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Xuan J, He L, Wen W, Feng Y. Hydrogenase and Nitrogenase: Key Catalysts in Biohydrogen Production. Molecules 2023; 28:molecules28031392. [PMID: 36771068 PMCID: PMC9919214 DOI: 10.3390/molecules28031392] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2022] [Revised: 01/28/2023] [Accepted: 01/29/2023] [Indexed: 02/05/2023] Open
Abstract
Hydrogen with high energy content is considered to be a promising alternative clean energy source. Biohydrogen production through microbes provides a renewable and immense hydrogen supply by utilizing raw materials such as inexhaustible natural sunlight, water, and even organic waste, which is supposed to solve the two problems of "energy supply and environment protection" at the same time. Hydrogenases and nitrogenases are two classes of key enzymes involved in biohydrogen production and can be applied under different biological conditions. Both the research on enzymatic catalytic mechanisms and the innovations of enzymatic techniques are important and necessary for the application of biohydrogen production. In this review, we introduce the enzymatic structures related to biohydrogen production, summarize recent enzymatic and genetic engineering works to enhance hydrogen production, and describe the chemical efforts of novel synthetic artificial enzymes inspired by the two biocatalysts. Continual studies on the two types of enzymes in the future will further improve the efficiency of biohydrogen production and contribute to the economic feasibility of biohydrogen as an energy source.
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Affiliation(s)
- Jinsong Xuan
- Department of Bioscience and Bioengineering, School of Chemistry and Biological Engineering, University of Science and Technology Beijing, 30 Xueyuan Road, Beijing 100083, China
- Correspondence: (J.X.); (Y.F.)
| | - Lingling He
- Department of Bioscience and Bioengineering, School of Chemistry and Biological Engineering, University of Science and Technology Beijing, 30 Xueyuan Road, Beijing 100083, China
| | - Wen Wen
- Department of Bioscience and Bioengineering, School of Chemistry and Biological Engineering, University of Science and Technology Beijing, 30 Xueyuan Road, Beijing 100083, China
| | - Yingang Feng
- CAS Key Laboratory of Biofuels, Shandong Provincial Key Laboratory of Synthetic Biology, Shandong Engineering Laboratory of Single Cell Oil, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, 189 Songling Road, Qingdao 266101, China
- Shandong Energy Institute, 189 Songling Road, Qingdao 266101, China
- Qingdao New Energy Shandong Laboratory, 189 Songling Road, Qingdao 266101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
- Correspondence: (J.X.); (Y.F.)
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Su Y, Michimori Y, Atomi H. Biochemical and genetic examination of two aminotransferases from the hyperthermophilic archaeon Thermococcus kodakarensis. Front Microbiol 2023; 14:1126218. [PMID: 36891395 PMCID: PMC9986279 DOI: 10.3389/fmicb.2023.1126218] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2022] [Accepted: 01/31/2023] [Indexed: 02/22/2023] Open
Abstract
The hyperthermophilic archaeon Thermococcus kodakarensis utilizes amino acids as a carbon and energy source. Multiple aminotransferases, along with glutamate dehydrogenase, are presumed to be involved in the catabolic conversion of amino acids. T. kodakarensis harbors seven Class I aminotransferase homologs on its genome. Here we examined the biochemical properties and physiological roles of two Class I aminotransferases. The TK0548 protein was produced in Escherichia coli and the TK2268 protein in T. kodakarensis. Purified TK0548 protein preferred Phe, Trp, Tyr, and His, and to a lower extent, Leu, Met and Glu. The TK2268 protein preferred Glu and Asp, with lower activities toward Cys, Leu, Ala, Met and Tyr. Both proteins recognized 2-oxoglutarate as the amino acceptor. The TK0548 protein exhibited the highest k cat/K m value toward Phe, followed by Trp, Tyr, and His. The TK2268 protein exhibited highest k cat/K m values for Glu and Asp. The TK0548 and TK2268 genes were individually disrupted, and both disruption strains displayed a retardation in growth on a minimal amino acid medium, suggesting their involvement in amino acid metabolism. Activities in the cell-free extracts of the disruption strains and the host strain were examined. The results suggested that the TK0548 protein contributes to the conversion of Trp, Tyr and His, and the TK2268 protein to that of Asp and His. Although other aminotransferases seem to contribute to the transamination of Phe, Trp, Tyr, Asp, and Glu, our results suggest that the TK0548 protein is responsible for the majority of aminotransferase activity toward His in T. kodakarensis. The genetic examination carried out in this study provides insight into the contributions of the two aminotransferases toward specific amino acids in vivo, an aspect which had not been thoroughly considered thus far.
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Affiliation(s)
- Yu Su
- Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Kyoto, Japan
| | - Yuta Michimori
- Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Kyoto, Japan
| | - Haruyuki Atomi
- Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Kyoto, Japan.,Integrated Research Center for Carbon Negative Science, Kyoto University, Kyoto, Japan
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Cao Y, Liu H, Liu W, Guo J, Xian M. Debottlenecking the biological hydrogen production pathway of dark fermentation: insight into the impact of strain improvement. Microb Cell Fact 2022; 21:166. [PMID: 35986320 PMCID: PMC9389701 DOI: 10.1186/s12934-022-01893-3] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Accepted: 07/26/2022] [Indexed: 11/26/2022] Open
Abstract
Confronted with the exhaustion of the earth’s fossil fuel reservoirs, bio-based process to produce renewable energy is receiving significant interest. Hydrogen is considered as an attractive energy carrier that can replace fossil fuels in the future mainly due to its high energy content, recyclability and environment-friendly nature. Biological hydrogen production from renewable biomass or waste materials by dark fermentation is a promising alternative to conventional routes since it is energy-saving and reduces environmental pollution. However, the current yield and evolution rate of fermentative hydrogen production are still low. Strain improvement of the microorganisms employed for hydrogen production is required to make the process competitive with traditional production methods. The present review summarizes recent progresses on the screening for highly efficient hydrogen-producing strains using various strategies. As the metabolic pathways for fermentative hydrogen production have been largely resolved, it is now possible to engineer the hydrogen-producing strains by rational design. The hydrogen yields and production rates by different genetically modified microorganisms are discussed. The key limitations and challenges faced in present studies are also proposed. We hope that this review can provide useful information for scientists in the field of fermentative hydrogen production. Hydrogen can be generated by microorganisms. Dark fermentation is efficient for biological hydrogen production. Strain improvement is critical to enhancing hydrogen-producing ability.
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Scott KA, Williams SA, Santangelo TJ. Thermococcus kodakarensis provides a versatile hyperthermophilic archaeal platform for protein expression. Methods Enzymol 2021; 659:243-273. [PMID: 34752288 PMCID: PMC8878339 DOI: 10.1016/bs.mie.2021.06.014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Hyperthermophiles, typically defined as organisms with growth optima ≥80°C, are dominated by the Archaea. Proteins that support life at the extremes of temperatures often retain substantial biotechnological and commercial value, but the recombinant expression of individual hyperthermophilic proteins is commonly complicated in non-native mesophilic hosts due to differences in codon bias, intracellular solutes and the requirement for accessory factors that aid in folding or deposition of metal centers within archaeal proteins. The development of versatile protein expression and facilitated protein purification systems in the model, genetically tractable, hyperthermophilic marine archaeon Thermococcus kodakarensis provides an attractive platform for protein expression within the hyperthermophiles. The assortment of T. kodakarensis genetic backgrounds and compatible selection markers allow iterative genetic manipulations that facilitate protein overexpression and expedite protein purifications. Expression vectors that stably replicate both in T. kodakarensis and Escherichia coli have been validated and permit high-level ectopic gene expression from a variety of controlled and constitutive promoters. Biologically relevant protein associations can be maintained during protein purifications to identify native protein partnerships and define protein interaction networks. T. kodakarensis thus provides a versatile platform for the expression and purification of thermostable proteins.
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Affiliation(s)
- Kristin A Scott
- Cell and Molecular Biology Graduate Program, Colorado State University, Fort Collins, CO, United States
| | - Sere A Williams
- Cell and Molecular Biology Graduate Program, Colorado State University, Fort Collins, CO, United States
| | - Thomas J Santangelo
- Cell and Molecular Biology Graduate Program, Colorado State University, Fort Collins, CO, United States; Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, CO, United States.
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Bhatia SK, Jagtap SS, Bedekar AA, Bhatia RK, Rajendran K, Pugazhendhi A, Rao CV, Atabani AE, Kumar G, Yang YH. Renewable biohydrogen production from lignocellulosic biomass using fermentation and integration of systems with other energy generation technologies. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 765:144429. [PMID: 33385808 DOI: 10.1016/j.scitotenv.2020.144429] [Citation(s) in RCA: 65] [Impact Index Per Article: 21.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/06/2020] [Revised: 12/05/2020] [Accepted: 12/05/2020] [Indexed: 06/12/2023]
Abstract
Biohydrogen is a clean and renewable source of energy. It can be produced by using technologies such as thermochemical, electrolysis, photoelectrochemical and biological, etc. Among these technologies, the biological method (dark fermentation) is considered more sustainable and ecofriendly. Dark fermentation involves anaerobic microbes which degrade carbohydrate rich substrate and produce hydrogen. Lignocellulosic biomass is an abundantly available raw material and can be utilized as an economic and renewable substrate for biohydrogen production. Although there are many hurdles, continuous advancements in lignocellulosic biomass pretreatment technology, microbial fermentation (mixed substrate and co-culture fermentation), the involvement of molecular biology techniques, and understanding of various factors (pH, T, addition of nanomaterials) effect on biohydrogen productivity and yield render this technology efficient and capable to meet future energy demands. Further integration of biohydrogen production technology with other products such as bio-alcohol, volatile fatty acids (VFAs), and methane have the potential to improve the efficiency and economics of the overall process. In this article, various methods used for lignocellulosic biomass pretreatment, technologies in trends to produce and improve biohydrogen production, a coproduction of other energy resources, and techno-economic analysis of biohydrogen production from lignocellulosic biomass are reviewed.
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Affiliation(s)
- Shashi Kant Bhatia
- Department of Biological Engineering, College of Engineering, Konkuk University, Seoul 05029, Republic of Korea; Institute for Ubiquitous Information Technology and Application, Konkuk University, Seoul 05029, Republic of Korea.
| | - Sujit Sadashiv Jagtap
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, 600 S. Mathews Ave., Urbana, IL 61801, USA; DOE Center for Advanced Bioenergy and Bioproducts Innovation, University of Illinois at Urbana-Champaign, 600 S. Mathews Ave., Urbana, IL 61801, USA
| | - Ashwini Ashok Bedekar
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, 600 S. Mathews Ave., Urbana, IL 61801, USA
| | - Ravi Kant Bhatia
- Department of Biotechnology, Himachal Pradesh University, Summer Hill 171005, H.P, India
| | - Karthik Rajendran
- Department of Environmental Science, SRM University-AP, Andhra Pradesh 522502, India
| | - Arivalagan Pugazhendhi
- Innovative Green Product Synthesis and Renewable Environment Development Research Group, Faculty of Environment and Labour Safety, Ton Duc Thang University, Ho Chi Minh City, Viet Nam.
| | - Christopher V Rao
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, 600 S. Mathews Ave., Urbana, IL 61801, USA; DOE Center for Advanced Bioenergy and Bioproducts Innovation, University of Illinois at Urbana-Champaign, 600 S. Mathews Ave., Urbana, IL 61801, USA
| | - A E Atabani
- Alternative Fuels Research Laboratory (AFRL), Energy Division, Department of Mechanical Engineering, Faculty of Engineering, Erciyes University, 38039 Kayseri, Turkey
| | - Gopalakrishnan Kumar
- Institute of Chemistry, Bioscience and Environmental Engineering, Faculty of Science and Technology, University of Stavanger, Box 8600 Forus, 4036 Stavanger, Norway
| | - Yung-Hun Yang
- Department of Biological Engineering, College of Engineering, Konkuk University, Seoul 05029, Republic of Korea; Institute for Ubiquitous Information Technology and Application, Konkuk University, Seoul 05029, Republic of Korea.
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Abstract
Volatolomics allows us to elucidate cell metabolic processes in real time. In particular, a volatile organic compound (VOC) excreted from our bodies may be specific for a certain disease, such that measuring this VOC may afford a simple, fast, accessible and safe diagnostic approach. Yet, finding the optimal endogenous volatile marker specific to a pathology is non-trivial because of interlaboratory disparities in sample preparation and analysis, as well as high interindividual variability. These limit the sensitivity and specificity of volatolomics and its applications in biological and clinical fields but have motivated the development of induced volatolomics. This approach aims to overcome issues by measuring VOCs that result not from an endogenous metabolite but, rather, from the pathogen-specific or metabolic-specific enzymatic metabolism of an exogenous biological or chemical probe. In this Review, we introduce volatile-compound-based probes and discuss how they can be exploited to detect and discriminate pathogenic infections, to assess organ function and to diagnose and monitor cancers in real time. We focus on cases in which labelled probes have informed us about metabolic processes and consider the potential and drawbacks of the probes for clinical trials. Beyond diagnostics, VOC-based probes may also be effective tools to explore biological processes more generally.
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Pfeifer K, Ergal İ, Koller M, Basen M, Schuster B, Rittmann SKMR. Archaea Biotechnology. Biotechnol Adv 2020; 47:107668. [PMID: 33271237 DOI: 10.1016/j.biotechadv.2020.107668] [Citation(s) in RCA: 45] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2020] [Revised: 11/19/2020] [Accepted: 11/20/2020] [Indexed: 12/13/2022]
Abstract
Archaea are a domain of prokaryotic organisms with intriguing physiological characteristics and ecological importance. In Microbial Biotechnology, archaea are historically overshadowed by bacteria and eukaryotes in terms of public awareness, industrial application, and scientific studies, although their biochemical and physiological properties show a vast potential for a wide range of biotechnological applications. Today, the majority of microbial cell factories utilized for the production of value-added and high value compounds on an industrial scale are bacterial, fungal or algae based. Nevertheless, archaea are becoming ever more relevant for biotechnology as their cultivation and genetic systems improve. Some of the main advantages of archaeal cell factories are the ability to cultivate many of these often extremophilic organisms under non-sterile conditions, and to utilize inexpensive feedstocks often toxic to other microorganisms, thus drastically reducing cultivation costs. Currently, the only commercially available products of archaeal cell factories are bacterioruberin, squalene, bacteriorhodopsin and diether-/tetraether-lipids, all of which are produced utilizing halophiles. Other archaeal products, such as carotenoids and biohydrogen, as well as polyhydroxyalkanoates and methane are in early to advanced development stages, respectively. The aim of this review is to provide an overview of the current state of Archaea Biotechnology by describing the actual state of research and development as well as the industrial utilization of archaeal cell factories, their role and their potential in the future of sustainable bioprocessing, and to illustrate their physiological and biotechnological potential.
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Affiliation(s)
- Kevin Pfeifer
- Archaea Physiology & Biotechnology Group, Department of Functional and Evolutionary Ecology, Universität Wien, Wien, Austria; Institute of Synthetic Bioarchitectures, Department of Nanobiotechnology, University of Natural Resources and Life Sciences, Wien, Austria
| | - İpek Ergal
- Archaea Physiology & Biotechnology Group, Department of Functional and Evolutionary Ecology, Universität Wien, Wien, Austria
| | - Martin Koller
- Office of Research Management and Service, c/o Institute of Chemistry, University of Graz, Austria
| | - Mirko Basen
- Microbial Physiology Group, Division of Microbiology, Institute of Biological Sciences, University of Rostock, Rostock, Germany
| | - Bernhard Schuster
- Institute of Synthetic Bioarchitectures, Department of Nanobiotechnology, University of Natural Resources and Life Sciences, Wien, Austria
| | - Simon K-M R Rittmann
- Archaea Physiology & Biotechnology Group, Department of Functional and Evolutionary Ecology, Universität Wien, Wien, Austria.
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8
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Song Y, Zhu Z, Zhou W, Zhang YHPJ. High-efficiency transformation of archaea by direct PCR products with its application to directed evolution of a thermostable enzyme. Microb Biotechnol 2020; 14:453-464. [PMID: 32602260 PMCID: PMC7936305 DOI: 10.1111/1751-7915.13613] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2020] [Revised: 05/16/2020] [Accepted: 05/31/2020] [Indexed: 01/09/2023] Open
Abstract
Hyperthermophilic archaea with unique biochemical and physiological characteristics are important organisms for fundamental research of life science and have great potential for biotechnological applications. However, low transformation efficiency of foreign DNA molecules impedes developments in genetic modification tools and industrial applications. In this study, we applied prolonged overlap extension PCR (POE-PCR) to generate multimeric DNA molecules and then transformed them into two hyperthermophilic archaea, Thermococcus kodakarensis KOD1 and Pyrococcus yayanosii A1. This study was the first example to demonstrate the enhanced transformation efficiencies of POE-PCR products by a factor of approximately 100 for T. kodakarensis KOD1 and 8 for P. yayanosii A1, respectively, relative to circular shuttle plasmids. Furthermore, directed evolution of a modestly thermophilic enzyme, Methanothermococcus okinawensis 3-hydroxy-3-methylglutaryl coenzyme A reductase (HMGR), was conducted to obtain more stable ones due to high transformation efficiency of T. kodakarensis (i.e. ~3 × 104 CFU per μg DNA). T. kodakarensis harbouring the most thermostable MoHMGR mutant can grow in the presence of a thermostable antibiotic simvastatin at 85°C and even higher temperatures. This high transformation efficiency technique could not only help develop more hyperthermophilic enzyme mutants via directed evolution but also simplify genetical modification of archaea, which could be novel hosts for industrial biotechnology.
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Affiliation(s)
- Yunhong Song
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, 32 West 7th Avenue, Tianjin Airport Economic Area, Tianjin, 300308, China
| | - Zhiguang Zhu
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, 32 West 7th Avenue, Tianjin Airport Economic Area, Tianjin, 300308, China
| | - Wei Zhou
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, 32 West 7th Avenue, Tianjin Airport Economic Area, Tianjin, 300308, China
| | - Yi-Heng P Job Zhang
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, 32 West 7th Avenue, Tianjin Airport Economic Area, Tianjin, 300308, China
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9
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Simons JR, Beppu H, Imanaka T, Kanai T, Atomi H. Effects of high-level expression of A 1-ATPase on H 2 production in Thermococcus kodakarensis. J Biosci Bioeng 2020; 130:149-158. [PMID: 32414665 DOI: 10.1016/j.jbiosc.2020.04.001] [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: 01/11/2020] [Revised: 03/18/2020] [Accepted: 04/01/2020] [Indexed: 10/24/2022]
Abstract
The hyperthermophilic archaeon Thermococcus kodakarensis can grow on pyruvate or maltooligosaccharides through H2 fermentation. H2 production levels of members of the Thermococcales are high, and studies to improve their production potential have been reported. Although H2 production is primary metabolism, here we aimed to partially uncouple cell growth and H2 production of T. kodakarensis. Additional A1-type ATPase genes were introduced into T. kodakarensis KU216 under the control of two promoters; the strong constitutive cell surface glycoprotein promoter, Pcsg, and the sugar-inducible fructose-1,6-bisphosphate aldolase promoter, Pfba. Whereas cells with the A1-type ATPase genes under the control of Pcsg displayed only trace levels of growth, cells with Pfba (strain KUA-PF) displayed growth sufficient for further analysis. Increased levels of A1-type ATPase protein were detected in KUA-PF cells grown on pyruvate or maltodextrin, when compared to the levels in the host strain KU216. The growth and H2 production levels of strain KUA-PF with pyruvate or maltodextrin as a carbon and electron source were analyzed and compared to those of the host strain KU216. Compared to a small decrease in total H2 production, significantly larger decreases in cell growth were observed, resulting in an increase in cell-specific H2 production. Quantification of the substrate also revealed that ATPase overexpression led to increased cell-specific pyruvate and maltodextrin consumptions. The results clearly indicate that ATPase production results in partial uncoupling of cell growth and H2 production in T. kodakarensis.
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Affiliation(s)
- Jan-Robert Simons
- Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Katsura, Nishikyo-ku, Kyoto 615-8510, Japan
| | - Haruki Beppu
- Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Katsura, Nishikyo-ku, Kyoto 615-8510, Japan
| | - Tadayuki Imanaka
- Research Organization of Science and Technology, Ritsumeikan University, 1-1-1 Noji-Higashi, Kusatsu 525-8577, Japan
| | - Tamotsu Kanai
- Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Katsura, Nishikyo-ku, Kyoto 615-8510, Japan
| | - Haruyuki Atomi
- Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Katsura, Nishikyo-ku, Kyoto 615-8510, Japan.
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10
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Wang S, Zhang T, Bao M, Su H, Xu P. Microbial Production of Hydrogen by Mixed Culture Technologies: A Review. Biotechnol J 2019; 15:e1900297. [PMID: 31556225 DOI: 10.1002/biot.201900297] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2019] [Revised: 09/05/2019] [Indexed: 12/18/2022]
Abstract
With its high energy content and clean combustion, hydrogen is recognized as a renewable clean energy source with enormous potential. Biological hydrogen production is a promising alternative with significant advantages over conventional petroleum-derived chemical processes. Sustainable hydrogen production from renewable resources such as cassava, wastewater, and other agricultural waste is economically feasible for industrial applications. So far, the major bottlenecks in large-scale biological hydrogen production are the low production rate and yield. This review discusses the various factors that affect the metabolic pathways of dark hydrogen production, and highlights the state-of-the-art development of mixed culture technology. The aim of this review is to provide suggestions for the future directions of mixed culture technology, as well as by-product valorization in dark fermentation.
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Affiliation(s)
- Shaojie Wang
- Beijing Advanced Innovation Center for Soft Matter Science and Engineering, Beijing Key Laboratory of Bioprocess, Beijing University of Chemical Technology, Beijing, 100029, P. R. China
| | - Ting Zhang
- Beijing Advanced Innovation Center for Soft Matter Science and Engineering, Beijing Key Laboratory of Bioprocess, Beijing University of Chemical Technology, Beijing, 100029, P. R. China
| | - Meidan Bao
- Beijing Advanced Innovation Center for Soft Matter Science and Engineering, Beijing Key Laboratory of Bioprocess, Beijing University of Chemical Technology, Beijing, 100029, P. R. China
| | - Haijia Su
- Beijing Advanced Innovation Center for Soft Matter Science and Engineering, Beijing Key Laboratory of Bioprocess, Beijing University of Chemical Technology, Beijing, 100029, P. R. China
| | - Ping Xu
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, P. R. China
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11
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A simple biosynthetic pathway for 2,3-butanediol production in Thermococcus onnurineus NA1. Appl Microbiol Biotechnol 2019; 103:3477-3485. [DOI: 10.1007/s00253-019-09724-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2018] [Revised: 02/05/2019] [Accepted: 02/24/2019] [Indexed: 11/25/2022]
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12
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Straub CT, Counts JA, Nguyen DMN, Wu CH, Zeldes BM, Crosby JR, Conway JM, Otten JK, Lipscomb GL, Schut GJ, Adams MWW, Kelly RM. Biotechnology of extremely thermophilic archaea. FEMS Microbiol Rev 2018; 42:543-578. [PMID: 29945179 DOI: 10.1093/femsre/fuy012] [Citation(s) in RCA: 53] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2018] [Accepted: 06/23/2018] [Indexed: 12/26/2022] Open
Abstract
Although the extremely thermophilic archaea (Topt ≥ 70°C) may be the most primitive extant forms of life, they have been studied to a limited extent relative to mesophilic microorganisms. Many of these organisms have unique biochemical and physiological characteristics with important biotechnological implications. These include methanogens that generate methane, fermentative anaerobes that produce hydrogen gas with high efficiency, and acidophiles that can mobilize base, precious and strategic metals from mineral ores. Extremely thermophilic archaea have also been a valuable source of thermoactive, thermostable biocatalysts, but their use as cellular systems has been limited because of the general lack of facile genetics tools. This situation has changed recently, however, thereby providing an important avenue for understanding their metabolic and physiological details and also opening up opportunities for metabolic engineering efforts. Along these lines, extremely thermophilic archaea have recently been engineered to produce a variety of alcohols and industrial chemicals, in some cases incorporating CO2 into the final product. There are barriers and challenges to these organisms reaching their full potential as industrial microorganisms but, if these can be overcome, a new dimension for biotechnology will be forthcoming that strategically exploits biology at high temperatures.
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Affiliation(s)
- Christopher T Straub
- Department of Chemical and Biomolecular Engineering North Carolina State University, Raleigh, NC 27695-7905, USA
| | - James A Counts
- Department of Chemical and Biomolecular Engineering North Carolina State University, Raleigh, NC 27695-7905, USA
| | - Diep M N Nguyen
- Department of Biochemistry and Molecular Biology University of Georgia, Athens, GA 30602, USA
| | - Chang-Hao Wu
- Department of Biochemistry and Molecular Biology University of Georgia, Athens, GA 30602, USA
| | - Benjamin M Zeldes
- Department of Chemical and Biomolecular Engineering North Carolina State University, Raleigh, NC 27695-7905, USA
| | - James R Crosby
- Department of Chemical and Biomolecular Engineering North Carolina State University, Raleigh, NC 27695-7905, USA
| | - Jonathan M Conway
- Department of Chemical and Biomolecular Engineering North Carolina State University, Raleigh, NC 27695-7905, USA
| | - Jonathan K Otten
- Department of Chemical and Biomolecular Engineering North Carolina State University, Raleigh, NC 27695-7905, USA
| | - Gina L Lipscomb
- Department of Biochemistry and Molecular Biology University of Georgia, Athens, GA 30602, USA
| | - Gerrit J Schut
- Department of Biochemistry and Molecular Biology University of Georgia, Athens, GA 30602, USA
| | - Michael W W Adams
- Department of Biochemistry and Molecular Biology University of Georgia, Athens, GA 30602, USA
| | - Robert M Kelly
- Department of Chemical and Biomolecular Engineering North Carolina State University, Raleigh, NC 27695-7905, USA
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13
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Song Y, Liu M, Xie L, You C, Sun J, Zhang YHPJ. A Recombinant 12-His Tagged Pyrococcus furiosus Soluble [NiFe]-Hydrogenase I Overexpressed in Thermococcus kodakarensis KOD1 Facilitates Hydrogen-Powered in vitro NADH Regeneration. Biotechnol J 2018; 14:e1800301. [PMID: 30307115 DOI: 10.1002/biot.201800301] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2018] [Revised: 09/27/2018] [Indexed: 01/11/2023]
Abstract
Soluble hydrogenase I (SHI) from the hyperthermophilic archaeon Pyrococcus furiosus is a heterotetrameric [NiFe] hydrogenase that catalyzes the reversible reduction of protons by NADPH into hydrogen gas (H2 ). Here, the authors expressed the four αβγδ subunits of SHI encoded by one gene cluster in another hyperthermophilic archaeon, Thermococcus kodakarensis KOD1, which uses its hydrogenase maturation apparatus without the coexpression of native P. furiosus hydrogenase endopeptidases (maturation proteases). The SHI overexpression of T. kodakarensis resulted in more than 1200-fold enhancement in the hydrogenase activity of the cell lysate compared to that of the host strain with an empty vector. An active, purified 12-His tagged recombinant SHI (rSHI) is obtained by one-step affinity adsorption on nickel-charged resin. Size-exclusion chromatography show that purified rSHI is heterotetrameric and has a molecular mass of 150 kDa. The purified rSHI has a half-life of 70 h at 80 °C. This rSHI is used to design a novel in vitro synthetic enzymatic biosystem to convert pyruvate and H2 gas into lactate in a theoretical yield, whereas rSHI is used for NADPH regeneration; an FMN-containing diaphorase (DI) is used to match NADP-preferred SHI and NAD-preferred lactate dehydrogenase (LDH). This study provides a cost-efficient method to obtain hyperthermostable hydrogenases, which can be used in in vitro synthetic enzymatic biosystems for cofactor regeneration and hydrogen production.
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Affiliation(s)
- Yunhong Song
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, 32 West 7th Avenue, Tianjin Airport Economic Area, Tianjin, 300308, China
| | - Meixia Liu
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, 32 West 7th Avenue, Tianjin Airport Economic Area, Tianjin, 300308, China
| | - Leipeng Xie
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, 32 West 7th Avenue, Tianjin Airport Economic Area, Tianjin, 300308, China.,College of Life Sciences, Henan Agricultural University, 95 Wenhua Road, Zhengzhou, 450002, China
| | - Chun You
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, 32 West 7th Avenue, Tianjin Airport Economic Area, Tianjin, 300308, China
| | - Junsong Sun
- Biorefinery Laboratory, Shanghai Advanced Research Institute, Chinese Academy of Sciences, Haike Road 99, Shanghai, 201210, China.,School of Life Science and Technology, Shanghai Tech University, Shanghai, 201210, China
| | - Yi-Heng P Job Zhang
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, 32 West 7th Avenue, Tianjin Airport Economic Area, Tianjin, 300308, China
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Freed E, Fenster J, Smolinski SL, Walker J, Henard CA, Gill R, Eckert CA. Building a genome engineering toolbox in nonmodel prokaryotic microbes. Biotechnol Bioeng 2018; 115:2120-2138. [PMID: 29750332 DOI: 10.1002/bit.26727] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2017] [Revised: 04/02/2018] [Accepted: 03/10/2018] [Indexed: 12/26/2022]
Abstract
The realization of a sustainable bioeconomy requires our ability to understand and engineer complex design principles for the development of platform organisms capable of efficient conversion of cheap and sustainable feedstocks (e.g., sunlight, CO2 , and nonfood biomass) into biofuels and bioproducts at sufficient titers and costs. For model microbes, such as Escherichia coli, advances in DNA reading and writing technologies are driving the adoption of new paradigms for engineering biological systems. Unfortunately, microbes with properties of interest for the utilization of cheap and renewable feedstocks, such as photosynthesis, autotrophic growth, and cellulose degradation, have very few, if any, genetic tools for metabolic engineering. Therefore, it is important to develop "design rules" for building a genetic toolbox for novel microbes. Here, we present an overview of our current understanding of these rules for the genetic manipulation of prokaryotic microbes and the available genetic tools to expand our ability to genetically engineer nonmodel systems.
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Affiliation(s)
- Emily Freed
- National Renewable Energy Laboratory, Biosciences Center, Golden, CO.,Renewable and Sustainable Energy Institute, University of Colorado, Boulder, CO
| | - Jacob Fenster
- Renewable and Sustainable Energy Institute, University of Colorado, Boulder, CO.,Chemical and Biological Engineering, University of Colorado, Boulder, CO
| | | | - Julie Walker
- Renewable and Sustainable Energy Institute, University of Colorado, Boulder, CO
| | - Calvin A Henard
- National Renewable Energy Laboratory, National Bioenergy Center, Golden, CO
| | - Ryan Gill
- National Renewable Energy Laboratory, Biosciences Center, Golden, CO.,Renewable and Sustainable Energy Institute, University of Colorado, Boulder, CO.,Chemical and Biological Engineering, University of Colorado, Boulder, CO
| | - Carrie A Eckert
- National Renewable Energy Laboratory, Biosciences Center, Golden, CO.,Renewable and Sustainable Energy Institute, University of Colorado, Boulder, CO
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15
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Engineering of the Hyperthermophilic Archaeon Thermococcus kodakarensis for Chitin-Dependent Hydrogen Production. Appl Environ Microbiol 2017; 83:AEM.00280-17. [PMID: 28550062 DOI: 10.1128/aem.00280-17] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2017] [Accepted: 05/16/2017] [Indexed: 11/20/2022] Open
Abstract
Thermococcus kodakarensis is a hyperthermophilic archaeon that harbors a complete set of genes for chitin degradation to fructose 6-phosphate. However, wild-type T. kodakarensis KOD1 does not display growth on chitin. In this study, we developed a T. kodakarensis strain that can grow on chitin via genetic and adaptive engineering. First, a chitinase overproduction strain (KC01) was constructed by replacing the chitinase gene promoter with a strong promoter from the cell surface glycoprotein gene, resulting in increased degradation of swollen chitin and accumulation of N-,N'-diacetylchitobiose in the medium. To enhance N-,N'-diacetylchitobiose assimilation in KC01, genes encoding diacetylchitobiose deacetylase, exo-β-d-glucosaminidase, and glucosamine-6-phosphate deaminase were also overexpressed to obtain strain KC04. To strengthen the glycolytic flux of KC04, the gene encoding Tgr (transcriptional repressor of glycolytic genes) was disrupted to obtain strain KC04Δt. In both KC04 and KC04Δt strains, degradation of swollen chitin was further enhanced. In the culture broth of these strains, the accumulation of glucosamine was observed. KC04Δt was repeatedly inoculated in a swollen-chitin-containing medium for 13 cultures. This adaptive engineering strategy resulted in the isolation of a strain (KC04ΔtM1) that showed almost complete degradation of 0.4% (wt/vol) swollen chitin after 90 h. The strain produced high levels of acetate and ammonium in the culture medium, and, moreover, molecular hydrogen was generated. This strongly suggests that strain KC04ΔtM1 has acquired the ability to convert chitin to fructose 6-phosphate via deacetylation and deamination and further convert fructose 6-phosphate to acetate via glycolysis coupled to hydrogen generation.IMPORTANCE Chitin is a linear homopolymer of β-1,4-linked N-acetylglucosamine and is the second most abundant biomass next to cellulose. Compared to the wealth of research focused on the microbial degradation and conversion of cellulose, studies addressing microbial chitin utilization are still limited. In this study, using the hyperthermophilic archaeon Thermococcus kodakarensis as a host, we have constructed a strain that displays chitin-dependent hydrogen generation. The apparent hydrogen yield per unit of sugar consumed was slightly higher with swollen chitin than with starch. As gene manipulation in T. kodakarensis is relatively simple, the strain constructed in this study can also be used as a parent strain for the development and expansion of chitin-dependent biorefinery, in addition to its capacity to produce hydrogen.
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Loder AJ, Zeldes BM, Conway JM, Counts JA, Straub CT, Khatibi PA, Lee LL, Vitko NP, Keller MW, Rhaesa AM, Rubinstein GM, Scott IM, Lipscomb GL, Adams MW, Kelly RM. Extreme Thermophiles as Metabolic Engineering Platforms: Strategies and Current Perspective. Ind Biotechnol (New Rochelle N Y) 2016. [DOI: 10.1002/9783527807796.ch14] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Affiliation(s)
- Andrew J. Loder
- North Carolina State University; Department of Chemical and Biomolecular Engineering; EB-1, 911 Partners Way Raleigh NC 27695-7905 USA
| | - Benjamin M. Zeldes
- North Carolina State University; Department of Chemical and Biomolecular Engineering; EB-1, 911 Partners Way Raleigh NC 27695-7905 USA
| | - Jonathan M. Conway
- North Carolina State University; Department of Chemical and Biomolecular Engineering; EB-1, 911 Partners Way Raleigh NC 27695-7905 USA
| | - James A. Counts
- North Carolina State University; Department of Chemical and Biomolecular Engineering; EB-1, 911 Partners Way Raleigh NC 27695-7905 USA
| | - Christopher T. Straub
- North Carolina State University; Department of Chemical and Biomolecular Engineering; EB-1, 911 Partners Way Raleigh NC 27695-7905 USA
| | - Piyum A. Khatibi
- North Carolina State University; Department of Chemical and Biomolecular Engineering; EB-1, 911 Partners Way Raleigh NC 27695-7905 USA
| | - Laura L. Lee
- North Carolina State University; Department of Chemical and Biomolecular Engineering; EB-1, 911 Partners Way Raleigh NC 27695-7905 USA
| | - Nicholas P. Vitko
- North Carolina State University; Department of Chemical and Biomolecular Engineering; EB-1, 911 Partners Way Raleigh NC 27695-7905 USA
| | - Matthew W. Keller
- University of Georgia; Department of Biochemistry and Molecular Biology; Life Sciences Bldg., University of Georgia, Athens GA 30602-7229, USA
| | - Amanda M. Rhaesa
- University of Georgia; Department of Biochemistry and Molecular Biology; Life Sciences Bldg., University of Georgia, Athens GA 30602-7229, USA
| | - Gabe M. Rubinstein
- University of Georgia; Department of Biochemistry and Molecular Biology; Life Sciences Bldg., University of Georgia, Athens GA 30602-7229, USA
| | - Israel M. Scott
- University of Georgia; Department of Biochemistry and Molecular Biology; Life Sciences Bldg., University of Georgia, Athens GA 30602-7229, USA
| | - Gina L. Lipscomb
- University of Georgia; Department of Biochemistry and Molecular Biology; Life Sciences Bldg., University of Georgia, Athens GA 30602-7229, USA
| | - Michael W.W. Adams
- University of Georgia; Department of Biochemistry and Molecular Biology; Life Sciences Bldg., University of Georgia, Athens GA 30602-7229, USA
| | - Robert M. Kelly
- North Carolina State University; Department of Chemical and Biomolecular Engineering; EB-1, 911 Partners Way Raleigh NC 27695-7905 USA
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17
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Matsuoka H. ELECTROCHEMISTRY 2016; 84:178-187. [DOI: 10.5796/electrochemistry.84.178] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] Open
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18
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Zeldes BM, Keller MW, Loder AJ, Straub CT, Adams MWW, Kelly RM. Extremely thermophilic microorganisms as metabolic engineering platforms for production of fuels and industrial chemicals. Front Microbiol 2015; 6:1209. [PMID: 26594201 PMCID: PMC4633485 DOI: 10.3389/fmicb.2015.01209] [Citation(s) in RCA: 107] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2015] [Accepted: 10/19/2015] [Indexed: 01/06/2023] Open
Abstract
Enzymes from extremely thermophilic microorganisms have been of technological interest for some time because of their ability to catalyze reactions of industrial significance at elevated temperatures. Thermophilic enzymes are now routinely produced in recombinant mesophilic hosts for use as discrete biocatalysts. Genome and metagenome sequence data for extreme thermophiles provide useful information for putative biocatalysts for a wide range of biotransformations, albeit involving at most a few enzymatic steps. However, in the past several years, unprecedented progress has been made in establishing molecular genetics tools for extreme thermophiles to the point that the use of these microorganisms as metabolic engineering platforms has become possible. While in its early days, complex metabolic pathways have been altered or engineered into recombinant extreme thermophiles, such that the production of fuels and chemicals at elevated temperatures has become possible. Not only does this expand the thermal range for industrial biotechnology, it also potentially provides biodiverse options for specific biotransformations unique to these microorganisms. The list of extreme thermophiles growing optimally between 70 and 100°C with genetic toolkits currently available includes archaea and bacteria, aerobes and anaerobes, coming from genera such as Caldicellulosiruptor, Sulfolobus, Thermotoga, Thermococcus, and Pyrococcus. These organisms exhibit unusual and potentially useful native metabolic capabilities, including cellulose degradation, metal solubilization, and RuBisCO-free carbon fixation. Those looking to design a thermal bioprocess now have a host of potential candidates to choose from, each with its own advantages and challenges that will influence its appropriateness for specific applications. Here, the issues and opportunities for extremely thermophilic metabolic engineering platforms are considered with an eye toward potential technological advantages for high temperature industrial biotechnology.
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Affiliation(s)
- Benjamin M Zeldes
- Department of Chemical and Biomolecular Engineering, North Carolina State University Raleigh, NC, USA
| | - Matthew W Keller
- Department of Biochemistry and Molecular Biology, University of Georgia Athens, GA, USA
| | - Andrew J Loder
- Department of Chemical and Biomolecular Engineering, North Carolina State University Raleigh, NC, USA
| | - Christopher T Straub
- Department of Chemical and Biomolecular Engineering, North Carolina State University Raleigh, NC, USA
| | - Michael W W Adams
- Department of Biochemistry and Molecular Biology, University of Georgia Athens, GA, USA
| | - Robert M Kelly
- Department of Chemical and Biomolecular Engineering, North Carolina State University Raleigh, NC, USA
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