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Harting C, Teleki A, Braakmann M, Jankowitsch F, Takors R. Systemic intracellular analysis for balancing complex biosynthesis in a transcriptionally deregulated Escherichia coli l-Methionine producer. Microb Biotechnol 2024; 17:e14433. [PMID: 38528766 DOI: 10.1111/1751-7915.14433] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2023] [Revised: 02/11/2024] [Accepted: 02/16/2024] [Indexed: 03/27/2024] Open
Abstract
l-Methionine (l-Met) has gained remarkable interest due to its multifaceted and versatile applications in the fields of nutrition, pharmaceuticals and clinical practice. In this study, the fluxes of the challenging l-Met biosynthesis in the producer strain Escherichia coli (E. coli) DM2853 were fine-tuned to enable improved l-Met production. The potential bottlenecks identified in sulfur assimilation and l-Met synthesis downstream of O-succinyl-l-homoserine (OSHS) were addressed by overexpressing glutaredoxin 1 (grxA), thiosulfate sulfurtransferase (pspE) and O-succinylhomoserine lyase (metB). Although deemed as a straightforward target for improving glucose-to-Met conversion, the yields remained at approximately 12%-13% (g/g). Instead, intracellular l-Met pools increased by up to four-fold with accelerated kinetics. Overexpression of the Met exporter ygaZH may serve as a proper valve for releasing the rising internal Met pressure. Interestingly, the export kinetics revealed maximum saturated export rates already at low growth rates. This scenario is particularly advantageous for large-scale fermentation when product formation is ideally uncoupled from biomass formation to achieve maximum performance within the technical limits of large-scale bioreactors.
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Ulmer A, Veit S, Erdemann F, Freund A, Loesch M, Teleki A, Zeidan AA, Takors R. A Two-Compartment Fermentation System to Quantify Strain-Specific Interactions in Microbial Co-Cultures. Bioengineering (Basel) 2023; 10:bioengineering10010103. [PMID: 36671675 PMCID: PMC9854596 DOI: 10.3390/bioengineering10010103] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/27/2022] [Revised: 12/19/2022] [Accepted: 12/21/2022] [Indexed: 01/14/2023]
Abstract
To fulfil the growing interest in investigating microbial interactions in co-cultures, a novel two-compartment bioreactor system was developed, characterised, and implemented. The system allowed for the exchange of amino acids and peptides via a polyethersulfone membrane that retained biomass. Further system characterisation revealed a Bodenstein number of 18, which hints at backmixing. Together with other physical settings, the existence of unwanted inner-compartment substrate gradients could be ruled out. Furthermore, the study of Damkoehler numbers indicated that a proper metabolite supply between compartments was enabled. Implementing the two-compartment system (2cs) for growing Streptococcus thermophilus and Lactobacillus delbrueckii subs. bulgaricus, which are microorganisms commonly used in yogurt starter cultures, revealed only a small variance between the one-compartment and two-compartment approaches. The 2cs enabled the quantification of the strain-specific production and consumption rates of amino acids in an interacting S. thermophilus-L. bulgaricus co-culture. Therefore, comparisons between mono- and co-culture performance could be achieved. Both species produce and release amino acids. Only alanine was produced de novo from glucose through potential transaminase activity by L. bulgaricus and consumed by S. thermophilus. Arginine availability in peptides was limited to S. thermophilus' growth, indicating active biosynthesis and dependency on the proteolytic activity of L. bulgaricus. The application of the 2cs not only opens the door for the quantification of exchange fluxes between microbes but also enables continuous production modes, for example, for targeted evolution studies.
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Affiliation(s)
- Andreas Ulmer
- Institute of Biochemical Engineering, University of Stuttgart, 70569 Stuttgart, Germany
| | - Stefan Veit
- Institute of Biochemical Engineering, University of Stuttgart, 70569 Stuttgart, Germany
| | - Florian Erdemann
- Institute of Biochemical Engineering, University of Stuttgart, 70569 Stuttgart, Germany
| | - Andreas Freund
- Institute of Biochemical Engineering, University of Stuttgart, 70569 Stuttgart, Germany
| | - Maren Loesch
- Institute of Biochemical Engineering, University of Stuttgart, 70569 Stuttgart, Germany
| | - Attila Teleki
- Institute of Biochemical Engineering, University of Stuttgart, 70569 Stuttgart, Germany
| | - Ahmad A. Zeidan
- Systems Biology, R&D Discovery, Chr. Hansen A/S, 2970 Hørsholm, Denmark
| | - Ralf Takors
- Institute of Biochemical Engineering, University of Stuttgart, 70569 Stuttgart, Germany
- Correspondence:
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3
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Hildenbrand JC, Sprenger GA, Teleki A, Takors R, Jendrossek D. Polyphosphate Kinases Phosphorylate Thiamine Phosphates. Microb Physiol 2022; 33:1-11. [PMID: 36041408 DOI: 10.1159/000526662] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2021] [Accepted: 08/12/2022] [Indexed: 12/23/2023]
Abstract
Polyphosphate kinases (PPKs) catalyze the reversible transfer of the γ-phosphate moiety of ATP (or of another nucleoside triphosphate) to a growing chain of polyphosphate (polyP). In this study, we describe that PPKs of various sources are additionally able to phosphorylate thiamine diphosphate (ThP2) to produce thiamine triphosphate (ThP3) and even thiamine tetraphosphate in vitro using polyP as phosphate donor. Furthermore, all tested PPK2s, but not PPK1s, were able to phosphorylate thiamine monophosphate (ThP1) to ThP2 and ThP3 although at low efficiency. The predicted masses and identities of the mono- and oligo-phosphorylated thiamine metabolites were identified by high-performance liquid chromatography tandem mass spectrometry. Moreover, the biological activity of ThP2, that was synthesized by phosphorylation of ThP1 with polyP and PPK, as a cofactor of ThP2-dependent enzymes (here transketolase TktA from Escherichia coli) was confirmed in a coupled enzyme assay. Our study shows that PPKs are promiscuous enzymes in vitro that could be involved in the formation of a variety of phosphorylated metabolites in vivo.
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Affiliation(s)
| | - Georg A Sprenger
- Institute of Microbiology, University of Stuttgart, Stuttgart, Germany
| | - Attila Teleki
- Institute of Biochemical Engineering, University of Stuttgart, Stuttgart, Germany
| | - Ralf Takors
- Institute of Biochemical Engineering, University of Stuttgart, Stuttgart, Germany
| | - Dieter Jendrossek
- Institute of Microbiology, University of Stuttgart, Stuttgart, Germany
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Minden S, Aniolek M, Sarkizi Shams Hajian C, Teleki A, Zerrer T, Delvigne F, van Gulik W, Deshmukh A, Noorman H, Takors R. Monitoring Intracellular Metabolite Dynamics in Saccharomyces cerevisiae during Industrially Relevant Famine Stimuli. Metabolites 2022; 12:metabo12030263. [PMID: 35323706 PMCID: PMC8953226 DOI: 10.3390/metabo12030263] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2022] [Revised: 03/08/2022] [Accepted: 03/16/2022] [Indexed: 11/16/2022] Open
Abstract
Carbon limitation is a common feeding strategy in bioprocesses to enable an efficient microbiological conversion of a substrate to a product. However, industrial settings inherently promote mixing insufficiencies, creating zones of famine conditions. Cells frequently traveling through such regions repeatedly experience substrate shortages and respond individually but often with a deteriorated production performance. A priori knowledge of the expected strain performance would enable targeted strain, process, and bioreactor engineering for minimizing performance loss. Today, computational fluid dynamics (CFD) coupled to data-driven kinetic models are a promising route for the in silico investigation of the impact of the dynamic environment in the large-scale bioreactor on microbial performance. However, profound wet-lab datasets are needed to cover relevant perturbations on realistic time scales. As a pioneering study, we quantified intracellular metabolome dynamics of Saccharomyces cerevisiae following an industrially relevant famine perturbation. Stimulus-response experiments were operated as chemostats with an intermittent feed and high-frequency sampling. Our results reveal that even mild glucose gradients in the range of 100 µmol·L−1 impose significant perturbations in adapted and non-adapted yeast cells, altering energy and redox homeostasis. Apparently, yeast sacrifices catabolic reduction charges for the sake of anabolic persistence under acute carbon starvation conditions. After repeated exposure to famine conditions, adapted cells show 2.7% increased maintenance demands.
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Affiliation(s)
- Steven Minden
- Institute of Biochemical Engineering, University of Stuttgart, 70569 Stuttgart, Germany; (S.M.); (M.A.); (C.S.S.H.); (A.T.); (T.Z.)
| | - Maria Aniolek
- Institute of Biochemical Engineering, University of Stuttgart, 70569 Stuttgart, Germany; (S.M.); (M.A.); (C.S.S.H.); (A.T.); (T.Z.)
| | - Christopher Sarkizi Shams Hajian
- Institute of Biochemical Engineering, University of Stuttgart, 70569 Stuttgart, Germany; (S.M.); (M.A.); (C.S.S.H.); (A.T.); (T.Z.)
| | - Attila Teleki
- Institute of Biochemical Engineering, University of Stuttgart, 70569 Stuttgart, Germany; (S.M.); (M.A.); (C.S.S.H.); (A.T.); (T.Z.)
| | - Tobias Zerrer
- Institute of Biochemical Engineering, University of Stuttgart, 70569 Stuttgart, Germany; (S.M.); (M.A.); (C.S.S.H.); (A.T.); (T.Z.)
| | - Frank Delvigne
- Microbial Processes and Interactions (MiPI), TERRA Research and Teaching Centre, Gembloux Agro Bio Tech, University of Liege, 5030 Gembloux, Belgium;
| | - Walter van Gulik
- Department of Biotechnology, Delft University of Technology, van der Maasweg 6, 2629 HZ Delft, The Netherlands;
| | - Amit Deshmukh
- Royal DSM, 2613 AX Delft, The Netherlands; (A.D.); (H.N.)
| | - Henk Noorman
- Royal DSM, 2613 AX Delft, The Netherlands; (A.D.); (H.N.)
- Department of Biotechnology, Delft University of Technology, 2628 CD Delft, The Netherlands
| | - Ralf Takors
- Institute of Biochemical Engineering, University of Stuttgart, 70569 Stuttgart, Germany; (S.M.); (M.A.); (C.S.S.H.); (A.T.); (T.Z.)
- Correspondence:
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Wijaya AW, Verhagen N, Teleki A, Takors R. Compartment-specific 13C metabolic flux analysis reveals boosted NADPH availability coinciding with increased cell-specific productivity for IgG1 producing CHO cells after MTA treatment. Eng Life Sci 2021; 21:832-847. [PMID: 34899120 PMCID: PMC8638276 DOI: 10.1002/elsc.202100057] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2021] [Revised: 10/05/2021] [Accepted: 10/08/2021] [Indexed: 01/26/2023] Open
Abstract
Increasing cell-specific productivities (CSPs) for the production of heterologous proteins in Chinese hamster ovary (CHO) cells is an omnipresent need in the biopharmaceutical industry. The novel additive 5'-deoxy-5'-(methylthio)adenosine (MTA), a chemical degradation product of S-(5'-adenosyl)-ʟ-methionine (SAM) and intermediate of polyamine biosynthesis, boosts the CSP of IgG1-producing CHO cells by 50%. Compartment-specific 13C flux analysis revealed a fundamental reprogramming of the central metabolism after MTA addition accompanied by cell-cycle arrest and increased cell volumes. Carbon fluxes into the pentose-phosphate pathway increased 22 fold in MTA-treated cells compared to that in non-MTA-treated reference cells. Most likely, cytosolic ATP inhibition of phosphofructokinase mediated the carbon detour. Mitochondrial shuttle activity of the α-ketoglurarate/malate antiporter (OGC) reversed, reducing cytosolic malate transport. In summary, NADPH supply in MTA-treated cells improved three fold compared to that in non-MTA-treated cells, which can be regarded as a major factor for explaining the boosted CSPs.
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Affiliation(s)
| | - Natascha Verhagen
- Institute of Biochemical EngineeringUniversity of StuttgartStuttgartGermany
| | - Attila Teleki
- Institute of Biochemical EngineeringUniversity of StuttgartStuttgartGermany
| | - Ralf Takors
- Institute of Biochemical EngineeringUniversity of StuttgartStuttgartGermany
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6
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Perpelea A, Wijaya AW, Martins LC, Rippert D, Klein M, Angelov A, Peltonen K, Teleki A, Liebl W, Richard P, Thevelein JM, Takors R, Sá-Correia I, Nevoigt E. Towards valorization of pectin-rich agro-industrial residues: Engineering of Saccharomyces cerevisiae for co-fermentation of d-galacturonic acid and glycerol. Metab Eng 2021; 69:1-14. [PMID: 34648971 DOI: 10.1016/j.ymben.2021.10.001] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2021] [Revised: 09/08/2021] [Accepted: 10/01/2021] [Indexed: 10/20/2022]
Abstract
Pectin-rich plant biomass residues represent underutilized feedstocks for industrial biotechnology. The conversion of the oxidized monomer d-galacturonic acid (d-GalUA) to highly reduced fermentation products such as alcohols is impossible due to the lack of electrons. The reduced compound glycerol has therefore been considered an optimal co-substrate, and a cell factory able to efficiently co-ferment these two carbon sources is in demand. Here, we inserted the fungal d-GalUA pathway in a strain of the yeast S. cerevisiae previously equipped with an NAD-dependent glycerol catabolic pathway. The constructed strain was able to consume d-GalUA with the highest reported maximum specific rate of 0.23 g gCDW-1 h-1 in synthetic minimal medium when glycerol was added. By means of a 13C isotope-labelling analysis, carbon from both substrates was shown to end up in pyruvate. The study delivers the proof of concept for a co-fermentation of the two 'respiratory' carbon sources to ethanol and demonstrates a fast and complete consumption of d-GalUA in crude sugar beet pulp hydrolysate under aerobic conditions. The future challenge will be to achieve co-fermentation under industrial, quasi-anaerobic conditions.
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Affiliation(s)
- Andreea Perpelea
- Department of Life Sciences and Chemistry, Jacobs University Bremen gGmbH, Campus Ring 1, 28759, Bremen, Germany
| | - Andy Wiranata Wijaya
- Department of Life Sciences and Chemistry, Jacobs University Bremen gGmbH, Campus Ring 1, 28759, Bremen, Germany; Institute of Biochemical Engineering, University of Stuttgart, Allmandring 31, 70569, Stuttgart, Germany
| | - Luís C Martins
- iBB - Institute for Bioengineering and Biosciences/i4HB-Associate Laboratory Institute for Health and Bioeconomy at Instituto Superior Técnico, Universidade de Lisboa, Av. Rovisco Pais, 1049-001, Lisbon, Portugal
| | - Dorthe Rippert
- Department of Life Sciences and Chemistry, Jacobs University Bremen gGmbH, Campus Ring 1, 28759, Bremen, Germany
| | - Mathias Klein
- Department of Life Sciences and Chemistry, Jacobs University Bremen gGmbH, Campus Ring 1, 28759, Bremen, Germany
| | - Angel Angelov
- Chair of Microbiology, TUM School of Life Sciences, Technical University of Munich, Emil-Ramann-Str 4, 85354, Freising-Weihenstephan, Germany; NGS Competence Center Tübingen, Universitätsklinikum Tübingen, Calwerstraße 7, 72076, Tübingen, Germany
| | - Kaisa Peltonen
- VTT Technical Research Centre of Finland Ltd., P.O. Box 1000, 02044, VTT Espoo, Finland
| | - Attila Teleki
- Institute of Biochemical Engineering, University of Stuttgart, Allmandring 31, 70569, Stuttgart, Germany
| | - Wolfgang Liebl
- Chair of Microbiology, TUM School of Life Sciences, Technical University of Munich, Emil-Ramann-Str 4, 85354, Freising-Weihenstephan, Germany
| | - Peter Richard
- VTT Technical Research Centre of Finland Ltd., P.O. Box 1000, 02044, VTT Espoo, Finland
| | - Johan M Thevelein
- NovelYeast bv, Open Bio-Incubator, Erasmus High School, Laarbeeklaan 121, 1090, Brussels (Jette), Belgium
| | - Ralf Takors
- Institute of Biochemical Engineering, University of Stuttgart, Allmandring 31, 70569, Stuttgart, Germany
| | - Isabel Sá-Correia
- iBB - Institute for Bioengineering and Biosciences/i4HB-Associate Laboratory Institute for Health and Bioeconomy at Instituto Superior Técnico, Universidade de Lisboa, Av. Rovisco Pais, 1049-001, Lisbon, Portugal; Department of Bioengineering, Instituto Superior Técnico, Universidade de Lisboa, Av. Rovisco Pais, 1049-001, Lisbon, Portugal
| | - Elke Nevoigt
- Department of Life Sciences and Chemistry, Jacobs University Bremen gGmbH, Campus Ring 1, 28759, Bremen, Germany.
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Wijaya AW, Ulmer A, Hundsdorfer L, Verhagen N, Teleki A, Takors R. Compartment-specific metabolome labeling enables the identification of subcellular fluxes that may serve as promising metabolic engineering targets in CHO cells. Bioprocess Biosyst Eng 2021; 44:2567-2578. [PMID: 34590184 PMCID: PMC8536584 DOI: 10.1007/s00449-021-02628-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2021] [Accepted: 08/27/2021] [Indexed: 11/30/2022]
Abstract
13C labeling data are used to calculate quantitative intracellular flux patterns reflecting in vivo conditions. Given that approaches for compartment-specific metabolomics exist, the benefits they offer compared to conventional non-compartmented 13C flux studies remain to be determined. Using compartment-specific labeling information of IgG1-producing Chinese hamster ovary cells, this study investigated differences of flux patterns exploiting and ignoring metabolic labeling data of cytosol and mitochondria. Although cellular analysis provided good estimates for the majority of intracellular fluxes, half of the mitochondrial transporters, and NADH and ATP balances, severe differences were found for some reactions. Accurate flux estimations of almost all iso-enzymes heavily depended on the sub-cellular labeling information. Furthermore, key discrepancies were found for the mitochondrial carriers vAGC1 (Aspartate/Glutamate antiporter), vDIC (Malate/H+ symporter), and vOGC (α-ketoglutarate/malate antiporter). Special emphasis is given to the flux of cytosolic malic enzyme (vME): it could not be estimated without the compartment-specific malate labeling information. Interesting enough, cytosolic malic enzyme is an important metabolic engineering target for improving cell-specific IgG1 productivity. Hence, compartment-specific 13C labeling analysis serves as prerequisite for related metabolic engineering studies.
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Affiliation(s)
- Andy Wiranata Wijaya
- Institute of Biochemical Engineering, University of Stuttgart, Allmandring 31, 70569, Stuttgart, Germany
| | - Andreas Ulmer
- Institute of Biochemical Engineering, University of Stuttgart, Allmandring 31, 70569, Stuttgart, Germany
| | - Lara Hundsdorfer
- Institute of Biochemical Engineering, University of Stuttgart, Allmandring 31, 70569, Stuttgart, Germany
| | - Natascha Verhagen
- Institute of Biochemical Engineering, University of Stuttgart, Allmandring 31, 70569, Stuttgart, Germany
| | - Attila Teleki
- Institute of Biochemical Engineering, University of Stuttgart, Allmandring 31, 70569, Stuttgart, Germany
| | - Ralf Takors
- Institute of Biochemical Engineering, University of Stuttgart, Allmandring 31, 70569, Stuttgart, Germany.
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Ankenbauer A, Nitschel R, Teleki A, Müller T, Favilli L, Blombach B, Takors R. Micro-aerobic production of isobutanol with engineered Pseudomonas putida. Eng Life Sci 2021; 21:475-488. [PMID: 34257629 PMCID: PMC8258000 DOI: 10.1002/elsc.202000116] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Revised: 02/14/2021] [Accepted: 02/16/2021] [Indexed: 11/29/2022] Open
Abstract
Pseudomonas putida KT2440 is emerging as a promising microbial host for biotechnological industry due to its broad range of substrate affinity and resilience to physicochemical stresses. Its natural tolerance towards aromatics and solvents qualifies this versatile microbe as promising candidate to produce next generation biofuels such as isobutanol. In this study, we scaled-up the production of isobutanol with P. putida from shake flask to fed-batch cultivation in a 30 L bioreactor. The design of a two-stage bioprocess with separated growth and production resulted in 3.35 gisobutanol L-1. Flux analysis revealed that the NADPH expensive formation of isobutanol exceeded the cellular catabolic supply of NADPH finally causing growth retardation. Concomitantly, the cell counteracted to the redox imbalance by increased formation of 2-ketogluconic thereby providing electrons for the respiratory ATP generation. Thus, P. putida partially uncoupled ATP formation from the availability of NADH. The quantitative analysis of intracellular pyridine nucleotides NAD(P)+ and NAD(P)H revealed elevated catabolic and anabolic reducing power during aerobic production of isobutanol. Additionally, the installation of micro-aerobic conditions during production doubled the integral glucose-to-isobutanol conversion yield to 60 mgisobutanol gglucose -1 while preventing undesired carbon loss as 2-ketogluconic acid.
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Affiliation(s)
- Andreas Ankenbauer
- Institute of Biochemical EngineeringUniversity of StuttgartStuttgartGermany
| | - Robert Nitschel
- Institute of Biochemical EngineeringUniversity of StuttgartStuttgartGermany
| | - Attila Teleki
- Institute of Biochemical EngineeringUniversity of StuttgartStuttgartGermany
| | - Tobias Müller
- Institute of Biochemical EngineeringUniversity of StuttgartStuttgartGermany
| | - Lorenzo Favilli
- Institute of Biochemical EngineeringUniversity of StuttgartStuttgartGermany
| | - Bastian Blombach
- Microbial BiotechnologyCampus Straubing for Biotechnology and SustainabilityTechnical University of MunichStraubingGermany
| | - Ralf Takors
- Institute of Biochemical EngineeringUniversity of StuttgartStuttgartGermany
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Hermann M, Teleki A, Weitz S, Niess A, Freund A, Bengelsdorf FR, Dürre P, Takors R. Identifying and Engineering Bottlenecks of Autotrophic Isobutanol Formation in Recombinant C. ljungdahlii by Systemic Analysis. Front Bioeng Biotechnol 2021; 9:647853. [PMID: 33748092 PMCID: PMC7968104 DOI: 10.3389/fbioe.2021.647853] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2020] [Accepted: 02/09/2021] [Indexed: 11/13/2022] Open
Abstract
Clostridium ljungdahlii (C. ljungdahlii, CLJU) is natively endowed producing acetic acid, 2,3-butandiol, and ethanol consuming gas mixtures of CO2, CO, and H2 (syngas). Here, we present the syngas-based isobutanol formation using C. ljungdahlii harboring the recombinant amplification of the "Ehrlich" pathway that converts intracellular KIV to isobutanol. Autotrophic isobutanol production was studied analyzing two different strains in 3-L gassed and stirred bioreactors. Physiological characterization was thoroughly applied together with metabolic profiling and flux balance analysis. Thereof, KIV and pyruvate supply were identified as key "bottlenecking" precursors limiting preliminary isobutanol formation in CLJU[KAIA] to 0.02 g L-1. Additional blocking of valine synthesis in CLJU[KAIA]:ilvE increased isobutanol production by factor 6.5 finally reaching 0.13 g L-1. Future metabolic engineering should focus on debottlenecking NADPH availability, whereas NADH supply is already equilibrated in the current generation of strains.
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Affiliation(s)
- Maria Hermann
- Institute of Biochemical Engineering, Faculty of Energy-, Process-, and Bio-Engineering, University of Stuttgart, Stuttgart, Germany
| | - Attila Teleki
- Institute of Biochemical Engineering, Faculty of Energy-, Process-, and Bio-Engineering, University of Stuttgart, Stuttgart, Germany
| | - Sandra Weitz
- Institute of Microbiology and Biotechnology, Faculty of Natural Sciences, University of Ulm, Ulm, Germany
| | - Alexander Niess
- Institute of Biochemical Engineering, Faculty of Energy-, Process-, and Bio-Engineering, University of Stuttgart, Stuttgart, Germany
| | - Andreas Freund
- Institute of Biochemical Engineering, Faculty of Energy-, Process-, and Bio-Engineering, University of Stuttgart, Stuttgart, Germany
| | - Frank Robert Bengelsdorf
- Institute of Microbiology and Biotechnology, Faculty of Natural Sciences, University of Ulm, Ulm, Germany
| | - Peter Dürre
- Institute of Microbiology and Biotechnology, Faculty of Natural Sciences, University of Ulm, Ulm, Germany
| | - Ralf Takors
- Institute of Biochemical Engineering, Faculty of Energy-, Process-, and Bio-Engineering, University of Stuttgart, Stuttgart, Germany
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Graf M, Haas T, Teleki A, Feith A, Cerff M, Wiechert W, Nöh K, Busche T, Kalinowski J, Takors R. Revisiting the Growth Modulon of Corynebacterium glutamicum Under Glucose Limited Chemostat Conditions. Front Bioeng Biotechnol 2020; 8:584614. [PMID: 33178676 PMCID: PMC7594717 DOI: 10.3389/fbioe.2020.584614] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2020] [Accepted: 09/23/2020] [Indexed: 11/13/2022] Open
Abstract
Increasing the growth rate of the industrial host Corynebacterium glutamicum is a promising target to rise productivities of growth coupled product formation. As a prerequisite, detailed knowledge about the tight regulation network is necessary for identifying promising metabolic engineering goals. Here, we present comprehensive metabolic and transcriptional analysis of C. glutamicum ATCC 13032 growing under glucose limited chemostat conditions with μ = 0.2, 0.3, and 0.4 h–1. Intermediates of central metabolism mostly showed rising pool sizes with increasing growth. 13C-metabolic flux analysis (13C-MFA) underlined the fundamental role of central metabolism for the supply of precursors, redox, and energy equivalents. Global, growth-associated, concerted transcriptional patterns were not detected giving rise to the conclusion that glycolysis, pentose-phosphate pathway, and citric acid cycle are predominately metabolically controlled under glucose-limiting chemostat conditions. However, evidence is found that transcriptional regulation takes control over glycolysis once glucose-rich growth conditions are installed.
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Affiliation(s)
- Michaela Graf
- Institute of Biochemical Engineering, University of Stuttgart, Stuttgart, Germany
| | - Thorsten Haas
- Institute of Biochemical Engineering, University of Stuttgart, Stuttgart, Germany
| | - Attila Teleki
- Institute of Biochemical Engineering, University of Stuttgart, Stuttgart, Germany
| | - André Feith
- Institute of Biochemical Engineering, University of Stuttgart, Stuttgart, Germany
| | - Martin Cerff
- Institute of Bio- and Geosciences, IBG-1: Biotechnology, Forschungszentrum Jülich GmbH, Jülich, Germany
| | - Wolfgang Wiechert
- Institute of Bio- and Geosciences, IBG-1: Biotechnology, Forschungszentrum Jülich GmbH, Jülich, Germany
| | - Katharina Nöh
- Institute of Bio- and Geosciences, IBG-1: Biotechnology, Forschungszentrum Jülich GmbH, Jülich, Germany
| | - Tobias Busche
- Center for Biotechnology, Bielefeld University, Bielefeld, Germany.,Institute for Biology-Microbiology, Freie Universität Berlin, Berlin, Germany
| | - Jörn Kalinowski
- Center for Biotechnology, Bielefeld University, Bielefeld, Germany
| | - Ralf Takors
- Institute of Biochemical Engineering, University of Stuttgart, Stuttgart, Germany
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11
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Hermann M, Teleki A, Weitz S, Niess A, Freund A, Bengelsdorf FR, Takors R. Electron availability in CO 2 , CO and H 2 mixtures constrains flux distribution, energy management and product formation in Clostridium ljungdahlii. Microb Biotechnol 2020; 13:1831-1846. [PMID: 32691533 PMCID: PMC7533319 DOI: 10.1111/1751-7915.13625] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2019] [Revised: 06/14/2020] [Accepted: 06/24/2020] [Indexed: 01/25/2023] Open
Abstract
Acetogens such as Clostridium ljungdahlii can play a crucial role reducing the human CO2 footprint by converting industrial emissions containing CO2 , CO and H2 into valuable products such as organic acids or alcohols. The quantitative understanding of cellular metabolism is a prerequisite to exploit the bacterial endowments and to fine-tune the cells by applying metabolic engineering tools. Studying the three gas mixtures CO2 + H2 , CO and CO + CO2 + H2 (syngas) by continuously gassed batch cultivation experiments and applying flux balance analysis, we identified CO as the preferred carbon and electron source for growth and producing alcohols. However, the total yield of moles of carbon (mol-C) per electrons consumed was almost identical in all setups which underlines electron availability as the main factor influencing product formation. The Wood-Ljungdahl pathway (WLP) showed high flexibility by serving as the key NAD+ provider for CO2 + H2, whereas this function was strongly compensated by the transhydrogenase-like Nfn complex when CO was metabolized. Availability of reduced ferredoxin (Fdred ) can be considered as a key determinant of metabolic control. Oxidation of CO via carbon monoxide dehydrogenase (CODH) is the main route of Fdred formation when CO is used as substrate, whereas Fdred is mainly regenerated via the methyl branch of WLP and the Nfn complex utilizing CO2 + H2 . Consequently, doubled growth rates, highest ATP formation rates and highest amounts of reduced products (ethanol, 2,3-butanediol) were observed when CO was the sole carbon and electron source.
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Affiliation(s)
- Maria Hermann
- Institute of Biochemical EngineeringUniversity of StuttgartAllmandring 31Stuttgart70569Germany
| | - Attila Teleki
- Institute of Biochemical EngineeringUniversity of StuttgartAllmandring 31Stuttgart70569Germany
| | - Sandra Weitz
- Institute of Microbiology and BiotechnologyUlm UniversityAlbert‐Einstein‐Allee 11Ulm89069Germany
| | - Alexander Niess
- Institute of Biochemical EngineeringUniversity of StuttgartAllmandring 31Stuttgart70569Germany
| | - Andreas Freund
- Institute of Biochemical EngineeringUniversity of StuttgartAllmandring 31Stuttgart70569Germany
| | - Frank R. Bengelsdorf
- Institute of Microbiology and BiotechnologyUlm UniversityAlbert‐Einstein‐Allee 11Ulm89069Germany
| | - Ralf Takors
- Institute of Biochemical EngineeringUniversity of StuttgartAllmandring 31Stuttgart70569Germany
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12
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Frank C, Teleki A, Jendrossek D. Characterization of Agrobacterium tumefaciens PPKs reveals the formation of oligophosphorylated products up to nucleoside nona-phosphates. Appl Microbiol Biotechnol 2020; 104:9683-9692. [PMID: 33025129 PMCID: PMC7595981 DOI: 10.1007/s00253-020-10891-7] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2020] [Revised: 08/28/2020] [Accepted: 09/04/2020] [Indexed: 12/29/2022]
Abstract
Agrobacterium tumefaciens synthesizes polyphosphate (polyP) in the form of one or two polyP granules per cell during growth. The A. tumefaciens genome codes for two polyphosphate kinase genes, ppk1AT and ppk2AT, of which only ppk1AT is essential for polyP granule formation in vivo. Biochemical characterization of the purified PPK1AT and PPK2AT proteins revealed a higher substrate specificity of PPK1AT (in particular for adenine nucleotides) than for PPK2AT. In contrast, PPK2AT accepted all nucleotides at comparable rates. Most interestingly, PPK2AT catalyzed also the formation of tetra-, penta-, hexa-, hepta-, and octa-phosphorylated nucleosides from guanine, cytosine, desoxy-thymidine, and uridine nucleotides and even nona-phosphorylated adenosine. Our data-in combination with in vivo results-suggest that PPK1AT is important for the formation of polyP whereas PPK2AT has the function to replenish nucleoside triphosphate pools during times of enhanced demand. The potential physiological function(s) of the detected oligophosphorylated nucleotides await clarification. KEY POINTS: •PPK1AT and PPK2AT have different substrate specificities, •PPK2AT is a subgroup 1 member of PPK2s, •PPK2AT catalyzes the formation of polyphosphorylated nucleosides.
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Affiliation(s)
- Celina Frank
- Institute of Microbiology, University of Stuttgart, Allmandring 31, 70569, Stuttgart, Germany
| | - Attila Teleki
- Institute of Biochemical Engineering, University of Stuttgart, Stuttgart, Germany
| | - Dieter Jendrossek
- Institute of Microbiology, University of Stuttgart, Allmandring 31, 70569, Stuttgart, Germany.
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13
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Verhagen N, Wijaya AW, Teleki A, Fadhlullah M, Unsöld A, Schilling M, Heinrich C, Takors R. Comparison of l-tyrosine containing dipeptides reveals maximum ATP availability for l-prolyl-l-tyrosine in CHO cells. Eng Life Sci 2020; 20:384-394. [PMID: 32944013 PMCID: PMC7481768 DOI: 10.1002/elsc.202000017] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2020] [Revised: 05/10/2020] [Accepted: 05/18/2020] [Indexed: 12/12/2022] Open
Abstract
Increasing markets for biopharmaceuticals, including monoclonal antibodies, have triggered a permanent need for bioprocess optimization. Biochemical engineering approaches often include the optimization of basal and feed media to improve productivities of Chinese hamster ovary (CHO) cell cultures. Often, l-tyrosine is added as dipeptide to deal with its poor solubility at neutral pH. Showcasing IgG1 production with CHO cells, we investigated the supplementation of three l-tyrosine (TYR, Y) containing dipeptides: glycyl-l-tyrosine (GY), l-tyrosyl-l-valine (YV), and l-prolyl-l-tyrosine (PY). While GY and YV led to almost no phenotypic and metabolic differences compared to reference samples, PY significantly amplified TYR uptake thus maximizing related catabolic activity. Consequently, ATP formation was roughly four times higher upon PY application than in reference samples.
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Affiliation(s)
- Natascha Verhagen
- Institute of Biochemical EngineeringUniversity of StuttgartStuttgartGermany
| | | | - Attila Teleki
- Institute of Biochemical EngineeringUniversity of StuttgartStuttgartGermany
| | | | - Andreas Unsöld
- Boehringer Ingelheim Pharma GmbH & Co. KGBiberachGermany
| | | | | | - Ralf Takors
- Institute of Biochemical EngineeringUniversity of StuttgartStuttgartGermany
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14
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Hildenbrand JC, Teleki A, Jendrossek D. A universal polyphosphate kinase: PPK2c of Ralstonia eutropha accepts purine and pyrimidine nucleotides including uridine diphosphate. Appl Microbiol Biotechnol 2020; 104:6659-6667. [PMID: 32500270 PMCID: PMC7347700 DOI: 10.1007/s00253-020-10706-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2020] [Revised: 05/19/2020] [Accepted: 05/24/2020] [Indexed: 01/15/2023]
Abstract
Polyphosphosphate kinases (PPKs) catalyse the reversible transfer of the γ-phosphate group of a nucleoside-triphosphate to a growing chain of polyphosphate. Most known PPKs are specific for ATP, but some can also use GTP as a phosphate donor. In this study, we describe the properties of a PPK2-type PPK of the β-proteobacterium Ralstonia eutropha. The purified enzyme (PPK2c) is highly unspecific and accepts purine nucleotides as well as the pyridine nucleotides including UTP as substrates. The presence of a polyP primer is not necessary for activity. The corresponding nucleoside diphosphates and microscopically detectable polyphosphate granules were identified as reaction products. PPK2c also catalyses the formation of ATP, GTP, CTP, dTTP and UTP from the corresponding nucleoside diphosphates, if polyP is present as a phosphate donor. Remarkably, the nucleoside-tetraphosphates AT(4)P, GT(4)P, CT(4)P, dTT(4)P and UT(4)P were also detected in substantial amounts. The low nucleotide specificity of PPK2c predestines this enzyme in combination with polyP to become a powerful tool for the regeneration of ATP and other nucleotides in biotechnological applications. As an example, PPK2c and polyP were used to replace ATP and to fuel the hexokinase-catalysed phosphorylation of glucose with only catalytic amounts of ADP. KEY POINTS: • PPK2c of R. eutropha can be used for regeneration of any NTP or dNTP. • PPK2c is highly unspecific and accepts all purine and pyrimidine nucleotides. • PPK2c forms polyphosphate granules in vitro from any NTP.
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Affiliation(s)
- Jennie C Hildenbrand
- Institute of Microbiology, University of Stuttgart, Allmandring 31, 70569, Stuttgart, Germany
| | - Attila Teleki
- Institute of Biochemical Engineering, University of Stuttgart, Stuttgart, Germany
| | - Dieter Jendrossek
- Institute of Microbiology, University of Stuttgart, Allmandring 31, 70569, Stuttgart, Germany.
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15
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Verhagen N, Teleki A, Heinrich C, Schilling M, Unsöld A, Takors R. S-adenosylmethionine and methylthioadenosine boost cellular productivities of antibody forming Chinese hamster ovary cells. Biotechnol Bioeng 2020; 117:3239-3247. [PMID: 32644191 DOI: 10.1002/bit.27484] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2020] [Revised: 06/22/2020] [Accepted: 07/07/2020] [Indexed: 01/28/2023]
Abstract
The improvement of cell specific productivities for the formation of therapeutic proteins is an important step towards intensified production processes. Among others, the induction of the desired production phenotype via proper media additives is a feasible solution provided that said compounds adequately trigger metabolic and regulatory programs inside the cells. In this study, S-(5'-adenosyl)- l-methionine (SAM) and 5'-deoxy-5'-(methylthio)adenosine (MTA) were found to stimulate cell specific productivities up to approx. 50% while keeping viable cell densities transiently high and partially arresting the cell cycle in an anti-IL-8-producing CHO-DP12 cell line. Noteworthy, MTA turned out to be the chemical degradation product of the methyl group donor SAM and is consumed by the cells.
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Affiliation(s)
- Natascha Verhagen
- Institute of Biochemical Engineering, University of Stuttgart, Allmandring, Stuttgart, Germany
| | - Attila Teleki
- Institute of Biochemical Engineering, University of Stuttgart, Allmandring, Stuttgart, Germany
| | | | | | - Andreas Unsöld
- Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach, Germany
| | - Ralf Takors
- Institute of Biochemical Engineering, University of Stuttgart, Allmandring, Stuttgart, Germany
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16
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Becker M, Junghans L, Teleki A, Bechmann J, Takors R. The Less the Better: How Suppressed Base Addition Boosts Production of Monoclonal Antibodies With Chinese Hamster Ovary Cells. Front Bioeng Biotechnol 2019; 7:76. [PMID: 31032253 PMCID: PMC6470187 DOI: 10.3389/fbioe.2019.00076] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2018] [Accepted: 03/25/2019] [Indexed: 11/30/2022] Open
Abstract
Biopharmaceutical production processes strive for the optimization of economic efficiency. Among others, the maximization of volumetric productivity is a key criterion. Typical parameters such as partial pressure of CO2 (pCO2) and pH are known to influence the performance although reasons are not yet fully elucidated. In this study the effects of pCO2 and pH shifts on the phenotypic performance were linked to metabolic and energetic changes. Short peak performance of qmAb (23 pg/cell/day) was achieved by early pCO2 shifts up to 200 mbar but followed by declining intracellular ATP levels to 2.5 fmol/cell and 80% increase of qLac. On the contrary, steadily rising qmAb could be installed by slight pH down-shifts ensuring constant cell specific ATP production (qATP) of 27 pmol/cell/day and high intracellular ATP levels of about 4 fmol/cell. As a result, maximum productivity was achieved combining highest qmAb (20 pg/cell/day) with maximum cell density and no lactate formation. Our results indicate that the energy availability in form of intracellular ATP is crucial for maintaining antibody synthesis and reacts sensitive to pCO2 and pH-process parameters typically responsible for inhomogeneities after scaling up.
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Affiliation(s)
- Max Becker
- Institute of Biochemical Engineering, University of Stuttgart, Stuttgart, Germany
| | - Lisa Junghans
- Institute of Biochemical Engineering, University of Stuttgart, Stuttgart, Germany
| | - Attila Teleki
- Institute of Biochemical Engineering, University of Stuttgart, Stuttgart, Germany
| | - Jan Bechmann
- Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach an der Riss, Germany
| | - Ralf Takors
- Institute of Biochemical Engineering, University of Stuttgart, Stuttgart, Germany
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17
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Feith A, Teleki A, Graf M, Favilli L, Takors R. HILIC-Enabled 13C Metabolomics Strategies: Comparing Quantitative Precision and Spectral Accuracy of QTOF High- and QQQ Low-Resolution Mass Spectrometry. Metabolites 2019; 9:metabo9040063. [PMID: 30986989 PMCID: PMC6523712 DOI: 10.3390/metabo9040063] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2019] [Revised: 03/21/2019] [Accepted: 03/28/2019] [Indexed: 11/16/2022] Open
Abstract
Dynamic 13C-tracer-based flux analyses of in vivo reaction networks still require a continuous development of advanced quantification methods applying state-of-the-art mass spectrometry platforms. Utilizing alkaline HILIC chromatography, we adapt strategies for a systematic quantification study in non- and 13C-labeled multicomponent endogenous Corynebacterium glutamicum extracts by LC-QTOF high resolution (HRMS) and LC-QQQ tandem mass spectrometry (MS/MS). Without prior derivatization, a representative cross-section of 17 central carbon and anabolic key intermediates were analyzed with high selectivity and sensitivity under optimized ESI-MS settings. In column detection limits for the absolute quantification range were between 6.8-304.7 (QQQ) and 28.7-881.5 fmol (QTOF) with comparable linearities (3-5 orders of magnitude) and enhanced precision using QQQ-MRM detection. Tailor-made preparations of uniformly (U)13C-labeled cultivation extracts for isotope dilution mass spectrometry enabled the accurate quantification in complex sample matrices and extended linearities without effect on method parameters. Furthermore, evaluation of metabolite-specific m+1-to-m+0 ratios (ISR1:0) in non-labeled extracts exhibited sufficient methodical spectral accuracies with mean deviations of 3.89 ± 3.54% (QTOF) and 4.01 ± 3.01% (QQQ). Based on the excellent HILIC performance, conformity analysis of time-resolved isotopic enrichments in 13C-tracer experiments revealed sufficient spectral accuracy for QQQ-SIM detection. However, only QTOF-HRMS ensures determination of the full isotopologue space in complex matrices without mass interferences.
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Affiliation(s)
- André Feith
- Institute of Biochemical Engineering, University of Stuttgart, Allmandring 31, 70569 Stuttgart, Germany.
| | - Attila Teleki
- Institute of Biochemical Engineering, University of Stuttgart, Allmandring 31, 70569 Stuttgart, Germany.
| | - Michaela Graf
- Institute of Biochemical Engineering, University of Stuttgart, Allmandring 31, 70569 Stuttgart, Germany.
| | - Lorenzo Favilli
- Institute of Biochemical Engineering, University of Stuttgart, Allmandring 31, 70569 Stuttgart, Germany.
| | - Ralf Takors
- Institute of Biochemical Engineering, University of Stuttgart, Allmandring 31, 70569 Stuttgart, Germany.
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18
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Junghans L, Teleki A, Wijaya AW, Becker M, Schweikert M, Takors R. From nutritional wealth to autophagy: In vivo metabolic dynamics in the cytosol, mitochondrion and shuttles of IgG producing CHO cells. Metab Eng 2019; 54:145-159. [PMID: 30930288 DOI: 10.1016/j.ymben.2019.02.005] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2018] [Revised: 01/27/2019] [Accepted: 02/27/2019] [Indexed: 10/27/2022]
Abstract
To fulfil the optimization needs of current biopharmaceutical processes the knowledge how to improve cell specific productivities is of outmost importance. This requires a detailed understanding of cellular metabolism on a subcellular level inside compartments such as cytosol and mitochondrion. Using IgG1 producing Chinese hamster ovary (CHO) cells, a pioneering protocol for compartment-specific metabolome analysis was applied. Various production-like growth conditions ranging from ample glucose and amino acid supply via moderate to severe nitrogen limitation were investigated in batch cultures. The combined application of quantitative metabolite pool analysis, 13C tracer studies and non-stationary flux calculations revealed that Pyr/H+ symport (MPC1/2) bore the bulk of the mitochondrial transport under ample nutrient supply. Glutamine limitation induced the concerted adaptation of the bidirectional Mal/aKG (OGC) and the Mal/HPO42- antiporter (DIC), even installing completely reversed shuttle fluxes. As a result, NADPH and ATP formation were adjusted to cellular needs unraveling the key role of cytosolic malic enzyme for NADPH production. Highest cell specific IgG1 productivities were closely correlated to a strong mitochondrial malate export according to the anabolic demands. The requirement to install proper NADPH supply for optimizing the production of monoclonal antibodies is clearly outlined. Interestingly, it was observed that mitochondrial citric acid cycle activity was always maintained enabling constant cytosolic adenylate energy charges at physiological levels, even under autophagy conditions.
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Affiliation(s)
- Lisa Junghans
- Institute of Biochemical Engineering, University of Stuttgart, Allmandring 31, 70569, Stuttgart, Germany
| | - Attila Teleki
- Institute of Biochemical Engineering, University of Stuttgart, Allmandring 31, 70569, Stuttgart, Germany
| | - Andy Wiranata Wijaya
- Institute of Biochemical Engineering, University of Stuttgart, Allmandring 31, 70569, Stuttgart, Germany
| | - Max Becker
- Institute of Biochemical Engineering, University of Stuttgart, Allmandring 31, 70569, Stuttgart, Germany
| | - Michael Schweikert
- Institute of Biomaterials and Biomolecular Systems, Department of Biobased Materials, University of Stuttgart, Pfaffenwaldring 57, 70569, Stuttgart, Germany
| | - Ralf Takors
- Institute of Biochemical Engineering, University of Stuttgart, Allmandring 31, 70569, Stuttgart, Germany.
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19
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Becker M, Junghans L, Teleki A, Bechmann J, Takors R. Perfusion cultures require optimum respiratory ATP supply to maximize cell-specific and volumetric productivities. Biotechnol Bioeng 2019; 116:951-960. [PMID: 30659583 DOI: 10.1002/bit.26926] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2018] [Revised: 01/12/2019] [Accepted: 01/16/2019] [Indexed: 01/16/2023]
Abstract
Perfusion processes are an emerging alternative to common fed-batch processes in the growing biopharmaceutical industry. However, the challenge of maintaining high cell-specific productivities remains. In this study, glucose limitation was applied to two perfusion steady states and compared with a third steady state without any detectable limitation. The metabolic phenotype was enhanced under glucose limitation with a decrease of 30% in glucose uptake and 75% in lactate formation. Cell-specific productivities were substantially improved by 50%. Remarkably, the productivities showed a strong correlation to respiratory adenosine triphosphate (ATP) supply. As less reduced nicotinamide adenine dinucleotide (NADH) remained in the cytosol, the ATP generation from oxidative phosphorylation was increased by almost 30%. Consequently, the efficiency of carbon metabolism and the resulting respiratory ATP supply was crucial for maintaining the highly productive cellular state. This study highlights that glucose limitation can be used for process intensification in perfusion cultures as ATP generation via respiration is significantly increased, leading to elevated productivities.
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Affiliation(s)
- Max Becker
- Institute of Biochemical Engineering, University of Stuttgart, Stuttgart, Germany
| | - Lisa Junghans
- Institute of Biochemical Engineering, University of Stuttgart, Stuttgart, Germany
| | - Attila Teleki
- Institute of Biochemical Engineering, University of Stuttgart, Stuttgart, Germany
| | - Jan Bechmann
- Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach, Germany
| | - Ralf Takors
- Institute of Biochemical Engineering, University of Stuttgart, Stuttgart, Germany
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20
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Verhagen N, Teleki A, Takors R. Identifizierung der Funktionen und Mechanismen von Mediumadditiven zur Optimierung der Zellkulturleistung. CHEM-ING-TECH 2018. [DOI: 10.1002/cite.201855337] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- N. Verhagen
- Universität Stuttgart; Institut für Bioverfahrenstechnik; Allmandring 31 70569 Stuttgart Deutschland
| | - A. Teleki
- Universität Stuttgart; Institut für Bioverfahrenstechnik; Allmandring 31 70569 Stuttgart Deutschland
| | - R. Takors
- Universität Stuttgart; Institut für Bioverfahrenstechnik; Allmandring 31 70569 Stuttgart Deutschland
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21
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Teleki A, Rahnert M, Bungart O, Gann B, Ochrombel I, Takors R. Robust identification of metabolic control for microbial l-methionine production following an easy-to-use puristic approach. Metab Eng 2017; 41:159-172. [PMID: 28389396 DOI: 10.1016/j.ymben.2017.03.008] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2016] [Revised: 02/15/2017] [Accepted: 03/31/2017] [Indexed: 11/28/2022]
Abstract
The identification of promising metabolic engineering targets is a key issue in metabolic control analysis (MCA). Conventional approaches make intensive use of model-based studies, such as exploiting post-pulse metabolic dynamics after proper perturbation of the microbial system. Here, we present an easy-to-use, purely data-driven approach, defining pool efflux capacities (PEC) for identifying reactions that exert the highest flux control in linear pathways. Comparisons with linlog-based MCA and data-driven substrate elasticities (DDSE) showed that similar key control steps were identified using PEC. Using the example of l-methionine production with recombinant Escherichia coli, PEC consistently and robustly identified main flux controls using perturbation data after a non-labeled 12C-l-serine stimulus. Furthermore, the application of full-labeled 13C-l-serine stimuli yielded additional insights into stimulus propagation to l-methionine. PEC analysis performed on the 13C data set revealed the same targets as the 12C data set. Notably, the typical drawback of metabolome analysis, namely, the omnipresent leakage of metabolites, was excluded using the 13C PEC approach.
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Affiliation(s)
- A Teleki
- Institute of Biochemical Engineering, University of Stuttgart, Allmandring 31, 70569 Stuttgart, Germany
| | - M Rahnert
- Institute of Biochemical Engineering, University of Stuttgart, Allmandring 31, 70569 Stuttgart, Germany
| | - O Bungart
- Institute of Biochemical Engineering, University of Stuttgart, Allmandring 31, 70569 Stuttgart, Germany
| | - B Gann
- Institute of Biochemical Engineering, University of Stuttgart, Allmandring 31, 70569 Stuttgart, Germany
| | - I Ochrombel
- Evonik Nutrition & Care GmbH, Kantstr. 2, 33790 Halle, Germany
| | - R Takors
- Institute of Biochemical Engineering, University of Stuttgart, Allmandring 31, 70569 Stuttgart, Germany.
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22
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Becker M, Junghans L, Teleki A, Bechmann J, Studts J, Voges R, Takors R. In-depth Metabolic Analysis of CHO Perfusion Processes Using Flux Balance Analysis and Intracellular Metabolomics. CHEM-ING-TECH 2016. [DOI: 10.1002/cite.201650194] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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23
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Junghans L, Teleki A, Becker M, Takors R. LC–MS-based compartment-specific metabolome analysis in CHO. N Biotechnol 2016. [DOI: 10.1016/j.nbt.2016.06.842] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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24
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Pfizenmaier J, Junghans L, Teleki A, Takors R. Hyperosmotic stimulus study discloses benefits in ATP supply and reveals miRNA/mRNA targets to improve recombinant protein production of CHO cells. Biotechnol J 2016; 11:1037-47. [PMID: 27214792 DOI: 10.1002/biot.201500606] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2015] [Revised: 03/07/2016] [Accepted: 05/12/2016] [Indexed: 01/02/2023]
Abstract
Biopharmaceuticals are predominantly produced by Chinese hamster ovary (CHO) cells cultivated in fed-batch mode. Hyperosmotic culture conditions (≥ 350 mOsmol kg(∑1) ) resulting from feeding of nutrients may enhance specific product formation rates (qp ). As an improved ATP supply was anticipated to enhance qp this study focused on the identification of suitable miRNA/mRNA targets to increase ATP levels. Therefor next generation sequencing and a compartment specific metabolomics approach were applied to analyze the response of an antibody (mAB) producing CHO cell line upon osmotic shift (280 → 430 mOsmol kg(-1) ). Hyperosmotic culture conditions caused a ∼2.6-fold increase of specific ATP formation rates together with a ∼1.7-fold rise in cytosolic and mitochondrial ATP-pools, thus showing increased ATP supply. mRNA expression analysis identified several genes encoding glycosylated proteins with strictly tissue related function. In addition, hyperosmotic culture conditions induced an upregulation of miR-132-3p, miR-132-5p, miR-182, miR-183, miR-194, miR-215-3p, miR-215-5p which have all been related to cell cycle arrest/proliferation in cancer studies. In relation to a previous independent CHO study miR-183 may be the most promising target to enhance qp by stable overexpression. Furthermore, deletion of genes with presumably dispensable function in suspension growing CHO cells may enhance mAB formation by increased ATP levels.
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Affiliation(s)
- Jennifer Pfizenmaier
- University of Stuttgart, Institute of Biochemical Engineering, Stuttgart, Germany
| | - Lisa Junghans
- University of Stuttgart, Institute of Biochemical Engineering, Stuttgart, Germany
| | - Attila Teleki
- University of Stuttgart, Institute of Biochemical Engineering, Stuttgart, Germany
| | - Ralf Takors
- University of Stuttgart, Institute of Biochemical Engineering, Stuttgart, Germany.
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Matuszczyk JC, Teleki A, Pfizenmaier J, Takors R. Compartment-specific metabolomics for CHO reveals that ATP pools in mitochondria are much lower than in cytosol. Biotechnol J 2015; 10:1639-50. [PMID: 26179617 DOI: 10.1002/biot.201500060] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2015] [Revised: 04/26/2015] [Accepted: 07/06/2015] [Indexed: 01/06/2023]
Abstract
Mammalian cells show a compartmented metabolism. Getting access to subcellular metabolite pools is of high interest to understand the cells' metabolomic state. Therefore a protocol is developed and applied for monitoring compartment-specific metabolite and nucleotide pool sizes in Chinese hamster ovary (CHO) cells. The approach consists of a subtracting filtering method separating cytosolic components from physically intact mitochondrial compartments. The internal standards glucose-6-phosphate and cis-aconitate were chosen to quantify cytosolic secession and mitochondrial membrane integrity. Extracts of related fractions were studied by liquid chromatography-isotope dilution mass spectrometry for the absolute quantification of a subset of glycolytic and tricarboxylic acid cycle intermediates together with the adenylate nucleotides ATP, ADP and AMP. The application of the protocol revealed highly dynamic changes in the related pool sizes as a function of distinct cultivation periods of IgG1 producing CHO cells. Mitochondrial and cytosolic pool dynamics were in agreement with anticipated metabolite pools of independent studies. The analysis of adenosine phosphate levels unraveled significantly higher ATP levels in the cytosol leading to the hypothesis that mitochondria predominantly serve for fueling ATP into the cytosol where it is tightly controlled at physiological adenylate energy charges about 0.9.
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Affiliation(s)
| | - Attila Teleki
- Institute of Biochemical Engineering, Stuttgart University, Stuttgart, Germany
| | | | - Ralf Takors
- Institute of Biochemical Engineering, Stuttgart University, Stuttgart, Germany.
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Ergeneman O, Sivaraman K, Pané S, Pellicer E, Teleki A, Hirt A, Baró M, Nelson B. Morphology, structure and magnetic properties of cobalt–nickel films obtained from acidic electrolytes containing glycine. Electrochim Acta 2011. [DOI: 10.1016/j.electacta.2010.10.068] [Citation(s) in RCA: 83] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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Hilty FM, Teleki A, Krumeich F, Büchel R, Hurrell RF, Pratsinis SE, Zimmermann MB. Development and optimization of iron- and zinc-containing nanostructured powders for nutritional applications. Nanotechnology 2009; 20:475101. [PMID: 19875869 DOI: 10.1088/0957-4484/20/47/475101] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
Reducing the size of low-solubility iron (Fe)-containing compounds to nanoscale has the potential to improve their bioavailability. Because Fe and zinc (Zn) deficiencies often coexist in populations, combined Fe/Zn-containing nanostructured compounds may be useful for nutritional applications. Such compounds are developed here and their solubility in dilute acid, a reliable indicator of iron bioavailability in humans, and sensory qualities in sensitive food matrices are investigated. Phosphates and oxides of Fe and atomically mixed Fe/Zn-containing (primarily ZnFe2O4) nanostructured powders were produced by flame spray pyrolysis (FSP). Chemical composition and surface area were systematically controlled by varying precursor concentration and feed rate during powder synthesis to increase solubility to the level of ferrous sulfate at maximum Fe and Zn content. Solubility of the nanostructured compounds was dependent on their particle size and crystallinity. The new nanostructured powders produced minimal color changes when added to dairy products containing chocolate or fruit compared to the changes produced when ferrous sulfate or ferrous fumarate were added to these foods. Flame-made Fe- and Fe/Zn-containing nanostructured powders have solubilities comparable to ferrous and Zn sulfate but may produce fewer color changes when added to difficult-to-fortify foods. Thus, these powders are promising for food fortification and other nutritional applications.
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Affiliation(s)
- F M Hilty
- Human Nutrition Laboratory, Institute of Food Science and Nutrition, ETH Zurich, Switzerland
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Wengeler R, Teleki A, Vetter M, Wengeler L, Pratsinis SE, Nirschl H. Dispergierung und Fragmentierung pyrogener SiO2- und TiO2-Nanopartikel. CHEM-ING-TECH 2006. [DOI: 10.1002/cite.200650034] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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