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Zhang DK, Song KY, Yan YQ, Zheng JT, Xu J, Da LT, Xu MJ. Structural and mechanistic investigations on CC bond forming α-oxoamine synthase allowing L-glutamate as substrate. Int J Biol Macromol 2024; 268:131696. [PMID: 38642679 DOI: 10.1016/j.ijbiomac.2024.131696] [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: 01/07/2024] [Revised: 03/23/2024] [Accepted: 04/17/2024] [Indexed: 04/22/2024]
Abstract
Carbon‑carbon (C-C) bonds serve as the fundamental structural backbone of organic molecules. As a critical CC bond forming enzyme, α-oxoamine synthase is responsible for the synthesis of α-amino ketones by performing the condensation reaction between amino acids and acyl-CoAs. We previously identified an α-oxoamine synthase (AOS), named as Alb29, involved in albogrisin biosynthesis in Streptomyces albogriseolus MGR072. This enzyme belongs to the α-oxoamine synthase family, a subfamily under the pyridoxal 5'-phosphate (PLP) dependent enzyme superfamily. In this study, we report the crystal structures of Alb29 bound to PLP and L-Glu, which provide the atomic-level structural insights into the substrate recognition by Alb29. We discover that Alb29 can catalyze the amino transformation from L-Gln to L-Glu, besides the condensation of L-Glu with β-methylcrotonyl coenzyme A. Subsequent structural analysis has revealed that one flexible loop in Alb29 plays an important role in both amino transformation and condensation. Based on the crystal structure of the S87G mutant in the loop region, we capture two distinct conformations of the flexible loop in the active site, compared with the wild-type Alb29. Our study offers valuable insights into the catalytic mechanism underlying substrate recognition of Alb29.
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Affiliation(s)
- Dai-Ke Zhang
- Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Centre for Systems Biomedicine, Shanghai Jiao Tong University, Shanghai 200240, P. R. China
| | - Kai-Yuan Song
- Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Centre for Systems Biomedicine, Shanghai Jiao Tong University, Shanghai 200240, P. R. China
| | - Ya-Qian Yan
- Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Centre for Systems Biomedicine, Shanghai Jiao Tong University, Shanghai 200240, P. R. China
| | - Jian-Ting Zheng
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, P. R. China
| | - Jun Xu
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, P. R. China
| | - Lin-Tai Da
- Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Centre for Systems Biomedicine, Shanghai Jiao Tong University, Shanghai 200240, P. R. China.
| | - Min-Juan Xu
- Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Centre for Systems Biomedicine, Shanghai Jiao Tong University, Shanghai 200240, P. R. China.
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2
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Zhu LL, Yang Q, Wang DG, Niu L, Pan Z, Li S, Li YZ, Zhang W, Wu C. Deciphering the Biosynthesis and Physiological Function of 5-Methylated Pyrazinones Produced by Myxobacteria. ACS CENTRAL SCIENCE 2024; 10:555-568. [PMID: 38559311 PMCID: PMC10979478 DOI: 10.1021/acscentsci.3c01363] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/02/2023] [Revised: 12/25/2023] [Accepted: 01/16/2024] [Indexed: 04/04/2024]
Abstract
Myxobacteria are a prolific source of secondary metabolites with sheer chemical complexity, intriguing biosynthetic enzymology, and diverse biological activities. In this study, we report the discovery, biosynthesis, biomimetic total synthesis, physiological function, structure-activity relationship, and self-resistance mechanism of the 5-methylated pyrazinone coralinone from a myxobacterium Corallococcus exiguus SDU70. A single NRPS/PKS gene corA was genetically and biochemically demonstrated to orchestrate coralinone, wherein the integral PKS part is responsible for installing the 5-methyl group. Intriguingly, coralinone exacerbated cellular aggregation of myxobacteria grown in liquid cultures by enhancing the secretion of extracellular matrix, and the 5-methylation is indispensable for the alleged activity. We provided an evolutionary landscape of the corA-associated biosynthetic gene clusters (BGCs) distributed in the myxobacterial realm, revealing the divergent evolution for the diversity-oriented biosynthesis of 5-alkyated pyrazinones. This phylogenetic contextualization provoked us to identify corB located in the proximity of corA as a self-resistance gene. CorB was experimentally verified to be a protease that hydrolyzes extracellular proteins to antagonize the agglutination-inducing effect of coralinone. Overall, we anticipate these findings will provide new insights into the chemical ecology of myxobacteria and lay foundations for the maximal excavation of these largely underexplored resources.
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Affiliation(s)
| | | | | | - Luo Niu
- State Key Laboratory of Microbial Technology,
Institute of Microbial Technology, Shandong
University, 266237 Qingdao, P.R. China
| | - Zhuo Pan
- State Key Laboratory of Microbial Technology,
Institute of Microbial Technology, Shandong
University, 266237 Qingdao, P.R. China
| | - Shengying Li
- State Key Laboratory of Microbial Technology,
Institute of Microbial Technology, Shandong
University, 266237 Qingdao, P.R. China
| | - Yue-Zhong Li
- State Key Laboratory of Microbial Technology,
Institute of Microbial Technology, Shandong
University, 266237 Qingdao, P.R. China
| | - Wei Zhang
- State Key Laboratory of Microbial Technology,
Institute of Microbial Technology, Shandong
University, 266237 Qingdao, P.R. China
| | - Changsheng Wu
- State Key Laboratory of Microbial Technology,
Institute of Microbial Technology, Shandong
University, 266237 Qingdao, P.R. China
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3
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Liu XX, Wang Y, Zhang JH, Lu YF, Dong ZX, Yue C, Huang XQ, Zhang SP, Li DD, Yao LG, Tang CD. Engineering Escherichia coli for high-yielding 2,5-Dimethylpyrazine synthesis from L-Threonine by reconstructing metabolic pathways and enhancing cofactors regeneration. BIOTECHNOLOGY FOR BIOFUELS AND BIOPRODUCTS 2024; 17:44. [PMID: 38500189 PMCID: PMC10949639 DOI: 10.1186/s13068-024-02487-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2023] [Accepted: 03/04/2024] [Indexed: 03/20/2024]
Abstract
2,5-Dimethylpyrazine (2,5-DMP) is important pharmaceutical raw material and food flavoring agent. Recently, engineering microbes to produce 2,5-DMP has become an attractive alternative to chemical synthesis approach. In this study, metabolic engineering strategies were used to optimize the modified Escherichia coli BL21 (DE3) strain for efficient synthesis of 2,5-DMP using L-threonine dehydrogenase (EcTDH) from Escherichia coli BL21, NADH oxidase (EhNOX) from Enterococcus hirae, aminoacetone oxidase (ScAAO) from Streptococcus cristatus and L-threonine transporter protein (EcSstT) from Escherichia coli BL21, respectively. We further optimized the reaction conditions for synthesizing 2,5-DMP. In optimized conditions, the modified strain can convert L-threonine to obtain 2,5-DMP with a yield of 2897.30 mg/L. Therefore, the strategies used in this study contribute to the development of high-level cell factories for 2,5-DMP.
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Affiliation(s)
- Xin-Xin Liu
- Henan Provincial Engineering Laboratory of Insect Bio-Reactor, Henan International Joint Laboratory of Insect Biology and Henan Key Laboratory of Insect Biology in Funiu Mountain, Nanyang Normal University, 1638 Wolong Road, Nanyang, Henan, 473061, People's Republic of China
| | - Yao Wang
- Henan Provincial Engineering Laboratory of Insect Bio-Reactor, Henan International Joint Laboratory of Insect Biology and Henan Key Laboratory of Insect Biology in Funiu Mountain, Nanyang Normal University, 1638 Wolong Road, Nanyang, Henan, 473061, People's Republic of China
| | - Jian-Hui Zhang
- Postdoctoral Innovation Practice Base, She Dian Lao Jiu Co. Ltd., 2 Liquor Avenue, Nanyang, Henan, 473300, People's Republic of China
| | - Yun-Feng Lu
- Henan Provincial Engineering Laboratory of Insect Bio-Reactor, Henan International Joint Laboratory of Insect Biology and Henan Key Laboratory of Insect Biology in Funiu Mountain, Nanyang Normal University, 1638 Wolong Road, Nanyang, Henan, 473061, People's Republic of China
| | - Zi-Xing Dong
- Henan Provincial Engineering Laboratory of Insect Bio-Reactor, Henan International Joint Laboratory of Insect Biology and Henan Key Laboratory of Insect Biology in Funiu Mountain, Nanyang Normal University, 1638 Wolong Road, Nanyang, Henan, 473061, People's Republic of China
| | - Chao Yue
- Henan Provincial Engineering Laboratory of Insect Bio-Reactor, Henan International Joint Laboratory of Insect Biology and Henan Key Laboratory of Insect Biology in Funiu Mountain, Nanyang Normal University, 1638 Wolong Road, Nanyang, Henan, 473061, People's Republic of China
| | - Xian-Qing Huang
- College of Food Science and Technology, Henan Agricultural University, 63 Agricultural Road, Zhengzhou, Henan, 450002, People's Republic of China
| | - Si-Pu Zhang
- Henan Academy of Agricultural Sciences, Zhengzhou, 450002, People's Republic of China
| | - Dan-Dan Li
- Henan Provincial Engineering Laboratory of Insect Bio-Reactor, Henan International Joint Laboratory of Insect Biology and Henan Key Laboratory of Insect Biology in Funiu Mountain, Nanyang Normal University, 1638 Wolong Road, Nanyang, Henan, 473061, People's Republic of China.
| | - Lun-Guang Yao
- Henan Provincial Engineering Laboratory of Insect Bio-Reactor, Henan International Joint Laboratory of Insect Biology and Henan Key Laboratory of Insect Biology in Funiu Mountain, Nanyang Normal University, 1638 Wolong Road, Nanyang, Henan, 473061, People's Republic of China.
| | - Cun-Duo Tang
- Henan Provincial Engineering Laboratory of Insect Bio-Reactor, Henan International Joint Laboratory of Insect Biology and Henan Key Laboratory of Insect Biology in Funiu Mountain, Nanyang Normal University, 1638 Wolong Road, Nanyang, Henan, 473061, People's Republic of China.
- Postdoctoral Innovation Practice Base, She Dian Lao Jiu Co. Ltd., 2 Liquor Avenue, Nanyang, Henan, 473300, People's Republic of China.
- College of Food Science and Technology, Henan Agricultural University, 63 Agricultural Road, Zhengzhou, Henan, 450002, People's Republic of China.
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Ashley B, Baslé A, Sajjad M, el Ashram A, Kelis P, Marles-Wright J, Campopiano DJ. Versatile Chemo-Biocatalytic Cascade Driven by a Thermophilic and Irreversible C-C Bond-Forming α-Oxoamine Synthase. ACS SUSTAINABLE CHEMISTRY & ENGINEERING 2023; 11:7997-8002. [PMID: 37266354 PMCID: PMC10230504 DOI: 10.1021/acssuschemeng.3c00243] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Revised: 04/24/2023] [Indexed: 06/03/2023]
Abstract
We report a chemo-biocatalytic cascade for the synthesis of substituted pyrroles, driven by the action of an irreversible, thermostable, pyridoxal 5'-phosphate (PLP)-dependent, C-C bond-forming biocatalyst (ThAOS). The ThAOS catalyzes the Claisen-like condensation between various amino acids and acyl-CoA substrates to generate a range of α-aminoketones. These products are reacted with β-keto esters in an irreversible Knorr pyrrole reaction. The determination of the 1.6 Å resolution crystal structure of the PLP-bound form of ThAOS lays the foundation for future engineering and directed evolution. This report establishes the AOS family as useful and versatile C-C bond-forming biocatalysts.
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Affiliation(s)
- Ben Ashley
- School
of Chemistry, University of Edinburgh, Joseph Black Building, David Brewster
Road, Edinburgh EH9 3FJ, United Kingdom
| | - Arnaud Baslé
- Biosciences
Institute, Faculty of Medical Sciences, Newcastle University, Newcastle
upon Tyne NE2 4HH, United Kingdom
| | - Mariyah Sajjad
- School
of Chemistry, University of Edinburgh, Joseph Black Building, David Brewster
Road, Edinburgh EH9 3FJ, United Kingdom
| | - Ahmed el Ashram
- School
of Chemistry, University of Edinburgh, Joseph Black Building, David Brewster
Road, Edinburgh EH9 3FJ, United Kingdom
| | - Panayiota Kelis
- School
of Chemistry, University of Edinburgh, Joseph Black Building, David Brewster
Road, Edinburgh EH9 3FJ, United Kingdom
| | - Jon Marles-Wright
- Biosciences
Institute, Faculty of Medical Sciences, Newcastle University, Newcastle
upon Tyne NE2 4HH, United Kingdom
| | - Dominic J. Campopiano
- School
of Chemistry, University of Edinburgh, Joseph Black Building, David Brewster
Road, Edinburgh EH9 3FJ, United Kingdom
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5
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Combined analysis of silk synthesis and hemolymph amino acid metabolism reveal key roles for glycine in increasing silkworm silk yields. Int J Biol Macromol 2022; 209:1760-1770. [PMID: 35490768 DOI: 10.1016/j.ijbiomac.2022.04.143] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2022] [Revised: 04/08/2022] [Accepted: 04/19/2022] [Indexed: 11/20/2022]
Abstract
Rearing silkworms (Bombyx mori) using formula feed has revolutionized traditional mulberry feed strategies. However, low silk production efficiencies persist and have caused bottlenecks, hindering the industrial application of formula feed sericulture. Here, we investigated the effects of formula feed amino acid composition on silk yields. We showed that imbalanced amino acids reduced DNA proliferation, decreased Fib-H, Fib-L, and P25 gene expression, and caused mild autophagy in the posterior silk gland, reducing cocoon shell weight and ratio. When compared with mulberry leaves, Gly, Ala, Ser, and Tyr percentages of total amino acids in formula feed were decreased by 5.26%, while Glu and Arg percentages increased by 9.56%. These changes increased uric acid and several amino acids levels in the hemolymph of silkworms on formula feed. Further analyses showed that Gly and Thr (important synthetic Gly sources) increased silk yields, with Gly increasing amino acid conversion efficiencies to silk protein, and reducing urea levels in hemolymph. Also, Gly promoted endomitotic DNA synthesis in silk gland cells via phosphoinositide 3-kinase (PI3K)/Akt/target of rapamycin (TOR) signaling. In this study, we highlighted the important role of Gly in regulating silk yields in silkworms.
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Attanayake G, Mao G, Walker KD. Semibiocatalytic Approach toward Regioisomerically Enriched Ethyl Dimethylpyrazines Important in Flavor Industries. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2021; 69:15314-15324. [PMID: 34874714 DOI: 10.1021/acs.jafc.1c05786] [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: 06/13/2023]
Abstract
Alkylpyrazines are important heterocyclic compounds used as flavorants in food and beverage industries. In this study, a regioselective semibiocatalytic process was developed to synthesize 2-ethyl-3,5-dimethylpyrazine (235-EDMP) over its 3-ethyl-2,5-dimethyl pyrazine (325-EDMP) isomer and vice versa. We initially explored how sterics could direct the coupling orientations between diamines and diketones to access 235- or 325-EDMP selectively. Also, the physical parameters of the reaction conditions were changed, such as reduced temperature, the order-of-addition of the reactants, and supplementation with chiral zeolites to template the orientation of the coupling partners to direct the reaction regiochemistry. Each reaction trial resulted in 50:50 mixtures of the EDMP isomers. An alternative approach was explored to control the regioselectivity of the reactions; α-hydroxy ketones replaced the diketones as the electrophilic coupling reactant used in previous trial experiments. The hydroxy ketone reactants were made biocatalytically with pyruvate decarboxylase. The coupling reaction between 2-hydroxypentan-3-one and propane-1,2-diamine resulted in the desired 235-EDMP at >70% (∼77 mg) relative to 325-EDMP in the mixture. The 3-hydroxypentan-2-one congener was biocatalyzed and reacted with propane-1,2-diamine as a proof of principle to synthesize 325-EDMP (∼60% relative abundance, ∼73 mg) over 235-EDMP. These results suggested a mechanism that was directed by the hydroxy ketone electrophilicity and the sterics at the diamine nucleophilic centers.
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Affiliation(s)
- Gayanthi Attanayake
- Department of Chemistry, Michigan State University, East Lansing, Michigan 48824, United States
| | - Guohong Mao
- Conagen, Inc., Bedford, Massachusetts 01730, United States
| | - Kevin D Walker
- Department of Chemistry, Michigan State University, East Lansing, Michigan 48824, United States
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan 48824, United States
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