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Shinmori A, Guo Z, Maeda T, Fukiya S, Wada M, Yokota A. Contributions of the anaplerotic reaction enzymes pyruvate carboxylase and phosphoenolpyruvate carboxylase to l-lysine production in Corynebacterium glutamicum. J Biosci Bioeng 2024:S1389-1723(24)00163-4. [PMID: 38937154 DOI: 10.1016/j.jbiosc.2024.05.015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2024] [Revised: 05/24/2024] [Accepted: 05/30/2024] [Indexed: 06/29/2024]
Abstract
Anaplerotic reactions catalyzed by pyruvate carboxylase (PC) and phosphoenolpyruvate carboxylase (PEPC) have important roles in the production of l-lysine to replenish oxaloacetic acid (OAA) in Corynebacterium glutamicum. However, the relative contributions of these enzymes to l-lysine production in C. glutamicum are not fully understood. In this study, using a parent strain (P) carrying a feedback inhibition-resistant aspartokinase with the T311I mutation, we constructed a PC gene-deleted mutant strain (PΔPC) and a PEPC gene-deleted mutant strain (PΔPEPC). Although the growth of both mutant strains was comparable to the growth of strain P, the maximum l-lysine production in strains PΔPC and PΔPEPC decreased by 14% and 49%, respectively, indicating that PEPC strongly contributed to OAA supply. l-Lysine production in strain PΔPC slightly decreased during the logarithmic phase, while production during the early stationary phase was comparable to production in strain P. By contrast, strain PΔPEPC produced l-lysine in an amount comparable to the production of strain P during the logarithmic phase; l-lysine production after the early stationary phase was completely stopped in strain PΔPEPC. These results indicate that OAA is supplied by both PC and PEPC during the logarithmic phase, while only PEPC can continuously supply OAA after the logarithmic phase.
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Affiliation(s)
- Akinobu Shinmori
- Laboratory of Microbial Physiology, Research Faculty of Agriculture, Hokkaido University, Kita 9, Nishi 9, Kita-ku, Sapporo, Hokkaido 060-8589, Japan
| | - Zhen Guo
- Laboratory of Microbial Physiology, Research Faculty of Agriculture, Hokkaido University, Kita 9, Nishi 9, Kita-ku, Sapporo, Hokkaido 060-8589, Japan
| | - Tomoya Maeda
- Laboratory of Microbial Physiology, Research Faculty of Agriculture, Hokkaido University, Kita 9, Nishi 9, Kita-ku, Sapporo, Hokkaido 060-8589, Japan
| | - Satoru Fukiya
- Laboratory of Microbial Physiology, Research Faculty of Agriculture, Hokkaido University, Kita 9, Nishi 9, Kita-ku, Sapporo, Hokkaido 060-8589, Japan
| | - Masaru Wada
- Laboratory of Microbial Physiology, Research Faculty of Agriculture, Hokkaido University, Kita 9, Nishi 9, Kita-ku, Sapporo, Hokkaido 060-8589, Japan; Faculty of Agriculture, Setsunan University, 45-1 Nagaotouge-cho, Hirakata, Osaka 573-0101, Japan
| | - Atsushi Yokota
- Laboratory of Microbial Physiology, Research Faculty of Agriculture, Hokkaido University, Kita 9, Nishi 9, Kita-ku, Sapporo, Hokkaido 060-8589, Japan.
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Yin L, Zhou Y, Ding N, Fang Y. Recent Advances in Metabolic Engineering for the Biosynthesis of Phosphoenol Pyruvate-Oxaloacetate-Pyruvate-Derived Amino Acids. Molecules 2024; 29:2893. [PMID: 38930958 PMCID: PMC11206799 DOI: 10.3390/molecules29122893] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2024] [Revised: 06/06/2024] [Accepted: 06/11/2024] [Indexed: 06/28/2024] Open
Abstract
The phosphoenol pyruvate-oxaloacetate-pyruvate-derived amino acids (POP-AAs) comprise native intermediates in cellular metabolism, within which the phosphoenol pyruvate-oxaloacetate-pyruvate (POP) node is the switch point among the major metabolic pathways existing in most living organisms. POP-AAs have widespread applications in the nutrition, food, and pharmaceutical industries. These amino acids have been predominantly produced in Escherichia coli and Corynebacterium glutamicum through microbial fermentation. With the rapid increase in market requirements, along with the global food shortage situation, the industrial production capacity of these two bacteria has encountered two bottlenecks: low product conversion efficiency and high cost of raw materials. Aiming to push forward the update and upgrade of engineered strains with higher yield and productivity, this paper presents a comprehensive summarization of the fundamental strategy of metabolic engineering techniques around phosphoenol pyruvate-oxaloacetate-pyruvate node for POP-AA production, including L-tryptophan, L-tyrosine, L-phenylalanine, L-valine, L-lysine, L-threonine, and L-isoleucine. Novel heterologous routes and regulation methods regarding the carbon flux redistribution in the POP node and the formation of amino acids should be taken into consideration to improve POP-AA production to approach maximum theoretical values. Furthermore, an outlook for future strategies of low-cost feedstock and energy utilization for developing amino acid overproducers is proposed.
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Affiliation(s)
- Lianghong Yin
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou 311300, China; (L.Y.); (Y.Z.)
- Zhejiang Provincial Key Laboratory of Resources Protection and Innovation of Traditional Chinese Medicine, Zhejiang A&F University, Hangzhou 311300, China
| | - Yanan Zhou
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou 311300, China; (L.Y.); (Y.Z.)
- Zhejiang Provincial Key Laboratory of Resources Protection and Innovation of Traditional Chinese Medicine, Zhejiang A&F University, Hangzhou 311300, China
| | - Nana Ding
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou 311300, China; (L.Y.); (Y.Z.)
- Zhejiang Provincial Key Laboratory of Resources Protection and Innovation of Traditional Chinese Medicine, Zhejiang A&F University, Hangzhou 311300, China
| | - Yu Fang
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou 311300, China; (L.Y.); (Y.Z.)
- Zhejiang Provincial Key Laboratory of Resources Protection and Innovation of Traditional Chinese Medicine, Zhejiang A&F University, Hangzhou 311300, China
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Gu S, Wu T, Zhao J, Sun T, Zhao Z, Zhang L, Li J, Tian C. Rewiring metabolic flux to simultaneously improve malate production and eliminate by-product succinate accumulation by Myceliophthora thermophila. Microb Biotechnol 2024; 17:e14410. [PMID: 38298109 PMCID: PMC10884987 DOI: 10.1111/1751-7915.14410] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2023] [Revised: 12/07/2023] [Accepted: 01/05/2024] [Indexed: 02/02/2024] Open
Abstract
Although a high titre of malic acid is achieved by filamentous fungi, by-product succinic acid accumulation leads to a low yield of malic acid and is unfavourable for downstream processing. Herein, we conducted a series of metabolic rewiring strategies in a previously constructed Myceliophthora thermophila to successfully improve malate production and abolish succinic acid accumulation. First, a pyruvate carboxylase CgPYC variant with increased activity was obtained using a high-throughput system and introduced to improve malic acid synthesis. Subsequently, shifting metabolic flux to malate synthesis from mitochondrial metabolism by deleing mitochondrial carriers of pyruvate and malate, led to a 53.7% reduction in succinic acid accumulation. The acceleration of importing cytosolic succinic acid into the mitochondria for consumption further decreased succinic acid formation by 53.3%, to 2.12 g/L. Finally, the importer of succinic acid was discovered and used to eliminate by-product accumulation. In total, malic acid production was increased by 26.5%, relative to the start strain JG424, to 85.23 g/L and 89.02 g/L on glucose and Avicel, respectively, in the flasks. In a 5-L fermenter, the titre of malic acid reached 182.7 g/L using glucose and 115.8 g/L using raw corncob, without any by-product accumulation. This study would accelerate the industrial production of biobased malic acid from renewable plant biomass.
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Affiliation(s)
- Shuying Gu
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of SciencesTianjinChina
- National Technology Innovation Center of Synthetic BiologyTianjinChina
| | - Taju Wu
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of SciencesTianjinChina
- National Technology Innovation Center of Synthetic BiologyTianjinChina
- School of Life Science, Bengbu Medical CollegeBengbuChina
| | - Junqi Zhao
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of SciencesTianjinChina
- National Technology Innovation Center of Synthetic BiologyTianjinChina
| | - Tao Sun
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of SciencesTianjinChina
- National Technology Innovation Center of Synthetic BiologyTianjinChina
| | - Zhen Zhao
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of SciencesTianjinChina
- National Technology Innovation Center of Synthetic BiologyTianjinChina
| | - Lu Zhang
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of SciencesTianjinChina
- National Technology Innovation Center of Synthetic BiologyTianjinChina
| | - Jingen Li
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of SciencesTianjinChina
- National Technology Innovation Center of Synthetic BiologyTianjinChina
| | - Chaoguang Tian
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of SciencesTianjinChina
- National Technology Innovation Center of Synthetic BiologyTianjinChina
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Laseke AJ, Boram TJ, Schneider NO, Lohman JR, Maurice MS. Allosteric Site at the Biotin Carboxylase Dimer Interface Mediates Activation and Inhibition in Staphylococcus aureus Pyruvate Carboxylase. Biochemistry 2023; 62:2632-2644. [PMID: 37603581 PMCID: PMC10693930 DOI: 10.1021/acs.biochem.3c00280] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/23/2023]
Abstract
Allosteric regulation of the essential anaplerotic enzyme, pyruvate carboxylase (PC), is vital for metabolic homeostasis. PC catalyzes the bicarbonate- and ATP-dependent carboxylation of pyruvate to form oxaloacetate. Dysregulation of PC activity can impact glucose and redox metabolism, which contributes to the pathogenicity of many diseases. To maintain homeostasis, PC is allosterically activated by acetyl-CoA and allosterically inhibited by l-aspartate. In this study, we further characterize the molecular basis of allosteric regulation in Staphylococcus aureus PC (SaPC) using slowly/nonhydrolyzable dethia analogues of acetyl-CoA and site-directed mutagenesis of residues at the biotin carboxylase homodimer interface. The dethia analogues fully activate SaPC but demonstrate significantly reduced binding affinities relative to acetyl-CoA. Residues Arg21, Lys46, and Glu418 of SaPC are located at the biotin carboxylase dimer interface and play a critical role in both allosteric activation and inhibition. A structure of R21A SaPC in complex with acetyl-CoA reveals an intact molecule of acetyl-CoA bound at the allosteric site, offering new molecular insights into the acetyl-CoA binding site. This study demonstrates that the biotin carboxylase domain dimer interface is a critical allosteric site in PC, serving as a convergence point for allosteric activation by acetyl-CoA and inhibition by l-aspartate.
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Affiliation(s)
- Amanda J. Laseke
- Department of Biological Sciences, Marquette University, Milwaukee, WI 53201-1881, USA
| | - Trevor J. Boram
- Department of Biochemistry, Purdue University, 175 S. University St., West Lafayette, IN 47907, United States
| | - Nicholas O. Schneider
- Department of Biological Sciences, Marquette University, Milwaukee, WI 53201-1881, USA
| | - Jeremy R. Lohman
- Department of Biochemistry, Purdue University, 175 S. University St., West Lafayette, IN 47907, United States
- Current Address: Department of Biochemistry and Molecular Biology, Michigan State University, 603 Wilson Road, East Lansing, MI 48824
| | - Martin St. Maurice
- Department of Biological Sciences, Marquette University, Milwaukee, WI 53201-1881, USA
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Taylor SK, Kostic N, Stojanovic MN. Oligonucleotide-Blocked Streptavidin for Biotinylation Analysis. Bioconjug Chem 2023; 34:92-96. [PMID: 36006852 DOI: 10.1021/acs.bioconjchem.2c00255] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
Binding between streptavidin, or its homologues, to biotin is one of the most widely exploited biological interactions in the biomedical sciences. Controlling the extent of biotinylation is important for meeting the requirements of the intended design and to preserve the native function of the biotin recipient. Within the protein world, a"trial-and-error" optimization approach toward biotinylation reaction conditions is often necessary due to widely varying properties of proteins. Therefore, product analysis is important. We show here that a oligonucleotide-blocked streptavidin, effectively "monovalent streptavidin", can tag biotin moieties individually and the tagged products visualized via a polyacrylamide gel shift assay to reveal the product distribution, i.e., [protein-(biotin)n] products where n = 1, 2, 3, etc. This is in contrast, and complementary, to current commercially available analytical reagents for biotinylation characterization, which use an absorbance or fluorescence signal to yield the mean number of biotin moieties.
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Luo S, Lin PP, Nieh LY, Liao GB, Tang PW, Chen C, Liao JC. A cell-free self-replenishing CO2-fixing system. Nat Catal 2022. [DOI: 10.1038/s41929-022-00746-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
AbstractBiological CO2 fixation is so far the most effective means for CO2 reduction at scale and accounts for most of the CO2 fixed on Earth. Through this process, carbon is fixed in cellular components and biomass during organismal growth. To uncouple CO2 fixation from growth and cellular regulation, cell-free CO2 fixation systems represent an alternative approach since the rate can be independently manipulated. Here we designed an oxygen-insensitive, self-replenishing CO2 fixation system with opto-sensing. The system comprises a synthetic reductive glyoxylate and pyruvate synthesis (rGPS) cycle and the malyl-CoA-glycerate (MCG) pathway to produce acetyl-coenzyme A (CoA), pyruvate and malate from CO2, which are also intermediates in the cycle. We solved various problems associated with the in vitro system, and implemented opto-sensing modules to control the regeneration of cofactors. We accomplished sustained operation for 6 hours with a CO2-fixing rate comparable to or greater than typical CO2 fixation rates of photosynthetic or lithoautotrophic organisms.
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Fan X, Zhang T, Ji Y, Li J, Long K, Yuan Y, Li Y, Xu Q, Chen N, Xie X. Pathway engineering of Escherichia coli for one-step fermentative production of L-theanine from sugars and ethylamine. Metab Eng Commun 2020; 11:e00151. [PMID: 33251110 PMCID: PMC7677707 DOI: 10.1016/j.mec.2020.e00151] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2020] [Revised: 10/26/2020] [Accepted: 11/03/2020] [Indexed: 01/08/2023] Open
Abstract
L-theanine is the most abundant free amino acid in tea that offers various favorable physiological and pharmacological effects. Bacterial enzyme of γ-glutamylmethylamide synthetase (GMAS) can catalyze the synthesis of theanine from glutamate, ethylamine and ATP, but the manufacturing cost is uncompetitive due to the expensive substrates and complex processes. In this study, we described pathway engineering of wild-type Escherichia coli for one-step fermentative production of theanine from sugars and ethylamine. First, the synthetic pathway of theanine was conducted by heterologous introduction of a novel GMAS from Paracoccus aminovorans. A xylose-induced T7 RNA polymerase-PT7 promoter system was used to enhance and control gmas gene expression. Next, the precursor glutamate pool was increased by overexpression of native citrate synthase and introduction of glutamate dehydrogenase from Corynebacterium glutamicum. Then, in order to push more carbon flux towards theanine synthesis, the tricarboxylic acid cycle was interrupted and pyruvate carboxylase from C. glutamicum was introduced as a bypath supplying oxaloacetate from pyruvate. Finally, an energy-conserving phosphoenolpyruvate carboxykinase from Mannheimia succiniciproducens was introduced to increase ATP yield for theanine synthesis. After optimizing the addition time and concentration of ethylamine hydrochloride in the fed-batch fermentation, the recombinant strain TH11 produced 70.6 g/L theanine in a 5-L bioreactor with a yield and productivity of 0.42 g/g glucose and 2.72 g/L/h, respectively. To our knowledge, this is the first report regarding the pathway engineering of E. coli for fermentative production of theanine. The high production capacity of recombinant strain, combined with the easy processes, will hold attractive industrial application potential for the future. γ-Glutamylmethylamide synthetase from P. aminovorans showed high ligation activity. Xylose-induced T7 RNA polymerase-PT7 promoter system was used to control gene expression. TCA cycle was rewired to push more carbon flux toward theanine synthesis. Ethylamine feeding strategy was optimized to balance cell growth and theanine production.
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Affiliation(s)
- Xiaoguang Fan
- Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, Tianjin University of Science & Technology, Tianjin, 300457, PR China.,College of Biotechnology, Tianjin University of Science & Technology, Tianjin, 300457, PR China
| | - Tong Zhang
- College of Biotechnology, Tianjin University of Science & Technology, Tianjin, 300457, PR China
| | - Yuanqing Ji
- College of Biotechnology, Tianjin University of Science & Technology, Tianjin, 300457, PR China
| | - Jie Li
- College of Biotechnology, Tianjin University of Science & Technology, Tianjin, 300457, PR China
| | - Keyi Long
- College of Biotechnology, Tianjin University of Science & Technology, Tianjin, 300457, PR China
| | - Yue Yuan
- College of Biotechnology, Tianjin University of Science & Technology, Tianjin, 300457, PR China
| | - Yanjun Li
- Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, Tianjin University of Science & Technology, Tianjin, 300457, PR China.,College of Biotechnology, Tianjin University of Science & Technology, Tianjin, 300457, PR China
| | - Qingyang Xu
- Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, Tianjin University of Science & Technology, Tianjin, 300457, PR China.,College of Biotechnology, Tianjin University of Science & Technology, Tianjin, 300457, PR China
| | - Ning Chen
- Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, Tianjin University of Science & Technology, Tianjin, 300457, PR China.,College of Biotechnology, Tianjin University of Science & Technology, Tianjin, 300457, PR China
| | - Xixian Xie
- Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, Tianjin University of Science & Technology, Tianjin, 300457, PR China.,College of Biotechnology, Tianjin University of Science & Technology, Tianjin, 300457, PR China
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