生物学杂志

生物学杂志 ›› 2020, Vol. 37 ›› Issue (3): 26-.doi: 10.3969/j.issn.2095-1736.2020.03.026

• 研究报告 • 上一篇    下一篇

菜青虫中肠表达基因密码子使用偏好性分析

  

  1. 西南交通大学 生命科学与工程学院， 成都 610031
  • 出版日期:2020-06-18 发布日期:2020-06-10
  • 通讯作者: 廖海, 副教授, 主要从事植物和昆虫分子方面研究, E-mail: ddliaohai@home.swjtu.edu.cn;周嘉裕, 副教授，主要从事植物和昆虫分子方面研究, E-mail: spinezhou@home.swjtu.edu.cn
  • 基金资助:
    国家自然科学基金（31500276）; 四川省重点研发项目（2018SZ0061）; 四川省应用基础研究项目（2017JY0222）; 成都市科技技术研发项目（2016-HM01-00260-SF）

Analysis of the codon usage preference of genes in midgut of Pieris rapae

  1. School of Life Science and Engineering, Southwest Jiaotong University, Chengdu 610031, China
  • Online:2020-06-18 Published:2020-06-10
  • About author:张娴, 硕士, 主要从事菜青虫丝氨酸蛋白酶研究, E-mail: 897145102@qq.com

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摘要： 为了解菜青虫(Pieris rapae)中肠表达基因密码子使用偏好性特点，为运用基因工程技术异源表达菜青虫丝氨酸蛋白酶提供理论依据，对菜青虫中肠转录组中共51 457条全长序列，使用CodonW、CUSP、CHIPS软件分析其密码子GC含量特点、有效密码子数（Effective number of codons，ENC）、相对同义密码子使用概率（Relative synonymous codon usage，RSCU）和密码子使用频率等参数，来衡量菜青虫的密码子使用偏好性。结果显示，平均总GC含量为40.43%，平均第3位碱基的GC含量（GC3）为38.16%；ENC数值在22.81～61.00之间，平均ENC为53.12，ENC小于35的有1160条，占总数的2.25%，表明基因密码子整体偏好性程度不高，但不同基因之间存在明显密码子使用偏好性；转录组密码子对以A或U结尾的密码子有明显的使用偏好性，GAA、UUU、AAU和UAU 4个密码子为菜青虫中肠表达基因的最优密码子。比较分析了菜青虫中肠参与消化的丝氨酸蛋白酶(胰凝乳蛋白酶和胰蛋白酶)与6种不同异源表达宿主密码子使用偏好性，结果显示表达最困难宿主是大肠杆菌B，其次是昆虫High5细胞和哺乳动物HEK293S细胞，烟草、毕赤酵母和拟南芥表达难度相对较低。

关键词: 菜青虫, 密码子偏好性, 丝氨酸蛋白酶, 异源表达

Abstract: In order to understand the preference characteristics of codon usage in the midgut expression genes of Pieris rapae, and to provide a theoretical basis for application of genetic engineering technology to achieve the heterologous expression of serine protease from P. rapae, in this paper, 51 457 full-length sequences in the midgut transcriptome of P. rapae were calculated and counted for GC content, effective number of codons(ENC), relative synonymous codon usage(RSCU), codon usage frequency and other parameters to measure the codon usage preference of P. rapae by using bioinformatics softwares including CodonW, CHIP and CUSP. The results showed that the total GC content was 40.43%, and the average GC content of the third nucleotide of the codon (GC3) was 38.16%. The distribution of ENC ranged from 22.81 to 61.00 with an average ENC of 53.12. There were 1160 unigenes with ENC less than 35 which accounted for 2.25% of the total. The overall codon preference of genes was not high, but there were still differences in codon usage preference among different genes. The transcriptome codon has obvious preference for codons ending in A or U. The four codons of GAA, UUU, AAU and UAU were the optimal codons for the midgut expression genes of P. rapae. The codon usage preferences of serine proteases (chymotrypsin and trypsin) involved in digestion in the midgut of P. rapae and six different heterologous expression hosts were compared and analyzed. The results showed that Escherichia coli B was the most difficult host to heterologous expression, followed by insects High 5 cells and mammalian HEK293S cells. The expression difficulty of tobacco, Pichia pastoris and Arabidopsis thaliana was relatively low.

Key words: Pieris rapae, codon preference, serine protease, heterologous expression

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