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Kim SM, Kang SH, Jeon BW, Kim YH. Tunnel engineering of gas-converting enzymes for inhibitor retardation and substrate acceleration. BIORESOURCE TECHNOLOGY 2024; 394:130248. [PMID: 38158090 DOI: 10.1016/j.biortech.2023.130248] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/07/2023] [Revised: 12/20/2023] [Accepted: 12/21/2023] [Indexed: 01/03/2024]
Abstract
Carbon monoxide dehydrogenase (CODH), formate dehydrogenase (FDH), hydrogenase (H2ase), and nitrogenase (N2ase) are crucial enzymatic catalysts that facilitate the conversion of industrially significant gases such as CO, CO2, H2, and N2. The tunnels in the gas-converting enzymes serve as conduits for these low molecular weight gases to access deeply buried catalytic sites. The identification of the substrate tunnels is imperative for comprehending the substrate selectivity mechanism underlying these gas-converting enzymes. This knowledge also holds substantial value for industrial applications, particularly in addressing the challenges associated with separation and utilization of byproduct gases. In this comprehensive review, we delve into the emerging field of tunnel engineering, presenting a range of approaches and analyses. Additionally, we propose methodologies for the systematic design of enzymes, with the ultimate goal of advancing protein engineering strategies.
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Affiliation(s)
- Suk Min Kim
- School of Energy and Chemical Engineering, Ulsan National Institute of Science and Technology (UNIST), 50 UNIST-gil, Ulsan 44919, Republic of Korea.
| | - Sung Heuck Kang
- School of Energy and Chemical Engineering, Ulsan National Institute of Science and Technology (UNIST), 50 UNIST-gil, Ulsan 44919, Republic of Korea
| | - Byoung Wook Jeon
- School of Energy and Chemical Engineering, Ulsan National Institute of Science and Technology (UNIST), 50 UNIST-gil, Ulsan 44919, Republic of Korea
| | - Yong Hwan Kim
- School of Energy and Chemical Engineering, Ulsan National Institute of Science and Technology (UNIST), 50 UNIST-gil, Ulsan 44919, Republic of Korea; Graduate School of Carbon Neutrality, Ulsan National Institute of Science and Technology (UNIST), 50 UNIST-gil, Ulsan 44919, Republic of Korea.
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Yu Y, Pi S, Ke T, Zhou B, Chao W, Yang Y, Li Z, Li G, Ren N, Gao X, Lu L. Artificial Soil-Like Material Enhances CO 2 Bio-Valorization into Chemicals in Gas Fermentation. ACS APPLIED MATERIALS & INTERFACES 2023; 15:53488-53497. [PMID: 37929338 DOI: 10.1021/acsami.3c12627] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/07/2023]
Abstract
Gas fermentation offers a carbon-neutral route for producing industrial feedstocks using autotrophic microbes to convert carbon dioxide (CO2) in waste gases, such as industrial emissions and biogas, into valuable chemicals or biofuels. However, slow microbial metabolism owing to low gaseous solubility causes significant challenges in gas fermentation. Although chemical or genetic manipulations have been explored to improve gas fermentation, they are either nonsustainable or complex. Herein, an artificial soil-like material (SLM) inspired by natural soil was fabricated to improve the growth and metabolism ofCupriavidus necatorfor enhanced poly-β-hydroxybutyrate (PHB) biosynthesis from CO2 and hydrogen (H2). Porous SLM comprises low-cost nanoclay, boehmite, and starch and serves as a biocarrier to facilitate the colonization of bacteria and delivery of CO2 to bacteria. With 3.0 g/L SLM addition, the solubility of CO2 in water increased by ∼4 times and biomass and PHB production boosted by 29 and 102%, respectively, in the 24 h culture. In addition, a positive modulation was observed in the metabolism of PHB biosynthesis. PHB biosynthesis-associated gene expression was found to be enhanced in response to the SLM addition. The concentrations of intermediates in the metabolic pathway of PHB biosynthesis, such as pyruvate and acetyl-CoA, as well as reducing energy (ATP and NADPH) significantly increased with SLM addition. SLM also demonstrated the merits of easy fabrication, high stability, recyclability, and plasticity, thereby indicating its considerable potential for large-scale application in gas fermentation.
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Affiliation(s)
- Yongjie Yu
- State Key Laboratory of Urban Water Resource and Environment, School of Civil and Environmental Engineering, Harbin Institute of Technology, Shenzhen 518055, China
| | - Shanshan Pi
- State Key Laboratory of Urban Water Resource and Environment, School of Civil and Environmental Engineering, Harbin Institute of Technology, Shenzhen 518055, China
| | - Tan Ke
- State Key Laboratory of Urban Water Resource and Environment, School of Civil and Environmental Engineering, Harbin Institute of Technology, Shenzhen 518055, China
| | - Baiqin Zhou
- State Key Laboratory of Urban Water Resource and Environment, School of Civil and Environmental Engineering, Harbin Institute of Technology, Shenzhen 518055, China
| | - Weixiang Chao
- State Key Laboratory of Urban Water Resource and Environment, School of Civil and Environmental Engineering, Harbin Institute of Technology, Shenzhen 518055, China
| | - Yang Yang
- State Key Laboratory of Urban Water Resource and Environment, School of Civil and Environmental Engineering, Harbin Institute of Technology, Shenzhen 518055, China
| | - Zhida Li
- State Key Laboratory of Urban Water Resource and Environment, School of Civil and Environmental Engineering, Harbin Institute of Technology, Shenzhen 518055, China
| | - Guifeng Li
- State Key Laboratory of Urban Water Resource and Environment, School of Civil and Environmental Engineering, Harbin Institute of Technology, Shenzhen 518055, China
| | - Nanqi Ren
- State Key Laboratory of Urban Water Resource and Environment, School of Civil and Environmental Engineering, Harbin Institute of Technology, Shenzhen 518055, China
| | - Xiang Gao
- Center for Materials Synthetic Biology, CAS Key Laboratory of Quantitative Engineering Biology of CAS, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academic of Science, Shenzhen 518000, China
| | - Lu Lu
- State Key Laboratory of Urban Water Resource and Environment, School of Civil and Environmental Engineering, Harbin Institute of Technology, Shenzhen 518055, China
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Safaeian P, Yazdian F, Khosravi-Darani K, Rashedi H, Lackner M. P3HB from CH 4 using methanotrophs: aspects of bioreactor, fermentation process and modelling for cost-effective biopolymer production. Front Bioeng Biotechnol 2023; 11:1137749. [PMID: 37404685 PMCID: PMC10315628 DOI: 10.3389/fbioe.2023.1137749] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2023] [Accepted: 06/01/2023] [Indexed: 07/06/2023] Open
Abstract
P3HB (poly-β-hydroxybutyrate), an energy-storage compound of several microorganisms, can be used as bioplastics material. P3HB is completely biodegradable under aerobic and aerobic conditions, also in the marine environment. The intracellular agglomeration of P3HB was examined employing a methanotrophic consortium. Supplanting fossil, non-degradable polymers by P3HB can significantly reduce the environmental impact of plastics. Utilizing inexpensive carbon sources like CH4 (natural gas, biogas) is a fundamental methodology to make P3HB production less costly, and to avoid the use of primary agricultural products such as sugar or starch. Biomass growth in polyhydroxyalkanoates (PHA) in general and in Poly (3-hydroxybutyrate) manufacture in specific could be a foremost point, so here the authors focus on natural gas as a proper carbon source and on the selection of bioreactors to produceP3HB, and in future further PHA, from that substrate. CH4 can also be obtained from biomass, e.g., biogas, syngas methanation or power-to-gas (synthetic natural gas, SNG). Simulation software can be utilized for examination, optimizing and scale-up of the process as shown in this paper. The fermentation systems continuously stirred tank reactor (CSTR), forced-liquid vertical loop bioreactor (VTLB), forced-liquid horizontal tubular loop bioreactor (HTLB), airlift (AL) fermenter and bubble column (BC) fermenter were compared for their methane conversion, kLa value, productivity, advantages and disadvantages. Methane is compared to methanol and other feedstocks. It was discovered that under optimum processing circumstances and using Methylocystis hirsuta, the cells accumulated 51.6% cell dry mass of P3HB in the VTLB setup.
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Affiliation(s)
- Parya Safaeian
- Department of Life Science Engineering, Faculty of New Sciences and Technologies, University of Tehran, Tehran, Iran
| | - Fatemeh Yazdian
- Department of Life Science Engineering, Faculty of New Sciences and Technologies, University of Tehran, Tehran, Iran
| | - Kianoush Khosravi-Darani
- Department of Food Technology Research, National Nutrition and Food Technology Research Institute, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Hamid Rashedi
- School of Chemical Engineering, College of Engineering, University of Tehran, Tehran, Iran
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Fuchs W, Rachbauer L, Rittmann SKMR, Bochmann G, Ribitsch D, Steger F. Eight Up-Coming Biotech Tools to Combat Climate Crisis. Microorganisms 2023; 11:1514. [PMID: 37375016 DOI: 10.3390/microorganisms11061514] [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: 05/19/2023] [Revised: 06/02/2023] [Accepted: 06/05/2023] [Indexed: 06/29/2023] Open
Abstract
Biotechnology has a high potential to substantially contribute to a low-carbon society. Several green processes are already well established, utilizing the unique capacity of living cells or their instruments. Beyond that, the authors believe that there are new biotechnological procedures in the pipeline which have the momentum to add to this ongoing change in our economy. Eight promising biotechnology tools were selected by the authors as potentially impactful game changers: (i) the Wood-Ljungdahl pathway, (ii) carbonic anhydrase, (iii) cutinase, (iv) methanogens, (v) electro-microbiology, (vi) hydrogenase, (vii) cellulosome and, (viii) nitrogenase. Some of them are fairly new and are explored predominantly in science labs. Others have been around for decades, however, with new scientific groundwork that may rigorously expand their roles. In the current paper, the authors summarize the latest state of research on these eight selected tools and the status of their practical implementation. We bring forward our arguments on why we consider these processes real game changers.
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Affiliation(s)
- Werner Fuchs
- Department IFA-Tulln, Institute of Environmental Biotechnology, University of Natural Resources and Life Sciences, Vienna, Konrad-Lorenz-Strasse 20, 3430 Tulln, Austria
| | - Lydia Rachbauer
- Lawrence Berkeley National Laboratory, Deconstruction Division at the Joint Bioenergy Institute, 5885 Hollis Street, Emeryville, CA 94608, USA
| | - Simon K-M R Rittmann
- Archaea Physiology & Biotechnology Group, Department of Functional and Evolutionary Ecology, Universität Wien, Djerassiplatz 1, 1030 Wien, Austria
| | - Günther Bochmann
- Department IFA-Tulln, Institute of Environmental Biotechnology, University of Natural Resources and Life Sciences, Vienna, Konrad-Lorenz-Strasse 20, 3430 Tulln, Austria
| | - Doris Ribitsch
- ACIB-Austrian Centre of Industrial Biotechnology, Krenngasse 37, 8010 Graz, Austria
| | - Franziska Steger
- Department IFA-Tulln, Institute of Environmental Biotechnology, University of Natural Resources and Life Sciences, Vienna, Konrad-Lorenz-Strasse 20, 3430 Tulln, Austria
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Moreira JPC, Heap JT, Alves JI, Domingues L. Developing a genetic engineering method for Acetobacterium wieringae to expand one-carbon valorization pathways. BIOTECHNOLOGY FOR BIOFUELS AND BIOPRODUCTS 2023; 16:24. [PMID: 36788587 PMCID: PMC9930230 DOI: 10.1186/s13068-023-02259-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Figures] [Subscribe] [Scholar Register] [Received: 05/05/2022] [Accepted: 01/05/2023] [Indexed: 02/16/2023]
Abstract
BACKGROUND Developing new bioprocesses to produce chemicals and fuels with reduced production costs will greatly facilitate the replacement of fossil-based raw materials. In most fermentation bioprocesses, the feedstock usually represents the highest cost, which becomes the target for cost reduction. Additionally, the biorefinery concept advocates revenue growth from the production of several compounds using the same feedstock. Taken together, the production of bio commodities from low-cost gas streams containing CO, CO2, and H2, obtained from the gasification of any carbon-containing waste streams or off-gases from heavy industry (steel mills, processing plants, or refineries), embodies an opportunity for affordable and renewable chemical production. To achieve this, by studying non-model autotrophic acetogens, current limitations concerning low growth rates, toxicity by gas streams, and low productivity may be overcome. The Acetobacterium wieringae strain JM is a novel autotrophic acetogen that is capable of producing acetate and ethanol. It exhibits faster growth rates on various gaseous compounds, including carbon monoxide, compared to other Acetobacterium species, making it potentially useful for industrial applications. The species A. wieringae has not been genetically modified, therefore developing a genetic engineering method is important for expanding its product portfolio from gas fermentation and overall improving the characteristics of this acetogen for industrial demands. RESULTS This work reports the development and optimization of an electrotransformation protocol for A. wieringae strain JM, which can also be used in A. wieringae DSM 1911, and A. woodii DSM 1030. We also show the functionality of the thiamphenicol resistance marker, catP, and the functionality of the origins of replication pBP1, pCB102, pCD6, and pIM13 in all tested Acetobacterium strains, with transformation efficiencies of up to 2.0 × 103 CFU/μgDNA. Key factors affecting electrotransformation efficiency include OD600 of cell harvesting, pH of resuspension buffer, the field strength of the electric pulse, and plasmid amount. Using this method, the acetone production operon from Clostridium acetobutylicum was efficiently introduced in all tested Acetobacterium spp., leading to non-native biochemical acetone production via plasmid-based expression. CONCLUSIONS A. wieringae can be electrotransformed at high efficiency using different plasmids with different replication origins. The electrotransformation procedure and tools reported here unlock the genetic and metabolic manipulation of the biotechnologically relevant A. wieringae strains. For the first time, non-native acetone production is shown in A. wieringae.
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Affiliation(s)
- João P. C. Moreira
- grid.10328.380000 0001 2159 175XCEB - Centre of Biological Engineering, University of Minho, 4710-057 Braga, Portugal ,LABBELS - Associate Laboratory, Braga/Guimarães, Portugal
| | - John T. Heap
- grid.4563.40000 0004 1936 8868School of Life Sciences, University of Nottingham, Biodiscovery Institute, University Park, Nottingham, NG7 2RD UK
| | - Joana I. Alves
- grid.10328.380000 0001 2159 175XCEB - Centre of Biological Engineering, University of Minho, 4710-057 Braga, Portugal ,LABBELS - Associate Laboratory, Braga/Guimarães, Portugal
| | - Lucília Domingues
- CEB - Centre of Biological Engineering, University of Minho, 4710-057, Braga, Portugal. .,LABBELS - Associate Laboratory, Braga/Guimarães, Portugal.
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Bierbaumer S, Nattermann M, Schulz L, Zschoche R, Erb TJ, Winkler CK, Tinzl M, Glueck SM. Enzymatic Conversion of CO 2: From Natural to Artificial Utilization. Chem Rev 2023; 123:5702-5754. [PMID: 36692850 PMCID: PMC10176493 DOI: 10.1021/acs.chemrev.2c00581] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Enzymatic carbon dioxide fixation is one of the most important metabolic reactions as it allows the capture of inorganic carbon from the atmosphere and its conversion into organic biomass. However, due to the often unfavorable thermodynamics and the difficulties associated with the utilization of CO2, a gaseous substrate that is found in comparatively low concentrations in the atmosphere, such reactions remain challenging for biotechnological applications. Nature has tackled these problems by evolution of dedicated CO2-fixing enzymes, i.e., carboxylases, and embedding them in complex metabolic pathways. Biotechnology employs such carboxylating and decarboxylating enzymes for the carboxylation of aromatic and aliphatic substrates either by embedding them into more complex reaction cascades or by shifting the reaction equilibrium via reaction engineering. This review aims to provide an overview of natural CO2-fixing enzymes and their mechanistic similarities. We also discuss biocatalytic applications of carboxylases and decarboxylases for the synthesis of valuable products and provide a separate summary of strategies to improve the efficiency of such processes. We briefly summarize natural CO2 fixation pathways, provide a roadmap for the design and implementation of artificial carbon fixation pathways, and highlight examples of biocatalytic cascades involving carboxylases. Additionally, we suggest that biochemical utilization of reduced CO2 derivates, such as formate or methanol, represents a suitable alternative to direct use of CO2 and provide several examples. Our discussion closes with a techno-economic perspective on enzymatic CO2 fixation and its potential to reduce CO2 emissions.
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Affiliation(s)
- Sarah Bierbaumer
- Institute of Chemistry, University of Graz, NAWI Graz, Heinrichstraße 28, 8010 Graz, Austria
| | - Maren Nattermann
- Department of Biochemistry and Synthetic Metabolism, Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch Straße 10, 35043 Marburg, Germany
| | - Luca Schulz
- Department of Biochemistry and Synthetic Metabolism, Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch Straße 10, 35043 Marburg, Germany
| | | | - Tobias J Erb
- Department of Biochemistry and Synthetic Metabolism, Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch Straße 10, 35043 Marburg, Germany
| | - Christoph K Winkler
- Institute of Chemistry, University of Graz, NAWI Graz, Heinrichstraße 28, 8010 Graz, Austria
| | - Matthias Tinzl
- Department of Biochemistry and Synthetic Metabolism, Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch Straße 10, 35043 Marburg, Germany
| | - Silvia M Glueck
- Institute of Chemistry, University of Graz, NAWI Graz, Heinrichstraße 28, 8010 Graz, Austria
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Zeldes B, Poehlein A, Jain S, Baum C, Daniel R, Müller V, Basen M. DNA uptake from a laboratory environment drives unexpected adaptation of a thermophile to a minor medium component. ISME COMMUNICATIONS 2023; 3:2. [PMID: 37938748 PMCID: PMC9834392 DOI: 10.1038/s43705-022-00211-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/10/2022] [Revised: 12/19/2022] [Accepted: 12/22/2022] [Indexed: 06/01/2023]
Abstract
DNA uptake is widespread among microorganisms and considered a strategy for rapid adaptation to new conditions. While both DNA uptake and adaptation are referred to in the context of natural environments, they are often studied in laboratories under defined conditions. For example, a strain of the thermophile Thermoanaerobacter kivui had been adapted to growth on high concentrations of carbon monoxide (CO). Unusual phenotypes of the CO-adapted strain prompted us to examine it more closely, revealing a horizontal gene transfer (HGT) event from another thermophile, Thermoanaerobacter sp. strain X514, being cultured in the same laboratory. The transferred genes conferred on T. kivui the ability to utilize trehalose, a trace component of the yeast-extract added to the media during CO-adaptation. This same HGT event simultaneously deleted a native operon for thiamine biosynthesis, which likely explains why the CO-adapted strain grows poorly without added vitamins. Attempts to replicate this HGT by providing T. kivui with genomic DNA from Thermoanaerobacter sp. strain X514 revealed that it is easily reproducible in the lab. This subtle form of "genome contamination" is difficult to detect, since the genome remains predominantly T. kivui, and no living cells from the original contamination remain. Unexpected HGT between two microorganisms as well as simultaneous adaptation to several conditions may occur often and unrecognized in laboratory environments, requiring caution and careful monitoring of phenotype and genotype of microorganisms that are naturally-competent for DNA uptake.
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Affiliation(s)
- Benjamin Zeldes
- Microbiology, Institute of Biological Sciences, University of Rostock, Rostock, Germany
| | - Anja Poehlein
- Genomic and Applied Microbiology & Göttingen Genomics Laboratory, Georg-August University, Göttingen, Germany
| | - Surbhi Jain
- Molecular Microbiology & Bioenergetics, Institute of Molecular Biosciences, Goethe University, Frankfurt/Main, Germany
| | - Christoph Baum
- Microbiology, Institute of Biological Sciences, University of Rostock, Rostock, Germany
| | - Rolf Daniel
- Genomic and Applied Microbiology & Göttingen Genomics Laboratory, Georg-August University, Göttingen, Germany
| | - Volker Müller
- Molecular Microbiology & Bioenergetics, Institute of Molecular Biosciences, Goethe University, Frankfurt/Main, Germany
| | - Mirko Basen
- Microbiology, Institute of Biological Sciences, University of Rostock, Rostock, Germany.
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Lee S, Rim Lee Y, Lee WH, Youn Lee S, Moon M, Woo Park G, Min K, Lee J, Lee JS. Valorization of CO 2 to β-farnesene in Rhodobacter sphaeroides. BIORESOURCE TECHNOLOGY 2022; 363:127955. [PMID: 36115510 DOI: 10.1016/j.biortech.2022.127955] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/03/2022] [Revised: 09/06/2022] [Accepted: 09/08/2022] [Indexed: 06/15/2023]
Abstract
The valorization of CO2 into valuable products is a sustainable strategy to help overcome the climate crisis. In particular, biological conversion is attractive as it can produce long-chain hydrocarbons such as terpenoids. This study reports the high yield of β-farnesene production from CO2 by expressing heterologous β-farnesene synthase (FS) into Rhodobacter sphaeroides. To increase the expression of FS, a strong active promoter and a ribosome binding site (RBS) were engineered. Moreover, β-farnesene production was improved further through the supply of exogenous antioxidants and additional nutrients. Finally, β-farnesene was produced from CO2 at a titer of 44.53 mg/L and yield of 234.08 mg/g, values that were correspondingly 23 times and 46 times higher than those from the initial production of β-farnesene. Altogether, the results here suggest that the autotrophic production of β-farnesene can provide a starting point for achieving a circular carbon economy.
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Affiliation(s)
- Sangmin Lee
- Gwangju Bio/Energy Research and Development Center, Korea Institute of Energy Research, Gwangju 61003, Republic of Korea
| | - Yu Rim Lee
- Gwangju Bio/Energy Research and Development Center, Korea Institute of Energy Research, Gwangju 61003, Republic of Korea; Interdisciplinary Program of Agriculture and Life Sciences, Chonnam National University, Gwangju 61186, Republic of Korea
| | - Won-Heong Lee
- Interdisciplinary Program of Agriculture and Life Sciences, Chonnam National University, Gwangju 61186, Republic of Korea; Department of Integrative Food, Bioscience and Biotechnology, Chonnam National University, Gwangju 61186, Republic of Korea
| | - Soo Youn Lee
- Gwangju Bio/Energy Research and Development Center, Korea Institute of Energy Research, Gwangju 61003, Republic of Korea
| | - Myounghoon Moon
- Gwangju Bio/Energy Research and Development Center, Korea Institute of Energy Research, Gwangju 61003, Republic of Korea
| | - Gwon Woo Park
- Gwangju Bio/Energy Research and Development Center, Korea Institute of Energy Research, Gwangju 61003, Republic of Korea
| | - Kyoungseon Min
- Gwangju Bio/Energy Research and Development Center, Korea Institute of Energy Research, Gwangju 61003, Republic of Korea
| | - Juah Lee
- Gwangju Bio/Energy Research and Development Center, Korea Institute of Energy Research, Gwangju 61003, Republic of Korea
| | - Jin-Suk Lee
- Gwangju Bio/Energy Research and Development Center, Korea Institute of Energy Research, Gwangju 61003, Republic of Korea.
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Carruthers DN, Lee TS. Translating advances in microbial bioproduction to sustainable biotechnology. Front Bioeng Biotechnol 2022; 10:968437. [PMID: 36082166 PMCID: PMC9445250 DOI: 10.3389/fbioe.2022.968437] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2022] [Accepted: 07/21/2022] [Indexed: 11/24/2022] Open
Abstract
Advances in synthetic biology have radically changed our ability to rewire microorganisms and significantly improved the scalable production of a vast array of drop-in biopolymers and biofuels. The success of a drop-in bioproduct is contingent on market competition with petrochemical analogues and weighted upon relative economic and environmental metrics. While the quantification of comparative trade-offs is critical for accurate process-level decision making, the translation of industrial ecology to synthetic biology is often ambiguous and assessment accuracy has proven challenging. In this review, we explore strategies for evaluating industrial biotechnology through life cycle and techno-economic assessment, then contextualize how recent developments in synthetic biology have improved process viability by expanding feedstock availability and the productivity of microbes. By juxtaposing biological and industrial constraints, we highlight major obstacles between the disparate disciplines that hinder accurate process evaluation. The convergence of these disciplines is crucial in shifting towards carbon neutrality and a circular bioeconomy.
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Affiliation(s)
- David N. Carruthers
- Joint BioEnergy Institute, Emeryville, CA, United States
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Taek Soon Lee
- Joint BioEnergy Institute, Emeryville, CA, United States
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
- *Correspondence: Taek Soon Lee,
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10
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A comparative evaluation of machine learning algorithms for predicting syngas fermentation outcomes. Biochem Eng J 2022. [DOI: 10.1016/j.bej.2022.108578] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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11
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Upscale fermenter design for lactic acid production from cheese whey permeate focusing on impeller selection and energy optimization. JOURNAL OF FOOD SCIENCE AND TECHNOLOGY 2022; 59:2263-2273. [PMID: 35602439 PMCID: PMC9114246 DOI: 10.1007/s13197-021-05239-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Revised: 08/03/2021] [Accepted: 08/10/2021] [Indexed: 11/26/2022]
Abstract
This study focusses on the design and scale-up of industrial lactic acid production by fermentation of dairy cheese whey permeate based on standard methodological parameters. The aim was to address the shortcomings of standard scale-up methodologies and provide a framework for fermenter scale-up that enables the accurate estimation of energy consumption by suitable selection of turbine and speed for industrial deployment. Moreover, life cycle assessment (LCA) was carried out to identify the potential impacts and possibilities to reduce the operation associated emissions at an early stage. The findings showed that a 3000 times scale-up strategy assuming constant geometric dimensions and specific energy consumption (P/Vw) resulted in lower impeller speed and energy demand. The Rushton turbine blade (RTB) and LightninA315 four-blade hydrofoil (LA315) were found to have the highest and lowest torque output, respectively, at a similar P/Vw of 2.8 kWm−3, with agitation speeds of 1.33 and 2.5 s−1, respectively. RTB demonstrating lower shear damage towards cells (up to 1.33 s−1) was selected because it permits high torque, low-power and acceptable turbulence. The LCA results showed a strong relation between the number of impellers installed and associated emissions suggesting a trade-off between mixing performance and environmental impacts.
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12
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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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13
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Reznichenko A, Harlin A. Next generation of polyolefin plastics: improving sustainability with existing and novel feedstock base. SN APPLIED SCIENCES 2022. [DOI: 10.1007/s42452-022-04991-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
Abstract
In this account, we present an overview of existing and emerging olefin production technologies, comparing them from the standpoint of carbon intensity, efficiency, feedstock type and availability. Olefins are indispensable feedstock for manufacture of polyolefin plastics and other base chemicals. Current methods of olefin production are associated with significant CO2 emissions and almost entirely rely of fossil feedstock. In order to assess potential alternatives, technical and economic maturity of six principal olefin production routes are compared in this paper. Coal (brown), oil and gas (grey), biomass (green), recycled plastic (pink) as well as carbon capture and storage (purple) and carbon capture and utilization (blue) technologies are considered. We conclude that broader adoption of biomass based “green” feedstock and introduction of recycled plastic based olefins may lead to reduced carbon footprint, however adoption of best available technologies and introduction of electrocracking to existing fossil-based “grey” olefin manufacture process can be the way to achieve highest impact most rapidly. Adoption of Power-to-X approaches to olefins starting from biogenic or atmospheric CO2 and renewable H2 can lead to ultimately carbon–neutral “blue” olefins in the long term, however substantial development and additional regulatory incentives are necessary to make the solution economically viable.
Article highlights
In this account, we introduce a color coding scheme to differentiate and compare carbon intensity and feedstock types for some of the main commercial and emerging olefin production routes.
Most viable short term improvements in CO2 emissions of olefin production will be achieved by discouraging “brown” coal based production and improving efficiency of “grey” oil and gas based processes.
Gradual incorporation of green and recycled feedstock to existing olefin production assets will allow to achieve substantial improvements in carbon efficiency in longer term.
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14
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Park GW, Moon M, Park JH, Jo JH, Kim HJ, Lee JY, Lee HS, Lee JP, Lee S, Lee SY, Lee J, Na JG, Kim MS, Lee JS. Improving hydrogen production by pH adjustment in pressurized gas fermentation. BIORESOURCE TECHNOLOGY 2022; 346:126605. [PMID: 34953994 DOI: 10.1016/j.biortech.2021.126605] [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: 12/13/2021] [Accepted: 12/17/2021] [Indexed: 06/14/2023]
Abstract
Gas fermentation utilizes syngas converted from biomass or waste as feedstock. A bubble column reactor for pressurizing was designed to increase the mass transfer rate between gas and liquid, and reduce energy consumption by medium agitation. Thermococcus onnurineus, a hydrogenic CO-oxidizer, was cultured initially under ambient pressure with the initial inlet gas composition; 60% CO and 40% N2. The maximum H2 productivity was 363 mmol/l/h, without pH adjustment. When additional pressure was applied, the pH rapidly declined; this may be attributed to the increased CO2 solubility under pressure. By controlling pH, H2 productivity increased up to 450 mmol/l/h; which is comparable to the previously reported H2 productivity in a continuous stirred tank reactor. The results may suggest energy saving potentials of bubble column reactors in gas fermentation. This finding may be applied to other gas fermentation processes, as syngas itself contains CO2 and many microbial processes also release CO2.
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Affiliation(s)
- Gwon Woo Park
- Gwangju Bio/Energy R&D Center, Korea Institute of Energy Research, Gwangju 61003, Republic of Korea
| | - Myounghoon Moon
- Gwangju Bio/Energy R&D Center, Korea Institute of Energy Research, Gwangju 61003, Republic of Korea
| | - Jeong-Ho Park
- Gwangju Bio/Energy R&D Center, Korea Institute of Energy Research, Gwangju 61003, Republic of Korea; Interdisciplinary Program for Agriculture and Life Sciences, Chonnam National University, Gwangju 61186, Republic of Korea
| | - Jae-Hwan Jo
- Gwangju Bio/Energy R&D Center, Korea Institute of Energy Research, Gwangju 61003, Republic of Korea; Interdisciplinary Program for Agriculture and Life Sciences, Chonnam National University, Gwangju 61186, Republic of Korea
| | - Hyouck Ju Kim
- Energy ICT Convergence Research Department, Korea Institute of Energy Research, Daejeon 34129, Republic of Korea
| | - Jae Yong Lee
- Energy ICT Convergence Research Department, Korea Institute of Energy Research, Daejeon 34129, Republic of Korea
| | - Hyun Sook Lee
- Marine Biotechnology Research Center, Korea Institute of Ocean Science and Technology, Busan 49111, Republic of Korea; Department of Marine Biotechnology, University of Science and Technology, Daejeon 34113, Republic of Korea
| | - Joon-Pyo Lee
- Gwangju Bio/Energy R&D Center, Korea Institute of Energy Research, Gwangju 61003, Republic of Korea
| | - Sangmin Lee
- Gwangju Bio/Energy R&D Center, Korea Institute of Energy Research, Gwangju 61003, Republic of Korea
| | - Soo Youn Lee
- Gwangju Bio/Energy R&D Center, Korea Institute of Energy Research, Gwangju 61003, Republic of Korea
| | - Jiye Lee
- Gwangju Bio/Energy R&D Center, Korea Institute of Energy Research, Gwangju 61003, Republic of Korea
| | - Jeong-Geol Na
- Department of Chemical and Biomolecular Engineering, Sogang University, Seoul 04107, Republic of Korea
| | - Min-Sik Kim
- Energy Resources Upcycling Research Laboratory, Korea Institute of Energy Research, Daejeon 34129, Republic of Korea.
| | - Jin-Suk Lee
- Gwangju Bio/Energy R&D Center, Korea Institute of Energy Research, Gwangju 61003, Republic of Korea
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15
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Abstract
Schism is the new normal for the bioeconomy concept. Since its proliferation in governments, the concept has been adapted to fit national or regional exigencies. Earlier this century the knowledge-based bioeconomy (KBBE) in Europe was seen as a technical and knowledge fix in the evolving sustainability landscape. At the OECD, the concept was further honed by imagining a future where biotechnologies contribute significantly to economic growth and development. Countries started to make national bioeconomy strategies. Some countries have diverged and made the bioeconomy both much larger and more general, involving a wide variety of sectors, such as industry, energy, healthcare, agriculture, aquaculture, forestry and fishing. Whatever the approach, what seems to be consistent is the need to reconcile environmental, social and economic sustainability. This paper attempts to establish one schism that could have ramifications for the future development of the bioeconomy. Some countries, including some of the largest economies but not exclusively so, are clearly following a biotechnology model, whereas others are clearly not. In the wake of the COVID-19 pandemic, biotechnologies offer outstanding potential in healthcare, although this sector is by no means included in all bioeconomy strategies. The paper also attempts to clarify how biotechnologies can address the grand challenges and the United Nations Sustainable Development Goals. The communities of scientists seem to have no difficulty with this, but citizens and governments find it more difficult. In fact, some biotechnologies are already well established, whereas others are emerging and more controversial.
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16
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Ntagia E, Chatzigiannidou I, Carvajal-Arroyo JM, Arends JBA, Rabaey K. Continuous H 2/CO 2 fermentation for acetic acid production under transient and continuous sulfide inhibition. CHEMOSPHERE 2021; 285:131536. [PMID: 34273695 DOI: 10.1016/j.chemosphere.2021.131536] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Revised: 07/08/2021] [Accepted: 07/09/2021] [Indexed: 06/13/2023]
Abstract
Waste gas fermentation powered by renewable H2 is reaching kiloton scale. The presence of sulfide, inherent to many waste gases, can cause inhibition, requiring additional gas treatment. In this work, acetogenesis and methanogenesis inhibition by sulfide were studied in a 10-L mixed-culture fermenter, supplied with CO2 and connected with a water electrolysis unit for electricity-powered H2 supply. Three cycles of inhibition (1.3 mM total dissolved sulfide (TDS)) and recovery were applied, then the fermenter was operated at 0.5 mM TDS for 35 days. During operation at 0.5 mM TDS the acetate production rate reached 7.1 ± 1.5 mmol C L-1 d-1. Furthermore, 43.7 ± 15.6% of the electrons, provided as H2, were distributed to acetate and 7.7 ± 4.1% to butyrate, the second most abundant fermentation product. Selectivity of sulfide as inhibitor was demonstrated by a 7 days lag-phase of methanogenesis recovery, compared to 48 h for acetogenesis and by the less than 1% electrons distribution to CH4, under 0.5 mM TDS. The microbial community was dominated by Eubacterium, Proteiniphilum and an unclassified member of the Eggerthellaceae family. The taxonomic diversity of the community decreased and conversely the phenotypic diversity increased, during operation. This work illustrated the scale-up potential of waste gas fermentations, by elucidating the effect of sulfide as a common gas impurity, and by demonstrating continuous, potentially renewable supply of electrons.
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Affiliation(s)
- Eleftheria Ntagia
- Center for Microbial Ecology and Technology (CMET), Ghent University, Coupure Links 653, 9000, Gent, Belgium; CAPTURE, www.capture-resources.be, Belgium
| | - Ioanna Chatzigiannidou
- Center for Microbial Ecology and Technology (CMET), Ghent University, Coupure Links 653, 9000, Gent, Belgium
| | - Jose M Carvajal-Arroyo
- Center for Microbial Ecology and Technology (CMET), Ghent University, Coupure Links 653, 9000, Gent, Belgium
| | - Jan B A Arends
- Center for Microbial Ecology and Technology (CMET), Ghent University, Coupure Links 653, 9000, Gent, Belgium; CAPTURE, www.capture-resources.be, Belgium
| | - Korneel Rabaey
- Center for Microbial Ecology and Technology (CMET), Ghent University, Coupure Links 653, 9000, Gent, Belgium; CAPTURE, www.capture-resources.be, Belgium.
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17
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Process Engineering Aspects for the Microbial Conversion of C1 Gases. ADVANCES IN BIOCHEMICAL ENGINEERING/BIOTECHNOLOGY 2021; 180:33-56. [PMID: 34291298 DOI: 10.1007/10_2021_172] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
Industrially applied bioprocesses for the reduction of C1 gases (CO2 and/or CO) are based in particular on (syn)gas fermentation with acetogenic bacteria and on photobioprocesses with microalgae. In each case, process engineering characteristics of the autotrophic microorganisms are specified and process engineering aspects for improving gas and electron supply are summarized before suitable bioreactor configurations are discussed for the production of organic products under given economic constraints. Additionally, requirements for the purity of C1 gases are summarized briefly. Finally, similarities and differences in microbial CO2 valorization are depicted comparing gas fermentations with acetogenic bacteria and photobioprocesses with microalgae.
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18
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Growth Enhancement Facilitated by Gaseous CO2 through Heterologous Expression of Reductive Tricarboxylic Acid Cycle Genes in Escherichia coli. FERMENTATION 2021. [DOI: 10.3390/fermentation7020098] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
The enzymatic mechanisms of carbon fixation by autotrophs, such as the reductive tricarboxylic acid cycle (rTCA), have inspired biotechnological approaches to producing bio-based chemicals directly through CO2. To explore the possibility of constructing an rTCA cycle in Escherichia coli and to investigate their potential for CO2 assimilation, a total of ten genes encoding the key rTCA cycle enzymes, including α-ketoglutarate:ferredoxin oxidoreductase, ATP-dependent citrate lyase, and fumarate reductase/succinate dehydrogenase, were cloned into E. coli. The transgenic E. coli strain exhibited enhanced growth and the ability to assimilate external inorganic carbon with a gaseous CO2 supply. Further experiments conducted in sugar-free medium containing hydrogen as the electron donor and dimethyl sulfoxide (DMSO) as the electron acceptor proved that the strain is able to undergo anaerobic respiration, using CO2 as the major carbon source. The transgenic stain demonstrated CO2-enhanced growth, whereas the genes involved in chemotaxis, flagellar assembly, and acid-resistance were upregulated under the anaerobic respiration. Furthermore, metabolomic analysis demonstrated that the total concentrations of ATP, ADP, and AMP in the transgenic strain were higher than those in the vector control strain and these results coincided with the enhanced growth. Our approach offers a novel strategy to engineer E. coli for assimilating external gaseous CO2.
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Abstract
Currently, the world is faced with two fundamental issues of great importance, namely climate change and the coronavirus pandemic. These are intimately involved with the need to control climate change and the need to switch from high carbon, unsustainable economies to low carbon economies. Inherent in this approach are the concepts of the bioeconomy and the Green Industrial Revolution. The article addresses both issues, but it, principally, focusses on the development of the bioeconomy. It considers how nations are divided in relation to the use of biotechnology and synthetic biology in terms of their bioeconomy strategies. The article addresses, as a central theme, the nature and role of engineering biology in these developments. Engineering biology is addressed in terms of BioDesign, coupled with high levels of automation (including AI and machine learning) to increase reproducibility and reliability to meet industrial standards. This lends itself to distributed manufacturing of products in a range of fields. Engineering biology is a platform technology that can be applied in a range of sectors. The bioeconomy, as an engine for economic growth is addressed—in terms of moving from oil‐based economies to bio‐based economies—using biomass, for example, using selected lignocellulosic waste as a feedstock.
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Affiliation(s)
| | - Jim Philp
- Directorate for Science, Technology and Innovation OECD Paris France
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20
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Capture and Reuse of Carbon Dioxide (CO2) for a Plastics Circular Economy: A Review. Processes (Basel) 2021. [DOI: 10.3390/pr9050759] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Plastic production has been increasing at enormous rates. Particularly, the socioenvironmental problems resulting from the linear economy model have been widely discussed, especially regarding plastic pieces intended for single use and disposed improperly in the environment. Nonetheless, greenhouse gas emissions caused by inappropriate disposal or recycling and by the many production stages have not been discussed thoroughly. Regarding the manufacturing processes, carbon dioxide is produced mainly through heating of process streams and intrinsic chemical transformations, explaining why first-generation petrochemical industries are among the top five most greenhouse gas (GHG)-polluting businesses. Consequently, the plastics market must pursue full integration with the circular economy approach, promoting the simultaneous recycling of plastic wastes and sequestration and reuse of CO2 through carbon capture and utilization (CCU) strategies, which can be employed for the manufacture of olefins (among other process streams) and reduction of fossil-fuel demands and environmental impacts. Considering the previous remarks, the present manuscript’s purpose is to provide a review regarding CO2 emissions, capture, and utilization in the plastics industry. A detailed bibliometric review of both the scientific and the patent literature available is presented, including the description of key players and critical discussions and suggestions about the main technologies. As shown throughout the text, the number of documents has grown steadily, illustrating the increasing importance of CCU strategies in the field of plastics manufacture.
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21
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Guo S, Asset T, Atanassov P. Catalytic Hybrid Electrocatalytic/Biocatalytic Cascades for Carbon Dioxide Reduction and Valorization. ACS Catal 2021. [DOI: 10.1021/acscatal.0c04862] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Affiliation(s)
- Shengyuan Guo
- Department of Chemical and Biomolecular Engineering, National Fuel Cell Research Center, University of California Irvine, Irvine, California 92697, United States
| | - Tristan Asset
- Department of Chemical and Biomolecular Engineering, National Fuel Cell Research Center, University of California Irvine, Irvine, California 92697, United States
| | - Plamen Atanassov
- Department of Chemical and Biomolecular Engineering, National Fuel Cell Research Center, University of California Irvine, Irvine, California 92697, United States
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22
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Cellulose nanocrystals coated with a tannic acid-Fe 3+ complex as a significant medium for efficient CH 4 microbial biotransformation. Carbohydr Polym 2021; 258:117733. [PMID: 33593529 DOI: 10.1016/j.carbpol.2021.117733] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2020] [Revised: 01/06/2021] [Accepted: 01/26/2021] [Indexed: 11/21/2022]
Abstract
Microbial biotransformation of CH4 gas has been attractive for the production of energy and high-value chemicals. However, insufficient supply of CH4 in a culture medium needs to be overcome for the efficient utilization of CH4. Here, we utilized cellulose nanocrystals coated with a tannic acid-Fe3+ complex (TA-Fe3+CNCs) as a medium component to enhance the gas-liquid mass-transfer performance. TA-Fe3+CNCs were well suspended in water without agglomeration, stabilized gas bubbles without coalescence, and increased the gas solubility by 20 % and the kLa value at a rapid inlet gas flow rate. Remarkably, the cell growth rate of Methylomonas sp. DH-1 as model CH4-utilizing bacteria improved with TA-Fe3+CNC concentration without any cytotoxic or antibacterial properties, resulting in higher metabolite production ability such as methanol, pyruvate, formate, and succinate. These results showed that TA-Fe3+CNCs could be utilized as a significant component in the culture medium applicable as a promising nanofluid for efficient CH4 microbial biotransformation.
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23
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Engineering an efficient H2 utilizing Escherichia coli platform by modulation of endogenous hydrogenases. Biochem Eng J 2021. [DOI: 10.1016/j.bej.2020.107851] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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24
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Shi XC, Tremblay PL, Wan L, Zhang T. Improved robustness of microbial electrosynthesis by adaptation of a strict anaerobic microbial catalyst to molecular oxygen. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 754:142440. [PMID: 33254866 DOI: 10.1016/j.scitotenv.2020.142440] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/22/2020] [Revised: 08/24/2020] [Accepted: 09/13/2020] [Indexed: 06/12/2023]
Abstract
Microbial electrosynthesis (MES) and other bioprocesses such as syngas fermentation developed for energy storage and the conversion of carbon dioxide into valuable chemicals often employs acetogens as microbial catalysts. Acetogens are sensitive to molecular oxygen, which means that bioproduction reactors must be maintained under strict anaerobic conditions. This requirement increases cost and does not eliminate the possibility of O2 leakage. For MES, the risk is even greater since the system generates O2 when water splitting is the anodic reaction. Here, we show that O2 from the anode of a MES reactor diffuses into the cathode chamber where strict anaerobes reduce CO2. To overcome this drawback, a stepwise adaptive laboratory evolution (ALE) strategy is used to develop the O2 tolerance of the acetogen Sporomusa ovata. Two heavily-mutated S. ovata strains growing well autotrophically in the presence of 0.5 to 5% O2 were obtained. The adapted strains were more performant in the MES system than the wild type converting electrical energy and CO2 into acetate 1.5 fold faster. This study shows that the O2 tolerance of acetogens can be increased, which leads to improvement of the performance and robustness of energy-storage bioprocesses such as MES where O2 is an inhibitor.
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Affiliation(s)
- Xiao-Chen Shi
- State Key Laboratory of Silicate Materials for Architectures, Wuhan University of Technology, Wuhan 430070, PR China; School of Chemistry, Chemical Engineering and Life Science, Wuhan University of Technology, Wuhan 430070, PR China; School of Materials Science and Engineering, Wuhan University of Technology, Wuhan 430070, PR China
| | - Pier-Luc Tremblay
- State Key Laboratory of Silicate Materials for Architectures, Wuhan University of Technology, Wuhan 430070, PR China; School of Chemistry, Chemical Engineering and Life Science, Wuhan University of Technology, Wuhan 430070, PR China
| | - Lulu Wan
- State Key Laboratory of Silicate Materials for Architectures, Wuhan University of Technology, Wuhan 430070, PR China; School of Chemistry, Chemical Engineering and Life Science, Wuhan University of Technology, Wuhan 430070, PR China; School of Materials Science and Engineering, Wuhan University of Technology, Wuhan 430070, PR China
| | - Tian Zhang
- State Key Laboratory of Silicate Materials for Architectures, Wuhan University of Technology, Wuhan 430070, PR China; School of Chemistry, Chemical Engineering and Life Science, Wuhan University of Technology, Wuhan 430070, PR China; School of Materials Science and Engineering, Wuhan University of Technology, Wuhan 430070, PR China.
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25
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Katsyv A, Müller V. Overcoming Energetic Barriers in Acetogenic C1 Conversion. Front Bioeng Biotechnol 2020; 8:621166. [PMID: 33425882 PMCID: PMC7793690 DOI: 10.3389/fbioe.2020.621166] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2020] [Accepted: 11/19/2020] [Indexed: 11/13/2022] Open
Abstract
Currently one of the biggest challenges for society is to combat global warming. A solution to this global threat is the implementation of a CO2-based bioeconomy and a H2-based bioenergy economy. Anaerobic lithotrophic bacteria such as the acetogenic bacteria are key players in the global carbon and H2 cycle and thus prime candidates as driving forces in a H2- and CO2-bioeconomy. Naturally, they convert two molecules of CO2via the Wood-Ljungdahl pathway (WLP) to one molecule of acetyl-CoA which can be converted to different C2-products (acetate or ethanol) or elongated to C4 (butyrate) or C5-products (caproate). Since there is no net ATP generation from acetate formation, an electron-transport phosphorylation (ETP) module is hooked up to the WLP. ETP provides the cell with additional ATP, but the ATP gain is very low, only a fraction of an ATP per mol of acetate. Since acetogens live at the thermodynamic edge of life, metabolic engineering to obtain high-value products is currently limited by the low energy status of the cells that allows for the production of only a few compounds with rather low specificity. To set the stage for acetogens as production platforms for a wide range of bioproducts from CO2, the energetic barriers have to be overcome. This review summarizes the pathway, the energetics of the pathway and describes ways to overcome energetic barriers in acetogenic C1 conversion.
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Affiliation(s)
- Alexander Katsyv
- Department of Molecular Microbiology & Bioenergetics, Institute of Molecular Biosciences, Johann Wolfgang Goethe University, Frankfurt am Main, Germany
| | - Volker Müller
- Department of Molecular Microbiology & Bioenergetics, Institute of Molecular Biosciences, Johann Wolfgang Goethe University, Frankfurt am Main, Germany
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26
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Synthetic Biology on Acetogenic Bacteria for Highly Efficient Conversion of C1 Gases to Biochemicals. Int J Mol Sci 2020; 21:ijms21207639. [PMID: 33076477 PMCID: PMC7589590 DOI: 10.3390/ijms21207639] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2020] [Revised: 10/13/2020] [Accepted: 10/13/2020] [Indexed: 12/13/2022] Open
Abstract
Synthesis gas, which is mainly produced from fossil fuels or biomass gasification, consists of C1 gases such as carbon monoxide, carbon dioxide, and methane as well as hydrogen. Acetogenic bacteria (acetogens) have emerged as an alternative solution to recycle C1 gases by converting them into value-added biochemicals using the Wood-Ljungdahl pathway. Despite the advantage of utilizing acetogens as biocatalysts, it is difficult to develop industrial-scale bioprocesses because of their slow growth rates and low productivities. To solve these problems, conventional approaches to metabolic engineering have been applied; however, there are several limitations owing to the lack of required genetic bioparts for regulating their metabolic pathways. Recently, synthetic biology based on genetic parts, modules, and circuit design has been actively exploited to overcome the limitations in acetogen engineering. This review covers synthetic biology applications to design and build industrial platform acetogens.
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27
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Köpke M, Simpson SD. Pollution to products: recycling of ‘above ground’ carbon by gas fermentation. Curr Opin Biotechnol 2020; 65:180-189. [DOI: 10.1016/j.copbio.2020.02.017] [Citation(s) in RCA: 72] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2020] [Revised: 02/21/2020] [Accepted: 02/26/2020] [Indexed: 02/01/2023]
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28
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Vees CA, Neuendorf CS, Pflügl S. Towards continuous industrial bioprocessing with solventogenic and acetogenic clostridia: challenges, progress and perspectives. J Ind Microbiol Biotechnol 2020; 47:753-787. [PMID: 32894379 PMCID: PMC7658081 DOI: 10.1007/s10295-020-02296-2] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2020] [Accepted: 07/20/2020] [Indexed: 12/11/2022]
Abstract
The sustainable production of solvents from above ground carbon is highly desired. Several clostridia naturally produce solvents and use a variety of renewable and waste-derived substrates such as lignocellulosic biomass and gas mixtures containing H2/CO2 or CO. To enable economically viable production of solvents and biofuels such as ethanol and butanol, the high productivity of continuous bioprocesses is needed. While the first industrial-scale gas fermentation facility operates continuously, the acetone-butanol-ethanol (ABE) fermentation is traditionally operated in batch mode. This review highlights the benefits of continuous bioprocessing for solvent production and underlines the progress made towards its establishment. Based on metabolic capabilities of solvent producing clostridia, we discuss recent advances in systems-level understanding and genome engineering. On the process side, we focus on innovative fermentation methods and integrated product recovery to overcome the limitations of the classical one-stage chemostat and give an overview of the current industrial bioproduction of solvents.
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Affiliation(s)
- Charlotte Anne Vees
- Institute of Chemical, Environmental and Bioscience Engineering, Research Area Biochemical Engineering, Technische Universität Wien, Gumpendorfer Straße 1a, 1060 Vienna, Austria
| | - Christian Simon Neuendorf
- Institute of Chemical, Environmental and Bioscience Engineering, Research Area Biochemical Engineering, Technische Universität Wien, Gumpendorfer Straße 1a, 1060 Vienna, Austria
| | - Stefan Pflügl
- Institute of Chemical, Environmental and Bioscience Engineering, Research Area Biochemical Engineering, Technische Universität Wien, Gumpendorfer Straße 1a, 1060 Vienna, Austria
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29
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Geinitz B, Hüser A, Mann M, Büchs J. Gas Fermentation Expands the Scope of a Process Network for Material Conversion. CHEM-ING-TECH 2020. [DOI: 10.1002/cite.202000086] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Affiliation(s)
- Bertram Geinitz
- RWTH Aachen University, AVT – Biochemical Engineering Forckenbeckstraße 51 52074 Aachen Germany
| | - Aline Hüser
- RWTH Aachen University, AVT – Biochemical Engineering Forckenbeckstraße 51 52074 Aachen Germany
| | - Marcel Mann
- RWTH Aachen University, AVT – Biochemical Engineering Forckenbeckstraße 51 52074 Aachen Germany
| | - Jochen Büchs
- RWTH Aachen University, AVT – Biochemical Engineering Forckenbeckstraße 51 52074 Aachen Germany
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30
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Affiliation(s)
- Cláudio J. R. Frazão
- TU Dresden Institute of Natural Materials Technology Bergstraße 120 01062 Dresden Germany
| | - Thomas Walther
- TU Dresden Institute of Natural Materials Technology Bergstraße 120 01062 Dresden Germany
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31
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Jang N, Lee M, Yasin M, Chang IS. Behavior of CO-water mass transfer coefficient in membrane sparger-integrated bubble column for synthesis gas fermentation. BIORESOURCE TECHNOLOGY 2020; 311:123594. [PMID: 32485601 DOI: 10.1016/j.biortech.2020.123594] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/18/2020] [Revised: 05/24/2020] [Accepted: 05/25/2020] [Indexed: 06/11/2023]
Abstract
The gas-liquid mass transfer coefficient (kLa) of O2 was investigated in a bubble column reactor (BCR) using a sintered gas filter (SF), ceramic membrane module (CMM), and hollow fiber membrane module (HFM), which have different ranges of gas supply areas. kLa was enhanced by increasing flow rate in all of the spargers. Different responses when changing the gas supply area were obtained depending on the sparger type. Average values of kLa that were 52 and 258% higher were obtained using a CMM-integrated BCR compared to SFs and HFMs. CO-water kLa was investigated using CMMs for application to gas fermentation. The CO-water kLa ranged from 28.3 to 113.7/h under the experimental conditions. Based on the experimental data from CO and O2, a model to predict kLa was constructed for CMM-integrated BCRs. A dimensionless number indicating a gas supply area of the sparger was newly defined and included in the developed model.
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Affiliation(s)
- Nulee Jang
- School of Earth Sciences and Environmental Engineering, Gwangju Institute of Science and Technology (GIST), Gwangju 61005, Republic of Korea
| | - Mungyu Lee
- School of Earth Sciences and Environmental Engineering, Gwangju Institute of Science and Technology (GIST), Gwangju 61005, Republic of Korea
| | - Muhammad Yasin
- School of Earth Sciences and Environmental Engineering, Gwangju Institute of Science and Technology (GIST), Gwangju 61005, Republic of Korea; Bioenergy & Environmental Sustainable Technology (BEST) Research Group, Department of Chemical Engineering, COMSATS University Islamabad (CUI), Lahore Campus, Defense Road, Off Raiwind Road, Lahore, Pakistan
| | - In Seop Chang
- School of Earth Sciences and Environmental Engineering, Gwangju Institute of Science and Technology (GIST), Gwangju 61005, Republic of Korea.
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32
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Development of a clostridia-based cell-free system for prototyping genetic parts and metabolic pathways. Metab Eng 2020; 62:95-105. [PMID: 32540392 DOI: 10.1016/j.ymben.2020.06.004] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2020] [Revised: 05/15/2020] [Accepted: 06/07/2020] [Indexed: 02/04/2023]
Abstract
Gas fermentation by autotrophic bacteria, such as clostridia, offers a sustainable path to numerous bioproducts from a range of local, highly abundant, waste and low-cost feedstocks, such as industrial flue gases or syngas generated from biomass or municipal waste. Unfortunately, designing and engineering clostridia remains laborious and slow. The ability to prototype individual genetic part function, gene expression patterns, and biosynthetic pathway performance in vitro before implementing designs in cells could help address these bottlenecks by speeding up design. Unfortunately, a high-yielding cell-free gene expression (CFE) system from clostridia has yet to be developed. Here, we report the development and optimization of a high-yielding (236 ± 24 μg/mL) batch CFE platform from the industrially relevant anaerobe, Clostridium autoethanogenum. A key feature of the platform is that both circular and linear DNA templates can be applied directly to the CFE reaction to program protein synthesis. We demonstrate the ability to prototype gene expression, and quantitatively map aerobic cell-free metabolism in lysates from this system. We anticipate that the C. autoethanogenum CFE platform will not only expand the protein synthesis toolkit for synthetic biology, but also serve as a platform in expediting the screening and prototyping of gene regulatory elements in non-model, industrially relevant microbes.
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33
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Kochetkova TV, Mardanov AV, Sokolova TG, Bonch-Osmolovskaya EA, Kublanov IV, Kevbrin VV, Beletsky AV, Ravin NV, Lebedinsky AV. The first crenarchaeon capable of growth by anaerobic carbon monoxide oxidation coupled with H2 production. Syst Appl Microbiol 2020; 43:126064. [DOI: 10.1016/j.syapm.2020.126064] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2019] [Revised: 12/01/2019] [Accepted: 12/13/2019] [Indexed: 12/12/2022]
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34
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Mohr T, Infantes A, Biebinger L, de Maayer P, Neumann A. Acetogenic Fermentation From Oxygen Containing Waste Gas. Front Bioeng Biotechnol 2020; 7:433. [PMID: 31921833 PMCID: PMC6932952 DOI: 10.3389/fbioe.2019.00433] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2019] [Accepted: 12/05/2019] [Indexed: 11/24/2022] Open
Abstract
The microbial production of bulk chemicals from waste gas is becoming a pertinent alternative to industrial strategies that rely on fossil fuels as substrate. Acetogens can use waste gas substrates or syngas (CO, CO2, H2) to produce chemicals, such as acetate or ethanol, but as the feed gas often contains oxygen, which inhibits acetogen growth and product formation, a cost-prohibitive chemical oxygen removal step is necessary. Here, we have developed a two-phase microbial system to facilitate acetate production using a gas mixture containing CO and O2. In the first phase the facultative anaerobic carboxydotroph Parageobacillus thermoglucosidasius was used to consume residual O2 and produce H2 and CO2, which was subsequently utilized by the acetogen Clostridium ljungdahlii for the production of acetate. From a starting amount of 3.3 mmol of CO, 0.52 mmol acetate was produced in the second phase by C. ljungdahlii. In this set-up, the yield achieved was 0.16 mol acetate/mol CO, a 63% of the theoretical maximum. This system has the potential to be developed for the production of a broad range of bulk chemicals from oxygen-containing waste gas by using P. thermoglucosidasius as an oxygen scrubbing tool.
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Affiliation(s)
- Teresa Mohr
- Technical Biology, Institute of Process Engineering in Life Science, Karlsruhe Institute of Technology, Karlsruhe, Germany
| | - Alba Infantes
- Technical Biology, Institute of Process Engineering in Life Science, Karlsruhe Institute of Technology, Karlsruhe, Germany
| | - Lars Biebinger
- Technical Biology, Institute of Process Engineering in Life Science, Karlsruhe Institute of Technology, Karlsruhe, Germany
| | - Pieter de Maayer
- Faculty of Science, School of Molecular & Cell Biology, University of the Witwatersrand, Johannesburg, South Africa
| | - Anke Neumann
- Technical Biology, Institute of Process Engineering in Life Science, Karlsruhe Institute of Technology, Karlsruhe, Germany
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35
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Utturkar S, Dassanayake A, Nagaraju S, Brown SD. Bacterial Differential Expression Analysis Methods. Methods Mol Biol 2020; 2096:89-112. [PMID: 32720149 DOI: 10.1007/978-1-0716-0195-2_8] [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] [Indexed: 12/13/2022]
Abstract
RNA-Seq examines global gene expression to provide insights into cellular processes, and it can be particularly informative when comparing contrasting physiological states or strains. Although relatively routine in many laboratories, there are many steps involved in performing a transcriptomics experiment to ensure representative and high-quality results are generated for analysis. In this chapter, we present the application of widely used bioinformatic methodologies to assess, trim, and filter RNA-seq reads for quality using FastQC and Trim Galore, respectively. High-quality reads are mapped using Bowtie2 and differentially expressed genes across different groups were estimated using the DEseq2 R-Bioconductor package. In addition, we describe the various steps to perform the sample-wise data quality assessment by generating exploratory plots through the DESeq2 package. Simple steps to calculate the significant differentially expressed genes, up- and down-regulated genes, and exporting the data and images are also included. A Venn diagram is a useful method to compare the differentially expressed genes across various comparisons and steps to generate the Venn diagram from DESeq2 results are provided. Finally, the output from DESeq2 is compared to published results from EdgeR. The Clostridium autoethanogenum data are published and publicly available.
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Affiliation(s)
- Sagar Utturkar
- Purdue University Center for Cancer Research, West Lafayette, IN, USA
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36
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Stoll IK, Boukis N, Sauer J. Syngas Fermentation to Alcohols: Reactor Technology and Application Perspective. CHEM-ING-TECH 2020. [DOI: 10.1002/cite.201900118] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- I. Katharina Stoll
- Karlsruhe Institute of Technology (KIT)Institute of Catalysis Research and Technology (IKFT) Hermann-von-Helmholtz-Platz 1 76344 Eggenstein-Leopoldshafen Germany
| | - Nikolaos Boukis
- Karlsruhe Institute of Technology (KIT)Institute of Catalysis Research and Technology (IKFT) Hermann-von-Helmholtz-Platz 1 76344 Eggenstein-Leopoldshafen Germany
| | - Jörg Sauer
- Karlsruhe Institute of Technology (KIT)Institute of Catalysis Research and Technology (IKFT) Hermann-von-Helmholtz-Platz 1 76344 Eggenstein-Leopoldshafen Germany
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37
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Van Hecke W, Bockrath R, De Wever H. Effects of moderately elevated pressure on gas fermentation processes. BIORESOURCE TECHNOLOGY 2019; 293:122129. [PMID: 31558339 DOI: 10.1016/j.biortech.2019.122129] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/25/2019] [Revised: 09/04/2019] [Accepted: 09/05/2019] [Indexed: 06/10/2023]
Abstract
Industrial biotechnology has a potential to tackle harmful CO2 emissions and turn CO2 into a valuable commodity. However, a major technical obstacle in gas fermentations is the limited gas mass transfer rate. Increasing system pressure is a way to increase the driving force for mass transfer. This review presents critical aspects of gas fermentation at elevated pressure, with a specific focus on results obtained at 5-10 bar. While a solid foundation for high pressure fermentations has already been laid in the past, mainly to enhance oxygen transfer rates, it can be concluded that fermentations at moderately elevated pressures using gases such as CO2, CH4, CO, H2, O2 are still underexplored. Microbial growth rates and product formation can be improved at higher pressures, but in general, titers and productivities need to be increased to allow a further industrialization. Hence, more systematic investigations and techno-economic assessments are required.
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Affiliation(s)
- Wouter Van Hecke
- Separation and Conversion Technology, Flemish Institute for Technological Research (VITO), Boeretang 200, Mol, Belgium
| | | | - Heleen De Wever
- Separation and Conversion Technology, Flemish Institute for Technological Research (VITO), Boeretang 200, Mol, Belgium.
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38
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Renewable methanol and formate as microbial feedstocks. Curr Opin Biotechnol 2019; 62:168-180. [PMID: 31733545 DOI: 10.1016/j.copbio.2019.10.002] [Citation(s) in RCA: 140] [Impact Index Per Article: 28.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2019] [Revised: 09/23/2019] [Accepted: 10/01/2019] [Indexed: 12/20/2022]
Abstract
Methanol and formate are attractive microbial feedstocks as they can be sustainably produced from CO2 and renewable energy, are completely miscible, and are easy to store and transport. Here, we provide a biochemical perspective on microbial growth and bioproduction using these compounds. We show that anaerobic growth of acetogens on methanol and formate is more efficient than on H2/CO2 or CO. We analyze the aerobic C1 assimilation pathways and suggest that new-to-nature routes could outperform their natural counterparts. We further discuss practical bioprocessing aspects related to growth on methanol and formate, including feedstock toxicity. While challenges in realizing sustainable production from methanol and formate still exist, the utilization of these feedstocks paves the way towards a truly circular carbon economy.
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39
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Grand Research Challenges for Sustainable Industrial Biotechnology. Trends Biotechnol 2019; 37:1042-1050. [DOI: 10.1016/j.tibtech.2019.04.002] [Citation(s) in RCA: 67] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2019] [Revised: 04/02/2019] [Accepted: 04/03/2019] [Indexed: 01/23/2023]
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40
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Norman RO, Millat T, Schatschneider S, Henstra AM, Breitkopf R, Pander B, Annan FJ, Piatek P, Hartman HB, Poolman MG, Fell DA, Winzer K, Minton NP, Hodgman C. Genome‐scale model of
C. autoethanogenum
reveals optimal bioprocess conditions for high‐value chemical production from carbon monoxide. ENGINEERING BIOLOGY 2019. [DOI: 10.1049/enb.2018.5003] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Affiliation(s)
- Rupert O.J. Norman
- Synthetic Biology Research CentreUniversity of Nottingham, University ParkNottinghamNG7 2RDUK
- School of BiosciencesUniversity of NottinghamSutton Bonington Campus, Sutton BoningtonLeicestershireLE12 5RDUK
| | - Thomas Millat
- Synthetic Biology Research CentreUniversity of Nottingham, University ParkNottinghamNG7 2RDUK
| | - Sarah Schatschneider
- Synthetic Biology Research CentreUniversity of Nottingham, University ParkNottinghamNG7 2RDUK
- Evonik Nutrition and Care GmbHKantstr. 233798Halle‐KinsbeckGermany
| | - Anne M. Henstra
- Synthetic Biology Research CentreUniversity of Nottingham, University ParkNottinghamNG7 2RDUK
| | - Ronja Breitkopf
- Synthetic Biology Research CentreUniversity of Nottingham, University ParkNottinghamNG7 2RDUK
| | - Bart Pander
- Synthetic Biology Research CentreUniversity of Nottingham, University ParkNottinghamNG7 2RDUK
| | - Florence J. Annan
- Synthetic Biology Research CentreUniversity of Nottingham, University ParkNottinghamNG7 2RDUK
| | - Pawel Piatek
- Synthetic Biology Research CentreUniversity of Nottingham, University ParkNottinghamNG7 2RDUK
| | - Hassan B. Hartman
- Department of Biology and Medical SciencesOxford Brookes UniversityOxfordOX3 0BPUK
- Public Health England61 Colindale AvenueLondonNW9 5EQUK
| | - Mark G. Poolman
- Department of Biology and Medical SciencesOxford Brookes UniversityOxfordOX3 0BPUK
| | - David A. Fell
- Department of Biology and Medical SciencesOxford Brookes UniversityOxfordOX3 0BPUK
| | - Klaus Winzer
- Synthetic Biology Research CentreUniversity of Nottingham, University ParkNottinghamNG7 2RDUK
| | - Nigel P. Minton
- Synthetic Biology Research CentreUniversity of Nottingham, University ParkNottinghamNG7 2RDUK
| | - Charlie Hodgman
- Synthetic Biology Research CentreUniversity of Nottingham, University ParkNottinghamNG7 2RDUK
- School of BiosciencesUniversity of NottinghamSutton Bonington Campus, Sutton BoningtonLeicestershireLE12 5RDUK
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41
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Pinu FR, Goldansaz SA, Jaine J. Translational Metabolomics: Current Challenges and Future Opportunities. Metabolites 2019; 9:E108. [PMID: 31174372 PMCID: PMC6631405 DOI: 10.3390/metabo9060108] [Citation(s) in RCA: 104] [Impact Index Per Article: 20.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2019] [Revised: 06/04/2019] [Accepted: 06/04/2019] [Indexed: 02/06/2023] Open
Abstract
Metabolomics is one of the latest omics technologies that has been applied successfully in many areas of life sciences. Despite being relatively new, a plethora of publications over the years have exploited the opportunities provided through this data and question driven approach. Most importantly, metabolomics studies have produced great breakthroughs in biomarker discovery, identification of novel metabolites and more detailed characterisation of biological pathways in many organisms. However, translation of the research outcomes into clinical tests and user-friendly interfaces has been hindered due to many factors, some of which have been outlined hereafter. This position paper is the summary of discussion on translational metabolomics undertaken during a peer session of the Australian and New Zealand Metabolomics Conference (ANZMET 2018) held in Auckland, New Zealand. Here, we discuss some of the key areas in translational metabolomics including existing challenges and suggested solutions, as well as how to expand the clinical and industrial application of metabolomics. In addition, we share our perspective on how full translational capability of metabolomics research can be explored.
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Affiliation(s)
- Farhana R Pinu
- The New Zealand Institute for Plant and Food Research, Private Bag 92169, Auckland 1142, New Zealand.
| | - Seyed Ali Goldansaz
- Department of Agriculture, Food and Nutritional Sciences, University of Alberta, Edmonton, AB T6G 2P5, Canada.
- Department of Biological Sciences, University of Alberta, Edmonton, AB T6G 2E9, Canada.
| | - Jacob Jaine
- Analytica Laboratories Ltd., Ruakura Research Centre, Hamilton 3216, New Zealand.
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42
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History, Current State, and Emerging Applications of Industrial Biotechnology. ADVANCES IN BIOCHEMICAL ENGINEERING/BIOTECHNOLOGY 2019; 173:13-51. [PMID: 30671594 DOI: 10.1007/10_2018_81] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
The past 150 years have seen remarkable discoveries, rapidly growing biological knowledge, and giant technological leaps providing biotechnological solutions for healthcare, food production, and other societal needs. Genetic engineering, miniaturization, and ever-increasing computing power, in particular, have been key technological drivers for the past few decades. Looking ahead, the eventual transition from fossil resources to biomass and CO2 demands a shift toward a 'bio-economy' based on novel production processes and engineered organisms.
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43
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Cheng HH, Syu JC, Tien SY, Whang LM. Biological acetate production from carbon dioxide by Acetobacterium woodii and Clostridium ljungdahlii: The effect of cell immobilization. BIORESOURCE TECHNOLOGY 2018; 262:229-234. [PMID: 29709841 DOI: 10.1016/j.biortech.2018.04.069] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/27/2018] [Revised: 04/16/2018] [Accepted: 04/17/2018] [Indexed: 06/08/2023]
Abstract
This study investigated the acetate production from gas mixture of hydrogen (H2) and carbon dioxide (CO2) in the ratio of 7:3 using two acetogens: Acetobacterium woodii and Clostridium ljungdahlii. Batch result shows A. woodii performed two-phase degradation with the presence of glucose that lactate was produced from glucose and was reutilized for the production of butyrate and few acetate, while only acetate was detected when providing gas mixture. C. ljungdahlii produced butyrate and ethanol along with acetate when glucose was introduced, while only ethanol and acetate were found by feeding gas mixture. The acetate-to-ethanol (A/E) ratio can be enhanced by cell immobilization, while GAC immobilization produced only acetate and the production rate reached 0.072 mmol/d under fed-batch operation. Acetate production rate increased from 18 to 28 mmol/L/d with GAC immobilization when gas flowrate increased from 100 to 300 mL/min in anaerobic fluidized membrane bioreactor (AFMBR), and a highest A/E ratio of 30 implies the possible application of acetate recovery from H2 and CO2.
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Affiliation(s)
- Hai-Hsuan Cheng
- Department of Environmental Engineering, National Cheng Kung University, No. 1, University Road, Tainan 701, Taiwan
| | - Jyun-Cyuan Syu
- Department of Environmental Engineering, National Cheng Kung University, No. 1, University Road, Tainan 701, Taiwan
| | - Shih-Yuan Tien
- Department of Environmental Engineering, National Cheng Kung University, No. 1, University Road, Tainan 701, Taiwan
| | - Liang-Ming Whang
- Department of Environmental Engineering, National Cheng Kung University, No. 1, University Road, Tainan 701, Taiwan; Sustainable Environment Research Center (SERC), National Cheng Kung University, No. 1, University Road, Tainan 701, Taiwan; Research Center for Energy Technology and Strategy (RCETS), National Cheng Kung University, No. 1, University Road, Tainan 701, Taiwan.
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44
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Takors R, Kopf M, Mampel J, Bluemke W, Blombach B, Eikmanns B, Bengelsdorf FR, Weuster-Botz D, Dürre P. Using gas mixtures of CO, CO 2 and H 2 as microbial substrates: the do's and don'ts of successful technology transfer from laboratory to production scale. Microb Biotechnol 2018; 11:606-625. [PMID: 29761637 PMCID: PMC6011938 DOI: 10.1111/1751-7915.13270] [Citation(s) in RCA: 88] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2018] [Revised: 03/26/2018] [Accepted: 03/28/2018] [Indexed: 01/26/2023] Open
Abstract
The reduction of CO2 emissions is a global effort which is not only supported by the society and politicians but also by the industry. Chemical producers worldwide follow the strategic goal to reduce CO2 emissions by replacing existing fossil-based production routes with sustainable alternatives. The smart use of CO and CO2 /H2 mixtures even allows to produce important chemical building blocks consuming the said gases as substrates in carboxydotrophic fermentations with acetogenic bacteria. However, existing industrial infrastructure and market demands impose constraints on microbes, bioprocesses and products that require careful consideration to ensure technical and economic success. The mini review provides scientific and industrial facets finally to enable the successful implementation of gas fermentation technologies in the industrial scale.
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Affiliation(s)
- Ralf Takors
- Institute of Biochemical Engineering, University of Stuttgart, Allmandring 31, 70569, Stuttgart, Germany
| | - Michael Kopf
- BASF SE, Bio-Process Development, Carl-Bosch-Str. 38, 67056, Ludwigshafen, Germany
| | - Joerg Mampel
- BRAIN AG, Darmstädter Straße 34-36, 64673, Zwingenberg, Germany
| | - Wilfried Bluemke
- Evonik Technology and Infrastructure GmbH, Process Technology & Engineering, Rodenbacher Chaussee 4, 63457, Hanau-Wolfgang, Germany
| | - Bastian Blombach
- Institute of Biochemical Engineering, University of Stuttgart, Allmandring 31, 70569, Stuttgart, Germany
| | - Bernhard Eikmanns
- Institute of Microbiology and Biotechnology, University of Ulm, Albert-Einstein-Allee 11, 89081, Ulm, Germany
| | - Frank R Bengelsdorf
- Institute of Microbiology and Biotechnology, University of Ulm, Albert-Einstein-Allee 11, 89081, Ulm, Germany
| | - Dirk Weuster-Botz
- Department of Mechanical Engineering, Institute of Biochemical Engineering, Technical University of Munich, Boltzmannstr. 15, 85748, Garching, Germany
| | - Peter Dürre
- Institute of Microbiology and Biotechnology, University of Ulm, Albert-Einstein-Allee 11, 89081, Ulm, Germany
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45
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Overcoming the energetic limitations of syngas fermentation. Curr Opin Chem Biol 2017; 41:84-92. [DOI: 10.1016/j.cbpa.2017.10.003] [Citation(s) in RCA: 44] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2017] [Revised: 09/28/2017] [Accepted: 10/03/2017] [Indexed: 01/05/2023]
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