An optimized yeast cell-free lysate system for in vitro translation of human virus mRNA

Multiple Gene Expression in Cell-Free Protein Synthesis Systems for Reconstructing Bacteriophages and Metabolic Pathways

As a fast and reliable technology with applications in diverse biological studies, cell-free protein synthesis has become popular in recent decades. The cell-free protein synthesis system can be considered a complex chemical reaction system that is also open to exogenous manipulation, including that which could otherwise potentially harm the cell's viability. On the other hand, since the technology depends on the cell lysates by which genetic information is transformed into active proteins, the whole system resembles the cell to some extent. These features make cell-free protein synthesis a valuable addition to synthetic biology technologies, expediting the design-build-test-learn cycle of synthetic biology routines. While the system has traditionally been used to synthesize one protein product from one gene addition, recent studies have employed multiple gene products in order to, for example, develop novel bacteriophages, viral particles, or synthetic metabolisms. Thus, we would like to review recent advancements in applying cell-free protein synthesis technology to synthetic biology, with an emphasis on multiple gene expressions.

Genome-Scale Analysis of Perturbations in Translation Elongation Based on a Computational Model

Perturbations play an important role both in engineered systems and cellular processes. Thus, understanding their effect on protein synthesis should contribute to all biomedical disciplines. Here we describe the first genome-scale analysis of perturbations in translation-related factors in S. cerevisiae. To this end, we used simulations based on a computational model that takes into consideration the fundamental stochastic and bio-physical nature of translation. We found that the initiation rate has a key role in determining the sensitivity to perturbations. For low initiation rates, the first codons of the coding region dominate the sensitivity, which is highly correlated with the ratio between initiation rate and mean elongation rate (r = −0.95), with the open reading frame (ORF) length (r = 0.6) and with protein abundance (r = 0.45). For high initiation rates (that may rise, for example, due to cellular growth), the sensitivity of a gene is dominated by all internal codons and is correlated with the decoding rate. We found that various central intracellular functions are associated with the sensitivity: for example, both genes that are sensitive and genes that are robust to perturbations are over-represented in the group of genes related to translation regulation; this may suggest that robustness to perturbations is a trait that undergoes evolutionary selection in relation to the function of the encoded protein. We believe that the reported results, due to their quantitative value and genome-wide perspective, should contribute to disciplines such as synthetic biology, functional genomics, comparative genomics and molecular evolution.

Performance benchmarking of four cell-free protein expression systems

Over the last half century, a range of cell-free protein expression systems based on pro- and eukaryotic organisms have 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 characterize 87 N-terminally GFP-tagged human cytosolic proteins of different sizes in E. coli, wheat 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 assessed the expression yields, the fraction of full-length translation product, and 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 systems 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, whereas the LTE-produced proteins have the lowest aggregation propensity among the systems analyzed. 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.