IRES-mediated Pichia pastoris cell-free protein synthesis

Efficient Incorporation of DOPA into Proteins Free from Competition with Endogenous Translation Termination Machinery

3,4-Dihydroxy-L-phenylalanine (DOPA) is a promising noncanonical amino acid (ncAA) that introduces novel catechol chemical features into proteins, expanding their functional potential. However, the most common approach to incorporating ncAAs into proteins relies on stop codon suppression, which is often limited by the competition of endogenous translational termination machinery. Here, we employed a special in vitro protein expression system that facilitates the efficiency of DOPA incorporation into proteins by removing essential Class I peptide release factors through targeted degradation. In the absence of both RF1 and RF2, we successfully demonstrated DOPA incorporation at all three stop codons (TAG, TAA, and TGA). By optimizing the concentration of engineered DOPA-specific aminoacyl-tRNA synthetase (DOPARS), DOPA, and DNA template, we achieved a synthesis yield of 2.24 µg of sfGFP with 100% DOPA incorporation in a 20 μL reaction system. DOPARS exhibited a dissociation constant (Kd) of 11.7 μM for DOPA but showed no detectable binding to its native counterpart, tyrosine. Additionally, DOPA was successfully incorporated into a reverse transcriptase, which interfered with its activity. This system demonstrates a fast and efficient approach for precise DOPA incorporation into proteins, paving the way for advanced protein engineering applications.

Cell-Free Gene Expression: Methods and Applications

Cell-free gene expression (CFE) systems empower synthetic biologists to build biological molecules and processes outside of living intact cells. The foundational principle is that precise, complex biomolecular transformations can be conducted in purified enzyme or crude cell lysate systems. This concept circumvents mechanisms that have evolved to facilitate species survival, bypasses limitations on molecular transport across the cell wall, and provides a significant departure from traditional, cell-based processes that rely on microscopic cellular "reactors." In addition, cell-free systems are inherently distributable through freeze-drying, which allows simple distribution before rehydration at the point-of-use. Furthermore, as cell-free systems are nonliving, they provide built-in safeguards for biocontainment without the constraints attendant on genetically modified organisms. These features have led to a significant increase in the development and use of CFE systems over the past two decades. Here, we discuss recent advances in CFE systems and highlight how they are transforming efforts to build cells, control genetic networks, and manufacture biobased products.

In silico characterization of Rhodotorula toruloides ELO-like elongases and production of very-long-chain fatty acids by expressing Rtelo2, RtKCR, RtHCD, and RtECR through IRES-mediated bicistrons

Rhodotorula toruloides, an oleaginous yeast known for its high lipid productivity, produces lipids with low very-long-chain fatty acid (VLCFA) content. Meanwhile, the roles of enzymes, particularly the condensing enzymes, involved in VLCFA biosynthesis in R. toruloides remained unclear. In this study, two elongases, RtELO1 and RtELO2, were identified from R. toruloides U13N3 and their tertiary structure and catalytic mechanism were investigated using molecular dynamic methods. Both enzymes exhibited typical ELO-like characteristics, with active sites located within cavities formed by seven transmembrane helixes. RtELO2 displayed higher binding affinity to acyl-CoAs compared to RtELO1, and at least seven amino acid residues, including two crucial histidines in the "HXXHH" box, were identified as important for the condensation reaction. To enhance VLCFA production, an internal ribosome entry site (IRES)-mediated bicistronic strategy was developed to integrate multiple genes into the R. toruloides genome. The efficiency of IRES-mediated translation initiation reached 85.4% of cap-dependent upstream translation, based on EGFP fluorescent intensity. Using this strategy, four genes encoding enzymes involved in the VLCFA biosynthesis cycle (Rtelo2, RtKCR, RtHCD, and RtECR) were introduced into the U13N3 genome in various combinations. The results indicated that the expression of a single elongase had a modest effect on VLCFA production, but the simultaneous expression of multiple genes resulted in cumulative effects. Notably, the transformant harboring four genes exhibited a remarkable 436.8% increase in C22 and C24 VLCFA yield compared to the original strain.

Promoting the production of challenging proteins via induced expression in CHO cells and modified cell-free lysates harboring T7 RNA polymerase and mutant eIF2α

Chinese hamster ovary (CHO) cells are crucial in biopharmaceutical production due to their scalability and capacity for human-like post-translational modifications. However, toxic proteins and membrane proteins are often difficult-to-express in living cells. Alternatively, cell-free protein synthesis can be employed. This study explores innovative strategies for enhancing the production of challenging proteins through the modification of CHO cells by investigating both, cell-based and cell-free approaches. A major result in our study involves the integration of a mutant eIF2 translation initiation factor and T7 RNA polymerase into CHO cell lysates for cell-free protein synthesis. This resulted in elevated yields, while eliminating the necessity for exogenous additions during cell-free production, thereby substantially enhancing efficiency. Additionally, we explore the potential of the Rosa26 genomic site for the integration of T7 RNA polymerase and cell-based tetracycline-controlled protein expression. These findings provide promising advancements in bioproduction technologies, offering flexibility to switch between cell-free and cell-based protein production as needed.

Engineering cell-free systems by chemoproteomic-assisted phenotypic screening

Phenotypic screening is a valuable tool to both understand and engineer complex biological systems. We demonstrate the functionality of this approach in the development of cell-free protein synthesis (CFPS) technology. Phenotypic screening identified numerous compounds that enhanced protein production in yeast lysate CFPS reactions. Notably, many of these were competitive ATP kinase inhibitors, with the exploitation of their inherent substrate promiscuity redirecting ATP flux towards heterologous protein expression. Chemoproteomic-guided strain engineering partially phenocopied drug effects, with a 30% increase in protein yield observed upon deletion of the ATP-consuming SSA1 component of the HSP70 chaperone. Moreover, drug-mediated metabolic rewiring coupled with template optimization generated the highest protein yields in yeast CFPS to date using a hitherto less efficient, but more cost-effective glucose energy regeneration system. Our approach highlights the utility of target-agnostic phenotypic screening and target identification to deconvolute cell-lysate complexity, adding to the expanding repertoire of strategies for improving CFPS.

A Cost-Effective Pichia pastoris Cell-Free System Driven by Glycolytic Intermediates Enables the Production of Complex Eukaryotic Proteins

Cell-free systems are particularly attractive for screening applications and the production of difficult-to-express proteins. However, the production of cell lysates is difficult to implement on a larger scale due to large time requirements, cultivation costs, and the supplementation of cell-free reactions with energy regeneration systems. Consequently, the methylotrophic yeast Pichia pastoris, which is widely used in recombinant protein production, was utilized in the present study to realize cell-free synthesis in a cost-effective manner. Sensitive disruption conditions were evaluated, and appropriate signal sequences for translocation into ER vesicles were identified. An alternative energy regeneration system based on fructose-1,6-bisphosphate was developed and a ~2-fold increase in protein production was observed. Using a statistical experiment design, the optimal composition of the cell-free reaction milieu was determined. Moreover, functional ion channels could be produced, and a G-protein-coupled receptor was site-specifically modified using the novel cell-free system. Finally, the established P. pastoris cell-free protein production system can economically produce complex proteins for biotechnological applications in a short time.

Toward Minimal Transcription-Translation Machinery

With the advantages of simple genetic composition, low metabolic background, low energy waste, and high genetic stability, genome-reduced strains, as promising functional chassis, have become an intensive direction for constructing potent biosynthesis factories. Herein, an innovative Genome-Reduced strain-based Active Cell-free Easy-to-make-protein (GRACE) system is built as minimal transcription-translation machinery. In this study, two Escherichia coli genome-reduced strains, ΔW3110 and ΔMG1655, with genome reduction of 11.53% and 37.85%, are fused with the cell-free transcription-translation (CFTT) system. The GRACE systems perform better than the corresponding CFTT systems derived from their parental strains in representative valuable applications, such as the expression and solubilization of membrane proteins or protein polymers, biosensing of inorganic or organic molecules based on different principles, and unnatural amino acid embedding. Obviously, the GRACE system has provided a brand-new enabling platform for cell-free transcription-translation basic and applied studies and also would inspire the potential of genome-reduced strains for versatile applications.