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Improvement of FK506 production by synthetic biology approaches. Biotechnol Lett 2016; 38:2015-2021. [DOI: 10.1007/s10529-016-2202-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2016] [Accepted: 08/23/2016] [Indexed: 12/25/2022]
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Liu Y, Link H, Liu L, Du G, Chen J, Sauer U. A dynamic pathway analysis approach reveals a limiting futile cycle in N-acetylglucosamine overproducing Bacillus subtilis. Nat Commun 2016; 7:11933. [PMID: 27324299 PMCID: PMC5512609 DOI: 10.1038/ncomms11933] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2015] [Accepted: 05/13/2016] [Indexed: 01/24/2023] Open
Abstract
Recent advances in genome engineering have further widened the gap between our ability to implement essentially any genetic change and understanding the impact of these changes on cellular function. We lack efficient methods to diagnose limiting steps in engineered pathways. Here, we develop a generally applicable approach to reveal limiting steps within a synthetic pathway. It is based on monitoring metabolite dynamics and simplified kinetic modelling to differentiate between putative causes of limiting product synthesis during the start-up phase of the pathway with near-maximal rates. We examine the synthetic N-acetylglucosamine (GlcNAc) pathway in Bacillus subtilis and find none of the acetyl-, amine- or glucose-moiety precursors to limit synthesis. Our dynamic metabolomics approach predicts an energy-dissipating futile cycle between GlcNAc6P and GlcNAc as the primary problem in the pathway. Deletion of the responsible glucokinase more than doubles GlcNAc productivity by restoring healthy growth of the overproducing strain. Rate-limiting steps in synthetic metabolic pathways are difficult to identify. Here, the authors monitor metabolite dynamics and apply kinetic modelling during the start-up phase of the Bacillus subtilis GlcNAc pathway to discover a futile cycle, allowing them to identify a more productive strain.
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Affiliation(s)
- Yanfeng Liu
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Lihu Road 1800, Wuxi 214122, China.,Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Lihu Road 1800, Wuxi 214122, China.,Institute of Molecular Systems Biology, ETH Zurich, Zurich 8093, Switzerland
| | - Hannes Link
- Max Planck Institute for terrestrial Microbiology, Marburg 35043, Germany
| | - Long Liu
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Lihu Road 1800, Wuxi 214122, China.,Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Lihu Road 1800, Wuxi 214122, China
| | - Guocheng Du
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Lihu Road 1800, Wuxi 214122, China.,Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Lihu Road 1800, Wuxi 214122, China
| | - Jian Chen
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Lihu Road 1800, Wuxi 214122, China.,Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Lihu Road 1800, Wuxi 214122, China
| | - Uwe Sauer
- Institute of Molecular Systems Biology, ETH Zurich, Zurich 8093, Switzerland
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Liu H, Huang D, Wen J. Integrated intracellular metabolic profiling and pathway analysis approaches reveal complex metabolic regulation by Clostridium acetobutylicum. Microb Cell Fact 2016; 15:36. [PMID: 26879529 PMCID: PMC4753663 DOI: 10.1186/s12934-016-0436-4] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2015] [Accepted: 02/01/2016] [Indexed: 01/27/2023] Open
Abstract
BACKGROUND Clostridium acetobutylicum is one of the most important butanol producing strains. However, environmental stress in the fermentation process usually leads to a lower yield, seriously hampering its industrialization. In order to systematically investigate the key intracellular metabolites that influence the strain growth and butanol production, and find out the critical regulation nodes, an integrated analysis approach has been carried out in this study. RESULTS Based on the gas chromatography-mass spectrometry technology, the partial least square discriminant analysis and the pathway analysis, 40 metabolic pathways linked with 43 key metabolic nodes were identified. In-depth analysis showed that lots of amino acids metabolism promoted cell growth but exerted slight influence on butanol production, while sugar metabolism was favorable for cell growth but unfavorable for butanol synthesis. Besides, both lysine and succinic acid metabolism generated a complex effect on the whole metabolic network. Dicarboxylate metabolism exerted an indispensable role on cell growth and butanol production. Subsequently, rational feeding strategies were proposed to verify these conclusions and facilitate the butanol biosynthesis. Feeding amino acids, especially glycine and serine, could obviously improve cell growth while yeast extract, citric acid and ethylene glycol could significantly enhance both growth and butanol production. CONCLUSIONS The feeding experiment confirmed that metabolic profiling combined with pathway analysis provided an accurate, reasonable and practical approach to explore the cellular metabolic activity and supplied a basis for improving butanol production. These strategies can also be extended for the production of other important bio-chemical compounds.
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Affiliation(s)
- Huanhuan Liu
- Key Laboratory of System Bioengineering (Tianjin University), Ministry of Education, Tianjin, 300072, People's Republic of China.
- SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, People's Republic of China.
| | - Di Huang
- TEDA Institute of Biological Sciences and Biotechnology, Nankai University, TEDA, Tianjin, 300457, People's Republic of China.
- Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, Tianjin, 300071, People's Republic of China.
- Tianjin Key Laboratory of Microbial Functional Genomics, Tianjin, 300457, People's Republic of China.
| | - Jianping Wen
- Key Laboratory of System Bioengineering (Tianjin University), Ministry of Education, Tianjin, 300072, People's Republic of China.
- SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, People's Republic of China.
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GUO ML, LIU XY, HUANG MZ, LI MC, CHU J, ZHUANG YP, ZHANG SL. 13C-assisted Ultra-High Performance Liquid Chromatography-Triple Quadrupole Mass Spectrometry Method for Precise Determination of Intracellular Metabolites in Pichia pastoris. CHINESE JOURNAL OF ANALYTICAL CHEMISTRY 2016. [DOI: 10.1016/s1872-2040(16)60906-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Xia ML, Wang L, Yang ZX, Chen HZ. Periodic-peristole agitation for process enhancement of butanol fermentation. BIOTECHNOLOGY FOR BIOFUELS 2015; 8:225. [PMID: 26702300 PMCID: PMC4689062 DOI: 10.1186/s13068-015-0409-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/02/2015] [Accepted: 12/04/2015] [Indexed: 06/05/2023]
Abstract
BACKGROUND Mass transfer plays an important role in determining the efficiency of the biofuel conversion. However, adverse effect of shear stress from traditional agitation inhibits the cell growth and production of biofuels. How to enhance the mass transfer with less adverse effect is considered as one of the important bioengineering issues. RESULTS In this study, a novel agitation type, named periodic-peristole was applied to butanol fermentation with Clostridium acetobutylicum ATCC 824. Meanwhile, the enhancement mechanism was studied. Initially, the fermentation performance of periodic-peristole agitation was compared with the traditional Rushton impeller and stationary cultivation. Result showed that the biomass, butanol and total solvent in periodic-peristole group (PPG) was enhanced to 1.92-, 2.06-, and 2.4-fold of those in the traditional Rushton impeller group (TIG), as well as 1.64-, 1.19- and 1.41-fold of those in the stationary group (SG). Subsequently, to get in-depth insight into enhancement mechanism, hydromechanics analysis and metabolic flux analysis (MFA) were carried out. The periodic-peristole agitation exhibits significant difference on velocity distribution, shear force, and mixing efficiency from the traditional Rushton impeller agitation. And the shear force in PPG is only 74 % of that in TIG. According to MFA result, fructose 6-phosphate, pyruvate, acetyl-CoA, oxaloacetate and α-ketoglutarate were determined the key nodes of cells in response to hydrodynamic mechanical stress. Based on such key information, rational enhancement strategies were proposed and butanol production was further improved. CONCLUSION The agitation associated with three issues which resulted in significant changes in cell metabolic behaviors: first, a rebalanced redox status; second, the energy (ATP) acquirement and consumption; third, the tolerance mechanism of the cell for survival of solvent. Periodic-peristole agitation provides an answer to address a long-standing problem of biofuel engineering. Key information derived from current study deepens the understanding of agitation, which can guide the designment of new bioreactors and development of enhancement strategies for biofuel refinery.
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Affiliation(s)
- Meng-lei Xia
- />State Key Laboratory of Biochemical Engineering, Institute of Process Engineering, Chinese Academy of Sciences, No. 1 Beiertiao, Zhongguancun, Haidian District, Beijing, 100190 China
- />University of Chinese Academy of Sciences, No. 80 Zhongguancun East Road, Haidian District, Beijing, 100039 China
| | - Lan Wang
- />State Key Laboratory of Biochemical Engineering, Institute of Process Engineering, Chinese Academy of Sciences, No. 1 Beiertiao, Zhongguancun, Haidian District, Beijing, 100190 China
| | - Zhi-xia Yang
- />College of Mathematics and System Science, Xinjiang University, No. 14 Shengli Road, Urumchi, 830046 China
| | - Hong-zhang Chen
- />State Key Laboratory of Biochemical Engineering, Institute of Process Engineering, Chinese Academy of Sciences, No. 1 Beiertiao, Zhongguancun, Haidian District, Beijing, 100190 China
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Huang D, Wang R, Du W, Wang G, Xia M. Activation of glycerol metabolic pathway by evolutionary engineering of Rhizopus oryzae to strengthen the fumaric acid biosynthesis from crude glycerol. BIORESOURCE TECHNOLOGY 2015; 196:263-272. [PMID: 26253910 DOI: 10.1016/j.biortech.2015.07.104] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/24/2015] [Revised: 07/26/2015] [Accepted: 07/27/2015] [Indexed: 06/04/2023]
Abstract
Rhizopus oryzae is strictly inhibited by biodiesel-based by-product crude glycerol, which results in low fumaric acid production. In this study, evolutionary engineering was employed to activate the glycerol utilization pathway for fumaric acid production. An evolved strain G80 was selected, which could tolerate and utilize high concentrations of crude glycerol to produce 14.9g/L fumaric acid with a yield of 0.248g/g glycerol. Key enzymes activity analysis revealed that the evolved strain displayed a significant upregulation in glycerol dissimilation, pyruvate consumption and reductive tricarboxylic acid pathways, compared with the parent strain. Subsequently, intracellular metabolic profiling analysis showed that amino acid biosynthesis, tricarboxylic acid cycle, fatty acid and stress response metabolites accounted for metabolic difference between two strains. Moreover, a glycerol fed-batch strategy was optimized to obtain the highest fumaric acid production of 25.5g/L, significantly increased by 20.9-fold than that of the parent strain of 1.2g/L.
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Affiliation(s)
- Di Huang
- TEDA Institute of Biological Sciences and Biotechnology, Nankai University, TEDA, Tianjin 300457, PR China; Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, Tianjin 300071, PR China; Tianjin Key Laboratory of Microbial Functional Genomics, Tianjin 300457, PR China.
| | - Ru Wang
- TEDA Institute of Biological Sciences and Biotechnology, Nankai University, TEDA, Tianjin 300457, PR China; Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, Tianjin 300071, PR China
| | - Wenjie Du
- Key Laboratory of System Bioengineering, Ministry of Education, Tianjin University, Tianjin 300072, PR China
| | - Guanyi Wang
- Key Laboratory of System Bioengineering, Ministry of Education, Tianjin University, Tianjin 300072, PR China
| | - Menglei Xia
- State Key Laboratory of Biochemical Engineering, Institute of Process Engineering, Chinese Academy of Sciences, Beijing 100190, PR China; University of Chinese Academy of Sciences, Beijing 100039, PR China
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Lu H, Liu X, Huang M, Xia J, Chu J, Zhuang Y, Zhang S, Noorman H. Integrated isotope-assisted metabolomics and (13)C metabolic flux analysis reveals metabolic flux redistribution for high glucoamylase production by Aspergillus niger. Microb Cell Fact 2015; 14:147. [PMID: 26383080 PMCID: PMC4574132 DOI: 10.1186/s12934-015-0329-y] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2015] [Accepted: 08/31/2015] [Indexed: 11/10/2022] Open
Abstract
Background Aspergillus niger is widely used for enzyme production and achievement of high enzyme production depends on the comprehensive understanding of cell’s metabolic regulation mechanisms. Results In this paper, we investigate the metabolic differences and regulation mechanisms between a high glucoamylase-producing strain A. niger DS03043 and its wild-type parent strain A. niger CBS513.88 via an integrated isotope-assisted metabolomics and 13C metabolic flux analysis approach. We found that A. niger DS03043 had higher cell growth, glucose uptake, and glucoamylase production rates but lower oxalic acid and citric acid secretion rates. In response to above phenotype changes, A. niger DS03043 was characterized by an increased carbon flux directed to the oxidative pentose phosphate pathway in contrast to reduced flux through TCA cycle, which were confirmed by consistent changes in pool sizes of metabolites. A higher ratio of ATP over AMP in the high producing strain might contribute to the increase in the PP pathway flux as glucosephosphate isomerase was inhibited at higher ATP concentrations. A. niger CBS513.88, however, was in a higher redox state due to the imbalance of NADH regeneration and consumption, resulting in the secretion of oxalic acid and citric acid, as well as the accumulation of intracellular OAA and PEP, which may in turn result in the decrease in the glucose uptake rate. Conclusions The application of integrated metabolomics and 13C metabolic flux analysis highlights the regulation mechanisms of energy and redox metabolism on flux redistribution in A. niger. An integrated isotope-assisted metabolomics and 13C metabolic flux analysis was was firstly systematically performed in A. niger. In response to enzyme production, the metabolic flux in A. niger DS03043 (high-producing) was redistributed, characterized by an increased carbon flux directed to the oxidative pentose phosphate pathway as well as an increased pool size of pentose. The consistency in 13C metabolic flux analysis and metabolites quantification indicated that an imbalance of NADH formation and consumption led to the accumulation and secretion of organic acids in A. niger CBS513.88 (wild-type) ![]() Electronic supplementary material The online version of this article (doi:10.1186/s12934-015-0329-y) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Hongzhong Lu
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, 200237, Shanghai, People's Republic of China.
| | - Xiaoyun Liu
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, 200237, Shanghai, People's Republic of China.
| | - Mingzhi Huang
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, 200237, Shanghai, People's Republic of China.
| | - Jianye Xia
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, 200237, Shanghai, People's Republic of China.
| | - Ju Chu
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, 200237, Shanghai, People's Republic of China.
| | - Yingping Zhuang
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, 200237, Shanghai, People's Republic of China.
| | - Siliang Zhang
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, 200237, Shanghai, People's Republic of China.
| | - Henk Noorman
- DSM Biotechnology Center, P.O. Box1, 2600 MA, Delft, The Netherlands.
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Ban YH, Park SR, Yoon YJ. The biosynthetic pathway of FK506 and its engineering: from past achievements to future prospects. J Ind Microbiol Biotechnol 2015; 43:389-400. [PMID: 26342319 DOI: 10.1007/s10295-015-1677-7] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2015] [Accepted: 08/19/2015] [Indexed: 11/28/2022]
Abstract
FK506, a 23-membered macrolide produced by several Streptomyces species, is an immunosuppressant widely used to prevent the rejection of transplanted organs. In addition, FK506 and its analogs possess numerous promising therapeutic potentials including antifungal, neuroprotective, and neuroregenerative activities. Herein, we introduce the biological activities and mechanisms of action of FK506 and discuss recent progress made in understanding its biosynthetic pathway, improving production, and in the mutasynthesis of diverse analogs. Perspectives highlighting further strain improvement and structural diversification aimed at generating more analogs with improved pharmaceutical properties will be emphasized.
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Affiliation(s)
- Yeon Hee Ban
- Department of Chemistry and Nano Science, Ewha Womans University, Seoul, 120-750, Republic of Korea
| | - Sung Ryeol Park
- Life Sciences Institute, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Yeo Joon Yoon
- Department of Chemistry and Nano Science, Ewha Womans University, Seoul, 120-750, Republic of Korea.
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Xia ML, Wang L, Yang ZX, Chen HZ. A novel digital color analysis method for rapid glucose detection. ANALYTICAL METHODS : ADVANCING METHODS AND APPLICATIONS 2015; 7:6654-6663. [PMID: 39044376 DOI: 10.1039/c5ay01233c] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/25/2024]
Abstract
The spectrophotometer is the most used analysis equipment in traditional colorimetric methods. However, the operation of using a spectrophotometer is time-consuming and labor-intensive, which presents practical difficulties in rapid detection. To this end, we present a digital color analysis method, using the typical 3,5-dinitrosalicylic acid (DNS) method for glucose detection as an example. The primary colors from 3 color spaces (Red-Green-Blue, Hue-Saturation-Value, Hue-Saturation-Intensity) were studied as quantitative analytical parameters for the glucose concentration and the red color (from the Red-Green-Blue colorspace) of the assay image provides superior prediction precision (>99.8%). Combined with the color analysis, two calculation algorithms, nonlinear regression and artificial neural networks, were compared for the detection of a high concentration of glucose. Then a microtiter plate (48-well plate) platform, based on the color analysis, was set up. Compared to existing methods using a spectrophotometer, the digital color analysis method has a large detection range (0-10 g L-1), high accuracy (0.07 g L-1) and fast detection rate (150 samples detected within about 15 min). It also shows great promise for use in a variety of reducing sugar measurements such as xylose, fructose and maltose. These aforementioned features render this newly developed method highly suitable for quick detection applications.
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Affiliation(s)
- Meng-Lei Xia
- State Key Laboratory of Biochemical Engineering, Institute of Process Engineering, Chinese Academy of Sciences, Beijing 100190, China.
- University of Chinese Academy of Sciences, Beijing 100039, China
| | - Lan Wang
- State Key Laboratory of Biochemical Engineering, Institute of Process Engineering, Chinese Academy of Sciences, Beijing 100190, China.
| | - Zhi-Xia Yang
- College of Mathematics and System Science, Xinjiang University, Urumchi, 830046, China
| | - Hong-Zhang Chen
- State Key Laboratory of Biochemical Engineering, Institute of Process Engineering, Chinese Academy of Sciences, Beijing 100190, China.
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Comparative metabolic profiling reveals the key role of amino acids metabolism in the rapamycin overproduction by Streptomyces hygroscopicus. ACTA ACUST UNITED AC 2015; 42:949-63. [DOI: 10.1007/s10295-015-1611-z] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2015] [Accepted: 03/23/2015] [Indexed: 01/06/2023]
Abstract
Abstract
Rapamycin is an important natural macrolide antibiotic with antifungal, immunosuppressive and anticancer activity produced by Streptomyces hygroscopicus. In this study, a mutant strain obtained by ultraviolet mutagenesis displayed higher rapamycin production capacity compared to the wild-type S. hygroscopicus ATCC 29253. To gain insights into the mechanism of rapamycin overproduction, comparative metabolic profiling between the wild-type and mutant strain was performed. A total of 86 metabolites were identified by gas chromatography–mass spectrometry. Pattern recognition methods, including principal component analysis, partial least squares and partial least squares discriminant analysis, were employed to determine the key biomarkers. The results showed that 22 potential biomarkers were closely associated with the increase of rapamycin production and the tremendous metabolic difference was observed between the two strains. Furthermore, metabolic pathway analysis revealed that amino acids metabolism played an important role in the synthesis of rapamycin, especially lysine, valine, tryptophan, isoleucine, glutamate, arginine and ornithine. The inadequate supply of amino acids, or namely “nitrogen starvation” occurred in the mutant strain. Subsequently, the exogenous addition of amino acids into the fermentation medium of the mutant strain confirmed the above conclusion, and rapamycin production of the mutant strain increased to 426.7 mg/L after adding lysine, approximately 5.8-fold of that in the wild-type strain. Finally, the results of real-time PCR and enzyme activity assays demonstrated that dihydrodipicolinate synthase involved with lysine metabolism played vital role in the biosynthesis of rapamycin. These findings will provide a theoretical basis for further improving production of rapamycin.
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Wang G, Huang D, Li Y, Wen J, Jia X. A metabolic-based approach to improve xylose utilization for fumaric acid production from acid pretreated wheat bran by Rhizopus oryzae. BIORESOURCE TECHNOLOGY 2015; 180:119-127. [PMID: 25594507 DOI: 10.1016/j.biortech.2014.12.091] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/28/2014] [Revised: 12/24/2014] [Accepted: 12/26/2014] [Indexed: 06/04/2023]
Abstract
In this work, wheat bran (WB) was utilized as feedstock to synthesize fumaric acid by Rhizopus oryzae. Firstly, the pretreatment process of WB by dilute sulfuric acid hydrolysis undertaken at 100°C for 30min offered the best performance for fumaric acid production. Subsequently, through optimizing the seed culture medium, a suitable morphology (0.55mm pellets diameter) of R. oryzae was obtained. Furthermore, a metabolic-based approach was developed to profile the differences of intracellular metabolites concentration of R. oryzae between xylose (the abundant sugar in wheat bran hydrolysate (WBH)) and glucose metabolism. The xylitol, sedoheptulose 7-phosphate, ribulose 5-phosphate, glucose 6-phosphate, proline and serine were responsible for fumaric acid biosynthesis limitation in xylose fermentation. Consequently, regulation strategies were proposed, leading to a 149% increase in titer (up to 15.4g/L). Finally, by combinatorial regulation strategies the highest production was 20.2g/L from WBH, 477% higher than that of initial medium.
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Affiliation(s)
- Guanyi Wang
- Key Laboratory of System Bioengineering (Tianjin University), Ministry of Education, Tianjin 300072, People's Republic of China; SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), 300072, People's Republic of China
| | - Di Huang
- TEDA School of Biological Sciences and Biotechnology, Nankai University, TEDA, Tianjin 300457, People's Republic of China
| | - Yong Li
- Key Laboratory of System Bioengineering (Tianjin University), Ministry of Education, Tianjin 300072, People's Republic of China; SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), 300072, People's Republic of China
| | - Jianping Wen
- Key Laboratory of System Bioengineering (Tianjin University), Ministry of Education, Tianjin 300072, People's Republic of China; SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), 300072, People's Republic of China.
| | - Xiaoqiang Jia
- Key Laboratory of System Bioengineering (Tianjin University), Ministry of Education, Tianjin 300072, People's Republic of China; SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), 300072, People's Republic of China
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Sévin DC, Kuehne A, Zamboni N, Sauer U. Biological insights through nontargeted metabolomics. Curr Opin Biotechnol 2014; 34:1-8. [PMID: 25461505 DOI: 10.1016/j.copbio.2014.10.001] [Citation(s) in RCA: 94] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2014] [Revised: 10/03/2014] [Accepted: 10/03/2014] [Indexed: 01/10/2023]
Abstract
Metabolomics is increasingly employed to investigate metabolism and its reciprocal crosstalk with cellular signaling and regulation. In recent years, several nontargeted metabolomics methods providing substantial metabolome coverage have been developed. Here, we review and compare the contributions of traditional targeted and nontargeted metabolomics in advancing different research areas ranging from biotechnology to human health. Although some studies demonstrated the power of nontargeted profiling in generating unexpected and yet highly important insights, we found that most mechanistic links were still revealed by hypothesis-driven targeted methods. Novel computational approaches for formal interpretation of complex metabolic patterns and integration of complementary molecular layers are required to tap the full potential of nontargeted metabolomics for data-driven, discovery-oriented research and rapidly nucleating novel biological insights.
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Affiliation(s)
- Daniel C Sévin
- Institute of Molecular Systems Biology, ETH Zurich, Switzerland; PhD Program on Systems Biology, Life Science Zurich, Switzerland
| | - Andreas Kuehne
- Institute of Molecular Systems Biology, ETH Zurich, Switzerland; PhD Program on Systems Biology, Life Science Zurich, Switzerland
| | - Nicola Zamboni
- Institute of Molecular Systems Biology, ETH Zurich, Switzerland
| | - Uwe Sauer
- Institute of Molecular Systems Biology, ETH Zurich, Switzerland.
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Pan X, Qi H, Mu L, Wen J, Jia X. Comparative metabolomic-based metabolic mechanism hypothesis for microbial mixed cultures utilizing cane molasses wastewater for higher 2-phenylethanol production. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2014; 62:9927-9935. [PMID: 25199087 DOI: 10.1021/jf502239d] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
The mixed microbes coculture method in cane molasses wastewater (CMW) was adopted to produce 2-phenylethanol (2-PE). Comparative metabolomics combined with multivariate statistical analysis was performed to profile the differences of overall intracellular metabolites concentration for the mixed microbes cocultured under two different fermentation conditions with low and high 2-PE production. In total 102 intracellular metabolites were identified, and 17 of them involved in six pathways were responsible for 2-PE biosynthesis. After further analysis of metabolites and verification by feeding experiment, an overall metabolic mechanism hypothesis for the microbial mixed cultures (MMC) utilizing CMW for higher 2-PE production was presented. The results demonstrated that the branches of intracellular pyruvate metabolic flux, as well as the flux of phenylalanine, tyrosine, tryptophan, glutamate, proline, leucine, threonine, and oleic acid, were closely related to 2-PE production and cell growth, which provided theoretical guidance for domestication and selection of species as well as medium optimization for MMC metabolizing CMW to enhance 2-PE yield.
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Affiliation(s)
- Xinrong Pan
- Key Laboratory of Systems Bioengineering (Ministry of Education) and SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), School of Chemical Engineering and Technology, Tianjin University , Tianjin 300072, People's Republic of China
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Gao P, Xu G. Mass-spectrometry-based microbial metabolomics: recent developments and applications. Anal Bioanal Chem 2014; 407:669-80. [PMID: 25216964 DOI: 10.1007/s00216-014-8127-7] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2014] [Revised: 08/04/2014] [Accepted: 08/20/2014] [Indexed: 12/20/2022]
Abstract
Metabolomics is an omics technique aiming at qualitatively and quantitatively describing a metabolome by various analytical platforms. It is an indispensable component of modern systems biology. Microbial metabolomics can be roughly classified as metabolic footprint analysis and metabolic fingerprint analysis depending on the analyte origins. Both of them have been beneficial to microbiological research for different reasons. Mass spectrometry and nuclear magnetic resonance spectroscopy techniques are popular analytical strategies prevailing in the metabolomics field. In this review, chromatography-mass-spectrometry-based microbial metabolomic analysis steps are summarized, including sample collection, metabolite extraction, instrument analysis, and data analysis. Moreover, their applications in some representative fields are discussed as examples. The aim of this review is to present briefly recent technical advances in mass-spectrometry-based analysis, and to highlight the value of modern applications of microbial metabolomics.
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Affiliation(s)
- Peng Gao
- Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, China
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Enhancement of ascomycin production in Streptomyces hygroscopicus var. ascomyceticus by combining resin HP20 addition and metabolic profiling analysis. ACTA ACUST UNITED AC 2014; 41:1365-74. [DOI: 10.1007/s10295-014-1473-9] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2014] [Accepted: 06/09/2014] [Indexed: 10/25/2022]
Abstract
Abstract
Combinatorial approach of adsorbent resin HP20 addition and metabolic profiling analysis were carried out to enhance ascomycin production. Under the optimal condition of 5 % m/v HP20 added at 24 h, ascomycin production was increased to 380 from 300 mg/L. To further rationally guide the improvement of ascomycin production, metabolic profiling analysis was employed to investigate the intracellular metabolite changes of Streptomyces hygroscopicus var. ascomyceticus FS35 in response to HP20 addition. A correlation between the metabolic profiles and ascomycin accumulation was revealed by partial least-squares to latent structures discriminant analysis, and 11 key metabolites that most contributed to metabolism differences and ascomycin biosynthesis were identified. Based on the analysis of metabolite changes together with their pathways, the potential key factors associated with ascomycin overproduction were determined. Finally, rationally designed fermentation strategies based on HP20 addition were performed as follows: 2 % v/v n-hexadecane was added at 24 h; 1.0 g/L valine was supplemented at 48 h; 1.0 g/L lysine was added at 72 h. The ascomycin production was ultimately improved to 460 mg/L, a 53.3 % enhancement compared with that obtained in initial condition. These results demonstrated that the combination of HP20 addition and metabolic profiling analysis could be successfully applied to the rational guidance of production improvement of ascomycin, as well as other clinically important compounds.
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Metabolic profiling analysis of the degradation of phenol and 4-chlorophenol by Pseudomonas sp. cbp1-3. Biochem Eng J 2014. [DOI: 10.1016/j.bej.2014.06.026] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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67
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Trends in the biosynthesis and production of the immunosuppressant tacrolimus (FK506). Appl Microbiol Biotechnol 2013; 98:497-507. [PMID: 24272367 DOI: 10.1007/s00253-013-5362-3] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2013] [Revised: 10/26/2013] [Accepted: 10/28/2013] [Indexed: 01/03/2023]
Abstract
The current off-patent state of tacrolimus (FK506) has opened the hunting season for new generic pharmaceutical formulations of this immunosuppressant. This fact has boosted the scientific and industrial research on tacrolimus for the last 5 years in order to improve its production. The fast discovery of tacrolimus producer strains has generated a huge number of producers, which presents the biosynthetic cluster of FK506 as a high promiscuous genetic region. For the first time, the current state-of-the-art on the tacrolimus biosynthesis, production improvements and drug purification is reviewed. On one hand, all the genes involved in the tacrolimus biosynthesis, in addition to the traditional PKS/NRPS, as well as their regulation are analysed. On the other hand, tacrolimus direct and indirect precursors are reviewed as a straight manner to improve the final yield, which is a current trend in the field. Twenty years of industrial and scientific improvements on tacrolimus production are summarised, whereas future trends are also drafted.
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Combined gene cluster engineering and precursor feeding to improve gougerotin production in Streptomyces graminearus. Appl Microbiol Biotechnol 2013; 97:10469-77. [DOI: 10.1007/s00253-013-5270-6] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2013] [Revised: 09/12/2013] [Accepted: 09/16/2013] [Indexed: 01/13/2023]
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