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Kurpejović E, Sariyar Akbulut B, Avci FG. Tailoring Corynebacterium glutamicum for Sustainable Biomanufacturing: From Traditional to Cutting-Edge Technologies. Mol Biotechnol 2025:10.1007/s12033-025-01447-z. [PMID: 40493161 DOI: 10.1007/s12033-025-01447-z] [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: 11/12/2024] [Accepted: 05/05/2025] [Indexed: 06/12/2025]
Abstract
As the workhorse of industrial amino acid production, Corynebacterium glutamicum is the focus of this review, which provides a comprehensive overview of available techniques employed to engineer strains with desired traits. The review highlights both traditional and cutting-edge approaches with a brief introduction to the bacterium's physiology, serving as a foundation for understanding its metabolic capabilities and potential applications. Genome modulation techniques by contrasting traditional methods with CRISPR-based approaches, as well as transcription modulation strategies that enhance gene expression and metabolic flux, and high-throughput techniques that streamline strain development processes are summarized. Furthermore, the roles of artificial intelligence and machine learning in genetic engineering are explored, emphasizing their growing impact on strain development.
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Affiliation(s)
- Eldin Kurpejović
- Department of Bioengineering, Faculty of Engineering, Marmara University, Istanbul, Türkiye
- Acies Bio d.o.o., Tehnološki Park 21, 1000, Ljubljana, Slovenia
| | - Berna Sariyar Akbulut
- Department of Bioengineering, Faculty of Engineering, Marmara University, Istanbul, Türkiye
| | - Fatma Gizem Avci
- Department of Bioengineering, Faculty of Engineering and Natural Sciences, Üsküdar University, Istanbul, Türkiye.
- Genetics of Prokaryotes, Faculty of Biology and Center for Biotechnology (CeBiTec), Bielefeld University, Bielefeld, Germany.
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Dodelin JK, Rose AE, Rajpurohit H, Eiteman MA. Increased Mevalonate Production Using Engineered Citrate Synthase and Phosphofructokinase Variants of Escherichia coli. Biotechnol Bioeng 2025; 122:548-560. [PMID: 39654318 PMCID: PMC11808435 DOI: 10.1002/bit.28902] [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: 07/24/2024] [Revised: 11/11/2024] [Accepted: 11/25/2024] [Indexed: 02/11/2025]
Abstract
Mevalonate is a biochemical precursor to a wide range of isoprenoids. The mevalonate pathway uses three moles of acetyl-CoA, and therefore native pathways which metabolize acetyl-CoA compete with mevalonate synthesis. Moreover, the final step in mevalonate formation, mediated by hydroxymethylglutaryl-CoA reductase, requires NADPH as a co-substrate. This study focuses on chromosomal modification of citrate synthase (GltA) involved in acetyl-CoA utilization and phosphofructokinase (PfkA) involved in NADPH formation to increase the yield and productivity of mevalonate in Escherichia coli overexpressing the three genes of the heterologous mevalonate pathway. Nine GltA variants were compared for mevalonate production with the ΔgltA knockout and the wild-type GltA strain in shake flasks in the absence and presence of casamino acids. In the presence of casamino acids, all variants generated mevalonate at a greater yield than the wild-type control, but less than the GltA knockout. In the absence of casamino acids, the strain expressing wild-type GltA generated the greatest yield of mevalonate, while most variants instead accumulated primarily acetate. Using the wild-type strain and two citrate synthase variants, four phosphofructokinase variants were also compared with the ΔpfkA knockout and the wild-type strain, but PfkA variants generated less mevalonate than the corresponding wild-type PfkA strain. Controlled processes at the 1-liter scale comparing five strains demonstrated the inverse relationship between yield and productivity, with the GltA[K167A] variant showing the best balance for the yield (0.20 g/g) and productivity (0.87 g/L h). A nitrogen-limited process using the GltA[K167A] variant generated 36.9 g/L mevalonate in 31 h at a yield of 0.31 g/g. This study demonstrates that GltA variants offer a means to affect intracellular acetyl-CoA pools for the generation of acetyl-CoA derived products and that the acetyl-CoA pool rather than NADPH availability is the important limiting factor for mevalonate production.
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Affiliation(s)
| | - Abigail E. Rose
- Department of MicrobiologyUniversity of GeorgiaAthensGeorgiaUSA
| | - Hemshikha Rajpurohit
- School of Chemical, Materials and Biomedical EngineeringUniversity of GeorgiaAthensGeorgiaUSA
| | - Mark A. Eiteman
- Department of MicrobiologyUniversity of GeorgiaAthensGeorgiaUSA
- School of Chemical, Materials and Biomedical EngineeringUniversity of GeorgiaAthensGeorgiaUSA
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Jamal QMS, Ahmad V. Bacterial metabolomics: current applications for human welfare and future aspects. JOURNAL OF ASIAN NATURAL PRODUCTS RESEARCH 2025; 27:207-230. [PMID: 39078342 DOI: 10.1080/10286020.2024.2385365] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/20/2024] [Revised: 07/22/2024] [Accepted: 07/24/2024] [Indexed: 07/31/2024]
Abstract
An imbalanced microbiome is linked to several diseases, such as cancer, inflammatory bowel disease, obesity, and even neurological disorders. Bacteria and their by-products are used for various industrial and clinical purposes. The metabolites under discussion were chosen based on their biological impacts on host and gut microbiota interactions as established by metabolome research. The separation of bacterial metabolites by using statistics and machine learning analysis creates new opportunities for applications of bacteria and their metabolites in the environmental and medical sciences. Thus, the metabolite production strategies, methodologies, and importance of bacterial metabolites for human well-being are discussed in this review.
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Affiliation(s)
- Qazi Mohammad Sajid Jamal
- Department of Health Informatics, College of Applied Medical Sciences, Qassim University, Buraydah 51452, Saudi Arabia
| | - Varish Ahmad
- Health Information Technology Department, The Applied College, King Abdulaziz University, Jeddah 21589, Saudi Arabia
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Li MH, Li H, Zhang X, Liang YC, Li C, Sun ML, Li K, Liu CG, Sinskey AJ. Metabolic engineering of Corynebacterium glutamicum: Unlocking its potential as a key cell factory platform for organic acid production. Biotechnol Adv 2024; 77:108475. [PMID: 39515670 DOI: 10.1016/j.biotechadv.2024.108475] [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: 07/16/2024] [Revised: 11/04/2024] [Accepted: 11/05/2024] [Indexed: 11/16/2024]
Abstract
Corynebacterium glutamicum, a well-studied industrial model microorganism, has garnered widespread attention due to its ability for producing amino acids with a long history. In recent years, research efforts have been increasingly focused on exploring its potential for producing various organic acids beyond amino acids. Organic acids, which are characterized by their acidic functional groups, have diverse applications across industries such as food, agriculture, pharmaceuticals, and biobased materials. Leveraging advancements in metabolic engineering and synthetic biology, the metabolic pathways of C. glutamicum have been broadened to facilitate the production of numerous high-value organic acids. This review summarizes the recent progress in metabolic engineering for the production of both amino acids and other organic acids by C. glutamicum. Notably, these acids include, amino acids (lysine, isoleucine, and phenylalanine), TCA cycle-derived organic acids (succinic acid, α-ketoglutaric acid), aromatic organic acids (protocatechuate, 4-amino-3-hydroxybenzoic acid, anthranilate, and para-coumaric acid), and other organic acids (itaconic acid and cis, cis-muconic acid).
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Affiliation(s)
- Ming-Hou Li
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Han Li
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Xue Zhang
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Yu-Chen Liang
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Cheng Li
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Disruptive & Sustainable Technologies for Agricultural Precision, Singapore-MIT Alliance for Research and Technology, Singapore 138602, Singapore
| | - Meng-Lin Sun
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Kai Li
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China.
| | - Chen-Guang Liu
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Anthony J Sinskey
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Disruptive & Sustainable Technologies for Agricultural Precision, Singapore-MIT Alliance for Research and Technology, Singapore 138602, Singapore
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Zhao Z, You J, Shi X, Zhu R, Yang F, Xu M, Shao M, Zhang R, Zhao Y, Rao Z. Engineering Escherichia coli for l-Threonine Hyperproduction Based on Multidimensional Optimization Strategies. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2024. [PMID: 39356799 DOI: 10.1021/acs.jafc.4c07607] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/04/2024]
Abstract
Exploring effective remodeling strategies to further improve the productivity of high-yield strains is the goal of biomanufacturing. However, the lack of insight into host-specific metabolic networks prevents timely identification of useful engineering targets. Here, multidimensional engineering strategies were implemented to optimize the global metabolic network for improving l-threonine production. First, the metabolic bottleneck for l-threonine synthesis was eliminated by synergistic utilization of NADH and an enhanced ATP supply. Carbon fluxes were redistributed into the TCA cycle by rationally regulating the GltA activity. Subsequently, the stress global response regulator UspA was identified to enhance l-threonine production by a transcriptomic analysis. Then, l-threonine productivity was improved by enhancing the host's stress resistance and releasing the inhibitory reaction of glucose utilization. Eventually, the l-threonine yield of THRH16 reached 170.3 g/L and 3.78 g/L/h in a 5 L bioreactor, which is the highest production index reported. This study provides rational guidance for increasing the productivity of other chemicals.
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Affiliation(s)
- Zhenqiang Zhao
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, Jiangsu 214122, China
- Institute of Future Food Technology, Yixing, JITRI 214200, China
| | - Jiajia You
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, Jiangsu 214122, China
- Institute of Future Food Technology, Yixing, JITRI 214200, China
| | - Xuanping Shi
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, Jiangsu 214122, China
- Institute of Future Food Technology, Yixing, JITRI 214200, China
| | - Rongshuai Zhu
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, Jiangsu 214122, China
- Institute of Future Food Technology, Yixing, JITRI 214200, China
| | - Fengyu Yang
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, Jiangsu 214122, China
- Institute of Future Food Technology, Yixing, JITRI 214200, China
| | - Meijuan Xu
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, Jiangsu 214122, China
- Institute of Future Food Technology, Yixing, JITRI 214200, China
| | - Minglong Shao
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, Jiangsu 214122, China
- Institute of Future Food Technology, Yixing, JITRI 214200, China
| | - Rongzhen Zhang
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, Jiangsu 214122, China
| | - Youxi Zhao
- College of Biochemical Engineering, Beijing Union University, Beijing 100023, China
| | - Zhiming Rao
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, Jiangsu 214122, China
- Institute of Future Food Technology, Yixing, JITRI 214200, China
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Wang L, Yang H, Wu M, Zhang H, Zhang J, Chen X. Enhanced ε-Poly-L-Lysine Production in Streptomyces albulus through Multi-Omics-Guided Metabolic Engineering. Biomolecules 2024; 14:752. [PMID: 39062465 PMCID: PMC11274744 DOI: 10.3390/biom14070752] [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: 05/14/2024] [Revised: 06/08/2024] [Accepted: 06/10/2024] [Indexed: 07/28/2024] Open
Abstract
Safe and eco-friendly preservatives are crucial to preventing food spoilage and illnesses, as foodborne diseases caused by pathogens result in approximately 600 million cases of illness and 420,000 deaths annually. ε-Poly-L-lysine (ε-PL) is a novel food preservative widely used in many countries. However, its commercial application has been hindered by high costs and low production. In this study, ε-PL's biosynthetic capacity was enhanced in Streptomyces albulus WG608 through metabolic engineering guided by multi-omics techniques. Based on transcriptome and metabolome data, differentially expressed genes (fold change >2 or <0.5; p < 0.05) and differentially expressed metabolites (fold change >1.2 or <0.8) were separately subjected to gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis. The integrative analysis of transcriptome, metabolome, and overexpression revealed the essential roles of isocitrate lyase, succinate dehydrogenase, flavoprotein subunit, diaminopimelate dehydrogenase, polyphosphate kinase, and polyP:AMP phosphotransferase in ε-PL biosynthesis. Subsequently, a strain with enhanced ATP supply, L-lysine supply, and ε-PL synthetase expression was constructed to improve its production. Finally, the resulting strain, S. albulus WME10, achieved an ε-PL production rate of 77.16 g/L in a 5 L bioreactor, which is the highest reported ε-PL production to date. These results suggest that the integrative analysis of the transcriptome and metabolome can facilitate the identification of key pathways and genetic elements affecting ε-PL synthesis, guiding further metabolic engineering and thus significantly enhancing ε-PL production. The method presented in this study could be applicable to other valuable natural antibacterial agents.
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Affiliation(s)
| | | | | | | | | | - Xusheng Chen
- Key Laboratory of Industrial Biotechnology, School of Biotechnology, Jiangnan University, Ministry of Education, Wuxi 214122, China; (L.W.); (M.W.); (J.Z.)
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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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Rajpurohit H, Eiteman MA. Citrate synthase variants improve yield of acetyl-CoA derived 3-hydroxybutyrate in Escherichia coli. Microb Cell Fact 2024; 23:173. [PMID: 38867236 PMCID: PMC11167817 DOI: 10.1186/s12934-024-02444-8] [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: 02/11/2024] [Accepted: 05/29/2024] [Indexed: 06/14/2024] Open
Abstract
BACKGROUND The microbial chiral product (R)-3-hydroxybutyrate (3-HB) is a gateway to several industrial and medical compounds. Acetyl-CoA is the key precursor for 3-HB, and several native pathways compete with 3-HB production. The principal competing pathway in wild-type Escherichia coli for acetyl-CoA is mediated by citrate synthase (coded by gltA), which directs over 60% of the acetyl-CoA into the tricarboxylic acid cycle. Eliminating citrate synthase activity (deletion of gltA) prevents growth on glucose as the sole carbon source. In this study, an alternative approach is used to generate an increased yield of 3-HB: citrate synthase activity is reduced but not eliminated by targeted substitutions in the chromosomally expressed enzyme. RESULTS Five E. coli GltA variants were examined for 3-HB production via heterologous overexpression of a thiolase (phaA) and NADPH-dependent acetoacetyl-CoA reductase (phaB) from Cupriavidus necator. In shake flask studies, four variants showed nearly 5-fold greater 3-HB yield compared to the wild-type, although pyruvate accumulated. Overexpression of either native thioesterases TesB or YciA eliminated pyruvate formation, but diverted acetyl-CoA towards acetate formation. Overexpression of pantothenate kinase similarly decreased pyruvate formation but did not improve 3-HB yield. Controlled batch studies at the 1.25 L scale demonstrated that the GltA[A267T] variant produced the greatest 3-HB titer of 4.9 g/L with a yield of 0.17 g/g. In a phosphate-starved repeated batch process, E. coli ldhA poxB pta-ackA gltA::gltA[A267T] generated 15.9 g/L 3-HB (effective concentration of 21.3 g/L with dilution) with yield of 0.16 g/g from glucose as the sole carbon source. CONCLUSIONS This study demonstrates that GltA variants offer a means to affect the generation of acetyl-CoA derived products. This approach should benefit a wide range of acetyl-CoA derived biochemical products in E. coli and other microbes. Enhancing substrate affinity of the introduced pathway genes like thiolase towards acetyl-CoA will likely further increase the flux towards 3-HB while reducing pyruvate and acetate accumulation.
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Affiliation(s)
| | - Mark A Eiteman
- School of Chemical, Materials and Biomedical Engineering, Athens, GA, USA.
- Department of Microbiology, University of Georgia, Athens, GA, 30602, USA.
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Tian S, Zhao G, Lv G, Wu C, Su R, Wang F, Wang Z, Liu Y, Chen N, Li Y. Efficient Fermentative Production of d-Alanine and Other d-Amino Acids by Metabolically Engineered Corynebacterium glutamicum. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2024; 72:8039-8051. [PMID: 38545740 DOI: 10.1021/acs.jafc.4c00914] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/11/2024]
Abstract
d-Amino acids (d-AAs) have wide applications in industries such as pharmaceutical, food, and cosmetics due to their unique properties. Currently, the production of d-AAs has relied on chemical synthesis or enzyme catalysts, and it is challenging to produce d-AAs via direct fermentation from glucose. We observed that Corynebacterium glutamicum exhibits a remarkable tolerance to high concentrations of d-Ala, a crucial characteristic for establishing a successful fermentation process. By optimizing meso-diaminopilmelate dehydrogenases in different C. glutamicum strains and successively deleting l-Ala biosynthetic pathways, we developed an efficient d-Ala fermentation system. The d-Ala titer was enhanced through systems metabolic engineering, which involved strengthening glucose assimilation and pyruvate supply, reducing the formation of organic acid byproducts, and attenuating the TCA cycle. During fermentation in a 5-L bioreactor, a significant accumulation of l-Ala was observed in the broth, which was subsequently diminished by introducing an l-amino acid deaminase. Ultimately, the engineered strain DA-11 produced 85 g/L d-Ala with a yield of 0.30 g/g glucose, accompanied by an optical purity exceeding 99%. The fermentation platform has the potential to be extended for the synthesis of other d-AAs, as demonstrated by the production of d-Val and d-Glu.
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Affiliation(s)
- Siyu Tian
- College of Biotechnology, Tianjin University of Science and Technology, No. 29, 13th Avenue, TEDA, Tianjin 300457, China
| | - Guihong Zhao
- College of Biotechnology, Tianjin University of Science and Technology, No. 29, 13th Avenue, TEDA, Tianjin 300457, China
| | - Gengcheng Lv
- College of Biotechnology, Tianjin University of Science and Technology, No. 29, 13th Avenue, TEDA, Tianjin 300457, China
| | - Chen Wu
- College of Biotechnology, Tianjin University of Science and Technology, No. 29, 13th Avenue, TEDA, Tianjin 300457, China
| | - Rui Su
- College of Biotechnology, Tianjin University of Science and Technology, No. 29, 13th Avenue, TEDA, Tianjin 300457, China
| | - Feiao Wang
- College of Biotechnology, Tianjin University of Science and Technology, No. 29, 13th Avenue, TEDA, Tianjin 300457, China
| | - Zeting Wang
- College of Biotechnology, Tianjin University of Science and Technology, No. 29, 13th Avenue, TEDA, Tianjin 300457, China
| | - Yuexiang Liu
- College of Biotechnology, Tianjin University of Science and Technology, No. 29, 13th Avenue, TEDA, Tianjin 300457, China
| | - Ning Chen
- College of Biotechnology, Tianjin University of Science and Technology, No. 29, 13th Avenue, TEDA, Tianjin 300457, China
- Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, Tianjin University of Science and Technology, No. 29, 13th Avenue, TEDA, Tianjin 300457, China
| | - Yanjun Li
- College of Biotechnology, Tianjin University of Science and Technology, No. 29, 13th Avenue, TEDA, Tianjin 300457, China
- Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, Tianjin University of Science and Technology, No. 29, 13th Avenue, TEDA, Tianjin 300457, China
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Mutz M, Kösters D, Wynands B, Wierckx N, Marienhagen J. Microbial synthesis of the plant natural product precursor p-coumaric acid with Corynebacterium glutamicum. Microb Cell Fact 2023; 22:209. [PMID: 37833813 PMCID: PMC10576375 DOI: 10.1186/s12934-023-02222-y] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2023] [Accepted: 10/04/2023] [Indexed: 10/15/2023] Open
Abstract
BACKGROUND Phenylpropanoids such as p-coumaric acid represent important precursors for the synthesis of a broad range of plant secondary metabolites including stilbenoids, flavonoids, and lignans, which are of pharmacological interest due to their health-promoting properties. Although extraction from plant material or chemical synthesis is possible, microbial synthesis of p-coumaric acid from glucose has the advantage of being less expensive and more resource efficient. In this study, Corynebacterium glutamicum was engineered for the production of the plant polyphenol precursor p-coumaric acid from glucose. RESULTS Heterologous expression of the tyrosine ammonia-lyase encoding gene from Flavobacterium johnsoniae enabled the conversion of endogenously provided tyrosine to p-coumaric acid. Product consumption was avoided by abolishing essential reactions of the phenylpropanoid degradation pathway. Accumulation of anthranilate as a major byproduct was eliminated by reducing the activity of anthranilate synthase through targeted mutagenesis to avoid tryptophan auxotrophy. Subsequently, the carbon flux into the shikimate pathway was increased, phenylalanine biosynthesis was reduced, and phosphoenolpyruvate availability was improved to boost p-coumaric acid accumulation. A maximum titer of 661 mg/L p-coumaric acid (4 mM) in defined mineral medium was reached. Finally, the production strain was utilized in co-cultivations with a C. glutamicum strain previously engineered for the conversion of p-coumaric acid into the polyphenol resveratrol. These co-cultivations enabled the synthesis of 31.2 mg/L (0.14 mM) resveratrol from glucose without any p-coumaric acid supplementation. CONCLUSIONS The utilization of a heterologous tyrosine ammonia-lyase in combination with optimization of the shikimate pathway enabled the efficient production of p-coumaric acid with C. glutamicum. Reducing the carbon flux into the phenylalanine and tryptophan branches was the key to success along with the introduction of feedback-resistant enzyme variants.
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Affiliation(s)
- Mario Mutz
- Institute of Bio- and Geosciences, IBG-1: Biotechnology, Forschungszentrum Jülich, 52425 Jülich, Germany
- Institute of Biotechnology, RWTH Aachen University, Worringer Weg 3, 52074 Aachen, Germany
| | - Dominic Kösters
- Institute of Bio- and Geosciences, IBG-1: Biotechnology, Forschungszentrum Jülich, 52425 Jülich, Germany
- Institute of Biotechnology, RWTH Aachen University, Worringer Weg 3, 52074 Aachen, Germany
| | - Benedikt Wynands
- Institute of Bio- and Geosciences, IBG-1: Biotechnology, Forschungszentrum Jülich, 52425 Jülich, Germany
| | - Nick Wierckx
- Institute of Bio- and Geosciences, IBG-1: Biotechnology, Forschungszentrum Jülich, 52425 Jülich, Germany
| | - Jan Marienhagen
- Institute of Bio- and Geosciences, IBG-1: Biotechnology, Forschungszentrum Jülich, 52425 Jülich, Germany
- Institute of Biotechnology, RWTH Aachen University, Worringer Weg 3, 52074 Aachen, Germany
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Jeung K, Kim S, Yeon Lee J, Yeol Jung G. Optimization of mevalonate production using acetate by precursor balancing and flux redistribution in Escherichia coli. J IND ENG CHEM 2023. [DOI: 10.1016/j.jiec.2022.12.049] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
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Wang L, Yang H, Wu M, Zhang J, Zhang H, Mao Z, Chen X. Integrative transcriptome and proteome revealed high-yielding mechanisms of epsilon-poly-L-lysine by Streptomyces albulus. Front Microbiol 2023; 14:1123050. [PMID: 37152744 PMCID: PMC10157215 DOI: 10.3389/fmicb.2023.1123050] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2022] [Accepted: 03/27/2023] [Indexed: 05/09/2023] Open
Abstract
Introduction ε-poly-L-lysine (ε-PL) is a high value, widely used natural antimicrobial peptide additive for foods and cosmetic products that is mainly produced by Streptomyces albulus. In previous work, we developed the high-yield industrial strain S. albulus WG-608 through successive rounds of engineering. Methods Here, we use integrated physiological, transcriptomic, and proteomics association analysis to resolve the complex mechanisms underlying high ε-PL production by comparing WG-608 with the progenitor strain M-Z18. Results Our results show that key genes in the glycolysis, pentose phosphate pathway, glyoxylate pathway, oxidative phosphorylation, and L-lysine biosynthesis pathways are differentially upregulated in WG-608, while genes in the biosynthetic pathways for fatty acids, various branched amino acids, and secondary metabolite by-products are downregulated. This regulatory pattern results in the introduction of more carbon atoms into L-lysine biosynthesis and ε-PL production. In addition, significant changes in the regulation of DNA replication, transcription, and translation, two component systems, and quorum sensing may facilitate the adaptability to environmental pressure and the biosynthesis of ε-PL. Overexpression of ppk gene and addition of polyP6 further enhanced the ε-PL production. Discussion This study enables comprehensive understanding of the biosynthetic mechanisms of ε-PL in S. albulus WG-608, while providing some genetic modification and fermentation strategies to further improve the ε-PL production.
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Kim GY, Kim J, Park G, Kim HJ, Yang J, Seo SW. Synthetic biology tools for engineering Corynebacterium glutamicum. Comput Struct Biotechnol J 2023; 21:1955-1965. [PMID: 36942105 PMCID: PMC10024154 DOI: 10.1016/j.csbj.2023.03.004] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2022] [Revised: 03/03/2023] [Accepted: 03/04/2023] [Indexed: 03/08/2023] Open
Abstract
Corynebacterium glutamicum is a promising organism for the industrial production of amino acids, fuels, and various value-added chemicals. From the whole genome sequence release, C. glutamicum has been valuable in the field of industrial microbiology and biotechnology. Continuous discovery of genetic manipulations and regulation mechanisms has developed C. glutamicum as a synthetic biology platform chassis. This review summarized diverse genomic manipulation technologies and gene expression tools for static, dynamic, and multiplex control at transcription and translation levels. Moreover, we discussed the current challenges and applicable tools to C. glutamicum for future advancements.
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Affiliation(s)
- Gi Yeon Kim
- Interdisciplinary Program in Bioengineering, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul 08826, South Korea
| | - Jinyoung Kim
- School of Chemical and Biological Engineering, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul 08826, South Korea
| | - Geunyung Park
- Interdisciplinary Program in Bioengineering, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul 08826, South Korea
| | - Hyeon Jin Kim
- Interdisciplinary Program in Bioengineering, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul 08826, South Korea
| | - Jina Yang
- Department of Chemical Engineering, Jeju National University, 102, Jejudaehak-ro, Jeju-si, Jeju-do 63243, South Korea
- Corresponding author.
| | - Sang Woo Seo
- Interdisciplinary Program in Bioengineering, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul 08826, South Korea
- School of Chemical and Biological Engineering, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul 08826, South Korea
- Institute of Chemical Processes, 1 Gwanak-ro, Gwanak-gu, Seoul 08826, South Korea
- Bio-MAX Institute, 1 Gwanak-ro, Gwanak-gu, Seoul 08826, South Korea
- Institute of Engineering Research Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul 08826, South Korea
- Corresponding author at: School of Chemical and Biological Engineering, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul 08826, South Korea.
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Niu J, Mao Z, Mao Y, Wu K, Shi Z, Yuan Q, Cai J, Ma H. Construction and Analysis of an Enzyme-Constrained Metabolic Model of Corynebacterium glutamicum. Biomolecules 2022; 12:1499. [PMID: 36291707 PMCID: PMC9599660 DOI: 10.3390/biom12101499] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2022] [Revised: 10/08/2022] [Accepted: 10/14/2022] [Indexed: 05/25/2024] Open
Abstract
The genome-scale metabolic model (GEM) is a powerful tool for interpreting and predicting cellular phenotypes under various environmental and genetic perturbations. However, GEM only considers stoichiometric constraints, and the simulated growth and product yield values will show a monotonic linear increase with increasing substrate uptake rate, which deviates from the experimentally measured values. Recently, the integration of enzymatic constraints into stoichiometry-based GEMs was proven to be effective in making novel discoveries and predicting new engineering targets. Here, we present the first genome-scale enzyme-constrained model (ecCGL1) for Corynebacterium glutamicum reconstructed by integrating enzyme kinetic data from various sources using a ECMpy workflow based on the high-quality GEM of C. glutamicum (obtained by modifying the iCW773 model). The enzyme-constrained model improved the prediction of phenotypes and simulated overflow metabolism, while also recapitulating the trade-off between biomass yield and enzyme usage efficiency. Finally, we used the ecCGL1 to identify several gene modification targets for l-lysine production, most of which agree with previously reported genes. This study shows that incorporating enzyme kinetic information into the GEM enhances the cellular phenotypes prediction of C. glutamicum, which can help identify key enzymes and thus provide reliable guidance for metabolic engineering.
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Affiliation(s)
- Jinhui Niu
- School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230026, China
- Biodesign Center, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
- National Technology Innovation Center of Synthetic Biology, Tianjin 300308, China
| | - Zhitao Mao
- Biodesign Center, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
- National Technology Innovation Center of Synthetic Biology, Tianjin 300308, China
| | - Yufeng Mao
- Biodesign Center, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
- National Technology Innovation Center of Synthetic Biology, Tianjin 300308, China
| | - Ke Wu
- Biodesign Center, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
- National Technology Innovation Center of Synthetic Biology, Tianjin 300308, China
| | - Zhenkun Shi
- Biodesign Center, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
- National Technology Innovation Center of Synthetic Biology, Tianjin 300308, China
| | - Qianqian Yuan
- Biodesign Center, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
- National Technology Innovation Center of Synthetic Biology, Tianjin 300308, China
| | - Jingyi Cai
- Biodesign Center, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
- National Technology Innovation Center of Synthetic Biology, Tianjin 300308, China
| | - Hongwu Ma
- School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230026, China
- Biodesign Center, 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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15
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Kranz A, Polen T, Kotulla C, Arndt A, Bosco G, Bussmann M, Chattopadhyay A, Cramer A, Davoudi CF, Degner U, Diesveld R, Freiherr von Boeselager R, Gärtner K, Gätgens C, Georgi T, Geraths C, Haas S, Heyer A, Hünnefeld M, Ishige T, Kabus A, Kallscheuer N, Kever L, Klaffl S, Kleine B, Kočan M, Koch-Koerfges A, Kraxner KJ, Krug A, Krüger A, Küberl A, Labib M, Lange C, Mack C, Maeda T, Mahr R, Majda S, Michel A, Morosov X, Müller O, Nanda AM, Nickel J, Pahlke J, Pfeifer E, Platzen L, Ramp P, Rittmann D, Schaffer S, Scheele S, Spelberg S, Schulte J, Schweitzer JE, Sindelar G, Sorger-Herrmann U, Spelberg M, Stansen C, Tharmasothirajan A, Ooyen JV, van Summeren-Wesenhagen P, Vogt M, Witthoff S, Zhu L, Eikmanns BJ, Oldiges M, Schaumann G, Baumgart M, Brocker M, Eggeling L, Freudl R, Frunzke J, Marienhagen J, Wendisch VF, Bott M. A manually curated compendium of expression profiles for the microbial cell factory Corynebacterium glutamicum. Sci Data 2022; 9:594. [PMID: 36182956 PMCID: PMC9526701 DOI: 10.1038/s41597-022-01706-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2022] [Accepted: 08/18/2022] [Indexed: 11/12/2022] Open
Abstract
Corynebacterium glutamicum is the major host for the industrial production of amino acids and has become one of the best studied model organisms in microbial biotechnology. Rational strain construction has led to an improvement of producer strains and to a variety of novel producer strains with a broad substrate and product spectrum. A key factor for the success of these approaches is detailed knowledge of transcriptional regulation in C. glutamicum. Here, we present a large compendium of 927 manually curated microarray-based transcriptional profiles for wild-type and engineered strains detecting genome-wide expression changes of the 3,047 annotated genes in response to various environmental conditions or in response to genetic modifications. The replicates within the 927 experiments were combined to 304 microarray sets ordered into six categories that were used for differential gene expression analysis. Hierarchical clustering confirmed that no outliers were present in the sets. The compendium provides a valuable resource for future fundamental and applied research with C. glutamicum and contributes to a systemic understanding of this microbial cell factory. Measurement(s) Gene Expression Analysis Technology Type(s) Two Color Microarray Factor Type(s) WT condition A vs. WT condition B • Plasmid-based gene overexpression in parental strain vs. parental strain with empty vector control • Deletion mutant vs. parental strain Sample Characteristic - Organism Corynebacterium glutamicum Sample Characteristic - Environment laboratory environment Sample Characteristic - Location Germany.
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Affiliation(s)
- Angela Kranz
- IBG-1: Biotechnology, Institute of Bio- and Geosciences, Forschungszentrum Jülich, D-52425, Jülich, Germany.
- IBG-4: Bioinformatics, Institute of Bio- and Geosciences, Forschungszentrum Jülich, D-52425, Jülich, Germany.
| | - Tino Polen
- IBG-1: Biotechnology, Institute of Bio- and Geosciences, Forschungszentrum Jülich, D-52425, Jülich, Germany
| | - Christian Kotulla
- IBG-1: Biotechnology, Institute of Bio- and Geosciences, Forschungszentrum Jülich, D-52425, Jülich, Germany
| | - Annette Arndt
- Institute of Microbiology and Biotechnology, University of Ulm, D-89069, Ulm, Germany
| | - Graziella Bosco
- IBG-1: Biotechnology, Institute of Bio- and Geosciences, Forschungszentrum Jülich, D-52425, Jülich, Germany
| | - Michael Bussmann
- IBG-1: Biotechnology, Institute of Bio- and Geosciences, Forschungszentrum Jülich, D-52425, Jülich, Germany
| | - Ava Chattopadhyay
- IBG-1: Biotechnology, Institute of Bio- and Geosciences, Forschungszentrum Jülich, D-52425, Jülich, Germany
| | - Annette Cramer
- Institute of Microbiology and Biotechnology, University of Ulm, D-89069, Ulm, Germany
| | - Cedric-Farhad Davoudi
- IBG-1: Biotechnology, Institute of Bio- and Geosciences, Forschungszentrum Jülich, D-52425, Jülich, Germany
| | - Ursula Degner
- IBG-1: Biotechnology, Institute of Bio- and Geosciences, Forschungszentrum Jülich, D-52425, Jülich, Germany
| | - Ramon Diesveld
- IBG-1: Biotechnology, Institute of Bio- and Geosciences, Forschungszentrum Jülich, D-52425, Jülich, Germany
| | | | - Kim Gärtner
- IBG-1: Biotechnology, Institute of Bio- and Geosciences, Forschungszentrum Jülich, D-52425, Jülich, Germany
| | - Cornelia Gätgens
- IBG-1: Biotechnology, Institute of Bio- and Geosciences, Forschungszentrum Jülich, D-52425, Jülich, Germany
| | - Tobias Georgi
- IBG-1: Biotechnology, Institute of Bio- and Geosciences, Forschungszentrum Jülich, D-52425, Jülich, Germany
| | - Christian Geraths
- IBG-1: Biotechnology, Institute of Bio- and Geosciences, Forschungszentrum Jülich, D-52425, Jülich, Germany
| | - Sabine Haas
- IBG-1: Biotechnology, Institute of Bio- and Geosciences, Forschungszentrum Jülich, D-52425, Jülich, Germany
| | - Antonia Heyer
- IBG-1: Biotechnology, Institute of Bio- and Geosciences, Forschungszentrum Jülich, D-52425, Jülich, Germany
| | - Max Hünnefeld
- IBG-1: Biotechnology, Institute of Bio- and Geosciences, Forschungszentrum Jülich, D-52425, Jülich, Germany
| | - Takeru Ishige
- IBG-1: Biotechnology, Institute of Bio- and Geosciences, Forschungszentrum Jülich, D-52425, Jülich, Germany
| | - Armin Kabus
- IBG-1: Biotechnology, Institute of Bio- and Geosciences, Forschungszentrum Jülich, D-52425, Jülich, Germany
| | - Nicolai Kallscheuer
- IBG-1: Biotechnology, Institute of Bio- and Geosciences, Forschungszentrum Jülich, D-52425, Jülich, Germany
| | - Larissa Kever
- IBG-1: Biotechnology, Institute of Bio- and Geosciences, Forschungszentrum Jülich, D-52425, Jülich, Germany
| | - Simon Klaffl
- IBG-1: Biotechnology, Institute of Bio- and Geosciences, Forschungszentrum Jülich, D-52425, Jülich, Germany
| | - Britta Kleine
- IBG-1: Biotechnology, Institute of Bio- and Geosciences, Forschungszentrum Jülich, D-52425, Jülich, Germany
| | - Martina Kočan
- IBG-1: Biotechnology, Institute of Bio- and Geosciences, Forschungszentrum Jülich, D-52425, Jülich, Germany
| | - Abigail Koch-Koerfges
- IBG-1: Biotechnology, Institute of Bio- and Geosciences, Forschungszentrum Jülich, D-52425, Jülich, Germany
| | - Kim J Kraxner
- IBG-1: Biotechnology, Institute of Bio- and Geosciences, Forschungszentrum Jülich, D-52425, Jülich, Germany
| | - Andreas Krug
- IBG-1: Biotechnology, Institute of Bio- and Geosciences, Forschungszentrum Jülich, D-52425, Jülich, Germany
| | - Aileen Krüger
- IBG-1: Biotechnology, Institute of Bio- and Geosciences, Forschungszentrum Jülich, D-52425, Jülich, Germany
| | - Andreas Küberl
- IBG-1: Biotechnology, Institute of Bio- and Geosciences, Forschungszentrum Jülich, D-52425, Jülich, Germany
| | - Mohamed Labib
- IBG-1: Biotechnology, Institute of Bio- and Geosciences, Forschungszentrum Jülich, D-52425, Jülich, Germany
| | - Christian Lange
- IBG-1: Biotechnology, Institute of Bio- and Geosciences, Forschungszentrum Jülich, D-52425, Jülich, Germany
| | - Christina Mack
- IBG-1: Biotechnology, Institute of Bio- and Geosciences, Forschungszentrum Jülich, D-52425, Jülich, Germany
| | - Tomoya Maeda
- IBG-1: Biotechnology, Institute of Bio- and Geosciences, Forschungszentrum Jülich, D-52425, Jülich, Germany
| | - Regina Mahr
- IBG-1: Biotechnology, Institute of Bio- and Geosciences, Forschungszentrum Jülich, D-52425, Jülich, Germany
| | - Stephan Majda
- IBG-1: Biotechnology, Institute of Bio- and Geosciences, Forschungszentrum Jülich, D-52425, Jülich, Germany
| | - Andrea Michel
- IBG-1: Biotechnology, Institute of Bio- and Geosciences, Forschungszentrum Jülich, D-52425, Jülich, Germany
| | - Xenia Morosov
- IBG-1: Biotechnology, Institute of Bio- and Geosciences, Forschungszentrum Jülich, D-52425, Jülich, Germany
| | - Olga Müller
- IBG-1: Biotechnology, Institute of Bio- and Geosciences, Forschungszentrum Jülich, D-52425, Jülich, Germany
| | - Arun M Nanda
- IBG-1: Biotechnology, Institute of Bio- and Geosciences, Forschungszentrum Jülich, D-52425, Jülich, Germany
| | - Jens Nickel
- IBG-1: Biotechnology, Institute of Bio- and Geosciences, Forschungszentrum Jülich, D-52425, Jülich, Germany
| | - Jennifer Pahlke
- IBG-1: Biotechnology, Institute of Bio- and Geosciences, Forschungszentrum Jülich, D-52425, Jülich, Germany
| | - Eugen Pfeifer
- IBG-1: Biotechnology, Institute of Bio- and Geosciences, Forschungszentrum Jülich, D-52425, Jülich, Germany
| | - Laura Platzen
- IBG-1: Biotechnology, Institute of Bio- and Geosciences, Forschungszentrum Jülich, D-52425, Jülich, Germany
| | - Paul Ramp
- IBG-1: Biotechnology, Institute of Bio- and Geosciences, Forschungszentrum Jülich, D-52425, Jülich, Germany
| | - Doris Rittmann
- IBG-1: Biotechnology, Institute of Bio- and Geosciences, Forschungszentrum Jülich, D-52425, Jülich, Germany
| | - Steffen Schaffer
- IBG-1: Biotechnology, Institute of Bio- and Geosciences, Forschungszentrum Jülich, D-52425, Jülich, Germany
| | - Sandra Scheele
- IBG-1: Biotechnology, Institute of Bio- and Geosciences, Forschungszentrum Jülich, D-52425, Jülich, Germany
| | - Stephanie Spelberg
- IBG-1: Biotechnology, Institute of Bio- and Geosciences, Forschungszentrum Jülich, D-52425, Jülich, Germany
| | - Julia Schulte
- IBG-1: Biotechnology, Institute of Bio- and Geosciences, Forschungszentrum Jülich, D-52425, Jülich, Germany
| | - Jens-Eric Schweitzer
- IBG-1: Biotechnology, Institute of Bio- and Geosciences, Forschungszentrum Jülich, D-52425, Jülich, Germany
| | - Georg Sindelar
- IBG-1: Biotechnology, Institute of Bio- and Geosciences, Forschungszentrum Jülich, D-52425, Jülich, Germany
| | - Ulrike Sorger-Herrmann
- IBG-1: Biotechnology, Institute of Bio- and Geosciences, Forschungszentrum Jülich, D-52425, Jülich, Germany
| | - Markus Spelberg
- IBG-1: Biotechnology, Institute of Bio- and Geosciences, Forschungszentrum Jülich, D-52425, Jülich, Germany
| | - Corinna Stansen
- IBG-1: Biotechnology, Institute of Bio- and Geosciences, Forschungszentrum Jülich, D-52425, Jülich, Germany
| | - Apilaasha Tharmasothirajan
- IBG-1: Biotechnology, Institute of Bio- and Geosciences, Forschungszentrum Jülich, D-52425, Jülich, Germany
| | - Jan van Ooyen
- IBG-1: Biotechnology, Institute of Bio- and Geosciences, Forschungszentrum Jülich, D-52425, Jülich, Germany
| | | | - Michael Vogt
- IBG-1: Biotechnology, Institute of Bio- and Geosciences, Forschungszentrum Jülich, D-52425, Jülich, Germany
| | - Sabrina Witthoff
- IBG-1: Biotechnology, Institute of Bio- and Geosciences, Forschungszentrum Jülich, D-52425, Jülich, Germany
| | - Lingfeng Zhu
- IBG-1: Biotechnology, Institute of Bio- and Geosciences, Forschungszentrum Jülich, D-52425, Jülich, Germany
| | - Bernhard J Eikmanns
- Institute of Microbiology and Biotechnology, University of Ulm, D-89069, Ulm, Germany
| | - Marco Oldiges
- IBG-1: Biotechnology, Institute of Bio- and Geosciences, Forschungszentrum Jülich, D-52425, Jülich, Germany
| | - Georg Schaumann
- SenseUp GmbH, c/o Campus Forschungszentrum, Wilhelm-Johnen-Strasse, D-52425, Jülich, Germany
| | - Meike Baumgart
- IBG-1: Biotechnology, Institute of Bio- and Geosciences, Forschungszentrum Jülich, D-52425, Jülich, Germany
| | - Melanie Brocker
- IBG-1: Biotechnology, Institute of Bio- and Geosciences, Forschungszentrum Jülich, D-52425, Jülich, Germany
| | - Lothar Eggeling
- IBG-1: Biotechnology, Institute of Bio- and Geosciences, Forschungszentrum Jülich, D-52425, Jülich, Germany
| | - Roland Freudl
- IBG-1: Biotechnology, Institute of Bio- and Geosciences, Forschungszentrum Jülich, D-52425, Jülich, Germany
| | - Julia Frunzke
- IBG-1: Biotechnology, Institute of Bio- and Geosciences, Forschungszentrum Jülich, D-52425, Jülich, Germany
| | - Jan Marienhagen
- IBG-1: Biotechnology, Institute of Bio- and Geosciences, Forschungszentrum Jülich, D-52425, Jülich, Germany
| | - Volker F Wendisch
- Genetics of Prokaryotes, Biology & CeBiTec, Bielefeld University, Universitaetsstr. 25, D-33615, Bielefeld, Germany
| | - Michael Bott
- IBG-1: Biotechnology, Institute of Bio- and Geosciences, Forschungszentrum Jülich, D-52425, Jülich, Germany.
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16
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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: 0.3] [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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17
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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: 1.5] [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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18
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Wang Y, Xu J, Jin Z, Xia X, Zhang W. Improvement of acetyl-CoA supply and glucose utilization increases l-leucine production in Corynebacterium glutamicum. Biotechnol J 2021; 17:e2100349. [PMID: 34870372 DOI: 10.1002/biot.202100349] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2021] [Revised: 12/02/2021] [Accepted: 12/03/2021] [Indexed: 11/11/2022]
Abstract
BACKGROUND l-Leucine is one of important essential amino acids with multiple industrial applications, whose market requirements cannot be met because of the lower productivity. MAIN METHODS AND MAJOR RESULTS In this study, a strain of Corynebacterium glutamicum with high l-leucine yield was constructed to enhance its acetyl-CoA supply and glucose utilization. One copy of leuA under the control of a strong promoter was incorporated into the C. glutamicum genome. Then, acetyl-CoA supply was increased by the integration of a terminator in front of gltA and by the heterogeneous overexpression of acetyl-CoA synthetase (Acs) and deacetylase (CobB) derived from Escherichia coli. Next, the transcriptional regulator SugR was deleted to enhance glucose uptake via a phosphotransferase-mediated route. In fed-batch fermentation performed in a 5-L reactor, l-leucine production of 40.11±0.73 g/L was achieved under the optimized conditions, with the l-leucine yield and productivity of 0.25 g/g glucose and 0.59 g/L/h, respectively. CONCLUSIONS AND IMPLICATIONS These results represent a significant improvement in the l-leucine titer of C. glutamicum, indicating that the process possesses highly potential for industrial application. These strategies can be also expanded to enable the production of other value-added biochemicals derived from the intermediates of central carbon metabolism. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Yingyu Wang
- State Key Laboratory of Food Science and Technology, School of Food Science and Technology, Jiangnan University, WuXi, 214122, China.,The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, WuXi, 214122, China
| | - Jianzhong Xu
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, WuXi, 214122, China
| | - Zhengyu Jin
- State Key Laboratory of Food Science and Technology, School of Food Science and Technology, Jiangnan University, WuXi, 214122, China
| | - Xiaole Xia
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, WuXi, 214122, China
| | - Weiguo Zhang
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, WuXi, 214122, China
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19
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Feierabend M, Renz A, Zelle E, Nöh K, Wiechert W, Dräger A. High-Quality Genome-Scale Reconstruction of Corynebacterium glutamicum ATCC 13032. Front Microbiol 2021; 12:750206. [PMID: 34867870 PMCID: PMC8634658 DOI: 10.3389/fmicb.2021.750206] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Accepted: 10/19/2021] [Indexed: 11/30/2022] Open
Abstract
Corynebacterium glutamicum belongs to the microbes of enormous biotechnological relevance. In particular, its strain ATCC 13032 is a widely used producer of L-amino acids at an industrial scale. Its apparent robustness also turns it into a favorable platform host for a wide range of further compounds, mainly because of emerging bio-based economies. A deep understanding of the biochemical processes in C. glutamicum is essential for a sustainable enhancement of the microbe's productivity. Computational systems biology has the potential to provide a valuable basis for driving metabolic engineering and biotechnological advances, such as increased yields of healthy producer strains based on genome-scale metabolic models (GEMs). Advanced reconstruction pipelines are now available that facilitate the reconstruction of GEMs and support their manual curation. This article presents iCGB21FR, an updated and unified GEM of C. glutamicum ATCC 13032 with high quality regarding comprehensiveness and data standards, built with the latest modeling techniques and advanced reconstruction pipelines. It comprises 1042 metabolites, 1539 reactions, and 805 genes with detailed annotations and database cross-references. The model validation took place using different media and resulted in realistic growth rate predictions under aerobic and anaerobic conditions. The new GEM produces all canonical amino acids, and its phenotypic predictions are consistent with laboratory data. The in silico model proved fruitful in adding knowledge to the metabolism of C. glutamicum: iCGB21FR still produces L-glutamate with the knock-out of the enzyme pyruvate carboxylase, despite the common belief to be relevant for the amino acid's production. We conclude that integrating high standards into the reconstruction of GEMs facilitates replicating validated knowledge, closing knowledge gaps, and making it a useful basis for metabolic engineering. The model is freely available from BioModels Database under identifier MODEL2102050001.
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Affiliation(s)
- Martina Feierabend
- Computational Systems Biology of Infections and Antimicrobial-Resistant Pathogens, Institute for Bioinformatics and Medical Informatics (IBMI), University of Tübingen, Tübingen, Germany
- Department of Computer Science, University of Tübingen, Tübingen, Germany
| | - Alina Renz
- Computational Systems Biology of Infections and Antimicrobial-Resistant Pathogens, Institute for Bioinformatics and Medical Informatics (IBMI), University of Tübingen, Tübingen, Germany
- Department of Computer Science, University of Tübingen, Tübingen, Germany
| | - Elisabeth Zelle
- Institute of Bio- and Geosciences, IBG-1: Biotechnology, Forschungszentrum Jülich GmbH, Jülich, Germany
| | - Katharina Nöh
- Institute of Bio- and Geosciences, IBG-1: Biotechnology, Forschungszentrum Jülich GmbH, Jülich, Germany
| | - Wolfgang Wiechert
- Institute of Bio- and Geosciences, IBG-1: Biotechnology, Forschungszentrum Jülich GmbH, Jülich, Germany
- Computational Systems Biotechnology (AVT.CSB), RWTH Aachen University, Aachen, Germany
| | - Andreas Dräger
- Computational Systems Biology of Infections and Antimicrobial-Resistant Pathogens, Institute for Bioinformatics and Medical Informatics (IBMI), University of Tübingen, Tübingen, Germany
- Department of Computer Science, University of Tübingen, Tübingen, Germany
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20
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Wang Z, Guo F, Dong T, Tan Z, Abdelraof M, Wang Z, Cui J, Jia S. Metabolomic Analysis of Biosynthesis Mechanism of ε-Polylysine Produced by Streptomyces diastatochromogenes. Front Bioeng Biotechnol 2021; 9:698022. [PMID: 34395404 PMCID: PMC8363252 DOI: 10.3389/fbioe.2021.698022] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2021] [Accepted: 06/25/2021] [Indexed: 12/21/2022] Open
Abstract
ε-Polylysine (ε-PL), a natural preservative with broad-spectrum antimicrobial activity, has been widely used as a green food additive, and it is now mainly produced by Streptomyces in industry. In the previous study, strain 6#-7 of high-yield ε-PL was obtained from the original strain TUST by mutagenesis. However, the biosynthesis mechanism of ε-PL in 6#-7 is still unclear. In this study, the metabolomic analyses of the biosynthesis mechanism of ε-PL in both strains are investigated. Results show that the difference in metabolisms between TUST and 6#-7 is significant. Based on the results of both metabolomic and enzymatic activities, a metabolic regulation mechanism of the high-yield strain is revealed. The transport and absorption capacity for glucose of 6#-7 is improved. The enzymatic activity benefits ε-PL synthesis, such as pyruvate kinase and aspartokinase, is strengthened. On the contrary, the activity of homoserine dehydrogenase in the branched-chain pathways is decreased. Meanwhile, the increase of trehalose, glutamic acid, etc. makes 6#-7 more resistant to ε-PL. Thus, the ability of the mutagenized strain 6#-7 to synthesize ε-PL is enhanced, and it can produce more ε-PLs compared with the original strain. For the first time, the metabolomic analysis of the biosynthesis mechanism of ε-PL in the high-yield strain 6#-7 is investigated, and a possible mechanism is then revealed. These findings provide a theoretical basis for further improving the production of ε-PL.
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Affiliation(s)
- Ziyuan Wang
- State Key Laboratory of Food Nutrition and Safety, Laboratory of Industrial Fermentation Microbiology, Ministry of Education, College of Biotechnology, Tianjin University of Science and Technology, Tianjin, China
- Tianjin Beiyang Baichuan Biotechnology Co., Ltd., Tianjin, China
| | - Fengzhu Guo
- State Key Laboratory of Food Nutrition and Safety, Laboratory of Industrial Fermentation Microbiology, Ministry of Education, College of Biotechnology, Tianjin University of Science and Technology, Tianjin, China
| | - Tianyu Dong
- State Key Laboratory of Food Nutrition and Safety, Laboratory of Industrial Fermentation Microbiology, Ministry of Education, College of Biotechnology, Tianjin University of Science and Technology, Tianjin, China
| | - Zhilei Tan
- State Key Laboratory of Food Nutrition and Safety, Laboratory of Industrial Fermentation Microbiology, Ministry of Education, College of Biotechnology, Tianjin University of Science and Technology, Tianjin, China
| | - Mohamed Abdelraof
- Genetic Engineering and Biotechnology Research Division, National Research Centre, Dokki, Giza, Egypt
| | - Zichen Wang
- State Key Laboratory of Food Nutrition and Safety, Laboratory of Industrial Fermentation Microbiology, Ministry of Education, College of Biotechnology, Tianjin University of Science and Technology, Tianjin, China
| | - Jiandong Cui
- State Key Laboratory of Food Nutrition and Safety, Laboratory of Industrial Fermentation Microbiology, Ministry of Education, College of Biotechnology, Tianjin University of Science and Technology, Tianjin, China
| | - Shiru Jia
- State Key Laboratory of Food Nutrition and Safety, Laboratory of Industrial Fermentation Microbiology, Ministry of Education, College of Biotechnology, Tianjin University of Science and Technology, Tianjin, China
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21
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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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22
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Zhang X, Zhang X, Wang T, Li C. Metabolic response of soybean leaves induced by short-term exposure of ozone. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2021; 213:112033. [PMID: 33582415 DOI: 10.1016/j.ecoenv.2021.112033] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/23/2020] [Revised: 12/31/2020] [Accepted: 02/03/2021] [Indexed: 06/12/2023]
Abstract
The ever-increasing ozone (O3) concentration has led to reduced production and altered quality of soybean. Abundant reports have explored the damage mechanisms of O3 on soybean. However, how the elevated O3 affects metabolite profiling of soybean remains to be poorly understood. Here, we compare the metabolic profile of soybean leaves under charcoal filtered air (CF, <20 ppb) and short-term elevated O3 concentration (EO, 100 ppb). High level of O3 affects metabolites for the tricarbonic acid (TCA) cycle, reactive oxygen species, cell wall composition and amino acids. Significantly, jasmonic acid-related metabolite promoting stomata closure is highly induced with 125-fold change. Furthermore, O3 fumigation alters the expression of genes contributing to the biosynthesis of certain metabolites in TCA cycle. Together, these findings identify a wide range of changed metabolites in response to O3 pollution. Our results pave the way for the genetic improvement of soybean to adapt to O3 pollution to maintain stable yields.
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Affiliation(s)
- Xinxin Zhang
- State Key Laboratory of Vegetation and Environmental Change, Institute of Botany, the Chinese Academy of Sciences, Beijing, China
| | - Xiaofan Zhang
- Institute for Interdisciplinary Information Sciences, Tsinghua University, Beijing, China
| | - Tianzuo Wang
- State Key Laboratory of Vegetation and Environmental Change, Institute of Botany, the Chinese Academy of Sciences, Beijing, China; College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, China
| | - Caihong Li
- State Key Laboratory of Vegetation and Environmental Change, Institute of Botany, the Chinese Academy of Sciences, Beijing, China.
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23
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Göttl VL, Schmitt I, Braun K, Peters-Wendisch P, Wendisch VF, Henke NA. CRISPRi-Library-Guided Target Identification for Engineering Carotenoid Production by Corynebacterium glutamicum. Microorganisms 2021; 9:670. [PMID: 33805131 PMCID: PMC8064071 DOI: 10.3390/microorganisms9040670] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Revised: 03/19/2021] [Accepted: 03/21/2021] [Indexed: 01/24/2023] Open
Abstract
Corynebacterium glutamicum is a prominent production host for various value-added compounds in white biotechnology. Gene repression by dCas9/clustered regularly interspaced short palindromic repeats (CRISPR) interference (CRISPRi) allows for the identification of target genes for metabolic engineering. In this study, a CRISPRi-based library for the repression of 74 genes of C. glutamicum was constructed. The chosen genes included genes encoding enzymes of glycolysis, the pentose phosphate pathway, and the tricarboxylic acid cycle, regulatory genes, as well as genes of the methylerythritol phosphate and carotenoid biosynthesis pathways. As expected, CRISPRi-mediated repression of the carotenogenesis repressor gene crtR resulted in increased pigmentation and cellular content of the native carotenoid pigment decaprenoxanthin. CRISPRi screening identified 14 genes that affected decaprenoxanthin biosynthesis when repressed. Carotenoid biosynthesis was significantly decreased upon CRISPRi-mediated repression of 11 of these genes, while repression of 3 genes was beneficial for decaprenoxanthin production. Largely, but not in all cases, deletion of selected genes identified in the CRISPRi screen confirmed the pigmentation phenotypes obtained by CRISPRi. Notably, deletion of pgi as well as of gapA improved decaprenoxanthin levels 43-fold and 9-fold, respectively. The scope of the designed library to identify metabolic engineering targets, transfer of gene repression to stable gene deletion, and limitations of the approach were discussed.
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Affiliation(s)
| | | | | | | | - Volker F. Wendisch
- Genetics of Prokaryotes, Faculty of Biology & CeBiTec, Bielefeld University, 33615 Bielefeld, Germany; (V.L.G.); (I.S.); (K.B.); (P.P.-W.); (N.A.H.)
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24
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Sonntag CK, Flachbart LK, Maass C, Vogt M, Marienhagen J. A unified design allows fine-tuning of biosensor parameters and application across bacterial species. Metab Eng Commun 2020; 11:e00150. [PMID: 33145168 PMCID: PMC7593625 DOI: 10.1016/j.mec.2020.e00150] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2020] [Revised: 10/09/2020] [Accepted: 10/12/2020] [Indexed: 11/23/2022] Open
Abstract
In recent years, transcriptional biosensors have become valuable tools in metabolic engineering as they allow semiquantitative determination of metabolites in single cells. Although being perfectly suitable tools for high-throughput screenings, application of transcriptional biosensors is often limited by the intrinsic characteristics of the individual sensor components and their interplay. In addition, biosensors often fail to work properly in heterologous host systems due to signal saturation at low intracellular metabolite concentrations, which typically limits their use in high-level producer strains at advanced engineering stages. We here introduce a biosensor design, which allows fine-tuning of important sensor parameters and restores the sensor response in a heterologous expression host. As a key feature of our design, the regulator activity is controlled through the expression level of the respective gene by different (synthetic) constitutive promoters selected for the used expression host. In this context, we constructed biosensors responding to basic amino acids or ring-hydroxylated phenylpropanoids for applications in Corynebacterium glutamicum and Escherichia coli. Detailed characterization of these biosensors in liquid cultures and during single-cell analysis using flow cytometry showed that the presented sensor design enables customization of important biosensor parameters as well as application of these sensors in relevant heterologous hosts. Development of a unified biosensor design for C. glutamicum and E. coli. Gradual expression of the regulator gene allows for biosensor fine-tuning. Biosensor response in a heterologous host can be restored. Biosensor characterization on the single-cell level prior to FACS is mandatory.
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Affiliation(s)
| | - Lion Konstantin Flachbart
- Institute of Bio- and Geosciences, IBG-1: Biotechnology, Forschungszentrum Jülich, D-52425, Jülich, Germany
| | - Celine Maass
- Institute of Bio- and Geosciences, IBG-1: Biotechnology, Forschungszentrum Jülich, D-52425, Jülich, Germany
| | - Michael Vogt
- Institute of Bio- and Geosciences, IBG-1: Biotechnology, Forschungszentrum Jülich, D-52425, Jülich, Germany
| | - Jan Marienhagen
- Institute of Bio- and Geosciences, IBG-1: Biotechnology, Forschungszentrum Jülich, D-52425, Jülich, Germany.,Institute of Biotechnology, RWTH Aachen University, Worringer Weg 3, D-52074, Aachen, Germany
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25
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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: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
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26
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Engineered citrate synthase alters Acetate Accumulation in Escherichia coli. Metab Eng 2020; 61:171-180. [PMID: 32569710 DOI: 10.1016/j.ymben.2020.06.006] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2020] [Revised: 05/24/2020] [Accepted: 06/10/2020] [Indexed: 12/15/2022]
Abstract
Metabolic engineering is used to improve titers, yields and generation rates for biochemical products in host microbes such as Escherichia coli. A wide range of biochemicals are derived from the central carbon metabolite acetyl-CoA, and the largest native drain of acetyl-CoA in most microbes including E. coli is entry into the tricarboxylic acid (TCA) cycle via citrate synthase (coded by the gltA gene). Since the pathway to any biochemical derived from acetyl-CoA must ultimately compete with citrate synthase, a reduction in citrate synthase activity should facilitate the increased formation of products derived from acetyl-CoA. To test this hypothesis, we integrated into E. coli C ΔpoxB twenty-eight citrate synthase variants having specific point mutations that were anticipated to reduce citrate synthase activity. These variants were assessed in shake flasks for growth and the production of acetate, a model product derived from acetyl-CoA. Mutations in citrate synthase at residues W260, A267 and V361 resulted in the greatest acetate yields (approximately 0.24 g/g glucose) compared to the native citrate synthase (0.05 g/g). These variants were further examined in controlled batch and continuous processes. The results provide important insights on improving the production of compounds derived from acetyl-CoA.
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27
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Wu X, Tovilla‐Coutiño DB, Eiteman MA. Engineered citrate synthase improves citramalic acid generation in
Escherichia coli. Biotechnol Bioeng 2020; 117:2781-2790. [DOI: 10.1002/bit.27450] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2020] [Revised: 05/24/2020] [Accepted: 06/02/2020] [Indexed: 12/20/2022]
Affiliation(s)
- Xianghao Wu
- School of Chemical, Materials and Biomedical Engineering University of Georgia Athens Georgia
| | | | - Mark A. Eiteman
- School of Chemical, Materials and Biomedical Engineering University of Georgia Athens Georgia
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28
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Lu L, Mao Y, Kou M, Cui Z, Jin B, Chang Z, Wang Z, Ma H, Chen T. Engineering central pathways for industrial-level (3R)-acetoin biosynthesis in Corynebacterium glutamicum. Microb Cell Fact 2020; 19:102. [PMID: 32398078 PMCID: PMC7216327 DOI: 10.1186/s12934-020-01363-8] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2020] [Accepted: 05/05/2020] [Indexed: 01/24/2023] Open
Abstract
BACKGROUND Acetoin, especially the optically pure (3S)- or (3R)-enantiomer, is a high-value-added bio-based platform chemical and important potential pharmaceutical intermediate. Over the past decades, intense efforts have been devoted to the production of acetoin through green biotechniques. However, efficient and economical methods for the production of optically pure acetoin enantiomers are rarely reported. Previously, we systematically engineered the GRAS microorganism Corynebacterium glutamicum to efficiently produce (3R)-acetoin from glucose. Nevertheless, its yield and average productivity were still unsatisfactory for industrial bioprocesses. RESULTS In this study, cellular carbon fluxes in the acetoin producer CGR6 were further redirected toward acetoin synthesis using several metabolic engineering strategies, including blocking anaplerotic pathways, attenuating key genes of the TCA cycle and integrating additional copies of the alsSD operon into the genome. Among them, the combination of attenuation of citrate synthase and inactivation of phosphoenolpyruvate carboxylase showed a significant synergistic effect on acetoin production. Finally, the optimal engineered strain CGS11 produced a titer of 102.45 g/L acetoin with a yield of 0.419 g/g glucose at a rate of 1.86 g/L/h in a 5 L fermenter. The optical purity of the resulting (3R)-acetoin surpassed 95%. CONCLUSION To the best of our knowledge, this is the highest titer of highly enantiomerically enriched (3R)-acetoin, together with a competitive product yield and productivity, achieved in a simple, green processes without expensive additives or substrates. This process therefore opens the possibility to achieve easy, efficient, economical and environmentally-friendly production of (3R)-acetoin via microbial fermentation in the near future.
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Affiliation(s)
- Lingxue Lu
- Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering of Ministry of Education, SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, China
| | - Yufeng Mao
- Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China
| | - Mengyun Kou
- Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering of Ministry of Education, SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, China
| | - Zhenzhen Cui
- Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering of Ministry of Education, SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, China
| | - Biao Jin
- Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering of Ministry of Education, SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, China
| | - Zhishuai Chang
- Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering of Ministry of Education, SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, China
| | - Zhiwen Wang
- Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering of Ministry of Education, SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, China
| | - Hongwu Ma
- Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China
| | - Tao Chen
- Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering of Ministry of Education, SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, China.
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29
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Increasing L-homoserine production in Escherichia coli by engineering the central metabolic pathways. J Biotechnol 2020; 314-315:1-7. [DOI: 10.1016/j.jbiotec.2020.03.010] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2019] [Revised: 03/07/2020] [Accepted: 03/25/2020] [Indexed: 01/05/2023]
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30
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Li M, Chen J, Wang Y, Liu J, Huang J, Chen N, Zheng P, Sun J. Efficient Multiplex Gene Repression by CRISPR-dCpf1 in Corynebacterium glutamicum. Front Bioeng Biotechnol 2020; 8:357. [PMID: 32391351 PMCID: PMC7193084 DOI: 10.3389/fbioe.2020.00357] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2020] [Accepted: 03/31/2020] [Indexed: 01/14/2023] Open
Abstract
Corynebacterium glutamicum is an important workhorse for industrial production of diversiform bioproducts. Multiplex control of metabolic pathway genes is crucial for maximizing biosynthesis of desired products. However, few tools for simultaneously regulating multiple genes in C. glutamicum have been reported. Here, a CRISPR-dCpf1-based multiplex gene repression system was developed for C. glutamicum. This system successfully repressed two fluorescent reporter genes simultaneously by expressing a dCpf1 (E1006A, D917A) and a designed single crRNA array. To demonstrate applications of this CRISPR-dCpf1 system in metabolic engineering, we applied this system to repress four genes involved in lysine biosynthesis (gltA, pck, pgi, and hom) with a single array, which increased the lysine titer and yield for over 4.0-fold. Quantitative PCR demonstrated that transcription of all the four endogenous target genes were repressed by over 90%. Thus, the CRISPR-dCpf1 system is a simple and effective technique for multiplex gene repression in C. glutamicum and holds promise for metabolic engineering of C. glutamicum to produce valuable chemicals and fuels.
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Affiliation(s)
- Mingyue Li
- College of Biotechnology, Tianjin University of Science and Technology, Tianjin, China.,Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
| | - Jiuzhou Chen
- Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
| | - Yu Wang
- Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
| | - Jiao Liu
- Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
| | - Jingwen Huang
- Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China.,School of Biology and Biological Engineering, South China University of Technology, Guangzhou, China
| | - Ning Chen
- College of Biotechnology, Tianjin University of Science and Technology, Tianjin, China
| | - Ping Zheng
- Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
| | - Jibin Sun
- Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
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31
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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: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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32
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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: 26] [Impact Index Per Article: 5.2] [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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33
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Li Y, Ai Y, Zhang J, Fei J, Liu B, Wang J, Li M, Zhao Q, Song J. A novel expression vector for Corynebacterium glutamicum with an auxotrophy complementation system. Plasmid 2019; 107:102476. [PMID: 31758959 DOI: 10.1016/j.plasmid.2019.102476] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2019] [Revised: 10/28/2019] [Accepted: 11/13/2019] [Indexed: 01/27/2023]
Abstract
Corynebacterium glutamicum is an important industrial strain used for the production of amino acids and vitamins. Most tools developed for overexpression of genes in C. glutamicum are based on the inducible promoter regulated by the lacIq gene or contain an antibiotic resistance gene as a selection marker. These vectors are essential for rapid identification of recombinant strains and detailed study of gene functions, but, as a considerable disadvantage, these vectors are not suitable for large-scale industrial production due to the need for the addition of isopropyl-β-D-thiogalactopyranoside (IPTG) and antibiotics. In this study, the novel Escherichia coli-C. glutamicum shuttle expression vector pLY-4, derived from the expression vector pXMJ19, was constructed. The constitutive vector pLY-4 contains a large multiple cloning site, the strong promoter tacM and two selective markers: the original chloramphenicol resistance gene cat is used for molecular cloning operations, and the auxotrophy complementation marker alr, which can be stably replicated in the auxotrophic host strain without antibiotic selection pressure, is used for industrial fermentation. Heterologous expression of the gapC gene using the vector pLY-4 in C. glutamicum for L-methionine production indicated the potential application of pLY-4 in the development of C. glutamicum strain engineering and industrial fermentation.
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Affiliation(s)
- Ying Li
- College of Food Science and Engineering, Dalian Ocean University, Dalian 116023, PR China; Collaborative Innovation Center of Seafood Deep Processing, Dalian Polytechnic University, Dalian 116034, PR China
| | - Yuqing Ai
- College of Food Science and Engineering, Dalian Ocean University, Dalian 116023, PR China
| | - Junzheng Zhang
- School of Chemical Engineering and Technology, Harbin Institute of Technology, Harbin, 150001, PR China
| | - Jingxuan Fei
- College of Food Science and Engineering, Dalian Ocean University, Dalian 116023, PR China
| | - Bingnan Liu
- School of Life Science and Technology, Harbin Institute of Technology, Harbin 150001, PR China
| | - Jing Wang
- School of Life Science and Technology, Harbin Institute of Technology, Harbin 150001, PR China
| | - Meng Li
- College of Food Science and Engineering, Dalian Ocean University, Dalian 116023, PR China
| | - Qiancheng Zhao
- Liaoning Key Laboratory Aquatic Product Processing and Utilization, Dalian Ocean University, Dalian 116023, PR China; Collaborative Innovation Center of Seafood Deep Processing, Dalian Polytechnic University, Dalian 116034, PR China.
| | - Jinzhu Song
- School of Life Science and Technology, Harbin Institute of Technology, Harbin 150001, PR China.
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Xu JZ, Yu HB, Han M, Liu LM, Zhang WG. Metabolic engineering of glucose uptake systems in Corynebacterium glutamicum for improving the efficiency of l-lysine production. ACTA ACUST UNITED AC 2019; 46:937-949. [DOI: 10.1007/s10295-019-02170-w] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2018] [Accepted: 03/27/2019] [Indexed: 11/25/2022]
Abstract
Abstract
Traditional amino acid producers typically exhibit the low glucose uptake rate and growth deficiency, resulting in a long fermentation time because of the accumulation of side mutations in breeding of strains. In this study, we demonstrate that the efficiency of l-lysine production in traditional l-lysine producer Corynebacterium glutamicum ZL-9 can be improved by rationally engineering glucose uptake systems. To do this, different bypasses for glucose uptake were investigated to reveal the best glucose uptake system for l-lysine production in traditional l-lysine producer. This study showed that overexpression of the key genes in PTSGlc or non-PTSGlc increased the glucose consumption, growth rate, and l-lysine production. However, increasing the function of PTSGlc in glucose uptake led to the increase of by-products, especially for plasmid-mediated expression system. Increasing the participation of non-PTSGlc in glucose utilization showed the best glucose uptake system for l-lysine production. The final strain ZL-92 with increasing the expression level of iolT1, iolT2 and ppgK could produce 201.6 ± 13.8 g/L of l-lysine with a productivity of 5.04 g/L/h and carbon yield of 0.65 g/(g glucose) in fed-batch culture. This is the first report of a rational modification of glucose uptake systems that improve the efficiency of l-lysine production through increasing the participation of non-PTSGlc in glucose utilization in traditional l-lysine producer. Similar strategies can be also used for producing other amino acids or their derivatives.
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Affiliation(s)
- Jian-Zhong Xu
- 0000 0001 0708 1323 grid.258151.a The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology Jiangnan University 1800 Lihu Road 214122 Wuxi People’s Republic of China
| | - Hai-Bo Yu
- 0000 0001 0708 1323 grid.258151.a The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology Jiangnan University 1800 Lihu Road 214122 Wuxi People’s Republic of China
| | - Mei Han
- 0000 0004 0431 6539 grid.469163.f Shanghai Business School 2271 Zhongsha West-Road 200235 Shanghai People’s Republic of China
| | - Li-Ming Liu
- 0000 0001 0708 1323 grid.258151.a State Key Laboratory of Food Science and Technology, School of Biotechnology Jiangnan University 1800 Lihu Road 214122 Wuxi People’s Republic of China
| | - Wei-Guo Zhang
- 0000 0001 0708 1323 grid.258151.a The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology Jiangnan University 1800 Lihu Road 214122 Wuxi People’s Republic of China
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Noh M, Yoo SM, Yang D, Lee SY. Broad-Spectrum Gene Repression Using Scaffold Engineering of Synthetic sRNAs. ACS Synth Biol 2019; 8:1452-1461. [PMID: 31132322 DOI: 10.1021/acssynbio.9b00165] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Gene expression regulation in broad-spectrum range is critical for constructing cell factories and genetic circuits to balance and control system-wide fluxes. Synthetic small regulatory RNAs (sRNAs) effectively regulate gene expression at the translational level by modulating an mRNA-binding chance and sRNA abundance; however, it can control target gene expression only within the limit of the intrinsic repression ability of sRNAs. Here, we systematically mutated a SgrS scaffold as a model sRNA by dividing the Hfq-binding module of the sRNA into the three regions: the A/U-rich sequence, the stem, and the hairpin loop, and examined how efficiently the mutants suppressed DsRed2 expression. By doing this, we found that a scaffold with an altered A/U-rich sequence (CUUU) and stem length and that with altered A/U-rich sequence (GCAC) showed a 3-fold stronger and a 3-fold weaker repression than the original scaffold, respectively. For practical application of altered scaffolds, proof-of-concept experiments were performed by constructing a library of 67 synthetic sRNAs with the strongest scaffold, each one targeting a different rationally selected gene, and using this library to enhance cadaverine production in Escherichia coli, yielding in 27% increase (1.67 g/L in flask cultivation, 13.7 g/L in fed-batch cultivation). Synthetic sRNAs with engineered sRNA scaffolds could be useful in modulating gene expression for strain improvement.
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Affiliation(s)
- Minho Noh
- Department of Chemical and Biomolecular Engineering (BK21 Plus Program), KAIST, 291 Daehak-ro, Yuseong-gu, Daejeon 34141, Republic of Korea
| | - Seung Min Yoo
- School of Integrative Engineering, Chung-Ang University, 84 Heukseok-ro, Dongjak-gu, Seoul 06974, Republic of Korea
- BioProcess Engineering Research Center, KAIST, 291 Daehak-ro, Yuseong-gu, Daejeon 34141, Republic of Korea
| | - Dongsoo Yang
- Department of Chemical and Biomolecular Engineering (BK21 Plus Program), KAIST, 291 Daehak-ro, Yuseong-gu, Daejeon 34141, Republic of Korea
- Systems Metabolic Engineering and Systems Healthcare Cross-Generation Collaborative Laboratory, KAIST, 291 Daehak-ro, Yuseong-gu, Daejeon 34141, Republic of Korea
| | - Sang Yup Lee
- Department of Chemical and Biomolecular Engineering (BK21 Plus Program), KAIST, 291 Daehak-ro, Yuseong-gu, Daejeon 34141, Republic of Korea
- BioProcess Engineering Research Center, KAIST, 291 Daehak-ro, Yuseong-gu, Daejeon 34141, Republic of Korea
- Systems Metabolic Engineering and Systems Healthcare Cross-Generation Collaborative Laboratory, KAIST, 291 Daehak-ro, Yuseong-gu, Daejeon 34141, Republic of Korea
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Milke L, Kallscheuer N, Kappelmann J, Marienhagen J. Tailoring Corynebacterium glutamicum towards increased malonyl-CoA availability for efficient synthesis of the plant pentaketide noreugenin. Microb Cell Fact 2019; 18:71. [PMID: 30975146 PMCID: PMC6460773 DOI: 10.1186/s12934-019-1117-x] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2019] [Accepted: 04/03/2019] [Indexed: 12/28/2022] Open
Abstract
Background In the last years, different biotechnologically relevant microorganisms have been engineered for the synthesis of plant polyphenols such as flavonoids and stilbenes. However, low intracellular availability of malonyl-CoA as essential precursor for most plant polyphenols of interest is regarded as the decisive bottleneck preventing high product titers. Results In this study, Corynebacterium glutamicum, which emerged as promising cell factory for plant polyphenol production, was tailored by rational metabolic engineering towards providing significantly more malonyl-CoA for product synthesis. This was achieved by improving carbon source uptake, transcriptional deregulation of accBC and accD1 encoding the two subunits of the acetyl-CoA carboxylase (ACC), reduced flux into the tricarboxylic acid (TCA) cycle, and elimination of anaplerotic carboxylation of pyruvate. The constructed strains were used for the synthesis of the pharmacologically interesting plant pentaketide noreugenin, which is produced by plants such as Aloe arborescens from five molecules of malonyl-CoA. In this context, accumulation of the C1/C6 cyclized intermediate 1-(2,4,6-trihydroxyphenyl)butane-1,3-dione (TPBD) was observed, which could be fully cyclized to the bicyclic product noreugenin by acidification. Conclusion The best strain C. glutamicum Nor2 C5 mufasOBCD1 PO6-iolT1 ∆pyc allowed for synthesis of 53.32 mg/L (0.278 mM) noreugenin in CGXII medium supplemented with casamino acids within 24 h. Electronic supplementary material The online version of this article (10.1186/s12934-019-1117-x) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Lars Milke
- Institute of Bio- and Geosciences, IBG-1: Biotechnology, Forschungszentrum Jülich, 52425, Jülich, Germany
| | - Nicolai Kallscheuer
- Institute of Bio- and Geosciences, IBG-1: Biotechnology, Forschungszentrum Jülich, 52425, Jülich, Germany.,Bioeconomy Science Center (BioSC), Forschungszentrum Jülich GmbH, 52425, Jülich, Germany
| | - Jannick Kappelmann
- Institute of Bio- and Geosciences, IBG-1: Biotechnology, Forschungszentrum Jülich, 52425, Jülich, Germany
| | - Jan Marienhagen
- Institute of Bio- and Geosciences, IBG-1: Biotechnology, Forschungszentrum Jülich, 52425, Jülich, Germany. .,Bioeconomy Science Center (BioSC), Forschungszentrum Jülich GmbH, 52425, Jülich, Germany. .,Institute of Biotechnology, RWTH Aachen University, Worringer Weg 3, 52074, Aachen, Germany.
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Milke L, Ferreira P, Kallscheuer N, Braga A, Vogt M, Kappelmann J, Oliveira J, Silva AR, Rocha I, Bott M, Noack S, Faria N, Marienhagen J. Modulation of the central carbon metabolism of Corynebacterium glutamicum improves malonyl-CoA availability and increases plant polyphenol synthesis. Biotechnol Bioeng 2019; 116:1380-1391. [PMID: 30684355 DOI: 10.1002/bit.26939] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2018] [Revised: 12/10/2018] [Accepted: 01/22/2019] [Indexed: 12/21/2022]
Abstract
In recent years microorganisms have been engineered towards synthesizing interesting plant polyphenols such as flavonoids and stilbenes from glucose. Currently, the low endogenous supply of malonyl-CoA, indispensable for plant polyphenol synthesis, impedes high product titers. Usually, limited malonyl-CoA availability during plant polyphenol production is avoided by supplementing fatty acid synthesis-inhibiting antibiotics such as cerulenin, which are known to increase the intracellular malonyl-CoA pool as a side effect. Motivated by the goal of microbial polyphenol synthesis being independent of such expensive additives, we used rational metabolic engineering approaches to modulate regulation of fatty acid synthesis and flux into the tricarboxylic acid cycle (TCA cycle) in Corynebacterium glutamicum strains capable of flavonoid and stilbene synthesis. Initial experiments showed that sole overexpression of genes coding for the native malonyl-CoA-forming acetyl-CoA carboxylase is not sufficient for increasing polyphenol production in C. glutamicum. Hence, the intracellular acetyl-CoA availability was also increased by reducing the flux into the TCA cycle through reduction of citrate synthase activity. In defined cultivation medium, the constructed C. glutamicum strains accumulated 24 mg·L -1 (0.088 mM) naringenin or 112 mg·L -1 (0.49 mM) resveratrol from glucose without supplementation of phenylpropanoid precursor molecules or any inhibitors of fatty acid synthesis.
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Affiliation(s)
- Lars Milke
- Institute of Bio- and Geosciences, IBG-1: Biotechnology, Forschungszentrum Jülich, Jülich, Germany
| | - Patrícia Ferreira
- Biotempo, Guimarães, Portugal.,Centre of Biological Engineering, University of Minho-Campus de Gualtar, Braga, Portugal
| | - Nicolai Kallscheuer
- Institute of Bio- and Geosciences, IBG-1: Biotechnology, Forschungszentrum Jülich, Jülich, Germany
| | - Adelaide Braga
- Biotempo, Guimarães, Portugal.,Centre of Biological Engineering, University of Minho-Campus de Gualtar, Braga, Portugal
| | - Michael Vogt
- Institute of Bio- and Geosciences, IBG-1: Biotechnology, Forschungszentrum Jülich, Jülich, Germany
| | - Jannick Kappelmann
- Institute of Bio- and Geosciences, IBG-1: Biotechnology, Forschungszentrum Jülich, Jülich, Germany
| | - Joana Oliveira
- Biotempo, Guimarães, Portugal.,Centre of Biological Engineering, University of Minho-Campus de Gualtar, Braga, Portugal
| | - Ana Rita Silva
- Biotempo, Guimarães, Portugal.,Centre of Biological Engineering, University of Minho-Campus de Gualtar, Braga, Portugal
| | - Isabel Rocha
- Biotempo, Guimarães, Portugal.,Centre of Biological Engineering, University of Minho-Campus de Gualtar, Braga, Portugal.,Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Oeiras, Portugal
| | - Michael Bott
- Institute of Bio- and Geosciences, IBG-1: Biotechnology, Forschungszentrum Jülich, Jülich, Germany
| | - Stephan Noack
- Institute of Bio- and Geosciences, IBG-1: Biotechnology, Forschungszentrum Jülich, Jülich, Germany
| | - Nuno Faria
- Biotempo, Guimarães, Portugal.,Centre of Biological Engineering, University of Minho-Campus de Gualtar, Braga, Portugal
| | - Jan Marienhagen
- Institute of Bio- and Geosciences, IBG-1: Biotechnology, Forschungszentrum Jülich, Jülich, Germany
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Burmeister A, Hilgers F, Langner A, Westerwalbesloh C, Kerkhoff Y, Tenhaef N, Drepper T, Kohlheyer D, von Lieres E, Noack S, Grünberger A. A microfluidic co-cultivation platform to investigate microbial interactions at defined microenvironments. LAB ON A CHIP 2018; 19:98-110. [PMID: 30488920 DOI: 10.1039/c8lc00977e] [Citation(s) in RCA: 62] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Interspecies interactions inside microbial communities bear a tremendous diversity of complex chemical processes that are by far not understood. Even for simplified, often synthetic systems, the interactions between two microbes are barely revealed in detail. Here, we present a microfluidic co-cultivation platform for the analysis of growth and interactions inside microbial consortia with single-cell resolution. Our device allows the spatial separation of two different microbial organisms inside adjacent microchambers facilitating sufficient exchange of metabolites via connecting nanochannels. Inside the cultivation chambers cell growth can be observed with high spatio-temporal resolution by live-cell imaging. In contrast to conventional approaches, in which single-cell activity is typically fully masked by the average bulk behavior, the small dimensions of the microfluidic cultivation chambers enable accurate environmental control and observation of cellular interactions with full spatio-temporal resolution. Our method enables one to study phenomena in microbial interactions, such as gene transfer or metabolic cross-feeding. We chose two different microbial model systems to demonstrate the wide applicability of the technology. First, we investigated commensalistic interactions between an industrially relevant l-lysine-producing Corynebacterium glutamicum strain and an l-lysine auxotrophic variant of the same species. Spatially separated co-cultivation of both strains resulted in growth of the auxotrophic strain due to secreted l-lysine supplied by the producer strain. As a second example we investigated bacterial conjugation between Escherichia coli S17-1 and Pseudomonas putida KT2440 cells. We could show that direct cell contact is essential for the successful gene transfer via conjugation and was hindered when cells were spatially separated. The presented device lays the foundation for further studies on contactless and contact-based interactions of natural and synthetic microbial communities.
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Affiliation(s)
- Alina Burmeister
- Institute of Bio- and Geosciences, IBG-1: Biotechnology, Forschungszentrum Jülich, 52425 Jülich, Germany
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Leistra AN, Curtis NC, Contreras LM. Regulatory non-coding sRNAs in bacterial metabolic pathway engineering. Metab Eng 2018; 52:190-214. [PMID: 30513348 DOI: 10.1016/j.ymben.2018.11.013] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2018] [Revised: 10/31/2018] [Accepted: 11/29/2018] [Indexed: 12/11/2022]
Abstract
Non-coding RNAs (ncRNAs) are versatile and powerful controllers of gene expression that have been increasingly linked to cellular metabolism and phenotype. In bacteria, identified and characterized ncRNAs range from trans-acting, multi-target small non-coding RNAs to dynamic, cis-encoded regulatory untranslated regions and riboswitches. These native regulators have inspired the design and construction of many synthetic RNA devices. In this work, we review the design, characterization, and impact of ncRNAs in engineering both native and exogenous metabolic pathways in bacteria. We also consider the opportunities afforded by recent high-throughput approaches for characterizing sRNA regulators and their corresponding networks to showcase their potential applications and impact in engineering bacterial metabolism.
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Affiliation(s)
- Abigail N Leistra
- McKetta Department of Chemical Engineering, University of Texas at Austin, 200 E. Dean Keeton Street Stop C0400, Austin, TX 78712, USA
| | - Nicholas C Curtis
- McKetta Department of Chemical Engineering, University of Texas at Austin, 200 E. Dean Keeton Street Stop C0400, Austin, TX 78712, USA
| | - Lydia M Contreras
- McKetta Department of Chemical Engineering, University of Texas at Austin, 200 E. Dean Keeton Street Stop C0400, Austin, TX 78712, USA.
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40
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Ma Y, Cui Y, Du L, Liu X, Xie X, Chen N. Identification and application of a growth-regulated promoter for improving L-valine production in Corynebacterium glutamicum. Microb Cell Fact 2018; 17:185. [PMID: 30474553 PMCID: PMC6260661 DOI: 10.1186/s12934-018-1031-7] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2018] [Accepted: 11/16/2018] [Indexed: 12/02/2022] Open
Abstract
Background Promoters are commonly used to regulate the expression of specific target genes or operons. Although a series of promoters have been developed in Corynebacterium glutamicum, more precise and unique expression patterns are needed that the current selection of promoters cannot produce. RNA-Seq technology is a powerful tool for helping us to screen out promoters with expected transcriptional strengths. Results The promoter PCP_2836 of an aldehyde dehydrogenase coding gene from Corynebacterium glutamicum CP was identified via RNA-seq and RT-PCR as a growth-regulated promoter. Comparing with the strong constitutive promoter Ptuf, the transcriptional strength of PCP_2836 showed a significant decrease that from about 75 to 8% in the stationary phase. By replacing the native promoters of the aceE and gltA genes with PCP_2836 in the C. glutamicum ATCC 13032-derived l-valine-producing strain AN02, the relative transcriptional levels of the aceE and gltA genes decreased from 1.2 and 1.1 to 0.35 and 0.3, and the activity of their translation products decreased to 43% and 35%, respectively. After 28 h flask fermentation, the final cell density of the obtained strains, GRaceE and GRgltA, exhibited a 7–10% decrease. However, l-valine production increased by 23.9% and 27.3%, and the yield of substrate to product increased 43.8% and 62.5%, respectively. In addition, in the stationary phase, the intracellular citrate levels in GRaceE and GRgltA decreased to 27.0% and 33.6% of AN02, and their intracellular oxaloacetate levels increased to 2.7 and 3.0 times that of AN02, respectively. Conclusions The PCP_2836 promoter displayed a significant difference on its transcriptional strength in different cell growth phases. With using PCP_2836 to replace the native promoters of aceE and gltA genes, both the transcriptional levels of the aceE and gltA genes and the activity of their translation products demonstrated a significant decrease in the stationary phase. Thus, the availability of pyruvate was significantly increased for the synthesis of l-valine without any apparent irreversible negative impacts on cell growth. Use of this promoter can enhance the selectivity and control of gene expression and could serve as a useful research tool for metabolic engineering. ![]() Electronic supplementary material The online version of this article (10.1186/s12934-018-1031-7) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Yuechao Ma
- National and Local United Engineering Lab of Metabolic Control Fermentation Technology, Tianjin University of Science & Technology, Tianjin, 300457, People's Republic of China.,College of Biotechnology, Tianjin University of Science & Technology, No. 29, 13 Main Street, Tianjin Economic and Technological Development Area, Tianjin, 300457, People's Republic of China
| | - Yi Cui
- National and Local United Engineering Lab of Metabolic Control Fermentation Technology, Tianjin University of Science & Technology, Tianjin, 300457, People's Republic of China.,College of Biotechnology, Tianjin University of Science & Technology, No. 29, 13 Main Street, Tianjin Economic and Technological Development Area, Tianjin, 300457, People's Republic of China
| | - Lihong Du
- National and Local United Engineering Lab of Metabolic Control Fermentation Technology, Tianjin University of Science & Technology, Tianjin, 300457, People's Republic of China.,College of Biotechnology, Tianjin University of Science & Technology, No. 29, 13 Main Street, Tianjin Economic and Technological Development Area, Tianjin, 300457, People's Republic of China
| | - Xiaoqian Liu
- National and Local United Engineering Lab of Metabolic Control Fermentation Technology, Tianjin University of Science & Technology, Tianjin, 300457, People's Republic of China.,College of Biotechnology, Tianjin University of Science & Technology, No. 29, 13 Main Street, Tianjin Economic and Technological Development Area, Tianjin, 300457, People's Republic of China
| | - Xixian Xie
- National and Local United Engineering Lab of Metabolic Control Fermentation Technology, Tianjin University of Science & Technology, Tianjin, 300457, People's Republic of China. .,College of Biotechnology, Tianjin University of Science & Technology, No. 29, 13 Main Street, Tianjin Economic and Technological Development Area, Tianjin, 300457, People's Republic of China.
| | - Ning Chen
- National and Local United Engineering Lab of Metabolic Control Fermentation Technology, Tianjin University of Science & Technology, Tianjin, 300457, People's Republic of China. .,College of Biotechnology, Tianjin University of Science & Technology, No. 29, 13 Main Street, Tianjin Economic and Technological Development Area, Tianjin, 300457, People's Republic of China.
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Metabolically engineered Corynebacterium glutamicum for bio-based production of chemicals, fuels, materials, and healthcare products. Metab Eng 2018; 50:122-141. [DOI: 10.1016/j.ymben.2018.07.008] [Citation(s) in RCA: 173] [Impact Index Per Article: 24.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2018] [Revised: 07/17/2018] [Accepted: 07/18/2018] [Indexed: 01/15/2023]
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42
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Lee MJ, Kim P. Recombinant Protein Expression System in Corynebacterium glutamicum and Its Application. Front Microbiol 2018; 9:2523. [PMID: 30416490 PMCID: PMC6213972 DOI: 10.3389/fmicb.2018.02523] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2018] [Accepted: 10/03/2018] [Indexed: 01/01/2023] Open
Abstract
Corynebacterium glutamicum, a soil-derived gram-positive actinobacterium, has been widely used for the production of biochemical molecules such as amino acids (i.e., L-glutamate and L-lysine), nucleic acids, alcohols, and organic acids. The metabolism of the bacterium has been engineered to increase the production of the target biochemical molecule, which requires a cytosolic enzyme expression. As recent demand for new proteinaceous biologics (such as antibodies, growth factors, and hormones) increase, C. glutamicum is attracting industrial interest as a recombinant protein expression host for therapeutic protein production due to the advantages such as low protease activity without endotoxin activity. In this review, we have summarized the recent studies on the heterologous expression of the recombinant protein in C. glutamicum for metabolic engineering, expansion of substrate availability, and recombinant protein secretion. We have also outlined the advances in genetic components such as promoters, surface anchoring systems, and secretory signal sequences in C. glutamicum for effective recombinant protein expression.
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Affiliation(s)
| | - Pil Kim
- Department of Biotechnology, The Catholirc University of Korea, Bucheon, South Korea
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43
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Xu JZ, Wu ZH, Gao SJ, Zhang W. Rational modification of tricarboxylic acid cycle for improving L-lysine production in Corynebacterium glutamicum. Microb Cell Fact 2018; 17:105. [PMID: 29981572 PMCID: PMC6035423 DOI: 10.1186/s12934-018-0958-z] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2018] [Accepted: 07/02/2018] [Indexed: 12/18/2022] Open
Abstract
BACKGROUND Oxaloacetate (OAA) and L-glutamate are essential precursors for the biosynthesis of L-lysine. Reasonable control of all potentially rate-limiting steps, including the precursors supply rate, is of vital importance to maximize the efficiency of L-lysine fermentation process. RESULTS In this paper, we have rationally engineered the tricarboxylic acid (TCA) cycle that increased the carbon yield (from 36.18 to 59.65%), final titer (from 14.47 ± 0.41 to 23.86 ± 2.16 g L-1) and productivity (from 0.30 to 0.50 g L-1 h-1) of L-lysine by Corynebacterium glutamicum in shake-flask fermentation because of improving the OAA and L-glutamate availability. To do this, the phosphoenolpyruvate-pyruvate-oxaloacetate (PEP-pyruvate-OAA) node's genes ppc and pyc were inserted in the genes pck and odx loci, the P1 promoter of the TCA cycle's gene gltA was deleted, and the nature promoter of glutamate dehydrogenase-coding gene gdh was replaced by Ptac-M promoter that resulted in the final engineered strain C. glutamicum JL-69Ptac-M gdh. Furthermore, the suitable addition of biotin accelerates the L-lysine production in strain JL-69Ptac-M gdh because it elastically adjusts the carbon flux for cell growth and precursor supply. The final strain JL-69Ptac-M gdh could produce 181.5 ± 11.74 g L-1 of L-lysine with a productivity of 3.78 g L-1 h-1 and maximal specific production rate (qLys, max.) of 0.73 ± 0.16 g g-1 h-1 in fed-batch culture during adding 2.4 mg L-1 biotin with four times. CONCLUSIONS Our results reveal that sufficient biomass, OAA and L-glutamate are equally important in the development of L-lysine high-yielding strain, and it is the first time to verify that fed-batch biotin plays a positive role in improving L-lysine production.
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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 People’s Republic of China
| | - Ze-Hua Wu
- Research and Development Department, Shandong Shouguang Juneng Golden Corn Co., Ltd., 1199# Xinxing Street, Shouguang, 262700 People’s Republic of China
| | - Shi-Jun Gao
- Research and Development Department, Shandong Shouguang Juneng Golden Corn Co., Ltd., 1199# Xinxing Street, Shouguang, 262700 People’s Republic of China
| | - Weiguo Zhang
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, 1800# Lihu Road, Wuxi, 214122 People’s Republic of China
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Genomic analysis of a Streptomyces tsukubaensis mutant with reduced FR900525 production isolated by selection for S-(2-aminoethyl) l-cysteine resistance. J Biosci Bioeng 2018; 126:580-585. [PMID: 29871825 DOI: 10.1016/j.jbiosc.2018.05.009] [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: 12/02/2017] [Revised: 04/13/2018] [Accepted: 05/11/2018] [Indexed: 11/23/2022]
Abstract
FK506 (tacrolimus), a macrolide compound with immunosuppressant activity, has been shown to be of clinical importance and has been manufactured industrially since 1993 using mutants with high FK506 production ability. These mutants have been developed from the wild strain Streptomyces tsukubaensis No. 9993. FR900525 is one of the by-products of FK506 production, and we previously established a mutant strain that produces reduced levels of FR900525 by selecting for S-(2-aminoethyl) l-cysteine (AEC) resistance. In this study, we conducted a genomic analysis of this strain to identify the changes associated with AEC resistance and to determine its metabolism. Three mutated genes were identified by comparing the genome sequences of the parental strain (A) and the AEC-resistant mutant (B). From the metabolite pathway, it was speculated that citric acid synthase was the most relevant to AEC resistance. To investigate the effect of the mutation in citric acid synthase, we added citric acid, an inhibitor of citric acid synthase, to strain A culture, which induced strain A to exhibit a strain B-like phenotype. We conclude that the mutation in citric acid synthase enhances the carbon flow into aspartic acid, increasing lysine synthesis and resulting in AEC resistance in strain B, as well as high production of FK506 and low production of FR900525.
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Kawaguchi H, Yoshihara K, Hara KY, Hasunuma T, Ogino C, Kondo A. Metabolome analysis-based design and engineering of a metabolic pathway in Corynebacterium glutamicum to match rates of simultaneous utilization of D-glucose and L-arabinose. Microb Cell Fact 2018; 17:76. [PMID: 29773073 PMCID: PMC5956887 DOI: 10.1186/s12934-018-0927-6] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2018] [Accepted: 05/11/2018] [Indexed: 11/24/2022] Open
Abstract
Background l-Arabinose is the second most abundant component of hemicellulose in lignocellulosic biomass, next to d-xylose. However, few microorganisms are capable of utilizing pentoses, and catabolic genes and operons enabling bacterial utilization of pentoses are typically subject to carbon catabolite repression by more-preferred carbon sources, such as d-glucose, leading to a preferential utilization of d-glucose over pentoses. In order to simultaneously utilize both d-glucose and l-arabinose at the same rate, a modified metabolic pathway was rationally designed based on metabolome analysis. Results Corynebacterium glutamicum ATCC 31831 utilized d-glucose and l-arabinose simultaneously at a low concentration (3.6 g/L each) but preferentially utilized d-glucose over l-arabinose at a high concentration (15 g/L each), although l-arabinose and d-glucose were consumed at comparable rates in the absence of the second carbon source. Metabolome analysis revealed that phosphofructokinase and pyruvate kinase were major bottlenecks for d-glucose and l-arabinose metabolism, respectively. Based on the results of metabolome analysis, a metabolic pathway was engineered by overexpressing pyruvate kinase in combination with deletion of araR, which encodes a repressor of l-arabinose uptake and catabolism. The recombinant strain utilized high concentrations of d-glucose and l-arabinose (15 g/L each) at the same consumption rate. During simultaneous utilization of both carbon sources at high concentrations, intracellular levels of phosphoenolpyruvate declined and acetyl-CoA levels increased significantly as compared with the wild-type strain that preferentially utilized d-glucose. These results suggest that overexpression of pyruvate kinase in the araR deletion strain increased the specific consumption rate of l-arabinose and that citrate synthase activity becomes a new bottleneck in the engineered pathway during the simultaneous utilization of d-glucose and l-arabinose. Conclusions Metabolome analysis identified potential bottlenecks in d-glucose and l-arabinose metabolism and was then applied to the following rational metabolic engineering. Manipulation of only two genes enabled simultaneous utilization of d-glucose and l-arabinose at the same rate in metabolically engineered C. glutamicum. This is the first report of rational metabolic design and engineering for simultaneous hexose and pentose utilization without inactivating the phosphotransferase system. Electronic supplementary material The online version of this article (10.1186/s12934-018-0927-6) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Hideo Kawaguchi
- Graduate School of Science, Technology and Innovation, Kobe University, 1-1 Rokkodai, Nada, Kobe, 657-8501, Japan
| | - Kumiko Yoshihara
- Graduate School of Science, Technology and Innovation, Kobe University, 1-1 Rokkodai, Nada, Kobe, 657-8501, Japan
| | - Kiyotaka Y Hara
- Graduate School of Science, Technology and Innovation, Kobe University, 1-1 Rokkodai, Nada, Kobe, 657-8501, Japan.,Department of Environmental and Life Sciences, School of Food and Nutritional Sciences, University of Shizuoka, 52-1 Yada, Suruga, Shizuoka, 422-8526, Japan
| | - Tomohisa Hasunuma
- Graduate School of Science, Technology and Innovation, Kobe University, 1-1 Rokkodai, Nada, Kobe, 657-8501, Japan
| | - Chiaki Ogino
- Department of Chemical Science and Engineering, Graduate School of Engineering, Kobe University, 1-1 Rokkodai, Nada, Kobe, 657-8501, Japan
| | - Akihiko Kondo
- Graduate School of Science, Technology and Innovation, Kobe University, 1-1 Rokkodai, Nada, Kobe, 657-8501, Japan. .,Department of Chemical Science and Engineering, Graduate School of Engineering, Kobe University, 1-1 Rokkodai, Nada, Kobe, 657-8501, Japan. .,Biomass Engineering Research Division, RIKEN, 1-7-22 Suehiro, Turumi, Yokohama, Kanagawa, 230-0045, Japan.
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Kallscheuer N, Marienhagen J. Corynebacterium glutamicum as platform for the production of hydroxybenzoic acids. Microb Cell Fact 2018; 17:70. [PMID: 29753327 PMCID: PMC5948850 DOI: 10.1186/s12934-018-0923-x] [Citation(s) in RCA: 54] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2018] [Accepted: 05/05/2018] [Indexed: 11/10/2022] Open
Abstract
Background Hydroxybenzoic acids are industrially relevant aromatic compounds, which also play key roles in the microbial carbon metabolism, e.g., as precursors for the synthesis of cofactors or metal-chelating molecules. Due to its pronounced resistance to aromatics Corynebacterium glutamicum represents an interesting platform for production of these compounds. Unfortunately, a complex catabolic network for aromatic molecules prevents application of C. glutamicum for microbial production of aromatic compounds other than aromatic amino acids, which cannot be metabolized by this microorganism. Results We completed the construction of the platform strain C. glutamicum DelAro5, in which the deletion of altogether 27 genes in five gene clusters abolished most of the peripheral and central catabolic pathways for aromatic compounds known in this microorganism. The obtained strain was subsequently applied for the production of 2-hydroxybenzoate (salicylate), 3-hydroxybenzoate, 4-hydroxybenzoate and protocatechuate, which all derive from intermediates of the aromatic amino acid-forming shikimate pathway. For an optimal connection of the designed hydroxybenzoate production pathways to the host metabolism, C. glutamicum was additionally engineered towards increased supply of the shikimate pathway substrates erythrose-4-phosphate and phosphoenolpyruvate by manipulation of the glucose transport and key enzymatic activities of the central carbon metabolism. With an optimized genetic background the constructed strains produced 0.01 g/L (0.07 mM) 2-hydroxybenzoate, 0.3 g/L (2.2 mM) 3-hydroxybenzoate, 2.0 g/L (13.0 mM) protocatechuate and 3.3 g/L (23.9 mM) 4-hydroxybenzoate in shaking flasks. Conclusion By abolishing its natural catabolic network for aromatic compounds, C. glutamicum was turned into a versatile microbial platform for aromatics production, which could be exemplarily demonstrated by rapidly engineering this platform organism towards producing four biotechnologically interesting hydroxybenzoates. Production of these compounds was optimized following different metabolic engineering strategies leading to increased precursor availability. The constructed C. glutamicum strains are promising hosts for the production of hydroxybenzoates and other aromatic compounds at larger scales. Electronic supplementary material The online version of this article (10.1186/s12934-018-0923-x) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Nicolai Kallscheuer
- Institute of Bio- and Geosciences, IBG-1: Biotechnology, Forschungszentrum Jülich GmbH, 52425, Jülich, Germany.,Bioeconomy Science Center (BioSC), Forschungszentrum Jülich GmbH, 52425, Jülich, Germany
| | - Jan Marienhagen
- Institute of Bio- and Geosciences, IBG-1: Biotechnology, Forschungszentrum Jülich GmbH, 52425, Jülich, Germany. .,Bioeconomy Science Center (BioSC), Forschungszentrum Jülich GmbH, 52425, Jülich, Germany.
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Golubeva LI, Shupletsov MS, Mashko SV. Metabolic Flux Analysis using 13C Isotopes: III. Significance for Systems Biology and Metabolic Engineering. APPL BIOCHEM MICRO+ 2018. [DOI: 10.1134/s0003683817090058] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Golubeva LI, Shupletsov MS, Mashko SV. Metabolic Flux Analysis Using 13C Isotopes (13C-MFA). 1. Experimental Basis of the Method and the Present State of Investigations. APPL BIOCHEM MICRO+ 2018. [DOI: 10.1134/s0003683817070031] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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Investigation of specific interactions between T7 promoter and T7 RNA polymerase by force spectroscopy using atomic force microscope. Biochem J 2018; 475:319-328. [DOI: 10.1042/bcj20170616] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2017] [Revised: 11/23/2017] [Accepted: 11/29/2017] [Indexed: 12/30/2022]
Abstract
The specific recognition and binding of promoter and RNA polymerase is the first step of transcription initiation in bacteria and largely determines transcription activity. Therefore, direct analysis of the interaction between promoter and RNA polymerase in vitro may be a new strategy for promoter characterization, to avoid interference due to the cell's biophysical condition and other regulatory elements. In the present study, the specific interaction between T7 promoter and T7 RNA polymerase was studied as a model system using force spectroscopy based on atomic force microscope (AFM). The specific interaction between T7 promoter and T7 RNA polymerase was verified by control experiments, and the rupture force in this system was measured as 307.2 ± 6.7 pN. The binding between T7 promoter mutants with various promoter activities and T7 RNA polymerase was analyzed. Interaction information including rupture force, rupture distance and binding percentage were obtained in vitro, and reporter gene expression regulated by these promoters was also measured according to a traditional promoter activity characterization method in vivo. Using correlation analysis, it was found that the promoter strength characterized by reporter gene expression was closely correlated with rupture force and the binding percentage by force spectroscopy. These results indicated that the analysis of the interaction between promoter and RNA polymerase using AFM-based force spectroscopy was an effective and valid approach for the quantitative characterization of promoters.
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Park J, Shin H, Lee SM, Um Y, Woo HM. RNA-guided single/double gene repressions in Corynebacterium glutamicum using an efficient CRISPR interference and its application to industrial strain. Microb Cell Fact 2018; 17:4. [PMID: 29316926 PMCID: PMC5759794 DOI: 10.1186/s12934-017-0843-1] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2017] [Accepted: 12/12/2017] [Indexed: 12/22/2022] Open
Abstract
BACKGROUND The construction of microbial cell factories requires cost-effective and rapid strain development through metabolic engineering. Recently, RNA-guided CRISPR technologies have been developed for metabolic engineering of industrially-relevant host. RESULTS To demonstrate the application of the CRISPR interference (CRISPRi), we developed two-plasmid CRISPRi vectors and applied the CRISPRi in Corynebacterium glutamicum to repress single target genes and double target genes simultaneously. Four-different single genes (the pyc, gltA, idsA, and glgC genes) repressions were successfully performed using the CRISPRi vectors, resulting significant mRNA reductions of the targets compared to a control. Subsequently, the phenotypes for the target gene-repressed strains were analyzed, showing the expected cell growth behaviors with different carbon sources. In addition, double gene repression (the idsA and glgC genes in a different order) by the CRISPRi resulted in an independent gene repression to each target gene simultaneously. To demonstrate an industrial application of the CRISPRi, citrate synthase (CS)-targeting DM1919 (L-lysine producer) strains with a sgRNA-gltA-r showed reduced CS activity, resulting in the improvement of L-lysine yield by 1.39-fold than the parental DM1919 (a lysine producer). CONCLUSIONS Single or double gene repression were successfully performed using the CRISPRi vectors and sequence specific sgRNAs. The CRISPRi can be applied for multiplex metabolic engineering to enhanced lysine production and it will promote the further rapid development of microbial cell factories of C. glutamicum.
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Affiliation(s)
- Jaehyun Park
- Department of Food Science and Biotechnology, Sungkyunkwan University (SKKU), 2066 Seobu-ro, Jangan-gu, Suwon, 16419 Republic of Korea
| | - Hyojung Shin
- Clean Energy Research Center, Korea Institute of Science and Technology, Hwarang-ro 14-gil 5, Seongbuk-gu, Seoul, 02792 Republic of Korea
- Present Address: GyeongSangBukdo Government Public Institute of Health & Environment, 22, Gosugol-gil Geumho-eup, Yeongcheon-si, 38874 Republic of Korea
| | - Sun-Mi Lee
- Clean Energy Research Center, Korea Institute of Science and Technology, Hwarang-ro 14-gil 5, Seongbuk-gu, Seoul, 02792 Republic of Korea
| | - Youngsoon Um
- Clean Energy Research Center, Korea Institute of Science and Technology, Hwarang-ro 14-gil 5, Seongbuk-gu, Seoul, 02792 Republic of Korea
| | - Han Min Woo
- Department of Food Science and Biotechnology, Sungkyunkwan University (SKKU), 2066 Seobu-ro, Jangan-gu, Suwon, 16419 Republic of Korea
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