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Mazzoli R, Pescarolo S, Gilli G, Gilardi G, Valetti F. Hydrogen production pathways in Clostridia and their improvement by metabolic engineering. Biotechnol Adv 2024; 73:108379. [PMID: 38754796 DOI: 10.1016/j.biotechadv.2024.108379] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2023] [Revised: 05/13/2024] [Accepted: 05/13/2024] [Indexed: 05/18/2024]
Abstract
Biological production of hydrogen has a tremendous potential as an environmentally sustainable technology to generate a clean fuel. Among the different available methods to produce biohydrogen, dark fermentation features the highest productivity and can be used as a means to dispose of organic waste biomass. Within this approach, Clostridia have the highest theoretical H2 production yield. Nonetheless, most strains show actual yields far lower than the theoretical maximum: improving their efficiency becomes necessary for achieving cost-effective fermentation processes. This review aims at providing a survey of the metabolic network involved in H2 generation in Clostridia and strategies used to improve it through metabolic engineering. Together with current achievements, a number of future perspectives to implement these results will be illustrated.
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Affiliation(s)
- Roberto Mazzoli
- Structural and Functional Biochemistry, Laboratory of Proteomics and Metabolic Engineering of Prokaryotes, Department of Life Sciences and Systems Biology, University of Torino, Via Accademia Albertina 13, 10123 Torino, Italy.
| | - Simone Pescarolo
- Biology applied to the environment, Laboratories of microbiology and ecotoxicology, Ecobioqual, Environment Park. Via Livorno 60, 10144 Torino, Italy
| | - Giorgio Gilli
- Department of Sciences of Public Health and Pediatrics, School of Medicine, University of Torino, Via Santena 5 bis, 10126 Torino, Italy
| | - Gianfranco Gilardi
- Structural and Functional Biochemistry, Laboratory of Proteomics and Metabolic Engineering of Prokaryotes, Department of Life Sciences and Systems Biology, University of Torino, Via Accademia Albertina 13, 10123 Torino, Italy
| | - Francesca Valetti
- Structural and Functional Biochemistry, Laboratory of Proteomics and Metabolic Engineering of Prokaryotes, Department of Life Sciences and Systems Biology, University of Torino, Via Accademia Albertina 13, 10123 Torino, Italy.
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2
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Dai K, Qu C, Li X, Lan Y, Fu H, Wang J. Cofactor engineering in Thermoanaerobacterium aotearoense SCUT27 for maximizing ethanol yield and revealing an enzyme complex with high ferredoxin-NAD + reductase activity. BIORESOURCE TECHNOLOGY 2024; 402:130784. [PMID: 38701976 DOI: 10.1016/j.biortech.2024.130784] [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: 02/28/2024] [Revised: 04/03/2024] [Accepted: 04/30/2024] [Indexed: 05/06/2024]
Abstract
Thermoanaerobacterium aotearoense SCUT27 is a prominent producer of biofuels from lignocellulosic materials. To provide sufficient NAD(P)H for ethanol production, redox-related genes, including lactate dehydrogenase (ldh), redox-sensing transcriptional repressor (rex), and hydrogenase (hfsB), were knocked out. However, the growth of strain PRH (Δldh/Δrex/ΔhfsB) was suppressed due to the intracellular redox state imbalance with the increased NADH concentration. Coincidentally, when the Bcd-EtfAB (BCD) complex was overexpressed, the resulting strain PRH-B3 (Δldh/Δrex/ΔhfsB::BCD) grew rapidly and produced ethanol with a high yield. With lignocellulosic hydrolysates, PRH-BA (Δldh/Δrex/ΔhfsB::BCD::adhE) demonstrated high ethanol productivity and yield, reaching levels of 0.45-0.51 g/L/h and 0.46-0.53 g/g sugars, respectively. The study results shed light on the cofactor balance for cell stability and the high ferredoxin-NAD+ reductase activity of the BCD complex under an intracellular low redox state. They also provide an essential reference for developing strains for improved biofuel production.
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Affiliation(s)
- Kaiqun Dai
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510006, China
| | - Chunyun Qu
- College of Light Industry and Food Science, Guangdong Provincial Key Laboratory of Science and Technology of Lingnan Special Food Science and Technology, Zhongkai University of Agriculture and Engineering, Guangzhou 510225, China
| | - Xin Li
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510006, China
| | - Yang Lan
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510006, China
| | - Hongxin Fu
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510006, China; Guangdong Provincial Key Laboratory of Fermentation and Enzyme Engineering, South China University of Technology, Guangzhou 510006, China; State Key Laboratory of Pulp and Paper Engineering, South China University of Technology, Guangzhou 510006, China.
| | - Jufang Wang
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510006, China; Guangdong Provincial Key Laboratory of Fermentation and Enzyme Engineering, South China University of Technology, Guangzhou 510006, China; State Key Laboratory of Pulp and Paper Engineering, South China University of Technology, Guangzhou 510006, China.
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3
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Joseph RC, Sandoval NR. Single and multiplexed gene repression in solventogenic Clostridium via Cas12a-based CRISPR interference. Synth Syst Biotechnol 2022; 8:148-156. [PMID: 36687471 PMCID: PMC9842803 DOI: 10.1016/j.synbio.2022.12.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2022] [Revised: 11/28/2022] [Accepted: 12/20/2022] [Indexed: 12/25/2022] Open
Abstract
The Gram-positive, spore-forming, obligate anaerobic firmicute species that make up the Clostridium genus have broad feedstock consumption capabilities and produce value-added metabolic products, but genetic manipulation is difficult, limiting their broad appeal. CRISPR-Cas systems have recently been applied to Clostridium species, primarily using Cas9 as a counterselection marker in conjunction with plasmid-based homologous recombination. CRISPR interference is a method that reduces gene expression of specific genes via precision targeting of a nuclease deficient Cas effector protein. Here, we develop a dCas12a-based CRISPR interference system for transcriptional gene repression in multiple mesophilic Clostridium species. We show the Francisella novicida Cas12a-based system has a broader applicability due to the low GC content in Clostridium species compared to CRISPR Cas systems derived from other bacteria. We demonstrate >99% reduction in transcript levels of targeted genes in Clostridium acetobutylicum and >75% reduction in Clostridium pasteurianum. We also demonstrate multiplexed repression via use of a single synthetic CRISPR array, achieving 99% reduction in targeted gene expression and elucidating a unique metabolic profile for their reduced expression. Overall, this work builds a foundation for high throughput genetic screens without genetic editing, a key limitation in current screening methods used in the Clostridium community.
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Affiliation(s)
| | - Nicholas R. Sandoval
- Corresponding author. Department of Chemical and Biomolecular Engineering, Tulane University, St. Charles Ave, New Orleans, LA, 70118, United States.
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Mechanistic modeling of redox balance effects on the fermentation of eucalyptus wood-derived xylose to acetone-butanol-ethanol. Biochem Eng J 2022. [DOI: 10.1016/j.bej.2022.108738] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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5
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Giri DD, Dwivedi H, Khalaf D Alsukaibi A, Pal DB, Otaibi AA, Areeshi MY, Haque S, Gupta VK. Sustainable production of algae-bacteria granular consortia based biological hydrogen: New insights. BIORESOURCE TECHNOLOGY 2022; 352:127036. [PMID: 35331885 DOI: 10.1016/j.biortech.2022.127036] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/06/2022] [Revised: 03/15/2022] [Accepted: 03/17/2022] [Indexed: 06/14/2023]
Abstract
Microbes recycling nutrient and detoxifying ecosystems are capable to fulfil the future energy need by producing biohydrogen by due to the coupling of autotrophic and heterotrophic microbes. In granules microbes mutualy exchanging nutrients and electrons for hydrogen production. The consortial biohydrogen production depend upon constituent microbes, their interdependence, competition for resources, and other operating parameters while remediating a waste material in nature or bioreactor. The present review deals with development of granular algae-bacteria consortia, hydrogen yield in coculture, important enzymes and possible engineering for improved hydrogen production.
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Affiliation(s)
- Deen Dayal Giri
- Department of Botany, Maharaj Singh College, Saharanpur-247001,Uttar Pradesh, India
| | - Himanshu Dwivedi
- Department of Botany, Maharaj Singh College, Saharanpur-247001,Uttar Pradesh, India
| | | | - Dan Bahadur Pal
- Department of Chemical Engineering, Birla Institute of Technology, Mesra, Ranchi-835215, Jharkhand, India
| | - Ahmed Al Otaibi
- Department of Chemistry, College of Sciences, University of Ha'il, Ha'il 2440, Saudi Arabia
| | - Mohammed Y Areeshi
- Research and Scientific Studies Unit, College of Nursing, Jazan University, Jazan 45142, Saudi Arabia; Medical Laboratory Technology Department, College of Applied Medical Sciences, Jazan University, Jazan 45142, Saudi Arabia
| | - Shafiul Haque
- Research and Scientific Studies Unit, College of Nursing, Jazan University, Jazan 45142, Saudi Arabia; Bursa Uludağ University Faculty of Medicine,Görükle Campus, 16059, Nilüfer, Bursa, Turkey
| | - Vijai Kumar Gupta
- Center for Safe and Improved Food, SRUC, Kings Buildings, West Mains Road, Edinburgh, EH9 3JG, UK; Biorefining and Advanced Materials Research Center, SRUC, Kings Buildings, West Mains Road, Edinburgh, EH9 3JG, UK.
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6
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Bai SK, Hong Y, Wu YR. Emerging technologies for genetic modification of solventogenic clostridia: From tool to strategy development. BIORESOURCE TECHNOLOGY 2021; 334:125222. [PMID: 33951568 DOI: 10.1016/j.biortech.2021.125222] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/05/2021] [Revised: 04/20/2021] [Accepted: 04/21/2021] [Indexed: 06/12/2023]
Abstract
Solventogenic clostridia has been considered as one of the most potential microbial cell factories for biofuel production in the biorefinery industry. However, the inherent shortcomings of clostridia strains such as low productivity, by-products formation and toxic tolerance still strongly restrict the large-scale application. Therefore, concerns regarding the genetic modification of solventogenic clostridia have spurred interests into the development of modern gene-editing tools. In this review, we summarize the latest advances of genetic tools involved in modifying solventogenic clostridia. Following a systematic comparison on their respective characteristics, we then review the corresponding strategies for overcoming the obstacles to the enhanced production. Discussing the progress of other microbial cell factories for solventogenesis, we finally describe the key challenges and trends with valuable recommendations for future large-scale biosolvent industrial application.
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Affiliation(s)
- Sheng-Kai Bai
- Department of Biology, Shantou University, Shantou, Guangdong 515063, China
| | - Ying Hong
- Department of Biology, Shantou University, Shantou, Guangdong 515063, China
| | - Yi-Rui Wu
- Department of Biology, Shantou University, Shantou, Guangdong 515063, China; Guangdong Provincial Key Laboratory of Marine Biotechnology, Shantou University, Shantou, Guangdong 515063, China; Institute of Marine Sciences, Shantou University, Shantou, Guangdong 515063, China.
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Zhang Y, Li J, Meng J, Sun K, Yan H. A neutral red mediated electro-fermentation system of Clostridium beijerinckii for effective co-production of butanol and hydrogen. BIORESOURCE TECHNOLOGY 2021; 332:125097. [PMID: 33845318 DOI: 10.1016/j.biortech.2021.125097] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/01/2021] [Revised: 03/25/2021] [Accepted: 03/26/2021] [Indexed: 06/12/2023]
Abstract
To enhance the co-production of butanol and hydrogen by the acetone-butanol-ethanol (ABE) fermentation of Clostridium beijerinckii, a novel cathodic electro-fermentation (CEF) system was constructed with neutral red (NR) as electron mediator. With the mediation of NR, production of butanol and hydrogen from glucose in the CEF system achieved 5.49 ± 0.28 g/L and 3.74 ± 0.16 L/L, 569.5% and 325.0% higher than that in the open circuit (OC) system, respectively. The butanol and hydrogen yield of 0.30 ± 0.02 g/g and 206.53 ± 8.20 mL/g was 172.7% and 71.4% higher than that in the OC system, respectively. The effective co-production of butanol and hydrogen in the NR-mediated CEF system was attributed to the cooperation of the introduced polarized electrode and the additional NR. With the control of the polarized electrode, a feasible ORP was available for the effective hydrogen production. And the additional NR had induced more carbon source and electrons to the synthesis of butanol.
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Affiliation(s)
- Yafei Zhang
- State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology, 73 Huanghe Road, Harbin 150090, China
| | - Jianzheng Li
- State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology, 73 Huanghe Road, Harbin 150090, China
| | - Jia Meng
- State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology, 73 Huanghe Road, Harbin 150090, China.
| | - Kai Sun
- State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology, 73 Huanghe Road, Harbin 150090, China
| | - Han Yan
- State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology, 73 Huanghe Road, Harbin 150090, China
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8
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Zhang Y, Li J, Meng J, Wang X. A cathodic electro-fermentation system for enhancing butyric acid production from rice straw with a mixed culture. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 767:145011. [PMID: 33636772 DOI: 10.1016/j.scitotenv.2021.145011] [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: 08/31/2020] [Revised: 12/24/2020] [Accepted: 12/29/2020] [Indexed: 06/12/2023]
Abstract
Bio-electrochemical system (BES) emerges as a versatile approach to handling environmental problems with the harvest of sustainable energy and value-added chemicals. To enhance the butyric acid production from rice straw, microbial fuel cell (MFC) and cathodic electro-fermentation (CEF) systems were constructed in this study. Inoculated with the same mixed culture, fermentative butyric acid production efficiency of the two BESs were evaluated with/without neutral red (NR) as electron mediator, respectively. It was found that the butyric acid fermentation efficiency in the MFC system was inefficient. While, the CEF system presented an evident positive effect on butyric acid production. The production and specific yield of butyric acid in the CEF system reached 5.54 g/L and 0.41 g/g, higher than that in the open circuit (OC) system by 17.37% and 28.13%, respectively. Mass percentage of butyric acid in the produced total volatile fatty acids (VFAs) was also increased from 44.74% to 52.76%. The addition of NR had no positive effect on the butyric acid production, due to the low contribution of electric current to the end-products. With the cathode potential of -0.80 V (vs Ag/AgCl), relative abundance of the butyric acid fermenting bacteria (Clostridium cluster IV and cluster XIVa) in the microbial mixture was increased from 20.25% in the OC system to 33.61% in the CEF system. This research work not only presents a novel method for enhancing butyric acid production by rice straw fermentation, but also aids an understanding of the fermentation mechanism in CEF systems.
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Affiliation(s)
- Yafei Zhang
- State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, 73 Huanghe Road, Harbin 150090, China
| | - Jianzheng Li
- State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, 73 Huanghe Road, Harbin 150090, China
| | - Jia Meng
- State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, 73 Huanghe Road, Harbin 150090, China.
| | - Xin Wang
- State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, 73 Huanghe Road, Harbin 150090, China
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9
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Bao T, Hou W, Wu X, Lu L, Zhang X, Yang ST. Engineering Clostridium cellulovorans for highly selective n-butanol production from cellulose in consolidated bioprocessing. Biotechnol Bioeng 2021; 118:2703-2718. [PMID: 33844271 DOI: 10.1002/bit.27789] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2020] [Revised: 03/06/2021] [Accepted: 04/09/2021] [Indexed: 01/05/2023]
Abstract
Cellulosic n-butanol from renewable lignocellulosic biomass has gained increased interest. Previously, we have engineered Clostridium cellulovorans, a cellulolytic acidogen, to overexpress the bifunctional butyraldehyde/butanol dehydrogenase gene adhE2 from C. acetobutylicum for n-butanol production from crystalline cellulose. However, butanol production by this engineered strain had a relatively low yield of approximately 0.22 g/g cellulose due to the coproduction of ethanol and acids. We hypothesized that strengthening the carbon flux through the central butyryl-CoA biosynthesis pathway and increasing intracellular NADH availability in C. cellulovorans adhE2 would enhance n-butanol production. In this study, thiolase (thlACA ) from C. acetobutylicum and 3-hydroxybutyryl-CoA dehydrogenase (hbdCT ) from C. tyrobutyricum were overexpressed in C. cellulovorans adhE2 to increase the flux from acetyl-CoA to butyryl-CoA. In addition, ferredoxin-NAD(P)+ oxidoreductase (fnr), which can regenerate the intracellular NAD(P)H and thus increase butanol biosynthesis, was also overexpressed. Metabolic flux analyses showed that mutants overexpressing these genes had a significantly increased carbon flux toward butyryl-CoA, which resulted in increased production of butyrate and butanol. The addition of methyl viologen as an electron carrier in batch fermentation further directed more carbon flux towards n-butanol biosynthesis due to increased reducing equivalent or NADH. The engineered strain C. cellulovorans adhE2-fnrCA -thlACA -hbdCT produced n-butanol from cellulose at a 50% higher yield (0.34 g/g), the highest ever obtained in batch fermentation by any known bacterial strain. The engineered C. cellulovorans is thus a promising host for n-butanol production from cellulosic biomass in consolidated bioprocessing.
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Affiliation(s)
- Teng Bao
- William G. Lowrie Department of Chemical and Biomolecular Engineering, The Ohio State University, Columbus, Ohio, USA
| | - Wenjie Hou
- William G. Lowrie Department of Chemical and Biomolecular Engineering, The Ohio State University, Columbus, Ohio, USA.,College of Life Sciences, Northwest A&F University, Yangling, Shanxi, China
| | - Xuefeng Wu
- William G. Lowrie Department of Chemical and Biomolecular Engineering, The Ohio State University, Columbus, Ohio, USA.,School of Food and Biological Engineering, Hefei University of Technology, Hefei, China
| | - Li Lu
- William G. Lowrie Department of Chemical and Biomolecular Engineering, The Ohio State University, Columbus, Ohio, USA
| | - Xian Zhang
- William G. Lowrie Department of Chemical and Biomolecular Engineering, The Ohio State University, Columbus, Ohio, USA.,School of Biotechnology, Jiangnan University, Wuxi, China
| | - Shang-Tian Yang
- William G. Lowrie Department of Chemical and Biomolecular Engineering, The Ohio State University, Columbus, Ohio, USA
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De Anda V, Chen LX, Dombrowski N, Hua ZS, Jiang HC, Banfield JF, Li WJ, Baker BJ. Brockarchaeota, a novel archaeal phylum with unique and versatile carbon cycling pathways. Nat Commun 2021; 12:2404. [PMID: 33893309 PMCID: PMC8065059 DOI: 10.1038/s41467-021-22736-6] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2020] [Accepted: 03/18/2021] [Indexed: 02/02/2023] Open
Abstract
Geothermal environments, such as hot springs and hydrothermal vents, are hotspots for carbon cycling and contain many poorly described microbial taxa. Here, we reconstructed 15 archaeal metagenome-assembled genomes (MAGs) from terrestrial hot spring sediments in China and deep-sea hydrothermal vent sediments in Guaymas Basin, Gulf of California. Phylogenetic analyses of these MAGs indicate that they form a distinct group within the TACK superphylum, and thus we propose their classification as a new phylum, 'Brockarchaeota', named after Thomas Brock for his seminal research in hot springs. Based on the MAG sequence information, we infer that some Brockarchaeota are uniquely capable of mediating non-methanogenic anaerobic methylotrophy, via the tetrahydrofolate methyl branch of the Wood-Ljungdahl pathway and reductive glycine pathway. The hydrothermal vent genotypes appear to be obligate fermenters of plant-derived polysaccharides that rely mostly on substrate-level phosphorylation, as they seem to lack most respiratory complexes. In contrast, hot spring lineages have alternate pathways to increase their ATP yield, including anaerobic methylotrophy of methanol and trimethylamine, and potentially use geothermally derived mercury, arsenic, or hydrogen. Their broad distribution and their apparent anaerobic metabolic versatility indicate that Brockarchaeota may occupy previously overlooked roles in anaerobic carbon cycling.
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Affiliation(s)
- Valerie De Anda
- Department of Marine Science, University of Texas Austin, Port Aransas, TX, 78373, USA
| | - Lin-Xing Chen
- Department of Earth and Planetary Sciences, University of California, Berkeley, CA, USA
| | - Nina Dombrowski
- Department of Marine Science, University of Texas Austin, Port Aransas, TX, 78373, USA
- NIOZ, Royal Netherlands Institute for Sea Research, Department of Marine Microbiology and Biogeochemistry, and Utrecht University, Den Burg, Netherlands
| | - Zheng-Shuang Hua
- Department of Environmental Science and Engineering, University of Science and Technology of China, Hefei, PR China
| | - Hong-Chen Jiang
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Wuhan, People's Republic of China
| | - Jillian F Banfield
- Department of Earth and Planetary Sciences, University of California, Berkeley, CA, USA
- Department of Environmental Science, Policy and Management, University of California, Berkeley, CA, USA
| | - Wen-Jun Li
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou, People's Republic of China.
- State Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, People's Republic of China.
| | - Brett J Baker
- Department of Marine Science, University of Texas Austin, Port Aransas, TX, 78373, USA.
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Wu H, Yang J, Shen P, Li Q, Wu W, Jiang X, Qin L, Huang J, Cao X, Qi F. High-Level Production of Indole-3-acetic Acid in the Metabolically Engineered Escherichia coli. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2021; 69:1916-1924. [PMID: 33541074 DOI: 10.1021/acs.jafc.0c08141] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Indole-3-acetic acid (IAA) is a critical plant hormone that regulates cell division, development, and metabolism. IAA synthesis in plants and plant-associated microorganisms cannot fulfill the requirement for large-scale agricultural production. Here, two novel IAA biosynthesis pathways, tryptamine (TAM) and indole-3-acetamide (IAM), were developed for IAA production by whole-cell catalysis and de novo biosynthesis in an engineered Escherichia coli MG1655. When 10 g/L l-tryptophan was used as a substrate, an MIA-6 strain containing a heterologous IAM pathway had the highest IAA titer of 7.10 g/L (1.34 × 103 mg/g DCW), which was 98.4 times more than MTAI-5 containing the TAM pathway by whole-cell catalysis. De novo IAA biosynthesis was optimized by improving NAD(P)H availability, resulting in an increased IAA titer of 906 mg/L obtained by the MGΔadhE::icd strain, which is 29.7% higher than the control. These strategies exhibit the potential for IAA production in engineered E. coli and possible industrial applications.
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Affiliation(s)
- Hongxuan Wu
- Engineering Research Center of Industrial Microbiology of Ministry of Education, College of Life Sciences, Fujian Normal University, Fuzhou 350117, Fujian, China
| | - Jinhua Yang
- Engineering Research Center of Industrial Microbiology of Ministry of Education, College of Life Sciences, Fujian Normal University, Fuzhou 350117, Fujian, China
| | - Peijie Shen
- Engineering Research Center of Industrial Microbiology of Ministry of Education, College of Life Sciences, Fujian Normal University, Fuzhou 350117, Fujian, China
| | - Qingchen Li
- Provincial University Key Laboratory of Cellular Stress Response and Metabolic Regulation and Provincial University Engineering Research Center of Industrial Biocatalysis, Fujian Normal University, Fuzhou, Fujian 350117, China
| | - Weibin Wu
- Fujian Vocational College of Bio-engineering, Fuzhou, Fujian 350002, China
| | - Xianzhang Jiang
- Engineering Research Center of Industrial Microbiology of Ministry of Education, College of Life Sciences, Fujian Normal University, Fuzhou 350117, Fujian, China
| | - Lina Qin
- Engineering Research Center of Industrial Microbiology of Ministry of Education, College of Life Sciences, Fujian Normal University, Fuzhou 350117, Fujian, China
| | - Jianzhong Huang
- Engineering Research Center of Industrial Microbiology of Ministry of Education, College of Life Sciences, Fujian Normal University, Fuzhou 350117, Fujian, China
| | - Xiao Cao
- Fujian Vocational College of Bio-engineering, Fuzhou, Fujian 350002, China
| | - Feng Qi
- Engineering Research Center of Industrial Microbiology of Ministry of Education, College of Life Sciences, Fujian Normal University, Fuzhou 350117, Fujian, China
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12
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Optimization of the supply chain for the production of biomass-based fuels and high-added value products in Mexico. Comput Chem Eng 2021. [DOI: 10.1016/j.compchemeng.2020.107181] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
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13
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Li W, Cheng C, Cao G, Yang ST, Ren N. Comparative transcriptome analysis of Clostridium tyrobutyricum expressing a heterologous uptake hydrogenase. THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 749:142022. [PMID: 33370888 DOI: 10.1016/j.scitotenv.2020.142022] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/17/2020] [Revised: 08/25/2020] [Accepted: 08/25/2020] [Indexed: 06/12/2023]
Abstract
Clostridium tyrobutyricum is a promising microbial cell factory to produce biofuels. In this study, an uptake hydrogenase (hyd2293) from Ethanoligenens harbinense was overexpressed in C. tyrobutyricum and significantly affected the redox reactions and metabolic profiles. Compared to the parental strain (Ct-WT), the mutant strain Ct-Hyd2293 produced ~34% less butyrate, ~148% more acetate, and ~11% less hydrogen, accompanied by the emerging genesis of butanol. Comparative transcriptome analysis revealed that 666 genes were significantly differentially expressed after the overexpression of hyd2293, including 82 up-regulated genes and 584 down-regulated genes. The up-regulated genes were mainly involved in carbohydrate and energy metabolisms while the down-regulated genes were distributed in nearly all pathways. Genes involved in glucose transportation, glycolysis, different fermentation pathways and hydrogen metabolism were studied and the gene expression changes showed the mechanism of the metabolic flux redistribution in Ct-Hyd2293. The overexpression of uptake hydrogenase redirected electrons from hydrogen and butyrate to butanol. The key enzymes participating in the energy conservation and sporulation were also identified and their transcription levels were generally reduced. This study demonstrated the transcriptomic responses of C. tyrobutyricum to the expression of a heterologous uptake hydrogenase, which provided a better understanding of the metabolic characteristics of C. tyrobutyricum and demonstrated the potential role of redox manipulation in metabolic engineering for biofuel productions.
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Affiliation(s)
- Weiming Li
- State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Harbin 150090, China; Department of Chemical and Biomolecular Engineering, The Ohio State University, Columbus, OH 43210, USA
| | - Chi Cheng
- Department of Chemical and Biomolecular Engineering, The Ohio State University, Columbus, OH 43210, USA; School of Bioengineering, Dalian University of Technology, Dalian 116024, China
| | - Guangli Cao
- State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Harbin 150090, China
| | - Shang-Tian Yang
- Department of Chemical and Biomolecular Engineering, The Ohio State University, Columbus, OH 43210, USA
| | - Nanqi Ren
- State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Harbin 150090, China.
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Han S, Kim Y, Karanjikar M, San KY, Bennett GN. Genetic sensor-regulators functional in Clostridia. J Ind Microbiol Biotechnol 2020; 47:609-620. [DOI: 10.1007/s10295-020-02303-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2020] [Accepted: 08/18/2020] [Indexed: 11/30/2022]
Abstract
Abstract
This study addressed the functionality of genetic circuits carrying natural regulatory elements of Clostridium acetobutylicum ATCC 824 in the presence of the respective inducer molecules. Specifically, promoters and their regulators involved in diverse carbon source utilization were characterized using mCherryOpt or beta-galactosidase as a reporter. Consequently, most of the genetic circuits tested in this study were functional in Clostridium acetobutylicum ATCC 824 in the presence of an inducer, leading to the expression of reporter proteins. These genetic sensor-regulators were found to be transferable to another Clostridium species, such as Clostridium beijerinckii NCIMB 8052. The gradual expression of reporter protein was observed as a function of the carbohydrates of interest. A xylose-inducible promoter allows a titratable and robust expression of a reporter protein with stringency and efficacy. This xylose-inducible circuit was seen to enable induction of the expression of reporter proteins in the presence of actual sugar mixtures incorporated in woody hydrolysate wherein glucose and xylose are present as predominant carbon sources.
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Affiliation(s)
- SongI Han
- grid.21940.3e 0000 0004 1936 8278 Department of Bioengineering Rice University 77005 Houston TX USA
| | - Younghwan Kim
- grid.427405.0 Technology Holding LLC 84119 West Valley City UT USA
| | | | - Ka-Yiu San
- grid.21940.3e 0000 0004 1936 8278 Department of Bioengineering Rice University 77005 Houston TX USA
- grid.21940.3e 0000 0004 1936 8278 Department of Chemical and Biomolecular Engineering Rice University 77005 Houston TX USA
| | - George N Bennett
- grid.21940.3e 0000 0004 1936 8278 Department of Chemical and Biomolecular Engineering Rice University 77005 Houston TX USA
- grid.21940.3e 0000 0004 1936 8278 Department of BioSciences Rice University 77005 Houston TX USA
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15
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Karim AS, Dudley QM, Juminaga A, Yuan Y, Crowe SA, Heggestad JT, Garg S, Abdalla T, Grubbe WS, Rasor BJ, Coar DN, Torculas M, Krein M, Liew F, Quattlebaum A, Jensen RO, Stuart JA, Simpson SD, Köpke M, Jewett MC. In vitro prototyping and rapid optimization of biosynthetic enzymes for cell design. Nat Chem Biol 2020; 16:912-919. [DOI: 10.1038/s41589-020-0559-0] [Citation(s) in RCA: 93] [Impact Index Per Article: 23.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2019] [Revised: 04/10/2020] [Accepted: 05/06/2020] [Indexed: 01/27/2023]
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16
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The significance of aspartate on NAD(H) biosynthesis and ABE fermentation in Clostridium acetobutylicum ATCC 824. AMB Express 2019; 9:142. [PMID: 31506849 PMCID: PMC6737123 DOI: 10.1186/s13568-019-0874-6] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2019] [Accepted: 09/05/2019] [Indexed: 01/25/2023] Open
Abstract
The co-factor NADH plays an important role in butanol biosynthesis. In this study, we found that aspartate could effectively improve the butanol production of Clostridium acetobutylicum ATCC 824. Further study showed that aspartate could be used as the precursor of NADH de novo synthesis in C. acetobutylicum ATCC 824. When 2 g/L aspartate was added, the transcription levels of essential genes (nadA, nadB and nadC) for NADH de novo synthesis were significantly higher than that of without aspartate addition. The levels of intracellular NAD+, NADH, total NAD(H) and the ratio of NADH/NAD+ were also significantly increased, which were 63.9 ± 8.0%, 85.0 ± %, 77.7 ± 8.0% and 12.7 ± 2.9% higher than those of without aspartate addition, respectively. Furthermore, the butanol production was improved by overexpressing the NADH de novo synthesis genes, and the fermentation performance could be further enhanced by strengthening the VB1 biosynthesis and NADH de novo synthesis pathway simultaneously. As a result, the butanol titer of the engineered strain 824(thiCGE–nadC) reached 13.96 ± 0.11 g/L, 7.2 ± 0.4%, 18.1 ± 0.1%, 34.1 ± 0.1% higher than that of 824(thiCGE), 824(nadC) and the wild type strain, respectively. This study has a reference value for the NADH related researches of other microbes, and the engineering strategy used in this study provides a new idea for construction of efficient fuel-producing strains.
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Nimbalkar PR, Khedkar MA, Kulkarni RK, Chavan PV, Bankar SB. Strategic intensification in butanol production by exogenous amino acid supplementation: Fermentation kinetics and thermodynamic studies. BIORESOURCE TECHNOLOGY 2019; 288:121521. [PMID: 31154278 DOI: 10.1016/j.biortech.2019.121521] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/20/2019] [Revised: 05/17/2019] [Accepted: 05/18/2019] [Indexed: 06/09/2023]
Abstract
Amino acids are vital precursors in many biochemical production pathways in addition to efficient nitrogen source which could enhance microbial growth yields. Therefore, in present study, the effect of amino acids from aliphatic and aromatic family was comprehensively evaluated in batch and integrated fed batch fermentation system. Clostridium acetobutylicum NRRL B-527 was able to utilize 54.15 ± 1.0 g/L glucose to produce 12.43 ± 0.10 g/L butanol under batch cultivation. Interestingly, a significant step up in butanol titer (20.82 ± 0.33 g/L) was achieved by using fed-batch fermentation process integrated with liquid-liquid extraction module. Besides, mathematical modeling studies demonstrated the best fitting of experimental data with first order reaction kinetics. Overall, an enhancement in solvent titer by induction of essential cellular components coupled with advance bioprocess strategy was successfully utilized in this study for its further applications.
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Affiliation(s)
- Pranhita R Nimbalkar
- Department of Bioproducts and Biosystems, School of Chemical Engineering, Aalto University, P.O. Box 16100, FI-00076 Aalto, Finland; Department of Chemical Engineering, Bharati Vidyapeeth Deemed University College of Engineering, Pune 411043, India
| | - Manisha A Khedkar
- Department of Chemical Engineering, Bharati Vidyapeeth Deemed University College of Engineering, Pune 411043, India
| | - Rahul K Kulkarni
- Department of Chemical Engineering, Bharati Vidyapeeth Deemed University College of Engineering, Pune 411043, India
| | - Prakash V Chavan
- Department of Chemical Engineering, Bharati Vidyapeeth Deemed University College of Engineering, Pune 411043, India
| | - Sandip B Bankar
- Department of Bioproducts and Biosystems, School of Chemical Engineering, Aalto University, P.O. Box 16100, FI-00076 Aalto, Finland.
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18
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Systems Metabolic Engineering Strategies: Integrating Systems and Synthetic Biology with Metabolic Engineering. Trends Biotechnol 2019; 37:817-837. [DOI: 10.1016/j.tibtech.2019.01.003] [Citation(s) in RCA: 226] [Impact Index Per Article: 45.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2018] [Revised: 01/07/2019] [Accepted: 01/10/2019] [Indexed: 12/12/2022]
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