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Chen C, Chen L, Liu X, Ma S, Chen K. Study on anti-BmNPV mechanism of branched-chain amino acid aminotransferases in silkworm. DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY 2024; 156:105183. [PMID: 38636699 DOI: 10.1016/j.dci.2024.105183] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/07/2024] [Revised: 04/14/2024] [Accepted: 04/15/2024] [Indexed: 04/20/2024]
Abstract
Bombyx mori nucleopolyhedrovirus (BmNPV) is the most important virus that threatens sericulture industry. At present, there is no effective treatment for BmNPV infection in silkworms, and lncRNA plays an important role in biological immune response and host-virus interaction, but there are relatively few studies in silkworms. In this study, the four midgut tissue samples of the resistance strain NB (NB) and susceptible strain 306 (306) and the NB and 306 continuously infected with BmNPV for 96 h are used for whole transcriptome sequencing to analyze the differences in the genetic background of NB and 306 and the differences after inoculation of BmNPV, and the significantly different mRNA, miRNA and lnRNA between NB and 306 after BmNPV inoculation were screened. By comparing NB and 306, 2651 significantly different mRNAs, 57 significantly different miRNAs and 198 significantly different lncRNAs were screened. By comparing NB and 306 after BmNPV inoculation, 2684 significantly different mRNAs, 39 significantly different miRNAs and 125 significantly different lncRNAs were screened. According to the significantly different mRNA, miRNA and lncRNA screened from NB and 306 and NB and 306 after virus inoculation, the mRNA-miRNA-lncRNA regulatory network was constructed before and after virus inoculation, and the BmBCAT-Bomo_chr7_8305-MSTRG.3236.2 regulatory axis was screened from them, and it was found that BmBCAT was not Bomo_chr7_8305 regulated in the genetic background, after viral infection, MSTRG.3236.2 competes for binding Bomo_chr7_8305 regulates BmBCAT. The whole transcriptome sequencing results were verified by qPCR and the time-series expression analysis was performed to prove the reliability of the regulatory network. The BmBCAT-Bomo_chr7_8305-MSTRG.3236.2 regulatory axis may play a potential role in the interaction between silkworms and BmNPV. These results provide new insights into the interaction mechanism between silkworms and BmNPV.
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Affiliation(s)
- Can Chen
- School of Life Sciences, Jiangsu University, Zhenjiang, 212013, China
| | - Liang Chen
- School of Life Sciences, Jiangsu University, Zhenjiang, 212013, China
| | - Xiaoyong Liu
- School of Life Sciences, Jiangsu University, Zhenjiang, 212013, China
| | - Shangshang Ma
- School of Life Sciences, Jiangsu University, Zhenjiang, 212013, China
| | - Keping Chen
- School of Life Sciences, Jiangsu University, Zhenjiang, 212013, China.
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Ren Y, Fu S, Dong W, Chen J, Xue H, Bu W. The ncRNA-mediated regulatory networks of defensins and lysozymes in Riptortus pedestris: involvement in response to gut bacterial disturbances. Front Microbiol 2024; 15:1386345. [PMID: 38827147 PMCID: PMC11140134 DOI: 10.3389/fmicb.2024.1386345] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2024] [Accepted: 04/23/2024] [Indexed: 06/04/2024] Open
Abstract
Insects depend on humoral immunity against intruders through the secretion of antimicrobial peptides (AMPs) and immune effectors via NF-κB transcription factors, and their fitness is improved by gut bacterial microbiota. Although there are growing numbers of reports on noncoding RNAs (ncRNAs) involving in immune responses against pathogens, comprehensive studies of ncRNA-AMP regulatory networks in Riptortus pedestris, which is one of the widely distributed pests in East Asia, are still not well understood under feeding environmental changes. The objective of this study employed the whole-transcriptome sequencing (WTS) to systematically identify the lncRNAs (long noncoding RNA) and circRNAs (circular RNA) and to obtain their differential expression from the R. pedestris gut under different feeding conditions. Functional annotation indicated that they were mainly enriched in various biological processes with the GO and KEGG databases, especially in immune signaling pathways. Five defensin (four novel members) and eleven lysozyme (nine novel members) family genes were identified and characterized from WTS data, and meanwhile, phylogenetic analysis confirmed their classification. Subsequently, the miRNA-mRNA interaction network of above two AMPs and lncRNA-involved ceRNA (competing endogenous RNA) regulatory network of one lysozyme were predicted and built based on bioinformatic prediction and calculation, and the expression patterns of differentially expressed (DE) defensins, and DE lysozymes and related DE ncRNAs were estimated and selected among all the comparison groups. Finally, to integrate the analyses of WTS and previous 16S rRNA amplicon sequencing, we conducted the Pearson correlation analysis to reveal the significantly positive or negative correlation between above DE AMPs and ncRNAs, as well as most changes in the gut bacterial microbiota at the genus level of R. pedestris. Taken together, the present observations provide great insights into the ncRNA regulatory networks of AMPs in response to rearing environmental changes in insects and uncover new potential strategies for pest control in the future.
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Affiliation(s)
- Yipeng Ren
- Institute of Entomology, College of Life Sciences, Nankai University, Tianjin, China
| | - Siying Fu
- Institute of Entomology, College of Life Sciences, Nankai University, Tianjin, China
| | - Wenhao Dong
- Tianjin Key Laboratory of Food and Biotechnology, School of Biotechnology and Food Science, Tianjin University of Commerce, Tianjin, China
| | - Juhong Chen
- Institute of Entomology, College of Life Sciences, Nankai University, Tianjin, China
| | - Huaijun Xue
- Institute of Entomology, College of Life Sciences, Nankai University, Tianjin, China
| | - Wenjun Bu
- Institute of Entomology, College of Life Sciences, Nankai University, Tianjin, China
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Ackah M, Jin X, Zhang Q, Amoako FK, Wang L, Attaribo T, Zhao M, Yuan F, Herman RA, Qiu C, Lin Q, Yin Z, Zhao W. Long noncoding RNA transcriptome analysis reveals novel lncRNAs in Morus alba 'Yu-711' response to drought stress. THE PLANT GENOME 2024; 17:e20273. [PMID: 36285722 DOI: 10.1002/tpg2.20273] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/04/2022] [Accepted: 09/13/2022] [Indexed: 06/16/2023]
Abstract
Drought stress has been a key environmental factor affecting plant growth and development. The plant genome is capable of producing long noncoding RNAs (lncRNAs). To better understand white mulberry (Morus alba L.) drought response mechanism, we conducted a comparative transcriptome study comparing two treatments: drought-stressed (EG) and well-watered (CK) plants. A total of 674 differentially expressed lncRNAs (DElncRNAs) were identified. In addition, 782 differentially expressed messenger RNAs (DEmRNAs) were identified. We conducted Gene Ontology (GO) and KEGG enrichment analyses focusing on the differential lncRNAs cis-target genes. The target genes of the DElncRNAs were most significantly involved in the biosynthesis of secondary metabolites. Gene regulatory networks of the target genes involving DElncRNAs-mRNAs-DEmRNAs and DElncRNA-miRNA-DEmRNA were constructed. In the DElncRNAs-DEmRNAs network, 30 DEmRNAs involved in the biosynthesis of secondary metabolites are collocated with 46 DElncRNAs. The interaction between DElncRNAs and candidate genes was identified using LncTar. In summary, quantitative real-time polymerase chain reaction (qRT-PCR) validated nine candidate genes and seven target lncRNAs including those identified by LncTar. We predicted that the DElncRNAs-DEmRNAs might recruit microRNAs (miRNAs) to interact with gene regulatory networks under the drought stress response in mulberry. The findings will contribute to our understanding of the regulatory functions of lncRNAs under drought stress and will shed new light on the mulberry-drought stress interactions.
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Affiliation(s)
- Michael Ackah
- Jiangsu Key Laboratory of Sericultural Biology and Biotechnology, School of Biotechnology, Jiangsu Univ. of Science and Technology, Zhenjiang, 212100, China
- School of Food and Biological Engineering, Jiangsu Univ., Zhenjiang, Jiangsu, 212013, People's Republic of China
| | - Xin Jin
- Jiangsu Key Laboratory of Sericultural Biology and Biotechnology, School of Biotechnology, Jiangsu Univ. of Science and Technology, Zhenjiang, 212100, China
| | - Qiaonan Zhang
- Jiangsu Key Laboratory of Sericultural Biology and Biotechnology, School of Biotechnology, Jiangsu Univ. of Science and Technology, Zhenjiang, 212100, China
| | - Frank Kwarteng Amoako
- Institute of Plant Nutrition and Soil Science, Kiel Univ., Hermann-Rodewald-Straße 2, Kiel, 24118, Germany
| | - Lei Wang
- Jiangsu Key Laboratory of Sericultural Biology and Biotechnology, School of Biotechnology, Jiangsu Univ. of Science and Technology, Zhenjiang, 212100, China
| | - Thomas Attaribo
- School of Agriculture, C. K. Tedam Univ. of Technology and Applied Sciences, Navrongo, UK-0215-5321, Ghana
| | - Mengdi Zhao
- Dep. of Materials Science and Engineering, Suzhou Univ. of Science and Technology, 99 Xuefu Road, Huqiu District, Suzhou, 215004, China
| | - Feng Yuan
- Jiangsu Key Laboratory of Sericultural Biology and Biotechnology, School of Biotechnology, Jiangsu Univ. of Science and Technology, Zhenjiang, 212100, China
| | - Richard Ansah Herman
- Jiangsu Key Laboratory of Sericultural Biology and Biotechnology, School of Biotechnology, Jiangsu Univ. of Science and Technology, Zhenjiang, 212100, China
| | - Changyu Qiu
- Sericultural Research Institute, Guangxi Zhuang Autonomous Region, Nanning, 530007, China
| | - Qiang Lin
- Sericultural Research Institute, Guangxi Zhuang Autonomous Region, Nanning, 530007, China
| | - Zhi Yin
- Nanjing Univ. of Finance & Economics, Nanjing, 210023, China
| | - Weiguo Zhao
- Jiangsu Key Laboratory of Sericultural Biology and Biotechnology, School of Biotechnology, Jiangsu Univ. of Science and Technology, Zhenjiang, 212100, China
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Chen Y, Chen Y, Yu XQ, Feng Q, Wang X, Liu L. Expression profiles of lncRNAs, miRNAs, and mRNAs and interaction analysis indicate their potential involvement during testicular fusion in Spodoptera litura. Genomics 2024; 116:110758. [PMID: 38065236 DOI: 10.1016/j.ygeno.2023.110758] [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: 08/25/2023] [Revised: 11/29/2023] [Accepted: 12/05/2023] [Indexed: 01/22/2024]
Abstract
Testicular fusion of Spodoptera litura occures during metamorphosis, which benefits sperms development. Previous research identified involvement of ECM-integrin interaction pathways, MMPs in testicular fusion, but the regulatory mechanism remains unclear. RNA-seq was performed to analyze long non-coding RNAs (lncRNAs) and microRNAs (miRNAs) in testes, aiming to uncover potential regulatory mechanisms of testicular fusion. 2150 lncRNAs, 2742 targeted mRNAs, and 347 miRNAs were identified in testes at three different developmental stages. Up-regulated DElncRNAs and DEmRNAs, as well as down-regulated DEmiRNAs, were observed during testicular fusion, while the opposite expression pattern was observed after fusion. Enrichment analysis of DEmRNAs revealed that cAMP signal pathway, ECM remodeling enzymes, ECM-integrin interaction pathways, and cell adhesion molecules were potentially associated with testicular fusion. The identified DElncRNA-DEmiRNA-DEmRNA regulatory network related to cAMP signal pathway, ECM remodeling enzymes suggests their roles during testicular fusion. Our research will provide new targets for studying the mechanism of testicular fusion.
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Affiliation(s)
- Yaqing Chen
- Guangdong Provincial Key Laboratory of Insect Developmental Biology and Applied Technology, Guangzhou Key Laboratory of Insect Development Regulation and Application Research, Institute of Insect Science and Technology, School of Life Sciences, South China Normal University, Guangzhou 510631, China
| | - Yu Chen
- Guangdong Provincial Key Laboratory of Insect Developmental Biology and Applied Technology, Guangzhou Key Laboratory of Insect Development Regulation and Application Research, Institute of Insect Science and Technology, School of Life Sciences, South China Normal University, Guangzhou 510631, China.
| | - Xiao-Qiang Yu
- Guangdong Provincial Key Laboratory of Insect Developmental Biology and Applied Technology, Guangzhou Key Laboratory of Insect Development Regulation and Application Research, Institute of Insect Science and Technology, School of Life Sciences, South China Normal University, Guangzhou 510631, China.
| | - Qili Feng
- Guangdong Provincial Key Laboratory of Insect Developmental Biology and Applied Technology, Guangzhou Key Laboratory of Insect Development Regulation and Application Research, Institute of Insect Science and Technology, School of Life Sciences, South China Normal University, Guangzhou 510631, China.
| | - Xiaoyun Wang
- Guangdong Provincial Key Laboratory of Insect Developmental Biology and Applied Technology, Guangzhou Key Laboratory of Insect Development Regulation and Application Research, Institute of Insect Science and Technology, School of Life Sciences, South China Normal University, Guangzhou 510631, China.
| | - Lin Liu
- Guangdong Provincial Key Laboratory of Insect Developmental Biology and Applied Technology, Guangzhou Key Laboratory of Insect Development Regulation and Application Research, Institute of Insect Science and Technology, School of Life Sciences, South China Normal University, Guangzhou 510631, China.
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5
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Chen Y, Wang Z, Wu C, Li H, Qian H, Wang M, Wu P, Guo X, Zhang Z. Identification of long noncoding RNAs of silkworm at the early stage of Bombyx mori bidensovirus infection. ARCHIVES OF INSECT BIOCHEMISTRY AND PHYSIOLOGY 2024; 115:e22082. [PMID: 38288492 DOI: 10.1002/arch.22082] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/01/2023] [Revised: 12/23/2023] [Accepted: 01/02/2024] [Indexed: 02/01/2024]
Abstract
Bombyx mori bidensovirus (BmBDV) is one of the most important pathogens of silkworm. It mainly infects midgut cells of silkworm and causes losses to the sericulture industry. Long noncoding RNAs (lncRNAs) have been reported to play an important role in the regulation of antiviral immune response in silkworm. To explore whether lncRNAs are involved in BmBDV infection and immune response of silkworm, we performed a comparative transcriptome analysis to identify the lncRNAs and mRNAs between the BmBDV infected and noninfected silkworm larvae at the early stage. A total of 16,069 genes and 974 candidate lncRNAs were identified, among which 142 messenger RNA (mRNAs) and four lncRNAs were differentially expressed (DE). Target gene prediction revealed that 142 DEmRNAs were coexpressed with four DElncRNAs, suggesting that the expression of mRNA is mainly affected through trans-regulation activities. A regulatory network of DElncRNAs and DEmRNAs was constructed, showing that many genes targeted by different DElncRNAs are involved in metabolism and immunity, which implies that these genes and lncRNAs play an important role in the replication of BmBDV. Our results will help us to improve our understanding of lncRNA-mediated regulatory roles in BmBDV infection, providing a new perspective for further exploring the interaction between host and BmBDV.
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Affiliation(s)
- Yeping Chen
- Jiangsu Key Laboratory of Sericultural Biology and Biotechnology, School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang, China
- Key Laboratory of Silkworm and Mulberry Genetic Improvement, Ministry of Agriculture and Rural Affairs, The Sericultural Research Institute, Chinese Academy of Agricultural Sciences, Zhenjiang, China
| | - Zihe Wang
- Jiangsu Key Laboratory of Sericultural Biology and Biotechnology, School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang, China
- Key Laboratory of Silkworm and Mulberry Genetic Improvement, Ministry of Agriculture and Rural Affairs, The Sericultural Research Institute, Chinese Academy of Agricultural Sciences, Zhenjiang, China
| | - Chengyue Wu
- Jiangsu Key Laboratory of Sericultural Biology and Biotechnology, School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang, China
- Key Laboratory of Silkworm and Mulberry Genetic Improvement, Ministry of Agriculture and Rural Affairs, The Sericultural Research Institute, Chinese Academy of Agricultural Sciences, Zhenjiang, China
| | - Hao Li
- Jiangsu Key Laboratory of Sericultural Biology and Biotechnology, School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang, China
- Key Laboratory of Silkworm and Mulberry Genetic Improvement, Ministry of Agriculture and Rural Affairs, The Sericultural Research Institute, Chinese Academy of Agricultural Sciences, Zhenjiang, China
| | - Heying Qian
- Jiangsu Key Laboratory of Sericultural Biology and Biotechnology, School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang, China
- Key Laboratory of Silkworm and Mulberry Genetic Improvement, Ministry of Agriculture and Rural Affairs, The Sericultural Research Institute, Chinese Academy of Agricultural Sciences, Zhenjiang, China
| | - Mengdong Wang
- Jiangsu Key Laboratory of Sericultural Biology and Biotechnology, School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang, China
- Key Laboratory of Silkworm and Mulberry Genetic Improvement, Ministry of Agriculture and Rural Affairs, The Sericultural Research Institute, Chinese Academy of Agricultural Sciences, Zhenjiang, China
| | - Ping Wu
- Jiangsu Key Laboratory of Sericultural Biology and Biotechnology, School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang, China
- Key Laboratory of Silkworm and Mulberry Genetic Improvement, Ministry of Agriculture and Rural Affairs, The Sericultural Research Institute, Chinese Academy of Agricultural Sciences, Zhenjiang, China
| | - Xijie Guo
- Jiangsu Key Laboratory of Sericultural Biology and Biotechnology, School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang, China
- Key Laboratory of Silkworm and Mulberry Genetic Improvement, Ministry of Agriculture and Rural Affairs, The Sericultural Research Institute, Chinese Academy of Agricultural Sciences, Zhenjiang, China
| | - Zhendong Zhang
- Jiangsu Key Laboratory of Sericultural Biology and Biotechnology, School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang, China
- Key Laboratory of Silkworm and Mulberry Genetic Improvement, Ministry of Agriculture and Rural Affairs, The Sericultural Research Institute, Chinese Academy of Agricultural Sciences, Zhenjiang, China
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Zafar J, Wu H, Xu Y, Lin L, Kang Z, Zhang J, Zhang R, Lu Y, Jin F, Xu X. Transcriptomic Analysis of Metarhizium anisopliae-Induced Immune-Related Long Non-Coding RNAs in Polymorphic Worker Castes of Solenopsis invicta. Int J Mol Sci 2023; 24:13983. [PMID: 37762284 PMCID: PMC10531276 DOI: 10.3390/ijms241813983] [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: 07/17/2023] [Revised: 09/03/2023] [Accepted: 09/10/2023] [Indexed: 09/29/2023] Open
Abstract
Long non-coding RNAs (lncRNAs) represent a class of RNA molecules that do not encode proteins. Generally studied for their regulatory potential in model insects, relatively little is known about their immunoregulatory functions in different castes of eusocial insects, including Solenopsis invicta, a notoriously invasive insect pest. In the current study, we used Metarhizium anisopliae, an entomopathogenic fungus, to infect the polymorphic worker castes (Major and Minor Workers) and subjected them to RNA sequencing at different intervals (6, 24, and 48 h post-infection (hpi)). Comprehensive bioinformatic analysis identified 5719 (1869 known and 3850 novel) lncRNAs in all libraries. Genomic characteristics analysis showed that S. invicta lncRNAs exhibited structural similarities with lncRNAs from other eusocial insects, including lower exon numbers, shorter intron and exon lengths, and a lower expression profile. A comparison of lncRNAs in major and minor worker ants revealed that several lncRNAs were exclusively expressed in one worker caste and remained absent in the other. LncRNAs such as MSTRG.12029.1, XR_005575440.1 (6 h), MSTRG.16728.1, XR_005575440.1 (24 h), MSTRG.20263.41, and MSTRG.11994.5 (48 h) were only present in major worker ants, while lncRNAs such as MSTRG.8896.1, XR_005574239.1 (6 h), MSTRG.20289.8, XR_005575051.1 (24 h), MSTRG.20289.8, and MSTRG.6682.1 (48 h) were only detected in minor workers. Additionally, we performed real-time quantitative PCR and experimentally validated these findings. Functional annotation of cis-acting lncRNAs in major worker ants showed that lncRNAs targeted genes such as serine protease, trypsin, melanization protease-1, spaetzle-3, etc. In contrast, apoptosis and autophagy-related genes were identified as targets of lncRNAs in minor ants. Lastly, we identified several lncRNAs as precursors of microRNAs (miRNAs), such as miR-8, miR-14, miR-210, miR-6038, etc., indicating a regulatory relationship between lncRNAs, miRNAs, and mRNAs in antifungal immunity. These findings will serve as a genetic resource for lncRNAs in polymorphic eusocial ants and provide a theoretical basis for exploring the function of lncRNAs from a unique and novel perspective.
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Affiliation(s)
| | | | | | | | | | | | | | | | - Fengliang Jin
- National Key Laboratory of Green Pesticide, “Belt and Road” Technology Industry and Innovation Institute for Green and Biological Control of Agricultural Pests, College of Plant Protection, South China Agricultural University, Guangzhou 510642, China; (J.Z.); (H.W.); (Y.X.); (L.L.); (Z.K.); (J.Z.); (R.Z.); (Y.L.)
| | - Xiaoxia Xu
- National Key Laboratory of Green Pesticide, “Belt and Road” Technology Industry and Innovation Institute for Green and Biological Control of Agricultural Pests, College of Plant Protection, South China Agricultural University, Guangzhou 510642, China; (J.Z.); (H.W.); (Y.X.); (L.L.); (Z.K.); (J.Z.); (R.Z.); (Y.L.)
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Ren Y, Chen J, Wang Y, Fu S, Bu W, Xue H. The lncRNA-mediated ceRNA network of Altica viridicyanea is involved in the regulation of the Toll/Imd signaling pathway under antibiotic treatment. Front Physiol 2023; 14:1244190. [PMID: 37664435 PMCID: PMC10470016 DOI: 10.3389/fphys.2023.1244190] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2023] [Accepted: 08/02/2023] [Indexed: 09/05/2023] Open
Abstract
Long noncoding RNAs (lncRNAs) play significant roles in the regulation of mRNA expression or in shaping the competing endogenous RNA (ceRNA) network by targeting miRNA. The insect gut is one of the most important tissues due to direct contact with external pathogens and functions in the immune defense against pathogen infection through the innate immune system and symbionts, but there are limited observations on the role of the lncRNA-involved ceRNA network of the Toll/Imd pathway and correlation analysis between this network and bacterial microbiota in the Altica viridicyanea gut. In this research, we constructed and sequenced six RNA sequencing libraries using normal and antibiotic-reared samples, generating a total of 17,193 lncRNAs and 26,361 mRNAs from massive clean data by quality control and bioinformatic analysis. Furthermore, a set of 8,539 differentially expressed lncRNAs (DELs) and 13,263 differentially expressed mRNAs (DEMs), of which related to various immune signaling pathways, such as the Toll/Imd, JAK/STAT, NF-κB, and PI3K-Akt signaling pathways, were obtained between the two experimental groups in A. viridicyanea. In addition, numerous GO and KEGG enrichment analyses were used to annotate the DELs and their target genes. Moreover, six Toll family members and nineteen signal genes from the Toll/Imd signaling pathway were identified and characterized using online tools, and phylogenetic analyses of the above genes proved their classification. Next, a lncRNA-miRNA-mRNA network of the Toll/Imd pathway was built, and it contained different numbers of DEMs in this pathway and related DELs based on prediction and annotation. In addition, qRT-PCR validation and sequencing data were conducted to show the expression patterns of the above DELs and DEMs related to the Toll/Imd signaling pathway. Finally, the correlated investigations between DELs or DEMs of the Toll/Imd signaling pathway and most changes in the gut bacterial microbiota revealed significantly positive or negative relationships between them. The present findings provide essential evidence for innate immune ceRNAs in the beetle gut and uncover new potential relationships between innate immune pathways and the gut bacterial microbiota in insects.
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Affiliation(s)
| | | | | | | | - Wenjun Bu
- Institute of Entomology, College of Life Sciences, Nankai University, Tianjin, China
| | - Huaijun Xue
- Institute of Entomology, College of Life Sciences, Nankai University, Tianjin, China
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8
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Fan YX, Andoh V, Chen L. Multi-omics study and ncRNA regulation of anti-BmNPV in silkworms, Bombyx mori: an update. Front Microbiol 2023; 14:1123448. [PMID: 37275131 PMCID: PMC10232802 DOI: 10.3389/fmicb.2023.1123448] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Accepted: 05/02/2023] [Indexed: 06/07/2023] Open
Abstract
Bombyx mori silkworm is an important economic insect which has a significant contribution to the improvement of the economy. Bombyx mori nucleopolyhedrovirus (BmNPV) is a vitally significant purulent virus that impedes the sustainable and stable development of the silkworm industry, resulting in substantial economic losses. In recent years, with the development of biotechnology, transcriptomics, proteomics, metabolomics, and the related techniques have been used to select BmNPV-resistant genes, proteins, and metabolites. The regulatory networks between viruses and hosts have been gradually clarified with the discovery of ncRNAs, such as miRNA, lncRNA, and circRNA in cells. Thus, this paper aims to highlight the results of current multi-omics and ncRNA studies on BmNPV resistance in the silkworm, providing some references for resistant strategies in the silkworm to BmNPV.
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Lin S, Yin HT, Zhao ZM, Chen ZK, Zhou XMI, Zhang ZD, Guo XJ, Zhao WG, Wu P. LincRNA_XR209691.3 could promote Bombyx mori nucleopolyhedrovirus replication by interacting with BmHSP70. INSECT MOLECULAR BIOLOGY 2023; 32:160-172. [PMID: 36482511 DOI: 10.1111/imb.12821] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Accepted: 11/29/2022] [Indexed: 06/17/2023]
Abstract
Long non-coding RNAs (lncRNAs), a class of transcripts exceeding 200 nucleotides and lacking protein coding potential, have been proven to play important roles in viral infection and host immunity. Bombyx mori nucleopolyhedrovirus (BmNPV) is an important pathogen, which causes the silkworm disease and leads to a huge challenge to the sericultural industry. At present, research on the roles of insect lncRNAs in host-virus interaction are relatively few. In this study, we explored the function of lincRNA_XR209691.3 that was significantly up-regulated in the silkworm fat body upon BmNPV infection. Firstly, the subcellular localization experiment confirmed that lincRNA_XR209691.3 was present in both the nucleus and cytoplasm. Enhancing the expression of lincRNA_XR209691.3 in BmN cells could promote the proliferation of BmNPV, while inhibition of lincRNA_XR209691.3 by RNA interference suppresses the proliferation of BmNPV. Combining RNA pull-down and mass spectrometry, we identified the host and BmNPV proteins that could interact with lincRNA_XR209691.3. Next, by using truncation experiment and RNA immunoprecipitation (RIP) assay, it was found that lincRNA_XR209691.3 could bind to the Actin domain of BmHSP70. Subsequently, overexpression of lncRNA_XR209691.3 in BmN cells promoted the expression of BmHSP70, while knockdown of BmHsp70 suppressed the replication of BmNPV. Based on the above results, it is speculated that lincRNA_XR209691.3 could promote the proliferation of BmNPV through interaction with BmHSP70, possibly by improving the stability of BmHSP70 and thereby enhancing the expression of BmHSP70. Our results shed light on the lncRNA function in insect-pathogen interactions and provide a new clue to elucidate the molecular mechanism of BmNPV infection.
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Affiliation(s)
- Su Lin
- School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang, China
| | - Hao Tong Yin
- School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang, China
| | - Zhi Meng Zhao
- School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang, China
| | - Zi Kang Chen
- School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang, China
| | - Xue MIng Zhou
- School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang, China
| | - Zheng Dong Zhang
- School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang, China
| | - Xi Jie Guo
- School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang, China
- Key Laboratory of Silkworm and Mulberry Genetic Improvement, Ministry of Agriculture and Rural Affairs, Sericultural Research Institute, Chinese Academy of Agricultural Sciences, Zhenjiang, China
| | - Wei Guo Zhao
- School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang, China
- Key Laboratory of Silkworm and Mulberry Genetic Improvement, Ministry of Agriculture and Rural Affairs, Sericultural Research Institute, Chinese Academy of Agricultural Sciences, Zhenjiang, China
| | - Ping Wu
- School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang, China
- Key Laboratory of Silkworm and Mulberry Genetic Improvement, Ministry of Agriculture and Rural Affairs, Sericultural Research Institute, Chinese Academy of Agricultural Sciences, Zhenjiang, China
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Chen P, Cai M, Feng YJ, Li C, Dong ZQ, Xiao WF, Tang L, Zhu Y, Tian T, Deng BY, Pan MH, Lu C. Apoptosis-related long non-coding RNA LINC5438 of Bombyx mori promotes the proliferation of BmNPV. PESTICIDE BIOCHEMISTRY AND PHYSIOLOGY 2023; 191:105380. [PMID: 36963947 DOI: 10.1016/j.pestbp.2023.105380] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/25/2022] [Revised: 02/12/2023] [Accepted: 02/26/2023] [Indexed: 06/18/2023]
Abstract
Apoptosis, as an important part of the immune response, is one of the core events in the host-virus interaction. Studies have shown that long non-coding RNAs (lncRNAs) play important roles in the process of cell apoptosis and pathophysiology. To investigate the apoptosis-related lncRNAs involved in Bombyx mori nucleopolyhedrovirus (BmNPV) infecting silkworms, transcriptome sequencing was conducted based on silkworm cells infected with BmNPV before and after B. mori inhibitor of apoptosis (Bmiap) gene knockout. A total of 23 differentially expressed lncRNAs were identified as being associated with the mitochondrial apoptosis pathway. Moreover, we demonstrated that B. mori LINC5438 has the function of inhibiting apoptosis in silkworm cells. Overexpression of LINC5438 promoted the proliferation of BmNPV, while interference with LINC5438 inhibited its proliferation, indicating that LINC5438 plays an important role in BmNPV infection. Our results also showed that LINC5438 can regulate the expression of Bmiap, BmDronc, BmICE, and its predicted target gene BmAIF, suggesting that LINC5438 may function through the mitochondrial pathway. These findings provide important insights into the mechanisms of virus-host interaction and the applications of baculoviruses as biological insecticides.
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Affiliation(s)
- Peng Chen
- State Key Laboratory of Silkworm Genome Biology, Key Laboratory of Sericultural Biology and Genetic Breeding, Ministry of Agriculture and Rural Affairs, Southwest University, Beibei 400715, China
| | - Min Cai
- State Key Laboratory of Silkworm Genome Biology, Key Laboratory of Sericultural Biology and Genetic Breeding, Ministry of Agriculture and Rural Affairs, Southwest University, Beibei 400715, China
| | - Yu-Jie Feng
- State Key Laboratory of Silkworm Genome Biology, Key Laboratory of Sericultural Biology and Genetic Breeding, Ministry of Agriculture and Rural Affairs, Southwest University, Beibei 400715, China
| | - Cong Li
- State Key Laboratory of Silkworm Genome Biology, Key Laboratory of Sericultural Biology and Genetic Breeding, Ministry of Agriculture and Rural Affairs, Southwest University, Beibei 400715, China
| | - Zhan-Qi Dong
- State Key Laboratory of Silkworm Genome Biology, Key Laboratory of Sericultural Biology and Genetic Breeding, Ministry of Agriculture and Rural Affairs, Southwest University, Beibei 400715, China
| | - Wen-Fu Xiao
- State Key Laboratory of Silkworm Genome Biology, Key Laboratory of Sericultural Biology and Genetic Breeding, Ministry of Agriculture and Rural Affairs, Southwest University, Beibei 400715, China; Sericultural Research Institute Sichuan Academy of Agricultural Sciences, Nanchong 637000, China
| | - Liang Tang
- Sericulture Technology Promotion Station of Guangxi, Nanning 530007, China
| | - Yan Zhu
- State Key Laboratory of Silkworm Genome Biology, Key Laboratory of Sericultural Biology and Genetic Breeding, Ministry of Agriculture and Rural Affairs, Southwest University, Beibei 400715, China
| | - Ting Tian
- State Key Laboratory of Silkworm Genome Biology, Key Laboratory of Sericultural Biology and Genetic Breeding, Ministry of Agriculture and Rural Affairs, Southwest University, Beibei 400715, China
| | - Bo-Yuan Deng
- State Key Laboratory of Silkworm Genome Biology, Key Laboratory of Sericultural Biology and Genetic Breeding, Ministry of Agriculture and Rural Affairs, Southwest University, Beibei 400715, China
| | - Min-Hui Pan
- State Key Laboratory of Silkworm Genome Biology, Key Laboratory of Sericultural Biology and Genetic Breeding, Ministry of Agriculture and Rural Affairs, Southwest University, Beibei 400715, China.
| | - Cheng Lu
- State Key Laboratory of Silkworm Genome Biology, Key Laboratory of Sericultural Biology and Genetic Breeding, Ministry of Agriculture and Rural Affairs, Southwest University, Beibei 400715, China.
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11
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Wang Z, Wang S, Fan X, Zhang K, Zhang J, Zhao H, Gao X, Zhang Y, Guo S, Zhou D, Li Q, Na Z, Chen D, Guo R. Systematic Characterization and Regulatory Role of lncRNAs in Asian Honey Bees Responding to Microsporidian Infestation. Int J Mol Sci 2023; 24:ijms24065886. [PMID: 36982959 PMCID: PMC10058195 DOI: 10.3390/ijms24065886] [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: 01/08/2023] [Revised: 03/09/2023] [Accepted: 03/17/2023] [Indexed: 03/30/2023] Open
Abstract
Long noncoding RNAs (lncRNAs) are pivotal regulators in gene expression and diverse biological processes, such as immune defense and host-pathogen interactions. However, little is known about the roles of lncRNAs in the response of the Asian honey bee (Apis cerana) to microsporidian infestation. Based on our previously obtained high-quality transcriptome datasets from the midgut tissues of Apis cerana cerana workers at 7 days post inoculation (dpi) and 10 dpi with Nosema ceranae (AcT7 and AcT10 groups) and the corresponding un-inoculated midgut tissues (AcCK7 and AcCK10 groups), the transcriptome-wide identification and structural characterization of lncRNAs were conducted, and the differential expression pattern of lncRNAs was then analyzed, followed by investigation of the regulatory roles of differentially expressed lncRNAs (DElncRNAs) in host response. Here, 2365, 2322, 2487, and 1986 lncRNAs were, respectively, identified in the AcCK7, AcT7, AcCK7, and AcT10 groups. After removing redundant ones, a total of 3496 A. c. cerana lncRNAs were identified, which shared similar structural characteristics with those discovered in other animals and plants, such as shorter exons and introns than mRNAs. Additionally, 79 and 73 DElncRNAs were screened from the workers' midguts at 7 dpi and 10 dpi, respectively, indicating the alteration of the overall expression pattern of lncRNAs in host midguts after N. ceranae infestation. These DElncRNAs could, respectively, regulate 87 and 73 upstream and downstream genes, involving a suite of functional terms and pathways, such as metabolic process and Hippo signaling pathway. Additionally, 235 and 209 genes co-expressed with DElncRNAs were found to enrich in 29 and 27 terms, as well as 112 and 123 pathways, such as ABC transporters and the cAMP signaling pathway. Further, it was detected that 79 (73) DElncRNAs in the host midguts at 7 (10) dpi could target 321 (313) DEmiRNAs and further target 3631 (3130) DEmRNAs. TCONS_00024312 and XR_001765805.1 were potential precursors for ame-miR-315 and ame-miR-927, while TCONS_00006120 was the putative precursor for both ame-miR-87-1 and ame-miR-87-2. These results together suggested that DElncRNAs are likely to play regulatory roles in the host response to N. ceranae infestation through the regulation of neighboring genes via a cis-acting effect, modulation of co-expressed mRNAs via trans-acting effect, and control of downstream target genes' expression via competing endogenous RNA networks. Our findings provide a basis for disclosing the mechanism underlying DElncRNA-mediated host N. ceranae response and a new perspective into the interaction between A. c. cerana and N. ceranae.
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Affiliation(s)
- Zixin Wang
- College of Animal Sciences (College of Bee Science), Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Siyi Wang
- College of Animal Sciences (College of Bee Science), Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Xiaoxue Fan
- College of Animal Sciences (College of Bee Science), Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Kaiyao Zhang
- College of Animal Sciences (College of Bee Science), Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Jiaxin Zhang
- College of Animal Sciences (College of Bee Science), Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Haodong Zhao
- College of Animal Sciences (College of Bee Science), Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Xuze Gao
- College of Animal Sciences (College of Bee Science), Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Yiqiong Zhang
- College of Animal Sciences (College of Bee Science), Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Sijia Guo
- College of Animal Sciences (College of Bee Science), Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Dingding Zhou
- College of Animal Sciences (College of Bee Science), Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Qiming Li
- College of Animal Sciences (College of Bee Science), Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Zhihao Na
- College of Animal Sciences (College of Bee Science), Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Dafu Chen
- College of Animal Sciences (College of Bee Science), Fujian Agriculture and Forestry University, 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
- Apitherapy Research Institute of Fujian Province, Fuzhou 350002, China
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12
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Recent Advances and Future Potential of Long Non-Coding RNAs in Insects. Int J Mol Sci 2023; 24:ijms24032605. [PMID: 36768922 PMCID: PMC9917219 DOI: 10.3390/ijms24032605] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2022] [Revised: 12/28/2022] [Accepted: 01/04/2023] [Indexed: 01/31/2023] Open
Abstract
Over the last decade, long non-coding RNAs (lncRNAs) have witnessed a steep rise in interest amongst the scientific community. Because of their functional significance in several biological processes, i.e., alternative splicing, epigenetics, cell cycle, dosage compensation, and gene expression regulation, lncRNAs have transformed our understanding of RNA's regulatory potential. However, most knowledge concerning lncRNAs comes from mammals, and our understanding of the potential role of lncRNAs amongst insects remains unclear. Technological advances such as RNA-seq have enabled entomologists to profile several hundred lncRNAs in insect species, although few are functionally studied. This article will review experimentally validated lncRNAs from different insects and the lncRNAs identified via bioinformatic tools. Lastly, we will discuss the existing research challenges and the future of lncRNAs in insects.
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Hu Z, Zhu F, Chen K. The Mechanisms of Silkworm Resistance to the Baculovirus and Antiviral Breeding. ANNUAL REVIEW OF ENTOMOLOGY 2023; 68:381-399. [PMID: 36689303 DOI: 10.1146/annurev-ento-120220-112317] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Abstract
Silkworm (Bombyx mori) is not only an economic insect but also a model organism for life science research. Bombyx mori nucleopolyhedrovirus (BmNPV) disease is a major infectious disease in the world's sericulture industry. The cocoon loss caused by this disease accounts for more than 60% of the total loss caused by all silkworm diseases. To date, there has been no effective solution for preventing and treating this disease. The most effective measure is to breed disease-resistant varieties. The quickest way to breed disease-resistant varieties is to apply genetic modification. However, this requires that we obtain disease resistance genes and know the mechanism of disease resistance. Since the discovery of disease-resistant resources in 1989, scholars in the sericulture industry around the world have been inspired to search for resistance genes. In the past two decades, with the help of multi-omics technologies, screening of resistance genes, gene localization, protein modification, virus-host interactions, etc., researchers have found some candidate genes that have been proposed to function at the cellular or individual level. Several disease-resistant varieties have been obtained and used in production through hybrid breeding, RNA interference, and genetic modification. This article summarizes and reviews the discovery of and research advances related to silkworm resistance to BmNPV. It is anticipated that the review will inspire scientific researchers to continue searching for disease resistance genes, clarify the molecular mechanism of silkworm disease resistance, and promote disease-resistant silkworm breeding.
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Affiliation(s)
- Zhaoyang Hu
- School of Life Sciences, Jiangsu University, Zhenjiang, China;
| | - Feifei Zhu
- School of Life Sciences, Jiangsu University, Zhenjiang, China;
| | - Keping Chen
- School of Life Sciences, Jiangsu University, Zhenjiang, China;
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14
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Ye Y, Fan X, Long Q, Wang J, Zhang W, Cai Z, Sun M, Gu X, Zou P, Chen D, Guo R. Comprehensive investigation and regulatory function of lncRNAs engaged in western honey bee larval immune response to Ascosphaera apis invasion. Front Physiol 2022; 13:1082522. [PMID: 36589426 PMCID: PMC9800914 DOI: 10.3389/fphys.2022.1082522] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Accepted: 12/01/2022] [Indexed: 12/23/2022] Open
Abstract
Ascosphaera apis is a fungal pathogen that exclusively infects bee larvae, causing chalkbrood disease, which results in severe damage for beekeeping industry. Long non-coding RNAs (lncRNAs) are versatile regulators in various biological processes such as immune defense and host-pathogen interaction. However, expression pattern and regulatory role of lncRNAs involved in immune response of bee host to A. apis invasion is still very limited. Here, the gut tissues of Apis mellifera ligustica 4-, 5-, and 6-day-old larvae inoculated by A. apis spores (AmT1, AmT2, and AmT3 groups) and corresponding un-inoculated larval guts (AmCK1, AmCK2, and AmCK3 groups) were prepared and subjected to deep sequencing, followed by identification of lncRNAs, analysis of differentially expressed lncRNAs (DElncRNAs), and investigation of competing endogenous RNA (ceRNA) network. In total, 3,746 A. m. ligustica lncRNAs were identified, including 78 sense lncRNAs, 891 antisense lncRNAs, 1,893 intergenic lncRNAs, 346 bidirectional lncRNAs, and 210 intronic lncRNAs. In the 4-, 5-, and 6- comparison groups, 357, 236, and 505 DElncRNAs were discovered. Additionally, 217, 129, and 272 DElncRNAs were respectively predicted to regulate neighboring genes via cis-acting manner, and these targets were associated with a series of GO terms and KEGG pathways of great importance, such as response to stimulus and Jak-STAT signaling pathway. Moreover, 197, 95, and 356 DElncRNAs were observed to target 10, eight, and 21 DEmiRNAs and further target 147, 79, and 315 DEmRNAs, forming complex regulatory networks. Further investigation suggested that these targets were engaged in several key cellular and humoral immune pathways, such as phagosome and MAPK signaling pathway. Ultimately, the expression trends of nine randomly selected DElncRNAs were verified by RT-qPCR, confirming the authenticity and reliability of our transcriptome data. Findings in this current work not only provide candidate DElncRNAs for functional study, but also lay a foundation for unclosing the mechanism underlying DElncRNA-regulated larval immune responses to A. apis invasion.
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Affiliation(s)
- Yaping Ye
- College of Animal Sciences (College of Bee Science), Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
| | - Xiaoxue Fan
- College of Animal Sciences (College of Bee Science), Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
| | - Qi Long
- College of Animal Sciences (College of Bee Science), Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
| | - Jie Wang
- College of Animal Sciences (College of Bee Science), Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
| | - Wende Zhang
- College of Animal Sciences (College of Bee Science), Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
| | - Zongbing Cai
- College of Animal Sciences (College of Bee Science), Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
| | - Minghui Sun
- College of Animal Sciences (College of Bee Science), Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
| | - Xiaoyu Gu
- College of Animal Sciences (College of Bee Science), Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
| | - Peiyuan Zou
- College of Animal Sciences (College of Bee Science), Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
| | - Dafu Chen
- College of Animal Sciences (College of Bee Science), Fujian Agriculture and Forestry University, Fuzhou, Fujian, China,Apitherapy Research Institute, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
| | - Rui Guo
- College of Animal Sciences (College of Bee Science), Fujian Agriculture and Forestry University, Fuzhou, Fujian, China,Apitherapy Research Institute, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China,*Correspondence: Rui Guo,
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15
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Zafar J, Huang J, Xu X, Jin F. Analysis of Long Non-Coding RNA-Mediated Regulatory Networks of Plutella xylostella in Response to Metarhizium anisopliae Infection. INSECTS 2022; 13:916. [PMID: 36292864 PMCID: PMC9604237 DOI: 10.3390/insects13100916] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Revised: 09/30/2022] [Accepted: 09/30/2022] [Indexed: 06/16/2023]
Abstract
Long non-coding RNAs (lncRNAs) represent a diverse class of RNAs that are structurally similar to messenger RNAs (mRNAs) but do not encode proteins. Growing evidence suggests that in response to biotic and abiotic stresses, the lncRNAs play crucial regulatory roles in plants and animals. However, the potential role of lncRNAs during fungal infection has yet to be characterized in Plutella xylostella, a devastating pest of cruciferous crops. In the current study, we performed a strand-specific RNA sequencing of Metarhizium anisopliae-infected (Px36hT, Px72hT) and uninfected (Px36hCK, Px72hCK) P. xylostella fat body tissues. Comprehensive bioinformatic analysis revealed a total of 5665 and 4941 lncRNAs at 36 and 72-h post-infection (hpi), including 563 (Px36hT), 532 (Px72hT) known and 5102 (Px36hT), 4409 (Px72hT) novel lncRNA transcripts. These lncRNAs shared structural similarities with their counterparts in other species, including shorter exon and intron length, fewer exon numbers, and a lower expression profile than mRNAs. LncRNAs regulate the expression of neighboring protein-coding genes by acting in a cis and trans manner. Functional annotation and pathway analysis of cis-acting lncRNAs revealed their role in several immune-related genes, including Toll, serpin, transferrin, βGRP etc. Furthermore, we identified multiple lncRNAs acting as microRNA (miRNA) precursors. These miRNAs can potentially regulate the expression of mRNAs involved in immunity and development, suggesting a crucial lncRNA-miRNA-mRNA complex. Our findings will provide a genetic resource for future functional studies of lncRNAs involved in P. xylostella immune responses to M. anisopliae infection and shed light on understanding insect host-pathogen interactions.
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Affiliation(s)
| | | | - Xiaoxia Xu
- Correspondence: (X.X.); (F.J.); Tel.: +86-135-6047-8369 (F.J.)
| | - Fengliang Jin
- Correspondence: (X.X.); (F.J.); Tel.: +86-135-6047-8369 (F.J.)
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Whole Transcriptome-Based Study to Speculate upon the Silkworm Yellow Blood Inhibitor (I) Gene and Analyze the miRNA-Mediated Gene Regulatory Network. Processes (Basel) 2022. [DOI: 10.3390/pr10081556] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
White cocoon is developed and used as a natural fiber, and different silkworm strains have different cocoon colors. Natural-colored cocoons are preferred by people, however, the cocoon color mainly settles on sericin and it basically falls off after reeling. Currently, there are no varieties applied to production due to the formation mechanism of cocoon color is not clear. The formation of cocoon color involves multiple gene regulations. Previous studies have shown that the main genes regulating cocoon traits are the yellow blood (Y) gene, yellow blood inhibitor (I) gene, and yellow cocoon (C) gene. Among them, the products of the Y gene and C gene have been studied, but the I gene is still unclear. In this study, the midgut tissues of the yellow (NB) and the white (306) cocoon silkworm were analyzed by whole transcriptome sequencing. The results showed that there are 1639 DE-circRNAs, 70 DE-miRNAs, and 3225 DE-mRNAs, including 1785 up-regulated genes and 1440 down-regulated genes. GO and KEGG annotation results indicated that DE-mRNAs are mainly involved in intracellular transport, signal transduction, lipid transport, and metabolic processes. Two key genes, KWMTBOMO10339 and KWMTBOMO16553, were screened out according to the annotation results, which were involved in amino acid transport and ion exchange function, respectively. The interaction analysis between ncRNA and target genes showed that there were five miRNAs regulating these two genes. The qPCR analysis showed that the I gene was down-regulated, and the miRNA expression profiles were most up-regulated. Therefore, during the yellow and white cocoon formation, KWMTBOMO10339 and KWMTBOMO16553 may be regulated by miRNA, resulting in the non-expression of KWMTBOMO10339 and KWMTBOMO16553 in yellow cocoon silkworm, and the pigment molecules can enter hemolymph from the midgut to form yellow blood, then transport to the middle silk gland to finally form yellow cocoons.
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17
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Wang KX, Chen CB, Wan QX, Zha XF. Long Non-Coding RNA Bmdsx-AS1 Effects on Male External Genital Development in Silkworm. INSECTS 2022; 13:insects13020188. [PMID: 35206761 PMCID: PMC8875567 DOI: 10.3390/insects13020188] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/11/2022] [Revised: 02/08/2022] [Accepted: 02/09/2022] [Indexed: 12/07/2022]
Abstract
Simple Summary LncRNAs are a class of non-coding RNAs longer than 200 nt that are involved in a variety of biological processes. Studies on lncRNAs in Bombyx mori have shown that some lncRNAs are involved in brain development, silk production and the response to virus infection of the host. However, the roles of lncRNAs are still largely unknown in the silkworm. In this study, we analyzed the function of lncRNAs Bmdsx-AS1 in silkworm by transgenic overexpression, which not only affects the development of male silkworm external genitalia, but also participates in the regulation of EGFR signaling pathway. Moreover, we studied the upstream promoter of Bmdsx-AS1 and found that the BmAbd-B transcription factor of the Hox gene family can negatively regulate the expression of Bmdsx-AS1. These results laid a substantial foundation for in-depth study of the function of lncRNAs in the silkworm. Abstract Long non-coding RNAs (lncRNAs) have been suggested to play important roles in some biological processes. However, the detailed mechanisms are not fully understood. We previously identified an antisense lncRNA, Bmdsx-AS1, that is involved in pre-mRNA splicing of the sex-determining gene Bmdsx in the silkworm. In this study, we analyzed the changes in the male external genitalia of transgenic overexpressed Bmdsx-AS1 silkworm lines and analyzed downstream and upstream responses. We found that Bmdsx-AS1 transgenic silkworms, compared with wild type, showed more claspers in the male external genitalia. Quantitative real-time PCR (qPCR) results indicated that overexpression of Bmdsx-AS1 decreased the expression of genes in the EGFR signaling pathway. Knockdown of Bmdsx-AS1 increased the activity of the EGFR pathway. Through promoter prediction, promoter truncation and electrophoretic mobility shift assay (EMSA) analyses, we found that the protein encoded by the Hox gene BmAbd-B specifically binds to the promoter of Bmdsx-AS1. Moreover, overexpression of BmAbd-B in the silkworm BmE cell line indicated that BmAbd-B negatively regulates the mRNA expression of Bmdsx-AS1. Our study provides insights into the regulatory mechanism of the lncRNA in the silkworm.
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Shang F, Ding BY, Zhang YT, Wu JJ, Pan ST, Wang JJ. Genome-wide analysis of long non-coding RNAs and their association with wing development in Aphis citricidus (Hemiptera: Aphididae). INSECT BIOCHEMISTRY AND MOLECULAR BIOLOGY 2021; 139:103666. [PMID: 34619323 DOI: 10.1016/j.ibmb.2021.103666] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/03/2021] [Revised: 09/28/2021] [Accepted: 09/28/2021] [Indexed: 06/13/2023]
Abstract
Long non-coding RNAs (lncRNAs) play critical roles in the various physiological processes of insects. The wing is a successful adaptation allowing insects to escape from unfavorable environments, while information on lncRNAs related to wing development is limited. In this study, we constructed 12 libraries from two RNA-seq comparisons: 4th instar winged nymphs versus winged adults and 4th instar wingless nymphs versus wingless adults in the brown citrus aphid Aphis citricidus, to identify the wing development-associated lncRNAs. A total of 2914 lncRNAs were identified and 50 lncRNAs were differentially expressed during the 4th instar winged nymphs to winged adults transition, and 28 lncRNAs changed during the 4th instar wingless nymphs to wingless adults transition. The differentially expressed lncRNAs were grouped into six clusters according to the expression patterns in the combined two-winged morphs. lncRNA Ac_lnc54106.1 was up-regulated during 4th instar winged nymphs to winged adults transition, but a lack of change during the 4th instar wingless nymphs to wingless adults transition implied a critical role in the specific regulation of wing development. RNA interference of Ac_lnc54106.1 resulted in malformed wings. Targets prediction, expression patterns, and RNAi assay results showed that Ac_lnc54106.1 may target the PiggyBac transposable element-derived protein 4 (PGBD4) gene, decrease expression of the canonical wing development-related genes, and finally regulate wing development. The systematic identification of lncRNAs in an aphid increases our understanding of how non-coding RNA mediates the wing plasticity of insects.
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Affiliation(s)
- Feng Shang
- Key Laboratory of Entomology and Pest Control Engineering, College of Plant Protection, Southwest University, Chongqing, 400716, China; State Cultivation Base of Crop Stress Biology for Southern Mountainous Land, Academy of Agricultural Sciences, Southwest University, Chongqing, China.
| | - Bi-Yue Ding
- Key Laboratory of Entomology and Pest Control Engineering, College of Plant Protection, Southwest University, Chongqing, 400716, China; State Cultivation Base of Crop Stress Biology for Southern Mountainous Land, Academy of Agricultural Sciences, Southwest University, Chongqing, China.
| | - Yong-Te Zhang
- Key Laboratory of Entomology and Pest Control Engineering, College of Plant Protection, Southwest University, Chongqing, 400716, China.
| | - Jin-Jin Wu
- Key Laboratory of Entomology and Pest Control Engineering, College of Plant Protection, Southwest University, Chongqing, 400716, China.
| | - Si-Tong Pan
- Key Laboratory of Entomology and Pest Control Engineering, College of Plant Protection, Southwest University, Chongqing, 400716, China.
| | - Jin-Jun Wang
- Key Laboratory of Entomology and Pest Control Engineering, College of Plant Protection, Southwest University, Chongqing, 400716, China; State Cultivation Base of Crop Stress Biology for Southern Mountainous Land, Academy of Agricultural Sciences, Southwest University, Chongqing, China.
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Comparative Transcriptome Analysis of Bombyx mori (Lepidoptera) Larval Hemolymph in Response to Autographa californica Nucleopolyhedrovirus in Differentially Resistant Strains. Processes (Basel) 2021. [DOI: 10.3390/pr9081401] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Bombyx mori nucleopolyhedrovirus (BmNPV) is a kind of pathogen that causes huge economic losses to silkworm production. Although Autographa californica nucleopolyhedrovirus (AcMNPV) and BmNPV are both baculoviruses, the host domains of these two viruses have almost no intersection in nature. Recently, it has been found that some silkworms could be infected by recombinant AcMNPV through a puncture, which provided valuable material for studying the infection mechanism of baculovirus to silkworm. In this study, comparative transcriptomics was used to analyse the hemolymph of two differentially resistant strains following AcMNPV inoculation. There were 678 DEGs in p50 and 515 DEGs in C108 following viral infection. Among them, the upregulation and downregulation of DEGs were similar in p50; however, the upregulated DEGs were nearly twice as numerous as the downregulated DEGs in C108. The DEGs in different resistant strains differed by GO enrichment. Based on KEGG enrichment, DEGs were mainly enriched in metabolic pathways in p50 and the apoptosis pathway in C108. Moreover, 13 genes involved in metabolic pathways and 11 genes involved in the apoptosis pathway were analysed. Among the DEGs involved in apoptosis, the function of BmTex261 in viral infection was analysed. The BmTex261 showed the highest expression in hemolymph and a significant response to viral infection in the hemolymph of C108, indicating that it is involved in anti-AcMNPV infection. This was further validated by the significantly decreased expression of viral gene lef3 after overexpression of BmTex261 in BmN cells. The results provide a theoretical reference for the molecular mechanism of resistance to BmNPV in silkworms.
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Qiao H, Wang J, Wang Y, Yang J, Wei B, Li M, Wang B, Li X, Cao Y, Tian L, Li D, Yao L, Kan Y. Transcriptome analysis reveals potential function of long non-coding RNAs in 20-hydroxyecdysone regulated autophagy in Bombyx mori. BMC Genomics 2021; 22:374. [PMID: 34022797 PMCID: PMC8140452 DOI: 10.1186/s12864-021-07692-1] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Accepted: 05/06/2021] [Indexed: 12/13/2022] Open
Abstract
Background 20-hydroxyecdysone (20E) plays important roles in insect molting and metamorphosis. 20E-induced autophagy has been detected during the larval–pupal transition in different insects. In Bombyx mori, autophagy is induced by 20E in the larval fat body. Long non-coding RNAs (lncRNAs) function in various biological processes in many organisms, including insects. Many lncRNAs have been reported to be potential for autophagy occurrence in mammals, but it has not been investigated in insects. Results RNA libraries from the fat body of B. mori dissected at 2 and 6 h post-injection with 20E were constructed and sequenced, and comprehensive analysis of lncRNAs and mRNAs was performed. A total of 1035 lncRNAs were identified, including 905 lincRNAs and 130 antisense lncRNAs. Compared with mRNAs, lncRNAs had longer transcript length and fewer exons. 132 lncRNAs were found differentially expressed at 2 h post injection, compared with 64 lncRNAs at 6 h post injection. Thirty differentially expressed lncRNAs were common at 2 and 6 h post-injection, and were hypothesized to be associated with the 20E response. Target gene analysis predicted 6493 lncRNA-mRNA cis pairs and 42,797 lncRNA-mRNA trans pairs. The expression profiles of LNC_000560 were highly consistent with its potential target genes, Atg4B, and RNAi of LNC_000560 significantly decreased the expression of LNC_000560 and Atg4B. These results indicated that LNC_000560 was potentially involved in the 20E-induced autophagy of the fat body by regulating Atg4B. Conclusions This study provides the genome-wide identification and functional characterization of lncRNAs associated with 20E-induced autophagy in the fat body of B. mori. LNC_000560 and its potential target gene were identified to be related to 20-regulated autophagy in B. mori. These results will be helpful for further studying the regulatory mechanisms of lncRNAs in autophagy and other biological processes in this insect model. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-021-07692-1.
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Affiliation(s)
- Huili Qiao
- China-UK-NYNU-RRes Joint Laboratory of insect biology, Henan Key Laboratory of Insect Biology in Funiu Mountain, Nanyang Normal University, 473061, Nanyang, Henan, China
| | - Jingya Wang
- China-UK-NYNU-RRes Joint Laboratory of insect biology, Henan Key Laboratory of Insect Biology in Funiu Mountain, Nanyang Normal University, 473061, Nanyang, Henan, China.,School of Life Science, Zhengzhou University, 450001, Zhengzhou, Henan, China
| | - Yuanzhuo Wang
- China-UK-NYNU-RRes Joint Laboratory of insect biology, Henan Key Laboratory of Insect Biology in Funiu Mountain, Nanyang Normal University, 473061, Nanyang, Henan, China
| | - Juanjuan Yang
- China-UK-NYNU-RRes Joint Laboratory of insect biology, Henan Key Laboratory of Insect Biology in Funiu Mountain, Nanyang Normal University, 473061, Nanyang, Henan, China
| | - Bofan Wei
- China-UK-NYNU-RRes Joint Laboratory of insect biology, Henan Key Laboratory of Insect Biology in Funiu Mountain, Nanyang Normal University, 473061, Nanyang, Henan, China
| | - Miaomiao Li
- China-UK-NYNU-RRes Joint Laboratory of insect biology, Henan Key Laboratory of Insect Biology in Funiu Mountain, Nanyang Normal University, 473061, Nanyang, Henan, China.,School of Life Science, Zhengzhou University, 450001, Zhengzhou, Henan, China
| | - Bo Wang
- China-UK-NYNU-RRes Joint Laboratory of insect biology, Henan Key Laboratory of Insect Biology in Funiu Mountain, Nanyang Normal University, 473061, Nanyang, Henan, China
| | - Xiaozhe Li
- China-UK-NYNU-RRes Joint Laboratory of insect biology, Henan Key Laboratory of Insect Biology in Funiu Mountain, Nanyang Normal University, 473061, Nanyang, Henan, China
| | - Yang Cao
- State Key Laboratory of Silkworm Genome Biology / Biological Science Research Center, Southwest University, 400716, Chongqing, China.,Guangdong Laboratory for Lingnan Modern Agriculture/Guangdong Provincial Key Laboratory of Agro-animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, 510642, Guangzhou, Guangdong, China
| | - Ling Tian
- Guangdong Laboratory for Lingnan Modern Agriculture/Guangdong Provincial Key Laboratory of Agro-animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, 510642, Guangzhou, Guangdong, China
| | - Dandan Li
- China-UK-NYNU-RRes Joint Laboratory of insect biology, Henan Key Laboratory of Insect Biology in Funiu Mountain, Nanyang Normal University, 473061, Nanyang, Henan, China
| | - Lunguang Yao
- China-UK-NYNU-RRes Joint Laboratory of insect biology, Henan Key Laboratory of Insect Biology in Funiu Mountain, Nanyang Normal University, 473061, Nanyang, Henan, China
| | - Yunchao Kan
- China-UK-NYNU-RRes Joint Laboratory of insect biology, Henan Key Laboratory of Insect Biology in Funiu Mountain, Nanyang Normal University, 473061, Nanyang, Henan, China.
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21
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Awais MM, Shakeel M, Sun J. MicroRNA-Mediated Host-Pathogen Interactions Between Bombyx mori and Viruses. Front Physiol 2021; 12:672205. [PMID: 34025458 PMCID: PMC8137832 DOI: 10.3389/fphys.2021.672205] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2021] [Accepted: 04/14/2021] [Indexed: 12/14/2022] Open
Abstract
MicroRNAs (miRNAs), small non-coding RNAs of about 22 nucleotides, have been reported to regulate gene expression at the posttranscriptional level and are involved in several biological processes such as immunity, development, metabolism, and host-pathogen interactions. Apart from miRNAs encoded by the host, miRNAs produced by pathogens also regulate host genes to facilitate virus replication and evasion of the host defense responses. In recent years, accumulated studies suggest that viral infections alter the host miRNAs expression profile, and both cellular and viral miRNAs may play vital roles in host-pathogen interactions. Bombyx mori, one of the critical lepidopteran model species, is an economically important insect for silk production. The mechanism of interaction between B. mori and its pathogens and their regulation by miRNAs has been extensively studied. Therefore, in this review, we aim to highlight the recent information and understanding of the virus-encoding miRNAs and their functions in modulating viral and host (B. mori) genes. Additionally, the response of B. mori derived miRNAs to viral infection is also discussed. A detailed critical view about miRNAs’ regulatory roles in B. mori-virus interactions will help us understand molecular networks and develop a sustainable antiviral strategy.
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Affiliation(s)
- Mian Muhammad Awais
- Guangdong Provincial Key Laboratory of Agro-animal Genomics and Molecular Breeding and Sub-Tropical Sericulture and Mulberry Resources Protection and Safety Engineering Research Center, College of Animal Science, South China Agricultural University, Guangzhou, China
| | - Muhammad Shakeel
- Laboratory of Bio-Pesticide Innovation and Application of Guandong Province, College of Plant Protection, South China Agricultural University, Guangzhou, China
| | - Jingchen Sun
- Guangdong Provincial Key Laboratory of Agro-animal Genomics and Molecular Breeding and Sub-Tropical Sericulture and Mulberry Resources Protection and Safety Engineering Research Center, College of Animal Science, South China Agricultural University, Guangzhou, China
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22
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Feng M, Xia J, Fei S, Peng R, Wang X, Zhou Y, Wang P, Swevers L, Sun J. Identification of Silkworm Hemocyte Subsets and Analysis of Their Response to Baculovirus Infection Based on Single-Cell RNA Sequencing. Front Immunol 2021; 12:645359. [PMID: 33995363 PMCID: PMC8119652 DOI: 10.3389/fimmu.2021.645359] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2020] [Accepted: 04/14/2021] [Indexed: 01/04/2023] Open
Abstract
A wide range of hemocyte types exist in insects but a full definition of the different subclasses is not yet established. The current knowledge of the classification of silkworm hemocytes mainly comes from morphology rather than specific markers, so our understanding of the detailed classification, hemocyte lineage and functions of silkworm hemocytes is very incomplete. Bombyx mori nucleopolyhedrovirus (BmNPV) is a representative member of the baculoviruses and a major pathogen that specifically infects silkworms (Bombyx mori) and causes serious losses in sericulture industry. Here, we performed single-cell RNA sequencing (scRNA-seq) of hemocytes in BmNPV and mock-infected larvae to comprehensively identify silkworm hemocyte subsets and determined specific molecular and cellular characteristics in each hemocyte subset before and after viral infectmadion. A total of 20 cell clusters and their potential marker genes were identified in silkworm hemocytes. All of the hemocyte clusters were infected by BmNPV at 3 days after inoculation. Interestingly, BmNPV infection can cause great changes in the distribution of hemocyte types. The cells appearing in the infection group mainly belong to prohemocytes (PR), while plasmatocytes (PL) and granulocytes (GR) are very much reduced. Furthermore, we found that BmNPV infection suppresses the RNA interference (RNAi) and immune response in the major hemocyte types. In summary, our results revealed the diversity of silkworm hemocytes and provided a rich resource of gene expression profiles for a systems-level understanding of their functions in the uninfected condition and as a response to BmNPV.
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Affiliation(s)
- Min Feng
- Guangdong Provincial Key Laboratory of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou, China
| | - Junming Xia
- Guangdong Provincial Key Laboratory of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou, China
| | - Shigang Fei
- Guangdong Provincial Key Laboratory of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou, China
| | - Ruoxuan Peng
- Guangdong Provincial Key Laboratory of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou, China
| | - Xiong Wang
- Guangdong Provincial Key Laboratory of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou, China
| | - Yaohong Zhou
- Guangdong Provincial Key Laboratory of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou, China
| | - Pengwei Wang
- Guangdong Provincial Key Laboratory of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou, China
| | - Luc Swevers
- Insect Molecular Genetics and Biotechnology, National Centre for Scientific Research Demokritos, Institute of Biosciences and Applications, Athens, Greece
| | - Jingchen Sun
- Guangdong Provincial Key Laboratory of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou, China
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23
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Choudhary C, Sharma S, Meghwanshi KK, Patel S, Mehta P, Shukla N, Do DN, Rajpurohit S, Suravajhala P, Shukla JN. Long Non-Coding RNAs in Insects. Animals (Basel) 2021; 11:1118. [PMID: 33919662 PMCID: PMC8069800 DOI: 10.3390/ani11041118] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2021] [Revised: 03/30/2021] [Accepted: 04/06/2021] [Indexed: 12/27/2022] Open
Abstract
Only a small subset of all the transcribed RNAs are used as a template for protein translation, whereas RNA molecules that are not translated play a very important role as regulatory non-coding RNAs (ncRNAs). Besides traditionally known RNAs (ribosomal and transfer RNAs), ncRNAs also include small non-coding RNAs (sncRNAs) and long non-coding RNAs (lncRNAs). The lncRNAs, which were initially thought to be junk, have gained a great deal attention because of their regulatory roles in diverse biological processes in animals and plants. Insects are the most abundant and diverse group of animals on this planet. Recent studies have demonstrated the role of lncRNAs in almost all aspects of insect development, reproduction, and genetic plasticity. In this review, we describe the function and molecular mechanisms of the mode of action of different insect lncRNAs discovered up to date.
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Affiliation(s)
- Chhavi Choudhary
- Department of Biotechnology, School of Life Sciences, Central University of Rajasthan, Bandarsindari, Ajmer 305801, India; (C.C.); (K.K.M.)
| | - Shivasmi Sharma
- Department of Biotechnology, Amity University Jaipur, Jaipur 303002, India; (S.S.); (S.P.)
| | - Keshav Kumar Meghwanshi
- Department of Biotechnology, School of Life Sciences, Central University of Rajasthan, Bandarsindari, Ajmer 305801, India; (C.C.); (K.K.M.)
| | - Smit Patel
- Department of Biotechnology, Amity University Jaipur, Jaipur 303002, India; (S.S.); (S.P.)
| | - Prachi Mehta
- Division of Biological & Life Sciences, School of Arts and Sciences, Ahmedabad University, Gujarat 380009, India; (P.M.); (S.R.)
| | - Nidhi Shukla
- Department of Biotechnology and Bioinformatics, Birla Institute of Scientific Research, Jaipur 302001, India;
| | - Duy Ngoc Do
- Institute of Research and Development, Duy Tan University, Danang 550000, Vietnam;
| | - Subhash Rajpurohit
- Division of Biological & Life Sciences, School of Arts and Sciences, Ahmedabad University, Gujarat 380009, India; (P.M.); (S.R.)
| | - Prashanth Suravajhala
- Department of Biotechnology and Bioinformatics, Birla Institute of Scientific Research, Jaipur 302001, India;
- Bioclues.org, Vivekananda Nagar, Kukatpally, Hyderabad, Telangana 500072, India
| | - Jayendra Nath Shukla
- Department of Biotechnology, School of Life Sciences, Central University of Rajasthan, Bandarsindari, Ajmer 305801, India; (C.C.); (K.K.M.)
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24
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Zhang Z, Zhao Z, Lin S, Wu W, Tang W, Dong Y, Shen M, Wu P, Guo X. Identification of long noncoding RNAs in silkworm larvae infected with Bombyx mori cypovirus. ARCHIVES OF INSECT BIOCHEMISTRY AND PHYSIOLOGY 2021; 106:1-12. [PMID: 33619747 DOI: 10.1002/arch.21777] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Revised: 01/31/2021] [Accepted: 02/03/2021] [Indexed: 06/12/2023]
Abstract
Bombyx mori cypovirus (BmCPV) is one of the most important pathogens causing severe disease to silkworm. Emerging evidence indicates that long noncoding RNAs (lncRNAs) play importantly regulatory roles in virus infection and host immune response. To better understand the interaction between silkworm, Bombyx mori and BmCPV, we performed a comparative transcriptome analysis on lncRNAs and mRNAs between the virus-infected and noninfected silkworm larvae midgut at two time points postinoculation. A total of 16,753 genes and 1845 candidate lncRNAs were identified, among which 356 messenger RNA (mRNAs) and 41 lncRNAs were differentially expressed (DE). Target gene prediction revealed that most of DEmRNAs (123) were coexpressed with 28 DElncRNAs, suggesting that the expression of mRNA is mainly affected through trans- regulation by BmCPV-induced lncRNAs, and a regulatory network of DElncRNAs and DEmRNAs was then constructed. According to the network, many genes involved in apoptosis, autophagy, and antiviral response, such as ATG3, PDCD6, IBP2, and MFB1, could be targeted by different DElncRNAs, implying the essential roles of these genes and lncRNAs in BmCPV infection. In all, our studies revealed for the first time the alteration of lncRNA expression in BmCPV-infected larvae and its potential influence on BmCPV replication, providing a new perspective for host-cypovirus interaction studies.
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Affiliation(s)
- Zhendong Zhang
- School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang, Jiangsu, China
- Sericultural Research Institute, Chinese Academy of Agricultural Sciences, Zhenjiang, Jiangsu, China
| | - Ze Zhao
- School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang, Jiangsu, China
- Sericultural Research Institute, Chinese Academy of Agricultural Sciences, Zhenjiang, Jiangsu, China
| | - Su Lin
- School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang, Jiangsu, China
- Sericultural Research Institute, Chinese Academy of Agricultural Sciences, Zhenjiang, Jiangsu, China
| | - Wanming Wu
- School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang, Jiangsu, China
- Sericultural Research Institute, Chinese Academy of Agricultural Sciences, Zhenjiang, Jiangsu, China
| | - Weiming Tang
- School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang, Jiangsu, China
- Sericultural Research Institute, Chinese Academy of Agricultural Sciences, Zhenjiang, Jiangsu, China
| | - Youfu Dong
- School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang, Jiangsu, China
- Sericultural Research Institute, Chinese Academy of Agricultural Sciences, Zhenjiang, Jiangsu, China
| | - Manman Shen
- School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang, Jiangsu, China
- Sericultural Research Institute, Chinese Academy of Agricultural Sciences, Zhenjiang, Jiangsu, China
| | - Ping Wu
- School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang, Jiangsu, China
- Sericultural Research Institute, Chinese Academy of Agricultural Sciences, Zhenjiang, Jiangsu, China
| | - Xijie Guo
- School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang, Jiangsu, China
- Sericultural Research Institute, Chinese Academy of Agricultural Sciences, Zhenjiang, Jiangsu, China
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25
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Zhang S, Shen M, Yin H, Huang H, Li T, Zhao W, Guo X, Wu P. Expression profile analysis of circular RNAs in BmN cells (Bombyx mori) upon BmNPV infection. ARCHIVES OF INSECT BIOCHEMISTRY AND PHYSIOLOGY 2020; 105:e21735. [PMID: 32881053 DOI: 10.1002/arch.21735] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/16/2020] [Revised: 08/08/2020] [Accepted: 08/14/2020] [Indexed: 06/11/2023]
Abstract
The disease caused by Bombyx mori nucleopolyhedrovirus (BmNPV) has always been difficult to control, resulting in tremendous economic losses in the sericulture industry. Although much has been learned about the impact of noncoding RNAs on pathogenesis, the role of circular RNA (circRNA) in insect immunity remains unclear. To explore circRNA regulation involved in BmNPV infection, we used transcriptome analysis of BmN cells with or without BmNPV infection to generate circRNA data set. A total of 444 novel circRNAs were identified in BmN cells, with 198 pervasively distributed both in the control group and BmNPV-infection group. The host genes were enriched inMAPK signaling pathway, dorso-ventral axis formation, and ECM-receptor interaction, which were required for the normal larval growth. A total of 75 circRNAs were differentially expressed (DE) on BmNPV infection. Six downregulated circRNAs were validated by Sanger sequencing and qRT-PCR. DEcircRNA-miRNA-DEmRNA network was constructed based on the six validated circRNAs. Pathway analysis indicated that the predicted target genes were mainly enriched in the metabolic pathway and immune-related signaling pathway. Our results may provide a basis for further studies on circRNA function in BmN cells challenged by BmNPV infection and offer an insight into the molecular mechanism on silkworm-virus interaction.
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Affiliation(s)
- Shaolun Zhang
- Jiangsu Key Laboratory of Sericultural Biology and Biotechnology, School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang, Jiangsu, China
| | - Manman Shen
- Jiangsu Key Laboratory of Sericultural Biology and Biotechnology, School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang, Jiangsu, China
- Key Laboratory of Silkworm and Mulberry Genetic Improvement, Ministry of Agriculture and Rural Affairs, Sericultural Research Institute, Chinese Academy of Agricultural Sciences, Zhenjiang, Jiangsu, China
| | - Haotong Yin
- Jiangsu Key Laboratory of Sericultural Biology and Biotechnology, School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang, Jiangsu, China
| | - Haoling Huang
- Jiangsu Key Laboratory of Sericultural Biology and Biotechnology, School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang, Jiangsu, China
| | - Tao Li
- Jiangsu Key Laboratory of Sericultural Biology and Biotechnology, School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang, Jiangsu, China
| | - Weiguo Zhao
- Jiangsu Key Laboratory of Sericultural Biology and Biotechnology, School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang, Jiangsu, China
- Key Laboratory of Silkworm and Mulberry Genetic Improvement, Ministry of Agriculture and Rural Affairs, Sericultural Research Institute, Chinese Academy of Agricultural Sciences, Zhenjiang, Jiangsu, China
| | - Xijie Guo
- Jiangsu Key Laboratory of Sericultural Biology and Biotechnology, School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang, Jiangsu, China
- Key Laboratory of Silkworm and Mulberry Genetic Improvement, Ministry of Agriculture and Rural Affairs, Sericultural Research Institute, Chinese Academy of Agricultural Sciences, Zhenjiang, Jiangsu, China
| | - Ping Wu
- Jiangsu Key Laboratory of Sericultural Biology and Biotechnology, School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang, Jiangsu, China
- Key Laboratory of Silkworm and Mulberry Genetic Improvement, Ministry of Agriculture and Rural Affairs, Sericultural Research Institute, Chinese Academy of Agricultural Sciences, Zhenjiang, Jiangsu, China
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Yin H, Shang Q, Zhang S, Shen M, Huang H, Zhao W, Xijie G, Wu P. Comprehensive analysis of lncRNA-mRNA regulatory network in BmNPV infected cells treated with Hsp90 inhibitor. Mol Immunol 2020; 127:230-237. [PMID: 33022580 DOI: 10.1016/j.molimm.2020.09.014] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2020] [Revised: 09/16/2020] [Accepted: 09/21/2020] [Indexed: 11/16/2022]
Abstract
Bombyx mori nucleopolyhedrovirus (BmNPV) is one of the main pathogens that seriously affect the sustainable development of sericulture industry. Inhibition of Hsp90 by Hsp90 inhibitor, geldanamycin (GA) significantly suppresses BmNPV proliferation in Bombyx mori, while the functional mechanism is not clear. LncRNA has been widely reported to play an important role in immune responses and host-virus interactions in mammalian. However, related research has been rarely reported on silkworm. In this study, firstly, we confirmed the decrease of BmNPV ORF75 protein in the BmNPV-infected BmN cells treated with GA. Next, by using a genome-wide transcriptome analysis, we compared the lncRNA and mRNA expression profiles in BmNPV infected BmN cells treated with or without GA and identified a total of 282 differentially expressed lncRNAs (DElncRNAs) and 523 DEmRNAs. KEGG pathway analysis revealed DEmRNA were mainly involved in ubiquitin mediated proteolysis, spliceosome, RNA transport and oxidative phosphorylation. Further, we selected 27 immune-related DEmRNAs, which displayed the similar changes of expression patterns on both protein level and transcript level to construct DElncRNA-DEmRNA network. In addition, based on the DElncRNA-bmo-miR-278-3p-BmHSC70 regulatory network, we explored the potential function of several lncRNAs as sponges to inhibit the regulatory effect of bmo-278-3p on Bombyx mori heat shock protein cognate 70 (BmHSC70). Our finding suggests that lncRNAs play a role in the regulation of BmNPV proliferation by Hsp90.
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Affiliation(s)
- Haotong Yin
- School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang, Jiangsu 212018, China
| | - Qi Shang
- School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang, Jiangsu 212018, China
| | - Shaolun Zhang
- School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang, Jiangsu 212018, China
| | - Manman Shen
- School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang, Jiangsu 212018, China
| | - Haoling Huang
- School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang, Jiangsu 212018, China
| | - Weiguo Zhao
- Jiangsu Key Laboratory of Sericutural Biology and Biotechnology, School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang, Jiangsu 212018, China; Key Laboratory of Silkworm and Mulberry Genetic Improvement, Ministry of Agriculture and Rural Affairs, Sericultural Research Institute, Chinese Academy of Agricultural Sciences, Zhenjiang, Jiangsu 212018, China
| | - Guo Xijie
- Jiangsu Key Laboratory of Sericutural Biology and Biotechnology, School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang, Jiangsu 212018, China; Key Laboratory of Silkworm and Mulberry Genetic Improvement, Ministry of Agriculture and Rural Affairs, Sericultural Research Institute, Chinese Academy of Agricultural Sciences, Zhenjiang, Jiangsu 212018, China
| | - Ping Wu
- Jiangsu Key Laboratory of Sericutural Biology and Biotechnology, School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang, Jiangsu 212018, China; Key Laboratory of Silkworm and Mulberry Genetic Improvement, Ministry of Agriculture and Rural Affairs, Sericultural Research Institute, Chinese Academy of Agricultural Sciences, Zhenjiang, Jiangsu 212018, China.
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