High-throughput cloning, expression, and purification

Macromolecular Crystallography: Conventional and high-throughput methods

Volumn 9780198520979, Issue , 2007, Pages

  Owens, Raymond J ^a   Nettleship, Joanne E ^a   Berrow, Nick S ^a   Sainsbury, Sarah ^a   Aricescu, A Radu ^a   Stuart, David I ^a   Stammers, David K ^a  

^a UNIVERSITY OF OXFORD   (United Kingdom)

Author keywords

Cloning; Expression; Genome sequencing; Purification; Structural proteomics

Indexed keywords

AUTOMATION; CLONING; GENES; MOLECULAR BIOLOGY; PROTEINS; THROUGHPUT;

EXPRESSION; GENOME SEQUENCING; HIGH-THROUGHPUT SEQUENCING; PROTEIN PRODUCTION TECHNOLOGY; PROTEOMICS; PURIFICATION PROCEDURES; STRUCTURE DETERMINATION; STRUCTURE-FUNCTION ANALYSIS;

PURIFICATION;

EID: 84920752433     PISSN: None     EISSN: None     Source Type: Book    
DOI: 10.1093/acprof:oso/9780198520979.003.0002     Document Type: Chapter

References (55)

1. Abergel, C., Coutard, B., Byrne, D., Chenivesse, S., Claude, J. B., Deregnaucourt, C., et al. (2003). Structural genomics of highly conserved microbial genes of unknown function in search of new antibacterial targets. J. Struct. Funct. Genomics 4, 141-157.
2. Alexandrov, A., Dutta, K. and Pascal, S. M. (2001). MBP fusion protein with a viral protease cleavage site: one-step cleavage/purification of insoluble proteins. Biotechniques 30, 1194-1198.
3. Aslandis, C. D. and de Jong, P. J. (1990). Ligation-independent cloning of PCR products (LIC-PCR). Nucleic Acids Res. 18, 6069-6074.
4. Bahia, D., Cheung, R., Buchs, M., Geisse, S. and Hunt, I. (2005). Optimisation of insect cell growth in deep-well blocks: development of a high-throughput insect cell expression screen. Protein Expr. Purif. 39, 61-70.
5. Baker, R. T. (1996). Protein expression using ubiquitin fusion and cleavage. Curr. Opin. Biotechnol. 7, 541-546.
6. Baldi, L., Muller, N., Picasso, S., Jacquet, R., Girard, P., Thanh, H. P., et al. (2005). Transient gene expression in suspension HEK-293 cells: application to large-scale protein production. Biotechnol. Prog. 21, 148-153.
7. Berrow, N. S., Alderton, D., Sainsbury, S., Nettleship, J., Assenberg, R., Rahman, N., Stuart, D. I. and Owens, R. J. (2007). A versatile ligationindependent cloning method suitable for high-throughput expression screening applications. Nucleic Acids Res. 35, E45, 1-12.
8. Boettner, M., Prinz, B., Holz, C., Stahl, U. and Lang, C. (2002). Highthroughput screening for expression of heterologous proteins in the yeast Pichia pastoris. J. Biotechnol 99, 51-62.
9. Braun, P., Hu, Y., Shen, B., Halleck, A., Koundinya, M., Harlow, E. and LaBaer, J. (2002). Proteome-scale purification of human proteins from bacteria. Proc. Natl. Acad. Sci. USA 99, 2654-2659.
10. Butt, T. R., Jonnalagadda, S., Monia, B. P., Sternberg, E. J., Marsh, J. A., Stadel, J. M., Ecker, D. J. and Crooke, S. T. (1989). Ubiquitin fusion augments the yield of cloned gene products in Escherichia coli. Proc. Natl. Acad. Sci. USA 86, 2540-2544.
11. Catanzariti, A. M., Soboleva, T. A., Jans, D. A., Board, P. G. and Baker, R. T. (2004). An efficient system for high-level expression and easy purification of authentic recombinant proteins. Protein Sci. 13, 1331-1339.
12. Chambers, S. P., Austen, D. A., Fulghum, J. R. and Kim, W. M. (2004). High-throughput screening for soluble recombinant expressed kinases in Escherichia coli and insect cells. Protein Expr. Purif. 36, 40-47.
13. Cohen, S. L. and Chait, B. T. (2001). Mass spectrometry as a tool for protein crystallography. Annu. Rev. Biophys. Biomol. Struct. 30, 67-85.
14. Cordingley, M. G., Register, R. B., Callahan, P. L., Garsky, V. M. and Colonno, R. J. (1989). Cleavage of small peptides in vitro by human rhinovirus 14 3C protease expressed in Escherichia coli. J. Virol. 63, 5037-5045.
15. Davies, A., et al. (2005). Optimisation and evaluation of a high-throughput mammalian protein expression system. Protein Expr. Purif. 42, 111-121.
16. Davis, S. J., Greene, A., Lullau, E. and Abbott, W. M. (1993). Expression of soluble recombinant glycoproteins with predefined glycosylation: application to the crystallization of the T-cell glycoprotein CD2. Protein Eng. 6, 229-232.
17. Davis, S. J., Ikemizu, S., Collins, A. V., Fennelly, J. A., Harlos, K., Jones, E. Y. and Stuart, D. I. (2001). Crystallization and functional analysis of a soluble deglycosylated form of the human costimulatory molecule B7-1. Acta Crystallogr. D 57, 605-608.
18. Durocher, Y., Perret, S. and Kamen, A. (2002). High-level and highthroughput recombinant protein production by transient transfection of suspension-growing human 293-EBNA1 cells. Nucleic Acids Res. 30, E9.
19. Dyson, M. R., Shadbolt, S. P., Vincent, K. J., Perera, R. L. and McCafferty, J. (2004). Production of soluble mammalian proteins in Escherichia coli:identification of protein features that correlate with successful expression. BMC Biotechnol. 4, 32.
20. Feliu, J. X., Cubarsi, R. and Villaverde, A. (1998). Optimized release of recombinant proteins by ultrasonication of E. coli cells. Biotechnol. Bioeng. 58, 536-540.
21. Folkers, G. E., van Buuren, B. N. and Kaptein, R. (2004). Expression screening, protein purification and NMR analysis of human protein domains for structural genomics. J. Struct. Funct. Genomics 5, 119-131.
22. Gia-Fen, T. C. and Inouye, M. (1990). Suppression of the negative effect of minor arginine codons on gene expression; preferential usage of minor codons within the first 25 codons of the Escherichia coli genes. Nucleic Acids Res. 18, 1465-1473.
23. Habel, J. E., Ohren, J. F. and Borgstahl, G. E. (2001). Dynamic light-scattering analysis of full-length human RPA14/32 dimer: purification, crystallization and self-association. Acta Crystallogr. D 57, 254-259.
24. Hammarstrom, M., Hellgren, N., van Den Berg, S., Berglund, H. and Hard, T. (2002). Rapid screening for improved solubility of small human proteins produced as fusion proteins in Escherichia coli. Protein Sci. 11, 313-321.
25. Hartley, J. L., Temple, G. F. and Brasch, M. A. (2000). DNA cloning using in vitro site-specific recombination. Genome Res. 10, 1788-1795.
26. Haun, R. S., Serventi, I. M. and Moss, J. (1992). Rapid, reliable ligationindependent cloning of PCR products using modified plasmid vectors. Biotechniques 13, 515-518.
27. Hendrickson, W. A., Horton, J. R. and LeMaster, D. M. (1990). Selenomethionyl proteins produced for analysis by multiwavelength anomalous diffraction (MAD): a vehicle for direct determination of threedimensional structure. EMBO J. 9, 1665-1672.
28. Holz, C., Hesse, O., Bolotina, N., Stahl, U. and Lang, C. (2002). A microscale process for high-throughput expression of cDNAs in the yeast Saccharomyces cerevisiae. Protein Expr. Purif. 25, 372-378.
29. Holz, C., Prinz, B., Bolotina, N., Sievert, V., Bussow, K., Simon, B., Stahl, U. and Lang, C. (2003). Establishing the yeast Saccharomyces cerevisiae as a system for expression of human proteins on a proteome-scale. J. Struct. Funct. Genomics 4, 97-108.
30. Huang, R. Y., Boulton, S. J., Vidal, M., Almo, S. C., Bresnick, A. R. and Chance, M. R. (2003). High-throughput expression, purification, and characterization of recombinant Caenorhabditis elegans proteins. Biochem. Biophys. Res. Commun. 307, 928-934.
31. Kim, Y., Dementieva, I., Zhou, M., Wu, R., Lezondra, L., Quartey, P., et al. (2004). Automation of protein purification for structural genomics. J. Struct. Funct. Genomics 5, 111-118.
32. Knaust, R. K. and Nordlund, P. (2001). Screening for soluble expression of recombinant proteins in a 96-well format. Anal. Biochem. 297, 79-85.
33. Laurila, M. R., Salgado, P. S., Makeyev, E. V., Nettleship, J., Stuart, D. I., Grimes, J. M. and Bamford, D. H. (2005). Gene silencing pathway RNAdependent RNA polymerase of Neurospora crassa: yeast expression and crystallization of selenomethionated QDE-1 protein. J. Struct. Biol. 149, 111-115.
34. Lesley, S. A., Kuhn, P., Godzik, A., Deacon, A. M., Mathews, I., Kreusch, A., et al. (2002). Structural genomics of the Thermotoga maritima proteome implemented in a high-throughput structure determination pipeline. Proc. Natl. Acad. Sci. USA 99, 11664-11669.
35. Luan, C. H., Qiu, S., Finley, J. B., Carson, M., Gray, R. J., Huang, W., et al. (2004). High-throughput expression of C. elegans proteins. Genome Res. 14, 2102-2110.
36. Malakhov, M. P., Mattern, M. R., Malakhova, O. A., Drinker, M., Weeks, S. D. and Butt, T. R. (2004). SUMO fusions and SUMO-specific protease for efficient expression and purification of proteins. J. Struct. Funct. Genomics 5, 75-86.
37. Marsischky, G. and LaBaer, J. (2004). Many paths to many clones; a comparative look at high-throughput cloning methods. Genome Research 14, 2020-2028.
38. McWhirter, S. M., Pullen, S. S., Holton, J. M., Crute, J. J., Kehry, M. R. and Alber, T. (1999). Crystallographic analysis of CD40 recognition and signaling by human TRAF2. Proc. Natl. Acad. Sci. USA 96, 8408-8413.
39. Millard, C. S., Stols, L., Quartey, P., Kim, Y., Dementieva, I. and Donnelly, M. I. (2003). A less laborious approach to the high-throughput production of recombinant proteins in Escherichia coli using 2-liter plastic bottles. Protein Expr. Purif. 29, 311-320.
40. Parks, T. D., Leuther, K. K., Howard, E. D., Johnston, S. A. and Dougherty, W. G. (1994). Release of proteins and peptides from fusion proteins using a recombinant plant virus proteinase. Anal. Biochem. 216, 413-417.
41. Pham, P. L., Perret, S., Doan, H. C., Cass, B., St-Laurent, G., Kamen, A. and Durocher, Y. (2003). Large-scale transient transfection of serum-free suspension-growing HEK293 EBNA1 cells: peptone additives improve cell growth and transfection efficiency. Biotechnol. Bioeng. 84, 332-342.
42. Porath, J. (1992). Immobilized metal ion affinity chromatography. Protein Expr. Purif. 3, 263-281.
43. Prinz, B., Schultchen, J., Rydzewski, R., Holz, C., Boettner, M., Stahl, U. and Lang, C. (2004). Establishing a versatile fermentation and purification procedure for human proteins expressed in the yeasts Saccharomyces cerevisiae and Pichia pastoris for structural genomics. J. Struct. Funct. Genomics 5, 29-44.
44. Reeves, P. J., Callewaert, N., Contreras, R. and Khorana, H. G. (2002). Structure and function in rhodopsin: high-level expression of rhodopsin with restricted and homogeneous N-glycosylation by a tetracycline-inducible Nacetylglucosaminyltransferase I-negative HEK293S stable mammalian cell line. Proc. Natl. Acad. Sci. USA 99, 13419-13424.
45. Sigrell, J. A., Eklund, P., Galin, M., Hedkvist, L., Liljedahl, P., Johansson, C. M., Pless, T. and Torstenson, K. (2003). Automated multi-dimensional purification of tagged proteins. J. Struct. Funct. Genomics 4, 109-114.
46. Smith, D. B. and Johnson, K. S. (1988). Single-step purification of polypeptides expressed in Escherichia coli as fusions with glutathione Stransferase. Gene 67, 31-40.
47. Sreenath, H. K., Bingman, C. A., Buchan, B. W., Seder, K. D., Burns, B. T., Geetha, H. V., et al. (2005). Protocols for production of selenomethioninelabeled proteins in 2-L polyethylene terephthalate bottles using autoinduction medium. Protein Expr. Purif. 40, 256-267.
48. Stols, L., Gu, M., Dieckman, L., Raffen, R., Collart, F. R. and Donnelly, M. I. (2002). Anew vector for high-throughput, ligation-independent cloning encoding a tobacco etch virus protease cleavage site. Protein Expr. Purif. 25, 8-15.
49. Stols, L., Millard, C. S., Dementieva, I. and Donnelly, M. I. (2004). Production of selenomethionine-labeled proteins in two-liter plastic bottles for structure determination. J. Struct. Funct. Genomics 5, 95-102.
50. Studier, F. W. (2005). Protein production by auto-induction in high density shaking cultures. Protein Expr. Purif. 41, 207-234.
51. Studier, F. W., Rosenberg, A. H., Dunn, J. J. and Dubendorff, J. W. (1990). Use of T7 RNA polymerase to direct expression of cloned genes. Method Enzymol. 185, 60-89.
52. Vincentelli, R., Bignon, C., Gruez, A., Canaan, S., Sulzenbacher, G., Tegoni, M., et al. (2003). Medium-scale structural genomics: strategies for protein expression and crystallization. Acc. Chem. Res. 36, 165-172.
53. Walhout, A. J., Temple, G. F., Brasch, M. A., Hartley, J. L., Lorson, M. A., van den Heuvel, S. and Vidal, M. (2000). GATEWAY recombinational cloning:application to the cloning of large numbers of open reading frames or ORFeomes. Method Enzymol. 328, 575-92.
54. Weber, W., Weber, E., Geisse, S. and Memmert, K. (2002). Optimisation of protein expression and establishment of the Wave Bioreactor system for Baculovirus/insect cell culture. Cytotechnology 38, 77-85.
55. Xu, X. and Jones, I. M. (2004). Rapid parallel expression in E. coli and insect cells: analysis of five lef gene products of the Autographa californica multiple nuclear polyhedrosis virus (AcMNPV). Virus Genes 29, 191-197.