A PCR-directed cell-free approach to optimize protein expression using diverse fusion tags

N-terminal fusion tags that enhance translation initiation or protein solubility are often used to facilitate protein overexpression. As the optimal tag for a given target protein cannot be predicted a priori, valuable time can be lost in cloning and manipulating the corresponding gene to generate different fusion constructs for expression analysis. We have developed a cell-free strategy that consolidates these steps, enabling the utility of a panel of nine fusion-tags to be determined within one to two days. This approach exploits the fact that PCR-amplified DNA can be used as a template for cell-free protein synthesis. Overlap/extension PCR using the TEV protease site as the overlap region allows the fusion of different T7 promoter (T7p)-tag-TEV DNA fragments with a TEV-gene–T7 terminator (T7ter) fragment. For tag sequences where the TEV site is not compatible, a short C3G3 repeat (CGr) sequence can be used as the overlap region. The resulting T7p-tag-TEV-gene–T7ter constructs are then used as templates for PCR-directed cell-free protein synthesis to identify which tag-TEV-gene fusion protein produces the highest amount of soluble protein. We have successfully applied this approach to the overexpression of the Adiponectin hypervariable domain (AHD). Five of the nine N-terminal fusion tags tested enabled the synthesis of soluble recombinant protein. The best of these was the Peptidyl-prolylcis-trans isomerise B (PpiB) fusion tag which produces 1 mg/ml amounts of soluble fusion protein. PpiB is an example of a new class of fusion tag known as the “stress-responsive proteins”. Our results suggest that this cell-free fusion-tag expression screen facilitates the rapid identification of suitable fusion-tags that overcome issues such as poor expression and insolubility, often encountered using conventional approaches.

► A cell-free fusion-tag screen can identify the best tag for protein expression.
► Overlap/extension PCR is used to fuse nine different tags with a target gene.
► PCR templates are prepared in a day and their cell-free expression done overnight.
► Approach is applied to the expression of the Adiponectin hypervariable domain.
► The novel PpiB tag is the best tag yielding mg/ml of soluble fusion protein.