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Jiang S, Wang R, Wang D, Zhao C, Ma Q, Wu H, Xie X. Metabolic reprogramming and biosensor-assisted mutagenesis screening for high-level production of L-arginine in Escherichia coli. Metab Eng 2023; 76:146-157. [PMID: 36758663 DOI: 10.1016/j.ymben.2023.02.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2022] [Revised: 01/14/2023] [Accepted: 02/07/2023] [Indexed: 02/11/2023]
Abstract
L-arginine is a value-added amino acid with promising applications in the pharmaceutical and nutraceutical industries. Further unleashing the potential of microbial cell factories to make L-arginine production more competitive remains challenging due to the sophisticated intracellular interaction networks and the insufficient knowledge of global metabolic regulation. Here, we combined multilevel rational metabolic engineering with biosensor-assisted mutagenesis screening to exploit the L-arginine production potential of Escherichia coli. First, multiple metabolic pathways were systematically reprogrammed to redirect the metabolic flux into L-arginine synthesis, including the L-arginine biosynthesis, TCA cycle, and L-arginine export. Specifically, a toggle switch responding to special cellular physiological conditions was designed to dynamically control the expression of sucA and pull more carbon flux from the TCA cycle toward L-arginine biosynthesis. Subsequently, a biosensor-assisted high-throughput screening platform was designed and applied to further exploit the L-arginine production potential. The best-engineered ARG28 strain produced 132 g/L L-arginine in a 5-L bioreactor with a yield of 0.51 g/g glucose and productivity of 2.75 g/(L ⋅ h), which were the highest values reported so far. Through whole genome sequencing and reverse engineering, Frc frameshift mutant, PqiB A78P mutant, and RpoB P564T mutant were revealed for enhancing the L-arginine biosynthesis. Our study exhibited the power of coupling rational metabolic reprogramming and biosensor-assisted mutagenesis screening to unleash the cellular potential for value-added metabolite production.
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Affiliation(s)
- Shuai Jiang
- Key Laboratory of Industrial Fermentation Microbiology of the Ministry of Education, Tianjin University of Science & Technology, Tianjin, 300457, PR China; College of Biotechnology, Tianjin University of Science & Technology, Tianjin, 300457, PR China
| | - Ruirui Wang
- Key Laboratory of Industrial Fermentation Microbiology of the Ministry of Education, Tianjin University of Science & Technology, Tianjin, 300457, PR China; College of Biotechnology, Tianjin University of Science & Technology, Tianjin, 300457, PR China
| | - Dehu Wang
- Key Laboratory of Industrial Fermentation Microbiology of the Ministry of Education, Tianjin University of Science & Technology, Tianjin, 300457, PR China; College of Biotechnology, Tianjin University of Science & Technology, Tianjin, 300457, PR China
| | - Chunguang Zhao
- Ningxia Eppen Biotech Co., Ltd, Ningxia, 750000, PR China
| | - Qian Ma
- Key Laboratory of Industrial Fermentation Microbiology of the Ministry of Education, Tianjin University of Science & Technology, Tianjin, 300457, PR China; College of Biotechnology, Tianjin University of Science & Technology, Tianjin, 300457, PR China
| | - Heyun Wu
- Key Laboratory of Industrial Fermentation Microbiology of the Ministry of Education, Tianjin University of Science & Technology, Tianjin, 300457, PR China; College of Biotechnology, Tianjin University of Science & Technology, Tianjin, 300457, PR China.
| | - Xixian Xie
- Key Laboratory of Industrial Fermentation Microbiology of the Ministry of Education, Tianjin University of Science & Technology, Tianjin, 300457, PR China; College of Biotechnology, Tianjin University of Science & Technology, Tianjin, 300457, PR China.
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2
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Lu J, Wang Y, Xu M, Fei Q, Gu Y, Luo Y, Wu H. Efficient biosynthesis of 3-hydroxypropionic acid from ethanol in metabolically engineered Escherichia coli. BIORESOURCE TECHNOLOGY 2022; 363:127907. [PMID: 36087655 DOI: 10.1016/j.biortech.2022.127907] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/26/2022] [Revised: 08/30/2022] [Accepted: 09/02/2022] [Indexed: 06/15/2023]
Abstract
Engineering microbial cell factories to convert CO2-based feedstock into chemicals and fuels provide a feasible carbon-neutral route for the third-generation biorefineries. Ethanol became one of the major products of syngas fermentation by engineered acetogens. The key building block chemical 3-hydroxypropionic acid (3-HP) can be synthesized from ethanol by the malonyl-CoA pathway with CO2 fixation. In this study, the effect of two ethanol consumption pathways on 3-HP synthesis were studied as well as the effect of TCA cycle, gluconeogenesis pathway, and transhydrogenase. And the 3-HP synthesis pathway was also optimized. The engineered strain synthesized 1.66 g/L of 3-HP with a yield of 0.24 g/g. Furthermore, the titer and the yield of 3-HP increased to 13.17 g/L and 0.57 g/g in the whole-cell biocatalysis system. This study indicated that ethanol as feedstock had the potential to synthesize 3-HP, which provided an alternative route for future biorefinery.
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Affiliation(s)
- Juefeng Lu
- State Key Laboratory of Bioreactor Engineering, School of Biotechnology, East China University of Science and Technology, 130 Meilong Road, Shanghai 200237, China
| | - Yuying Wang
- State Key Laboratory of Bioreactor Engineering, School of Biotechnology, East China University of Science and Technology, 130 Meilong Road, Shanghai 200237, China
| | - Mingcheng Xu
- State Key Laboratory of Bioreactor Engineering, School of Biotechnology, East China University of Science and Technology, 130 Meilong Road, Shanghai 200237, China
| | - Qiang Fei
- School of Chemical Engineering and Technology, Xi'an Jiaotong University, Xi'an, China
| | - Yang Gu
- Key Laboratory of Synthetic Biology, The State Key Laboratory of Plant Carbon-Nitrogen Assimilation, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China
| | - Yuanchan Luo
- State Key Laboratory of Bioreactor Engineering, School of Biotechnology, East China University of Science and Technology, 130 Meilong Road, Shanghai 200237, China
| | - Hui Wu
- State Key Laboratory of Bioreactor Engineering, School of Biotechnology, East China University of Science and Technology, 130 Meilong Road, Shanghai 200237, China; Shanghai Collaborative Innovation Center for Biomanufacturing Technology, 130 Meilong Road, Shanghai 200237, China; Key Laboratory of Bio-based Material Engineering of China National Light Industry Council, 130 Meilong Road, Shanghai 200237, China.
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3
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LeBlanc N, Charles TC. Bacterial genome reductions: Tools, applications, and challenges. Front Genome Ed 2022; 4:957289. [PMID: 36120530 PMCID: PMC9473318 DOI: 10.3389/fgeed.2022.957289] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2022] [Accepted: 07/29/2022] [Indexed: 11/16/2022] Open
Abstract
Bacterial cells are widely used to produce value-added products due to their versatility, ease of manipulation, and the abundance of genome engineering tools. However, the efficiency of producing these desired biomolecules is often hindered by the cells’ own metabolism, genetic instability, and the toxicity of the product. To overcome these challenges, genome reductions have been performed, making strains with the potential of serving as chassis for downstream applications. Here we review the current technologies that enable the design and construction of such reduced-genome bacteria as well as the challenges that limit their assembly and applicability. While genomic reductions have shown improvement of many cellular characteristics, a major challenge still exists in constructing these cells efficiently and rapidly. Computational tools have been created in attempts at minimizing the time needed to design these organisms, but gaps still exist in modelling these reductions in silico. Genomic reductions are a promising avenue for improving the production of value-added products, constructing chassis cells, and for uncovering cellular function but are currently limited by their time-consuming construction methods. With improvements to and the creation of novel genome editing tools and in silico models, these approaches could be combined to expedite this process and create more streamlined and efficient cell factories.
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Affiliation(s)
- Nicole LeBlanc
- Department of Biology, University of Waterloo, Waterloo, ON, Canada
- *Correspondence: Nicole LeBlanc,
| | - Trevor C. Charles
- Department of Biology, University of Waterloo, Waterloo, ON, Canada
- Metagenom Bio Life Science Inc., Waterloo, ON, Canada
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Man MY, Mohamad MS, Choon YW, Ismail MA. In silico gene knockout prediction using a hybrid of Bat algorithm and minimization of metabolic adjustment. J Integr Bioinform 2021; 18:jib-2020-0037. [PMID: 34348418 PMCID: PMC8573224 DOI: 10.1515/jib-2020-0037] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2020] [Accepted: 06/21/2021] [Indexed: 11/17/2022] Open
Abstract
Microorganisms commonly produce many high-demand industrial products like fuels, food, vitamins, and other chemicals. Microbial strains are the strains of microorganisms, which can be optimized to improve their technological properties through metabolic engineering. Metabolic engineering is the process of overcoming cellular regulation in order to achieve a desired product or to generate a new product that the host cells do not usually need to produce. The prediction of genetic manipulations such as gene knockout is part of metabolic engineering. Gene knockout can be used to optimize the microbial strains, such as to maximize the production rate of chemicals of interest. Metabolic and genetic engineering is important in producing the chemicals of interest as, without them, the product yields of many microorganisms are normally low. As a result, the aim of this paper is to propose a combination of the Bat algorithm and the minimization of metabolic adjustment (BATMOMA) to predict which genes to knock out in order to increase the succinate and lactate production rates in Escherichia coli (E. coli).
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Affiliation(s)
- Mei Yen Man
- School of Computing, Faculty of Engineering, Universiti Teknologi Malaysia, Skudai, Johor, Malaysia
| | - Mohd Saberi Mohamad
- Department of Genetics and Genomics, College of Medical and Health Sciences, United Arab Emirates University, Al Ain17666, Abu Dhabi, United Arab Emirates
| | - Yee Wen Choon
- Institute for Artificial Intelligence and Big Data, Universiti Malaysia Kelantan, Kota Bharu 16100, Kelantan, Malaysia; and Department of Data Science, Universiti Malaysia Kelantan, Kota Bharu 16100, Kelantan, Malaysia
| | - Mohd Arfian Ismail
- Faculty of Computing (FKOM), College of Computing and Applied Sciences, Universiti Malaysia Pahang, Lebuhraya Tun Razak, 26300 Gambang, Kuantan, Pahang, Malaysia
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5
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Vaud S, Pearcy N, Hanževački M, Van Hagen AMW, Abdelrazig S, Safo L, Ehsaan M, Jonczyk M, Millat T, Craig S, Spence E, Fothergill J, Bommareddy RR, Colin PY, Twycross J, Dalby PA, Minton NP, Jäger CM, Kim DH, Yu J, Maness PC, Lynch S, Eckert CA, Conradie A, Bryan SJ. Engineering improved ethylene production: Leveraging systems biology and adaptive laboratory evolution. Metab Eng 2021; 67:308-320. [PMID: 34245888 DOI: 10.1016/j.ymben.2021.07.001] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2021] [Revised: 05/26/2021] [Accepted: 07/02/2021] [Indexed: 10/20/2022]
Abstract
Ethylene is a small hydrocarbon gas widely used in the chemical industry. Annual worldwide production currently exceeds 150 million tons, producing considerable amounts of CO2 contributing to climate change. The need for a sustainable alternative is therefore imperative. Ethylene is natively produced by several different microorganisms, including Pseudomonas syringae pv. phaseolicola via a process catalyzed by the ethylene-forming enzyme (EFE), subsequent heterologous expression of EFE has led to ethylene production in non-native bacterial hosts including Escherichia coli and cyanobacteria. However, solubility of EFE and substrate availability remain rate-limiting steps in biological ethylene production. We employed a combination of genome-scale metabolic modelling, continuous fermentation, and protein evolution to enable the accelerated development of a high efficiency ethylene producing E. coli strain, yielding a 49-fold increase in production, the most significant improvement reported to date. Furthermore, we have clearly demonstrated that this increased yield resulted from metabolic adaptations that were uniquely linked to EFE (wild type versus mutant). Our findings provide a novel solution to deregulate metabolic bottlenecks in key pathways, which can be readily applied to address other engineering challenges.
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Affiliation(s)
- Sophie Vaud
- BBSRC/EPSRC Synthetic Biology Research Centre, The Biodiscovery Institute, University of Nottingham, Nottingham, NG7 2RD, UK
| | - Nicole Pearcy
- BBSRC/EPSRC Synthetic Biology Research Centre, The Biodiscovery Institute, University of Nottingham, Nottingham, NG7 2RD, UK
| | - Marko Hanževački
- Department of Chemical and Environmental Engineering, Faculty of Engineering, University of Nottingham, Nottingham, NG7 2RD, UK
| | - Alexander M W Van Hagen
- Department of Chemical and Environmental Engineering, Faculty of Engineering, University of Nottingham, Nottingham, NG7 2RD, UK
| | - Salah Abdelrazig
- Centre for Analytical Bioscience, Advanced Materials and Healthcare Technologies Division, School of Pharmacy, University of Nottingham, NG7 2RD, UK
| | - Laudina Safo
- Centre for Analytical Bioscience, Advanced Materials and Healthcare Technologies Division, School of Pharmacy, University of Nottingham, NG7 2RD, UK
| | - Muhammad Ehsaan
- BBSRC/EPSRC Synthetic Biology Research Centre, The Biodiscovery Institute, University of Nottingham, Nottingham, NG7 2RD, UK
| | - Magdalene Jonczyk
- BBSRC/EPSRC Synthetic Biology Research Centre, The Biodiscovery Institute, University of Nottingham, Nottingham, NG7 2RD, UK
| | - Thomas Millat
- BBSRC/EPSRC Synthetic Biology Research Centre, The Biodiscovery Institute, University of Nottingham, Nottingham, NG7 2RD, UK
| | - Sean Craig
- Department of Chemical and Environmental Engineering, Faculty of Engineering, University of Nottingham, Nottingham, NG7 2RD, UK
| | - Edward Spence
- Department of Chemical and Environmental Engineering, Faculty of Engineering, University of Nottingham, Nottingham, NG7 2RD, UK
| | - James Fothergill
- BBSRC/EPSRC Synthetic Biology Research Centre, The Biodiscovery Institute, University of Nottingham, Nottingham, NG7 2RD, UK
| | - Rajesh Reddy Bommareddy
- Department of Chemical and Environmental Engineering, Faculty of Engineering, University of Nottingham, Nottingham, NG7 2RD, UK
| | - Pierre-Yves Colin
- Department of Biochemical Engineering, Bernard Katz Building, University College London, WC1E 6BT, UK
| | - Jamie Twycross
- BBSRC/EPSRC Synthetic Biology Research Centre, The Biodiscovery Institute, University of Nottingham, Nottingham, NG7 2RD, UK; School of Computer Science, University of Nottingham, Nottingham, NG7 2RD, UK
| | - Paul A Dalby
- Department of Biochemical Engineering, Bernard Katz Building, University College London, WC1E 6BT, UK
| | - Nigel P Minton
- BBSRC/EPSRC Synthetic Biology Research Centre, The Biodiscovery Institute, University of Nottingham, Nottingham, NG7 2RD, UK
| | - Christof M Jäger
- Department of Chemical and Environmental Engineering, Faculty of Engineering, University of Nottingham, Nottingham, NG7 2RD, UK
| | - Dong-Hyun Kim
- Centre for Analytical Bioscience, Advanced Materials and Healthcare Technologies Division, School of Pharmacy, University of Nottingham, NG7 2RD, UK
| | - Jianping Yu
- Biosciences Center, National Renewable Energy Laboratory (NREL), Golden, CO, USA
| | - Pin-Ching Maness
- Biosciences Center, National Renewable Energy Laboratory (NREL), Golden, CO, USA
| | - Sean Lynch
- Biosciences Center, National Renewable Energy Laboratory (NREL), Golden, CO, USA; Renewable and Sustainable Energy Institute (RASEI), University of Colorado Boulder, USA; Somalogic, Inc., Boulder, CO, USA
| | - Carrie A Eckert
- Biosciences Center, National Renewable Energy Laboratory (NREL), Golden, CO, USA; Renewable and Sustainable Energy Institute (RASEI), University of Colorado Boulder, USA
| | - Alex Conradie
- Department of Chemical and Environmental Engineering, Faculty of Engineering, University of Nottingham, Nottingham, NG7 2RD, UK
| | - Samantha J Bryan
- Department of Chemical and Environmental Engineering, Faculty of Engineering, University of Nottingham, Nottingham, NG7 2RD, UK.
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6
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Li Q, Zhao P, Yin H, Liu Z, Zhao H, Tian P. CRISPR interference-guided modulation of glucose pathways to boost aconitic acid production in Escherichia coli. Microb Cell Fact 2020; 19:174. [PMID: 32883305 PMCID: PMC7470443 DOI: 10.1186/s12934-020-01435-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2020] [Accepted: 08/27/2020] [Indexed: 12/26/2022] Open
Abstract
Background One major mission of microbial breeding is high-level production of desired metabolites. Overproduction of intermediate metabolites in core pathways is challenging as it may impair cell growth and viability. Results Here we report that aconitic acid, an intermediate metabolite in tricarboxylic acid (TCA) cycle, can be overproduced by an engineered CRISPR interference (CRISPRi) system in Escherichia coli. This CRISPRi system was designed to simultaneously target pyruvate kinase (PK) and isocitrate dehydrogenase (IDH), two enzymes in glycolytic pathway and TCA cycle, respectively. Reverse transcription and quantitative PCR and enzyme activity assays showed that this engineered CRISPRi system significantly repressed the genes encoding IDH and PK, resulting in simultaneous reduction in the activities of IDH and PK. In shake-flask and fed-batch cultivation, this CRISPRi strain produced 60-fold (362.80 ± 22.05 mg/L) and 15-fold (623.80 ± 20.05 mg/L) of aconitic acid relative to the control strain, respectively. In addition, this two-target CRISPRi strain maintained low levels of acetate and lactate, two problematic byproducts. Conclusions This work demonstrates that CRISPRi system can improve aconitic acid production by coordinating glycolysis and TCA cycle. This study provides insights for high-level production of the intermediate metabolites in central pathways.
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Affiliation(s)
- Qingyang Li
- School of Food Science and Engineering, South China University of Technology, Guangzhou, 510641, China
| | - Peng Zhao
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, 100029, China
| | - Hang Yin
- School of Food Science and Engineering, South China University of Technology, Guangzhou, 510641, China
| | - Zhaonan Liu
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, 100029, China
| | - Haifeng Zhao
- School of Food Science and Engineering, South China University of Technology, Guangzhou, 510641, China
| | - Pingfang Tian
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, 100029, China.
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Miscevic D, Srirangan K, Kefale T, Kilpatrick S, Chung DA, Moo-Young M, Chou CP. Heterologous production of 3-hydroxyvalerate in engineered Escherichia coli. Metab Eng 2020; 61:141-151. [DOI: 10.1016/j.ymben.2019.11.005] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2019] [Revised: 10/25/2019] [Accepted: 11/09/2019] [Indexed: 10/25/2022]
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8
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Miscevic D, Mao JY, Moo-Young M, Chou CHP. High-level heterologous production of propionate in engineered Escherichia coli. Biotechnol Bioeng 2020; 117:1304-1315. [PMID: 31956980 DOI: 10.1002/bit.27276] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2019] [Revised: 01/13/2020] [Accepted: 01/16/2020] [Indexed: 12/14/2022]
Abstract
A propanologenic (i.e., 1-propanol-producing) bacterium Escherichia coli strain was previously derived by activating the genomic sleeping beauty mutase (Sbm) operon. The activated Sbm pathway branches out of the tricarboxylic acid (TCA) cycle at the succinyl-CoA node to form propionyl-CoA and its derived metabolites of 1-propanol and propionate. In this study, we targeted several TCA cycle genes encoding enzymes near the succinyl-CoA node for genetic manipulation to identify the individual contribution of the carbon flux into the Sbm pathway from the three TCA metabolic routes, that is, oxidative TCA cycle, reductive TCA branch, and glyoxylate shunt. For the control strain CPC-Sbm, in which propionate biosynthesis occurred under relatively anaerobic conditions, the carbon flux into the Sbm pathway was primarily derived from the reductive TCA branch, and both succinate availability and the SucCD-mediated interconversion of succinate/succinyl-CoA were critical for such carbon flux redirection. Although the oxidative TCA cycle normally had a minimal contribution to the carbon flux redirection, the glyoxylate shunt could be an alternative and effective carbon flux contributor under aerobic conditions. With mechanistic understanding of such carbon flux redirection, metabolic strategies based on blocking the oxidative TCA cycle (via ∆sdhA mutation) and deregulating the glyoxylate shunt (via ∆iclR mutation) were developed to enhance the carbon flux redirection and therefore propionate biosynthesis, achieving a high propionate titer of 30.9 g/L with an overall propionate yield of 49.7% upon fed-batch cultivation of the double mutant strain CPC-Sbm∆sdhA∆iclR under aerobic conditions. The results also suggest that the Sbm pathway could be metabolically active under both aerobic and anaerobic conditions.
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Affiliation(s)
- Dragan Miscevic
- Department of Chemical Engineering, University of Waterloo, Waterloo, Ontario, Canada
| | - Ju-Yi Mao
- Department of Bioscience and Biotechnology, National Taiwan Ocean University, Keelung, Taiwan
| | - Murray Moo-Young
- Department of Chemical Engineering, University of Waterloo, Waterloo, Ontario, Canada
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9
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Mærk M, Jakobsen ØM, Sletta H, Klinkenberg G, Tøndervik A, Ellingsen TE, Valla S, Ertesvåg H. Identification of Regulatory Genes and Metabolic Processes Important for Alginate Biosynthesis in Azotobacter vinelandii by Screening of a Transposon Insertion Mutant Library. Front Bioeng Biotechnol 2020; 7:475. [PMID: 32010681 PMCID: PMC6979010 DOI: 10.3389/fbioe.2019.00475] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2019] [Accepted: 12/23/2019] [Indexed: 12/23/2022] Open
Abstract
Azotobacter vinelandii produces the biopolymer alginate, which has a wide range of industrial and pharmaceutical applications. A random transposon insertion mutant library was constructed from A. vinelandii ATCC12518Tc in order to identify genes and pathways affecting alginate biosynthesis, and about 4,000 mutant strains were screened for altered alginate production. One mutant, containing a mucA disruption, displayed an elevated alginate production level, and several mutants with decreased or abolished alginate production were identified. The regulatory proteins AlgW and AmrZ seem to be required for alginate production in A. vinelandii, similarly to Pseudomonas aeruginosa. An algB mutation did however not affect alginate yield in A. vinelandii although its P. aeruginosa homolog is needed for full alginate production. Inactivation of the fructose phosphoenolpyruvate phosphotransferase system protein FruA resulted in a mutant that did not produce alginate when cultivated in media containing various carbon sources, indicating that this system could have a role in regulation of alginate biosynthesis. Furthermore, impaired or abolished alginate production was observed for strains with disruptions of genes involved in peptidoglycan biosynthesis/recycling and biosynthesis of purines, isoprenoids, TCA cycle intermediates, and various vitamins, suggesting that sufficient access to some of these compounds is important for alginate production. This hypothesis was verified by showing that addition of thiamine, succinate or a mixture of lysine, methionine and diaminopimelate increases alginate yield in the non-mutagenized strain. These results might be used in development of optimized alginate production media or in genetic engineering of A. vinelandii strains for alginate bioproduction.
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Affiliation(s)
- Mali Mærk
- Department of Biotechnology and Food Science, Norwegian University of Science and Technology, Trondheim, Norway
| | | | | | | | | | | | - Svein Valla
- Department of Biotechnology and Food Science, Norwegian University of Science and Technology, Trondheim, Norway
| | - Helga Ertesvåg
- Department of Biotechnology and Food Science, Norwegian University of Science and Technology, Trondheim, Norway
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10
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Daud KM, Mohamad MS, Zakaria Z, Hassan R, Shah ZA, Deris S, Ibrahim Z, Napis S, Sinnott RO. A non-dominated sorting Differential Search Algorithm Flux Balance Analysis (ndsDSAFBA) for in silico multiobjective optimization in identifying reactions knockout. Comput Biol Med 2019; 113:103390. [PMID: 31450056 DOI: 10.1016/j.compbiomed.2019.103390] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2019] [Revised: 08/15/2019] [Accepted: 08/15/2019] [Indexed: 01/06/2023]
Abstract
Metabolic engineering is defined as improving the cellular activities of an organism by manipulating the metabolic, signal or regulatory network. In silico reaction knockout simulation is one of the techniques applied to analyse the effects of genetic perturbations on metabolite production. Many methods consider growth coupling as the objective function, whereby it searches for mutants that maximise the growth and production rate. However, the final goal is to increase the production rate. Furthermore, they produce one single solution, though in reality, cells do not focus on one objective and they need to consider various different competing objectives. In this work, a method, termed ndsDSAFBA (non-dominated sorting Differential Search Algorithm and Flux Balance Analysis), has been developed to find the reaction knockouts involved in maximising the production rate and growth rate of the mutant, by incorporating Pareto dominance concepts. The proposed ndsDSAFBA method was validated using three genome-scale metabolic models. We obtained a set of non-dominated solutions, with each solution representing a different mutant strain. The results obtained were compared with the single objective optimisation (SOO) and multi-objective optimisation (MOO) methods. The results demonstrate that ndsDSAFBA is better than the other methods in terms of production rate and growth rate.
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Affiliation(s)
- Kauthar Mohd Daud
- Artificial Intelligence and Bioinformatics Research Group, School of Computing, Faculty of Engineering, Universiti Teknologi Malaysia, 81310, Skudai, Johor, Malaysia
| | - Mohd Saberi Mohamad
- Institute for Artificial Intelligence and Big Data, Universiti Malaysia Kelantan, City Campus, Pengkalan Chepa, 16100, Kota Bharu, Kelantan, Malaysia; Faculty of Bioengineering and Technology, Universiti Malaysia Kelantan, Jeli Campus, Lock Bag 100, 17600, Jeli, Kelantan, Malaysia.
| | - Zalmiyah Zakaria
- Artificial Intelligence and Bioinformatics Research Group, School of Computing, Faculty of Engineering, Universiti Teknologi Malaysia, 81310, Skudai, Johor, Malaysia
| | - Rohayanti Hassan
- Software Engineering Research Group, School of Computing, Faculty of Engineering, Universiti Teknologi Malaysia, 81310, Johor Bahru, Malaysia
| | - Zuraini Ali Shah
- Artificial Intelligence and Bioinformatics Research Group, School of Computing, Faculty of Engineering, Universiti Teknologi Malaysia, 81310, Skudai, Johor, Malaysia
| | - Safaai Deris
- Institute for Artificial Intelligence and Big Data, Universiti Malaysia Kelantan, City Campus, Pengkalan Chepa, 16100, Kota Bharu, Kelantan, Malaysia; Faculty of Bioengineering and Technology, Universiti Malaysia Kelantan, Jeli Campus, Lock Bag 100, 17600, Jeli, Kelantan, Malaysia
| | - Zuwairie Ibrahim
- Faculty of Electrical and Electronic Engineering, Universiti Malaysia Pahang, Pekan, Pahang, Malaysia
| | - Suhaimi Napis
- Department of Cell and Molecular Biology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, Universiti Putra Malaysia, 43400, Serdang, Selangor, Malaysia
| | - Richard O Sinnott
- School of Computing and Information Systems, Melbourne School of Engineering, University of Melbourne, Victoria, 3010, Australia
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11
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Identification of novel genes involved in high hydrostatic pressure resistance of Escherichia coli. Food Microbiol 2019; 78:171-178. [DOI: 10.1016/j.fm.2018.10.007] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2018] [Revised: 09/19/2018] [Accepted: 10/21/2018] [Indexed: 12/16/2022]
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12
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Sun D, Gao D, Liu X, Zhu M, Li C, Chen Y, Zhu Z, Lu F, Qin HM. Redesign and engineering of a dioxygenase targeting biocatalytic synthesis of 5-hydroxyl leucine. Catal Sci Technol 2019. [DOI: 10.1039/c9cy00110g] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
The protein engineering and metabolic engineering strategies are performed to solve rate-limiting steps in the biosynthesis of 5-HLeu.
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Affiliation(s)
- Dengyue Sun
- Key Laboratory of Industrial Fermentation Microbiology
- Ministry of Education
- Tianjin 300457
- People's Republic of China
- College of Biotechnology
| | - Dengke Gao
- College of Biotechnology
- Tianjin University of Science and Technology
- Tianjin 300457
- People's Republic of China
| | - Xin Liu
- College of Biotechnology
- Tianjin University of Science and Technology
- Tianjin 300457
- People's Republic of China
| | - Menglu Zhu
- College of Biotechnology
- Tianjin University of Science and Technology
- Tianjin 300457
- People's Republic of China
| | - Chao Li
- College of Biotechnology
- Tianjin University of Science and Technology
- Tianjin 300457
- People's Republic of China
| | - Ying Chen
- College of Biotechnology
- Tianjin University of Science and Technology
- Tianjin 300457
- People's Republic of China
| | - Zhangliang Zhu
- Key Laboratory of Industrial Fermentation Microbiology
- Ministry of Education
- Tianjin 300457
- People's Republic of China
- College of Biotechnology
| | - Fuping Lu
- Key Laboratory of Industrial Fermentation Microbiology
- Ministry of Education
- Tianjin 300457
- People's Republic of China
- College of Biotechnology
| | - Hui-Min Qin
- Key Laboratory of Industrial Fermentation Microbiology
- Ministry of Education
- Tianjin 300457
- People's Republic of China
- College of Biotechnology
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13
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Wang J, Wu Y, Sun X, Yuan Q, Yan Y. De Novo Biosynthesis of Glutarate via α-Keto Acid Carbon Chain Extension and Decarboxylation Pathway in Escherichia coli. ACS Synth Biol 2017; 6:1922-1930. [PMID: 28618222 DOI: 10.1021/acssynbio.7b00136] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Microbial based bioplastics are promising alternatives to petroleum based synthetic plastics due to their renewability and economic feasibility. Glutarate is one of the most potential building blocks for bioplastics. The recent biosynthetic routes for glutarate were mostly based on the l-lysine degradation pathway from Pseudomonas putida that required lysine either by feeding or lysine overproduction via genetic manipulations. Herein, we established a novel glutarate biosynthetic pathway by incorporation of a "+1" carbon chain extension pathway from α-ketoglutarate (α-KG) in combination with α-keto acid decarboxylation pathway in Escherichia coli. Introduction of homocitrate synthase (HCS), homoaconitase (HA) and homoisocitrate dehydrogenase (HICDH) from Saccharomyces cerevisiae into E. coli enabled "+1" carbon extension from α-KG to α-ketoadipate (α-KA), which was subsequently converted into glutarate by a promiscuous α-keto acid decarboxylase (KivD) and a succinate semialdehyde dehydrogenase (GabD). The recombinant E. coli coexpressing all five genes produced 0.3 g/L glutarate from glucose. To further improve the titers, α-KG was rechanneled into carbon chain extension pathway via the clustered regularly interspersed palindromic repeats system mediated interference (CRISPRi) of essential genes sucA and sucB in tricarboxylic acid (TCA) cycle. The final strain could produce 0.42 g/L glutarate, which was increased by 40% compared with the parental strain.
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Affiliation(s)
- Jian Wang
- College
of Engineering, The University of Georgia, Athens, Georgia 30602, United States
| | - Yifei Wu
- State
Key Laboratory of Chemical Resource Engineering, Beijing University of Chemical Technology, Beijing 100029, China
- Beijing
Advanced Innovation Center for Soft Matter Science and Engineering, Beijing University of Chemical Technology, Beijing 100029, China
| | - Xinxiao Sun
- State
Key Laboratory of Chemical Resource Engineering, Beijing University of Chemical Technology, Beijing 100029, China
- Beijing
Advanced Innovation Center for Soft Matter Science and Engineering, Beijing University of Chemical Technology, Beijing 100029, China
| | - Qipeng Yuan
- State
Key Laboratory of Chemical Resource Engineering, Beijing University of Chemical Technology, Beijing 100029, China
- Beijing
Advanced Innovation Center for Soft Matter Science and Engineering, Beijing University of Chemical Technology, Beijing 100029, China
| | - Yajun Yan
- College
of Engineering, The University of Georgia, Athens, Georgia 30602, United States
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14
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Theodosiou E, Breisch M, Julsing MK, Falcioni F, Bühler B, Schmid A. An artificial TCA cycle selects for efficient α-ketoglutarate dependent hydroxylase catalysis in engineered Escherichia coli. Biotechnol Bioeng 2017; 114:1511-1520. [PMID: 28266022 DOI: 10.1002/bit.26281] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2016] [Revised: 02/13/2017] [Accepted: 03/01/2017] [Indexed: 01/24/2023]
Abstract
Amino acid hydroxylases depend directly on the cellular TCA cycle via their cosubstrate α-ketoglutarate (α-KG) and are highly useful for the selective biocatalytic oxyfunctionalization of amino acids. This study evaluates TCA cycle engineering strategies to force and increase α-KG flux through proline-4-hydroxylase (P4H). The genes sucA (α-KG dehydrogenase E1 subunit) and sucC (succinyl-CoA synthetase β subunit) were alternately deleted together with aceA (isocitrate lyase) in proline degradation-deficient Escherichia coli strains (ΔputA) expressing the p4h gene. Whereas, the ΔsucCΔaceAΔputA strain grew in minimal medium in the absence of P4H, relying on the activity of fumarate reductase, growth of the ΔsucAΔaceAΔputA strictly depended on P4H activity, thus coupling growth to proline hydroxylation. P4H restored growth, even when proline was not externally added. However, the reduced succinyl-CoA pool caused a 27% decrease of the average cell size compared to the wildtype strain. Medium supplementation partially restored the morphology and, in some cases, enhanced proline hydroxylation activity. The specific proline hydroxylation rate doubled when putP, encoding the Na+ /l-proline transporter, was overexpressed in the ΔsucAΔaceAΔputA strain. This is in contrast to wildtype and ΔputA single-knock out strains, in which α-KG availability obviously limited proline hydroxylation. Such α-KG limitation was relieved in the ΔsucAΔaceAΔputA strain. Furthermore, the ΔsucAΔaceAΔputA strain was used to demonstrate an agar plate-based method for the identification and selection of active α-KG dependent hydroxylases. This together with the possibility to waive selection pressure and overcome α-KG limitation in respective hydroxylation processes based on living cells emphasizes the potential of TCA cycle engineering for the productive application of α-KG dependent hydroxylases. Biotechnol. Bioeng. 2017;114: 1511-1520. © 2017 Wiley Periodicals, Inc.
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Affiliation(s)
- Eleni Theodosiou
- Department of Solar Materials, Helmholtz Centre for Environmental Research-UFZ, Permoserstr. 15, Leipzig 04318, Germany
| | - Marina Breisch
- Laboratory of Chemical Biotechnology, Department of Biochemical and Chemical Engineering, TU Dortmund University, Dortmund, Germany
| | - Mattijs K Julsing
- Laboratory of Chemical Biotechnology, Department of Biochemical and Chemical Engineering, TU Dortmund University, Dortmund, Germany
| | - Francesco Falcioni
- Laboratory of Chemical Biotechnology, Department of Biochemical and Chemical Engineering, TU Dortmund University, Dortmund, Germany
| | - Bruno Bühler
- Department of Solar Materials, Helmholtz Centre for Environmental Research-UFZ, Permoserstr. 15, Leipzig 04318, Germany
| | - Andreas Schmid
- Department of Solar Materials, Helmholtz Centre for Environmental Research-UFZ, Permoserstr. 15, Leipzig 04318, Germany
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15
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Construction of a minimal genome as a chassis for synthetic biology. Essays Biochem 2016; 60:337-346. [DOI: 10.1042/ebc20160024] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2016] [Revised: 09/26/2016] [Accepted: 09/29/2016] [Indexed: 12/15/2022]
Abstract
Microbial diversity and complexity pose challenges in understanding the voluminous genetic information produced from whole-genome sequences, bioinformatics and high-throughput ‘-omics’ research. These challenges can be overcome by a core blueprint of a genome drawn with a minimal gene set, which is essential for life. Systems biology and large-scale gene inactivation studies have estimated the number of essential genes to be ∼300–500 in many microbial genomes. On the basis of the essential gene set information, minimal-genome strains have been generated using sophisticated genome engineering techniques, such as genome reduction and chemical genome synthesis. Current size-reduced genomes are not perfect minimal genomes, but chemically synthesized genomes have just been constructed. Some minimal genomes provide various desirable functions for bioindustry, such as improved genome stability, increased transformation efficacy and improved production of biomaterials. The minimal genome as a chassis genome for synthetic biology can be used to construct custom-designed genomes for various practical and industrial applications.
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16
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E1 of α-ketoglutarate dehydrogenase defends Mycobacterium tuberculosis against glutamate anaplerosis and nitroxidative stress. Proc Natl Acad Sci U S A 2015; 112:E5834-43. [PMID: 26430237 DOI: 10.1073/pnas.1510932112] [Citation(s) in RCA: 49] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Enzymes of central carbon metabolism (CCM) in Mycobacterium tuberculosis (Mtb) make an important contribution to the pathogen's virulence. Evidence is emerging that some of these enzymes are not simply playing the metabolic roles for which they are annotated, but can protect the pathogen via additional functions. Here, we found that deficiency of 2-hydroxy-3-oxoadipate synthase (HOAS), the E1 component of the α-ketoglutarate (α-KG) dehydrogenase complex (KDHC), did not lead to general metabolic perturbation or growth impairment of Mtb, but only to the specific inability to cope with glutamate anaplerosis and nitroxidative stress. In the former role, HOAS acts to prevent accumulation of aldehydes, including growth-inhibitory succinate semialdehyde (SSA). In the latter role, HOAS can participate in an alternative four-component peroxidase system, HOAS/dihydrolipoyl acetyl transferase (DlaT)/alkylhydroperoxide reductase colorless subunit gene (ahpC)-neighboring subunit (AhpD)/AhpC, using α-KG as a previously undescribed source of electrons for reductase action. Thus, instead of a canonical role in CCM, the E1 component of Mtb's KDHC serves key roles in situational defense that contribute to its requirement for virulence in the host. We also show that pyruvate decarboxylase (AceE), the E1 component of pyruvate dehydrogenase (PDHC), can participate in AceE/DlaT/AhpD/AhpC, using pyruvate as a source of electrons for reductase action. Identification of these systems leads us to suggest that Mtb can recruit components of its CCM for reactive nitrogen defense using central carbon metabolites.
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17
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Bhatia SK, Yi DH, Kim HJ, Jeon JM, Kim YH, Sathiyanarayanan G, Seo HM, Lee JH, Kim JH, Park K, Brigham CJ, Yang YH. Overexpression of succinyl-CoA synthase for poly (3-hydroxybutyrate-co-3-hydroxyvalerate) production in engineered Escherichia coli BL21(DE3). J Appl Microbiol 2015; 119:724-35. [PMID: 26109231 DOI: 10.1111/jam.12880] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2015] [Revised: 06/04/2015] [Accepted: 06/11/2015] [Indexed: 01/27/2023]
Abstract
AIM This study aims to increase the 3-hydroxyvalerate (3HV) fraction in poly(3-hydroxybutyrate-co-3-hydroxyvalerate) [P(HB-co-HV)] using succinyl-CoA synthase. METHODS AND RESULTS Escherichia coli YH090, a polyhydroxyalkonate (PHA)-producing strain, was further engineered for overexpression of succinyl-CoA synthase genes (sucCD), and examined for P(HB-co-HV) copolymer production in the presence of various precursor molecules using mixture analysis. Glycerol, succinate and propionate were screened as important factors for controlling intracellular PHA accumulation and monomer composition. Glycerol concentrations exerted the greatest influence on the overall biomass concentration and the intracellular PHA content, while propionate concentrations in the presence of succinate influenced the 3HV content of the copolymer. Mixture analysis also demonstrated that the engineered strain has the capacity to accumulate up to 80% of its cell dry weight (CDW) as PHA with a variable fraction of 3HV monomer (maximum of 72 wt %) depending on the controlled conditions. CONCLUSIONS Propionate is the principal precursor for 3HV monomer in P(HB-co-HV) biopolymer and its utilization requires conversion to propionyl-CoA. Engineered E. coli YHY99, overexpressing sucCD genes, leads to an increase of the succinyl-CoA pool, which enhances the conversion rate of propionate by providing a CoA supply to other acyltransferase enzymes that have a role in propionate utilization. SIGNIFICANCE AND IMPACT OF THE STUDY Engineered E. coli YHY99 was able to utilize propionate with a 4·5-fold increase in rate, as compared to the control strain, and resulted in the synthesis of a copolymer with high 3HV monomer content.
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Affiliation(s)
- S K Bhatia
- Department of Biological Engineering, College of Engineering, Konkuk University, Seoul, South Korea
| | - D-H Yi
- Department of Biological Engineering, College of Engineering, Konkuk University, Seoul, South Korea
| | - H-J Kim
- Department of Biological Engineering, College of Engineering, Konkuk University, Seoul, South Korea
| | - J-M Jeon
- Department of Biological Engineering, College of Engineering, Konkuk University, Seoul, South Korea
| | - Y-H Kim
- Department of Biological Engineering, College of Engineering, Konkuk University, Seoul, South Korea
| | - G Sathiyanarayanan
- Department of Biological Engineering, College of Engineering, Konkuk University, Seoul, South Korea
| | - H M Seo
- Department of Biological Engineering, College of Engineering, Konkuk University, Seoul, South Korea
| | - J H Lee
- Department of Biological Engineering, College of Engineering, Konkuk University, Seoul, South Korea
| | - J-H Kim
- Department of Biological Engineering, College of Engineering, Konkuk University, Seoul, South Korea
| | - K Park
- Department of Biological and Chemical Engineering, Hongik University, Jochiwon, Sejong City, Korea
| | - C J Brigham
- Department of Bioengineering, University of Massachusetts Dartmouth, North Dartmouth, MA, USA
| | - Y-H Yang
- Department of Biological Engineering, College of Engineering, Konkuk University, Seoul, South Korea.,Institute for Ubiquitous Information Technology and Applications (CBRU), Konkuk University, Seoul, South Korea
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18
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Lv L, Ren YL, Chen JC, Wu Q, Chen GQ. Application of CRISPRi for prokaryotic metabolic engineering involving multiple genes, a case study: Controllable P(3HB-co-4HB) biosynthesis. Metab Eng 2015; 29:160-168. [PMID: 25838211 DOI: 10.1016/j.ymben.2015.03.013] [Citation(s) in RCA: 192] [Impact Index Per Article: 21.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2014] [Revised: 03/21/2015] [Accepted: 03/23/2015] [Indexed: 01/08/2023]
Abstract
Clustered regularly interspaced short palindromic repeats interference (CRISPRi) is used to edit eukaryotic genomes. Here, we show that CRISPRi can also be used for fine-tuning prokaryotic gene expression while simultaneously regulating multiple essential gene expression with less labor and time consumption. As a case study, CRISPRi was used to control polyhydroxyalkanoate (PHA) biosynthesis pathway flux and to adjust PHA composition. A pathway was constructed in Escherichia coli for the production of poly(3-hydroxybutyrate-co-4-hydroxybutyrate) [P(3HB-co-4HB)] from glucose. The native gene sad encoding E. coli succinate semi-aldehyde dehydrogenase was expressed under the control of CRISPRi using five specially designed single guide RNAs (sgRNAs) for regulating carbon flux to 4-hydroxybutyrate (4HB) biosynthesis. The system allowed formation of P(3HB-co-4HB) consisting of 1-9mol% 4HB. Additionally, succinate, generated by succinyl-coA synthetase and succinate dehydrogenase (respectively encoded by genes sucC, sucD and sdhA, sdhB) was channeled preferentially to the 4HB precursor by using selected sgRNAs such as sucC2, sucD2, sdhB2 and sdhA1 via CRISPRi. The resulting 4HB content in P(3HB-co-4HB) was found to range from 1.4 to 18.4mol% depending on the expression levels of down-regulated genes. The results show that CRISPRi is a feasible method to simultaneously manipulate multiple genes in E. coli.
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Affiliation(s)
- Li Lv
- MOE Key Lab of Bioinformatics, Department of Biological Science and Biotechnology, School of Life Science, Tsinghua-Peking Center for Life Sciences, Tsinghua University, Beijing 100084, China
| | - Yi-Lin Ren
- MOE Key Lab of Bioinformatics, Department of Biological Science and Biotechnology, School of Life Science, Tsinghua-Peking Center for Life Sciences, Tsinghua University, Beijing 100084, China
| | - Jin-Chun Chen
- MOE Key Lab of Bioinformatics, Department of Biological Science and Biotechnology, School of Life Science, Tsinghua-Peking Center for Life Sciences, Tsinghua University, Beijing 100084, China
| | - Qiong Wu
- MOE Key Lab of Bioinformatics, Department of Biological Science and Biotechnology, School of Life Science, Tsinghua-Peking Center for Life Sciences, Tsinghua University, Beijing 100084, China
| | - Guo-Qiang Chen
- MOE Key Lab of Bioinformatics, Department of Biological Science and Biotechnology, School of Life Science, Tsinghua-Peking Center for Life Sciences, Tsinghua University, Beijing 100084, China; Center for Nano and Micro-Mechanics, Tsinghua University, Beijing 100084, China.
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19
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Optimising the production of succinate and lactate in Escherichia coli using a hybrid of artificial bee colony algorithm and minimisation of metabolic adjustment. J Biosci Bioeng 2015; 119:363-8. [DOI: 10.1016/j.jbiosc.2014.08.004] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2013] [Revised: 07/02/2014] [Accepted: 08/08/2014] [Indexed: 11/19/2022]
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20
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Hartman HB, Fell DA, Rossell S, Jensen PR, Woodward MJ, Thorndahl L, Jelsbak L, Olsen JE, Raghunathan A, Daefler S, Poolman MG. Identification of potential drug targets in Salmonella enterica sv. Typhimurium using metabolic modelling and experimental validation. MICROBIOLOGY-SGM 2014; 160:1252-1266. [PMID: 24777662 DOI: 10.1099/mic.0.076091-0] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Salmonella enterica sv. Typhimurium is an established model organism for Gram-negative, intracellular pathogens. Owing to the rapid spread of resistance to antibiotics among this group of pathogens, new approaches to identify suitable target proteins are required. Based on the genome sequence of S. Typhimurium and associated databases, a genome-scale metabolic model was constructed. Output was based on an experimental determination of the biomass of Salmonella when growing in glucose minimal medium. Linear programming was used to simulate variations in the energy demand while growing in glucose minimal medium. By grouping reactions with similar flux responses, a subnetwork of 34 reactions responding to this variation was identified (the catabolic core). This network was used to identify sets of one and two reactions that when removed from the genome-scale model interfered with energy and biomass generation. Eleven such sets were found to be essential for the production of biomass precursors. Experimental investigation of seven of these showed that knockouts of the associated genes resulted in attenuated growth for four pairs of reactions, whilst three single reactions were shown to be essential for growth.
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Affiliation(s)
- Hassan B Hartman
- Department of Medical and Biological Sciences, Oxford Brookes University, Gipsy Lane, Headington, Oxford OX3 OBP, UK
| | - David A Fell
- Department of Medical and Biological Sciences, Oxford Brookes University, Gipsy Lane, Headington, Oxford OX3 OBP, UK
| | - Sergio Rossell
- Department of Systems Biology, Technical University of Denmark, Lyngby, Denmark
| | - Peter Ruhdal Jensen
- Department of Systems Biology, Technical University of Denmark, Lyngby, Denmark
| | - Martin J Woodward
- Department of Food and Nutritional Sciences, University of Reading, Reading, UK
| | - Lotte Thorndahl
- Department of Veterinary Disease Biology, University of Copenhagen, Copenhagen, Denmark
| | - Lotte Jelsbak
- Department of Veterinary Disease Biology, University of Copenhagen, Copenhagen, Denmark
| | - John Elmerdahl Olsen
- Department of Veterinary Disease Biology, University of Copenhagen, Copenhagen, Denmark
| | - Anu Raghunathan
- Department of Infectious Diseases, Mount Sinai School of Medicine, New York, NY, USA
| | - Simon Daefler
- Department of Infectious Diseases, Mount Sinai School of Medicine, New York, NY, USA
| | - Mark G Poolman
- Department of Medical and Biological Sciences, Oxford Brookes University, Gipsy Lane, Headington, Oxford OX3 OBP, UK
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21
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Behrends V, Maharjan RP, Ryall B, Feng L, Liu B, Wang L, Bundy JG, Ferenci T. A metabolic trade-off between phosphate and glucose utilization in Escherichia coli. ACTA ACUST UNITED AC 2014; 10:2820-2. [DOI: 10.1039/c4mb00313f] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Using full genome sequencing and metabolomics we show that adaptation to chronic nutrient starvation reduces metabolic flexibility inEscherichia coli.
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Affiliation(s)
- Volker Behrends
- Department of Surgery and Cancer
- Imperial College London
- London SW7 2AZ, UK
| | - Ram P. Maharjan
- School of Molecular Bioscience
- University of Sydney
- , Australia
| | - Ben Ryall
- School of Molecular Bioscience
- University of Sydney
- , Australia
| | - Lu Feng
- TEDA Institute of Biological Sciences and Biotechnology
- Nankai University
- Tianjin 300457, P. R. China
- Key Laboratory of Molecular Microbiology and Technology
- Ministry of Education
| | - Bin Liu
- TEDA Institute of Biological Sciences and Biotechnology
- Nankai University
- Tianjin 300457, P. R. China
- Key Laboratory of Molecular Microbiology and Technology
- Ministry of Education
| | - Lei Wang
- TEDA Institute of Biological Sciences and Biotechnology
- Nankai University
- Tianjin 300457, P. R. China
- Key Laboratory of Molecular Microbiology and Technology
- Ministry of Education
| | - Jacob G. Bundy
- Department of Surgery and Cancer
- Imperial College London
- London SW7 2AZ, UK
| | - Thomas Ferenci
- School of Molecular Bioscience
- University of Sydney
- , Australia
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22
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Minato Y, Fassio SR, Wolfe AJ, Häse CC. Central metabolism controls transcription of a virulence gene regulator in Vibrio cholerae. MICROBIOLOGY-SGM 2013; 159:792-802. [PMID: 23429745 DOI: 10.1099/mic.0.064865-0] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
ToxT is the central regulatory protein involved in activation of the main virulence genes in Vibrio cholerae. We have identified transposon insertions in central metabolism genes, whose disruption increases toxT transcription. These disrupted genes encode the primary respiration-linked sodium pump (NADH:ubiquinone oxidoreductase or NQR) and certain tricarboxylic acid (TCA) cycle enzymes. Observations made following stimulation of respiration in the nqr mutant or chemical inhibition of NQR activity in the TCA cycle mutants led to the hypothesis that NQR affects toxT transcription via the TCA cycle. That toxT transcription increased when the growth medium was supplemented with citrate, but decreased with oxaloacetate, focused our attention on the TCA cycle substrate acetyl-CoA and its non-TCA cycle metabolism. Indeed, both the nqr and the TCA cycle mutants increased acetate excretion. A similar correlation between acetate excretion and toxT transcription was observed in a tolC mutant and upon amino acid (NRES) supplementation. As acetate and its tendency to decrease pH exerted no strong effect on toxT transcription, and because disruption of the major acetate excretion pathway increased toxT transcription, we propose that toxT transcription is regulated by either acetyl-CoA or some close derivative.
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Affiliation(s)
- Yusuke Minato
- Department of Biomedical Sciences, College of Veterinary Medicine, Oregon State University, Corvallis, OR, USA
| | - Sara R Fassio
- Department of Microbiology, College of Science, Oregon State University, Corvallis, OR, USA
| | - Alan J Wolfe
- Department of Microbiology and Immunology, Health Sciences Division, Loyola University Chicago, Maywood, IL, USA
| | - Claudia C Häse
- Department of Microbiology, College of Science, Oregon State University, Corvallis, OR, USA.,Department of Biomedical Sciences, College of Veterinary Medicine, Oregon State University, Corvallis, OR, USA
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23
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Mattozzi MD, Ziesack M, Voges MJ, Silver PA, Way JC. Expression of the sub-pathways of the Chloroflexus aurantiacus 3-hydroxypropionate carbon fixation bicycle in E. coli: Toward horizontal transfer of autotrophic growth. Metab Eng 2013; 16:130-9. [PMID: 23376595 DOI: 10.1016/j.ymben.2013.01.005] [Citation(s) in RCA: 60] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2012] [Revised: 01/08/2013] [Accepted: 01/17/2013] [Indexed: 01/11/2023]
Abstract
The 3-hydroxypropionate (3-HPA) bicycle is unique among CO2-fixing systems in that none of its enzymes appear to be affected by oxygen. Moreover, the bicycle includes a number of enzymes that produce novel intermediates of biotechnological interest, and the CO2-fixing steps in this pathway are relatively rapid. We expressed portions of the 3-HPA bicycle in a heterologous organism, E. coli K12. We subdivided the 3-HPA bicycle into four sub-pathways: (1) synthesis of propionyl-CoA from acetyl-CoA, (2) synthesis of succinate from propionyl-CoA, (3) glyoxylate production and regeneration of acetyl-CoA, and (4) assimilation of glyoxylate and propionyl-CoA to form pyruvate and regenerate acetyl-CoA. We expressed the novel enzymes of the 3-HPA bicycle in operon form and used phenotypic tests for activity. Sub-pathway 1 activated a propionate-specific biosensor. Sub-pathway 2, found in non-CO2-fixing bacteria, was reassembled in E. coli using genes from diverse sources. Sub-pathway 3, operating in reverse, generated succinyl-CoA sufficient to rescue a sucAD(-) double mutant of its diaminopimelic acid (DAP) auxotrophy. Sub-pathway 4 was able to reduce the toxicity of propionate and allow propionate to contribute to cell biomass in a prpC(-)(2 methylcitrate synthase) mutant strain. These results indicate that all of the sub-pathways of the 3-HPA bicycle can function to some extent in vivo in a heterologous organism, as indicated by growth tests. Overexpression of certain enzymes was deleterious to cell growth, and, in particular, expression of MMC-CoA lyase caused a mucoid phenotype. These results have implications for metabolic engineering and for bacterial evolution through horizontal gene transfer.
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Affiliation(s)
- Matthew d Mattozzi
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA 02115, USA.
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24
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Cheng C, Wakefield MJ, Yang J, Tauschek M, Robins-Browne RM. Genome-wide analysis of the Pho regulon in a pstCA mutant of Citrobacter rodentium. PLoS One 2012; 7:e50682. [PMID: 23226353 PMCID: PMC3511308 DOI: 10.1371/journal.pone.0050682] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2012] [Accepted: 10/26/2012] [Indexed: 11/19/2022] Open
Abstract
The phosphate-specific transport operon, pstSCAB-phoU, of Gram-negative bacteria is an essential part of the Pho regulon. Its key roles are to encode a high-affinity inorganic phosphate transport system and to prevent activation of PhoB in phosphate-rich environments. In general, mutations in pstSCAB-phoU lead to the constitutive expression of the Pho regulon. Previously, we constructed a pstCA deletion mutant of Citrobacter rodentium and found it to be attenuated for virulence in mice, its natural host. This attenuation was dependent on PhoB or PhoB-regulated gene(s) because a phoB mutation restored virulence for mice to the pstCA mutant. To investigate how downstream genes may contribute to the virulence of C. rodentium, we used microarray analysis to investigate global gene expression of C. rodentium strain ICC169 and its isogenic pstCA mutant when grown in phosphate-rich medium. Overall 323 genes of the pstCA mutant were differentially expressed by at least 1.5-fold compared to the wild-type C. rodentium. Of these 145 were up-regulated and 178 were down-regulated. Differentially expressed genes included some involved in phosphate homoeostasis, cellular metabolism and protein metabolism. A large number of genes involved in stress responses and of unknown function were also differentially expressed, as were some virulence-associated genes. Up-regulated virulence-associated genes in the pstCA mutant included that for DegP, a serine protease, which appeared to be directly regulated by PhoB. Down-regulated genes included those for the production of the urease, flagella, NleG8 (a type III-secreted protein) and the tad focus (which encodes type IVb pili in Yersinia enterocolitica). Infection studies using C57/BL6 mice showed that DegP and NleG8 play a role in bacterial virulence. Overall, our study provides evidence that Pho is a global regulator of gene expression in C. rodentium and indicates the presence of at least two previously unrecognized virulence determinants of C. rodentium, namely, DegP and NleG8.
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Affiliation(s)
- Catherine Cheng
- Department of Microbiology and Immunology, The University of Melbourne, Parkville, Victoria, Australia
| | - Matthew J. Wakefield
- Bioinformatics Division, Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
- Department of Genetics, The University of Melbourne, Parkville, Victoria, Australia
| | - Ji Yang
- Department of Microbiology and Immunology, The University of Melbourne, Parkville, Victoria, Australia
| | - Marija Tauschek
- Department of Microbiology and Immunology, The University of Melbourne, Parkville, Victoria, Australia
| | - Roy M. Robins-Browne
- Department of Microbiology and Immunology, The University of Melbourne, Parkville, Victoria, Australia
- Murdoch Childrens Research Institute, Royal Children’s Hospital, Parkville, Victoria, Australia
- * E-mail:
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Novel reaction of succinyl coenzyme A (Succinyl-CoA) synthetase: activation of 3-sulfinopropionate to 3-sulfinopropionyl-CoA in Advenella mimigardefordensis strain DPN7T during degradation of 3,3'-dithiodipropionic acid. J Bacteriol 2011; 193:3078-89. [PMID: 21515777 DOI: 10.1128/jb.00049-11] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The sucCD gene of Advenella mimigardefordensis strain DPN7(T) encodes a succinyl coenzyme A (succinyl-CoA) synthetase homologue (EC 6.2.1.4 or EC 6.2.1.5) that recognizes, in addition to succinate, the structural analogues 3-sulfinopropionate (3SP) and itaconate as substrates. Accumulation of 3SP during 3,3'-dithiodipropionic acid (DTDP) degradation was observed in Tn5::mob-induced mutants of A. mimigardefordensis strain DPN7(T) disrupted in sucCD and in the defined deletion mutant A. mimigardefordensis ΔsucCD. These mutants were impaired in growth with DTDP and 3SP as the sole carbon source. Hence, it was proposed that the succinyl-CoA synthetase homologue in A. mimigardefordensis strain DPN7(T) activates 3SP to the corresponding CoA-thioester (3SP-CoA). The putative genes coding for A. mimigardefordensis succinyl-CoA synthetase (SucCD(Am)) were cloned and heterologously expressed in Escherichia coli BL21(DE3)/pLysS. Purification and characterization of the enzyme confirmed its involvement during degradation of DTDP. 3SP, the cleavage product of DTDP, was converted into 3SP-CoA by the purified enzyme, as demonstrated by in vitro enzyme assays. The structure of 3SP-CoA was verified by using liquid chromatography-electrospray ionization-mass spectrometry. SucCD(Am) is Mg²⁺ or Mn²⁺ dependent and unspecific regarding ATP or GTP. In kinetic studies the enzyme showed highest enzyme activity and substrate affinity with succinate (V(max) = 9.85 ± 0.14 μmol min⁻¹ mg⁻¹, K(m) = 0.143 ± 0.001 mM). In comparison to succinate, activity with 3SP was only ca. 1.2% (V(max) = 0.12 ± 0.01 μmol min⁻¹ mg⁻¹) and the affinity was 6-fold lower (K(m) = 0.818 ± 0.046 mM). Based on the present results, we conclude that SucCD(Am) is physiologically associated with the citric acid cycle but is mandatory for the catabolic pathway of DTDP and its degradation intermediate 3SP.
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Cho HY, Lee SG, Hyeon JE, Han SO. Identification and characterization of a transcriptional regulator, SucR, that influences sucCD transcription in Corynebacterium glutamicum. Biochem Biophys Res Commun 2010; 401:300-5. [DOI: 10.1016/j.bbrc.2010.09.057] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2010] [Accepted: 09/14/2010] [Indexed: 12/01/2022]
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Lone AG, Deslandes V, Nash JHE, Jacques M, MacInnes JI. Modulation of gene expression in Actinobacillus pleuropneumoniae exposed to bronchoalveolar fluid. PLoS One 2009; 4:e6139. [PMID: 19578537 PMCID: PMC2700959 DOI: 10.1371/journal.pone.0006139] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2009] [Accepted: 06/08/2009] [Indexed: 12/31/2022] Open
Abstract
BACKGROUND Actinobacillus pleuropneumoniae, the causative agent of porcine contagious pleuropneumonia, is an important pathogen of swine throughout the world. It must rapidly overcome the innate pulmonary immune defenses of the pig to cause disease. To better understand this process, the objective of this study was to identify genes that are differentially expressed in a medium that mimics the lung environment early in the infection process. METHODS AND PRINCIPAL FINDINGS Since bronchoalveolar lavage fluid (BALF) contains innate immune and other components found in the lungs, we examined gene expression of a virulent serovar 1 strain of A. pleuropneumoniae after a 30 min exposure to BALF, using DNA microarrays and real-time PCR. The functional classes of genes found to be up-regulated most often in BALF were those encoding proteins involved in energy metabolism, especially anaerobic metabolism, and in cell envelope, DNA, and protein biosynthesis. Transcription of a number of known virulence genes including apxIVA and the gene for SapF, a protein which is involved in resistance to antimicrobial peptides, was also up-regulated in BALF. Seventy-nine percent of the genes that were up-regulated in BALF encoded a known protein product, and of these, 44% had been reported to be either expressed in vivo and/or involved in virulence. CONCLUSIONS The results of this study suggest that in early stages of infection, A. pleuropneumoniae may modulate expression of genes involved in anaerobic energy generation and in the synthesis of proteins involved in cell wall biogenesis, as well as established virulence factors. Given that many of these genes are thought to be expressed in vivo or involved in virulence, incubation in BALF appears, at least partially, to simulate in vivo conditions and may provide a useful medium for the discovery of novel vaccine or therapeutic targets.
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Affiliation(s)
- Abdul G. Lone
- Department of Pathobiology, Ontario Veterinary College, University of Guelph, Guelph, Ontario, Canada
| | - Vincent Deslandes
- Groupe de Recherche sur les Maladies Infectieuses du Porc, Université de Montréal, St-Hyacinthe, Québec, Canada
- Centre de Recherche en Infectiologie Porcine, Université de Montréal, St-Hyacinthe, Québec, Canada
| | - John H. E. Nash
- Institute for Biological Sciences, National Research Council of Canada, Ottawa, Ontario, Canada
| | - Mario Jacques
- Groupe de Recherche sur les Maladies Infectieuses du Porc, Université de Montréal, St-Hyacinthe, Québec, Canada
- Centre de Recherche en Infectiologie Porcine, Université de Montréal, St-Hyacinthe, Québec, Canada
| | - Janet I. MacInnes
- Department of Pathobiology, Ontario Veterinary College, University of Guelph, Guelph, Ontario, Canada
- * E-mail:
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Abstract
Background Metabolic networks present a complex interconnected structure, whose understanding is in general a non-trivial task. Several formal approaches have been developed to support the investigation of such networks. One of the relevant problems in this context is the comprehension of causality dependencies amongst the molecules involved in the metabolic process. Results We apply techniques from formal methods and computational logic to develop an abstract qualitative model of metabolic networks in order to determine possible causal dependencies. Keeping in mind both expressiveness and ease of use, we aimed at providing: i) a minimal notation to represent causality in biochemical interactions, and ii) an automated tool allowing human experts to easily vary conditions of in silico experiments. We exploit a reading of chemical reactions in terms of logical implications: starting from a description of a metabolic network in terms of reaction rules and initial conditions, chains of reactions, causally depending one from the another, can be automatically deduced. Both the components of the initial state and the clauses ruling reactions can be easily varied and a new trial of the experiment started, according to a what-if investigation strategy. Our approach aims at exploiting computational logic as a formal modeling framework, amongst the several available, that is naturally close to human reasoning. It directly leads to executable implementations and may support, in perspective, various reasoning schemata. Indeed, our abstractions are supported by a computational counterpart, based on a Prolog implementation, which allows for a representation language closely correspondent to the adopted chemical abstract notation. The proposed approach has been validated by results regarding gene knock-out and essentiality for a model of the metabolic network of Escherichia coli K12, which show a relevant coherence with available wet-lab experimental data. Conclusions Starting from the presented work, our goal is to provide an effective analysis toolkit, supported by an efficient full-fledged computational counterpart, with the aim of fruitfully driving in vitro experiments by effectively pruning non promising directions.
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Affiliation(s)
- Chiara Bodei
- Dipartimento di Informatica, Università di Pisa, I-56127, Pisa, Italy.
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