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Yadav SA, Vats VK, Sharma R, Chauhan N, Subramanian M, Das A, Satpati D. 177Lu-labeling of nuclear localization sequence (NLS)-grafted HER2-receptor affine peptide. Bioorg Med Chem 2024; 112:117883. [PMID: 39180861 DOI: 10.1016/j.bmc.2024.117883] [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: 07/01/2024] [Revised: 08/13/2024] [Accepted: 08/16/2024] [Indexed: 08/27/2024]
Abstract
Tagging of cell permeable nuclear localization sequence (NLS) with receptor targeting peptide vectors is an attractive strategy for selectively targeted translocation of therapeutic cargoes. The present study aimed at grafting nuclear localization sequence (NLS) onto breast cancer targeting rL-A9 peptide. Molecular docking analysis revealed higher binding affinity of the peptide, DOTA-NLS-rL-A9 (-26.1 kJ/mol) towards HER2 receptor in comparison to DOTA-rL-A9 peptide (-22.2 kJ/mol). Confocal microscopy data suggested significantly enhanced cellular internalization of NLS-tagged peptide. The engineered HER2-selective, DOTA-NLS-rL-A9 peptide scaffold was radiolabeled with Lu-177 for intracellular delivery of the theranostic radionuclide into tumor cells. [177Lu]Lu-DOTA-NLS-rL-A9 exhibited significantly enhanced binding affinity (4.58 ± 1.77 nM) towards human breast carcinoma SKBR3 cells and cellular internalization (85 % at 24 h) compared to its original analog, [177Lu]Lu-DOTA-rL-A9. In vivo biodistribution studies showed consistent retention of [177Lu]Lu-DOTA-NLS-rL-A9 in the tumor with negligible washout of radioactivity (∼4.1 % ID/g at 48 h). Prolonged tumor activity with rapid off-target tissue clearance resulted in significantly high tumor-to-background ratios. The radiopeptide, [177Lu]Lu-DOTA-NLS-rL-A9 thus, being precisely confined into HER2-expressing tumor cells and exhibiting favourable pharmacokinetic features is an efficient candidate for further screening.
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Affiliation(s)
| | - V Kusum Vats
- Radiopharmaceuticals Division, Bhabha Atomic Research Centre, Mumbai, India
| | - Rohit Sharma
- Radiopharmaceuticals Division, Bhabha Atomic Research Centre, Mumbai, India; Homi Bhabha National Institute, Mumbai, India
| | - Nitish Chauhan
- Bio-organic Division, Bhabha Atomic Research Centre, Mumbai, India
| | | | - Amit Das
- Protein Crystallography Section, Bio-Science Group, Bhabha Atomic Research Centre, Mumbai, India; Homi Bhabha National Institute, Mumbai, India
| | - Drishty Satpati
- Radiopharmaceuticals Division, Bhabha Atomic Research Centre, Mumbai, India; Homi Bhabha National Institute, Mumbai, India.
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2
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Armour EM, Thomas CM, Greco G, Bhatnagar A, Elefant F. Experience-dependent Tip60 nucleocytoplasmic transport is regulated by its NLS/NES sequences for neuroplasticity gene control. Mol Cell Neurosci 2023; 127:103888. [PMID: 37598897 PMCID: PMC11337217 DOI: 10.1016/j.mcn.2023.103888] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2023] [Revised: 08/14/2023] [Accepted: 08/16/2023] [Indexed: 08/22/2023] Open
Abstract
Nucleocytoplasmic transport (NCT) in neurons is critical for enabling proteins to enter the nucleus and regulate plasticity genes in response to environmental cues. Such experience-dependent (ED) neural plasticity is central for establishing memory formation and cognitive function and can influence the severity of neurodegenerative disorders like Alzheimer's disease (AD). ED neural plasticity is driven by histone acetylation (HA) mediated epigenetic mechanisms that regulate dynamic activity-dependent gene transcription profiles in response to neuronal stimulation. Yet, how histone acetyltransferases (HATs) respond to extracellular cues in the in vivo brain to drive HA-mediated activity-dependent gene control remains unclear. We previously demonstrated that extracellular stimulation of rat hippocampal neurons in vitro triggers Tip60 HAT nuclear import with concomitant synaptic gene induction. Here, we focus on investigating Tip60 HAT subcellular localization and NCT specifically in neuronal activity-dependent gene control by using the learning and memory mushroom body (MB) region of the Drosophila brain as a powerful in vivo cognitive model system. We used immunohistochemistry (IHC) to compare the subcellular localization of Tip60 HAT in the Drosophila brain under normal conditions and in response to stimulation of fly brain neurons in vivo either by genetically inducing potassium channels activation or by exposure to natural positive ED conditions. Furthermore, we found that both inducible and ED condition-mediated neural induction triggered Tip60 nuclear import with concomitant induction of previously identified Tip60 target genes and that Tip60 levels in both the nucleus and cytoplasm were significantly decreased in our well-characterized Drosophila AD model. Mutagenesis of a putative nuclear localization signal (NLS) sequence and nuclear export signal (NES) sequence that we identified in the Drosophila Tip60 protein revealed that both are functionally required for appropriate Tip60 subcellular localization. Our results support a model by which neuronal stimulation triggers Tip60 NCT via its NLS and NES sequences to promote induction of activity-dependent neuroplasticity gene transcription and that this process may be disrupted in AD.
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Affiliation(s)
- Ellen M Armour
- Department of Biology, Drexel University, Philadelphia, PA, United States of America
| | - Christina M Thomas
- Department of Biology, Drexel University, Philadelphia, PA, United States of America
| | - Gabrielle Greco
- Department of Biology, Drexel University, Philadelphia, PA, United States of America
| | - Akanksha Bhatnagar
- Department of Biology, Drexel University, Philadelphia, PA, United States of America
| | - Felice Elefant
- Department of Biology, Drexel University, Philadelphia, PA, United States of America.
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3
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Bashkeran T, Kamaruddin AH, Ngo TX, Suda K, Umakoshi H, Watanabe N, Nadzir MM. Niosomes in cancer treatment: A focus on curcumin encapsulation. Heliyon 2023; 9:e18710. [PMID: 37593605 PMCID: PMC10428065 DOI: 10.1016/j.heliyon.2023.e18710] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2022] [Revised: 07/24/2023] [Accepted: 07/25/2023] [Indexed: 08/19/2023] Open
Abstract
Curcumin is widely used as a therapeutic drug for cancer treatment. However, its limited absorption and rapid excretion are the major therapeutic limitations to its clinical use. Using niosomes as a curcumin delivery system is a cheap, easy, and less toxic strategy for enhancing the absorption of curcumin by cells and delaying its excretion. Thus, there is a vital need to explore curcumin niosomes to configure the curcumin to suitably serve and aid current pharmacokinetics in treatments for cancer. To date, no comprehensive review has focused on the cytotoxic effects of curcumin niosomes on malignant cells. Thus, this review provides a critical analysis of the curcumin niosomes in cancer treatment, formulations of curcumin niosomes, characterizations of curcumin niosomes, and factors influencing their performance. The findings from this review article can strongly accelerate the understanding of curcumin niosomes and pave a brighter direction towards advances in the pharmaceutical, biotechnology, and medical industries.
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Affiliation(s)
- Thaaranni Bashkeran
- School of Chemical Engineering, Universiti Sains Malaysia, Engineering Campus, 14300, Nibong Tebal, Pulau Pinang, Malaysia
| | - Azlina Harun Kamaruddin
- School of Chemical Engineering, Universiti Sains Malaysia, Engineering Campus, 14300, Nibong Tebal, Pulau Pinang, Malaysia
| | - Trung Xuan Ngo
- Rohto Pharmaceutical Co., Ltd., Basic Research Division, Research Village Kyoto, 6-5-4 Kunimidai, Kizugawa, Kyoto, 619-0216, Japan
| | - Kazuma Suda
- Rohto Pharmaceutical Co., Ltd., Basic Research Division, Research Village Kyoto, 6-5-4 Kunimidai, Kizugawa, Kyoto, 619-0216, Japan
| | - Hiroshi Umakoshi
- Division of Chemical Engineering, Graduate School of Engineering Science, Osaka University, 1-3 Machikaneyama-cho, Toyonaka, 560-8531, Japan
| | - Nozomi Watanabe
- Division of Chemical Engineering, Graduate School of Engineering Science, Osaka University, 1-3 Machikaneyama-cho, Toyonaka, 560-8531, Japan
| | - Masrina Mohd Nadzir
- School of Chemical Engineering, Universiti Sains Malaysia, Engineering Campus, 14300, Nibong Tebal, Pulau Pinang, Malaysia
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4
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Udi Y, Zhang W, Stein ME, Ricardo-Lax I, Pasolli HA, Chait BT, Rout MP. A general method for quantitative fractionation of mammalian cells. J Cell Biol 2023; 222:213941. [PMID: 36920247 PMCID: PMC10040634 DOI: 10.1083/jcb.202209062] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Revised: 01/11/2023] [Accepted: 02/24/2023] [Indexed: 03/16/2023] Open
Abstract
Subcellular fractionation in combination with mass spectrometry-based proteomics is a powerful tool to study localization of key proteins in health and disease. Here we offered a reliable and rapid method for mammalian cell fractionation, tuned for such proteomic analyses. This method proves readily applicable to different cell lines in which all the cellular contents are accounted for, while maintaining nuclear and nuclear envelope integrity. We demonstrated the method's utility by quantifying the effects of a nuclear export inhibitor on nucleoplasmic and cytoplasmic proteomes.
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Affiliation(s)
- Yael Udi
- Laboratory of Cellular and Structural Biology, The Rockefeller University , New York, NY, USA
| | - Wenzhu Zhang
- Laboratory of Mass Spectrometry and Gaseous Ion Chemistry, The Rockefeller University , New York, NY, USA
| | - Milana E Stein
- Laboratory of Cellular and Structural Biology, The Rockefeller University , New York, NY, USA
| | - Inna Ricardo-Lax
- Laboratory of Virology and Infectious Disease, The Rockefeller University , New York, NY, USA
| | - Hilda A Pasolli
- Electron Microscopy Resource Center, The Rockefeller University , New York, NY, USA
| | - Brian T Chait
- Laboratory of Mass Spectrometry and Gaseous Ion Chemistry, The Rockefeller University , New York, NY, USA
| | - Michael P Rout
- Laboratory of Cellular and Structural Biology, The Rockefeller University , New York, NY, USA
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5
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Pereira Sena P, Weber JJ, Bayezit S, Saup R, Incebacak Eltemur RD, Li X, Velic A, Jung J, Macek B, Nguyen HP, Riess O, Schmidt T. Implications of specific lysine residues within ataxin-3 for the molecular pathogenesis of Machado-Joseph disease. Front Mol Neurosci 2023; 16:1133271. [PMID: 37273907 PMCID: PMC10235640 DOI: 10.3389/fnmol.2023.1133271] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2022] [Accepted: 05/03/2023] [Indexed: 06/06/2023] Open
Abstract
Lysine residues are one of the main sites for posttranslational modifications of proteins, and lysine ubiquitination of the Machado-Joseph disease protein ataxin-3 is implicated in its cellular function and polyglutamine expansion-dependent toxicity. Despite previously undertaken efforts, the individual roles of specific lysine residues of the ataxin-3 sequence are not entirely understood and demand further analysis. By retaining single lysine residues of otherwise lysine-free wild-type and polyglutamine-expanded ataxin-3, we assessed the effects of a site-limited modifiability on ataxin-3 protein levels, aggregation propensity, localization, and stability. We confirmed earlier findings that levels of lysine-free ataxin-3 are reduced due to its decreased stability, which led to a diminished load of SDS-insoluble species of its polyglutamine-expanded form. The isolated presence of several single lysine residues within the N-terminus of polyglutamine-expanded ataxin-3 significantly restored its aggregate levels, with highest fold changes induced by the presence of lysine 8 or lysine 85, respectively. Ataxin-3 lacking all lysine residues presented a slightly increased nuclear localization, which was counteracted by the reintroduction of lysine 85, whereas presence of either lysine 8 or lysine 85 led to a significantly higher ataxin-3 stability. Moreover, lysine-free ataxin-3 showed increased toxicity and binding to K48-linked polyubiquitin chains, whereas the reintroduction of lysine 85, located between the ubiquitin-binding sites 1 and 2 of ataxin-3, normalized its binding affinity. Overall, our data highlight the relevance of lysine residues 8 and 85 of ataxin-3 and encourage further analyses, to evaluate the potential of modulating posttranslational modifications of these sites for influencing pathophysiological characteristics of the Machado-Joseph disease protein.
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Affiliation(s)
- Priscila Pereira Sena
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, Tübingen, Germany
| | - Jonasz Jeremiasz Weber
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, Tübingen, Germany
- Department of Human Genetics, Ruhr University Bochum, Bochum, Germany
| | - Sercan Bayezit
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, Tübingen, Germany
| | - Rafael Saup
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, Tübingen, Germany
| | - Rana Dilara Incebacak Eltemur
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, Tübingen, Germany
- Department of Human Genetics, Ruhr University Bochum, Bochum, Germany
| | - Xiaoling Li
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, Tübingen, Germany
| | - Ana Velic
- Proteome Center Tübingen, University of Tübingen, Tübingen, Germany
| | - Jaqueline Jung
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, Tübingen, Germany
| | - Boris Macek
- Proteome Center Tübingen, University of Tübingen, Tübingen, Germany
| | - Huu Phuc Nguyen
- Department of Human Genetics, Ruhr University Bochum, Bochum, Germany
| | - Olaf Riess
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, Tübingen, Germany
| | - Thorsten Schmidt
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, Tübingen, Germany
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6
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Raterman ST, Von Den Hoff JW, Dijkstra S, De Vriend C, Te Morsche T, Broekman S, Zethof J, De Vrieze E, Wagener FADTG, Metz JR. Disruption of the foxe1 gene in zebrafish reveals conserved functions in development of the craniofacial skeleton and the thyroid. Front Cell Dev Biol 2023; 11:1143844. [PMID: 36994096 PMCID: PMC10040582 DOI: 10.3389/fcell.2023.1143844] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2023] [Accepted: 02/28/2023] [Indexed: 03/14/2023] Open
Abstract
Introduction: Mutations in the FOXE1 gene are implicated in cleft palate and thyroid dysgenesis in humans.Methods: To investigate whether zebrafish could provide meaningful insights into the etiology of developmental defects in humans related to FOXE1, we generated a zebrafish mutant that has a disruption in the nuclear localization signal in the foxe1 gene, thereby restraining nuclear access of the transcription factor. We characterized skeletal development and thyroidogenesis in these mutants, focusing on embryonic and larval stages.Results: Mutant larvae showed aberrant skeletal phenotypes in the ceratohyal cartilage and had reduced whole body levels of Ca, Mg and P, indicating a critical role for foxe1 in early skeletal development. Markers of bone and cartilage (precursor) cells were differentially expressed in mutants in post-migratory cranial neural crest cells in the pharyngeal arch at 1 dpf, at induction of chondrogenesis at 3 dpf and at the start of endochondral bone formation at 6 dpf. Foxe1 protein was detected in differentiated thyroid follicles, suggesting a role for the transcription factor in thyroidogenesis, but thyroid follicle morphology or differentiation were unaffected in mutants.Discussion: Taken together, our findings highlight the conserved role of Foxe1 in skeletal development and thyroidogenesis, and show differential signaling of osteogenic and chondrogenic genes related to foxe1 mutation.
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Affiliation(s)
- Sophie T. Raterman
- Department of Dentistry—Orthodontics and Craniofacial Biology, Radboud Institute of Molecular Life Sciences (RIMLS), Radboud University Medical Center, Nijmegen, Netherlands
- Department of Animal Ecology and Physiology, Radboud Institute for Biological and Environmental Sciences (RIBES), Radboud University, Nijmegen, Netherlands
- *Correspondence: Sophie T. Raterman,
| | - Johannes W. Von Den Hoff
- Department of Dentistry—Orthodontics and Craniofacial Biology, Radboud Institute of Molecular Life Sciences (RIMLS), Radboud University Medical Center, Nijmegen, Netherlands
| | - Sietske Dijkstra
- Department of Animal Ecology and Physiology, Radboud Institute for Biological and Environmental Sciences (RIBES), Radboud University, Nijmegen, Netherlands
| | - Cheyenne De Vriend
- Department of Animal Ecology and Physiology, Radboud Institute for Biological and Environmental Sciences (RIBES), Radboud University, Nijmegen, Netherlands
| | - Tim Te Morsche
- Department of Animal Ecology and Physiology, Radboud Institute for Biological and Environmental Sciences (RIBES), Radboud University, Nijmegen, Netherlands
| | - Sanne Broekman
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, Netherlands
| | - Jan Zethof
- Department of Animal Ecology and Physiology, Radboud Institute for Biological and Environmental Sciences (RIBES), Radboud University, Nijmegen, Netherlands
| | - Erik De Vrieze
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, Netherlands
| | - Frank A. D. T. G. Wagener
- Department of Dentistry—Orthodontics and Craniofacial Biology, Radboud Institute of Molecular Life Sciences (RIMLS), Radboud University Medical Center, Nijmegen, Netherlands
| | - Juriaan R. Metz
- Department of Animal Ecology and Physiology, Radboud Institute for Biological and Environmental Sciences (RIBES), Radboud University, Nijmegen, Netherlands
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7
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Gupta S, Kumar A, Tamuli R. CRZ1 transcription factor is involved in cell survival, stress tolerance, and virulence in fungi. J Biosci 2022. [DOI: 10.1007/s12038-022-00294-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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8
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G Protein Subunit β1 Facilitates Influenza A Virus Replication by Promoting the Nuclear Import of PB2. J Virol 2022; 96:e0049422. [PMID: 35604143 DOI: 10.1128/jvi.00494-22] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
G protein subunit β1 (GNB1), the beta subunit of the G protein family, plays an important role in regulating transmembrane signal transduction. Although a recent study has demonstrated that GNB1 can bind the matrix protein 1 (M1) to facilitate M1 transport to budding sites and promote the release of progeny influenza A virus (IAV), whether the GNB1 protein has other functions in IAV replication requires further study. Here, we found that GNB1 promoted IAV replication, as virus yield decreased in GNB1 knockdown or knockout cells. GNB1 interacted with polymerase subunits PB2, PB1, and PA. Overexpressed GNB1 facilitated PB2 binding to importin α3, α5, and α7 promoting the nuclear import of PB2, enhancing viral RNA synthesis and polymerase activity. Altogether, our results demonstrated that GNB1 positively regulates virus replication by interacting with polymerase subunits and facilitating the nuclear import of PB2, which provide novel insights into the molecular mechanism of IAV. IMPORTANCE Until now, there has been only one article on the role of GNB1 in IAV budding. No study has investigated the role of GNB1 in IAV replication. In this study, our research demonstrated that GNB1 could increase the interaction between PB2 and the importin α isoform and mediate the nuclear import of PB2. Therefore, GNB1 could promote viral replication and transcription. Our results provide a better understanding of the molecular mechanisms of viral replication and provide potential antiviral drug targets.
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9
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Kural Mangit E, Boustanabadimaralan Düz N, Dinçer P. A cytoplasmic escapee: desmin is going nuclear. Turk J Biol 2022; 45:711-719. [PMID: 35068951 PMCID: PMC8733954 DOI: 10.3906/biy-2107-54] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2021] [Accepted: 11/04/2021] [Indexed: 11/03/2022] Open
Abstract
It has been a long time since researchers have focused on the cytoskeletal proteins' unconventional functions in the nucleus. Subcellular localization of a protein not only affects its functions but also determines the accessibility for cellular processes. Desmin is a muscle-specific, cytoplasmic intermediate filament protein, the cytoplasmic roles of which are defined. Yet, there is some evidence pointing out nuclear functions for desmin. In silico and wet lab analysis shows that desmin can enter and function in the nucleus. Furthermore, the candidate nuclear partners of desmin support the notion that desmin can serve as a transcriptional regulator inside the nucleus. Uncovering the nuclear functions and partners of desmin will provide a new insight into the biological significance of desmin.
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Affiliation(s)
- Ecem Kural Mangit
- Department of Medical Biology, Faculty of Medicine, Hacettepe University, Ankara Turkey.,Laboratory Animals Research and Application Centre, Hacettepe University, Ankara Turkey
| | | | - Pervin Dinçer
- Department of Medical Biology, Faculty of Medicine, Hacettepe University, Ankara Turkey
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10
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Peukes J, Xiong X, Briggs JAG. New structural insights into the multifunctional influenza A matrix protein 1. FEBS Lett 2021; 595:2535-2543. [PMID: 34547821 PMCID: PMC8835727 DOI: 10.1002/1873-3468.14194] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2021] [Revised: 09/10/2021] [Accepted: 09/10/2021] [Indexed: 11/18/2022]
Abstract
Influenza A virus matrix protein 1 (M1) is the most abundant protein within virions and functions at multiple steps of the virus life cycle, including nuclear RNA export, virus particle assembly, and virus disassembly. Two recent publications have presented the first structures of full‐length M1 and show that it assembles filaments in vitro via an interface between the N‐ and C‐terminal domains of adjacent monomers. These filaments were found to be similar to those that form the endoskeleton of assembled virions. The structures provide a molecular basis to understand the functions of M1 during the virus life cycle. Here, we compare and discuss the two structures, and explore their implications for the mechanisms by which the multifunctional M1 protein can mediate virus assembly, interact with viral ribonucleoproteins and act during infection of a new cell.
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Affiliation(s)
- Julia Peukes
- Structural Studies Division, Medical Research Council Laboratory of Molecular Biology, Cambridge, UK.,California Institute for Quantitative Biosciences (QB3), University of California, Berkeley, CA, USA
| | - Xiaoli Xiong
- Structural Studies Division, Medical Research Council Laboratory of Molecular Biology, Cambridge, UK.,Bioland Laboratory (Guangzhou Regenerative Medicine and Health - Guangdong Laboratory), Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
| | - John A G Briggs
- Structural Studies Division, Medical Research Council Laboratory of Molecular Biology, Cambridge, UK.,Department of Cell and Virus Structure, Max Planck Institute of Biochemistry, Martinsried, Germany
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11
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Novev JK, Heltberg ML, Jensen MH, Doostmohammadi A. Spatiotemporal model of cellular mechanotransduction via Rho and YAP. Integr Biol (Camb) 2021; 13:197-209. [PMID: 34278428 DOI: 10.1093/intbio/zyab012] [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] [Received: 01/06/2021] [Revised: 04/29/2021] [Accepted: 06/15/2021] [Indexed: 01/20/2023]
Abstract
How cells sense and respond to mechanical stimuli remains an open question. Recent advances have identified the translocation of Yes-associated protein (YAP) between nucleus and cytoplasm as a central mechanism for sensing mechanical forces and regulating mechanotransduction. We formulate a spatiotemporal model of the mechanotransduction signalling pathway that includes coupling of YAP with the cell force-generation machinery through the Rho family of GTPases. Considering the active and inactive forms of a single Rho protein (GTP/GDP-bound) and of YAP (non-phosphorylated/phosphorylated), we study the cross-talk between cell polarization due to active Rho and YAP activation through its nuclear localization. For fixed mechanical stimuli, our model predicts stationary nuclear-to-cytoplasmic YAP ratios consistent with experimental data at varying adhesive cell area. We further predict damped and even sustained oscillations in the YAP nuclear-to-cytoplasmic ratio by accounting for recently reported positive and negative YAP-Rho feedback. Extending the framework to time-varying mechanical stimuli that simulate cyclic stretching and compression, we show that the YAP nuclear-to-cytoplasmic ratio's time dependence follows that of the cyclic mechanical stimulus. The model presents one of the first frameworks for understanding spatiotemporal YAP mechanotransduction, providing several predictions of possible YAP localization dynamics, and suggesting new directions for experimental and theoretical studies.
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Affiliation(s)
- Javor K Novev
- Niels Bohr Institute, University of Copenhagen, Blegdamsvej 17, 2100 Copenhagen Ø, Denmark
| | - Mathias L Heltberg
- Niels Bohr Institute, University of Copenhagen, Blegdamsvej 17, 2100 Copenhagen Ø, Denmark.,Laboratoire de Physique, Ecole Normale Superieure, Rue Lhomond 15, Paris 07505, France
| | - Mogens H Jensen
- Niels Bohr Institute, University of Copenhagen, Blegdamsvej 17, 2100 Copenhagen Ø, Denmark
| | - Amin Doostmohammadi
- Niels Bohr Institute, University of Copenhagen, Blegdamsvej 17, 2100 Copenhagen Ø, Denmark
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12
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Kumar R, Santa Chalarca CF, Bockman MR, Bruggen CV, Grimme CJ, Dalal RJ, Hanson MG, Hexum JK, Reineke TM. Polymeric Delivery of Therapeutic Nucleic Acids. Chem Rev 2021; 121:11527-11652. [PMID: 33939409 DOI: 10.1021/acs.chemrev.0c00997] [Citation(s) in RCA: 152] [Impact Index Per Article: 50.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The advent of genome editing has transformed the therapeutic landscape for several debilitating diseases, and the clinical outlook for gene therapeutics has never been more promising. The therapeutic potential of nucleic acids has been limited by a reliance on engineered viral vectors for delivery. Chemically defined polymers can remediate technological, regulatory, and clinical challenges associated with viral modes of gene delivery. Because of their scalability, versatility, and exquisite tunability, polymers are ideal biomaterial platforms for delivering nucleic acid payloads efficiently while minimizing immune response and cellular toxicity. While polymeric gene delivery has progressed significantly in the past four decades, clinical translation of polymeric vehicles faces several formidable challenges. The aim of our Account is to illustrate diverse concepts in designing polymeric vectors towards meeting therapeutic goals of in vivo and ex vivo gene therapy. Here, we highlight several classes of polymers employed in gene delivery and summarize the recent work on understanding the contributions of chemical and architectural design parameters. We touch upon characterization methods used to visualize and understand events transpiring at the interfaces between polymer, nucleic acids, and the physiological environment. We conclude that interdisciplinary approaches and methodologies motivated by fundamental questions are key to designing high-performing polymeric vehicles for gene therapy.
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Affiliation(s)
- Ramya Kumar
- Department of Chemistry, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | | | - Matthew R Bockman
- Department of Chemistry, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Craig Van Bruggen
- Department of Chemistry, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Christian J Grimme
- Department of Chemical Engineering and Materials Science, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Rishad J Dalal
- Department of Chemistry, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Mckenna G Hanson
- Department of Chemistry, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Joseph K Hexum
- Department of Chemistry, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Theresa M Reineke
- Department of Chemistry, University of Minnesota, Minneapolis, Minnesota 55455, United States
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13
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McLane LM, Ngiow SF, Chen Z, Attanasio J, Manne S, Ruthel G, Wu JE, Staupe RP, Xu W, Amaravadi RK, Xu X, Karakousis GC, Mitchell TC, Schuchter LM, Huang AC, Freedman BD, Betts MR, Wherry EJ. Role of nuclear localization in the regulation and function of T-bet and Eomes in exhausted CD8 T cells. Cell Rep 2021; 35:109120. [PMID: 33979613 PMCID: PMC8195461 DOI: 10.1016/j.celrep.2021.109120] [Citation(s) in RCA: 54] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2018] [Revised: 10/06/2020] [Accepted: 04/21/2021] [Indexed: 12/15/2022] Open
Abstract
The transcription factors T-bet and Eomesodermin (Eomes) regulate CD8 T cell exhaustion through undefined mechanisms. Here, we show that the subcellular localization of T-bet and Eomes dictate their regulatory activity in exhausted T cells (TEXs). TEXs had a higher ratio of nuclear Eomes:T-bet than memory T cells (TMEMs) during chronic lymphocytic choriomeningitis virus (LCMV) infection in preclinical cancer models and in human tumors. Biochemically, T-bet and Eomes compete for the same DNA sequences, including the Pdcd1 T-box. High nuclear T-bet strongly represses Pdcd1 transcription in TMEM, whereas low nuclear T-bet in TEX leads to a dominant effect of Eomes that acts as a weaker repressor of Pdcd1. Blocking PD-1 signaling in TEXs increases nuclear T-bet, restoring stronger repression of Pdcd1, and driving T-bet-associated gene expression programs of chemotaxis, homing, and activation. These data identify a mechanism whereby the T-bet-Eomes axis regulates exhaustion through their nuclear localization, providing insights into how these transcription factors regulate TEX biology. McLane et al. demonstrate that T-bet and Eomes expression contributes to exhaustion, but also their nuclear localization, and therefore functional activity, plays a key role. PD-1 blockade restores nuclear T-bet and promotes T cell homing and activation through direct competition with Eomes at gene promoters, such as Pdcd1.
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Affiliation(s)
- Laura M McLane
- Department of Systems Pharmacology and Translational Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Institute for Immunology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Shin Foong Ngiow
- Department of Systems Pharmacology and Translational Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Institute for Immunology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Parker Institute for Cancer Immunotherapy, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Zeyu Chen
- Department of Systems Pharmacology and Translational Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Institute for Immunology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Parker Institute for Cancer Immunotherapy, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - John Attanasio
- Department of Systems Pharmacology and Translational Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Institute for Immunology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Sasikanth Manne
- Department of Systems Pharmacology and Translational Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Institute for Immunology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Gordon Ruthel
- Department of Pathobiology, University of Pennsylvania School of Veterinary Medicine, Philadelphia, PA 19104, USA
| | - Jennifer E Wu
- Department of Systems Pharmacology and Translational Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Institute for Immunology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Parker Institute for Cancer Immunotherapy, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Ryan P Staupe
- Department of Systems Pharmacology and Translational Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Institute for Immunology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Wei Xu
- Abramson Cancer Center, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Ravi K Amaravadi
- Abramson Cancer Center, University of Pennsylvania, Philadelphia, PA 19104, USA; Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Xiaowei Xu
- Abramson Cancer Center, University of Pennsylvania, Philadelphia, PA 19104, USA; Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Giorgos C Karakousis
- Abramson Cancer Center, University of Pennsylvania, Philadelphia, PA 19104, USA; Department of Surgery, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Tara C Mitchell
- Abramson Cancer Center, University of Pennsylvania, Philadelphia, PA 19104, USA; Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Lynn M Schuchter
- Abramson Cancer Center, University of Pennsylvania, Philadelphia, PA 19104, USA; Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Alexander C Huang
- Department of Systems Pharmacology and Translational Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Institute for Immunology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Parker Institute for Cancer Immunotherapy, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Bruce D Freedman
- Institute for Immunology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Department of Pathobiology, University of Pennsylvania School of Veterinary Medicine, Philadelphia, PA 19104, USA
| | - Michael R Betts
- Department of Systems Pharmacology and Translational Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Institute for Immunology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - E John Wherry
- Department of Systems Pharmacology and Translational Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Institute for Immunology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Parker Institute for Cancer Immunotherapy, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA.
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14
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Li L, He L, Wu B, Yu C, Zhao H, Zhou Y, Wang J, Zhu L. Structural Determinants for Light-Dependent Membrane Binding of a Photoswitchable Polybasic Domain. ACS Synth Biol 2021; 10:542-551. [PMID: 33689308 DOI: 10.1021/acssynbio.0c00571] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
OptoPB is an optogenetic tool engineered by fusion of the phosphoinositide (PI)-binding polybasic domain of Rit1 (Rit-PB) to a photoreactive light-oxygen-voltage (LOV) domain. OptoPB selectively and reversibly binds the plasma membrane (PM) under blue light excitation, and in the dark, it releases back to the cytoplasm. However, the molecular mechanism of optical regulation and lipid recognition is still unclear. Here using nuclear magnetic resonance (NMR) spectroscopy, liposome pulldown assay, and surface plasmon resonance (SPR), we find that OptoPB binds to membrane mimetics containing di- or triphosphorylated phosphatidylinositols, particularly phosphatidylinositol 4,5-bisphosphate (PI(4,5)P2), an acidic phospholipid predominantly located in the eukaryotic PM. In the dark, steric hindrance prevented this protein-membrane interaction, while 470 nm blue light illumination activated it. NMR titration and site-directed mutagenesis revealed that both cationic and hydrophobic Rit-PB residues are essential to the membrane interaction, indicating that OptoPB binds the membrane via a specific PI(4,5)P2-dependent mechanism.
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Affiliation(s)
- Ling Li
- High Magnetic Field Laboratory, CAS Key Laboratory of High Magnetic Field and Ion Beam Physical Biology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei 230031, China
- University of Science and Technology of China, Hefei 230026, China
| | - Lian He
- Center for Translational Cancer Research, Institute of Biosciences and Technology, Texas A&M University, Houston, Texas 77030, United States
| | - Bo Wu
- High Magnetic Field Laboratory, CAS Key Laboratory of High Magnetic Field and Ion Beam Physical Biology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei 230031, China
| | - Chuandi Yu
- High Magnetic Field Laboratory, CAS Key Laboratory of High Magnetic Field and Ion Beam Physical Biology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei 230031, China
- University of Science and Technology of China, Hefei 230026, China
| | - Hongxin Zhao
- High Magnetic Field Laboratory, CAS Key Laboratory of High Magnetic Field and Ion Beam Physical Biology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei 230031, China
| | - Yubin Zhou
- Center for Translational Cancer Research, Institute of Biosciences and Technology, Texas A&M University, Houston, Texas 77030, United States
| | - Junfeng Wang
- High Magnetic Field Laboratory, CAS Key Laboratory of High Magnetic Field and Ion Beam Physical Biology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei 230031, China
- University of Science and Technology of China, Hefei 230026, China
- Institute of Physical Science and Information Technology, Anhui University, Hefei 230031, China
| | - Lei Zhu
- High Magnetic Field Laboratory, CAS Key Laboratory of High Magnetic Field and Ion Beam Physical Biology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei 230031, China
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15
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Ma Y, Weng J, Wang N, Zhang Y, Minato N, Su L. A novel nuclear localization region in SIPA1 determines protein nuclear distribution and epirubicin-sensitivity of breast cancer cells. Int J Biol Macromol 2021; 180:718-728. [PMID: 33753200 DOI: 10.1016/j.ijbiomac.2021.03.101] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2020] [Revised: 02/26/2021] [Accepted: 03/17/2021] [Indexed: 01/03/2023]
Abstract
Signal-induced proliferation-associated protein 1 (SIPA1) is highly expressed and mainly located in the nucleus in some breast cancer cell lines and clinical tumor tissues. Previous study revealed that nuclear localization of SIPA1 is functionally involved in breast cancer metastasis in the lymphatic gland. In the current study, we identified a non-typical region (140-179aa) of SIPA1 as a novel nuclear localization region (NLR) which is crucial for translocating the proteins into the nucleus in HEK293 cells and breast cancer cells. This region contained one basic amino acid, His160, and had no common features of typical nuclear localization signals. In addition, overexpressing SIPA1 without NLR could suppress breast cancer cell proliferation but could not promote cell migration in MCF7 cells. Furthermore, we found that a high expression of SIPA1 upregulated the expression of ABCB1, encoding multi-drug resistance protein MDR1, and promoted the resistance to epirubicin in breast cancer cells, while this effect was largely abolished in the cells with the expression of NLR-deleted SIPA1. This study overall, identified a nuclear localization-dependent region determining the nuclear distribution of SIPA1 and its regulation on epirubicin-sensitivity in breast cancer cells, which could be a potential drug target to facilitate the development of breast cancer chemotherapy.
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Affiliation(s)
- Ying Ma
- Key Laboratory of Molecular Biophysics of Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, China
| | - Jun Weng
- Key Laboratory of Molecular Biophysics of Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, China
| | - Ning Wang
- Key Laboratory of Molecular Biophysics of Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, China
| | - Yilei Zhang
- Department of Experimental Radiation Oncology, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Nagahiro Minato
- Department of Immunology and Cell Biology, Graduate School of Medicine, Kyoto University, Kyoto 606-8501, Japan
| | - Li Su
- Key Laboratory of Molecular Biophysics of Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, China.
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16
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Cao Y, Di X, Zhang Q, Li R, Wang K. RBM10 Regulates Tumor Apoptosis, Proliferation, and Metastasis. Front Oncol 2021; 11:603932. [PMID: 33718153 PMCID: PMC7943715 DOI: 10.3389/fonc.2021.603932] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2020] [Accepted: 01/12/2021] [Indexed: 12/15/2022] Open
Abstract
The RNA-binding motif protein 10 (RBM10) is involved in alternative splicing and modifies mRNA post-transcriptionally. RBM10 is abnormally expressed in the lung, breast, and colorectal cancer, female genital tumors, osteosarcoma, and other malignant tumors. It can inhibit proliferation, promote apoptosis, and inhibit invasion and metastasis. RBM10 has long been considered a tumor suppressor because it promotes apoptosis through the regulation of the MDM2-p53 negative feedback loop, Bcl-2, Bax, and other apoptotic proteins and inhibits proliferation through the Notch signaling and rap1a/Akt/CREB pathways. However, it has been recently demonstrated that RBM10 can also promote cancer. Given these different views, it is necessary to summarize the research progress of RBM10 in various fields to reasonably analyze the underlying molecular mechanisms, and provide new ideas and directions for the clinical research of RBM10 in various cancer types. In this review, we provide a new perspective on the reasons for these opposing effects on cancer biology, molecular mechanisms, research progress, and clinical value of RBM10.
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Affiliation(s)
- Yingshu Cao
- Department of Respiratory Medicine, The Second Hospital of Jilin University, Changchun, China
| | - Xin Di
- Department of Respiratory Medicine, The Second Hospital of Jilin University, Changchun, China
| | - Qinghua Zhang
- Department of Respiratory Medicine, The Second Hospital of Jilin University, Changchun, China
| | - Ranwei Li
- Department of Urinary Surgery, The Second Hospital of Jilin University, Changchun, China
| | - Ke Wang
- Department of Respiratory Medicine, The Second Hospital of Jilin University, Changchun, China
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17
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Li Y, Ren H, Zhao Y, Sun J, Fan Y, Jin D, Pei Y. Characterization of three FK506-binding proteins in the entomopathogenic fungus Beauveria bassiana. J Invertebr Pathol 2020; 171:107334. [PMID: 32006551 DOI: 10.1016/j.jip.2020.107334] [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: 12/11/2019] [Revised: 01/26/2020] [Accepted: 01/28/2020] [Indexed: 10/25/2022]
Abstract
FK506 binding proteins (FKBPs) participate in regulation of diverse biological processes. However, the role of these proteins in insect-pathogenic fungi is far from well understood. To investigate the functions of FKBPs in Beauveria bassiana, a widely used entomopathogenic fungus for control of insect pests, we identify three putative FKBP genes, Bbfkbp12, Bbfkbp15, and Bbfkbp50, in the fungus. Gene-disruption experiments show that loss of Bbfkbp12 results in a significant increase of resistance of B. bassiana against the immunosuppressive compounds FK506 and rapamycin, while loss of Bbfkbp50 leads to the resistance to the ergosterol synthesis inhibitor lovastatin. Transcription assays of calcineurin (CaN)- and mTOR (mammalian target of rapamycin)-downstream target genes confirm that BbFKBP12 is the target of both FK506 and rapamycin, associated with CaN- and mTOR-signal pathways in B. bassiana. GFP-tagging of the proteins shows that BbFKBP12 and BbFKBP15 localize in cytoplasm while BbFKBP50 in nucleus. Our results provide useful information for the study of functions of CaN- and mTOR-mediated signaling, and ergosterol synthesis in the entomopathogenic fungi.
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Affiliation(s)
- Yujie Li
- Biotechnology Research Center, Southwest University, Beibei, Chongqing 400716, China
| | - Hui Ren
- Biotechnology Research Center, Southwest University, Beibei, Chongqing 400716, China
| | - Yutao Zhao
- Biotechnology Research Center, Southwest University, Beibei, Chongqing 400716, China
| | - Jiyuan Sun
- Biotechnology Research Center, Southwest University, Beibei, Chongqing 400716, China
| | - Yanhua Fan
- Biotechnology Research Center, Southwest University, Beibei, Chongqing 400716, China
| | - Dan Jin
- Biotechnology Research Center, Southwest University, Beibei, Chongqing 400716, China
| | - Yan Pei
- Biotechnology Research Center, Southwest University, Beibei, Chongqing 400716, China.
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18
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Affinity for DNA Contributes to NLS Independent Nuclear Localization of MeCP2. Cell Rep 2020; 24:2213-2220. [PMID: 30157418 PMCID: PMC6130050 DOI: 10.1016/j.celrep.2018.07.099] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2017] [Revised: 06/22/2018] [Accepted: 07/26/2018] [Indexed: 12/14/2022] Open
Abstract
MeCP2 is a nuclear protein that is mutated in the severe neurological disorder Rett syndrome (RTT). The ability to target β-galactosidase to the nucleus was previously used to identify a conserved nuclear localization signal (NLS) in MeCP2 that interacts with the nuclear import factors KPNA3 and KPNA4. Here, we report that nuclear localization of MeCP2 does not depend on its NLS. Instead, our data reveal that an intact methyl-CpG binding domain (MBD) is sufficient for nuclear localization, suggesting that MeCP2 can be retained in the nucleus by its affinity for DNA. Consistent with these findings, we demonstrate that disease progression in a mouse model of RTT is unaffected by an inactivating mutation in the NLS of MeCP2. Taken together, our work reveals an unexpected redundancy between functional domains of MeCP2 in targeting this protein to the nucleus, potentially explaining why NLS-inactivating mutations are rarely associated with disease. Nuclear localization of MeCP2 does not require its NLS DNA binding by MeCP2 contributes to its NLS-independent nuclear localization MeCP2 NLS mutation does not affect pathology in a mouse model of Rett syndrome
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19
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Frączyk T, Bonna A, Stefaniak E, Wezynfeld NE, Bal W. Peptide Bond Cleavage by Ni(II) Ions within the Nuclear Localization Signal Sequence. Chem Biodivers 2019; 17:e1900652. [PMID: 31869504 DOI: 10.1002/cbdv.201900652] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2019] [Accepted: 12/20/2019] [Indexed: 12/30/2022]
Abstract
Nickel is harmful to humans, being both carcinogenic and allergenic. However, the mechanisms of this toxicity are still unresolved. We propose that Ni(II) ions disintegrate proteins by hydrolysis of peptide bonds preceding the Ser/Thr-Xaa-His sequences. Such sequences occur in nuclear localization signals (NLSs) of human phospholipid scramblase 1, Sam68-like mammalian protein 2, and CLK3 kinase. We performed spectroscopic experiments showing that model nonapeptides derived from these NLSs bind Ni(II) at physiological pH. We also proved that these sequences are prone to Ni(II) hydrolysis. Thus, the aforementioned NLSs may be targets for nickel toxicity. This implies that Ni(II) ions disrupt the transport of some proteins from cytoplasm to cell nucleus.
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Affiliation(s)
- Tomasz Frączyk
- Department of Immunology, Transplantology and Internal Medicine, Medical University of Warsaw, Nowogrodzka 59, 02-006, Warsaw, Poland.,Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawińskiego 5a, 02-106, Warsaw, Poland
| | - Arkadiusz Bonna
- Department of Biochemistry, University of Cambridge, Tennis Court Road, CB2 1QW, Cambridge, United Kingdom
| | - Ewelina Stefaniak
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawińskiego 5a, 02-106, Warsaw, Poland
| | - Nina E Wezynfeld
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawińskiego 5a, 02-106, Warsaw, Poland.,Faculty of Chemistry, Warsaw University of Technology, Noakowskiego 3, 00-664, Warsaw, Poland
| | - Wojciech Bal
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawińskiego 5a, 02-106, Warsaw, Poland
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20
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Chen JH, Zhang RH, Lin SL, Li PF, Lan JJ, Gao JM, Xie ZJ, Li FC, Jiang SJ. Identification of a functional nuclear localization signal in 3D pol/3CD of duck hepatitis A virus 1. Virus Res 2019; 270:197670. [PMID: 31330206 DOI: 10.1016/j.virusres.2019.197670] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2019] [Revised: 07/16/2019] [Accepted: 07/17/2019] [Indexed: 10/26/2022]
Abstract
The nuclear localization signals (NLS) were usually composed of basic residues (K and R) and played an important role in delivery of genomes and structural protein into nucleus. In this research, we identified that 3Dpol/3CD entered into nucleus during viral propagation of duck hepatitis A virus type 1 (DHAV-1). To investigate the reason that 3Dpol/3CD entered into nucleus, the amino acid sequence of 3CD was analyzed through NLS Mapper program. The basic region 17PRKTAYMRS25 was subsequently proved to be a functional NLS to guide 3Dpol/3CD into nucleus. 18R, 19K and 24R were found essential for maintaining the nuclear targeting activity, and exchange between 24R and 24K had no impact on cellular localization of 3Dpol. Since the entry of 3Dpol/3CD into nucleus was essential for shutoff of host cell transcription and maintaining the viral propagation of picornavirus numbers, our study provided new insights into the mechanism of DHAV-1 propagation.
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Affiliation(s)
- Jun-Hao Chen
- College of Veterinary Medicine, Shandong Agricultural University, Shandong Taian, 271018, China; Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, Taian, 271018, China
| | - Rui-Hua Zhang
- College of Veterinary Medicine, Shandong Agricultural University, Shandong Taian, 271018, China; Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, Taian, 271018, China
| | - Shao-Li Lin
- College of Veterinary Medicine, Shandong Agricultural University, Shandong Taian, 271018, China; Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, Taian, 271018, China
| | - Peng-Fei Li
- College of Veterinary Medicine, Shandong Agricultural University, Shandong Taian, 271018, China; Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, Taian, 271018, China
| | - Jing-Jing Lan
- College of Veterinary Medicine, Shandong Agricultural University, Shandong Taian, 271018, China; Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, Taian, 271018, China
| | - Ji-Ming Gao
- Department of Basic Medical Sciences, Taishan Medical College, Taian, 271000, China
| | - Zhi-Jing Xie
- College of Veterinary Medicine, Shandong Agricultural University, Shandong Taian, 271018, China; Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, Taian, 271018, China
| | - Fu-Chang Li
- College of Animal Science and Technology, Shandong Agricultural University, Taian, 271018, China
| | - Shi-Jin Jiang
- College of Veterinary Medicine, Shandong Agricultural University, Shandong Taian, 271018, China; Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, Taian, 271018, China.
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21
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Ni R, Feng R, Chau Y. Synthetic Approaches for Nucleic Acid Delivery: Choosing the Right Carriers. Life (Basel) 2019; 9:E59. [PMID: 31324016 PMCID: PMC6789897 DOI: 10.3390/life9030059] [Citation(s) in RCA: 44] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2019] [Revised: 07/02/2019] [Accepted: 07/03/2019] [Indexed: 12/12/2022] Open
Abstract
The discovery of the genetic roots of various human diseases has motivated the exploration of different exogenous nucleic acids as therapeutic agents to treat these genetic disorders (inherited or acquired). However, the physicochemical properties of nucleic acids render them liable to degradation and also restrict their cellular entrance and gene translation/inhibition at the correct cellular location. Therefore, gene condensation/protection and guided intracellular trafficking are necessary for exogenous nucleic acids to function inside cells. Diversified cationic formulation materials, including natural and synthetic lipids, polymers, and proteins/peptides, have been developed to facilitate the intracellular transportation of exogenous nucleic acids. The chemical properties of different formulation materials determine their special features for nucleic acid delivery, so understanding the property-function correlation of the formulation materials will inspire the development of next-generation gene delivery carriers. Therefore, in this review, we focus on the chemical properties of different types of formulation materials and discuss how these formulation materials function as protectors and cellular pathfinders for nucleic acids, bringing them to their destination by overcoming different cellular barriers.
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Affiliation(s)
- Rong Ni
- Department of Chemical and Biological Engineering, the Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong 999077, China
- Institute for Advanced Study, the Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong 999077, China
| | - Ruilu Feng
- Department of Chemical and Biological Engineering, the Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong 999077, China
| | - Ying Chau
- Department of Chemical and Biological Engineering, the Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong 999077, China.
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22
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Gu Y, Zhang AC, Han Y, Li J, Chen C, Lo YH. Machine Learning Based Real-Time Image-Guided Cell Sorting and Classification. Cytometry A 2019; 95:499-509. [PMID: 30958640 PMCID: PMC6520141 DOI: 10.1002/cyto.a.23764] [Citation(s) in RCA: 48] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2018] [Revised: 03/06/2019] [Accepted: 03/25/2019] [Indexed: 01/05/2023]
Abstract
Cell classification based on phenotypical, spatial, and genetic information greatly advances our understanding of the physiology and pathology of biological systems. Technologies derived from next generation sequencing and fluorescent activated cell sorting are cornerstones for cell- and genomic-based assays supporting cell classification and mapping. However, there exists a deficiency in technology space to rapidly isolate cells based on high content image information. Fluorescence-activated cell sorting can only resolve cell-to-cell variation in fluorescence and optical scattering. Utilizing microfluidics, photonics, computation microscopy, real-time image processing and machine learning, we demonstrate an image-guided cell sorting and classification system possessing the high throughput of flow cytometer and high information content of microscopy. We demonstrate the utility of this technology in cell sorting based on (1) nuclear localization of glucocorticoid receptors, (2) particle binding to the cell membrane, and (3) DNA damage induced γ-H2AX foci. © 2019 International Society for Advancement of Cytometry.
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Affiliation(s)
- Yi Gu
- Department of Electrical and Computer Engineering, University of California, San Diego, La Jolla, California 92093-0407, USA
| | - Alex Ce Zhang
- Department of Electrical and Computer Engineering, University of California, San Diego, La Jolla, California 92093-0407, USA
| | - Yuanyuan Han
- Department of Electrical and Computer Engineering, University of California, San Diego, La Jolla, California 92093-0407, USA
| | - Jie Li
- Department of Neurosurgery, University of Minnesota, Minneapolis, D429 Mayo Memorial Building, 420 Delaware Street S.E., MMC 96MN 55455, USA
| | - Clark Chen
- Department of Neurosurgery, University of Minnesota, Minneapolis, D429 Mayo Memorial Building, 420 Delaware Street S.E., MMC 96MN 55455, USA
| | - Yu-Hwa Lo
- Department of Electrical and Computer Engineering, University of California, San Diego, La Jolla, California 92093-0407, USA,To whom correspondence should be addressed.
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23
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Transient Receptor Potential Mucolipin-1 Channels in Glioblastoma: Role in Patient's Survival. Cancers (Basel) 2019; 11:cancers11040525. [PMID: 31013784 PMCID: PMC6521337 DOI: 10.3390/cancers11040525] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2019] [Accepted: 04/09/2019] [Indexed: 02/06/2023] Open
Abstract
A link between mucolipin channels and tumors has been recently suggested. Herein, we aim to investigate the transient receptor potential mucolipin (TRPML)-1 relevance in glioblastoma. The expression of this channel was evaluated via qRT-PCR and immunohistochemistry in biopsies from 66 glioblastoma patients and two human glioblastoma cell lines and compared to normal human brain, astrocytes, and epileptic tissues. The subcellular distribution of TRPML-1 was examined via confocal microscopy in the glioma cell lines. Then, to assess the role of TRPML-1, cell viability assays have been conducted in T98 and U251 cell lines treated with the specific TRPML-1 agonist, MK6-83. We found that MK6-83 reduced cell viability and induced caspase-3-dependent apoptosis. Indeed, the TRPML-1 silencing or the blockage of TRPML-1 dependent [Ca2+]i release abrogated these effects. In addition, exposure of glioma cells to the reactive oxygen species (ROS) inducer, carbonyl cyanide m-chlorophenylhydrazone (CCCP), stimulated a TRPML-1-dependent autophagic cell death, as demonstrated by the ability of the autophagic inhibitor bafilomycin A, the TRPML-1 inhibitor sphingomyelin, and the TRPML-1 silencing to completely inhibit the CCCP-mediated effects. To test a possible correlation with patient’s survival, Kaplan–Meier, univariate, and multivariate analysis have been performed. Data showed that the loss/reduction of TRPML-1 mRNA expression strongly correlates with short survival in glioblastoma (GBM) patients, suggesting that the reduction of TRPML-1 expression represents a negative prognostic factor in GBM patients.
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Polyphosphoinositides in the nucleus: Roadmap of their effectors and mechanisms of interaction. Adv Biol Regul 2019; 72:7-21. [PMID: 31003946 DOI: 10.1016/j.jbior.2019.04.001] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2019] [Revised: 04/02/2019] [Accepted: 04/03/2019] [Indexed: 01/01/2023]
Abstract
Biomolecular interactions between proteins and polyphosphoinositides (PPIn) are essential in the regulation of the vast majority of cellular processes. Consequently, alteration of these interactions is implicated in the development of many diseases. PPIn are phosphorylated derivatives of phosphatidylinositol and consist of seven species with different phosphate combinations. PPIn signal by recruiting proteins via canonical domains or short polybasic motifs. Although their actions are predominantly documented on cytoplasmic membranes, six of the seven PPIn are present within the nucleus together with the PPIn kinases, phosphatases and phospholipases that regulate their turnover. Importantly, the contribution of nuclear PPIn in the regulation of nuclear processes has led to an increased recognition of their importance compared to their more accepted cytoplasmic roles. This review summarises our knowledge on the identification and functional characterisation of nuclear PPIn-effector proteins as well as their mode of interactions, which tend to favour polybasic motifs.
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Dominguez-Berrocal L, Cirri E, Zhang X, Andrini L, Marin GH, Lebel-Binay S, Rebollo A. New Therapeutic Approach for Targeting Hippo Signalling Pathway. Sci Rep 2019; 9:4771. [PMID: 30886324 PMCID: PMC6423280 DOI: 10.1038/s41598-019-41404-w] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2018] [Accepted: 03/08/2019] [Indexed: 12/29/2022] Open
Abstract
Nuclear localization signals are short amino acid sequences that target proteins for nuclear import. In this manuscript, we have generated a chimeric tri-functional peptide composed of a cell penetrating peptide (CPP), a nuclear localization sequence and an interfering peptide blocking the interaction between TEAD and YAP, two transcription factors involved in the Hippo signalling pathway, whose deregulation is related to several types of cancer. We have validated the cell penetration and nuclear localization by flow cytometry and fluorescence microscopy and shown that the new generated peptide displays an apoptotic effect in tumor cell lines thanks to the specific nuclear delivery of the cargo, which targets a protein/protein interaction in the nucleus. In addition, the peptide has an anti-tumoral effect in vivo in xenograft models of breast cancer. The chimeric peptide designed in the current study shows encouraging prospects for developing nuclear anti- neoplastic drugs.
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Affiliation(s)
| | - Erica Cirri
- PEP Therapy, 45 rue du Cardinal Lemoine, 75005, Paris, France
| | - Xiguang Zhang
- CIMI Paris, Inserm U1135, 91, bd de l'hôpital, 75013, Paris, France
| | - Laura Andrini
- Facultad de Ciencias Medicas, UNLP-CONICET, 60 and 120, Code, 1900, La Plata, Argentina
| | - Gustavo H Marin
- Facultad de Ciencias Medicas, UNLP-CONICET, 60 and 120, Code, 1900, La Plata, Argentina
| | | | - Angelita Rebollo
- CIMI Paris, Inserm U1135, 91, bd de l'hôpital, 75013, Paris, France.
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26
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Dey KK. Dynamic Coupling at Low Reynolds Number. Angew Chem Int Ed Engl 2019; 58:2208-2228. [DOI: 10.1002/anie.201804599] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2018] [Indexed: 01/10/2023]
Affiliation(s)
- Krishna Kanti Dey
- Discipline of PhysicsIndian Institute of Technology Gandhinagar Gandhinagar Gujarat 382355 India
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Qadir A, Gao Y, Suryaji P, Tian Y, Lin X, Dang K, Jiang S, Li Y, Miao Z, Qian A. Non-Viral Delivery System and Targeted Bone Disease Therapy. Int J Mol Sci 2019; 20:ijms20030565. [PMID: 30699924 PMCID: PMC6386958 DOI: 10.3390/ijms20030565] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2018] [Revised: 01/25/2019] [Accepted: 01/27/2019] [Indexed: 01/01/2023] Open
Abstract
Skeletal systems provide support, movement, and protection to the human body. It can be affected by several life suffering bone disorders such as osteoporosis, osteoarthritis, and bone cancers. It is not an easy job to treat bone disorders because of avascular cartilage regions. Treatment with non-specific drug delivery must utilize high doses of systemic administration, which may result in toxicities in non-skeletal tissues and low therapeutic efficacy. Therefore, in order to overcome such limitations, developments in targeted delivery systems are urgently needed. Although the idea of a general targeted delivery system using bone targeting moieties like bisphosphonates, tetracycline, and calcium phosphates emerged a few decades ago, identification of carrier systems like viral and non-viral vectors is a recent approach. Viral vectors have high transfection efficiency but are limited by inducing immunogenicity and oncogenicity. Although non-viral vectors possess low transfection efficiency they are comparatively safe. A number of non-viral vectors including cationic lipids, cationic polymers, and cationic peptides have been developed and used for targeted delivery of DNA, RNA, and drugs to bone tissues or cells with successful consequences. Here we mainly discuss such various non-viral delivery systems with respect to their mechanisms and applications in the specific targeting of bone tissues or cells. Moreover, we discuss possible therapeutic agents that can be delivered against various bone related disorders.
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Affiliation(s)
- Abdul Qadir
- Lab for Bone Metabolism, Key Lab for Space Biosciences and Biotechnology, School of Life Sciences, Northwestern Polytechnical University, Xi'an 710072, Shaanxi, China.
- Research Center for Special Medicine and Health Systems Engineering, School of Life Sciences, Northwestern Polytechnical University, Xi'an 710072, Shaanxi, China.
- NPU-UAB Joint Laboratory for Bone Metabolism, School of Life Sciences, Northwestern Polytechnical University, Xi'an 710072, Shaanxi, China.
| | - Yongguang Gao
- Lab for Bone Metabolism, Key Lab for Space Biosciences and Biotechnology, School of Life Sciences, Northwestern Polytechnical University, Xi'an 710072, Shaanxi, China.
- Research Center for Special Medicine and Health Systems Engineering, School of Life Sciences, Northwestern Polytechnical University, Xi'an 710072, Shaanxi, China.
- NPU-UAB Joint Laboratory for Bone Metabolism, School of Life Sciences, Northwestern Polytechnical University, Xi'an 710072, Shaanxi, China.
| | - Patil Suryaji
- Lab for Bone Metabolism, Key Lab for Space Biosciences and Biotechnology, School of Life Sciences, Northwestern Polytechnical University, Xi'an 710072, Shaanxi, China.
- Research Center for Special Medicine and Health Systems Engineering, School of Life Sciences, Northwestern Polytechnical University, Xi'an 710072, Shaanxi, China.
- NPU-UAB Joint Laboratory for Bone Metabolism, School of Life Sciences, Northwestern Polytechnical University, Xi'an 710072, Shaanxi, China.
| | - Ye Tian
- Lab for Bone Metabolism, Key Lab for Space Biosciences and Biotechnology, School of Life Sciences, Northwestern Polytechnical University, Xi'an 710072, Shaanxi, China.
- Research Center for Special Medicine and Health Systems Engineering, School of Life Sciences, Northwestern Polytechnical University, Xi'an 710072, Shaanxi, China.
- NPU-UAB Joint Laboratory for Bone Metabolism, School of Life Sciences, Northwestern Polytechnical University, Xi'an 710072, Shaanxi, China.
| | - Xiao Lin
- Lab for Bone Metabolism, Key Lab for Space Biosciences and Biotechnology, School of Life Sciences, Northwestern Polytechnical University, Xi'an 710072, Shaanxi, China.
- Research Center for Special Medicine and Health Systems Engineering, School of Life Sciences, Northwestern Polytechnical University, Xi'an 710072, Shaanxi, China.
- NPU-UAB Joint Laboratory for Bone Metabolism, School of Life Sciences, Northwestern Polytechnical University, Xi'an 710072, Shaanxi, China.
| | - Kai Dang
- Lab for Bone Metabolism, Key Lab for Space Biosciences and Biotechnology, School of Life Sciences, Northwestern Polytechnical University, Xi'an 710072, Shaanxi, China.
- Research Center for Special Medicine and Health Systems Engineering, School of Life Sciences, Northwestern Polytechnical University, Xi'an 710072, Shaanxi, China.
- NPU-UAB Joint Laboratory for Bone Metabolism, School of Life Sciences, Northwestern Polytechnical University, Xi'an 710072, Shaanxi, China.
| | - Shanfeng Jiang
- Lab for Bone Metabolism, Key Lab for Space Biosciences and Biotechnology, School of Life Sciences, Northwestern Polytechnical University, Xi'an 710072, Shaanxi, China.
- Research Center for Special Medicine and Health Systems Engineering, School of Life Sciences, Northwestern Polytechnical University, Xi'an 710072, Shaanxi, China.
- NPU-UAB Joint Laboratory for Bone Metabolism, School of Life Sciences, Northwestern Polytechnical University, Xi'an 710072, Shaanxi, China.
| | - Yu Li
- Lab for Bone Metabolism, Key Lab for Space Biosciences and Biotechnology, School of Life Sciences, Northwestern Polytechnical University, Xi'an 710072, Shaanxi, China.
- Research Center for Special Medicine and Health Systems Engineering, School of Life Sciences, Northwestern Polytechnical University, Xi'an 710072, Shaanxi, China.
- NPU-UAB Joint Laboratory for Bone Metabolism, School of Life Sciences, Northwestern Polytechnical University, Xi'an 710072, Shaanxi, China.
| | - Zhiping Miao
- Lab for Bone Metabolism, Key Lab for Space Biosciences and Biotechnology, School of Life Sciences, Northwestern Polytechnical University, Xi'an 710072, Shaanxi, China.
- Research Center for Special Medicine and Health Systems Engineering, School of Life Sciences, Northwestern Polytechnical University, Xi'an 710072, Shaanxi, China.
- NPU-UAB Joint Laboratory for Bone Metabolism, School of Life Sciences, Northwestern Polytechnical University, Xi'an 710072, Shaanxi, China.
| | - Airong Qian
- Lab for Bone Metabolism, Key Lab for Space Biosciences and Biotechnology, School of Life Sciences, Northwestern Polytechnical University, Xi'an 710072, Shaanxi, China.
- Research Center for Special Medicine and Health Systems Engineering, School of Life Sciences, Northwestern Polytechnical University, Xi'an 710072, Shaanxi, China.
- NPU-UAB Joint Laboratory for Bone Metabolism, School of Life Sciences, Northwestern Polytechnical University, Xi'an 710072, Shaanxi, China.
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Affiliation(s)
- Krishna Kanti Dey
- Discipline of Physics; Indian Institute of Technology Gandhinagar; Gandhinagar Gujarat 382355 Indien
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29
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Sumoylated α-synuclein translocates into the nucleus by karyopherin α6. Mol Cell Toxicol 2018. [DOI: 10.1007/s13273-019-0012-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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Kirby TW, Pedersen LC, Gabel SA, Gassman NR, London RE. Variations in nuclear localization strategies among pol X family enzymes. Traffic 2018; 19:10.1111/tra.12600. [PMID: 29931796 PMCID: PMC6684861 DOI: 10.1111/tra.12600] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2017] [Revised: 06/19/2018] [Accepted: 06/20/2018] [Indexed: 12/22/2022]
Abstract
Despite the essential roles of pol X family enzymes in DNA repair, information about the structural basis of their nuclear import is limited. Recent studies revealed the unexpected presence of a functional nuclear localization signal (NLS) in DNA polymerase β, indicating the importance of active nuclear targeting, even for enzymes likely to leak into and out of the nucleus. The current studies further explore the active nuclear transport of these enzymes by identifying and structurally characterizing the functional NLS sequences in the three remaining human pol X enzymes: terminal deoxynucleotidyl transferase (TdT), DNA polymerase mu (pol μ) and DNA polymerase lambda (pol λ). NLS identifications are based on Importin α (Impα) binding affinity determined by fluorescence polarization of fluorescein-labeled NLS peptides, X-ray crystallographic analysis of the Impα∆IBB•NLS complexes and fluorescence-based subcellular localization studies. All three polymerases use NLS sequences located near their N-terminus; TdT and pol μ utilize monopartite NLS sequences, while pol λ utilizes a bipartite sequence, unique among the pol X family members. The pol μ NLS has relatively weak measured affinity for Impα, due in part to its proximity to the N-terminus that limits non-specific interactions of flanking residues preceding the NLS. However, this effect is partially mitigated by an N-terminal sequence unsupportive of Met1 removal by methionine aminopeptidase, leading to a 3-fold increase in affinity when the N-terminal methionine is present. Nuclear targeting is unique to each pol X family enzyme with variations dependent on the structure and unique functional role of each polymerase.
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Affiliation(s)
- Thomas W Kirby
- National Institute of Environmental Health Sciences, Genome Integrity and Structural Biology Laboratory, National Institutes of Health, Research Triangle Park, North Carolina
| | - Lars C Pedersen
- National Institute of Environmental Health Sciences, Genome Integrity and Structural Biology Laboratory, National Institutes of Health, Research Triangle Park, North Carolina
| | - Scott A Gabel
- National Institute of Environmental Health Sciences, Genome Integrity and Structural Biology Laboratory, National Institutes of Health, Research Triangle Park, North Carolina
| | - Natalie R Gassman
- Molecular & Metabolic Oncology, University of South Alabama Mitchell Cancer Institute, Mobile, Alabama
| | - Robert E London
- National Institute of Environmental Health Sciences, Genome Integrity and Structural Biology Laboratory, National Institutes of Health, Research Triangle Park, North Carolina
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Wu P, Chen H, Jin R, Weng T, Ho JK, You C, Zhang L, Wang X, Han C. Non-viral gene delivery systems for tissue repair and regeneration. J Transl Med 2018; 16:29. [PMID: 29448962 PMCID: PMC5815227 DOI: 10.1186/s12967-018-1402-1] [Citation(s) in RCA: 64] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2017] [Accepted: 02/07/2018] [Indexed: 12/11/2022] Open
Abstract
Critical tissue defects frequently result from trauma, burns, chronic wounds and/or surgery. The ideal treatment for such tissue loss is autografting, but donor sites are often limited. Tissue engineering (TE) is an inspiring alternative for tissue repair and regeneration (TRR). One of the current state-of-the-art methods for TRR is gene therapy. Non-viral gene delivery systems (nVGDS) have great potential for TE and have several advantages over viral delivery including lower immunogenicity and toxicity, better cell specificity, better modifiability, and higher productivity. However, there is no ideal nVGDS for TRR, hence, there is widespread research to improve their properties. This review introduces the basic principles and key aspects of commonly-used nVGDSs. We focus on recent advances in their applications, current challenges, and future directions.
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Affiliation(s)
- Pan Wu
- Department of Burns & Wound Care Center, Second Affiliated Hospital of Medical College, Zhejiang University, Hangzhou, 310009, China
| | - Haojiao Chen
- Department of Burns & Wound Care Center, Second Affiliated Hospital of Medical College, Zhejiang University, Hangzhou, 310009, China
| | - Ronghua Jin
- Department of Burns & Wound Care Center, Second Affiliated Hospital of Medical College, Zhejiang University, Hangzhou, 310009, China
| | - Tingting Weng
- Department of Burns & Wound Care Center, Second Affiliated Hospital of Medical College, Zhejiang University, Hangzhou, 310009, China
| | - Jon Kee Ho
- Department of Burns & Wound Care Center, Second Affiliated Hospital of Medical College, Zhejiang University, Hangzhou, 310009, China
| | - Chuangang You
- Department of Burns & Wound Care Center, Second Affiliated Hospital of Medical College, Zhejiang University, Hangzhou, 310009, China
| | - Liping Zhang
- Department of Burns & Wound Care Center, Second Affiliated Hospital of Medical College, Zhejiang University, Hangzhou, 310009, China
| | - Xingang Wang
- Department of Burns & Wound Care Center, Second Affiliated Hospital of Medical College, Zhejiang University, Hangzhou, 310009, China.
| | - Chunmao Han
- Department of Burns & Wound Care Center, Second Affiliated Hospital of Medical College, Zhejiang University, Hangzhou, 310009, China.
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Bridges RJ, Bradbury NA. Cystic Fibrosis, Cystic Fibrosis Transmembrane Conductance Regulator and Drugs: Insights from Cellular Trafficking. Handb Exp Pharmacol 2018; 245:385-425. [PMID: 29460152 DOI: 10.1007/164_2018_103] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
The eukaryotic cell is organized into membrane-delineated compartments that are characterized by specific cadres of proteins sustaining biochemically distinct cellular processes. The appropriate subcellular localization of proteins is key to proper organelle function and provides a physiological context for cellular processes. Disruption of normal trafficking pathways for proteins is seen in several genetic diseases, where a protein's absence for a specific subcellular compartment leads to organelle disruption, and in the context of an individual, a disruption of normal physiology. Importantly, several drug therapies can also alter protein trafficking, causing unwanted side effects. Thus, a deeper understanding of trafficking pathways needs to be appreciated as novel therapeutic modalities are proposed. Despite the promising efficacy of novel therapeutic agents, the intracellular bioavailability of these compounds has proved to be a potential barrier, leading to failures in treatments for various diseases and disorders. While endocytosis of drug moieties provides an efficient means of getting material into cells, the subsequent release and endosomal escape of materials into the cytosol where they need to act has been a barrier. An understanding of cellular protein/lipid trafficking pathways has opened up strategies for increasing drug bioavailability. Approaches to enhance endosomal exit have greatly increased the cytosolic bioavailability of drugs and will provide a means of investigating previous drugs that may have been shelved due to their low cytosolic concentration.
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Affiliation(s)
- Robert J Bridges
- Department of Physiology and Biophysics, Chicago Medical School, North Chicago, IL, USA
| | - Neil A Bradbury
- Department of Physiology and Biophysics, Chicago Medical School, North Chicago, IL, USA.
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33
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Lai WF, Rogach AL, Wong WT. Molecular design of upconversion nanoparticles for gene delivery. Chem Sci 2017; 8:7339-7358. [PMID: 29163885 PMCID: PMC5672820 DOI: 10.1039/c7sc02956j] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2017] [Accepted: 08/29/2017] [Indexed: 12/17/2022] Open
Abstract
Due to their large anti-Stokes shifts, sharp emission spectra and long excited-state lifetimes, upconversion nanoparticles (UCNPs) have attracted an increasing amount of research interests, and have shown great potential for enhancing the practical utility of gene therapy, whose versatility has been limited by existing gene delivery technologies that are basically mono-functional in nature. Despite this, up to now in-depth analysis of the development of UCNPs for gene delivery has been scant in the literature, even though there has been an upsurge of reviews on the chemistry of UCNPs and their applications in bioimaging and drug delivery. To fill this gap, this review aims to present the latest advances in the development and applications of UCNPs as gene carriers. Prior to describing the prominent works published in the field, a critical view on the properties, chemistry and molecular design of UCNPs for gene delivery is provided. With a synopsis of the recent advances in UCNP-mediated gene delivery, challenges and opportunities could be illuminated for clinical translation of works in this nascent field of research.
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Affiliation(s)
- Wing-Fu Lai
- School of Pharmaceutical Sciences , Health Science Centre , Shenzhen University , Shenzhen , China
- Department of Applied Biology & Chemical Technology , The Hong Kong Polytechnic University , Hong Kong . ;
| | - Andrey L Rogach
- Department of Materials Science and Engineering & Centre for Functional Photonics (CFP) , City University of Hong Kong , Hong Kong
| | - Wing-Tak Wong
- Department of Applied Biology & Chemical Technology , The Hong Kong Polytechnic University , Hong Kong . ;
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Kirby TW, Gassman NR, Smith CE, Zhao ML, Horton JK, Wilson SH, London RE. DNA polymerase β contains a functional nuclear localization signal at its N-terminus. Nucleic Acids Res 2017; 45:1958-1970. [PMID: 27956495 PMCID: PMC5389473 DOI: 10.1093/nar/gkw1257] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2016] [Accepted: 12/02/2016] [Indexed: 12/23/2022] Open
Abstract
DNA polymerase β (pol β) requires nuclear localization to fulfil its DNA repair function. Although its small size has been interpreted to imply the absence of a need for active nuclear import, sequence and structural analysis suggests that a monopartite nuclear localization signal (NLS) may reside in the N-terminal lyase domain. Binding of this domain to Importin α1 (Impα1) was confirmed by gel filtration and NMR studies. Affinity was quantified by fluorescence polarization analysis of a fluorescein-tagged peptide corresponding to pol β residues 2–13. These studies indicate high affinity binding, characterized by a low micromolar Kd, that is selective for the murine Importin α1 (mImpα1) minor site, with the Kd strengthening to ∼140 nM for the full lyase domain (residues 2–87). A further reduction in Kd obtains in binding studies with human Importin α5 (hImpα5), which in some cases has been demonstrated to bind small domains connected to the NLS. The role of this NLS was confirmed by fluorescent imaging of wild-type and NLS-mutated pol β(R4S,K5S) in mouse embryonic fibroblasts lacking endogenous pol β. Together these data demonstrate that pol β contains a specific NLS sequence in the N-terminal lyase domain that promotes transport of the protein independent of its interaction partners. Active nuclear uptake allows development of a nuclear/cytosolic concentration gradient against a background of passive diffusion.
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Affiliation(s)
- Thomas W Kirby
- National Institute of Environmental Health Sciences, Genome Integrity and Structural Biology Laboratory, National Institutes of Health, Research Triangle Park, NC 27709, USA
| | - Natalie R Gassman
- National Institute of Environmental Health Sciences, Genome Integrity and Structural Biology Laboratory, National Institutes of Health, Research Triangle Park, NC 27709, USA
| | - Cassandra E Smith
- National Institute of Environmental Health Sciences, Genome Integrity and Structural Biology Laboratory, National Institutes of Health, Research Triangle Park, NC 27709, USA
| | - Ming-Lang Zhao
- National Institute of Environmental Health Sciences, Genome Integrity and Structural Biology Laboratory, National Institutes of Health, Research Triangle Park, NC 27709, USA
| | - Julie K Horton
- National Institute of Environmental Health Sciences, Genome Integrity and Structural Biology Laboratory, National Institutes of Health, Research Triangle Park, NC 27709, USA
| | - Samuel H Wilson
- National Institute of Environmental Health Sciences, Genome Integrity and Structural Biology Laboratory, National Institutes of Health, Research Triangle Park, NC 27709, USA
| | - Robert E London
- National Institute of Environmental Health Sciences, Genome Integrity and Structural Biology Laboratory, National Institutes of Health, Research Triangle Park, NC 27709, USA
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Sun Y, Yang Z, Wang C, Yang T, Cai C, Zhao X, Yang L, Ding P. Exploring the role of peptides in polymer-based gene delivery. Acta Biomater 2017; 60:23-37. [PMID: 28778533 DOI: 10.1016/j.actbio.2017.07.043] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2017] [Revised: 07/14/2017] [Accepted: 07/31/2017] [Indexed: 12/15/2022]
Abstract
Polymers are widely studied as non-viral gene vectors because of their strong DNA binding ability, capacity to carry large payload, flexibility of chemical modifications, low immunogenicity, and facile processes for manufacturing. However, high cytotoxicity and low transfection efficiency substantially restrict their application in clinical trials. Incorporating functional peptides is a promising approach to address these issues. Peptides demonstrate various functions in polymer-based gene delivery systems, such as targeting to specific cells, breaching membrane barriers, facilitating DNA condensation and release, and lowering cytotoxicity. In this review, we systematically summarize the role of peptides in polymer-based gene delivery, and elaborate how to rationally design polymer-peptide based gene delivery vectors. STATEMENT OF SIGNIFICANCE Polymers are widely studied as non-viral gene vectors, but suffer from high cytotoxicity and low transfection efficiency. Incorporating short, bioactive peptides into polymer-based gene delivery systems can address this issue. Peptides demonstrate various functions in polymer-based gene delivery systems, such as targeting to specific cells, breaching membrane barriers, facilitating DNA condensation and release, and lowering cytotoxicity. In this review, we highlight the peptides' roles in polymer-based gene delivery, and elaborate how to utilize various functional peptides to enhance the transfection efficiency of polymers. The optimized peptide-polymer vectors should be able to alter their structures and functions according to biological microenvironments and utilize inherent intracellular pathways of cells, and consequently overcome the barriers during gene delivery to enhance transfection efficiency.
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Affiliation(s)
- Yanping Sun
- School of Pharmacy, Shenyang Pharmaceutical University, Shenyang 110016, China
| | - Zhen Yang
- School of Pharmacy, Shenyang Pharmaceutical University, Shenyang 110016, China
| | - Chunxi Wang
- School of Pharmacy, Shenyang Pharmaceutical University, Shenyang 110016, China
| | - Tianzhi Yang
- Department of Basic Pharmaceutical Sciences, School of Pharmacy, Husson University, Bangor, ME, USA
| | - Cuifang Cai
- School of Pharmacy, Shenyang Pharmaceutical University, Shenyang 110016, China
| | - Xiaoyun Zhao
- Department of Microbiology and Cell Biology, School of Life Science and Biopharmaceutics, Shenyang Pharmaceutical University, Shenyang 110016, China
| | - Li Yang
- School of Pharmacy, Shenyang Pharmaceutical University, Shenyang 110016, China.
| | - Pingtian Ding
- School of Pharmacy, Shenyang Pharmaceutical University, Shenyang 110016, China.
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Kim YH, Han ME, Oh SO. The molecular mechanism for nuclear transport and its application. Anat Cell Biol 2017; 50:77-85. [PMID: 28713609 PMCID: PMC5509903 DOI: 10.5115/acb.2017.50.2.77] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2017] [Accepted: 03/31/2017] [Indexed: 12/30/2022] Open
Abstract
Transportation between the cytoplasm and the nucleoplasm is critical for many physiological and pathophysiological processes including gene expression, signal transduction, and oncogenesis. So, the molecular mechanism for the transportation needs to be studied not only to understand cell physiological processes but also to develop new diagnostic and therapeutic targets. Recent progress in the research of the nuclear transportation (import and export) via nuclear pore complex and four important factors affecting nuclear transport (nucleoporins, Ran, karyopherins, and nuclear localization signals/nuclear export signals) will be discussed. Moreover, the clinical significance of nuclear transport and its application will be reviewed. This review will provide some critical insight for the molecular design of therapeutics which need to be targeted inside the nucleus.
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Affiliation(s)
- Yun Hak Kim
- Department of Anatomy, Pusan National University School of Medicine, Yangsan, Korea.,BEER, Busan Society of Evidence-Based mEdicine and Research, Busan, Korea.,Gene and Cell Therapy Research Center for Vessel-associated Diseases, Pusan National University, Yangsan, Korea
| | - Myoung-Eun Han
- Department of Anatomy, Pusan National University School of Medicine, Yangsan, Korea.,Gene and Cell Therapy Research Center for Vessel-associated Diseases, Pusan National University, Yangsan, Korea
| | - Sae-Ock Oh
- Department of Anatomy, Pusan National University School of Medicine, Yangsan, Korea.,Gene and Cell Therapy Research Center for Vessel-associated Diseases, Pusan National University, Yangsan, Korea
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Zhang J, Roggero VR, Allison LA. Nuclear Import and Export of the Thyroid Hormone Receptor. VITAMINS AND HORMONES 2017; 106:45-66. [PMID: 29407444 DOI: 10.1016/bs.vh.2017.04.002] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
The thyroid hormone receptors, TRα1 and TRβ1, are members of the nuclear receptor superfamily that forms one of the most abundant classes of transcription factors in multicellular organisms. Although primarily localized to the nucleus, TRα1 and TRβ1 shuttle rapidly between the nucleus and cytoplasm. The fine balance between nuclear import and export of TRs has emerged as a critical control point for modulating thyroid hormone-responsive gene expression. Mutagenesis studies have defined two nuclear localization signal (NLS) motifs that direct nuclear import of TRα1: NLS-1 in the hinge domain and NLS-2 in the N-terminal A/B domain. Three nuclear export signal (NES) motifs reside in the ligand-binding domain. A combined approach of shRNA-mediated knockdown and coimmunoprecipitation assays revealed that nuclear entry of TRα1 is facilitated by importin 7, likely through interactions with NLS-2, and importin β1 and the adapter importin α1 interacting with both NLS-1 and NLS-2. Interestingly, TRβ1 lacks NLS-2 and nuclear import depends solely on the importin α1/β1 heterodimer. Heterokaryon and fluorescence recovery after photobleaching shuttling assays identified multiple exportins that play a role in nuclear export of TRα1, including CRM1 (exportin 1), and exportins 4, 5, and 7. Even single amino acid changes in TRs dramatically alter their intracellular distribution patterns. We conclude that mutations within NLS and NES motifs affect nuclear shuttling activity, and propose that TR mislocalization contributes to the development of some types of cancer and Resistance to Thyroid Hormone syndrome.
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Affiliation(s)
- Jibo Zhang
- College of William and Mary, Williamsburg, VA, United States
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Sharip A, Abdukhakimova D, Wang X, Kim A, Kim Y, Sharip A, Orakov A, Miao L, Sun Q, Chen Y, Chen Z, Xie Y. Analysis of origin and protein-protein interaction maps suggests distinct oncogenic role of nuclear EGFR during cancer evolution. J Cancer 2017; 8:903-912. [PMID: 28382154 PMCID: PMC5381180 DOI: 10.7150/jca.17961] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2016] [Accepted: 12/30/2016] [Indexed: 02/07/2023] Open
Abstract
Receptor tyrosine kinase EGFR usually is localized on plasma membrane to induce progression of many cancers including cancers in children (Bodey et al. In Vivo. 2005, 19:931-41), but it contains a nuclear localization signal (NLS) that mediates EGFR nuclear translocation (Lin et al. Nat Cell Biol. 2001, 3:802-8). Here we report that NLS of EGFR has its old evolutionary origin. Protein-protein interaction maps suggests that nEGFR pathways are different from membrane EGFR and EGF is not found in nEGFR network while androgen receptor (AR) is found, which suggests the evolution of prostate cancer, a well-known AR driven cancer, through changes in androgen- or EGF-dependence. Database analysis suggests that nEGFR correlates with the tumor grades especially in prostate cancer patients. Structural predication analysis suggests that NLS can compromise the differential protein binding to EGFR through stretch linkers with evolutionary mutation from N to V. In experiment, elevation of nEGFR but not membrane EGFR was found in castration resistant prostate cancer cells. Finally, systems analysis of NLS and transmembrane domain (TM) suggests that NLS has old origin while NLS neighboring domain of TM has been undergone accelerated evolution. Thus nEGFR has an old origin resembling the cancer evolution but TM may interfere with NLS driven signaling for natural selection of survival to evade NLS induced aggressive cancers. Our data suggest NLS is a dynamic inducer of EGFR oncogenesis during evolution for advanced cancers. Our model provides novel insights into the evolutionary role of NLS of oncogenic kinases in cancers.
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Affiliation(s)
- Ainur Sharip
- Department of Biology, School of Science and Technology, Nazarbayev University, Astana, 010000, Republic of Kazakhstan
| | - Diyora Abdukhakimova
- Department of Biology, School of Science and Technology, Nazarbayev University, Astana, 010000, Republic of Kazakhstan
| | - Xiao Wang
- Shandong Analysis and Test Center, Shandong Academy of Sciences, 19 Keyuan Street, Jinan, 250014, P.R. China
| | - Alexey Kim
- Department of Biology, School of Science and Technology, Nazarbayev University, Astana, 010000, Republic of Kazakhstan
| | - Yevgeniy Kim
- Department of Biology, School of Science and Technology, Nazarbayev University, Astana, 010000, Republic of Kazakhstan
| | - Aigul Sharip
- Department of Biology, School of Science and Technology, Nazarbayev University, Astana, 010000, Republic of Kazakhstan
| | - Askarbek Orakov
- Department of Biology, School of Science and Technology, Nazarbayev University, Astana, 010000, Republic of Kazakhstan
| | - Lixia Miao
- College of Basic Medicine, Wuhan University, Wuhan, 430071, P.R. China
| | - Qinglei Sun
- Shandong Analysis and Test Center, Shandong Academy of Sciences, 19 Keyuan Street, Jinan, 250014, P.R. China
| | - Yue Chen
- Department of Mechanical Engineering, Vanderbilt University, Nashville, TN, 37203, USA
| | - Zhenbang Chen
- Department of Biochemistry and Cancer Biology, Meharry Medical College, Nashville, TN, 37201, USA
| | - Yingqiu Xie
- Department of Biology, School of Science and Technology, Nazarbayev University, Astana, 010000, Republic of Kazakhstan
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Munsell EV, Ross NL, Sullivan MO. Journey to the Center of the Cell: Current Nanocarrier Design Strategies Targeting Biopharmaceuticals to the Cytoplasm and Nucleus. Curr Pharm Des 2016; 22:1227-44. [PMID: 26675220 DOI: 10.2174/1381612822666151216151420] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2015] [Accepted: 12/15/2015] [Indexed: 01/06/2023]
Abstract
New biopharmaceutical molecules, potentially able to provide more personalized and effective treatments, are being identified through the advent of advanced synthetic biology strategies, sophisticated chemical synthesis approaches, and new analytical methods to assess biological potency. However, translation of many of these structures has been significantly limited due to the need for more efficient strategies to deliver macromolecular therapeutics to desirable intracellular sites of action. Engineered nanocarriers that encapsulate peptides, proteins, or nucleic acids are generally internalized into target cells via one of several endocytic pathways. These nanostructures, entrapped within endosomes, must navigate the intracellular milieu to orchestrate delivery to the intended destination, typically the cytoplasm or nucleus. For therapeutics active in the cytoplasm, endosomal escape continues to represent a limiting step to effective treatment, since a majority of nanocarriers trapped within endosomes are ultimately marked for enzymatic degradation in lysosomes. Therapeutics active in the nucleus have the added challenges of reaching and penetrating the nuclear envelope, and nuclear delivery remains a preeminent challenge preventing clinical translation of gene therapy applications. Herein, we review cutting-edge peptide- and polymer-based design strategies with the potential to enable significant improvements in biopharmaceutical efficacy through improved intracellular targeting. These strategies often mimic the activities of pathogens, which have developed innate and highly effective mechanisms to penetrate plasma membranes and enter the nucleus of host cells. Understanding these mechanisms has enabled advances in synthetic peptide and polymer design that may ultimately improve intracellular trafficking and bioavailability, leading to increased access to new classes of biotherapeutics.
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Affiliation(s)
| | | | - Millicent O Sullivan
- Department of Chemical and Biomolecular Engineering, University of Delaware, 150 Academy Street, Newark, DE 19716, Delaware.
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Ross C, Upfold N, Luke GA, Bishop ÖT, Knox C. Subcellular localisation of Theiler's murine encephalomyelitis virus (TMEV) capsid subunit VP1 vis-á-vis host protein Hsp90. Virus Res 2016; 222:53-63. [PMID: 27269472 DOI: 10.1016/j.virusres.2016.06.003] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2016] [Revised: 05/30/2016] [Accepted: 06/02/2016] [Indexed: 01/25/2023]
Abstract
The VP1 subunit of the picornavirus capsid is the major antigenic determinant and mediates host cell attachment and virus entry. To investigate the localisation of Theiler's murine encephalomyelitis virus (TMEV) VP1 during infection, a bioinformatics approach was used to predict a surface-exposed, linear epitope region of the protein for subsequent expression and purification. This region, comprising the N-terminal 112 amino acids of the protein, was then used for rabbit immunisation, and the resultant polyclonal antibodies were able to recognise full length VP1 in infected cell lysates by Western blot. Following optimisation, the antibodies were used to investigate the localisation of VP1 in relation to Hsp90 in infected cells by indirect immunofluorescence and confocal microscopy. At 5h post infection, VP1 was distributed diffusely in the cytoplasm with strong perinuclear staining but was absent from the nucleus of all cells analysed. Dual-label immunofluorescence using anti-TMEV VP1 and anti-Hsp90 antibodies indicated that the distribution of both proteins colocalised in the cytoplasm and perinuclear region of infected cells. This is the first report describing the localisation of TMEV VP1 in infected cells, and the antibodies produced provide a valuable tool for investigating the poorly understood mechanisms underlying the early steps of picornavirus assembly.
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Affiliation(s)
- Caroline Ross
- Research Unit in Bioinformatics (RUBi), Department of Biochemistry and Microbiology, Rhodes University, Grahamstown, 6140, South Africa
| | - Nicole Upfold
- Department of Biochemistry and Microbiology, Rhodes University, Grahamstown, 6140, South Africa
| | - Garry A Luke
- Centre for Biomolecular Sciences, School of Biology, Biomolecular Sciences Building, University of St. Andrews, North Haugh, St. Andrews, Scotland KY16 9ST, UK
| | - Özlem Tastan Bishop
- Research Unit in Bioinformatics (RUBi), Department of Biochemistry and Microbiology, Rhodes University, Grahamstown, 6140, South Africa
| | - Caroline Knox
- Department of Biochemistry and Microbiology, Rhodes University, Grahamstown, 6140, South Africa.
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Duan J, Tang Z, Mu H, Zhang G. Nuclear import of prototype foamy virus transactivator Bel1 is mediated by KPNA1, KPNA6 and KPNA7. Int J Mol Med 2016; 38:399-406. [PMID: 27277550 PMCID: PMC4935454 DOI: 10.3892/ijmm.2016.2635] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2015] [Accepted: 05/31/2016] [Indexed: 01/01/2023] Open
Abstract
Bel1, a transactivator of the prototype foamy virus (PFV), plays pivotal roles in the replication of PFV. Previous studies have demonstrated that Bel1 bears a nuclear localization signal (NLS); however, its amino acid sequence remains unclear and the corresponding adaptor importins have not yet been identified. In this study, we inserted various fragments of Bel1 into an EGFP-GST fusion protein and investigated their subcellular localization by fluorescence microscopy. We found that the 215PRQKRPR221 fragment, which accords with the consensus sequence K(K/R)X(K/R) of the monopartite NLS, directed the nuclear translocation of Bel1. Point mutation experiments revealed that K218, R219 and R221 were essential for the nuclear localization of Bel1. The results of GST pull-down assay revealed that the Bel1 peptide 215-221, which bears the NLS, interacted with the nucleocytoplasmic transport receptors, karyopherin alpha 1 (importin alpha 5) (KPNA1), karyopherin alpha 6 (importin alpha 7) (KPNA6) and karyopherin alpha 7 (importin alpha 8) (KPNA7). Finally, in vitro nuclear import assays demonstrated that KPNA1, KPNA6 or KPNA7, along with other necessary nuclear factors, caused Bel1 to localize to the nucleus. Thus, the findings of our study indicate that KPNA1, KPNA6 and KPNA7 are involved in Bel1 nuclear distribution.
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Affiliation(s)
- Jihui Duan
- Clinical Laboratory, Tianjin First Center Hospital, Tianjin 300192, P.R. China
| | - Zhiqin Tang
- Clinical Laboratory, Tianjin First Center Hospital, Tianjin 300192, P.R. China
| | - Hong Mu
- Clinical Laboratory, Tianjin First Center Hospital, Tianjin 300192, P.R. China
| | - Guojun Zhang
- Clinical Laboratory, Tianjin First Center Hospital, Tianjin 300192, P.R. China
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Namvar A, Bolhassani A, Khairkhah N, Motevalli F. Physicochemical properties of polymers: An important system to overcome the cell barriers in gene transfection. Biopolymers 2016; 103:363-75. [PMID: 25761628 DOI: 10.1002/bip.22638] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2014] [Revised: 03/04/2015] [Accepted: 03/04/2015] [Indexed: 12/22/2022]
Abstract
Delivery of the macromolecules including DNA, miRNA, and antisense oligonucleotides is typically mediated by carriers due to the large size and negative charge. Different physical (e.g., gene gun or electroporation), and chemical (e.g., cationic polymer or lipid) vectors have been already used to improve the efficiency of gene transfer. Polymer-based DNA delivery systems have attracted special interest, in particular via intravenous injection with many intra- and extracellular barriers. The recent progress has shown that stimuli-responsive polymers entitled as multifunctional nucleic acid vehicles can act to target specific cells. These nonviral carriers are classified by the type of stimulus including reduction potential, pH, and temperature. Generally, the physicochemical characterization of DNA-polymer complexes is critical to enhance the transfection potency via protection of DNA from nuclease digestion, endosomal escape, and nuclear localization. The successful clinical applications will depend on an exact insight of barriers in gene delivery and development of carriers overcoming these barriers. Consequently, improvement of novel cationic polymers with low toxicity and effective for biomedical use has attracted a great attention in gene therapy. This article summarizes the main physicochemical and biological properties of polyplexes describing their gene transfection behavior, in vitro and in vivo. In this line, the relative efficiencies of various cationic polymers are compared.
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Affiliation(s)
- Ali Namvar
- Department of Hepatitis and AIDS, Pasteur Institute of Iran, Tehran, Iran
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Schröder B. The multifaceted roles of the invariant chain CD74--More than just a chaperone. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2016; 1863:1269-81. [PMID: 27033518 DOI: 10.1016/j.bbamcr.2016.03.026] [Citation(s) in RCA: 140] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/23/2016] [Revised: 03/22/2016] [Accepted: 03/23/2016] [Indexed: 01/13/2023]
Abstract
The invariant chain (CD74) is well known for its essential role in antigen presentation by mediating assembly and subcellular trafficking of the MHCII complex. Beyond this, CD74 has also been implicated in a number of processes independent of MHCII. These include the regulation of endosomal trafficking, cell migration and cellular signalling as surface receptor of the pro-inflammatory cytokine macrophage migration inhibitory factor (MIF). In several forms of cancer, CD74 is up-regulated and associated with enhanced proliferation and metastatic potential. In this review, an overview of the diverse biological functions of the CD74 protein is provided with a particular focus on how these may be regulated. In particular, proteolysis of CD74 will be discussed as a central mechanism to control the actions of this important protein at different levels.
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Affiliation(s)
- Bernd Schröder
- Biochemical Institute, Christian Albrechts University of Kiel, Otto-Hahn-Platz 9, D-24118 Kiel, Germany.
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44
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Ross NL, Sullivan MO. Importin-4 Regulates Gene Delivery by Enhancing Nuclear Retention and Chromatin Deposition by Polyplexes. Mol Pharm 2015; 12:4488-97. [PMID: 26465823 PMCID: PMC4733562 DOI: 10.1021/acs.molpharmaceut.5b00645] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
For successful gene delivery, plasmid DNA must be able to access the nucleus in order to be transcribed. Numerous studies have shown that gene delivery occurs more readily in dividing cells, which is attributed to increased nuclear access when the nuclear envelope disassembles during mitosis; however, nonviral carriers continue to have low transfection efficiencies and require large quantities of DNA per cell to achieve reasonable gene transfer, even in dividing cells. Therefore, we hypothesized that using histone-derived nuclear localization sequences (NLS)s to target polyplexes might enhance nuclear delivery by facilitating interactions with histone effectors that mediate nuclear partitioning and retention during mitosis. We discovered a novel interaction between polyplexes linked to histone 3 (H3) N-terminal tail peptides and the histone nuclear import protein importin-4, as evidenced by strong spatial colocalization as well as significantly decreased transfection when importin-4 expression was reduced. A fraction of the histone-targeted polyplexes was also found to colocalize with the retrotranslocon of the endoplasmic reticulum, Sec61. Super resolution microscopy demonstrated a high level of polyplex binding to chromatin postmitosis, and there also was a significant decrease in the amount of chromatin binding following importin-4 knockdown. These results provide evidence that natural histone effectors mediate both nuclear entry and deposition on chromatin by histone-targeted polyplexes, and a translocation event from the endoplasmic reticulum into the cytosol may occur before mitosis to enable the polyplexes to interact with these essential cytoplasmic proteins.
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Affiliation(s)
- Nikki L Ross
- Department of Chemical and Biomolecular Engineering, University of Delaware , 150 Academy Street, Newark, Delaware 19716, United States
| | - Millicent O Sullivan
- Department of Chemical and Biomolecular Engineering, University of Delaware , 150 Academy Street, Newark, Delaware 19716, United States
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Christie M, Chang CW, Róna G, Smith KM, Stewart AG, Takeda AAS, Fontes MRM, Stewart M, Vértessy BG, Forwood JK, Kobe B. Structural Biology and Regulation of Protein Import into the Nucleus. J Mol Biol 2015; 428:2060-90. [PMID: 26523678 DOI: 10.1016/j.jmb.2015.10.023] [Citation(s) in RCA: 181] [Impact Index Per Article: 20.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2015] [Revised: 10/16/2015] [Accepted: 10/24/2015] [Indexed: 11/28/2022]
Abstract
Proteins are translated in the cytoplasm, but many need to access the nucleus to perform their functions. Understanding how these nuclear proteins are transported through the nuclear envelope and how the import processes are regulated is therefore an important aspect of understanding cell function. Structural biology has played a key role in understanding the molecular events during the transport processes and their regulation, including the recognition of nuclear targeting signals by the corresponding receptors. Here, we review the structural basis of the principal nuclear import pathways and the molecular basis of their regulation. The pathways involve transport factors that are members of the β-karyopherin family, which can bind cargo directly (e.g., importin-β, transportin-1, transportin-3, importin-13) or through adaptor proteins (e.g., importin-α, snurportin-1, symportin-1), as well as unrelated transport factors such as Hikeshi, involved in the transport of heat-shock proteins, and NTF2, involved in the transport of RanGDP. Solenoid proteins feature prominently in these pathways. Nuclear transport factors recognize nuclear targeting signals on the cargo proteins, including the classical nuclear localization signals, recognized by the adaptor importin-α, and the PY nuclear localization signals, recognized by transportin-1. Post-translational modifications, particularly phosphorylation, constitute key regulatory mechanisms operating in these pathways.
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Affiliation(s)
- Mary Christie
- The Garvan Institute of Medical Research, 384 Victoria Street, Darlinghurst, NSW 2010, Australia; St Vincent's Clinical School, University of New South Wales Faculty of Medicine, Darlinghurst, NSW 2010, Australia
| | - Chiung-Wen Chang
- School of Chemistry and Molecular Biosciences, Institute for Molecular Bioscience and Australian Infectious Diseases Research Centre, University of Queensland, Brisbane, QLD 4072, Australia; Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Gergely Róna
- Institute of Enzymology, Research Centre for Natural Sciences, Hungarian Academy of Sciences, Budapest H-1117, Hungary; Department of Applied Biotechnology and Food Sciences, Budapest University of Technology and Economics, Budapest H-1111, Hungary
| | - Kate M Smith
- School of Biomedical Sciences, Charles Sturt University, Wagga Wagga, NSW 2650, Australia
| | - Alastair G Stewart
- School of Molecular Bioscience, The University of Sydney, Sydney, NSW 2006, Australia
| | - Agnes A S Takeda
- Department of Physics and Biophysics, Institute of Biosciences, Universidade Estadual Paulista, Botucatu, São Paulo 18618-000, Brazil
| | - Marcos R M Fontes
- Department of Physics and Biophysics, Institute of Biosciences, Universidade Estadual Paulista, Botucatu, São Paulo 18618-000, Brazil
| | - Murray Stewart
- School of Chemistry and Molecular Biosciences, Institute for Molecular Bioscience and Australian Infectious Diseases Research Centre, University of Queensland, Brisbane, QLD 4072, Australia; MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge CB2 0QH, United Kingdom
| | - Beáta G Vértessy
- Institute of Enzymology, Research Centre for Natural Sciences, Hungarian Academy of Sciences, Budapest H-1117, Hungary; Department of Applied Biotechnology and Food Sciences, Budapest University of Technology and Economics, Budapest H-1111, Hungary
| | - Jade K Forwood
- School of Biomedical Sciences, Charles Sturt University, Wagga Wagga, NSW 2650, Australia
| | - Bostjan Kobe
- School of Chemistry and Molecular Biosciences, Institute for Molecular Bioscience and Australian Infectious Diseases Research Centre, University of Queensland, Brisbane, QLD 4072, Australia.
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Lim PS, Sutton CR, Rao S. Protein kinase C in the immune system: from signalling to chromatin regulation. Immunology 2015; 146:508-22. [PMID: 26194700 DOI: 10.1111/imm.12510] [Citation(s) in RCA: 77] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2015] [Revised: 06/29/2015] [Accepted: 07/15/2015] [Indexed: 12/12/2022] Open
Abstract
Protein kinase C (PKC) form a key family of enzymes involved in signalling pathways that specifically phosphorylates substrates at serine/threonine residues. Phosphorylation by PKC is important in regulating a variety of cellular events such as cell proliferation and the regulation of gene expression. In the immune system, PKCs are involved in regulating signal transduction pathways important for both innate and adaptive immunity, ultimately resulting in the expression of key immune genes. PKCs act as mediators during immune cell signalling through the immunological synapse. PKCs are traditionally known to be cytoplasmic signal transducers and are well embedded in the signalling pathways of cells to mediate the cells' response to a stimulus from the plasma membrane to the nucleus. PKCs are also found to transduce signals within the nucleus, a process that is distinct from the cytoplasmic signalling pathway. There is now growing evidence suggesting that PKC can directly regulate gene expression programmes through a non-traditional role as nuclear kinases. In this review, we will focus on the role of PKCs as key cytoplasmic signal transducers in immune cell signalling, as well as its role in nuclear signal transduction. We will also highlight recent evidence for its newly discovered regulatory role in the nucleus as a chromatin-associated kinase.
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Affiliation(s)
- Pek Siew Lim
- Discipline of Biomedical Sciences, Faculty of Applied Science, University of Canberra, Canberra, ACT, Australia
| | - Christopher Ray Sutton
- Discipline of Biomedical Sciences, Faculty of Applied Science, University of Canberra, Canberra, ACT, Australia
| | - Sudha Rao
- Discipline of Biomedical Sciences, Faculty of Applied Science, University of Canberra, Canberra, ACT, Australia
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Mentrup T, Häsler R, Fluhrer R, Saftig P, Schröder B. A Cell-Based Assay Reveals Nuclear Translocation of Intracellular Domains Released by SPPL Proteases. Traffic 2015; 16:871-92. [DOI: 10.1111/tra.12287] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2014] [Revised: 03/26/2015] [Accepted: 03/26/2015] [Indexed: 12/27/2022]
Affiliation(s)
- Torben Mentrup
- Biochemical Institute; Christian Albrechts University of Kiel; Otto-Hahn-Platz 9 D-24118 Kiel Germany
| | - Robert Häsler
- Institute of Clinical Molecular Biology; Christian Albrechts University of Kiel; Schittenhelmstr. 12 D-24105 Kiel Germany
| | - Regina Fluhrer
- Biomedizinisches Centrum (BMC); Ludwig Maximilians University of Munich; Feodor-Lynen-Strasse 17 D-81377 Munich Germany
- DZNE - German Center for Neurodegenerative Diseases; Feodor-Lynen-Strasse 17 D-81377 Munich Germany
| | - Paul Saftig
- Biochemical Institute; Christian Albrechts University of Kiel; Otto-Hahn-Platz 9 D-24118 Kiel Germany
| | - Bernd Schröder
- Biochemical Institute; Christian Albrechts University of Kiel; Otto-Hahn-Platz 9 D-24118 Kiel Germany
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48
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Pentecost M, Vashisht AA, Lester T, Voros T, Beaty SM, Park A, Wang YE, Yun TE, Freiberg AN, Wohlschlegel JA, Lee B. Evidence for ubiquitin-regulated nuclear and subnuclear trafficking among Paramyxovirinae matrix proteins. PLoS Pathog 2015; 11:e1004739. [PMID: 25782006 PMCID: PMC4363627 DOI: 10.1371/journal.ppat.1004739] [Citation(s) in RCA: 48] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2014] [Accepted: 02/10/2015] [Indexed: 11/24/2022] Open
Abstract
The paramyxovirus matrix (M) protein is a molecular scaffold required for viral morphogenesis and budding at the plasma membrane. Transient nuclear residence of some M proteins hints at non-structural roles. However, little is known regarding the mechanisms that regulate the nuclear sojourn. Previously, we found that the nuclear-cytoplasmic trafficking of Nipah virus M (NiV-M) is a prerequisite for budding, and is regulated by a bipartite nuclear localization signal (NLSbp), a leucine-rich nuclear export signal (NES), and monoubiquitination of the K258 residue within the NLSbp itself (NLSbp-lysine). To define whether the sequence determinants of nuclear trafficking identified in NiV-M are common among other Paramyxovirinae M proteins, we generated the homologous NES and NLSbp-lysine mutations in M proteins from the five major Paramyxovirinae genera. Using quantitative 3D confocal microscopy, we determined that the NES and NLSbp-lysine are required for the efficient nuclear export of the M proteins of Nipah virus, Hendra virus, Sendai virus, and Mumps virus. Pharmacological depletion of free ubiquitin or mutation of the conserved NLSbp-lysine to an arginine, which inhibits M ubiquitination, also results in nuclear and nucleolar retention of these M proteins. Recombinant Sendai virus (rSeV-eGFP) bearing the NES or NLSbp-lysine M mutants rescued at similar efficiencies to wild type. However, foci of cells expressing the M mutants displayed marked fusogenicity in contrast to wild type, and infection did not spread. Recombinant Mumps virus (rMuV-eGFP) bearing the homologous mutations showed similar defects in viral morphogenesis. Finally, shotgun proteomics experiments indicated that the interactomes of Paramyxovirinae M proteins are significantly enriched for components of the nuclear pore complex, nuclear transport receptors, and nucleolar proteins. We then synthesize our functional and proteomics data to propose a working model for the ubiquitin-regulated nuclear-cytoplasmic trafficking of cognate paramyxovirus M proteins that show a consistent nuclear trafficking phenotype. Elucidating virus-cell interactions is fundamental to understanding viral replication and identifying targets for therapeutic control of viral infection. Paramyxoviruses include human and animal pathogens of medical and agricultural significance. Their matrix (M) structural protein organizes virion assembly at the plasma membrane and mediates viral budding. While nuclear localization of M proteins has been described for some paramyxoviruses, the underlying mechanisms of nuclear trafficking and the biological relevance of this observation have remained largely unexamined. Through comparative analyses of M proteins across five Paramyxovirinae genera, we identify M proteins from at least three genera that exhibit similar nuclear trafficking phenotypes regulated by an NLSbp as well as an NES sequence within M that may mediate the interaction of M with host nuclear transport receptors. Additionally, a conserved lysine within the NLSbp of some M proteins is required for nuclear export by regulating M ubiquitination. Sendai virus engineered to express a ubiquitination-defective M does not produce infectious virus but instead displays extensive cell-cell fusion while M is retained in the nucleolus. Thus, some Paramyxovirinae M proteins undergo regulated and active nuclear and subnuclear transport, a prerequisite for viral morphogenesis, which also suggests yet to be discovered roles for M in the nucleus.
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Affiliation(s)
- Mickey Pentecost
- Department of Microbiology, Immunology, and Molecular Genetics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, California, United States of America
| | - Ajay A. Vashisht
- Department of Biological Chemistry, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, California, United States of America
| | - Talia Lester
- Department of Microbiology, Immunology, and Molecular Genetics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, California, United States of America
| | - Tim Voros
- Department of Microbiology, Immunology, and Molecular Genetics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, California, United States of America
| | - Shannon M. Beaty
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
| | - Arnold Park
- Department of Microbiology, Immunology, and Molecular Genetics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, California, United States of America
| | - Yao E. Wang
- Department of Microbiology, Immunology, and Molecular Genetics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, California, United States of America
| | - Tatyana E Yun
- Department of Pathology, University of Texas Medical Branch, Galveston, Texas, United States of America
| | - Alexander N. Freiberg
- Department of Pathology, University of Texas Medical Branch, Galveston, Texas, United States of America
| | - James A. Wohlschlegel
- Department of Biological Chemistry, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, California, United States of America
| | - Benhur Lee
- Department of Microbiology, Immunology, and Molecular Genetics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, California, United States of America
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
- * E-mail:
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Negi S, Pandey S, Srinivasan SM, Mohammed A, Guda C. LocSigDB: a database of protein localization signals. DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION 2015; 2015:bav003. [PMID: 25725059 PMCID: PMC4343182 DOI: 10.1093/database/bav003] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
LocSigDB (http://genome.unmc.edu/LocSigDB/) is a manually curated database of experimental protein localization signals for eight distinct subcellular locations; primarily in a eukaryotic cell with brief coverage of bacterial proteins. Proteins must be localized at their appropriate subcellular compartment to perform their desired function. Mislocalization of proteins to unintended locations is a causative factor for many human diseases; therefore, collection of known sorting signals will help support many important areas of biomedical research. By performing an extensive literature study, we compiled a collection of 533 experimentally determined localization signals, along with the proteins that harbor such signals. Each signal in the LocSigDB is annotated with its localization, source, PubMed references and is linked to the proteins in UniProt database along with the organism information that contain the same amino acid pattern as the given signal. From LocSigDB webserver, users can download the whole database or browse/search for data using an intuitive query interface. To date, LocSigDB is the most comprehensive compendium of protein localization signals for eight distinct subcellular locations. Database URL: http://genome.unmc.edu/LocSigDB/
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Affiliation(s)
- Simarjeet Negi
- Department of Genetics, Cell Biology and Anatomy, Bioinformatics and Systems Biology Core, Department of Biochemistry and Molecular Biology, Fred and Pamela Buffet Cancer Center and Eppley Institute for Research in Cancer and Allied Diseases, University of Nebraska Medical Center, Omaha, NE 68198, USA
| | - Sanjit Pandey
- Department of Genetics, Cell Biology and Anatomy, Bioinformatics and Systems Biology Core, Department of Biochemistry and Molecular Biology, Fred and Pamela Buffet Cancer Center and Eppley Institute for Research in Cancer and Allied Diseases, University of Nebraska Medical Center, Omaha, NE 68198, USA Department of Genetics, Cell Biology and Anatomy, Bioinformatics and Systems Biology Core, Department of Biochemistry and Molecular Biology, Fred and Pamela Buffet Cancer Center and Eppley Institute for Research in Cancer and Allied Diseases, University of Nebraska Medical Center, Omaha, NE 68198, USA
| | - Satish M Srinivasan
- Department of Genetics, Cell Biology and Anatomy, Bioinformatics and Systems Biology Core, Department of Biochemistry and Molecular Biology, Fred and Pamela Buffet Cancer Center and Eppley Institute for Research in Cancer and Allied Diseases, University of Nebraska Medical Center, Omaha, NE 68198, USA
| | - Akram Mohammed
- Department of Genetics, Cell Biology and Anatomy, Bioinformatics and Systems Biology Core, Department of Biochemistry and Molecular Biology, Fred and Pamela Buffet Cancer Center and Eppley Institute for Research in Cancer and Allied Diseases, University of Nebraska Medical Center, Omaha, NE 68198, USA
| | - Chittibabu Guda
- Department of Genetics, Cell Biology and Anatomy, Bioinformatics and Systems Biology Core, Department of Biochemistry and Molecular Biology, Fred and Pamela Buffet Cancer Center and Eppley Institute for Research in Cancer and Allied Diseases, University of Nebraska Medical Center, Omaha, NE 68198, USA Department of Genetics, Cell Biology and Anatomy, Bioinformatics and Systems Biology Core, Department of Biochemistry and Molecular Biology, Fred and Pamela Buffet Cancer Center and Eppley Institute for Research in Cancer and Allied Diseases, University of Nebraska Medical Center, Omaha, NE 68198, USA Department of Genetics, Cell Biology and Anatomy, Bioinformatics and Systems Biology Core, Department of Biochemistry and Molecular Biology, Fred and Pamela Buffet Cancer Center and Eppley Institute for Research in Cancer and Allied Diseases, University of Nebraska Medical Center, Omaha, NE 68198, USA Department of Genetics, Cell Biology and Anatomy, Bioinformatics and Systems Biology Core, Department of Biochemistry and Molecular Biology, Fred and Pamela Buffet Cancer Center and Eppley Institute for Research in Cancer and Allied Diseases, University of Nebraska Medical Center, Omaha, NE 68198, USA Department of Genetics, Cell Biology and Anatomy, Bioinformatics and Systems Biology Core, Department of Biochemistry and Molecular Biology, Fred and Pamela Buffet Cancer Center and Eppley Institute for Research in Cancer and Allied Diseases, University of Nebraska Medical Center, Omaha, NE 68198, USA
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Lin JR, Liu Z, Hu J. Computational identification of post-translational modification-based nuclear import regulations by characterizing nuclear localization signal-import receptor interaction. Proteins 2014; 82:2783-96. [DOI: 10.1002/prot.24642] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2014] [Revised: 06/18/2014] [Accepted: 06/26/2014] [Indexed: 12/16/2022]
Affiliation(s)
- Jhih-Rong Lin
- Department of Computer Science and Engineering; University of South Carolina; Columbia South Carolina 29208
| | - Zhonghao Liu
- Department of Computer Science and Engineering; University of South Carolina; Columbia South Carolina 29208
| | - Jianjun Hu
- Department of Computer Science and Engineering; University of South Carolina; Columbia South Carolina 29208
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