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Kumar V, Kumar P, Maity SK, Agrawal D, Narisetty V, Jacob S, Kumar G, Bhatia SK, Kumar D, Vivekanand V. Recent advances in bio-based production of top platform chemical, succinic acid: an alternative to conventional chemistry. BIOTECHNOLOGY FOR BIOFUELS AND BIOPRODUCTS 2024; 17:72. [PMID: 38811976 PMCID: PMC11137917 DOI: 10.1186/s13068-024-02508-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/17/2024] [Accepted: 04/20/2024] [Indexed: 05/31/2024]
Abstract
Succinic acid (SA) is one of the top platform chemicals with huge applications in diverse sectors. The presence of two carboxylic acid groups on the terminal carbon atoms makes SA a highly functional molecule that can be derivatized into a wide range of products. The biological route for SA production is a cleaner, greener, and promising technological option with huge potential to sequester the potent greenhouse gas, carbon dioxide. The recycling of renewable carbon of biomass (an indirect form of CO2), along with fixing CO2 in the form of SA, offers a carbon-negative SA manufacturing route to reduce atmospheric CO2 load. These attractive attributes compel a paradigm shift from fossil-based to microbial SA manufacturing, as evidenced by several commercial-scale bio-SA production in the last decade. The current review article scrutinizes the existing knowledge and covers SA production by the most efficient SA producers, including several bacteria and yeast strains. The review starts with the biochemistry of the major pathways accumulating SA as an end product. It discusses the SA production from a variety of pure and crude renewable sources by native as well as engineered strains with details of pathway/metabolic, evolutionary, and process engineering approaches for enhancing TYP (titer, yield, and productivity) metrics. The review is then extended to recent progress on separation technologies to recover SA from fermentation broth. Thereafter, SA derivatization opportunities via chemo-catalysis are discussed for various high-value products, which are only a few steps away. The last two sections are devoted to the current scenario of industrial production of bio-SA and associated challenges, along with the author's perspective.
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Affiliation(s)
- Vinod Kumar
- School of Water, Energy and Environment, Cranfield University, Cranfield, MK43 0AL, UK.
- Department of Bioscience and Bioengineering, Indian Institute of Technology Roorkee, Roorkee, Uttarakhand, 247667, India.
| | - Pankaj Kumar
- Department of Chemical Engineering, School of Studies of Engineering and Technology, Guru Ghasidas Vishwavidyalaya (A Central University), Bilaspur, Chhattisgarh, 495009, India
| | - Sunil K Maity
- Department of Chemical Engineering, Indian Institute of Technology Hyderabad, Kandi, Sangareddy, Hyderabad, Telangana, 502284, India.
| | - Deepti Agrawal
- Biochemistry and Biotechnology Area, Material Resource Efficiency Division, CSIR-Indian Institute of Petroleum, Dehradun, Uttarakhand, 248005, India
| | - Vivek Narisetty
- School of Water, Energy and Environment, Cranfield University, Cranfield, MK43 0AL, UK
| | - Samuel Jacob
- Department of Biotechnology, School of Bioengineering, SRM Institute of Science and Technology, Kattankulathur, Chennai, Tamil Nadu, 603203, India
| | - Gopalakrishnan Kumar
- School of Civil and Environmental Engineering, Yonsei University, Seoul, 03722, Republic of Korea
| | - Shashi Kant Bhatia
- Department of Biological Engineering, College of Engineering, Konkuk University, Seoul, 05029, Republic of Korea
| | - Dinesh Kumar
- School of Bioengineering & Food Technology, Shoolini University of Biotechnology and Management Sciences, Solan, Himachal Pradesh, 173229, India
| | - Vivekanand Vivekanand
- Centre for Energy and Environment, Malaviya National Institute of Technology Jaipur, Jaipur, Rajasthan, 302017, India
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Rawat M, Chauhan M, Pandey A. Extremophiles and their expanding biotechnological applications. Arch Microbiol 2024; 206:247. [PMID: 38713374 DOI: 10.1007/s00203-024-03981-x] [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: 02/22/2024] [Revised: 04/16/2024] [Accepted: 04/25/2024] [Indexed: 05/08/2024]
Abstract
Microbial life is not restricted to any particular setting. Over the past several decades, it has been evident that microbial populations can exist in a wide range of environments, including those with extremes in temperature, pressure, salinity, and pH. Bacteria and Archaea are the two most reported types of microbes that can sustain in extreme environments, such as hot springs, ice caves, acid drainage, and salt marshes. Some can even grow in toxic waste, organic solvents, and heavy metals. These microbes are called extremophiles. There exist certain microorganisms that are found capable of thriving in two or more extreme physiological conditions simultaneously, and are regarded as polyextremophiles. Extremophiles possess several physiological and molecular adaptations including production of extremolytes, ice nucleating proteins, pigments, extremozymes and exopolysaccharides. These metabolites are used in many biotechnological industries for making biofuels, developing new medicines, food additives, cryoprotective agents etc. Further, the study of extremophiles holds great significance in astrobiology. The current review summarizes the diversity of microorganisms inhabiting challenging environments and the biotechnological and therapeutic applications of the active metabolites obtained as a response to stress conditions. Bioprospection of extremophiles provides a progressive direction with significant enhancement in economy. Moreover, the introduction to omics approach including whole genome sequencing, single cell genomics, proteomics, metagenomics etc., has made it possible to find many unique microbial communities that could be otherwise difficult to cultivate using traditional methods. These findings might be capable enough to state that discovery of extremophiles can bring evolution to biotechnology.
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Affiliation(s)
- Manvi Rawat
- Department of Biotechnology, Graphic Era (Deemed to be University), Dehradun, Uttarakhand, 248002, India
| | - Mansi Chauhan
- Department of Microbiology, Graphic Era (Deemed to be University), Dehradun, Uttarakhand, 248002, India
| | - Anita Pandey
- Department of Biotechnology, Graphic Era (Deemed to be University), Dehradun, Uttarakhand, 248002, India.
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Li Z, Zhang L, Zhang X, Chen T, Yang P, Chen Y, Lin H, Zhuang W, Wu J, Ying H. Long-Chain Bio-Based Nylon 514 Salt: Crystal Structure, Phase Transformation, and Polymerization. Polymers (Basel) 2024; 16:480. [PMID: 38399858 PMCID: PMC10892662 DOI: 10.3390/polym16040480] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Revised: 01/29/2024] [Accepted: 02/06/2024] [Indexed: 02/25/2024] Open
Abstract
Nylon 514 is one of the new long-chain bio-based nylon materials; its raw material, 1,5-pentanediamine (PDA), is prepared by biological techniques, using biomass as the raw material. The high-performance monomer of nylon 514, 1,5-pentanediamine-tetradecanedioate (PDA-TDA) salt, was obtained through efficient crystallization methods. Here, two crystal forms of PDA-TDA, anhydrous and dihydrate, were identified and studied in this paper. From the characterization data, their crystal structures and thermal behaviors were investigated. Lattice energy was calculated to gain further insight into the relationship between thermal stability and crystal structures. The contribution of hydrogen bonds and other intermolecular interactions to the crystal structure stability have been quantified according to detailed Hirshfeld and IRI analyses. Additionally, the transformation mechanism of the anhydrate and dihydrate was established through a series of well-designed stability experiments, in which the temperature and water activity play a significant role in the structural stability of crystalline forms. Eventually, we obtained nylon 514 products with good thermal stability and low absorption using stable dihydrate powders as monomers. The properties of nylon 514 products prepared by different polymerization methods were also compared.
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Affiliation(s)
- Zihan Li
- National Engineering Technique Research Center for Biotechnology, State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, No. 30, Puzhu South Road, Nanjing 211816, China; (Z.L.); (X.Z.); (P.Y.); (Y.C.); (W.Z.); (J.W.); (H.Y.)
| | - Lei Zhang
- Nanjing Biotogether Co., Ltd., No. 8, Shuangfeng Road, Nanjing 211806, China;
| | - Xiaohan Zhang
- National Engineering Technique Research Center for Biotechnology, State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, No. 30, Puzhu South Road, Nanjing 211816, China; (Z.L.); (X.Z.); (P.Y.); (Y.C.); (W.Z.); (J.W.); (H.Y.)
| | - Tianpeng Chen
- National Engineering Technique Research Center for Biotechnology, State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, No. 30, Puzhu South Road, Nanjing 211816, China; (Z.L.); (X.Z.); (P.Y.); (Y.C.); (W.Z.); (J.W.); (H.Y.)
| | - Pengpeng Yang
- National Engineering Technique Research Center for Biotechnology, State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, No. 30, Puzhu South Road, Nanjing 211816, China; (Z.L.); (X.Z.); (P.Y.); (Y.C.); (W.Z.); (J.W.); (H.Y.)
| | - Yong Chen
- National Engineering Technique Research Center for Biotechnology, State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, No. 30, Puzhu South Road, Nanjing 211816, China; (Z.L.); (X.Z.); (P.Y.); (Y.C.); (W.Z.); (J.W.); (H.Y.)
| | - Huajie Lin
- SINOPEC Ningbo Research Institute of New Materials, No. 88, Mianfeng Road, Ningbo 315200, China
| | - Wei Zhuang
- National Engineering Technique Research Center for Biotechnology, State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, No. 30, Puzhu South Road, Nanjing 211816, China; (Z.L.); (X.Z.); (P.Y.); (Y.C.); (W.Z.); (J.W.); (H.Y.)
| | - Jinglan Wu
- National Engineering Technique Research Center for Biotechnology, State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, No. 30, Puzhu South Road, Nanjing 211816, China; (Z.L.); (X.Z.); (P.Y.); (Y.C.); (W.Z.); (J.W.); (H.Y.)
| | - Hanjie Ying
- National Engineering Technique Research Center for Biotechnology, State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, No. 30, Puzhu South Road, Nanjing 211816, China; (Z.L.); (X.Z.); (P.Y.); (Y.C.); (W.Z.); (J.W.); (H.Y.)
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Wang R, Huang D, Chen C, Song D, Peng H, He M, Huang X, Huang Z, Wang B, Lan H, Tang P. From transients to permanent residents: the existence of obligate aerobic microorganisms in the goat rumen. Front Microbiol 2024; 15:1325505. [PMID: 38318339 PMCID: PMC10839086 DOI: 10.3389/fmicb.2024.1325505] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2023] [Accepted: 01/09/2024] [Indexed: 02/07/2024] Open
Abstract
The rumen serves as a complex ecosystem, harboring diverse microbial communities that play crucial ecological roles. Because previous studies have predominantly focused on anaerobic microorganisms, limited attention has been given to aerobic microorganisms in the goat rumen. This study aims to explore the diversity of aerobic microorganisms in the rumen and understand their niche and ecological roles. Rumen fluid samples were collected from 6 goats at different time points post-morning feeding. pH, NH3-N, and volatile fatty acid (TVFA) concentrations were measured, while In vitro cultivation of aerobic microorganisms was performed using PDA medium. Internal Transcribed Spacer (ITS) and 16S sequencing unveiled microbial diversity within the rumen fluid samples. Evidence of obligate aerobic microorganisms in the goat rumen suggests their potential contribution to ecological functionalities. Significantly, certain aerobic microorganisms exhibited correlations with TVFA levels, implying their involvement in TVFA metabolism. This study provides evidence of the existence and potential ecological roles of obligate aerobic microorganisms in the goat rumen. The findings underscore the significance of comprehensively deciphering goat rumen microbial communities and their interactions, with aerobes regarded as permanent residents rather than transients. These insights form a solid foundation for advancing our understanding of the intricate interplay between goat and their aerobic microorganisms in the rumen.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | - Ping Tang
- Panzhihua Academy of Agricultural and Forestry Sciences, Panzhihua, China
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Luo Y, Huang W. Base-mediated carboxylation of C-nucleophiles with CO 2. Org Biomol Chem 2023; 21:8628-8641. [PMID: 37860946 DOI: 10.1039/d3ob01367g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2023]
Abstract
Carbon dioxide (CO2) is an available, abundant, and renewable C1 resource, which could be converted into value-added chemicals. Due to its inherent thermodynamic stability and kinetic inertness, it is difficult to realize its efficient utilization. Nevertheless, many elegant strategies for the utilization of CO2 have been developed using Lewis bases, frustrated Lewis pairs, hydroxyl-containing compounds, amino-group-containing compounds or transition metal catalysis. Among them, base-mediated carboxylation of C-nucleophiles is an environmentally friendly strategy for CO2 conversion, which is operationally simple, using low-toxicity bases and economical available promoters, without the use of complex ligands or cocatalysts. This review summarizes related work on the base-mediated carboxylation of C-nucleophiles with CO2, based on the effects of nucleophiles, promoters, additives, and solvents. The types of pronucleophile are categorized as follows: hydrocarbon with C(sp3)-H, C(sp2)-H or C(sp)-H bonds, organosilanes, organotin, organoboron, and N-tosylhydrazones. Typical mechanisms and applications of these carboxylation reactions are also depicted. Moreover, mechanistic comprehension of CO2 activation and conversion at a molecular level aims to further expand the repertoire of carboxylation transformations mediated by bases.
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Affiliation(s)
- Yanlong Luo
- School of Chemical Engineering and Technology, Tianshui Normal University, Tianshui, Gansu 741001, China.
| | - Wenbin Huang
- Department of Chemistry, Southern University of Science and Technology, Shenzhen 518055, China.
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Son J, Sohn YJ, Baritugo KA, Jo SY, Song HM, Park SJ. Recent advances in microbial production of diamines, aminocarboxylic acids, and diacids as potential platform chemicals and bio-based polyamides monomers. Biotechnol Adv 2023; 62:108070. [PMID: 36462631 DOI: 10.1016/j.biotechadv.2022.108070] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2022] [Revised: 11/16/2022] [Accepted: 11/24/2022] [Indexed: 12/03/2022]
Abstract
Recently, bio-based manufacturing processes of value-added platform chemicals and polymers in biorefineries using renewable resources have extensively been developed for sustainable and carbon dioxide (CO2) neutral-based industry. Among them, bio-based diamines, aminocarboxylic acids, and diacids have been used as monomers for the synthesis of polyamides having different carbon numbers and ubiquitous and versatile industrial polymers and also as precursors for further chemical and biological processes to afford valuable chemicals. Until now, these platform bio-chemicals have successfully been produced by biorefinery processes employing enzymes and/or microbial host strains as main catalysts. In this review, we discuss recent advances in bio-based production of diamines, aminocarboxylic acids, and diacids, which has been developed and improved by systems metabolic engineering strategies of microbial consortia and optimization of microbial conversion processes including whole cell bioconversion and direct fermentative production.
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Affiliation(s)
- Jina Son
- Department of Chemical Engineering and Materials Science, Graduate Program in System Health Science and Engineering, Ewha Womans University, 52 Ewhayeodae-gil, Seodaemun-gu, Seoul 03760, Republic of Korea
| | - Yu Jung Sohn
- Department of Chemical Engineering and Materials Science, Graduate Program in System Health Science and Engineering, Ewha Womans University, 52 Ewhayeodae-gil, Seodaemun-gu, Seoul 03760, Republic of Korea
| | - Kei-Anne Baritugo
- Department of Chemical Engineering and Materials Science, Graduate Program in System Health Science and Engineering, Ewha Womans University, 52 Ewhayeodae-gil, Seodaemun-gu, Seoul 03760, Republic of Korea
| | - Seo Young Jo
- Department of Chemical Engineering and Materials Science, Graduate Program in System Health Science and Engineering, Ewha Womans University, 52 Ewhayeodae-gil, Seodaemun-gu, Seoul 03760, Republic of Korea
| | - Hye Min Song
- Department of Chemical Engineering and Materials Science, Graduate Program in System Health Science and Engineering, Ewha Womans University, 52 Ewhayeodae-gil, Seodaemun-gu, Seoul 03760, Republic of Korea
| | - Si Jae Park
- Department of Chemical Engineering and Materials Science, Graduate Program in System Health Science and Engineering, Ewha Womans University, 52 Ewhayeodae-gil, Seodaemun-gu, Seoul 03760, Republic of Korea.
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Li Z, Li S, Yang P, Fang X, Wen Q, Li M, Zhuang W, Wu J, Ying H. The effect of polymorphism on polymer properties: crystal structure, stability and polymerization of the short-chain bio-based nylon 52 monomer 1,5-pentanediamine oxalate. IUCRJ 2023; 10:52-65. [PMID: 36598502 PMCID: PMC9812218 DOI: 10.1107/s2052252522010442] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/23/2022] [Accepted: 10/31/2022] [Indexed: 06/17/2023]
Abstract
The compound 1,5-pentanediamine (PDA) is prepared by biological methods using biomass as raw material. The salt of 1,5-pentanediamine oxalate (PDA-OXA) was used directly as the monomer for the preparation of a new bio-based nylon 52 material. High-performance polymer materials require initial high-quality monomers, and crystallization is an essential approach to preparing such a monomer. In this work, three crystal forms of PDA-OXA, the anhydrate, dihydrate and trihydrate, were found and the single crystals of two hydrates were obtained. Their crystal structures were determined using single-crystal and powder X-ray diffraction. The thermal behaviors were characterized by thermodynamic analysis, and the lattice energy was calculated to further explore the relationship between the thermal stability and crystal structure. Detailed computational calculations, Hirshfeld analyses and lattice energy calculations were performed to quantify both the contribution of intra- and intermolecular interactions to the supramolecular assembly, as well as the influence on the stability of the structure. The structure-property relationship between the PDA-OXA crystal forms was established. Moreover, the phase transformation mechanism between the crystalline forms of PDA-OXA has been established, and the control strategy of specific crystal forms was developed from the water activity-temperature phase diagram and relevant thermodynamic data. Finally, the influence of the polymorphism of the monomer and the polymerization methods on the properties of the polymer was investigated. The nylon 52 product obtained showed good appearance, high hardness and thermal stability, the polymer made using the anhydrate as the monomer has better thermodynamic properties than that prepared from the dihydrate, indicating practical industrial application prospects.
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Affiliation(s)
- Zihan Li
- National Engineering Technique Research Center for Biotechnology, State Key Laboratory of Materials-Oriented Chemical Engineering, Jiangsu Synergetic Innovation Center for Advanced Bio-Manufacture, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, No. 30, Puzhu South Road, Nanjing 211816, People’s Republic of China
| | - Shushu Li
- National Engineering Technique Research Center for Biotechnology, State Key Laboratory of Materials-Oriented Chemical Engineering, Jiangsu Synergetic Innovation Center for Advanced Bio-Manufacture, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, No. 30, Puzhu South Road, Nanjing 211816, People’s Republic of China
| | - Pengpeng Yang
- National Engineering Technique Research Center for Biotechnology, State Key Laboratory of Materials-Oriented Chemical Engineering, Jiangsu Synergetic Innovation Center for Advanced Bio-Manufacture, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, No. 30, Puzhu South Road, Nanjing 211816, People’s Republic of China
| | - Xincao Fang
- National Engineering Technique Research Center for Biotechnology, State Key Laboratory of Materials-Oriented Chemical Engineering, Jiangsu Synergetic Innovation Center for Advanced Bio-Manufacture, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, No. 30, Puzhu South Road, Nanjing 211816, People’s Republic of China
| | - Qingshi Wen
- Industrial Biotechnology Institute of Jiangsu Industrial Technology Research Institute, Nanjing 211816, People’s Republic of China
| | - Ming Li
- National Engineering Technique Research Center for Biotechnology, State Key Laboratory of Materials-Oriented Chemical Engineering, Jiangsu Synergetic Innovation Center for Advanced Bio-Manufacture, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, No. 30, Puzhu South Road, Nanjing 211816, People’s Republic of China
| | - Wei Zhuang
- National Engineering Technique Research Center for Biotechnology, State Key Laboratory of Materials-Oriented Chemical Engineering, Jiangsu Synergetic Innovation Center for Advanced Bio-Manufacture, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, No. 30, Puzhu South Road, Nanjing 211816, People’s Republic of China
| | - Jinglan Wu
- National Engineering Technique Research Center for Biotechnology, State Key Laboratory of Materials-Oriented Chemical Engineering, Jiangsu Synergetic Innovation Center for Advanced Bio-Manufacture, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, No. 30, Puzhu South Road, Nanjing 211816, People’s Republic of China
| | - Hanjie Ying
- National Engineering Technique Research Center for Biotechnology, State Key Laboratory of Materials-Oriented Chemical Engineering, Jiangsu Synergetic Innovation Center for Advanced Bio-Manufacture, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, No. 30, Puzhu South Road, Nanjing 211816, People’s Republic of China
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Lee JA, Ahn JH, Kim GB, Choi S, Kim JY, Lee SY. Metabolic engineering of Mannheimia succiniciproducens for malic acid production using dimethylsulfoxide as an electron acceptor. Biotechnol Bioeng 2023; 120:203-215. [PMID: 36128631 DOI: 10.1002/bit.28242] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2022] [Revised: 09/14/2022] [Accepted: 09/16/2022] [Indexed: 11/12/2022]
Abstract
Microbial production of various TCA intermediates and related chemicals through the reductive TCA cycle has been of great interest. However, rumen bacteria that naturally possess strong reductive TCA cycle have been rarely studied to produce these chemicals, except for succinic acid, due to their dependence on fumarate reduction to transport electrons for ATP synthesis. In this study, malic acid (MA), a dicarboxylic acid of industrial importance, was selected as a target chemical for mass production using Mannheimia succiniciproducens, a rumen bacterium possessing a strong reductive branch of the TCA cycle. The metabolic pathway was reconstructed by eliminating fumarase to prevent MA conversion to fumarate. The respiration system of M. succiniciproducens was reconstructed by introducing the Actinobacillus succinogenes dimethylsulfoxide (DMSO) reductase to improve cell growth using DMSO as an electron acceptor. Also, the cell membrane was engineered by employing Pseudomonas aeruginosa cis-trans isomerase to enhance MA tolerance. High inoculum fed-batch fermentation of the final engineered strain produced 61 g/L of MA with an overall productivity of 2.27 g/L/h, which is the highest MA productivity reported to date. The systems metabolic engineering strategies reported in this study will be useful for developing anaerobic bioprocesses for the production of various industrially important chemicals.
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Affiliation(s)
- Jong An Lee
- Department of Chemical and Biomolecular Engineering (BK21 Four Program), Metabolic and Biomolecular Engineering National Research Laboratory, Systems Metabolic Engineering and Systems Healthcare Cross-Generation Collaborative Laboratory, Institute for the BioCentury, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, Korea
| | - Jung Ho Ahn
- Department of Chemical and Biomolecular Engineering (BK21 Four Program), Metabolic and Biomolecular Engineering National Research Laboratory, Systems Metabolic Engineering and Systems Healthcare Cross-Generation Collaborative Laboratory, Institute for the BioCentury, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, Korea
| | - Gi Bae Kim
- Department of Chemical and Biomolecular Engineering (BK21 Four Program), Metabolic and Biomolecular Engineering National Research Laboratory, Systems Metabolic Engineering and Systems Healthcare Cross-Generation Collaborative Laboratory, Institute for the BioCentury, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, Korea
| | - Sol Choi
- Department of Chemical and Biomolecular Engineering (BK21 Four Program), Metabolic and Biomolecular Engineering National Research Laboratory, Systems Metabolic Engineering and Systems Healthcare Cross-Generation Collaborative Laboratory, Institute for the BioCentury, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, Korea
| | - Ji Yeon Kim
- Department of Chemical and Biomolecular Engineering (BK21 Four Program), Metabolic and Biomolecular Engineering National Research Laboratory, Systems Metabolic Engineering and Systems Healthcare Cross-Generation Collaborative Laboratory, Institute for the BioCentury, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, Korea
| | - Sang Yup Lee
- Department of Chemical and Biomolecular Engineering (BK21 Four Program), Metabolic and Biomolecular Engineering National Research Laboratory, Systems Metabolic Engineering and Systems Healthcare Cross-Generation Collaborative Laboratory, Institute for the BioCentury, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, Korea.,BioInformatics Research Center and BioProcess Engineering Research Center, KAIST, Daejeon, Korea
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Liu X, Zhao G, Sun S, Fan C, Feng X, Xiong P. Biosynthetic Pathway and Metabolic Engineering of Succinic Acid. Front Bioeng Biotechnol 2022; 10:843887. [PMID: 35350186 PMCID: PMC8957974 DOI: 10.3389/fbioe.2022.843887] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2021] [Accepted: 02/16/2022] [Indexed: 11/25/2022] Open
Abstract
Succinic acid, a dicarboxylic acid produced as an intermediate of the tricarboxylic acid (TCA) cycle, is one of the most important platform chemicals for the production of various high value-added derivatives. As traditional chemical synthesis processes suffer from nonrenewable resources and environment pollution, succinic acid biosynthesis has drawn increasing attention as a viable, more environmentally friendly alternative. To date, several metabolic engineering approaches have been utilized for constructing and optimizing succinic acid cell factories. In this review, different succinic acid biosynthesis pathways are summarized, with a focus on the key enzymes and metabolic engineering approaches, which mainly include redirecting carbon flux, balancing NADH/NAD+ ratios, and optimizing CO2 supplementation. Finally, future perspectives on the microbial production of succinic acid are discussed.
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Affiliation(s)
- Xiutao Liu
- School of Life Sciences and Medicine, Shandong University of Technology, Zibo, China
| | - Guang Zhao
- State Key Lab of Microbial Technology, Shandong University, Qingdao, China
| | - Shengjie Sun
- School of Life Sciences and Medicine, Shandong University of Technology, Zibo, China
| | - Chuanle Fan
- CAS Key Laboratory of Biobased Materials, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, China.,School of Chemical Engineering, University of Chinese Academy of Sciences, Beijing, China
| | - Xinjun Feng
- CAS Key Laboratory of Biobased Materials, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, China
| | - Peng Xiong
- School of Life Sciences and Medicine, Shandong University of Technology, Zibo, China
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Insights on the Advancements of In Silico Metabolic Studies of Succinic Acid Producing Microorganisms: A Review with Emphasis on Actinobacillus succinogenes. FERMENTATION-BASEL 2021. [DOI: 10.3390/fermentation7040220] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Succinic acid (SA) is one of the top candidate value-added chemicals that can be produced from biomass via microbial fermentation. A considerable number of cell factories have been proposed in the past two decades as native as well as non-native SA producers. Actinobacillus succinogenes is among the best and earliest known natural SA producers. However, its industrial application has not yet been realized due to various underlying challenges. Previous studies revealed that the optimization of environmental conditions alone could not entirely resolve these critical problems. On the other hand, microbial in silico metabolic modeling approaches have lately been the center of attention and have been applied for the efficient production of valuable commodities including SA. Then again, literature survey results indicated the absence of up-to-date reviews assessing this issue, specifically concerning SA production. Hence, this review was designed to discuss accomplishments and future perspectives of in silico studies on the metabolic capabilities of SA producers. Herein, research progress on SA and A. succinogenes, pathways involved in SA production, metabolic models of SA-producing microorganisms, and status, limitations and prospects on in silico studies of A. succinogenes were elaborated. All in all, this review is believed to provide insights to understand the current scenario and to develop efficient mathematical models for designing robust SA-producing microbial strains.
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Li Z, Xu M, Liu H, Wen Q, Fu J, Zhuang W, Yang P, Wu J, Ying H. Monohydrate and anhydrate of nylon 5I monomer 1,5-pentanediamine-isophthalate. RSC Adv 2020; 10:44774-44784. [PMID: 35516270 PMCID: PMC9058625 DOI: 10.1039/d0ra08767j] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2020] [Accepted: 11/11/2020] [Indexed: 11/21/2022] Open
Abstract
Nylon 5I is one of the new bio-based nylon materials. Its raw material 1,5-pentanediamine (PDA) is prepared by biological methods using biomass as the raw material. The high-performance polymer materials require the original high-quality monomers. 1,5-Pentanediamine–isophthalate (PDA–IPA) was taken as the direct monomer for the preparation of nylon 5I, and the crystallization was a valuable and essential approach to preparing the good-performance monomer salt. In this report, we found and obtained two crystal forms of PDA–IPA, monohydrate and an anhydrous form. Their crystal structures were determined and analyzed by single crystal X-ray diffraction (SCXRD), powder X-ray diffraction (PXRD), and Fourier transform infrared spectroscopy (FTIR). Hirshfeld surface maps were employed to capture the differences in the interactions present in the two forms. The thermal behaviors were characterized by differential scanning calorimetry (DSC) and thermogravimetric analysis (TGA). Moreover, the monohydrate and anhydrous phase can transform to each other through solid–solid transformation or solution-mediated phase transformation, and the critical values of the phase transformation were determined. Finally, the relative stability of the two forms under different thermodynamic conditions was discussed, especially the influence of temperature and water activity on the stability. Monohydrate and anhydrous phases of PDA–IPA single crystals have been identified by single crystal X-ray diffraction. The monohydrate and anhydrate phases can achieve mutual transformation under certain conditions, and depend strongly on the temperature and water activity.![]()
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Affiliation(s)
- Zihan Li
- National Engineering Technique Research Center for Biotechnology, State Key Laboratory of Materials-Oriented Chemical Engineering, Jiangsu Synergetic Innovation Center for Advanced Bio-Manufacture, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University No. 30, Puzhu South Road 211816 Nanjing China
| | - Mengjie Xu
- National Engineering Technique Research Center for Biotechnology, State Key Laboratory of Materials-Oriented Chemical Engineering, Jiangsu Synergetic Innovation Center for Advanced Bio-Manufacture, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University No. 30, Puzhu South Road 211816 Nanjing China
| | - Haodong Liu
- National Engineering Technique Research Center for Biotechnology, State Key Laboratory of Materials-Oriented Chemical Engineering, Jiangsu Synergetic Innovation Center for Advanced Bio-Manufacture, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University No. 30, Puzhu South Road 211816 Nanjing China
| | - Qingshi Wen
- Industrial Biotechnology Institute of Jiangsu Industrial Technology Research Institute 211816 Nanjing China
| | - Jinqiu Fu
- School of Chemical Engineering, Zhengzhou University Zhengzhou 450001 China
| | - Wei Zhuang
- National Engineering Technique Research Center for Biotechnology, State Key Laboratory of Materials-Oriented Chemical Engineering, Jiangsu Synergetic Innovation Center for Advanced Bio-Manufacture, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University No. 30, Puzhu South Road 211816 Nanjing China
| | - Pengpeng Yang
- National Engineering Technique Research Center for Biotechnology, State Key Laboratory of Materials-Oriented Chemical Engineering, Jiangsu Synergetic Innovation Center for Advanced Bio-Manufacture, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University No. 30, Puzhu South Road 211816 Nanjing China
| | - Jinglan Wu
- National Engineering Technique Research Center for Biotechnology, State Key Laboratory of Materials-Oriented Chemical Engineering, Jiangsu Synergetic Innovation Center for Advanced Bio-Manufacture, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University No. 30, Puzhu South Road 211816 Nanjing China
| | - Hanjie Ying
- National Engineering Technique Research Center for Biotechnology, State Key Laboratory of Materials-Oriented Chemical Engineering, Jiangsu Synergetic Innovation Center for Advanced Bio-Manufacture, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University No. 30, Puzhu South Road 211816 Nanjing China
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12
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Fermentation of organic wastes and CO2 + H2 off-gas by microbiotas provides short-chain fatty acids and ethanol for n-caproate production. J CO2 UTIL 2020. [DOI: 10.1016/j.jcou.2020.101314] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
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13
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Li Z, Yang P, Liu H, Liu J, Zhu S, Li X, Zhuang W, Wu J, Ying H. Crystal forms and phase transformation of 1,5-pentanediamine-terephthalate: a bio-based nylon 5T monomer. ACTA CRYSTALLOGRAPHICA SECTION B, STRUCTURAL SCIENCE, CRYSTAL ENGINEERING AND MATERIALS 2020; 76:524-533. [PMID: 32831271 DOI: 10.1107/s2052520620006265] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/20/2020] [Accepted: 05/08/2020] [Indexed: 06/11/2023]
Abstract
Nylon 5T is one of the bio-based nylons, its raw material 1,5-pentanediamine is derived from biomass resources and produced by biological methods. 1,5-pentanediamine-terephthalate (PDA-TPA) is the monomeric salt for nylon 5T polymerization, and its own product quality has a significant impact on the performance of nylon 5T. PDA-TPA was prepared by anti-solvent crystallization in this study. It exists in two solid forms, a monohydrate [form (I)] and an anhydrous phase [form (II)]. The transition temperature of the two phases was around 65°C in the given ethanol-water binary (7:1) mixture. The characterization of monohydrate and anhydrate phases regarding structures and stabilities was carefully carried out using powder X-ray diffraction, single crystal X-ray diffraction, differential scanning calorimetry, thermogravimetric analysis, hot-stage microscopy and Fourier transform infrared spectroscopy. The relationship between the molecular interactions of monohydrate and anhydrate phases under different packing architectures and their thermal behaviours was analysed and established. In addition, the relationships between the structures and thermal behaviours for the two solid forms were analysed and established. In addition, the effect of solvent on phase conversion, the relationships between the temperature and water activity, as well as the relative stability of monohydrate and anhydrate phases under different thermodynamic conditions, were investigated by solid-solid transformation and solvent-mediated transformation experiments. It was obvious that the transition temperature of monohydrate and anhydrate phases of PDA-TPA was significantly influenced by water activity, and the larger the value of water activity is, the higher is the transition temperature. These studies give insight into the transformation of nylon 5T monomer salt and contribute to the control of target crystal preparation.
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Affiliation(s)
- Zihan Li
- National Engineering Technique Research Center for Biotechnology, State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, and Jiangsu Synergetic Innovation Center for Advanced Bio-Manufacture, Nanjing Tech University, Nanjing, 210009, People's Republic of China
| | - Pengpeng Yang
- National Engineering Technique Research Center for Biotechnology, State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, and Jiangsu Synergetic Innovation Center for Advanced Bio-Manufacture, Nanjing Tech University, Nanjing, 210009, People's Republic of China
| | - Haodong Liu
- National Engineering Technique Research Center for Biotechnology, State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, and Jiangsu Synergetic Innovation Center for Advanced Bio-Manufacture, Nanjing Tech University, Nanjing, 210009, People's Republic of China
| | - Jun Liu
- Central South University of Forestry and Technology, Shaoshan Nan Road No. 498, Changsha, Hunan 41000, People's Republic of China
| | - Sha Zhu
- National Engineering Technique Research Center for Biotechnology, State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, and Jiangsu Synergetic Innovation Center for Advanced Bio-Manufacture, Nanjing Tech University, Nanjing, 210009, People's Republic of China
| | - Xiaojie Li
- National Engineering Technique Research Center for Biotechnology, State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, and Jiangsu Synergetic Innovation Center for Advanced Bio-Manufacture, Nanjing Tech University, Nanjing, 210009, People's Republic of China
| | - Wei Zhuang
- National Engineering Technique Research Center for Biotechnology, State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, and Jiangsu Synergetic Innovation Center for Advanced Bio-Manufacture, Nanjing Tech University, Nanjing, 210009, People's Republic of China
| | - Jinglan Wu
- National Engineering Technique Research Center for Biotechnology, State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, and Jiangsu Synergetic Innovation Center for Advanced Bio-Manufacture, Nanjing Tech University, Nanjing, 210009, People's Republic of China
| | - Hanjie Ying
- National Engineering Technique Research Center for Biotechnology, State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, and Jiangsu Synergetic Innovation Center for Advanced Bio-Manufacture, Nanjing Tech University, Nanjing, 210009, People's Republic of China
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14
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Enhanced succinic acid production by Mannheimia employing optimal malate dehydrogenase. Nat Commun 2020; 11:1970. [PMID: 32327663 PMCID: PMC7181634 DOI: 10.1038/s41467-020-15839-z] [Citation(s) in RCA: 44] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2019] [Accepted: 03/31/2020] [Indexed: 02/06/2023] Open
Abstract
Succinic acid (SA), a dicarboxylic acid of industrial importance, can be efficiently produced by metabolically engineered Mannheimia succiniciproducens. Malate dehydrogenase (MDH) is one of the key enzymes for SA production, but has not been well characterized. Here we report biochemical and structural analyses of various MDHs and development of hyper-SA producing M. succiniciproducens by introducing the best MDH. Corynebacterium glutamicum MDH (CgMDH) shows the highest specific activity and least substrate inhibition, whereas M. succiniciproducens MDH (MsMDH) shows low specific activity at physiological pH and strong uncompetitive inhibition toward oxaloacetate (ki of 67.4 and 588.9 μM for MsMDH and CgMDH, respectively). Structural comparison of the two MDHs reveals a key residue influencing the specific activity and susceptibility to substrate inhibition. A high-inoculum fed-batch fermentation of the final strain expressing cgmdh produces 134.25 g L-1 of SA with the maximum productivity of 21.3 g L-1 h-1, demonstrating the importance of enzyme optimization in strain development.
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15
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Zhou N, Zhang A, Wei G, Yang S, Xu S, Chen K, Ouyang P. Cadaverine Production From L-Lysine With Chitin-Binding Protein-Mediated Lysine Decarboxylase Immobilization. Front Bioeng Biotechnol 2020; 8:103. [PMID: 32195228 PMCID: PMC7062646 DOI: 10.3389/fbioe.2020.00103] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2019] [Accepted: 02/03/2020] [Indexed: 12/26/2022] Open
Abstract
Lysine decarboxylase (CadA) can directly convert L-lysine to cadaverine, which is an important platform chemical that can be used to produce polyamides. However, the non-recyclable and the poor pH tolerance of pure CadA hampered its practical application. Herein, a one-step purification and immobilization procedure of CadA was established to investigate the cadaverine production from L-lysine. Renewable biomass chitin was used as a carrier for lysine decarboxylase (CadA) immobilization via fusion of a chitin-binding domain (ChBD). Scanning electron microscopy, laser scanning confocal microscopy, fourier transform infrared spectra, elemental analysis, and thermal gravimetric analysis proved that the fusion protein ChBD-CadA can be adsorbed on chitin effectively. Furthermore, the fusion protein (ChBD-CadA) existed better pH stability compared to wild CadA, and kept over 73% of the highest activity at pH 8.0. Meanwhile, the ChBD-CadA showed high specificity toward chitin and reached 93% immobilization yield within 10 min under the optimum conditions. The immobilized ChBD-CadA (I-ChBD-CadA) could efficiently converted L-lysine at 200.0 g/L to cadaverine at 135.6 g/L in a batch conversion within 120 min, achieving a 97% molar yield of the substrate L-lysine. In addition, the I-ChBD-CadA was able to be reused under a high concentration of L-lysine and retained over 57% of its original activity after four cycles of use without acid addition to maintain pH. These results demonstrate that immobilization of CadA using chitin-binding domain has the potential in cadaverine production on an industrial scale.
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Affiliation(s)
- Ning Zhou
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, China
| | - Alei Zhang
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, China
| | - Guoguang Wei
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, China
| | - Sai Yang
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, China
| | - Sheng Xu
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, China
| | - Kequan Chen
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, China
| | - Pingkai Ouyang
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, China
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16
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Link between Heterotrophic Carbon Fixation and Virulence in the Porcine Lung Pathogen Actinobacillus pleuropneumoniae. Infect Immun 2019; 87:IAI.00768-18. [PMID: 31285248 DOI: 10.1128/iai.00768-18] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2018] [Accepted: 06/24/2019] [Indexed: 01/01/2023] Open
Abstract
Actinobacillus pleuropneumoniae is a capnophilic pathogen of the porcine respiratory tract lacking enzymes of the oxidative branch of the tricarboxylic acid (TCA) cycle. We previously claimed that A. pleuropneumoniae instead uses the reductive branch in order to generate energy and metabolites. Here, we show that bicarbonate and oxaloacetate supported anaerobic growth of A. pleuropneumoniae Isotope mass spectrometry revealed heterotrophic fixation of carbon from stable isotope-labeled bicarbonate by A. pleuropneumoniae, which was confirmed by nano-scale secondary ion mass spectrometry at a single-cell level. By gas chromatography-combustion-isotope ratio mass spectrometry we could further show that the labeled carbon atom is mainly incorporated into the amino acids aspartate and lysine, which are derived from the TCA metabolite oxaloacetate. We therefore suggest that carbon fixation occurs at the interface of glycolysis and the reductive branch of the TCA cycle. The heme precursor δ-aminolevulinic acid supported growth of A. pleuropneumoniae, similar to bicarbonate, implying that anaplerotic carbon fixation is needed for heme synthesis. However, deletion of potential carbon-fixing enzymes, including PEP-carboxylase (PEPC), PEP-carboxykinase (PEPCK), malic enzyme, and oxaloacetate decarboxylase, as well as various combinations thereof, did not affect carbon fixation. Interestingly, generation of a deletion mutant lacking all four enzymes was not possible, suggesting that carbon fixation in A. pleuropneumoniae is an essential metabolic pathway controlled by a redundant set of enzymes. A double deletion mutant lacking PEPC and PEPCK was not impaired in carbon fixation in vitro but showed reduction of virulence in a pig infection model.
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17
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Röhl A, Bockmayr A. Finding MEMo: minimum sets of elementary flux modes. J Math Biol 2019; 79:1749-1777. [PMID: 31388689 DOI: 10.1007/s00285-019-01409-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2018] [Revised: 07/15/2019] [Indexed: 10/26/2022]
Abstract
Metabolic network reconstructions are widely used in computational systems biology for in silico studies of cellular metabolism. A common approach to analyse these models are elementary flux modes (EFMs), which correspond to minimal functional units in the network. Already for medium-sized networks, it is often impossible to compute the set of all EFMs, due to their huge number. From a practical point of view, this might also not be necessary because a subset of EFMs may already be sufficient to answer relevant biological questions. In this article, we study MEMos or minimum sets of EFMs that can generate all possible steady-state behaviours of a metabolic network. The number of EFMs in a MEMo may be by several orders of magnitude smaller than the total number of EFMs. Using MEMos, we can compute generating sets of EFMs in metabolic networks where the whole set of EFMs is too large to be enumerated.
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Affiliation(s)
- Annika Röhl
- Department of Mathematics and Computer Science, Freie Universität Berlin, Arnimallee 6, 14195, Berlin, Germany.
| | - Alexander Bockmayr
- Department of Mathematics and Computer Science, Freie Universität Berlin, Arnimallee 6, 14195, Berlin, Germany
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18
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Liu J, Li H, Xiong H, Xie X, Chen N, Zhao G, Caiyin Q, Zhu H, Qiao J. Two-stage carbon distribution and cofactor generation for improving l-threonine production of Escherichia coli. Biotechnol Bioeng 2018; 116:110-120. [PMID: 30252940 DOI: 10.1002/bit.26844] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2018] [Revised: 09/09/2018] [Accepted: 09/21/2018] [Indexed: 12/14/2022]
Abstract
L-Threonine, a kind of essential amino acid, has numerous applications in food, pharmaceutical, and aquaculture industries. Fermentative l-threonine production from glucose has been achieved in Escherichia coli. However, there are still several limiting factors hindering further improvement of l-threonine productivity, such as the conflict between cell growth and production, byproduct accumulation, and insufficient availability of cofactors (adenosine triphosphate, NADH, and NADPH). Here, a metabolic modification strategy of two-stage carbon distribution and cofactor generation was proposed to address the above challenges in E. coli THRD, an l-threonine producing strain. The glycolytic fluxes towards tricarboxylic acid cycle were increased in growth stage through heterologous expression of pyruvate carboxylase, phosphoenolpyruvate carboxykinase, and citrate synthase, leading to improved glucose utilization and growth performance. In the production stage, the carbon flux was redirected into l-threonine synthetic pathway via a synthetic genetic circuit. Meanwhile, to sustain the transaminase reaction for l-threonine production, we developed an l-glutamate and NADPH generation system through overexpression of glutamate dehydrogenase, formate dehydrogenase, and pyridine nucleotide transhydrogenase. This strategy not only exhibited 2.02- and 1.21-fold increase in l-threonine production in shake flask and bioreactor fermentation, respectively, but had potential to be applied in the production of many other desired oxaloacetate derivatives, especially those involving cofactor reactions.
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Affiliation(s)
- Jiaheng Liu
- Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin, China.,School of Chemical Engineering and Technology, Tianjin University, Tianjin, China.,SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin) Tianjin University, Tianjin, China
| | - Huiling Li
- Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin, China.,School of Chemical Engineering and Technology, Tianjin University, Tianjin, China.,SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin) Tianjin University, Tianjin, China
| | - Hui Xiong
- Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin, China.,School of Chemical Engineering and Technology, Tianjin University, Tianjin, China.,SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin) Tianjin University, Tianjin, China
| | - Xixian Xie
- National and Local United Engineering Lab of Metabolic Control Fermentation Technology, Tianjin University of Science and Technology, Tianjin, China
| | - Ning Chen
- National and Local United Engineering Lab of Metabolic Control Fermentation Technology, Tianjin University of Science and Technology, Tianjin, China
| | - Guangrong Zhao
- Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin, China.,School of Chemical Engineering and Technology, Tianjin University, Tianjin, China.,SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin) Tianjin University, Tianjin, China
| | - Qinggele Caiyin
- Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin, China.,School of Chemical Engineering and Technology, Tianjin University, Tianjin, China
| | - Hongji Zhu
- Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin, China.,School of Chemical Engineering and Technology, Tianjin University, Tianjin, China
| | - Jianjun Qiao
- Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin, China.,School of Chemical Engineering and Technology, Tianjin University, Tianjin, China.,SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin) Tianjin University, Tianjin, China
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19
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Opportunities, challenges, and future perspectives of succinic acid production by Actinobacillus succinogenes. Appl Microbiol Biotechnol 2018; 102:9893-9910. [PMID: 30259101 DOI: 10.1007/s00253-018-9379-5] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2018] [Revised: 09/04/2018] [Accepted: 09/06/2018] [Indexed: 12/21/2022]
Abstract
Due to environmental issues and the depletion of fossil-based resources, ecofriendly sustainable biomass-based chemical production has been given more attention recently. Succinic acid (SA) is one of the top value added bio-based chemicals. It can be synthesized through microbial fermentation using various waste steam bioresources. Production of chemicals from waste streams has dual function as it alleviates environmental concerns; they could have caused because of their improper disposal and transform them into valuable products. To date, Actinobacillus succinogenes is termed as the best natural SA producer. However, few reviews regarding SA production by A. succinogenes were reported. Herewith, pathways and metabolic engineering strategies, biomass pretreatment and utilization, and process optimization related with SA fermentation by A. succinogenes were discussed in detail. In general, this review covered vital information including merits, achievements, progresses, challenges, and future perspectives in SA production using A. succinogenes. Therefore, it is believed that this review will provide platform to understand the potential of the strain and tackle existing hurdles so as to develop superior strain for industrial applications. It will also be used as a baseline for identification, isolation, and improvement of other SA-producing microbes.
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20
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Chen X, Zhou Y, Zhang D. EngineeringCorynebacterium crenatumfor enhancing succinic acid production. J Food Biochem 2018. [DOI: 10.1111/jfbc.12645] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Xiaoju Chen
- College of Chemistry and Material Engineering Chaohu University Chaohu China
| | - Yaojie Zhou
- School of Food and Biological Engineering Jiangsu University Zhenjiang China
| | - Di Zhang
- School of Food and Biological Engineering Jiangsu University Zhenjiang China
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21
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Genome-Scale In Silico Analysis for Enhanced Production of Succinic Acid in Zymomonas mobilis. Processes (Basel) 2018. [DOI: 10.3390/pr6040030] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
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22
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Rhie MN, Park B, Ko H, Choi I, Kim OB. Transcriptome analysis and anaerobic C 4 -dicarboxylate transport in Actinobacillus succinogenes. Microbiologyopen 2017; 7:e00565. [PMID: 29230966 PMCID: PMC6011838 DOI: 10.1002/mbo3.565] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2017] [Revised: 10/26/2017] [Accepted: 10/30/2017] [Indexed: 11/07/2022] Open
Abstract
A global transcriptome analysis of the natural succinate producer Actinobacillus succinogenes revealed that 353 genes were differentially expressed when grown on various carbon and energy sources, which were categorized into six functional groups. We then analyzed the expression pattern of 37 potential C4‐dicarboxylate transporters in detail. A total of six transporters were considered potential fumarate transporters: three transporters, Asuc_1999 (Dcu), Asuc_0304 (DASS), and Asuc_0270‐0273 (TRAP), were constitutively expressed, whereas three others, Asuc_1568 (DASS), Asuc_1482 (DASS), and Asuc_0142 (Dcu), were differentially expressed during growth on fumarate. Transport assays under anaerobic conditions with [14C]fumarate and [14C]succinate were performed to experimentally verify that A. succinogenes possesses multiple C4‐dicarboxlayte transport systems with different substrate affinities. Upon uptake of 5 mmol/L fumarate, the systems had substrate specificity for fumarate, oxaloacetate, and malate, but not for succinate. Uptake was optimal at pH 7, and was dependent on both proton and sodium gradients. Asuc_1999 was suspected to be a major C4‐dicarboxylate transporter because of its noticeably high and constitutive expression. An Asuc_1999 deletion (∆1999) decreased fumarate uptake significantly at approximately 5 mmol/L fumarate, which was complemented by the introduction of Asuc_1999. Asuc_1999 expressed in Escherichia coli catalyzed fumarate uptake at a level of 21.6 μmol·gDW−1·min−1. These results suggest that C4‐dicarboxylate transport in A. succinogenes is mediated by multiple transporters, which transport various types and concentrations of C4‐dicarboxylates.
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Affiliation(s)
- Mi Na Rhie
- Department of Life Science, and Interdisciplinary Program of EcoCreativeEwha Womans UniversitySeoulKorea
| | - Byeonghyeok Park
- Department of BiotechnologyCollege of Life Sciences and BiotechnologyKorea UniversitySeoulKorea
| | - Hyeok‐Jin Ko
- Department of BiotechnologyCollege of Life Sciences and BiotechnologyKorea UniversitySeoulKorea
| | - In‐Geol Choi
- Department of BiotechnologyCollege of Life Sciences and BiotechnologyKorea UniversitySeoulKorea
| | - Ok Bin Kim
- Department of Life Science, and Interdisciplinary Program of EcoCreativeEwha Womans UniversitySeoulKorea
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23
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Abstract
Systems metabolic engineering, which recently emerged as metabolic engineering integrated with systems biology, synthetic biology, and evolutionary engineering, allows engineering of microorganisms on a systemic level for the production of valuable chemicals far beyond its native capabilities. Here, we review the strategies for systems metabolic engineering and particularly its applications in Escherichia coli. First, we cover the various tools developed for genetic manipulation in E. coli to increase the production titers of desired chemicals. Next, we detail the strategies for systems metabolic engineering in E. coli, covering the engineering of the native metabolism, the expansion of metabolism with synthetic pathways, and the process engineering aspects undertaken to achieve higher production titers of desired chemicals. Finally, we examine a couple of notable products as case studies produced in E. coli strains developed by systems metabolic engineering. The large portfolio of chemical products successfully produced by engineered E. coli listed here demonstrates the sheer capacity of what can be envisioned and achieved with respect to microbial production of chemicals. Systems metabolic engineering is no longer in its infancy; it is now widely employed and is also positioned to further embrace next-generation interdisciplinary principles and innovation for its upgrade. Systems metabolic engineering will play increasingly important roles in developing industrial strains including E. coli that are capable of efficiently producing natural and nonnatural chemicals and materials from renewable nonfood biomass.
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24
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25
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Thuy NTH, Kongkaew A, Flood A, Boontawan A. Fermentation and crystallization of succinic acid from Actinobacillus succinogenes ATCC55618 using fresh cassava root as the main substrate. BIORESOURCE TECHNOLOGY 2017; 233:342-352. [PMID: 28285227 DOI: 10.1016/j.biortech.2017.02.114] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/16/2016] [Revised: 02/23/2017] [Accepted: 02/24/2017] [Indexed: 05/25/2023]
Abstract
The fermentation of succinic acid from fresh cassava root using Actinobacillus succinogenes ATCC55618, and the recovery of the product using crystallization were investigated. Fresh cassava root is an ideal succinic acid feedstock due to its low price and high starch content. Saccharification was carried out using commercially available enzymes and diammonium phosphate was used as an inexpensive nitrogen source. Different fermentation modes were compared in terms of product yield and productivity. Results for fed-batch fermentations showed that a succinic acid titer of 151.44g/L, with yield and productivity of 1.51gSA/gglucose and 3.22g/L/h could be obtained. Seeded batch cooling crystallization was investigated after pre-treatment using nanofiltration. A succinic acid crystal purity of 99.35% with a relative crystallinity of 96.77% was obtained from high seeding experiments. These results indicated that fresh cassava roots could be an economically alternative feedstock for a high quality succinic acid production.
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Affiliation(s)
- Nguyen Thi Huong Thuy
- School of Biotechnology, Institute of Agricultural Technology, Suranaree University of Technology, 111 University avenue, Muang district, Nakhon Ratchasima 30000, Thailand
| | - Artit Kongkaew
- School of Biotechnology, Institute of Agricultural Technology, Suranaree University of Technology, 111 University avenue, Muang district, Nakhon Ratchasima 30000, Thailand
| | - Adrian Flood
- Department of Chemical and Biomolecular Engineering, Vidyasirimedhi Institute of Science and Technology (VISTEC), Wangchan District, Rayong 21210, Thailand
| | - Apichat Boontawan
- School of Biotechnology, Institute of Agricultural Technology, Suranaree University of Technology, 111 University avenue, Muang district, Nakhon Ratchasima 30000, Thailand; Cassava Research Center, Suranaree University of Technology, 111 University avenue, Muang district, Nakhon Ratchasima 30000, Thailand.
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Biotechnological route for sustainable succinate production utilizing oil palm frond and kenaf as potential carbon sources. Appl Microbiol Biotechnol 2017; 101:3055-3075. [PMID: 28280869 DOI: 10.1007/s00253-017-8210-z] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2017] [Revised: 02/20/2017] [Accepted: 02/21/2017] [Indexed: 10/20/2022]
Abstract
Due to the world's dwindling energy supplies, greater thrust has been placed on the utilization of renewable resources for global succinate production. Exploration of such biotechnological route could be seen as an act of counterbalance to the continued fossil fuel dominance. Malaysia being a tropical country stands out among many other nations for its plenty of resources in the form of lignocellulosic biomass. To date, oil palm frond (OPF) contributes to the largest fraction of agricultural residues in Malaysia, while kenaf, a newly introduced fiber crop with relatively high growth rate, holds great potential for developing sustainable succinate production, apart from OPF. Utilization of non-food, inexhaustible, and low-cost derived biomass in the form of OPF and kenaf for bio-based succinate production remains largely untapped. Owing to the richness of carbohydrates in OPF and kenaf, bio-succinate commercialization using these sources appears as an attractive proposition for future sustainable developments. The aim of this paper was to review some research efforts in developing a biorefinery system based on OPF and kenaf as processing inputs. It presents the importance of the current progress in bio-succinate commercialization, in addition to describing the potential use of different succinate production hosts and various pretreatments-saccharifications under development for OPF and kenaf. Evaluations on the feasibility of OPF and kenaf as fermentation substrates are also discussed.
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Improvement of succinate production by release of end-product inhibition in Corynebacterium glutamicum. Metab Eng 2017; 40:157-164. [DOI: 10.1016/j.ymben.2017.02.004] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2016] [Revised: 01/31/2017] [Accepted: 02/12/2017] [Indexed: 11/20/2022]
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Kim WJ, Ahn JH, Kim HU, Kim TY, Lee SY. Metabolic engineering of Mannheimia succiniciproducens
for succinic acid production based on elementary mode analysis with clustering. Biotechnol J 2017; 12. [DOI: 10.1002/biot.201600701] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2016] [Revised: 12/12/2016] [Accepted: 12/13/2016] [Indexed: 11/06/2022]
Affiliation(s)
- Won Jun Kim
- Metabolic and Biomolecular Engineering National Research Laboratory; Department of Chemical and Biomolecular Engineering (BK21 Plus Program); Center for Systems and Synthetic Biotechnology; Institute for the BioCentury; Korea Advanced Institute of Science and Technology (KAIST); Daejeon Republic of Korea
| | - Jung Ho Ahn
- Metabolic and Biomolecular Engineering National Research Laboratory; Department of Chemical and Biomolecular Engineering (BK21 Plus Program); Center for Systems and Synthetic Biotechnology; Institute for the BioCentury; Korea Advanced Institute of Science and Technology (KAIST); Daejeon Republic of Korea
| | - Hyun Uk Kim
- Metabolic and Biomolecular Engineering National Research Laboratory; Department of Chemical and Biomolecular Engineering (BK21 Plus Program); Center for Systems and Synthetic Biotechnology; Institute for the BioCentury; Korea Advanced Institute of Science and Technology (KAIST); Daejeon Republic of Korea
- BioInformatics Research Center; Korea Advanced Institute of Science and Technology (KAIST); Daejeon Republic of Korea
| | - Tae Yong Kim
- Metabolic and Biomolecular Engineering National Research Laboratory; Department of Chemical and Biomolecular Engineering (BK21 Plus Program); Center for Systems and Synthetic Biotechnology; Institute for the BioCentury; Korea Advanced Institute of Science and Technology (KAIST); Daejeon Republic of Korea
- BioInformatics Research Center; Korea Advanced Institute of Science and Technology (KAIST); Daejeon Republic of Korea
| | - Sang Yup Lee
- Metabolic and Biomolecular Engineering National Research Laboratory; Department of Chemical and Biomolecular Engineering (BK21 Plus Program); Center for Systems and Synthetic Biotechnology; Institute for the BioCentury; Korea Advanced Institute of Science and Technology (KAIST); Daejeon Republic of Korea
- BioInformatics Research Center; Korea Advanced Institute of Science and Technology (KAIST); Daejeon Republic of Korea
- BioProcess Engineering Research Center; Korea Advanced Institute of Science and Technology (KAIST); Daejeon Republic of Korea
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29
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Affiliation(s)
- Jung Ho Ahn
- Metabolic and Biomolecular Engineering National Research Laboratory, Department of Chemical and Biomolecular Engineering (BK21 Plus Program), BioProcess Engineering Research Center, and Center for Systems and Synthetic Biotechnology, Institute for the BioCentury; KAIST; 291 Daehak-ro, Yuseong-gu Daejeon 34141 Republic of Korea
| | - Yu-Sin Jang
- Metabolic and Biomolecular Engineering National Research Laboratory, Department of Chemical and Biomolecular Engineering (BK21 Plus Program), BioProcess Engineering Research Center, and Center for Systems and Synthetic Biotechnology, Institute for the BioCentury; KAIST; 291 Daehak-ro, Yuseong-gu Daejeon 34141 Republic of Korea
| | - Sang Yup Lee
- Metabolic and Biomolecular Engineering National Research Laboratory, Department of Chemical and Biomolecular Engineering (BK21 Plus Program), BioProcess Engineering Research Center, and Center for Systems and Synthetic Biotechnology, Institute for the BioCentury; KAIST; 291 Daehak-ro, Yuseong-gu Daejeon 34141 Republic of Korea
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30
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Lee JW, Yi J, Kim TY, Choi S, Ahn JH, Song H, Lee MH, Lee SY. Homo-succinic acid production by metabolically engineered Mannheimia succiniciproducens. Metab Eng 2016; 38:409-417. [PMID: 27746096 DOI: 10.1016/j.ymben.2016.10.004] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2016] [Revised: 09/18/2016] [Accepted: 10/10/2016] [Indexed: 10/20/2022]
Abstract
Succinic acid (SA) is a four carbon dicarboxylic acid of great industrial interest that can be produced by microbial fermentation. Here we report development of a high-yield homo-SA producing Mannheimia succiniciproducens strain by metabolic engineering. The PALFK strain (ldhA-, pta-, ackA-, fruA-) was developed based on optimization of carbon flux towards SA production while minimizing byproducts formation through the integrated application of in silico genome-scale metabolic flux analysis, omics analyses, and reconstruction of central carbon metabolism. Based on in silico simulation, utilization of sucrose would enhance the SA production and cell growth rates, while consumption of glycerol would reduce the byproduct formation rates. Thus, sucrose and glycerol were selected as dual carbon sources to improve the SA yield and productivity, while deregulation of catabolite-repression was also performed in engineered M. succiniciproducens. Fed-batch fermentations of PALFK with low- and medium-density (OD600 of 0.4 and 9.0, respectively) inocula produced 69.2 and 78.4g/L of homo-SA with yields of 1.56 and 1.64mol/mol glucose equivalent and overall volumetric SA productivities of 2.50 and 6.02g/L/h, respectively, using sucrose and glycerol as dual carbon sources. The SA productivity could be further increased to 38.6g/L/h by employing a membrane cell recycle bioreactor system. The systems metabolic engineering strategies employed here for achieving homo-SA production with the highest overall performance indices reported to date will be generally applicable for developing superior industrial microorganisms and competitive processes for the bio-based production of other chemicals as well.
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Affiliation(s)
- Jeong Wook Lee
- Metabolic and Biomolecular Engineering National Research Laboratory, Department of Chemical and Biomolecular Engineering (BK21 Plus program), BioProcess Engineering Research Center, KAIST, 291 Daehak-ro, Yuseong-gu, Daejeon 34141, Republic of Korea
| | - Jongho Yi
- Metabolic and Biomolecular Engineering National Research Laboratory, Department of Chemical and Biomolecular Engineering (BK21 Plus program), BioProcess Engineering Research Center, KAIST, 291 Daehak-ro, Yuseong-gu, Daejeon 34141, Republic of Korea
| | - Tae Yong Kim
- Metabolic and Biomolecular Engineering National Research Laboratory, Department of Chemical and Biomolecular Engineering (BK21 Plus program), BioProcess Engineering Research Center, KAIST, 291 Daehak-ro, Yuseong-gu, Daejeon 34141, Republic of Korea
| | - Sol Choi
- Metabolic and Biomolecular Engineering National Research Laboratory, Department of Chemical and Biomolecular Engineering (BK21 Plus program), BioProcess Engineering Research Center, KAIST, 291 Daehak-ro, Yuseong-gu, Daejeon 34141, Republic of Korea; Center for Systems and Synthetic Biotechnology, Institute for the BioCentury, KAIST, 291 Daehak-ro, Yuseong-gu, Daejeon 34141, Republic of Korea
| | - Jung Ho Ahn
- Metabolic and Biomolecular Engineering National Research Laboratory, Department of Chemical and Biomolecular Engineering (BK21 Plus program), BioProcess Engineering Research Center, KAIST, 291 Daehak-ro, Yuseong-gu, Daejeon 34141, Republic of Korea; Center for Systems and Synthetic Biotechnology, Institute for the BioCentury, KAIST, 291 Daehak-ro, Yuseong-gu, Daejeon 34141, Republic of Korea
| | - Hyohak Song
- Metabolic and Biomolecular Engineering National Research Laboratory, Department of Chemical and Biomolecular Engineering (BK21 Plus program), BioProcess Engineering Research Center, KAIST, 291 Daehak-ro, Yuseong-gu, Daejeon 34141, Republic of Korea
| | - Moon-Hee Lee
- Metabolic and Biomolecular Engineering National Research Laboratory, Department of Chemical and Biomolecular Engineering (BK21 Plus program), BioProcess Engineering Research Center, KAIST, 291 Daehak-ro, Yuseong-gu, Daejeon 34141, Republic of Korea; Center for Systems and Synthetic Biotechnology, Institute for the BioCentury, KAIST, 291 Daehak-ro, Yuseong-gu, Daejeon 34141, Republic of Korea
| | - Sang Yup Lee
- Metabolic and Biomolecular Engineering National Research Laboratory, Department of Chemical and Biomolecular Engineering (BK21 Plus program), BioProcess Engineering Research Center, KAIST, 291 Daehak-ro, Yuseong-gu, Daejeon 34141, Republic of Korea; Center for Systems and Synthetic Biotechnology, Institute for the BioCentury, KAIST, 291 Daehak-ro, Yuseong-gu, Daejeon 34141, Republic of Korea.
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Pateraki C, Patsalou M, Vlysidis A, Kopsahelis N, Webb C, Koutinas AA, Koutinas M. Actinobacillus succinogenes : Advances on succinic acid production and prospects for development of integrated biorefineries. Biochem Eng J 2016. [DOI: 10.1016/j.bej.2016.04.005] [Citation(s) in RCA: 107] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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32
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Engineered biosynthesis of biodegradable polymers. ACTA ACUST UNITED AC 2016; 43:1037-58. [DOI: 10.1007/s10295-016-1785-z] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2015] [Accepted: 05/21/2016] [Indexed: 10/21/2022]
Abstract
Abstract
Advances in science and technology have resulted in the rapid development of biobased plastics and the major drivers for this expansion are rising environmental concerns of plastic pollution and the depletion of fossil-fuels. This paper presents a broad view on the recent developments of three promising biobased plastics, polylactic acid (PLA), polyhydroxyalkanoate (PHA) and polybutylene succinate (PBS), well known for their biodegradability. The article discusses the natural and recombinant host organisms used for fermentative production of monomers, alternative carbon feedstocks that have been used to lower production cost, different metabolic engineering strategies used to improve product titers, various fermentation technologies employed to increase productivities and finally, the different downstream processes used for recovery and purification of the monomers and polymers.
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33
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Choi S, Song H, Lim SW, Kim TY, Ahn JH, Lee JW, Lee MH, Lee SY. Highly selective production of succinic acid by metabolically engineeredMannheimia succiniciproducensand its efficient purification. Biotechnol Bioeng 2016; 113:2168-77. [DOI: 10.1002/bit.25988] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2016] [Revised: 03/09/2016] [Accepted: 04/06/2016] [Indexed: 02/04/2023]
Affiliation(s)
- Sol Choi
- Department of Chemical and Biomolecular Engineering (BK21 Plus Program), Metabolic and Biomolecular Engineering National Research Laboratory, BioProcess Engineering Research Center, and Center for Systems and Synthetic Biotechnology; Institute for the BioCentury; KAIST; 291 Daehak-ro Yuseong-gu Daejeon 34141 Republic of Korea
| | - Hyohak Song
- Department of Chemical and Biomolecular Engineering (BK21 Plus Program), Metabolic and Biomolecular Engineering National Research Laboratory, BioProcess Engineering Research Center, and Center for Systems and Synthetic Biotechnology; Institute for the BioCentury; KAIST; 291 Daehak-ro Yuseong-gu Daejeon 34141 Republic of Korea
| | - Sung Won Lim
- Department of Chemical and Biomolecular Engineering (BK21 Plus Program), Metabolic and Biomolecular Engineering National Research Laboratory, BioProcess Engineering Research Center, and Center for Systems and Synthetic Biotechnology; Institute for the BioCentury; KAIST; 291 Daehak-ro Yuseong-gu Daejeon 34141 Republic of Korea
| | - Tae Yong Kim
- Department of Chemical and Biomolecular Engineering (BK21 Plus Program), Metabolic and Biomolecular Engineering National Research Laboratory, BioProcess Engineering Research Center, and Center for Systems and Synthetic Biotechnology; Institute for the BioCentury; KAIST; 291 Daehak-ro Yuseong-gu Daejeon 34141 Republic of Korea
| | - Jung Ho Ahn
- Department of Chemical and Biomolecular Engineering (BK21 Plus Program), Metabolic and Biomolecular Engineering National Research Laboratory, BioProcess Engineering Research Center, and Center for Systems and Synthetic Biotechnology; Institute for the BioCentury; KAIST; 291 Daehak-ro Yuseong-gu Daejeon 34141 Republic of Korea
| | - Jeong Wook Lee
- Department of Chemical and Biomolecular Engineering (BK21 Plus Program), Metabolic and Biomolecular Engineering National Research Laboratory, BioProcess Engineering Research Center, and Center for Systems and Synthetic Biotechnology; Institute for the BioCentury; KAIST; 291 Daehak-ro Yuseong-gu Daejeon 34141 Republic of Korea
| | - Moon-Hee Lee
- Department of Chemical and Biomolecular Engineering (BK21 Plus Program), Metabolic and Biomolecular Engineering National Research Laboratory, BioProcess Engineering Research Center, and Center for Systems and Synthetic Biotechnology; Institute for the BioCentury; KAIST; 291 Daehak-ro Yuseong-gu Daejeon 34141 Republic of Korea
| | - Sang Yup Lee
- Department of Chemical and Biomolecular Engineering (BK21 Plus Program), Metabolic and Biomolecular Engineering National Research Laboratory, BioProcess Engineering Research Center, and Center for Systems and Synthetic Biotechnology; Institute for the BioCentury; KAIST; 291 Daehak-ro Yuseong-gu Daejeon 34141 Republic of Korea
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34
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Ahn JH, Jang YS, Lee SY. Production of succinic acid by metabolically engineered microorganisms. Curr Opin Biotechnol 2016; 42:54-66. [PMID: 26990278 DOI: 10.1016/j.copbio.2016.02.034] [Citation(s) in RCA: 168] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2016] [Revised: 02/25/2016] [Accepted: 02/26/2016] [Indexed: 01/07/2023]
Abstract
Succinic acid (SA) has been recognized as one of the most important bio-based building block chemicals due to its numerous potential applications. For the economical bio-based production of SA, extensive research works have been performed on developing microbial strains by metabolic engineering as well as fermentation and downstream processes. Here we review metabolic engineering strategies applied for bio-based production of SA using representative microorganisms, including Saccharomyces cerevisiae, Pichia kudriavzevii, Escherichia coli, Mannheimia succiniciproducens, Basfia succiniciproducens, Actinobacillus succinogenes, and Corynebacterium glutamicum. In particular, strategies employed for developing engineered strains of these microorganisms leading to the best performance indices (titer, yield, and productivity) are showcased based on the published papers as well as patents. Those processes currently under commercialization are also analyzed and future perspectives are provided.
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Affiliation(s)
- Jung Ho Ahn
- Metabolic and Biomolecular Engineering National Research Laboratory, Department of Chemical and Biomolecular Engineering (BK21 Plus Program), BioProcess Engineering Research Center, and Center for Systems and Synthetic Biotechnology, Institute for the BioCentury, KAIST, 291 Daehak-ro, Yuseong-gu, Daejeon 34141, Republic of Korea
| | - Yu-Sin Jang
- Metabolic and Biomolecular Engineering National Research Laboratory, Department of Chemical and Biomolecular Engineering (BK21 Plus Program), BioProcess Engineering Research Center, and Center for Systems and Synthetic Biotechnology, Institute for the BioCentury, KAIST, 291 Daehak-ro, Yuseong-gu, Daejeon 34141, Republic of Korea
| | - Sang Yup Lee
- Metabolic and Biomolecular Engineering National Research Laboratory, Department of Chemical and Biomolecular Engineering (BK21 Plus Program), BioProcess Engineering Research Center, and Center for Systems and Synthetic Biotechnology, Institute for the BioCentury, KAIST, 291 Daehak-ro, Yuseong-gu, Daejeon 34141, Republic of Korea.
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35
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Valdes N, Soto P, Cottet L, Alarcon P, Gonzalez A, Castillo A, Corsini G, Tello M. Draft genome sequence of Janthinobacterium lividum strain MTR reveals its mechanism of capnophilic behavior. Stand Genomic Sci 2015; 10:110. [PMID: 26605004 PMCID: PMC4657372 DOI: 10.1186/s40793-015-0104-z] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2015] [Accepted: 11/17/2015] [Indexed: 11/10/2022] Open
Abstract
Janthinobacterium lividum is a Gram-negative bacterium able to produce violacein, a pigment with antimicrobial and antitumor properties. Janthinobacterium lividum colonizes the skin of some amphibians and confers protection against fungal pathogens. The mechanisms underlying this association are not well understood. In order to identify the advantages for the bacterium to colonize amphibian skin we sequenced Janthinobacterium lividum strain MTR, a strain isolated from Cajón del Maipo, Chile. The strain has capnophilic behavior, with growth favored by high concentrations (5 %) of carbon dioxide. Its genome is 6,535,606 bp in size, with 5,362 coding sequences and a G + C content of 62.37 %. The presence of genes encoding for products that participate in the carbon fixation pathways (dark CAM pathways), and the entire set of genes encoding for the enzymes of the glyoxylate cycle may explain the capnophilic behavior and allow us to propose that the CO2 secreted by the skin of amphibians is the signal molecule that guides colonization by Janthinobacterium lividum.
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Affiliation(s)
- Natalia Valdes
- Unidad de Apoyo Bioinformático, Departamento de Biología, Facultad de Química y Biología, Universidad de Santiago de Chile, Alameda, 3363 Santiago, Chile
| | - Paola Soto
- Laboratorio de Metagenómica Bacteriana, Centro de Biotecnología Acuícola, Departamento de Biología, Facultad de Química y Biología, Universidad de Santiago de Chile, Alameda, 3363 Santiago, Chile
| | - Luis Cottet
- Laboratorio de Virología de Hongos, Departamento de Biología, Facultad de Química y Biología, Universidad de Santiago de Chile, Alameda, 3363 Santiago, Chile
| | - Paula Alarcon
- Laboratorio de Metagenómica Bacteriana, Centro de Biotecnología Acuícola, Departamento de Biología, Facultad de Química y Biología, Universidad de Santiago de Chile, Alameda, 3363 Santiago, Chile
| | - Alex Gonzalez
- Laboratorio de Microbiología Ambiental y Extremófilos, Departamento de Ciencias Biológicas y Biodiversidad, Universidad de los Lagos, Fuchslocher, 1305 Osorno, Chile
| | - Antonio Castillo
- Laboratorio de Virología de Hongos, Departamento de Biología, Facultad de Química y Biología, Universidad de Santiago de Chile, Alameda, 3363 Santiago, Chile
| | - Gino Corsini
- Centro de Investigación Biomédica, Instituto de Ciencias Biomédicas, Facultad de Ciencias de la Salud, Universidad Autónoma de Chile, El Llano Subercaseaux, 2801 Santiago, Chile ; Universidad Científica del Sur, Panamericana Sur Km. 19, Lima, Perú
| | - Mario Tello
- Laboratorio de Metagenómica Bacteriana, Centro de Biotecnología Acuícola, Departamento de Biología, Facultad de Química y Biología, Universidad de Santiago de Chile, Alameda, 3363 Santiago, Chile
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36
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Yin X, Li J, Shin HD, Du G, Liu L, Chen J. Metabolic engineering in the biotechnological production of organic acids in the tricarboxylic acid cycle of microorganisms: Advances and prospects. Biotechnol Adv 2015; 33:830-41. [DOI: 10.1016/j.biotechadv.2015.04.006] [Citation(s) in RCA: 103] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2015] [Revised: 04/08/2015] [Accepted: 04/11/2015] [Indexed: 01/15/2023]
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37
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Osanai T, Shirai T, Iijima H, Nakaya Y, Okamoto M, Kondo A, Hirai MY. Genetic manipulation of a metabolic enzyme and a transcriptional regulator increasing succinate excretion from unicellular cyanobacterium. Front Microbiol 2015; 6:1064. [PMID: 26500619 PMCID: PMC4594341 DOI: 10.3389/fmicb.2015.01064] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2015] [Accepted: 09/15/2015] [Indexed: 11/13/2022] Open
Abstract
Succinate is a building block compound that the U.S. Department of Energy (DOE) has declared as important in biorefineries, and it is widely used as a commodity chemical. Here, we identified the two genes increasing succinate production of the unicellular cyanobacterium Synechocystis sp. PCC 6803. Succinate was excreted under dark, anaerobic conditions, and its production level increased by knocking out ackA, which encodes an acetate kinase, and by overexpressing sigE, which encodes an RNA polymerase sigma factor. Glycogen catabolism and organic acid biosynthesis were enhanced in the mutant lacking ackA and overexpressing sigE, leading to an increase in succinate production reaching five times of the wild-type levels. Our genetic and metabolomic analyses thus demonstrated the effect of genetic manipulation of a metabolic enzyme and a transcriptional regulator on succinate excretion from this cyanobacterium with the data based on metabolomic technique.
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Affiliation(s)
- Takashi Osanai
- RIKEN Center for Sustainable Resource Science Yokohama, Japan ; Department of Agricultural Chemistry, School of Agriculture, Meiji University Kawasaki, Japan
| | | | - Hiroko Iijima
- RIKEN Center for Sustainable Resource Science Yokohama, Japan ; Department of Agricultural Chemistry, School of Agriculture, Meiji University Kawasaki, Japan
| | - Yuka Nakaya
- RIKEN Center for Sustainable Resource Science Yokohama, Japan ; Biomass Engineering Program, RIKEN Yokohama, Japan
| | - Mami Okamoto
- Biomass Engineering Program, RIKEN Yokohama, Japan
| | - Akihiko Kondo
- Biomass Engineering Program, RIKEN Yokohama, Japan ; Department of Chemical Science and Engineering, Graduate School of Engineering, Kobe University Kobe, Japan
| | - Masami Y Hirai
- RIKEN Center for Sustainable Resource Science Yokohama, Japan
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38
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Bhatia SK, Kim YH, Kim HJ, Seo HM, Kim JH, Song HS, Sathiyanarayanan G, Park SH, Park K, Yang YH. Biotransformation of lysine into cadaverine using barium alginate-immobilized Escherichia coli overexpressing CadA. Bioprocess Biosyst Eng 2015; 38:2315-22. [PMID: 26314400 DOI: 10.1007/s00449-015-1465-9] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2015] [Accepted: 08/22/2015] [Indexed: 11/26/2022]
Abstract
In this study, Escherichia coli cells overexpressing lysine decarboxylase (CadA) were used for cadaverine production. Barium alginate was selected as a matrix for immobilization of E. coli YH91. Free cells and immobilized cells (IC) were characterized for their physiochemical properties, and the optimum pH and temperature were determined as 6 and 37 °C, respectively. Immobilized cells were three times more thermally stable compared to free cells at the optimum temperature and had a half-life (t 1/2) of 131 h. The free cells lost most of lysine decarboxylase activity after nine cycles, but in contrast immobilized cells retained 56% of their residual activity even after the 18th cycle. The immobilized cells gave a maximum production of cadaverine (75.8 g/L) with 84% conversion.
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Affiliation(s)
- Shashi Kant Bhatia
- Department of Biological Engineering, College of Engineering, Konkuk University, Seoul, 143-701, Republic of Korea
| | - Yong Hyun Kim
- Department of Biological Engineering, College of Engineering, Konkuk University, Seoul, 143-701, Republic of Korea
| | - Hyun Joong Kim
- Department of Biological Engineering, College of Engineering, Konkuk University, Seoul, 143-701, Republic of Korea
| | - Hyung-Min Seo
- Department of Biological Engineering, College of Engineering, Konkuk University, Seoul, 143-701, Republic of Korea
| | - Jung-Ho Kim
- Department of Biological Engineering, College of Engineering, Konkuk University, Seoul, 143-701, Republic of Korea
| | - Hun-Seok Song
- Department of Biological Engineering, College of Engineering, Konkuk University, Seoul, 143-701, Republic of Korea
| | - Ganesan Sathiyanarayanan
- Department of Biological Engineering, College of Engineering, Konkuk University, Seoul, 143-701, Republic of Korea
| | - Sung-Hee Park
- Food Ingredients Center, Foods R&D, CheilJedang, Guro-dong, Guro-Gu, Seoul, 152-051, Republic of Korea
| | - Kyungmoon Park
- Department of Biological and Chemical Engineering, Hongik University, Sejong Ro 2639, Jochiwon, Sejong, 339-701, Republic of Korea
| | - Yung-Hun Yang
- Department of Biological Engineering, College of Engineering, Konkuk University, Seoul, 143-701, Republic of Korea.
- Microbial Carbohydrate Resource Bank, Konkuk University, Seoul, 143-701, Republic of Korea.
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39
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Phylogenomic and molecular demarcation of the core members of the polyphyletic pasteurellaceae genera actinobacillus, haemophilus, and pasteurella. Int J Genomics 2015; 2015:198560. [PMID: 25821780 PMCID: PMC4363679 DOI: 10.1155/2015/198560] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2014] [Revised: 01/19/2015] [Accepted: 01/26/2015] [Indexed: 12/18/2022] Open
Abstract
The genera Actinobacillus, Haemophilus, and Pasteurella exhibit extensive polyphyletic branching in phylogenetic trees and do not represent coherent clusters of species. In this study, we have utilized molecular signatures identified through comparative genomic analyses in conjunction with genome based and multilocus sequence based phylogenetic analyses to clarify the phylogenetic and taxonomic boundary of these genera. We have identified large clusters of Actinobacillus, Haemophilus, and Pasteurella species which represent the “sensu stricto” members of these genera. We have identified 3, 7, and 6 conserved signature indels (CSIs), which are specifically shared by sensu stricto members of Actinobacillus, Haemophilus, and Pasteurella, respectively. We have also identified two different sets of CSIs that are unique characteristics of the pathogen containing genera Aggregatibacter and Mannheimia, respectively. It is now possible to demarcate the genera Actinobacillus sensu stricto, Haemophilus sensu stricto, and Pasteurella sensu stricto on the basis of discrete molecular signatures. The other members of the genera Actinobacillus, Haemophilus, and Pasteurella that do not fall within the “sensu stricto” clades and do not contain these molecular signatures should be reclassified as other genera. The CSIs identified here also provide useful diagnostic targets for the identification of current and novel members of the indicated genera.
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Choi S, Song CW, Shin JH, Lee SY. Biorefineries for the production of top building block chemicals and their derivatives. Metab Eng 2015; 28:223-239. [PMID: 25576747 DOI: 10.1016/j.ymben.2014.12.007] [Citation(s) in RCA: 244] [Impact Index Per Article: 27.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2014] [Revised: 12/27/2014] [Accepted: 12/29/2014] [Indexed: 01/11/2023]
Abstract
Due to the growing concerns on the climate change and sustainability on petrochemical resources, DOE selected and announced the bio-based top 12 building blocks and discussed the needs for developing biorefinery technologies to replace the current petroleum based industry in 2004. Over the last 10 years after its announcement, many studies have been performed for the development of efficient technologies for the bio-based production of these chemicals and derivatives. Now, ten chemicals among these top 12 chemicals, excluding the l-aspartic acid and 3-hydroxybutyrolactone, have already been commercialized or are close to commercialization. In this paper, we review the current status of biorefinery development for the production of these platform chemicals and their derivatives. In addition, current technological advances on industrial strain development for the production of platform chemicals using micro-organisms will be covered in detail with case studies on succinic acid and 3-hydroxypropionic acid as examples.
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Affiliation(s)
- Sol Choi
- Metabolic and Biomolecular Engineering National Research Laboratory, Department of Chemical and Biomolecular Engineering (BK21 Plus program), Center for Systems and Synthetic Biotechnology, Institute for the BioCentury, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 305-701, Republic of Korea; BioProcess Engineering Research Center, KAIST, Daejeon 305-701, Republic of Korea
| | - Chan Woo Song
- Metabolic and Biomolecular Engineering National Research Laboratory, Department of Chemical and Biomolecular Engineering (BK21 Plus program), Center for Systems and Synthetic Biotechnology, Institute for the BioCentury, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 305-701, Republic of Korea
| | - Jae Ho Shin
- Metabolic and Biomolecular Engineering National Research Laboratory, Department of Chemical and Biomolecular Engineering (BK21 Plus program), Center for Systems and Synthetic Biotechnology, Institute for the BioCentury, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 305-701, Republic of Korea
| | - Sang Yup Lee
- Metabolic and Biomolecular Engineering National Research Laboratory, Department of Chemical and Biomolecular Engineering (BK21 Plus program), Center for Systems and Synthetic Biotechnology, Institute for the BioCentury, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 305-701, Republic of Korea; BioProcess Engineering Research Center, KAIST, Daejeon 305-701, Republic of Korea; BioInformatics Research Center, KAIST, Daejeon 305-701, Republic of Korea; The Novo Nordisk Foundation Center for Biosustainability, Technical University Denmark, Hørsholm, Denmark.
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Wang C, Yan D, Li Q, Sun W, Xing J. Ionic liquid pretreatment to increase succinic acid production from lignocellulosic biomass. BIORESOURCE TECHNOLOGY 2014; 172:283-289. [PMID: 25270043 DOI: 10.1016/j.biortech.2014.09.045] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/10/2014] [Revised: 09/09/2014] [Accepted: 09/10/2014] [Indexed: 05/25/2023]
Abstract
In this study, pinewood and corn stover pretreated with the ionic liquid (IL) 1-allyl-3-methylimidazolium chloride (AmimCl) were used as a feedstock for succinic acid production. Results reveal that 5% (v/v) AmimCl inhibited bacterial growth, whereas 0.01% (v/v) AmimCl inhibited succinic acid production. AmimCl was effective in extracting cellulose from pinewood and in degrading pinewood into a uniform pulp, as revealed by scanning electron microscopy (SEM). The rate of enzymatic hydrolysis of pinewood extract reached 72.16%. The combinations of AmimCl pretreatment with steam explosion or with hot compressed water were effective in treating corn stover, whereas AmimCl treatment alone did not result in a significant improvement. Pinewood extract produced 20.7g/L succinic acid with an average yield of 0.37g per gram of biomass. Workflow calculations indicated pine wood pretreated with IL has a theoretical yield of succinic acid of 57.1%. IL pretreatment led to increase in succinic acid yields.
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Affiliation(s)
- Caixia Wang
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, No. 16, Nanxiaojie, Dongzhimennei, Beijing 100700, China; National Key Laboratory of Biochemical Engineering, Institute of Process Engineering, Chinese Academy of Sciences, Beijing 100190, China
| | - Daojiang Yan
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, China
| | - Qiang Li
- National Key Laboratory of Biochemical Engineering, Institute of Process Engineering, Chinese Academy of Sciences, Beijing 100190, China
| | - Wei Sun
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, No. 16, Nanxiaojie, Dongzhimennei, Beijing 100700, China
| | - Jianmin Xing
- National Key Laboratory of Biochemical Engineering, Institute of Process Engineering, Chinese Academy of Sciences, Beijing 100190, China.
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Yun S, Lee EG, Kim SY, Shin JM, Jung WS, Oh DB, Lee SY, Kwon O. The CpxRA two-component system is involved in the maintenance of the integrity of the cell envelope in the rumen bacterium Mannheimia succiniciproducens. Curr Microbiol 2014; 70:103-9. [PMID: 25231942 DOI: 10.1007/s00284-014-0686-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2014] [Accepted: 07/29/2014] [Indexed: 11/28/2022]
Abstract
In this study, we characterized the CpxRA two-component signal transduction system of the rumen bacterium Mannheimia succiniciproducens. The truncated form of the CpxA sensor kinase protein without its transmembrane domain was able to autophosphorylate and transphosphorylate the CpxR response regulator protein in vitro. We identified 152 putative target genes for the Cpx system in M. succiniciproducens, which were differentially expressed by more than twofold upon overexpression of the CpxR protein. Genes of a putative 16-gene operon related to the cell wall and lipopolysaccharide biosynthesis were induced strongly upon CpxR overexpression. The promoter region of the first gene of this operon, wecC encoding UDP-N-acetyl-D-mannosaminuronate dehydrogenase, was analyzed and found to contain a sequence homologous to the CpxR box of Escherichia coli. An electrophoretic mobility shift assay showed that the phosphorylated CpxR proteins were able to bind specifically to PCR-amplified DNA fragments containing the promoter sequence of wecC. Furthermore, a cpxR-disrupted mutant strain exhibited increased envelope permeability compared with a wild-type strain. These results suggest that the Cpx system of M. succiniciproducens is involved in the maintenance of the integrity of the cell envelope.
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Affiliation(s)
- Seulgi Yun
- Synthetic Biology and Bioengineering Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, Republic of Korea
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Kind S, Neubauer S, Becker J, Yamamoto M, Völkert M, Abendroth GV, Zelder O, Wittmann C. From zero to hero – Production of bio-based nylon from renewable resources using engineered Corynebacterium glutamicum. Metab Eng 2014; 25:113-23. [DOI: 10.1016/j.ymben.2014.05.007] [Citation(s) in RCA: 203] [Impact Index Per Article: 20.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2014] [Revised: 04/03/2014] [Accepted: 05/05/2014] [Indexed: 01/06/2023]
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Park SJ, David Y, Baylon MG, Hong SH, Oh YH, Yang JE, Choi SY, Lee SH, Lee SY. Development of Metabolic Engineering Strategies for Microbial Platform to Produce Bioplastics. APPLIED CHEMISTRY FOR ENGINEERING 2014. [DOI: 10.14478/ace.2014.1031] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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REVIEW: The rumen microbiome: Composition, abundance, diversity, and new investigative tools. ACTA ACUST UNITED AC 2014. [DOI: 10.15232/s1080-7446(15)30076-0] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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Genome sequencing of rumen bacteria and archaea and its application to methane mitigation strategies. Animal 2013; 7 Suppl 2:235-43. [PMID: 23739466 DOI: 10.1017/s1751731113000700] [Citation(s) in RCA: 67] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Ruminant-derived methane (CH4), a potent greenhouse gas, is a consequence of microbial fermentation in the digestive tract of livestock. Development of mitigation strategies to reduce CH4 emissions from farmed animals is currently the subject of both scientific and environmental interest. Methanogens are the sole producers of ruminant CH4, and therefore CH4 abatement strategies can either target the methanogens themselves or target the other members of the rumen microbial community that produce substrates necessary for methanogenesis. Understanding the relationship that methanogens have with other rumen microbes is crucial when considering CH4 mitigation strategies for ruminant livestock. Genome sequencing of rumen microbes is an important tool to improve our knowledge of the processes that underpin those relationships. Currently, several rumen bacterial and archaeal genome projects are either complete or underway. Genome sequencing is providing information directly applicable to CH4 mitigation strategies based on vaccine and small molecule inhibitor approaches. In addition, genome sequencing is contributing information relevant to other CH4 mitigation strategies. These include the selection and breeding of low CH4-emitting animals through the interpretation of large-scale DNA and RNA sequencing studies and the modification of other microbial groups within the rumen, thereby changing the dynamics of microbial fermentation.
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Yang JE, Choi SY, Shin JH, Park SJ, Lee SY. Microbial production of lactate-containing polyesters. Microb Biotechnol 2013; 6:621-36. [PMID: 23718266 PMCID: PMC3815930 DOI: 10.1111/1751-7915.12066] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2013] [Revised: 04/19/2013] [Accepted: 04/22/2013] [Indexed: 12/31/2022] Open
Abstract
Due to our increasing concerns on environmental problems and limited fossil resources, biobased production of chemicals and materials through biorefinery has been attracting much attention. Optimization of the metabolic performance of microorganisms, the key biocatalysts for the efficient production of the desired target bioproducts, has been achieved by metabolic engineering. Metabolic engineering allowed more efficient production of polyhydroxyalkanoates, a family of microbial polyesters. More recently, non-natural polyesters containing lactate as a monomer have also been produced by one-step fermentation of engineered bacteria. Systems metabolic engineering integrating traditional metabolic engineering with systems biology, synthetic biology, protein/enzyme engineering through directed evolution and structural design, and evolutionary engineering, enabled microorganisms to efficiently produce natural and non-natural products. Here, we review the strategies for the metabolic engineering of microorganisms for the in vivo biosynthesis of lactate-containing polyesters and for the optimization of whole cell metabolism to efficiently produce lactate-containing polyesters. Also, major problems to be solved to further enhance the production of lactate-containing polyesters are discussed.
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Affiliation(s)
- Jung Eun Yang
- Metabolic and Biomolecular Engineering National Research Laboratory, Department of Chemical and Biomolecular Engineering (BK21 Program), Center for Systems and Synthetic Biotechnology, KAIST291 Daehak-ro, Yuseong-gu, Daejeon, 305-701, Korea
- Institute for the BioCentury, KAIST291 Daehak-ro, Yuseong-gu, Daejeon, 305-701, Korea
| | - So Young Choi
- Metabolic and Biomolecular Engineering National Research Laboratory, Department of Chemical and Biomolecular Engineering (BK21 Program), Center for Systems and Synthetic Biotechnology, KAIST291 Daehak-ro, Yuseong-gu, Daejeon, 305-701, Korea
- Institute for the BioCentury, KAIST291 Daehak-ro, Yuseong-gu, Daejeon, 305-701, Korea
| | - Jae Ho Shin
- Metabolic and Biomolecular Engineering National Research Laboratory, Department of Chemical and Biomolecular Engineering (BK21 Program), Center for Systems and Synthetic Biotechnology, KAIST291 Daehak-ro, Yuseong-gu, Daejeon, 305-701, Korea
- Institute for the BioCentury, KAIST291 Daehak-ro, Yuseong-gu, Daejeon, 305-701, Korea
| | - Si Jae Park
- Department of Environmental Engineering and Energy (Undergraduate program), Myongji UniversitySan 38-2, Nam-dong, Cheoin-gu, Yongin-si, Gyeonggido, 449-728, Korea
- Department of Energy Science and Technology (Graduate program), Myongji UniversitySan 38-2, Nam-dong, Cheoin-gu, Yongin-si, Gyeonggido, 449-728, Korea
| | - Sang Yup Lee
- Metabolic and Biomolecular Engineering National Research Laboratory, Department of Chemical and Biomolecular Engineering (BK21 Program), Center for Systems and Synthetic Biotechnology, KAIST291 Daehak-ro, Yuseong-gu, Daejeon, 305-701, Korea
- Institute for the BioCentury, KAIST291 Daehak-ro, Yuseong-gu, Daejeon, 305-701, Korea
- Department of Bio and Brain Engineering, Department of Biological Sciences, BioProcess Engineering Research Center, KAIST291 Daehak-ro, Yuseong-gu, Daejeon, 305-701, Korea
- Bioinformatics Research Center, KAIST291 Daehak-ro, Yuseong-gu, Daejeon, 305-701, Korea
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Becker J, Reinefeld J, Stellmacher R, Schäfer R, Lange A, Meyer H, Lalk M, Zelder O, von Abendroth G, Schröder H, Haefner S, Wittmann C. Systems-wide analysis and engineering of metabolic pathway fluxes in bio-succinate producing Basfia succiniciproducens. Biotechnol Bioeng 2013; 110:3013-23. [PMID: 23832568 DOI: 10.1002/bit.24963] [Citation(s) in RCA: 78] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2012] [Revised: 04/03/2013] [Accepted: 05/06/2013] [Indexed: 12/18/2022]
Abstract
Basfia succiniciproducens has been recently isolated as novel producer for succinate, an important platform chemical. In batch culture, the wild type exhibited a high natural yield of 0.75 mol succinate (mol glucose)⁻¹. Systems-wide ¹³C metabolic flux analysis identified undesired fluxes through pyruvate-formate lyase (PflD) and lactate dehydrogenase (LdhA). The double deletion strain B. succiniciproducens ΔldhA ΔpflD revealed a 45% improved product yield of 1.08 mol mol⁻¹. In addition, metabolic flux analysis unraveled the parallel in vivo activity of the oxidative and reductive branch of the TCA cycle in B. succiniciproducens, whereby the oxidative part mainly served for anabolism. The wild type re-directed surplus NADH via a cycle involving malic enzyme or via transhydrogenase, respectively, to supply NADPH for anabolism, because the fluxes through the oxidative PPP and isocitrate dehydrogenase, that also provide this cofactor, were not sufficient. This was not observed for the deletion mutants, B. succiniciproducens ΔpflD and ΔldhA ΔpflD, where PPP and isocitrate dehydrogenase flux alone matched with the reduced anabolic NADPH demand. The integration of the production performance into the theoretical flux space, computed by elementary flux mode analysis, revealed that B. succiniciproducens ΔldhA ΔpflD reached 62% of the theoretical maximum yield.
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Affiliation(s)
- Judith Becker
- Institute of Biochemical Engineering, Technische Universität Braunschweig, Gaußstraße 17, Braunschweig, D-38106, Germany
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Park SJ, Kim EY, Noh W, Park HM, Oh YH, Lee SH, Song BK, Jegal J, Lee SY. Metabolic engineering of Escherichia coli for the production of 5-aminovalerate and glutarate as C5 platform chemicals. Metab Eng 2013; 16:42-7. [DOI: 10.1016/j.ymben.2012.11.011] [Citation(s) in RCA: 118] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2012] [Revised: 11/07/2012] [Accepted: 11/30/2012] [Indexed: 02/07/2023]
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Improved production of L-threonine in Escherichia coli by use of a DNA scaffold system. Appl Environ Microbiol 2012; 79:774-82. [PMID: 23160128 DOI: 10.1128/aem.02578-12] [Citation(s) in RCA: 55] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Despite numerous approaches for the development of l-threonine-producing strains, strain development is still hampered by the intrinsic inefficiency of metabolic reactions caused by simple diffusion and random collisions of enzymes and metabolites. A scaffold system, which can promote the proximity of metabolic enzymes and increase the local concentration of intermediates, was reported to be one of the most promising solutions. Here, we report an improvement in l-threonine production in Escherichia coli using a DNA scaffold system, in which a zinc finger protein serves as an adapter for the site-specific binding of each enzyme involved in l-threonine production to a precisely ordered location on a DNA double helix to increase the proximity of enzymes and the local concentration of metabolites to maximize production. The optimized DNA scaffold system for l-threonine production significantly increased the efficiency of the threonine biosynthetic pathway in E. coli, substantially reducing the production time for l-threonine (by over 50%). In addition, this DNA scaffold system enhanced the growth rate of the host strain by reducing the intracellular concentration of toxic intermediates, such as homoserine. Our DNA scaffold system can be used as a platform technology for the construction and optimization of artificial metabolic pathways as well as for the production of many useful biomaterials.
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