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Yang Z, Wu W, Zhao Q, Angelidaki I, Arhin SG, Hua D, Zhao Y, Sun H, Liu G, Wang W. Enhanced direct gaseous CO 2 fixation into higher bio-succinic acid production and selectivity. J Environ Sci (China) 2024; 143:164-175. [PMID: 38644014 DOI: 10.1016/j.jes.2023.05.035] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Revised: 05/24/2023] [Accepted: 05/24/2023] [Indexed: 04/23/2024]
Abstract
Utilizing CO2 for bio-succinic acid production is an attractive approach to achieve carbon capture and recycling (CCR) with simultaneous production of a useful platform chemical. Actinobacillus succinogenes and Basfia succiniciproducens were selected and investigated as microbial catalysts. Firstly, the type and concentration of inorganic carbon concentration and glucose concentration were evaluated. 6 g C/L MgCO3 and 24 g C/L glucose were found to be the optimal basic operational conditions, with succinic acid production and carbon yield of over 30 g/L and over 40%, respectively. Then, for maximum gaseous CO2 fixation, carbonate was replaced with CO2 at different ratios. The "less carbonate more CO2" condition of the inorganic carbon source was set as carbonate: CO2 = 1:9 (based on the mass of carbon). This condition presented the highest availability of CO2 by well-balanced chemical reaction equilibrium and phase equilibrium, showing the best performance with regarding CO2 fixation (about 15 mg C/(L·hr)), with suppressed lactic acid accumulation. According to key enzymes analysis, the ratio of phosphoenolpyruvate carboxykinase to lactic dehydrogenase was enhanced at high ratios of gaseous CO2, which could promote glucose conversion through the succinic acid path. To further increase gaseous CO2 fixation and succinic acid production and selectivity, stepwise CO2 addition was evaluated. 50%-65% increase in inorganic carbon utilization was obtained coupled with 20%-30% increase in succinic acid selectivity. This was due to the promotion of the succinic acid branch of the glucose metabolism, while suppressing the pyruvate branch, along with the inhibition on the conversion from glucose to lactic acid.
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Affiliation(s)
- Ziyi Yang
- Biomass Energy and Environmental Engineering Research Center, Beijing University of Chemical Technology, Beijing 100029, China; College of Chemical Engineering, Beijing University of Chemical Technology, Beijing 100029, China
| | - Wanling Wu
- Biomass Energy and Environmental Engineering Research Center, Beijing University of Chemical Technology, Beijing 100029, China; College of Chemical Engineering, Beijing University of Chemical Technology, Beijing 100029, China
| | - Qing Zhao
- Biomass Energy and Environmental Engineering Research Center, Beijing University of Chemical Technology, Beijing 100029, China; College of Chemical Engineering, Beijing University of Chemical Technology, Beijing 100029, China
| | - Irini Angelidaki
- Department of Chemical and Biochemical Environmental Engineering, Technical University of Denmark, DK-2800, Kgs Lyngby, Denmark
| | - Samuel Gyebi Arhin
- Biomass Energy and Environmental Engineering Research Center, Beijing University of Chemical Technology, Beijing 100029, China; College of Chemical Engineering, Beijing University of Chemical Technology, Beijing 100029, China
| | - Dongliang Hua
- Energy Research Institute, Qilu University of Technology (Shandong Academy of Sciences), Shandong Provincial Key Laboratory of Biomass Gasification Technology, Jinan 250014, China
| | - Yuxiao Zhao
- Energy Research Institute, Qilu University of Technology (Shandong Academy of Sciences), Shandong Provincial Key Laboratory of Biomass Gasification Technology, Jinan 250014, China
| | - Hangyu Sun
- Biomass Energy and Environmental Engineering Research Center, Beijing University of Chemical Technology, Beijing 100029, China; College of Chemical Engineering, Beijing University of Chemical Technology, Beijing 100029, China
| | - Guangqing Liu
- Biomass Energy and Environmental Engineering Research Center, Beijing University of Chemical Technology, Beijing 100029, China
| | - Wen Wang
- Biomass Energy and Environmental Engineering Research Center, Beijing University of Chemical Technology, Beijing 100029, China; College of Chemical Engineering, Beijing University of Chemical Technology, Beijing 100029, China.
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Meyer S, Tilloy V, Durand-Fontanier S, Lafon T, Garnier F, Martin C, Ploy MC, Barraud O. Emayella augustorita, New Member of Pasteurellaceae, Isolated from Blood Cultures of Septic Patient. Emerg Infect Dis 2024; 30:1719-1721. [PMID: 38907366 PMCID: PMC11286039 DOI: 10.3201/eid3008.231651] [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] [Indexed: 06/24/2024] Open
Abstract
We report discovery of a new bacterial genus and species of the family Pasteurellaceae by using phylogenetic and metabolic analysis. The bacterium, Emayella augustorita, was isolated from blood cultures of a patient in France diagnosed with an adenocarcinoma of the intestines and who was treated with a biliary prosthesis placement.
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Jia M, Zhu S, Xue MY, Chen H, Xu J, Song M, Tang Y, Liu X, Tao Y, Zhang T, Liu JX, Wang Y, Sun HZ. Single-cell transcriptomics across 2,534 microbial species reveals functional heterogeneity in the rumen microbiome. Nat Microbiol 2024; 9:1884-1898. [PMID: 38866938 DOI: 10.1038/s41564-024-01723-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2023] [Accepted: 05/07/2024] [Indexed: 06/14/2024]
Abstract
Deciphering the activity of individual microbes within complex communities and environments remains a challenge. Here we describe the development of microbiome single-cell transcriptomics using droplet-based single-cell RNA sequencing and pangenome-based computational analysis to characterize the functional heterogeneity of the rumen microbiome. We generated a microbial genome database (the Bovine Gastro Microbial Genome Map) as a functional reference map for the construction of a single-cell transcriptomic atlas of the rumen microbiome. The atlas includes 174,531 microbial cells and 2,534 species, of which 172 are core active species grouped into 12 functional clusters. We detected single-cell-level functional roles, including a key role for Basfia succiniciproducens in the carbohydrate metabolic niche of the rumen microbiome. Furthermore, we explored functional heterogeneity and reveal metabolic niche trajectories driven by biofilm formation pathway genes within B. succiniciproducens. Our results provide a resource for studying the rumen microbiome and illustrate the diverse functions of individual microbial cells that drive their ecological niche stability or adaptation within the ecosystem.
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Affiliation(s)
- Minghui Jia
- Institute of Dairy Science, College of Animal Sciences, Zhejiang University, Hangzhou, China
- Key Laboratory of Molecular Animal Nutrition, Ministry of Education, Zhejiang University, Hangzhou, China
- Key Laboratory of Dairy Cow Genetic Improvement and Milk Quality Research of Zhejiang Province, Zhejiang University, Hangzhou, China
| | - Senlin Zhu
- Institute of Dairy Science, College of Animal Sciences, Zhejiang University, Hangzhou, China
- Key Laboratory of Molecular Animal Nutrition, Ministry of Education, Zhejiang University, Hangzhou, China
- Key Laboratory of Dairy Cow Genetic Improvement and Milk Quality Research of Zhejiang Province, Zhejiang University, Hangzhou, China
| | - Ming-Yuan Xue
- Institute of Dairy Science, College of Animal Sciences, Zhejiang University, Hangzhou, China
- Key Laboratory of Molecular Animal Nutrition, Ministry of Education, Zhejiang University, Hangzhou, China
- Xianghu Laboratory, Hangzhou, China
| | - Hongyi Chen
- Institute of Dairy Science, College of Animal Sciences, Zhejiang University, Hangzhou, China
- Key Laboratory of Molecular Animal Nutrition, Ministry of Education, Zhejiang University, Hangzhou, China
| | - Jinghong Xu
- Institute of Dairy Science, College of Animal Sciences, Zhejiang University, Hangzhou, China
- Key Laboratory of Molecular Animal Nutrition, Ministry of Education, Zhejiang University, Hangzhou, China
| | - Mengdi Song
- Liangzhu Laboratory, Zhejiang University, Hangzhou, China
- Department of Laboratory Medicine, the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
- M20 Genomics, Hangzhou, China
| | - Yifan Tang
- Institute of Dairy Science, College of Animal Sciences, Zhejiang University, Hangzhou, China
- Key Laboratory of Molecular Animal Nutrition, Ministry of Education, Zhejiang University, Hangzhou, China
| | - Xiaohan Liu
- Institute of Dairy Science, College of Animal Sciences, Zhejiang University, Hangzhou, China
- Key Laboratory of Molecular Animal Nutrition, Ministry of Education, Zhejiang University, Hangzhou, China
| | - Ye Tao
- Shanghai Biozeron Biotechnology Company, Shanghai, China
| | - Tianyu Zhang
- Liangzhu Laboratory, Zhejiang University, Hangzhou, China
- Department of Laboratory Medicine, the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
- M20 Genomics, Hangzhou, China
| | - Jian-Xin Liu
- Institute of Dairy Science, College of Animal Sciences, Zhejiang University, Hangzhou, China
- Key Laboratory of Molecular Animal Nutrition, Ministry of Education, Zhejiang University, Hangzhou, China
| | - Yongcheng Wang
- Liangzhu Laboratory, Zhejiang University, Hangzhou, China.
- Department of Laboratory Medicine, the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China.
| | - Hui-Zeng Sun
- Institute of Dairy Science, College of Animal Sciences, Zhejiang University, Hangzhou, China.
- Key Laboratory of Molecular Animal Nutrition, Ministry of Education, Zhejiang University, Hangzhou, China.
- Key Laboratory of Dairy Cow Genetic Improvement and Milk Quality Research of Zhejiang Province, Zhejiang University, Hangzhou, China.
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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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Hackmann TJ, Zhang B. The phenotype and genotype of fermentative prokaryotes. SCIENCE ADVANCES 2023; 9:eadg8687. [PMID: 37756392 PMCID: PMC10530074 DOI: 10.1126/sciadv.adg8687] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Accepted: 08/25/2023] [Indexed: 09/29/2023]
Abstract
Fermentation is a type of metabolism pervasive in oxygen-deprived environments. Despite its importance, we know little about the range and traits of organisms that carry out this metabolism. Our study addresses this gap with a comprehensive analysis of the phenotype and genotype of fermentative prokaryotes. We assembled a dataset with phenotypic records of 8350 organisms plus 4355 genomes and 13.6 million genes. Our analysis reveals fermentation is both widespread (in ~30% of prokaryotes) and complex (forming ~300 combinations of metabolites). Furthermore, it points to previously uncharacterized proteins involved in this metabolism. Previous studies suggest that metabolic pathways for fermentation are well understood, but metabolic models built in our study show gaps in our knowledge. This study demonstrates the complexity of fermentation while showing that there is still much to learn about this metabolism. All resources in our study can be explored by the scientific community with an online, interactive tool.
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Affiliation(s)
| | - Bo Zhang
- Department of Chemical Engineering, University of California, Santa Barbara, CA, USA
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Balázs M, Bartos H, Lányi S, Bodor Z, Miklóssy I. Substrate type and CO 2 addition significantly influence succinic acid production of Basfia succiniciproducens. Biotechnol Lett 2023; 45:1133-1145. [PMID: 37395870 PMCID: PMC10432361 DOI: 10.1007/s10529-023-03406-7] [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: 11/18/2022] [Revised: 05/28/2023] [Accepted: 06/10/2023] [Indexed: 07/04/2023]
Abstract
Metabolic engineering has shown that optimizing metabolic pathways' fluxes for industrial purposes requires a methodical approach. Accordingly, in this study, in silico metabolic modeling was utilized to characterize the lesser-known strain Basfia succiniciproducens under different environmental conditions, followed by the use of industrially relevant substrates for succinic acid synthesis. Based on RT-qPCR carried out in flask experiments, we discovered a relatively large difference in the expression levels of ldhA gene compared to glucose in both xylose and glycerol cultures. In bioreactor-scale fermentations, the impact of different gas phases (CO2, CO2/AIR) on biomass yield, substrate consumption, and metabolite profiles was also investigated. In the case of glycerol, the addition of CO2 increased biomass as well as target product formation, while using CO2/AIR gas phase resulted in higher target product yield (0.184 mM⋅mM-1). In case of xylose, using CO2 alone would result in higher succinic acid production (0.277 mM⋅mM-1). The promising rumen bacteria, B. succiniciproducens, has shown to be suitable for succinic acid production from both xylose and glycerol. As a result, our findings present new opportunities for broadening the range of raw materials used in this significant biochemical process. Our study also sheds light on fermentation parameter optimization for this strain, namely that, CO2/AIR supply has a positive effect on target product formation.
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Affiliation(s)
- Márta Balázs
- Faculty of Science, University of Pécs, Ifjúság 6, 7624, Pécs, Hungary
| | - Hunor Bartos
- Faculty of Science, University of Pécs, Ifjúság 6, 7624, Pécs, Hungary
| | - Szabolcs Lányi
- Department of Bioengineering, Sapientia Hungarian University of Transylvania, Piata Libertatii, 530104, Miercurea Ciuc, Romania
| | - Zsolt Bodor
- Department of Bioengineering, Sapientia Hungarian University of Transylvania, Piata Libertatii, 530104, Miercurea Ciuc, Romania.
- Institute for Research and Development of Hunting and Mountain Resources, St. Progresului 35B, 530240, Miercurea Ciuc, Romania.
| | - Ildikó Miklóssy
- Department of Bioengineering, Sapientia Hungarian University of Transylvania, Piata Libertatii, 530104, Miercurea Ciuc, Romania
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7
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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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9
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D’ambrosio S, Alfano A, Cimini D. Production of Succinic Acid From Basfia succiniciproducens. FRONTIERS IN CHEMICAL ENGINEERING 2021. [DOI: 10.3389/fceng.2021.785691] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Basfia succiniciproducens is a facultative anaerobic capnophilic bacterium, isolated from rumen, that naturally produces high amounts of succinic acid by fixing CO2 and using fumarate as final electron acceptor. This metabolic feature makes it one of the ideal candidates for developing biotechnological industrial routes that could eventually replace the polluting and environment unfriendly petrochemical ones that are still main sources for the production of this value-added compound. In fact, due to the large number of applications of succinic acid that range from the more traditional ones as food additive or pharmaceutical intermediate to the most recent as building block for biopolymers and bioplastic, increasing demand and market size growth are expected in the next years. In line with a “green revolution” needed to preserve our environment, the great challenge is the establishment of commercially viable production processes that exploit renewable materials and in particular preferably non-food lignocellulosic biomasses and waste products. In this review, we describe the currently available literature concerning B. succiniciproducens since the strain was first isolated, focusing on the different renewable materials and fermentation strategies used to improve succinic acid production titers to date. Moreover, an insight into the metabolic engineering approaches and the key physiological characteristics of B. succiniciproducens deduced from the different studies are presented.
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10
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Influence of the Initial Sugar Concentration and Supplementation with Yeast Extract on Succinic Acid Fermentation in a Lactose-Based Medium. FERMENTATION 2021. [DOI: 10.3390/fermentation7040221] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
The aim of this study was to investigate the production of succinic acid from lactose concentrate, a by-product of cheese-making, using Actinobacillus succinogenes and Basfia succiniciproducens. Although the ability of these strains to metabolize different sugars is already known, their application in the conversion of lactose bears high potential for optimization. With regard to B. succiniciproducens, this approach is completely novel. In particular, the effect of the medium’s sugar concentration as well as the ability of its supplementation with yeast extract to prevent a lack of essential nutrient proteins and vitamins was examined. Lactose-based media containing sugar concentrations of between 20 and 65 g L−1 and 5 g L−1 of yeast extract were fermented, with both strains showing comparable performances. The best results in terms of succinic acid yield and acid concentration—0.57 g g−1 initial sugar and 23 g L−1—were achieved at an initial sugar concentration of 43 g L−1. The necessity of yeast extract was demonstrated using the sugar-optimized medium without supplementation. As a result, the yield and concentration of succinic acid dropped to 0.34 g g−1 and 13 g L−1 and the sugar consumption decreased from more than 99 to less than 55%. Therefore, the supplementation amount of 5 g L−1 of yeast extract can be regarded as well-balanced.
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11
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Hoff B, Plassmeier J, Blankschien M, Letzel AC, Kourtz L, Schröder H, Koch W, Zelder O. Unlocking Nature's Biosynthetic Power-Metabolic Engineering for the Fermentative Production of Chemicals. Angew Chem Int Ed Engl 2021; 60:2258-2278. [PMID: 33026132 DOI: 10.1002/anie.202004248] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2020] [Revised: 07/08/2020] [Indexed: 01/03/2023]
Abstract
Fermentation as a production method for chemicals is especially attractive, as it is based on cheap renewable raw materials and often exhibits advantages in terms of costs and sustainability. The tremendous development of technology in bioscience has resulted in an exponentially increasing knowledge about biological systems and has become the main driver for innovations in the field of metabolic engineering. Progress in recombinant DNA technology, genomics, and computational methods open new, cheaper, and faster ways to metabolically engineer microorganisms. Existing biosynthetic pathways for natural products, such as vitamins, organic acids, amino acids, or secondary metabolites, can be discovered and optimized efficiently, thereby enabling competitive commercial production processes. Novel biosynthetic routes can now be designed by the rearrangement of nature's unlimited number of enzymes and metabolic pathways in microbial strains. This expands the range of chemicals accessible by biotechnology and has yielded the first commercial products, while new fermentation technologies targeting novel active ingredients, commodity chemicals, and CO2 -fixation methods are on the horizon.
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Affiliation(s)
- Birgit Hoff
- RBW, White Biotechnology Research, BASF SE, building: A30, Carl-Bosch-Strasse 38, 67056, Ludwigshafen am Rhein, Germany
| | - Jens Plassmeier
- Biomaterials, Conagen, Inc., 15 DeAngelo Drive, 01730, Bedford, MA, USA
| | - Matthew Blankschien
- James R. Randall Research Center, ADM, 1001 North Brush College Road, 62521, Decatur, Il, USA
| | - Anne-Catrin Letzel
- RBW, White Biotechnology Research, BASF SE, building: A30, Carl-Bosch-Strasse 38, 67056, Ludwigshafen am Rhein, Germany
| | - Lauralynn Kourtz
- R&D, Allied Microbiota, 1345 Ave of Americas, 10105, New York, NY, USA
| | - Hartwig Schröder
- RBW, White Biotechnology Research, BASF SE, building: A30, Carl-Bosch-Strasse 38, 67056, Ludwigshafen am Rhein, Germany
| | - Walter Koch
- RBW, White Biotechnology Research, BASF SE, building: A30, Carl-Bosch-Strasse 38, 67056, Ludwigshafen am Rhein, Germany
| | - Oskar Zelder
- RBW, White Biotechnology Research, BASF SE, building: A30, Carl-Bosch-Strasse 38, 67056, Ludwigshafen am Rhein, Germany
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12
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Liu Y, Esen O, Pronk JT, van Gulik WM. Uncoupling growth and succinic acid production in an industrial Saccharomyces cerevisiae strain. Biotechnol Bioeng 2021; 118:1576-1586. [PMID: 33410171 PMCID: PMC8048565 DOI: 10.1002/bit.27672] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2020] [Revised: 12/13/2020] [Accepted: 12/29/2020] [Indexed: 12/12/2022]
Abstract
This study explores the relation between biomass‐specific succinic acid (SA) production rate and specific growth rate of an engineered industrial strain of Saccharomyces cerevisiae, with the aim to investigate the extent to which growth and product formation can be uncoupled. Ammonium‐limited aerobic chemostat and retentostat cultures were grown at different specific growth rates under industrially relevant conditions, that is, at a culture pH of 3 and with sparging of a 1:1 CO2–air mixture. Biomass‐specific SA production rates decreased asymptotically with decreasing growth rate. At near‐zero growth rates, the engineered strain maintained a stable biomass‐specific SA production rate for over 500 h, with a SA yield on glucose of 0.61 mol mol−1. These results demonstrate that uncoupling of growth and SA production could indeed be achieved. A linear relation between the biomass‐specific SA production rate and glucose consumption rate indicated the coupling of SA production rate and the flux through primary metabolism. The low culture pH resulted in an increased death rate, which was lowest at near‐zero growth rates. Nevertheless, a significant amount of non‐viable biomass accumulated in the retentostat cultures, thus underlining the importance of improving low‐pH tolerance in further strain development for industrial SA production with S. cerevisiae.
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Affiliation(s)
- Yaya Liu
- Department of Biotechnology, Delft University of Technology, Delft, The Netherlands
| | - Osman Esen
- Department of Biotechnology, Delft University of Technology, Delft, The Netherlands
| | - Jack T Pronk
- Department of Biotechnology, Delft University of Technology, Delft, The Netherlands
| | - Walter M van Gulik
- Department of Biotechnology, Delft University of Technology, Delft, The Netherlands
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Hoff B, Plassmeier J, Blankschien M, Letzel A, Kourtz L, Schröder H, Koch W, Zelder O. Unlocking Nature's Biosynthetic Power—Metabolic Engineering for the Fermentative Production of Chemicals. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.202004248] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Affiliation(s)
- Birgit Hoff
- RBW, White Biotechnology Research BASF SE building: A30, Carl-Bosch-Strasse 38 67056 Ludwigshafen am Rhein Germany
| | - Jens Plassmeier
- Biomaterials Conagen, Inc. 15 DeAngelo Drive 01730 Bedford, MA USA
| | - Matthew Blankschien
- James R. Randall Research Center ADM 1001 North Brush College Road 62521 Decatur, Il USA
| | - Anne‐Catrin Letzel
- RBW, White Biotechnology Research BASF SE building: A30, Carl-Bosch-Strasse 38 67056 Ludwigshafen am Rhein Germany
| | - Lauralynn Kourtz
- R&D Allied Microbiota 1345 Ave of Americas 10105 New York, NY USA
| | - Hartwig Schröder
- RBW, White Biotechnology Research BASF SE building: A30, Carl-Bosch-Strasse 38 67056 Ludwigshafen am Rhein Germany
| | - Walter Koch
- RBW, White Biotechnology Research BASF SE building: A30, Carl-Bosch-Strasse 38 67056 Ludwigshafen am Rhein Germany
| | - Oskar Zelder
- RBW, White Biotechnology Research BASF SE building: A30, Carl-Bosch-Strasse 38 67056 Ludwigshafen am Rhein Germany
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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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Metabolic engineering for the production of dicarboxylic acids and diamines. Metab Eng 2020; 58:2-16. [DOI: 10.1016/j.ymben.2019.03.005] [Citation(s) in RCA: 60] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2019] [Revised: 03/15/2019] [Accepted: 03/15/2019] [Indexed: 11/18/2022]
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16
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Dickerman A, Bandara AB, Inzana TJ. Phylogenomic analysis of Haemophilus parasuis and proposed reclassification to Glaesserella parasuis, gen. nov., comb. nov. Int J Syst Evol Microbiol 2020; 70:180-186. [PMID: 31592757 DOI: 10.1099/ijsem.0.003730] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The Gram-negative bacterium Haemophilus parasuis is the etiologic agent of Glässer's disease in pigs, and causes significant economic losses to the swine industry. This bacterium has been classified as a member of the family Pasteurellaceae in the genus Haemophilus, but phylogenetic relatedness has not been adequately examined to support this genus classification. Phenotypically, all 38 strains of H. parasuis tested were positive for catalase activity, oxidase activity, V-factor requirement, and acid formation from maltose and d-galactose without gas. All strains were negative for X-factor requirement, formation of indole from tryptophan, urease, l-arabinose, and α-glucosidase activity. To determine whether H. parasuis belongs to one of the current Pasteurellaceae genera 40 H. parasuis genomes, plus those of representative Pasteurellaceae, were subjected to phylogenetic analysis of concatenated, multi-protein alignments. Sequence variation at 16S rRNA and rpoB loci allowed the 15 reference serovars of H. parasuis to be integrated into the whole-genome tree. The phylogenetic analysis showed H. parasuis to be a distinct and tight clade whose sister taxon is the genus Bibersteinia. Within H. parasuis two clades were identified with individual serovars distributed between the two. As a result, H. parasuis was confirmed as a member of the family Pasteurellaceae, but was distinct from other genera in this family. Therefore, we propose the name Glaesserella parasuis, gen. nov., comb. nov. for bacterial strains currently classified as H. parasuis. The reference strain of this species is ATCC 19417 (1374)T, NCTC 4557T, DSM 21448T, CCUG 3712T.
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Affiliation(s)
- Allan Dickerman
- Biocomplexity Institute, Virginia Tech, Blacksburg, VA 24061, USA
| | - Aloka B Bandara
- Department of Biomedical Sciences and Pathobiology, Virginia Tech, Blacksburg, VA 24061, USA
| | - Thomas J Inzana
- College of Veterinary Medicine, Long Island University, Brookville, NY 11548, USA
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17
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Snelling TJ, Auffret MD, Duthie CA, Stewart RD, Watson M, Dewhurst RJ, Roehe R, Walker AW. Temporal stability of the rumen microbiota in beef cattle, and response to diet and supplements. Anim Microbiome 2019; 1:16. [PMID: 33499961 PMCID: PMC7807515 DOI: 10.1186/s42523-019-0018-y] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2019] [Accepted: 10/28/2019] [Indexed: 12/31/2022] Open
Abstract
BACKGROUND Dietary intake is known to be a driver of microbial community dynamics in ruminants. Beef cattle go through a finishing phase that typically includes very high concentrate ratios in their feed, with consequent effects on rumen metabolism including methane production. This longitudinal study was designed to measure dynamics of the rumen microbial community in response to the introduction of high concentrate diets fed to beef cattle during the finishing period. A cohort of 50 beef steers were fed either of two basal diet formulations consisting of approximately 10:90 or 50:50 forage:concentrate ratios respectively. Nitrate and oil rich supplements were also added either individually or in combination. Digesta samples were taken at time points over ~ 200 days during the finishing period of the cattle to measure the adaptation to the basal diet and long-term stability of the rumen microbiota. RESULTS 16S rRNA gene amplicon libraries were prepared from 313 rumen digesta samples and analysed at a depth of 20,000 sequences per library. Bray Curtis dissimilarity with analysis of molecular variance (AMOVA) revealed highly significant (p < 0.001) differences in microbiota composition between cattle fed different basal diets, largely driven by reduction of fibre degrading microbial groups and increased relative abundance of an unclassified Gammaproteobacteria OTU in the high concentrate fed animals. Conversely, the forage-based diet was significantly associated with methanogenic archaea. Within basal diet groups, addition of the nitrate and combined supplements had lesser, although still significant, impacts on microbiota dissimilarity compared to pre-treatment time points and controls. Measurements of the response and stability of the microbial community over the time course of the experiment showed continuing adaptation up to 25 days in the high concentrate groups. After this time point, however, no significant variability was detected. CONCLUSIONS High concentrate diets that are typically fed to finishing beef cattle can have a significant effect on the microbial community in the rumen. Inferred metabolic activity of the different microbial communities associated with each of the respective basal diets explained differences in methane and short chain fatty acid production between cattle. Longitudinal sampling revealed that once adapted to a change in diet, the rumen microbial community remains in a relatively stable alternate state.
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Affiliation(s)
| | | | | | - Robert D. Stewart
- The Roslin Institute and R(D)SVS, University of Edinburgh, Edinburgh, EH25 9RG UK
| | - Mick Watson
- The Roslin Institute and R(D)SVS, University of Edinburgh, Edinburgh, EH25 9RG UK
| | | | | | - Alan W. Walker
- Rowett Institute, University of Aberdeen, Aberdeen, AB25 2ZD UK
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18
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Babaei M, Tsapekos P, Alvarado-Morales M, Hosseini M, Ebrahimi S, Niaei A, Angelidaki I. Valorization of organic waste with simultaneous biogas upgrading for the production of succinic acid. Biochem Eng J 2019. [DOI: 10.1016/j.bej.2019.04.012] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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19
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Ferone M, Raganati F, Olivieri G, Marzocchella A. Bioreactors for succinic acid production processes. Crit Rev Biotechnol 2019; 39:571-586. [DOI: 10.1080/07388551.2019.1592105] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Mariateresa Ferone
- Dipartimento di Ingegneria Chimica, dei Materiali e della Produzione Industriale, Università degli Studi di Napoli Federico II, Napoli, Italy
- UCD School of Agriculture & Food Science, University College Dublin, Dublin, Ireland
| | - Francesca Raganati
- Dipartimento di Ingegneria Chimica, dei Materiali e della Produzione Industriale, Università degli Studi di Napoli Federico II, Napoli, Italy
| | - Giuseppe Olivieri
- Dipartimento di Ingegneria Chimica, dei Materiali e della Produzione Industriale, Università degli Studi di Napoli Federico II, Napoli, Italy
- Department of Agrotechnology and Food Sciences, Wageningen University and Research Centre, Wageningen, The Netherlands
| | - Antonio Marzocchella
- Dipartimento di Ingegneria Chimica, dei Materiali e della Produzione Industriale, Università degli Studi di Napoli Federico II, Napoli, Italy
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20
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Membrane engineering via trans-unsaturated fatty acids production improves succinic acid production in Mannheimia succiniciproducens. J Ind Microbiol Biotechnol 2018; 45:555-566. [PMID: 29380151 DOI: 10.1007/s10295-018-2016-6] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2017] [Accepted: 01/23/2018] [Indexed: 12/11/2022]
Abstract
Engineering of microorganisms to produce desired bio-products with high titer, yield, and productivity is often limited by product toxicity. This is also true for succinic acid (SA), a four carbon dicarboxylic acid of industrial importance. Acid products often cause product toxicity to cells through several different factors, membrane damage being one of the primary factors. In this study, cis-trans isomerase from Pseudomonas aeruginosa was expressed in Mannheimia succiniciproducens to produce trans-unsaturated fatty acid (TUFA) and to reinforce the cell membrane of M. succiniciproducens. The engineered strain showed significant decrease in membrane fluidity as production of TUFA enabled tight packing of fatty acids, which made cells to possess more rigid cell membrane. As a result, the membrane-engineered M. succiniciproducens strain showed higher tolerance toward SA and increased production of SA compared with the control strain without membrane engineering. The membrane engineering approach employed in this study will be useful for increasing tolerance to, and consequently enhancing production of acid products.
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21
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Adhikary S, Bisgaard M, Nicklas W, Christensen H. Reclassification of Bisgaard taxon 5 as Caviibacterium pharyngocola gen. nov., sp. nov. and Bisgaard taxon 7 as Conservatibacter flavescens gen. nov., sp. nov. Int J Syst Evol Microbiol 2018; 68:643-650. [PMID: 29303698 DOI: 10.1099/ijsem.0.002558] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A total of 29 strains mainly from guinea pigs were investigated by a polyphasic approach that included previously published data. The strains were classified as Bisgaard taxa 5 and 7 by comparison of phenotypic characteristics and the strains showed typical cultural characteristics for members of family Pasteurellaceae and the strains formed two monophyletic groups based on 16S rRNA gene sequence comparison. Partial rpoB sequence analysis as well as published data on DNA-DNA hybridization showed high genotypic relationships within both groups. A new genus with one species, Caviibacterium pharyngocola gen. nov., sp. nov., is proposed to accommodate members of taxon 5 of Bisgaard, whereas members of taxon 7 are proposed as Conservatibacter flavescens gen. nov., sp. nov. The two genera are clearly separated by phenotype from each other and from existing genera of the family Pasteurellaceae. The type strain of Caviibacterium pharyngocola is 7.3T (=CCUG 16493T=DSM 105478T) and the type strain of Conservatibacter flavescens is 7.4T (=CCUG 24852T=DSM 105479T=HIM 794-7T), both were isolated from the pharynx of guinea pigs.
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Affiliation(s)
- Sadhana Adhikary
- Department of Veterinary Animal Sciences, University of Copenhagen, 4 Stigbøjlen, DK-1870 Frederiksberg C, Denmark
| | - Magne Bisgaard
- Professor emeritus, Horsevænget 40, Viby Sjælland, Denmark
| | - Werner Nicklas
- Microbiological Diagnostics, German Cancer Research Centre, D-69120 Heidelberg, Germany
| | - Henrik Christensen
- Department of Veterinary Animal Sciences, University of Copenhagen, 4 Stigbøjlen, DK-1870 Frederiksberg C, Denmark
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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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Lange A, Becker J, Schulze D, Cahoreau E, Portais JC, Haefner S, Schröder H, Krawczyk J, Zelder O, Wittmann C. Bio-based succinate from sucrose: High-resolution 13C metabolic flux analysis and metabolic engineering of the rumen bacterium Basfia succiniciproducens. Metab Eng 2017; 44:198-212. [PMID: 29037780 DOI: 10.1016/j.ymben.2017.10.003] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2017] [Revised: 09/10/2017] [Accepted: 10/04/2017] [Indexed: 01/12/2023]
Abstract
Succinic acid is a platform chemical of recognized industrial value and accordingly faces a continuous challenge to enable manufacturing from most attractive raw materials. It is mainly produced from glucose, using microbial fermentation. Here, we explore and optimize succinate production from sucrose, a globally applied substrate in biotechnology, using the rumen bacterium Basfia succiniciproducens DD1. As basis of the strain optimization, the yet unknown sucrose metabolism of the microbe was studied, using 13C metabolic flux analyses. When grown in batch culture on sucrose, the bacterium exhibited a high succinate yield of 1molmol-1 and a by-product spectrum, which did not match the expected PTS-mediated sucrose catabolism. This led to the discovery of a fructokinase, involved in sucrose catabolism. The flux approach unraveled that the fructokinase and the fructose PTS both contribute to phosphorylation of the fructose part of sucrose. The contribution of the fructokinase reduces the undesired loss of the succinate precursor PEP into pyruvate and into pyruvate-derived by-products and enables increased succinate production, exclusively via the reductive TCA cycle branch. These findings were used to design superior producers. Mutants, which (i) overexpress the beneficial fructokinase, (II) lack the competing fructose PTS, and (iii) combine both traits, produce significantly more succinate. In a fed-batch process, B. succiniciproducens ΔfruA achieved a titer of 71gL-1 succinate and a yield of 2.5molmol-1 from sucrose.
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Affiliation(s)
- Anna Lange
- Institute of Systems Biotechnology, Saarland University, Germany
| | - Judith Becker
- Institute of Systems Biotechnology, Saarland University, Germany
| | - Dennis Schulze
- Institute of Systems Biotechnology, Saarland University, Germany
| | - Edern Cahoreau
- Université de Toulouse, INSA, UPS, INP, Toulouse, France; INRA, UMR792 Ingénierie des Systèmes Biologiques et des Procédés, Toulouse, France; CNRS, UMR5504, Toulouse, France
| | - Jean-Charles Portais
- Université de Toulouse, INSA, UPS, INP, Toulouse, France; INRA, UMR792 Ingénierie des Systèmes Biologiques et des Procédés, Toulouse, France; CNRS, UMR5504, Toulouse, France
| | - Stefan Haefner
- BASF SE, Fine Chemicals and Biotechnology, Ludwigshafen, Germany
| | - Hartwig Schröder
- BASF SE, Fine Chemicals and Biotechnology, Ludwigshafen, Germany
| | - Joanna Krawczyk
- BASF SE, Fine Chemicals and Biotechnology, Ludwigshafen, Germany
| | - Oskar Zelder
- BASF SE, Fine Chemicals and Biotechnology, Ludwigshafen, Germany
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25
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Adhikary S, Nicklas W, Bisgaard M, Boot R, Kuhnert P, Waberschek T, Aalbæk B, Korczak B, Christensen H. Rodentibacter gen. nov. including Rodentibacter pneumotropicus comb. nov., Rodentibacter heylii sp. nov., Rodentibacter myodis sp. nov., Rodentibacter ratti sp. nov., Rodentibacter heidelbergensis sp. nov., Rodentibacter trehalosifermentans sp. nov., Rodentibacter rarus sp. nov., Rodentibacter mrazii and two genomospecies. Int J Syst Evol Microbiol 2017. [DOI: 10.1099/ijsem.0.001866] [Citation(s) in RCA: 69] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Sadhana Adhikary
- Department of Veterinary Disease Biology, University of Copenhagen, 4 Stigbøjlen, DK-1870 Frederiksberg C, Denmark
| | - Werner Nicklas
- Microbiological Diagnostics, German Cancer Research Centre, D-69120 Heidelberg, Germany
| | - Magne Bisgaard
- Professor emeritus, Horsevænget 40, Viby Sjælland, Denmark
| | - Ron Boot
- Mr. Tripkade 51, 3571 SW, Utrecht, The Netherlands
| | - Peter Kuhnert
- Institute of Veterinary Bacteriology, Vetsuisse Faculty, University of Bern, Laenggass-Strasse 122, CH-3001 Bern, Switzerland
| | - Torsten Waberschek
- Microbiological Diagnostics, German Cancer Research Centre, D-69120 Heidelberg, Germany
| | - Bent Aalbæk
- Department of Veterinary Disease Biology, University of Copenhagen, 4 Stigbøjlen, DK-1870 Frederiksberg C, Denmark
| | - Bozena Korczak
- Institute of Veterinary Bacteriology, Vetsuisse Faculty, University of Bern, Laenggass-Strasse 122, CH-3001 Bern, Switzerland
| | - Henrik Christensen
- Department of Veterinary Disease Biology, University of Copenhagen, 4 Stigbøjlen, DK-1870 Frederiksberg C, Denmark
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26
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Wahl SA, Bernal Martinez C, Zhao Z, van Gulik WM, Jansen MLA. Intracellular product recycling in high succinic acid producing yeast at low pH. Microb Cell Fact 2017; 16:90. [PMID: 28535757 PMCID: PMC5442661 DOI: 10.1186/s12934-017-0702-0] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2017] [Accepted: 05/12/2017] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The metabolic engineering of Saccharomyces cerevisiae for the production of succinic acid has progressed dramatically, and a series of high-producing hosts are available. At low cultivation pH and high titers, the product transport can become bidirectional, i.e. the acid is reentering the cell and is again exported or even catabolized. Here, a quantitative approach for the identification of product recycling fluxes is developed. RESULTS The metabolic flux distributions at two time-points of the fermentation process were analyzed. 13C labeled succinic acid was added to the extracellular space and intracellular enrichments were measured and subsequently used for the estimation of metabolic fluxes. The labeling was introduced by a labeling switch experiment, leading to an immediate labeling of about 85% of the acid while keeping the total acid concentration constant. Within 100 s significant labeling enrichment of the TCA cycle intermediates fumarate, iso-citrate and α-ketoglutarate was observed, while no labeling was detected for malate and citrate. These findings suggest that succinic acid is rapidly exchanged over the cellular membrane and enters the oxidative TCA cycle. Remarkably, in the oxidative direction malate 13C enrichment was not detected, indicating that there is no flux going through this metabolite pool. Using flux modeling and thermodynamic assumptions on compartmentation it was concluded that malate must be predominantly cytosolic while fumarate and iso-citrate were more dominant in the mitochondria. CONCLUSIONS Adding labeled product without changing the extracellular environment allowed to quantify intracellular metabolic fluxes under high producing conditions and identify product degradation cycles. In the specific case of succinic acid production, compartmentation was found to play a major role, i.e. the presence of metabolic activity in two different cellular compartments lead to intracellular product degradation reducing the yield. We also observed that the flux from glucose to succinic acid branches at two points in metabolism: (1) At the level of pyruvate, and (2) at cytosolic malate which was not expected.
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Affiliation(s)
- S Aljoscha Wahl
- Department of Biotechnology, Delft University of Technology, Van der Maasweg 9, 2629 HZ, Delft, The Netherlands.
| | - Cristina Bernal Martinez
- Department of Biotechnology, Delft University of Technology, Van der Maasweg 9, 2629 HZ, Delft, The Netherlands.,Applikon Biotechnology B.V., Heertjeslaan 2, 2629 JG, Delft, The Netherlands
| | - Zheng Zhao
- DSM Biotechnology Center, Alexander Fleminglaan 1, 2613 AX, Delft, The Netherlands
| | - Walter M van Gulik
- Department of Biotechnology, Delft University of Technology, Van der Maasweg 9, 2629 HZ, Delft, The Netherlands
| | - Mickel L A Jansen
- DSM Biotechnology Center, Alexander Fleminglaan 1, 2613 AX, Delft, The Netherlands
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27
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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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Cimini D, Argenzio O, D'Ambrosio S, Lama L, Finore I, Finamore R, Pepe O, Faraco V, Schiraldi C. Production of succinic acid from Basfia succiniciproducens up to the pilot scale from Arundo donax hydrolysate. BIORESOURCE TECHNOLOGY 2016; 222:355-360. [PMID: 27741473 DOI: 10.1016/j.biortech.2016.10.004] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/07/2016] [Revised: 09/30/2016] [Accepted: 10/01/2016] [Indexed: 05/03/2023]
Abstract
In the present work the recently isolated strain Basfia succiniciproducens BPP7 was evaluated for the production of succinic acid up to the pilot fermentation scale in separate hydrolysis and fermentation experiments on Arundo donax, a non-food dedicated energy crop. An average concentration of about 17g/L of succinic acid and a yield on consumed sugars of 0.75mol/mol were obtained demonstrating strain potential for further process improvement. Small scale experiments indicated that the concentration of acetic acid in the medium is crucial to improve productivity; on the other hand, interestingly, short-term (24h) adaptation to higher acetic acid concentrations, and strain recovery, were also observed.
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Affiliation(s)
- Donatella Cimini
- Second University of Naples, Department of Experimental Medicine, Via de Crecchio 7, 80138 Naples, Italy.
| | - Ottavia Argenzio
- Second University of Naples, Department of Experimental Medicine, Via de Crecchio 7, 80138 Naples, Italy
| | - Sergio D'Ambrosio
- Second University of Naples, Department of Experimental Medicine, Via de Crecchio 7, 80138 Naples, Italy
| | - Licia Lama
- National Research Council, Institute of Biomolecular Chemistry (ICB), Via Campi Flegrei 34, 80078 Pozzuoli, Naples, Italy
| | - Ilaria Finore
- National Research Council, Institute of Biomolecular Chemistry (ICB), Via Campi Flegrei 34, 80078 Pozzuoli, Naples, Italy
| | - Rosario Finamore
- Second University of Naples, Department of Experimental Medicine, Via de Crecchio 7, 80138 Naples, Italy
| | - Olimpia Pepe
- Department of Agricultural Sciences, Division of Microbiology, University of Naples Federico II, Via Università 100, 80055 Portici (Naples), Italy
| | - Vincenza Faraco
- Department of Chemical Sciences, University of Naples Federico II, Complesso Universitario Monte S. Angelo, via Cinthia, 4, 80126 Naples, Italy
| | - Chiara Schiraldi
- Second University of Naples, Department of Experimental Medicine, Via de Crecchio 7, 80138 Naples, Italy
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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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Salvachúa D, Smith H, St John PC, Mohagheghi A, Peterson DJ, Black BA, Dowe N, Beckham GT. Succinic acid production from lignocellulosic hydrolysate by Basfia succiniciproducens. BIORESOURCE TECHNOLOGY 2016; 214:558-566. [PMID: 27179951 DOI: 10.1016/j.biortech.2016.05.018] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/03/2016] [Revised: 05/05/2016] [Accepted: 05/06/2016] [Indexed: 05/03/2023]
Abstract
The production of chemicals alongside fuels will be essential to enhance the feasibility of lignocellulosic biorefineries. Succinic acid (SA), a naturally occurring C4-diacid, is a primary intermediate of the tricarboxylic acid cycle and a promising building block chemical that has received significant industrial attention. Basfia succiniciproducens is a relatively unexplored SA-producing bacterium with advantageous features such as broad substrate utilization, genetic tractability, and facultative anaerobic metabolism. Here B. succiniciproducens is evaluated in high xylose-content hydrolysates from corn stover and different synthetic media in batch fermentation. SA titers in hydrolysate at an initial sugar concentration of 60g/L reached up to 30g/L, with metabolic yields of 0.69g/g, and an overall productivity of 0.43g/L/h. These results demonstrate that B. succiniciproducens may be an attractive platform organism for bio-SA production from biomass hydrolysates.
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Affiliation(s)
- Davinia Salvachúa
- National Bioenergy Center, National Renewable Energy Laboratory, 15013 Denver West Parkway, Golden, CO 80401, USA
| | - Holly Smith
- National Bioenergy Center, National Renewable Energy Laboratory, 15013 Denver West Parkway, Golden, CO 80401, USA
| | - Peter C St John
- National Bioenergy Center, National Renewable Energy Laboratory, 15013 Denver West Parkway, Golden, CO 80401, USA
| | - Ali Mohagheghi
- National Bioenergy Center, National Renewable Energy Laboratory, 15013 Denver West Parkway, Golden, CO 80401, USA
| | - Darren J Peterson
- National Bioenergy Center, National Renewable Energy Laboratory, 15013 Denver West Parkway, Golden, CO 80401, USA
| | - Brenna A Black
- National Bioenergy Center, National Renewable Energy Laboratory, 15013 Denver West Parkway, Golden, CO 80401, USA
| | - Nancy Dowe
- National Bioenergy Center, National Renewable Energy Laboratory, 15013 Denver West Parkway, Golden, CO 80401, USA
| | - Gregg T Beckham
- National Bioenergy Center, National Renewable Energy Laboratory, 15013 Denver West Parkway, Golden, CO 80401, USA.
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32
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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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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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34
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Testudinibacter aquarius gen. nov., sp. nov., a member of the family Pasteurellaceae isolated from the oral cavity of freshwater turtles. Int J Syst Evol Microbiol 2016; 66:567-573. [DOI: 10.1099/ijsem.0.000759] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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McAtee AG, Jazmin LJ, Young JD. Application of isotope labeling experiments and 13C flux analysis to enable rational pathway engineering. Curr Opin Biotechnol 2015; 36:50-6. [DOI: 10.1016/j.copbio.2015.08.004] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2015] [Revised: 08/06/2015] [Accepted: 08/09/2015] [Indexed: 12/24/2022]
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36
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37
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Nicklas W, Bisgaard M, Aalbæk B, Kuhnert P, Christensen H. Reclassification of Actinobacillus muris as Muribacter muris gen. nov., comb. nov. Int J Syst Evol Microbiol 2015; 65:3344-3351. [DOI: 10.1099/ijsem.0.000417] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
To reinvestigate the taxonomy of [Actinobacillus] muris, 474 strains, mainly from mice and rats, were characterized by phenotype and 130 strains selected for genotypic characterization by 16S rRNA and partial rpoB gene sequencing. The type strain was further investigated by whole-genome sequencing. Phylogenetic analysis of the DNA sequences showed one monophyletic group with intragroup similarities of 96.7 and 97.2 % for the 16S rRNA and rpoB genes, respectively. The highest 16S rRNA gene sequence similarity to a taxon with a validly published name outside the group was 95.9 %, to the type strain of [Pasteurella] pneumotropica. The closest related taxon based on rpoB sequence comparison was ‘Haemophilus influenzae-murium’, with 88.4 % similarity. A new genus and a new combination, Muribacter muris gen. nov., comb. nov., are proposed based on a distinct phylogenetic position based on 16S rRNA and rpoB gene sequence comparisons, with major divergence from the existing genera of the family Pasteurellaceae. The new genus has the characteristics of [A.] muris with the emendation that acid formation from ( − )-d-mannitol and hydrolysis of aesculin are variable, while the α-glucosidase test is positive. There is no requirement for exogenously supplied NAD (V factor) for the majority of strains investigated; however, one strain was found to require NAD. The major fatty acids of the type strain of Muribacter muris were C14 : 0, C14 : 0 3-OH/iso-C16 : 1 I, C16 : 1ω7c and C16 : 0, which is in line with most genera of the Pasteurellaceae. The type strain of Muribacter muris is CCUG 16938T ( = NCTC 12432T = ATCC 49577T).
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Affiliation(s)
- Werner Nicklas
- Microbiological Diagnostics, German Cancer Research Centre, D-69120 Heidelberg, Germany
| | - Magne Bisgaard
- Professor emeritus, Horsevænget 40, DK-4130 Viby Sjælland, Denmark
| | - Bent Aalbæk
- Department of Veterinary Disease Biology, VetSchool, University of Copenhagen, 4 Stigbøjlen, DK-1870 Frederiksberg C, Denmark
| | - Peter Kuhnert
- Institute of Veterinary Bacteriology, Vetsuisse Faculty, University of Bern, Laenggass-Strasse 122, CH-3001 Bern, Switzerland
| | - Henrik Christensen
- Department of Veterinary Disease Biology, VetSchool, University of Copenhagen, 4 Stigbøjlen, DK-1870 Frederiksberg C, Denmark
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38
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Johanne Hansen M, Strøm Braaten M, Miki Bojesen A, Christensen H, Sonne C, Dietz R, Frost Bertelsen M. Ursidibacter maritimus gen. nov., sp. nov. and Ursidibacter arcticus sp. nov., two new members of the family Pasteurellaceae isolated from the oral cavity of bears. Int J Syst Evol Microbiol 2015. [DOI: 10.1099/ijsem.0.000476] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Thirty-three suspected strains of the family Pasteurellaceae isolated from the oral cavity of polar and brown bears were characterized by genotypic and phenotypic tests. Phylogenetic analysis of partial 16S rRNA gene and rpoB sequences showed that the investigated isolates formed two closely related monophyletic groups, representing two novel species of a new genus. Based on 16S rRNA gene sequence comparison Bibersteinia trehalosi was the closest related species with a validly published name, with 95.4 % similarity to the polar bear group and 94.4 % similarity to the brown bear group. Otariodibacter oris was the closest related species based on rpoB sequence comparison with a similarity of 89.8 % with the polar bear group and 90 % with the brown bear group. The new genus could be separated from existing genera of the family Pasteurellaceae by three to ten phenotypic characters, and the two novel species could be separated from each other by two phenotypic characters. It is proposed that the strains should be classified as representatives of a new genus, Ursidibacter gen. nov., with two novel species: the type species Ursidibacter maritimus sp. nov., isolated from polar bears (type strain Pb43106T = CCUG 65144T = DSM 28137T, DNA G+C content 39.3 mol%), and Ursidibacter arcticus sp. nov., isolated from brown bears (type strain Bamse61T = CCUG 65145T = DSM 28138T).
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Affiliation(s)
- Mie Johanne Hansen
- Department of Veterinary Disease Biology, Faculty of Health and Medical Sciences, University of Copenhagen, Stigboejlen 4, 1870 Frederiksberg C, Denmark
- Center for Zoo and Wild Animal Health, Copenhagen Zoo, 2000 Frederiksberg, Denmark
| | - Mira Strøm Braaten
- Department of Veterinary Disease Biology, Faculty of Health and Medical Sciences, University of Copenhagen, Stigboejlen 4, 1870 Frederiksberg C, Denmark
- Center for Zoo and Wild Animal Health, Copenhagen Zoo, 2000 Frederiksberg, Denmark
| | - Anders Miki Bojesen
- Department of Veterinary Disease Biology, Faculty of Health and Medical Sciences, University of Copenhagen, Stigboejlen 4, 1870 Frederiksberg C, Denmark
| | - Henrik Christensen
- Department of Veterinary Disease Biology, Faculty of Health and Medical Sciences, University of Copenhagen, Stigboejlen 4, 1870 Frederiksberg C, Denmark
| | - Christian Sonne
- Department of Bioscience, Faculty of Science and Technology, Arctic Research Centre, Frederiksborgvej 399, PO Box 358, Aarhus University, 4000 Roskilde, Denmark
| | - Rune Dietz
- Department of Bioscience, Faculty of Science and Technology, Arctic Research Centre, Frederiksborgvej 399, PO Box 358, Aarhus University, 4000 Roskilde, Denmark
| | - Mads Frost Bertelsen
- Department of Veterinary Disease Biology, Faculty of Health and Medical Sciences, University of Copenhagen, Stigboejlen 4, 1870 Frederiksberg C, Denmark
- Center for Zoo and Wild Animal Health, Copenhagen Zoo, 2000 Frederiksberg, Denmark
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Zuo G, Hao B. CVTree3 Web Server for Whole-genome-based and Alignment-free Prokaryotic Phylogeny and Taxonomy. GENOMICS, PROTEOMICS & BIOINFORMATICS 2015; 13:321-31. [PMID: 26563468 PMCID: PMC4678791 DOI: 10.1016/j.gpb.2015.08.004] [Citation(s) in RCA: 146] [Impact Index Per Article: 16.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/22/2015] [Accepted: 08/10/2015] [Indexed: 01/15/2023]
Abstract
A faithful phylogeny and an objective taxonomy for prokaryotes should agree with each other and ultimately follow the genome data. With the number of sequenced genomes reaching tens of thousands, both tree inference and detailed comparison with taxonomy are great challenges. We now provide one solution in the latest Release 3.0 of the alignment-free and whole-genome-based web server CVTree3. The server resides in a cluster of 64 cores and is equipped with an interactive, collapsible, and expandable tree display. It is capable of comparing the tree branching order with prokaryotic classification at all taxonomic ranks from domains down to species and strains. CVTree3 allows for inquiry by taxon names and trial on lineage modifications. In addition, it reports a summary of monophyletic and non-monophyletic taxa at all ranks as well as produces print-quality subtree figures. After giving an overview of retrospective verification of the CVTree approach, the power of the new server is described for the mega-classification of prokaryotes and determination of taxonomic placement of some newly-sequenced genomes. A few discrepancies between CVTree and 16S rRNA analyses are also summarized with regard to possible taxonomic revisions. CVTree3 is freely accessible to all users at http://tlife.fudan.edu.cn/cvtree3/ without login requirements.
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Affiliation(s)
- Guanghong Zuo
- T-Life Research Center, Department of Physics, Fudan University, Shanghai 200433, China
| | - Bailin Hao
- T-Life Research Center, Department of Physics, Fudan University, Shanghai 200433, China.
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40
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Dill-McFarland KA, Weimer PJ, Pauli JN, Peery MZ, Suen G. Diet specialization selects for an unusual and simplified gut microbiota in two- and three-toed sloths. Environ Microbiol 2015; 18:1391-402. [DOI: 10.1111/1462-2920.13022] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2015] [Accepted: 08/12/2015] [Indexed: 01/03/2023]
Affiliation(s)
| | - Paul J. Weimer
- Department of Bacteriology; University of Wisconsin-Madison; Madison WI 53706 USA
- US Department of Agriculture; Agricultural Research Service; Madison WI 53706 USA
| | - Jonathan N. Pauli
- Department of Forest and Wildlife Ecology; University of Wisconsin-Madison; Madison WI 53706 USA
| | - M. Zachariah Peery
- Department of Forest and Wildlife Ecology; University of Wisconsin-Madison; Madison WI 53706 USA
| | - Garret Suen
- Department of Bacteriology; University of Wisconsin-Madison; Madison WI 53706 USA
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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: 250] [Impact Index Per Article: 27.8] [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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42
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Li Q, Xing J. Microbial Succinic Acid Production Using Different Bacteria Species. MICROORGANISMS IN BIOREFINERIES 2015. [DOI: 10.1007/978-3-662-45209-7_7] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
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43
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Draft Genome Sequence of Chelonobacter oris Strain 1662T, Associated with Respiratory Disease in Hermann's Tortoises. GENOME ANNOUNCEMENTS 2014; 2:2/6/e01322-14. [PMID: 25523777 PMCID: PMC4271167 DOI: 10.1128/genomea.01322-14] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Chelonobacter oris 1662T is a type strain of the recently described species of the Pasteurellaceae family. The strain was isolated from the choanae of a captive tortoise with signs of respiratory tract infection. The genome reported here is approximately 2.6 Mb in size and has a G+C content of 47.1%.
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44
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Jansen MLA, van Gulik WM. Towards large scale fermentative production of succinic acid. Curr Opin Biotechnol 2014; 30:190-7. [DOI: 10.1016/j.copbio.2014.07.003] [Citation(s) in RCA: 151] [Impact Index Per Article: 15.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2014] [Revised: 06/18/2014] [Accepted: 07/21/2014] [Indexed: 01/04/2023]
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45
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Christensen H, Nicklas W, Bisgaard M. Investigation of taxa of the family Pasteurellaceae isolated from Syrian and European hamsters and proposal of Mesocricetibacter intestinalis gen. nov., sp. nov. and Cricetibacter osteomyelitidis gen. nov., sp. nov. Int J Syst Evol Microbiol 2014; 64:3636-3643. [DOI: 10.1099/ijs.0.067470-0] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Eleven strains from hamster of Bisgaard taxa 23 and 24, also referred to as Krause’s groups 2 and 1, respectively, were investigated by a polyphasic approach including data published previously. Strains showed small, regular and circular colonies with smooth and shiny appearance, typical of members of the family
Pasteurellaceae
. The strains formed two monophyletic groups based on 16S rRNA gene sequence comparison to other members of the family
Pasteurellaceae
. Partial rpoB sequencing as well as published data on DNA–DNA hybridization showed high genotypic relationships within both groups. Menaquinone 7 (MK7) was found in strains of both groups as well as an unknown ubiquinone with shorter chain length than previously reported for any other member of the family
Pasteurellaceae
. A new genus with one species, Mesocricetibacter intestinalis gen. nov., sp. nov., is proposed to accommodate members of taxon 24 of Bisgaard whereas members of taxon 23 of Bisgaard are proposed to represent Cricetibacter osteomyelitidis gen. nov., sp. nov. Major fatty acids of type strains of type species of both genera are C14 : 0, C14 : 0 3-OH/iso-C16 : 1 I, C16 : 1ω7c and C16 : 0. The two genera are clearly separated by phenotype from each other and from existing genera of the family
Pasteurellaceae
. The type strain of Mesocricetibacter intestinalis is HIM 933/7T ( = Kunstyr 246/85T = CCUG 28030T = DSM 28403T) while the type strain of Cricetibacter osteomyelitidis is HIM943/7T ( = Kunstyr 507/85T = CCUG 36451T = DSM 28404T).
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Affiliation(s)
- H. Christensen
- Department of Veterinary Disease Biology, Faculty of Health and Medical Sciences, University of Copenhagen, 4 Stigbøjlen, DK-1870 Frederiksberg C, Denmark
| | - W. Nicklas
- Microbiological Diagnostics, German Cancer Research Centre, D-69120 Heidelberg, Germany
| | - M. Bisgaard
- Horsevænget 40, DK-4130 Viby Sjælland, Denmark
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Mühldorfer K, Speck S, Wibbelt G. Proposal of Vespertiliibacter pulmonis gen. nov., sp. nov. and two genomospecies as new members of the family Pasteurellaceae isolated from European bats. Int J Syst Evol Microbiol 2014; 64:2424-2430. [PMID: 24776530 DOI: 10.1099/ijs.0.062786-0] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Five bacterial strains isolated from bats of the family Vespertilionidae were characterized by phenotypic tests and multilocus sequence analysis (MLSA) using the 16S rRNA gene and four housekeeping genes (rpoA, rpoB, infB, recN). Phylogenetic analyses of individual and combined datasets indicated that the five strains represent a monophyletic cluster within the family Pasteurellaceae. Comparison of 16S rRNA gene sequences demonstrated a high degree of similarity (98.3-99.9%) among the group of bat-derived strains, while searches in nucleotide databases indicated less than 96% sequence similarity to known members of the Pasteurellaceae. The housekeeping genes rpoA, rpoB, infB and recN provided higher resolution compared with the 16S rRNA gene and subdivided the group according to the bat species from which the strains were isolated. Three strains derived from noctule bats shared 98.6-100% sequence similarity in all four genes investigated, whereas, based on rpoB, infB and recN gene sequences, 91.8-96% similarity was observed with and between the remaining two strains isolated from a serotine bat and a pipistrelle bat, respectively. Genome relatedness as deduced from recN gene sequences correlated well with the results of MLSA and indicated that the five strains represent a new genus. Based on these results, it is proposed to classify the five strains derived from bats within Vespertiliibacter pulmonis gen. nov., sp. nov. (the type species), Vespertiliibacter genomospecies 1 and Vespertiliibacter genomospecies 2. The genus can be distinguished phenotypically from recognized genera of the Pasteurellaceae by at least three characteristics. All strains are nutritionally fastidious and require a chemically defined supplement with NAD for growth. The DNA G+C content of strain E127/08(T) is 38.2 mol%. The type strain of Vespertiliibacter pulmonis gen. nov., sp. nov. is E127/08(T) ( = CCUG 64585(T) = DSM 27238(T)). The reference strains of Vespertiliibacter genomospecies 1 and 2 are E145/08 and E157/08, respectively.
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Affiliation(s)
- Kristin Mühldorfer
- Department of Wildlife Diseases, Leibniz Institute for Zoo and Wildlife Research, Berlin, Germany
| | - Stephanie Speck
- Institute for Animal Hygiene and Veterinary Public Health, University of Leipzig, Leipzig, Germany
| | - Gudrun Wibbelt
- Department of Wildlife Diseases, Leibniz Institute for Zoo and Wildlife Research, Berlin, Germany
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Korczak BM, Bisgaard M, Christensen H, Kuhnert P. Frederiksenia canicola gen. nov., sp. nov. isolated from dogs and human dog-bite wounds. Antonie van Leeuwenhoek 2014; 105:731-41. [DOI: 10.1007/s10482-014-0129-0] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/19/2013] [Accepted: 01/28/2014] [Indexed: 11/28/2022]
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Abstract
Many bacteria are naturally competent, able to actively transport environmental DNA fragments across their cell envelope and into their cytoplasm. Because incoming DNA fragments can recombine with and replace homologous segments of the chromosome, competence provides cells with a potent mechanism of horizontal gene transfer as well as access to the nutrients in extracellular DNA. This review starts with an introductory overview of competence and continues with a detailed consideration of the DNA uptake specificity of competent proteobacteria in the Pasteurellaceae and Neisseriaceae. Species in these distantly related families exhibit strong preferences for genomic DNA from close relatives, a self-specificity arising from the combined effects of biases in the uptake machinery and genomic overrepresentation of the sequences this machinery prefers. Other competent species tested lack obvious uptake bias or uptake sequences, suggesting that strong convergent evolutionary forces have acted on these two families. Recent results show that uptake sequences have multiple "dialects," with clades within each family preferring distinct sequence variants and having corresponding variants enriched in their genomes. Although the genomic consensus uptake sequences are 12 and 29 to 34 bp, uptake assays have found that only central cores of 3 to 4 bp, conserved across dialects, are crucial for uptake. The other bases, which differ between dialects, make weaker individual contributions but have important cooperative interactions. Together, these results make predictions about the mechanism of DNA uptake across the outer membrane, supporting a model for the evolutionary accumulation and stability of uptake sequences and suggesting that uptake biases may be more widespread than currently thought.
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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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Abstract
In a world where most emerging and reemerging infectious diseases are zoonotic in nature and our contacts with both domestic and wild animals abound, there is growing awareness of the potential for human acquisition of animal diseases. Like other Pasteurellaceae, Pasteurella species are highly prevalent among animal populations, where they are often found as part of the normal microbiota of the oral, nasopharyngeal, and upper respiratory tracts. Many Pasteurella species are opportunistic pathogens that can cause endemic disease and are associated increasingly with epizootic outbreaks. Zoonotic transmission to humans usually occurs through animal bites or contact with nasal secretions, with P. multocida being the most prevalent isolate observed in human infections. Here we review recent comparative genomics and molecular pathogenesis studies that have advanced our understanding of the multiple virulence mechanisms employed by Pasteurella species to establish acute and chronic infections. We also summarize efforts being explored to enhance our ability to rapidly and accurately identify and distinguish among clinical isolates and to control pasteurellosis by improved development of new vaccines and treatment regimens.
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Affiliation(s)
- Brenda A Wilson
- Department of Microbiology and Host-Microbe Systems Theme of the Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA.
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