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

Journal of Tianjin Agricultural University ›› 2024, Vol. 31 ›› Issue (5): 1-10.doi: 10.19640/j.cnki.jtau.2024.05.001

• Researches and Scientific Notes • Next Articles

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

Abstract

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

CLC Number:

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

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