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Gong Z, Zhang W, Chen J, Li J, Tan T. Upcycling CO2 into succinic acid via electrochemical and engineered Escherichia coli. BIORESOURCE TECHNOLOGY 2024; 406:130956. [PMID: 38871229 DOI: 10.1016/j.biortech.2024.130956] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/07/2024] [Revised: 06/04/2024] [Accepted: 06/10/2024] [Indexed: 06/15/2024]
Abstract
Converting CO2 into value-added chemicals still remains a grand challenge. Succinic acid has long been considered as one of the top building block chemicals. This study reported efficiently upcycling CO2 into succinic acid by combining between electrochemical and engineered Escherichia coli. In this process, the Cu-organic framework catalyst was synthesized for electrocatalytic CO2-to-ethanol conversion with high Faradaic efficiency (FE, 84.7 %) and relative purity (RP, 95 wt%). Subsequently, an engineered E. coli with efficiently assimilating CO2-derived ethanol to produce succinic acid was constructed by combining computational design and metabolic engineering, and the succinic acid titer reached 53.8 mM with the yield of 0.41 mol/mol, which is 82 % of the theoretical yield. This study effort to link the two processes of efficient ethanol synthesis by electrocatalytic CO2 and succinic acid production from CO2-derived ethanol, paving a way for the production of succinic acid and other value-added chemicals by converting CO2 into ethanol.
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Affiliation(s)
- Zhijin Gong
- National Energy R&D Center for Biorefinery, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, China; Beijing Key Laboratory of Bioprocess, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, China
| | - Wei Zhang
- National Energy R&D Center for Biorefinery, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, China; Beijing Key Laboratory of Bioprocess, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, China
| | - Jiayao Chen
- National Energy R&D Center for Biorefinery, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, China; Beijing Key Laboratory of Bioprocess, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, China
| | - Jingchuan Li
- National Energy R&D Center for Biorefinery, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, China; Beijing Key Laboratory of Bioprocess, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, China
| | - Tianwei Tan
- National Energy R&D Center for Biorefinery, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, China; Beijing Key Laboratory of Bioprocess, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, China.
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Meng J, Liu S, Wu X. Engineered probiotics as live biotherapeutics for diagnosis and treatment of human diseases. Crit Rev Microbiol 2024; 50:300-314. [PMID: 36946080 DOI: 10.1080/1040841x.2023.2190392] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2022] [Accepted: 01/09/2023] [Indexed: 03/23/2023]
Abstract
The use of probiotics to regulate the intestinal microbiota to prevent and treat a large number of disorders and diseases has been an international research hotspot. Although conventional probiotics have a certain regulatory role in nutrient metabolism, inhibiting pathogens, inducing immune regulation, and maintaining intestinal epithelial barrier function, they are unable to treat certain diseases. In recent years, aided by the continuous development of synthetic biology, engineering probiotics with desired characteristics and functionalities to benefit human health has made significant progress. In this article, we summarise the mechanism of action of conventional probiotics and their limitations and highlight the latest developments in the design and construction of probiotics as living diagnostics and therapeutics for the detection and treatment of a series of diseases, including pathogen infections, cancer, intestinal inflammation, metabolic disorders, vaccine delivery, cognitive health, and fatty liver. Besides we discuss the concerns regarding engineered probiotics and corresponding countermeasures and outline the desired features in the future development of engineered live biotherapeutics.
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Affiliation(s)
- Jiao Meng
- Laboratory of Nutrient Resources and Synthetic Biology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Science, Tianjin, China
| | - Shufan Liu
- Laboratory of Nutrient Resources and Synthetic Biology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Science, Tianjin, China
- Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, Tianjin University of Science and Technology; College of Bioengineering, Tianjin University of Science and Technology, Tianjin, China
| | - Xin Wu
- Laboratory of Nutrient Resources and Synthetic Biology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Science, Tianjin, China
- CAS Key Laboratory of Agro-Ecological Processes in Subtropical Region, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha, China
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Meng J, Liu S, Gao L, Hong K, Liu S, Wu X. Economical production of Pichia pastoris single cell protein from methanol at industrial pilot scale. Microb Cell Fact 2023; 22:198. [PMID: 37770920 PMCID: PMC10540378 DOI: 10.1186/s12934-023-02198-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Accepted: 09/06/2023] [Indexed: 09/30/2023] Open
Abstract
BACKGROUND Methanol, synthesized from CO2, is a potentially sustainable one-carbon (C1) resource for biomanufacturing. The use of methanol as a feedstock to produce single cell protein (SCP) has been investigated for decades as an alternative to alleviate the high global demand for animal-derived proteins. The methylotrophic yeast Pichia pastoris is an ideal host for methanol-based SCP synthesis due to its natural methanol assimilation ability. However, improving methanol utilization, tolerance to higher temperature, and the protein content of P. pastoris are also current challenges, which are of great significance to the economical industrial application using methanol as a feedstock for SCP production. RESULTS In the present work, adaptive laboratory evolution (ALE) has been employed to overcome the low methanol utilization efficiency and intolerance to a higher temperature of 33 °C in P. pastoris, associated with reduced carbon loss due to the lessened detoxification of intracellular formaldehyde through the dissimilation pathway and cell wall rearrangement to temperature stress resistance following long-term evolution as revealed by transcriptomic and phenotypic analysis. By strengthening nitrogen metabolism and impairing cell wall synthesis, metabolic engineering further increased protein content. Finally, the engineered strain via multi-strategy produced high levels of SCP from methanol in a pilot-scale fed-batch culture at 33 °C with a biomass of 63.37 g DCW/L, methanol conversion rate of 0.43 g DCW/g, and protein content of 0.506 g/g DCW. SCP obtained from P. pastoris contains a higher percentage of protein compared to conventional foods like soy, fish, meat, whole milk, and is a source of essential amino acids, including methionine, lysine, and branched-chain amino acids (BCAAs: valine, isoleucine, leucine). CONCLUSIONS This study clarified the unique mechanism of P. pastoris for efficient methanol utilization, higher temperature resistance, and high protein synthesis, providing a P. pastoris cell factory for SCP production with environmental, economic, and nutritional benefits.
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Affiliation(s)
- Jiao Meng
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, National Technology Innovation Center of Synthetic Biology, No. 32, Xiqi Road, Tianjin Airport Economic Park, 300308, Tianjin, Tianjin, China
| | - Shufan Liu
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, National Technology Innovation Center of Synthetic Biology, No. 32, Xiqi Road, Tianjin Airport Economic Park, 300308, Tianjin, Tianjin, China
| | - Le Gao
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, National Technology Innovation Center of Synthetic Biology, No. 32, Xiqi Road, Tianjin Airport Economic Park, 300308, Tianjin, Tianjin, China
| | - Kai Hong
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, National Technology Innovation Center of Synthetic Biology, No. 32, Xiqi Road, Tianjin Airport Economic Park, 300308, Tianjin, Tianjin, China
| | - Shuguang Liu
- Ningxia Future Biotechnology Co., Ltd, Jingsan Road, Ningdong Linhe Industrial Zone, Ningdong Town, Ningxia, China
| | - Xin Wu
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, National Technology Innovation Center of Synthetic Biology, No. 32, Xiqi Road, Tianjin Airport Economic Park, 300308, Tianjin, Tianjin, China.
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Ye DY, Moon JH, Jung GY. Recent Progress in Metabolic Engineering of Escherichia coli for the Production of Various C4 and C5-Dicarboxylic Acids. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2023; 71:10916-10931. [PMID: 37458388 DOI: 10.1021/acs.jafc.3c02156] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/27/2023]
Abstract
As an alternative to petrochemical synthesis, well-established industrial microbes, such as Escherichia coli, are employed to produce a wide range of chemicals, including dicarboxylic acids (DCAs), which have significant potential in diverse areas including biodegradable polymers. The demand for biodegradable polymers has been steadily rising, prompting the development of efficient production pathways on four- (C4) and five-carbon (C5) DCAs derived from central carbon metabolism to meet the increased demand via the biosynthesis. In this context, E. coli is utilized to produce these DCAs through various metabolic engineering strategies, including the design or selection of metabolic pathways, pathway optimization, and enhancement of catalytic activity. This review aims to highlight the recent advancements in metabolic engineering techniques for the production of C4 and C5 DCAs in E. coli.
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Affiliation(s)
- Dae-Yeol Ye
- Department of Chemical Engineering, Pohang University of Science and Technology, 77 Cheongam-Ro, Nam-Gu, Pohang, Gyeongbuk 37673, Republic of Korea
| | - Jo Hyun Moon
- Department of Chemical Engineering, Pohang University of Science and Technology, 77 Cheongam-Ro, Nam-Gu, Pohang, Gyeongbuk 37673, Republic of Korea
| | - Gyoo Yeol Jung
- Department of Chemical Engineering, Pohang University of Science and Technology, 77 Cheongam-Ro, Nam-Gu, Pohang, Gyeongbuk 37673, Republic of Korea
- School of Interdisciplinary Bioscience and Bioengineering, Pohang University of Science and Technology, 77 Cheongam-Ro, Nam-Gu, Pohang, Gyeongbuk 37673, Republic of Korea
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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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Mhatre A, Shinde S, Jha AK, Rodriguez A, Wardak Z, Jansen A, Gladden JM, George A, Davis RW, Varman AM. Corynebacterium glutamicum as an Efficient Omnivorous Microbial Host for the Bioconversion of Lignocellulosic Biomass. Front Bioeng Biotechnol 2022; 10:827386. [PMID: 35433642 PMCID: PMC9011048 DOI: 10.3389/fbioe.2022.827386] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2021] [Accepted: 03/03/2022] [Indexed: 01/07/2023] Open
Abstract
Corynebacterium glutamicum has been successfully employed for the industrial production of amino acids and other bioproducts, partially due to its native ability to utilize a wide range of carbon substrates. We demonstrated C. glutamicum as an efficient microbial host for utilizing diverse carbon substrates present in biomass hydrolysates, such as glucose, arabinose, and xylose, in addition to its natural ability to assimilate lignin-derived aromatics. As a case study to demonstrate its bioproduction capabilities, L-lactate was chosen as the primary fermentation end product along with acetate and succinate. C. glutamicum was found to grow well in different aromatics (benzoic acid, cinnamic acid, vanillic acid, and p-coumaric acid) up to a concentration of 40 mM. Besides, 13C-fingerprinting confirmed that carbon from aromatics enter the primary metabolism via TCA cycle confirming the presence of β-ketoadipate pathway in C. glutamicum. 13C-fingerprinting in the presence of both glucose and aromatics also revealed coumarate to be the most preferred aromatic by C. glutamicum contributing 74 and 59% of its carbon for the synthesis of glutamate and aspartate respectively. 13C-fingerprinting also confirmed the activity of ortho-cleavage pathway, anaplerotic pathway, and cataplerotic pathways. Finally, the engineered C. glutamicum strain grew well in biomass hydrolysate containing pentose and hexose sugars and produced L-lactate at a concentration of 47.9 g/L and a yield of 0.639 g/g from sugars with simultaneous utilization of aromatics. Succinate and acetate co-products were produced at concentrations of 8.9 g/L and 3.2 g/L, respectively. Our findings open the door to valorize all the major carbon components of biomass hydrolysate by using C. glutamicum as a microbial host for biomanufacturing.
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Affiliation(s)
- Apurv Mhatre
- Chemical Engineering Program, School for Engineering of Matter, Transport, and Energy, Arizona State University, Tempe, AZ, United States
| | - Somnath Shinde
- Department of Bioresource and Environmental Security, Sandia National Laboratories, Livermore, CA, United States
| | - Amit Kumar Jha
- Chemical Engineering Program, School for Engineering of Matter, Transport, and Energy, Arizona State University, Tempe, AZ, United States,Department of Bioresource and Environmental Security, Sandia National Laboratories, Livermore, CA, United States
| | - Alberto Rodriguez
- Department of Biomaterials and Biomanufacturing, Sandia National Laboratories, Livermore, CA, United States,Joint BioEnergy Institute, Emeryville, CA, United States
| | - Zohal Wardak
- Department of Bioresource and Environmental Security, Sandia National Laboratories, Livermore, CA, United States
| | - Abigail Jansen
- Chemical Engineering Program, School for Engineering of Matter, Transport, and Energy, Arizona State University, Tempe, AZ, United States
| | - John M. Gladden
- Department of Biomaterials and Biomanufacturing, Sandia National Laboratories, Livermore, CA, United States,Joint BioEnergy Institute, Emeryville, CA, United States
| | - Anthe George
- Department of Bioresource and Environmental Security, Sandia National Laboratories, Livermore, CA, United States,Department of Biomaterials and Biomanufacturing, Sandia National Laboratories, Livermore, CA, United States
| | - Ryan W. Davis
- Department of Bioresource and Environmental Security, Sandia National Laboratories, Livermore, CA, United States,*Correspondence: Ryan W. Davis, ; Arul M. Varman,
| | - Arul M. Varman
- Chemical Engineering Program, School for Engineering of Matter, Transport, and Energy, Arizona State University, Tempe, AZ, United States,*Correspondence: Ryan W. Davis, ; Arul M. Varman,
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Imdad S, Lim W, Kim JH, Kang C. Intertwined Relationship of Mitochondrial Metabolism, Gut Microbiome and Exercise Potential. Int J Mol Sci 2022; 23:ijms23052679. [PMID: 35269818 PMCID: PMC8910986 DOI: 10.3390/ijms23052679] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2022] [Revised: 02/25/2022] [Accepted: 02/25/2022] [Indexed: 02/04/2023] Open
Abstract
The microbiome has emerged as a key player contributing significantly to the human physiology over the past decades. The potential microbial niche is largely unexplored in the context of exercise enhancing capacity and the related mitochondrial functions. Physical exercise can influence the gut microbiota composition and diversity, whereas a sedentary lifestyle in association with dysbiosis can lead to reduced well-being and diseases. Here, we have elucidated the importance of diverse microbiota, which is associated with an individual's fitness, and moreover, its connection with the organelle, the mitochondria, which is the hub of energy production, signaling, and cellular homeostasis. Microbial by-products, such as short-chain fatty acids, are produced during regular exercise that can enhance the mitochondrial capacity. Therefore, exercise can be employed as a therapeutic intervention to circumvent or subside various metabolic and mitochondria-related diseases. Alternatively, the microbiome-mitochondria axis can be targeted to enhance exercise performance. This review furthers our understanding about the influence of microbiome on the functional capacity of the mitochondria and exercise performance, and the interplay between them.
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Affiliation(s)
- Saba Imdad
- Molecular Metabolism in Health & Disease, Exercise Physiology Laboratory, Sport Science Research Institute, Inha University, Incheon 22212, Korea;
- Department of Biomedical Laboratory Science, College of Health Science, Cheongju University, Cheongju 28503, Korea
| | - Wonchung Lim
- Department of Sports Medicine, College of Health Science, Cheongju University, Cheongju 28503, Korea;
| | - Jin-Hee Kim
- Department of Biomedical Laboratory Science, College of Health Science, Cheongju University, Cheongju 28503, Korea
- Correspondence: (J.-H.K.); (C.K.)
| | - Chounghun Kang
- Molecular Metabolism in Health & Disease, Exercise Physiology Laboratory, Sport Science Research Institute, Inha University, Incheon 22212, Korea;
- Department of Physical Education, College of Education, Inha University, Incheon 22212, Korea
- Correspondence: (J.-H.K.); (C.K.)
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8
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Fordjour E, Mensah EO, Hao Y, Yang Y, Liu X, Li Y, Liu CL, Bai Z. Toward improved terpenoids biosynthesis: strategies to enhance the capabilities of cell factories. BIORESOUR BIOPROCESS 2022; 9:6. [PMID: 38647812 PMCID: PMC10992668 DOI: 10.1186/s40643-022-00493-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2021] [Accepted: 01/04/2022] [Indexed: 02/22/2023] Open
Abstract
Terpenoids form the most diversified class of natural products, which have gained application in the pharmaceutical, food, transportation, and fine and bulk chemical industries. Extraction from naturally occurring sources does not meet industrial demands, whereas chemical synthesis is often associated with poor enantio-selectivity, harsh working conditions, and environmental pollutions. Microbial cell factories come as a suitable replacement. However, designing efficient microbial platforms for isoprenoid synthesis is often a challenging task. This has to do with the cytotoxic effects of pathway intermediates and some end products, instability of expressed pathways, as well as high enzyme promiscuity. Also, the low enzymatic activity of some terpene synthases and prenyltransferases, and the lack of an efficient throughput system to screen improved high-performing strains are bottlenecks in strain development. Metabolic engineering and synthetic biology seek to overcome these issues through the provision of effective synthetic tools. This review sought to provide an in-depth description of novel strategies for improving cell factory performance. We focused on improving transcriptional and translational efficiencies through static and dynamic regulatory elements, enzyme engineering and high-throughput screening strategies, cellular function enhancement through chromosomal integration, metabolite tolerance, and modularization of pathways.
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Affiliation(s)
- Eric Fordjour
- National Engineering Laboratory for Cereal Fermentation Technology, Jiangnan University, 1800 Lihu Road, Wuxi, 214122, Jiangsu, China
- Jiangsu Provincial Research Centre for Bioactive Product Processing Technology, Jiangnan University, Wuxi, China
| | - Emmanuel Osei Mensah
- National Engineering Laboratory for Cereal Fermentation Technology, Jiangnan University, 1800 Lihu Road, Wuxi, 214122, Jiangsu, China
- Jiangsu Provincial Research Centre for Bioactive Product Processing Technology, Jiangnan University, Wuxi, China
| | - Yunpeng Hao
- National Engineering Laboratory for Cereal Fermentation Technology, Jiangnan University, 1800 Lihu Road, Wuxi, 214122, Jiangsu, China
- Jiangsu Provincial Research Centre for Bioactive Product Processing Technology, Jiangnan University, Wuxi, China
| | - Yankun Yang
- National Engineering Laboratory for Cereal Fermentation Technology, Jiangnan University, 1800 Lihu Road, Wuxi, 214122, Jiangsu, China
- Jiangsu Provincial Research Centre for Bioactive Product Processing Technology, Jiangnan University, Wuxi, China
| | - Xiuxia Liu
- National Engineering Laboratory for Cereal Fermentation Technology, Jiangnan University, 1800 Lihu Road, Wuxi, 214122, Jiangsu, China
- Jiangsu Provincial Research Centre for Bioactive Product Processing Technology, Jiangnan University, Wuxi, China
| | - Ye Li
- National Engineering Laboratory for Cereal Fermentation Technology, Jiangnan University, 1800 Lihu Road, Wuxi, 214122, Jiangsu, China
- Jiangsu Provincial Research Centre for Bioactive Product Processing Technology, Jiangnan University, Wuxi, China
| | - Chun-Li Liu
- National Engineering Laboratory for Cereal Fermentation Technology, Jiangnan University, 1800 Lihu Road, Wuxi, 214122, Jiangsu, China.
- Jiangsu Provincial Research Centre for Bioactive Product Processing Technology, Jiangnan University, Wuxi, China.
| | - Zhonghu Bai
- National Engineering Laboratory for Cereal Fermentation Technology, Jiangnan University, 1800 Lihu Road, Wuxi, 214122, Jiangsu, China.
- Jiangsu Provincial Research Centre for Bioactive Product Processing Technology, Jiangnan University, Wuxi, China.
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Yamada S, Takamatsu Y, Ikeda S, Kouzuma A, Watanabe K. Towards Application of Electro-Fermentation for the Production of Value-Added Chemicals From Biomass Feedstocks. Front Chem 2022; 9:805597. [PMID: 35127650 PMCID: PMC8807546 DOI: 10.3389/fchem.2021.805597] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2021] [Accepted: 12/24/2021] [Indexed: 12/03/2022] Open
Abstract
According to recent social demands for sustainable developments, the value of biomass as feedstocks for chemical industry is increasing. With the aid of metabolic engineering and genome editing, microbial fermentation has been developed for producing value-added chemicals from biomass feedstocks, while further improvements are desired for producing more diverse chemicals and increasing the production efficiency. The major intrinsic limitation in conventional fermentation technologies is associated with the need for balancing the net redox equivalents between substrates and products, resulting in limited repertories of fermentation products. One solution for this limitation would be “electro-fermentation (EF)” that utilizes bioelectrochemical systems for modifying the intracellular redox state of electrochemically active bacteria, thereby overcoming the redox constraint of fermentation. Recent studies have attempted the production of chemicals based on the concept of EF, while its utility has not been sufficiently demonstrated in terms of low production efficiencies. Here we discuss EF in terms of its concept, current status and future directions, which help us develop its practical applications to sustainable chemical industries.
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Systems Metabolic Engineering of Methanotrophic Bacteria for Biological Conversion of Methane to Value-Added Compounds. ADVANCES IN BIOCHEMICAL ENGINEERING/BIOTECHNOLOGY 2022; 180:91-126. [DOI: 10.1007/10_2021_184] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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11
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Identification and Characterization of a Novel Soluble Pyridine Nucleotide Transhydrogenase from Streptomyces avermitilis. Curr Microbiol 2021; 79:32. [PMID: 34931264 DOI: 10.1007/s00284-021-02727-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2021] [Accepted: 11/25/2021] [Indexed: 10/19/2022]
Abstract
Soluble pyridine nucleotide transhydrogenase (STH) transfers hydride between NADH and NADPH to maintain redox balance. In the present study, the sth gene from Gram-positive bacterium Streptomyces avermitilis (SaSTH) was expressed in Escherichia coli, and the recombinant STH protein was purified to homogeneity. Activity assays indicated that SaSTH was able to catalyze transhydrogenase reactions by using NADH or NADPH as reductants and thio-NAD+ as an oxidant. The apparent Km value for NADPH (74.5 μM) was lower than that for NADH (104.0 μM) and the apparent kcat/Km for NADPH (2704.7 mM-1 s-1) was higher than that for NADH (1129.8 mM-1 s-1). SaSTH showed optimal activity at 25 °C and at a pH of 6.2. Heat-inactivation studies revealed that SaSTH remained stable below 55 °C and that approximately 50% activity was preserved at 57 °C for 20 min. Analyses also showed that SaSTH activity was inhibited by divalent ions, particularly Co2+, Ni2+, and Zn2+. In addition, the transhydrogenase activity of SaSTH was inhibited by ATP and strongly stimulated by ADP and AMP. In summary, we characterized a recombinant enzyme exhibiting STH activity from Gram-positive bacteria for the first time. Our findings provide new options for cofactor engineering and industrial biocatalytic processes.
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12
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Well Knowledge of the Physiology of Actinobacillus succinogenes to Improve Succinic Acid Production. Appl Microbiol 2021. [DOI: 10.3390/applmicrobiol1020022] [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
The anaerobic fermentation of glucose and fructose was performed by Actinobacillus succinogenes 130Z in batch mode using three different volume of bioreactors (0.25, 1 and 3 L). The strategy used was the addition of MgCO3 and fumaric acid (FA) as mineral carbon and the precursor of succinic acid, respectively, in the culture media. Kinetics and yields of succinic acid (SA) production in the presence of sugars in a relevant synthetic medium were investigated. Work on the bench scale (3 L) showed the best results when compared to the small anaerobic reactor’s succinic acid yield and productivity after 96 h of fermentation. For an equal mixture of glucose and fructose used as substrate at 0.4 mol L−1 with the addition of FA as enhancer and under proven optimal conditions (pH 6.8, T = 37 °C, anaerobic condition and 1% v/v of biomass), about 0.5 mol L−1 of SA was obtained, while the theoretical production of succinic acid was 0.74 mol L−1. This concentration corresponded to an experimental yield of 0.88 (mol-C SA/mol-C sugars consumed anaerobically) and a volumetric productivity of 0.48 g-SA L−1 h−1. The succinic acid yield and concentration obtained were significant and in the order of those reported in the literature.
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Zhan J, Wang S, Li F, Ji C, Wu H. Dose-dependent responses of metabolism and tissue injuries in clam Ruditapes philippinarum after subchronic exposure to cadmium. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 779:146479. [PMID: 33744590 DOI: 10.1016/j.scitotenv.2021.146479] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/23/2020] [Revised: 03/05/2021] [Accepted: 03/11/2021] [Indexed: 06/12/2023]
Abstract
Marine cadmium (Cd) pollution has been globally occurring, which creates a pressing need to characterize toxicological effects and develop biomarkers for Cd. However, the dose-response relationships challenge toxicity characterization and biomarkers selection. Metabolic processes have been frequently targeted by Cd. In this work, we investigated the dose-dependent effects of Cd on metabolic endpoints in whole soft tissues as well as gill and hepatopancreas injuries in clam Ruditapes philippinarum, aiming to better understand the metabolic responses and develop biomarkers. Nuclear magnetic resonance (NMR)-based metabolomic analysis was conducted on clam whole soft tissues to identify metabolites. The enzymes and metabolites associated with tricarboxylic acid (TCA) cycle, glycolysis, and oxidative phosphorylation showed both monotonic and non-monotonic curves with the increase of Cd dose. In details, glutamine, glucose-1-phosphate, hexokinase (HK), and citrate synthase (CS) presented monotonic decreases with the increase of Cd dose, among which glutamine and CS were preferable biomarkers to Cd exposure based on lower benchmark dose (BMD) values. The monotonic decreases of HK and CS activities suggested Cd exposure potentially disrupted glycolysis and TCA cycle via inhibiting rate-limiting enzymes. In contrast, the non-monotonic responses of succinate dehydrogenase (SDH), alanine aminotransferase (ALT), and their substrates (succinate and alanine) were approximate to U- or J-shaped curves, suggesting the adaptive strategy of metabolic responses to different degrees of Cd stress, like induction of anaerobiosis as energy compensation. Especially, the alterations of succinate and SDH presented typical hormetic dose-response curves. What is more, clam hepatopancreas was more sensitive to Cd than gill in terms of injury occurrence. Overall, characterization of dose-dependent effect of Cd on metabolism and tissue injuries provides a new insight into understanding the metabolic adaptation in marine clams and risk assessment of Cd pollution.
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Affiliation(s)
- Junfei Zhan
- CAS Key Laboratory of Coastal Environmental Processes and Ecological Remediation, Yantai Institute of Coastal Zone Research (YIC), Chinese Academy of Sciences(CAS); Shandong Key Laboratory of Coastal Environmental Processes, YICCAS, Yantai Shandong 264003, PR China; University of Chinese Academy of Sciences, Beijing 100049, PR China
| | - Shuang Wang
- CAS Key Laboratory of Coastal Environmental Processes and Ecological Remediation, Yantai Institute of Coastal Zone Research (YIC), Chinese Academy of Sciences(CAS); Shandong Key Laboratory of Coastal Environmental Processes, YICCAS, Yantai Shandong 264003, PR China; University of Chinese Academy of Sciences, Beijing 100049, PR China
| | - Fei Li
- CAS Key Laboratory of Coastal Environmental Processes and Ecological Remediation, Yantai Institute of Coastal Zone Research (YIC), Chinese Academy of Sciences(CAS); Shandong Key Laboratory of Coastal Environmental Processes, YICCAS, Yantai Shandong 264003, PR China; Center for Ocean Mega-Science, Chinese Academy of Sciences (CAS), Qingdao 266071, PR China
| | - Chenglong Ji
- CAS Key Laboratory of Coastal Environmental Processes and Ecological Remediation, Yantai Institute of Coastal Zone Research (YIC), Chinese Academy of Sciences(CAS); Shandong Key Laboratory of Coastal Environmental Processes, YICCAS, Yantai Shandong 264003, PR China; Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, PR China; Center for Ocean Mega-Science, Chinese Academy of Sciences (CAS), Qingdao 266071, PR China
| | - Huifeng Wu
- CAS Key Laboratory of Coastal Environmental Processes and Ecological Remediation, Yantai Institute of Coastal Zone Research (YIC), Chinese Academy of Sciences(CAS); Shandong Key Laboratory of Coastal Environmental Processes, YICCAS, Yantai Shandong 264003, PR China; Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, PR China; Center for Ocean Mega-Science, Chinese Academy of Sciences (CAS), Qingdao 266071, PR China.
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14
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Guo H, Chen Y, Guo W, Chen J. Effects of extracellular DNA on dual-species biofilm formed by Streptococcus mutans and Candida albicans. Microb Pathog 2021; 154:104838. [PMID: 33691176 DOI: 10.1016/j.micpath.2021.104838] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2020] [Revised: 01/28/2021] [Accepted: 02/25/2021] [Indexed: 12/12/2022]
Abstract
Streptococcus mutans is the most important acid-producing pathogen that causes dental caries, while Candida albicans is an opportunistic fungal pathogen that is frequently detected in conjunction with heavy infection by S. mutans. Their interactions in dental plaque biofilms remain unclear. Extracellular DNA (eDNA) is found in oral biofilms, but its effects have not been thoroughly defined. In this study, the role of eDNA in dual-species biofilms formed by S. mutans and C. albicans was investigated. With eDNA removal, the growth of both strains was not affected, but the formation of dual-species biofilms obviously decreased. In addition, the removal of eDNA spatially disrupted the structure of the dual-species biofilm. It was also shown that eDNA mainly affected the initial attachment and development stages of the dual-species biofilms but not the well-developed biofilms. A similar phenomenon was also observed in the cell viability of dual-species biofilms after DNase I treatment. To further exploration, we analyzed the expression of genes associated with biofilm formation in both S. mutans and C. albicans. We determined that the co-cultivation of S. mutans and C. albicans promotes the expression of genes related to extracellular polysaccharide production (e.g., gtfC), adhesion (e.g., spaP, epa1), mycelial transformation (e.g., hwp1), and drug resistance (e.g., cdr2). However, these genes were significantly downregulated when the eDNA of the dual-species biofilm was removed by adding DNase I compared to those untreated groups. Altogether, eDNA removal, such as that by DNase I treatment, could be considered a promising strategy to control oral biofilms and biofilm-associated oral diseases.
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Affiliation(s)
- Haoran Guo
- Beijing Laboratory for Food Quality and Safety, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, 100083, China
| | - Yitong Chen
- Beijing Laboratory for Food Quality and Safety, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, 100083, China
| | - Wenjin Guo
- Beijing Chong Wen Stomatological Hospital, Beijing, 100062, China
| | - Jingyu Chen
- Beijing Laboratory for Food Quality and Safety, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, 100083, China.
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15
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Cao Z, Meng R, Wang P, Zhu G. Heterologous expression and enzymatic identification of two novel soluble pyridine nucleotide transhydrogenases from Acidobacteria bacterium KBS 146 and Nocardia jiangxiensis. BIOTECHNOL BIOTEC EQ 2021. [DOI: 10.1080/13102818.2021.1988708] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022] Open
Affiliation(s)
- Zhengyu Cao
- Anhui Provincial Key Laboratory of Molecular Enzymology and Mechanism of Major Diseases and Key Laboratory of Biomedicine in Gene Diseases and Health of Anhui Higher Education Institutes, College of Life Sciences, Anhui Normal University, Wuhu, Anhui, PR China
| | - Rui Meng
- Anhui Provincial Key Laboratory of Molecular Enzymology and Mechanism of Major Diseases and Key Laboratory of Biomedicine in Gene Diseases and Health of Anhui Higher Education Institutes, College of Life Sciences, Anhui Normal University, Wuhu, Anhui, PR China
| | - Peng Wang
- Anhui Provincial Key Laboratory of Molecular Enzymology and Mechanism of Major Diseases and Key Laboratory of Biomedicine in Gene Diseases and Health of Anhui Higher Education Institutes, College of Life Sciences, Anhui Normal University, Wuhu, Anhui, PR China
| | - Guoping Zhu
- Anhui Provincial Key Laboratory of Molecular Enzymology and Mechanism of Major Diseases and Key Laboratory of Biomedicine in Gene Diseases and Health of Anhui Higher Education Institutes, College of Life Sciences, Anhui Normal University, Wuhu, Anhui, PR China
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16
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Abstract
Biological wax esters offer a sustainable, renewable and biodegradable alternative to many fossil fuel derived chemicals including plastics and paraffins. Many species of bacteria accumulate waxes with similar structure and properties to highly desirable animal and plant waxes such as Spermaceti and Jojoba oils, the use of which is limited by resource requirements, high cost and ethical concerns. While bacterial fermentations overcome these issues, a commercially viable bacterial wax production process would require high yields and renewable, affordable feedstock to make it economically competitive and environmentally beneficial. This review describes recent progress in wax ester generation in both wild type and genetically engineered bacteria, with a focus on comparing substrates and quantifying obtained waxes. The full breadth of wax accumulating species is discussed, with emphasis on species generating high yields and utilising renewable substrates. Key areas of the field that have, thus far, received limited attention are highlighted, such as waste stream valorisation, mixed microbial cultures and efficient wax extraction, as, until effectively addressed, these will slow progress in creating commercially viable wax production methods.
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17
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Rcs Phosphorelay Responses to Truncated Lipopolysaccharide-Induced Cell Envelope Stress in Yersinia enterocolitica. Molecules 2020; 25:molecules25235718. [PMID: 33287412 PMCID: PMC7730088 DOI: 10.3390/molecules25235718] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2020] [Revised: 11/28/2020] [Accepted: 11/30/2020] [Indexed: 01/22/2023] Open
Abstract
Lipopolysaccharide (LPS) is the major component of the outer membrane of Gram-negative bacteria, and its integrity is monitored by various stress response systems. Although the Rcs system is involved in the envelope stress response and regulates genes controlling numerous bacterial cell functions of Yersinia enterocolitica, whether it can sense the truncated LPS in Y. enterocolitica remains unclear. In this study, the deletion of the Y. enterocolitica waaF gene truncated the structure of LPS and produced a deep rough LPS. The truncated LPS increased the cell surface hydrophobicity and outer membrane permeability, generating cell envelope stress. The truncated LPS also directly exposed the smooth outer membrane to the external environment and attenuated the resistance to adverse conditions, such as impaired survival under polymyxin B and sodium dodecyl sulfate (SDS) exposure. Further phenotypic experiment and gene expression analysis indicated that the truncated LPS was correlated with the activation of the Rcs phosphorelay, thereby repressing cell motility and biofilm formation. Our findings highlight the importance of LPS integrity in maintaining membrane function and broaden the understanding of Rcs phosphorelay signaling in response to cell envelope stress, thus opening new avenues to develop effective antimicrobial agents for combating Y. enterocolitica infections.
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18
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Pateraki C, Skliros D, Flemetakis E, Koutinas A. Succinic acid production from pulp and paper industry waste: A transcriptomic approach. J Biotechnol 2020; 325:250-260. [PMID: 33069778 DOI: 10.1016/j.jbiotec.2020.10.015] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2020] [Revised: 09/21/2020] [Accepted: 10/12/2020] [Indexed: 01/29/2023]
Abstract
The fermentative production of biobased chemicals and polymers using crude lignocellulose hydrolysates is challenging due to the presence of various inhibitory compounds and multiple sugars. This study evaluates the metabolic response of Actinobacillus succinogenes for the production of succinic acid using spent sulphite liquor (SSL) as feedstock derived from industrial acidic sulphite pulping of Eucalyptus globulus hardwood. A transcriptomic approach led to significant insights on gene regulation of the major metabolic pathways (glycolysis, pentose phosphate pathway, TCA cycle, pyruvate metabolism and oxidative phosphorylation) in batch cultures carried out on SSL and compared with glucose and xylose. Significantly overexpressed genes in SSL compared to glucose and xylose were fructose biphosphate aldolase (> 1.18-fold change) in the catabolism, phosphoenolpyruvate carboxykinase (> 1.59-fold change) and malate dehydrogenase (> 1.49-fold change) in the TCA cycle, citrate lyase (> 1.7-fold change), dihydrolipoamide dehydrogenase (> 0.88-fold change), pyruvate dehydrogenase E2 (> 1.63-fold change) and pyruvate formate lyase (> 0.61-fold change), involved in acetyl-CoA pathways. Finally, C4 tricarboxylic transporters were overexpressed (DCU (> 1.61-fold change) and 0079 (> 4.19-fold change). SSL was responsible for the upregulation of genes involved in the TCA cycle and oxidative phosphorylation, while xylose showed similar results with SSL in the oxidative phosphorylation.
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Affiliation(s)
- Chrysanthi Pateraki
- Department of Food Science and Human Nutrition, Agricultural University of Athens, Iera Odos 75, 118 55 Athens, Greece.
| | - Dimitrios Skliros
- Department of Biotechnology, Agricultural University of Athens, Iera Odos 75, 118 55 Athens, Greece
| | - Emmanouil Flemetakis
- Department of Biotechnology, Agricultural University of Athens, Iera Odos 75, 118 55 Athens, Greece
| | - Apostolis Koutinas
- Department of Food Science and Human Nutrition, Agricultural University of Athens, Iera Odos 75, 118 55 Athens, Greece
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19
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Weusthuis RA, Folch PL, Pozo-Rodríguez A, Paul CE. Applying Non-canonical Redox Cofactors in Fermentation Processes. iScience 2020; 23:101471. [PMID: 32891057 PMCID: PMC7479625 DOI: 10.1016/j.isci.2020.101471] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2020] [Revised: 07/29/2020] [Accepted: 08/14/2020] [Indexed: 01/29/2023] Open
Abstract
Fermentation processes are used to sustainably produce chemicals and as such contribute to the transition to a circular economy. The maximum theoretical yield of a conversion can only be approached if all electrons present in the substrate end up in the product. Control over the electrons is therefore crucial. However, electron transfer via redox cofactors results in a diffuse distribution of electrons over metabolism. To overcome this challenge, we propose to apply non-canonical redox cofactors (NRCs) in metabolic networks: cofactors that channel electrons exclusively from substrate to product, forming orthogonal circuits for electron transfer.
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Affiliation(s)
- Ruud A. Weusthuis
- Bioprocess Engineering, Wageningen University & Research, Post Office Box 16, 6700 AA Wageningen, the Netherlands
| | - Pauline L. Folch
- Bioprocess Engineering, Wageningen University & Research, Post Office Box 16, 6700 AA Wageningen, the Netherlands
| | - Ana Pozo-Rodríguez
- Bioprocess Engineering, Wageningen University & Research, Post Office Box 16, 6700 AA Wageningen, the Netherlands
| | - Caroline E. Paul
- Biocatalysis, Department of Biotechnology, Delft University of Technology, Van der Maasweg 9, 2629 HZ Delft, the Netherlands
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20
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Feng J, Jiang M, Li K, Lu Q, Xu S, Wang X, Chen K, Ouyang P. Direct electron uptake from a cathode using the inward Mtr pathway in Escherichia coli. Bioelectrochemistry 2020; 134:107498. [DOI: 10.1016/j.bioelechem.2020.107498] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2019] [Revised: 02/20/2020] [Accepted: 03/02/2020] [Indexed: 02/07/2023]
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21
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Meng J, Xu J, Chen J. The role of osmoregulated periplasmic glucans in the biofilm antibiotic resistance of Yersinia enterocolitica. Microb Pathog 2020; 147:104284. [PMID: 32492459 DOI: 10.1016/j.micpath.2020.104284] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2020] [Revised: 05/27/2020] [Accepted: 05/27/2020] [Indexed: 12/28/2022]
Abstract
The formation of biofilms by bacteria is of great significance because it involves many physiological changes that serve to protect the cells from various stresses. One of the best-known biofilm-specific properties of bacteria is that bacteria that grow in biofilms are generally more resistant to antibiotics than their planktonic counterparts. In a previous study, osmoregulated periplasmic glucans (OPGs), catalyzed by the opgGH operon, were identified and found to function in Rcs signalling in Yersinia enterocolitica. In this study, the possible contribution of OPGs to antimicrobial resistance of Y. enterocolitica biofilms were investigated, and the results showed that OPGs, especially when overexpressed, conferred a high level of biofilm resistance to two different classes of antibiotics onto Y. enterocolitica. Subsequent analysis revealed that OPGs regulated the biofilm architecture in Y. enterocolitica by promoting the bacteria to form large cell aggregates. Moreover, the opgGH genes in biofilms showed higher expression than in planktonic cultures. OPGs were required to induce the expression of genes related to flagella, extracellular polysaccharide, and c-di-GMP biosynthesis in Y. enterocolitica biofilms and this effect was more significant when OPGs were overproduced. The current investigation showed an extension in the biological role of OPGs in Y. enterocolitica and provided a strong theoretical basis to further study this resistance mechanism at the molecular level to identify new drug targets or disinfectants for the treatment of infections caused by Y. enterocolitica within biofilms.
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Affiliation(s)
- Jiao Meng
- Beijing Laboratory for Food Quality and Safety, College of Food Science & Nutritional Engineering, China Agricultural University, Beijing, 100083, China
| | - Jingguo Xu
- Beijing Laboratory for Food Quality and Safety, College of Food Science & Nutritional Engineering, China Agricultural University, Beijing, 100083, China
| | - Jingyu Chen
- Beijing Laboratory for Food Quality and Safety, College of Food Science & Nutritional Engineering, China Agricultural University, Beijing, 100083, China.
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22
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Transcriptomic analysis reveals the role of RcsB in suppressing bacterial chemotaxis, flagellar assembly and infection in Yersinia enterocolitica. Curr Genet 2020; 66:971-988. [PMID: 32488337 DOI: 10.1007/s00294-020-01083-x] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2020] [Revised: 05/01/2020] [Accepted: 05/01/2020] [Indexed: 12/17/2022]
Abstract
Defining the Rcs (Regulator of Capsule Synthesis) regulon in Enterobacteriaceae has been the major focus of several recent studies. The overall role of the Rcs system in Yersinia enterocolitica is largely unknown. Our previous study showed that RcsB inhibits motility, biofilm formation and c-di-GMP production by negatively regulating flhDC, hmsHFRS and hmsT expression. To identify other cellular functions regulated by the RcsB, gene expression profiles of the wild type and ΔrcsB mutant were compared by RNA-Seq in this study. A total of 132 differentially expressed genes regulated by the RcsB have been identified, of which 114 were upregulated and 18 were downregulated. Further, the results of RNA sequencing were discussed with a focus on the predictive roles of RcsB in the inhibition of bacterial chemotaxis, flagellar assembly and infection. To confirm these predictions, we experimentally verified that the ΔrcsB mutant activated chemotactic behavior and flagella biosynthesis, and exhibited enhanced adhesion and invasion of Y. enterocolitica to Caco-2 cells. Although RcsB largely inhibits these physiological activities, the presence of RcsB is still of great significance for optimizing the survival of Y. enterocolitica as evidenced by our previous report that RcsB confers some level of resistance to the cationic antimicrobial peptide polymyxin B in Y. enterocolitica. Overall, the information provided in this study complements our understanding of Rcs phosphorelay in the regulation of Y. enterocolitica pathogenicity, and, simultaneously, provides clues to additional roles of the Rcs system in other members of family Enterobacteriaceae.
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23
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Meng J, Huang C, Huang X, Liu D, Han B, Chen J. Osmoregulated Periplasmic Glucans Transmit External Signals Through Rcs Phosphorelay Pathway in Yersinia enterocolitica. Front Microbiol 2020; 11:122. [PMID: 32117145 PMCID: PMC7013093 DOI: 10.3389/fmicb.2020.00122] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2019] [Accepted: 01/20/2020] [Indexed: 01/13/2023] Open
Abstract
Fast response to environmental changes plays a key role in the transmission and pathogenesis of Yersinia enterocolitica. Osmoregulated periplasmic glucans (OPGs) are known to be involved in environmental perception of several Enterobacteriaceae pathogens; however, the biological function of OPGs in Y. enterocolitica is still unclear. In this study, we investigated the role of OPGs in Y. enterocolitica by deleting the opgGH operon encoding enzymes responsible for OPGs biosynthesis. Complete loss of OPGs in the ΔopgGH mutant resulted in decreased motility, c-di-GMP production, biofilm formation and smaller cell size, whereas the overproduction of OPGs through restoration of opgGH expression promoted c-di-GMP/biofilm production and increased antibiotic resistance of Y. enterocolitica. Gene expression analysis revealed that opgGH deletion reduced transcription of flhDC, ftsAZ, hmsT and hmsHFRS genes regulated by the Rcs phosphorelay system, whereas additional deletion of rcs family genes (rcsF, rcsC, or rcsB) reversed this effect and restored motility and c-di-GMP/biofilm production but further reduced cell size. Furthermore, disruption of the Rcs phosphorelay increased the motility and promoted the induction of biofilm and c-di-GMP production regulated by OPGs through upregulating the expression of flhDC, hmsHFRS, and hmsT. However, deletion of genes encoding the EnvZ/OmpR phosphorelay downregulated the flhDC, hmsHFRS and hmsT expression, leading to the decreased motility and prevented the induction of biofilm and c-di-GMP production regulated by OPGs. These results indicated that Rcs phosphorelay had the effect on OPGs-mediated functional responses in Y. enterocolitica. Our findings disclose part of the biological role of OPGs and the underlying molecular mechanisms associated with Rcs system in the regulation of the pathogenic phenotype in Y. enterocolitica.
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Affiliation(s)
- Jiao Meng
- Beijing Laboratory for Food Quality and Safety, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, China.,Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, China
| | - Can Huang
- Beijing Laboratory for Food Quality and Safety, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, China.,Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, China
| | - Xiaoning Huang
- Beijing Laboratory for Food Quality and Safety, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, China.,Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, China
| | - Dingyu Liu
- Department of Biochemical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin, China
| | - Beizhong Han
- Beijing Laboratory for Food Quality and Safety, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, China.,Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, China
| | - Jingyu Chen
- Beijing Laboratory for Food Quality and Safety, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, China.,Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, China
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24
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Zhao C, Zhang Y, Li Y. Production of fuels and chemicals from renewable resources using engineered Escherichia coli. Biotechnol Adv 2019; 37:107402. [DOI: 10.1016/j.biotechadv.2019.06.001] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2018] [Revised: 05/23/2019] [Accepted: 06/02/2019] [Indexed: 02/06/2023]
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25
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Jin L, Nawab S, Xia M, Ma X, Huo Y. Context-dependency of synthetic minimal promoters in driving gene expression: a case study. Microb Biotechnol 2019; 12:1476-1486. [PMID: 31578818 PMCID: PMC6801132 DOI: 10.1111/1751-7915.13489] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2019] [Accepted: 09/09/2019] [Indexed: 12/13/2022] Open
Abstract
Synthetic promoters are considered ideal candidates in driving robust gene expression. Most of the available synthetic promoters are minimal promoters, for which the upstream sequence of the 5' end of the core region is usually excluded. Although the upstream sequence has been shown to mediate transcription of natural promoters, its impact on synthetic promoters has not been widely studied. Here, a library of chromosomal DNA fragments is randomly fused with the 5' end of the J23119 synthetic promoter, and the transcriptional performance of the promoter is evaluated through β-galactosidase assay, fluorescence intensity and chemical biosynthesis. Results show that changes in the upstream sequence can induce significant variation in the promoter strength of up to 5.8-fold. The effect is independent of the length of the insertions and the number of potential transcription factor binding sites. Several DNA fragments that are able to enhance the transcription of both the natural and the synthetic promoters are identified. This study indicates that the synthetic minimal promoters are susceptible to the surrounding sequence context. Therefore, the upstream sequence should be treated as an indispensable component in the design and application of synthetic promoters, or as an independent genetic part for the fine-tuning of gene expression.
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Affiliation(s)
- Liyuan Jin
- Key Laboratory of Molecular Medicine and BiotherapySchool of Life ScienceBeijing Institute of Technology5 South Zhongguancun Street, Haidian DistrictBeijing100081China
| | - Said Nawab
- Key Laboratory of Molecular Medicine and BiotherapySchool of Life ScienceBeijing Institute of Technology5 South Zhongguancun Street, Haidian DistrictBeijing100081China
| | - Mengli Xia
- Key Laboratory of Molecular Medicine and BiotherapySchool of Life ScienceBeijing Institute of Technology5 South Zhongguancun Street, Haidian DistrictBeijing100081China
| | - Xiaoyan Ma
- Key Laboratory of Molecular Medicine and BiotherapySchool of Life ScienceBeijing Institute of Technology5 South Zhongguancun Street, Haidian DistrictBeijing100081China
| | - Yi‐Xin Huo
- Key Laboratory of Molecular Medicine and BiotherapySchool of Life ScienceBeijing Institute of Technology5 South Zhongguancun Street, Haidian DistrictBeijing100081China
- UCLA Institute for Technology Advancement (Suzhou)10 Yueliangwan Road, Suzhou Industrial ParkSuzhou215123China
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26
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Metabolic engineering of the type I methanotroph Methylomonas sp. DH-1 for production of succinate from methane. Metab Eng 2019; 54:170-179. [DOI: 10.1016/j.ymben.2019.03.013] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2018] [Revised: 03/21/2019] [Accepted: 03/31/2019] [Indexed: 12/20/2022]
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27
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Altering the sensitivity of Escherichia coli pyruvate dehydrogenase complex to NADH inhibition by structure-guided design. Enzyme Microb Technol 2018; 119:52-57. [PMID: 30243387 DOI: 10.1016/j.enzmictec.2018.09.002] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2018] [Revised: 08/20/2018] [Accepted: 09/03/2018] [Indexed: 11/22/2022]
Abstract
A sufficient supply of reducing equivalents is essential for obtaining the maximum yield of target products in anaerobic fermentation. The pyruvate dehydrogenase (PDH) complex controls the critical step in pyruvate conversion to acetyl-CoA and NADH. However, in anaerobic Escherichia coli, PDH residing in the dihydrolipoamide dehydrogenase (LPD) component is normally inactive due to inhibition by NADH. In this study, the protein engineering of LPD by structural analysis was explored to eliminate this inhibition. A novel IAA350/351/358VVV triple mutant was successfully verified to be more effective than other LPD mutants reported till date. Notably, PDH activity with the triple mutant at an [NADH]/[NAD+] ratio of 0.15 was still higher than that of the wild-type without NADH addition. The altered enzyme of the PDH complex was also active in the presence of such high NADH levels. This is the first study concerning protein engineering of PDH by structure-guided design. The presence and functional activity of such an NADH-insensitive PDH complex provides a useful metabolic element for fermentation products and has potential for biotechnological application.
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28
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Kyselova L, Kreitmayer D, Kremling A, Bettenbrock K. Type and capacity of glucose transport influences succinate yield in two-stage cultivations. Microb Cell Fact 2018; 17:132. [PMID: 30153840 PMCID: PMC6112142 DOI: 10.1186/s12934-018-0980-1] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2018] [Accepted: 08/22/2018] [Indexed: 12/03/2022] Open
Abstract
Background Glucose is the main carbon source of E. coli and a typical substrate in production processes. The main glucose uptake system is the glucose specific phosphotransferase system (Glc-PTS). The PTS couples glucose uptake with its phosphorylation. This is achieved by the concomitant conversion of phosphoenolpyruvate (PEP) to pyruvate. The Glc-PTS is hence unfavorable for the production of succinate as this product is derived from PEP. Results We studied, in a systematic manner, the effect of knocking out the Glc-PTS and of replacing it with the glucose facilitator (Glf) of Zymomonas mobilis on succinate yield and productivity. For this study a set of strains derived from MG1655, carrying deletions of ackA-pta, adhE and ldhA that prevent the synthesis of competing fermentation products, were constructed and tested in two-stage cultivations. The data show that inactivation of the Glc-PTS achieved a considerable increase in succinate yield and productivity. On the other hand, aerobic growth of this strain on glucose was strongly decreased. Expression of the alternative glucose transporter, Glf, in this strain enhanced aerobic growth but productivity and yield under anaerobic conditions were slightly decreased. This decrease in succinate yield was accompanied by pyruvate production. Yield could be increased in both Glc-PTS mutants by overexpressing phosphoenolpyruvate carboxykinase (Pck). Productivity on the other hand, was decreased in the strain without alternative glucose transporter but strongly increased in the strain expressing Glf. The experiments were complemented by flux balance analysis in order to check the observed yields against the maximal theoretical yields. Furthermore, the phosphorylation state of EIIAGlc was determined. The data indicate that the ratio of PEP to pyruvate is correlating with pyruvate excretion. This ratio is affected by the PTS reaction as well as by further reactions at the PEP/pyruvate node. Conclusions The results show that for optimization of succinate yield and productivity it is not sufficient to knock out or introduce single reactions. Rather, balancing of the fluxes of central metabolism most important at the PEP/pyruvate node is important. Electronic supplementary material The online version of this article (10.1186/s12934-018-0980-1) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- L Kyselova
- Team Experimental Systems Biology, Max Planck Institute for Dynamics of Complex Technical Systems, Sandtorstr.1, 39106, Magdeburg, Germany
| | - D Kreitmayer
- Systembiotechnologie, Technische Universität München, Bolzmannstr. 15, 85748, Garching, Germany
| | - A Kremling
- Systembiotechnologie, Technische Universität München, Bolzmannstr. 15, 85748, Garching, Germany
| | - K Bettenbrock
- Team Experimental Systems Biology, Max Planck Institute for Dynamics of Complex Technical Systems, Sandtorstr.1, 39106, Magdeburg, Germany.
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Li Q, Huang B, He Q, Lu J, Li X, Li Z, Wu H, Ye Q. Production of succinate from simply purified crude glycerol by engineered Escherichia coli using two-stage fermentation. BIORESOUR BIOPROCESS 2018. [DOI: 10.1186/s40643-018-0227-3] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
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Kallscheuer N. Engineered Microorganisms for the Production of Food Additives Approved by the European Union-A Systematic Analysis. Front Microbiol 2018; 9:1746. [PMID: 30123195 PMCID: PMC6085563 DOI: 10.3389/fmicb.2018.01746] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2018] [Accepted: 07/12/2018] [Indexed: 01/16/2023] Open
Abstract
In the 1950s, the idea of a single harmonized list of food additives for the European Union arose. Already in 1962, the E-classification system, a robust food safety system intended to protect consumers from possible food-related risks, was introduced. Initially, it was restricted to colorants, but at later stages also preservatives, antioxidants, emulsifiers, stabilizers, thickeners, gelling agents, sweeteners, and flavorings were included. Currently, the list of substances authorized by the European Food Safety Authority (EFSA) (referred to as "E numbers") comprises 316 natural or artificial substances including small organic molecules, metals, salts, but also more complex compounds such as plant extracts and polymers. Low overall concentrations of such compounds in natural producers due to inherent regulation mechanisms or production processes based on non-regenerative carbon sources led to an increasing interest in establishing more reliable and sustainable production platforms. In this context, microorganisms have received significant attention as alternative sources providing access to these compounds. Scientific advancements in the fields of molecular biology and genetic engineering opened the door toward using engineered microorganisms for overproduction of metabolites of their carbon metabolism such as carboxylic acids and amino acids. In addition, entire pathways, e.g., of plant origin, were functionally introduced into microorganisms, which holds the promise to get access to an even broader range of accessible products. The aim of this review article is to give a systematic overview on current efforts during construction and application of microbial cell factories for the production of food additives listed in the EU "E numbers" catalog. The review is focused on metabolic engineering strategies of industrially relevant production hosts also discussing current bottlenecks in the underlying metabolic pathways and how they can be addressed in the future.
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Affiliation(s)
- Nicolai Kallscheuer
- Institute of Bio- and Geosciences, IBG-1: Biotechnology, Forschungszentrum Jülich GmbH, Jülich, Germany
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31
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Liu D, Mao Z, Guo J, Wei L, Ma H, Tang Y, Chen T, Wang Z, Zhao X. Construction, Model-Based Analysis, and Characterization of a Promoter Library for Fine-Tuned Gene Expression in Bacillus subtilis. ACS Synth Biol 2018; 7:1785-1797. [PMID: 29944832 DOI: 10.1021/acssynbio.8b00115] [Citation(s) in RCA: 58] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Promoters are among the most-important and most-basic tools for the control of metabolic pathways. However, previous research mainly focused on the screening and characterization of some native promoters in Bacillus subtilis. To develop a broadly applicable promoter system for this important platform organism, we created a de novo synthetic promoter library (SPL) based on consensus sequences by analyzing the microarray transcriptome data of B. subtilis 168. A total of 214 potential promoters spanning a gradient of strengths was isolated and characterized by a green fluorescence assay. Among these, a detailed intensity analysis was conducted on nine promoters with different strengths by reverse-transcription polymerase chain reaction (RT-PCR) and sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS-PAGE). Furthermore, reconstructed promoters and promoter cassettes (tandem promoter cluster) were designed via statistical model-based analysis and tandem dual promoters, which showed strength that was increased 1.2- and 2.77-fold compared to that of promoter P43, respectively. Finally, the SPL was employed in the production of inosine and acetoin by repressing and over-expressing the relevant metabolic pathways, yielding a 700% and 44% increase relative to the respective control strains. This is the first report of a de novo synthetic promoter library for B. subtilis, which is independent of any native promoter. The strategy of improving and fine-tuning promoter strengths will contribute to future metabolic engineering and synthetic biology projects in B. subtilis.
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Affiliation(s)
| | - Zhitao Mao
- Key Laboratory of System Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | | | | | - Hongwu Ma
- Key Laboratory of System Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yajie Tang
- Key Laboratory of Fermentation Engineering (Ministry of Education), Hubei Key Laboratory of Industrial Microbiology, Hubei Provincial Cooperative Innovation Center of Industrial Fermentation, Hubei University of Technology, Wuhan 430068, China
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Hasunuma T, Matsuda M, Kato Y, Vavricka CJ, Kondo A. Temperature enhanced succinate production concurrent with increased central metabolism turnover in the cyanobacterium Synechocystis sp. PCC 6803. Metab Eng 2018; 48:109-120. [DOI: 10.1016/j.ymben.2018.05.013] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2018] [Revised: 05/25/2018] [Accepted: 05/25/2018] [Indexed: 12/22/2022]
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Current advances of succinate biosynthesis in metabolically engineered Escherichia coli. Biotechnol Adv 2017; 35:1040-1048. [DOI: 10.1016/j.biotechadv.2017.09.007] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2017] [Revised: 09/14/2017] [Accepted: 09/15/2017] [Indexed: 01/19/2023]
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Wang M, Chen B, Fang Y, Tan T. Cofactor engineering for more efficient production of chemicals and biofuels. Biotechnol Adv 2017; 35:1032-1039. [DOI: 10.1016/j.biotechadv.2017.09.008] [Citation(s) in RCA: 68] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2017] [Revised: 09/14/2017] [Accepted: 09/15/2017] [Indexed: 01/04/2023]
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35
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Improving metabolic efficiency of the reverse beta-oxidation cycle by balancing redox cofactor requirement. Metab Eng 2017; 44:313-324. [PMID: 29122703 DOI: 10.1016/j.ymben.2017.11.001] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2017] [Revised: 09/29/2017] [Accepted: 11/04/2017] [Indexed: 12/15/2022]
Abstract
Previous studies have made many exciting achievements on pushing the functional reversal of beta-oxidation cycle (r-BOX) to more widespread adoption for synthesis of a wide variety of fuels and chemicals. However, the redox cofactor requirement for the efficient operation of r-BOX remains unclear. In this work, the metabolic efficiency of r-BOX for medium-chain fatty acid (C6-C10, MCFA) production was optimized by redox cofactor engineering. Stoichiometric analysis of the r-BOX pathway and further experimental examination identified NADH as a crucial determinant of r-BOX process yield. Furthermore, the introduction of formate dehydrogenase from Candida boidinii using fermentative inhibitor byproduct formate as a redox NADH sink improved MCFA titer from initial 1.2g/L to 3.1g/L. Moreover, coupling of increasing the supply of acetyl-CoA with NADH to achieve fermentative redox balance enabled product synthesis at maximum titers. To this end, the acetate re-assimilation pathway was further optimized to increase acetyl-CoA availability associated with the new supply of NADH. It was found that the acetyl-CoA synthetase activity and intracellular ATP levels constrained the activity of acetate re-assimilation pathway, and 4.7g/L of MCFA titer was finally achieved after alleviating these two limiting factors. To the best of our knowledge, this represented the highest titer reported to date. These results demonstrated that the key constraint of r-BOX was redox imbalance and redox engineering could further unleash the lipogenic potential of this cycle. The redox engineering strategies could be applied to acetyl-CoA-derived products or other bio-products requiring multiple redox cofactors for biosynthesis.
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Gonzalez-Garcia RA, McCubbin T, Wille A, Plan M, Nielsen LK, Marcellin E. Awakening sleeping beauty: production of propionic acid in Escherichia coli through the sbm operon requires the activity of a methylmalonyl-CoA epimerase. Microb Cell Fact 2017; 16:121. [PMID: 28716098 PMCID: PMC5512728 DOI: 10.1186/s12934-017-0735-4] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2017] [Accepted: 07/05/2017] [Indexed: 11/29/2022] Open
Abstract
BACKGROUND Propionic acid is used primarily as a food preservative with smaller applications as a chemical building block for the production of many products including fabrics, cosmetics, drugs, and plastics. Biological production using propionibacteria would be competitive against chemical production through hydrocarboxylation of ethylene if native producers could be engineered to reach near-theoretical yield and good productivity. Unfortunately, engineering propionibacteria has proven very challenging. It has been suggested that activation of the sleeping beauty operon in Escherichia coli is sufficient to achieve propionic acid production. Optimising E. coli production should be much easier than engineering propionibacteria if tolerance issues can be addressed. RESULTS Propionic acid is produced in E. coli via the sleeping beauty mutase operon under anaerobic conditions in rich medium via amino acid degradation. We observed that the sbm operon enhances amino acids degradation to propionic acid and allows E. coli to degrade isoleucine. However, we show here that the operon lacks an epimerase reaction that enables propionic acid production in minimal medium containing glucose as the sole carbon source. Production from glucose can be restored by engineering the system with a methylmalonyl-CoA epimerase from Propionibacterium acidipropionici (0.23 ± 0.02 mM). 1-Propanol production was also detected from the promiscuous activity of the native alcohol dehydrogenase (AdhE). We also show that aerobic conditions are favourable for propionic acid production. Finally, we increase titre 65 times using a combination of promoter engineering and process optimisation. CONCLUSIONS The native sbm operon encodes an incomplete pathway. Production of propionic acid from glucose as sole carbon source is possible when the pathway is complemented with a methylmalonyl-CoA epimerase. Although propionic acid via the restored succinate dissimilation pathway is considered a fermentative process, the engineered pathway was shown to be functional under anaerobic and aerobic conditions.
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Affiliation(s)
| | - Tim McCubbin
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, Brisbane, QLD 4072 Australia
| | - Annalena Wille
- Bielefeld University, Universitätsstraße 25, 33615 Bielefeld, Germany
| | - Manuel Plan
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, Brisbane, QLD 4072 Australia
| | - Lars Keld Nielsen
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, Brisbane, QLD 4072 Australia
| | - Esteban Marcellin
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, Brisbane, QLD 4072 Australia
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Enhancement of succinate yield by manipulating NADH/NAD + ratio and ATP generation. Appl Microbiol Biotechnol 2017; 101:3153-3161. [PMID: 28108762 DOI: 10.1007/s00253-017-8127-6] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2016] [Revised: 01/04/2017] [Accepted: 01/10/2017] [Indexed: 10/20/2022]
Abstract
We previously engineered Escherichia coli YL104 to efficiently produce succinate from glucose. In this study, we investigated the relationships between the NADH/NAD+ ratio, ATP level, and overall yield of succinate production by using glucose as the carbon source in YL104. First, the use of sole NADH dehydrogenases increased the overall yield of succinate by 7% and substantially decreased the NADH/NAD+ ratio. Second, the soluble fumarate reductase from Saccharomyces cerevisiae was overexpressed to manipulate the anaerobic NADH/NAD+ ratio and ATP level. Third, another strategy for reducing the ATP level was applied by introducing ATP futile cycling for improving succinate production. Finally, a combination of these methods exerted a synergistic effect on improving the overall yield of succinate, which was 39% higher than that of the previously engineered strain YL104. The study results indicated that regulation of the NADH/NAD+ ratio and ATP level is an efficient strategy for succinate production.
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Application of theoretical methods to increase succinate production in engineered strains. Bioprocess Biosyst Eng 2016; 40:479-497. [PMID: 28040871 DOI: 10.1007/s00449-016-1729-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2016] [Accepted: 12/16/2016] [Indexed: 12/19/2022]
Abstract
Computational methods have enabled the discovery of non-intuitive strategies to enhance the production of a variety of target molecules. In the case of succinate production, reviews covering the topic have not yet analyzed the impact and future potential that such methods may have. In this work, we review the application of computational methods to the production of succinic acid. We found that while a total of 26 theoretical studies were published between 2002 and 2016, only 10 studies reported the successful experimental implementation of any kind of theoretical knowledge. None of the experimental studies reported an exact application of the computational predictions. However, the combination of computational analysis with complementary strategies, such as directed evolution and comparative genome analysis, serves as a proof of concept and demonstrates that successful metabolic engineering can be guided by rational computational methods.
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