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Nalivaiko EY, Seebeck FP. A Rhodanese-Like Enzyme that Catalyzes Desulfination of Ergothioneine Sulfinic Acid. Chembiochem 2024; 25:e202400131. [PMID: 38597743 DOI: 10.1002/cbic.202400131] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2024] [Revised: 03/12/2024] [Indexed: 04/11/2024]
Abstract
Many actinobacterial species contain structural genes for iron-dependent enzymes that consume ergothioneine by way of O2-dependent dioxygenation. The resulting product ergothioneine sulfinic acid is stable under physiological conditions unless cleavage to sulfur dioxide and trimethyl histidine is catalyzed by a dedicated desulfinase. This report documents that two types of ergothioneine sulfinic desulfinases have evolved by convergent evolution. One type is related to metal-dependent decarboxylases while the other belongs to the superfamily of rhodanese-like enzymes. Pairs of ergothioneine dioxygenases (ETDO) and ergothioneine sulfinic acid desulfinase (ETSD) occur in thousands of sequenced actinobacteria, suggesting that oxidative ergothioneine degradation is a common activity in this phylum.
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Affiliation(s)
- Egor Y Nalivaiko
- Department of Chemistry, University of Basel, Mattenstrasse 24a, Basel, 4002, Switzerland
| | - Florian P Seebeck
- Department of Chemistry, University of Basel, Mattenstrasse 24a, Basel, 4002, Switzerland
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2
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Fan Y, Wu S, Shi J, Li X, Yang Y, Feng Y, Xue S. The catalytic mechanism of direction-dependent interactions for 2,3-dihydroxybenzoate decarboxylase. Appl Microbiol Biotechnol 2023; 107:7451-7462. [PMID: 37851105 DOI: 10.1007/s00253-023-12813-9] [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: 05/11/2023] [Revised: 09/14/2023] [Accepted: 09/21/2023] [Indexed: 10/19/2023]
Abstract
Benzoic acid decarboxylases offer an elegant alternative to CO2 fixation by reverse reaction-carboxylation, which is named the bio-Kolbe-Schmitt reaction, but they are unfavorable to carboxylation. Enhancing the carboxylation efficiency of reversible benzoic acid decarboxylases is restricted by the unexplained carboxylation mechanisms. The direction of reversible enzyme catalytic reactions depends on whether catalytic residues at the active center of the enzyme are protonated, which is subjected by the pH. Therefore, the forward and reverse reactions could be separated at different pH values. Reversible 2,3-dihydroxybenzoate acid decarboxylase undergoes decarboxylation at pH 5.0 and carboxylation at pH 8.6. However, it is unknown whether the interaction of enzymes with substrates and products in the forward and reverse reactions can be exploited to improve the catalytic activity of reversible enzymes in the unfavorable direction. Here, we identify a V-shaped tunnel of 2,3-dihydroxybenzoic acid decarboxylase from Aspergillus oryzae (2,3-DHBD_Ao) through which the substrate travels in the enzyme, and demonstrate that the side chain conformation of a tyrosine residue controls the entry and exit of substrate/product during reversible reactions. Together with the kinetic studies of the mutants, it is clarified that interactions between substrate/product traveling through the enzyme tunnel in 2,3-DHBD_Ao are direction-dependent. These results enrich the understanding of the interactions of substrates/products with macromolecular reversible enzymes in different reaction directions, thereby demonstrating a possible path for engineering decarboxylases with higher carboxylation efficiency. KEY POINTS: • The residue Trp23 of 2,3-DHBD_Ao served as a switch to control the entry and exit of catechol • A V-shaped tunnel of 2,3-DHBD_Ao for decarboxylation and carboxylation reactions was identified • The results provide a promising strategy for engineering decarboxylases with direction-dependent residues inside the substrate/product traveling tunnel of the enzyme.
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Affiliation(s)
- Yan Fan
- School of Bioengineering, Dalian University of Technology, Dalian, 116024, China
- Guangdong Provincial Key Laboratory of Lingnan Specialty Food Science and Technology, Zhongkai University of Agriculture and Engineering, Guangzhou, 510225, China
- Department of Biotechnology, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, China
| | - Sijin Wu
- Laboratory of Molecular Modeling and Design, State Key Laboratory of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, China
| | - Jianping Shi
- School of Bioengineering, Dalian University of Technology, Dalian, 116024, China
| | - Xianglong Li
- School of Bioengineering, Dalian University of Technology, Dalian, 116024, China
| | - Yongliang Yang
- School of Bioengineering, Dalian University of Technology, Dalian, 116024, China
| | - Yanbin Feng
- School of Bioengineering, Dalian University of Technology, Dalian, 116024, China.
| | - Song Xue
- School of Bioengineering, Dalian University of Technology, Dalian, 116024, China.
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Zhou Y, Zhang S, Huang S, Fan X, Su H, Tan T. De novo biosynthesis of 2-hydroxyterephthalic acid, the monomer for high-performance hydroxyl modified PBO fiber, by enzymatic Kolbe-Schmitt reaction with CO 2 fixation. BIOTECHNOLOGY FOR BIOFUELS AND BIOPRODUCTS 2023; 16:179. [PMID: 37986026 PMCID: PMC10662693 DOI: 10.1186/s13068-023-02413-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/01/2023] [Accepted: 10/18/2023] [Indexed: 11/22/2023]
Abstract
BACKGROUND High-performance poly(p-phenylenebenzobisoxazole) (PBO) fiber, with excellent mechanical properties (stiffness, strength, and toughness), high thermal stability combined and light weight, are widely employed in automotive and aerospace composites, body armor and sports goods. Hydroxyl modified PBO (HPBO) fiber shows better photostability and interfacial shear strength. 2-Hydroxyterephthalic acid (2-HTA), the monomer for the HPBO fiber, is usually synthesized by chemical method, which has poor space selectivity and high energy consumption. The enzymatic Kolbe-Schmitt reaction, which carboxylates phenolic substrates to generate hydroxybenzoic acids with bicarbonate/CO2, was applied in de novo biosynthesis of 2-HTA with CO2 fixation. RESULTS The biosynthesis of 2-HTA was achieved by the innovative application of hydroxybenzoic acid (de)carboxylases to carboxylation of 3-hydroxybenzoic acid (3-HBA) at the para-position of the benzene carboxyl group, known as enzymatic Kolbe-Schmitt reaction. 2,3-Dihydroxybenzoic acid decarboxylase from Aspergillus oryzae (2,3-DHBD_Ao) were expressed in recombinant E. coli and showed highest activity. The yield of 2-HTA was 108.97 ± 2.21 μg/L/mg protein in the whole-cell catalysis. In addition, two amino acid substitutions, F27G and T62A, proved to be of great help in improving 2,3-DHBD activity. The double site mutation F27G/T62A increased the production of 2-HTA in the whole-cell catalysis by 24.7-fold, reaching 2.69 ± 0.029 mg/L/mg protein. Moreover, de novo biosynthetic pathway of 2-HTA was constructed by co-expression of 2,3-DHBD_Ao and 3-hydroxybenzoate synthase Hyg5 in S. cerevisiae S288C with Ura3, Aro7 and Trp3 knockout. The engineered strain synthesized 45.40 ± 0.28 μg/L 2-HTA at 36 h in the CO2 environment. CONCLUSIONS De novo synthesis of 2-HTA has been achieved, using glucose as a raw material to generate shikimic acid, chorismic acid, and 3-HBA, and finally 2-HTA. We demonstrate the strong potential of hydroxybenzoate (de)carboxylase to produce terephthalic acid and its derivatives with CO2 fixation.
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Affiliation(s)
- Yali Zhou
- National Energy R&D Center for Biorefnery, Beijing Key Lab of Bioprocess, College of Life Science and Technology, Beijing University of Chemical Technology, No. 15 North 3Rd Ring Rd East, Beijing, 100029, People's Republic of China
| | - Shiding Zhang
- National Energy R&D Center for Biorefnery, Beijing Key Lab of Bioprocess, College of Life Science and Technology, Beijing University of Chemical Technology, No. 15 North 3Rd Ring Rd East, Beijing, 100029, People's Republic of China
| | - Shiming Huang
- National Energy R&D Center for Biorefnery, Beijing Key Lab of Bioprocess, College of Life Science and Technology, Beijing University of Chemical Technology, No. 15 North 3Rd Ring Rd East, Beijing, 100029, People's Republic of China
| | - Xuanhe Fan
- National Energy R&D Center for Biorefnery, Beijing Key Lab of Bioprocess, College of Life Science and Technology, Beijing University of Chemical Technology, No. 15 North 3Rd Ring Rd East, Beijing, 100029, People's Republic of China
| | - Haijia Su
- National Energy R&D Center for Biorefnery, Beijing Key Lab of Bioprocess, College of Life Science and Technology, Beijing University of Chemical Technology, No. 15 North 3Rd Ring Rd East, Beijing, 100029, People's Republic of China
| | - Tianwei Tan
- National Energy R&D Center for Biorefnery, Beijing Key Lab of Bioprocess, College of Life Science and Technology, Beijing University of Chemical Technology, No. 15 North 3Rd Ring Rd East, Beijing, 100029, People's Republic of China.
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Cui M, Wei Y, Tan J, Li T, Jiao X, Zhou Y. Biochemical investigations of polyphenol degradation enzymes in the phototrophic bacterium Rubrivivax gelatinosus. Biochem J 2023; 480:1753-1766. [PMID: 37903000 DOI: 10.1042/bcj20230387] [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: 09/13/2023] [Revised: 10/27/2023] [Accepted: 10/30/2023] [Indexed: 11/01/2023]
Abstract
Phloroglucinol (1,3,5-trihydroxybenzene) is an important intermediate in the degradation of flavonoids and tannins by anaerobic bacteria. Recent studies have shed light on the enzymatic mechanism of phloroglucinol degradation in butyrate-forming anaerobic bacteria, including environmental and intestinal bacteria such as Clostridium and Flavonifractor sp. Phloroglucinol degradation gene clusters have also been identified in other metabolically diverse bacteria, although the polyphenol metabolism of these microorganisms remain largely unexplored. Here, we describe biochemical studies of polyphenol degradation enzymes found in the purple non-sulfur bacterium Rubrivivax gelatinosus IL144, an anaerobic photoheterotroph reported to utilize diverse organic compounds as carbon sources for growth. In addition to the phloroglucinol reductase and dihydrophloroglucinol cyclohydrolase that catalyze phloroglucinol degradation, we characterize a Mn2+-dependent phloretin hydrolase that catalyzes the cleavage of phloretin into phloroglucinol and phloretic acid. We also report a Mn2+-dependent decarboxylase (DeC) that catalyzes the reversible decarboxylation of 2,4,6-trihydroxybenzoate to form phloroglucinol. A bioinformatics search led to the identification of DeC homologs in diverse soil and gut bacteria, and biochemical studies of a DeC homolog from the human gut bacterium Flavonifractor plautii demonstrated that it is also a 2,4,6-trihydroxybenzoate decarboxylase. Our study expands the range of enzymatic mechanisms for phloroglucinol formation, and provides further biochemical insight into polyphenol metabolism in the anaerobic biosphere.
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Affiliation(s)
- Mengyu Cui
- Jiangsu Key Laboratory of Zoonosis, Yangzhou University, Yangzhou 225009, China
- Key Laboratory of Prevention and Control of Biological Hazard Factors (Animal Origin) for Agrifood Safety and Quality, Ministry of Agriculture of China, Yangzhou University, Yangzhou 225009, China
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou 225009, Jiangsu Province, China
| | - Yifeng Wei
- Singapore Institute of Food and Biotechnology Innovation, Agency for Science, Technology and Research (A*STAR), Singapore 138669, Singapore
| | - Jason Tan
- Singapore Institute of Food and Biotechnology Innovation, Agency for Science, Technology and Research (A*STAR), Singapore 138669, Singapore
| | - Tong Li
- Jiangsu Key Laboratory of Zoonosis, Yangzhou University, Yangzhou 225009, China
- Key Laboratory of Prevention and Control of Biological Hazard Factors (Animal Origin) for Agrifood Safety and Quality, Ministry of Agriculture of China, Yangzhou University, Yangzhou 225009, China
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou 225009, Jiangsu Province, China
| | - Xinan Jiao
- Jiangsu Key Laboratory of Zoonosis, Yangzhou University, Yangzhou 225009, China
- Key Laboratory of Prevention and Control of Biological Hazard Factors (Animal Origin) for Agrifood Safety and Quality, Ministry of Agriculture of China, Yangzhou University, Yangzhou 225009, China
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou 225009, Jiangsu Province, China
| | - Yan Zhou
- Jiangsu Key Laboratory of Zoonosis, Yangzhou University, Yangzhou 225009, China
- Key Laboratory of Prevention and Control of Biological Hazard Factors (Animal Origin) for Agrifood Safety and Quality, Ministry of Agriculture of China, Yangzhou University, Yangzhou 225009, China
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou 225009, Jiangsu Province, China
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Song Y, Hu Y, Li J, Wang L, Jing W, Zhang L, Dai Y, Jia S, Meng X, Zhang H. Site-Directed Mutation of Salicylate Decarboxylase Gene and Mechanism of Ginkgo Acid Decarboxylation. Protein J 2023; 42:1-13. [PMID: 36527585 DOI: 10.1007/s10930-022-10086-1] [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] [Accepted: 11/18/2022] [Indexed: 12/23/2022]
Abstract
Ginkgo seed is an important Chinese medicine and food resource in China, but the toxicity of ginkgo acid in it limits its application. Previous studies have found that salicylic acid decarboxylase (Sdc) has a decarboxylation degradation effect on ginkgo acid. In order to improve the decarboxylation ability of Sdc to Ginkgo acid, 11 residues of the Sdc around the substrate (salicylic acid) were determined as mutation targets according to the analysis of crystal structure of Sdc (PDB ID:6JQX), from Trichosporon moniliiforme WU-0401, and a total of 30 single point mutant enzymes and one compound mutant enzyme were obtained. With Ginkgo acid C15:1 as the substrate, it was found from activity assay that Sdc-Y64T and Sdc-P191A had higher decarboxylation activity, which increased by 105.18% and 116.74% compared with that of wild type Sdc, respectively. The optimal pH for Sdc Y64T and Sdc-P191A to decarboxylate Ginkgo acid C15:1 was 5.5, which is the same as the wild type Sdc. The optimal temperature of Sdc-P191A was 50 °C, which was consistent with that of the wild type Sdc, but the optimal temperature of the mutant Sdc-Y64T was 40 °C, which was 10 °C lower than that of wild type Sdc.
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Affiliation(s)
- Yuanyuan Song
- Tianjin Key Laboratory of Industrial Microbiology, Teda Campus, Tianjin University of Science and Technology, No. 9 of 13th Street, Tianjin Economic and Technological Development Zone TEDA, Tianjin, 300457, People's Republic of China
| | - Yanying Hu
- Jining University, Xingtan Road, New District, Qufu City, Shandong Province, People's Republic of China
| | - Jiaxin Li
- Tianjin Key Laboratory of Industrial Microbiology, Teda Campus, Tianjin University of Science and Technology, No. 9 of 13th Street, Tianjin Economic and Technological Development Zone TEDA, Tianjin, 300457, People's Republic of China
| | - Lin Wang
- Tianjin Key Laboratory of Industrial Microbiology, Teda Campus, Tianjin University of Science and Technology, No. 9 of 13th Street, Tianjin Economic and Technological Development Zone TEDA, Tianjin, 300457, People's Republic of China
| | - Wenjie Jing
- Tianjin Key Laboratory of Industrial Microbiology, Teda Campus, Tianjin University of Science and Technology, No. 9 of 13th Street, Tianjin Economic and Technological Development Zone TEDA, Tianjin, 300457, People's Republic of China
| | - Liming Zhang
- Tianjin Key Laboratory of Industrial Microbiology, Teda Campus, Tianjin University of Science and Technology, No. 9 of 13th Street, Tianjin Economic and Technological Development Zone TEDA, Tianjin, 300457, People's Republic of China
| | - Yujie Dai
- Tianjin Key Laboratory of Industrial Microbiology, Teda Campus, Tianjin University of Science and Technology, No. 9 of 13th Street, Tianjin Economic and Technological Development Zone TEDA, Tianjin, 300457, People's Republic of China.
| | - Shiru Jia
- Tianjin Key Laboratory of Industrial Microbiology, Teda Campus, Tianjin University of Science and Technology, No. 9 of 13th Street, Tianjin Economic and Technological Development Zone TEDA, Tianjin, 300457, People's Republic of China
| | - Xuan Meng
- Tianjin Key Laboratory of Industrial Microbiology, Teda Campus, Tianjin University of Science and Technology, No. 9 of 13th Street, Tianjin Economic and Technological Development Zone TEDA, Tianjin, 300457, People's Republic of China
| | - Huitu Zhang
- Tianjin Key Laboratory of Industrial Microbiology, Teda Campus, Tianjin University of Science and Technology, No. 9 of 13th Street, Tianjin Economic and Technological Development Zone TEDA, Tianjin, 300457, People's Republic of China
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A Combined Computational–Experimental Study on the Substrate Binding and Reaction Mechanism of Salicylic Acid Decarboxylase. Catalysts 2022. [DOI: 10.3390/catal12121577] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Salicylic acid decarboxylase (SDC) from the amidohydrolase superfamily (AHS) catalyzes the reversible decarboxylation of salicylic acid to form phenol. In this study, the substrate binding mode and reaction mechanism of SDC were investigated using computational and crystallographic methods. Quantum chemical calculations show that the enzyme follows the general mechanism of AHS decarboxylases. Namely, the reaction begins with proton transfer from a metal-coordinated aspartic acid residue (Asp298 in SDC) to the C1 of salicylic acid, which is followed by the C–C bond cleavage, to generate the phenol product and release CO2. Interestingly, the calculations show that SDC is a Mg-dependent enzyme rather than the previously proposed Zn-dependent, and the substrate is shown to be bidentately coordinated to the metal center in the catalysis, which is also different from the previous proposal. These predictions are corroborated by the crystal structure of SDC solved in complex with the substrate analogue 2-nitrophenol. The mechanistic insights into SDC in the present study provide important information for the rational design of the enzyme.
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Wang D, Zheng P, Chen P, Dan Wu. Engineering an α-L-rhamnosidase from Aspergillus niger for efficient conversion of rutin substrate. Biochem Eng J 2022. [DOI: 10.1016/j.bej.2022.108572] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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