| 引用本文: | 鲍麒,张晓兰,黄纯,梁春年,李吉叶,褚敏,阎萍.牦牛NLRP基因家族全基因组鉴定及转录组分析[J].生物信息学,2022,20(2):113-123. |
| BAO Qi,ZHANG Xiaolan,HUANG Chun,LIANG Chunnian,LI Jiye,CHU Min,YAN Ping.Genome-wide identification and transcriptome analysis of NLRPgene family of yak[J].Chinese Journal of Bioinformatics,2022,20(2):113-123. |
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| 牦牛NLRP基因家族全基因组鉴定及转录组分析 |
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鲍麒1,2,张晓兰1,2,黄纯1,2,梁春年1,2,李吉叶3,褚敏1,2,阎萍1,2
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(1.中国农业科学院 兰州畜牧与兽药研究所,兰州 730050;2.甘肃省牦牛繁育工程重点实验室,兰州 730050;3.青海大通种牛场,西宁 810000)
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| 摘要: |
| NLRP基因家族在哺乳动物基因组中分布广泛,在免疫应答和生殖相关过程中发挥重要作用。本研究根据已报道的人类NLRP基因,利用PFAM、CDD、UniProt等数据库,采用ClustalW、MEGA X、ExPASy、MEME、GSDS和STRING等软件对牦牛NLRP家族成员进行全基因组鉴定和分析,并且基于高通量测序数据分析NLRP基因在牦牛不同组织中的表达情况。研究共鉴定出8个不同的NLRP基因家族成员,包括NLRP2、NLRP3、NLRP5、NLRP6、NLRP8、NLRP9、NLRP12、NLRP14,其中NLRP9有2个可变剪切。牦牛NLRP蛋白均有多个磷酸化位点,GRAVY值均小于0,属于亲水性蛋白；不稳定系数均大于40,均为不稳定蛋白,无跨膜结构。系统进化树显示同一家族成员氨基酸序列相似性高,在 6个物种中都聚在一起,免疫相关基因与生殖发育相关基因在进化中已经分开。蛋白互作网络显示牦牛NLRP蛋白与其他物种已经研究的功能相似,不仅与参与免疫相关的蛋白互作,也与生殖标记蛋白互作。如NLRP3与多种参与炎症反应的蛋白PYCARD、MLKL、GSDMD互作,NLRP5也与生殖细胞标记蛋白GDF9、BMP15、ZAR1等互作。转录组分析结果显示,牦牛NLRP基因在6种组织中的表达较为微弱或者不表达,具有组织特异性。牦牛NLRP家族在结构及理化性质上与其他物种同源基因具有相同的特点,部分试验和预测证实其同样参与了免疫和生殖相关过程。本研究结论不仅对牦牛NLRP基因家族进行了系统分析,同时为进一步研究牦牛先天免疫和生殖相关过程提供理论依据。 |
| 关键词: NLRP 牦牛 生物信息 基因家族 全基因组鉴定 |
| DOI：10.12113/202012013 |
| 分类号:S828 |
| 文献标识码:A |
| 基金项目:中国农业科学院创新工程项目(No.CAAS-ASTIP-2014-LIHPS-01)；科技援青合作专项(No.2020-QY-212)；现代农业(肉牛牦牛)产业技术体系建设专项资金(No.CARS-37)；甘肃省科技计划资助(No.20JR5RA580). |
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| Genome-wide identification and transcriptome analysis of NLRPgene family of yak |
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BAO Qi1,2,ZHANG Xiaolan1,2,HUANG Chun1,2,LIANG Chunnian1,2,LI Jiye3,CHU Min1,2,YAN Ping1,2
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(1.Lanzhou Institute of Husbandry and Pharmaceutical Sciences,Chinese Academy of Agricultural Sciences,Lanzhou 730050,China; 2.Key Laboratory of Yak Breeding Engineering,Lanzhou 730050,China; 3.Datong Cattle Farm in Qinghai Province, Xining 810000,China)
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| Abstract: |
| NLRPgenes are widely distributed in mammalian genomes and play an important role in immune response and reproduction-related processes. According to the reported human NLRPgenes, based on PFAM, CDD, UniProt, and other databases, the ClustalW, MEGA X, ExPASy, MEME, GSDS, and STRING software systems were used to identify and analyze the NLRPfamily members of yak, and based on high-throughput sequencing data, the NLRPgene expression in different tissues of yak was analyzed. A total of eight different NLRPgene family members were identified, including NLRP2, NLRP3, NLRP5, NLRP6, NLRP8, NLRP9, NLRP12, and NLRP14, among which NLRP9had two variable splicings. The NLRPproteins had multiple phosphorylation sites, and the GRAVY values were all less than 0, which were hydrophilic proteins; the instability coefficients were all greater than 40, and they were all unstable proteins with no transmembrane structure. The phylogenetic tree showed that the amino acid sequences of members of the same family were highly similar, and they were clustered in six species. The immune-related genes and the genes related to reproductive development had been separated in evolution. The protein interaction network showed that members of the yak NLRPfamily had similar functions with those studied in other species. They not only interacted with immune-related proteins but also with reproductive marker proteins. For example, NLRP3 interacted with a variety of proteins (PYCARD, MLKL, and GSDMD) involved in inflammation, and NLRP5 also interacts with germ cell marker proteins such as GDF9, BMP15, and ZAR1. The results of transcriptome analysis showed that the expression of yak NLRPgene in six kinds of tissues was weak or not expressed, which was tissue-specific. The yak NLRPfamily had the same characteristics as homologous genes of other species in terms of structure and physical and chemical properties. Some experiments and predictions have confirmed that it is also involved in immune and reproduction-related processes. The study not only conducted a systematic analysis of the yak NLRPgene family, but also provided theoretical basis for further research on the innate immunity and reproduction-related processes of yak. |
| Key words: NLRP Yak Bioinformatics Gene family Genome-wide identification |
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