1
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Ewerling A, May-Simera HL. Evolutionary trajectory for nuclear functions of ciliary transport complex proteins. Microbiol Mol Biol Rev 2024:e0000624. [PMID: 38995044 DOI: 10.1128/mmbr.00006-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/13/2024] Open
Abstract
SUMMARYCilia and the nucleus were two defining features of the last eukaryotic common ancestor. In early eukaryotic evolution, these structures evolved through the diversification of a common membrane-coating ancestor, the protocoatomer. While in cilia, the descendants of this protein complex evolved into parts of the intraflagellar transport complexes and BBSome, the nucleus gained its selectivity by recruiting protocoatomer-like proteins to the nuclear envelope to form the selective nuclear pore complexes. Recent studies show a growing number of proteins shared between the proteomes of the respective organelles, and it is currently unknown how ciliary transport proteins could acquire nuclear functions and vice versa. The nuclear functions of ciliary proteins are still observable today and remain relevant for the understanding of the disease mechanisms behind ciliopathies. In this work, we review the evolutionary history of cilia and nucleus and their respective defining proteins and integrate current knowledge into theories for early eukaryotic evolution. We postulate a scenario where both compartments co-evolved and that fits current models of eukaryotic evolution, explaining how ciliary proteins and nucleoporins acquired their dual functions.
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Affiliation(s)
- Alexander Ewerling
- Faculty of Biology, Institute of Molecular Physiology, Johannes Gutenberg-University, Mainz, Germany
| | - Helen Louise May-Simera
- Faculty of Biology, Institute of Molecular Physiology, Johannes Gutenberg-University, Mainz, Germany
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2
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Shrikondawar AN, Chennoju K, Ghosh DK, Ranjan A. Identification and characterization of nuclear localization signals in the circumsporozoite protein of Plasmodium falciparum. FEBS Lett 2024; 598:801-817. [PMID: 38369616 DOI: 10.1002/1873-3468.14829] [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: 11/09/2023] [Revised: 12/30/2023] [Accepted: 01/15/2024] [Indexed: 02/20/2024]
Abstract
Secretory proteins of Plasmodium exhibit differential spatial and functional activity within the host cell nucleus. However, the nuclear localization signals (NLSs) for these proteins remain largely uncharacterized. In this study, we have identified and characterized two NLSs in the circumsporozoite protein of Plasmodium falciparum (Pf-CSP). Both NLSs in the Pf-CSP contain clusters of lysine and arginine residues essential for specific interactions with the conserved tryptophan and asparagine residues of importin-α, facilitating nuclear translocation of Pf-CSP. While the two NLSs of Pf-CSP function independently and are both crucial for nuclear localization, a single NLS of Pf-CSP leads to weak nuclear localization. These findings shed light on the mechanism of nuclear penetrability of secretory proteins of Plasmodium proteins.
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Affiliation(s)
- Akshaykumar Nanaji Shrikondawar
- Computational and Functional Genomics Group, Centre for DNA Fingerprinting and Diagnostics, Hyderabad, India
- Graduate Studies, Regional Centre for Biotechnology, Faridabad, India
| | - Kiranmai Chennoju
- Computational and Functional Genomics Group, Centre for DNA Fingerprinting and Diagnostics, Hyderabad, India
- Graduate Studies, Manipal Academy of Higher Education, Manipal, India
| | | | - Akash Ranjan
- Computational and Functional Genomics Group, Centre for DNA Fingerprinting and Diagnostics, Hyderabad, India
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3
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Boo A, Toth T, Yu Q, Pfotenhauer A, Fields BD, Lenaghan SC, Stewart CN, Voigt CA. Synthetic microbe-to-plant communication channels. Nat Commun 2024; 15:1817. [PMID: 38418817 PMCID: PMC10901793 DOI: 10.1038/s41467-024-45897-6] [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: 02/10/2023] [Accepted: 02/07/2024] [Indexed: 03/02/2024] Open
Abstract
Plants and microbes communicate to collaborate to stop pests, scavenge nutrients, and react to environmental change. Microbiota consisting of thousands of species interact with each other and plants using a large chemical language that is interpreted by complex regulatory networks. In this work, we develop modular interkingdom communication channels, enabling bacteria to convey environmental stimuli to plants. We introduce a "sender device" in Pseudomonas putida and Klebsiella pneumoniae, that produces the small molecule p-coumaroyl-homoserine lactone (pC-HSL) when the output of a sensor or circuit turns on. This molecule triggers a "receiver device" in the plant to activate gene expression. We validate this system in Arabidopsis thaliana and Solanum tuberosum (potato) grown hydroponically and in soil, demonstrating its modularity by swapping bacteria that process different stimuli, including IPTG, aTc and arsenic. Programmable communication channels between bacteria and plants will enable microbial sentinels to transmit information to crops and provide the building blocks for designing artificial consortia.
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Affiliation(s)
- Alice Boo
- Department of Biological Engineering, Synthetic Biology Center, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Tyler Toth
- Department of Biological Engineering, Synthetic Biology Center, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Qiguo Yu
- Department of Biological Engineering, Synthetic Biology Center, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Alexander Pfotenhauer
- Center for Agricultural Synthetic Biology, University of Tennessee, Knoxville, TN, 37996, USA
| | - Brandon D Fields
- Department of Biological Engineering, Synthetic Biology Center, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Scott C Lenaghan
- Center for Agricultural Synthetic Biology, University of Tennessee, Knoxville, TN, 37996, USA
| | - C Neal Stewart
- Center for Agricultural Synthetic Biology, University of Tennessee, Knoxville, TN, 37996, USA
| | - Christopher A Voigt
- Department of Biological Engineering, Synthetic Biology Center, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA.
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4
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Moraes IR, de Oliveira HC, Fontes MRM. Structural basis of nuclear transport for NEIL DNA glycosylases mediated by importin-alpha. BIOCHIMICA ET BIOPHYSICA ACTA. PROTEINS AND PROTEOMICS 2024; 1872:140974. [PMID: 38065227 DOI: 10.1016/j.bbapap.2023.140974] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/29/2023] [Revised: 11/18/2023] [Accepted: 11/30/2023] [Indexed: 01/10/2024]
Abstract
NEIL glycosylases, including NEIL1, NEIL2, and NEIL3, play a crucial role in the base excision DNA repair pathway (BER). The classical importin pathway mediated by importin α/β and cargo proteins containing nuclear localization sequences (NLS) is the most common transport mechanism of DNA repair proteins to the nucleus. Previous studies have identified putative NLSs located at the C-terminus of NEIL3 and NEIL1. Crystallographic, bioinformatics, calorimetric (ITC), and fluorescence assays were used to investigate the interaction between NEIL1 and NEIL3 putative NLSs and importin-α (Impα). Our findings showed that NEIL3 contains a typical cNLS, with medium affinity for the major binding site of Impα. In contrast, crystallographic analysis of NEIL1 NLS revealed its binding to Impα, but with high B-factors and a lack of electron density at the linker region. ITC and fluorescence assays indicated no detectable affinity between NEIL1 NLS and Impα. These data suggest that NEIL1 NLS is a non-classical NLS with low affinity to Impα. Additionally, we compared the binding mode of NEIL3 and NEIL1 with Mus musculus Impα to human isoforms HsImpα1 and HsImpα3, which revealed interesting binding differences for HsImpα3 variant. NEIL3 is a classical medium affinity monopartite NLS, while NEIL1 is likely to be an unclassical low-affinity bipartite NLS. The base excision repair pathway is one of the primary systems involved in repairing DNA. Thus, understanding the mechanisms of nuclear transport of NEIL proteins is crucial for comprehending the role of these proteins in DNA repair and disease development.
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Affiliation(s)
- Ivan R Moraes
- Departamento de Biofísica e Farmacologia, Instituto de Biociências, Universidade Estadual Paulista (UNESP), Botucatu, SP, Brazil
| | - Hamine C de Oliveira
- Departamento de Biofísica e Farmacologia, Instituto de Biociências, Universidade Estadual Paulista (UNESP), Botucatu, SP, Brazil
| | - Marcos R M Fontes
- Departamento de Biofísica e Farmacologia, Instituto de Biociências, Universidade Estadual Paulista (UNESP), Botucatu, SP, Brazil; Instituto de Estudos Avançados do Mar (IEAMar), Universidade Estadual Paulista (UNESP), São Vicente, SP, Brazil.
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5
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Kumar M, Michael S, Alvarado-Valverde J, Zeke A, Lazar T, Glavina J, Nagy-Kanta E, Donagh J, Kalman Z, Pascarelli S, Palopoli N, Dobson L, Suarez C, Van Roey K, Krystkowiak I, Griffin J, Nagpal A, Bhardwaj R, Diella F, Mészáros B, Dean K, Davey N, Pancsa R, Chemes L, Gibson T. ELM-the Eukaryotic Linear Motif resource-2024 update. Nucleic Acids Res 2024; 52:D442-D455. [PMID: 37962385 PMCID: PMC10767929 DOI: 10.1093/nar/gkad1058] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2023] [Revised: 10/22/2023] [Accepted: 10/24/2023] [Indexed: 11/15/2023] Open
Abstract
Short Linear Motifs (SLiMs) are the smallest structural and functional components of modular eukaryotic proteins. They are also the most abundant, especially when considering post-translational modifications. As well as being found throughout the cell as part of regulatory processes, SLiMs are extensively mimicked by intracellular pathogens. At the heart of the Eukaryotic Linear Motif (ELM) Resource is a representative (not comprehensive) database. The ELM entries are created by a growing community of skilled annotators and provide an introduction to linear motif functionality for biomedical researchers. The 2024 ELM update includes 346 novel motif instances in areas ranging from innate immunity to both protein and RNA degradation systems. In total, 39 classes of newly annotated motifs have been added, and another 17 existing entries have been updated in the database. The 2024 ELM release now includes 356 motif classes incorporating 4283 individual motif instances manually curated from 4274 scientific publications and including >700 links to experimentally determined 3D structures. In a recent development, the InterPro protein module resource now also includes ELM data. ELM is available at: http://elm.eu.org.
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Affiliation(s)
- Manjeet Kumar
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg 69117, Germany
| | - Sushama Michael
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg 69117, Germany
| | - Jesús Alvarado-Valverde
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg 69117, Germany
- Collaboration for joint PhD degree between EMBL and Heidelberg University, Faculty of Biosciences, Germany
| | - András Zeke
- Institute of Enzymology, HUN-REN Research Centre for Natural Sciences, Budapest 1117, Hungary
| | - Tamas Lazar
- VIB-VUB Center for Structural Biology, Vlaams Instituut voor Biotechnologie, Pleinlaan 2, 1050 Brussels, Belgium
- Structural Biology Brussels, Department of Bioengineering, Vrije Universiteit Brussel, Pleinlaan 2, 1050 Brussels, Belgium
| | - Juliana Glavina
- Instituto de Investigaciones Biotecnológicas, Universidad Nacional de San Martín (UNSAM), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), CP 1650, Buenos Aires, Argentina
- Escuela de Bio y Nanotecnologías (EByN), Universidad Nacional de San Martín, Av. 25 de Mayo y Francia, CP1650 San Martín, Buenos Aires, Argentina
| | - Eszter Nagy-Kanta
- Faculty of Information Technology and Bionics, Pázmány Péter Catholic University, Práter u. 50/A, Budapest 1083, Hungary
| | - Juan Mac Donagh
- Departamento de Ciencia y Tecnología, Universidad Nacional de Quilmes - Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Bernal, Buenos Aires, Argentina
| | - Zsofia E Kalman
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg 69117, Germany
- Faculty of Information Technology and Bionics, Pázmány Péter Catholic University, Práter u. 50/A, Budapest 1083, Hungary
| | - Stefano Pascarelli
- Department of Computational Biology, University of Lausanne, Lausanne, Switzerland
- Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Nicolas Palopoli
- Departamento de Ciencia y Tecnología, Universidad Nacional de Quilmes - Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Bernal, Buenos Aires, Argentina
| | - László Dobson
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg 69117, Germany
- Department of Bioinformatics, Semmelweis University, Tűzoltó u. 7, Budapest 1094, Hungary
| | - Carmen Florencia Suarez
- Instituto de Investigaciones Biotecnológicas, Universidad Nacional de San Martín (UNSAM), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), CP 1650, Buenos Aires, Argentina
- Escuela de Bio y Nanotecnologías (EByN), Universidad Nacional de San Martín, Av. 25 de Mayo y Francia, CP1650 San Martín, Buenos Aires, Argentina
| | - Kim Van Roey
- Health Services Research, Sciensano, Brussels, Belgium
| | - Izabella Krystkowiak
- Institute of Cancer Research, Chester Beatty Laboratories, 237 Fulham Rd, Chelsea, London SW3 6JB, UK
| | - Juan Esteban Griffin
- Departamento de Ciencia y Tecnología, Universidad Nacional de Quilmes - Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Bernal, Buenos Aires, Argentina
| | - Anurag Nagpal
- Department of Biological Sciences, BITS Pilani, K. K. Birla Goa campus, Zuarinagar, Goa 403726, India
| | - Rajesh Bhardwaj
- Inselspital, University of Bern, Freiburgstrasse 15, CH-3010 Bern, Switzerland
| | - Francesca Diella
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg 69117, Germany
| | - Bálint Mészáros
- Department of Structural Biology and Center of Excellence for Data Driven Discovery, St Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA
| | - Kellie Dean
- School of Biochemistry and Cell Biology, 3.91 Western Gateway Building, University College Cork, Cork, Ireland
| | - Norman E Davey
- Institute of Cancer Research, Chester Beatty Laboratories, 237 Fulham Rd, Chelsea, London SW3 6JB, UK
| | - Rita Pancsa
- Institute of Enzymology, HUN-REN Research Centre for Natural Sciences, Budapest 1117, Hungary
| | - Lucía B Chemes
- Instituto de Investigaciones Biotecnológicas, Universidad Nacional de San Martín (UNSAM), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), CP 1650, Buenos Aires, Argentina
- Escuela de Bio y Nanotecnologías (EByN), Universidad Nacional de San Martín, Av. 25 de Mayo y Francia, CP1650 San Martín, Buenos Aires, Argentina
| | - Toby J Gibson
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg 69117, Germany
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6
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Liu D, Wang L, Ha W, Li K, Shen R, Wang D. HIF-1α: A potential therapeutic opportunity in renal fibrosis. Chem Biol Interact 2024; 387:110808. [PMID: 37980973 DOI: 10.1016/j.cbi.2023.110808] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2023] [Revised: 11/04/2023] [Accepted: 11/14/2023] [Indexed: 11/21/2023]
Abstract
Renal fibrosis is a common outcome of various renal injuries, leading to structural destruction and functional decline of the kidney, and is also a critical prognostic indicator and determinant in renal diseases therapy. Hypoxia is induced in different stress and injuries in kidney, and the hypoxia inducible factors (HIFs) are activated in the context of hypoxia in response and regulation the hypoxia in time. Under stress and hypoxia conditions, HIF-1α increases rapidly and regulates intracellular energy metabolism, cell proliferation, apoptosis, and inflammation. Through reprogramming cellular metabolism, HIF-1α can directly or indirectly induce abnormal accumulation of metabolites, changes in cellular epigenetic modifications, and activation of fibrotic signals. HIF-1α protein expression and activity are regulated by various posttranslational modifications. The drugs targeting HIF-1α can regulate the downstream cascade signals by inhibiting HIF-1α activity or promoting its degradation. As the renal fibrosis is affected by renal diseases, different diseases may trigger different mechanisms which will affect the therapy effect. Therefore, comprehensive analysis of the role and contribution of HIF-1α in occurrence and progression of renal fibrosis, and determination the appropriate intervention time of HIF-1α in the process of renal fibrosis are important ideas to explore effective treatment strategies. This study reviews the regulation of HIF-1α and its mediated complex cascade reactions in renal fibrosis, and lists some drugs targeting HIF-1α that used in preclinical studies, to provide new insight for the study of the renal fibrosis mechanism.
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Affiliation(s)
- Disheng Liu
- The First Hospital of Lanzhou University, Lanzhou University, Gansu, 730000, China
| | - Lu Wang
- The First Hospital of Lanzhou University, Lanzhou University, Gansu, 730000, China
| | - Wuhua Ha
- The First Hospital of Lanzhou University, Lanzhou University, Gansu, 730000, China
| | - Kan Li
- The First Hospital of Lanzhou University, Lanzhou University, Gansu, 730000, China
| | - Rong Shen
- School of Basic Medical Sciences, Lanzhou University, Gansu, 730000, China.
| | - Degui Wang
- School of Basic Medical Sciences, Lanzhou University, Gansu, 730000, China.
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7
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Vogel OA, Forwood JK, Leung DW, Amarasinghe GK, Basler CF. Viral Targeting of Importin Alpha-Mediated Nuclear Import to Block Innate Immunity. Cells 2023; 13:71. [PMID: 38201275 PMCID: PMC10778312 DOI: 10.3390/cells13010071] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2023] [Revised: 12/22/2023] [Accepted: 12/27/2023] [Indexed: 01/12/2024] Open
Abstract
Cellular nucleocytoplasmic trafficking is mediated by the importin family of nuclear transport proteins. The well-characterized importin alpha (IMPA) and importin beta (IMPB) nuclear import pathway plays a crucial role in the innate immune response to viral infection by mediating the nuclear import of transcription factors such as IRF3, NFκB, and STAT1. The nuclear transport of these transcription factors ultimately leads to the upregulation of a wide range of antiviral genes, including IFN and IFN-stimulated genes (ISGs). To replicate efficiently in cells, viruses have developed mechanisms to block these signaling pathways. One strategy to evade host innate immune responses involves blocking the nuclear import of host antiviral transcription factors. By binding IMPA proteins, these viral proteins prevent the nuclear transport of key transcription factors and suppress the induction of antiviral gene expression. In this review, we describe examples of proteins encoded by viruses from several different families that utilize such a competitive inhibition strategy to suppress the induction of antiviral gene expression.
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Affiliation(s)
- Olivia A. Vogel
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA;
| | - Jade K. Forwood
- School of Dentistry and Medical Sciences, Charles Sturt University, Wagga Wagga, NSW 2678, Australia;
| | - Daisy W. Leung
- Department of Internal Medicine, Washington University School of Medicine in St. Louis, St. Louis, MO 63110, USA;
| | - Gaya K. Amarasinghe
- Department of Pathology and Immunology, Washington University School of Medicine in St. Louis, St. Louis, MO 63110, USA;
| | - Christopher F. Basler
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA;
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8
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Casper J, Schenk SH, Parhizkar E, Detampel P, Dehshahri A, Huwyler J. Polyethylenimine (PEI) in gene therapy: Current status and clinical applications. J Control Release 2023; 362:667-691. [PMID: 37666302 DOI: 10.1016/j.jconrel.2023.09.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2023] [Revised: 08/24/2023] [Accepted: 09/01/2023] [Indexed: 09/06/2023]
Abstract
Polyethlyenimine (PEI) was introduced 1995 as a cationic polymer for nucleic acid delivery. PEI and its derivatives are extensively used in basic research and as reference formulations in the field of polymer-based gene delivery. Despite its widespread use, the number of clinical applications to date is limited. Thus, this review aims to consolidate the past applications of PEI in DNA delivery, elucidate the obstacles that hinder its transition to clinical use, and highlight potential prospects for novel iterations of PEI derivatives. The present review article is divided into three sections. The first section examines the mechanism of action employed by PEI, examining fundamental aspects of cellular delivery including uptake mechanisms, release from endosomes, and transport into the cell nucleus, along with potential strategies for enhancing these delivery phases. Moreover, an in-depth analysis is conducted concerning the mechanism underlying cellular toxicity, accompanied with approaches to overcome this major challenge. The second part is devoted to the in vivo performance of PEI and its application in various therapeutic indications. While systemic administration has proven to be challenging, alternative localized delivery routes hold promise, such as treatment of solid tumors, application as a vaccine, or serving as a therapeutic agent for pulmonary delivery. In the last section, the outcome of completed and ongoing clinical trials is summarized. Finally, an expert opinion is provided on the potential of PEI and its future applications. PEI-based formulations for nucleic acid delivery have a promising potential, it will be an important task for the years to come to introduce innovations that address PEI-associated shortcomings by introducing well-designed PEI formulations in combination with an appropriate route of administration.
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Affiliation(s)
- Jens Casper
- Division of Pharmaceutical Technology, Department of Pharmaceutical Sciences, University of Basel, Klingelbergstrasse 50, 4056 Basel, Switzerland
| | - Susanne H Schenk
- Division of Pharmaceutical Technology, Department of Pharmaceutical Sciences, University of Basel, Klingelbergstrasse 50, 4056 Basel, Switzerland
| | - Elahehnaz Parhizkar
- Department of Pharmaceutics, School of Pharmacy, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Pascal Detampel
- Division of Pharmaceutical Technology, Department of Pharmaceutical Sciences, University of Basel, Klingelbergstrasse 50, 4056 Basel, Switzerland
| | - Ali Dehshahri
- Department of Pharmaceutical Biotechnology, School of Pharmacy, Shiraz University of Medical Sciences, Shiraz, Iran.
| | - Jörg Huwyler
- Division of Pharmaceutical Technology, Department of Pharmaceutical Sciences, University of Basel, Klingelbergstrasse 50, 4056 Basel, Switzerland.
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9
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Bhambid M, Dey V, Walunj S, Patankar S. Toxoplasma Gondii Importin α Shows Weak Auto-Inhibition. Protein J 2023:10.1007/s10930-023-10128-2. [PMID: 37284905 DOI: 10.1007/s10930-023-10128-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/18/2023] [Indexed: 06/08/2023]
Abstract
Importin α is a nuclear transporter that binds to nuclear localization signals (NLSs), consisting of 7-20 positively charged amino acids found within cargo proteins. In addition to cargo binding, intramolecular interactions also occur within the importin α protein due to binding between the importin β-binding (IBB) domain and the NLS-binding sites, a phenomenon called auto-inhibition. The interactions causing auto-inhibition are driven by a stretch of basic residues, similar to an NLS, in the IBB domain. Consistent with this, importin α proteins that do not have some of these basic residues lack auto-inhibition; a naturally occurring example of such a protein is found in the apicomplexan parasite Plasmodium falciparum. In this report, we show that importin α from another apicomplexan parasite, Toxoplasma gondii, harbors basic residues (KKR) in the IBB domain and exhibits auto-inhibition. This protein has a long, unstructured hinge motif (between the IBB domain and the NLS-binding sites) that does not contribute to auto-inhibition. However, the IBB domain may have a higher propensity to form an α-helical structure, positioning the wild-type KKR motif in an orientation that results in weaker interactions with the NLS-binding site than a KRR mutant. We conclude that the importin α protein from T. gondii shows auto-inhibition, exhibiting a different phenotype from that of P. falciparum importin α. However, our data indicate that T. gondii importin α may have a low strength of auto-inhibition. We hypothesize that low levels of auto-inhibition may confer an advantage to these important human pathogens.
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Affiliation(s)
- Manasi Bhambid
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai, India
| | - Vishakha Dey
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai, India
- Indiana University School of Medicine, Indianapolis, USA
| | - Sujata Walunj
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai, India
- Department of Biochemistry and Molecular Biology, Monash University, Clayton, Australia
- IITB-Monash Research Academy, IIT Bombay, Mumbai, India
| | - Swati Patankar
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai, India.
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10
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Jiang Y, Jiang L, Akhil CS, Wang D, Zhang Z, Zhang W, Xu D. MULocDeep web service for protein localization prediction and visualization at subcellular and suborganellar levels. Nucleic Acids Res 2023:7161528. [PMID: 37178004 DOI: 10.1093/nar/gkad374] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2023] [Revised: 04/12/2023] [Accepted: 04/27/2023] [Indexed: 05/15/2023] Open
Abstract
Predicting protein localization and understanding its mechanisms are critical in biology and pathology. In this context, we propose a new web application of MULocDeep with improved performance, result interpretation, and visualization. By transferring the original model into species-specific models, MULocDeep achieved competitive prediction performance at the subcellular level against other state-of-the-art methods. It uniquely provides a comprehensive localization prediction at the suborganellar level. Besides prediction, our web service quantifies the contribution of single amino acids to localization for individual proteins; for a group of proteins, common motifs or potential targeting-related regions can be derived. Furthermore, the visualizations of targeting mechanism analyses can be downloaded for publication-ready figures. The MULocDeep web service is available at https://www.mu-loc.org/.
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Affiliation(s)
- Yuexu Jiang
- Department of Electrical Engineer and Computer Science, Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, USA
| | - Lei Jiang
- Department of Electrical Engineer and Computer Science, Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, USA
| | - Chopparapu Sai Akhil
- Department of Electrical Engineer and Computer Science, Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, USA
| | - Duolin Wang
- Department of Electrical Engineer and Computer Science, Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, USA
| | - Ziyang Zhang
- Department of Electrical Engineer and Computer Science, Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, USA
| | - Weinan Zhang
- Department of Electrical Engineer and Computer Science, Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, USA
| | - Dong Xu
- Department of Electrical Engineer and Computer Science, Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, USA
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11
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Sushmita K, Sharma S, Singh Kaushik M, Kateriya S. Algal rhodopsins encoding diverse signal sequence holds potential for expansion of organelle optogenetics. Biophys Physicobiol 2023; 20:e201008. [PMID: 38362319 PMCID: PMC10865886 DOI: 10.2142/biophysico.bppb-v20.s008] [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: 12/22/2022] [Accepted: 01/20/2023] [Indexed: 01/24/2023] Open
Abstract
Rhodopsins have been extensively employed for optogenetic regulation of bioelectrical activity of excitable cells and other cellular processes across biological systems. Various strategies have been adopted to attune the cellular processes at the desired subcellular compartment (plasma membrane, endoplasmic reticulum, Golgi, mitochondria, lysosome) within the cell. These strategies include-adding signal sequences, tethering peptides, specific interaction sites, or mRNA elements at different sites in the optogenetic proteins for plasma membrane integration and subcellular targeting. However, a single approach for organelle optogenetics was not suitable for the relevant optogenetic proteins and often led to the poor expression, mislocalization, or altered physical and functional properties. Therefore, the current study is focused on the native subcellular targeting machinery of algal rhodopsins. The N- and C-terminus signal prediction led to the identification of rhodopsins with diverse organelle targeting signal sequences for the nucleus, mitochondria, lysosome, endosome, vacuole, and cilia. Several identified channelrhodopsins and ion-pumping rhodopsins possess effector domains associated with DNA metabolism (repair, replication, and recombination) and gene regulation. The identified algal rhodopsins with diverse effector domains and encoded native subcellular targeting sequences hold immense potential to establish expanded organelle optogenetic regulation and associated cellular signaling.
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Affiliation(s)
- Kumari Sushmita
- Laboratory of Optobiotechnology, School of Biotechnology, Jawaharlal Nehru University, New Delhi 110067, India
| | - Sunita Sharma
- Laboratory of Optobiotechnology, School of Biotechnology, Jawaharlal Nehru University, New Delhi 110067, India
| | - Manish Singh Kaushik
- Laboratory of Optobiotechnology, School of Biotechnology, Jawaharlal Nehru University, New Delhi 110067, India
| | - Suneel Kateriya
- Laboratory of Optobiotechnology, School of Biotechnology, Jawaharlal Nehru University, New Delhi 110067, India
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12
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Bahari A, Castillo AG, Safaie N, Bejarano ER, Luna AP, Shams-Bakhsh M. Functional Analysis of V2 Protein of Beet Curly Top Iran Virus. PLANTS (BASEL, SWITZERLAND) 2022; 11:3351. [PMID: 36501393 PMCID: PMC9736138 DOI: 10.3390/plants11233351] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/21/2022] [Revised: 11/23/2022] [Accepted: 11/26/2022] [Indexed: 06/17/2023]
Abstract
Geminivirus beet curly top Iran virus (BCTIV) is one of the main causal agents of the beet curly top disease in Iran and the newly established Becurtovirus genus type species. Although the biological features of known becurtoviruses are similar to those of curtoviruses, they only share a limited sequence identity, and no information is available on the function of their viral genes. In this work, we demonstrate that BCTIV V2, as the curtoviral V2, is also a local silencing suppressor in Nicotiana benthamiana and can delay the systemic silencing spreading, although it cannot block the cell-to-cell movement of the silencing signal to adjacent cells. BCTIV V2 shows the same subcellular localization as curtoviral V2, being detected in the nucleus and perinuclear region, and its ectopic expression from a PVX-derived vector also causes the induction of necrotic lesions in N. benthamiana, such as the ones produced during the HR, both at the local and systemic levels. The results from the infection of N. benthamiana with a V2 BCTIV mutant showed that V2 is required for systemic infection, but not for viral replication, in a local infection. Considering all these results, we can conclude that BCTIV V2 is a functional homologue of curtoviral V2 and plays a crucial role in viral pathogenicity and systemic movement.
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Affiliation(s)
- Atiyeh Bahari
- Plant Pathology Department, Faculty of Agriculture, Tarbiat Modares University (TMU), Tehran 336-14115, Iran
| | - Araceli G. Castillo
- Consejo Superior de Investigaciones Científicas (IHSM-UMA-CSIC), Departamento Biología Celular, Genética y Fisiología, Universidad de Málaga, 29010 Malaga, Spain
| | - Naser Safaie
- Plant Pathology Department, Faculty of Agriculture, Tarbiat Modares University (TMU), Tehran 336-14115, Iran
| | - Eduardo R. Bejarano
- Consejo Superior de Investigaciones Científicas (IHSM-UMA-CSIC), Departamento Biología Celular, Genética y Fisiología, Universidad de Málaga, 29010 Malaga, Spain
| | - Ana P. Luna
- Consejo Superior de Investigaciones Científicas (IHSM-UMA-CSIC), Departamento Biología Celular, Genética y Fisiología, Universidad de Málaga, 29010 Malaga, Spain
| | - Masoud Shams-Bakhsh
- Plant Pathology Department, Faculty of Agriculture, Tarbiat Modares University (TMU), Tehran 336-14115, Iran
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13
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Chakraborty C, Das A, Basak C, Roy S, Agarwal T, Ray S. Chloroplastic RecA protein from Physcomitrium patens is able to repair chloroplastic DNA damage by homologous recombination but unable to repair nuclear DNA damage. PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS : AN INTERNATIONAL JOURNAL OF FUNCTIONAL PLANT BIOLOGY 2022; 28:2057-2067. [PMID: 36573145 PMCID: PMC9789214 DOI: 10.1007/s12298-022-01264-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/10/2021] [Revised: 12/05/2022] [Accepted: 12/05/2022] [Indexed: 06/17/2023]
Abstract
Plants are unavoidably exposed to a range of environmental stress factors throughout their life. In addition to the external environmental factors, the production of reactive oxygen species as a product of the cellular metabolic process often causes DNA damage and thus affects genome stability. Homologous recombination (HR) is an essential mechanism used for DNA damage repair that helps to maintain genome integrity. Here we report that the recombinase, PpRecA2, a bacterial RecA homolog from moss Physcomitrium patens can partially complement the function of Escherichia coli RecA in the bacterial system. Transcript analysis showed induced expression of PpRecA2 upon experiencing DNA damaging stressors indicating its involvement in DNA damage sensing and repair mechanism. Over-expressing the chloroplast localizing PpRecA2 confers protection to the chloroplast genome against DNA damage by enhancing the chloroplastic HR frequency in transgenic tobacco plants. Although it fails to protect against nuclear DNA damage when engineered for nuclear localization due to the non-availability of interacting partners. Our results indicate that the chloroplastic HR repair mechanism differs from the nucleus, where chloroplastic HR involves RecA as a key player that resembles the bacterial system. Supplementary Information The online version contains supplementary material available at 10.1007/s12298-022-01264-7.
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Affiliation(s)
- Chandrima Chakraborty
- Plant Functional Genomics Laboratory, Department of Botany, University of Calcutta, 35 Ballygunge Circular Road, Kolkata, West Bengal 700019 India
| | - Arup Das
- Plant Functional Genomics Laboratory, Department of Botany, University of Calcutta, 35 Ballygunge Circular Road, Kolkata, West Bengal 700019 India
| | - Chandra Basak
- Plant Functional Genomics Laboratory, Department of Botany, University of Calcutta, 35 Ballygunge Circular Road, Kolkata, West Bengal 700019 India
| | - Shuddhanjali Roy
- Plant Functional Genomics Laboratory, Department of Botany, University of Calcutta, 35 Ballygunge Circular Road, Kolkata, West Bengal 700019 India
| | - Tanushree Agarwal
- Plant Functional Genomics Laboratory, Department of Botany, University of Calcutta, 35 Ballygunge Circular Road, Kolkata, West Bengal 700019 India
| | - Sudipta Ray
- Plant Functional Genomics Laboratory, Department of Botany, University of Calcutta, 35 Ballygunge Circular Road, Kolkata, West Bengal 700019 India
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14
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Krossa I, Strub T, Aplin AE, Ballotti R, Bertolotto C. Lysine Methyltransferase NSD1 and Cancers: Any Role in Melanoma? Cancers (Basel) 2022; 14:cancers14194865. [PMID: 36230787 PMCID: PMC9563040 DOI: 10.3390/cancers14194865] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Revised: 09/27/2022] [Accepted: 09/29/2022] [Indexed: 11/23/2022] Open
Abstract
Simple Summary Epigenetic events, which comprise post-translational modifications of histone tails or DNA methylation, control gene expression by altering chromatin structure without change in the DNA sequence. Histone tails modifications are driven by specific cellular enzymes such as histone methyltransferases or histone acetylases, which play a key role in regulating diverse biological processes. Their alteration may have consequences on growth and tumorigenesis. Abstract Epigenetic regulations, that comprise histone modifications and DNA methylation, are essential to processes as diverse as development and cancer. Among the histone post-translational modifications, lysine methylation represents one of the most important dynamic marks. Here, we focused on methyltransferases of the nuclear binding SET domain 1 (NSD) family, that catalyze the mono- and di-methylation of histone H3 lysine 36. We review the loss of function mutations of NSD1 in humans that are the main cause of SOTOS syndrome, a disease associated with an increased risk of developing cancer. We then report the role of NSD1 in triggering tumor suppressive or promoter functions according to the tissue context and we discuss the role of NSD1 in melanoma. Finally, we examine the ongoing efforts to target NSD1 signaling in cancers.
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Affiliation(s)
- Imène Krossa
- Université Côte d’Azur, 06100 Nice, France
- Team 1, Biology and Pathologies of melanocytes, Inserm, Equipe labellisée Ligue 2020 and Equipe labellisée ARC 2022, Centre Méditerranéen de Médecine Moléculaire, 06200 Nice, France
- Correspondence: (I.K.); (C.B.)
| | - Thomas Strub
- Université Côte d’Azur, 06100 Nice, France
- Team 1, Biology and Pathologies of melanocytes, Inserm, Equipe labellisée Ligue 2020 and Equipe labellisée ARC 2022, Centre Méditerranéen de Médecine Moléculaire, 06200 Nice, France
| | - Andrew E. Aplin
- Department of Pharmacology, Physiology, and Cancer Biology, Thomas Jefferson University, Philadelphia, PA 19107, USA
| | - Robert Ballotti
- Université Côte d’Azur, 06100 Nice, France
- Team 1, Biology and Pathologies of melanocytes, Inserm, Equipe labellisée Ligue 2020 and Equipe labellisée ARC 2022, Centre Méditerranéen de Médecine Moléculaire, 06200 Nice, France
| | - Corine Bertolotto
- Université Côte d’Azur, 06100 Nice, France
- Team 1, Biology and Pathologies of melanocytes, Inserm, Equipe labellisée Ligue 2020 and Equipe labellisée ARC 2022, Centre Méditerranéen de Médecine Moléculaire, 06200 Nice, France
- Correspondence: (I.K.); (C.B.)
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15
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Muñoz-Díaz E, Sáez-Vásquez J. Nuclear dynamics: Formation of bodies and trafficking in plant nuclei. FRONTIERS IN PLANT SCIENCE 2022; 13:984163. [PMID: 36082296 PMCID: PMC9445803 DOI: 10.3389/fpls.2022.984163] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Accepted: 08/04/2022] [Indexed: 06/01/2023]
Abstract
The existence of the nucleus distinguishes prokaryotes and eukaryotes. Apart from containing most of the genetic material, the nucleus possesses several nuclear bodies composed of protein and RNA molecules. The nucleus is separated from the cytoplasm by a double membrane, regulating the trafficking of molecules in- and outwards. Here, we investigate the composition and function of the different plant nuclear bodies and molecular clues involved in nuclear trafficking. The behavior of the nucleolus, Cajal bodies, dicing bodies, nuclear speckles, cyclophilin-containing bodies, photobodies and DNA damage foci is analyzed in response to different abiotic stresses. Furthermore, we research the literature to collect the different protein localization signals that rule nucleocytoplasmic trafficking. These signals include the different types of nuclear localization signals (NLSs) for nuclear import, and the nuclear export signals (NESs) for nuclear export. In contrast to these unidirectional-movement signals, the existence of nucleocytoplasmic shuttling signals (NSSs) allows bidirectional movement through the nuclear envelope. Likewise, nucleolar signals are also described, which mainly include the nucleolar localization signals (NoLSs) controlling nucleolar import. In contrast, few examples of nucleolar export signals, called nucleoplasmic localization signals (NpLSs) or nucleolar export signals (NoESs), have been reported. The existence of consensus sequences for these localization signals led to the generation of prediction tools, allowing the detection of these signals from an amino acid sequence. Additionally, the effect of high temperatures as well as different post-translational modifications in nuclear and nucleolar import and export is discussed.
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Affiliation(s)
- Eduardo Muñoz-Díaz
- Centre National de la Recherche Scientifique (CNRS), Laboratoire Génome et Développement des Plantes, UMR 5096, Perpignan, France
- Univ. Perpignan Via Domitia, Laboratoire Génome et Développement des Plantes, UMR 5096, Perpignan, France
| | - Julio Sáez-Vásquez
- Centre National de la Recherche Scientifique (CNRS), Laboratoire Génome et Développement des Plantes, UMR 5096, Perpignan, France
- Univ. Perpignan Via Domitia, Laboratoire Génome et Développement des Plantes, UMR 5096, Perpignan, France
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16
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Brophy JAN, Magallon KJ, Duan L, Zhong V, Ramachandran P, Kniazev K, Dinneny JR. Synthetic genetic circuits as a means of reprogramming plant roots. Science 2022; 377:747-751. [PMID: 35951698 DOI: 10.1126/science.abo4326] [Citation(s) in RCA: 52] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
The shape of a plant's root system influences its ability to reach essential nutrients in the soil and to acquire water during drought. Progress in engineering plant roots to optimize water and nutrient acquisition has been limited by our capacity to design and build genetic programs that alter root growth in a predictable manner. We developed a collection of synthetic transcriptional regulators for plants that can be compiled to create genetic circuits. These circuits control gene expression by performing Boolean logic operations and can be used to predictably alter root structure. This work demonstrates the potential of synthetic genetic circuits to control gene expression across tissues and reprogram plant growth.
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Affiliation(s)
- Jennifer A N Brophy
- Department of Biology, Stanford University, Stanford, CA, USA.,Department of Bioengineering, Stanford University, Stanford, CA, USA
| | | | - Lina Duan
- Department of Biology, Stanford University, Stanford, CA, USA
| | - Vivian Zhong
- Department of Bioengineering, Stanford University, Stanford, CA, USA
| | | | - Kiril Kniazev
- Department of Biology, Stanford University, Stanford, CA, USA
| | - José R Dinneny
- Department of Biology, Stanford University, Stanford, CA, USA
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17
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Mo L, Meng L, Huang Z, Yi L, Yang N, Li G. An analysis of the role of HnRNP C dysregulation in cancers. Biomark Res 2022; 10:19. [PMID: 35395937 PMCID: PMC8994388 DOI: 10.1186/s40364-022-00366-4] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2022] [Accepted: 03/20/2022] [Indexed: 12/21/2022] Open
Abstract
Heterogeneous nuclear ribonucleoproteins C (HnRNP C) is part of the hnRNP family of RNA-binding proteins. The relationship between hnRNP C and cancers has been extensively studied, and dysregulation of hnRNP C has been found in many cancers. According to existing public data, hnRNP C could promote the maturation of new heterogeneous nuclear RNAs (hnRNA s, also referred to as pre-mRNAs) into mRNAs and could stabilize mRNAs, controlling their translation. This paper reviews the regulation and dysregulation of hnRNP C in cancers. It interacts with some cancer genes and other biological molecules, such as microRNAs (miRNAs), long noncoding RNAs (lncRNAs), and double-stranded RNAs (dsRNAs). Even directly binds to them. The effects of hnRNP C on biological processes such as alternative cleavage and polyadenylation (APA) and N6-methyladenosine (m6A) modification differ among cancers. Its main function is regulating stability and level of translation of cancer genes, and the hnRNP C is regarded as a candidate biomarker and might be valuable for prognosis evaluation.
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Affiliation(s)
- Liyi Mo
- The Hengyang Key Laboratory of Cellular Stress Biology, Institute of Cytology and Genetics, Hengyang Medical School, University of South China, Hengyang, 421001, Hunan, China
| | - Lijuan Meng
- Department of Ultrasonography, Second Affiliated Hospital, University of South China, Hengyang, 421001, Hunan, China
| | - Zhicheng Huang
- The Hengyang Key Laboratory of Cellular Stress Biology, Institute of Cytology and Genetics, Hengyang Medical School, University of South China, Hengyang, 421001, Hunan, China
| | - Lan Yi
- The Hengyang Key Laboratory of Cellular Stress Biology, Institute of Cytology and Genetics, Hengyang Medical School, University of South China, Hengyang, 421001, Hunan, China
| | - Nanyang Yang
- The Hengyang Key Laboratory of Cellular Stress Biology, Institute of Cytology and Genetics, Hengyang Medical School, University of South China, Hengyang, 421001, Hunan, China.
| | - Guoqing Li
- The Hengyang Key Laboratory of Cellular Stress Biology, Institute of Cytology and Genetics, Hengyang Medical School, University of South China, Hengyang, 421001, Hunan, China.
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18
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Grabarczyk P, Delin M, Rogińska D, Schulig L, Forkel H, Depke M, Link A, Machaliński B, Schmidt CA. Nuclear import of BCL11B is mediated by a classical nuclear localization signal and not the Krüppel-like zinc fingers. J Cell Sci 2021; 134:272659. [PMID: 34714335 DOI: 10.1242/jcs.258655] [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: 03/17/2021] [Accepted: 10/24/2021] [Indexed: 11/20/2022] Open
Abstract
The Krüppel-like transcription factor BCL11B is characterized by wide tissue distribution and crucial functions in key developmental and cellular processes and various pathologies including cancer or HIV infection. Although basics of BCL11B activity and relevant interactions with other proteins were uncovered, how this exclusively nuclear protein localizes to its compartment remained unclear. Here, we demonstrate that unlike other KLFs, BCL11B does not require the C-terminal DNA-binding domain to pass through the nuclear envelope but encodes an independent, previously unidentified nuclear localization signal (NLS) which is located distantly from the zinc finger domains and fulfills the essential criteria of an autonomous NLS. First, it can redirect a heterologous cytoplasmic protein to the nucleus. Second, its mutations cause aberrant localization of the protein of origin. Finally, we provide experimental and in silico evidences of the direct interaction with importin alpha. The relative conservation of this motif allows formulating a consensus sequence (K/R)K-X13-14-KR+K++ which can be found in all BCL11B orthologues among vertebrates and in the closely related protein BCL11A.
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Affiliation(s)
- Piotr Grabarczyk
- Clinic of Hematology and Oncology, University Medicine Greifswald, Greifswald, Germany
| | - Martin Delin
- Clinic of Hematology and Oncology, University Medicine Greifswald, Greifswald, Germany
| | - Dorota Rogińska
- Department of General Pathology, Pomeranian Medical University, Szczecin, Poland
| | - Lukas Schulig
- Department of Pharmaceutical and Medicinal Chemistry, Institute of Pharmacy, University of Greifswald, Greifswald, Germany
| | - Hannes Forkel
- Clinic of Hematology and Oncology, University Medicine Greifswald, Greifswald, Germany
| | - Maren Depke
- Clinic of Hematology and Oncology, University Medicine Greifswald, Greifswald, Germany
| | - Andreas Link
- Department of Pharmaceutical and Medicinal Chemistry, Institute of Pharmacy, University of Greifswald, Greifswald, Germany
| | - Bogusław Machaliński
- Department of General Pathology, Pomeranian Medical University, Szczecin, Poland
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19
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Liu S, Zhang Q, Shy AN, Yi M, He H, Lu S, Xu B. Enzymatically Forming Intranuclear Peptide Assemblies for Selectively Killing Human Induced Pluripotent Stem Cells. J Am Chem Soc 2021; 143:15852-15862. [PMID: 34528792 DOI: 10.1021/jacs.1c07923] [Citation(s) in RCA: 41] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Tumorigenic risk of undifferentiated human induced pluripotent stem cells (iPSCs), being a major obstacle for clinical application of iPSCs, requires novel approaches for selectively eliminating undifferentiated iPSCs. Here, we show that an l-phosphopentapeptide, upon the dephosphorylation catalyzed by alkaline phosphatase (ALP) overexpressed by iPSCs, rapidly forms intranuclear peptide assemblies made of α-helices to selectively kill iPSCs. The phosphopentapeptide, consisting of four l-leucine residues and a C-terminal l-phosphotyrosine, self-assembles to form micelles/nanoparticles, which transform into peptide nanofibers/nanoribbons after enzymatic dephosphorylation removes the phosphate group from the l-phosphotyrosine. The concentration of ALP and incubation time dictates the morphology of the peptide assemblies. Circular dichroism and FTIR indicate that the l-pentapeptide in the assemblies contains a mixture of an α-helix and aggregated strands. Incubating the l-phosphopentapeptide with human iPSCs results in rapid killing of the iPSCs (=<2 h) due to the significant accumulation of the peptide assemblies in the nuclei of iPSCs. The phosphopentapeptide is innocuous to normal cells (e.g., HEK293 and hematopoietic progenitor cell (HPC)) because normal cells hardly overexpress ALP. Inhibiting ALP, mutating the l-phosphotyrosine from the C-terminal to the middle of the phosphopentapeptides, or replacing l-leucine to d-leucine in the phosphopentapeptide abolishes the intranuclear assemblies of the pentapeptides. Treating the l-phosphopentapeptide with cell lysate of normal cells (e.g., HS-5) confirms the proteolysis of the l-pentapeptide. This work, as the first case of intranuclear assemblies of peptides, not only illustrates the application of enzymatic noncovalent synthesis for selectively targeting nuclei of cells but also may lead to a new way to eliminate other pathological cells that express a high level of certain enzymes.
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Affiliation(s)
- Shuang Liu
- Department of Chemistry, Brandeis University, 415 South Street, Waltham, Massachusetts 02454, United States.,School of Materials Science and Engineering, Wuhan University of Technology, 122 Luoshi Road, Wuhan, Hubei 430070, China
| | - Qiuxin Zhang
- Department of Chemistry, Brandeis University, 415 South Street, Waltham, Massachusetts 02454, United States
| | - Adrianna N Shy
- Department of Chemistry, Brandeis University, 415 South Street, Waltham, Massachusetts 02454, United States
| | - Meihui Yi
- Department of Chemistry, Brandeis University, 415 South Street, Waltham, Massachusetts 02454, United States
| | - Hongjian He
- Department of Chemistry, Brandeis University, 415 South Street, Waltham, Massachusetts 02454, United States
| | - Shijiang Lu
- HebeCell, 21 Strathmore Road, Natick, Massachusetts 01760, United States
| | - Bing Xu
- Department of Chemistry, Brandeis University, 415 South Street, Waltham, Massachusetts 02454, United States
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20
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Jiang Y, Wang D, Yao Y, Eubel H, Künzler P, Møller IM, Xu D. MULocDeep: A deep-learning framework for protein subcellular and suborganellar localization prediction with residue-level interpretation. Comput Struct Biotechnol J 2021; 19:4825-4839. [PMID: 34522290 PMCID: PMC8426535 DOI: 10.1016/j.csbj.2021.08.027] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2021] [Revised: 08/16/2021] [Accepted: 08/16/2021] [Indexed: 12/18/2022] Open
Abstract
Prediction of protein localization plays an important role in understanding protein function and mechanisms. In this paper, we propose a general deep learning-based localization prediction framework, MULocDeep, which can predict multiple localizations of a protein at both subcellular and suborganellar levels. We collected a dataset with 44 suborganellar localization annotations in 10 major subcellular compartments—the most comprehensive suborganelle localization dataset to date. We also experimentally generated an independent dataset of mitochondrial proteins in Arabidopsis thaliana cell cultures, Solanum tuberosum tubers, and Vicia faba roots and made this dataset publicly available. Evaluations using the above datasets show that overall, MULocDeep outperforms other major methods at both subcellular and suborganellar levels. Furthermore, MULocDeep assesses each amino acid’s contribution to localization, which provides insights into the mechanism of protein sorting and localization motifs. A web server can be accessed at http://mu-loc.org.
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Affiliation(s)
- Yuexu Jiang
- Department of Electrical Engineering and Computer Science, Bond Life Sciences Center, Columbia, MO, USA
| | - Duolin Wang
- Department of Electrical Engineering and Computer Science, Bond Life Sciences Center, Columbia, MO, USA
| | - Yifu Yao
- Department of Electrical Engineering and Computer Science, Bond Life Sciences Center, Columbia, MO, USA
| | - Holger Eubel
- Institute of Plant Genetics, Leibniz University Hannover, Hannover, Germany
| | - Patrick Künzler
- Institute of Plant Genetics, Leibniz University Hannover, Hannover, Germany
| | - Ian Max Møller
- Department of Molecular Biology and Genetics, Aarhus University, Forsøgsvej 1, DK-4200 Slagelse, Denmark
| | - Dong Xu
- Department of Electrical Engineering and Computer Science, Bond Life Sciences Center, Columbia, MO, USA
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21
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Liu L, Wang Z, Li J, Wang Y, Yuan J, Zhan J, Wang P, Lin Y, Li F, Ge X. Verticillium dahliae secreted protein Vd424Y is required for full virulence, targets the nucleus of plant cells, and induces cell death. MOLECULAR PLANT PATHOLOGY 2021; 22:1109-1120. [PMID: 34233072 PMCID: PMC8358993 DOI: 10.1111/mpp.13100] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/12/2020] [Revised: 05/09/2021] [Accepted: 05/27/2021] [Indexed: 05/26/2023]
Abstract
Fungal pathogens secrete effector proteins that regulate host immunity and can suppress basal defence mechanisms against colonization in plants. Verticillium dahliae is a widespread and destructive soilborne fungus that can cause vascular wilt disease and reduces plant yields. However, little is currently known about how the effectors secreted by V. dahliae function. In this study, we analysed and identified 34 candidate effectors in the V. dahliae secretome and found that Vd424Y, a glycoside hydrolase family 11 protein, was highly upregulated during the early stages of V. dahliae infection in cotton plants. This protein was located in the nucleus and its deletion compromised the virulence of the fungus. The transient expression of Vd424Y in Nicotiana benthamiana induced BAK1- and SOBIR1-dependent cell death and activated both salicylic acid and jasmonic acid signalling. This enhanced its resistance to the oomycetes Phytophthora capsici in a way that depended on its nuclear localization signal and signal peptides. Our results demonstrate that Vd424Y is an important effector protein targeting the host nucleus to regulate and activate effector-triggered immunity in plants.
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Affiliation(s)
- Lisen Liu
- Institute of Cotton ResearchHenan Normal University Research Base of State Key Laboratory of Cotton BiologyHenanChina
- National Key Laboratory of Crop Genetic ImprovementHuazhong Agricultural UniversityWuhanChina
| | - Zhaohan Wang
- Institute of Cotton ResearchHenan Normal University Research Base of State Key Laboratory of Cotton BiologyHenanChina
| | - Jianing Li
- Institute of Cotton ResearchHenan Normal University Research Base of State Key Laboratory of Cotton BiologyHenanChina
| | - Ye Wang
- Institute of Cotton ResearchHenan Normal University Research Base of State Key Laboratory of Cotton BiologyHenanChina
| | - Jiachen Yuan
- Institute of Cotton ResearchHenan Normal University Research Base of State Key Laboratory of Cotton BiologyHenanChina
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, School of Agricultural SciencesZhengzhou UniversityZhengzhouChina
| | - Jingjing Zhan
- Institute of Cotton ResearchHenan Normal University Research Base of State Key Laboratory of Cotton BiologyHenanChina
| | - Peng Wang
- Institute of Cotton ResearchHenan Normal University Research Base of State Key Laboratory of Cotton BiologyHenanChina
| | - Yongjun Lin
- National Key Laboratory of Crop Genetic ImprovementHuazhong Agricultural UniversityWuhanChina
| | - Fuguang Li
- Institute of Cotton ResearchHenan Normal University Research Base of State Key Laboratory of Cotton BiologyHenanChina
| | - Xiaoyang Ge
- Institute of Cotton ResearchHenan Normal University Research Base of State Key Laboratory of Cotton BiologyHenanChina
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, School of Agricultural SciencesZhengzhou UniversityZhengzhouChina
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Distinct mutations in importin-β family nucleocytoplasmic transport receptors transportin-SR and importin-13 affect specific cargo binding. Sci Rep 2021; 11:15649. [PMID: 34341383 PMCID: PMC8329185 DOI: 10.1038/s41598-021-94948-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2020] [Accepted: 07/20/2021] [Indexed: 01/25/2023] Open
Abstract
Importin-(Imp)β family nucleocytoplasmic transport receptors (NTRs) are supposed to bind to their cargoes through interaction between a confined interface on an NTR and a nuclear localization or export signal (NLS/NES) on a cargo. Although consensus NLS/NES sequence motifs have been defined for cargoes of some NTRs, many experimentally identified cargoes of those NTRs lack those motifs, and consensus NLSs/NESs have been reported for only a few NTRs. Crystal structures of NTR–cargo complexes have exemplified 3D structure-dependent binding of cargoes lacking a consensus NLS/NES to different sites on an NTR. Since only a limited number of NTR–cargo interactions have been studied, whether most cargoes lacking a consensus NLS/NES bind to the same confined interface or to various sites on an NTR is still unclear. Addressing this issue, we generated four mutants of transportin-(Trn)SR, of which many cargoes lack a consensus NLS, and eight mutants of Imp13, where no consensus NLS has been defined, and we analyzed their binding to as many as 40 cargo candidates that we previously identified by a nuclear import reaction-based method. The cargoes bind differently to the NTR mutants, suggesting that positions on an NTR contribute differently to the binding of respective cargoes.
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Structural and calorimetric studies reveal specific determinants for the binding of a high-affinity NLS to mammalian importin-alpha. Biochem J 2021; 478:2715-2732. [PMID: 34195786 DOI: 10.1042/bcj20210401] [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: 06/01/2021] [Revised: 06/21/2021] [Accepted: 06/25/2021] [Indexed: 11/17/2022]
Abstract
The classical nuclear import pathway is mediated by importin (Impα and Impβ), which recognizes the cargo protein by its nuclear localization sequence (NLS). NLSs have been extensively studied resulting in different proposed consensus; however, recent studies showed that exceptions may occur. This mechanism may be also dependent on specific characteristics of different Impα. Aiming to better understand the importance of specific residues from consensus and adjacent regions of NLSs, we studied different mutations of a high-affinity NLS complexed to Impα by crystallography and calorimetry. We showed that although the consensus sequence allows Lys or Arg residues at the second residue of a monopartite sequence, the presence of Arg is very important to its binding in major and minor sites of Impα. Mutations in the N or C-terminus (position P1 or P6) of the NLS drastically reduces their affinity to the receptor, which is corroborated by the loss of hydrogen bonds and hydrophobic interactions. Surprisingly, a mutation in the far N-terminus of the NLS led to an increase in the affinity for both binding sites, corroborated by the structure with an additional hydrogen bond. The binding of NLSs to the human variant Impα1 revealed that these are similar to those found in structures presented here. For human variant Impα3, the bindings are only relevant for the major site. This study increases understanding of specific issues sparsely addressed in previous studies that are important to the task of predicting NLSs, which will be relevant in the eventual design of synthetic NLSs.
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Wang X, Greenblatt HM, Bigman LS, Yu B, Pletka CC, Levy Y, Iwahara J. Dynamic Autoinhibition of the HMGB1 Protein via Electrostatic Fuzzy Interactions of Intrinsically Disordered Regions. J Mol Biol 2021; 433:167122. [PMID: 34181980 DOI: 10.1016/j.jmb.2021.167122] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2021] [Revised: 06/03/2021] [Accepted: 06/22/2021] [Indexed: 10/21/2022]
Abstract
Highly negatively charged segments containing only aspartate or glutamate residues ("D/E repeats") are found in many eukaryotic proteins. For example, the C-terminal 30 residues of the HMGB1 protein are entirely D/E repeats. Using nuclear magnetic resonance (NMR), fluorescence, and computational approaches, we investigated how the D/E repeats causes the autoinhibition of HMGB1 against its specific binding to cisplatin-modified DNA. By varying ionic strength in a wide range (40-900 mM), we were able to shift the conformational equilibrium between the autoinhibited and uninhibited states toward either of them to the full extent. This allowed us to determine the macroscopic and microscopic equilibrium constants for the HMGB1 autoinhibition at various ionic strengths. At a macroscopic level, a model involving the autoinhibited and uninhibited states can explain the salt concentration-dependent binding affinity data. Our data at a microscopic level show that the D/E repeats and other parts of HMGB1 undergo electrostatic fuzzy interactions, each of which is weaker than expected from the macroscopic autoinhibitory effect. This discrepancy suggests that the multivalent nature of the fuzzy interactions enables strong autoinhibition at a macroscopic level despite the relatively weak intramolecular interaction at each site. Both experimental and computational data suggest that the D/E repeats interact preferentially with other intrinsically disordered regions (IDRs) of HMGB1. We also found that mutations mimicking post-translational modifications relevant to nuclear export of HMGB1 can moderately modulate DNA-binding affinity, possibly by impacting the autoinhibition. This study illuminates a functional role of the fuzzy interactions of D/E repeats.
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Affiliation(s)
- Xi Wang
- Department of Biochemistry and Molecular Biology, Sealy Center for Structural Biology and Molecular Biophysics, University of Texas Medical Branch, Galveston, TX 77555-1068, USA
| | - Harry M Greenblatt
- Department of Chemical and Structural Biology, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Lavi S Bigman
- Department of Chemical and Structural Biology, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Binhan Yu
- Department of Biochemistry and Molecular Biology, Sealy Center for Structural Biology and Molecular Biophysics, University of Texas Medical Branch, Galveston, TX 77555-1068, USA
| | - Channing C Pletka
- Department of Biochemistry and Molecular Biology, Sealy Center for Structural Biology and Molecular Biophysics, University of Texas Medical Branch, Galveston, TX 77555-1068, USA
| | - Yaakov Levy
- Department of Chemical and Structural Biology, Weizmann Institute of Science, Rehovot 76100, Israel.
| | - Junji Iwahara
- Department of Biochemistry and Molecular Biology, Sealy Center for Structural Biology and Molecular Biophysics, University of Texas Medical Branch, Galveston, TX 77555-1068, USA.
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25
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The DNA Sensor IFIX Drives Proteome Alterations To Mobilize Nuclear and Cytoplasmic Antiviral Responses, with Its Acetylation Acting as a Localization Toggle. mSystems 2021; 6:e0039721. [PMID: 34156286 PMCID: PMC8269231 DOI: 10.1128/msystems.00397-21] [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] [Indexed: 12/11/2022] Open
Abstract
DNA sensors are critical components of innate immunity that enable cells to recognize infection by pathogens with DNA genomes. The interferon-inducible protein X (IFIX), a member of the PYHIN protein family, is a DNA sensor capable of promoting immune signaling after binding to double-stranded DNA (dsDNA) within either the nucleus or cytoplasm. Here, we investigate the impact of IFIX on the cellular proteome upon introduction of foreign DNA to the nucleus or the cytoplasm as well as regulatory hubs that control IFIX subcellular localization. Using quantitative mass spectrometry, we define the effect of CRISPR-mediated IFIX knockout on nuclear and cytoplasmic proteomes in fibroblasts. Proteomes are probed in response to either nuclear viral DNA, during herpes simplex virus 1 (HSV-1) infection, or cytoplasmic viral DNA, following transfection with dsDNA derived from vaccinia virus (VACV 70-mer). We show that IFIX broadly impacts nuclear and cytoplasmic proteomes, inducing alterations in the abundances of immune signaling, DNA damage response, and vesicle-mediated transport proteins. To characterize IFIX properties that regulate its localization during DNA sensing, we perform deletion and mutagenesis assays. We find that IFIX contains a multipartite nuclear localization signal (NLS) and highlight the main contributing motif for its nuclear localization. Using immunoaffinity purification, we identify IFIX acetylation and phosphorylation sites. Mutations to acetyl or charge mimics demonstrate that K138 acetylation, positioned within the NLS, affects nuclear localization. Altogether, our study establishes a mechanism regulating IFIX subcellular localization and contextualizes this localization with the involvement of IFIX in host cell responses to pathogenic DNA. IMPORTANCE Mammalian cells must be able to detect and respond to invading pathogens to prevent the spread of infection. DNA sensors, such as IFIX, are proteins that bind to pathogen-derived double-stranded DNA and induce antiviral cytokine expression. Here, we characterize the host proteome changes that require IFIX during both viral infection and DNA transfection. We show IFIX mobilizes numerous pathways and proteome alterations within the nucleus and the cytoplasm, pointing to a multifunctional protein with roles in immune signaling, DNA damage response, and transcriptional regulation. We next interrogate the IFIX domains required for nuclear localization, discovering its regulation via a multipartite nuclear localization motif. The acetylation of this motif promotes IFIX cytoplasmic localization, in agreement with its detection of pathogenic DNA in both the nucleus and the cytoplasm. This study established NLS acetylation as a conserved mechanism for regulating the localization of nuclear DNA sensors from the PYHIN family of proteins.
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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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27
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Nuclear localization of non-structural protein 3 (NS3) during dengue virus infection. Arch Virol 2021; 166:1439-1446. [PMID: 33682072 DOI: 10.1007/s00705-021-05026-w] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2020] [Accepted: 01/21/2021] [Indexed: 12/21/2022]
Abstract
Although dengue virus (DENV) replication occurs in the cytoplasm, the nucleus plays an essential role during infection. Both the capsid protein (C) and non-structural protein 5 (NS5) are translocated into the infected cell nucleus to favor viral replication. Previously, our group reported the nuclear localization of the NS3 protein during DENV infection of mosquito cells; however, the nuclear localization of the DENV NS3 protein in human host cells has not been described. Here, we demonstrated that NS3 is present in the nucleus of Huh7 cells at early infection times, and later, it is mainly located in the cytoplasm.
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Lagan Tregaskis P, Devaney R, Smyth VJ. The First Whole Genome Sequence and Characterisation of Avian Nephritis Virus Genotype 3. Viruses 2021; 13:v13020235. [PMID: 33546203 PMCID: PMC7913312 DOI: 10.3390/v13020235] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2020] [Revised: 01/22/2021] [Accepted: 01/27/2021] [Indexed: 12/22/2022] Open
Abstract
Avian nephritis virus (ANV) is classified in the Avastroviridae family with disease associations with nephritis, uneven flock growth and runting stunting syndrome (RSS) in chicken and turkey flocks, and other avian species. The whole genome of ANV genotype 3 (ANV-3) of 6959 nucleotides including the untranslated 5′ and 3′ regions and polyadenylated tail was detected in a metagenomic virome investigation of RSS-affected chicken broiler flocks. This report characterises the ANV-3 genome, identifying partially overlapping open reading frames (ORFs), ORF1a and ORF1b, and an opposing secondary pseudoknot prior to a ribosomal frameshift stemloop structure, with a separate ORF2, whilst observing conserved astrovirus motifs. Phylogenetic analysis of the Avastroviridae whole genome and ORF2 capsid polyprotein classified the first complete whole genome of ANV-3 within Avastroviridae genogroup 2.
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Motifs of the C-terminal domain of MCM9 direct localization to sites of mitomycin-C damage for RAD51 recruitment. J Biol Chem 2021; 296:100355. [PMID: 33539926 PMCID: PMC7949153 DOI: 10.1016/j.jbc.2021.100355] [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: 01/11/2021] [Accepted: 01/28/2021] [Indexed: 11/20/2022] Open
Abstract
The MCM8/9 complex is implicated in aiding fork progression and facilitating homologous recombination (HR) in response to several DNA damage agents. MCM9 itself is an outlier within the MCM family containing a long C-terminal extension (CTE) comprising 42% of the total length, but with no known functional components and high predicted disorder. In this report, we identify and characterize two unique motifs within the primarily unstructured CTE that are required for localization of MCM8/9 to sites of mitomycin C (MMC)-induced DNA damage. First, an unconventional “bipartite-like” nuclear localization (NLS) motif consisting of two positively charged amino acid stretches separated by a long intervening sequence is required for the nuclear import of both MCM8 and MCM9. Second, a variant of the BRC motif (BRCv) similar to that found in other HR helicases is necessary for localization to sites of MMC damage. The MCM9-BRCv directly interacts with and recruits RAD51 downstream to MMC-induced damage to aid in DNA repair. Patient lymphocytes devoid of functional MCM9 and discrete MCM9 knockout cells have a significantly impaired ability to form RAD51 foci after MMC treatment. Therefore, the disordered CTE in MCM9 is functionally important in promoting MCM8/9 activity and in recruiting downstream interactors; thus, requiring full-length MCM9 for proper DNA repair.
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Ye G, Feng Y, Mi Z, Wang D, Lin S, Chen F, Cui J, Yu Y. Expression and Functional Characterization of c-Fos Gene in Chinese Fire-Bellied Newt Cynops Orientalis. Genes (Basel) 2021; 12:genes12020205. [PMID: 33573315 PMCID: PMC7912203 DOI: 10.3390/genes12020205] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2021] [Revised: 01/27/2021] [Accepted: 01/28/2021] [Indexed: 11/16/2022] Open
Abstract
c-Fos is an immediate-early gene that modulates cellular responses to a wide variety of stimuli and also plays an important role in tissue regeneration. However, the sequence and functions of c-Fos are still poorly understood in newts. This study describes the molecular cloning and characterization of the c-Fos gene (Co-c-Fos) of the Chinese fire-bellied newt, Cynops orientalis. The full-length Co-c-Fos cDNA sequence consists of a 1290 bp coding sequence that encoded 429 amino acids. The alignment and phylogenetic analyses reveal that the amino acid sequence of Co-c-Fos shared a conserved basic leucine zipper domain, including a nuclear localization sequence and a leucine heptad repeat. The Co-c-Fos mRNA is widely expressed in various tissues and is highly and uniformly expressed along the newt limb. After limb amputation, the expression of Co-c-Fos mRNA was immediately upregulated, but rapidly declined. However, the significant upregulation of Co-c-Fos protein expression was sustained for 24 h, overlapping with the wound healing stage of C. orientalis limb regeneration. To investigate if Co-c-Fos participate in newt wound healing, a skin wound healing model is employed. The results show that the treatment of T-5224, a selective c-Fos inhibitor, could largely impair the healing process of newt’s skin wound, as well as the injury-induced matrix metalloproteinase-3 upregulation, which is fundamental to wound epithelium formation. These data suggest that Co-c-Fos might participate in wound healing by modulating the expression of its potential target gene matrix metalloproteinase-3. Our study provides important insights into mechanisms that are responsible for the initiation of newt limb regeneration.
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Affiliation(s)
- Gang Ye
- Lab of Tissue Engineering, College of Life Sciences, Northwest University, Xi’an 710069, China; (G.Y.); (Y.F.); (Z.M.); (D.W.); (S.L.); (F.C.); (J.C.)
| | - Yalong Feng
- Lab of Tissue Engineering, College of Life Sciences, Northwest University, Xi’an 710069, China; (G.Y.); (Y.F.); (Z.M.); (D.W.); (S.L.); (F.C.); (J.C.)
| | - Zhaoxiang Mi
- Lab of Tissue Engineering, College of Life Sciences, Northwest University, Xi’an 710069, China; (G.Y.); (Y.F.); (Z.M.); (D.W.); (S.L.); (F.C.); (J.C.)
| | - Du Wang
- Lab of Tissue Engineering, College of Life Sciences, Northwest University, Xi’an 710069, China; (G.Y.); (Y.F.); (Z.M.); (D.W.); (S.L.); (F.C.); (J.C.)
| | - Shuai Lin
- Lab of Tissue Engineering, College of Life Sciences, Northwest University, Xi’an 710069, China; (G.Y.); (Y.F.); (Z.M.); (D.W.); (S.L.); (F.C.); (J.C.)
| | - Fulin Chen
- Lab of Tissue Engineering, College of Life Sciences, Northwest University, Xi’an 710069, China; (G.Y.); (Y.F.); (Z.M.); (D.W.); (S.L.); (F.C.); (J.C.)
- Provincial Key Laboratory of Biotechnology of Shaanxi, Northwest University, Xi’an 710069, China
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, School of Medicine, Northwest University, Xi’an 710069, China
| | - Jihong Cui
- Lab of Tissue Engineering, College of Life Sciences, Northwest University, Xi’an 710069, China; (G.Y.); (Y.F.); (Z.M.); (D.W.); (S.L.); (F.C.); (J.C.)
- Provincial Key Laboratory of Biotechnology of Shaanxi, Northwest University, Xi’an 710069, China
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, School of Medicine, Northwest University, Xi’an 710069, China
| | - Yuan Yu
- Lab of Tissue Engineering, College of Life Sciences, Northwest University, Xi’an 710069, China; (G.Y.); (Y.F.); (Z.M.); (D.W.); (S.L.); (F.C.); (J.C.)
- Provincial Key Laboratory of Biotechnology of Shaanxi, Northwest University, Xi’an 710069, China
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, School of Medicine, Northwest University, Xi’an 710069, China
- Correspondence:
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Kondrashov A, Karpova E. Notes on Functional Modules in the Assembly of CRISPR/Cas9-Mediated Epigenetic Modifiers. Methods Mol Biol 2021; 2198:401-428. [PMID: 32822047 DOI: 10.1007/978-1-0716-0876-0_30] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
CRISPR/cas9 is a popular tool, widely used today for genome editing. However, the modular organization of this tool allows it to be used not only for DNA modifications but also for introducing epigenetic modifications both in DNA (methylation/demethylation) and in histones (acetylation/deacetylation). In these notes we will concentrate on the ways to adapt the CRISPR/cas9 system for epigenetic DNA modification of specific regions of interest. The modular organization represents a universal principal, that allows to create infinite number of functions with a limited number of tools. CRISPR/cas9, in which each subunit can be adapted for a particular task, is an excellent example of this rule. Made of two main subunits, it can be modified for targeted delivery of foreign activity (effector, an epigenetic enzyme in our case) to a selected part of the genome. In doing this the CRISPR/cas9 system represents a unique method that allows the introduction of both genomic and epigenetic modifications. This chapter gives a detailed review of how to prepare DNA for the fully functional CRISPR/cas9 system, able to introduce required modifications in the region of interest. We will discuss specific requirements for each structural component of the system as well as for auxiliary elements (modules), which are needed to ensure efficient expression of the elements of the system within the cell and the needs of selection and visualization.
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Affiliation(s)
- Alexander Kondrashov
- Division of Cancer and Stem Cells, School of Medicine, University of Nottingham Biodiscovery Institute, Nottingham, UK.
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32
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Akishina AA, Kuvaeva EE, Vorontsova YE, Simonova OB. NAP Family Histone Chaperones: Characterization and Role in Ontogenesis. Russ J Dev Biol 2020. [DOI: 10.1134/s1062360420060028] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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Wang J, Nan N, Shi L, Li N, Huang S, Zhang A, Liu Y, Guo P, Liu B, Xu ZY. Arabidopsis BRCA1 represses RRTF1-mediated ROS production and ROS-responsive gene expression under dehydration stress. THE NEW PHYTOLOGIST 2020; 228:1591-1610. [PMID: 32621388 DOI: 10.1111/nph.16786] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/31/2019] [Accepted: 06/22/2020] [Indexed: 06/11/2023]
Abstract
Reactive oxygen species (ROS) act as important secondary messengers in abscisic acid (ABA) signaling and induce stomatal closure under dehydration stress. The breast cancer susceptibility gene 1 (BRCA1), an important tumor suppressor in animals, functions primarily in the maintenance of genome integrity in animals and plants. However, whether and how the plant BRCA1 regulates intracellular ROS homeostasis in guard cells under dehydration stress remains unknown. Here, we found that Arabidopsis atbrca1 loss-of-function mutants showed dehydration stress tolerance. This stress tolerant phenotype of atbrca1 was a result of ABA- and ROS-induced stomatal closure, which was enhanced in atbrca1 mutants compared with the wild-type. AtBRCA1 downregulated the expression of ROS-responsive and marker genes. Notably, these genes were also the targets of the AP2/ERF transcriptional activator RRTF1/ERF109. Under normal conditions, AtBRCA1 physically interacted with RRTF1 and inhibited its binding to the GCC-box-like sequence in target gene promoters. Under dehydration stress, the expression of AtBRCA1 was dramatically reduced and that of RRTF1 was activated, thus inducing the expression of ROS-responsive genes. Overall, our study reveals a novel molecular function of AtBRCA1 in the transcriptional regulation of intracellular ROS homeostasis under dehydration stress.
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Affiliation(s)
- Jie Wang
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, 130024, China
| | - Nan Nan
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, 130024, China
| | - Lulu Shi
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, 130024, China
| | - Ning Li
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, 130024, China
| | - Shuangzhan Huang
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, 130024, China
| | - Ai Zhang
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, 130024, China
| | - Yutong Liu
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, 130024, China
| | - Peng Guo
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, 130024, China
| | - Bao Liu
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, 130024, China
| | - Zheng-Yi Xu
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, 130024, China
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Suárez M, Canclini L, Esteves A. Identification of a non-classical three-dimensional nuclear localization signal in the intestinal fatty acid binding protein. PLoS One 2020; 15:e0242312. [PMID: 33180886 PMCID: PMC7660557 DOI: 10.1371/journal.pone.0242312] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2020] [Accepted: 10/30/2020] [Indexed: 11/18/2022] Open
Abstract
The intestinal fatty acid binding protein (FABP) is a small protein expressed along the small intestine that bind long-chain fatty acids and other hydrophobic ligands. Several lines of evidence suggest that, once in the nucleus, it interacts with nuclear receptors, activating them and thus transferring the bound ligand into the nucleus. Previous work by our group suggests that FABP2 would participate in the cytoplasm-nucleus translocation of fatty acids. Because the consensus NLS is absent in the sequence of FABP2, we propose that a 3D signal could be responsible for its nuclear translocation. The results obtained by transfection assays of recombinant wild type and mutated forms of Danio rerio Fabp2 in Caco-2 cell cultures, showed that lysine 17, arginine 29 and lysine 30 residues, which are located in the helix-turn-helix region, would constitute a functional non-classical three-dimensional NLS.
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Affiliation(s)
- Mariana Suárez
- Sección Bioquímica, Facultad de Ciencias, Universidad de la República, Montevideo, Uruguay
| | - Lucía Canclini
- Departamento de Genética, Instituto de Investigaciones Biológicas Clemente Estable, Montevideo, Uruguay
| | - Adriana Esteves
- Sección Bioquímica, Facultad de Ciencias, Universidad de la República, Montevideo, Uruguay
- * E-mail:
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35
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Marchand C, Lemay G, Archambault D. Identification of the nuclear and nucleolar localization signals of the Feline immunodeficiency virus Rev protein. Virus Res 2020; 290:198153. [PMID: 33010374 DOI: 10.1016/j.virusres.2020.198153] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Revised: 08/30/2020] [Accepted: 08/31/2020] [Indexed: 10/23/2022]
Abstract
Lentivirus genomes code for a regulatory protein essential for virus replication termed Rev. The Rev protein binds to partially spliced and unspliced viral RNAs and mediates their nuclear export. Therefore, Rev possesses functional domains that enable its shuttling between the cytoplasm and the nucleus. The Feline immunodeficiency virus (FIV), a lentivirus, can lead to an immunodeficiency syndrome after a long incubation period, similar to that associated with the human immunodeficiency virus type 1 (HIV-1). The FIV Rev functional domains have been predicted only by homology with those of HIV-1 Rev. In the present study, the nuclear and nucleolar localization signals (NLS and NoLS, respectively) of the FIV Rev were examined. A series of FIV Rev deletion mutants fused to the enhanced green fluorescent protein (EGFP) were used to localize the NLS in a region spanning amino acids (aa) 81-100. By using alanine substitution mutants, basic residues present between the amino acids (aa) 84-99 of the FIV Rev protein sequence were identified to form the NLS, whereas those between aa 82-95 were associated with the NoLS function. These results further enhance our understanding of how Rev exerts its role in the replication cycle of lentiviruses.
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Affiliation(s)
- Claude Marchand
- Département des Sciences Biologiques, Université du Québec à Montréal, Montréal, Québec, Canada; Département de Microbiologie, Infectiologie et Immunologie, Université de Montréal, Montréal, Québec, Canada
| | - Guy Lemay
- Département de Microbiologie, Infectiologie et Immunologie, Université de Montréal, Montréal, Québec, Canada
| | - Denis Archambault
- Département des Sciences Biologiques, Université du Québec à Montréal, Montréal, Québec, Canada.
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36
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Belcher MS, Vuu KM, Zhou A, Mansoori N, Agosto Ramos A, Thompson MG, Scheller HV, Loqué D, Shih PM. Design of orthogonal regulatory systems for modulating gene expression in plants. Nat Chem Biol 2020; 16:857-865. [PMID: 32424304 DOI: 10.1038/s41589-020-0547-4] [Citation(s) in RCA: 46] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2019] [Accepted: 04/09/2020] [Indexed: 11/08/2022]
Abstract
Agricultural biotechnology strategies often require the precise regulation of multiple genes to effectively modify complex plant traits. However, most efforts are hindered by a lack of characterized tools that allow for reliable and targeted expression of transgenes. We have successfully engineered a library of synthetic transcriptional regulators that modulate expression strength in planta. By leveraging orthogonal regulatory systems from Saccharomyces spp., we have developed a strategy for the design of synthetic activators, synthetic repressors, and synthetic promoters and have validated their use in Nicotiana benthamiana and Arabidopsis thaliana. This characterization of contributing genetic elements that dictate gene expression represents a foundation for the rational design of refined synthetic regulators. Our findings demonstrate that these tools provide variation in transcriptional output while enabling the concerted expression of multiple genes in a tissue-specific and environmentally responsive manner, providing a basis for generating complex genetic circuits that process endogenous and environmental stimuli.
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Affiliation(s)
- Michael S Belcher
- Feedstocks Division, Joint BioEnergy Institute, Emeryville, CA, USA
- Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, CA, USA
| | - Khanh M Vuu
- Feedstocks Division, Joint BioEnergy Institute, Emeryville, CA, USA
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Andy Zhou
- Feedstocks Division, Joint BioEnergy Institute, Emeryville, CA, USA
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- Department of Plant Biology, University of California, Davis, Davis, CA, USA
| | - Nasim Mansoori
- Feedstocks Division, Joint BioEnergy Institute, Emeryville, CA, USA
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Amanda Agosto Ramos
- Feedstocks Division, Joint BioEnergy Institute, Emeryville, CA, USA
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Mitchell G Thompson
- Feedstocks Division, Joint BioEnergy Institute, Emeryville, CA, USA
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- Department of Plant Biology, University of California, Davis, Davis, CA, USA
| | - Henrik V Scheller
- Feedstocks Division, Joint BioEnergy Institute, Emeryville, CA, USA
- Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, CA, USA
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Dominique Loqué
- Feedstocks Division, Joint BioEnergy Institute, Emeryville, CA, USA
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Patrick M Shih
- Feedstocks Division, Joint BioEnergy Institute, Emeryville, CA, USA.
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.
- Department of Plant Biology, University of California, Davis, Davis, CA, USA.
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Mackey AS, Redd PS, DeLaurier A, Hancock CN. Codon optimized Tol2 transposase results in increased transient expression of a crystallin-GFP transgene in zebrafish. MICROPUBLICATION BIOLOGY 2020; 2020:10.17912/micropub.biology.000268. [PMID: 32626847 PMCID: PMC7326334 DOI: 10.17912/micropub.biology.000268] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Grants] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/13/2020] [Revised: 06/08/2020] [Accepted: 06/11/2020] [Indexed: 02/02/2023]
Affiliation(s)
- Allison S. Mackey
- University of South Carolina Aiken, Department of Biology and Geology, Aiken, SC
- University of Utah Bioscience Program, Salt Lake City, UT
| | - Priscilla S. Redd
- University of South Carolina Aiken, Department of Biology and Geology, Aiken, SC
| | - April DeLaurier
- University of South Carolina Aiken, Department of Biology and Geology, Aiken, SC
| | - C. Nathan Hancock
- University of South Carolina Aiken, Department of Biology and Geology, Aiken, SC
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Singh R, Low ETL, Ooi LCL, Ong-Abdullah M, Ting NC, Nookiah R, Ithnin M, Marjuni M, Mustaffa S, Yaakub Z, Amiruddin MD, Manaf MAA, Chan KL, Halim MAA, Sanusi NSNM, Lakey N, Sachdeva M, Bacher B, Garner PA, MacDonald JD, Smith SW, Wischmeyer C, Budiman MA, Beil M, Stroff C, Reed J, Van Brunt A, Berg H, Ordway JM, Sambanthamurthi R. Variation for heterodimerization and nuclear localization among known and novel oil palm SHELL alleles. THE NEW PHYTOLOGIST 2020; 226:426-440. [PMID: 31863488 DOI: 10.1111/nph.16387] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/16/2019] [Accepted: 12/06/2019] [Indexed: 06/10/2023]
Abstract
Oil palm breeding involves crossing dura and pisifera palms to produce tenera progeny with greatly improved oil yield. Oil yield is controlled by variant alleles of a type II MADS-box gene, SHELL, that impact the presence and thickness of the endocarp, or shell, surrounding the fruit kernel. We identified six novel SHELL alleles in noncommercial African germplasm populations from the Malaysian Palm Oil Board. These populations provide extensive diversity to harness genetic, mechanistic and phenotypic variation associated with oil yield in a globally critical crop. We investigated phenotypes in heteroallelic combinations, as well as SHELL heterodimerization and subcellular localization by yeast two-hybrid, bimolecular fluorescence complementation and gene expression analyses. Four novel SHELL alleles were associated with fruit form phenotype. Candidate heterodimerization partners were identified, and interactions with EgSEP3 and subcellular localization were SHELL allele-specific. Our findings reveal allele-specific mechanisms by which variant SHELL alleles impact yield, as well as speculative insights into the potential role of SHELL in single-gene oil yield heterosis. Future field trials for combinability and introgression may further optimize yield and improve sustainability.
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Affiliation(s)
- Rajinder Singh
- Advanced Biotechnology and Breeding Centre, Malaysian Palm Oil Board, 6, Persiaran Institusi Bandar Baru Bangi, Kajang, Selangor, 43000, Malaysia
| | - Eng-Ti Leslie Low
- Advanced Biotechnology and Breeding Centre, Malaysian Palm Oil Board, 6, Persiaran Institusi Bandar Baru Bangi, Kajang, Selangor, 43000, Malaysia
| | - Leslie Cheng-Li Ooi
- Advanced Biotechnology and Breeding Centre, Malaysian Palm Oil Board, 6, Persiaran Institusi Bandar Baru Bangi, Kajang, Selangor, 43000, Malaysia
| | - Meilina Ong-Abdullah
- Advanced Biotechnology and Breeding Centre, Malaysian Palm Oil Board, 6, Persiaran Institusi Bandar Baru Bangi, Kajang, Selangor, 43000, Malaysia
| | - Ngoot-Chin Ting
- Advanced Biotechnology and Breeding Centre, Malaysian Palm Oil Board, 6, Persiaran Institusi Bandar Baru Bangi, Kajang, Selangor, 43000, Malaysia
| | - Rajanaidu Nookiah
- Advanced Biotechnology and Breeding Centre, Malaysian Palm Oil Board, 6, Persiaran Institusi Bandar Baru Bangi, Kajang, Selangor, 43000, Malaysia
| | - Maizura Ithnin
- Advanced Biotechnology and Breeding Centre, Malaysian Palm Oil Board, 6, Persiaran Institusi Bandar Baru Bangi, Kajang, Selangor, 43000, Malaysia
| | - Marhalil Marjuni
- Advanced Biotechnology and Breeding Centre, Malaysian Palm Oil Board, 6, Persiaran Institusi Bandar Baru Bangi, Kajang, Selangor, 43000, Malaysia
| | - Suzana Mustaffa
- Advanced Biotechnology and Breeding Centre, Malaysian Palm Oil Board, 6, Persiaran Institusi Bandar Baru Bangi, Kajang, Selangor, 43000, Malaysia
| | - Zulkifli Yaakub
- Advanced Biotechnology and Breeding Centre, Malaysian Palm Oil Board, 6, Persiaran Institusi Bandar Baru Bangi, Kajang, Selangor, 43000, Malaysia
| | - Mohd Din Amiruddin
- Advanced Biotechnology and Breeding Centre, Malaysian Palm Oil Board, 6, Persiaran Institusi Bandar Baru Bangi, Kajang, Selangor, 43000, Malaysia
| | - Mohamad Arif Abdul Manaf
- Advanced Biotechnology and Breeding Centre, Malaysian Palm Oil Board, 6, Persiaran Institusi Bandar Baru Bangi, Kajang, Selangor, 43000, Malaysia
| | - Kuang-Lim Chan
- Advanced Biotechnology and Breeding Centre, Malaysian Palm Oil Board, 6, Persiaran Institusi Bandar Baru Bangi, Kajang, Selangor, 43000, Malaysia
| | - Mohd Amin Ab Halim
- Advanced Biotechnology and Breeding Centre, Malaysian Palm Oil Board, 6, Persiaran Institusi Bandar Baru Bangi, Kajang, Selangor, 43000, Malaysia
| | - Nik Shazana Nik Mohd Sanusi
- Advanced Biotechnology and Breeding Centre, Malaysian Palm Oil Board, 6, Persiaran Institusi Bandar Baru Bangi, Kajang, Selangor, 43000, Malaysia
| | | | | | | | | | | | | | | | | | | | | | - Jerry Reed
- Orion Genomics, St Louis, MO, 63108, USA
| | | | - Howard Berg
- Donald Danforth Plant Science Center, St Louis, MO, 63132, USA
| | | | - Ravigadevi Sambanthamurthi
- Advanced Biotechnology and Breeding Centre, Malaysian Palm Oil Board, 6, Persiaran Institusi Bandar Baru Bangi, Kajang, Selangor, 43000, Malaysia
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39
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Day AH, Übler MH, Best HL, Lloyd-Evans E, Mart RJ, Fallis IA, Allemann RK, Al-Wattar EAH, Keymer NI, Buurma NJ, Pope SJA. Targeted cell imaging properties of a deep red luminescent iridium(iii) complex conjugated with a c-Myc signal peptide. Chem Sci 2020; 11:1599-1606. [PMID: 32206278 PMCID: PMC7069228 DOI: 10.1039/c9sc05568a] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2019] [Accepted: 12/14/2019] [Indexed: 12/05/2022] Open
Abstract
A nuclear localisation sequence (NLS) peptide, PAAKRVKLD, derived from the human c-Myc regulator gene, has been functionalised with a long wavelength (λ ex = 550 nm; λ em = 677 nm) cyclometalated organometallic iridium(iii) complex to give the conjugate Ir-CMYC. Confocal fluorescence microscopy studies on human fibroblast cells imaged after 18-24 h incubation show that Ir-CMYC concentrations of 80-100 μM promote good cell uptake and nuclear localisation, which was confirmed though co-localisation studies using Hoechst 33342. In comparison, a structurally related, photophysically analogous iridium(iii) complex lacking the peptide sequence, Ir-PYR, showed very different biological behaviour, with no evidence of nuclear, lysosomal or autophagic vesicle localisation and significantly increased toxicity to the cells at concentrations >10 μM that induced mitochondrial dysfunction. Supporting UV-visible and circular dichroism spectroscopic studies show that Ir-PYR and Ir-CMYC display similarly low affinities for DNA (ca. 103 M-1), consistent with electrostatic binding. Therefore the translocation and nuclear uptake properties of Ir-CMYC are attributed to the presence of the PAAKRVKLD nuclear localisation sequence in this complex.
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Affiliation(s)
- Adam H Day
- School of Chemistry , Cardiff University , Main Building , Cardiff , CF10 3AT , UK .
| | - Martin H Übler
- School of Chemistry , Cardiff University , Main Building , Cardiff , CF10 3AT , UK .
| | - Hannah L Best
- School of Biosciences , Cardiff University , Sir Martin Evans Building , Cardiff , UK
| | - Emyr Lloyd-Evans
- School of Biosciences , Cardiff University , Sir Martin Evans Building , Cardiff , UK
| | - Robert J Mart
- School of Chemistry , Cardiff University , Main Building , Cardiff , CF10 3AT , UK .
| | - Ian A Fallis
- School of Chemistry , Cardiff University , Main Building , Cardiff , CF10 3AT , UK .
| | - Rudolf K Allemann
- School of Chemistry , Cardiff University , Main Building , Cardiff , CF10 3AT , UK .
| | - Eman A H Al-Wattar
- School of Chemistry , Cardiff University , Main Building , Cardiff , CF10 3AT , UK .
| | - Nathaniel I Keymer
- School of Chemistry , Cardiff University , Main Building , Cardiff , CF10 3AT , UK .
| | - Niklaas J Buurma
- School of Chemistry , Cardiff University , Main Building , Cardiff , CF10 3AT , UK .
| | - Simon J A Pope
- School of Chemistry , Cardiff University , Main Building , Cardiff , CF10 3AT , UK .
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40
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Huang B, Li WX, Wang ZX, Liang Y, Huang WS, Nie P. Identification of a novel splice variant isoform of interferon regulatory factor 10, IRF10, in orange spotted grouper Epinephelus coioides. FISH & SHELLFISH IMMUNOLOGY 2020; 97:637-647. [PMID: 31866452 DOI: 10.1016/j.fsi.2019.12.056] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/16/2019] [Revised: 12/16/2019] [Accepted: 12/18/2019] [Indexed: 06/10/2023]
Abstract
Interferon regulatory factors (IRFs) are a family of transcription factors essential to the control of antiviral immune response, cell growth, differentiation and apoptosis. IRF10 was originally found in chicken, which was induced by the v-Rel oncoprotein in lymphoid cell lines and involved in the upregulation of major histocompatibility complex (MHC) class I and guanylate-binding protein. In fish, IRF10 plays negative roles in regulation of the interferon (IFN) response. Here, we identified a splice variant of IRF10, named as EcIRF10-SF in orange spotted grouper, which shares the first three exons with the long form (EcIRF10-LF) and retains part of intron 3, creating a premature termination codon. Furthermore, we observed that the EcIRF10-SF exhibits similar expression pattern compared to its native counterparts. Functional studies demonstrate that the two EcIRF10 isoforms repress DrIFNϕ1 and DrIFNϕ3 promoter activity and negatively regulate fish antiviral gene expression. Subcellular localization analysis shows that the amino acids from 57 to 86 within DBD are required for IRF10 nuclear import. Overall, our description of transcript diversification of IRF10 in the grouper provides a coherent framework to further dissect its roles in immune response.
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Affiliation(s)
- B Huang
- Fisheries College, Jimei University, Xiamen, 361021, China; Engineering Research Center of the Modern Technology for Eel Industry, Ministry of Education, PR China
| | - W X Li
- Fisheries College, Jimei University, Xiamen, 361021, China
| | - Z X Wang
- Fisheries College, Jimei University, Xiamen, 361021, China
| | - Y Liang
- Fisheries College, Jimei University, Xiamen, 361021, China
| | - W S Huang
- Fisheries College, Jimei University, Xiamen, 361021, China; Engineering Research Center of the Modern Technology for Eel Industry, Ministry of Education, PR China.
| | - P Nie
- Laboratory for Marine Biology and Biotechnology, Pilot National Laboratory for Marine Science and Technology (Qingdao), Qingdao, Shandong Province, 266237, China; School of Marine Science and Engineering, Qingdao Agricultural University, Qingdao, Shandong Province, 266109, China.
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41
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Zhou Z, Wang J, Zhang S, Yu Q, Lan H. Investigation of the Nature of CgCDPK and CgbHLH001 Interaction and the Function of bHLH Transcription Factor in Stress Tolerance in Chenopodium glaucum. FRONTIERS IN PLANT SCIENCE 2020; 11:603298. [PMID: 33552098 PMCID: PMC7862342 DOI: 10.3389/fpls.2020.603298] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/06/2020] [Accepted: 12/11/2020] [Indexed: 05/22/2023]
Abstract
Calcium-dependent protein kinase (CDPK) and its substrates play important roles in plant response to stress. So far, the documentation on the characterization of the CDPK and downstream interaction components (especially transcription factors, TFs) is limited. In the present study, an interaction between CgCDPK (protein kinase) (accession no. MW26306) and CgbHLH001 (TF) (accession no. MT797813) from a halophyte Chenopodium glaucum was further dissected. Firstly, we revealed that the probable nature between the CgCDPK and CgbHLH001 interaction was the phosphorylation, and the N-terminus of CgbHLH001, especially the 96th serine (the potential phosphorylation site) within it, was essential for the interaction, whereas the mutation of 96Ser to alanine did not change its nuclear localization, which was determined by the N-terminus and bHLH domain together. Furthermore, we verified the function of CgbHLH001 gene in response to stress by ectopic overexpression in tobacco; the transgenic lines presented enhanced stress tolerance probably by improving physiological performance and stress-related gene expression. In conclusion, we characterized the biological significance of the interaction between CDPK and bHLH in C. glaucum and verified the positive function of CgbHLH001 in stress tolerance, which may supply more evidence in better understanding of the CDPK signaling pathway in response to adversity.
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Affiliation(s)
- Zixin Zhou
- Xinjiang Key Laboratory of Biological Resources and Genetic Engineering, College of Life Science and Technology, Xinjiang University, Urumqi, China
| | - Juan Wang
- Institute of Horticulture Crops, Xinjiang Academy of Agricultural Sciences, Urumqi, China
| | - Shiyue Zhang
- Xinjiang Key Laboratory of Biological Resources and Genetic Engineering, College of Life Science and Technology, Xinjiang University, Urumqi, China
| | - Qinghui Yu
- Institute of Horticulture Crops, Xinjiang Academy of Agricultural Sciences, Urumqi, China
- *Correspondence: Qinghui Yu,
| | - Haiyan Lan
- Xinjiang Key Laboratory of Biological Resources and Genetic Engineering, College of Life Science and Technology, Xinjiang University, Urumqi, China
- Haiyan Lan,
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42
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Alvite G, Riera X, Cancela S, Paulino M, Esteves A. Bioinformatic analysis of a novel Echinococcus granulosus nuclear receptor with two DNA binding domains. PLoS One 2019; 14:e0224703. [PMID: 31710619 PMCID: PMC6844482 DOI: 10.1371/journal.pone.0224703] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2019] [Accepted: 10/18/2019] [Indexed: 12/12/2022] Open
Abstract
Nuclear receptors are ligand-activated transcription factors capable of regulating the expression of complex gene networks. The family includes seven subfamilies of proteins with a wide phylogenetic distribution. A novel subfamily with two DNA-binding domains (2DBDs) has been reported in Schistosoma mansoni (Platyhelminth, Trematoda). This work describes the cDNA cloning and bioinformatics analysis of Eg2DBDα, a 2DBD nuclear receptor isoform from the parasite Echinococcus granulosus (Platyhelminth, Cestoda). The Eg2DBDα gene coding domain structure was analysed. Although two additional 2DBD nuclear receptors are reported in the parasite database GeneDB, they are unlikely to be expressed in the larval stage. Phylogenetic relationships between these atypical proteins from different cestodes are also analysed including S. mansoni 2DBD nuclear receptors. The presence of two DNA binding domains confers particular interest to these nuclear receptors, not only concerning their function but to the development of new antihelminthic drugs.
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Affiliation(s)
- Gabriela Alvite
- Biochemistry Section, Faculty of Sciences, Universidad de la República, Montevideo, Uruguay
| | - Ximena Riera
- Biochemistry Section, Faculty of Sciences, Universidad de la República, Montevideo, Uruguay
| | - Saira Cancela
- Biochemistry Section, Faculty of Sciences, Universidad de la República, Montevideo, Uruguay
| | - Margot Paulino
- Center of Bioinformatics, Departamento de Experimentación y Teoría de la Materia, Faculty of Chemistry, Universidad de la República, Montevideo, Uruguay
| | - Adriana Esteves
- Biochemistry Section, Faculty of Sciences, Universidad de la República, Montevideo, Uruguay
- * E-mail:
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43
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Saribas AS, Datta PK, Safak M. A comprehensive proteomics analysis of JC virus Agnoprotein-interacting proteins: Agnoprotein primarily targets the host proteins with coiled-coil motifs. Virology 2019; 540:104-118. [PMID: 31765920 DOI: 10.1016/j.virol.2019.10.005] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2019] [Revised: 10/13/2019] [Accepted: 10/16/2019] [Indexed: 11/29/2022]
Abstract
JC virus (JCV) Agnoprotein (Agno) plays critical roles in successful completion of the viral replication cycle. Understanding its regulatory roles requires a complete map of JCV-host protein interactions. Here, we report the first Agno interactome with host cellular targets utilizing "Two-Strep-Tag" affinity purification system coupled with mass spectroscopy (AP/MS). Proteomics data revealed that Agno primarily targets 501 cellular proteins, most of which contain "coiled-coil" motifs. Agno-host interactions occur in several cellular networks including those involved in protein synthesis and degradation; and cellular transport; and in organelles, including mitochondria, nucleus and ER-Golgi network. Among the Agno interactions, Rab11B, Importin and Crm-1 were first validated biochemically and further characterization was done for Crm-1, using a HIV-1 Rev-M10-like Agno mutant (L33D + E34L), revealing the critical roles of L33 and E34 residues in Crm-1 interaction. This comprehensive proteomics data provides new foundations to unravel the critical regulatory roles of Agno during the JCV life cycle.
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Affiliation(s)
- A Sami Saribas
- Department of Neuroscience, Laboratory of Molecular Neurovirology, Lewis Katz School of Medicine at Temple University, 3500 N. Broad Street, Philadelphia, PA, 19140, USA
| | - Prasun K Datta
- Department of Neuroscience, Laboratory of Molecular Neurovirology, Lewis Katz School of Medicine at Temple University, 3500 N. Broad Street, Philadelphia, PA, 19140, USA
| | - Mahmut Safak
- Department of Neuroscience, Laboratory of Molecular Neurovirology, Lewis Katz School of Medicine at Temple University, 3500 N. Broad Street, Philadelphia, PA, 19140, USA.
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44
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Candelori A, Yamamoto TG, Iwamoto M, Montani M, Amici A, Vallesi A. Subcellular Targeting of the Euplotes raikovi Kinase Er-MAPK1, as Revealed by Expression in Different Cell Systems. Front Cell Dev Biol 2019; 7:244. [PMID: 31681773 PMCID: PMC6811501 DOI: 10.3389/fcell.2019.00244] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2019] [Accepted: 10/04/2019] [Indexed: 11/13/2022] Open
Abstract
In the ciliate Euplotes raikovi, a 631-amino acid Er-MAPK1 protein kinase was found to localize in nucleoli of the transcriptionally active nucleus (macronucleus) and act as a key component of an autocrine, cell-growth promoting self-signaling mechanism. While its 283-amino acid N-terminal domain includes all the structural specificities of the mitogen-activated protein kinases required for a catalytic function, the 348-amino acid C-terminal domain is structurally unique with undetermined functions. By expressing the two Er-MAPK1 domains tagged with the green fluorescent protein in mammalian fibroblasts, the yeast Schizosaccharomyces pombe and the ciliate Tetrahymena thermophila, evidence was obtained that the C-terminal domain contains all the sequence information responsible for the Er-MAPK1 subcellular localization. However, in fibroblasts and S. pombe this information determined a nucleolar localization of the GFP-tagged C-terminal domain, and a ciliary localization in T. thermophila. In the light of these findings, the Er-MAPK1 localization in E. raikovi was re-examined via immunoreactions and shown to be ciliary besides that nuclear, as is the case for the mammalian intestinal cell kinase with which the Er-MAPK1 N-terminal domain shares a strong sequence identity and a catalytic function.
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Affiliation(s)
- Annalisa Candelori
- School of Biosciences and Veterinary Medicine, University of Camerino, Camerino, Italy
| | - Takaharu G Yamamoto
- Advanced ICT Research Institute, National Institute of Information and Communications Technology, Kobe, Japan
| | - Masaaki Iwamoto
- Advanced ICT Research Institute, National Institute of Information and Communications Technology, Kobe, Japan
| | - Maura Montani
- School of Biosciences and Veterinary Medicine, University of Camerino, Camerino, Italy
| | - Augusto Amici
- School of Biosciences and Veterinary Medicine, University of Camerino, Camerino, Italy
| | - Adriana Vallesi
- School of Biosciences and Veterinary Medicine, University of Camerino, Camerino, Italy
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45
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Contreras R, Kallemi P, González-García MP, Lazarova A, Sánchez-Serrano JJ, Sanmartín M, Rojo E. Identification of Domains and Factors Involved in MINIYO Nuclear Import. FRONTIERS IN PLANT SCIENCE 2019; 10:1044. [PMID: 31552063 PMCID: PMC6748027 DOI: 10.3389/fpls.2019.01044] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/22/2019] [Accepted: 07/29/2019] [Indexed: 05/28/2023]
Abstract
The transition of stem cells from self-renewal into differentiation is tightly regulated to assure proper development of the organism. Arabidopsis MINIYO (IYO) and its mammalian orthologue RNA polymerase II associated protein 1 (RPAP1) are essential factors for initiating stem cell differentiation in plants and animals. Moreover, there is evidence suggesting that the translocation of IYO and RPAP1 from the cytosol into the nucleus functions as a molecular switch to initiate this cell fate transition. Identifying the determinants of IYO subcellular localization would allow testing if, indeed, nuclear IYO migration triggers cell differentiation and could provide tools to control this crucial developmental transition. Through transient and stable expression assays in Nicotiana benthamiana and Arabidopsis thaliana, we demonstrate that IYO contains two nuclear localization signals (NLSs), located at the N- and C-terminus of the protein, which mediate the interaction with the NLS-receptor IMPA4 and the import of the protein into the nucleus. Interestingly, IYO also interacts with GPN GTPases, which are involved in selective nuclear import of RNA polymerase II. This interaction is prevented when the G1 motif in GPN1 is mutated, suggesting that IYO binds specifically to the nucleotide-bound form of GPN1. In contrast, deleting the NLSs in IYO does not prevent the interaction with GPN1, but it interferes with import of GPN1 into the nucleus, indicating that IYO and GPN1 are co-transported as a complex that requires the IYO NLSs for import. This work unveils key domains and factors involved in IYO nuclear import, which may prove instrumental to determine how IYO and RPAP1 control stem cell differentiation.
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Affiliation(s)
| | | | | | | | | | | | - Enrique Rojo
- *Correspondence: Maite Sanmartín, , ; Enrique Rojo,
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46
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The Jembrana disease virus Rev protein: Identification of nuclear and novel lentiviral nucleolar localization and nuclear export signals. PLoS One 2019; 14:e0221505. [PMID: 31437223 PMCID: PMC6706053 DOI: 10.1371/journal.pone.0221505] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2018] [Accepted: 08/08/2019] [Indexed: 11/19/2022] Open
Abstract
The lentiviral Rev protein, which is a regulatory protein essential for virus replication, has been first studied in the human immunodeficiency virus type 1 (HIV-1). The main function of Rev is to mediate the nuclear exportation of viral RNAs. To fulfill its function, Rev shuttles between the cytoplasm and the nucleus. The Jembrana disease virus (JDV), a lentivirus, is the etiologic agent of the Jembrana disease which was first described in Bali cattle in Indonesia in 1964. Despite the high mortality rate associated with JDV, this virus remains poorly studied. Herein the subcellular distribution of JDV Rev, the nuclear and nucleolar localization signals (NLS and NoLS, respectively) and the nuclear export signal (NES) of the protein were examined. JDV Rev fused to the enhanced green fluorescent protein (EGFP) predominantly localized to the cytoplasm and nucleolus of transfected cells, as determined by fluorescence microscopy analyses. Through transfection of a series of deletion mutants of JDV Rev, it was possible to localize the NLS/NoLS region between amino acids (aa) 74 to 105. By substituting basic residues with alanine within this sequence, we demonstrated that the JDV Rev NLS encompasses aa 76 to 86, and is exclusively composed of arginine residues, whereas a bipartite NoLS was observed for the first time in any retroviral Rev/Rev-like proteins. Finally, a NES was identified downstream of the NLS/NoLS and encompasses aa 116 to 128 of the JDV Rev protein. The JDV Rev NES was found to be of the protein kinase A inhibitor (PKI) class instead of the HIV-1 Rev class. It also corresponds to the most optimal consensus sequence of PKI NES and, as such, is novel among lentiviral Rev NES.
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Zhang H, Zhang L, Han J, Qian Z, Zhou B, Xu Y, Wu G. The nuclear localization signal is required for the function of squamosa promoter binding protein-like gene 9 to promote vegetative phase change in Arabidopsis. PLANT MOLECULAR BIOLOGY 2019; 100:571-578. [PMID: 30953277 DOI: 10.1007/s11103-019-00863-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/29/2019] [Accepted: 03/27/2019] [Indexed: 05/14/2023]
Abstract
A mutation in the nuclear localization signal of squamosa promoter binding like-protein 9 (SPL9) delays vegetative phase change by disrupting its nuclear localization. The juvenile-to-adult phase transition is a critical developmental process in plant development, and it is regulated by a decrease in miR156/157 and a corresponding increase in their targets, squamosa promoter binding protein-like (SPL) genes. SPL proteins contain a conserved SBP domain with putative nuclear localization signals (NLSs) at their C-terminals. Some SPLs promote vegetative phase change by promoting miR172 expression, but the function of nuclear localization signals in those SPLs remains unknown. Here, we identified a loss-of-function mutant, which we named del6, with delayed vegetative phase change phenotypes in a forward genetic screen. Map-based cloning, the whole genome resequencing, and allelic complementation test demonstrate that a G-to-A substitution in the SPL9 gene is responsible for the delayed vegetative phase change phenotypes. In del6, the mutation causes a substitution of the glutamine (Gln) for the conserved basic amino acid arginine (Arg) in the NLS of the SBP domain, and disrupts the normal nuclear localization and function of SPL9. Therefore, our work demonstrates that the NLSs in the SBP domain of SPL9 are indispensable for its nuclear localization and normal function in Arabidopsis.
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Affiliation(s)
- Hui Zhang
- State Key Laboratory of Subtropical Silviculture, Laboratory of Plant Molecular and Developmental Biology, Zhejiang Agriculture and Forestry University, Hangzhou, China
| | - Lu Zhang
- State Key Laboratory of Subtropical Silviculture, Laboratory of Plant Molecular and Developmental Biology, Zhejiang Agriculture and Forestry University, Hangzhou, China
| | - Junyou Han
- College of Plant Science, Jilin University, Changchun, 130062, China
| | - Zhiyuan Qian
- State Key Laboratory of Subtropical Silviculture, Laboratory of Plant Molecular and Developmental Biology, Zhejiang Agriculture and Forestry University, Hangzhou, China
| | - Bingying Zhou
- State Key Laboratory of Subtropical Silviculture, Laboratory of Plant Molecular and Developmental Biology, Zhejiang Agriculture and Forestry University, Hangzhou, China
| | - Yunmin Xu
- State Key Laboratory of Subtropical Silviculture, Laboratory of Plant Molecular and Developmental Biology, Zhejiang Agriculture and Forestry University, Hangzhou, China.
| | - Gang Wu
- State Key Laboratory of Subtropical Silviculture, Laboratory of Plant Molecular and Developmental Biology, Zhejiang Agriculture and Forestry University, Hangzhou, China.
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48
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Huang S, Zhang A, Jin JB, Zhao B, Wang TJ, Wu Y, Wang S, Liu Y, Wang J, Guo P, Ahmad R, Liu B, Xu ZY. Arabidopsis histone H3K4 demethylase JMJ17 functions in dehydration stress response. THE NEW PHYTOLOGIST 2019; 223:1372-1387. [PMID: 31038749 DOI: 10.1111/nph.15874] [Citation(s) in RCA: 57] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/21/2018] [Accepted: 04/18/2019] [Indexed: 06/09/2023]
Abstract
Under dehydration in plants, antagonistic activities of histone 3 lysine 4 (H3K4) methyltransferase and histone demethylase maintain a dynamic and homeostatic state of gene expression by orientating transcriptional reprogramming toward growth or stress tolerance. However, the histone demethylase that specifically controls histone methylation homeostasis under dehydration stress remains unknown. Here, we document that a histone demethylase, JMJ17, belonging to the KDM5/JARID1 family, plays crucial roles in response to dehydration stress and abscisic acid (ABA) in Arabidopsis thaliana. jmj17 loss-of-function mutants displayed dehydration stress tolerance and ABA hypersensitivity in terms of stomatal closure. JMJ17 specifically demethylated H3K4me1/2/3 via conserved iron-binding amino acids in vitro and in vivo. Moreover, H3K4 demethylase activity of JMJ17 was required for dehydration stress response. Systematic combination of genome-wide chromatin immunoprecipitation coupled with massively parallel DNA sequencing (ChIP-seq) and RNA-sequencing (RNA-seq) analyses revealed that a loss-of-function mutation in JMJ17 caused an ectopic increase in genome-wide H3K4me3 levels and activated a plethora of dehydration stress-responsive genes. Importantly, JMJ17 bound directly to the chromatin of OPEN STOMATA 1 (OST1) and demethylated H3K4me3 for the regulation of OST1 mRNA abundance, thereby modulating the dehydration stress response. Our results demonstrate a new function of a histone demethylase under dehydration stress in plants.
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Affiliation(s)
- Shuangzhan Huang
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, 130024, China
| | - Ai Zhang
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, 130024, China
| | - Jing Bo Jin
- Key Laboratory of Molecular Physiology, Institute of Botany, the Chinese Academy of Sciences, Beijing, 100093, China
| | - Bo Zhao
- Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, TX, 78712, USA
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, 78712, USA
| | - Tian-Jing Wang
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, 130024, China
| | - Yifan Wu
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, 130024, China
| | - Shuang Wang
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, 130024, China
| | - Yutong Liu
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, 130024, China
| | - Jie Wang
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, 130024, China
| | - Peng Guo
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, 130024, China
| | - Rafiq Ahmad
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, 130024, China
| | - Bao Liu
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, 130024, China
| | - Zheng-Yi Xu
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, 130024, China
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Li J, Dong Y, Sun Y, Lai Z, Zhao Y, Liu P, Gao Y, Chen X, Gu J. A Novel Densovirus Isolated From the Asian Tiger Mosquito Displays Varied Pathogenicity Depending on Its Host Species. Front Microbiol 2019; 10:1549. [PMID: 31333635 PMCID: PMC6624781 DOI: 10.3389/fmicb.2019.01549] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2019] [Accepted: 06/20/2019] [Indexed: 11/18/2022] Open
Abstract
Mosquito-borne viral diseases (MBVDs) continue to pose a significant global public health burden. Mosquito control remains a core intervention strategy in integrated mosquito management (IMM) programs to reduce the transmission of MBVDs. Mosquito densoviruses (MDVs) are mosquito-specific entomopathogenic viruses, and their attractive biological and pathogenic characteristics make MDVs potential biological control agents as alternatives to traditional chemical pesticides. However, different viral strains vary greatly in their pathogenicity against different mosquito species, which poses an obstacle for the wide application of MDVs in vector control. In this study, a novel MDV, Aedes albopictus densovirus-7 (AalDV-7), was isolated from field-collected Aedes albopictus in the dengue-endemic area of Guangzhou, China. The complete 4,048 nt genome of AalDV-7 was cloned and sequenced, and the transcription and translation of three open reading frames (ORFs) were characterized. Phylogenetic analysis indicated that AalDV-7 clustered with MDVs mostly isolated from indigenous mosquitoes. The pathogenicity of AalDV-7 to A. albopictus, Aedes aegypti, and Culex quinquefasciatus larvae was completely different, and the median lethal dose (LD50) of AalDV-7 in A. albopictus which was 109.48 genome equivalents per ml (geq/ml) was 12 and 46 times lower than those in A. aegypti (1010.56 geq/ml) and C. quinquefasciatus (1011.15 geq/ml). Furthermore, the median lethal time (LT50) value in A. albopictus (7.72 days) was 25% and 26% shorter than those in A. aegypti (10.24 days) and C. quinquefasciatus (10.42 days) at a titer of 1011 geq/ml. Furthermore, the mortality of AalDV-7-infected mosquitoes increased in a dose-dependent manner, and the highest mortality was found in A. albopictus larvae exposed to 1011 geq/ml AalDV-7 (82.00%). Sublethal effects analysis also showed that AalDV-7 infection significantly decreased pupation and emergence rates. The 1st–2nd instar larvae of all three mosquito species showed a near 100% infection rate, and the highest relative vial titer (305.97 ± 67.57 geq/ng) was observed in the 1st–2nd instar larvae of C. quinquefasciatus. These pathogenic characteristics make AalDV-7 a potential MBVDs control agent in China, whereas its negligible pathogenicity and high infection rate and viral dose in vivo make it a good candidate for gene delivery vectors in C. quinquefasciatus gene function analysis. In conclusion, the continuous discovery and isolation of new MDVs enrich the pool of mosquito entomopathogenic viruses and provide a variety of choices for optimal MDVs or combinations of MDVs to target certain mosquitoes.
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Affiliation(s)
- Jing Li
- Guangdong Provincial Key Laboratory of Tropical Disease Research, Department of Pathogen Biology, School of Public Health, Southern Medical University, Guangzhou, China
| | - Yunqiao Dong
- Reproductive Medical Centre of Guangdong Women and Children's Hospital, Guangzhou, China
| | - Yan Sun
- Guangdong Provincial Key Laboratory of Tropical Disease Research, Department of Pathogen Biology, School of Public Health, Southern Medical University, Guangzhou, China
| | - Zetian Lai
- Guangdong Provincial Key Laboratory of Tropical Disease Research, Department of Pathogen Biology, School of Public Health, Southern Medical University, Guangzhou, China
| | - Yijie Zhao
- Guangdong Provincial Key Laboratory of Tropical Disease Research, Department of Pathogen Biology, School of Public Health, Southern Medical University, Guangzhou, China
| | - Peiwen Liu
- Guangdong Provincial Key Laboratory of Tropical Disease Research, Department of Pathogen Biology, School of Public Health, Southern Medical University, Guangzhou, China
| | - Yonghui Gao
- Guangdong Provincial Key Laboratory of Tropical Disease Research, Department of Pathogen Biology, School of Public Health, Southern Medical University, Guangzhou, China
| | - Xiaoguang Chen
- Guangdong Provincial Key Laboratory of Tropical Disease Research, Department of Pathogen Biology, School of Public Health, Southern Medical University, Guangzhou, China
| | - Jinbao Gu
- Guangdong Provincial Key Laboratory of Tropical Disease Research, Department of Pathogen Biology, School of Public Health, Southern Medical University, Guangzhou, China
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50
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Xiao Y, Chen J, Wan Y, Gao Q, Jing N, Zheng Y, Zhu X. Regulation of zebrafish dorsoventral patterning by phase separation of RNA-binding protein Rbm14. Cell Discov 2019; 5:37. [PMID: 31636951 PMCID: PMC6796953 DOI: 10.1038/s41421-019-0106-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2019] [Revised: 06/13/2019] [Accepted: 06/14/2019] [Indexed: 02/08/2023] Open
Abstract
RNA-binding proteins with intrinsically disordered regions (IDRs) such as Rbm14 can phase separate in vitro. To what extent the phase separation contributes to their physiological functions is however unclear. Here we show that zebrafish Rbm14 regulates embryonic dorsoventral patterning through phase separation. Zebrafish rbm14 morphants displayed dorsalized phenotypes associated with attenuated BMP signaling. Consistently, depletion of mammalian Rbm14 downregulated BMP regulators and effectors Nanog, Smad4/5, and Id1/2, whereas overexpression of the BMP-related proteins in the morphants significantly restored the developmental defects. Importantly, the IDR of zebrafish Rbm14 demixed into liquid droplets in vitro despite poor sequence conservation with its mammalian counterpart. While its phase separation mutants or IDR failed to rescue the morphants, its chimeric proteins containing an IDR from divergent phase separation proteins were effective. Rbm14 complexed with proteins involved in RNA metabolism and phase separated into cellular ribonucleoprotein compartments. Consistently, RNA deep sequencing analysis on the morphant embryos revealed increased alternative splicing events as well as large-scale transcriptomic downregulations. Our results suggest that Rbm14 functions in ribonucleoprotein compartments through phase separation to modulate multiple aspects of RNA metabolism. Furthermore, IDRs conserve in phase separation ability but not primary sequence and can be functionally interchangeable.
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Affiliation(s)
- Yue Xiao
- State Key Laboratory of Cell Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, 320 Yueyang Road, 200031 Shanghai, China
| | - Jiehui Chen
- State Key Laboratory of Cell Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, 320 Yueyang Road, 200031 Shanghai, China
| | - Yihan Wan
- State Key Laboratory of Cell Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, 320 Yueyang Road, 200031 Shanghai, China
- Department of Embryology, Carnegie Institution for Science, 3520 San Martin Dr., Baltimore, MD 21218 USA
| | - Qi Gao
- State Key Laboratory of Cell Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, 320 Yueyang Road, 200031 Shanghai, China
| | - Naihe Jing
- State Key Laboratory of Cell Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, 320 Yueyang Road, 200031 Shanghai, China
| | - Yixian Zheng
- Department of Embryology, Carnegie Institution for Science, 3520 San Martin Dr., Baltimore, MD 21218 USA
| | - Xueliang Zhu
- State Key Laboratory of Cell Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, 320 Yueyang Road, 200031 Shanghai, China
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