1
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King MR, Ruff KM, Pappu RV. Emergent microenvironments of nucleoli. Nucleus 2024; 15:2319957. [PMID: 38443761 PMCID: PMC10936679 DOI: 10.1080/19491034.2024.2319957] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2023] [Accepted: 02/13/2024] [Indexed: 03/07/2024] Open
Abstract
In higher eukaryotes, the nucleolus harbors at least three sub-phases that facilitate multiple functionalities including ribosome biogenesis. The three prominent coexisting sub-phases are the fibrillar center (FC), the dense fibrillar component (DFC), and the granular component (GC). Here, we review recent efforts in profiling sub-phase compositions that shed light on the types of physicochemical properties that emerge from compositional biases and territorial organization of specific types of macromolecules. We highlight roles played by molecular grammars which refers to protein sequence features including the substrate binding domains, the sequence features of intrinsically disordered regions, and the multivalence of these distinct types of domains / regions. We introduce the concept of a barcode of emergent physicochemical properties of nucleoli. Although our knowledge of the full barcode remains incomplete, we hope that the concept prompts investigations into undiscovered emergent properties and engenders an appreciation for how and why unique microenvironments control biochemical reactions.
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Affiliation(s)
- Matthew R. King
- Department of Biomedical Engineering and Center for Biomolecular Condensates, Washington University in St. Louis, Campus, MO, USA
| | - Kiersten M. Ruff
- Department of Biomedical Engineering and Center for Biomolecular Condensates, Washington University in St. Louis, Campus, MO, USA
| | - Rohit V. Pappu
- Department of Biomedical Engineering and Center for Biomolecular Condensates, Washington University in St. Louis, Campus, MO, USA
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2
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González-Arzola K. The nucleolus: Coordinating stress response and genomic stability. BIOCHIMICA ET BIOPHYSICA ACTA. GENE REGULATORY MECHANISMS 2024; 1867:195029. [PMID: 38642633 DOI: 10.1016/j.bbagrm.2024.195029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/15/2023] [Revised: 03/25/2024] [Accepted: 04/12/2024] [Indexed: 04/22/2024]
Abstract
The perception that the nucleoli are merely the organelles where ribosome biogenesis occurs is challenged. Only around 30 % of nucleolar proteins are solely involved in producing ribosomes. Instead, the nucleolus plays a critical role in controlling protein trafficking during stress and, according to its dynamic nature, undergoes continuous protein exchange with nucleoplasm under various cellular stressors. Hence, the concept of nucleolar stress has evolved as cellular insults that disrupt the structure and function of the nucleolus. Considering the emerging role of this organelle in DNA repair and the fact that rDNAs are the most fragile genomic loci, therapies targeting the nucleoli are increasingly being developed. Besides, drugs that target ribosome synthesis and induce nucleolar stress can be used in cancer therapy. In contrast, agents that regulate nucleolar activity may be a potential treatment for neurodegeneration caused by abnormal protein accumulation in the nucleolus. Here, I explore the roles of nucleoli beyond their ribosomal functions, highlighting the factors triggering nucleolar stress and their impact on genomic stability.
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Affiliation(s)
- Katiuska González-Arzola
- Centro Andaluz de Biología Molecular y Medicina Regenerativa (CABIMER), Universidad de Sevilla, Consejo Superior de Investigaciones Científicas, Junta de Andalucía, Universidad Pablo de Olavide, 41092 Seville, Spain; Departamento de Bioquímica Vegetal y Biología Molecular, Universidad de Sevilla, 41012 Seville, Spain.
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3
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Sirozh O, Saez-Mas A, Jung B, Sanchez-Burgos L, Zarzuela E, Rodrigo-Perez S, Ventoso I, Lafarga V, Fernandez-Capetillo O. Nucleolar stress caused by arginine-rich peptides triggers a ribosomopathy and accelerates aging in mice. Mol Cell 2024; 84:1527-1540.e7. [PMID: 38521064 DOI: 10.1016/j.molcel.2024.02.031] [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: 09/15/2023] [Revised: 01/11/2024] [Accepted: 02/26/2024] [Indexed: 03/25/2024]
Abstract
Nucleolar stress (NS) has been associated with age-related diseases such as cancer or neurodegeneration. To investigate how NS triggers toxicity, we used (PR)n arginine-rich peptides present in some neurodegenerative diseases as inducers of this perturbation. We here reveal that whereas (PR)n expression leads to a decrease in translation, this occurs concomitant with an accumulation of free ribosomal (r) proteins. Conversely, (PR)n-resistant cells have lower rates of r-protein synthesis, and targeting ribosome biogenesis by mTOR inhibition or MYC depletion alleviates (PR)n toxicity in vitro. In mice, systemic expression of (PR)97 drives widespread NS and accelerated aging, which is alleviated by rapamycin. Notably, the generalized accumulation of orphan r-proteins is a common outcome of chemical or genetic perturbations that induce NS. Together, our study presents a general model to explain how NS induces cellular toxicity and provides in vivo evidence supporting a role for NS as a driver of aging in mammals.
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Affiliation(s)
- Oleksandra Sirozh
- Genomic Instability Group, Spanish National Cancer Research Centre (CNIO), Madrid 28029, Spain
| | - Anabel Saez-Mas
- Genomic Instability Group, Spanish National Cancer Research Centre (CNIO), Madrid 28029, Spain
| | - Bomi Jung
- Science for Life Laboratory, Division of Genome Biology, Department of Medical Biochemistry and Biophysics, Karolinska Institute, 171 21 Stockholm, Sweden
| | - Laura Sanchez-Burgos
- Genomic Instability Group, Spanish National Cancer Research Centre (CNIO), Madrid 28029, Spain
| | - Eduardo Zarzuela
- Proteomics Unit, Spanish National Cancer Research Centre (CNIO), Madrid 28029, Spain
| | - Sara Rodrigo-Perez
- Genomic Instability Group, Spanish National Cancer Research Centre (CNIO), Madrid 28029, Spain
| | - Ivan Ventoso
- Centro de Biologia Molecular Severo Ochoa (CSIC-UAM), Departamento de Biologia Molecular, Universidad Autonoma de Madrid (UAM), Madrid, Spain
| | - Vanesa Lafarga
- Genomic Instability Group, Spanish National Cancer Research Centre (CNIO), Madrid 28029, Spain.
| | - Oscar Fernandez-Capetillo
- Genomic Instability Group, Spanish National Cancer Research Centre (CNIO), Madrid 28029, Spain; Science for Life Laboratory, Division of Genome Biology, Department of Medical Biochemistry and Biophysics, Karolinska Institute, 171 21 Stockholm, Sweden.
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4
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Szelenyi ER, Navarrete JS, Murry AD, Zhang Y, Girven KS, Kuo L, Cline MM, Bernstein MX, Burdyniuk M, Bowler B, Goodwin NL, Juarez B, Zweifel LS, Golden SA. An arginine-rich nuclear localization signal (ArgiNLS) strategy for streamlined image segmentation of single-cells. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.11.22.568319. [PMID: 38045271 PMCID: PMC10690249 DOI: 10.1101/2023.11.22.568319] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/05/2023]
Abstract
High-throughput volumetric fluorescent microscopy pipelines can spatially integrate whole-brain structure and function at the foundational level of single-cells. However, conventional fluorescent protein (FP) modifications used to discriminate single-cells possess limited efficacy or are detrimental to cellular health. Here, we introduce a synthetic and non-deleterious nuclear localization signal (NLS) tag strategy, called 'Arginine-rich NLS' (ArgiNLS), that optimizes genetic labeling and downstream image segmentation of single-cells by restricting FP localization near-exclusively in the nucleus through a poly-arginine mechanism. A single N-terminal ArgiNLS tag provides modular nuclear restriction consistently across spectrally separate FP variants. ArgiNLS performance in vivo displays functional conservation across major cortical cell classes, and in response to both local and systemic brain wide AAV administration. Crucially, the high signal-to-noise ratio afforded by ArgiNLS enhances ML-automated segmentation of single-cells due to rapid classifier training and enrichment of labeled cell detection within 2D brain sections or 3D volumetric whole-brain image datasets, derived from both staining-amplified and native signal. This genetic strategy provides a simple and flexible basis for precise image segmentation of genetically labeled single-cells at scale and paired with behavioral procedures.
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Affiliation(s)
- Eric R. Szelenyi
- University of Washington Center of Excellence in Neurobiology of Addiction, Pain, and Emotion (NAPE), Seattle, WA, USA
- University of Washington, Department of Biological Structure, Seattle, WA, USA
| | - Jovana S. Navarrete
- University of Washington Center of Excellence in Neurobiology of Addiction, Pain, and Emotion (NAPE), Seattle, WA, USA
- University of Washington, Department of Biological Structure, Seattle, WA, USA
- University of Washington, Graduate Program in Neuroscience, Seattle, WA, USA
| | - Alexandria D. Murry
- University of Washington Center of Excellence in Neurobiology of Addiction, Pain, and Emotion (NAPE), Seattle, WA, USA
- University of Washington, Department of Biological Structure, Seattle, WA, USA
| | - Yizhe Zhang
- University of Washington Center of Excellence in Neurobiology of Addiction, Pain, and Emotion (NAPE), Seattle, WA, USA
- University of Washington, Department of Biological Structure, Seattle, WA, USA
| | - Kasey S. Girven
- University of Washington, Department of Anesthesiology and Pain Medicine
| | - Lauren Kuo
- University of Washington Center of Excellence in Neurobiology of Addiction, Pain, and Emotion (NAPE), Seattle, WA, USA
- University of Washington Undergraduate Program in Biochemistry
- Allen Institute for Cell Science, Seattle, WA, USA
| | - Marcella M. Cline
- University of Washington Center of Excellence in Neurobiology of Addiction, Pain, and Emotion (NAPE), Seattle, WA, USA
- University of Washington, Department of Pharmacology, Seattle, WA, USA
- Cajal Neuroscience, Seattle, WA, USA
| | - Mollie X. Bernstein
- University of Washington Center of Excellence in Neurobiology of Addiction, Pain, and Emotion (NAPE), Seattle, WA, USA
- University of Washington, Department of Pharmacology, Seattle, WA, USA
| | | | - Bryce Bowler
- University of Washington, Department of Biological Structure, Seattle, WA, USA
| | - Nastacia L. Goodwin
- University of Washington Center of Excellence in Neurobiology of Addiction, Pain, and Emotion (NAPE), Seattle, WA, USA
- University of Washington, Department of Biological Structure, Seattle, WA, USA
- University of Washington, Graduate Program in Neuroscience, Seattle, WA, USA
| | - Barbara Juarez
- University of Washington Center of Excellence in Neurobiology of Addiction, Pain, and Emotion (NAPE), Seattle, WA, USA
- University of Washington, Department of Psychiatry and Behavioral Sciences, Seattle, WA, USA
- University of Washington, Department of Pharmacology, Seattle, WA, USA
- University of Maryland School of Medicine, Department of Neurobiology, Baltimore, MD, USA
| | - Larry S. Zweifel
- University of Washington Center of Excellence in Neurobiology of Addiction, Pain, and Emotion (NAPE), Seattle, WA, USA
- University of Washington, Department of Psychiatry and Behavioral Sciences, Seattle, WA, USA
- University of Washington, Department of Pharmacology, Seattle, WA, USA
| | - Sam A. Golden
- University of Washington Center of Excellence in Neurobiology of Addiction, Pain, and Emotion (NAPE), Seattle, WA, USA
- University of Washington, Department of Biological Structure, Seattle, WA, USA
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5
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Aryan F, Detrés D, Luo CC, Kim SX, Shah AN, Bartusel M, Flynn RA, Calo E. Nucleolus activity-dependent recruitment and biomolecular condensation by pH sensing. Mol Cell 2023; 83:4413-4423.e10. [PMID: 37979585 PMCID: PMC10803072 DOI: 10.1016/j.molcel.2023.10.031] [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: 11/15/2022] [Revised: 06/20/2023] [Accepted: 10/23/2023] [Indexed: 11/20/2023]
Abstract
DEAD-box ATPases are major regulators of biomolecular condensates and orchestrate diverse biochemical processes that are critical for the functioning of cells. How DEAD-box proteins are selectively recruited to their respective biomolecular condensates is unknown. We explored this in the context of the nucleolus and DEAD-box protein DDX21. We find that the pH of the nucleolus is intricately linked to the transcriptional activity of the organelle and facilitates the recruitment and condensation of DDX21. We identify an evolutionarily conserved feature of the C terminus of DDX21 responsible for nucleolar localization. This domain is essential for zebrafish development, and its intrinsically disordered and isoelectric properties are necessary and sufficient for the ability of DDX21 to respond to changes in pH and form condensates. Molecularly, the enzymatic activities of poly(ADP-ribose) polymerases contribute to maintaining the nucleolar pH and, consequently, DDX21 recruitment and nucleolar partitioning. These observations reveal an activity-dependent physicochemical mechanism for the selective recruitment of biochemical activities to biomolecular condensates.
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Affiliation(s)
- Fardin Aryan
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Diego Detrés
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Claire C Luo
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Skylar X Kim
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Arish N Shah
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Michaela Bartusel
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Ryan A Flynn
- Stem Cell Program and Division of Hematology/Oncology, Boston Children's Hospital, Boston, MA, USA; Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA
| | - Eliezer Calo
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.
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6
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Martin RM, de Almeida MR, Gameiro E, de Almeida SF. Live-cell imaging unveils distinct R-loop populations with heterogeneous dynamics. Nucleic Acids Res 2023; 51:11010-11023. [PMID: 37819055 PMCID: PMC10639055 DOI: 10.1093/nar/gkad812] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2023] [Revised: 09/08/2023] [Accepted: 09/20/2023] [Indexed: 10/13/2023] Open
Abstract
We have developed RHINO, a genetically encoded sensor that selectively binds RNA:DNA hybrids enabling live-cell imaging of cellular R-loops. RHINO comprises a tandem array of three copies of the RNA:DNA hybrid binding domain of human RNase H1 connected by optimized linker segments and fused to a fluorescent protein. This tool allows the measurement of R-loop abundance and dynamics in live cells with high specificity and sensitivity. Using RHINO, we provide a kinetic framework for R-loops at nucleoli, telomeres and protein-coding genes. Our findings demonstrate that R-loop dynamics vary significantly across these regions, potentially reflecting the distinct roles R-loops play in different chromosomal contexts. RHINO is a powerful tool for investigating the role of R-loops in cellular processes and their contribution to disease development and progression.
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Affiliation(s)
- Robert M Martin
- Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina da Universidade de Lisboa, Lisboa, Portugal
| | - Madalena R de Almeida
- Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina da Universidade de Lisboa, Lisboa, Portugal
| | - Eduardo Gameiro
- Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina da Universidade de Lisboa, Lisboa, Portugal
| | - Sérgio F de Almeida
- Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina da Universidade de Lisboa, Lisboa, Portugal
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7
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Lavering ED, Gandhamaneni M, Weeks DL. Intrinsically disordered regions are not sufficient to direct the compartmental localization of nucleolar proteins in the nucleus. PLoS Biol 2023; 21:e3002378. [PMID: 37943867 PMCID: PMC10662738 DOI: 10.1371/journal.pbio.3002378] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2023] [Revised: 11/21/2023] [Accepted: 10/12/2023] [Indexed: 11/12/2023] Open
Abstract
The nucleolus is a non-membrane bound organelle central to ribosome biogenesis. The nucleolus contains a mix of proteins and RNA and has 3 known nucleolar compartments: the fibrillar center (FC), the dense fibrillar component (DFC), and the granular component (GC). The spatial organization of the nucleolus is influenced by the phase separation properties of nucleolar proteins, the presence of RNA, protein modification, and cellular activity. Many nucleolar proteins appear to concentrate within the borders of the compartments. We investigated whether the intrinsically disordered regions from several proteins provided the information needed to establish specific compartment localization using Xenopus laevis oocytes. For the proteins we tested, the disordered regions were not sufficient to direct specific domain localization and appear dispensable with respect to compartmentalization. Among the proteins that colocalize to the DFC are the quartet that comprise the box H/ACA pseudouridylation complex. In contrast to the insufficiency of IDRs to direct compartment localization, we found that the DFC accumulation of 2 box H/ACA proteins, Gar1 and Nhp2, was disrupted by mutations that were previously shown to reduce their ability to join the box H/ACA complex. Using a nanobody to introduce novel binding to a different DFC localized protein, we restored the localization of the mutated forms of Gar1 and Nhp2.
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Affiliation(s)
- Emily D. Lavering
- Biochemistry and Molecular Biology Department, Carver College of Medicine, University of Iowa, Iowa City, United States of America
| | | | - Daniel L. Weeks
- Biochemistry and Molecular Biology Department, Carver College of Medicine, University of Iowa, Iowa City, United States of America
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8
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Dai Y, Zhou Z, Kim K, Rivera N, Mohammed J, Hsu-Kim H, Chilkoti A, You L. Global control of cellular physiology by biomolecular condensates through modulation of electrochemical equilibria. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.10.19.563018. [PMID: 37904914 PMCID: PMC10614965 DOI: 10.1101/2023.10.19.563018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/01/2023]
Abstract
Control of the electrochemical environment in living cells is typically attributed to ion channels. Here we show that the formation of biomolecular condensates can modulate the electrochemical environment in cells, which affects processes globally within the cell and interactions of the cell with its environment. Condensate formation results in the depletion or enrichment of certain ions, generating intracellular ion gradients. These gradients directly affect the electrochemical properties of a cell, including the cytoplasmic pH and hyperpolarization of the membrane potential. The modulation of the electrochemical equilibria between the intra- and extra-cellular environments by biomolecular condensates governs charge-dependent uptake of small molecules by cells, and thereby directly influences bacterial survival under antibiotic stress. The shift of the intracellular electrochemical equilibria by condensate formation also drives a global change of the gene expression profile. The control of the cytoplasmic environment by condensates is correlated with their volume fraction, which can be highly variable between cells due to the stochastic nature of gene expression at the single cell level. Thus, condensate formation can amplify cell-cell variability of the environmental effects induced by the shift of cellular electrochemical equilibria. Our work reveals new biochemical functions of condensates, which extend beyond the biomolecules driving and participating in condensate formation, and uncovers a new role of biomolecular condensates in cellular regulation.
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Affiliation(s)
- Yifan Dai
- Department of Biomedical Engineering, Duke University, Durham, NC, 27708
- Department of Biomedical Engineering, Center for Biomolecular Condensates, Washington University in St. Louis, Saint Louis, MO, 63130
| | - Zhengqing Zhou
- Department of Biomedical Engineering, Duke University, Durham, NC, 27708
| | - Kyeri Kim
- Department of Biomedical Engineering, Duke University, Durham, NC, 27708
| | - Nelson Rivera
- Department of Civil and Environmental Engineering, Duke University, Durham, NC, 27708
| | - Javid Mohammed
- Department of Immunology, Duke University, Durham, NC, 27705
| | - Heileen Hsu-Kim
- Department of Civil and Environmental Engineering, Duke University, Durham, NC, 27708
| | - Ashutosh Chilkoti
- Department of Biomedical Engineering, Duke University, Durham, NC, 27708
- Center for Quantitative Biodesign, Duke University, Durham, NC 27708
| | - Lingchong You
- Department of Biomedical Engineering, Duke University, Durham, NC, 27708
- Center for Quantitative Biodesign, Duke University, Durham, NC 27708
- Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, NC 27710
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9
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Frion J, Meller A, Marbach G, Lévesque D, Roucou X, Boisvert FM. CRISPR/Cas9-mediated knockout of the ubiquitin variant UbKEKS reveals a role in regulating nucleolar structures and composition. Biol Open 2023; 12:bio059984. [PMID: 37670689 PMCID: PMC10537958 DOI: 10.1242/bio.059984] [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: 04/24/2023] [Accepted: 08/25/2023] [Indexed: 09/07/2023] Open
Abstract
Ubiquitination is a post-translational modification responsible for one of the most complex multilayered communication and regulation systems in the cell. Over the past decades, new ubiquitin variants and ubiquitin-like proteins arose to further enrich this mechanism. Recently discovered ubiquitin variant UbKEKS can specifically target several proteins and yet, functional consequences of this new modification remain unknown. Depletion of UbKEKS induces accumulation of lamin A in the nucleoli, highlighting the need for deeper investigations about protein composition and functions regulation of this highly dynamic and membrane-less compartment. Using data-independent acquisition mass spectrometry and microscopy, we show that despite not impacting protein stability, UbKEKS is required to maintain a normal nucleolar organization. The absence of UbKEKS increases nucleoli's size and accentuate their circularity while disrupting dense fibrillar component and fibrillar centre structures. Moreover, depletion of UbKEKS leads to distinct changes in nucleolar composition. Lack of UbKEKS favours nucleolar sequestration of known apoptotic regulators such as IFI16 or p14ARF, resulting in an increase of apoptosis observed by flow cytometry and real-time monitoring. Overall, these results identify the first cellular functions of the UbKEKS variant and lay the foundation stone to establish UbKEKS as a new universal layer of regulation in the ubiquitination system.
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Affiliation(s)
- Julie Frion
- Department of Immunology and Cell Biology, Université de Sherbrooke, Sherbrooke, QC, J1E 4K8, Canada
| | - Anna Meller
- Department of Immunology and Cell Biology, Université de Sherbrooke, Sherbrooke, QC, J1E 4K8, Canada
| | - Gwendoline Marbach
- Department of Immunology and Cell Biology, Université de Sherbrooke, Sherbrooke, QC, J1E 4K8, Canada
| | - Dominique Lévesque
- Department of Immunology and Cell Biology, Université de Sherbrooke, Sherbrooke, QC, J1E 4K8, Canada
| | - Xavier Roucou
- Department of Biochemistry and Functional Genomics, Université de Sherbrooke, Sherbrooke, QC, J1E 4K8, Canada
| | - François-Michel Boisvert
- Department of Immunology and Cell Biology, Université de Sherbrooke, Sherbrooke, QC, J1E 4K8, Canada
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10
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Wang JW, Squire HJ, Goh NS, Ni HM, Lien E, Wong C, González-Grandío E, Landry MP. Delivered complementation in planta (DCIP) enables measurement of peptide-mediated protein delivery efficiency in plants. Commun Biol 2023; 6:840. [PMID: 37573467 PMCID: PMC10423278 DOI: 10.1038/s42003-023-05191-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Accepted: 07/28/2023] [Indexed: 08/14/2023] Open
Abstract
Using a fluorescence complementation assay, Delivered Complementation in Planta (DCIP), we demonstrate cell-penetrating peptide-mediated cytosolic delivery of peptides and recombinant proteins in Nicotiana benthamiana. We show that DCIP enables quantitative measurement of protein delivery efficiency and enables functional screening of cell-penetrating peptides for in-planta protein delivery. Finally, we demonstrate that DCIP detects cell-penetrating peptide-mediated delivery of recombinantly expressed proteins such as mCherry and Lifeact into intact leaves. We also demonstrate delivery of a recombinant plant transcription factor, WUSCHEL (AtWUS), into N. benthamiana. RT-qPCR analysis of AtWUS delivery in Arabidopsis seedlings also suggests delivered WUS can recapitulate transcriptional changes induced by overexpression of AtWUS. Taken together, our findings demonstrate that DCIP offers a new and powerful tool for interrogating cytosolic delivery of proteins in plants and highlights future avenues for engineering plant physiology.
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Affiliation(s)
- Jeffrey W Wang
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, Berkeley, CA, 94720, USA
| | - Henry J Squire
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, Berkeley, CA, 94720, USA
| | - Natalie S Goh
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, Berkeley, CA, 94720, USA
| | - Heyuan Michael Ni
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, 94720, USA
| | - Edward Lien
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, 94720, USA
| | - Cerise Wong
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, Berkeley, CA, 94720, USA
| | - Eduardo González-Grandío
- Plant Molecular Genetics Department, Centro Nacional de Biotecnología-CSIC, Campus Universidad Autónoma de Madrid, Madrid, Spain
| | - Markita P Landry
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, Berkeley, CA, 94720, USA.
- Innovative Genomics Institute, Berkeley, CA, 94720, USA.
- California Institute for Quantitative Biosciences, University of California, Berkeley, Berkeley, CA, 94720, USA.
- Chan Zuckerberg Biohub, San Francisco, CA, 94063, USA.
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11
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Miyagi T, Ueda K, Sugimoto M, Yagi T, Ito D, Yamazaki R, Narumi S, Hayamizu Y, Uji-i H, Kuroda M, Kanekura K. Differential toxicity and localization of arginine-rich C9ORF72 dipeptide repeat proteins depend on de-clustering of positive charges. iScience 2023; 26:106957. [PMID: 37332605 PMCID: PMC10275993 DOI: 10.1016/j.isci.2023.106957] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2023] [Revised: 03/30/2023] [Accepted: 05/22/2023] [Indexed: 06/20/2023] Open
Abstract
Arginine-rich dipeptide repeat proteins (R-DPRs), poly(PR) and poly(GR), translated from the hexanucleotide repeat expansion in the amyotrophic lateral sclerosis (ALS)-causative C9ORF72 gene, contribute significantly to pathogenesis of ALS. Although both R-DPRs share many similarities, there are critical differences in their subcellular localization, phase separation, and toxicity mechanisms. We analyzed localization, protein-protein interactions, and phase separation of R-DPR variants and found that sufficient segregation of arginine charges is necessary for nucleolar distribution. Proline not only efficiently separated the charges, but also allowed for weak, but highly multivalent binding. In contrast, because of its high flexibility, glycine cannot fully separate the charges, and poly(GR) behaves similarly to the contiguous arginines, being trapped in the cytoplasm. We conclude that the amino acid that spaces the arginine charges determines the strength and multivalency of the binding, leading to differences in localization and toxicity mechanisms.
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Affiliation(s)
- Tamami Miyagi
- Department of Molecular Pathology, Tokyo Medical University, 6-1-1 Shinjuku, Shinjuku-ku, Tokyo 160-8402, Japan
- Department of Pharmacology, Tokyo Medical University, 6-1-1 Shinjuku, Shinjuku-ku, Tokyo 160-8402, Japan
| | - Koji Ueda
- Cancer Proteomics Group, Cancer Precision Medicine Center, Japanese Foundation for Cancer Research, 3-8-31 Ariake, Koto-ku, Tokyo 135-8550, Japan
| | - Masahiro Sugimoto
- Research and Development Center for Minimally Invasive Therapies, Tokyo Medical University, 6-1-1 Shinjuku, Shinjuku-ku, Tokyo 160-8402, Japan
- Institute for Advanced Biosciences, KEIO University, 246-2 Mizukami, Kakuganji, Tsuruoka, Yamagata 997-0052, Japan
| | - Takuya Yagi
- Department of Neurology, KEIO University School of Medicine, 35 Shinanomachi, Shinjuku-ku, Tokyo 160-8582, Japan
| | - Daisuke Ito
- Department of Physiology, KEIO University School of Medicine, 35 Shinanomachi, Shinjuku-ku, Tokyo 160-8582, Japan
| | - Rio Yamazaki
- Department of Molecular Pathology, Tokyo Medical University, 6-1-1 Shinjuku, Shinjuku-ku, Tokyo 160-8402, Japan
- Department of Pharmacology, Tokyo Medical University, 6-1-1 Shinjuku, Shinjuku-ku, Tokyo 160-8402, Japan
| | - Satoshi Narumi
- Department of Molecular Endocrinology, National Research Institute for Child Health and Development, 2-10-1 Okura, Setagaya-ku, Tokyo 157-8535, Japan
| | - Yuhei Hayamizu
- Department of Materials Science and Engineering, School of Materials and Chemical Technology, Tokyo Institute of Technology, 2-12-1, Ookayama, Meguro-ku, Tokyo 152-8550, Japan
| | - Hiroshi Uji-i
- Department of Nanomaterials and Nanoscopy, Research Institute for Electronic Science, Hokkaido University, Kita 10 Nishi 20, North Ward, Sapporo, Hokkaido 001-0020, Japan
- Department of Chemistry, KU Leuven Celestijnenlaan 200F, Heverlee, 3001 Leuven, Belgium
| | - Masahiko Kuroda
- Department of Molecular Pathology, Tokyo Medical University, 6-1-1 Shinjuku, Shinjuku-ku, Tokyo 160-8402, Japan
| | - Kohsuke Kanekura
- Department of Molecular Pathology, Tokyo Medical University, 6-1-1 Shinjuku, Shinjuku-ku, Tokyo 160-8402, Japan
- Department of Pharmacology, Tokyo Medical University, 6-1-1 Shinjuku, Shinjuku-ku, Tokyo 160-8402, Japan
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12
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Mohd Jaafar F, Monsion B, Mertens PPC, Attoui H. Identification of Orbivirus Non-Structural Protein 5 (NS5), Its Role and Interaction with RNA/DNA in Infected Cells. Int J Mol Sci 2023; 24:ijms24076845. [PMID: 37047816 PMCID: PMC10095184 DOI: 10.3390/ijms24076845] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2023] [Accepted: 03/31/2023] [Indexed: 04/09/2023] Open
Abstract
Bioinformatic analyses have predicted that orbiviruses encode an additional, small non-structural protein (NS5) from a secondary open reading frame on genome segment 10. However, this protein has not previously been detected in infected mammalian or insect cells. NS5-specific antibodies were generated in mice and were used to identify NS5 synthesised in orbivirus-infected BSR cells or cells transfected with NS5 expression plasmids. Confocal microscopy shows that although NS5 accumulates in the nucleus, particularly in the nucleolus, which becomes disrupted, it also appears in the cell cytoplasm, co-localising with mitochondria. NS5 helps to prevent the degradation of ribosomal RNAs during infection and reduces host-cell protein synthesis However, it helps to extend cell viability by supporting viral protein synthesis and virus replication. Pulldown studies showed that NS5 binds to ssRNAs and supercoiled DNAs and demonstrates interactions with ZBP1, suggesting that it modulates host-cell responses.
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Affiliation(s)
- Fauziah Mohd Jaafar
- UMR1161 VIROLOGIE, INRAE, Ecole Nationale Vétérinaire d’Alfort, ANSES, Université Paris-Est, F-94700 Maisons-Alfort, France
| | - Baptiste Monsion
- UMR1161 VIROLOGIE, INRAE, Ecole Nationale Vétérinaire d’Alfort, ANSES, Université Paris-Est, F-94700 Maisons-Alfort, France
| | - Peter P. C. Mertens
- One Virology, The Wolfson Centre for Global Virus Research, School of Veterinary Medicine and Science, University of Nottingham, Sutton Bonington Campus, Leicestershire LE12 5RD, UK
| | - Houssam Attoui
- UMR1161 VIROLOGIE, INRAE, Ecole Nationale Vétérinaire d’Alfort, ANSES, Université Paris-Est, F-94700 Maisons-Alfort, France
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13
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Gonskikh Y, Stoute J, Shen H, Budinich K, Pingul B, Schultz K, Elashal H, Marmorstein R, Shi J, Liu KF. Noncatalytic regulation of 18 S rRNA methyltransferase DIMT1 in acute myeloid leukemia. Genes Dev 2023; 37:321-335. [PMID: 37024283 PMCID: PMC10153457 DOI: 10.1101/gad.350298.122] [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: 12/08/2022] [Accepted: 03/21/2023] [Indexed: 04/08/2023]
Abstract
Several rRNA-modifying enzymes install rRNA modifications while participating in ribosome assembly. Here, we show that 18S rRNA methyltransferase DIMT1 is essential for acute myeloid leukemia (AML) proliferation through a noncatalytic function. We reveal that targeting a positively charged cleft of DIMT1, remote from the catalytic site, weakens the binding of DIMT1 to rRNA and mislocalizes DIMT1 to the nucleoplasm, in contrast to the primarily nucleolar localization of wild-type DIMT1. Mechanistically, rRNA binding is required for DIMT1 to undergo liquid-liquid phase separation, which explains the distinct nucleoplasm localization of the rRNA binding-deficient DIMT1. Re-expression of wild-type or a catalytically inactive mutant E85A, but not the rRNA binding-deficient DIMT1, supports AML cell proliferation. This study provides a new strategy to target DIMT1-regulated AML proliferation via targeting this essential noncatalytic region.
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Affiliation(s)
- Yulia Gonskikh
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Julian Stoute
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
- Graduate Group in Biochemistry and Molecular Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Hui Shen
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Krista Budinich
- Department of Cancer Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
- Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
- Abramson Family Cancer Research Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Bianca Pingul
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
- Graduate Group in Biochemistry and Molecular Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Kollin Schultz
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
- Graduate Group in Biochemistry and Molecular Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Heidi Elashal
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
- Graduate Group in Biochemistry and Molecular Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Ronen Marmorstein
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
- Graduate Group in Biochemistry and Molecular Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Junwei Shi
- Department of Cancer Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
- Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
- Abramson Family Cancer Research Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Kathy Fange Liu
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA;
- Graduate Group in Biochemistry and Molecular Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
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14
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Suzuki M, Sato Y, Togashi N, Nishizawa S. Cationic Oligopeptides with Amino Groups as Synthetic Nucleolar Localization Signals for the Rational Design of Nucleolus-Staining Probes. ACS OMEGA 2023; 8:9592-9596. [PMID: 36936342 PMCID: PMC10018684 DOI: 10.1021/acsomega.3c00116] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/06/2023] [Accepted: 01/20/2023] [Indexed: 06/18/2023]
Abstract
Cationic oligopeptides with amino groups were found to function as synthetic nucleolar localization signals for directing various fluorophores to the nucleolus with high selectivity in the cells with a view toward the development of nucleolus-staining probes.
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15
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Lavogina D, Nasirova N, Sõrmus T, Tähtjärv T, Enkvist E, Viht K, Haljasorg T, Herodes K, Jaal J, Uri A. Conjugates of adenosine mimetics and arginine-rich peptides serve as inhibitors and fluorescent probes but not as long-lifetime photoluminescent probes for protein arginine methyltransferases. J Pept Sci 2023; 29:e3456. [PMID: 36208424 DOI: 10.1002/psc.3456] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2022] [Revised: 09/30/2022] [Accepted: 10/04/2022] [Indexed: 11/06/2022]
Abstract
The conjugates of an adenosine mimetic and oligo-l-arginine or oligo-d-arginine (ARCs) were initially designed in our research group as inhibitors and photoluminescent probes targeting basophilic protein kinases. Here, we explored a panel of ARCs and their fluorescent derivatives in biochemical assays with members of the protein arginine methyltransferase (PRMT) family, focusing specifically on PRMT1. In the binding/displacement assay with detection of fluorescence anisotropy, we found that ARCs and arginine-rich peptides could serve as high-affinity ligands for PRMT1, whereas the equilibrium dissociation constant values depended dramatically on the number of arginine residues within the compounds. The fluorescently labeled probe ARC-1081 was displaced from its complex with PRMT1 by both S-adenosyl-l-methionine (SAM) and S-adenosyl-l-homocysteine (SAH), indicating binding of the adenosine mimetic of ARCs to the SAM/SAH-binding site within PRMT1. The ARCs that had previously shown microsecond-lifetime photoluminescence in complex with protein kinases did not feature such property in complex with PRMT1, demonstrating the selectivity of the time-resolved readout format. When tested against a panel of PRMT family members in single-dose inhibition experiments, a micromolar concentration of ARC-902 was required for the inhibition of PRMT1 and PRMT7. Overall, our results suggest that the compounds containing multiple arginine residues (including the well-known cell-penetrating peptides) are likely to inhibit PRMT and thus interfere with the epigenetic modification status in complex biological systems, which should be taken into consideration during interpretation of the experimental data.
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Affiliation(s)
- Darja Lavogina
- Institute of Chemistry, University of Tartu, Tartu, Estonia.,Institute of Clinical Medicine, University of Tartu, Tartu, Estonia
| | - Naila Nasirova
- Institute of Chemistry, University of Tartu, Tartu, Estonia
| | - Tanel Sõrmus
- Institute of Chemistry, University of Tartu, Tartu, Estonia
| | - Taavo Tähtjärv
- Institute of Chemistry, University of Tartu, Tartu, Estonia
| | - Erki Enkvist
- Institute of Chemistry, University of Tartu, Tartu, Estonia
| | - Kaido Viht
- Institute of Chemistry, University of Tartu, Tartu, Estonia
| | - Tõiv Haljasorg
- Institute of Chemistry, University of Tartu, Tartu, Estonia
| | - Koit Herodes
- Institute of Chemistry, University of Tartu, Tartu, Estonia
| | - Jana Jaal
- Institute of Clinical Medicine, University of Tartu, Tartu, Estonia.,Department of Radiotherapy and Oncological Therapy, Tartu University Hospital, Tartu, Estonia
| | - Asko Uri
- Institute of Chemistry, University of Tartu, Tartu, Estonia
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16
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Rawlinson SM, Zhao T, Ardipradja K, Zhang Y, Veugelers PF, Harper JA, David CT, Sundaramoorthy V, Moseley GW. Henipaviruses and lyssaviruses target nucleolar treacle protein and regulate ribosomal RNA synthesis. Traffic 2023; 24:146-157. [PMID: 36479968 PMCID: PMC10947316 DOI: 10.1111/tra.12877] [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: 04/21/2022] [Revised: 11/24/2022] [Accepted: 11/28/2022] [Indexed: 12/14/2022]
Abstract
The nucleolus is a common target of viruses and viral proteins, but for many viruses the functional outcomes and significance of this targeting remains unresolved. Recently, the first intranucleolar function of a protein of a cytoplasmically-replicating negative-sense RNA virus (NSV) was identified, with the finding that the matrix (M) protein of Hendra virus (HeV) (genus Henipavirus, family Paramyxoviridae) interacts with Treacle protein within nucleolar subcompartments and mimics a cellular mechanism of the nucleolar DNA-damage response (DDR) to suppress ribosomal RNA (rRNA) synthesis. Whether other viruses utilise this mechanism has not been examined. We report that sub-nucleolar Treacle targeting and modulation is conserved between M proteins of multiple Henipaviruses, including Nipah virus and other potentially zoonotic viruses. Furthermore, this function is also evident for P3 protein of rabies virus, the prototype virus of a different RNA virus family (Rhabdoviridae), with Treacle depletion in cells also found to impact virus production. These data indicate that unrelated proteins of viruses from different families have independently developed nucleolar/Treacle targeting function, but that modulation of Treacle has distinct effects on infection. Thus, subversion of Treacle may be an important process in infection by diverse NSVs, and so could provide novel targets for antiviral approaches with broad specificity.
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Affiliation(s)
- Stephen M. Rawlinson
- Department of Microbiology, Biomedicine Discovery InstituteMonash UniversityMelbourneVictoriaAustralia
| | - Tianyue Zhao
- Department of Microbiology, Biomedicine Discovery InstituteMonash UniversityMelbourneVictoriaAustralia
| | - Katie Ardipradja
- Commonwealth Scientific and Industrial Research Organisation (CSIRO)Australian Centre for Disease Preparedness (ACDP)East GeelongVictoriaAustralia
| | - Yilin Zhang
- Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology InstituteThe University of MelbourneMelbourneAustralia
| | - Patrick F. Veugelers
- Department of Microbiology, Biomedicine Discovery InstituteMonash UniversityMelbourneVictoriaAustralia
| | - Jennifer A. Harper
- Commonwealth Scientific and Industrial Research Organisation (CSIRO)Australian Centre for Disease Preparedness (ACDP)East GeelongVictoriaAustralia
| | - Cassandra T. David
- Department of Microbiology, Biomedicine Discovery InstituteMonash UniversityMelbourneVictoriaAustralia
| | - Vinod Sundaramoorthy
- Commonwealth Scientific and Industrial Research Organisation (CSIRO)Australian Centre for Disease Preparedness (ACDP)East GeelongVictoriaAustralia
- School of MedicineDeakin UniversityGeelongVictoriaAustralia
| | - Gregory W. Moseley
- Department of Microbiology, Biomedicine Discovery InstituteMonash UniversityMelbourneVictoriaAustralia
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17
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Ntefidou M, Eklund DM, Le Bail A, Schulmeister S, Scherbel F, Brandl L, Dörfler W, Eichstädt C, Bannmüller A, Ljung K, Kost B. Physcomitrium patens PpRIC, an ancestral CRIB-domain ROP effector, inhibits auxin-induced differentiation of apical initial cells. Cell Rep 2023; 42:112130. [PMID: 36790931 DOI: 10.1016/j.celrep.2023.112130] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2022] [Revised: 12/03/2022] [Accepted: 02/01/2023] [Indexed: 02/16/2023] Open
Abstract
RHO guanosine triphosphatases are important eukaryotic regulators of cell differentiation and behavior. Plant ROP (RHO of plant) family members activate specific, incompletely characterized downstream signaling. The structurally simple land plant Physcomitrium patens is missing homologs of key animal and flowering plant RHO effectors but contains a single CRIB (CDC42/RAC interactive binding)-domain-containing RIC (ROP-interacting CRIB-containing) protein (PpRIC). Protonemal P. patens filaments elongate based on regular division and PpROP-dependent tip growth of apical initial cells, which upon stimulation by the hormone auxin differentiate caulonemal characteristics. PpRIC interacts with active PpROP1, co-localizes with this protein at the plasma membrane at the tip of apical initial cells, and accumulates in the nucleus. Remarkably, PpRIC is not required for tip growth but is targeted to the nucleus to block caulonema differentiation downstream of auxin-controlled gene expression. These observations establish functions of PpRIC in mediating crosstalk between ROP and auxin signaling, which contributes to the maintenance of apical initial cell identity.
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Affiliation(s)
- Maria Ntefidou
- Cell Biology, Department of Biology, University Erlangen-Nuremberg, 91058 Erlangen, Germany
| | - D Magnus Eklund
- Physiology and Environmental Toxicology, Department of Organismal Biology, Uppsala University, 75236 Uppsala, Sweden
| | - Aude Le Bail
- Cell Biology, Department of Biology, University Erlangen-Nuremberg, 91058 Erlangen, Germany
| | - Sylwia Schulmeister
- Cell Biology, Department of Biology, University Erlangen-Nuremberg, 91058 Erlangen, Germany
| | - Franziska Scherbel
- Cell Biology, Department of Biology, University Erlangen-Nuremberg, 91058 Erlangen, Germany
| | - Lisa Brandl
- Cell Biology, Department of Biology, University Erlangen-Nuremberg, 91058 Erlangen, Germany
| | - Wolfgang Dörfler
- Cell Biology, Department of Biology, University Erlangen-Nuremberg, 91058 Erlangen, Germany
| | - Chantal Eichstädt
- Cell Biology, Department of Biology, University Erlangen-Nuremberg, 91058 Erlangen, Germany
| | - Anna Bannmüller
- Cell Biology, Department of Biology, University Erlangen-Nuremberg, 91058 Erlangen, Germany
| | - Karin Ljung
- Umeå Plant Science Centre, Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, 90183 Umeå, Sweden
| | - Benedikt Kost
- Cell Biology, Department of Biology, University Erlangen-Nuremberg, 91058 Erlangen, Germany.
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18
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Jevitt AM, Rankin BD, Chen J, Rankin S. The cohesin modifier ESCO2 is stable during DNA replication. Chromosome Res 2023; 31:6. [PMID: 36708487 PMCID: PMC9884251 DOI: 10.1007/s10577-023-09711-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2022] [Revised: 11/01/2022] [Accepted: 12/13/2022] [Indexed: 01/29/2023]
Abstract
Cohesion between sister chromatids by the cohesin protein complex ensures accurate chromosome segregation and enables recombinational DNA repair. Sister chromatid cohesion is promoted by acetylation of the SMC3 subunit of cohesin by the ESCO2 acetyltransferase, inhibiting cohesin release from chromatin. The interaction of ESCO2 with the DNA replication machinery, in part through PCNA-interacting protein (PIP) motifs in ESCO2, is required for full cohesion establishment. Recent reports have suggested that Cul4-dependent degradation regulates the level of ESCO2 protein following replication. To follow up on these observations, we have characterized ESCO2 stability in Xenopus egg extracts, a cell-free system that recapitulates cohesion establishment in vitro. We found that ESCO2 was stable during DNA replication in this system. Indeed, further challenging the system by inducing DNA damage signaling or increasing the number of nuclei undergoing DNA replication had no significant impact on the stability of ESCO2. In transgenic somatic cell lines, we also did not see evidence of GFP-ESCO2 degradation during S phase of the cell cycle using both flow cytometry and live-cell imaging. We conclude that ESCO2 is stable during DNA replication in both embryonic and somatic cells.
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Affiliation(s)
- Allison M Jevitt
- Cell Cycle and Cancer Biology Program, Oklahoma Medical Research Foundation, Oklahoma City, OK, 73104, USA
| | - Brooke D Rankin
- Department of Cell Biology, University of Oklahoma Health Sciences Center, Oklahoma City, OK, 73104, USA
| | - Jingrong Chen
- Cell Cycle and Cancer Biology Program, Oklahoma Medical Research Foundation, Oklahoma City, OK, 73104, USA
| | - Susannah Rankin
- Cell Cycle and Cancer Biology Program, Oklahoma Medical Research Foundation, Oklahoma City, OK, 73104, USA.
- Department of Cell Biology, University of Oklahoma Health Sciences Center, Oklahoma City, OK, 73104, USA.
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19
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Saini N, Bheeshmachar G, Sarin A. Sirtuin1 meditated modification of Notch1 intracellular domain regulates nucleolar localization and activation of distinct signaling cascades. Front Cell Dev Biol 2022; 10:988816. [PMID: 36211456 PMCID: PMC9539544 DOI: 10.3389/fcell.2022.988816] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2022] [Accepted: 08/29/2022] [Indexed: 11/13/2022] Open
Abstract
Notch signaling is involved in cell fate decisions in the development and maintenance of tissue homeostasis. Spatial regulation of the Notch1 intracellular domain (NIC1), has been shown to underpin signaling outcomes mediated by this receptor. We recently reported a putative Nucleolar Localization Sequence (NoLS) in NIC1. Here we investigate if the putative NoLS identified in NIC1 regulates localization in the nucleolus and anti-apoptotic activity. Confocal imaging of live cells expressing NIC1 or forms modified by deletion or site-directed mutagenesis established that the putative NoLS in NIC1 is required for nucleolar localization and regulated by the deacetylase Sirtuin1. Subsequent analysis of anti-apoptotic activity revealed signaling cascades linked to nucleolar localization. For this, etoposide and 4-Nitroquinoline 1-oxide, an inhibitor of topoisomerase-II and a UV mimetic drug respectively, were used as prototypic triggers of genomic damage in a mammalian cell line. While NIC1 blocked apoptosis regardless of its localization to the nucleoplasm or nucleolus, modifications of NIC1 which promoted localization to the nucleolus triggered a dependence on the nucleolar proteins fibrillarin and nucleolin for anti-apoptotic activity. Further, cells co-expressing NIC1 and Sirtuin1 (but not its catalytically inactive form), confirmed both spatial regulation and the switch to dependence on the nucleolar proteins. Finally, site-directed mutagenesis showed that the NoLS lysine residues are targets of Sirtuin1 activity. NIC1 mediated transcription is not similarly regulated. Thus, NIC1 localization to the nucleolus is regulated by Sirtuin1 modification of the lysine residues in NoLS and triggers a distinct signaling cascade involving nucleolar intermediates for anti-apoptotic activity.
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20
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Lacroix E, Audas TE. Keeping up with the condensates: The retention, gain, and loss of nuclear membrane-less organelles. Front Mol Biosci 2022; 9:998363. [PMID: 36203874 PMCID: PMC9530788 DOI: 10.3389/fmolb.2022.998363] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Accepted: 08/19/2022] [Indexed: 12/04/2022] Open
Abstract
In recent decades, a growing number of biomolecular condensates have been identified in eukaryotic cells. These structures form through phase separation and have been linked to a diverse array of cellular processes. While a checklist of established membrane-bound organelles is present across the eukaryotic domain, less is known about the conservation of membrane-less subcellular structures. Many of these structures can be seen throughout eukaryotes, while others are only thought to be present in metazoans or a limited subset of species. In particular, the nucleus is a hub of biomolecular condensates. Some of these subnuclear domains have been found in a broad range of organisms, which is a characteristic often attributed to essential functionality. However, this does not always appear to be the case. For example, the nucleolus is critical for ribosomal biogenesis and is present throughout the eukaryotic domain, while the Cajal bodies are believed to be similarly conserved, yet these structures are dispensable for organismal survival. Likewise, depletion of the Drosophila melanogaster omega speckles reduces viability, despite the apparent absence of this domain in higher eukaryotes. By reviewing primary research that has analyzed the presence of specific condensates (nucleoli, Cajal bodies, amyloid bodies, nucleolar aggresomes, nuclear speckles, nuclear paraspeckles, nuclear stress bodies, PML bodies, omega speckles, NUN bodies, mei2 dots) in a cross-section of organisms (e.g., human, mouse, D. melanogaster, Caenorhabditis elegans, yeast), we adopt a human-centric view to explore the emergence, retention, and absence of a subset of nuclear biomolecular condensates. This overview is particularly important as numerous biomolecular condensates have been linked to human disease, and their presence in additional species could unlock new and well characterized model systems for health research.
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Affiliation(s)
- Emma Lacroix
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC, Canada
- Centre for Cell Biology, Development, and Disease, Simon Fraser University, Burnaby, BC, Canada
| | - Timothy E. Audas
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC, Canada
- Centre for Cell Biology, Development, and Disease, Simon Fraser University, Burnaby, BC, Canada
- *Correspondence: Timothy E. Audas,
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21
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Schmidt A, Frei J, Poetsch A, Chittka A, Zhang H, Aßmann C, Lehmkuhl A, Bauer UM, Nuber UA, Cardoso MC. MeCP2 heterochromatin organization is modulated by arginine methylation and serine phosphorylation. Front Cell Dev Biol 2022; 10:941493. [PMID: 36172281 PMCID: PMC9510713 DOI: 10.3389/fcell.2022.941493] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2022] [Accepted: 08/19/2022] [Indexed: 11/23/2022] Open
Abstract
Rett syndrome is a human intellectual disability disorder that is associated with mutations in the X-linked MECP2 gene. The epigenetic reader MeCP2 binds to methylated cytosines on the DNA and regulates chromatin organization. We have shown previously that MECP2 Rett syndrome missense mutations are impaired in chromatin binding and heterochromatin reorganization. Here, we performed a proteomics analysis of post-translational modifications of MeCP2 isolated from adult mouse brain. We show that MeCP2 carries various post-translational modifications, among them phosphorylation on S80 and S421, which lead to minor changes in either heterochromatin binding kinetics or clustering. We found that MeCP2 is (di)methylated on several arginines and that this modification alters heterochromatin organization. Interestingly, we identified the Rett syndrome mutation site R106 as a dimethylation site. In addition, co-expression of protein arginine methyltransferases (PRMT)1 and PRMT6 lead to a decrease of heterochromatin clustering. Altogether, we identified and validated novel modifications of MeCP2 in the brain and show that these can modulate its ability to bind as well as reorganize heterochromatin, which may play a role in the pathology of Rett syndrome.
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Affiliation(s)
- Annika Schmidt
- Cell Biology and Epigenetics, Department of Biology, Technical University of Darmstadt, Darmstadt, Germany
| | - Jana Frei
- Stem Cell and Developmental Biology, Department of Biology, Technical University of Darmstadt, Darmstadt, Germany
| | - Ansgar Poetsch
- Queen Mary School, Medical College, Nanchang University, Nanchang, China
- Plant Biochemistry, Ruhr University Bochum, Bochum, Germany
- College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Alexandra Chittka
- Division of Medicine, The Wolfson Institute for Biomedical Research, University College London, London, United Kingdom
- Department of Neuromuscular Diseases, Queen Square Institute of Neurology, University College London, London, United Kingdom
| | - Hui Zhang
- Cell Biology and Epigenetics, Department of Biology, Technical University of Darmstadt, Darmstadt, Germany
| | - Chris Aßmann
- Institute of Molecular Biology and Tumor Research, Philipps University Marburg, Marburg, Germany
| | - Anne Lehmkuhl
- Cell Biology and Epigenetics, Department of Biology, Technical University of Darmstadt, Darmstadt, Germany
| | - Uta-Maria Bauer
- Institute of Molecular Biology and Tumor Research, Philipps University Marburg, Marburg, Germany
| | - Ulrike A. Nuber
- Stem Cell and Developmental Biology, Department of Biology, Technical University of Darmstadt, Darmstadt, Germany
- *Correspondence: Ulrike A. Nuber, ; M. Cristina Cardoso,
| | - M. Cristina Cardoso
- Cell Biology and Epigenetics, Department of Biology, Technical University of Darmstadt, Darmstadt, Germany
- *Correspondence: Ulrike A. Nuber, ; M. Cristina Cardoso,
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22
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Muñoz-Díaz E, Sáez-Vásquez J. Nuclear dynamics: Formation of bodies and trafficking in plant nuclei. FRONTIERS IN PLANT SCIENCE 2022; 13:984163. [PMID: 36082296 PMCID: PMC9445803 DOI: 10.3389/fpls.2022.984163] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Accepted: 08/04/2022] [Indexed: 06/01/2023]
Abstract
The existence of the nucleus distinguishes prokaryotes and eukaryotes. Apart from containing most of the genetic material, the nucleus possesses several nuclear bodies composed of protein and RNA molecules. The nucleus is separated from the cytoplasm by a double membrane, regulating the trafficking of molecules in- and outwards. Here, we investigate the composition and function of the different plant nuclear bodies and molecular clues involved in nuclear trafficking. The behavior of the nucleolus, Cajal bodies, dicing bodies, nuclear speckles, cyclophilin-containing bodies, photobodies and DNA damage foci is analyzed in response to different abiotic stresses. Furthermore, we research the literature to collect the different protein localization signals that rule nucleocytoplasmic trafficking. These signals include the different types of nuclear localization signals (NLSs) for nuclear import, and the nuclear export signals (NESs) for nuclear export. In contrast to these unidirectional-movement signals, the existence of nucleocytoplasmic shuttling signals (NSSs) allows bidirectional movement through the nuclear envelope. Likewise, nucleolar signals are also described, which mainly include the nucleolar localization signals (NoLSs) controlling nucleolar import. In contrast, few examples of nucleolar export signals, called nucleoplasmic localization signals (NpLSs) or nucleolar export signals (NoESs), have been reported. The existence of consensus sequences for these localization signals led to the generation of prediction tools, allowing the detection of these signals from an amino acid sequence. Additionally, the effect of high temperatures as well as different post-translational modifications in nuclear and nucleolar import and export is discussed.
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Affiliation(s)
- Eduardo Muñoz-Díaz
- Centre National de la Recherche Scientifique (CNRS), Laboratoire Génome et Développement des Plantes, UMR 5096, Perpignan, France
- Univ. Perpignan Via Domitia, Laboratoire Génome et Développement des Plantes, UMR 5096, Perpignan, France
| | - Julio Sáez-Vásquez
- Centre National de la Recherche Scientifique (CNRS), Laboratoire Génome et Développement des Plantes, UMR 5096, Perpignan, France
- Univ. Perpignan Via Domitia, Laboratoire Génome et Développement des Plantes, UMR 5096, Perpignan, France
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Kuznetsov VI, Liu WH, Klein MA, Denu JM. Potent Activation of NAD +-Dependent Deacetylase Sirt7 by Nucleosome Binding. ACS Chem Biol 2022; 17:2248-2261. [PMID: 35939806 PMCID: PMC9499614 DOI: 10.1021/acschembio.2c00348] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Sirtuin-7 (Sirt7) is a nuclear NAD+-dependent deacetylase with a broad spectrum of biological functions. Sirt7 overexpression is linked to several pathological states and enhances anticancer drug resistance, making the enzyme a promising target for the development of novel therapeutics. Despite a plethora of reported in vivo functions, the biochemical characterization of recombinant Sirt7 remains inadequate for the development of novel drug candidates. Here, we conduct an extensive biochemical analysis of Sirt7 using newly developed binding and kinetic assays to reveal that the enzyme preferentially interacts with and is activated by nucleosomes. Sirt7 activation by nucleic acids alone is effective toward long-chain acylated hydrophobic substrates, while only nucleosome binding leads to 105-fold activation of the deacetylase activity. Using endogenous chromatin and recombinant acetylated nucleosomes, we reveal that Sirt7 is one of the most efficient deacetylases in the sirtuin family and that its catalytic activity is limited by the rate of dissociation from deacetylated nucleosomes.
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Affiliation(s)
- Vyacheslav I. Kuznetsov
- Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, WI, 53706, USA
- Wisconsin Institute for Discovery, University of Wisconsin-Madison, Madison, WI, 53715, USA
| | - Wallace H. Liu
- Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, WI, 53706, USA
- Wisconsin Institute for Discovery, University of Wisconsin-Madison, Madison, WI, 53715, USA
| | - Mark A. Klein
- Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, WI, 53706, USA
- Wisconsin Institute for Discovery, University of Wisconsin-Madison, Madison, WI, 53715, USA
| | - John M. Denu
- Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, WI, 53706, USA
- Wisconsin Institute for Discovery, University of Wisconsin-Madison, Madison, WI, 53715, USA
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24
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The Patterning and Proportion of Charged Residues in the Arginine-Rich Mixed-Charge Domain Determine the Membrane-Less Organelle Targeted by the Protein. Int J Mol Sci 2022; 23:ijms23147658. [PMID: 35887012 PMCID: PMC9324279 DOI: 10.3390/ijms23147658] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2022] [Revised: 07/08/2022] [Accepted: 07/08/2022] [Indexed: 11/17/2022] Open
Abstract
Membrane-less organelles (MLOs) are formed by biomolecular liquid–liquid phase separation (LLPS). Proteins with charged low-complexity domains (LCDs) are prone to phase separation and localize to MLOs, but the mechanism underlying the distributions of such proteins to specific MLOs remains poorly understood. Recently, proteins with Arg-enriched mixed-charge domains (R-MCDs), primarily composed of R and Asp (D), were found to accumulate in nuclear speckles via LLPS. However, the process by which R-MCDs selectively incorporate into nuclear speckles is unknown. Here, we demonstrate that the patterning of charged amino acids and net charge determines the targeting of specific MLOs, including nuclear speckles and the nucleolus, by proteins. The redistribution of R and D residues from an alternately sequenced pattern to uneven blocky sequences caused a shift in R-MCD distribution from nuclear speckles to the nucleolus. In addition, the incorporation of basic residues in the R-MCDs promoted their localization to the MLOs and their apparent accumulation in the nucleolus. The R-MCD peptide with alternating amino acids did not undergo LLPS, whereas the blocky R-MCD peptide underwent LLPS with affinity to RNA, acidic poly-Glu, and the acidic nucleolar protein nucleophosmin, suggesting that the clustering of R residues helps avoid their neutralization by D residues and eventually induces R-MCD migration to the nucleolus. Therefore, the distribution of proteins to nuclear speckles requires the proximal positioning of D and R for the mutual neutralization of their charges.
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25
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Tan P, Hong T, Cai X, Li W, Huang Y, He L, Zhou Y. Optical control of protein delivery and partitioning in the nucleolus. Nucleic Acids Res 2022; 50:e69. [PMID: 35325178 PMCID: PMC9262612 DOI: 10.1093/nar/gkac191] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2021] [Revised: 02/12/2022] [Accepted: 03/11/2022] [Indexed: 11/14/2022] Open
Abstract
The nucleolus is a subnuclear membraneless compartment intimately involved in ribosomal RNA synthesis, ribosome biogenesis and stress response. Multiple optogenetic devices have been developed to manipulate nuclear protein import and export, but molecular tools tailored for remote control over selective targeting or partitioning of cargo proteins into subnuclear compartments capable of phase separation are still limited. Here, we report a set of single-component photoinducible nucleolus-targeting tools, designated pNUTs, to enable rapid and reversible nucleoplasm-to-nucleolus shuttling, with the half-lives ranging from milliseconds to minutes. pNUTs allow both global protein infiltration into nucleoli and local delivery of cargoes into the outermost layer of the nucleolus, the granular component. When coupled with the amyotrophic lateral sclerosis (ALS)-associated C9ORF72 proline/arginine-rich dipeptide repeats, pNUTs allow us to photomanipulate poly-proline-arginine nucleolar localization, perturb nucleolar protein nucleophosmin 1 and suppress nascent protein synthesis. pNUTs thus expand the optogenetic toolbox by permitting light-controllable interrogation of nucleolar functions and precise induction of ALS-associated toxicity in cellular models.
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Affiliation(s)
- Peng Tan
- Center for Translational Cancer Research, Institute of Biosciences and Technology, Texas A&M University, Houston, TX 77030, USA
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Tingting Hong
- Center for Epigenetics and Disease Prevention, Institute of Biosciences and Technology, Texas A&M University, Houston, TX 77030, USA
| | - Xiaoli Cai
- Center for Epigenetics and Disease Prevention, Institute of Biosciences and Technology, Texas A&M University, Houston, TX 77030, USA
| | - Wenbo Li
- Department of Biochemistry and Molecular Biology, McGovern Medical School, University of Texas Health Science Center, Houston, TX 77030, USA
| | - Yun Huang
- Center for Epigenetics and Disease Prevention, Institute of Biosciences and Technology, Texas A&M University, Houston, TX 77030, USA
| | - Lian He
- Center for Translational Cancer Research, Institute of Biosciences and Technology, Texas A&M University, Houston, TX 77030, USA
| | - Yubin Zhou
- Center for Translational Cancer Research, Institute of Biosciences and Technology, Texas A&M University, Houston, TX 77030, USA
- Department of Translational Medical Sciences, College of Medicine, Texas A&M University, Houston, TX 77030, USA
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Abstract
The nucleolus is best known for housing the highly ordered assembly line that produces ribosomal subunits. The >100 ribosome assembly factors in the nucleolus are thought to cycle between two states: an operative state (when integrated into subunit assembly intermediates) and a latent state (upon release from intermediates). Although it has become commonplace to refer to the nucleolus as "being a multilayered condensate," and this may be accurate for latent factors, there is little reason to think that such assertions pertain to the operative state of assembly factors.
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Affiliation(s)
- Alan Tartakoff
- Case Western Reserve University, Cleveland, Ohio 44106, USA
| | - Patrick DiMario
- Louisiana State University, Baton Rouge, Louisiana 70803, USA
| | - Eduard Hurt
- Universität Heidelberg, Biochemistry Center, Heidelberg, Baden Württemberg 69120, Germany
| | - Brian McStay
- Centre for Chromosome Biology, Galway H91 TK33, Ireland
| | - Vikram Govind Panse
- Institute of Medical Microbiology, University of Zurich, Zurich CH-8057, Switzerland
| | - David Tollervey
- Wellcome Trust Centre for Cell Biology, Edinburgh EH9 3BF, United Kingdom
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Somashekara SC, Muniyappa K. Dual targeting of Saccharomyces cerevisiae Pso2 to mitochondria and the nucleus, and its functional relevance in the repair of DNA interstrand crosslinks. G3 (BETHESDA, MD.) 2022; 12:jkac066. [PMID: 35482533 PMCID: PMC9157068 DOI: 10.1093/g3journal/jkac066] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Accepted: 03/15/2022] [Indexed: 11/12/2022]
Abstract
Repair of DNA interstrand crosslinks involves a functional interplay among different DNA surveillance and repair pathways. Previous work has shown that interstrand crosslink-inducing agents cause damage to Saccharomyces cerevisiae nuclear and mitochondrial DNA, and its pso2/snm1 mutants exhibit a petite phenotype followed by loss of mitochondrial DNA integrity and copy number. Complex as it is, the cause and underlying molecular mechanisms remains elusive. Here, by combining a wide range of approaches with in vitro and in vivo analyses, we interrogated the subcellular localization and function of Pso2. We found evidence that the nuclear-encoded Pso2 contains 1 mitochondrial targeting sequence and 2 nuclear localization signals (NLS1 and NLS2), although NLS1 resides within the mitochondrial targeting sequence. Further analysis revealed that Pso2 is a dual-localized interstrand crosslink repair protein; it can be imported into both nucleus and mitochondria and that genotoxic agents enhance its abundance in the latter. While mitochondrial targeting sequence is essential for mitochondrial Pso2 import, either NLS1 or NLS2 is sufficient for its nuclear import; this implies that the 2 nuclear localization signal motifs are functionally redundant. Ablation of mitochondrial targeting sequence abrogated mitochondrial Pso2 import, and concomitantly, raised its levels in the nucleus. Strikingly, mutational disruption of both nuclear localization signal motifs blocked the nuclear Pso2 import; at the same time, they enhanced its translocation into the mitochondria, consistent with the notion that the relationship between mitochondrial targeting sequence and nuclear localization signal motifs is competitive. However, the nuclease activity of import-deficient species of Pso2 was not impaired. The potential relevance of dual targeting of Pso2 into 2 DNA-bearing organelles is discussed.
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Affiliation(s)
| | - Kalappa Muniyappa
- Department of Biochemistry, Indian Institute of Science, Bangalore 560 012, India
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28
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Cecchini NM, Torres JR, López IL, Cobo S, Nota F, Alvarez ME. Alternative splicing of an exitron determines the subnuclear localization of the Arabidopsis DNA glycosylase MBD4L under heat stress. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2022; 110:377-388. [PMID: 35061303 DOI: 10.1111/tpj.15675] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/09/2021] [Accepted: 01/15/2022] [Indexed: 06/14/2023]
Affiliation(s)
- Nicolás Miguel Cecchini
- Centro de Investigaciones en Química Biológica de Córdoba, CIQUIBIC, CONICET, Departamento de Química Biológica Ranwel Caputto, Facultad de Ciencias Químicas, Universidad Nacional de Córdoba, Haya de la Torre y Medina Allende, Ciudad Universitaria, Córdoba, Argentina
| | - José Roberto Torres
- Centro de Investigaciones en Química Biológica de Córdoba, CIQUIBIC, CONICET, Departamento de Química Biológica Ranwel Caputto, Facultad de Ciencias Químicas, Universidad Nacional de Córdoba, Haya de la Torre y Medina Allende, Ciudad Universitaria, Córdoba, Argentina
| | - Ignacio Lescano López
- Centro de Investigaciones en Química Biológica de Córdoba, CIQUIBIC, CONICET, Departamento de Química Biológica Ranwel Caputto, Facultad de Ciencias Químicas, Universidad Nacional de Córdoba, Haya de la Torre y Medina Allende, Ciudad Universitaria, Córdoba, Argentina
| | - Santiago Cobo
- Centro de Investigaciones en Química Biológica de Córdoba, CIQUIBIC, CONICET, Departamento de Química Biológica Ranwel Caputto, Facultad de Ciencias Químicas, Universidad Nacional de Córdoba, Haya de la Torre y Medina Allende, Ciudad Universitaria, Córdoba, Argentina
| | - Florencia Nota
- Centro de Investigaciones en Química Biológica de Córdoba, CIQUIBIC, CONICET, Departamento de Química Biológica Ranwel Caputto, Facultad de Ciencias Químicas, Universidad Nacional de Córdoba, Haya de la Torre y Medina Allende, Ciudad Universitaria, Córdoba, Argentina
| | - María Elena Alvarez
- Centro de Investigaciones en Química Biológica de Córdoba, CIQUIBIC, CONICET, Departamento de Química Biológica Ranwel Caputto, Facultad de Ciencias Químicas, Universidad Nacional de Córdoba, Haya de la Torre y Medina Allende, Ciudad Universitaria, Córdoba, Argentina
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29
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Abstract
In eukaryotic cells, protein and RNA factors involved in genome activities like transcription, RNA processing, DNA replication, and repair accumulate in self-organizing membraneless chromatin subcompartments. These structures contribute to efficiently conduct chromatin-mediated reactions and to establish specific cellular programs. However, the underlying mechanisms for their formation are only partly understood. Recent studies invoke liquid-liquid phase separation (LLPS) of proteins and RNAs in the establishment of chromatin activity patterns. At the same time, the folding of chromatin in the nucleus can drive genome partitioning into spatially distinct domains. Here, the interplay between chromatin organization, chromatin binding, and LLPS is discussed by comparing and contrasting three prototypical chromatin subcompartments: the nucleolus, clusters of active RNA polymerase II, and pericentric heterochromatin domains. It is discussed how the different ways of chromatin compartmentalization are linked to transcription regulation, the targeting of soluble factors to certain parts of the genome, and to disease-causing genetic aberrations.
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Affiliation(s)
- Karsten Rippe
- Division of Chromatin Networks, German Cancer Research Center (DKFZ) and Bioquant, 69120 Heidelberg, Germany
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30
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Cerrato CP, Langel Ü. An update on cell-penetrating peptides with intracellular organelle targeting. Expert Opin Drug Deliv 2022; 19:133-146. [PMID: 35086398 DOI: 10.1080/17425247.2022.2034784] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
INTRODUCTION Cell-penetrating peptide (CPP) technologies represent an important strategy to address drug delivery to specific intracellular compartments by covalent conjugation to targeting sequences, potentially enabling strategies to combat most diseases. AREAS COVERED This updated review article provides an overview of current intracellular organelle targeting by CPP. The targeting strategies of CPP and CPP/cargo complexes to specific cells or intracellular organelles are summarized, and the review provides an update on the current data for their pharmacological and therapeutical applications. EXPERT OPINION Targeted drug delivery is moving from the level of tissue or specific pathogenic cell to the level of specific organelle that is the target of the drug, an important aspect in drug design and development. Organelle-targeted drug delivery results in improved efficacy, ability to control mode of action, reduction of undesired toxicities and side effects, and possibility to overcome drug resistance mechanisms.
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Affiliation(s)
| | - Ülo Langel
- Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden.,Laboratory of Molecular Biotechnology, Institute of Technology, University of Tartu, Tartu, Estonia
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31
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Hidaka C, Soda K, Ito T, Ito H. Contribution of mutation I142M in fusion protein and Q44R in matrix protein of Newcastle disease virus to virulence in ducks. J Vet Med Sci 2021; 84:121-128. [PMID: 34853197 PMCID: PMC8810335 DOI: 10.1292/jvms.21-0527] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Although verogenic Newcastle disease viruses (NDVs) generally cause subclinical infection in waterfowls such as ducks, NDVs with high virulence in waterfowl have been sporadically reported.
We previously reported that the NDV d5a20b strain, which is obtained by serial passaging of the velogenic 9a5b strain in domestic ducks, showed increased virulence in ducks (Hidaka
et al., 2021). The d5a20b strain had 11 amino acid substitutions in its P/V, M, F, HN, and L proteins as compared to 9a5b. In the present study, we generated a series of
recombinant (r) NDVs with these amino acid substitutions to identify the molecular basis of virulence of NDV in ducks, and evaluated their influences on virulence and in
vitro viral properties. Each of the single amino acid substitutions in either the F protein I142M or the M protein Q44R contributed to the enhancement of intracerebral and
intranasal pathogenicity in domestic ducks. The cell-cell fusion activity of the virus with F I142M was five times higher than that of the parental r9a5b. The virus with M Q44R rapidly
replicated in duck embryo fibroblasts. Additionally, the rM+F+HN strain, which has the same amino acid sequences as d5a20b in M, F, and HN proteins, showed the highest level of virulence and
replication efficiency among the generated recombinant viruses, nearly comparable to rd5a20b. These results suggest that multiple factors are involved in the high growth ability of NDV in
duck cells, leading to increased virulence in vivo.
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Affiliation(s)
- Chiharu Hidaka
- Joint Department of Veterinary Medicine, Faculty of Agriculture, Tottori University.,The United Graduate School of Veterinary Science, Yamaguchi University
| | - Kosuke Soda
- Joint Department of Veterinary Medicine, Faculty of Agriculture, Tottori University.,The United Graduate School of Veterinary Science, Yamaguchi University.,Avian Zoonosis Research Center, Faculty of Agriculture, Tottori University
| | - Toshihiro Ito
- Joint Department of Veterinary Medicine, Faculty of Agriculture, Tottori University.,The United Graduate School of Veterinary Science, Yamaguchi University.,Avian Zoonosis Research Center, Faculty of Agriculture, Tottori University
| | - Hiroshi Ito
- Joint Department of Veterinary Medicine, Faculty of Agriculture, Tottori University.,The United Graduate School of Veterinary Science, Yamaguchi University.,Avian Zoonosis Research Center, Faculty of Agriculture, Tottori University
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32
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Rashid FZM, Mahlandt E, van der Vaart M, Boer DEC, Varela Alvarez M, Henneman B, Brocken DJW, Voskamp P, Blok A, Shimizu T, Meijer A, Luijsterburg M, Goedhart J, Crémazy FGE, Dame R. HI-NESS: a family of genetically encoded DNA labels based on a bacterial nucleoid-associated protein. Nucleic Acids Res 2021; 50:e10. [PMID: 34734265 PMCID: PMC8789088 DOI: 10.1093/nar/gkab993] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2020] [Revised: 10/06/2021] [Accepted: 10/08/2021] [Indexed: 02/02/2023] Open
Abstract
The interplay between three-dimensional chromosome organisation and genomic processes such as replication and transcription necessitates in vivo studies of chromosome dynamics. Fluorescent organic dyes are often used for chromosome labelling in vivo. The mode of binding of these dyes to DNA cause its distortion, elongation, and partial unwinding. The structural changes induce DNA damage and interfere with the binding dynamics of chromatin-associated proteins, consequently perturbing gene expression, genome replication, and cell cycle progression. We have developed a minimally-perturbing, genetically encoded fluorescent DNA label consisting of a (photo-switchable) fluorescent protein fused to the DNA-binding domain of H-NS — a bacterial nucleoid-associated protein. We show that this DNA label, abbreviated as HI-NESS (H-NS-based indicator for nucleic acid stainings), is minimally-perturbing to genomic processes and labels chromosomes in eukaryotic cells in culture, and in zebrafish embryos with preferential binding to AT-rich chromatin.
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Affiliation(s)
- Fatema-Zahra M Rashid
- Macromolecular Biochemistry, Leiden Institute of Chemistry, Leiden University, Leiden 2333CC, The Netherlands
- Centre for Microbial Cell Biology, Leiden University, Leiden, The Netherlands
| | - Eike Mahlandt
- Molecular Cytology, Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam 1098XH, The Netherlands
| | - Michiel van der Vaart
- Animal Sciences, Institute of Biology Leiden, Leiden University, Leiden 2333CC, The Netherlands
| | - Daphne E C Boer
- Department of Human Genetics, Leiden University Medical Center, Leiden 2333ZC, The Netherlands
| | - Monica Varela Alvarez
- Animal Sciences, Institute of Biology Leiden, Leiden University, Leiden 2333CC, The Netherlands
| | - Bram Henneman
- Macromolecular Biochemistry, Leiden Institute of Chemistry, Leiden University, Leiden 2333CC, The Netherlands
| | - Daan J W Brocken
- Macromolecular Biochemistry, Leiden Institute of Chemistry, Leiden University, Leiden 2333CC, The Netherlands
| | - Patrick Voskamp
- Biophysical Structural Chemistry, Leiden Institute of Chemistry, Leiden University, Leiden 2333CC, The Netherlands
| | - Anneloes J Blok
- Macromolecular Biochemistry, Leiden Institute of Chemistry, Leiden University, Leiden 2333CC, The Netherlands
| | - Thomas S Shimizu
- Systems Biology, AMOLF Institute, Amsterdam 1098XG, The Netherlands
| | - Annemarie H Meijer
- Animal Sciences, Institute of Biology Leiden, Leiden University, Leiden 2333CC, The Netherlands
| | - Martijn S Luijsterburg
- Department of Human Genetics, Leiden University Medical Center, Leiden 2333ZC, The Netherlands
| | - Joachim Goedhart
- Molecular Cytology, Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam 1098XH, The Netherlands
| | - Frédéric G E Crémazy
- Macromolecular Biochemistry, Leiden Institute of Chemistry, Leiden University, Leiden 2333CC, The Netherlands
| | - Remus T Dame
- To whom correspondence should be addressed. Tel: +31 71 527 5605;
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Molecular coevolution of nuclear and nucleolar localization signals inside basic domain of HIV-1 Tat. J Virol 2021; 96:e0150521. [PMID: 34613791 DOI: 10.1128/jvi.01505-21] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
During evolution, viruses had to adapt to an increasingly complex environment of eukaryotic cells. Viral proteins that need to enter the cell nucleus or associate with nucleoli possess nuclear localization signals (NLSs) and nucleolar localization signals (NoLSs) for nuclear and nucleolar accumulation, respectively. As viral proteins are relatively small, acquisition of novel sequences seems to be a more complicated task for viruses than for eukaryotes. Here, we carried out a comprehensive analysis of the basic domain (BD) of HIV-1 Tat to show how viral proteins might evolve with NLSs and NoLSs without an increase in protein size. The HIV-1 Tat BD is involved in several functions, the most important being the transactivation of viral transcription. The BD also functions as an NLS, although it is substantially longer than a typical NLS. It seems that different regions in the BD could function as NLSs due to its enrichment with positively charged amino acids. Additionally, the high positive net charge inevitably causes the BD to function as an NoLS through a charge-specific mechanism. The integration of NLSs and NoLSs into functional domains enriched with positively charged amino acids might be a mechanism that allows the condensation of different functional sequences in small protein regions and, as a result, to reduce protein size, influencing the origin and evolution of NLSs and NoLSs in viruses. IMPORTANCE Here, we investigated the molecular mechanism of NLS and NoLS integration into the basic domain of HIV-1 Tat (49RKKRRQRRR57), and found that these two supplementary functions (i.e., function of NLS and NoLS) are embedded in the basic domain amino acid sequence. The integration of NLSs and NoLSs into functional domains of viral proteins enriched with positively charged amino acids is a mechanism that allows the concentration of different functions within small protein regions. Integration of NLS and NoLS into functional protein domains might have influenced the viral evolution, as this could prevent an increase in the protein size.
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34
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Du Y, Chen Z, Yan P, Zhang C, Duan X, Chen X, Liu M, Kang L, Yang X, Fan Y, Zhang J, Wang R. Arginine-Arginine-Leucine Peptide Targeting Heat Shock Protein 70 for Cancer Imaging. Mol Pharm 2021; 18:3750-3762. [PMID: 34491767 DOI: 10.1021/acs.molpharmaceut.1c00273] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Arg-Arg-Leu (RRL) is a potent tumor-homing tripeptide. However, the binding target is unclear. In this study, we intended to identify the binding target of RRL and evaluate the tumor targeting of 99mTc-MAG3-RRL in vivo. Biotin-RRL, 5-TAMRA-RRL, and 99mTc-MAG3-RRL were designed to trace the binding target and tumor lesion. Immunoprecipitation-mass spectrometry was conducted to identify the candidate proteins and determination of the subcellular localization was also performed. A pull-down assay was performed to demonstrate the immunoprecipitate. Fluorescence colocalization and cell uptake assays were performed to elucidate the correlation between the selected binding protein and RRL, and the internalization mechanism of RRL. Biodistribution and in vivo imaging were performed to evaluate the tumor accumulation and targeting of 99mTc-MAG3-RRL. The target for RRL was screened to be heat shock protein 70 (HSP70). The prominent uptake distribution of RRL was concentrated in the membrane and cytoplasm. A pull-down assay demonstrated the existence of HSP70 in the biotin-RRL captured complex. Regarding fluorescence colocalization and cell uptake assays, RRL may interact with HSP70 at the nucleotide-binding domain (NBD). Clathrin-dependent endocytosis and macropinocytosis could be a vital internalization mechanism of RRL. In vivo imaging and biodistribution both demonstrated that 99mTc-MAG3-RRL can trace tumors with satisfactory accumulation in hepatoma xenograft mice. The radioactive signals accumulated in tumor lesions can be blocked by VER-155008, which can bind to the NBD of HSP70. Our findings revealed that RRL may interact with HSP70 and that 99mTc-MAG3-RRL could be a prospective probe for visualizing overexpressed HSP70 tumor sections.
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Affiliation(s)
- Yujing Du
- Department of Nuclear Medicine, Peking University First Hospital, Beijing 100034, China
| | - Zhao Chen
- Department of Nuclear Medicine, Peking University First Hospital, Beijing 100034, China
| | - Ping Yan
- Department of Nuclear Medicine, Peking University First Hospital, Beijing 100034, China
| | - Chunli Zhang
- Department of Nuclear Medicine, Peking University First Hospital, Beijing 100034, China
| | - Xiaojiang Duan
- Department of Nuclear Medicine, Peking University First Hospital, Beijing 100034, China
| | - Xueqi Chen
- Department of Nuclear Medicine, Peking University First Hospital, Beijing 100034, China
| | - Meng Liu
- Department of Nuclear Medicine, Peking University First Hospital, Beijing 100034, China
| | - Lei Kang
- Department of Nuclear Medicine, Peking University First Hospital, Beijing 100034, China
| | - Xing Yang
- Department of Nuclear Medicine, Peking University First Hospital, Beijing 100034, China
| | - Yan Fan
- Department of Nuclear Medicine, Peking University First Hospital, Beijing 100034, China
| | - Jianhua Zhang
- Department of Nuclear Medicine, Peking University First Hospital, Beijing 100034, China
| | - Rongfu Wang
- Department of Nuclear Medicine, Peking University First Hospital, Beijing 100034, China.,Department of Nuclear Medicine, Peking University International Hospital, Beijing 102206, China
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35
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Ákos Z, Dunipace L, Stathopoulos A. NaNuTrap: a technique for in vivo cell nucleus labelling using nanobodies. Development 2021; 148:dev199822. [PMID: 34328170 PMCID: PMC10656463 DOI: 10.1242/dev.199822] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2021] [Accepted: 07/12/2021] [Indexed: 11/20/2022]
Abstract
In vivo cell labelling is challenging in fast developmental processes because many cell types differentiate more quickly than the maturation time of fluorescent proteins, making visualization of these tissues impossible with standard techniques. Here, we present a nanobody-based method, Nanobody Nuclear Trap (NaNuTrap), which works with the existing Gal4/UAS system in Drosophila and allows for early in vivo cell nuclei labelling independently of the maturation time of the fluorescent protein. This restores the utility of fluorescent proteins that have longer maturation times, such as those used in two-photon imaging, for live imaging of fast or very early developmental processes. We also present a more general application of this system, whereby NaNuTrap can convert cytoplasmic GFP expressed in any existing transgenic fly line into a nuclear label. This nuclear re-localization of the fluorescent signal can improve the utility of the GFP label, e.g. in cell counting, as well as resulting in a general increase in intensity of the live fluorescent signal. We demonstrate these capabilities of NaNuTrap by effectively tracking subsets of cells during the fast movements associated with gastrulation.
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Affiliation(s)
- Zsuzsa Ákos
- California Institute of Technology, 1200 East California Blvd, Pasadena, CA 91125, USA
| | - Leslie Dunipace
- California Institute of Technology, 1200 East California Blvd, Pasadena, CA 91125, USA
| | - Angelike Stathopoulos
- California Institute of Technology, 1200 East California Blvd, Pasadena, CA 91125, USA
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36
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Rodríguez-Fernández L, Company S, Zaragozá R, Viña JR, García-Trevijano ER. Cleavage and activation of LIM kinase 1 as a novel mechanism for calpain 2-mediated regulation of nuclear dynamics. Sci Rep 2021; 11:16339. [PMID: 34381117 PMCID: PMC8358030 DOI: 10.1038/s41598-021-95797-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2021] [Accepted: 07/30/2021] [Indexed: 12/26/2022] Open
Abstract
Calpain-2 (CAPN2) is a processing enzyme ubiquitously expressed in mammalian tissues whose pleiotropic functions depend on the role played by its cleaved-products. Nuclear interaction networks, crucial for a number of molecular processes, could be modified by CAPN2 activity. However, CAPN2 functions in cell nucleus are poorly understood. To unveil CAPN2 functions in this compartment, the result of CAPN2-mediated interactions in cell nuclei was studied in breast cancer cell (BCC) lines. CAPN2 abundance was found to be determinant for its nucleolar localization during interphase. Those CAPN2-dependent components of nucleolar proteome, including the actin-severing protein cofilin-1 (CFL1), were identified by proteomic approaches. CAPN2 binding, cleavage and activation of LIM Kinase-1 (LIMK1), followed by CFL1 phosphorylation was studied. Upon CAPN2-depletion, full-length LIMK1 levels increased and CFL1/LIMK1 binding was inhibited. In addition, LIMK1 accumulated at the cell periphery and perinucleolar region and, the mitosis-specific increase of CFL1 phosphorylation and localization was altered, leading to aberrant mitosis and cell multinucleation. These findings uncover a mechanism for the role of CAPN2 during mitosis, unveil the critical role of CAPN2 in the interactions among nuclear components and, identifying LIMK1 as a new CAPN2-target, provide a novel mechanism for LIMK1 activation. CFL1 is crucial for cytoskeleton remodeling and mitosis, but also for the maintenance of nuclear structure, the movement of chromosomes and the modulation of transcription frequently altered in cancer cells. Consequently, the role of CAPN2 in the nuclear compartment might be extended to other actin-associated biological and pathological processes.
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Affiliation(s)
- L Rodríguez-Fernández
- Departamento de Bioquímica y Biología Molecular, Facultad de Medicina, Universidad de Valencia, Avda. Blasco Ibañez, 15, 46010, Valencia, Spain
| | - S Company
- Departamento de Bioquímica y Biología Molecular, Facultad de Medicina, Universidad de Valencia, Avda. Blasco Ibañez, 15, 46010, Valencia, Spain
| | - R Zaragozá
- Fundación Investigación Hospital Clínico-INCLIVA, Valencia, Spain.,Departamento de Anatomía y Embriología Humana, Facultad de Medicina, Universidad de Valencia, Valencia, Spain
| | - J R Viña
- Departamento de Bioquímica y Biología Molecular, Facultad de Medicina, Universidad de Valencia, Avda. Blasco Ibañez, 15, 46010, Valencia, Spain.,Fundación Investigación Hospital Clínico-INCLIVA, Valencia, Spain
| | - E R García-Trevijano
- Departamento de Bioquímica y Biología Molecular, Facultad de Medicina, Universidad de Valencia, Avda. Blasco Ibañez, 15, 46010, Valencia, Spain. .,Fundación Investigación Hospital Clínico-INCLIVA, Valencia, Spain.
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37
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Pochechuev MS, Lanin AA, Kelmanson IV, Chebotarev AS, Fetisova ES, Bilan DS, Shevchenko EK, Ivanov AA, Fedotov AB, Belousov VV, Zheltikov AM. Multimodal nonlinear-optical imaging of nucleoli. OPTICS LETTERS 2021; 46:3608-3611. [PMID: 34329236 DOI: 10.1364/ol.416300] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Accepted: 02/12/2021] [Indexed: 06/13/2023]
Abstract
Multimodal nonlinear microscopy combining third-harmonic generation (THG) with two- and three-photon-excited fluorescence (2PEF and 3PEF) is shown to provide a powerful resource for high-fidelity imaging of nucleoli and nucleolar proteins. We demonstrate that, with a suitably tailored genetically encoded fluorescent stain, the 2PEF/3PEF readout from specific nucleolar proteins can be reliably detected against the extranucleolar 2PEF/3PEF signal, enabling high-contrast imaging of the key nucleolar ribosome biogenesis components, such as fibrillarin. THG is shown to provide a versatile readout for unstained nucleolus imaging in a vast class of biological systems as different as neurons in brain slices and cultured HeLa cells.
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38
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Iarovaia OV, Ioudinkova ES, Velichko AK, Razin SV. Manipulation of Cellular Processes via Nucleolus Hijaking in the Course of Viral Infection in Mammals. Cells 2021; 10:cells10071597. [PMID: 34202380 PMCID: PMC8303250 DOI: 10.3390/cells10071597] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2021] [Revised: 06/22/2021] [Accepted: 06/23/2021] [Indexed: 12/16/2022] Open
Abstract
Due to their exceptional simplicity of organization, viruses rely on the resources, molecular mechanisms, macromolecular complexes, regulatory pathways, and functional compartments of the host cell for an effective infection process. The nucleolus plays an important role in the process of interaction between the virus and the infected cell. The interactions of viral proteins and nucleic acids with the nucleolus during the infection process are universal phenomena and have been described for almost all taxonomic groups. During infection, proteins of the nucleolus in association with viral components can be directly used for the processes of replication and transcription of viral nucleic acids and the assembly and transport of viral particles. In the course of a viral infection, the usurpation of the nucleolus functions occurs and the usurpation is accompanied by profound changes in ribosome biogenesis. Recent studies have demonstrated that the nucleolus is a multifunctional and dynamic compartment. In addition to the biogenesis of ribosomes, it is involved in regulating the cell cycle and apoptosis, responding to cellular stress, repairing DNA, and transcribing RNA polymerase II-dependent genes. A viral infection can be accompanied by targeted transport of viral proteins to the nucleolus, massive release of resident proteins of the nucleolus into the nucleoplasm and cytoplasm, the movement of non-nucleolar proteins into the nucleolar compartment, and the temporary localization of viral nucleic acids in the nucleolus. The interaction of viral and nucleolar proteins interferes with canonical and non-canonical functions of the nucleolus and results in a change in the physiology of the host cell: cell cycle arrest, intensification or arrest of ribosome biogenesis, induction or inhibition of apoptosis, and the modification of signaling cascades involved in the stress response. The nucleolus is, therefore, an important target during viral infection. In this review, we discuss the functional impact of viral proteins and nucleic acid interaction with the nucleolus during infection.
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39
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Zarębski M, Bosire R, Wesołowska J, Szelest O, Eatmann A, Jasińska-Konior K, Kepp O, Kroemer G, Szabo G, Dobrucki JW. Translocation of chromatin proteins to nucleoli-The influence of protein dynamics on post-fixation localization. Cytometry A 2021; 99:1230-1239. [PMID: 34110091 PMCID: PMC9543561 DOI: 10.1002/cyto.a.24464] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2021] [Revised: 05/16/2021] [Accepted: 05/19/2021] [Indexed: 11/23/2022]
Abstract
It is expected that the subnuclear localization of a protein in a fixed cell, detected by microscopy, reflects its position in the living cell. We demonstrate, however, that some dynamic nuclear proteins can change their localization upon fixation by either crosslinking or non‐crosslinking methods. We examined the subnuclear localization of the chromatin architectural protein HMGB1, linker histone H1, and core histone H2B in cells fixed by formaldehyde, glutaraldehyde, glyoxal, ethanol, or zinc salts. We demonstrate that some dynamic, weakly binding nuclear proteins, like HMGB1 and H1, may not only be unexpectedly lost from their original binding sites during the fixation process, but they can also diffuse through the nucleus and eventually bind in nucleoli. Such translocation to nucleoli does not occur in the case of core histone H2B, which is more stably bound to DNA and other histones. We suggest that the diminished binding of some dynamic proteins to DNA during fixation, and their subsequent translocation to nucleoli, is induced by changes of DNA structure, arising from interaction with a fixative. Detachment of dynamic proteins from chromatin can also be induced in cells already fixed by non‐crosslinking methods when DNA structure is distorted by intercalating molecules. The proteins translocated during fixation from chromatin to nucleoli bind there to RNA‐containing structures.
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Affiliation(s)
- Mirosław Zarębski
- Department of Cell Biophysics, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University in Kraków, Poland
| | - Rosevalentine Bosire
- Department of Biophysics and Cell Biology, Faculty of Medicine, University of Debrecen, Debrecen, Hungary.,Doctoral School of Molecular Cell and Immune Biology, University of Debrecen, Debrecen, Hungary
| | - Julita Wesołowska
- Department of Cell Biophysics, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University in Kraków, Poland
| | - Oskar Szelest
- Department of Cell Biophysics, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University in Kraków, Poland
| | - Ahmed Eatmann
- Department of Cell Biophysics, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University in Kraków, Poland
| | - Katarzyna Jasińska-Konior
- Department of Cell Biophysics, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University in Kraków, Poland
| | - Oliver Kepp
- Centre de Recherche des Cordeliers, Equipe labellisée par la Ligue contre le cancer, Université de Paris, Sorbonne Université, Paris, France.,Metabolomics and Cell Biology Platforms, Institut Gustave Roussy, Villejuif, France
| | - Guido Kroemer
- Centre de Recherche des Cordeliers, Equipe labellisée par la Ligue contre le cancer, Université de Paris, Sorbonne Université, Paris, France.,Metabolomics and Cell Biology Platforms, Institut Gustave Roussy, Villejuif, France.,Pôle de Biologie, Hôpital Européen Georges Pompidou, Paris, AP-HP, France.,Suzhou Institute for Systems Medicine, Chinese Academy of Medical Sciences, Suzhou, China.,Karolinska Institute, Department of Women's and Children's Health, Karolinska University Hospital, Stockholm, Sweden
| | - Gabor Szabo
- Department of Biophysics and Cell Biology, Faculty of Medicine, University of Debrecen, Debrecen, Hungary
| | - Jurek W Dobrucki
- Department of Cell Biophysics, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University in Kraków, Poland
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40
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Sapio RT, Burns CJ, Pestov DG. Effects of Hydrogen Peroxide Stress on the Nucleolar Redox Environment and Pre-rRNA Maturation. Front Mol Biosci 2021; 8:678488. [PMID: 33981726 PMCID: PMC8107432 DOI: 10.3389/fmolb.2021.678488] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2021] [Accepted: 04/06/2021] [Indexed: 12/16/2022] Open
Abstract
Identifying biologically relevant molecular targets of oxidative stress may provide new insights into disease mechanisms and accelerate development of novel biomarkers. Ribosome biogenesis is a fundamental prerequisite for cellular protein synthesis, but how oxidative stress affects ribosome biogenesis has not been clearly established. To monitor and control the redox environment of ribosome biogenesis, we targeted a redox-sensitive roGFP reporter and catalase, a highly efficient H2O2 scavenger, to the nucleolus, the primary site for transcription and processing of rRNA in eukaryotic cells. Imaging of mouse 3T3 cells exposed to non-cytotoxic H2O2 concentrations revealed increased oxidation of the nucleolar environment accompanied by a detectable increase in the oxidative damage marker 8-oxo-G in nucleolar RNA. Analysis of pre-rRNA processing showed a complex pattern of alterations in pre-rRNA maturation in the presence of H2O2, including inhibition of the transcription and processing of the primary 47S transcript, accumulation of 18S precursors, and inefficient 3'-end processing of 5.8S rRNA. This work introduces new tools for studies of the redox biology of the mammalian nucleolus and identifies pre-rRNA maturation steps sensitive to H2O2 stress.
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Affiliation(s)
- Russell T Sapio
- Graduate School of Biomedical Sciences, Rowan University School of Osteopathic Medicine, Stratford, NJ, United States.,Department of Cell Biology and Neuroscience, Rowan University School of Osteopathic Medicine, Stratford, NJ, United States
| | - Chelsea J Burns
- Graduate School of Biomedical Sciences, Rowan University School of Osteopathic Medicine, Stratford, NJ, United States
| | - Dimitri G Pestov
- Department of Cell Biology and Neuroscience, Rowan University School of Osteopathic Medicine, Stratford, NJ, United States
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41
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Law ASY, Lee LCC, Lo KKW, Yam VWW. Aggregation and Supramolecular Self-Assembly of Low-Energy Red Luminescent Alkynylplatinum(II) Complexes for RNA Detection, Nucleolus Imaging, and RNA Synthesis Inhibitor Screening. J Am Chem Soc 2021; 143:5396-5405. [PMID: 33813827 DOI: 10.1021/jacs.0c13327] [Citation(s) in RCA: 42] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
As an important nuclear substructure, the nucleolus has received increasing attention because of its significant functions in the transcription and processing of ribosomal RNA in eukaryotic cells. In this work, we introduce a proof-of-concept luminescence assay to detect RNA and to accomplish nucleolus imaging with the use of the supramolecular self-assembly of platinum(II) complexes. Noncovalent interactions between platinum(II) complexes and RNA can be induced by the introduction of a guanidinium group into the complexes, and accordingly, a high RNA affinity can be achieved. Interestingly, the aggregation affinities of platinum(II) complexes enable them to display remarkable luminescence turn-on upon RNA binding, which is a result of the strengthening of noncovalent Pt(II)···Pt(II) and π-π stacking interactions. The complexes exhibit not only intriguing spectroscopic changes and luminescence enhancement after RNA binding but also specific nucleolus imaging in cells. As compared to fluorescent dyes, the low-energy red luminescence and large Stokes shifts of platinum(II) complexes afford a high signal-to-background autofluorescence ratio in nucleolus imaging. Additional properties, including long phosphorescence lifetimes and low cytotoxicity, have endowed the platinum(II) complexes with the potential for biological applications. Also, platinum(II) complexes have been adopted to monitor the dynamics of the nucleolus induced by the addition of RNA synthesis inhibitors. This capability allows the screening of inhibitors and can be advantageous for the development of antineoplastic agents. This work provides a novel strategy for exploring the application of platinum(II) complex-based cell imaging agents based on the mechanism of supramolecular self-assembly. It is envisaged that platinum(II) complexes can be utilized as valuable probes because of the aforementioned appealing advantages.
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Affiliation(s)
- Angela Sin-Yee Law
- Institute of Molecular Functional Materials, State Key Laboratory of Synthetic Chemistry and Department of Chemistry, The University of Hong Kong, Pokfulam Road, Hong Kong, People's Republic of China
| | - Lawrence Cho-Cheung Lee
- Department of Chemistry, City University of Hong Kong, Tat Chee Avenue, Kowloon, Hong Kong, People's Republic of China
| | - Kenneth Kam-Wing Lo
- Department of Chemistry, City University of Hong Kong, Tat Chee Avenue, Kowloon, Hong Kong, People's Republic of China
| | - Vivian Wing-Wah Yam
- Institute of Molecular Functional Materials, State Key Laboratory of Synthetic Chemistry and Department of Chemistry, The University of Hong Kong, Pokfulam Road, Hong Kong, People's Republic of China
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42
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Rothmund-Thomson Syndrome-Like RECQL4 Truncating Mutations Cause a Haploinsufficient Low-Bone-Mass Phenotype in Mice. Mol Cell Biol 2021; 41:e0059020. [PMID: 33361189 PMCID: PMC8088275 DOI: 10.1128/mcb.00590-20] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Rothmund-Thomson syndrome (RTS) is an autosomal recessive disorder characterized by defects in the skeletal system, such as bone hypoplasia, short stature, low bone mass, and an increased incidence of osteosarcoma. RTS type 2 patients have germ line compound biallelic protein-truncating mutations of RECQL4. As existing murine models employ Recql4 null alleles, we have attempted to more accurately model RTS by generating mice with patient-mimicking truncating Recql4 mutations. Truncating mutations impaired the stability and subcellular localization of RECQL4 and resulted in homozygous embryonic lethality and a haploinsufficient low-bone mass phenotype. Combination of a truncating mutation with a conditional Recql4 null allele demonstrated that the skeletal defects were intrinsic to the osteoblast lineage. However, the truncating mutations did not promote tumorigenesis. We utilized murine Recql4 null cells to assess the impact of human RECQL4 mutations using an in vitro complementation assay. While some mutations created unstable protein products, others altered subcellular localization of the protein. Interestingly, the severity of the phenotypes correlated with the extent of protein truncation. Collectively, our results reveal that truncating RECQL4 mutations in mice lead to an osteoporosis-like phenotype through defects in early osteoblast progenitors and identify RECQL4 gene dosage as a novel regulator of bone mass.
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43
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Garcia J, Fernández‐Pradas JM, Lladó A, Serra P, Zalvidea D, Kogan MJ, Giralt E, Sánchez‐Navarro M. The Combined Use of Gold Nanoparticles and Infrared Radiation Enables Cytosolic Protein Delivery. Chemistry 2021; 27:4670-4675. [DOI: 10.1002/chem.202005000] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2020] [Indexed: 12/16/2022]
Affiliation(s)
- Josep Garcia
- Institute for Research in Biomedicine Barcelona Institute of, Science and Technology Baldiri Reixac 10 08028 Barcelona Spain
| | - J. Marcos Fernández‐Pradas
- Department of Applied Physics University of Barcelona Martí i Franquès 1 08028 Barcelona Spain
- Institute of Nanoscience and Nanotechnology (IN2UB) University of Barcelona Av. Diagonal 645 08028 Barcelona Spain
| | - Anna Lladó
- Institute for Research in Biomedicine Barcelona Institute of, Science and Technology Baldiri Reixac 10 08028 Barcelona Spain
| | - Pere Serra
- Department of Applied Physics University of Barcelona Martí i Franquès 1 08028 Barcelona Spain
- Institute of Nanoscience and Nanotechnology (IN2UB) University of Barcelona Av. Diagonal 645 08028 Barcelona Spain
| | - Dobryna Zalvidea
- Institute for Bioengineering of Catalonia (IBEC) Barcelona Institute of Technology (BIST) Barcelona Spain
| | - Marcelo J. Kogan
- Departamento de Química Farmacológica y Toxicológica Facultad de Ciencias Químicas y Farmacéuticas Universidad de Chile Santiago Chile
- Advanced Center for Chronic Diseases (ACCDiS) Sergio Livingstone 1007, Independencia Santiago Chile
| | - Ernest Giralt
- Institute for Research in Biomedicine Barcelona Institute of, Science and Technology Baldiri Reixac 10 08028 Barcelona Spain
- Department of Inorganic and Organic Chemistry University of Barcelona Martí i Franquès 1–11 08028 Barcelona Spain
| | - Macarena Sánchez‐Navarro
- Institute for Research in Biomedicine Barcelona Institute of, Science and Technology Baldiri Reixac 10 08028 Barcelona Spain
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44
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Anson F, Kanjilal P, Thayumanavan S, Hardy JA. Tracking exogenous intracellular casp-3 using split GFP. Protein Sci 2021; 30:366-380. [PMID: 33165988 PMCID: PMC7784757 DOI: 10.1002/pro.3992] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2020] [Revised: 09/28/2020] [Accepted: 11/03/2020] [Indexed: 11/08/2022]
Abstract
Cytosolic protein delivery promises diverse applications from therapeutics, to genetic modification and precision research tools. To achieve effective cellular and subcellular delivery, approaches that allow protein visualization and accurate localization with greater sensitivity are essential. Fluorescently tagging proteins allows detection, tracking and visualization in cellulo. However, undesired consequences from fluorophores or fluorescent protein tags, such as nonspecific interactions and high background or perturbation to native protein's size and structure, are frequently observed, or more troublingly, overlooked. Distinguishing cytosolically released molecules from those that are endosomally entrapped upon cellular uptake is particularly challenging and is often complicated by the inherent pH-sensitive and hydrophobic properties of the fluorophore. Monitoring localization is more complex in delivery of proteins with inherent protein-modifying activities like proteases, transacetylases, kinases, etc. Proteases are among the toughest cargos due to their inherent propensity for self-proteolysis. To implement a reliable, but functionally silent, tagging technology in a protease, we have developed a caspase-3 variant tagged with the 11th strand of GFP that retains both enzymatic activity and structural characteristics of wild-type caspase-3. Only in the presence of cytosolic GFP strands 1-10 will the tagged caspase-3 generate fluorescence to signal a non-endosomal location. This methodology facilitates easy screening of cytosolic vs. endosomally-entrapped proteins due to low probabilities for false positive results, and further, allows tracking of the resultant cargo's translocation. The development of this tagged casp-3 cytosolic reporter lays the foundation to probe caspase therapeutic properties, charge-property relationships governing successful escape, and the precise number of caspases required for apoptotic cell death.
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Affiliation(s)
- Francesca Anson
- Department of ChemistryUniversity of MassachusettsAmherstMassachusettsUSA
| | - Pintu Kanjilal
- Department of ChemistryUniversity of MassachusettsAmherstMassachusettsUSA
| | - S. Thayumanavan
- Department of ChemistryUniversity of MassachusettsAmherstMassachusettsUSA
- The Center for Bioactive Delivery at the Institute for Applied Life SciencesUniversity of MassachusettsAmherstMassachusettsUSA
| | - Jeanne A. Hardy
- Department of ChemistryUniversity of MassachusettsAmherstMassachusettsUSA
- The Center for Bioactive Delivery at the Institute for Applied Life SciencesUniversity of MassachusettsAmherstMassachusettsUSA
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45
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Tycko J, DelRosso N, Hess GT, Aradhana, Banerjee A, Mukund A, Van MV, Ego BK, Yao D, Spees K, Suzuki P, Marinov GK, Kundaje A, Bassik MC, Bintu L. High-Throughput Discovery and Characterization of Human Transcriptional Effectors. Cell 2020; 183:2020-2035.e16. [PMID: 33326746 PMCID: PMC8178797 DOI: 10.1016/j.cell.2020.11.024] [Citation(s) in RCA: 55] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2020] [Revised: 09/22/2020] [Accepted: 11/13/2020] [Indexed: 02/07/2023]
Abstract
Thousands of proteins localize to the nucleus; however, it remains unclear which contain transcriptional effectors. Here, we develop HT-recruit, a pooled assay where protein libraries are recruited to a reporter, and their transcriptional effects are measured by sequencing. Using this approach, we measure gene silencing and activation for thousands of domains. We find a relationship between repressor function and evolutionary age for the KRAB domains, discover that Homeodomain repressor strength is collinear with Hox genetic organization, and identify activities for several domains of unknown function. Deep mutational scanning of the CRISPRi KRAB maps the co-repressor binding surface and identifies substitutions that improve stability/silencing. By tiling 238 proteins, we find repressors as short as ten amino acids. Finally, we report new activator domains, including a divergent KRAB. These results provide a resource of 600 human proteins containing effectors and demonstrate a scalable strategy for assigning functions to protein domains.
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Affiliation(s)
- Josh Tycko
- Department of Genetics, Stanford University, Stanford, CA 94305, USA
| | - Nicole DelRosso
- Biophysics Program, Stanford University, Stanford, CA 94305, USA
| | - Gaelen T Hess
- Department of Genetics, Stanford University, Stanford, CA 94305, USA
| | - Aradhana
- Department of Genetics, Stanford University, Stanford, CA 94305, USA
| | | | - Aditya Mukund
- Biophysics Program, Stanford University, Stanford, CA 94305, USA
| | - Mike V Van
- Department of Biology, Stanford University, Stanford, CA 94305, USA
| | - Braeden K Ego
- Department of Genetics, Stanford University, Stanford, CA 94305, USA
| | - David Yao
- Department of Genetics, Stanford University, Stanford, CA 94305, USA
| | - Kaitlyn Spees
- Department of Genetics, Stanford University, Stanford, CA 94305, USA
| | - Peter Suzuki
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA
| | - Georgi K Marinov
- Department of Genetics, Stanford University, Stanford, CA 94305, USA
| | - Anshul Kundaje
- Department of Genetics, Stanford University, Stanford, CA 94305, USA; Department of Computer Science, Stanford University, Stanford, CA 94305, USA
| | - Michael C Bassik
- Department of Genetics, Stanford University, Stanford, CA 94305, USA.
| | - Lacramioara Bintu
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA.
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46
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Xiao Y, Hu F, Luo X, Zhao M, Sun Z, Qian X, Yang Y. Modulating the pKa Values of Hill-Type pH Probes for Biorelevant Acidic pH Range. ACS APPLIED BIO MATERIALS 2020; 4:2097-2103. [DOI: 10.1021/acsabm.0c01262] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- Yansheng Xiao
- State Key Laboratory of Bioreactor Engineering, School of Pharmacy, East China University of Science and Technology, Shanghai 200237, China
| | - Fang Hu
- State Key Laboratory of Bioreactor Engineering, School of Pharmacy, East China University of Science and Technology, Shanghai 200237, China
| | - Xiao Luo
- School of Chemistry and Molecular Engineering, East China Normal University, Shanghai 200241, China
| | - Mingming Zhao
- Beijing Hospital, National Center of Gerontology, Institute of Geriatric Medicine Chinese Academy of Medical Science, Beijing 100730, China
| | - Zhenglong Sun
- Suzhou Institute of Biomedical Engineering and Technology (SIBET), Chinese Academy of Sciences, Suzhou 215163, China
| | - Xuhong Qian
- State Key Laboratory of Bioreactor Engineering, School of Pharmacy, East China University of Science and Technology, Shanghai 200237, China
| | - Youjun Yang
- State Key Laboratory of Bioreactor Engineering, School of Pharmacy, East China University of Science and Technology, Shanghai 200237, China
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Bachollet SPJT, Addi C, Pietrancosta N, Mallet JM, Dumat B. Fluorogenic Protein Probes with Red and Near-Infrared Emission for Genetically Targeted Imaging*. Chemistry 2020; 26:14467-14473. [PMID: 32691883 DOI: 10.1002/chem.202002911] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2020] [Indexed: 11/09/2022]
Abstract
Fluorogenic probes are important tools to image proteins with high contrast and no wash protocols. In this work, we rationally designed and synthesized a small set of four protein fluorogens with red or near-infrared emission. The fluorophores were characterized in the presence of albumin as a model protein environment and exhibited good fluorogenicity and brightness (fluorescence quantum yield up to 36 %). Once conjugated to a haloalkane ligand, the probes reacted with the protein self-labeling tag HaloTag with a high fluorescence enhancement (up to 156-fold). The spectroscopic properties of the fluorogens and their reaction with HaloTag were investigated experimentally in vitro and with the help of molecular dynamics. The two most promising probes, one in the red and one in the near-infrared range, were finally applied to image the nucleus or actin in live-cell and in wash-free conditions using fluorogenic and chemogenetic targeting of HaloTag fusion proteins.
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Affiliation(s)
- Sylvestre P J T Bachollet
- Laboratoire des Biomolécules, LBM, Département de chimie, École Normale Supérieure, PSL University, Sorbonne Université, CNRS, 75005, Paris, France
| | - Cyril Addi
- Membrane Traffic and Cell Division Lab, Cell Biology and Infection Department, Institut Pasteur, CNRS UMR3691, Sorbonne Université, 75005, Paris, France
| | - Nicolas Pietrancosta
- Laboratoire des Biomolécules, LBM, Département de chimie, École Normale Supérieure, PSL University, Sorbonne Université, CNRS, 75005, Paris, France.,Neuroscience Paris Seine-Institut de Biologie Paris Seine (NPS-IBPS) INSERM, CNRS, Sorbonne Université, Paris, France
| | - Jean-Maurice Mallet
- Laboratoire des Biomolécules, LBM, Département de chimie, École Normale Supérieure, PSL University, Sorbonne Université, CNRS, 75005, Paris, France
| | - Blaise Dumat
- Laboratoire des Biomolécules, LBM, Département de chimie, École Normale Supérieure, PSL University, Sorbonne Université, CNRS, 75005, Paris, France
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Marchand C, Lemay G, Archambault D. Identification of the nuclear and nucleolar localization signals of the Feline immunodeficiency virus Rev protein. Virus Res 2020; 290:198153. [PMID: 33010374 DOI: 10.1016/j.virusres.2020.198153] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Revised: 08/30/2020] [Accepted: 08/31/2020] [Indexed: 10/23/2022]
Abstract
Lentivirus genomes code for a regulatory protein essential for virus replication termed Rev. The Rev protein binds to partially spliced and unspliced viral RNAs and mediates their nuclear export. Therefore, Rev possesses functional domains that enable its shuttling between the cytoplasm and the nucleus. The Feline immunodeficiency virus (FIV), a lentivirus, can lead to an immunodeficiency syndrome after a long incubation period, similar to that associated with the human immunodeficiency virus type 1 (HIV-1). The FIV Rev functional domains have been predicted only by homology with those of HIV-1 Rev. In the present study, the nuclear and nucleolar localization signals (NLS and NoLS, respectively) of the FIV Rev were examined. A series of FIV Rev deletion mutants fused to the enhanced green fluorescent protein (EGFP) were used to localize the NLS in a region spanning amino acids (aa) 81-100. By using alanine substitution mutants, basic residues present between the amino acids (aa) 84-99 of the FIV Rev protein sequence were identified to form the NLS, whereas those between aa 82-95 were associated with the NoLS function. These results further enhance our understanding of how Rev exerts its role in the replication cycle of lentiviruses.
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Affiliation(s)
- Claude Marchand
- Département des Sciences Biologiques, Université du Québec à Montréal, Montréal, Québec, Canada; Département de Microbiologie, Infectiologie et Immunologie, Université de Montréal, Montréal, Québec, Canada
| | - Guy Lemay
- Département de Microbiologie, Infectiologie et Immunologie, Université de Montréal, Montréal, Québec, Canada
| | - Denis Archambault
- Département des Sciences Biologiques, Université du Québec à Montréal, Montréal, Québec, Canada.
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Stevenson BW, Gorman MA, Koach J, Cheung BB, Marshall GM, Parker MW, Holien JK. A structural view of PA2G4 isoforms with opposing functions in cancer. J Biol Chem 2020; 295:16100-16112. [PMID: 32952126 DOI: 10.1074/jbc.rev120.014293] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2020] [Revised: 09/17/2020] [Indexed: 01/04/2023] Open
Abstract
The role of proliferation-associated protein 2G4 (PA2G4), alternatively known as ErbB3-binding protein 1 (EBP1), in cancer has become apparent over the past 20 years. PA2G4 expression levels are correlated with prognosis in a range of human cancers, including neuroblastoma, cervical, brain, breast, prostate, pancreatic, hepatocellular, and other tumors. There are two PA2G4 isoforms, PA2G4-p42 and PA2G4-p48, and although both isoforms of PA2G4 regulate cellular growth and differentiation, these isoforms often have opposing roles depending on the context. Therefore, PA2G4 can function either as a contextual tumor suppressor or as an oncogene, depending on the tissue being studied. However, it is unclear how distinct structural features of the two PA2G4 isoforms translate into different functional outcomes. In this review, we examine published structures to identify important structural and functional components of PA2G4 and consider how they may explain its crucial role in the malignant phenotype. We will highlight the lysine-rich regions, protein-protein interaction sites, and post-translational modifications of the two PA2G4 isoforms and relate these to the functional cellular role of PA2G4. These data will enable a better understanding of the function and structure relationship of the two PA2G4 isoforms and highlight the care that will need to be undertaken for those who wish to conduct isoform-specific structure-based drug design campaigns.
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Affiliation(s)
| | - Michael A Gorman
- Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, Victoria, Australia
| | - Jessica Koach
- Department of Pediatrics, Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, California, USA; Children's Cancer Institute Australia for Medical Research, Lowy Cancer Research Centre, University of New South Wales, Sydney, New South Wales, Australia
| | - Belamy B Cheung
- Children's Cancer Institute Australia for Medical Research, Lowy Cancer Research Centre, University of New South Wales, Sydney, New South Wales, Australia; School of Women's and Children's Health, University of New South Wales, Randwick, New South Wales, Australia
| | - Glenn M Marshall
- School of Women's and Children's Health, University of New South Wales, Randwick, New South Wales, Australia; Kids Cancer Centre, Sydney Children's Hospital, Randwick, New South Wales, Australia
| | - Michael W Parker
- St. Vincent's Institute of Medical Research, Fitzroy, Victoria, Australia; Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, Victoria, Australia
| | - Jessica K Holien
- St. Vincent's Institute of Medical Research, Fitzroy, Victoria, Australia; Department of Surgery, University of Melbourne, Parkville, Victoria, Australia; School of Science, College of Science, Engineering, and Health, RMIT University, Melbourne, Victoria, Australia.
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Frank L, Rippe K. Repetitive RNAs as Regulators of Chromatin-Associated Subcompartment Formation by Phase Separation. J Mol Biol 2020; 432:4270-4286. [DOI: 10.1016/j.jmb.2020.04.015] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2019] [Revised: 04/14/2020] [Accepted: 04/14/2020] [Indexed: 12/21/2022]
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