It is true that cell-free protein synthesis works with genetic materials such as plasmid DNA but also with PCR-amplified linear DNA sequences. However, when cell-free expression assays started with PCR fragments, the expression yields were much lower than from plasmid DNA. This was due to the DNase activity present in the cell extract that decreased the lifetime of linear DNA. However, as protein production from PCR-products was already much faster due to the elimination of cloning, screening and selection steps, several approaches have been investigated to improve productivity by decreasing linear DNA degradation or by stabilizing mRNA (Lee et al., 2018; Schinn et al. 2016).
In cell-free systems, the use of PCR fragments now reaches the equivalent efficacy than working with plasmid DNA.
One such approach is to remove gene encoding endonuclease I and exonuclease V, two major nucleases of double-stranded DNA, from the genome of E. coli strain used for cell extract preparation (Michel-Reydellet et al., 2005). In this approach, endA gene encoding for endonuclease I was suppressed and the recCBD operon, which is part of the E. coli recombination system and encodes for the exonuclease V, was replaced by the lambda phage Red recombination system. Bacterial growth rate was not affected by these mutations and PCR product stability was increased. As a result, CAT (chloramphenicol acetyltransferase) was produced with similar yields (500-600 µg/mL) from PCR products or from plasmids.
Other approaches improved productivity using linear DNA templates: for example the addition of bacteriophage lambda Gam protein, an inhibitor of RecBCD protein (Sitaraman et al., 2004) or the introduction of chi-sites in linear DNA. Since RecBCD stops on DNA chi-sites as part of homologous recombination (Marshall et al., 2017), both strategies increased the stability of the linear DNA in the bacterial cell extract.
Prolonging the lifetime of the mRNA is another approach that aims to improve productivity when using PCR products. By preparing a cell extract lacking RNase E activity and introducing a stem-loop structure at the 3’-end of the mRNA (Ahn et al., 2005), mRNA were protected from endonucleases and exonucleases, mRNA half-lives were significantly prolonged and translation occurred even with the rapid degradation of DNA template. CAT was produced at 685 µg/mL, a yield comparable to that observed when using plasmid DNA.
Thus, the enhanced productivity in cell-free systems, using PCR fragments, enables its use as a high-throughput tool to screen libraries or engineered proteins. Indeed, the proteins can be rapidly produced from a linear PCR product through microscale reactions allowing high throughput screening of a protein library in 384 well-plates format, as well as by using plasmids. These protocols can be automated with the use of a liquid handling robot but can also be performed manually.
Authors & sources :
Ahn J.H., Chu H.S., Kim T.W., Oh I.S., Choi C.Y., Hahn G.H., Park C.G., Kim D.M. 2005. Cell-free synthesis of recombinant proteins from PCR-amplified genes at a comparable productivity to that of plasmid-based reactions. Biochemical and Biophysical Research Communications 338:1346–1352.
Lee K.H., Kim D.M. 2018. Recent advances in development of cell-free protein synthesis systems for fast and efficient production of recombinant proteins. FEMS Microbiology Letters 365(17):1-7.
Marshall R., Maxwell C.S., Collins S.P., Beisel C.L., Noireaux V. 2017. Short DNA containing chi sites enhances DNA stability and gene expression in E. coli cell-free transcription-translation systems. Biotechnology and Bioengineering 114:2137–2141.
Michel-Reydellet N., Woodrow K., Swartz J. 2005. Increasing PCR Fragment Stability and Protein Yields in a Cell-Free System with Genetically Modified Escherichia coli Extracts. Journal of Molecular Microbiology and Biotechnology 9:26–34.
Schinn S.M., Broadbent A., Bradley W.T., Bundy B.C. 2016. Protein Synthesis Directly from PCR: Progress and Applications of Cell-Free Protein Synthesis with Linear DNA. New Biotechnology 33(4):480-7.
Seki E., Matsuda N., Yokoyama S., Kigawa T. 2008. Cell-free protein synthesis system from Escherichia coli cells cultured at decreased temperatures improves productivity by decreasing DNA template degradation. Analytical Biochemistry 377:156–161.