Experimental k
Corynebacterium glutamicum
Monod growth kinetics
affinity constant
cell-to-cell heterogeneity
microfluidic single-cell cultivation
respiratory activity monitoring
Journal
Biotechnology and bioengineering
ISSN: 1097-0290
Titre abrégé: Biotechnol Bioeng
Pays: United States
ID NLM: 7502021
Informations de publication
Date de publication:
05 2023
05 2023
Historique:
revised:
16
01
2023
received:
25
08
2022
accepted:
02
02
2023
medline:
14
4
2023
pubmed:
7
2
2023
entrez:
6
2
2023
Statut:
ppublish
Résumé
Knowledge about the specific affinity of whole cells toward a substrate, commonly referred to as k
Substances chimiques
Oxygen
S88TT14065
Carbon Dioxide
142M471B3J
Types de publication
Journal Article
Research Support, Non-U.S. Gov't
Langues
eng
Sous-ensembles de citation
IM
Pagination
1288-1302Informations de copyright
© 2023 The Authors. Biotechnology and Bioengineering published by Wiley Periodicals LLC.
Références
Arnoldini, M., Vizcarra, I. A., Peña-Miller, R., Stocker, N., Diard, M., Vogel, V., Beardmore, R. E., Hardt, W. D., & Ackermann, M. (2014). Bistable expression of virulence genes in salmonella leads to the formation of an antibiotic-tolerant subpopulation. PLoS Biology, 12(8), e1001928. https://doi.org/10.1371/journal.pbio.1001928
Bäumchen, C., Knoll, A., Husemann, B., Seletzky, J., Maier, B., Dietrich, C., Amoabediny, G., & Büchs, J. (2007). Effect of elevated dissolved carbon dioxide concentrations on growth of Corynebacterium glutamicum on D-glucose and L-lactate. Journal of Biotechnology, 128(4), 868-874. https://doi.org/10.1016/j.jbiotec.2007.01.001
Becker, J., Rohles, C. M., & Wittmann, C. (2018). Metabolically engineered Corynebacterium glutamicum for bio-based production of chemicals, fuels, materials, and healthcare products. Metabolic Engineering, 50, 122-141. https://doi.org/10.1016/j.ymben.2018.07.008
Bettenworth, V., Steinfeld, B., Duin, H., Petersen, K., Streit, W. R., Bischofs, I., & Becker, A. (2019). Phenotypic heterogeneity in bacterial quorum sensing systems. Journal of Molecular Biology, 431(23), 4530-4546. https://doi.org/10.1016/j.jmb.2019.04.036
Burmeister, A., Akhtar, Q., Hollmann, L., Tenhaef, N., Hilgers, F., Hogenkamp, F., Sokolowsky, S., Marienhagen, J., Noack, S., Kohlheyer, D., & Grünberger, A. (2021). (Optochemical) control of synthetic microbial coculture interactions on a microcolony level. ACS Synthetic Biology, 10(6), 1308-1319. https://doi.org/10.1021/acssynbio.0c00382
Bylund, F., Collet, E., Enfors, S. O., & Larsson, G. (1998). Substrate gradient formation in the large-scale bioreactor lowers cell yield and increases by-product formation. Bioprocess Engineering, 18(3), 171-180. https://doi.org/10.1007/s004490050427
Dinger, R., Lattermann, C., Flitsch, D., Fischer, J. P., Kosfeld, U., & Büchs, J. (2022). Device for respiration activity measurement enables the determination of oxygen transfer rates of microbial cultures in shaken 96-deepwell microtiter plates. Biotechnology and Bioengineering, 119(3), 881-894. https://doi.org/10.1002/bit.28022
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., Manelius, Å. (2001). Physiological responses to mixing in large scale bioreactors. Journal of Biotechnology, 85(2), 175-185. https://doi.org/10.1016/S0168-1656(00)00365-5
Farwick, M., Siewe, R. M., & Krämer, R. (1995). Glycine betaine uptake after hyperosmotic shift in Corynebacterium glutamicum. Journal of Bacteriology, 177(16), 4690-4695. https://doi.org/10.1128/jb.177.16.4690-4695.1995
Ferenci, T. (1999). Growth of bacterial cultures' 50 years on: Towards an uncertainty principle instead of constants in bacterial growth kinetics. Research in Microbiology, 150(7), 431-438. https://doi.org/10.1016/s0923-2508(99)00114-x
Freudl, R. (2017). Beyond amino acids: Use of the Corynebacterium glutamicum cell factory for the secretion of heterologous proteins. Journal of Biotechnology, 258, 101-109. https://doi.org/10.1016/j.jbiotec.2017.02.023
Goudar, C. T., & Strevett, K. A. (1998). Estimating growth kinetics of Penicillium chrysogenum through the use of respirometry. Journal of Chemical Technology & Biotechnology, 72(3), 207-212. https://doi.org/10.1002/(SICI)1097-4660(199807)72:3<207::AID-JCTB899>3.0.CO;2-B
Graf, M., Haas, T., Teleki, A., Feith, A., Cerff, M., Wiechert, W., Nöh, K., Busche, T., Kalinowski, J., & Takors, R. (2020). Revisiting the growth modulon of Corynebacterium glutamicum under glucose limited chemostat conditions. Frontiers in Bioengineering and Biotechnology, 8, 584614. https://doi.org/10.3389/fbioe.2020.584614
Grünberger, A., Probst, C., Heyer, A., Wiechert, W., Frunzke, J., & Kohlheyer, D. (2013). Microfluidic picoliter bioreactor for microbial single-cell analysis: Fabrication, system setup, and operation. Journal of Visualized Experiments: JoVE, 82, 50560. https://doi.org/10.3791/50560
Harrison, D. E. F. (1973). Studies on the affinity of methanol- and methane-utilizing bacteria for their carbon substrates. Journal of Applied Bacteriology, 36(2), 301-308. https://doi.org/10.1111/j.1365-2672.1973.tb04106.x
Helleckes, L. M., Osthege, M., Wiechert, W., von Lieres, E., & Oldiges, M. (2022). Bayesian calibration, process modeling and uncertainty quantification in biotechnology. PLoS Computational Biology, 18(3), e1009223. https://doi.org/10.1371/journal.pcbi.1009223
Hermann, T. (2003). Industrial production of amino acids by coryneform bacteria. Journal of Biotechnology, 104(1-3), 155-172. https://doi.org/10.1016/S0168-1656(03)00149-4
Ho, P., Täuber, S., Stute, B., Grünberger, A., & von Lieres, E. (2022). Microfluidic reproduction of dynamic bioreactor environment based on computational lifelines. Frontiers in Chemical Engineering, 4, 826485. https://doi.org/10.3389/fceng.2022.826485
Ihling, N., Munkler, L. P., Berg, C., Reichenbächer, B., Wirth, J., Lang, D., Wagner, R., & Büchs, J. (2021). Time-resolved monitoring of the oxygen transfer rate of Chinese hamster ovary cells provides insights into culture behavior in shake flasks. Frontiers in Bioengineering and Biotechnology, 9, 725498. https://doi.org/10.3389/fbioe.2021.725498
Junker, B. H. (2004). Scale-up methodologies for Escherichia coli and yeast fermentation processes. Journal of Bioscience and Bioengineering, 97(6), 347-364. https://doi.org/10.1016/S1389-1723(04)70218-2
Kell, D. B., & Sonnleitner, B. (1995). GMP-good modelling practice: An essential component of good manufacturing practice. Trends in Biotechnology, 13(11), 481-492. https://doi.org/10.1016/S0167-7799(00)89006-X
Koch, A. L. (1983). The surface stress theory of microbial morphogenesis. Advances in Microbial Physiology, 24, 301-366. https://doi.org/10.1016/S0065-2911(08)60388-4
Kovárová-Kovar, K., & Egli, T. (1998). Growth kinetics of suspended microbial cells: From single-substrate-controlled growth to mixed-substrate kinetics. Microbiology and Molecular Biology Reviews, 62(3), 646-666. https://doi.org/10.1128/MMBR.62.3.646-666.1998
Legan, J. D., & Owens, J. D. (1987). Determination of growth parameters of methylamine-using bacteria. Microbiology, 133(4), 1075-1080. https://doi.org/10.1099/00221287-133-4-1075
Li, Y., Jin, M., O'Laughlin, R., Bittihn, P., Tsimring, L. S., Pillus, L., Hasty, J., & Hao, N. (2017). Multigenerational silencing dynamics control cell aging. Proceedings of the National Academy of Sciences, 114(42), 11253-11258. https://doi.org/10.1073/pnas.1703379114
Liebl, W., Klamer, R., & Schleifer, K. H. (1989). Requirement of chelating compounds for the growth of Corynebacterium glutamicum in synthetic media. Applied Microbiology and Biotechnology, 32(2), 205-210. https://doi.org/10.1007/BF00165889
Lindemann, D., Westerwalbesloh, C., Kohlheyer, D., Grünberger, A., & von Lieres, E. (2019). Microbial single-cell growth response at defined carbon limiting conditions. RSC Advances, 9(25), 14040-14050. https://doi.org/10.1039/c9ra02454a
Lindner, S. N., Seibold, G. M., Henrich, A., Krämer, R., & Wendisch, V. F. (2011). Phosphotransferase system-independent glucose utilization in Corynebacterium glutamicum by inositol permeases and glucokinases. Applied and Environmental Microbiology, 77(11), 3571-3581. https://doi.org/10.1128/AEM.02713-10
Mandenius, C.-F. (Ed.). (2016). Bioreactors: Design, operation and novel applications (1st ed.). Wiley-VCH. http://nbn-resolving.org/urn:nbn:de:bsz:31-epflicht-1081908
Martin, O., Hartikainen, A., Abril-Pla, C. O., Kumar, R., Gautam, P., Arroyuelo, A., Naeem, R., Banerjea, R. A., Pasricha, N., Gruevski, P., Sanjay, R., Rochford, A., Phan, D., Mahweshwari, U., Kazantsev, V., Arunava, Andorra, A., & Lozada, R. P. (2021). ArviZ. Zenodo.
Martins, B. M., & Locke, J. C. (2015). Microbial individuality: How single-cell heterogeneity enables population level strategies. Current Opinion in Microbiology, 24, 104-112. https://doi.org/10.1016/j.mib.2015.01.003
Monod, J. (1949). The growth of bacterial cultures. Annual Review of Microbiology, 3(1), 371-394. https://doi.org/10.1146/annurev.mi.03.100149.002103
Mühlmann, M. J., Forsten, E., Noack, S., & Büchs, J. (2018). Prediction of recombinant protein production by Escherichia coli derived online from indicators of metabolic burden. Biotechnology Progress, 34(6), 1543-1552. https://doi.org/10.1002/btpr.2704
Oliveira, C. S., Ordaz, A., Alba, J., Alves, M., Ferreira, E. C., & Thalasso, F. (2009). Determination of kinetic and stoichiometric parameters of Pseudomonas putida F1 by chemostat and in situ pulse respirometry. Chemical Product and Process Modeling, 4(2). https://doi.org/10.2202/1934-2659.1304
Ordaz, A., Oliveira, C. S., Aguilar, R., Carrión, M., Ferreira, E. C., Alves, M., & Thalasso, F. (2008). Kinetic and stoichiometric parameters estimation in a nitrifying bubble column through “in-situ” pulse respirometry. Biotechnology and Bioengineering, 100(1), 94-102. https://doi.org/10.1002/bit.21723
Osthege, M., & Helleckes, L. M. (2022a). JuBiotech/calibr8: v6.4.0. Zenodo.
Osthege, M., & Helleckes, L. M. (2022b). JuBiotech/murefi: v5.1.0. Zenodo.
Osthege, M., & Schito, S. (2022). Supplement to Experimental kS estimation: A comparison of methods for Corynebacterium glutamicum from lab to microfluidic scale. Zenodo.
Osthege, M., Tenhaef, N., Helleckes, L. M., & Müller, C. (2022). JuBiotech/bletl: v1.1.0. Zenodo.
Osthege, M., Tenhaef, N., Zyla, R., Müller, C., Hemmerich, J., Wiechert, W., Noack, S., & Oldiges, M. (2022). bletl - A Python package for integrating BioLector microcultivation devices in the Design-Build-Test-Learn cycle. Engineering in Life Sciences, 22(3-4), 242-259. https://doi.org/10.1002/elsc.202100108
Phoenix, D. (1997). Introductory mathematics for the life sciences. Modules in life sciences. CRC Press.
Schindelin, J., Arganda-Carreras, I., Frise, E., Kaynig, V., Longair, M., Pietzsch, T., Preibisch, S., Rueden, C., Saalfeld, S., Schmid, B., Tinevez, J. Y., White, D. J., Hartenstein, V., Eliceiri, K., Tomancak, P., & Cardona, A. (2012). Fiji: An open-source platform for biological-image analysis. Nature Methods, 9(7), 676-682. https://doi.org/10.1038/nmeth.2019
Schmideder, A., Severin, T. S., Cremer, J. H., & Weuster-Botz, D. (2015). A novel milliliter-scale chemostat system for parallel cultivation of microorganisms in stirred-tank bioreactors. Journal of Biotechnology, 210, 19-24. https://doi.org/10.1016/j.jbiotec.2015.06.402
Senn, H., Lendenmann, U., Snozzi, M., Hamer, G., & Egli, T. (1994). The growth of Escherichia coli in glucose-limited chemostat cultures: A re-examination of the kinetics. Biochimica Et Biophysica Acta (BBA)-General Subjects, 1201(3), 424-436. https://doi.org/10.1016/0304-4165(94)90072-8
Stöckmann, C., Maier, U., Anderlei, T., Knocke, C., Gellissen, G., & Büchs, J. (2003). The oxygen transfer rate as key parameter for the characterization of Hansenula polymorpha screening cultures. Journal of Industrial Microbiology & Biotechnology, 30(10), 613-622. https://doi.org/10.1007/s10295-003-0090-9
Takors, R. (2012). Scale-up of microbial processes: Impacts, tools and open questions. Journal of Biotechnology, 160(1-2), 3-9. https://doi.org/10.1016/j.jbiotec.2011.12.010
Täuber, S., Golze, C., Ho, P., von Lieres, E., & Grünberger, A. (2020). dMSCC: a microfluidic platform for microbial single-cell cultivation of Corynebacterium glutamicum under dynamic environmental medium conditions. Lab on a Chip, 20(23), 4442-4455. https://doi.org/10.1101/2020.07.10.188938
ter Braak, C. J. F., & Vrugt, J. A. (2008). Differential evolution Markov chain with snooker updater and fewer chains. Statistics and Computing, 18(4), 435-446. https://doi.org/10.1007/s11222-008-9104-9
Toepke, M. W., & Beebe, D. J. (2006). PDMS absorption of small molecules and consequences in microfluidic applications. Lab on a Chip, 6(12), 1484-1486. https://doi.org/10.1039/b612140c
Uhde, A., Youn, J. W., Maeda, T., Clermont, L., Matano, C., Krämer, R., Wendisch, V. F., Seibold, G. M., & Marin, K. (2013). Glucosamine as carbon source for amino acid-producing Corynebacterium glutamicum. Applied Microbiology and Biotechnology, 97(4), 1679-1687. https://doi.org/10.1007/s00253-012-4313-8
Unthan, S., Grünberger, A., van Ooyen, J., Gätgens, J., Heinrich, J., Paczia, N., Wiechert, W., Kohlheyer, D., & Noack, S. (2014). Beyond growth rate 0.6: What drives Corynebacterium glutamicum to higher growth rates in defined medium. Biotechnology and Bioengineering, 111(2), 359-371. https://doi.org/10.1002/bit.25103
Vertès, A. A., Inui,M., & Yukawa, H. (2012). Postgenomic approaches to using corynebacteria as biocatalysts. Annual Review of Microbiology, 66, 521-550. https://doi.org/10.1146/annurev-micro-010312-105506
von der Osten, C. H., Gioannetti, C., & Sinskey, A. J. (1989). Design of a defined medium for growth of Corynebacterium glutamicum in which citrate facilitates iron uptake. Biotechnology Letters, 11(1), 11-16. https://doi.org/10.1007/BF01026778
Wang, P., Robert, L., Pelletier, J., Dang, W. L., Taddei, F., Wright, A., & Jun, S. (2010). Robust growth of Escherichia coli. Current Biology, 20(12), 1099-1103. https://doi.org/10.1016/j.cub.2010.04.045
Wechselberger, P., Sagmeister, P., & Herwig, C. (2013). Real-time estimation of biomass and specific growth rate in physiologically variable recombinant fed-batch processes. Bioprocess and Biosystems Engineering, 36(9), 1205-1218. https://doi.org/10.1007/s00449-012-0848-4
Wendisch, V. F., Bott, M., & Eikmanns, B. J. (2006). Metabolic engineering of Escherichia coli and Corynebacterium glutamicum for biotechnological production of organic acids and amino acids. Current Opinion in Microbiology, 9(3), 268-274. https://doi.org/10.1016/j.mib.2006.03.001
Wendisch, V. F., Jorge, J., Pérez-García, F., & Sgobba, E. (2016). Updates on industrial production of amino acids using Corynebacterium glutamicum. World Journal of Microbiology & Biotechnology, 32(6), 105. https://doi.org/10.1007/s11274-016-2060-1
Wiecki, T., Salvatier, J., Patil, A., Kochurov, M., Engels, B., Lao, J., Colin Martin, O., Ricardo, V., Willard, B. T., & Osthege, M. (2022). pymc-devs/pymc: v4.0.0b2. Zenodo.
Wolf, A., Krämer, R., & Morbach, S. (2003). Three pathways for trehalose metabolism in Corynebacterium glutamicum ATCC13032 and their significance in response to osmotic stress. Molecular Microbiology, 49(4), 1119-1134. https://doi.org/10.1046/j.1365-2958.2003.03625.x