Bargoti Taniya, Nain Divya Pratap, Kumar Rajesh, Awasthi Amit Kumar, Singh Deepali, Nain Vikrant
University School of Biotechnology, Department of Biotechnology, Gautam Buddha University, Greater Noida, Uttar Pradesh (201312), India.
University School of Vocational Studies and Applied Sciences, Department of Mathematical Science, Gautam Buddha University, Greater Noida, Uttar Pradesh (201312), India.
J Genet Eng Biotechnol. 2024 Dec;22(4):100441. doi: 10.1016/j.jgeb.2024.100441. Epub 2024 Nov 13.
Over the past three decades species-specific codon usage bias has been used to optimize heterologous gene expression in the target host. However, synthesizing codon optimized gene for multiple species is not achievable due to the prohibitive expense of DNA synthesis. To address this challenge, grouping species with similar codon usage can reduce the need for species-specific codon optimised gene synthesis. We introduced Scaled Codon Usage Similarity (SCUS) index to standardize species similarity assessments based on codon usage profiles. By analysing the SCUS index of 77 plant nuclear genomes from 13 families, we identified codon usage patterns and similarities. We developed an online SCUS index database and a Consensus Relative Synonymous Codon Usage (CRSCU) calculator, available at https://pcud.plantcodon.info. The CRSCU calculator helps determine the most suitable codon usage pattern among two or more species. The SCUS index and CRSCU calculator will facilitate the development of multi-species expression systems, enabling the efficient expression of a single synthetic gene across various crop species. This innovation paves the way for cost-effective and efficient heterologous gene expression across diverse crop species.
在过去三十年中，物种特异性密码子使用偏好已被用于优化目标宿主中的异源基因表达。然而，由于DNA合成成本过高，为多个物种合成密码子优化基因是无法实现的。为应对这一挑战，将密码子使用相似的物种分组可以减少对物种特异性密码子优化基因合成的需求。我们引入了比例密码子使用相似性（SCUS）指数，以基于密码子使用谱标准化物种相似性评估。通过分析来自13个科的77个植物核基因组的SCUS指数，我们确定了密码子使用模式和相似性。我们开发了一个在线SCUS指数数据库和一个一致相对同义密码子使用（CRSCU）计算器，可在https://pcud.plantcodon.info获取。CRSCU计算器有助于确定两个或多个物种之间最合适的密码子使用模式。SCUS指数和CRSCU计算器将促进多物种表达系统的开发，使单个合成基因能够在各种作物物种中高效表达。这一创新为跨多种作物物种进行经济高效的异源基因表达铺平了道路。
