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Su Z, Guo B, Xu H, Yuan Z, Liu H, Guo T, Deng Z, Zhang Y, Yin D, Liu C, Chen JH, Rao Y. Synthetic Biology-based Construction of Unnatural Perylenequinones with Improved Photodynamic Anticancer Activities. Angew Chem Int Ed Engl 2024; 63:e202317726. [PMID: 38258338 DOI: 10.1002/anie.202317726] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2023] [Revised: 01/03/2024] [Accepted: 01/22/2024] [Indexed: 01/24/2024]
Abstract
The construction of structural complexity and diversity of natural products is crucial for drug discovery and development. To overcome high dark toxicity and poor photostability of natural photosensitizer perylenequinones (PQs) for photodynamic therapy, herein, we aim to introduce the structural complexity and diversity to biosynthesize the desired unnatural PQs in fungus Cercospora through synthetic biology-based strategy. Thus, we first elucidate the intricate biosynthetic pathways of class B PQs and reveal how the branching enzymes create their structural complexity and diversity from a common ancestor. This enables the rational reprogramming of cercosporin biosynthetic pathway in Cercospora to generate diverse unnatural PQs without chemical modification. Among them, unnatural cercosporin A displays remarkably low dark toxicity and high photostability with retention of great photodynamic anticancer and antimicrobial activities. Moreover, it is found that, unlike cercosporin, unnatural cercosporin A could be selectively accumulated in cancer cells, providing potential targets for drug development. Therefore, this work provides a comprehensive foundation for preparing unnatural products with customized functions through synthetic biology-based strategies, thus facilitating drug discovery pipelines from nature.
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Affiliation(s)
- Zengping Su
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, 214122, P. R. China
| | - Baodang Guo
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, 214122, P. R. China
| | - Huibin Xu
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, 214122, P. R. China
| | - Zhenbo Yuan
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, 214122, P. R. China
| | - Huiling Liu
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, 214122, P. R. China
| | - Tao Guo
- Wuxi School of Medicine, Jiangnan University, Wuxi, 214122, P. R. China
| | - Zhiwei Deng
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, 214122, P. R. China
| | - Yan Zhang
- School of Life Sciences and Health Engineering, Jiangnan University, Wuxi, 214122, P. R. China
| | - Dejing Yin
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, 214122, P. R. China
| | - Changmei Liu
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, 214122, P. R. China
| | - Jian-Huan Chen
- Wuxi School of Medicine, Jiangnan University, Wuxi, 214122, P. R. China
| | - Yijian Rao
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, 214122, P. R. China
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2
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Naz S, Liu P, Liu C, Cui M, Ma H. In silico prediction of mutation sites for anthranilate synthase from Serratia marcesens to deregulate tryptophan feedback inhibition. J Biomol Struct Dyn 2023:1-11. [PMID: 37676253 DOI: 10.1080/07391102.2023.2253910] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2023] [Accepted: 08/24/2023] [Indexed: 09/08/2023]
Abstract
Allosteric feedback inhibition of the committed step in amino acid biosynthetic pathways is a major concern for production of amino acids at industrial scale. Anthranilate synthase (AS) catalyzes the first reaction of tryptophan biosynthetic pathway found in microorganisms and is feedback inhibited by its own product i.e. tryptophan. Here, we identified new mutant sites in AS using computational mutagenesis approach. MD simulations (20 ns) followed by MMPBSA and per residue decomposition energy analysis identified seven amino acid residues with best binding affinity for tryptophan. All 19 mutant structures were generated for each identified amino acid residue followed by simulation to evaluate effect of mutation on protein stability. Later, molecular docking studies were employed to generate mutant-tryptophan complex and structures with binding energies (kcal/mol) much higher than wild-type AS were selected. Finally, two mutants i.e., S37W and S37H were identified on the basis of positive binding scores and loss of tryptophan binding inside pocket. Further, MD simulations run for 200 ns were performed over these mutant-tryptophan complexes followed by RMSD, RMSF, radius of gyration , solvent accessible surface area , intra-protein hydrogen bond numbers, principal component analysis, free energy landscape (FEL) and secondary structure analysis to rationale effect of mutations on stability of protein. Cross correlation analysis of mutant site amino acids (S37W) with key residues of catalytic site (G325, T326, H395 and G482) was done to evaluate the effect of mutations on catalytic site conformation. Current computational mutagenesis approach predicted two mutants S37W and S37H with proposed deregulated feedback inhibition by tryptophan and retained catalytic activity.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Sadia Naz
- Biodesign Center, Key Laboratory of Engineering Biology for Low-carbon Manufacturing, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
| | - Pi Liu
- Biodesign Center, Key Laboratory of Engineering Biology for Low-carbon Manufacturing, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
| | - Cui Liu
- Biodesign Center, Key Laboratory of Engineering Biology for Low-carbon Manufacturing, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
| | - Mengfei Cui
- Biodesign Center, Key Laboratory of Engineering Biology for Low-carbon Manufacturing, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
| | - Hongwu Ma
- Biodesign Center, Key Laboratory of Engineering Biology for Low-carbon Manufacturing, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
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3
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Qiu Y, Lei P, Wang R, Sun L, Luo Z, Li S, Xu H. Kluyveromyces as promising yeast cell factories for industrial bioproduction: From bio-functional design to applications. Biotechnol Adv 2023; 64:108125. [PMID: 36870581 DOI: 10.1016/j.biotechadv.2023.108125] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2022] [Revised: 02/26/2023] [Accepted: 02/27/2023] [Indexed: 03/06/2023]
Abstract
As the two most widely used Kluyveromyces yeast, Kluyveromyces marxianus and K. lactis have gained increasing attention as microbial chassis in biocatalysts, biomanufacturing and the utilization of low-cost raw materials owing to their high suitability to these applications. However, due to slow progress in the development of molecular genetic manipulation tools and synthetic biology strategies, Kluyveromyces yeast cell factories as biological manufacturing platforms have not been fully developed. In this review, we provide a comprehensive overview of the attractive characteristics and applications of Kluyveromyces cell factories, with special emphasis on the development of molecular genetic manipulation tools and systems engineering strategies for synthetic biology. In addition, future avenues in the development of Kluyveromyces cell factories for the utilization of simple carbon compounds as substrates, the dynamic regulation of metabolic pathways, and for rapid directed evolution of robust strains are proposed. We expect that more synthetic systems, synthetic biology tools and metabolic engineering strategies will adapt to and optimize for Kluyveromyces cell factories to achieve green biofabrication of multiple products with higher efficiency.
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Affiliation(s)
- Yibin Qiu
- College of Food Science and Light Industry, Nanjing Tech University, Nanjing 211816, PR China; State Key Laboratory of Materials-Oriented Chemical Engineering, Nanjing Tech University, Nanjing 211816, PR China
| | - Peng Lei
- College of Food Science and Light Industry, Nanjing Tech University, Nanjing 211816, PR China; State Key Laboratory of Materials-Oriented Chemical Engineering, Nanjing Tech University, Nanjing 211816, PR China
| | - Rui Wang
- College of Food Science and Light Industry, Nanjing Tech University, Nanjing 211816, PR China; State Key Laboratory of Materials-Oriented Chemical Engineering, Nanjing Tech University, Nanjing 211816, PR China
| | - Liang Sun
- College of Food Science and Light Industry, Nanjing Tech University, Nanjing 211816, PR China; State Key Laboratory of Materials-Oriented Chemical Engineering, Nanjing Tech University, Nanjing 211816, PR China
| | - Zhengshan Luo
- College of Food Science and Light Industry, Nanjing Tech University, Nanjing 211816, PR China; State Key Laboratory of Materials-Oriented Chemical Engineering, Nanjing Tech University, Nanjing 211816, PR China
| | - Sha Li
- College of Food Science and Light Industry, Nanjing Tech University, Nanjing 211816, PR China; State Key Laboratory of Materials-Oriented Chemical Engineering, Nanjing Tech University, Nanjing 211816, PR China.
| | - Hong Xu
- College of Food Science and Light Industry, Nanjing Tech University, Nanjing 211816, PR China; State Key Laboratory of Materials-Oriented Chemical Engineering, Nanjing Tech University, Nanjing 211816, PR China.
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4
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Lu S, Zheng F, Wen L, He Y, Wang D, Wu M, Wang B. Yeast engineering technologies and their applications to the food industry. FOOD BIOTECHNOL 2021. [DOI: 10.1080/08905436.2021.1942037] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Affiliation(s)
- Siyan Lu
- Department of Food Science and Engineering, Jilin Agricultural University, Changchun, China
| | - Fei Zheng
- Jilin Ginseng Academy, Changchun University of Chinese Medicine, Changchun, China
| | - Liankui Wen
- Department of Food Science and Engineering, Jilin Agricultural University, Changchun, China
| | - Yang He
- Department of Food Science and Engineering, Jilin Agricultural University, Changchun, China
| | - Donghui Wang
- SBU of Agriculture, Sinochem Group Co., Ltd., Beijing, China
| | - Manyu Wu
- Department of Food Science and Engineering, Jilin Agricultural University, Changchun, China
| | - Bixiang Wang
- Department of Food Science and Engineering, Jilin Agricultural University, Changchun, China
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Mehrshahi P, Nguyen GTDT, Gorchs Rovira A, Sayer A, Llavero-Pasquina M, Lim Huei Sin M, Medcalf EJ, Mendoza-Ochoa GI, Scaife MA, Smith AG. Development of Novel Riboswitches for Synthetic Biology in the Green Alga Chlamydomonas. ACS Synth Biol 2020; 9:1406-1417. [PMID: 32496044 PMCID: PMC7309327 DOI: 10.1021/acssynbio.0c00082] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Riboswitches are RNA regulatory elements that bind specific ligands to control gene expression. Because of their modular composition, where a ligand-sensing aptamer domain is combined with an expression platform, riboswitches offer unique tools for synthetic biology applications. Here we took a mutational approach to determine functionally important nucleotide residues in the thiamine pyrophosphate (TPP) riboswitch in the THI4 gene of the model alga Chlamydomonas reinhardtii, allowing us to carry out aptamer swap using THIC aptamers from Chlamydomonas and Arabidopsis thaliana. These chimeric riboswitches displayed a distinct specificity and dynamic range of responses to different ligands. Our studies demonstrate ease of assembly as 5'UTR DNA parts, predictability of output, and utility for controlled production of a high-value compound in Chlamydomonas. The simplicity of riboswitch incorporation in current design platforms will facilitate the generation of genetic circuits to advance synthetic biology and metabolic engineering of microalgae.
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Affiliation(s)
- Payam Mehrshahi
- Department of Plant Sciences, University of Cambridge, Downing Street, Cambridge CB2 3EA, U.K
| | - Ginnie Trinh D. T. Nguyen
- Glanbia Performance Nutrition Canada Inc., 3500 Lacey Road, Suite 1200, Downers Grove, Illinois 60515, United States
| | - Aleix Gorchs Rovira
- Department of Plant Sciences, University of Cambridge, Downing Street, Cambridge CB2 3EA, U.K
| | - Andrew Sayer
- Department of Plant Sciences, University of Cambridge, Downing Street, Cambridge CB2 3EA, U.K
| | - Marcel Llavero-Pasquina
- Department of Plant Sciences, University of Cambridge, Downing Street, Cambridge CB2 3EA, U.K
| | - Michelle Lim Huei Sin
- John Swire & Sons (H.K.) Ltd. 33/F One Pacific Place, 88 Queensway, Hong Kong, China
| | - Elliot J. Medcalf
- Department of Plant Sciences, University of Cambridge, Downing Street, Cambridge CB2 3EA, U.K
| | | | - Mark A. Scaife
- Mara Renewables Corporation, 101A Research Drive, Dartmouth, Nova Scotia B2Y 4T6, Canada
| | - Alison G. Smith
- Department of Plant Sciences, University of Cambridge, Downing Street, Cambridge CB2 3EA, U.K
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6
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Antelo-Varela M, Aguilar Suárez R, Bartel J, Bernal-Cabas M, Stobernack T, Sura T, van Dijl JM, Maaß S, Becher D. Membrane Modulation of Super-Secreting "midi Bacillus" Expressing the Major Staphylococcus aureus Antigen - A Mass-Spectrometry-Based Absolute Quantification Approach. Front Bioeng Biotechnol 2020; 8:143. [PMID: 32185169 PMCID: PMC7059095 DOI: 10.3389/fbioe.2020.00143] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2019] [Accepted: 02/12/2020] [Indexed: 01/18/2023] Open
Abstract
Bacillus subtilis has been extensively used as a microbial cell factory for industrial enzymes due to its excellent capacities for protein secretion and large-scale fermentation. This bacterium is also an attractive host for biopharmaceutical production. However, the secretion potential of this organism is not fully utilized yet, mostly due to a limited understanding of critical rearrangements in the membrane proteome upon high-level protein secretion. Recently, it was shown that bottlenecks in heterologous protein secretion can be resolved by genome minimization. Here, we present for the first time absolute membrane protein concentrations of a genome-reduced B. subtilis strain ("midiBacillus") expressing the immunodominant Staphylococcus aureus antigen A (IsaA). We quantitatively characterize the membrane proteome adaptation of midiBacillus during production stress on the level of molecules per cell for more than 400 membrane proteins, including determination of protein concentrations for ∼61% of the predicted transporters. We demonstrate that ∼30% of proteins with unknown functions display a significant increase in abundance, confirming the crucial role of membrane proteins in vital biological processes. In addition, our results show an increase of proteins dedicated to translational processes in response to IsaA induction. For the first time reported, we provide accumulation rates of a heterologous protein, demonstrating that midiBacillus secretes 2.41 molecules of IsaA per minute. Despite the successful secretion of this protein, it was found that there is still some IsaA accumulation occurring in the cytosol and membrane fraction, leading to a severe secretion stress response, and a clear adjustment of the cell's array of transporters. This quantitative dataset offers unprecedented insights into bioproduction stress responses in a synthetic microbial cell.
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Affiliation(s)
- Minia Antelo-Varela
- Centre of Functional Genomics of Microbes, Department of Microbial Proteomics, Institute of Microbiology, University of Greifswald, Greifswald, Germany
| | - Rocío Aguilar Suárez
- Department of Medical Microbiology, University Medical Center Groningen, University of Groningen, Groningen, Netherlands
| | - Jürgen Bartel
- Centre of Functional Genomics of Microbes, Department of Microbial Proteomics, Institute of Microbiology, University of Greifswald, Greifswald, Germany
| | - Margarita Bernal-Cabas
- Department of Medical Microbiology, University Medical Center Groningen, University of Groningen, Groningen, Netherlands
| | - Tim Stobernack
- Department of Medical Microbiology, University Medical Center Groningen, University of Groningen, Groningen, Netherlands
| | - Thomas Sura
- Centre of Functional Genomics of Microbes, Department of Microbial Proteomics, Institute of Microbiology, University of Greifswald, Greifswald, Germany
| | - Jan Maarten van Dijl
- Department of Medical Microbiology, University Medical Center Groningen, University of Groningen, Groningen, Netherlands
| | - Sandra Maaß
- Centre of Functional Genomics of Microbes, Department of Microbial Proteomics, Institute of Microbiology, University of Greifswald, Greifswald, Germany
| | - Dörte Becher
- Centre of Functional Genomics of Microbes, Department of Microbial Proteomics, Institute of Microbiology, University of Greifswald, Greifswald, Germany
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7
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Wege C, Koch C. From stars to stripes: RNA-directed shaping of plant viral protein templates-structural synthetic virology for smart biohybrid nanostructures. WILEY INTERDISCIPLINARY REVIEWS-NANOMEDICINE AND NANOBIOTECHNOLOGY 2019; 12:e1591. [PMID: 31631528 DOI: 10.1002/wnan.1591] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 06/04/2019] [Revised: 08/04/2019] [Accepted: 08/26/2019] [Indexed: 12/12/2022]
Abstract
The self-assembly of viral building blocks bears exciting prospects for fabricating new types of bionanoparticles with multivalent protein shells. These enable a spatially controlled immobilization of functionalities at highest surface densities-an increasing demand worldwide for applications from vaccination to tissue engineering, biocatalysis, and sensing. Certain plant viruses hold particular promise because they are sustainably available, biodegradable, nonpathogenic for mammals, and amenable to in vitro self-organization of virus-like particles. This offers great opportunities for their redesign into novel "green" carrier systems by spatial and structural synthetic biology approaches, as worked out here for the robust nanotubular tobacco mosaic virus (TMV) as prime example. Natural TMV of 300 x 18 nm is built from more than 2,100 identical coat proteins (CPs) helically arranged around a 6,395 nucleotides ssRNA. In vitro, TMV-like particles (TLPs) may self-assemble also from modified CPs and RNAs if the latter contain an Origin of Assembly structure, which initiates a bidirectional encapsidation. By way of tailored RNA, the process can be reprogrammed to yield uncommon shapes such as branched nanoobjects. The nonsymmetric mechanism also proceeds on 3'-terminally immobilized RNA and can integrate distinct CP types in blends or serially. Other emerging plant virus-deduced systems include the usually isometric cowpea chlorotic mottle virus (CCMV) with further strikingly altered structures up to "cherrybombs" with protruding nucleic acids. Cartoon strips and pictorial descriptions of major RNA-based strategies induct the reader into a rare field of nanoconstruction that can give rise to utile soft-matter architectures for complex tasks. This article is categorized under: Biology-Inspired Nanomaterials > Protein and Virus-Based Structures Nanotechnology Approaches to Biology > Nanoscale Systems in Biology Biology-Inspired Nanomaterials > Nucleic Acid-Based Structures.
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Affiliation(s)
- Christina Wege
- Department of Molecular Biology and Plant Virology, Institute of Biomaterials and Biomolecular Systems, University of Stuttgart, Stuttgart, Germany
| | - Claudia Koch
- Department of Molecular Biology and Plant Virology, Institute of Biomaterials and Biomolecular Systems, University of Stuttgart, Stuttgart, Germany
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8
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Lee SY, Kim HU, Chae TU, Cho JS, Kim JW, Shin JH, Kim DI, Ko YS, Jang WD, Jang YS. A comprehensive metabolic map for production of bio-based chemicals. Nat Catal 2019. [DOI: 10.1038/s41929-018-0212-4] [Citation(s) in RCA: 282] [Impact Index Per Article: 56.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
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9
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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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10
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Mora-Villalobos JA, Zeng AP. Protein and pathway engineering for the biosynthesis of 5-hydroxytryptophan in Escherichia coli. Eng Life Sci 2017; 17:892-899. [PMID: 32624837 DOI: 10.1002/elsc.201700064] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2017] [Revised: 05/16/2017] [Accepted: 05/29/2017] [Indexed: 11/06/2022] Open
Abstract
The hydroxylation of tryptophan is an important reaction in the biosynthesis of natural products. 5-Hydroxytryptophan (5HTP) is not only an important compound for its pharmaceutical value but also because it is the precursor of other molecules, such as serotonin. In this study, we have extended the metabolism of an E. coli strain to produce 5HTP. Aromatic amino acid hydroxylase from Cupriavidus taiwanensis (CtAAAH) was selected using an in silico structure-based approach. We have predicted and selected several substrate-determining residues using sequence, phylogenetic and functional divergence analyses; we also did rational design on CtAAAH to shift the enzyme preference from phenylalanine to tryptophan. Whole cell bioconversion assays were used to show the effect of predicted sites. In general, all of them decreased the preference toward phenylalanine and increased the tryptophan synthesis activity. The best performer, CtAAAH-W192F, was transformed into a strain that had the tryptophanase gene disrupted and carried a human tetrahydrobiopterin (BH4) regeneration pathway. The resulting strain was capable of synthesizing 2.5 mM 5HTP after 24 hours. This work demonstrates the application of computational approaches for protein engineering and further coupling with the bacterial metabolism.
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Affiliation(s)
- José-Aníbal Mora-Villalobos
- Institute of Bioprocess and Biosystems Engineering Hamburg University of Technology Hamburg Germany.,Centro Nacional de Innovaciones Biotecnológicas Centro Nacional de Alta Tecnología San Jose Costa Rica
| | - An-Ping Zeng
- Institute of Bioprocess and Biosystems Engineering Hamburg University of Technology Hamburg Germany
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Chen X, Gao C, Guo L, Hu G, Luo Q, Liu J, Nielsen J, Chen J, Liu L. DCEO Biotechnology: Tools To Design, Construct, Evaluate, and Optimize the Metabolic Pathway for Biosynthesis of Chemicals. Chem Rev 2017; 118:4-72. [DOI: 10.1021/acs.chemrev.6b00804] [Citation(s) in RCA: 109] [Impact Index Per Article: 15.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Xiulai Chen
- State
Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, China
- Key
Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China
| | - Cong Gao
- State
Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, China
- Key
Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China
| | - Liang Guo
- State
Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, China
- Key
Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China
| | - Guipeng Hu
- State
Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, China
- Key
Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China
| | - Qiuling Luo
- State
Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, China
- Key
Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China
| | - Jia Liu
- State
Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, China
- Key
Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China
| | - Jens Nielsen
- Department
of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg SE-412 96, Sweden
- Novo
Nordisk Foundation Center for Biosustainability, Technical University of Denmark, DK2800 Lyngby, Denmark
| | - Jian Chen
- State
Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, China
- Key
Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China
| | - Liming Liu
- State
Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, China
- Department
of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg SE-412 96, Sweden
- Key
Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China
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12
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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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13
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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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14
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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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15
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Metabolic engineering of Corynebacterium glutamicum for the de novo production of ethylene glycol from glucose. Metab Eng 2016; 33:12-18. [DOI: 10.1016/j.ymben.2015.10.013] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2015] [Revised: 09/14/2015] [Accepted: 10/30/2015] [Indexed: 11/23/2022]
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16
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Chen Z, Wu Y, Huang J, Liu D. Metabolic engineering of Klebsiella pneumoniae for the de novo production of 2-butanol as a potential biofuel. BIORESOURCE TECHNOLOGY 2015; 197:260-5. [PMID: 26342337 DOI: 10.1016/j.biortech.2015.08.086] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/08/2015] [Revised: 08/14/2015] [Accepted: 08/17/2015] [Indexed: 05/14/2023]
Abstract
Butanol isomers are important bulk chemicals and promising fuel substitutes. The inevitable toxicity of n-butanol and isobutanol to microbial cells hinders their final titers. In this study, we attempt to engineer Klebsiella pneumoniae for the de novo production of 2-butanol, another butanol isomer which shows lower toxicity than n-butanol and isobutanol. 2-Butanol synthesis was realized by the extension of the native meso-2,3-butanediol synthesis pathway with the introduction of diol dehydratase and secondary alcohol dehydrogenase. By the screening of different secondary alcohol dehydrogenases and diol dehydratases, 320mg/L of 2-butanol was produced by the best engineered K. pneumoniae. The production was increased to 720mg/L by knocking out the ldhA gene and appropriate addition of coenzyme B12. Further improvement of 2-butanol to 1030mg/L was achieved by protein engineering of diol dehydratase. This work lays the basis for the metabolic engineering of microorganism for the production of 2-butanol as potential biofuel.
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Affiliation(s)
- Zhen Chen
- Institute of Applied Chemistry, Department of Chemical Engineering, Tsinghua University, Beijing 100084, China; Tsinghua Innovation Center in Dongguan, Dongguan 523808, China.
| | - Yao Wu
- 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
| | - Dehua Liu
- 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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17
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Marine extremophiles: a source of hydrolases for biotechnological applications. Mar Drugs 2015; 13:1925-65. [PMID: 25854643 PMCID: PMC4413194 DOI: 10.3390/md13041925] [Citation(s) in RCA: 121] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2014] [Revised: 03/22/2015] [Accepted: 03/25/2015] [Indexed: 12/26/2022] Open
Abstract
The marine environment covers almost three quarters of the planet and is where evolution took its first steps. Extremophile microorganisms are found in several extreme marine environments, such as hydrothermal vents, hot springs, salty lakes and deep-sea floors. The ability of these microorganisms to support extremes of temperature, salinity and pressure demonstrates their great potential for biotechnological processes. Hydrolases including amylases, cellulases, peptidases and lipases from hyperthermophiles, psychrophiles, halophiles and piezophiles have been investigated for these reasons. Extremozymes are adapted to work in harsh physical-chemical conditions and their use in various industrial applications such as the biofuel, pharmaceutical, fine chemicals and food industries has increased. The understanding of the specific factors that confer the ability to withstand extreme habitats on such enzymes has become a priority for their biotechnological use. The most studied marine extremophiles are prokaryotes and in this review, we present the most studied archaea and bacteria extremophiles and their hydrolases, and discuss their use for industrial applications.
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Chen Z, Rappert S, Zeng AP. Rational design of allosteric regulation of homoserine dehydrogenase by a nonnatural inhibitor L-lysine. ACS Synth Biol 2015; 4:126-31. [PMID: 24344690 DOI: 10.1021/sb400133g] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
Allosteric proteins, which can sense different signals, are interesting biological parts for synthetic biology. In particular, the design of an artificial allosteric enzyme to sense an unnatural signal is both challenging and highly desired, for example, for a precise and dynamical control of fluxes of growth-essential but byproduct pathways in metabolic engineering of industrial microorganisms. In this work, we used homoserine dehydrogenase (HSDH) of Corynebacterium glutamicum, which is naturally allosterically regulated by threonine and isoleucine, as an example to demonstrate the feasibility of reengineering an allosteric enzyme to respond to an unnatural inhibitor L-lysine. For this purpose, the natural threonine binding sites of HSD were first predicted and verified by mutagenesis experiments. The threonine binding sites were then engineered to a lysine binding pocket. The reengineered HSD only responds to lysine inhibition but not to threonine. This is a significant step toward the construction of artificial molecular circuits for dynamic control of growth-essential byproduct formation pathway for lysine biosynthesis.
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Affiliation(s)
- Zhen Chen
- Institute
of Bioprocess and
Biosystems Engineering, Hamburg University of Technology Denickestrasse
15, D-21073 Hamburg, Germany
| | - Sugima Rappert
- 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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19
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Chen Z, Geng F, Zeng AP. Protein design and engineering of a de novo pathway for microbial production of 1,3-propanediol from glucose. Biotechnol J 2014; 10:284-9. [DOI: 10.1002/biot.201400235] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2014] [Revised: 05/25/2014] [Accepted: 06/06/2014] [Indexed: 01/25/2023]
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20
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Yin J, Chen JC, Wu Q, Chen GQ. Halophiles, coming stars for industrial biotechnology. Biotechnol Adv 2014; 33:1433-42. [PMID: 25447783 DOI: 10.1016/j.biotechadv.2014.10.008] [Citation(s) in RCA: 163] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2014] [Revised: 10/10/2014] [Accepted: 10/19/2014] [Indexed: 10/24/2022]
Abstract
Industrial biotechnology aims to produce chemicals, materials and biofuels to ease the challenges of shortage on petroleum. However, due to the disadvantages of bioprocesses including energy consuming sterilization, high fresh water consumption, discontinuous fermentation to avoid microbial contamination, highly expensive stainless steel fermentation facilities and competing substrates for human consumption, industrial biotechnology is less competitive compared with chemical processes. Recently, halophiles have shown promises to overcome these shortcomings. Due to their unique halophilic properties, some halophiles are able to grow in high pH and high NaCl containing medium under higher temperature, allowing fermentation processes to run contamination free under unsterile conditions and continuous way. At the same time, genetic manipulation methods have been developed for halophiles. So far, halophiles have been used to produce bioplastics polyhydroxyalkanoates (PHA), ectoines, enzymes, and bio-surfactants. Increasing effects have been made to develop halophiles into a low cost platform for bioprocessing with advantages of low energy, less fresh water consumption, low fixed capital investment, and continuous production.
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Affiliation(s)
- Jin Yin
- MOE Key Lab of Bioinformatics, School of Life Science, Tsinghua-Peking Center for Life Sciences, Tsinghua University, Beijing 100084, China
| | - Jin-Chun Chen
- MOE Key Lab of Bioinformatics, School of Life Science, Tsinghua-Peking Center for Life Sciences, Tsinghua University, Beijing 100084, China
| | - Qiong Wu
- MOE Key Lab of Bioinformatics, School of Life Science, Tsinghua-Peking Center for Life Sciences, Tsinghua University, Beijing 100084, China
| | - Guo-Qiang Chen
- MOE Key Lab of Bioinformatics, School of Life Science, Tsinghua-Peking Center for Life Sciences, Tsinghua University, Beijing 100084, China.
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21
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A de novo NADPH generation pathway for improving lysine production of Corynebacterium glutamicum by rational design of the coenzyme specificity of glyceraldehyde 3-phosphate dehydrogenase. Metab Eng 2014; 25:30-7. [PMID: 24953302 DOI: 10.1016/j.ymben.2014.06.005] [Citation(s) in RCA: 115] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2014] [Revised: 05/15/2014] [Accepted: 06/11/2014] [Indexed: 11/20/2022]
Abstract
Engineering the cofactor availability is a common strategy of metabolic engineering to improve the production of many industrially important compounds. In this work, a de novo NADPH generation pathway is proposed by altering the coenzyme specificity of a native NAD-dependent glyceraldehyde 3-phosphate dehydrogenase (GAPDH) to NADP, which consequently has the potential to produce additional NADPH in the glycolytic pathway. Specifically, the coenzyme specificity of GAPDH of Corynebacterium glutamicum is systematically manipulated by rational protein design and the effect of the manipulation for cellular metabolism and lysine production is evaluated. By a combinatorial modification of four key residues within the coenzyme binding sites, different GAPDH mutants with varied coenzyme specificity were constructed. While increasing the catalytic efficiency of GAPDH towards NADP enhanced lysine production in all of the tested mutants, the most significant improvement of lysine production (~60%) was achieved with the mutant showing similar preference towards both NAD and NADP. Metabolic flux analysis with (13)C isotope studies confirmed that there was no significant change of flux towards the pentose phosphate pathway and the increased lysine yield was mainly attributed to the NADPH generated by the mutated GAPDH. The present study highlights the importance of protein engineering as a key strategy in de novo pathway design and overproduction of desired products.
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22
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Engineering redox balance through cofactor systems. Trends Biotechnol 2014; 32:337-43. [DOI: 10.1016/j.tibtech.2014.04.003] [Citation(s) in RCA: 117] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2013] [Revised: 03/26/2014] [Accepted: 04/02/2014] [Indexed: 12/12/2022]
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23
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Kang Z, Zhang C, Zhang J, Jin P, Zhang J, Du G, Chen J. Small RNA regulators in bacteria: powerful tools for metabolic engineering and synthetic biology. Appl Microbiol Biotechnol 2014; 98:3413-24. [DOI: 10.1007/s00253-014-5569-y] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2013] [Revised: 01/22/2014] [Accepted: 01/23/2014] [Indexed: 12/17/2022]
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24
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Deregulation of feedback inhibition of phosphoenolpyruvate carboxylase for improved lysine production in Corynebacterium glutamicum. Appl Environ Microbiol 2013; 80:1388-93. [PMID: 24334667 DOI: 10.1128/aem.03535-13] [Citation(s) in RCA: 77] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Allosteric regulation of phosphoenolpyruvate carboxylase (PEPC) controls the metabolic flux distribution of anaplerotic pathways. In this study, the feedback inhibition of Corynebacterium glutamicum PEPC was rationally deregulated, and its effect on metabolic flux redistribution was evaluated. Based on rational protein design, six PEPC mutants were designed, and all of them showed significantly reduced sensitivity toward aspartate and malate inhibition. Introducing one of the point mutations (N917G) into the ppc gene, encoding PEPC of the lysine-producing strain C. glutamicum LC298, resulted in ∼37% improved lysine production. In vitro enzyme assays and (13)C-based metabolic flux analysis showed ca. 20 and 30% increases in the PEPC activity and corresponding flux, respectively, in the mutant strain. Higher demand for NADPH in the mutant strain increased the flux toward pentose phosphate pathway, which increased the supply of NADPH for enhanced lysine production. The present study highlights the importance of allosteric regulation on the flux control of central metabolism. The strategy described here can also be implemented to improve other oxaloacetate-derived products.
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25
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Chen Z, Zeng AP. Protein design in systems metabolic engineering for industrial strain development. Biotechnol J 2013; 8:523-33. [PMID: 23589416 DOI: 10.1002/biot.201200238] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2012] [Revised: 01/24/2013] [Accepted: 02/27/2013] [Indexed: 12/20/2022]
Abstract
Accelerating the process of industrial bacterial host strain development, aimed at increasing productivity, generating new bio-products or utilizing alternative feedstocks, requires the integration of complementary approaches to manipulate cellular metabolism and regulatory networks. Systems metabolic engineering extends the concept of classical metabolic engineering to the systems level by incorporating the techniques used in systems biology and synthetic biology, and offers a framework for the development of the next generation of industrial strains. As one of the most useful tools of systems metabolic engineering, protein design allows us to design and optimize cellular metabolism at a molecular level. Here, we review the current strategies of protein design for engineering cellular synthetic pathways, metabolic control systems and signaling pathways, and highlight the challenges of this subfield within the context of systems metabolic engineering.
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Affiliation(s)
- Zhen Chen
- Institute of Bioprocess and Biosystems Engineering, Hamburg University of Technology, Hamburg, Germany
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26
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Marcheschi RJ, Gronenberg LS, Liao JC. Protein engineering for metabolic engineering: current and next-generation tools. Biotechnol J 2013; 8:545-55. [PMID: 23589443 DOI: 10.1002/biot.201200371] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2012] [Revised: 03/07/2013] [Accepted: 03/20/2013] [Indexed: 11/10/2022]
Abstract
Protein engineering in the context of metabolic engineering is increasingly important to the field of industrial biotechnology. As the demand for biologically produced food, fuels, chemicals, food additives, and pharmaceuticals continues to grow, the ability to design and modify proteins to accomplish new functions will be required to meet the high productivity demands for the metabolism of engineered organisms. We review advances in selecting, modeling, and engineering proteins to improve or alter their activity. Some of the methods have only recently been developed for general use and are just beginning to find greater application in the metabolic engineering community. We also discuss methods of generating random and targeted diversity in proteins to generate mutant libraries for analysis. Recent uses of these techniques to alter cofactor use; produce non-natural amino acids, alcohols, and carboxylic acids; and alter organism phenotypes are presented and discussed as examples of the successful engineering of proteins for metabolic engineering purposes.
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Affiliation(s)
- Ryan J Marcheschi
- Department of Chemical and Biomolecular Engineering, University of California, Los Angeles, CA, USA
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27
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Chen Z, Jandt U, Rappert S, Zeng AP. Proteindesign für die Entwicklung von industriellen Mikroorganismen. ACTA ACUST UNITED AC 2013. [DOI: 10.1007/s12268-013-0276-2] [Citation(s) in RCA: 3] [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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28
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Compartmentalization and metabolic channeling for multienzymatic biosynthesis: practical strategies and modeling approaches. ADVANCES IN BIOCHEMICAL ENGINEERING/BIOTECHNOLOGY 2013; 137:41-65. [PMID: 23934361 DOI: 10.1007/10_2013_221] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
: The construction of efficient enzyme complexes for multienzymatic biosynthesis is of increasing interest in order to achieve maximum yield and to minimize the interference due to shortcomings that are typical for straightforward one-pot multienzyme catalysis. These include product or intermediate feedback inhibition, degeneration, and diffusive losses of reaction intermediates, consumption of co-factors, and others. The main mechanisms in nature to tackle these effects in transient or stable protein associations are the formation of metabolic channeling and microcompartments, processes that are desirable also for multienzymatic biosynthesis in vitro. This chapter provides an overview over two main aspects. First, numerous recent strategies for establishing compartmentalized multienzyme associations and constructed synthetic enzyme complexes are reviewed. Second, the computational methods at hand to investigate and optimize such associations systematically, especially with focus on large multienzyme complexes and metabolic channeling, are discussed. Perspectives on future studies of multienzymatic biosynthesis concerning compartmentalization and metabolic channeling are presented.
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29
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Systems metabolic engineering, industrial biotechnology and microbial cell factories. Microb Cell Fact 2012; 11:156. [PMID: 23232052 PMCID: PMC3539922 DOI: 10.1186/1475-2859-11-156] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2012] [Accepted: 12/09/2012] [Indexed: 11/24/2022] Open
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30
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Geng F, Chen Z, Zheng P, Sun J, Zeng AP. Exploring the allosteric mechanism of dihydrodipicolinate synthase by reverse engineering of the allosteric inhibitor binding sites and its application for lysine production. Appl Microbiol Biotechnol 2012; 97:1963-71. [PMID: 22644522 DOI: 10.1007/s00253-012-4062-8] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2012] [Revised: 03/23/2012] [Accepted: 03/27/2012] [Indexed: 12/20/2022]
Abstract
Dihydrodipicolinate synthase (DHDPS, EC 4.2.1.52) catalyzes the first committed reaction of L-lysine biosynthesis in bacteria and plants and is allosterically regulated by L-lysine. In previous studies, DHDPSs from different species were proved to have different sensitivity to L-lysine inhibition. In this study, we investigated the key determinants of feedback regulation between two industrially important DHDPSs, the L-lysine-sensitive DHDPS from Escherichia coli and L-lysine-insensitive DHDPS from Corynebacterium glutamicum, by sequence and structure comparisons and site-directed mutation. Feedback inhibition of E. coli DHDPS was successfully alleviated after substitution of the residues around the inhibitor's binding sites with those of C. glutamicum DHDPS. Interestingly, mutagenesis of the lysine binding sites of C. glutamicum DHDPS according to E. coli DHDPS did not recover the expected feedback inhibition but an activation of DHDPS by L-lysine, probably due to differences in the allosteic signal transduction in the DHDPS of these two organisms. Overexpression of L-lysine-insensitive E. coli DHDPS mutants in E. coli MG1655 resulted in an improvement of L-lysine production yield by 46 %.
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Affiliation(s)
- Feng Geng
- Department of Biopharmaceutic Engineering, School of Chemical Engineering and Technology, Tianjin University, 92 Weijin Road, Nankai District, Tianjin 300072, China
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31
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Structural and functional characterization of α-isopropylmalate synthase and citramalate synthase, members of the LeuA dimer superfamily. Arch Biochem Biophys 2012; 519:202-9. [DOI: 10.1016/j.abb.2011.10.009] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2011] [Revised: 10/12/2011] [Accepted: 10/13/2011] [Indexed: 11/19/2022]
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32
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Bubela T, Hagen G, Einsiedel E. Synthetic biology confronts publics and policy makers: challenges for communication, regulation and commercialization. Trends Biotechnol 2011; 30:132-7. [PMID: 22119159 DOI: 10.1016/j.tibtech.2011.10.003] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2011] [Revised: 10/17/2011] [Accepted: 10/21/2011] [Indexed: 11/28/2022]
Abstract
The novelty of synthetic biology lies in the use of synthesized parts that can be arranged to make useful products. Such advanced, high-throughput genetic engineering projects redesign and fabricate existing biological systems as well as new biological parts, devices and systems that do not occur in nature. This Opinion discusses challenges raised by synthetic biology for public acceptance, regulation, commercialization and the emerging global issue of access to genetic resources and information. As with all new fields of research, maintaining the trust of the public and policy regulators is paramount. Hype and exaggerated claims are counterproductive to developing adaptive and ethically sound regulatory models responsive to stakeholder concerns.
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Affiliation(s)
- Tania Bubela
- Department of Public Health Sciences, School of Public Health, University of Alberta, Edmonton Clinic Health Academy, 11405-87 Avenue, Edmonton, Alberta, Canada, T6G 1C9.
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33
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Carbonell P, Planson AG, Fichera D, Faulon JL. A retrosynthetic biology approach to metabolic pathway design for therapeutic production. BMC SYSTEMS BIOLOGY 2011; 5:122. [PMID: 21819595 PMCID: PMC3163555 DOI: 10.1186/1752-0509-5-122] [Citation(s) in RCA: 92] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/18/2011] [Accepted: 08/05/2011] [Indexed: 01/10/2023]
Abstract
BACKGROUND Synthetic biology is used to develop cell factories for production of chemicals by constructively importing heterologous pathways into industrial microorganisms. In this work we present a retrosynthetic approach to the production of therapeutics with the goal of developing an in situ drug delivery device in host cells. Retrosynthesis, a concept originally proposed for synthetic chemistry, iteratively applies reversed chemical transformations (reversed enzyme-catalyzed reactions in the metabolic space) starting from a target product to reach precursors that are endogenous to the chassis. So far, a wider adoption of retrosynthesis into the manufacturing pipeline has been hindered by the complexity of enumerating all feasible biosynthetic pathways for a given compound. RESULTS In our method, we efficiently address the complexity problem by coding substrates, products and reactions into molecular signatures. Metabolic maps are represented using hypergraphs and the complexity is controlled by varying the specificity of the molecular signature. Furthermore, our method enables candidate pathways to be ranked to determine which ones are best to engineer. The proposed ranking function can integrate data from different sources such as host compatibility for inserted genes, the estimation of steady-state fluxes from the genome-wide reconstruction of the organism's metabolism, or the estimation of metabolite toxicity from experimental assays. We use several machine-learning tools in order to estimate enzyme activity and reaction efficiency at each step of the identified pathways. Examples of production in bacteria and yeast for two antibiotics and for one antitumor agent, as well as for several essential metabolites are outlined. CONCLUSIONS We present here a unified framework that integrates diverse techniques involved in the design of heterologous biosynthetic pathways through a retrosynthetic approach in the reaction signature space. Our engineering methodology enables the flexible design of industrial microorganisms for the efficient on-demand production of chemical compounds with therapeutic applications.
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Affiliation(s)
- Pablo Carbonell
- Institute of Systems and Synthetic Biology, University of Evry, Genopole Campus 1, Genavenir 6, 5 rue Henri Desbruères, Evry Cedex, France
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34
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Chen Z, Rappert S, Sun J, Zeng AP. Integrating molecular dynamics and co-evolutionary analysis for reliable target prediction and deregulation of the allosteric inhibition of aspartokinase for amino acid production. J Biotechnol 2011; 154:248-54. [DOI: 10.1016/j.jbiotec.2011.05.005] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2011] [Revised: 05/02/2011] [Accepted: 05/09/2011] [Indexed: 10/18/2022]
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35
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Coevolutionary analysis enabled rational deregulation of allosteric enzyme inhibition in Corynebacterium glutamicum for lysine production. Appl Environ Microbiol 2011; 77:4352-60. [PMID: 21531824 DOI: 10.1128/aem.02912-10] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Product feedback inhibition of allosteric enzymes is an essential issue for the development of highly efficient microbial strains for bioproduction. Here we used aspartokinase from Corynebacterium glutamicum (CgAK), a key enzyme controlling the biosynthesis of industrially important aspartate family amino acids, as a model to demonstrate a fast and efficient approach to the deregulation of allostery. In the last 50 years many researchers and companies have made considerable efforts to deregulate this enzyme from allosteric inhibition by lysine and threonine. However, only a limited number of positive mutants have been identified so far, almost exclusively by random mutation and selection. In this study, we used statistical coupling analysis of protein sequences, a method based on coevolutionary analysis, to systematically clarify the interaction network within the regulatory domain of CgAK that is essential for allosteric inhibition. A cluster of interconnected residues linking different inhibitors' binding sites as well as other regions of the protein have been identified, including most of the previously reported positions of successful mutations. Beyond these mutation positions, we have created another 14 mutants that can partially or completely desensitize CgAK from allosteric inhibition, as shown by enzyme activity assays. The introduction of only one of the inhibition-insensitive CgAK mutations (here Q298G) into a wild-type C. glutamicum strain by homologous recombination resulted in an accumulation of 58 g/liter L-lysine within 30 h of fed-batch fermentation in a bioreactor.
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36
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Pleiss J. Protein design in metabolic engineering and synthetic biology. Curr Opin Biotechnol 2011; 22:611-7. [PMID: 21514140 DOI: 10.1016/j.copbio.2011.03.004] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2011] [Revised: 03/08/2011] [Accepted: 03/09/2011] [Indexed: 11/18/2022]
Abstract
Starting from experimental data on sequence, structure or biochemical properties of enzymes, protein design seeks to construct enzymes with desired activity, stability, specificity and selectivity. Two strategies are widely used to investigate sequence-structure-function relationships: statistical methods to analyse protein families or mutant libraries, and molecular modelling methods to study proteins and their interaction with ligands or substrates. On the basis of these methods, protein design has been successfully applied to fine-tune bottleneck enzymes in metabolic engineering and to design enzymes with new substrate spectra and new functions. However, constructing efficient metabolic pathways by integrating individual enzymes into a complex system is challenging. The field of synthetic biology is still in its infancy, but promising results have demonstrated the feasibility and usefulness of the concept.
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Affiliation(s)
- Jürgen Pleiss
- Institute of Technical Biochemistry, University of Stuttgart, Allmandring 31, D-70569 Stuttgart, Germany.
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