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Frohwitter J, Behrendt G, Klamt S, Bettenbrock K. A new Zymomonas mobilis platform strain for the efficient production of chemicals. Microb Cell Fact 2024; 23:143. [PMID: 38773442 PMCID: PMC11110354 DOI: 10.1186/s12934-024-02419-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2024] [Accepted: 05/07/2024] [Indexed: 05/23/2024] Open
Abstract
BACKGROUND Zymomonas mobilis is well known for its outstanding ability to produce ethanol with both high specific productivity and with high yield close to the theoretical maximum. The key enzyme in the ethanol production pathway is the pyruvate decarboxylase (PDC) which is converting pyruvate to acetaldehyde. Since it is widely considered that its gene pdc is essential, metabolic engineering strategies aiming to produce other compounds derived from pyruvate need to find ways to reduce PDC activity. RESULTS Here, we present a new platform strain (sGB027) of Z. mobilis in which the native promoter of pdc was replaced with the IPTG-inducible PT7A1, allowing for a controllable expression of pdc. Expression of lactate dehydrogenase from E. coli in sGB027 allowed the production of D-lactate with, to the best of our knowledge, the highest reported specific productivity of any microbial lactate producer as well as with the highest reported lactate yield for Z. mobilis so far. Additionally, by expressing the L-alanine dehydrogenase of Geobacillus stearothermophilus in sGB027 we produced L-alanine, further demonstrating the potential of sGB027 as a base for the production of compounds other than ethanol. CONCLUSION We demonstrated that our new platform strain can be an excellent starting point for the efficient production of various compounds derived from pyruvate with Z. mobilis and can thus enhance the establishment of this organism as a workhorse for biotechnological production processes.
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Affiliation(s)
- Jonas Frohwitter
- Analysis and Redesign of Biological Networks, Max Planck Institute for Dynamics of Complex Technical Systems, Sandtorstr. 1, 39106, Magdeburg, Germany
| | - Gerrich Behrendt
- Analysis and Redesign of Biological Networks, Max Planck Institute for Dynamics of Complex Technical Systems, Sandtorstr. 1, 39106, Magdeburg, Germany
| | - Steffen Klamt
- Analysis and Redesign of Biological Networks, Max Planck Institute for Dynamics of Complex Technical Systems, Sandtorstr. 1, 39106, Magdeburg, Germany
| | - Katja Bettenbrock
- Analysis and Redesign of Biological Networks, Max Planck Institute for Dynamics of Complex Technical Systems, Sandtorstr. 1, 39106, Magdeburg, Germany.
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2
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Ahmadpanah H, Motamedian E, Mardanpour MM. Metabolic regulation boosts bioelectricity generation in Zymomonas mobilis microbial fuel cell, surpassing ethanol production. Sci Rep 2023; 13:20673. [PMID: 38001147 PMCID: PMC10673858 DOI: 10.1038/s41598-023-47846-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2023] [Accepted: 11/19/2023] [Indexed: 11/26/2023] Open
Abstract
Zymomonas mobilis (Z. mobilis), a bacterium known for its ethanol production capabilities, can also generate electricity by transitioning from ethanol production to electron generation. The purpose of this study is to investigate the ability of Z. mobilis to produce bioelectricity when utilized as a biocatalyst in a single-chamber microbial fuel cell (MFC). Given the bacterium's strong inclination towards ethanol production, a metabolic engineering strategy was devised to identify key reactions responsible for redirecting electrons from ethanol towards electricity generation. To evaluate the electroactivity of cultured Z. mobilis and its ethanol production in the presence of regulators, the reduction of soluble Fe(III) was utilized. Among the regulators tested, CuCl2 demonstrated superior effectiveness. Consequently, the MFC was employed to analyze the electrochemical properties of Z. mobilis using both a minimal and modified medium. By modifying the bacterial medium, the maximum current and power density of the MFC fed with Z. mobilis increased by more than 5.8- and sixfold, respectively, compared to the minimal medium. These findings highlight the significant impact of metabolic redirection in enhancing the performance of MFCs. Furthermore, they establish Z. mobilis as an active electrogenesis microorganism capable of power generation in MFCs.
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Affiliation(s)
- Hananeh Ahmadpanah
- Department of Biotechnology, Faculty of Chemical Engineering, Tarbiat Modares University, P.O. Box 14115‑143, Tehran, Iran
| | - Ehsan Motamedian
- Department of Biotechnology, Faculty of Chemical Engineering, Tarbiat Modares University, P.O. Box 14115‑143, Tehran, Iran.
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3
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Graf von Westarp W, Wiesenthal J, Spöring JD, Mengers HG, Kasterke M, Koß HJ, Blank LM, Rother D, Klankermayer J, Jupke A. Interdisciplinary development of an overall process concept from glucose to 4,5-dimethyl-1,3-dioxolane via 2,3-butanediol. Commun Chem 2023; 6:253. [PMID: 37974008 PMCID: PMC10654704 DOI: 10.1038/s42004-023-01052-8] [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: 05/19/2023] [Accepted: 11/06/2023] [Indexed: 11/19/2023] Open
Abstract
To reduce carbon dioxide emissions, carbon-neutral fuels have recently gained renewed attention. Here we show the development and evaluation of process routes for the production of such a fuel, the cyclic acetal 4,5-dimethyl-1,3-dioxolane, from glucose via 2,3-butanediol. The selected process routes are based on the sequential use of microbes, enzymes and chemo-catalysts in order to exploit the full potential of the different catalyst systems through a tailor-made combination. The catalysts (microbes, enzymes, chemo-catalysts) and the reaction medium selected for each conversion step are key factors in the development of the respective production methods. The production of the intermediate 2,3-butanediol by combined microbial and enzyme catalysis is compared to the conventional microbial route from glucose in terms of specific energy demand and overall yield, with the conventional route remaining more efficient. In order to be competitive with current 2,3-butanediol production, the key performance indicator, enzyme stability to high aldehyde concentrations, needs to be increased. The target value for the enzyme stability is an acetaldehyde concentration of 600 mM, which is higher than the current maximum concentration (200 mM) by a factor of three.
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Affiliation(s)
- William Graf von Westarp
- Fluid Process Engineering (AVT.FVT), RWTH Aachen University, Forckenbeckstraße 51, 52074, Aachen, Germany
| | - Jan Wiesenthal
- Institute of Technical and Macromolecular Chemistry (ITMC), RWTH Aachen University, Worringerweg 2, 52074, Aachen, Germany
| | - Jan-Dirk Spöring
- Institute for Bio- and Geosciences Plant Sciences (IBG-1), Forschungszentrum Jülich GmbH, Wilhelm-Johnen-Straße, 52428, Jülich, Germany
- Aachen Biology and Biotechnology (ABBt), RWTH Aachen University, Worringerweg 3, 52074, Aachen, Germany
| | - Hendrik G Mengers
- Aachen Biology and Biotechnology (ABBt), RWTH Aachen University, Worringerweg 3, 52074, Aachen, Germany
- Institute of Applied Microbiology (iAMB), Aachen Biology and Biotechnology (ABBt), RWTH Aachen University, Worringerweg 1, 52074, Aachen, Germany
| | - Marvin Kasterke
- Institute of Technical Thermodynamics (LTT), RWTH Aachen University, Schinkelstraße 8, 52062, Aachen, Germany
| | - Hans-Jürgen Koß
- Institute of Technical Thermodynamics (LTT), RWTH Aachen University, Schinkelstraße 8, 52062, Aachen, Germany
| | - Lars M Blank
- Aachen Biology and Biotechnology (ABBt), RWTH Aachen University, Worringerweg 3, 52074, Aachen, Germany
- Institute of Applied Microbiology (iAMB), Aachen Biology and Biotechnology (ABBt), RWTH Aachen University, Worringerweg 1, 52074, Aachen, Germany
| | - Dörte Rother
- Institute for Bio- and Geosciences Plant Sciences (IBG-1), Forschungszentrum Jülich GmbH, Wilhelm-Johnen-Straße, 52428, Jülich, Germany
- Aachen Biology and Biotechnology (ABBt), RWTH Aachen University, Worringerweg 3, 52074, Aachen, Germany
| | - Jürgen Klankermayer
- Institute of Technical and Macromolecular Chemistry (ITMC), RWTH Aachen University, Worringerweg 2, 52074, Aachen, Germany.
| | - Andreas Jupke
- Fluid Process Engineering (AVT.FVT), RWTH Aachen University, Forckenbeckstraße 51, 52074, Aachen, Germany.
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4
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Pentjuss A, Bolmanis E, Suleiko A, Didrihsone E, Suleiko A, Dubencovs K, Liepins J, Kazaks A, Vanags J. Pichia pastoris growth-coupled heme biosynthesis analysis using metabolic modelling. Sci Rep 2023; 13:15816. [PMID: 37739976 PMCID: PMC10516909 DOI: 10.1038/s41598-023-42865-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Accepted: 09/15/2023] [Indexed: 09/24/2023] Open
Abstract
Soy leghemoglobin is one of the most important and key ingredients in plant-based meat substitutes that can imitate the colour and flavour of the meat. To improve the high-yield production of leghemoglobin protein and its main component-heme in the yeast Pichia pastoris, glycerol and methanol cultivation conditions were studied. Additionally, in-silico metabolic modelling analysis of growth-coupled enzyme quantity, suggests metabolic gene up/down-regulation strategies for heme production. First, cultivations and metabolic modelling analysis of P. pastoris were performed on glycerol and methanol in different growth media. Glycerol cultivation uptake and production rates can be increased by 50% according to metabolic modelling results, but methanol cultivation-is near the theoretical maximum. Growth-coupled metabolic optimisation results revealed the best feasible upregulation (33 reactions) (1.47% of total reactions) and 66 downregulation/deletion (2.98% of total) reaction suggestions. Finally, we describe reaction regulation suggestions with the highest potential to increase heme production yields.
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Affiliation(s)
- Agris Pentjuss
- Microbiology and Biotechnology Institute, University of Latvia, Jelgavas Street 1, Riga, 1004, Latvia.
- Latvian State Institute of Wood Chemistry, Dzerbenes Street 27, Riga, 1006, Latvia.
| | - Emils Bolmanis
- Latvian Biomedical Research and Study Centre, Ratsupites Street 1 K-1, Riga, 1067, Latvia
| | - Anastasija Suleiko
- Latvian State Institute of Wood Chemistry, Dzerbenes Street 27, Riga, 1006, Latvia
- Bioreactors.Net AS, Dzerbenes Street 27, Riga, 1006, Latvia
| | - Elina Didrihsone
- Latvian State Institute of Wood Chemistry, Dzerbenes Street 27, Riga, 1006, Latvia
| | - Arturs Suleiko
- Latvian State Institute of Wood Chemistry, Dzerbenes Street 27, Riga, 1006, Latvia
- Bioreactors.Net AS, Dzerbenes Street 27, Riga, 1006, Latvia
| | - Konstantins Dubencovs
- Latvian State Institute of Wood Chemistry, Dzerbenes Street 27, Riga, 1006, Latvia
- Bioreactors.Net AS, Dzerbenes Street 27, Riga, 1006, Latvia
| | - Janis Liepins
- Microbiology and Biotechnology Institute, University of Latvia, Jelgavas Street 1, Riga, 1004, Latvia
| | - Andris Kazaks
- Latvian Biomedical Research and Study Centre, Ratsupites Street 1 K-1, Riga, 1067, Latvia
| | - Juris Vanags
- Latvian State Institute of Wood Chemistry, Dzerbenes Street 27, Riga, 1006, Latvia
- Bioreactors.Net AS, Dzerbenes Street 27, Riga, 1006, Latvia
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5
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Wu Y, Yuan Q, Yang Y, Liu D, Yang S, Ma H. Construction and application of high-quality genome-scale metabolic model of Zymomonas mobilis to guide rational design of microbial cell factories. Synth Syst Biotechnol 2023; 8:498-508. [PMID: 37554249 PMCID: PMC10404502 DOI: 10.1016/j.synbio.2023.07.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2023] [Revised: 07/04/2023] [Accepted: 07/04/2023] [Indexed: 08/10/2023] Open
Abstract
High-quality genome-scale metabolic models (GEMs) could play critical roles on rational design of microbial cell factories in the classical Design-Build-Test-Learn cycle of synthetic biology studies. Despite of the constant establishment and update of GEMs for model microorganisms such as Escherichia coli and Saccharomyces cerevisiae, high-quality GEMs for non-model industrial microorganisms are still scarce. Zymomonas mobilis subsp. mobilis ZM4 is a non-model ethanologenic microorganism with many excellent industrial characteristics that has been developing as microbial cell factories for biochemical production. Although five GEMs of Z. mobilis have been constructed, these models are either generating ATP incorrectly, or lacking information of plasmid genes, or not providing standard format file. In this study, a high-quality GEM iZM516 of Z. mobilis ZM4 was constructed. The information from the improved genome annotation, literature, datasets of Biolog Phenotype Microarray studies, and recently updated Gene-Protein-Reaction information was combined for the curation of iZM516. Finally, 516 genes, 1389 reactions, 1437 metabolites, and 3 cell compartments are included in iZM516, which also had the highest MEMOTE score of 91% among all published GEMs of Z. mobilis. Cell growth was then predicted by iZM516, which had 79.4% agreement with the experimental results of the substrate utilization. In addition, the potential endogenous succinate synthesis pathway of Z. mobilis ZM4 was proposed through simulation and analysis using iZM516. Furthermore, metabolic engineering strategies to produce succinate and 1,4-butanediol (1,4-BDO) were designed and then simulated under anaerobic condition using iZM516. The results indicated that 1.68 mol/mol succinate and 1.07 mol/mol 1,4-BDO can be achieved through combinational metabolic engineering strategies, which was comparable to that of the model species E. coli. Our study thus not only established a high-quality GEM iZM516 to help understand and design microbial cell factories for economic biochemical production using Z. mobilis as the chassis, but also provided guidance on building accurate GEMs for other non-model industrial microorganisms.
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Affiliation(s)
- Yalun Wu
- State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Wuhan, 430062, Hubei, China
| | - Qianqian Yuan
- Biodesign Center, Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China
| | - Yongfu Yang
- State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Wuhan, 430062, Hubei, China
- Hubei Key Laboratory of Applied Mathematics, Faculty of Mathematics and Statistics, Hubei University, Wuhan, 430062, Hubei, China
- Artificial Intelligence and Knowledge Engineering Lab, School of Computer Science and Information Engineering, Hubei University, Wuhan, 430062, Hubei, China
| | - Defei Liu
- Biodesign Center, Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China
| | - Shihui Yang
- State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Wuhan, 430062, Hubei, China
| | - Hongwu Ma
- Biodesign Center, Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China
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6
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Grausa K, Siddiqui SA, Lameyer N, Wiesotzki K, Smetana S, Pentjuss A. Metabolic Modeling of Hermetia illucens Larvae Resource Allocation for High-Value Fatty Acid Production. Metabolites 2023; 13:724. [PMID: 37367882 DOI: 10.3390/metabo13060724] [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: 03/21/2023] [Revised: 05/31/2023] [Accepted: 06/01/2023] [Indexed: 06/28/2023] Open
Abstract
All plant and animal kingdom organisms use highly connected biochemical networks to facilitate sustaining, proliferation, and growth functions. While the biochemical network details are well known, the understanding of the intense regulation principles is still limited. We chose to investigate the Hermetia illucens fly at the larval stage because this stage is a crucial period for the successful accumulation and allocation of resources for the subsequent organism's developmental stages. We combined iterative wet lab experiments and innovative metabolic modeling design approaches to simulate and explain the H. illucens larval stage resource allocation processes and biotechnology potential. We performed time-based growth and high-value chemical compound accumulation wet lab chemical analysis experiments on larvae and the Gainesville diet composition. We built and validated the first H. illucens medium-size, stoichiometric metabolic model to predict the effects of diet-based alterations on fatty acid allocation potential. Using optimization methods such as flux balance and flux variability analysis on the novel insect metabolic model, we predicted that doubled essential amino acid consumption increased the growth rate by 32%, but pure glucose consumption had no positive impact on growth. In the case of doubled pure valine consumption, the model predicted a 2% higher growth rate. In this study, we describe a new framework for researching the impact of dietary alterations on the metabolism of multi-cellular organisms at different developmental stages for improved, sustainable, and directed high-value chemicals.
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Affiliation(s)
- Kristina Grausa
- Department of Computer Systems, Latvia University of Life Sciences and Technologies, LV-3001 Jelgava, Latvia
- Institute of Microbiology and Biotechnology, University of Latvia, LV-1050 Riga, Latvia
| | - Shahida A Siddiqui
- Campus Straubing for Biotechnology and Sustainability, Technical University of Munich, Essigberg 3, D-94315 Straubing, Germany
- German Institute of Food Technologies (DIL e.V.), 49610 Quakenbrück, Germany
| | - Norbert Lameyer
- German Institute of Food Technologies (DIL e.V.), 49610 Quakenbrück, Germany
| | - Karin Wiesotzki
- German Institute of Food Technologies (DIL e.V.), 49610 Quakenbrück, Germany
| | - Sergiy Smetana
- German Institute of Food Technologies (DIL e.V.), 49610 Quakenbrück, Germany
| | - Agris Pentjuss
- Department of Computer Systems, Latvia University of Life Sciences and Technologies, LV-3001 Jelgava, Latvia
- Institute of Microbiology and Biotechnology, University of Latvia, LV-1050 Riga, Latvia
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Improved Hydrogen Peroxide Stress Resistance of Zymomonas mobilis NADH Dehydrogenase (ndh) and Alcohol Dehydrogenase (adhB) Mutants. FERMENTATION-BASEL 2022. [DOI: 10.3390/fermentation8060289] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Unintended shifts in stress resistance of microbial strains with engineered central metabolism may impact their growth and production performance under oxidative, lignocellulosic, solvent, and other stress conditions, and as such, must be taken into account in bioprocess design. In the present work, we studied oxidative stress resistance in mutant strains of the facultatively anaerobic, ethanologenic bacterium Zymomonas mobilis with modified respiratory (inactivated NADH dehydrogenase Ndh, by disruption of ndh) and ethanologenic (inactivated iron-containing alcohol dehydrogenase isoenzyme ADH II, by disruption of adhB) catabolism, using exogenously added H2O2 in the concentration range of 2–6 mM as the oxidative stressor. Both mutations improved H2O2 resistance and enhanced catalase activity by a factor of 2–5, while the overexpression of Ndh had an opposite effect. Strains with a catalase-negative background were unable to grow already at 1 mM hydrogen peroxide, and their H2O2 resistance did not depend on AdhB or Ndh expression levels. Hence, the improved resistance of the ndh and adhB mutants to H2O2 resulted from their elevated catalase activity. The interrelation between these mutations, the catabolic redox balance, catalase activity, and oxidative stress defense in Z. mobilis is discussed.
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Grausa K, Mozga I, Pleiko K, Pentjuss A. Integrative Gene Expression and Metabolic Analysis Tool IgemRNA. Biomolecules 2022; 12:biom12040586. [PMID: 35454176 PMCID: PMC9029533 DOI: 10.3390/biom12040586] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2022] [Revised: 04/11/2022] [Accepted: 04/14/2022] [Indexed: 01/27/2023] Open
Abstract
Genome-scale metabolic modeling is widely used to study the impact of metabolism on the phenotype of different organisms. While substrate modeling reflects the potential distribution of carbon and other chemical elements within the model, the additional use of omics data, e.g., transcriptome, has implications when researching the genotype–phenotype responses to environmental changes. Several algorithms for transcriptome analysis using genome-scale metabolic modeling have been proposed. Still, they are restricted to specific objectives and conditions and lack flexibility, have software compatibility issues, and require advanced user skills. We classified previously published algorithms, summarized transcriptome pre-processing, integration, and analysis methods, and implemented them in the newly developed transcriptome analysis tool IgemRNA, which (1) has a user-friendly graphical interface, (2) tackles compatibility issues by combining previous data input and pre-processing algorithms in MATLAB, and (3) introduces novel algorithms for the automatic comparison of different transcriptome datasets with or without Cobra Toolbox 3.0 optimization algorithms. We used publicly available transcriptome datasets from Saccharomyces cerevisiae BY4741 and H4-S47D strains for validation. We found that IgemRNA provides a means for transcriptome and environmental data validation on biochemical network topology since the biomass function varies for different phenotypes. Our tool can detect problematic reaction constraints.
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Affiliation(s)
- Kristina Grausa
- Department of Computer Systems, Latvia University of Life Sciences and Technologies, Liela Street 2, LV-3001 Jelgava, Latvia; (K.G.); (I.M.)
| | - Ivars Mozga
- Department of Computer Systems, Latvia University of Life Sciences and Technologies, Liela Street 2, LV-3001 Jelgava, Latvia; (K.G.); (I.M.)
| | - Karlis Pleiko
- Laboratory of Precision and Nanomedicine, Institute of Biomedicine and Translational Medicine, University of Tartu, 50411 Tartu, Estonia;
- Faculty of Medicine, University of Latvia, LV-1586 Riga, Latvia
| | - Agris Pentjuss
- Institute of Microbiology and Biotechnology, University of Latvia, Jelgavas Street 1, LV-1004 Riga, Latvia
- Correspondence:
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Zymomonas mobilis ZM4 Utilizes an NADP +-Dependent Acetaldehyde Dehydrogenase To Produce Acetate. J Bacteriol 2022; 204:e0056321. [PMID: 35258321 PMCID: PMC9017298 DOI: 10.1128/jb.00563-21] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Zymomonas mobilis is a promising bacterial host for biofuel production, but further improvement has been hindered because some aspects of its metabolism remain poorly understood. For example, one of the main by-products generated by Z. mobilis is acetate, but the pathway for acetate production is unknown. Acetaldehyde oxidation has been proposed as the major source of acetate, and an acetaldehyde dehydrogenase was previously isolated from Z. mobilis via activity guided fractionation, but the corresponding gene has never been identified. We determined that the locus ZMO1754 (also known as ZMO_RS07890) encodes an NADP+-dependent acetaldehyde dehydrogenase that is responsible for acetate production by Z. mobilis. Deletion of this gene from the chromosome resulted in a growth defect in oxic conditions, suggesting that acetaldehyde detoxification is an important role of acetaldehyde dehydrogenase. The deletion strain also exhibited a near complete abolition of acetate production, both in typical laboratory conditions and during lignocellulosic hydrolysate fermentation. Our results show that ZMO1754 encodes the major acetate-forming acetaldehyde dehydrogenase in Z. mobilis, and we therefore rename the gene aldB based on functional similarity to the Escherichia coli acetaldehyde dehydrogenase. IMPORTANCE Biofuel production from nonfood crops is an important strategy for reducing carbon emissions from the transportation industry, but it has not yet become commercially viable. An important avenue to improve biofuel production is to enhance the characteristics of fermentation organisms by decreasing by-product formation via genetic engineering. Here, we identified and deleted a metabolic pathway and associated gene that lead to acetate formation in Zymomonas mobilis. Acetate is one of the major by-products generated during ethanol production by Z. mobilis, so this information may be used in the future to develop better strains for commercial biofuel production.
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10
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Antimicrobial Activity of Zymomonas mobilis Is Related to Its Aerobic Catabolism and Acid Resistance. FERMENTATION-BASEL 2022. [DOI: 10.3390/fermentation8020077] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Zymomonas mobilis is an ethanologenic, facultatively anaerobic alpha-proteobacterium, known for its inhibitory effect on the growth of a wide variety of microorganisms. This property might be interesting for the design of novel antimicrobials, yet it has negative implications for biotechnology, as it hinders the use of Z. mobilis as a producer microorganism in cocultivation. So far, the chemical nature of its inhibitory compound(s) has not been established. In the present study, we demonstrate that the putative inhibitor is a low-molecular-weight (below 3 kDa), thermostable compound, resistant to protease treatment, which is synthesized under aerobic conditions in Z. mobilis strains via the active respiratory chain. It is also synthesized by aerated nongrowing, glucose-consuming cells in the presence of chloramphenicol, thus ruling out its bacteriocin-like peptide nature. The inhibitory activity is pH-dependent and strongly correlated with the accumulation of propionate and acetate in the culture medium. Although, in Z. mobilis, the synthesis pathways of these acids still need to be identified, the acid production depends on respiration, and is much less pronounced in the non-respiring mutant strain, which shows low inhibitory activity. We conclude that propionate and acetate play a central role in the antimicrobial effects of Z. mobilis, which itself is known to bear high resistance to organic acids.
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Yeast-based production and in situ purification of acetaldehyde. Bioprocess Biosyst Eng 2022; 45:761-769. [PMID: 35137261 PMCID: PMC8948146 DOI: 10.1007/s00449-022-02697-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2021] [Accepted: 01/19/2022] [Indexed: 12/31/2022]
Abstract
Acetaldehyde is a platform chemical with a production volume of more than 1 Mt/a, but is chiefly synthesized from petrochemical feedstocks. We propose the fermentative conversion of glucose towards acetaldehyde via genetically modified S. cerevisiae. This allows for ethanol-free bioactaldehyde production. Exploiting the high volatility of the product, in situ gas stripping in an aerated reactor is inevitable and crucial due to the respiratory toxicity effects of the acetaldehyde overproduction. We devise a lab-scale setup for the recovery of the product from the off-gas. Water was chosen as a suitable solvent and the Henry coefficient of acetaldehyde in water was validated experimentally. Based on an experimentally verified capture efficiency of 75%, an acetaldehyde production rate of over 100 mg/g/h was reached in 200 mL lab-scale fermentations.
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12
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Martien JI, Trujillo EA, Jacobson TB, Tatli M, Hebert AS, Stevenson DM, Coon JJ, Amador-Noguez D. Metabolic Remodeling during Nitrogen Fixation in Zymomonas mobilis. mSystems 2021; 6:e0098721. [PMID: 34783580 PMCID: PMC8594446 DOI: 10.1128/msystems.00987-21] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2021] [Accepted: 10/06/2021] [Indexed: 11/20/2022] Open
Abstract
Zymomonas mobilis is an ethanologenic bacterium currently being developed for production of advanced biofuels. Recent studies have shown that Z. mobilis can fix dinitrogen gas (N2) as a sole nitrogen source. During N2 fixation, Z. mobilis exhibits increased biomass-specific rates of ethanol production. In order to better understand the physiology of Z. mobilis during N2 fixation and during changes in ammonium (NH4+) availability, we performed liquid chromatography-mass spectrometry (LC-MS)-based targeted metabolomics and shotgun proteomics under three regimes of nitrogen availability: continuous N2 fixation, gradual NH4+ depletion, and acute NH4+ addition to N2-fixing cells. We report dynamic changes in abundance of proteins and metabolites related to nitrogen fixation, motility, ammonium assimilation, amino acid biosynthesis, nucleotide biosynthesis, isoprenoid biosynthesis, and Entner-Doudoroff (ED) glycolysis, providing insight into the regulatory mechanisms that control these processes in Z. mobilis. Our analysis identified potential physiological mechanisms that may contribute to increased specific ethanol production during N2 fixation, including decreased activity of biosynthetic pathways, increased protein abundance of alcohol dehydrogenase (ADHI), and increased thermodynamic favorability of the ED pathway. Of particular relevance to advanced biofuel production, we found that intermediates in the methylerythritol phosphate (MEP) pathway for isoprenoid biosynthesis were depleted during N2 fixation, coinciding with decreased protein abundance of deoxyxylulose 5-phosphate synthase (DXS), the first enzyme in the pathway. This implies that DXS protein abundance serves as a native control point in regulating MEP pathway activity in Z. mobilis. The results of this study will inform metabolic engineering to further develop Z. mobilis as a platform organism for biofuel production. IMPORTANCE Biofuels and bioproducts have the potential to serve as environmentally sustainable replacements for petroleum-derived fuels and commodity molecules. Advanced fuels such as higher alcohols and isoprenoids are more suitable gasoline replacements than bioethanol. Developing microbial systems to generate advanced biofuels requires metabolic engineering to reroute carbon away from ethanol and other native products and toward desired pathways, such as the MEP pathway for isoprenoid biosynthesis. However, rational engineering of microbial metabolism relies on understanding metabolic control points, in terms of both enzyme activity and thermodynamic favorability. In Z. mobilis, the factors that control glycolytic rates, ethanol production, and isoprenoid production are still not fully understood. In this study, we performed metabolomic, proteomic, and thermodynamic analysis of Z. mobilis during N2 fixation. This analysis identified key changes in metabolite levels, enzyme abundance, and glycolytic thermodynamic favorability that occurred during changes in NH4+ availability, helping to inform future efforts in metabolic engineering.
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Affiliation(s)
- Julia I. Martien
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin–Madison, Madison, Wisconsin, USA
- Department of Bacteriology, University of Wisconsin–Madison, Madison, Wisconsin, USA
| | - Edna A. Trujillo
- Department of Chemistry, University of Wisconsin–Madison, Madison, Wisconsin, USA
- National Center for Quantitative Biology of Complex Systems, University of Wisconsin–Madison, Madison, Wisconsin, USA
| | - Tyler B. Jacobson
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin–Madison, Madison, Wisconsin, USA
- Department of Bacteriology, University of Wisconsin–Madison, Madison, Wisconsin, USA
| | - Mehmet Tatli
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin–Madison, Madison, Wisconsin, USA
- Department of Bacteriology, University of Wisconsin–Madison, Madison, Wisconsin, USA
| | - Alexander S. Hebert
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin–Madison, Madison, Wisconsin, USA
- Department of Chemistry, University of Wisconsin–Madison, Madison, Wisconsin, USA
| | - David M. Stevenson
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin–Madison, Madison, Wisconsin, USA
- Department of Bacteriology, University of Wisconsin–Madison, Madison, Wisconsin, USA
| | - Joshua J. Coon
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin–Madison, Madison, Wisconsin, USA
- Department of Chemistry, University of Wisconsin–Madison, Madison, Wisconsin, USA
- National Center for Quantitative Biology of Complex Systems, University of Wisconsin–Madison, Madison, Wisconsin, USA
- Department of Biomolecular Chemistry, University of Wisconsin–Madison, Madison, Wisconsin, USA
- Morgridge Institute for Research, Madison, Wisconsin, USA
| | - Daniel Amador-Noguez
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin–Madison, Madison, Wisconsin, USA
- Department of Bacteriology, University of Wisconsin–Madison, Madison, Wisconsin, USA
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Petrovs R, Stalidzans E, Pentjuss A. IMFLer: A Web Application for Interactive Metabolic Flux Analysis and Visualization. J Comput Biol 2021; 28:1021-1032. [PMID: 34424732 DOI: 10.1089/cmb.2021.0056] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Increasing genome-wide data in biological sciences and medicine has contributed to the development of a variety of visualization tools. Several automatic, semiautomatic, and manual visualization tools have already been developed. Some even have integrated flux balance analysis (FBA), but in most cases, it depends on separately installed third party software that is proprietary and does not allow customization of its functionality and has many restrictions for easy data distribution and analysis. In this study, we present an interactive metabolic flux analyzer and visualizer (IMFLer)-a static single-page web application that enables the reading and management of metabolic model layout maps, as well as immediate visualization of results from both FBA and flux variability analysis (FVA). IMFLer uses the Escher Builder tool to load, show, edit, and save metabolic pathway maps. This makes IMFLer an attractive and easily applicable tool with a user-friendly interface. Moreover, it allows to faster interpret results from FBA and FVA and improves data interoperability by using a standardized file format for the genome-scale metabolic model. IMFLer is a fully open-source tool that enables the rapid visualization and interpretation of the results of FBA and FVA with no time setup and no programming skills required, available at https://lv-csbg.github.io/IMFLer/.
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Affiliation(s)
- Rudolfs Petrovs
- Computational Systems Biology Group, Institute of Microbiology and Biotechnology, University of Latvia, Riga, Latvia
| | - Egils Stalidzans
- Computational Systems Biology Group, Institute of Microbiology and Biotechnology, University of Latvia, Riga, Latvia.,Biosystems Group, Department of Computer Systems, Latvia University of Life Sciences and Technologies, Jelgava, Latvia
| | - Agris Pentjuss
- Computational Systems Biology Group, Institute of Microbiology and Biotechnology, University of Latvia, Riga, Latvia
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Fuchino K, Wasser D, Soppa J. Genome Copy Number Quantification Revealed That the Ethanologenic Alpha-Proteobacterium Zymomonas mobilis Is Polyploid. Front Microbiol 2021; 12:705895. [PMID: 34408736 PMCID: PMC8365228 DOI: 10.3389/fmicb.2021.705895] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2021] [Accepted: 07/07/2021] [Indexed: 11/20/2022] Open
Abstract
The alpha-proteobacterium Zymomonas mobilis is a promising biofuel producer, based on its native metabolism that efficiently converts sugars to ethanol. Therefore, it has a high potential for industrial-scale biofuel production. Two previous studies suggested that Z. mobilis strain Zm4 might not be monoploid. However, a systematic analysis of the genome copy number is still missing, in spite of the high potential importance of Z. mobilis. To get a deep insight into the ploidy level of Z. mobilis and its regulation, the genome copy numbers of three strains were quantified. The analyses revealed that, during anaerobic growth, the lab strain Zm6, the Zm6 type strain obtained from DSMZ (German Collection of Microorganisms), and the lab strain Zm4, have copy numbers of 18.9, 22.3 and 16.2, respectively, of an origin-adjacent region. The copy numbers of a terminus-adjacent region were somewhat lower with 9.3, 15.8, and 12.9, respectively. The values were similar throughout the growth curves, and they were only slightly downregulated in late stationary phase. During aerobic growth, the copy numbers of the lab strain Zm6 were much higher with around 40 origin-adjacent copies and 17 terminus-adjacent copies. However, the cells were larger during aerobic growth, and the copy numbers per μm3 cell volume were rather similar. Taken together, this first systematic analysis revealed that Z. mobilis is polyploid under regular laboratory growth conditions. The copy number is constant during growth, in contrast to many other polyploid bacteria. This knowledge should be considered in further engineering of the strain for industrial applications.
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Affiliation(s)
- Katsuya Fuchino
- Institute for Molecular Biosciences, Goethe-University, Frankfurt, Germany.,Department of Biotechnology and Food Science, NTNU Norwegian University of Science and Technology, Trondheim, Norway
| | - Daniel Wasser
- Institute for Molecular Biosciences, Goethe-University, Frankfurt, Germany
| | - Jörg Soppa
- Institute for Molecular Biosciences, Goethe-University, Frankfurt, Germany
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15
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Strazdina I, Klavins L, Galinina N, Shvirksts K, Grube M, Stalidzans E, Kalnenieks U. Syntrophy of Crypthecodinium cohnii and immobilized Zymomonas mobilis for docosahexaenoic acid production from sucrose-containing substrates. J Biotechnol 2021; 338:63-70. [PMID: 34280360 DOI: 10.1016/j.jbiotec.2021.07.008] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2021] [Revised: 07/10/2021] [Accepted: 07/13/2021] [Indexed: 11/17/2022]
Abstract
Marine heterotrophic dinoflagellate Crypthecodinium cohnii is an aerobic oleaginous microorganism that accumulates intracellular lipid with high content of 4,7,10,13,16,19-docosahexaenoic acid (DHA), a polyunsaturated ω-3 (22:6) fatty acid with multiple health benefits. C. cohnii can grow on glucose and ethanol, but not on sucrose or fructose. For conversion of sucrose-containing renewables to C. cohnii DHA, we investigated a syntrophic process, involving immobilized cells of ethanologenic bacterium Zymomonas mobilis for fermenting sucrose to ethanol. The non-respiring, NADH dehydrogenase-deficient Z. mobilis strain Zm6-ndh, with high ethanol yield both under anaerobic and aerobic conditions, was taken as the genetic background for inactivation of levansucrase (sacB). SacB mutation eliminated the levan-forming activity on sucrose. The double mutant Zm6-ndh-sacB cells were immobilized in Ca alginate, and applied for syntrophic conversion of sucrose to DHA of C. cohnii, either taking the ethanol-containing fermentation medium from the immobilized Z. mobilis for feeding to the C. cohnii fed-batch culture, or directly coculturing the immobilized Zm6-ndh-sacB with C. cohnii on sucrose. Both modes of cultivation produced C. cohnii CCMP 316 biomass with DHA content around 2-3 % of cell dry weight, corresponding to previously reported results for this strain on glucose.
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Affiliation(s)
- Inese Strazdina
- University of Latvia, Institute of Microbiology and Biotechnology, Riga, Latvia
| | - Linards Klavins
- University of Latvia, Natural Resource Research Centre, Riga, Latvia
| | - Nina Galinina
- University of Latvia, Institute of Microbiology and Biotechnology, Riga, Latvia
| | - Karlis Shvirksts
- University of Latvia, Institute of Microbiology and Biotechnology, Riga, Latvia
| | - Mara Grube
- University of Latvia, Institute of Microbiology and Biotechnology, Riga, Latvia
| | - Egils Stalidzans
- University of Latvia, Institute of Microbiology and Biotechnology, Riga, Latvia
| | - Uldis Kalnenieks
- University of Latvia, Institute of Microbiology and Biotechnology, Riga, Latvia.
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Rutkis R, Strazdina I, Lasa Z, Bruheim P, Kalnenieks U. Ethanologenesis and respiration in a pyruvate decarboxylase-deficient Zymomonas mobilis. BMC Res Notes 2021; 14:208. [PMID: 34049566 PMCID: PMC8161578 DOI: 10.1186/s13104-021-05625-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2021] [Accepted: 05/19/2021] [Indexed: 11/10/2022] Open
Abstract
Objective Zymomonas mobilis is an alpha-proteobacterium with a rapid ethanologenic pathway, involving Entner–Doudoroff (E–D) glycolysis, pyruvate decarboxylase (Pdc) and two alcohol dehydrogenase (ADH) isoenzymes. Pyruvate is the end-product of the E–D pathway and the substrate for Pdc. Construction and study of Pdc-deficient strains is of key importance for Z. mobilis metabolic engineering, because the pyruvate node represents the central branching point, most novel pathways divert from ethanol synthesis. In the present work, we examined the aerobic metabolism of a strain with partly inactivated Pdc. Results Relative to its parent strain the mutant produced more pyruvate. Yet, it also yielded more acetaldehyde, the product of the Pdc reaction and the substrate for ADH, although the bulk ADH activity was similar in both strains, while the Pdc activity in the mutant was reduced by half. Simulations with the kinetic model of Z. mobilis E-D pathway indicated that, for the observed acetaldehyde to ethanol production ratio in the mutant, the ratio between its respiratory NADH oxidase and ADH activities should be significantly higher, than the measured values. Implications of this finding for the directionality of the ADH isoenzyme operation in vivo and interactions between ADH and Pdc are discussed. Supplementary Information The online version contains supplementary material available at 10.1186/s13104-021-05625-5.
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Affiliation(s)
- Reinis Rutkis
- Institute of Microbiology and Biotechnology, University of Latvia, Riga, Latvia
| | - Inese Strazdina
- Institute of Microbiology and Biotechnology, University of Latvia, Riga, Latvia
| | - Zane Lasa
- Institute of Microbiology and Biotechnology, University of Latvia, Riga, Latvia
| | - Per Bruheim
- Department of Biotechnology and Food Science, NTNU Norwegian University of Science and Technology, Trondheim, Norway
| | - Uldis Kalnenieks
- Institute of Microbiology and Biotechnology, University of Latvia, Riga, Latvia.
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17
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The Ethanologenic Bacterium Zymomonas mobilis Divides Asymmetrically and Exhibits Heterogeneity in DNA Content. Appl Environ Microbiol 2021; 87:AEM.02441-20. [PMID: 33452021 DOI: 10.1128/aem.02441-20] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2020] [Accepted: 12/23/2020] [Indexed: 02/04/2023] Open
Abstract
The alphaproteobacterium Zymomonas mobilis exhibits extreme ethanologenic physiology, making this species a promising biofuel producer. Numerous studies have investigated its biology relevant to industrial applications and mostly at the population level. However, the organization of single cells in this industrially important polyploid species has been largely uncharacterized. In the present study, we characterized basic cellular behavior of Z. mobilis strain Zm6 under anaerobic conditions at the single-cell level. We observed that growing Z. mobilis cells often divided at a nonmidcell position, which contributed to variant cell size at birth. However, the cell size variance was regulated by a modulation of cell cycle span, mediated by a correlation of bacterial tubulin homologue FtsZ ring accumulation with cell growth. The Z. mobilis culture also exhibited heterogeneous cellular DNA content among individual cells, which might have been caused by asynchronous replication of chromosome that was not coordinated with cell growth. Furthermore, slightly angled divisions might have resulted in temporary curvatures of attached Z. mobilis cells. Overall, the present study uncovers a novel bacterial cell organization in Z. mobilis IMPORTANCE With increasing environmental concerns about the use of fossil fuels, development of a sustainable biofuel production platform has been attracting significant public attention. Ethanologenic Z. mobilis species are endowed with an efficient ethanol fermentation capacity that surpasses, in several respects, that of baker's yeast (Saccharomyces cerevisiae), the most-used microorganism for ethanol production. For development of a Z. mobilis culture-based biorefinery, an investigation of its uncharacterized cell biology is important, because bacterial cellular organization and metabolism are closely associated with each other in a single cell compartment. In addition, the current work demonstrates that the polyploid bacterium Z. mobilis exhibits a distinctive mode of bacterial cell organization, likely reflecting its unique metabolism that does not prioritize incorporation of nutrients for cell growth. Thus, another significant result of this work is to advance our general understanding in the diversity of bacterial cell architecture.
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18
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Xing C, Liu Y, Zhang Y, Wang X, Guardia P, Yao L, Han X, Zhang T, Arbiol J, Soler L, Chen Y, Sivula K, Guijarro N, Cabot A, Llorca J. A Direct Z-Scheme for the Photocatalytic Hydrogen Production from a Water Ethanol Mixture on CoTiO 3/TiO 2 Heterostructures. ACS APPLIED MATERIALS & INTERFACES 2021; 13:449-457. [PMID: 33386057 DOI: 10.1021/acsami.0c17004] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Photocatalytic H2 evolution from ethanol dehydrogenation is a convenient strategy to store solar energy in a highly valuable fuel with potential zero net CO2 balance. Herein, we report on the synthesis of CoTiO3/TiO2 composite catalysts with controlled amounts of highly distributed CoTiO3 nanodomains for photocatalytic ethanol dehydrogenation. We demonstrate these materials to provide outstanding hydrogen evolution rates under UV and visible illumination. The origin of this enhanced activity is extensively analyzed. In contrast to previous assumptions, UV-vis absorption spectra and ultraviolet photoelectron spectroscopy (UPS) prove CoTiO3/TiO2 heterostructures to have a type II band alignment, with the conduction band minimum of CoTiO3 below the H2/H+ energy level. Additional steady-state photoluminescence (PL) spectra, time-resolved PL spectra (TRPLS), and electrochemical characterization prove such heterostructures to result in enlarged lifetimes of the photogenerated charge carriers. These experimental evidence point toward a direct Z-scheme as the mechanism enabling the high photocatalytic activity of CoTiO3/TiO2 composites toward ethanol dehydrogenation. In addition, we probe small changes of temperature to strongly modify the photocatalytic activity of the materials tested, which could be used to further promote performance in a solar thermophotocatalytic reactor.
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Affiliation(s)
- Congcong Xing
- Catalonia Institute for Energy Research (IREC), Sant Adriá de Besós 08930, Barcelona, Spain
- Institute of Energy Technologies, Department of Chemical Engineering and Barcelona Research Center in Multiscale Science and Engineering, Universitat Politècnica de Catalunya, EEBE, 08019 Barcelona, Spain
| | - Yongpeng Liu
- Laboratory for Molecular Engineering of Optoelectronic Nanomaterials (LIMNO), École Polytechnique Fédérale de Lausanne (EPFL), Station 6, CH-1015 Lausanne, Switzerland
| | - Yu Zhang
- Catalonia Institute for Energy Research (IREC), Sant Adriá de Besós 08930, Barcelona, Spain
| | - Xiang Wang
- Catalonia Institute for Energy Research (IREC), Sant Adriá de Besós 08930, Barcelona, Spain
| | - Pablo Guardia
- Catalonia Institute for Energy Research (IREC), Sant Adriá de Besós 08930, Barcelona, Spain
| | - Liang Yao
- Laboratory for Molecular Engineering of Optoelectronic Nanomaterials (LIMNO), École Polytechnique Fédérale de Lausanne (EPFL), Station 6, CH-1015 Lausanne, Switzerland
| | - Xu Han
- Catalan Institute of Nanoscience and Nanotechnology (ICN2), CSIC and BIST, Campus UAB, Bellaterra, 08193 Barcelona, Catalonia, Spain
| | - Ting Zhang
- Catalan Institute of Nanoscience and Nanotechnology (ICN2), CSIC and BIST, Campus UAB, Bellaterra, 08193 Barcelona, Catalonia, Spain
| | - Jordi Arbiol
- Catalan Institute of Nanoscience and Nanotechnology (ICN2), CSIC and BIST, Campus UAB, Bellaterra, 08193 Barcelona, Catalonia, Spain
- ICREA, Pg. Lluis Companys 23, 08010 Barcelona, Spain
| | - Lluís Soler
- Institute of Energy Technologies, Department of Chemical Engineering and Barcelona Research Center in Multiscale Science and Engineering, Universitat Politècnica de Catalunya, EEBE, 08019 Barcelona, Spain
| | - Yufen Chen
- Institute of Energy Technologies, Department of Chemical Engineering and Barcelona Research Center in Multiscale Science and Engineering, Universitat Politècnica de Catalunya, EEBE, 08019 Barcelona, Spain
| | - Kevin Sivula
- Laboratory for Molecular Engineering of Optoelectronic Nanomaterials (LIMNO), École Polytechnique Fédérale de Lausanne (EPFL), Station 6, CH-1015 Lausanne, Switzerland
| | - Néstor Guijarro
- Laboratory for Molecular Engineering of Optoelectronic Nanomaterials (LIMNO), École Polytechnique Fédérale de Lausanne (EPFL), Station 6, CH-1015 Lausanne, Switzerland
| | - Andreu Cabot
- Catalonia Institute for Energy Research (IREC), Sant Adriá de Besós 08930, Barcelona, Spain
- ICREA, Pg. Lluis Companys 23, 08010 Barcelona, Spain
| | - Jordi Llorca
- Institute of Energy Technologies, Department of Chemical Engineering and Barcelona Research Center in Multiscale Science and Engineering, Universitat Politècnica de Catalunya, EEBE, 08019 Barcelona, Spain
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Fuchino K, Bruheim P. An assessment of serial co-cultivation approach for generating novel Zymomonas mobilis strains. BMC Res Notes 2020; 13:422. [PMID: 32894180 PMCID: PMC7487726 DOI: 10.1186/s13104-020-05261-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2020] [Accepted: 08/28/2020] [Indexed: 11/21/2022] Open
Abstract
Objective The alphaproteobacterium Zymomonas mobilis is an efficient ethanol producer, and Z. mobilis-based biorefinery shows great potential for biofuel production. Serial co-cultivation is an emerging approach that promotes inter-species interactions which can improve or rewire the metabolic features in industrially useful microorganisms by inducing frequent mutations. We applied this method to assess if it improves or rewires the desirable physiological features of Z. mobilis, especially ethanol production. Results We performed serial co-culture of Z. mobilis with the baker’s yeast, Saccharomyces cerevisiae. We observed filamentation of Z. mobilis cells in the co-culture, indicating that the Z. mobilis cells were exposed to stress due to the presence of a competitor. After 50 times of serial transfers, we characterized the generated Z. mobilis strains, showing that long term co-culture did not drive significant changes in either the growth or profile of excreted metabolites in the generated strains. In line with this, whole genome sequencing of the generated Z. mobilis strains revealed only minor genetic variations from the parental strain. 50 generations of Z. mobilis monoculture did not induce morphological changes or any significant genetic variations. The result indicates that the method needs to be carefully optimized for Z. mobilis strain improvement.
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Affiliation(s)
- Katsuya Fuchino
- Department of Biotechnology and Food Science, Norwegian University of Science and Technology, Trondheim, Norway.
| | - Per Bruheim
- Department of Biotechnology and Food Science, Norwegian University of Science and Technology, Trondheim, Norway
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Fuchino K, Bruheim P. Increased salt tolerance in Zymomonas mobilis strain generated by adaptative evolution. Microb Cell Fact 2020; 19:147. [PMID: 32690090 PMCID: PMC7372843 DOI: 10.1186/s12934-020-01406-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2020] [Accepted: 07/13/2020] [Indexed: 12/16/2022] Open
Abstract
BACKGROUND Ethanologenic alphaproteobacterium Zymomonas mobilis has been acknowledged as a promising biofuel producer. There have been numerous efforts to engineer this species applicable for an industrial-scale bioethanol production. Although Z. mobilis is robustly resilient to certain abiotic stress such as ethanol, the species is known to be sensitive to saline stress at a mild concentration, which hampers its industrial use as an efficient biocatalyst. To overcome this issue, we implemented a laboratory adaptive evolution approach to obtain salt tolerant Z. mobilis strain. RESULTS During an adaptive evolution, we biased selection by cell morphology to exclude stressed cells. The evolved strains significantly improved growth and ethanol production in the medium supplemented with 0.225 M NaCl. Furthermore, comparative metabolomics revealed that the evolved strains did not accumulate prototypical osmolytes, such as proline, to counter the stress during their growth. The sequenced genomes of the studied strains suggest that the disruption of ZZ6_1149 encoding carboxyl-terminal protease was likely responsible for the improved phenotype. CONCLUSIONS The present work successfully generated strains able to grow and ferment glucose under the saline condition that severely perturbs parental strain physiology. Our approach to generate strains, cell shape-based diagnosis and selection, might be applicable to other kinds of strain engineering in Z. mobilis.
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Affiliation(s)
- Katsuya Fuchino
- Department of Biotechnology and Food Science, Norwegian University of Science and Technology, Trondheim, Norway.
| | - Per Bruheim
- Department of Biotechnology and Food Science, Norwegian University of Science and Technology, Trondheim, Norway
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Bioaldehydes and beyond: Expanding the realm of bioderived chemicals using biogenic aldehydes as platforms. Curr Opin Chem Biol 2020; 59:37-46. [PMID: 32454426 DOI: 10.1016/j.cbpa.2020.04.007] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2020] [Revised: 04/04/2020] [Accepted: 04/12/2020] [Indexed: 01/06/2023]
Abstract
Biofuels and biochemicals derived from renewable resources are sconsidered as potential solutions for the energy crisis and associated environmental problems that human beings are facing today. However, so far the available types of bioderived chemicals are rather limited, and production efficiency is generally low. Expanding the realm of bioderived chemicals and relevant derivatives can help motivate the development of bioenergy and the general bioeconomy. Aldehydes, possessing unique reactivity, hold great promise as platform chemicals for producing a large portfolio of bioproducts. In this review, we focus on production of aldehydes from renewable bioresources and derivatization of aldehydes through chemocatalysis, biocatalysis, or de novo biosynthesis. Perspectives on combining protein engineering and cascade reactions for advanced aldehyde derivatization are also provided.
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Metabolic Profiling of Glucose-Fed Metabolically Active Resting Zymomonas mobilis Strains. Metabolites 2020; 10:metabo10030081. [PMID: 32110884 PMCID: PMC7142471 DOI: 10.3390/metabo10030081] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2020] [Revised: 02/17/2020] [Accepted: 02/24/2020] [Indexed: 11/17/2022] Open
Abstract
Zymomonas mobilis is the most efficient bacterial ethanol producer and its physiology is potentially applicable to industrial-scale bioethanol production. However, compared to other industrially important microorganisms, the Z. mobilis metabolome and adaptation to various nutritional and genetic perturbations have been poorly characterized. For rational metabolic engineering, it is essential to understand how central metabolism and intracellular redox balance are maintained in Z. mobilis under various conditions. In this study, we applied quantitative mass spectrometry-based metabolomics to explore how glucose-fed non-growing Z. mobilis Zm6 cells metabolically adapt to change of oxygen availability. Mutants partially impaired in ethanol synthesis (Zm6 adhB) or oxidative stress response (Zm6 cat) were also examined. Distinct patterns of adaptation of central metabolite pools due to the change in cultivation condition and between the mutants and Zm6 reference strain were observed. Decreased NADH/NAD ratio under aerobic incubation corresponded to higher concentrations of the phosphorylated glycolytic intermediates, in accordance with predictions of the kinetic model of Entner–Doudoroff pathway. The effects on the metabolite pools of aerobic to anaerobic transition were similar in the mutants, yet less pronounced. The present data on metabolic plasticity of non-growing Z. mobilis cells will facilitate the further metabolic engineering of the respective strains and their application as biocatalysts.
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Zymomonas mobilis metabolism: Novel tools and targets for its rational engineering. Adv Microb Physiol 2020; 77:37-88. [PMID: 34756211 DOI: 10.1016/bs.ampbs.2020.08.001] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Zymomonas mobilis is an α-proteobacterium that interests the biofuel industry due to its perfect ethanol fermentation yields. From its first description as a bacterial isolate in fermented alcoholic beverages to date, Z. mobilis has been rigorously studied in directions basic and applied. The Z. mobilis powerful Entner-Doudoroff glycolytic pathway has been the center of rigorous biochemical studies and, aside from ethanol, it has attracted interest in terms of high-added-value chemical manufacturing. Energetic balances and the effects of respiration have been explored in fundamental directions as also in applications pursuing strain enhancement and the utilization of alternative carbon sources. Metabolic modeling has addressed the optimization of the biochemical circuitry at various conditions of growth and/or substrate utilization; it has been also critical in predicting desirable end-product yields via flux redirection. Lastly, stress tolerance has received particular attention, since it directly determines biocatalytical performance at challenging bioreactor conditions. At a genetic level, advances in the genetic engineering of the organism have brought forth beneficial manipulations in the Z. mobilis gene pool, e.g., knock-outs, knock-ins and gene stacking, aiming to broaden the metabolic repertoire and increase robustness. Recent omic and expressional studies shed light on the genomic content of the most applied strains and reveal landscapes of activity manifested at ambient or reactor-based conditions. Studies such as those reviewed in this work, contribute to the understanding of the biology of Z. mobilis, enable insightful strain development, and pave the way for the transformation of Z. mobilis into a consummate organism for biomass conversion.
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Kalnenieks U, Balodite E, Rutkis R. Metabolic Engineering of Bacterial Respiration: High vs. Low P/O and the Case of Zymomonas mobilis. Front Bioeng Biotechnol 2019; 7:327. [PMID: 31781557 PMCID: PMC6861446 DOI: 10.3389/fbioe.2019.00327] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2019] [Accepted: 10/28/2019] [Indexed: 11/13/2022] Open
Abstract
Respiratory chain plays a pivotal role in the energy and redox balance of aerobic bacteria. By engineering respiration, it is possible to alter the efficiency of energy generation and intracellular redox state, and thus affect the key bioprocess parameters: cell yield, productivity and stress resistance. Here we summarize the current metabolic engineering and synthetic biology approaches to bacterial respiratory metabolism, with a special focus on the respiratory chain of the ethanologenic bacterium Zymomonas mobilis. Electron transport in Z. mobilis can serve as a model system of bacterial respiration with low oxidative phosphorylation efficiency. Its application for redox balancing and relevance for improvement of stress tolerance are analyzed.
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Affiliation(s)
- Uldis Kalnenieks
- Institute of Microbiology and Biotechnology, University of Latvia, Riga, Latvia
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