Yeast knockout library allows for efficient testing of genomic mutations for cell-free protein synthesis

Synthetic and Systems Biotechnology - Tập 1 - Trang 2-6 - 2016
Jennifer A. Schoborg1,2, Lauren G. Clark1,2, Alaksh Choudhury1,2,3, C. Eric Hodgman1,2, Michael C. Jewett1,2,3,4,5
1Department of Chemical and Biological Engineering, Northwestern University, 2145 Sheridan Road Evanston, IL 60208-3120, USA
2Chemistry of Life Processes Institute, 2170 Campus Drive, Evanston, IL 60208-3120, USA
3Masters in Biotechnology Program, Northwestern University, 2145 Sheridan Road, Evanston, IL 60208-3120, USA
4Robert H. Lurie Comprehensive Cancer Center, Northwestern University, 676 N. St Clair St, Suite 1200, Chicago, IL 60611-3068, USA
5Simpson Querrey Institute, Northwestern University, 303 E. Superior St, Suite 11-131, Chicago, IL 60611-2875, USA

Tài liệu tham khảo

Nirenberg, 1961, The dependence of cell-free protein synthesis in E. coli upon naturally occurring or synthetic polyribonucleotides, Proc Natl Acad Sci U S A, 47, 1588, 10.1073/pnas.47.10.1588 Carlson, 2012, Cell-free protein synthesis: applications come of age, Biotechnol Adv, 30, 1185, 10.1016/j.biotechadv.2011.09.016 Katzen, 2009, Membrane protein expression: no cells required, Trends Biotechnol, 27, 455, 10.1016/j.tibtech.2009.05.005 Uhlemann, 2012, Cell-free synthesis of membrane subunits of ATP synthase in phospholipid bicelles: NMR shows subunit a fold similar to the protein in the cell membrane, Protein Sci, 21, 279, 10.1002/pro.2014 Sachse, 2014, Membrane protein synthesis in cell-free systems: from bio-mimetic systems to bio-membranes, FEBS Lett, 588, 2774, 10.1016/j.febslet.2014.06.007 Bundy, 2010, Site-specific incorporation of p-propargyloxyphenylalanine in a cell-free environment for direct protein-protein click conjugation, Bioconjug Chem, 21, 255, 10.1021/bc9002844 Albayrak, 2013, Cell-free co-production of an orthogonal transfer RNA activates efficient site-specific non-natural amino acid incorporation, Nucleic Acids Res, 41, 5949, 10.1093/nar/gkt226 Hong, 2014, Non-standard amino acid incorporation into proteins using Escherichia coli cell-free protein synthesis, Front Chem, 2, 34, 10.3389/fchem.2014.00034 Hong, 2015, Improving cell-free protein synthesis through genome engineering of Escherichia coli lacking release factor 1, Chembiochem, 16, 844, 10.1002/cbic.201402708 Quast, 2014, Synthesis and site-directed fluorescence labeling of azido proteins using eukaryotic cell-free orthogonal translation systems, Anal Biochem, 451, 4, 10.1016/j.ab.2014.01.013 Goshima, 2008, Human protein factory for converting the transcriptome into an in vitro-expressed proteome, Nat Methods, 5, 1011, 10.1038/nmeth.1273 Kwon, 2010, Cloning-independent expression and analysis of omega-transaminases by use of a cell-free protein synthesis system, Appl Environ Microbiol, 76, 6295, 10.1128/AEM.00029-10 Stafford, 2014, In vitro Fab display: a cell-free system for IgG discovery, Protein Eng Des Sel, 27, 97, 10.1093/protein/gzu002 Yang, 2004, Expression of active murine granulocyte-macrophage colony-stimulating factor in an Escherichia coli cell-free system, Biotechnol Prog, 20, 1689, 10.1021/bp034350b Yin, 2004, Enhancing multiple disulfide bonded protein folding in a cell-free system, Biotechnol Bioeng, 86, 188, 10.1002/bit.10827 Kanter, 2007, Cell-free production of scFv fusion proteins: an efficient approach for personalized lymphoma vaccines, Blood, 109, 3393, 10.1182/blood-2006-07-030593 Zawada, 2011, Microscale to manufacturing scale-up of cell-free cytokine production – a new approach for shortening protein production development timelines, Biotechnol Bioeng, 108, 1570, 10.1002/bit.23103 Yin, 2012, Aglycosylated antibodies and antibody fragments produced in a scalable in vitro transcription-translation system, MAbs, 4, 217, 10.4161/mabs.4.2.19202 Heinzelman, 2015, pH responsive granulocyte colony-stimulating factor variants with implications for treating Alzheimer's disease and other central nervous system disorders, Protein Eng Des Sel, 28, 481, 10.1093/protein/gzv022 Chappell, 2015, Creating small transcription activating RNAs, Nat Chem Biol, 11, 214, 10.1038/nchembio.1737 Siegal-Gaskins, 2014, Gene circuit performance characterization and resource usage in a cell-free “breadboard”, ACS Synth Biol, 3, 416, 10.1021/sb400203p Shin, 2012, An E. coli cell-free expression toolbox: application to synthetic gene circuits and artificial cells, ACS Synth Biol, 1, 29, 10.1021/sb200016s Bujara, 2010, Exploiting cell-free systems: implementation and debugging of a system of biotransformations, Biotechnol Bioeng, 106, 376 Chappell, 2013, Validation of an entirely in vitro approach for rapid prototyping of DNA regulatory elements for synthetic biology, Nucleic Acids Res, 41, 3471, 10.1093/nar/gkt052 Pardee, 2014, Paper-based synthetic gene networks, Cell, 159, 940, 10.1016/j.cell.2014.10.004 Caschera, 2014, Synthesis of 2.3 mg/ml of protein with an all Escherichia coli cell-free transcription-translation system, Biochimie, 99, 162, 10.1016/j.biochi.2013.11.025 Hodgman, 2013, Optimized extract preparation methods and reaction conditions for improved yeast cell-free protein synthesis, Biotechnol Bioeng, 110, 2643, 10.1002/bit.24942 Dondapati, 2014, Membrane assembly of the functional KcsA potassium channel in a vesicle-based eukaryotic cell-free translation system, Biosens Bioelectron, 59, 174, 10.1016/j.bios.2014.03.004 Kovtun, 2011, Leishmania cell-free protein expression system, Methods, 55, 58, 10.1016/j.ymeth.2011.06.006 Brodel, 2014, Cell-free protein expression based on extracts from CHO cells, Biotechnol Bioeng, 111, 25, 10.1002/bit.25013 Buntru, 2014, Tobacco BY-2 cell-free lysate: an alternative and highly-productive plant-based in vitro translation system, BMC Biotechnol, 14, 37, 10.1186/1472-6750-14-37 Madin, 2000, A highly efficient and robust cell-free protein synthesis system prepared from wheat embryos: plants apparently contain a suicide system directed at ribosomes, Proc Natl Acad Sci U S A, 97, 559, 10.1073/pnas.97.2.559 Michel-Reydellet, 2004, Amino acid stabilization for cell-free protein synthesis by modification of the Escherichia coli genome, Metab Eng, 6, 197, 10.1016/j.ymben.2004.01.003 Michel-Reydellet, 2005, Increasing PCR fragment stability and protein yields in a cell-free system with genetically modified Escherichia coli extracts, J Mol Microbiol Biotechnol, 9, 26, 10.1159/000088143 Calhoun, 2006, Total amino acid stabilization during cell-free protein synthesis reactions, J Biotechnol, 123, 193, 10.1016/j.jbiotec.2005.11.011 Jiang, 2002, Reduction of protein degradation by use of protease-deficient mutants in cell-free protein synthesis system of Escherichia coli, J Biosci Bioeng, 93, 151, 10.1016/S1389-1723(02)80007-X Gan, 2014, A combined cell-free transcription-translation system from Saccharomyces cerevisiae for rapid and robust protein synthesis, Biotechnol J, 9, 641, 10.1002/biot.201300545 Schoborg, 2014, Substrate replenishment and byproduct removal improve yeast cell-free protein synthesis, Biotechnol J, 9, 630, 10.1002/biot.201300383 Choudhury, 2014, Evaluating fermentation effects on cell growth and crude extract metabolic activity for improved yeast cell-free protein synthesis, Biochem Eng J, 91, 140, 10.1016/j.bej.2014.07.014 Anderson, 2015, Energizing eukaryotic cell-free protein synthesis with glucose metabolism, FEBS Lett, 589, 1723, 10.1016/j.febslet.2015.05.045 Schiestl, 1989, High efficiency transformation of intact yeast cells using single stranded nucleic acids as a carrier, Curr Genet, 16, 339, 10.1007/BF00340712 Ryan, 2014, Selection of chromosomal DNA libraries using a multiplex CRISPR system, eLife, 3, e03703, 10.7554/eLife.03703 Goffeau, 1996, Life with 6000 genes, Science, 274, 563 Winzeler, 1999, Functional characterization of the S. cerevisiae genome by gene deletion and parallel analysis, Science, 285, 901, 10.1126/science.285.5429.901 Hodgman, 2014, Characterizing IGR IRES-mediated translation initiation for use in yeast cell-free protein synthesis, N Biotechnol, 31, 499, 10.1016/j.nbt.2014.07.001 Teichert, 1989, Lysosomal (vacuolar) proteinases of yeast are essential catalysts for protein degradation, differentiation, and cell survival, J Biol Chem, 264, 16037, 10.1016/S0021-9258(18)71584-6 Kaufman, 2004, Regulation of mRNA translation by protein folding in the endoplasmic reticulum, Trends Biochem Sci, 29, 152, 10.1016/j.tibs.2004.01.004 Pavitt, 1998, eIF2 independently binds two distinct eIF2B subcomplexes that catalyze and regulate guanine-nucleotide exchange, Genes Dev, 12, 514, 10.1101/gad.12.4.514 Sonenberg, 2009, Regulation of translation initiation in eukaryotes: mechanisms and biological targets, Cell, 136, 731, 10.1016/j.cell.2009.01.042 Brachmann, 1998, Designer deletion strains derived from Saccharomyces cerevisiae S288C: a useful set of strains and plasmids for PCR-mediated gene disruption and other applications, Yeast, 14, 115, 10.1002/(SICI)1097-0061(19980130)14:2<115::AID-YEA204>3.0.CO;2-2 Dever, 2002, Gene-specific regulation by general translation factors, Cell, 108, 545, 10.1016/S0092-8674(02)00642-6 Baba, 2006, Construction of Escherichia coli K-12 in-frame, single-gene knockout mutants: the Keio collection, Mol Syst Biol, 2, 10.1038/msb4100050 Yamamoto, 2009, Update on the Keio collection of Escherichia coli single-gene deletion mutants, Mol Syst Biol, 5, 335, 10.1038/msb.2009.92 Cong, 2013, Multiplex genome engineering using CRISPR/Cas systems, Science, 339, 819, 10.1126/science.1231143 Jinek, 2012, A programmable dual-RNA-guided DNA endonuclease in adaptive bacterial immunity, Science, 337, 816, 10.1126/science.1225829 Grav, 2015, One-step generation of triple knockout CHO cell lines using CRISPR/Cas9 and fluorescent enrichment, Biotechnol J, 10, 1446, 10.1002/biot.201500027 Lee, 2015, Site-specific integration in CHO cells mediated by CRISPR/Cas9 and homology-directed DNA repair pathway, Sci Rep, 5, 8572, 10.1038/srep08572