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Ma Y, Guo X, He Q, Liu L, Li Z, Zhao X, Gu W, Zhong Q, Li N, Yao G, Ma X. Integrated analysis of microRNA and messenger RNA expression profiles reveals functional microRNA in infectious bovine rhinotracheitis virus-induced mitochondrial damage in Madin-Darby bovine kidney cells. BMC Genomics 2024; 25:158. [PMID: 38331736 PMCID: PMC10851472 DOI: 10.1186/s12864-024-10042-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2023] [Accepted: 01/22/2024] [Indexed: 02/10/2024] Open
Abstract
BACKGROUND Studies have confirmed that Infectious bovine rhinotracheitis virus (IBRV) infection induces mitochondrial damage. MicroRNAs (miRNAs) are a class of noncoding RNA molecules, which are involved in various biological processes and pathological changes associated with mitochondrial damage. It is currently unclear whether miRNAs participate in IBRV-induced mitochondrial damage in Madin-Darby bovine kidney (MDBK) cells. RESULTS In the present study, we used high-throughput sequencing technology, Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis to screen for mitochondria-related miRNAs and messenger RNAs (mRNAs). In total, 279 differentially expressed miRNAs and 832 differentially expressed mRNAs were identified in 6 hours (IBRV1) versus 24 hours (IBRV2) after IBRV infection in MDBK cells. GO and KEGG enrichment analysis revealed that 42 differentially expressed mRNAs and 348 target genes of differentially expressed miRNAs were correlated with mitochondrial damage, and the miRNA-mitochondria-related target genes regulatory network was constructed to elucidate their potential regulatory relationships. Among the 10 differentially expressed miRNAs, 8 showed expression patterns consistent with the high-throughput sequencing results. Functional validation results showed that overexpression of miR-10a and miR-182 aggravated mitochondrial damage, while inhibition of miR-10a and miR-182 alleviated mitochondrial damage. CONCLUSIONS This study not only revealed the expression changes of miRNAs and mRNAs in IBRV-infected MDBK cells, but also revealed possible biological regulatory relationship between them. MiR-10a and miR-182 may have the potential to be developed as biomarkers for the diagnosis and treatment of IBRV. Together, Together, these data and analyses provide additional insights into the roles of miRNA and mRNA in IBRV-induced mitochondria damage.
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Affiliation(s)
- Yingcai Ma
- College of Veterinary Medicine, Xinjiang Agricultural University, Urumqi, 830052, China
- Xinjiang key Laboratory of New Drug Study and Creation for Herbivorous Animal (XJ-KLNDSCHA), Xinjiang Agricultural University, Urumqi, 830052, China
| | - Xueping Guo
- College of Veterinary Medicine, Xinjiang Agricultural University, Urumqi, 830052, China
- Xinjiang key Laboratory of New Drug Study and Creation for Herbivorous Animal (XJ-KLNDSCHA), Xinjiang Agricultural University, Urumqi, 830052, China
| | - Qin He
- College of Veterinary Medicine, Xinjiang Agricultural University, Urumqi, 830052, China
- Xinjiang key Laboratory of New Drug Study and Creation for Herbivorous Animal (XJ-KLNDSCHA), Xinjiang Agricultural University, Urumqi, 830052, China
| | - Lu Liu
- College of Veterinary Medicine, Xinjiang Agricultural University, Urumqi, 830052, China
- Xinjiang key Laboratory of New Drug Study and Creation for Herbivorous Animal (XJ-KLNDSCHA), Xinjiang Agricultural University, Urumqi, 830052, China
| | - Zelong Li
- College of Veterinary Medicine, Xinjiang Agricultural University, Urumqi, 830052, China
- Xinjiang key Laboratory of New Drug Study and Creation for Herbivorous Animal (XJ-KLNDSCHA), Xinjiang Agricultural University, Urumqi, 830052, China
| | - Xiaomin Zhao
- College of Veterinary Medicine, Northwest A & F University, Yangling, 712100, China
| | - Wenxi Gu
- Institute of Animal Science, Xinjiang Academy of Animal Sciences, Urumqi, 830011, China
| | - Qi Zhong
- Institute of Animal Science, Xinjiang Academy of Animal Sciences, Urumqi, 830011, China
| | - Na Li
- College of Veterinary Medicine, Xinjiang Agricultural University, Urumqi, 830052, China
- Xinjiang key Laboratory of New Drug Study and Creation for Herbivorous Animal (XJ-KLNDSCHA), Xinjiang Agricultural University, Urumqi, 830052, China
| | - Gang Yao
- College of Veterinary Medicine, Xinjiang Agricultural University, Urumqi, 830052, China.
- Xinjiang key Laboratory of New Drug Study and Creation for Herbivorous Animal (XJ-KLNDSCHA), Xinjiang Agricultural University, Urumqi, 830052, China.
| | - Xuelian Ma
- College of Veterinary Medicine, Xinjiang Agricultural University, Urumqi, 830052, China.
- Xinjiang key Laboratory of New Drug Study and Creation for Herbivorous Animal (XJ-KLNDSCHA), Xinjiang Agricultural University, Urumqi, 830052, China.
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Deng J, Wu Z, Liu J, Ji Q, Ju C. The Role of Latency-Associated Transcripts in the Latent Infection of Pseudorabies Virus. Viruses 2022; 14:v14071379. [PMID: 35891360 PMCID: PMC9320458 DOI: 10.3390/v14071379] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2022] [Revised: 06/22/2022] [Accepted: 06/22/2022] [Indexed: 11/16/2022] Open
Abstract
Pseudorabies virus (PRV) can cause neurological, respiratory, and reproductive diseases in pigs and establish lifelong latent infection in the peripheral nervous system (PNS). Latent infection is a typical feature of PRV, which brings great difficulties to the prevention, control, and eradication of pseudorabies. The integral mechanism of latent infection is still unclear. Latency-associated transcripts (LAT) gene is the only transcriptional region during latent infection of PRV which plays the key role in regulating viral latent infection and inhibiting apoptosis. Here, we review the characteristics of PRV latent infection and the transcriptional characteristics of the LAT gene. We also analyzed the function of non-coding RNA (ncRNA) produced by the LAT gene and its importance in latent infection. Furthermore, we provided possible strategies to solve the problem of latent infection of virulent PRV strains in the host. In short, the detailed mechanism of PRV latent infection needs to be further studied and elucidated.
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Hoffmann W, Lipińska AD, Bieńkowska-Szewczyk K. Functional Analysis of a Frontal miRNA Cluster Located in the Large Latency Transcript of Pseudorabies Virus. Viruses 2022; 14:v14061147. [PMID: 35746619 PMCID: PMC9227234 DOI: 10.3390/v14061147] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2022] [Revised: 05/19/2022] [Accepted: 05/24/2022] [Indexed: 01/28/2023] Open
Abstract
MicroRNAs (miRNAs) have been identified as a class of crucial regulators of virus-host crosstalk, modulating such processes as viral replication, antiviral immune response, viral latency, and pathogenesis. Pseudorabies virus (PRV), a model for the study of alphaherpesvirus biology, codes for 11 distinct miRNAs mapped to the ~4.6 kb intron of Large Latency Transcript (LLT). Recent studies have revealed the role of clusters consisting of nine and eleven miRNA genes in the replication and virulence of PRV. The function of separate miRNA species in regulating PRV biology has not been thoroughly investigated. To analyze the regulatory potential of three PRV miRNAs located in the frontal cluster of the LLT intron, we generated a research model based on the constitutive expression of viral miRNAs in swine testis cells (ST_LLT [1–3] cell line). Using a cell culture system providing a stable production of individual miRNAs at high levels, we demonstrated that the LLT [1–3] miRNA cluster significantly downregulated IE180, EP0, and gE at the early stages of PRV infection. It was further determined that LLT [1–3] miRNAs could regulate the infection process, leading to a slight distortion in transmission and proliferation ability. Collectively, our findings indicate the potential of LLT [1–3] miRNAs to retard the host responses by reducing viral antigenic load and suppressing the expansion of progeny viruses at the early stages of infection.
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He W, Li C, Dong L, Yang G, Liu H. Tandem Mass Tag-Based Quantitative Proteomic Analysis of ISG15 Knockout PK15 Cells in Pseudorabies Virus Infection. Genes (Basel) 2021; 12:genes12101557. [PMID: 34680952 PMCID: PMC8535405 DOI: 10.3390/genes12101557] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2021] [Revised: 09/14/2021] [Accepted: 09/28/2021] [Indexed: 12/24/2022] Open
Abstract
Pseudorabies virus (PRV) is recognized as one of the most important pathogens of swine and poses a serious threat to the swine industry worldwide. Available commercial vaccines fail to protect against the emergence of new PRV strains. Therefore, the new protein targets against PRV highlight the urgent need for uncovering the molecular determinants of host cellular proteins following PRV infection. Interferon-stimulated gene 15 (ISG15) demonstrates an outstanding antiviral response. However, the molecular mechanism of ISG15 that affects PRV replication is incompletely known. Here, we performed a tandem mass tag (TMT)-based approach to quantitatively identify protein expression changes in PRV-infected ISG15 knockout PK15 (ISG15−/−-PK15) cells. In total, 4958 proteins were identified by using TMT coupled with LC-MS/MS in this study. In the PRV- and mock-infected groups, 241 differentially expressed proteins (DEPs) were identified, 162 upregulated and 79 downregulated proteins at 24 h post-infection (hpi), among which AFP, Vtn, Hsp40, Herc5, and Mccc1 may play important roles in PRV propagation. To ensure the validity and reliability of the proteomics data, the randomly selected DEPs were verified by RT-qPCR and Western blot analysis, and the results were consistent with the TMT results. Bioinformatics analyses further demonstrated that the DEPs are mainly involved in various biological processes and signaling pathways, such as signal transduction, the digestive system, and the PI3K-AKT pathway. These findings may provide new insight into molecular mechanisms for PRV infection, which is helpful for identifying potential protein targets for antiviral agents.
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Fang L, Gao Y, Liu X, Bai J, Jiang P, Wang X. Long non-coding RNA LNC_000641 regulates pseudorabies virus replication. Vet Res 2021; 52:52. [PMID: 33766129 PMCID: PMC7992786 DOI: 10.1186/s13567-021-00922-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2020] [Accepted: 03/01/2021] [Indexed: 01/06/2023] Open
Abstract
Long non-coding RNAs (lncRNAs) are a new arm of gene regulatory mechanism as discovered by sequencing techniques and follow-up functional studies. The lncRNAs regulation of pseudorabies virus (PRV) infection has rarely been reported so far. Using RNA sequencing analysis, 225 lncRNAs with significant altered expressions in 3D4/21 cells infected with PRV (ZJ01) were identified. Five lncRNAs upregulated in PRV-infected cells were verified in cells infected with different PRV strains by qRT-PCR. By down- and up-regulation of lnc641, the accelerating effect of lnc641 on PRV replication was confirmed. Furthermore, we found that lnc641 regulated PRV replication by inhibiting the JAK-STAT1 pathway. This study suggests that lnc641 could be a new host factor target for developing antiviral therapies against PRV infection.
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Affiliation(s)
- Linlin Fang
- Key Laboratory of Animal Diseases Diagnostic and Immunology, Ministry of Agriculture, MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, 210095, China
| | - Yanni Gao
- Key Laboratory of Animal Diseases Diagnostic and Immunology, Ministry of Agriculture, MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, 210095, China.,Jiangsu Co-Innovation Center for the Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, 225009, China
| | - Xing Liu
- Key Laboratory of Animal Diseases Diagnostic and Immunology, Ministry of Agriculture, MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, 210095, China.,Jiangsu Co-Innovation Center for the Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, 225009, China
| | - Juan Bai
- Key Laboratory of Animal Diseases Diagnostic and Immunology, Ministry of Agriculture, MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, 210095, China.,Jiangsu Co-Innovation Center for the Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, 225009, China
| | - Ping Jiang
- Key Laboratory of Animal Diseases Diagnostic and Immunology, Ministry of Agriculture, MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, 210095, China.,Jiangsu Co-Innovation Center for the Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, 225009, China
| | - XianWei Wang
- Key Laboratory of Animal Diseases Diagnostic and Immunology, Ministry of Agriculture, MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, 210095, China. .,Jiangsu Co-Innovation Center for the Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, 225009, China.
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Lan J, Zhang R, Yu H, Wang J, Xue W, Chen J, Lin S, Wang Y, Xie Z, Jiang S. Quantitative Proteomic Analysis Uncovers the Mediation of Endoplasmic Reticulum Stress-Induced Autophagy in DHAV-1-Infected DEF Cells. Int J Mol Sci 2019; 20:ijms20246160. [PMID: 31817666 PMCID: PMC6940786 DOI: 10.3390/ijms20246160] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2019] [Revised: 12/03/2019] [Accepted: 12/04/2019] [Indexed: 12/11/2022] Open
Abstract
Autophagy is a tightly regulated catabolic process and is activated in cells in response to stress signals. Despite extensive study, the interplay between duck hepatitis A virus type 1 (DHAV-1) and the autophagy of host cells is not clear. In this study, we applied proteomics analysis to investigate the interaction mechanism between DHAV-1 and duck embryo fibroblast (DEF) cells. In total, 507 differentially expressed proteins (DEPs) were identified, with 171 upregulated proteins and 336 downregulated proteins. The protein expression level of heat shock proteins (Hsps) and their response to stimulus proteins and zinc finger proteins (ZFPs) were significantly increased while the same aspects of ribosome proteins declined. Bioinformatics analysis indicated that DEPs were mainly involved in the “response to stimulus”, the “defense response to virus”, and the “phagosome pathway”. Furthermore, Western blot results showed that the conversion of microtubule-associated protein 1 light chain 3-I (LC3-I) to the lipidation form of LC3-II increased, and the conversion rate decreased when DEF cells were processed with 4-phenylbutyrate (4-PBA). These findings indicated that DHAV-1 infection could cause endoplasmic reticulum (ER) stress-induced autophagy in DEF cells, and that ER stress was an important regulatory factor in the activation of autophagy. Our data provide a new clue regarding the host cell response to DHAV-1 and identify proteins involved in the DHAV-1 infection process or the ER stress-induced autophagy process.
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Affiliation(s)
- Jingjing Lan
- College of Veterinary Medicine, Shandong Agricultural University, Taian 271000, China; (J.L.); (R.Z.); (H.Y.); (J.W.); (W.X.); (J.C.); (Z.X.)
- Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, Taian 271000, China
| | - Ruihua Zhang
- College of Veterinary Medicine, Shandong Agricultural University, Taian 271000, China; (J.L.); (R.Z.); (H.Y.); (J.W.); (W.X.); (J.C.); (Z.X.)
- Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, Taian 271000, China
| | - Honglei Yu
- College of Veterinary Medicine, Shandong Agricultural University, Taian 271000, China; (J.L.); (R.Z.); (H.Y.); (J.W.); (W.X.); (J.C.); (Z.X.)
- Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, Taian 271000, China
| | - Jingyu Wang
- College of Veterinary Medicine, Shandong Agricultural University, Taian 271000, China; (J.L.); (R.Z.); (H.Y.); (J.W.); (W.X.); (J.C.); (Z.X.)
- Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, Taian 271000, China
| | - Wenxiang Xue
- College of Veterinary Medicine, Shandong Agricultural University, Taian 271000, China; (J.L.); (R.Z.); (H.Y.); (J.W.); (W.X.); (J.C.); (Z.X.)
- Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, Taian 271000, China
| | - Junhao Chen
- College of Veterinary Medicine, Shandong Agricultural University, Taian 271000, China; (J.L.); (R.Z.); (H.Y.); (J.W.); (W.X.); (J.C.); (Z.X.)
- College of Public Health and Management, Weifang Medical University, Weifang 261042, China
| | - Shaoli Lin
- Molecular Virology Laboratory, VA-MD College of Veterinary Medicine and Maryland Pathogen Research Institute, University of Maryland, College Park, MD 20742, USA;
| | - Yu Wang
- Department of Basic Medical Sciences, Taishan Medical College, Taian 271000, China;
| | - Zhijing Xie
- College of Veterinary Medicine, Shandong Agricultural University, Taian 271000, China; (J.L.); (R.Z.); (H.Y.); (J.W.); (W.X.); (J.C.); (Z.X.)
- Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, Taian 271000, China
| | - Shijin Jiang
- College of Veterinary Medicine, Shandong Agricultural University, Taian 271000, China; (J.L.); (R.Z.); (H.Y.); (J.W.); (W.X.); (J.C.); (Z.X.)
- Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, Taian 271000, China
- Correspondence: ; Tel.: +86-538-8245799
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Guan X, Liu J, Jiang H, Wu CX, Chen HC, Liu ZF. Expression of pseudorabies virus-encoded long noncoding RNAs in epithelial cells and neurons. J Neurovirol 2018; 24:597-605. [PMID: 29987580 DOI: 10.1007/s13365-018-0651-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2017] [Revised: 05/18/2018] [Accepted: 05/23/2018] [Indexed: 11/30/2022]
Abstract
Long noncoding RNAs (lncRNAs) play important roles in regulating eukaryotic genome replication and gene expression in diverse biological systems. Here, we identified lncRNAs transcribed from pseudorabies virus (PRV)-infected PK-15 cells. Based on high-throughput sequencing data, we obtained 87,263,926 and 93,947,628 clean reads from mock-infected and PRV-infected PK-15 cells, respectively. Through a normalized analytic protocol, we identified three novel viral lncRNAs. According to an analysis of differential expression between the mock-infected and PRV-infected cells, 4151 host lncRNAs were significantly upregulated and 2327 host lncRNAs were significantly downregulated in the latter group. Viral lncRNAs and several host lncRNAs were verified by northern blotting and real-time PCR. The findings showed that the viral lncRNA LDI might regulate the expression of IE180, a potent transcriptional activator of viral genes. Furthermore, we characterized the expression of viral lncRNAs in a culture of infected primary chicken dorsal root ganglia (DRG). Collectively, the obtained data suggest that PRV generates lncRNAs in both epithelial cells and chick DRG neurons.
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Affiliation(s)
- Xiang Guan
- State Key Laboratory of Agricultural Microbiology and Key Laboratory of Preventive Veterinary Medicine in Hubei Province, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, 430070, China
| | - Jie Liu
- State Key Laboratory of Agricultural Microbiology and Key Laboratory of Preventive Veterinary Medicine in Hubei Province, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, 430070, China
| | - Hui Jiang
- State Key Laboratory of Agricultural Microbiology and Key Laboratory of Preventive Veterinary Medicine in Hubei Province, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, 430070, China
| | - Chang-Xian Wu
- State Key Laboratory of Agricultural Microbiology and Key Laboratory of Preventive Veterinary Medicine in Hubei Province, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, 430070, China
| | - Huan-Chun Chen
- State Key Laboratory of Agricultural Microbiology and Key Laboratory of Preventive Veterinary Medicine in Hubei Province, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, 430070, China
| | - Zheng-Fei Liu
- State Key Laboratory of Agricultural Microbiology and Key Laboratory of Preventive Veterinary Medicine in Hubei Province, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, 430070, China.
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Li L, Gao F, Zheng H, Jiang Y, Tong W, Zhou Y, Tong G. Utilizing host endogenous microRNAs to negatively regulate the replication of porcine reproductive and respiratory syndrome virus in MARC-145 cells. PLoS One 2018; 13:e0200029. [PMID: 29969475 PMCID: PMC6029797 DOI: 10.1371/journal.pone.0200029] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2018] [Accepted: 06/17/2018] [Indexed: 01/22/2023] Open
Abstract
MicroRNAs (miRNAs) contribute to gene regulation at the post-transcriptional level and are capable of mRNA silencing by binding to target sites exhibiting high degrees of complementarity. Therefore, cloning host miRNA-recognition sequences into the genome of RNA viruses represents a rational strategy for manipulating viral replication. Here, we performed deep sequencing to obtain small-RNA (sRNA)-expression profiles from in vitro-cultured MARC-145 cells post infection with porcine reproductive and respiratory syndrome virus (PRRSV) and chose six candidate miRNAs of different abundance (miR-21, miR-140-3p, miR-185, miR-26a, miR-505, and miR-199a) for further study. Based on the full-length cDNA clone p7USC, we constructed a number of PRRSV mutants that provided complementary base-pairing target sites for the miRNAs in 3′ untranslated regions. Our results showed that all low- and moderate- abundant miRNA-target mutants showed similar growth properties, whereas the highest-abundant miRNA-target mutant blocked both viral transcription and replication. Discontinuous mutations in high-abundant miRNA-target sites subsequently recovered viral viability and propagation. These results demonstrated the copy number of endogenous miRNAs and the extent of sRNA complementarity were key factors to silence potential mRNA expression/translation, thereby determining PRRSV viability. Interestingly, the mutant containing miR-140-target sites (v140-t) showed strong suppression of viral replication from P1 to P3 in vitro, as shown by virus titer, plaque morphology, and qRT-PCR assays. To assess genetic stability, sequencing of v140-t (P1, P3, P5 and P10) revealed spontaneous mutations preferentially located among several nucleotides near the 3′ end of the insertion region and corresponding to the “seed region” of miR-140-3p, explaining the induced viral repression and the direction of virus evolution. This approach provided a general silencing strategy for limiting PRRSV replication by endogenous miRNAs in MARC-145 cells.
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Affiliation(s)
- Liwei Li
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, PR China
| | - Fei Gao
- 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, PR China
| | - Hao Zheng
- 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, PR China
| | - Yifeng Jiang
- 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, PR China
| | - Wu Tong
- 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, PR China
| | - Yanjun Zhou
- 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, PR China
| | - Guangzhi Tong
- 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, PR China
- * E-mail:
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Wu X, Jia R, Zhou J, Wang M, Chen S, Liu M, Zhu D, Zhao X, Sun K, Yang Q, Wu Y, Yin Z, Chen X, Wang J, Cheng A. Virulent duck enteritis virus infected DEF cells generate a unique pattern of viral microRNAs and a novel set of host microRNAs. BMC Vet Res 2018; 14:144. [PMID: 29704894 PMCID: PMC5923184 DOI: 10.1186/s12917-018-1468-2] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2017] [Accepted: 04/20/2018] [Indexed: 12/12/2022] Open
Abstract
Background Duck enteritis virus (DEV) belongs to the family Herpesviridae and is an important epornitic agent that causes economic losses in the waterfowl industry. The Chinese virulent (CHv) and attenuate vaccines (VAC) are two different pathogenic DEV strains. MicroRNAs (miRNAs) are a class of non-coding RNAs that regulate gene expression in viral infection. Nonetheless, there is little information on virulent duck enteritis virus (DEV)-encoded miRNAs. Results Using high-throughput sequencing, we identified 39 mature viral miRNAs from CHv-infected duck embryo fibroblasts cells. Compared with the reported 33 VAC-encoded miRNAs, only 13 miRNA sequences and 22 “seed sequences” of miRNA were identical, and 8 novel viral miRNAs were detected and confirmed by stem-loop RT-qPCR in this study. Using RNAhybrid and PITA software, 38 CHv-encoded miRNAs were predicted to target 41 viral genes and formed a complex regulatory network. Dual luciferase reporter assay (DLRA) confirmed that viral dev-miR-D8-3p can directly target the 3’-UTR of CHv US1 gene (p < 0.05). Gene Ontology analysis on host target genes of viral miRNAs were mainly involved in biological regulation, cellular and metabolic processes. In addition, 598 novel duck-encoded miRNAs were detected in this study. Thirty-eight host miRNAs showed significant differential expression after CHv infection: 13 miRNAs were up-regulated, and 25 miRNAs were down-regulated, which may affect viral replication in the host cell. Conclusions These data suggested that CHv encoded a different set of microRNAs and formed a unique regulatory network compared with VAC. This is the first report of DEF miRNAs expression profile and an analysis of these miRNAs regulatory mechanisms during DEV infection. These data provide a basis for further exploring miRNA regulatory roles in the pathogenesis of DEV infection and contribute to the understanding of the CHv-host interaction at the miRNA level. Electronic supplementary material The online version of this article (10.1186/s12917-018-1468-2) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Xianglong Wu
- Research Center of Avian Disease, College of Veterinary, Medicine of Sichuan Agricultural University, Wenjiang District, Chengdu, 611130, Sichuan Province, China.,Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Wenjiang District, Chengdu, 611130, Sichuan Province, China
| | - Renyong Jia
- Research Center of Avian Disease, College of Veterinary, Medicine of Sichuan Agricultural University, Wenjiang District, Chengdu, 611130, Sichuan Province, China. .,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Wenjiang District, Chengdu, 611130, Sichuan Province, China. .,Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Wenjiang District, Chengdu, 611130, Sichuan Province, China.
| | - Jiakun Zhou
- Research Center of Avian Disease, College of Veterinary, Medicine of Sichuan Agricultural University, Wenjiang District, Chengdu, 611130, Sichuan Province, China.,Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Wenjiang District, Chengdu, 611130, Sichuan Province, China
| | - Mingshu Wang
- Research Center of Avian Disease, College of Veterinary, Medicine of Sichuan Agricultural University, Wenjiang District, Chengdu, 611130, Sichuan Province, China.,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Wenjiang District, Chengdu, 611130, Sichuan Province, China.,Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Wenjiang District, Chengdu, 611130, Sichuan Province, China
| | - Shun Chen
- Research Center of Avian Disease, College of Veterinary, Medicine of Sichuan Agricultural University, Wenjiang District, Chengdu, 611130, Sichuan Province, China.,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Wenjiang District, Chengdu, 611130, Sichuan Province, China.,Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Wenjiang District, Chengdu, 611130, Sichuan Province, China
| | - Mafeng Liu
- Research Center of Avian Disease, College of Veterinary, Medicine of Sichuan Agricultural University, Wenjiang District, Chengdu, 611130, Sichuan Province, China.,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Wenjiang District, Chengdu, 611130, Sichuan Province, China.,Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Wenjiang District, Chengdu, 611130, Sichuan Province, China
| | - Dekang Zhu
- Research Center of Avian Disease, College of Veterinary, Medicine of Sichuan Agricultural University, Wenjiang District, Chengdu, 611130, Sichuan Province, China.,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Wenjiang District, Chengdu, 611130, Sichuan Province, China.,Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Wenjiang District, Chengdu, 611130, Sichuan Province, China
| | - Xinxin Zhao
- Research Center of Avian Disease, College of Veterinary, Medicine of Sichuan Agricultural University, Wenjiang District, Chengdu, 611130, Sichuan Province, China.,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Wenjiang District, Chengdu, 611130, Sichuan Province, China.,Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Wenjiang District, Chengdu, 611130, Sichuan Province, China
| | - Kunfeng Sun
- Research Center of Avian Disease, College of Veterinary, Medicine of Sichuan Agricultural University, Wenjiang District, Chengdu, 611130, Sichuan Province, China.,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Wenjiang District, Chengdu, 611130, Sichuan Province, China.,Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Wenjiang District, Chengdu, 611130, Sichuan Province, China
| | - Qiao Yang
- Research Center of Avian Disease, College of Veterinary, Medicine of Sichuan Agricultural University, Wenjiang District, Chengdu, 611130, Sichuan Province, China.,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Wenjiang District, Chengdu, 611130, Sichuan Province, China.,Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Wenjiang District, Chengdu, 611130, Sichuan Province, China
| | - Ying Wu
- Research Center of Avian Disease, College of Veterinary, Medicine of Sichuan Agricultural University, Wenjiang District, Chengdu, 611130, Sichuan Province, China.,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Wenjiang District, Chengdu, 611130, Sichuan Province, China.,Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Wenjiang District, Chengdu, 611130, Sichuan Province, China
| | - Zhongqiong Yin
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Wenjiang District, Chengdu, 611130, Sichuan Province, China
| | - Xiaoyue Chen
- Research Center of Avian Disease, College of Veterinary, Medicine of Sichuan Agricultural University, Wenjiang District, Chengdu, 611130, Sichuan Province, China.,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Wenjiang District, Chengdu, 611130, Sichuan Province, China
| | - Jue Wang
- BGI Genomics Co,shenzhen Ltd, Shenzhen, 518083, Guangdong Province, China
| | - Anchun Cheng
- Research Center of Avian Disease, College of Veterinary, Medicine of Sichuan Agricultural University, Wenjiang District, Chengdu, 611130, Sichuan Province, China. .,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Wenjiang District, Chengdu, 611130, Sichuan Province, China. .,Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Wenjiang District, Chengdu, 611130, Sichuan Province, China.
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10
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Yang S, Pei Y, Zhao A. iTRAQ-based Proteomic Analysis of Porcine Kidney Epithelial PK15 cells Infected with Pseudorabies virus. Sci Rep 2017; 7:45922. [PMID: 28374783 PMCID: PMC5379687 DOI: 10.1038/srep45922] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2016] [Accepted: 03/03/2017] [Indexed: 12/18/2022] Open
Abstract
Pseudorabies virus (PRV) is one of the most important pathogens of swine, resulting in severe economic losses to the pig industry. To improve our understanding of the host responses to PRV infection, we applied isobaric tags for relative and absolute quantification (iTRAQ) labeling coupled with liquid chromatography-tandem mass spectrometry to quantitatively identify the differentially expressed cellular proteins in PRV-infected PK15 cells. In total, relative quantitative data were identified for 4333 proteins in PRV and mock- infected PK15 cells, among which 466 cellular proteins were differentially expressed, including 234 upregulated proteins and 232 downregulated proteins. Bioinformatics analysis disclosed that most of these differentially expressed proteins were involved in metabolic processes, cellular growth and proliferation, endoplasmic reticulum (ER) stress response, cell adhesion and cytoskeleton. Moreover, expression levels of four representative proteins, beta-catenin, STAT1, GRB2 and PCNA, were further confirmed by western blot analysis. This is the first attempt to analyze the protein profile of PRV-infected PK15 cells using iTRAQ technology, and our findings may provide valuable information to help understand the host response to PRV infection.
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Affiliation(s)
- Songbai Yang
- College of Animal Science and Technology, Zhejiang A&F University, Lin'an, Zhejiang 311300, China
| | - Yue Pei
- College of Animal Science and Technology, Zhejiang A&F University, Lin'an, Zhejiang 311300, China
| | - Ayong Zhao
- College of Animal Science and Technology, Zhejiang A&F University, Lin'an, Zhejiang 311300, China
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11
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Li Y, Zheng G, Zhang Y, Yang X, Liu H, Chang H, Wang X, Zhao J, Wang C, Chen L. MicroRNA analysis in mouse neuro-2a cells after pseudorabies virus infection. J Neurovirol 2017; 23:430-440. [PMID: 28130759 DOI: 10.1007/s13365-016-0511-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2016] [Revised: 12/23/2016] [Accepted: 12/29/2016] [Indexed: 11/30/2022]
Abstract
Pseudorabies virus (PRV), an alpha herpesvirus can enter the mammalian nervous system, causing Aujezsky's disease. Previous studies have reported an alteration of microRNA (miRNA) expression levels during PRV infections. However, knowledge regarding miRNA response in nervous cells to PRV infection is still unknown. To address this issue, small RNA libraries from infected and uninfected mouse neuroblastoma cells were assessed after Illumina deep sequencing. A total of eight viral miRNA were identified, and ten host miRNAs showed significantly different expression upon PRV infection. Among these, five were analyzed by stem-loop RT-qPCR, which confirmed the above data. Interestingly, these viral miRNAs were mainly found in the large latency transcript region of PRV, and predicted to target a variety of genes, forming a complicated regulatory network. Moreover, ten cellular miRNAs were expressed differently upon PRV infection, including nine upregulated and one downregulated miRNAs. Host targets of these miRNAs obtained by bioinformatics analysis belonged to large signaling networks, mainly encompassing calcium signaling pathway, cAMP signaling pathway, MAPK signaling pathway, and other nervous-associated pathways. These findings further highlighted miRNA features in nervous cells after PRV infection and contributed to unveil the underlying mechanisms of neurotropism as well as the neuropathogenesis of PRV.
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Affiliation(s)
- Yongtao Li
- College of Animal Husbandry and Veterinary Science, Henan Agricultural University, Zhengzhou, 450002, China
| | - Guanmin Zheng
- College of Animal Husbandry and Veterinary Science, Henan Agricultural University, Zhengzhou, 450002, China
| | - Yujuan Zhang
- College of Animal Husbandry and Veterinary Science, Henan Agricultural University, Zhengzhou, 450002, China
| | - Xia Yang
- College of Animal Husbandry and Veterinary Science, Henan Agricultural University, Zhengzhou, 450002, China
| | - Hongying Liu
- College of Animal Husbandry and Veterinary Science, Henan Agricultural University, Zhengzhou, 450002, China
| | - Hongtao Chang
- College of Animal Husbandry and Veterinary Science, Henan Agricultural University, Zhengzhou, 450002, China
| | - Xinwei Wang
- College of Animal Husbandry and Veterinary Science, Henan Agricultural University, Zhengzhou, 450002, China
| | - Jun Zhao
- College of Animal Husbandry and Veterinary Science, Henan Agricultural University, Zhengzhou, 450002, China
| | - Chuanqing Wang
- College of Animal Husbandry and Veterinary Science, Henan Agricultural University, Zhengzhou, 450002, China
| | - Lu Chen
- College of Animal Husbandry and Veterinary Science, Henan Agricultural University, Zhengzhou, 450002, China.
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