研究报告 Research Report 金鱼 ABC 转运蛋白基因家族成员鉴定及分析 刘含梅 崔文耀 宋诗颖 李伟明 任建峰 * 上海海洋大学, 科技部海洋生物科学国际联合研究中心, 水产种质资源发掘与利用教育部重点实验室, 水产科学国家级实验教学示范中心, 上 海, 201306 * 通信作者, [email protected]摘 要 腺苷三磷酸结合盒转运蛋白(ATP-binding cassette transporter, ABC transporter)基因家族在原核生物 和真核生物中广泛存在,该家族蛋白能够利用 ATP 裂解产生的能量将多种底物转运到膜上,参与多种生物 过程,如营养摄入、细胞解毒、脂质稳态、信号转导、病毒防御以及抗原呈递等。目前,鱼类中,只在斑马鱼、斑 点叉尾鮰和鲤鱼等少数鱼类中对该基因家族进行了系统的研究,关于金鱼 ABC 转运蛋白基因家族的详细 分析,未见报道。本研究中,我们利用三代结合二代测序技术构建的金鱼转录组参考基因集数据,鉴定出 55 个 ABC 转运蛋白基因,通过系统进化分析将它们分为 8 个亚家族(A~H)。即金鱼 ABC 转运蛋白基因是由 10 个 ABCA、 14 个 ABCB、 13 个 ABCC、 5 个 ABCD、 1 个 ABCE、 4 个 ABCF、 7 个 ABCG 和 1 个 ABCH 组成。同 时,我们将金鱼与斑马鱼、斑点叉尾鮰和鲤鱼等物种 ABC 转运蛋白基因家族成员的数目进行比较分析,推 测硬骨鱼类特异的第 3 次全基因复制(3R-WGD)和谱系特异的第 4 次全基因组复制(4R-WGD)对金鱼该基 因家族成员数目的影响。本研究结果为金鱼 ABC 转运蛋白基因功能的研究提供了理论依据。 关键词 金鱼, ABC 转运蛋白, 基因鉴定, 序列分析, 进化 Identification and Analysis of ABC Transporter Gene Family in Goldfish (Carassius auratus auratus ) Liu Hanmei Cui Wenyao Song Shiying Li Weiming Ren Jianfeng * National Demonstration Center for Experimental Fisheries Science Education, Key Laboratory of Exploration and Utilization of Aquatic Genetic Re sources, Ministry of Education, International Research Center for Marine Biosciences, Ministry of Science and Technology, Shanghai Ocean University, Shanghai, 201306 * Corresponding author, [email protected]DOI: 10.13417/j.gab.039.000001 Abstract The ATP-binding cassette (ABC) transporter gene family is considered to be one of the largest gene families in various forms of prokaryotes and eukaryotes, and they are able to transport various substrates to the membrane using the energy generated by ATP cleavage. Members of this family participate in a variety of biological processes such as nutrition uptake, cell detoxification, lipid homeostasis, signal transduction, viral defense, antigen presentation and so on. At present, systematical studies on this gene family have been carried out only in a few fish species, such as zebrafish (Danio rerio), catfish (Ietalurus punetaus ) and common carp (Cyprinus carpio). A detailed analysis of the ABC transporter gene family in goldfish (Carassius auratus auratus ) has not been investigated. In this study, with the goldfish transcriptome reference dataset generated by the sequencing technology of the third generation combined with the second generation, we identified 55 ABC transporter genes and divided them into 8 different subfamilies (A~H) according to the result from phylogenetic analysis. The ABC 基金项目:本研究由上海市科委国际科技合作项目(15410723300) 和上海海洋大学优秀本科生项目(A1-2041-18-0000) 共同资助 引用格式: Liu H.M., Cui W.Y., Song S.Y., Li W.M., and Ren J.F., 2020, FIdentification and analysis of ABC transporter gene family in goldfish ( Carassius auratus auratus), Jiyinzuxue Yu Yingyong Shengwuxue (Genomics and Applied Biology), 39(1): 1-10 (刘含梅, 崔文 耀, 宋诗颖, 李伟明, 任建峰, 2020, 金鱼 ABC 转运蛋白基因家族成员鉴定及分析, 基因组学与应用生物学, 39(1): 1-10) 基因组学与应用生物学, 2020 年,第 39 卷,第 1 期,第 1-10 页
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Identification and Analysis of ABC Transporter Gene Family in Goldfish(Carassius auratus auratus)Liu Hanmei Cui Wenyao Song Shiying Li Weiming Ren Jianfeng *
National Demonstration Center for Experimental Fisheries Science Education, Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Ministry of Education, International Research Center for Marine Biosciences, Ministry of Science and Technology, Shanghai Ocean University,Shanghai, 201306* Corresponding author, [email protected]: 10.13417/j.gab.039.000001
Abstract The ATP-binding cassette (ABC) transporter gene family is considered to be one of the largest genefamilies in various forms of prokaryotes and eukaryotes, and they are able to transport various substrates to themembrane using the energy generated by ATP cleavage. Members of this family participate in a variety ofbiological processes such as nutrition uptake, cell detoxification, lipid homeostasis, signal transduction, viraldefense, antigen presentation and so on. At present, systematical studies on this gene family have been carried outonly in a few fish species, such as zebrafish (Danio rerio), catfish (Ietalurus punetaus) and common carp (Cyprinuscarpio). A detailed analysis of the ABC transporter gene family in goldfish (Carassius auratus auratus) has notbeen investigated. In this study, with the goldfish transcriptome reference dataset generated by the sequencingtechnology of the third generation combined with the second generation, we identified 55 ABC transporter genesand divided them into 8 different subfamilies (A~H) according to the result from phylogenetic analysis. The ABC
引用格式:Liu H.M., Cui W.Y., Song S.Y., Li W.M., and Ren J.F., 2020, FIdentification and analysis of ABC transporter gene family ingoldfish (Carassius auratus auratus), Jiyinzuxue Yu Yingyong Shengwuxue (Genomics and Applied Biology), 39(1): 1-10 (刘含梅,崔文
作用,需要 ATP 的结合和水解以将许多底物(例如:简单离子,氨基酸,脂质,糖,肽和药物)从细胞质运输
到细胞内或细胞外区域(Liu et al., 2013; Dermauwand Leeuwen, 2014)。它们还参与许多其它重要的生
理过程,如营养摄入、细胞解毒、脂质稳态、信号转
导、病毒防御以及抗原呈递等(Wilkens, 2015)。此外,
ABC转运蛋白基因与人类多种疾病相关,如:ABCA1突变导致高密度脂蛋白缺乏症(Tangier Disease) (Bo-dzioch et al., 1999; Rust et al., 1999),ABCB1、ABCC1和 ABCG2 等蛋白与多种癌症耐药性的关系(Robeyet al., 2018)。
典型的 ABC 转运蛋白核心结构通常由 4 个结
构域组成,包括 2 个结合、水解 ATP 的胞质核苷酸
结合结构域(nucleotide binding domain, NBD)和 2 个
完整的跨膜结构域 (transmembrane domain, TMD)(Beek et al., 2014)。其中 NBD 结构域相对保守,由
Walker A 基序、Walker B 基序、Walker C 基序、
Q-loop、H-loop 和 ABC-signature 等组成,它们能够
结合 ATP并将其水解为主动运输的能量(刘艳青和
transporter gene family in the goldfish are comprised of 10 ABCA genes, 14 ABCB genes, 13 ABCC genes, fiveABCD genes, one ABCE gene, four ABCF genes, seven ABCG genes, and one ABCH gene. In addition, we alsocompared the ABC gene family members of goldfish with those of zebrafish, catfish and common carp; thenumber of ABC gene family in goldfish was affected by the teleost-specific third-round whole genome duplication(3R-WGD) and lineage-specific fourth-round whole genome duplication (4R-WGD). These results will provideessential genomic resources for functional studies of goldfish ABC transporter proteins in future.Keywords Goldfish, ABC transporter, Gene identification, Sequence analysis, Evolution
来在其它节肢动物(Dean et al., 2001; Annilo et al.,2006; Dermauw and Leeuwen, 2014)和斑马鱼(Daniorerio)中被发现,但在植物、蠕虫、酵母和哺乳动物基
因组中未发现(Dean and Annilo, 2005; Popovic et al.,2010; Guo et al., 2015)。
目前,脊椎动物中,只在人、小鼠、鱼类(斑马鱼,斑点叉尾鮰, 海水青鳉和鲤鱼)和七鳃鳗等少数物种
中进行了 ABC转运蛋白基因家族的系统研究(Deanet al., 2001; Dean and Annilo, 2005; Liu et al., 2013;Jeong et al., 2015; Ren et al., 2015; Liu et al., 2016),金鱼(Carassius auratus auratus)中该基因家族成员的详
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