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Song P, Yuan K, Qin T, Zhang K, Ji XJ, Ren L, Guan R, Wen J, Huang H. Metabolomics profiling reveals the mechanism of increased pneumocandin B 0 production by comparing mutant and parent strains. J Ind Microbiol Biotechnol 2018; 45:767-780. [PMID: 29948195 DOI: 10.1007/s10295-018-2047-z] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2018] [Accepted: 05/18/2018] [Indexed: 11/26/2022]
Abstract
Metabolic profiling was used to discover mechanisms of increased pneumocandin B0 production in a high-yield strain by comparing it with its parent strain. Initially, 79 intracellular metabolites were identified, and the levels of 15 metabolites involved in six pathways were found to be directly correlated with pneumocandin B0 biosynthesis. Then by combining the analysis of key enzymes, acetyl-CoA and NADPH were identified as the main factors limiting pneumocandin B0 biosynthesis. Other metabolites, such as pyruvate, α-ketoglutaric acid, lactate, unsaturated fatty acids and previously unreported metabolite γ-aminobutyric acid were shown to play important roles in pneumocandin B0 biosynthesis and cell growth. Finally, the overall metabolic mechanism hypothesis was formulated and a rational feeding strategy was implemented that increased the pneumocandin B0 yield from 1821 to 2768 mg/L. These results provide practical and theoretical guidance for strain selection, medium optimization, and genetic engineering for pneumocandin B0 production.
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Affiliation(s)
- Ping Song
- Department Biochemical Engineering, School Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, China
- College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, 211816, China
| | - Kai Yuan
- College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, 211816, China
| | - Tingting Qin
- College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, 211816, China
| | - Ke Zhang
- College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, 211816, China
| | - Xiao-Jun Ji
- College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, 211816, China
| | - Lujing Ren
- College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, 211816, China
| | - Rongfeng Guan
- Laboratory for Advanced Technology in Environmental Protection of Jiangsu Province, Yancheng Institute of Technology, Yancheng, 224051, China
| | - Jianping Wen
- Department Biochemical Engineering, School Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, China.
| | - He Huang
- School of Pharmaceutical Sciences, Nanjing Tech University, Nanjing, 211816, China.
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Comparative genomics and transcriptome analysis of Aspergillus niger and metabolic engineering for citrate production. Sci Rep 2017; 7:41040. [PMID: 28106122 PMCID: PMC5247736 DOI: 10.1038/srep41040] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2016] [Accepted: 12/15/2016] [Indexed: 01/01/2023] Open
Abstract
Despite a long and successful history of citrate production in Aspergillus niger, the molecular mechanism of citrate accumulation is only partially understood. In this study, we used comparative genomics and transcriptome analysis of citrate-producing strains—namely, A. niger H915-1 (citrate titer: 157 g L−1), A1 (117 g L−1), and L2 (76 g L−1)—to gain a genome-wide view of the mechanism of citrate accumulation. Compared with A. niger A1 and L2, A. niger H915-1 contained 92 mutated genes, including a succinate-semialdehyde dehydrogenase in the γ-aminobutyric acid shunt pathway and an aconitase family protein involved in citrate synthesis. Furthermore, transcriptome analysis of A. niger H915-1 revealed that the transcription levels of 479 genes changed between the cell growth stage (6 h) and the citrate synthesis stage (12 h, 24 h, 36 h, and 48 h). In the glycolysis pathway, triosephosphate isomerase was up-regulated, whereas pyruvate kinase was down-regulated. Two cytosol ATP-citrate lyases, which take part in the cycle of citrate synthesis, were up-regulated, and may coordinate with the alternative oxidases in the alternative respiratory pathway for energy balance. Finally, deletion of the oxaloacetate acetylhydrolase gene in H915-1 eliminated oxalate formation but neither influence on pH decrease nor difference in citrate production were observed.
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Guo H, Wan H, Chen H, Fang F, Liu S, Zhou J. Proteomic analysis of the response of α-ketoglutarate-producer Yarrowia lipolytica WSH-Z06 to environmental pH stimuli. Appl Microbiol Biotechnol 2016; 100:8829-41. [PMID: 27535241 DOI: 10.1007/s00253-016-7775-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2016] [Revised: 07/25/2016] [Accepted: 08/02/2016] [Indexed: 11/25/2022]
Abstract
During bioproduction of short-chain carboxylates, a shift in pH is a common strategy for enhancing the biosynthesis of target products. Based on two-dimensional gel electrophoresis, comparative proteomics analysis of general and mitochondrial protein samples was used to investigate the cellular responses to environmental pH stimuli in the α-ketoglutarate overproducer Yarrowia lipolytica WSH-Z06. The lower environmental pH stimuli tensioned intracellular acidification and increased the level of reactive oxygen species (ROS). A total of 54 differentially expressed protein spots were detected, and 11 main cellular processes were identified to be involved in the cellular response to environmental pH stimuli. Slight decrease in cytoplasmic pH enhanced the cellular acidogenicity by elevating expression level of key enzymes in tricarboxylic acid cycle (TCA cycle). Enhanced energy biosynthesis, ROS elimination, and membrane potential homeostasis processes were also employed as cellular defense strategies to compete with environmental pH stimuli. Owing to its antioxidant role of α-ketoglutarate, metabolic flux shifted to α-ketoglutarate under lower pH by Y. lipolytica in response to acidic pH stimuli. The identified differentially expressed proteins provide clues for understanding the mechanisms of the cellular responses and for enhancing short-chain carboxylate production through metabolic engineering or process optimization strategies in combination with manipulation of environmental conditions.
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Affiliation(s)
- Hongwei Guo
- Department of Biotechnology and Bioengineering, School of Chemical Engineering and Key Laboratory of Fujian Province for Biological Chemical Engineering, Huaqiao University, 668 Jimei Road, Amoy, Fujian, 361021, China.,School of Biotechnology and Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu, 214122, China
| | - Hui Wan
- School of Biotechnology and Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu, 214122, China
| | - Hongwen Chen
- Department of Biotechnology and Bioengineering, School of Chemical Engineering and Key Laboratory of Fujian Province for Biological Chemical Engineering, Huaqiao University, 668 Jimei Road, Amoy, Fujian, 361021, China
| | - Fang Fang
- School of Biotechnology and Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu, 214122, China
| | - Song Liu
- School of Biotechnology and Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu, 214122, China
| | - Jingwen Zhou
- School of Biotechnology and Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu, 214122, China.
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Guo H, Liu P, Madzak C, Du G, Zhou J, Chen J. Identification and application of keto acids transporters in Yarrowia lipolytica. Sci Rep 2015; 5:8138. [PMID: 25633653 PMCID: PMC4311248 DOI: 10.1038/srep08138] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2014] [Accepted: 01/08/2015] [Indexed: 01/18/2023] Open
Abstract
Production of organic acids by microorganisms is of great importance for obtaining building-block chemicals from sustainable biomass. Extracellular accumulation of organic acids involved a series of transporters, which play important roles in the accumulation of specific organic acid while lack of systematic demonstration in eukaryotic microorganisms. To circumvent accumulation of by-product, efforts have being orchestrated to carboxylate transport mechanism for potential clue in Yarrowia lipolytica WSH-Z06. Six endogenous putative transporter genes, YALI0B19470g, YALI0C15488g, YALI0C21406g, YALI0D24607g, YALI0D20108g and YALI0E32901g, were identified. Transport characteristics and substrate specificities were further investigated using a carboxylate-transport-deficient Saccharomyces cerevisiae strain. These transporters were expressed in Y. lipolytica WSH-Z06 to assess their roles in regulating extracellular keto acids accumulation. In a Y. lipolytica T1 line over expressing YALI0B19470g, α-ketoglutarate accumulated to 46.7 g·L−1, whereas the concentration of pyruvate decreased to 12.3 g·L−1. Systematic identification of these keto acids transporters would provide clues to further improve the accumulation of specific organic acids with higher efficiency in eukaryotic microorganisms.
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Affiliation(s)
- Hongwei Guo
- 1] School of Biotechnology and Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China [2] Synergetic Innovation Center of Food Safety and Nutrition, 1800 Lihu Road, Wuxi, Jiangsu 214122, China
| | - Peiran Liu
- School of Biotechnology and Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China
| | - Catherine Madzak
- UMR1238 Microbiologie et Génétique Moléculaire, INRA/CNRS/AgroPan's Tech, CBAI, BP 01, 78850 Thiverval-Grignon, France
| | - Guocheng Du
- 1] School of Biotechnology and Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China [2] Synergetic Innovation Center of Food Safety and Nutrition, 1800 Lihu Road, Wuxi, Jiangsu 214122, China
| | - Jingwen Zhou
- 1] School of Biotechnology and Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China [2] Synergetic Innovation Center of Food Safety and Nutrition, 1800 Lihu Road, Wuxi, Jiangsu 214122, China
| | - Jian Chen
- 1] School of Biotechnology and Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China [2] Synergetic Innovation Center of Food Safety and Nutrition, 1800 Lihu Road, Wuxi, Jiangsu 214122, China
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Hachama K, Khodja M, Moulay S, Boutoumi H, Hennig L, Sicker D. Novel 3-(2-Oxo-2 H-benzo[ b][1,4]oxazin-3-yl)propanoates from Dimethyl-2-oxoglutarate and Test of Their Biological Activity. J Heterocycl Chem 2013. [DOI: 10.1002/jhet.1520] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Kamel Hachama
- Laboratoire de Recherche Plantes Médicinales et Aromatiques, Département de Chimie Industrielle; Université Saâd Dahlab de Blida; 09000 Blida, B. P. 270; Algeria
| | - Mohamed Khodja
- Laboratoire de Recherche Plantes Médicinales et Aromatiques, Département de Chimie Industrielle; Université Saâd Dahlab de Blida; 09000 Blida, B. P. 270; Algeria
| | - Saad Moulay
- Laboratoire Chimie-Physique Moléculaire et Macromoléculaire, Département de Chimie Industrielle; Université Saâd Dahlab de Blida; 09000 Blida, B. P. 270; Algeria
| | - Hocine Boutoumi
- Laboratoire de Recherche Plantes Médicinales et Aromatiques, Département de Chimie Industrielle; Université Saâd Dahlab de Blida; 09000 Blida, B. P. 270; Algeria
| | - Lothar Hennig
- Institut für Organische Chemie der Universität Leipzig; Johannisallee 29; D-04103; Leipzig; Germany
| | - Dieter Sicker
- Institut für Organische Chemie der Universität Leipzig; Johannisallee 29; D-04103; Leipzig; Germany
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Yin X, Madzak C, Du G, Zhou J, Chen J. Enhanced alpha-ketoglutaric acid production in Yarrowia lipolytica WSH-Z06 by regulation of the pyruvate carboxylation pathway. Appl Microbiol Biotechnol 2012; 96:1527-37. [DOI: 10.1007/s00253-012-4192-z] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2012] [Revised: 05/13/2012] [Accepted: 05/16/2012] [Indexed: 10/28/2022]
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