1
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Song J, Zhuang M, Fang Y, Hu X, Wang X. Self-regulated efficient production of L-threonine via an artificial quorum sensing system in engineered Escherichia coli. Microbiol Res 2024; 284:127720. [PMID: 38640767 DOI: 10.1016/j.micres.2024.127720] [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: 12/28/2023] [Revised: 04/01/2024] [Accepted: 04/10/2024] [Indexed: 04/21/2024]
Abstract
Imbalance in carbon flux distribution is one of the most important factors affecting the further increase in the yield of high value-added natural products in microbial metabolic engineering. Meanwhile, the most common inducible expression systems are difficult to achieve industrial-scale production due to the addition of high-cost or toxic inducers during the fermentation process. Quorum sensing system, as a typical model for density-dependent induction of gene expression, has been widely applied in synthetic biology. However, there are currently few reports for efficient production of microbial natural products by using quorum sensing system to self-regulate carbon flux distribution. Here, we designed an artificial quorum sensing system to achieve efficient production of L-threonine in engineered Escherichia coli by altering the carbon flux distribution of the central metabolic pathways at specific periods. Under the combination of switch module and production module, the system was applied to divide the microbial fermentation process into two stages including growth and production, and improve the production of L-threonine by self-inducing the expression of pyruvate carboxylase and threonine extracellular transporter protease after a sufficient amount of cell growth. The final strain TWF106/pST1011, pST1042pr could produce 118.2 g/L L-threonine with a yield of 0.57 g/g glucose and a productivity of 2.46 g/(L· h). The establishment of this system has important guidance and application value for the production of other high value-added chemicals in microorganisms by self-regulation.
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Affiliation(s)
- Jie Song
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, China
| | - Miaomiao Zhuang
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, China
| | - Yu Fang
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, China
| | - Xiaoqing Hu
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, China
| | - Xiaoyuan Wang
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, China.
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2
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Su B, Lai P, Deng MR, Zhu H. Design of a dual-responding genetic circuit for high-throughput identification of L-threonine-overproducing Escherichia coli. BIORESOURCE TECHNOLOGY 2024; 395:130407. [PMID: 38295961 DOI: 10.1016/j.biortech.2024.130407] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/05/2023] [Revised: 01/04/2024] [Accepted: 01/27/2024] [Indexed: 02/18/2024]
Abstract
L-threonine is a crucial amino acid that is extensively employed in the realms of food, animal feed and pharmaceuticals. Unfortunately, the lack of an appropriate biosensor has hindered the establishment of a robust high-throughput screening (HTS) system for the identification of the desired strains from random mutants. In this study, a dual-responding genetic circuit that capitalizes on the L-threonine inducer-like effect, the L-threonine riboswitch, and a signal amplification system was designed for the purpose of screening L-threonine overproducers. This platform effectively enhanced the performance of the enzyme and facilitated the identification of high L-threonine-producing strains from a random mutant library. Consequently, pathway optimization and directed evolution of the key enzyme enhanced L-threonine production by 4 and 7-fold, respectively. These results demonstrate the potential of biosensor design for dynamic metabolite detection and offer a promising tool for HTS and metabolic regulation for the development of L-threonine-hyperproducing strains.
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Affiliation(s)
- Buli Su
- Key Laboratory of Agricultural Microbiomics and Precision Application (MARA), Key Laboratory of Agricultural Microbiome (MARA), State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou 510070, PR China.
| | - Peixuan Lai
- Key Laboratory of Agricultural Microbiomics and Precision Application (MARA), Key Laboratory of Agricultural Microbiome (MARA), State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou 510070, PR China.
| | - Ming-Rong Deng
- Key Laboratory of Agricultural Microbiomics and Precision Application (MARA), Key Laboratory of Agricultural Microbiome (MARA), State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou 510070, PR China.
| | - Honghui Zhu
- Key Laboratory of Agricultural Microbiomics and Precision Application (MARA), Key Laboratory of Agricultural Microbiome (MARA), State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou 510070, PR China.
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3
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Carpenter AC, Feist AM, Harrison FS, Paulsen IT, Williams TC. Have you tried turning it off and on again? Oscillating selection to enhance fitness-landscape traversal in adaptive laboratory evolution experiments. Metab Eng Commun 2023; 17:e00227. [PMID: 37538933 PMCID: PMC10393799 DOI: 10.1016/j.mec.2023.e00227] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2023] [Revised: 06/05/2023] [Accepted: 07/11/2023] [Indexed: 08/05/2023] Open
Abstract
Adaptive Laboratory Evolution (ALE) is a powerful tool for engineering and understanding microbial physiology. ALE relies on the selection and enrichment of mutations that enable survival or faster growth under a selective condition imposed by the experimental setup. Phenotypic fitness landscapes are often underpinned by complex genotypes involving multiple genes, with combinatorial positive and negative effects on fitness. Such genotype relationships result in mutational fitness landscapes with multiple local fitness maxima and valleys. Traversing local maxima to find a global maximum often requires an individual or sub-population of cells to traverse fitness valleys. Traversing involves gaining mutations that are not adaptive for a given local maximum but are necessary to 'peak shift' to another local maximum, or eventually a global maximum. Despite these relatively well understood evolutionary principles, and the combinatorial genotypes that underlie most metabolic phenotypes, the majority of applied ALE experiments are conducted using constant selection pressures. The use of constant pressure can result in populations becoming trapped within local maxima, and often precludes the attainment of optimum phenotypes associated with global maxima. Here, we argue that oscillating selection pressures is an easily accessible mechanism for traversing fitness landscapes in ALE experiments, and provide theoretical and practical frameworks for implementation.
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Affiliation(s)
- Alexander C. Carpenter
- Department of Molecular Sciences and ARC Centre of Excellence in Synthetic Biology, Centre Headquarters, Macquarie University, Sydney, SW, 2109, Australia
- CSIRO Synthetic Biology Future Science Platform, Canberra, ACT, 2601, Australia
| | - Adam M. Feist
- Department of Bioengineering, University of California San Diego, 9500 Gilman Dr., La Jolla, CA, 92093, USA
- Joint BioEnergy Institute, 5885 Hollis Street, 4th Floor, Emeryville, CA, 94608, USA
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800, Kgs, Lyngby, Denmark
| | - Fergus S.M. Harrison
- Department of Molecular Sciences and ARC Centre of Excellence in Synthetic Biology, Centre Headquarters, Macquarie University, Sydney, SW, 2109, Australia
| | - Ian T. Paulsen
- Department of Molecular Sciences and ARC Centre of Excellence in Synthetic Biology, Centre Headquarters, Macquarie University, Sydney, SW, 2109, Australia
| | - Thomas C. Williams
- Department of Molecular Sciences and ARC Centre of Excellence in Synthetic Biology, Centre Headquarters, Macquarie University, Sydney, SW, 2109, Australia
- CSIRO Synthetic Biology Future Science Platform, Canberra, ACT, 2601, Australia
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4
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Tellechea-Luzardo J, Stiebritz MT, Carbonell P. Transcription factor-based biosensors for screening and dynamic regulation. Front Bioeng Biotechnol 2023; 11:1118702. [PMID: 36814719 PMCID: PMC9939652 DOI: 10.3389/fbioe.2023.1118702] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2022] [Accepted: 01/26/2023] [Indexed: 02/09/2023] Open
Abstract
Advances in synthetic biology and genetic engineering are bringing into the spotlight a wide range of bio-based applications that demand better sensing and control of biological behaviours. Transcription factor (TF)-based biosensors are promising tools that can be used to detect several types of chemical compounds and elicit a response according to the desired application. However, the wider use of this type of device is still hindered by several challenges, which can be addressed by increasing the current metabolite-activated transcription factor knowledge base, developing better methods to identify new transcription factors, and improving the overall workflow for the design of novel biosensor circuits. These improvements are particularly important in the bioproduction field, where researchers need better biosensor-based approaches for screening production-strains and precise dynamic regulation strategies. In this work, we summarize what is currently known about transcription factor-based biosensors, discuss recent experimental and computational approaches targeted at their modification and improvement, and suggest possible future research directions based on two applications: bioproduction screening and dynamic regulation of genetic circuits.
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Affiliation(s)
- Jonathan Tellechea-Luzardo
- Institute of Industrial Control Systems and Computing (AI2), Universitat Politècnica de València (UPV), Valencia, Spain
| | - Martin T. Stiebritz
- Institute of Industrial Control Systems and Computing (AI2), Universitat Politècnica de València (UPV), Valencia, Spain
| | - Pablo Carbonell
- Institute of Industrial Control Systems and Computing (AI2), Universitat Politècnica de València (UPV), Valencia, Spain,Institute for Integrative Systems Biology I2SysBio, Universitat de València-CSIC, Paterna, Spain,*Correspondence: Pablo Carbonell,
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5
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Guo Y, Ji F, Qiao J, Dong X, Wu Y, Wang X. Overexpression of the key genes in the biosynthetic pathways of lipid A and peptidoglycan in Escherichia coli. Biotechnol Appl Biochem 2023; 70:374-386. [PMID: 35644907 DOI: 10.1002/bab.2364] [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: 01/07/2022] [Accepted: 05/01/2022] [Indexed: 11/09/2022]
Abstract
Gram-negative bacterium Escherichia coli has a tripartite cell envelope with a cytoplasmic membrane, a peptidoglycan layer, and an asymmetric outer membrane containing lipopolysaccharide in its outer leaflet. The biogenesis of peptidoglycan and lipopolysaccharide shares the same substrate UDP-GlcNAc. From UDP-GlcNAc, MurA catalyzes the first reaction for peptidoglycan biosynthesis, while LpxA catalyzes the first reaction for lipopolysaccharide biosynthesis. This study demonstrates that murA overexpression in E. coli MG1655 inhibited the cell growth and increased the cell length, whereas lpxA overexpression in MG1655 neither inhibited the cell growth nor increased the cell length. Further study showed that individual overexpression of the other eight genes encoding the enzymes to catalyze the initial reactions in the biosynthetic pathway of lipopolysaccharide did not inhibit the cell growth. When MG1655/pBad-lpxA, MG1655/pBad-lpxD, and MG1655/pBad-lpxH were transformed with pFW01-thrA*BC-rhtC that contains the key genes for L-threonine biosynthesis and transport, the L-threonine production was increased. The L-threonine production in MG1655/pFW01-thrA*BC-rhtC/pBad-lpxH increased 46.1% as compared to the control MG1655/pFW01-thrA*BC-rhtC/pBad.
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Affiliation(s)
- Yong Guo
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, China.,Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, China
| | - Fan Ji
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, China.,Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, China
| | - Jun Qiao
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, China.,Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, China
| | - Xiaofei Dong
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, China.,Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, China
| | - Yuanming Wu
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, China.,Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, China
| | - Xiaoyuan Wang
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, China.,Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, China.,International Joint Laboratory on Food Safety, Jiangnan University, Wuxi, China
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6
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Zhao Z, Cai M, Liu Y, Hu M, Yang F, Zhu R, Xu M, Rao Z. Genomics and transcriptomics-guided metabolic engineering Corynebacterium glutamicum for l-arginine production. BIORESOURCE TECHNOLOGY 2022; 364:128054. [PMID: 36184013 DOI: 10.1016/j.biortech.2022.128054] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/26/2022] [Revised: 09/27/2022] [Accepted: 09/27/2022] [Indexed: 06/16/2023]
Abstract
l-arginine is a semi-essential amino acid that is broadly used as food additives and pharmaceutical intermediates. The synthesis of l-arginine is restricted by complex metabolic mechanisms and suboptimal fermentation conditions. Initially, a mutant strain that accumulated 19.4 g/L l-arginine was generated by random mutagenesis. Subsequently, a mutation of the repressor protein (argRG159D) in the l-arginine operon and glutamate synthase (gltD) with 532-fold upregulation were identified to be vital for l-arginine production by multi-omic analysis. Systematic metabolic engineering was used to modify the strain, which included interfering with α-ketoglutarate dehydrogenase complex (ODHC) activity by knocking out serine/threonine-protein kinase (pknG), enhancing the expression of multiple key enzymes in the l-arginine synthesis pathway, and increasing the availability of intracellular cofactor (NADPH) and energy (ATP). Finally, C. glutamicum ARG12 produced 71.3 g/L l-arginine, with a yield of 0.43 g/g glucose by fermentation optimization. This study provides new ideas to boost l-arginine production.
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Affiliation(s)
- Zhenqiang Zhao
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, China
| | - Mengmeng Cai
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, China
| | - Yunran Liu
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, China
| | - Mengkai Hu
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, China
| | - Fengyu Yang
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, China
| | - Rongshuai Zhu
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, China
| | - Meijuan Xu
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, China
| | - Zhiming Rao
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, China.
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7
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Rational Metabolic Engineering Combined with Biosensor-Mediated Adaptive Laboratory Evolution for l-Cysteine Overproduction from Glycerol in Escherichia coli. FERMENTATION-BASEL 2022. [DOI: 10.3390/fermentation8070299] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
l-Cysteine is an important sulfur-containing amino acid with numerous applications in the pharmaceutical and cosmetic industries. The microbial production of l-cysteine has received substantial attention, and the supply of the precursor l-serine is important in l-cysteine biosynthesis. In this study, to achieve l-cysteine overproduction, we first increased l-serine production by deleting genes involved in the pathway of l-serine degradation to glycine (serine hydroxymethyl transferase, SHMT, encoded by glyA genes) in strain 4W (with l-serine titer of 1.1 g/L), thus resulting in strain 4WG with l-serine titer of 2.01 g/L. Second, the serine-biosensor based on the transcriptional regulator NCgl0581 of C. glutamicum was constructed in E. coli, and the validity and sensitivity of the biosensor were demonstrated in E. coli. Then 4WG was further evolved through adaptive laboratory evolution (ALE) combined with serine-biosensor, thus yielding the strain 4WGX with 4.13 g/L l-serine production. Moreover, the whole genome of the evolved strain 4WGX was sequenced, and ten non-synonymous mutations were found in the genome of strain 4WGX compared with strain 4W. Finally, 4WGX was used as the starting strain, and deletion of the l-cysteine desulfhydrases (encoded by tnaA), overexpression of serine acetyltransferase (encoded by cysE) and the key enzyme of transport pathway (encoded by ydeD) were performed in strain 4WGX. The recombinant strain 4WGX-∆tnaA-cysE-ydeD can produce 313.4 mg/L of l-cysteine using glycerol as the carbon source. This work provides an efficient method for the biosynthesis of value-added commodity products associated with glycerol conversion.
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8
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Dynamic Regulation of Transporter Expression to Increase L-Threonine Production Using L-Threonine Biosensors. FERMENTATION 2022. [DOI: 10.3390/fermentation8060250] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
The cytotoxicity of overexpressed transporters limits their application in biochemical production. To overcome this problem, we developed a feedback circuit for L-threonine production that uses a biosensor to regulate transporter expression. First, we used IPTG-induced rhtA regulation, L-threonine exporter, to simulate dynamic regulation for improving L-threonine production, and the results show that it had significant advantages compared with the constitutive overexpression of rhtA. To further construct a feedback circuit for rhtA auto-regulation, three L-threonine sensing promoters, PcysJ, PcysD, and PcysJH, were characterized with gradually decreasing strength. The dynamic expression of rhtA with a threonine-activated promoter considerably increased L-threonine production (21.19 g/L) beyond that attainable by the constitutive expression of rhtA (8.55 g/L). Finally, the autoregulation method was used in regulating rhtB and rhtC to improve L-threonine production and achieve a high titer of 26.78 g/L (a 161.01% increase), a yield of 0.627 g/g glucose, and a productivity of 0.743 g/L/h in shake-flask fermentation. This study analyzed in detail the influence of dynamic regulation and the constitutive expression of transporters on L-threonine production. For the first time, we confirmed that dynamically regulating transporter levels can efficiently promote L-threonine production by using the end-product biosensor.
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9
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Budniak L, Slobodianiuk L, Marchyshyn S, Potishnyi I. Determination of amino acids of plants from Angelica L. genus by HPLC method. PHARMACIA 2022. [DOI: 10.3897/pharmacia.69.e83705] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
One of the tasks of pharmaceutical science is to find new sources of effective drugs. Such sources include plants such as Angelica archangelica L. and Angelica sylvestris L., which have been used for many years to treat various diseases in folk medicine. Because the chemical composition of these plants is poorly understood, the aim of our study was to investigate the amino acid composition of the leaves of A. archangelica L. and A. sylvestris L. The amino acids of the leaves of the study species of the genus Angelica L. were determined by the HPLC method. Eighteen free and nineteen bound amino acids were identified in the leaves of A. archangelica L. The A. sylvestris L. leaves contained nineteen free and the same amount of bound amino acids. High concentrations of free and bound amino acids such as L-glutamic acid and L-aspartic acid predominate in A. archangelica L. and A. sylvestris L. This allowed these amino acids to be considered distinguishing markers of the study plants. Character metabolic processes in which these amino acids take part may be associated with the medicinal properties of these plants pursuant to their use in medicine and, therefore, may contribute to the insight of their therapeutic properties.
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10
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Shimizu K, Matsuoka Y. Feedback regulation and coordination of the main metabolism for bacterial growth and metabolic engineering for amino acid fermentation. Biotechnol Adv 2021; 55:107887. [PMID: 34921951 DOI: 10.1016/j.biotechadv.2021.107887] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Revised: 12/05/2021] [Accepted: 12/09/2021] [Indexed: 12/28/2022]
Abstract
Living organisms such as bacteria are often exposed to continuous changes in the nutrient availability in nature. Therefore, bacteria must constantly monitor the environmental condition, and adjust the metabolism quickly adapting to the change in the growth condition. For this, bacteria must orchestrate (coordinate and integrate) the complex and dynamically changing information on the environmental condition. In particular, the central carbon metabolism (CCM), monomer synthesis, and macromolecular synthesis must be coordinately regulated for the efficient growth. It is a grand challenge in bioscience, biotechnology, and synthetic biology to understand how living organisms coordinate the metabolic regulation systems. Here, we consider the integrated sensing of carbon sources by the phosphotransferase system (PTS), and the feed-forward/feedback regulation systems incorporated in the CCM in relation to the pool sizes of flux-sensing metabolites and αketoacids. We also consider the metabolic regulation of amino acid biosynthesis (as well as purine and pyrimidine biosyntheses) paying attention to the feedback control systems consisting of (fast) enzyme level regulation with (slow) transcriptional regulation. The metabolic engineering for the efficient amino acid production by bacteria such as Escherichia coli and Corynebacterium glutamicum is also discussed (in relation to the regulation mechanisms). The amino acid synthesis is important for determining the rate of ribosome biosynthesis. Thus, the growth rate control (growth law) is further discussed on the relationship between (p)ppGpp level and the ribosomal protein synthesis.
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Affiliation(s)
- Kazuyuki Shimizu
- Kyushu institute of Technology, Iizuka, Fukuoka 820-8502, Japan; Institute of Advanced Biosciences, Keio University, Tsuruoka, Yamagata 997-0017, Japan.
| | - Yu Matsuoka
- Department of Fisheries Distribution and Management, National Fisheries University, Shimonoseki, Yamaguchi 759-6595, Japan
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11
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Zhang G, Ren X, Liang X, Wang Y, Feng D, Zhang Y, Xian M, Zou H. Improving the Microbial Production of Amino Acids: From Conventional Approaches to Recent Trends. BIOTECHNOL BIOPROC E 2021. [DOI: 10.1007/s12257-020-0390-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
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12
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Huang J, Chen J, Wang Y, Shi T, Ni X, Pu W, Liu J, Zhou Y, Cai N, Han S, Zheng P, Sun J. Development of a Hyperosmotic Stress Inducible Gene Expression System by Engineering the MtrA/MtrB-Dependent NCgl1418 Promoter in Corynebacterium glutamicum. Front Microbiol 2021; 12:718511. [PMID: 34367120 PMCID: PMC8334368 DOI: 10.3389/fmicb.2021.718511] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2021] [Accepted: 06/28/2021] [Indexed: 11/13/2022] Open
Abstract
Corynebacterium glutamicum is an important workhorse for industrial production of diversiform bioproducts. Precise regulation of gene expression is crucial for metabolic balance and enhancing production of target molecules. Auto-inducible promoters, which can be activated without expensive inducers, are ideal regulatory tools for industrial-scale application. However, few auto-inducible promoters have been identified and applied in C. glutamicum. Here, a hyperosmotic stress inducible gene expression system was developed and used for metabolic engineering of C. glutamicum. The promoter of NCgl1418 (P NCgl1418 ) that was activated by the two-component signal transduction system MtrA/MtrB was found to exhibit a high inducibility under hyperosmotic stress conditions. A synthetic promoter library was then constructed by randomizing the flanking and space regions of P NCgl1418 , and mutant promoters exhibiting high strength were isolated via fluorescence activated cell sorting (FACS)-based high-throughput screening. The hyperosmotic stress inducible gene expression system was applied to regulate the expression of lysE encoding a lysine exporter and repress four genes involved in lysine biosynthesis (gltA, pck, pgi, and hom) by CRISPR interference, which increased the lysine titer by 64.7% (from 17.0 to 28.0 g/L) in bioreactors. The hyperosmotic stress inducible gene expression system developed here is a simple and effective tool for gene auto-regulation in C. glutamicum and holds promise for metabolic engineering of C. glutamicum to produce valuable chemicals and fuels.
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Affiliation(s)
- Jingwen Huang
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou, China.,Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
| | - Jiuzhou Chen
- Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
| | - Yu Wang
- Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
| | - Tuo Shi
- Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
| | - Xiaomeng Ni
- Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
| | - Wei Pu
- Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
| | - Jiao Liu
- Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
| | - Yingyu Zhou
- Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China.,College of Biotechnology, Tianjin University of Science and Technology, Tianjin, China
| | - Ningyun Cai
- Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
| | - Shuangyan Han
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou, China
| | - Ping Zheng
- Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
| | - Jibin Sun
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou, China.,Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
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13
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Yi D, Bayer T, Badenhorst CPS, Wu S, Doerr M, Höhne M, Bornscheuer UT. Recent trends in biocatalysis. Chem Soc Rev 2021; 50:8003-8049. [PMID: 34142684 PMCID: PMC8288269 DOI: 10.1039/d0cs01575j] [Citation(s) in RCA: 122] [Impact Index Per Article: 40.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2020] [Indexed: 12/13/2022]
Abstract
Biocatalysis has undergone revolutionary progress in the past century. Benefited by the integration of multidisciplinary technologies, natural enzymatic reactions are constantly being explored. Protein engineering gives birth to robust biocatalysts that are widely used in industrial production. These research achievements have gradually constructed a network containing natural enzymatic synthesis pathways and artificially designed enzymatic cascades. Nowadays, the development of artificial intelligence, automation, and ultra-high-throughput technology provides infinite possibilities for the discovery of novel enzymes, enzymatic mechanisms and enzymatic cascades, and gradually complements the lack of remaining key steps in the pathway design of enzymatic total synthesis. Therefore, the research of biocatalysis is gradually moving towards the era of novel technology integration, intelligent manufacturing and enzymatic total synthesis.
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Affiliation(s)
- Dong Yi
- Department of Biotechnology & Enzyme Catalysis, Institute of Biochemistry, University GreifswaldFelix-Hausdorff-Str. 4D-17487 GreifswaldGermany
| | - Thomas Bayer
- Department of Biotechnology & Enzyme Catalysis, Institute of Biochemistry, University GreifswaldFelix-Hausdorff-Str. 4D-17487 GreifswaldGermany
| | - Christoffel P. S. Badenhorst
- Department of Biotechnology & Enzyme Catalysis, Institute of Biochemistry, University GreifswaldFelix-Hausdorff-Str. 4D-17487 GreifswaldGermany
| | - Shuke Wu
- Department of Biotechnology & Enzyme Catalysis, Institute of Biochemistry, University GreifswaldFelix-Hausdorff-Str. 4D-17487 GreifswaldGermany
| | - Mark Doerr
- Department of Biotechnology & Enzyme Catalysis, Institute of Biochemistry, University GreifswaldFelix-Hausdorff-Str. 4D-17487 GreifswaldGermany
| | - Matthias Höhne
- Department of Biotechnology & Enzyme Catalysis, Institute of Biochemistry, University GreifswaldFelix-Hausdorff-Str. 4D-17487 GreifswaldGermany
| | - Uwe T. Bornscheuer
- Department of Biotechnology & Enzyme Catalysis, Institute of Biochemistry, University GreifswaldFelix-Hausdorff-Str. 4D-17487 GreifswaldGermany
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14
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Wu Y, Jameel A, Xing XH, Zhang C. Advanced strategies and tools to facilitate and streamline microbial adaptive laboratory evolution. Trends Biotechnol 2021; 40:38-59. [PMID: 33958227 DOI: 10.1016/j.tibtech.2021.04.002] [Citation(s) in RCA: 40] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2020] [Revised: 03/17/2021] [Accepted: 04/01/2021] [Indexed: 12/18/2022]
Abstract
Adaptive laboratory evolution (ALE) has served as a historic microbial engineering method that mimics natural selection to obtain desired microbes. The past decade has witnessed improvements in all aspects of ALE workflow, in terms of growth coupling, genotypic diversification, phenotypic selection, and genotype-phenotype mapping. The developing growth-coupling strategies facilitate ALE to a wider range of appealing traits. In vivo mutagenesis methods and multiplexed automated culture platforms open new gates to streamline its execution. Meanwhile, the application of multi-omics analyses and multiplexed genetic engineering promote efficient knowledge mining. This article provides a comprehensive and updated review of these advances, highlights newest significant applications, and discusses future improvements, aiming to provide a practical guide for implementation of novel, effective, and efficient ALE experiments.
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Affiliation(s)
- Yinan Wu
- MOE Key Laboratory for Industrial Biocatalysis, Institute of Biochemical Engineering, Department of Chemical Engineering, Tsinghua University, Beijing 100084, China
| | - Aysha Jameel
- MOE Key Laboratory for Industrial Biocatalysis, Institute of Biochemical Engineering, Department of Chemical Engineering, Tsinghua University, Beijing 100084, China
| | - Xin-Hui Xing
- MOE Key Laboratory for Industrial Biocatalysis, Institute of Biochemical Engineering, Department of Chemical Engineering, Tsinghua University, Beijing 100084, China; Center for Synthetic and Systems Biology, Tsinghua University, Beijing, 100084, China
| | - Chong Zhang
- MOE Key Laboratory for Industrial Biocatalysis, Institute of Biochemical Engineering, Department of Chemical Engineering, Tsinghua University, Beijing 100084, China; Center for Synthetic and Systems Biology, Tsinghua University, Beijing, 100084, China.
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15
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Sun X, Li Q, Wang Y, Zhou W, Guo Y, Chen J, Zheng P, Sun J, Ma Y. Isoleucyl-tRNA synthetase mutant based whole-cell biosensor for high-throughput selection of isoleucine overproducers. Biosens Bioelectron 2021; 172:112783. [PMID: 33157411 DOI: 10.1016/j.bios.2020.112783] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2020] [Revised: 10/29/2020] [Accepted: 10/30/2020] [Indexed: 02/02/2023]
Abstract
Whole-cell amino acid biosensors can sense the concentrations of certain amino acids and output easily detectable signals, which are important for construction of microbial producers. However, many reported biosensors have poor specificity because they also sense non-target amino acids. Besides, biosensors for many amino acids are still unavailable. In this study, we proposed a new strategy for constructing whole-cell biosensors based on aminoacyl-tRNA synthetases (aaRSs), which take the advantage of their universality and intrinsically specific binding ability to corresponding amino acids. Taking isoleucine biosensor as an example, we first mutated the isoleucyl-tRNA synthetase in Escherichia coli to dramatically decrease its affinity to isoleucine. The engineered cells specifically sensed isoleucine and output isoleucine dose-dependent cell growth as an easily detectable signal. To further expand the sensing range, an isoleucine exporter was overexpressed to enhance excretion of intracellular isoleucine. Since cells equipped with the optimized whole-cell biosensor showed accelerated growth when cells produced higher concentrations of isoleucine, the biosensor was successfully applied in high-throughput selection of isoleucine overproducers from random mutation libraries. This work demonstrates the feasibility of engineering aaRSs to construct a new kind of whole-cell biosensors for amino acids. Considering all twenty proteinogenic and many non-canonical amino acids have their specific aaRSs, this strategy should be useful for developing biosensors for various amino acids.
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Affiliation(s)
- Xue Sun
- Tianjin Institute of Industrial Biotechnology, Key Laboratory of Systems Microbial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China; National Technology Innovation Center of Synthetic Biology, Tianjin 300308, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Qinggang Li
- Tianjin Institute of Industrial Biotechnology, Key Laboratory of Systems Microbial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China; National Technology Innovation Center of Synthetic Biology, Tianjin 300308, China
| | - Yu Wang
- Tianjin Institute of Industrial Biotechnology, Key Laboratory of Systems Microbial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China; National Technology Innovation Center of Synthetic Biology, Tianjin 300308, China
| | - Wenjuan Zhou
- Tianjin Institute of Industrial Biotechnology, Key Laboratory of Systems Microbial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China; National Technology Innovation Center of Synthetic Biology, Tianjin 300308, China
| | - Yanmei Guo
- Tianjin Institute of Industrial Biotechnology, Key Laboratory of Systems Microbial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China; National Technology Innovation Center of Synthetic Biology, Tianjin 300308, China
| | - Jiuzhou Chen
- Tianjin Institute of Industrial Biotechnology, Key Laboratory of Systems Microbial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China; National Technology Innovation Center of Synthetic Biology, Tianjin 300308, China
| | - Ping Zheng
- Tianjin Institute of Industrial Biotechnology, Key Laboratory of Systems Microbial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China; National Technology Innovation Center of Synthetic Biology, Tianjin 300308, China.
| | - Jibin Sun
- Tianjin Institute of Industrial Biotechnology, Key Laboratory of Systems Microbial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China; National Technology Innovation Center of Synthetic Biology, Tianjin 300308, China.
| | - Yanhe Ma
- Tianjin Institute of Industrial Biotechnology, Key Laboratory of Systems Microbial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China; National Technology Innovation Center of Synthetic Biology, Tianjin 300308, China
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16
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Aburatani S, Ishiya K, Itoh T, Hayashi T, Taniguchi T, Takaku H. Inference of Regulatory System for TAG Biosynthesis in Lipomyces starkeyi. Bioengineering (Basel) 2020; 7:bioengineering7040148. [PMID: 33227954 PMCID: PMC7711605 DOI: 10.3390/bioengineering7040148] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2020] [Revised: 11/14/2020] [Accepted: 11/18/2020] [Indexed: 12/23/2022] Open
Abstract
Improving the bioproduction ability of efficient host microorganisms is a central aim in bioengineering. To control biosynthesis in living cells, the regulatory system of the whole biosynthetic pathway should be clearly understood. In this study, we applied our network modeling method to infer the regulatory system for triacylglyceride (TAG) biosynthesis in Lipomyces starkeyi, using factor analyses and structural equation modeling to construct a regulatory network model. By factor analysis, we classified 89 TAG biosynthesis-related genes into nine groups, which were considered different regulatory sub-systems. We constructed two different types of regulatory models. One is the regulatory model for oil productivity, and the other is the whole regulatory model for TAG biosynthesis. From the inferred oil productivity regulatory model, the well characterized genes DGA1 and ACL1 were detected as regulatory factors. Furthermore, we also found unknown feedback controls in oil productivity regulation. These regulation models suggest that the regulatory factor induction targets should be selected carefully. Within the whole regulatory model of TAG biosynthesis, some genes were detected as not related to TAG biosynthesis regulation. Using network modeling, we reveal that the regulatory system is helpful for the new era of bioengineering.
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Affiliation(s)
- Sachiyo Aburatani
- Computational Bio Big-Data Open Innovation Laboratory (CBBD-OIL), National Institute of Advanced Industrial Science and Technology (AIST), Tokyo 305-8568, Japan
- Correspondence: (S.A.); (H.T.); Tel.: +81-3-3599-8712 (S.A.); +81-250-25-5119 (H.T.)
| | - Koji Ishiya
- BPRI, National Institute of Advance Industrial Science and Technology (AIST), Sapporo 062-8517, Japan;
| | - Toshikazu Itoh
- Mitsubishi Research Institute, Inc., Chiyoda District, Tokyo 100-8141, Japan; (T.I.); (T.H.); (T.T.)
| | - Toshihiro Hayashi
- Mitsubishi Research Institute, Inc., Chiyoda District, Tokyo 100-8141, Japan; (T.I.); (T.H.); (T.T.)
| | - Takeaki Taniguchi
- Mitsubishi Research Institute, Inc., Chiyoda District, Tokyo 100-8141, Japan; (T.I.); (T.H.); (T.T.)
| | - Hiroaki Takaku
- Department of Applied Life Sciences, Niigata University of Pharmacy and Applied Life Sciences, Niigata 956-8603, Japan
- Correspondence: (S.A.); (H.T.); Tel.: +81-3-3599-8712 (S.A.); +81-250-25-5119 (H.T.)
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17
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Cheng L, Wang J, Zhao X, Yin H, Fang H, Lin C, Zhang S, Shen Z, Zhao C. An antiphage Escherichia coli mutant for higher production of L-threonine obtained by atmospheric and room temperature plasma mutagenesis. Biotechnol Prog 2020; 36:e3058. [PMID: 32735374 DOI: 10.1002/btpr.3058] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2020] [Revised: 07/27/2020] [Accepted: 07/27/2020] [Indexed: 12/21/2022]
Abstract
Phage infection is common during the production of L-threonine by E. coli, and low L-threonine production and glucose conversion percentage are bottlenecks for the efficient commercial production of L-threonine. In this study, 20 antiphage mutants producing high concentration of L-threonine were obtained by atmospheric and room temperature plasma (ARTP) mutagenesis, and an antiphage E. coli variant was characterized that exhibited the highest production of L-threonine Escherichia coli ([E. coli] TRFC-AP). The elimination of fhuA expression in E. coli TRFC-AP was responsible for phage resistance. The biomass and cell growth of E. coli TRFC-AP showed no significant differences from those of the parent strain (E. coli TRFC), and the production of L-threonine (159.3 g L-1 ) and glucose conversion percentage (51.4%) were increased by 10.9% and 9.1%, respectively, compared with those of E. coli TRFC. During threonine production (culture time of 20 h), E. coli TRFC-AP exhibited higher activities of key enzymes for glucose utilization (hexokinase, glucose phosphate dehydrogenase, phosphofructokinase, phosphoenolpyruvate carboxylase, and PYK) and threonine synthesis (glutamate synthase, aspartokinase, homoserine dehydrogenase, homoserine kinase and threonine synthase) compared to those of E. coli TRFC. The analysis of metabolic flux distribution indicated that the flux of threonine with E. coli TRFC-AP reached 69.8%, an increase of 16.0% compared with that of E. coli TRFC. Overall, higher L-threonine production and glucose conversion percentage were obtained with E. coli TRFC-AP due to increased activities of key enzymes and improved carbon flux for threonine synthesis.
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Affiliation(s)
- Likun Cheng
- Shandong Research Center of High Cell Density Fermentation and Efficient Expression Technology, Shandong Lvdu Bio-science and Technology Co., Ltd, Shandong Binzhou Animal Science and Veterinary Medicine Academy, Binzhou, China
| | - Jing Wang
- Department of Critical Care Medicine, Affiliated Hospital of Binzhou Medical University, Binzhou, China
| | - Xiubao Zhao
- Shandong Research Center of High Cell Density Fermentation and Efficient Expression Technology, Shandong Lvdu Bio-science and Technology Co., Ltd, Shandong Binzhou Animal Science and Veterinary Medicine Academy, Binzhou, China
| | - Huanhuan Yin
- Shandong Research Center of High Cell Density Fermentation and Efficient Expression Technology, Shandong Lvdu Bio-science and Technology Co., Ltd, Shandong Binzhou Animal Science and Veterinary Medicine Academy, Binzhou, China
| | - Haitian Fang
- Research and Development Center, Ningxia Eppen Biotech Co., Ltd, Yinchuan, China.,Ningxia Key Laboratory for Food Microbial-Applications Technology and Safety Control, School of Agriculture, Ningxia University, Yinchuan, China
| | - Chuwen Lin
- Shandong Research Center of High Cell Density Fermentation and Efficient Expression Technology, Shandong Lvdu Bio-science and Technology Co., Ltd, Shandong Binzhou Animal Science and Veterinary Medicine Academy, Binzhou, China
| | - Shasha Zhang
- Shandong Research Center of High Cell Density Fermentation and Efficient Expression Technology, Shandong Lvdu Bio-science and Technology Co., Ltd, Shandong Binzhou Animal Science and Veterinary Medicine Academy, Binzhou, China
| | - Zhiqiang Shen
- Shandong Research Center of High Cell Density Fermentation and Efficient Expression Technology, Shandong Lvdu Bio-science and Technology Co., Ltd, Shandong Binzhou Animal Science and Veterinary Medicine Academy, Binzhou, China
| | - Chunguang Zhao
- Research and Development Center, Ningxia Eppen Biotech Co., Ltd, Yinchuan, China.,Ningxia Key Laboratory for Food Microbial-Applications Technology and Safety Control, School of Agriculture, Ningxia University, Yinchuan, China
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18
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Genetic Biosensor Design for Natural Product Biosynthesis in Microorganisms. Trends Biotechnol 2020; 38:797-810. [PMID: 32359951 DOI: 10.1016/j.tibtech.2020.03.013] [Citation(s) in RCA: 69] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2019] [Revised: 03/26/2020] [Accepted: 03/26/2020] [Indexed: 12/28/2022]
Abstract
Low yield and low titer of natural products are common issues in natural product biosynthesis through microbial cell factories. One effective way to resolve such bottlenecks is to design genetic biosensors to monitor and regulate the biosynthesis of target natural products. In this review, we evaluate the most recent advances in the design of genetic biosensors for natural product biosynthesis in microorganisms. In particular, we examine strategies for selection of genetic parts and construction principles for the design and evaluation of genetic biosensors. We also review the latest applications of transcription factor- and riboswitch-based genetic biosensors in natural product biosynthesis. Lastly, we discuss challenges and solutions in designing genetic biosensors for the biosynthesis of natural products in microorganisms.
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19
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Han L, Han D, Li L, Huang S, He P, Wang Q. Discovery and identification of medium-chain fatty acid responsive promoters in Saccharomyces cerevisiae. Eng Life Sci 2020; 20:186-196. [PMID: 32874182 PMCID: PMC7447867 DOI: 10.1002/elsc.201900093] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2019] [Revised: 12/13/2019] [Accepted: 12/19/2019] [Indexed: 01/03/2023] Open
Abstract
Medium-chain fatty acids (MCFAs) and their derivatives are important chemicals that can be used in lubricants, detergents, and cosmetics. MCFAs can be produced in several microbes, although production is not high. Dynamic regulation by synthetic biology is a good method of improving production of chemicals that avoids toxic intermediates, but chemical-responsive promoters are required. Several MCFA sensors or promoters have been reported in Saccharomyces cerevisiae. In this study, by using transcriptomic analysis of S. cerevisiae exposed to fatty acids with 6-, 12-, and 16-carbon chains, we identified 58 candidate genes that may be responsive to MCFAs. Using a fluorescence-based screening method, we identified MCFA-responsive promoters, four that upregulated gene expression, and three that downregulated gene expression. Dose-response analysis revealed that some of the promoters were sensitive to fatty acid concentrations as low as 0.02-0.06 mM. The MCFA-responsive promoters reported in this study could be used in dynamic regulation of fatty acids and fatty acid-derived products in S. cerevisiae.
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Affiliation(s)
- Li Han
- Henan Collaborative Innovation Center for Food Production and SafetySchool of Food and BioengineeringZhengzhou University of Light IndustryZhengzhouP. R. China
- Henan Key Laboratory of Cold Chain Food Quality and Safety ControlZhengzhouP. R. China
| | - Danya Han
- Henan Collaborative Innovation Center for Food Production and SafetySchool of Food and BioengineeringZhengzhou University of Light IndustryZhengzhouP. R. China
| | - Lei Li
- Henan Collaborative Innovation Center for Food Production and SafetySchool of Food and BioengineeringZhengzhou University of Light IndustryZhengzhouP. R. China
| | - Shen Huang
- Henan Collaborative Innovation Center for Food Production and SafetySchool of Food and BioengineeringZhengzhou University of Light IndustryZhengzhouP. R. China
- Henan Key Laboratory of Cold Chain Food Quality and Safety ControlZhengzhouP. R. China
| | - Peixin He
- Henan Collaborative Innovation Center for Food Production and SafetySchool of Food and BioengineeringZhengzhou University of Light IndustryZhengzhouP. R. China
- Henan Key Laboratory of Cold Chain Food Quality and Safety ControlZhengzhouP. R. China
| | - Qinhong Wang
- CAS Key Laboratory of Systems Microbial BiotechnologyTianjin Institute of Industrial BiotechnologyChinese Academy of Sciences (CAS)TianjinP. R. China
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20
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Han G, Xu N, Sun X, Chen J, Chen C, Wang Q. Improvement of l-Valine Production by Atmospheric and Room Temperature Plasma Mutagenesis and High-Throughput Screening in Corynebacterium glutamicum. ACS OMEGA 2020; 5:4751-4758. [PMID: 32201760 PMCID: PMC7081258 DOI: 10.1021/acsomega.9b02747] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/25/2019] [Accepted: 02/13/2020] [Indexed: 06/10/2023]
Abstract
As one of the branched-chain amino acids, l-valine is an essential nutrient for most mammalian species. In this study, the l-valine producer Corynebacterium glutamicum ΔppcΔaceEΔalatΔpqo was first constructed. Additionally, an improved biosensor based on the Lrp-type transcriptional regulator and temperature-sensitive replication was built. Then, the C. glutamicum strain was mutagenized by atmospheric and room temperature plasma. A sequential three-step procedure was carried out to screen l-valine-producing strains, including the fluorescence-activated cell sorting (FACS), 96-well plate screening, and flask fermentation. The final mutant HL2-7 obtained by screening produced 3.20 g/L of l-valine, which was 21.47% higher than the titer produced by the starting strain. This study demonstrates that the l-valine-producing mutants can be successfully isolated based on the Lrp sensor system in combination with FACS screening after random mutagenesis.
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Affiliation(s)
- Guoqiang Han
- Life
Science and Technology Institute, Yangtze
Normal University, Chongqing 408100, P. R. China
- School
of Advanced Agriculture and Bioengineering, Yangtze Normal University, Chongqing 408100, P. R. China
| | - Ning Xu
- Tianjin
Institute of Industrial Biotechnology, Chinese
Academy of Sciences, Tianjin 300308, P. R. China
| | - Xieping Sun
- Life
Science and Technology Institute, Yangtze
Normal University, Chongqing 408100, P. R. China
| | - Jinzhao Chen
- Life
Science and Technology Institute, Yangtze
Normal University, Chongqing 408100, P. R. China
| | - Chun Chen
- Life
Science and Technology Institute, Yangtze
Normal University, Chongqing 408100, P. R. China
| | - Qing Wang
- Life
Science and Technology Institute, Yangtze
Normal University, Chongqing 408100, P. R. China
- School
of Advanced Agriculture and Bioengineering, Yangtze Normal University, Chongqing 408100, P. R. China
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21
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Zhao L, Lu Y, Yang J, Fang Y, Zhu L, Ding Z, Wang C, Ma W, Hu X, Wang X. Expression regulation of multiple key genes to improve L-threonine in Escherichia coli. Microb Cell Fact 2020; 19:46. [PMID: 32093713 PMCID: PMC7041290 DOI: 10.1186/s12934-020-01312-5] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2019] [Accepted: 02/18/2020] [Indexed: 11/28/2022] Open
Abstract
Background Escherichia coli is an important strain for l-threonine production. Genetic switch is a ubiquitous regulatory tool for gene expression in prokaryotic cells. To sense and regulate intracellular or extracellular chemicals, bacteria evolve a variety of transcription factors. The key enzymes required for l-threonine biosynthesis in E. coli are encoded by the thr operon. The thr operon could coordinate expression of these genes when l-threonine is in short supply in the cell. Results The thrL leader regulatory elements were applied to regulate the expression of genes iclR, arcA, cpxR, gadE, fadR and pykF, while the threonine-activating promoters PcysH, PcysJ and PcysD were applied to regulate the expression of gene aspC, resulting in the increase of l-threonine production in an l-threonine producing E. coli strain TWF001. Firstly, different parts of the regulator thrL were inserted in the iclR regulator region in TWF001, and the best resulting strain TWF063 produced 16.34 g l-threonine from 40 g glucose after 30 h cultivation. Secondly, the gene aspC following different threonine-activating promoters was inserted into the chromosome of TWF063, and the best resulting strain TWF066 produced 17.56 g l-threonine from 40 g glucose after 30 h cultivation. Thirdly, the effect of expression regulation of arcA, cpxR, gadE, pykF and fadR was individually investigated on l-threonine production in TWF001. Finally, using TWF066 as the starting strain, the expression of genes arcA, cpxR, gadE, pykF and fadR was regulated individually or in combination to obtain the best strain for l-threonine production. The resulting strain TWF083, in which the expression of seven genes (iclR, aspC, arcA, cpxR, gadE, pykF, fadR and aspC) was regulated, produced 18.76 g l-threonine from 30 g glucose, 26.50 g l-threonine from 40 g glucose, or 26.93 g l-threonine from 50 g glucose after 30 h cultivation. In 48 h fed-batch fermentation, TWF083 could produce 116.62 g/L l‐threonine with a yield of 0.486 g/g glucose and productivity of 2.43 g/L/h. Conclusion The genetic engineering through the expression regulation of key genes is a better strategy than simple deletion of these genes to improve l-threonine production in E. coli. This strategy has little effect on the intracellular metabolism in the early stage of the growth but could increase l-threonine biosynthesis in the late stage.
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Affiliation(s)
- Lei Zhao
- State Key Laboratory of Food Science and Technology, Jiangnan University, 1800 Lihu Avenue, Wuxi, 214122, China.,International Joint Laboratory on Food Safety, Jiangnan University, Wuxi, 214122, China
| | - Ying Lu
- Nanjing Customs District P. R. China, Wuxi, 214122, China
| | - Jun Yang
- State Key Laboratory of Food Science and Technology, Jiangnan University, 1800 Lihu Avenue, Wuxi, 214122, China.,International Joint Laboratory on Food Safety, Jiangnan University, Wuxi, 214122, China
| | - Yu Fang
- State Key Laboratory of Food Science and Technology, Jiangnan University, 1800 Lihu Avenue, Wuxi, 214122, China.,International Joint Laboratory on Food Safety, Jiangnan University, Wuxi, 214122, China
| | - Lifei Zhu
- State Key Laboratory of Food Science and Technology, Jiangnan University, 1800 Lihu Avenue, Wuxi, 214122, China.,International Joint Laboratory on Food Safety, Jiangnan University, Wuxi, 214122, China
| | - Zhixiang Ding
- State Key Laboratory of Food Science and Technology, Jiangnan University, 1800 Lihu Avenue, Wuxi, 214122, China.,International Joint Laboratory on Food Safety, Jiangnan University, Wuxi, 214122, China
| | - Chenhui Wang
- State Key Laboratory of Food Science and Technology, Jiangnan University, 1800 Lihu Avenue, Wuxi, 214122, China.,International Joint Laboratory on Food Safety, Jiangnan University, Wuxi, 214122, China
| | - Wenjian Ma
- State Key Laboratory of Food Science and Technology, Jiangnan University, 1800 Lihu Avenue, Wuxi, 214122, China.,International Joint Laboratory on Food Safety, Jiangnan University, Wuxi, 214122, China
| | - Xiaoqing Hu
- State Key Laboratory of Food Science and Technology, Jiangnan University, 1800 Lihu Avenue, Wuxi, 214122, China.,International Joint Laboratory on Food Safety, Jiangnan University, Wuxi, 214122, China
| | - Xiaoyuan Wang
- State Key Laboratory of Food Science and Technology, Jiangnan University, 1800 Lihu Avenue, Wuxi, 214122, China. .,International Joint Laboratory on Food Safety, Jiangnan University, Wuxi, 214122, China. .,Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, 214122, China.
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22
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Zhao L, Zhang H, Wang X, Han G, Ma W, Hu X, Li Y. Transcriptomic analysis of an l-threonine-producing Escherichia coli TWF001. Biotechnol Appl Biochem 2020; 67:414-429. [PMID: 31976571 DOI: 10.1002/bab.1890] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2019] [Accepted: 01/21/2020] [Indexed: 01/10/2023]
Abstract
Wild-type Escherichia coli usually does not accumulate l-threonine, but E. coli strain TWF001 could produce 30.35 g/L l-threonine after 23-H fed-batch fermentation. To understand the mechanism for the high yield of l-threonine production in TWF001, transcriptomic analyses of the TWF001 cell samples collected at the logarithmic and stationary phases were performed, using the wild-type E. coli strain W3110 as the control. Compared with W3110, 1739 and 2361 genes were differentially transcribed in the logarithmic and stationary phases, respectively. Most genes related to the biosynthesis of l-threonine were significantly upregulated. Some key genes related to the NAD(P)H regeneration were upregulated. Many genes relevant to glycolysis and TCA cycle were downregulated. The key genes involved in the l-threonine degradation were downregulated. The gene rhtA encoding the l-threonine exporter was upregulated, whereas the genes sstT and tdcC encoding the l-threonine importer were downregulated. The upregulated genes in the glutamate pathway might form an amino-providing loop, which is beneficial for the high yield of l-threonine production. Many genes encoding the 30S and 50S subunits of ribosomes were also upregulated. The findings are useful for gene engineering to increase l-threonine production in E. coli.
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Affiliation(s)
- Lei Zhao
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, 214122, China.,Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, 214122, China
| | - Hailing Zhang
- Department of Biological Engineering, College of Life Science, Yantai University, Shandong, 408100, China
| | - Xiaoyuan Wang
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, 214122, China.,Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, 214122, China.,International Joint Laboratory on Food Safety, Jiangnan University, Wuxi, 214122, China
| | - Guoqiang Han
- College of Modern Agriculture and Biological Engineering, Yangtze Normal University, Chongqing, 264005, China
| | - Wenjian Ma
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, 214122, China.,International Joint Laboratory on Food Safety, Jiangnan University, Wuxi, 214122, China
| | - Xiaoqing Hu
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, 214122, China.,International Joint Laboratory on Food Safety, Jiangnan University, Wuxi, 214122, China
| | - Ye Li
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, 214122, China
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23
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Zeng W, Guo L, Xu S, Chen J, Zhou J. High-Throughput Screening Technology in Industrial Biotechnology. Trends Biotechnol 2020; 38:888-906. [PMID: 32005372 DOI: 10.1016/j.tibtech.2020.01.001] [Citation(s) in RCA: 122] [Impact Index Per Article: 30.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2019] [Revised: 01/01/2020] [Accepted: 01/03/2020] [Indexed: 12/14/2022]
Abstract
Based on the development of automatic devices and rapid assay methods, various high-throughput screening (HTS) strategies have been established for improving the performance of industrial microorganisms. We discuss the most significant factors that can improve HTS efficiency, including the construction of screening libraries with high diversity and the use of new detection methods to expand the search range and highlight target compounds. We also summarize applications of HTS for enhancing the performance of industrial microorganisms. Current challenges and potential improvements to HTS in industrial biotechnology are discussed in the context of rapid developments in synthetic biology, nanotechnology, and artificial intelligence. Rational integration will be an important driving force for constructing more efficient industrial microorganisms with wider applications in biotechnology.
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Affiliation(s)
- Weizhu Zeng
- National Engineering Laboratory for Cereal Fermentation Technology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China; Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China
| | - Likun Guo
- National Engineering Laboratory for Cereal Fermentation Technology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China; Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China; Jiangsu Provisional Research Center for Bioactive Product Processing Technology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China
| | - Sha Xu
- National Engineering Laboratory for Cereal Fermentation Technology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China; Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China; Jiangsu Provisional Research Center for Bioactive Product Processing Technology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China
| | - Jian Chen
- National Engineering Laboratory for Cereal Fermentation Technology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China; Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China; Jiangsu Provisional Research Center for Bioactive Product Processing Technology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China
| | - Jingwen Zhou
- National Engineering Laboratory for Cereal Fermentation Technology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China; Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China; Jiangsu Provisional Research Center for Bioactive Product Processing Technology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China.
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Qiu C, Zhang A, Tao S, Li K, Chen K, Ouyang P. Combination of ARTP mutagenesis and color-mediated high-throughput screening to enhance 1-naphthol yield from microbial oxidation of naphthalene in aqueous system. Front Chem Sci Eng 2020. [DOI: 10.1007/s11705-019-1876-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
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25
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Tools and systems for evolutionary engineering of biomolecules and microorganisms. ACTA ACUST UNITED AC 2019; 46:1313-1326. [DOI: 10.1007/s10295-019-02191-5] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2019] [Accepted: 05/20/2019] [Indexed: 12/28/2022]
Abstract
Abstract
Evolutionary approaches have been providing solutions to various bioengineering challenges in an efficient manner. In addition to traditional adaptive laboratory evolution and directed evolution, recent advances in synthetic biology and fluidic systems have opened a new era of evolutionary engineering. Synthetic genetic circuits have been created to control mutagenesis and enable screening of various phenotypes, particularly metabolite production. Fluidic systems can be used for high-throughput screening and multiplexed continuous cultivation of microorganisms. Moreover, continuous directed evolution has been achieved by combining all the steps of evolutionary engineering. Overall, modern tools and systems for evolutionary engineering can be used to establish the artificial equivalent to natural evolution for various research applications.
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Wang J, Ma W, Fang Y, Yang J, Zhan J, Chen S, Wang X. Increasing L-threonine production in Escherichia coli by overexpressing the gene cluster phaCAB. J Ind Microbiol Biotechnol 2019; 46:1557-1568. [PMID: 31312942 DOI: 10.1007/s10295-019-02215-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2019] [Accepted: 07/11/2019] [Indexed: 10/26/2022]
Abstract
L-Threonine is an important branched-chain amino acid and could be applied in feed, drugs, and food. In this study, L-threonine production in an L-threonine-producing Escherichia coli strain TWF001 was significantly increased by overexpressing the gene cluster phaCAB from Ralstonia eutropha. TWF001/pFW01-phaCAB could produce 96.4-g/L L-threonine in 3-L fermenter and 133.5-g/L L-threonine in 10-L fermenter, respectively. In addition, TWF001/pFW01-phaCAB produced 216% more acetyl-CoA, 43% more malate, and much less acetate than the vector control TWF001/pFW01, and meanwhile, TWF001/pFW01-phaCAB produced poly-3-hydroxybutyrate, while TWF001/pFW01 did not. Transcription analysis showed that the key genes in the L-threonine biosynthetic pathway were up-regulated, the genes relevant to the acetate formation were down-regulated, and the gene acs encoding the enzyme which converts acetate to acetyl-CoA was up-regulated. The results suggested that overexpression of the gene cluster phaCAB in E. coli benefits the enhancement of L-threonine production.
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Affiliation(s)
- Jianli Wang
- State Key Laboratory of Food Science and Technology, Jiangnan University, 1800 Lihu Avenue, Wuxi, 214122, China.,International Joint Laboratory on Food Safety, Jiangnan University, Wuxi, 214122, China
| | - Wenjian Ma
- State Key Laboratory of Food Science and Technology, Jiangnan University, 1800 Lihu Avenue, Wuxi, 214122, China.,International Joint Laboratory on Food Safety, Jiangnan University, Wuxi, 214122, China
| | - Yu Fang
- State Key Laboratory of Food Science and Technology, Jiangnan University, 1800 Lihu Avenue, Wuxi, 214122, China.,International Joint Laboratory on Food Safety, Jiangnan University, Wuxi, 214122, China
| | - Jun Yang
- State Key Laboratory of Food Science and Technology, Jiangnan University, 1800 Lihu Avenue, Wuxi, 214122, China.,Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, 214122, China
| | - Jie Zhan
- State Key Laboratory of Food Science and Technology, Jiangnan University, 1800 Lihu Avenue, Wuxi, 214122, China.,International Joint Laboratory on Food Safety, Jiangnan University, Wuxi, 214122, China
| | - Shangwei Chen
- State Key Laboratory of Food Science and Technology, Jiangnan University, 1800 Lihu Avenue, Wuxi, 214122, China
| | - Xiaoyuan Wang
- State Key Laboratory of Food Science and Technology, Jiangnan University, 1800 Lihu Avenue, Wuxi, 214122, China. .,International Joint Laboratory on Food Safety, Jiangnan University, Wuxi, 214122, China. .,Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, 214122, China.
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27
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Wang X, Li Q, Sun C, Cai Z, Zheng X, Guo X, Ni X, Zhou W, Guo Y, Zheng P, Chen N, Sun J, Li Y, Ma Y. GREACE-assisted adaptive laboratory evolution in endpoint fermentation broth enhances lysine production by Escherichia coli. Microb Cell Fact 2019; 18:106. [PMID: 31186003 PMCID: PMC6560909 DOI: 10.1186/s12934-019-1153-6] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2019] [Accepted: 06/01/2019] [Indexed: 12/23/2022] Open
Abstract
BACKGROUND Late-stage fermentation broth contains high concentrations of target chemicals. Additionally, it contains various cellular metabolites which have leaked from lysed cells, which would exert multifactorial stress to industrial hyperproducers and perturb both cellular metabolism and product formation. Although adaptive laboratory evolution (ALE) has been wildly used to improve stress tolerance of microbial cell factories, single-factor stress condition (i.e. target product or sodium chloride at a high concentration) is currently provided. In order to enhance bacterial stress tolerance to actual industrial production conditions, ALE in late-stage fermentation broth is desired. Genome replication engineering assisted continuous evolution (GREACE) employs mutants of the proofreading element of DNA polymerase complex (DnaQ) to facilitate mutagenesis. Application of GREACE coupled-with selection under stress conditions is expected to accelerate the ALE process. RESULTS In this study, GREACE was first modified by expressing a DnaQ mutant KR5-2 using an arabinose inducible promoter on a temperature-sensitive plasmid, which resulted in timed mutagenesis introduction. Using this method, tolerance of a lysine hyperproducer E. coli MU-1 was improved by enriching mutants in a lysine endpoint fermentation broth. Afterwards, the KR5-2 expressing plasmid was cured to stabilize acquired genotypes. By subsequent fermentation evaluation, a mutant RS3 with significantly improved lysine production capacity was selected. The final titer, yield and total amount of lysine produced by RS3 in a 5-L batch fermentation reached 155.0 ± 1.4 g/L, 0.59 ± 0.02 g lysine/g glucose, and 605.6 ± 23.5 g, with improvements of 14.8%, 9.3%, and 16.7%, respectively. Further metabolomics and genomics analyses, coupled with molecular biology studies revealed that mutations SpeBA302V, AtpBS165N and SecYM145V mainly contributed both to improved cell integrity under stress conditions and enhanced metabolic flux into lysine synthesis. CONCLUSIONS Our present study indicates that improving a lysine hyperproducer by GREACE-assisted ALE in its stressful living environment is efficient and effective. Accordingly, this is a promising method for improving other valuable chemical hyperproducers.
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Affiliation(s)
- Xiaowei Wang
- College of Biotechnology, Tianjin University of Science and Technology, Tianjin, 300457, China.,Key Laboratory of Systems Microbial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China.,Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, People's Republic of China
| | - Qinggang Li
- Key Laboratory of Systems Microbial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China.,Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, People's Republic of China
| | - Cunmin Sun
- Key Laboratory of Systems Microbial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China.,Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, People's Republic of China
| | - Zhen Cai
- CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Xiaomei Zheng
- Key Laboratory of Systems Microbial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China.,Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, People's Republic of China
| | - Xuan Guo
- Key Laboratory of Systems Microbial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China.,Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, People's Republic of China
| | - Xiaomeng Ni
- Key Laboratory of Systems Microbial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China.,Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, People's Republic of China
| | - Wenjuan Zhou
- Key Laboratory of Systems Microbial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China.,Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, People's Republic of China
| | - Yanmei Guo
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, People's Republic of China
| | - Ping Zheng
- Key Laboratory of Systems Microbial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China. .,Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, People's Republic of China.
| | - Ning Chen
- College of Biotechnology, Tianjin University of Science and Technology, Tianjin, 300457, China
| | - Jibin Sun
- Key Laboratory of Systems Microbial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China. .,Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, People's Republic of China.
| | - Yin Li
- CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Yanhe Ma
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, People's Republic of China
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28
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Yang J, Fang Y, Wang J, Wang C, Zhao L, Wang X. Deletion of regulator-encoding genes fadR, fabR and iclR to increase L-threonine production in Escherichia coli. Appl Microbiol Biotechnol 2019; 103:4549-4564. [DOI: 10.1007/s00253-019-09818-8] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2019] [Revised: 03/19/2019] [Accepted: 03/31/2019] [Indexed: 12/25/2022]
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29
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Design and optimization of genetically encoded biosensors for high-throughput screening of chemicals. Curr Opin Biotechnol 2018; 54:18-25. [DOI: 10.1016/j.copbio.2018.01.011] [Citation(s) in RCA: 47] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2017] [Revised: 01/08/2018] [Accepted: 01/11/2018] [Indexed: 02/07/2023]
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30
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Liu L, Hu W, Li WJ, Wang SY, Lu D, Tian XJ, Mao YQ, Liu J, Chen JH. Heavy-ion mutagenesis significantly enhances enduracidin production by Streptomyces fungicidicus. Eng Life Sci 2018; 19:112-120. [PMID: 32624993 DOI: 10.1002/elsc.201800109] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2018] [Revised: 10/09/2018] [Accepted: 11/16/2018] [Indexed: 11/11/2022] Open
Abstract
To improve fermentative production of enduracidin, heavy-ion beams generated by the Heavy Ion Research Facility in Lanzhou (HIRFL), China, were employed for the first time to generate mutations in Streptomyces fungicidicus. Initial screening detected 44 positive mutants with larger inhibition zone, which were subsequently tested based on flask fermentation. Finally, 20 mutants showed 20% increase in enduracidin production, when compared with the original strain. Among them, enduracidin production by the three mutants (M13, M30, and M34) was significantly higher than that by the original strain. In particular, mutant M30 exhibited highest enduracidin production, which was 114% higher than that obtained with the original strain. Following culture optimization, the maximal enduracidin yield obtained by M30 reached 918.5 mg/L in 10 days, which was 34% higher than that noted in the control.
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Affiliation(s)
- Lu Liu
- Institute of Modern Physics Chinese Academy of Sciences Lanzhou P. R. China.,University of Chinese Academy of Sciences Beijing P. R. China
| | - Wei Hu
- Institute of Modern Physics Chinese Academy of Sciences Lanzhou P. R. China
| | - Wen-Jian Li
- Institute of Modern Physics Chinese Academy of Sciences Lanzhou P. R. China
| | - Shu-Yang Wang
- Institute of Modern Physics Chinese Academy of Sciences Lanzhou P. R. China
| | - Dong Lu
- Institute of Modern Physics Chinese Academy of Sciences Lanzhou P. R. China
| | - Xue-Jiao Tian
- Institute of Modern Physics Chinese Academy of Sciences Lanzhou P. R. China.,University of Chinese Academy of Sciences Beijing P. R. China
| | - Yan-Qin Mao
- Institute of Modern Physics Chinese Academy of Sciences Lanzhou P. R. China.,University of Chinese Academy of Sciences Beijing P. R. China
| | - Jing Liu
- Institute of Modern Physics Chinese Academy of Sciences Lanzhou P. R. China
| | - Ji-Hong Chen
- Institute of Modern Physics Chinese Academy of Sciences Lanzhou P. R. China
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31
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Hu W, Li WJ, Yang HQ, Chen JH. Current strategies and future prospects for enhancing microbial production of citric acid. Appl Microbiol Biotechnol 2018; 103:201-209. [PMID: 30421107 DOI: 10.1007/s00253-018-9491-6] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2018] [Accepted: 10/27/2018] [Indexed: 10/27/2022]
Abstract
Aspergillus niger and Yarrowia lipolytica are highly important in citric acid (CA) production. To further minimize the cost of CA bio-production using A. niger and Y. lipolytica, some strategies (e.g., metabolic engineering, efficient mutagenesis, and optimal fermentation strategies) were developed to enhance CA production and low-cost carbon sources were also utilized to decrease CA bio-production cost. In this review, we summarize the recent significant progresses in CA bio-production, including metabolic engineering, efficient mutagenesis and screening methods, optimal fermentation strategies, and use of low-cost carbon sources, and future prospects in this field are also discussed, which could help in the development of CA production industry.
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Affiliation(s)
- Wei Hu
- Institute of Modern Physics, Chinese Academy of Sciences, 509 Nanchang Road, Lanzhou, 730000, Gansu, China
| | - Wen-Jian Li
- Institute of Modern Physics, Chinese Academy of Sciences, 509 Nanchang Road, Lanzhou, 730000, Gansu, China
| | - Hai-Quan Yang
- The Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, 214122, Jiangsu, China.
| | - Ji-Hong Chen
- Institute of Modern Physics, Chinese Academy of Sciences, 509 Nanchang Road, Lanzhou, 730000, Gansu, China.
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32
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Jiang A, Hu W, Li W, Liu L, Tian X, Liu J, Wang S, Lu D, Chen J. Enhanced production of l-lactic acid by Lactobacillus thermophilus SRZ50 mutant generated by high-linear energy transfer heavy ion mutagenesis. Eng Life Sci 2018; 18:626-634. [PMID: 32624942 PMCID: PMC6999237 DOI: 10.1002/elsc.201800052] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2018] [Revised: 04/11/2018] [Accepted: 05/02/2018] [Indexed: 12/17/2022] Open
Abstract
The aim of this study was to improve l-lactic acid production of Lactobacillus thermophilus SRZ50. For this purpose, high efficient heavy-ion mutagenesis technique was performed using SRZ50 as the original strain. To enhance the screening efficiency for high yield l-lactic acid producers, a scale-down from shake flask to microtiter plate was developed. The results showed that 24-well U-bottom MTPs could well alternate shake flasks for L. thermophilus cultivation as a scale-down tool due to its a very good comparability to the shake flasks. Based on this microtiter plate screening method, two high l-lactic acid productivity mutants, A59 and A69, were successfully screened out, which presented, respectively, 15.8 and 16.2% higher productivities than that of the original strain. Based on fed-batch fermentation, the A69 mutant can accumulate 114.2 g/L l-lactic acid at 96 h. Hence, the proposed traditional microbial breeding method with efficient high-throughput screening assay was proved to be an appropriate strategy to obtain lactic acid-overproducing strain.
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Affiliation(s)
- Ai‐lian Jiang
- Department of BiophysicsInstitute of Modern PhysicsChinese Academy of SciencesLanzhouP. R. China
- University of Chinese Academy of SciencesBeijingP. R. China
| | - Wei Hu
- Department of BiophysicsInstitute of Modern PhysicsChinese Academy of SciencesLanzhouP. R. China
| | - Wen‐jian Li
- Department of BiophysicsInstitute of Modern PhysicsChinese Academy of SciencesLanzhouP. R. China
| | - Lu Liu
- Department of BiophysicsInstitute of Modern PhysicsChinese Academy of SciencesLanzhouP. R. China
- University of Chinese Academy of SciencesBeijingP. R. China
| | - Xue‐jiao Tian
- Department of BiophysicsInstitute of Modern PhysicsChinese Academy of SciencesLanzhouP. R. China
- University of Chinese Academy of SciencesBeijingP. R. China
| | - Jing Liu
- Department of BiophysicsInstitute of Modern PhysicsChinese Academy of SciencesLanzhouP. R. China
| | - Shu‐yang Wang
- Department of BiophysicsInstitute of Modern PhysicsChinese Academy of SciencesLanzhouP. R. China
| | - Dong Lu
- Department of BiophysicsInstitute of Modern PhysicsChinese Academy of SciencesLanzhouP. R. China
| | - Ji‐hong Chen
- Department of BiophysicsInstitute of Modern PhysicsChinese Academy of SciencesLanzhouP. R. China
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The Applications of Promoter-gene-Engineered Biosensors. SENSORS 2018; 18:s18092823. [PMID: 30150540 PMCID: PMC6164924 DOI: 10.3390/s18092823] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/15/2018] [Revised: 08/16/2018] [Accepted: 08/22/2018] [Indexed: 12/22/2022]
Abstract
A promoter is a small region of a DNA sequence that responds to various transcription factors, which initiates a particular gene expression. The promoter-engineered biosensor can activate or repress gene expression through a transcription factor recognizing specific molecules, such as polyamine, sugars, lactams, amino acids, organic acids, or a redox molecule; however, there are few reported applications of promoter-enhanced biosensors. This review paper highlights the strategies of construction of promoter gene-engineered biosensors with human and bacteria genetic promoter arrays with regard to high-throughput screening (HTS) molecular drugs, the study of the membrane protein’s localization and nucleocytoplasmic shuttling mechanism of regulating factors, enzyme activity, detection of the toxicity of intermediate chemicals, and probing bacteria density to improve value-added product titer. These biosensors’ sensitivity and specificity can be further improved by the proposed approaches of Mn2+ and Mg2+ added random error-prone PCR that is a technique used to generate randomized genomic libraries and site-directed mutagenesis approach, which is applied for the construction of bacteria’s “mutant library”. This is expected to establish a flexible HTS platform (biosensor array) to large-scale screen transcription factor-acting drugs, reduce the toxicity of intermediate compounds, and construct a gene-dynamic regulatory system in “push and pull” mode, in order to effectively regulate the valuable medicinal product production. These proposed novel promoter-engineered biosensors aiding in synthetic genetic circuit construction will maximize the efficiency of the bio-synthesis of medicinal compounds, which will greatly promote the development of microbial metabolic engineering and biomedical science.
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34
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In vivo biosensors: mechanisms, development, and applications. ACTA ACUST UNITED AC 2018; 45:491-516. [DOI: 10.1007/s10295-018-2004-x] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2017] [Accepted: 12/30/2017] [Indexed: 01/09/2023]
Abstract
Abstract
In vivo biosensors can recognize and respond to specific cellular stimuli. In recent years, biosensors have been increasingly used in metabolic engineering and synthetic biology, because they can be implemented in synthetic circuits to control the expression of reporter genes in response to specific cellular stimuli, such as a certain metabolite or a change in pH. There are many types of natural sensing devices, which can be generally divided into two main categories: protein-based and nucleic acid-based. Both can be obtained either by directly mining from natural genetic components or by engineering the existing genetic components for novel specificity or improved characteristics. A wide range of new technologies have enabled rapid engineering and discovery of new biosensors, which are paving the way for a new era of biotechnological progress. Here, we review recent advances in the design, optimization, and applications of in vivo biosensors in the field of metabolic engineering and synthetic biology.
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Zhang X, Zhang X, Xu G, Zhang X, Shi J, Xu Z. Integration of ARTP mutagenesis with biosensor-mediated high-throughput screening to improve l-serine yield in Corynebacterium glutamicum. Appl Microbiol Biotechnol 2018; 102:5939-5951. [DOI: 10.1007/s00253-018-9025-2] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2017] [Revised: 03/31/2018] [Accepted: 04/14/2018] [Indexed: 12/31/2022]
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36
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Zhao H, Fang Y, Wang X, Zhao L, Wang J, Li Y. Increasing L-threonine production in Escherichia coli by engineering the glyoxylate shunt and the L-threonine biosynthesis pathway. Appl Microbiol Biotechnol 2018; 102:5505-5518. [PMID: 29713792 DOI: 10.1007/s00253-018-9024-3] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2018] [Revised: 03/20/2018] [Accepted: 04/13/2018] [Indexed: 11/29/2022]
Abstract
L-threonine is an important amino acid that can be added in food, medicine, or feed. Here, the influence of glyoxylate shunt on an L-threonine producing strain Escherichia coli TWF001 has been studied. The gene iclR was deleted, and the native promoter of the aceBA operon was replaced by the trc promoter in the chromosome of TWF001, the resulting strainTWF004 could produce 0.39 g L-threonine from1 g glucose after 36-h flask cultivation. Further replacing the native promoter of aspC by the trc promoter in the chromosome of TWF004 resulted in the strain TWF006. TWF006 could produce 0.42 g L-threonine from 1 g glucose after 36-h flask cultivation. Three key genes in the biosynthetic pathway of L-threonine, thrA * (a mutated thrA), thrB, and thrC were overexpressed in TWF006, resulting the strain TWF006/pFW01-thrA * BC. TWF006/pFW01-thrA * BC could produce 0.49 g L-threonine from 1 g glucose after 36-h flask cultivation. Next, the genes asd, rhtA, rhtC, or thrE were inserted into the plasmid TWF006/pFW01-thrA * BC, and TWF006 was transformed with these plasmids, resulting the strains TWF006/pFW01-thrA * BC-asd, TWF006/pFW01-thrA * BC-rhtA, TWF006/pFW01-thrA * BC-rhtC, and TWF006/pFW01-thrA * BC-thrE, respectively. These four strains could produce more L-threonine than the control strain, and the highest yield was produced by TWF006/pFW01-thrA * BC-asd; after 36-h flask cultivation, TWF006/pFW01-thrA * BC-asd could produce 15.85 g/l L-threonine, i.e., 0.53 g L-threonine per 1 g glucose, which is a 70% increase relative to the control strain TWF001. The results suggested that the combined engineering of glyoxylate shunt and L-threonine biosynthesis pathway could significantly increase the L-threonine production in E. coli.
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Affiliation(s)
- Hui Zhao
- State Key Laboratory of Food Science and Technology, Jiangnan University, 1800 Lihu Avenue, Wuxi, 214122, China.,Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, 214122, China
| | - Yu Fang
- State Key Laboratory of Food Science and Technology, Jiangnan University, 1800 Lihu Avenue, Wuxi, 214122, China.,Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, 214122, China
| | - Xiaoyuan Wang
- State Key Laboratory of Food Science and Technology, Jiangnan University, 1800 Lihu Avenue, Wuxi, 214122, China. .,Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, 214122, China. .,International Joint Laboratory on Food Safety, Jiangnan University, Wuxi, 214122, China.
| | - Lei Zhao
- State Key Laboratory of Food Science and Technology, Jiangnan University, 1800 Lihu Avenue, Wuxi, 214122, China.,International Joint Laboratory on Food Safety, Jiangnan University, Wuxi, 214122, China
| | - Jianli Wang
- State Key Laboratory of Food Science and Technology, Jiangnan University, 1800 Lihu Avenue, Wuxi, 214122, China.,International Joint Laboratory on Food Safety, Jiangnan University, Wuxi, 214122, China
| | - Ye Li
- State Key Laboratory of Food Science and Technology, Jiangnan University, 1800 Lihu Avenue, Wuxi, 214122, China
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Promoter library-based module combination (PLMC) technology for optimization of threonine biosynthesis in Corynebacterium glutamicum. Appl Microbiol Biotechnol 2018; 102:4117-4130. [DOI: 10.1007/s00253-018-8911-y] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2017] [Revised: 02/24/2018] [Accepted: 03/03/2018] [Indexed: 12/20/2022]
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38
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A Novel Corynebacterium glutamicum l-Glutamate Exporter. Appl Environ Microbiol 2018; 84:AEM.02691-17. [PMID: 29330181 DOI: 10.1128/aem.02691-17] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2017] [Accepted: 01/07/2018] [Indexed: 01/24/2023] Open
Abstract
Besides metabolic pathways and regulatory networks, transport systems are also pivotal for cellular metabolism and hyperproduction of biochemicals using microbial cell factories. The identification and characterization of transporters are therefore of great significance for the understanding and engineering of transport reactions. Herein, a novel l-glutamate exporter, MscCG2, which exists extensively in Corynebacterium glutamicum strains but is distinct from the only known l-glutamate exporter, MscCG, was discovered in an industrial l-glutamate-producing C. glutamicum strain. MscCG2 was predicted to possess three transmembrane helices in the N-terminal region and located in the cytoplasmic membrane, which are typical structural characteristics of the mechanosensitive channel of small conductance. MscCG2 has a low amino acid sequence identity (23%) to MscCG and evolved separately from MscCG with four transmembrane helices. Despite the considerable differences between MscCG2 and MscCG in sequence and structure, gene deletion and complementation confirmed that MscCG2 also functioned as an l-glutamate exporter and an osmotic safety valve in C. glutamicum Besides, transcriptional analysis showed that MscCG2 and MscCG genes were transcribed in similar patterns and not induced by l-glutamate-producing conditions. It was also demonstrated that MscCG2-mediated l-glutamate excretion was activated by biotin limitation or penicillin treatment and that constitutive l-glutamate excretion was triggered by a gain-of-function mutation of MscCG2 (A151V). Discovery of MscCG2 will enrich the understanding of bacterial amino acid transport and provide additional targets for exporter engineering.IMPORTANCE The exchange of matter, energy, and information with surroundings is fundamental for cellular metabolism. Therefore, studying transport systems that are essential for these processes is of great significance. Besides, transport systems of bacterial cells are usually related to product excretion as well as product reuptake, making transporter engineering a useful strategy for strain improvement. The significance of our research is in identifying and characterizing a novel l-glutamate exporter from the industrial workhorse Corynebacterium glutamicum, which will enrich the understanding of l-glutamate excretion and provide a new target for studying bacterial amino acid transport and engineering transport reactions.
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Lee JH, Wendisch VF. Production of amino acids - Genetic and metabolic engineering approaches. BIORESOURCE TECHNOLOGY 2017; 245:1575-1587. [PMID: 28552565 DOI: 10.1016/j.biortech.2017.05.065] [Citation(s) in RCA: 61] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/25/2017] [Revised: 05/10/2017] [Accepted: 05/11/2017] [Indexed: 05/22/2023]
Abstract
The biotechnological production of amino acids occurs at the million-ton scale and annually about 6milliontons of l-glutamate and l-lysine are produced by Escherichia coli and Corynebacterium glutamicum strains. l-glutamate and l-lysine production from starch hydrolysates and molasses is very efficient and access to alternative carbon sources and new products has been enabled by metabolic engineering. This review focusses on genetic and metabolic engineering of amino acid producing strains. In particular, rational approaches involving modulation of transcriptional regulators, regulons, and attenuators will be discussed. To address current limitations of metabolic engineering, this article gives insights on recent systems metabolic engineering approaches based on functional tools and method such as genome reduction, amino acid sensors based on transcriptional regulators and riboswitches, CRISPR interference, small regulatory RNAs, DNA scaffolding, and optogenetic control, and discusses future prospects.
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Affiliation(s)
- Jin-Ho Lee
- Major in Food Science & Biotechnology, School of Food Biotechnology & Nutrition, Kyungsung University, 309, Suyeong-ro, Nam-gu, Busan 48434, Republic of Korea
| | - Volker F Wendisch
- Genetics of Prokaryotes, Faculty of Biology and Center for Biotechnology, Bielefeld University, Bielefeld, Germany.
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Shi S, Choi YW, Zhao H, Tan MH, Ang EL. Discovery and engineering of a 1-butanol biosensor in Saccharomyces cerevisiae. BIORESOURCE TECHNOLOGY 2017; 245:1343-1351. [PMID: 28712783 DOI: 10.1016/j.biortech.2017.06.114] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2017] [Revised: 06/20/2017] [Accepted: 06/21/2017] [Indexed: 06/07/2023]
Abstract
The present study aimed to develop a universal methodology for the discovery of biosensors sensitive to particular stresses or metabolites by using a transcriptome analysis, in order to address the need for in vivo biosensors to drive the engineering of microbial cell factories. The method was successfully applied to the discovery of 1-butanol sensors. In particular, the genome-wide transcriptome profiling of S. cerevisiae exposed to three similar short-chain alcohols, 1-butanol, 1-propanol, and ethanol, identified genes that were differentially expressed only under the treatment of 1-butanol. From these candidates, two promoters that responded specifically to 1-butanol were characterized in a dose-dependent manner and were used to distinguish differences in production levels among different 1-butanol producer strains. This strategy opens up new opportunities for the discovery of promoter-based biosensors and can potentially be used to identify biosensors for any metabolite that causes cellular transcriptomic changes.
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Affiliation(s)
- Shuobo Shi
- Metabolic Engineering Research Laboratory, Science and Engineering Institutes, Agency for Science, Technology and Research, Singapore.
| | - Yook Wah Choi
- Metabolic Engineering Research Laboratory, Science and Engineering Institutes, Agency for Science, Technology and Research, Singapore.
| | - Huimin Zhao
- Metabolic Engineering Research Laboratory, Science and Engineering Institutes, Agency for Science, Technology and Research, Singapore; Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA.
| | - Meng How Tan
- School of Chemical and Biomedical Engineering, Nanyang Technological University, Singapore; Genome Institute of Singapore, Agency for Science, Technology and Research, Singapore.
| | - Ee Lui Ang
- Metabolic Engineering Research Laboratory, Science and Engineering Institutes, Agency for Science, Technology and Research, Singapore.
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Liu Y, Liu Y, Wang M. Design, Optimization and Application of Small Molecule Biosensor in Metabolic Engineering. Front Microbiol 2017; 8:2012. [PMID: 29089935 PMCID: PMC5651080 DOI: 10.3389/fmicb.2017.02012] [Citation(s) in RCA: 58] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2017] [Accepted: 09/29/2017] [Indexed: 11/13/2022] Open
Abstract
The development of synthetic biology and metabolic engineering has painted a great future for the bio-based economy, including fuels, chemicals, and drugs produced from renewable feedstocks. With the rapid advance of genome-scale modeling, pathway assembling and genome engineering/editing, our ability to design and generate microbial cell factories with various phenotype becomes almost limitless. However, our lack of ability to measure and exert precise control over metabolite concentration related phenotypes becomes a bottleneck in metabolic engineering. Genetically encoded small molecule biosensors, which provide the means to couple metabolite concentration to measurable or actionable outputs, are highly promising solutions to the bottleneck. Here we review recent advances in the design, optimization and application of small molecule biosensor in metabolic engineering, with particular focus on optimization strategies for transcription factor (TF) based biosensors.
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Affiliation(s)
- Yang Liu
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
| | - Ye Liu
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
| | - Meng Wang
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
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42
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Sense and sensitivity in bioprocessing — detecting cellular metabolites with biosensors. Curr Opin Chem Biol 2017; 40:31-36. [DOI: 10.1016/j.cbpa.2017.05.014] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2017] [Revised: 05/23/2017] [Accepted: 05/26/2017] [Indexed: 11/23/2022]
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Hu W, Li W, Chen J. Recent advances of microbial breeding via heavy-ion mutagenesis at IMP. Lett Appl Microbiol 2017; 65:274-280. [PMID: 28741678 DOI: 10.1111/lam.12780] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2017] [Revised: 07/11/2017] [Accepted: 07/17/2017] [Indexed: 12/12/2022]
Abstract
Nowadays, the value of heavy-ion mutagenesis has been accepted as a novel powerful mutagen technique to generate new microbial mutants due to its high linear energy transfer and high relative biological effectiveness. This paper briefly reviews recent progress in developing a more efficient mutagenesis technique for microbial breeding using heavy-ion mutagenesis, and also presents the outline of the beam line for microbial breeding in Heavy Ion Research Facility of Lanzhou. Then, new insights into microbial biotechnology via heavy-ion mutagenesis are also further explored. We hope that our concerns will give deep insight into microbial breeding biotechnology via heavy-ion mutagenesis. We also believe that heavy-ion mutagenesis breeding will greatly contribute to the progress of a comprehensive study industrial strain engineering for bioindustry in the future. SIGNIFICANCE AND IMPACT OF THE STUDY There is currently a great interest in developing rapid and diverse microbial mutation tool for strain modification. Heavy-ion mutagenesis has been proved as a powerful technology for microbial breeding due to its broad spectrum of mutation phenotypes with high efficiency. In order to deeply understand heavy-ion mutagenesis technology, this paper briefly reviews recent progress in microbial breeding using heavy-ion mutagenesis at IMP, and also presents the outline of the beam line for microbial breeding in Heavy Ion Research Facility of Lanzhou (HIRFL) as well as new insights into microbial biotechnology via heavy-ion mutagenesis. Thus, this work can provide the guidelines to promote the development of novel microbial biotechnology cross-linking heavy-ion mutagenesis breeding that could make breeding process more efficiently in the future.
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Affiliation(s)
- W Hu
- Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou, China
| | - W Li
- Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou, China
| | - J Chen
- Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou, China
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Luo Z, Zeng W, Du G, Liu S, Fang F, Zhou J, Chen J. A high-throughput screening procedure for enhancing pyruvate production in Candida glabrata by random mutagenesis. Bioprocess Biosyst Eng 2017; 40:693-701. [DOI: 10.1007/s00449-017-1734-x] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2016] [Accepted: 01/07/2017] [Indexed: 12/30/2022]
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45
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Wang Y, Li Q, Zheng P, Guo Y, Wang L, Zhang T, Sun J, Ma Y. Evolving the L-lysine high-producing strain of Escherichia coli using a newly developed high-throughput screening method. J Ind Microbiol Biotechnol 2016; 43:1227-35. [PMID: 27369765 PMCID: PMC4983297 DOI: 10.1007/s10295-016-1803-1] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2016] [Accepted: 06/22/2016] [Indexed: 12/30/2022]
Abstract
This study provided a new method which applied a selected L-lysine-inducible promoter for evolving lysine industrial strains of E. coli. According to the intracellular levels of the enhanced green fluorescent protein (EGFP) whose expression was controlled by the promoter, 186 strains were preliminarily selected using fluorescence-activated cell sorting from a 10-million-mutant library generated from a L-lysine high-producing E. coli strain. By subsequent multiple parameter evaluation of the 186 selected strains according to the concentration and the yield of lysine, the productivity per unit of cell in 96-deep-well blocks, two mutants MU-1 and MU-2 were obtained. They produced 136.51 ± 1.55 and 133.2 9 ± 1.42 g/L of lysine, respectively, in 5-L jars. Compared with the lysine concentration and the yield of the original strain, those of strain MU-1 improved by 21.00 and 9.05 %, respectively, and those of strain MU-2 improved by 18.14 and 10.41 %, respectively. The mutant selection and evaluation system newly established in our study should be useful for continuous improvement of the current E. coli strains in the lysine industry.
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Affiliation(s)
- Yan Wang
- College of Biotechnology, Tianjin University of Science and Technology, Tianjin, People's Republic of China.,Key Laboratory of Systems Microbial Biotechnology, Chinese Academy of Sciences, Tianjin, People's Republic of China.,Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, People's Republic of China
| | - Qinggang Li
- Key Laboratory of Systems Microbial Biotechnology, Chinese Academy of Sciences, Tianjin, People's Republic of China.,Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, People's Republic of China
| | - Ping Zheng
- Key Laboratory of Systems Microbial Biotechnology, Chinese Academy of Sciences, Tianjin, People's Republic of China. .,Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, People's Republic of China.
| | - Yanmei Guo
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, People's Republic of China
| | - Lixian Wang
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, People's Republic of China
| | - Tongcun Zhang
- College of Biotechnology, Tianjin University of Science and Technology, Tianjin, People's Republic of China
| | - Jibin Sun
- Key Laboratory of Systems Microbial Biotechnology, Chinese Academy of Sciences, Tianjin, People's Republic of China. .,Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, People's Republic of China.
| | - Yanhe Ma
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, People's Republic of China
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Bassalo MC, Liu R, Gill RT. Directed evolution and synthetic biology applications to microbial systems. Curr Opin Biotechnol 2016; 39:126-133. [DOI: 10.1016/j.copbio.2016.03.016] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2015] [Revised: 03/12/2016] [Accepted: 03/20/2016] [Indexed: 10/22/2022]
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