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Zhao J, Muawiya MA, Zhuang Y, Wang G. Developing rational scale-down simulators for mimicking substrate heterogeneities based on cell lifelines in industrial-scale bioreactors. BIORESOURCE TECHNOLOGY 2024; 395:130354. [PMID: 38272147 DOI: 10.1016/j.biortech.2024.130354] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/19/2023] [Revised: 01/17/2024] [Accepted: 01/18/2024] [Indexed: 01/27/2024]
Abstract
The influence of extracellular variations on the cellular metabolism and thereby the process performance at large-scale can be evaluated using the so-called scale-down simulators. Nevertheless, the major challenge is to design an appropriate scale-down simulator, which can accurately mimic the cell lifelines that record the flow paths and experiences of cells circulating in large-scale bioreactors. To address this, a dedicated SDSA (scale-down simulator application) was purposedly developed on the basis of black box model and process reaction model established for Penicillium chrysogenum strain as well as cell lifelines or trajectories information in an industrial-scale fermentor. Guided by the SDSA, the industrial-relevant metabolic regimes for substrate availability, i.e., excess, limitation and starvation, were successfully reproduced at laboratory-scale three-compartment scale-down (SD) system. In addition, such SDSA can also display individual process dynamics in each compartment, and demonstrate how individual factors influence the entire bioprocess performance, thus serving both educational and research purposes.
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Affiliation(s)
- Jiachen Zhao
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology (ECUST), Shanghai, People's Republic of China
| | - Muhammad Alkali Muawiya
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology (ECUST), Shanghai, People's Republic of China
| | - Yingping Zhuang
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology (ECUST), Shanghai, People's Republic of China
| | - Guan Wang
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology (ECUST), Shanghai, People's Republic of China.
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2
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Chen LM, Erol Ö, Choi YH, Pronk M, van Loosdrecht M, Lin Y. The water-soluble fraction of extracellular polymeric substances from a resource recovery demonstration plant: characterization and potential application as an adhesive. Front Microbiol 2024; 15:1331120. [PMID: 38468850 PMCID: PMC10925790 DOI: 10.3389/fmicb.2024.1331120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Accepted: 02/07/2024] [Indexed: 03/13/2024] Open
Abstract
Currently, there is a growing interest in transforming wastewater treatment plants (WWTPs) into resource recovery plants. Microorganisms in aerobic granular sludge produce extracellular polymeric substances (EPS), which are considered sustainable resources to be extracted and can be used in diverse applications. Exploring applications in other high-value materials, such as adhesives, will not only enhance the valorization potential of the EPS but also promote resource recovery. This study aimed to characterize a water-soluble fraction extracted from the EPS collected at the demonstration plant in the Netherlands based on its chemical composition (amino acids, sugar, and fatty acids) and propose a proof-of-concept for its use as an adhesive. This fraction comprises a mixture of biomolecules, such as proteins (26.6 ± 0.3%), sugars (21.8 ± 0.2%), and fatty acids (0.9%). The water-soluble fraction exhibited shear strength reaching 36-51 kPa across a pH range of 2-10 without additional chemical treatment, suggesting a potential application as an adhesive. The findings from this study provide insights into the concept of resource recovery and the valorization of excess sludge at WWTPs.
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Affiliation(s)
- Le Min Chen
- Department of Biotechnology, Delft University of Technology, Delft, Netherlands
| | - Özlem Erol
- Natural Products Laboratory, Institute of Biology, Leiden University, Leiden, Netherlands
| | - Young Hae Choi
- Natural Products Laboratory, Institute of Biology, Leiden University, Leiden, Netherlands
| | - Mario Pronk
- Department of Biotechnology, Delft University of Technology, Delft, Netherlands
- Royal HaskoningDHV, Amersfoort, Netherlands
| | - Mark van Loosdrecht
- Department of Biotechnology, Delft University of Technology, Delft, Netherlands
| | - Yuemei Lin
- Department of Biotechnology, Delft University of Technology, Delft, Netherlands
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3
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Yuan Y, Xu F, Ke X, Lu J, Huang M, Chu J. Ammonium sulfate supplementation enhances erythromycin biosynthesis by augmenting intracellular metabolism and precursor supply in Saccharopolyspora erythraea. Bioprocess Biosyst Eng 2023:10.1007/s00449-023-02898-x. [PMID: 37392219 DOI: 10.1007/s00449-023-02898-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2023] [Accepted: 06/21/2023] [Indexed: 07/03/2023]
Abstract
In this study, the cellular metabolic mechanisms regarding ammonium sulfate supplementation on erythromycin production were investigated by employing targeted metabolomics and metabolic flux analysis. The results suggested that the addition of ammonium sulfate stimulates erythromycin biosynthesis. Targeted metabolomics analysis uncovered that the addition of ammonium sulfate during the late stage of fermentation resulted in an augmented intracellular amino acid metabolism pool, guaranteeing an ample supply of precursors for organic acids and coenzyme A-related compounds. Therefore, adequate precursors facilitated cellular maintenance and erythromycin biosynthesis. Subsequently, an optimal supplementation rate of 0.02 g/L/h was determined. The results exhibited that erythromycin titer (1311.1 μg/mL) and specific production rate (0.008 mmol/gDCW/h) were 101.3% and 41.0% higher than those of the process without ammonium sulfate supplementation, respectively. Moreover, the erythromycin A component proportion increased from 83.2% to 99.5%. Metabolic flux analysis revealed increased metabolic fluxes with the supplementation of three ammonium sulfate rates.
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Affiliation(s)
- Yujie Yuan
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, 130 Meilong Road, Shanghai, 200237, People's Republic of China
| | - Feng Xu
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, 130 Meilong Road, Shanghai, 200237, People's Republic of China
| | - Xiang Ke
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, 130 Meilong Road, Shanghai, 200237, People's Republic of China
| | - Ju Lu
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, 130 Meilong Road, Shanghai, 200237, People's Republic of China
| | - Mingzhi Huang
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, 130 Meilong Road, Shanghai, 200237, People's Republic of China.
| | - Ju Chu
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, 130 Meilong Road, Shanghai, 200237, People's Republic of China.
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Puiman L, Almeida Benalcázar E, Picioreanu C, Noorman HJ, Haringa C. Downscaling Industrial-Scale Syngas Fermentation to Simulate Frequent and Irregular Dissolved Gas Concentration Shocks. Bioengineering (Basel) 2023; 10:bioengineering10050518. [PMID: 37237589 DOI: 10.3390/bioengineering10050518] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2023] [Revised: 04/12/2023] [Accepted: 04/20/2023] [Indexed: 05/28/2023] Open
Abstract
In large-scale syngas fermentation, strong gradients in dissolved gas (CO, H2) concentrations are very likely to occur due to locally varying mass transfer and convection rates. Using Euler-Lagrangian CFD simulations, we analyzed these gradients in an industrial-scale external-loop gas-lift reactor (EL-GLR) for a wide range of biomass concentrations, considering CO inhibition for both CO and H2 uptake. Lifeline analyses showed that micro-organisms are likely to experience frequent (5 to 30 s) oscillations in dissolved gas concentrations with one order of magnitude. From the lifeline analyses, we developed a conceptual scale-down simulator (stirred-tank reactor with varying stirrer speed) to replicate industrial-scale environmental fluctuations at bench scale. The configuration of the scale-down simulator can be adjusted to match a broad range of environmental fluctuations. Our results suggest a preference for industrial operation at high biomass concentrations, as this would strongly reduce inhibitory effects, provide operational flexibility and enhance the product yield. The peaks in dissolved gas concentration were hypothesized to increase the syngas-to-ethanol yield due to the fast uptake mechanisms in C. autoethanogenum. The proposed scale-down simulator can be used to validate such results and to obtain data for parametrizing lumped kinetic metabolic models that describe such short-term responses.
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Affiliation(s)
- Lars Puiman
- Department of Biotechnology, Faculty of Applied Sciences, Delft University of Technology, Van der Maasweg 9, 2629 Delft, The Netherlands
| | - Eduardo Almeida Benalcázar
- Department of Biotechnology, Faculty of Applied Sciences, Delft University of Technology, Van der Maasweg 9, 2629 Delft, The Netherlands
| | - Cristian Picioreanu
- Biological and Environmental Science and Engineering, Water Desalination and Reuse Center, King Abdullah University of Science and Technology, Thuwal 23955-6900, Saudi Arabia
| | - Henk J Noorman
- Department of Biotechnology, Faculty of Applied Sciences, Delft University of Technology, Van der Maasweg 9, 2629 Delft, The Netherlands
- Royal DSM, Alexander Fleminglaan 1, 2613 Delft, The Netherlands
| | - Cees Haringa
- Department of Biotechnology, Faculty of Applied Sciences, Delft University of Technology, Van der Maasweg 9, 2629 Delft, The Netherlands
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5
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Janoska A, Buijs J, van Gulik WM. Predicting the influence of combined oxygen and glucose gradients based on scale-down and modelling approaches for the scale-up of penicillin fermentations. Process Biochem 2022. [DOI: 10.1016/j.procbio.2022.11.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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6
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Abstract
Saccharomyces cerevisiae, whose evolutionary past includes a whole-genome duplication event, is characterized by a mosaic genome configuration with substantial apparent genetic redundancy. This apparent redundancy raises questions about the evolutionary driving force for genomic fixation of “minor” paralogs and complicates modular and combinatorial metabolic engineering strategies. While isoenzymes might be important in specific environments, they could be dispensable in controlled laboratory or industrial contexts. The present study explores the extent to which the genetic complexity of the central carbon metabolism (CCM) in S. cerevisiae, here defined as the combination of glycolysis, the pentose phosphate pathway, the tricarboxylic acid cycle, and a limited number of related pathways and reactions, can be reduced by elimination of (iso)enzymes without major negative impacts on strain physiology. Cas9-mediated, groupwise deletion of 35 of the 111 genes yielded a “minimal CCM” strain which, despite the elimination of 32% of CCM-related proteins, showed only a minimal change in phenotype on glucose-containing synthetic medium in controlled bioreactor cultures relative to a congenic reference strain. Analysis under a wide range of other growth and stress conditions revealed remarkably few phenotypic changes from the reduction of genetic complexity. Still, a well-documented context-dependent role of GPD1 in osmotolerance was confirmed. The minimal CCM strain provides a model system for further research into genetic redundancy of yeast genes and a platform for strategies aimed at large-scale, combinatorial remodeling of yeast CCM.
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7
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Janoska A, Verheijen JJ, Tang W, Lee Q, Sikkema B, van Gulik WM. Influence of oxygen concentration on the metabolism of Penicillium chrysogenum. Eng Life Sci 2022; 23:e2100139. [PMID: 36619886 PMCID: PMC9815084 DOI: 10.1002/elsc.202100139] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2021] [Revised: 02/17/2022] [Accepted: 03/08/2022] [Indexed: 01/11/2023] Open
Abstract
In large-scale bioreactors, there is often insufficient mixing and as a consequence, cells experience uneven substrate and oxygen levels that influence product formation. In this study, the influence of dissolved oxygen (DO) gradients on the primary and secondary metabolism of a high producing industrial strain of Penicillium chrysogenum was investigated. Within a wide range of DO concentrations, obtained under chemostat conditions, we observed different responses from P. chrysogenum: (i) no influence on growth or penicillin production (>0.025 mmol L-1); (ii) reduced penicillin production, but no growth limitation (0.013-0.025 mmol L-1); and (iii) growth and penicillin production limitations (<0.013 mmol L-1). In addition, scale down experiments were performed by oscillating the DO concentration in the bioreactor. We found that during DO oscillation, the penicillin production rate decreased below the value observed when a constant DO equal to the average oscillating DO value was used. To understand and predict the influence of oxygen levels on primary metabolism and penicillin production, we developed a black box model that was linked to a detailed kinetic model of the penicillin pathway. The model simulations represented the experimental data during the step experiments; however, during the oscillation experiments the predictions deviated, indicating the involvement of the central metabolism in penicillin production.
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Affiliation(s)
- Agnes Janoska
- Department of BiotechnologyDelft University of TechnologyDelftThe Netherlands
| | - Jelle J. Verheijen
- Department of BiotechnologyDelft University of TechnologyDelftThe Netherlands
| | - Wenjung Tang
- Department of BiotechnologyDelft University of TechnologyDelftThe Netherlands,DSM Biotechnology CenterAlexander Fleminglaan 1DelftNetherlands
| | - Queenie Lee
- Department of BiotechnologyDelft University of TechnologyDelftThe Netherlands
| | - Baukje Sikkema
- Department of BiotechnologyDelft University of TechnologyDelftThe Netherlands
| | - Walter M. van Gulik
- Department of BiotechnologyDelft University of TechnologyDelftThe Netherlands
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8
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Haringa C, Tang W, Noorman HJ. Stochastic parcel tracking in an Euler-Lagrange compartment model for fast simulation of fermentation processes. Biotechnol Bioeng 2022; 119:1849-1860. [PMID: 35352339 PMCID: PMC9321588 DOI: 10.1002/bit.28094] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2021] [Accepted: 02/02/2022] [Indexed: 11/23/2022]
Abstract
The compartment model (CM) is a well‐known approach for computationally affordable, spatially resolved hydrodynamic modeling of unit operations. Recent implementations use flow profiles based on Computational Fluid Dynamics (CFD) simulations, and several authors included microbial kinetics to simulate gradients in bioreactors. However, these studies relied on black‐box kinetics that do not account for intracellular changes and cell population dynamics in response to heterogeneous environments. In this paper, we report the implementation of a Lagrangian reaction model, where the microbial phase is tracked as a set of biomass‐parcels, each linked with an intracellular composition vector and a structured reaction model describing their intracellular response to extracellular variations. A stochastic parcel tracking approach is adopted, in contrast to the resolved trajectories used in CFD implementations. A penicillin production process is used as a case study. We show good performance of the model compared with full CFD simulations, both regarding the extracellular gradients and intracellular pool response, using the mixing time as a matching criterion and taking into account that the mixing time is sensitive to the number of compartments. The sensitivity of the model output towards some of the inputs is explored. The coarsest representative CM requires a few minutes to solve 80 h of flow time, compared with approximately 2 weeks for a full Euler–Lagrange CFD simulation of the same case. This alleviates one of the major bottlenecks for the application of such CFD simulations towards the analysis and optimization of industrial fermentation processes.
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Affiliation(s)
- Cees Haringa
- Biotechnology Department, Bioprocess EngineeringDelft University of TechnologyDelftThe Netherlands
| | - Wenjun Tang
- Biotechnology Department, Bioprocess EngineeringDelft University of TechnologyDelftThe Netherlands
- Department of Biotechnology, Bioprocess Engineering group, Faculty of Applied Sciences, Delft University of TechnologyRoyal DSMDelftThe Netherlands
| | - Henk J. Noorman
- Biotechnology Department, Bioprocess EngineeringDelft University of TechnologyDelftThe Netherlands
- Department of Biotechnology, Bioprocess Engineering group, Faculty of Applied Sciences, Delft University of TechnologyRoyal DSMDelftThe Netherlands
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9
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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: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [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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10
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Haringa C. An analysis of organism lifelines in an industrial bioreactor using Lattice-Boltzmann CFD. Eng Life Sci 2022; 23:e2100159. [PMID: 36619885 PMCID: PMC9815090 DOI: 10.1002/elsc.202100159] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2021] [Revised: 02/03/2022] [Accepted: 02/24/2022] [Indexed: 01/11/2023] Open
Abstract
Euler-Lagrange CFD simulations, where the biotic phase is represented by computational particles (parcels), provide information on environmental gradients inside bioreactors from the microbial perspective. Such information is highly relevant for reactor scale-down and process optimization. One of the major challenges is the computational intensity of CFD simulations, especially when resolution of dynamics in the flowfield is required. Lattice-Boltzmann large-eddy simulations (LB-LES) form a very promising approach for simulating accurate, dynamic flowfields in stirred reactors, at strongly reduced computation times compared to finite volume approaches. In this work, the performance of LB-LES in resolving substrate gradients in large-scale bioreactors is explored, combined with the inclusion of a Lagrangian biotic phase to provide the microbial perspective. In addition, the hydrodynamic performance of the simulations is confirmed by verification of hydrodynamic characteristics (radial velocity, turbulent kinetic energy, energy dissipation) in the impeller discharge stream of a 29 cm diameter stirred tank. The results are compared with prior finite volume simulation results, both in terms of hydrodynamic and biokinetic observations, and time requirements.
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Affiliation(s)
- Cees Haringa
- Bioprocess EngineeringBiotechnology DepartmentDelft University of TechnologyDelftthe Netherlands
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11
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Yang Q, Lin W, Xu J, Guo N, Zhao J, Wang G, Wang Y, Chu J, Wang G. Changes in Oxygen Availability during Glucose-Limited Chemostat Cultivations of Penicillium chrysogenum Lead to Rapid Metabolite, Flux and Productivity Responses. Metabolites 2022; 12:metabo12010045. [PMID: 35050169 PMCID: PMC8780904 DOI: 10.3390/metabo12010045] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Revised: 01/02/2022] [Accepted: 01/03/2022] [Indexed: 02/01/2023] Open
Abstract
Bioreactor scale-up from the laboratory scale to the industrial scale has always been a pivotal step in bioprocess development. However, the transition of a bioeconomy from innovation to commercialization is often hampered by performance loss in titer, rate and yield. These are often ascribed to temporal variations of substrate and dissolved oxygen (for instance) in the environment, experienced by microorganisms at the industrial scale. Oscillations in dissolved oxygen (DO) concentration are not uncommon. Furthermore, these fluctuations can be exacerbated with poor mixing and mass transfer limitations, especially in fermentations with filamentous fungus as the microbial cell factory. In this work, the response of glucose-limited chemostat cultures of an industrial Penicillium chrysogenum strain to different dissolved oxygen levels was assessed under both DO shift-down (60% → 20%, 10% and 5%) and DO ramp-down (60% → 0% in 24 h) conditions. Collectively, the results revealed that the penicillin productivity decreased as the DO level dropped down below 20%, while the byproducts, e.g., 6-oxopiperidine-2-carboxylic acid (OPC) and 6-aminopenicillanic acid (6APA), accumulated. Following DO ramp-down, penicillin productivity under DO shift-up experiments returned to its maximum value in 60 h when the DO was reset to 60%. The result showed that a higher cytosolic redox status, indicated by NADH/NAD+, was observed in the presence of insufficient oxygen supply. Consistent with this, flux balance analysis indicated that the flux through the glyoxylate shunt was increased by a factor of 50 at a DO value of 5% compared to the reference control, favoring the maintenance of redox status. Interestingly, it was observed that, in comparison with the reference control, the penicillin productivity was reduced by 25% at a DO value of 5% under steady state conditions. Only a 14% reduction in penicillin productivity was observed as the DO level was ramped down to 0. Furthermore, intracellular levels of amino acids were less sensitive to DO levels at DO shift-down relative to DO ramp-down conditions; this difference could be caused by different timescales between turnover rates of amino acid pools (tens of seconds to minutes) and DO switches (hours to days at steady state and minutes to hours at ramp-down). In summary, this study showed that changes in oxygen availability can lead to rapid metabolite, flux and productivity responses, and dynamic DO perturbations could provide insight into understanding of metabolic responses in large-scale bioreactors.
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12
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Ziegler M, Zieringer J, Döring CL, Paul L, Schaal C, Takors R. Engineering of a robust Escherichia coli chassis and exploitation for large-scale production processes. Metab Eng 2021; 67:75-87. [PMID: 34098100 DOI: 10.1016/j.ymben.2021.05.011] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2020] [Revised: 05/30/2021] [Accepted: 05/31/2021] [Indexed: 11/28/2022]
Abstract
In large-scale bioprocesses microbes are exposed to heterogeneous substrate availability reducing the overall process performance. A series of deletion strains was constructed from E. coli MG1655 aiming for a robust phenotype in heterogeneous fermentations with transient starvation. Deletion targets were hand-picked based on a list of genes derived from previous large-scale simulation runs. Each gene deletion was conducted on the premise of strict neutrality towards growth parameters in glucose minimal medium. The final strain of the series, named E. coli RM214, was cultivated continuously in an STR-PFR (stirred tank reactor - plug flow reactor) scale-down reactor. The scale-down reactor system simulated repeated passages through a glucose starvation zone. When exposed to nutrient gradients, E. coli RM214 had a significantly lower maintenance coefficient than E. coli MG1655 (Δms = 0.038 gGlucose/gCDW/h, p < 0.05). In an exemplary protein production scenario E. coli RM214 remained significantly more productive than E. coli MG1655 reaching 44% higher eGFP yield after 28 h of STR-PFR cultivation. This study developed E. coli RM214 as a robust chassis strain and demonstrated the feasibility of engineering microbial hosts for large-scale applications.
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Affiliation(s)
- Martin Ziegler
- University of Stuttgart - Institute of Biochemical Engineering, Allmandring 31, 70569, Stuttgart, Germany.
| | - Julia Zieringer
- University of Stuttgart - Institute of Biochemical Engineering, Allmandring 31, 70569, Stuttgart, Germany.
| | - Clarissa-Laura Döring
- University of Stuttgart - Institute of Biochemical Engineering, Allmandring 31, 70569, Stuttgart, Germany.
| | - Liv Paul
- University of Stuttgart - Institute of Biochemical Engineering, Allmandring 31, 70569, Stuttgart, Germany.
| | - Christoph Schaal
- University of Stuttgart - Institute of Biochemical Engineering, Allmandring 31, 70569, Stuttgart, Germany.
| | - Ralf Takors
- University of Stuttgart - Institute of Biochemical Engineering, Allmandring 31, 70569, Stuttgart, Germany.
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13
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Ziegler M, Zieringer J, Takors R. Transcriptional profiling of the stringent response mutant strain E. coli SR reveals enhanced robustness to large-scale conditions. Microb Biotechnol 2021; 14:993-1010. [PMID: 33369128 PMCID: PMC8085953 DOI: 10.1111/1751-7915.13738] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2020] [Revised: 12/08/2020] [Accepted: 12/08/2020] [Indexed: 12/05/2022] Open
Abstract
In large-scale fed-batch production processes, microbes are exposed to heterogeneous substrate availability caused by long mixing times. Escherichia coli, the most common industrial host for recombinant protein production, reacts by recurring accumulation of the alarmone ppGpp and energetically wasteful transcriptional strategies. Here, we compare the regulatory responses of the stringent response mutant strain E. coli SR and its parent strain E. coli MG1655 to repeated nutrient starvation in a two-compartment scale-down reactor. Our data show that E. coli SR can withstand these stress conditions without a ppGpp-mediated stress response maintaining fully functional ammonium uptake and biomass formation. Furthermore, E. coli SR exhibited a substantially reduced short-term transcriptional response compared to E. coli MG1655 (less than half as many differentially expressed genes). E. coli SR proceeded adaptation via more general SOS response pathways by initiating negative regulation of transcription, translation and cell division. Our results show that locally induced stress responses propagating through the bioreactor do not result in cyclical induction and repression of genes in E. coli SR, but in a reduced and coordinated response, which makes it potentially suitable for large-scale production processes.
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Affiliation(s)
- Martin Ziegler
- Institute of Biochemical EngineeringUniversity of StuttgartStuttgartGermany
| | - Julia Zieringer
- Institute of Biochemical EngineeringUniversity of StuttgartStuttgartGermany
| | - Ralf Takors
- Institute of Biochemical EngineeringUniversity of StuttgartStuttgartGermany
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14
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Liu P, Wang S, Li C, Zhuang Y, Xia J, Noorman H. Dynamic response of Aspergillus niger to periodical glucose pulse stimuli in chemostat cultures. Biotechnol Bioeng 2021; 118:2265-2282. [PMID: 33666237 DOI: 10.1002/bit.27739] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2020] [Revised: 01/05/2021] [Accepted: 01/21/2021] [Indexed: 12/15/2022]
Abstract
In industrial large-scale bioreactors, microorganisms encounter heterogeneous substrate concentration conditions, which can impact growth or product formation. Here we carried out an extended (12 h) experiment of repeated glucose pulsing with a 10-min period to simulate fluctuating glucose concentrations with Aspergillus niger producing glucoamylase, and investigated its dynamic response by rapid sampling and quantitative metabolomics. The 10-min period represents worst-case conditions, as in industrial bioreactors the average cycling duration is usually in the order of 1 min. We found that cell growth and the glucoamylase productivity were not significantly affected, despite striking metabolomic dynamics. Periodical dynamic responses were found across all central carbon metabolism pathways, with different time scales, and the frequently reported ATP paradox was confirmed for this A. niger strain under the dynamic conditions. A thermodynamics analysis revealed that several reactions of the central carbon metabolism remained in equilibrium even under periodical dynamic conditions. The dynamic response profiles of the intracellular metabolites did not change during the pulse exposure, showing no significant adaptation of the strain to the more than 60 perturbation cycles applied. The apparent high tolerance of the glucoamylase producing A. niger strain for extreme variations in the glucose availability presents valuable information for the design of robust industrial microbial hosts.
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Affiliation(s)
- Peng Liu
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China
| | - Shuai Wang
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China
| | - Chao Li
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China
| | - Yingping Zhuang
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China
| | - Jianye Xia
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China
| | - Henk Noorman
- DSM Biotechnology Center, Delft, The Netherlands
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Impact of Altered Trehalose Metabolism on Physiological Response of Penicillium chrysogenum Chemostat Cultures during Industrially Relevant Rapid Feast/Famine Conditions. Processes (Basel) 2021. [DOI: 10.3390/pr9010118] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
Due to insufficient mass transfer and mixing issues, cells in the industrial-scale bioreactor are often forced to experience glucose feast/famine cycles, mostly resulting in reduced commercial metrics (titer, yield and productivity). Trehalose cycling has been confirmed as a double-edged sword in the Penicillium chrysogenum strain, which facilitates the maintenance of a metabolically balanced state, but it consumes extra amounts of the ATP responsible for the repeated breakdown and formation of trehalose molecules in response to extracellular glucose perturbations. This loss of ATP would be in competition with the high ATP-demanding penicillin biosynthesis. In this work, the role of trehalose metabolism was further explored under industrially relevant conditions by cultivating a high-yielding Penicillium chrysogenum strain, and the derived trehalose-null strains in the glucose-limited chemostat system where the glucose feast/famine condition was imposed. This dynamic feast/famine regime with a block-wise feed/no feed regime (36 s on, 324 s off) allows one to generate repetitive cycles of moderate changes in glucose availability. The results obtained using quantitative metabolomics and stoichiometric analysis revealed that the intact trehalose metabolism is vitally important for maintaining penicillin production capacity in the Penicillium chrysogenum strain under both steady state and dynamic conditions. Additionally, cells lacking such a key metabolic regulator would become more sensitive to industrially relevant conditions, and are more able to sustain metabolic rearrangements, which manifests in the shrinkage of the central metabolite pool size and the formation of ATP-consuming futile cycles.
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16
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Gelain L, Geraldo da Cruz Pradella J, Carvalho da Costa A, van der Wielen L, van Gulik WM. A possible influence of extracellular polysaccharides on the analysis of intracellular metabolites from Trichoderma harzianum grown under carbon-limited conditions. Fungal Biol 2020; 125:368-377. [PMID: 33910678 DOI: 10.1016/j.funbio.2020.12.002] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2020] [Revised: 10/30/2020] [Accepted: 12/08/2020] [Indexed: 11/19/2022]
Abstract
Intracellular metabolites were evaluated during the continuous growth of Trichoderma harzianum P49P11 under carbon-limited conditions. Four different conditions in duplicate were investigated (10 and 20 g/L of glucose, 5.26/5.26 g/L of fructose/glucose and 10 g/L of sucrose in the feed). Differences in the values of some specific concentrations of intracellular metabolites were observed at steady-state for the duplicates. The presence of extracellular polysaccharide was confirmed in the supernatant of all conditions based on FT-IR and proton NMR. Fragments of polysaccharides from the cell wall could be released due to the shear stress and since the cells can consume them under carbon-limited conditions, this could create an unpredictable carbon flow rate into the cells. According to the values of the metabolite concentrations, it was considered that the consumption of those fragments was interfering with the analysis.
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Affiliation(s)
- Lucas Gelain
- Delft University of Technology, Department of Biotechnology, Van der Maasweg 9, 2629HZ, Delft, the Netherlands; University of Campinas, School of Chemical Engineering, Av. Albert Einstein, 500, Campinas, Brazil.
| | - José Geraldo da Cruz Pradella
- Federal University of São Paulo, Institute of Science and Technology, Av. Cesare Mansueto Giulio Lattes, 1201, S. J. Campos, Brazil
| | - Aline Carvalho da Costa
- University of Campinas, School of Chemical Engineering, Av. Albert Einstein, 500, Campinas, Brazil
| | - Luuk van der Wielen
- Delft University of Technology, Department of Biotechnology, Van der Maasweg 9, 2629HZ, Delft, the Netherlands; University of Limerick, Bernal Institute, V94 T9PX, Limerick, Ireland
| | - Walter M van Gulik
- Delft University of Technology, Department of Biotechnology, Van der Maasweg 9, 2629HZ, Delft, the Netherlands
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17
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Understanding gradients in industrial bioreactors. Biotechnol Adv 2020; 46:107660. [PMID: 33221379 DOI: 10.1016/j.biotechadv.2020.107660] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2020] [Revised: 10/22/2020] [Accepted: 11/14/2020] [Indexed: 01/07/2023]
Abstract
Gradients in industrial bioreactors have attracted substantial research attention since exposure to fluctuating environmental conditions has been shown to lead to changes in the metabolome, transcriptome as well as population heterogeneity in industrially relevant microorganisms. Such changes have also been found to impact key process parameters like the yield on substrate and the productivity. Hence, understanding gradients is important from both the academic and industrial perspectives. In this review the causes of gradients are outlined, along with their impact on microbial physiology. Quantifying the impact of gradients requires a detailed understanding of both fluid flow inside industrial equipment and microbial physiology. This review critically examines approaches used to investigate gradients including large-scale experimental work, computational methods and scale-down approaches. Avenues for future work have been highlighted, particularly the need for further coordinated development of both in silico and experimental tools which can be used to further the current understanding of gradients in industrial equipment.
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18
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Analysis of the proteins secreted by Trichoderma harzianum P49P11 under carbon-limited conditions. J Proteomics 2020; 227:103922. [DOI: 10.1016/j.jprot.2020.103922] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2020] [Revised: 07/22/2020] [Accepted: 07/24/2020] [Indexed: 02/06/2023]
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19
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Wang G, Haringa C, Noorman H, Chu J, Zhuang Y. Developing a Computational Framework To Advance Bioprocess Scale-Up. Trends Biotechnol 2020; 38:846-856. [DOI: 10.1016/j.tibtech.2020.01.009] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2019] [Revised: 01/27/2020] [Accepted: 01/29/2020] [Indexed: 01/10/2023]
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20
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Vasilakou E, van Loosdrecht MCM, Wahl SA. Escherichia coli metabolism under short-term repetitive substrate dynamics: adaptation and trade-offs. Microb Cell Fact 2020; 19:116. [PMID: 32471427 PMCID: PMC7260802 DOI: 10.1186/s12934-020-01379-0] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2020] [Accepted: 05/25/2020] [Indexed: 12/04/2022] Open
Abstract
Background Microbial metabolism is highly dependent on the environmental conditions. Especially, the substrate concentration, as well as oxygen availability, determine the metabolic rates. In large-scale bioreactors, microorganisms encounter dynamic conditions in substrate and oxygen availability (mixing limitations), which influence their metabolism and subsequently their physiology. Earlier, single substrate pulse experiments were not able to explain the observed physiological changes generated under large-scale industrial fermentation conditions. Results In this study we applied a repetitive feast–famine regime in an aerobic Escherichia coli culture in a time-scale of seconds. The regime was applied for several generations, allowing cells to adapt to the (repetitive) dynamic environment. The observed response was highly reproducible over the cycles, indicating that cells were indeed fully adapted to the regime. We observed an increase of the specific substrate and oxygen consumption (average) rates during the feast–famine regime, compared to a steady-state (chemostat) reference environment. The increased rates at same (average) growth rate led to a reduced biomass yield (30% lower). Interestingly, this drop was not followed by increased by-product formation, pointing to the existence of energy-spilling reactions. During the feast–famine cycle, the cells rapidly increased their uptake rate. Within 10 s after the beginning of the feeding, the substrate uptake rate was higher (4.68 μmol/gCDW/s) than reported during batch growth (3.3 μmol/gCDW/s). The high uptake led to an accumulation of several intracellular metabolites, during the feast phase, accounting for up to 34% of the carbon supplied. Although the metabolite concentrations changed rapidly, the cellular energy charge remained unaffected, suggesting well-controlled balance between ATP producing and ATP consuming reactions. Conclusions The adaptation of the physiology and metabolism of E. coli under substrate dynamics, representative for large-scale fermenters, revealed the existence of several cellular mechanisms coping with stress. Changes in the substrate uptake system, storage potential and energy-spilling processes resulted to be of great importance. These metabolic strategies consist a meaningful step to further tackle reduced microbial performance, observed under large-scale cultivations.
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Affiliation(s)
- Eleni Vasilakou
- Department of Biotechnology, Delft University of Technology, Van der Maasweg, 2629 HZ, Delft, The Netherlands.
| | - Mark C M van Loosdrecht
- Department of Biotechnology, Delft University of Technology, Van der Maasweg, 2629 HZ, Delft, The Netherlands
| | - S Aljoscha Wahl
- Department of Biotechnology, Delft University of Technology, Van der Maasweg, 2629 HZ, Delft, The Netherlands.
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21
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Felz S, Neu TR, van Loosdrecht MCM, Lin Y. Aerobic granular sludge contains Hyaluronic acid-like and sulfated glycosaminoglycans-like polymers. WATER RESEARCH 2020; 169:115291. [PMID: 31734393 DOI: 10.1016/j.watres.2019.115291] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/23/2019] [Revised: 09/30/2019] [Accepted: 11/06/2019] [Indexed: 06/10/2023]
Abstract
Glycosaminoglycans (GAGs) are linear heteropolysaccharides containing a derivative of an amino sugar. The possibility of the presence of GAGs in aerobic granular sludge was studied by combining SDS-PAGE with Alcian Blue staining (at pH 2.5 and 1), FTIR, mammalian Hyaluronic acid and sulfated GAG analysis kits, enzymatic digestion and specific in situ visualization by Heparin Red and lectin staining. GAGs, including Hyaluronic acid-like and sulfated GAGs-like polymers were found in aerobic granular sludge. The sulfated GAGs-like polymers contained Chondroitin sulfate and Heparan sulfate/Heparin based on their sensitivity to the digestion by Chondroitinase ABC and Heparinase I & III. Heparin Red and lectin staining demonstrated that, the sulfated GAGs-like polymers were not only present in the extracellular matrix, but also filled in the space between the cells inside the microcolonies. The GAGs-like polymers in aerobic granules were different from those produced by pathogenic bacteria but resemble those produced by vertebrates. Findings reported here and in previous studies on granular sludge described in literature indicate that GAGs-like polymers might be widespread in granular sludge/biofilm and contribute to the stability of these systems. The extracellular polymeric substances (EPS) in granular sludge/biofilm are far more complicated than they are currently appreciated. Integrated and multidisciplinary analyses are significantly required to study the EPS.
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Affiliation(s)
- Simon Felz
- Department of Biotechnology, Delft University of Technology, Van der Maasweg 9, 2629 HZ, Delft, the Netherlands
| | - Thomas R Neu
- Microbiology of Interfaces, Department River Ecology, Helmholtz Centre for Environmental Research - UFZ, Brueckstrasse 3A, 39114, Magdeburg, Germany
| | - Mark C M van Loosdrecht
- Department of Biotechnology, Delft University of Technology, Van der Maasweg 9, 2629 HZ, Delft, the Netherlands
| | - Yuemei Lin
- Department of Biotechnology, Delft University of Technology, Van der Maasweg 9, 2629 HZ, Delft, the Netherlands.
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22
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Valk LC, Luttik MAH, de Ram C, Pabst M, van den Broek M, van Loosdrecht MCM, Pronk JT. A Novel D-Galacturonate Fermentation Pathway in Lactobacillus suebicus Links Initial Reactions of the Galacturonate-Isomerase Route With the Phosphoketolase Pathway. Front Microbiol 2020; 10:3027. [PMID: 32010092 PMCID: PMC6978723 DOI: 10.3389/fmicb.2019.03027] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2019] [Accepted: 12/17/2019] [Indexed: 11/13/2022] Open
Abstract
D-galacturonate, a key constituent of pectin, is a ubiquitous monomer in plant biomass. Anaerobic, fermentative conversion of D-galacturonate is therefore relevant in natural environments as well as in microbial processes for microbial conversion of pectin-containing agricultural residues. In currently known microorganisms that anaerobically ferment D-galacturonate, its catabolism occurs via the galacturonate-isomerase pathway. Redox-cofactor balancing in this pathway strongly constrains the possible range of products generated from anaerobic D-galacturonate fermentation, resulting in acetate as the predominant organic fermentation product. To explore metabolic diversity of microbial D-galacturonate fermentation, anaerobic enrichment cultures were performed at pH 4. Anaerobic batch and chemostat cultures of a dominant Lactobacillus suebicus strain isolated from these enrichment cultures produced near-equimolar amounts of lactate and acetate from D-galacturonate. A combination of whole-genome sequence analysis, quantitative proteomics, enzyme activity assays in cell extracts, and in vitro product identification demonstrated that D-galacturonate metabolism in L. suebicus occurs via a novel pathway. In this pathway, mannonate generated by the initial reactions of the canonical isomerase pathway is converted to 6-phosphogluconate by two novel biochemical reactions, catalyzed by a mannonate kinase and a 6-phosphomannonate 2-epimerase. Further catabolism of 6-phosphogluconate then proceeds via known reactions of the phosphoketolase pathway. In contrast to the classical isomerase pathway for D-galacturonate catabolism, the novel pathway enables redox-cofactor-neutral conversion of D-galacturonate to ribulose-5-phosphate. While further research is required to identify the structural genes encoding the key enzymes for the novel pathway, its redox-cofactor coupling is highly interesting for metabolic engineering of microbial cell factories for conversion of pectin-containing feedstocks into added-value fermentation products such as ethanol or lactate. This study illustrates the potential of microbial enrichment cultivation to identify novel pathways for the conversion of environmentally and industrially relevant compounds.
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Affiliation(s)
| | | | | | | | | | | | - Jack T. Pronk
- Department of Biotechnology, Delft University of Technology, Delft, Netherlands
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23
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Wang G, Haringa C, Tang W, Noorman H, Chu J, Zhuang Y, Zhang S. Coupled metabolic-hydrodynamic modeling enabling rational scale-up of industrial bioprocesses. Biotechnol Bioeng 2019; 117:844-867. [PMID: 31814101 DOI: 10.1002/bit.27243] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2019] [Revised: 11/28/2019] [Accepted: 11/30/2019] [Indexed: 12/13/2022]
Abstract
Metabolomics aims to address what and how regulatory mechanisms are coordinated to achieve flux optimality, different metabolic objectives as well as appropriate adaptations to dynamic nutrient availability. Recent decades have witnessed that the integration of metabolomics and fluxomics within the goal of synthetic biology has arrived at generating the desired bioproducts with improved bioconversion efficiency. Absolute metabolite quantification by isotope dilution mass spectrometry represents a functional readout of cellular biochemistry and contributes to the establishment of metabolic (structured) models required in systems metabolic engineering. In industrial practices, population heterogeneity arising from fluctuating nutrient availability frequently leads to performance losses, that is reduced commercial metrics (titer, rate, and yield). Hence, the development of more stable producers and more predictable bioprocesses can benefit from a quantitative understanding of spatial and temporal cell-to-cell heterogeneity within industrial bioprocesses. Quantitative metabolomics analysis and metabolic modeling applied in computational fluid dynamics (CFD)-assisted scale-down simulators that mimic industrial heterogeneity such as fluctuations in nutrients, dissolved gases, and other stresses can procure informative clues for coping with issues during bioprocessing scale-up. In previous studies, only limited insights into the hydrodynamic conditions inside the industrial-scale bioreactor have been obtained, which makes case-by-case scale-up far from straightforward. Tracking the flow paths of cells circulating in large-scale bioreactors is a highly valuable tool for evaluating cellular performance in production tanks. The "lifelines" or "trajectories" of cells in industrial-scale bioreactors can be captured using Euler-Lagrange CFD simulation. This novel methodology can be further coupled with metabolic (structured) models to provide not only a statistical analysis of cell lifelines triggered by the environmental fluctuations but also a global assessment of the metabolic response to heterogeneity inside an industrial bioreactor. For the future, the industrial design should be dependent on the computational framework, and this integration work will allow bioprocess scale-up to the industrial scale with an end in mind.
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Affiliation(s)
- Guan Wang
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, People's Republic of China
| | - Cees Haringa
- Transport Phenomena, Chemical Engineering Department, Delft University of Technology, Delft, The Netherlands.,DSM Biotechnology Center, Delft, The Netherlands
| | - Wenjun Tang
- DSM Biotechnology Center, Delft, The Netherlands
| | - Henk Noorman
- DSM Biotechnology Center, Delft, The Netherlands.,Bioprocess Engineering, Department of Biotechnology, Delft University of Technology, Delft, The Netherlands
| | - Ju Chu
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, People's Republic of China
| | - Yingping Zhuang
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, People's Republic of China
| | - Siliang Zhang
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, People's Republic of China
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24
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Liu X, Wang T, Sun X, Wang Z, Tian X, Zhuang Y, Chu J. Optimized sampling protocol for mass spectrometry-based metabolomics in Streptomyces. BIORESOUR BIOPROCESS 2019. [DOI: 10.1186/s40643-019-0269-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
Abstract
In quantitative metabolomics studies, the most crucial step was arresting snapshots of all interesting metabolites. However, the procedure customized for Streptomyces was so rare that most studies consulted the procedure from other bacteria even yeast, leading to inaccurate and unreliable metabolomics analysis. In this study, a base solution (acetone: ethanol = 1:1, mol/mol) was added to a quenching solution to keep the integrity of the cell membrane. Based on the molar transition energy (ET) of the organic solvents, five solutions were used to carry out the quenching procedures. These were acetone, isoamylol, propanol, methanol, and 60% (v/v) methanol. To the best of our knowledge, this is the first report which has utilized a quenching solution with ET values. Three procedures were also adopted for extraction. These were boiling, freezing–thawing, and grinding ethanol. Following the analysis of the mass balance, amino acids, organic acids, phosphate sugars, and sugar alcohols were measured using gas chromatography with an isotope dilution mass spectrometry. It was found that using isoamylol with a base solution (5:1, v/v) as a quenching solution and that freezing–thawing in liquid nitrogen within 50% (v/v) methanol as an extracting procedure were the best pairing for the quantitative metabolomics of Streptomyces ZYJ-6, and resulted in average recoveries of close to 100%. The concentration of intracellular metabolites obtained from this new quenching solution was between two and ten times higher than that from 60% (v/v) methanol, which until now has been the most commonly used solution. Our findings are the first systematic quantitative metabolomics tools for Streptomyces ZYJ-6 and, therefore, will be important references for research in fields such as 13C based metabolic flux analysis, multi-omic research and genome-scale metabolic model establishment, as well as for other Streptomyces.
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25
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Wang G, Wang X, Wang T, Gulik W, Noorman HJ, Zhuang Y, Chu J, Zhang S. Comparative Fluxome and Metabolome Analysis of Formate as an Auxiliary Substrate for Penicillin Production in Glucose‐Limited Cultivation of
Penicillium chrysogenum. Biotechnol J 2019; 14:e1900009. [DOI: 10.1002/biot.201900009] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2019] [Revised: 05/20/2019] [Indexed: 12/11/2022]
Affiliation(s)
- Guan Wang
- State Key Laboratory of Bioreactor EngineeringEast China University of Science and Technology (ECUST) 130 Meilong Road Shanghai 200237 P. R. China
| | - Xinxin Wang
- State Key Laboratory of Bioreactor EngineeringEast China University of Science and Technology (ECUST) 130 Meilong Road Shanghai 200237 P. R. China
| | - Tong Wang
- State Key Laboratory of Bioreactor EngineeringEast China University of Science and Technology (ECUST) 130 Meilong Road Shanghai 200237 P. R. China
| | - Walter Gulik
- Cell Systems Engineering, Department of BiotechnologyDelft University of Technology Delft The Netherlands
| | - Henk J. Noorman
- DSM Biotechnology Center Delft The Netherlands
- Department of BiotechnologyDelft University of Technology Delft The Netherlands
| | - Yingping Zhuang
- State Key Laboratory of Bioreactor EngineeringEast China University of Science and Technology (ECUST) 130 Meilong Road Shanghai 200237 P. R. China
| | - Ju Chu
- State Key Laboratory of Bioreactor EngineeringEast China University of Science and Technology (ECUST) 130 Meilong Road Shanghai 200237 P. R. China
| | - Siliang Zhang
- State Key Laboratory of Bioreactor EngineeringEast China University of Science and Technology (ECUST) 130 Meilong Road Shanghai 200237 P. R. China
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26
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Wang G, Zhao J, Wang X, Wang T, Zhuang Y, Chu J, Zhang S, Noorman HJ. Quantitative metabolomics and metabolic flux analysis reveal impact of altered trehalose metabolism on metabolic phenotypes of Penicillium chrysogenum in aerobic glucose-limited chemostats. Biochem Eng J 2019. [DOI: 10.1016/j.bej.2019.03.006] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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27
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Wang G, Chu J, Zhuang Y, van Gulik W, Noorman H. A dynamic model-based preparation of uniformly-13C-labeled internal standards facilitates quantitative metabolomics analysis of Penicillium chrysogenum. J Biotechnol 2019; 299:21-31. [DOI: 10.1016/j.jbiotec.2019.04.021] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2019] [Revised: 04/03/2019] [Accepted: 04/25/2019] [Indexed: 01/03/2023]
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28
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Wang S, Liu P, Shu W, Li C, Li H, Liu S, Xia J, Noorman H. Dynamic response of Aspergillus niger to single pulses of glucose with high and low concentrations. BIORESOUR BIOPROCESS 2019. [DOI: 10.1186/s40643-019-0251-y] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
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29
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Liu X, Sun X, He W, Tian X, Zhuang Y, Chu J. Dynamic changes of metabolomics and expression of candicidin biosynthesis gene cluster caused by the presence of a pleiotropic regulator AdpA in Streptomyces ZYJ-6. Bioprocess Biosyst Eng 2019; 42:1353-1365. [PMID: 31062087 DOI: 10.1007/s00449-019-02135-4] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2018] [Accepted: 04/15/2019] [Indexed: 10/26/2022]
Abstract
Candicidin is one of the frequent antibiotics for its high antifungal activity, but the productivity is still extremely low. Introduction of adpA into Streptomyces ZYJ-6 could improve candicidin productivity significantly and achieved 9338 μg/mL, which was the highest value ever reported in the literature. Combined analyses of transcriptional levels, metabolic flux and metabolomics indicate that para-aminobenzoic acid and the first step of shikimic acid metabolism were not the bottleneck for the candicidin production in the control. However, methylmalonyl-CoA played a central role in the candicidin production and the gene methB responsible for the biosynthesis of methylmalonyl-CoA might be the candidate gene target for further improving the production of candicidin.
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Affiliation(s)
- Xiaoyun Liu
- State Key Laboratory of Bioreactor Engineering, School of Biochemical Engineering, East China University of Science and Technology, Room 413, Building 18, Shanghai, 200237, People's Republic of China
| | - Xiaojuan Sun
- State Key Laboratory of Bioreactor Engineering, School of Biochemical Engineering, East China University of Science and Technology, Room 413, Building 18, Shanghai, 200237, People's Republic of China
| | - Weimin He
- State Key Laboratory of Bioreactor Engineering, School of Biochemical Engineering, East China University of Science and Technology, Room 413, Building 18, Shanghai, 200237, People's Republic of China
| | - Xiwei Tian
- State Key Laboratory of Bioreactor Engineering, School of Biochemical Engineering, East China University of Science and Technology, Room 413, Building 18, Shanghai, 200237, People's Republic of China
| | - Yingping Zhuang
- State Key Laboratory of Bioreactor Engineering, School of Biochemical Engineering, East China University of Science and Technology, Room 413, Building 18, Shanghai, 200237, People's Republic of China
| | - Ju Chu
- State Key Laboratory of Bioreactor Engineering, School of Biochemical Engineering, East China University of Science and Technology, Room 413, Building 18, Shanghai, 200237, People's Republic of China.
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30
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Wehrs M, Tanjore D, Eng T, Lievense J, Pray TR, Mukhopadhyay A. Engineering Robust Production Microbes for Large-Scale Cultivation. Trends Microbiol 2019; 27:524-537. [PMID: 30819548 DOI: 10.1016/j.tim.2019.01.006] [Citation(s) in RCA: 119] [Impact Index Per Article: 23.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2018] [Revised: 01/11/2019] [Accepted: 01/23/2019] [Indexed: 11/27/2022]
Abstract
Systems biology and synthetic biology are increasingly used to examine and modulate complex biological systems. As such, many issues arising during scaling-up microbial production processes can be addressed using these approaches. We review differences between laboratory-scale cultures and larger-scale processes to provide a perspective on those strain characteristics that are especially important during scaling. Systems biology has been used to examine a range of microbial systems for their response in bioreactors to fluctuations in nutrients, dissolved gases, and other stresses. Synthetic biology has been used both to assess and modulate strain response, and to engineer strains to improve production. We discuss these approaches and tools in the context of their use in engineering robust microbes for applications in large-scale production.
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Affiliation(s)
- Maren Wehrs
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA; Institut für Genetik, Technische Universität Braunschweig, Braunschweig, Germany; Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Emeryville, CA 94608, USA
| | - Deepti Tanjore
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA; Advanced Biofuels and Bioproducts Process Development Unit, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Thomas Eng
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA; Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Emeryville, CA 94608, USA
| | | | - Todd R Pray
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA; Advanced Biofuels and Bioproducts Process Development Unit, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Aindrila Mukhopadhyay
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA; Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Emeryville, CA 94608, USA; Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.
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Haringa C, Mudde RF, Noorman HJ. From industrial fermentor to CFD-guided downscaling: what have we learned? Biochem Eng J 2018. [DOI: 10.1016/j.bej.2018.09.001] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
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Enhancing candicidin biosynthesis by medium optimization and pH stepwise control strategy with process metabolomics analysis of Streptomyces ZYJ-6. Bioprocess Biosyst Eng 2018; 41:1743-1755. [DOI: 10.1007/s00449-018-1997-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2018] [Accepted: 08/02/2018] [Indexed: 10/28/2022]
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Li C, Shu W, Wang S, Liu P, Zhuang Y, Zhang S, Xia J. Dynamic metabolic response of Aspergillus niger to glucose perturbation: evidence of regulatory mechanism for reduced glucoamylase production. J Biotechnol 2018; 287:28-40. [PMID: 30134150 DOI: 10.1016/j.jbiotec.2018.08.005] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2018] [Revised: 06/20/2018] [Accepted: 08/18/2018] [Indexed: 01/14/2023]
Abstract
Environmental gradient is an important common issue during scale-up process for protein production. To address the dynamic regulatory mechanism of Aspergillus niger being exposed to inhomogeneous glucose concentrations, glucose perturbation were experimented on the steady state of A. niger chemostat culture, and dynamic profiles of the intracellular metabolites in central carbon metabolism were tracked in a time scale of seconds. The upper glycolysis and pentose phosphate pathway showed sharp variations after glucose perturbation, while the lower glycolysis, TCA cycle and amino acid pools represented a moderate and prolonged response due to the allosteric regulation of enzymes and buffering function of metabolites with large pool sizes. Improved glucose-6-phosphate enhanced the metabolic flux to PP pathway remarkably, which provided not only more redox cofactors (NADPH) for protein synthesis but also more precursors (phosphoribosyl pyrophosphate and ribose-5-phosphate) for cell growth. Moreover, reduction of the total adenine nucleotides and major precursor amino acids indicated the upregulated RNA synthesis was required to produce stress proteins, and partially explained the drop of glucoamylase production when A. niger experienced a fluctuated glucose concentration environment. These findings would be valuable for improving bioreactor operation, design, and scale-up from engineering or genetic aspects.
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Affiliation(s)
- Chao Li
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, China
| | - Wei Shu
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, China
| | - Shuai Wang
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, China
| | - Peng Liu
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, China
| | - Yingpping Zhuang
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, China
| | - Siliang Zhang
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, China
| | - Jianye Xia
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, China.
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Heins AL, Weuster-Botz D. Population heterogeneity in microbial bioprocesses: origin, analysis, mechanisms, and future perspectives. Bioprocess Biosyst Eng 2018. [PMID: 29541890 DOI: 10.1007/s00449-018-1922-3] [Citation(s) in RCA: 45] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Population heterogeneity is omnipresent in all bioprocesses even in homogenous environments. Its origin, however, is only so well understood that potential strategies like bet-hedging, noise in gene expression and division of labour that lead to population heterogeneity can be derived from experimental studies simulating the dynamics in industrial scale bioprocesses. This review aims at summarizing the current state of the different parts of single cell studies in bioprocesses. This includes setups to visualize different phenotypes of single cells, computational approaches connecting single cell physiology with environmental influence and special cultivation setups like scale-down reactors that have been proven to be useful to simulate large-scale conditions. A step in between investigation of populations and single cells is studying subpopulations with distinct properties that differ from the rest of the population with sub-omics methods which are also presented here. Moreover, the current knowledge about population heterogeneity in bioprocesses is summarized for relevant industrial production hosts and mixed cultures, as they provide the unique opportunity to distribute metabolic burden and optimize production processes in a way that is impossible in traditional monocultures. In the end, approaches to explain the underlying mechanism of population heterogeneity and the evidences found to support each hypothesis are presented. For instance, population heterogeneity serving as a bet-hedging strategy that is used as coordinated action against bioprocess-related stresses while at the same time spreading the risk between individual cells as it ensures the survival of least a part of the population in any environment the cells encounter.
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Affiliation(s)
- Anna-Lena Heins
- Institute of Biochemical Engineering, Technical University of Munich, Boltzmannstr. 15, 85748, Garching, Germany.
| | - Dirk Weuster-Botz
- Institute of Biochemical Engineering, Technical University of Munich, Boltzmannstr. 15, 85748, Garching, Germany
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Wang G, Zhao J, Haringa C, Tang W, Xia J, Chu J, Zhuang Y, Zhang S, Deshmukh AT, van Gulik W, Heijnen JJ, Noorman HJ. Comparative performance of different scale-down simulators of substrate gradients in Penicillium chrysogenum cultures: the need of a biological systems response analysis. Microb Biotechnol 2018; 11:486-497. [PMID: 29333753 PMCID: PMC5902331 DOI: 10.1111/1751-7915.13046] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2017] [Revised: 12/18/2017] [Accepted: 12/18/2017] [Indexed: 12/22/2022] Open
Abstract
In a 54 m3 large‐scale penicillin fermentor, the cells experience substrate gradient cycles at the timescales of global mixing time about 20–40 s. Here, we used an intermittent feeding regime (IFR) and a two‐compartment reactor (TCR) to mimic these substrate gradients at laboratory‐scale continuous cultures. The IFR was applied to simulate substrate dynamics experienced by the cells at full scale at timescales of tens of seconds to minutes (30 s, 3 min and 6 min), while the TCR was designed to simulate substrate gradients at an applied mean residence time (τc) of 6 min. A biological systems analysis of the response of an industrial high‐yielding P. chrysogenum strain has been performed in these continuous cultures. Compared to an undisturbed continuous feeding regime in a single reactor, the penicillin productivity (qPenG) was reduced in all scale‐down simulators. The dynamic metabolomics data indicated that in the IFRs, the cells accumulated high levels of the central metabolites during the feast phase to actively cope with external substrate deprivation during the famine phase. In contrast, in the TCR system, the storage pool (e.g. mannitol and arabitol) constituted a large contribution of carbon supply in the non‐feed compartment. Further, transcript analysis revealed that all scale‐down simulators gave different expression levels of the glucose/hexose transporter genes and the penicillin gene clusters. The results showed that qPenG did not correlate well with exposure to the substrate regimes (excess, limitation and starvation), but there was a clear inverse relation between qPenG and the intracellular glucose level.
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Affiliation(s)
- Guan Wang
- State key laboratory of Bioreactor Engineering, East China University of Science and Technology (ECUST), Shanghai, China
| | - Junfei Zhao
- State key laboratory of Bioreactor Engineering, East China University of Science and Technology (ECUST), Shanghai, China
| | - Cees Haringa
- Transport Phenomena, Chemical Engineering Department, Delft University of Technology, Delft, The Netherlands
| | - Wenjun Tang
- State key laboratory of Bioreactor Engineering, East China University of Science and Technology (ECUST), Shanghai, China
| | - Jianye Xia
- State key laboratory of Bioreactor Engineering, East China University of Science and Technology (ECUST), Shanghai, China
| | - Ju Chu
- State key laboratory of Bioreactor Engineering, East China University of Science and Technology (ECUST), Shanghai, China
| | - Yingping Zhuang
- State key laboratory of Bioreactor Engineering, East China University of Science and Technology (ECUST), Shanghai, China
| | - Siliang Zhang
- State key laboratory of Bioreactor Engineering, East China University of Science and Technology (ECUST), Shanghai, China
| | | | - Walter van Gulik
- Cell Systems Engineering, Department of Biotechnology, Delft University of Technology, Delft, The Netherlands
| | - Joseph J Heijnen
- Cell Systems Engineering, Department of Biotechnology, Delft University of Technology, Delft, The Netherlands
| | - Henk J Noorman
- DSM Biotechnology Center, Delft, The Netherlands.,Bio Process Engineering, Department of Biotechnology, Delft University of Technology, Delft, The Netherlands
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Computational fluid dynamics simulation of an industrial P. chrysogenum fermentation with a coupled 9-pool metabolic model: Towards rational scale-down and design optimization. Chem Eng Sci 2018. [DOI: 10.1016/j.ces.2017.09.020] [Citation(s) in RCA: 54] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
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37
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Wang G, Wu B, Zhao J, Haringa C, Xia J, Chu J, Zhuang Y, Zhang S, Heijnen JJ, van Gulik W, Deshmukh AT, Noorman HJ. Power input effects on degeneration in prolonged penicillin chemostat cultures: A systems analysis at flux, residual glucose, metabolite, and transcript levels. Biotechnol Bioeng 2017; 115:114-125. [DOI: 10.1002/bit.26447] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2017] [Revised: 07/14/2017] [Accepted: 09/01/2017] [Indexed: 12/28/2022]
Affiliation(s)
- Guan Wang
- State Key Laboratory of Bioreactor Engineering; East China University of Science and Technology (ECUST); Shanghai People's Republic of China
| | - Baofeng Wu
- State Key Laboratory of Bioreactor Engineering; East China University of Science and Technology (ECUST); Shanghai People's Republic of China
| | - Junfei Zhao
- State Key Laboratory of Bioreactor Engineering; East China University of Science and Technology (ECUST); Shanghai People's Republic of China
| | - Cees Haringa
- Transport Phenomena, Chemical Engineering Department; Delft University of Technology; Delft The Netherlands
| | - Jianye Xia
- State Key Laboratory of Bioreactor Engineering; East China University of Science and Technology (ECUST); Shanghai People's Republic of China
| | - Ju Chu
- State Key Laboratory of Bioreactor Engineering; East China University of Science and Technology (ECUST); Shanghai People's Republic of China
| | - Yingping Zhuang
- State Key Laboratory of Bioreactor Engineering; East China University of Science and Technology (ECUST); Shanghai People's Republic of China
| | - Siliang Zhang
- State Key Laboratory of Bioreactor Engineering; East China University of Science and Technology (ECUST); Shanghai People's Republic of China
| | - Joseph J. Heijnen
- Cell Systems Engineering, Department of Biotechnology; Delft University of Technology; Delft The Netherlands
| | - Walter van Gulik
- Cell Systems Engineering, Department of Biotechnology; Delft University of Technology; Delft The Netherlands
| | | | - Henk J. Noorman
- DSM Biotechnology Center; Delft The Netherlands
- Bio Process Engineering, Department of Biotechnology; Delft University of Technology; Delft The Netherlands
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Haringa C, Deshmukh AT, Mudde RF, Noorman HJ. Euler-Lagrange analysis towards representative down-scaling of a 22 m 3 aerobic S. cerevisiae fermentation. Chem Eng Sci 2017. [DOI: 10.1016/j.ces.2017.01.014] [Citation(s) in RCA: 56] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
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40
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Delvigne F, Takors R, Mudde R, van Gulik W, Noorman H. Bioprocess scale-up/down as integrative enabling technology: from fluid mechanics to systems biology and beyond. Microb Biotechnol 2017; 10:1267-1274. [PMID: 28805306 PMCID: PMC5609235 DOI: 10.1111/1751-7915.12803] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2017] [Accepted: 07/12/2017] [Indexed: 11/28/2022] Open
Abstract
Efficient optimization of microbial processes is a critical issue for achieving a number of sustainable development goals, considering the impact of microbial biotechnology in agrofood, environment, biopharmaceutical and chemical industries. Many of these applications require scale-up after proof of concept. However, the behaviour of microbial systems remains unpredictable (at least partially) when shifting from laboratory-scale to industrial conditions. The need for robust microbial systems is thus highly needed in this context, as well as a better understanding of the interactions between fluid mechanics and cell physiology. For that purpose, a full scale-up/down computational framework is already available. This framework links computational fluid dynamics (CFD), metabolic flux analysis and agent-based modelling (ABM) for a better understanding of the cell lifelines in a heterogeneous environment. Ultimately, this framework can be used for the design of scale-down simulators and/or metabolically engineered cells able to cope with environmental fluctuations typically found in large-scale bioreactors. However, this framework still needs some refinements, such as a better integration of gas-liquid flows in CFD, and taking into account intrinsic biological noise in ABM.
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Affiliation(s)
- Frank Delvigne
- TERRA Research CenterMicrobial Processes and Interactions (MiPI)University of LiègeLiègeBelgium
| | - Ralf Takors
- Institute of Biochemical EngineeringUniversity of StuttgartStuttgartGermany
| | - Rob Mudde
- Transport Phenomena SectionDepartment of Chemical EngineeringDelft University of TechnologyDelftThe Netherlands
| | - Walter van Gulik
- Department of BiotechnologyDelft University of TechnologyDelftThe Netherlands
| | - Henk Noorman
- Department of BiotechnologyDelft University of TechnologyDelftThe Netherlands
- DSM Biotechnology CenterDelftThe Netherlands
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41
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Tang W, Deshmukh AT, Haringa C, Wang G, van Gulik W, van Winden W, Reuss M, Heijnen JJ, Xia J, Chu J, Noorman HJ. A 9-pool metabolic structured kinetic model describing days to seconds dynamics of growth and product formation byPenicillium chrysogenum. Biotechnol Bioeng 2017; 114:1733-1743. [DOI: 10.1002/bit.26294] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2016] [Revised: 02/26/2017] [Accepted: 03/14/2017] [Indexed: 12/30/2022]
Affiliation(s)
- Wenjun Tang
- State Key Laboratory of Bioreactor Engineering; East China University of Science and Technology; P.O. Box 329#, No.130, Meilong Road Shanghai P.R. China
| | | | - Cees Haringa
- Cell Systems Engineering; Department of Biotechnology; Delft University of Technology; Delft The Netherlands
| | - Guan Wang
- State Key Laboratory of Bioreactor Engineering; East China University of Science and Technology; P.O. Box 329#, No.130, Meilong Road Shanghai P.R. China
| | - Walter van Gulik
- Cell Systems Engineering; Department of Biotechnology; Delft University of Technology; Delft The Netherlands
| | | | - Matthias Reuss
- Institute of Biochemical Engineering; University of Stuttgart; Stuttgart Germany
| | - Joseph J. Heijnen
- Cell Systems Engineering; Department of Biotechnology; Delft University of Technology; Delft The Netherlands
| | - Jianye Xia
- State Key Laboratory of Bioreactor Engineering; East China University of Science and Technology; P.O. Box 329#, No.130, Meilong Road Shanghai P.R. China
| | - Ju Chu
- State Key Laboratory of Bioreactor Engineering; East China University of Science and Technology; P.O. Box 329#, No.130, Meilong Road Shanghai P.R. China
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Cueto-Rojas HF, Milne N, van Helmond W, Pieterse MM, van Maris AJA, Daran JM, Wahl SA. Membrane potential independent transport of NH 3 in the absence of ammonium permeases in Saccharomyces cerevisiae. BMC SYSTEMS BIOLOGY 2017; 11:49. [PMID: 28412970 PMCID: PMC5392931 DOI: 10.1186/s12918-016-0381-1] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/19/2016] [Accepted: 12/20/2016] [Indexed: 01/08/2023]
Abstract
Background Microbial production of nitrogen containing compounds requires a high uptake flux and assimilation of the N-source (commonly ammonium), which is generally coupled with ATP consumption and negatively influences the product yield. In the industrial workhorse Saccharomyces cerevisiae, ammonium (NH4+) uptake is facilitated by ammonium permeases (Mep1, Mep2 and Mep3), which transport the NH4+ ion, resulting in ATP expenditure to maintain the intracellular charge balance and pH by proton export using the plasma membrane-bound H+-ATPase. Results To decrease the ATP costs for nitrogen assimilation, the Mep genes were removed, resulting in a strain unable to uptake the NH4+ ion. Subsequent analysis revealed that growth of this ∆mep strain was dependent on the extracellular NH3 concentrations. Metabolomic analysis revealed a significantly higher intracellular NHX concentration (3.3-fold) in the ∆mep strain than in the reference strain. Further proteomic analysis revealed significant up-regulation of vacuolar proteases and genes involved in various stress responses. Conclusions Our results suggest that the uncharged species, NH3, is able to diffuse into the cell. The measured intracellular/extracellular NHX ratios under aerobic nitrogen-limiting conditions were consistent with this hypothesis when NHx compartmentalization was considered. On the other hand, proteomic analysis indicated a more pronounced N-starvation stress response in the ∆mep strain than in the reference strain, which suggests that the lower biomass yield of the ∆mep strain was related to higher turnover rates of biomass components. Electronic supplementary material The online version of this article (doi:10.1186/s12918-016-0381-1) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Hugo F Cueto-Rojas
- Department of Biotechnology, Delft University of Technology, van der Maasweg 9, 2629HZ, Delft, The Netherlands
| | - Nicholas Milne
- Department of Biotechnology, Delft University of Technology, van der Maasweg 9, 2629HZ, Delft, The Netherlands.,Present Address: Evolva Biotech A/S, Lersø Parkallé 42, 2100, København Ø, Denmark
| | - Ward van Helmond
- Department of Biotechnology, Delft University of Technology, van der Maasweg 9, 2629HZ, Delft, The Netherlands.,Present Address: Nederlands Forensisch Instituut (NFI), Laan van Ypenburg 6, 2497 GB, Den Haag, The Netherlands
| | - Mervin M Pieterse
- Department of Biotechnology, Delft University of Technology, van der Maasweg 9, 2629HZ, Delft, The Netherlands
| | - Antonius J A van Maris
- Department of Biotechnology, Delft University of Technology, van der Maasweg 9, 2629HZ, Delft, The Netherlands.,Division of Industrial Biotechnology, School of Biotechnology, KTH Royal Institute of Technology, AlbaNova University Center, SE 106 91, Stockholm, Sweden
| | - Jean-Marc Daran
- Department of Biotechnology, Delft University of Technology, van der Maasweg 9, 2629HZ, Delft, The Netherlands.
| | - S Aljoscha Wahl
- Department of Biotechnology, Delft University of Technology, van der Maasweg 9, 2629HZ, Delft, The Netherlands.
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43
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Haringa C, Noorman HJ, Mudde RF. Lagrangian modeling of hydrodynamic–kinetic interactions in (bio)chemical reactors: Practical implementation and setup guidelines. Chem Eng Sci 2017. [DOI: 10.1016/j.ces.2016.07.031] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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Suarez-Mendez C, Hanemaaijer M, ten Pierick A, Wolters J, Heijnen J, Wahl S. Interaction of storage carbohydrates and other cyclic fluxes with central metabolism: A quantitative approach by non-stationary 13C metabolic flux analysis. Metab Eng Commun 2016; 3:52-63. [PMID: 29468113 PMCID: PMC5779734 DOI: 10.1016/j.meteno.2016.01.001] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2015] [Revised: 11/30/2015] [Accepted: 01/19/2016] [Indexed: 12/11/2022] Open
Abstract
13C labeling experiments in aerobic glucose limited cultures of Saccharomyces cerevisiae at four different growth rates (0.054; 0.101, 0.207, 0.307 h-1) are used for calculating fluxes that include intracellular cycles (e.g., storage carbohydrate cycles, exchange fluxes with amino acids), which are rearranged depending on the growth rate. At low growth rates the impact of the storage carbohydrate recycle is relatively more significant than at high growth rates due to a higher concentration of these materials in the cell (up to 560-fold) and higher fluxes relative to the glucose uptake rate (up to 16%). Experimental observations suggest that glucose can be exported to the extracellular space, and that its source is related to storage carbohydrates, most likely via the export and subsequent extracellular breakdown of trehalose. This hypothesis is strongly supported by 13C-labeling experimental data, measured extracellular trehalose, and the corresponding flux estimations.
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Key Words
- 2PG, 2-phosphoglycerate
- 3PG, 3-phosphoglycerate
- 6PG, 6-phospho gluconate
- ACO, aconitate hydratase
- AK, adenylate kinase
- ALA, alanine
- ASP, aspartate
- Amino acids
- CoA, coenzyme-A
- DHAP, dihydroxy acetone phosphate
- DO, dissolved oxygen
- E4P, erythrose-4-phosphate
- ENO, phosphopyruvate hydratase
- F6P, fructose-6-phosphate
- FBA, fructose-bisphosphate aldolase
- FBP, fructose-1,6-bis-phosphate
- FMH, fumarate hydratase
- FUM, fumarate
- Flux estimation
- G1P, glucose-1-phosphate
- G6P, glucose-6-phosphate
- G6PDH, glucose-6-phosphate dehydrogenase
- GAP, glyceraldehyde-3-phosphate
- GAPDH&PGK, glyceraldehyde-3-phosphate dehydrogenase+phosphoglycerate kinase
- GLN, glutamine
- GLU, glutamate
- GLY, glycine
- GPM, phosphoglycerate mutase
- Glycogen
- IDMS, Isotope dilution mass spectrometry
- Iso-Cit, isocitrate
- LEU, leucine
- LYS, lysine
- MAL, malate
- METH, methionine
- Non-stationary 13C labeling
- OAA, oxaloacetate
- OUR, Oxygen uptake rate
- PEP, phospho-enol-pyruvate
- PFK, 6-phosphofructokinase
- PGI, glucose-6-phosphate isomerase
- PGM, phosphoglucomutase
- PMI, mannose-6-phosphate isomerase
- PPP, pentose phosphate pathway
- PRO, proline
- PYK, pyruvate kinase
- PYR, pyruvate
- RPE, ribulose-phosphate 3-epimerase
- RPI, ribose-5-phosphate isomerase
- Rib5P, ribose-5-phosphate
- Ribu5P, ribulose-5-phosphate
- S7P, sedoheptulose-7-phosphate
- SER, serine
- SUC, succinate
- T6P, trehalose-6-phosphate
- TCA, tricarboxylic acid cycle.
- TPP, trehalose- phosphatase
- TPS, alpha,alpha-trehalose-phosphate synthase
- Trehalose
- UDP, uridine-5-diphosphate
- UDPG, UDP-glucose
- UTP, uridine-5-triphosphate
- X5P, xylulose-5-phosphate
- α-KG, oxoglutarate
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Affiliation(s)
- C.A. Suarez-Mendez
- Department of Biotechnology, Delft University of Technology, Julianalaan 67 – 2628 BC Delft, The Netherlands
- Kluyver Centre for Genomics of Industrial Fermentation, P.O. Box 5057, 2600 GA Delft, The Netherlands
| | - M. Hanemaaijer
- Department of Biotechnology, Delft University of Technology, Julianalaan 67 – 2628 BC Delft, The Netherlands
| | - Angela ten Pierick
- Department of Biotechnology, Delft University of Technology, Julianalaan 67 – 2628 BC Delft, The Netherlands
| | - J.C. Wolters
- Department of Analytical Biochemistry, University of Groningen, Antonius Deusinglaan 1, 9713 AV Groningen, The Netherlands
| | - J.J. Heijnen
- Department of Biotechnology, Delft University of Technology, Julianalaan 67 – 2628 BC Delft, The Netherlands
- Kluyver Centre for Genomics of Industrial Fermentation, P.O. Box 5057, 2600 GA Delft, The Netherlands
| | - S.A. Wahl
- Department of Biotechnology, Delft University of Technology, Julianalaan 67 – 2628 BC Delft, The Netherlands
- Kluyver Centre for Genomics of Industrial Fermentation, P.O. Box 5057, 2600 GA Delft, The Netherlands
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In Vivo Analysis of NH 4+ Transport and Central Nitrogen Metabolism in Saccharomyces cerevisiae during Aerobic Nitrogen-Limited Growth. Appl Environ Microbiol 2016; 82:6831-6845. [PMID: 27637876 DOI: 10.1128/aem.01547-16] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2016] [Accepted: 09/08/2016] [Indexed: 11/20/2022] Open
Abstract
Ammonium is the most common N source for yeast fermentations. Although its transport and assimilation mechanisms are well documented, there have been only a few attempts to measure the in vivo intracellular concentration of ammonium and assess its impact on gene expression. Using an isotope dilution mass spectrometry (IDMS)-based method, we were able to measure the intracellular ammonium concentration in N-limited aerobic chemostat cultivations using three different N sources (ammonium, urea, and glutamate) at the same growth rate (0.05 h-1). The experimental results suggest that, at this growth rate, a similar concentration of intracellular (IC) ammonium, about 3.6 mmol NH4+/literIC, is required to supply the reactions in the central N metabolism, independent of the N source. Based on the experimental results and different assumptions, the vacuolar and cytosolic ammonium concentrations were estimated. Furthermore, we identified a futile cycle caused by NH3 leakage into the extracellular space, which can cost up to 30% of the ATP production of the cell under N-limited conditions, and a futile redox cycle between Gdh1 and Gdh2 reactions. Finally, using shotgun proteomics with protein expression determined relative to a labeled reference, differences between the various environmental conditions were identified and correlated with previously identified N compound-sensing mechanisms.IMPORTANCE In our work, we studied central N metabolism using quantitative approaches. First, intracellular ammonium was measured under different N sources. The results suggest that Saccharomyces cerevisiae cells maintain a constant NH4+ concentration (around 3 mmol NH4+/literIC), independent of the applied nitrogen source. We hypothesize that this amount of intracellular ammonium is required to obtain sufficient thermodynamic driving force. Furthermore, our calculations based on thermodynamic analysis of the transport mechanisms of ammonium suggest that ammonium is not equally distributed, indicating a high degree of compartmentalization in the vacuole. Additionally, metabolomic analysis results were used to calculate the thermodynamic driving forces in the central N metabolism reactions, revealing that the main reactions in the central N metabolism are far from equilibrium. Using proteomics approaches, we were able to identify major changes, not only in N metabolism, but also in C metabolism and regulation.
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Haringa C, Tang W, Deshmukh AT, Xia J, Reuss M, Heijnen JJ, Mudde RF, Noorman HJ. Euler-Lagrange computational fluid dynamics for (bio)reactor scale down: An analysis of organism lifelines. Eng Life Sci 2016; 16:652-663. [PMID: 27917102 PMCID: PMC5129516 DOI: 10.1002/elsc.201600061] [Citation(s) in RCA: 76] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2016] [Revised: 07/11/2016] [Accepted: 07/18/2016] [Indexed: 12/28/2022] Open
Abstract
The trajectories, referred to as lifelines, of individual microorganisms in an industrial scale fermentor under substrate limiting conditions were studied using an Euler‐Lagrange computational fluid dynamics approach. The metabolic response to substrate concentration variations along these lifelines provides deep insight in the dynamic environment inside a large‐scale fermentor, from the point of view of the microorganisms themselves. We present a novel methodology to evaluate this metabolic response, based on transitions between metabolic “regimes” that can provide a comprehensive statistical insight in the environmental fluctuations experienced by microorganisms inside an industrial bioreactor. These statistics provide the groundwork for the design of representative scale‐down simulators, mimicking substrate variations experimentally. To focus on the methodology we use an industrial fermentation of Penicillium chrysogenum in a simplified representation, dealing with only glucose gradients, single‐phase hydrodynamics, and assuming no limitation in oxygen supply, but reasonably capturing the relevant timescales. Nevertheless, the methodology provides useful insight in the relation between flow and component fluctuation timescales that are expected to hold in physically more thorough simulations. Microorganisms experience substrate fluctuations at timescales of seconds, in the order of magnitude of the global circulation time. Such rapid fluctuations should be replicated in truly industrially representative scale‐down simulators.
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Affiliation(s)
- Cees Haringa
- Transport Phenomena Section Department of Chemical Engineering Delft University of Technology Delft The Netherlands
| | - Wenjun Tang
- State key laboratory of Bioreactor Engineering East China University of Science and Technology (ECUST) Shanghai People's Republic of China
| | | | - Jianye Xia
- State key laboratory of Bioreactor Engineering East China University of Science and Technology (ECUST) Shanghai People's Republic of China
| | - Matthias Reuss
- Stuttgart Research Center Systems Biology (SRCSB) University of Stuttgart Stuttgart Germany
| | - Joseph J Heijnen
- Cell Systems Engineering Department of Biotechnology Delft University of Technology Delft The Netherlands
| | - Robert F Mudde
- Transport Phenomena Section Department of Chemical Engineering Delft University of Technology Delft The Netherlands
| | - Henk J Noorman
- DSM Biotechnology Center Delft The Netherlands; Bio Separation Technology Department of Biotechnology Delft University of Technology Delft The Netherlands
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Accurate Measurement of the in vivo Ammonium Concentration in Saccharomyces cerevisiae. Metabolites 2016; 6:metabo6020012. [PMID: 27120628 PMCID: PMC4931543 DOI: 10.3390/metabo6020012] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2016] [Revised: 04/13/2016] [Accepted: 04/20/2016] [Indexed: 11/16/2022] Open
Abstract
Ammonium (NH4+) is the most common N-source for yeast fermentations, and N-limitation is frequently applied to reduce growth and increase product yields. While there is significant molecular knowledge on NH4+ transport and assimilation, there have been few attempts to measure the in vivo concentration of this metabolite. In this article, we present a sensitive and accurate analytical method to quantify the in vivo intracellular ammonium concentration in Saccharomycescerevisiae based on standard rapid sampling and metabolomics techniques. The method validation experiments required the development of a proper sample processing protocol to minimize ammonium production/consumption during biomass extraction by assessing the impact of amino acid degradation—an element that is often overlooked. The resulting cold chloroform metabolite extraction method, together with quantification using ultra high performance liquid chromatography-isotope dilution mass spectrometry (UHPLC-IDMS), was not only more sensitive than most of the existing methods but also more accurate than methods that use electrodes, enzymatic reactions, or boiling water or boiling ethanol biomass extraction because it minimized ammonium consumption/production during sampling processing and interference from other metabolites in the quantification of intracellular ammonium. Finally, our validation experiments showed that other metabolites such as pyruvate or 2-oxoglutarate (αKG) need to be extracted with cold chloroform to avoid measurements being biased by the degradation of other metabolites (e.g., amino acids).
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In vivo kinetic analysis of the penicillin biosynthesis pathway using PAA stimulus response experiments. Metab Eng 2015; 32:155-173. [DOI: 10.1016/j.ymben.2015.09.018] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2015] [Revised: 09/22/2015] [Accepted: 09/26/2015] [Indexed: 11/18/2022]
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Lu H, Liu X, Huang M, Xia J, Chu J, Zhuang Y, Zhang S, Noorman H. Integrated isotope-assisted metabolomics and (13)C metabolic flux analysis reveals metabolic flux redistribution for high glucoamylase production by Aspergillus niger. Microb Cell Fact 2015; 14:147. [PMID: 26383080 PMCID: PMC4574132 DOI: 10.1186/s12934-015-0329-y] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2015] [Accepted: 08/31/2015] [Indexed: 11/10/2022] Open
Abstract
Background Aspergillus niger is widely used for enzyme production and achievement of high enzyme production depends on the comprehensive understanding of cell’s metabolic regulation mechanisms. Results In this paper, we investigate the metabolic differences and regulation mechanisms between a high glucoamylase-producing strain A. niger DS03043 and its wild-type parent strain A. niger CBS513.88 via an integrated isotope-assisted metabolomics and 13C metabolic flux analysis approach. We found that A. niger DS03043 had higher cell growth, glucose uptake, and glucoamylase production rates but lower oxalic acid and citric acid secretion rates. In response to above phenotype changes, A. niger DS03043 was characterized by an increased carbon flux directed to the oxidative pentose phosphate pathway in contrast to reduced flux through TCA cycle, which were confirmed by consistent changes in pool sizes of metabolites. A higher ratio of ATP over AMP in the high producing strain might contribute to the increase in the PP pathway flux as glucosephosphate isomerase was inhibited at higher ATP concentrations. A. niger CBS513.88, however, was in a higher redox state due to the imbalance of NADH regeneration and consumption, resulting in the secretion of oxalic acid and citric acid, as well as the accumulation of intracellular OAA and PEP, which may in turn result in the decrease in the glucose uptake rate. Conclusions The application of integrated metabolomics and 13C metabolic flux analysis highlights the regulation mechanisms of energy and redox metabolism on flux redistribution in A. niger. An integrated isotope-assisted metabolomics and 13C metabolic flux analysis was was firstly systematically performed in A. niger. In response to enzyme production, the metabolic flux in A. niger DS03043 (high-producing) was redistributed, characterized by an increased carbon flux directed to the oxidative pentose phosphate pathway as well as an increased pool size of pentose. The consistency in 13C metabolic flux analysis and metabolites quantification indicated that an imbalance of NADH formation and consumption led to the accumulation and secretion of organic acids in A. niger CBS513.88 (wild-type) ![]() Electronic supplementary material The online version of this article (doi:10.1186/s12934-015-0329-y) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Hongzhong Lu
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, 200237, Shanghai, People's Republic of China.
| | - Xiaoyun Liu
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, 200237, Shanghai, People's Republic of China.
| | - Mingzhi Huang
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, 200237, Shanghai, People's Republic of China.
| | - Jianye Xia
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, 200237, Shanghai, People's Republic of China.
| | - Ju Chu
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, 200237, Shanghai, People's Republic of China.
| | - Yingping Zhuang
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, 200237, Shanghai, People's Republic of China.
| | - Siliang Zhang
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, 200237, Shanghai, People's Republic of China.
| | - Henk Noorman
- DSM Biotechnology Center, P.O. Box1, 2600 MA, Delft, The Netherlands.
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