Abstract
Protein leakage is induced in well-mixed fed-batch bioreactor by comparison with cultures carried out in scale-down conditions. This effect is attributed to a progressive increase of cell membrane permeability and the synthesis of several outer-membrane components allowing to cope with substrate limitation commonly found in high cell density culture. A comparative analysis of protein leakage has thus been performed in well-mixed bioreactors and in scale-down devices. The extracellular proteome of E.coli has been investigated by 2D-gel electrophoresis and identified by subsequent MALDI-TOF analysis. On 110 picked spots, 67 proteins have been identified and the sub-localisation and the molecular function of these proteins have been determined. A majority of the extracellular proteome was composed of outer-membrane and periplasmic proteins (64 %) confirming the fact that leakage is involved in high cell density cultures. About 50 % of this extracellular proteome was composed of transport and binding proteins. Furthermore, the more abundant spots on the gel corresponded to porin proteins and periplasmic transporters. In particular, the OmpC porin was found to be very abundant. Moreover, the scale-down effect on this extracellular proteome has been investigated by two-dimensional differential in-gel electrophoresis analysis (2D-DIGE), and significant differences have been observed by comparison with culture carried out in well-mixed systems. Indeed, since substrate limitation signal is alleviated in this kind of apparatus, cell permeability was lowered as shown by flow cytometry. In scale-down conditions, protein leakage was thus less abundant.
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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 (2001) Physiological responses to mixing in large scale bioreactors. J Biotechnol 85:175–185
Lapin A, Schmid J, Reuss M (2006) Modeling the dynamics of E. coli populations in the three-dimensional turbulent field of a stirred bioreactor—a structured-segregated approach. Chem Eng Sci 61:4783–4797
Delvigne F, Destain J, Thonart P (2006) Towards a stochastic formulation of the microbial growth in relation with the bioreactor performances: case study of an E. coli fed-batch process. Biotechnol Prog 22(4):1114–1124
Lapin A, Müller D, Reuss M (2004) Dynamic behavior of microbial populations in stirred bioreactors simulated with Euler-Lagrange methods: traveling along the lifelines of single cells. Ind Eng Chem Res 43:4647–4656
Neubauer P, Junne S (2010) Scale-down simulators for metabolic analysis of large-scale bioprocesses. Curr Opin Biotechnol 21:114–121
Eiteman MA, Altman E (2006) Overcoming acetate in Escherichia coli recombinant protein fermentations. Trends Biotechnol 24(11):530–536
Xu B, Jahic M, Blomsten G, Enfors SO (1999) Glucose overflow metabolism and mixed-acid fermentation in aerobic large-scale fed-batch processes with Escherichia coli. Appl Microbiol Biotechnol 51:564–571
Booth IR (2002) Stress and the single cell: intrapopulation diversity is a mechanism to ensure survival upon exposure to stress. Int J Food Microbiol 78:19–30
Aertsen A, Michiels CW (2004) Stress and how bacteria cope with death and survival. Crit Rev Microbiol 30:263–273
Roostalu J, Joers A, Luidalepp H, Kaldalu N, Tenson T (2008) Cell division in Escherichia coli cultures monitored at single cell resolution. BMC Microbiol 8:68
Chung HJ, Bang W, Drake MA (2006) Stress response of Escherichia coli. Compr Rev Food Sci Food Saf 5:52–64
Lara AR, Galindo E, Ramirez OT, Palomares LA (2006) Living with heterogeneities in bioreactors: understanding the effects of environmental gradients on cells. Mol Biotechnol 34:355–381
Lin HY, Neubauer P (2000) Influence of controlled glucose oscillations on a fed-batch process of recombinant Escherichia coli. J Biotechnol 79:27–37
Lara AR, Leal L, Flores N, Gosset G, Bolivar F, Ramirez OT (2005) Transcriptional and metabolic response of recombinant Escherichia coli to spatial dissolved oxygen tension gradients simulated in a scale-down system. Biotechnol Bioeng 93(2):372–385
Sandoval-Basurto EA, Gosset G, Bolivar F, Ramirez OT (2004) Culture of Escherichia coli under dissolved oxygen gradients simulated in a two-compartment scale-down system: metabolic response and production of recombinant protein. Biotechnol Bioeng 89(4):453–463
George S, Larsson G, Enfors SO (1993) A scale-down two compartment reactor with controlled substrate oscillations: metabolic response of Saccharomyces cerevisiae. Bioprocess Eng 9:249–257
Neubauer P, Häggström L, Enfors SO (1995) Influence of substrate oscillations on acetate formation and growth yield in Escherichia coli glucose limited fed-batch cultivations. Biotechnol Bioeng 47:139–146
Delvigne F, Brognaux A, Gorret N, Neubauer P, Delafosse A, Collignon ML, Toye D, Crine M, Thonart P (2011) Characterization of the response of GFP microbial biosensors sensitive to substrate limitation in scale-down bioreactors. Biochem Eng J 55:131–139
Delvigne F, Brognaux A, Francis F, Twizere JC, Gorret N, Sorensen SJ, Thonart P (2011) Green fluorescent protein (GFP) leakage from microbial biosensors provides useful information for the evaluation of the scale-down effect. Biotechnol J 6(8):968–978
Zaslaver A, Bren A, Ronen M, Itzkovitz S, Kikoin I, Shavit S, Liebermeister W, Surette MG, Alon U (2006) A comprehensive library of fluorescent transcriptional reporters for Escherichia coli. Nat Methods 3(8):623–628
Xia XX, Han MJ, Lee SY, Yoo JS (2008) Comparison of the extracellular proteomes of Eschercihia coli B and K-12 strains during high cell density cultivation. Proteomics 8:2089–2103
Rinas U, Hoffmann F (2004) Selective leakage of host-cell proteins during high-cell-density cultivation of recombinant and non-recombinant Escherichia coli. Biotechnol Prog 20:679–687
Song S, Kumar A, Saleh M (2009) Bioinformatics comparison of bacterial secretomes. Genomics Proteomics Bioinformatics 7:37–46
Hewitt CJ, Nienow AW (2007) The scale-up of microbial batch and fed-batch fermentation processes. Adv Appl Microbiol 62:105–135
Hewitt CJ, Nebe-Von Caron G, Axelsson B, Mc Farlane CM, Nienow AW (2000) 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 70(4):381–390
Nandakumar MP, Cheung A, Marten MR (2006) Proteomic analysis of extracellular proteins from Eschercihia coli W3110. J Proteome Res 5:1155–1161
Bäcklund E, Reeks D, Markland K, Weir N, Bowering L, Larsson G (2008) Fedbatch design for periplasmic product retention in Escherichia coli. J Biotechnol 135:358–365
Tsien RY (1998) The green fluorescent protein. Annual Rev Biochem 67:509–544
Castan A, Heidrich J, Enfors SO (2002) The use of flow cytometry to detect nucleic acid attached to the surface of Escherichia coli in high cell density fed-batch processes. Biotechnol Lett 24:219–224
Wick L, Quadroni M, Egli T (2001) Short- and long-term changes in proteome composition and kinetic properties in a culture of Escherichia coli during transition from glucose-excess to glucose limited growth conditions in continuous culture and vice versa. Environ Microbiol 3(9):588–599
Shokri A, Larsson G (2004) Characterisation of the Escherichia coli membrane structure and function during fedbatch cultivation. Microb Cell Fact 3:1–12
Shokri A, Sandén AM, Larsson G (2002) Growth rate-dependent changes in Escherichia coli membrane structure and protein leakage. Appl Microbiol Biotechnol 58:386–392
Davey HM, Hexley P (2011) Red but not dead ? Membranes of stressed Saccharomyces cerevisiae are permeable to propidium iodide. Environ Microbiol 13(1):163–171
Davey HM (2011) Life, death, and in-between: meaning and methods in microbiology. Appl Environ Microbiol 77(16):5571–5576
Egli T (2011) How to live at very low substrate concentrations. Water Res 44:4826–4837
Morchain J., Gabelle JC, Cockx A. (2013) A coupled population balance model and CFD approach for the simulation of mixing issues in lab-scale and industrial bioreactors. AIChE Journal in press
Nebe-von-Caron G, Stephens PJ, Hewitt CJ, Powell JR, Badley RA (2000) Analysis of bacterial function by multi-colour fluorescence flow cytometry and single cell sorting. J Microbiol Methods 42:97–114
Chen YC, Chen LA, Chen SJ, Chang MC, Chang MC, Chen TL (2004) A modified osmotic shock for periplasmic release of recombinant creatinase from Escherichia coli. Biochem Eng J 19:211–215
Vaara M (1992) Agents that increase the permeability of the outer membrane. Micrbiol Rev 56(3):395–411
Han L, Enfors SO, Häggström L (2003) Escherichia coli high-cell-density culture: carbon mass balances and release of outer membrane components. Bioprocess Biosyst Eng 25(4):205–212
Ferenci T (2001) Hungry bacteria—definition and properties of a nutritional state. Environ Microbiol 3(10):605–611
Ferenci T (1996) Adaptation to life at micromolar nutrient levels: the regulation of Escherichia coli glucose transport by endoinduction and cAMP. FEMS Microbiol Rev 18:301–317
Ferenci T (1999) Regulation by nutrient limitation. Curr Opin Microbiol 2:208–213
Liu X, Ferenci T (1998) Regulation of porin-mediated outer membrane permeability by nutrient limitation in Escherichia coli. J Bacteriol 180(5):3917–3922
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AB is recipient of a PhD FRIA grant provided by the Belgian Fund for Scientific Research (FRS-FNRS).
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Brognaux, A., Francis, F., Twizere, JC. et al. Scale-down effect on the extracellular proteome of Escherichia coli: correlation with membrane permeability and modulation according to substrate heterogeneities. Bioprocess Biosyst Eng 37, 1469–1485 (2014). https://doi.org/10.1007/s00449-013-1119-8
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DOI: https://doi.org/10.1007/s00449-013-1119-8