Yeast systems biotechnology for the production of heterologous proteins

FEMS Yeast Research

Volumn 9, Issue 3, 2009, Pages 335-348

  Graf, Alexandra ^a,b   Dragosits, Martin ^a   Gasser, Brigitte ^a   Mattanovich, Diethard ^a,b  

^a UNIVERSITY OF AGRICULTURAL SCIENCES   (Austria)

^b Fachhochschule Campus Wien   (Austria)

Author keywords

Heterologous protein; Metabolic engineering; Pichia pastoris; Systems biology; Systems biotechnology; Yeast

Indexed keywords

BACTERIAL PROTEIN; FUNGAL PROTEIN; RECOMBINANT PROTEIN;

ANALYTIC METHOD; ARTICLE; BIOPROCESS; BIOTECHNOLOGY; FUNGAL GENE; FUNGUS; GENE EXPRESSION SYSTEM; GENE SEQUENCE; GENOME ANALYSIS; MAMMAL CELL; METABOLOMICS; MODEL; NONHUMAN; PROTEIN ENGINEERING; PROTEIN SYNTHESIS; PROTEOMICS; SYSTEMS BIOLOGY; TRANSCRIPTOMICS; YEAST;

BIOTECHNOLOGY; GENETIC ENGINEERING; METABOLIC NETWORKS AND PATHWAYS; RECOMBINANT PROTEINS; SYSTEMS BIOLOGY; YEASTS;

BACTERIA (MICROORGANISMS); MAMMALIA; PICHIA PASTORIS;

EID: 64549111428     PISSN: 15671356     EISSN: 15671364     Source Type: Journal    
DOI: 10.1111/j.1567-1364.2009.00507.x     Document Type: Article

References (100)

1. Aldor I, Krawitz D, Forrest W, Chen C, Nishihara J, Joly J Champion K (2005) Proteomic profiling of recombinant Escherichia coli in high-cell-density fermentations for improved production of an antibody fragment biopharmaceutical. Appl Environ Microb 71 : 1717 1728.
2. Alper H, Moxley J, Nevoigt E, Fink G Stephanopoulos G (2006) Engineering yeast transcription machinery for improved ethanol tolerance and production. Science 314 : 1565 1568.
3. Andersen M, Nielsen M Nielsen J (2008) Metabolic model integration of the bibliome, genome, metabolome and reactome of Aspergillus niger. Mol Syst Biol 4 : 178.
4. Arga K, Onsan Z, Kirdar B, Ulgen K Nielsen J (2007) Understanding signaling in yeast: insights from network analysis. Biotechnol Bioeng 97 : 1246 1258.
5. Arvas M, Pakula T, Lanthaler K et al 2006) Common features and interesting differences in transcriptional responses to secretion stress in the fungi Trichoderma reesei and Saccharomyces cerevisiae. BMC Genomics 7 : 32.
6. Bachi A Bonaldi T (2008) Quantitative proteomics as a new piece of the systems biology puzzle. J Proteomics 71 : 357 367.
7. Bailey J (1991) Toward a science of metabolic engineering. Science 252 : 1668 1675.
8. Bailey J, Sburlati A, Hatzimanikatis V, Lee K, Renner W Tsai P (1996) Inverse metabolic engineering: a strategy for directed genetic engineering of useful phenotypes. Biotechnol Bioeng 52 : 109 121.
9. Beltran G, Novo M, Leberre V et al 2006) Integration of transcriptomic and metabolic analyses for understanding the global responses of low-temperature winemaking fermentations. FEMS Yeast Res 6 : 1167 1183.
10. Bino R, Hall R, Fiehn O et al 2004) Potential of metabolomics as a functional genomics tool. Trends Plant Sci 9 : 418 425.
11. Blank L, Lehmbeck F Sauer U (2005) Metabolic-flux and network analysis in fourteen hemiascomycetous yeasts. FEMS Yeast Res 5 : 545 558.
12. Blomberg A (1995) Global changes in protein synthesis during adaptation of the yeast Saccharomyces cerevisiae to 0.7 M NaCl. J Bacteriol 177 : 3563 3572.
13. Bonander N, Darby RAJ, Grgic L et al 2009) Altering the ribosomal subunit ratio in yeast maximizes recombinant protein yield. Microb Cell Fact 8 : 10.
14. Breakspear A Momany M (2007) The first fifty microarray studies in filamentous fungi. Microbiology 153 : 7 15.
15. Bro C Nielsen J (2004) Impact of 'ome' analyses on inverse metabolic engineering. Metab Eng 6 : 204 211.
16. Chen D, Toone W, Mata J et al 2003) Global transcriptional responses of fission yeast to environmental stress. Mol Biol Cell 14 : 214 229.
17. Chou C (2007) Engineering cell physiology to enhance recombinant protein production in Escherichia coli. Appl Microbiol Biot 76 : 521 532.
18. Dinnis D James D (2005) Engineering mammalian cell factories for improved recombinant monoclonal antibody production: lessons from nature? Biotechnol Bioeng 91 : 180 189.
19. Draghici S, Khatri P, Eklund A Szallasi Z (2006) Reliability and reproducibility issues in DNA microarray measurements. Trends Genet 22 : 101 109.
20. Dragosits M, Stadlmann J, Albiol J et al 2009) The effect of temperature on the proteome of recombinant Pichia pastoris. J Proteome Res 8 : 1380 1392.
21. Dujon B (2006) Yeasts illustrate the molecular mechanisms of eukaryotic genome evolution. Trends Genet 22 : 375 387.
22. Dürrschmid K, Reischer H, Schmidt-Heck W, Hrebicek T, Guthke R, Rizzi A Bayer K (2008) Monitoring of transcriptome and proteome profiles to investigate the cellular response of E. coli towards recombinant protein expression under defined chemostat conditions. J Biotechnol 135 : 34 44.
23. Edwards J Palsson B (2000) The Escherichia coli MG1655 in silico metabolic genotype: its definition, characteristics, and capabilities. P Natl Acad Sci USA 97 : 5528 5533.
24. Elrick M, Walgren J, Mitchell M Thompson D (2006) Proteomics: recent applications and new technologies. Basic Clin Pharmacol 98 : 432 441.
25. Fernandes P, Domitrovic T, Kao C Kurtenbach E (2004) Genomic expression pattern in Saccharomyces cerevisiae cells in response to high hydrostatic pressure. FEBS Lett 556 : 153 160.
26. Förster J, Famili I, Fu P, Palsson B Nielsen J (2003) Genome-scale reconstruction of the Saccharomyces cerevisiae metabolic network. Genome Res 13 : 244 253.
27. Fürch T, Wittmann C, Wang W, Franco-Lara E, Jahn D Deckwer W (2007) Effect of different carbon sources on central metabolic fluxes and the recombinant production of a hydrolase from Thermobifida fusca in Bacillus megaterium. J Biotechnol 132 : 385 394.
28. Gasch A, Spellman P, Kao C et al 2000) Genomic expression programs in the response of yeast cells to environmental changes. Mol Biol Cell 11 : 4241 4257.
29. Gasser B, Maurer M, Rautio J et al 2007a) Monitoring of transcriptional regulation in Pichia pastoris under protein production conditions. BMC Genomics 8 : 179.
30. Gasser B, Sauer M, Maurer M, Stadlmayr G Mattanovich D (2007b) Transcriptomics-based identification of novel factors enhancing heterologous protein secretion in yeasts. Appl Environ Microb 73 : 6499 6507.
31. Gonzalez R, Andrews B, Molitor J Asenjo J (2003) Metabolic analysis of the synthesis of high levels of intracellular human SOD in Saccharomyces cerevisiae rhSOD 2060 411 SGA122. Biotechnol Bioeng 82 : 152 169.
32. Gori K, Hébraud M, Chambon C, Mortensen H, Arneborg N Jespersen L (2007) Proteomic changes in Debaryomyces hansenii upon exposure to NaCl stress. FEMS Yeast Res 7 : 293 303.
33. Graf A, Gasser B, Dragosits M et al 2008) Novel insights into the unfolded protein response using Pichia pastoris specific DNA microarrays. BMC Genomics 9 : 390.
34. Griffin T, Seth G, Xie H, Bandhakavi S Hu W (2007) Advancing mammalian cell culture engineering using genome-scale technologies. Trends Biotechnol 25 : 401 408.
35. Guillemette T, van Peij N, Goosen T et al 2007) Genomic analysis of the secretion stress response in the enzyme-producing cell factory Aspergillus niger. BMC Genomics 8 : 158.
36. Gupta P (2009) Single-molecule DNA sequencing technologies for future genomics research. Trends Biotechnol 26 : 602 611.
37. Gupta P Lee K (2007) Genomics and proteomics in process development: opportunities and challenges. Trends Biotechnol 25 : 324 330.
38. Han M, Lee J, Lee S Yoo J (2008) Proteome-level responses of Escherichia coli to long-chain fatty acids and use of fatty acid inducible promoter in protein production. J Biomed Biotechnol 2008 : 735101.
39. Hartmann M, Roeraade J, Stoll D, Templin M Joos T (2008) Protein microarrays for diagnostic assays. Anal Bioanal Chem 393 : 1407 1416.
40. Herrgård M, Swainston N, Dobson P et al 2008) A consensus yeast metabolic network reconstruction obtained from a community approach to systems biology. Nat Biotechnol 26 : 1155 1160.
41. Hohenblum H, Borth N Mattanovich D (2003) Assessing viability and cell-associated product of recombinant protein producing Pichia pastoris with flow cytometry. J Biotechnol 102 : 281 290.
42. Jacobs DI, Olsthoorn MM, Maillet I et al 2009) Effective lead selection for improved protein production in Aspergillus niger based on integrated genomics. Fungal Genet Biol 46 : 141 152.
43. Jahic M, Wallberg F, Bollok M, Garcia P Enfors S (2003) Temperature limited fed-batch technique for control of proteolysis in Pichia pastoris bioreactor cultures. Microb Cell Fact 2 : 6.
44. Jaluria P, Chu C, Betenbaugh M Shiloach J (2008) Cells by design: a mini-review of targeting cell engineering using DNA microarrays. Mol Biotechnol 39 : 105 111.
45. Johnson D, Li W, Gordon D et al 2008) Systematic evaluation of variability in ChIP-chip experiments using predefined DNA targets. Genome Res 18 : 393 403.
46. Josic D Kovac S (2008) Application of proteomics in biotechnology - microbial proteomics. Biotechnol J 3 : 496 509.
47. Jürgen B, Lin H, Riemschneider S et al 2000) Monitoring of genes that respond to overproduction of an insoluble recombinant protein in Escherichia coli glucose-limited fed-batch fermentations. Biotechnol Bioeng 70 : 217 224.
48. Jürgen B, Hanschke R, Sarvas M, Hecker M Schweder T (2001) Proteome and transcriptome based analysis of Bacillus subtilis cells overproducing an insoluble heterologous protein. Appl Microbiol Biot 55 : 326 332.
49. Kawasaki E (2006) The end of the microarray Tower of Babel: will universal standards lead the way? J Biomol Tech 17 : 200 206.
50. Khan SU Schroder M (2008) Engineering of chaperone systems and of the unfolded protein response. Cytotechnology 57 : 207 231.
51. Kim T, Sohn S, Kim H Lee S (2008) Strategies for systems-level metabolic engineering. Biotechnol J 3 : 612 623.
52. Kim Y, Nandakumar M Marten M (2007) Proteome map of Aspergillus nidulans during osmoadaptation. Fungal Genet Biol 44 : 886 895.
53. Kimura S, Maruyama J, Takeuchi M Kitamoto K (2008) Monitoring global gene expression of proteases and improvement of human lysozyme production in the nptB gene disruptant of Aspergillus oryzae. Biosci Biotech Bioch 72 : 499 505.
54. Kobi D, Zugmeyer S, Potier S Jaquet-Gutfreund L (2004) Two-dimensional protein map of an "ale"-brewing yeast strain: proteome dynamics during fermentation. FEMS Yeast Res 5 : 213 230.
55. Kolkman A, Daran-Lapujade P, Fullaondo A, Olsthoorn M, Pronk J, Slijper M Heck A (2006) Proteome analysis of yeast response to various nutrient limitations. Mol Syst Biol 2 : 2006. 0026.
56. Korke R, Rink A, Seow T, Chung M, Beattie C Hu W (2002) Genomic and proteomic perspectives in cell culture engineering. J Biotechnol 94 : 73 92.
57. Kuystermans D, Krampe B, Swiderek H Al-Rubeai M (2007) Using cell engineering and omic tools for the improvement of cell culture processes. Cytotechnology 53 : 3 22.
58. Lee P Lee K (2005) Engineering HlyA hypersecretion in Escherichia coli based on proteomic and microarray analyses. Biotechnol Bioeng 89 : 195 205.
59. Lee S, Lee D Kim T (2005) Systems biotechnology for strain improvement. Trends Biotechnol 23 : 349 358.
60. Le Novère N, Finney A, Hucka M et al 2005) Minimum information requested in the annotation of biochemical models (MIRIAM). Nat Biotechnol 23 : 1509 1515.
61. Li Z, Xiong F, Lin Q, d'Anjou M, Daugulis A, Yang D Hew C (2001) Low-temperature increases the yield of biologically active herring antifreeze protein in Pichia pastoris. Protein Expres Purif 21 : 438 445.
62. Mardis E (2008) The impact of next-generation sequencing technology on genetics. Trends Genet 24 : 133 141.
63. Mattanovich D Borth N (2006) Applications of cell sorting in biotechnology. Microb Cell Fact 5 : 12.
64. Mattanovich D, Gasser B, Hohenblum H Sauer M (2004) Stress in recombinant protein producing yeasts. J Biotechnol 113 : 121 135.
65. Mukhopadhyay A, Redding A, Rutherford B Keasling J (2008) Importance of systems biology in engineering microbes for biofuel production. Curr Opin Biotech 19 : 228 234.
66. Nemecek S, Marisch K, Juric R Bayer K (2008) Design of transcriptional fusions of stress sensitive promoters and GFP to monitor the overburden of Escherichia coli hosts during recombinant protein production. Bioproc Biosyst Eng 31 : 47 53.
67. Nesvizhskii A, Vitek O Aebersold R (2007) Analysis and validation of proteomic data generated by tandem mass spectrometry. Nat Meth 4 : 787 797.
68. Nevoigt E (2008) Progress in metabolic engineering of Saccharomyces cerevisiae. Microbiol Mol Biol R 72 : 379 412.
69. Nielsen J (2001) Metabolic engineering. Appl Microbiol Biot 55 : 263 283.
70. Nielsen J Jewett M (2008) Impact of systems biology on metabolic engineering of Saccharomyces cerevisiae. FEMS Yeast Res 8 : 122 131.
71. Nookaew I, Jewett M, Meechai A et al 2008) The genome-scale metabolic model iIN800 of Saccharomyces cerevisiae and its validation: a scaffold to query lipid metabolism. BMC Syst Biol 2 : 71.
72. Ostergaard S, Olsson L Nielsen J (2000) Metabolic engineering of Saccharomyces cerevisiae. Microbiol Mol Biol R 64 : 34 50.
73. Park S, Lee S, Cho J, Kim T, Lee J, Park J Han M (2005) Global physiological understanding and metabolic engineering of microorganisms based on omics studies. Appl Microbiol Biot 68 : 567 579.
74. Payne T, Finnis C, Evans LR, Mead DJ, Avery SV, Archer DB Sleep D (2008) Modulation of chaperone gene expression in mutagenized Saccharomyces cerevisiae strains developed for recombinant human albumin production results in increased production of multiple heterologous proteins. Appl Environ Microb 74 : 7759 7766.
75. Pizarro F, Vargas F Agosin E (2007) A systems biology perspective of wine fermentations. Yeast 24 : 977 991.
76. Porro D, Sauer M, Branduardi P Mattanovich D (2005) Recombinant protein production in yeasts. Mol Biotechnol 31 : 245 259.
77. Qian Z, Xia X, Choi J Lee S (2008) Proteome-based identification of fusion partner for high-level extracellular production of recombinant proteins in Escherichia coli. Biotechnol Bioeng 101 : 587 601.
78. Rosende SS, Becerra M, Salgado MT, Lamas-Maceiras M, González M Picos MAF (2008) Growth phase-dependent expression of Kluyveromyces lactis genes and involvement of 3′-UTR elements. Process Biochem 43 : 1153 1157.
79. Sauer M, Branduardi P, Gasser B, Valli M, Maurer M, Porro D Mattanovich D (2004) Differential gene expression in recombinant Pichia pastoris analysed by heterologous DNA microarray hybridisation. Microb Cell Fact 3 : 17.
80. Schlitt T Brazma A (2005) Modelling gene networks at different organisational levels. FEBS Lett 579 : 1859 1866.
81. Seth G, Ozturk M Hu W (2006) Reverting cholesterol auxotrophy of NS0 cells by altering epigenetic gene silencing. Biotechnol Bioeng 93 : 820 827.
82. Seth G, Charaniya S, Wlaschin K Hu W (2007) In pursuit of a super producer-alternative paths to high producing recombinant mammalian cells. Curr Opin Biotechnol 18 : 557 564.
83. Shi X, Karkut T, Chamankhah M, Alting-Mees M, Hemmingsen S Hegedus D (2003) Optimal conditions for the expression of a single-chain antibody (scFv) gene in Pichia pastoris. Protein Expres Purif 28 : 321 330.
84. Sims AH, Gent ME, Lanthaler K, Dunn-Coleman NS, Oliver SG Robson GD (2005) Transcriptome analysis of recombinant protein secretion by Aspergillus nidulans and the unfolded-protein response in vivo. Appl Environ Microb 71 : 2737 2747.
85. Smith D, Quinlan A, Peckham H et al 2008) Rapid whole-genome mutational profiling using next-generation sequencing technologies. Genome Res 18 : 1638 1642.
86. Solà A, Maaheimo H, Ylönen K, Ferrer P Szyperski T (2004) Amino acid biosynthesis and metabolic flux profiling of Pichia pastoris. Eur J Biochem 271 : 2462 2470.
87. Solà A, Jouhten P, Maaheimo H, Sánchez-Ferrando F, Szyperski T Ferrer P (2007) Metabolic flux profiling of Pichia pastoris grown on glycerol/methanol mixtures in chemostat cultures at low and high dilution rates. Microbiology 153 : 281 290.
88. Sonderegger M Sauer U (2003) Evolutionary engineering of Saccharomyces cerevisiae for anaerobic growth on xylose. Appl Environ Microb 69 : 1990 1998.
89. Steuer R (2007) Computational approaches to the topology, stability and dynamics of metabolic networks. Phytochemistry 68 : 2139 2151.
90. Tai S, Daran-Lapujade P, Walsh M, Pronk J Daran J (2007) Acclimation of Saccharomyces cerevisiae to low temperature: a chemostat-based transcriptome analysis. Mol Biol Cell 18 : 5100 5112.
91. Takors R, Bathe B, Rieping M, Hans S, Kelle R Huthmacher K (2007) Systems biology for industrial strains and fermentation processes - example: amino acids. J Biotechnol 129 : 181 190.
92. Trummer E, Ernst W, Hesse F et al 2008) Transcriptional profiling of phenotypically different Epo-Fc expressing CHO clones by cross-species microarray analysis. Biotechnol J 3 : 924 937.
93. van Anken E, Romijn E, Maggioni C, Mezghrani A, Sitia R, Braakman I Heck A (2003) Sequential waves of functionally related proteins are expressed when B cells prepare for antibody secretion. Immunity 18 : 243 253.
94. van Ooyen A, Dekker P, Huang M, Olsthoorn M, Jacobs D, Colussi P Taron C (2006) Heterologous protein production in the yeast Kluyveromyces lactis. FEMS Yeast Res 6 : 381 392.
95. Wang W, Hollmann R Deckwer W (2006) Comparative proteomic analysis of high cell density cultivations with two recombinant Bacillus megaterium strains for the production of a heterologous dextransucrase. Proteome Sci 4 : 19.
96. Wang Y, Xue W, Sims AH et al 2008) Isolation of four pepsin-like protease genes from Aspergillus niger and analysis of the effect of disruptions on heterologous laccase expression. Fungal Genet Biol 45 : 17 27.
97. Westerhoff H Palsson B (2004) The evolution of molecular biology into systems biology. Nat Biotechnol 22 : 1249 1252.
98. Wong D, Wong K, Nissom P, Heng C Yap M (2006) Targeting early apoptotic genes in batch and fed-batch CHO cell cultures. Biotechnol Bioeng 95 : 350 361.
99. Yee J, de Leon Gatti M, Philp R, Yap M Hu W (2008) Genomic and proteomic exploration of CHO and hybridoma cells under sodium butyrate treatment. Biotechnol Bioeng 99 : 1186 1204.
100. Zuzuarregui A, Monteoliva L, Gil C del Olmo M (2006) Transcriptomic and proteomic approach for understanding the molecular basis of adaptation of Saccharomyces cerevisiae to wine fermentation. Appl Environ Microb 72 : 836 847.