Transcriptome Dynamics of BmN Cells During the Early Phase of Bombyx mori Nucleopolyhedrovirus Infection
Simple Summary
Abstract
1. Introduction
2. Materials and Methods
2.1. Genes, Plasmids, Strains, and Cells
2.2. Construction of Recombinant Baculovirus rBmNPV-mCherry
2.3. Sample Preparation and RNA Sequencing
2.4. Reads Filtering, Transcription Assembly, and Basic Annotation of Unigenes
2.5. Differential Expression Genes Analysis and Enrichment
2.6. The Vector plex4-Map3k12 Construction for Overexpression
2.7. RNAi
2.8. Reverse Transcription Quantitative Real-Time PCR (RT-qPCR)
3. Results
3.1. Construction of Recombinant Baculovirus rBmBV-mCherry
3.2. RNA Sequencing Analysis
3.3. Differental Expression Analysis of Genes
3.4. Enrichment Analysis of DEGs
3.5. RT-qPCR Validation for Genes Expression Patterns
3.6. The Role of Map3k12 in BmNPV Proliferation
4. Discussion
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Data Availability Statement
Conflicts of Interest
References
- Chen, Z.K.; Lin, S.; Wu, Y.X.; Zhao, Z.M.; Zhou, X.M.; Sadiq, S.; Zhang, Z.; Guo, X.; Wu, P. Hsp90 could promote BmNPV proliferation by interacting with Actin-4 and enhance its expression. Dev. Comp. Immunol. 2023, 142, 104667. [Google Scholar] [CrossRef] [Scilit] [PubMed]
- Gomi, S.; Majima, K.; Maeda, S. Sequence analysis of the genome of Bombyx mori nucleopolyhedrovirus. J. Gen. Virol. 1999, 80, 1323–1337. [Google Scholar] [CrossRef] [Scilit]
- Meng, H.; Ai, H.; Li, D.; Jiang, X.; Zhang, H.; Xu, J.; Huang, S. Bombyx mori UFBP1 regulates apoptosis and promotes BmNPV proliferation by affecting the expression of ER chaperone BmBIP. Int. J. Biol. Macromol. 2024, 283, 137681. [Google Scholar] [CrossRef] [Scilit]
- Wang, X.; Ma, G.; Ren, F.; Awais, M.M.; Sun, J. Bombyx mori nucleopolyhedrovirus induces BmFABP1 downregulation to promote viral proliferation. Insect Sci. 2023, 30, 1595–1606. [Google Scholar] [CrossRef] [Scilit]
- Hu, Z.; Zhu, F.; Chen, K. The Mechanisms of Silkworm Resistance to the Baculovirus and Antiviral Breeding. Annu. Rev. Entomol. 2023, 68, 381–399. [Google Scholar] [CrossRef] [Scilit]
- Fan, Y.X.; Andoh, V.; Chen, L. Multi-omics study and ncRNA regulation of anti-BmNPV in silkworms, Bombyx mori: An update. Front. Microbiol. 2023, 14, 1123448. [Google Scholar] [CrossRef] [Scilit] [PubMed]
- Fan, Y.; Bao, J.; Fu, X.; Wu, P.; Chen, J.; Huang, Y.; Wei, J.; Pan, G.; Li, C. The NPC Families Mediate BmNPV Entry. Microbiol. Spectr. 2022, 10, e0091722. [Google Scholar] [CrossRef] [Scilit] [PubMed]
- Wang, X.; Zhang, Y.; Fei, S.; Awais, M.M.; Zheng, H.; Feng, M.; Sun, J. Heat Shock Protein 75 (TRAP1) facilitate the proliferation of the Bombyx mori nucleopolyhedrovirus. Int. J. Biol. Macromol. 2021, 175, 372–378. [Google Scholar] [CrossRef] [Scilit]
- Jiang, L.; Xia, Q. The progress and future of enhancing antiviral capacity by transgenic technology in the silkworm Bombyx mori. Insect Biochem. Mol. Biol. 2014, 48, 1–7. [Google Scholar] [CrossRef] [Scilit]
- Jiang, L. Insights into the Antiviral Pathways of the Silkworm Bombyx mori. Front. Immunol. 2021, 12, 639092. [Google Scholar] [CrossRef] [Scilit] [PubMed]
- Keddie, B.A.; Aponte, G.W.; Volkman, L.E. The pathway of infection of Autographa californica nuclear polyhedrosis virus in an insect host. Science 1989, 243, 1728–1730. [Google Scholar] [CrossRef] [Scilit] [PubMed]
- Yuan, Y.; Zhu, F.; Xiao, R.; Ge, Q.; Tang, H.; Kong, M.; Taha, R.H.; Chen, K. Increased expression of Suppressor of cytokine signaling 2 (BmSOCS2) is correlated with suppression of Bombyx mori nucleopolyhedrovirus replication in silkworm larval tissues and cells. J. Invertebr. Pathol. 2020, 174, 107419. [Google Scholar] [CrossRef] [Scilit]
- Xia, D.; Jiang, D.; Yu, P.; Jia, K.; Wang, J.; Shen, D.; Zhao, Q.; Cheng, L. Ras3 in Bombyx mori with antiviral function against B. mori nucleopolyhedrovirus. Dev. Comp. Immunol. 2024, 152, 105114. [Google Scholar] [CrossRef] [Scilit]
- Yao, L.; Wang, S.; Su, S.; Yao, N.; He, J.; Peng, L.; Sun, J. Construction of a baculovirus-silkworm multigene expression system and its application on producing virus-like particles. PLoS ONE 2012, 7, e32510. [Google Scholar] [CrossRef] [Scilit] [PubMed]
- Chen, S.; Zhou, Y.; Chen, Y.; Gu, J. fastp: An ultra-fast all-in-one FASTQ preprocessor. Bioinformatics 2018, 34, i884–i890. [Google Scholar] [CrossRef] [Scilit]
- Kim, D.; Langmead, B.; Salzberg, S.L. HISAT: A fast spliced aligner with low memory requirements. Nat. Methods 2015, 12, 357–360. [Google Scholar] [CrossRef] [Scilit] [PubMed]
- Pertea, M.; Pertea, G.M.; Antonescu, C.M.; Chang, T.C.; Mendell, J.T.; Salzberg, S.L. StringTie enables improved reconstruction of a transcriptome from RNA-seq reads. Nat. Biotechnol. 2015, 33, 290–295. [Google Scholar] [CrossRef] [Scilit]
- Robinson, M.D.; McCarthy, D.J.; Smyth, G.K. edgeR: A Bioconductor package for differential expression analysis of digital gene expression data. Bioinformatics 2010, 26, 139–140. [Google Scholar] [CrossRef] [Scilit]
- Stewart, P.L.; Nemerow, G.R. Cell integrins: Commonly used receptors for diverse viral pathogens. Trends Microbiol. 2007, 15, 500–507. [Google Scholar] [CrossRef] [Scilit]
- Nogalski, M.T.; Chan, G.; Stevenson, E.V.; Gray, S.; Yurochko, A.D. Human cytomegalovirus-regulated paxillin in monocytes links cellular pathogenic motility to the process of viral entry. J. Virol. 2011, 85, 1360–1369. [Google Scholar] [CrossRef] [Scilit]
- Morrison, D.K. MAP kinase pathways. Cold Spring Harb. Perspect. Biol. 2012, 4, a011254. [Google Scholar] [CrossRef] [Scilit]
- Tafesh-Edwards, G.; Eleftherianos, I. JNK signaling in Drosophila immunity and homeostasis. Immunol. Lett. 2020, 226, 7–11. [Google Scholar] [CrossRef] [Scilit] [PubMed]
- Fung, T.S.; Liu, D.X. Activation of the c-Jun NH(2)-terminal kinase pathway by coronavirus infectious bronchitis virus promotes apoptosis independently of c-Jun. Cell Death Dis. 2017, 8, 3215. [Google Scholar] [CrossRef] [Scilit]
- Merritt, S.E.; Mata, M.; Nihalani, D.; Zhu, C.; Hu, X.; Holzman, L.B. The mixed lineage kinase DLK utilizes MKK7 and not MKK4 as substrate. J. Biol. Chem. 1999, 274, 10195–10202. [Google Scholar] [CrossRef] [Scilit] [PubMed]
- Katsuma, S.; Mita, K.; Shimada, T. ERK- and JNK-dependent signaling pathways contribute to Bombyx mori nucleopolyhedrovirus infection. J. Virol. 2007, 81, 13700–13709. [Google Scholar] [CrossRef] [Scilit]
- Liu, Y.X.; Yang, J.Y.; Sun, J.L.; Wang, A.C.; Wang, X.Y.; Zhu, L.B.; Cao, H.H.; Huang, Z.H.; Liu, S.H.; Xu, J.P. Reactive oxygen species-mediated phosphorylation of JNK is involved in the regulation of BmFerHCH on Bombyx mori nucleopolyhedrovirus proliferation. Int. J. Biol. Macromol. 2023, 235, 123834. [Google Scholar] [CrossRef] [Scilit] [PubMed]
- Wilson, A.; McCormick, C. Reticulophagy and viral infection. Autophagy 2025, 21, 3–20. [Google Scholar] [CrossRef] [Scilit]
- Cagno, V.; Tseligka, E.D.; Jones, S.T.; Tapparel, C. Heparan Sulfate Proteoglycans and Viral Attachment: True Receptors or Adaptation Bias? Viruses 2019, 11, 596. [Google Scholar] [CrossRef] [Scilit]
- Vassilaki, N.; Frakolaki, E. Virus-host interactions under hypoxia. Microbes Infect. 2017, 19, 193–203. [Google Scholar] [CrossRef] [Scilit]
- Clem, R.J.; Fechheimer, M.; Miller, L.K. Prevention of apoptosis by a baculovirus gene during infection of insect cells. Science 1991, 254, 1388–1390. [Google Scholar] [CrossRef] [Scilit]
- Crook, N.E.; Clem, R.J.; Miller, L.K. An apoptosis-inhibiting baculovirus gene with a zinc finger-like motif. J. Virol. 1993, 67, 2168–2174. [Google Scholar] [CrossRef] [Scilit] [PubMed]
- Sun, Y.; Ji, L.; Liu, W.; Sun, J.; Liu, P.; Wang, X.; Liu, X.; Xu, X. Influenza virus infection activates TAK1 to suppress RIPK3-independent apoptosis and RIPK1-dependent necroptosis. Cell Commun. Signal. 2024, 22, 372. [Google Scholar] [CrossRef] [Scilit] [PubMed]
- Yin, C.; Fedorov, A.; Guo, H.; Crawford, J.C.; Rousseau, C.; Zhong, X.; Williams, R.M.; Gautam, A.; Koehler, H.S.; Whisnant, A.W.; et al. Host cell Z-RNAs activate ZBP1 during virus infections. Nature 2025, 648, 707–716. [Google Scholar] [CrossRef] [Scilit] [PubMed]







| Primer Name | Primer Sequence |
|---|---|
| mCherry-F | 5′-AAGTCGACATGGTGAG-CAAGGGCGAGGAGCTGT-3′ |
| mCherry-R | 5′-AAGAGCTCTTACTTGTACAGCTCGTCCAT-3′ |
| Map3k12-F | 5′-AAGGTACCATGCTTTTTTTATCA-3′ |
| Map3k12-R | 5′-AAGCGGCCGCTTAGACGTGAGC-3′ |
| Map3k12 for dsRNA synthesis-F | 5′-GTAATACGACTCAC-TATAGGGAGCGGCAACCTTA-GAGGTGAAATGG-3′ |
| Map3k12 for dsRNA synthesis-R | 5′-GTAATACGACTCACTATAGGGCGGA-GACTTACCGTCCGACG-3′ |
| EGFP for dsRNA synthesis-F | 5′-GGATCCTAATACGACTCACTATAGGATGGTGAGCAAGGGC-3′ |
| EGFP for dsRNA synthesis-R | 5′-GGATCCTAATACGACTCACTATAGGTTACTTGTACAGCTCGTC-3′ |
| Map3k12 for RT-qPCR-F | 5′-GGGAAGTGCCATTTGAG-3′ |
| Map3k12 for RT-qPCR-R | 5′-CTATGTTGTCGTGGTTGAGT-3′ |
| VP39 for RT-qPCR-F | 5′-CTAATGCCCGTGGGTATGG-3′ |
| VP39 for RT-qPCR-R | 5′-TTGATGAGGTGGCTGTTGC-3′ |
| GAPDH for RT-qPCR-F | 5′-CATTCCGCGTCCCCTGTTGCTAAT-3′ |
| GAPDH for RT-qPCR-R | 5′-GCTGCCTCCTTGACCTTTTGC-3′ |
| Sample | Raw Data | Clean Reads | Q20 (%) | Q30 (%) | GC (%) | Total Mapped (%) |
|---|---|---|---|---|---|---|
| BmN-12h-1 | 52,801,132 | 52,491,010 | 97.53 | 92.91 | 42.20 | 46.97 |
| BmN-12h-2 | 50,967,124 | 50,628,832 | 97.57 | 92.90 | 42.17 | 47.40 |
| BmN-12h-3 | 49,408,250 | 49,114,190 | 97.83 | 93.51 | 42.11 | 48.12 |
| BmN-12h-1-ck | 59,107,832 | 58,728,882 | 97.76 | 93.27 | 41.84 | 82.83 |
| BmN-12h-2-ck | 51,707,854 | 51,382,778 | 97.56 | 92.94 | 41.91 | 82.48 |
| BmN-12h-3-ck | 54,139,170 | 53,794,204 | 97.74 | 93.37 | 41.73 | 82.01 |
| BmN-24h-1 | 39,745,074 | 39,516,804 | 96.90 | 91.49 | 42.29 | 15.56 |
| BmN-24h-2 | 71,026,758 | 70,625,640 | 97.57 | 92.94 | 42.23 | 15.60 |
| BmN-24h-3 | 65,696,490 | 65,337,122 | 97.89 | 93.61 | 41.95 | 15.27 |
| BmN-24h-1-ck | 57,915,664 | 57,557,250 | 97.45 | 92.69 | 42.07 | 82.99 |
| BmN-24h-2-ck | 36,151,820 | 35,909,688 | 98.06 | 94.19 | 42.47 | 83.87 |
| BmN-24h-3-ck | 49,561,852 | 49,246,990 | 97.92 | 93.83 | 42.82 | 83.99 |
| DEGs | log2Fold Change | Adjust p Value | Regulated |
|---|---|---|---|
| Itgbn | 1.82 | 2.32 × 10−4 | up |
| Sv2a | −1.26 | 2.20 × 10−88 | down |
| Itga9 | −1.70 | 9.68 × 10−57 | down |
| Thbs3b | 2.57 | 2.78 × 10−5 | up |
| Map3k12 | 5.04 | 5.21 × 10−5 | up |
| DEGs | log2Fold Change | Adjust p Value | Regulated |
|---|---|---|---|
| Itgbn | 1.68 | 0.0002 | up |
| Sv2a | −2.51 | 5.72 × 10−82 | down |
| Itga9 | −3.25 | 7.12 × 10−45 | down |
| Thbs3b | 1.59 | 0.0007 | up |
| Map3k12 | 3.31 | 1.14 × 10−8 | up |
Disclaimer/Publisher’s Note: The statements, opinions and data contained in all publications are solely those of the individual author(s) and contributor(s) and not of MDPI and/or the editor(s). MDPI and/or the editor(s) disclaim responsibility for any injury to people or property resulting from any ideas, methods, instructions or products referred to in the content. |
© 2026 by the authors. Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license.
Share and Cite
Wang, X.; Miao, F.; Wang, W.; Sun, J.; Yao, L. Transcriptome Dynamics of BmN Cells During the Early Phase of Bombyx mori Nucleopolyhedrovirus Infection. Insects 2026, 17, 80. https://doi.org/10.3390/insects17010080
Wang X, Miao F, Wang W, Sun J, Yao L. Transcriptome Dynamics of BmN Cells During the Early Phase of Bombyx mori Nucleopolyhedrovirus Infection. Insects. 2026; 17(1):80. https://doi.org/10.3390/insects17010080
Chicago/Turabian StyleWang, Xiong, Fangyu Miao, Wei Wang, Jingchen Sun, and Lunguang Yao. 2026. "Transcriptome Dynamics of BmN Cells During the Early Phase of Bombyx mori Nucleopolyhedrovirus Infection" Insects 17, no. 1: 80. https://doi.org/10.3390/insects17010080
APA StyleWang, X., Miao, F., Wang, W., Sun, J., & Yao, L. (2026). Transcriptome Dynamics of BmN Cells During the Early Phase of Bombyx mori Nucleopolyhedrovirus Infection. Insects, 17(1), 80. https://doi.org/10.3390/insects17010080

