微小杆菌冷激蛋白（CSP）基因密码子偏好性分析

doi:10.19640/j.cnki.jtau.2024.05.001

天津农学院学报 ›› 2024, Vol. 31 ›› Issue (5): 1-10.doi: 10.19640/j.cnki.jtau.2024.05.001

• 研究与简报 • 下一篇

微小杆菌冷激蛋白（CSP）基因密码子偏好性分析

钟迎兰, 罗希帆, 杜锦, 陈帅君, 黄海东, 吴疆^通信作者

天津农学院农学与资源环境学院,天津 300392

收稿日期:2023-08-16 出版日期:2024-10-31 发布日期:2024-11-05
通讯作者: 吴疆（1976—）,男,副教授,博士,主要从事植物分子生物学方面的研究。E-mail：wujiangjack@tjau.edu.cn。
作者简介:钟迎兰（1995—）,女,硕士在读,主要从事植物转基因方面的研究。E-mail：yinglanzhong@163.com。
基金资助:
天津市优秀企业科技特派员项目（22YDTPJC00960）

Analysis of codon use features of cold shock protein（CSP）gene in Exobacterium profundaum

Zhong Yinglan, Luo Xifan, Du Jin, Chen Shuaijun, Huang Haidong, Wu Jiang^{Corresponding Author}

College of Agronomy and Resources Environment, Tianjin Agricultural University, Tianjin 300392, China

Received:2023-08-16 Online:2024-10-31 Published:2024-11-05

摘要/Abstract

摘要： 对微小杆菌（Exobacterium profundaum）冷激蛋白（CSP）基因（EpCSP）密码子偏好性进行分析,为后续EpCSP基因的功能验证及遗传转化等研究提供理论依据。结果表明：EpCSP基因的密码子偏好性较弱,偏好使用A/T结尾的密码子;比较分析不同物种CSP基因的密码子偏好性参数发现,大多数物种CSP基因密码子偏好使用G/C结尾的密码子;21个物种CSP基因的CDS序列及RSCU值聚类分析表明,微小杆菌与另外20个不同物种CSP基因密码子使用偏好性存在一定差异;中性分析、PR2-plot分析、ENc-plot等都证实了自然选择是影响CSP基因密码子偏好性形成的最主要原因;与7种模式生物的基因组密码子使用频率对比研究表明,在筛选异源转化受体时,作为真核表达系统的酿酒酵母比作为原核表达系统的大肠杆菌更利于EpCSP基因异源表达,而在选择植物遗传转化受体时,拟南芥和小麦比烟草和水稻更适合作为EpCSP基因的遗传转化受体。本研究初步探索了EpCSP基因密码子使用偏好性,对以后开展基因功能验证有重要的指导作用,同时也可为研究微小杆菌分子进化提供一定的理论基础。

关键词: 微小杆菌, CSP基因, 密码子偏好性, 异源表达, 外源宿主

Abstract: Analyzing the codon preference of the EpCSP gene in Exobacterium profundum provides a theoretical basis for subsequent functional verification and genetic transformation research of the EpCSP gene. The research results indicated that the codon preference of the EpCSP gene in E. profundum was weak, preferring to use codons ending in A/T. By comparing and analyzing the codon preference parameters of CSP genes in different species, it was found that most species prefer to use codons ending in G/C. Cluster analysis of CDS sequences and RSCU values of CSP genes in 21 species showed that there were certain differences in codon usage preferences between E. profundum and 20 other different species. Neutrality analysis, PR2 plot analysis, ENc plot analysis, etc. all confirmed that natural selection was the most important factor affecting the formation of codon preference in CSP genes. Compared with the frequency of genomic codon usage in seven model organisms, it was found that in the selection of heterologous transformation receptors, the yeast eukaryotic expression system was more suitable for heterologous expression of EpCSP in E. profundum than the Escherichia coli prokaryotic expression system. Arabidopsis and wheat were more suitable as genetic transformation receptors for EpCSP genes in E. profundum than tobacco and rice. This study preliminarily revealed the usage patterns of the EpCSP gene codon in E. profundum, which has important guidance for subsequent gene function verification and can also provide a certain scientific basis for studying the molecular evolution of E. profundum.

Key words: Exiguobacterium profundum, CSP gene, codon preference, heterologous expression, exogenous host

中图分类号:

钟迎兰, 罗希帆, 杜锦, 陈帅君, 黄海东, 吴疆. 微小杆菌冷激蛋白（CSP）基因密码子偏好性分析[J]. 天津农学院学报, 2024, 31(5): 1-10.

Zhong Yinglan, Luo Xifan, Du Jin, Chen Shuaijun, Huang Haidong, Wu Jiang. Analysis of codon use features of cold shock protein（CSP）gene in Exobacterium profundaum[J]. Journal of Tianjin Agricultural University, 2024, 31(5): 1-10.

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微小杆菌冷激蛋白（CSP）基因密码子偏好性分析

Analysis of codon use features of cold shock protein（CSP）gene in Exobacterium profundaum

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