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Fekry M, Stenberg G, Dobritzsch D, Danielson UH. Production of stable and pure ZC3H11A - An extensively disordered RNA binding protein. Protein Expr Purif 2024; 222:106542. [PMID: 38969281 DOI: 10.1016/j.pep.2024.106542] [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: 05/21/2024] [Revised: 07/02/2024] [Accepted: 07/03/2024] [Indexed: 07/07/2024]
Abstract
Human ZC3H11A is an RNA-binding zinc finger protein involved in mRNA export and required for the efficient growth of human nuclear replicating viruses. Its biochemical properties are largely unknown so our goal has been to produce the protein in a pure and stable form suitable for its characterization. This has been challenging since the protein is large (810 amino acids) and with only the N-terminal zinc finger domain (amino acids 1-86) being well structured, the remainder is intrinsically disordered. Our production strategies have encompassed recombinant expression of full-length, truncated and mutated ZC3H11A variants with varying purification tags and fusion proteins in several expression systems, with or without co-expression of chaperones and putative interaction partners. A range of purification schemes have been explored. Initially, only truncated ZC3H11A encompassing the zinc finger domain could successfully be produced in a stable form. It required recombinant expression in insect cells since expression in E. coli gave a protein that aggregated. To reduce problematic nucleic acid contaminations, Cys8, located in one of the zinc fingers, was substituted by Ala and Ser. Interestingly, this did not affect nucleic acid binding, but the full-length protein was stabilised while the truncated version was insoluble. Ultimately, we discovered that when using alkaline buffers (pH 9) for purification, full-length ZC3H11A expressed in Sf9 insect cells was obtained in a stable and >90 % pure form, and as a mixture of monomers, dimers, tetramers and hexamers. Many of the challenges experienced are consistent with its predicted structure and unusual charge distribution.
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Affiliation(s)
- Mostafa Fekry
- Department of Chemistry - BMC, Uppsala University, Uppsala, Sweden; Biophysics Department, Faculty of Science, Cairo University, Giza, Egypt
| | - Gun Stenberg
- Department of Chemistry - BMC, Uppsala University, Uppsala, Sweden
| | | | - U Helena Danielson
- Department of Chemistry - BMC, Uppsala University, Uppsala, Sweden; Science for Life Laboratory, Drug Discovery & Development Platform, Uppsala University, SE 751 23 Uppsala, Sweden.
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Rich J, Bennaroch M, Notel L, Patalakh P, Alberola J, Issa F, Opolon P, Bawa O, Rondof W, Marchais A, Dessen P, Meurice G, Le-Gall M, Polrot M, Ser-Le Roux K, Mamchaoui K, Droin N, Raslova H, Maire P, Geoerger B, Pirozhkova I. DiPRO1 distinctly reprograms muscle and mesenchymal cancer cells. EMBO Mol Med 2024; 16:1840-1885. [PMID: 39009887 PMCID: PMC11319797 DOI: 10.1038/s44321-024-00097-z] [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: 01/10/2023] [Revised: 06/13/2024] [Accepted: 06/18/2024] [Indexed: 07/17/2024] Open
Abstract
We have recently identified the uncharacterized ZNF555 protein as a component of a productive complex involved in the morbid function of the 4qA locus in facioscapulohumeral dystrophy. Subsequently named DiPRO1 (Death, Differentiation, and PROliferation related PROtein 1), our study provides substantial evidence of its role in the differentiation and proliferation of human myoblasts. DiPRO1 operates through the regulatory binding regions of SIX1, a master regulator of myogenesis. Its relevance extends to mesenchymal tumors, such as rhabdomyosarcoma (RMS) and Ewing sarcoma, where DiPRO1 acts as a repressor via the epigenetic regulators TIF1B and UHRF1, maintaining methylation of cis-regulatory elements and gene promoters. Loss of DiPRO1 mimics the host defense response to virus, awakening retrotransposable repeats and the ZNF/KZFP gene family. This enables the eradication of cancer cells, reprogramming the cellular decision balance towards inflammation and/or apoptosis by controlling TNF-α via NF-kappaB signaling. Finally, our results highlight the vulnerability of mesenchymal cancer tumors to si/shDiPRO1-based nanomedicines, positioning DiPRO1 as a potential therapeutic target.
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Affiliation(s)
- Jeremy Rich
- UMR8126 CNRS, Gustave Roussy Cancer campus, Université Paris-Saclay, Villejuif, France
| | - Melanie Bennaroch
- UMR8126 CNRS, Gustave Roussy Cancer campus, Université Paris-Saclay, Villejuif, France
| | - Laura Notel
- UMR8126 CNRS, Gustave Roussy Cancer campus, Université Paris-Saclay, Villejuif, France
| | - Polina Patalakh
- UMR8126 CNRS, Gustave Roussy Cancer campus, Université Paris-Saclay, Villejuif, France
| | - Julien Alberola
- UMR8126 CNRS, Gustave Roussy Cancer campus, Université Paris-Saclay, Villejuif, France
| | - Fayez Issa
- INSERM U1016, CNRS UMR 8104, Institut Cochin, Université Paris-Cité, Paris, France
| | - Paule Opolon
- Pathology and Cytology Section, UMS AMMICA, CNRS, INSERM, Gustave Roussy Cancer campus, Université Paris-Saclay, Villejuif, France
| | - Olivia Bawa
- Pathology and Cytology Section, UMS AMMICA, CNRS, INSERM, Gustave Roussy Cancer campus, Université Paris-Saclay, Villejuif, France
| | - Windy Rondof
- Bioinformatics Platform, UMS AMMICA, CNRS, INSERM, Gustave Roussy Cancer campus, Université Paris-Saclay, Villejuif, France
- Department of Pediatric and Adolescent Oncology, Gustave Roussy Cancer campus, INSERM U1015, Université Paris-Saclay, Villejuif, France
| | - Antonin Marchais
- Bioinformatics Platform, UMS AMMICA, CNRS, INSERM, Gustave Roussy Cancer campus, Université Paris-Saclay, Villejuif, France
- Department of Pediatric and Adolescent Oncology, Gustave Roussy Cancer campus, INSERM U1015, Université Paris-Saclay, Villejuif, France
| | - Philippe Dessen
- Bioinformatics Platform, UMS AMMICA, CNRS, INSERM, Gustave Roussy Cancer campus, Université Paris-Saclay, Villejuif, France
| | - Guillaume Meurice
- Bioinformatics Platform, UMS AMMICA, CNRS, INSERM, Gustave Roussy Cancer campus, Université Paris-Saclay, Villejuif, France
| | - Morgane Le-Gall
- Proteom'IC facility, Université Paris Cité, CNRS, INSERM, Institut Cochin, F-75014, Paris, France
| | - Melanie Polrot
- Pre-clinical Evaluation Unit (PFEP), INSERM, Gustave Roussy Cancer campus, Université Paris-Saclay, Villejuif, France
| | - Karine Ser-Le Roux
- Pre-clinical Evaluation Unit (PFEP), INSERM, Gustave Roussy Cancer campus, Université Paris-Saclay, Villejuif, France
| | - Kamel Mamchaoui
- Sorbonne Université, Inserm, Institut de Myologie, Centre de Recherche en Myologie, F-75013, Paris, France
| | - Nathalie Droin
- Genomic Platform, UMS AMMICA US 23 INSERM UAR 3655 CNRS, Gustave Roussy Cancer campus, Université Paris-Saclay, Villejuif, France
- UMR1287 INSERM, Gustave Roussy Cancer campus, Université Paris-Saclay, Villejuif, France
| | - Hana Raslova
- UMR1287 INSERM, Gustave Roussy Cancer campus, Université Paris-Saclay, Villejuif, France
| | - Pascal Maire
- INSERM U1016, CNRS UMR 8104, Institut Cochin, Université Paris-Cité, Paris, France
| | - Birgit Geoerger
- Department of Pediatric and Adolescent Oncology, Gustave Roussy Cancer campus, INSERM U1015, Université Paris-Saclay, Villejuif, France
| | - Iryna Pirozhkova
- UMR8126 CNRS, Gustave Roussy Cancer campus, Université Paris-Saclay, Villejuif, France.
- INSERM U1016, CNRS UMR 8104, Institut Cochin, Université Paris-Cité, Paris, France.
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Alfaro-Sifuentes R, Lares-Jiménez LF, Rojas-Hernández S, Carrasco-Yépez MM, Rojas-Ortega DA, Rodriguez-Anaya LZ, Gonzalez-Galaviz JR, Lares-Villa F. Immunogens in Balamuthia mandrillaris: a proteomic exploration. Parasitol Res 2024; 123:173. [PMID: 38536506 DOI: 10.1007/s00436-024-08193-2] [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: 02/01/2024] [Accepted: 03/20/2024] [Indexed: 04/04/2024]
Abstract
Balamuthia mandrillaris is the causative agent of granulomatous amoebic encephalitis, a rare and often fatal infection affecting the central nervous system. The amoeba is isolated from diverse environmental sources and can cause severe infections in both immunocompromised and immunocompetent individuals. Given the limited understanding of B. mandrillaris, our research aimed to explore its protein profile, identifying potential immunogens crucial for early granulomatous amoebic encephalitis diagnosis. Cultures of B. mandrillaris and other amoebas were grown under axenic conditions, and total amoebic extracts were obtained. Proteomic analyses, including two-dimensional electrophoresis and mass spectrometry, were performed. A 50-kDa band showed a robust recognition of antibodies from immunized BALB/c mice; peptides contained in this band were matched with elongation factor-1 alpha, which emerged as a putative key immunogen. Besides, lectin blotting revealed the presence of glycoproteins in B. mandrillaris, and confocal microscopy demonstrated the focal distribution of the 50-kDa band throughout trophozoites. Cumulatively, these observations suggest the participation of the 50-kDa band in adhesion and recognition mechanisms. Thus, these collective findings demonstrate some protein characteristics of B. mandrillaris, opening avenues for understanding its pathogenicity and developing diagnostic and therapeutic strategies.
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Affiliation(s)
- Rosalía Alfaro-Sifuentes
- Programa de Doctorado en Ciencias Especialidad en Biotecnología, Departamento de Biotecnología y Ciencias Alimentarias, Instituto Tecnológico de Sonora, 85000, Ciudad Obregón, Sonora, México.
| | - Luis Fernando Lares-Jiménez
- Departamento de Ciencias Agronómicas y Veterinarias, Instituto Tecnológico de Sonora, 85000, Ciudad Obregón, Sonora, México
| | - Saul Rojas-Hernández
- Laboratorio de Inmunología Molecular, Instituto Politécnico Nacional, Escuela Superior de Medicina, Salvador Díaz Mirón Esq. Plan de San Luis S/N, Miguel Hidalgo, Casco de Santo Tomas, Ciudad de México, México
| | | | - Diego Alexander Rojas-Ortega
- Centro de Investigación en Ciencias de La Salud (CICSA), FCS, Universidad Anáhuac México, 52786, Huixquilucan, Estado de México, México
| | | | | | - Fernando Lares-Villa
- Departamento de Ciencias Agronómicas y Veterinarias, Instituto Tecnológico de Sonora, 85000, Ciudad Obregón, Sonora, México.
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Hussein HE, Johnson WC, Taus NS, Ueti MW. Expression of sex-specific molecular markers by Babesia bovis gametes. Parasit Vectors 2024; 17:75. [PMID: 38374075 PMCID: PMC10877833 DOI: 10.1186/s13071-024-06185-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2023] [Accepted: 02/07/2024] [Indexed: 02/21/2024] Open
Abstract
BACKGROUND Bovine babesiosis caused by Babesia bovis is one of the most important tick-borne diseases of cattle in tropical and subtropical regions. Babesia bovis parasites have a complex lifecycle, including development within the mammalian host and tick vector. In the tick midgut, extracellular Babesia parasites transform into gametes that fuse to form zygotes. To date, little is known about genes and proteins expressed by male gametes. METHODS AND RESULTS We developed a method to separate male gametes from in vitro induced B. bovis culture. Separation enabled the validation of sex-specific markers. Collected male gametocytes were observed by Giemsa-stained smear and live-cell fluorescence microscopy. Babesia male gametes were used to confirm sex-specific markers by quantitative real-time PCR. Some genes were found to be male gamete specific genes including pka, hap2, α-tubulin II and znfp2. However, α-tubulin I and ABC transporter, trap2-4 and ccp1-3 genes were found to be upregulated in culture depleted of male gametes (female-enriched). Live immunofluorescence analysis using polyclonal antibodies confirmed surface expression of HAP2 by male and TRAP2-4 by female gametes. These results revealed strong markers to distinguish between B. bovis male and female gametes. CONCLUSIONS Herein, we describe the identification of sex-specific molecular markers essential for B. bovis sexual reproduction. These tools will enhance our understanding of the biology of sexual stages and, consequently, the development of additional strategies to control bovine babesiosis.
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Affiliation(s)
- Hala E Hussein
- Department of Veterinary Microbiology and Pathology, Washington State University, Pullman, WA, USA.
- Department of Biology, College of Arts and Sciences, Gonzaga University, Spokane, WA, USA.
| | - Wendell C Johnson
- Department of Veterinary Microbiology and Pathology, Washington State University, Pullman, WA, USA
| | - Naomi S Taus
- Department of Veterinary Microbiology and Pathology, Washington State University, Pullman, WA, USA
- The U.S. Department of Agriculture-ARS-Animal Disease Research Unit, Pullman, WA, USA
| | - Massaro W Ueti
- Department of Veterinary Microbiology and Pathology, Washington State University, Pullman, WA, USA
- The U.S. Department of Agriculture-ARS-Animal Disease Research Unit, Pullman, WA, USA
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Jin J, He J, Li X, Ni X, Jin X. The role of ubiquitination and deubiquitination in PI3K/AKT/mTOR pathway: A potential target for cancer therapy. Gene 2023; 889:147807. [PMID: 37722609 DOI: 10.1016/j.gene.2023.147807] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2023] [Revised: 09/12/2023] [Accepted: 09/15/2023] [Indexed: 09/20/2023]
Abstract
The PI3K/AKT/mTOR pathway controls key cellular processes, including proliferation and tumor progression, and abnormally high activation of this pathway is a hallmark in human cancers. The post-translational modification, such as Ubiquitination and deubiquitination, fine-tuning the protein level and the activity of members in this pathway play a pivotal role in maintaining normal physiological process. Emerging evidence show that the unbalanced ubiquitination/deubiquitination modification leads to human diseases via PI3K/AKT/mTOR pathway. Therefore, a comprehensive understanding of the ubiquitination/deubiquitination regulation of PI3K/AKT/mTOR pathway may be helpful to uncover the underlying mechanism and improve the potential treatment of cancer via targeting this pathway. Herein, we summarize the latest research progress of ubiquitination and deubiquitination of PI3K/AKT/mTOR pathway, systematically discuss the associated crosstalk between them, as well as focus the clinical transformation via targeting ubiquitination process.
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Affiliation(s)
- Jiabei Jin
- Department of Biochemistry and Molecular Biology, Zhejiang Key Laboratory of Pathophysiology, Health Science Center, Ningbo University, Ningbo, Zhejiang 315211, China
| | - Jian He
- Department of Biochemistry and Molecular Biology, Zhejiang Key Laboratory of Pathophysiology, Health Science Center, Ningbo University, Ningbo, Zhejiang 315211, China
| | - Xinming Li
- Department of Biochemistry and Molecular Biology, Zhejiang Key Laboratory of Pathophysiology, Health Science Center, Ningbo University, Ningbo, Zhejiang 315211, China
| | - Xiaoqi Ni
- Department of Biochemistry and Molecular Biology, Zhejiang Key Laboratory of Pathophysiology, Health Science Center, Ningbo University, Ningbo, Zhejiang 315211, China
| | - Xiaofeng Jin
- Department of Biochemistry and Molecular Biology, Zhejiang Key Laboratory of Pathophysiology, Health Science Center, Ningbo University, Ningbo, Zhejiang 315211, China.
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Li J, Song M, Liu Z, Nan F, Wang B, Qian D, Hu M. Analysis of the mRNA export protein ZC3H11A in HCMV infection and pan-cancer. Front Microbiol 2023; 14:1296725. [PMID: 38033582 PMCID: PMC10684726 DOI: 10.3389/fmicb.2023.1296725] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2023] [Accepted: 10/16/2023] [Indexed: 12/02/2023] Open
Abstract
Background We have previously reported that human cytomegalovirus (HCMV) infection could promote the progression of glioma. Here we discovered a stress-induced nuclear protein ZC3H11A (ZC3) through high-throughput sequencing after HCMV infection, which has been reported recently by our research group in regulating mRNA export under stress conditions. And also, a thorough analysis of ZC3 in pan-cancer and the omics data of ZC3 are yet to be conducted. Methods The transcriptomes of glioma cells after HCMV infection were assessed by RNA sequencing. ZC3 mRNA and protein level following HCMV infection were validated and measured by qRT-PCR and Western-blot. The RNA sequencing and protein expression information of ZC3 across pan-cancer were analyzed and visualized by R packages. The localization of ZC3 protein was assessed by IHC images from HPA. The ZC3 proteomics and transcriptomics data in different cancers were extracted through the CPTAC data portal, and comparisons were conducted with a Python script. The genetic alteration, survival prognosis, immune infiltration analysis of ZC3 in pan-cancer were analyzed by cBioPortal, TCGA, and TIMER2 databases. The protein interaction networks were revealed by STRING, GEPIA2 and TCGA. Results Genes in mRNA processing pathways were upregulated after HCMV infection and ZC3 expression in mRNA and protein level was validated. We also discovered that the status of ZC3 were generally at high levels in cancers, although varied among different cancer types. ZC3 protein in tumor cells localized to the nuclear whereas in normal cells it was mainly found in cytoplasmic/membranous. However, from ZC3 proteomics and transcriptomics data in some cancer types, the increase in ZC3 protein was not accompanied by a significant elevation in mRNA level. Additionally, our analysis indicated that elevated ZC3 expression was primarily linked to a negative prognosis in majority cancers but still varied depending on the cancer types. Our annotation analysis suggested that ZC3-related proteins are mainly involved in mRNA processing clusters. Conclusion We demonstrated that ZC3 significantly impacted by HCMV infection in gliomas. Furthermore, we identified a set of genes exhibiting analogous expression patterns to ZC3H11A in TCGA pan-cancer cohorts, implying a potential functional role for ZC3H11A in mRNA processing. Our study provided valuable insights into the role of a new mRNA export protein ZC3 in HCMV infection and pan-cancer progression. These results lay the foundation for our next research on the regulatory mechanism of ZC3 in virus-infected tumors.
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Affiliation(s)
- Jiawen Li
- Department of Special Medicine, School of Basic Medicine, Qingdao University, Qingdao, Shandong, China
| | - Min Song
- Department of Digestive Endoscopy, Qingdao Hospital, University of Health and Rehabilitation Sciences (Qingdao Municipal Hospital), Qingdao, Shandong, China
| | - Zhen Liu
- Department of Special Medicine, School of Basic Medicine, Qingdao University, Qingdao, Shandong, China
| | - Fulong Nan
- Department of Special Medicine, School of Basic Medicine, Qingdao University, Qingdao, Shandong, China
| | - Bin Wang
- Department of Special Medicine, School of Basic Medicine, Qingdao University, Qingdao, Shandong, China
| | - Dongmeng Qian
- Department of Special Medicine, School of Basic Medicine, Qingdao University, Qingdao, Shandong, China
| | - Ming Hu
- Department of Special Medicine, School of Basic Medicine, Qingdao University, Qingdao, Shandong, China
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Gao J, Wu XJ, Zheng XN, Li TT, Kou YJ, Wang XC, Wang M, Zhu XQ. Functional Characterization of Eight Zinc Finger Motif-Containing Proteins in Toxoplasma gondii Type I RH Strain Using the CRISPR-Cas9 System. Pathogens 2023; 12:1232. [PMID: 37887748 PMCID: PMC10609756 DOI: 10.3390/pathogens12101232] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2023] [Revised: 10/03/2023] [Accepted: 10/06/2023] [Indexed: 10/28/2023] Open
Abstract
The Zinc finger protein (ZFP) family is widely distributed in eukaryotes and interacts with DNA, RNA, and various proteins to participate in many molecular processes. In the present study, the biological functions of eight ZFP genes in the lytic cycle and the pathogenicity of Toxoplasma gondii were examined using the CRISPR-Cas9 system. Immunofluorescence showed that four ZFPs (RH248270-HA, RH255310-HA, RH309200-HA, and RH236640-HA) were localized in the cytoplasm, and one ZFP (RH273150-HA) was located in the nucleus, while the expression level of RH285190-HA, RH260870-HA, and RH248450-HA was undetectable. No significant differences were detected between seven RHΔzfp strains (RHΔ285190, RHΔ248270, RHΔ260870, RHΔ255310, RHΔ309200, RHΔ248450, and RHΔ236640) and the wild-type (WT) strain in the T. gondii lytic cycle, including plaque formation, invasion, intracellular replication, and egress, as well as in vitro virulence (p > 0.05). However, the RHΔ273150 strain exhibited significantly lower replication efficiency compared to the other seven RHΔzfp strains and the WT strain, while in vivo virulence in mice was not significantly affected. Comparative expression analysis of the eight zfp genes indicates that certain genes may have essential functions in the sexual reproductive stage of T. gondii. Taken together, these findings expand our current understanding of the roles of ZFPs in T. gondii.
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Affiliation(s)
- Jin Gao
- Laboratory of Parasitic Diseases, College of Veterinary Medicine, Shanxi Agricultural University, Taigu, Jinzhong 030801, China; (J.G.); (X.-J.W.); (X.-N.Z.); (Y.-J.K.)
- State Key Laboratory for Animal Disease Control and Prevention, Key Laboratory of Veterinary Parasitology of Gansu Province, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou 730046, China; (T.-T.L.); (X.-C.W.)
| | - Xiao-Jing Wu
- Laboratory of Parasitic Diseases, College of Veterinary Medicine, Shanxi Agricultural University, Taigu, Jinzhong 030801, China; (J.G.); (X.-J.W.); (X.-N.Z.); (Y.-J.K.)
- State Key Laboratory for Animal Disease Control and Prevention, Key Laboratory of Veterinary Parasitology of Gansu Province, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou 730046, China; (T.-T.L.); (X.-C.W.)
| | - Xiao-Nan Zheng
- Laboratory of Parasitic Diseases, College of Veterinary Medicine, Shanxi Agricultural University, Taigu, Jinzhong 030801, China; (J.G.); (X.-J.W.); (X.-N.Z.); (Y.-J.K.)
| | - Ting-Ting Li
- State Key Laboratory for Animal Disease Control and Prevention, Key Laboratory of Veterinary Parasitology of Gansu Province, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou 730046, China; (T.-T.L.); (X.-C.W.)
| | - Yong-Jie Kou
- Laboratory of Parasitic Diseases, College of Veterinary Medicine, Shanxi Agricultural University, Taigu, Jinzhong 030801, China; (J.G.); (X.-J.W.); (X.-N.Z.); (Y.-J.K.)
- State Key Laboratory for Animal Disease Control and Prevention, Key Laboratory of Veterinary Parasitology of Gansu Province, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou 730046, China; (T.-T.L.); (X.-C.W.)
| | - Xin-Cheng Wang
- State Key Laboratory for Animal Disease Control and Prevention, Key Laboratory of Veterinary Parasitology of Gansu Province, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou 730046, China; (T.-T.L.); (X.-C.W.)
| | - Meng Wang
- State Key Laboratory for Animal Disease Control and Prevention, Key Laboratory of Veterinary Parasitology of Gansu Province, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou 730046, China; (T.-T.L.); (X.-C.W.)
| | - Xing-Quan Zhu
- Laboratory of Parasitic Diseases, College of Veterinary Medicine, Shanxi Agricultural University, Taigu, Jinzhong 030801, China; (J.G.); (X.-J.W.); (X.-N.Z.); (Y.-J.K.)
- Key Laboratory of Veterinary Public Health of Higher Education of Yunnan Province, College of Veterinary Medicine, Yunnan Agricultural University, Kunming 650201, China
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Xue JC, Yuan S, Hou XT, Meng H, Liu BH, Cheng WW, Zhao M, Li HB, Guo XF, Di C, Li MJ, Zhang QG. Natural products modulate NLRP3 in ulcerative colitis. Front Pharmacol 2023; 14:1265825. [PMID: 37849728 PMCID: PMC10577194 DOI: 10.3389/fphar.2023.1265825] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2023] [Accepted: 09/21/2023] [Indexed: 10/19/2023] Open
Abstract
Ulcerative colitis (UC) is a clinically common, progressive, devastating, chronic inflammatory disease of the intestine that is recurrent and difficult to treat. Nod-like receptor protein 3 (NLRP3) is a protein complex composed of multiple proteins whose formation activates cysteine aspartate protease-1 (caspase-1) to induce the maturation and secretion of inflammatory mediators such as interleukin (IL)-1β and IL-18, promoting the development of inflammatory responses. Recent studies have shown that NLRP3 is associated with UC susceptibility, and that it maintains a stable intestinal environment by responding to a wide range of pathogenic microorganisms. The mainstay of treatment for UC is to control inflammation and relieve symptoms. Despite a certain curative effect, there are problems such as easy recurrence after drug withdrawal and many side effects associated with long-term medication. NLRP3 serves as a core link in the inflammatory response. If the relationship between NLRP3 and gut microbes and inflammation-associated factors can be analyzed concerning its related inflammatory signaling pathways, its expression status as well as specific mechanism in the course of IBD can be elucidated and further considered for clinical diagnosis and treatment of IBD, it is expected that the development of lead compounds targeting the NLRP3 inflammasome can be developed for the treatment of IBD. Research into the prevention and treatment of UC, which has become a hotbed of research in recent years, has shown that natural products are rich in therapeutic means, and multi-targets, with fewer adverse effects. Natural products have shown promise in treating UC in numerous basic and clinical trials over the past few years. This paper describes the regulatory role of the NLRP3 inflammasome in UC and the mechanism of recent natural products targeting NLRP3 against UC, which provides a reference for the clinical treatment of this disease.
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Affiliation(s)
- Jia-Chen Xue
- Department of Nuclear Medicine, Affiliated Zhongshan Hospital of Dalian University, Dalian, Liaoning, China
- Chronic Disease Research Center, Medical College, Dalian University, Dalian, Liaoning, China
- Department of Immunology and Pathogenic Biology, Yanbian University College of Basic Medicine, Yanji, Jilin, China
| | - Shuo Yuan
- Chronic Disease Research Center, Medical College, Dalian University, Dalian, Liaoning, China
- Key Laboratory of Natural Medicines of the Changbai Mountain, Ministry of Education, College of Pharmacy, Yanbian University, Yanji, Jilin, China
| | - Xiao-Ting Hou
- Chronic Disease Research Center, Medical College, Dalian University, Dalian, Liaoning, China
| | - Huan Meng
- Chronic Disease Research Center, Medical College, Dalian University, Dalian, Liaoning, China
| | - Bao-Hong Liu
- Chronic Disease Research Center, Medical College, Dalian University, Dalian, Liaoning, China
| | - Wen-Wen Cheng
- Chronic Disease Research Center, Medical College, Dalian University, Dalian, Liaoning, China
| | - Ming Zhao
- Department of Nuclear Medicine, Affiliated Zhongshan Hospital of Dalian University, Dalian, Liaoning, China
| | - Hong-Ben Li
- Department of Nuclear Medicine, Affiliated Zhongshan Hospital of Dalian University, Dalian, Liaoning, China
| | - Xue-Fen Guo
- Department of Nuclear Medicine, Affiliated Zhongshan Hospital of Dalian University, Dalian, Liaoning, China
| | - Chang Di
- Department of Nuclear Medicine, Affiliated Zhongshan Hospital of Dalian University, Dalian, Liaoning, China
| | - Min-Jie Li
- Department of Nuclear Medicine, Affiliated Zhongshan Hospital of Dalian University, Dalian, Liaoning, China
| | - Qing-Gao Zhang
- Chronic Disease Research Center, Medical College, Dalian University, Dalian, Liaoning, China
- Department of Immunology and Pathogenic Biology, Yanbian University College of Basic Medicine, Yanji, Jilin, China
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Zhang Y, Li QS, Liu HL, Tang HT, Yang HL, Wu DQ, Huang YY, Li LC, Liu LH, Li MX. MKRN1 promotes colorectal cancer metastasis by activating the TGF-β signalling pathway through SNIP1 protein degradation. J Exp Clin Cancer Res 2023; 42:219. [PMID: 37620897 PMCID: PMC10464235 DOI: 10.1186/s13046-023-02788-w] [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: 04/13/2023] [Accepted: 08/03/2023] [Indexed: 08/26/2023] Open
Abstract
BACKGROUND The Makorin ring finger protein 1 (MKRN1) gene, also called RNF61, is located on the long arm of chromosome 7 and is a member of the RING finger protein family. The E3 ubiquitin ligase MKRN1 is closely linked to tumour development, but the exact mechanism needs to be elucidated. In this study, we aimed to investigate the specific mechanism and role of MKRN1 in colorectal cancer (CRC) development. METHODS MKRN1 expression in CRC was analysed using the Cancer Cell Line Encyclopaedia and the Cancer Genome Atlas (TCGA) databases. Rectal tumour tissues were frozen to explore the MKRN1 expression in CRC and its clinical significance. The impact of MKRN1 on CRC cell proliferation and migration was observed using CCK8, colony formation, wound healing, and transwell assays. A combination of MKRN1 quantitative proteomics, ubiquitination modification omics analysis, and a string of in vitro and in vivo experiments revealed the potential mechanisms by which MKRN1 regulates CRC metastasis. RESULTS MKRN1 expression was significantly elevated in CRC tissues compared to paracancerous tissues and was positively linked with prognosis (P < 0.01). MKRN1 downregulation inhibits CRC cell proliferation, migration, and invasion. Conversely, MKRN1 overexpression promotes the proliferation, migration, and invasion of CRC cells. Mechanistically, MKRN1 induces epithelial-mesenchymal transition (EMT) in CRC cells via ubiquitination and degradation of Smad nuclear-interacting protein 1 (SNIP1). Furthermore, SNIP1 inhibits transforming growth factor-β (TGF-β) signalling, and MKRN1 promotes TGF-β signalling by degrading SNIP1 to induce EMT in CRC cells. Finally, using conditional knockout mice, intestinal lesions and metastatic liver microlesions were greatly reduced in the intestinal knockout MKRN1 group compared to that in the control group. CONCLUSIONS High MKRN1 levels promote TGF-β signalling through ubiquitination and degradation of SNIP1, thereby facilitating CRC metastasis, and supporting MKRN1 as a CRC pro-cancer factor. The MKRN1/SNIP1/TGF-β axis may be a potential therapeutic target in CRC.
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Affiliation(s)
- Yi Zhang
- Guizhou Prenatal Diagnosis Center, Affiliated Hospital of Guizhou Medical University, Guiyang, 550004, Guizhou, People's Republic of China
- Department of Clinical Biochemistry, School of Medical Laboratory Science, Guizhou Medical University, Guizhou, Guiyang, 550004, People's Republic of China
| | - Qin-Shan Li
- Guizhou Prenatal Diagnosis Center, Affiliated Hospital of Guizhou Medical University, Guiyang, 550004, Guizhou, People's Republic of China.
- Department of Clinical Biochemistry, School of Medical Laboratory Science, Guizhou Medical University, Guizhou, Guiyang, 550004, People's Republic of China.
| | - Hong-Lin Liu
- Institute of Clinical Medical Sciences, China-Japan Friendship Hospital, Beijing, 100000, People's Republic of China
| | - Hong-Ting Tang
- Department of Clinical Biochemistry, School of Medical Laboratory Science, Guizhou Medical University, Guizhou, Guiyang, 550004, People's Republic of China
| | - Han-Lin Yang
- Department of Clinical Biochemistry, School of Medical Laboratory Science, Guizhou Medical University, Guizhou, Guiyang, 550004, People's Republic of China
| | - Dao-Qiu Wu
- Department of Clinical Biochemistry, School of Medical Laboratory Science, Guizhou Medical University, Guizhou, Guiyang, 550004, People's Republic of China
| | - Yu-Ying Huang
- Department of Clinical Biochemistry, School of Medical Laboratory Science, Guizhou Medical University, Guizhou, Guiyang, 550004, People's Republic of China
| | - Li-Cheng Li
- Clinical Medical College, Guizhou Medical University, Guizhou, Guiyang, 550004, People's Republic of China
- Department of HematologyGuizhou Province Laboratory of Hematopoietic Stem Cell Transplantation Centre, Affiliated Hospital of Guizhou Medical University, Guizhou Province Institute of Hematology, Guizhou, Guiyang, People's Republic of China
| | - Li-Hong Liu
- Department of Pharmacy, China-Japan Friendship Hospital, Beijing, 100029, People's Republic of China.
| | - Meng-Xing Li
- Clinical Medical College, Guizhou Medical University, Guizhou, Guiyang, 550004, People's Republic of China.
- Department of HematologyGuizhou Province Laboratory of Hematopoietic Stem Cell Transplantation Centre, Affiliated Hospital of Guizhou Medical University, Guizhou Province Institute of Hematology, Guizhou, Guiyang, People's Republic of China.
- Department of Pathophysiology, Guizhou Medical University, Guizhou, Guiyang, 550004, People's Republic of China.
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10
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Kases K, Schubert E, Hajikhezri Z, Larsson M, Devi P, Darweesh M, Andersson L, Akusjärvi G, Punga T, Younis S. The RNA-binding protein ZC3H11A interacts with the nuclear poly(A)-binding protein PABPN1 and alters polyadenylation of viral transcripts. J Biol Chem 2023; 299:104959. [PMID: 37356722 PMCID: PMC10371797 DOI: 10.1016/j.jbc.2023.104959] [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: 03/09/2023] [Revised: 06/09/2023] [Accepted: 06/14/2023] [Indexed: 06/27/2023] Open
Abstract
Nuclear mRNA metabolism is regulated by multiple proteins, which either directly bind to RNA or form multiprotein complexes. The RNA-binding protein ZC3H11A is involved in nuclear mRNA export, NF-κB signaling, and is essential during mouse embryo development. Furthermore, previous studies have shown that ZC3H11A is important for nuclear-replicating viruses. However, detailed biochemical characterization of the ZC3H11A protein has been lacking. In this study, we established the ZC3H11A protein interactome in human and mouse cells. We demonstrate that the nuclear poly(A)-binding protein PABPN1 interacts specifically with the ZC3H11A protein and controls ZC3H11A localization into nuclear speckles. We report that ZC3H11A specifically interacts with the human adenovirus type 5 (HAdV-5) capsid mRNA in a PABPN1-dependent manner. Notably, ZC3H11A uses the same zinc finger motifs to interact with PABPN1 and viral mRNA. Further, we demonstrate that the lack of ZC3H11A alters the polyadenylation of HAdV-5 capsid mRNA. Taken together, our results suggest that the ZC3H11A protein may act as a novel regulator of polyadenylation of nuclear mRNA.
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Affiliation(s)
- Katharina Kases
- Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
| | - Erik Schubert
- Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
| | - Zamaneh Hajikhezri
- Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
| | - Mårten Larsson
- Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
| | - Priya Devi
- Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
| | - Mahmoud Darweesh
- Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden; Department of Microbiology and Immunology, Al-Azhr University, Assiut, Egypt
| | - Leif Andersson
- Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
| | - Göran Akusjärvi
- Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
| | - Tanel Punga
- Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden.
| | - Shady Younis
- Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden; Division of Immunology and Rheumatology, Stanford University, Stanford, California, USA.
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11
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Morozov SY, Lezzhov AA, Solovyev AG. Predicted Membrane-Associated Domains in Proteins Encoded by Novel Monopartite Plant RNA Viruses Related to Members of the Family Benyviridae. Int J Mol Sci 2023; 24:12161. [PMID: 37569537 PMCID: PMC10418960 DOI: 10.3390/ijms241512161] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2023] [Revised: 07/17/2023] [Accepted: 07/27/2023] [Indexed: 08/13/2023] Open
Abstract
As a continuation of our previous work, in this paper, we examine in greater detail the genome organization and some protein properties of the members of a potential group named Reclovirids and belonging to Benyviridae-related viruses. It can be proposed that the single-component Reclovirid genomes encode previously undiscovered transport genes. Indeed, analysis of the coding potential of these novel viral genomes reveals one or more cistrons ranging in size from 40 to 80 to about 600 codons, located in the 3'-terminal region of the genomic RNA, encoding proteins with predicted hydrophobic segments that are structurally diverse among Reclovirids and have no analogues in other plant RNA viruses. Additionally, in many cases, the possible methyltransferase domain of Reclovirid replicases is preceded by membrane-embedded protein segments that are not present in annotated members of the Benyviridae family. These observations suggest a general association of most Reclovirid proteins with cell membranes.
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Affiliation(s)
- Sergey Y. Morozov
- A. N. Belozersky Institute of Physico-Chemical Biology, Moscow State University, 119992 Moscow, Russia; (A.A.L.); (A.G.S.)
- Department of Virology, Biological Faculty, Moscow State University, 119234 Moscow, Russia
| | - Alexander A. Lezzhov
- A. N. Belozersky Institute of Physico-Chemical Biology, Moscow State University, 119992 Moscow, Russia; (A.A.L.); (A.G.S.)
| | - Andrey G. Solovyev
- A. N. Belozersky Institute of Physico-Chemical Biology, Moscow State University, 119992 Moscow, Russia; (A.A.L.); (A.G.S.)
- Department of Virology, Biological Faculty, Moscow State University, 119234 Moscow, Russia
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12
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Licon MH, Giuliano CJ, Chan AW, Chakladar S, Eberhard JN, Shallberg LA, Chandrasekaran S, Waldman BS, Koshy AA, Hunter CA, Lourido S. A positive feedback loop controls Toxoplasma chronic differentiation. Nat Microbiol 2023; 8:889-904. [PMID: 37081202 PMCID: PMC10520893 DOI: 10.1038/s41564-023-01358-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2022] [Accepted: 03/07/2023] [Indexed: 04/22/2023]
Abstract
Successful infection strategies must balance pathogen amplification and persistence. In the obligate intracellular parasite Toxoplasma gondii this is accomplished through differentiation into dedicated cyst-forming chronic stages that avoid clearance by the host immune system. The transcription factor BFD1 is both necessary and sufficient for stage conversion; however, its regulation is not understood. In this study we examine five factors that are transcriptionally activated by BFD1. One of these is a cytosolic RNA-binding protein of the CCCH-type zinc-finger family, which we name bradyzoite formation deficient 2 (BFD2). Parasites lacking BFD2 fail to induce BFD1 and are consequently unable to fully differentiate in culture or in mice. BFD2 interacts with the BFD1 transcript under stress, and deletion of BFD2 reduces BFD1 protein levels but not messenger RNA abundance. The reciprocal effects on BFD2 transcription and BFD1 translation outline a positive feedback loop that enforces the chronic-stage gene-expression programme. Thus, our findings help explain how parasites both initiate and commit to chronic differentiation. This work provides new mechanistic insight into the regulation of T. gondii persistence, and can be exploited in the design of strategies to prevent and treat these key reservoirs of human infection.
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Affiliation(s)
| | - Christopher J Giuliano
- Whitehead Institute, Cambridge, MA, USA
- Biology Department, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Alex W Chan
- Whitehead Institute, Cambridge, MA, USA
- Biology Department, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Sundeep Chakladar
- Biology Department, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Julia N Eberhard
- Department of Pathobiology, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Lindsey A Shallberg
- Department of Pathobiology, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | | | - Benjamin S Waldman
- Whitehead Institute, Cambridge, MA, USA
- Department of Microbiology and Immunology, School of Medicine, Stanford University, Stanford, CA, USA
| | - Anita A Koshy
- BIO5 Institute, University of Arizona, Tucson, AZ, USA
- Department of Neurology, Department of Immunobiology, University of Arizona, Tucson, AZ, USA
| | - Christopher A Hunter
- Department of Pathobiology, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Sebastian Lourido
- Whitehead Institute, Cambridge, MA, USA.
- Biology Department, Massachusetts Institute of Technology, Cambridge, MA, USA.
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13
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Momin T, Villasenor A, Singh A, Darweesh M, Singh A, Rajput M. ZFP36 ring finger protein like 1 significantly suppresses human coronavirus OC43 replication. PeerJ 2023; 11:e14776. [PMID: 36846448 PMCID: PMC9948753 DOI: 10.7717/peerj.14776] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2022] [Accepted: 01/03/2023] [Indexed: 02/22/2023] Open
Abstract
CCCH-type zinc figure proteins (ZFP) are small cellular proteins that are structurally maintained by zinc ions. Zinc ions coordinate the protein structure in a tetrahedral geometry by binding to cystine-cystine or cysteines-histidine amino acids. ZFP's unique structure enables it to interact with a wide variety of molecules including RNA; thus, ZFP modulates several cellular processes including the host immune response and virus replication. CCCH-type ZFPs have shown their antiviral efficacy against several DNA and RNA viruses. However, their role in the human coronavirus is little explored. We hypothesized that ZFP36L1 also suppresses the human coronavirus. To test our hypothesis, we used OC43 human coronavirus (HCoV) strain in our study. We overexpressed and knockdown ZFP36L1 in HCT-8 cells using lentivirus transduction. Wild type, ZFP36L1 overexpressed, and ZFP36L1 knockdown cells were each infected with HCoV-OC43, and the virus titer in each cell line was measured over 96 hours post-infection (p.i.). Our results show that HCoV-OC43 replication was significantly reduced with ZFP36L1 overexpression while ZFP36L1 knockdown significantly enhanced virus replication. ZFP36L1 knockdown HCT-8 cells started producing infectious virus at 48 hours p.i. which was an earlier timepoint as compared to wild -type and ZFP36L1 overexpressed cells. Wild-type and ZFP36L1 overexpressed HCT-8 cells started producing infectious virus at 72 hours p.i. Overall, the current study showed that overexpression of ZFP36L1 suppressed human coronavirus (OC43) production.
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Affiliation(s)
- Tooba Momin
- Department of Biology, University of Dayton, Dayton, OH, United States of America
| | - Andrew Villasenor
- Department of Biology, University of Dayton, Dayton, OH, United States of America
| | - Amit Singh
- Department of Biology, University of Dayton, Dayton, OH, United States of America
| | - Mahmoud Darweesh
- Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Uppsala, Sweden
- Department of Microbiology and Immunology, Faculty of Pharmacy, Al-Azhr University, Assiut, Egypt
| | - Aditi Singh
- Department of Biology, University of Dayton, Dayton, OH, United States of America
| | - Mrigendra Rajput
- Department of Biology, University of Dayton, Dayton, OH, United States of America
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14
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Darweesh M, Younis S, Hajikhezri Z, Ali A, Jin C, Punga T, Gupta S, Essand M, Andersson L, Akusjärvi G. ZC3H11A loss of function enhances NF-κB signaling through defective IκBα protein expression. Front Immunol 2022; 13:1002823. [PMID: 36439101 PMCID: PMC9681899 DOI: 10.3389/fimmu.2022.1002823] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2022] [Accepted: 10/05/2022] [Indexed: 12/02/2023] Open
Abstract
ZC3H11A is a cellular protein associated with the transcription export (TREX) complex that is induced during heat-shock. Several nuclear-replicating viruses exploit the mRNA export mechanism of ZC3H11A protein for their efficient replication. Here we show that ZC3H11A protein plays a role in regulation of NF-κB signal transduction. Depletion of ZC3H11A resulted in enhanced NF-κB mediated signaling, with upregulation of numerous innate immune related mRNAs, including IL-6 and a large group of interferon-stimulated genes. IL-6 upregulation in the absence of the ZC3H11A protein correlated with an increased NF-κB transcription factor binding to the IL-6 promoter and decreased IL-6 mRNA decay. The enhanced NF-κB signaling pathway in ZC3H11A deficient cells correlated with a defect in IκBα inhibitory mRNA and protein accumulation. Upon ZC3H11A depletion The IκBα mRNA was retained in the cell nucleus resulting in failure to maintain normal levels of the cytoplasmic IκBα mRNA and protein that is essential for its inhibitory feedback loop on NF-κB activity. These findings indicate towards a previously unknown mechanism of ZC3H11A in regulating the NF-κB pathway at the level of IkBα mRNA export.
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Affiliation(s)
- Mahmoud Darweesh
- Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
- Department of Microbiology and Immunology, Faculty of Pharmacy, Alazhr University, Assiut, Egypt
| | - Shady Younis
- Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
- Division of Immunology and Rheumatology, Stanford University, Stanford, CA, United States
| | - Zamaneh Hajikhezri
- Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
| | - Arwa Ali
- Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden
| | - Chuan Jin
- Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden
| | - Tanel Punga
- Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
| | - Soham Gupta
- Division of Clinical Microbiology, Department of Laboratory Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Magnus Essand
- Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden
| | - Leif Andersson
- Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
- Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, Uppsala, Sweden
- Department of Veterinary Integrative Biosciences, Texas A&M University, College Station, TX, United States
| | - Göran Akusjärvi
- Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
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15
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Benites LF, Stephens TG, Bhattacharya D. Multiple waves of viral invasions in Symbiodiniaceae algal genomes. Virus Evol 2022; 8:veac101. [PMID: 36381231 PMCID: PMC9651163 DOI: 10.1093/ve/veac101] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2022] [Revised: 08/29/2022] [Accepted: 10/25/2022] [Indexed: 08/13/2023] Open
Abstract
Dinoflagellates from the family Symbiodiniaceae are phototrophic marine protists that engage in symbiosis with diverse hosts. Their large and distinct genomes are characterized by pervasive gene duplication and large-scale retroposition events. However, little is known about the role and scale of horizontal gene transfer (HGT) in the evolution of this algal family. In other dinoflagellates, high levels of HGTs have been observed, linked to major genomic transitions, such as the appearance of a viral-acquired nucleoprotein that originated via HGT from a large DNA algal virus. Previous work showed that Symbiodiniaceae from different hosts are actively infected by viral groups, such as giant DNA viruses and ssRNA viruses, that may play an important role in coral health. Latent viral infections may also occur, whereby viruses could persist in the cytoplasm or integrate into the host genome as a provirus. This hypothesis received experimental support; however, the cellular localization of putative latent viruses and their taxonomic affiliation are still unknown. In addition, despite the finding of viral sequences in some genomes of Symbiodiniaceae, viral origin, taxonomic breadth, and metabolic potential have not been explored. To address these questions, we searched for putative viral-derived proteins in thirteen Symbiodiniaceae genomes. We found fifty-nine candidate viral-derived HGTs that gave rise to twelve phylogenies across ten genomes. We also describe the taxonomic affiliation of these virus-related sequences, their structure, and their genomic context. These results lead us to propose a model to explain the origin and fate of Symbiodiniaceae viral acquisitions.
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Affiliation(s)
- L Felipe Benites
- Department of Biochemistry and Microbiology, Rutgers University, 102 Foran Hall, 59 Dudley Road, New Brunswick, NJ 08901-8520, USA
| | - Timothy G Stephens
- Department of Biochemistry and Microbiology, Rutgers University, 102 Foran Hall, 59 Dudley Road, New Brunswick, NJ 08901-8520, USA
| | - Debashish Bhattacharya
- Department of Biochemistry and Microbiology, Rutgers University, 102 Foran Hall, 59 Dudley Road, New Brunswick, NJ 08901-8520, USA
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16
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He Z, Ye L, Yang D, Ma Z, Deng F, He Z, Hu J, Chen H, Zheng L, Pu Y, Jiao Y, Chen Q, Gao K, Xiong J, Lai B, Gu X, Huang X, Yang S, Zhang M, Yan T. Identification, characterization and functional analysis of gonadal long noncoding RNAs in a protogynous hermaphroditic teleost fish, the ricefield eel (Monopterus albus). BMC Genomics 2022; 23:450. [PMID: 35725373 PMCID: PMC9208217 DOI: 10.1186/s12864-022-08679-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2022] [Accepted: 06/09/2022] [Indexed: 11/11/2022] Open
Abstract
Background An increasing number of long noncoding RNAs (lncRNAs) have been found to play important roles in sex differentiation and gonad development by regulating gene expression at the epigenetic, transcriptional and posttranscriptional levels. The ricefield eel, Monopterus albus, is a protogynous hermaphroditic fish that undergoes a sequential sex change from female to male. However, the roles of lncRNA in the sex change is unclear. Results Herein, we performed RNA sequencing to analyse lncRNA expression patterns in five different stages of M. albus development to investigate the roles of lncRNAs in the sex change process. A total of 12,746 lncRNAs (1503 known lncRNAs and 11,243 new lncRNAs) and 2901 differentially expressed lncRNAs (DE-lncRNAs) were identified in the gonads. The target genes of the DE-lncRNAs included foxo1, foxm1, smad3, foxr1, camk4, ar and tgfb3, which were mainly enriched in signalling pathways related to gonadal development, such as the insulin signalling pathway, MAPK signalling pathway, and calcium signalling pathway. We selected 5 highly expressed DE-lncRNAs (LOC109952131, LOC109953466, LOC109954337, LOC109954360 and LOC109958454) for full length amplification and expression pattern verification. They were all expressed at higher levels in ovaries and intersex gonads than in testes, and exhibited specific time-dependent expression in ovarian tissue incubated with follicle-stimulating hormone (FSH) and human chorionic gonadotropin (hCG). The results of quantitative real-time PCR (qRT-PCR) analysis and a dual-luciferase assay showed that znf207, as the gene targeted by LOC109958454, was expressed in multiple tissues and gonadal developmental stages of M. albus, and its expression was also inhibited by the hormones FSH and hCG. Conclusions These results provide new insights into the role of lncRNAs in gonad development, especially regarding natural sex changes in fish, which will be useful for enhancing our understanding of sequential hermaphroditism and sex changes in the ricefield eel (M. albus) and other teleosts. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-022-08679-2.
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Affiliation(s)
- Zhi He
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
| | - Lijuan Ye
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
| | - Deying Yang
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
| | - Zhijun Ma
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
| | - Faqiang Deng
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
| | - Zhide He
- Luzhou Municipal Bureau of Agriculture and Rural Affairs, Luzhou, 646000, Sichuan, China
| | - Jiaxiang Hu
- Sichuan Water Conservancy Vocational College, Chengdu, 611231, Sichuan, China
| | - Hongjun Chen
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
| | - Li Zheng
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
| | - Yong Pu
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
| | - Yuanyuan Jiao
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
| | - Qiqi Chen
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
| | - Kuo Gao
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
| | - Jinxin Xiong
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
| | - Bolin Lai
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
| | - Xiaobin Gu
- College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
| | - Xiaoli Huang
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
| | - Shiyong Yang
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
| | - Mingwang Zhang
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
| | - Taiming Yan
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China.
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17
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Chen X, Shan T, Sun D, Zhai H, Dong S, Kong N, Zheng H, Tong W, Tong G. Host Zinc-finger CCHC-type containing protein 3 inhibits pseudorabies virus proliferation by regulating type I interferon signaling. Gene X 2022; 827:146480. [PMID: 35390445 DOI: 10.1016/j.gene.2022.146480] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2021] [Revised: 03/25/2022] [Accepted: 04/01/2022] [Indexed: 11/04/2022] Open
Abstract
Zinc finger CCHC-type containing protein 3 (ZCCHC3) acts as an antiviral factor that interacts with RIG-I and cGAS to modulate innate signaling against viral infections. Here, we investigated the role of porcine ZCCHC3 during pseudorabies virus (PRV) proliferation. We found that porcine ZCCHC3 plays an inhibitory role in the proliferation of PRV by regulating cellular innate immune responses. Further, overexpression of ZCCHC3 inhibited gB protein levels and viral titers, whereas knockdown of ZCCHC3 promoted viral growth. ZCCHC3 overexpression increased IFN-β expression to upregulate downstream gene expression, thus leading to the suppression of viral replication. However, PRV infection reduced the endogenous expression of ZCCHC3 in permissive cells. Importantly, PRV-encoded UL13 and UL24 proteins were identified to inhibit the expression of ZCCHC3, thus antagonizing its antiviral effect. Collectively, our data underscore the important role of ZCCHC3 against PRV infection and promote understandings of viral proteins in PRV pathogenesis.
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Affiliation(s)
- Xiaoyong Chen
- Institute of Animal Sciences, Wenzhou Academy of Agricultural Sciences, Wenzhou, Zhejiang, PR China; Department of Swine Infectious Diseases, Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, PR China
| | - Tongling Shan
- Department of Swine Infectious Diseases, Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, PR China
| | - Dage Sun
- Department of Swine Infectious Diseases, Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, PR China
| | - Huanjie Zhai
- Department of Swine Infectious Diseases, Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, PR China
| | - Sujie Dong
- Department of Swine Infectious Diseases, Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, PR China
| | - Ning Kong
- Department of Swine Infectious Diseases, Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, PR China
| | - Hao Zheng
- Department of Swine Infectious Diseases, Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, PR China
| | - Wu Tong
- Department of Swine Infectious Diseases, Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, PR China
| | - Guangzhi Tong
- Department of Swine Infectious Diseases, Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, PR China; Jiangsu Co-Innovation Center for the Prevention and Control of Important Animal Infectious Disease and Zoonose, Yangzhou University, Yangzhou, Jiangsu, PR China.
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The Plasmodium falciparum CCCH Zinc Finger Protein ZNF4 Plays an Important Role in Gametocyte Exflagellation through the Regulation of Male Enriched Transcripts. Cells 2022; 11:cells11101666. [PMID: 35626703 PMCID: PMC9139750 DOI: 10.3390/cells11101666] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Revised: 04/28/2022] [Accepted: 05/13/2022] [Indexed: 11/26/2022] Open
Abstract
CCCH zinc finger proteins (ZFPs) function mainly as RNA-binding proteins (RBPs) and play a central role in the mRNA metabolism. Over twenty seven CCCH-ZFPs are encoded in the genome of the human malaria parasite Plasmodium falciparum, the causative agent of malaria tropica. However, little is known about their functions. In this study, we characterize one member of the PfCCCH-ZFP named ZNF4. We show that ZNF4 is highly expressed in mature gametocytes, where it predominantly localizes to the cytoplasm. Targeted gene disruption of ZNF4 showed no significant effect in asexual blood stage replication and gametocyte development while male gametocyte exflagellation was significantly impaired, leading to reduced malaria transmission in the mosquito. Comparative transcriptomics between wildtype (WT) and the ZNF4-deficient line (ZNF4-KO) demonstrated the deregulation of about 473 genes (274 upregulated and 199 downregulated) in mature gametocytes. Most of the downregulated genes show peak expression in mature gametocyte with male enriched genes associated to the axonemal dynein complex formation, and cell projection organization is highly affected, pointing to the phenotype in male gametocyte exflagellation. Upregulated genes are associated to ATP synthesis. Our combined data therefore indicate that ZNF4 is a CCCH zinc finger protein which plays an important role in male gametocyte exflagellation through the regulation of male gametocyte-enriched genes.
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Bu S, Lv Y, Liu Y, Qiao S, Wang H. Zinc Finger Proteins in Neuro-Related Diseases Progression. Front Neurosci 2021; 15:760567. [PMID: 34867169 PMCID: PMC8637543 DOI: 10.3389/fnins.2021.760567] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2021] [Accepted: 10/11/2021] [Indexed: 01/02/2023] Open
Abstract
Zinc finger proteins (ZNF) are among the most abundant proteins in eukaryotic genomes. It contains several zinc finger domains that can selectively bind to certain DNA or RNA and associate with proteins, therefore, ZNF can regulate gene expression at the transcriptional and translational levels. In terms of neurological diseases, numerous studies have shown that many ZNF are associated with neurological diseases. The purpose of this review is to summarize the types and roles of ZNF in neuropsychiatric disorders. We will describe the structure and classification of ZNF, then focus on the pathophysiological role of ZNF in neuro-related diseases and summarize the mechanism of action of ZNF in neuro-related diseases.
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Affiliation(s)
- Siyuan Bu
- Department of Pharmacology, School of Medicine, Southeast University, Nanjing, China
| | - Yihan Lv
- Department of Pharmacology, School of Medicine, Southeast University, Nanjing, China
| | - Yusheng Liu
- Department of Pharmacology, School of Medicine, Southeast University, Nanjing, China
| | - Sen Qiao
- Department of Pharmacology, Center for Molecular Signaling (PZMS), School of Medicine, Saarland University, Homburg, Germany
| | - Hongmei Wang
- Department of Pharmacology, School of Medicine, Southeast University, Nanjing, China
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20
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Ngwa CJ, Farrukh A, Pradel G. Zinc finger proteins of Plasmodium falciparum. Cell Microbiol 2021; 23:e13387. [PMID: 34418264 DOI: 10.1111/cmi.13387] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Revised: 07/19/2021] [Accepted: 07/24/2021] [Indexed: 01/14/2023]
Abstract
Zinc finger proteins (ZFPs) are a large diverse family of proteins with one or more zinc finger domains in which zinc is important in stabilising the domain. ZFPs can interact with DNA, RNA, lipids or even other proteins and therefore contribute to diverse cellular processes including transcriptional regulation, ubiquitin-mediated protein degradation, mRNA decay and stability. In this review, we provide the first comprehensive classification of ZFPs of the malaria parasite Plasmodium falciparum and provide a state of knowledge on the main ZFPs in the parasite, which include the C2H2, CCCH, RING finger and the PHD finger proteins. TAKE AWAYS: The Plasmodium falciparum genome encodes 170 putative Zinc finger proteins (ZFPs). The C2H2, CCCH, RING finger and PHD finger subfamilies of ZFPs are most represented. Known ZFP functions include the regulation of mRNA metabolism and proteostasis.
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Affiliation(s)
- Che Julius Ngwa
- Division of Cellular and Applied Infection Biology, Institute of Zoology, RWTH Aachen University, Aachen, Germany
| | - Afia Farrukh
- Division of Cellular and Applied Infection Biology, Institute of Zoology, RWTH Aachen University, Aachen, Germany
| | - Gabriele Pradel
- Division of Cellular and Applied Infection Biology, Institute of Zoology, RWTH Aachen University, Aachen, Germany
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21
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Arnberg N, Lenman A. Special Issue "Adenovirus Pathogenesis". Viruses 2021; 13:v13061112. [PMID: 34200540 PMCID: PMC8227180 DOI: 10.3390/v13061112] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2021] [Accepted: 06/09/2021] [Indexed: 11/16/2022] Open
Affiliation(s)
- Niklas Arnberg
- Section of Virology, Department of Clinical Microbiology, Umeå University, SE-90185 Umeå, Sweden
- Correspondence: (N.A.); (A.L.)
| | - Annasara Lenman
- Section of Virology, Department of Clinical Microbiology, Umeå University, SE-90185 Umeå, Sweden
- Institute for Experimental Virology, TWINCORE, Centre for Experimental and Clinical Infection Research, 30625 Hannover, Germany
- Correspondence: (N.A.); (A.L.)
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