刚地弓形虫蛋白磷酸酶的全蛋白质组鉴定及生物信息学分析

doi:10.12140/j.issn.1000-7423.2021.01.018

中国寄生虫学与寄生虫病杂志 ›› 2021, Vol. 39 ›› Issue (1): 120-124.doi: 10.12140/j.issn.1000-7423.2021.01.018

刚地弓形虫蛋白磷酸酶的全蛋白质组鉴定及生物信息学分析

何成(), 潘帅, 许妹珍, 原飞, 何静妹, 刘转转^*()

1 徐州医科大学病原生物学与免疫学教研室,江苏省免疫与代谢重点实验室,基础医学国家级实验教学示范中心,徐州 221004

收稿日期:2020-04-28 修回日期:2020-12-06 出版日期:2021-02-28 发布日期:2021-03-10
通讯作者: 刘转转
作者简介:何成（1988-）,男,博士研究生,从事弓形虫与宿主相互作用研究。E-mail： hechengchoice@163.com
基金资助:
江苏省自然科学基金青年基金(BK20190983);江苏省高校自然科学基金(19KJB310022);江苏省高校自然科学基金(D2019018)

Proteome-based identification and bioinformatics analysis of protein phosphatases of Toxoplasma gondii

HE Cheng(), PAN Shuai, XU Mei-zhen, YUAN Fei, HE Jing-mei, LIU Zhuan-zhuan^*()

1 National Experimental Demonstration Center for Basic Medicine Education, Jiangsu Key Laboratory of Immunity and Metabolism, Department of Pathogen Biology and Immunology, Xuzhou Medical University, Xuzhou 221004, China

Received:2020-04-28 Revised:2020-12-06 Online:2021-02-28 Published:2021-03-10
Contact: LIU Zhuan-zhuan
Supported by:
Natural Science Foundation of Jiangsu Province(BK20190983);Natural Science Foundation of the Jiangsu Higher Education Institutions of China(19KJB310022);Natural Science Foundation of the Jiangsu Higher Education Institutions of China(D2019018)

摘要/Abstract

摘要：

从相关数据库分别下载刚地弓形虫GT1、ME49、VEG虫株,疟原虫以及44个其他真核生物物种的全蛋白质组氨基酸序列,应用HMMER3软件搜索弓形虫不同虫株及其他物种氨基酸序列,鉴定出弓形虫及其他物种磷酸酶家族蛋白。对所有鉴定出的磷酸酶家族蛋白进行聚类分析,提取相对保守的磷酸酶家族蛋白氨基酸序列,分别用邻接法和最大似然法构建系统进化树。应用Pfam在线工具对鉴定出的弓形虫磷酸酶蛋白的结构域进行注释,并进行基因本体(GO)和京都基因与基因组百科全书(KEGG)富集分析,利用基因芯片数据分析并比较蛋白磷酸酶在不同虫株及ME49虫株不同发育时期的转录水平。共鉴定出64个弓形虫磷酸酶蛋白,分属5个磷酸酶亚家族,其中,磷蛋白磷酸酶家族蛋白11个,酪氨酸磷酸酶样蛋白A家族蛋白1个,天冬氨酸依赖的酪氨酸磷酸酶家族蛋白8个,双特异性磷酸酶家族蛋白9个,Mg ²⁺或Mn ²⁺依赖的磷酸酶家族蛋白35个。系统进化树分析结果显示,蛋白磷酸酶在不同弓形虫虫株间高度保守,仅有2个蛋白磷酸酶无直系同源蛋白,为VEG虫株所特有。GO富集分析结果显示,弓形虫蛋白磷酸酶主要具有磷酸酶、水解酶及催化活性的分子功能,参与调节去磷酸化的生物学过程。芯片分析结果显示,蛋白磷酸酶在弓形虫不同虫株速殖子时期的表达谱相似,虫株间表达水平差异最大的为TG_312200,其在ME49虫株中的表达水平约为GT1和VEG虫株的4倍;部分蛋白磷酸酶的转录水平在ME49虫株不同发育阶段差异显著,如TG_318660在未孢子化的卵囊中低表达,TG_304955在速殖子和缓殖子期高表达,这些在不同发育时期差异表达的蛋白磷酸酶可能在虫体发育过程中发挥重要作用。

关键词: 刚地弓形虫, 磷酸酶, 生物信息学分析

Abstract:

The proteomic amino acids of Toxoplasma gondii strains GT1, ME49 and VEG, Plasmodium, and 44 other eukaryote species were downloaded from related databases. The amino acid sequences of various T. gondii strains and other species were searched using the HMMER3 software to identify the phosphatases of. T. gondii and other species. Cluster analysis was performed for all of the identified phosphatases to extract the conserved amino acid sequences of phosphatases, and phylogenetic trees were constructed with the neighbor-joining method and maximum likelihood method, respectively. Meanwhile, the catalytic domains of these identified phosphatases were annotated using the Pfam online tool, and gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses were performed. Gene array data were used to analyze and compare the transcription levels of protein phosphatases in different strains and at different developmental stages of ME49 strain. Results showed that 64 phosphatases were identified, which were classified into 5 subfamilies: phosphoprotein phosphatase (PPP) family (11 proteins), protein tyrosine phosphatase-like A (PTPLA) family (1 protein), ASP-dependent tyrosine phosphatase (APP) family (8 proteins), dual-specificity phosphatase (DSP) family (9 proteins) and Mg ²⁺ or Mn ²⁺-dependent protein phosphatase (PPM) family (35 proteins). The bioinformatics analysis revealed that the identified phosphatases mainly possessed phosphatase activity, hydrolase activity and catalytic activity, and participated in the regulation of dephosphorylation. The phylogenetic analysis suggested that the phosphatases were conserved among the T. gondii strains. In addition, similar protein phosphatase expression profiles were found at the tachyzoite stage of different T. gondii strains. The most significant difference was found in TG_312200 among different stains. Its expression in ME49 was 4 times as that in the GT1 strain and VEG strains. However, the transcription levels of some phosphatases varied significantly among various developmental stages of the ME49 strain. For example, TG_318660 transcription was at a low level in unsporulated oocysts while TG_304955 transcription was at a high level in both tachyzoites and bradyzoites. These results suggested that these differentially expressed phosphatases may play essential roles in the development of T. gondii.

Key words: Toxoplasma gondii, Phosphatase, Bioinformatics analysis

中图分类号:

382.5

何成, 潘帅, 许妹珍, 原飞, 何静妹, 刘转转. 刚地弓形虫蛋白磷酸酶的全蛋白质组鉴定及生物信息学分析[J]. 中国寄生虫学与寄生虫病杂志, 2021, 39(1): 120-124.

HE Cheng, PAN Shuai, XU Mei-zhen, YUAN Fei, HE Jing-mei, LIU Zhuan-zhuan. Proteome-based identification and bioinformatics analysis of protein phosphatases of Toxoplasma gondii[J]. Chinese Journal of Parasitology and Parasitic Diseases, 2021, 39(1): 120-124.

图/表 3

参考文献 17

[1]	Wei HX, He C, Yang PL, et al. Relationship between cat contant and infection by Toxoplasma gondii in human: a meta-analysis[J]. Comp Parasitol, 2016,83(1):11-19. doi: 10.1654/1525-2647-83.1.11
[2]	Shen JL, Wang L. Genotypes and main effectors of Toxoplasma gondii and their pathogenic mechanism[J]. Chin J Parasitol Parasit Dis, 2015,33(6):429-435. (in Chinese)
	( 沈继龙, 王林. 弓形虫的基因型及其主要效应分子的致病机制[J]. 中国寄生虫学与寄生虫病杂志, 2015,33(6):429-435.)
[3]	Fentress SJ, Behnke MS, Dunay IR, et al. Phosphorylation of immunity-related GTPases by a Toxoplasma gondii-secreted kinase promotes macrophage survival and virulence[J]. Cell Host Microbe, 2010,8(6):484-495. doi: 10.1016/j.chom.2010.11.005
[4]	Yang C, Arrizabalaga G. The serine/threonine phosphatases of apicomplexan parasites[J]. Mol Microbiol, 2017,106(1):1-21. doi: 10.1111/mmi.13715 pmid: 28556455
[5]	Guttery DS, Poulin B, Ramaprasad A, et al. Genome-wide functional analysis of Plasmodium protein phosphatases reveals key regulators of parasite development and differentiation[J]. Cell Host Microbe, 2014,16(1):128-140. doi: 10.1016/j.chom.2014.05.020
[6]	Eddy SR. Profile hidden Markov models[J]. Bioinformatics, 1998,14(9):755-763. doi: 10.1093/bioinformatics/14.9.755 pmid: 9918945
[7]	Li L, Stoeckert CJ, Roos DS. OrthoMCL: identification of ortholog groups for eukaryotic genomes[J]. Genome Res, 2003,13(9):2178-2189. doi: 10.1101/gr.1224503 pmid: 12952885
[8]	Katoh K, Toh H. Parallelization of the MAFFT multiple sequence alignment program[J]. Bioinformatics, 2010,26(15):1899-1900. doi: 10.1093/bioinformatics/btq224 pmid: 20427515
[9]	Tamura K, Stecher G, Peterson D, et al. MEGA6: molecular evolutionary eenetics analysis version 6.0[J]. Mol Biol Evol, 2013,30(12):2725-2729. doi: 10.1093/molbev/mst197
[10]	Guindon S, Dufayard JF, Lefort V, et al. New algorithms and methods to estimate maximum-likelihood phylogenies: assessing the performance of PhyML 3.0[J]. Syst Biol, 2010,59(3):307-321. doi: 10.1093/sysbio/syq010 pmid: 20525638
[11]	Madeira F, Park YM, Lee J, et al. The EMBL-EBI search and sequence analysis tools APIs in 2019[J]. Nucleic Acids Res, 2019,47(W1):W636-W641. doi: 10.1093/nar/gkz268 pmid: 30976793
[12]	Letunic I, Bork P. Interactive tree of life (iTOL): an online tool for phylogenetic tree display and annotation[J]. Bioinformatics, 2007,23(1):127-128. doi: 10.1093/bioinformatics/btl529 pmid: 17050570
[13]	Sidik SM, Huet D, Ganesan SM, et al. A genome-wide CRISPR screen in Toxoplasma identifies essential apicomplexan genes[J]. Cell, 2016, 166(6): 1423-1435.e12. doi: 10.1016/j.cell.2016.08.019 pmid: 27594426
[14]	Deng W, Wang Y, Liu Z, et al. HemI: a toolkit for illustrating heatmaps[J]. PLoS One, 2014,9(11):e111988. doi: 10.1371/journal.pone.0111988 pmid: 25372567
[15]	Delorme V, Cayla X, Faure G, et al. Actin dynamics is controlled by a casein kinase Ⅱ and phosphatase 2C interplay on Toxoplasma gondii toxofilin[J]. Mol Biol Cell, 2003,14(5):1900-1912. doi: 10.1091/mbc.e02-08-0462 pmid: 12802063
[16]	Paul AS, Saha S, Engelberg K, et al. Parasite calcineurin regulates host cell recognition and attachment by apicomplexans[J]. Cell Host Microbe, 2015,18(1):49-60. doi: 10.1016/j.chom.2015.06.003 pmid: 26118996
[17]	Gilbert LA, Ravindran S, Turetzky JM, et al. Toxoplasma gondii targets a protein phosphatase 2C to the nuclei of infected host cells[J]. Eukaryot Cell, 2007,6(1):73-83. doi: 10.1128/EC.00309-06 pmid: 17085638

刚地弓形虫蛋白磷酸酶的全蛋白质组鉴定及生物信息学分析

Proteome-based identification and bioinformatics analysis of protein phosphatases of Toxoplasma gondii

RichHTML

PDF (PC)

可视化

摘要/Abstract

引用本文

使用本文

图/表 3

参考文献 17

相关文章 15

编辑推荐

Metrics

本文评价

[1]	薛羽珊, 林萍, 程训佳, 冯萌. 慢性弓形虫感染对宿主中枢神经系统的损伤及其作用机制[J]. 中国寄生虫学与寄生虫病杂志, 2023, 41(5): 527-531.
[2]	姜文静, 孟雅莉, 赵利娜, 王春苗, 张晓磊. 刚地弓形虫棒状体蛋白18和膜表面抗原30复合核酸疫苗对小鼠的免疫保护作用[J]. 中国寄生虫学与寄生虫病杂志, 2023, 41(5): 532-538.
[3]	赵紫琪, 吕芳丽. 蒿甲醚脂质体体外抑制刚地弓形虫增殖作用的研究[J]. 中国寄生虫学与寄生虫病杂志, 2023, 41(4): 446-451.
[4]	张驰, 陈嘉婷, 辛紫萱, 杨莉莉, 杨梓瀚, 彭鸿娟. 弓形虫慢性感染小鼠脑转录组分析及与抑郁相关的犬尿氨酸通路的验证[J]. 中国寄生虫学与寄生虫病杂志, 2023, 41(3): 270-278.
[5]	杜鹃, 李佳, 吴迪, 余琦, 张玮, 白如念, 郭俊林, 刘庆斌, 雷琪莉, 谷传慧, 王萌, 赵浩军. 2022年北京市犬猫刚地弓形虫感染血清流行病学调查[J]. 中国寄生虫学与寄生虫病杂志, 2023, 41(3): 389-392.
[6]	李佳铭, 王艺璇, 杨宁爱, 马慧慧, 兰敏, 刘春兰, 赵志军. 刚地弓形虫ROP16蛋白对MH-S细胞极化和凋亡的影响及其相关机制[J]. 中国寄生虫学与寄生虫病杂志, 2022, 40(5): 579-586.
[7]	邹伟浩, 吴蔚玲, 廖远鹏, 陈敏, 彭鸿娟. 刚地弓形虫抗缓殖子期抗原1单克隆抗体的制备与应用[J]. 中国寄生虫学与寄生虫病杂志, 2022, 40(5): 587-593.
[8]	代莉莎, 张丽新, 尹昆. 刚地弓形虫诱导宿主精神行为障碍的研究进展[J]. 中国寄生虫学与寄生虫病杂志, 2022, 40(5): 642-646.
[9]	王杰, 温红阳, 陈滢, 安然, 罗庆礼, 沈继龙, 都建. 刚地弓形虫巨噬细胞迁移抑制因子基因敲除虫株的构建与鉴定[J]. 中国寄生虫学与寄生虫病杂志, 2022, 40(3): 349-354.
[10]	王振勋, 熊思思, 孙夏慧, 王永亮, 潘格, 何深一, 丛华. 刚地弓形虫慢性感染小鼠脑组织中lncRNA102796的差异表达及其作用机制[J]. 中国寄生虫学与寄生虫病杂志, 2022, 40(2): 187-193.
[11]	蒋峰, 陈润, 都宁宁, 朱梦怡, 钟昊, 陈辉, 奚旭霞, 湛孝东, 李朝品. 芜湖市区宠物犬、猫刚地弓形虫感染情况调查[J]. 中国寄生虫学与寄生虫病杂志, 2022, 40(1): 124-126.
[12]	鲁飞, 卓洵辉, 陆绍红. 顶复门原虫感染与宿主细胞自噬相互作用的研究进展[J]. 中国寄生虫学与寄生虫病杂志, 2021, 39(6): 826-831.
[13]	王龙江, 李瑾, 尹昆, 徐超, 刘功振, 黄炳成, 魏庆宽, 孙慧. 刚地弓形虫入侵人包皮成纤维细胞前后转录组差异分析[J]. 中国寄生虫学与寄生虫病杂志, 2021, 39(4): 480-486.
[14]	廖文中, 徐李清, 姚礼捷, 陈敏, 彭鸿娟. 弓形虫感染后宿主细胞泛素化蛋白谱变化的特征分析[J]. 中国寄生虫学与寄生虫病杂志, 2021, 39(4): 487-493.
[15]	张丽新, 赵桂华, 徐超, 肖婷, 孙慧, 李瑾, 刘功振, 尹昆. 刚地弓形虫RH株速殖子体外入侵小鼠巨噬细胞系感染模型的构建[J]. 中国寄生虫学与寄生虫病杂志, 2021, 39(4): 494-501.