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Niu J, Yan R, Zhou H, Ma B, Lu Z, Meng F, Lu F, Zhu P. Self-cascade deoxynivalenol detoxification by an artificial enzyme with bifunctions of dehydrogenase and aldo/keto reductase from genome mining. Int J Biol Macromol 2024; 261:129512. [PMID: 38246466 DOI: 10.1016/j.ijbiomac.2024.129512] [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: 10/09/2023] [Revised: 12/05/2023] [Accepted: 01/12/2024] [Indexed: 01/23/2024]
Abstract
Due to the severe health risks for human and animal caused by the intake of toxic deoxynivalenol (DON) derived from Fusarium species, elimination DON in food and feed has been initiated as a critical issue. Enzymatic cascade catalysis by dehydrogenase and aldo-keto reductase represents a fascinating strategy for DON detoxification. Here, one quinone-dpendent alcohol dehydrogenase DADH oxidized DON into less-toxic 3-keto-DON and NADPH-dependent aldo-keto reductase AKR13B3 reduced 3-keto-DON into relatively non-toxic 3-epi-DON were identified from Devosia strain A6-243, indicating that degradation of DON on C3 are two-step sequential cascade processes. To establish the bifunctions, fusion enzyme linking DADH and AKR13B3 was successfully assembled to promote one-step DON degradations with accelerated specific activity and efficiency, resulting 93.29 % of DON removal rate in wheat sample. Three-dimensional simulation analysis revealed that the bifunctional enzyme forms an artificial intramolecular channel to minimize the distance of intermediate from DADH to AKR13B3 for two-step enzymatic reactions, and thereby accelerates this enzymatic process. As the first report of directing single step DON detoxification by an interesting bifunctional artificial enzyme, this work revealed a facile and eco-friendly approach to detoxify DON with application potential and gave valuable insights into execute other mycotoxin detoxification for ensuring food safety.
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Affiliation(s)
- Jiafeng Niu
- College of Food Science and Technology, Nanjing Agricultural University, Nanjing 210095, China
| | - Ruxue Yan
- College of Food Science and Technology, Nanjing Agricultural University, Nanjing 210095, China
| | - Huimin Zhou
- College of Food Science and Technology, Nanjing Agricultural University, Nanjing 210095, China
| | - Bin Ma
- College of Food Science and Technology, Nanjing Agricultural University, Nanjing 210095, China
| | - Zhaoxin Lu
- College of Food Science and Technology, Nanjing Agricultural University, Nanjing 210095, China
| | - Fanqiang Meng
- College of Food Science and Technology, Nanjing Agricultural University, Nanjing 210095, China
| | - Fengxia Lu
- College of Food Science and Technology, Nanjing Agricultural University, Nanjing 210095, China.
| | - Ping Zhu
- College of Food Science and Technology, Nanjing Agricultural University, Nanjing 210095, China.
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2
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Niu J, Ma B, Shen J, Chi H, Zhou H, Lu Z, Lu F, Zhu P. Structure-Guided Steric Hindrance Engineering of Devosia Strain A6-243 Quinone-Dependent Dehydrogenase to Enhance Its Catalytic Efficiency. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2024; 72:549-558. [PMID: 38153089 DOI: 10.1021/acs.jafc.3c07179] [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: 12/29/2023]
Abstract
Deoxynivalenol (DON), the most widely distributed mycotoxin worldwide, causes severe health risks for humans and animals. Quinone-dependent dehydrogenase derived from Devosia strain A6-243 (DADH) can degrade DON into less toxic 3-keto-DON and then aldo-keto reductase AKR13B3 can reduce 3-keto-DON into relatively nontoxic 3-epi-DON. However, the poor catalytic efficiency of DADH made it unsuitable for practical applications, and it has become the rate-limiting step of the two-step enzymatic cascade catalysis. Here, structure-guided steric hindrance engineering was employed to enhance the catalytic efficiency of DADH. After the steric hindrance engineering, the best mutant, V429G/N431V/T432V/L434V/F537A (M5-1), showed an 18.17-fold increase in specific activity and an 11.04-fold increase in catalytic efficiency (kcat/Km) compared with that of wild-type DADH. Structure-based computational analysis provided information on the increased catalytic efficiency in the directions that attenuated steric hindrance, which was attributed to the reshaped substrate-binding pocket with an expanded catalytic binding cavity and a favorable attack distance. Tunnel analysis suggested that reshaping the active cavity by mutation might alter the shape and size of the enzyme tunnels or form one new enzyme tunnel, which might contribute to the improved catalytic efficiency of M5-1. These findings provide a promising strategy to enhance the catalytic efficiency by steric hindrance engineering.
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Affiliation(s)
- Jiafeng Niu
- College of Food Science and Technology, Nanjing Agricultural University, Nanjing 210095, China
| | - Bin Ma
- College of Food Science and Technology, Nanjing Agricultural University, Nanjing 210095, China
| | - Juan Shen
- College of Food Science and Technology, Nanjing Agricultural University, Nanjing 210095, China
| | - Huibing Chi
- College of Food Science and Technology, Nanjing Agricultural University, Nanjing 210095, China
| | - Huimin Zhou
- College of Food Science and Technology, Nanjing Agricultural University, Nanjing 210095, China
| | - Zhaoxin Lu
- College of Food Science and Technology, Nanjing Agricultural University, Nanjing 210095, China
| | - Fengxia Lu
- College of Food Science and Technology, Nanjing Agricultural University, Nanjing 210095, China
| | - Ping Zhu
- College of Food Science and Technology, Nanjing Agricultural University, Nanjing 210095, China
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3
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Li D, Liang G, Mu P, Lin J, Huang J, Guo C, Li Y, Lin R, Jiang J, Wu J, Deng Y, Wen J. Improvement of catalytic activity of sorbose dehydrogenase for deoxynivalenol degradation by rational design. Food Chem 2023; 423:136274. [PMID: 37159968 DOI: 10.1016/j.foodchem.2023.136274] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2022] [Revised: 02/27/2023] [Accepted: 04/27/2023] [Indexed: 05/11/2023]
Abstract
Deoxynivalenol (DON) is the most frequently contaminated mycotoxin in food and feed worldwide, causing significant economic losses and health risks. Physical and chemical detoxification methods are widely used, but they cannot efficiently and specifically remove DON. In the study, the combination of bioinformatics screening and experimental verification confirmed that sorbose dehydrogenase (SDH) can effectively convert DON to 3-keto-DON and a substance that removes four hydrogen atoms for DON. Through rational design, the Vmax of the mutants F103L and F103A were increased by 5 and 23 times, respectively. Furthermore, we identified catalytic sites W218 and D281. SDH and its mutants have broad application conditions, including temperature ranges of 10-45 °C and pH levels of 4-9. Additionally, the half-lives of F103A at 90 °C (processing temperature) and 30 °C (storage temperature) were 60.1 min and 100.5 d, respectively. These results suggest that F103A has significant potential in the detoxification application of DON.
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Affiliation(s)
- Danyang Li
- Guangdong Provincial Key Laboratory of Protein Function and Regulation in Agricultural Organisms, College of Life Sciences, South China Agricultural University, Guangzhou, Guangdong 510642, PR China; Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University, Guangzhou, Guangdong 510642, PR China; Key Laboratory of Zoonosis of Ministry of Agriculture and Rural Affairs, South China Agricultural University, Guangzhou, Guangdong 510642, PR China.
| | - Guoqiang Liang
- Guangdong Provincial Key Laboratory of Protein Function and Regulation in Agricultural Organisms, College of Life Sciences, South China Agricultural University, Guangzhou, Guangdong 510642, PR China; Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University, Guangzhou, Guangdong 510642, PR China; Key Laboratory of Zoonosis of Ministry of Agriculture and Rural Affairs, South China Agricultural University, Guangzhou, Guangdong 510642, PR China.
| | - Peiqiang Mu
- Guangdong Provincial Key Laboratory of Protein Function and Regulation in Agricultural Organisms, College of Life Sciences, South China Agricultural University, Guangzhou, Guangdong 510642, PR China; Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University, Guangzhou, Guangdong 510642, PR China; Key Laboratory of Zoonosis of Ministry of Agriculture and Rural Affairs, South China Agricultural University, Guangzhou, Guangdong 510642, PR China.
| | - Jinquan Lin
- Guangdong Provincial Key Laboratory of Protein Function and Regulation in Agricultural Organisms, College of Life Sciences, South China Agricultural University, Guangzhou, Guangdong 510642, PR China; Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University, Guangzhou, Guangdong 510642, PR China; Key Laboratory of Zoonosis of Ministry of Agriculture and Rural Affairs, South China Agricultural University, Guangzhou, Guangdong 510642, PR China.
| | - Jiarun Huang
- Guangdong Provincial Key Laboratory of Protein Function and Regulation in Agricultural Organisms, College of Life Sciences, South China Agricultural University, Guangzhou, Guangdong 510642, PR China; Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University, Guangzhou, Guangdong 510642, PR China; Key Laboratory of Zoonosis of Ministry of Agriculture and Rural Affairs, South China Agricultural University, Guangzhou, Guangdong 510642, PR China.
| | - Chongwen Guo
- Guangdong Provincial Key Laboratory of Protein Function and Regulation in Agricultural Organisms, College of Life Sciences, South China Agricultural University, Guangzhou, Guangdong 510642, PR China; Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University, Guangzhou, Guangdong 510642, PR China; Key Laboratory of Zoonosis of Ministry of Agriculture and Rural Affairs, South China Agricultural University, Guangzhou, Guangdong 510642, PR China.
| | - Yang Li
- Guangdong Provincial Key Laboratory of Protein Function and Regulation in Agricultural Organisms, College of Life Sciences, South China Agricultural University, Guangzhou, Guangdong 510642, PR China; Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University, Guangzhou, Guangdong 510642, PR China; Key Laboratory of Zoonosis of Ministry of Agriculture and Rural Affairs, South China Agricultural University, Guangzhou, Guangdong 510642, PR China.
| | - Ruqin Lin
- Guangdong Provincial Key Laboratory of Protein Function and Regulation in Agricultural Organisms, College of Life Sciences, South China Agricultural University, Guangzhou, Guangdong 510642, PR China; Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University, Guangzhou, Guangdong 510642, PR China; Key Laboratory of Zoonosis of Ministry of Agriculture and Rural Affairs, South China Agricultural University, Guangzhou, Guangdong 510642, PR China.
| | - Jun Jiang
- Guangdong Provincial Key Laboratory of Protein Function and Regulation in Agricultural Organisms, College of Life Sciences, South China Agricultural University, Guangzhou, Guangdong 510642, PR China; Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University, Guangzhou, Guangdong 510642, PR China; Key Laboratory of Zoonosis of Ministry of Agriculture and Rural Affairs, South China Agricultural University, Guangzhou, Guangdong 510642, PR China.
| | - Jun Wu
- Guangdong Provincial Key Laboratory of Protein Function and Regulation in Agricultural Organisms, College of Life Sciences, South China Agricultural University, Guangzhou, Guangdong 510642, PR China; Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University, Guangzhou, Guangdong 510642, PR China; Key Laboratory of Zoonosis of Ministry of Agriculture and Rural Affairs, South China Agricultural University, Guangzhou, Guangdong 510642, PR China.
| | - Yiqun Deng
- Guangdong Provincial Key Laboratory of Protein Function and Regulation in Agricultural Organisms, College of Life Sciences, South China Agricultural University, Guangzhou, Guangdong 510642, PR China; Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University, Guangzhou, Guangdong 510642, PR China; Key Laboratory of Zoonosis of Ministry of Agriculture and Rural Affairs, South China Agricultural University, Guangzhou, Guangdong 510642, PR China.
| | - Jikai Wen
- Guangdong Provincial Key Laboratory of Protein Function and Regulation in Agricultural Organisms, College of Life Sciences, South China Agricultural University, Guangzhou, Guangdong 510642, PR China; Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University, Guangzhou, Guangdong 510642, PR China; Key Laboratory of Zoonosis of Ministry of Agriculture and Rural Affairs, South China Agricultural University, Guangzhou, Guangdong 510642, PR China.
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4
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Yang H, Yan R, Li Y, Lu Z, Bie X, Zhao H, Lu F, Chen M. Structure-Function Analysis of a Quinone-Dependent Dehydrogenase Capable of Deoxynivalenol Detoxification. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2022; 70:6764-6774. [PMID: 35613468 DOI: 10.1021/acs.jafc.2c01083] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
The pyrroloquinoline quinone (PQQ)-dependent dehydrogenase DepA detoxifies deoxynivalenol (DON) by converting the C3-OH into a keto group. Herein, two crystal structures of DepA and its complex with PQQ were determined, together with biochemical evidence confirming the interactions of DepA with PQQ and DON and revealing a unique tyrosine residue important for substrate selection. Furthermore, four loops over the active site essential for DepA activity were identified, of which three loops were stabilized by PQQ, and the fourth loop invisible in both structures was considered important for binding DON, together constituting a lid for the active site. Preliminary engineering of the loop showed its potential for enzyme improvement. This study provides structural insights into how a PQQ-dependent dehydrogenase is equipped with the function of DON conversion and for the first time shows the necessity of a lid structure for PQQ-dependent dehydrogenase activity, laying foundation for structure-based design to enhance catalysis efficiency.
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Affiliation(s)
- Hua Yang
- College of Food Science and Technology, Nanjing Agricultural University, Nanjing 210095, China
| | - Ruxue Yan
- College of Food Science and Technology, Nanjing Agricultural University, Nanjing 210095, China
| | - Yue Li
- College of Food Science and Technology, Nanjing Agricultural University, Nanjing 210095, China
| | - Zhaoxin Lu
- College of Food Science and Technology, Nanjing Agricultural University, Nanjing 210095, China
| | - Xiaomei Bie
- College of Food Science and Technology, Nanjing Agricultural University, Nanjing 210095, China
| | - Haizhen Zhao
- College of Food Science and Technology, Nanjing Agricultural University, Nanjing 210095, China
| | - Fengxia Lu
- College of Food Science and Technology, Nanjing Agricultural University, Nanjing 210095, China
| | - Meirong Chen
- School of Pharmacy, China Pharmaceutical University, Nanjing 211198, China
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5
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Ito T, Masaki H, Fujita K, Murakami H, Shizuma M, Kiso T, Kiryu T. Identification of Enzymes from Pseudogluconobacter saccharoketogenes Producing d-Glucaric Acid from d-Glucose. Biosci Biotechnol Biochem 2021; 86:56-67. [PMID: 34669931 DOI: 10.1093/bbb/zbab182] [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: 08/19/2021] [Accepted: 10/08/2021] [Indexed: 11/14/2022]
Abstract
In 2004, the US Department of Energy listed d-glucaric acid as one of the top 12 bio-based chemicals and a potential biopolymer building block. In this study, we show that Pseudogluconobacter saccharoketogenes strains can produce d-glucaric acid from d-glucose, although in low yield because of the generation of the byproduct 2-keto-d-gluconic acid in large quantities. To improve d-glucaric acid yield, we generated Rh47-3, a P. saccharoketogenes IFO14464 mutant, which produced d-glucaric acid from d-gluconic acid and d-glucose with 81 and 53 mol% yields, respectively. Furthermore, the key enzymes involved in d-glucaric acid production, alcohol dehydrogenase (Ps-ADH), aldehyde dehydrogenase (Ps-ALDH), and gluconate 2-dehydrogenase (Ps-GADH), were purified and their roles in d-glucaric acid synthesis were evaluated. Ps-ADH and Ps-ALDH catalyzed d-glucaric acid production, which was mediated by d-gluconic acid and d-glucuronic acid pathways. In contrast, Ps-GADH inhibited d-glucaric acid production by promoting the formation of 2-keto-d-gluconic acid from d-glucose.
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Affiliation(s)
- Tetsuya Ito
- ENSUIKO Sugar Refining Co., Ltd., Tokyo, Japan
| | | | - Koki Fujita
- ENSUIKO Sugar Refining Co., Ltd., Tokyo, Japan
| | - Hiromi Murakami
- Osaka Research Institute of Industrial Science and Technology, Osaka, Japan
| | - Motohiro Shizuma
- Osaka Research Institute of Industrial Science and Technology, Osaka, Japan
| | - Taro Kiso
- Osaka Research Institute of Industrial Science and Technology, Osaka, Japan
| | - Takaaki Kiryu
- Osaka Research Institute of Industrial Science and Technology, Osaka, Japan
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6
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Qin Z, Yu S, Chen J, Zhou J. Dehydrogenases of acetic acid bacteria. Biotechnol Adv 2021; 54:107863. [PMID: 34793881 DOI: 10.1016/j.biotechadv.2021.107863] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2021] [Revised: 10/26/2021] [Accepted: 10/26/2021] [Indexed: 12/13/2022]
Abstract
Acetic acid bacteria (AAB) are a group of bacteria that can oxidize many substrates such as alcohols and sugar alcohols and play important roles in industrial biotechnology. A majority of industrial processes that involve AAB are related to their dehydrogenases, including PQQ/FAD-dependent membrane-bound dehydrogenases and NAD(P)+-dependent cytoplasmic dehydrogenases. These cofactor-dependent dehydrogenases must effectively regenerate their cofactors in order to function continuously. For PQQ, FAD and NAD(P)+ alike, regeneration is directly or indirectly related to the electron transport chain (ETC) of AAB, which plays an important role in energy generation for aerobic cell growth. Furthermore, in changeable natural habitats, ETC components of AAB can be regulated so that the bacteria survive in different environments. Herein, the progressive cascade in an application of AAB, including key dehydrogenases involved in the application, regeneration of dehydrogenase cofactors, ETC coupling with cofactor regeneration and ETC regulation, is systematically reviewed and discussed. As they have great application value, a deep understanding of the mechanisms through which AAB function will not only promote their utilization and development but also provide a reference for engineering of other industrial strains.
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Affiliation(s)
- Zhijie Qin
- School of Biotechnology and Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China; National Engineering Laboratory for Cereal Fermentation Technology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China; Jiangsu Provisional Research Center for Bioactive Product Processing Technology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China
| | - Shiqin Yu
- School of Biotechnology and Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China
| | - Jian Chen
- School of Biotechnology and Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China; National Engineering Laboratory for Cereal Fermentation Technology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China; Science Center for Future Foods, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China; Jiangsu Provisional Research Center for Bioactive Product Processing Technology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China
| | - Jingwen Zhou
- School of Biotechnology and Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China; National Engineering Laboratory for Cereal Fermentation Technology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China; Jiangsu Provisional Research Center for Bioactive Product Processing Technology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China.
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7
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Sarmiento-Pavía PD, Sosa-Torres ME. Bioinorganic insights of the PQQ-dependent alcohol dehydrogenases. J Biol Inorg Chem 2021; 26:177-203. [PMID: 33606117 DOI: 10.1007/s00775-021-01852-0] [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: 10/09/2020] [Accepted: 01/07/2021] [Indexed: 12/19/2022]
Abstract
Among the several alcohol dehydrogenases, PQQ-dependent enzymes are mainly found in the α, β, and γ-proteobacteria. These proteins are classified into three main groups. Type I ADHs are localized in the periplasm and contain one Ca2+-PQQ moiety, being the methanol dehydrogenase (MDH) the most representative. In recent years, several lanthanide-dependent MDHs have been discovered exploding the understanding of the natural role of lanthanide ions. Type II ADHs are localized in the periplasm and possess one Ca2+-PQQ moiety and one heme c group. Finally, type III ADHs are complexes of two or three subunits localized in the cytoplasmic membrane and possess one Ca2+-PQQ moiety and four heme c groups, and in one of these proteins, an additional [2Fe-2S] cluster has been discovered recently. From the bioinorganic point of view, PQQ-dependent alcohol dehydrogenases have been revived recently mainly due to the discovery of the lanthanide-dependent enzymes. Here, we review the three types of PQQ-dependent ADHs with special focus on their structural features and electron transfer processes. The PQQ-Alcohol dehydrogenases are classified into three main groups. Type I and type II ADHs are located in the periplasm, while type III ADHs are in the cytoplasmic membrane. ADH-I have a Ca-PQQ or a Ln-PQQ, ADH-II a Ca-PQQ and one heme-c and ADH-III a Ca-PQQ and four hemes-c. This review focuses on their structural features and electron transfer processes.
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Affiliation(s)
- Pedro D Sarmiento-Pavía
- Facultad de Química, Universidad Nacional Autónoma de México, Cd. Universitaria, Coyoacán, 04510, Ciudad de México, Mexico
| | - Martha E Sosa-Torres
- Facultad de Química, Universidad Nacional Autónoma de México, Cd. Universitaria, Coyoacán, 04510, Ciudad de México, Mexico.
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8
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Gandomkar S, Rocha R, Sorgenfrei FA, Montero LM, Fuchs M, Kroutil W. PQQ-dependent Dehydrogenase Enables One-pot Bi-enzymatic Enantio-convergent Biocatalytic Amination of Racemic sec-Allylic Alcohols. ChemCatChem 2021; 13:1290-1293. [PMID: 33777250 PMCID: PMC7986696 DOI: 10.1002/cctc.202001707] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2020] [Revised: 11/20/2020] [Indexed: 12/28/2022]
Abstract
The asymmetric amination of secondary racemic allylic alcohols bears several challenges like the reactivity of the bi-functional substrate/product as well as of the α,β-unsaturated ketone intermediate in an oxidation-reductive amination sequence. Heading for a biocatalytic amination cascade with a minimal number of enzymes, an oxidation step was implemented relying on a single PQQ-dependent dehydrogenase with low enantioselectivity. This enzyme allowed the oxidation of both enantiomers at the expense of iron(III) as oxidant. The stereoselective amination of the α,β-unsaturated ketone intermediate was achieved with transaminases using 1-phenylethylamine as formal reducing agent as well as nitrogen source. Choosing an appropriate transaminase, either the (R)- or (S)-enantiomer was obtained in optically pure form (>98 % ee). The enantio-convergent amination of the racemic allylic alcohols to one single allylic amine enantiomer was achieved in one pot in a sequential cascade.
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Affiliation(s)
| | - Raquel Rocha
- Institute of ChemistryUniversity of Graz, NAWI Graz8010GrazAustria
| | - Frieda A. Sorgenfrei
- Institute of ChemistryUniversity of Graz, NAWI Graz8010GrazAustria
- Austrian Centre of Industrial Biotechnology c/oUniversity of Graz8010GrazAustria
| | | | - Michael Fuchs
- Institute of ChemistryUniversity of Graz, NAWI Graz8010GrazAustria
| | - Wolfgang Kroutil
- Institute of ChemistryUniversity of Graz, NAWI Graz8010GrazAustria
- Field of Excellence BioHealthUniversity of Graz8010GrazAustria
- BioTechMed Graz8010GrazAustria
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9
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Aylward FO, Santoro AE. Heterotrophic Thaumarchaea with Small Genomes Are Widespread in the Dark Ocean. mSystems 2020; 5:e00415-20. [PMID: 32546674 PMCID: PMC7300363 DOI: 10.1128/msystems.00415-20] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2020] [Accepted: 05/28/2020] [Indexed: 01/01/2023] Open
Abstract
The Thaumarchaeota is a diverse archaeal phylum comprising numerous lineages that play key roles in global biogeochemical cycling, particularly in the ocean. To date, all genomically characterized marine thaumarchaea are reported to be chemolithoautotrophic ammonia oxidizers. In this study, we report a group of putatively heterotrophic marine thaumarchaea (HMT) with small genome sizes that is globally abundant in the mesopelagic, apparently lacking the ability to oxidize ammonia. We assembled five HMT genomes from metagenomic data and show that they form a deeply branching sister lineage to the ammonia-oxidizing archaea (AOA). We identify this group in metagenomes from mesopelagic waters in all major ocean basins, with abundances reaching up to 6% of that of AOA. Surprisingly, we predict the HMT have small genomes of ∼1 Mbp, and our ancestral state reconstruction indicates this lineage has undergone substantial genome reduction compared to other related archaea. The genomic repertoire of HMT indicates a versatile metabolism for aerobic chemoorganoheterotrophy that includes a divergent form III-a RuBisCO, a 2M respiratory complex I that has been hypothesized to increase energetic efficiency, and a three-subunit heme-copper oxidase complex IV that is absent from AOA. We also identify 21 pyrroloquinoline quinone (PQQ)-dependent dehydrogenases that are predicted to supply reducing equivalents to the electron transport chain and are among the most highly expressed HMT genes, suggesting these enzymes play an important role in the physiology of this group. Our results suggest that heterotrophic members of the Thaumarchaeota are widespread in the ocean and potentially play key roles in global chemical transformations.IMPORTANCE It has been known for many years that marine Thaumarchaeota are abundant constituents of dark ocean microbial communities, where their ability to couple ammonia oxidation and carbon fixation plays a critical role in nutrient dynamics. In this study, we describe an abundant group of putatively heterotrophic marine Thaumarchaeota (HMT) in the ocean with physiology distinct from those of their ammonia-oxidizing relatives. HMT lack the ability to oxidize ammonia and fix carbon via the 3-hydroxypropionate/4-hydroxybutyrate pathway but instead encode a form III-a RuBisCO and diverse PQQ-dependent dehydrogenases that are likely used to conserve energy in the dark ocean. Our work expands the scope of known diversity of Thaumarchaeota in the ocean and provides important insight into a widespread marine lineage.
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Affiliation(s)
- Frank O Aylward
- Department of Biological Sciences, Virginia Tech, Blacksburg, Virginia, USA
| | - Alyson E Santoro
- Department of Ecology, Evolution and Marine Biology, University of California, Santa Barbara, California, USA
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10
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He WJ, Shi MM, Yang P, Huang T, Zhao Y, Wu AB, Dong WB, Li HP, Zhang JB, Liao YC. A quinone-dependent dehydrogenase and two NADPH-dependent aldo/keto reductases detoxify deoxynivalenol in wheat via epimerization in a Devosia strain. Food Chem 2020; 321:126703. [PMID: 32247890 DOI: 10.1016/j.foodchem.2020.126703] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2019] [Revised: 03/26/2020] [Accepted: 03/26/2020] [Indexed: 11/16/2022]
Abstract
The Fusarium mycotoxin deoxynivalenol (DON) is typically controlled by fungicides. Here, we report DON detoxification using enzymes from the highly active Devosia strain D6-9 which degraded DON at 2.5 μg/min/108 cells. Strain D6-9 catabolized DON to 3-keto-DON and 3-epi-DON, completely removing DON in wheat. Genome analysis of three Devosia strains (D6-9, D17, and D13584), with strain D6-9 transcriptomes, identified three genes responsible for DON epimerization. One gene encodes a quinone-dependent DON dehydrogenase QDDH which oxidized DON into 3-keto-DON. Two genes encode the NADPH-dependent aldo/keto reductases AKR13B2 and AKR6D1 that convert 3-keto-DON into 3-epi-DON. Recombinant proteins expressed in Escherichia coli efficiently degraded DON in wheat grains. Molecular docking and site-directed mutagenesis revealed that residues S497, E499, and E535 function in QDDH's DON-oxidizing activity. These results advance potential microbial and enzymatic elimination of DON in agricultural samples and lend insight into the underlying mechanisms and molecular evolution of DON detoxification.
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Affiliation(s)
- Wei-Jie He
- Molecular Biotechnology Laboratory of Triticeae Crops, Huazhong Agricultural University, Wuhan 430070, People's Republic of China; Hubei Engineering and Technology Research Center of Wheat/Wheat Disease Biology Research Station for Central China, Food Crops Institute, Hubei Academy of Agricultural Sciences, Wuhan 430064, People's Republic of China
| | - Meng-Meng Shi
- Molecular Biotechnology Laboratory of Triticeae Crops, Huazhong Agricultural University, Wuhan 430070, People's Republic of China; College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, People's Republic of China
| | - Peng Yang
- Molecular Biotechnology Laboratory of Triticeae Crops, Huazhong Agricultural University, Wuhan 430070, People's Republic of China; College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, People's Republic of China
| | - Tao Huang
- Molecular Biotechnology Laboratory of Triticeae Crops, Huazhong Agricultural University, Wuhan 430070, People's Republic of China; College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, People's Republic of China
| | - Yue Zhao
- Molecular Biotechnology Laboratory of Triticeae Crops, Huazhong Agricultural University, Wuhan 430070, People's Republic of China; College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, People's Republic of China
| | - Ai-Bo Wu
- Key Laboratory of Food Safety Research Institute for Nutritional Sciences, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, People's Republic of China
| | - Wu-Bei Dong
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, People's Republic of China
| | - He-Ping Li
- Molecular Biotechnology Laboratory of Triticeae Crops, Huazhong Agricultural University, Wuhan 430070, People's Republic of China; College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, People's Republic of China
| | - Jing-Bo Zhang
- Molecular Biotechnology Laboratory of Triticeae Crops, Huazhong Agricultural University, Wuhan 430070, People's Republic of China; College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, People's Republic of China.
| | - Yu-Cai Liao
- Molecular Biotechnology Laboratory of Triticeae Crops, Huazhong Agricultural University, Wuhan 430070, People's Republic of China; College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, People's Republic of China.
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11
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Carere J, Hassan YI, Lepp D, Zhou T. The enzymatic detoxification of the mycotoxin deoxynivalenol: identification of DepA from the DON epimerization pathway. Microb Biotechnol 2018; 11:1106-1111. [PMID: 29148251 PMCID: PMC6196400 DOI: 10.1111/1751-7915.12874] [Citation(s) in RCA: 59] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2017] [Revised: 09/18/2017] [Accepted: 09/20/2017] [Indexed: 01/10/2023] Open
Abstract
The biological detoxification of mycotoxins, including deoxynivalenol (DON), represents a very promising approach to address the challenging problem of cereal grain contamination. The recent discovery of Devosia mutans 17-2-E-8 (Devosia spp. 17-2-E-8), a bacterial isolate capable of transforming DON to the non-toxic stereoisomer 3-epi-deoxynivalenol, along with earlier reports of bacterial species capable of oxidizing DON to 3-keto-DON, has generated interest in the possible mechanism and enzyme(s) involved. An understanding of these details could pave the way for novel strategies to manage this widely present toxin. It was previously shown that DON epimerization proceeds through a two-step biocatalysis. Significantly, this report describes the identification of the first enzymatic step in this pathway. The enzyme, a dehydrogenase responsible for the selective oxidation of DON at the C3 position, was shown to readily convert DON to 3-keto-DON, a less toxic intermediate in the DON epimerization pathway. Furthermore, this study provides insights into the PQQ dependence of the enzyme. This enzyme may be part of a feasible strategy for DON mitigation within the near future.
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Affiliation(s)
- Jason Carere
- Guelph Research and Development CentreAgriculture and Agri‐Food Canada93 Stone Road WestGuelphONN1G 5C9Canada
| | - Yousef I. Hassan
- Guelph Research and Development CentreAgriculture and Agri‐Food Canada93 Stone Road WestGuelphONN1G 5C9Canada
| | - Dion Lepp
- Guelph Research and Development CentreAgriculture and Agri‐Food Canada93 Stone Road WestGuelphONN1G 5C9Canada
| | - Ting Zhou
- Guelph Research and Development CentreAgriculture and Agri‐Food Canada93 Stone Road WestGuelphONN1G 5C9Canada
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12
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Detheridge AP, Griffith GW, Hopper DJ. Genome Sequence Analysis of Two Pseudomonas putida Strains to Identify a 17-Hydroxylase Putatively Involved in Sparteine Degradation. Curr Microbiol 2018; 75:1649-1654. [PMID: 30267141 PMCID: PMC6208669 DOI: 10.1007/s00284-018-1573-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2018] [Accepted: 08/29/2018] [Indexed: 11/28/2022]
Abstract
Two strains of Pseudomonas putida, Psp-LUP and Psp-SPAR, capable of growth on the quinolizidine alkaloids, lupanine and sparteine respectively, were studied here. We report the isolation of Psp-SPAR and the complete genome sequencing of both bacteria. Both were confirmed to belong to P. putida, Psp-LUP close to the type isolate of the species (NBRC14164T) and Psp-SPAR close to strains KT2440 and F1. Psp-SPAR did not grow on lupanine but did contain a gene encoding a putative quinolizidine-17-hydroxylase peptide which exhibited high similarity (76%identity) to the lupanine-17-hydroxylase characterised from Psp-LUP.
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Affiliation(s)
- Andrew P Detheridge
- Institute of Biological, Environmental and Rural Sciences, Aberystwyth University, Aberystwyth, Ceredigion, Wales, UK
| | - Gareth W Griffith
- Institute of Biological, Environmental and Rural Sciences, Aberystwyth University, Aberystwyth, Ceredigion, Wales, UK.
| | - David J Hopper
- Institute of Biological, Environmental and Rural Sciences, Aberystwyth University, Aberystwyth, Ceredigion, Wales, UK
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13
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Ikemoto K, Mori S, Mukai K. Synthesis and crystal structure of pyrroloquinoline quinol (PQQH2) and pyrroloquinoline quinone (PQQ). ACTA CRYSTALLOGRAPHICA SECTION B-STRUCTURAL SCIENCE CRYSTAL ENGINEERING AND MATERIALS 2017; 73:489-497. [DOI: 10.1107/s2052520617002281] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/20/2016] [Accepted: 02/10/2017] [Indexed: 11/10/2022]
Abstract
Pyrroloquinoline quinone (PQQ) is a water-soluble quinone compound first identified as a cofactor of alcohol- and glucose-dehydrogenases (ADH and GDH) in bacteria. For example, in the process of ADH reaction, alcohol is oxidized to the corresponding aldehyde, and inversely PQQ is reduced to pyrroloquinoline quinol (PQQH2). PQQ and PQQH2molecules play an important role as a cofactor in ADH and GDH reactions. However, crystal structure analysis has not been performed for PQQ and PQQH2. In the present study, the synthesis of PQQH2powder crystals was performed under air, by utilizing vitamin C as a reducing agent. By reacting a trihydrate of disodium salt of PQQ (PQQNa2·3H2O) with excess vitamin C in H2O at 293 and 343 K, yellowish brown and black powder crystals of PQQH2having different properties were obtained in high yield, respectively. The former was PQQH2trihydrate (PQQH2·3H2O) and the latter was PQQH2anhydrate (PQQH2). Furthermore, sodium-free red PQQ powder crystal (a monohydrate of PQQ, PQQ·H2O) was prepared by the reaction of PQQNa2·3H2O with HCl in H2O. Single crystals of PQQH2and PQQ were prepared from Me2SO/CH3CN mixed solvent, and we have succeeded in the crystal structure analyses of PQQH2and PQQ for the first time.
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