Performance benchmarking of four cell‐free protein expression systems

Dejan Gagoski, Mark E. Polinkovsky, Sergey Mureev, Anne Kunert, Wayne Johnston, Yann Gambin, Kirill Alexandrov

Over the last half a century, a range of cell-free protein expression systems based on pro- and eukaryotic organisms havehas been developed and have found a range of applications, from structural biology to directed protein evolution. While it is generally accepted that significant differences in performance among systems exist, there is a paucity of systematic experimental studies supporting this notion. Here, we took advantage of the Species- Independent Translation Initiation sequence to express and characterise 88 N-terminallyterminaly GFP- tagged human cytosolic proteins of different sizes in E. coli, wheat germWheat Germ (WGE),), HeLa and Leishmania-based (LTE) cell-free systems. Using a combination of single- molecule fluorescence spectroscopy, SDS-PAGE and Western blot analysis we assessedas assess the expression yields, the fraction of full- length translation product and its aggregation propensity for each of these systems. Our results demonstrate that the E. coli system has the highest expression yields. However, we observe that high expression levels are accompanied by production of truncated species- particularly pronounced in the case of proteins larger than 70 kDa. Furthermore, proteins produced in the E. coli system display high aggregation propensity, with only 10% of tested proteins being produced in predominantly monodispersed form. The WGE system was the most productive among eukaryotic systemssystem tested. Finally, HeLa and LTE show comparable protein yields that are considerably lower than the ones achieved in the E. coli and WGE systems. The protein products produced in the HeLa system display slightly higher integrity, while the LTE- produced proteins have the lowest aggregation propensity among the systems analysed. The high quality of HeLa- and LTE-produced proteins enable their analysis without purification and make them suitable for analysis of multi-domain eukaryotic proteins. This article is protected by copyright. All rights reserved.