microbial stress; scale-up; scale-down; fluorescent reporter; protein leakage
Abstract :
[en] Substrate limitation responsive biosensors have been used for the development of a mini-bioreactor platform that can be used as a scale-down tool. Three green fluorescent protein (GFP) transcriptional reporters have been chosen in Escherichia coli, i.e., uspA::gfp, csiE::gfp and yciG::gfp. Our previous studies have shown that these kinds of promoters are induced in response to substrate limitation and are significantly repressed when cultures are carried out in heterogeneous bioreactors. This sensitivity to substrate limitation has been confirmed in the case of the csiE and yciG biosensors. A mini-scale-down platform is proposed as a high throughput tool to rapidly investigate the usefulness of a given microbial biosensor. This platform is composed of shake flasks able to operate in fed-batch mode either using the slow release or the intermittent feeding principle. Local heterogeneities were reproduced at the level of these mini-bioreactors (operating under the intermittent feeding principle) and caused a decrease in GFP expression as in conventional scale-down reactors. The presence of GFP in supernatants was also noted and seems to be correlated with the substrate limitation signal for the three cultivation systems considered in this work (i.e., chemostat, conventional and mini-bioreactors) and with membrane permeability.
Disciplines :
Biotechnology
Author, co-author :
Brognaux, Alison ; Université de Liège - ULiège > Département des sciences de la vie > Biochimie et microbiologie industrielles
Neubauer, Peter
Twizere, Jean-Claude ; Université de Liège - ULiège > Chimie et bio-industries > Biologie cell. et moléc.
Francis, Frédéric ; Université de Liège - ULiège > Sciences agronomiques > Entomologie fonctionnelle et évolutive
Gorret, Nathalie
Thonart, Philippe ; Université de Liège - ULiège > Département des sciences de la vie > Biochimie et microbiologie industrielles
Delvigne, Frank ; Université de Liège - ULiège > Chimie et bio-industries > Bio-industries
Language :
English
Title :
Direct and indirect use of GFP whole cell biosensors for the assessment of bioprocess performances: design of milliliter scale-down bioreactors
Publication date :
2013
Journal title :
Biotechnology Progress
ISSN :
8756-7938
eISSN :
1520-6033
Publisher :
American Chemical Society
Volume :
29
Issue :
1
Pages :
48-59
Peer reviewed :
Peer Reviewed verified by ORBi
Funders :
FRIA - Fonds pour la Formation à la Recherche dans l'Industrie et dans l'Agriculture [BE]
Betts JI, Baganz F. Miniature bioreactors: Current practices and future opportunities. Microb Cell Fact. 2006; 5: 21.
Kunze M, Huber R, Gutjahr C, Müllner S, Büch J. Predictive tool for recombinant protein production in Escherichia coli shake-flask cultures using an on-line monitoring system. Biotechnol Prog. 2011; 28: 103-113.
Cyril PP, Suzuki Y, Rachinskiy K, Lotter S, Büchs J. Volumetric power consumption in baffled shake flasks. Chem Eng Sci. 2006; 61: 3771-3779.
Lotter S, Büchs J. Utilization of specific power input measurements for optimization of culture conditions in shaking flasks. Biochem Eng J. 2004; 17: 195-203.
Seletzky JM, Noak U, Fricke J, Welk E, Eberhard W, Knocke C, Büchs J. Scale-up from shake flasks to fermenters in batch and continuous mode with Corynebacterium glutamicum on lactic acid based on oxygen transfer and pH. Biotechnol Bioeng. 2007; 98: 800-811.
Takors R. Scale-up of microbial processes: Impacts, tools and open questions. J Biotechnol. 2012; 160: 3-9.
Patnaik PR. Can imperfections help to improve bioreactor performance? Trends Biotechnol. 2002; 20: 135-137.
Patnaik PR. External, extrinsic and intrinsic noise in cellular systems: Analogies and implications for protein synthesis. Biotechnol Mol Biol Rev. 2006; 1: 121-127.
Enfors SO, Jahic M, Rozkov A, Xu B, Hecker M, Jürgen B, Krüger E, Schweder T, Hamer G, O'Beirne D, Noisommit-Rizzi N, Reuss M, Boone L, Hewitt C, McFarlane C, Nienow A, Kovacs T, Trägardh C, Fuchs L, Revstedt J, Friberg PC, Hjertager B, Blomsten G, Skogman H, Hjort S, Hoeks F, Lin HY, Neubauer P, van der Lans R, Luyben K, Vrabel P, Manelius A. Physiological responses to mixing in large scale bioreactors. J Biotechnol. 2001; 85: 175-185.
Hewitt CJ, Nienow AW. The scale-up of microbial batch and fed-batch fermentation processes. Adv Appl Microbiol. 2007; 62: 105-135.
Lencastre Fernandes RM, Nierychlo L, Lundin AE, Pedersen PE, PuentesTellez A, Dutta M, Carlquist A, Bolic D, Schäpper AC, Brunetti S, Helmark AL, Heins AD, Jensen I, Nopens K, Rottwitt N, Szita JD, van Elsas PH, Nielsen J, Martinussen SJ, Sørensen AE, Lantz KV, Gernaey. Experimental methods and modeling techniques for description of cell population heterogeneity. Biotechnol Adv. 2011; 29: 575-599.
Krause M, Ukkonen K, Haataja T, Ruottinen M, Glumoff T, Neubauer A, Neubauer P, Vasala A. A novel fed-batch based cultivation method provides high cell-density and improves yield of soluble recombinant proteins in shaken cultures. Microb Cell Fact. 2010; 9: 11.
Weuster-Botz D, Altenbach-Rhem J, Arnold M. Parallel substrate feeding and pH control in shaking flasks. Biochem Eng J. 2001; 7: 163-170.
Delvigne F, Ingels S, Thonart P. Evaluation of a set of E. coli reporter strains as physiological tracer for estimating bioreactor hydrodynamic efficiency. Process Biochem. 2010; 45: 1769-1778.
Delvigne F, Brognaux A, Gorret N, Neubauer P, Delafosse A, Collignon ML, Toye D, Crine M, Thonart P. Characterization of the response of GFP microbial biosensors sensitive to substrate limitation in scale-down bioreactors. Biochem Eng J. 2011; 55: 131-139.
Delvigne F, Boxus M, Ingels S, Thonart P. Bioreactor mixing efficiency modulates the activity of a prpoS::GFP reporter gene in E. coli. Microb Cell Fact. 2009; 8: 15.
Delvigne F, Brognaux A, Francis F, Twizere JC, Gorret N, Sorensen S.J, Thonart P. Green fluorescent protein (GFP) leakage from microbial biosensors provides useful information for the estimation of the scale-down effect. Biotechnol J. 2011; 6: 968-978.
Zaslaver A, Bren A, Ronen M, Itzkovitz S, Kikoin I, Shavit S, Liebermeister W, Surette MG, Alon U. A comprehensive library of fluorescent transcriptional reporters for Escherichia coli. Nat Methods. 2006; 3: 623-628.
Dremel LSY, Schmid RD. On-line determination of glucose and lactate concentrations in animal cell culture based on fibre optic detection of oxygen in flow-detection. Biosens Bioelectron. 1992; 7: 133-139.
Lara AR, Galindo E, Ramirez OT, Palomares L.A. Living with heterogeneities in bioreactors-Understanding the effects of environmental gradients on cells. Mol Biotechnol. 2006; 34: 355-381.
Hewitt CJ, Nebe-Von Caron G, Axelsson B, Mc Farlane CM, Nienow AW. Studies related to the scale-up of high-cell-density E. coli fed-batch fermentations using multiparameter flow cytometry: effect of a changing microenvironment with respect to glucose and dissolved oxygen concentration. Biotechnol Bioeng. 2000; 70: 381-390.
John GT, Klimant I, Wittmann C, Heinzle E. Integrated optical sensing of dissolved oxygen in microtiter plates: A novel tool for microbial cultivation. Biotechnol Bioeng. 2003; 81: 830-836.
Schäpper D, Alam MN, Szita N, Lantz AE, Gernaey KV. Application of microbioreactors in fermentation process development: A review. Anal Bioanal Chem. 2009; 395: 679-695.
Panula-Perälä J, Siurkus J, Vasala A, Wilmanowski R, Casteleijn MG, Neubauer P. Enzyme controlled glucose auto-delivery for high cell density cultivations in microplates and shake flasks. Microb Cell Fact. 2008; 7: 31.
Schneider K, Schütz V, John GT, Heinzle E. Optical device for parallel online measurement of dissolved oxygen and pH in shake flask cultures. Bioprocess Biosyst Eng. 2010; 33: 541-547.
Cormack BP, Valdivia RH, Falkow R. FACS-optimized mutants of the green fluorescent protein (GFP). Gene. 1996; 173: 33-38.
Galbraith DW, Anderson MT, Herzenberg LA. Flow cytometry analysis and FACS sorting of cells based on GFP accumulation. Methods Cell Biol. 1999; 58: 315-341.
Freestone P, Nyström T, Trinei M, Norris V. The universal stress protein uspA, of Escherichia coli is phosphorylated in response to stasis. J Mol Biol. 1997; 274: 318-324.
Sorensen SJ, Burmolle M, Hansen L.H. Making bio-sense of toxicity: New developments in whole-cell biosensors. Curr Opin Biotechnol. 2006; 17: 11-16.
Sunya S, Gorret N, Delvigne F, Uribellarea JL, Jouve C. Real-time monitoring of metabolic shift and transcriptional induction of yciG::luxCDABE E. coli reporter strain to a glucose pulse of different concentrations. J Biotechnol. 2012; 157: 379-390.
Neubauer P, Junne S. Scale-down simulators for metabolic analysis of large-scale bioprocesses. Curr Opin Biotechnol. 2010; 21: 114-121.
DeLisa MP, Bentley WE. Bacterial autoinduction: Looking outside the cell for new metabolic engineering targets. Microb Cell Fact. 2002; 1: 5.
Büchs J. Introduction to advantages and problems of shaken cultures. Biochem Eng J. 2001; 7: 91-98.
Hengge-Aronis R. Recent insigths into the general stress response regulatory network in E. coli. J Mol Biol Biotechnol. 2002; 4: 341-346.
Marschall C, Hengge-Aronis R. Regulatory characteristics and pormoter analysis of csiE, a stationary phase-inducible gene under the control of sigma S and the cAMP-CRP complex in Escherichia coli. Mol Microbiol. 1995; 18: 175-184.
Ma HW, Buer J, Zeng AP. Hierarchical structure and modules in the Escherichia coli transcriptional regulatory network revealed by a new top-down approach. BMC Bioinformatics. 2004; 5: 199.
Teich A, Meyer S, Lin HY, Andersson L, Enfors SO, Neubauer P. Growth rate related concentration changes of the starvation response regulators sigma S and ppGpp in glucose-limited fed-batch and continuous cultures of Escherichia coli. Biotechnol Prog. 1999; 15: 123-129.
Funke M, Buchenauer A, Mokwa W, Kluge S, Hein L, Müller C, Kensy F, Büchs J. Bioprocess control in microscale: Scalable fermentations in disposable and user-friendly microfluidic systems. Microb Cell Fact. 2011; 9: 86.
Hewitt CJ, Nebe-Von Caron G, Nienow AW, Mc Farlane CM. The use of multi-parameter flow cytomerty to compare the physiological response of Escerichia coli W3110 to glucose limitation during batch, fed-batch and continuous culture cultivations. J Biotechnol. 1999; 75: 251-264.
Sundstrom H, Wallberg F, Ledung E, Norrman B, Hewitt CJ, Enfors SO. Segregation to non-dividing cells in recombinant Escherichia coli fed-batch fermentation processes. Biotechnol Lett. 2004; 26: 1533-1539.
Xia XX, Han MJ, Lee SY, Yoo JS. Comparison of the extracellular proteomes of Eschercihia coli B and K-12 strains during high cell density cultivation. Proteomics. 2008; 8: 2089-2103.
Castan A, Heidrich J, Enfors SO. The use of flow cytometry to detect nucleic acids attached to the surface of Escherichia coli in high cell density fed-batch processes. Biotechnol Lett. 2002; 24: 219-224.
Bäcklund E, Reeks D, Marklanda K, Weir N, Bowering L, Larsson G. Fedbatch design for periplasmic product retention in Escherichia coli. J Biotechnol. 2008; 135: 358-365.
Shokri A, Sanden AM, Larsson G. Growth rate dependent changes in Escherichia coli membrane structure and protein leakage. Appl Microbiol Biotechnol. 2002; 58: 386-392.
Shokri A, Larsson G. Characterisation of the Escherichia coli membrane structure and function during fedbatch cultivation. Microb Cell Fact. 2004; 3: 9.
