1
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Bhat EH, Henard JM, Lee SA, McHalffey D, Ravulapati MS, Rogers EV, Yu L, Skiles D, Henard CA. Construction of a broad-host-range Anderson promoter series and particulate methane monooxygenase promoter variants expand the methanotroph genetic toolbox. Synth Syst Biotechnol 2024; 9:250-258. [PMID: 38435708 PMCID: PMC10909576 DOI: 10.1016/j.synbio.2024.02.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2024] [Revised: 02/02/2024] [Accepted: 02/06/2024] [Indexed: 03/05/2024] Open
Abstract
Methanotrophic bacteria are currently used industrially for the bioconversion of methane-rich natural gas and anaerobic digestion-derived biogas to valuable products. These bacteria may also serve to mitigate the negative effects of climate change by capturing atmospheric greenhouse gases. Several genetic tools have previously been developed for genetic and metabolic engineering of methanotrophs. However, the available tools for use in methanotrophs are significantly underdeveloped compared to many other industrially relevant bacteria, which hinders genetic and metabolic engineering of these biocatalysts. As such, expansion of the methanotroph genetic toolbox is needed to further our understanding of methanotrophy and develop biotechnologies that leverage these unique microbes for mitigation and conversion of methane to valuable products. Here, we determined the copy number of three broad-host-range plasmids in Methylococcus capsulatus Bath and Methylosinus trichosporium OB3b, representing phylogenetically diverse Gammaproteobacterial and Alphaproteobacterial methanotrophs, respectively. Further, we show that the commonly used synthetic Anderson series promoters are functional and exhibit similar relative activity in M. capsulatus and M. trichosporium OB3b, but the synthetic series had limited range. Thus, we mutagenized the native M. capsulatus particulate methane monooxygenase promoter and identified variants with activity that expand the activity range of synthetic, constitutive promoters functional not only in M. capsulatus, but also in Escherichia coli. Collectively, the tools developed here advance the methanotroph genetic engineering toolbox and represent additional synthetic genetic parts that may have broad applicability in Pseudomonadota bacteria.
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Affiliation(s)
| | | | | | - Dustin McHalffey
- Department of Biological Sciences and BioDiscovery Institute, University of North Texas, Denton, TX, USA
| | - Mahith S. Ravulapati
- Department of Biological Sciences and BioDiscovery Institute, University of North Texas, Denton, TX, USA
| | - Elle V. Rogers
- Department of Biological Sciences and BioDiscovery Institute, University of North Texas, Denton, TX, USA
| | - Logan Yu
- Department of Biological Sciences and BioDiscovery Institute, University of North Texas, Denton, TX, USA
| | - David Skiles
- Department of Biological Sciences and BioDiscovery Institute, University of North Texas, Denton, TX, USA
| | - Calvin A. Henard
- Department of Biological Sciences and BioDiscovery Institute, University of North Texas, Denton, TX, USA
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2
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Goswami S, Singer SW, Simmons BA, Awasthi D. Optimization of electroporation method and promoter evaluation for type-1 methanotroph, Methylotuvimicrobium alcaliphilum. Front Bioeng Biotechnol 2024; 12:1412410. [PMID: 38812915 PMCID: PMC11133525 DOI: 10.3389/fbioe.2024.1412410] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2024] [Accepted: 04/26/2024] [Indexed: 05/31/2024] Open
Abstract
Methanotrophic bacteria are promising hosts for methane bioconversion to biochemicals or bioproducts. However, due to limitations associated with long genetic manipulation timelines and, lack of choice in genetic tools required for strain engineering, methanotrophs are currently not employed for bioconversion technologies. In this study, a rapid and reproducible electroporation protocol is developed for type 1 methanotroph, Methylotuvimicrobium alcaliphilum using common laboratory solutions, analyzing optimal electroshock voltages and post-shock cell recovery time. Successful reproducibility of the developed method was achieved when different replicative plasmids were assessed on lab adapted vs. wild-type M. alcaliphilum strains (DASS vs. DSM19304). Overall, a ∼ 3-fold decrease in time is reported with use of electroporation protocol developed here, compared to conjugation, which is the traditionally employed approach. Additionally, an inducible (3-methyl benzoate) and a constitutive (sucrose phosphate synthase) promoter is characterized for their strength in driving gene expression.
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Affiliation(s)
- Shubhasish Goswami
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Steven W. Singer
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
- Joint BioEnergy Institute, Emeryville, CA, United States
| | - Blake A. Simmons
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
- Joint BioEnergy Institute, Emeryville, CA, United States
| | - Deepika Awasthi
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
- Joint BioEnergy Institute, Emeryville, CA, United States
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3
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Wutkowska M, Tláskal V, Bordel S, Stein LY, Nweze JA, Daebeler A. Leveraging genome-scale metabolic models to understand aerobic methanotrophs. THE ISME JOURNAL 2024; 18:wrae102. [PMID: 38861460 PMCID: PMC11195481 DOI: 10.1093/ismejo/wrae102] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/04/2024] [Revised: 05/20/2024] [Accepted: 06/10/2024] [Indexed: 06/13/2024]
Abstract
Genome-scale metabolic models (GEMs) are valuable tools serving systems biology and metabolic engineering. However, GEMs are still an underestimated tool in informing microbial ecology. Since their first application for aerobic gammaproteobacterial methane oxidizers less than a decade ago, GEMs have substantially increased our understanding of the metabolism of methanotrophs, a microbial guild of high relevance for the natural and biotechnological mitigation of methane efflux to the atmosphere. Particularly, GEMs helped to elucidate critical metabolic and regulatory pathways of several methanotrophic strains, predicted microbial responses to environmental perturbations, and were used to model metabolic interactions in cocultures. Here, we conducted a systematic review of GEMs exploring aerobic methanotrophy, summarizing recent advances, pointing out weaknesses, and drawing out probable future uses of GEMs to improve our understanding of the ecology of methane oxidizers. We also focus on their potential to unravel causes and consequences when studying interactions of methane-oxidizing bacteria with other methanotrophs or members of microbial communities in general. This review aims to bridge the gap between applied sciences and microbial ecology research on methane oxidizers as model organisms and to provide an outlook for future studies.
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Affiliation(s)
- Magdalena Wutkowska
- Institute of Soil Biology and Biogeochemistry, Biology Centre CAS, 370 05 České Budějovice, Czech Republic
| | - Vojtěch Tláskal
- Institute of Soil Biology and Biogeochemistry, Biology Centre CAS, 370 05 České Budějovice, Czech Republic
| | - Sergio Bordel
- Department of Chemical Engineering and Environmental Technology, School of Industrial Engineering, University of Valladolid, Valladolid 47011, Spain
- Institute of Sustainable Processes, Valladolid 47011, Spain
| | - Lisa Y Stein
- Department of Biological Sciences, Faculty of Science, University of Alberta, Edmonton, AB T6G 2E9, Canada
| | - Justus Amuche Nweze
- Institute of Soil Biology and Biogeochemistry, Biology Centre CAS, 370 05 České Budějovice, Czech Republic
- Department of Ecosystem Biology, Faculty of Science, University of South Bohemia, 370 05 České Budějovice, Czech Republic
- Department of Science Laboratory Technology, Faculty of Physical Sciences, University of Nigeria, Nsukka 410001, Nigeria
| | - Anne Daebeler
- Institute of Soil Biology and Biogeochemistry, Biology Centre CAS, 370 05 České Budějovice, Czech Republic
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4
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Yang X, Zhang Y, Zhao G. Artificial carbon assimilation: From unnatural reactions and pathways to synthetic autotrophic systems. Biotechnol Adv 2024; 70:108294. [PMID: 38013126 DOI: 10.1016/j.biotechadv.2023.108294] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Revised: 10/26/2023] [Accepted: 11/18/2023] [Indexed: 11/29/2023]
Abstract
Synthetic biology is being increasingly used to establish novel carbon assimilation pathways and artificial autotrophic strains that can be used in low-carbon biomanufacturing. Currently, artificial pathway design has made significant progress from advocacy to practice within a relatively short span of just over ten years. However, there is still huge scope for exploration of pathway diversity, operational efficiency, and host suitability. The accelerated research process will bring greater opportunities and challenges. In this paper, we provide a comprehensive summary and interpretation of representative one-carbon assimilation pathway designs and artificial autotrophic strain construction work. In addition, we propose some feasible design solutions based on existing research results and patterns to promote the development and application of artificial autotrophy.
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Affiliation(s)
- Xue Yang
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China; National Center of Technology Innovation for Synthetic Biology, Tianjin 300308, China; Haihe Laboratory of Synthetic Biology, Tianjin 300308, China
| | - Yanfei Zhang
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China; National Center of Technology Innovation for Synthetic Biology, Tianjin 300308, China.
| | - Guoping Zhao
- National Center of Technology Innovation for Synthetic Biology, Tianjin 300308, China; CAS-Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China.
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5
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Lee OK, Kang SG, Choi TR, Yang YH, Lee EY. Production and characterization of a biodegradable polymer, poly(3-hydroxybutyrate-co-3-hydroxyvalerate), using the type II methanotroph, Methylocystis sp. MJC1. BIORESOURCE TECHNOLOGY 2023; 389:129853. [PMID: 37813313 DOI: 10.1016/j.biortech.2023.129853] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/09/2023] [Revised: 10/06/2023] [Accepted: 10/06/2023] [Indexed: 10/11/2023]
Abstract
The production of polyhydroxyalkanoates (PHAs) through the biological conversion of methane is a promising solution to address both methane emissions and plastic waste. Type II methanotrophs naturally accumulate a representative PHA, poly(3-hydroxybutyrate) (PHB), using methane as the sole carbon source. In this study, we aimed to produce poly(3-hydroxybutyrate-co-3-hydroxyvalerate) (PHBV copolymer) with improved properties compared with PHB, using the type II methanotroph, Methylocystis sp. MJC1. We optimized the pH, valerate concentration, and valerate supply time in a one-step cultivation process using a gas bioreactor to enhance PHBV copolymer production yield and the 3-hydroxyvalerate (3HV) molar fraction. Under the optimal conditions, the biomass reached 21.3 g DCW/L, and PHBV copolymer accumulation accounted for 41.9 % of the dried cell weight, with a 3HV molar fraction of 28.4 %. The physicochemical properties of the purified PHBV copolymer were characterized using NMR, FTIR, TGA, DSC, and GPC.
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Affiliation(s)
- Ok Kyung Lee
- Department of Chemical Engineering (BK21 FOUR Integrated Engineering Program), Kyung Hee University, Yongin-si, Gyeonggi-do 17104, Republic of Korea
| | - Seung Gi Kang
- Department of Chemical Engineering (BK21 FOUR Integrated Engineering Program), Kyung Hee University, Yongin-si, Gyeonggi-do 17104, Republic of Korea
| | - Tae-Rim Choi
- Department of Biological Engineering, College of Engineering, Konkuk University, Seoul 05029, Republic of Korea
| | - Yung-Hun Yang
- Department of Biological Engineering, College of Engineering, Konkuk University, Seoul 05029, 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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6
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Sahoo KK, Katari JK, Das D. Recent advances in methanol production from methanotrophs. World J Microbiol Biotechnol 2023; 39:360. [PMID: 37891430 DOI: 10.1007/s11274-023-03813-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2023] [Accepted: 10/19/2023] [Indexed: 10/29/2023]
Abstract
Methanol, the simplest aliphatic molecule of the alcohol family, finds diverse range of applications as an industrial solvent, a precursor for producing other chemicals (e.g., dimethyl ether, acetic acid and formaldehyde), and a potential fuel. There are conventional chemical routes for methanol production such as, steam reforming of natural gas to form syngas, followed by catalytic conversion into methanol; direct catalytic oxidation of methane, or hydrogenation of carbon dioxide. However, these chemical routes are limited by the requirement for expensive catalysts and extreme process conditions, and plausible environmental implications. Alternatively, methanotrophic microorganisms are being explored as biological alternative for methanol production, under milder process conditions, bypassing the requirement for chemical catalysts, and without imposing any adverse environmental impact. Methanotrophs possess inherent metabolic pathways for methanol production via biological methane oxidation or carbon dioxide reduction, thus offering a surplus advantage pertaining to the sequestration of two major greenhouse gases. This review sheds light on the recent advances in methanotrophic methanol production including metabolic pathways, feedstocks, metabolic engineering, and bioprocess engineering approaches. Furthermore, various reactor configurations are discussed in view of the challenges associated with solubility and mass transfer limitations in methanotrophic gas fermentation systems.
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Affiliation(s)
- Krishna Kalyani Sahoo
- Department of Biosciences & Bioengineering, Indian Institute of Technology, Guwahati, 781039, Assam, India
| | - John Kiran Katari
- School of Energy Science & Engineering, Indian Institute of Technology, Guwahati, 781039, Assam, India
| | - Debasish Das
- Department of Biosciences & Bioengineering, Indian Institute of Technology, Guwahati, 781039, Assam, India.
- School of Energy Science & Engineering, Indian Institute of Technology, Guwahati, 781039, Assam, India.
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7
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Weng C, Peng X, Han Y. From methane to value-added bioproducts: microbial metabolism, enzymes, and metabolic engineering. ADVANCES IN APPLIED MICROBIOLOGY 2023; 124:119-146. [PMID: 37597946 DOI: 10.1016/bs.aambs.2023.07.004] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/21/2023]
Abstract
Methane is abundant in nature, and excessive emissions will cause the greenhouse effect. Methane is also an ideal carbon and energy feedstock for biosynthesis. In the review, the microorganisms, metabolism, and enzymes for methane utilization, and the advances of conversion to value-added bioproducts were summarized. First, the physiological characteristics, classification, and methane oxidation process of methanotrophs were introduced. The metabolic pathways for methane utilization and key intermediate metabolites of native and synthetic methanotrophs were summarized. Second, the enzymatic properties, crystal structures, and catalytic mechanisms of methane-oxidizing and metabolizing enzymes in methanotrophs were described. Third, challenges and prospects in metabolic pathways and enzymatic catalysis for methane utilization and conversion to value-added bioproducts were discussed. Finally, metabolic engineering of microorganisms for methane biooxidation and bioproducts synthesis based on different pathways were summarized. Understanding the metabolism and challenges of microbial methane utilization will provide insights into possible strategies for efficient methane-based synthesis.
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Affiliation(s)
- Caihong Weng
- National Key Laboratory of Biochemical Engineering, Institute of Process Engineering, Chinese Academy of Sciences, Beijing, P.R. China; School of Chemical Engineering, University of Chinese Academy of Sciences, Beijing, P.R. China
| | - Xiaowei Peng
- National Key Laboratory of Biochemical Engineering, Institute of Process Engineering, Chinese Academy of Sciences, Beijing, P.R. China; School of Chemical Engineering, University of Chinese Academy of Sciences, Beijing, P.R. China
| | - Yejun Han
- National Key Laboratory of Biochemical Engineering, Institute of Process Engineering, Chinese Academy of Sciences, Beijing, P.R. China; School of Chemical Engineering, University of Chinese Academy of Sciences, Beijing, P.R. China.
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8
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Thi Quynh Le H, Yeol Lee E. Methanotrophs: Metabolic versatility from utilization of methane to multi-carbon sources and perspectives on current and future applications. BIORESOURCE TECHNOLOGY 2023:129296. [PMID: 37302766 DOI: 10.1016/j.biortech.2023.129296] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/03/2023] [Revised: 05/29/2023] [Accepted: 06/07/2023] [Indexed: 06/13/2023]
Abstract
The development of biorefineries for a sustainable bioeconomy has been driven by the concept of utilizing environmentally friendly and cost-effective renewable energy sources. Methanotrophic bacteria with a unique capacity to utilize methane as a carbon and energy source can serve as outstanding biocatalysts to develop C1 bioconversion technology. By establishing the utilization of diverse multi-carbon sources, integrated biorefinery platforms can be created for the concept of the circular bioeconomy. An understanding of physiology and metabolism could help to overcome challenges for biomanufacturing. This review summaries fundamental gaps for methane oxidation and the capability to utilize multi-carbon sources in methanotrophic bacteria. Subsequently, breakthroughs and challenges in harnessing methanotrophs as robust microbial chassis for industrial biotechnology were compiled and overviewed. Finally, capabilities to exploit the inherent advantages of methanotrophs to synthesize various target products in higher titers are proposed.
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Affiliation(s)
- Hoa Thi Quynh Le
- Department of Chemical Engineering (BK21 FOUR Integrated Engineering Program), Kyung Hee University, Yongin 17104, Republic of Korea
| | - Eun Yeol Lee
- Department of Chemical Engineering (BK21 FOUR Integrated Engineering Program), Kyung Hee University, Yongin 17104, Republic of Korea.
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9
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Lv X, Yu W, Zhang C, Ning P, Li J, Liu Y, Du G, Liu L. C1-based biomanufacturing: Advances, challenges and perspectives. BIORESOURCE TECHNOLOGY 2023; 367:128259. [PMID: 36347475 DOI: 10.1016/j.biortech.2022.128259] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/04/2022] [Revised: 10/29/2022] [Accepted: 10/29/2022] [Indexed: 06/16/2023]
Abstract
One-carbon (C1) compounds have emerged as a key research focus due to the growth of metabolic engineering and synthetic biology as affordable and sustainable nonfood sugar feedstocks for energy-efficient and environmentally friendly biomanufacturing. This paper summarizes and discusses current developments in C1 compounds for biomanufacturing. First, two primary groups of microbes that use C1 compounds (native and synthetic) are introduced, and the traits, categorization, and functions of C1 microbes are summarized. Second, engineering strategies for C1 utilization are compiled and reviewed, including reconstruction of C1-utilization pathway, enzyme engineering, cofactor engineering, genome-scale modeling, and adaptive laboratory evolution. Third, a review of C1 compounds' uses in the synthesis of biofuels and high-value compounds is presented. Finally, potential obstacles to C1-based biomanufacturing are highlighted along with future research initiatives.
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Affiliation(s)
- Xueqin Lv
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China; Science Center for Future Foods, Jiangnan University, Wuxi 214122, China; Baima Future Foods Research Institute, Nanjing 211225, China
| | - Wenwen Yu
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China; Science Center for Future Foods, Jiangnan University, Wuxi 214122, China
| | - Chenyang Zhang
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China; Science Center for Future Foods, Jiangnan University, Wuxi 214122, China
| | - Peng Ning
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China; Science Center for Future Foods, Jiangnan University, Wuxi 214122, China
| | - Jianghua Li
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China; Science Center for Future Foods, Jiangnan University, Wuxi 214122, China
| | - Yanfeng Liu
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China; Science Center for Future Foods, Jiangnan University, Wuxi 214122, China
| | - Guocheng Du
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China; Science Center for Future Foods, Jiangnan University, Wuxi 214122, China
| | - Long Liu
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China; Science Center for Future Foods, Jiangnan University, Wuxi 214122, China.
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10
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Naizabekov S, Hyun SW, Na JG, Yoon S, Lee OK, Lee EY. Comparative genomic analysis of Methylocystis sp. MJC1 as a platform strain for polyhydroxybutyrate biosynthesis. PLoS One 2023; 18:e0284846. [PMID: 37163531 PMCID: PMC10171618 DOI: 10.1371/journal.pone.0284846] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2023] [Accepted: 04/06/2023] [Indexed: 05/12/2023] Open
Abstract
Biodegradable polyhydroxybutyrate (PHB) can be produced from methane by some type II methanotroph such as the genus Methylocystis. This study presents the comparative genomic analysis of a newly isolated methanotroph, Methylocystis sp. MJC1 as a biodegradable PHB-producing platform strain. Methylocystis sp. MJC1 accumulates up to 44.5% of PHB based on dry cell weight under nitrogen-limiting conditions. To facilitate its development as a PHB-producing platform strain, the complete genome sequence of Methylocystis sp. MJC1 was assembled, functionally annotated, and compared with genomes of other Methylocystis species. Phylogenetic analysis has shown that Methylocystis parvus to be the closest species to Methylocystis sp. MJC1. Genome functional annotation revealed that Methylocystis sp. MJC1 contains all major type II methanotroph biochemical pathways such as the serine cycle, EMC pathway, and Krebs cycle. Interestingly, Methylocystis sp. MJC1 has both particulate and soluble methane monooxygenases, which are not commonly found among Methylocystis species. In addition, this species also possesses most of the RuMP pathway reactions, a characteristic of type I methanotrophs, and all PHB biosynthetic genes. These comparative analysis would open the possibility of future practical applications such as the development of organism-specific genome-scale models and application of metabolic engineering strategies to Methylocystis sp. MJC1.
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Affiliation(s)
- Sanzhar Naizabekov
- Department of Chemical Engineering (BK21 FOUR Integrated Engineering Program), Kyung Hee University, Yongin-si, Gyeonggi-do, Republic of Korea
| | - Seung Woon Hyun
- Department of Chemical Engineering (BK21 FOUR Integrated Engineering Program), Kyung Hee University, Yongin-si, Gyeonggi-do, Republic of Korea
| | - Jeong-Geol Na
- Department of Chemical and Biomolecular Engineering, Sogang University, Seoul, Republic of Korea
| | - Sukhwan Yoon
- Department of Civil & Environmental Engineering, Korea Advanced Institute of Science & Technology, Daejeon, Republic of Korea
| | - Ok Kyung Lee
- Department of Chemical Engineering (BK21 FOUR Integrated Engineering Program), Kyung Hee University, Yongin-si, Gyeonggi-do, Republic of Korea
| | - Eun Yeol Lee
- Department of Chemical Engineering (BK21 FOUR Integrated Engineering Program), Kyung Hee University, Yongin-si, Gyeonggi-do, Republic of Korea
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11
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Huang X, Song Q, Guo S, Fei Q. Transcription regulation strategies in methylotrophs: progress and challenges. BIORESOUR BIOPROCESS 2022; 9:126. [PMID: 38647763 PMCID: PMC10992012 DOI: 10.1186/s40643-022-00614-3] [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: 08/30/2022] [Accepted: 11/22/2022] [Indexed: 12/14/2022] Open
Abstract
As a promising industrial microorganism, methylotroph is capable of using methane or methanol as the sole carbon source natively, which has been utilized in the biosynthesis of various bioproducts. However, the relatively low efficiency of carbon conversion has become a limiting factor throughout the development of methanotrophic cell factories due to the unclear genetic background. To better highlight their advantages in methane or methanol-based biomanufacturing, some metabolic engineering strategies, including upstream transcription regulation projects, are being popularized in methylotrophs. In this review, several strategies of transcription regulations applied in methylotrophs are summarized and their applications are discussed and prospected.
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Affiliation(s)
- Xiaohan Huang
- School of Chemical Engineering and Technology, Xi'an Jiaotong University, Xi'an, 710049, China
| | - Qiaoqiao Song
- School of Chemical Engineering and Technology, Xi'an Jiaotong University, Xi'an, 710049, China
| | - Shuqi Guo
- 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.
- Shaanxi Key Laboratory of Energy Chemical Process Intensification, Xi'an Jiaotong University, Xi'an, 710049, China.
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12
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Le HTQ, Lee EY. Insights into C1 and C3 assimilation pathways in type I methanotrophic bacterium from co-production of 1,2-propanediol and lactate. BIORESOURCE TECHNOLOGY 2022; 365:128172. [PMID: 36279980 DOI: 10.1016/j.biortech.2022.128172] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/21/2022] [Revised: 10/15/2022] [Accepted: 10/17/2022] [Indexed: 06/16/2023]
Abstract
Methanotrophic bacteria are attractive hosts for mining metabolic pathways of C1 assimilation to produce value-added products. Herein, the type I methanotroph Methylotuvimicrobium alcaliphilum 20Z was employed to explore the carbon flux from methane and methanol via the EMP pathway to produce 1,2-propanediol (1,2-PDO). The production of 1,2-PDO on methane was found to be mainly restricted by the lower carbon flux toward the EMP pathway. The co-utilization of C1 substrates and glycerol (C3) could contribute to enhance 1,2-PDO. Lactate was co-produced in much higher amounts than 1,2-PDO. This unexpected product was probably derived from lactaldehyde by inherent aldehyde dehydrogenases. The 1,2-PDO production without increased accumulation of lactate was observed via establishing the acetol-based pathway by propane utilization with the overexpression of pmoD. This is the first study to provide experimental insights into the operation of metabolic routes for 1,2-PDO and lactate co-production from C1 and C3 compounds in methanotrophs.
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Affiliation(s)
- Hoa Thi Quynh Le
- Department of Chemical Engineering (BK21 FOUR Integrated Engineering Program), Kyung Hee University, Yongin 17104, Republic of Korea
| | - Eun Yeol Lee
- Department of Chemical Engineering (BK21 FOUR Integrated Engineering Program), Kyung Hee University, Yongin 17104, Republic of Korea.
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13
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Khmelenina VN, But SY, Rozova ON, Oshkin IY, Pimenov NV, Dedysh SN. Genome Editing in Methanotrophic Bacteria: Potential Targets and Available Tools. Microbiology (Reading) 2022. [DOI: 10.1134/s0026261722602196] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
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14
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Thi Quynh Le H, Lee EY. Biological production of 2-propanol from propane using a metabolically engineered type I methanotrophic bacterium. BIORESOURCE TECHNOLOGY 2022; 362:127835. [PMID: 36031125 DOI: 10.1016/j.biortech.2022.127835] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/06/2022] [Revised: 08/21/2022] [Accepted: 08/22/2022] [Indexed: 06/15/2023]
Abstract
2-Propanol is a widely used industrial solvents. Herein, we employed a unique feature of type I methanotrophic bacterium Methylotuvimicrobium alcaliphilum 20Z possessing only particulate methane monooxygenase (pMMO) for one-step direct production of pure 2-propanol from propane. By maintaining cell growth on glycerol, and after deletion of both Ca2+-dependent and La3+-dependent methanol dehydrogenases, propane was converted to 2-propanol by pMMO. Although most of the 2-propanol produced was further oxidized to acetone, deletion of active alcohol dehydrogenase, concomitant with synchronous overexpression of secondary alcohol dehydrogenase, significantly inhibited such undesirable oxidation. As a result, a remarkable enhancement (263 mg/L) of 2-propanol was achieved for 120 h by increasing cell growth with a supply of 50% (v/v) propane in headspace. This is the first demonstration to develop an engineered methanotrophic strain for the one-step direct production of pure 2-propanol from propane using one-phase cultivation without the supply of chemical inhibitors or additional reducing-power sources.
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Affiliation(s)
- Hoa Thi Quynh Le
- Department of Chemical Engineering (BK21 FOUR Integrated Engineering Program), Kyung Hee University, Yongin 17104, Republic of Korea
| | - Eun Yeol Lee
- Department of Chemical Engineering (BK21 FOUR Integrated Engineering Program), Kyung Hee University, Yongin 17104, Republic of Korea.
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15
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Comesaña-Gándara B, García-Depraect O, Santos-Beneit F, Bordel S, Lebrero R, Muñoz R. Recent trends and advances in biogas upgrading and methanotrophs-based valorization. CHEMICAL ENGINEERING JOURNAL ADVANCES 2022. [DOI: 10.1016/j.ceja.2022.100325] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
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16
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Enhancement of 2,3-Butanediol Production by Klebsiella pneumoniae: Emphasis on the Mediation of sRNA-SgrS on the Carbohydrate Utilization. FERMENTATION-BASEL 2022. [DOI: 10.3390/fermentation8080359] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
The demand for renewable energy is increasing. Klebsiella pneumoniae is one of the most promising strains to produce 2,3-butanediol (2,3-BD). Compared with chemical methods, the biological production of 2,3-BD has the characteristics of substrate safety, low cost, and low energy consumption. However, excessive glucose concentrations can cause damage to cells. Therefore, this study investigated the effect of sRNA-SgrS as a sugar transport regulator on the fermentative production of 2,3-BD by K. pneumoniae in response to sugar stress. We designed multiple mutants of K. pneumoniae HD79 to redistribute its carbon flux to produce 2,3-BD. It was found that the 2,3-BD yield of sgrS overexpressed strain decreased by 44% compared with the original strain. The results showed that a high concentration of sRNA-SgrS could accelerate the degradation of ptsG mRNA (encoding the glucose transporter EIICBGlc) and downregulate the expression levels of the budA gene (encoding the α-acetyllactate decarboxylase) and the budB gene (encoding the α-acetyllactate synthase) and budC gene (encoding the 2,3-BD dehydrogenase) but had no effect on the ack gene (encoding the acetate kinase) and the ldh gene (encoding the lactate dehydrogenase). It provides a theoretical basis and a technical reference for understanding the complex regulation mechanism of sRNA in microorganisms and the genetics and breeding in industrial fermentation engineering.
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17
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Metabolic Engineering and Regulation of Diol Biosynthesis from Renewable Biomass in Escherichia coli. Biomolecules 2022; 12:biom12050715. [PMID: 35625642 PMCID: PMC9138338 DOI: 10.3390/biom12050715] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2022] [Revised: 05/15/2022] [Accepted: 05/16/2022] [Indexed: 02/01/2023] Open
Abstract
As bulk chemicals, diols have wide applications in many fields, such as clothing, biofuels, food, surfactant and cosmetics. The traditional chemical synthesis of diols consumes numerous non-renewable energy resources and leads to environmental pollution. Green biosynthesis has emerged as an alternative method to produce diols. Escherichia coli as an ideal microbial factory has been engineered to biosynthesize diols from carbon sources. Here, we comprehensively summarized the biosynthetic pathways of diols from renewable biomass in E. coli and discussed the metabolic-engineering strategies that could enhance the production of diols, including the optimization of biosynthetic pathways, improvement of cofactor supplementation, and reprogramming of the metabolic network. We then investigated the dynamic regulation by multiple control modules to balance the growth and production, so as to direct carbon sources for diol production. Finally, we proposed the challenges in the diol-biosynthesis process and suggested some potential methods to improve the diol-producing ability of the host.
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18
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Govindaraju A, Good NM, Zytnick AM, Martinez-Gomez NC. Employing methylotrophs for a green economy: one-carbon to fuel them all and through metabolism redesign them. Curr Opin Microbiol 2022; 67:102145. [PMID: 35525169 DOI: 10.1016/j.mib.2022.102145] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2022] [Revised: 02/24/2022] [Accepted: 02/28/2022] [Indexed: 11/03/2022]
Abstract
Microbial platforms are currently being optimized to revolutionize industrial energy production while mitigating shortages of global resources and food supplies. Here, we address recent advances to develop bacterial methylotrophic platforms as promising platforms enabling the reuse of products and materials (at their highest value) while reducing waste and pollution.
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Affiliation(s)
- Alekhya Govindaraju
- Department of Plant and Microbial Biology, University of California, Berkeley, CA, USA
| | - Nathan M Good
- Department of Plant and Microbial Biology, University of California, Berkeley, CA, USA
| | - Alexa M Zytnick
- Department of Plant and Microbial Biology, University of California, Berkeley, CA, USA
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19
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Hu L, Guo S, Wang B, Fu R, Fan D, Jiang M, Fei Q, Gonzalez R. Bio-valorization of C1 gaseous substrates into bioalcohols: Potentials and challenges in reducing carbon emissions. Biotechnol Adv 2022; 59:107954. [DOI: 10.1016/j.biotechadv.2022.107954] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2021] [Revised: 03/29/2022] [Accepted: 04/04/2022] [Indexed: 11/02/2022]
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20
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Integrative Genome-Scale Metabolic Modeling Reveals Versatile Metabolic Strategies for Methane Utilization in Methylomicrobium album BG8. mSystems 2022; 7:e0007322. [PMID: 35258342 PMCID: PMC9040813 DOI: 10.1128/msystems.00073-22] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022] Open
Abstract
Methylomicrobium album BG8 is an aerobic methanotrophic bacterium with promising features as a microbial cell factory for the conversion of methane to value-added chemicals. However, the lack of a genome-scale metabolic model (GEM) of M. album BG8 has hindered the development of systems biology and metabolic engineering of this methanotroph. To fill this gap, a high-quality GEM was constructed to facilitate a system-level understanding of the biochemistry of M. album BG8. Flux balance analysis, constrained with time-series data derived from experiments with various levels of methane, oxygen, and biomass, was used to investigate the metabolic states that promote the production of biomass and the excretion of carbon dioxide, formate, and acetate. The experimental and modeling results indicated that M. album BG8 requires a ratio of ∼1.5:1 between the oxygen- and methane-specific uptake rates for optimal growth. Integrative modeling revealed that at ratios of >2:1 oxygen-to-methane uptake flux, carbon dioxide and formate were the preferred excreted compounds, while at ratios of <1.5:1 acetate accounted for a larger fraction of the total excreted flux. Our results showed a coupling between biomass production and the excretion of carbon dioxide that was linked to the ratio between the oxygen- and methane-specific uptake rates. In contrast, acetate excretion was experimentally detected during exponential growth only when the initial biomass concentration was increased. A relatively lower growth rate was also observed when acetate was produced in the exponential phase, suggesting a trade-off between biomass and acetate production. IMPORTANCE A genome-scale metabolic model (GEM) is an integrative platform that enables the incorporation of a wide range of experimental data. It is used to reveal system-level metabolism and, thus, clarify the link between the genotype and phenotype. The lack of a GEM for Methylomicrobium album BG8, an aerobic methane-oxidizing bacterium, has hindered its use in environmental and industrial biotechnology applications. The diverse metabolic states indicated by the GEM developed in this study demonstrate the versatility in the methane metabolic processes used by this strain. The integrative GEM presented here will aid the implementation of the design-build-test-learn paradigm in the metabolic engineering of M. album BG8. This advance will facilitate the development of a robust methane bioconversion platform and help to mitigate methane emissions from environmental systems.
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Paul Alphy M, Hakkim Hazeena S, Binoop M, Madhavan A, Arun KB, Vivek N, Sindhu R, Kumar Awasthi M, Binod P. Synthesis of C2-C4 diols from bioresources: Pathways and metabolic intervention strategies. BIORESOURCE TECHNOLOGY 2022; 346:126410. [PMID: 34838635 DOI: 10.1016/j.biortech.2021.126410] [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: 10/10/2021] [Revised: 11/17/2021] [Accepted: 11/19/2021] [Indexed: 06/13/2023]
Abstract
Diols are important platform chemicals with extensive industrial applications in biopolymer synthesis, cosmetics, and fuels. The increased dependence on non-renewable sources to meet the energy requirement of the population raised issues regarding fossil fuel depletion and environmental impacts. The utilization of biological methods for the synthesis of diols by utilizing renewable resources such as glycerol and agro-residual wastes gained attention worldwide because of its advantages. Among these, biotransformation of 1,3-propanediol (1,3-PDO) and 2,3-butanediol (2,3-BDO) were extensively studied and at present, these diols are produced commercially in large scale with high yield. Many important isomers of C2-C4 diols lack natural synthetic pathways and development of chassis strains for the synthesis can be accomplished by adopting synthetic biology approaches. This current review depicts an overall idea about the pathways involved in C2-C4 diol production, metabolic intervention strategies and technologies in recent years.
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Affiliation(s)
- Maria Paul Alphy
- Microbial Processes and Technology Division, CSIR-National Institute for Interdisciplinary Science and Technology (CSIR-NIIST), Trivandrum 695 019, Kerala, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Sulfath Hakkim Hazeena
- Microbial Processes and Technology Division, CSIR-National Institute for Interdisciplinary Science and Technology (CSIR-NIIST), Trivandrum 695 019, Kerala, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Mohan Binoop
- Microbial Processes and Technology Division, CSIR-National Institute for Interdisciplinary Science and Technology (CSIR-NIIST), Trivandrum 695 019, Kerala, India
| | - Aravind Madhavan
- Rajiv Gandhi Center for Biotechnology, Jagathy, Thiruvananthapuram 695 014, Kerala, India
| | - K B Arun
- Rajiv Gandhi Center for Biotechnology, Jagathy, Thiruvananthapuram 695 014, Kerala, India
| | - Narisetty Vivek
- Centre for Climate and Environmental Protection, School of Water, Energy and Environment, Cranfield University, Cranfield MK43 0AL, UK
| | - Raveendran Sindhu
- Microbial Processes and Technology Division, CSIR-National Institute for Interdisciplinary Science and Technology (CSIR-NIIST), Trivandrum 695 019, Kerala, India
| | - Mukesh Kumar Awasthi
- College of Natural Resources and Environment, Northwest A & F University, Yangling, Shaanxi 712 100, China
| | - Parameswaran Binod
- Microbial Processes and Technology Division, CSIR-National Institute for Interdisciplinary Science and Technology (CSIR-NIIST), Trivandrum 695 019, Kerala, India.
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22
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Kulkarni PP, Chavan SB, Deshpande MS, Sagotra D, Kumbhar PS, Ghosalkar AR. Enrichment of Methylocystis dominant mixed culture from rice field for PHB production. J Biotechnol 2022; 343:62-70. [PMID: 34838616 DOI: 10.1016/j.jbiotec.2021.11.007] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2021] [Revised: 11/16/2021] [Accepted: 11/20/2021] [Indexed: 11/16/2022]
Abstract
Presence of methanotrophs in diverse environmental habitats helps to reduce emissions of greenhouse gas like methane. Isolation and culture of undiscovered wealth of methanotrophic organisms can help in exploitation of these organisms in value added products. The present study focuses on the enrichment of methanotroph dominated mixed microbial community by use of three stage strategy of revival, proliferation, and segregation. During the enrichment process amplicon sequencing of 16 s rRNA V3-V4 region showed relative abundance of mixed culture comprising single methanotrophic species of Methylocystis genus (88.92%) along with only three other species. Methylocystis dominant mixed culture (MMI-11) was observed to produce polyhydroxyalkanoates (PHA). During studies to identify favourable culture conditions, nitrate was found to be preferred nitrogen source for growth and PHA production. Cell growth ability to produce PHA was also evaluated at 14 L fermentor by supplying gas using continuous bubbling and through pressurization in the headspace. The mixed methanotrophic culture was found to accumulate maximum of 22.20% polyhydroxybutyrate (PHB) under nitrate limited condition. The molecular weight of PHB was found to be 2.221 × 105 g mol-1 with polydispersity of 1.82.
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Affiliation(s)
- Pranav P Kulkarni
- Department of Technology, Savitribai Phule Pune University, Pune, India; Praj Matrix - R&D Centre, division of Praj Industries Limited, Urawade, Pune, India
| | - Sambhaji B Chavan
- Praj Matrix - R&D Centre, division of Praj Industries Limited, Urawade, Pune, India
| | - Mandar S Deshpande
- Praj Matrix - R&D Centre, division of Praj Industries Limited, Urawade, Pune, India
| | - Dhanishta Sagotra
- Department of Technology, Savitribai Phule Pune University, Pune, India
| | - Pramod S Kumbhar
- Praj Matrix - R&D Centre, division of Praj Industries Limited, Urawade, Pune, India
| | - Anand R Ghosalkar
- Department of Technology, Savitribai Phule Pune University, Pune, India; Praj Matrix - R&D Centre, division of Praj Industries Limited, Urawade, Pune, India.
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23
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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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24
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Systems Metabolic Engineering of Methanotrophic Bacteria for Biological Conversion of Methane to Value-Added Compounds. ADVANCES IN BIOCHEMICAL ENGINEERING/BIOTECHNOLOGY 2022; 180:91-126. [DOI: 10.1007/10_2021_184] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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25
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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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26
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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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Gregory GJ, Bennett RK, Papoutsakis ET. Recent advances toward the bioconversion of methane and methanol in synthetic methylotrophs. Metab Eng 2021; 71:99-116. [PMID: 34547453 DOI: 10.1016/j.ymben.2021.09.005] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2021] [Revised: 09/14/2021] [Accepted: 09/16/2021] [Indexed: 12/19/2022]
Abstract
Abundant natural gas reserves, along with increased biogas production, have prompted recent interest in harnessing methane as an industrial feedstock for the production of liquid fuels and chemicals. Methane can either be used directly for fermentation or first oxidized to methanol via biological or chemical means. Methanol is advantageous due to its liquid state under normal conditions. Methylotrophy, defined as the ability of microorganisms to utilize reduced one-carbon compounds like methane and methanol as sole carbon and energy sources for growth, is widespread in bacterial communities. However, native methylotrophs lack the extensive and well-characterized synthetic biology toolbox of platform microorganisms like Escherichia coli, which results in slow and inefficient design-build-test cycles. If a heterologous production pathway can be engineered, the slow growth and uptake rates of native methylotrophs generally limit their industrial potential. Therefore, much focus has been placed on engineering synthetic methylotrophs, or non-methylotrophic platform microorganisms, like E. coli, that have been engineered with synthetic methanol utilization pathways. These platform hosts allow for rapid design-build-test cycles and are well-suited for industrial application at the current time. In this review, recent progress made toward synthetic methylotrophy (including methanotrophy) is discussed. Specifically, the importance of amino acid metabolism and alternative one-carbon assimilation pathways are detailed. A recent study that has achieved methane bioconversion to liquid chemicals in a synthetic E. coli methanotroph is also briefly discussed. We also discuss strategies for the way forward in order to realize the industrial potential of synthetic methanotrophs and methylotrophs.
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Affiliation(s)
- Gwendolyn J Gregory
- Department of Chemical and Biomolecular Engineering, University of Delaware, Newark, DE, USA; The Delaware Biotechnology Institute, University of Delaware, Newark, DE, USA.
| | - R Kyle Bennett
- Department of Chemical and Biomolecular Engineering, University of Delaware, Newark, DE, USA; The Delaware Biotechnology Institute, University of Delaware, Newark, DE, USA.
| | - Eleftherios T Papoutsakis
- Department of Chemical and Biomolecular Engineering, University of Delaware, Newark, DE, USA; The Delaware Biotechnology Institute, University of Delaware, Newark, DE, USA.
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Selection of methanotrophic platform for methanol production using methane and biogas. J Biosci Bioeng 2021; 132:460-468. [PMID: 34462232 DOI: 10.1016/j.jbiosc.2021.07.007] [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: 06/08/2021] [Revised: 07/11/2021] [Accepted: 07/14/2021] [Indexed: 11/23/2022]
Abstract
To develop biotechnological process for methane to methanol conversion, selection of a suitable methanotrophic platform is an important aspect. Systematic approach based on literature and public databases was developed to select representative methanotrophs Methylotuvimicrobium alcaliphilum, Methylomonas methanica, Methylosinus trichosporium and Methylocella silvestris. Selected methanotrophs were further investigated for methanol tolerance and methanol production on pure methane as well as biogas along with key enzyme activities involved in methane utilization. Among selected methanotrophs M. alcaliphilum showed maximum methanol tolerance of 6% v/v along with maximum methanol production of 307.90 mg/L and 247.37 mg/L on pure methane and biogas respectively. Activity of methane monooxygenase and formate dehydrogenase enzymes in M.alcaliphilum was significantly higher up to 98.40 nmol/min/mg cells and 0.87 U/mg protein, respectively. Biotransformation trials in 14 L fermentor resulted in increased methanol production up to 418 and 331.20 mg/L, with yield coefficient 0.83 and 0.71 mg methanol/mg of pure methane and biogas respectively. The systematic selection resulted in haloalkaliphilic strain M. alcaliphilum as one of the potential methanotroph for bio-methanol production.
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29
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Nguyen TT, Lee EY. Methane-based biosynthesis of 4-hydroxybutyrate and P(3-hydroxybutyrate-co-4-hydroxybutyrate) using engineered Methylosinus trichosporium OB3b. BIORESOURCE TECHNOLOGY 2021; 335:125263. [PMID: 34020156 DOI: 10.1016/j.biortech.2021.125263] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/02/2021] [Revised: 05/05/2021] [Accepted: 05/06/2021] [Indexed: 06/12/2023]
Abstract
4-Hydroxybutyric acid (4-HB) is a key platform chemical that serves as a precursor in a wide variety of industrial applications including 1,4-butanediol and bioplastics production. In this study, we reconstructed 4-HB biosynthetic pathway including CoA-dependent succinate semialdehyde dehydrogenase and NADPH-dependent succinate semialdehyde reductase in Type II methanotrophs, Methylosinus trichosporium OB3b, to synthesize 4-HB. These engineered strains were able to synthesize 4-HB from methane via tricarboxylic acid cycle. 4-HB synthesis was further improved to 10.5 mg/L by overexpressing phosphoenolpyruvate carboxylase, isocitrate dehydrogenase and 2-oxoglutarate dehydrogenase genes in M. trichosporium OB3b. We combined the native poly(3-hydroxybutyrate) metabolic pathway and reconstructed 4-HB biosynthetic pathway to synthesize P(3-hydroxybutyrate-co-4-hydroxybutyrate) copolymer from structurally unrelated substrate methane as a single carbon source. These engineered strains could synthesize P(3HB-co-4HB) copolymer with 3.08 mol% 4-HB from methane. This study provides several engineering strategies to synthesize polyhydroxyalkanoates and their monomers from methane.
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Affiliation(s)
- Thu Thi Nguyen
- Department of Chemical Engineering (Integrated Engineering), Kyung Hee University, Yongin-si, Gyeonggi-do 17104, Republic of Korea
| | - Eun Yeol Lee
- Department of Chemical Engineering (Integrated Engineering), Kyung Hee University, Yongin-si, Gyeonggi-do 17104, Republic of Korea.
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Hu L, Guo S, Yan X, Zhang T, Xiang J, Fei Q. Exploration of an Efficient Electroporation System for Heterologous Gene Expression in the Genome of Methanotroph. Front Microbiol 2021; 12:717033. [PMID: 34421878 PMCID: PMC8373458 DOI: 10.3389/fmicb.2021.717033] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2021] [Accepted: 07/07/2021] [Indexed: 11/20/2022] Open
Abstract
One-carbon (C1) substrates such as methane and methanol have been considered as the next-generation carbon source in industrial biotechnology with the characteristics of low cost, availability, and bioconvertibility. Recently, methanotrophic bacteria naturally capable of converting C1 substrates have drawn attractive attention for their promising applications in C1-based biomanufacturing for the production of chemicals or fuels. Although genetic tools have been explored for metabolically engineered methanotroph construction, there is still a lack of efficient methods for heterologous gene expression in methanotrophs. Here, a rapid and efficient electroporation method with a high transformation efficiency was developed for a robust methanotroph of Methylomicrobium buryatense 5GB1. Based on the homologous recombination and high transformation efficiency, gene deletion and heterologous gene expression can be simultaneously achieved by direct electroporation of PCR-generated linear DNA fragments. In this study, the influence of several key parameters (competent cell preparation, electroporation condition, recovery time, and antibiotic concentration) on the transformation efficiency was investigated for optimum conditions. The maximum electroporation efficiency of 719 ± 22.5 CFU/μg DNA was reached, which presents a 10-fold improvement. By employing this method, an engineered M. buryatense 5GB1 was constructed to biosynthesize isobutyraldehyde by replacing an endogenous fadE gene in the genome with a heterologous kivd gene. This study provides a potential and efficient strategy and method to facilitate the cell factory construction of methanotrophs.
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Affiliation(s)
- Lizhen Hu
- School of Chemical Engineering and Technology, Xi'an Jiaotong University, Xi'an, China
| | - Shuqi Guo
- School of Chemical Engineering and Technology, Xi'an Jiaotong University, Xi'an, China
| | - Xin Yan
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, Nanjing, China
| | - Tianqing Zhang
- School of Chemical Engineering and Technology, Xi'an Jiaotong University, Xi'an, China
| | - Jing Xiang
- School of Chemical Engineering and Technology, Xi'an Jiaotong University, Xi'an, China
| | - Qiang Fei
- School of Chemical Engineering and Technology, Xi'an Jiaotong University, Xi'an, China.,Shaanxi Key Laboratory of Energy Chemical Process Intensification, Xi'an Jiaotong University, Xi'an, China
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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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Maina S, Prabhu AA, Vivek N, Vlysidis A, Koutinas A, Kumar V. Prospects on bio-based 2,3-butanediol and acetoin production: Recent progress and advances. Biotechnol Adv 2021; 54:107783. [PMID: 34098005 DOI: 10.1016/j.biotechadv.2021.107783] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2021] [Revised: 05/27/2021] [Accepted: 06/02/2021] [Indexed: 11/19/2022]
Abstract
The bio-based platform chemicals 2,3-butanediol (BDO) and acetoin have various applications in chemical, cosmetics, food, agriculture, and pharmaceutical industries, whereas the derivatives of BDO could be used as fuel additives, polymer and synthetic rubber production. This review summarizes the novel technological developments in adapting genetic and metabolic engineering strategies for selection and construction of chassis strains for BDO and acetoin production. The valorization of renewable feedstocks and bioprocess development for the upstream and downstream stages of bio-based BDO and acetoin production are discussed. The techno-economic aspects evaluating the viability and industrial potential of bio-based BDO production are presented. The commercialization of bio-based BDO and acetoin production requires the utilization of crude renewable resources, the chassis strains with high fermentation production efficiencies and development of sustainable purification or conversion technologies.
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Affiliation(s)
- Sofia Maina
- Department of Food Science and Human Nutrition, Agricultural University of Athens, Iera Odos, 75, 11855 Athens, Greece
| | - Ashish A Prabhu
- Centre for Climate and Environmental Protection, School of Water, Energy and Environment, Cranfield University, Cranfield MK43 0AL, UK
| | - Narisetty Vivek
- Centre for Climate and Environmental Protection, School of Water, Energy and Environment, Cranfield University, Cranfield MK43 0AL, UK
| | - Anestis Vlysidis
- Department of Food Science and Human Nutrition, Agricultural University of Athens, Iera Odos, 75, 11855 Athens, Greece
| | - Apostolis Koutinas
- Department of Food Science and Human Nutrition, Agricultural University of Athens, Iera Odos, 75, 11855 Athens, Greece.
| | - Vinod Kumar
- Centre for Climate and Environmental Protection, School of Water, Energy and Environment, Cranfield University, Cranfield MK43 0AL, UK.
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Costa RB, Lens PNL, Foresti E. Methanotrophic denitrification in wastewater treatment: microbial aspects and engineering strategies. Crit Rev Biotechnol 2021; 42:145-161. [PMID: 34157918 DOI: 10.1080/07388551.2021.1931014] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
Anaerobic technologies are consolidated for sewage treatment and are the core processes for mining marketable products from waste streams. However, anaerobic effluents are supersaturated with methane, which represents a liability regarding greenhouse gas emissions. Meanwhile, anaerobic technologies are not capable of nitrogen removal, which is required to ensure environmental protection. Methane oxidation and denitrification processes can be combined to address both issues concurrently. Aerobic methane oxidizers can release intermediate organic compounds that can be used by conventional denitrifiers as electron donors. Alternatively, anoxic methanotrophic species combine methane oxidation with either nitrate or nitrite reduction in the same metabolism. Engineered systems need to overcome the long doubling times and low NOx consumption rates of anoxic methanotrophic microorganisms. Another commonly reported bottleneck of methanotrophic denitrification relates to gas-liquid mass transfer limitations. Although anaerobic effluents are supersaturated with methane, experimental setups usually rely on methane supply in a gaseous mode. Hence, possibilities for the application of methane-oxidation coupled to denitrification in full scale might be overlooked. Moreover, syntrophic relationships among methane oxidizers, denitrifiers, nitrifiers, and other microorganisms (such as anammox) are not well understood. Integrating mixed populations with various metabolic abilities could allow for more robust methane-driven wastewater denitrification systems. This review presents an overview of the metabolic capabilities of methane oxidation and denitrification and discusses technological aspects that allow for the application of methanotrophic denitrification at larger scales.
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Affiliation(s)
- R B Costa
- Department of Hydraulics and Sanitation, São Carlos School of Engineering (EESC), University of São Paulo (USP), São Carlos, Brazil.,National University of Ireland, Galway, Ireland
| | - P N L Lens
- National University of Ireland, Galway, Ireland
| | - E Foresti
- Department of Hydraulics and Sanitation, São Carlos School of Engineering (EESC), University of São Paulo (USP), São Carlos, Brazil
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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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Nguyen DTN, Lee OK, Nguyen TT, Lee EY. Type II methanotrophs: A promising microbial cell-factory platform for bioconversion of methane to chemicals. Biotechnol Adv 2021; 47:107700. [PMID: 33548453 DOI: 10.1016/j.biotechadv.2021.107700] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2020] [Revised: 12/04/2020] [Accepted: 01/20/2021] [Indexed: 10/22/2022]
Abstract
Methane, the predominant element in natural gas and biogas, represents a promising alternative to carbon feedstocks in the biotechnological industry due to its low cost and high abundance. The bioconversion of methane to value-added products can enhance the value of gas and mitigate greenhouse gas emissions. Methanotrophs, methane-utilizing bacteria, can make a significant contribution to the production of various valuable biofuels and chemicals from methane. Type II methanotrophs in comparison with Type I methanotrophs have distinct advantages, including high acetyl-CoA flux and the co-incorporation of two important greenhouse gases (methane and CO2), making it a potential microbial cell-factory platform for methane-derived biomanufacturing. Herein, we review the most recent advances in Type II methanotrophs related to multi-omics studies and metabolic engineering. Representative examples and prospects of metabolic engineering strategies for the production of suitable products are also discussed.
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Affiliation(s)
- Diep Thi Ngoc Nguyen
- Department of Chemical Engineering (Integrated Engineering), Kyung Hee University, Gyeonggi-do 17104, Republic of Korea
| | - Ok Kyung Lee
- Department of Chemical Engineering (Integrated Engineering), Kyung Hee University, Gyeonggi-do 17104, Republic of Korea
| | - Thu Thi Nguyen
- Department of Chemical Engineering (Integrated Engineering), Kyung Hee University, Gyeonggi-do 17104, Republic of Korea
| | - Eun Yeol Lee
- Department of Chemical Engineering (Integrated Engineering), Kyung Hee University, Gyeonggi-do 17104, Republic of Korea.
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36
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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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Ogwugwa VH, Oyetibo GO, Amund OO. Taxonomic profiling of bacteria and fungi in freshwater sewer receiving hospital wastewater. ENVIRONMENTAL RESEARCH 2021; 192:110319. [PMID: 33069702 DOI: 10.1016/j.envres.2020.110319] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/15/2020] [Revised: 10/04/2020] [Accepted: 10/06/2020] [Indexed: 06/11/2023]
Abstract
Consistent discharges of hospital wastewaters (HWWs) pose ecological risk to the biome of the receiving environment with cumulative effect on its healthiness. Understanding the taxonomic profile of microorganisms in the impacted systems is required to establish taxa that are bio-indicators of toxicants, and provide possible taxa for mitigating ecotoxicity of the HWWs. Geochemistry, pollution status and ecotoxicity of heavy metals (HMs) in HWW-impacted sewer (LU) were assessed. The microbiome profiling was based on 16S rDNA and ITS of 18S rDNA metagenomes. The degree of HMs contamination exceeded 50 and HMs pollution load index of LU was severe (1,084), which consequently exerted severe risk (1,411,575 toxic response factors) with very high toxic responses of Co, Cu, Pb, and Cd. Eco-toxicological impact of the HMs on LU skewed microbiome towards Proteobacteria (43%), Actinobacteria (18%), and about 5% apiece for Chloroflexi, Acidobacteria, Plantomycetes, and Bacteroidetes. Likewise, the relative abundance of in LU inclined towards Ascomycota (59%), Basidiomycota (17%) and unclassified Eukarya_uc_p (16%). Exclusively found in LU sediments were 44,862 bacterial species and 42,881 fungi taxa, while 72,877 and 53,971 species of bacteria and fungi, respectively, were found missing. Extinction and emergence of bacteria and fungi taxa in LU were in response to HMs ecotoxicity and the need for natural attenuation processes respectively. The profiled taxa in LU may be plausible in bioremediation strategies of the impacted system, and in designing knowledge-based bioreactor system for the treatment of HWWs before discharge into the environment.
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Affiliation(s)
- Vincent Happy Ogwugwa
- Department of Microbiology, Faculty of Science, University of Lagos, Akoka, Yaba, Lagos State, 101017, Nigeria.
| | - Ganiyu Oladunjoye Oyetibo
- Department of Microbiology, Faculty of Science, University of Lagos, Akoka, Yaba, Lagos State, 101017, Nigeria.
| | - Olukayode Oladipupo Amund
- Department of Microbiology, Faculty of Science, University of Lagos, Akoka, Yaba, Lagos State, 101017, Nigeria.
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Seong W, Han GH, Lim HS, Baek JI, Kim SJ, Kim D, Kim SK, Lee H, Kim H, Lee SG, Lee DH. Adaptive laboratory evolution of Escherichia coli lacking cellular byproduct formation for enhanced acetate utilization through compensatory ATP consumption. Metab Eng 2020; 62:249-259. [PMID: 32931907 DOI: 10.1016/j.ymben.2020.09.005] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2020] [Revised: 08/18/2020] [Accepted: 09/08/2020] [Indexed: 10/23/2022]
Abstract
Acetate has attracted great attention as a carbon source to develop economically feasible bioprocesses for sustainable bioproducts. Acetate is a less-preferred carbon source and a well-known growth inhibitor of Escherichia coli. In this study, we carried out adaptive laboratory evolution of an E. coli strain lacking four genes (adhE, pta, ldhA, and frdA) involved in acetyl-CoA consumption, allowing the efficient utilization of acetate as its sole carbon and energy source. Four genomic mutations were found in the evolved strain through whole-genome sequencing, and two major mutations (in cspC and patZ) mainly contributed to efficient utilization of acetate and tolerance to acetate. Transcriptomic reprogramming was examined by analyzing the genome-wide transcriptome with different carbon sources. The evolved strain showed high levels of intracellular ATP by upregulation of genes involved in NADH and ATP biosynthesis, which facilitated the production of enhanced green fluorescent protein, mevalonate, and n-butanol using acetate alone. This new strain, given its high acetate tolerance and high ATP levels, has potential as a starting host for cell factories targeting the production of acetyl-CoA-derived products from acetate or of products requiring high ATP levels.
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Affiliation(s)
- Wonjae Seong
- 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 and Technology (UST), Daejeon, 34113, Republic of Korea
| | - Gui Hwan Han
- Synthetic Biology and Bioengineering Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, 34141, Republic of Korea; Center for Industrialization of Agricultural and Livestock Microorganism (CIALM), Jeongeup, 56212, Republic of Korea
| | - Hyun Seung Lim
- 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, Daejeon, 34134, Republic of Korea
| | - Soo-Jung Kim
- Department of Integrative Food, Bioscience and Technology, Chonnam National University, Gwangju, 61186, Republic of Korea
| | - Donghyuk Kim
- School of Energy and Chemical Engineering, Ulsan National Institute of Science and Technology (UNIST), Ulsan, 44919, Republic of Korea
| | - Seong Keun Kim
- Synthetic Biology and Bioengineering Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, 34141, Republic of Korea
| | - Hyewon Lee
- 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; Department of Biosystems and Bioengineering, KRIBB School of Biotechnology, University of Science and Technology (UST), Daejeon, 34113, 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 and Technology (UST), Daejeon, 34113, 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 and Technology (UST), Daejeon, 34113, Republic of Korea.
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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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40
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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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Bordel S, Pérez R, Rodríguez E, Cantera S, Fernández-González N, Martínez MA, Muñoz R. Halotolerance mechanisms of the methanotroph Methylomicrobium alcaliphilum. Biotechnol Bioeng 2020; 117:3459-3474. [PMID: 32672837 DOI: 10.1002/bit.27506] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2020] [Revised: 06/18/2020] [Accepted: 07/15/2020] [Indexed: 11/12/2022]
Abstract
Methylomicrobium alcaliphilum is an alkaliphilic and halotolerant methanotroph. The physiological responses of M. alcaliphilum to high NaCl concentrations, were studied using RNA sequencing and metabolic modeling. This study revealed that M. alcaliphilum possesses an unusual respiratory chain, in which complex I is replaced by a Na+ extruding NQR complex (highly upregulated under high salinity conditions) and a Na+ driven adenosine triphosphate (ATP) synthase coexists with a conventional H+ driven ATP synthase. A thermodynamic and metabolic model showing the interplay between these different components is presented. Ectoine is the main osmoprotector used by the cells. Ectoine synthesis is activated by the transcription of an ect operon that contains five genes, including the ectoine hydroxylase coding ectD gene. Enzymatic tests revealed that the product of ectD does not have catalytic activity. A new Genome Scale Metabolic Model for M. alcaliphilum revealed a higher flux in the oxidative branch of the pentose phosphate pathway leading to NADPH production and contributing to resistance to oxidative stress.
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Affiliation(s)
- Sergio Bordel
- Department of Chemical Engineering and Environmental Technology, School of Insdustrial Engineering, University of Valladolid, Valladolid, Spain.,Institute of Sustainable Processes, Valladolid, Spain
| | - Rebeca Pérez
- Department of Chemical Engineering and Environmental Technology, School of Insdustrial Engineering, University of Valladolid, Valladolid, Spain.,Institute of Sustainable Processes, Valladolid, Spain
| | - Elisa Rodríguez
- Department of Chemical Engineering and Environmental Technology, School of Insdustrial Engineering, University of Valladolid, Valladolid, Spain.,Institute of Sustainable Processes, Valladolid, Spain
| | - Sara Cantera
- Laboratory of Microbiology, Wageningen University and Research Center, Wageningen, The Netherlands
| | - Nuria Fernández-González
- Department of Chemical Engineering and Environmental Technology, School of Insdustrial Engineering, University of Valladolid, Valladolid, Spain.,Institute of Sustainable Processes, Valladolid, Spain
| | - María A Martínez
- Institute of Sustainable Processes, Valladolid, Spain.,PROIMI Planta Piloto de Procesos Industriales Microbiológicos, CONICET, San Miguel de Tucumán, Argentina.,Facultad de Ciencias Exactas y Tecnología, Universidad Nacional de Tucumán, San Miguel de Tucumán, Argentina
| | - Raúl Muñoz
- Department of Chemical Engineering and Environmental Technology, School of Insdustrial Engineering, University of Valladolid, Valladolid, Spain.,Institute of Sustainable Processes, Valladolid, Spain
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Kulyashov M, Peltek SE, Akberdin IR. A Genome-Scale Metabolic Model of 2,3-Butanediol Production by Thermophilic Bacteria Geobacillus icigianus. Microorganisms 2020; 8:E1002. [PMID: 32635563 PMCID: PMC7409357 DOI: 10.3390/microorganisms8071002] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2020] [Revised: 07/01/2020] [Accepted: 07/02/2020] [Indexed: 11/16/2022] Open
Abstract
The thermophilic strain of the genus Geobacillus, Geobacillus icigianus is a promising bacterial chassis for a wide range of biotechnological applications. In this study, we explored the metabolic potential of Geobacillus icigianus for the production of 2,3-butanediol (2,3-BTD), one of the cost-effective commodity chemicals. Here we present a genome-scale metabolic model iMK1321 for Geobacillus icigianus constructed using an auto-generating pipeline with consequent thorough manual curation. The model contains 1321 genes and includes 1676 reactions and 1589 metabolites, representing the most-complete and publicly available model of the genus Geobacillus. The developed model provides new insights into thermophilic bacterial metabolism and highlights new strategies for biotechnological applications of the strain. Our analysis suggests that Geobacillus icigianus has a potential for 2,3-butanediol production from a variety of utilized carbon sources, including glycerine, a common byproduct of biofuel production. We identified a set of solutions for enhancing 2,3-BTD production, including cultivation under anaerobic or microaerophilic conditions and decreasing the TCA flux to succinate via reducing citrate synthase activity. Both in silico predicted metabolic alternatives have been previously experimentally verified for closely related strains including the genus Bacillus.
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Affiliation(s)
- Mikhail Kulyashov
- Biosoft.ru, 630058 Novosibirsk, Russia;
- Department of Natural Sciences, Novosibirsk State University, 630090 Novosibirsk, Russia
- Department of Bioinformatics, Federal Research Center for Information and Computational Technologies, 630090 Novosibirsk, Russia
| | - Sergey E. Peltek
- Department of Molecular Biotechnology, Institute of Cytology and Genetics SB RAS, 630090 Novosibirsk, Russia;
| | - Ilya R. Akberdin
- Biosoft.ru, 630058 Novosibirsk, Russia;
- Department of Natural Sciences, Novosibirsk State University, 630090 Novosibirsk, Russia
- Department of Molecular Biotechnology, Institute of Cytology and Genetics SB RAS, 630090 Novosibirsk, Russia;
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43
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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: 6] [Impact Index Per Article: 1.5] [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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44
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Liu LY, Xie GJ, Xing DF, Liu BF, Ding J, Ren NQ. Biological conversion of methane to polyhydroxyalkanoates: Current advances, challenges, and perspectives. ENVIRONMENTAL SCIENCE AND ECOTECHNOLOGY 2020; 2:100029. [PMID: 36160923 PMCID: PMC9487992 DOI: 10.1016/j.ese.2020.100029] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/12/2020] [Revised: 04/20/2020] [Accepted: 04/22/2020] [Indexed: 05/13/2023]
Abstract
Methane emissions and plastic pollution are critical global challenges. The biological conversion of methane to poly-β-hydroxybutyrate (PHB) not only mitigates methane emissions but also provides biodegradable polymer substitutes for petroleum-based materials used in plastics production. This work provides an early overview of the methane-based PHB advances and discusses challenges and related strategies. Recent advances of PHB, including PHB biosynthetic pathways, methanotrophs, bioreactors, and the performances of PHB materials are introduced. Major challenges of methane-based PHB production are discussed in detail; these include low efficiency of methanotrophs, low gas-liquid mass transfer efficiency, and poor material properties. To overcome these limitations, various approaches are also explored, such as feast-famine regimes, engineered microorganisms, gas-permeable membrane bioreactors, two-phase partitioning bioreactors, poly-β-hydroxybutyrate-co-hydroxyvalerate synthesis, and molecular weight manipulation.
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45
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Liu Y, He X, Zhu P, Cheng M, Hong Q, Yan X. pheS AG Based Rapid and Efficient Markerless Mutagenesis in Methylotuvimicrobium. Front Microbiol 2020; 11:441. [PMID: 32296398 PMCID: PMC7136838 DOI: 10.3389/fmicb.2020.00441] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2019] [Accepted: 03/02/2020] [Indexed: 01/05/2023] Open
Abstract
Due to their fast growth rate and robustness, some haloalkalitolerant methanotrophs from the genus Methylotuvimicrobium have recently become not only promising biocatalysts for methane conversion but also favorable materials for obtaining fundamental knowledge on methanotrophs. Here, to realize unmarked genome modification in Methylotuvimicrobium bacteria, a counterselectable marker (CSM) was developed based on pheS, which encodes the α-subunit of phenylalanyl-tRNA synthetase. Two-point mutations (T252A and A306G) were introduced into PheS in Methylotuvimicrobium buryatense 5GB1C, generating PheS AG , which can recognize p-chloro-phenylalanine (p-Cl-Phe) as a substrate. Theoretically, the expression of PheS AG in a cell will result in the incorporation of p-Cl-Phe into proteins, leading to cell death. The P tac promoter and the ribosome-binding site region of mmoX were employed to control pheS AG , producing the pheS AG -3 CSM. M. buryatense 5GB1C harboring pheS AG -3 was extremely sensitive to 0.5 mM p-Cl-Phe. Then, a positive and counterselection cassette, PZ (only 1.5 kb in length), was constructed by combining pheS AG -3 and the zeocin resistance gene. A PZ- and PCR-based strategy was used to create the unmarked deletion of glgA1 or the whole smmo operon in M. buryatense 5GB1C and Methylotuvimicrobium alcaliphilum 20Z. The positive rates were over 92%, and the process could be accomplished in as few as eight days.
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Affiliation(s)
- Yongchuang Liu
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, Nanjing, China
| | - Xiangrong He
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, Nanjing, China
| | - Pingping Zhu
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, Nanjing, China
| | - Minggen Cheng
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, Nanjing, China
| | - Qing Hong
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, Nanjing, China
| | - Xin Yan
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, Nanjing, China
- Jiangsu Provincial Key Lab for Organic Solid Waste Utilization, Nanjing Agricultural University, Nanjing, China
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Naizabekov S, Lee EY. Genome-Scale Metabolic Model Reconstruction and in Silico Investigations of Methane Metabolism in Methylosinus trichosporium OB3b. Microorganisms 2020; 8:microorganisms8030437. [PMID: 32244934 PMCID: PMC7144005 DOI: 10.3390/microorganisms8030437] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2020] [Revised: 03/16/2020] [Accepted: 03/19/2020] [Indexed: 01/09/2023] Open
Abstract
Methylosinus trichosporium OB3b is an obligate aerobic methane-utilizing alpha-proteobacterium. Since its isolation, M. trichosporium OB3b has been established as a model organism to study methane metabolism in type II methanotrophs. M. trichosporium OB3b utilizes soluble and particulate methane monooxygenase (sMMO and pMMO respectively) for methane oxidation. While the source of electrons is known for sMMO, there is less consensus regarding electron donor to pMMO. To investigate this and other questions regarding methane metabolism, the genome-scale metabolic model for M. trichosporium OB3b (model ID: iMsOB3b) was reconstructed. The model accurately predicted oxygen: methane molar uptake ratios and specific growth rates on nitrate-supplemented medium with methane as carbon and energy source. The redox-arm mechanism which links methane oxidation with complex I of electron transport chain has been found to be the most optimal mode of electron transfer. The model was also qualitatively validated on ammonium-supplemented medium indicating its potential to accurately predict methane metabolism in different environmental conditions. Finally, in silico investigations regarding flux distribution in central carbon metabolism of M. trichosporium OB3b were performed. Overall, iMsOB3b can be used as an organism-specific knowledgebase and a platform for hypothesis-driven theoretical investigations of methane metabolism.
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Metabolic engineering of type II methanotroph, Methylosinus trichosporium OB3b, for production of 3-hydroxypropionic acid from methane via a malonyl-CoA reductase-dependent pathway. Metab Eng 2020; 59:142-150. [PMID: 32061966 DOI: 10.1016/j.ymben.2020.02.002] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2019] [Revised: 01/07/2020] [Accepted: 02/09/2020] [Indexed: 12/21/2022]
Abstract
We engineered a type II methanotroph, Methylosinus trichosporium OB3b, for 3-hydroxypropionic acid (3HP) production by reconstructing malonyl-CoA pathway through heterologous expression of Chloroflexus aurantiacus malonyl-CoA reductase (MCR), a bifunctional enzyme. Two strategies were designed and implemented to increase the malonyl-CoA pool and thus, increase in 3HP production. First, we engineered the supply of malonyl-CoA precursors by overexpressing endogenous acetyl-CoA carboxylase (ACC), substantially enhancing the production of 3HP. Overexpression of biotin protein ligase (BPL) and malic enzyme (NADP+-ME) led to a ∼22.7% and ∼34.5% increase, respectively, in 3HP titer in ACC-overexpressing cells. Also, the acetyl-CoA carboxylation bypass route was reconstructed to improve 3HP productivity. Co-expression of methylmalonyl-CoA carboxyltransferase (MMC) of Propionibacterium freudenreichii and phosphoenolpyruvate carboxylase (PEPC), which provides the MMC precursor, further improved the 3HP titer. The highest 3HP production of 49 mg/L in the OB3b-MCRMP strain overexpressing MCR, MMC and PEPC resulted in a 2.4-fold improvement of titer compared with that in the only MCR-overexpressing strain. Finally, we could obtain 60.59 mg/L of 3HP in 42 h using the OB3b-MCRMP strain through bioreactor operation, with a 6.36-fold increase of volumetric productivity compared than that in the flask cultures. This work demonstrates metabolic engineering of type II methanotrophs, opening the door for using type II methanotrophs as cell factories for biochemical production along with mitigation of greenhouse gases.
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48
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Cho S, Ha S, Kim HS, Han JH, Kim H, Yeon YJ, Na JG, Lee J. Stimulation of cell growth by addition of tungsten in batch culture of a methanotrophic bacterium, Methylomicrobium alcaliphilum 20Z on methane and methanol. J Biotechnol 2020; 309:81-84. [PMID: 31899249 DOI: 10.1016/j.jbiotec.2019.12.021] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2019] [Revised: 12/12/2019] [Accepted: 12/31/2019] [Indexed: 11/15/2022]
Abstract
It is carried out for researches to convert methane, the second most potent greenhouse gas, to high-value chemicals and fuels by using methanotrophs. In this study, we observed that cell growth of Methylomicrobium alcaliphilum 20Z in the batch cultures on methane or methanol was stimulated by the addition of tungsten (W) without formate accumulation. Not only biomass yield but also the total products yield (biomass and formate) on carbon basis increased up to 11.50-fold and 1.28-fold respectively in W-added medium. Furthermore, a significant decrease in CO2 yield from formate was observed in the W-added cells, which indicates that W might have affected the activity of certain enzymes involved in carbon assimilation as well as formate dehydrogenase (FDH). The results of this study suggest that M. alcaliphilum 20Z is a promising model system for studying the physiology of the aerobic methanotroph and for enabling its industrial use for methane conversion through high cell density cultivation.
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Affiliation(s)
- Sukhyeong Cho
- C1 Gas Refinery R&D Center, Sogang University, Seoul, Republic of Korea
| | - Seonyoung Ha
- Department of Chemical and Biomolecular Engineering, Sogang University, Seoul, Republic of Korea
| | - Hye Su Kim
- C1 Gas Refinery R&D Center, Sogang University, Seoul, Republic of Korea
| | - Jin Hee Han
- C1 Gas Refinery R&D Center, Sogang University, Seoul, Republic of Korea
| | - Hyeonsoo Kim
- Department of Chemical and Biomolecular Engineering, Sogang University, Seoul, Republic of Korea
| | - Young Joo Yeon
- Department of Biochemical Engineering, Gangneung-Wonju National University, Gangneung, Republic of Korea
| | - Jeong Geol Na
- Department of Chemical and Biomolecular Engineering, Sogang University, Seoul, Republic of Korea
| | - Jinwon Lee
- C1 Gas Refinery R&D Center, Sogang University, Seoul, Republic of Korea; Department of Chemical and Biomolecular Engineering, Sogang University, Seoul, Republic of Korea.
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Patel SKS, Kalia VC, Joo JB, Kang YC, Lee JK. Biotransformation of methane into methanol by methanotrophs immobilized on coconut coir. BIORESOURCE TECHNOLOGY 2020; 297:122433. [PMID: 31761623 DOI: 10.1016/j.biortech.2019.122433] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/22/2019] [Revised: 11/09/2019] [Accepted: 11/12/2019] [Indexed: 06/10/2023]
Abstract
This study aimed to establish a unique approach for the production of methanol from methane (CH4) in the presence of paraffin oil mediated by methanotrophs immobilized on coconut coir (CC). Immobilization of different methanotrophs through covalent method increased the immobilization yield and relative efficiency for methanol production to 48.6% and 96.8%, respectively. In the presence of paraffin oil, methanol production was 1.6-fold higher by Methylocystis bryophila than by control. Compared to free cells, whole cells immobilized on CC showed higher stability for methanol production. Under repeated batch conditions, cumulative methanol production by immobilized cells and free cells, after eight cycles of reuse, was 52.9 and 30.9 mmol/L, respectively. This study effectively demonstrated the beneficial influence of lignocellulosic biowaste CC as support for immobilization of methanotrophs and paraffin oil on bioconversion of CH4 to methanol.
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Affiliation(s)
- Sanjay K S Patel
- Department of Chemical Engineering, Konkuk University, Seoul 05029, Republic of Korea
| | - Vipin Chandra Kalia
- Department of Chemical Engineering, Konkuk University, Seoul 05029, Republic of Korea
| | - Ji Bong Joo
- Department of Chemical Engineering, Konkuk University, Seoul 05029, Republic of Korea
| | - Yun Chan Kang
- Department of Materials Science and Engineering, Korea University, Seoul 02841, Republic of Korea
| | - Jung-Kul Lee
- Department of Chemical Engineering, Konkuk University, Seoul 05029, Republic of Korea.
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50
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Disruption of the lactate dehydrogenase and acetate kinase genes in Klebsiella pneumoniae HD79 to enhance 2,3-butanediol production, and related transcriptomics analysis. Biotechnol Lett 2020; 42:537-549. [PMID: 31974647 DOI: 10.1007/s10529-020-02802-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2019] [Accepted: 01/13/2020] [Indexed: 12/18/2022]
Abstract
OBJECTIVES 2,3-Butanediol (2,3-BD) is widely used in several chemical syntheses as well as the manufacture of plastics, solvents, and antifreeze formulations, and can be manufactured by microbial glucose fermentation. Conventional (2,3-BD) fermentation typically has low productivity, yield, and purity, and is expensive for commercial applications. We aimed to delete the lactate dehydrogenase and acetate kinase (ldhA and ack) genes in Klebsiella pneumoniae HD79 by using λRed homologous recombination technology, to eliminate by-products and thereby improve (2,3-BD) production. We also analyzed the resulting gene changes by using transcriptomics. RESULTS The yield of (2,3-BD) from the mutant Klebsiella strain was 46.21 g/L, the conversion rate was 0.47 g/g, and the productivity was 0.64 g/L·h, which represented increases of 54.9%, 20.5%, and 106.5% respectively, compared to (WT) strains. Lactate and acetate decreased by 48.2% and 62.8%, respectively. Transcriptomics analysis showed that 4628 genes were differentially expressed (404 significantly up-regulated and 162 significantly down-regulated). Moreover, the (2,3-BD) operon genes were differentially expressed. CONCLUSION Our data showed that the biosynthesis of (2,3-BD) was regulated by inducers (lactate and acetate), a regulator (BudR), and carbon flux. Elimination of acidic by-products by ldhA and ack knockdown significantly improved (2,3-BD) production. Our results provide a deeper understanding of the mechanisms underlying (2,3-BD) production, and form a molecular basis for the improvement this process by genetic modification in the future.
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