1
|
Alavi-Borazjani SA, da Cruz Tarelho LA, Capela MI. Biohythane production via anaerobic digestion process: fundamentals, scale-up challenges, and techno-economic and environmental aspects. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2024:10.1007/s11356-024-34471-8. [PMID: 39090294 DOI: 10.1007/s11356-024-34471-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/25/2023] [Accepted: 07/20/2024] [Indexed: 08/04/2024]
Abstract
Biohythane, a balanced mixture comprising bioH2 (biohydrogen) and bioCH4 (biomethane) produced through anaerobic digestion, is gaining recognition as a promising energy source for the future. This article provides a comprehensive overview of biohythane production, covering production mechanisms, microbial diversity, and process parameters. It also explores different feedstock options, bioreactor designs, and scalability challenges, along with techno-economic and environmental assessments. Additionally, the article discusses the integration of biohythane into waste management systems and examines future prospects for enhancing production efficiency and applicability. This review serves as a valuable resource for researchers, engineers, and policymakers interested in advancing biohythane production as a sustainable and renewable energy solution.
Collapse
Affiliation(s)
- Seyedeh Azadeh Alavi-Borazjani
- Department of Environment and Planning/Centre for Environmental and Marine Studies (CESAM), University of Aveiro, Campus Universitário de Santiago, 3810-193, Aveiro, Portugal.
| | - Luís António da Cruz Tarelho
- Department of Environment and Planning/Centre for Environmental and Marine Studies (CESAM), University of Aveiro, Campus Universitário de Santiago, 3810-193, Aveiro, Portugal
| | - Maria Isabel Capela
- Department of Environment and Planning/Centre for Environmental and Marine Studies (CESAM), University of Aveiro, Campus Universitário de Santiago, 3810-193, Aveiro, Portugal
| |
Collapse
|
2
|
Shekhar C, Maeda T. Impaired glucose metabolism by deleting the operon of hydrogenase 2 in Escherichia coli. Arch Microbiol 2022; 204:627. [DOI: 10.1007/s00203-022-03245-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2022] [Revised: 08/23/2022] [Accepted: 09/08/2022] [Indexed: 11/25/2022]
|
3
|
Jayachandran V, Basak N, De Philippis R, Adessi A. Novel strategies towards efficient molecular biohydrogen production by dark fermentative mechanism: present progress and future perspective. Bioprocess Biosyst Eng 2022; 45:1595-1624. [PMID: 35713786 DOI: 10.1007/s00449-022-02738-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Accepted: 05/27/2022] [Indexed: 01/05/2023]
Abstract
In the scenario of alarming increase in greenhouse and toxic gas emissions from the burning of conventional fuels, it is high time that the population drifts towards alternative fuel usage to obviate pollution. Hydrogen is an environment-friendly biofuel with high energy content. Several production methods exist to produce hydrogen, but the least energy intensive processes are the fermentative biohydrogen techniques. Dark fermentative biohydrogen production (DFBHP) is a value-added, less energy-consuming process to generate biohydrogen. In this process, biohydrogen can be produced from sugars as well as complex substrates that are generally considered as organic waste. Yet, the process is constrained by many factors such as low hydrogen yield, incomplete conversion of substrates, accumulation of volatile fatty acids which lead to the drop of the system pH resulting in hindered growth and hydrogen production by the bacteria. To circumvent these drawbacks, researchers have come up with several strategies that improve the yield of DFBHP process. These strategies can be classified as preliminary methodologies concerned with the process optimization and the latter that deals with pretreatment of substrate and seed sludge, bioaugmentation, co-culture of bacteria, supplementation of additives, bioreactor design considerations, metabolic engineering, nanotechnology, immobilization of bacteria, etc. This review sums up some of the improvement techniques that profoundly enhance the biohydrogen productivity in a DFBHP process.
Collapse
Affiliation(s)
- Varsha Jayachandran
- Department of Biotechnology, Dr. B. R. Ambedkar National Institute of Technology, Jalandhar, 144 027, Punjab, India
| | - Nitai Basak
- Department of Biotechnology, Dr. B. R. Ambedkar National Institute of Technology, Jalandhar, 144 027, Punjab, India.
| | - Roberto De Philippis
- Department of Agriculture, Food, Environment and Forestry, Florence University, Florence, Italy
| | - Alessandra Adessi
- Department of Agriculture, Food, Environment and Forestry, Florence University, Florence, Italy
| |
Collapse
|
4
|
Enhanced Phenazine-1-Carboxamide Production in Pseudomonas chlororaphis H5△fleQ△relA through Fermentation Optimization. FERMENTATION 2022. [DOI: 10.3390/fermentation8040188] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Phenazine-1-carboxamide (PCN) is effective to control many plant pathogens, and improving PCN production would be of great significance in promoting its development as a biopesticide. This study was conducted to improve the PCN production of Pseudomonas chlororaphis H5△fleQ△relA through fermentation optimization in both shake flask and bioreactor. The PCN production of H5△fleQ△relA was improved from 2.75 ± 0.23 g/L to 5.51 ± 0.17 g/L by medium optimization in shake flask using Plackett-Burman design, the path of steepest ascent experiment and central composite design. Then, PCN production reached 8.58 ± 0.25 g/L through optimizing pH in 1 L bioreactor. After pH optimization, the transcriptional levels of ccoO_2 and ccoQ_2 genes related to microbial aerobic respiration were significantly upregulated, and the relative abundance of 3-oxo-C14-HSL was significantly enhanced 15-fold, and these changes were vital for cell activity and metabolites production. Furthermore, the PCN production reached 9.58 ± 0.57 g/L after optimization of the fed-batch fermentation strategy in 1 L bioreactor. Finally, the fermentation scale-up of the optimal medium and optimal feeding strategy were conducted in 30 L bioreactor at the optimal pH, and their PCN production reached 9.17 g/L and 9.62 g/L respectively, which were comparable to that in 1 L bioreactor. In this study, the high PCN production was achieved from the shake-flask fermentation to 30 L bioreactor, and the optimal feeding strategy improved PCN production in bioreactor without increasing total glycerol compared with in shake flask. It provides promising pathways for the optimization of processes for the production of other phenazines.
Collapse
|
5
|
Intasian P, Prakinee K, Phintha A, Trisrivirat D, Weeranoppanant N, Wongnate T, Chaiyen P. Enzymes, In Vivo Biocatalysis, and Metabolic Engineering for Enabling a Circular Economy and Sustainability. Chem Rev 2021; 121:10367-10451. [PMID: 34228428 DOI: 10.1021/acs.chemrev.1c00121] [Citation(s) in RCA: 63] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Since the industrial revolution, the rapid growth and development of global industries have depended largely upon the utilization of coal-derived chemicals, and more recently, the utilization of petroleum-based chemicals. These developments have followed a linear economy model (produce, consume, and dispose). As the world is facing a serious threat from the climate change crisis, a more sustainable solution for manufacturing, i.e., circular economy in which waste from the same or different industries can be used as feedstocks or resources for production offers an attractive industrial/business model. In nature, biological systems, i.e., microorganisms routinely use their enzymes and metabolic pathways to convert organic and inorganic wastes to synthesize biochemicals and energy required for their growth. Therefore, an understanding of how selected enzymes convert biobased feedstocks into special (bio)chemicals serves as an important basis from which to build on for applications in biocatalysis, metabolic engineering, and synthetic biology to enable biobased processes that are greener and cleaner for the environment. This review article highlights the current state of knowledge regarding the enzymatic reactions used in converting biobased wastes (lignocellulosic biomass, sugar, phenolic acid, triglyceride, fatty acid, and glycerol) and greenhouse gases (CO2 and CH4) into value-added products and discusses the current progress made in their metabolic engineering. The commercial aspects and life cycle assessment of products from enzymatic and metabolic engineering are also discussed. Continued development in the field of metabolic engineering would offer diversified solutions which are sustainable and renewable for manufacturing valuable chemicals.
Collapse
Affiliation(s)
- Pattarawan Intasian
- School of Biomolecular Science and Engineering, Vidyasirimedhi Institute of Science and Technology (VISTEC), Wangchan Valley, Rayong 21210, Thailand
| | - Kridsadakorn Prakinee
- School of Biomolecular Science and Engineering, Vidyasirimedhi Institute of Science and Technology (VISTEC), Wangchan Valley, Rayong 21210, Thailand
| | - Aisaraphon Phintha
- School of Biomolecular Science and Engineering, Vidyasirimedhi Institute of Science and Technology (VISTEC), Wangchan Valley, Rayong 21210, Thailand.,Department of Biochemistry and Center for Excellence in Protein and Enzyme Technology, Faculty of Science, Mahidol University, Bangkok 10400, Thailand
| | - Duangthip Trisrivirat
- School of Biomolecular Science and Engineering, Vidyasirimedhi Institute of Science and Technology (VISTEC), Wangchan Valley, Rayong 21210, Thailand
| | - Nopphon Weeranoppanant
- School of Biomolecular Science and Engineering, Vidyasirimedhi Institute of Science and Technology (VISTEC), Wangchan Valley, Rayong 21210, Thailand.,Department of Chemical Engineering, Faculty of Engineering, Burapha University, 169, Long-hard Bangsaen, Saensook, Muang, Chonburi 20131, Thailand
| | - Thanyaporn Wongnate
- School of Biomolecular Science and Engineering, Vidyasirimedhi Institute of Science and Technology (VISTEC), Wangchan Valley, Rayong 21210, Thailand
| | - Pimchai Chaiyen
- School of Biomolecular Science and Engineering, Vidyasirimedhi Institute of Science and Technology (VISTEC), Wangchan Valley, Rayong 21210, Thailand
| |
Collapse
|
6
|
Building cell factories for the production of advanced fuels. Biochem Soc Trans 2020; 47:1701-1714. [PMID: 31803925 DOI: 10.1042/bst20190168] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2019] [Revised: 11/13/2019] [Accepted: 11/15/2019] [Indexed: 12/31/2022]
Abstract
Synthetic biology-based engineering strategies are being extensively employed for microbial production of advanced fuels. Advanced fuels, being comparable in energy efficiency and properties to conventional fuels, have been increasingly explored as they can be directly incorporated into the current fuel infrastructure without the need for reconstructing the pre-existing set-up rendering them economically viable. Multiple metabolic engineering approaches have been used for rewiring microbes to improve existing or develop newly programmed cells capable of efficient fuel production. The primary challenge in using these approaches is improving the product yield for the feasibility of the commercial processes. Some of the common roadblocks towards enhanced fuel production include - limited availability of flux towards precursors and desired pathways due to presence of competing pathways, limited cofactor and energy supply in cells, the low catalytic activity of pathway enzymes, obstructed product transport, and poor tolerance of host cells for end products. Consequently, despite extensive studies on the engineering of microbial hosts, the costs of industrial-scale production of most of these heterologously produced fuel compounds are still too high. Though considerable progress has been made towards successfully producing some of these biofuels, a substantial amount of work needs to be done for improving the titers of others. In this review, we have summarized the different engineering strategies that have been successfully used for engineering pathways into commercial hosts for the production of advanced fuels and different approaches implemented for tuning host strains and pathway enzymes for scaling up production levels.
Collapse
|
7
|
Valle A, Cantero D, Bolívar J. Metabolic engineering for the optimization of hydrogen production in Escherichia coli: A review. Biotechnol Adv 2019; 37:616-633. [DOI: 10.1016/j.biotechadv.2019.03.006] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2018] [Revised: 03/05/2019] [Accepted: 03/07/2019] [Indexed: 12/29/2022]
|
8
|
Westbrook AW, Miscevic D, Kilpatrick S, Bruder MR, Moo-Young M, Chou CP. Strain engineering for microbial production of value-added chemicals and fuels from glycerol. Biotechnol Adv 2019; 37:538-568. [DOI: 10.1016/j.biotechadv.2018.10.006] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2017] [Revised: 10/03/2018] [Accepted: 10/10/2018] [Indexed: 12/22/2022]
|
9
|
Escherichia coli as a host for metabolic engineering. Metab Eng 2018; 50:16-46. [DOI: 10.1016/j.ymben.2018.04.008] [Citation(s) in RCA: 181] [Impact Index Per Article: 30.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2018] [Revised: 04/11/2018] [Accepted: 04/12/2018] [Indexed: 12/21/2022]
|
10
|
Zakaria MA, Mohd Yusoff MZ, Zakaria MR, Hassan MA, Wood TK, Maeda T. Pseudogene product YqiG is important for pflB expression and biohydrogen production in Escherichia coli BW25113. 3 Biotech 2018; 8:435. [PMID: 30306004 DOI: 10.1007/s13205-018-1461-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2018] [Accepted: 09/24/2018] [Indexed: 01/08/2023] Open
Abstract
Pseudogenes in the Escherichia coli genome are assumed to be non-functional. In this study, Keio collection BW25113∆yqiG and YqiG-producing strain (BW25113/pCA24N-YqiG) were used to evaluate the importance of pseudogene yqiG in hydrogen metabolism. Our results show pseudogene protein YqiG was identified as an essential protein in the production of biohydrogen from glucose. The mutant yqiG decreased biohydrogen production from 37 µmol mg-1 protein to 6 µmol mg-1 protein compared to the wild-type strain, and glucose consumption was reduced by 80%. Through transcriptional analysis, we found that the yqiG mutation represses pflB transcription tenfold; pflB encodes pyruvate-formate lyase, one of the key enzymes in the anaerobic metabolism of E. coli. Moreover, production of YqiG stimulated glycolysis and increased biohydrogen productivity 1.5-fold compared to that of the wild-type strain. Thus, YqiG is important for the central glycolysis reaction and is able to influence hydrogen metabolism activity in E. coli.
Collapse
Affiliation(s)
- Muhammad Azman Zakaria
- 1Department of Bioprocess Technology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400 UPM Serdang, Selangor Malaysia
| | - Mohd Zulkhairi Mohd Yusoff
- 1Department of Bioprocess Technology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400 UPM Serdang, Selangor Malaysia
- 2Laboratory of Biopolymer and Derivatives, Institute of Tropical Forestry and Forest Products, Universiti Putra Malaysia, 43400 UPM Serdang, Selangor Malaysia
| | - Mohd Rafein Zakaria
- 1Department of Bioprocess Technology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400 UPM Serdang, Selangor Malaysia
- 2Laboratory of Biopolymer and Derivatives, Institute of Tropical Forestry and Forest Products, Universiti Putra Malaysia, 43400 UPM Serdang, Selangor Malaysia
| | - Mohd Ali Hassan
- 1Department of Bioprocess Technology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400 UPM Serdang, Selangor Malaysia
| | - Thomas K Wood
- 3Department of Chemical Engineering and Biochemistry and Molecular Biology, Pennsylvania State University, 161 Fenske Laboratory, University Park, PA 16802 USA
| | - Toshinari Maeda
- 4Department of Biological Functions Engineering, Graduate School of Life Science and Systems Engineering, Kyushu Institute of Technology, 2-4 Hibikino, Wakamatsu-ku, Kitakyushu, Fukuoka 808-0196 Japan
| |
Collapse
|
11
|
Microbial Production of l-Serine from Renewable Feedstocks. Trends Biotechnol 2018; 36:700-712. [DOI: 10.1016/j.tibtech.2018.02.001] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2017] [Revised: 01/30/2018] [Accepted: 02/01/2018] [Indexed: 11/21/2022]
|
12
|
Current state and perspectives in hydrogen production by Escherichia coli: roles of hydrogenases in glucose or glycerol metabolism. Appl Microbiol Biotechnol 2018; 102:2041-2050. [DOI: 10.1007/s00253-018-8752-8] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2017] [Revised: 12/28/2017] [Accepted: 12/29/2017] [Indexed: 01/07/2023]
|
13
|
Soo CS, Yap WS, Hon WM, Ramli N, Md Shah UK, Phang LY. Co-production of hydrogen and ethanol by Escherichia coli SS1 and its recombinant. ELECTRON J BIOTECHN 2017. [DOI: 10.1016/j.ejbt.2017.09.002] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
|
14
|
Michalowski A, Siemann-Herzberg M, Takors R. Escherichia coli HGT: Engineered for high glucose throughput even under slowly growing or resting conditions. Metab Eng 2017; 40:93-103. [PMID: 28110078 DOI: 10.1016/j.ymben.2017.01.005] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2016] [Revised: 12/01/2016] [Accepted: 01/16/2017] [Indexed: 12/27/2022]
Abstract
Aerobic production-scale processes are constrained by the technical limitations of maximum oxygen transfer and heat removal. Consequently, microbial activity is often controlled via limited nutrient feeding to maintain it within technical operability. Here, we present an alternative approach based on a newly engineered Escherichia coli strain. This E. coli HGT (high glucose throughput) strain was engineered by modulating the stringent response regulation program and decreasing the activity of pyruvate dehydrogenase. The strain offers about three-fold higher rates of cell-specific glucose uptake under nitrogen-limitation (0.6gGlc gCDW-1h-1) compared to that of wild type, with a maximum glucose uptake rate of about 1.8gGlc gCDW-1h-1 already at a 0.3h-1 specific growth rate. The surplus of imported glucose is almost completely available via pyruvate and is used to fuel pyruvate and lactate formation. Thus, E. coli HGT represents a novel chassis as a host for pyruvate-derived products.
Collapse
Affiliation(s)
- Annette Michalowski
- University of Stuttgart, Institute of Biochemical Engineering, Allmandring 31, 70569, Stuttgart, Germany
| | - Martin Siemann-Herzberg
- University of Stuttgart, Institute of Biochemical Engineering, Allmandring 31, 70569, Stuttgart, Germany.
| | - Ralf Takors
- University of Stuttgart, Institute of Biochemical Engineering, Allmandring 31, 70569, Stuttgart, Germany.
| |
Collapse
|
15
|
Valle A, Cabrera G, Cantero D, Bolivar J. Heterologous expression of the human Phosphoenol Pyruvate Carboxykinase (hPEPCK-M) improves hydrogen and ethanol synthesis in the Escherichia coli dcuD mutant when grown in a glycerol-based medium. N Biotechnol 2016; 35:1-12. [PMID: 27780757 DOI: 10.1016/j.nbt.2016.10.007] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2016] [Revised: 09/02/2016] [Accepted: 10/17/2016] [Indexed: 01/06/2023]
Abstract
The production of biodiesel has emerged as an alternative to fossil fuels. However, this industry generates glycerol as a by-product in such large quantities that it has become an environmental problem. The biotransformation of this excess glycerol into other renewable bio-energy sources, like H2 and ethanol, by microorganisms such as Escherichia coli is an interesting possibility that warrants investigation. In this work we hypothesized that the conversion of oxaloacetate (OAA) to phosphoenolpyruvate (PEP) could be improved by a controlled expression of the human mitochondrial GTP-dependent PEP carboxykinase. This heterologous expression was tested in several E. coli mutant backgrounds with increased availability of C4 intermediates. It was found that this metabolic rewiring improved the synthesis of the target products in several mutants, with the dcuD mutant being the most suitable background for hydrogen and ethanol specific productions and glycerol consumption. These factors increased by 2.46, 1.73 and 1.95 times, respectively, when compared to those obtained for the wild-type strain.
Collapse
Affiliation(s)
- Antonio Valle
- Department of Biomedicine, Biotechnology and Public Health-Biochemistry and Molecular Biology, Campus de Excelencia Internacional Agroalimentario (ceiA3), University of Cádiz, Avda. República Saharui s/n, 11510 Puerto Real, Cádiz, Spain.
| | - Gema Cabrera
- Department of Chemical Engineering and Food Technology, Campus de Excelencia Internacional Agroalimentario (ceiA3), University of Cádiz, Avda. República Saharaui s/n, 11510 Puerto Real, Cádiz, Spain
| | - Domingo Cantero
- Department of Chemical Engineering and Food Technology, Campus de Excelencia Internacional Agroalimentario (ceiA3), University of Cádiz, Avda. República Saharaui s/n, 11510 Puerto Real, Cádiz, Spain
| | - Jorge Bolivar
- Department of Biomedicine, Biotechnology and Public Health-Biochemistry and Molecular Biology, Campus de Excelencia Internacional Agroalimentario (ceiA3), University of Cádiz, Avda. República Saharui s/n, 11510 Puerto Real, Cádiz, Spain.
| |
Collapse
|
16
|
Roy S, Das D. Biohythane production from organic wastes: present state of art. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2016; 23:9391-9410. [PMID: 26507735 DOI: 10.1007/s11356-015-5469-4] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/11/2015] [Accepted: 09/21/2015] [Indexed: 06/05/2023]
Abstract
The economy of an industrialized country is greatly dependent on fossil fuels. However, these nonrenewable sources of energy are nearing the brink of extinction. Moreover, the reliance on these fuels has led to increased levels of pollution which have caused serious adverse impacts on the environment. Hydrogen has emerged as a promising alternative since it does not produce CO2 during combustion and also has the highest calorific value. The biohythane process comprises of biohydrogen production followed by biomethanation. Biological H2 production has an edge over its chemical counterpart mainly because it is environmentally benign. Maximization of gaseous energy recovery could be achieved by integrating dark fermentative hydrogen production followed by biomethanation. Intensive research work has already been carried out on the advancement of biohydrogen production processes, such as the development of suitable microbial consortium (mesophiles or thermophiles), genetically modified microorganism, improvement of the reactor designs, use of different solid matrices for the immobilization of whole cells, and development of two-stage process for higher rate of H2 production. Scale-up studies of the dark fermentation process was successfully carried out in 20- and 800-L reactors. However, the total gaseous energy recovery for two stage process was found to be 53.6 %. From single-stage H2 production, gaseous energy recovery was only 28 %. Thus, two-stage systems not only help in improving gaseous energy recovery but also can make biohythane (mixture of H2 and CH4) concept commercially feasible.
Collapse
Affiliation(s)
- Shantonu Roy
- Department of Biotechnology, Indian Institute of Technology, Kharagpur, 721302, India
| | - Debabrata Das
- Department of Biotechnology, Indian Institute of Technology, Kharagpur, 721302, India.
| |
Collapse
|
17
|
Kalia VC, Prakash J, Koul S. Biorefinery for Glycerol Rich Biodiesel Industry Waste. Indian J Microbiol 2016; 56:113-25. [PMID: 27570302 DOI: 10.1007/s12088-016-0583-7] [Citation(s) in RCA: 50] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2016] [Accepted: 04/12/2016] [Indexed: 11/30/2022] Open
Abstract
The biodiesel industry has the potential to meet the fuel requirements in the future. A few inherent lacunae of this bioprocess are the effluent, which is 10 % of the actual product, and the fact that it is 85 % glycerol along with a few impurities. Biological treatments of wastes have been known as a dependable and economical direction of overseeing them and bring some value added products as well. A novel eco-biotechnological strategy employs metabolically diverse bacteria, which ensures higher reproducibility and economics. In this article, we have opined, which organisms and what bioproducts should be the focus, while exploiting glycerol as feed.
Collapse
Affiliation(s)
- Vipin Chandra Kalia
- Microbial Biotechnology and Genomics, CSIR - Institute of Genomics and Integrative Biology (IGIB), Delhi University Campus, Mall Road, Delhi, 110007 India ; Academy for Scientific and Innovative Research (AcSIR), 2 Rafi Marg, New Delhi, 110001 India
| | - Jyotsana Prakash
- Microbial Biotechnology and Genomics, CSIR - Institute of Genomics and Integrative Biology (IGIB), Delhi University Campus, Mall Road, Delhi, 110007 India ; Academy for Scientific and Innovative Research (AcSIR), 2 Rafi Marg, New Delhi, 110001 India
| | - Shikha Koul
- Microbial Biotechnology and Genomics, CSIR - Institute of Genomics and Integrative Biology (IGIB), Delhi University Campus, Mall Road, Delhi, 110007 India ; Academy for Scientific and Innovative Research (AcSIR), 2 Rafi Marg, New Delhi, 110001 India
| |
Collapse
|
18
|
Boboescu IZ, Gherman VD, Lakatos G, Pap B, Bíró T, Maróti G. Surpassing the current limitations of biohydrogen production systems: The case for a novel hybrid approach. BIORESOURCE TECHNOLOGY 2016; 204:192-201. [PMID: 26790867 DOI: 10.1016/j.biortech.2015.12.083] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/06/2015] [Revised: 12/22/2015] [Accepted: 12/28/2015] [Indexed: 06/05/2023]
Abstract
The steadily increase of global energy requirements has brought about a general agreement on the need for novel renewable and environmentally friendly energy sources and carriers. Among the alternatives to a fossil fuel-based economy, hydrogen gas is considered a game-changer. Certain methods of hydrogen production can utilize various low-priced industrial and agricultural wastes as substrate, thus coupling organic waste treatment with renewable energy generation. Among these approaches, different biological strategies have been investigated and successfully implemented in laboratory-scale systems. Although promising, several key aspects need further investigation in order to push these technologies towards large-scale industrial implementation. Some of the major scientific and technical bottlenecks will be discussed, along with possible solutions, including a thorough exploration of novel research combining microbial dark fermentation and algal photoheterotrophic degradation systems, integrated with wastewater treatment and metabolic by-products usage.
Collapse
Affiliation(s)
- Iulian Zoltan Boboescu
- Polytechnic University of Timisoara, Victoriei Square, nr. 2, 300006 Timisoara, Romania; Hungarian Academy of Sciences, Biological Research Centre Szeged, Temesvari krt. 62, 6726 Szeged, Hungary
| | - Vasile Daniel Gherman
- Polytechnic University of Timisoara, Victoriei Square, nr. 2, 300006 Timisoara, Romania
| | - Gergely Lakatos
- Hungarian Academy of Sciences, Biological Research Centre Szeged, Temesvari krt. 62, 6726 Szeged, Hungary
| | - Bernadett Pap
- Seqomics Biotechnology Ltd., Vállalkozók útja 7, 6782 Mórahalom, Hungary
| | - Tibor Bíró
- Szent István University, Faculty of Economics, Agricultural and Health Studies, Szarvas, Hungary
| | - Gergely Maróti
- Polytechnic University of Timisoara, Victoriei Square, nr. 2, 300006 Timisoara, Romania; Hungarian Academy of Sciences, Biological Research Centre Szeged, Temesvari krt. 62, 6726 Szeged, Hungary.
| |
Collapse
|
19
|
Sun X, Shen X, Jain R, Lin Y, Wang J, Sun J, Wang J, Yan Y, Yuan Q. Synthesis of chemicals by metabolic engineering of microbes. Chem Soc Rev 2016; 44:3760-85. [PMID: 25940754 DOI: 10.1039/c5cs00159e] [Citation(s) in RCA: 75] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Metabolic engineering is a powerful tool for the sustainable production of chemicals. Over the years, the exploration of microbial, animal and plant metabolism has generated a wealth of valuable genetic information. The prudent application of this knowledge on cellular metabolism and biochemistry has enabled the construction of novel metabolic pathways that do not exist in nature or enhance existing ones. The hand in hand development of computational technology, protein science and genetic manipulation tools has formed the basis of powerful emerging technologies that make the production of green chemicals and fuels a reality. Microbial production of chemicals is more feasible compared to plant and animal systems, due to simpler genetic make-up and amenable growth rates. Here, we summarize the recent progress in the synthesis of biofuels, value added chemicals, pharmaceuticals and nutraceuticals via metabolic engineering of microbes.
Collapse
Affiliation(s)
- Xinxiao Sun
- State Key Laboratory of Chemical Resource Engineering, Beijing University of Chemical Technology, 15#, Beisanhuan East Road, Chaoyang District, Beijing 100029, China.
| | | | | | | | | | | | | | | | | |
Collapse
|
20
|
Lu Y, Zhao H, Zhang C, Xing XH. Insights into the global regulation of anaerobic metabolism for improved biohydrogen production. BIORESOURCE TECHNOLOGY 2016; 200:35-41. [PMID: 26476162 DOI: 10.1016/j.biortech.2015.10.007] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/26/2015] [Revised: 10/02/2015] [Accepted: 10/06/2015] [Indexed: 06/05/2023]
Abstract
To improve the biohydrogen yield in bacterial dark fermentation, a new approach of global anaerobic regulation was introduced. Two cellular global regulators FNR and NarP were overexpressed in two model organisms: facultatively anaerobic Enterobacter aerogenes (Ea) and strictly anaerobic Clostridium paraputrificum (Cp). The overexpression of FNR and NarP greatly altered anaerobic metabolism and increased the hydrogen yield by 40%. Metabolic analysis showed that the global regulation caused more reducing environment inside the cell. To get a thorough understanding of the global metabolic regulation, more genes (fdhF, fhlA, ppk, Cb-fdh1, and Sc-fdh1) were overexpressed in different Ea and Cp mutants. For the first time, it demonstrated that there were approximately linear relationships between the relative change of hydrogen yield and the relative change of NADH yield or ATP yield. It implied that cellular reducing power and energy level played vital roles in the biohydrogen production.
Collapse
Affiliation(s)
- Yuan Lu
- Key Lab of Industrial Biocatalysis of Ministry of Education (Tsinghua University), China; Institute of Biochemical Engineering, Department of Chemical Engineering, Tsinghua University, Beijing 100084, China
| | - Hongxin Zhao
- Key Lab of Industrial Biocatalysis of Ministry of Education (Tsinghua University), China; Institute of Biochemical Engineering, Department of Chemical Engineering, Tsinghua University, Beijing 100084, China; Zhejiang Province Key Laboratory of Plant Secondary Metabolism and Regulation, College of Life Sciences, Zhejiang Sci-Tech University, Hangzhou 310018, China; College of Chemistry and Life Sciences, Shenyang Normal University, Shenyang 110034, China
| | - Chong Zhang
- Key Lab of Industrial Biocatalysis of Ministry of Education (Tsinghua University), China; Institute of Biochemical Engineering, Department of Chemical Engineering, Tsinghua University, Beijing 100084, China
| | - Xin-Hui Xing
- Key Lab of Industrial Biocatalysis of Ministry of Education (Tsinghua University), China; Institute of Biochemical Engineering, Department of Chemical Engineering, Tsinghua University, Beijing 100084, China.
| |
Collapse
|
21
|
Abstract
In Escherichia coli, hydrogen metabolism plays a prominent role in anaerobic physiology. The genome contains the capability to produce and assemble up to four [NiFe]-hydrogenases, each of which are known, or predicted, to contribute to different aspects of cellular metabolism. In recent years, there have been major advances in the understanding of the structure, function, and roles of the E. coli [NiFe]-hydrogenases. The membrane-bound, periplasmically oriented, respiratory Hyd-1 isoenzyme has become one of the most important paradigm systems for understanding an important class of oxygen-tolerant enzymes, as well as providing key information on the mechanism of hydrogen activation per se. The membrane-bound, periplasmically oriented, Hyd-2 isoenzyme has emerged as an unusual, bidirectional redox valve able to link hydrogen oxidation to quinone reduction during anaerobic respiration, or to allow disposal of excess reducing equivalents as hydrogen gas. The membrane-bound, cytoplasmically oriented, Hyd-3 isoenzyme is part of the formate hydrogenlyase complex, which acts to detoxify excess formic acid under anaerobic fermentative conditions and is geared towards hydrogen production under those conditions. Sequence identity between some Hyd-3 subunits and those of the respiratory NADH dehydrogenases has led to hypotheses that the activity of this isoenzyme may be tightly coupled to the formation of transmembrane ion gradients. Finally, the E. coli genome encodes a homologue of Hyd-3, termed Hyd-4, however strong evidence for a physiological role for E. coli Hyd-4 remains elusive. In this review, the versatile hydrogen metabolism of E. coli will be discussed and the roles and potential applications of the spectrum of different types of [NiFe]-hydrogenases available will be explored.
Collapse
|
22
|
Lin J, Zhang Y, Xu D, Xiang G, Jia Z, Fu S, Gong H. Deletion of poxB, pta, and ackA improves 1,3-propanediol production by Klebsiella pneumoniae. Appl Microbiol Biotechnol 2015; 100:2775-84. [DOI: 10.1007/s00253-015-7237-2] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2015] [Revised: 11/29/2015] [Accepted: 12/07/2015] [Indexed: 12/24/2022]
|
23
|
Kelly CL, Pinske C, Murphy BJ, Parkin A, Armstrong F, Palmer T, Sargent F. Integration of an [FeFe]-hydrogenase into the anaerobic metabolism of Escherichia coli. BIOTECHNOLOGY REPORTS (AMSTERDAM, NETHERLANDS) 2015; 8:94-104. [PMID: 26839796 PMCID: PMC4694547 DOI: 10.1016/j.btre.2015.10.002] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/01/2015] [Accepted: 10/06/2015] [Indexed: 01/19/2023]
Abstract
Biohydrogen is a potentially useful product of microbial energy metabolism. One approach to engineering biohydrogen production in bacteria is the production of non-native hydrogenase activity in a host cell, for example Escherichia coli. In some microbes, hydrogenase enzymes are linked directly to central metabolism via diaphorase enzymes that utilise NAD+/NADH cofactors. In this work, it was hypothesised that heterologous production of an NAD+/NADH-linked hydrogenase could connect hydrogen production in an E. coli host directly to its central metabolism. To test this, a synthetic operon was designed and characterised encoding an apparently NADH-dependent, hydrogen-evolving [FeFe]-hydrogenase from Caldanaerobacter subterranus. The synthetic operon was stably integrated into the E. coli chromosome and shown to produce an active hydrogenase, however no H2 production was observed. Subsequently, it was found that heterologous co-production of a pyruvate::ferredoxin oxidoreductase and ferredoxin from Thermotoga maritima was found to be essential to drive H2 production by this system. This work provides genetic evidence that the Ca.subterranus [FeFe]-hydrogenase could be operating in vivo as an electron-confurcating enzyme.
Collapse
Affiliation(s)
- Ciarán L. Kelly
- School of Life Sciences, University of Dundee, Dundee, Scotland DD1 5EH, UK
| | - Constanze Pinske
- School of Life Sciences, University of Dundee, Dundee, Scotland DD1 5EH, UK
| | - Bonnie J. Murphy
- Department of Chemistry, Inorganic Chemistry Laboratory, University of Oxford, Oxford OX1 3QR, UK
| | - Alison Parkin
- Department of Chemistry, University of York, Heslington, York YO10 5DD, UK
| | - Fraser Armstrong
- Department of Chemistry, Inorganic Chemistry Laboratory, University of Oxford, Oxford OX1 3QR, UK
| | - Tracy Palmer
- School of Life Sciences, University of Dundee, Dundee, Scotland DD1 5EH, UK
| | - Frank Sargent
- School of Life Sciences, University of Dundee, Dundee, Scotland DD1 5EH, UK
| |
Collapse
|
24
|
Khosraviani M, Saheb Zamani M, Bidkhori G. FogLight: an efficient matrix-based approach to construct metabolic pathways by search space reduction. Bioinformatics 2015; 32:398-408. [PMID: 26454274 DOI: 10.1093/bioinformatics/btv578] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2015] [Accepted: 10/02/2015] [Indexed: 12/31/2022] Open
Abstract
MOTIVATION A fundamental computational problem in the area of metabolic engineering is finding metabolic pathways between a pair of source and target metabolites efficiently. We present an approach, namely FogLight, for searching metabolic networks utilizing Boolean (AND-OR) operations represented in matrix notation to efficiently reduce the search space. This enables the enumeration of all pathways between metabolites that are too distant for the application of brute-force methods. RESULTS Benchmarking tests run with FogLight show that it can reduce the search space by up to 98%, after which the accelerated search for high accurate results is guaranteed. Using FogLight, several pathways between eight given pairs of metabolites are found of which the pathways from CO2 to ethanol are specifically discussed. Additionally, in comparison with three path-finding tools, namely PHT, FMM and RouteSearch, FogLight can find shorter and more pathways for attempted source-target metabolite pairs. CONTACT szamani@aut.ac.ir, gholamreza.bidkhori@vtt.fi SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
Collapse
Affiliation(s)
- Mehrshad Khosraviani
- Department of Computer Engineering & IT, Amirkabir University of Technology, Tehran, Iran and
| | - Morteza Saheb Zamani
- Department of Computer Engineering & IT, Amirkabir University of Technology, Tehran, Iran and
| | - Gholamreza Bidkhori
- Department of Computer Engineering & IT, Amirkabir University of Technology, Tehran, Iran and
| |
Collapse
|
25
|
Valle A, Cabrera G, Muhamadali H, Trivedi DK, Ratray NJW, Goodacre R, Cantero D, Bolivar J. A systematic analysis of TCA
Escherichia coli
mutants reveals suitable genetic backgrounds for enhanced hydrogen and ethanol production using glycerol as main carbon source. Biotechnol J 2015; 10:1750-61. [DOI: 10.1002/biot.201500005] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2015] [Revised: 03/29/2015] [Accepted: 06/04/2015] [Indexed: 01/14/2023]
Affiliation(s)
- Antonio Valle
- Department of Biomedicine, Biotechnology and Public Health‐Biochemistry and Molecular Biology. Campus de Excelencia Internacional Agroalimentario (ceiA3), Institute of Biomolecules (INBIO), University of Cádiz, Puerto Real (Cádiz), Spain
| | - Gema Cabrera
- Department of Chemical Engineering and Food Technology. Campus de Excelencia Internacional Agroalimentario (ceiA3), University of Cádiz, Puerto Real (Cádiz), Spain
| | - Howbeer Muhamadali
- Manchester Institute of Biotechnology, School of Chemistry, University of Manchester, Manchester, United Kingdom
| | - Drupad K. Trivedi
- Manchester Institute of Biotechnology, School of Chemistry, University of Manchester, Manchester, United Kingdom
| | - Nicholas J. W. Ratray
- Manchester Institute of Biotechnology, School of Chemistry, University of Manchester, Manchester, United Kingdom
| | - Royston Goodacre
- Manchester Institute of Biotechnology, School of Chemistry, University of Manchester, Manchester, United Kingdom
| | - Domingo Cantero
- Department of Chemical Engineering and Food Technology. Campus de Excelencia Internacional Agroalimentario (ceiA3), University of Cádiz, Puerto Real (Cádiz), Spain
| | - Jorge Bolivar
- Department of Biomedicine, Biotechnology and Public Health‐Biochemistry and Molecular Biology. Campus de Excelencia Internacional Agroalimentario (ceiA3), Institute of Biomolecules (INBIO), University of Cádiz, Puerto Real (Cádiz), Spain
| |
Collapse
|
26
|
Valle A, Cabrera G, Cantero D, Bolivar J. Identification of enhanced hydrogen and ethanol Escherichia coli producer strains in a glycerol-based medium by screening in single-knock out mutant collections. Microb Cell Fact 2015; 14:93. [PMID: 26122736 PMCID: PMC4485358 DOI: 10.1186/s12934-015-0285-6] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2015] [Accepted: 06/16/2015] [Indexed: 01/25/2023] Open
Abstract
BACKGROUND Earth's climate is warming as a result of anthropogenic emissions of greenhouse gases from fossil fuel combustion. Bioenergy, which includes biodiesel, biohydrogen and bioethanol, has emerged as a sustainable alternative fuel source. For this reason, in recent years biodiesel production has become widespread but this industry currently generates a huge amount of glycerol as a by-product, which has become an environmental problem in its own right. A feasible possibility to solve this problem is the use of waste glycerol as a carbon source for microbial transformation into biofuels such as hydrogen and ethanol. For instance, Escherichia coli is a microorganism that can synthesize these compounds under anaerobic conditions. RESULTS In this work an experimental procedure was established for screening E. coli single mutants to identify strains with enhanced ethanol and/or H2 productions compared to the wild type strain. In an initial screening of 150 single mutants, 12 novel strains (gnd, tdcE, rpiA nanE, tdcB, deoB, sucB, cpsG, frmA, glgC, fumA and gadB) were found to provide enhanced yields for at least one of the target products. The mutations, that improve most significantly the parameters evaluated (gnd and tdcE genes), were combined with other mutations in three engineered E. coli mutant strains in order to further redirect carbon flux towards the desired products. CONCLUSIONS This methodology can be a useful tool to disclose the metabolic pathways that are more susceptible to manipulation in order to obtain higher molar yields of hydrogen and ethanol using glycerol as main carbon source in multiple E. coli mutants.
Collapse
Affiliation(s)
- Antonio Valle
- Department of Biomedicine, Biotechnology and Public Health-Biochemistry and Molecular Biology, Campus de Excelencia Internacional Agroalimentario (ceiA3), Institute of Biomolecules, University of Cádiz, Avda República Saharui s/n, 11510, Puerto Real, Cádiz, Spain.
| | - Gema Cabrera
- Department of Chemical Engineering and Food Technology, Campus de Excelencia Internacional Agroalimentario (ceiA3), University of Cádiz, Avda República Saharui s/n, 11510, Puerto Real, Cádiz, Spain.
| | - Domingo Cantero
- Department of Chemical Engineering and Food Technology, Campus de Excelencia Internacional Agroalimentario (ceiA3), University of Cádiz, Avda República Saharui s/n, 11510, Puerto Real, Cádiz, Spain.
| | - Jorge Bolivar
- Department of Biomedicine, Biotechnology and Public Health-Biochemistry and Molecular Biology, Campus de Excelencia Internacional Agroalimentario (ceiA3), Institute of Biomolecules, University of Cádiz, Avda República Saharui s/n, 11510, Puerto Real, Cádiz, Spain.
| |
Collapse
|
27
|
Unthan S, Baumgart M, Radek A, Herbst M, Siebert D, Brühl N, Bartsch A, Bott M, Wiechert W, Marin K, Hans S, Krämer R, Seibold G, Frunzke J, Kalinowski J, Rückert C, Wendisch VF, Noack S. Chassis organism from Corynebacterium glutamicum--a top-down approach to identify and delete irrelevant gene clusters. Biotechnol J 2015; 10:290-301. [PMID: 25139579 PMCID: PMC4361050 DOI: 10.1002/biot.201400041] [Citation(s) in RCA: 89] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2014] [Revised: 07/25/2014] [Accepted: 08/19/2014] [Indexed: 01/05/2023]
Abstract
For synthetic biology applications, a robust structural basis is required, which can be constructed either from scratch or in a top-down approach starting from any existing organism. In this study, we initiated the top-down construction of a chassis organism from Corynebacterium glutamicum ATCC 13032, aiming for the relevant gene set to maintain its fast growth on defined medium. We evaluated each native gene for its essentiality considering expression levels, phylogenetic conservation, and knockout data. Based on this classification, we determined 41 gene clusters ranging from 3.7 to 49.7 kbp as target sites for deletion. 36 deletions were successful and 10 genome-reduced strains showed impaired growth rates, indicating that genes were hit, which are relevant to maintain biological fitness at wild-type level. In contrast, 26 deleted clusters were found to include exclusively irrelevant genes for growth on defined medium. A combinatory deletion of all irrelevant gene clusters would, in a prophage-free strain, decrease the size of the native genome by about 722 kbp (22%) to 2561 kbp. Finally, five combinatory deletions of irrelevant gene clusters were investigated. The study introduces the novel concept of relevant genes and demonstrates general strategies to construct a chassis suitable for biotechnological application.
Collapse
Affiliation(s)
- Simon Unthan
- Institute of Bio- and Geosciences, IBG-1: Biotechnology, Systems BiotechnologyForschungszentrum Jülich, Jülich, Germany
| | - Meike Baumgart
- Institute of Bio- and Geosciences, IBG-1: Biotechnology, Systemic MicrobiologyForschungszentrum Jülich, Jülich, Germany
| | - Andreas Radek
- Institute of Bio- and Geosciences, IBG-1: Biotechnology, Systems BiotechnologyForschungszentrum Jülich, Jülich, Germany
| | - Marius Herbst
- Chair of Genetics of Prokaryotes, Faculty of Biology & CeBiTec, Bielefeld UniversityBielefeld, Germany
| | - Daniel Siebert
- Chair of Genetics of Prokaryotes, Faculty of Biology & CeBiTec, Bielefeld UniversityBielefeld, Germany
| | - Natalie Brühl
- Institute of Biochemistry, University of CologneCologne, Germany
| | - Anna Bartsch
- Institute of Biochemistry, University of CologneCologne, Germany
| | - Michael Bott
- Institute of Bio- and Geosciences, IBG-1: Biotechnology, Systemic MicrobiologyForschungszentrum Jülich, Jülich, Germany
| | - Wolfgang Wiechert
- Institute of Bio- and Geosciences, IBG-1: Biotechnology, Systems BiotechnologyForschungszentrum Jülich, Jülich, Germany
| | - Kay Marin
- Evonik Degussa GmbHHalle/Westphalia, Germany
| | | | - Reinhard Krämer
- Institute of Biochemistry, University of CologneCologne, Germany
| | - Gerd Seibold
- Institute of Biochemistry, University of CologneCologne, Germany
| | - Julia Frunzke
- Institute of Bio- and Geosciences, IBG-1: Biotechnology, Systemic MicrobiologyForschungszentrum Jülich, Jülich, Germany
| | - Jörn Kalinowski
- Microbial Genomics and Biotechnology, Center for Biotechnology, Bielefeld UniversityBielefeld, Germany
| | - Christian Rückert
- Microbial Genomics and Biotechnology, Center for Biotechnology, Bielefeld UniversityBielefeld, Germany
| | - Volker F Wendisch
- Chair of Genetics of Prokaryotes, Faculty of Biology & CeBiTec, Bielefeld UniversityBielefeld, Germany
| | - Stephan Noack
- Institute of Bio- and Geosciences, IBG-1: Biotechnology, Systems BiotechnologyForschungszentrum Jülich, Jülich, Germany
| |
Collapse
|
28
|
Tran KT, Maeda T, Sanchez-Torres V, Wood TK. Beneficial knockouts in Escherichia coli for producing hydrogen from glycerol. Appl Microbiol Biotechnol 2015; 99:2573-81. [DOI: 10.1007/s00253-014-6338-7] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2014] [Revised: 12/12/2014] [Accepted: 12/14/2014] [Indexed: 12/28/2022]
|
29
|
Kurosawa K, Radek A, Plassmeier JK, Sinskey AJ. Improved glycerol utilization by a triacylglycerol-producing Rhodococcus opacus strain for renewable fuels. BIOTECHNOLOGY FOR BIOFUELS 2015; 8:31. [PMID: 25763105 PMCID: PMC4355421 DOI: 10.1186/s13068-015-0209-z] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/02/2014] [Accepted: 01/21/2015] [Indexed: 05/04/2023]
Abstract
BACKGROUND Glycerol generated during renewable fuel production processes is potentially an attractive substrate for the production of value-added materials by fermentation. An engineered strain MITXM-61 of the oleaginous bacterium Rhodococcus opacus produces large amounts of intracellular triacylglycerols (TAGs) for lipid-based biofuels on high concentrations of glucose and xylose. However, on glycerol medium, MITXM-61 does not produce TAGs and grows poorly. The aim of the present work was to construct a TAG-producing R. opacus strain capable of high-cell-density cultivation at high glycerol concentrations. RESULTS An adaptive evolution strategy was applied to improve the conversion of glycerol to TAGs in R. opacus MITXM-61. An evolved strain, MITGM-173, grown on a defined medium with 16 g L(-1) glycerol, produced 2.3 g L(-1) of TAGs, corresponding to 40.4% of the cell dry weight (CDW) and 0.144 g g(-1) of TAG yield per glycerol consumed. MITGM-173 was able to grow on high concentrations (greater than 150 g L(-1)) of glycerol. Cultivated in a medium containing an initial concentration of 20 g L(-1) glycerol, 40 g L(-1) glucose, and 40 g L(-1) xylose, MITGM-173 was capable of simultaneously consuming the mixed substrates and yielding 13.6 g L(-1) of TAGs, representing 51.2% of the CDM. In addition, when 20 g L(-1) glycerol was pulse-loaded into the culture with 40 g L(-1) glucose and 40 g L(-1) xylose at the stationary growth phase, MITGM-173 produced 14.3 g L(-1) of TAGs corresponding to 51.1% of the CDW although residual glycerol in the culture was observed. The addition of 20 g L(-1) glycerol in the glucose/xylose mix resulted in a TAG yield per glycerol consumed of 0.170 g g(-1) on the initial addition and 0.279 g g(-1) on the pulse addition of glycerol. CONCLUSION We have generated a TAG-producing R. opacus MITGM-173 strain that shows significantly improved glycerol utilization in comparison to the parental strain. The present study demonstrates that the evolved R. opacus strain shows significant promise for developing a cost-effective bioprocess to generate advanced renewable fuels from mixed sugar feedstocks supplemented with glycerol.
Collapse
Affiliation(s)
- Kazuhiko Kurosawa
- />Department of Biology, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139 USA
| | - Andreas Radek
- />Department of Biology, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139 USA
- />Present address: Institute of Bio- and Geosciences, IBG-1: Biotechnology, Systems Biotechnology, Forschungszentrum Juelich, 52425 Juelich, Germany
| | - Jens K Plassmeier
- />Department of Biology, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139 USA
| | - Anthony J Sinskey
- />Department of Biology, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139 USA
- />Engineering Systems Division, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139 USA
| |
Collapse
|
30
|
Physiology and bioenergetics of [NiFe]-hydrogenase 2-catalyzed H2-consuming and H2-producing reactions in Escherichia coli. J Bacteriol 2014; 197:296-306. [PMID: 25368299 DOI: 10.1128/jb.02335-14] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
Escherichia coli uptake hydrogenase 2 (Hyd-2) catalyzes the reversible oxidation of H2 to protons and electrons. Hyd-2 synthesis is strongly upregulated during growth on glycerol or on glycerol-fumarate. Membrane-associated Hyd-2 is an unusual heterotetrameric [NiFe]-hydrogenase that lacks a typical cytochrome b membrane anchor subunit, which transfers electrons to the quinone pool. Instead, Hyd-2 has an additional electron transfer subunit, termed HybA, with four predicted iron-sulfur clusters. Here, we examined the physiological role of the HybA subunit. During respiratory growth with glycerol and fumarate, Hyd-2 used menaquinone/demethylmenaquinone (MQ/DMQ) to couple hydrogen oxidation to fumarate reduction. HybA was essential for electron transfer from Hyd-2 to MQ/DMQ. H2 evolution catalyzed by Hyd-2 during fermentation of glycerol in the presence of Casamino Acids or in a fumarate reductase-negative strain growing with glycerol-fumarate was also shown to be dependent on both HybA and MQ/DMQ. The uncoupler carbonyl cyanide m-chlorophenylhydrazone (CCCP) inhibited Hyd-2-dependent H2 evolution from glycerol, indicating the requirement for a proton gradient. In contrast, CCCP failed to inhibit H2-coupled fumarate reduction. Although a Hyd-2 enzyme lacking HybA could not catalyze Hyd-2-dependent H2 oxidation or H2 evolution in whole cells, reversible H2-dependent reduction of viologen dyes still occurred. Finally, hydrogen-dependent dye reduction by Hyd-2 was reversibly inhibited in extracts derived from cells grown in H2 evolution mode. Our findings suggest that Hyd-2 switches between H2-consuming and H2-producing modes in response to the redox status of the quinone pool. Hyd-2-dependent H2 evolution from glycerol requires reverse electron transport.
Collapse
|
31
|
Kim J, Kim KJ. Cloning, expression, purification, crystallization and X-ray crystallographic analysis of the (S)-3-hydroxybutyryl-CoA dehydrogenase PaaH1 from Ralstonia eutropha H16. Acta Crystallogr F Struct Biol Commun 2014; 70:955-8. [PMID: 25005097 PMCID: PMC4089540 DOI: 10.1107/s2053230x14011881] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2014] [Accepted: 05/22/2014] [Indexed: 11/11/2022] Open
Abstract
The (S)-3-hydroxybutyryl-CoA dehydrogenase PaaH1 from Ralstonia eutropha (RePaaH1) is an enzyme used in the biosynthesis of n-butanol from acetyl-CoA by the reduction of acetoacetyl-CoA to (S)-3-hydroxybutyryl-CoA. The RePaaH1 protein was crystallized using the hanging-drop vapour-diffusion method in the presence of 1.4 M ammonium sulfate, 0.1 M sodium cacodylate pH 6.0, 0.2 M sodium chloride at 295 K. X-ray diffraction data were collected to a maximum resolution of 2.6 Å on a synchrotron beamline. The crystal belonged to space group P3221, with unit-cell parameters a=b=135.4, c=97.2 Å. With three molecules per asymmetric unit, the crystal volume per unit protein weight (VM) is 2.68 Å3 Da(-1), which corresponds to a solvent content of approximately 54.1%. The structure was solved by the single-wavelength anomalous dispersion method and refinement of the structure is in progress.
Collapse
Affiliation(s)
- Jieun Kim
- School of Life Sciences, KNU Creative BioResearch Group (BK21 plus program), Kyungpook National University, Daehak-ro 80, Buk-ku, Daegu 702-701, Republic of Korea
| | - Kyung-Jin Kim
- School of Life Sciences, KNU Creative BioResearch Group (BK21 plus program), Kyungpook National University, Daehak-ro 80, Buk-ku, Daegu 702-701, Republic of Korea
| |
Collapse
|
32
|
Kim J, Chang JH, Kim KJ. Crystal structure and biochemical properties of the (S)-3-hydroxybutyryl-CoA dehydrogenase PaaH1 from Ralstonia eutropha. Biochem Biophys Res Commun 2014; 448:163-8. [PMID: 24792376 DOI: 10.1016/j.bbrc.2014.04.101] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2014] [Accepted: 04/16/2014] [Indexed: 01/14/2023]
Abstract
3-Hydroxybutyryl-CoA dehydrogenase is an enzyme involved in the synthesis of the biofuel n-butanol by converting acetoacetyl-CoA to 3-hydroxybutyryl-CoA. To investigate the molecular mechanism of n-butanol biosynthesis, we determined crystal structures of the Ralstonia eutropha-derived 3-hydroxybutyryl-CoA dehydrogenase (RePaaH1) in complex with either its cofactor NAD(+) or its substrate acetoacetyl-CoA. While the biologically active structure is dimeric, the monomer of RePaaH1 comprises two separated domains with an N-terminal Rossmann fold and a C-terminal helical bundle for dimerization. In this study, we show that the cofactor-binding site is located on the Rossmann fold and is surrounded by five loops and one helix. The binding mode of the acetoacetyl-CoA substrate was found to be that the adenosine diphosphate moiety is not highly stabilized compared with the remainder of the molecule. Residues involved in catalysis and substrate binding were further confirmed by site-directed mutagenesis experiments, and kinetic properties of RePaaH1were examined as well. Our findings contribute to the understanding of 3-hydroxybutyryl-CoA dehydrogenase catalysis, and will be useful in enhancing the efficiency of n-butanol biosynthesis by structure based protein engineering.
Collapse
Affiliation(s)
- Jieun Kim
- School of Life Sciences, KNU Creative BioResearch Group (BK21 Plus Program), Kyungpook National University, Daehak-ro 80, Buk-ku, Daegu 702-701, Republic of Korea
| | - Jeong Ho Chang
- Department of Biology, Teachers College, Kyungpook National University, Daehak-ro 80, Buk-ku, Daegu 702-701, Republic of Korea
| | - Kyung-Jin Kim
- School of Life Sciences, KNU Creative BioResearch Group (BK21 Plus Program), Kyungpook National University, Daehak-ro 80, Buk-ku, Daegu 702-701, Republic of Korea.
| |
Collapse
|