Key Laboratory for Forest Resources Conservation and Utilization in the Southwest Mountains of China Ministry of Education, Southwest Forestry University, Kunming, 650224, China.
Key Laboratory for Forest Genetics and Tree Improvement and Propagation in Universities of Yunnan Province, Southwest Forestry University, Kunming, 650224, China.
BMC Plant Biol. 2024 May 20;24(1):424. doi: 10.1186/s12870-024-04999-5.
Rutaceae family comprises economically important plants due to their extensive applications in spices, food, oil, medicine, etc. The Rutaceae plants is able to better utilization through biotechnology. Modern biotechnological approaches primarily rely on the heterologous expression of functional proteins in different vectors. However, several proteins are difficult to express outside their native environment. The expression potential of functional genes in heterologous systems can be maximized by replacing the rare synonymous codons in the vector with preferred optimal codons of functional genes. Codon usage bias plays a critical role in biogenetic engineering-based research and development. In the current study, 727 coding sequences (CDSs) obtained from the chloroplast genomes of ten Rutaceae plant family members were analyzed for codon usage bias. The nucleotide composition analysis of codons showed that these codons were rich in A/T(U) bases and preferred A/T(U) endings. Analyses of neutrality plots, effective number of codons (ENC) plots, and correlations between ENC and codon adaptation index (CAI) were conducted, which revealed that natural selection is a major driving force for the Rutaceae plant family's codon usage bias, followed by base mutation. In the ENC vs. CAI plot, codon usage bias in the Rutaceae family had a negligible relationship with gene expression level. For each sample, we screened 12 codons as preferred and high-frequency codons simultaneously, of which GCU encoding Ala, UUA encoding Leu, and AGA encoding Arg were the most preferred codons. Taken together, our study unraveled the synonymous codon usage pattern in the Rutaceae family, providing valuable information for the genetic engineering of Rutaceae plant species in the future.
芸香科植物由于其在香料、食品、油、医药等方面的广泛应用而成为经济上重要的植物。通过生物技术，芸香科植物能够得到更好的利用。现代生物技术方法主要依赖于在不同载体中异源表达功能蛋白。然而，一些蛋白质在其天然环境之外很难表达。通过用功能基因的优选最佳密码子替换载体中的稀有同义密码子，可以最大限度地提高异源系统中功能基因的表达潜力。密码子使用偏性在基于生物发生工程的研究和开发中起着关键作用。在本研究中，分析了来自芸香科植物家族 10 个成员的叶绿体基因组中的 727 个编码序列（CDS），以研究密码子的使用偏性。密码子的核苷酸组成分析表明，这些密码子富含 A/T(U)碱基，并偏好 A/T(U)结尾。进行了中性作图、有效密码子数（ENC）作图和 ENC 与密码子适应指数（CAI）之间相关性的分析，结果表明自然选择是芸香科植物家族密码子使用偏性的主要驱动力，其次是碱基突变。在 ENC 与 CAI 图中，芸香科植物家族的密码子使用偏性与基因表达水平几乎没有关系。对于每个样本，我们同时筛选了 12 个作为优选和高频的密码子，其中编码 Ala 的 GCU、编码 Leu 的 UUA 和编码 Arg 的 AGA 是最优选的密码子。总之，我们的研究揭示了芸香科植物家族中的同义密码子使用模式，为未来芸香科植物物种的遗传工程提供了有价值的信息。
