1
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Chaisupa P, Wright RC. State-of-the-art in engineering small molecule biosensors and their applications in metabolic engineering. SLAS Technol 2024; 29:100113. [PMID: 37918525 DOI: 10.1016/j.slast.2023.10.005] [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: 07/07/2023] [Revised: 10/18/2023] [Accepted: 10/25/2023] [Indexed: 11/04/2023]
Abstract
Genetically encoded biosensors are crucial for enhancing our understanding of how molecules regulate biological systems. Small molecule biosensors, in particular, help us understand the interaction between chemicals and biological processes. They also accelerate metabolic engineering by increasing screening throughput and eliminating the need for sample preparation through traditional chemical analysis. Additionally, they offer significantly higher spatial and temporal resolution in cellular analyte measurements. In this review, we discuss recent progress in in vivo biosensors and control systems-biosensor-based controllers-for metabolic engineering. We also specifically explore protein-based biosensors that utilize less commonly exploited signaling mechanisms, such as protein stability and induced degradation, compared to more prevalent transcription factor and allosteric regulation mechanism. We propose that these lesser-used mechanisms will be significant for engineering eukaryotic systems and slower-growing prokaryotic systems where protein turnover may facilitate more rapid and reliable measurement and regulation of the current cellular state. Lastly, we emphasize the utilization of cutting-edge and state-of-the-art techniques in the development of protein-based biosensors, achieved through rational design, directed evolution, and collaborative approaches.
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Affiliation(s)
- Patarasuda Chaisupa
- Department of Biological Systems Engineering, Virginia Tech, Blacksburg, VA 24061, United States
| | - R Clay Wright
- Department of Biological Systems Engineering, Virginia Tech, Blacksburg, VA 24061, United States; Translational Plant Sciences Center (TPSC), Virginia Tech, Blacksburg, VA 24061, United States.
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2
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Liu X, Liu J, Liu Z, Qiao Q, Ni X, Yang J, Sun G, Li F, Zhou W, Guo X, Chen J, Jia S, Zheng Y, Zheng P, Sun J. Engineering allosteric inhibition of homoserine dehydrogenase by semi-rational saturation mutagenesis screening. Front Bioeng Biotechnol 2024; 11:1336215. [PMID: 38234301 PMCID: PMC10791936 DOI: 10.3389/fbioe.2023.1336215] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2023] [Accepted: 12/11/2023] [Indexed: 01/19/2024] Open
Abstract
Allosteric regulation by pathway products plays a vital role in amino acid metabolism. Homoserine dehydrogenase (HSD), the key enzyme for the biosynthesis of various aspartate family amino acids, is subject to feedback inhibition by l-threonine and l-isoleucine. The desensitized mutants with the potential for amino acid production remain limited. Herein, a semi-rational approach was proposed to relieve the feedback inhibition. HSD from Corynebacterium glutamicum (CgHSD) was first characterized as a homotetramer, and nine conservative sites at the tetramer interface were selected for saturation mutagenesis by structural simulations and sequence analysis. Then, we established a high-throughput screening (HTS) method based on resistance to l-threonine analog and successfully acquired two dominant mutants (I397V and A384D). Compared with the best-ever reported desensitized mutant G378E, both new mutants qualified the engineered strains with higher production of CgHSD-dependent amino acids. The mutant and wild-type enzymes were purified and assessed in the presence or absence of inhibitors. Both purified mutants maintained >90% activity with 10 mM l-threonine or 25 mM l-isoleucine. Moreover, they showed >50% higher specific activities than G378E without inhibitors. This work provides two competitive alternatives for constructing cell factories of CgHSD-related amino acids and derivatives. Moreover, the proposed approach can be applied to engineering other allosteric enzymes in the amino acid synthesis pathway.
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Affiliation(s)
- Xinyang Liu
- College of Biotechnology, Tianjin University of Science and Technology, Tianjin, China
- Key Laboratory of Engineering Biology for Low-carbon Manufacturing, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
- National Technology Innovation Center of Synthetic Biology, Tianjin, China
- State Key Laboratory of Food Nutrition and Safety, Tianjin University of Science and Technology, Tianjin, China
| | - Jiao Liu
- Key Laboratory of Engineering Biology for Low-carbon Manufacturing, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
- National Technology Innovation Center of Synthetic Biology, Tianjin, China
| | - Zhemin Liu
- Key Laboratory of Engineering Biology for Low-carbon Manufacturing, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
- National Technology Innovation Center of Synthetic Biology, Tianjin, China
| | - Qianqian Qiao
- College of Biotechnology, Tianjin University of Science and Technology, Tianjin, China
- Key Laboratory of Engineering Biology for Low-carbon Manufacturing, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
- National Technology Innovation Center of Synthetic Biology, Tianjin, China
- State Key Laboratory of Food Nutrition and Safety, Tianjin University of Science and Technology, Tianjin, China
| | - Xiaomeng Ni
- College of Biotechnology, Tianjin University of Science and Technology, Tianjin, China
- Key Laboratory of Engineering Biology for Low-carbon Manufacturing, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
- National Technology Innovation Center of Synthetic Biology, Tianjin, China
| | - Jinxing Yang
- Key Laboratory of Engineering Biology for Low-carbon Manufacturing, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
- National Technology Innovation Center of Synthetic Biology, Tianjin, China
| | - Guannan Sun
- Key Laboratory of Engineering Biology for Low-carbon Manufacturing, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
- National Technology Innovation Center of Synthetic Biology, Tianjin, China
| | - Fanghe Li
- Key Laboratory of Engineering Biology for Low-carbon Manufacturing, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
- National Technology Innovation Center of Synthetic Biology, Tianjin, China
| | - Wenjuan Zhou
- Key Laboratory of Engineering Biology for Low-carbon Manufacturing, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
- National Technology Innovation Center of Synthetic Biology, Tianjin, China
| | - Xuan Guo
- Key Laboratory of Engineering Biology for Low-carbon Manufacturing, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
- National Technology Innovation Center of Synthetic Biology, Tianjin, China
| | - Jiuzhou Chen
- Key Laboratory of Engineering Biology for Low-carbon Manufacturing, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
- National Technology Innovation Center of Synthetic Biology, Tianjin, China
| | - Shiru Jia
- College of Biotechnology, Tianjin University of Science and Technology, Tianjin, China
- State Key Laboratory of Food Nutrition and Safety, Tianjin University of Science and Technology, Tianjin, China
| | - Yu Zheng
- College of Biotechnology, Tianjin University of Science and Technology, Tianjin, China
- State Key Laboratory of Food Nutrition and Safety, Tianjin University of Science and Technology, Tianjin, China
| | - Ping Zheng
- College of Biotechnology, Tianjin University of Science and Technology, Tianjin, China
- Key Laboratory of Engineering Biology for Low-carbon Manufacturing, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
- National Technology Innovation Center of Synthetic Biology, Tianjin, China
| | - Jibin Sun
- College of Biotechnology, Tianjin University of Science and Technology, Tianjin, China
- Key Laboratory of Engineering Biology for Low-carbon Manufacturing, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
- National Technology Innovation Center of Synthetic Biology, Tianjin, China
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3
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Hayes G, Laurel M, MacKinnon D, Zhao T, Houck HA, Becer CR. Polymers without Petrochemicals: Sustainable Routes to Conventional Monomers. Chem Rev 2023; 123:2609-2734. [PMID: 36227737 PMCID: PMC9999446 DOI: 10.1021/acs.chemrev.2c00354] [Citation(s) in RCA: 23] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Access to a wide range of plastic materials has been rationalized by the increased demand from growing populations and the development of high-throughput production systems. Plastic materials at low costs with reliable properties have been utilized in many everyday products. Multibillion-dollar companies are established around these plastic materials, and each polymer takes years to optimize, secure intellectual property, comply with the regulatory bodies such as the Registration, Evaluation, Authorisation and Restriction of Chemicals and the Environmental Protection Agency and develop consumer confidence. Therefore, developing a fully sustainable new plastic material with even a slightly different chemical structure is a costly and long process. Hence, the production of the common plastic materials with exactly the same chemical structures that does not require any new registration processes better reflects the reality of how to address the critical future of sustainable plastics. In this review, we have highlighted the very recent examples on the synthesis of common monomers using chemicals from sustainable feedstocks that can be used as a like-for-like substitute to prepare conventional petrochemical-free thermoplastics.
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Affiliation(s)
- Graham Hayes
- Department of Chemistry, University of Warwick, CV4 7ALCoventry, United Kingdom
| | - Matthew Laurel
- Department of Chemistry, University of Warwick, CV4 7ALCoventry, United Kingdom
| | - Dan MacKinnon
- Department of Chemistry, University of Warwick, CV4 7ALCoventry, United Kingdom
| | - Tieshuai Zhao
- Department of Chemistry, University of Warwick, CV4 7ALCoventry, United Kingdom
| | - Hannes A Houck
- Department of Chemistry, University of Warwick, CV4 7ALCoventry, United Kingdom.,Institute of Advanced Study, University of Warwick, CV4 7ALCoventry, United Kingdom
| | - C Remzi Becer
- Department of Chemistry, University of Warwick, CV4 7ALCoventry, United Kingdom
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4
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Cen X, Liu Y, Zhu F, Liu D, Chen Z. Metabolic engineering of Escherichia coli for high production of 1,5-pentanediol via a cadaverine-derived pathway. Metab Eng 2022; 74:168-177. [DOI: 10.1016/j.ymben.2022.10.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2022] [Revised: 10/06/2022] [Accepted: 10/27/2022] [Indexed: 11/05/2022]
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5
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Löwe H, Kremling A. In-Depth Computational Analysis of Natural and Artificial Carbon Fixation Pathways. BIODESIGN RESEARCH 2021; 2021:9898316. [PMID: 37849946 PMCID: PMC10521678 DOI: 10.34133/2021/9898316] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2021] [Accepted: 08/02/2021] [Indexed: 10/19/2023] Open
Abstract
In the recent years, engineering new-to-nature CO2- and C1-fixing metabolic pathways made a leap forward. New, artificial pathways promise higher yields and activity than natural ones like the Calvin-Benson-Bassham (CBB) cycle. The question remains how to best predict their in vivo performance and what actually makes one pathway "better" than another. In this context, we explore aerobic carbon fixation pathways by a computational approach and compare them based on their specific activity and yield on methanol, formate, and CO2/H2 considering the kinetics and thermodynamics of the reactions. Besides pathways found in nature or implemented in the laboratory, this included two completely new cycles with favorable features: the reductive citramalyl-CoA cycle and the 2-hydroxyglutarate-reverse tricarboxylic acid cycle. A comprehensive kinetic data set was collected for all enzymes of all pathways, and missing kinetic data were sampled with the Parameter Balancing algorithm. Kinetic and thermodynamic data were fed to the Enzyme Cost Minimization algorithm to check for respective inconsistencies and calculate pathway-specific activities. The specific activities of the reductive glycine pathway, the CETCH cycle, and the new reductive citramalyl-CoA cycle were predicted to match the best natural cycles with superior product-substrate yield. However, the CBB cycle performed better in terms of activity compared to the alternative pathways than previously thought. We make an argument that stoichiometric yield is likely not the most important design criterion of the CBB cycle. Still, alternative carbon fixation pathways were paretooptimal for specific activity and product-substrate yield in simulations with C1 substrates and CO2/H2 and therefore hold great potential for future applications in Industrial Biotechnology and Synthetic Biology.
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Affiliation(s)
- Hannes Löwe
- Systems Biotechnology, Technical University of Munich, Germany
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6
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Tang W, Dong X, Meng J, Feng Y, Xie M, Xu H, Song P. Biochemical characterization and redesign of the coenzyme specificity of a novel monofunctional NAD +-dependent homoserine dehydrogenase from the human pathogen Neisseria gonorrhoeae. Protein Expr Purif 2021; 186:105909. [PMID: 34022392 DOI: 10.1016/j.pep.2021.105909] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2021] [Revised: 05/13/2021] [Accepted: 05/15/2021] [Indexed: 12/17/2022]
Abstract
Gonorrhoea, caused by Neisseria gonorrhoeae, is a major global public health concern. Homoserine dehydrogenase (HSD), a key enzyme in the aspartate pathway, is a promising metabolic target against pathogenic infections. In this study, a monofunctional HSD from N. gonorrhoeae (NgHSD) was overexpressed in Escherichia coli and purified to >95% homogeneity for biochemical characterization. Unlike the classic dimeric structure, the purified recombinant NgHSD exists as a tetramer in solution. We determined the enzymatic activity of recombinant NgHSD for l-homoserine oxidation, which revealed that this enzyme was NAD+ dependent, with an approximate 479-fold (kcat/Km) preference for NAD+ over NADP+, and that optimal activity for l-homoserine oxidation occurred at pH 10.5 and 40 °C. At 800 mM, neither NaCl nor KCl increased the activity of NgHSD, in contrast to the behavior of several reported NAD+-independent homologs. Moreover, threonine did not markedly inhibit the oxidation activity of NgHSD. To gain insight into the cofactor specificity, site-directed mutagenesis was used to alter coenzyme specificity. The double mutant L45R/S46R, showing the highest affinity for NADP+, caused a shift in coenzyme preference from NAD+ to NADP+ by a factor of ~974, with a catalytic efficiency comparable with naturally occurring NAD+-independent homologs. Collectively, our results should allow the exploration of drugs targeting NgHSD to treat gonococcal infections and contribute to the prediction of the coenzyme specificity of novel HSDs.
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Affiliation(s)
- Wanggang Tang
- Department of Biochemistry and Molecular Biology, School of Laboratory Medicine, Bengbu Medical College, Bengbu, Anhui, 233030, China.
| | - Xue Dong
- Research Center of Laboratory Medicine, School of Laboratory Medicine, Bengbu Medical College, Bengbu, Anhui, 233030, China
| | - Jiang Meng
- Research Center of Laboratory Medicine, School of Laboratory Medicine, Bengbu Medical College, Bengbu, Anhui, 233030, China
| | - Yanan Feng
- Research Center of Laboratory Medicine, School of Laboratory Medicine, Bengbu Medical College, Bengbu, Anhui, 233030, China
| | - Manman Xie
- Research Center of Laboratory Medicine, School of Laboratory Medicine, Bengbu Medical College, Bengbu, Anhui, 233030, China
| | - Haonan Xu
- Research Center of Laboratory Medicine, School of Laboratory Medicine, Bengbu Medical College, Bengbu, Anhui, 233030, China
| | - Ping Song
- College of Biological and Food Engineering, Anhui Polytechnic University, Wuhu, Anhui, 241000, China.
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7
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Wang S, Ma C, Zeng A. Dynamic energy correlation analysis of E. coli aspartokinase III and alteration of allosteric regulation by manipulating energy transduction pathways. Eng Life Sci 2021; 21:314-323. [PMID: 33976604 PMCID: PMC8092979 DOI: 10.1002/elsc.202000065] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2020] [Revised: 11/20/2020] [Accepted: 01/13/2021] [Indexed: 01/14/2023] Open
Abstract
Conformational change associated with allosteric regulation in a protein is ultimately driven by energy transformation. However, little is known about the latter process. In this work, we combined steered molecular dynamics simulations and sequence conservation analysis to investigate the conformational changes and energy transformation in the allosteric enzyme aspartokinase III (AK III) from Escherichia coli. Correlation analysis of energy change at residue level indicated significant transformation between electrostatic energy and dihedral angle energy during the allosteric regulation. Key amino acid residues located in the corresponding energy transduction pathways were identified by dynamic energy correlation analysis. To verify their functions, residues with a high energy correlation in the pathways were altered and their effects on allosteric regulation of AKIII were determined. This study sheds new insights into energy transformation during allosteric regulation of AK III and proposes a strategy to identify key residues that are involved in intramolecular energy transduction and thus in driving the allosteric process.
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Affiliation(s)
- Shizhen Wang
- Department of Chemical and Biochemical EngineeringCollege of Chemistry and Chemical EngineeringXiamen UniversityXiamenP. R. China
- Institute of Bioprocess and Biosystems EngineeringHamburg University of TechnologyHamburgGermany
| | - Chengwei Ma
- Institute of Bioprocess and Biosystems EngineeringHamburg University of TechnologyHamburgGermany
| | - An‐Ping Zeng
- Institute of Bioprocess and Biosystems EngineeringHamburg University of TechnologyHamburgGermany
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8
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Wu M, Sun Y, Zhu M, Zhu L, Lü J, Geng F. Molecular Dynamics-Based Allosteric Prediction Method to Design Key Residues in Threonine Dehydrogenase for Amino-Acid Production. ACS OMEGA 2021; 6:10975-10983. [PMID: 34056250 PMCID: PMC8153896 DOI: 10.1021/acsomega.1c00798] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/12/2021] [Accepted: 04/01/2021] [Indexed: 06/12/2023]
Abstract
Allosteric proteins are considered as one of the most critical targets to design cell factories via synthetic biology approaches. Here, we proposed a molecular dynamics-based allosteric prediction method (MBAP) to screen indirect-binding sites and potential mutations for protein re-engineering. Using this MBAP method, we have predicted new sites to relieve the allosteric regulation of threonine dehydrogenase (TD) by isoleucine. An obtained mutation P441L has been verified with the ability to significantly reduce the allosteric regulation of TD in vitro assays and with the fermentation application in vivo for amino-acid production. These findings have proved the MBAP method as an effective and efficient predicting tool to find new positions of the allosteric enzymes, thus opening a new path to constructing cell factories in synthetic biology.
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Affiliation(s)
- Mingyu Wu
- School
of Pharmacy, Binzhou Medical University, No. 346 Guanhai Road, Yantai 264003, China
| | - Yu Sun
- School
of Pharmacy, Binzhou Medical University, No. 346 Guanhai Road, Yantai 264003, China
| | - Meiru Zhu
- School
of Pharmacy, Binzhou Medical University, No. 346 Guanhai Road, Yantai 264003, China
| | - Laiyu Zhu
- School
of Pharmacy, Binzhou Medical University, No. 346 Guanhai Road, Yantai 264003, China
| | - Junhong Lü
- School
of Pharmacy, Binzhou Medical University, No. 346 Guanhai Road, Yantai 264003, China
- Zhangjiang
Laboratory, Shanghai Advanced Research Institute,
Chinese Academy of Sciences, No. 239 Zhangheng Road, Pudong New District, Shanghai 201203, China
| | - Feng Geng
- School
of Pharmacy, Binzhou Medical University, No. 346 Guanhai Road, Yantai 264003, China
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9
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Combining protein and metabolic engineering to construct efficient microbial cell factories. Curr Opin Biotechnol 2020; 66:27-35. [DOI: 10.1016/j.copbio.2020.06.001] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2020] [Revised: 05/25/2020] [Accepted: 06/01/2020] [Indexed: 11/17/2022]
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10
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Li N, Xu S, Du G, Chen J, Zhou J. Efficient production of L-homoserine in Corynebacterium glutamicum ATCC 13032 by redistribution of metabolic flux. Biochem Eng J 2020. [DOI: 10.1016/j.bej.2020.107665] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
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11
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Andriiash GS, Sekan OS, Tigunova OO, Blume YB, Shulga SM. Metabolic Engineering of Lysine Producing Corynebacterium glutamicum Strains. CYTOL GENET+ 2020. [DOI: 10.3103/s0095452720020024] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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12
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New Therapeutic Candidates for the Treatment of Malassezia pachydermatis -Associated Infections. Sci Rep 2020; 10:4860. [PMID: 32184419 PMCID: PMC7078309 DOI: 10.1038/s41598-020-61729-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2019] [Accepted: 02/24/2020] [Indexed: 11/26/2022] Open
Abstract
The opportunistic pathogen Malassezia pachydermatis causes bloodstream infections in preterm infants or individuals with immunodeficiency disorders and has been associated with a broad spectrum of diseases in animals such as seborrheic dermatitis, external otitis and fungemia. The current approaches to treat these infections are failing as a consequence of their adverse effects, changes in susceptibility and antifungal resistance. Thus, the identification of novel therapeutic targets against M. pachydermatis infections are highly relevant. Here, Gene Essentiality Analysis and Flux Variability Analysis was applied to a previously reported M. pachydermatis metabolic network to identify enzymes that, when absent, negatively affect biomass production. Three novel therapeutic targets (i.e., homoserine dehydrogenase (MpHSD), homocitrate synthase (MpHCS) and saccharopine dehydrogenase (MpSDH)) were identified that are absent in humans. Notably, L-lysine was shown to be an inhibitor of the enzymatic activity of MpHCS and MpSDH at concentrations of 1 mM and 75 mM, respectively, while L-threonine (1 mM) inhibited MpHSD. Interestingly, L- lysine was also shown to inhibit M. pachydermatis growth during in vitro assays with reference strains and canine isolates, while it had a negligible cytotoxic activity on HEKa cells. Together, our findings form the bases for the development of novel treatments against M. pachydermatis infections.
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13
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Nikolaev Y, Ripin N, Soste M, Picotti P, Iber D, Allain FHT. Systems NMR: single-sample quantification of RNA, proteins and metabolites for biomolecular network analysis. Nat Methods 2019; 16:743-749. [PMID: 31363225 PMCID: PMC6837886 DOI: 10.1038/s41592-019-0495-7] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2018] [Accepted: 06/17/2019] [Indexed: 12/14/2022]
Abstract
Cellular behavior is controlled by the interplay of diverse biomolecules. Most experimental methods, however, can only monitor a single molecule class or reaction type at a time. We developed an in vitro nuclear magnetic resonance spectroscopy (NMR) approach, which permitted dynamic quantification of an entire 'heterotypic' network-simultaneously monitoring three distinct molecule classes (metabolites, proteins and RNA) and all elementary reaction types (bimolecular interactions, catalysis, unimolecular changes). Focusing on an eight-reaction co-transcriptional RNA folding network, in a single sample we recorded over 35 time points with over 170 observables each, and accurately determined five core reaction constants in multiplex. This reconstruction revealed unexpected cross-talk between the different reactions. We further observed dynamic phase-separation in a system of five distinct RNA-binding domains in the course of the RNA transcription reaction. Our Systems NMR approach provides a deeper understanding of biological network dynamics by combining the dynamic resolution of biochemical assays and the multiplexing ability of 'omics'.
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Affiliation(s)
- Yaroslav Nikolaev
- Department of Biology, Institute of Molecular Biology & Biophysics, ETH Zurich, Zurich, Switzerland.
| | - Nina Ripin
- Department of Biology, Institute of Molecular Biology & Biophysics, ETH Zurich, Zurich, Switzerland
| | - Martin Soste
- Department of Biology, Institute of Biochemistry, ETH Zurich, Zurich, Switzerland
| | - Paola Picotti
- Department of Biology, Institute of Biochemistry, ETH Zurich, Zurich, Switzerland
| | - Dagmar Iber
- Department of Biosystems Science and Engineering, ETH Zurich, Zurich, Switzerland
| | - Frédéric H-T Allain
- Department of Biology, Institute of Molecular Biology & Biophysics, ETH Zurich, Zurich, Switzerland.
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14
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Akai S, Ikushiro H, Sawai T, Yano T, Kamiya N, Miyahara I. The crystal structure of homoserine dehydrogenase complexed with l-homoserine and NADPH in a closed form. J Biochem 2019; 165:185-195. [PMID: 30423116 DOI: 10.1093/jb/mvy094] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2018] [Accepted: 11/08/2018] [Indexed: 12/18/2022] Open
Abstract
Homoserine dehydrogenase from Thermus thermophilus (TtHSD) is a key enzyme in the aspartate pathway that catalyses the reversible conversion of l-aspartate-β-semialdehyde to l-homoserine (l-Hse) with NAD(P)H. We determined the crystal structures of unliganded TtHSD, TtHSD complexed with l-Hse and NADPH, and Lys99Ala and Lys195Ala mutant TtHSDs, which have no enzymatic activity, complexed with l-Hse and NADP+ at 1.83, 2.00, 1.87 and 1.93 Å resolutions, respectively. Binding of l-Hse and NADPH induced the conformational changes of TtHSD from an open to a closed form: the mobile loop containing Glu180 approached to fix l-Hse and NADPH, and both Lys99 and Lys195 could make hydrogen bonds with the hydroxy group of l-Hse. The ternary complex of TtHSDs in the closed form mimicked a Michaelis complex better than the previously reported open form structures from other species. In the crystal structure of Lys99Ala TtHSD, the productive geometry of the ternary complex was almost preserved with one new water molecule taking over the hydrogen bonds associated with Lys99, while the positions of Lys195 and l-Hse were significantly retained with those of the wild-type enzyme. These results propose new possibilities that Lys99 is the acid-base catalytic residue of HSDs.
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Affiliation(s)
- Shota Akai
- Graduate School of Science, Osaka City University, Osaka, Japan
| | - Hiroko Ikushiro
- Depertment of Biochemistry, Faculty of Medicine, Osaka Medical College, Osaka, Japan
| | - Taiki Sawai
- Depertment of Biochemistry, Faculty of Medicine, Osaka Medical College, Osaka, Japan
| | - Takato Yano
- Depertment of Biochemistry, Faculty of Medicine, Osaka Medical College, Osaka, Japan
| | - Nobuo Kamiya
- Graduate School of Science, Osaka City University, Osaka, Japan.,The OCU Advanced Research Institute for Natural Science and Technology, Osaka City University, Osaka, Japan
| | - Ikuko Miyahara
- Graduate School of Science, Osaka City University, Osaka, Japan
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15
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Li P, Liao ST, Wang JS, Zhang Q, Lv Y, Yang MH, Kong LY. Pharmacokinetic and NMR metabolomics approach to evaluate therapeutic effect of berberine and Coptidis Rhizoma for sepsis. CHINESE HERBAL MEDICINES 2019. [DOI: 10.1016/j.chmed.2018.05.005] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
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16
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Leistra AN, Curtis NC, Contreras LM. Regulatory non-coding sRNAs in bacterial metabolic pathway engineering. Metab Eng 2018; 52:190-214. [PMID: 30513348 DOI: 10.1016/j.ymben.2018.11.013] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2018] [Revised: 10/31/2018] [Accepted: 11/29/2018] [Indexed: 12/11/2022]
Abstract
Non-coding RNAs (ncRNAs) are versatile and powerful controllers of gene expression that have been increasingly linked to cellular metabolism and phenotype. In bacteria, identified and characterized ncRNAs range from trans-acting, multi-target small non-coding RNAs to dynamic, cis-encoded regulatory untranslated regions and riboswitches. These native regulators have inspired the design and construction of many synthetic RNA devices. In this work, we review the design, characterization, and impact of ncRNAs in engineering both native and exogenous metabolic pathways in bacteria. We also consider the opportunities afforded by recent high-throughput approaches for characterizing sRNA regulators and their corresponding networks to showcase their potential applications and impact in engineering bacterial metabolism.
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Affiliation(s)
- Abigail N Leistra
- McKetta Department of Chemical Engineering, University of Texas at Austin, 200 E. Dean Keeton Street Stop C0400, Austin, TX 78712, USA
| | - Nicholas C Curtis
- McKetta Department of Chemical Engineering, University of Texas at Austin, 200 E. Dean Keeton Street Stop C0400, Austin, TX 78712, USA
| | - Lydia M Contreras
- McKetta Department of Chemical Engineering, University of Texas at Austin, 200 E. Dean Keeton Street Stop C0400, Austin, TX 78712, USA.
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17
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Reznik E, Christodoulou D, Goldford JE, Briars E, Sauer U, Segrè D, Noor E. Genome-Scale Architecture of Small Molecule Regulatory Networks and the Fundamental Trade-Off between Regulation and Enzymatic Activity. Cell Rep 2018; 20:2666-2677. [PMID: 28903046 DOI: 10.1016/j.celrep.2017.08.066] [Citation(s) in RCA: 52] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2017] [Revised: 08/05/2017] [Accepted: 08/19/2017] [Indexed: 12/21/2022] Open
Abstract
Metabolic flux is in part regulated by endogenous small molecules that modulate the catalytic activity of an enzyme, e.g., allosteric inhibition. In contrast to transcriptional regulation of enzymes, technical limitations have hindered the production of a genome-scale atlas of small molecule-enzyme regulatory interactions. Here, we develop a framework leveraging the vast, but fragmented, biochemical literature to reconstruct and analyze the small molecule regulatory network (SMRN) of the model organism Escherichia coli, including the primary metabolite regulators and enzyme targets. Using metabolic control analysis, we prove a fundamental trade-off between regulation and enzymatic activity, and we combine it with metabolomic measurements and the SMRN to make inferences on the sensitivity of enzymes to their regulators. Generalizing the analysis to other organisms, we identify highly conserved regulatory interactions across evolutionarily divergent species, further emphasizing a critical role for small molecule interactions in the maintenance of metabolic homeostasis.
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Affiliation(s)
- Ed Reznik
- Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA; Department of Biomedical Engineering, Boston University, Boston, MA, USA; Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
| | - Dimitris Christodoulou
- Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland; Systems Biology Graduate School, Zurich 8057, Switzerland
| | | | - Emma Briars
- Bioinformatics Program, Boston University, Boston, MA, USA
| | - Uwe Sauer
- Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland
| | - Daniel Segrè
- Department of Biomedical Engineering, Boston University, Boston, MA, USA; Bioinformatics Program, Boston University, Boston, MA, USA; Department of Biology, Boston University, Boston, MA, USA
| | - Elad Noor
- Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland.
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18
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Wu W, Zhang Y, Huang J, Wu Y, Liu D, Chen Z. Discovery of a Potentially New Subfamily of ELFV Dehydrogenases Effective for l
-Arginine Deamination by Enzyme Mining. Biotechnol J 2017; 13. [DOI: 10.1002/biot.201700305] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2017] [Revised: 09/11/2017] [Accepted: 10/09/2017] [Indexed: 11/05/2022]
Affiliation(s)
- Wenjun Wu
- Institute of Applied Chemistry, Department of Chemical Engineering; Tsinghua University; Beijing 100084 China
| | - Ye Zhang
- Institute of Applied Chemistry, Department of Chemical Engineering; Tsinghua University; Beijing 100084 China
| | - Jinhai Huang
- Institute of Applied Chemistry, Department of Chemical Engineering; Tsinghua University; Beijing 100084 China
| | - Yao Wu
- Institute of Applied Chemistry, Department of Chemical Engineering; Tsinghua University; Beijing 100084 China
| | - Dehua Liu
- Institute of Applied Chemistry, Department of Chemical Engineering; Tsinghua University; Beijing 100084 China
- Tsinghua Innovation Center in Dongguan; Dongguan 523808 China
| | - Zhen Chen
- Institute of Applied Chemistry, Department of Chemical Engineering; Tsinghua University; Beijing 100084 China
- Tsinghua Innovation Center in Dongguan; Dongguan 523808 China
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19
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Metabolic engineering of Corynebacterium glutamicum for the production of 3-hydroxypropionic acid from glucose and xylose. Metab Eng 2017; 39:151-158. [DOI: 10.1016/j.ymben.2016.11.009] [Citation(s) in RCA: 87] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2016] [Revised: 10/21/2016] [Accepted: 11/26/2016] [Indexed: 12/29/2022]
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20
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Zhang Y, Liu D, Chen Z. Production of C2-C4 diols from renewable bioresources: new metabolic pathways and metabolic engineering strategies. BIOTECHNOLOGY FOR BIOFUELS 2017; 10:299. [PMID: 29255482 PMCID: PMC5727944 DOI: 10.1186/s13068-017-0992-9] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/28/2017] [Accepted: 12/05/2017] [Indexed: 05/17/2023]
Abstract
C2-C4 diols classically derived from fossil resource are very important bulk chemicals which have been used in a wide range of areas, including solvents, fuels, polymers, cosmetics, and pharmaceuticals. Production of C2-C4 diols from renewable resources has received significant interest in consideration of the reducing fossil resource and the increasing environmental issues. While bioproduction of certain diols like 1,3-propanediol has been commercialized in recent years, biosynthesis of many other important C2-C4 diol isomers is highly challenging due to the lack of natural synthesis pathways. Recent advances in synthetic biology have enabled the de novo design of completely new pathways to non-natural molecules from renewable feedstocks. In this study, we review recent advances in bioproduction of C2-C4 diols, focusing on new metabolic pathways and metabolic engineering strategies being developed. We also discuss the challenges and future trends toward the development of economically competitive processes for bio-based diol production.
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Affiliation(s)
- Ye Zhang
- Department of Chemical Engineering, Tsinghua University, Beijing, 100084 China
- Key Lab of Industrial Biocatalysis, Ministry of Education, Tsinghua University, Beijing, 100084 China
- Tsinghua Innovation Center in Dongguan, Dongguan, 523808 China
| | - Dehua Liu
- Department of Chemical Engineering, Tsinghua University, Beijing, 100084 China
- Key Lab of Industrial Biocatalysis, Ministry of Education, Tsinghua University, Beijing, 100084 China
- Tsinghua Innovation Center in Dongguan, Dongguan, 523808 China
- Center of Synthetic and Systems Biology, Tsinghua University, Beijing, 100084 China
| | - Zhen Chen
- Department of Chemical Engineering, Tsinghua University, Beijing, 100084 China
- Key Lab of Industrial Biocatalysis, Ministry of Education, Tsinghua University, Beijing, 100084 China
- Tsinghua Innovation Center in Dongguan, Dongguan, 523808 China
- Center of Synthetic and Systems Biology, Tsinghua University, Beijing, 100084 China
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21
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Liu Y, Li J, Du G, Chen J, Liu L. Metabolic engineering of Bacillus subtilis fueled by systems biology: Recent advances and future directions. Biotechnol Adv 2017; 35:20-30. [DOI: 10.1016/j.biotechadv.2016.11.003] [Citation(s) in RCA: 57] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2016] [Revised: 10/21/2016] [Accepted: 11/16/2016] [Indexed: 12/25/2022]
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22
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da Luz JA, Hans E, Frank D, Zeng AP. Analysis of intracellular metabolites of Corynebacterium glutamicum at high cell density with automated sampling and filtration and assessment of engineered enzymes for effective l-lysine production. Eng Life Sci 2016; 17:512-522. [PMID: 32624795 DOI: 10.1002/elsc.201600163] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2016] [Revised: 09/13/2016] [Accepted: 10/27/2016] [Indexed: 01/18/2023] Open
Abstract
Engineering of enzymes and pathways is generally required for the development of efficient strains for bioproduction processes. To this end, quantitative and reliable data of intracellular metabolites are highly desired, but often not available, especially for conditions more close to industrial applications, i.e. at high cell density and product concentration. Here, we investigated the intracellular metabolite profiles of an engineered l-lysine-producing Corynebacterium glutamicum strain and the corresponding wild-type strain to assess the impacts of deregulation of product inhibition of the key enzymes aspartate kinase and phosphoenolpyruvate carboxylase and to identify potentials for their further improvement. A bioreactor system with automated fast-sampling, filtration and on-filter quenching of the metabolism was used for a more reliable determination of intracellular metabolites in batch cultures with optical cell density (OD660) up to 40. The l-lysine-producing strain showed substantially different metabolite profiles in the amino acid metabolism, including increased intracellular pool sizes in the l-lysine-, l-homoserine- and l-threonine pathways and decreased intracellular pool sizes for all other determined amino acids. By comparing data of in vitro inhibition of the engineered enzymes and determined intracellular concentrations of the inhibitors it was found that the inferred in vivo activities of these enzymes are still significantly below their in vitro maximums. This work demonstrates the usefulness of metabolic analysis for assessing the impact of engineered enzymes and identifying targets for further strain development.
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Affiliation(s)
- Julian A da Luz
- Institute of Bioprocess- and Biosystems Engineering Hamburg University of Technology Hamburg Germany
| | - Enrico Hans
- Institute of Bioprocess- and Biosystems Engineering Hamburg University of Technology Hamburg Germany
| | - Doinita Frank
- Institute of Bioprocess- and Biosystems Engineering Hamburg University of Technology Hamburg Germany
| | - An-Ping Zeng
- Institute of Bioprocess- and Biosystems Engineering Hamburg University of Technology Hamburg Germany
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23
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Chen Z, Zeng AP. Protein engineering approaches to chemical biotechnology. Curr Opin Biotechnol 2016; 42:198-205. [DOI: 10.1016/j.copbio.2016.07.007] [Citation(s) in RCA: 62] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2016] [Revised: 06/10/2016] [Accepted: 07/30/2016] [Indexed: 01/09/2023]
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24
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Characterization of aspartate kinase and homoserine dehydrogenase from Corynebacterium glutamicum IWJ001 and systematic investigation of l-isoleucine biosynthesis. ACTA ACUST UNITED AC 2016; 43:873-85. [DOI: 10.1007/s10295-016-1763-5] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2015] [Accepted: 03/16/2016] [Indexed: 11/24/2022]
Abstract
Abstract
Previously we have characterized a threonine dehydratase mutant TDF383V (encoded by ilvA1) and an acetohydroxy acid synthase mutant AHASP176S, D426E, L575W (encoded by ilvBN1) in Corynebacterium glutamicum IWJ001, one of the best l-isoleucine producing strains. Here, we further characterized an aspartate kinase mutant AKA279T (encoded by lysC1) and a homoserine dehydrogenase mutant HDG378S (encoded by hom1) in IWJ001, and analyzed the consequences of all these mutant enzymes on amino acids production in the wild type background. In vitro enzyme tests confirmed that AKA279T is completely resistant to feed-back inhibition by l-threonine and l-lysine, and that HDG378S is partially resistant to l-threonine with the half maximal inhibitory concentration between 12 and 14 mM. In C. glutamicum ATCC13869, expressing lysC1 alone led to exclusive l-lysine accumulation, co-expressing hom1 and thrB1 with lysC1 shifted partial carbon flux from l-lysine (decreased by 50.1 %) to l-threonine (4.85 g/L) with minor l-isoleucine and no l-homoserine accumulation, further co-expressing ilvA1 completely depleted l-threonine and strongly shifted carbon flux from l-lysine (decreased by 83.0 %) to l-isoleucine (3.53 g/L). The results demonstrated the strongly feed-back resistant TDF383V might be the main driving force for l-isoleucine over-synthesis in this case, and the partially feed-back resistant HDG378S might prevent the accumulation of toxic intermediates. Information exploited from such mutation-bred production strain would be useful for metabolic engineering.
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25
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He F, Murabito E, Westerhoff HV. Synthetic biology and regulatory networks: where metabolic systems biology meets control engineering. J R Soc Interface 2016; 13:rsif.2015.1046. [PMID: 27075000 DOI: 10.1098/rsif.2015.1046] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2015] [Accepted: 03/21/2016] [Indexed: 12/25/2022] Open
Abstract
Metabolic pathways can be engineered to maximize the synthesis of various products of interest. With the advent of computational systems biology, this endeavour is usually carried out through in silico theoretical studies with the aim to guide and complement further in vitro and in vivo experimental efforts. Clearly, what counts is the result in vivo, not only in terms of maximal productivity but also robustness against environmental perturbations. Engineering an organism towards an increased production flux, however, often compromises that robustness. In this contribution, we review and investigate how various analytical approaches used in metabolic engineering and synthetic biology are related to concepts developed by systems and control engineering. While trade-offs between production optimality and cellular robustness have already been studied diagnostically and statically, the dynamics also matter. Integration of the dynamic design aspects of control engineering with the more diagnostic aspects of metabolic, hierarchical control and regulation analysis is leading to the new, conceptual and operational framework required for the design of robust and productive dynamic pathways.
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Affiliation(s)
- Fei He
- Department of Automatic Control and Systems Engineering, University of Sheffield, Sheffield S1 3JD, UK
| | - Ettore Murabito
- The Manchester Centre for Integrative Systems Biology, Manchester Institute for Biotechnology, School for Chemical Engineering and Analytical Science, University of Manchester, Manchester M1 7DN, UK
| | - Hans V Westerhoff
- The Manchester Centre for Integrative Systems Biology, Manchester Institute for Biotechnology, School for Chemical Engineering and Analytical Science, University of Manchester, Manchester M1 7DN, UK Department of Synthetic Systems Biology, Swammerdam Institute for Life Sciences, University of Amsterdam, Science Park 904, 1098 XH Amsterdam, The Netherlands Department of Molecular Cell Physiology, VU University Amsterdam, De Boelelaan 1085, 1081 HV Amsterdam, The Netherlands
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26
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Gu P, Su T, Qi Q. Novel technologies provide more engineering strategies for amino acid-producing microorganisms. Appl Microbiol Biotechnol 2016; 100:2097-105. [PMID: 26754821 DOI: 10.1007/s00253-015-7276-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2015] [Revised: 12/20/2015] [Accepted: 12/23/2015] [Indexed: 10/22/2022]
Abstract
Traditionally, amino acid-producing strains were obtained by random mutagenesis and subsequent selection. With the development of genetic and metabolic engineering techniques, various microorganisms with high amino acid production yields are now constructed by rational design of targeted biosynthetic pathways. Recently, novel technologies derived from systems and synthetic biology have emerged and open a new promising avenue towards the engineering of amino acid production microorganisms. In this review, these approaches, including rational engineering of rate-limiting enzymes, real-time sensing of end-products, pathway optimization on the chromosome, transcription factor-mediated strain improvement, and metabolic modeling and flux analysis, were summarized with regard to their application in microbial amino acid production.
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Affiliation(s)
- Pengfei Gu
- State Key Laboratory of Microbial Technology, Shandong University, Jinan, 250100, People's Republic of China
| | - Tianyuan Su
- State Key Laboratory of Microbial Technology, Shandong University, Jinan, 250100, People's Republic of China
| | - Qingsheng Qi
- State Key Laboratory of Microbial Technology, Shandong University, Jinan, 250100, People's Republic of China.
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27
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Chen Z, Liu D. Toward glycerol biorefinery: metabolic engineering for the production of biofuels and chemicals from glycerol. BIOTECHNOLOGY FOR BIOFUELS 2016; 9:205. [PMID: 27729943 PMCID: PMC5048440 DOI: 10.1186/s13068-016-0625-8] [Citation(s) in RCA: 51] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/12/2016] [Accepted: 09/24/2016] [Indexed: 05/03/2023]
Abstract
As an inevitable by-product of the biofuel industry, glycerol is becoming an attractive feedstock for biorefinery due to its abundance, low price and high degree of reduction. Converting crude glycerol into value-added products is important to increase the economic viability of the biofuel industry. Metabolic engineering of industrial strains to improve its performance and to enlarge the product spectrum of glycerol biotransformation process is highly important toward glycerol biorefinery. This review focuses on recent metabolic engineering efforts as well as challenges involved in the utilization of glycerol as feedstock for the production of fuels and chemicals, especially for the production of diols, organic acids and biofuels.
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Affiliation(s)
- Zhen Chen
- Department of Chemical Engineering, Tsinghua University, Beijing, 100084 China
- Tsinghua Innovation Center in Dongguan, Dongguan, 523808 China
| | - Dehua Liu
- Department of Chemical Engineering, Tsinghua University, Beijing, 100084 China
- Tsinghua Innovation Center in Dongguan, Dongguan, 523808 China
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28
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Ma CW, Zhou LB, Zeng AP. Engineering Biomolecular Switches for Dynamic Metabolic Control. ADVANCES IN BIOCHEMICAL ENGINEERING/BIOTECHNOLOGY 2016; 162:45-76. [DOI: 10.1007/10_2016_9] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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29
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Liu D, Evans T, Zhang F. Applications and advances of metabolite biosensors for metabolic engineering. Metab Eng 2015; 31:35-43. [DOI: 10.1016/j.ymben.2015.06.008] [Citation(s) in RCA: 136] [Impact Index Per Article: 15.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2015] [Revised: 06/23/2015] [Accepted: 06/23/2015] [Indexed: 01/01/2023]
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30
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Zhou LB, Zeng AP. Exploring lysine riboswitch for metabolic flux control and improvement of L-lysine synthesis in Corynebacterium glutamicum. ACS Synth Biol 2015; 4:729-34. [PMID: 25575181 DOI: 10.1021/sb500332c] [Citation(s) in RCA: 83] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Riboswitch, a regulatory part of an mRNA molecule that can specifically bind a metabolite and regulate gene expression, is attractive for engineering biological systems, especially for the control of metabolic fluxes in industrial microorganisms. Here, we demonstrate the use of lysine riboswitch and intracellular l-lysine as a signal to control the competing but essential metabolic by-pathways of lysine biosynthesis. To this end, we first examined the natural lysine riboswitches of Eschericia coli (ECRS) and Bacillus subtilis (BSRS) to control the expression of citrate synthase (gltA) and thus the metabolic flux in the tricarboxylic acid (TCA) cycle in E. coli. ECRS and BSRS were then successfully used to control the gltA gene and TCA cycle activity in a lysine producing strain Corynebacterium glutamicum LP917, respectively. Compared with the strain LP917, the growth of both lysine riboswitch-gltA mutants was slower, suggesting a reduced TCA cycle activity. The lysine production was 63% higher in the mutant ECRS-gltA and 38% higher in the mutant BSRS-gltA, indicating a higher metabolic flux into the lysine synthesis pathway. This is the first report on using an amino acid riboswitch for improvement of lysine biosynthesis. The lysine riboswitches can be easily adapted to dynamically control other essential but competing metabolic pathways or even be engineered as an "on-switch" to enhance the metabolic fluxes of desired metabolic pathways.
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Affiliation(s)
- Li-Bang Zhou
- Institute of Bioprocess and
Biosystems Engineering, Hamburg University of Technology Denickestrasse
15, D-21073 Hamburg, Germany
| | - An-Ping Zeng
- Institute of Bioprocess and
Biosystems Engineering, Hamburg University of Technology Denickestrasse
15, D-21073 Hamburg, Germany
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31
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Makhlynets OV, Raymond EA, Korendovych IV. Design of allosterically regulated protein catalysts. Biochemistry 2015; 54:1444-56. [PMID: 25642601 DOI: 10.1021/bi5015248] [Citation(s) in RCA: 48] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Activity of allosteric protein catalysts is regulated by an external stimulus, such as protein or small molecule binding, light activation, pH change, etc., at a location away from the active site of the enzyme. Since its original introduction in 1961, the concept of allosteric regulation has undergone substantial expansion, and many, if not most, enzymes have been shown to possess some degree of allosteric regulation. The ability to create new catalysts that can be turned on and off using allosteric interactions would greatly expand the chemical biology toolbox and will allow for detection of environmental pollutants and disease biomarkers and facilitate studies of cellular processes and metal homeostasis. Thus, design of allosterically regulated protein catalysts represents an actively growing area of research. In this paper, we describe various approaches to achieving regulation of catalysis.
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Affiliation(s)
- Olga V Makhlynets
- Department of Chemistry, Syracuse University , 111 College Place, Syracuse, New York 13244, United States
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