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Husain M. Influenza Virus Host Restriction Factors: The ISGs and Non-ISGs. Pathogens 2024; 13:127. [PMID: 38392865 PMCID: PMC10893265 DOI: 10.3390/pathogens13020127] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2023] [Revised: 01/18/2024] [Accepted: 01/26/2024] [Indexed: 02/25/2024] Open
Abstract
Influenza virus has been one of the most prevalent and researched viruses globally. Consequently, there is ample information available about influenza virus lifecycle and pathogenesis. However, there is plenty yet to be known about the determinants of influenza virus pathogenesis and disease severity. Influenza virus exploits host factors to promote each step of its lifecycle. In turn, the host deploys antiviral or restriction factors that inhibit or restrict the influenza virus lifecycle at each of those steps. Two broad categories of host restriction factors can exist in virus-infected cells: (1) encoded by the interferon-stimulated genes (ISGs) and (2) encoded by the constitutively expressed genes that are not stimulated by interferons (non-ISGs). There are hundreds of ISGs known, and many, e.g., Mx, IFITMs, and TRIMs, have been characterized to restrict influenza virus infection at different stages of its lifecycle by (1) blocking viral entry or progeny release, (2) sequestering or degrading viral components and interfering with viral synthesis and assembly, or (3) bolstering host innate defenses. Also, many non-ISGs, e.g., cyclophilins, ncRNAs, and HDACs, have been identified and characterized to restrict influenza virus infection at different lifecycle stages by similar mechanisms. This review provides an overview of those ISGs and non-ISGs and how the influenza virus escapes the restriction imposed by them and aims to improve our understanding of the host restriction mechanisms of the influenza virus.
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Affiliation(s)
- Matloob Husain
- Department of Microbiology and Immunology, University of Otago, P.O. Box 56, Dunedin 9054, New Zealand
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Yuan W, Qin H, Bi H, Zhao D, Zhang Y, Chen W. Ssc-mir-221-3p regulates melanin production in Xiang pigs melanocytes by targeting the TYRP1 gene. BMC Genomics 2023; 24:369. [PMID: 37393242 DOI: 10.1186/s12864-023-09451-w] [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: 11/14/2022] [Accepted: 06/14/2023] [Indexed: 07/03/2023] Open
Abstract
BACKGROUND MicroRNAs (miRNAs) are small endogenous non-coding RNAs that regulate gene expression by down-regulating it. Several studies have suggested that miRNAs plays a crucial role in mammalian skin color production. The TYRP1 gene, a member of the tyrosine family, is an important candidate gene that affects melanogenesis. This study aimed to identify genes and miRNAs that affect melanin production in Xiang pigs by transcriptome sequencing, and to validate their targeted regulatory relationships. RESULTS 17 miRNAs and 1,230 genes were significantly differentially expressed (P < 0.05) in the black and white skin tissues of Jianbai Xiang pigs. miRNA-221-3p was identified as a candidate miRNA for melanin formation and its target gene, TYRP1, was selected. The TYRP1 gene is a member of the TYR gene family, which evolved from the TYR gene through chromosome segmental duplication. The function of the gene was highly conserved throughout the evolutionary process. overexpression of TYRP1 gene significantly increased the expression of TYR, TYRP1, and DCT genes P < 0.01, which led to an increase in the relative content of melanin. Silencing of TYRP1 through the use of TYRP1-siRNA significantly reduced the expression of TYR, TYRP1, and DCT genes in Jianbai Xiang pig melanocytes P < 0.01, which in turn decreased the relative melanin content. The targeted binding relationship between ssc-miR-221-3p and TYRP1 gene was validated. After transfection of porcine melanocytes with ssc-miR-221-3p mimic, the expression of ssc-miR-221-3p was significantly up-regulated (P < 0.01). Furthermore, the mRNA and protein levels of TYR, TYRP1, and DCT genes were significantly down-regulated (P < 0.01), and melanin content in cells was significantly reduced (P < 0.01). CONCLUSION The TYRP1 gene affects melanogenesis in melanocytes of Jianbai Xiang pigs, and ssc-miR-221-3p targets the TYRP1 gene to regulate melanogenesis in melanocytes of Jianbai Xiang pigs.
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Affiliation(s)
- Wei Yuan
- Key Laboratory of Animal Genetics, Breeding and Reproduction in the Plateau Mountainous Region, Ministry of Education, Guizhou University, Guiyang, 550025, Guizhou Province, China
- Key Laboratory of Animal Genetics, Breeding and Reproduction, Guiyang, 550025, Guizhou Province, China
- College of Animal Science, Guizhou University, Guiyang, 550025, Guizhou Province, China
| | - Hai Qin
- Key Laboratory of Animal Genetics, Breeding and Reproduction in the Plateau Mountainous Region, Ministry of Education, Guizhou University, Guiyang, 550025, Guizhou Province, China
- Key Laboratory of Animal Genetics, Breeding and Reproduction, Guiyang, 550025, Guizhou Province, China
- College of Animal Science, Guizhou University, Guiyang, 550025, Guizhou Province, China
| | - Huan Bi
- Key Laboratory of Animal Genetics, Breeding and Reproduction in the Plateau Mountainous Region, Ministry of Education, Guizhou University, Guiyang, 550025, Guizhou Province, China
- Key Laboratory of Animal Genetics, Breeding and Reproduction, Guiyang, 550025, Guizhou Province, China
- College of Animal Science, Guizhou University, Guiyang, 550025, Guizhou Province, China
| | - Depeng Zhao
- Key Laboratory of Animal Genetics, Breeding and Reproduction in the Plateau Mountainous Region, Ministry of Education, Guizhou University, Guiyang, 550025, Guizhou Province, China
- Key Laboratory of Animal Genetics, Breeding and Reproduction, Guiyang, 550025, Guizhou Province, China
- College of Animal Science, Guizhou University, Guiyang, 550025, Guizhou Province, China
| | - Yiyu Zhang
- Key Laboratory of Animal Genetics, Breeding and Reproduction in the Plateau Mountainous Region, Ministry of Education, Guizhou University, Guiyang, 550025, Guizhou Province, China
- Key Laboratory of Animal Genetics, Breeding and Reproduction, Guiyang, 550025, Guizhou Province, China
- College of Animal Science, Guizhou University, Guiyang, 550025, Guizhou Province, China
| | - Wei Chen
- Key Laboratory of Animal Genetics, Breeding and Reproduction in the Plateau Mountainous Region, Ministry of Education, Guizhou University, Guiyang, 550025, Guizhou Province, China.
- Key Laboratory of Animal Genetics, Breeding and Reproduction, Guiyang, 550025, Guizhou Province, China.
- College of Animal Science, Guizhou University, Guiyang, 550025, Guizhou Province, China.
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Cai W, Pan Y, Cheng A, Wang M, Yin Z, Jia R. Regulatory Role of Host MicroRNAs in Flaviviruses Infection. Front Microbiol 2022; 13:869441. [PMID: 35479613 PMCID: PMC9036177 DOI: 10.3389/fmicb.2022.869441] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2022] [Accepted: 03/16/2022] [Indexed: 12/15/2022] Open
Abstract
MicroRNAs (miRNAs) are small non-coding RNA that affect mRNA abundance or translation efficiency by binding to the 3′UTR of the mRNA of the target gene, thereby participating in multiple biological processes, including viral infection. Flavivirus genus consists of small, positive-stranded, single-stranded RNA viruses transmitted by arthropods, especially mosquitoes and ticks. The genus contains several globally significant human/animal pathogens, such as Dengue virus, Japanese encephalitis virus, West Nile virus, Zika virus, Yellow fever virus, Tick-borne encephalitis virus, and Tembusu virus. After flavivirus invades, the expression of host miRNA changes, exerting the immune escape mechanism to create an environment conducive to its survival, and the altered miRNA in turn affects the life cycle of the virus. Accumulated evidence suggests that host miRNAs influence flavivirus replication and host–virus interactions through direct binding of viral genomes or through virus-mediated host transcriptome changes. Furthermore, miRNA can also interweave with other non-coding RNAs, such as long non-coding RNA and circular RNA, to form an interaction network to regulate viral replication. A variety of non-coding RNAs produced by the virus itself exert similar function by interacting with cellular RNA and viral RNA. Understanding the interaction sites between non-coding RNA, especially miRNA, and virus/host genes will help us to find targets for antiviral drugs and viral therapy.
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Affiliation(s)
- Wenjun Cai
- Research Center of Avian Disease, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, China
| | - Yuhong Pan
- Research Center of Avian Disease, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, China
| | - Anchun Cheng
- Research Center of Avian Disease, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, China
- *Correspondence: Anchun Cheng,
| | - Mingshu Wang
- Research Center of Avian Disease, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, China
| | - Zhongqiong Yin
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, China
| | - Renyong Jia
- Research Center of Avian Disease, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, China
- Renyong Jia,
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Sui N, Zhang R, Jiang Y, Yu H, Xu G, Wang J, Zhu Y, Xie Z, Hu J, Jiang S. Integrated miRNA and mRNA Expression Profiles Reveal Differentially Expressed miR-222a as an Antiviral Factor Against Duck Hepatitis A Virus Type 1 Infection. Front Cell Infect Microbiol 2022; 11:811556. [PMID: 35047423 PMCID: PMC8761743 DOI: 10.3389/fcimb.2021.811556] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2021] [Accepted: 12/06/2021] [Indexed: 12/11/2022] Open
Abstract
Duck hepatitis A virus 1 (DHAV-1) is a highly contagious etiological agent that causes acute hepatitis in young ducklings. MicroRNAs (miRNAs) play important regulatory roles in response to pathogens. However, the interplay between DHAV-1 infection and miRNAs remains ambiguous. We characterized and compared miRNA and mRNA expression profiles in duck embryo fibroblasts cells (DEFs) infected with DHAV-1. In total, 36 and 96 differentially expressed (DE) miRNAs, and 4110 and 2595 DE mRNAs, were identified at 12 and 24 h after infection. In particular, 126 and 275 miRNA-mRNA pairs with a negative correlation were chosen to construct an interaction network. Subsequently, we identified the functional annotation of DE mRNAs and target genes of DE miRNAs enriched in diverse Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways, which may be important for virus resistance, cell proliferation, and metabolism. Moreover, upregulated miR-222a could negatively regulate DHAV-1 replication in DEFs and downregulate integrin subunit beta 3 (ITGB3) expression by targeting the 3' untranslated region (3'UTR), indicating that miR-222a may modulate DHAV-1 replication via interaction with ITGB3. In conclusion, the results reveal changes of mRNAs and miRNAs during DHAV-1 infection and suggest miR-222a as an antiviral factor against DHAV-1.
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Affiliation(s)
- Nana Sui
- College of Veterinary Medicine, Shandong Agricultural University, Taian, China.,Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, Taian, China
| | - Ruihua Zhang
- College of Veterinary Medicine, Shandong Agricultural University, Taian, China.,Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, Taian, China
| | - Yue Jiang
- College of Veterinary Medicine, Shandong Agricultural University, Taian, China.,Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, Taian, China
| | - Honglei Yu
- College of Veterinary Medicine, Shandong Agricultural University, Taian, China.,Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, Taian, China
| | - Guige Xu
- College of Veterinary Medicine, Shandong Agricultural University, Taian, China.,Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, Taian, China
| | - Jingyu Wang
- College of Veterinary Medicine, Shandong Agricultural University, Taian, China.,Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, Taian, China
| | - Yanli Zhu
- College of Veterinary Medicine, Shandong Agricultural University, Taian, China.,Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, Taian, China
| | - Zhijing Xie
- College of Veterinary Medicine, Shandong Agricultural University, Taian, China.,Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, Taian, China
| | - Jiaqing Hu
- College of Veterinary Medicine, Shandong Agricultural University, Taian, China.,Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, Taian, China.,Shandong GreenBlue Biotechnology Co. Ltd. Economic Development Zone, Ningyang County, Taian, China
| | - Shijin Jiang
- College of Veterinary Medicine, Shandong Agricultural University, Taian, China.,Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, Taian, China
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Liao Y, Guo S, Liu G, Qiu Z, Wang J, Yang D, Tian X, Qiao Z, Ma Z, Liu Z. Host Non-Coding RNA Regulates Influenza A Virus Replication. Viruses 2021; 14:v14010051. [PMID: 35062254 PMCID: PMC8779696 DOI: 10.3390/v14010051] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2021] [Revised: 12/21/2021] [Accepted: 12/21/2021] [Indexed: 12/12/2022] Open
Abstract
Outbreaks of influenza, caused by the influenza A virus (IAV), occur almost every year in various regions worldwide, seriously endangering human health. Studies have shown that host non-coding RNA is an important regulator of host-virus interactions in the process of IAV infection. In this paper, we comprehensively analyzed the research progress on host non-coding RNAs with regard to the regulation of IAV replication. According to the regulation mode of host non-coding RNAs, the signal pathways involved, and the specific target genes, we found that a large number of host non-coding RNAs directly targeted the PB1 and PB2 proteins of IAV. Nonstructural protein 1 and other key genes regulate the replication of IAV and indirectly participate in the regulation of the retinoic acid-induced gene I-like receptor signaling pathway, toll-like receptor signaling pathway, Janus kinase signal transducer and activator of transcription signaling pathway, and other major intracellular viral response signaling pathways to regulate the replication of IAV. Based on the above findings, we mapped the regulatory network of host non-coding RNAs in the innate immune response to the influenza virus. These findings will provide a more comprehensive understanding of the function and mechanism of host non-coding RNAs in the cellular anti-virus response as well as clues to the mechanism of cell-virus interactions and the discovery of antiviral drug targets.
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Affiliation(s)
- Yuejiao Liao
- Gansu Tech Innovation Center of Animal Cell, Biomedical Research Center, Northwest Minzu University, Lanzhou 730030, China; (Y.L.); (S.G.); (G.L.); (Z.Q.); (J.W.); (D.Y.); (Z.Q.); (Z.M.)
- Life Science and Engineering College, Northwest Minzu University, Lanzhou 730030, China;
| | - Shouqing Guo
- Gansu Tech Innovation Center of Animal Cell, Biomedical Research Center, Northwest Minzu University, Lanzhou 730030, China; (Y.L.); (S.G.); (G.L.); (Z.Q.); (J.W.); (D.Y.); (Z.Q.); (Z.M.)
- Life Science and Engineering College, Northwest Minzu University, Lanzhou 730030, China;
| | - Geng Liu
- Gansu Tech Innovation Center of Animal Cell, Biomedical Research Center, Northwest Minzu University, Lanzhou 730030, China; (Y.L.); (S.G.); (G.L.); (Z.Q.); (J.W.); (D.Y.); (Z.Q.); (Z.M.)
- Life Science and Engineering College, Northwest Minzu University, Lanzhou 730030, China;
| | - Zhenyu Qiu
- Gansu Tech Innovation Center of Animal Cell, Biomedical Research Center, Northwest Minzu University, Lanzhou 730030, China; (Y.L.); (S.G.); (G.L.); (Z.Q.); (J.W.); (D.Y.); (Z.Q.); (Z.M.)
- Life Science and Engineering College, Northwest Minzu University, Lanzhou 730030, China;
| | - Jiamin Wang
- Gansu Tech Innovation Center of Animal Cell, Biomedical Research Center, Northwest Minzu University, Lanzhou 730030, China; (Y.L.); (S.G.); (G.L.); (Z.Q.); (J.W.); (D.Y.); (Z.Q.); (Z.M.)
- Key Laboratory of Biotechnology & Bioengineering of State Ethnic Affairs Commission, Biomedical Research Center, Northwest Minzu University, Lanzhou 730030, China
| | - Di Yang
- Gansu Tech Innovation Center of Animal Cell, Biomedical Research Center, Northwest Minzu University, Lanzhou 730030, China; (Y.L.); (S.G.); (G.L.); (Z.Q.); (J.W.); (D.Y.); (Z.Q.); (Z.M.)
- Key Laboratory of Biotechnology & Bioengineering of State Ethnic Affairs Commission, Biomedical Research Center, Northwest Minzu University, Lanzhou 730030, China
| | - Xiaojing Tian
- Life Science and Engineering College, Northwest Minzu University, Lanzhou 730030, China;
- Key Laboratory of Biotechnology & Bioengineering of State Ethnic Affairs Commission, Biomedical Research Center, Northwest Minzu University, Lanzhou 730030, China
| | - Ziling Qiao
- Gansu Tech Innovation Center of Animal Cell, Biomedical Research Center, Northwest Minzu University, Lanzhou 730030, China; (Y.L.); (S.G.); (G.L.); (Z.Q.); (J.W.); (D.Y.); (Z.Q.); (Z.M.)
- Key Laboratory of Biotechnology & Bioengineering of State Ethnic Affairs Commission, Biomedical Research Center, Northwest Minzu University, Lanzhou 730030, China
| | - Zhongren Ma
- Gansu Tech Innovation Center of Animal Cell, Biomedical Research Center, Northwest Minzu University, Lanzhou 730030, China; (Y.L.); (S.G.); (G.L.); (Z.Q.); (J.W.); (D.Y.); (Z.Q.); (Z.M.)
- Key Laboratory of Biotechnology & Bioengineering of State Ethnic Affairs Commission, Biomedical Research Center, Northwest Minzu University, Lanzhou 730030, China
| | - Zhenbin Liu
- Gansu Tech Innovation Center of Animal Cell, Biomedical Research Center, Northwest Minzu University, Lanzhou 730030, China; (Y.L.); (S.G.); (G.L.); (Z.Q.); (J.W.); (D.Y.); (Z.Q.); (Z.M.)
- Key Laboratory of Biotechnology & Bioengineering of State Ethnic Affairs Commission, Biomedical Research Center, Northwest Minzu University, Lanzhou 730030, China
- Correspondence:
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Sajjad N, Wang S, Liu P, Chen JL, Chi X, Liu S, Ma S. Functional Roles of Non-coding RNAs in the Interaction Between Host and Influenza A Virus. Front Microbiol 2021; 12:742984. [PMID: 34745043 PMCID: PMC8569443 DOI: 10.3389/fmicb.2021.742984] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2021] [Accepted: 10/04/2021] [Indexed: 11/13/2022] Open
Abstract
Non-coding RNAs (ncRNAs) are extensively expressed in various cells and tissues, and studies have shown that ncRNAs play significant roles in cell regulation. However, in the past few decades, the knowledge of ncRNAs has been increased dramatically due to their transcriptional ability and multiple regulatory functions. Typically, regulatory ncRNAs include long ncRNAs (lncRNAs), miRNAs, piRNAs, Y RNAs, vault RNAs, and circular RNAs (circRNAs), etc. Previous studies have revealed that various ncRNAs are involved in the host responses to virus infection and play critical roles in the regulation of host-virus interactions. In this review, we discuss the conceptual framework and biological regulations of ncRNAs to elucidate their functions in response to viral infection, especially influenza A virus (IAV) infection. In addition, we summarize the ncRNAs that are associated with innate immunity and involvement of interferons and their stimulated genes (ISGs) during IAV infection.
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Affiliation(s)
- Nelam Sajjad
- Key Laboratory of Fujian-Taiwan Animal Pathogen Biology, College of Animal Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Song Wang
- Key Laboratory of Fujian-Taiwan Animal Pathogen Biology, College of Animal Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Ping Liu
- Key Laboratory of Fujian-Taiwan Animal Pathogen Biology, College of Animal Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Ji-Long Chen
- Key Laboratory of Fujian-Taiwan Animal Pathogen Biology, College of Animal Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Xiaojuan Chi
- Key Laboratory of Fujian-Taiwan Animal Pathogen Biology, College of Animal Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Shasha Liu
- Key Laboratory of Fujian-Taiwan Animal Pathogen Biology, College of Animal Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Shujie Ma
- Key Laboratory of Fujian-Taiwan Animal Pathogen Biology, College of Animal Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
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