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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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Stegmüller J, Rodríguez Estévez M, Shu W, Gläser L, Myronovskyi M, Rückert-Reed C, Kalinowski J, Luzhetskyy A, Wittmann C. Systems metabolic engineering of the primary and secondary metabolism of Streptomyces albidoflavus enhances production of the reverse antibiotic nybomycin against multi-resistant Staphylococcus aureus. Metab Eng 2024; 81:123-143. [PMID: 38072358 DOI: 10.1016/j.ymben.2023.12.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2023] [Revised: 11/17/2023] [Accepted: 12/01/2023] [Indexed: 01/23/2024]
Abstract
Nybomycin is an antibiotic compound with proven activity against multi-resistant Staphylococcus aureus, making it an interesting candidate for combating these globally threatening pathogens. For exploring its potential, sufficient amounts of nybomycin and its derivatives must be synthetized to fully study its effectiveness, safety profile, and clinical applications. As native isolates only accumulate low amounts of the compound, superior producers are needed. The heterologous cell factory S. albidoflavus 4N24, previously derived from the cluster-free chassis S. albidoflavus Del14, produced 860 μg L-1 of nybomycin, mainly in the stationary phase. A first round of strain development modulated expression of genes involved in supply of nybomycin precursors under control of the common Perm* promoter in 4N24, but without any effect. Subsequent studies with mCherry reporter strains revealed that Perm* failed to drive expression during the product synthesis phase but that use of two synthetic promoters (PkasOP* and P41) enabled strong constitutive expression during the entire process. Using PkasOP*, several rounds of metabolic engineering successively streamlined expression of genes involved in the pentose phosphate pathway, the shikimic acid pathway, supply of CoA esters, and nybomycin biosynthesis and export, which more than doubled the nybomycin titer to 1.7 mg L-1 in the sixth-generation strain NYB-6B. In addition, we identified the minimal set of nyb genes needed to synthetize the molecule using single-gene-deletion strains. Subsequently, deletion of the regulator nybW enabled nybomycin production to begin during the growth phase, further boosting the titer and productivity. Based on RNA sequencing along the created strain genealogy, we discovered that the nyb gene cluster was unfavorably downregulated in all advanced producers. This inspired removal of a part and the entire set of the four regulatory genes at the 3'-end nyb of the cluster. The corresponding mutants NYB-8 and NYB-9 exhibited marked further improvement in production, and the deregulated cluster was combined with all beneficial targets from primary metabolism. The best strain, S. albidoflavus NYB-11, accumulated up to 12 mg L-1 nybomycin, fifteenfold more than the basic strain. The absence of native gene clusters in the host and use of a lean minimal medium contributed to a selective production process, providing an important next step toward further development of nybomycin.
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Affiliation(s)
- Julian Stegmüller
- Institute of Systems Biotechnology, Saarland University, Saarbrücken, Germany
| | | | - Wei Shu
- Institute of Systems Biotechnology, Saarland University, Saarbrücken, Germany
| | - Lars Gläser
- Institute of Systems Biotechnology, Saarland University, Saarbrücken, Germany
| | - Maksym Myronovskyi
- Department of Pharmaceutical Biotechnology, Saarland University, Saarbrücken, Germany
| | | | - Jörn Kalinowski
- Center for Biotechnology, Bielefeld University, Bielefeld, Germany
| | - Andriy Luzhetskyy
- Department of Pharmaceutical Biotechnology, Saarland University, Saarbrücken, Germany
| | - Christoph Wittmann
- Institute of Systems Biotechnology, Saarland University, Saarbrücken, Germany.
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Seo K, Shu W, Rückert-Reed C, Gerlinger P, Erb TJ, Kalinowski J, Wittmann C. From waste to health-supporting molecules: biosynthesis of natural products from lignin-, plastic- and seaweed-based monomers using metabolically engineered Streptomyces lividans. Microb Cell Fact 2023; 22:262. [PMID: 38114944 PMCID: PMC10731712 DOI: 10.1186/s12934-023-02266-0] [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: 11/02/2023] [Accepted: 12/05/2023] [Indexed: 12/21/2023] Open
Abstract
BACKGROUND Transforming waste and nonfood materials into bulk biofuels and chemicals represents a major stride in creating a sustainable bioindustry to optimize the use of resources while reducing environmental footprint. However, despite these advancements, the production of high-value natural products often continues to depend on the use of first-generation substrates, underscoring the intricate processes and specific requirements of their biosyntheses. This is also true for Streptomyces lividans, a renowned host organism celebrated for its capacity to produce a wide array of natural products, which is attributed to its genetic versatility and potent secondary metabolic activity. Given this context, it becomes imperative to assess and optimize this microorganism for the synthesis of natural products specifically from waste and nonfood substrates. RESULTS We metabolically engineered S. lividans to heterologously produce the ribosomally synthesized and posttranslationally modified peptide bottromycin, as well as the polyketide pamamycin. The modified strains successfully produced these compounds using waste and nonfood model substrates such as protocatechuate (derived from lignin), 4-hydroxybenzoate (sourced from plastic waste), and mannitol (from seaweed). Comprehensive transcriptomic and metabolomic analyses offered insights into how these substrates influenced the cellular metabolism of S. lividans. In terms of production efficiency, S. lividans showed remarkable tolerance, especially in a fed-batch process using a mineral medium containing the toxic aromatic 4-hydroxybenzoate, which led to enhanced and highly selective bottromycin production. Additionally, the strain generated a unique spectrum of pamamycins when cultured in mannitol-rich seaweed extract with no additional nutrients. CONCLUSION Our study showcases the successful production of high-value natural products based on the use of varied waste and nonfood raw materials, circumventing the reliance on costly, food-competing resources. S. lividans exhibited remarkable adaptability and resilience when grown on these diverse substrates. When cultured on aromatic compounds, it displayed a distinct array of intracellular CoA esters, presenting promising avenues for polyketide production. Future research could be focused on enhancing S. lividans substrate utilization pathways to process the intricate mixtures commonly found in waste and nonfood sources more efficiently.
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Affiliation(s)
- Kyoyoung Seo
- Institute of Systems Biotechnology, Saarland University, Saarbrücken, Germany
| | - Wei Shu
- Institute of Systems Biotechnology, Saarland University, Saarbrücken, Germany
| | | | | | - Tobias J Erb
- Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
| | | | - Christoph Wittmann
- Institute of Systems Biotechnology, Saarland University, Saarbrücken, Germany.
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Beganovic S, Rückert-Reed C, Sucipto H, Shu W, Gläser L, Patschkowski T, Struck B, Kalinowski J, Luzhetskyy A, Wittmann C. Systems biology of industrial oxytetracycline production in Streptomyces rimosus: the secrets of a mutagenized hyperproducer. Microb Cell Fact 2023; 22:222. [PMID: 37898787 PMCID: PMC10612213 DOI: 10.1186/s12934-023-02215-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2023] [Accepted: 09/26/2023] [Indexed: 10/30/2023] Open
Abstract
BACKGROUND Oxytetracycline which is derived from Streptomyces rimosus, inhibits a wide range of bacteria and is industrially important. The underlying biosynthetic processes are complex and hinder rational engineering, so industrial manufacturing currently relies on classical mutants for production. While the biochemistry underlying oxytetracycline synthesis is known to involve polyketide synthase, hyperproducing strains of S. rimosus have not been extensively studied, limiting our knowledge on fundamental mechanisms that drive production. RESULTS In this study, a multiomics analysis of S. rimosus is performed and wild-type and hyperproducing strains are compared. Insights into the metabolic and regulatory networks driving oxytetracycline formation were obtained. The overproducer exhibited increased acetyl-CoA and malonyl CoA supply, upregulated oxytetracycline biosynthesis, reduced competing byproduct formation, and streamlined morphology. These features were used to synthesize bhimamycin, an antibiotic, and a novel microbial chassis strain was created. A cluster deletion derivative showed enhanced bhimamycin production. CONCLUSIONS This study suggests that the precursor supply should be globally increased to further increase the expression of the oxytetracycline cluster while maintaining the natural cluster sequence. The mutagenized hyperproducer S. rimosus HP126 exhibited numerous mutations, including large genomic rearrangements, due to natural genetic instability, and single nucleotide changes. More complex mutations were found than those typically observed in mutagenized bacteria, impacting gene expression, and complicating rational engineering. Overall, the approach revealed key traits influencing oxytetracycline production in S. rimosus, suggesting that similar studies for other antibiotics could uncover general mechanisms to improve production.
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Affiliation(s)
- Selma Beganovic
- Institute of Systems Biotechnology, Saarland University, Campus A1 5, 66123, Saarbrücken, Germany
| | | | - Hilda Sucipto
- Department of Pharmacy, Saarland University, Saarbrücken, Germany
| | - Wei Shu
- Institute of Systems Biotechnology, Saarland University, Campus A1 5, 66123, Saarbrücken, Germany
| | - Lars Gläser
- Institute of Systems Biotechnology, Saarland University, Campus A1 5, 66123, Saarbrücken, Germany
| | | | - Ben Struck
- Centre for Biotechnology, Bielefeld University, Bielefeld, Germany
| | - Jörn Kalinowski
- Centre for Biotechnology, Bielefeld University, Bielefeld, Germany
| | | | - Christoph Wittmann
- Institute of Systems Biotechnology, Saarland University, Campus A1 5, 66123, Saarbrücken, Germany. *
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Pauli S, Kohlstedt M, Lamber J, Weiland F, Becker J, Wittmann C. Systems metabolic engineering upgrades Corynebacterium glutamicum for selective high-level production of the chiral drug precursor and cell-protective extremolyte L-pipecolic acid. Metab Eng 2023; 77:100-117. [PMID: 36931556 DOI: 10.1016/j.ymben.2023.03.006] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2022] [Revised: 03/02/2023] [Accepted: 03/14/2023] [Indexed: 03/17/2023]
Abstract
The nonproteinogenic cyclic metabolite l-pipecolic acid is a chiral precursor for the synthesis of various commercial drugs and functions as a cell-protective extremolyte and mediator of defense in plants, enabling high-value applications in the pharmaceutical, medical, cosmetic, and agrochemical markets. To date, the production of the compound is unfavorably fossil-based. Here, we upgraded the strain Corynebacterium glutamicum for l-pipecolic acid production using systems metabolic engineering. Heterologous expression of the l-lysine 6-dehydrogenase pathway, apparently the best route to be used in the microbe, yielded a family of strains that enabled successful de novo synthesis from glucose but approached a limit of performance at a yield of 0.18 mol mol-1. Detailed analysis of the producers at the transcriptome, proteome, and metabolome levels revealed that the requirements of the introduced route were largely incompatible with the cellular environment, which could not be overcome after several further rounds of metabolic engineering. Based on the gained knowledge, we based the strain design on l-l-lysine 6-aminotransferase instead, which enabled a substantially higher in vivo flux toward l-pipecolic acid. The tailormade producer C. glutamicum PIA-7 formed l-pipecolic acid up to a yield of 562 mmol mol-1, representing 75% of the theoretical maximum. Ultimately, the advanced mutant PIA-10B achieved a titer of 93 g L-1 in a fed-batch process on glucose, outperforming all previous efforts to synthesize this valuable molecule de novo and even approaching the level of biotransformation from l-lysine. Notably, the use of C. glutamicum allows the safe production of GRAS-designated l-pipecolic acid, providing extra benefit toward addressing the high-value pharmaceutical, medical, and cosmetic markets. In summary, our development sets a milestone toward the commercialization of biobased l-pipecolic acid.
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Affiliation(s)
- Sarah Pauli
- Institute for Systems Biotechnology, Saarland University, Saarbrücken, Germany
| | - Michael Kohlstedt
- Institute for Systems Biotechnology, Saarland University, Saarbrücken, Germany
| | - Jessica Lamber
- Institute for Systems Biotechnology, Saarland University, Saarbrücken, Germany
| | - Fabia Weiland
- Institute for Systems Biotechnology, Saarland University, Saarbrücken, Germany
| | - Judith Becker
- Institute for Systems Biotechnology, Saarland University, Saarbrücken, Germany
| | - Christoph Wittmann
- Institute for Systems Biotechnology, Saarland University, Saarbrücken, Germany.
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Christmann J, Cao P, Becker J, Desiderato CK, Goldbeck O, Riedel CU, Kohlstedt M, Wittmann C. High-efficiency production of the antimicrobial peptide pediocin PA-1 in metabolically engineered Corynebacterium glutamicum using a microaerobic process at acidic pH and elevated levels of bivalent calcium ions. Microb Cell Fact 2023; 22:41. [PMID: 36849884 PMCID: PMC9969654 DOI: 10.1186/s12934-023-02044-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2022] [Accepted: 02/16/2023] [Indexed: 03/01/2023] Open
Abstract
BACKGROUND Pediocin PA-1 is a bacteriocin of recognized value with applications in food bio-preservation and the medical sector for the prevention of infection. To date, industrial manufacturing of pediocin PA-1 is limited by high cost and low-performance. The recent establishment of the biotechnological workhorse Corynebacterium glutamicum as recombinant host for pediocin PA-1 synthesis displays a promising starting point towards more efficient production. RESULTS Here, we optimized the fermentative production process. Following successful simplification of the production medium, we carefully investigated the impact of dissolved oxygen, pH value, and the presence of bivalent calcium ions on pediocin production. It turned out that the formation of the peptide was strongly supported by an acidic pH of 5.7 and microaerobic conditions at a dissolved oxygen level of 2.5%. Furthermore, elevated levels of CaCl2 boosted production. The IPTG-inducible producer C. glutamicum CR099 pXMJ19 Ptac pedACDCg provided 66 mg L-1 of pediocin PA-1 in a two-phase batch process using the optimized set-up. In addition, the novel constitutive strain Ptuf pedACDCg allowed successful production without the need for IPTG. CONCLUSIONS The achieved pediocin titer surpasses previous efforts in various microbes up to almost seven-fold, providing a valuable step to further explore and develop this important bacteriocin. In addition to its high biosynthetic performance C. glutamicum proved to be highly robust under the demanding producing conditions, suggesting its further use as host for bacteriocin production.
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Affiliation(s)
- Jens Christmann
- grid.11749.3a0000 0001 2167 7588Institute for Systems Biotechnology, Saarland University, Saarbrücken, Germany
| | - Peng Cao
- grid.11749.3a0000 0001 2167 7588Institute for Systems Biotechnology, Saarland University, Saarbrücken, Germany
| | - Judith Becker
- grid.11749.3a0000 0001 2167 7588Institute for Systems Biotechnology, Saarland University, Saarbrücken, Germany
| | - Christian K. Desiderato
- grid.6582.90000 0004 1936 9748Institute of Microbiology and Biotechnology, University of Ulm, Ulm, Germany
| | - Oliver Goldbeck
- grid.6582.90000 0004 1936 9748Institute of Microbiology and Biotechnology, University of Ulm, Ulm, Germany
| | - Christian U. Riedel
- grid.6582.90000 0004 1936 9748Institute of Microbiology and Biotechnology, University of Ulm, Ulm, Germany
| | - Michael Kohlstedt
- grid.11749.3a0000 0001 2167 7588Institute for Systems Biotechnology, Saarland University, Saarbrücken, Germany
| | - Christoph Wittmann
- Institute for Systems Biotechnology, Saarland University, Saarbrücken, Germany.
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Li N, Li L, Yu S, Zhou J. Dual-channel glycolysis balances cofactor supply for l-homoserine biosynthesis in Corynebacterium glutamicum. BIORESOURCE TECHNOLOGY 2023; 369:128473. [PMID: 36509305 DOI: 10.1016/j.biortech.2022.128473] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Revised: 12/05/2022] [Accepted: 12/06/2022] [Indexed: 06/17/2023]
Abstract
l-Homoserine is an important platform compound that is widely used to produce many valuable bio-based products, but production of l-homoserine in Corynebacterium glutamicum remains low. In this study, an efficient l-homoserine-producing strain was constructed. Native pentose phosphate pathway (PPP) was enhanced and heterologous Entner-Doudoroff (ED) pathway was carefully introduced into l-homoserine-producing strain, which increased the l-homoserine titer. Coexpression of NADH-dependent aspartate-4-semialdehyde dehydrogenase and aspartate dehydrogenase could increase the titer from 11.3 to 13.3 g/L. Next, NADP+-dependent glyceraldehyde-3-phosphate dehydrogenase (NADP-GPD) was coexpressed with that of NAD+-dependent (NAD-GPD) to construct dual-channel glycolysis for balance of intracellular cofactors, which increased the l-homoserine titer by 48.6 % to 16.8 g/L. Finally, engineered strain Cg18-1 accumulated 63.5 g/L l-homoserine after 96 h in a 5 L bioreactor, the highest titer reported to date for C. glutamicum. This dual-channel glycolysis strategy provides a reference for automatic cofactor regulation to promote efficient biosynthesis of other target products.
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Affiliation(s)
- Ning Li
- Science Center for Future Foods, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China; National Engineering Research Center of Cereal Fermentation and Food Biomanufacturing, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China; School of Food Science and Technology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China
| | - Lihong Li
- Science Center for Future Foods, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China; National Engineering Research Center of Cereal Fermentation and Food Biomanufacturing, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China
| | - Shiqin Yu
- Science Center for Future Foods, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China; National Engineering Research Center of Cereal Fermentation and Food Biomanufacturing, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China
| | - Jingwen Zhou
- Science Center for Future Foods, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China; National Engineering Research Center of Cereal Fermentation and Food Biomanufacturing, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China; Engineering Research Center of Ministry of Education on Food Synthetic Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China; Jiangsu Province Engineering Research Center of Food Synthetic Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China.
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Xin B, Zhong C, Wang Y. Integrating the marine carbon resource mannitol into biomanufacturing. Trends Biotechnol 2023; 41:745-749. [PMID: 36610892 DOI: 10.1016/j.tibtech.2022.12.010] [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: 11/24/2022] [Revised: 12/15/2022] [Accepted: 12/16/2022] [Indexed: 01/07/2023]
Abstract
Mannitol is a readily accessible component of seaweed with higher energy content than glucose, making it a promising feedstock for biomanufacturing. Microorganisms have been engineered for converting mannitol into various bioproducts. Microbial strain discovery and synthetic biology approach will advance biomanufacturing using mannitol and other complex components of marine biomass.
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Affiliation(s)
- Bo Xin
- State Key Laboratory of Food Nutrition and Safety, Tianjin University of Science and Technology, Tianjin 300457, China; Key Laboratory of Industrial Fermentation Microbiology (Ministry of Education), Tianjin University of Science and Technology, Tianjin 300457, China
| | - Cheng Zhong
- State Key Laboratory of Food Nutrition and Safety, Tianjin University of Science and Technology, Tianjin 300457, China; Key Laboratory of Industrial Fermentation Microbiology (Ministry of Education), Tianjin University of Science and Technology, Tianjin 300457, China.
| | - Yu Wang
- Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China; National Technology Innovation Center of Synthetic Biology, Tianjin 300308, China.
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Systems metabolic engineering upgrades Corynebacterium glutamicum to high-efficiency cis, cis-muconic acid production from lignin-based aromatics. Metab Eng 2023; 75:153-169. [PMID: 36563956 DOI: 10.1016/j.ymben.2022.12.005] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Revised: 12/14/2022] [Accepted: 12/17/2022] [Indexed: 12/24/2022]
Abstract
Lignin displays a highly challenging renewable. To date, massive amounts of lignin, generated in lignocellulosic processing facilities, are for the most part merely burned due to lacking value-added alternatives. Aromatic lignin monomers of recognized relevance are in particular vanillin, and to a lesser extent vanillate, because they are accessible at high yield from softwood-lignin using industrially operated alkaline oxidative depolymerization. Here, we metabolically engineered C. glutamicum towards cis, cis-muconate (MA) production from these key aromatics. Starting from the previously created catechol-based producer C. glutamicum MA-2, systems metabolic engineering first discovered an unspecific aromatic aldehyde reductase that formed aromatic alcohols from vanillin, protocatechualdehyde, and p- hydroxybenzaldehyde, and was responsible for the conversion up to 57% of vanillin into vanillyl alcohol. The alcohol was not re-consumed by the microbe later, posing a strong drawback on the producer. The identification and subsequent elimination of the encoding fudC gene completely abolished vanillyl alcohol formation. Second, the initially weak flux through the native vanillin and vanillate metabolism was enhanced up to 2.9-fold by implementing synthetic pathway modules. Third, the most efficient protocatechuate decarboxylase AroY for conversion of the midstream pathway intermediate protocatechuate into catechol was identified out of several variants in native and codon optimized form and expressed together with the respective helper proteins. Fourth, the streamlined modules were all genomically combined which yielded the final strain MA-9. MA-9 produced bio-based MA from vanillin, vanillate, and seven structurally related aromatics at maximum selectivity. In addition, MA production from softwood-based vanillin, obtained through alkaline depolymerization, was demonstrated.
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10
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Woo S, Moon JH, Sung J, Baek D, Shon YJ, Jung GY. Recent Advances in the Utilization of Brown Macroalgae as Feedstock for Microbial Biorefinery. BIOTECHNOL BIOPROC E 2022. [DOI: 10.1007/s12257-022-0301-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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11
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Wei X, Yang L, Wang H, Chen Z, Xu Y, Weng Y, Cao M, Li Q, He N. Genomic and metabolomic analysis of Bacillus licheniformis with enhanced poly-γ-glutamic acid production through atmospheric and room temperature plasma mutagenesis. Front Chem Sci Eng 2022. [DOI: 10.1007/s11705-022-2211-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/14/2022]
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12
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Nie L, He Y, Hu L, Zhu X, Wu X, Zhang B. Improvement in L-ornithine production from mannitol via transcriptome-guided genetic engineering in Corynebacterium glutamicum. BIOTECHNOLOGY FOR BIOFUELS AND BIOPRODUCTS 2022; 15:97. [PMID: 36123702 PMCID: PMC9484086 DOI: 10.1186/s13068-022-02198-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/16/2022] [Accepted: 09/10/2022] [Indexed: 06/15/2023]
Abstract
BACKGROUND L-Ornithine is an important medicinal intermediate that is mainly produced by microbial fermentation using glucose as the substrate. To avoid competition with human food resources, there is an urgent need to explore alternative carbon sources for L-ornithine production. In a previous study, we constructed an engineered strain, Corynebacterium glutamicum MTL13, which produces 54.56 g/L of L-ornithine from mannitol. However, compared with the titers produced using glucose as a substrate, the results are insufficient, and further improvement is required. RESULTS In this study, comparative transcriptome profiling of MTL01 cultivated with glucose or mannitol was performed to identify novel targets for engineering L-ornithine-producing strains. Guided by the transcriptome profiling results, we modulated the expression of qsuR (encoding a LysR-type regulator QsuR), prpC (encoding 2-methylcitrate synthase PrpC), pdxR (encoding a MocR-type regulator PdxR), acnR (encoding a TetR-type transcriptional regulator AcnR), CGS9114_RS08985 (encoding a hypothetical protein), and CGS9114_RS09730 (encoding a TetR/AcrR family transcriptional regulator), thereby generating the engineered strain MTL25 that can produce L-ornithine at a titer of 93.6 g/L, representing a 71.6% increase as compared with the parent strain MTL13 and the highest L-ornithine titer reported so far for C. glutamicum. CONCLUSIONS This study provides novel indirect genetic targets for enhancing L-ornithine accumulation on mannitol and lays a solid foundation for the biosynthesis of L-ornithine from marine macroalgae, which is farmed globally as a promising alternative feedstock.
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Affiliation(s)
- Libin Nie
- Jiangxi Engineering Laboratory for the Development and Utilization of Agricultural Microbial Resources, Jiangxi Agricultural University, Nanchang, 330045, China
- College of Bioscience and Bioengineering, Jiangxi Agricultural University, Nanchang, 330045, China
| | - Yutong He
- Jiangxi Engineering Laboratory for the Development and Utilization of Agricultural Microbial Resources, Jiangxi Agricultural University, Nanchang, 330045, China
- College of Bioscience and Bioengineering, Jiangxi Agricultural University, Nanchang, 330045, China
| | - Lirong Hu
- Jiangxi Engineering Laboratory for the Development and Utilization of Agricultural Microbial Resources, Jiangxi Agricultural University, Nanchang, 330045, China
- College of Bioscience and Bioengineering, Jiangxi Agricultural University, Nanchang, 330045, China
| | - Xiangdong Zhu
- Jiangxi Engineering Laboratory for the Development and Utilization of Agricultural Microbial Resources, Jiangxi Agricultural University, Nanchang, 330045, China
- College of Bioscience and Bioengineering, Jiangxi Agricultural University, Nanchang, 330045, China
| | - Xiaoyu Wu
- Jiangxi Engineering Laboratory for the Development and Utilization of Agricultural Microbial Resources, Jiangxi Agricultural University, Nanchang, 330045, China
- College of Bioscience and Bioengineering, Jiangxi Agricultural University, Nanchang, 330045, China
| | - Bin Zhang
- Jiangxi Engineering Laboratory for the Development and Utilization of Agricultural Microbial Resources, Jiangxi Agricultural University, Nanchang, 330045, China.
- College of Bioscience and Bioengineering, Jiangxi Agricultural University, Nanchang, 330045, China.
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13
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Rohles C, Pauli S, Gießelmann G, Kohlstedt M, Becker J, Wittmann C. Systems metabolic engineering of Corynebacterium glutamicum eliminates all by-products for selective and high-yield production of the platform chemical 5-aminovalerate. Metab Eng 2022; 73:168-181. [PMID: 35917915 DOI: 10.1016/j.ymben.2022.07.005] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Revised: 07/01/2022] [Accepted: 07/13/2022] [Indexed: 11/29/2022]
Abstract
5-aminovalerate (AVA) is a platform chemical of substantial commercial value to derive nylon-5 and five-carbon derivatives like δ-valerolactam, 1,5-pentanediol, glutarate, and 5-hydroxyvalerate. De-novo bio-production synthesis of AVA using metabolically engineered cell factories is regarded as exemplary route to provide this chemical in a sustainable way. So far, this route is limited by low titers, rates and yields and suffers from high levels of by-products. To overcome these limitations, we developed a novel family of AVA producing C. glutamicum cell factories. Stepwise optimization included (i) improved AVA biosynthesis by expression balancing of the heterologous davAB genes from P. putida, (ii) reduced formation of the by-product glutarate by disruption of the catabolic y-aminobutyrate pathway (iii), increased AVA export, and (iv) reduced AVA re-import via native and heterologous transporters to account for the accumulation of intracellular AVA up to 300 mM. Strain C. glutamicum AVA-5A, obtained after several optimization rounds, produced 48.3 g L-1 AVA in a fed-batch process and achieved a high yield of 0.21 g g-1. Surprisingly in later stages, the mutant suddenly accumulated glutarate to an extent equivalent to 30% of the amount of AVA formed, tenfold more than in the early process, displaying a severe drawback toward industrial production. Further exploration led to the discovery that ArgD, naturally aminating N-acetyl-l-ornithine during l-arginine biosynthesis, exhibits deaminating side activity on AVA toward glutarate formation. This promiscuity became relevant because of the high intracellular AVA level and the fact that ArgD became unoccupied with the gradually stronger switch-off of anabolism during production. Glutarate formation was favorably abolished in the advanced strains AVA-6A, AVA-6B, and AVA-7, all lacking argD. In a fed-batch process, C. glutamicum AVA-7 produced 46.5 g L-1 AVA at a yield of 0.34 g g-1 and a maximum productivity of 1.52 g L-1 h-1, outperforming all previously reported efforts and stetting a milestone toward industrial manufacturing of AVA. Notably, the novel cell factories are fully genome-based, offering high genetic stability and requiring no selection markers.
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Affiliation(s)
- Christina Rohles
- Institute of Systems Biotechnology, Saarland University, Germany
| | - Sarah Pauli
- Institute of Systems Biotechnology, Saarland University, Germany
| | | | | | - Judith Becker
- Institute of Systems Biotechnology, Saarland University, Germany
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14
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Jie-Liu, Xu JZ, Rao ZM, Zhang WG. Industrial production of L-lysine in Corynebacterium glutamicum: progress and prospects. Microbiol Res 2022; 262:127101. [DOI: 10.1016/j.micres.2022.127101] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2022] [Revised: 06/11/2022] [Accepted: 06/22/2022] [Indexed: 11/24/2022]
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15
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Pérez-García F, Klein VJ, Brito LF, Brautaset T. From Brown Seaweed to a Sustainable Microbial Feedstock for the Production of Riboflavin. Front Bioeng Biotechnol 2022; 10:863690. [PMID: 35497351 PMCID: PMC9049185 DOI: 10.3389/fbioe.2022.863690] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Accepted: 03/09/2022] [Indexed: 12/11/2022] Open
Abstract
The increasing global demand for food and energy production encourages the development of new production strategies focused on sustainability. Often, microbial bioprocesses rely on food or feed competitive feedstocks; hence, there is a trending need for green substrates. Here, we have proven the potential of brown seaweed biomass as microbial feedstock on account of its content of mannitol and the glucose polymer laminarin. Our host, Corynebacterium glutamicum, was engineered to enable access to mannitol as a carbon source through the heterologous expression of the mannitol-specific phosphotransferase system and the mannitol-1-phosphate-5-dehydrogenase from Bacillus subtilis. Overproduction of riboflavin was coupled with mannitol and glucose consumption via constitutive overexpression of the biosynthetic riboflavin operon ribGCAH from C. glutamicum. Brown seaweed extract and brown seaweed hydrolysate from Laminaria hyperborea, containing mannitol and glucose, were used as a carbon source for flask and bioreactor fermentations. In a seaweed-based fed-batch fermentation, the riboflavin final titer, yield, and volumetric productivity values of 1,291.2 mg L−1, 66.1 mg g−1, and 17.2 mg L−1 h−1, respectively, were achieved.
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16
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Wendisch VF, Nampoothiri KM, Lee JH. Metabolic Engineering for Valorization of Agri- and Aqua-Culture Sidestreams for Production of Nitrogenous Compounds by Corynebacterium glutamicum. Front Microbiol 2022; 13:835131. [PMID: 35211108 PMCID: PMC8861201 DOI: 10.3389/fmicb.2022.835131] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Accepted: 01/13/2022] [Indexed: 01/06/2023] Open
Abstract
Corynebacterium glutamicum is used for the million-ton-scale production of amino acids. Valorization of sidestreams from agri- and aqua-culture has focused on the production of biofuels and carboxylic acids. Nitrogen present in various amounts in sidestreams may be valuable for the production of amines, amino acids and other nitrogenous compounds. Metabolic engineering of C. glutamicum for valorization of agri- and aqua-culture sidestreams addresses to bridge this gap. The product portfolio accessible via C. glutamicum fermentation primarily features amino acids and diamines for large-volume markets in addition to various specialty amines. On the one hand, this review covers metabolic engineering of C. glutamicum to efficiently utilize components of various sidestreams. On the other hand, examples of the design and implementation of synthetic pathways not present in native metabolism to produce sought after nitrogenous compounds will be provided. Perspectives and challenges of this concept will be discussed.
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Affiliation(s)
- Volker F Wendisch
- Genetics of Prokaryotes, Faculty of Biology and Center for Biotechnology, Bielefeld University, Bielefeld, Germany
| | - K Madhavan Nampoothiri
- Microbial Processes and Technology Division, Council of Scientific and Industrial Research-National Institute for Interdisciplinary Science and Technology, Thiruvananthapuram, India
| | - Jin-Ho Lee
- Department of Food Science & Biotechnology, Kyungsung University, Busan, South Korea
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17
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Sasaki Y, Yoshikuni Y. Metabolic engineering for valorization of macroalgae biomass. Metab Eng 2022; 71:42-61. [PMID: 35077903 DOI: 10.1016/j.ymben.2022.01.005] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2021] [Revised: 01/10/2022] [Accepted: 01/12/2022] [Indexed: 12/18/2022]
Abstract
Marine macroalgae have huge potential as feedstocks for production of a wide spectrum of chemicals used in biofuels, biomaterials, and bioactive compounds. Harnessing macroalgae in these ways could promote wellbeing for people while mitigating climate change and environmental destruction linked to use of fossil fuels. Microorganisms play pivotal roles in converting macroalgae into valuable products, and metabolic engineering technologies have been developed to extend their native capabilities. This review showcases current achievements in engineering the metabolisms of various microbial chassis to convert red, green, and brown macroalgae into bioproducts. Unique features of macroalgae, such as seasonal variation in carbohydrate content and salinity, provide the next challenges to advancing macroalgae-based biorefineries. Three emerging engineering strategies are discussed here: (1) designing dynamic control of metabolic pathways, (2) engineering strains of halophilic (salt-tolerant) microbes, and (3) developing microbial consortia for conversion. This review illuminates opportunities for future research communities by elucidating current approaches to engineering microbes so they can become cell factories for the utilization of macroalgae feedstocks.
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Affiliation(s)
- Yusuke Sasaki
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Yasuo Yoshikuni
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA; Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA; Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA; Center for Advanced Bioenergy and Bioproducts Innovation, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA; Global Institution for Collaborative Research and Education, Hokkaido University, Hokkaido, 060-8589, Japan.
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18
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Advances in microbial production of feed amino acid. ADVANCES IN APPLIED MICROBIOLOGY 2022; 119:1-33. [DOI: 10.1016/bs.aambs.2022.05.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
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19
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Dookeran ZA, Nielsen DR. Systematic Engineering of Synechococcus elongatus UTEX 2973 for Photosynthetic Production of l-Lysine, Cadaverine, and Glutarate. ACS Synth Biol 2021; 10:3561-3575. [PMID: 34851612 DOI: 10.1021/acssynbio.1c00492] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Amino acids and related targets are typically produced by well-characterized heterotrophs including Corynebacterium glutamicum and Escherichia coli. Cyanobacteria offer an opportunity to supplant these sugar-intensive processes by instead directly utilizing atmospheric CO2 and sunlight. Synechococcus elongatus UTEX 2973 (hereafter UTEX 2973) is a particularly promising photoautotrophic platform due to its fast growth rate. Here, we first engineered UTEX 2973 to overproduce l-lysine (hereafter lysine), after which both cadaverine and glutarate production were achieved through further pathway engineering. To facilitate metabolic engineering, the relative activities of a subset of previously uncharacterized promoters were investigated, in each case, while also comparing the effects of both chromosomal (from neutral site NS3) and episomal (from pAM4788) expressions. Using these parts, lysine overproduction in UTEX 2973 was engineered by introducing a feedback-resistant copy of aspartate kinase (encoded by lysCfbr) and a lysine exporter (encoded by ybjE), both from E. coli. While chromosomal expression resulted in lysine production up to just 325.3 ± 14.8 mg/L after 120 h, this was then increased to 556.3 ± 62.3 mg/L via plasmid-based expression, also surpassing prior reports of photoautotrophic lysine bioproduction. Lastly, additional products of interest were then targeted by modularly extending the lysine pathway to glutarate and cadaverine, two 5-carbon, bioplastic monomers. By this approach, glutarate has so far been produced at final titers reaching 67.5 ± 2.2 mg/L by 96 h, whereas cadaverine has been produced at up to 55.3 ± 6.7 mg/L. Overcoming pathway and/or transport bottlenecks, meanwhile, will be important to improving upon these initial outputs.
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Affiliation(s)
- Zachary A. Dookeran
- Chemical Engineering, School for Engineering of Matter, Transport, and Energy, Arizona State University, P.O. Box 876106, Tempe, Arizona 85287-6106, United States
| | - David R. Nielsen
- Chemical Engineering, School for Engineering of Matter, Transport, and Energy, Arizona State University, P.O. Box 876106, Tempe, Arizona 85287-6106, United States
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20
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Establishing recombinant production of pediocin PA-1 in Corynebacterium glutamicum. Metab Eng 2021; 68:34-45. [PMID: 34492380 PMCID: PMC8593837 DOI: 10.1016/j.ymben.2021.09.002] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2021] [Revised: 07/30/2021] [Accepted: 09/01/2021] [Indexed: 11/21/2022]
Abstract
Bacteriocins are antimicrobial peptides produced by bacteria to inhibit competitors in their natural environments. Some of these peptides have emerged as commercial food preservatives and, due to the rapid increase in antibiotic resistant bacteria, are also discussed as interesting alternatives to antibiotics for therapeutic purposes. Currently, commercial bacteriocins are produced exclusively with natural producer organisms on complex substrates and are sold as semi-purified preparations or crude fermentates. To allow clinical application, efficacy of production and purity of the product need to be improved. This can be achieved by shifting production to recombinant microorganisms. Here, we identify Corynebacterium glutamicum as a suitable production host for the bacteriocin pediocin PA-1. C. glutamicum CR099 shows resistance to high concentrations of pediocin PA-1 and the bacteriocin was not inactivated when spiked into growing cultures of this bacterium. Recombinant C. glutamicum expressing a synthetic pedACDCgl operon releases a compound that has potent antimicrobial activity against Listeria monocytogenes and Listeria innocua and matches size and mass:charge ratio of commercial pediocin PA-1. Fermentations in shake flasks and bioreactors suggest that low levels of dissolved oxygen are favorable for production of pediocin. Under these conditions, however, reduced activity of the TCA cycle resulted in decreased availability of the important pediocin precursor l-asparagine suggesting options for further improvement. Overall, we demonstrate that C. glutamicum is a suitable host for recombinant production of bacteriocins of the pediocin family. C. glutamicum CR099 is resistant to high concentrations of pediocin PA-1. Recombinant C. glutamicum CR099/pEKEx-pedACDCg produces of a compound with antimicrobial activity against Listeria sp. The purified compound matches size and mass:charge ratio of commercial pediocin PA-1. Low oxygen levels are favorable for production of active pediocin by C. glutamicum in batch fermentations.
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21
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Advances in metabolic engineering of Corynebacterium glutamicum to produce high-value active ingredients for food, feed, human health, and well-being. Essays Biochem 2021; 65:197-212. [PMID: 34096577 PMCID: PMC8313993 DOI: 10.1042/ebc20200134] [Citation(s) in RCA: 49] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2021] [Revised: 04/26/2021] [Accepted: 04/27/2021] [Indexed: 12/12/2022]
Abstract
The soil microbe Corynebacterium glutamicum is a leading workhorse in industrial biotechnology and has become famous for its power to synthetise amino acids and a range of bulk chemicals at high titre and yield. The product portfolio of the microbe is continuously expanding. Moreover, metabolically engineered strains of C. glutamicum produce more than 30 high value active ingredients, including signature molecules of raspberry, savoury, and orange flavours, sun blockers, anti-ageing sugars, and polymers for regenerative medicine. Herein, we highlight recent advances in engineering of the microbe into novel cell factories that overproduce these precious molecules from pioneering proofs-of-concept up to industrial productivity.
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22
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Becker J, Wittmann C. Metabolic Engineering of
Corynebacterium glutamicum. Metab Eng 2021. [DOI: 10.1002/9783527823468.ch12] [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]
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23
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Hoffmann SL, Kohlstedt M, Jungmann L, Hutter M, Poblete-Castro I, Becker J, Wittmann C. Cascaded valorization of brown seaweed to produce l-lysine and value-added products using Corynebacterium glutamicum streamlined by systems metabolic engineering. Metab Eng 2021; 67:293-307. [PMID: 34314893 DOI: 10.1016/j.ymben.2021.07.010] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2020] [Revised: 06/23/2021] [Accepted: 07/22/2021] [Indexed: 12/15/2022]
Abstract
Seaweeds emerge as promising third-generation renewable for sustainable bioproduction. In the present work, we valorized brown seaweed to produce l-lysine, the world's leading feed amino acid, using Corynebacterium glutamicum, which was streamlined by systems metabolic engineering. The mutant C. glutamicum SEA-1 served as a starting point for development because it produced small amounts of l-lysine from mannitol, a major seaweed sugar, because of the deletion of its arabitol repressor AtlR and its engineered l-lysine pathway. Starting from SEA-1, we systematically optimized the microbe to redirect excess NADH, formed on the sugar alcohol, towards NADPH, required for l-lysine synthesis. The mannitol dehydrogenase variant MtlD D75A, inspired by 3D protein homology modelling, partly generated NADPH during the oxidation of mannitol to fructose, leading to a 70% increased l-lysine yield in strain SEA-2C. Several rounds of strain engineering further increased NADPH supply and l-lysine production. The best strain, SEA-7, overexpressed the membrane-bound transhydrogenase pntAB together with codon-optimized gapN, encoding NADPH-dependent glyceraldehyde 3-phosphate dehydrogenase, and mak, encoding fructokinase. In a fed-batch process, SEA-7 produced 76 g L-1l-lysine from mannitol at a yield of 0.26 mol mol-1 and a maximum productivity of 2.1 g L-1 h-1. Finally, SEA-7 was integrated into seaweed valorization cascades. Aqua-cultured Laminaria digitata, a major seaweed for commercial alginate, was extracted and hydrolyzed enzymatically, followed by recovery and clean-up of pure alginate gum. The residual sugar-based mixture was converted to l-lysine at a yield of 0.27 C-mol C-mol-1 using SEA-7. Second, stems of the wild-harvested seaweed Durvillaea antarctica, obtained as waste during commercial processing of the blades for human consumption, were extracted using acid treatment. Fermentation of the hydrolysate using SEA-7 provided l-lysine at a yield of 0.40 C-mol C-mol-1. Our findings enable improvement of the efficiency of seaweed biorefineries using tailor-made C. glutamicum strains.
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Affiliation(s)
- Sarah Lisa Hoffmann
- Institute of Systems Biotechnology, Saarland University, Saarbrücken, Germany
| | - Michael Kohlstedt
- Institute of Systems Biotechnology, Saarland University, Saarbrücken, Germany
| | - Lukas Jungmann
- Institute of Systems Biotechnology, Saarland University, Saarbrücken, Germany
| | - Michael Hutter
- Centre for Bioinformatics, Saarland University, Saarbrücken, Germany
| | | | - Judith Becker
- Institute of Systems Biotechnology, Saarland University, Saarbrücken, Germany
| | - Christoph Wittmann
- Institute of Systems Biotechnology, Saarland University, Saarbrücken, Germany.
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24
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Huang Y, Ji X, Ma Z, Łężyk M, Xue Y, Zhao H. Green chemical and biological synthesis of cadaverine: recent development and challenges. RSC Adv 2021; 11:23922-23942. [PMID: 35479032 PMCID: PMC9036910 DOI: 10.1039/d1ra02764f] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2021] [Accepted: 06/29/2021] [Indexed: 11/21/2022] Open
Abstract
Cadaverine has great potential to be used as an important monomer for the development of a series of high value-added products with market prospects. The most promising strategies for cadaverine synthesis involve using green chemical and bioconversion technologies. Herein, the review focuses on the progress and strategies towards the green chemical synthesis and biosynthesis of cadaverine. Specifically, we address the specific biosynthetic pathways of cadaverine from different substrates as well as extensively discussing the origination, structure and catalytic mechanism of the key lysine decarboxylases. The advanced strategies for process intensification, the separation and purification of cadaverine have been summarized. Furthermore, the challenging issues of the environmental, economic, and applicable impact for cadaverine production are also highlighted. This review concludes with the promising outlooks of state-of-the-art applications of cadaverine along with some insights toward their challenges and potential improvements. Progress and strategies towards the green chemo/bio-synthesis of cadaverine with special attention to their environmental, economic, and applicable impact are reviewed.![]()
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Affiliation(s)
- Yuhong Huang
- Beijing Key Laboratory of Ionic Liquids Clean Process, CAS Key Laboratory of Green Process and Engineering, State Key Laboratory of Multiphase Complex Systems, Institute of Process Engineering, Chinese Academy of Sciences Beijing 100190 China .,Innovation Academy for Green Manufacture, Chinese Academy of Sciences Beijing 100190 China.,Zhengzhou Institute of Emerging Industrial Technology Zhengzhou City Henan 450000 China.,Zhongke Langfang Institute of Process Engineering Langfang 065001 China
| | - Xiuling Ji
- Beijing Key Laboratory of Ionic Liquids Clean Process, CAS Key Laboratory of Green Process and Engineering, State Key Laboratory of Multiphase Complex Systems, Institute of Process Engineering, Chinese Academy of Sciences Beijing 100190 China
| | - Zhanling Ma
- Zhengzhou Institute of Emerging Industrial Technology Zhengzhou City Henan 450000 China
| | - Mateusz Łężyk
- Water Supply and Bioeconomy Division, Faculty of Environmental Engineering and Energy, Poznan University of Technology Berdychowo 4 60-965 Poznan Poland
| | - Yaju Xue
- Beijing Key Laboratory of Ionic Liquids Clean Process, CAS Key Laboratory of Green Process and Engineering, State Key Laboratory of Multiphase Complex Systems, Institute of Process Engineering, Chinese Academy of Sciences Beijing 100190 China
| | - Hai Zhao
- Innovation Academy for Green Manufacture, Chinese Academy of Sciences Beijing 100190 China
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25
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Li N, Wang M, Yu S, Zhou J. Optimization of CRISPR-Cas9 through promoter replacement and efficient production of L-homoserine in Corynebacterium glutamicum. Biotechnol J 2021; 16:e2100093. [PMID: 34018325 DOI: 10.1002/biot.202100093] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2021] [Revised: 05/04/2021] [Accepted: 05/11/2021] [Indexed: 12/18/2022]
Abstract
BACKGROUND Corynebacterium glutamicum is an important chassis for industrial applications. The low efficiency of commonly used genome editing methods for C. glutamicum limits the rapid multiple engineering of the bacterium. MAIN METHODS AND MAJOR RESULTS In this study, chromosome-borne expression of cas9 and recET from Escherichia coli K12-MG1655 was achieved to avoid toxicity to the strain, increase the probability of homologous recombination, and reduce loss of viability caused by double-strand breaks. Constitutive strong promoters, such as P45 , Ptrc , and PH36 , were used to replace PglyA and to expand the application of the CRISPR-Cas9 system. By using this system, a C. glutamicum strain producing L-homoserine to 22.1 g per L in a 5-L bioreactor after 96 h was obtained. CONCLUSIONS AND IMPLICATIONS Through the application of visualized fluorescent protein, the process of plasmid curing was optimized, obtain a continuous and rapid CRISPR-Cas9 genome editing system. The method described here could be useful to construct C. glutamicum mutant rapidly.
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Affiliation(s)
- Ning Li
- National Engineering Laboratory for Cereal Fermentation Technology, Jiangnan University, Wuxi, Jiangsu, China.,State Key Laboratory of Food Science and Technology, School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu, China.,Science Center for Future Foods, Jiangnan University, Wuxi, Jiangsu, China.,Jiangsu Provisional Research Center for Bioactive Product Processing Technology, Jiangnan University, Wuxi, Jiangsu, China
| | - Miao Wang
- State Key Laboratory of Food Science and Technology, School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu, China
| | - Shiqin Yu
- National Engineering Laboratory for Cereal Fermentation Technology, Jiangnan University, Wuxi, Jiangsu, China.,Science Center for Future Foods, Jiangnan University, Wuxi, Jiangsu, China.,Jiangsu Provisional Research Center for Bioactive Product Processing Technology, Jiangnan University, Wuxi, Jiangsu, China
| | - Jingwen Zhou
- National Engineering Laboratory for Cereal Fermentation Technology, Jiangnan University, Wuxi, Jiangsu, China.,Science Center for Future Foods, Jiangnan University, Wuxi, Jiangsu, China.,Jiangsu Provisional Research Center for Bioactive Product Processing Technology, Jiangnan University, Wuxi, Jiangsu, China
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26
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Gläser L, Kuhl M, Stegmüller J, Rückert C, Myronovskyi M, Kalinowski J, Luzhetskyy A, Wittmann C. Superior production of heavy pamamycin derivatives using a bkdR deletion mutant of Streptomyces albus J1074/R2. Microb Cell Fact 2021; 20:111. [PMID: 34082758 PMCID: PMC8176718 DOI: 10.1186/s12934-021-01602-6] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2021] [Accepted: 05/27/2021] [Indexed: 11/17/2022] Open
Abstract
Background Pamamycins are macrodiolides of polyketide origin which form a family of differently large homologues with molecular weights between 579 and 663. They offer promising biological activity against pathogenic fungi and gram-positive bacteria. Admittedly, production titers are very low, and pamamycins are typically formed as crude mixture of mainly smaller derivatives, leaving larger derivatives rather unexplored so far. Therefore, strategies that enable a more efficient production of pamamycins and provide increased fractions of the rare large derivatives are highly desired. Here we took a systems biology approach, integrating transcription profiling by RNA sequencing and intracellular metabolite analysis, to enhance pamamycin production in the heterologous host S. albus J1074/R2. Results Supplemented with l-valine, the recombinant producer S. albus J1074/R2 achieved a threefold increased pamamycin titer of 3.5 mg L−1 and elevated fractions of larger derivatives: Pam 649 was strongly increased, and Pam 663 was newly formed. These beneficial effects were driven by increased availability of intracellular CoA thioesters, the building blocks for the polyketide, resulting from l-valine catabolism. Unfavorably, l-valine impaired growth of the strain, repressed genes of mannitol uptake and glycolysis, and suppressed pamamycin formation, despite the biosynthetic gene cluster was transcriptionally activated, restricting production to the post l-valine phase. A deletion mutant of the transcriptional regulator bkdR, controlling a branched-chain amino acid dehydrogenase complex, revealed decoupled pamamycin biosynthesis. The regulator mutant accumulated the polyketide independent of the nutrient status. Supplemented with l-valine, the novel strain enabled the biosynthesis of pamamycin mixtures with up to 55% of the heavy derivatives Pam 635, Pam 649, and Pam 663: almost 20-fold more than the wild type. Conclusions Our findings open the door to provide rare heavy pamamycins at markedly increased efficiency and facilitate studies to assess their specific biological activities and explore this important polyketide further. Supplementary Information The online version contains supplementary material available at 10.1186/s12934-021-01602-6.
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Affiliation(s)
- Lars Gläser
- Institute of Systems Biotechnology, Saarland University, Saarbrücken, Germany
| | - Martin Kuhl
- Institute of Systems Biotechnology, Saarland University, Saarbrücken, Germany
| | - Julian Stegmüller
- Institute of Systems Biotechnology, Saarland University, Saarbrücken, Germany
| | | | - Maksym Myronovskyi
- Department of Pharmacy, Pharmaceutical Biotechnology, Saarland University, Saarbrücken, Germany
| | - Jörn Kalinowski
- Center for Biotechnology, Bielefeld University, Bielefeld, Germany
| | - Andriy Luzhetskyy
- Department of Pharmacy, Pharmaceutical Biotechnology, Saarland University, Saarbrücken, Germany
| | - Christoph Wittmann
- Institute of Systems Biotechnology, Saarland University, Saarbrücken, Germany.
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Sheng Q, Wu X, Jiang Y, Li Z, Wang F, Zhang B. Highly efficient biosynthesis of l-ornithine from mannitol by using recombinant Corynebacterium glutamicum. BIORESOURCE TECHNOLOGY 2021; 327:124799. [PMID: 33582518 DOI: 10.1016/j.biortech.2021.124799] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/11/2020] [Revised: 01/26/2021] [Accepted: 01/27/2021] [Indexed: 06/12/2023]
Abstract
Mannitol is a promising six-carbon sugar alcohol that is widely found in macroalgae. The potential of mannitol as a renewable raw material is of interest due to the advantages of ocean farms. Herein, the biobased production of l-ornithine from mannitol was resoundingly demonstrated for the first time in engineered Corynebacterium glutamicum S9114 through the deletion of the mannitol repressor MtlR. By modulating the expression of mtlD and reinforcing the fructose metabolic pathway, we generated the strain MTL13 that produced 54.56 g/L of l-ornithine with a yield of 0.47 g/g on mannitol. These results illustrate the robust conversion from mannitol to l-ornithine using engineered Corynebacterium glutamicum, providing a reference for the biobased production of additional chemicals from mannitol.
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Affiliation(s)
- Qi Sheng
- College of Bioscience and Bioengineering, Jiangxi Agricultural University, Nanchang 330045, China; Jiangxi Engineering Laboratory for the Development and Utilization of Agricultural Microbial Resources, Jiangxi Agricultural University, Nanchang 330045, China
| | - Xiaoyu Wu
- College of Bioscience and Bioengineering, Jiangxi Agricultural University, Nanchang 330045, China; Jiangxi Engineering Laboratory for the Development and Utilization of Agricultural Microbial Resources, Jiangxi Agricultural University, Nanchang 330045, China
| | - Yan Jiang
- College of Bioscience and Bioengineering, Jiangxi Agricultural University, Nanchang 330045, China; Jiangxi Engineering Laboratory for the Development and Utilization of Agricultural Microbial Resources, Jiangxi Agricultural University, Nanchang 330045, China
| | - Zhimin Li
- College of Bioscience and Bioengineering, Jiangxi Agricultural University, Nanchang 330045, China; Jiangxi Engineering Laboratory for the Development and Utilization of Agricultural Microbial Resources, Jiangxi Agricultural University, Nanchang 330045, China
| | - Fei Wang
- College of Bioscience and Bioengineering, Jiangxi Agricultural University, Nanchang 330045, China; Jiangxi Engineering Laboratory for the Development and Utilization of Agricultural Microbial Resources, Jiangxi Agricultural University, Nanchang 330045, China
| | - Bin Zhang
- College of Bioscience and Bioengineering, Jiangxi Agricultural University, Nanchang 330045, China; Jiangxi Engineering Laboratory for the Development and Utilization of Agricultural Microbial Resources, Jiangxi Agricultural University, Nanchang 330045, China.
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28
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Cen X, Liu Y, Chen B, Liu D, Chen Z. Metabolic Engineering of Escherichia coli for De Novo Production of 1,5-Pentanediol from Glucose. ACS Synth Biol 2021; 10:192-203. [PMID: 33301309 DOI: 10.1021/acssynbio.0c00567] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
1,5-Pentanediol (1,5-PDO) is an important C5 building block for the synthesis of different value-added polyurethanes and polyesters. However, no natural metabolic pathway exists for the biosynthesis of 1,5-PDO. Herein we designed and constructed a promising nonnatural pathway for de novo production of 1,5-PDO from cheap carbohydrates. This biosynthesis route expands natural lysine pathways and employs two artificial metabolic modules to sequentially convert lysine into 5-hydroxyvalerate (5-HV) and 1,5-PDO via 5-hydroxyvaleryl-CoA. Theoretically, the 5-hydroxyvaleryl-CoA-based pathway is more energy-efficient than a recently published carboxylic acid reductase-based pathway for 1,5-PDO production. By combining strategies of systematic enzyme screening, pathway balancing, and transporter engineering, we successfully constructed a minimally engineered Escherichia coli strain capable of producing 3.19 g/L of 5-HV and 0.35 g/L of 1,5-PDO in a medium containing 20 g/L of glucose and 5 g/L lysine. Introducing the synthetic modules into a lysine producer and enhancing NADPH supply enabled the strain to accumulate 1.04 g/L of 5-HV and 0.12 g/L of 1,5-PDO using glucose as the main carbon source. This work lays the basis for the development of a biological route for 1,5-PDO production from renewable bioresources.
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Affiliation(s)
- Xuecong Cen
- Key Laboratory of Industrial Biocatalysis (Ministry of Education), Department of Chemical Engineering, Tsinghua University, Beijing 100084, China
| | - Yu Liu
- Key Laboratory of Industrial Biocatalysis (Ministry of Education), Department of Chemical Engineering, Tsinghua University, Beijing 100084, China
| | - Bo Chen
- Nutrition & Health Research Institute, China National Cereals, Oils and Foodstuffs Corporation (COFCO), Beijing 102209, China
| | - Dehua Liu
- Key Laboratory of Industrial Biocatalysis (Ministry of Education), Department of Chemical Engineering, Tsinghua University, Beijing 100084, China
- Tsinghua Innovation Center in Dongguan, Dongguan 523808, China
- Center for Synthetic and Systems Biology, Tsinghua University, Beijing 100084, China
| | - Zhen Chen
- Key Laboratory of Industrial Biocatalysis (Ministry of Education), Department of Chemical Engineering, Tsinghua University, Beijing 100084, China
- Tsinghua Innovation Center in Dongguan, Dongguan 523808, China
- Center for Synthetic and Systems Biology, Tsinghua University, Beijing 100084, China
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Zhang B, Jiang Y, Li Z, Wang F, Wu XY. Recent Progress on Chemical Production From Non-food Renewable Feedstocks Using Corynebacterium glutamicum. Front Bioeng Biotechnol 2021; 8:606047. [PMID: 33392171 PMCID: PMC7775722 DOI: 10.3389/fbioe.2020.606047] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2020] [Accepted: 10/31/2020] [Indexed: 11/13/2022] Open
Abstract
Due to the non-renewable nature of fossil fuels, microbial fermentation is considered a sustainable approach for chemical production using glucose, xylose, menthol, and other complex carbon sources represented by lignocellulosic biomass. Among these, xylose, methanol, arabinose, glycerol, and other alternative feedstocks have been identified as superior non-food sustainable carbon substrates that can be effectively developed for microbe-based bioproduction. Corynebacterium glutamicum is a model gram-positive bacterium that has been extensively engineered to produce amino acids and other chemicals. Recently, in order to reduce production costs and avoid competition for human food, C. glutamicum has also been engineered to broaden its substrate spectrum. Strengthening endogenous metabolic pathways or assembling heterologous ones enables C. glutamicum to rapidly catabolize a multitude of carbon sources. This review summarizes recent progress in metabolic engineering of C. glutamicum toward a broad substrate spectrum and diverse chemical production. In particularly, utilization of lignocellulosic biomass-derived complex hybrid carbon source represents the futural direction for non-food renewable feedstocks was discussed.
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Affiliation(s)
- Bin Zhang
- College of Bioscience and Bioengineering, Jiangxi Agricultural University, Nanchang, China.,Jiangxi Engineering Laboratory for the Development and Utilization of Agricultural Microbial Resources, Jiangxi Agricultural University, Nanchang, China
| | - Yan Jiang
- College of Bioscience and Bioengineering, Jiangxi Agricultural University, Nanchang, China.,Jiangxi Engineering Laboratory for the Development and Utilization of Agricultural Microbial Resources, Jiangxi Agricultural University, Nanchang, China
| | - Zhimin Li
- College of Bioscience and Bioengineering, Jiangxi Agricultural University, Nanchang, China.,Jiangxi Engineering Laboratory for the Development and Utilization of Agricultural Microbial Resources, Jiangxi Agricultural University, Nanchang, China
| | - Fei Wang
- College of Bioscience and Bioengineering, Jiangxi Agricultural University, Nanchang, China.,Jiangxi Engineering Laboratory for the Development and Utilization of Agricultural Microbial Resources, Jiangxi Agricultural University, Nanchang, China
| | - Xiao-Yu Wu
- College of Bioscience and Bioengineering, Jiangxi Agricultural University, Nanchang, China.,Jiangxi Engineering Laboratory for the Development and Utilization of Agricultural Microbial Resources, Jiangxi Agricultural University, Nanchang, China
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30
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Jiang Y, Sheng Q, Wu XY, Ye BC, Zhang B. l-arginine production in Corynebacterium glutamicum: manipulation and optimization of the metabolic process. Crit Rev Biotechnol 2020; 41:172-185. [PMID: 33153325 DOI: 10.1080/07388551.2020.1844625] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
As an important semi-essential amino acid, l-arginine is extensively used in the food and pharmaceutical fields. At present, l-arginine production depends on cost-effective, green, and sustainable microbial fermentation by using a renewable carbon source. To enhance its fermentative production, various metabolic engineering strategies have been employed, which provide valid paths for reducing the cost of l-arginine production. This review summarizes recent advances in molecular biology strategies for the optimization of l-arginine-producing strains, including manipulating the principal metabolic pathway, modulating the carbon metabolic pathway, improving the intracellular biosynthesis of cofactors and energy usage, manipulating the assimilation of ammonia, improving the transportation and membrane permeability, and performing biosensor-assisted high throughput screening, providing useful insight into the current state of l-arginine production.
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Affiliation(s)
- Yan Jiang
- Jiangxi Engineering Laboratory for the Development and Utilization of Agricultural Microbial Resources, Jiangxi Agricultural University, Nanchang, China
| | - Qi Sheng
- Jiangxi Engineering Laboratory for the Development and Utilization of Agricultural Microbial Resources, Jiangxi Agricultural University, Nanchang, China.,College of Bioscience and Bioengineering, Jiangxi Agricultural University, Nanchang, China
| | - Xiao-Yu Wu
- Jiangxi Engineering Laboratory for the Development and Utilization of Agricultural Microbial Resources, Jiangxi Agricultural University, Nanchang, China.,College of Bioscience and Bioengineering, Jiangxi Agricultural University, Nanchang, China
| | - Bang-Ce Ye
- Laboratory of Biosystems and Microanalysis, State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China
| | - Bin Zhang
- Jiangxi Engineering Laboratory for the Development and Utilization of Agricultural Microbial Resources, Jiangxi Agricultural University, Nanchang, China.,College of Bioscience and Bioengineering, Jiangxi Agricultural University, Nanchang, China
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31
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Marques F, Luzhetskyy A, Mendes MV. Engineering Corynebacterium glutamicum with a comprehensive genomic library and phage-based vectors. Metab Eng 2020; 62:221-234. [DOI: 10.1016/j.ymben.2020.08.007] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2020] [Revised: 07/17/2020] [Accepted: 08/10/2020] [Indexed: 12/18/2022]
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32
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Becker J, Wittmann C. Microbial production of extremolytes — high-value active ingredients for nutrition, health care, and well-being. Curr Opin Biotechnol 2020; 65:118-128. [DOI: 10.1016/j.copbio.2020.02.010] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2020] [Revised: 02/14/2020] [Accepted: 02/17/2020] [Indexed: 01/09/2023]
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33
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Cascaded valorization of seaweed using microbial cell factories. Curr Opin Biotechnol 2020; 65:102-113. [DOI: 10.1016/j.copbio.2020.02.008] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2020] [Revised: 02/14/2020] [Accepted: 02/17/2020] [Indexed: 11/17/2022]
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34
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Liu Y, Su A, Li J, Ledesma-Amaro R, Xu P, Du G, Liu L. Towards next-generation model microorganism chassis for biomanufacturing. Appl Microbiol Biotechnol 2020; 104:9095-9108. [DOI: 10.1007/s00253-020-10902-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2020] [Revised: 09/03/2020] [Accepted: 09/10/2020] [Indexed: 11/29/2022]
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35
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Li N, Xu S, Du G, Chen J, Zhou J. Efficient production of L-homoserine in Corynebacterium glutamicum ATCC 13032 by redistribution of metabolic flux. Biochem Eng J 2020. [DOI: 10.1016/j.bej.2020.107665] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
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36
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Gläser L, Kuhl M, Jovanovic S, Fritz M, Vögeli B, Erb TJ, Becker J, Wittmann C. A common approach for absolute quantification of short chain CoA thioesters in prokaryotic and eukaryotic microbes. Microb Cell Fact 2020; 19:160. [PMID: 32778124 PMCID: PMC7418318 DOI: 10.1186/s12934-020-01413-1] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2020] [Accepted: 07/20/2020] [Indexed: 02/08/2023] Open
Abstract
BACKGROUND Thioesters of coenzyme A participate in 5% of all enzymatic reactions. In microbial cell factories, they function as building blocks for products of recognized commercial value, including natural products such as polyketides, polyunsaturated fatty acids, biofuels, and biopolymers. A core spectrum of approximately 5-10 short chain thioesters is present in many microbes, as inferred from their genomic repertoire. The relevance of these metabolites explains the high interest to trace and quantify them in microbial cells. RESULTS Here, we describe a common workflow for extraction and absolute quantification of short chain CoA thioesters in different gram-positive and gram-negative bacteria and eukaryotic yeast, i.e. Corynebacterium glutamicum, Streptomyces albus, Pseudomonas putida, and Yarrowia lipolytica. The approach assessed intracellular CoA thioesters down to the picomolar level and exhibited high precision and reproducibility for all microbes, as shown by principal component analysis. Furthermore, it provided interesting insights into microbial CoA metabolism. A succinyl-CoA synthase defective mutant of C. glutamicum exhibited an unaffected level of succinyl-CoA that indicated a complete compensation by the L-lysine pathway to bypass the disrupted TCA cycle. Methylmalonyl-CoA, an important building block of high-value polyketides, was identified as dominant CoA thioester in the actinomycete S. albus. The microbe revealed a more than 10,000-fold difference in the abundance of intracellular CoA thioesters. A recombinant strain of S. albus, which produced different derivatives of the antituberculosis polyketide pamamycin, revealed a significant depletion of CoA thioesters of the ethylmalonyl CoA pathway, influencing product level and spectrum. CONCLUSIONS The high relevance of short chain CoA thioesters to synthetize industrial products and the interesting insights gained from the examples shown in this work, suggest analyzing these metabolites in microbial cell factories more routinely than done so far. Due to its broad application range, the developed approach appears useful to be applied this purpose. Hereby, the possibility to use one single protocol promises to facilitate automatized efforts, which rely on standardized workflows.
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Affiliation(s)
- Lars Gläser
- Institute of Systems Biotechnology, Saarland University, Saarbrücken, Germany
| | - Martin Kuhl
- Institute of Systems Biotechnology, Saarland University, Saarbrücken, Germany
| | - Sofija Jovanovic
- Institute of Systems Biotechnology, Saarland University, Saarbrücken, Germany
| | - Michel Fritz
- Institute of Systems Biotechnology, Saarland University, Saarbrücken, Germany
| | - Bastian Vögeli
- Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
| | - Tobias J. Erb
- Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
| | - Judith Becker
- Institute of Systems Biotechnology, Saarland University, Saarbrücken, Germany
| | - Christoph Wittmann
- Institute of Systems Biotechnology, Saarland University, Saarbrücken, Germany
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37
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Li N, Zeng W, Xu S, Zhou J. Obtaining a series of native gradient promoter-5'-UTR sequences in Corynebacterium glutamicum ATCC 13032. Microb Cell Fact 2020; 19:120. [PMID: 32493332 PMCID: PMC7268698 DOI: 10.1186/s12934-020-01376-3] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2020] [Accepted: 05/25/2020] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Corynebacterium glutamicum is an important industrial microorganism used for the production of many valuable compounds, especially amino acids and their derivatives. For fine-tuning of metabolic pathways, synthetic biological tools are largely based on the rational application of promoters. However, the limited number of promoters make it difficult. RESULTS In this study, according to the analysis of RNA-Seq data, 90 DNA fragments with lengths of 200-500 bp that may contain promoter-5'-UTR (PUTR) sequences were amplified and linked to a fluorescent protein gene. When compared with the common strong PUTR PsodUTR, 17 strong PUTRs were obtained, which maintained stable expression strengths from the early to post stationary phase. Among them, PNCgl1676UTR was the strongest and its fluorescent protein expression level was more than five times higher than that of PsodUTR. Furthermore, nine typical chemicals related to the biosynthesis of sulfur-containing amino acids (such as L-methionine, L-cysteine) were selected as stress substances to preliminarily explore the stress on these PUTRs. The results showed that the expression of PbrnFUTR was activated by L-methionine, while that of PNCgl1202UTR was severely inhibited by L-lysine. CONCLUSIONS These findings demonstrated that the selected PUTRs can stably express different genes, such as the red fluorescence protein gene, and can be useful for fine-tuning regulation of metabolic networks in C. glutamicum or for establishing high-throughput screening strategies through biosensor for the production of useful compounds.
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Affiliation(s)
- Ning Li
- Key Laboratory of Industrial Biotechnology, Ministry of Education and School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, 214122, Jiangsu, China.,National Engineering Laboratory for Cereal Fermentation Technology, Jiangnan University, 1800 Lihu Road, Wuxi, 214122, Jiangsu, China.,Jiangsu Provisional Research Center for Bioactive Product Processing Technology, Jiangnan University, 1800 Lihu Road, Wuxi, 214122, Jiangsu, China
| | - Weizhu Zeng
- Key Laboratory of Industrial Biotechnology, Ministry of Education and School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, 214122, Jiangsu, China.,National Engineering Laboratory for Cereal Fermentation Technology, Jiangnan University, 1800 Lihu Road, Wuxi, 214122, Jiangsu, China.,Jiangsu Provisional Research Center for Bioactive Product Processing Technology, Jiangnan University, 1800 Lihu Road, Wuxi, 214122, Jiangsu, China
| | - Sha Xu
- Key Laboratory of Industrial Biotechnology, Ministry of Education and School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, 214122, Jiangsu, China.,National Engineering Laboratory for Cereal Fermentation Technology, Jiangnan University, 1800 Lihu Road, Wuxi, 214122, Jiangsu, China.,Jiangsu Provisional Research Center for Bioactive Product Processing Technology, Jiangnan University, 1800 Lihu Road, Wuxi, 214122, Jiangsu, China
| | - Jingwen Zhou
- Key Laboratory of Industrial Biotechnology, Ministry of Education and School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, 214122, Jiangsu, China. .,National Engineering Laboratory for Cereal Fermentation Technology, Jiangnan University, 1800 Lihu Road, Wuxi, 214122, Jiangsu, China. .,Jiangsu Provisional Research Center for Bioactive Product Processing Technology, Jiangnan University, 1800 Lihu Road, Wuxi, 214122, Jiangsu, China.
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Hakvåg S, Nærdal I, Heggeset TMB, Kristiansen KA, Aasen IM, Brautaset T. Production of Value-Added Chemicals by Bacillus methanolicus Strains Cultivated on Mannitol and Extracts of Seaweed Saccharina latissima at 50°C. Front Microbiol 2020; 11:680. [PMID: 32328058 PMCID: PMC7161427 DOI: 10.3389/fmicb.2020.00680] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2019] [Accepted: 03/24/2020] [Indexed: 11/13/2022] Open
Abstract
The facultative methylotroph Bacillus methanolicus MGA3 has previously been genetically engineered to overproduce the amino acids L-lysine and L-glutamate and their derivatives cadaverine and γ-aminobutyric acid (GABA) from methanol at 50°C. We here explored the potential of utilizing the sugar alcohol mannitol and seaweed extract (SWE) containing mannitol, as alternative feedstocks for production of chemicals by fermentation using B. methanolicus. Extracts of the brown algae Saccharina latissima harvested in the Trondheim Fjord in Norway were prepared and found to contain 12–13 g/l of mannitol, with conductivities corresponding to a salt content of ∼2% NaCl. Initially, 12 B. methanolicus wild type strains were tested for tolerance to various SWE concentrations, and some strains including MGA3 could grow on 50% SWE medium. Non-methylotrophic and methylotrophic growth of B. methanolicus rely on differences in regulation of metabolic pathways, and we compared production titers of GABA and cadaverine under such growth conditions. Shake flask experiments showed that recombinant MGA3 strains could produce similar and higher titers of cadaverine during growth on 50% SWE and mannitol, compared to on methanol. GABA production levels under these conditions were however low compared to growth on methanol. We present the first fed-batch mannitol fermentation of B. methanolicus and production of 6.3 g/l cadaverine. Finally, we constructed a recombinant MGA3 strain synthesizing the C30 terpenoids 4,4′-diaponeurosporene and 4,4′-diapolycopene, experimentally confirming that B. methanolicus has a functional methylerythritol phosphate (MEP) pathway. Together, our results contribute to extending the range of both the feedstocks for growth and products that can be synthesized by B. methanolicus.
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Affiliation(s)
- Sigrid Hakvåg
- Department of Biotechnology and Food Sciences, Norwegian University of Science and Technology, Trondheim, Norway
| | - Ingemar Nærdal
- Department of Biotechnology and Nanomedicine, SINTEF Industry, Trondheim, Norway
| | - Tonje M B Heggeset
- Department of Biotechnology and Nanomedicine, SINTEF Industry, Trondheim, Norway
| | - Kåre A Kristiansen
- Department of Biotechnology and Food Sciences, Norwegian University of Science and Technology, Trondheim, Norway
| | - Inga M Aasen
- Department of Biotechnology and Nanomedicine, SINTEF Industry, Trondheim, Norway
| | - Trygve Brautaset
- Department of Biotechnology and Food Sciences, Norwegian University of Science and Technology, Trondheim, Norway
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Andriiash GS, Sekan OS, Tigunova OO, Blume YB, Shulga SM. Metabolic Engineering of Lysine Producing Corynebacterium glutamicum Strains. CYTOL GENET+ 2020. [DOI: 10.3103/s0095452720020024] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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40
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Han G, Xu N, Sun X, Chen J, Chen C, Wang Q. Improvement of l-Valine Production by Atmospheric and Room Temperature Plasma Mutagenesis and High-Throughput Screening in Corynebacterium glutamicum. ACS OMEGA 2020; 5:4751-4758. [PMID: 32201760 PMCID: PMC7081258 DOI: 10.1021/acsomega.9b02747] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/25/2019] [Accepted: 02/13/2020] [Indexed: 06/10/2023]
Abstract
As one of the branched-chain amino acids, l-valine is an essential nutrient for most mammalian species. In this study, the l-valine producer Corynebacterium glutamicum ΔppcΔaceEΔalatΔpqo was first constructed. Additionally, an improved biosensor based on the Lrp-type transcriptional regulator and temperature-sensitive replication was built. Then, the C. glutamicum strain was mutagenized by atmospheric and room temperature plasma. A sequential three-step procedure was carried out to screen l-valine-producing strains, including the fluorescence-activated cell sorting (FACS), 96-well plate screening, and flask fermentation. The final mutant HL2-7 obtained by screening produced 3.20 g/L of l-valine, which was 21.47% higher than the titer produced by the starting strain. This study demonstrates that the l-valine-producing mutants can be successfully isolated based on the Lrp sensor system in combination with FACS screening after random mutagenesis.
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Affiliation(s)
- Guoqiang Han
- Life
Science and Technology Institute, Yangtze
Normal University, Chongqing 408100, P. R. China
- School
of Advanced Agriculture and Bioengineering, Yangtze Normal University, Chongqing 408100, P. R. China
| | - Ning Xu
- Tianjin
Institute of Industrial Biotechnology, Chinese
Academy of Sciences, Tianjin 300308, P. R. China
| | - Xieping Sun
- Life
Science and Technology Institute, Yangtze
Normal University, Chongqing 408100, P. R. China
| | - Jinzhao Chen
- Life
Science and Technology Institute, Yangtze
Normal University, Chongqing 408100, P. R. China
| | - Chun Chen
- Life
Science and Technology Institute, Yangtze
Normal University, Chongqing 408100, P. R. China
| | - Qing Wang
- Life
Science and Technology Institute, Yangtze
Normal University, Chongqing 408100, P. R. China
- School
of Advanced Agriculture and Bioengineering, Yangtze Normal University, Chongqing 408100, P. R. China
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Xu JZ, Ruan HZ, Yu HB, Liu LM, Zhang W. Metabolic engineering of carbohydrate metabolism systems in Corynebacterium glutamicum for improving the efficiency of L-lysine production from mixed sugar. Microb Cell Fact 2020; 19:39. [PMID: 32070345 PMCID: PMC7029506 DOI: 10.1186/s12934-020-1294-7] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2019] [Accepted: 01/23/2020] [Indexed: 01/08/2023] Open
Abstract
The efficiency of industrial fermentation process mainly depends on carbon yield, final titer and productivity. To improve the efficiency of l-lysine production from mixed sugar, we engineered carbohydrate metabolism systems to enhance the effective use of sugar in this study. A functional metabolic pathway of sucrose and fructose was engineered through introduction of fructokinase from Clostridium acetobutylicum. l-lysine production was further increased through replacement of phosphoenolpyruvate-dependent glucose and fructose uptake system (PTSGlc and PTSFru) by inositol permeases (IolT1 and IolT2) and ATP-dependent glucokinase (ATP-GlK). However, the shortage of intracellular ATP has a significantly negative impact on sugar consumption rate, cell growth and l-lysine production. To overcome this defect, the recombinant strain was modified to co-express bifunctional ADP-dependent glucokinase (ADP-GlK/PFK) and NADH dehydrogenase (NDH-2) as well as to inactivate SigmaH factor (SigH), thus reducing the consumption of ATP and increasing ATP regeneration. Combination of these genetic modifications resulted in an engineered C. glutamicum strain K-8 capable of producing 221.3 ± 17.6 g/L l-lysine with productivity of 5.53 g/L/h and carbon yield of 0.71 g/g glucose in fed-batch fermentation. As far as we know, this is the best efficiency of l-lysine production from mixed sugar. This is also the first report for improving the efficiency of l-lysine production by systematic modification of carbohydrate metabolism systems.
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Affiliation(s)
- Jian-Zhong Xu
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, 1800# Lihu Road, Wuxi, 214122, China.
| | - Hao-Zhe Ruan
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, 1800# Lihu Road, Wuxi, 214122, China
| | - Hai-Bo Yu
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, 1800# Lihu Road, Wuxi, 214122, China
| | - Li-Ming Liu
- State Key Laboratory of Food Science and Technology, School of Biotechnology, Jiangnan University, 1800# Lihu Road, Wuxi, 214122, China
| | - Weiguo Zhang
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, 1800# Lihu Road, Wuxi, 214122, China
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Wu XY, Guo XY, Zhang B, Jiang Y, Ye BC. Recent Advances of L-ornithine Biosynthesis in Metabolically Engineered Corynebacterium glutamicum. Front Bioeng Biotechnol 2020; 7:440. [PMID: 31998705 PMCID: PMC6962107 DOI: 10.3389/fbioe.2019.00440] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2019] [Accepted: 12/11/2019] [Indexed: 12/31/2022] Open
Abstract
L-ornithine, a valuable non-protein amino acid, has a wide range of applications in the pharmaceutical and food industries. Currently, microbial fermentation is a promising, sustainable, and environment-friendly method to produce L-ornithine. However, the industrial production capacity of L-ornithine by microbial fermentation is low and rarely meets the market demands. Various strategies have been employed to improve the L-ornithine production titers in the model strain, Corynebacterium glutamicum, which serves as a major indicator for improving the cost-effectiveness of L-ornithine production by microbial fermentation. This review focuses on the development of high L-ornithine-producing strains by metabolic engineering and reviews the recent advances in breeding strategies, such as reducing by-product formation, improving the supplementation of precursor glutamate, releasing negative regulation and negative feedback inhibition, increasing the supply of intracellular cofactors, modulating the central metabolic pathway, enhancing the transport system, and adaptive evolution for improving L-ornithine production.
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Affiliation(s)
- Xiao-Yu Wu
- Jiangxi Engineering Laboratory for the Development and Utilization of Agricultural Microbial Resources, College of Bioscience and Engineering, Jiangxi Agricultural University, Nanchang, China
| | - Xiao-Yan Guo
- Jiangxi Engineering Laboratory for the Development and Utilization of Agricultural Microbial Resources, College of Bioscience and Engineering, Jiangxi Agricultural University, Nanchang, China
| | - Bin Zhang
- Jiangxi Engineering Laboratory for the Development and Utilization of Agricultural Microbial Resources, College of Bioscience and Engineering, Jiangxi Agricultural University, Nanchang, China
| | - Yan Jiang
- Jiangxi Engineering Laboratory for the Development and Utilization of Agricultural Microbial Resources, College of Bioscience and Engineering, Jiangxi Agricultural University, Nanchang, China
| | - Bang-Ce Ye
- Laboratory of Biosystems and Microanalysis, State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China
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Becker J, Wittmann C. A field of dreams: Lignin valorization into chemicals, materials, fuels, and health-care products. Biotechnol Adv 2019; 37:107360. [DOI: 10.1016/j.biotechadv.2019.02.016] [Citation(s) in RCA: 207] [Impact Index Per Article: 41.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2018] [Revised: 02/18/2019] [Accepted: 02/22/2019] [Indexed: 02/07/2023]
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Production of nonnatural straight-chain amino acid 6-aminocaproate via an artificial iterative carbon-chain-extension cycle. Metab Eng 2019; 55:23-32. [DOI: 10.1016/j.ymben.2019.06.009] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2019] [Revised: 06/13/2019] [Accepted: 06/15/2019] [Indexed: 12/23/2022]
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Systems Metabolic Engineering Strategies: Integrating Systems and Synthetic Biology with Metabolic Engineering. Trends Biotechnol 2019; 37:817-837. [DOI: 10.1016/j.tibtech.2019.01.003] [Citation(s) in RCA: 226] [Impact Index Per Article: 45.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2018] [Revised: 01/07/2019] [Accepted: 01/10/2019] [Indexed: 12/12/2022]
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Wang Y, Liu Y, Li J, Yang Y, Ni X, Cheng H, Huang T, Guo Y, Ma H, Zheng P, Wang M, Sun J, Ma Y. Expanding targeting scope, editing window, and base transition capability of base editing in
Corynebacterium glutamicum. Biotechnol Bioeng 2019; 116:3016-3029. [DOI: 10.1002/bit.27121] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2019] [Revised: 07/03/2019] [Accepted: 07/08/2019] [Indexed: 01/02/2023]
Affiliation(s)
- Yu Wang
- Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial BiotechnologyChinese Academy of Sciences Tianjin China
| | - Ye Liu
- Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial BiotechnologyChinese Academy of Sciences Tianjin China
| | - Junwei Li
- Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial BiotechnologyChinese Academy of Sciences Tianjin China
- College of BiotechnologyTianjin University of Science and Technology Tianjin China
| | - Yi Yang
- Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial BiotechnologyChinese Academy of Sciences Tianjin China
| | - Xiaomeng Ni
- Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial BiotechnologyChinese Academy of Sciences Tianjin China
| | - Haijiao Cheng
- Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial BiotechnologyChinese Academy of Sciences Tianjin China
| | - Teng Huang
- Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial BiotechnologyChinese Academy of Sciences Tianjin China
| | - Yanmei Guo
- Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial BiotechnologyChinese Academy of Sciences Tianjin China
| | - Hongwu Ma
- Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial BiotechnologyChinese Academy of Sciences Tianjin China
| | - Ping Zheng
- Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial BiotechnologyChinese Academy of Sciences Tianjin China
| | - Meng Wang
- Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial BiotechnologyChinese Academy of Sciences Tianjin China
| | - Jibin Sun
- Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial BiotechnologyChinese Academy of Sciences Tianjin China
| | - Yanhe Ma
- Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial BiotechnologyChinese Academy of Sciences Tianjin China
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GC-MS-based 13C metabolic flux analysis resolves the parallel and cyclic glucose metabolism of Pseudomonas putida KT2440 and Pseudomonas aeruginosa PAO1. Metab Eng 2019; 54:35-53. [DOI: 10.1016/j.ymben.2019.01.008] [Citation(s) in RCA: 74] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2018] [Revised: 01/16/2019] [Accepted: 01/16/2019] [Indexed: 01/05/2023]
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Wendisch VF. Metabolic engineering advances and prospects for amino acid production. Metab Eng 2019; 58:17-34. [PMID: 30940506 DOI: 10.1016/j.ymben.2019.03.008] [Citation(s) in RCA: 141] [Impact Index Per Article: 28.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2019] [Revised: 03/26/2019] [Accepted: 03/26/2019] [Indexed: 11/18/2022]
Abstract
Amino acid fermentation is one of the major pillars of industrial biotechnology. The multi-billion USD amino acid market is rising steadily and is diversifying. Metabolic engineering is no longer focused solely on strain development for the bulk amino acids L-glutamate and L-lysine that are produced at the million-ton scale, but targets specialty amino acids. These demands are met by the development and application of new metabolic engineering tools including CRISPR and biosensor technologies as well as production processes by enabling a flexible feedstock concept, co-production and co-cultivation schemes. Metabolic engineering advances are exemplified for specialty proteinogenic amino acids, cyclic amino acids, omega-amino acids, and amino acids functionalized by hydroxylation, halogenation and N-methylation.
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Affiliation(s)
- Volker F Wendisch
- Genetics of Prokaryotes, Faculty of Biology and Center for Biotechnology (CeBiTec), Bielefeld University, Bielefeld, Germany.
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Poblete-Castro I, Wittmann C, Nikel PI. Biochemistry, genetics and biotechnology of glycerol utilization in Pseudomonas species. Microb Biotechnol 2019; 13:32-53. [PMID: 30883020 PMCID: PMC6922529 DOI: 10.1111/1751-7915.13400] [Citation(s) in RCA: 49] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2019] [Revised: 02/17/2019] [Accepted: 02/23/2019] [Indexed: 11/30/2022] Open
Abstract
The use of renewable waste feedstocks is an environment‐friendly choice contributing to the reduction of waste treatment costs and increasing the economic value of industrial by‐products. Glycerol (1,2,3‐propanetriol), a simple polyol compound widely distributed in biological systems, constitutes a prime example of a relatively cheap and readily available substrate to be used in bioprocesses. Extensively exploited as an ingredient in the food and pharmaceutical industries, glycerol is also the main by‐product of biodiesel production, which has resulted in a progressive drop in substrate price over the years. Consequently, glycerol has become an attractive substrate in biotechnology, and several chemical commodities currently produced from petroleum have been shown to be obtained from this polyol using whole‐cell biocatalysts with both wild‐type and engineered bacterial strains. Pseudomonas species, endowed with a versatile and rich metabolism, have been adopted for the conversion of glycerol into value‐added products (ranging from simple molecules to structurally complex biopolymers, e.g. polyhydroxyalkanoates), and a number of metabolic engineering strategies have been deployed to increase the number of applications of glycerol as a cost‐effective substrate. The unique genetic and metabolic features of glycerol‐grown Pseudomonas are presented in this review, along with relevant examples of bioprocesses based on this substrate – and the synthetic biology and metabolic engineering strategies implemented in bacteria of this genus aimed at glycerol valorization.
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Affiliation(s)
- Ignacio Poblete-Castro
- Biosystems Engineering Laboratory, Center for Bioinformatics and Integrative Biology, Faculty of Natural Sciences, Universidad Andrés Bello, Santiago de Chile, Chile
| | - Christoph Wittmann
- Institute of Systems Biotechnology, Universität des Saarlandes, Saarbrücken, Germany
| | - Pablo I Nikel
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kgs Lyngby, Denmark
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Wu W, Zhang Y, Liu D, Chen Z. Efficient mining of natural NADH-utilizing dehydrogenases enables systematic cofactor engineering of lysine synthesis pathway of Corynebacterium glutamicum. Metab Eng 2018; 52:77-86. [PMID: 30458240 DOI: 10.1016/j.ymben.2018.11.006] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2018] [Revised: 10/22/2018] [Accepted: 11/16/2018] [Indexed: 12/01/2022]
Abstract
Increasing the availability of NADPH is commonly used to improve lysine production by Corynebacterium glutamicum since 4 mol of NADPH are required for the synthesis of 1 mol of lysine. Alternatively, engineering of enzymes in lysine synthesis pathway to utilize NADH directly can also be explored for cofactor balance during lysine overproduction. To achieve such a goal, enzyme mining was used in this study to quickly identify a full set of NADH-utilizing dehydrogenases, namely aspartate dehydrogenase from Pseudomonas aeruginosa (PaASPDH), aspartate-semialdehyde dehydrogenase from Tistrella mobilis (TmASADH), dihydrodipicolinate reductase from Escherichia coli (EcDHDPR), and diaminopimelate dehydrogenase from Pseudothermotoga thermarum (PtDAPDH). This allowed us to systematically perturb cofactor utilization of lysine synthesis pathway of C. glutamicum for the first time. Individual overexpression of PaASPDH, TmASADH, EcDHDPR, and PtDAPDH in C. glutamicum LC298, a basic lysine producer, increased the production of lysine by 30.7%, 32.4%, 17.4%, and 36.8%, respectively. Combinatorial replacement of NADPH-dependent dehydrogenases in C. glutamicum ATCC 21543, a lysine hyperproducer, also resulted in significantly improved lysine production. The highest increase of lysine production (30.7%) was observed for a triple-mutant strain (27.7 g/L, 0.35 g/g glucose) expressing PaASPDH, TmASADH, and EcDHDPR. A quadruple-mutant strain expressing all of the four NADH-utilizing enzymes allowed high lysine production (24.1 g/L, 0.30 g/g glucose) almost independent of the oxidative pentose phosphate pathway. Collectively, our results demonstrated that a combination of enzyme mining and cofactor engineering was a highly efficient approach to improve lysine production. Similar strategies can be applied for the production of other amino acids or their derivatives.
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Affiliation(s)
- Wenjun Wu
- Key Laboratory of Industrial Biocatalysis (Ministry of Education), Department of Chemical Engineering, Tsinghua University, Beijing 100084, China
| | - Ye Zhang
- Key Laboratory of Industrial Biocatalysis (Ministry of Education), Department of Chemical Engineering, Tsinghua University, Beijing 100084, China
| | - Dehua Liu
- Key Laboratory of Industrial Biocatalysis (Ministry of Education), Department of Chemical Engineering, Tsinghua University, Beijing 100084, China; Tsinghua Innovation Center in Dongguan, Dongguan 523808, China; Center for Synthetic and Systems Biology, Tsinghua University, Beijing 100084, China
| | - Zhen Chen
- Key Laboratory of Industrial Biocatalysis (Ministry of Education), Department of Chemical Engineering, Tsinghua University, Beijing 100084, China; Tsinghua Innovation Center in Dongguan, Dongguan 523808, China; Center for Synthetic and Systems Biology, Tsinghua University, Beijing 100084, China.
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