Yeast systems biotechnology for the production of heterologous proteins
Tóm tắt
Từ khóa
Tài liệu tham khảo
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: 1717â1728.
Alper H , Moxley J , Nevoigt E , Fink G & Stephanopoulos G (2006) Engineering yeast transcription machinery for improved ethanol tolerance and production. Science 314: 1565â1568.
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.
Arga K , Onsan Z , Kirdar B , Ulgen K & Nielsen J (2007) Understanding signaling in yeast: insights from network analysis. Biotechnol Bioeng 97: 1246â1258.
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.
Bachi A & Bonaldi T (2008) Quantitative proteomics as a new piece of the systems biology puzzle. J Proteomics 71: 357â367.
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: 109â121.
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: 1167â1183.
Bino R , Hall R , Fiehn O et al. (2004) Potential of metabolomics as a functional genomics tool. Trends Plant Sci 9: 418â425.
Blank L , Lehmbeck F & Sauer U (2005) Metabolic-flux and network analysis in fourteen hemiascomycetous yeasts. FEMS Yeast Res 5: 545â558.
Blomberg A (1995) Global changes in protein synthesis during adaptation of the yeast Saccharomyces cerevisiae to 0.7âM NaCl. J Bacteriol 177: 3563â3572.
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.
Breakspear A & Momany M (2007) The first fifty microarray studies in filamentous fungi. Microbiology 153: 7â15.
Bro C & Nielsen J (2004) Impact of âomeâ analyses on inverse metabolic engineering. Metab Eng 6: 204â211.
Chen D , Toone W , Mata J et al. (2003) Global transcriptional responses of fission yeast to environmental stress. Mol Biol Cell 14: 214â229.
Chou C (2007) Engineering cell physiology to enhance recombinant protein production in Escherichia coli. Appl Microbiol Biot 76: 521â532.
Dinnis D & James D (2005) Engineering mammalian cell factories for improved recombinant monoclonal antibody production: lessons from nature? Biotechnol Bioeng 91: 180â189.
Draghici S , Khatri P , Eklund A & Szallasi Z (2006) Reliability and reproducibility issues in DNA microarray measurements. Trends Genet 22: 101â109.
Dragosits M , Stadlmann J , Albiol J et al. (2009) The effect of temperature on the proteome of recombinant Pichia pastoris. J Proteome Res 8: 1380â1392.
Dujon B (2006) Yeasts illustrate the molecular mechanisms of eukaryotic genome evolution. Trends Genet 22: 375â387.
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: 34â44.
Edwards J & Palsson B (2000) The Escherichia coli MG1655 in silico metabolic genotype: its definition, characteristics, and capabilities. P Natl Acad Sci USA 97: 5528â5533.
Elrick M , Walgren J , Mitchell M & Thompson D (2006) Proteomics: recent applications and new technologies. Basic Clin Pharmacol 98: 432â441.
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: 153â160.
Förster J , Famili I , Fu P , Palsson B & Nielsen J (2003) Genome-scale reconstruction of the Saccharomyces cerevisiae metabolic network. Genome Res 13: 244â253.
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: 385â394.
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: 4241â4257.
Gasser B , Maurer M , Rautio J et al. (2007a) Monitoring of transcriptional regulation in Pichia pastoris under protein production conditions. BMC Genomics 8: 179.
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: 6499â6507.
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: 152â169.
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: 293â303.
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.
Griffin T , Seth G , Xie H , Bandhakavi S & Hu W (2007) Advancing mammalian cell culture engineering using genome-scale technologies. Trends Biotechnol 25: 401â408.
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.
Gupta P (2009) Single-molecule DNA sequencing technologies for future genomics research. Trends Biotechnol 26: 602â611.
Gupta P & Lee K (2007) Genomics and proteomics in process development: opportunities and challenges. Trends Biotechnol 25: 324â330.
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.
Hartmann M , Roeraade J , Stoll D , Templin M & Joos T (2008) Protein microarrays for diagnostic assays. Anal Bioanal Chem 393: 1407â1416.
HerrgÃ¥rd 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: 1155â1160.
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: 281â290.
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: 141â152.
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.
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: 105â111.
Johnson D , Li W , Gordon D et al. (2008) Systematic evaluation of variability in ChIP-chip experiments using predefined DNA targets. Genome Res 18: 393â403.
Josic D & Kovac S (2008) Application of proteomics in biotechnology â microbial proteomics. Biotechnol J 3: 496â509.
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: 217â224.
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: 326â332.
Kawasaki E (2006) The end of the microarray Tower of Babel: will universal standards lead the way? J Biomol Tech 17: 200â206.
Khan SU & Schroder M (2008) Engineering of chaperone systems and of the unfolded protein response. Cytotechnology 57: 207â231.
Kim T , Sohn S , Kim H & Lee S (2008) Strategies for systems-level metabolic engineering. Biotechnol J 3: 612â623.
Kim Y , Nandakumar M & Marten M (2007) Proteome map of Aspergillus nidulans during osmoadaptation. Fungal Genet Biol 44: 886â895.
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: 499â505.
Kobi D , Zugmeyer S , Potier S & Jaquet-Gutfreund L (2004) Two-dimensional protein map of an âaleâ-brewing yeast strain: proteome dynamics during fermentation. FEMS Yeast Res 5: 213â230.
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.
Korke R , Rink A , Seow T , Chung M , Beattie C & Hu W (2002) Genomic and proteomic perspectives in cell culture engineering. J Biotechnol 94: 73â92.
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: 3â22.
Lee P & Lee K (2005) Engineering HlyA hypersecretion in Escherichia coli based on proteomic and microarray analyses. Biotechnol Bioeng 89: 195â205.
Lee S , Lee D & Kim T (2005) Systems biotechnology for strain improvement. Trends Biotechnol 23: 349â358.
Le Novère N , Finney A , Hucka M et al. (2005) Minimum information requested in the annotation of biochemical models (MIRIAM). Nat Biotechnol 23: 1509â1515.
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: 438â445.
Mardis E (2008) The impact of next-generation sequencing technology on genetics. Trends Genet 24: 133â141.
Mattanovich D & Borth N (2006) Applications of cell sorting in biotechnology. Microb Cell Fact 5: 12.
Mattanovich D , Gasser B , Hohenblum H & Sauer M (2004) Stress in recombinant protein producing yeasts. J Biotechnol 113: 121â135.
Mukhopadhyay A , Redding A , Rutherford B & Keasling J (2008) Importance of systems biology in engineering microbes for biofuel production. Curr Opin Biotech 19: 228â234.
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: 47â53.
Nesvizhskii A , Vitek O & Aebersold R (2007) Analysis and validation of proteomic data generated by tandem mass spectrometry. Nat Meth 4: 787â797.
Nevoigt E (2008) Progress in metabolic engineering of Saccharomyces cerevisiae. Microbiol Mol Biol R 72: 379â412.
Nielsen J & Jewett M (2008) Impact of systems biology on metabolic engineering of Saccharomyces cerevisiae. FEMS Yeast Res 8: 122â131.
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.
Ostergaard S , Olsson L & Nielsen J (2000) Metabolic engineering of Saccharomyces cerevisiae. Microbiol Mol Biol R 64: 34â50.
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: 567â579.
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: 7759â7766.
Pizarro F , Vargas F & Agosin E (2007) A systems biology perspective of wine fermentations. Yeast 24: 977â991.
Porro D , Sauer M , Branduardi P & Mattanovich D (2005) Recombinant protein production in yeasts. Mol Biotechnol 31: 245â259.
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: 587â601.
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 3â²-UTR elements. Process Biochem 43: 1153â1157.
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.
Schlitt T & Brazma A (2005) Modelling gene networks at different organisational levels. FEBS Lett 579: 1859â1866.
Seth G , Ozturk M & Hu W (2006) Reverting cholesterol auxotrophy of NS0 cells by altering epigenetic gene silencing. Biotechnol Bioeng 93: 820â827.
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: 557â564.
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: 321â330.
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: 2737â2747.
Smith D , Quinlan A , Peckham H et al. (2008) Rapid whole-genome mutational profiling using next-generation sequencing technologies. Genome Res 18: 1638â1642.
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: 2462â2470.
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: 281â290.
Sonderegger M & Sauer U (2003) Evolutionary engineering of Saccharomyces cerevisiae for anaerobic growth on xylose. Appl Environ Microb 69: 1990â1998.
Steuer R (2007) Computational approaches to the topology, stability and dynamics of metabolic networks. Phytochemistry 68: 2139â2151.
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: 5100â5112.
Takors R , Bathe B , Rieping M , Hans S , Kelle R & Huthmacher K (2007) Systems biology for industrial strains and fermentation processes â example: amino acids. J Biotechnol 129: 181â190.
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: 924â937.
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: 243â253.
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: 381â392.
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.
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: 17â27.
Westerhoff H & Palsson B (2004) The evolution of molecular biology into systems biology. Nat Biotechnol 22: 1249â1252.
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: 350â361.
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: 1186â1204.