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Zhai Y, Tong S, Chen L, Zhang Y, Amin FR, Khalid H, Liu F, Duan Y, Chen W, Chen G, Li D. The enhancement of energy supply in syngas-fermenting microorganisms. ENVIRONMENTAL RESEARCH 2024; 252:118813. [PMID: 38574985 DOI: 10.1016/j.envres.2024.118813] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/29/2023] [Revised: 03/25/2024] [Accepted: 03/26/2024] [Indexed: 04/06/2024]
Abstract
After the second industrial revolution, social productivity developed rapidly, and the use of fossil fuels such as coal, oil, and natural gas increased greatly in industrial production. The burning of these fossil fuels releases large amounts of greenhouse gases such as CO2, which has caused greenhouse effects and global warming. This has endangered the planet's ecological balance and brought many species, including animals and plants, to the brink of extinction. Thus, it is crucial to address this problem urgently. One potential solution is the use of syngas fermentation with microbial cell factories. This process can produce chemicals beneficial to humans, such as ethanol as a fuel while consuming large quantities of harmful gases, CO and CO2. However, syngas-fermenting microorganisms often face a metabolic energy deficit, resulting in slow cell growth, metabolic disorders, and low product yields. This problem limits the large-scale industrial application of engineered microorganisms. Therefore, it is imperative to address the energy barriers of these microorganisms. This paper provides an overview of the current research progress in addressing energy barriers in bacteria, including the efficient capture of external energy and the regulation of internal energy metabolic flow. Capturing external energy involves summarizing studies on overexpressing natural photosystems and constructing semiartificial photosynthesis systems using photocatalysts. The regulation of internal energy metabolic flows involves two parts: regulating enzymes and metabolic pathways. Finally, the article discusses current challenges and future perspectives, with a focus on achieving both sustainability and profitability in an economical and energy-efficient manner. These advancements can provide a necessary force for the large-scale industrial application of syngas fermentation microbial cell factories.
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Affiliation(s)
- Yida Zhai
- School of Marine Science and Technology, Harbin Institute of Technology (Weihai), Weihai, 264209, PR China; School of Environment, Harbin Institute of Technology, Harbin, 150090, PR China; Tianjin Key Laboratory for Industrial Biological System and Bioprocessing Engineering, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, PR China
| | - Sheng Tong
- Tianjin Key Laboratory for Industrial Biological System and Bioprocessing Engineering, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, PR China
| | - Limei Chen
- Tianjin Key Laboratory for Industrial Biological System and Bioprocessing Engineering, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, PR China
| | - Yuan Zhang
- Tianjin Key Laboratory for Industrial Biological System and Bioprocessing Engineering, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, PR China
| | - Farrukh Raza Amin
- Tianjin Key Laboratory for Industrial Biological System and Bioprocessing Engineering, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, PR China
| | - Habiba Khalid
- Tianjin Key Laboratory for Industrial Biological System and Bioprocessing Engineering, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, PR China
| | - Fuguo Liu
- School of Marine Science and Technology, Harbin Institute of Technology (Weihai), Weihai, 264209, PR China; School of Environment, Harbin Institute of Technology, Harbin, 150090, PR China
| | - Yu Duan
- School of Marine Science and Technology, Harbin Institute of Technology (Weihai), Weihai, 264209, PR China; School of Environment, Harbin Institute of Technology, Harbin, 150090, PR China; Tianjin Key Laboratory for Industrial Biological System and Bioprocessing Engineering, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, PR China
| | - Wuxi Chen
- Tianjin Key Laboratory for Industrial Biological System and Bioprocessing Engineering, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, PR China
| | - Guofu Chen
- School of Marine Science and Technology, Harbin Institute of Technology (Weihai), Weihai, 264209, PR China.
| | - Demao Li
- Tianjin Key Laboratory for Industrial Biological System and Bioprocessing Engineering, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, PR China.
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Ingelman H, Heffernan JK, Harris A, Brown SD, Shaikh KM, Saqib AY, Pinheiro MJ, de Lima LA, Martinez KR, Gonzalez-Garcia RA, Hawkins G, Daleiden J, Tran L, Zeleznik H, Jensen RO, Reynoso V, Schindel H, Jänes J, Simpson SD, Köpke M, Marcellin E, Valgepea K. Autotrophic adaptive laboratory evolution of the acetogen Clostridium autoethanogenum delivers the gas-fermenting strain LAbrini with superior growth, products, and robustness. N Biotechnol 2024; 83:S1871-6784(24)00023-2. [PMID: 38871051 DOI: 10.1016/j.nbt.2024.06.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2024] [Revised: 06/05/2024] [Accepted: 06/10/2024] [Indexed: 06/15/2024]
Abstract
Microbes able to convert gaseous one-carbon (C1) waste feedstocks are increasingly important to transition to the sustainable production of renewable chemicals and fuels. Acetogens are interesting biocatalysts since gas fermentation using Clostridium autoethanogenum has been commercialised. However, most acetogen strains need complex nutrients, display slow growth, and are not robust for bioreactor fermentations. In this work, we used three different and independent adaptive laboratory evolution (ALE) strategies to evolve the wild-type C. autoethanogenum to grow faster, without yeast extract and to be robust in operating continuous bioreactor cultures. Multiple evolved strains with improved phenotypes were isolated on minimal media with one strain, named "LAbrini", exhibiting superior performance regarding the maximum specific growth rate, product profile, and robustness in continuous cultures. Whole-genome sequencing of the evolved strains identified 25 mutations. Of particular interest are two genes that acquired seven different mutations across the three ALE strategies, potentially as a result of convergent evolution. Reverse genetic engineering of mutations in potentially sporulation-related genes CLAU_3129 (spo0A) and CLAU_1957 recovered all three superior features of our ALE strains through triggering significant proteomic rearrangements. This work provides a robust C. autoethanogenum strain "LAbrini" to accelerate phenotyping and genetic engineering and to better understand acetogen metabolism.
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Affiliation(s)
- Henri Ingelman
- ERA Chair in Gas Fermentation Technologies, Institute of Bioengineering, University of Tartu, 50411 Tartu, Estonia
| | - James K Heffernan
- Australian Institute for Bioengineering and Nanotechnology (AIBN), The University of Queensland, 4072 St. Lucia, Australia
| | | | | | | | - Asfand Yar Saqib
- ERA Chair in Gas Fermentation Technologies, Institute of Bioengineering, University of Tartu, 50411 Tartu, Estonia
| | - Marina J Pinheiro
- ERA Chair in Gas Fermentation Technologies, Institute of Bioengineering, University of Tartu, 50411 Tartu, Estonia
| | - Lorena Azevedo de Lima
- ERA Chair in Gas Fermentation Technologies, Institute of Bioengineering, University of Tartu, 50411 Tartu, Estonia
| | - Karen Rodriguez Martinez
- Australian Institute for Bioengineering and Nanotechnology (AIBN), The University of Queensland, 4072 St. Lucia, Australia
| | - Ricardo A Gonzalez-Garcia
- Australian Institute for Bioengineering and Nanotechnology (AIBN), The University of Queensland, 4072 St. Lucia, Australia
| | | | | | | | | | | | | | | | - Jürgen Jänes
- Institute of Molecular Systems Biology, ETH Zürich, 8049 Zürich, Switzerland
| | | | | | - Esteban Marcellin
- Australian Institute for Bioengineering and Nanotechnology (AIBN), The University of Queensland, 4072 St. Lucia, Australia.
| | - Kaspar Valgepea
- ERA Chair in Gas Fermentation Technologies, Institute of Bioengineering, University of Tartu, 50411 Tartu, Estonia.
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Deantas-Jahn C, Mendoza SN, Licona-Cassani C, Orellana C, Saa PA. Metabolic modeling of Halomonas campaniensis improves polyhydroxybutyrate production under nitrogen limitation. Appl Microbiol Biotechnol 2024; 108:310. [PMID: 38662130 PMCID: PMC11045607 DOI: 10.1007/s00253-024-13111-8] [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: 08/21/2023] [Revised: 02/25/2024] [Accepted: 03/18/2024] [Indexed: 04/26/2024]
Abstract
Poly-hydroxybutyrate (PHB) is an environmentally friendly alternative for conventional fossil fuel-based plastics that is produced by various microorganisms. Large-scale PHB production is challenging due to the comparatively higher biomanufacturing costs. A PHB overproducer is the haloalkaliphilic bacterium Halomonas campaniensis, which has low nutritional requirements and can grow in cultures with high salt concentrations, rendering it resistant to contamination. Despite its virtues, the metabolic capabilities of H. campaniensis as well as the limitations hindering higher PHB production remain poorly studied. To address this limitation, we present HaloGEM, the first high-quality genome-scale metabolic network reconstruction, which encompasses 888 genes, 1528 reactions (1257 gene-associated), and 1274 metabolites. HaloGEM not only displays excellent agreement with previous growth data and experiments from this study, but it also revealed nitrogen as a limiting nutrient when growing aerobically under high salt concentrations using glucose as carbon source. Among different nitrogen source mixtures for optimal growth, HaloGEM predicted glutamate and arginine as a promising mixture producing increases of 54.2% and 153.4% in the biomass yield and PHB titer, respectively. Furthermore, the model was used to predict genetic interventions for increasing PHB yield, which were consistent with the rationale of previously reported strategies. Overall, the presented reconstruction advances our understanding of the metabolic capabilities of H. campaniensis for rationally engineering this next-generation industrial biotechnology platform. KEY POINTS: A comprehensive genome-scale metabolic reconstruction of H. campaniensis was developed. Experiments and simulations predict N limitation in minimal media under aerobiosis. In silico media design increased experimental biomass yield and PHB titer.
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Affiliation(s)
- Carolina Deantas-Jahn
- Departamento de Ingeniería Química y Bioprocesos, Escuela de Ingeniería, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Sebastián N Mendoza
- Departamento de Ingeniería Química y Bioprocesos, Escuela de Ingeniería, Pontificia Universidad Católica de Chile, Santiago, Chile
- Systems Biology Lab, Vrije Universiteit Amsterdam, Amsterdam, Netherlands
| | - Cuauhtemoc Licona-Cassani
- Núcleo de Innovación de Sistemas Biológicos (NISB), FEMSA Biotechnology Center, Tecnológico de Monterrey, Monterrey, Mexico
- Escuela de Ingeniería y Ciencias, Tecnológico de Monterrey, Monterrey, Mexico
| | - Camila Orellana
- Departamento de Ingeniería Química y Bioprocesos, Escuela de Ingeniería, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Pedro A Saa
- Departamento de Ingeniería Química y Bioprocesos, Escuela de Ingeniería, Pontificia Universidad Católica de Chile, Santiago, Chile.
- Instituto de Ingeniería Matemática y Computacional, Pontificia Universidad Católica de Chile, Santiago, Chile.
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Heffernan J, Garcia Gonzalez RA, Mahamkali V, McCubbin T, Daygon D, Liu L, Palfreyman R, Harris A, Koepke M, Valgepea K, Nielsen LK, Marcellin E. Adaptive laboratory evolution of Clostridium autoethanogenum to metabolize CO 2 and H 2 enhances growth rates in chemostat and unravels proteome and metabolome alterations. Microb Biotechnol 2024; 17:e14452. [PMID: 38568755 PMCID: PMC10990044 DOI: 10.1111/1751-7915.14452] [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: 08/17/2023] [Revised: 03/03/2024] [Accepted: 03/06/2024] [Indexed: 04/05/2024] Open
Abstract
Gas fermentation of CO2 and H2 is an attractive means to sustainably produce fuels and chemicals. Clostridium autoethanogenum is a model organism for industrial CO to ethanol and presents an opportunity for CO2-to-ethanol processes. As we have previously characterized its CO2/H2 chemostat growth, here we use adaptive laboratory evolution (ALE) with the aim of improving growth with CO2/H2. Seven ALE lineages were generated, all with improved specific growth rates. ALE conducted in the presence of 2% CO along with CO2/H2 generated Evolved lineage D, which showed the highest ethanol titres amongst all the ALE lineages during the fermentation of CO2/H2. Chemostat comparison against the parental strain shows no change in acetate or ethanol production, while Evolved D could achieve a higher maximum dilution rate. Multi-omics analyses at steady state revealed that Evolved D has widespread proteome and intracellular metabolome changes. However, the uptake and production rates and titres remain unaltered until investigating their maximum dilution rate. Yet, we provide numerous insights into CO2/H2 metabolism via these multi-omics data and link these results to mutations, suggesting novel targets for metabolic engineering in this bacterium.
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Affiliation(s)
- James Heffernan
- Australian Institute of Bioengineering and NanotechnologyThe University of QueenslandSt. LuciaQueenslandAustralia
- ARC Centre of Excellence in Synthetic BiologyThe University of QueenslandSt. LuciaQueenslandAustralia
| | - R. Axayactl Garcia Gonzalez
- Australian Institute of Bioengineering and NanotechnologyThe University of QueenslandSt. LuciaQueenslandAustralia
- ARC Centre of Excellence in Synthetic BiologyThe University of QueenslandSt. LuciaQueenslandAustralia
| | | | - Tim McCubbin
- Queensland Metabolomics and Proteomics Q‐MAPThe University of QueenslandSt. LuciaQueenslandAustralia
| | - Dara Daygon
- Queensland Metabolomics and Proteomics Q‐MAPThe University of QueenslandSt. LuciaQueenslandAustralia
| | - Lian Liu
- Queensland Metabolomics and Proteomics Q‐MAPThe University of QueenslandSt. LuciaQueenslandAustralia
| | - Robin Palfreyman
- Queensland Metabolomics and Proteomics Q‐MAPThe University of QueenslandSt. LuciaQueenslandAustralia
| | | | | | - Kaspar Valgepea
- ERA Chair in Gas Fermentation Technologies, Institute of TechnologyUniversity of TartuTartuEstonia
| | - Lars Keld Nielsen
- Australian Institute of Bioengineering and NanotechnologyThe University of QueenslandSt. LuciaQueenslandAustralia
- ARC Centre of Excellence in Synthetic BiologyThe University of QueenslandSt. LuciaQueenslandAustralia
- Queensland Metabolomics and Proteomics Q‐MAPThe University of QueenslandSt. LuciaQueenslandAustralia
- The Novo Nordisk Foundation Center for BiosustainabilityTechnical University of DenmarkKgs. LyngbyDenmark
| | - Esteban Marcellin
- Australian Institute of Bioengineering and NanotechnologyThe University of QueenslandSt. LuciaQueenslandAustralia
- ARC Centre of Excellence in Synthetic BiologyThe University of QueenslandSt. LuciaQueenslandAustralia
- Queensland Metabolomics and Proteomics Q‐MAPThe University of QueenslandSt. LuciaQueenslandAustralia
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Carrasco Muriel J, Cowie N, Taylor Parkins S, Mansouvar M, Groves T, Nielsen LK. Shu: visualization of high-dimensional biological pathways. Bioinformatics 2024; 40:btae140. [PMID: 38452346 PMCID: PMC10957514 DOI: 10.1093/bioinformatics/btae140] [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: 04/14/2023] [Revised: 01/03/2024] [Accepted: 03/06/2024] [Indexed: 03/09/2024] Open
Abstract
SUMMARY Shu is a visualization tool that integrates diverse data types into a metabolic map, with a focus on supporting multiple conditions and visualizing distributions. The goal is to provide a unified platform for handling the growing volume of multi-omics data, leveraging the metabolic maps developed by the metabolic modeling community. In addition, shu offers a streamlined python API, based on the Grammar of Graphics, for easy integration with data pipelines. AVAILABILITY AND IMPLEMENTATION Freely available at https://github.com/biosustain/shu under MIT/Apache 2.0 license. Binaries are available in the release page of the repository and the web application is deployed at https://biosustain.github.io/shu.
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Affiliation(s)
- Jorge Carrasco Muriel
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, DK-2800 Kgs. Lyngby, Denmark
| | - Nicholas Cowie
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, DK-2800 Kgs. Lyngby, Denmark
| | - Shannara Taylor Parkins
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, DK-2800 Kgs. Lyngby, Denmark
| | - Marjan Mansouvar
- Department of Biotechnology and Biomedicine, Technical University of Denmark, DK-2800 Kgs. Lyngby, Denmark
| | - Teddy Groves
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, DK-2800 Kgs. Lyngby, Denmark
| | - Lars Keld Nielsen
- Australian Institute for Bioengineering and Nanotechnology (AIBN), The University of Queensland, St Lucia, QLD 4067, Australia
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Wan S, Lai M, Gao X, Zhou M, Yang S, Li Q, Li F, Xia L, Tan Y. Recent progress in engineering Clostridium autoethanogenum to synthesize the biochemicals and biocommodities. Synth Syst Biotechnol 2024; 9:19-25. [PMID: 38205027 PMCID: PMC10776380 DOI: 10.1016/j.synbio.2023.12.001] [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: 09/21/2023] [Revised: 11/15/2023] [Accepted: 12/07/2023] [Indexed: 01/12/2024] Open
Abstract
Excessive mining and utilization fossil fuels has led to drastic environmental consequences, which will contribute to global warming and cause further climate change with severe consequences for the human population. The magnitude of these challenges requires several approaches to develop sustainable alternatives for chemicals and fuels production. In this context, biological processes, mainly microbial fermentation, have gained particular interest. For example, autotrophic gas-fermenting acetogenic bacteria are capable of converting CO, CO2 and H2 into biomass and multiple metabolites through Wood-Ljungdahl pathway, which can be exploited for large-scale fermentation processes to sustainably produce bulk biochemicals and biofuels (e.g. acetate and ethanol) from syngas. Clostridium autoethanogenum is one representative of these chemoautotrophic bacteria and considered as the model for the gas fermentation. Recently, the development of synthetic biology toolbox for this strain has enabled us to study and genetically improve their metabolic capability in gas fermentation. In this review, we will summarize the recent progress involved in the understanding of physiological mechanism and strain engineering for C. autoethanogenum, and provide our perspectives on the future development about the basic biology and engineering biology of this strain.
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Affiliation(s)
- Sai Wan
- Qingdao C1 Refinery Engineering Research Center, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266101, Shandong, China
| | - Mingchi Lai
- Qingdao C1 Refinery Engineering Research Center, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266101, Shandong, China
- School of Life Sciences, Qingdao Agricultural University, Qingdao, 266109, Shandong, China
| | - Xinyu Gao
- Qingdao C1 Refinery Engineering Research Center, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266101, Shandong, China
- School of Biological Science and Technology, University of Jinan, Jinan, 250022, Shandong, China
| | - Mingxin Zhou
- CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Science, Shenzhen, 518055, China
- Shenzhen Powered Carbon Biotechnology Co., Ltd, Shenzhen, 518055, China
| | - Song Yang
- School of Life Sciences, Qingdao Agricultural University, Qingdao, 266109, Shandong, China
| | - Qiang Li
- School of Biological Science and Technology, University of Jinan, Jinan, 250022, Shandong, China
| | - Fuli Li
- Qingdao C1 Refinery Engineering Research Center, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266101, Shandong, China
| | - Lin Xia
- Shenzhen Powered Carbon Biotechnology Co., Ltd, Shenzhen, 518055, China
| | - Yang Tan
- Qingdao C1 Refinery Engineering Research Center, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266101, Shandong, China
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Müller M, Van Liefferinge E, Tilbrook A, van Barneveld R, Roura E. Excess dietary Lys reduces feed intake, stimulates jejunal CCK secretion and alters essential and non-essential blood AA profile in pigs. J Anim Sci Biotechnol 2024; 15:24. [PMID: 38369505 PMCID: PMC10874532 DOI: 10.1186/s40104-023-00971-9] [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: 07/29/2023] [Accepted: 12/06/2023] [Indexed: 02/20/2024] Open
Abstract
BACKGROUND Commercial diets are frequently formulated to meet or exceed nutrient levels including those of limiting essential amino acids (AA) covering potential individual variations within the herd. However, the provision of dietary excess of AA, such as Lys, may lead to reduced appetite and growth in pigs. The mechanisms modulating these responses have not been extensively investigated. This study evaluated the effect of Lys dietary excesses on performance and satiety biomarkers in post weaning pigs. METHODS Twenty-four pigs aged 21 d and weighing 6.81 ± 0.12 kg (mean ± SEM) were individually housed and offered 1 of 4 dietary treatments for 3 weeks: a diet containing a standardized ileal digestible Lys reaching 100% (T0), 120% (T1), 150% (T2) or 200% (T3) of the NRC (2012) requirements. At the end of the experiment, blood samples from the cephalic vein of the T0 and T3 groups were obtained for AA analysis. In addition, primary intestinal cultures from T0 pigs were used, following their humane killing, to evaluate the effect of Lys on gut hormone secretion and AA sensors gene expression under ex vivo conditions. RESULTS Feed intake was linearly reduced (P < 0.001) and the weight gain to feed ratio reduced (P < 0.10) with increased dietary levels of Lys during the third- and first-week post weaning, respectively. Cholecystokinin concentration (P < 0.05) and the metabotropic glutamate receptor 1 and the solute carrier family 7 member 2 (P < 0.10) gene expression was enhanced in proximal jejunum tissues incubated with Lys at 20 mmol/L when compared to the control (Lys 0 mmol/L). Plasma Lys and Glu (P < 0.05) concentration increased in the T3 compared to T0 pigs. In contrast, plasma levels of His, Val, Thr, Leu (P < 0.05) and Gln (P < 0.10) were lower in T3 than T0 pigs. CONCLUSION The present results confirm that excess dietary Lys inhibits hunger in pigs. Moreover, the results provide evidence of pre- and post-absorptive mechanisms modulating these responses. Lys dietary excesses should be narrowed, when possible, to avoid negative effects of the AA on appetite in pigs.
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Affiliation(s)
- Maximiliano Müller
- Centre for Nutrition and Food Sciences, Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Brisbane, Queensland, 4072, Australia
| | - Elout Van Liefferinge
- Laboratory of Animal Nutrition and Animal Product Quality (LANUPRO), Department of Animal Sciences and Aquatic Ecology, Ghent University, 339000, Ghent, Flanders, Belgium
| | - Alan Tilbrook
- Centre for Animal Science, Queensland Alliance for Agriculture and Food Innovation and the School of Veterinary Science, The University of Queensland, Brisbane, Queensland, 4072, Australia
| | | | - Eugeni Roura
- Centre for Nutrition and Food Sciences, Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Brisbane, Queensland, 4072, Australia.
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Casini I, McCubbin T, Esquivel-Elizondo S, Luque GG, Evseeva D, Fink C, Beblawy S, Youngblut ND, Aristilde L, Huson DH, Dräger A, Ley RE, Marcellin E, Angenent LT, Molitor B. An integrated systems biology approach reveals differences in formate metabolism in the genus Methanothermobacter. iScience 2023; 26:108016. [PMID: 37854702 PMCID: PMC10579436 DOI: 10.1016/j.isci.2023.108016] [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: 07/27/2023] [Revised: 08/29/2023] [Accepted: 09/19/2023] [Indexed: 10/20/2023] Open
Abstract
Methanogenesis allows methanogenic archaea to generate cellular energy for their growth while producing methane. Thermophilic hydrogenotrophic species of the genus Methanothermobacter have been recognized as robust biocatalysts for a circular carbon economy and are already applied in power-to-gas technology with biomethanation, which is a platform to store renewable energy and utilize captured carbon dioxide. Here, we generated curated genome-scale metabolic reconstructions for three Methanothermobacter strains and investigated differences in the growth performance of these same strains in chemostat bioreactor experiments with hydrogen and carbon dioxide or formate as substrates. Using an integrated systems biology approach, we identified differences in formate anabolism between the strains and revealed that formate anabolism influences the diversion of carbon between biomass and methane. This finding, together with the omics datasets and the metabolic models we generated, can be implemented for biotechnological applications of Methanothermobacter in power-to-gas technology, and as a perspective, for value-added chemical production.
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Affiliation(s)
- Isabella Casini
- Environmental Biotechnology Group, Department of Geosciences, University of Tübingen, Schnarrenbergstraße 94-96, 72076 Tübingen, Germany
| | - Tim McCubbin
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, Brisbane, QLD 4072, Australia
- Queensland Metabolomics and Proteomics (Q-MAP), The University of Queensland, Brisbane, QLD 4072, Australia
- ARC Centre of Excellence in Synthetic Biology (COESB), The University of Queensland, Brisbane, QLD 4072, Australia
| | - Sofia Esquivel-Elizondo
- Department of Microbiome Science, Max Planck Institute for Biology Tübingen, Max-Planck-Ring 5, 72076 Tübingen, Germany
| | - Guillermo G. Luque
- Department of Microbiome Science, Max Planck Institute for Biology Tübingen, Max-Planck-Ring 5, 72076 Tübingen, Germany
| | - Daria Evseeva
- Department of Computer Science, University of Tübingen, Sand 14, 72076 Tübingen, Germany
- Institute for Bioinformatics and Medical Informatics (IBMI), University of Tübingen, 72076 Tübingen, Germany
| | - Christian Fink
- Environmental Biotechnology Group, Department of Geosciences, University of Tübingen, Schnarrenbergstraße 94-96, 72076 Tübingen, Germany
| | - Sebastian Beblawy
- Environmental Biotechnology Group, Department of Geosciences, University of Tübingen, Schnarrenbergstraße 94-96, 72076 Tübingen, Germany
| | - Nicholas D. Youngblut
- Department of Microbiome Science, Max Planck Institute for Biology Tübingen, Max-Planck-Ring 5, 72076 Tübingen, Germany
| | - Ludmilla Aristilde
- Department of Civil and Environmental Engineering, Northwestern University, Evanston, IL 60208, USA
| | - Daniel H. Huson
- Department of Computer Science, University of Tübingen, Sand 14, 72076 Tübingen, Germany
- Institute for Bioinformatics and Medical Informatics (IBMI), University of Tübingen, 72076 Tübingen, Germany
- Cluster of Excellence – Controlling Microbes to Fight Infections, University of Tübingen, Auf der Morgenstelle 28, 72076 Tübingen, Germany
| | - Andreas Dräger
- Department of Computer Science, University of Tübingen, Sand 14, 72076 Tübingen, Germany
- Institute for Bioinformatics and Medical Informatics (IBMI), University of Tübingen, 72076 Tübingen, Germany
- Cluster of Excellence – Controlling Microbes to Fight Infections, University of Tübingen, Auf der Morgenstelle 28, 72076 Tübingen, Germany
| | - Ruth E. Ley
- Department of Microbiome Science, Max Planck Institute for Biology Tübingen, Max-Planck-Ring 5, 72076 Tübingen, Germany
- Cluster of Excellence – Controlling Microbes to Fight Infections, University of Tübingen, Auf der Morgenstelle 28, 72076 Tübingen, Germany
| | - Esteban Marcellin
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, Brisbane, QLD 4072, Australia
- Queensland Metabolomics and Proteomics (Q-MAP), The University of Queensland, Brisbane, QLD 4072, Australia
- ARC Centre of Excellence in Synthetic Biology (COESB), The University of Queensland, Brisbane, QLD 4072, Australia
| | - Largus T. Angenent
- Environmental Biotechnology Group, Department of Geosciences, University of Tübingen, Schnarrenbergstraße 94-96, 72076 Tübingen, Germany
- Cluster of Excellence – Controlling Microbes to Fight Infections, University of Tübingen, Auf der Morgenstelle 28, 72076 Tübingen, Germany
- AG Angenent, Max Planck Institute for Biology Tübingen, Max-Planck-Ring 5, 72076 Tübingen, Germany
- Department of Biological and Chemical Engineering, Aarhus University, Gustav Wieds Vej 10D, 8000 Aarhus C, Denmark
- The Novo Nordisk Foundation CO2 Research Center (CORC), Aarhus University, Gustav Wieds Vej 10C, 8000 Aarhus C, Denmark
| | - Bastian Molitor
- Environmental Biotechnology Group, Department of Geosciences, University of Tübingen, Schnarrenbergstraße 94-96, 72076 Tübingen, Germany
- Cluster of Excellence – Controlling Microbes to Fight Infections, University of Tübingen, Auf der Morgenstelle 28, 72076 Tübingen, Germany
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9
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Xu J, Zhao N, Meng X, Zhang T, Li J, Dong H, Wei X, Fan M. Contribution of amino acids to Alicyclobacillus acidoterrestris DSM 3922T resistance towards acid stress. Food Microbiol 2023; 113:104273. [PMID: 37098432 DOI: 10.1016/j.fm.2023.104273] [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: 11/28/2022] [Revised: 03/26/2023] [Accepted: 04/01/2023] [Indexed: 04/08/2023]
Abstract
Spoilage of juice and beverages by a thermo-acidophilic bacterium, Alicyclobacillus acidoterrestris, has been considered to be a major and widespread concern for juice industry. Acid-resistant property of A. acidoterrestris supports its survival and multiplication in acidic juice and challenges the development of corresponding control measures. In this study, intracellular amino acid differences caused by acid stress (pH 3.0, 1 h) were determined by targeted metabolomics. The effect of exogenous amino acids on acid resistance of A. acidoterrestris and the related mechanisms were also investigated. The results showed that acid stress affected the amino acid metabolism of A. acidoterrestris, and the selected glutamate, arginine, and lysine contributed to its survival under acid stress. Exogenous glutamate, arginine, and lysine significantly increased the intracellular pH and ATP level, alleviated cell membrane damage, reduced surface roughness, and suppressed deformation caused by acid stress. Additionally, the up-regulated gadA and speA genes and the enhanced enzymatic activity confirmed that glutamate and arginine decarboxylase systems played a crucial role in maintaining pH homeostasis of A. acidoterrestris under acid stress. Our research reveals an important factor contributing to acid resistance of A. acidoterrestris, which provides an alternative target for effectively controlling this contaminant in fruit juices.
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Affiliation(s)
- Junnan Xu
- College of Food Science and Engineering, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Ning Zhao
- College of Food Science and Engineering, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Xuemei Meng
- College of Food Science and Engineering, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Tong Zhang
- College of Food Science and Engineering, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Jun Li
- College of Food Science and Engineering, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Huayu Dong
- College of Food Science and Engineering, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Xinyuan Wei
- College of Food Science and Engineering, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Mingtao Fan
- College of Food Science and Engineering, Northwest A&F University, Yangling, Shaanxi, 712100, China.
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10
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Scott WT, Benito-Vaquerizo S, Zimmermann J, Bajić D, Heinken A, Suarez-Diez M, Schaap PJ. A structured evaluation of genome-scale constraint-based modeling tools for microbial consortia. PLoS Comput Biol 2023; 19:e1011363. [PMID: 37578975 PMCID: PMC10449394 DOI: 10.1371/journal.pcbi.1011363] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2023] [Revised: 08/24/2023] [Accepted: 07/17/2023] [Indexed: 08/16/2023] Open
Abstract
Harnessing the power of microbial consortia is integral to a diverse range of sectors, from healthcare to biotechnology to environmental remediation. To fully realize this potential, it is critical to understand the mechanisms behind the interactions that structure microbial consortia and determine their functions. Constraint-based reconstruction and analysis (COBRA) approaches, employing genome-scale metabolic models (GEMs), have emerged as the state-of-the-art tool to simulate the behavior of microbial communities from their constituent genomes. In the last decade, many tools have been developed that use COBRA approaches to simulate multi-species consortia, under either steady-state, dynamic, or spatiotemporally varying scenarios. Yet, these tools have not been systematically evaluated regarding their software quality, most suitable application, and predictive power. Hence, it is uncertain which tools users should apply to their system and what are the most urgent directions that developers should take in the future to improve existing capacities. This study conducted a systematic evaluation of COBRA-based tools for microbial communities using datasets from two-member communities as test cases. First, we performed a qualitative assessment in which we evaluated 24 published tools based on a list of FAIR (Findability, Accessibility, Interoperability, and Reusability) features essential for software quality. Next, we quantitatively tested the predictions in a subset of 14 of these tools against experimental data from three different case studies: a) syngas fermentation by C. autoethanogenum and C. kluyveri for the static tools, b) glucose/xylose fermentation with engineered E. coli and S. cerevisiae for the dynamic tools, and c) a Petri dish of E. coli and S. enterica for tools incorporating spatiotemporal variation. Our results show varying performance levels of the best qualitatively assessed tools when examining the different categories of tools. The differences in the mathematical formulation of the approaches and their relation to the results were also discussed. Ultimately, we provide recommendations for refining future GEM microbial modeling tools.
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Affiliation(s)
- William T. Scott
- Laboratory of Systems and Synthetic Biology, Wageningen University & Research, Wageningen, the Netherlands
- UNLOCK, Wageningen University & Research and Delft University of Technology, Wageningen, the Netherlands
| | - Sara Benito-Vaquerizo
- Laboratory of Systems and Synthetic Biology, Wageningen University & Research, Wageningen, the Netherlands
| | - Johannes Zimmermann
- Christian-Albrechts-University Kiel, Institute of Experimental Medicine, Research Group Medical Systems Biology, Kiel, Germany
| | - Djordje Bajić
- Department of Biotechnology, Delft University of Technology, Delft, the Netherlands
| | - Almut Heinken
- Inserm U1256 Laboratoire nGERE, Université de Lorraine, Nancy, France
| | - Maria Suarez-Diez
- Laboratory of Systems and Synthetic Biology, Wageningen University & Research, Wageningen, the Netherlands
| | - Peter J. Schaap
- Laboratory of Systems and Synthetic Biology, Wageningen University & Research, Wageningen, the Netherlands
- UNLOCK, Wageningen University & Research and Delft University of Technology, Wageningen, the Netherlands
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11
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Shrestha S, van 't Hag L, Haritos V, Dhital S. Comparative study on molecular and higher-order structures of legume seed protein isolates: Lentil, mungbean and yellow pea. Food Chem 2023; 411:135464. [PMID: 36669335 DOI: 10.1016/j.foodchem.2023.135464] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2022] [Revised: 12/14/2022] [Accepted: 01/09/2023] [Indexed: 01/13/2023]
Abstract
Lentils and mungbean proteins are under-researched compared to pea and soybean. Lentils (green, red and black-lentils), mungbean and yellow pea protein isolates were obtained by alkaline extraction (pH 9)-isoelectric precipitation (pH 4.5) and investigated for molecular and higher-order structures using complementary and novel approaches. These extracted isolates showed comparable protein content but significantly greater nitrogen solubility index (NSI > 85 %) than commercial pea and soy protein isolates (NSI < 60 %). Based on molecular weight estimations from sodium dodecyl sulphate-polyacrylamide gel electrophoresis analysis, the soluble proteins of lentils and yellow pea were identified as legumin-like and vicilin-like, while mungbean was dominated by vicilin-like proteins. The soluble extracts were confirmed to be in native structural condition by size exclusion chromatography and nano-differential scanning calorimetry, unlike commercial extracts. Further differences in secondary structure were evident on circular dichroism spectra of the soluble extracts and deconvolution of the Amide I region (1700-1600 cm-1) from Fourier Transform Infrared of the total protein.
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Affiliation(s)
- Smriti Shrestha
- Department of Chemical and Biological Engineering, Monash University, Clayton, VIC 3800, Australia
| | - Leonie van 't Hag
- Department of Chemical and Biological Engineering, Monash University, Clayton, VIC 3800, Australia.
| | - Victoria Haritos
- Department of Chemical and Biological Engineering, Monash University, Clayton, VIC 3800, Australia
| | - Sushil Dhital
- Department of Chemical and Biological Engineering, Monash University, Clayton, VIC 3800, Australia.
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12
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Nwaokorie UJ, Reinmets K, de Lima LA, Pawar PR, Shaikh KM, Harris A, Köpke M, Valgepea K. Deletion of genes linked to the C 1-fixing gene cluster affects growth, by-products, and proteome of Clostridium autoethanogenum. Front Bioeng Biotechnol 2023; 11:1167892. [PMID: 37265994 PMCID: PMC10230548 DOI: 10.3389/fbioe.2023.1167892] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2023] [Accepted: 05/03/2023] [Indexed: 06/03/2023] Open
Abstract
Gas fermentation has emerged as a sustainable route to produce fuels and chemicals by recycling inexpensive one-carbon (C1) feedstocks from gaseous and solid waste using gas-fermenting microbes. Currently, acetogens that utilise the Wood-Ljungdahl pathway to convert carbon oxides (CO and CO2) into valuable products are the most advanced biocatalysts for gas fermentation. However, our understanding of the functionalities of the genes involved in the C1-fixing gene cluster and its closely-linked genes is incomplete. Here, we investigate the role of two genes with unclear functions-hypothetical protein (hp; LABRINI_07945) and CooT nickel binding protein (nbp; LABRINI_07950)-directly adjacent and expressed at similar levels to the C1-fixing gene cluster in the gas-fermenting model-acetogen Clostridium autoethanogenum. Targeted deletion of either the hp or nbp gene using CRISPR/nCas9, and phenotypic characterisation in heterotrophic and autotrophic batch and autotrophic bioreactor continuous cultures revealed significant growth defects and altered by-product profiles for both ∆hp and ∆nbp strains. Variable effects of gene deletion on autotrophic batch growth on rich or minimal media suggest that both genes affect the utilisation of complex nutrients. Autotrophic chemostat cultures showed lower acetate and ethanol production rates and higher carbon flux to CO2 and biomass for both deletion strains. Additionally, proteome analysis revealed that disruption of either gene affects the expression of proteins of the C1-fixing gene cluster and ethanol synthesis pathways. Our work contributes to a better understanding of genotype-phenotype relationships in acetogens and offers engineering targets to improve carbon fixation efficiency in gas fermentation.
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Affiliation(s)
- Ugochi Jennifer Nwaokorie
- ERA Chair in Gas Fermentation Technologies, Institute of Technology, University of Tartu, Tartu, Estonia
| | - Kristina Reinmets
- ERA Chair in Gas Fermentation Technologies, Institute of Technology, University of Tartu, Tartu, Estonia
| | - Lorena Azevedo de Lima
- ERA Chair in Gas Fermentation Technologies, Institute of Technology, University of Tartu, Tartu, Estonia
| | - Pratik Rajendra Pawar
- ERA Chair in Gas Fermentation Technologies, Institute of Technology, University of Tartu, Tartu, Estonia
| | | | | | | | - Kaspar Valgepea
- ERA Chair in Gas Fermentation Technologies, Institute of Technology, University of Tartu, Tartu, Estonia
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13
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Xu J, Wang J, Ma C, Wei Z, Zhai Y, Tian N, Zhu Z, Xue M, Li D. Embracing a low-carbon future by the production and marketing of C1 gas protein. Biotechnol Adv 2023; 63:108096. [PMID: 36621726 DOI: 10.1016/j.biotechadv.2023.108096] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2022] [Revised: 12/14/2022] [Accepted: 01/03/2023] [Indexed: 01/07/2023]
Abstract
Food scarcity and environmental deterioration are two major problems that human populations currently face. Fortunately, the disruptive innovation of raw food materials has been stimulated by the rapid evolution of biomanufacturing. Therefore, it is expected that the new trends in technology will not only alter the natural resource-dependent food production systems and the traditional way of life but also reduce and assimilate the greenhouse gases released into the atmosphere. This review article summarizes the metabolic pathways associated with C1 gas conversion and the production of single-cell protein for animal feed. Moreover, the protein function, worldwide authorization, market access, and methods to overcome challenges in C1 gas assimilation microbial cell factory construction are also provided. With widespread attention and increasing policy support, the production of C1 gas protein will bring more opportunities and make tremendous contributions to our sustainable future.
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Affiliation(s)
- Jian Xu
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China; National Centre of Technology Innovation for Synthetic Biology, Tianjin, China; Tianjin Key Laboratory for Industrial Biological Systems and Bioprocessing Engineering, Tianjin, China
| | - Jie Wang
- Institute of Feed Research, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Chunling Ma
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China; Haihe Laboratory of Synthetic Biology, Tianjin, China; National Centre of Technology Innovation for Synthetic Biology, Tianjin, China
| | - Zuoxi Wei
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China; National Centre of Technology Innovation for Synthetic Biology, Tianjin, China; Tianjin Key Laboratory for Industrial Biological Systems and Bioprocessing Engineering, Tianjin, China
| | - Yida Zhai
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China; National Centre of Technology Innovation for Synthetic Biology, Tianjin, China; Tianjin Key Laboratory for Industrial Biological Systems and Bioprocessing Engineering, Tianjin, China
| | - Na Tian
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China; National Centre of Technology Innovation for Synthetic Biology, Tianjin, China; Tianjin Key Laboratory for Industrial Biological Systems and Bioprocessing Engineering, Tianjin, China
| | - Zhiguang Zhu
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China; National Centre of Technology Innovation for Synthetic Biology, Tianjin, China.
| | - Min Xue
- Institute of Feed Research, Chinese Academy of Agricultural Sciences, Beijing, China.
| | - Demao Li
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China; National Centre of Technology Innovation for Synthetic Biology, Tianjin, China; Tianjin Key Laboratory for Industrial Biological Systems and Bioprocessing Engineering, Tianjin, China.
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14
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Devkota L, Kyriakopoulou K, Bergia R, Dhital S. Structural and Thermal Characterization of Protein Isolates from Australian Lupin Varieties as Affected by Processing Conditions. Foods 2023; 12:foods12050908. [PMID: 36900425 PMCID: PMC10001375 DOI: 10.3390/foods12050908] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2022] [Revised: 02/08/2023] [Accepted: 02/13/2023] [Indexed: 02/23/2023] Open
Abstract
Proteins from the full and defatted flours of L. angustifolius cv Jurien and L. albus cv Murringo were prepared using alkaline extraction and iso-electric precipitation. Isolates were either freeze dried or spray dried or pasteurized at 75 ± 3 °C/5 min before freeze-drying. Various structural properties were investigated to elucidate the varietal and processing-induced effect on molecular and secondary structure. Irrespective of processing, isolated proteins had a similar molecular size, with α-conglutin (412 kDa) and β-conglutin (210 kDa) being principal fractions for the albus and angustifolius variety, respectively. Smaller peptide fragments were observed for the pasteurized and spray dried samples, indicating some degree of processing-induced changes. Furthermore, secondary structure characterization by Fourier-transform-infrared and circular dichroism spectroscopy showed β-sheet and α-helical structure being the dominant structure, respectively. Thermal characterization showed two denaturation peaks corresponding to β-conglutin (Td = 85-89 °C) and α-conglutin (Td = 102-105 °C) fractions. However, the enthalpy values for α-conglutin denaturation were significantly higher for albus species, which corroborates well with higher amounts of heat stable α-conglutin present. Amino acid profile was similar for all samples with limiting sulphur amino acid. In summary, commercial processing conditions did not have a profound effect on the various structural properties of lupin protein isolates, and properties were mainly determined by varietal differences.
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Affiliation(s)
- Lavaraj Devkota
- Department of Chemical and Biological Engineering, Monash University, Clayton, VIC 3800, Australia
| | | | - Robert Bergia
- Archer-Daniels-Midland (ADM), James R. Randall Research Centre, Decatur, IL 62521, USA
| | - Sushil Dhital
- Department of Chemical and Biological Engineering, Monash University, Clayton, VIC 3800, Australia
- Correspondence: ; Tel.: +61-3-9905-9344
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15
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Lv X, Yu W, Zhang C, Ning P, Li J, Liu Y, Du G, Liu L. C1-based biomanufacturing: Advances, challenges and perspectives. BIORESOURCE TECHNOLOGY 2023; 367:128259. [PMID: 36347475 DOI: 10.1016/j.biortech.2022.128259] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/04/2022] [Revised: 10/29/2022] [Accepted: 10/29/2022] [Indexed: 06/16/2023]
Abstract
One-carbon (C1) compounds have emerged as a key research focus due to the growth of metabolic engineering and synthetic biology as affordable and sustainable nonfood sugar feedstocks for energy-efficient and environmentally friendly biomanufacturing. This paper summarizes and discusses current developments in C1 compounds for biomanufacturing. First, two primary groups of microbes that use C1 compounds (native and synthetic) are introduced, and the traits, categorization, and functions of C1 microbes are summarized. Second, engineering strategies for C1 utilization are compiled and reviewed, including reconstruction of C1-utilization pathway, enzyme engineering, cofactor engineering, genome-scale modeling, and adaptive laboratory evolution. Third, a review of C1 compounds' uses in the synthesis of biofuels and high-value compounds is presented. Finally, potential obstacles to C1-based biomanufacturing are highlighted along with future research initiatives.
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Affiliation(s)
- Xueqin Lv
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China; Science Center for Future Foods, Jiangnan University, Wuxi 214122, China; Baima Future Foods Research Institute, Nanjing 211225, China
| | - Wenwen Yu
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China; Science Center for Future Foods, Jiangnan University, Wuxi 214122, China
| | - Chenyang Zhang
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China; Science Center for Future Foods, Jiangnan University, Wuxi 214122, China
| | - Peng Ning
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China; Science Center for Future Foods, Jiangnan University, Wuxi 214122, China
| | - Jianghua Li
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China; Science Center for Future Foods, Jiangnan University, Wuxi 214122, China
| | - Yanfeng Liu
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China; Science Center for Future Foods, Jiangnan University, Wuxi 214122, China
| | - Guocheng Du
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China; Science Center for Future Foods, Jiangnan University, Wuxi 214122, China
| | - Long Liu
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China; Science Center for Future Foods, Jiangnan University, Wuxi 214122, China.
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16
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Benito-Vaquerizo S, Nouse N, Schaap PJ, Hugenholtz J, Brul S, López-Contreras AM, Martins dos Santos VAP, Suarez-Diez M. Model-driven approach for the production of butyrate from CO 2/H 2 by a novel co-culture of C. autoethanogenum and C. beijerinckii. Front Microbiol 2022; 13:1064013. [PMID: 36620068 PMCID: PMC9815533 DOI: 10.3389/fmicb.2022.1064013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2022] [Accepted: 12/05/2022] [Indexed: 12/24/2022] Open
Abstract
One-carbon (C1) compounds are promising feedstocks for the sustainable production of commodity chemicals. CO2 is a particularly advantageous C1-feedstock since it is an unwanted industrial off-gas that can be converted into valuable products while reducing its atmospheric levels. Acetogens are microorganisms that can grow on CO2/H2 gas mixtures and syngas converting these substrates into ethanol and acetate. Co-cultivation of acetogens with other microbial species that can further process such products, can expand the variety of products to, for example, medium chain fatty acids (MCFA) and longer chain alcohols. Solventogens are microorganisms known to produce MCFA and alcohols via the acetone-butanol-ethanol (ABE) fermentation in which acetate is a key metabolite. Thus, co-cultivation of an acetogen and a solventogen in a consortium provides a potential platform to produce valuable chemicals from CO2. In this study, metabolic modeling was implemented to design a new co-culture of an acetogen and a solventogen to produce butyrate from CO2/H2 mixtures. The model-driven approach suggested the ability of the studied solventogenic species to grow on lactate/glycerol with acetate as co-substrate. This ability was confirmed experimentally by cultivation of Clostridium beijerinckii on these substrates in batch serum bottles and subsequently in pH-controlled bioreactors. Community modeling also suggested that a novel microbial consortium consisting of the acetogen Clostridium autoethanogenum, and the solventogen C. beijerinckii would be feasible and stable. On the basis of this prediction, a co-culture was experimentally established. C. autoethanogenum grew on CO2/H2 producing acetate and traces of ethanol. Acetate was in turn, consumed by C. beijerinckii together with lactate, producing butyrate. These results show that community modeling of metabolism is a valuable tool to guide the design of microbial consortia for the tailored production of chemicals from renewable resources.
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Affiliation(s)
- Sara Benito-Vaquerizo
- Laboratory of Systems and Synthetic Biology, Wageningen University and Research, Wageningen, Netherlands
| | - Niels Nouse
- Molecular Biology and Microbial Food Safety, University of Amsterdam, Amsterdam, Netherlands
| | - Peter J. Schaap
- Laboratory of Systems and Synthetic Biology, Wageningen University and Research, Wageningen, Netherlands,UNLOCK Large Scale Infrastructure for Microbial Communities, Wageningen University and Research and Delft University of Technology, Wageningen, Netherlands
| | - Jeroen Hugenholtz
- Molecular Biology and Microbial Food Safety, University of Amsterdam, Amsterdam, Netherlands
| | - Stanley Brul
- Molecular Biology and Microbial Food Safety, University of Amsterdam, Amsterdam, Netherlands
| | - Ana M. López-Contreras
- Wageningen Food and Biobased Research, Wageningen University and Research, Wageningen, Netherlands
| | | | - Maria Suarez-Diez
- Laboratory of Systems and Synthetic Biology, Wageningen University and Research, Wageningen, Netherlands,*Correspondence: Maria Suarez-Diez ✉
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17
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Kwon SJ, Lee J, Lee HS. Metabolic changes of the acetogen Clostridium sp. AWRP through adaptation to acetate challenge. Front Microbiol 2022; 13:982442. [PMID: 36569090 PMCID: PMC9768041 DOI: 10.3389/fmicb.2022.982442] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Accepted: 11/14/2022] [Indexed: 12/12/2022] Open
Abstract
In this study, we report the phenotypic changes that occurred in the acetogenic bacterium Clostridium sp. AWRP as a result of an adaptive laboratory evolution (ALE) under the acetate challenge. Acetate-adapted strain 46 T-a displayed acetate tolerance to acetate up to 10 g L-1 and increased ethanol production in small-scale cultures. The adapted strain showed a higher cell density than AWRP even without exogenous acetate supplementation. 46 T-a was shown to have reduced gas consumption rate and metabolite production. It was intriguing to note that 46 T-a, unlike AWRP, continued to consume H2 at low CO2 levels. Genome sequencing revealed that the adapted strain harbored three point mutations in the genes encoding an electron-bifurcating hydrogenase (Hyt) crucial for autotrophic growth in CO2 + H2, in addition to one in the dnaK gene. Transcriptome analysis revealed that most genes involved in the CO2-fixation Wood-Ljungdahl pathway and auxiliary pathways for energy conservation (e.g., Rnf complex, Nfn, etc.) were significantly down-regulated in 46 T-a. Several metabolic pathways involved in dissimilation of nucleosides and carbohydrates were significantly up-regulated in 46 T-a, indicating that 46 T-a evolved to utilize organic substrates rather than CO2 + H2. Further investigation into degeneration in carbon fixation of the acetate-adapted strain will provide practical implications for CO2 + H2 fermentation using acetogenic bacteria for long-term continuous fermentation.
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Affiliation(s)
- Soo Jae Kwon
- Marine Biotechnology Research Center, Korea Institute of Ocean Science and Technology, Busan, South Korea,Department of Marine Biotechnology, University of Science and Technology, Daejeon, South Korea
| | - Joungmin Lee
- Marine Biotechnology Research Center, Korea Institute of Ocean Science and Technology, Busan, South Korea,*Correspondence: Joungmin Lee,
| | - Hyun Sook Lee
- Marine Biotechnology Research Center, Korea Institute of Ocean Science and Technology, Busan, South Korea,Department of Marine Biotechnology, University of Science and Technology, Daejeon, South Korea,Hyun Sook Lee,
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18
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de Lima LA, Reinmets K, Nielsen LK, Marcellin E, Harris A, Köpke M, Valgepea K. RNA-seq Sample Preparation Kits Strongly Affect Transcriptome Profiles of a Gas-Fermenting Bacterium. Microbiol Spectr 2022; 10:e0230322. [PMID: 35894617 PMCID: PMC9431689 DOI: 10.1128/spectrum.02303-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2022] [Accepted: 07/06/2022] [Indexed: 11/20/2022] Open
Abstract
Transcriptome analysis via RNA sequencing (RNA-seq) has become a standard technique employed across various biological fields of study. The rapid adoption of the RNA-seq approach has been mediated, in part, by the development of different commercial RNA-seq library preparation kits compatible with standard next-generation sequencing (NGS) platforms. Generally, the essential steps of library preparation, such as rRNA depletion and first-strand cDNA synthesis, are tailored to a specific group of organisms (e.g., eukaryotes versus prokaryotes) or genomic GC content. Therefore, the selection of appropriate commercial products is of crucial importance to capture the transcriptome of interest as closely to the native state as possible without introduction of technical bias. However, researchers rarely have the resources and time to test various commercial RNA-seq kits for their samples. This work reports a side-by-side comparison of RNA-seq data from Clostridium autoethanogenum obtained using three commercial rRNA removal and strand-specific library construction products of NuGEN Technologies, Qiagen, and Zymo Research and assesses their performance relative to published data. While all three vendors advertise their products as suitable for prokaryotes, we found significant differences in their performance regarding rRNA removal, strand specificity, and most importantly, transcript abundance distribution profiles. Notably, RNA-seq data obtained with Qiagen products were most similar to published data and delivered the best results in terms of library strandedness and transcript abundance distribution range. Our results highlight the importance of finding appropriate organism-specific workflows and library preparation products for RNA-seq studies. IMPORTANCE RNA-seq is a powerful technique for transcriptome profiling while involving elaborate sample processing before library sequencing. We show that RNA-seq library preparation kits can strongly affect the outcome of an RNA-seq experiment. Although library preparation benefits from the availability of various commercial kits, choosing appropriate products for the specific samples can be challenging for new users or for users working with unconventional organisms. Evaluating the performance of different commercial products requires significant financial and time investments infeasible for most researchers. Therefore, users are often guided in their choice of kits by published data involving similar input samples. We conclude that important consideration should be given to selecting sample processing workflows for any given organism.
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Affiliation(s)
- Lorena Azevedo de Lima
- ERA Chair in Gas Fermentation Technologies, Institute of Technology, University of Tartu, Tartu, Estonia
| | - Kristina Reinmets
- ERA Chair in Gas Fermentation Technologies, Institute of Technology, University of Tartu, Tartu, Estonia
| | - Lars Keld Nielsen
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, St. Lucia, Australia
- ARC Centre of Excellence in Synthetic Biology, The University of Queensland, St. Lucia, Australia
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Esteban Marcellin
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, St. Lucia, Australia
- ARC Centre of Excellence in Synthetic Biology, The University of Queensland, St. Lucia, Australia
| | | | | | - Kaspar Valgepea
- ERA Chair in Gas Fermentation Technologies, Institute of Technology, University of Tartu, Tartu, Estonia
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19
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An T, Kim YK. Effect of selenium and tungsten on cell growth and metabolite production in syngas fermentation using "Clostridium autoethanogenum". J Biotechnol 2022; 356:60-64. [PMID: 35878811 DOI: 10.1016/j.jbiotec.2022.07.004] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2022] [Revised: 06/16/2022] [Accepted: 07/20/2022] [Indexed: 11/18/2022]
Abstract
The effect of tungsten and selenium on cell growth and production of metabolites such as acetic acid and ethanol when fermenting syngas using "Clostridium autoethanogenum" was investigated to improve the process efficiency. General concentrations of selenium and tungsten in the medium are 0.01µM during acetogenic syngas fermentation. We conducted culture experiments at concentrations of 0, 0.001, 0.01 and 0.1µM for each heavy metal. The effect of selenium on cell growth and total metabolite production was greater than that of tungsten as the effect of selenium on formate dehydrogenase, an important enzyme of the Wood-Ljungdahl pathway, is greater than that of tungsten. Although an increase in tungsten had a marginal effect on total metabolite production, the ethanol/acetic acid production ratio increased significantly due to a decrease in acetic acid and an increase in ethanol production. Thus, tungsten plays a key role in activating aldehyde:ferredoxin oxidoreductase, a key enzyme in the reduction of acetate to ethanol. A specific ethanol productivity of 0.462g ethanol/g DCW∙d was obtained in a culture using 0.01µM selenium and 0.1µM tungsten, which was 2.18 times higher than when using 0.01µM of both selenium and tungsten.
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Affiliation(s)
- Taegwang An
- Department of Chemical Engineering, Research Center of Chemical Technology, Hankyong National University, Anseong, Gyeonggi-do 17579, Republic of Korea
| | - Young-Kee Kim
- Department of Chemical Engineering, Research Center of Chemical Technology, Hankyong National University, Anseong, Gyeonggi-do 17579, Republic of Korea.
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20
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Benito-Vaquerizo S, Parera Olm I, de Vroet T, Schaap PJ, Sousa DZ, Martins Dos Santos VAP, Suarez-Diez M. Genome-scale metabolic modelling enables deciphering ethanol metabolism via the acrylate pathway in the propionate-producer Anaerotignum neopropionicum. Microb Cell Fact 2022; 21:116. [PMID: 35710409 PMCID: PMC9205015 DOI: 10.1186/s12934-022-01841-1] [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: 04/12/2022] [Accepted: 05/26/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Microbial production of propionate from diluted streams of ethanol (e.g., deriving from syngas fermentation) is a sustainable alternative to the petrochemical production route. Yet, few ethanol-fermenting propionigenic bacteria are known, and understanding of their metabolism is limited. Anaerotignum neopropionicum is a propionate-producing bacterium that uses the acrylate pathway to ferment ethanol and CO2 to propionate and acetate. In this work, we used computational and experimental methods to study the metabolism of A. neopropionicum and, in particular, the pathway for conversion of ethanol into propionate. RESULTS Our work describes iANEO_SB607, the first genome-scale metabolic model (GEM) of A. neopropionicum. The model was built combining the use of automatic tools with an extensive manual curation process, and it was validated with experimental data from this and published studies. The model predicted growth of A. neopropionicum on ethanol, lactate, sugars and amino acids, matching observed phenotypes. In addition, the model was used to implement a dynamic flux balance analysis (dFBA) approach that accurately predicted the fermentation profile of A. neopropionicum during batch growth on ethanol. A systematic analysis of the metabolism of A. neopropionicum combined with model simulations shed light into the mechanism of ethanol fermentation via the acrylate pathway, and revealed the presence of the electron-transferring complexes NADH-dependent reduced ferredoxin:NADP+ oxidoreductase (Nfn) and acryloyl-CoA reductase-EtfAB, identified for the first time in this bacterium. CONCLUSIONS The realisation of the GEM iANEO_SB607 is a stepping stone towards the understanding of the metabolism of the propionate-producer A. neopropionicum. With it, we have gained insight into the functioning of the acrylate pathway and energetic aspects of the cell, with focus on the fermentation of ethanol. Overall, this study provides a basis to further exploit the potential of propionigenic bacteria as microbial cell factories.
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Affiliation(s)
- Sara Benito-Vaquerizo
- Laboratory of Systems and Synthetic Biology, Wageningen University & Research, Stippeneng 4, Wageningen, 6708WE, The Netherlands
| | - Ivette Parera Olm
- Laboratory of Microbiology, Wageningen University & Research, Stippeneng 4, Wageningen, 6708WE, The Netherlands
| | - Thijs de Vroet
- Laboratory of Microbiology, Wageningen University & Research, Stippeneng 4, Wageningen, 6708WE, The Netherlands
| | - Peter J Schaap
- Laboratory of Systems and Synthetic Biology, Wageningen University & Research, Stippeneng 4, Wageningen, 6708WE, The Netherlands
| | - Diana Z Sousa
- Laboratory of Microbiology, Wageningen University & Research, Stippeneng 4, Wageningen, 6708WE, The Netherlands.,Centre for Living Technologies, Alliance TU/e, WUR, UU, UMC Utrecht, Vening Meinesz building C, Princetonlaan 6, Utrecht, 3584 CB, The Netherlands
| | - Vitor A P Martins Dos Santos
- Laboratory of Systems and Synthetic Biology, Wageningen University & Research, Stippeneng 4, Wageningen, 6708WE, The Netherlands.,Bioprocess Engineering, Wageningen University & Research, Droevendaalsesteeg 1, 6708 PB, Wageningen, The Netherlands
| | - Maria Suarez-Diez
- Laboratory of Systems and Synthetic Biology, Wageningen University & Research, Stippeneng 4, Wageningen, 6708WE, The Netherlands.
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21
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de Lima LA, Ingelman H, Brahmbhatt K, Reinmets K, Barry C, Harris A, Marcellin E, Köpke M, Valgepea K. Faster Growth Enhances Low Carbon Fuel and Chemical Production Through Gas Fermentation. Front Bioeng Biotechnol 2022; 10:879578. [PMID: 35497340 PMCID: PMC9039284 DOI: 10.3389/fbioe.2022.879578] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2022] [Accepted: 03/14/2022] [Indexed: 12/13/2022] Open
Abstract
Gas fermentation offers both fossil carbon-free sustainable production of fuels and chemicals and recycling of gaseous and solid waste using gas-fermenting microbes. Bioprocess development, systems-level analysis of biocatalyst metabolism, and engineering of cell factories are advancing the widespread deployment of the commercialised technology. Acetogens are particularly attractive biocatalysts but effects of the key physiological parameter–specific growth rate (μ)—on acetogen metabolism and the gas fermentation bioprocess have not been established yet. Here, we investigate the μ-dependent bioprocess performance of the model-acetogen Clostridium autoethanogenum in CO and syngas (CO + CO2+H2) grown chemostat cultures and assess systems-level metabolic responses using gas analysis, metabolomics, transcriptomics, and metabolic modelling. We were able to obtain steady-states up to μ ∼2.8 day−1 (∼0.12 h−1) and show that faster growth supports both higher yields and productivities for reduced by-products ethanol and 2,3-butanediol. Transcriptomics data revealed differential expression of 1,337 genes with increasing μ and suggest that C. autoethanogenum uses transcriptional regulation to a large extent for facilitating faster growth. Metabolic modelling showed significantly increased fluxes for faster growing cells that were, however, not accompanied by gene expression changes in key catabolic pathways for CO and H2 metabolism. Cells thus seem to maintain sufficient “baseline” gene expression to rapidly respond to CO and H2 availability without delays to kick-start metabolism. Our work advances understanding of transcriptional regulation in acetogens and shows that faster growth of the biocatalyst improves the gas fermentation bioprocess.
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Affiliation(s)
- Lorena Azevedo de Lima
- ERA Chair in Gas Fermentation Technologies, Institute of Technology, University of Tartu, Tartu, Estonia
| | - Henri Ingelman
- ERA Chair in Gas Fermentation Technologies, Institute of Technology, University of Tartu, Tartu, Estonia
| | - Kush Brahmbhatt
- ERA Chair in Gas Fermentation Technologies, Institute of Technology, University of Tartu, Tartu, Estonia
| | - Kristina Reinmets
- ERA Chair in Gas Fermentation Technologies, Institute of Technology, University of Tartu, Tartu, Estonia
| | - Craig Barry
- Australian Institute for Bioengineering and Nanotechnology (AIBN), The University of Queensland, St. Lucia, QLD, Australia
| | | | - Esteban Marcellin
- Australian Institute for Bioengineering and Nanotechnology (AIBN), The University of Queensland, St. Lucia, QLD, Australia
| | | | - Kaspar Valgepea
- ERA Chair in Gas Fermentation Technologies, Institute of Technology, University of Tartu, Tartu, Estonia
- *Correspondence: Kaspar Valgepea,
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22
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Metabolic Engineering Interventions for Sustainable 2,3-Butanediol Production in Gas-Fermenting Clostridium autoethanogenum. mSystems 2022; 7:e0111121. [PMID: 35323044 PMCID: PMC9040633 DOI: 10.1128/msystems.01111-21] [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] [Indexed: 11/20/2022] Open
Abstract
Gas fermentation provides a promising platform to turn low-cost and readily available single-carbon waste gases into commodity chemicals, such as 2,3-butanediol. Clostridium autoethanogenum is usually used as a robust and flexible chassis for gas fermentation. Here, we leveraged constraint-based stoichiometric modeling and kinetic ensemble modeling of the C. autoethanogenum metabolic network to provide a systematic in silico analysis of metabolic engineering interventions for 2,3-butanediol overproduction and low carbon substrate loss in dissipated CO2. Our analysis allowed us to identify and to assess comparatively the expected performances for a wide range of single, double, and triple interventions. Our analysis managed to individuate bottleneck reactions in relevant metabolic pathways when suggesting intervening strategies. Besides recapitulating intuitive and/or previously attempted genetic modifications, our analysis neatly outlined that interventions-at least partially-impinging on by-products branching from acetyl coenzyme A (acetyl-CoA) and pyruvate (acetate, ethanol, amino acids) offer valuable alternatives to the interventions focusing directly on the specific branch from pyruvate to 2,3-butanediol. IMPORTANCE Envisioning value chains inspired by environmental sustainability and circularity in economic models is essential to counteract the alterations in the global natural carbon cycle induced by humans. Recycling carbon-based waste gas streams into chemicals by devising gas fermentation bioprocesses mediated by acetogens of the genus Clostridium is one component of the solution. Carbon monoxide originates from multiple biogenic and abiogenic sources and bears a significant environmental impact. This study aims at identifying metabolic engineering interventions for increasing 2,3-butanediol production and avoiding carbon loss in CO2 dissipation via C. autoethanogenum fermenting a substrate comprising CO and H2. 2,3-Butanediol is a valuable biochemical by-product since, due to its versatility, can be transformed quite easily into chemical compounds such as butadiene, diacetyl, acetoin, and methyl ethyl ketone. These compounds are usable as building blocks to manufacture a vast range of industrially produced chemicals.
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23
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Heffernan JK, Mahamkali V, Valgepea K, Marcellin E, Nielsen LK. Analytical tools for unravelling the metabolism of gas-fermenting Clostridia. Curr Opin Biotechnol 2022; 75:102700. [PMID: 35240422 DOI: 10.1016/j.copbio.2022.102700] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Revised: 01/24/2022] [Accepted: 02/05/2022] [Indexed: 12/23/2022]
Abstract
Acetogens harness the Wood-Ljungdahl Pathway, a unique metabolic pathway for C1 capture close to the thermodynamic limit. Gas fermentation using acetogens is already used for CO-to-ethanol conversion at industrial-scale and has the potential to valorise a range of C1 and waste substrates to short-chain and medium-chain carboxylic acids and alcohols. Advances in analytical quantification and metabolic modelling have helped guide industrial gas fermentation designs. Further advances in the measurements of difficult to measure metabolites are required to improve kinetic modelling and understand the regulation of acetogen metabolism. This will help guide future synthetic biology designs needed to realise the full potential of gas fermentation in stimulating a circular bioeconomy.
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Affiliation(s)
- James K Heffernan
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Vishnu Mahamkali
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Kaspar Valgepea
- ERA Chair in Gas Fermentation Technologies, Institute of Technology, University of Tartu, Tartu 50411, Estonia
| | - Esteban Marcellin
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, Brisbane, QLD 4072, Australia; Queensland Node of Metabolomics Australia, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Lars K Nielsen
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, Brisbane, QLD 4072, Australia; Queensland Node of Metabolomics Australia, The University of Queensland, Brisbane, QLD 4072, Australia; The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kgs. Lyngby DK-2800, Denmark.
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24
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Carbon-negative production of acetone and isopropanol by gas fermentation at industrial pilot scale. Nat Biotechnol 2022; 40:335-344. [DOI: 10.1038/s41587-021-01195-w] [Citation(s) in RCA: 45] [Impact Index Per Article: 22.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2020] [Accepted: 12/09/2021] [Indexed: 12/21/2022]
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25
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Yi Z, Xie J. Assessment of spoilage potential and amino acids deamination & decarboxylation activities of Shewanella putrefaciens in bigeye tuna (Thunnus obesus). Lebensm Wiss Technol 2022. [DOI: 10.1016/j.lwt.2021.113016] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
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26
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Barry CP, Gillane R, Talbo GH, Plan M, Palfreyman R, Haber-Stuk AK, Power J, Nielsen LK, Marcellin E. Multi-omic characterisation of Streptomyces hygroscopicus NRRL 30439: detailed assessment of its secondary metabolic potential. Mol Omics 2022; 18:226-236. [PMID: 34989730 DOI: 10.1039/d1mo00150g] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
The emergence of multidrug-resistant pathogenic bacteria creates a demand for novel antibiotics with distinct mechanisms of action. Advances in next-generation genome sequencing promised a paradigm shift in the quest to find new bioactive secondary metabolites. Genome mining has proven successful for predicting putative biosynthetic elements in secondary metabolite superproducers such as Streptomycetes. However, genome mining approaches do not inform whether biosynthetic gene clusters are dormant or active under given culture conditions. Here we show that using a multi-omics approach in combination with antiSMASH, it is possible to assess the secondary metabolic potential of a Streptomyces strain capable of producing mannopeptimycin, an important cyclic peptide effective against Gram-positive infections. The genome of Streptomyces hygroscopicus NRRL 30439 was first sequenced using PacBio RSII to obtain a closed genome. A chemically defined medium was then used to elicit a nutrient stress response in S. hygroscopicus NRRL 30439. Detailed extracellular metabolomics and intracellular proteomics were used to profile and segregate primary and secondary metabolism. Our results demonstrate that the combination of genomics, proteomics and metabolomics enables rapid evaluation of a strain's performance in bioreactors for industrial production of secondary metabolites.
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Affiliation(s)
- Craig P Barry
- Australian Institute for Bioengineering and Nanotechnology (AIBN), The University of Queensland, 4072 St. Lucia, Australia.
| | - Rosemary Gillane
- Australian Institute for Bioengineering and Nanotechnology (AIBN), The University of Queensland, 4072 St. Lucia, Australia.
| | - Gert H Talbo
- Australian Institute for Bioengineering and Nanotechnology (AIBN), The University of Queensland, 4072 St. Lucia, Australia. .,The Queensland Node of Metabolomics Australia, AIBN, The University of Queensland, 4072 St. Lucia, Australia
| | - Manual Plan
- Australian Institute for Bioengineering and Nanotechnology (AIBN), The University of Queensland, 4072 St. Lucia, Australia. .,The Queensland Node of Metabolomics Australia, AIBN, The University of Queensland, 4072 St. Lucia, Australia
| | - Robin Palfreyman
- Australian Institute for Bioengineering and Nanotechnology (AIBN), The University of Queensland, 4072 St. Lucia, Australia. .,The Queensland Node of Metabolomics Australia, AIBN, The University of Queensland, 4072 St. Lucia, Australia
| | | | - John Power
- Zoetis, 333 Portage Street, Kalamazoo, MI 49007, USA
| | - Lars K Nielsen
- Australian Institute for Bioengineering and Nanotechnology (AIBN), The University of Queensland, 4072 St. Lucia, Australia. .,The Queensland Node of Metabolomics Australia, AIBN, The University of Queensland, 4072 St. Lucia, Australia.,The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, DK-2800 Kgs. Lyngby, Denmark
| | - Esteban Marcellin
- Australian Institute for Bioengineering and Nanotechnology (AIBN), The University of Queensland, 4072 St. Lucia, Australia. .,The Queensland Node of Metabolomics Australia, AIBN, The University of Queensland, 4072 St. Lucia, Australia
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27
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Systems Biology on Acetogenic Bacteria for Utilizing C1 Feedstocks. ADVANCES IN BIOCHEMICAL ENGINEERING/BIOTECHNOLOGY 2022; 180:57-90. [DOI: 10.1007/10_2021_199] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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28
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Pavan M, Reinmets K, Garg S, Mueller AP, Marcellin E, Köpke M, Valgepea K. Advances in systems metabolic engineering of autotrophic carbon oxide-fixing biocatalysts towards a circular economy. Metab Eng 2022; 71:117-141. [DOI: 10.1016/j.ymben.2022.01.015] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2021] [Revised: 01/24/2022] [Accepted: 01/25/2022] [Indexed: 12/16/2022]
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29
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Liu Y, Zhang Z, Jiang W, Gu Y. Protein acetylation-mediated cross-regulation of acetic acid and ethanol synthesis in the gas-fermenting Clostridium ljungdahlii. J Biol Chem 2021; 298:101538. [PMID: 34954142 PMCID: PMC8814400 DOI: 10.1016/j.jbc.2021.101538] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2021] [Revised: 12/16/2021] [Accepted: 12/20/2021] [Indexed: 01/23/2023] Open
Abstract
The autotrophic acetogen Clostridium ljungdahlii has emerged as a major candidate in the biological conversion of one-carbon gases (CO2/CO) to bulk chemicals and fuels. Nevertheless, the regulatory pathways and downstream metabolic changes responsible for product formation and distribution in this bacterium remain minimally explored. Protein lysine acetylation (PLA), a prevalent posttranslational modification, controls numerous crucial cellular functions. Herein, we revealed a novel cross-regulatory mechanism that uses both the PLA system and transcription factors to regulate the carbon flow distribution for product formation in C. ljungdahlii. The dominant acetylation/deacetylation system (At2/Dat1) in C. ljungdahlii was found to regulate the ratio of two major products, acetic acid and ethanol. Subsequent genetic and biochemical analyses revealed that the activities of Pta and AdhE1, two crucial enzymes responsible for acetic acid and ethanol synthesis, respectively, were greatly affected by their levels of PLA. We found that the acetylation statuses of Pta and AdhE1 underwent significant dynamic changes during the fermentation process, leading to differential synthesis of acetic acid and ethanol. Furthermore, the crucial redox-sensing protein Rex was shown to be regulated by PLA, which subsequently altered its transcriptional regulation on genes responsible for acetic acid and ethanol formation and distribution. Based on our understanding of this cross-regulatory module, we optimized the ethanol synthetic pathway by modifying the acetylation status (deacetylation-mimicked mutations of crucial lysine residues) of the related key enzyme, achieving significantly increased titer and yield of ethanol, an important chemical and fuel, by C. ljungdahlii in gas fermentation.
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Affiliation(s)
- Yanqiang Liu
- Key Laboratory of Synthetic Biology, The State Key Laboratory of Plant Carbon-Nitrogen Assimilation, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 200032, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Ziwen Zhang
- Key Laboratory of Synthetic Biology, The State Key Laboratory of Plant Carbon-Nitrogen Assimilation, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 200032, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Weihong Jiang
- Key Laboratory of Synthetic Biology, The State Key Laboratory of Plant Carbon-Nitrogen Assimilation, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 200032, China.
| | - Yang Gu
- Key Laboratory of Synthetic Biology, The State Key Laboratory of Plant Carbon-Nitrogen Assimilation, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 200032, China.
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30
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Yi Z, Xie J. Comparative Proteomics Reveals the Spoilage-Related Factors of Shewanella putrefaciens Under Refrigerated Condition. Front Microbiol 2021; 12:740482. [PMID: 34925259 PMCID: PMC8678035 DOI: 10.3389/fmicb.2021.740482] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2021] [Accepted: 11/09/2021] [Indexed: 11/13/2022] Open
Abstract
Shewanella putrefaciens is a microorganism with strong spoilage potential for aquatic products. This study aimed to investigate the potential spoilage factors of S. putrefaciens by comparative proteomic analysis. The spoilage potential of two strains of S. putrefaciens (00A and 00B) isolated from chilled spoiled bigeye tuna was investigated. The results of total volatile basic nitrogen (TVB-N), trimethylamine (TMA) in fish inoculated with S. putrefaciens, extracellular protease activity of S. putrefaciens, and degradation of fish proteins indicated that the spoilage potential of S. putrefaciens 00A was much higher than that of 00B. Fish proteins are usually degraded by spoilage microorganism proteases into small molecular peptides and amino acids, which are subsequently degraded into spoilage metabolites in bacterial cells, leading to deterioration of fish quality. Thus, proteomic analysis of the extracellular and intracellular proteins of 00A vs. 00B was performed. The results indicated that the intracellular differentially expressed protein (IDEP) contained 243 upregulated proteins and 308 downregulated proteins, while 78 upregulated proteins and 4 downregulated proteins were found in the extracellular differentially expressed protein (EDEP). GO annotation revealed that IDEP and EDEP were mainly involved in cellular and metabolic processes. KEGG annotation results showed that the upregulated proteins in IDEP were mainly involved in sulfur metabolism, amino acid metabolism, and aminoacyl-tRNA biosynthesis, while downregulated proteins were related to propanoate metabolism. In contrast, EDEP of KEGG annotation was mainly involved in ribosomes, quorum sensing, and carbohydrate metabolism. Proteins associated with spoilage containing sulfur metabolism (sulfite reductase, sulfate adenylyltransferase, adenylyl-sulfate kinase), amino acid metabolism (biosynthetic arginine decarboxylase, histidine ammonia-lyase), trimethylamine metabolism (trimethylamine-N-oxide reductase), and extracellular proteins (ATP-dependent Clp protease proteolytic subunit) were identified as upregulated. These proteins may play a key role in the spoilage potential of S. putrefaciens. These findings would contribute to the identification of key spoilage factors and understanding of the spoilage mechanism of microorganisms.
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Affiliation(s)
- Zhengkai Yi
- College of Food Science and Technology, Shanghai Ocean University, Shanghai, China
- Shanghai Professional Technology Service Platform on Cold Chain Equipment Performance and Energy Saving Evaluation, Shanghai Ocean University, Shanghai, China
- National Experimental Teaching Demonstration Center for Food Science and Engineering, Shanghai Ocean University, Shanghai, China
| | - Jing Xie
- College of Food Science and Technology, Shanghai Ocean University, Shanghai, China
- Shanghai Professional Technology Service Platform on Cold Chain Equipment Performance and Energy Saving Evaluation, Shanghai Ocean University, Shanghai, China
- National Experimental Teaching Demonstration Center for Food Science and Engineering, Shanghai Ocean University, Shanghai, China
- Shanghai Engineering Research Center of Aquatic Product Processing and Preservation, Shanghai Ocean University, Shanghai, China
- Collaborative Innovation Center of Seafood Deep Processing, Ministry of Education, Dalian, China
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31
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Li X, Han R, Bao T, Osire T, Zhang X, Xu M, Yang T, Rao Z. Citrulline deiminase pathway provides ATP and boosts growth of Clostridium carboxidivorans P7. BIOTECHNOLOGY FOR BIOFUELS 2021; 14:204. [PMID: 34656154 PMCID: PMC8520249 DOI: 10.1186/s13068-021-02051-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Accepted: 10/02/2021] [Indexed: 06/13/2023]
Abstract
BACKGROUND Clostridium carboxidivorans P7 is capable of producing ethanol and butanol from inexpensive and non-food feedstock, such as syngas. Achieving improved ethanol and butanol production in the strain for industrial application depends on the energetics and biomass, especially ATP availability. RESULTS This study found that exogenous addition of citrulline promoted accumulation of ATP, increased specific growth rate, and reduced the doubling time of C. carboxidivorans P7. In heterotrophic fermentation experiments, the addition of citrulline increased intracellular ATP by 3.39-fold, significantly enhancing the production of total alcohol (ethanol + butanol) by 20%. Moreover, in the syngas fermentation experiments, the addition of citrulline improved the level of intracellular ATP and the biomass by 80.5% and 31.6%, respectively, resulting in an 18.6% and 60.3% increase in ethanol and the alcohol/acid production ratio, respectively. CONCLUSIONS This is the first report that citrulline could promote the growth of C. carboxidivorans P7 and increase the level of intracellular ATP, which is of great significance for the use of C. carboxidivorans P7 to synthesize biofuels.
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Affiliation(s)
- Xiangfei Li
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, 214122, Jiangsu, China
| | - Rumeng Han
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, 214122, Jiangsu, China
| | - Teng Bao
- Department of Chemical and Biomolecular Engineering, The Ohio State University, Columbus, OH, 43210, USA
| | - Tolbert Osire
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, 214122, Jiangsu, China
| | - Xian Zhang
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, 214122, Jiangsu, China
| | - Meijuan Xu
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, 214122, Jiangsu, China
| | - Taowei Yang
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, 214122, Jiangsu, China.
| | - Zhiming Rao
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, 214122, Jiangsu, China.
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32
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Abstract
Botulinum neurotoxins (BoNTs) are the most toxic substances known to humankind and are the causative agents of the neuroparalytic disease botulism. Despite the overall importance of BoNTs in public health and safety, as a bioterrorism concern, and in pharmaceutical development, little is known about the molecular mechanisms mediating BoNT stability and degradation in various environments. Previous studies using Clostridium botulinum strain ATCC 3502 revealed that high levels of arginine (20 g/liter) repressed BoNT production approximately 1,000-fold. In the present study, the mechanisms of toxin reduction in arginine-enriched cultures of C. botulinum strain Hall A-hyper, which we have previously genetically manipulated using ClosTron technology, were explored. Cultures were grown in toxin production medium (TPM) and TPM enriched with arginine. Cultures were analyzed for growth (optical density at 600 nm [OD600]), changes in pH, and BoNT formation and stability. Our data indicate that arginine enrichment of C. botulinum strain Hall A-hyper cultures results in a pH shift that induces pH-dependent posttranslational control mechanisms. We further show that independent of arginine, maintenance of an acidic culture pH during growth of C. botulinum strain Hall A-hyper plays a central role in toxin stability and that an extracellular metalloprotease produced by the culture results in BoNT degradation at pH levels between ⁓6.5 and 8.0. IMPORTANCE Botulinum neurotoxin (BoNT) is a public health and bioterrorism concern as well as an important and widely used pharmaceutical, yet the regulation of its synthesis by BoNT-producing clostridia is not well understood. This paper highlights the role of environmentally controlled posttranslational regulatory mechanisms influencing processing and stability of biologically active BoNTs produced by C. botulinum. The results of this work will help enhance public health and safety measures and our ability to evaluate safety risks of novel BoNTs and improve production and quality of BoNTs for pharmaceutical use.
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Debabov VG. Acetogens: Biochemistry, Bioenergetics, Genetics, and Biotechnological Potential. Microbiology (Reading) 2021. [DOI: 10.1134/s0026261721030024] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
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Li X, Henson MA. Dynamic metabolic modelling predicts efficient acetogen-gut bacterium cocultures for CO-to-butyrate conversion. J Appl Microbiol 2021; 131:2899-2917. [PMID: 34008274 DOI: 10.1111/jam.15155] [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: 11/04/2020] [Revised: 04/19/2021] [Accepted: 05/04/2021] [Indexed: 12/19/2022]
Abstract
AIMS While gas-fermenting acetogens have been engineered to secrete non-native metabolites such as butyrate, acetate remains the most thermodynamically favourable product. An alternative to metabolic engineering is to exploit native capabilities for CO-to-acetate conversion by coculturing an acetogen with a second bacterium that provides efficient acetate-butyrate conversion. METHODS AND RESULTS We used dynamic metabolic modelling to computationally evaluate the CO-to-butyrate conversion capabilities of candidate coculture systems by exploiting the diversity of human gut bacteria for anaerobic synthesis of butyrate from acetate and ethanol. A preliminary screening procedure based on flux balance analysis was developed to identify 48 gut bacteria which satisfied minimal growth rate and acetate-to-butyrate conversion requirements when cultured on minimal medium containing acetate and a simple sugar not consumed by the paired acetogen. A total of 170 acetogen/gut bacterium/sugar combinations were dynamically simulated for continuous growth using a 70/30 CO/CO2 feed gas mixture and minimal medium computationally determined for each combination. CONCLUSIONS While coculture systems involving the acetogens Eubacterium limosum or Blautia producta yielded low butyrate productivities and CO-to-ethanol conversion had minimal impact on system performance, dynamic simulations predicted a large number of promising coculture designs with Clostridium ljungdahlii or C. autoethanogenum as the CO-to-acetate converter. Pairings with the gut bacterium Clostridium hylemonae or Roseburia hominis were particularly promising due to their ability to generate high butyrate productivities over a range of dilution rates with a variety of sugars. The higher specific acetate secretion rate of C. ljungdahlii proved more beneficial than the elevated growth rate of C. autoethanogenum for coculture butyrate productivity. SIGNIFICANCE AND IMPACT OF THE STUDY Our study demonstrated that metabolic modelling could provide useful insights into coculture design that can guide future experimental studies. More specifically, our predictions generated several favourable designs, which could serve as the first coculture systems realized experimentally.
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Affiliation(s)
- X Li
- Department of Chemical Engineering and Institute for Applied Life Sciences, University of Massachusetts, Amherst, MA, USA
| | - M A Henson
- Department of Chemical Engineering and Institute for Applied Life Sciences, University of Massachusetts, Amherst, MA, USA
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Flaiz M, Ludwig G, Bengelsdorf FR, Dürre P. Production of the biocommodities butanol and acetone from methanol with fluorescent FAST-tagged proteins using metabolically engineered strains of Eubacterium limosum. BIOTECHNOLOGY FOR BIOFUELS 2021; 14:117. [PMID: 33971948 PMCID: PMC8111989 DOI: 10.1186/s13068-021-01966-2] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Accepted: 04/29/2021] [Indexed: 05/12/2023]
Abstract
BACKGROUND The interest in using methanol as a substrate to cultivate acetogens increased in recent years since it can be sustainably produced from syngas and has the additional benefit of reducing greenhouse gas emissions. Eubacterium limosum is one of the few acetogens that can utilize methanol, is genetically accessible and, therefore, a promising candidate for the recombinant production of biocommodities from this C1 carbon source. Although several genetic tools are already available for certain acetogens including E. limosum, the use of brightly fluorescent reporter proteins is still limited. RESULTS In this study, we expanded the genetic toolbox of E. limosum by implementing the fluorescence-activating and absorption shifting tag (FAST) as a fluorescent reporter protein. Recombinant E. limosum strains that expressed the gene encoding FAST in an inducible and constitutive manner were constructed. Cultivation of these recombinant strains resulted in brightly fluorescent cells even under anaerobic conditions. Moreover, we produced the biocommodities butanol and acetone from methanol with recombinant E. limosum strains. Therefore, we used E. limosum cultures that produced FAST-tagged fusion proteins of the bifunctional acetaldehyde/alcohol dehydrogenase or the acetoacetate decarboxylase, respectively, and determined the fluorescence intensity and product concentrations during growth. CONCLUSIONS The addition of FAST as an oxygen-independent fluorescent reporter protein expands the genetic toolbox of E. limosum. Moreover, our results show that FAST-tagged fusion proteins can be constructed without negatively impacting the stability, functionality, and productivity of the resulting enzyme. Finally, butanol and acetone can be produced from methanol using recombinant E. limosum strains expressing genes encoding fluorescent FAST-tagged fusion proteins.
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Affiliation(s)
- Maximilian Flaiz
- Institute of Microbiology and Biotechnology, Ulm University, Albert-Einstein-Allee 11, 89081, Ulm, Germany.
| | - Gideon Ludwig
- Institute of Microbiology and Biotechnology, Ulm University, Albert-Einstein-Allee 11, 89081, Ulm, Germany
| | - Frank R Bengelsdorf
- Institute of Microbiology and Biotechnology, Ulm University, Albert-Einstein-Allee 11, 89081, Ulm, Germany
| | - Peter Dürre
- Institute of Microbiology and Biotechnology, Ulm University, Albert-Einstein-Allee 11, 89081, Ulm, Germany
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Fackler N, Heijstra BD, Rasor BJ, Brown H, Martin J, Ni Z, Shebek KM, Rosin RR, Simpson SD, Tyo KE, Giannone RJ, Hettich RL, Tschaplinski TJ, Leang C, Brown SD, Jewett MC, Köpke M. Stepping on the Gas to a Circular Economy: Accelerating Development of Carbon-Negative Chemical Production from Gas Fermentation. Annu Rev Chem Biomol Eng 2021; 12:439-470. [PMID: 33872517 DOI: 10.1146/annurev-chembioeng-120120-021122] [Citation(s) in RCA: 41] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Owing to rising levels of greenhouse gases in our atmosphere and oceans, climate change poses significant environmental, economic, and social challenges globally. Technologies that enable carbon capture and conversion of greenhouse gases into useful products will help mitigate climate change by enabling a new circular carbon economy. Gas fermentation usingcarbon-fixing microorganisms offers an economically viable and scalable solution with unique feedstock and product flexibility that has been commercialized recently. We review the state of the art of gas fermentation and discuss opportunities to accelerate future development and rollout. We discuss the current commercial process for conversion of waste gases to ethanol, including the underlying biology, challenges in process scale-up, and progress on genetic tool development and metabolic engineering to expand the product spectrum. We emphasize key enabling technologies to accelerate strain development for acetogens and other nonmodel organisms.
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Affiliation(s)
- Nick Fackler
- LanzaTech Inc., Skokie, Illinois 60077, USA; , , , , , ,
| | | | - Blake J Rasor
- Department of Chemical and Biological Engineering, Chemistry of Life Processes Institute, and Center for Synthetic Biology, Northwestern University, Evanston, Illinois 60208, USA; , , , , , ,
| | - Hunter Brown
- Department of Chemical and Biological Engineering, Chemistry of Life Processes Institute, and Center for Synthetic Biology, Northwestern University, Evanston, Illinois 60208, USA; , , , , , ,
| | - Jacob Martin
- Department of Chemical and Biological Engineering, Chemistry of Life Processes Institute, and Center for Synthetic Biology, Northwestern University, Evanston, Illinois 60208, USA; , , , , , ,
| | - Zhuofu Ni
- Department of Chemical and Biological Engineering, Chemistry of Life Processes Institute, and Center for Synthetic Biology, Northwestern University, Evanston, Illinois 60208, USA; , , , , , ,
| | - Kevin M Shebek
- Department of Chemical and Biological Engineering, Chemistry of Life Processes Institute, and Center for Synthetic Biology, Northwestern University, Evanston, Illinois 60208, USA; , , , , , ,
| | - Rick R Rosin
- LanzaTech Inc., Skokie, Illinois 60077, USA; , , , , , ,
| | - Séan D Simpson
- LanzaTech Inc., Skokie, Illinois 60077, USA; , , , , , ,
| | - Keith E Tyo
- Department of Chemical and Biological Engineering, Chemistry of Life Processes Institute, and Center for Synthetic Biology, Northwestern University, Evanston, Illinois 60208, USA; , , , , , ,
| | - Richard J Giannone
- Chemical Sciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, USA; ,
| | - Robert L Hettich
- Chemical Sciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, USA; ,
| | | | - Ching Leang
- LanzaTech Inc., Skokie, Illinois 60077, USA; , , , , , ,
| | - Steven D Brown
- LanzaTech Inc., Skokie, Illinois 60077, USA; , , , , , ,
| | - Michael C Jewett
- Department of Chemical and Biological Engineering, Chemistry of Life Processes Institute, and Center for Synthetic Biology, Northwestern University, Evanston, Illinois 60208, USA; , , , , , , .,Robert H. Lurie Comprehensive Cancer Center and Simpson Querrey Institute, Northwestern University, Chicago, Illinois 60611, USA
| | - Michael Köpke
- LanzaTech Inc., Skokie, Illinois 60077, USA; , , , , , ,
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Cyclic di-AMP Oversight of Counter-Ion Osmolyte Pools Impacts Intrinsic Cefuroxime Resistance in Lactococcus lactis. mBio 2021; 12:mBio.00324-21. [PMID: 33832972 PMCID: PMC8092236 DOI: 10.1128/mbio.00324-21] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
The bacterial second messenger cyclic di-AMP (c-di-AMP) is a global regulator of potassium homeostasis and compatible solute uptake in many Gram-positive bacteria, making it essential for osmoregulation. The role that c-di-AMP plays in β-lactam resistance, however, is unclear despite being first identified a decade ago. The broadly conserved cyclic di-AMP (c-di-AMP) is a conditionally essential bacterial second messenger. The pool of c-di-AMP is fine-tuned through diadenylate cyclase and phosphodiesterase activities, and direct binding of c-di-AMP to proteins and riboswitches allows the regulation of a broad spectrum of cellular processes. c-di-AMP has a significant impact on intrinsic β-lactam antibiotic resistance in Gram-positive bacteria; however, the reason for this is currently unclear. In this work, genetic studies revealed that suppressor mutations that decrease the activity of the potassium (K+) importer KupB or the glutamine importer GlnPQ restore cefuroxime (CEF) resistance in diadenylate cyclase (cdaA) mutants of Lactococcus lactis. Metabolite analyses showed that glutamine is imported by GlnPQ and then rapidly converted to glutamate, and GlnPQ mutations or c-di-AMP negatively affects the pools of the most abundant free amino acids (glutamate and aspartate) during growth. In a high-c-di-AMP mutant, GlnPQ activity could be increased by raising the internal K+ level through the overexpression of a c-di-AMP-insensitive KupB variant. These results demonstrate that c-di-AMP reduces GlnPQ activity and, therefore, the level of the major free anions in L. lactis through its inhibition of K+ import. Excessive ion accumulation in cdaA mutants results in greater spontaneous cell lysis under hypotonic conditions, while CEF-resistant suppressors exhibit reduced cell lysis and lower osmoresistance. This work demonstrates that the overaccumulation of major counter-ion osmolyte pools in c-di-AMP-defective mutants of L. lactis causes cefuroxime sensitivity.
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Bourgade B, Minton NP, Islam MA. Genetic and metabolic engineering challenges of C1-gas fermenting acetogenic chassis organisms. FEMS Microbiol Rev 2021; 45:fuab008. [PMID: 33595667 PMCID: PMC8351756 DOI: 10.1093/femsre/fuab008] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Accepted: 01/15/2021] [Indexed: 12/11/2022] Open
Abstract
Unabated mining and utilisation of petroleum and petroleum resources and their conversion to essential fuels and chemicals have drastic environmental consequences, contributing to global warming and climate change. In addition, fossil fuels are finite resources, with a fast-approaching shortage. Accordingly, research efforts are increasingly focusing on developing sustainable alternatives for chemicals and fuels production. In this context, bioprocesses, relying on microorganisms, have gained particular interest. For example, acetogens use the Wood-Ljungdahl pathway to grow on single carbon C1-gases (CO2 and CO) as their sole carbon source and produce valuable products such as acetate or ethanol. These autotrophs can, therefore, be exploited for large-scale fermentation processes to produce industrially relevant chemicals from abundant greenhouse gases. In addition, genetic tools have recently been developed to improve these chassis organisms through synthetic biology approaches. This review will focus on the challenges of genetically and metabolically modifying acetogens. It will first discuss the physical and biochemical obstacles complicating successful DNA transfer in these organisms. Current genetic tools developed for several acetogens, crucial for strain engineering to consolidate and expand their catalogue of products, will then be described. Recent tool applications for metabolic engineering purposes to allow redirection of metabolic fluxes or production of non-native compounds will lastly be covered.
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Affiliation(s)
- Barbara Bourgade
- Department of Chemical Engineering, Loughborough University, Loughborough, Leicestershire, LE11 3TU, UK
| | - Nigel P Minton
- BBSRC/EPSRC Synthetic Biology Research Centre (SBRC), School of Life Sciences, University Park, University of Nottingham, Nottingham, Nottinghamshire, NG7 2RD, UK
| | - M Ahsanul Islam
- Department of Chemical Engineering, Loughborough University, Loughborough, Leicestershire, LE11 3TU, UK
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Modeling Growth Kinetics, Interspecies Cell Fusion, and Metabolism of a Clostridium acetobutylicum/Clostridium ljungdahlii Syntrophic Coculture. mSystems 2021; 6:6/1/e01325-20. [PMID: 33622858 PMCID: PMC8573953 DOI: 10.1128/msystems.01325-20] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Clostridium acetobutylicum and Clostridium ljungdahlii grown in a syntrophic culture were recently shown to fuse membranes and exchange cytosolic contents, yielding hybrid cells with significant shifts in gene expression and growth phenotypes. Here, we introduce a dynamic genome-scale metabolic modeling framework to explore how cell fusion alters the growth phenotype and panel of metabolites produced by this binary community. Computational results indicate C. ljungdahlii persists in the coculture through proteome exchange during fusing events, which endow C. ljungdahlii cells with expanded substrate utilization, and access to additional reducing equivalents from C. acetobutylicum-evolved H2 and through acquisition of C. acetobutylicum-native cofactor-reducing enzymes. Simulations predict maximum theoretical ethanol and isopropanol yields that are increased by 0.64 mmol and 0.39 mmol per mmol hexose sugar consumed, respectively, during exponential growth when cell fusion is active. This modeling effort provides a mechanistic explanation for the metabolic outcome of cellular fusion and altered homeostasis achieved in this syntrophic clostridial community.IMPORTANCE Widespread cell fusion and protein exchange between microbial organisms as observed in synthetic C. acetobutylicum/C. ljungdahlii culture is a novel observation that has not been explored in silico The mechanisms responsible for the observed cell fusion events in this culture are still unknown. In this work, we develop a modeling framework that captures the observed culture composition and metabolic phenotype, use it to offer a mechanistic explanation for how the culture achieves homeostasis, and identify C. ljungdahlii as primary beneficiary of fusion events. The implications for the events described in this study are far reaching, with potential to reshape our understanding of microbial community behavior synthetically and in nature.
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Göbbels L, Poehlein A, Dumnitch A, Egelkamp R, Kröger C, Haerdter J, Hackl T, Feld A, Weller H, Daniel R, Streit WR, Schoelmerich MC. Cysteine: an overlooked energy and carbon source. Sci Rep 2021; 11:2139. [PMID: 33495538 PMCID: PMC7835215 DOI: 10.1038/s41598-021-81103-z] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Accepted: 12/31/2020] [Indexed: 11/09/2022] Open
Abstract
Biohybrids composed of microorganisms and nanoparticles have emerged as potential systems for bioenergy and high-value compound production from CO2 and light energy, yet the cellular and metabolic processes within the biological component of this system are still elusive. Here we dissect the biohybrid composed of the anaerobic acetogenic bacterium Moorella thermoacetica and cadmium sulphide nanoparticles (CdS) in terms of physiology, metabolism, enzymatics and transcriptomic profiling. Our analyses show that while the organism does not grow on l-cysteine, it is metabolized to acetate in the biohybrid system and this metabolism is independent of CdS or light. CdS cells have higher metabolic activity, despite an inhibitory effect of Cd2+ on key enzymes, because of an intracellular storage compound linked to arginine metabolism. We identify different routes how cysteine and its oxidized form can be innately metabolized by the model acetogen and what intracellular mechanisms are triggered by cysteine, cadmium or blue light.
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Affiliation(s)
- Luise Göbbels
- Microbiology and Biotechnology, Institute of Plant Sciences and Microbiology, University of Hamburg, 22609, Hamburg, Germany
| | - Anja Poehlein
- Genomic and Applied Microbiology and Göttingen Genomics Laboratory, Georg-August University Göttingen, Grisebachstraße 8, 37077, Göttingen, Germany
| | - Albert Dumnitch
- Microbiology and Biotechnology, Institute of Plant Sciences and Microbiology, University of Hamburg, 22609, Hamburg, Germany
| | - Richard Egelkamp
- Genomic and Applied Microbiology and Göttingen Genomics Laboratory, Georg-August University Göttingen, Grisebachstraße 8, 37077, Göttingen, Germany
| | - Cathrin Kröger
- Microbiology and Biotechnology, Institute of Plant Sciences and Microbiology, University of Hamburg, 22609, Hamburg, Germany
| | - Johanna Haerdter
- Institute of Organic Chemistry, University of Hamburg, Martin-Luther-King-Platz 6, 20146, Hamburg, Germany
| | - Thomas Hackl
- Institute of Organic Chemistry, University of Hamburg, Martin-Luther-King-Platz 6, 20146, Hamburg, Germany
| | - Artur Feld
- Institute of Physical Chemistry, University of Hamburg, Grindelallee 117, 20146, Hamburg, Germany
| | - Horst Weller
- Institute of Physical Chemistry, University of Hamburg, Grindelallee 117, 20146, Hamburg, Germany
| | - Rolf Daniel
- Genomic and Applied Microbiology and Göttingen Genomics Laboratory, Georg-August University Göttingen, Grisebachstraße 8, 37077, Göttingen, Germany
| | - Wolfgang R Streit
- Microbiology and Biotechnology, Institute of Plant Sciences and Microbiology, University of Hamburg, 22609, Hamburg, Germany
| | - Marie Charlotte Schoelmerich
- Microbiology and Biotechnology, Institute of Plant Sciences and Microbiology, University of Hamburg, 22609, Hamburg, Germany.
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Benito-Vaquerizo S, Diender M, Parera Olm I, Martins Dos Santos VAP, Schaap PJ, Sousa DZ, Suarez-Diez M. Modeling a co-culture of Clostridium autoethanogenum and Clostridium kluyveri to increase syngas conversion to medium-chain fatty-acids. Comput Struct Biotechnol J 2020; 18:3255-3266. [PMID: 33240469 PMCID: PMC7658664 DOI: 10.1016/j.csbj.2020.10.003] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2020] [Revised: 10/01/2020] [Accepted: 10/02/2020] [Indexed: 12/17/2022] Open
Abstract
We model a co-culture of C. autoethanogenum and C. kluyveri for syngas fermentation. Biomass species ratio affects ethanol and acetate profiles in the co-culture. The model predicts that addition of succinate increases caproate production. Genetic interventions in C. autoethanogenum could increase caproate production.
Microbial fermentation of synthesis gas (syngas) is becoming more attractive for sustainable production of commodity chemicals. To date, syngas fermentation focuses mainly on the use of Clostridium species for the production of small organic molecules such as ethanol and acetate. The co-cultivation of syngas-fermenting microorganisms with chain-elongating bacteria can expand the range of possible products, allowing, for instance, the production of medium-chain fatty acids (MCFA) and alcohols from syngas. To explore these possibilities, we report herein a genome-scale, constraint-based metabolic model to describe growth of a co-culture of Clostridium autoethanogenum and Clostridium kluyveri on syngas for the production of valuable compounds. Community flux balance analysis was used to gain insight into the metabolism of the two strains and their interactions, and to reveal potential strategies enabling production of butyrate and hexanoate. The model suggests that one strategy to optimize the production of medium-chain fatty-acids from syngas would be the addition of succinate. According to the prediction, addition of succinate would increase the pool of crotonyl-CoA and the ethanol/acetate uptake ratio in C. kluyveri, resulting in a flux of up to 60% of electrons into hexanoate. Another potential way to further optimize butyrate and hexanoate production would be an increase of C. autoethanogenum ethanol production. Blocking either acetaldehyde dehydrogenase or formate dehydrogenase (ferredoxin) activity or formate transport, in the C. autoethanogenum metabolic model could potentially lead to an up to 150% increase in ethanol production.
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Affiliation(s)
- Sara Benito-Vaquerizo
- Laboratory of Systems and Synthetic Biology, Wageningen University & Research, Stippeneng 4, 6708 WE Wageningen, The Netherlands
| | - Martijn Diender
- Laboratory of Microbiology, Wageningen University & Research, Stippeneng 4, 6708 WE Wageningen, The Netherlands
| | - Ivette Parera Olm
- Laboratory of Microbiology, Wageningen University & Research, Stippeneng 4, 6708 WE Wageningen, The Netherlands
| | - Vitor A P Martins Dos Santos
- Laboratory of Systems and Synthetic Biology, Wageningen University & Research, Stippeneng 4, 6708 WE Wageningen, The Netherlands
| | - Peter J Schaap
- Laboratory of Systems and Synthetic Biology, Wageningen University & Research, Stippeneng 4, 6708 WE Wageningen, The Netherlands
| | - Diana Z Sousa
- Laboratory of Microbiology, Wageningen University & Research, Stippeneng 4, 6708 WE Wageningen, The Netherlands
| | - Maria Suarez-Diez
- Laboratory of Systems and Synthetic Biology, Wageningen University & Research, Stippeneng 4, 6708 WE Wageningen, The Netherlands
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Köpke M, Simpson SD. Pollution to products: recycling of ‘above ground’ carbon by gas fermentation. Curr Opin Biotechnol 2020; 65:180-189. [DOI: 10.1016/j.copbio.2020.02.017] [Citation(s) in RCA: 72] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2020] [Revised: 02/21/2020] [Accepted: 02/26/2020] [Indexed: 02/01/2023]
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Vees CA, Neuendorf CS, Pflügl S. Towards continuous industrial bioprocessing with solventogenic and acetogenic clostridia: challenges, progress and perspectives. J Ind Microbiol Biotechnol 2020; 47:753-787. [PMID: 32894379 PMCID: PMC7658081 DOI: 10.1007/s10295-020-02296-2] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2020] [Accepted: 07/20/2020] [Indexed: 12/11/2022]
Abstract
The sustainable production of solvents from above ground carbon is highly desired. Several clostridia naturally produce solvents and use a variety of renewable and waste-derived substrates such as lignocellulosic biomass and gas mixtures containing H2/CO2 or CO. To enable economically viable production of solvents and biofuels such as ethanol and butanol, the high productivity of continuous bioprocesses is needed. While the first industrial-scale gas fermentation facility operates continuously, the acetone-butanol-ethanol (ABE) fermentation is traditionally operated in batch mode. This review highlights the benefits of continuous bioprocessing for solvent production and underlines the progress made towards its establishment. Based on metabolic capabilities of solvent producing clostridia, we discuss recent advances in systems-level understanding and genome engineering. On the process side, we focus on innovative fermentation methods and integrated product recovery to overcome the limitations of the classical one-stage chemostat and give an overview of the current industrial bioproduction of solvents.
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Affiliation(s)
- Charlotte Anne Vees
- Institute of Chemical, Environmental and Bioscience Engineering, Research Area Biochemical Engineering, Technische Universität Wien, Gumpendorfer Straße 1a, 1060 Vienna, Austria
| | - Christian Simon Neuendorf
- Institute of Chemical, Environmental and Bioscience Engineering, Research Area Biochemical Engineering, Technische Universität Wien, Gumpendorfer Straße 1a, 1060 Vienna, Austria
| | - Stefan Pflügl
- Institute of Chemical, Environmental and Bioscience Engineering, Research Area Biochemical Engineering, Technische Universität Wien, Gumpendorfer Straße 1a, 1060 Vienna, Austria
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Hülsen T, Sander EM, Jensen PD, Batstone DJ. Application of purple phototrophic bacteria in a biofilm photobioreactor for single cell protein production: Biofilm vs suspended growth. WATER RESEARCH 2020; 181:115909. [PMID: 32492592 DOI: 10.1016/j.watres.2020.115909] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/14/2020] [Revised: 05/01/2020] [Accepted: 05/02/2020] [Indexed: 06/11/2023]
Abstract
Single cell protein (SCP), has been proposed as alternative to effectively upgrade and recycle organics and nutrients from wastewater. Biomass recovery is a critical issue, and recovery as a biofilm is effective in comparison with sedimentation of suspended biomass. This study aims to determine the applicability of purple phototrophic bacteria (PPB) biofilm on infra-red irradiated, submerged surfaces for the treatment of pre-settled red meat processing wastewater, and SCP generation. PPB removed up to 66% of COD and 42% of TN and TP during batch operation with total areal productivities between 15 and 20 gVS m-2 d-1 achieved. More than 60% of the total biomass grew attached (as biofilm) with the remainder being suspended. The biofilm can be harvested at around 160 gTS L-1 with high protein (>96 g L-1) and low ash contents (>4.0% compared to >30% in the wastewater). The compositions of attached and suspended biomass differed significantly, where the suspended fraction resembled the wastewater composition (e.g. in terms of inert components). The PPB community was similar in the suspended and biofilm fractions while the biofilm had higher relative abundance of PPB representatives (57% vs 43%). A consistent product composition is highly relevant for the manufacturer and ultimately determines the value as feed, feed additive, or supplement.
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Affiliation(s)
- Tim Hülsen
- Advanced Water Management Centre, The University of Queensland, Gehrmann Building, Brisbane, Queensland, 4072, Australia.
| | - Elisa Marx Sander
- Advanced Water Management Centre, The University of Queensland, Gehrmann Building, Brisbane, Queensland, 4072, Australia
| | - Paul D Jensen
- Advanced Water Management Centre, The University of Queensland, Gehrmann Building, Brisbane, Queensland, 4072, Australia
| | - Damien J Batstone
- Advanced Water Management Centre, The University of Queensland, Gehrmann Building, Brisbane, Queensland, 4072, Australia
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Ethanol Metabolism Dynamics in Clostridium ljungdahlii Grown on Carbon Monoxide. Appl Environ Microbiol 2020; 86:AEM.00730-20. [PMID: 32414802 DOI: 10.1128/aem.00730-20] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2020] [Accepted: 05/11/2020] [Indexed: 01/10/2023] Open
Abstract
Bioethanol production from syngas using acetogenic bacteria has attracted considerable attention in recent years. However, low ethanol yield is the biggest challenge that prevents the commercialization of syngas fermentation into biofuels using microbial catalysts. The present study demonstrated that ethanol metabolism plays an important role in recycling NADH/NAD+ during autotrophic growth. Deletion of bifunctional aldehyde/alcohol dehydrogenase (adhE) genes leads to significant growth deficiencies in gas fermentation. Using specific fermentation technology in which the gas pressure and pH were constantly controlled at 0.1 MPa and 6.0, respectively, we revealed that ethanol was formed during the exponential phase, closely accompanied by biomass production. Then, ethanol was oxidized to acetate via the aldehyde ferredoxin oxidoreductase pathway in Clostridium ljungdahlii A metabolic experiment using 13C-labeled ethanol and acetate, redox balance analysis, and comparative transcriptomic analysis demonstrated that ethanol production and reuse shared the metabolic pathway but occurred at different growth phases.IMPORTANCE Ethanol production from carbon monoxide (CO) as a carbon and energy source by Clostridium ljungdahlii and "Clostridium autoethanogenum" is currently being commercialized. During gas fermentation, ethanol synthesis is NADH-dependent. However, ethanol oxidation and its regulatory mechanism remain incompletely understood. Energy metabolism analysis demonstrated that reduced ferredoxin is the sole source of NADH formation by the Rnf-ATPase system, which provides ATP for cell growth during CO fermentation. Therefore, ethanol production is tightly linked to biomass production (ATP production). Clarification of the mechanism of ethanol oxidation and biosynthesis can provide an important reference for generating high-ethanol-yield strains of C. ljungdahlii in the future.
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Mahamkali V, Valgepea K, de Souza Pinto Lemgruber R, Plan M, Tappel R, Köpke M, Simpson SD, Nielsen LK, Marcellin E. Redox controls metabolic robustness in the gas-fermenting acetogen Clostridium autoethanogenum. Proc Natl Acad Sci U S A 2020; 117:13168-13175. [PMID: 32471945 PMCID: PMC7293625 DOI: 10.1073/pnas.1919531117] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Living biological systems display a fascinating ability to self-organize their metabolism. This ability ultimately determines the metabolic robustness that is fundamental to controlling cellular behavior. However, fluctuations in metabolism can affect cellular homeostasis through transient oscillations. For example, yeast cultures exhibit rhythmic oscillatory behavior in high cell-density continuous cultures. Oscillatory behavior provides a unique opportunity for quantitating the robustness of metabolism, as cells respond to changes by inherently compromising metabolic efficiency. Here, we quantify the limits of metabolic robustness in self-oscillating autotrophic continuous cultures of the gas-fermenting acetogen Clostridium autoethanogenum Online gas analysis and high-resolution temporal metabolomics showed oscillations in gas uptake rates and extracellular byproducts synchronized with biomass levels. The data show initial growth on CO, followed by growth on CO and H2 Growth on CO and H2 results in an accelerated growth phase, after which a downcycle is observed in synchrony with a loss in H2 uptake. Intriguingly, oscillations are not linked to translational control, as no differences were observed in protein expression during oscillations. Intracellular metabolomics analysis revealed decreasing levels of redox ratios in synchrony with the cycles. We then developed a thermodynamic metabolic flux analysis model to investigate whether regulation in acetogens is controlled at the thermodynamic level. We used endo- and exo-metabolomics data to show that the thermodynamic driving force of critical reactions collapsed as H2 uptake is lost. The oscillations are coordinated with redox. The data indicate that metabolic oscillations in acetogen gas fermentation are controlled at the thermodynamic level.
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Affiliation(s)
- Vishnuvardhan Mahamkali
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, 4072 Brisbane, Australia
| | - Kaspar Valgepea
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, 4072 Brisbane, Australia
- ERA Chair in Gas Fermentation Technologies, Institute of Technology, University of Tartu, 50411 Tartu, Estonia
| | | | - Manuel Plan
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, 4072 Brisbane, Australia
- Queensland Node of Metabolomics Australia, The University of Queensland, 4072 Brisbane, Australia
| | | | | | | | - Lars Keld Nielsen
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, 4072 Brisbane, Australia
- Queensland Node of Metabolomics Australia, The University of Queensland, 4072 Brisbane, Australia
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800 Kongens Lyngby, Denmark
| | - Esteban Marcellin
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, 4072 Brisbane, Australia;
- Queensland Node of Metabolomics Australia, The University of Queensland, 4072 Brisbane, Australia
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Almeida Benalcázar E, Noorman H, Maciel Filho R, Posada JA. Modeling ethanol production through gas fermentation: a biothermodynamics and mass transfer-based hybrid model for microbial growth in a large-scale bubble column bioreactor. BIOTECHNOLOGY FOR BIOFUELS 2020; 13:59. [PMID: 32231709 PMCID: PMC7102449 DOI: 10.1186/s13068-020-01695-y] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/06/2019] [Accepted: 03/05/2020] [Indexed: 05/08/2023]
Abstract
BACKGROUND Ethanol production through fermentation of gas mixtures containing CO, CO2 and H2 has just started operating at commercial scale. However, quantitative schemes for understanding and predicting productivities, yields, mass transfer rates, gas flow profiles and detailed energy requirements have been lacking in literature; such are invaluable tools for process improvements and better systems design. The present study describes the construction of a hybrid model for simulating ethanol production inside a 700 m3 bubble column bioreactor fed with gas of two possible compositions, i.e., pure CO and a 3:1 mixture of H2 and CO2. RESULTS Estimations made using the thermodynamics-based black-box model of microbial reactions on substrate threshold concentrations, biomass yields, as well as CO and H2 maximum specific uptake rates agreed reasonably well with data and observations reported in literature. According to the bioreactor simulation, there is a strong dependency of process performance on mass transfer rates. When mass transfer coefficients were estimated using a model developed from oxygen transfer to water, ethanol productivity reached 5.1 g L-1 h-1; when the H2/CO2 mixture is fed to the bioreactor, productivity of CO fermentation was 19% lower. Gas utilization reached 23 and 17% for H2/CO2 and CO fermentations, respectively. If mass transfer coefficients were 100% higher than those estimated, ethanol productivity and gas utilization may reach 9.4 g L-1 h-1 and 38% when feeding the H2/CO2 mixture at the same process conditions. The largest energetic requirements for a complete manufacturing plant were identified for gas compression and ethanol distillation, being higher for CO fermentation due to the production of CO2. CONCLUSIONS The thermodynamics-based black-box model of microbial reactions may be used to quantitatively assess and consolidate the diversity of reported data on CO, CO2 and H2 threshold concentrations, biomass yields, maximum substrate uptake rates, and half-saturation constants for CO and H2 for syngas fermentations by acetogenic bacteria. The maximization of ethanol productivity in the bioreactor may come with a cost: low gas utilization. Exploiting the model flexibility, multi-objective optimizations of bioreactor performance might reveal how process conditions and configurations could be adjusted to guide further process development.
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Affiliation(s)
- Eduardo Almeida Benalcázar
- Department of Product and Process Development, Faculty of Chemical Engineering, State University of Campinas, Av. Albert Einstein 500, Cidade Universitária, Campinas, SP 13083-852 Brazil
- Department of Biotechnology, Faculty of Applied Sciences, Delft University of Technology, Van der Maasweg 9, 2629 HZ Delft, The Netherlands
| | - Henk Noorman
- Department of Biotechnology, Faculty of Applied Sciences, Delft University of Technology, Van der Maasweg 9, 2629 HZ Delft, The Netherlands
- DSM Biotechnology Center, A. Fleminglaan 1, 2613 AX Delft, The Netherlands
| | - Rubens Maciel Filho
- Department of Product and Process Development, Faculty of Chemical Engineering, State University of Campinas, Av. Albert Einstein 500, Cidade Universitária, Campinas, SP 13083-852 Brazil
| | - John A. Posada
- Department of Biotechnology, Faculty of Applied Sciences, Delft University of Technology, Van der Maasweg 9, 2629 HZ Delft, The Netherlands
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BCAT1 and BCAT2 disruption in CHO cells has cell line-dependent effects. J Biotechnol 2019; 306:24-31. [PMID: 31465797 DOI: 10.1016/j.jbiotec.2019.08.017] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2019] [Revised: 08/18/2019] [Accepted: 08/25/2019] [Indexed: 11/20/2022]
Abstract
In recombinant protein expression using Chinese hamster ovary (CHO) cells, chemically defined media contain essential amino acids such as branched chain amino acids (BCAAs) leucine, isoleucine and valine. Availability of amino acids is critical as these are building blocks for protein synthesis. However, breakdown of amino acids can lead to build up of toxic intermediates and metabolites that decrease cell growth, productivity and product quality. BCAA catabolism also hampers the usage of BCAAs for protein synthesis. In this work we studied the effects of disrupting the genes responsible for the first step of BCAA catabolism: branched chain aminotransferase 1 (Bcat1) and branched chain aminotransferase 2 (Bcat2). We evaluated the effect of disrupting the genes individually and in combination, and examined the effects in producer and non-producer host cells. Our experiments show that Bcat1 disruption improves cell growth in producer cells, but not in non-producers. Conversely, Bcat2 has a minor negative effect on growth in producer cells, and none in non-producers. Combined Bcat1 and Bcat2 disruption improves growth in producer cells. By-product metabolism is cell line-, clone- and producer-dependent. Overall, our results show that the effects of targeting Bcat1 and/or Bcat2 are cell line-dependent, and seemingly linked to the burden of recombinant protein expression.
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Beck MH, Flaiz M, Bengelsdorf FR, Dürre P. Induced heterologous expression of the arginine deiminase pathway promotes growth advantages in the strict anaerobe Acetobacterium woodii. Appl Microbiol Biotechnol 2019; 104:687-699. [DOI: 10.1007/s00253-019-10248-9] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2019] [Revised: 09/30/2019] [Accepted: 11/05/2019] [Indexed: 01/12/2023]
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Müller V. New Horizons in Acetogenic Conversion of One-Carbon Substrates and Biological Hydrogen Storage. Trends Biotechnol 2019; 37:1344-1354. [DOI: 10.1016/j.tibtech.2019.05.008] [Citation(s) in RCA: 75] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2019] [Revised: 05/17/2019] [Accepted: 05/23/2019] [Indexed: 01/12/2023]
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