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Stalidzans E, Muiznieks R, Dubencovs K, Sile E, Berzins K, Suleiko A, Vanags J. A Fermentation State Marker Rule Design Task in Metabolic Engineering. Bioengineering (Basel) 2023; 10:1427. [PMID: 38136018 PMCID: PMC10740952 DOI: 10.3390/bioengineering10121427] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2023] [Revised: 12/12/2023] [Accepted: 12/13/2023] [Indexed: 12/24/2023] Open
Abstract
There are several ways in which mathematical modeling is used in fermentation control, but mechanistic mathematical genome-scale models of metabolism within the cell have not been applied or implemented so far. As part of the metabolic engineering task setting, we propose that metabolite fluxes and/or biomass growth rate be used to search for a fermentation steady state marker rule. During fermentation, the bioreactor control system can automatically detect the desired steady state using a logical marker rule. The marker rule identification can be also integrated with the production growth coupling approach, as presented in this study. A design of strain with marker rule is demonstrated on genome scale metabolic model iML1515 of Escherichia coli MG1655 proposing two gene deletions enabling a measurable marker rule for succinate production using glucose as a substrate. The marker rule example at glucose consumption 10.0 is: IF (specific growth rate μ is above 0.060 h-1, AND CO2 production under 1.0, AND ethanol production above 5.5), THEN succinate production is within the range 8.2-10, where all metabolic fluxes units are mmol ∗ gDW-1 ∗ h-1. An objective function for application in metabolic engineering, including productivity features and rule detecting sensor set characterizing parameters, is proposed. Two-phase approach to implementing marker rules in the cultivation control system is presented to avoid the need for a modeler during production.
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Affiliation(s)
- Egils Stalidzans
- Institute of Microbiology and Biotechnology, University of Latvia, Jelgavas Street 1, LV-1004 Riga, Latvia; (R.M.); (K.B.)
| | - Reinis Muiznieks
- Institute of Microbiology and Biotechnology, University of Latvia, Jelgavas Street 1, LV-1004 Riga, Latvia; (R.M.); (K.B.)
| | - Konstantins Dubencovs
- Bioreactors.net AS, Dzerbenes Street 27, LV-1006 Riga, Latvia (E.S.); (A.S.); (J.V.)
- Laboratory of Bioengineering, Latvian State Institute of Wood Chemistry, Dzerbenes Street 27, LV-1006 Riga, Latvia
| | - Elina Sile
- Bioreactors.net AS, Dzerbenes Street 27, LV-1006 Riga, Latvia (E.S.); (A.S.); (J.V.)
| | - Kristaps Berzins
- Institute of Microbiology and Biotechnology, University of Latvia, Jelgavas Street 1, LV-1004 Riga, Latvia; (R.M.); (K.B.)
| | - Arturs Suleiko
- Bioreactors.net AS, Dzerbenes Street 27, LV-1006 Riga, Latvia (E.S.); (A.S.); (J.V.)
- Laboratory of Bioengineering, Latvian State Institute of Wood Chemistry, Dzerbenes Street 27, LV-1006 Riga, Latvia
| | - Juris Vanags
- Bioreactors.net AS, Dzerbenes Street 27, LV-1006 Riga, Latvia (E.S.); (A.S.); (J.V.)
- Laboratory of Bioengineering, Latvian State Institute of Wood Chemistry, Dzerbenes Street 27, LV-1006 Riga, Latvia
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Motamedian E, Berzins K, Muiznieks R, Stalidzans E. OptEnvelope: A target point guided method for growth-coupled production using knockouts. PLoS One 2023; 18:e0294313. [PMID: 37972019 PMCID: PMC10653430 DOI: 10.1371/journal.pone.0294313] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2023] [Accepted: 10/29/2023] [Indexed: 11/19/2023] Open
Abstract
Finding the best knockout strategy for coupling biomass growth and production of a target metabolite using a mathematic model of metabolism is a challenge in biotechnology. In this research, a three-step method named OptEnvelope is presented based on finding minimal set of active reactions for a target point in the feasible solution space (envelope) using a mixed-integer linear programming formula. The method initially finds the reduced desirable solution space envelope in the product versus biomass plot by removing all inactive reactions. Then, with reinsertion of the deleted reactions, OptEnvelope attempts to reduce the number of knockouts so that the desirable production envelope is preserved. Additionally, OptEnvelope searches for envelopes with higher minimum production rates or fewer knockouts by evaluating different target points within the desired solution space. It is possible to limit the maximal number of knockouts. The method was implemented on metabolic models of E. coli and S. cerevisiae to test the method benchmarking the capability of these industrial microbes for overproduction of acetate and glycerol under aerobic conditions and succinate and ethanol under anaerobic conditions. The results illustrate that OptEnvelope is capable to find multiple strong coupled envelopes located in the desired solution space because of its novel target point oriented strategy of envelope search. The results indicate that E. coli is more appropriate to produce acetate and succinate while S. cerevisiae is a better host for glycerol production. Gene deletions for some of the proposed reaction knockouts have been previously reported to increase the production of these metabolites in experiments. Both organisms are suitable for ethanol production, however, more knockouts for the adaptation of E. coli are required. OptEnvelope is available at https://github.com/lv-csbg/optEnvelope.
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Affiliation(s)
- Ehsan Motamedian
- Institute of Microbiology and Biotechnology, Computational Systems Biology Group, University of Latvia, Riga, Latvia
| | - Kristaps Berzins
- Institute of Microbiology and Biotechnology, Computational Systems Biology Group, University of Latvia, Riga, Latvia
| | - Reinis Muiznieks
- Institute of Microbiology and Biotechnology, Computational Systems Biology Group, University of Latvia, Riga, Latvia
| | - Egils Stalidzans
- Institute of Microbiology and Biotechnology, Computational Systems Biology Group, University of Latvia, Riga, Latvia
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Arevalo Villa C, Marienhagen J, Noack S, Wahl SA. Achieving net zero CO 2 emission in the biobased production of reduced platform chemicals using defined co-feeding of methanol. Curr Opin Biotechnol 2023; 82:102967. [PMID: 37441841 DOI: 10.1016/j.copbio.2023.102967] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Revised: 06/13/2023] [Accepted: 06/20/2023] [Indexed: 07/15/2023]
Abstract
Next-generation bioprocesses of a future bio-based economy will rely on a flexible mix of readily available feedstocks. Renewable energy can be used to generate sustainable CO2-derived substrates. Metabolic engineering already enables the functional implementation of different pathways for the assimilation of C1 substrates in various microorganisms. In addition to feedstocks, the benchmark for all future bioprocesses will be sustainability, including the avoidance of CO2 emissions. Here we review recent advances in the utilization of C1-compounds from different perspectives, considering both strain and bioprocess engineering technologies. In particular, we evaluate methanol as a co-feed for enabling the CO2 emission-free production of acetyl-CoA-derived compounds. The possible metabolic strategies are analyzed using stoichiometric modeling combined with thermodynamic analysis and prospects for industrial-scale implementation are discussed.
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Affiliation(s)
- Carlos Arevalo Villa
- Lehrstuhl für Bioverfahrenstechnik, Friedrich Alexander Universität Erlangen-Nürnberg, D-91052 Erlangen, Germany
| | - Jan Marienhagen
- Institute of Bio, and Geosciences (IBG-1): Biotechnology, Forschungszentrum Jülich GmbH, D-52425 Jülich, Germany; Institute of Biotechnology, RWTH Aachen University, D-52074 Aachen, Germany
| | - Stephan Noack
- Institute of Bio, and Geosciences (IBG-1): Biotechnology, Forschungszentrum Jülich GmbH, D-52425 Jülich, Germany
| | - Sebastian Aljoscha Wahl
- Lehrstuhl für Bioverfahrenstechnik, Friedrich Alexander Universität Erlangen-Nürnberg, D-91052 Erlangen, Germany.
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Lopes A, Azevedo-Silva J, Carsanba E, Pintado M, Oliveira AS, Ferreira C, Pereira JO, Carvalho AP, Oliveira C. Peptide extract from spent yeast improves resistance of Saccharomyces cerevisiae to oxidative stress. Appl Microbiol Biotechnol 2023; 107:3405-3417. [PMID: 37086282 PMCID: PMC10175367 DOI: 10.1007/s00253-023-12514-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2022] [Revised: 03/24/2023] [Accepted: 03/29/2023] [Indexed: 04/23/2023]
Abstract
Yeast cells face various stress factors during industrial fermentations, since they are exposed to harsh environmental conditions, which may impair biomolecules productivity and yield. In this work, the use of an antioxidant peptide extract obtained from industrial spent yeast was explored as supplement for Saccharomyces cerevisiae fermentation to prevent a common bottleneck: oxidative stress. For that, a recombinant yeast strain, producer of β-farnesene, was firstly incubated with 0.5 and 0.7 g/L peptide extract, in the presence and absence of hydrogen peroxide (an oxidative stress inducer), for 1-5 h, and then assayed for intracellular reactive oxygen species, and growth ability in agar spot assays. Results showed that under 2 mM H2O2, the peptide extract could improve cells growth and reduce reactive oxygen species production. Therefore, this antioxidant effect was further evaluated in shake-flasks and 2-L bioreactor batch fermentations. Peptide extract (0.7 g/L) was able to increase yeast resistance to the oxidative stress promoted by 2 mM H2O2, by reducing reactive oxygen species levels between 1.2- and 1.7-fold in bioreactor and between 1.2- and 3-fold in shake-flask fermentations. Moreover, improvements on yeast cell density of up to 1.5-fold and 2-fold, and on biomolecule concentration of up to 1.6-fold and 2.8-fold, in bioreactor and shake-flasks, respectively, were obtained. Thus, culture medium supplementation with antioxidant peptide extracted from industrial spent yeast is a promising strategy to improve fermentation performance while valuing biomass waste. This valorization can promote a sustainable and eco-friendly solution for the biotechnology industry by the implementation of a circular economy model. KEY POINTS: • Peptide extract from spent yeast applied for the first time on yeast fermentation. • Antioxidant peptide extract enhanced S. cerevisiae oxidative stress resistance. • Fermentation performance under stress improved by peptide extract supplementation.
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Affiliation(s)
- Ana Lopes
- Amyris BioProducts Portugal, Unipessoal, Lda. Rua Diogo Botelho 1327, 4169-005, Porto, Portugal
- Universidade Católica Portuguesa, CBQF - Centro de Biotecnologia e Química Fina - Laboratório Associado, Escola Superior de Biotecnologia, Rua Diogo Botelho 1327, 4169-005, Porto, Portugal
| | - João Azevedo-Silva
- Universidade Católica Portuguesa, CBQF - Centro de Biotecnologia e Química Fina - Laboratório Associado, Escola Superior de Biotecnologia, Rua Diogo Botelho 1327, 4169-005, Porto, Portugal
| | - Erdem Carsanba
- Amyris BioProducts Portugal, Unipessoal, Lda. Rua Diogo Botelho 1327, 4169-005, Porto, Portugal.
- Universidade Católica Portuguesa, CBQF - Centro de Biotecnologia e Química Fina - Laboratório Associado, Escola Superior de Biotecnologia, Rua Diogo Botelho 1327, 4169-005, Porto, Portugal.
| | - Manuela Pintado
- Universidade Católica Portuguesa, CBQF - Centro de Biotecnologia e Química Fina - Laboratório Associado, Escola Superior de Biotecnologia, Rua Diogo Botelho 1327, 4169-005, Porto, Portugal
| | - Ana Sofia Oliveira
- Universidade Católica Portuguesa, CBQF - Centro de Biotecnologia e Química Fina - Laboratório Associado, Escola Superior de Biotecnologia, Rua Diogo Botelho 1327, 4169-005, Porto, Portugal
| | - Carlos Ferreira
- Amyris BioProducts Portugal, Unipessoal, Lda. Rua Diogo Botelho 1327, 4169-005, Porto, Portugal
- Universidade Católica Portuguesa, CBQF - Centro de Biotecnologia e Química Fina - Laboratório Associado, Escola Superior de Biotecnologia, Rua Diogo Botelho 1327, 4169-005, Porto, Portugal
| | - Joana Odila Pereira
- Amyris BioProducts Portugal, Unipessoal, Lda. Rua Diogo Botelho 1327, 4169-005, Porto, Portugal
- Universidade Católica Portuguesa, CBQF - Centro de Biotecnologia e Química Fina - Laboratório Associado, Escola Superior de Biotecnologia, Rua Diogo Botelho 1327, 4169-005, Porto, Portugal
| | - Ana P Carvalho
- Universidade Católica Portuguesa, CBQF - Centro de Biotecnologia e Química Fina - Laboratório Associado, Escola Superior de Biotecnologia, Rua Diogo Botelho 1327, 4169-005, Porto, Portugal
| | - Carla Oliveira
- Universidade Católica Portuguesa, CBQF - Centro de Biotecnologia e Química Fina - Laboratório Associado, Escola Superior de Biotecnologia, Rua Diogo Botelho 1327, 4169-005, Porto, Portugal.
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Stikane A, Dace E, Stalidzans E. Closing the loop in bioproduction: Spent Microbial Biomass as a resource within circular bioeconomy. N Biotechnol 2022; 70:109-115. [DOI: 10.1016/j.nbt.2022.06.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Revised: 04/15/2022] [Accepted: 06/03/2022] [Indexed: 11/30/2022]
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A Review on the Production of C4 Platform Chemicals from Biochemical Conversion of Sugar Crop Processing Products and By-Products. FERMENTATION-BASEL 2022. [DOI: 10.3390/fermentation8050216] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
The development and commercialization of sustainable chemicals from agricultural products and by-products is necessary for a circular economy built on renewable natural resources. Among the largest contributors to the final cost of a biomass conversion product is the cost of the initial biomass feedstock, representing a significant challenge in effective biomass utilization. Another major challenge is in identifying the correct products for development, which must be able to satisfy the need for both low-cost, drop-in fossil fuel replacements and novel, high-value fine chemicals (and/or commodity chemicals). Both challenges can be met by utilizing wastes or by-products from biomass processing, which have very limited starting cost, to yield platform chemicals. Specifically, sugar crop processing (e.g., sugarcane, sugar beet) is a mature industry that produces high volumes of by-products with significant potential for valorization. This review focuses specifically on the production of acetoin (3-hydroxybutanone), 2,3-butanediol, and C4 dicarboxylic (succinic, malic, and fumaric) acids with emphasis on biochemical conversion and targeted upgrading of sugar crop products/by-products. These C4 compounds are easily derived from fermentations and can be converted into many different final products, including food, fragrance, and cosmetic additives, as well as sustainable biofuels and other chemicals. State-of-the-art literature pertaining to optimization strategies for microbial conversion of sugar crop byproducts to C4 chemicals (e.g., bagasse, molasses) is reviewed, along with potential routes for upgrading and valorization. Directions and opportunities for future research and industrial biotechnology development are discussed.
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Berzins K, Muiznieks R, Baumanis MR, Strazdina I, Shvirksts K, Prikule S, Galvanauskas V, Pleissner D, Pentjuss A, Grube M, Kalnenieks U, Stalidzans E. Kinetic and Stoichiometric Modeling-Based Analysis of Docosahexaenoic Acid (DHA) Production Potential by C. cohnii from Glycerol, Glucose and Ethanol. Mar Drugs 2022; 20:md20020115. [PMID: 35200644 PMCID: PMC8879253 DOI: 10.3390/md20020115] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2022] [Revised: 01/26/2022] [Accepted: 01/28/2022] [Indexed: 11/16/2022] Open
Abstract
Docosahexaenoic acid (DHA) is one of the most important long-chain polyunsaturated fatty acids (LC-PUFAs), with numerous health benefits. Crypthecodinium cohnii, a marine heterotrophic dinoflagellate, is successfully used for the industrial production of DHA because it can accumulate DHA at high concentrations within the cells. Glycerol is an interesting renewable substrate for DHA production since it is a by-product of biodiesel production and other industries, and is globally generated in large quantities. The DHA production potential from glycerol, ethanol and glucose is compared by combining fermentation experiments with the pathway-scale kinetic modeling and constraint-based stoichiometric modeling of C. cohnii metabolism. Glycerol has the slowest biomass growth rate among the tested substrates. This is partially compensated by the highest PUFAs fraction, where DHA is dominant. Mathematical modeling reveals that glycerol has the best experimentally observed carbon transformation rate into biomass, reaching the closest values to the theoretical upper limit. In addition to our observations, the published experimental evidence indicates that crude glycerol is readily consumed by C. cohnii, making glycerol an attractive substrate for DHA production.
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Affiliation(s)
- Kristaps Berzins
- Institute of Microbiology and Biotechnology, University of Latvia, Jelgavas Street 1, LV-1004 Riga, Latvia; (K.B.); (R.M.); (M.R.B.); (I.S.); (K.S.); (S.P.); (A.P.); (M.G.); (U.K.)
| | - Reinis Muiznieks
- Institute of Microbiology and Biotechnology, University of Latvia, Jelgavas Street 1, LV-1004 Riga, Latvia; (K.B.); (R.M.); (M.R.B.); (I.S.); (K.S.); (S.P.); (A.P.); (M.G.); (U.K.)
| | - Matiss R. Baumanis
- Institute of Microbiology and Biotechnology, University of Latvia, Jelgavas Street 1, LV-1004 Riga, Latvia; (K.B.); (R.M.); (M.R.B.); (I.S.); (K.S.); (S.P.); (A.P.); (M.G.); (U.K.)
| | - Inese Strazdina
- Institute of Microbiology and Biotechnology, University of Latvia, Jelgavas Street 1, LV-1004 Riga, Latvia; (K.B.); (R.M.); (M.R.B.); (I.S.); (K.S.); (S.P.); (A.P.); (M.G.); (U.K.)
| | - Karlis Shvirksts
- Institute of Microbiology and Biotechnology, University of Latvia, Jelgavas Street 1, LV-1004 Riga, Latvia; (K.B.); (R.M.); (M.R.B.); (I.S.); (K.S.); (S.P.); (A.P.); (M.G.); (U.K.)
| | - Santa Prikule
- Institute of Microbiology and Biotechnology, University of Latvia, Jelgavas Street 1, LV-1004 Riga, Latvia; (K.B.); (R.M.); (M.R.B.); (I.S.); (K.S.); (S.P.); (A.P.); (M.G.); (U.K.)
| | - Vytautas Galvanauskas
- Biotehniskais Centrs AS, Dzerbenes Street 27, LV-1006 Riga, Latvia;
- Department of Automation, Kaunas University of Technology, LT-51367 Kaunas, Lithuania
| | - Daniel Pleissner
- Sustainable Chemistry (Resource Efciency), Institute of Sustainable and Environmental Chemistry, Leuphana University of Lüneburg, Universitätsallee 1, C13.203, 21335 Luneburg, Germany;
- Institute for Food and Environmental Research (ILU), Papendorfer Weg 3, 14806 Bad Belzig, Germany
| | - Agris Pentjuss
- Institute of Microbiology and Biotechnology, University of Latvia, Jelgavas Street 1, LV-1004 Riga, Latvia; (K.B.); (R.M.); (M.R.B.); (I.S.); (K.S.); (S.P.); (A.P.); (M.G.); (U.K.)
| | - Mara Grube
- Institute of Microbiology and Biotechnology, University of Latvia, Jelgavas Street 1, LV-1004 Riga, Latvia; (K.B.); (R.M.); (M.R.B.); (I.S.); (K.S.); (S.P.); (A.P.); (M.G.); (U.K.)
| | - Uldis Kalnenieks
- Institute of Microbiology and Biotechnology, University of Latvia, Jelgavas Street 1, LV-1004 Riga, Latvia; (K.B.); (R.M.); (M.R.B.); (I.S.); (K.S.); (S.P.); (A.P.); (M.G.); (U.K.)
| | - Egils Stalidzans
- Institute of Microbiology and Biotechnology, University of Latvia, Jelgavas Street 1, LV-1004 Riga, Latvia; (K.B.); (R.M.); (M.R.B.); (I.S.); (K.S.); (S.P.); (A.P.); (M.G.); (U.K.)
- Biotehniskais Centrs AS, Dzerbenes Street 27, LV-1006 Riga, Latvia;
- Correspondence: ; Tel.: +371-29575510
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