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Zheng Y, Zhang R, Chen M, Zhou Q, Wu Y, Xue W. Design, Synthesis, and Antibacterial Evaluation of Novel Isoindolin-1-ones Derivatives Containing Piperidine Fragments. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2024; 72:12434-12444. [PMID: 38775141 DOI: 10.1021/acs.jafc.3c09928] [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: 06/06/2024]
Abstract
A series of novel isoindoline-1-one derivatives containing piperidine moiety were designed and synthesized using natural compounds as raw materials, and their biological activities were tested for three bacterial and three fungal pathogens. These derivatives exhibited good against phytopathogenic bacteria activities against Pseudomonas syringae pv actinidiae (Psa) and Xanthomonas axonopodis pv.citri (Xac). Some compounds exhibited excellent antibacterial activities against Xanthomonas oryzae pv oryzae (Xoo). The dose of Y8 against Xoo (the maximum half lethal effective concentration (EC50) = 21.3 μg/mL) was better than that of the thiediazole copper dose (EC50 = 53.3 μg/mL). Excitingly, further studies have shown that the molecular docking of Y8 with 2FBW indicates that it can fully locate the interior of the binding pocket through hydrogen bonding and hydrophobic interactions, thereby enhancing its anti-Xoo activity. Scanning electron microscopy (SEM) studies revealed that Y8 induced the Xoo cell membrane collapse. Moreover, the proteomic results also indicate that Y8 may be a multifunctional candidate as it affects the formation of bacterial Xoo biofilms, thereby exerting antibacterial effects.
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Affiliation(s)
- Yuguo Zheng
- State Key Laboratory of Green Pesticide, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Center for R&D of Fine Chemical of Guizhou University, Huaxi District Guiyang 550025, China
- The Key Laboratory of Chemical Synthesis and Environmental Pollution Control-Remediation Technology of Guizhou Province, Xingyi Normal University for Nationalities, Xingyi 562400, China
| | - Renfeng Zhang
- The Key Laboratory of Chemical Synthesis and Environmental Pollution Control-Remediation Technology of Guizhou Province, Xingyi Normal University for Nationalities, Xingyi 562400, China
| | - Mei Chen
- The Key Laboratory of Chemical Synthesis and Environmental Pollution Control-Remediation Technology of Guizhou Province, Xingyi Normal University for Nationalities, Xingyi 562400, China
| | - Qing Zhou
- State Key Laboratory of Green Pesticide, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Center for R&D of Fine Chemical of Guizhou University, Huaxi District Guiyang 550025, China
| | - Yongjun Wu
- State Key Laboratory of Green Pesticide, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Center for R&D of Fine Chemical of Guizhou University, Huaxi District Guiyang 550025, China
| | - Wei Xue
- State Key Laboratory of Green Pesticide, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Center for R&D of Fine Chemical of Guizhou University, Huaxi District Guiyang 550025, China
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2
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A clean in-frame knockout system for gene deletion in Acetobacterium woodii. J Biotechnol 2022; 353:9-18. [PMID: 35659892 DOI: 10.1016/j.jbiotec.2022.05.013] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2022] [Revised: 05/27/2022] [Accepted: 05/28/2022] [Indexed: 11/24/2022]
Abstract
Acetogenic bacteria produce acetate following the fixation of CO2 via the Wood-Ljungdahl pathway. As such, they represent excellent process organisms for the production of novel chemicals and fuels from this waste greenhouse gas. Acetobacterium woodii is the model acetogen and numerous studies have been conducted investigating its biochemistry, gas consumption and use as a production chassis. However, there are a dearth of available tools for A. woodii gene modification which limits the research options available for genetic studies. Here, the previously proposed Clostridia Roadmap is implemented in A. woodii leading to the derivation of a knockout system for the generation of clean, in-frame deletions. The replicon of the Gram-positive plasmid pCD6 that originated in Clostridioides difficile was identified as being replication-defective in A. woodii, a property that was exploited to construct a pseudo-suicide knockout plasmid which was used to generate an auxotrophic, pyrE mutant. This allowed the subsequent use of a heterologous pyrE gene (from Clostridium acetobutylicum) as a counter selection marker and the deletion of a number of genes by allelic exchange. Specific mutants generated were affected in growth on glucose, fructose and ethanol as a consequence of deletion of fruA, pstG and adhE, respectively.
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Patakova P, Branska B, Vasylkivska M, Jureckova K, Musilova J, Provaznik I, Sedlar K. Transcriptomic studies of solventogenic clostridia, Clostridium acetobutylicum and Clostridium beijerinckii. Biotechnol Adv 2021; 58:107889. [PMID: 34929313 DOI: 10.1016/j.biotechadv.2021.107889] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2021] [Revised: 12/10/2021] [Accepted: 12/14/2021] [Indexed: 12/13/2022]
Abstract
Solventogenic clostridia are not a strictly defined group within the genus Clostridium but its representatives share some common features, i.e. they are anaerobic, non-pathogenic, non-toxinogenic and endospore forming bacteria. Their main metabolite is typically 1-butanol but depending on species and culture conditions, they can form other metabolites such as acetone, isopropanol, ethanol, butyric, lactic and acetic acids, and hydrogen. Although these organisms were previously used for the industrial production of solvents, they later fell into disuse, being replaced by more efficient chemical production. A return to a more biological production of solvents therefore requires a thorough understanding of clostridial metabolism. Transcriptome analysis, which reflects the involvement of individual genes in all cellular processes within a population, at any given (sampling) moment, is a valuable tool for gaining a deeper insight into clostridial life. In this review, we describe techniques to study transcription, summarize the evolution of these techniques and compare methods for data processing and visualization of solventogenic clostridia, particularly the species Clostridium acetobutylicum and Clostridium beijerinckii. Individual approaches for evaluating transcriptomic data are compared and their contributions to advancements in the field are assessed. Moreover, utilization of transcriptomic data for reconstruction of computational clostridial metabolic models is considered and particular models are described. Transcriptional changes in glucose transport, central carbon metabolism, the sporulation cycle, butanol and butyrate stress responses, the influence of lignocellulose-derived inhibitors on growth and solvent production, and other respective topics, are addressed and common trends are highlighted.
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Affiliation(s)
- Petra Patakova
- University of Chemistry and Technology Prague, Technicka 5, 16628 Prague 6, Czech Republic.
| | - Barbora Branska
- University of Chemistry and Technology Prague, Technicka 5, 16628 Prague 6, Czech Republic
| | - Maryna Vasylkivska
- University of Chemistry and Technology Prague, Technicka 5, 16628 Prague 6, Czech Republic
| | | | - Jana Musilova
- Brno University of Technology, Technicka 10, 61600 Brno, Czech Republic
| | - Ivo Provaznik
- Brno University of Technology, Technicka 10, 61600 Brno, Czech Republic
| | - Karel Sedlar
- Brno University of Technology, Technicka 10, 61600 Brno, Czech Republic
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4
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Wang Q, Al Makishah NH, Li Q, Li Y, Liu W, Sun X, Wen Z, Yang S. Developing Clostridia as Cell Factories for Short- and Medium-Chain Ester Production. Front Bioeng Biotechnol 2021; 9:661694. [PMID: 34164382 PMCID: PMC8215697 DOI: 10.3389/fbioe.2021.661694] [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: 01/31/2021] [Accepted: 04/19/2021] [Indexed: 11/21/2022] Open
Abstract
Short- and medium-chain volatile esters with flavors and fruity fragrances, such as ethyl acetate, butyl acetate, and butyl butyrate, are usually value-added in brewing, food, and pharmacy. The esters can be naturally produced by some microorganisms. As ester-forming reactions are increasingly deeply understood, it is possible to produce esters in non-natural but more potential hosts. Clostridia are a group of important industrial microorganisms since they can produce a variety of volatile organic acids and alcohols with high titers, especially butanol and butyric acid through the CoA-dependent carbon chain elongation pathway. This implies sufficient supplies of acyl-CoA, organic acids, and alcohols in cells, which are precursors for ester production. Besides, some Clostridia could utilize lignocellulosic biomass, industrial off-gas, or crude glycerol to produce other branched or straight-chain alcohols and acids. Therefore, Clostridia offer great potential to be engineered to produce short- and medium-chain volatile esters. In the review, the efforts to produce esters from Clostridia via in vitro lipase-mediated catalysis and in vivo alcohol acyltransferase (AAT)-mediated reaction are comprehensively revisited. Besides, the advantageous characteristics of several Clostridia and clostridial consortia for bio-ester production and the driving force of synthetic biology to clostridial chassis development are also discussed. It is believed that synthetic biotechnology should enable the future development of more effective Clostridia for ester production.
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Affiliation(s)
- Qingzhuo Wang
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing, China
| | - Naief H Al Makishah
- Department of Environmental Sciences, Faculty of Meteorology, Environment and Arid Land Agriculture, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Qi Li
- College of Life Sciences, Sichuan Normal University, Chengdu, China
| | - Yanan Li
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing, China
| | - Wenzheng Liu
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing, China
| | - Xiaoman Sun
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing, China
| | - Zhiqiang Wen
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing, China
| | - Sheng Yang
- Huzhou Center of Industrial Biotechnology, Shanghai Institutes of Biological Sciences, Chinese Academy of Sciences, Shanghai, China.,Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China
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5
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Enhancing acetic acid and 5‐hydroxymethyl furfural tolerance of C. saccharoperbutylacetonicum through adaptive laboratory evolution. Process Biochem 2021. [DOI: 10.1016/j.procbio.2020.11.013] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
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6
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Fonseca BC, Bortolucci J, da Silva TM, dos Passos VF, de Gouvêa PF, Dinamarco TM, Reginatto V. Butyric acid as sole product from xylose fermentation by a non-solventogenic Clostridium beijerinckii strain under controlled pH and nutritional conditions. ACTA ACUST UNITED AC 2020. [DOI: 10.1016/j.biteb.2020.100426] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
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7
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Wu Y, Wang Z, Xin X, Bai F, Xue C. Synergetic Engineering of Central Carbon, Energy, and Redox Metabolisms for High Butanol Production and Productivity by Clostridium acetobutylicum. Ind Eng Chem Res 2020. [DOI: 10.1021/acs.iecr.0c01187] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Youduo Wu
- School of Bioengineering, Dalian University of Technology, Dalian 116024, China
- Engineering Research Center of Application and Transformation for Synthetic Biology, Dalian University of Technology, Dalian 116024, China
| | - Zhenzhong Wang
- School of Bioengineering, Dalian University of Technology, Dalian 116024, China
| | - Xin Xin
- School of Bioengineering, Dalian University of Technology, Dalian 116024, China
| | - Fengwu Bai
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Chuang Xue
- School of Bioengineering, Dalian University of Technology, Dalian 116024, China
- Engineering Research Center of Application and Transformation for Synthetic Biology, Dalian University of Technology, Dalian 116024, China
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8
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Wen Z, Li Q, Liu J, Jin M, Yang S. Consolidated bioprocessing for butanol production of cellulolytic Clostridia: development and optimization. Microb Biotechnol 2020; 13:410-422. [PMID: 31448546 PMCID: PMC7017829 DOI: 10.1111/1751-7915.13478] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2019] [Revised: 08/02/2019] [Accepted: 08/04/2019] [Indexed: 12/20/2022] Open
Abstract
Butanol is an important bulk chemical, as well as a promising renewable gasoline substitute, that is commonly produced by solventogenic Clostridia. The main cost of cellulosic butanol fermentation is caused by cellulases that are required to saccharify lignocellulose, since solventogenic Clostridia cannot efficiently secrete cellulases. However, cellulolytic Clostridia can natively degrade lignocellulose and produce ethanol, acetate, butyrate and even butanol. Therefore, cellulolytic Clostridia offer an alternative to develop consolidated bioprocessing (CBP), which combines cellulase production, lignocellulose hydrolysis and co-fermentation of hexose/pentose into butanol in one step. This review focuses on CBP advances for butanol production of cellulolytic Clostridia and various synthetic biotechnologies that drive these advances. Moreover, the efforts to optimize the CBP-enabling cellulolytic Clostridia chassis are also discussed. These include the development of genetic tools, pentose metabolic engineering and the improvement of butanol tolerance. Designer cellulolytic Clostridia or consortium provide a promising approach and resource to accelerate future CBP for butanol production.
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Affiliation(s)
- Zhiqiang Wen
- School of Environmental and Biological EngineeringNanjing University of Science and TechnologyNanjing210094China
| | - Qi Li
- College of Life SciencesSichuan Normal UniversityLongquan, Chengdu610101China
| | - Jinle Liu
- Key Laboratory of Synthetic BiologyCAS Center for Excellence in Molecular Plant SciencesShanghai Institute of Plant Physiology and EcologyChinese Academy of SciencesShanghai200032China
| | - Mingjie Jin
- School of Environmental and Biological EngineeringNanjing University of Science and TechnologyNanjing210094China
| | - Sheng Yang
- Key Laboratory of Synthetic BiologyCAS Center for Excellence in Molecular Plant SciencesShanghai Institute of Plant Physiology and EcologyChinese Academy of SciencesShanghai200032China
- Huzhou Center of Industrial BiotechnologyShanghai Institutes of Biological SciencesChinese Academy of SciencesShanghai200032China
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9
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Wen Z, Ledesma-Amaro R, Lu M, Jin M, Yang S. Metabolic Engineering of Clostridium cellulovorans to Improve Butanol Production by Consolidated Bioprocessing. ACS Synth Biol 2020; 9:304-315. [PMID: 31940438 DOI: 10.1021/acssynbio.9b00331] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Clostridium cellulovorans DSM 743B can produce butyrate when grown on lignocellulose, but it can hardly synthesize butanol. In a previous study, C. cellulovorans was successfully engineered to switch the metabolism from butyryl-CoA to butanol by overexpressing an alcohol aldehyde dehydrogenase gene adhE1 from Clostridium acetobutylicum ATCC 824; however, its full potential in butanol production is still unexplored. In the study, a metabolic engineering approach based on a push-pull strategy was developed to further enhance cellulosic butanol production. In order to accomplish this, the carbon flux from acetyl-CoA to butyryl-CoA was pulled by overexpressing a trans-enoyl-coenzyme A reductase gene (ter), which can irreversibly catalyze crotonyl-CoA to butyryl-CoA. Then an acid reassimilation pathway uncoupled with acetone production was introduced to redirect the carbon flow from butyrate and acetate toward butyryl-CoA. Finally, xylose metabolism engineering was implemented by inactivating xylR (Clocel_0594) and araR (Clocel_1253), as well as overexpressing xylT (CA_C1345), which is expected to supply additional carbon and reducing power for CoA and butanol synthesis pathways. The final engineered strain produced 4.96 g/L of n-butanol from alkali extracted corn cobs (AECC), increasing by 235-fold compared to that of the wild type. It serves as a promising butanol producer by consolidated bioprocessing.
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Affiliation(s)
- Zhiqiang Wen
- School of Environmental and Biological Engineering, Nanjing University of Science & Technology, Nanjing 210094, China
| | | | - Minrui Lu
- School of Environmental and Biological Engineering, Nanjing University of Science & Technology, Nanjing 210094, China
| | - Mingjie Jin
- School of Environmental and Biological Engineering, Nanjing University of Science & Technology, Nanjing 210094, China
| | - Sheng Yang
- Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China
- Huzhou Center of Industrial Biotechnology, Shanghai Institutes of Biological Sciences, Chinese Academy of Sciences, Shanghai 200032, China
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10
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Menezes L, Sardaro MS, Duarte R, Mazzon R, Neviani E, Gatti M, De Dea Lindner J. Sourdough bacterial dynamics revealed by metagenomic analysis in Brazil. Food Microbiol 2020; 85:103302. [DOI: 10.1016/j.fm.2019.103302] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2019] [Revised: 08/02/2019] [Accepted: 08/10/2019] [Indexed: 12/12/2022]
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11
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Zhao T, Tashiro Y, Sonomoto K. Smart fermentation engineering for butanol production: designed biomass and consolidated bioprocessing systems. Appl Microbiol Biotechnol 2019; 103:9359-9371. [PMID: 31720773 DOI: 10.1007/s00253-019-10198-2] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2019] [Revised: 10/08/2019] [Accepted: 10/15/2019] [Indexed: 12/18/2022]
Abstract
There is a renewed interest in acetone-butanol-ethanol (ABE) fermentation from renewable substrates for the sustainable and environment-friendly production of biofuel and platform chemicals. However, the ABE fermentation is associated with several challenges due to the presence of heterogeneous components in the renewable substrates and the intrinsic characteristics of ABE fermentation process. Hence, there is a need to select optimal substrates and modify their characteristics suitable for the ABE fermentation process or microbial strain. This "designed biomass" can be used to establish the consolidated bioprocessing systems. As there are very few reports on designed biomass, the main objectives of this review are to summarize the main challenges associated with ABE fermentation from renewable substrates and to introduce feasible strategies for designing the substrates through pretreatment and hydrolysis technologies as well as through the establishment of consolidated bioprocessing systems. This review offers new insights on improving the efficiency of ABE fermentation from designed renewable substrates.
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Affiliation(s)
- Tao Zhao
- Laboratory of Microbial Technology, Division of Systems Bioengineering, Department of Bioscience and Biotechnology, Faculty of Agriculture, Graduate School, Kyushu University, 744, Motooka, Nishi-ku, Fukuoka, 819-0395, Japan.,Energy-rich Compounds Production by Photosynthetic Carbon Fixation Research Center, College of Life Science, Qingdao Agricultural University, No. 700 Changcheng Road, Chengyang District, Qingdao, 266109, China
| | - Yukihiro Tashiro
- Laboratory of Soil and Environmental Microbiology, Division of Systems Bioengineering, Department of Bioscience and Biotechnology, Faculty of Agriculture, Graduate School, Kyushu University, 744, Motooka, Nishi-ku, Fukuoka, 819-0395, Japan.,Laboratory of Microbial Environmental Protection, Tropical Microbiology Unit, Center for International Education and Research of Agriculture, Faculty of Agriculture, Kyushu University, 744, Motooka, Nishi-ku, Fukuoka, 819-0395, Japan
| | - Kenji Sonomoto
- Laboratory of Microbial Technology, Division of Systems Bioengineering, Department of Bioscience and Biotechnology, Faculty of Agriculture, Graduate School, Kyushu University, 744, Motooka, Nishi-ku, Fukuoka, 819-0395, Japan.
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12
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Vasylkivska M, Jureckova K, Branska B, Sedlar K, Kolek J, Provaznik I, Patakova P. Transcriptional analysis of amino acid, metal ion, vitamin and carbohydrate uptake in butanol-producing Clostridium beijerinckii NRRL B-598. PLoS One 2019; 14:e0224560. [PMID: 31697692 PMCID: PMC6837493 DOI: 10.1371/journal.pone.0224560] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2019] [Accepted: 10/16/2019] [Indexed: 11/19/2022] Open
Abstract
In-depth knowledge of cell metabolism and nutrient uptake mechanisms can lead to the development of a tool for improving acetone-butanol-ethanol (ABE) fermentation performance and help to overcome bottlenecks in the process, such as the high cost of substrates and low production rates. Over 300 genes potentially encoding transport of amino acids, metal ions, vitamins and carbohydrates were identified in the genome of the butanol-producing strain Clostridium beijerinckii NRRL B-598, based on similarity searches in protein function databases. Transcriptomic data of the genes were obtained during ABE fermentation by RNA-Seq experiments and covered acidogenesis, solventogenesis and sporulation. The physiological roles of the selected 81 actively expressed transport genes were established on the basis of their expression profiles at particular stages of ABE fermentation. This article describes how genes encoding the uptake of glucose, iron, riboflavin, glutamine, methionine and other nutrients take part in growth, production and stress responses of C. beijerinckii NRRL B-598. These data increase our knowledge of transport mechanisms in solventogenic Clostridium and may be used in the selection of individual genes for further research.
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Affiliation(s)
- Maryna Vasylkivska
- Department of Biotechnology, University of Chemistry and Technology Prague, Prague, Czech Republic
- * E-mail:
| | - Katerina Jureckova
- Department of Biomedical Engineering, Brno University of Technology, Brno, Czech Republic
| | - Barbora Branska
- Department of Biotechnology, University of Chemistry and Technology Prague, Prague, Czech Republic
| | - Karel Sedlar
- Department of Biomedical Engineering, Brno University of Technology, Brno, Czech Republic
| | - Jan Kolek
- Department of Biotechnology, University of Chemistry and Technology Prague, Prague, Czech Republic
| | - Ivo Provaznik
- Department of Biomedical Engineering, Brno University of Technology, Brno, Czech Republic
| | - Petra Patakova
- Department of Biotechnology, University of Chemistry and Technology Prague, Prague, Czech Republic
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13
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Wen Z, Lu M, Ledesma-Amaro R, Li Q, Jin M, Yang S. TargeTron Technology Applicable in Solventogenic Clostridia: Revisiting 12 Years' Advances. Biotechnol J 2019; 15:e1900284. [PMID: 31475782 DOI: 10.1002/biot.201900284] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2019] [Revised: 08/20/2019] [Indexed: 12/11/2022]
Abstract
Clostridium has great potential in industrial application and medical research. But low DNA repair capacity and plasmids transformation efficiency severely delay development and application of genetic tools based on homologous recombination (HR). TargeTron is a gene editing technique dependent on the mobility of group II introns, rather than homologous recombination, which makes it very suitable for gene disruption of Clostridium. The application of TargeTron technology in solventogenic Clostridium is academically reported in 2007 and this tool has been introduced in various clostridia as it is easy to operate, time saving, and reliable. TargeTron has made great progress in solventogenic Clostridium in the aspects of acetone-butanol-ethanol (ABE) fermentation pathway modification, important functional genes identification, and xylose metabolic pathway analysis and reconstruction. In the review, 12 years' advances of TargeTron technology applicable in solventogenic Clostridium, including its principle, technical characteristics, application, and efforts to expand its capabilities, or to avoid potential drawbacks, are revisisted. Some other technologies as putative competitors or collaborators are also discussed. It is believed that TargeTron combined with CRISPR/Cas-assisted gene/base editing and gene-expression regulation system will make a better future for clostridial genetic modification.
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Affiliation(s)
- Zhiqiang Wen
- School of Environmental and Biological Engineering, Nanjing University of Science & Technology, Nanjing, 210094, China
| | - Minrui Lu
- School of Environmental and Biological Engineering, Nanjing University of Science & Technology, Nanjing, 210094, China
| | | | - Qi Li
- College of Life Sciences, Sichuan Normal University, Longquan, Chengdu, 610101, China
| | - Mingjie Jin
- School of Environmental and Biological Engineering, Nanjing University of Science & Technology, Nanjing, 210094, China
| | - Sheng Yang
- Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 200032, China.,Huzhou Center of Industrial Biotechnology, Shanghai Institutes of Biological Sciences, Chinese Academy of Sciences, Zhejiang, 313000, China
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14
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ABC Transporters Required for Hexose Uptake by Clostridium phytofermentans. J Bacteriol 2019; 201:JB.00241-19. [PMID: 31109990 DOI: 10.1128/jb.00241-19] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2019] [Accepted: 05/13/2019] [Indexed: 01/02/2023] Open
Abstract
The mechanisms by which bacteria uptake solutes across the cell membrane broadly impact their cellular energetics. Here, we use functional genomic, genetic, and biophysical approaches to reveal how Clostridium (Lachnoclostridium) phytofermentans, a model bacterium that ferments lignocellulosic biomass, uptakes plant hexoses using highly specific, nonredundant ATP-binding cassette (ABC) transporters. We analyze the transcription patterns of its 173 annotated sugar transporter genes to find those upregulated on specific carbon sources. Inactivation of these genes reveals that individual ABC transporters are required for uptake of hexoses and hexo-oligosaccharides and that distinct ABC transporters are used for oligosaccharides versus their constituent monomers. The thermodynamics of sugar binding shows that substrate specificity of these transporters is encoded by the extracellular solute-binding subunit. As sugars are not phosphorylated during ABC transport, we identify intracellular hexokinases based on in vitro activities. These mechanisms used by Clostridia to uptake plant hexoses are key to understanding soil and intestinal microbiomes and to engineer strains for industrial transformation of lignocellulose.IMPORTANCE Plant-fermenting Clostridia are anaerobic bacteria that recycle plant matter in soil and promote human health by fermenting dietary fiber in the intestine. Clostridia degrade plant biomass using extracellular enzymes and then uptake the liberated sugars for fermentation. The main sugars in plant biomass are hexoses, and here, we identify how hexoses are taken in to the cell by the model organism Clostridium phytofermentans We show that this bacterium uptakes hexoses using a set of highly specific, nonredundant ABC transporters. Once in the cell, the hexoses are phosphorylated by intracellular hexokinases. This study provides insight into the functioning of abundant members of soil and intestinal microbiomes and identifies gene targets to engineer strains for industrial lignocellulosic fermentation.
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15
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Niglio S, Marzocchella A, Rehmann L. Clostridial conversion of corn syrup to Acetone-Butanol-Ethanol (ABE) via batch and fed-batch fermentation. Heliyon 2019; 5:e01401. [PMID: 30963127 PMCID: PMC6434287 DOI: 10.1016/j.heliyon.2019.e01401] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2018] [Revised: 03/17/2019] [Accepted: 03/18/2019] [Indexed: 11/28/2022] Open
Abstract
Corn syrup - a commercial product derived from saccharification of corn starch - was used to produce acetone-butanol-ethanol (ABE) by Clostridium spp. Screening of commercial Clostridium spp., substrate inhibition tests and fed-batch experiments were carried out to improve ABE production using corn syrup as only carbon source. The screening tests carried out in batch mode using a production media containing 50 g/L corn syrup revealed that C. saccharobutylicum was the best performer in terms of total solvent concentration (12.46 g/L), yield (0.30 g/g) and productivity (0.19 g/L/h) and it was selected for successive experiments. Concentration of corn syrup higher than 50 g/L resulted in no solvents production. Fed-batch fermentation improved ABE production with respect to batch fermentation: the butanol and solvent concentration increased up to 8.70 and 16.68 g/L, respectively. The study demonstrated the feasibility of producing solvents via ABE fermentation using corn syrup as a model substrate of concentrated sugar mixtures.
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Affiliation(s)
- Saverio Niglio
- Dipartimento di Ingegneria Chimica, Dei Materiali e della Produzione Industriale, Università degli Studi di Napoli Federico II, P.le V. Tecchio 80, 80125 Napoli, Italy
| | - Antonio Marzocchella
- Dipartimento di Ingegneria Chimica, Dei Materiali e della Produzione Industriale, Università degli Studi di Napoli Federico II, P.le V. Tecchio 80, 80125 Napoli, Italy
| | - Lars Rehmann
- Department of Chemical and Biochemical Engineering, University of Western Ontario, 1151 Richmond Street, London, ON, Canada
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Acidogenesis, solventogenesis, metabolic stress response and life cycle changes in Clostridium beijerinckii NRRL B-598 at the transcriptomic level. Sci Rep 2019; 9:1371. [PMID: 30718562 PMCID: PMC6362236 DOI: 10.1038/s41598-018-37679-0] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2018] [Accepted: 12/13/2018] [Indexed: 01/16/2023] Open
Abstract
Clostridium beijerinckii NRRL B-598 is a sporulating, butanol and hydrogen producing strain that utilizes carbohydrates by the acetone-butanol-ethanol (ABE) fermentative pathway. The pathway consists of two metabolic phases, acidogenesis and solventogenesis, from which the latter one can be coupled with sporulation. Thorough transcriptomic profiling during a complete life cycle and both metabolic phases completed with flow cytometry, microscopy and a metabolites analysis helped to find out key genes involved in particular cellular events. The description of genes/operons that are closely involved in metabolism or the cell cycle is a necessary condition for metabolic engineering of the strain and will be valuable for all C. beijerinckii strains and other Clostridial species. The study focused on glucose transport and catabolism, hydrogen formation, metabolic stress response, binary fission, motility/chemotaxis and sporulation, which resulted in the composition of the unique image reflecting clostridial population changes. Surprisingly, the main change in expression of individual genes was coupled with the sporulation start and not with the transition from acidogenic to solventogenic metabolism. As expected, solvents formation started at pH decrease and the accumulation of butyric and acetic acids in the cultivation medium.
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Clostridial whole cell and enzyme systems for hydrogen production: current state and perspectives. Appl Microbiol Biotechnol 2018; 103:567-575. [PMID: 30446778 DOI: 10.1007/s00253-018-9514-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2018] [Revised: 11/06/2018] [Accepted: 11/09/2018] [Indexed: 10/27/2022]
Abstract
Strictly anaerobic bacteria of the Clostridium genus have attracted great interest as potential cell factories for molecular hydrogen production purposes. In addition to being a useful approach to this process, dark fermentation has the advantage of using the degradation of cheap agricultural residues and industrial wastes for molecular hydrogen production. However, many improvements are still required before large-scale hydrogen production from clostridial metabolism is possible. Here we review the literature on the basic biological processes involved in clostridial hydrogen production, and present the main advances obtained so far in order to enhance the hydrogen productivity, as well as suggesting some possible future prospects.
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Sun C, Zhang S, Xin F, Shanmugam S, Wu YR. Genomic comparison of Clostridium species with the potential of utilizing red algal biomass for biobutanol production. BIOTECHNOLOGY FOR BIOFUELS 2018; 11:42. [PMID: 29467820 PMCID: PMC5815214 DOI: 10.1186/s13068-018-1044-9] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/28/2017] [Accepted: 02/05/2018] [Indexed: 05/17/2023]
Abstract
BACKGROUND Sustainable biofuels, which are widely considered as an attractive alternative to fossil fuels, can be generated by utilizing various biomass from the environment. Marine biomass, such as red algal biomass, is regarded as one potential renewable substrate source for biofuels conversion due to its abundance of fermentable sugars (e.g., galactose). Previous studies focused on the enhancement of biofuels production from different Clostridium species; however, there has been limited investigation into their metabolic pathways, especially on the conversion of biofuels from galactose, via whole genomic comparison and evolutionary analysis. RESULTS Two galactose-utilizing Clostridial strains were examined and identified as Clostridium acetobutylicum strain WA and C. beijerinckii strain WB. Via the genomic sequencing of both strains, the comparison of the whole genome together with the relevant protein prediction of 33 other Clostridium species was established to reveal a clear genome profile based upon various genomic features. Among them, five representative strains, including C. beijerinckii NCIMB14988, C. diolis DSM 15410, C. pasteurianum BC1, strain WA and WB, were further discussed to demonstrate the main differences among their respective metabolic pathways, especially in their carbohydrate metabolism. The metabolic pathways involved in the generation of biofuels and other potential products (e.g., riboflavin) were also reconstructed based on the utilization of marine biomass. Finally, a batch fermentation process was performed to verify the fermentative products from strains WA and WB using 60 g/L of galactose, which is the main hydrolysate from algal biomass. It was observed that strain WA and WB could produce up to 16.98 and 12.47 g/L of biobutanol, together with 21,560 and 10,140 mL/L biohydrogen, respectively. CONCLUSIONS The determination of the production of various biofuels by both strains WA and WB and their genomic comparisons with other typical Clostridium species on the analysis of various metabolic pathways was presented. Through the identification of their metabolic pathways, which are involved in the conversion of galactose into various potential products, such as biobutanol, the obtained results extend the current insight into the potential capability of utilizing marine red algal biomass and provide a systematic investigation into the relationship between this genus and the generation of sustainable bioenergy.
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Affiliation(s)
- Chongran Sun
- Department of Biology, Shantou University, Shantou, 515063 Guangdong China
| | - Shuangfei Zhang
- Department of Biology, Shantou University, Shantou, 515063 Guangdong China
| | - Fengxue Xin
- Guangdong Provincial Key Laboratory of Marine Biotechnology, Shantou University, Shantou, 515063 Guangdong China
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, 211816 Jiangsu China
| | | | - Yi-Rui Wu
- Department of Biology, Shantou University, Shantou, 515063 Guangdong China
- Guangdong Provincial Key Laboratory of Marine Biotechnology, Shantou University, Shantou, 515063 Guangdong China
- STU-UNIVPM Joint Algal Research Center, Shantou University, Shantou, 515063 Guangdong China
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Chen LJ, Wu YD, Xue C, Bai FW. Improving Fructose Utilization and Butanol Production by Clostridium acetobutylicum via Extracellular Redox Potential Regulation and Intracellular Metabolite Analysis. Biotechnol J 2017; 12. [PMID: 28731563 DOI: 10.1002/biot.201700198] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2017] [Revised: 06/30/2017] [Indexed: 12/15/2022]
Abstract
Jerusalem artichoke (JA) can grow well in marginal lands with high biomass yield, and thus is a potential energy crop for biorefinery. The major biomass of JA is from tubers, which contain inulin that can be easily hydrolyzed into a mixture of fructose and glucose, but fructose utilization for producing butanol as an advanced biofuel is poor compared to glucose-based ABE fermentation by Clostridium acetobutylicum. In this article, the impact of extracellular redox potential (ORP) on the process is studied using a mixture of fructose and glucose to simulate the hydrolysate of JA tubers. When the extracellular ORP is controlled above -460 mV, 13.2 g L-1 butanol is produced from 51.0 g L-1 total sugars (40.1 g L-1 fructose and 10.9 g L-1 glucose), leading to dramatically increased butanol yield and butanol/ABE ratio of 0.26 g g-1 and 0.67, respectively. Intracellular metabolite and q-PCR analysis further indicate that intracellular ATP and NADH availabilities are significantly improved together with the fructose-specific PTS expression at the lag phase, which consequently facilitate fructose transport, metabolic shift toward solventogenesis and carbon flux redistribution for butanol biosynthesis. Therefore, the extracellular ORP control can be an effective strategy to improve butanol production from fructose-based feedstock.
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Affiliation(s)
- Li-Jie Chen
- School of Life Science and Biotechnology, Dalian University of Technology, Dalian, China
| | - You-Duo Wu
- School of Life Science and Biotechnology, Dalian University of Technology, Dalian, China
| | - Chuang Xue
- School of Life Science and Biotechnology, Dalian University of Technology, Dalian, China
| | - Feng-Wu Bai
- School of Life Science and Biotechnology, Dalian University of Technology, Dalian, China.,School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
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Xue C, Zhao J, Chen L, Yang ST, Bai F. Recent advances and state-of-the-art strategies in strain and process engineering for biobutanol production by Clostridium acetobutylicum. Biotechnol Adv 2017; 35:310-322. [DOI: 10.1016/j.biotechadv.2017.01.007] [Citation(s) in RCA: 177] [Impact Index Per Article: 25.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2016] [Revised: 01/06/2017] [Accepted: 01/25/2017] [Indexed: 12/20/2022]
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Effect of Trehalose and Trehalose Transport on the Tolerance of Clostridium perfringens to Environmental Stress in a Wild Type Strain and Its Fluoroquinolone-Resistant Mutant. Int J Microbiol 2017; 2016:4829716. [PMID: 28058047 PMCID: PMC5183799 DOI: 10.1155/2016/4829716] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2016] [Accepted: 10/10/2016] [Indexed: 11/17/2022] Open
Abstract
Trehalose has been shown to protect bacterial cells from environmental stress. Its uptake and osmoprotective effect in Clostridium perfringens were investigated by comparing wild type C. perfringens ATCC 13124 with a fluoroquinolone- (gatifloxacin-) resistant mutant. In a chemically defined medium, trehalose and sucrose supported the growth of the wild type but not that of the mutant. Microarray data and qRT-PCR showed that putative genes for the phosphorylation and transport of sucrose and trehalose (via phosphoenolpyruvate-dependent phosphotransferase systems, PTS) and some regulatory genes were downregulated in the mutant. The wild type had greater tolerance than the mutant to salts and low pH; trehalose and sucrose further enhanced the osmotolerance of the wild type to NaCl. Expression of the trehalose-specific PTS was lower in the fluoroquinolone-resistant mutant. Protection of C. perfringens from environmental stress could therefore be correlated with the ability to take up trehalose.
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Aristilde L. Metabolite labelling reveals hierarchies in Clostridium acetobutylicum that selectively channel carbons from sugar mixtures towards biofuel precursors. Microb Biotechnol 2016; 10:162-174. [PMID: 27878973 PMCID: PMC5270725 DOI: 10.1111/1751-7915.12459] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2016] [Accepted: 10/23/2016] [Indexed: 12/30/2022] Open
Abstract
Clostridial fermentation of cellulose and hemicellulose relies on the cellular physiology controlling the metabolism of the cellulosic hexose sugar (glucose) with respect to the hemicellulosic pentose sugars (xylose and arabinose) and the hemicellulosic hexose sugars (galactose and mannose). Here, liquid chromatography–mass spectrometry and stable isotope tracers in Clostridium acetobutylicum were applied to investigate the metabolic hierarchy of glucose relative to the different hemicellulosic sugars towards two important biofuel precursors, acetyl‐coenzyme A and butyryl‐coenzyme A. The findings revealed constitutive metabolic hierarchies in C. acetobutylicum that facilitate (i) selective investment of hemicellulosic pentoses towards ribonucleotide biosynthesis without substantial investment into biofuel production and (ii) selective contribution of hemicellulosic hexoses through the glycolytic pathway towards biofuel precursors. Long‐term isotopic enrichment demonstrated incorporation of both pentose sugars into pentose‐phosphates and ribonucleotides in the presence of glucose. Kinetic labelling data, however, showed that xylose was not routed towards the biofuel precursors but there was minor contribution from arabinose. Glucose hierarchy over the hemicellulosic hexoses was substrate‐dependent. Kinetic labelling of hexose‐phosphates and triose‐phosphates indicated that mannose was assimilated but not galactose. Labelling of both biofuel precursors confirmed this metabolic preference. These results highlight important metabolic considerations in the accounting of clostridial mixed‐sugar utilization.
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Affiliation(s)
- Ludmilla Aristilde
- Department of Biological and Environmental Engineering, College of Agriculture and Life Sciences, Cornell University, Ithaca, NY, 14853, USA
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Kök MS. An integrated approach: advances in the use ofClostridiumfor biofuel. Biotechnol Genet Eng Rev 2016; 31:69-81. [DOI: 10.1080/02648725.2016.1168075] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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