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Fan L, Wang Y, Huang H, Wang Z, Liang C, Yang X, Ye P, Lin J, Shi W, Zhou Y, Yan H, Long Z, Wang Z, Liu L, Qian J. RNA binding motif 4 inhibits the replication of ebolavirus by directly targeting 3'-leader region of genomic RNA. Emerg Microbes Infect 2024; 13:2300762. [PMID: 38164794 PMCID: PMC10773643 DOI: 10.1080/22221751.2023.2300762] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2023] [Accepted: 12/26/2023] [Indexed: 01/03/2024]
Abstract
Ebola virus (EBOV) belongs to Filoviridae family possessing single-stranded negative-sense RNA genome, which is a serious threat to human health. Nowadays, no therapeutics have been proven to be successful in efficiently decreasing the mortality rate. RNA binding proteins (RBPs) are reported to participate in maintaining cell integrity and regulation of viral replication. However, little is known about whether and how RBPs participate in regulating the life cycle of EBOV. In our study, we found that RNA binding motif protein 4 (RBM4) inhibited the replication of EBOV in HEK293T and Huh-7 cells by suppressing viral mRNA production. Such inhibition resulted from the direct interaction between the RRM1 domain of RBM4 and the "CU" enrichment elements located in the PE1 and TSS of the 3'-leader region within the viral genome. Simultaneously, RBM4 could upregulate the expression of some cytokines involved in the host innate immune responses to synergistically exert its antiviral function. The findings therefore suggest that RBM4 might serve as a novel target of anti-EBOV strategy.
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Affiliation(s)
- Linjin Fan
- Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, People’s Republic of China
- Key Laboratory of Tropical Disease Control (Sun Yat-sen University), Ministry of Education, Guangzhou, People’s Republic of China
| | - Yulong Wang
- Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, People’s Republic of China
- Key Laboratory of Tropical Disease Control (Sun Yat-sen University), Ministry of Education, Guangzhou, People’s Republic of China
| | - Hongxin Huang
- Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, People’s Republic of China
- Key Laboratory of Tropical Disease Control (Sun Yat-sen University), Ministry of Education, Guangzhou, People’s Republic of China
| | - Zequn Wang
- Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, People’s Republic of China
- Key Laboratory of Tropical Disease Control (Sun Yat-sen University), Ministry of Education, Guangzhou, People’s Republic of China
| | - Chudan Liang
- Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, People’s Republic of China
- Key Laboratory of Tropical Disease Control (Sun Yat-sen University), Ministry of Education, Guangzhou, People’s Republic of China
| | - Xiaofeng Yang
- Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, People’s Republic of China
- Key Laboratory of Tropical Disease Control (Sun Yat-sen University), Ministry of Education, Guangzhou, People’s Republic of China
| | - Pengfei Ye
- Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, People’s Republic of China
- Key Laboratory of Tropical Disease Control (Sun Yat-sen University), Ministry of Education, Guangzhou, People’s Republic of China
| | - Jingyan Lin
- Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, People’s Republic of China
- Key Laboratory of Tropical Disease Control (Sun Yat-sen University), Ministry of Education, Guangzhou, People’s Republic of China
| | - Wendi Shi
- Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, People’s Republic of China
- Key Laboratory of Tropical Disease Control (Sun Yat-sen University), Ministry of Education, Guangzhou, People’s Republic of China
| | - Yuandong Zhou
- Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, People’s Republic of China
- Key Laboratory of Tropical Disease Control (Sun Yat-sen University), Ministry of Education, Guangzhou, People’s Republic of China
| | - Huijun Yan
- Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, People’s Republic of China
- Key Laboratory of Tropical Disease Control (Sun Yat-sen University), Ministry of Education, Guangzhou, People’s Republic of China
| | - Zhenyu Long
- Institute of Infectious Diseases, Guangzhou Eighth People's Hospital, Guangzhou Medical University, Guangzhou, People’s Republic of China
| | - Zhongyi Wang
- Beijing Institute of Biotechnology, Beijing, People’s Republic of China
| | - Linna Liu
- Institute of Infectious Diseases, Guangzhou Eighth People's Hospital, Guangzhou Medical University, Guangzhou, People’s Republic of China
| | - Jun Qian
- Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, People’s Republic of China
- Key Laboratory of Tropical Disease Control (Sun Yat-sen University), Ministry of Education, Guangzhou, People’s Republic of China
- School of Public Health (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Shenzhen, People’s Republic of China
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Shang Z, Zhang S, Wang J, Zhou L, Zhang X, Billadeau DD, Yang P, Zhang L, Zhou F, Bai P, Jia D. TRIM25 predominately associates with anti-viral stress granules. Nat Commun 2024; 15:4127. [PMID: 38750080 PMCID: PMC11096359 DOI: 10.1038/s41467-024-48596-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2023] [Accepted: 05/07/2024] [Indexed: 05/18/2024] Open
Abstract
Stress granules (SGs) are induced by various environmental stressors, resulting in their compositional and functional heterogeneity. SGs play a crucial role in the antiviral process, owing to their potent translational repressive effects and ability to trigger signal transduction; however, it is poorly understood how these antiviral SGs differ from SGs induced by other environmental stressors. Here we identify that TRIM25, a known driver of the ubiquitination-dependent antiviral innate immune response, is a potent and critical marker of the antiviral SGs. TRIM25 undergoes liquid-liquid phase separation (LLPS) and co-condenses with the SG core protein G3BP1 in a dsRNA-dependent manner. The co-condensation of TRIM25 and G3BP1 results in a significant enhancement of TRIM25's ubiquitination activity towards multiple antiviral proteins, which are mainly located in SGs. This co-condensation is critical in activating the RIG-I signaling pathway, thus restraining RNA virus infection. Our studies provide a conceptual framework for better understanding the heterogeneity of stress granule components and their response to distinct environmental stressors.
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Affiliation(s)
- Zehua Shang
- Key Laboratory of Birth Defects and Related Diseases of Women and Children, Department of Pediatrics, West China Second University Hospital, State Key Laboratory of Biotherapy, Sichuan University, Chengdu, 610041, China
| | - Sitao Zhang
- Key Laboratory of Birth Defects and Related Diseases of Women and Children, Department of Pediatrics, West China Second University Hospital, State Key Laboratory of Biotherapy, Sichuan University, Chengdu, 610041, China
| | - Jinrui Wang
- Key Laboratory of Birth Defects and Related Diseases of Women and Children, Department of Pediatrics, West China Second University Hospital, State Key Laboratory of Biotherapy, Sichuan University, Chengdu, 610041, China
| | - Lili Zhou
- Institutes of Biology and Medical Science, Soochow University, Suzhou, 215000, China
| | - Xinyue Zhang
- Key Laboratory of Birth Defects and Related Diseases of Women and Children, Department of Pediatrics, West China Second University Hospital, State Key Laboratory of Biotherapy, Sichuan University, Chengdu, 610041, China
| | - Daniel D Billadeau
- Division of Oncology Research and Schulze Center for Novel Therapeutics, Mayo Clinic, Rochester, MN, 55905, USA
| | - Peiguo Yang
- School of Life Sciences, Westlake University, Hangzhou, 310024, 310030, China
| | - Lingqiang Zhang
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, 100850, Beijing, China
| | - Fangfang Zhou
- Institutes of Biology and Medical Science, Soochow University, Suzhou, 215000, China
| | - Peng Bai
- Department of Forensic Genetics, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu, 610041, China.
| | - Da Jia
- Key Laboratory of Birth Defects and Related Diseases of Women and Children, Department of Pediatrics, West China Second University Hospital, State Key Laboratory of Biotherapy, Sichuan University, Chengdu, 610041, China.
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3
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Carlson RJ, Patten JJ, Stefanakis G, Soong BY, Radhakrishnan A, Singh A, Thakur N, Amarasinghe GK, Hacohen N, Basler CF, Leung D, Uhler C, Davey RA, Blainey PC. Single-cell image-based genetic screens systematically identify regulators of Ebola virus subcellular infection dynamics. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.06.588168. [PMID: 38617272 PMCID: PMC11014611 DOI: 10.1101/2024.04.06.588168] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/16/2024]
Abstract
Ebola virus (EBOV) is a high-consequence filovirus that gives rise to frequent epidemics with high case fatality rates and few therapeutic options. Here, we applied image-based screening of a genome-wide CRISPR library to systematically identify host cell regulators of Ebola virus infection in 39,085,093 million single cells. Measuring viral RNA and protein levels together with their localization in cells identified over 998 related host factors and provided detailed information about the role of each gene across the virus replication cycle. We trained a deep learning model on single-cell images to associate each host factor with predicted replication steps, and confirmed the predicted relationship for select host factors. Among the findings, we showed that the mitochondrial complex III subunit UQCRB is a post-entry regulator of Ebola virus RNA replication, and demonstrated that UQCRB inhibition with a small molecule reduced overall Ebola virus infection with an IC50 of 5 μM. Using a random forest model, we also identified perturbations that reduced infection by disrupting the equilibrium between viral RNA and protein. One such protein, STRAP, is a spliceosome-associated factor that was found to be closely associated with VP35, a viral protein required for RNA processing. Loss of STRAP expression resulted in a reduction in full-length viral genome production and subsequent production of non-infectious virus particles. Overall, the data produced in this genome-wide high-content single-cell screen and secondary screens in additional cell lines and related filoviruses (MARV and SUDV) revealed new insights about the role of host factors in virus replication and potential new targets for therapeutic intervention.
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Affiliation(s)
- Rebecca J Carlson
- Massachusetts Institute of Technology, Department of Health Sciences and Technology, Cambridge, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - J J Patten
- Department of Virology, Immunology, and Microbiology, Boston University School of Medicine, Boston, MA, USA
- National Emerging Infectious Diseases Laboratories, Boston University, Boston, MA, USA
| | - George Stefanakis
- Laboratory for Information & Decision Systems, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Brian Y Soong
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Adityanarayanan Radhakrishnan
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Harvard School of Engineering and Applied Sciences, Cambridge, MA, USA
| | - Avtar Singh
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Naveen Thakur
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Gaya K Amarasinghe
- Division of Infectious Diseases, Washington University School of Medicine, St. Louis, MO, USA
| | - Nir Hacohen
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Massachusetts General Hospital, Cancer Center, Boston, MA, USA
| | - Christopher F Basler
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Daisy Leung
- Division of Infectious Diseases, Washington University School of Medicine, St. Louis, MO, USA
| | - Caroline Uhler
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Laboratory for Information & Decision Systems, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Robert A Davey
- Department of Virology, Immunology, and Microbiology, Boston University School of Medicine, Boston, MA, USA
- National Emerging Infectious Diseases Laboratories, Boston University, Boston, MA, USA
| | - Paul C Blainey
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Massachusetts Institute of Technology, Department of Biological Engineering, Cambridge, MA, USA
- Koch Institute for Integrative Cancer Research, MIT, Cambridge, MA, USA
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4
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Vogel OA, Nafziger E, Sharma A, Pasolli HA, Davey RA, Basler CF. The Role of Ebola Virus VP24 Nuclear Trafficking Signals in Infectious Particle Production. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.13.584761. [PMID: 38559040 PMCID: PMC10980025 DOI: 10.1101/2024.03.13.584761] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/04/2024]
Abstract
Ebola virus (EBOV) protein VP24 carries out at least two critical functions. It promotes condensation of viral nucleocapsids, which is crucial for infectious virus production, and it suppresses interferon (IFN) signaling, which requires interaction with the NPI-1 subfamily of importin-α (IMPA) nuclear transport proteins. Interestingly, over-expressed IMPA leads to VP24 nuclear accumulation and a carboxy-terminus nuclear export signal (NES) has been reported, suggesting that VP24 may undergo nuclear trafficking. For the first time, we demonstrate that NPI-1 IMPA overexpression leads to the nuclear accumulation of VP24 during EBOV infection. To assess the functional impact of nuclear trafficking, we generated tetracistronic minigenomes encoding VP24 nuclear import and/or export signal mutants. The minigenomes, which also encode Renilla luciferase and viral proteins VP40 and GP, were used to generate transcription and replication competent virus-like particles (trVLPs) that can be used to assess EBOV RNA synthesis, gene expression, entry and viral particle production. With this system, we confirmed that NES or IMPA binding site mutations altered VP24 nuclear localization, demonstrating functional trafficking signals. While these mutations minimally affected transcription and replication, the trVLPs exhibited impaired infectivity and formation of shortened nucleocapsids for the IMPA binding mutant. For the NES mutants, infectivity was reduced approximately 1000-fold. The NES mutant could still suppress IFN signaling but failed to promote nucleocapsid formation. To determine whether VP24 nuclear export is required for infectivity, the residues surrounding the wildtype NES were mutated to alanine or the VP24 NES was replaced with the Protein Kinase A Inhibitor NES. While nuclear export remained intact for these mutants, infectivity was severely impaired. These data demonstrate that VP24 undergoes nuclear trafficking and illuminates a separate and critical role for the NES and surrounding sequences in infectivity and nucleocapsid assembly.
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Affiliation(s)
- Olivia A. Vogel
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029
| | - Elias Nafziger
- National Emerging Infectious Diseases Laboratories and Department of Virology, Immunology, and Microbiology, Boston University, Boston, MA 02118
| | - Anurag Sharma
- Electron Microscopy Resource Center, The Rockefeller University, New York ,NY 10065, USA
| | - H. Amalia Pasolli
- Electron Microscopy Resource Center, The Rockefeller University, New York ,NY 10065, USA
| | - Robert A. Davey
- National Emerging Infectious Diseases Laboratories and Department of Virology, Immunology, and Microbiology, Boston University, Boston, MA 02118
| | - Christopher F. Basler
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029
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5
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Rodríguez-Salazar CA, van Tol S, Mailhot O, Gonzalez-Orozco M, Galdino GT, Warren AN, Teruel N, Behera P, Afreen KS, Zhang L, Juelich TL, Smith JK, Zylber MI, Freiberg AN, Najmanovich RJ, Giraldo MI, Rajsbaum R. Ebola virus VP35 interacts non-covalently with ubiquitin chains to promote viral replication. PLoS Biol 2024; 22:e3002544. [PMID: 38422166 PMCID: PMC10942258 DOI: 10.1371/journal.pbio.3002544] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2024] [Revised: 03/15/2024] [Accepted: 02/09/2024] [Indexed: 03/02/2024] Open
Abstract
Ebolavirus (EBOV) belongs to a family of highly pathogenic viruses that cause severe hemorrhagic fever in humans. EBOV replication requires the activity of the viral polymerase complex, which includes the cofactor and Interferon antagonist VP35. We previously showed that the covalent ubiquitination of VP35 promotes virus replication by regulating interactions with the polymerase complex. In addition, VP35 can also interact non-covalently with ubiquitin (Ub); however, the function of this interaction is unknown. Here, we report that VP35 interacts with free (unanchored) K63-linked polyUb chains. Ectopic expression of Isopeptidase T (USP5), which is known to degrade unanchored polyUb chains, reduced VP35 association with Ub and correlated with diminished polymerase activity in a minigenome assay. Using computational methods, we modeled the VP35-Ub non-covalent interacting complex, identified the VP35-Ub interacting surface, and tested mutations to validate the interface. Docking simulations identified chemical compounds that can block VP35-Ub interactions leading to reduced viral polymerase activity. Treatment with the compounds reduced replication of infectious EBOV in cells and in vivo in a mouse model. In conclusion, we identified a novel role of unanchored polyUb in regulating Ebola virus polymerase function and discovered compounds that have promising anti-Ebola virus activity.
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Affiliation(s)
- Carlos A. Rodríguez-Salazar
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, Texas, United States of America
- Molecular Biology and Virology Laboratory, Faculty of Medicine and Health Sciences, Corporación Universitaria Empresarial Alexander von Humboldt, Armenia, Colombia
| | - Sarah van Tol
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, Texas, United States of America
| | - Olivier Mailhot
- Department of Pharmacology and Physiology, Faculty of Medicine, Université de Montréal, Montreal, Canada
| | - Maria Gonzalez-Orozco
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, Texas, United States of America
| | - Gabriel T. Galdino
- Department of Pharmacology and Physiology, Faculty of Medicine, Université de Montréal, Montreal, Canada
| | - Abbey N. Warren
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, Texas, United States of America
- Center for Virus-Host-Innate Immunity and Department of Medicine; Rutgers Biomedical and Health Sciences, Institute for Infectious and Inflammatory Diseases, Rutgers University, Newark, New Jersey, United States of America
| | - Natalia Teruel
- Department of Pharmacology and Physiology, Faculty of Medicine, Université de Montréal, Montreal, Canada
| | - Padmanava Behera
- Center for Virus-Host-Innate Immunity and Department of Medicine; Rutgers Biomedical and Health Sciences, Institute for Infectious and Inflammatory Diseases, Rutgers University, Newark, New Jersey, United States of America
| | - Kazi Sabrina Afreen
- Center for Virus-Host-Innate Immunity and Department of Medicine; Rutgers Biomedical and Health Sciences, Institute for Infectious and Inflammatory Diseases, Rutgers University, Newark, New Jersey, United States of America
| | - Lihong Zhang
- Department of Pathology, University of Texas Medical Branch, Galveston, Texas, United States of America
| | - Terry L. Juelich
- Department of Pathology, University of Texas Medical Branch, Galveston, Texas, United States of America
| | - Jennifer K. Smith
- Department of Pathology, University of Texas Medical Branch, Galveston, Texas, United States of America
| | - María Inés Zylber
- Department of Pharmacology and Physiology, Faculty of Medicine, Université de Montréal, Montreal, Canada
| | - Alexander N. Freiberg
- Department of Pathology, University of Texas Medical Branch, Galveston, Texas, United States of America
| | - Rafael J. Najmanovich
- Department of Pharmacology and Physiology, Faculty of Medicine, Université de Montréal, Montreal, Canada
| | - Maria I. Giraldo
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, Texas, United States of America
| | - Ricardo Rajsbaum
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, Texas, United States of America
- Center for Virus-Host-Innate Immunity and Department of Medicine; Rutgers Biomedical and Health Sciences, Institute for Infectious and Inflammatory Diseases, Rutgers University, Newark, New Jersey, United States of America
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6
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de Andrade KQ, Cirne-Santos CC. Antiviral Activity of Zinc Finger Antiviral Protein (ZAP) in Different Virus Families. Pathogens 2023; 12:1461. [PMID: 38133344 PMCID: PMC10747524 DOI: 10.3390/pathogens12121461] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2023] [Revised: 12/14/2023] [Accepted: 12/15/2023] [Indexed: 12/23/2023] Open
Abstract
The CCCH-type zinc finger antiviral protein (ZAP) in humans, specifically isoforms ZAP-L and ZAP-S, is a crucial component of the cell's intrinsic immune response. ZAP acts as a post-transcriptional RNA restriction factor, exhibiting its activity during infections caused by retroviruses and alphaviruses. Its function involves binding to CpG (cytosine-phosphate-guanine) dinucleotide sequences present in viral RNA, thereby directing it towards degradation. Since vertebrate cells have a suppressed frequency of CpG dinucleotides, ZAP is capable of distinguishing foreign genetic elements. The expression of ZAP leads to the reduction of viral replication and impedes the assembly of new virus particles. However, the specific mechanisms underlying these effects have yet to be fully understood. Several questions regarding ZAP's mechanism of action remain unanswered, including the impact of CpG dinucleotide quantity on ZAP's activity, whether this sequence is solely required for the binding between ZAP and viral RNA, and whether the recruitment of cofactors is dependent on cell type, among others. This review aims to integrate the findings from studies that elucidate ZAP's antiviral role in various viral infections, discuss gaps that need to be filled through further studies, and shed light on new potential targets for therapeutic intervention.
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Affiliation(s)
- Kívia Queiroz de Andrade
- Laboratory of Immunology of Infectious Disease, Immunology Department, Institute of Biomedical Sciences, University of São Paulo, São Paulo 05508-000, SP, Brazil
| | - Claudio Cesar Cirne-Santos
- Laboratory of Molecular Virology and Marine Biotechnology, Department of Cellular and Molecular Biology, Institute of Biology, Federal Fluminense University, Niterói 24020-150, RJ, Brazil
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7
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Yang C, Shu J, Miao Y, Liu X, Zheng T, Hou R, Xiao J, Feng H. TRIM25 negatively regulates IKKε-mediated interferon signaling in black carp. FISH & SHELLFISH IMMUNOLOGY 2023; 142:109095. [PMID: 37730077 DOI: 10.1016/j.fsi.2023.109095] [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: 07/28/2023] [Revised: 09/11/2023] [Accepted: 09/17/2023] [Indexed: 09/22/2023]
Abstract
IKKε plays an important role in the activation of IRF3/IRF7 and the production of interferon (IFN), however, its regulation remains obscure in human. E3 ligase TRIM25 has been reported to manipulate the K63-linked ubiquitination of RIG-I, leading to the activation of RIG-I/IFN signaling. To elucidate the role of TRIM25 in teleost, a TRIM25 homolog (bcTRIM25) was cloned and characterized from black carp (Mylopharyngodon piceus). bcTRIM25 contains 653 amino acids, possessing conservative RING, B-box and SPRY domain, which is highly expressed in muscle, spleen and skin. bcTRIM25 knock-down enhanced the antiviral ability of host cells. bcTRIM25 over-expression alone in EPC cells attenuated bcIFNa promoter transcription in the reporter assays and impeded PKR and MX1 expression in qRT-PCR. Interestingly, co-IP assays indicated that bcTRIM25 interacted with bcIKKε and the induced bcIFNa promoter transcription by bcIKKε was notably hindered by bcTRIM25. Furthermore, bcIKKε-induced expression of interferon stimulated genes (ISGs) and antiviral activity were dampened by bcTRIM25. Further exploration showed that bcTRIM25 visibly enhanced the ubiquitination of bcIKKε but significantly attenuated the phosphorylation of bcIKKε. Thus, our data demonstrate for the first time in vertebrate that TRIM25 negatively regulates IKKε through enhancing its ubiquitination, which sheds a light on the regulation of IKKε/IFN signaling.
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Affiliation(s)
- Can Yang
- State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Science, Hunan Normal University, Changsha, 410081, China
| | - Juanjuan Shu
- State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Science, Hunan Normal University, Changsha, 410081, China
| | - Yujia Miao
- State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Science, Hunan Normal University, Changsha, 410081, China
| | - Xiaoyu Liu
- State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Science, Hunan Normal University, Changsha, 410081, China
| | - Tianle Zheng
- State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Science, Hunan Normal University, Changsha, 410081, China
| | - Ruixin Hou
- State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Science, Hunan Normal University, Changsha, 410081, China
| | - Jun Xiao
- State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Science, Hunan Normal University, Changsha, 410081, China.
| | - Hao Feng
- State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Science, Hunan Normal University, Changsha, 410081, China.
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8
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Lo R, Gonçalves-Carneiro D. Sensing nucleotide composition in virus RNA. Biosci Rep 2023; 43:BSR20230372. [PMID: 37606964 PMCID: PMC10500230 DOI: 10.1042/bsr20230372] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2023] [Revised: 08/10/2023] [Accepted: 08/22/2023] [Indexed: 08/23/2023] Open
Abstract
Nucleotide composition plays a crucial role in the structure, function and recognition of RNA molecules. During infection, virus RNA is exposed to multiple endogenous proteins that detect local or global compositional biases and interfere with virus replication. Recent advancements in RNA:protein mapping technologies have enabled the identification of general RNA-binding preferences in the human proteome at basal level and in the context of virus infection. In this review, we explore how cellular proteins recognise nucleotide composition in virus RNA and the impact these interactions have on virus replication. Protein-binding G-rich and C-rich sequences are common examples of how host factors detect and limit infection, and, in contrast, viruses may have evolved to purge their genomes from such motifs. We also give examples of how human RNA-binding proteins inhibit virus replication, not only by destabilising virus RNA, but also by interfering with viral protein translation and genome encapsidation. Understanding the interplay between cellular proteins and virus RNA composition can provide insights into host-virus interactions and uncover potential targets for antiviral strategies.
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Affiliation(s)
- Raymon Lo
- Imperial College London, Department of Infectious Disease, Imperial College London, London, U.K
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9
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Rodríguez-Salazar CA, van Tol S, Mailhot O, Galdino G, Teruel N, Zhang L, Warren AN, González-Orozco M, Freiberg AN, Najmanovich RJ, Giraldo MI, Rajsbaum R. Ebola Virus VP35 Interacts Non-Covalently with Ubiquitin Chains to Promote Viral Replication Creating New Therapeutic Opportunities. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.07.14.549057. [PMID: 37503276 PMCID: PMC10369991 DOI: 10.1101/2023.07.14.549057] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/29/2023]
Abstract
Ebolavirus (EBOV) belongs to a family of highly pathogenic viruses that cause severe hemorrhagic fever in humans. EBOV replication requires the activity of the viral polymerase complex, which includes the co-factor and Interferon antagonist VP35. We previously showed that the covalent ubiquitination of VP35 promotes virus replication by regulating interactions with the polymerase complex. In addition, VP35 can also interact non-covalently with ubiquitin (Ub); however, the function of this interaction is unknown. Here, we report that VP35 interacts with free (unanchored) K63-linked polyUb chains. Ectopic expression of Isopeptidase T (USP5), which is known to degrade unanchored polyUb chains, reduced VP35 association with Ub and correlated with diminished polymerase activity in a minigenome assay. Using computational methods, we modeled the VP35-Ub non-covalent interacting complex, identified the VP35-Ub interacting surface and tested mutations to validate the interface. Docking simulations identified chemical compounds that can block VP35-Ub interactions leading to reduced viral polymerase activity that correlated with reduced replication of infectious EBOV. In conclusion, we identified a novel role of unanchored polyUb in regulating Ebola virus polymerase function and discovered compounds that have promising anti-Ebola virus activity.
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Affiliation(s)
- Carlos A. Rodríguez-Salazar
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston 77555, Texas, USA
- Molecular Biology and Virology Laboratory, Faculty of Medicine and Health Sciences, Corporación Universitaria Empresarial Alexander von Humboldt, Armenia 630003, Colombia
| | - Sarah van Tol
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston 77555, Texas, USA
| | - Olivier Mailhot
- Department of Pharmacology and Physiology, Faculty of Medicine, Université de Montréal, Montreal, Canada
| | - Gabriel Galdino
- Department of Pharmacology and Physiology, Faculty of Medicine, Université de Montréal, Montreal, Canada
| | - Natalia Teruel
- Department of Pharmacology and Physiology, Faculty of Medicine, Université de Montréal, Montreal, Canada
| | - Lihong Zhang
- Department of Pathology, University of Texas Medical Branch, Galveston 77555, Texas, USA
| | - Abbey N. Warren
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston 77555, Texas, USA
- Center for Virus-Host-Innate Immunity and Department of Medicine; Rutgers Biomedical and Health Sciences, Institute for Infectious and Inflammatory Diseases, Rutgers University, Newark, New Jersey 07103
| | - María González-Orozco
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston 77555, Texas, USA
| | - Alexander N. Freiberg
- Department of Pathology, University of Texas Medical Branch, Galveston 77555, Texas, USA
| | - Rafael J. Najmanovich
- Department of Pharmacology and Physiology, Faculty of Medicine, Université de Montréal, Montreal, Canada
| | - María I. Giraldo
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston 77555, Texas, USA
| | - Ricardo Rajsbaum
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston 77555, Texas, USA
- Center for Virus-Host-Innate Immunity and Department of Medicine; Rutgers Biomedical and Health Sciences, Institute for Infectious and Inflammatory Diseases, Rutgers University, Newark, New Jersey 07103
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10
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Goodier JL, Wan H, Soares AO, Sanchez L, Selser JM, Pereira GC, Karma S, García-Pérez JL, Kazazian HH, García Cañadas MM. ZCCHC3 is a stress granule zinc knuckle protein that strongly suppresses LINE-1 retrotransposition. PLoS Genet 2023; 19:e1010795. [PMID: 37405998 DOI: 10.1371/journal.pgen.1010795] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2022] [Accepted: 05/23/2023] [Indexed: 07/07/2023] Open
Abstract
Retrotransposons have generated about half of the human genome and LINE-1s (L1s) are the only autonomously active retrotransposons. The cell has evolved an arsenal of defense mechanisms to protect against retrotransposition with factors we are only beginning to understand. In this study, we investigate Zinc Finger CCHC-Type Containing 3 (ZCCHC3), a gag-like zinc knuckle protein recently reported to function in the innate immune response to infecting viruses. We show that ZCCHC3 also severely restricts human retrotransposons and associates with the L1 ORF1p ribonucleoprotein particle. We identify ZCCHC3 as a bona fide stress granule protein, and its association with LINE-1 is further supported by colocalization with L1 ORF1 protein in stress granules, dense cytoplasmic aggregations of proteins and RNAs that contain stalled translation pre-initiation complexes and form when the cell is under stress. Our work also draws links between ZCCHC3 and the anti-viral and retrotransposon restriction factors Mov10 RISC Complex RNA Helicase (MOV10) and Zinc Finger CCCH-Type, Antiviral 1 (ZC3HAV1, also called ZAP). Furthermore, collective evidence from subcellular localization, co-immunoprecipitation, and velocity gradient centrifugation connects ZCCHC3 with the RNA exosome, a multi-subunit ribonuclease complex capable of degrading various species of RNA molecules and that has previously been linked with retrotransposon control.
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Affiliation(s)
- John L Goodier
- McKusick-Nathans Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
| | - Han Wan
- McKusick-Nathans Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
| | - Alisha O Soares
- McKusick-Nathans Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
| | - Laura Sanchez
- GENYO, Centre for Genomics and Oncological Research: Pfizer, University of Granada, Andalusian Regional Government, Granada, Spain
| | - John Michael Selser
- McKusick-Nathans Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
| | - Gavin C Pereira
- McKusick-Nathans Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
| | - Sadik Karma
- McKusick-Nathans Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
| | - Jose Luis García-Pérez
- GENYO, Centre for Genomics and Oncological Research: Pfizer, University of Granada, Andalusian Regional Government, Granada, Spain
| | - Haig H Kazazian
- McKusick-Nathans Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
| | - Marta M García Cañadas
- GENYO, Centre for Genomics and Oncological Research: Pfizer, University of Granada, Andalusian Regional Government, Granada, Spain
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11
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Pinto RM, Bakshi S, Lytras S, Zakaria MK, Swingler S, Worrell JC, Herder V, Hargrave KE, Varjak M, Cameron-Ruiz N, Collados Rodriguez M, Varela M, Wickenhagen A, Loney C, Pei Y, Hughes J, Valette E, Turnbull ML, Furnon W, Gu Q, Orr L, Taggart A, Diebold O, Davis C, Boutell C, Grey F, Hutchinson E, Digard P, Monne I, Wootton SK, MacLeod MKL, Wilson SJ, Palmarini M. BTN3A3 evasion promotes the zoonotic potential of influenza A viruses. Nature 2023; 619:338-347. [PMID: 37380775 DOI: 10.1038/s41586-023-06261-8] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2023] [Accepted: 05/25/2023] [Indexed: 06/30/2023]
Abstract
Spillover events of avian influenza A viruses (IAVs) to humans could represent the first step in a future pandemic1. Several factors that limit the transmission and replication of avian IAVs in mammals have been identified. There are several gaps in our understanding to predict which virus lineages are more likely to cross the species barrier and cause disease in humans1. Here, we identified human BTN3A3 (butyrophilin subfamily 3 member A3)2 as a potent inhibitor of avian IAVs but not human IAVs. We determined that BTN3A3 is expressed in human airways and its antiviral activity evolved in primates. We show that BTN3A3 restriction acts primarily at the early stages of the virus life cycle by inhibiting avian IAV RNA replication. We identified residue 313 in the viral nucleoprotein (NP) as the genetic determinant of BTN3A3 sensitivity (313F or, rarely, 313L in avian viruses) or evasion (313Y or 313V in human viruses). However, avian IAV serotypes, such as H7 and H9, that spilled over into humans also evade BTN3A3 restriction. In these cases, BTN3A3 evasion is due to substitutions (N, H or Q) in NP residue 52 that is adjacent to residue 313 in the NP structure3. Thus, sensitivity or resistance to BTN3A3 is another factor to consider in the risk assessment of the zoonotic potential of avian influenza viruses.
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Affiliation(s)
- Rute Maria Pinto
- MRC-University of Glasgow Centre for Virus Research, Glasgow, UK
- The Roslin Institute, University of Edinburgh, Edinburgh, UK
| | - Siddharth Bakshi
- MRC-University of Glasgow Centre for Virus Research, Glasgow, UK
| | - Spyros Lytras
- MRC-University of Glasgow Centre for Virus Research, Glasgow, UK
| | | | - Simon Swingler
- MRC-University of Glasgow Centre for Virus Research, Glasgow, UK
| | - Julie C Worrell
- School of Infection and Immunity, University of Glasgow, Glasgow, UK
| | - Vanessa Herder
- MRC-University of Glasgow Centre for Virus Research, Glasgow, UK
| | - Kerrie E Hargrave
- School of Infection and Immunity, University of Glasgow, Glasgow, UK
| | - Margus Varjak
- MRC-University of Glasgow Centre for Virus Research, Glasgow, UK
- Faculty of Science and Technology, Institute of Technology, University of Tartu, Tartu, Estonia
| | | | | | - Mariana Varela
- MRC-University of Glasgow Centre for Virus Research, Glasgow, UK
| | | | - Colin Loney
- MRC-University of Glasgow Centre for Virus Research, Glasgow, UK
| | - Yanlong Pei
- Department of Pathobiology, University of Guelph, Guelph, Ontario, Canada
| | - Joseph Hughes
- MRC-University of Glasgow Centre for Virus Research, Glasgow, UK
| | - Elise Valette
- MRC-University of Glasgow Centre for Virus Research, Glasgow, UK
| | | | - Wilhelm Furnon
- MRC-University of Glasgow Centre for Virus Research, Glasgow, UK
| | - Quan Gu
- MRC-University of Glasgow Centre for Virus Research, Glasgow, UK
| | - Lauren Orr
- MRC-University of Glasgow Centre for Virus Research, Glasgow, UK
| | - Aislynn Taggart
- MRC-University of Glasgow Centre for Virus Research, Glasgow, UK
| | - Ola Diebold
- The Roslin Institute, University of Edinburgh, Edinburgh, UK
| | - Chris Davis
- MRC-University of Glasgow Centre for Virus Research, Glasgow, UK
| | - Chris Boutell
- MRC-University of Glasgow Centre for Virus Research, Glasgow, UK
| | - Finn Grey
- The Roslin Institute, University of Edinburgh, Edinburgh, UK
| | | | - Paul Digard
- The Roslin Institute, University of Edinburgh, Edinburgh, UK
| | - Isabella Monne
- Istituto Zooprofilattico Sperimentale delle Venezie (IZSVe), Legnaro, Italy
| | - Sarah K Wootton
- Department of Pathobiology, University of Guelph, Guelph, Ontario, Canada
| | - Megan K L MacLeod
- School of Infection and Immunity, University of Glasgow, Glasgow, UK
| | - Sam J Wilson
- MRC-University of Glasgow Centre for Virus Research, Glasgow, UK
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12
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Kiss L, Rhinesmith T, Luptak J, Dickson CF, Weidenhausen J, Smyly S, Yang JC, Maslen SL, Sinning I, Neuhaus D, Clift D, James LC. Trim-Away ubiquitinates and degrades lysine-less and N-terminally acetylated substrates. Nat Commun 2023; 14:2160. [PMID: 37061529 PMCID: PMC10105713 DOI: 10.1038/s41467-023-37504-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Accepted: 03/20/2023] [Indexed: 04/17/2023] Open
Abstract
TRIM proteins are the largest family of E3 ligases in mammals. They include the intracellular antibody receptor TRIM21, which is responsible for mediating targeted protein degradation during Trim-Away. Despite their importance, the ubiquitination mechanism of TRIM ligases has remained elusive. Here we show that while Trim-Away activation results in ubiquitination of both ligase and substrate, ligase ubiquitination is not required for substrate degradation. N-terminal TRIM21 RING ubiquitination by the E2 Ube2W can be inhibited by N-terminal acetylation, but this doesn't prevent substrate ubiquitination nor degradation. Instead, uncoupling ligase and substrate degradation prevents ligase recycling and extends functional persistence in cells. Further, Trim-Away degrades substrates irrespective of whether they contain lysines or are N-terminally acetylated, which may explain the ability of TRIM21 to counteract fast-evolving pathogens and degrade diverse substrates.
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Affiliation(s)
- Leo Kiss
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge, CB2 0QH, UK.
- Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152, Martinsried, Germany.
| | - Tyler Rhinesmith
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge, CB2 0QH, UK
| | - Jakub Luptak
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge, CB2 0QH, UK
| | - Claire F Dickson
- EMBL Australia Node in Single Molecule Science and ARC Centre of Excellence in Advanced Molecular Imaging School of Medical Sciences, UNSW Sydney, NSW, 2052, Australia
| | - Jonas Weidenhausen
- Biochemiezentrum der Universität Heidelberg (BZH), INF328, D-69120, Heidelberg, Germany
- EMBL Heidelberg, Meyerhofstraße 1, 69117, Heidelberg, Germany
| | - Shannon Smyly
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge, CB2 0QH, UK
| | - Ji-Chun Yang
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge, CB2 0QH, UK
| | - Sarah L Maslen
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge, CB2 0QH, UK
- The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
| | - Irmgard Sinning
- Biochemiezentrum der Universität Heidelberg (BZH), INF328, D-69120, Heidelberg, Germany
| | - David Neuhaus
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge, CB2 0QH, UK
| | - Dean Clift
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge, CB2 0QH, UK.
| | - Leo C James
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge, CB2 0QH, UK.
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13
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Lu J, Gullett JM, Kanneganti TD. Filoviruses: Innate Immunity, Inflammatory Cell Death, and Cytokines. Pathogens 2022; 11:pathogens11121400. [PMID: 36558734 PMCID: PMC9785368 DOI: 10.3390/pathogens11121400] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2022] [Revised: 11/17/2022] [Accepted: 11/19/2022] [Indexed: 11/24/2022] Open
Abstract
Filoviruses are a group of single-stranded negative sense RNA viruses. The most well-known filoviruses that affect humans are ebolaviruses and marburgviruses. During infection, they can cause life-threatening symptoms such as inflammation, tissue damage, and hemorrhagic fever, with case fatality rates as high as 90%. The innate immune system is the first line of defense against pathogenic insults such as filoviruses. Pattern recognition receptors (PRRs), including toll-like receptors, retinoic acid-inducible gene-I-like receptors, C-type lectin receptors, AIM2-like receptors, and NOD-like receptors, detect pathogens and activate downstream signaling to induce the production of proinflammatory cytokines and interferons, alert the surrounding cells to the threat, and clear infected and damaged cells through innate immune cell death. However, filoviruses can modulate the host inflammatory response and innate immune cell death, causing an aberrant immune reaction. Here, we discuss how the innate immune system senses invading filoviruses and how these deadly pathogens interfere with the immune response. Furthermore, we highlight the experimental difficulties of studying filoviruses as well as the current state of filovirus-targeting therapeutics.
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14
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Małkowska P, Niedźwiedzka-Rystwej P. Factors affecting RIG-I-Like receptors activation - New research direction for viral hemorrhagic fevers. Front Immunol 2022; 13:1010635. [PMID: 36248895 PMCID: PMC9557057 DOI: 10.3389/fimmu.2022.1010635] [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: 08/03/2022] [Accepted: 09/13/2022] [Indexed: 11/13/2022] Open
Abstract
Viral hemorrhagic fever (VHF) is a term referring to a group of life-threatening infections caused by several virus families (Arenaviridae, Bunyaviridae, Filoviridae and Flaviviridae). Depending on the virus, the infection can be mild and can be also characterized by an acute course with fever accompanied by hypervolemia and coagulopathy, resulting in bleeding and shock. It has been suggested that the course of the disease is strongly influenced by the activation of signaling pathways leading to RIG-I-like receptor-dependent interferon production. RIG-I-like receptors (RLRs) are one of two major receptor families that detect viral nucleic acid. RLR receptor activation is influenced by a number of factors that may have a key role in the differences that occur during the antiviral immune response in VHF. In the present study, we collected data on RLR receptors in viral hemorrhagic fevers and described factors that may influence the activation of the antiviral response. RLR receptors seem to be a good target for VHF research, which may contribute to better therapeutic and diagnostic strategies. However, due to the difficulty of conducting such studies in humans, we suggest using Lagovirus europaeus as an animal model for VHF.
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Affiliation(s)
- Paulina Małkowska
- Doctoral School, University of Szczecin, Szczecin, Poland
- Institute of Biology, University of Szczecin, Szczecin, Poland
- *Correspondence: Paulina Małkowska,
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