 59 (LRRC59), and SEC62) previously implicated in associating with ribosomes. We observed labeling of ER-bound ribosomes with the SEC61β and LRRC59 BioID reporters, comparatively modest labeling with the ribophorin I reporter, and no labeling with the SEC62 reporter. A biotin pulse-chase/subcellular fractionation approach to examine ribosome exchange at the SEC61β and LRRC59 sites revealed that, at steady state, ribosomes at these sites comprise both rapid- and slow-exchanging pools. Global translational initiation arrest elicited by the inhibitor harringtonine accelerated SEC61β reporter-labeled ribosome exchange. RNA-Seq analyses of the mRNAs associated with SEC61β- and LRRC59-labeled ribosomes revealed both site-enriched and shared mRNAs and further established that the ER has a transcriptome-wide role in regulating proteome composition. These results provide evidence that ribosomes interact with the ER membrane via multiple modes and suggest regulatory mechanisms that control global proteome composition via ER membrane-bound ribosomes.
Collapse
Affiliation(s)
| | - Qiang Chen
- Cell Biology, Duke University School of Medicine, Durham, North Carolina 27710
| | - Tianli Zheng
- Cell Biology, Duke University School of Medicine, Durham, North Carolina 27710
| | - Christopher V Nicchitta
- From the Departments of Biochemistry and .,Cell Biology, Duke University School of Medicine, Durham, North Carolina 27710
| |
Collapse
|
50
|
Wilbertz JH, Voigt F, Horvathova I, Roth G, Zhan Y, Chao JA. Single-Molecule Imaging of mRNA Localization and Regulation during the Integrated Stress Response. Mol Cell 2019; 73:946-958.e7. [PMID: 30661979 DOI: 10.1016/j.molcel.2018.12.006] [Citation(s) in RCA: 97] [Impact Index Per Article: 19.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2018] [Revised: 10/24/2018] [Accepted: 12/11/2018] [Indexed: 12/31/2022]
Abstract
Biological phase transitions form membrane-less organelles that generate distinct cellular environments. How molecules are partitioned between these compartments and the surrounding cellular space and the functional consequence of this localization is not well understood. Here, we report the localization of mRNA to stress granules (SGs) and processing bodies (PBs) and its effect on translation and degradation during the integrated stress response. Using single mRNA imaging in living human cells, we find that the interactions of mRNAs with SGs and PBs have different dynamics, very few mRNAs directly move between SGs and PBs, and that specific RNA-binding proteins can anchor mRNAs within these compartments. During recovery from stress, we show that mRNAs that were within SGs and PBs are translated and degraded at similar rates as their cytosolic counterparts. Our work provides a framework for using single-molecule measurements to directly investigate the molecular mechanisms of phase-separated compartments within their cellular environment.
Collapse
Affiliation(s)
- Johannes H Wilbertz
- Friedrich Miescher Institute for Biomedical Research, 4058 Basel, Switzerland; University of Basel, 4003 Basel, Switzerland
| | - Franka Voigt
- Friedrich Miescher Institute for Biomedical Research, 4058 Basel, Switzerland
| | - Ivana Horvathova
- Friedrich Miescher Institute for Biomedical Research, 4058 Basel, Switzerland; University of Basel, 4003 Basel, Switzerland
| | - Gregory Roth
- Friedrich Miescher Institute for Biomedical Research, 4058 Basel, Switzerland
| | - Yinxiu Zhan
- Friedrich Miescher Institute for Biomedical Research, 4058 Basel, Switzerland; University of Basel, 4003 Basel, Switzerland
| | - Jeffrey A Chao
- Friedrich Miescher Institute for Biomedical Research, 4058 Basel, Switzerland.
| |
Collapse
|