Development of a full-length human protein production pipeline

Protein Science

Volumn 23, Issue 8, 2014, Pages 1123-1135

  Saul, Justin ^a   Petritis, Brianne ^a   Sau, Sujay ^b   Rauf, Femina ^a   Gaskin, Michael ^a   Ober Reynolds, Benjamin ^a   Mineyev, Irina ^c   Magee, Mitch ^a   Chaput, John ^b   Qiu, Ji ^a   LaBaer, Joshua ^a  

^a ARIZONA STATE UNIVERSITY   (United States)

^b Arizona State University   (United States)

^c PERKINELMER INC   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

PROTEIN;

CHEMISTRY; FLUORESCENCE; GENETICS; HELA CELL LINE; HIGH THROUGHPUT SCREENING; HUMAN; ISOLATION AND PURIFICATION; PROTEIN SYNTHESIS; PROTEOMICS;

FLUORESCENCE; HELA CELLS; HIGH-THROUGHPUT SCREENING ASSAYS; HUMANS; PROTEIN BIOSYNTHESIS; PROTEINS; PROTEOMICS;

EID: 84906853591     PISSN: 09618368     EISSN: 1469896X     Source Type: Journal    
DOI: 10.1002/pro.2484     Document Type: Article

References (41)

1. Terwilliger TC, Stuart D, Yokoyama S (2009). Lessons from structural genomics. Annu Rev Biophys 38:371- 383.
2. Fasolo J, Sboner A, Sun MG, Yu H, Chen R, Sharon D, Kim PM, Gerstein M, Snyder M (2011). Diverse protein kinase interactions identified by protein microarrays reveal novel connections between cellular processes. Genes Dev 25:767-778.
3. Anastassiadis T, Deacon SW, Devarajan K, Ma H, Peterson JR (2011). Comprehensive assay of kinase catalytic activity reveals features of kinase inhibitor selectivity. Nat Biotechnol 29:1039-1045.
4. Davis MI, Hunt JP, Herrgard S, Ciceri P, Wodicka LM, Pallares G, Hocker M, Treiber DK, Zarrinkar PP (2011). Comprehensive analysis of kinase inhibitor selectivity. Nat Biotechnol 29:1046-1051.
5. Stergachis AB, MacLean B, Lee K, Stamatoyannopoulos JA, MacCoss MJ (2011). Rapid empirical discovery of optimal peptides for targeted proteomics. Nat Methods 8:1041-1043.
6. Marx V (2013). Calling the next generation of affinity reagents. Nat Methods 10:829-833.
7. Vincentelli R, Romier C (2013). Expression in Escherichia coli: becoming faster and more complex. Curr Opin Struct Biol 23:326-334.
8. Terpe K (2006). Overview of bacterial expression systems for heterologous protein production: from molecular and biochemical fundamentals to commercial systems. Appl Microbiol Biotechnol 72:211-222.
9. Braun P, Hu Y, Shen B, Halleck A, Koundinya M, Harlow E, LaBaer J (2002). Proteome-scale purification of human proteins from bacteria. Proc Natl Acad Sci USA 99:2654-2659.
10. Langlais C, Guilleaume B, Wermke N, Scheuermann T, Ebert L, LaBaer J, Korn B (2007). A systematic approach for testing expression of human full-length proteins in cell-free expression systems. BMC Biotechnol 7:64.
11. Bird LE (2011). High throughput construction and small scale expression screening of multi-tag vectors in Escherichia coli. Methods 55:29-37.
12. Bussow K, Scheich C, Sievert V, Harttig U, Schultz J, Simon B, Bork P, Lehrach H, Heinemann U (2005). Structural genomics of human proteins-target selection and generation of a public catalogue of expression clones. Microb Cell Fact 4:21.
13. Graslund S, Sagemark J, Berglund H, Dahlgren LG, Flores A, Hammarstrom M, Johansson I, Kotenyova T, Nilsson M, Nordlund P, Weigelt J (2008). The use of systematic N- And C-terminal deletions to promote production and structural studies of recombinant proteins. Protein Expr Purif 58:210-221.
14. Pacheco B, Crombet L, Loppnau P, Cossar D (2012). A screening strategy for heterologous protein expression in Escherichia coli with the highest return of investment. Protein Expr Purif 81:33-41.
15. Dessailly BH, Nair R, Jaroszewski L, Fajardo JE, Kouranov A, Lee D, Fiser A, Godzik A, Rost B, Orengo C (2009). PSI-2: structural genomics to cover protein domain family space. Structure 17:869-881.
16. Acton TB, Xiao R, Anderson S, Aramini J, Buchwald WA, Ciccosanti C, Conover K, Everett J, Hamilton K, Huang YJ, Janjua H, Kornhaber G, Lau J, Lee DY, Liu G, Maglaqui M, Ma L, Mao L, Patel D, Rossi P, Sahdev S, Shastry R, Swapna GV, Tang Y, Tong S, Wang D, Wang H, Zhao L, Montelione GT (2011). Preparation of protein samples for NMR structure, function, and small-molecule screening studies. Methods Enzymol 493:21-60.
17. Xiao R, Anderson S, Aramini J, Belote R, Buchwald WA, Ciccosanti C, Conover K, Everett JK, Hamilton K, Huang YJ, Janjua H, Jiang M, Kornhaber GJ, Lee DY, Locke JY, Ma LC, Maglaqui M, Mao L, Mitra S, Patel D, Rossi P, Sahdev S, Sharma S, Shastry R, Swapna GV, Tong SN, Wang D, Wang H, Zhao L, Montelione GT, Acton TB. (2010). The high-throughput protein sample production platform of the Northeast Structural Genomics Consortium. J Struct Biol 172:21-33.
18. Takai K, Sawasaki T, Endo Y (2010). Practical cell-free protein synthesis system using purified wheat embryos. Nat Protoc 5:227-238.
19. Guild K, Zhang Y, Stacy R, Mundt E, Benbow S, Green A, Myler PJ (2011). Wheat germ cell-free expression system as a pathway to improve protein yield and solubility for the SSGCID pipeline. Acta Crystallogr Sect F Struct Biol Cryst Commun 67:1027-1031.
20. Fernandez FJ, Vega MC (2013). Technologies to keep an eye on: Alternative hosts for protein production in structural biology. Curr Opin Struct Biol 23:365-373.
21. Wellensiek BP, Larsen AC, Flores J, Jacobs BL, Chaput JC (2013). A leader sequence capable of enhancing RNA expression and protein synthesis in mammalian cells. Protein Sci 22:1392-1398.
22. Barford D, Takagi Y, Schultz P, Berger I (2013). Baculovirus expression: Tackling the complexity challenge. Curr Opin Struct Biol 23:357-364.
23. Hunt I (2005). From gene to protein: A review of new and enabling technologies for multi-parallel protein expression. Protein Expr Purif 4:1-22.
24. Possee RD, Hitchman RB, Richards KS, Mann SG, Siaterli E, Nixon CP, Irving H, Assenberg R, Alderton D, Owens RJ, King LA. (2008). Generation of baculovirus vectors for the high-throughput production of proteins in insect cells. Biotechnol Bioeng 101:1115-1122.
25. Seal AJ, Collingridge GL, Henley JM (1995). An investigation of the membrane topology of the ionotropic glutamate receptor subunit GluR1 in a cell-free system. Biochem J 312:451-456.
26. Festa F, Rollins SM, Vattem K, Hathaway M, Lorenz P, Mendoza EA, Yu X, Qiu J, Kilmer G, Jensen P, Webb B, Ryan ET, Labaer J (2013). Robust microarray production of freshly expressed proteins in a human milieu. Proteomics Clin Appl 7:372-377.
27. Beebe ET, Makino S, Nozawa A, Matsubara Y, Frederick RO, Primm JG, Goren MA, Fox BG (2011). Robotic large-scale application of wheat cell-free translation to structural studies including membrane proteins. Nat Biotechnol 28:239-249.
28. Tyler RC, Aceti DJ, Bingman CA, Cornilescu CC, Fox BG, Frederick RO, Jeon WB, Lee MS, Newman CS, Peterson FC, Phillips GN Jr., Shahan MN, Singh S, Song J, Sreenath HK, Tyler EM, Ulrich EL, Vinarov DA, Vojtik FC, Volkman BF, Wrobel RL, Zhao Q, Markley JL (2005). Comparison of cell-based and cellfree protocols for producing target proteins from the Arabidopsis thaliana genome for structural studies. Proteins 59:633-643.
29. Ohana RF, Encell LP, Zhao K, Simpson D, Slater MR, Urh M, Wood KV (2009). HaloTag7: A genetically engineered tag that enhances bacterial expression of soluble proteins and improves protein purification. Protein Expr Purif 68:110-120.
30. Ohana RF, Hurst R, Vidugiriene J, Slater MR, Wood KV, Urh M (2011). HaloTag-based purification of functional human kinases from mammalian cells. Protein Expr Purif 76:154-164.
31. Lamesch P, Li N, Milstein S, Fan C, Hao T, Szabo G, Hu Z, Venkatesan K, Bethel G, Martin P, Rogers J, Lawlor S, McLaren S, Dricot A, Borick H, Cusick ME, Vandenhaute J, Dunham I, Hill DE, Vidal M (2007). hORFeome v3.1: A resource of human open reading frames representing over 10, 000 human genes. Genomics 89:307-315.
32. Seiler CY, Park JG, Sharma A, Hunter P, Surapaneni P, Sedillo C, Field J, Algar R, Price A, Steel J, Throop A, Fiacco M, Labaer J (2014). DNASU plasmid and PSI:Biology-Materials repositories: resources to accelerate biological research. Nucleic Acids Res 42:1253- 1260.
33. Hanahan D, Weinberg RA (2011). Hallmarks of cancer: The next generation. Cell 144:646-674.
34. Wang J, Barker K, Steel J, Park J, Saul J, Festa F, Wallstrom G, Yu X, Bian X, Anderson KS, Figueroa JD, LaBaer J, Qiu J (2013). A versatile protein microarray platform enabling antibody profiling against denatured proteins. Proteomics Clin Appl 7:378-383.
35. Rustandi RR, Loughney JW, Hamm M, Hamm C, Lancaster C, Mach A, Ha S (2012). Qualitative and quantitative evaluation of Simon, a new CE-based automated Western blot system as applied to vaccine development. Electrophoresis 33:2790-2797.
36. Brasher BB, Van Etten, RA (2000). c-Abl has high intrinsic tyrosine kinase activity that is stimulated by mutation of the Src homology 3 domain and by autophosphorylation at two distinct regulatory tyrosines. J Biol Chem 275:35631-35637.
37. Persons DL, Yazlovitskaya EM, Pelling JC (2000). Effect of extracellular signal-regulated kinase on p53 accumulation in response to cisplatin. J Biol Chem 275:35778-35785.
38. Carlson ED, Gan R, Hodgman CE, Jewett MC (2012). Cell-free protein synthesis: Applications come of age. Biotechnol Adv 30:1185-1194.
39. Zhao L, Zhao KQ, Hurst R, Slater MR, Acton TB, Swapna GV, Shastry R, Kornhaber GJ, Montelione GT (2010). Engineering of a wheat germ expression system to provide compatibility with a high throughput pET-based cloning platform. J Struct Funct Genomics 11:201-209.
40. Aramini JM, Rossi P, Anklin C, Xiao R, Montelione GT (2007). Microgram-scale protein structure determination by NMR. Nat Methods 4:491-493.
41. Boutet S, Lomb L, Williams GJ, Barends TR, Aquila A, Doak RB, Weierstall U, DePonte DP, Steinbrener J, Shoeman RL, Messerschmidt M, Barty A, White TA, Kassemeyer S, Kirian RA, Seibert MM, Montanez PA, Kenney C, Herbst R, Hart P, Pines J, Haller G, Gruner SM, Philipp HT, Tate MW, Hromalik M, Koerner LJ, van Bakel N, Morse J, Ghonsalves W, Arnlund D, Bogan MJ, Caleman C, Fromme R, Hampton CY, Hunter MS, Johansson LC, Katona G, Kupitz C, Liang M, Martin AV, Nass K, Redecke L, Stellato F, Timneanu N, Wang D, Zatsepin NA, Schafer D, Defever J, Neutze R, Fromme P, Spence JC, Chapman HN, Schlichting I (2012). High-resolution protein structure determination by serial femtosecond crystallography. Science 337:362-364.