Real-time monitoring of metabolic shift and transcriptional induction of yciG::luxCDABE E. coli reporter strain to a glucose pulse of different concentrations
Delvigne, Frank ; Université de Liège - ULiège > Chimie et bio-industries > Bio-industries
Uribellarea, Jean-Louis; INSA Toulouse
Molina-Jouve, Carole; INSA Toulouse
Language :
English
Title :
Real-time monitoring of metabolic shift and transcriptional induction of yciG::luxCDABE E. coli reporter strain to a glucose pulse of different concentrations
Al-Homoud A., Hondzo M., LaPara T. Fluid dynamics impact on bacterial physiology: biochemical oxygen demand. J. Environ. Eng.: ASCE 2007, 133:226-236.
Bearson S., Bearson B., Foster J.W. Acid stress responses in Enterobacteria. FEMS Microbiol. Lett. 1997, 147:173-180.
Bechor O., Smulski D.R., Van Dyk T.K., LaRossa R.A., Belkin S. Recombinant microorganisms as environmental biosensors: pollutants detection by Escherichia coli bearing fabA: lux fusions. J. Biotechnol. 2002, 94:125-132.
Belkin S. A panel of stress-responsive luminous bacteria for monitoring wastewater toxicity. Methods in Molecular Biology: Bioluminescence Methods and Protocols 1998, pp. 247-258.
Bendriaa L., Picart P., Daniel P., Horry H., Durand M.J., Thouand G. Versatile device for on-line and in situ measurement of growth and light production of bioluminescent cells. Sens. Actuators B: Chem. 2004, 103:115-121.
Buchholz A., Hurlebaus J., Wandrey C., Takors R. Metabolomics: quantification of intracellular metabolite dynamics. Biomol. Eng 2002, 19:5-15.
Burton N.A., Johnson M.D., Antczak P., Robinson A., Lund P.A. Novel aspects of the acid response network of E. coli K-12 are revealed by a study of transcriptional dynamics. J. Mol. Biol. 2010, 401:726-742.
Christensen L.H., Schulze U., Nielsen J., Villadsen J. Acoustic off-gas analyzer for bioreactors - precision, accuracy and dynamics of detection. Chem. Eng. Sci. 1995, 50:2601-2610.
Clark B., Holms W.H. Control of sequential utilization of glucose and fructose by Escherichia coli. J. Gen. Microbiol. 1976, 95:191-201.
de Jong H., Ranquet C., Ropers D., Pinel C., Geiselmann J. Experimental and computational validation of models of fluorescent and luminescent reporter genes in bacteria. BMC Syst. Biol. 2010, 4.
De Mey M., Taymaz-Nikerel H., Baart G., Waegeman H., Maertens J., Heijnen J.J., van Gulik W.M. Catching prompt metabolite dynamics in Escherichia coli with the BioScope at oxygen rich conditions. Metab. Eng. 2010, 12:477-487.
Delafosse A., Delvigne F., Collignon M.L., Crine M., Thonart P., Toye D. Development of a compartment model based on CFD simulations for description of mixing in bioreactors. Biotechnol. Agron. Soc. 2010, 14:517-522.
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.
Delvigne F., Destain J., Thonart P. Bioreactor hydrodynamic effect on Escherichia coli physiology: experimental results and stochastic simulations. Bioprocess Biosyst. Eng. 2005, 28:131-137.
Delvigne F., Destain J., Thonart P. Structured mixing model for stirred bioreactors: an extension to the stochastic approach. Chem. Eng. J. 2005, 113:1-12.
Delvigne F., Destain J., Thonart P. Elaboration of a biased random walk model with a high spatial resolution for the simulation of the microorganisms exposure to gradient stress in scale-down reactors. Biochem. Eng. J. 2008, 39:105-114.
Delvigne F., Lejeune A., Destain J., Thonart P. Modelling of the substrate heterogeneities experienced by a limited microbial population in scale-down and in large-scale bioreactors. Chem. Eng. J. 2006, 120:157-167.
Delvigne F., Lejeune A., Destain J., Thonart P. Stochastic models to study the impact of mixing on a fed-batch culture of Saccharomyces cerevisiae. Biotechnol. Prog. 2006, 22:259-269.
Douma R.D., Verheijen P.J.T., de Laat W., Heijnen J.J., van Gulik W.M. Dynamic gene expression regulation model for growth and penicillin production in Penicillium chrysogenum. Biotechnol. Bioeng. 2010, 106:608-618.
Elsemore D.A. Insertion of promoter region: luxCDABE fusions into the Escherichia coli chromosome. Methods in Molecular Biology: Bioluminescence Methods and Protocols 1998, pp. 97-104.
Enfors S.-O., 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., Trägårdh C., Fuchs L., Revstedt J., Friberg P.C., Hjertager B., Blomsten G., Skogman H., Hjort S., Hoeks F., Lin H.-Y., 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.
Galluzzi L., Karp M. Intracellular redox equilibrium and growth phase affect the performance of luciferase-based biosensors. J. Biotechnol. 2007, 127:188-198.
Gil G.C., Mitchell R.J., Chang S.T., Gu M.B. A biosensor for the detection of gas toxicity using a recombinant bioluminescent bacterium. Biosens. Bioelectron. 2000, 15:23-30.
Gu M.B., Dhurjati P.S., VanDyk T.K., LaRossa R.A. A miniature bioreactor for sensing toxicity using recombinant bioluminescent Escherichia coli cells. Biotechnol. Prog. 1996, 12:393-397.
Guillard F., Tragardh C. Modeling of the performance of industrial bioreactors with a dynamic microenvironmental approach: a critical review. Chem. Eng. Technol. 1999, 22:187-195.
Hakkila K., Maksimow M., Karp M., Virta M. Reporter genes lucFF, luxCDABE, gfp, and dsred have different characteristics in whole-cell bacterial sensors. Anal. Biochem. 2002, 301:235-242.
Hautefort I., Hinton J.C.D. Measurement of bacterial gene expression in vivo. Philos. Trans. R. Soc. Lond. B: Biol. Sci. 2000, 355:601-611.
Heitzer A., Applegate B., Kehrmeyer S., Pinkart H., Webb O.F., Phelps T.J., White D.C., Sayler G.S. Physiological considerations of environmental applications of lux reporter fusions. J. Microbiol. Methods 1998, 33:45-57.
Hengge-Aronis R. Signal transduction and regulatory mechanisms involved in control of the sigma(S) (RpoS) subunit of RNA polymerase. Microbiol. Mol. Biol. Rev. 2002, 66:373.
Hengge R. The two-component network and the general stress sigma factor RpoS (sigma(S)) in Escherichia coli. Bacterial Signal Transduction: Networks and Drug Targets 2008, Springer, New York, pp. 40-53.
Hewitt C.J., Nebe-Von Caron G., Axelsson B., McFarlane C.M., Nienow A.W. 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.
Hoque M.A., Ushiyama H., Tomita M., Shimizu K. Dynamic responses of the intracellular metabolite concentrations of the wild type and pykA mutant Escherichia coli against pulse addition of glucose or NH 3 under those limiting continuous cultures. Biochem. Eng. J. 2005, 26:38-49.
Ivask A., Rolova T., Kahru A. A suite of recombinant luminescent bacterial strains for the quantification of bioavailable heavy metals and toxicity testing. BMC Biotechnol. 2009, 9.
Jahreis K., Bentler L., Bockmann J., Hans S., Meyer A., Siepelmeyer J., Lengeler J.W. Adaptation of sucrose metabolism in the Escherichia coli wild-type strain EC3132. J. Bacteriol. 2002, 184:5307-5316.
Kelly C.J., Bienkowski P.R., Sayler G.S. Kinetic analysis of a tod-lux bacterial reporter for toluene degradation and trichloroethylene cometabolism. Biotechnol. Bioeng. 2000, 69:256-265.
Kelly C.J., Hsiung C.J., Lajoie C.A. Kinetic analysis of bacterial bioluminescence. Biotechnol. Bioeng. 2003, 81:370-378.
Kim B.C., Gu M.B. Expression analysis of stress-specific responsive genes in two-stage continuous cultures of Escherichia coli using cDNA microarray and real-time RT-PCR analysis. Enzyme Microb. Technol. 2006, 39:440-446.
Koga K., Harada T., Shimizu H., Tanaka K. Bacterial luciferase activity and the intracellular redox pool in Escherichia coli. Mol. Genet. Genomics 2005, 274:180-188.
Lange R., Henggearonis R. The cellular concentration of the sigma(S) subunit of RNA-polymerase in Escherichia coli is controlled at the levels of transcription translation, and protein stability. Genes Dev. 1994, 8:1600-1612.
Lapin A., Muller D., Reuss M. Dynamic behavior of microbial populations in stirred bioreactors simulated with Euler-Lagrange methods: traveling along the lifelines of single cells. Ind. Eng. Chem. Res. 2004, 43:4647-4656.
Lapin A., Schmid J., Reuss M. Modeling the dynamics of E. coli populations in the three-dimensional turbulent field of a stirred-tank bioreactor - a structured-segregated approach. Chem. Eng. Sci. 2006, 61:4783-4797.
Lara A.R., Galindo E., Ramirez O.T., Palomares L.A. Living with heterogeneities in bioreactors. Mol. Biotechnol. 2006, 34:355-381.
Lara A.R., Leal L., Flores N., Gosset G., Bolivar F., Ramirez O.T. Transcriptional and metabolic response of recombinant Escherichia coli to spatial dissolved oxygen tension gradients simulated in a scale-down system. Biotechnol. Bioeng. 2006, 93:372-385.
Lara A.R., Taymaz-Nikerel H., Mashego M.R., van Gulik W.M., Heijnen J.J., Ramirez O.T., van Winden W.A. Fast dynamic response of the fermentative metabolism of Escherichia coli to aerobic and anaerobic glucose pulses. Biotechnol. Bioeng. 2009, 104:1153-1161.
Larossa R., Van Dyk T. Application of stress responses for environmental monitoring and molecular toxicology. Bacterial Stress Responses 2000, pp. 453-468.
Larsson G., Tornkvist M., Wernersson E.S., Tragardh C., Noorman H., Enfors S.O. Substrate gradients in bioreactors: origin and consequences. Bioprocess Eng. 1996, 14:281-289.
Lee J.W., Choi S., Park J.H., Vickers C.E., Nielsen L.K., Lee S.Y. Development of sucrose-utilizing Escherichia coli K-12 strain by cloning beta-fructofuranosidases and its application for l-threonine production. Appl. Microbiol. Biotechnol. 2010, 88:905-913.
Lemuth K., Hardiman T., Winter S., Pfeiffer D., Keller M.A., Lange S., Reuss M., Schmid R.D., Siemann-Herzberg M. Global transcription and metabolic flux analysis of Escherichia coli in glucose-limited fed-batch cultivations. Appl. Environ. Microbiol. 2008, 74:7002-7015.
Loewen P.C., Hu B., Strutinsky J., Sparling R. Regulation in the rpoS regulon of Escherichia coli. Can. J. Microbiol. 1998, 44:707-717.
Marincs F. On-line monitoring of growth of Escherichia coli in batch cultures by bioluminescence. Appl. Microbiol. Biotechnol. 2000, 53:536-541.
Meighen E.A. Bacterial bioluminescence - organization, regulation, and application of the lux genes. FASEB J. 1993, 7:1016-1022.
Meighen E.A., Dunlap P.V. Physiological, biochemical and genetic-control of bacterial bioluminescence. Advances in Microbial Physiology 1993, vol. 34. Academic Press Ltd., London, pp. 1-67.
Monod J. Recherches sur la croissance des cultures bactériennes 1942, Hermann and Cie ed, Paris.
Neidhardt F.C. Multigene systems and regulons. Escherichia coli and Salmonella typhimurium: Cellular and Molecular Biology 1987, 1313-1317. American Society for Microbiology, Washington, DC. F.C. Neidhardt (Ed.).
Notley L., Ferenci T. Induction of RpoS-dependent functions in glucose-limited continuous culture: what level of nutrient limitation induces the stationary phase of Escherichia coli?. J. Bacteriol. 1996, 178:1465-1468.
Poilpre E., Tronquit D., Goma G., Guillou V. On-line estimation of biomass concentration during transient growth on yeast chemostat culture using light reflectance. Biotechnol. Lett. 2002, 24:2075-2081.
Postma P.W., Lengeler J.W., Jacobson G.R. Phosphoenolpyruvate - carbohydrate phosphotransferase systems of bacteria. Microbiol. Rev. 1993, 57:543-594.
Roels J.A. Energetics and Kinetics in Biotechnology 1983, Elsevier Biomedical Press BV, Amsterdam, New York, Oxford.
Roustan, M., Pharamond, J.C., Line, A., 1999. Agitation Mélange Concepts théoriques de base. Technique-Ingénieur.
Rupani S.P., Gu M.R., Konstantinov K.B., Dhurjati P.S., VanDyk T.K., LaRossa R.A. Characterization of the stress response of a bioluminescent biological sensor in batch and continuous cultures. Biotechnol. Prog. 1996, 12:387-392.
Scheerer S., Gomez F., Lloyd D. Bioluminescence of Vibrio fischeri in continuous culture: optimal conditions for stability and intensity of photoemission. J. Microbiol. Methods 2006, 67:321-329.
Schmalzriedt S., Jenne M., Mauch K., Reuss M. Integration of physiology and fluid dynamics. Process Integration Biochem. Eng. 2003, 80:19-68.
Taymaz-Nikerel H., Van Gulik W.M., Heijnen J.J. Escherichia coli responds with a rapid and large change in growth rate upon a shift from glucose-limited to glucose-excess conditions. Metab. Eng. 2011, 13:307-318.
Teich A., Meyer S., Lin H.Y., Andersson L., Enfors S.O., 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.
Trezzani I., Nadri M., Dorel C., Lejeune P., Bellalou J., Lieto J., Hammouri H., Longin R., Dhurjati P. Monitoring of recombinant protein production using bioluminescence in a semiautomated fermentation process. Biotechnol. Prog. 2003, 19:1377-1382.
Ulitzur S., Reinhertz A., Hastings J.W. Factors affecting the cellular expression of bacterial luciferase. Arch. Microbiol. 1981, 129:67-71.
Van Dyk T.K., Ayers B.L., Morgan R.W., Larossa R.A. Constricted flux through the branched-chain amino acid biosynthetic enzyme acetolactate synthase triggers elevated expression of genes regulated by rpoS and internal acidification. J. Bacteriol. 1998, 180:785-792.
Van Dyk T.K., Reed T.R., Vollmer A.C., Larossa R.A. Synergistic induction of the heat shock response in Escherichia coli by simultaneous treatment with chemical inducers. J. Bacteriol. 1995, 177:6001-6004.
Van Dyk T.K., Rosson R.A. Photorhabdus luminescens luxCDABE promoter probe vectors. Methods in Molecular Biology: Bioluminescence Methods and Protocols 1998, pp. 85-95.
Van Dyk T.K., Wei Y., Hanafey M.K., Dolan M., Reeve M.J.G., Rafalski J.A., Rothman-Denes L.B., LaRossa R.A. A genomic approach to gene fusion technology. Proc. Natl. Acad. Sci. U.S.A. 2001, 98:2555-2560.
Vollmer A.C., Van Dyk T.K. Stress responsive bacteria: biosensors as environmental monitors. Adv. Microb. Physiol. 2004, 49:131-174.
Vrabel P., van der Lans R., van der Schot F.N., Luyben K., Xu B., Enfors S.O. CMA: integration of fluid dynamics and microbial kinetics in modelling of large-scale fermentations. Chem. Eng. J. 2001, 84:463-474.
Weber J., Kayser A., Rinas U. Metabolic flux analysis of Escherichia coli in glucose-limited continuous culture. II. Dynamic response to famine and feast activation of the methylglyoxal pathway and oscillatory behaviour. Microbiology (UK) 2005, 151:707-716.
Weitz H.J., Ritchie J.M., Bailey D.A., Horsburgh A.M., Killham K., Glover L.A. Construction of a modified mini-Tn5 luxCDABE transposon for the development of bacterial biosensors for ecotoxicity testing. FEMS Microbiol. Lett. 2001, 197:159-165.
Wick L., Egli T. Molecular components of physiological stress responses in Escherichia coli. Physiological Stress Responses in Bioprocesses 2004, Springer, Berlin/Heidelberg, p. 1.
Yagur-Kroll S., Bilic B., Belkin S. Strategies for enhancing bioluminescent bacterial sensor performance by promoter region manipulation. Microb. Biotechnol. 2010, 3:300-310.
Zahradnik J., Mann R., Fialova M., Vlaev D., Vlaev S.D., Lossev V., Seichter P. A networks-of-zones analysis of mixing and mass transfer in three industrial bioreactors. Chem. Eng. Sci. 2001, 56:485-492.
Zanzotto A., Boccazzi P., Gorret N., Van Dyk T.K., Sinskey A.J., Jensen K.F. In situ measurement of bioluminescence and fluorescence in an integrated microbioreactor. Biotechnol. Bioeng. 2006, 93:40-47.
Zgurskaya H.I., Keyhan M., Matin A. The sigma(s) level in starving Escherichia coli cells increases solely as a result of its increased stability, despite decreased synthesis. Mol. Microbiol. 1997, 24:643-651.
