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Ding Q, Ye C. Microbial cell factories based on filamentous bacteria, yeasts, and fungi. Microb Cell Fact 2023; 22:20. [PMID: 36717860 PMCID: PMC9885587 DOI: 10.1186/s12934-023-02025-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2022] [Accepted: 01/20/2023] [Indexed: 01/31/2023] Open
Abstract
BACKGROUND Advanced DNA synthesis, biosensor assembly, and genetic circuit development in synthetic biology and metabolic engineering have reinforced the application of filamentous bacteria, yeasts, and fungi as promising chassis cells for chemical production, but their industrial application remains a major challenge that needs to be solved. RESULTS As important chassis strains, filamentous microorganisms can synthesize important enzymes, chemicals, and niche pharmaceutical products through microbial fermentation. With the aid of metabolic engineering and synthetic biology, filamentous bacteria, yeasts, and fungi can be developed into efficient microbial cell factories through genome engineering, pathway engineering, tolerance engineering, and microbial engineering. Mutant screening and metabolic engineering can be used in filamentous bacteria, filamentous yeasts (Candida glabrata, Candida utilis), and filamentous fungi (Aspergillus sp., Rhizopus sp.) to greatly increase their capacity for chemical production. This review highlights the potential of using biotechnology to further develop filamentous bacteria, yeasts, and fungi as alternative chassis strains. CONCLUSIONS In this review, we recapitulate the recent progress in the application of filamentous bacteria, yeasts, and fungi as microbial cell factories. Furthermore, emphasis on metabolic engineering strategies involved in cellular tolerance, metabolic engineering, and screening are discussed. Finally, we offer an outlook on advanced techniques for the engineering of filamentous bacteria, yeasts, and fungi.
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Affiliation(s)
- Qiang Ding
- grid.252245.60000 0001 0085 4987School of Life Sciences, Anhui University, Hefei, 230601 China ,grid.252245.60000 0001 0085 4987Key Laboratory of Human Microenvironment and Precision Medicine of Anhui Higher Education Institutes, Anhui University, Hefei, 230601 Anhui China ,Anhui Key Laboratory of Modern Biomanufacturing, Hefei, 230601 Anhui China
| | - Chao Ye
- grid.260474.30000 0001 0089 5711School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing, 210023 China
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Li X, Chen J, Andersen JM, Chu J, Jensen PR. Cofactor Engineering Redirects Secondary Metabolism and Enhances Erythromycin Production in Saccharopolyspora erythraea. ACS Synth Biol 2020; 9:655-670. [PMID: 32078772 DOI: 10.1021/acssynbio.9b00528] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Saccharopolyspora erythraea is used for industrial erythromycin production. To explore the physiological role of intracellular energy state in metabolic regulation by S. erythraea, we initially overexpressed the F1 part of the endogenous F1F0-ATPase in the high yielding erythromycin producing strain E3. The F1-ATPase expression resulted in lower [ATP]/[ADP] ratios, which was accompanied by a strong increase in the production of a reddish pigment and a decreased erythromycin production. Subsequent transcriptional analysis revealed that the lower intracellular [ATP]/[ADP] ratios exerted a pleotropic regulation on the metabolism of S. erythraea. The lower [ATP]/[ADP] ratios induced physiological changes to restore the energy balance, mainly via pathways that tend to produce ATP or regenerate NADH. The F1-ATPase overexpression strain exhibited a state of redox stress, which was correlated to an alteration of electron transport at the branch of the terminal oxidases, and S. erythraea channeled the enhanced glycolytic flux toward a reddish pigment in order to reduce NADH formation. The production of erythromycin was decreased, which is in accordance with the net ATP requirement and the excess NADH formed through this pathway. Partial growth inhibition by apramycin increased the intracellular [ATP]/[ADP] ratios and demonstrated a positive correlation between [ATP]/[ADP] ratios and erythromycin synthesis. Finally, overexpression of the entire F1F0-ATPase complex resulted in 28% enhanced erythromycin production and markedly reduced pigment synthesis in E3. The work illustrates a feasible strategy to optimize the distribution of fluxes in secondary metabolism.
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Affiliation(s)
- Xiaobo Li
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, 130 Meilong Road, Shanghai 200237, People’s Republic of China
- National Food Institute, Technical University of Denmark, Kemitorvet Building 201, DK2800 Kongens Lyngby, Denmark
| | - Jun Chen
- National Food Institute, Technical University of Denmark, Kemitorvet Building 201, DK2800 Kongens Lyngby, Denmark
| | - Joakim M. Andersen
- National Food Institute, Technical University of Denmark, Kemitorvet Building 201, DK2800 Kongens Lyngby, Denmark
| | - Ju Chu
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, 130 Meilong Road, Shanghai 200237, People’s Republic of China
| | - Peter R. Jensen
- National Food Institute, Technical University of Denmark, Kemitorvet Building 201, DK2800 Kongens Lyngby, Denmark
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3
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Luo Z, Zeng W, Du G, Chen J, Zhou J. Enhancement of pyruvic acid production in Candida glabrata by engineering hypoxia-inducible factor 1. BIORESOURCE TECHNOLOGY 2020; 295:122248. [PMID: 31627065 DOI: 10.1016/j.biortech.2019.122248] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/28/2019] [Revised: 10/04/2019] [Accepted: 10/05/2019] [Indexed: 06/10/2023]
Abstract
Dissolved oxygen (DO) supply plays essential roles in microbial organic acid production. Candida glabrata, as a dominant strain for producing pyruvic acid, principally converts glucose to pyruvic acid through glycolysis. However, this process relies excessively on high extracellular DO content. In this study, in combination with specific motif analysis of gene promoters, hypoxia-inducible factor 1 (HIF1) was engineered to improve the transcription level of some enzymes related to pyruvic acid synthesis under low DO level and directly led to increased pyruvic acid production and glycolysis efficiency. Moreover, the intracellular stability of HIF1 was further optimized from different aspects to maximize pyruvic acid accumulation. Finally, the pyruvic acid titer in a 5-L batch bioreactor with 10% DO level reached 53.1 g/L. As pyruvic acid is involved in the biosynthesis of various products, these findings suggest that HIF1-enabled regulation method has significant potential for increasing the synthesis of other chemicals in microorganisms.
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Affiliation(s)
- Zhengshan Luo
- 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; State Key Laboratory of Materials-Oriented Chemical Engineering, College of Food Science and Light Industry, Nanjing Tech University, Nanjing 211816, China
| | - Weizhu Zeng
- National Engineering Laboratory for Cereal Fermentation Technology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China
| | - Guocheng Du
- National Engineering Laboratory for Cereal Fermentation Technology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China; The Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, 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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4
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Luo Z, Zeng W, Du G, Chen J, Zhou J. Enhanced Pyruvate Production in Candida glabrata by Engineering ATP Futile Cycle System. ACS Synth Biol 2019; 8:787-795. [PMID: 30856339 DOI: 10.1021/acssynbio.8b00479] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Energy metabolism plays an important role in the growth and central metabolic pathways of cells. Manipulating energy metabolism is an efficient strategy to improve the formation of target products and to understand the effects of altering intracellular energy levels on global metabolic networks. Candida glabrata, as a dominant yeast strain for producing pyruvate, principally converts glucose to pyruvate through the glycolytic pathway. However, this process can be severely inhibited by a high intracellular ATP content. Here, in combination with the physiological characteristics of C. glabrata, efforts have been made to construct an ATP futile cycle system (ATP-FCS) in C. glabrata to decrease the intracellular ATP level without destroying F0F1-ATPase function. ATP-FCS was capable of decreasing the intracellular ATP level by 51.0% in C. glabrata. The decrease in the ATP level directly led to an increased pyruvate production and glycolysis efficiency. Moreover, we further optimized different aspects of the ATP-FCS to maximize pyruvate accumulation. Combining ATP-FCS with further genetic optimization strategies, we achieved a final pyruvate titer of 40.2 g/L, with 4.35 g pyruvate/g dry cell weight and a 0.44 g/g substrate conversion rate in 500 mL flasks, which represented increases of 98.5%, 322.3%, and 160%, respectively, compared with the original strain. Thus, these strategies hold great potential for increasing the synthesis of other organic acids in microbes.
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Shimizu K, Matsuoka Y. Regulation of glycolytic flux and overflow metabolism depending on the source of energy generation for energy demand. Biotechnol Adv 2018; 37:284-305. [PMID: 30576718 DOI: 10.1016/j.biotechadv.2018.12.007] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2018] [Revised: 11/06/2018] [Accepted: 12/15/2018] [Indexed: 12/11/2022]
Abstract
Overflow metabolism is a common phenomenon observed at higher glycolytic flux in many bacteria, yeast (known as Crabtree effect), and mammalian cells including cancer cells (known as Warburg effect). This phenomenon has recently been characterized as the trade-offs between protein costs and enzyme efficiencies based on coarse-graining approaches. Moreover, it has been recognized that the glycolytic flux increases as the source of energy generation changes from energetically efficient respiration to inefficient respiro-fermentative or fermentative metabolism causing overflow metabolism. It is highly desired to clarify the metabolic regulation mechanisms behind such phenomena. Metabolic fluxes are located on top of the hierarchical regulation systems, and represent the outcome of the integrated response of all levels of cellular regulation systems. In the present article, we discuss about the different levels of regulation systems for the modulation of fluxes depending on the growth rate, growth condition such as oxygen limitation that alters the metabolism towards fermentation, and genetic perturbation affecting the source of energy generation from respiration to respiro-fermentative metabolism in relation to overflow metabolism. The intracellular metabolite of the upper glycolysis such as fructose 1,6-bisphosphate (FBP) plays an important role not only for flux sensing, but also for the regulation of the respiratory activity either directly or indirectly (via transcription factors) at higher growth rate. The glycolytic flux regulation is backed up (enhanced) by unphosphorylated EIIA and HPr of the phosphotransferase system (PTS) components, together with the sugar-phosphate stress regulation, where the transcriptional regulation is further modulated by post-transcriptional regulation via the degradation of mRNA (stability of mRNA) in Escherichia coli. Moreover, the channeling may also play some role in modulating the glycolytic cascade reactions.
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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
- Kyushu Institute of Technology, Iizuka, Fukuoka 820-8502, Japan
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Enhancement of Pyruvate Productivity in Candida glabrata by Deleting the CgADE13 Gene to Improve Acid Tolerance. BIOTECHNOL BIOPROC E 2018. [DOI: 10.1007/s12257-018-0201-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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7
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Wu J, Luo Q, Liu J, Chen X, Liu L. Enhanced pyruvate production in Candida glabrata by overexpressing the CgAMD1 gene to improve acid tolerance. Biotechnol Lett 2017; 40:143-149. [PMID: 28983762 DOI: 10.1007/s10529-017-2452-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2017] [Accepted: 09/27/2017] [Indexed: 10/18/2022]
Abstract
OBJECTIVES To enhance acid tolerance of Candida glabrata for pyruvate production by engineering AMP metabolism. RESULTS The physiological function of AMP deaminase in AMP metabolism from C. glabrata was investigated by deleting or overexpresseing the corresponding gene, CgAMD1. At pH 4, CgAMD1 overexpression resulted in 59 and 51% increases in biomass and cell viability compared to those of wild type strain, respectively. In addition, the intracellular ATP level of strain Cgamd1Δ/CgAMD1 was down-regulated by 22%, which led to a 94% increase in pyruvate production. Further, various strengths of CgAMD1 expression cassettes were designed, thus resulting in a 59% increase in pyruvate production at pH 4. Strain Cgamd1Δ/CgAMD1 (H) was grown in a 30 l batch bioreactor at pH 4, and pyruvate reached 46.1 g/l. CONCLUSION CgAMD1 overexpression plays an active role in improving acid tolerance and pyruvate fermentation performance of C. glabrata at pH 4.
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Affiliation(s)
- Jing Wu
- School of Pharmaceutical Science, Jiangnan University, Wuxi, 214122, China
| | - Qiuling Luo
- School of Pharmaceutical Science, Jiangnan University, Wuxi, 214122, China.,State Key Laboratory of Food Science and Technology, Jiangnan University, 1800 Lihu Road, Wuxi, 214122, China
| | - Jia Liu
- State Key Laboratory of Food Science and Technology, Jiangnan University, 1800 Lihu Road, Wuxi, 214122, China
| | - Xiulai Chen
- State Key Laboratory of Food Science and Technology, Jiangnan University, 1800 Lihu Road, Wuxi, 214122, China. .,Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi, 214122, China.
| | - Liming Liu
- State Key Laboratory of Food Science and Technology, Jiangnan University, 1800 Lihu Road, Wuxi, 214122, China.,Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi, 214122, China
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Xu N, Ye C, Chen X, Liu J, Liu L. Genome-scale metabolic modelling common cofactors metabolism in microorganisms. J Biotechnol 2017; 251:1-13. [PMID: 28385592 DOI: 10.1016/j.jbiotec.2017.04.004] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2017] [Revised: 04/02/2017] [Accepted: 04/03/2017] [Indexed: 12/20/2022]
Abstract
The common cofactors ATP/ADP, NAD(P)(H), and acetyl-CoA/CoA are indispensable participants in biochemical reactions in industrial microbes. To systematically explore the effects of these cofactors on cell growth and metabolic phenotypes, the first genome-scale cofactor metabolic model, icmNX6434, including 6434 genes, 1782 metabolites, and 6877 reactions, was constructed from 14 genome-scale metabolic models of 14 industrial strains. The origin, consumption, and interactions of these common cofactors in microbial cells were elucidated by the icmNX6434 model, and they played important roles in cell growth. The essential cofactor modules contained 2480 genes and 2948 reactions; therefore, improving cofactor biosynthesis, directing these cofactors into essential metabolic pathways, as well as avoiding cofactor utilization during byproduct biosynthesis and futile cycles, are three ways to increase cell growth. The effects of these common cofactors on the distribution and rate of the carbon flux in four universal modes, as well as an optimized metabolic flux, could be obtained by manipulating cofactor availability and balance. Significant changes in the ATP, NAD(H), NADP(H), or acetyl-CoA concentrations triggered relevant metabolic responses to acidic, oxidative, heat, and osmotic stress. Globally, the model icmNX6434 provides a comprehensive platform to elucidate the physiological effects of these cofactors on cell growth, metabolic flux, and industrial robustness. Moreover, the results of this study are a further example of using a consensus genome-scale metabolic model to increase our understanding of key biological processes.
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Affiliation(s)
- Nan Xu
- State Key Laboratory of Food Science and Technology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China; College of Bioscience and Biotechnology, Yangzhou University, Yangzhou, Jiangsu 225009, China; The Laboratory of Food Microbial-Manufacturing Engineering, Jiangnan University, Wuxi 214122, China
| | - Chao Ye
- State Key Laboratory of Food Science and 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; The Laboratory of Food Microbial-Manufacturing Engineering, Jiangnan University, Wuxi 214122, China
| | - Xiulai Chen
- State Key Laboratory of Food Science and 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; The Laboratory of Food Microbial-Manufacturing Engineering, Jiangnan University, Wuxi 214122, China
| | - Jia Liu
- State Key Laboratory of Food Science and 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; The Laboratory of Food Microbial-Manufacturing Engineering, Jiangnan University, Wuxi 214122, China
| | - Liming Liu
- State Key Laboratory of Food Science and 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; The Laboratory of Food Microbial-Manufacturing Engineering, Jiangnan University, Wuxi 214122, China.
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Xu N, Ye C, Chen X, Liu J, Liu L, Chen J. Genome Sequencing of the Pyruvate-producing Strain Candida glabrata CCTCC M202019 and Genomic Comparison with Strain CBS138. Sci Rep 2016; 6:34893. [PMID: 27713500 PMCID: PMC5054605 DOI: 10.1038/srep34893] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2016] [Accepted: 09/21/2016] [Indexed: 11/22/2022] Open
Abstract
Candida glabrata CCTCC M202019 as an industrial yeast strain that is widely used to produce α-oxocarboxylic acid. Strain M202019 has been proven to have a higher pyruvate-producing capacity than the reference strain CBS138. To characterize the genotype of the M202019 strain, we generated a draft sequence of its genome, which has a size of 12.1 Mbp and a GC content of 38.47%. Evidence accumulated during genome annotation suggests that strain M202019 has strong capacities for glucose transport and pyruvate biosynthesis, defects in pyruvate catabolism, as well as variations in genes involved in nutrient and dicarboxylic acid transport, oxidative phosphorylation, and other relevant aspects of carbon metabolism, which might promote pyruvate accumulation. In addition to differences in its central carbon metabolism, a genomic analysis revealed genetic differences in adhesion metabolism. Forty-nine adhesin-like proteins of strain M202019 were identified classified into seven subfamilies. Decreased amounts of adhesive proteins, and deletions or changes of low-complexity repeats and functional domains might lead to lower adhesion and reduced pathogenicity. Further virulence experiments validated the biological safety of strain M202019. Analysis of the C. glabrata CCTCC M202019 genome sequence provides useful insights into its genetic context, physical characteristics, and potential metabolic capacity.
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Affiliation(s)
- Nan Xu
- State Key Laboratory of Food Science and 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
| | - Chao Ye
- State Key Laboratory of Food Science and 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
| | - Xiulai Chen
- State Key Laboratory of Food Science and 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
| | - Jia Liu
- State Key Laboratory of Food Science and 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
| | - Liming Liu
- State Key Laboratory of Food Science and 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
| | - Jian Chen
- State Key Laboratory of Food Science and 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
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Cheng L, Wang J, Fu Q, Miao L, Yang X, Li S, Li F, Shen Z. Optimization of carbon and nitrogen sources and substrate feeding strategy to increase the cell density ofStreptococcus suis. BIOTECHNOL BIOTEC EQ 2015. [DOI: 10.1080/13102818.2015.1039465] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022] Open
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11
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Li S, Liu L, Chen J. Compartmentalizing metabolic pathway in Candida glabrata for acetoin production. Metab Eng 2015; 28:1-7. [DOI: 10.1016/j.ymben.2014.11.008] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2014] [Revised: 11/11/2014] [Accepted: 11/20/2014] [Indexed: 01/28/2023]
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12
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Wang L, Zhang J, Cao Z, Wang Y, Gao Q, Zhang J, Wang D. Inhibition of oxidative phosphorylation for enhancing citric acid production by Aspergillus niger. Microb Cell Fact 2015; 14:7. [PMID: 25592678 PMCID: PMC4320542 DOI: 10.1186/s12934-015-0190-z] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2014] [Accepted: 01/05/2015] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The spore germination rate and growth characteristics were compared between the citric acid high-yield strain Aspergillus niger CGMCC 5751 and A. niger ATCC 1015 in media containing antimycin A or DNP. We inferred that differences in citric acid yield might be due to differences in energy metabolism between these strains. To explore the impact of energy metabolism on citric acid production, the changes in intracellular ATP, NADH and NADH/NAD+ were measured at various fermentation stages. In addition, the effects of antimycin A or DNP on energy metabolism and citric acid production was investigated by CGMCC 5751. RESULTS By comparing the spore germination rate and the extent of growth on PDA plates containing antimycin A or DNP, CGMCC 5751 was shown to be more sensitive to antimycin A than ATCC 1015. The substrate-level phosphorylation of CGMCC 5751 was greater than that of ATCC 1015 on PDA plates with DNP. DNP at tested concentrations had no apparent effect on the growth of CGMCC 5751. There were no apparent effects on the mycelial morphology, the growth of mycelial pellets or the dry cell mass when 0.2 mg L(-1) antimycin A or 0.1 mg L(-1) DNP was added to medium at the 24-h time point. The concentrations of intracellular ATP, NADH and NADH/NAD+ of CGMCC 5751 were notably lower than those of ATCC 1015 at several fermentation stages. Moreover, at 96 h of fermentation, the citric acid production of CGMCC 5751 reached up to 151.67 g L(-1) and 135.78 g L(-1) by adding 0.2 mg L(-1) antimycin A or 0.1 mg L(-1) DNP, respectively, at the 24-h time point of fermentation. Thus, the citric acid production of CGMCC 5751 was increased by 19.89% and 7.32%, respectively. CONCLUSIONS The concentrations of intracellular ATP, NADH and NADH/NAD+ of the citric acid high-yield strain CGMCC 5751 were notably lower than those of ATCC 1015. The excessive ATP has a strong inhibitory effect on citric acid accumulation by A. niger. Increasing NADH oxidation and appropriately reducing the concentration of intracellular ATP can accelerate glycolysis and the TCA cycle to enhance citric acid yield.
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Affiliation(s)
- Lu Wang
- Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, Tianjin, 300457, P. R. China. .,College of Biotechnology, Tianjin University of Science & Technology, Tianjin, 300457, P. R. China.
| | - Jianhua Zhang
- Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, Tianjin, 300457, P. R. China. .,College of Biotechnology, Tianjin University of Science & Technology, Tianjin, 300457, P. R. China.
| | - Zhanglei Cao
- Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, Tianjin, 300457, P. R. China. .,College of Biotechnology, Tianjin University of Science & Technology, Tianjin, 300457, P. R. China.
| | - Yajun Wang
- Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, Tianjin, 300457, P. R. China. .,College of Biotechnology, Tianjin University of Science & Technology, Tianjin, 300457, P. R. China.
| | - Qiang Gao
- Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, Tianjin, 300457, P. R. China. .,College of Biotechnology, Tianjin University of Science & Technology, Tianjin, 300457, P. R. China. .,Tianjin Key Laboratory of Industrial Microbiology, Tianjin, 300457, P. R. China.
| | - Jian Zhang
- Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, Tianjin, 300457, P. R. China. .,College of Biotechnology, Tianjin University of Science & Technology, Tianjin, 300457, P. R. China. .,Tianjin Key Laboratory of Industrial Microbiology, Tianjin, 300457, P. R. China.
| | - Depei Wang
- Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, Tianjin, 300457, P. R. China. .,College of Biotechnology, Tianjin University of Science & Technology, Tianjin, 300457, P. R. China. .,Tianjin Key Laboratory of Industrial Microbiology, Tianjin, 300457, P. R. China.
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Improved vitamin B12 fermentation process by adding rotenone to regulate the metabolism of Pseudomonas denitrificans. Appl Biochem Biotechnol 2014; 173:673-81. [PMID: 24687557 DOI: 10.1007/s12010-014-0878-2] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2013] [Accepted: 03/24/2014] [Indexed: 01/08/2023]
Abstract
Our previous research had revealed that the dissolved oxygen limitation was more favorable for vitamin B12 fermentation, due to its inducement to the increased glycolytic flux in Pseudomonas denitrificans. In this paper, a novel strategy was implemented to further investigate the metabolic characteristics of P. denitrificans under different oxygen supply levels, by exogenously adding rotenone (a respiratory chain inhibitor interfering with the oxygen consumption) to the fermentation broths. Compared to the fermentation process without rotenone treatment, it was observed that 5 mg/L rotenone treatment could significantly strengthen the glycolytic flux of P. denitrificans via activating the key glycolytic enzymes (phosphofructokinase and pyruvate kinase), resulting in the accelerated generations of anterior precursors (glutamate and 5-aminolevulinic acid) for vitamin B12 biosynthesis. Although 5 mg/L rotenone treatment had a negative effect on cell growth of P. denitrificans, the vitamin B12 yield was increased from 48.28 ± 0.62 mg/L to 54.70 ± 0.45 mg/L, which further proved that an increased glycolytic flux in P. denitrificans was a consequence of higher vitamin B12 production.
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Li S, Chen X, Liu L, Chen J. Pyruvate production inCandida glabrata: manipulation and optimization of physiological function. Crit Rev Biotechnol 2013; 36:1-10. [DOI: 10.3109/07388551.2013.811636] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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Xu N, Liu L, Zou W, Liu J, Hua Q, Chen J. Reconstruction and analysis of the genome-scale metabolic network of Candida glabrata. ACTA ACUST UNITED AC 2013; 9:205-16. [DOI: 10.1039/c2mb25311a] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
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16
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The shock of vacuolar PrA on glycolytic flux, oxidative phosphorylation, and cell morphology by industrial Saccharomyces cerevisiae WZ65. Eur Food Res Technol 2011. [DOI: 10.1007/s00217-011-1586-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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17
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Qin Y, Johnson CH, Liu L, Chen J. Introduction of heterogeneous NADH reoxidation pathways into Torulopsis glabrata significantly increases pyruvate production efficiency. KOREAN J CHEM ENG 2011. [DOI: 10.1007/s11814-010-0483-1] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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18
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Qin Y, Liu LM, Li CH, Xu S, Chen J. Accelerating glycolytic flux of Torulopsis glabrata CCTCC M202019 at high oxidoreduction potential created using potassium ferricyanide. Biotechnol Prog 2010; 26:1551-7. [PMID: 20886645 DOI: 10.1002/btpr.496] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2010] [Revised: 06/29/2010] [Indexed: 11/06/2022]
Abstract
This study aimed to increase the glycolytic flux of the multivitamin auxotrophic yeast Torulopsis glabrata by redirecting NADH oxidation from oxidative phosphorylation to membrane-bound ferric reductase. We added potassium ferricyanide as electron acceptor to T. glabrata culture broth at 20% dissolved oxygen (DO) concentration, which resulted in: (1) decreases in the NADH content, NADH/NAD(+) ratio, and ATP level of 45.3%, 60.3%, and 15.2%, respectively; (2) high activities of the key glycolytic enzymes hexokinase, phosphofructokinase, and pyruvate kinase, as well as high expression levels of the genes encoding these enzymes; and (3) increases in the specific glucose consumption rate and pyruvate yield of T. glabrata was by 45.5% and 23.1%, respectively. Our results showed that membrane-bound ferric reductase offers an alternative and efficient NADH oxidation pathway at lower DO concentration, which increases the glycolytic flux of T. glabrata.
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Affiliation(s)
- Yi Qin
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, China
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19
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Effect of PrA encoding gene-PEP4 deletion in industrial S. cerevisiae WZ65 on key enzymes in relation to the glycolytic pathway. Eur Food Res Technol 2010. [DOI: 10.1007/s00217-010-1355-y] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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20
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Liu L, Agren R, Bordel S, Nielsen J. Use of genome-scale metabolic models for understanding microbial physiology. FEBS Lett 2010; 584:2556-64. [PMID: 20420838 DOI: 10.1016/j.febslet.2010.04.052] [Citation(s) in RCA: 69] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2010] [Revised: 04/18/2010] [Accepted: 04/20/2010] [Indexed: 11/17/2022]
Abstract
The exploitation of microorganisms in industrial, medical, food and environmental biotechnology requires a comprehensive understanding of their physiology. The availability of genome sequences and accumulation of high-throughput data allows gaining understanding of microbial physiology at the systems level, and genome-scale metabolic models represent a valuable framework for integrative analysis of metabolism of microorganisms. Genome-scale metabolic models are reconstructed based on a combination of genome sequence information and detailed biochemical information, and these reconstructed models can be used for analyzing and simulating the operation of metabolism in response to different stimuli. Here we discuss the requirement for having detailed physiological insight in order to exploit microorganisms for production of fuels, chemicals and pharmaceuticals. We further describe the reconstruction process of genome-scale metabolic models and different algorithms that can be used to apply these models to gain improved insight into microbial physiology.
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Affiliation(s)
- Liming Liu
- Department of Chemical and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
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21
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Mitochondrial DNA heteroplasmy in Candida glabrata after mitochondrial transformation. EUKARYOTIC CELL 2010; 9:806-14. [PMID: 20207853 DOI: 10.1128/ec.00349-09] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
Genetic manipulation of mitochondrial DNA (mtDNA) is the most direct method for investigating mtDNA, but until now, this has been achieved only in the diploid yeast Saccharomyces cerevisiae. In this study, the ATP6 gene on mtDNA of the haploid yeast Candida glabrata (Torulopsis glabrata) was deleted by biolistic transformation of DNA fragments with a recoded ARG8(m) mitochondrial genetic marker, flanked by homologous arms to the ATP6 gene. Transformants were identified by arginine prototrophy. However, in the transformants, the original mtDNA was not lost spontaneously, even under arginine selective pressure. Moreover, the mtDNA transformants selectively lost the transformed mtDNA under aerobic conditions. The mtDNA heteroplasmy in the transformants was characterized by PCR, quantitative PCR, and Southern blotting, showing that the heteroplasmy was relatively stable in the absence of arginine. Aerobic conditions facilitated the loss of the original mtDNA, and anaerobic conditions favored loss of the transformed mtDNA. Moreover, detailed investigations showed that increases in reactive oxygen species in mitochondria lacking ATP6, along with their equal cell division, played important roles in determining the dynamics of heteroplasmy. Based on our analysis of mtDNA heteroplasmy in C. glabrata, we were able to generate homoplasmic Deltaatp6 mtDNA strains.
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Zhou J, Huang L, Liu L, Chen J. Enhancement of pyruvate productivity by inducible expression of a F(0)F(1)-ATPase inhibitor INH1 in Torulopsis glabrata CCTCC M202019. J Biotechnol 2009; 144:120-6. [PMID: 19761804 DOI: 10.1016/j.jbiotec.2009.09.005] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2009] [Revised: 09/01/2009] [Accepted: 09/04/2009] [Indexed: 11/28/2022]
Abstract
The aim of this study is to establish a controllable intracellular ATP content regulation system applied to the enhancement of pyruvate production in Torulopsis glabrata. The INH1 gene, which encodes a F(0)F(1)-ATPase inhibitor from Saccharomyces cerevisiae, was expressed under a copper ion inducible promoter in the pyruvate producer Torulopsis glabrata CCTCC M202019. The resultant strain was designated as T. glabrata INH1. The induction efficiency was measured by the inducible expression of an enhanced green fluorescence protein. The copper inducible INH1 gene could control the intracellular ATP content (24 h) in an extensive range between 0.192 mmol/mg protein and 0.642 mmol/mg protein in a flask culture. With T. glabrataINH1, induction with 30 microM of Cu(2+) at 12 h in a 3 L fermentor improved pyruvate yield from glucose on biomass by 29% and its yield by 20%, respectively.
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Affiliation(s)
- Jingwen Zhou
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu, China
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23
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Zhou J, Liu L, Shi Z, Du G, Chen J. ATP in current biotechnology: regulation, applications and perspectives. Biotechnol Adv 2008; 27:94-101. [PMID: 19026736 DOI: 10.1016/j.biotechadv.2008.10.005] [Citation(s) in RCA: 86] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2008] [Revised: 08/13/2008] [Accepted: 10/14/2008] [Indexed: 11/25/2022]
Abstract
Adenosine tri-phosphate (ATP), the most important energy source for metabolic reactions and pathways, plays a vital role in the growth of industrial strain and the production of target metabolites. In this review, current advances in manipulating ATP in industrial strains, including altering NADH availability, and regulating NADH oxidation pathway, oxygen supply, proton gradient, the electron transfer chain activity and the F(0)F(1)-ATPase activity, are summarized and discussed. By applying these strategies, optimal product concentrations, yields and productivity in industrial biotechnology have been achieved. Furthermore, the mechanisms by which ATP extends the substrate utilization spectra and enhances the ability to challenge harsh environmental stress have been elucidated. Finally, three critical issues related to ATP manipulation have been addressed.
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Affiliation(s)
- Jingwen Zhou
- The Key Laboratory of Industrial Biotechnology, School of Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China
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Postmus J, Canelas AB, Bouwman J, Bakker BM, van Gulik W, de Mattos MJT, Brul S, Smits GJ. Quantitative analysis of the high temperature-induced glycolytic flux increase in Saccharomyces cerevisiae reveals dominant metabolic regulation. J Biol Chem 2008; 283:23524-32. [PMID: 18562308 DOI: 10.1074/jbc.m802908200] [Citation(s) in RCA: 56] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
A major challenge in systems biology lies in the integration of processes occurring at different levels, such as transcription, translation, and metabolism, to understand the functioning of a living cell in its environment. We studied the high temperature-induced glycolytic flux increase in Saccharomyces cerevisiae and investigated the regulatory mechanisms underlying this increase. We used glucose-limited chemostat cultures to separate regulatory effects of temperature from effects on growth rate. Growth at increased temperature (38 degrees C versus 30 degrees C) resulted in a strongly increased glycolytic flux, accompanied by a switch from respiration to a partially fermentative metabolism. We observed an increased flux through all enzymes, ranging from 5- to 10-fold. We quantified the contributions of direct temperature effects on enzyme activities, the gene expression cascade and shifts in the metabolic network, to the increased flux through each enzyme. To do this we adapted flux regulation analysis. We show that the direct effect of temperature on enzyme kinetics can be included as a separate term. Together with hierarchical regulation and metabolic regulation, this term explains the total flux change between two steady states. Surprisingly, the effect of the cultivation temperature on enzyme catalytic capacity, both directly through the Arrhenius effect and indirectly through adapted gene expression, is only a moderate contribution to the increased glycolytic flux for most enzymes. The changes in flux are therefore largely caused by changes in the interaction of the enzymes with substrates, products, and effectors.
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Affiliation(s)
- Jarne Postmus
- Department of Molecular Biology and Microbial Food Safety, University of Amsterdam, Nieuwe Achtergracht 166, Amsterdam
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25
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Current awareness on yeast. Yeast 2007. [DOI: 10.1002/yea.1328] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
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