Strategies for Tag Design and Removal in the Expression and Purification of Recombinant Proteins

Review Strategies for Tag Design and Removal in the Expression and Purification of Recombinant Proteins Jiayi Xie 1,2, Hongyi Fan 3, and Qingshan Bill Fu 1,2,* 1 School of Pharmaceutical Sciences, Southern Medical University, Guangzhou 510515, China 2 Shanghai Institute of Materia Medica, Zhongshan Institute for Drug Discovery, Chinese Academy of Sciences, Zhongshan 528400, China 3 School of Pharmacy, Guangdong Pharmaceutical University, Guangzhou 511400, China * Correspondence: fuqingshan@simm.ac.cn Received: 19 December 2024; Revised: 10 January 2025; Accepted: 14 February 2025; Published: 8 April 2025 Abstract: Recombinant proteins find extensive applications in the biomedical and industrial fields, and efficient protein purification is often critical for achieving their functional value. Adding specific tags to the target proteins significantly enhances expression and purification efficiency and reduces time and costs. Tags can be classified into interfering and non-interfering tags, based on their effect on protein function during purification. However, interfering tags may need to be removed after purification to prevent interference with the protein’s function in downstream applications, presenting challenges for the design and utilization of tagged fusion proteins. In this article, we discuss the recent advancements in solubility tags and controllable aggregation tags, which have emerged as powerful tools to improve purification efficiency and address these challenges. We further outline strategies for optimal tag design and on-demand cleavage, and emphasize emerging trends, technical features, and forthcoming challenges that are shaping the future of tagged fusion protein production.