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Guo S, Song Q, Song X, Zhang C, Fei Q. Sustainable production of C50 carotenoid bacterioruberin from methane using soil-enriched microbial consortia. BIORESOURCE TECHNOLOGY 2024; 412:131415. [PMID: 39233184 DOI: 10.1016/j.biortech.2024.131415] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/19/2024] [Revised: 08/30/2024] [Accepted: 08/31/2024] [Indexed: 09/06/2024]
Abstract
Bacterioruberin is widely used in medicine, food, and cosmetics owing to its prominent characteristics of antioxidants and bioactivities. Bioconversion of methane into bacterioruberin is a promising way to address biomanufacturing substrate costs and greenhouse gas emissions but has not been achieved yet. Herein, this study aimed to upcycle methane to bacterioruberin by microbial consortia. The microbial consortia consist of Methylomonas and Methylophilus capable of synthesizing carotenoids from methane was firstly enriched from paddy soil. Through this microbial community, methane was successfully converted into C50 bacterioruberin for the first time. The bioconversion process was then optimized by the response surface methodology. Finally, the methane-derived bacterioruberin reached a record yield of 280.88 ± 2.94 μg/g DCW. This study presents a cost-effective and eco-friendly approach for producing long-chain carotenoids from methane, offering a significant advancement in the direct conversion of greenhouse gases into value-added products.
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Affiliation(s)
- Shuqi Guo
- School of Chemical Engineering and Technology, Xi'an Jiaotong University, Xi'an 710049, PR China; Xi'an Key Laboratory of C1 Compound Bioconversion Technology, Xi'an 710049, PR China
| | - Qiaoqiao Song
- School of Chemical Engineering and Technology, Xi'an Jiaotong University, Xi'an 710049, PR China
| | - Xungong Song
- School of Chemical Engineering and Technology, Xi'an Jiaotong University, Xi'an 710049, PR China
| | - Chenyue Zhang
- School of Chemical Engineering and Technology, Xi'an Jiaotong University, Xi'an 710049, PR China
| | - Qiang Fei
- School of Chemical Engineering and Technology, Xi'an Jiaotong University, Xi'an 710049, PR China; Xi'an Key Laboratory of C1 Compound Bioconversion Technology, Xi'an 710049, PR China.
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2
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Guo W, He R, Zhao Y, Li D. Imbalanced metabolism induced NH 4+ accumulation and its effect on the central metabolism of Methylomonas sp. ZR1. Int Microbiol 2024; 27:49-66. [PMID: 38038804 DOI: 10.1007/s10123-023-00457-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2022] [Revised: 07/23/2023] [Accepted: 11/14/2023] [Indexed: 12/02/2023]
Abstract
Nitrogen and carbon are the two most essential nutrient elements, and their metabolism is tightly coupled in single carbon metabolic microorganisms. However, the nitrogen metabolism and the nitrogen/carbon (N/C) metabolic balance in single-carbon metabolism is poorly studied. In this study, the nitrogen metabolism pattern of the fast growing methanotrophs Methylomonas sp. ZR1 grown in methane and methanol was studied. Effect study of different nitrogen sources on the cell growth of ZR1 indicates that nitrate salts are the best nitrogen source supporting the growth of ZR1 using methane and methanol as carbon source. However, its metabolic intermediate ammonium was found to accumulate with high N/C ratio in the medium and consequently inhibit the growth of ZR1. Studies of carbon and nitrogen metabolic kinetic under different N/C ratio conditions indicate that the accumulation of NH4+ is caused by the imbalanced nitrogen and carbon metabolism in ZR1. Feeding carbon skeleton α-ketoglutaric acid could effectively relieve the inhibition effect of NH4+ on the growth of ZR1, which further confirms this assumption. qPCR analysis of the expression level of the central metabolic key enzyme gene indicates that the nitrogen metabolic intermediate ammonium has strong regulation effect on the central nitrogen and carbon metabolism in ZR1. qPCR-combined genomic analysis confirms that a third ammonium assimilation pathway glycine synthesis system is operated in ZR1 to balance the nitrogen and carbon metabolism. Based on the qPCR result, it was also found that ZR1 employs two strategies to relieve ammonium stress in the presence of ammonium: assimilating excess ammonium or cutting off the nitrogen reduction reactions according to the available C1 substrate. Validating the connections between single-carbon and nitrogen metabolism and studying the accumulation and assimilation mechanism of ammonium will contribute to understand how nitrogen regulates cellular growth in single-carbon metabolic microorganisms.
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Affiliation(s)
- Wei Guo
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Science, 32 West 7Th Avenue, Tianjin Airport Economic Area, Tianjin, 300308, China.
| | - Ronglin He
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Science, 32 West 7Th Avenue, Tianjin Airport Economic Area, Tianjin, 300308, China
| | - Yujie Zhao
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Science, 32 West 7Th Avenue, Tianjin Airport Economic Area, Tianjin, 300308, China
| | - Demao Li
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Science, 32 West 7Th Avenue, Tianjin Airport Economic Area, Tianjin, 300308, China
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3
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Oshkin IY, Tikhonova EN, Suleimanov RZ, Ashikhmin AA, Ivanova AA, Pimenov NV, Dedysh SN. All Kinds of Sunny Colors Synthesized from Methane: Genome-Encoded Carotenoid Production by Methylomonas Species. Microorganisms 2023; 11:2865. [PMID: 38138009 PMCID: PMC10745290 DOI: 10.3390/microorganisms11122865] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2023] [Revised: 11/23/2023] [Accepted: 11/24/2023] [Indexed: 12/24/2023] Open
Abstract
Carotenoids are secondary metabolites that exhibit antioxidant properties and are characterized by a striking range of colorations from red to yellow. These natural pigments are synthesized by a wide range of eukaryotic and prokaryotic organisms. Among the latter, carotenoid-producing methanotrophic bacteria, which display fast growth on methane or natural gas, are of particular interest as potential producers of a feed protein enriched with carotenoids. Until recently, Methylomonas strain 16a and Methylomonas sp. ZR1 remained the only representatives of the genus for which detailed carotenoid profile was determined. In this study, we analyzed the genome sequences of five strains of Methylomonas species whose pigmentation varied from white and yellow to orange and red, and identified carotenoids produced by these bacteria. Carotenoids synthesized using four pigmented strains included C30 fraction, primarily composed of 4,4'-diaplycopene-4,4'-dioic acid and 4,4'-diaplycopenoic acid, as well as C40 fraction with the major compound represented by 1,1'-dihydroxy-3,4-didehydrolycopene. The genomes of studied Methylomonas strains varied in size between 4.59 and 5.45 Mb and contained 4201-4735 protein-coding genes. These genomes and 35 reference Methylomonas genomes available in the GenBank were examined for the presence of genes encoding carotenoid biosynthesis. Genomes of all pigmented Methylomonas strains harbored genes necessary for the synthesis of 4,4'-diaplycopene-4,4'-dioic acid. Non-pigmented "Methylomonas montana" MW1T lacked the crtN gene required for carotenoid production. Nearly all strains possessed phytoene desaturases, which explained their ability to naturally synthesize lycopene. Thus, members of the genus Methylomonas can potentially be considered as producers of C30 and C40 carotenoids from methane.
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Affiliation(s)
- Igor Y. Oshkin
- Winogradsky Institute of Microbiology, Research Center of Biotechnology of the Russian Academy of Sciences, Moscow 117312, Russia
| | - Ekaterina N. Tikhonova
- Winogradsky Institute of Microbiology, Research Center of Biotechnology of the Russian Academy of Sciences, Moscow 117312, Russia
| | - Ruslan Z. Suleimanov
- Winogradsky Institute of Microbiology, Research Center of Biotechnology of the Russian Academy of Sciences, Moscow 117312, Russia
| | - Aleksandr A. Ashikhmin
- Institute of Basic Biological Problems, Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences, Pushchino 142290, Russia
| | - Anastasia A. Ivanova
- Winogradsky Institute of Microbiology, Research Center of Biotechnology of the Russian Academy of Sciences, Moscow 117312, Russia
| | - Nikolai V. Pimenov
- Winogradsky Institute of Microbiology, Research Center of Biotechnology of the Russian Academy of Sciences, Moscow 117312, Russia
| | - Svetlana N. Dedysh
- Winogradsky Institute of Microbiology, Research Center of Biotechnology of the Russian Academy of Sciences, Moscow 117312, Russia
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4
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Sarwar A, Lee EY. Methanol-based biomanufacturing of fuels and chemicals using native and synthetic methylotrophs. Synth Syst Biotechnol 2023; 8:396-415. [PMID: 37384124 PMCID: PMC10293595 DOI: 10.1016/j.synbio.2023.06.001] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2023] [Revised: 06/03/2023] [Accepted: 06/04/2023] [Indexed: 06/30/2023] Open
Abstract
Methanol has recently gained significant attention as a potential carbon substrate for the production of fuels and chemicals, owing to its high degree of reduction, abundance, and low price. Native methylotrophic yeasts and bacteria have been investigated for the production of fuels and chemicals. Alternatively, synthetic methylotrophic strains are also being developed by reconstructing methanol utilization pathways in model microorganisms, such as Escherichia coli. Owing to the complex metabolic pathways, limited availability of genetic tools, and methanol/formaldehyde toxicity, the high-level production of target products for industrial applications are still under development to satisfy commercial feasibility. This article reviews the production of biofuels and chemicals by native and synthetic methylotrophic microorganisms. It also highlights the advantages and limitations of both types of methylotrophs and provides an overview of ways to improve their efficiency for the production of fuels and chemicals from methanol.
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Methylomonas rapida sp. nov., a novel species of fast-growing, carotenoid-producing obligate methanotrophs with high biotechnological potential. Syst Appl Microbiol 2023; 46:126398. [PMID: 36724672 DOI: 10.1016/j.syapm.2023.126398] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2022] [Revised: 12/31/2022] [Accepted: 01/11/2023] [Indexed: 01/26/2023]
Abstract
The genus Methylomonas accommodates strictly aerobic, obligate methanotrophs, with their sole carbon and energy sources restricted to methane and methanol. These bacteria inhabit oxic-anoxic interfaces of various freshwater habitats and have attracted considerable attention as potential producers of a single-cell protein. Here, we characterize two fast-growing representatives of this genus, strains 12 and MP1T, which are phylogenetically distinct from the currently described Methylomonas species (94.0-97.3 % 16S rRNA gene sequence similarity). Strains 12 and MP1T were isolated from freshwater sediments collected in Moscow and Krasnodar regions, respectively. Cells of these strains are Gram-negative, red-pigmented, highly motile thick rods that contain a type I intracytoplasmic membrane system and possess a particulate methane monooxygenase (pMMO) enzyme. These bacteria grow between 8 and 45 °C (optimum 35 °C) in a relatively narrow pH range of 5.5-7.3 (optimum pH 6.6-7.2). Major carotenoids synthesized by these methanotrophs are 4,4'-diaplycopene-4,4'-dioic acid, 1,1'-dihydroxy-3,4-didehydrolycopene and 4,4'-diaplycopenoic acid. High biomass yield, of up to 3.26 g CDW/l, is obtained during continuous cultivation of MP1T on natural gas in a bioreactor at a dilution rate of 0.22 h-1. The complete genome sequence of strain MP1T is 4.59 Mb in size; the DNA G + C content is 52.8 mol%. The genome encodes four rRNA operons, one pMMO operon and 4,216 proteins. The genome sequence displays 82-85 % average nucleotide identity to those of earlier described Methylomonas species. We propose to classify these bacteria as representing a novel species of the genus Methylomonas, M. rapida sp. nov., with the type strain MP1T (=KCTC 92586T = VKM B-3663T).
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6
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Mrudulakumari Vasudevan U, Mai DHA, Krishna S, Lee EY. Methanotrophs as a reservoir for bioactive secondary metabolites: Pitfalls, insights and promises. Biotechnol Adv 2023; 63:108097. [PMID: 36634856 DOI: 10.1016/j.biotechadv.2023.108097] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2022] [Revised: 12/10/2022] [Accepted: 01/06/2023] [Indexed: 01/11/2023]
Abstract
Methanotrophs are potent natural producers of several bioactive secondary metabolites (SMs) including isoprenoids, polymers, peptides, and vitamins. Cryptic biosynthetic gene clusters identified from these microbes via genome mining hinted at the vast and hidden SM biosynthetic potential of these microbes. Central carbon metabolism in methanotrophs offers rare pathway intermediate pools that could be further diversified using advanced synthetic biology tools to produce valuable SMs; for example, plant polyketides, rare carotenoids, and fatty acid-derived SMs. Recent advances in pathway reconstruction and production of isoprenoids, squalene, ectoine, polyhydroxyalkanoate copolymer, cadaverine, indigo, and shinorine serve as proof-of-concept. This review provides theoretical guidance for developing methanotrophs as microbial chassis for high-value SMs. We summarize the distinct secondary metabolic potentials of type I and type II methanotrophs, with specific attention to products relevant to biomedical applications. This review also includes native and non-native SMs from methanotrophs, their therapeutic potential, strategies to induce silent biosynthetic gene clusters, and challenges.
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Affiliation(s)
- Ushasree Mrudulakumari Vasudevan
- Department of Chemical Engineering (BK21 FOUR Integrated Engineering Program), Kyung Hee University, Yongin-si, Gyeonggi-do 17104, Republic of Korea
| | - Dung Hoang Anh Mai
- Department of Chemical Engineering (BK21 FOUR Integrated Engineering Program), Kyung Hee University, Yongin-si, Gyeonggi-do 17104, Republic of Korea
| | - Shyam Krishna
- Department of Chemical Engineering (BK21 FOUR Integrated Engineering Program), Kyung Hee University, Yongin-si, Gyeonggi-do 17104, Republic of Korea
| | - Eun Yeol Lee
- Department of Chemical Engineering (BK21 FOUR Integrated Engineering Program), Kyung Hee University, Yongin-si, Gyeonggi-do 17104, Republic of Korea.
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7
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Khalaf RA, Awad M. Lycopene as a Potential Bioactive Compound: Chemistry, Extraction, and Anticancer Prospective. Curr Cancer Drug Targets 2023; 23:634-642. [PMID: 36718971 DOI: 10.2174/1568009623666230131124236] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2022] [Revised: 12/01/2022] [Accepted: 12/05/2022] [Indexed: 02/01/2023]
Abstract
Lycopene, a potential bioactive agent, is a non-pro-vitamin A carotenoid recognized as a potent antioxidant. It is extracted from plants like tomatoes, watermelons, red carrots and papayas and has remarkable health benefits. A significant amount of research has been assisted to date to establish the anticancer activity of lycopene. Our review enhances information about the promising anticancer potential of this compound. The biological activity of lycopene has been described in several studies in regard to pancreatic, breast, prostate, liver, gastric, ovarian, kidney, skin, intestine, brain and spinal cord cancers. Lycopene resists cancer by inhibition of apoptosis, induction of cell proliferation, cell invasion, cell cycle development, metastasis and angiogenesis. The mechanisms of anticancer action of lycopene are attributed to the management of certain signal transduction pathways, such as modulation of insulin-like growth factors system, PI3K/Akt pathway, modification of important gene expression, inhibit the activity of sex steroid hormones, and the conversation of mitochondrial behavior. Hence, this review focuses on current knowledge of sources, extraction techniques, and chemistry of lycopene, as well as the prospective mechanisms of action related with its anticancer activity. Also, it summarizes the background information about lycopene and the most current research with consideration to its aspect in treating several types of cancer together with future directions.
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Affiliation(s)
- Reema Abu Khalaf
- Department of Pharmacy, Faculty of Pharmacy, Al-Zaytoonah University of Jordan, Amman, Jordan
| | - Maha Awad
- Department of Pharmacy, Faculty of Pharmacy, Al-Zaytoonah University of Jordan, Amman, Jordan
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8
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Oshkin IY, Danilova OV, Suleimanov RZ, Tikhonova EN, Malakhova TV, Murashova IA, Pimenov NV, Dedysh SN. Thermotolerant Methanotrophic Bacteria from Sediments of the River Chernaya, Crimea, and Assessment of Their Growth Characteristics. Microbiology (Reading) 2021. [DOI: 10.1134/s0026261721050131] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
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9
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Salem R, ElDyasti A, Audette GF. Biomedical Applications of Biomolecules Isolated from Methanotrophic Bacteria in Wastewater Treatment Systems. Biomolecules 2021; 11:1217. [PMID: 34439884 PMCID: PMC8392503 DOI: 10.3390/biom11081217] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2021] [Revised: 08/05/2021] [Accepted: 08/11/2021] [Indexed: 11/16/2022] Open
Abstract
Wastewater treatment plants and other remediation facilities serve important roles, both in public health, but also as dynamic research platforms for acquiring useful resources and biomolecules for various applications. An example of this is methanotrophic bacteria within anaerobic digestion processes in wastewater treatment plants. These bacteria are an important microbial source of many products including ectoine, polyhydroxyalkanoates, and methanobactins, which are invaluable to the fields of biotechnology and biomedicine. Here we provide an overview of the methanotrophs' unique metabolism and the biochemical pathways involved in biomolecule formation. We also discuss the potential biomedical applications of these biomolecules through creation of beneficial biocompatible products including vaccines, prosthetics, electronic devices, drug carriers, and heart stents. We highlight the links between molecular biology, public health, and environmental science in the advancement of biomedical research and industrial applications using methanotrophic bacteria in wastewater treatment systems.
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Affiliation(s)
- Rana Salem
- Department of Chemistry, York University, Toronto, ON M3J 1P3, Canada;
| | - Ahmed ElDyasti
- Department of Civil Engineering, York University, Toronto, ON M3J 1P3, Canada;
| | - Gerald F. Audette
- Department of Chemistry, York University, Toronto, ON M3J 1P3, Canada;
- The Centre for Research on Biomolecular Interactions, York University, 4700 Keele Street, Toronto, ON M3J 1P3, Canada
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10
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Nguyen AD, Pham DN, Chau THT, Lee EY. Enhancing Sesquiterpenoid Production from Methane via Synergy of the Methylerythritol Phosphate Pathway and a Short-Cut Route to 1-Deoxy-D-xylulose 5-Phosphate in Methanotrophic Bacteria. Microorganisms 2021; 9:microorganisms9061236. [PMID: 34200225 PMCID: PMC8227265 DOI: 10.3390/microorganisms9061236] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2021] [Revised: 06/01/2021] [Accepted: 06/03/2021] [Indexed: 12/29/2022] Open
Abstract
Sesquiterpenoids are one of the most diverse classes of isoprenoids which exhibit numerous potentials in industrial biotechnology. The methanotrophs-based methane bioconversion is a promising approach for sustainable production of chemicals and fuels from methane. With intrinsic high carbon flux though the ribulose monophosphate cycle in Methylotuvimicrobium alcaliphilum 20Z, we demonstrated here that employing a short-cut route from ribulose 5-phosphate to 1-deoxy-d-xylulose 5-phosphate (DXP) could enable a more efficient isoprenoid production via the methylerythritol 4-phosphate (MEP) pathway, using α-humulene as a model compound. An additional 2.8-fold increase in α-humulene production yield was achieved by the fusion of the nDXP enzyme and DXP reductase. Additionally, we utilized these engineering strategies for the production of another sesquiterpenoid, α-bisabolene. The synergy of the nDXP and MEP pathways improved the α-bisabolene titer up to 12.24 ± 0.43 mg/gDCW, twofold greater than that of the initial strain. This study expanded the suite of sesquiterpenoids that can be produced from methane and demonstrated the synergistic uses of the nDXP and MEP pathways for improving sesquiterpenoid production in methanotrophic bacteria.
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Affiliation(s)
| | | | | | - Eun Yeol Lee
- Correspondence: ; Tel.: +82-31-201-3839; Fax: +82-31-204-8114
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11
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Yasuda S, Suenaga T, Orschler L, Agrawal S, Lackner S, Terada A. Metagenomic Insights Into Functional and Taxonomic Compositions of an Activated Sludge Microbial Community Treating Leachate of a Completed Landfill: A Pathway-Based Analysis. Front Microbiol 2021; 12:640848. [PMID: 33995301 PMCID: PMC8121002 DOI: 10.3389/fmicb.2021.640848] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2020] [Accepted: 04/01/2021] [Indexed: 11/13/2022] Open
Abstract
Upcycling wastes into valuable products by mixed microbial communities has recently received considerable attention. Sustainable production of high-value substances from one-carbon (C1) compounds, e.g., methanol supplemented as an external electron donor in bioreactors for wastewater treatment, is a promising application of upcycling. This study undertook a gene-centric approach to screen valuable production potentials from mixed culture biomass, removing organic carbon and nitrogen from landfill leachate. To this end, the microbial community of the activated sludge from a landfill leachate treatment plant and its metabolic potential for the production of seven valuable products were investigated. The DNA extracted from the activated sludge was subjected to shotgun metagenome sequencing to analyze the microbial taxonomy and functions associated with producing the seven products. The functional analysis confirmed that the activated sludge could produce six of the valuable products, ectoine, polyhydroxybutyrate (PHB), zeaxanthin, astaxanthin, acetoin, and 2,3-butanediol. Quantification of the detected functional gene hit numbers for these valuable products as a primary trial identified a potential rate-limiting metabolic pathway, e.g., conversion of L-2,4-diaminobutyrate into N-γ-acetyl-L2,4,-diaminobutyrate during the ectoine biosynthesis. Overall, this study demonstrated that primary screening by the proposed gene-centric approach can be used to evaluate the potential for the production of valuable products using mixed culture or single microbe in engineered systems. The proposed approach can be expanded to sites where water purification is highly required, but resource recovery, or upcycling has not been implemented.
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Affiliation(s)
- Shohei Yasuda
- Department of Chemical Engineering, Tokyo University of Agriculture and Technology, Koganei, Japan
| | - Toshikazu Suenaga
- Global Innovation Research Institute, Tokyo University of Agriculture and Technology, Fuchu, Japan
| | - Laura Orschler
- Department of Civil and Environmental Engineering Science, Institute IWAR, Chair of Wastewater Engineering, Technical University of Darmstadt, Darmstadt, Germany
| | - Shelesh Agrawal
- Department of Civil and Environmental Engineering Science, Institute IWAR, Chair of Wastewater Engineering, Technical University of Darmstadt, Darmstadt, Germany
| | - Susanne Lackner
- Department of Civil and Environmental Engineering Science, Institute IWAR, Chair of Wastewater Engineering, Technical University of Darmstadt, Darmstadt, Germany
| | - Akihiko Terada
- Department of Chemical Engineering, Tokyo University of Agriculture and Technology, Koganei, Japan.,Global Innovation Research Institute, Tokyo University of Agriculture and Technology, Fuchu, Japan
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12
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Genome-scale revealing the central metabolic network of the fast growing methanotroph Methylomonas sp. ZR1. World J Microbiol Biotechnol 2021; 37:29. [PMID: 33452942 DOI: 10.1007/s11274-021-02995-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2019] [Accepted: 01/05/2021] [Indexed: 10/22/2022]
Abstract
Methylomonas sp. ZR1 was an isolated new methanotrophs that could utilize methane and methanol growing fast and synthesizing value added compounds such as lycopene. In this study, the genomic study integrated with the comparative transcriptome analysis were taken to understanding the metabolic characteristic of ZR1 grown on methane and methanol at normal and high temperature regime. Complete Embden-Meyerhof-Parnas pathway (EMP), Entner-Doudoroff pathway (ED), Pentose Phosphate Pathway (PP) and Tricarboxy Acid Cycle (TCA) were found to be operated in ZR1. In addition, the energy saving ppi-dependent EMP enzyme, coupled with the complete and efficient central carbon metabolic network might be responsible for its fast growing nature. Transcript level analysis of the central carbon metabolism indicated that formaldehyde metabolism was a key nod that may be in charge of the carbon conversion efficiency (CCE) divergent of ZR1 grown on methanol and methane. Flexible nitrogen and carotene metabolism pattern were also investigated in ZR1. Nitrogenase genes in ZR1 were found to be highly expressed with methane even in the presence of sufficient nitrate. It appears that, higher lycopene production in ZR1 grown on methane might be attributed to the higher proportion of transcript level of C40 to C30 metabolic gene. Higher transcript level of exopolysaccharides metabolic gene and stress responding proteins indicated that ZR1 was confronted with severer growth stress with methanol than with methane. Additionally, lower transcript level of the TCA cycle, the dramatic high expression level of the nitric oxide reductase and stress responding protein, revealed the imbalance of the central carbon and nitrogen metabolic status, which would result in the worse growth of ZR1 with methanol at 30 °C.
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13
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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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14
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Nguyen AD, Kim D, Lee EY. A comparative transcriptome analysis of the novel obligate methanotroph Methylomonas sp. DH-1 reveals key differences in transcriptional responses in C1 and secondary metabolite pathways during growth on methane and methanol. BMC Genomics 2019; 20:130. [PMID: 30755173 PMCID: PMC6373157 DOI: 10.1186/s12864-019-5487-6] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2018] [Accepted: 01/28/2019] [Indexed: 12/21/2022] Open
Abstract
Background Methanotrophs play an important role in biotechnological applications, with their ability to utilize single carbon (C1) feedstock such as methane and methanol to produce a range of high-value compounds. A newly isolated obligate methanotroph strain, Methylomonas sp. DH-1, became a platform strain for biotechnological applications because it has proven capable of producing chemicals, fuels, and secondary metabolites from methane and methanol. In this study, transcriptome analysis with RNA-seq was used to investigate the transcriptional change of Methylomonas sp. DH-1 on methane and methanol. This was done to improve knowledge about C1 assimilation and secondary metabolite pathways in this promising, but under-characterized, methane-bioconversion strain. Results We integrated genomic and transcriptomic analysis of the newly isolated Methylomonas sp. DH-1 grown on methane and methanol. Detailed transcriptomic analysis indicated that (i) Methylomonas sp. DH-1 possesses the ribulose monophosphate (RuMP) cycle and the Embden–Meyerhof–Parnas (EMP) pathway, which can serve as main pathways for C1 assimilation, (ii) the existence and the expression of a complete serine cycle and a complete tricarboxylic acid (TCA) cycle might contribute to methane conversion and energy production, and (iii) the highly active endogenous plasmid pDH1 may code for essential metabolic processes. Comparative transcriptomic analysis on methane and methanol as a sole carbon source revealed different transcriptional responses of Methylomonas sp. DH-1, especially in C1 assimilation, secondary metabolite pathways, and oxidative stress. Especially, these results suggest a shift of central metabolism when substrate changed from methane to methanol in which formaldehyde oxidation pathway and serine cycle carried more flux to produce acetyl-coA and NADH. Meanwhile, downregulation of TCA cycle when grown on methanol may suggest a shift of its main function is to provide de novo biosynthesis, but not produce NADH. Conclusions This study provides insights into the transcriptomic profile of Methylomonas sp. DH-1 grown on major carbon sources for C1 assimilation, providing in-depth knowledge on the metabolic pathways of this strain. These observations and analyses can contribute to future metabolic engineering with the newly isolated, yet under-characterized, Methylomonas sp. DH-1 to enhance its biochemical application in relevant industries. Electronic supplementary material The online version of this article (10.1186/s12864-019-5487-6) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Anh Duc Nguyen
- Department of Chemical Engineering, Kyung Hee University, Yongin, 17104, Republic of Korea
| | - Donghyuk Kim
- School of Energy and Chemical Engineering & School of Biological Sciences, Ulsan National Institute of Science and Technology (UNIST), Ulsan, 44919, Republic of Korea.
| | - Eun Yeol Lee
- Department of Chemical Engineering, Kyung Hee University, Yongin, 17104, Republic of Korea.
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