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Hughes SR, Dowd PF, Hector RE, Riedmuller SB, Bartolett S, Mertens JA, Qureshi N, Liu S, Bischoff KM, Li XL, Jackson JS, Sterner D, Panavas T, Rich JO, Farrelly PJ, Butt T, Cotta MA. Cost-Effective High-Throughput Fully Automated Construction of a Multiplex Library of Mutagenized Open Reading Frames for an Insecticidal Peptide Using a Plasmid-Based Functional Proteomic Robotic Workcell with Improved Vacuum System. ACTA ACUST UNITED AC 2016. [DOI: 10.1016/j.jala.2007.04.007] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
Robotic platforms are essential for production of large numbers of expression-ready plasmid sets to develop optimized clones and improved microbial strains for crucial bioenergy applications and simultaneous high-value peptide expression. Here we demonstrate a plasmid-based integrated robotic workcell, modified with a motorized vacuum filtration system, for performing fully automated molecular biology protocols, including assembly of mutagenized gene sequences, purification of PCR amplicons, ligation of PCR products into vectors, transformation of competent Escherichia coli, plating of recovered transformants, plasmid preparation, cloning, and expression of optimized genes. A library of genes encoding variants of wolf spider lycotoxin-1, a candidate bioinsecticide, was produced using PCR mutagenesis in an amino acid scanning strategy to generate a complete set of mutations across the lycotoxin-1 gene. The improved vacuum filtration system permits automated purification of PCR products. Methods for recovery and growth of bacteria containing plasmids with PCR inserts allow individual colony formation on a novel solid medium in a deepwell plate. Inserts are cloned into a bacterial vector to verify expression. These protocols form the core of a fully automated molecular biology platform that reduces the cost and time required to perform all operations. (JALA 2007;12:202–12)
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Affiliation(s)
- Stephen R. Hughes
- United States Department of Agriculture (USDA), Agricultural Research Service (ARS), National Center for Agricultural Utilization Research (NCAUR), Peoria, IL
| | - Patrick F. Dowd
- United States Department of Agriculture (USDA), Agricultural Research Service (ARS), National Center for Agricultural Utilization Research (NCAUR), Peoria, IL
| | - Ronald E. Hector
- United States Department of Agriculture (USDA), Agricultural Research Service (ARS), National Center for Agricultural Utilization Research (NCAUR), Peoria, IL
| | | | | | - Jeffrey A. Mertens
- United States Department of Agriculture (USDA), Agricultural Research Service (ARS), National Center for Agricultural Utilization Research (NCAUR), Peoria, IL
| | - Nasib Qureshi
- United States Department of Agriculture (USDA), Agricultural Research Service (ARS), National Center for Agricultural Utilization Research (NCAUR), Peoria, IL
| | - Siqing Liu
- United States Department of Agriculture (USDA), Agricultural Research Service (ARS), National Center for Agricultural Utilization Research (NCAUR), Peoria, IL
| | - Kenneth M. Bischoff
- United States Department of Agriculture (USDA), Agricultural Research Service (ARS), National Center for Agricultural Utilization Research (NCAUR), Peoria, IL
| | - Xin-Liang Li
- United States Department of Agriculture (USDA), Agricultural Research Service (ARS), National Center for Agricultural Utilization Research (NCAUR), Peoria, IL
| | - John S. Jackson
- United States Department of Agriculture (USDA), Agricultural Research Service (ARS), National Center for Agricultural Utilization Research (NCAUR), Peoria, IL
| | | | | | - Joseph O. Rich
- United States Department of Agriculture (USDA), Agricultural Research Service (ARS), National Center for Agricultural Utilization Research (NCAUR), Peoria, IL
| | | | | | - Michael A. Cotta
- United States Department of Agriculture (USDA), Agricultural Research Service (ARS), National Center for Agricultural Utilization Research (NCAUR), Peoria, IL
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Hughes SR, Riedmuller SB, Mertens JA, Li XL, Bischoff KM, Cotta MA, Farrelly PJ. Development of a Liquid Handler Component for a Plasmid-Based Functional Proteomic Robotic Workcell. ACTA ACUST UNITED AC 2016. [DOI: 10.1016/j.jala.2005.06.009] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
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.
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Affiliation(s)
- Stephen R. Hughes
- BBC Research Unit, USDA, ARS, NCAUR, 1815 North University Street, Peoria, IL 61604
| | | | - Jeffrey A. Mertens
- FBT Research Unit, USDA, ARS, NCAUR, 1815 North University Street, Peoria, IL 61604
| | - Xin-Liang Li
- FBT Research Unit, USDA, ARS, NCAUR, 1815 North University Street, Peoria, IL 61604
| | - Kenneth M. Bischoff
- BBC Research Unit, USDA, ARS, NCAUR, 1815 North University Street, Peoria, IL 61604
| | - Michael A. Cotta
- FBT Research Unit, USDA, ARS, NCAUR, 1815 North University Street, Peoria, IL 61604
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Hughes SR, Cox EJ, Bang SS, Pinkelman RJ, López-Núñez JC, Saha BC, Qureshi N, Gibbons WR, Fry MR, Moser BR, Bischoff KM, Liu S, Sterner DE, Butt TR, Riedmuller SB, Jones MA, Riaño-Herrera NM. Process for Assembly and Transformation into Saccharomyces cerevisiae of a Synthetic Yeast Artificial Chromosome Containing a Multigene Cassette to Express Enzymes That Enhance Xylose Utilization Designed for an Automated Platform. ACTA ACUST UNITED AC 2015; 20:621-35. [PMID: 25720598 DOI: 10.1177/2211068215573188] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2014] [Indexed: 01/26/2023]
Abstract
A yeast artificial chromosome (YAC) containing a multigene cassette for expression of enzymes that enhance xylose utilization (xylose isomerase [XI] and xylulokinase [XKS]) was constructed and transformed into Saccharomyces cerevisiae to demonstrate feasibility as a stable protein expression system in yeast and to design an assembly process suitable for an automated platform. Expression of XI and XKS from the YAC was confirmed by Western blot and PCR analyses. The recombinant and wild-type strains showed similar growth on plates containing hexose sugars, but only recombinant grew on D-xylose and L-arabinose plates. In glucose fermentation, doubling time (4.6 h) and ethanol yield (0.44 g ethanol/g glucose) of recombinant were comparable to wild type (4.9 h and 0.44 g/g). In whole-corn hydrolysate, ethanol yield (0.55 g ethanol/g [glucose + xylose]) and xylose utilization (38%) for recombinant were higher than for wild type (0.47 g/g and 12%). In hydrolysate from spent coffee grounds, yield was 0.46 g ethanol/g (glucose + xylose), and xylose utilization was 93% for recombinant. These results indicate introducing a YAC expressing XI and XKS enhanced xylose utilization without affecting integrity of the host strain, and the process provides a potential platform for automated synthesis of a YAC for expression of multiple optimized genes to improve yeast strains.
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Affiliation(s)
- Stephen R Hughes
- United States Department of Agriculture (USDA), Agricultural Research Service (ARS), National Center for Agricultural Utilization Research (NCAUR), Renewable Product Technology Research Unit, Peoria, IL, USA
| | - Elby J Cox
- United States Department of Agriculture (USDA), Agricultural Research Service (ARS), National Center for Agricultural Utilization Research (NCAUR), Renewable Product Technology Research Unit, Peoria, IL, USA Department of Chemistry and Biochemistry, Bradley University, Peoria, IL, USA
| | - Sookie S Bang
- South Dakota School of Mines & Technology, Chemical and Biological Engineering, Rapid City, SD, USA
| | - Rebecca J Pinkelman
- South Dakota School of Mines & Technology, Chemical and Biological Engineering, Rapid City, SD, USA
| | - Juan Carlos López-Núñez
- National Coffee Research Centre (Cenicafe), National Federation of Coffee Growers of Colombia (FNC), Manizales, Caldas, Colombia
| | - Badal C Saha
- USDA, ARS, NCAUR, Bioenergy Research Unit, Peoria, IL, USA
| | - Nasib Qureshi
- USDA, ARS, NCAUR, Bioenergy Research Unit, Peoria, IL, USA
| | - William R Gibbons
- Department of Biology and Microbiology, South Dakota State University, Brookings, SD, USA
| | - Michelle R Fry
- Department of Chemistry and Biochemistry, Bradley University, Peoria, IL, USA
| | - Bryan R Moser
- USDA, ARS, NCAUR, Bio-Oils Research Unit, Peoria, IL, USA
| | - Kenneth M Bischoff
- United States Department of Agriculture (USDA), Agricultural Research Service (ARS), National Center for Agricultural Utilization Research (NCAUR), Renewable Product Technology Research Unit, Peoria, IL, USA
| | - Siqing Liu
- United States Department of Agriculture (USDA), Agricultural Research Service (ARS), National Center for Agricultural Utilization Research (NCAUR), Renewable Product Technology Research Unit, Peoria, IL, USA
| | | | | | | | - Marjorie A Jones
- Department of Chemistry, Illinois State University, Normal, IL, USA
| | - Néstor M Riaño-Herrera
- National Coffee Research Centre (Cenicafe), National Federation of Coffee Growers of Colombia (FNC), Manizales, Caldas, Colombia
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Hughes SR, Dowd PF, Hector RE, Panavas T, Sterner DE, Qureshi N, Bischoff KM, Bang SS, Mertens JA, Johnson ET, Li XL, Jackson JS, Caughey RJ, Riedmuller SB, Bartolett S, Liu S, Rich JO, Farrelly PJ, Butt TR, Labaer J, Cotta MA. Lycotoxin-1 insecticidal peptide optimized by amino acid scanning mutagenesis and expressed as a coproduct in an ethanologenic Saccharomyces cerevisiae strain. J Pept Sci 2008; 14:1039-50. [PMID: 18465835 DOI: 10.1002/psc.1040] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
New methods of safe biological pest control are required as a result of evolution of insect resistance to current biopesticides. Yeast strains being developed for conversion of cellulosic biomass to ethanol are potential host systems for expression of commercially valuable peptides, such as bioinsecticides, to increase the cost-effectiveness of the process. Spider venom is one of many potential sources of novel insect-specific peptide toxins. Libraries of mutants of the small amphipathic peptide lycotoxin-1 from the wolf spider were produced in high throughput using an automated integrated plasmid-based functional proteomic platform and screened for ability to kill fall armyworms, a significant cause of damage to corn (maize) and other crops in the United States. Using amino acid scanning mutagenesis (AASM) we generated a library of mutagenized lycotoxin-1 open reading frames (ORF) in a novel small ubiquitin-like modifier (SUMO) yeast expression system. The SUMO technology enhanced expression and improved generation of active lycotoxins. The mutants were engineered to be expressed at high level inside the yeast and ingested by the insect before being cleaved to the active form (so-called Trojan horse strategy). These yeast strains expressing mutant toxin ORFs were also carrying the xylose isomerase (XI) gene and were capable of aerobic growth on xylose. Yeast cultures expressing the peptide toxins were prepared and fed to armyworm larvae to identify the mutant toxins with greatest lethality. The most lethal mutations appeared to increase the ability of the toxin alpha-helix to interact with insect cell membranes or to increase its pore-forming ability, leading to cell lysis. The toxin peptides have potential as value-added coproducts to increase the cost-effectiveness of fuel ethanol bioproduction.
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Affiliation(s)
- Stephen R Hughes
- United States Department of Agriculture, Agricultural Research Service, National Center for Agricultural Utilization Research, Bioproducts and Biocatalysis Research Unit, Peoria, IL 61604, USA.
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Hughes SR, Riedmuller SB, Mertens JA, Li XL, Bischoff KM, Qureshi N, Cotta MA, Farrelly PJ. High-throughput screening of cellulase F mutants from multiplexed plasmid sets using an automated plate assay on a functional proteomic robotic workcell. Proteome Sci 2006; 4:10. [PMID: 16670026 PMCID: PMC1479318 DOI: 10.1186/1477-5956-4-10] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2005] [Accepted: 05/02/2006] [Indexed: 11/23/2022] Open
Abstract
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.
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Affiliation(s)
- Stephen R Hughes
- United States Department of Agriculture (USDA), Agricultural Research Service (ARS), National Center for Agricultural Utilization Research (NCAUR), Bioproducts and Biocatalysis (BBC) Research Unit, 1815 North University Street, Peoria, IL 61604, USA
| | | | - Jeffrey A Mertens
- USDA, ARS, NCAUR, Fermentation Biotechnology (FBT) Research Unit, 1815 North University Street, Peoria, IL 61604, USA
| | - Xin-Liang Li
- USDA, ARS, NCAUR, Fermentation Biotechnology (FBT) Research Unit, 1815 North University Street, Peoria, IL 61604, USA
| | - Kenneth M Bischoff
- United States Department of Agriculture (USDA), Agricultural Research Service (ARS), National Center for Agricultural Utilization Research (NCAUR), Bioproducts and Biocatalysis (BBC) Research Unit, 1815 North University Street, Peoria, IL 61604, USA
| | - Nasib Qureshi
- USDA, ARS, NCAUR, Fermentation Biotechnology (FBT) Research Unit, 1815 North University Street, Peoria, IL 61604, USA
| | - Michael A Cotta
- USDA, ARS, NCAUR, Fermentation Biotechnology (FBT) Research Unit, 1815 North University Street, Peoria, IL 61604, USA
| | - Philip J Farrelly
- Hudson Control Group, Inc., 10 Stern Avenue, Springfield, NJ 07081, USA
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Carlton JM, Angiuoli SV, Suh BB, Kooij TW, Pertea M, Silva JC, Ermolaeva MD, Allen JE, Selengut JD, Koo HL, Peterson JD, Pop M, Kosack DS, Shumway MF, Bidwell SL, Shallom SJ, van Aken SE, Riedmuller SB, Feldblyum TV, Cho JK, Quackenbush J, Sedegah M, Shoaibi A, Cummings LM, Florens L, Yates JR, Raine JD, Sinden RE, Harris MA, Cunningham DA, Preiser PR, Bergman LW, Vaidya AB, van Lin LH, Janse CJ, Waters AP, Smith HO, White OR, Salzberg SL, Venter JC, Fraser CM, Hoffman SL, Gardner MJ, Carucci DJ. Genome sequence and comparative analysis of the model rodent malaria parasite Plasmodium yoelii yoelii. Nature 2002; 419:512-9. [PMID: 12368865 DOI: 10.1038/nature01099] [Citation(s) in RCA: 532] [Impact Index Per Article: 24.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2002] [Accepted: 08/30/2002] [Indexed: 12/18/2022]
Abstract
Species of malaria parasite that infect rodents have long been used as models for malaria disease research. Here we report the whole-genome shotgun sequence of one species, Plasmodium yoelii yoelii, and comparative studies with the genome of the human malaria parasite Plasmodium falciparum clone 3D7. A synteny map of 2,212 P. y. yoelii contiguous DNA sequences (contigs) aligned to 14 P. falciparum chromosomes reveals marked conservation of gene synteny within the body of each chromosome. Of about 5,300 P. falciparum genes, more than 3,300 P. y. yoelii orthologues of predominantly metabolic function were identified. Over 800 copies of a variant antigen gene located in subtelomeric regions were found. This is the first genome sequence of a model eukaryotic parasite, and it provides insight into the use of such systems in the modelling of Plasmodium biology and disease.
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Affiliation(s)
- Jane M Carlton
- The Institute for Genomic Research, 9712 Medical Center Drive, Rockville, Maryland 20850, USA.
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