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Tan JN, Ratra K, Singer SW, Simmons BA, Goswami S, Awasthi D. Methane to bioproducts: unraveling the potential of methanotrophs for biomanufacturing. Curr Opin Biotechnol 2024; 90:103210. [PMID: 39368401 DOI: 10.1016/j.copbio.2024.103210] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2024] [Revised: 06/24/2024] [Accepted: 09/11/2024] [Indexed: 10/07/2024]
Abstract
With the continuous increase in the world population, anthropogenic activities will generate more waste and create greenhouse gases such as methane, amplifying global warming. The biological conversion of methane into biochemicals is a sustainable solution to sequester and convert this greenhouse gas. Methanotrophic bacteria fulfill this role by utilizing methane as a feedstock while manufacturing various bioproducts. Recently, methanotrophs have made their mark in industrial biomanufacturing. However, unlike glucose-utilizing model organisms such as Escherichia coli and Saccharomyces cerevisiae, methanotrophs do not have established transformation methods and genetic tools, making these organisms challenging to engineer. Despite these challenges, recent advancements in methanotroph engineering demonstrate great promise, showcasing these C1-carbon-utilizing microbes as prospective hosts for bioproduction. This review discusses the recent developments and challenges in strain engineering, biomolecule production, and process development methodologies in the methanotroph field.
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Affiliation(s)
- Justin N Tan
- College of Arts and Sciences, University of California, Berkeley, CA 94720, USA
| | - Keshav Ratra
- College of Arts and Sciences, University of California, Berkeley, CA 94720, USA
| | - Steven W Singer
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA; Joint BioEnergy Institute, Emeryville, CA 94608, USA
| | - Blake A Simmons
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA; Joint BioEnergy Institute, Emeryville, CA 94608, USA
| | - Shubhasish Goswami
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.
| | - Deepika Awasthi
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA; Joint BioEnergy Institute, Emeryville, CA 94608, USA.
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2
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Ma Y, Liu S, Cui L, Fei Q, Wang Q. Turning food waste to microbial lipid towards a superb economic and environmental sustainability: An innovative integrated biological route. ENVIRONMENTAL RESEARCH 2024; 255:119125. [PMID: 38740293 DOI: 10.1016/j.envres.2024.119125] [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: 03/14/2024] [Revised: 05/06/2024] [Accepted: 05/09/2024] [Indexed: 05/16/2024]
Abstract
With the drastic growth of the economic and population, the global energy requirement is on the rise, and massive human and material resources have been put into the development of alternative and renewable energy sources. Biodiesel has been recognized as a green and sustainable alternative energy, but the raw materials-associated source and cost makes it difficult to achieve large-scale commercial production. Microbial lipids (ML) produced by oleaginous microbes have attracted more and more topics as feedstocks for biodiesel production because of their unique advantages (fast growth cycle, small footprint and so on). However, there are still many problems and challenges ahead towards commercialization of ML-based biodiesel, especially the cost of feedstock for ML production. Food waste (FW) rich in organic matters and nutrients is an excellent and almost zero-cost feedstock for ML production. However, current biological routes of FW-based ML production have some defects, which make it impossible to achieve full industrialization at present. Therefore, this review intends to provide a critical and comprehensive analysis of current biological routes of FW-based ML production with the focus on the challenges and solutions forward. The biological routes towards future FW-based ML production must be able to concurrently achieve economic feasibility and environmental sustainability. On this condition, an innovative integrated biological route for FW-based ML production has thus been put forward, which is also elucidated on its economic and environmental sustainability. Moreover, the prospective advantages, limitations and challenges for future scale-up of FW-based ML production have also been outlined, together with the perspectives and directions forward.
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Affiliation(s)
- Yingqun Ma
- School of Chemical Engineering and Technology, Xi'an Jiaotong University, Xi'an, 710049, China; Xi'an Key Laboratory of C1 Compound Bioconversion Technology, Xi'an Jiaotong University, Xi'an, 710049, China; Shaanxi Key Laboratory of Energy Chemical Process Intensification, Xi'an Jiaotong University, Xi'an, 710049, China.
| | - Shiman Liu
- School of Chemical Engineering and Technology, Xi'an Jiaotong University, Xi'an, 710049, China
| | - Lihui Cui
- School of Chemical Engineering and Technology, Xi'an Jiaotong University, Xi'an, 710049, China
| | - Qiang Fei
- School of Chemical Engineering and Technology, Xi'an Jiaotong University, Xi'an, 710049, China; Xi'an Key Laboratory of C1 Compound Bioconversion Technology, Xi'an Jiaotong University, Xi'an, 710049, China; Shaanxi Key Laboratory of Energy Chemical Process Intensification, Xi'an Jiaotong University, Xi'an, 710049, China.
| | - Qunhui Wang
- School of Energy and Environmental Engineering, University of Science and Technology Beijing, Beijing, 100083, China
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Huang C, Chen Y, Cheng S, Li M, Wang L, Cheng M, Li F, Cao Y, Song H. Enhanced acetate utilization for value-added chemicals production in Yarrowia lipolytica by integration of metabolic engineering and microbial electrosynthesis. Biotechnol Bioeng 2023; 120:3013-3024. [PMID: 37306471 DOI: 10.1002/bit.28465] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2023] [Revised: 05/19/2023] [Accepted: 05/31/2023] [Indexed: 06/13/2023]
Abstract
The limited supply of reducing power restricts the efficient utilization of acetate in Yarrowia lipolytica. Here, microbial electrosynthesis (MES) system, enabling direct conversion of inward electrons to NAD(P)H, was used to improve the production of fatty alcohols from acetate based on pathway engineering. First, the conversion efficiency of acetate to acetyl-CoA was reinforced by heterogenous expression of ackA-pta genes. Second, a small amount of glucose was used as cosubstrate to activate the pentose phosphate pathway and promote intracellular reducing cofactors synthesis. Third, through the employment of MES system, the final fatty alcohols production of the engineered strain YLFL-11 reached 83.8 mg/g dry cell weight (DCW), which was 6.17-fold higher than the initial production of YLFL-2 in shake flask. Furthermore, these strategies were also applied for the elevation of lupeol and betulinic acid synthesis from acetate in Y. lipolytica, demonstrating that our work provides a practical solution for cofactor supply and the assimilation of inferior carbon sources.
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Affiliation(s)
- Congcong Huang
- Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin, China
- Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin, China
| | - Yaru Chen
- Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin, China
- Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin, China
| | - Shuai Cheng
- Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin, China
- Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin, China
| | - Mengxu Li
- Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin, China
- Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin, China
| | - Luxin Wang
- Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin, China
- Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin, China
| | - Meijie Cheng
- Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin, China
- Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin, China
| | - Feng Li
- Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin, China
- Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin, China
| | - Yingxiu Cao
- Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin, China
- Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin, China
| | - Hao Song
- Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin, China
- Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin, China
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4
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Yang Y, Liu Y, Zhao H, Liu D, Zhang J, Cheng J, Yang Q, Chu H, Lu X, Luo M, Sheng X, Zhang YHPJ, Jiang H, Ma Y. Construction of an artificial phosphoketolase pathway that efficiently catabolizes multiple carbon sources to acetyl-CoA. PLoS Biol 2023; 21:e3002285. [PMID: 37733785 PMCID: PMC10547157 DOI: 10.1371/journal.pbio.3002285] [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: 01/10/2023] [Revised: 10/03/2023] [Accepted: 07/31/2023] [Indexed: 09/23/2023] Open
Abstract
The canonical glycolysis pathway is responsible for converting glucose into 2 molecules of acetyl-coenzyme A (acetyl-CoA) through a cascade of 11 biochemical reactions. Here, we have designed and constructed an artificial phosphoketolase (APK) pathway, which consists of only 3 types of biochemical reactions. The core enzyme in this pathway is phosphoketolase, while phosphatase and isomerase act as auxiliary enzymes. The APK pathway has the potential to achieve a 100% carbon yield to acetyl-CoA from any monosaccharide by integrating a one-carbon condensation reaction. We tested the APK pathway in vitro, demonstrating that it could efficiently catabolize typical C1-C6 carbohydrates to acetyl-CoA with yields ranging from 83% to 95%. Furthermore, we engineered Escherichia coli stain capable of growth utilizing APK pathway when glycerol act as a carbon source. This novel catabolic pathway holds promising route for future biomanufacturing and offering a stoichiometric production platform using multiple carbon sources.
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Affiliation(s)
- Yiqun Yang
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
- National Center of Technology Innovation for Synthetic Biology, Tianjin, China
| | - Yuwan Liu
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
- National Center of Technology Innovation for Synthetic Biology, Tianjin, China
- Haihe Laboratory of Synthetic Biology, Tianjin, China
| | - Haodong Zhao
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
- National Center of Technology Innovation for Synthetic Biology, Tianjin, China
- School of Life Sciences, University of Science and Technology of China, Hefei, Anhui, China
| | - Dingyu Liu
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
- National Center of Technology Innovation for Synthetic Biology, Tianjin, China
| | - Jie Zhang
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
- National Center of Technology Innovation for Synthetic Biology, Tianjin, China
- School of Life Sciences, University of Science and Technology of China, Hefei, Anhui, China
| | - Jian Cheng
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
- National Center of Technology Innovation for Synthetic Biology, Tianjin, China
| | - Qiaoyu Yang
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
- National Center of Technology Innovation for Synthetic Biology, Tianjin, China
| | - Huanyu Chu
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
- National Center of Technology Innovation for Synthetic Biology, Tianjin, China
| | - Xiaoyun Lu
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
- National Center of Technology Innovation for Synthetic Biology, Tianjin, China
| | - Mengting Luo
- School of Life Science and Technology, Wuhan Polytechnic University, Wuhan, China
| | - Xiang Sheng
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
- National Center of Technology Innovation for Synthetic Biology, Tianjin, China
| | - Yi-Heng P. J. Zhang
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
- National Center of Technology Innovation for Synthetic Biology, Tianjin, China
| | - Huifeng Jiang
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
- National Center of Technology Innovation for Synthetic Biology, Tianjin, China
- Haihe Laboratory of Synthetic Biology, Tianjin, China
| | - Yanhe Ma
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
- National Center of Technology Innovation for Synthetic Biology, Tianjin, China
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Chai A, Wong YS, Ong SA, Lutpi NA, Sam ST, Wirach T, Kee WC, Khoo HC. Exploring the potential of thermophilic anaerobic co-digestion between agro-industrial waste and water hyacinth: operational performance, kinetic study and degradation pathway. Bioprocess Biosyst Eng 2023:10.1007/s00449-023-02879-0. [PMID: 37160769 DOI: 10.1007/s00449-023-02879-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2022] [Accepted: 04/26/2023] [Indexed: 05/11/2023]
Abstract
Anaerobic co-digestion (co-AD) of agro-industrial waste, namely, palm oil mill effluent (POME) and sugarcane vinasse (Vn), with water hyacinth (WH) as co-substrate was carried out in two separate Anaerobic Suspended Growth Closed Bioreactors (ASGCBs) under thermophilic (55 °C) conditions. The highest chemical oxygen demand (COD) and soluble COD reduction in co-AD of POME-WH (78.61%, 78.86%) is slightly higher than co-AD of Vn-WH (75.75%, 78.24%). However, VFA reduction in co-AD of POME-WH (96.41%) is higher compared to co-AD of Vn-WH (85.94%). Subsequently, biogas production peaked at 13438 mL/day values and 16122 mL/day for co-AD of POME-WH and Vn-WH, respectively. However, the methane content was higher in the co-AD of POME-WH (72.04%) than in the co-AD of Vn-WH (69.86%). Growth yield (YG), maximum specific substrate utilization rate (rx,max) and maximum specific biomass growth rate (μmax) are higher in co-AD of POME-WH, as supported by the higher mixed liquor volatile suspended solids (MLVSS) and COD reduction efficiency compared to co-AD of Vn-WH. However, methane yield ([Formula: see text]) reported in the co-AD of POME-WH and Vn-WH are 0.2748 and 0.3112 L CH4/g CODreduction, respectively, which suggests that WH is a more suitable co-substrate for Vn compared to POME.
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Affiliation(s)
- Audrey Chai
- Faculty of Civil Engineering Technology, Universiti Malaysia Perlis, 02600, Arau, Perlis, Malaysia
| | - Yee-Shian Wong
- Faculty of Civil Engineering Technology, Universiti Malaysia Perlis, 02600, Arau, Perlis, Malaysia.
- Water Research and Environmental Sustainability Growth, Centre of Excellence (WAREG), Universiti Malaysia Perlis (UniMAP), Perlis, Malaysia.
| | - Soon-An Ong
- Faculty of Civil Engineering Technology, Universiti Malaysia Perlis, 02600, Arau, Perlis, Malaysia
- Water Research and Environmental Sustainability Growth, Centre of Excellence (WAREG), Universiti Malaysia Perlis (UniMAP), Perlis, Malaysia
| | - Nabilah Aminah Lutpi
- Faculty of Civil Engineering Technology, Universiti Malaysia Perlis, 02600, Arau, Perlis, Malaysia
- Water Research and Environmental Sustainability Growth, Centre of Excellence (WAREG), Universiti Malaysia Perlis (UniMAP), Perlis, Malaysia
| | - Sung-Ting Sam
- Faculty of Chemical Engineering Technology, Universiti Malaysia Perlis, 02600, Arau, Perlis, Malaysia
| | - Taweepreda Wirach
- Division of Physical Science, Faculty of Science, Prince of Songkla University, Songkhla, 90112, Thailand
| | - Wei-Chin Kee
- Faculty of Civil Engineering Technology, Universiti Malaysia Perlis, 02600, Arau, Perlis, Malaysia
| | - Hwa-Chuan Khoo
- Bio Synergy Laboratories Sdn Bhd, Lot 1109, Mukim Malau, Daerah Kubang PasuJitra, 06000, Kedah, Malaysia
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Bruinsma L, Martin-Pascual M, Kurnia K, Tack M, Hendriks S, van Kranenburg R, dos Santos VAPM. Increasing cellular fitness and product yields in Pseudomonas putida through an engineered phosphoketolase shunt. Microb Cell Fact 2023; 22:14. [PMID: 36658566 PMCID: PMC9850600 DOI: 10.1186/s12934-022-02015-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2022] [Accepted: 12/31/2022] [Indexed: 01/20/2023] Open
Abstract
BACKGROUND Pseudomonas putida has received increasing interest as a cell factory due to its remarkable features such as fast growth, a versatile and robust metabolism, an extensive genetic toolbox and its high tolerance to oxidative stress and toxic compounds. This interest is driven by the need to improve microbial performance to a level that enables biologically possible processes to become economically feasible, thereby fostering the transition from an oil-based economy to a more sustainable bio-based one. To this end, one of the current strategies is to maximize the product-substrate yield of an aerobic biocatalyst such as P. putida during growth on glycolytic carbon sources, such as glycerol and xylose. We demonstrate that this can be achieved by implementing the phosphoketolase shunt, through which pyruvate decarboxylation is prevented, and thus carbon loss is minimized. RESULTS In this study, we introduced the phosphoketolase shunt in the metabolism of P. putida KT2440. To maximize the effect of this pathway, we first tested and selected a phosphoketolase (Xfpk) enzyme with high activity in P. putida. Results of the enzymatic assays revealed that the most efficient Xfpk was the one isolated from Bifidobacterium breve. Using this enzyme, we improved the P. putida growth rate on glycerol and xylose by 44 and 167%, respectively, as well as the biomass yield quantified by OD600 by 50 and 30%, respectively. Finally, we demonstrated the impact on product formation and achieved a 38.5% increase in mevalonate and a 25.9% increase in flaviolin yield from glycerol. A similar effect was observed on the mevalonate-xylose and flaviolin-xylose yields, which increased by 48.7 and 49.4%, respectively. CONCLUSIONS Pseudomonas putida with the implemented Xfpk shunt grew faster, reached a higher final OD600nm and provided better product-substrate yields than the wild type. By reducing the pyruvate decarboxylation flux, we significantly improved the performance of this important workhorse for industrial applications. This work encompasses the first steps towards full implementation of the non-oxidative glycolysis (NOG) or the glycolysis alternative high carbon yield cycle (GATCHYC), in which a substrate is converted into products without CO2 loss These enhanced properties of P. putida will be crucial for its subsequent use in a range of industrial processes.
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Affiliation(s)
- Lyon Bruinsma
- grid.4818.50000 0001 0791 5666Laboratory of Systems and Synthetic Biology, Wageningen University & Research, 6708 WE Wageningen, The Netherlands
| | - Maria Martin-Pascual
- grid.4818.50000 0001 0791 5666Laboratory of Systems and Synthetic Biology, Wageningen University & Research, 6708 WE Wageningen, The Netherlands
| | - Kesi Kurnia
- grid.4818.50000 0001 0791 5666Laboratory of Systems and Synthetic Biology, Wageningen University & Research, 6708 WE Wageningen, The Netherlands ,grid.502801.e0000 0001 2314 6254Present Address: Faculty of Engineering and Natural Sciences, Tampere University, 33100 Tampere, Finland
| | - Marieken Tack
- grid.4818.50000 0001 0791 5666Laboratory of Systems and Synthetic Biology, Wageningen University & Research, 6708 WE Wageningen, The Netherlands
| | - Simon Hendriks
- grid.4818.50000 0001 0791 5666Laboratory of Systems and Synthetic Biology, Wageningen University & Research, 6708 WE Wageningen, The Netherlands
| | - Richard van Kranenburg
- grid.425710.50000 0004 4907 2152Corbion, 4206 AC Gorinchem, The Netherlands ,grid.4818.50000 0001 0791 5666Laboratory of Microbiology, Wageningen University & Research, 6708 WE Wageningen, The Netherlands
| | - Vitor A. P. Martins dos Santos
- grid.4818.50000 0001 0791 5666Laboratory of Systems and Synthetic Biology, Wageningen University & Research, 6708 WE Wageningen, The Netherlands ,grid.4818.50000 0001 0791 5666Laboratory Bioprocess Engineering, Wageningen University & Research, 6708 WE Wageningen, The Netherlands ,grid.435730.6LifeGlimmer GmbH, 12163 Berlin, Germany
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7
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Using the Mixed Culture of Fodder Mallow (Malva verticillata L.) and White Sweet Clover (Melilotus albus Medik.) for Methane Production. FERMENTATION 2022. [DOI: 10.3390/fermentation8030094] [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
The ever-growing number of biogas plants also leads to an increasing demand for suitable, alternative plant substrates. A currently dominant plant substrate is maize silage. However, intensive cultivation of maize (Zea mays L.) as an energy crop in monocultures poses risk to the environment (soil erosion, depletion of soil nutrient supplies, increased concentration of pests—Ostrinia nubilalis). In this study, results of experimental methane production from silages of alternative substrates, such as fodder mallow (Malva verticillata var. crispa L.; FM), white sweet clover (Melilotus albus Medik.; WSC) and their mixture, are presented. Based on the dry matter yield of a mixed culture of mallow and sweet clover, the value of the land equivalent ratio parameter (LER) was set as 1.05. The obtained LER (>1) value shows that the cultivation of the two tested crops in the mixed culture is more beneficial than their monocultures. Methane production from all three silage variants was fully comparable with results of methane production from the maize silage. Anaerobic fermentation of the mixture of FM and WSC did not result in higher methane yield than the average result of monosubstrates.
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8
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Klein VJ, Irla M, Gil López M, Brautaset T, Fernandes Brito L. Unravelling Formaldehyde Metabolism in Bacteria: Road towards Synthetic Methylotrophy. Microorganisms 2022; 10:microorganisms10020220. [PMID: 35208673 PMCID: PMC8879981 DOI: 10.3390/microorganisms10020220] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2021] [Revised: 01/14/2022] [Accepted: 01/17/2022] [Indexed: 12/26/2022] Open
Abstract
Formaldehyde metabolism is prevalent in all organisms, where the accumulation of formaldehyde can be prevented through the activity of dissimilation pathways. Furthermore, formaldehyde assimilatory pathways play a fundamental role in many methylotrophs, which are microorganisms able to build biomass and obtain energy from single- and multicarbon compounds with no carbon–carbon bonds. Here, we describe how formaldehyde is formed in the environment, the mechanisms of its toxicity to the cells, and the cell’s strategies to circumvent it. While their importance is unquestionable for cell survival in formaldehyde rich environments, we present examples of how the modification of native formaldehyde dissimilation pathways in nonmethylotrophic bacteria can be applied to redirect carbon flux toward heterologous, synthetic formaldehyde assimilation pathways introduced into their metabolism. Attempts to engineer methylotrophy into nonmethylotrophic hosts have gained interest in the past decade, with only limited successes leading to the creation of autonomous synthetic methylotrophy. Here, we discuss how native formaldehyde assimilation pathways can additionally be employed as a premise to achieving synthetic methylotrophy. Lastly, we discuss how emerging knowledge on regulation of formaldehyde metabolism can contribute to creating synthetic regulatory circuits applied in metabolic engineering strategies.
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9
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Awasthi D, Tang YH, Amer B, Baidoo EEK, Gin J, Chen Y, Petzold CJ, Kalyuzhnaya M, Singer SW. OUP accepted manuscript. J Ind Microbiol Biotechnol 2022; 49:6521446. [PMID: 35134957 PMCID: PMC9118986 DOI: 10.1093/jimb/kuac002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Accepted: 01/19/2022] [Indexed: 11/15/2022]
Abstract
Rhamnolipids (RLs) are well-studied biosurfactants naturally produced by pathogenic strains of Pseudomonas aeruginosa. Current methods to produce RLs in native and heterologous hosts have focused on carbohydrates as production substrate; however, methane (CH4) provides an intriguing alternative as a substrate for RL production because it is low cost and may mitigate greenhouse gas emissions. Here, we demonstrate RL production from CH4 by Methylotuvimicrobium alcaliphilum DSM19304. RLs are inhibitory to M. alcaliphilum growth (<0.05 g/l). Adaptive laboratory evolution was performed by growing M. alcaliphilum in increasing concentrations of RLs, producing a strain that grew in the presence of 5 g/l of RLs. Metabolomics and proteomics of the adapted strain grown on CH4 in the absence of RLs revealed metabolic changes, increase in fatty acid production and secretion, alterations in gluconeogenesis, and increased secretion of lactate and osmolyte products compared with the parent strain. Expression of plasmid-borne RL production genes in the parent M. alcaliphilum strain resulted in cessation of growth and cell death. In contrast, the adapted strain transformed with the RL production genes showed no growth inhibition and produced up to 1 μM of RLs, a 600-fold increase compared with the parent strain, solely from CH4. This work has promise for developing technologies to produce fatty acid-derived bioproducts, including biosurfactants, from CH4.
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Affiliation(s)
- Deepika Awasthi
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Yung-Hsu Tang
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Bashar Amer
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Edward E K Baidoo
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Jennifer Gin
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Yan Chen
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Christopher J Petzold
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Marina Kalyuzhnaya
- Department of Biology, San Diego State University, San Diego, CA 92182, USA
| | - Steven W Singer
- Correspondence should be addressed to: Steven W. Singer. Tel: 510-486-5556; Fax: 510-486-4252; E-mail:
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10
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Jo SY, Son J, Sohn YJ, Lim SH, Lee JY, Yoo JI, Park SY, Na JG, Park SJ. A shortcut to carbon-neutral bioplastic production: Recent advances in microbial production of polyhydroxyalkanoates from C1 resources. Int J Biol Macromol 2021; 192:978-998. [PMID: 34656544 DOI: 10.1016/j.ijbiomac.2021.10.066] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2021] [Revised: 10/04/2021] [Accepted: 10/09/2021] [Indexed: 12/18/2022]
Abstract
Since the 20th century, plastics that are widely being used in general life and industries are causing enormous plastic waste problems since improperly discarded plastics barely degrade and decompose. Thus, the demand for polyhydroxyalkanoates (PHAs), biodegradable polymers with material properties similar to conventional petroleum-based plastics, has been increased so far. The microbial production of PHAs is an environment-friendly solution for the current plastic crisis, however, the carbon sources for the microbial PHA production is a crucial factor to be considered in terms of carbon-neutrality. One‑carbon (C1) resources, such as methane, carbon monoxide, and carbon dioxide, are greenhouse gases and are abundantly found in nature and industry. C1 resources as the carbon sources for PHA production have a completely closed carbon loop with much advances; i) fast carbon circulation with direct bioconversion process and ii) simple fermentation procedure without sterilization as non-preferable nutrients. This review discusses the biosynthesis of PHAs based on C1 resource utilization by wild-type and metabolically engineered microbial host strains via biorefinery processes.
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Affiliation(s)
- Seo Young Jo
- Department of Chemical Engineering and Materials Science, Graduate Program in System Health Science and Engineering, Ewha Womans University, Seoul, 03760, Republic of Korea
| | - Jina Son
- Department of Chemical Engineering and Materials Science, Graduate Program in System Health Science and Engineering, Ewha Womans University, Seoul, 03760, Republic of Korea
| | - Yu Jung Sohn
- Department of Chemical Engineering and Materials Science, Graduate Program in System Health Science and Engineering, Ewha Womans University, Seoul, 03760, Republic of Korea
| | - Seo Hyun Lim
- Department of Chemical Engineering and Materials Science, Graduate Program in System Health Science and Engineering, Ewha Womans University, Seoul, 03760, Republic of Korea
| | - Ji Yeon Lee
- Department of Chemical Engineering and Materials Science, Graduate Program in System Health Science and Engineering, Ewha Womans University, Seoul, 03760, Republic of Korea
| | - Jee In Yoo
- Department of Chemical Engineering and Materials Science, Graduate Program in System Health Science and Engineering, Ewha Womans University, Seoul, 03760, Republic of Korea
| | - Se Young Park
- Department of Chemical Engineering and Materials Science, Graduate Program in System Health Science and Engineering, Ewha Womans University, Seoul, 03760, Republic of Korea
| | - Jeong-Geol Na
- Department of Chemical and Biomolecular Engineering, Sogang University, Seoul, Republic of Korea.
| | - Si Jae Park
- Department of Chemical Engineering and Materials Science, Graduate Program in System Health Science and Engineering, Ewha Womans University, Seoul, 03760, Republic of Korea.
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11
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Le HTQ, Nguyen AD, Park YR, Lee EY. Sustainable biosynthesis of chemicals from methane and glycerol via reconstruction of multi-carbon utilizing pathway in obligate methanotrophic bacteria. Microb Biotechnol 2021; 14:2552-2565. [PMID: 33830652 PMCID: PMC8601198 DOI: 10.1111/1751-7915.13809] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2020] [Revised: 03/19/2021] [Accepted: 03/19/2021] [Indexed: 01/26/2023] Open
Abstract
Obligate methanotrophic bacteria can utilize methane, an inexpensive carbon feedstock, as a sole energy and carbon substrate, thus are considered as the only nature-provided biocatalyst for sustainable biomanufacturing of fuels and chemicals from methane. To address the limitation of native C1 metabolism of obligate type I methanotrophs, we proposed a novel platform strain that can utilize methane and multi-carbon substrates, such as glycerol, simultaneously to boost growth rates and chemical production in Methylotuvimicrobium alcaliphilum 20Z. To demonstrate the uses of this concept, we reconstructed a 2,3-butanediol biosynthetic pathway and achieved a fourfold higher titer of 2,3-butanediol production by co-utilizing methane and glycerol compared with that of methanotrophic growth. In addition, we reported the creation of a methanotrophic biocatalyst for one-step bioconversion of methane to methanol in which glycerol was used for cell growth, and methane was mainly used for methanol production. After the deletion of genes encoding methanol dehydrogenase (MDH), 11.6 mM methanol was obtained after 72 h using living cells in the absence of any chemical inhibitors of MDH and exogenous NADH source. A further improvement of this bioconversion was attained by using resting cells with a significantly increased titre of 76 mM methanol after 3.5 h with the supply of 40 mM formate. The work presented here provides a novel framework for a variety of approaches in methane-based biomanufacturing.
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Affiliation(s)
- Hoa Thi Quynh Le
- Department of Chemical Engineering (Integrated Engineering)Kyung Hee University17104Yongin‐siGyeonggi‐doSouth Korea
| | - Anh Duc Nguyen
- Department of Chemical Engineering (Integrated Engineering)Kyung Hee University17104Yongin‐siGyeonggi‐doSouth Korea
| | - Ye Rim Park
- Department of Chemical Engineering (Integrated Engineering)Kyung Hee University17104Yongin‐siGyeonggi‐doSouth Korea
| | - Eun Yeol Lee
- Department of Chemical Engineering (Integrated Engineering)Kyung Hee University17104Yongin‐siGyeonggi‐doSouth Korea
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12
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Gęsicka A, Oleskowicz-Popiel P, Łężyk M. Recent trends in methane to bioproduct conversion by methanotrophs. Biotechnol Adv 2021; 53:107861. [PMID: 34710553 DOI: 10.1016/j.biotechadv.2021.107861] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2021] [Revised: 10/11/2021] [Accepted: 10/20/2021] [Indexed: 12/26/2022]
Abstract
Methane is an abundant and low-cost gas with high global warming potential and its use as a feedstock can help mitigate climate change. Variety of valuable products can be produced from methane by methanotrophs in gas fermentation processes. By using methane as a sole carbon source, methanotrophic bacteria can produce bioplastics, biofuels, feed additives, ectoine and variety of other high-value chemical compounds. A lot of studies have been conducted through the years for natural methanotrophs and engineered strains as well as methanotrophic consortia. These have focused on increasing yields of native products as well as proof of concept for the synthesis of new range of chemicals by metabolic engineering. This review shows trends in the research on key methanotrophic bioproducts since 2015. Despite certain limitations of the known production strategies that makes commercialization of methane-based products challenging, there is currently much attention placed on the promising further development.
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Affiliation(s)
- Aleksandra Gęsicka
- Water Supply and Bioeconomy Division, Faculty of Environmental Engineering and Energy, Poznan University of Technology, Berdychowo 4, 60-965 Poznan, Poland
| | - Piotr Oleskowicz-Popiel
- Water Supply and Bioeconomy Division, Faculty of Environmental Engineering and Energy, Poznan University of Technology, Berdychowo 4, 60-965 Poznan, Poland.
| | - Mateusz Łężyk
- Water Supply and Bioeconomy Division, Faculty of Environmental Engineering and Energy, Poznan University of Technology, Berdychowo 4, 60-965 Poznan, Poland.
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13
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Oshkin IY, Danilova OV, But SY, Miroshnikov KK, Suleimanov RZ, Belova SE, Tikhonova EN, Kuznetsov NN, Khmelenina VN, Pimenov NV, Dedysh SN. Expanding Characterized Diversity and the Pool of Complete Genome Sequences of Methylococcus Species, the Bacteria of High Environmental and Biotechnological Relevance. Front Microbiol 2021; 12:756830. [PMID: 34691008 PMCID: PMC8527097 DOI: 10.3389/fmicb.2021.756830] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2021] [Accepted: 09/13/2021] [Indexed: 11/18/2022] Open
Abstract
The bacterial genus Methylococcus, which comprises aerobic thermotolerant methanotrophic cocci, was described half-a-century ago. Over the years, a member of this genus, Methylococcus capsulatus Bath, has become a major model organism to study genomic and metabolic basis of obligate methanotrophy. High biotechnological potential of fast-growing Methylococcus species, mainly as a promising source of feed protein, has also been recognized. Despite this big research attention, the currently cultured Methylococcus diversity is represented by members of the two species, M. capsulatus and M. geothermalis, while finished genome sequences are available only for two strains of these methanotrophs. This study extends the pool of phenotypically characterized Methylococcus strains with good-quality genome sequences by contributing four novel isolates of these bacteria from activated sludge, landfill cover soil, and freshwater sediments. The determined genome sizes of novel isolates varied between 3.2 and 4.0Mb. As revealed by the phylogenomic analysis, strains IO1, BH, and KN2 affiliate with M. capsulatus, while strain Mc7 may potentially represent a novel species. Highest temperature optima (45-50°C) and highest growth rates in bioreactor cultures (up to 0.3h-1) were recorded for strains obtained from activated sludge. The comparative analysis of all complete genomes of Methylococcus species revealed 4,485 gene clusters. Of these, pan-genome core comprised 2,331 genes (on average 51.9% of each genome), with the accessory genome containing 846 and 1,308 genes in the shell and the cloud, respectively. Independently of the isolation source, all strains of M. capsulatus displayed surprisingly high genome synteny and a striking similarity in gene content. Strain Mc7 from a landfill cover soil differed from other isolates by the high content of mobile genetic elements in the genome and a number of genome-encoded features missing in M. capsulatus, such as sucrose biosynthesis and the ability to scavenge phosphorus and sulfur from the environment.
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Affiliation(s)
- Igor Y. Oshkin
- Winogradsky Institute of Microbiology, Research Center of Biotechnology, Russian Academy of Sciences, Moscow, Russia
| | - Olga V. Danilova
- Winogradsky Institute of Microbiology, Research Center of Biotechnology, Russian Academy of Sciences, Moscow, Russia
| | - Sergey Y. But
- Winogradsky Institute of Microbiology, Research Center of Biotechnology, Russian Academy of Sciences, Moscow, Russia
- G. K. Skryabin Institute of Biochemistry and Physiology of Microorganisms, Pushchino Scientific Center for Biological Research, Russian Academy of Sciences, Pushchino, Russia
| | - Kirill K. Miroshnikov
- Winogradsky Institute of Microbiology, Research Center of Biotechnology, Russian Academy of Sciences, Moscow, Russia
| | - Ruslan Z. Suleimanov
- Winogradsky Institute of Microbiology, Research Center of Biotechnology, Russian Academy of Sciences, Moscow, Russia
| | - Svetlana E. Belova
- Winogradsky Institute of Microbiology, Research Center of Biotechnology, Russian Academy of Sciences, Moscow, Russia
| | - Ekaterina N. Tikhonova
- Winogradsky Institute of Microbiology, Research Center of Biotechnology, Russian Academy of Sciences, Moscow, Russia
| | - Nikolai N. Kuznetsov
- Winogradsky Institute of Microbiology, Research Center of Biotechnology, Russian Academy of Sciences, Moscow, Russia
| | - Valentina N. Khmelenina
- G. K. Skryabin Institute of Biochemistry and Physiology of Microorganisms, Pushchino Scientific Center for Biological Research, Russian Academy of Sciences, Pushchino, Russia
| | - Nikolai V. Pimenov
- Winogradsky Institute of Microbiology, Research Center of Biotechnology, Russian Academy of Sciences, Moscow, Russia
| | - Svetlana N. Dedysh
- Winogradsky Institute of Microbiology, Research Center of Biotechnology, Russian Academy of Sciences, Moscow, Russia
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14
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Bioconversion of Methanol by Synthetic Methylotrophy. ADVANCES IN BIOCHEMICAL ENGINEERING/BIOTECHNOLOGY 2021; 180:149-168. [PMID: 34545421 DOI: 10.1007/10_2021_176] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
As an important building block in the chemical industry, methanol has become an attractive substrate in biorefinery owing to its abundance and low cost. With the development of synthetic biology, metabolic engineering of non-methylotrophy to construct synthetic methylotrophy has drawn increased attention. As for the metabolic construction of methanol assimilation pathway in some industrial hosts, several artificial methanol assimilation pathways have recently been designed and constructed based on the computer-aided design. Particularly, these artificial methanol assimilation pathways possess advantages of shorter reaction steps, stronger driving forces, and independence on oxygen. Accordingly, this chapter reviewed strategies of constructing synthetic methylotrophs, including introducing methanol metabolic modules derived from natural methylotrophs and designing artificial methanol assimilation pathways. Future challenges and prospects were also discussed.
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15
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Lee H, Baek JI, Lee JY, Jeong J, Kim H, Lee DH, Kim DM, Lee SG. Syntrophic co-culture of a methanotroph and heterotroph for the efficient conversion of methane to mevalonate. Metab Eng 2021; 67:285-292. [PMID: 34298134 DOI: 10.1016/j.ymben.2021.07.008] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2021] [Revised: 06/07/2021] [Accepted: 07/18/2021] [Indexed: 10/20/2022]
Abstract
As the bioconversion of methane becomes increasingly important for bio-industrial and environmental applications, methanotrophs have received much attention for their ability to convert methane under ambient conditions. This includes the extensive reporting of methanotroph engineering for the conversion of methane to biochemicals. To further increase methane usability, we demonstrated a highly flexible and efficient modular approach based on a synthetic consortium of methanotrophs and heterotrophs mimicking the natural methane ecosystem to produce mevalonate (MVA) from methane. In the methane-conversion module, we used Methylococcus capsulatus Bath as a highly efficient methane biocatalyst and optimized the culture conditions for the production of high amounts of organic acids. In the MVA-synthesis module, we used Escherichia coli SBA01, an evolved strain with high organic acid tolerance and utilization ability, to convert organic acids to MVA. Using recombinant E. coli SBA01 possessing genes for the MVA pathway, 61 mg/L (0.4 mM) of MVA was successfully produced in 48 h without any addition of nutrients except methane. Our platform exhibited high stability and reproducibility with regard to cell growth and MVA production. We believe that this versatile system can be easily extended to many other value-added processes and has a variety of potential applications.
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Affiliation(s)
- Hyewon Lee
- Synthetic Biology and Bioengineering Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, 34141, Republic of Korea
| | - Ji In Baek
- Synthetic Biology and Bioengineering Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, 34141, Republic of Korea; Department of Chemical Engineering and Applied Chemistry, Chungnam National University, 99 Daehak-ro, 34134, Republic of Korea
| | - Jin-Young Lee
- Synthetic Biology and Bioengineering Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, 34141, Republic of Korea
| | - Jiyeong Jeong
- Synthetic Biology and Bioengineering Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, 34141, Republic of Korea
| | - Haseong Kim
- Synthetic Biology and Bioengineering Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, 34141, Republic of Korea
| | - Dae-Hee Lee
- Synthetic Biology and Bioengineering Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, 34141, Republic of Korea; Department of Biosystems and Bioengineering, KRIBB School of Biotechnology, University of Science & Technology (UST), Daejeon, 34113, Republic of Korea
| | - Dong-Myung Kim
- Department of Chemical Engineering and Applied Chemistry, Chungnam National University, 99 Daehak-ro, 34134, Republic of Korea
| | - Seung-Goo Lee
- Synthetic Biology and Bioengineering Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, 34141, Republic of Korea; Department of Biosystems and Bioengineering, KRIBB School of Biotechnology, University of Science & Technology (UST), Daejeon, 34113, Republic of Korea.
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16
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Microbial lipid biosynthesis from lignocellulosic biomass pyrolysis products. Biotechnol Adv 2021; 54:107791. [PMID: 34192583 DOI: 10.1016/j.biotechadv.2021.107791] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2021] [Revised: 05/18/2021] [Accepted: 06/24/2021] [Indexed: 01/08/2023]
Abstract
Lipids are a biorefinery platform to prepare fuel, food and health products. They are traditionally obtained from plants, but those of microbial origin allow for a better use of land and C resources, among other benefits. Several (thermo)chemical and biochemical strategies are used for the conversion of C contained in lignocellulosic biomass into lipids. In particular, pyrolysis can process virtually any biomass and is easy to scale up. Products offer cost-effective, renewable C in the form of readily fermentable molecules and other upgradable intermediates. Although the production of microbial lipids has been studied for 30 years, their incorporation into biorefineries was only described a few years ago. As pyrolysis becomes a profitable technology to depolymerize lignocellulosic biomass into assimilable C, the number of investigations on it raises significantly. This article describes the challenges and opportunities resulting from the combination of lignocellulosic biomass pyrolysis and lipid biosynthesis with oleaginous microorganisms. First, this work presents the basics of the individual processes, and then it shows state-of-the-art processes for the preparation of microbial lipids from biomass pyrolysis products. Advanced knowledge on separation techniques, structure analysis, and fermentability is detailed for each biomass pyrolysis fraction. Finally, the microbial fatty acid platform comprising biofuel, human food and animal feed products, and others, is presented. Literature shows that the microbial lipid production from anhydrosugars, like levoglucosan, and short-chain organic acids, like acetic acid, is straightforward. Indeed, processes achieving nearly theoretical yields form the latter have been described. Some authors have shown that lipid biosynthesis from different lignin sources is biochemically feasible. However, it still imposes major challenges regarding strain performance. No report on the fermentation of pyrolytic lignin is yet available. Research on the microbial uptake of pyrolytic humins remains vacant. Microorganisms that make use of methane show promising results at the proof-of-concept level. Overall, despite some issues need to be tackled, it is now possible to conceive new versatile biorefinery models by combining lignocellulosic biomass pyrolysis products and robust oleaginous microbial cell factories.
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17
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Zhu L, Zhang J, Yang J, Jiang Y, Yang S. Strategies for optimizing acetyl-CoA formation from glucose in bacteria. Trends Biotechnol 2021; 40:149-165. [PMID: 33965247 DOI: 10.1016/j.tibtech.2021.04.004] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2020] [Revised: 04/02/2021] [Accepted: 04/02/2021] [Indexed: 12/17/2022]
Abstract
Acetyl CoA is an important precursor for various chemicals. We provide a metabolic engineering guideline for the production of acetyl-CoA and other end products from a bacterial chassis. Among 13 pathways that produce acetyl-CoA from glucose, 11 lose carbon in the process, and two do not. The first 11 use the Embden-Meyerhof-Parnas (EMP) pathway to produce redox cofactors and gain or lose ATP. The other two pathways function via phosphoketolase with net consumption of ATP, so they must therefore be combined with one of the 11 glycolytic pathways or auxiliary pathways. Optimization of these pathways can maximize the theoretical acetyl-CoA yield, thereby minimizing the overall cost of subsequent acetyl-CoA-derived molecules. Other strategies for generating hyper-producer strains are also addressed.
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Affiliation(s)
- Li Zhu
- Shanghai Laiyi Center for Biopharmaceutical R&D, Shanghai 200240, China
| | - Jieze Zhang
- Department of Chemistry, University of Southern California, Los Angeles, CA 90089, USA
| | - Jiawei Yang
- College of Life Science, University of Chinese Academy of Sciences, Beijing 100049, China; Key Laboratory of Synthetic Biology, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200032, China
| | - Yu Jiang
- Huzhou Center of Industrial Biotechnology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Huzhou 313000, China; Shanghai Taoyusheng Biotechnology Company Ltd, Shanghai 200032, China
| | - Sheng Yang
- Key Laboratory of Synthetic Biology, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200032, China; Huzhou Center of Industrial Biotechnology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Huzhou 313000, China.
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18
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Song X, Diao J, Yao J, Cui J, Sun T, Chen L, Zhang W. Engineering a Central Carbon Metabolism Pathway to Increase the Intracellular Acetyl-CoA Pool in Synechocystis sp. PCC 6803 Grown under Photomixotrophic Conditions. ACS Synth Biol 2021; 10:836-846. [PMID: 33779148 DOI: 10.1021/acssynbio.0c00629] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
In cyanobacteria, photomixotrophic growth is considered as a promising strategy to achieve both high cell density and product accumulation. However, the conversion of glucose to acetyl coenzyme A (acetyl-CoA) in the native glycolytic pathway is insufficient, which decreases the carbon utilization and productivity of engineered cyanobacteria under photomixotrophic conditions. To increase the carbon flux from glucose to key intracellular precursor acetyl-CoA in Synechocystis sp. PCC 6803 (hereafter, Synechocystis 6803) under photomixotrophic conditions, a synthetic nonoxidative cyclic glycolysis (NOG) pathway was introduced into the wild type strain, which successfully increased the intracellular pool of acetyl-CoA by approximately 1-fold. To minimize the competition for glucose, the native Embden-Meyerhof-Parnas (EMP) and Entner-Doudoroff (ED) pathways were knocked out, respectively. Notably, eliminating the native ED pathway in the engineered strain carrying the NOG pathway further increased the intracellular pool of acetyl-CoA up to 2.8-fold. Another carbon consuming pathway in Synechocystis 6803, the glycogen biosynthesis pathway, was additionally knocked out in the above-mentioned engineered strain, which enabled an increase of the intracellular acetyl-CoA pool by up to 3.5-fold when compared with the wild type strain. Finally, the content of intracellular lipids was analyzed as an index of the productive capacity of the engineered Synechocystis 6803 cell factory under photomixotrophic conditions. The results showed the total lipids yield increased about 26% compared to the wild type (from 15.71% to 34.12%, g/g glucose), demonstrating that this integrated approach could represent a general strategy not only for the improvement of the intracellular concentration of acetyl-CoA, but also for the production of value-added chemicals that require acetyl-CoA as a key precursor in cyanobacteria.
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Affiliation(s)
- Xinyu Song
- Center for Biosafety Research and Strategy, Tianjin University, Tianjin 300072, People’s Republic of China
- Laboratory of Synthetic Microbiology, School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, People’s Republic of China
- Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (MOE), School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, People’s Republic of China
- Law School of Tianjin University, Tianjin 300072, P.R. China
| | - Jinjin Diao
- Laboratory of Synthetic Microbiology, School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, People’s Republic of China
- Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (MOE), School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, People’s Republic of China
- SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering, Tianjin 300072, People’s Republic of China
| | - Jiaqi Yao
- Laboratory of Synthetic Microbiology, School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, People’s Republic of China
- Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (MOE), School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, People’s Republic of China
- SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering, Tianjin 300072, People’s Republic of China
| | - Jinyu Cui
- Laboratory of Synthetic Microbiology, School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, People’s Republic of China
- Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (MOE), School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, People’s Republic of China
- SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering, Tianjin 300072, People’s Republic of China
| | - Tao Sun
- Center for Biosafety Research and Strategy, Tianjin University, Tianjin 300072, People’s Republic of China
- Laboratory of Synthetic Microbiology, School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, People’s Republic of China
- Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (MOE), School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, People’s Republic of China
- Law School of Tianjin University, Tianjin 300072, P.R. China
| | - Lei Chen
- Laboratory of Synthetic Microbiology, School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, People’s Republic of China
- Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (MOE), School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, People’s Republic of China
- SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering, Tianjin 300072, People’s Republic of China
| | - Weiwen Zhang
- Center for Biosafety Research and Strategy, Tianjin University, Tianjin 300072, People’s Republic of China
- Laboratory of Synthetic Microbiology, School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, People’s Republic of China
- Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (MOE), School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, People’s Republic of China
- Law School of Tianjin University, Tianjin 300072, P.R. China
- SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering, Tianjin 300072, People’s Republic of China
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19
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Yuan XJ, Chen WJ, Ma ZX, Yuan QQ, Zhang M, He L, Mo XH, Zhang C, Zhang CT, Wang MY, Xing XH, Yang S. Rewiring the native methanol assimilation metabolism by incorporating the heterologous ribulose monophosphate cycle into Methylorubrum extorquens. Metab Eng 2021; 64:95-110. [PMID: 33493644 DOI: 10.1016/j.ymben.2021.01.009] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2020] [Revised: 01/05/2021] [Accepted: 01/18/2021] [Indexed: 10/22/2022]
Abstract
Methanol is assimilated through the serine cycle to generate acetyl-CoA without carbon loss. However, a highly active serine cycle requires high consumption of reducing equivalents and ATP, thereby leading to the impaired efficiency of methanol conversion to reduced chemicals. In the present study, a genome-scale flux balance analysis (FBA) predicted that the introduction of the heterologous ribulose monophosphate (RuMP) cycle, a more energy-efficient pathway for methanol assimilation, could theoretically increase growth rate by 31.3% for the model alphaproteobacterial methylotroph Methylorubrum extorquens AM1. Based on this analysis, we constructed a novel synergistic assimilation pathway in vivo by incorporating the RuMP cycle into M. extroquens metabolism with the intrinsic serine cycle. We demonstrated that the operation of the synergistic pathway could increase cell growth rate by 16.5% and methanol consumption rate by 13.1%. This strategy rewired the central methylotrophic metabolism through adjusting core gene transcription, leading to a pool size increase of C2 to C5 central intermediates by 1.2- to 3.6-fold and an NADPH cofactor improvement by 1.3-fold. The titer of 3-hydroxypropionic acid (3-HP), a model product in the newly engineered chassis of M. extorquens AM1, was increased to 91.2 mg/L in shake-flask culture, representing a 3.1-fold increase compared with the control strain with only the serine cycle. The final titer of 3-HP was significantly improved to 0.857 g/L in the fed-batch bioreactor, which was more competitive compared with the other 3-HP producers using methane and CO2 as C1 sources. Collectively, our current study demonstrated that engineering the synergistic methanol assimilation pathway was a promising strategy to increase the carbon assimilation and the yields of reduced chemicals in diverse host strains for C1 microbial cell factories.
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Affiliation(s)
- Xiao-Jie Yuan
- School of Life Sciences, Shandong Province Key Laboratory of Applied Mycology, And Qingdao International Center on Microbes Utilizing Biogas, Qingdao Agricultural University, Qingdao, Shandong Province, People's Republic of China; Department of Molecular Biology, Qingdao Vland Biotech Inc., Qingdao, Shandong Province, People's Republic of China
| | - Wen-Jing Chen
- School of Life Sciences, Shandong Province Key Laboratory of Applied Mycology, And Qingdao International Center on Microbes Utilizing Biogas, Qingdao Agricultural University, Qingdao, Shandong Province, People's Republic of China
| | - Zeng-Xin Ma
- School of Life Sciences, Shandong Province Key Laboratory of Applied Mycology, And Qingdao International Center on Microbes Utilizing Biogas, Qingdao Agricultural University, Qingdao, Shandong Province, People's Republic of China
| | - Qian-Qian Yuan
- Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, People's Republic of China
| | - Min Zhang
- School of Life Sciences, Shandong Province Key Laboratory of Applied Mycology, And Qingdao International Center on Microbes Utilizing Biogas, Qingdao Agricultural University, Qingdao, Shandong Province, People's Republic of China
| | - Lian He
- Department of Chemical Engineering, University of Washington, Seattle, WA, USA
| | - Xu-Hua Mo
- School of Life Sciences, Shandong Province Key Laboratory of Applied Mycology, And Qingdao International Center on Microbes Utilizing Biogas, Qingdao Agricultural University, Qingdao, Shandong Province, People's Republic of China
| | - Chong Zhang
- Key Laboratory of Industrial Biocatalysis, Ministry of Education, Department of Chemical Engineering, Tsinghua University, Beijing, People's Republic of China; Center for Synthetic and Systems Biology, Tsinghua University, Beijing, People's Republic of China
| | - Chang-Tai Zhang
- School of Life Sciences, Shandong Province Key Laboratory of Applied Mycology, And Qingdao International Center on Microbes Utilizing Biogas, Qingdao Agricultural University, Qingdao, Shandong Province, People's Republic of China
| | - Meng-Ying Wang
- School of Life Sciences, Shandong Province Key Laboratory of Applied Mycology, And Qingdao International Center on Microbes Utilizing Biogas, Qingdao Agricultural University, Qingdao, Shandong Province, People's Republic of China
| | - Xin-Hui Xing
- Key Laboratory of Industrial Biocatalysis, Ministry of Education, Department of Chemical Engineering, Tsinghua University, Beijing, People's Republic of China; Center for Synthetic and Systems Biology, Tsinghua University, Beijing, People's Republic of China; Institute of Biopharmaceutical and Health Engineering, Tsinghua Shenzhen International Graduate School, And Institute of Biomedical Health Technology and Engineering, Shenzhen Bay Laboratory, Shenzhen, China
| | - Song Yang
- School of Life Sciences, Shandong Province Key Laboratory of Applied Mycology, And Qingdao International Center on Microbes Utilizing Biogas, Qingdao Agricultural University, Qingdao, Shandong Province, People's Republic of China; Key Laboratory of Systems Bioengineering, Ministry of Education, Tianjin University, Tianjin, People's Republic of China.
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20
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Liu Y, Su A, Li J, Ledesma-Amaro R, Xu P, Du G, Liu L. Towards next-generation model microorganism chassis for biomanufacturing. Appl Microbiol Biotechnol 2020; 104:9095-9108. [DOI: 10.1007/s00253-020-10902-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2020] [Revised: 09/03/2020] [Accepted: 09/10/2020] [Indexed: 11/29/2022]
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Nguyen AD, Kim D, Lee EY. Unlocking the biosynthesis of sesquiterpenoids from methane via the methylerythritol phosphate pathway in methanotrophic bacteria, using α-humulene as a model compound. Metab Eng 2020; 61:69-78. [PMID: 32387228 DOI: 10.1016/j.ymben.2020.04.011] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2020] [Revised: 03/21/2020] [Accepted: 04/25/2020] [Indexed: 11/22/2022]
Abstract
Isoprenoids are an abundant and diverse class of natural products with various applications in the pharmaceutical, cosmetics and biofuel industries. A methanotroph-based biorefinery is an attractive scenario for the production of a variety of value-added compounds from methane, because methane is a promising alternative feedstock for industrial biomanufacturing. In this study, we metabolically engineered Methylotuvimicrobium alcaliphilum 20Z for de novo synthesis of a sesquiterpenoid from methane, using α-humulene as a model compound, via optimization of the native methylerythritol phosphate (MEP) pathway. Expression of codon-optimized α-humulene synthase from Zingiber zerumbet in M. alcaliphilum 20Z resulted in an initial yield of 0.04 mg/g dry cell weight. Overexpressing key enzymes (IspA, IspG, and Dxs) for debottlenecking of the MEP pathway increased α-humulene production 5.2-fold compared with the initial strain. Subsequently, redirecting the carbon flux through the Embden-Meyerhof-Parnas pathway resulted in an additional 3-fold increase in α-humulene production. Additionally, a genome-scale model using flux scanning based on enforced objective flux method was used to identify potential overexpression targets to increase flux towards isoprenoid production. Several target reactions from cofactor synthesis pathways were probed and evaluated for their effects on α-humulene synthesis, resulting in α-humulene yield up to 0.75 mg/g DCW with 18.8-fold enhancement from initial yield. This study first demonstrates production of a sesquiterpenoid from methane using methanotrophs as the biocatalyst and proposes potential strategies to enhance production of sesquiterpenoid and related isoprenoid products in engineered methanotrophic bacteria.
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Affiliation(s)
- Anh Duc Nguyen
- Department of Chemical Engineering, Kyung Hee University, Yongin-si, Gyeonggi-do, 17104, South Korea
| | - Donghyuk Kim
- School of Energy and Chemical Engineering, Ulsan National Institute of Science and Technology (UNIST), Ulsan, 44919, South Korea
| | - Eun Yeol Lee
- Department of Chemical Engineering, Kyung Hee University, Yongin-si, Gyeonggi-do, 17104, South Korea.
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22
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Nguyen AD, Lee EY. Engineered Methanotrophy: A Sustainable Solution for Methane-Based Industrial Biomanufacturing. Trends Biotechnol 2020; 39:381-396. [PMID: 32828555 DOI: 10.1016/j.tibtech.2020.07.007] [Citation(s) in RCA: 42] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2020] [Revised: 07/16/2020] [Accepted: 07/17/2020] [Indexed: 12/22/2022]
Abstract
Methane is a promising feedstock with high abundance and low cost for the sustainable production of biochemicals and biofuels. Methanotrophic bacteria are particularly interesting platforms for methane bioconversion as they can utilize methane as a carbon substrate. Recently, breakthroughs in the understanding of methane metabolism in methanotrophs as well as critical advances in systems metabolic engineering of methanotrophic bacteria have been reported. Here, we discuss the important gaps in the understanding of methanotrophic metabolism that have been uncovered recently and the current trends in systems metabolic engineering in both methanotrophic bacteria and non-native hosts to advance the potential of methane-based biomanufacturing.
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Affiliation(s)
- Anh Duc Nguyen
- Department of Chemical Engineering, Kyung Hee University, Yongin-si, Gyeonggi-do 17104, South Korea
| | - Eun Yeol Lee
- Department of Chemical Engineering, Kyung Hee University, Yongin-si, Gyeonggi-do 17104, South Korea.
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23
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Nguyen AD, Nam G, Kim D, Lee EY. Metabolic role of pyrophosphate-linked phosphofructokinase pfk for C1 assimilation in Methylotuvimicrobium alcaliphilum 20Z. Microb Cell Fact 2020; 19:131. [PMID: 32546161 PMCID: PMC7298851 DOI: 10.1186/s12934-020-01382-5] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2019] [Accepted: 05/30/2020] [Indexed: 01/02/2023] Open
Abstract
BACKGROUND Methanotrophs is a promising biocatalyst in biotechnological applications with their ability to utilize single carbon (C1) feedstock to produce high-value compounds. Understanding the behavior of biological networks of methanotrophic bacteria in different parameters is vital to systems biology and metabolic engineering. Interestingly, methanotrophic bacteria possess the pyrophosphate-dependent 6-phosphofructokinase (PPi-PFK) instead of the ATP-dependent 6-phosphofructokinase, indicating their potentials to serve as promising model for investigation the role of inorganic pyrophosphate (PPi) and PPi-dependent glycolysis in bacteria. Gene knockout experiments along with global-omics approaches can be used for studying gene functions as well as unraveling regulatory networks that rely on the gene product. RESULTS In this study, we performed gene knockout and RNA-seq experiments in Methylotuvimicrobium alcaliphilum 20Z to investigate the functional roles of PPi-PFK in C1 metabolism when cells were grown on methane and methanol, highlighting its metabolic importance in C1 assimilation in M. alcaliphilum 20Z. We further conducted adaptive laboratory evolution (ALE) to investigate regulatory architecture in pfk knockout strain. Whole-genome resequencing and RNA-seq approaches were performed to characterize the genetic and metabolic responses of adaptation to pfk knockout. A number of mutations, as well as gene expression profiles, were identified in pfk ALE strain to overcome insufficient C1 assimilation pathway which limits the growth in the unevolved strain. CONCLUSIONS This study first revealed the regulatory roles of PPi-PFK on C1 metabolism and then provided novel insights into mechanism of adaptation to the loss of this major metabolic enzyme as well as an improved basis for future strain design in type I methanotrophs.
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Affiliation(s)
- Anh Duc Nguyen
- Department of Chemical Engineering, Kyung Hee University, Yongin-si, Gyeonggi-do, 17104, South Korea
| | - Gayoung Nam
- School of Energy and Chemical Engineering, Ulsan National Institute of Science and Technology (UNIST), Ulsan, 44919, South Korea
| | - Donghyuk Kim
- School of Energy and Chemical Engineering, Ulsan National Institute of Science and Technology (UNIST), Ulsan, 44919, South Korea.
| | - Eun Yeol Lee
- Department of Chemical Engineering, Kyung Hee University, Yongin-si, Gyeonggi-do, 17104, South Korea.
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Oshkin IY, Khmelenina VN, But SY, Miroshnikov KK, Belova SE, Khokhlachev NS, Chernushkin DV, Beletsky AV, Mardanov AV, Ravin NV, Popov VO, Dedysh SN, Pimenov NV. Analysis of the Complete Genome Sequence of Strain Concept-8, a Novel Representative of the Genus Methylococcus. Microbiology (Reading) 2020. [DOI: 10.1134/s0026261720030121] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
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25
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Fei Q, Liang B, Tao L, Tan EC, Gonzalez R, Henard CA, Guarnieri MT. Biological valorization of natural gas for the production of lactic acid: Techno-economic analysis and life cycle assessment. Biochem Eng J 2020. [DOI: 10.1016/j.bej.2020.107500] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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26
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Response Surface Methodology to Optimize Methane Production from Mesophilic Anaerobic Co-Digestion of Oily-Biological Sludge and Sugarcane Bagasse. SUSTAINABILITY 2020. [DOI: 10.3390/su12052116] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Oily-biological sludge (OBS) generated from petroleum refineries has high toxicity. Therefore, it needs an appropriate disposal method to reduce the negative impacts on the environment. The anaerobic co-digestion process is an effective method that manages and converts organic waste to energy. For effective anaerobic digestion, a co-substrate would be required to provide a suitable environment for anaerobic bacteria. In oily-biological sludge, the carbon/nitrogen (C/N) ratio and volatile solids (VS) content are very low. Therefore, it needs to be digested with organic waste that has a high C/N ratio and high VS content. This study investigates the use of sugarcane bagasse (SB) as an effective co-substrate due to its high C/N ratio and high VS content to improve the anaerobic co-digestion process with oily-biological sludge. The sugarcane bagasse also helps to delay the toxicity effect of the methane bacteria. Batch anaerobic co-digestion of oily-biological sludge was conducted with sugarcane bagasse as a co-substrate in twelve reactors with two-liter capacity, each under mesophilic conditions. The interaction effect of a C/N ratio of 20-30 and a VS co-substrate/VS inoculum ratio of 0.06-0.18 on the methane yield (mL CH4/g VSremoved) was investigated. Before the anaerobic digestion, thermochemical pre-treatment of the inoculum and co-substrate was conducted using sodium hydroxide to balance their acidic nature and provide a suitable pH environment for methane bacteria. Design and optimization for the mixing ratios were carried out by central composite design-response surface methodology (CCD-RSM). The highest predicted methane yield was found to be 63.52 mL CH4/g VSremoved, under optimum conditions (C/N ratio of 30 and co-substrate/inoculum ratio of 0.18).
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Rozova ON, Mustakhimov II, But SY, Reshetnikov AS, Khmelenina VN. Role of the malic enzyme in metabolism of the halotolerant methanotroph Methylotuvimicrobium alcaliphilum 20Z. PLoS One 2019; 14:e0225054. [PMID: 31738793 PMCID: PMC6860931 DOI: 10.1371/journal.pone.0225054] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2019] [Accepted: 10/28/2019] [Indexed: 01/10/2023] Open
Abstract
The bacteria utilizing methane as a growth substrate (methanotrophs) are important constituents of the biosphere. Methanotrophs mitigate the emission of anthropogenic and natural greenhouse gas methane to the environment and are the promising agents for future biotechnologies. Many aspects of CH4 bioconversion by methanotrophs require further clarification. This study was aimed at characterizing the biochemical properties of the malic enzyme (Mae) from the halotolerant obligate methanotroph Methylotuvimicrobium alcaliphilum 20Z. The His6-tagged Mae was obtained by heterologous expression in Escherichia coli BL21 (DE3) and purified by affinity metal chelating chromatography. As determined by gel filtration and non-denaturating gradient gel electrophoresis, the molecular mass of the native enzyme is 260 kDa. The homotetrameric Mae (65x4 kDa) catalyzed an irreversible NAD+-dependent reaction of L-malate decarboxylation into pyruvate with a specific activity of 32 ± 2 units mg-1 and Km value of 5.5 ± 0.8 mM for malate and 57 ± 5 μM for NAD+. The disruption of the mae gene by insertion mutagenesis resulted in a 20-fold increase in intracellular malate level in the mutant compared to the wild type strain. Based on both enzyme and mutant properties, we conclude that the malic enzyme is involved in the control of intracellular L-malate level in Mtm. alcaliphilum 20Z. Genomic analysis has revealed that Maes present in methanotrophs fall into two different clades in the amino acid-based phylogenetic tree, but no correlation of the division with taxonomic affiliations of the host bacteria was observed.
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Affiliation(s)
- Olga N. Rozova
- Federal Research Center “Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences”, G.K. Skryabin Institute of Biochemistry and Physiology of Microorganisms, Russian Academy of Sciences, Pushchino, Moscow Region, Russia
| | - Ildar I. Mustakhimov
- Federal Research Center “Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences”, G.K. Skryabin Institute of Biochemistry and Physiology of Microorganisms, Russian Academy of Sciences, Pushchino, Moscow Region, Russia
| | - Sergei Y. But
- Federal Research Center “Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences”, G.K. Skryabin Institute of Biochemistry and Physiology of Microorganisms, Russian Academy of Sciences, Pushchino, Moscow Region, Russia
| | - Aleksandr S. Reshetnikov
- Federal Research Center “Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences”, G.K. Skryabin Institute of Biochemistry and Physiology of Microorganisms, Russian Academy of Sciences, Pushchino, Moscow Region, Russia
| | - Valentina N. Khmelenina
- Federal Research Center “Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences”, G.K. Skryabin Institute of Biochemistry and Physiology of Microorganisms, Russian Academy of Sciences, Pushchino, Moscow Region, Russia
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28
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A Review on Anaerobic Digestion of Lignocellulosic Wastes: Pretreatments and Operational Conditions. APPLIED SCIENCES-BASEL 2019. [DOI: 10.3390/app9214655] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Anaerobic digestion (AD) has become extremely popular in the last years to treat and valorize organic wastes both at laboratory and industrial scales, for a wide range of highly produced organic wastes: municipal wastes, wastewater sludge, manure, agrowastes, food industry residuals, etc. Although the principles of AD are well known, it is very important to highlight that knowing the biochemical composition of waste is crucial in order to know its anaerobic biodegradability, which makes an AD process economically feasible. In this paper, we review the main principles of AD, moving to the specific features of lignocellulosic wastes, especially regarding the pretreatments that can enhance the biogas production of such wastes. The main point to consider is that lignocellulosic wastes are present in any organic wastes, and sometimes are the major fraction. Therefore, improving their AD could cause a boost in the development in this technology. The conclusions are that there is no unique strategy to improve the anaerobic biodegradability of lignocellulosic wastes, but pretreatments and codigestion both have an important role on this issue.
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29
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Bioproduction of Isoprenoids and Other Secondary Metabolites Using Methanotrophic Bacteria as an Alternative Microbial Cell Factory Option: Current Stage and Future Aspects. Catalysts 2019. [DOI: 10.3390/catal9110883] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
Methane is a promising carbon feedstock for industrial biomanufacturing because of its low price and high abundance. Recent advances in metabolic engineering and systems biology in methanotrophs have made it possible to produce a variety of value-added compounds from methane, including secondary metabolites. Isoprenoids are one of the largest family of secondary metabolites and have many useful industrial applications. In this review, we highlight the current efforts invested to methanotrophs for the production of isoprenoids and other secondary metabolites, including riboflavin and ectoine. The future outlook for improving secondary metabolites production (especially of isoprenoids) using metabolic engineering of methanotrophs is also discussed.
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30
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Antoniewicz MR. Synthetic methylotrophy: Strategies to assimilate methanol for growth and chemicals production. Curr Opin Biotechnol 2019; 59:165-174. [PMID: 31437746 DOI: 10.1016/j.copbio.2019.07.001] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2019] [Revised: 07/12/2019] [Accepted: 07/17/2019] [Indexed: 11/29/2022]
Abstract
Methanol is an attractive and broadly available substrate for large-scale bioproduction of fuels and chemicals. It contains more energy and electrons per carbon than carbohydrates and can be cheaply produced from natural gas. Synthetic methylotrophy refers to the development of non-native methylotrophs such as Escherichia coli and Corynebacterium glutamicum to utilize methanol as a carbon source. Here, we discuss recent advances in engineering these industrial hosts to assimilate methanol for growth and chemicals production through the introduction of the ribulose monophosphate (RuMP) cycle. In addition, we present novel strategies based on flux coupling and adaptive laboratory evolution to engineer new strains that can grow exclusively on methanol.
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Affiliation(s)
- Maciek R Antoniewicz
- Department of Chemical and Biomolecular Engineering, Metabolic Engineering and Systems Biology Laboratory, University of Delaware, Newark DE 19716, USA.
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31
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Growth-coupled evolution of phosphoketolase to improve l-glutamate production by Corynebacterium glutamicum. Appl Microbiol Biotechnol 2019; 103:8413-8425. [DOI: 10.1007/s00253-019-10043-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2019] [Revised: 07/13/2019] [Accepted: 07/23/2019] [Indexed: 01/14/2023]
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32
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Henard CA, Franklin TG, Youhenna B, But S, Alexander D, Kalyuzhnaya MG, Guarnieri MT. Biogas Biocatalysis: Methanotrophic Bacterial Cultivation, Metabolite Profiling, and Bioconversion to Lactic Acid. Front Microbiol 2018; 9:2610. [PMID: 30429839 PMCID: PMC6220066 DOI: 10.3389/fmicb.2018.02610] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2018] [Accepted: 10/12/2018] [Indexed: 12/19/2022] Open
Abstract
Anaerobic digestion (AD) of waste substrates, and renewable biomass and crop residues offers a means to generate energy-rich biogas. However, at present, AD-derived biogas is primarily flared or used for combined heat and power (CHP), in part due to inefficient gas-to-liquid conversion technologies. Methanotrophic bacteria are capable of utilizing methane as a sole carbon and energy source, offering promising potential for biological gas-to-liquid conversion of AD-derived biogas. Here, we report cultivation of three phylogenetically diverse methanotrophic bacteria on biogas streams derived from AD of a series of energy crop residues. Strains maintained comparable central metabolic activity and displayed minimal growth inhibition when cultivated under batch configuration on AD biogas streams relative to pure methane, although metabolite analysis suggested biogas streams increase cellular oxidative stress. In contrast to batch cultivation, growth arrest was observed under continuous cultivation configuration, concurrent with increased biosynthesis and excretion of lactate. We examined the potential for enhanced lactate production via the employ of a pyruvate dehydrogenase mutant strain, ultimately achieving 0.027 g lactate/g DCW/h, the highest reported lactate specific productivity from biogas to date.
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Affiliation(s)
- Calvin A Henard
- National Renewable Energy Laboratory, National Bioenergy Center, Golden, CO, United States
| | - Tyler G Franklin
- National Renewable Energy Laboratory, National Bioenergy Center, Golden, CO, United States
| | - Batool Youhenna
- Biology Department, San Diego State University, San Diego, CA, United States
| | - Sergey But
- Skryabin Institute of Biochemistry and Physiology of Microorganisms, Moscow, Russia
| | | | | | - Michael T Guarnieri
- National Renewable Energy Laboratory, National Bioenergy Center, Golden, CO, United States
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Lieven C, Herrgård MJ, Sonnenschein N. Microbial Methylotrophic Metabolism: Recent Metabolic Modeling Efforts and Their Applications In Industrial Biotechnology. Biotechnol J 2018; 13:e1800011. [PMID: 29917330 DOI: 10.1002/biot.201800011] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2018] [Revised: 05/31/2018] [Indexed: 11/08/2022]
Abstract
Developing methylotrophic bacteria into cell factories that meet the chemical demand of the future could be both economical and environmentally friendly. Methane is not only an abundant, low-cost resource but also a potent greenhouse gas, the capture of which could help to reduce greenhouse gas emissions. Rational strain design workflows rely on the availability of carefully combined knowledge often in the form of genome-scale metabolic models to construct high-producer organisms. In this review, the authors present the most recent genome-scale metabolic models in aerobic methylotrophy and their applications. Further, the authors present models for the study of anaerobic methanotrophy through reverse methanogenesis and suggest organisms that may be of interest for expanding one-carbon industrial biotechnology. Metabolic models of methylotrophs are scarce, yet they are important first steps toward rational strain-design in these organisms.
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Affiliation(s)
- Christian Lieven
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800 Kgs. Lyngby, Denmark
| | - Markus J Herrgård
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800 Kgs. Lyngby, Denmark
| | - Nikolaus Sonnenschein
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800 Kgs. Lyngby, Denmark
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Bioconversion of methane to C-4 carboxylic acids using carbon flux through acetyl-CoA in engineered Methylomicrobium buryatense 5GB1C. Metab Eng 2018; 48:175-183. [PMID: 29883803 DOI: 10.1016/j.ymben.2018.06.001] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2017] [Revised: 05/31/2018] [Accepted: 06/01/2018] [Indexed: 11/24/2022]
Abstract
Methane, the primary component of natural gas, is the second most abundant greenhouse gas (GHG) and contributes significantly to climate change. The conversion of methane to industrial platform chemicals provides an attractive opportunity to decrease GHG emissions and utilize this inexpensive and abundantly available gas as a carbon feedstock. While technologies exist for chemical conversion of methane to liquid fuels, the technical complexity of these processes mandate high capital expenditure, large-scale commercial facilities to leverage economies of scale that cannot be efficiently scaled down. Alternatively, bioconversion technologies capable of efficient small-scale operation with high carbon and energy efficiency can enable deployment at remote methane resources inaccessible to current chemical technologies. Aerobic obligate methanotrophs, specifically Methylomicrobium buryatense 5GB1, have recently garnered increased research interest for development of such bio-technologies. In this study, we demonstrate production of C-4 carboxylic acids non-native to the host, specifically crotonic and butyric acids, from methane in an engineered M. buryatense 5GB1C by diversion of carbon flux through the acetyl-CoA node of central 'sugar' linked metabolic pathways using reverse β-oxidation pathway genes. The synthesis of short chain carboxylic acids through the acetyl-CoA node demonstrates the potential for engineering M. buryatense 5GB1 as a platform for bioconversion of methane to a number of value added industrial chemicals, and presents new opportunities for further diversifying the products obtainable from methane as the feedstock.
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Wang CY, Li Y, Gao ZW, Liu LC, Zhang MY, Zhang TY, Wu CF, Zhang YX. Establishing an innovative carbohydrate metabolic pathway for efficient production of 2-keto-L-gulonic acid in Ketogulonicigenium robustum initiated by intronic promoters. Microb Cell Fact 2018; 17:81. [PMID: 29778095 PMCID: PMC5960096 DOI: 10.1186/s12934-018-0932-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2017] [Accepted: 05/15/2018] [Indexed: 12/21/2022] Open
Abstract
Background 2-Keto-l-gulonic acid (2-KGA), the precursor of vitamin C, is currently produced by two-step fermentation. In the second step, l-sorbose is transformed into 2-KGA by the symbiosis system composed of Ketogulonicigenium vulgare and Bacillus megaterium. Due to the different nutrient requirements and the uncertain ratio of the two strains, the symbiosis system significantly limits strain improvement and fermentation optimization. Results In this study, Ketogulonicigenium robustum SPU_B003 was reported for its capability to grow well independently and to produce more 2-KGA than that of K. vulgare in a mono-culture system. The complete genome of K. robustum SPU_B003 was sequenced, and the metabolic characteristics were analyzed. Compared to the four reported K. vulgare genomes, K. robustum SPU_B003 contained more tRNAs, rRNAs, NAD and NADP biosynthetic genes, as well as regulation- and cell signaling-related genes. Moreover, the amino acid biosynthesis pathways were more complete. Two species-specific internal promoters, P1 (orf_01408 promoter) and P2 (orf_02221 promoter), were predicted and validated by detecting their initiation activity. To efficiently produce 2-KGA with decreased CO2 release, an innovative acetyl-CoA biosynthetic pathway (XFP-PTA pathway) was introduced into K. robustum SPU_B003 by expressing heterologous phosphoketolase (xfp) and phosphotransacetylase (pta) initiated by internal promoters. After gene optimization, the recombinant strain K. robustum/pBBR-P1_xfp2502-P2_pta2145 enhanced acetyl-CoA approximately 2.4-fold and increased 2-KGA production by 22.27% compared to the control strain K. robustum/pBBR1MCS-2. Accordingly, the transcriptional level of the 6-phosphogluconate dehydrogenase (pgd) and pyruvate dehydrogenase genes (pdh) decreased by 24.33 ± 6.67 and 8.67 ± 5.51%, respectively. The key genes responsible for 2-KGA biosynthesis, sorbose dehydrogenase gene (sdh) and sorbosone dehydrogenase gene (sndh), were up-regulated to different degrees in the recombinant strain. Conclusions The genome-based functional analysis of K. robustum SPU_B003 provided a new understanding of the specific metabolic characteristics. The new XFP-PTA pathway was an efficient route to enhance acetyl-CoA levels and to therefore promote 2-KGA production. Electronic supplementary material The online version of this article (10.1186/s12934-018-0932-9) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Cai-Yun Wang
- School of Life Science and Biopharmaceutics, Shenyang Pharmaceutical University, 103 Wenhua Road, Shenyang, 110016, Liaoning, People's Republic of China
| | - Ye Li
- School of Life Science and Biopharmaceutics, Shenyang Pharmaceutical University, 103 Wenhua Road, Shenyang, 110016, Liaoning, People's Republic of China.,Northeast Pharmaceutical Group Co., Ltd, Shenyang, 110026, People's Republic of China
| | - Zi-Wei Gao
- Department of Biotechnology, School of Engineering, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, 464-8603, Japan
| | - Li-Cheng Liu
- School of Life Science and Biopharmaceutics, Shenyang Pharmaceutical University, 103 Wenhua Road, Shenyang, 110016, Liaoning, People's Republic of China
| | - Meng-Yue Zhang
- School of Life Science and Biopharmaceutics, Shenyang Pharmaceutical University, 103 Wenhua Road, Shenyang, 110016, Liaoning, People's Republic of China
| | - Tian-Yuan Zhang
- School of Life Science and Biopharmaceutics, Shenyang Pharmaceutical University, 103 Wenhua Road, Shenyang, 110016, Liaoning, People's Republic of China
| | - Chun-Fu Wu
- School of Life Science and Biopharmaceutics, Shenyang Pharmaceutical University, 103 Wenhua Road, Shenyang, 110016, Liaoning, People's Republic of China
| | - Yi-Xuan Zhang
- School of Life Science and Biopharmaceutics, Shenyang Pharmaceutical University, 103 Wenhua Road, Shenyang, 110016, Liaoning, People's Republic of China.
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36
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Fei Q, Puri AW, Smith H, Dowe N, Pienkos PT. Enhanced biological fixation of methane for microbial lipid production by recombinant Methylomicrobium buryatense. BIOTECHNOLOGY FOR BIOFUELS 2018; 11:129. [PMID: 29755588 PMCID: PMC5934843 DOI: 10.1186/s13068-018-1128-6] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/22/2017] [Accepted: 04/23/2018] [Indexed: 05/24/2023]
Abstract
BACKGROUND Due to the success of shale gas development in the US, the production cost of natural gas has been reduced significantly, which in turn has made methane (CH4), the major component of natural gas, a potential alternative substrate for bioconversion processes compared with other high-price raw material sources or edible feedstocks. Therefore, exploring effective ways to use CH4 for the production of biofuels is attractive. Biological fixation of CH4 by methanotrophic bacteria capable of using CH4 as their sole carbon and energy source has obtained great attention for biofuel production from this resource. RESULTS In this study, a fast-growing and lipid-rich methanotroph, Methylomicrobium buryatense 5GB1 and its glycogen-knock-out mutant (AP18) were investigated for the production of lipids derived from intracellular membranes, which are key precursors for the production of green diesel. The effects of culture conditions on cell growth and lipid production were investigated in high cell density cultivation with continuous feeding of CH4 and O2. The highest dry cell weight observed was 21.4 g/L and the maximum lipid productivity observed was 45.4 mg/L/h obtained in batch cultures, which corresponds to a 2-fold enhancement in cell density and 3-fold improvement in lipid production, compared with previous reported data from cultures of 5GB1. A 90% enhancement of lipid content was achieved by limiting the biosynthesis of glycogen in strain AP18. Increased CH4/O2 uptake and CO2 evaluation rates were observed in AP18 cultures suggesting that more carbon substrate and energy are needed for AP18 growth while producing lipids. The lipid produced by M. buryatense was estimated to have a cetane number of 75, which is 50% higher than biofuel standards requested by US and EU. CONCLUSIONS Cell growth and lipid production were significantly influenced by culture conditions for both 5GB1 and AP18. Enhanced lipid production in terms of titer, productivity, and content was achieved under high cell density culture conditions by blocking glycogen accumulation as a carbon sink in the strain AP18. Differences observed in CH4/O2 gas uptake and CO2 evolution rates as well as cell growth and glycogen accumulation between 5GB1 and AP18 suggest changes in the metabolic network between these strains. This bioconversion process provides a promising opportunity to transform CH4 into biofuel molecules and encourages further investigation to elucidate the remarkable CH4 biofixation mechanism used by these bacteria.
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Affiliation(s)
- Qiang Fei
- School of Chemical Engineering and Technology, Xi’an Jiaotong University, Xi’an, China
- National Bioenergy Center, National Renewable Energy Laboratory, Golden, CO USA
| | - Aaron W. Puri
- Department of Chemical Engineering, University of Washington, Seattle, WA USA
| | - Holly Smith
- National Bioenergy Center, National Renewable Energy Laboratory, Golden, CO USA
| | - Nancy Dowe
- National Bioenergy Center, National Renewable Energy Laboratory, Golden, CO USA
| | - Philip. T. Pienkos
- National Bioenergy Center, National Renewable Energy Laboratory, Golden, CO USA
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37
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Garg S, Clomburg JM, Gonzalez R. A modular approach for high-flux lactic acid production from methane in an industrial medium using engineered Methylomicrobium buryatense 5GB1. J Ind Microbiol Biotechnol 2018; 45:379-391. [PMID: 29675615 DOI: 10.1007/s10295-018-2035-3] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2018] [Accepted: 04/03/2018] [Indexed: 12/01/2022]
Abstract
Convergence of market drivers such as abundant availability of inexpensive natural gas and increasing awareness of its global warming effects have created new opportunities for the development of small-scale gas-to-liquid (GTL) conversion technologies that can efficiently utilize methane, the primary component of natural gas. Leveraging the unique ability of methanotrophs that use methane as carbon and energy source, biological GTL platforms can be envisioned that are readily deployable at remote petroleum drilling sites where large chemical GTL infrastructure is uneconomical to set-up. Methylomicrobium buryatense, an obligate methanotroph, has gained traction as a potential industrial methanotrophic host because of availability of genetic tools and recent advances in its metabolic engineering. However, progress is impeded by low strain performance and lack of an industrial medium. In this study, we first established a small-scale cultivation platform using Hungate tubes for growth of M. buryatense at medium-to-high-throughput that also enabled 2X faster growth compared to that obtained in traditional glass serum bottles. Then, employing a synthetic biology approach we engineered M. buryatense with varying promoter (inducible and constitutive) and ribosome-binding site combinations, and obtained a strain capable of producing L-lactate from methane at a flux 14-fold higher than previously reported. Finally, we demonstrated L-lactate production in an industrial medium by replacing nitrate with less-expensive ammonium as the nitrogen source. Under these conditions, L-lactate was synthesized at a flux approximately 50-fold higher than that reported previously in a bioreactor system while achieving a titer of 0.6 g/L. These findings position M. buryatense closer to becoming an industrial host strain of choice, and pave new avenues for accelerating methane-to-chemical conversion using synthetic biology.
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Affiliation(s)
- Shivani Garg
- Department of Chemical and Biomolecular Engineering, Rice University, 6100 Main Street MS-667, Houston, TX, 77005, USA
| | - James M Clomburg
- Department of Chemical and Biomolecular Engineering, Rice University, 6100 Main Street MS-667, Houston, TX, 77005, USA
| | - Ramon Gonzalez
- Department of Chemical and Biomolecular Engineering, Rice University, 6100 Main Street MS-667, Houston, TX, 77005, USA. .,Department of Bioengineering, Rice University, Houston, 77005, USA.
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38
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Chistoserdova L, Kalyuzhnaya MG. Current Trends in Methylotrophy. Trends Microbiol 2018; 26:703-714. [PMID: 29471983 DOI: 10.1016/j.tim.2018.01.011] [Citation(s) in RCA: 87] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2017] [Revised: 01/18/2018] [Accepted: 01/30/2018] [Indexed: 11/26/2022]
Abstract
Methylotrophy is a field of study dealing with microorganisms capable of utilization of compounds devoid of carbon-carbon bonds (C1 compounds). In this review, we highlight several emerging trends in methylotrophy. First, we discuss the significance of the recent discovery of lanthanide-dependent alcohol dehydrogenases for understanding both the occurrence and the distribution of methylotrophy functions among bacteria, and then we discuss the newly appreciated role of lanthanides in biology. Next, we describe the detection of other methylotrophy pathways across novel bacterial taxa and insights into the evolution of methylotrophy. Further, data are presented on the occurrence and activity of aerobic methylotrophs in hypoxic and anoxic environments, questioning the prior assumptions on niche separation of aerobic and anaerobic methylotrophy. The concept of communal function in aerobic methane oxidation is also briefly discussed. Finally, we review recent research in engineering methylotrophs for biotechnological applications as well as recent progress in engineering synthetic methylotrophy.
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39
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Methane utilization in Methylomicrobium alcaliphilum 20Z R: a systems approach. Sci Rep 2018; 8:2512. [PMID: 29410419 PMCID: PMC5802761 DOI: 10.1038/s41598-018-20574-z] [Citation(s) in RCA: 57] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2017] [Accepted: 01/22/2018] [Indexed: 12/20/2022] Open
Abstract
Biological methane utilization, one of the main sinks of the greenhouse gas in nature, represents an attractive platform for production of fuels and value-added chemicals. Despite the progress made in our understanding of the individual parts of methane utilization, our knowledge of how the whole-cell metabolic network is organized and coordinated is limited. Attractive growth and methane-conversion rates, a complete and expert-annotated genome sequence, as well as large enzymatic, 13C-labeling, and transcriptomic datasets make Methylomicrobium alcaliphilum 20ZR an exceptional model system for investigating methane utilization networks. Here we present a comprehensive metabolic framework of methane and methanol utilization in M. alcaliphilum 20ZR. A set of novel metabolic reactions governing carbon distribution across central pathways in methanotrophic bacteria was predicted by in-silico simulations and confirmed by global non-targeted metabolomics and enzymatic evidences. Our data highlight the importance of substitution of ATP-linked steps with PPi-dependent reactions and support the presence of a carbon shunt from acetyl-CoA to the pentose-phosphate pathway and highly branched TCA cycle. The diverged TCA reactions promote balance between anabolic reactions and redox demands. The computational framework of C1-metabolism in methanotrophic bacteria can represent an efficient tool for metabolic engineering or ecosystem modeling.
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Chistoserdova L. Applications of methylotrophs: can single carbon be harnessed for biotechnology? Curr Opin Biotechnol 2018; 50:189-194. [PMID: 29414059 DOI: 10.1016/j.copbio.2018.01.012] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2017] [Revised: 12/07/2017] [Accepted: 01/11/2018] [Indexed: 02/06/2023]
Abstract
This review summarizes developments in the field of applied research involving microbial conversion of single carbon compounds (methane, methanol, CO2). The potential of the microorganisms involved in biotechnological applications could be realized via engineering native C1 utilizers toward higher output of value-added compounds, including biofuels, or via production of value chemicals as parts of novel, heterologously expressed biochemical pathways. Alternatively, C1 metabolism could be implemented in traditional industrial platforms (Escherichia coli, yeast), via introduction of specific metabolic modules. Most recent research spanning both approaches is covered. The potential of C1 utilizers in biomining of rare Earth elements, as well as the potential of C1 consuming microbial consortia in industrial applications are discussed.
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Affiliation(s)
- Ludmila Chistoserdova
- Department of Chemical Engineering, University of Washington, Seattle, WA, United States.
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41
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Bennett RK, Steinberg LM, Chen W, Papoutsakis ET. Engineering the bioconversion of methane and methanol to fuels and chemicals in native and synthetic methylotrophs. Curr Opin Biotechnol 2017; 50:81-93. [PMID: 29216497 DOI: 10.1016/j.copbio.2017.11.010] [Citation(s) in RCA: 68] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2017] [Revised: 11/14/2017] [Accepted: 11/15/2017] [Indexed: 10/18/2022]
Abstract
Methylotrophy describes the ability of organisms to utilize reduced one-carbon compounds, notably methane and methanol, as growth and energy sources. Abundant natural gas supplies, composed primarily of methane, have prompted interest in using these compounds, which are more reduced than sugars, as substrates to improve product titers and yields of bioprocesses. Engineering native methylotophs or developing synthetic methylotrophs are emerging fields to convert methane and methanol into fuels and chemicals under aerobic and anaerobic conditions. This review discusses recent progress made toward engineering native methanotrophs for aerobic and anaerobic methane utilization and synthetic methylotrophs for methanol utilization. Finally, strategies to overcome the limitations involved with synthetic methanol utilization, notably methanol dehydrogenase kinetics and ribulose 5-phosphate regeneration, are discussed.
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Affiliation(s)
- R Kyle Bennett
- Department of Chemical and Biomolecular Engineering, University of Delaware, 150 Academy St., Newark, DE 19716, USA; The Delaware Biotechnology Institute, Molecular Biotechnology Laboratory, University of Delaware, 15 Innovation Way, Newark, DE 19711, USA
| | - Lisa M Steinberg
- Department of Chemical and Biomolecular Engineering, University of Delaware, 150 Academy St., Newark, DE 19716, USA; The Delaware Biotechnology Institute, Molecular Biotechnology Laboratory, University of Delaware, 15 Innovation Way, Newark, DE 19711, USA
| | - Wilfred Chen
- Department of Chemical and Biomolecular Engineering, University of Delaware, 150 Academy St., Newark, DE 19716, USA
| | - Eleftherios T Papoutsakis
- Department of Chemical and Biomolecular Engineering, University of Delaware, 150 Academy St., Newark, DE 19716, USA; The Delaware Biotechnology Institute, Molecular Biotechnology Laboratory, University of Delaware, 15 Innovation Way, Newark, DE 19711, USA.
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42
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Gilman A, Fu Y, Hendershott M, Chu F, Puri AW, Smith AL, Pesesky M, Lieberman R, Beck DAC, Lidstrom ME. Oxygen-limited metabolism in the methanotroph Methylomicrobium buryatense 5GB1C. PeerJ 2017; 5:e3945. [PMID: 29062611 PMCID: PMC5652258 DOI: 10.7717/peerj.3945] [Citation(s) in RCA: 51] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2017] [Accepted: 09/30/2017] [Indexed: 11/20/2022] Open
Abstract
The bacteria that grow on methane aerobically (methanotrophs) support populations of non-methanotrophs in the natural environment by excreting methane-derived carbon. One group of excreted compounds are short-chain organic acids, generated in highest abundance when cultures are grown under O2-starvation. We examined this O2-starvation condition in the methanotroph Methylomicrobium buryatense 5GB1. The M. buryatense 5GB1 genome contains homologs for all enzymes necessary for a fermentative metabolism, and we hypothesize that a metabolic switch to fermentation can be induced by low-O2 conditions. Under prolonged O2-starvation in a closed vial, this methanotroph increases the amount of acetate excreted about 10-fold, but the formate, lactate, and succinate excreted do not respond to this culture condition. In bioreactor cultures, the amount of each excreted product is similar across a range of growth rates and limiting substrates, including O2-limitation. A set of mutants were generated in genes predicted to be involved in generating or regulating excretion of these compounds and tested for growth defects, and changes in excretion products. The phenotypes and associated metabolic flux modeling suggested that in M. buryatense 5GB1, formate and acetate are excreted in response to redox imbalance. Our results indicate that even under O2-starvation conditions, M. buryatense 5GB1 maintains a metabolic state representing a combination of fermentation and respiration metabolism.
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Affiliation(s)
- Alexey Gilman
- Department of Chemical Engineering, University of Washington, Seattle, WA, United States of America
| | - Yanfen Fu
- Department of Chemical Engineering, University of Washington, Seattle, WA, United States of America
| | | | | | - Aaron W Puri
- Department of Chemical Engineering, University of Washington, Seattle, WA, United States of America
| | | | - Mitchell Pesesky
- Department of Chemical Engineering, University of Washington, Seattle, WA, United States of America
| | - Rose Lieberman
- Department of Biology, George Washington University, Washington, D.C., USA
| | - David A C Beck
- Department of Chemical Engineering, University of Washington, Seattle, WA, United States of America.,eScience Institute, University of Washington, Seattle, WA, USA
| | - Mary E Lidstrom
- Department of Chemical Engineering, University of Washington, Seattle, WA, United States of America.,Department of Microbiology, University of Washington, Seattle, WA, USA
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43
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Ishikawa M, Tanaka Y, Suzuki R, Kimura K, Tanaka K, Kamiya K, Ito H, Kato S, Kamachi T, Hori K, Nakanishi S. Real-time monitoring of intracellular redox changes in Methylococcus capsulatus (Bath) for efficient bioconversion of methane to methanol. BIORESOURCE TECHNOLOGY 2017; 241:1157-1161. [PMID: 28578808 DOI: 10.1016/j.biortech.2017.05.107] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/30/2017] [Revised: 05/16/2017] [Accepted: 05/17/2017] [Indexed: 06/07/2023]
Abstract
This study aimed to develop a novel method for real-time monitoring of the intracellular redox states in a methanotroph Methylococcus capsulatus, using Peredox as a genetically encoded fluorescent sensor of the NADH:NAD+ ratio. As expected, the fluorescence derived from the Peredox-expressing M. capsulatus transformant increased by supplementation of electron donor compounds (methane and formate), while it decreased by specifically inhibiting the methanol oxidation reaction. Electrochemical measurements confirmed that the Peredox fluorescence reliably represents the intracellular redox changes. This study is the first to construct a reliable redox-monitoring method for methanotrophs, which will facilitate to develop more efficient methane-to-methanol bioconversion processes.
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Affiliation(s)
- Masahito Ishikawa
- Department of Biotechnology, Graduate School of Engineering, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8603, Japan; Research Center for Solar Energy Chemistry, Osaka University, 1-3 Machikaneyama, Toyonaka, Osaka 560-8531, Japan
| | - Yuya Tanaka
- Department of Chemistry, Graduate School of Engineering Science, Osaka University, Machikaneyama, Toyonaka, Osaka 560-8531, Japan
| | - Risa Suzuki
- Department of Biotechnology, Graduate School of Engineering, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8603, Japan
| | - Kota Kimura
- Department of Chemistry, Graduate School of Engineering Science, Osaka University, Machikaneyama, Toyonaka, Osaka 560-8531, Japan
| | - Kenya Tanaka
- Department of Chemistry, Graduate School of Engineering Science, Osaka University, Machikaneyama, Toyonaka, Osaka 560-8531, Japan
| | - Kazuhide Kamiya
- Research Center for Solar Energy Chemistry, Osaka University, 1-3 Machikaneyama, Toyonaka, Osaka 560-8531, Japan; Department of Chemistry, Graduate School of Engineering Science, Osaka University, Machikaneyama, Toyonaka, Osaka 560-8531, Japan
| | - Hidehiro Ito
- Education Academy of Computational Life Sciences, Tokyo Institute of Technology, 2-12-1 Ookayama, Meguro-ku, Tokyo 152-8550, Japan
| | - Souichiro Kato
- Research Center for Solar Energy Chemistry, Osaka University, 1-3 Machikaneyama, Toyonaka, Osaka 560-8531, Japan; Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), 2-17-2-1 Tsukisamu-Higashi, Toyohira-ku, Sapporo, Hokkaido 062-8517, Japan
| | - Toshiaki Kamachi
- Department of Life Science and Technology, Graduated School of Bioscience and Biotechnology, Tokyo Institute of Technology, 2-12-1 Ookayama, Meguro-ku, Tokyo 152-8550, Japan
| | - Katsutoshi Hori
- Department of Biotechnology, Graduate School of Engineering, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8603, Japan
| | - Shuji Nakanishi
- Research Center for Solar Energy Chemistry, Osaka University, 1-3 Machikaneyama, Toyonaka, Osaka 560-8531, Japan; Department of Chemistry, Graduate School of Engineering Science, Osaka University, Machikaneyama, Toyonaka, Osaka 560-8531, Japan.
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