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主管单位 工业和信息化部 主办单位 哈尔滨工业大学 主编 任南琪 国际刊号ISSN 1672-5565 国内刊号CN 23-1513/Q

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引用本文:王冰清,关中夏,王亚丽,石莎莎,郭梦可,宋成义,高波.Y1转座酶关联转座子在大肠杆菌和沙门氏菌基因组中的分布和结构特征[J].生物信息学,2024,22(3):217-224.
WANG Bingqing,GUAN Zhongxia,WANG Yali,SHI Shasha,GUO Mengke,SONG Chengyi,GAO Bo.Distribution and structural characteristics of Y1 transposase associated transposons in Escherichia coliand Salmonella entericagenomes[J].Chinese Journal of Bioinformatics,2024,22(3):217-224.
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Y1转座酶关联转座子在大肠杆菌和沙门氏菌基因组中的分布和结构特征
王冰清,关中夏,王亚丽,石莎莎,郭梦可,宋成义,高波
(扬州大学 动物科学与技术学院,江苏 扬州 225002)
摘要:
Y1转座酶关联转座子(Y1ATs)的活性催化位点为一个酪氨酸,能够切割和连接单链DNA,在原核生物分布广泛。为探究Y1转座酶关联转座子在大肠杆菌(Escherichia coli, E. coli)与沙门氏菌(Salmonella enterica, S. ente)基因组中系统进化特性,通过Hmmsearch程序对Y1转座酶关联转座子进行了挖掘分析。结果表明,Y1转座酶关联转座子广泛分布于96.84%大肠杆菌基因组和80.4%沙门氏菌基因组。根据序列比对和蛋白结构域预测将Y1转座酶关联转座子分为10类,均隶属于IS200/IS605超家族,其中11 645个属于IS200家族,4 811个属于IS605家族。IS200家族广泛分布于S. ente基因组中(72.24%),而IS605家族广泛分布于E. coli基因组中(89.38%)。IS200拷贝数以及完整拷贝数显著高于IS605。IS200家族仅含有一个Y1转座酶编码区,而IS605家族含两个开放阅读框,分别编码Y1转座酶和TnpB蛋白。IS200家族的Y1氨基酸序列高度保守(95.3%),而IS605家族的Y1和TnpB具有较高遗传多样性,为研究转座子在原核生物的遗传进化模式提供重要参考。IS200家族具有高度保守的Y1转座酶,且完整拷贝数比例较高,提示该类转座子可能具有转座活性,对其活性的挖掘有利于研制转座子介导的新型高效基因编辑工具。
关键词:  转座子  Y1  TnpB  IS200  IS605  大肠杆菌(E. coli)  沙门氏菌(S. ente)
DOI:10.12113/202304017
分类号:Q311
文献标识码:A
基金项目:
Distribution and structural characteristics of Y1 transposase associated transposons in Escherichia coliand Salmonella entericagenomes
WANG Bingqing, GUAN Zhongxia, WANG Yali, SHI Shasha, GUO Mengke, SONG Chengyi, GAO Bo
(College of Animal Science and Technology, Yangzhou University, Yangzhou 225002, Jiangsu, China)
Abstract:
Y1 is a transposase that contains one tyrosine in its catalytic center, and it is capable of cleaving and ligating single-stranded DNA. Y1-associated transposons (Y1ATs) are widely distributed among prokaryotes. To explore the systematic evolutionary characteristics of Y1ATs in the genomes of two bacterial strains, Escherichia coli(E. coli) and Salmonella enterica(S. ente), which is done by mining and analyzing Y1ATs using the Hmmsearch program. The results indicate that Y1ATs are widely distributed in 96.84% of the E. coligenome and 80.4% of the S. entegenome. Based on sequence alignment and protein structure domain prediction, Y1ATs are classified into 10 classes, all belonging to the IS200/IS605superfamily, with 11 645 belonging to the IS200family and 4,1 belonging to the IS605family. The IS200family is widely distributed in the S. entegenome (72.24%), while the IS605family is highly distributed in the E. coligenome (89.38%). The number of IS200copies and intact copies are significantly higher than that of IS605. The IS200family has only one Y1 transposase coding region, while the IS605family has two open reading frames, encoding Y1 transposase and TnpB protein, respectively. The amino acid sequence of Y1 in the IS200family is highly conserved (95.3%). In contrast, Y1 and TnpB in the IS605family exhibit genetic diversity, which can provide significant insights into the genetic evolutionary pattern of transposons among prokaryotes. The IS200family containing a highly conserves Y1 transposase with a high proportion of intact copies suggests that this type of transposon may have transpositional activity. Exploring its activity could be beneficial in developing novel and efficient transposon-mediated gene editing tools.
Key words:  Tansposon  Y1  TnpB  IS200  IS605  Escherichia coli (E. coli)  Salmonella enterica (S. ente)

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