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Duran K, Kohlstedt M, van Erven G, Klostermann CE, America AHP, Bakx E, Baars JJP, Gorissen A, de Visser R, de Vries RP, Wittmann C, Comans RNJ, Kuyper TW, Kabel MA. From 13C-lignin to 13C-mycelium: Agaricus bisporus uses polymeric lignin as a carbon source. Sci Adv 2024; 10:eadl3419. [PMID: 38640242 PMCID: PMC11029805 DOI: 10.1126/sciadv.adl3419] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/13/2023] [Accepted: 03/19/2024] [Indexed: 04/21/2024]
Abstract
Plant biomass conversion by saprotrophic fungi plays a pivotal role in terrestrial carbon (C) cycling. The general consensus is that fungi metabolize carbohydrates, while lignin is only degraded and mineralized to CO2. Recent research, however, demonstrated fungal conversion of 13C-monoaromatic compounds into proteinogenic amino acids. To unambiguously prove that polymeric lignin is not merely degraded, but also metabolized, carefully isolated 13C-labeled lignin served as substrate for Agaricus bisporus, the world's most consumed mushroom. The fungus formed a dense mycelial network, secreted lignin-active enzymes, depolymerized, and removed lignin. With a lignin carbon use efficiency of 0.14 (g/g) and fungal biomass enrichment in 13C, we demonstrate that A. bisporus assimilated and further metabolized lignin when offered as C-source. Amino acids were high in 13C-enrichment, while fungal-derived carbohydrates, fatty acids, and ergosterol showed traces of 13C. These results hint at lignin conversion via aromatic ring-cleaved intermediates to central metabolites, underlining lignin's metabolic value for fungi.
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Affiliation(s)
- Katharina Duran
- Laboratory of Food Chemistry, Wageningen University & Research, Bornse Weilanden 9, 6708 WG Wageningen, Netherlands
| | - Michael Kohlstedt
- Institute of Systems Biotechnology, Saarland University, Campus A 1.5, 66123 Saarbrücken, Germany
| | - Gijs van Erven
- Laboratory of Food Chemistry, Wageningen University & Research, Bornse Weilanden 9, 6708 WG Wageningen, Netherlands
- Wageningen Food and Biobased Research, Wageningen University & Research, Bornse Weilanden 9, 6708 WG Wageningen, Netherlands
| | - Cynthia E. Klostermann
- Laboratory of Food Chemistry, Wageningen University & Research, Bornse Weilanden 9, 6708 WG Wageningen, Netherlands
- Biobased Chemistry and Technology, Wageningen University & Research, Bornse Weilanden 9, 6708 WG Wageningen Netherlands
| | - Antoine H. P. America
- Bioscience, Wageningen University & Research, Droevendaalsesteeg 1, 6708 PB Wageningen, Netherlands
| | - Edwin Bakx
- Laboratory of Food Chemistry, Wageningen University & Research, Bornse Weilanden 9, 6708 WG Wageningen, Netherlands
| | - Johan J. P. Baars
- Plant Breeding, Wageningen University & Research, 6708 PB Wageningen, Netherlands
- CNC Grondstoffen, Driekronenstraat 6, 6596 MA Milsbeek, Netherlands
| | - Antonie Gorissen
- IsoLife bv, Droevendaalsesteeg 1, 6708 PB Wageningen, Netherlands
| | - Ries de Visser
- IsoLife bv, Droevendaalsesteeg 1, 6708 PB Wageningen, Netherlands
| | - Ronald P. de Vries
- Fungal Physiology, Westerdijk Fungal Biodiversity Institute & Fungal Molecular Physiology, Utrecht University, Uppsalalaan 8, 3584 CT Utrecht, Netherlands
| | - Christoph Wittmann
- Institute of Systems Biotechnology, Saarland University, Campus A 1.5, 66123 Saarbrücken, Germany
| | - Rob N. J. Comans
- Soil Chemistry and Chemical Soil Quality Group, Wageningen University & Research, Droevendaalsesteeg 3a, 6708 PB Wageningen, Netherlands
| | - Thomas W. Kuyper
- Soil Biology Group, Wageningen University & Research, Droevendaalsesteeg 3a, 6708 PB Wageningen, Netherlands
| | - Mirjam A. Kabel
- Laboratory of Food Chemistry, Wageningen University & Research, Bornse Weilanden 9, 6708 WG Wageningen, Netherlands
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Weiland F, Kohlstedt M, Wittmann C. Biobased de novo synthesis, upcycling, and recycling - the heartbeat toward a green and sustainable polyethylene terephthalate industry. Curr Opin Biotechnol 2024; 86:103079. [PMID: 38422776 DOI: 10.1016/j.copbio.2024.103079] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2023] [Revised: 01/19/2024] [Accepted: 01/24/2024] [Indexed: 03/02/2024]
Abstract
Polyethylene terephthalate (PET) has revolutionized the industrial sector because of its versatility, with its predominant uses in the textiles and packaging materials industries. Despite the various advantages of this polymer, its synthesis is, unfavorably, tightly intertwined with nonrenewable fossil resources. Additionally, given its widespread use, accumulating PET waste poses a significant environmental challenge. As a result, current research in the areas of biological recycling, upcycling, and de novo synthesis is intensifying. Biological recycling involves the use of micro-organisms or enzymes to breakdown PET into monomers, offering a sustainable alternative to traditional recycling. Upcycling transforms PET waste into value-added products, expanding its potential application range and promoting a circular economy. Moreover, studies of cascading biological and chemical processes driven by microbial cell factories have explored generating PET using renewable, biobased feedstocks such as lignin. These avenues of research promise to mitigate the environmental footprint of PET, underlining the importance of sustainable innovations in the industry.
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Affiliation(s)
- Fabia Weiland
- Institute of Systems Biotechnology, Saarland University, Germany
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3
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Pause L, Weimer A, Wirth NT, Nguyen AV, Lenz C, Kohlstedt M, Wittmann C, Nikel PI, Lai B, Krömer JO. Anaerobic glucose uptake in Pseudomonas putida KT2440 in a bioelectrochemical system. Microb Biotechnol 2024; 17:e14375. [PMID: 37990843 PMCID: PMC10832537 DOI: 10.1111/1751-7915.14375] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2023] [Revised: 11/01/2023] [Accepted: 11/07/2023] [Indexed: 11/23/2023] Open
Abstract
Providing an anodic potential in a bio-electrochemical system to the obligate aerobe Pseudomonas putida enables anaerobic survival and allows the cells to overcome redox imbalances. In this setup, the bacteria could be exploited to produce chemicals via oxidative pathways at high yield. However, the absence of anaerobic growth and low carbon turnover rates remain as obstacles for the application of such an electro-fermentation technology. Growth and carbon turnover start with carbon uptake into the periplasm and cytosol. P. putida KT2440 has three native transporting systems for glucose, each differing in energy and redox demand. This architecture previously led to the hypothesis that internal redox and energy constraints ultimately limit cytoplasmic carbon utilization in a bio-electrochemical system. However, it remains largely unclear which uptake route is predominantly used by P. putida under electro-fermentative conditions. To elucidate this, we created three gene deletion mutants of P. putida KT2440, forcing the cells to exclusively utilize one of the routes. When grown in a bio-electrochemical system, the pathway mutants were heavily affected in terms of sugar consumption, current output and product formation. Surprisingly, however, we found that about half of the acetate formed in the cytoplasm originated from carbon that was put into the system via the inoculation biomass, while the other half came from the consumption of substrate. The deletion of individual sugar uptake routes did not alter significantly the secreted acetate concentrations among different strains even with different carbon sources. This means that the stoichiometry of the sugar uptake routes is not a limiting factor during electro-fermentation and that the low rates might be caused by other reasons, for example energy limitations or a yet-to-be-identified oxygen-dependent regulatory mechanism.
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Affiliation(s)
- Laura Pause
- Systems Biotechnology groupHelmholtz Centre for Environmental Research – UFZLeipzigGermany
| | - Anna Weimer
- Institute of Systems BiotechnologySaarland UniversitySaarbrückenGermany
| | - Nicolas T. Wirth
- Systems Environmental Microbiology Group, The Novo Nordisk Foundation Center for BiosustainabilityTechnical University of DenmarkLyngbyDenmark
| | - Anh Vu Nguyen
- Systems Biotechnology groupHelmholtz Centre for Environmental Research – UFZLeipzigGermany
| | - Claudius Lenz
- Systems Biotechnology groupHelmholtz Centre for Environmental Research – UFZLeipzigGermany
| | - Michael Kohlstedt
- Institute of Systems BiotechnologySaarland UniversitySaarbrückenGermany
| | | | - Pablo I. Nikel
- Systems Environmental Microbiology Group, The Novo Nordisk Foundation Center for BiosustainabilityTechnical University of DenmarkLyngbyDenmark
| | - Bin Lai
- BMBF Junior Research Group BiophotovoltaicsHelmholtz Centre for Environmental Research – UFZLeipzigGermany
| | - Jens O. Krömer
- Systems Biotechnology groupHelmholtz Centre for Environmental Research – UFZLeipzigGermany
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Jovanovic Gasovic S, Dietrich D, Gläser L, Cao P, Kohlstedt M, Wittmann C. Multi-omics view of recombinant Yarrowia lipolytica: Enhanced ketogenic amino acid catabolism increases polyketide-synthase-driven docosahexaenoic production to high selectivity at the gram scale. Metab Eng 2023; 80:45-65. [PMID: 37683719 DOI: 10.1016/j.ymben.2023.09.003] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2023] [Revised: 09/04/2023] [Accepted: 09/04/2023] [Indexed: 09/10/2023]
Abstract
DHA is a marine PUFA of commercial value, given its multiple health benefits. The worldwide emerging shortage in DHA supply has increased interest in microbial cell factories that can provide the compound de novo. In this regard, the present work aimed to improve DHA production in the oleaginous yeast strain Y. lipolytica Af4, which synthetized the PUFA via a heterologous myxobacterial polyketide synthase (PKS)-like gene cluster. As starting point, we used transcriptomics, metabolomics, and 13C-based metabolic pathway profiling to study the cellular dynamics of Y. lipolytica Af4. The shift from the growth to the stationary DHA-production phase was associated with fundamental changes in carbon core metabolism, including a strong upregulation of the PUFA gene cluster, as well as an increase in citrate and fatty acid degradation. At the same time, the intracellular levels of the two DHA precursors acetyl-CoA and malonyl-CoA dropped by up to 98% into the picomolar range. Interestingly, the degradation pathways for the ketogenic amino acids l-lysine, l-leucine, and l-isoleucine were transcriptionally activated, presumably to provide extra acetyl-CoA. Supplementation with small amounts of these amino acids at the beginning of the DHA production phase beneficially increased the intracellular CoA-ester pools and boosted the DHA titer by almost 40%. Isotopic 13C-tracer studies revealed that the supplements were efficiently directed toward intracellular CoA-esters and DHA. Hereby, l-lysine was found to be most efficient, as it enabled long-term activation, due to storage within the vacuole and continuous breakdown. The novel strategy enabled DHA production in Y. lipolytica at the gram scale for the first time. DHA was produced at a high selectivity (27% of total fatty acids) and free of the structurally similar PUFA DPA, which facilitates purification for high-value medical applications that require API-grade DHA. The assembled multi-omics picture of the central metabolism of Y. lipolytica provides valuable insights into this important yeast. Beyond our work, the enhanced catabolism of ketogenic amino acids seems promising for the overproduction of other compounds in Y. lipolytica, whose synthesis is limited by the availability of CoA ester precursors.
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Affiliation(s)
| | - Demian Dietrich
- Institute of Systems Biotechnology, Saarland University, Germany
| | - Lars Gläser
- Institute of Systems Biotechnology, Saarland University, Germany
| | - Peng Cao
- Institute of Systems Biotechnology, Saarland University, Germany
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Dietrich D, Jovanovic-Gasovic S, Cao P, Kohlstedt M, Wittmann C. Refactoring the architecture of a polyketide gene cluster enhances docosahexaenoic acid production in Yarrowia lipolytica through improved expression and genetic stability. Microb Cell Fact 2023; 22:199. [PMID: 37773137 PMCID: PMC10540379 DOI: 10.1186/s12934-023-02209-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2023] [Accepted: 09/20/2023] [Indexed: 10/01/2023] Open
Abstract
BACKGROUND Long-chain polyunsaturated fatty acids (LC-PUFAs), such as docosahexaenoic acid (DHA), are essential for human health and have been widely used in the food and pharmaceutical industries. However, the limited availability of natural sources, such as oily fish, has led to the pursuit of microbial production as a promising alternative. Yarrowia lipolytica can produce various PUFAs via genetic modification. A recent study upgraded Y. lipolytica for DHA production by expressing a four-gene cluster encoding a myxobacterial PKS-like PUFA synthase, reducing the demand for redox power. However, the genetic architecture of gene expression in Y. lipolytica is complex and involves various control elements, offering space for additional improvement of DHA production. This study was designed to optimize the expression of the PUFA cluster using a modular cloning approach. RESULTS Expression of the monocistronic cluster with each gene under the control of the constitutive TEF promoter led to low-level DHA production. By using the minLEU2 promoter instead and incorporating additional upstream activating UAS1B4 sequences, 5' promoter introns, and intergenic spacers, DHA production was increased by 16-fold. The producers remained stable over 185 h of cultivation. Beneficially, the different genetic control elements acted synergistically: UAS1B elements generally increased expression, while the intron caused gene-specific effects. Mutants with UAS1B16 sequences within 2-8 kb distance, however, were found to be genetically unstable, which limited production performance over time, suggesting the avoidance of long repetitive sequence blocks in synthetic multigene clusters and careful monitoring of genetic stability in producing strains. CONCLUSIONS Overall, the results demonstrate the effectiveness of synthetic heterologous gene clusters to drive DHA production in Y. lipolytica. The combinatorial exploration of different genetic control elements allowed the optimization of DHA production. These findings have important implications for developing Y. lipolytica strains for the industrial-scale production of valuable polyunsaturated fatty acids.
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Affiliation(s)
- Demian Dietrich
- Institute of Systems Biotechnology, Saarland University, Saarbrücken, Germany
| | | | - Peng Cao
- Institute of Systems Biotechnology, Saarland University, Saarbrücken, Germany
| | - Michael Kohlstedt
- Institute of Systems Biotechnology, Saarland University, Saarbrücken, Germany
| | - Christoph Wittmann
- Institute of Systems Biotechnology, Saarland University, Saarbrücken, Germany.
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Pauli S, Kohlstedt M, Lamber J, Weiland F, Becker J, Wittmann C. Systems metabolic engineering upgrades Corynebacterium glutamicum for selective high-level production of the chiral drug precursor and cell-protective extremolyte L-pipecolic acid. Metab Eng 2023; 77:100-117. [PMID: 36931556 DOI: 10.1016/j.ymben.2023.03.006] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2022] [Revised: 03/02/2023] [Accepted: 03/14/2023] [Indexed: 03/17/2023]
Abstract
The nonproteinogenic cyclic metabolite l-pipecolic acid is a chiral precursor for the synthesis of various commercial drugs and functions as a cell-protective extremolyte and mediator of defense in plants, enabling high-value applications in the pharmaceutical, medical, cosmetic, and agrochemical markets. To date, the production of the compound is unfavorably fossil-based. Here, we upgraded the strain Corynebacterium glutamicum for l-pipecolic acid production using systems metabolic engineering. Heterologous expression of the l-lysine 6-dehydrogenase pathway, apparently the best route to be used in the microbe, yielded a family of strains that enabled successful de novo synthesis from glucose but approached a limit of performance at a yield of 0.18 mol mol-1. Detailed analysis of the producers at the transcriptome, proteome, and metabolome levels revealed that the requirements of the introduced route were largely incompatible with the cellular environment, which could not be overcome after several further rounds of metabolic engineering. Based on the gained knowledge, we based the strain design on l-l-lysine 6-aminotransferase instead, which enabled a substantially higher in vivo flux toward l-pipecolic acid. The tailormade producer C. glutamicum PIA-7 formed l-pipecolic acid up to a yield of 562 mmol mol-1, representing 75% of the theoretical maximum. Ultimately, the advanced mutant PIA-10B achieved a titer of 93 g L-1 in a fed-batch process on glucose, outperforming all previous efforts to synthesize this valuable molecule de novo and even approaching the level of biotransformation from l-lysine. Notably, the use of C. glutamicum allows the safe production of GRAS-designated l-pipecolic acid, providing extra benefit toward addressing the high-value pharmaceutical, medical, and cosmetic markets. In summary, our development sets a milestone toward the commercialization of biobased l-pipecolic acid.
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Affiliation(s)
- Sarah Pauli
- Institute for Systems Biotechnology, Saarland University, Saarbrücken, Germany
| | - Michael Kohlstedt
- Institute for Systems Biotechnology, Saarland University, Saarbrücken, Germany
| | - Jessica Lamber
- Institute for Systems Biotechnology, Saarland University, Saarbrücken, Germany
| | - Fabia Weiland
- Institute for Systems Biotechnology, Saarland University, Saarbrücken, Germany
| | - Judith Becker
- Institute for Systems Biotechnology, Saarland University, Saarbrücken, Germany
| | - Christoph Wittmann
- Institute for Systems Biotechnology, Saarland University, Saarbrücken, Germany.
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Christmann J, Cao P, Becker J, Desiderato CK, Goldbeck O, Riedel CU, Kohlstedt M, Wittmann C. High-efficiency production of the antimicrobial peptide pediocin PA-1 in metabolically engineered Corynebacterium glutamicum using a microaerobic process at acidic pH and elevated levels of bivalent calcium ions. Microb Cell Fact 2023; 22:41. [PMID: 36849884 PMCID: PMC9969654 DOI: 10.1186/s12934-023-02044-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2022] [Accepted: 02/16/2023] [Indexed: 03/01/2023] Open
Abstract
BACKGROUND Pediocin PA-1 is a bacteriocin of recognized value with applications in food bio-preservation and the medical sector for the prevention of infection. To date, industrial manufacturing of pediocin PA-1 is limited by high cost and low-performance. The recent establishment of the biotechnological workhorse Corynebacterium glutamicum as recombinant host for pediocin PA-1 synthesis displays a promising starting point towards more efficient production. RESULTS Here, we optimized the fermentative production process. Following successful simplification of the production medium, we carefully investigated the impact of dissolved oxygen, pH value, and the presence of bivalent calcium ions on pediocin production. It turned out that the formation of the peptide was strongly supported by an acidic pH of 5.7 and microaerobic conditions at a dissolved oxygen level of 2.5%. Furthermore, elevated levels of CaCl2 boosted production. The IPTG-inducible producer C. glutamicum CR099 pXMJ19 Ptac pedACDCg provided 66 mg L-1 of pediocin PA-1 in a two-phase batch process using the optimized set-up. In addition, the novel constitutive strain Ptuf pedACDCg allowed successful production without the need for IPTG. CONCLUSIONS The achieved pediocin titer surpasses previous efforts in various microbes up to almost seven-fold, providing a valuable step to further explore and develop this important bacteriocin. In addition to its high biosynthetic performance C. glutamicum proved to be highly robust under the demanding producing conditions, suggesting its further use as host for bacteriocin production.
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Affiliation(s)
- Jens Christmann
- grid.11749.3a0000 0001 2167 7588Institute for Systems Biotechnology, Saarland University, Saarbrücken, Germany
| | - Peng Cao
- grid.11749.3a0000 0001 2167 7588Institute for Systems Biotechnology, Saarland University, Saarbrücken, Germany
| | - Judith Becker
- grid.11749.3a0000 0001 2167 7588Institute for Systems Biotechnology, Saarland University, Saarbrücken, Germany
| | - Christian K. Desiderato
- grid.6582.90000 0004 1936 9748Institute of Microbiology and Biotechnology, University of Ulm, Ulm, Germany
| | - Oliver Goldbeck
- grid.6582.90000 0004 1936 9748Institute of Microbiology and Biotechnology, University of Ulm, Ulm, Germany
| | - Christian U. Riedel
- grid.6582.90000 0004 1936 9748Institute of Microbiology and Biotechnology, University of Ulm, Ulm, Germany
| | - Michael Kohlstedt
- grid.11749.3a0000 0001 2167 7588Institute for Systems Biotechnology, Saarland University, Saarbrücken, Germany
| | - Christoph Wittmann
- Institute for Systems Biotechnology, Saarland University, Saarbrücken, Germany.
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Jungmann L, Hoffmann SL, Lang C, De Agazio R, Becker J, Kohlstedt M, Wittmann C. High-efficiency production of 5-hydroxyectoine using metabolically engineered Corynebacterium glutamicum. Microb Cell Fact 2022; 21:274. [PMID: 36578077 PMCID: PMC9798599 DOI: 10.1186/s12934-022-02003-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2022] [Accepted: 12/17/2022] [Indexed: 12/29/2022] Open
Abstract
BACKGROUND Extremolytes enable microbes to withstand even the most extreme conditions in nature. Due to their unique protective properties, the small organic molecules, more and more, become high-value active ingredients for the cosmetics and the pharmaceutical industries. While ectoine, the industrial extremolyte flagship, has been successfully commercialized before, an economically viable route to its highly interesting derivative 5-hydroxyectoine (hydroxyectoine) is not existing. RESULTS Here, we demonstrate high-level hydroxyectoine production, using metabolically engineered strains of C. glutamicum that express a codon-optimized, heterologous ectD gene, encoding for ectoine hydroxylase, to convert supplemented ectoine in the presence of sucrose as growth substrate into the desired derivative. Fourteen out of sixteen codon-optimized ectD variants from phylogenetically diverse bacterial and archaeal donors enabled hydroxyectoine production, showing the strategy to work almost regardless of the origin of the gene. The genes from Pseudomonas stutzeri (PST) and Mycobacterium smegmatis (MSM) worked best and enabled hydroxyectoine production up to 97% yield. Metabolic analyses revealed high enrichment of the ectoines inside the cells, which, inter alia, reduced the synthesis of other compatible solutes, including proline and trehalose. After further optimization, C. glutamicum Ptuf ectDPST achieved a titre of 74 g L-1 hydroxyectoine at 70% selectivity within 12 h, using a simple batch process. In a two-step procedure, hydroxyectoine production from ectoine, previously synthesized fermentatively with C. glutamicum ectABCopt, was successfully achieved without intermediate purification. CONCLUSIONS C. glutamicum is a well-known and industrially proven host, allowing the synthesis of commercial products with granted GRAS status, a great benefit for a safe production of hydroxyectoine as active ingredient for cosmetic and pharmaceutical applications. Because ectoine is already available at commercial scale, its use as precursor appears straightforward. In the future, two-step processes might provide hydroxyectoine de novo from sugar.
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Affiliation(s)
- Lukas Jungmann
- grid.11749.3a0000 0001 2167 7588Institute of Systems Biotechnology, Saarland University, Campus A1.5, Saarbrücken, Germany
| | - Sarah Lisa Hoffmann
- grid.11749.3a0000 0001 2167 7588Institute of Systems Biotechnology, Saarland University, Campus A1.5, Saarbrücken, Germany
| | - Caroline Lang
- grid.11749.3a0000 0001 2167 7588Institute of Systems Biotechnology, Saarland University, Campus A1.5, Saarbrücken, Germany
| | - Raphaela De Agazio
- grid.11749.3a0000 0001 2167 7588Institute of Systems Biotechnology, Saarland University, Campus A1.5, Saarbrücken, Germany
| | - Judith Becker
- grid.11749.3a0000 0001 2167 7588Institute of Systems Biotechnology, Saarland University, Campus A1.5, Saarbrücken, Germany
| | - Michael Kohlstedt
- grid.11749.3a0000 0001 2167 7588Institute of Systems Biotechnology, Saarland University, Campus A1.5, Saarbrücken, Germany
| | - Christoph Wittmann
- grid.11749.3a0000 0001 2167 7588Institute of Systems Biotechnology, Saarland University, Campus A1.5, Saarbrücken, Germany
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Rohles C, Pauli S, Gießelmann G, Kohlstedt M, Becker J, Wittmann C. Systems metabolic engineering of Corynebacterium glutamicum eliminates all by-products for selective and high-yield production of the platform chemical 5-aminovalerate. Metab Eng 2022; 73:168-181. [PMID: 35917915 DOI: 10.1016/j.ymben.2022.07.005] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Revised: 07/01/2022] [Accepted: 07/13/2022] [Indexed: 11/29/2022]
Abstract
5-aminovalerate (AVA) is a platform chemical of substantial commercial value to derive nylon-5 and five-carbon derivatives like δ-valerolactam, 1,5-pentanediol, glutarate, and 5-hydroxyvalerate. De-novo bio-production synthesis of AVA using metabolically engineered cell factories is regarded as exemplary route to provide this chemical in a sustainable way. So far, this route is limited by low titers, rates and yields and suffers from high levels of by-products. To overcome these limitations, we developed a novel family of AVA producing C. glutamicum cell factories. Stepwise optimization included (i) improved AVA biosynthesis by expression balancing of the heterologous davAB genes from P. putida, (ii) reduced formation of the by-product glutarate by disruption of the catabolic y-aminobutyrate pathway (iii), increased AVA export, and (iv) reduced AVA re-import via native and heterologous transporters to account for the accumulation of intracellular AVA up to 300 mM. Strain C. glutamicum AVA-5A, obtained after several optimization rounds, produced 48.3 g L-1 AVA in a fed-batch process and achieved a high yield of 0.21 g g-1. Surprisingly in later stages, the mutant suddenly accumulated glutarate to an extent equivalent to 30% of the amount of AVA formed, tenfold more than in the early process, displaying a severe drawback toward industrial production. Further exploration led to the discovery that ArgD, naturally aminating N-acetyl-l-ornithine during l-arginine biosynthesis, exhibits deaminating side activity on AVA toward glutarate formation. This promiscuity became relevant because of the high intracellular AVA level and the fact that ArgD became unoccupied with the gradually stronger switch-off of anabolism during production. Glutarate formation was favorably abolished in the advanced strains AVA-6A, AVA-6B, and AVA-7, all lacking argD. In a fed-batch process, C. glutamicum AVA-7 produced 46.5 g L-1 AVA at a yield of 0.34 g g-1 and a maximum productivity of 1.52 g L-1 h-1, outperforming all previously reported efforts and stetting a milestone toward industrial manufacturing of AVA. Notably, the novel cell factories are fully genome-based, offering high genetic stability and requiring no selection markers.
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Affiliation(s)
- Christina Rohles
- Institute of Systems Biotechnology, Saarland University, Germany
| | - Sarah Pauli
- Institute of Systems Biotechnology, Saarland University, Germany
| | | | | | - Judith Becker
- Institute of Systems Biotechnology, Saarland University, Germany
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10
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Dahlem C, Chanda S, Hemmer J, Schymik HS, Kohlstedt M, Wittmann C, Kiemer AK. Characterization of Anti-Cancer Activities of Violacein: Actions on Tumor Cells and the Tumor Microenvironment. Front Oncol 2022; 12:872223. [PMID: 35646663 PMCID: PMC9130777 DOI: 10.3389/fonc.2022.872223] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2022] [Accepted: 04/12/2022] [Indexed: 11/13/2022] Open
Abstract
Natural products have been shown to serve as promising starting points for novel anti-cancer drugs. In this study, the anti-cancer activities of the purple compound violacein, initially isolated from Chromobacterium violaceum, were investigated. To highlight the crucial role of the tumor microenvironment on the effectiveness of cancer therapies, this study includes effects on macrophages as prototypic cells of the microenvironment in addition to the investigation of tumor-centric activities. Using 2D and 3D cell culture models, automated live-cell microscopy, and biochemical analyses, violacein was demonstrated to inhibit tumor cell proliferation and migration. The violacein-triggered tumor cell death was further associated with caspase 3-like activation and ATP release. Stimuli released from dead cells resulted in inflammatory activation of macrophages, as shown by NF-κB reporter cell assays, macrophage morphology, and gene expression analysis. Moreover, macrophages deficient in the inflammasome component Nlrp3 were found to be significantly less sensitive towards treatment with violacein and doxorubicin. Taken together, this study provides new insights into the biological activity of violacein against cancer. In addition, the in vitro data suggest immunogenic features of induced cell death, making violacein an interesting candidate for further studies investigating the compound as an inducer of immunogenic cell death.
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Affiliation(s)
- Charlotte Dahlem
- Pharmaceutical Biology, Department of Pharmacy, Saarland University, Saarbruecken, Germany
| | - Shilpee Chanda
- Pharmaceutical Biology, Department of Pharmacy, Saarland University, Saarbruecken, Germany
| | - Jan Hemmer
- Pharmaceutical Biology, Department of Pharmacy, Saarland University, Saarbruecken, Germany
| | - Hanna S Schymik
- Pharmaceutical Biology, Department of Pharmacy, Saarland University, Saarbruecken, Germany
| | - Michael Kohlstedt
- Institute of Systems Biotechnology, Saarland University, Saarbruecken, Germany
| | - Christoph Wittmann
- Institute of Systems Biotechnology, Saarland University, Saarbruecken, Germany
| | - Alexandra K Kiemer
- Pharmaceutical Biology, Department of Pharmacy, Saarland University, Saarbruecken, Germany
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11
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Kohlstedt M, Weimer A, Weiland F, Stolzenberger J, Selzer M, Sanz M, Kramps L, Wittmann C. Biobased PET from lignin using an engineered cis, cis-muconate-producing Pseudomonas putida strain with superior robustness, energy and redox properties. Metab Eng 2022; 72:337-352. [DOI: 10.1016/j.ymben.2022.05.001] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2022] [Revised: 04/18/2022] [Accepted: 05/04/2022] [Indexed: 11/26/2022]
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12
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Schulze D, Kohlstedt M, Becker J, Cahoreau E, Peyriga L, Makowka A, Hildebrandt S, Gutekunst K, Portais JC, Wittmann C. GC/MS-based 13C metabolic flux analysis resolves the parallel and cyclic photomixotrophic metabolism of Synechocystis sp. PCC 6803 and selected deletion mutants including the Entner-Doudoroff and phosphoketolase pathways. Microb Cell Fact 2022; 21:69. [PMID: 35459213 PMCID: PMC9034593 DOI: 10.1186/s12934-022-01790-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2021] [Accepted: 04/05/2022] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND Cyanobacteria receive huge interest as green catalysts. While exploiting energy from sunlight, they co-utilize sugar and CO2. This photomixotrophic mode enables fast growth and high cell densities, opening perspectives for sustainable biomanufacturing. The model cyanobacterium Synechocystis sp. PCC 6803 possesses a complex architecture of glycolytic routes for glucose breakdown that are intertwined with the CO2-fixing Calvin-Benson-Bassham (CBB) cycle. To date, the contribution of these pathways to photomixotrophic metabolism has remained unclear. RESULTS Here, we developed a comprehensive approach for 13C metabolic flux analysis of Synechocystis sp. PCC 6803 during steady state photomixotrophic growth. Under these conditions, the Entner-Doudoroff (ED) and phosphoketolase (PK) pathways were found inactive but the microbe used the phosphoglucoisomerase (PGI) (63.1%) and the oxidative pentose phosphate pathway (OPP) shunts (9.3%) to fuel the CBB cycle. Mutants that lacked the ED pathway, the PK pathway, or phosphofructokinases were not affected in growth under metabolic steady-state. An ED pathway-deficient mutant (Δeda) exhibited an enhanced CBB cycle flux and increased glycogen formation, while the OPP shunt was almost inactive (1.3%). Under fluctuating light, ∆eda showed a growth defect, different to wild type and the other deletion strains. CONCLUSIONS The developed approach, based on parallel 13C tracer studies with GC-MS analysis of amino acids, sugars, and sugar derivatives, optionally adding NMR data from amino acids, is valuable to study fluxes in photomixotrophic microbes to detail. In photomixotrophic cells, PGI and OPP form glycolytic shunts that merge at switch points and result in synergistic fueling of the CBB cycle for maximized CO2 fixation. However, redirected fluxes in an ED shunt-deficient mutant and the impossibility to delete this shunt in a GAPDH2 knockout mutant, indicate that either minor fluxes (below the resolution limit of 13C flux analysis) might exist that could provide catalytic amounts of regulatory intermediates or alternatively, that EDA possesses additional so far unknown functions. These ideas require further experiments.
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Affiliation(s)
- Dennis Schulze
- Institute of Systems Biotechnology, Saarland University, Saarbrücken, Germany
| | - Michael Kohlstedt
- Institute of Systems Biotechnology, Saarland University, Saarbrücken, Germany
| | - Judith Becker
- Institute of Systems Biotechnology, Saarland University, Saarbrücken, Germany
| | - Edern Cahoreau
- Toulouse Biotechnology Institute, Université de Toulouse, CNRS, INRAE, INSA, Toulouse, France.,MetaboHUB-MetaToul, National Infrastructure of Metabolomics & Fluxomics, Toulouse, France.,RESTORE, Université de Toulouse, Inserm U1031, CNRS 5070, UPS, EFS, Toulouse, France
| | - Lindsay Peyriga
- Toulouse Biotechnology Institute, Université de Toulouse, CNRS, INRAE, INSA, Toulouse, France.,MetaboHUB-MetaToul, National Infrastructure of Metabolomics & Fluxomics, Toulouse, France.,RESTORE, Université de Toulouse, Inserm U1031, CNRS 5070, UPS, EFS, Toulouse, France
| | | | | | - Kirstin Gutekunst
- Institute of Botany, Christian-Albrecht University, Kiel, Germany.,Molecular Plant Physiology, Bioenergetics in Photoautotrophs, University of Kassel, Kassel, Germany
| | - Jean-Charles Portais
- Toulouse Biotechnology Institute, Université de Toulouse, CNRS, INRAE, INSA, Toulouse, France.,MetaboHUB-MetaToul, National Infrastructure of Metabolomics & Fluxomics, Toulouse, France.,RESTORE, Université de Toulouse, Inserm U1031, CNRS 5070, UPS, EFS, Toulouse, France
| | - Christoph Wittmann
- Institute of Systems Biotechnology, Saarland University, Saarbrücken, Germany.
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13
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Weiland F, Kohlstedt M, Wittmann C. Guiding stars to the field of dreams: Metabolically engineered pathways and microbial platforms for a sustainable lignin-based industry. Metab Eng 2021; 71:13-41. [PMID: 34864214 DOI: 10.1016/j.ymben.2021.11.011] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2021] [Revised: 11/25/2021] [Accepted: 11/29/2021] [Indexed: 12/19/2022]
Abstract
Lignin is an important structural component of terrestrial plants and is readily generated during biomass fractionation in lignocellulose processing facilities. Due to lacking alternatives the majority of technical lignins is industrially simply burned into heat and energy. However, regarding its vast abundance and a chemically interesting richness in aromatics, lignin is presently regarded as the most under-utilized and promising feedstock for value-added applications. Notably, microbes have evolved powerful enzymes and pathways that break down lignin and metabolize its various aromatic components. This natural pathway atlas meanwhile serves as a guiding star for metabolic engineers to breed designed cell factories and efficiently upgrade this global waste stream. The metabolism of aromatic compounds, in combination with success stories from systems metabolic engineering, as reviewed here, promises a sustainable product portfolio from lignin, comprising bulk and specialty chemicals, biomaterials, and fuels.
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Affiliation(s)
- Fabia Weiland
- Institute of Systems Biotechnology, Saarland University, Saarbrücken, Germany
| | - Michael Kohlstedt
- Institute of Systems Biotechnology, Saarland University, Saarbrücken, Germany
| | - Christoph Wittmann
- Institute of Systems Biotechnology, Saarland University, Saarbrücken, Germany.
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14
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Borrero‐de Acuña JM, Gutierrez‐Urrutia I, Hidalgo‐Dumont C, Aravena‐Carrasco C, Orellana‐Saez M, Palominos‐Gonzalez N, van Duuren JBJH, Wagner V, Gläser L, Becker J, Kohlstedt M, Zacconi FC, Wittmann C, Poblete‐Castro I. Channelling carbon flux through the meta-cleavage route for improved poly(3-hydroxyalkanoate) production from benzoate and lignin-based aromatics in Pseudomonas putida H. Microb Biotechnol 2021; 14:2385-2402. [PMID: 33171015 PMCID: PMC8601166 DOI: 10.1111/1751-7915.13705] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2020] [Revised: 10/14/2020] [Accepted: 10/23/2020] [Indexed: 12/22/2022] Open
Abstract
Lignin-based aromatics are attractive raw materials to derive medium-chain length poly(3-hydroxyalkanoates) (mcl-PHAs), biodegradable polymers of commercial value. So far, this conversion has exclusively used the ortho-cleavage route of Pseudomonas putida KT2440, which results in the secretion of toxic intermediates and limited performance. Pseudomonas putida H exhibits the ortho- and the meta-cleavage pathways where the latter appears promising because it stoichiometrically yields higher levels of acetyl-CoA. Here, we created a double-mutant H-ΔcatAΔA2 that utilizes the meta route exclusively and synthesized 30% more PHA on benzoate than the parental strain but suffered from catechol accumulation. The single deletion of the catA2 gene in the H strain provoked a slight attenuation on the enzymatic capacity of the ortho route (25%) and activation of the meta route by nearly 8-fold, producing twice as much mcl-PHAs compared to the wild type. Inline, the mutant H-ΔcatA2 showed a 2-fold increase in the intracellular malonyl-CoA abundance - the main precursor for mcl-PHAs synthesis. As inferred from flux simulation and enzyme activity assays, the superior performance of H-ΔcatA2 benefited from reduced flux through the TCA cycle and malic enzyme and diminished by-product formation. In a benzoate-based fed-batch, P. putida H-ΔcatA2 achieved a PHA titre of 6.1 g l-1 and a volumetric productivity of 1.8 g l-1 day-1 . Using Kraft lignin hydrolysate as feedstock, the engineered strain formed 1.4 g l- 1 PHA. The balancing of carbon flux between the parallel catechol-degrading routes emerges as an important strategy to prevent intermediate accumulation and elevate mcl-PHA production in P. putida H and, as shown here, sets the next level to derive this sustainable biopolymer from lignin hydrolysates and aromatics.
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Affiliation(s)
- José Manuel Borrero‐de Acuña
- Biosystems Engineering LaboratoryCenter for Bioinformatics and Integrative Biology (CBIB)Faculty of Life SciencesUniversidad Andres BelloSantiagoChile
- Present address:
Institute of MicrobiologyTechnical University of BraunschweigBraunschweigGermany
| | - Izabook Gutierrez‐Urrutia
- Biosystems Engineering LaboratoryCenter for Bioinformatics and Integrative Biology (CBIB)Faculty of Life SciencesUniversidad Andres BelloSantiagoChile
- Institute of Systems BiotechnologySaarland UniversitySaarbrückenGermany
| | - Cristian Hidalgo‐Dumont
- Biosystems Engineering LaboratoryCenter for Bioinformatics and Integrative Biology (CBIB)Faculty of Life SciencesUniversidad Andres BelloSantiagoChile
| | - Carla Aravena‐Carrasco
- Biosystems Engineering LaboratoryCenter for Bioinformatics and Integrative Biology (CBIB)Faculty of Life SciencesUniversidad Andres BelloSantiagoChile
| | - Matias Orellana‐Saez
- Biosystems Engineering LaboratoryCenter for Bioinformatics and Integrative Biology (CBIB)Faculty of Life SciencesUniversidad Andres BelloSantiagoChile
| | - Nestor Palominos‐Gonzalez
- Biosystems Engineering LaboratoryCenter for Bioinformatics and Integrative Biology (CBIB)Faculty of Life SciencesUniversidad Andres BelloSantiagoChile
| | | | - Viktoria Wagner
- Institute of Systems BiotechnologySaarland UniversitySaarbrückenGermany
| | - Lars Gläser
- Institute of Systems BiotechnologySaarland UniversitySaarbrückenGermany
| | - Judith Becker
- Institute of Systems BiotechnologySaarland UniversitySaarbrückenGermany
| | - Michael Kohlstedt
- Institute of Systems BiotechnologySaarland UniversitySaarbrückenGermany
| | - Flavia C. Zacconi
- Facultad de Química y de FarmaciaPontificia Universidad Católica de ChileSantiagoChile
- Institute for Biological and Medical EngineeringSchools of Engineering, Medicine and Biological SciencesPontificia Universidad Católica de ChileSantiagoChile
| | | | - Ignacio Poblete‐Castro
- Biosystems Engineering LaboratoryCenter for Bioinformatics and Integrative Biology (CBIB)Faculty of Life SciencesUniversidad Andres BelloSantiagoChile
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15
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Hoffmann SL, Kohlstedt M, Jungmann L, Hutter M, Poblete-Castro I, Becker J, Wittmann C. Cascaded valorization of brown seaweed to produce l-lysine and value-added products using Corynebacterium glutamicum streamlined by systems metabolic engineering. Metab Eng 2021; 67:293-307. [PMID: 34314893 DOI: 10.1016/j.ymben.2021.07.010] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2020] [Revised: 06/23/2021] [Accepted: 07/22/2021] [Indexed: 12/15/2022]
Abstract
Seaweeds emerge as promising third-generation renewable for sustainable bioproduction. In the present work, we valorized brown seaweed to produce l-lysine, the world's leading feed amino acid, using Corynebacterium glutamicum, which was streamlined by systems metabolic engineering. The mutant C. glutamicum SEA-1 served as a starting point for development because it produced small amounts of l-lysine from mannitol, a major seaweed sugar, because of the deletion of its arabitol repressor AtlR and its engineered l-lysine pathway. Starting from SEA-1, we systematically optimized the microbe to redirect excess NADH, formed on the sugar alcohol, towards NADPH, required for l-lysine synthesis. The mannitol dehydrogenase variant MtlD D75A, inspired by 3D protein homology modelling, partly generated NADPH during the oxidation of mannitol to fructose, leading to a 70% increased l-lysine yield in strain SEA-2C. Several rounds of strain engineering further increased NADPH supply and l-lysine production. The best strain, SEA-7, overexpressed the membrane-bound transhydrogenase pntAB together with codon-optimized gapN, encoding NADPH-dependent glyceraldehyde 3-phosphate dehydrogenase, and mak, encoding fructokinase. In a fed-batch process, SEA-7 produced 76 g L-1l-lysine from mannitol at a yield of 0.26 mol mol-1 and a maximum productivity of 2.1 g L-1 h-1. Finally, SEA-7 was integrated into seaweed valorization cascades. Aqua-cultured Laminaria digitata, a major seaweed for commercial alginate, was extracted and hydrolyzed enzymatically, followed by recovery and clean-up of pure alginate gum. The residual sugar-based mixture was converted to l-lysine at a yield of 0.27 C-mol C-mol-1 using SEA-7. Second, stems of the wild-harvested seaweed Durvillaea antarctica, obtained as waste during commercial processing of the blades for human consumption, were extracted using acid treatment. Fermentation of the hydrolysate using SEA-7 provided l-lysine at a yield of 0.40 C-mol C-mol-1. Our findings enable improvement of the efficiency of seaweed biorefineries using tailor-made C. glutamicum strains.
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Affiliation(s)
- Sarah Lisa Hoffmann
- Institute of Systems Biotechnology, Saarland University, Saarbrücken, Germany
| | - Michael Kohlstedt
- Institute of Systems Biotechnology, Saarland University, Saarbrücken, Germany
| | - Lukas Jungmann
- Institute of Systems Biotechnology, Saarland University, Saarbrücken, Germany
| | - Michael Hutter
- Centre for Bioinformatics, Saarland University, Saarbrücken, Germany
| | | | - Judith Becker
- Institute of Systems Biotechnology, Saarland University, Saarbrücken, Germany
| | - Christoph Wittmann
- Institute of Systems Biotechnology, Saarland University, Saarbrücken, Germany.
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16
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Millard P, Sokol S, Kohlstedt M, Wittmann C, Létisse F, Lippens G, Portais JC. IsoSolve: An Integrative Framework to Improve Isotopic Coverage and Consolidate Isotopic Measurements by Mass Spectrometry and/or Nuclear Magnetic Resonance. Anal Chem 2021; 93:9428-9436. [PMID: 34197087 DOI: 10.1021/acs.analchem.1c01064] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Stable-isotope labeling experiments are widely used to investigate the topology and functioning of metabolic networks. Label incorporation into metabolites can be quantified using a broad range of mass spectrometry (MS) and nuclear magnetic resonance (NMR) spectroscopy methods, but in general, no single approach can completely cover isotopic space, even for small metabolites. The number of quantifiable isotopic species could be increased and the coverage of isotopic space improved by integrating measurements obtained by different methods; however, this approach has remained largely unexplored because no framework able to deal with partial, heterogeneous isotopic measurements has yet been developed. Here, we present a generic computational framework based on symbolic calculus that can integrate any isotopic data set by connecting measurements to the chemical structure of the molecules. As a test case, we apply this framework to isotopic analyses of amino acids, which are ubiquitous to life, central to many biological questions, and can be analyzed by a broad range of MS and NMR methods. We demonstrate how this integrative framework helps to (i) clarify and improve the coverage of isotopic space, (ii) evaluate the complementarity and redundancy of different techniques, (iii) consolidate isotopic data sets, (iv) design experiments, and (v) guide future analytical developments. This framework, which can be applied to any labeled element, isotopic tracer, metabolite, and analytical platform, has been implemented in IsoSolve (available at https://github.com/MetaSys-LISBP/IsoSolve and https://pypi.org/project/IsoSolve), an open-source software that can be readily integrated into data analysis pipelines.
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Affiliation(s)
- Pierre Millard
- TBI, Université de Toulouse, CNRS, INRAE, INSA, Toulouse 31077, France.,MetaboHUB-MetaToul, National Infrastructure of Metabolomics and Fluxomics, Toulouse 31077, France
| | - Serguei Sokol
- TBI, Université de Toulouse, CNRS, INRAE, INSA, Toulouse 31077, France.,MetaboHUB-MetaToul, National Infrastructure of Metabolomics and Fluxomics, Toulouse 31077, France
| | - Michael Kohlstedt
- Institute of Systems Biotechnology, Saarland University, Saarbrücken 66123, Germany
| | - Christoph Wittmann
- Institute of Systems Biotechnology, Saarland University, Saarbrücken 66123, Germany
| | - Fabien Létisse
- TBI, Université de Toulouse, CNRS, INRAE, INSA, Toulouse 31077, France.,Université Toulouse III - Paul Sabatier, Toulouse 31077, France
| | - Guy Lippens
- TBI, Université de Toulouse, CNRS, INRAE, INSA, Toulouse 31077, France
| | - Jean-Charles Portais
- TBI, Université de Toulouse, CNRS, INRAE, INSA, Toulouse 31077, France.,MetaboHUB-MetaToul, National Infrastructure of Metabolomics and Fluxomics, Toulouse 31077, France.,Université Toulouse III - Paul Sabatier, Toulouse 31077, France.,RESTORE, Université de Toulouse, INSERM U1031, CNRS 5070, Université Toulouse III - Paul Sabatier, EFS, Toulouse 31077, France
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17
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Jovanovic S, Dietrich D, Becker J, Kohlstedt M, Wittmann C. Microbial production of polyunsaturated fatty acids - high-value ingredients for aquafeed, superfoods, and pharmaceuticals. Curr Opin Biotechnol 2021; 69:199-211. [PMID: 33540327 DOI: 10.1016/j.copbio.2021.01.009] [Citation(s) in RCA: 41] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2020] [Revised: 01/01/2021] [Accepted: 01/10/2021] [Indexed: 12/26/2022]
Abstract
Polyunsaturated fatty acids (PUFAs), primarily docosahexaenoic acid (DHA) and eicosapentaenoic acid (EPA), have received worldwide attention in recent years due to an increasing awareness of their uniqueness in improving diet and human health and their apparently inevitable shortage in global availability. Microbial cell factories are a major solution to supplying these precious molecules in sufficient amounts and providing PUFA-rich aquafeed, superfoods, and medical formulations. This review assesses the PUFA world markets and highlights recent advances in upgrading and streamlining microalgae, yeasts, fungi, and bacteria for high-level PUFA production and broadening of the PUFA spectrum.
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Affiliation(s)
- Sofija Jovanovic
- Institute of Systems Biotechnology, Universität des Saarlandes, Germany
| | - Demian Dietrich
- Institute of Systems Biotechnology, Universität des Saarlandes, Germany
| | - Judith Becker
- Institute of Systems Biotechnology, Universität des Saarlandes, Germany
| | - Michael Kohlstedt
- Institute of Systems Biotechnology, Universität des Saarlandes, Germany
| | - Christoph Wittmann
- Institute of Systems Biotechnology, Universität des Saarlandes, Germany.
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18
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Weimer A, Kohlstedt M, Volke DC, Nikel PI, Wittmann C. Industrial biotechnology of Pseudomonas putida: advances and prospects. Appl Microbiol Biotechnol 2020; 104:7745-7766. [PMID: 32789744 PMCID: PMC7447670 DOI: 10.1007/s00253-020-10811-9] [Citation(s) in RCA: 86] [Impact Index Per Article: 21.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2020] [Revised: 07/23/2020] [Accepted: 08/02/2020] [Indexed: 11/17/2022]
Abstract
Pseudomonas putida is a Gram-negative, rod-shaped bacterium that can be encountered in diverse ecological habitats. This ubiquity is traced to its remarkably versatile metabolism, adapted to withstand physicochemical stress, and the capacity to thrive in harsh environments. Owing to these characteristics, there is a growing interest in this microbe for industrial use, and the corresponding research has made rapid progress in recent years. Hereby, strong drivers are the exploitation of cheap renewable feedstocks and waste streams to produce value-added chemicals and the steady progress in genetic strain engineering and systems biology understanding of this bacterium. Here, we summarize the recent advances and prospects in genetic engineering, systems and synthetic biology, and applications of P. putida as a cell factory. KEY POINTS: • Pseudomonas putida advances to a global industrial cell factory. • Novel tools enable system-wide understanding and streamlined genomic engineering. • Applications of P. putida range from bioeconomy chemicals to biosynthetic drugs.
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Affiliation(s)
- Anna Weimer
- Institute of Systems Biotechnology, Saarland University, Campus A1.5, 66123, Saarbrücken, Germany
| | - Michael Kohlstedt
- Institute of Systems Biotechnology, Saarland University, Campus A1.5, 66123, Saarbrücken, Germany
| | - Daniel C Volke
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Lyngby, Denmark
| | - Pablo I Nikel
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Lyngby, Denmark
| | - Christoph Wittmann
- Institute of Systems Biotechnology, Saarland University, Campus A1.5, 66123, Saarbrücken, Germany.
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19
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Duuren JBJH, Wild PJ, Starck S, Bradtmöller C, Selzer M, Mehlmann K, Schneider R, Kohlstedt M, Poblete‐Castro I, Stolzenberger J, Barton N, Fritz M, Scholl S, Venus J, Wittmann C. Cover Image. Biotechnol Bioeng 2020. [DOI: 10.1002/bit.27049] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Affiliation(s)
| | - Paul J. Wild
- Biomass & Energy Efficiency, TNOPetten The Netherlands
| | - Sören Starck
- Institute of Systems BiotechnologySaarland UniversitySaarbrücken Germany
| | - Christian Bradtmöller
- Institute for Chemical and Thermal Process EngineeringTechnische Universität BraunschweigBraunschweig Germany
| | - Mirjam Selzer
- Institute of Systems BiotechnologySaarland UniversitySaarbrücken Germany
| | - Kerstin Mehlmann
- Department of BioengineeringLeibniz Institute for Agricultural Engineering and Bioeconomy (ATB)Potsdam Germany
| | - Roland Schneider
- Department of BioengineeringLeibniz Institute for Agricultural Engineering and Bioeconomy (ATB)Potsdam Germany
| | - Michael Kohlstedt
- Institute of Systems BiotechnologySaarland UniversitySaarbrücken Germany
| | - Ignacio Poblete‐Castro
- Biosystems Engineering Laboratory, Center for Bioinformatics and Integrative Biology, Faculty of Natural SciencesUniversidad Andres BelloSantiago de Chile Chile
| | | | - Nadja Barton
- Institute of Systems BiotechnologySaarland UniversitySaarbrücken Germany
| | - Michel Fritz
- Institute of Systems BiotechnologySaarland UniversitySaarbrücken Germany
| | - Stephan Scholl
- Institute for Chemical and Thermal Process EngineeringTechnische Universität BraunschweigBraunschweig Germany
| | - Joachim Venus
- Department of BioengineeringLeibniz Institute for Agricultural Engineering and Bioeconomy (ATB)Potsdam Germany
| | - Christoph Wittmann
- Institute of Systems BiotechnologySaarland UniversitySaarbrücken Germany
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20
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Duuren JBJH, Wild PJ, Starck S, Bradtmöller C, Selzer M, Mehlmann K, Schneider R, Kohlstedt M, Poblete‐Castro I, Stolzenberger J, Barton N, Fritz M, Scholl S, Venus J, Wittmann C. Limited life cycle and cost assessment for the bioconversion of lignin‐derived aromatics into adipic acid. Biotechnol Bioeng 2020; 117:1381-1393. [DOI: 10.1002/bit.27299] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2019] [Accepted: 02/03/2020] [Indexed: 01/20/2023]
Affiliation(s)
| | - Paul J. Wild
- Biomass & Energy Efficiency, TNOPetten The Netherlands
| | - Sören Starck
- Institute of Systems BiotechnologySaarland UniversitySaarbrücken Germany
| | - Christian Bradtmöller
- Institute for Chemical and Thermal Process EngineeringTechnische Universität BraunschweigBraunschweig Germany
| | - Mirjam Selzer
- Institute of Systems BiotechnologySaarland UniversitySaarbrücken Germany
| | - Kerstin Mehlmann
- Department of BioengineeringLeibniz Institute for Agricultural Engineering and Bioeconomy (ATB)Potsdam Germany
| | - Roland Schneider
- Department of BioengineeringLeibniz Institute for Agricultural Engineering and Bioeconomy (ATB)Potsdam Germany
| | - Michael Kohlstedt
- Institute of Systems BiotechnologySaarland UniversitySaarbrücken Germany
| | - Ignacio Poblete‐Castro
- Biosystems Engineering Laboratory, Center for Bioinformatics and Integrative Biology, Faculty of Natural SciencesUniversidad Andres BelloSantiago de Chile Chile
| | | | - Nadja Barton
- Institute of Systems BiotechnologySaarland UniversitySaarbrücken Germany
| | - Michel Fritz
- Institute of Systems BiotechnologySaarland UniversitySaarbrücken Germany
| | - Stephan Scholl
- Institute for Chemical and Thermal Process EngineeringTechnische Universität BraunschweigBraunschweig Germany
| | - Joachim Venus
- Department of BioengineeringLeibniz Institute for Agricultural Engineering and Bioeconomy (ATB)Potsdam Germany
| | - Christoph Wittmann
- Institute of Systems BiotechnologySaarland UniversitySaarbrücken Germany
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Gießelmann G, Dietrich D, Jungmann L, Kohlstedt M, Jeon EJ, Yim SS, Sommer F, Zimmer D, Mühlhaus T, Schroda M, Jeong KJ, Becker J, Wittmann C. Metabolic Engineering of
Corynebacterium glutamicum
for High‐Level Ectoine Production: Design, Combinatorial Assembly, and Implementation of a Transcriptionally Balanced Heterologous Ectoine Pathway. Biotechnol J 2019; 14:e1800417. [DOI: 10.1002/biot.201800417] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2018] [Revised: 05/03/2019] [Indexed: 12/27/2022]
Affiliation(s)
- Gideon Gießelmann
- Institute of Systems BiotechnologySaarland University 66123 Saarbrücken Germany
| | - Demian Dietrich
- Institute of Systems BiotechnologySaarland University 66123 Saarbrücken Germany
| | - Lukas Jungmann
- Institute of Systems BiotechnologySaarland University 66123 Saarbrücken Germany
| | - Michael Kohlstedt
- Institute of Systems BiotechnologySaarland University 66123 Saarbrücken Germany
| | - Eun J. Jeon
- Department of Chemical and Biomolecular EngineeringKAIST 335 Gwahagno Yuseong‐gu Daejeon 305‐701 Republic of Korea
| | - Sung S. Yim
- Department of Chemical and Biomolecular EngineeringKAIST 335 Gwahagno Yuseong‐gu Daejeon 305‐701 Republic of Korea
| | - Frederik Sommer
- Department of Molecular Biotechnology and Systems BiologyTU Kaiserslautern Kaiserslautern 67663 Germany
| | - David Zimmer
- Department of Molecular Biotechnology and Systems BiologyTU Kaiserslautern Kaiserslautern 67663 Germany
| | - Timo Mühlhaus
- Department of Molecular Biotechnology and Systems BiologyTU Kaiserslautern Kaiserslautern 67663 Germany
| | - Michael Schroda
- Department of Molecular Biotechnology and Systems BiologyTU Kaiserslautern Kaiserslautern 67663 Germany
| | - Ki J. Jeong
- Department of Chemical and Biomolecular EngineeringKAIST 335 Gwahagno Yuseong‐gu Daejeon 305‐701 Republic of Korea
| | - Judith Becker
- Institute of Systems BiotechnologySaarland University 66123 Saarbrücken Germany
| | - Christoph Wittmann
- Institute of Systems BiotechnologySaarland University 66123 Saarbrücken Germany
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Becker J, Kuhl M, Kohlstedt M, Starck S, Wittmann C. Metabolic engineering of Corynebacterium glutamicum for the production of cis, cis-muconic acid from lignin. Microb Cell Fact 2018; 17:115. [PMID: 30029656 PMCID: PMC6054733 DOI: 10.1186/s12934-018-0963-2] [Citation(s) in RCA: 101] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2018] [Accepted: 07/13/2018] [Indexed: 11/25/2022] Open
Abstract
Background Cis, cis-muconic acid (MA) is a dicarboxylic acid of recognized industrial value. It provides direct access to adipic acid and terephthalic acid, prominent monomers of commercial plastics. Results In the present work, we engineered the soil bacterium Corynebacterium glutamicum into a stable genome-based cell factory for high-level production of bio-based MA from aromatics and lignin hydrolysates. The elimination of muconate cycloisomerase (catB) in the catechol branch of the β-ketoadipate pathway provided a mutant, which accumulated MA at 100% molar yield from catechol, phenol, and benzoic acid, using glucose as additional growth substrate. The production of MA was optimized by constitutive overexpression of catA, which increased the activity of the encoded catechol 1,2-dioxygenase, forming MA from catechol, tenfold. Intracellular levels of catechol were more than 30-fold lower than extracellular levels, minimizing toxicity, but still saturating the high affinity CatA enzyme. In a fed-batch process, the created strain C. glutamicum MA-2 accumulated 85 g L−1 MA from catechol in 60 h and achieved a maximum volumetric productivity of 2.4 g L−1 h−1. The strain was furthermore used to demonstrate the production of MA from lignin in a cascade process. Following hydrothermal depolymerization of softwood lignin into small aromatics, the MA-2 strain accumulated 1.8 g L−1 MA from the obtained hydrolysate. Conclusions Our findings open the door to valorize lignin, the second most abundant polymer on earth, by metabolically engineered C. glutamicum for industrial production of MA and potentially other chemicals. Electronic supplementary material The online version of this article (10.1186/s12934-018-0963-2) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Judith Becker
- Institute of Systems Biotechnology, Saarland University, Campus A1.5, Saarbrücken, Germany
| | - Martin Kuhl
- Institute of Systems Biotechnology, Saarland University, Campus A1.5, Saarbrücken, Germany
| | - Michael Kohlstedt
- Institute of Systems Biotechnology, Saarland University, Campus A1.5, Saarbrücken, Germany
| | - Sören Starck
- Institute of Systems Biotechnology, Saarland University, Campus A1.5, Saarbrücken, Germany
| | - Christoph Wittmann
- Institute of Systems Biotechnology, Saarland University, Campus A1.5, Saarbrücken, Germany.
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Kohlstedt M, Starck S, Barton N, Stolzenberger J, Selzer M, Mehlmann K, Schneider R, Pleissner D, Rinkel J, Dickschat JS, Venus J, B.J.H. van Duuren J, Wittmann C. From lignin to nylon: Cascaded chemical and biochemical conversion using metabolically engineered Pseudomonas putida. Metab Eng 2018; 47:279-293. [DOI: 10.1016/j.ymben.2018.03.003] [Citation(s) in RCA: 121] [Impact Index Per Article: 20.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2017] [Revised: 03/02/2018] [Accepted: 03/04/2018] [Indexed: 12/31/2022]
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Affiliation(s)
- Ignacio Poblete-Castro
- Universidad Andrés Bello; Center for Bioinformatics and Integrative Biology, Biosystems Engineering Laboratory, Faculty of Biological Sciences; Av. República 239 8340176 Santiago de Chile Chile
| | - José M. Borrero-de Acuña
- Universidad Andrés Bello; Center for Bioinformatics and Integrative Biology, Biosystems Engineering Laboratory, Faculty of Biological Sciences; Av. República 239 8340176 Santiago de Chile Chile
| | - Pablo I. Nikel
- Systems and Synthetic Biology Program; National Spanish Center for Biotechnology (CNB-CSIC); Calle Darwin, 3 28049 Madrid, Spain
| | - Michael Kohlstedt
- Saarland University; Institute of Systems Biology, Biosciences; Campus A1.5 66123 Saarbrücken, Germany
| | - Christoph Wittmann
- Saarland University; Institute of Systems Biology, Biosciences; Campus A1.5 66123 Saarbrücken, Germany
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25
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Rohles CM, Gießelmann G, Kohlstedt M, Wittmann C, Becker J. Systems metabolic engineering of Corynebacterium glutamicum for the production of the carbon-5 platform chemicals 5-aminovalerate and glutarate. Microb Cell Fact 2016; 15:154. [PMID: 27618862 PMCID: PMC5020477 DOI: 10.1186/s12934-016-0553-0] [Citation(s) in RCA: 90] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2016] [Accepted: 09/02/2016] [Indexed: 11/30/2022] Open
Abstract
Background The steadily growing world population and our ever luxurious life style, along with the simultaneously decreasing fossil resources has confronted modern society with the issue and need of finding renewable routes to accommodate for our demands. Shifting the production pipeline from raw oil to biomass requires efficient processes for numerous platform chemicals being produced with high yield, high titer and high productivity. Results In the present work, we established a de novo bio-based production process for the two carbon-5 platform chemicals 5-aminovalerate and glutarate on basis of the lysine-hyperproducing strain Corynebacterium glutamicum LYS-12. Upon heterologous implementation of the Pseudomonas putida genes davA, encoding 5-aminovaleramidase and davB, encoding lysine monooxygenase, 5-aminovalerate production was established. Related to the presence of endogenous genes coding for 5-aminovalerate transaminase (gabT) and glutarate semialdehyde dehydrogenase, 5-aminovalerate was partially converted to glutarate. Moreover, residual l-lysine was secreted as by-product. The issue of by-product formation was then addressed by deletion of the lysE gene, encoding the l-lysine exporter. Additionally, a putative gabT gene was deleted to enhance 5-aminovalerate production. To fully exploit the performance of the optimized strain, fed-batch fermentation was carried out producing 28 g L−1 5-aminovalerate with a maximal space–time yield of 0.9 g L−1 h−1. Conclusions The present study describes the construction of a recombinant microbial cell factory for the production of carbon-5 platform chemicals. Beyond a basic proof-of-concept, we were able to specifically increase the production flux of 5-aminovalerate thereby generating a strain with excellent production performance. Additional improvement can be expected by removal of remaining by-product formation and bottlenecks, associated to the terminal pathway, to generate a strain being applicable as centerpiece for a bio-based production of 5-aminovalerate.
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Affiliation(s)
| | - Gideon Gießelmann
- Institute of Systems Biotechnology, Saarland University, Saarbrücken, Germany
| | - Michael Kohlstedt
- Institute of Systems Biotechnology, Saarland University, Saarbrücken, Germany
| | - Christoph Wittmann
- Institute of Systems Biotechnology, Saarland University, Saarbrücken, Germany
| | - Judith Becker
- Institute of Systems Biotechnology, Saarland University, Saarbrücken, Germany.
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Kohlstedt M, Sappa PK, Meyer H, Maaß S, Zaprasis A, Hoffmann T, Becker J, Steil L, Hecker M, van Dijl JM, Lalk M, Mäder U, Stülke J, Bremer E, Völker U, Wittmann C. Adaptation ofBacillus subtiliscarbon core metabolism to simultaneous nutrient limitation and osmotic challenge: a multi-omics perspective. Environ Microbiol 2014; 16:1898-917. [DOI: 10.1111/1462-2920.12438] [Citation(s) in RCA: 71] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2013] [Accepted: 02/18/2014] [Indexed: 01/24/2023]
Affiliation(s)
- Michael Kohlstedt
- Institute of Systems Biotechnology; Saarland University; Campus A1 5 66123 Saarbrücken Germany
- Institute of Biochemical Engineering; Braunschweig University of Technology; Braunschweig Germany
| | - Praveen K. Sappa
- Interfaculty Institute of Genetics and Functional Genomics; Department Functional Genomics; University Medicine Greifswald; Germany
| | - Hanna Meyer
- Institutes of Biochemistry; Ernst-Moritz-Arndt-University Greifswald; Greifswald Germany
| | - Sandra Maaß
- Microbiology; Ernst-Moritz-Arndt-University Greifswald; Greifswald Germany
| | - Adrienne Zaprasis
- Department of Biology; Laboratory of Microbiology; Philipps-University Marburg; Marburg Germany
| | - Tamara Hoffmann
- Department of Biology; Laboratory of Microbiology; Philipps-University Marburg; Marburg Germany
| | - Judith Becker
- Institute of Systems Biotechnology; Saarland University; Campus A1 5 66123 Saarbrücken Germany
- Institute of Biochemical Engineering; Braunschweig University of Technology; Braunschweig Germany
| | - Leif Steil
- Interfaculty Institute of Genetics and Functional Genomics; Department Functional Genomics; University Medicine Greifswald; Germany
| | - Michael Hecker
- Microbiology; Ernst-Moritz-Arndt-University Greifswald; Greifswald Germany
| | - Jan Maarten van Dijl
- Department of Medical Microbiology; University of Groningen; University Medical Center Groningen; Groningen The Netherlands
| | - Michael Lalk
- Institutes of Biochemistry; Ernst-Moritz-Arndt-University Greifswald; Greifswald Germany
| | - Ulrike Mäder
- Interfaculty Institute of Genetics and Functional Genomics; Department Functional Genomics; University Medicine Greifswald; Germany
| | - Jörg Stülke
- Department for General Microbiology; Georg-August-University Göttingen; Göttingen Germany
| | - Erhard Bremer
- Department of Biology; Laboratory of Microbiology; Philipps-University Marburg; Marburg Germany
| | - Uwe Völker
- Interfaculty Institute of Genetics and Functional Genomics; Department Functional Genomics; University Medicine Greifswald; Germany
| | - Christoph Wittmann
- Institute of Systems Biotechnology; Saarland University; Campus A1 5 66123 Saarbrücken Germany
- Institute of Biochemical Engineering; Braunschweig University of Technology; Braunschweig Germany
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Becker J, Schäfer R, Kohlstedt M, Harder BJ, Borchert NS, Stöveken N, Bremer E, Wittmann C. Systems metabolic engineering of Corynebacterium glutamicum for production of the chemical chaperone ectoine. Microb Cell Fact 2013; 12:110. [PMID: 24228689 PMCID: PMC4225761 DOI: 10.1186/1475-2859-12-110] [Citation(s) in RCA: 71] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2013] [Accepted: 11/05/2013] [Indexed: 11/14/2022] Open
Abstract
Background The stabilizing and function-preserving effects of ectoines have attracted considerable biotechnological interest up to industrial scale processes for their production. These rely on the release of ectoines from high-salinity-cultivated microbial producer cells upon an osmotic down-shock in rather complex processor configurations. There is growing interest in uncoupling the production of ectoines from the typical conditions required for their synthesis, and instead design strains that naturally release ectoines into the medium without the need for osmotic changes, since the use of high-salinity media in the fermentation process imposes notable constraints on the costs, design, and durability of fermenter systems. Results Here, we used a Corynebacterium glutamicum strain as a cellular chassis to establish a microbial cell factory for the biotechnological production of ectoines. The implementation of a mutant aspartokinase enzyme ensured efficient supply of L-aspartate-beta-semialdehyde, the precursor for ectoine biosynthesis. We further engineered the genome of the basic C. glutamicum strain by integrating a codon-optimized synthetic ectABCD gene cluster under expressional control of the strong and constitutive C. glutamicum tuf promoter. The resulting recombinant strain produced ectoine and excreted it into the medium; however, lysine was still found as a by-product. Subsequent inactivation of the L-lysine exporter prevented the undesired excretion of lysine while ectoine was still exported. Using the streamlined cell factory, a fed-batch process was established that allowed the production of ectoine with an overall productivity of 6.7 g L-1 day-1 under growth conditions that did not rely on the use of high-salinity media. Conclusions The present study describes the construction of a stable microbial cell factory for recombinant production of ectoine. We successfully applied metabolic engineering strategies to optimize its synthetic production in the industrial workhorse C. glutamicum and thereby paved the way for further improvements in ectoine yield and biotechnological process optimization.
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Affiliation(s)
- Judith Becker
- Institute of Biochemical Engineering, Technische Universität Braunschweig, Braunschweig, Germany.
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Demming S, Peterat G, Llobera A, Schmolke H, Bruns A, Kohlstedt M, Al-Halhouli A, Klages CP, Krull R, Büttgenbach S. Vertical microbubble column-A photonic lab-on-chip for cultivation and online analysis of yeast cell cultures. Biomicrofluidics 2012; 6:34106. [PMID: 23882299 PMCID: PMC3416849 DOI: 10.1063/1.4738587] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/20/2012] [Accepted: 07/03/2012] [Indexed: 05/11/2023]
Abstract
This paper presents a vertically positioned microfluidic system made of poly(dimethylsiloxane) (PDMS) and glass, which can be applied as a microbubble column (μBC) for biotechnological screening in suspension. In this μBC, microbubbles are produced in a cultivation chamber through an integrated nozzle structure. Thus, homogeneous suspension of biomass is achieved in the cultivation chamber without requiring additional mixing elements. Moreover, blockage due to produced carbon dioxide by the microorganisms-a problem predominant in common, horizontally positioned microbioreactors (MBRs)-is avoided, as the gas bubbles are released by buoyancy at the upper part of the microsystem. The patterned PDMS layer is based on an optimized two-lithographic process. Since the naturally hydrophobic PDMS causes problems for the sufficient production of microbubbles, a method based on polyelectrolyte multilayers is applied in order to allow continuous hydrophilization of the already bonded PDMS-glass-system. The μBC comprises various microelements, including stabilization of temperature, control of continuous bubble formation, and two optical configurations for measurement of optical density with two different sensitivities. In addition, the simple and robust application and handling of the μBC is achieved via a custom-made modular plug-in adapter. To validate the scalability from laboratory scale to microscale, and thus to demonstrate the successful application of the μBC as a screening instrument, a batch cultivation of Saccharomyces cerevisiae is performed in the μBC and compared to shake flask cultivation. Monitoring of the biomass growth in the μBC with the integrated online analytics resulted in a specific growth rate of 0.32 h(-1), which is almost identical to the one achieved in the shake flask cultivation (0.31 h(-1)). Therefore, the validity of the μBC as an alternative screening tool compared to other conventional laboratory scale systems in bioprocess development is proven. In addition, vertically positioned microbioreactors show high potential in comparison to conventional screening tools, since they allow for high density of integrated online analytics and therefore minimize time and cost for screening and guarantee improved control and analysis of cultivation parameters.
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Affiliation(s)
- Stefanie Demming
- Institut für Mikrotechnik, Technische Universität Braunschweig, 38106 Braunschweig, Germany
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