1
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Rong Y, Jensen SI, Woodley JM, Nielsen AT. Modulating metabolism through synthetic biology: Opportunities for two-stage fermentation. Biotechnol Bioeng 2024; 121:3001-3008. [PMID: 38970785 DOI: 10.1002/bit.28791] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2022] [Revised: 04/23/2024] [Accepted: 06/19/2024] [Indexed: 07/08/2024]
Abstract
Bio-based production of fuels, chemicals and materials is needed to replace current fossil fuel based production. However, bio-based production processes are very costly, so the process needs to be as efficient as possible. Developments in synthetic biology tools has made it possible to dynamically modulate cellular metabolism during a fermentation. This can be used towards two-stage fermentations, where the process is separated into a growth and a production phase, leading to more efficient feedstock utilization and thus potentially lower costs. This article reviews the current status and some recent results in application of synthetic biology tools towards two-stage fermentations, and compares this approach to pre-existing ones, such as nutrient limitation and addition of toxins/inhibitors.
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Affiliation(s)
- Yixin Rong
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Sheila Ingemann Jensen
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kongens Lyngby, Denmark
| | - John M Woodley
- Department of Chemical and Biochemical Engineering, Technical University of Denmark (DTU), Kongens Lyngby, Denmark
| | - Alex Toftgaard Nielsen
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kongens Lyngby, Denmark
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2
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Duport C, Armengaud J, Schmitt C, Morin D, Lacapère JJ. Elucidating the pivotal role of TSPO in porphyrin-related cellular processes, in Bacillus cereus. Biochimie 2024; 224:51-61. [PMID: 38423451 DOI: 10.1016/j.biochi.2024.02.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2024] [Revised: 02/19/2024] [Accepted: 02/21/2024] [Indexed: 03/02/2024]
Abstract
A structural homolog of the mammalian TSPO has been identified in the human pathogen Bacillus cereus. BcTSPO, in its recombinant form, has previously been shown to bind and degrade porphyrins. In this study, we generated a ΔtspO mutant strain in B. cereus ATCC 14579 and assessed the impact of the absence of BcTSPO on cellular proteomics and physiological characteristics. The proteomic analysis revealed correlations between the lack of BcTSPO and the observed growth defects, increased oxygen consumption, ATP deficiency, heightened tryptophan catabolism, reduced motility, and impaired biofilm formation in the ΔtspO mutant strain. Our results also suggested that BcTSPO plays a crucial role in regulating intracellular levels of metabolites from the coproporphyrin-dependent branch of the heme biosynthetic pathway. This regulation potentially underlies alterations in the metabolic landscape, emphasizing the pivotal role of BcTSPO in B. cereus aerobic metabolism. Notably, our study unveils, for the first time, the involvement of TSPO in tryptophan metabolism. These findings underscore the multifaceted role of TSPO, not only in metabolic pathways but also potentially in the microorganism's virulence mechanisms.
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Affiliation(s)
| | - Jean Armengaud
- Université Paris Saclay, CEA, INRAE, Département Médicaments et Technologies pour la Santé (DMTS), SPI, 30200, Bagnols-sur-Cèze, France
| | - Caroline Schmitt
- Assistance Publique Hôpitaux de Paris (AP-HP), Centre Français des Porphyries, Hôpital Louis Mourier, 92700, Colombes, France; INSERM U1149, Center for Research on Inflammation (CRI), Université de Paris, 75018, Paris, France
| | - Didier Morin
- INSERM, U955, équipe 3, Faculté de Médecine, Université Paris Est, 94010, Creteil, France
| | - Jean-Jacques Lacapère
- Sorbonne Université, Ecole Normale Supérieure, PSL University, CNRS UMR 7203, Laboratoire des BioMolécules (LBM), 4 place Jussieu, F-75005, Paris, France
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3
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Yang W, Feng Y, Yan J, Kang C, Yao T, Sun H, Cheng Z. Phosphate (Pi) Transporter PIT1 Induces Pi Starvation in Salmonella-Containing Vacuole in HeLa Cells. Int J Mol Sci 2023; 24:17216. [PMID: 38139044 PMCID: PMC10743064 DOI: 10.3390/ijms242417216] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2023] [Revised: 12/04/2023] [Accepted: 12/05/2023] [Indexed: 12/24/2023] Open
Abstract
Salmonella enterica serovar Typhimurium (S. Typhimurium), an important foodborne pathogen, causes diarrheal illness and gastrointestinal diseases. S. Typhimurium survives and replicates in phagocytic and non-phagocytic cells for acute or chronic infections. In these cells, S. Typhimurium resides within Salmonella-containing vacuoles (SCVs), in which the phosphate (Pi) concentration is low. S. Typhimurium senses low Pi and expresses virulence factors to modify host cells. However, the mechanism by which host cells reduce the Pi concentration in SCVs is not clear. In this study, we show that through the TLR4-MyD88-NF-κB signaling pathway, S. Typhimurium upregulates PIT1, which in turn transports Pi from SCVs into the cytosol and results in Pi starvation in SCVs. Immunofluorescence and western blotting analysis reveal that after the internalization of S. Typhimurium, PIT1 is located on SCV membranes. Silencing or overexpressing PIT1 inhibits or promotes Pi starvation, Salmonella pathogenicity island-2 (SPI-2) gene expression, and replication in SCVs. The S. Typhimurium ΔmsbB mutant or silenced TLR4-MyD88-NF-κB pathway suppresses the expression of the SPI-2 genes and promotes the fusion of SCVs with lysosomes. Our results illustrate that S. Typhimurium exploits the host innate immune responses as signals to promote intracellular replication, and they provide new insights for the development of broad-spectrum therapeutics to combat bacterial infections.
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Affiliation(s)
- Wen Yang
- The Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, Nankai University, Tianjin 300071, China; (W.Y.); (Y.F.); (J.Y.); (C.K.); (T.Y.); (H.S.)
- TEDA Institute of Biological Sciences and Biotechnology, Tianjin Key Laboratory of Microbial Functional Genomics, Nankai University, Tianjin 300457, China
| | - Yingxing Feng
- The Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, Nankai University, Tianjin 300071, China; (W.Y.); (Y.F.); (J.Y.); (C.K.); (T.Y.); (H.S.)
- Department of Microbiology, College of Life Sciences, Nankai University, Tianjin 300071, China
| | - Jun Yan
- The Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, Nankai University, Tianjin 300071, China; (W.Y.); (Y.F.); (J.Y.); (C.K.); (T.Y.); (H.S.)
- TEDA Institute of Biological Sciences and Biotechnology, Tianjin Key Laboratory of Microbial Functional Genomics, Nankai University, Tianjin 300457, China
| | - Chenbo Kang
- The Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, Nankai University, Tianjin 300071, China; (W.Y.); (Y.F.); (J.Y.); (C.K.); (T.Y.); (H.S.)
- TEDA Institute of Biological Sciences and Biotechnology, Tianjin Key Laboratory of Microbial Functional Genomics, Nankai University, Tianjin 300457, China
| | - Ting Yao
- The Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, Nankai University, Tianjin 300071, China; (W.Y.); (Y.F.); (J.Y.); (C.K.); (T.Y.); (H.S.)
- TEDA Institute of Biological Sciences and Biotechnology, Tianjin Key Laboratory of Microbial Functional Genomics, Nankai University, Tianjin 300457, China
| | - Hongmin Sun
- The Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, Nankai University, Tianjin 300071, China; (W.Y.); (Y.F.); (J.Y.); (C.K.); (T.Y.); (H.S.)
- TEDA Institute of Biological Sciences and Biotechnology, Tianjin Key Laboratory of Microbial Functional Genomics, Nankai University, Tianjin 300457, China
| | - Zhihui Cheng
- The Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, Nankai University, Tianjin 300071, China; (W.Y.); (Y.F.); (J.Y.); (C.K.); (T.Y.); (H.S.)
- Department of Microbiology, College of Life Sciences, Nankai University, Tianjin 300071, China
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4
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Yu Z, Li W, Ge C, Sun X, Wang J, Shen X, Yuan Q. Functional expansion of the natural inorganic phosphorus starvation response system in Escherichia coli. Biotechnol Adv 2023; 66:108154. [PMID: 37062526 DOI: 10.1016/j.biotechadv.2023.108154] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2022] [Revised: 04/08/2023] [Accepted: 04/09/2023] [Indexed: 04/18/2023]
Abstract
Phosphorus, an indispensable nutrient, plays an essential role in cell composition, metabolism, and signal transduction. When inorganic phosphorus (Pi) is scarce, the Pi starvation response in E. coli is activated to increase phosphorus acquisition and drive the cells into a non-growing state to reduce phosphorus consumption. In the six decades of research history, the initiation, output, and shutdown processes of the Pi starvation response have been extensively studied. Simultaneously, Pi starvation has been used in biosensor development, recombinant protein production, and natural product biosynthesis. In this review, we focus on the output process and the applications of the Pi starvation response that have not been summarized before. Meanwhile, based on the current status of mechanistic studies and applications, we propose practical strategies to develop the natural Pi starvation response into a multifunctional and standardized regulatory system in four aspects, including response threshold, temporal expression, intensity range, and bifunctional regulation, which will contribute to its broader application in more fields such as industrial production, medical analysis, and environmental protection.
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Affiliation(s)
- Zheng Yu
- State Key Laboratory of Chemical Resource Engineering, Beijing University of Chemical Technology, Beijing 100029, China
| | - Wenna Li
- State Key Laboratory of Chemical Resource Engineering, Beijing University of Chemical Technology, Beijing 100029, China
| | - Chang Ge
- State Key Laboratory of Chemical Resource Engineering, Beijing University of Chemical Technology, Beijing 100029, China
| | - Xinxiao Sun
- State Key Laboratory of Chemical Resource Engineering, Beijing University of Chemical Technology, Beijing 100029, China
| | - Jia Wang
- State Key Laboratory of Chemical Resource Engineering, Beijing University of Chemical Technology, Beijing 100029, China
| | - Xiaolin Shen
- State Key Laboratory of Chemical Resource Engineering, Beijing University of Chemical Technology, Beijing 100029, China.
| | - Qipeng Yuan
- State Key Laboratory of Chemical Resource Engineering, Beijing University of Chemical Technology, Beijing 100029, China.
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5
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Müller T, Schick S, Beck J, Sprenger G, Takors R. Synthetic mutualism in engineered E. coli mutant strains as functional basis for microbial production consortia. Eng Life Sci 2023; 23:e2100158. [PMID: 36619882 PMCID: PMC9815082 DOI: 10.1002/elsc.202100158] [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: 12/01/2021] [Revised: 03/02/2022] [Accepted: 04/25/2022] [Indexed: 01/11/2023] Open
Abstract
In nature, microorganisms often reside in symbiotic co-existence providing nutrition, stability, and protection for each partner by applying "division of labor." This principle may also be used for the overproduction of targeted compounds in bioprocesses. It requires the engineering of a synthetic co-culture with distributed tasks for each partner. Thereby, the competition on precursors, redox cofactors, and energy-which occurs in a single host-is prevented. Current applications often focus on unidirectional interactions, that is, the product of partner A is used for the completion of biosynthesis by partner B. Here, we present a synthetically engineered Escherichia coli co-culture of two engineered mutant strains marked by the essential interaction of the partners which is achieved by implemented auxotrophies. The tryptophan auxotrophic strain E. coli ANT-3, only requiring small amounts of the aromatic amino acid, provides the auxotrophic anthranilate for the tryptophan producer E. coli TRP-3. The latter produces a surplus of tryptophan which is used to showcase the suitability of the co-culture to access related products in future applications. Co-culture characterization revealed that the microbial consortium is remarkably functionally stable for a broad range of inoculation ratios. The range of robust and functional interaction may even be extended by proper glucose feeding which was shown in a two-compartment bioreactor setting with filtrate exchange. This system even enables the use of the co-culture in a parallel two-level temperature setting which opens the door to access temperature sensitive products via heterologous production in E. coli in a continuous manner.
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Affiliation(s)
- Tobias Müller
- Institute of Biochemical EngineeringUniversity of StuttgartStuttgartGermany
| | - Simon Schick
- Institute of MicrobiologyUniversity of StuttgartStuttgartGermany
| | - Jonathan Beck
- Institute of Biochemical EngineeringUniversity of StuttgartStuttgartGermany
| | - Georg Sprenger
- Institute of MicrobiologyUniversity of StuttgartStuttgartGermany
| | - Ralf Takors
- Institute of Biochemical EngineeringUniversity of StuttgartStuttgartGermany
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6
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Rajpurohit H, Eiteman MA. Nutrient-Limited Operational Strategies for the Microbial Production of Biochemicals. Microorganisms 2022; 10:2226. [PMID: 36363817 PMCID: PMC9695796 DOI: 10.3390/microorganisms10112226] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Revised: 10/31/2022] [Accepted: 11/07/2022] [Indexed: 08/24/2023] Open
Abstract
Limiting an essential nutrient has a profound impact on microbial growth. The notion of growth under limited conditions was first described using simple Monod kinetics proposed in the 1940s. Different operational modes (chemostat, fed-batch processes) were soon developed to address questions related to microbial physiology and cell maintenance and to enhance product formation. With more recent developments of metabolic engineering and systems biology, as well as high-throughput approaches, the focus of current engineers and applied microbiologists has shifted from these fundamental biochemical processes. This review draws attention again to nutrient-limited processes. Indeed, the sophisticated gene editing tools not available to pioneers offer the prospect of metabolic engineering strategies which leverage nutrient limited processes. Thus, nutrient- limited processes continue to be very relevant to generate microbially derived biochemicals.
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Affiliation(s)
| | - Mark A. Eiteman
- School of Chemical, Materials and Biomedical Engineering, University of Georgia, Athens, GA 30602, USA
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7
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Saez-Jimenez V, Scrima S, Lambrughi M, Papaleo E, Mapelli V, Engqvist MKM, Olsson L. Directed Evolution of ( R)-2-Hydroxyglutarate Dehydrogenase Improves 2-Oxoadipate Reduction by 2 Orders of Magnitude. ACS Synth Biol 2022; 11:2779-2790. [PMID: 35939387 PMCID: PMC9396657 DOI: 10.1021/acssynbio.2c00162] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
![]()
Pathway engineering is commonly employed to improve the
production
of various metabolites but may incur in bottlenecks due to the low
catalytic activity of a particular reaction step. The reduction of
2-oxoadipate to (R)-2-hydroxyadipate is a key reaction
in metabolic pathways that exploit 2-oxoadipate conversion via α-reduction
to produce adipic acid, an industrially important platform chemical.
Here, we engineered (R)-2-hydroxyglutarate dehydrogenase
from Acidaminococcus fermentans (Hgdh)
with the aim of improving 2-oxoadipate reduction. Using a combination
of computational analysis, saturation mutagenesis, and random mutagenesis,
three mutant variants with a 100-fold higher catalytic efficiency
were obtained. As revealed by rational analysis of the mutations found
in the variants, this improvement could be ascribed to a general synergistic
effect where mutation A206V played a key role since it boosted the
enzyme’s activity by 4.8-fold. The Hgdh variants with increased
activity toward 2-oxoadipate generated within this study pave the
way for the bio-based production of adipic acid.
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Affiliation(s)
- Veronica Saez-Jimenez
- Division of Industrial Biotechnology, Department of Biology and Biological Engineering, Chalmers University of Technology, 412 96 Gothenburg, Sweden
| | - Simone Scrima
- Cancer Structural Biology, Danish Cancer Society Research Center, 2100 Copenhagen, Denmark.,Cancer Systems Biology, Section for Bioinformatics, Department of Health and Technology, Technical University of Denmark, 2800 Lyngby, Denmark
| | - Matteo Lambrughi
- Cancer Structural Biology, Danish Cancer Society Research Center, 2100 Copenhagen, Denmark
| | - Elena Papaleo
- Cancer Structural Biology, Danish Cancer Society Research Center, 2100 Copenhagen, Denmark.,Cancer Systems Biology, Section for Bioinformatics, Department of Health and Technology, Technical University of Denmark, 2800 Lyngby, Denmark
| | - Valeria Mapelli
- Division of Industrial Biotechnology, Department of Biology and Biological Engineering, Chalmers University of Technology, 412 96 Gothenburg, Sweden
| | - Martin K M Engqvist
- Division of Systems and Synthetic Biology, Department of Biology and Biological Engineering, Chalmers University of Technology, 412 96 Gothenburg, Sweden
| | - Lisbeth Olsson
- Division of Industrial Biotechnology, Department of Biology and Biological Engineering, Chalmers University of Technology, 412 96 Gothenburg, Sweden
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8
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Abstract
Auto-inducible promoter systems have been reported to increase soluble product formation in the periplasm of E. coli compared to inducer-dependent systems. In this study, we investigated the phosphate (PO4)-sensitive phoA expression system (pAT) for the production of a recombinant model antigen-binding fragment (Fab) in the periplasm of E. coli in detail. We explored the impact of non-limiting and limiting PO4 conditions on strain physiology as well as Fab productivity. We compared different methods for extracellular PO4 detection, identifying automated colorimetric measurement to be most suitable for at-line PO4 monitoring. We showed that PO4 limitation boosts phoA-based gene expression, however, the product was already formed at non-limiting PO4 conditions, indicating leaky expression. Furthermore, cultivation under PO4 limitation caused physiological changes ultimately resulting in a metabolic breakdown at PO4 starvation. Finally, we give recommendations for process optimization with the phoA expression system. In summary, our study provides very detailed information on the E. coli phoA expression system, thus extending the existing knowledge of this system, and underlines its high potential for the successful production of periplasmic products in E. coli.
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9
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Phosphate starvation controls lactose metabolism to produce recombinant protein in Escherichia coli. Appl Microbiol Biotechnol 2020; 104:9707-9718. [PMID: 33001250 DOI: 10.1007/s00253-020-10935-y] [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: 05/06/2020] [Revised: 09/14/2020] [Accepted: 09/27/2020] [Indexed: 10/23/2022]
Abstract
Phosphate is one of the major constituents in growth media. It closely regulates central carbon and energy metabolism. Biochemical reactions in central carbon metabolism are known to be regulated by phosphorylation and dephosphorylation of enzymes. Phosphate scarcity can limit microbial productivity. However, microorganisms are evolved to grow in phosphate starvation environments. This study investigates the effect of phosphate-starved response (PSR) stimuli in wild-type and recombinant Escherichia coli cells cultivated in two different substrates, lactose, and glycerol. Phosphate-starved E. coli culture sustained bacterial growth despite the metabolic burden that emanated from recombinant protein expression albeit with altered dynamics of substrate utilisation. Induction of lactose in phosphate-starved culture led to a 2-fold improvement in product titre of rSymlin and a 2.3-fold improvement in product titre of rLTNF as compared with phosphate-unlimited culture. The results obtained in the study are in agreement with the literature to infer that phosphate starvation or limitation can slow down the microbial growth rate in order to produce recombinant proteins. Further, under PSR conditions, gene expression analysis demonstrated that while selected genes (gapdh, pykF, ppsA, icdA) in glycolysis and pentose phosphate pathway (zwf, gnd, talB, tktA) were up-regulated, other genes in lactose (lacY, lacA) and acetate (ackA, pta) pathway were down-regulated. We have demonstrated that cra, crp, phoB, and phoR are involved in the regulation of central carbon metabolism. We propose a novel cross-regulation between lactose metabolism and phosphate starvation. UDP-galactose, a toxic metabolite that is known to cause cell lysis, has been shown to be significantly reduced due to slow uptake of lactose under PSR conditions. Therefore, E. coli employs a decoupling strategy by limiting growth and redirecting metabolic resources to survive and produce recombinant protein under phosphate starvation conditions. KEY POINTS: • Phosphate starvation controls lactose metabolism, which results in less galactose accumulation. • Phosphate starvation modulates metabolic flow of central carbon metabolism. • Product titre improves by 2-fold due to phosphate starvation. • The approach has been successfully applied to production of two different proteins.
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10
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Agbogbo FK, Ramsey P, George R, Joy J, Srivastava S, Huang M, McCool J. Upstream development of Escherichia coli fermentation process with PhoA promoter using design of experiments (DoE). J Ind Microbiol Biotechnol 2020; 47:789-799. [PMID: 32844325 PMCID: PMC7658055 DOI: 10.1007/s10295-020-02302-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2020] [Accepted: 08/14/2020] [Indexed: 02/08/2023]
Abstract
In this work, a fed-batch fermentation development was performed with recombinant E. coli carrying the PhoA promoter system. The phosphate concentrations tested for this PhoA strain, 2.79 mM to 86.4 mM, were beyond the concentrations previously evaluated for cell growth and product titer. The results from the scouting work was used for design of experiments (DoE) where a range of phosphate levels from 27.1 mM to 86.4 mM was simultaneously evaluated with temperature, pH and DO set points. Definitive screening was used to evaluate these parameters simultaneously and the results indicate that fermentation temperature and phosphate content are the major contributors of product titer. The other factors tested such as pH had a minimal effect and DO had no impact on product titer.
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Affiliation(s)
- Frank K Agbogbo
- Cytovance Biologics, 800 Research Parkway, Suite 200, Oklahoma City, OK, 73104, USA.
| | - Phil Ramsey
- Predictum Inc., Austin, TX, USA
- University of New Hampshire, Durham, NH, USA
| | - Renija George
- Cytovance Biologics, 800 Research Parkway, Suite 200, Oklahoma City, OK, 73104, USA
| | - Jobin Joy
- Cytovance Biologics, 800 Research Parkway, Suite 200, Oklahoma City, OK, 73104, USA
| | - Shikha Srivastava
- Cytovance Biologics, 800 Research Parkway, Suite 200, Oklahoma City, OK, 73104, USA
| | - Mian Huang
- BioMarin Pharmaceutical Inc., 770 Lindaro Street, San Rafael, CA, 94901, USA
| | - Jesse McCool
- Cytovance Biologics, 800 Research Parkway, Suite 200, Oklahoma City, OK, 73104, USA
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11
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Man Z, Guo J, Zhang Y, Cai Z. Regulation of intracellular ATP supply and its application in industrial biotechnology. Crit Rev Biotechnol 2020; 40:1151-1162. [PMID: 32862717 DOI: 10.1080/07388551.2020.1813071] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Efficient cell factories are the core of industrial biotechnology. In recent years, synthetic biology develops rapidly, and more and more modified microbial cell factories are employed in industrial biotechnology. ATP plays vital roles in biosynthesis, metabolism regulation, and cellular maintenance. Regulating cellular ATP supply can effectively modify cellular metabolism. This paper presents a review of recent studies on the regulation of the intracellular ATP supply and its application in industrial biotechnology. Detailed strategies for regulating the ATP supply and the resulting impact on bioproduction are introduced. It is observed that regulating the cellular ATP supply can provide great possibilities for making microbial cells into efficient factories. Future perspectives for further understanding the function of ATP are also discussed.
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Affiliation(s)
- Zaiwei Man
- Advanced Catalysis and Green Manufacturing Collaborative Innovation Center, School of Petrochemical Engineering, Changzhou University, Changzhou, China.,Zaozhuang Key Laboratory of Corn Bioengineering, Zaozhuang Science and Technology Collaborative Innovation Center of Enzyme, Shandong Hengren Gongmao Co. Ltd, Zaozhuang, China
| | - Jing Guo
- Advanced Catalysis and Green Manufacturing Collaborative Innovation Center, School of Petrochemical Engineering, Changzhou University, Changzhou, China.,School of Pharmaceutical Engineering and Life Science, Changzhou University, Changzhou, China
| | - Yingyang Zhang
- Advanced Catalysis and Green Manufacturing Collaborative Innovation Center, School of Petrochemical Engineering, Changzhou University, Changzhou, China
| | - Zhiqiang Cai
- Advanced Catalysis and Green Manufacturing Collaborative Innovation Center, School of Petrochemical Engineering, Changzhou University, Changzhou, China.,School of Pharmaceutical Engineering and Life Science, Changzhou University, Changzhou, China
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12
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Nitta N, Tajima Y, Katashkina J, Yamamoto Y, Onuki A, Rachi H, Kazieva E, Nishio Y. Application of inorganic phosphate limitation to efficient isoprene production in
Pantoea ananatis. J Appl Microbiol 2019; 128:763-774. [DOI: 10.1111/jam.14521] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2019] [Revised: 11/08/2019] [Accepted: 11/15/2019] [Indexed: 01/11/2023]
Affiliation(s)
- N. Nitta
- Institute for Innovation Ajinomoto Co., Inc. Kawasaki Japan
| | - Y. Tajima
- Institute for Innovation Ajinomoto Co., Inc. Kawasaki Japan
| | | | - Y. Yamamoto
- Institute for Innovation Ajinomoto Co., Inc. Kawasaki Japan
| | - A. Onuki
- Institute for Innovation Ajinomoto Co., Inc. Kawasaki Japan
| | - H. Rachi
- Institute for Innovation Ajinomoto Co., Inc. Kawasaki Japan
| | - E. Kazieva
- Ajinomoto‐Genetika Research Institute Moscow Russia
| | - Y. Nishio
- Institute for Innovation Ajinomoto Co., Inc. Kawasaki Japan
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13
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Kalnenieks U, Balodite E, Rutkis R. Metabolic Engineering of Bacterial Respiration: High vs. Low P/O and the Case of Zymomonas mobilis. Front Bioeng Biotechnol 2019; 7:327. [PMID: 31781557 PMCID: PMC6861446 DOI: 10.3389/fbioe.2019.00327] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2019] [Accepted: 10/28/2019] [Indexed: 11/13/2022] Open
Abstract
Respiratory chain plays a pivotal role in the energy and redox balance of aerobic bacteria. By engineering respiration, it is possible to alter the efficiency of energy generation and intracellular redox state, and thus affect the key bioprocess parameters: cell yield, productivity and stress resistance. Here we summarize the current metabolic engineering and synthetic biology approaches to bacterial respiratory metabolism, with a special focus on the respiratory chain of the ethanologenic bacterium Zymomonas mobilis. Electron transport in Z. mobilis can serve as a model system of bacterial respiration with low oxidative phosphorylation efficiency. Its application for redox balancing and relevance for improvement of stress tolerance are analyzed.
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Affiliation(s)
- Uldis Kalnenieks
- Institute of Microbiology and Biotechnology, University of Latvia, Riga, Latvia
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14
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15
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Xu Y, Yang L, Zhao S, Wang Z. Large-scale production of tauroursodeoxycholic acid products through fermentation optimization of engineered Escherichia coli cell factory. Microb Cell Fact 2019; 18:34. [PMID: 30736766 PMCID: PMC6368744 DOI: 10.1186/s12934-019-1076-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2018] [Accepted: 01/29/2019] [Indexed: 12/25/2022] Open
Abstract
Background Bear bile powder is a valuable medicinal material characterized by high content of tauroursodeoxycholic acid (TUDCA) at a certain ratio to taurochenodeoxycholic acid (TCDCA). We had created an engineered E. coli harboring two-step bidirectional oxidative and reductive enzyme-catalyzing pathway that could rapidly convert TCDCA to TUDCA at a specific percentage in shake flasks. Results We reported here the large-scale production of TUDCA containing products by balancing the bidirectional reactions through optimizing fermentation process of the engineered E. coli in fermenters. The fermentation medium was firstly optimized based on M9 medium using response surface methodology, leading to a glycerol and yeast extract modified M9-GY medium benefits for both cell growth and product conversion efficiency. Then isopropylthio-β-galactoside induction and fed-stock stage was successively optimized. Finally, a special deep-tank static process was developed to promote the conversion from TCDCA to TUDCA. Applying the optimal condition, fermentation was performed by separately supplementing 30 g refined chicken bile powder and 35 g crude chicken bile powder as substrates, resulting in 29.35 ± 2.83 g and 30.78 ± 3.04 g powder products containing 35.85 ± 3.85% and 27.14 ± 4.23% of TUDCA at a ratio of 1.49 ± 0.14 and 1.55 ± 0.19 to TCDCA, respectively, after purification and evaporation of the fermentation broth. The recovery yield was 92.84 ± 4.21% and 91.83 ± 2.56%, respectively. Conclusion This study provided a practical and environment friendly industrialized process for producing artificial substitute of bear bile powder from cheap and readily available chicken bile powder using engineered E. coli microbial cell factory. It also put forward an interesting deep-tank static process to promote the enzyme-catalyzing reactions toward target compounds in synthetic biology-based fermentation. Electronic supplementary material The online version of this article (10.1186/s12934-019-1076-2) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Yingpeng Xu
- The SATCM Key Laboratory for New Resources & Quality Evaluation of Chinese Medicine, The MOE Key Laboratory for Standardization of Chinese Medicines and Shanghai Key Laboratory of Compound Chinese Medicines, Institute of Chinese Materia Medica, Shanghai University of Traditional Chinese Medicine, Shanghai, 201203, People's Republic of China
| | - Li Yang
- The SATCM Key Laboratory for New Resources & Quality Evaluation of Chinese Medicine, The MOE Key Laboratory for Standardization of Chinese Medicines and Shanghai Key Laboratory of Compound Chinese Medicines, Institute of Chinese Materia Medica, Shanghai University of Traditional Chinese Medicine, Shanghai, 201203, People's Republic of China
| | - Shujuan Zhao
- The SATCM Key Laboratory for New Resources & Quality Evaluation of Chinese Medicine, The MOE Key Laboratory for Standardization of Chinese Medicines and Shanghai Key Laboratory of Compound Chinese Medicines, Institute of Chinese Materia Medica, Shanghai University of Traditional Chinese Medicine, Shanghai, 201203, People's Republic of China.
| | - Zhengtao Wang
- The SATCM Key Laboratory for New Resources & Quality Evaluation of Chinese Medicine, The MOE Key Laboratory for Standardization of Chinese Medicines and Shanghai Key Laboratory of Compound Chinese Medicines, Institute of Chinese Materia Medica, Shanghai University of Traditional Chinese Medicine, Shanghai, 201203, People's Republic of China
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16
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Mohammadi Nargesi B, Trachtmann N, Sprenger GA, Youn JW. Production of p-amino-L-phenylalanine (L-PAPA) from glycerol by metabolic grafting of Escherichia coli. Microb Cell Fact 2018; 17:149. [PMID: 30241531 PMCID: PMC6148955 DOI: 10.1186/s12934-018-0996-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2018] [Accepted: 09/12/2018] [Indexed: 11/17/2022] Open
Abstract
BACKGROUND The non-proteinogenic aromatic amino acid, p-amino-L-phenylalanine (L-PAPA) is a high-value product with a broad field of applications. In nature, L-PAPA occurs as an intermediate of the chloramphenicol biosynthesis pathway in Streptomyces venezuelae. Here we demonstrate that the model organism Escherichia coli can be transformed with metabolic grafting approaches to result in an improved L-PAPA producing strain. RESULTS Escherichia coli K-12 cells were genetically engineered for the production of L-PAPA from glycerol as main carbon source. To do so, genes for a 4-amino-4-deoxychorismate synthase (pabAB from Corynebacterium glutamicum), and genes encoding a 4-amino-4-deoxychorismate mutase and a 4-amino-4-deoxyprephenate dehydrogenase (papB and papC, both from Streptomyces venezuelae) were cloned and expressed in E. coli W3110 (lab strain LJ110). In shake flask cultures with minimal medium this led to the formation of ca. 43 ± 2 mg l-1 of L-PAPA from 5 g l-1 glycerol. By expression of additional chromosomal copies of the tktA and glpX genes, and of plasmid-borne aroFBL genes in a tyrR deletion strain, an improved L-PAPA producer was obtained which gave a titer of 5.47 ± 0.4 g l-1 L-PAPA from 33.3 g l-1 glycerol (0.16 g L-PAPA/g of glycerol) in fed-batch cultivation (shake flasks). Finally, in a fed-batch fermenter cultivation, a titer of 16.7 g l-1 L-PAPA was obtained which is the highest so far reported value for this non-proteinogenic amino acid. CONCLUSION Here we show that E. coli is a suitable chassis strain for L-PAPA production. Modifying the flux to the product and improved supply of precursor, by additional gene copies of glpX, tkt and aroFBL together with the deletion of the tyrR gene, increased the yield and titer.
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Affiliation(s)
| | - Natalie Trachtmann
- Institute of Microbiology, University of Stuttgart, Allmandring 31, 70569 Stuttgart, Germany
| | - Georg A. Sprenger
- Institute of Microbiology, University of Stuttgart, Allmandring 31, 70569 Stuttgart, Germany
| | - Jung-Won Youn
- Institute of Microbiology, University of Stuttgart, Allmandring 31, 70569 Stuttgart, Germany
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17
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A Proteomic View of Salmonella Typhimurium in Response to Phosphate Limitation. Proteomes 2018; 6:proteomes6020019. [PMID: 29693629 PMCID: PMC6027262 DOI: 10.3390/proteomes6020019] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2018] [Revised: 04/22/2018] [Accepted: 04/23/2018] [Indexed: 11/17/2022] Open
Abstract
Salmonella enterica serovar Typhimurium (S. Typhimurium), an important foodborne pathogen, often encounters phosphate (Pi) shortage both in the environment and inside host cells. To gain a global view on its physiological responses to Pi starvation, we performed proteomic profiling of S. Typhimurium upon the shift from Pi-rich to Pi-low conditions. In addition to the Pho regulon, many metabolic processes were up-regulated, such as glycolysis, pentose phosphate pathway, pyrimidine degradation, glycogen, and trehalose metabolism, allowing us to chart an overview of S. Typhimurium carbon metabolism under Pi starvation. Furthermore, proteomic analysis of a mutant lacking phoB (that encodes a key regulator of Pi shortage response) suggested that only a small subset of the altered proteins upon Pi limitation was PhoB-dependent. Importantly, we present evidence that S. Typhimurium N-acetylglucosamine catabolism was induced under Pi-limiting conditions in a PhoB-dependent manner. Immunoblotting and β-galactosidase assays demonstrated that PhoB was required for the full activation of NagB, a key enzyme of this pathway, in response to low Pi. Thus, our study reveals that N-acetylglucosamine catabolism may represent an additional PhoB-regulated pathway to tackle bacterial Pi shortage.
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18
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Vrabl P, Schinagl CW, Artmann DJ, Krüger A, Ganzera M, Pötsch A, Burgstaller W. The Dynamics of Plasma Membrane, Metabolism and Respiration (PM-M-R) in Penicillium ochrochloron CBS 123824 in Response to Different Nutrient Limitations-A Multi-level Approach to Study Organic Acid Excretion in Filamentous Fungi. Front Microbiol 2017; 8:2475. [PMID: 29312185 PMCID: PMC5732977 DOI: 10.3389/fmicb.2017.02475] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2017] [Accepted: 11/29/2017] [Indexed: 11/23/2022] Open
Abstract
Filamentous fungi are important cell factories. In contrast, we do not understand well even basic physiological behavior in these organisms. This includes the widespread phenomenon of organic acid excretion. One strong hurdle to fully exploit the metabolic capacity of these organisms is the enormous, highly environment sensitive phenotypic plasticity. In this work we explored organic acid excretion in Penicillium ochrochloron from a new point of view by simultaneously investigating three essential metabolic levels: the plasma membrane H+-ATPase (PM); energy metabolism, in particular adenine and pyridine nucleotides (M); and respiration, in particular the alternative oxidase (R). This was done in strictly standardized chemostat culture with different nutrient limitations (glucose, ammonium, nitrate, and phosphate). These different nutrient limitations led to various quantitative phenotypes (as represented by organic acid excretion, oxygen consumption, glucose consumption, and biomass formation). Glucose-limited grown mycelia were used as the reference point (very low organic acid excretion). Both ammonium and phosphate grown mycelia showed increased organic acid excretion, although the patterns of excreted acids were different. In ammonium-limited grown mycelia amount and activity of the plasma membrane H+-ATPase was increased, nucleotide concentrations were decreased, energy charge (EC) and catabolic reduction charge (CRC) were unchanged and alternative respiration was present but not quantifiable. In phosphate-limited grown mycelia (no data on the H+-ATPase) nucleotide concentrations were still lower, EC was slightly decreased, CRC was distinctly decreased and alternative respiration was present and quantifiable. Main conclusions are: (i) the phenotypic plasticity of filamentous fungi demands adaptation of sample preparation and analytical methods at the phenotype level; (ii) each nutrient condition is unique and its metabolic situation must be considered separately; (iii) organic acid excretion is inversely related to nucleotide concentration (but not EC); (iv) excretion of organic acids is the outcome of a simultaneous adjustment of several metabolic levels to nutrient conditions.
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Affiliation(s)
- Pamela Vrabl
- Institute of Microbiology, University of Innsbruck, Innsbruck, Austria
| | | | | | - Anja Krüger
- Institute of Pharmacy/Pharmacognosy, University of Innsbruck, Innsbruck, Austria
| | - Markus Ganzera
- Institute of Pharmacy/Pharmacognosy, University of Innsbruck, Innsbruck, Austria
| | - Ansgar Pötsch
- Plant Biochemistry, Ruhr University Bochum, Bochum, Germany
- School of Biomedical and Healthcare Sciences, Plymouth University, Plymouth, United Kingdom
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19
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Rodriguez A, Martínez JA, Millard P, Gosset G, Portais JC, Létisse F, Bolivar F. Plasmid-encoded biosynthetic genes alleviate metabolic disadvantages while increasing glucose conversion to shikimate in an engineeredEscherichia colistrain. Biotechnol Bioeng 2017; 114:1319-1330. [DOI: 10.1002/bit.26264] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2016] [Revised: 01/17/2017] [Accepted: 02/08/2017] [Indexed: 12/31/2022]
Affiliation(s)
- Alberto Rodriguez
- Instituto de Biotecnología; Universidad Nacional Autónoma de México (UNAM); Cuernavaca Morelos Mexico
| | - Juan A. Martínez
- Instituto de Biotecnología; Universidad Nacional Autónoma de México (UNAM); Cuernavaca Morelos Mexico
| | - Pierre Millard
- LISBP, Université de Toulouse, CNRS, INRA; INSA; Toulouse France
| | - Guillermo Gosset
- Instituto de Biotecnología; Universidad Nacional Autónoma de México (UNAM); Cuernavaca Morelos Mexico
| | | | - Fabien Létisse
- LISBP, Université de Toulouse, CNRS, INRA; INSA; Toulouse France
| | - Francisco Bolivar
- Instituto de Biotecnología; Universidad Nacional Autónoma de México (UNAM); Cuernavaca Morelos Mexico
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20
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Michalowski A, Siemann-Herzberg M, Takors R. Escherichia coli HGT: Engineered for high glucose throughput even under slowly growing or resting conditions. Metab Eng 2017; 40:93-103. [PMID: 28110078 DOI: 10.1016/j.ymben.2017.01.005] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2016] [Revised: 12/01/2016] [Accepted: 01/16/2017] [Indexed: 12/27/2022]
Abstract
Aerobic production-scale processes are constrained by the technical limitations of maximum oxygen transfer and heat removal. Consequently, microbial activity is often controlled via limited nutrient feeding to maintain it within technical operability. Here, we present an alternative approach based on a newly engineered Escherichia coli strain. This E. coli HGT (high glucose throughput) strain was engineered by modulating the stringent response regulation program and decreasing the activity of pyruvate dehydrogenase. The strain offers about three-fold higher rates of cell-specific glucose uptake under nitrogen-limitation (0.6gGlc gCDW-1h-1) compared to that of wild type, with a maximum glucose uptake rate of about 1.8gGlc gCDW-1h-1 already at a 0.3h-1 specific growth rate. The surplus of imported glucose is almost completely available via pyruvate and is used to fuel pyruvate and lactate formation. Thus, E. coli HGT represents a novel chassis as a host for pyruvate-derived products.
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Affiliation(s)
- Annette Michalowski
- University of Stuttgart, Institute of Biochemical Engineering, Allmandring 31, 70569, Stuttgart, Germany
| | - Martin Siemann-Herzberg
- 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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21
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D'Alessandro M, Turina P, Melandri BA, Dunn SD. Modulation of coupling in the Escherichia coli ATP synthase by ADP and P i: Role of the ε subunit C-terminal domain. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2016; 1858:34-44. [PMID: 27751906 DOI: 10.1016/j.bbabio.2016.10.004] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 12/31/2015] [Revised: 08/06/2016] [Accepted: 10/13/2016] [Indexed: 01/28/2023]
Abstract
The ε-subunit of ATP-synthase is an endogenous inhibitor of the hydrolysis activity of the complex and its α-helical C-terminal domain (εCTD) undergoes drastic changes among at least two different conformations. Even though this domain is not essential for ATP synthesis activity, there is evidence for its involvement in the coupling mechanism of the pump. Recently, it was proposed that coupling of the ATP synthase can vary as a function of ADP and Pi concentration. In the present work, we have explored the possible role of the εCTD in this ADP- and Pi-dependent coupling, by examining an εCTD-lacking mutant of Escherichia coli. We show that the loss of Pi-dependent coupling can be observed also in the εCTD-less mutant, but the effects of Pi on both proton pumping and ATP hydrolysis were much weaker in the mutant than in the wild-type. We also show that the εCTD strongly influences the binding of ADP to a very tight binding site (half-maximal effect≈1nM); binding at this site induces higher coupling in EFOF1 and increases responses to Pi. It is proposed that one physiological role of the εCTD is to regulate the kinetics and affinity of ADP/Pi binding, promoting ADP/Pi-dependent coupling.
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Affiliation(s)
- M D'Alessandro
- Department of Biology, Laboratory of Biochemistry and Biophysics, University of Bologna, Via Irnerio 42, 40126 Bologna, Italy
| | - P Turina
- Department of Biology, Laboratory of Biochemistry and Biophysics, University of Bologna, Via Irnerio 42, 40126 Bologna, Italy.
| | - B A Melandri
- Department of Biology, Laboratory of Biochemistry and Biophysics, University of Bologna, Via Irnerio 42, 40126 Bologna, Italy
| | - S D Dunn
- Department of Biochemistry, University of Western Ontario, London, Ontario N6A 5C1, Canada
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22
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Falke D, Fischer M, Sawers RG. Phosphate and oxygen limitation induce respiratory nitrate reductase 3 synthesis in stationary-phase mycelium of Streptomyces coelicolor A3(2). MICROBIOLOGY-SGM 2016; 162:1689-1697. [PMID: 27499000 DOI: 10.1099/mic.0.000349] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
The saprophytic actinobacterium Streptomyces coelicolor A3(2) requires oxygen for filamentous growth. Surprisingly, the bacterium also synthesizes three active respiratory nitrate reductases (Nar), which are believed to contribute to survival, or general fitness, of the bacterium in soil when oxygen becomes limiting. In this study, we analysed Nar3 and showed that activity of the enzyme is restricted to stationary-phase mycelium of S. coelicolor. Phosphate limitation was shown to be necessary for induction of enzyme synthesis. Nar3 synthesis was inhibited by inclusion of 20 mM phosphate in a defined 'switch assay' in which highly dispersed mycelium from exponentially growing cultures was shifted to neutral MOPS-glucose buffer to induce Nar3 synthesis and activity. Quantitative assessment of nar3 transcripts revealed a 30-fold induction of gene expression in stationary-phase mycelium. Transcript levels in stationary-phase mycelium incubated with phosphate were reduced by a little more than twofold, suggesting that the negative influence of phosphate on Nar3 synthesis was mainly at the post-transcriptional level. Furthermore, it was demonstrated that oxygen limitation was necessary to induce high levels of Nar3 activity. However, an abrupt shift from aerobic to anaerobic conditions prevented appearance of Nar3 activity. This suggests that the bacterium regulates Nar3 synthesis in response to the energy status of the mycelium. Nitrate had little impact on regulation of the Nar3 level. Together, these data identify Nar3 as a stationary-phase nitrate reductase in S. coelicolor and demonstrate that enzyme synthesis is induced in response to both phosphate limitation and hypoxia.
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Affiliation(s)
- Dörte Falke
- Institute of Biology/Microbiology, Martin-Luther University Halle-Wittenberg, Kurt-Mothes-Str. 3, 06120 Halle (Saale), Germany
| | - Marco Fischer
- Institute of Biology/Microbiology, Martin-Luther University Halle-Wittenberg, Kurt-Mothes-Str. 3, 06120 Halle (Saale), Germany
| | - R Gary Sawers
- Institute of Biology/Microbiology, Martin-Luther University Halle-Wittenberg, Kurt-Mothes-Str. 3, 06120 Halle (Saale), Germany
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23
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Löffler M, Simen JD, Jäger G, Schäferhoff K, Freund A, Takors R. Engineering E. coli for large-scale production - Strategies considering ATP expenses and transcriptional responses. Metab Eng 2016; 38:73-85. [PMID: 27378496 DOI: 10.1016/j.ymben.2016.06.008] [Citation(s) in RCA: 60] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2016] [Revised: 06/20/2016] [Accepted: 06/30/2016] [Indexed: 01/18/2023]
Abstract
Microbial producers such as Escherichia coli are evolutionarily trained to adapt to changing substrate availabilities. Being exposed to large-scale production conditions, their complex, multilayered regulatory programs are frequently activated because they face changing substrate supply due to limited mixing. Here, we show that E. coli can adopt both short- and long-term strategies to withstand these stress conditions. Experiments in which glucose availability was changed over a short time scale were performed in a two-compartment bioreactor system. Quick metabolic responses were observed during the first 30s of glucose shortage, and after 70s, fundamental transcriptional programs were initiated. Since cells are fluctuating under simulated large-scale conditions, this scenario represents a continuous on/off switching of about 600 genes. Furthermore, the resulting ATP maintenance demands were increased by about 40-50%, allowing us to conclude that hyper-producing strains could become ATP-limited under large-scale production conditions. Based on the observed transcriptional patterns, we identified a number of candidate gene deletions that may reduce unwanted ATP losses. In summary, we present a theoretical framework that provides biological targets that could be used to engineer novel E. coli strains such that large-scale performance equals laboratory-scale expectations.
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Affiliation(s)
- Michael Löffler
- University of Stuttgart, Institute of Biochemical Engineering, Allmandring 31, 70569 Stuttgart, Germany
| | - Joana Danica Simen
- University of Stuttgart, Institute of Biochemical Engineering, Allmandring 31, 70569 Stuttgart, Germany
| | - Günter Jäger
- University of Tübingen, Institute of Medical Genetics and Applied Genomics, Calwerstr. 7, 72076 Tübingen, Germany
| | - Karin Schäferhoff
- University of Tübingen, Institute of Medical Genetics and Applied Genomics, Calwerstr. 7, 72076 Tübingen, Germany
| | - Andreas Freund
- 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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