In vitro construction and screening of a Burkholderia cepacia lipase library using single-molecule PCR and cell-free protein synthesis

Expanding biological applications using cell-free metabolic engineering: An overview

Expanding the concept of cell-free biology, implemented both with purified components and crude extracts, is continuing to deepen our appreciation of biological fundamentals while enlarging the range of applications. We are no longer intimidated by the complexity of crude extracts and complicated reaction systems with hundreds of active components, and, instead, coordinately activate and inactivate metabolic processes to focus and expand the capabilities of natural biological processes. This, in turn, dramatically increases the range of benefits offered by new products, both natural and supernatural, that were previously infeasible and/or unimaginable. This overview of cell-free metabolic engineering provides a broad range of examples and insights to guide and motivate continued research that will further expand fundamental understanding and beneficial applications. However, this survey also reveals how far we are from fully unlocking the potential offered by natural and engineered biological components and systems. This is an exciting conclusion, but metabolic engineering by itself is not sufficient. Going forward, innovative metabolic engineering must be intimately combined with creative process engineering to fully realize potential contributions toward a sustainable global civilization.

Microcompartmentalized cell-free protein synthesis in semipermeable microcapsules composed of polyethylenimine-coated alginate

We describe microcompartmentalized cell-free protein synthesis in semipermeable microcapsules prepared from water-in-oil-in-water droplets by a rupture-induced encapsulation method. An aqueous solution of template DNA coding for green fluorescent protein and enzymes for the cell-free protein synthesis was aliquoted into water-in-oil droplets using a microfluidic device, and the droplets were transformed into semipermeable microcapsules. Substrates for protein synthesis diffused into the microcapsules through their semipermeable polyion complex membranes composed of polyethylenimine-coated alginate. Cell-free protein synthesis was confirmed by detection of the fluorescence of the synthesized green fluorescence protein in the microcapsules. We also used this microcompartmentalized system to synthesize protein from a single molecule of template DNA encapsulated by limiting dilution.

Cell-free synthesis and multifold screening of Candida antarctica lipase B (CalB) variants after combinatorial mutagenesis of hot spots

We have developed a strategy for rapid and combinatorial optimization of the hot spot residues of enzymes. After combinatorial randomization of target locations in the Candida antarctica lipase B (CalB) gene, the individual variant genes isolated in the E.coli cells were expressed in the cell-free protein synthesis system to analyze different parameters of the resulting CalB variants. The enzymatic assays for the hydrolysis of para-nitrophenyl-ester (pNP-ester) and triglyceride, synthesis of wax ester, and thermal stability of the variant enzymes were carried out simultaneously in 96-well microtiter plates. From the 1,000 variant genes tested in each assay, we were able to identify a series of the variant enzymes having markedly improved hydrolytic, synthetic activity, or thermal stability. The improved traits of the cell-free selected CalB variants were well reproduced when the corresponding genes were expressed in Pichia pastoris. Therefore, we expect that the proposed strategy of cell-free expression screening can serve as a viable option for rapid and precise tuning of enzyme molecules, not only for analytical purposes but also for industrial applications through large scale production using microbial cells transformed with variant genes selected from the cell-free expression screening.

A completely in vitro system for obtaining scFv using mRNA display, PCR, direct sequencing, and wheat embryo cell-free translation

Using mRNA display followed by in vitro sequencing and translation, a complete in vitro system for obtaining scFv has been developed. An mRNA display library for synthetic scFv was panned against human TNF receptor (TNFR). The nucleotide portion of the enriched molecules was subjected to limiting dilution, and PCR-amplified. Three of the proteins encoded by the amplified fragments were synthesized in a wheat embryo (WE) cell-free system using a batch method. They were shown to bind TNFR by ELISA. One of their sequences was identified in vitro. The identified clone was further synthesized at approx. 0.5 mg/ml reaction mixture in a WE system with dialysis as a totally soluble protein.

SIMPLEX: single-molecule PCR-linked in vitro expression: a novel method for high-throughput construction and screening of protein libraries

A novel strategy for construction of protein libraries called "SIMPLEX: single-molecule PCR-linked in vitro expression" is described. A pool of genes is prepared and thereafter extensively diluted to give one molecule of DNA per well. Each individual molecule is separately amplified by PCR (single-molecule PCR) yielding a one-well-one-gene PCR library. Subsequently, the PCR library is directly transformed into a protein library by means of in vitro-coupled transcription/translation in an array format. Individual proteins in the library can be screened for target functions directly without further purification. The generated protein library is compatible with various selection methods. The strategy provides high-throughput construction and screening of protein libraries, and suits automation.

Inverting enantioselectivity of Burkholderia cepacia KWI-56 lipase by combinatorial mutation and high-throughput screening using single-molecule PCR and in vitro expression

The enantioselectivity of lipase from Burkhorderia cepacia KWI-56 has been inverted using a novel in vitro technique for construction and screening of a protein library by single-molecule DNA amplification by PCR followed by in vitro coupled transcription/translation system termed single-molecule-PCR-linked in vitro expression (SIMPLEX). Four amino acid residues (L17, F119, L167, and L266) in the hydrophobic substrate-binding pocket of the lipase were selected for mutation based on a structural model of a substrate-enzyme complex, and a combinatorial mutation library was constructed by SIMPLEX and screened for (R) and (S)-configurations of p-nitrophenyl 3-phenylbutyrate. Some combinations of amino acid substitutions in the four positions of the lipase were found as effective for changing the enantiopreference from the (S)-form substrate to the (R)-form. Two variants were expressed in the original host cells and purified to homogeneity, showing completely reversed enantioselectivity for the (R)-form of ethyl 3-phenylbutyrate (selectivity factor E(R)=38 or 33), whereas the wild-type lipase was (S)-selective (selectivity factor E(S)=33). Thus the semi-rational and semi-random combinatorial design of a mutant library followed by a high-throughput screening based on their enzymatic activity should be a powerful tool to engineer the enantioselectivity of enzymes.

PCR-linked in vitro expression: a novel system for high-throughput construction and screening of protein libraries

A novel entirely in vitro strategy for generation and screening of a combinatorial protein library in an array format has been developed and is experimentally demonstrated. The strategy exploits virtues of PCR and in vitro coupled transcription/translation. Our new approach provides high-throughput construction and screening of the in vitro protein library, and compatibility with various selection methods.