Semi-Automated Sample Preparation for Plasma Proteomics

Development of a Liquid Handler Component for a Plasmid-Based Functional Proteomic Robotic Workcell

A Hudson Control Group, Inc. ProLink Express™ robotic workcell to conduct plasmid-based functional proteomics is being developed for optimization of protein open reading frames (ORF). The initial phase of this project is to design and assemble a Xantus liquid handler from Sias, Inc. modified by Hudson so that a workcell track component can be placed within the Xantus® gripper tool work area. The liquid handler is designed to produce plasmids using the Qiagen Turbo® plasmid preparation kit. This design allows processing of up to four 96-well plates in one run. The procedure eliminates disposable tips and provides an advanced wash system to prevent cross contamination. To evaluate liquid handler operation, a mutagenized cellulase F ORF plasmid library was prepared from wild-type cellulase F (Chen, H.; Li, X.-L.; Blum, D. L.; Ximenes, E. A.; Ljungdahl, L. G. CelF of Orpinomyces PC-2 has an intron and encodes a cellulase (CelF) containing a carbohydrate-binding module. Applied Biochemistry and Biotechnology 2003, 105–108, 775–785; Li, X.-L.; Chen, H.; Ljungdahl, L. G. Two cellulases, CelA and CelC, from the polycentric anaerobic fungus Orpinomyces strain PC-2 contain N-terminal docking domains for a cellulase-hemicellulase complex. Applied and Environmental Microbiology 1997, 63(12), 4721–4728) using a novel Invitrogen Gateway® cloning strategy. For the automated reproducibility run, the average yield of plasmid was 5.35 μg per well from 1.347 mL of starting culture. Four plates were processed automatically on the liquid handler in 374 min compared to at least 441 min for the same plate operations performed manually. The quality and quantity of plasmids prepared on the liquid handler made the implementation of the following workcell protocols possible: DNA sequencing, in vitro transcription/translation, and transformation of bacterial and yeast strains for protein expression.

Strategies for discovery and improvement of enzyme function: state of the art and opportunities

Developments in biocatalysis have been largely fuelled by consumer demands for new products, industrial attempts to improving existing process and minimizing waste, coupled with governmental measures to regulate consumer safety along with scientific advancements. One of the major hurdles to application of biocatalysis to chemical synthesis is unavailability of the desired enzyme to catalyse the reaction to allow for a viable process development. Even when the desired enzyme is available it often forces the process engineers to alter process parameters due to inadequacies of the enzyme, such as instability, inhibition, low yield or selectivity, etc. Developments in the field of enzyme or reaction engineering have allowed access to means to achieve the ends, such as directed evolution, de novo protein design, use of non‐conventional media, using new substrates for old enzymes, active‐site imprinting, altering temperature, etc. Utilization of enzyme discovery and improvement tools therefore provides a feasible means to overcome this problem. Judicious employment of these tools has resulted in significant advancements that have leveraged the research from laboratory to market thus impacting economic growth; however, there are further opportunities that have not yet been explored. The present review attempts to highlight some of these achievements and potential opportunities.

Design and Construction of a First-Generation High-Throughput Integrated Robotic Molecular Biology Platform for Bioenergy Applications

The molecular biological techniques for plasmid-based assembly and cloning of gene open reading frames are essential for elucidating the function of the proteins encoded by the genes. High-throughput integrated robotic molecular biology platforms that have the capacity to rapidly clone and express heterologous gene open reading frames in bacteria and yeast and to screen large numbers of expressed proteins for optimized function are an important technology for improving microbial strains Published by Elsevier Inc. on behalf of the Society for Laboratory Automation and Screening for biofuel production. The process involves the production of full-length complementary DNA libraries as a source of plasmid-based clones to express the desired proteins in active form for determination of their functions. Proteins that were identified by high-throughput screening as having desired characteristics are overexpressed in microbes to enable them to perform functions that will allow more cost-effective and sustainable production of biofuels. Because the plasmid libraries are composed of several thousand unique genes, automation of the process is essential. This review describes the design and implementation of an automated integrated programmable robotic workcell capable of producing complementary DNA libraries, colony picking, isolating plasmid DNA, transforming yeast and bacteria, expressing protein, and performing appropriate functional assays. These operations will allow tailoring microbial strains to use renewable feedstocks for production of biofuels, bioderived chemicals, fertilizers, and other coproducts for profitable and sustainable biorefineries.

High-throughput screening of cellulase F mutants from multiplexed plasmid sets using an automated plate assay on a functional proteomic robotic workcell

Background

The field of plasmid-based functional proteomics requires the rapid assay of proteins expressed from plasmid libraries. Automation is essential since large sets of mutant open reading frames are being cloned for evaluation. To date no integrated automated platform is available to carry out the entire process including production of plasmid libraries, expression of cloned genes, and functional testing of expressed proteins.

Results

We used a functional proteomic assay in a multiplexed setting on an integrated plasmid-based robotic workcell for high-throughput screening of mutants of cellulase F, an endoglucanase from the anaerobic fungus Orpinomyces PC-2. This allowed us to identify plasmids containing optimized clones expressing mutants with improved activity at lower pH. A plasmid library of mutagenized clones of the celF gene with targeted variations in the last four codons was constructed by site-directed PCR mutagenesis and transformed into Escherichia coli. A robotic picker integrated into the workcell was used to inoculate medium in a 96-well deep well plate, combining the transformants into a multiplexed set in each well, and the plate was incubated on the workcell. Plasmids were prepared from the multiplexed culture on the liquid handler component of the workcell and used for in vitro transcription/translation. The multiplexed expressed recombinant proteins were screened for improved activity and stability in an azo-carboxymethylcellulose plate assay. The multiplexed wells containing mutants with improved activity were identified and linked back to the corresponding multiplexed cultures stored in glycerol. Spread plates were prepared from the glycerol stocks and the workcell was used to pick single colonies from the spread plates, prepare plasmid, produce recombinant protein, and assay for activity. The screening assay and subsequent deconvolution of the multiplexed wells resulted in identification of improved CelF mutants and corresponding optimized clones in expression-ready plasmids.

Conclusion

The multiplex method using an integrated automated platform for high-throughput screening in a functional proteomic assay allows rapid identification of plasmids containing optimized clones ready for use in subsequent applications including transformations to produce improved strains or cell lines.