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Xu X, Xu J, Qiu M, Yu Y, Gou M, Pang Y, Li Q, Su P. A Comparative Transcriptomic Study and Key Gene Targeting of Lamprey Gonadal Immune Response. Immunol Invest 2024; 53:241-260. [PMID: 38078455 DOI: 10.1080/08820139.2023.2289070] [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] [Indexed: 03/23/2024]
Abstract
The mammalian testis and ovary possess special immunocompetence, which is central to provide protection against pathogens. However, the innate immune responses to immune challenges in lamprey gonads are poorly understood. In this study, we extracted RNA from testis and ovary tissues of lampreys at 0 hour, 8 hours and 17 days after lipopolysaccharides (LPS) stimulation and performed transcriptome sequencing. While the transcriptome profiles of the two tissues were different for the most part, genes LIP, LECT2, LAL2, GRN, ITLN, and C1q were found to be the most significantly up-regulated genes in both. Quantitative Real-time PCR (qRT-PCR) analysis confirmed that these genes were upregulated after stimulation. Furthermore, immunohistochemical staining showed that these genes in lamprey gonads are expressed in high quantities and have a specific distribution. Taken together, our results suggest that these genes could play an essential role in response of the gonads to LPS induction. This research establishes a basis for investigating the immune mechanism of vertebrate gonads and presents a fresh concept for gaining insight into the evolutionary development of jawless vertebrates.
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Affiliation(s)
- Xiangting Xu
- College of Life Science, Liaoning Normal University, Dalian, China
- Lamprey Research Center, Liaoning Normal University, Dalian, China
- Collaborative Innovation Center of Seafood Deep Processing, Dalian Polytechnic University, Dalian, China
| | - Jing Xu
- College of Life Science, Liaoning Normal University, Dalian, China
- Lamprey Research Center, Liaoning Normal University, Dalian, China
- Collaborative Innovation Center of Seafood Deep Processing, Dalian Polytechnic University, Dalian, China
- Functional laboratory, College of Basic Medical Sciences, Dalian Medical University, Dalian, China
| | - Mingyue Qiu
- College of Life Science, Liaoning Normal University, Dalian, China
- Lamprey Research Center, Liaoning Normal University, Dalian, China
- Collaborative Innovation Center of Seafood Deep Processing, Dalian Polytechnic University, Dalian, China
| | - Yang Yu
- College of Life Science, Liaoning Normal University, Dalian, China
- Lamprey Research Center, Liaoning Normal University, Dalian, China
- Collaborative Innovation Center of Seafood Deep Processing, Dalian Polytechnic University, Dalian, China
- Department of Urology, The Second Hospital of Dalian Medical University, Dalian, Liaoning, China
| | - Meng Gou
- College of Life Science, Liaoning Normal University, Dalian, China
- Lamprey Research Center, Liaoning Normal University, Dalian, China
- Collaborative Innovation Center of Seafood Deep Processing, Dalian Polytechnic University, Dalian, China
| | - Yue Pang
- College of Life Science, Liaoning Normal University, Dalian, China
- Lamprey Research Center, Liaoning Normal University, Dalian, China
- Collaborative Innovation Center of Seafood Deep Processing, Dalian Polytechnic University, Dalian, China
| | - Qingwei Li
- College of Life Science, Liaoning Normal University, Dalian, China
- Lamprey Research Center, Liaoning Normal University, Dalian, China
- Collaborative Innovation Center of Seafood Deep Processing, Dalian Polytechnic University, Dalian, China
| | - Peng Su
- College of Life Science, Liaoning Normal University, Dalian, China
- Lamprey Research Center, Liaoning Normal University, Dalian, China
- Collaborative Innovation Center of Seafood Deep Processing, Dalian Polytechnic University, Dalian, China
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Yao H, Sun J, Zhang T, Wang L, Song L. Syk regulates the haemocyte autophagy through inducing the mRNA expressions of autophagy-related genes and the cleavage of CgLC3 in oyster antibacterial immunity. FISH AND SHELLFISH IMMUNOLOGY REPORTS 2023; 4:100085. [PMID: 37065179 PMCID: PMC10102855 DOI: 10.1016/j.fsirep.2023.100085] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2022] [Revised: 01/07/2023] [Accepted: 01/16/2023] [Indexed: 01/18/2023] Open
Abstract
Spleen tyrosine kinase (Syk) is reported to be involved in activating the autophagy. Recently, a homologue of Syk was identified from Pacific oyster Crassostrea gigas (defined as CgSyk). In the present study, the molecular characteristics of CgSyk and its regulation mechanism in autophagy were investigated in oyster C. gigas. The full-length cDNA of CgSyk was of 4566 bp with an open reading frame (ORF) of 1989 bp. CgSyk encoded a polypeptide of 662 amino acids, containing two Src homology 2 (SH2) domains and one tyrosine kinase catalytic (TyrKc) domain. The deduced amino acid sequence of CgSyk shared low similarity with the previously identified Syks from other species. In the phylogenetic tree, CgSyk was first clustered with Crassostrea virginica CvSyk, and then classified into a branch of invertebrate Syks. In CgSyk-RNAi oysters, the mRNA expressions of CgLC3, CgP62, CgBeclin-1 and CgATG5 in haemocytes decreased significantly at 12 h after Vibrio splendidus stimulation. At the same time, the abundance of CgLC3Ⅱ in haemocytes, and the autophagy rate of haemocytes in CgSyk-RNAi oysters decreased significantly at 12 h after V. splendidus stimulation. All the results collectively suggested that CgSyk regulated the autophagy through inducing the mRNA expressions of autophagy-related genes and the cleavage of CgLC3 to defend against bacterial invasion in oysters.
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Affiliation(s)
- Hongsheng Yao
- Liaoning Key Laboratory of Marine Animal Immunology, Dalian Ocean University, 52 Heishijiao Street, Dalian 116023, China
- Liaoning Key Laboratory of Marine Animal Immunology and Disease Control, Dalian Ocean University, Dalian 116023, China
| | - Jiejie Sun
- Liaoning Key Laboratory of Marine Animal Immunology, Dalian Ocean University, 52 Heishijiao Street, Dalian 116023, China
- Liaoning Key Laboratory of Marine Animal Immunology and Disease Control, Dalian Ocean University, Dalian 116023, China
- Corresponding author at: Liaoning Key Laboratory of Marine Animal Immunology, Dalian Ocean University, 52 Heishijiao Street, Dalian 116023, China.
| | - Tong Zhang
- Liaoning Key Laboratory of Marine Animal Immunology, Dalian Ocean University, 52 Heishijiao Street, Dalian 116023, China
- Liaoning Key Laboratory of Marine Animal Immunology and Disease Control, Dalian Ocean University, Dalian 116023, China
| | - Lingling Wang
- Liaoning Key Laboratory of Marine Animal Immunology, Dalian Ocean University, 52 Heishijiao Street, Dalian 116023, China
- Laboratory of Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266235, China
- Liaoning Key Laboratory of Marine Animal Immunology and Disease Control, Dalian Ocean University, Dalian 116023, China
- Dalian Key Laboratory of Aquatic Animal Disease Prevention and Control, Dalian Ocean University, Dalian 116023, China
| | - Linsheng Song
- Liaoning Key Laboratory of Marine Animal Immunology, Dalian Ocean University, 52 Heishijiao Street, Dalian 116023, China
- Laboratory of Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266235, China
- Liaoning Key Laboratory of Marine Animal Immunology and Disease Control, Dalian Ocean University, Dalian 116023, China
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Molecular Characterization of a B Cell Adaptor for Phosphoinositide 3-Kinase Homolog in Lamprey ( Lampetra japonica) and Its Function in the Immune Response. Int J Mol Sci 2022; 23:ijms232214449. [PMID: 36430927 PMCID: PMC9695028 DOI: 10.3390/ijms232214449] [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: 10/31/2022] [Revised: 11/17/2022] [Accepted: 11/18/2022] [Indexed: 11/22/2022] Open
Abstract
Human B cell adaptor for phosphoinositide 3-kinase (BCAP) is identified as an adaptor protein expressed in B cells and plays a critical immunomodulatory role in B cell receptor signaling and humoral immune response. In the current study, a homolog of BCAP (Lja-BCAP) was identified in Lampetra japonica. The open reading frame of Lja-BCAP contains 2181bp nucleotides and encodes a protein of 726 amino acids. After being stimulated by mixed bacteria, the mRNA and protein expression levels of Lja-BCAP and the activation levels of tyrosine kinases increased significantly in peripheral blood lymphocytes, gills and supraneural myeloid bodies, respectively. However, after the knockdown of Lja-BCAP by RNAi in vivo, the activation of tyrosine kinases was inhibited in the above tissues, which indicated that Lja-BCAP participated in the anti-bacterial immune response of lampreys. After lipopolysaccharide (LPS) stimulation, the expression of Lja-BCAP in peripheral blood lymphocytes, gills and supraneural myeloid bodies were significantly up-regulated 2.5, 2.2, and 11.1 times (p < 0.05) compared to the control group, respectively; while after phytohemagglutinin (PHA) stimulation, the up-regulation of Lja-BCAP was only detected in peripheral blood lymphocytes. The above results show that Lja-BCAP mainly participates in the LPS-mediated immune response of lampreys.
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Wang L, Xu X, Zhang Z, Li K, Yang Y, Zheng W, Sun H, Chen S. Transcriptome analysis and protein-protein interaction in resistant and susceptible families of Japanese flounder (Paralichthys olivaceus) to understand the mechanism against Edwardsiella tarda. FISH & SHELLFISH IMMUNOLOGY 2022; 123:265-281. [PMID: 35272057 DOI: 10.1016/j.fsi.2022.02.055] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Revised: 02/25/2022] [Accepted: 02/28/2022] [Indexed: 06/14/2023]
Abstract
Edwardsiella tarda is one of the most harmful bacterial pathogens for aquaculture flatfish. After artificial infection of 47 Japanese flounder (Paralichthys olivaceus) families, resistant and susceptible families were identified in this study. High-throughput sequencing was performed on the liver transcriptome of uninfected groups (PoRU and PoSU) and infected groups (PoRC and PoSC). Through assembly and annotation, a total of 3012 and 1386 differentially expressed genes (DEGs) were identified in PoRU vs. PoSU and PoRC vs. PoSC. The significant enrichment pathways between PoRU and PoSU were mainly in metabolic and biosynthesis pathways. A total of thirty dominant enrichment pathways between PoRC and PoSC mainly focused on some immune-related pathways, including the hematopoietic cell lineage, cytokine-cytokine receptor interaction, complement and coagulation cascades, antigen processing and presentation, the intestinal immune network for immunoglobulin A (IgA) production and T/B cell receptor signaling pathway. Under the protein-protein interaction (PPI) analysis, hub genes, including CD molecules, complement component factors and chemokines, were identified in the network, and 16 core genes were differentially expressed in resistant and sustainable families in quantitative polymerase chain reaction (qPCR) validation. This study represents the first transcriptome analysis based on resistant and susceptible families and provides resistant genes to understand the potential molecular mechanisms of antibacterial function in marine fish. The results obtained in this study provide crucial information on gene markers for resistant breeding of Japanese flounder.
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Affiliation(s)
- Lei Wang
- Key Laboratory for Sustainable Development of Marine Fisheries, Ministry of Agriculture, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences (CAFS), Qingdao, 266071, China; Key Laboratory for Sustainable Development of Marine Fisheries, Ministry of Agriculture, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences (CAFS), Qingdao, 266071, China
| | - Xiwen Xu
- Key Laboratory for Sustainable Development of Marine Fisheries, Ministry of Agriculture, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences (CAFS), Qingdao, 266071, China; Key Laboratory for Sustainable Development of Marine Fisheries, Ministry of Agriculture, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences (CAFS), Qingdao, 266071, China
| | - Ziwei Zhang
- Key Laboratory for Sustainable Development of Marine Fisheries, Ministry of Agriculture, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences (CAFS), Qingdao, 266071, China; Key Laboratory for Sustainable Development of Marine Fisheries, Ministry of Agriculture, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences (CAFS), Qingdao, 266071, China; Wuxi Fisheries College, Nanjing Agricultural University, Wuxi, 214081, China
| | - Kaimin Li
- Key Laboratory for Sustainable Development of Marine Fisheries, Ministry of Agriculture, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences (CAFS), Qingdao, 266071, China; Key Laboratory for Sustainable Development of Marine Fisheries, Ministry of Agriculture, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences (CAFS), Qingdao, 266071, China; Shandong Normal University, Jinan, 250014, China
| | - Yingming Yang
- Key Laboratory for Sustainable Development of Marine Fisheries, Ministry of Agriculture, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences (CAFS), Qingdao, 266071, China; Key Laboratory for Sustainable Development of Marine Fisheries, Ministry of Agriculture, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences (CAFS), Qingdao, 266071, China
| | - Weiwei Zheng
- Key Laboratory for Sustainable Development of Marine Fisheries, Ministry of Agriculture, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences (CAFS), Qingdao, 266071, China; Key Laboratory for Sustainable Development of Marine Fisheries, Ministry of Agriculture, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences (CAFS), Qingdao, 266071, China
| | - Hejun Sun
- Key Laboratory for Sustainable Development of Marine Fisheries, Ministry of Agriculture, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences (CAFS), Qingdao, 266071, China; Key Laboratory for Sustainable Development of Marine Fisheries, Ministry of Agriculture, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences (CAFS), Qingdao, 266071, China
| | - Songlin Chen
- Key Laboratory for Sustainable Development of Marine Fisheries, Ministry of Agriculture, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences (CAFS), Qingdao, 266071, China; Key Laboratory for Sustainable Development of Marine Fisheries, Ministry of Agriculture, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences (CAFS), Qingdao, 266071, China.
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Bian X, Wu L, Mu L, Yin X, Wei X, Zhong X, Yang Y, Wang J, Li Y, Guo Z, Ye J. Spleen tyrosine kinase from Nile tilapia (Oreochromis niloticus): Molecular characterization, expression pattern upon bacterial infection and the potential role in BCR signaling and inflammatory response. FISH & SHELLFISH IMMUNOLOGY 2018; 82:162-172. [PMID: 30114435 DOI: 10.1016/j.fsi.2018.08.015] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/12/2018] [Revised: 07/31/2018] [Accepted: 08/07/2018] [Indexed: 06/08/2023]
Abstract
Spleen tyrosine kinase (SYK), a member of non-receptor tyrosine kinase family, plays an important role in immune responses against pathogen infection, which is capable of activating B cells signaling pathway and regulating inflammatory response. In this study, Nile tilapia (Oreochromis niloticus) ortholog (OnSYK) was identified and characterized at expression pattern against bacterial infection, function in B cells activation pathway and inflammatory response. The cDNA of OnSYK ORF contained 1851 bp of nucleotide sequence encoding polypeptides of 616 amino acids. The deduced OnSYK protein was highly homologous to other species SYK, containing two SH2 domains and a TyrKc domain. Spatial mRNA expression analysis revealed that OnSYK had wide tissue distribution and was highly expressed in the liver. After challenge of Streptococcus agalactiae (S. agalactiae) in vivo, mRNA expression of OnSYK was significantly up-regulated in the head kidney, spleen and liver. The up-regulation of OnSYK transcript was also displayed in the head kidney and spleen leukocytes stimulation with S. agalactiae and LPS in vitro, which was confirmed at protein level in the head kidney leukocytes by FACS analysis. In addition, after induction with mouse anti-OnIgM monoclonal antibody in vitro, the expressions of OnSYK and its downstream molecules (OnLYN, OnBLNK and OnAP-1) were significantly up-regulated in the head kidney leukocytes, and pharmacological inhibition of SYK activity with inhibitor (P505-15) significantly attenuated the expressions of OnLYN, OnBLNK and OnAP-1. Moreover, upon LPS challenge, the expressions of OnSYK, OnTNF-α, OnIL-6 and OnAP-1 were also up-regulated in the head kidney monocytes/macrophages. After treatment with SYK inhibitor (BAY 61-3606), the expressions of OnTNF-α, OnIL-6 and OnAP-1 were inhibited in the LPS-challenged head kidney monocytes/macrophages. Taken together, the results of this study indicated that OnSYK, playing potential roles in BCR signaling and inflammatory response, was likely to get involved in host defense against bacterial infection in Nile tilapia.
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Affiliation(s)
- Xia Bian
- Guangdong Provincial Key Laboratory for Healthy and Safe Aquaculture, Guangdong Provincial Engineering Technology Research Center for Environmentally-Friendly Aquaculture, College of Life Sciences, South China Normal University, Guangdong, 510631, PR China
| | - Liting Wu
- Guangdong Provincial Key Laboratory for Healthy and Safe Aquaculture, Guangdong Provincial Engineering Technology Research Center for Environmentally-Friendly Aquaculture, College of Life Sciences, South China Normal University, Guangdong, 510631, PR China
| | - Liangliang Mu
- Guangdong Provincial Key Laboratory for Healthy and Safe Aquaculture, Guangdong Provincial Engineering Technology Research Center for Environmentally-Friendly Aquaculture, College of Life Sciences, South China Normal University, Guangdong, 510631, PR China
| | - Xiaoxue Yin
- Guangdong Provincial Key Laboratory for Healthy and Safe Aquaculture, Guangdong Provincial Engineering Technology Research Center for Environmentally-Friendly Aquaculture, College of Life Sciences, South China Normal University, Guangdong, 510631, PR China
| | - Xiufang Wei
- Guangdong Provincial Key Laboratory for Healthy and Safe Aquaculture, Guangdong Provincial Engineering Technology Research Center for Environmentally-Friendly Aquaculture, College of Life Sciences, South China Normal University, Guangdong, 510631, PR China
| | - Xiaofang Zhong
- Guangdong Provincial Key Laboratory for Healthy and Safe Aquaculture, Guangdong Provincial Engineering Technology Research Center for Environmentally-Friendly Aquaculture, College of Life Sciences, South China Normal University, Guangdong, 510631, PR China
| | - Yanjian Yang
- Guangdong Provincial Key Laboratory for Healthy and Safe Aquaculture, Guangdong Provincial Engineering Technology Research Center for Environmentally-Friendly Aquaculture, College of Life Sciences, South China Normal University, Guangdong, 510631, PR China
| | - Junru Wang
- Guangdong Provincial Key Laboratory for Healthy and Safe Aquaculture, Guangdong Provincial Engineering Technology Research Center for Environmentally-Friendly Aquaculture, College of Life Sciences, South China Normal University, Guangdong, 510631, PR China
| | - Yuan Li
- Guangdong Provincial Key Laboratory for Healthy and Safe Aquaculture, Guangdong Provincial Engineering Technology Research Center for Environmentally-Friendly Aquaculture, College of Life Sciences, South China Normal University, Guangdong, 510631, PR China
| | - Zheng Guo
- Guangdong Provincial Key Laboratory for Healthy and Safe Aquaculture, Guangdong Provincial Engineering Technology Research Center for Environmentally-Friendly Aquaculture, College of Life Sciences, South China Normal University, Guangdong, 510631, PR China
| | - Jianmin Ye
- Guangdong Provincial Key Laboratory for Healthy and Safe Aquaculture, Guangdong Provincial Engineering Technology Research Center for Environmentally-Friendly Aquaculture, College of Life Sciences, South China Normal University, Guangdong, 510631, PR China.
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A Novel Vav3 Homolog Identified in Lamprey, Lampetra japonica, with Roles in Lipopolysaccharide-Mediated Immune Response. Int J Mol Sci 2017; 18:ijms18102035. [PMID: 28937614 PMCID: PMC5666717 DOI: 10.3390/ijms18102035] [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: 09/04/2017] [Revised: 09/19/2017] [Accepted: 09/20/2017] [Indexed: 11/16/2022] Open
Abstract
Vav guanine nucleotide exchange factor 3 (Vav3), a Rho family GTPase, regulates multiple cell signaling pathways including those of T- and B-cell receptors in vertebrates through mediating the activities of the Rho family members. Whether the lamprey possesses Vav3 homolog and what role it plays in immune response remain unknown. Gene cloning, recombinant expression, antibody production and expression pattern analyses were performed to characterize the lamprey Vav3 in the current study. The lamprey Vav3 is closer to jawed vertebrates' Vav3 molecules (about 53% identities in general) than to Vav2 molecules of jawless and jawed vertebrates (about 51% identities in general) in sequence similarity. Conserved motif analysis showed that the most distinguished parts between Vav3 and Vav2 proteins are their two Src-homology 3 domains. The relative expression levels of lamprey vav3 mRNA and protein were significantly up-regulated in lamprey lymphocytes and supraneural myeloid bodies after mixed-antigens stimulation, respectively. In addition, lamprey Vav3 were up-regulated drastically in lymphocytes and supraneural myeloid bodies after lipopolysaccharide (LPS) rather than phytohemagglutinin (PHA) stimulation. Lamprey Vav3 distributed in the cytoplasm of variable lymphocyte receptor B positive (VLRB⁺) lymphocytes, and the number of plasmacytes (VLRB and lamprey Vav3 double positive) in blood lymphocytes also increased after LPS stimulation. Our results proved that lamprey Vav3 was involved in the LPS-mediated immune reaction of lamprey and provided a clue for the further study of the precise role lamprey Vav3 played in the signaling pathway of lamprey VLRB⁺ lymphocytes.
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In Silico Prediction of Gamma-Aminobutyric Acid Type-A Receptors Using Novel Machine-Learning-Based SVM and GBDT Approaches. BIOMED RESEARCH INTERNATIONAL 2016; 2016:2375268. [PMID: 27579307 PMCID: PMC4992803 DOI: 10.1155/2016/2375268] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/24/2016] [Revised: 06/08/2016] [Accepted: 06/19/2016] [Indexed: 11/17/2022]
Abstract
Gamma-aminobutyric acid type-A receptors (GABAARs) belong to multisubunit membrane spanning ligand-gated ion channels (LGICs) which act as the principal mediators of rapid inhibitory synaptic transmission in the human brain. Therefore, the category prediction of GABAARs just from the protein amino acid sequence would be very helpful for the recognition and research of novel receptors. Based on the proteins' physicochemical properties, amino acids composition and position, a GABAAR classifier was first constructed using a 188-dimensional (188D) algorithm at 90% cd-hit identity and compared with pseudo-amino acid composition (PseAAC) and ProtrWeb web-based algorithms for human GABAAR proteins. Then, four classifiers including gradient boosting decision tree (GBDT), random forest (RF), a library for support vector machine (libSVM), and k-nearest neighbor (k-NN) were compared on the dataset at cd-hit 40% low identity. This work obtained the highest correctly classified rate at 96.8% and the highest specificity at 99.29%. But the values of sensitivity, accuracy, and Matthew's correlation coefficient were a little lower than those of PseAAC and ProtrWeb; GBDT and libSVM can make a little better performance than RF and k-NN at the second dataset. In conclusion, a GABAAR classifier was successfully constructed using only the protein sequence information.
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Han Y, Liu X, Shi B, Xiao R, Gou M, Wang H, Li Q. Identification and characterisation of the immune response properties of Lampetra japonica BLNK. Sci Rep 2016; 6:25308. [PMID: 27126461 PMCID: PMC4850452 DOI: 10.1038/srep25308] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2015] [Accepted: 04/14/2016] [Indexed: 01/01/2023] Open
Abstract
B cell linker protein (BLNK) is a central linker protein involved in B cell signal transduction in jawed vertebrates. In a previous study, we have reported the identification of a BLNK homolog named Lj-BLNK in lampreys. In this study, a 336 bp cDNA fragment encoding the Lj-BLNK Src homology 2 (SH2) domain was cloned into the vector pET-28a(+) and overexpressed in Escherichia coli BL21. The recombinant fragment of Lj-BLNK (rLj-BLNK) was purifiedby His-Bind affinity chromatography, and polyclonal antibodies against rLj-BLNK were raised in male New Zealand rabbits. Fluorescenceactivated cell sorting (FACS) analysisrevealed that Lj-BLNK was expressed in approximately 48% of the lymphocyte-like cells of control lampreys, and a significant increase in Lj-BLNK expression was observed in lampreys stimulated with lipopolysaccharide (LPS). Western blotting analysis showed that variable lymphocyte receptor B (VLRB) and Lj-BLNKwere distributed in the same immune-relevant tissues, and the levels of both were upregulated in supraneural myeloid bodies and lymphocyte-like cells after LPS stimulation. Immunofluorescence demonstrated that Lj-BLNK was localized in VLRB(+) lymphocyte-like cells. These results indicate that the Lj-BLNK protein identified in lampreys might play an important role in the VLRB-mediated adaptive immune response.
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Affiliation(s)
- Yinglun Han
- College of Life Science, Liaoning Normal University, Dalian 116029, China.,Lamprey Research Center, Liaoning Normal University, Dalian 116029, China
| | - Xin Liu
- College of Life Science, Liaoning Normal University, Dalian 116029, China.,Lamprey Research Center, Liaoning Normal University, Dalian 116029, China
| | - Biyue Shi
- College of Life Science, Liaoning Normal University, Dalian 116029, China.,Lamprey Research Center, Liaoning Normal University, Dalian 116029, China
| | - Rong Xiao
- College of Life Science, Liaoning Normal University, Dalian 116029, China.,Lamprey Research Center, Liaoning Normal University, Dalian 116029, China
| | - Meng Gou
- College of Life Science, Liaoning Normal University, Dalian 116029, China.,Lamprey Research Center, Liaoning Normal University, Dalian 116029, China
| | - Hao Wang
- College of Life Science, Liaoning Normal University, Dalian 116029, China.,Lamprey Research Center, Liaoning Normal University, Dalian 116029, China
| | - Qingwei Li
- College of Life Science, Liaoning Normal University, Dalian 116029, China.,Lamprey Research Center, Liaoning Normal University, Dalian 116029, China
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