메뉴 건너뛰기




Volumn 12, Issue 6, 2017, Pages

Experimental validation of in silico estimated biomass yields of Pseudomonas putida KT2440

Author keywords

Batch cultivation process; Biomass yield; Flux balance analysis; Genome scale model; Stirred tank bioreactor

Indexed keywords

BACTERIA; BIOREACTORS; ECOLOGY; GENES; GLYCEROL; TANKS (CONTAINERS);

EID: 85018987676     PISSN: 18606768     EISSN: 18607314     Source Type: Journal    
DOI: 10.1002/biot.201600720     Document Type: Article
Times cited : (17)

References (40)
  • 1
    • 0036933705 scopus 로고    scopus 로고
    • Complete genome sequence and comparative analysis of the metabolically versatile Pseudomonas putida KT2440
    • Nelson, K. E., Weinel, C., Paulsen, I. T., Dodson, R. J. et al., Complete genome sequence and comparative analysis of the metabolically versatile Pseudomonas putida KT2440. Environ. Microbiol. 2002, 4, 799–808.
    • (2002) Environ. Microbiol. , vol.4 , pp. 799-808
    • Nelson, K.E.1    Weinel, C.2    Paulsen, I.T.3    Dodson, R.J.4
  • 2
    • 0019995020 scopus 로고
    • The metabolic versatility of pseudomonads
    • Clarke, P. H., The metabolic versatility of pseudomonads. Antonie Van Leeuwenhoek 1982, 48, 105–130.
    • (1982) Antonie Van Leeuwenhoek , vol.48 , pp. 105-130
    • Clarke, P.H.1
  • 3
    • 54449092307 scopus 로고    scopus 로고
    • A genome-scale metabolic reconstruction of Pseudomonas putida KT2440: iJN746 as a cell factory
    • Nogales, J., Palsson, B. Ø., Thiele, I., A genome-scale metabolic reconstruction of Pseudomonas putida KT2440: iJN746 as a cell factory. BMC Syst. Biol. 2008, 2, 79.
    • (2008) BMC Syst. Biol. , vol.2 , pp. 79
    • Nogales, J.1    Palsson, B.Ø.2    Thiele, I.3
  • 4
    • 84964313870 scopus 로고    scopus 로고
    • Pseudomonas 2.0: Genetic upgrading of P. putida KT2440 as an enhanced host for heterologous gene expression
    • Martínez-García E, Nikel PI, Aparicio T, de Lorenzo V. Pseudomonas 2.0: Genetic upgrading of P. putida KT2440 as an enhanced host for heterologous gene expression. Microb. Cell Fact. 2014, 13, 159.
    • (2014) Microb. Cell Fact. , vol.13 , pp. 159
    • Martínez-García, E.1    Nikel, P.I.2    Aparicio, T.3    de Lorenzo, V.4
  • 5
    • 84866172978 scopus 로고    scopus 로고
    • Enhanced Tolerance to Naphthalene and Enhanced Rhizoremediation Performance for Pseudomonas putida KT2440 via the NAH7 Catabolic Plasmid
    • Fernandez, M., Niqui-Arroyo, J. L., Conde, S., Ramos, J. L. et al., Enhanced Tolerance to Naphthalene and Enhanced Rhizoremediation Performance for Pseudomonas putida KT2440 via the NAH7 Catabolic Plasmid. Appl. Environ. Microbiol. 2012, 78, 5104–5110.
    • (2012) Appl. Environ. Microbiol. , vol.78 , pp. 5104-5110
    • Fernandez, M.1    Niqui-Arroyo, J.L.2    Conde, S.3    Ramos, J.L.4
  • 6
    • 33645791055 scopus 로고    scopus 로고
    • A Two step chemo-biotechnological conversion of polystyrene to a biodegradable thermoplastic
    • Ward, P. G., Goff, M., Donner, M., Kaminsky, W. et al., A Two step chemo-biotechnological conversion of polystyrene to a biodegradable thermoplastic. Environ. Sci. Technol. 2006, 40, 2433–2437.
    • (2006) Environ. Sci. Technol. , vol.40 , pp. 2433-2437
    • Ward, P.G.1    Goff, M.2    Donner, M.3    Kaminsky, W.4
  • 7
    • 84865167599 scopus 로고    scopus 로고
    • Production host selection for asymmetric styrene epoxidation: Escherichia coli vs. solvent-tolerant Pseudomonas
    • Kuhn, D., Bühler, B., Schmid, A., Production host selection for asymmetric styrene epoxidation: Escherichia coli vs. solvent-tolerant Pseudomonas. J. Ind. Microbiol. Biotechnol. 2012, 39, 1125–1133.
    • (2012) J. Ind. Microbiol. Biotechnol. , vol.39 , pp. 1125-1133
    • Kuhn, D.1    Bühler, B.2    Schmid, A.3
  • 8
    • 33744951971 scopus 로고    scopus 로고
    • Transcriptional tradeoff between metabolic and stress-response programs in Pseudomonas putida KT2440 Cells Exposed to Toluene
    • Dominguez-Cuevas, P., Gonzalez-Pastor, J.-E., Marques, S., Ramos, J.-L. et al., Transcriptional tradeoff between metabolic and stress-response programs in Pseudomonas putida KT2440 Cells Exposed to Toluene. J. Biol. Chem. 2006, 281, 11981–11991.
    • (2006) J. Biol. Chem. , vol.281 , pp. 11981-11991
    • Dominguez-Cuevas, P.1    Gonzalez-Pastor, J.-E.2    Marques, S.3    Ramos, J.-L.4
  • 9
    • 0346936145 scopus 로고    scopus 로고
    • Proteome reference map of Pseudomonas putida strain KT2440 for genome expression profiling: Distinct responses of KT2440 and Pseudomonas aeruginosa strain PAO1 to iron deprivation and a new form of superoxide dismutase
    • Heim, S., Ferrer, M., Heuer, H., Regenhardt, D. et al., Proteome reference map of Pseudomonas putida strain KT2440 for genome expression profiling: Distinct responses of KT2440 and Pseudomonas aeruginosa strain PA O1 to iron deprivation and a new form of superoxide dismutase. Environ. Microbiol. 2003, 5, 1257–1269.
    • (2003) Environ. Microbiol. , vol.5 , pp. 1257-1269
    • Heim, S.1    Ferrer, M.2    Heuer, H.3    Regenhardt, D.4
  • 10
    • 0041358749 scopus 로고    scopus 로고
    • Use of proteomics and physiological characteristics to elucidate ecotoxic effects of methyltert-butyl ether in Pseudomonas putida KT2440
    • Krayl, M., Benndorf, D., Loffhagen, N., Babel, W., Use of proteomics and physiological characteristics to elucidate ecotoxic effects of methyltert-butyl ether in Pseudomonas putida KT2440. Proteomics 2003, 3, 1544–1552.
    • (2003) Proteomics , vol.3 , pp. 1544-1552
    • Krayl, M.1    Benndorf, D.2    Loffhagen, N.3    Babel, W.4
  • 11
    • 34249088019 scopus 로고    scopus 로고
    • Sampling for metabolome analysis of microorganisms
    • Bolten, C. J., Kiefer, P., Letisse, F., Portais, J.-C. et al., Sampling for metabolome analysis of microorganisms. Anal. Chem. 2007, 79, 3843–3849.
    • (2007) Anal. Chem. , vol.79 , pp. 3843-3849
    • Bolten, C.J.1    Kiefer, P.2    Letisse, F.3    Portais, J.-C.4
  • 12
    • 14244256095 scopus 로고    scopus 로고
    • Experimental Identification and Quantification of Glucose Metabolism in Seven Bacterial Species
    • Fuhrer, T., Fischer, E., Sauer, U., Experimental Identification and Quantification of Glucose Metabolism in Seven Bacterial Species. J. Bacteriol. 2005, 187, 1581–1590.
    • (2005) J. Bacteriol. , vol.187 , pp. 1581-1590
    • Fuhrer, T.1    Fischer, E.2    Sauer, U.3
  • 13
    • 34548548565 scopus 로고    scopus 로고
    • Simultaneous catabolite repression between glucose and toluene metabolism in Pseudomonas putida is channeled through different signaling pathways
    • del Castillo, T., Ramos, J. L., Simultaneous catabolite repression between glucose and toluene metabolism in Pseudomonas putida is channeled through different signaling pathways. J. Bacteriol. 2007, 189, 6602–6610.
    • (2007) J. Bacteriol. , vol.189 , pp. 6602-6610
    • del Castillo, T.1    Ramos, J.L.2
  • 14
    • 52449130902 scopus 로고    scopus 로고
    • Metabolic response of Pseudomonas putida during redox biocatalysis in the presence of a second octanol phase
    • Blank, L. M., Ionidis, G., Ebert, B. E., Bühler, B. et al., Metabolic response of Pseudomonas putida during redox biocatalysis in the presence of a second octanol phase. FEBS J. 2008, 275, 5173–5190.
    • (2008) FEBS J. , vol.275 , pp. 5173-5190
    • Blank, L.M.1    Ionidis, G.2    Ebert, B.E.3    Bühler, B.4
  • 15
    • 67649622058 scopus 로고    scopus 로고
    • Selected Pseudomonas putida strains able to grow in the presence of high butanol concentrations
    • Ruhl, J., Schmid, A., Blank, L. M., Selected Pseudomonas putida strains able to grow in the presence of high butanol concentrations. Appl. Environ. Microbiol. 2009, 75, 4653–4656.
    • (2009) Appl. Environ. Microbiol. , vol.75 , pp. 4653-4656
    • Ruhl, J.1    Schmid, A.2    Blank, L.M.3
  • 17
    • 55449096123 scopus 로고    scopus 로고
    • Genome-scale reconstruction and analysis of the Pseudomonas putida KT2440 metabolic network facilitates applications in biotechnology
    • Puchałka, J., Oberhardt, M. A., Godinho, M., Bielecka, A. et al., Genome-scale reconstruction and analysis of the Pseudomonas putida KT2440 metabolic network facilitates applications in biotechnology. PLoS Comput. Biol. 2008, 4, e1000210.
    • (2008) PLoS Comput. Biol. , vol.4
    • Puchałka, J.1    Oberhardt, M.A.2    Godinho, M.3    Bielecka, A.4
  • 18
    • 77954714441 scopus 로고    scopus 로고
    • In silico genome-scale metabolic analysis of Pseudomonas putida KT2440 for polyhydroxyalkanoate synthesis, degradation of aromatics and anaerobic survival
    • Sohn, S. B., Kim, T. Y., Park, J. M., Lee, S. Y., In silico genome-scale metabolic analysis of Pseudomonas putida KT2440 for polyhydroxyalkanoate synthesis, degradation of aromatics and anaerobic survival. Biotechnol. J. 2010, 5, 739–750.
    • (2010) Biotechnol. J. , vol.5 , pp. 739-750
    • Sohn, S.B.1    Kim, T.Y.2    Park, J.M.3    Lee, S.Y.4
  • 19
    • 79953649492 scopus 로고    scopus 로고
    • Reconciliation of genome-scale metabolic reconstructions for comparative systems analysis
    • Oberhardt, M. A., Puchałka, J., Martins dos Santos, Vítor A. P., Papin, J. A. et al., Reconciliation of genome-scale metabolic reconstructions for comparative systems analysis. PLoS Comput. Biol. 2011, 7, e1001116.
    • (2011) PLoS Comput. Biol. , vol.7
    • Oberhardt, M.A.1    Puchałka, J.2    Martins dos Santos, V.A.P.3    Papin, J.A.4
  • 20
    • 84964771581 scopus 로고    scopus 로고
    • The revisited genome of Pseudomonas putida KT2440 enlightens its value as a robust metabolic chassis
    • Belda, E., van Heck, R. G., Jose, L.-S. M., Cruveiller, S. et al., The revisited genome of Pseudomonas putida KT2440 enlightens its value as a robust metabolic chassis. Environ. Microbiol. 2016, 18, 3403–3424.
    • (2016) Environ. Microbiol. , vol.18 , pp. 3403-3424
    • Belda, E.1    van Heck, R.G.2    Jose, L.-S.M.3    Cruveiller, S.4
  • 21
    • 84886422324 scopus 로고    scopus 로고
    • Reconciling in vivo and in silico key biological parameters of Pseudomonas putida KT2440 during growth on glucose under carbon-limited condition
    • van Duuren, J., Puchałka, J., Mars, A. E., Bücker, R. et al., Reconciling in vivo and in silico key biological parameters of Pseudomonas putida KT2440 during growth on glucose under carbon-limited condition. BMC Biotechnol. 2013, 13, 93.
    • (2013) BMC Biotechnol. , vol.13 , pp. 93
    • van Duuren, J.1    Puchałka, J.2    Mars, A.E.3    Bücker, R.4
  • 22
    • 33646578756 scopus 로고    scopus 로고
    • Overflow metabolism in Escherichia coli during steady-state growth: Transcriptional regulation and effect of the redox ratio
    • Vemuri, G. N., Altman, E., Sangurdekar, D. P., Khodursky, A. B. et al., Overflow metabolism in Escherichia coli during steady-state growth: Transcriptional regulation and effect of the redox ratio. Appl. Environ. Microbiol. 2006, 72, 3653–3661.
    • (2006) Appl. Environ. Microbiol. , vol.72 , pp. 3653-3661
    • Vemuri, G.N.1    Altman, E.2    Sangurdekar, D.P.3    Khodursky, A.B.4
  • 23
    • 73149109962 scopus 로고    scopus 로고
    • Shifts in growth strategies reflect tradeoffs in cellular economics
    • Molenaar, D., van Berlo, R., Ridder, D.de, Teusink, B., Shifts in growth strategies reflect tradeoffs in cellular economics. Mol. Syst. Biol. 2009, 5, 323.
    • (2009) Mol. Syst. Biol. , vol.5 , pp. 323
    • Molenaar, D.1    van Berlo, R.2    de Ridder, D.3    Teusink, B.4
  • 24
    • 84864584520 scopus 로고    scopus 로고
    • Prediction of microbial growth rate versus biomass yield by a metabolic network with kinetic parameters
    • Adadi, R., Volkmer, B., Milo, R., Heinemann, M. et al., Prediction of microbial growth rate versus biomass yield by a metabolic network with kinetic parameters. PLoS Comput. Biol. 2012, 8, e1002575.
    • (2012) PLoS Comput. Biol. , vol.8
    • Adadi, R.1    Volkmer, B.2    Milo, R.3    Heinemann, M.4
  • 25
    • 84858394287 scopus 로고    scopus 로고
    • The metabolic response of P. putida KT2442 producing high levels of polyhydroxyalkanoate under single- and multiple-nutrient-limited growth: Highlights from a multi-level omics approach
    • Poblete-Castro, I., Escapa, I. F., Jäger, C., Puchalka, J. et al., The metabolic response of P. putida KT2442 producing high levels of polyhydroxyalkanoate under single- and multiple-nutrient-limited growth: Highlights from a multi-level omics approach. Microb. Cell Fact. 2012, 11, 34.
    • (2012) Microb. Cell Fact. , vol.11 , pp. 34
    • Poblete-Castro, I.1    Escapa, I.F.2    Jäger, C.3    Puchalka, J.4
  • 26
    • 80052787409 scopus 로고    scopus 로고
    • Response of Pseudomonas putida KT2440 to Increased NADH and ATP Demand
    • Ebert, B. E., Kurth, F., Grund, M., Blank, L. M. et al., Response of Pseudomonas putida KT2440 to Increased NADH and ATP Demand. Appl. Environ. Microbiol. 2011, 77, 6597–6605.
    • (2011) Appl. Environ. Microbiol. , vol.77 , pp. 6597-6605
    • Ebert, B.E.1    Kurth, F.2    Grund, M.3    Blank, L.M.4
  • 27
    • 0004246963 scopus 로고
    • Wild, C. J., (Ed.),, John Wiley & Sons, Inc
    • Seber, G. A. F., Wild, C. J. (Ed.), Nonlinear Regression, John Wiley & Sons, Inc, 1989.
    • (1989) Nonlinear Regression
    • Seber, G.A.F.1
  • 28
    • 84982699549 scopus 로고    scopus 로고
    • Anodic respiration of Pseudomonas putida KT2440 in a stirred-tank bioreactor
    • Hintermayer, S., Yu, S., Krömer, J. O., Weuster-Botz, D., Anodic respiration of Pseudomonas putida KT2440 in a stirred-tank bioreactor. Biochem. Eng. J. 2016, 115, 1–13.
    • (2016) Biochem. Eng. J. , vol.115 , pp. 1-13
    • Hintermayer, S.1    Yu, S.2    Krömer, J.O.3    Weuster-Botz, D.4
  • 29
    • 80054070941 scopus 로고    scopus 로고
    • Growth independent rhamnolipid production from glucose using the non-pathogenic Pseudomonas putida KT2440
    • Wittgens, A., Tiso, T., Arndt, T. T., Wenk, P. et al., Growth independent rhamnolipid production from glucose using the non-pathogenic Pseudomonas putida KT2440. Microb. Cell Fact. 2011, 10, 80.
    • (2011) Microb. Cell Fact. , vol.10 , pp. 80
    • Wittgens, A.1    Tiso, T.2    Arndt, T.T.3    Wenk, P.4
  • 30
    • 79551662521 scopus 로고    scopus 로고
    • Quantitative prediction of cellular metabolism with constraint-based models: The COBRA Toolbox v2.0
    • Schellenberger, J., Que, R., Fleming, R. M. T., Thiele, I. et al., Quantitative prediction of cellular metabolism with constraint-based models: The COBRA Toolbox v2.0. Nat. Protoc. 2011, 6, 1290–1307.
    • (2011) Nat. Protoc. , vol.6 , pp. 1290-1307
    • Schellenberger, J.1    Que, R.2    Fleming, R.M.T.3    Thiele, I.4
  • 32
    • 0022129930 scopus 로고
    • Acetate inhibition of Pseudomonas putida
    • Fieschko, J., Humphrey, A. E., Acetate inhibition of Pseudomonas putida. Biotechnol. Bioeng. 1985, 27, 1362–1366.
    • (1985) Biotechnol. Bioeng. , vol.27 , pp. 1362-1366
    • Fieschko, J.1    Humphrey, A.E.2
  • 33
    • 84928793736 scopus 로고    scopus 로고
    • The glycerol-dependent metabolic persistence of Pseudomonas putida KT2440 reflects the regulatory logic of the GlpR repressor
    • Nikel, P. I., Romero-Campero, F. J., Zeidman, J. A., Goni-Moreno, A. et al., The glycerol-dependent metabolic persistence of Pseudomonas putida KT2440 reflects the regulatory logic of the GlpR repressor. MBio 2015, 6, e00340-15.
    • (2015) MBio , vol.6
    • Nikel, P.I.1    Romero-Campero, F.J.2    Zeidman, J.A.3    Goni-Moreno, A.4
  • 34
    • 84891635026 scopus 로고    scopus 로고
    • Metabolic and regulatory rearrangements underlying glycerol metabolism in Pseudomonas putida KT2440
    • Nikel, P. I., Kim, J., Lorenzo, V. de, Metabolic and regulatory rearrangements underlying glycerol metabolism in Pseudomonas putida KT2440. Environ. Microbiol. 2014, 16, 239–254.
    • (2014) Environ. Microbiol. , vol.16 , pp. 239-254
    • Nikel, P.I.1    Kim, J.2    de Lorenzo, V.3
  • 35
    • 84964313870 scopus 로고    scopus 로고
    • Pseudomonas 2.0: Genetic upgrading of P. putida KT2440 as an enhanced host for heterologous gene expression
    • Martínez-García, E., Nikel, P. I., Aparicio, T., Lorenzo, V. de, Pseudomonas 2.0: Genetic upgrading of P. putida KT2440 as an enhanced host for heterologous gene expression. Microb. Cell Fact. 2014, 13, 1.
    • (2014) Microb. Cell Fact. , vol.13 , pp. 1
    • Martínez-García, E.1    Nikel, P.I.2    Aparicio, T.3    de Lorenzo, V.4
  • 36
    • 0037079023 scopus 로고    scopus 로고
    • Escherichia coli K-12 undergoes adaptive evolution to achieve in silico predicted optimal growth
    • Ibarra, R. U., Edwards, J. S., Palsson, B. O., Escherichia coli K-12 undergoes adaptive evolution to achieve in silico predicted optimal growth. Nature 2002, 420, 186–189.
    • (2002) Nature , vol.420 , pp. 186-189
    • Ibarra, R.U.1    Edwards, J.S.2    Palsson, B.O.3
  • 37
    • 0042853224 scopus 로고    scopus 로고
    • Formate-stimulated oxidation of methanol by Pseudomonas putida 9816
    • Riis, V., Miethe, D., Babel, W., Formate-stimulated oxidation of methanol by Pseudomonas putida 9816. Biosci. Biotechnol. Biochem. 2014, 67, 684–690.
    • (2014) Biosci. Biotechnol. Biochem. , vol.67 , pp. 684-690
    • Riis, V.1    Miethe, D.2    Babel, W.3
  • 38
    • 84877832640 scopus 로고    scopus 로고
    • Regulation of Pichia pastoris promoters and its consequences for protein production
    • Vogl, T., Glieder, A., Regulation of Pichia pastoris promoters and its consequences for protein production. New Biotechnol. 2013, 30, 385–404.
    • (2013) New Biotechnol. , vol.30 , pp. 385-404
    • Vogl, T.1    Glieder, A.2
  • 39
    • 59649117138 scopus 로고    scopus 로고
    • Physiological responses of Pseudomonas putida to formaldehyde during detoxification
    • Roca, A., Rodríguez-Herva, J.-J., Duque, E., Ramos, J. L., Physiological responses of Pseudomonas putida to formaldehyde during detoxification. Microb. Biotechnol. 2008, 1, 158–169.
    • (2008) Microb. Biotechnol. , vol.1 , pp. 158-169
    • Roca, A.1    Rodríguez-Herva, J.-J.2    Duque, E.3    Ramos, J.L.4
  • 40
    • 84944910018 scopus 로고    scopus 로고
    • Pseudomonas putida KT2440 strain metabolizes glucose through a cycle formed by enzymes of the Entner-Doudoroff, Embden-Meyerhof-Parnas, and Pentose Phosphate Pathways
    • Nikel, P. I., Chavarría, M., Fuhrer, T., Sauer, U. et al., Pseudomonas putida KT2440 strain metabolizes glucose through a cycle formed by enzymes of the Entner-Doudoroff, Embden-Meyerhof-Parnas, and Pentose Phosphate Pathways. J. Biol. Chem. 2015, 290, 25920–25932.
    • (2015) J. Biol. Chem. , vol.290 , pp. 25920-25932
    • Nikel, P.I.1    Chavarría, M.2    Fuhrer, T.3    Sauer, U.4


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.