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Du R, Zheng X, Liu Y, Lu P, Hong Y, Wang P. Molecular and functional characterization of a type-1 cystatin in amphioxus (Branchiostoma japonicum). FISH & SHELLFISH IMMUNOLOGY 2024; 147:109423. [PMID: 38341117 DOI: 10.1016/j.fsi.2024.109423] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/19/2023] [Revised: 02/01/2024] [Accepted: 02/01/2024] [Indexed: 02/12/2024]
Abstract
Cystatins comprise a vast superfamily of evolutionary conserved proteins, predominantly recognized for their roles as endogenous inhibitors by regulating the activity of cysteine proteases. Emerging lines of research evidence also provides insight into their alternative roles in a spectrum of biological and pathological processes, including neurodegenerative disorders, tumor progression, inflammatory diseases, and immune response. Nowadays, various type-1 cystatins (stefins) have been demonstrated among a variety of discovered vertebrate groups, while little is known about the related homologue in cephalochordate amphioxus, which are repositioned at the base of the chordate phylum. In the present study, a single type-1 cystatin homologue in Branchiostoma japonicum was first successfully cloned and designated as Bjcystatin-1. The deduced Bjcystatin-1 protein is structurally characterized by the presence of typical wedge-shaped cystatin features, including the 'QxVxG' and 'Px' motif, as well as the conserved N-terminal glycine residue. Phylogenomic analyses utilizing different cystatin counterparts affirmed the close evolutionary relationship of Bjcystatin-1 and type-1 cystatin homologue. Bjcystatin-1 was predominantly expressed in the gills and hind-gut in a tissue-specific pattern, and its expression was remarkably up-regulated in response to challenge with bacteria or their signature molecules LPS and LTA, suggesting the involvement in immune response. Additionally, the recombinant Bjcystatin-1 (rBjcystatin-1) protein showed significant inhibitory activity towards papain and binding ability to LPS and LTA, indicating its hypothesized role as a pattern recognition receptor in immune response. Subcellular localization results also showed that Bjcystatin-1 was located in the cytoplasm and nucleus, and its overexpression could attenuate the activation of LPS-induced nuclear transcription factors NF-κB. Taken together, our study suggests that amphioxus Bjcystatin-1 acts as a dual role in protease inhibitor and an immunocompetent factor, providing new insights into the immune defense effect of type-1 cystatin in amphioxus.
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Affiliation(s)
- Ronghuan Du
- Department of Nutrition and Food Hygiene, College of Public Health, Qingdao University, Ning Xia Road 308, Qingdao, 266071, China
| | - Xian Zheng
- Department of Nutrition and Food Hygiene, College of Public Health, Qingdao University, Ning Xia Road 308, Qingdao, 266071, China
| | - Yudan Liu
- Department of Nutrition and Food Hygiene, College of Public Health, Qingdao University, Ning Xia Road 308, Qingdao, 266071, China
| | - Pei Lu
- Department of Nutrition and Food Hygiene, College of Public Health, Qingdao University, Ning Xia Road 308, Qingdao, 266071, China
| | - Yuxiang Hong
- Zhejiang Fangyuan Testing Group Co., Ltd., Hangzhou, Zhejiang, 310020, China
| | - Peng Wang
- Department of Nutrition and Food Hygiene, College of Public Health, Qingdao University, Ning Xia Road 308, Qingdao, 266071, China.
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Chai W, Qu H, Ma Q, Zhu M, Li M, Zhan Y, Liu Z, Xu J, Yao H, Li Z, Wang C. RNA-seq analysis identifies differentially expressed gene in different types of donkey skeletal muscles. Anim Biotechnol 2023; 34:1786-1795. [PMID: 35302433 DOI: 10.1080/10495398.2022.2050920] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/01/2022]
Abstract
The main component of donkey meat is skeletal muscle, and different muscle fibers have been found to be associated with meat quality. However, RNA-seq technology has yet to be used to profile the transcriptomic changes of different muscles of the donkey. In this study, the characterizations of different muscles on the gene expression profiles of Dezhou donkey were obtained, the aim was to identify the important genes in donkey muscles, and aid in improving donkey meat quality via RNA-seq. In the donkey gluteus (DG) and donkey longissimus dorsi (DL) group, GO enrichment indicated that DEGs were mainly involved in the biological regulation and metabolic process, and KEGG analysis shows that a total of 427 DEGs were mapped to 216 KEGG pathways and 23 KEGG pathways were significantly enriched such as the ribosome, glycolysis/gluconeogenesis, glucagon signaling pathway and biosynthesis of amino acids pathways. Meanwhile, 504 DEGs were mapped to 223 KEGG pathways, in which 17 were significantly enriched including cardiac muscle contraction and oxytocin signaling pathway in donkey hamstring muscles (DH) and DL group. In addition, the tenderness in donkey meat might involve muscle fiber type and glucose metabolism, which might profit from the DEGs including MYH1, MYH7, TNNC1, TNNI3, TPM3, ALDOA, ENO3, and PGK1. The genes found in this study will provide some ideas for further understanding the molecular mechanism of donkey meat quality.
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Affiliation(s)
- Wenqiong Chai
- Liaocheng Research Institute of Donkey High-efficiency Breeding and Ecological Feeding, Liaocheng University, Liaocheng, China
| | - Honglei Qu
- State Key Laboratory of Animal Nutrition, College of Animal Science and Technology, China Agricultural University, Beijing, China
- National Engineering Research Center for Gelatin-based Traditional Chinese Medicine, Dong-E-E-Jiao Co. Ltd, Liaocheng, China
| | - Qiugang Ma
- State Key Laboratory of Animal Nutrition, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Mingxia Zhu
- Liaocheng Research Institute of Donkey High-efficiency Breeding and Ecological Feeding, Liaocheng University, Liaocheng, China
| | - Mengmeng Li
- Liaocheng Research Institute of Donkey High-efficiency Breeding and Ecological Feeding, Liaocheng University, Liaocheng, China
| | - Yandong Zhan
- Liaocheng Research Institute of Donkey High-efficiency Breeding and Ecological Feeding, Liaocheng University, Liaocheng, China
| | - Ziwen Liu
- Liaocheng Research Institute of Donkey High-efficiency Breeding and Ecological Feeding, Liaocheng University, Liaocheng, China
| | - Jing Xu
- Liaocheng Research Institute of Donkey High-efficiency Breeding and Ecological Feeding, Liaocheng University, Liaocheng, China
| | - Huanfen Yao
- Liaocheng Research Institute of Donkey High-efficiency Breeding and Ecological Feeding, Liaocheng University, Liaocheng, China
| | - Zeyu Li
- Liaocheng Research Institute of Donkey High-efficiency Breeding and Ecological Feeding, Liaocheng University, Liaocheng, China
| | - Changfa Wang
- Liaocheng Research Institute of Donkey High-efficiency Breeding and Ecological Feeding, Liaocheng University, Liaocheng, China
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Yang LY, Zhu QH, Chen JY, Lin LB, Liang MZ, Zhang QL. Genome-wide transcriptomics and microRNAomics analyses uncover multi-faceted mechanisms to cope with copper stress in ancient macrobenthos amphioxus. JOURNAL OF HAZARDOUS MATERIALS 2023; 458:131594. [PMID: 37330373 DOI: 10.1016/j.jhazmat.2023.131594] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Revised: 04/20/2023] [Accepted: 05/05/2023] [Indexed: 06/19/2023]
Abstract
The mechanisms underlying the toxicity of environmental stress are unclear for marine macrobenthos. Copper/Cu has posed the most serious threats to amphioxus, an ancient and model benthic cephalochordate. Herein, a dynamic change in the physiological parameters (GR, SOD, ATP, and MDA) was detected with ROS accumulation in Branchiostoma belcheri exposed to 0.3 mg·L-1 Cu. Transcriptomes and microRNAomes of B. belcheri were generated to investigate the molecular mechanisms by which this amphioxus copes with Cu exposure. Time-specific genes identified at different time points after exposure were involved in the stimulus and immune response, detoxification and ionic homeostasis, aging and the nervous system, sequentially, with prolongation of exposure time, forming a dynamic process of molecular response to Cu stress. In total, 57 differentially expressed miRNAs were identified under Cu stress. Transcriptomics-miRNAomics analyses indicate that these miRNAs targeted genes associated with many key biological processes such as xenobiotics degradation, oxidative stress, and energy metabolism. The constructed miRNA-mRNA-pathway network uncovered a broad post-transcriptional regulatory mechanism in B. belcheri to cope with Cu stress. Overall, this integrated analyses show that enhanced defense response, accelerated ROS elimination, and repressed ATP production constitute a comprehensive strategy to cope with Cu toxicity in the ancient macrobenthos.
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Affiliation(s)
- Lin-Yu Yang
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming 650500, China; Guangxi Key Laboratory of Marine Disaster in the Beibu Gulf, Beibu Gulf University, Qinzhou 535011, China
| | - Qian-Hua Zhu
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming 650500, China
| | - Jun-Yuan Chen
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Science, Nanjing University, Nanjing 210023, China
| | - Lian-Bing Lin
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming 650500, China
| | - Ming-Zhong Liang
- Guangxi Key Laboratory of Marine Disaster in the Beibu Gulf, Beibu Gulf University, Qinzhou 535011, China.
| | - Qi-Lin Zhang
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming 650500, China.
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Comprehensive transcriptomics and proteomics analysis of Carassius auratus gills in response to Aeromonas hydrophila. FISH AND SHELLFISH IMMUNOLOGY REPORTS 2022; 4:100077. [PMID: 36589261 PMCID: PMC9798182 DOI: 10.1016/j.fsirep.2022.100077] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2022] [Revised: 12/11/2022] [Accepted: 12/13/2022] [Indexed: 12/15/2022] Open
Abstract
As one of the mucosal barriers, fish gills represent the first line of defense against pathogen infection. However, the exact mechanism of gill mucosal immune response to bacterial infection still needs further investigation in fish. Here, to investigate pathological changes and molecular mechanisms of the mucosal immune response in the gills of crucian carp (Carassius auratus) challenged by Aeromonas hydrophila, the transcriptomics and proteomics were performed by using multi-omics analyses of RNA-seq coupled with iTRAQ techniques. The results demonstrated gill immune response were mostly related to the activation of complement and coagulation cascades, antigen processing and presentation, phagosome, NOD-like receptor (NLR) and nuclear factor κB (NFκB) signaling pathway. Selected 21 immune-related DEGs (ie., Clam, nfyal, snrpf, acin1b, psme, sf3b5, rbm8a, rbm25, prpf18, g3bp2, snrpd3l, tecrem-2, cfl-A, C7, lysC, ddx5, hsp90, α-2M, C9, C3 and slc4a1a) were verified for their immune roles in the A. hydrophila infection via using qRT-PCR assay. Meanwhile, some complement (C3, C7, C9, CFD, DF and FH) and antigen presenting (HSP90, MHC Ⅱ, CALR, CANX and PSME) proteins were significantly participated in the process of defense against infections in gill tissues, and protein-protein interaction (PPI) network displayed the immune signaling pathways and interactions among these DEPs. The correlation analysis indicated that the iTRAQ and qRT-PCR results was significantly correlated (Pearson's correlation coefficient = 0.70, p < 0.01). To our knowledge, the transcriptomics and proteomics of gills firstly identified by multi-omics analyses contribute to understanding on the molecular mechanisms of local mucosal immunity in cyprinid species.
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Wang W, Wang C, Chen W, Ding S. Advances in immunological research of amphioxus. DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY 2021; 118:103992. [PMID: 33387559 DOI: 10.1016/j.dci.2020.103992] [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: 10/12/2020] [Revised: 12/17/2020] [Accepted: 12/26/2020] [Indexed: 06/12/2023]
Abstract
Amphioxus, one of the most closely related invertebrates to vertebrates, is an important animal model for studying the origin and evolution of vertebrate immunity, especially the transition from innate immunity to adaptive immunity. The current research progresses of amphioxus in the field of immune organs, immune cells, complement system, cytokines, nuclear factor kappa B, immune-related lectins and enzymes are summarized, and some issues that remain to be understood or are in need of further clarification are highlighted. We hope to provide references for more in-depth study of the amphioxus immune system and lay a solid foundation for the construction of three-dimensional immune network in amphioxus from ontogeny to phylogeny.
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Affiliation(s)
- Wenjun Wang
- School of Life Sciences, Ludong University, Yantai, 264025, People's Republic of China
| | - Changliu Wang
- School of Life Sciences, Ludong University, Yantai, 264025, People's Republic of China.
| | - Wei Chen
- School of Life Sciences, Ludong University, Yantai, 264025, People's Republic of China; Yantai Productivity Promotion Center, Yantai, 264003, People's Republic of China
| | - Shuo Ding
- School of Life Sciences, Ludong University, Yantai, 264025, People's Republic of China
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6
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Jiao T, Chu XH, Gao ZQ, Yang TT, Liu Y, Yang L, Zhang DZ, Wang JL, Tang BP, Wu K, Liu QN, Dai LS. New insight into the molecular basis of Fe (III) stress responses of Procambarus clarkii by transcriptome analysis. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2019; 182:109388. [PMID: 31299477 DOI: 10.1016/j.ecoenv.2019.109388] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/02/2019] [Revised: 06/22/2019] [Accepted: 06/24/2019] [Indexed: 06/10/2023]
Abstract
Iron in excess can have toxic effects on living organisms. In China, the freshwater crayfish Procambarus clarkii is a source of aquatic food with high-quality protein and has significant commercial value. P. clarkii shows oxidative stress on exposure to heavy metals, and antioxidant enzymes, such as ubiquitination enzymes and proteasomes, play important roles in oxidative stress. To understand the antioxidant defense system of P. clarkii, we analyzed the hepatopancreas transcriptomes of P. clarkii after stimulation with FeCl3. In total, 5199 differentially expressed genes (DEGs) were identified (2747 upregulated and 2452 downregulated). GO analysis revealed that these DEGs belonged to 16 cellular component, 16 molecular function, and 19 biological process subcategories. A total of 1069 DEGs were classified into 25 categories by using COG. Some antioxidant defense pathways, such as "Ubiquitin mediated proteolysis" and "Glutathione metabolism," were identified using KEGG. In addition, quantitative real time-PCR (qRT-PCR) substantiated the up-regulation of a random selection of DEGs including antioxidant and immune defense genes. We obtained information for P. clarkii transcriptome databases and new insights into the responses of P. clarkii hepatopancreas to heavy metals.
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Affiliation(s)
- Ting Jiao
- Jiangsu Key Laboratory for Bioresources of Saline Soils, Jiangsu Synthetic Innovation Center for Coastal Bio-agriculture, Jiangsu Provincial Key Laboratory of Coastal Wetland Bioresources and Environmental Protection, School of Ocean and Biological Engineering, Yancheng Teachers University, Yancheng, 224007, People's Republic of China; School of Pharmaceutical Sciences, Wenzhou Medical University, Wenzhou, 325035, People's Republic of China
| | - Xiao-Hua Chu
- Jiangsu Key Laboratory for Bioresources of Saline Soils, Jiangsu Synthetic Innovation Center for Coastal Bio-agriculture, Jiangsu Provincial Key Laboratory of Coastal Wetland Bioresources and Environmental Protection, School of Ocean and Biological Engineering, Yancheng Teachers University, Yancheng, 224007, People's Republic of China; School of Pharmaceutical Sciences, Wenzhou Medical University, Wenzhou, 325035, People's Republic of China
| | - Zhen-Qiu Gao
- School of Pharmacy, Yancheng Teachers University, Yancheng, 224007, People's Republic of China
| | - Ting-Ting Yang
- Jiangsu Key Laboratory for Bioresources of Saline Soils, Jiangsu Synthetic Innovation Center for Coastal Bio-agriculture, Jiangsu Provincial Key Laboratory of Coastal Wetland Bioresources and Environmental Protection, School of Ocean and Biological Engineering, Yancheng Teachers University, Yancheng, 224007, People's Republic of China; College of Biotechnology and Pharmaceutical Engineering, Nanjing University of Technology, Nanjing, 210009, People's Republic of China
| | - Yu Liu
- Jiangsu Key Laboratory for Bioresources of Saline Soils, Jiangsu Synthetic Innovation Center for Coastal Bio-agriculture, Jiangsu Provincial Key Laboratory of Coastal Wetland Bioresources and Environmental Protection, School of Ocean and Biological Engineering, Yancheng Teachers University, Yancheng, 224007, People's Republic of China; College of Biotechnology and Pharmaceutical Engineering, Nanjing University of Technology, Nanjing, 210009, People's Republic of China
| | - Li Yang
- Jiangsu Key Laboratory for Bioresources of Saline Soils, Jiangsu Synthetic Innovation Center for Coastal Bio-agriculture, Jiangsu Provincial Key Laboratory of Coastal Wetland Bioresources and Environmental Protection, School of Ocean and Biological Engineering, Yancheng Teachers University, Yancheng, 224007, People's Republic of China
| | - Dai-Zhen Zhang
- Jiangsu Key Laboratory for Bioresources of Saline Soils, Jiangsu Synthetic Innovation Center for Coastal Bio-agriculture, Jiangsu Provincial Key Laboratory of Coastal Wetland Bioresources and Environmental Protection, School of Ocean and Biological Engineering, Yancheng Teachers University, Yancheng, 224007, People's Republic of China
| | - Jia-Lian Wang
- Jiangsu Key Laboratory for Bioresources of Saline Soils, Jiangsu Synthetic Innovation Center for Coastal Bio-agriculture, Jiangsu Provincial Key Laboratory of Coastal Wetland Bioresources and Environmental Protection, School of Ocean and Biological Engineering, Yancheng Teachers University, Yancheng, 224007, People's Republic of China
| | - Bo-Ping Tang
- Jiangsu Key Laboratory for Bioresources of Saline Soils, Jiangsu Synthetic Innovation Center for Coastal Bio-agriculture, Jiangsu Provincial Key Laboratory of Coastal Wetland Bioresources and Environmental Protection, School of Ocean and Biological Engineering, Yancheng Teachers University, Yancheng, 224007, People's Republic of China
| | - Kai Wu
- College of Life Sciences, Shangrao Normal University, Shangrao, 334001, People's Republic of China.
| | - Qiu-Ning Liu
- Jiangsu Key Laboratory for Bioresources of Saline Soils, Jiangsu Synthetic Innovation Center for Coastal Bio-agriculture, Jiangsu Provincial Key Laboratory of Coastal Wetland Bioresources and Environmental Protection, School of Ocean and Biological Engineering, Yancheng Teachers University, Yancheng, 224007, People's Republic of China; Key Laboratory of Insect Developmental and Evolutionary Biology, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 200032, People's Republic of China.
| | - Li-Shang Dai
- School of Pharmaceutical Sciences, Wenzhou Medical University, Wenzhou, 325035, People's Republic of China.
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Zhang QL, Guo J, Deng XY, Wang F, Chen JY, Lin LB. Comparative transcriptomic analysis provides insights into the response to the benzo(a)pyrene stress in aquatic firefly (Luciola leii). THE SCIENCE OF THE TOTAL ENVIRONMENT 2019; 661:226-234. [PMID: 30677670 DOI: 10.1016/j.scitotenv.2019.01.156] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/13/2018] [Revised: 01/07/2019] [Accepted: 01/13/2019] [Indexed: 06/09/2023]
Abstract
Many studies have reported that behavior and bioluminescence of fireflies could be affected by changes in environment conditions. However, little is known about how the deterioration of the aquatic environment affects aquatic fireflies, particularly with respect to molecular responses following exposure to water pollutants, such as benzo(a)pyrene (BaP), which is a key indicator in environmental risk assessment because of the hazards it poses. Here, whole transcriptome sequencing and gene expression analysis were performed on freshwater fireflies (Luciola leii) exposed to BaP (concentration of 0.01 mg/L). Four transcriptomic libraries were constructed for the control and treatment groups, including two biological replicates. From the mixed pools (each pool contains 60 individuals from three time points), a total of 54,282 unigenes were assembled. Furthermore, 329,337 of Single-nucleotide Polymorphisms (SNPs) and 1324 of Simple Sequence Repeats (SSRs) were predicted using bioinformatics, which is useful for the future development of molecular markers. Subsequently, 2414 differently expressed genes (DEGs) were identified in response to BaP stress in comparison to the control, including 1350 up-regulated and 1064 down-regulated DEGs. Functional enrichment showed that these DEGs are primarily related to innate immunity; xenobiotic biodegradation and response, biomacromolecule metabolism, biosynthesis, and absorption. Eight key BaP-responsive DEGs were screened to survey the dynamic changes of expression in response to BaP stress at different time points, and to validate the RNA sequencing data using quantitative real-time PCR. The results indicate that the expression of genes encoding UGT, CYP3A, CYP9, CYP6AS5 and ADHP were induced, while those encoding UGT2B10L, PTGDS, and ALDH were reduced, to participate in response to the BaP exposure and potentially help counteract the adverse effects of BaP. This investigation provides insight into the toxicological response of fireflies to the occurrence of water deterioration.
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Affiliation(s)
- Qi-Lin Zhang
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming 650500, China.
| | - Jun Guo
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming 650500, China
| | - Xian-Yu Deng
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming 650500, China
| | - Feng Wang
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming 650500, China
| | - Jun-Yuan Chen
- LPS, Nanjing Institute of Geology and Paleontology, Chinese Academy of Sciences (CAS), Nanjing 210008, China
| | - Lian-Bing Lin
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming 650500, China.
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Zhang QL, Zhang GL, Xiong Y, Li HW, Guo J, Wang F, Deng XY, Chen JY, Wang YJ, Lin LB. Genome-wide gene expression analysis reveals novel insights into the response to nitrite stress in gills of Branchiostoma belcheri. CHEMOSPHERE 2019; 218:609-615. [PMID: 30502699 DOI: 10.1016/j.chemosphere.2018.11.156] [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: 10/14/2018] [Revised: 11/23/2018] [Accepted: 11/24/2018] [Indexed: 06/09/2023]
Abstract
Amphioxus has been widely used as a model for the comparative immunology of vertebrates. Studies have reported that gene expression changes in the amphioxus gill in response to biotic stress, such as microbial and their mimic challenge, but little is known about how gene expression is affected by abiotic stress in the marine environment, such as nitrite. A lack of information regarding gene expression response to abiotic stress hinders a comprehensive understanding of gill defense response in amphioxus. Here, RNA sequencing was used to carry out gene expression profiling analyses of Branchiostoma belcheri gills under nitrite stress. Six libraries were created for the control and treatment groups, including three biological replicates. In total, 2416 differently expressed genes (DEGs) were detected in response to nitrite stress, of which 1522 DEGs were up-regulated in the treatment group in comparison to the control, while the remaining 894 DEGs were down-regulated genes. Functional enrichment revealed that these DEGs are primarily involved in disease, innate immunity, xenobiotic biodegradation and metabolism, and biomolecular processes and apoptosis. We screened 11 key nitrite-responsive DEGs to detect their expression responses to nitrite stress at different time points, and validate the sequencing data using real time quantitative PCR. The results indicated that the expression of gene encoding CYP3A, POD, CASPR1, GST, MAO, DDH, and XDH/XO were induced, while those encoding MRC, GT, DNASE1L, and RIPK5 were reduced, to participate in the anti-nitrite response. This study provides a useful resource for research of molecular toxicology in amphioxus under environmental stress.
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Affiliation(s)
- Qi-Lin Zhang
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming 650500 China.
| | - Guan-Ling Zhang
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming 650500 China
| | - Yan Xiong
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming 650500 China
| | - Hong-Wei Li
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming 650500 China
| | - Jun Guo
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming 650500 China
| | - Feng Wang
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming 650500 China
| | - Xian-Yu Deng
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming 650500 China
| | - Jun-Yuan Chen
- LPS, Nanjing Institute of Geology and Paleontology, Chinese Academy of Sciences, Nanjing 210008 China; State Key Laboratory of Pharmaceutical Biotechnology, School of Life Science, Nanjing University, Nanjing, 210023 China
| | - Yu-Jun Wang
- Guangxi Key Laboratory of Beibu Gulf Marine Biodiversity Conservation, Ocean College, Qinzhou University, Qinzhou 535011 China.
| | - Lian-Bing Lin
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming 650500 China.
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Zhang QL, Ji XY, Li HW, Guo J, Wang F, Deng XY, Chen JY, Lin LB. Identification of circular RNAs and their altered expression under poly(I:C) challenge in key antiviral immune pathways in amphioxus. FISH & SHELLFISH IMMUNOLOGY 2019; 86:1053-1057. [PMID: 30590167 DOI: 10.1016/j.fsi.2018.12.061] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/19/2018] [Revised: 12/11/2018] [Accepted: 12/24/2018] [Indexed: 06/09/2023]
Abstract
Amphioxus is a key model for studying comparative immunity of vertebrates. Circular RNA (circRNA), as RNAs with a circular structure, has received little attention until recently, where several studies have reported that circRNA expression changes are involved in the immune response in animals. However, circRNA and its immune role in amphioxus have not been previously studied. Here, circRNAs in Chinese amphioxus (Branchiostoma belcheri) were sequenced, and 1859 circRNAs were identified using two algorithms (find_circ and CIRI). The analysis of miRNA target sites on circRNAs showed that 332 circRNAs may function as miRNA sponges. Furthermore, we identified circRNAs that were conserved between B. belcheri and vertebrates, tracing the origin of these circRNAs within chordates. Additionally, in combination with several key antiviral immune (poly(I:C), pIC) pathways identified in our previous B. belcheri studies, nine circRNAs potentially involved in these pathways were identified using bioinformatic predictions. Among these nine circRNAs, eight were selected to examine their expression response in B. belcheri challenged by pIC in comparison to control using real-time quantitative PCR. The results showed that four circRNAs were induced as part of the antiviral response against pIC, while expression of two circRNAs was decreased, and the expression levels of the remaining two were not significantly altered after pIC challenge. This work is the first to identify circRNAs and reveal their antiviral role in amphioxus. Therefore, it opens a new window to explore the comparative immunology of circRNAs in chordates and the regulatory roles of circRNAs in antiviral immunity in amphioxus.
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Affiliation(s)
- Qi-Lin Zhang
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, 650500, China
| | - Xin-Yu Ji
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, 650500, China
| | - Hong-Wei Li
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, 650500, China
| | - Jun Guo
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, 650500, China
| | - Feng Wang
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, 650500, China
| | - Xian-Yu Deng
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, 650500, China
| | - Jun-Yuan Chen
- LPS, Nanjing Institute of Geology and Paleontology, Chinese Academy of Sciences, Nanjing, 210008, China; State Key Laboratory of Pharmaceutical Biotechnology, School of Life Science, Nanjing University, Nanjing, 210023, China
| | - Lian-Bing Lin
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, 650500, China.
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Zhang QL, Wang F, Guo J, Deng XY, Chen JY, Lin LB. Characterization of ladybird Henosepilachna vigintioctopunctata transcriptomes across various life stages. Sci Data 2018; 5:180093. [PMID: 29870033 PMCID: PMC5987669 DOI: 10.1038/sdata.2018.93] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2017] [Accepted: 03/27/2018] [Indexed: 12/17/2022] Open
Abstract
Henosepilachna vigintioctopunctata is a vegetable pest that has spread worldwide. It belongs to the Coccinellidae family, whose members exhibit remarkable diversity, both in terms of their diets and the colored spots that appear on the elytra in the adult stage. Transcriptomic data from H. vigintioctopunctata at different life stages would be useful for further investigating the genetic basis of this dietary diversity and the formation of the colored spots in ladybird beetles, as well as revealing the population dynamics of H. vigintioctopunctata, which could be useful in pest control. Here, we generated a comprehensive RNA-seq data set (a total of ~24 Gb of clean data) for H. vigintioctopunctata by sequencing samples collected at different life stages. We characterized the transcriptomes of each of the four life stages (egg, larva, pupa, adult) and generated a high-coverage pool by combining all the RNA-seq reads. Furthermore, we identified a catalog of simple sequence repeat (SSR) markers. This represents the first study to collect transcriptome data from all life stages of a ladybird beetle.
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Affiliation(s)
- Qi-Lin Zhang
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming 650500, China
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Science, Nanjing University, Nanjing 210023, China
| | - Feng Wang
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming 650500, China
| | - Jun Guo
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming 650500, China
| | - Xian-Yu Deng
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming 650500, China
| | - Jun-Yuan Chen
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Science, Nanjing University, Nanjing 210023, China
- LPS, Nanjing Institute of Geology and Paleontology, CAS, Nanjing 210008, China
| | - Lian-Bing Lin
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming 650500, China
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Zhang QL, Zhu QH, Liang MZ, Wang F, Guo J, Deng XY, Chen JY, Wang YJ, Lin LB. Comparative transcriptomic analysis provides insights into antibacterial mechanisms of Branchiostoma belcheri under Vibrio parahaemolyticus infection. FISH & SHELLFISH IMMUNOLOGY 2018; 76:196-205. [PMID: 29510259 DOI: 10.1016/j.fsi.2018.03.007] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/08/2018] [Revised: 02/24/2018] [Accepted: 03/02/2018] [Indexed: 06/08/2023]
Abstract
UNLABELLED Amphioxus, a basal chordate, is widely considered to be an existing proxy of the invertebrate ancestor of vertebrates, and it exhibits susceptibility to various pathogen infections and pathogenic mimic challenges. Here, in order to understand more clearly its antibacterial mechanisms, we analyzed the ribosomal RNA (rRNA)-depleted transcriptome of Chinese amphioxus (Branchiostoma belcheri) infected with Vibrio parahaemolyticus (V. p.) via next-generation deep sequencing technology (RNA-seq). We identified a total of 3214 differentially expressed genes (DEGs) by comparing V. p.-infected and control transcriptome libraries, including 2219 significantly up-regulated and 995 significantly down-regulated DEGs in V. p.-infected amphioxus. The DEGs with the top 10 most dramatic expression fold changes after V. p. infection, as well as 53 immune-related DEGs (IRDs) belonging to four primary categories of innate immunity were analyzed further. Through gene ontology (GO) and pathway enrichment analysis, DEGs were found to be primarily related to immune processes, apoptosis, catabolic and metabolic processes, binding and enzyme activity, while pathways involving bacterial infection, immune signaling, immune response, cancer, and apoptosis were overrepresented. We validated the RNA-seq results by detecting the expression levels of 10 IRDs using qRT-PCR, and we surveyed the dynamic variation in gene expression for these IRDs at 0, 6, 12, 24, and 48 h after V. p. TREATMENT Subsequently, according to the RNA-seq results, the presence of a primitive Toll-like receptor (TLR)-mediated antibacterial immune signaling pathway was predicted in B. belcheri. This study provides valuable information regarding antibacterial immunity for further research into the evolution of immunity in vertebrates and broadens our understanding of the innate immune response against bacterial invasion in amphioxus.
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Affiliation(s)
- Qi-Lin Zhang
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, 650500, China; State Key Laboratory of Pharmaceutical Biotechnology, School of Life Science, Nanjing University, Nanjing, 210023, China
| | - Qian-Hua Zhu
- BGI Genomics, BGI-Shenzhen, Shenzhen, 518083, China
| | - Ming-Zhong Liang
- Department of Marine Science, Qinzhou University, Qinzhou, 535000, China
| | - Feng Wang
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, 650500, China
| | - Jun Guo
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, 650500, China
| | - Xian-Yu Deng
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, 650500, China
| | - Jun-Yuan Chen
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Science, Nanjing University, Nanjing, 210023, China
| | - Yu-Jun Wang
- Department of Marine Science, Qinzhou University, Qinzhou, 535000, China.
| | - Lian-Bing Lin
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, 650500, China.
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Zhang QL, Xie ZQ, Liang MZ, Luo B, Wang XQ, Chen JY. Genome-wide gene expression analysis in the amphioxus, Branchiostoma belcheri after poly (I: C) challenge using strand-specific RNA-seq. Oncotarget 2017; 8:108392-108405. [PMID: 29312538 PMCID: PMC5752451 DOI: 10.18632/oncotarget.21553] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2017] [Accepted: 10/02/2017] [Indexed: 02/07/2023] Open
Abstract
The gene expression associated with immune response to bacteria/bacterial mimic has been extensively analyzed in amphioxus, but remains largely unknown about how gene are involved in the immune response to viral invasion at expression level. Here, we analyze the rRNA-depleted transcriptomes of Branchiostoma belcheri using strand-specific RNA-seq in response to the viral mimic, poly (I:C) (pIC). A total of 5,317 differentially expressed genes were detected at treatment group by comparing with control. The gene with the most significant expression changes (top 15) after pIC challenge and 7 immune-related categories involving 58 differently expressed genes were scrutinized. By functional enrichment analysis of differently expressed genes, gene ontology terms involving response to stress and stimulus, apoptosis, catabolic and metabolic processes and enzyme activity were overrepresented, and several pathways related to immune signaling, immune response, cancer, apoptosis, viral disease, metabolism were activated after pIC injection. A positive correlation between the qRT-PCR and strand-specific RNA-seq data confirmed the accuracy of the RNA-seq results. Additionally, the expression of genes encoding NLRC5, CASP1, CASP6, CYP450, CAT, and MDA5 were induced in B. belcheri under pIC challenge. Our experiments provide insight into the immune response of amphioxus to pIC and valuable gene expression information for studying the evolution of antiviral immunity in vertebrates.
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Affiliation(s)
- Qi-Lin Zhang
- LPS, Nanjing Institute of Geology and Paleontology, Chinese Academy of Science, Nanjing, China.,State Key Laboratory of Pharmaceutical Biotechnology, School of Life Science, Nanjing University, Nanjing, China
| | - Zheng-Qing Xie
- LPS, Nanjing Institute of Geology and Paleontology, Chinese Academy of Science, Nanjing, China.,State Key Laboratory of Pharmaceutical Biotechnology, School of Life Science, Nanjing University, Nanjing, China
| | - Ming-Zhong Liang
- Department of Marine Science, Qinzhou University, Qinzhou, China
| | - Bang Luo
- Guangxi Academy of Fishery Sciences, Nanning, China
| | - Xiu-Qiang Wang
- LPS, Nanjing Institute of Geology and Paleontology, Chinese Academy of Science, Nanjing, China
| | - Jun-Yuan Chen
- LPS, Nanjing Institute of Geology and Paleontology, Chinese Academy of Science, Nanjing, China
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