1
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Rahman MS, Shimul MEK, Parvez MAK. Comprehensive analysis of genomic variation, pan-genome and biosynthetic potential of Corynebacterium glutamicum strains. PLoS One 2024; 19:e0299588. [PMID: 38718091 PMCID: PMC11078359 DOI: 10.1371/journal.pone.0299588] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2023] [Accepted: 02/13/2024] [Indexed: 05/12/2024] Open
Abstract
Corynebacterium glutamicum is a non-pathogenic species of the Corynebacteriaceae family. It has been broadly used in industrial biotechnology for the production of valuable products. Though it is widely accepted at the industrial level, knowledge about the genomic diversity of the strains is limited. Here, we investigated the comparative genomic features of the strains and pan-genomic characteristics. We also observed phylogenetic relationships among the strains based on average nucleotide identity (ANI). We found diversity between strains at the genomic and pan-genomic levels. Less than one-third of the C. glutamicum pan-genome consists of core genes and soft-core genes. Whereas, a large number of strain-specific genes covered about half of the total pan-genome. Besides, C. glutamicum pan-genome is open and expanding, which indicates the possible addition of new gene families to the pan-genome. We also investigated the distribution of biosynthetic gene clusters (BGCs) among the strains. We discovered slight variations of BGCs at the strain level. Several BGCs with the potential to express novel bioactive secondary metabolites have been identified. Therefore, by utilizing the characteristic advantages of C. glutamicum, different strains can be potential applicants for natural drug discovery.
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Affiliation(s)
- Md. Shahedur Rahman
- Department of Genetic Engineering and Biotechnology, Jashore University of Science and Technology, Jashore, Bangladesh
- Department of Genetic Engineering and Biotechnology, Bioinformatics and Microbial Biotechnology Laboratory, Jashore University of Science and Technology, Jashore, Bangladesh
| | - Md. Ebrahim Khalil Shimul
- Department of Genetic Engineering and Biotechnology, Jashore University of Science and Technology, Jashore, Bangladesh
- Department of Genetic Engineering and Biotechnology, Bioinformatics and Microbial Biotechnology Laboratory, Jashore University of Science and Technology, Jashore, Bangladesh
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2
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Täuber S, Blöbaum L, Steier V, Oldiges M, Grünberger A. Microfluidic single-cell scale-down bioreactors: A proof-of-concept for the growth of Corynebacterium glutamicum at oscillating pH values. Biotechnol Bioeng 2022; 119:3194-3209. [PMID: 35950295 DOI: 10.1002/bit.28208] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2022] [Revised: 06/30/2022] [Accepted: 07/29/2022] [Indexed: 11/07/2022]
Abstract
In large-scale bioreactors, gradients in cultivation parameter such as oxygen, substrate and pH result in fluctuating cell environments. pH fluctuations were identified as a critical parameter for bioprocess performance. Traditionally, scale-down systems at the laboratory scale are used to analyze the effects of fluctuating pH values on strain and thus process performance. Here, we demonstrate the application of dynamic microfluidic single-cell cultivation (dMSCC) as a novel scale-down system for the characterization of Corynebacterium glutamicum growth using oscillating pH conditions as a model stress-factor. A detailed comparison between two-compartment reactor (two-CR) scale-down experiments and dMSCC was performed for one specific pH oscillation between reference pH 7 (~ 8 min) and disturbed pH 6 (~2 min). Similar reductions in growth rates were observed in both systems (dMSCC 21% and two-CR 27%) compared to undisturbed cultivation at pH 7. Afterwards, systematic experiments at symmetric and asymmetric pH oscillations between pH ranges of 4-6 and 8-11 and different intervals from 1 minute to 20 minutes, were performed to demonstrate the unique application range and throughput of the dMSCC system. Finally, the strength of the dMSCC application was demonstrated by mimicking fluctuating environmental conditions of a putative large-scale bioprocesse, which is difficult to conduct using two-CRs. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Sarah Täuber
- Multiscale Bioengineering, Technical Faculty, Bielefeld University, Universitätsstraße 25, 33615, Bielefeld, Germany.,Center for Biotechnology (CeBiTec), Bielefeld University, Universitätsstraße 25, 33615, Bielefeld, Germany
| | - Luisa Blöbaum
- Multiscale Bioengineering, Technical Faculty, Bielefeld University, Universitätsstraße 25, 33615, Bielefeld, Germany.,Center for Biotechnology (CeBiTec), Bielefeld University, Universitätsstraße 25, 33615, Bielefeld, Germany
| | - Valentin Steier
- Institute of Bio- and Geosciences, Forschungszentrum Jülich GmbH, IBG-1: Biotechnology, Jülich, Germany.,Institute of Biotechnology, RWTH Aachen University, Aachen, Germany
| | - Marco Oldiges
- Institute of Bio- and Geosciences, Forschungszentrum Jülich GmbH, IBG-1: Biotechnology, Jülich, Germany.,Institute of Biotechnology, RWTH Aachen University, Aachen, Germany
| | - Alexander Grünberger
- Multiscale Bioengineering, Technical Faculty, Bielefeld University, Universitätsstraße 25, 33615, Bielefeld, Germany.,Center for Biotechnology (CeBiTec), Bielefeld University, Universitätsstraße 25, 33615, Bielefeld, Germany
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3
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Hartmann FSF, Udugama IA, Seibold GM, Sugiyama H, Gernaey KV. Digital models in biotechnology: Towards multi-scale integration and implementation. Biotechnol Adv 2022; 60:108015. [PMID: 35781047 DOI: 10.1016/j.biotechadv.2022.108015] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2022] [Revised: 06/03/2022] [Accepted: 06/27/2022] [Indexed: 12/28/2022]
Abstract
Industrial biotechnology encompasses a large area of multi-scale and multi-disciplinary research activities. With the recent megatrend of digitalization sweeping across all industries, there is an increased focus in the biotechnology industry on developing, integrating and applying digital models to improve all aspects of industrial biotechnology. Given the rapid development of this field, we systematically classify the state-of-art modelling concepts applied at different scales in industrial biotechnology and critically discuss their current usage, advantages and limitations. Further, we critically analyzed current strategies to couple cell models with computational fluid dynamics to study the performance of industrial microorganisms in large-scale bioprocesses, which is of crucial importance for the bio-based production industries. One of the most challenging aspects in this context is gathering intracellular data under industrially relevant conditions. Towards comprehensive models, we discuss how different scale-down concepts combined with appropriate analytical tools can capture intracellular states of single cells. We finally illustrated how the efforts could be used to develop digitals models suitable for both cell factory design and process optimization at industrial scales in the future.
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Affiliation(s)
- Fabian S F Hartmann
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Søltofts Plads, Building 223, 2800 Kgs. Lyngby, Denmark
| | - Isuru A Udugama
- Department of Chemical System Engineering, The University of Tokyo, 7-3-1, Hongo, Bunkyo-ku, 113-8656 Tokyo, Japan; Department of Chemical and Biochemical Engineering, Technical University of Denmark, Søltofts Plads, Building 228 A, 2800 Kgs. Lyngby, Denmark.
| | - Gerd M Seibold
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Søltofts Plads, Building 223, 2800 Kgs. Lyngby, Denmark
| | - Hirokazu Sugiyama
- Department of Chemical System Engineering, The University of Tokyo, 7-3-1, Hongo, Bunkyo-ku, 113-8656 Tokyo, Japan
| | - Krist V Gernaey
- Department of Chemical and Biochemical Engineering, Technical University of Denmark, Søltofts Plads, Building 228 A, 2800 Kgs. Lyngby, Denmark.
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4
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Mirzabe AH, Hajiahmad A, Fadavi A, Rafiee S. Design of nutrient gas-phase bioreactors: a critical comprehensive review. Bioprocess Biosyst Eng 2022; 45:1239-1265. [PMID: 35562481 DOI: 10.1007/s00449-022-02728-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2022] [Accepted: 04/13/2022] [Indexed: 11/28/2022]
Abstract
To reach an efficient and economical gas-phase bioreactor is still one of the most critical challenges in biotechnology engineering. The numerous advantages of gas-phase bioreactors (GPBs) as well as disadvantages of these bioreactors should be exactly recognized, and efforts should be made to eliminate these defects. The first step in upgrading these bioreactors is to identify their types and the results of previous research. In the present work, a summary of the studies carried out in the field of cultivation in these bioreactors, their classification, their components, their principles and relations governing elements, modeling them, and some of their inherent engineering aspects are presented. Literature review showed that inoculation of shoots, roots, adventurous roots, callus, nodal explants, anther, nodal segment, somatic embryo, hairy roots, and fungus is reported in 15, 2, 2, 2, 3, 2, 1, 1, 37, and 5 cases, respectively.
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Affiliation(s)
- Amir Hossein Mirzabe
- Department of Mechanics of Biosystem Engineering, Faculty of Engineering and Technology, College of Agriculture and Natural Resources, University of Tehran, Karaj, Alborz, Iran
| | - Ali Hajiahmad
- Department of Mechanics of Biosystem Engineering, Faculty of Engineering and Technology, College of Agriculture and Natural Resources, University of Tehran, Karaj, Alborz, Iran. .,Department of Mechanical Engineering of Biosystems, Faculty of Agricultural Engineering and Technology, University of Tehran, Karaj, Alborz, Iran.
| | - Ali Fadavi
- Department of Food Technology, College of Aburaihan, University of Tehran, Tehran, Iran
| | - Shahin Rafiee
- Department of Mechanics of Biosystem Engineering, Faculty of Engineering and Technology, College of Agriculture and Natural Resources, University of Tehran, Karaj, Alborz, Iran
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5
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Ho P, Täuber S, Stute B, Grünberger A, von Lieres E. Microfluidic Reproduction of Dynamic Bioreactor Environment Based on Computational Lifelines. FRONTIERS IN CHEMICAL ENGINEERING 2022. [DOI: 10.3389/fceng.2022.826485] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The biotechnological production of fine chemicals, proteins and pharmaceuticals is usually hampered by loss of microbial performance during scale-up. This challenge is mainly caused by discrepancies between homogeneous environmental conditions at laboratory scale, where bioprocesses are optimized, and inhomogeneous conditions in large-scale bioreactors, where production takes place. Therefore, to improve strain selection and process development, it is of great interest to characterize these fluctuating conditions at large-scale and to study their effects on microbial cells. In this paper, we demonstrate the potential of computational fluid dynamics (CFD) simulation of large-scale bioreactors combined with dynamic microfluidic single-cell cultivation (dMSCC). Environmental conditions in a 200 L bioreactor were characterized with CFD simulations. Computational lifelines were determined by combining simulated turbulent multiphase flow, mass transport and particle tracing. Glucose availability for Corynebacterium glutamicum cells was determined. The reactor was simulated with average glucose concentrations of 6 g m−3, 10 g m−3 and 16 g m−3. The resulting computational lifelines, discretized into starvation and abundance regimes, were used as feed profiles for the dMSCC to investigate how varying glucose concentration affects cell physiology and growth rate. In this study, each colony in the dMSCC device represents a single cell as it travels through the reactor. Under oscillating conditions reproduced in the dMSCC device, a decrease in growth rate of about 40% was observed compared to continuous supply with the same average glucose availability. The presented approach provides insights into environmental conditions observed by microorganisms in large-scale bioreactors. It also paves the way for an improved understanding of how inhomogeneous environmental conditions influence cellular physiology, growth and production.
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6
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Hoang MD, Doan DT, Schmidt M, Kranz H, Kremling A, Heins A. Application of an Escherichia coli triple reporter strain for at-line monitoring of single-cell physiology during L-phenylalanine production. Eng Life Sci 2022; 23:e2100162. [PMID: 36619877 PMCID: PMC9815085 DOI: 10.1002/elsc.202100162] [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: 12/03/2021] [Revised: 01/24/2022] [Accepted: 02/07/2022] [Indexed: 01/11/2023] Open
Abstract
Biotechnological production processes are sustainable approaches for the production of biobased components such as amino acids for food and feed industry. Scale-up from ideal lab-scale bioreactors to large-scale processes is often accompanied by loss in productivity. This may be related to population heterogeneities of cells originating from isogenic cultures that arise due to dynamic non-ideal conditions in the bioreactor. To better understand this phenomenon, deeper insights into single-cell physiologies in bioprocesses are mandatory before scale-up. Here, a triple reporter strain (3RP) was developed by chromosomally integrating the fluorescent proteins mEmerald, CyOFP1, and mTagBFP2 into the L-phenylalanine producing Escherichia coli strain FUS4 (pF81kan) to allow monitoring of growth, oxygen availability, and general stress response of the single cells. Functionality of the 3RP was confirmed in well-mixed lab-scale fed-batch processes with glycerol as carbon source in comparison to the strain without fluorescent proteins, leading to no difference in process performance. Fluorescence levels could successfully reflect the course of related process state variables, revealed population heterogeneities during the transition between different process phases and potentially subpopulations that exhibit superior process performance. Furthermore, indications were found for noise in gene expression as regulation strategy against environmental perturbation.
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Affiliation(s)
- Manh Dat Hoang
- Chair of Biochemical EngineeringDepartment of Energy and Process EngineeringTUM School of Engineering and DesignTechnical University of MunichGarchingGermany
| | - Dieu Thi Doan
- Systems BiotechnologyDepartment of Energy and Process EngineeringTUM School of Engineering and DesignTechnical University of MunichGarchingGermany
| | - Marlen Schmidt
- Gen‐H Genetic Engineering Heidelberg GmbHHeidelbergGermany
| | - Harald Kranz
- Gen‐H Genetic Engineering Heidelberg GmbHHeidelbergGermany
| | - Andreas Kremling
- Systems BiotechnologyDepartment of Energy and Process EngineeringTUM School of Engineering and DesignTechnical University of MunichGarchingGermany
| | - Anna‐Lena Heins
- Chair of Biochemical EngineeringDepartment of Energy and Process EngineeringTUM School of Engineering and DesignTechnical University of MunichGarchingGermany
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7
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Becker J, Wittmann C. Metabolic Engineering of
Corynebacterium glutamicum. Metab Eng 2021. [DOI: 10.1002/9783527823468.ch12] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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8
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Zelle E, Pfelzer N, Oldiges M, Koch-Koerfges A, Bott M, Nöh K, Wiechert W. An energetic profile of Corynebacterium glutamicum underpinned by measured biomass yield on ATP. Metab Eng 2021; 65:66-78. [PMID: 33722651 DOI: 10.1016/j.ymben.2021.03.006] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2020] [Revised: 02/17/2021] [Accepted: 03/06/2021] [Indexed: 11/17/2022]
Abstract
The supply and usage of energetic cofactors in metabolism is a central concern for systems metabolic engineering, particularly in case of energy intensive products. One of the most important parameters for systems wide balancing of energetic cofactors is the ATP requirement for biomass formation YATP/Biomass. Despite its fundamental importance, YATP/Biomass values for non-fermentative organisms are still rough estimates deduced from theoretical considerations. For the first time, we present an approach for the experimental determination of YATP/Biomass using comparative 13C metabolic flux analysis (13C MFA) of a wild type strain and an ATP synthase knockout mutant. We show that the energetic profile of a cell can then be deduced from a genome wide stoichiometric model and experimental maintenance data. Particularly, the contributions of substrate level phosphorylation (SLP) and electron transport phosphorylation (ETP) to ATP generation become available which enables the overall energetic efficiency of a cell to be characterized. As a model organism, the industrial platform organism Corynebacterium glutamicum is used. C. glutamicum uses a respiratory type of energy metabolism, implying that ATP can be synthesized either by SLP or by ETP with the membrane-bound F1FO-ATP synthase using the proton motive force (pmf) as driving force. The presence of two terminal oxidases, which differ in their proton translocation efficiency by a factor of three, further complicates energy balancing for this organism. By integration of experimental data and network models, we show that in the wild type SLP and ETP contribute equally to ATP generation. Thus, the role of ETP in respiring bacteria may have been overrated in the past. Remarkably, in the genome wide setting 65% of the pmf is actually not used for ATP synthesis. However, it turns out that, compared to other organisms C. glutamicum still uses its energy budget rather efficiently.
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Affiliation(s)
- E Zelle
- Institute of Bio- and Geosciences, IBG-1: Biotechnology, Forschungszentrum Jülich GmbH, D, 52425, Jülich, Germany
| | - N Pfelzer
- Institute of Bio- and Geosciences, IBG-1: Biotechnology, Forschungszentrum Jülich GmbH, D, 52425, Jülich, Germany
| | - M Oldiges
- Institute of Bio- and Geosciences, IBG-1: Biotechnology, Forschungszentrum Jülich GmbH, D, 52425, Jülich, Germany
| | - A Koch-Koerfges
- Institute of Bio- and Geosciences, IBG-1: Biotechnology, Forschungszentrum Jülich GmbH, D, 52425, Jülich, Germany
| | - M Bott
- Institute of Bio- and Geosciences, IBG-1: Biotechnology, Forschungszentrum Jülich GmbH, D, 52425, Jülich, Germany
| | - K Nöh
- Institute of Bio- and Geosciences, IBG-1: Biotechnology, Forschungszentrum Jülich GmbH, D, 52425, Jülich, Germany
| | - W Wiechert
- Institute of Bio- and Geosciences, IBG-1: Biotechnology, Forschungszentrum Jülich GmbH, D, 52425, Jülich, Germany.
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9
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Xia J, Wang G, Fan M, Chen M, Wang Z, Zhuang Y. Understanding the scale-up of fermentation processes from the viewpoint of the flow field in bioreactors and the physiological response of strains. Chin J Chem Eng 2021. [DOI: 10.1016/j.cjche.2020.12.004] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
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10
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Potential of Integrating Model-Based Design of Experiments Approaches and Process Analytical Technologies for Bioprocess Scale-Down. ADVANCES IN BIOCHEMICAL ENGINEERING/BIOTECHNOLOGY 2021. [PMID: 33381857 DOI: 10.1007/10_2020_154] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/18/2023]
Abstract
Typically, bioprocesses on an industrial scale are dynamic systems with a certain degree of variability, system inhomogeneities, and even population heterogeneities. Therefore, the scaling of such processes from laboratory to industrial scale and vice versa is not a trivial task. Traditional scale-down methodologies consider several technical parameters, so that systems on the laboratory scale tend to qualitatively reflect large-scale effects, but not the dynamic situation in an industrial bioreactor over the entire process, from the perspective of a cell. Supported by the enormous increase in computing power, the latest scientific focus is on the application of dynamic models, in combination with computational fluid dynamics to quantitatively describe cell behavior. These models allow the description of possible cellular lifelines which in turn can be used to derive a regime analysis for scale-down experiments. However, the approaches described so far, which were for a very few process examples, are very labor- and time-intensive and cannot be validated easily. In parallel, alternatives have been developed based on the description of the industrial process with hybrid process models, which describe a process mechanistically as far as possible in order to determine the essential process parameters with their respective variances. On-line analytical methods allow the characterization of population heterogeneity directly in the process. This detailed information from the industrial process can be used in laboratory screening systems to select relevant conditions in which the cell and process related parameters reflect the situation in the industrial scale. In our opinion, these technologies, which are available in research for modeling biological systems, in combination with process analytical techniques are so far developed that they can be implemented in industrial routines for faster development of new processes and optimization of existing ones.
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11
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Täuber S, Golze C, Ho P, von Lieres E, Grünberger A. dMSCC: a microfluidic platform for microbial single-cell cultivation of Corynebacterium glutamicum under dynamic environmental medium conditions. LAB ON A CHIP 2020; 20:4442-4455. [PMID: 33095214 DOI: 10.1039/d0lc00711k] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
In nature and in technical systems, microbial cells are often exposed to rapidly fluctuating environmental conditions. These conditions can vary in quality, e.g., the existence of a starvation zone, and quantity, e.g., the average residence time in this zone. For strain development and process design, cellular response to such fluctuations needs to be systematically analysed. However, the existing methods for physically imitating rapidly changing environmental conditions are limited in spatio-temporal resolution. Hence, we present a novel microfluidic system for cultivation of single cells and small cell clusters under dynamic environmental conditions (dynamic microfluidic single-cell cultivation (dMSCC)). This system enables the control of nutrient availability and composition between two media with second to minute resolution. We validate our technology using the industrially relevant model organism Corynebacterium glutamicum. The organism was exposed to different oscillation frequencies between nutrient excess (feasts) and scarcity (famine). The resulting changes in cellular physiology, such as the colony growth rate and cell morphology, were analysed and revealed significant differences in the growth rate and cell length between the different conditions. dMSCC also allows the application of defined but randomly changing nutrient conditions, which is important for reproducing more complex conditions from natural habitats and large-scale bioreactors. The presented system lays the foundation for the cultivation of cells under complex changing environmental conditions.
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Affiliation(s)
- Sarah Täuber
- Multiscale Bioengineering, Technical Faculty, Bielefeld University, Universitätsstraße 25, 33615 Bielefeld, Germany.
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12
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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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13
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Hemmerich J, Labib M, Steffens C, Reich SJ, Weiske M, Baumgart M, Rückert C, Ruwe M, Siebert D, Wendisch VF, Kalinowski J, Wiechert W, Oldiges M. Screening of a genome-reduced Corynebacterium glutamicum strain library for improved heterologous cutinase secretion. Microb Biotechnol 2020; 13:2020-2031. [PMID: 32893457 PMCID: PMC7533341 DOI: 10.1111/1751-7915.13660] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2019] [Revised: 08/14/2020] [Accepted: 08/17/2020] [Indexed: 12/19/2022] Open
Abstract
The construction of microbial platform organisms by means of genome reduction is an ongoing topic in biotechnology. In this study, we investigated whether the deletion of single or multiple gene clusters has a positive effect on the secretion of cutinase from Fusarium solani pisi in the industrial workhorse Corynebacterium glutamicum. A total of 22 genome-reduced strain variants were compared applying two Sec signal peptides from Bacillus subtilis. High-throughput phenotyping using robotics-integrated microbioreactor technology with automated harvesting revealed distinct cutinase secretion performance for a specific combination of signal peptide and genomic deletions. The biomass-specific cutinase yield for strain GRS41_51_NprE was increased by ~ 200%, although the growth rate was reduced by ~ 60%. Importantly, the causative deletions of genomic clusters cg2801-cg2828 and rrnC-cg3298 could not have been inferred a priori. Strikingly, bioreactor fed-batch cultivations at controlled growth rates resulted in a complete reversal of the screening results, with the cutinase yield for strain GRS41_51_NprE dropping by ~ 25% compared to the reference strain. Thus, the choice of bioprocess conditions may turn a 'high-performance' strain from batch screening into a 'low-performance' strain in fed-batch cultivation. In conclusion, future studies are needed in order to understand metabolic adaptations of C. glutamicum to both genomic deletions and different bioprocess conditions.
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Affiliation(s)
- Johannes Hemmerich
- Institute of Bio‐ and Geosciences – Biotechnology (IBG‐1)Forschungszentrum Jülich, Institute of Bio‐ and Geosciences ‐ Biotechnology (IBG‐1)Jülich52425Germany
- Bioeconomy Science Center (BioSC)Forschungszentrum JülichJülich52425Germany
| | - Mohamed Labib
- Institute of Bio‐ and Geosciences – Biotechnology (IBG‐1)Forschungszentrum Jülich, Institute of Bio‐ and Geosciences ‐ Biotechnology (IBG‐1)Jülich52425Germany
| | - Carmen Steffens
- Institute of Bio‐ and Geosciences – Biotechnology (IBG‐1)Forschungszentrum Jülich, Institute of Bio‐ and Geosciences ‐ Biotechnology (IBG‐1)Jülich52425Germany
| | - Sebastian J. Reich
- Institute of Bio‐ and Geosciences – Biotechnology (IBG‐1)Forschungszentrum Jülich, Institute of Bio‐ and Geosciences ‐ Biotechnology (IBG‐1)Jülich52425Germany
- Present address:
Institute of Microbiology and BiotechnologyUlm UniversityUlm89081Germany
| | - Marc Weiske
- Institute of Bio‐ and Geosciences – Biotechnology (IBG‐1)Forschungszentrum Jülich, Institute of Bio‐ and Geosciences ‐ Biotechnology (IBG‐1)Jülich52425Germany
| | - Meike Baumgart
- Institute of Bio‐ and Geosciences – Biotechnology (IBG‐1)Forschungszentrum Jülich, Institute of Bio‐ and Geosciences ‐ Biotechnology (IBG‐1)Jülich52425Germany
| | - Christian Rückert
- Microbial Genomics and BiotechnologyCenter for BiotechnologyBielefeld UniversityBielefeld33615Germany
| | - Matthias Ruwe
- Microbial Genomics and BiotechnologyCenter for BiotechnologyBielefeld UniversityBielefeld33615Germany
| | - Daniel Siebert
- Faculty of Biology, Chair of Genetics of ProkaryotesBielefeld UniversityBielefeld33615Germany
- Present address:
Microbial BiotechnologyCampus Straubing for Biotechnology and SustainabilityTechnical University of MunichStraubing94315Germany
| | - Volker F. Wendisch
- Faculty of Biology, Chair of Genetics of ProkaryotesBielefeld UniversityBielefeld33615Germany
| | - Jörn Kalinowski
- Microbial Genomics and BiotechnologyCenter for BiotechnologyBielefeld UniversityBielefeld33615Germany
| | - Wolfgang Wiechert
- Institute of Bio‐ and Geosciences – Biotechnology (IBG‐1)Forschungszentrum Jülich, Institute of Bio‐ and Geosciences ‐ Biotechnology (IBG‐1)Jülich52425Germany
- Bioeconomy Science Center (BioSC)Forschungszentrum JülichJülich52425Germany
- Computational Systems Biotechnology (AVT.CSB)RWTH Aachen UniversityAachen52074Germany
| | - Marco Oldiges
- Institute of Bio‐ and Geosciences – Biotechnology (IBG‐1)Forschungszentrum Jülich, Institute of Bio‐ and Geosciences ‐ Biotechnology (IBG‐1)Jülich52425Germany
- Bioeconomy Science Center (BioSC)Forschungszentrum JülichJülich52425Germany
- Institute of BiotechnologyRWTH Aachen UniversityAachen52074Germany
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14
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The Industrial Organism Corynebacterium glutamicum Requires Mycothiol as Antioxidant to Resist Against Oxidative Stress in Bioreactor Cultivations. Antioxidants (Basel) 2020; 9:antiox9100969. [PMID: 33050339 PMCID: PMC7599745 DOI: 10.3390/antiox9100969] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2020] [Revised: 09/28/2020] [Accepted: 09/29/2020] [Indexed: 12/27/2022] Open
Abstract
In aerobic environments, bacteria are exposed to reactive oxygen species (ROS). To avoid an excess of ROS, microorganisms are equipped with powerful enzymatic and non-enzymatic antioxidants. Corynebacterium glutamicum, a widely used industrial platform organism, uses mycothiol (MSH) as major low molecular weight (LMW) thiol and non-enzymatic antioxidant. In aerobic bioreactor cultivations, C. glutamicum becomes exposed to oxygen concentrations surpassing the air saturation, which are supposed to constitute a challenge for the intracellular MSH redox balance. In this study, the role of MSH was investigated at different oxygen levels (pO2) in bioreactor cultivations in C. glutamicum. Despite the presence of other highly efficient antioxidant systems, such as catalase, the MSH deficient ΔmshC mutant was impaired in growth in bioreactor experiments performed at pO2 values of 30%. At a pO2 level of 20%, this growth defect was abolished, indicating a high susceptibility of the MSH-deficient mutant towards elevated oxygen concentrations. Bioreactor experiments with C. glutamicum expressing the Mrx1-roGFP2 redox biosensor revealed a strong oxidative shift in the MSH redox potential (EMSH) at pO2 values above 20%. This indicates that the LMW thiol MSH is an essential antioxidant to maintain the robustness and industrial performance of C. glutamicum during aerobic fermentation processes.
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Wehrs M, Thompson MG, Banerjee D, Prahl JP, Morella NM, Barcelos CA, Moon J, Costello Z, Keasling JD, Shih PM, Tanjore D, Mukhopadhyay A. Investigation of Bar-seq as a method to study population dynamics of Saccharomyces cerevisiae deletion library during bioreactor cultivation. Microb Cell Fact 2020; 19:167. [PMID: 32811554 PMCID: PMC7437010 DOI: 10.1186/s12934-020-01423-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2020] [Accepted: 08/11/2020] [Indexed: 12/15/2022] Open
Abstract
Background Despite the latest advancements in metabolic engineering for genome editing and characterization of host performance, the successful development of robust cell factories used for industrial bioprocesses and accurate prediction of the behavior of microbial systems, especially when shifting from laboratory-scale to industrial conditions, remains challenging. To increase the probability of success of a scale-up process, data obtained from thoroughly performed studies mirroring cellular responses to typical large-scale stimuli may be used to derive crucial information to better understand potential implications of large-scale cultivation on strain performance. This study assesses the feasibility to employ a barcoded yeast deletion library to assess genome-wide strain fitness across a simulated industrial fermentation regime and aims to understand the genetic basis of changes in strain physiology during industrial fermentation, and the corresponding roles these genes play in strain performance. Results We find that mutant population diversity is maintained through multiple seed trains, enabling large scale fermentation selective pressures to act upon the community. We identify specific deletion mutants that were enriched in all processes tested in this study, independent of the cultivation conditions, which include MCK1, RIM11, MRK1, and YGK3 that all encode homologues of mammalian glycogen synthase kinase 3 (GSK-3). Ecological analysis of beta diversity between all samples revealed significant population divergence over time and showed feed specific consequences of population structure. Further, we show that significant changes in the population diversity during fed-batch cultivations reflect the presence of significant stresses. Our observations indicate that, for this yeast deletion collection, the selection of the feeding scheme which affects the accumulation of the fermentative by-product ethanol impacts the diversity of the mutant pool to a higher degree as compared to the pH of the culture broth. The mutants that were lost during the time of most extreme population selection suggest that specific biological processes may be required to cope with these specific stresses. Conclusions Our results demonstrate the feasibility of Bar-seq to assess fermentation associated stresses in yeast populations under industrial conditions and to understand critical stages of a scale-up process where variability emerges, and selection pressure gets imposed. Overall our work highlights a promising avenue to identify genetic loci and biological stress responses required for fitness under industrial conditions.
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Affiliation(s)
- Maren Wehrs
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA.,Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Emeryville, CA, 94608, USA
| | - Mitchell G Thompson
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA.,Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Emeryville, CA, 94608, USA.,Department of Plant and Microbial Biology, University of California, Berkeley, CA, 94720, USA
| | - Deepanwita Banerjee
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA.,Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Emeryville, CA, 94608, USA
| | - Jan-Philip Prahl
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA.,Advanced Biofuels and Bioproducts Process Development Unit, Lawrence Berkeley National Laboratory, Emeryville, CA, 94608, USA
| | - Norma M Morella
- Fred Hutchinson Cancer Research Center, Seattle, WA, 98109, USA
| | - Carolina A Barcelos
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA.,Advanced Biofuels and Bioproducts Process Development Unit, Lawrence Berkeley National Laboratory, Emeryville, CA, 94608, USA
| | - Jadie Moon
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA.,Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Emeryville, CA, 94608, USA
| | - Zak Costello
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA.,Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Emeryville, CA, 94608, USA.,Department of Energy Agile BioFoundry, Emeryville, CA, 94608, USA
| | - Jay D Keasling
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA.,Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Emeryville, CA, 94608, USA.,Department of Bioengineering, University of California, Berkeley, CA, 94720, USA.,Department of Chemical and Biomolecular Engineering, University of California, Berkeley, CA, 94720, USA.,Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, DK 2970, Horsholm, Denmark.,Synthetic Biochemistry Center, Institute for Synthetic Biology, Shenzhen Institutes for Advanced Technologies, Shenzhen, China
| | - Patrick M Shih
- 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.,Department of Plant Biology, University of California-Davis, Davis, CA, 95616, 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, Emeryville, CA, 94608, 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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Olughu W, Nienow A, Hewitt C, Rielly C. Scale-down studies for the scale-up of a recombinant Corynebacterium glutamicum fed-batch fermentation: loss of homogeneity leads to lower levels of cadaverine production. JOURNAL OF CHEMICAL TECHNOLOGY AND BIOTECHNOLOGY (OXFORD, OXFORDSHIRE : 1986) 2020; 95:675-685. [PMID: 32139953 PMCID: PMC7043379 DOI: 10.1002/jctb.6248] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/07/2019] [Revised: 09/30/2019] [Accepted: 10/14/2019] [Indexed: 06/10/2023]
Abstract
BACKGROUND The loss of efficiency and performance of bioprocesses on scale-up is well known, but not fully understood. This work addresses this problem, by studying the effect of some fermentation gradients (pH, glucose and oxygen) that occur at the larger scale in a bench-scale two-compartment reactor [plug flow reactor (PFR) + stirred tank reactor (STR)] using the cadaverine-producing recombinant Corynebacterium glutamicum DM1945 Δact3 Ptuf-ldcC_OPT. The new scale-down strategy developed here studied the effect of increasing the magnitude of fermentation gradients by considering not only the average cell residence time in the PFR (τ PFR), but also the mean frequency at which the bacterial cells entered the PFR (f m) section of the two-compartment reactor. RESULTS On implementing this strategy the cadaverine production decreased on average by 26%, 49% and 59% when the τ PFR was increased from 1 to 2 min and then 5 min respectively compared to the control fermentation. The carbon dioxide productivity was highest (3.1-fold that of the control) at a τ PFR of 5 min, but no losses were observed in biomass production. However, the population of viable but non-culturable cells increased as the magnitude of fermentation gradients was increased. The new scale-down approach was also shown to have a bigger impact on fermentation performance than the traditional one. CONCLUSION This study demonstrated that C. glutamicum DM1945 Δact3 Ptuf-ldcC_OPT physiological response was a function of the magnitude of fermentation gradients simulated. The adaptations of a bacterial cell within a heterogeneous environment ultimately result in losses in fermentation productivity as observed here. © 2019 The Authors. Journal of Chemical Technology & Biotechnology published by John Wiley & Sons Ltd on behalf of Society of Chemical Industry.
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Affiliation(s)
- Williams Olughu
- Department of Chemical EngineeringLoughborough UniversityLoughboroughUK
- Ipsen Biopharma LtdWrexhamUK
| | - Alvin Nienow
- Department of Chemical EngineeringLoughborough UniversityLoughboroughUK
- School of Chemical EngineeringUniversity of BirminghamBirminghamUK
- School of Life and Health SciencesAston UniversityBirminghamUK
| | - Chris Hewitt
- School of Life and Health SciencesAston UniversityBirminghamUK
| | - Chris Rielly
- Department of Chemical EngineeringLoughborough UniversityLoughboroughUK
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Harnessing microbial metabolomics for industrial applications. World J Microbiol Biotechnol 2019; 36:1. [DOI: 10.1007/s11274-019-2775-x] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2019] [Accepted: 11/21/2019] [Indexed: 10/25/2022]
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18
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Lee D, Hong J, Kim KJ. Crystal Structure and Biochemical Characterization of Ketol-Acid Reductoisomerase from Corynebacterium glutamicum. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2019; 67:8527-8535. [PMID: 31298526 DOI: 10.1021/acs.jafc.9b03262] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
l-Valine belongs to the branched-chain amino acids (BCAAs) and is an essential amino acid that is crucial for all living organisms. l-Valine is industrially produced by the nonpathogenic bacterium Corynebacterium glutamicum and is synthesized by the BCAA biosynthetic pathway. Ketol-acid reductoisomerase (KARI) is the second enzyme in the BCAA pathway and catalyzes the conversion of (S)-2-acetolactate into (R)-2,3-dihydroxy-isovalerate, or the conversion of (S)-2-aceto-2-hydroxybutyrate into (R)-2,3-dihydroxy-3-methylvalerate. To elucidate the enzymatic properties of KARI from C. glutamicum (CgKARI), we successfully produced CgKARI protein and determined its crystal structure in complex with NADP+ and two Mg2+ ions. Based on the complex structure, docking simulations, and site-directed mutagenesis experiments, we revealed that CgKARI belongs to Class I KARI and identified key residues involved in stabilization of the substrate, metal ions, and cofactor. Furthermore, we confirmed the difference in the binding of metal ions that depended on the conformational change.
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Affiliation(s)
- Donghoon Lee
- School of Life Sciences, BK21 Plus KNU Creative BioResearch Group , Kyungpook National University , Daehak-ro 80, Buk-ku , Daegu 702-701 , Korea
- KNU Institute for Microorganisms , Kyungpook National University , Daegu 41566 , Republic of Korea
| | - Jiyeon Hong
- School of Life Sciences, BK21 Plus KNU Creative BioResearch Group , Kyungpook National University , Daehak-ro 80, Buk-ku , Daegu 702-701 , Korea
- KNU Institute for Microorganisms , Kyungpook National University , Daegu 41566 , Republic of Korea
| | - Kyung-Jin Kim
- School of Life Sciences, BK21 Plus KNU Creative BioResearch Group , Kyungpook National University , Daehak-ro 80, Buk-ku , Daegu 702-701 , Korea
- KNU Institute for Microorganisms , Kyungpook National University , Daegu 41566 , Republic of Korea
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Conrady M, Lemoine A, Limberg MH, Oldiges M, Neubauer P, Junne S. Carboxylic acid consumption and production by Corynebacterium glutamicum. Biotechnol Prog 2019; 35:e2804. [PMID: 30851150 DOI: 10.1002/btpr.2804] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2018] [Revised: 03/01/2019] [Accepted: 03/05/2019] [Indexed: 11/07/2022]
Abstract
Corynebacterium glutamicum is well-known as an industrial workhorse, most notably for its use in the bulk production of amino acids in the feed and food sector. Previous studies of the effect of gradients in scale-down reactors with complex media disclosed an accumulation of several carboxylic acids and a parallel decrease of growth and product accumulation. This study, therefore, addresses the impact of carboxylic acids, for example, acetate and l-lactate, on the cultivation of the cadaverine producing strain C. glutamicum DM1945Δact3:Ptuf -ldcCopt and their potential role in scale up related performance losses. A fluctuating power input in shake flask and stirred tank cultivations with mineral salt was applied to mimic discontinuous oxygen availability. Results demonstrate, whenever sufficient oxygen was available, C. glutamicum recovered from previously occurring stressful conditions like an oxygen limiting phase. Reassimilation of acids was detected simultaneously. In cultures, which were supplemented with either acetate or l-lactate, a rapid cometabolization of both acids in presence of glucose was observed, showing conversion rates of 7.8 and 3.8 mmol gcell dry weight -1 hr-1 , respectively. Uptake of these acids was accompanied by increased oxygen consumption. Proteins related to oxidative stress response, glycogen synthesis, and the main carbon metabolism were found in altered concentrations under oscillatory cultivation conditions. (Proteomics data are available via ProteomeXchange with identifier PXD012760). Virtually no impact on growth or product formation was observed. We conclude that the reduced growth and product formation in scale-down cultivations when complex media was used is not caused by the accumulation of carboxylic acids.
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Affiliation(s)
- Marius Conrady
- Department of Biotechnology, Bioprocess Engineering, Technische Universität Berlin, Berlin, Germany
| | - Anja Lemoine
- Department of Biotechnology, Bioprocess Engineering, Technische Universität Berlin, Berlin, Germany
| | - Michael H Limberg
- Research Centre Juelich, IBG-1-Institute of Bio- and Geosciences, Biotechnology, Juelich, Germany.,Department of Molecular Biotechnology, Fraunhofer Institute for Molecular Biology and Applied Ecology (IME), Aachen, Germany
| | - Marco Oldiges
- Research Centre Juelich, IBG-1-Institute of Bio- and Geosciences, Biotechnology, Juelich, Germany
| | - Peter Neubauer
- Department of Biotechnology, Bioprocess Engineering, Technische Universität Berlin, Berlin, Germany
| | - Stefan Junne
- Department of Biotechnology, Bioprocess Engineering, Technische Universität Berlin, Berlin, Germany
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20
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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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21
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Kaboré AK, Delaunay S, Blanchard F, Guedon E, Fick M, Olmos E. Study and modeling of fluctuating dissolved oxygen concentration impact on Corynebacterium glutamicum growth in a scale-down bioreactor. Process Biochem 2019. [DOI: 10.1016/j.procbio.2018.10.016] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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22
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Hemmerich J, Moch M, Jurischka S, Wiechert W, Freudl R, Oldiges M. Combinatorial impact of Sec signal peptides fromBacillus subtilisand bioprocess conditions on heterologous cutinase secretion byCorynebacterium glutamicum. Biotechnol Bioeng 2018; 116:644-655. [DOI: 10.1002/bit.26873] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2018] [Revised: 09/11/2018] [Accepted: 10/26/2018] [Indexed: 12/12/2022]
Affiliation(s)
- Johannes Hemmerich
- Forschungszentrum JülichInstitute of Bio‐ and Geosciences—Biotechnology (IBG‐1)Jülich Germany
- Bioeconomy Science Center (BioSC)c/o Forschungszentrum JülichJülich Germany
| | - Matthias Moch
- Forschungszentrum JülichInstitute of Bio‐ and Geosciences—Biotechnology (IBG‐1)Jülich Germany
| | - Sarah Jurischka
- Forschungszentrum JülichInstitute of Bio‐ and Geosciences—Biotechnology (IBG‐1)Jülich Germany
- Bioeconomy Science Center (BioSC)c/o Forschungszentrum JülichJülich Germany
| | - Wolfgang Wiechert
- Forschungszentrum JülichInstitute of Bio‐ and Geosciences—Biotechnology (IBG‐1)Jülich Germany
- Bioeconomy Science Center (BioSC)c/o Forschungszentrum JülichJülich Germany
- Computational Systems Biotechnology (AVT.CSB)RWTH Aachen UniversityAachen Germany
| | - Roland Freudl
- Forschungszentrum JülichInstitute of Bio‐ and Geosciences—Biotechnology (IBG‐1)Jülich Germany
- Bioeconomy Science Center (BioSC)c/o Forschungszentrum JülichJülich Germany
| | - Marco Oldiges
- Forschungszentrum JülichInstitute of Bio‐ and Geosciences—Biotechnology (IBG‐1)Jülich Germany
- Bioeconomy Science Center (BioSC)c/o Forschungszentrum JülichJülich Germany
- Institute of BiotechnologyRWTH Aachen UniversityAachen Germany
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Graf M, Zieringer J, Haas T, Nieß A, Blombach B, Takors R. Physiological Response of Corynebacterium glutamicum to Increasingly Nutrient-Rich Growth Conditions. Front Microbiol 2018; 9:2058. [PMID: 30210489 PMCID: PMC6123352 DOI: 10.3389/fmicb.2018.02058] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2018] [Accepted: 08/13/2018] [Indexed: 01/31/2023] Open
Abstract
To ensure economic competitiveness, bioprocesses should achieve maximum productivities enabled by high growth rates (μ) and equally high substrate consumption rates (qS) as a prerequisite of sufficient carbon-to-product conversion. Both traits were investigated and improved via bioprocess engineering approaches studying the industrial work horse Corynebacterium glutamicum. Standard minimal medium CGXII with glucose as sole carbon source was supplemented with complex brain-heart-infusion (BHI) or amino acid (AA) cocktails. Maximum μ of 0.67 h-1 was exclusively observed in 37 g BHI L-1 whereas only minor growth stimulation was found after AA supplementation (μ = 0.468 h-1). Increasing glucose consumption rates (qGlc) were solely observed in certain dosages of BHI (1-10 g L-1), while 37 g BHI L-1 and AA addition revealed qGlc below the reference experiments. Moreover, BHI supplementation revealed Monod-type saturation kinetics of μ (KBHI = 2.73 g BHI L-1) referring to the preference of non-AAs as key boosting nutrients. ATP-demands under reference, 1 g BHI L-1, and AA conditions were nearly constant but halved in BHI concentrations above 5 g L-1 reflecting the energetic advantage of consuming complex nutrient components in addition to "simple" building blocks such as AAs. Furthermore, C. glutamicum revealed maximum biomass per carbon yields of about 18 gCDW C-mol-1 irrespective of the medium. In AA supplementation experiments, simultaneous uptake of 17 AAs was observed, maximum individual consumption rates determined, and L-asparagine and L-glutamine were distinguished as compounds with the highest consumption rates. Employment of the expanded stoichiometric model iMG481 successfully reproduced experimental results and revealed the importance of C. glutamicum's transaminase network to compensate needs of limiting AA supply. Model-based sensitivity studies attributed the highest impact on μ to AAs with high ATP and NADPH demands such as L-tryptophan or L-phenylalanine.
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Affiliation(s)
| | | | | | | | | | - Ralf Takors
- Institute of Biochemical Engineering, University of Stuttgart, Stuttgart, Germany
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Lange J, Münch E, Müller J, Busche T, Kalinowski J, Takors R, Blombach B. Deciphering the Adaptation of Corynebacterium glutamicum in Transition from Aerobiosis via Microaerobiosis to Anaerobiosis. Genes (Basel) 2018; 9:E297. [PMID: 29899275 PMCID: PMC6027265 DOI: 10.3390/genes9060297] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2018] [Revised: 05/31/2018] [Accepted: 06/07/2018] [Indexed: 01/02/2023] Open
Abstract
Zero-growth processes are a promising strategy for the production of reduced molecules and depict a steady transition from aerobic to anaerobic conditions. To investigate the adaptation of Corynebacterium glutamicum to altering oxygen availabilities, we conceived a triple-phase fermentation process that describes a gradual reduction of dissolved oxygen with a shift from aerobiosis via microaerobiosis to anaerobiosis. The distinct process phases were clearly bordered by the bacteria’s physiologic response such as reduced growth rate, biomass substrate yield and altered yield of fermentation products. During the process, sequential samples were drawn at six points and analyzed via RNA-sequencing, for metabolite concentrations and for enzyme activities. We found transcriptional alterations of almost 50% (1421 genes) of the entire protein coding genes and observed an upregulation of fermentative pathways, a rearrangement of respiration, and mitigation of the basic cellular mechanisms such as transcription, translation and replication as a transient response related to the installed oxygen dependent process phases. To investigate the regulatory regime, 18 transcriptionally altered (putative) transcriptional regulators were deleted, but none of the deletion strains showed noticeable growth kinetics under an oxygen restricted environment. However, the described transcriptional adaptation of C. glutamicum resolved to varying oxygen availabilities provides a useful basis for future process and strain engineering.
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Affiliation(s)
- Julian Lange
- Institute of Biochemical Engineering, University of Stuttgart, Allmandring 31, 70569 Stuttgart, Germany.
| | - Eugenia Münch
- Institute of Biochemical Engineering, University of Stuttgart, Allmandring 31, 70569 Stuttgart, Germany.
| | - Jan Müller
- Institute of Biochemical Engineering, University of Stuttgart, Allmandring 31, 70569 Stuttgart, Germany.
| | - Tobias Busche
- Center for Biotechnology, Bielefeld University, Universitätsstraße 27, 33615 Bielefeld, Germany.
- Institute for Biology-Microbiology, Freie Universität Berlin, Königin-Luise-Str. 12-16, 14195 Berlin, Germany.
| | - Jörn Kalinowski
- Center for Biotechnology, Bielefeld University, Universitätsstraße 27, 33615 Bielefeld, Germany.
| | - Ralf Takors
- Institute of Biochemical Engineering, University of Stuttgart, Allmandring 31, 70569 Stuttgart, Germany.
| | - Bastian Blombach
- Institute of Biochemical Engineering, University of Stuttgart, Allmandring 31, 70569 Stuttgart, Germany.
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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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26
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Son HF, Kim KJ. Structural basis for substrate specificity of meso-diaminopimelic acid decarboxylase from Corynebacterium glutamicum. Biochem Biophys Res Commun 2018; 495:1815-1821. [DOI: 10.1016/j.bbrc.2017.11.097] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2017] [Accepted: 11/15/2017] [Indexed: 11/28/2022]
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27
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Hemmerich J, Freier L, Wiechert W, von Lieres E, Oldiges M. Generic Protocol for Optimization of Heterologous Protein Production Using Automated Microbioreactor Technology. J Vis Exp 2017. [PMID: 29286407 PMCID: PMC5755569 DOI: 10.3791/56234] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
A core business in industrial biotechnology using microbial production cell factories is the iterative process of strain engineering and optimization of bioprocess conditions. One important aspect is the improvement of cultivation medium to provide an optimal environment for microbial formation of the product of interest. It is well accepted that the media composition can dramatically influence overall bioprocess performance. Nutrition medium optimization is known to improve recombinant protein production with microbial systems and thus, this is a rewarding step in bioprocess development. However, very often standard media recipes are taken from literature, since tailor-made design of the cultivation medium is a tedious task that demands microbioreactor technology for sufficient cultivation throughput, fast product analytics, as well as support by lab robotics to enable reliability in liquid handling steps. Furthermore, advanced mathematical methods are required for rationally analyzing measurement data and efficiently designing parallel experiments such as to achieve optimal information content. The generic nature of the presented protocol allows for easy adaption to different lab equipment, other expression hosts, and target proteins of interest, as well as further bioprocess parameters. Moreover, other optimization objectives like protein production rate, specific yield, or product quality can be chosen to fit the scope of other optimization studies. The applied Kriging Toolbox (KriKit) is a general tool for Design of Experiments (DOE) that contributes to improved holistic bioprocess optimization. It also supports multi-objective optimization which can be important in optimizing both upstream and downstream processes.
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Affiliation(s)
- Johannes Hemmerich
- IBG-1: Biotechnology, Forschungszentrum Jülich; Research Center Jülich, Bioeconomy Science Center (BioSC)
| | - Lars Freier
- IBG-1: Biotechnology, Forschungszentrum Jülich; Research Center Jülich, Bioeconomy Science Center (BioSC)
| | - Wolfgang Wiechert
- IBG-1: Biotechnology, Forschungszentrum Jülich; Research Center Jülich, Bioeconomy Science Center (BioSC); Computational Systems Biotechnology (AVT.CSB), RWTH Aachen University
| | - Eric von Lieres
- IBG-1: Biotechnology, Forschungszentrum Jülich; Research Center Jülich, Bioeconomy Science Center (BioSC);
| | - Marco Oldiges
- IBG-1: Biotechnology, Forschungszentrum Jülich; Research Center Jülich, Bioeconomy Science Center (BioSC); Institute for Biotechnology, RWTH Aachen University;
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Limberg MH, Joachim M, Klein B, Wiechert W, Oldiges M. pH fluctuations imperil the robustness of C. glutamicum to short term oxygen limitation. J Biotechnol 2017; 259:248-260. [DOI: 10.1016/j.jbiotec.2017.08.018] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2017] [Revised: 08/15/2017] [Accepted: 08/16/2017] [Indexed: 11/16/2022]
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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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30
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Oliva R, Ortenzi MA, Salvini A, Papacchini A, Giomi D. One-pot oligoamides syntheses from l-lysine and l-tartaric acid. RSC Adv 2017. [DOI: 10.1039/c7ra00676d] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Oligoamides based on natural raw materials, l-lysine and l-tartaric acid, were synthesized using one-pot processes. A l-lysine diketopiperazine structure was obtained with good selectivity without protection/deprotection steps.
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Affiliation(s)
- R. Oliva
- Dipartimento di Chimica “Ugo Schiff”
- Università di Firenze
- 50019 Sesto Fiorentino (FI)
- Italy
| | - M. A. Ortenzi
- CRC Materiali Polimerici (LaMPo)
- Dipartimento di Chimica
- 19 – 20133 Milano
- Italy
| | - A. Salvini
- Dipartimento di Chimica “Ugo Schiff”
- Università di Firenze
- 50019 Sesto Fiorentino (FI)
- Italy
| | - A. Papacchini
- Dipartimento di Chimica “Ugo Schiff”
- Università di Firenze
- 50019 Sesto Fiorentino (FI)
- Italy
| | - D. Giomi
- Dipartimento di Chimica “Ugo Schiff”
- Università di Firenze
- 50019 Sesto Fiorentino (FI)
- Italy
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32
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Becker J, Wittmann C. Industrial Microorganisms: Corynebacterium glutamicum. Ind Biotechnol (New Rochelle N Y) 2016. [DOI: 10.1002/9783527807796.ch6] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Affiliation(s)
- Judith Becker
- Saarland University; Institute of Systems Biotechnology; Campus A 15 66123 Saarbrücken Germany
| | - Christoph Wittmann
- Saarland University; Institute of Systems Biotechnology; Campus A 15 66123 Saarbrücken Germany
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33
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Limberg MH, Schulte J, Aryani T, Mahr R, Baumgart M, Bott M, Wiechert W, Oldiges M. Metabolic profile of 1,5-diaminopentane producing Corynebacterium glutamicum
under scale-down conditions: Blueprint for robustness to bioreactor inhomogeneities. Biotechnol Bioeng 2016; 114:560-575. [DOI: 10.1002/bit.26184] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2016] [Revised: 09/08/2016] [Accepted: 09/16/2016] [Indexed: 11/10/2022]
Affiliation(s)
- Michael H. Limberg
- Forschungszentrum Jülich GmbH, Institute of Bio- and Geosciences; IBG-1: Biotechnology; Wilhelm-Johnen-Straße 52425 Jülich Germany
| | - Julia Schulte
- Forschungszentrum Jülich GmbH, Institute of Bio- and Geosciences; IBG-1: Biotechnology; Wilhelm-Johnen-Straße 52425 Jülich Germany
| | - Tita Aryani
- Forschungszentrum Jülich GmbH, Institute of Bio- and Geosciences; IBG-1: Biotechnology; Wilhelm-Johnen-Straße 52425 Jülich Germany
| | - Regina Mahr
- Forschungszentrum Jülich GmbH, Institute of Bio- and Geosciences; IBG-1: Biotechnology; Wilhelm-Johnen-Straße 52425 Jülich Germany
| | - Meike Baumgart
- Forschungszentrum Jülich GmbH, Institute of Bio- and Geosciences; IBG-1: Biotechnology; Wilhelm-Johnen-Straße 52425 Jülich Germany
| | - Michael Bott
- Forschungszentrum Jülich GmbH, Institute of Bio- and Geosciences; IBG-1: Biotechnology; Wilhelm-Johnen-Straße 52425 Jülich Germany
| | - Wolfgang Wiechert
- Forschungszentrum Jülich GmbH, Institute of Bio- and Geosciences; IBG-1: Biotechnology; Wilhelm-Johnen-Straße 52425 Jülich Germany
| | - Marco Oldiges
- Forschungszentrum Jülich GmbH, Institute of Bio- and Geosciences; IBG-1: Biotechnology; Wilhelm-Johnen-Straße 52425 Jülich Germany
- Institute of Biotechnology; RWTH Aachen University; Aachen Germany
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34
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Limberg MH, Pooth V, Wiechert W, Oldiges M. Plug flow versus stirred tank reactor flow characteristics in two-compartment scale-down bioreactor: Setup-specific influence on the metabolic phenotype and bioprocess performance ofCorynebacterium glutamicum. Eng Life Sci 2016. [DOI: 10.1002/elsc.201500142] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022] Open
Affiliation(s)
- Michael H. Limberg
- Forschungszentrum Jülich GmbH; Institute of Bio- and Geosciences; IBG-1: Biotechnology Jülich Germany
| | - Viola Pooth
- Forschungszentrum Jülich GmbH; Institute of Bio- and Geosciences; IBG-1: Biotechnology Jülich Germany
| | - Wolfgang Wiechert
- Forschungszentrum Jülich GmbH; Institute of Bio- and Geosciences; IBG-1: Biotechnology Jülich Germany
| | - Marco Oldiges
- Forschungszentrum Jülich GmbH; Institute of Bio- and Geosciences; IBG-1: Biotechnology Jülich Germany
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35
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Bai Y, Zhou PP, Fan P, Zhu YM, Tong Y, Wang HB, Yu LJ. Four-stage dissolved oxygen strategy based on multi-scale analysis for improving spinosad yield by Saccharopolyspora spinosa ATCC49460. Microb Biotechnol 2015; 8:561-8. [PMID: 25808914 PMCID: PMC4408188 DOI: 10.1111/1751-7915.12264] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2014] [Revised: 11/24/2014] [Accepted: 12/26/2014] [Indexed: 11/29/2022] Open
Abstract
Dissolved oxygen (DO) is an important influencing factor in the process of aerobic microbial fermentation. Spinosad is an aerobic microbial-derived secondary metabolite. In our study, spinosad was used as an example to establish a DO strategy by multi-scale analysis, which included a reactor, cell and gene scales. We changed DO conditions that are related to the characteristics of cell metabolism (glucose consumption rate, biomass accumulation and spinosad production). Consequently, cell growth was promoted by maintaining DO at 40% in the first 24 h and subsequently increasing DO to 50% in 24 h to 96 h. In an in-depth analysis of the key enzyme genes (gtt, spn A, spn K and spn O), expression of spinosad and specific Adenosine Triphosphate (ATP), the spinosad yield was increased by regulating DO to 30% within 96 h to 192 h and then changing it to 25% in 192 h to 240 h. Under the four-phase DO strategy, spinosad yield increased by 652.1%, 326.1%, 546.8%, and 781.4% compared with the yield obtained under constant DO control at 50%, 40%, 30%, and 20% respectively. The proposed method provides a novel way to develop a precise DO strategy for fermentation.
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Affiliation(s)
- Yun Bai
- Institute of Resource Biology and Biotechnology, Department of Biotechnology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, 430074, China; Key Laboratory of Molecular Biophysics Ministry of Education, Huazhong University of Science and Technology, Wuhan, 430074, China
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36
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Eggeling L, Bott M. A giant market and a powerful metabolism: L-lysine provided by Corynebacterium glutamicum. Appl Microbiol Biotechnol 2015; 99:3387-94. [PMID: 25761623 DOI: 10.1007/s00253-015-6508-2] [Citation(s) in RCA: 150] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2015] [Revised: 02/23/2015] [Accepted: 02/23/2015] [Indexed: 11/30/2022]
Abstract
L-lysine is made in an exceptional large quantity of currently 2,200,000 tons/year and belongs therefore to one of the leading biotechnological products. Production is done almost exclusively with mutants of Corynebacterium glutamicum. The increasing L-lysine market forces companies to improve the production process fostering also a deeper understanding of the microbial physiology of C. glutamicum. Current major challenges are the identification of ancillary mutations not intuitively related with product increase. This review gives insights on how cellular characteristics enable to push the carbon flux in metabolism towards its theoretical maximum, and this example may also serve as a guide to achieve and increase the formation of other products of interest in microbial biotechnology.
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Affiliation(s)
- Lothar Eggeling
- IBG-1: Biotechnology, Institute of Bio- and Geosciences, Forschungszentrum Jülich, 52458, Jülich, Germany,
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37
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CO2/HCO3 − perturbations of simulated large scale gradients in a scale-down device cause fast transcriptional responses in Corynebacterium glutamicum. Appl Microbiol Biotechnol 2014; 98:8563-72. [DOI: 10.1007/s00253-014-6014-y] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2014] [Revised: 08/03/2014] [Accepted: 08/05/2014] [Indexed: 10/24/2022]
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