E. coli; continuous biomanufacturing; mixed-feeding; productivity recovery; recombinant protein production
Abstract :
[en] Continuous cultivation with Escherichia coli has several benefits compared to classical fed-batch cultivation. The economic benefits would be a stable process, which leads to time independent quality of the product, and hence ease the downstream process. However, continuous biomanufacturing with E. coli is known to exhibit a drop of productivity after about 4-5 days of cultivation depending on dilution rate. These cultivations are generally performed on glucose, being the favorite carbon source for E. coli and used in combination with isopropyl β-D-1 thiogalactopyranoside (IPTG) for induction. In recent works, harsh induction with IPTG was changed to softer induction using lactose for T7-based plasmids, with the result of reducing the metabolic stress and tunability of productivity. These mixed feed systems based on glucose and lactose result in high amounts of correctly folded protein. In this study we used different mixed feed systems with glucose/lactose and glycerol/lactose to investigate productivity of E. coli based chemostats. We tested different strains producing three model proteins, with the final aim of a stable long-time protein expression. While glucose fed chemostats showed the well-known drop in productivity after a certain process time, glycerol fed cultivations recovered productivity after about 150 h of induction, which corresponds to around 30 generation times. We want to further highlight that the cellular response upon galactose utilization in E. coli BL21(DE3), might be causing fluctuating productivity, as galactose is referred to be a weak inducer. This "Lazarus" phenomenon has not been described in literature before and may enable a stabilization of continuous cultivation with E. coli using different carbon sources.
Disciplines :
Biotechnology
Author, co-author :
Kittler, Stefan; Research Division Biochemical Engineering, Research Group Integrated Bioprocess
Kopp, Julian; Christian Doppler Laboratory for Mechanistic and Physiological Methods for
Veelenturf, Patrick Gwen; Christian Doppler Laboratory for Mechanistic and Physiological Methods for
Spadiut, Oliver; Research Division Biochemical Engineering, Research Group Integrated Bioprocess
Delvigne, Frank ; Université de Liège - ULiège > Département GxABT > Microbial technologies ; TERRA Teaching and Research Centre, Microbial Processes and Interactions (MiPI),
Herwig, Christoph; Research Division Biochemical Engineering, Research Group Integrated Bioprocess ; Christian Doppler Laboratory for Mechanistic and Physiological Methods for
Slouka, Christoph; Research Division Biochemical Engineering, Research Group Integrated Bioprocess
Language :
English
Title :
The Lazarus Escherichia coli Effect: Recovery of Productivity on Glycerol/Lactose Mixed Feed in Continuous Biomanufacturing.
Baeshen M. N., Al-Hejin A. M., Bora R. S., Ahmed M. M., Ramadan H. A., Saini K. S., et al. (2015). Production of biopharmaceuticals in E. coli: current scenario and future perspectives. J. Microbiol. Biotechnol. 25 953–962. 10.4014/jmb.1412.12079 25737124
Berlec A., Strukelj B., (2013). Current state and recent advances in biopharmaceutical production in Escherichia coli, yeasts and mammalian cells. J. Ind. Microbiol. Biotechnol. 40 257–274. 10.1007/s10295-013-1235-1230
Binder D., Drepper T., Jaeger K.-E., Delvigne F., Wiechert W., Kohlheyer D., et al. (2017). Homogenizing bacterial cell factories: analysis and engineering of phenotypic heterogeneity. Metab. Eng. 42 145–156. 10.1016/j.ymben.2017.06.009 28645641
Blommel P. G., Becker K. J., Duvnjak P., Fox B. G., (2007). Enhanced bacterial protein expression during auto-induction obtained by alteration of lac repressor dosage and medium composition. Biotechnol. Prog. 23 585–598. 10.1021/bp070011x 17506520
Burstein C., Cohn M., Kepes A., Monod J., (1965). Role du lactose et de ses produits metaboliques dans l’induction de l’operon lactose chez Escherichia coli. Biochimica et Biophysica Acta (BBA)-Nucleic Acids and Protein Synthesis 95 634–639. 10.1016/0005-2787(65)90517-90514
Ceroni A., Passerini A., Vullo A., Frasconi P., (2006). DISULFIND: a disulfide bonding state and cysteine connectivity prediction server. Nucleic Acids Res. 34(Suppl._2), W177–W181.
Daegelen P., Studier F. W., Lenski R. E., Cure S., Kim J. F., (2009). Tracing ancestors and relatives of Escherichia coli B, and the derivation of B strains REL606 and BL21(DE3). J. Mol. Biol. 394 634–643. 10.1016/j.jmb.2009.09.022 19765591
DeLisa M. P., Li J., Rao G., Weigand W. A., Bentley W. E., (1999). Monitoring GFP-operon fusion protein expression during high cell density cultivation of Escherichia coli using an on-line optical sensor. Biotechnol. Bioeng. 65 54–64. 10.1002/(SICI)1097-0290(19991005)65:1<54::AID-BIT7<3.0.CO;2-R
Delvigne F., Baert J., Sassi H., Fickers P., Grünberger A., Dusny C., (2017). Taking control over microbial populations: current approaches for exploiting biological noise in bioprocesses. Biotechnol. J. 12:1600549. 10.1002/biot.201600549 28544731
Deutscher J., Francke C., Postma P. W., (2006). How phosphotransferase system-related protein phosphorylation regulates carbohydrate metabolism in bacteria. Microbiol. Mol. Biol. Rev. 70 939–1031. 10.1128/MMBR.00024-26
Diers I., Rasmussen E., Larsen P., Kjaersig I., (1991). Yeast fermentation processes for insulin production. Bioprocess. Technol. 13:166.
Dubendorff J. W., Studier F. W., (1991). Controlling basal expression in an inducible T7 expression system by blocking the target T7 promoter with lac repressor. J. Mol. Biol. 219 45–59. 10.1016/0022-2836(91)90856-90852
Dvorak P., Chrast L., Nikel P. I., Fedr R., Soucek K., Sedlackova M., et al. (2015). Exacerbation of substrate toxicity by IPTG in Escherichia coli BL21(DE3) carrying a synthetic metabolic pathway. Microb Cell Fact 14:201. 10.1186/s12934-015-0393-393
Fernández-Castané A., Vine C. E., Caminal G., López-Santín J., (2012). Evidencing the role of lactose permease in IPTG uptake by Escherichia coli in fed-batch high cell density cultures. J. Biotechnol. 157 391–398. 10.1016/j.jbiotec.2011.12.007 22202176
Goyon A., Sciascera L., Clarke A., Guillarme D., Pell R., (2018). Extending the limits of size exclusion chromatography: simultaneous separation of free payloads and related species from antibody drug conjugates and their aggregates. J. Chromatogr. A 1539 19–29. 10.1016/j.chroma.2018.01.039 29397979
Gupta S. K., Shukla P., (2016). Microbial platform technology for recombinant antibody fragment production: a review. Crit. Rev. Microbiol. 43 31–42. 10.3109/1040841X.2016.1150959 27387055
Hansen R., Eriksen N. T., (2007). Activity of recombinant GST in Escherichia coli grown on glucose and glycerol. Process Biochem. 42 1259–1263. 10.1016/j.procbio.2007.05.022
Hausjell J., Weissensteiner J., Molitor C., Halbwirth H., Spadiut O., (2018). E. coli HMS174 (DE3) is a sustainable alternative to BL21 (DE3). Microb Cell Fact 17:169. 10.1186/s12934-018-1016-1016
Hebisch E., Knebel J., Landsberg J., Frey E., Leisner M., (2013). High variation of fluorescence protein maturation times in closely related Escherichia coli strains. PLoS One 8:e75991. 10.1371/journal.pone.0075991 24155882
Heins A.-L., Johanson T., Han S., Lundin L., Carlquist M., Gernaey K. V., et al. (2019). Quantitative flow cytometry to understand population heterogeneity in response to changes in substrate availability in Escherichia coli and saccharomyces cerevisiae chemostats. Front. Bioeng. Biotech. 7:187. 10.3389/fbioe.2019.00187 31448270
Hoffmann F., Rinas U., (2004). Stress induced by recombinant protein production in Escherichia coli. Adv. Biochem. Eng. Biotechnol. 89 73–92. 10.1007/b93994 15217156
Inada T., Kimata K., Aiba H., (1996). Mechanism responsible for glucose–lactose diauxie in Escherichia coli: challenge to the cAMP model. Genes Cells 1 293–301. 10.1046/j.1365-2443.1996.24025.x 9133663
Jeong H., Barbe V., Lee C. H., Vallenet D., Yu D. S., Choi S. H., et al. (2009). Genome sequences of Escherichia coli B strains REL606 and BL21(DE3). J. Mol. Biol. 394 644–652. 10.1016/j.jmb.2009.09.052 19786035
Jeong H., Kim H. J., Lee S. J., (2015). Complete genome sequence of Escherichia coli strain BL21. Genome Announc. 3:e00134-15. 10.1128/genomeA.00134-115
Jia B., Jeon C. O., (2016). High-throughput recombinant protein expression in Escherichia coli: current status and future perspectives. Open Biol. 6:160196. 10.1098/rsob.160196 27581654
Kopp J., Kolkmann A.-M., Veleenturf P. G., Spadiut O., Herwig C., Slouka C., (2019a). Boosting recombinant inclusion body production-from classical fed-batch approach to continuous cultivation. Front. Bioeng. Biotech. 7:297. 10.3389/fbioe.2019.00297 31737617
Kopp J., Slouka C., Spadiut O., Herwig C., (2019b). The rocky road from fed-batch to continuous processing with E. coli. Front. Bioeng. Biotech. 7:328. 10.3389/fbioe.2019.00328 31824931
Kopp J., Slouka C., Strohmer D., Kager J., Spadiut O., Herwig C., (2018). Inclusion Body Bead Size in E. coli controlled by physiological feeding. Microorganisms 6:116. 10.3390/microorganisms6040116 30477255
Kopp J., Slouka C., Ulonska S., Kager J., Fricke J., Spadiut O., et al. (2017). Impact of glycerol as carbon source onto specific sugar and inducer uptake rates and inclusion body productivity in E. coli BL21 (DE3). Bioengineering 5:1. 10.3390/bioengineering5010001 29267215
Kopp J., Zauner F. B., Pell A., Hausjell J., Humer D., Ebner J., et al. (2020). Development of a generic reversed-phase liquid chromatography method for protein quantification using analytical quality-by-design principles. J. Pharmaceut. Biomed. 188:113412. 10.1016/j.jpba.2020.113412 32590301
Liu J.-F., Zhang Z.-J., Li A.-T., Pan J., Xu J.-H., (2011). Significantly enhanced production of recombinant nitrilase by optimization of culture conditions and glycerol feeding. Appl. Microbiol. Biot. 89 665–672. 10.1007/s00253-010-2866-y 20862583
Llanes B., McFall E., (1969). Effect of galactose on β-Galactosidase synthesis in Escherichia coli K-12. J. Bacteriol. 97 217–222. 10.1128/jb.97.1.217-222.1969 4884812
Loomis W. F., Magasanik B., (1967). Glucose-lactose diauxie in Escherichia coli. J. Bacteriol. 93 1397–1401. 10.1128/JB.93.4.1397-1401.1967 5340309
Lyakhov D. L., He B., Zhang X., Studier F. W., Dunn J. J., McAllister W. T., (1998). Pausing and termination by bacteriophage T7 RNA polymerase. J. Mol. Biol. 280 201–213. 10.1006/jmbi.1998.1854 9654445
Malakar P., Venkatesh K., (2012). Effect of substrate and IPTG concentrations on the burden to growth of Escherichia coli on glycerol due to the expression of Lac proteins. Appl. Microbiol. Biot. 93 2543–2549. 10.1007/s00253-011-3642-3643
Marbach A., Bettenbrock K., (2012). lac operon induction in Escherichia coli: systematic comparison of IPTG and TMG induction and influence of the transacetylase LacA. J. Biotechnol. 157 82–88. 10.1016/j.jbiotec.2011.10.009 22079752
Martínez-Gómez K., Flores N., Castañeda H. M., Martínez-Batallar G., Hernández-Chávez G., Ramírez O. T., et al. (2012). New insights into Escherichia coli metabolism: carbon scavenging, acetate metabolism and carbon recycling responses during growth on glycerol. Microb. Cell Fact 11:46. 10.1186/1475-2859-11-46 22513097
Monod J., (1949). The growth of bacterial cultures. Annu. Rev. Microbiol. 3 371–394.
Murarka A., Dharmadi Y., Yazdani S. S., Gonzalez R., (2008). Fermentative utilization of glycerol by Escherichia coli and its implications for the production of fuels and chemicals. Appl. Environ. Microbiol. 74 1124–1135. 10.1128/AEM.02192-2197
Neubauer P., Hofmann K., (1994). Efficient use of lactose for the lac promoter-controlled overexpression of the main antigenic protein of the foot and mouth disease virus in Escherichia coli under fed-batch fermentation conditions. FEMS Microbiol. Rev. 14 99–102. 10.1111/j.1574-6976.1994.tb00080.x 8011364
Neubauer P., Lin H., Mathiszik B., (2003). Metabolic load of recombinant protein production: inhibition of cellular capacities for glucose uptake and respiration after induction of a heterologous gene in Escherichia coli. Biotechnol. Bioeng. 83 53–64. 10.1002/bit.10645 12740933
Ozbudak E. M., Thattai M., Lim H. N., Shraiman B. I., Van Oudenaarden A., (2004). Multistability in the lactose utilization network of Escherichia coli. Nature 427:737. 10.1038/nature02298 14973486
Peebo K., Neubauer P., (2018). Application of continuous culture methods to recombinant protein production in microorganisms. Microorganisms 6:56. 10.3390/microorganisms6030056 29933583
Portaccio M., Stellato S., Rossi S., Bencivenga U., Eldin M. M., Gaeta F., et al. (1998). Galactose competitive inhibition of β-galactosidase (Aspergillus oryzae) immobilized on chitosan and nylon supports. Enzyme Microb Tech. 23 101–106. 10.1016/S0141-0229(98)00018-10
Postma P. W., Lengeler J. W., Jacobson G. R., (1993). Phosphoenolpyruvate:carbohydrate phosphotransferase systems of bacteria. Microbiol. Rev. 57 543–594.
Reinikainen P., Virkajärvi I., (1989). Escherichia coli growth and plasmid copy numbers in continuous cultivations. Biotechnol. Lett. 11 225–230. 10.1007/BF01031568
Ronimus R. S., Morgan H. W., (2003). Distribution and phylogenies of enzymes of the Embden-Meyerhof-Parnas pathway from archaea and hyperthermophilic bacteria support a gluconeogenic origin of metabolism. Archaea 1 199–221. 10.1155/2003/162593 15803666
Rosano G. L., Ceccarelli E. A., (2014). Recombinant protein expression in Escherichia coli: advances and challenges. Front. Microbiol. 5:172. 10.3389/fmicb.2014.00172 24860555
Schmideder A., Weuster-Botz D., (2017). High-performance recombinant protein production with Escherichia coli in continuously operated cascades of stirred-tank reactors. J. Ind. Microbiol. Biotechnol. 44 1021–1029. 10.1007/s10295-017-1927-y 28251388
Seo J. H., Bailey J. E., (1986). Continuous cultivation of recombinant Escherichia coli: existence of an optimum dilution rate for maximum plasmid and gene product concentration. Biotechnol. Bioeng. 28 1590–1594. 10.1002/bit.260281018 18553877
Shaner N. C., Campbell R. E., Steinbach P. A., Giepmans B. N., Palmer A. E., Tsien R. Y., (2004). Improved monomeric red, orange and yellow fluorescent proteins derived from Discosoma sp. red fluorescent protein. Nat. Biotechnol. 22 1567–1572. 10.1038/nbt1037 15558047
Shiloach J., Fass R., (2005). Growing E. coli to high cell density—a historical perspective on method development. Biotechnol. Adv. 23 345–357. 10.1016/j.biotechadv.2005.04.004 15899573
Sieben M., Steinhorn G., Müller C., Fuchs S., Chin L. A., Regestein L., et al. (2016). Testing plasmid stability of Escherichia coli using the continuously operated shaken BIOreactor system. Biotechnol. Prog. 32 1418–1425. 10.1002/btpr.2341 27593226
Slouka C., Kopp J., Hutwimmer S., Strahammer M., Strohmer D., Eitenberger E., et al. (2018). Custom made inclusion bodies: impact of classical process parameters and physiological parameters on inclusion body quality attributes. Microb Cell Fact 17:148. 10.1186/s12934-018-0997-995
Slouka C., Kopp J., Strohmer D., Kager J., Spadiut O., Herwig C., (2019). Monitoring and control strategies for inclusion body production in E. coli based on glycerol consumption. J. Biotechnol. 296 75–82. 10.1016/j.jbiotec.2019.03.014 30904592
Slouka C., Wurm D. J., Brunauer G., Welzl-Wachter A., Spadiut O., Fleig J., et al. (2016). A novel application for low frequency electrochemical impedance spectroscopy as an online process monitoring tool for viable cell concentrations. Sensors (Basel) 16:1900. 10.3390/s16111900 27845720
Spadiut O., Capone S., Krainer F., Glieder A., Herwig C., (2014). Microbials for the production of monoclonal antibodies and antibody fragments. Trends Biotechnol. 32 54–60. 10.1016/j.tibtech.2013.10.002 24183828
Steen R., Dahlberg A. E., Lade B. N., Studier F. W., Dunn J. J., (1986). T7 RNA polymerase directed expression of the Escherichia coli rrnB operon. EMBO J. 5 1099–1103. 10.1002/j.1460-2075.1986.tb04328.x
Striedner G., Pfaffenzeller I., Markus L., Nemecek S., Grabherr R., Bayer K., (2010). Plasmid-free T7-based Escherichia coli expression systems. Biotechnol. Bioeng. 105 786–794. 10.1002/bit.22598 19891007
Studier F. W., Moffatt B. A., (1986). Use of bacteriophage T7 RNA polymerase to direct selective high-level expression of cloned genes. J. Mol. Biol. 189 113–130. 10.1016/0022-2836(86)90385-2
Studier F. W., Rosenberg A. H., Dunn J. J., Dubendorff J. W., (1990). Use of T7 RNA polymerase to direct expression of cloned genes. Methods Enzymol. 185 60–89. 10.1016/0076-6879(90)85008-c
Tseng T. T., Tyler B. M., Setubal J. C., (2009). Protein secretion systems in bacterial-host associations, and their description in the gene ontology. BMC Microbiol. 9(Suppl. 1):S2. 10.1186/1471-2180-9-S1-S2 19278550
Ukkonen K., Mayer S., Vasala A., Neubauer P., (2013). Use of slow glucose feeding as supporting carbon source in lactose autoinduction medium improves the robustness of protein expression at different aeration conditions. Protein Expr. Purif. 91 147–154. 10.1016/j.pep.2013.07.016 23938950
Vaiphei S. T., Pandey G., Mukherjee K. J., (2009). Kinetic studies of recombinant human interferon-gamma expression in continuous cultures of E. coli. J. Ind. Microbiol. Biotechnol. 36:1453. 10.1007/s10295-009-0632-x 19727876
Viitanen M. I., Vasala A., Neubauer P., Alatossava T., (2003). Cheese whey-induced high-cell-density production of recombinant proteins in Escherichia coli. Microb Cell Fact 2:2. 10.1186/1475-2859-2-2 12740045
Wang Z., Yang S.-T., (2013). Propionic acid production in glycerol/glucose co-fermentation by Propionibacterium freudenreichii subsp. shermanii. Bioresour. Technol. 137 116–123. 10.1016/j.biortech.2013.03.012 23584412
Weikert C., Sauer U., Bailey J. E., (1997). Use of a glycerol-limited, long-term chemostat for isolation of Escherichia coli mutants with improved physiological properties. Microbiology 143 1567–1574. 10.1099/00221287-143-5-1567 9168607
Wick L. M., 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. 3 588–599. 10.1046/j.1462-2920.2001.00231.x 11683869
Wurm D. J., Hausjell J., Ulonska S., Herwig C., Spadiut O., (2017a). Mechanistic platform knowledge of concomitant sugar uptake in Escherichia coli BL21 (DE3) strains. Sci. Rep. 7:45072. 10.1038/srep45072 28332595
Wurm D. J., Herwig C., Spadiut O., (2017b). How to determine interdependencies of glucose and lactose uptake rates for heterologous protein production with E. coli. Methods Mol. Biol. 1586 397–408. 10.1007/978-1-4939-6887-9_26
Wurm D. J., Quehenberger J., Mildner J., Eggenreich B., Slouka C., Schwaighofer A., et al. (2018). Teaching an old pET new tricks: tuning of inclusion body formation and properties by a mixed feed system in E. coli. Appl. Microbiol. Biot. 102 667–676. 10.1007/s00253-017-8641-8646
Wurm D. J., Veiter L., Ulonska S., Eggenreich B., Herwig C., Spadiut O., (2016). The E. coli pET expression system revisited-mechanistic correlation between glucose and lactose uptake. Appl. Microbiol. Biotechnol. 100 8721–8729. 10.1007/s00253-016-7620-7627
Yao R., Xiong D., Hu H., Wakayama M., Yu W., Zhang X., et al. (2016). Elucidation of the co-metabolism of glycerol and glucose in Escherichia coli by genetic engineering, transcription profiling, and 13C metabolic flux analysis. Biotechnol. Biofuels 9:175. 10.1186/s13068-016-0591-591