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Chi X, Huang G, Wang L, Zhang X, Liu J, Yin Z, Guo G, Chen Y, Wang S, Chen JL. A small protein encoded by PCBP1-AS1 is identified as a key regulator of influenza virus replication via enhancing autophagy. PLoS Pathog 2024; 20:e1012461. [PMID: 39137200 PMCID: PMC11343454 DOI: 10.1371/journal.ppat.1012461] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2024] [Revised: 08/23/2024] [Accepted: 07/29/2024] [Indexed: 08/15/2024] Open
Abstract
Many annotated long noncoding RNAs (lncRNAs) contain small open reading frames (sORFs), some of which have been demonstrated to encode small proteins or micropeptides with fundamental biological importance. However, functions of lncRNAs-encoded small proteins or micropeptides in viral pathogenesis remain largely unexplored. Here, we identified a 110-amino acid small protein as a key regulator of influenza A virus (IAV) replication. This small protein that we call PESP was encoded by the putative lncRNA PCBP1-AS1. It was observed that both PCBP1-AS1 and PESP were significantly upregulated by IAV infection. Furthermore, they were markedly induced by treatment with either type I or type III interferon. Overexpression of either PCBP1-AS1 or PESP alone significantly enhanced IAV replication. In contrast, shRNA-mediated knockdown of PCBP1-AS1 or CRISPR/Cas9-mediated knockout of PESP markedly inhibited the viral production. Moreover, the targeted deletion or mutation of the sORF within the PCBP1-AS1 transcript, which resulted in the disruption of PESP expression, significantly diminished the capacity of PCBP1-AS1 to enhance IAV replication, underscoring the indispensable role of PESP in the facilitation of IAV replication by PCBP1-AS1. Interestingly, overexpression of PESP enhanced the IAV-induced autophagy by increasing the expression of ATG7, an essential autophagy effector enzyme. We also found that the 7-22 amino acids at the N-terminus of PESP were crucial for its functionality in modulating ATG7 expression and action as an enhancer of IAV replication. Additionally, HSP90AA1, a protein identified previously as a facilitator of autophagy, was found to interact with PESP, resulting in the stabilization of PESP and consequently an increase in the production of IAV. These data reveal a critical lncRNA-encoded small protein that is induced and exploited by IAV during its infection, and provide a significant insight into IAV-host interaction network.
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Affiliation(s)
- Xiaojuan Chi
- Fujian Agriculture and Forestry University, Fuzhou, China
- Key Laboratory of Animal Pathogen Infection and Immunology of Fujian Province, College of Animal Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
- Key Laboratory of Fujian-Taiwan Animal Pathogen Biology, College of Animal Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Guiying Huang
- Fujian Agriculture and Forestry University, Fuzhou, China
- Key Laboratory of Animal Pathogen Infection and Immunology of Fujian Province, College of Animal Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Liwei Wang
- Fujian Agriculture and Forestry University, Fuzhou, China
- Key Laboratory of Animal Pathogen Infection and Immunology of Fujian Province, College of Animal Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Xinge Zhang
- Fujian Agriculture and Forestry University, Fuzhou, China
- Key Laboratory of Animal Pathogen Infection and Immunology of Fujian Province, College of Animal Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Jiayin Liu
- Fujian Agriculture and Forestry University, Fuzhou, China
- Key Laboratory of Fujian-Taiwan Animal Pathogen Biology, College of Animal Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Zhihui Yin
- Fujian Agriculture and Forestry University, Fuzhou, China
- Key Laboratory of Fujian-Taiwan Animal Pathogen Biology, College of Animal Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Guijie Guo
- Fujian Agriculture and Forestry University, Fuzhou, China
- Key Laboratory of Animal Pathogen Infection and Immunology of Fujian Province, College of Animal Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
- Key Laboratory of Fujian-Taiwan Animal Pathogen Biology, College of Animal Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Yuhai Chen
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Song Wang
- Fujian Agriculture and Forestry University, Fuzhou, China
- Key Laboratory of Animal Pathogen Infection and Immunology of Fujian Province, College of Animal Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
- Key Laboratory of Fujian-Taiwan Animal Pathogen Biology, College of Animal Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Ji-Long Chen
- Fujian Agriculture and Forestry University, Fuzhou, China
- Key Laboratory of Animal Pathogen Infection and Immunology of Fujian Province, College of Animal Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
- Key Laboratory of Fujian-Taiwan Animal Pathogen Biology, College of Animal Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
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Suleiman AA, Al-Chalabi R, Shaban SA. Integrative role of small non-coding RNAs in viral immune response: a systematic review. Mol Biol Rep 2024; 51:107. [PMID: 38227137 DOI: 10.1007/s11033-023-09141-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2023] [Accepted: 12/11/2023] [Indexed: 01/17/2024]
Abstract
Various viruses cause viral infection, and these viruses have different microscopic sizes, genetic material, and morphological forms. Due to a viral infection, the host body induces defense mechanisms that activate the innate and adaptive immune system. sncRNAs are involved in various biological processes and play an essential role in antiviral response in viruses including ZIKV, HCV, DENV, SARS-CoV, and West Nile virus, and regulate the complex interactions between the viruses and host cells. This review discusses the role of miRNAs, siRNAs, piRNAs, and tiRNAs in antiviral response. Cellular miRNAs bind with virus mRNA and perform their antiviral response in multiple viruses. However, the chemical modifications of miRNA necessary to avoid nuclease attack, which is then involved with intracellular processing, have proven challenging for therapeutic replacement of miRNAs. siRNAs have significant antiviral responses by targeting any gene of interest along the correct nucleotide of targeting mRNA. Due to this ability, siRNAs have valuable characteristics in antiviral response for therapeutic purposes. Additionally, the researchers noted the involvement of piRNAs and tiRNAs in the antiviral response, yet their findings were deemed insignificant.
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Affiliation(s)
| | | | - Semaa A Shaban
- Biology Department, College of Sciences, Tikrit University, Tikrit, Iraq
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Sun M, Fan X, Long Q, Zang H, Zhang Y, Liu X, Feng P, Song Y, Li K, Wu Y, Jiang H, Chen D, Guo R. First Characterization and Regulatory Function of piRNAs in the Apis mellifera Larval Response to Ascosphaera apis Invasion. Int J Mol Sci 2023; 24:16358. [PMID: 38003547 PMCID: PMC10671575 DOI: 10.3390/ijms242216358] [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: 09/21/2023] [Revised: 11/09/2023] [Accepted: 11/12/2023] [Indexed: 11/26/2023] Open
Abstract
piRNAs are a class of small non-coding RNAs that play essential roles in modulating gene expression and abundant biological processes. To decode the piRNA-regulated larval response of western honeybees (Apis mellifera) to Ascosphaera apis infection, the expression pattern of piRNAs in Apis mellifera ligustica larval guts after A. apis inoculation was analyzed based on previously obtained high-quality small RNA-seq datasets, followed by structural characterization, target prediction, regulatory network investigation, and functional dissection. Here, 504, 657, and 587 piRNAs were respectively identified in the 4-, 5-, and 6-day-old larval guts after inoculation with A. apis, with 411 ones shared. These piRNAs shared a similar length distribution and first base bias with mammal piRNAs. Additionally, 96, 103, and 143 DEpiRNAs were detected in the 4-, 5-, and 6-day-old comparison groups. Targets of the DEpiRNAs were engaged in diverse pathways such as the phosphatidylinositol signaling system, inositol phosphate metabolism, and Wnt signaling pathway. These targets were involved in three energy metabolism-related pathways, eight development-associated signaling pathways, and seven immune-relevant pathways such as the Jak-STAT signaling pathway. The expression trends of five randomly selected DEpiRNAs were verified using a combination of RT-PCR and RT-qPCR. The effective overexpression and knockdown of piR-ame-945760 in A. apis-infected larval guts were achieved by feeding a specific mimic and inhibitor. Furthermore, piR-ame-945760 negatively regulated the expression of two target immune mRNAs, SOCS5 and ARF1, in the larval gut during the A. apis infection. These findings indicated that the overall expression level of piRNAs was increased and the expression pattern of piRNAs in larval guts was altered due to the A. apis infection, DEpiRNAs were putative regulators in the A. apis-response of A. m. ligustica worker larvae. Our data provide not only a platform for the functional investigation of piRNAs in honeybees, especially in bee larvae, but also a foundation for illuminating the piRNA-involved mechanisms underlying the host response to the A. apis infection.
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Affiliation(s)
- Minghui Sun
- College of Animal Sciences (College of Bee Science), Fujian Agriculture and Forestry University, Fuzhou 350002, China; (M.S.); (X.F.); (Q.L.); (H.Z.); (Y.Z.); (X.L.); (P.F.); (Y.S.); (K.L.); (D.C.)
| | - Xiaoxue Fan
- College of Animal Sciences (College of Bee Science), Fujian Agriculture and Forestry University, Fuzhou 350002, China; (M.S.); (X.F.); (Q.L.); (H.Z.); (Y.Z.); (X.L.); (P.F.); (Y.S.); (K.L.); (D.C.)
| | - Qi Long
- College of Animal Sciences (College of Bee Science), Fujian Agriculture and Forestry University, Fuzhou 350002, China; (M.S.); (X.F.); (Q.L.); (H.Z.); (Y.Z.); (X.L.); (P.F.); (Y.S.); (K.L.); (D.C.)
| | - He Zang
- College of Animal Sciences (College of Bee Science), Fujian Agriculture and Forestry University, Fuzhou 350002, China; (M.S.); (X.F.); (Q.L.); (H.Z.); (Y.Z.); (X.L.); (P.F.); (Y.S.); (K.L.); (D.C.)
| | - Yiqiong Zhang
- College of Animal Sciences (College of Bee Science), Fujian Agriculture and Forestry University, Fuzhou 350002, China; (M.S.); (X.F.); (Q.L.); (H.Z.); (Y.Z.); (X.L.); (P.F.); (Y.S.); (K.L.); (D.C.)
| | - Xiaoyu Liu
- College of Animal Sciences (College of Bee Science), Fujian Agriculture and Forestry University, Fuzhou 350002, China; (M.S.); (X.F.); (Q.L.); (H.Z.); (Y.Z.); (X.L.); (P.F.); (Y.S.); (K.L.); (D.C.)
| | - Peilin Feng
- College of Animal Sciences (College of Bee Science), Fujian Agriculture and Forestry University, Fuzhou 350002, China; (M.S.); (X.F.); (Q.L.); (H.Z.); (Y.Z.); (X.L.); (P.F.); (Y.S.); (K.L.); (D.C.)
| | - Yuxuan Song
- College of Animal Sciences (College of Bee Science), Fujian Agriculture and Forestry University, Fuzhou 350002, China; (M.S.); (X.F.); (Q.L.); (H.Z.); (Y.Z.); (X.L.); (P.F.); (Y.S.); (K.L.); (D.C.)
| | - Kunze Li
- College of Animal Sciences (College of Bee Science), Fujian Agriculture and Forestry University, Fuzhou 350002, China; (M.S.); (X.F.); (Q.L.); (H.Z.); (Y.Z.); (X.L.); (P.F.); (Y.S.); (K.L.); (D.C.)
| | - Ying Wu
- Apiculture Science Institute of Jilin Province, Jilin 132000, China; (Y.W.); (H.J.)
| | - Haibin Jiang
- Apiculture Science Institute of Jilin Province, Jilin 132000, China; (Y.W.); (H.J.)
| | - Dafu Chen
- College of Animal Sciences (College of Bee Science), Fujian Agriculture and Forestry University, Fuzhou 350002, China; (M.S.); (X.F.); (Q.L.); (H.Z.); (Y.Z.); (X.L.); (P.F.); (Y.S.); (K.L.); (D.C.)
- National & Local United Engineering Laboratory of Natural Biotoxin, Fuzhou 350002, China
- Apitherapy Research Institute of Fujian Province, Fuzhou 350002, China
| | - Rui Guo
- College of Animal Sciences (College of Bee Science), Fujian Agriculture and Forestry University, Fuzhou 350002, China; (M.S.); (X.F.); (Q.L.); (H.Z.); (Y.Z.); (X.L.); (P.F.); (Y.S.); (K.L.); (D.C.)
- National & Local United Engineering Laboratory of Natural Biotoxin, Fuzhou 350002, China
- Apitherapy Research Institute of Fujian Province, Fuzhou 350002, China
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Zhang Y, Yang J, Liu P, Zhang RJ, Li JD, Bi YH, Li Y. Regulatory role of ncRNAs in pulmonary epithelial and endothelial barriers: Molecular therapy clues of influenza-induced acute lung injury. Pharmacol Res 2022; 185:106509. [DOI: 10.1016/j.phrs.2022.106509] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/31/2022] [Revised: 09/23/2022] [Accepted: 10/10/2022] [Indexed: 10/31/2022]
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Yang Y, Li M, Ma Y, Ye W, Si Y, Zheng X, Liu H, Cheng L, Zhang L, Zhang H, Zhang X, Lei Y, Shen L, Zhang F, Ma H. LncRNA NEAT1 Potentiates SREBP2 Activity to Promote Inflammatory Macrophage Activation and Limit Hantaan Virus Propagation. Front Microbiol 2022; 13:849020. [PMID: 35495674 PMCID: PMC9044491 DOI: 10.3389/fmicb.2022.849020] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2022] [Accepted: 03/10/2022] [Indexed: 11/17/2022] Open
Abstract
As the global prototypical zoonotic hantavirus, Hantaan virus (HTNV) is prevalent in Asia and is the leading causative agent of severe hemorrhagic fever with renal syndrome (HFRS), which has profound morbidity and mortality. Macrophages are crucial components of the host innate immune system and serve as the first line of defense against HTNV infection. Previous studies indicated that the viral replication efficiency in macrophages determines hantavirus pathogenicity, but it remains unknown which factor manipulates the macrophage activation pattern and the virus-host interaction process. Here, we performed the transcriptomic analysis of HTNV-infected mouse bone marrow-derived macrophages and identified the long noncoding RNA (lncRNA) nuclear enriched abundant transcript 1 (NEAT1), especially the isoform NEAT1-2, as one of the lncRNAs that is differentially expressed at the early phase. Based on coculture experiments, we revealed that silencing NEAT1-2 hinders inflammatory macrophage activation and facilitates HTNV propagation, while enhancing NEAT1-2 transcription effectively restrains viral replication. Furthermore, sterol response element binding factor-2 (SREBP2), which controls the cholesterol metabolism process, was found to stimulate macrophages by promoting the production of multiple inflammatory cytokines upon HTNV infection. NEAT1-2 could potentiate SREBP2 activity by upregulating Srebf1 expression and interacting with SREBP2, thus stimulating inflammatory macrophages and limiting HTNV propagation. More importantly, we demonstrated that the NEAT1-2 expression level in patient monocytes was negatively correlated with viral load and HFRS disease progression. Our results identified a function and mechanism of action for the lncRNA NEAT1 in heightening SREBP2-mediated macrophage activation to restrain hantaviral propagation and revealed the association of NEAT1 with HFRS severity.
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Affiliation(s)
- Yongheng Yang
- College of Life Sciences, Northwest University, Xi'an, China.,Department of Microbiology, School of Basic Medicine, The Fourth Military Medical University, Xi'an, China
| | - Mengyun Li
- College of Life Sciences, Northwest University, Xi'an, China.,Department of Microbiology, School of Basic Medicine, The Fourth Military Medical University, Xi'an, China
| | - Yongtao Ma
- Department of Emergency, Children's Hospital of Kaifeng City, Kaifeng, China
| | - Wei Ye
- Department of Microbiology, School of Basic Medicine, The Fourth Military Medical University, Xi'an, China
| | - Yue Si
- Department of Microbiology, School of Basic Medicine, The Fourth Military Medical University, Xi'an, China
| | - Xuyang Zheng
- Department of Microbiology, School of Basic Medicine, The Fourth Military Medical University, Xi'an, China.,Department of Infectious Diseases, Tangdu Hospital, The Fourth Military Medical University, Xi'an, China
| | - He Liu
- Department of Microbiology, School of Basic Medicine, The Fourth Military Medical University, Xi'an, China
| | - Linfeng Cheng
- Department of Microbiology, School of Basic Medicine, The Fourth Military Medical University, Xi'an, China
| | - Liang Zhang
- Department of Microbiology, School of Basic Medicine, The Fourth Military Medical University, Xi'an, China
| | - Hui Zhang
- Department of Microbiology, School of Basic Medicine, The Fourth Military Medical University, Xi'an, China
| | - Xijing Zhang
- Department of Anesthesiology and Critical Care Medicine, Xijing Hospital, The Fourth Military Medical University, Xi'an, China
| | - Yingfeng Lei
- Department of Microbiology, School of Basic Medicine, The Fourth Military Medical University, Xi'an, China
| | - Lixin Shen
- College of Life Sciences, Northwest University, Xi'an, China
| | - Fanglin Zhang
- Department of Microbiology, School of Basic Medicine, The Fourth Military Medical University, Xi'an, China
| | - Hongwei Ma
- Department of Microbiology, School of Basic Medicine, The Fourth Military Medical University, Xi'an, China.,Department of Anesthesiology and Critical Care Medicine, Xijing Hospital, The Fourth Military Medical University, Xi'an, China
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