Protein production in Saccharomyces cerevisiae for systems biology studies

Methods in Enzymology

Volumn 500, Issue , 2011, Pages 197-212

  Malys, Naglis ^a   Wishart, Jill A ^a   Oliver, Stephen G ^a,b   McCarthy, John E G ^a,c  

^a UNIVERSITY OF MANCHESTER   (United Kingdom)

^b UNIVERSITY OF CAMBRIDGE   (United Kingdom)

^c UNIVERSITY OF WARWICK   (United Kingdom)

Author keywords

Affinity purification; expression systems; Protein production; Systems biology; Yeast tagged collections

Indexed keywords

PROTEIN;

BACTERIUM; CELL DISRUPTION; CELL FREE SYSTEM; CELL GROWTH; ENZYME KINETICS; ENZYME PURIFICATION; ENZYME SYNTHESIS; GENE EXPRESSION SYSTEM; INSECT; INTERMETHOD COMPARISON; MAMMAL; MOLECULAR LIBRARY; NONHUMAN; PLANT; POLYACRYLAMIDE GEL ELECTROPHORESIS; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN EXPRESSION; PROTEIN ISOLATION; PROTEIN PURIFICATION; PROTEIN SYNTHESIS; PROTEOMICS; QUANTITATIVE ANALYSIS; REVIEW; SACCHAROMYCES CEREVISIAE; SYSTEMS BIOLOGY; YEAST;

SACCHAROMYCES CEREVISIAE;

EID: 80053056359     PISSN: 00766879     EISSN: 15577988     Source Type: Book Series    
DOI: 10.1016/B978-0-12-385118-5.00011-6     Document Type: Chapter

References (46)

1. C. Boone, H. Bussey, and B.J. Andrews Exploring genetic interactions and networks with yeast Nat. Rev. Genet. 8 2007 437 449 (Pubitemid 46789246)
2. W.H. Brondyk Selecting an appropriate method for expressing a recombinant protein Methods Enzymol. 463 2009 131 147
3. K.M. Carroll, F. Lanucara, and C.E. Eyers Quantification of proteins and their modifications using QconCAT technology Methods Enzymol. 500 2011 113 131
4. G. Chua, Q.D. Morris, R. Sopko, M.D. Robinson, O. Ryan, E.T. Chan, B.J. Frey, B.J. Andrews, C. Boone, and T.R. Hughes Identifying transcription factor functions and targets by phenotypic activation Proc. Natl. Acad. Sci. USA 103 2006 12045 12050 (Pubitemid 44215808)
5. J.M. Cregg, I. Tolstorukov, A. Kusari, J. Sunga, K. Madden, and T. Chappell Expression in the yeast Pichia pastoris Methods Enzymol. 463 2009 169 189
6. A. Fatica, A.D. Cronshaw, M. Dlakić, and D. Tollervey Ssf1p prevents premature processing of an early pre-60S ribosomal particle Mol. Cell 9 2002 341 351 (Pubitemid 34195559)
7. J.B. Franklin, and E. Ullu Biochemical analysis of PIFTC3, the Trypanosoma brucei orthologue of nematode DYF-13, reveals interactions with established and putative intraflagellar transport components Mol. Microbiol. 78 2010 173 186
8. A.-C. Gavin, P. Aloy, P. Grandi, R. Krause, M. Boesche, M. Marzioch, C. Rau, L.J. Jensen, S. Bastuck, B. Dümpelfeld, A. Edelmann, and M.-A. Heurtier Proteome survey reveals modularity of the yeast cell machinery Nature 440 2006 631 636
9. D.M. Gelperin, M.A. White, M.L. Wilkinson, Y. Kon, L.A. Kung, K.J. Wise, N. Lopez-Hoyo, L. Jiang, S. Piccirillo, H. Yu, M. Gerstein, and M.E. Dumont Biochemical and genetic analysis of the yeast proteome with a movable ORF collection Genes Dev. 19 2005 2816 2826 (Pubitemid 41739967)
10. R. George, H.-L. Chan, Z. Ahmed, K.M. Suen, C.N. Stevens, J.A. Levitt, K. Suhling, J. Timms, and J.E. Ladbury A complex of Shc and Ran-GTPase localises to the cell nucleus Cell. Mol. Life Sci. 66 2009 711 720
11. S. Ghaemmaghami, W.K. Huh, K. Bower, R.W. Howson, A. Belle, N. Dephoure, E.K. O'Shea, and J.S. Weissman Global analysis of protein expression in yeast Nature 425 2003 737 741 (Pubitemid 37314318)
12. L. Gold Expression of heterologous proteins in Escherichia coli Methods Enzymol. 185 1990 11 14 (Pubitemid 20219807)
13. H. Hernández, A. Dziembowski, T. Taverner, B. Séraphin, and C.V. Robinson Subunit architecture of multimeric complexes isolated directly from cells EMBO Rep. 7 2006 605 610 (Pubitemid 43827327)
14. J.E. Jackman, L. Kotelawala, E.J. Grayhack, and E.M. Phizicky Identification and characterization of modification enzymes by biochemical analysis of the proteome Methods Enzymol. 425 2007 139 152
15. J.E. Jackman, E.J. Grayhack, and E.M. Phizicky The use of Saccharomyces cerevisiae proteomic libraries to identify RNA-modifying proteins Methods Mol. Biol. 488 2008 383 393
16. D.L. Jarvis Baculovirus-insect cell expression Methods Enzymol. 463 2009 191 222
17. F. Junge, B. Schneider, S. Reckel, D. Schwarz, V. Dötsch, and F. Bernhard Large-scale production of functional membrane proteins Cell. Mol. Life Sci. 65 2008 1729 1755
18. F. Katzen, G. Chang, and W. Kudlicki The past, present and future of cell-free protein synthesis Trends Biotechnol. 23 2005 150 156 (Pubitemid 40269848)
19. D.B. Kell Metabolomics and systems biology: Making sense of the soup Curr. Opin. Microbiol. 7 2004 296 307 (Pubitemid 38765114)
20. D.B. Kell Metabolomics, modelling and machine learning in systems biology - Towards an understanding of the languages of cells. The 2005 Theodor Bücher Lecture FEBS J. 273 2006 873 894
21. R.D. King, J. Rowland, S.G. Oliver, M. Young, W. Aubrey, E. Byrne, M. Liakata, M. Markham, P. Pir, L.N. Soldatova, A. Sparkes, and K.E. Whelan The automation of science Science 324 2009 85 89
22. N.J. Krogan, G. Cagney, H. Yu, G. Zhong, X. Guo, A. Ignatchenko, J. Li, S. Pu, N. Datta, N.P. Tikuisis, T. Punna, and J.M. Peregrín-Alvarez Global landscape of protein complexes in the yeast Saccharomyces cerevisiae Nature 440 2006 637 643
23. L.A. Kung, and M. Snyder Proteome chips for whole-organism assays Nat. Rev. Mol. Cell Biol. 7 2006 617 622 (Pubitemid 44325353)
24. U.K. Laemmli Cleavage of structural proteins during the assembly of the head of bacteriophage T4 Nature 227 1970 680 685
25. Z. Li, D. Barajas, T. Panavas, D.A. Herbst, and P.D. Nagy Cdc34p ubiquitin-conjugating enzyme is a component of the tombusvirus replicase complex and ubiquitinates p33 replication protein J. Virol. 82 2008 6911 6926 (Pubitemid 351977712)
26. J.A. Lindbo High-efficiency protein expression in plants from agroinfection-compatible tobacco mosaic virus expression vectors BMC Biotechnol. 7 2007 52
27. S.C. Makrides Strategies for achieving high-level expression of genes in Escherichia coli Microbiol. Rev. 60 1996 512 538 (Pubitemid 26303477)
28. A. Malhotra Tagging for protein expression Methods Enzymol. 463 2009 239 258
29. N. Malys, and J.E.G. McCarthy Dcs2, a novel stress-induced modulator of m7G pppX pyrophosphatase activity that locates to P bodies J. Mol. Biol. 363 2006 370 382 (Pubitemid 44436253)
30. N. Malys, and J.E.G. McCarthy Translation initiation: Variations in the mechanism can be anticipated Cell. Mol. Life Sci. 68 2011 991 1003
31. N. Malys, D.-Y. Chang, R.G. Baumann, D. Xie, and L.W. Black A bipartite bacteriophage T4 SOC and HOC randomized peptide display library: Detection and analysis of phage T4 terminase (gp17) and late σ factor (gp55) interaction J. Mol. Biol. 319 2002 289 304 (Pubitemid 34729458)
32. N. Malys, K. Carroll, J. Miyan, D. Tollervey, and J.E.G. McCarthy The 'scavenger' m7G pppX pyrophosphatase activity of Dcs1 modulates nutrient-induced responses in yeast Nucleic Acids Res. 32 2004 3590 3600 (Pubitemid 39157707)
33. P. Mendes, H. Messiha, N. Malys, and S. Hoops Enzyme kinetics and computational modeling for systems biology Methods Enzymol. 467 2009 583 599
34. H.L. Messiha, N. Malys, and K.M. Carroll Towards a full quantitative description of yeast metabolism: A systematic approach for estimating the kinetic parameters of isoenzymes under in-vivo like conditions Methods Enzymol. 500 2011 215 231
35. M.G. Norris, and N. Malys What is the true enzyme kinetics in the biological system? An investigation of macromolecular crowding effect upon enzyme kinetics of glucose-6-phosphate dehydrogenase Biochem. Biophys. Res. Commun. 405 2011 388 392
36. A.K. Panigrahi, A. Schnaufer, and K.D. Stuart Isolation and compositional analysis of trypanosomatid editosomes Methods Enzymol. 424 2007 3 24
37. O. Puig, F. Caspary, G. Rigaut, B. Rutz, E. Bouveret, E. Bragado-Nilsson, M. Wilm, and B. Seraphin The tandem affinity purification (TAP) method: A general procedure of protein complex purification Methods 24 2001 218 229 (Pubitemid 32846428)
38. G. Rigaut, A. Shevchenko, B. Rutz, M. Wilm, M. Mann, and B. Seraphin A generic protein purification method for protein complex characterization and proteome exploration Nat. Biotechnol. 17 1999 1030 1032 (Pubitemid 29474865)
39. R. Sabate, N.S. De Groot, and S. Ventura Protein folding and aggregation in bacteria Cell. Mol. Life Sci. 67 2010 2695 2715
40. K. Smallbone, N. Malys, H.L. Messiha, J.A. Wishart, and E. Simeonidis Building a kinetic model of trehalose biosynthesis in Saccharomyces cerevisiae Methods Enzymol. 500 2011 355 370
41. P.K. Smith, R.I. Krohn, G.T. Hermanson, A.K. Mallia, F.H. Gartner, M.D. Provenzano, E.K. Fujimoto, N.M. Goeke, B.J. Olson, and D.C. Klenk Measurement of protein using bicinchoninic acid Anal. Biochem. 150 1985 76 85 (Pubitemid 16258399)
42. R. Sopko, D. Huang, N. Preston, G. Chua, B. Papp, K. Kafadar, M. Snyder, S.G. Oliver, M. Cyert, T.R. Hughes, C. Boone, and B. Andrews Mapping pathways and phenotypes by systematic gene overexpression Mol. Cell 21 2006 319 330 (Pubitemid 43163527)
43. S. Tabor, and C.C. Richardson A bacteriophage T7 RNA polymerase/promoter system for controlled exclusive expression of specific genes Proc. Natl. Acad. Sci. USA 82 1985 1074 1078 (Pubitemid 15100497)
44. J. Yin, G. Li, X. Ren, and G. Herrler Select what you need: A comparative evaluation of the advantages and limitations of frequently used expression systems for foreign genes J. Biotechnol. 127 2007 335 347 (Pubitemid 44827384)
45. S. Zerbs, A.M. Frank, and F.R. Collart Bacterial systems for production of heterologous proteins Methods Enzymol. 463 2009 149 168
46. H. Zhu, M. Bilgin, R. Bangham, D. Hall, A. Casamayor, P. Bertone, N. Lan, R. Jansen, S. Bidlingmaier, T. Houfek, T. Mitchell, and P. Miller Global analysis of protein activities using proteome chips Science 293 2001 2101 2105 (Pubitemid 32848060)