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Li N, Wang Y, Meng Y, Lv Y, Zhang S, Wei S, Ma P, Hu Y, Lin H. Structural and functional characterization of a new thermophilic-like OYE from Aspergillus flavus. Appl Microbiol Biotechnol 2024; 108:134. [PMID: 38229304 DOI: 10.1007/s00253-023-12963-w] [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: 08/28/2023] [Revised: 10/19/2023] [Accepted: 10/24/2023] [Indexed: 01/18/2024]
Abstract
Old yellow enzymes (OYEs) have been proven as powerful biocatalysts for the asymmetric reduction of activated alkenes. Fungi appear to be valuable sources of OYEs, but most of the fungal OYEs are unexplored. To expand the OYEs toolbox, a new thermophilic-like OYE (AfOYE1) was identified from Aspergillus flavus strain NRRL3357. The thermal stability analysis showed that the T1/2 of AfOYE1 was 60 °C, and it had the optimal temperature at 45 °C. Moreover, AfOYE1 exhibited high reduction activity in a wide pH range (pH 5.5-8.0). AfOYE1 could accept cyclic enones, acrylamide, nitroalkenes, and α, β-unsaturated aldehydes as substrates and had excellent enantioselectivity toward prochiral alkenes (> 99% ee). Interestingly, an unexpected (S)-stereoselectivity bioreduction toward 2-methylcyclohexenone was observed. The further crystal structure of AfOYE1 revealed that the "cap" region from Ala132 to Thr182, the loop of Ser316 to Gly325, α short helix of Arg371 to Gln375, and the C-terminal "finger" structure endow the catalytic cavity of AfOYE1 quite deep and narrow, and flavin mononucleotide (FMN) heavily buried at the bottom of the active site tunnel. Furthermore, the catalytic mechanism of AfOYE1 was also investigated, and the results confirmed that the residues His211, His214, and Tyr216 compose its catalytic triad. This newly identified thermophilic-like OYE would thus be valuable for asymmetric alkene hydrogenation in industrial processes. KEY POINTS: A new thermophilic-like OYE AfOYE1 was identified from Aspergillus flavus, and the T1/2 of AfOYE1 was 60 °C AfOYE1 catalyzed the reduction of 2-methylcyclohexenone with (S)-stereoselectivity The crystal structure of AfOYE1 was revealedv.
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Affiliation(s)
- Na Li
- College of Biological Engineering, Henan Unsssiversity of Technology, 100 Lianhua Street, Zhengzhou, 450001, Henan, China
| | - Yuan Wang
- College of Biological Engineering, Henan Unsssiversity of Technology, 100 Lianhua Street, Zhengzhou, 450001, Henan, China
| | - Yinyin Meng
- Henan International Joint Laboratory of Biocatalysis and Bio-Based Products, College of Life Sciences, Henan Agricultural University, 95 Wenhua Road, Zhengzhou, 450002, China
| | - Yangyong Lv
- College of Biological Engineering, Henan Unsssiversity of Technology, 100 Lianhua Street, Zhengzhou, 450001, Henan, China
| | - Shuaibing Zhang
- College of Biological Engineering, Henan Unsssiversity of Technology, 100 Lianhua Street, Zhengzhou, 450001, Henan, China
| | - Shan Wei
- College of Biological Engineering, Henan Unsssiversity of Technology, 100 Lianhua Street, Zhengzhou, 450001, Henan, China
| | | | - Yuansen Hu
- College of Biological Engineering, Henan Unsssiversity of Technology, 100 Lianhua Street, Zhengzhou, 450001, Henan, China.
| | - Hui Lin
- Henan International Joint Laboratory of Biocatalysis and Bio-Based Products, College of Life Sciences, Henan Agricultural University, 95 Wenhua Road, Zhengzhou, 450002, China.
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2
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Li Y, Liu C, Han X, Sheng R, Bao L, Lei L, Wu Y, Li Q, Zhang Y, Zhang J, Wang W, Zhang Y, Li S, Wang C, Wei X, Wang J, Peng Z, Xu Y, Si S. The novel small molecule E0924G dually regulates bone formation and bone resorption through activating the PPARδ signaling pathway to prevent bone loss in ovariectomized rats and senile mice. Bioorg Chem 2024; 147:107364. [PMID: 38636434 DOI: 10.1016/j.bioorg.2024.107364] [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: 01/14/2024] [Revised: 03/24/2024] [Accepted: 04/10/2024] [Indexed: 04/20/2024]
Abstract
Osteoporosis is particularly prevalent among postmenopausal women and the elderly. In the present study, we investigated the effect of the novel small molecule E0924G (N-(4-methoxy-pyridine-2-yl)-5-methylfuran-2-formamide) on osteoporosis. E0924G significantly increased the protein expression levels of osteoprotegerin (OPG) and runt-related transcription factor 2 (RUNX2), and thus significantly promoted osteogenesis in MC3T3-E1 cells. E0924G also significantly decreased osteoclast differentiation and inhibited bone resorption and F-actin ring formation in receptor activator of NF-κB ligand (RANKL)-induced osteoclasts from RAW264.7 macrophages. Importantly, oral administration of E0924G in both ovariectomized (OVX) rats and SAMP6 senile mice significantly increased bone mineral density and decreased bone loss compared to OVX controls or SAMR1 mice. Further mechanistic studies showed that E0924G could bind to and then activate peroxisome proliferator-activated receptor delta (PPARδ), and the pro-osteoblast effect and the inhibition of osteoclast differentiation induced by E0924G were significantly abolished when PPARδ was knocked down or inhibited. In conclusion, these data strongly suggest that E0924G has the potential to prevent OVX-induced and age-related osteoporosis by dual regulation of bone formation and bone resorption through activation of the PPARδ signaling pathway.
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Affiliation(s)
- Yining Li
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, NHC Key Laboratory of Biotechnology for Microbial Drugs, National Center for Screening Novel Microbial Drugs, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College (CAMS & PUMC), Tiantan Xili 1#, Beijing 100050, China
| | - Chao Liu
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, NHC Key Laboratory of Biotechnology for Microbial Drugs, National Center for Screening Novel Microbial Drugs, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College (CAMS & PUMC), Tiantan Xili 1#, Beijing 100050, China
| | - Xiaowan Han
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, NHC Key Laboratory of Biotechnology for Microbial Drugs, National Center for Screening Novel Microbial Drugs, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College (CAMS & PUMC), Tiantan Xili 1#, Beijing 100050, China
| | - Ren Sheng
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, NHC Key Laboratory of Biotechnology for Microbial Drugs, National Center for Screening Novel Microbial Drugs, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College (CAMS & PUMC), Tiantan Xili 1#, Beijing 100050, China
| | - Li Bao
- Department of Orthopedics, Beijing Friendship Hospital, Capital Medical University, Beijing, China
| | - Lijuan Lei
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, NHC Key Laboratory of Biotechnology for Microbial Drugs, National Center for Screening Novel Microbial Drugs, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College (CAMS & PUMC), Tiantan Xili 1#, Beijing 100050, China
| | - Yexiang Wu
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, NHC Key Laboratory of Biotechnology for Microbial Drugs, National Center for Screening Novel Microbial Drugs, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College (CAMS & PUMC), Tiantan Xili 1#, Beijing 100050, China
| | - Quanjie Li
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, NHC Key Laboratory of Biotechnology for Microbial Drugs, National Center for Screening Novel Microbial Drugs, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College (CAMS & PUMC), Tiantan Xili 1#, Beijing 100050, China
| | - Yuyan Zhang
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, NHC Key Laboratory of Biotechnology for Microbial Drugs, National Center for Screening Novel Microbial Drugs, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College (CAMS & PUMC), Tiantan Xili 1#, Beijing 100050, China
| | - Jing Zhang
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, NHC Key Laboratory of Biotechnology for Microbial Drugs, National Center for Screening Novel Microbial Drugs, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College (CAMS & PUMC), Tiantan Xili 1#, Beijing 100050, China
| | - Weizhi Wang
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, NHC Key Laboratory of Biotechnology for Microbial Drugs, National Center for Screening Novel Microbial Drugs, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College (CAMS & PUMC), Tiantan Xili 1#, Beijing 100050, China
| | - Yuhao Zhang
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, NHC Key Laboratory of Biotechnology for Microbial Drugs, National Center for Screening Novel Microbial Drugs, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College (CAMS & PUMC), Tiantan Xili 1#, Beijing 100050, China
| | - Shunwang Li
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, NHC Key Laboratory of Biotechnology for Microbial Drugs, National Center for Screening Novel Microbial Drugs, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College (CAMS & PUMC), Tiantan Xili 1#, Beijing 100050, China
| | - Chenyin Wang
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, NHC Key Laboratory of Biotechnology for Microbial Drugs, National Center for Screening Novel Microbial Drugs, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College (CAMS & PUMC), Tiantan Xili 1#, Beijing 100050, China
| | - Xinwei Wei
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, NHC Key Laboratory of Biotechnology for Microbial Drugs, National Center for Screening Novel Microbial Drugs, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College (CAMS & PUMC), Tiantan Xili 1#, Beijing 100050, China
| | - Jingrui Wang
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, NHC Key Laboratory of Biotechnology for Microbial Drugs, National Center for Screening Novel Microbial Drugs, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College (CAMS & PUMC), Tiantan Xili 1#, Beijing 100050, China
| | - Zonggen Peng
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, NHC Key Laboratory of Biotechnology for Microbial Drugs, National Center for Screening Novel Microbial Drugs, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College (CAMS & PUMC), Tiantan Xili 1#, Beijing 100050, China.
| | - Yanni Xu
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, NHC Key Laboratory of Biotechnology for Microbial Drugs, National Center for Screening Novel Microbial Drugs, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College (CAMS & PUMC), Tiantan Xili 1#, Beijing 100050, China.
| | - Shuyi Si
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, NHC Key Laboratory of Biotechnology for Microbial Drugs, National Center for Screening Novel Microbial Drugs, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College (CAMS & PUMC), Tiantan Xili 1#, Beijing 100050, China.
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Gu Y, Li T, Zhou NY. Redundant and scattered genetic determinants for coumarin biodegradation in Pseudomonas sp. strain NyZ480. Appl Environ Microbiol 2023; 89:e0110923. [PMID: 37815346 PMCID: PMC10617510 DOI: 10.1128/aem.01109-23] [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: 06/30/2023] [Accepted: 08/18/2023] [Indexed: 10/11/2023] Open
Abstract
Coumarin (COU) is both a naturally derived phytotoxin and a synthetic pollutant which causes hepatotoxicity in susceptible humans. Microbes have potentials in COU biodegradation; however, its underlying genetic determinants remain unknown. Pseudomonas sp. strain NyZ480, a robust COU degrader, has been isolated and proven to grow on COU as its sole carbon source. In this study, five homologs of xenobiotic reductase A scattered throughout the chromosome of strain NyZ480 were identified, which catalyzed the conversion of COU to dihydrocoumarin (DHC) in vitro. Phylogenetic analysis indicated that these COU reductases belong to different subgroups of the old yellow enzyme family. Moreover, two hydrolases (CouB1 and CouB2) homologous to the 3,4-dihydrocoumarin hydrolase in the fluorene degradation were found to accelerate the generation of melilotic acid (MA) from DHC. CouC, a new member from the group A flavin monooxygenase, was heterologously expressed and purified, catalyzing the hydroxylation of MA to produce 3-(2,3-dihydroxyphenyl)propionate (DHPP). Gene deletion and complementation of couC indicated that couC played an essential role in the COU catabolism in strain NyZ480, considering that the genes involved in the downstream catabolism of DHPP have been characterized (Y. Xu and N. Y. Zhou, Appl Environ Microbiol 86:e02385-19, 2020) and homologous catabolic cluster exists in strain NyZ480. This study elucidated the genetic determinants for complete degradation of COU by Pseudomonas sp. strain NyZ480.IMPORTANCECoumarin (COU) is a phytochemical widely distributed in the plant kingdom and also artificially produced as an ingredient for personal care products. Hence, the environmental occurrence of COU has been reported in different places. Toxicologically, COU was proven hepatotoxic to individuals with mutations in the CYP2A6 gene and listed as a group 3 carcinogen by the International Agency for Research on Cancer and thus has raised increasing concerns. Until now, different physicochemical methods have been developed for the removal of COU, whereas their practical applications were hampered due to high cost and the risk of secondary contamination. In this study, genetic evidence and biochemical characterization of the COU degradation by Pseudomonas sp. strain NyZ480 are presented. With the gene and strain resources provided here, better managements of the hazards that humans face from COU could be achieved, and the possible microbiota-plant interaction mediated by the COU-utilizing rhizobacteria could also be investigated.
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Affiliation(s)
- Yichao Gu
- State Key Laboratory of Microbial Metabolism & School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
- Joint International Research Laboratory of Metabolic and Developmental Sciences, Shanghai Jiao Tong University, Shanghai, China
| | - Tao Li
- State Key Laboratory of Microbial Metabolism & School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
- Joint International Research Laboratory of Metabolic and Developmental Sciences, Shanghai Jiao Tong University, Shanghai, China
| | - Ning-Yi Zhou
- State Key Laboratory of Microbial Metabolism & School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
- Joint International Research Laboratory of Metabolic and Developmental Sciences, Shanghai Jiao Tong University, Shanghai, China
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4
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Breukelaar W, Polidori N, Singh A, Daniel B, Glueck SM, Gruber K, Kroutil W. Mechanistic Insights into the Ene-Reductase-Catalyzed Promiscuous Reduction of Oximes to Amines. ACS Catal 2023; 13:2610-2618. [PMID: 36846821 PMCID: PMC9942197 DOI: 10.1021/acscatal.2c06137] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2022] [Revised: 01/18/2023] [Indexed: 02/08/2023]
Abstract
The biocatalytic reduction of the oxime moiety to the corresponding amine group has only recently been found to be a promiscuous activity of ene-reductases transforming α-oximo β-keto esters. However, the reaction pathway of this two-step reduction remained elusive. By studying the crystal structures of enzyme oxime complexes, analyzing molecular dynamics simulations, and investigating biocatalytic cascades and possible intermediates, we obtained evidence that the reaction proceeds via an imine intermediate and not via the hydroxylamine intermediate. The imine is reduced further by the ene-reductase to the amine product. Remarkably, a non-canonical tyrosine residue was found to contribute to the catalytic activity of the ene-reductase OPR3, protonating the hydroxyl group of the oxime in the first reduction step.
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Affiliation(s)
- Willem
B. Breukelaar
- Department
of Chemistry, NAWI Graz, University of Graz, Heinrichstraße 28, 8010 Graz, Austria
| | - Nakia Polidori
- Institute
of Molecular Biosciences, University of
Graz, Humboldtstraße 50, 8010 Graz, Austria
| | - Amit Singh
- Institute
of Molecular Biosciences, University of
Graz, Humboldtstraße 50, 8010 Graz, Austria
| | - Bastian Daniel
- Institute
of Molecular Biosciences, University of
Graz, Humboldtstraße 50, 8010 Graz, Austria
| | - Silvia M. Glueck
- Department
of Chemistry, NAWI Graz, University of Graz, Heinrichstraße 28, 8010 Graz, Austria
| | - Karl Gruber
- Institute
of Molecular Biosciences, University of
Graz, Humboldtstraße 50, 8010 Graz, Austria,Field
of Excellence BioHealth, University of Graz, 8010 Graz, Austria,BioTechMed
Graz, 8010 Graz, Austria,
| | - Wolfgang Kroutil
- Department
of Chemistry, NAWI Graz, University of Graz, Heinrichstraße 28, 8010 Graz, Austria,Field
of Excellence BioHealth, University of Graz, 8010 Graz, Austria,BioTechMed
Graz, 8010 Graz, Austria,
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5
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Zhao Q, Hu Q, Qiu Z, Yu C. Biodegradation characteristics and mechanism of quinoline by Ochrobactrum sp. strain C2. WATER SCIENCE AND TECHNOLOGY : A JOURNAL OF THE INTERNATIONAL ASSOCIATION ON WATER POLLUTION RESEARCH 2022; 86:1284-1298. [PMID: 36358061 DOI: 10.2166/wst.2022.249] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
A quinoline-degrading strain, C2, which could completely degrade 250 mg/L of quinoline within 24 h, was isolated from coking wastewater. Strain C2 was identified as Ochrobactrum sp. on the basis of 16S rDNA sequence analysis According to 16S rDNA gene sequence analysis, Strain C2 was identified as Ochrobactrum sp. Strain C2 could utilize quinoline as the sole carbon sources and nitrogen sources to grow and degrade quinoline well under acidic conditions. The optimum inoculum concentration, temperature and shaking speed for quinoline degradation were 10%, 30 °C and 150 r/min, respectively. The degradation of quinoline at low concentration by the strain followed the first-order kinetic model. The growth process of strain C2 was more consistent with the Haldane model than the Monod model, and the kinetic parameters were: Vmax = 0.08 h-1, Ks = 131.5 mg/L, Ki = 183.1 mg/L. Compared with suspended strains, strain C2 immobilized by sodium alginate had better degradation efficiency of quinoline and COD. The metabolic pathway of quinoline by Strain C2 was tentatively proposed, quinoline was firstly converted into 2(1H) quinolone, then the benzene ring was opened with the action of catechol 1,2-dioxygenase and subsequently transformed into benzaldehyde, 2-pentanone, hydroxyphenyl propionic acid and others.
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Affiliation(s)
- Qiancheng Zhao
- School of Chemical and Environmental Engineering, China University of Mining and Technology (Beijing), Beijing 100083, China E-mail:
| | - Qiaoyu Hu
- School of Chemical and Environmental Engineering, China University of Mining and Technology (Beijing), Beijing 100083, China E-mail:
| | - Ziliang Qiu
- School of Chemical and Environmental Engineering, China University of Mining and Technology (Beijing), Beijing 100083, China E-mail:
| | - Caihong Yu
- School of Chemical and Environmental Engineering, China University of Mining and Technology (Beijing), Beijing 100083, China E-mail:
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Comparative Genomic Analysis of Antarctic Pseudomonas Isolates with 2,4,6-Trinitrotoluene Transformation Capabilities Reveals Their Unique Features for Xenobiotics Degradation. Genes (Basel) 2022; 13:genes13081354. [PMID: 36011267 PMCID: PMC9407559 DOI: 10.3390/genes13081354] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2022] [Revised: 07/25/2022] [Accepted: 07/25/2022] [Indexed: 12/04/2022] Open
Abstract
The nitroaromatic explosive 2,4,6-trinitrotoluene (TNT) is a highly toxic and persistent environmental pollutant. Since physicochemical methods for remediation are poorly effective, the use of microorganisms has gained interest as an alternative to restore TNT-contaminated sites. We previously demonstrated the high TNT-transforming capability of three novel Pseudomonas spp. isolated from Deception Island, Antarctica, which exceeded that of the well-characterized TNT-degrading bacterium Pseudomonas putida KT2440. In this study, a comparative genomic analysis was performed to search for the metabolic functions encoded in the genomes of these isolates that might explain their TNT-transforming phenotype, and also to look for differences with 21 other selected pseudomonads, including xenobiotics-degrading species. Comparative analysis of xenobiotic degradation pathways revealed that our isolates have the highest abundance of key enzymes related to the degradation of fluorobenzoate, TNT, and bisphenol A. Further comparisons considering only TNT-transforming pseudomonads revealed the presence of unique genes in these isolates that would likely participate directly in TNT-transformation, and others involved in the β-ketoadipate pathway for aromatic compound degradation. Lastly, the phylogenomic analysis suggested that these Antarctic isolates likely represent novel species of the genus Pseudomonas, which emphasizes their relevance as potential agents for the bioremediation of TNT and other xenobiotics.
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The First Step of Biodegradation of 7-Hydroxycoumarin in Pseudomonas mandelii 7HK4 Depends on an Alcohol Dehydrogenase-Type Enzyme. Int J Mol Sci 2021; 22:ijms22041552. [PMID: 33557119 PMCID: PMC7913881 DOI: 10.3390/ijms22041552] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2021] [Revised: 01/27/2021] [Accepted: 02/01/2021] [Indexed: 11/23/2022] Open
Abstract
Coumarins are well known secondary metabolites widely found in various plants. However, the degradation of these compounds in the environment has not been studied in detail, and, especially, the initial stages of the catabolic pathways of coumarins are not fully understood. A soil isolate Pseudomonas mandelii 7HK4 is able to degrade 7-hydroxycoumarin (umbelliferone) via the formation of 3-(2,4-dihydroxyphenyl)propionic acid, but the enzymes catalyzing the α-pyrone ring transformations have not been characterized. To elucidate an upper pathway of the catabolism of 7-hydroxycoumarin, 7-hydroxycoumarin-inducible genes hcdD, hcdE, hcdF, and hcdG were identified by RT-qPCR analysis. The DNA fragment encoding a putative alcohol dehydrogenase HcdE was cloned, and the recombinant protein catalyzed the NADPH-dependent reduction of 7-hydroxycoumarin both in vivo and in vitro. The reaction product was isolated and characterized as a 7-hydroxy-3,4-dihydrocoumarin based on HPLC-MS and NMR analyses. In addition, the HcdE was active towards 6,7-dihydroxycoumarin, 6-hydroxycoumarin, 6-methylcoumarin and coumarin. Thus, in contrast to the well-known fact that the ene-reductases usually participate in the reduction of the double bond, an alcohol dehydrogenase catalyzing such reaction has been identified, and, for P. mandelii 7HK4, 7-hydroxycoumarin degradation via a 7-hydroxy-3,4-dihydrocoumarin pathway has been proposed.
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Old yellow enzymes: structures and structure-guided engineering for stereocomplementary bioreduction. Appl Microbiol Biotechnol 2020; 104:8155-8170. [PMID: 32830294 DOI: 10.1007/s00253-020-10845-z] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2020] [Revised: 08/07/2020] [Accepted: 08/17/2020] [Indexed: 10/23/2022]
Abstract
Since the first discovery of old yellow enzyme 1 (OYE1) from Saccharomyces pastorianus in 1932, biocatalytic asymmetric reduction of activated alkenes by OYEs has become a valuable reaction in organic synthesis. To access stereocomplementary C=C-bond bioreduction, the mining of novel OYEs and especially the protein engineering of existing OYEs have been performed, which successfully achieved the stereocomplementary reduction in several cases and further raise the potential of applications. In this review, we analyzed the structures, active sites, and substrate recognition of OYEs, which are the bases for their substrate specificity and stereospecificity. Sequence similarity network of OYEs superfamily was also constructed to investigate the scope of characterized OYEs. The structure-guided engineering to switch the stereoselectivity of OYEs and thus access stereocomplementary bioreduction over the last decade (2009-2020) was then reviewed and discussed, which might give new insights into the mining and engineering of related biocatalysts. KEY POINTS: • The sequence similarity network of OYEs superfamily was constructed and annotated. • The structures and active sites of OYEs from different classes were compared. • "Left/right" binding mode was used to explain the stereopreferences of OYEs. • Structure-guided engineering of OYEs to switch their stereoselectivity was reviewed.
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Barros CHN, Devlin H, Hiebner DW, Vitale S, Quinn L, Casey E. Enhancing curcumin's solubility and antibiofilm activity via silica surface modification. NANOSCALE ADVANCES 2020; 2:1694-1708. [PMID: 36132306 PMCID: PMC9418611 DOI: 10.1039/d0na00041h] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/15/2020] [Accepted: 03/19/2020] [Indexed: 06/15/2023]
Abstract
Bacterial biofilms are microbial communities in which bacterial cells in sessile state are mechanically and chemically protected against foreign agents, thus enhancing antibiotic resistance. The delivery of active compounds to the inside of biofilms is often hindered due to the existence of the biofilm extracellular polymeric substances (EPS) and to the poor solubility of drugs and antibiotics. A possible strategy to overcome the EPS barrier is the incorporation of antimicrobial agents into a nanocarrier, able to penetrate the matrix and deliver the active substance to the cells. Here, we report the synthesis of antimicrobial curcumin-conjugated silica nanoparticles (curc-NPs) as a possibility for dealing with these issues. Curcumin is a known antimicrobial agent and to overcome its low solubility in water it was grafted onto the surface of silica nanoparticles, the latter functioning as nanocarrier for curcumin into the biofilm. Curc-NPs were able to impede the formation of model P. putida biofilms up to 50% and disrupt mature biofilms up to 54% at 2.5 mg mL-1. Cell viability of sessile cells in both cases was also considerably affected, which is not observed for curcumin delivered as a free compound at the same concentration. Furthermore, proteomics of extracted EPS matrix of biofilms grown in the presence of free curcumin and curc-NPs revealed differences in the expression of key proteins related to cell detoxification and energy production. Therefore, curc-NPs are presented here as an alternative for curcumin delivery that can be exploited not only to other bacterial strains but also to further biological applications.
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Affiliation(s)
- Caio H N Barros
- School of Chemical and Bioprocess Engineering, University College Dublin Ireland
| | - Henry Devlin
- School of Chemical and Bioprocess Engineering, University College Dublin Ireland
| | - Dishon W Hiebner
- School of Chemical and Bioprocess Engineering, University College Dublin Ireland
| | - Stefania Vitale
- School of Chemical and Bioprocess Engineering, University College Dublin Ireland
| | - Laura Quinn
- School of Chemical and Bioprocess Engineering, University College Dublin Ireland
| | - Eoin Casey
- School of Chemical and Bioprocess Engineering, University College Dublin Ireland
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10
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Outer membrane vesicles catabolize lignin-derived aromatic compounds in Pseudomonas putida KT2440. Proc Natl Acad Sci U S A 2020; 117:9302-9310. [PMID: 32245809 DOI: 10.1073/pnas.1921073117] [Citation(s) in RCA: 64] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Lignin is an abundant and recalcitrant component of plant cell walls. While lignin degradation in nature is typically attributed to fungi, growing evidence suggests that bacteria also catabolize this complex biopolymer. However, the spatiotemporal mechanisms for lignin catabolism remain unclear. Improved understanding of this biological process would aid in our collective knowledge of both carbon cycling and microbial strategies to valorize lignin to value-added compounds. Here, we examine lignin modifications and the exoproteome of three aromatic-catabolic bacteria: Pseudomonas putida KT2440, Rhodoccocus jostii RHA1, and Amycolatopsis sp. ATCC 39116. P. putida cultivation in lignin-rich media is characterized by an abundant exoproteome that is dynamically and selectively packaged into outer membrane vesicles (OMVs). Interestingly, many enzymes known to exhibit activity toward lignin-derived aromatic compounds are enriched in OMVs from early to late stationary phase, corresponding to the shift from bioavailable carbon to oligomeric lignin as a carbon source. In vivo and in vitro experiments demonstrate that enzymes contained in the OMVs are active and catabolize aromatic compounds. Taken together, this work supports OMV-mediated catabolism of lignin-derived aromatic compounds as an extracellular strategy for nutrient acquisition by soil bacteria and suggests that OMVs could potentially be useful tools for synthetic biology and biotechnological applications.
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11
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Xu H, Sun W, Yan N, Li D, Wang X, Yu T, Zhang Y, Rittmann BE. Competition for electrons between pyridine and quinoline during their simultaneous biodegradation. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2017; 24:25082-25091. [PMID: 28921046 DOI: 10.1007/s11356-017-0082-3] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/28/2017] [Accepted: 09/03/2017] [Indexed: 06/07/2023]
Abstract
Biodegradation of pyridine and quinoline is initiated with mono-oxygenation reactions that require an intracellular electron donor. Simultaneous biodegradation of both substrates should set up competition for the intracellular electron donor that may inhibit one or more of the mono-oxygenation steps. An internal circulation baffled biofilm reactor (ICBBR) was used to evaluate the impacts of competition during pyridine and quinoline biodegradation. Compared with independent biodegradation, pyridine and quinoline removal rates were slowed when biodegraded simultaneously, although the pyridine removal rate decreased more than for quinoline. The first mono-oxygenation of quinoline (to 2-hydroxyquinoline) always was faster than the first mono-oxygenation of pyridine (to 2-hydroxypyridine), and the difference was accentuated with pyridine and quinoline which were biodegraded simultaneously due to the competition for intracellular electron donor. Competition also existed between the second mono-oxygenations, and the removal rate of 2-hydroxypyridine was faster than the rate for 2-hydroxyquinoline, even though the rate was faster for quinoline than pyridine. Adding an exogenous electron donor accelerated all mono-oxygenations in proportion to the amount of donor added, but the increments were greater for quinoline due to its higher affinity for intracellular electron donors than pyridine. When actual coking wastewater was used as the background matrix, removals of pyridine and quinoline exhibited the same competitive trends.
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Affiliation(s)
- Hua Xu
- Department of Environmental Science and Engineering, College of Life and Environmental Science, Shanghai Normal University, Shanghai, 200234, People's Republic of China
| | - Weihua Sun
- Department of Environmental Science and Engineering, College of Life and Environmental Science, Shanghai Normal University, Shanghai, 200234, People's Republic of China.
| | - Ning Yan
- Department of Environmental Science and Engineering, College of Life and Environmental Science, Shanghai Normal University, Shanghai, 200234, People's Republic of China
| | - Danni Li
- Department of Environmental Science and Engineering, College of Life and Environmental Science, Shanghai Normal University, Shanghai, 200234, People's Republic of China
| | - Xueqi Wang
- Department of Environmental Science and Engineering, College of Life and Environmental Science, Shanghai Normal University, Shanghai, 200234, People's Republic of China
| | - Tingting Yu
- Department of Environmental Science and Engineering, College of Life and Environmental Science, Shanghai Normal University, Shanghai, 200234, People's Republic of China
| | - Yongming Zhang
- Department of Environmental Science and Engineering, College of Life and Environmental Science, Shanghai Normal University, Shanghai, 200234, People's Republic of China.
| | - Bruce E Rittmann
- Biodesign Swette Center for Environmental Biotechnology, Arizona State University, Tempe, AZ, 85287-5701, USA
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12
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Opperman DJ. Structural investigation into the C-terminal extension of the ene-reductase from Ralstonia (Cupriavidus) metallidurans. Proteins 2017; 85:2252-2257. [PMID: 28833623 DOI: 10.1002/prot.25372] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2017] [Revised: 08/16/2017] [Accepted: 08/18/2017] [Indexed: 01/25/2023]
Abstract
Ene-reductases (ERs), or Old Yellow Enzymes, catalyze the asymmetric reduction of various activated alkenes. This class of biocatalysts is considered an attractive alternative to current chemical technologies for hydrogenation due to their high selectivity and specificity. Here the X-ray crystal structure of RmER, a "thermophilic"-like ER from Ralstonia (Cupriavidus) metallidurans, is reported. Unlike other members of this class of ERs, RmER is monomeric in solution which we previously related to its atypical elongated C-terminus. A typical dimer interface was however observed in our crystal structure, with the conserved Arg-"finger" forming part of the adjacent monomer's active site and the elongated C-terminus extending into the active site through contacting the "capping" domain. This dimerization also resulted in the loss of one FMN cofactor from each dimer pair. This potential transient dimerization and dissociation of FMN could conceivably explain the rapid rates previously observed when an FMN light-driven cofactor regeneration system was used during catalysis with RmER.
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Affiliation(s)
- Diederik J Opperman
- Department of Biotechnology, University of the Free State, 205 Nelson Mandela Drive, Bloemfontein, 9300, South Africa
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13
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Werther T, Wahlefeld S, Salewski J, Kuhlmann U, Zebger I, Hildebrandt P, Dobbek H. Redox-dependent substrate-cofactor interactions in the Michaelis-complex of a flavin-dependent oxidoreductase. Nat Commun 2017. [PMCID: PMC5519977 DOI: 10.1038/ncomms16084] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
How an enzyme activates its substrate for turnover is fundamental for catalysis but incompletely understood on a structural level. With redox enzymes one typically analyses structures of enzyme–substrate complexes in the unreactive oxidation state of the cofactor, assuming that the interaction between enzyme and substrate is independent of the cofactors oxidation state. Here, we investigate the Michaelis complex of the flavoenzyme xenobiotic reductase A with the reactive reduced cofactor bound to its substrates by X-ray crystallography and resonance Raman spectroscopy and compare it to the non-reactive oxidized Michaelis complex mimics. We find that substrates bind in different orientations to the oxidized and reduced flavin, in both cases flattening its structure. But only authentic Michaelis complexes display an unexpected rich vibrational band pattern uncovering a strong donor–acceptor complex between reduced flavin and substrate. This interaction likely activates the catalytic ground state of the reduced flavin, accelerating the reaction within a compressed cofactor–substrate complex. Due to their transient nature, enzyme-substrate complexes are difficult to characterize structurally. Here, the authors capture the reactive reduced form of xenobiotic reductase A bound to its substrate and show that the oxidation state of the flavin cofactor affects the interaction of the substrate with the enzyme.
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14
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Ma X, Bian L, Ding J, Wu Y, Xia H, Li J. Electrochemical oxidation of quinoline aqueous solution on β-PbO 2 anode and the evolution of phytotoxicity on duckweed. WATER SCIENCE AND TECHNOLOGY : A JOURNAL OF THE INTERNATIONAL ASSOCIATION ON WATER POLLUTION RESEARCH 2017; 75:1820-1829. [PMID: 28452774 DOI: 10.2166/wst.2017.053] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Electrochemical oxidation of quinoline on a β-PbO2 electrode modified with fluoride resin and the comprehensive toxicity of intermediates formed during oxidation on duckweed were investigated in detail. The results showed that quinoline was initially hydroxylated at the C-2 and C-8 positions by hydroxyl radicals (·OH) electro-generated on a β-PbO2 anode, yielding 2(1H)-quinolinone and 8-hydroxyquinoline, then undergoing ring cleavage to form pyridine, nicotinic acid, pyridine-2-carboxaldehyde and acetophenone, which were ultimately converted to biodegradable organic acids. NO3- was the final form of quinoline-N. The growth of duckweed exposed to the oxidized quinoline solution was gradually inhibited with the decrease in pH and the formation of intermediates. However, the growth inhibition of duckweed could be eliminated beyond 120 min of oxidation, indicating the comprehensive toxicity of the quinoline solution reduced when the amount of quinoline removed was above 80%. Additionally, the adjustment of the pH to 7.5 and the addition of nutrients to the treated quinoline solution before culturing duckweed could obviously alleviate the inhibition on duckweed. Thus, partial electrochemical degradation of quinoline offers a cost-effective and clean alternative for pretreatment of wastewater containing nitrogen-heterocyclic compounds before biological treatment. The duckweed test presents a simple method for assessing the comprehensive toxicity of intermediates.
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Affiliation(s)
- Xiangjuan Ma
- School of Environmental Science and Engineering, Zhejiang Gongshang University, Hangzhou 310018, China E-mail:
| | - Lixia Bian
- School of Environmental Science and Engineering, Zhejiang Gongshang University, Hangzhou 310018, China E-mail: ; Aqseptence Group (Hangzhou) Co., Ltd, Hangzhou 310053, China
| | - Jingfeng Ding
- School of Environmental Science and Engineering, Zhejiang Gongshang University, Hangzhou 310018, China E-mail:
| | - Yaping Wu
- School of Environmental Science and Engineering, Zhejiang Gongshang University, Hangzhou 310018, China E-mail:
| | - Huilong Xia
- School of Environmental Science and Engineering, Zhejiang Gongshang University, Hangzhou 310018, China E-mail:
| | - Jionghui Li
- School of Environmental Science and Engineering, Zhejiang Gongshang University, Hangzhou 310018, China E-mail:
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15
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Catucci G, Romagnolo A, Spina F, Varese GC, Gilardi G, Di Nardo G. Enzyme-substrate matching in biocatalysis: in silico studies to predict substrate preference of ten putative ene-reductases from Mucor circinelloides MUT44. ACTA ACUST UNITED AC 2016. [DOI: 10.1016/j.molcatb.2016.06.008] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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16
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Geddes A, Paul CE, Hay S, Hollmann F, Scrutton NS. Donor–Acceptor Distance Sampling Enhances the Performance of “Better than Nature” Nicotinamide Coenzyme Biomimetics. J Am Chem Soc 2016; 138:11089-92. [DOI: 10.1021/jacs.6b05625] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Alexander Geddes
- BBSRC/EPSRC
Centre for Synthetic Biology of Fine and Speciality Chemicals (SYNBIOCHEM),
Manchester Institute of Biotechnology and School of Chemistry, The University of Manchester, 131 Princess Street, Manchester M1 7DN, United Kingdom
| | - Caroline E. Paul
- Department
of Biotechnology, Delft University of Technology, Julianalaan 136, 2628BL Delft, The Netherlands
| | - Sam Hay
- BBSRC/EPSRC
Centre for Synthetic Biology of Fine and Speciality Chemicals (SYNBIOCHEM),
Manchester Institute of Biotechnology and School of Chemistry, The University of Manchester, 131 Princess Street, Manchester M1 7DN, United Kingdom
| | - Frank Hollmann
- Department
of Biotechnology, Delft University of Technology, Julianalaan 136, 2628BL Delft, The Netherlands
| | - Nigel S. Scrutton
- BBSRC/EPSRC
Centre for Synthetic Biology of Fine and Speciality Chemicals (SYNBIOCHEM),
Manchester Institute of Biotechnology and School of Chemistry, The University of Manchester, 131 Princess Street, Manchester M1 7DN, United Kingdom
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17
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Bai Q, Yang L, Li R, Chen B, Zhang L, Zhang Y, Rittmann BE. Accelerating Quinoline Biodegradation and Oxidation with Endogenous Electron Donors. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2015; 49:11536-42. [PMID: 26327306 DOI: 10.1021/acs.est.5b03293] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
Quinoline, a recalcitrant heterocyclic compound, is biodegraded by a series of reactions that begin with mono-oxygenations, which require an intracellular electron donor. Photolysis of quinoline can generate readily biodegradable products, such as oxalate, whose bio-oxidation can generate endogenous electron donors that ought to accelerate quinoline biodegradation and, ultimately, mineralization. To test this hypothesis, we compared three protocols for the biodegradation of quinoline: direct biodegradation (B), biodegradation after photolysis of 1 h (P1h+B) or 2 h (P2h+B), and biodegradation by adding oxalate commensurate to the amount generated from photolysis of 1 h (O1+B) or 2 h (O2+B). The experimental results show that P1h+B and P2h+B accelerated quinoline biodegradation by 19% and 50%, respectively, compared to B. Protocols O1+B and O2+B also gave 19% and 50% increases, respectively. During quinoline biodegradation, its first intermediate, 2-hydroxyquinoline, accumulated gradually in parallel to quinoline loss but declined once quinoline was depleted. Mono-oxygenation of 2-hydroxyquinoline competed with mono-oxygenation of quinoline, but the inhibition was relieved when extra electrons donors were added from oxalate, whether formed by UV photolysis or added exogenously. Rapid oxalate oxidation stimulated both mono-oxygenations, which accelerated the overall quinoline oxidation that provided the bulk of the electron donor.
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Affiliation(s)
- Qi Bai
- Department of Environmental Science and Engineering, College of Life and Environmental Science, Shanghai Normal University , Shanghai 200234, PR China
| | - Lihui Yang
- Department of Environmental Science and Engineering, College of Life and Environmental Science, Shanghai Normal University , Shanghai 200234, PR China
| | - Rongjie Li
- Department of Environmental Science and Engineering, College of Life and Environmental Science, Shanghai Normal University , Shanghai 200234, PR China
| | - Bin Chen
- Department of Environmental Science and Engineering, College of Life and Environmental Science, Shanghai Normal University , Shanghai 200234, PR China
| | - Lili Zhang
- Department of Environmental Science and Engineering, College of Life and Environmental Science, Shanghai Normal University , Shanghai 200234, PR China
| | - Yongming Zhang
- Department of Environmental Science and Engineering, College of Life and Environmental Science, Shanghai Normal University , Shanghai 200234, PR China
| | - Bruce E Rittmann
- Swette Center for Environmental Biotechnology, Biodesign Institute, Arizona State University , Tempe, AZ 85287-5701, United States
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18
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Kong X, Yang Y, Wu W, Wan H, Li X, Zhong M, Su X, Jia S, Lin N. Triterpenoid Saponin W3 from Anemone flaccida Suppresses Osteoclast Differentiation through Inhibiting Activation of MAPKs and NF-κB Pathways. Int J Biol Sci 2015; 11:1204-14. [PMID: 26327814 PMCID: PMC4551756 DOI: 10.7150/ijbs.12296] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2015] [Accepted: 07/17/2015] [Indexed: 11/05/2022] Open
Abstract
Excessive bone resorption by osteoclasts within inflamed joints is the most specific hallmark of rheumatoid arthritis. A. flaccida has long been used for the treatment of arthritis in folk medicine of China; however, the active ingredients responsible for the anti-arthritis effects of A. flaccida are still elusive. In this study, W3, a saponin isolated from the extract of A. flaccida was identified as the major active ingredient by using an osteoclast formation model induced by receptor activator of nuclear factor kappa-B ligand (RANKL). W3 dose-dependently suppressed the actin ring formation and lacunar resorption. Mechanistic investigation revealed that W3 inhibited the RANKL-induced TRAF6 expression, decreased phosphorylation of mitogen-activated protein kinases (MAPKs) and IκB-α, and suppressed NF-κB p65 DNA binding activity. Furthermore, W3 almost abrogated the expression of c-Fos and nuclear factor of activated T cells (NFATc1). Therefore, our results suggest that W3 is a potential agent for treating lytic bone diseases although further evaluation in vivo and in clinical trials is needed.
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Affiliation(s)
- Xiangying Kong
- 1. Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, 100700 Beijing, China
| | - Yue Yang
- 1. Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, 100700 Beijing, China
| | - Wenbin Wu
- 1. Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, 100700 Beijing, China
| | - Hongye Wan
- 1. Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, 100700 Beijing, China
| | - Xiaomin Li
- 1. Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, 100700 Beijing, China
| | - Michun Zhong
- 1. Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, 100700 Beijing, China
| | - Xiaohui Su
- 1. Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, 100700 Beijing, China
| | - Shiwei Jia
- 2. Guangzhou Kanghe Pharmaceutical Limited Company, 511440 Guangzhou, China
| | - Na Lin
- 1. Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, 100700 Beijing, China
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19
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Kong X, Wu W, Yang Y, Wan H, Li X, Zhong M, Zhao H, Su X, Jia S, Ju D, Lin N. Total saponin from Anemone flaccida Fr. Schmidt abrogates osteoclast differentiation and bone resorption via the inhibition of RANKL-induced NF-κB, JNK and p38 MAPKs activation. J Transl Med 2015; 13:91. [PMID: 25889035 PMCID: PMC4372222 DOI: 10.1186/s12967-015-0440-1] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2014] [Accepted: 02/17/2015] [Indexed: 11/16/2022] Open
Abstract
Osteoclasts, bone-specialized multinucleated cells, are responsible for bone destructive diseases such as rheumatoid arthritis and osteoporosis. Natural plant-derived products have received substantial attention given their potential therapeutic and preventive activities against bone destructive diseases. In the present study, we investigated the effects of total saponin (TS) from Anemone flaccida Fr. Schmidt, on receptor activator of nuclear factor-κB ligand (RANKL)-induced in vitro osteoclast differentiation. We observed that TS concentration-dependently inhibited RANKL-induced osteoclast formation from RAW 264.7 cell and bone marrow-derived macrophages (BMMs), as well as decreased extent of actin ring formation and lacunar resorption. The RANKL-stimulated expression of osteoclast-related transcription factors were also diminished by TS. Moreover, TS blocked the RANKL-triggered TRAF6 expression, phosphorylation of mitogen-activated protein kinases (MAPKs) and IκB-α, and inhibited NF-κB p65 DNA binding activity. Furthermore, TS almost abrogated the nuclear factor of activated T cells (NFATc1) and c-Fos expression. Taken together, our results demonstrated that TS suppresses RANKL-induced osteoclast differentiation and inflammatory bone loss via the down-regulation of TRAF6 level, suppression of JNK and p38 MAPKs and NF-κB activation, and subsequent decreased expression of c-Fos and NFATc1. Therefore, TS may be a potential agent and needs to be more evaluated in vivo or in clinical trials to become a therapeutic for lytic bone diseases.
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Affiliation(s)
- Xiangying Kong
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, No. 16, Nanxiaojie, Dongzhimennei, Beijing, 100700, China.
| | - Wenbin Wu
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, No. 16, Nanxiaojie, Dongzhimennei, Beijing, 100700, China.
| | - Yue Yang
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, No. 16, Nanxiaojie, Dongzhimennei, Beijing, 100700, China.
| | - Hongye Wan
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, No. 16, Nanxiaojie, Dongzhimennei, Beijing, 100700, China.
| | - Xiaomin Li
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, No. 16, Nanxiaojie, Dongzhimennei, Beijing, 100700, China.
| | - Michun Zhong
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, No. 16, Nanxiaojie, Dongzhimennei, Beijing, 100700, China.
| | - Hongyan Zhao
- Institute of Basic Theory, China Academy of Chinese Medical Sciences, Beijing, 100700, China.
| | - Xiaohui Su
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, No. 16, Nanxiaojie, Dongzhimennei, Beijing, 100700, China.
| | - Shiwei Jia
- Guangzhou Kanghe Pharmaceutical Limited Company, Guangzhou, 511440, China.
| | - Dahong Ju
- Institute of Basic Theory, China Academy of Chinese Medical Sciences, Beijing, 100700, China.
| | - Na Lin
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, No. 16, Nanxiaojie, Dongzhimennei, Beijing, 100700, China.
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20
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Park JT, Gómez Ramos LM, Bommarius AS. Engineering towards Nitroreductase Functionality in Ene-Reductase Scaffolds. Chembiochem 2015; 16:811-8. [DOI: 10.1002/cbic.201402667] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2014] [Indexed: 11/10/2022]
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21
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22
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Xu MY, Pei XQ, Wu ZL. Identification and characterization of a novel “thermophilic-like” Old Yellow Enzyme from the genome of Chryseobacterium sp. CA49. ACTA ACUST UNITED AC 2014. [DOI: 10.1016/j.molcatb.2014.07.002] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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23
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Nizam S, Gazara RK, Verma S, Singh K, Verma PK. Comparative structural modeling of six old yellow enzymes (OYEs) from the necrotrophic fungus Ascochyta rabiei: insight into novel OYE classes with differences in cofactor binding, organization of active site residues and stereopreferences. PLoS One 2014; 9:e95989. [PMID: 24776850 PMCID: PMC4002455 DOI: 10.1371/journal.pone.0095989] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2014] [Accepted: 04/02/2014] [Indexed: 11/29/2022] Open
Abstract
Old Yellow Enzyme (OYE1) was the first flavin-dependent enzyme identified and characterized in detail by the entire range of physical techniques. Irrespective of this scrutiny, true physiological role of the enzyme remains a mystery. In a recent study, we systematically identified OYE proteins from various fungi and classified them into three classes viz. Class I, II and III. However, there is no information about the structural organization of Class III OYEs, eukaryotic Class II OYEs and Class I OYEs of filamentous fungi. Ascochyta rabiei, a filamentous phytopathogen which causes Ascochyta blight (AB) in chickpea possesses six OYEs (ArOYE1-6) belonging to the three OYE classes. Here we carried out comparative homology modeling of six ArOYEs representing all the three classes to get an in depth idea of structural and functional aspects of fungal OYEs. The predicted 3D structures of A. rabiei OYEs were refined and evaluated using various validation tools for their structural integrity. Analysis of FMN binding environment of Class III OYE revealed novel residues involved in interaction. The ligand para-hydroxybenzaldehyde (PHB) was docked into the active site of the enzymes and interacting residues were analyzed. We observed a unique active site organization of Class III OYE in comparison to Class I and II OYEs. Subsequently, analysis of stereopreference through structural features of ArOYEs was carried out, suggesting differences in R/S selectivity of these proteins. Therefore, our comparative modeling study provides insights into the FMN binding, active site organization and stereopreference of different classes of ArOYEs and indicates towards functional differences of these enzymes. This study provides the basis for future investigations towards the biochemical and functional characterization of these enigmatic enzymes.
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Affiliation(s)
- Shadab Nizam
- Plant Immunity Laboratory, National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, India
| | - Rajesh Kumar Gazara
- Plant Immunity Laboratory, National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, India
| | - Sandhya Verma
- Plant Immunity Laboratory, National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, India
| | - Kunal Singh
- Plant Immunity Laboratory, National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, India
| | - Praveen Kumar Verma
- Plant Immunity Laboratory, National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, India
- * E-mail:
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24
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Peters C, Kölzsch R, Kadow M, Skalden L, Rudroff F, Mihovilovic MD, Bornscheuer UT. Identification, Characterization, and Application of Three Enoate Reductases fromPseudomonas putidain In Vitro Enzyme Cascade Reactions. ChemCatChem 2014. [DOI: 10.1002/cctc.201300957] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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25
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Nizam S, Verma S, Borah NN, Gazara RK, Verma PK. Comprehensive genome-wide analysis reveals different classes of enigmatic old yellow enzyme in fungi. Sci Rep 2014; 4:4013. [PMID: 24500274 PMCID: PMC3915301 DOI: 10.1038/srep04013] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2013] [Accepted: 01/17/2014] [Indexed: 11/09/2022] Open
Abstract
In this study, we systematically identify Old Yellow Enzymes (OYEs) from a diverse range of economically important fungi representing different ecology and lifestyle. Using active site residues and sequence alignments, we present a classification for these proteins into three distinct classes including a novel class (Class III) and assign names to sequences. Our in-depth phylogenetic analysis suggests a complex history of lineage-specific expansion and contraction for the OYE gene family in fungi. Comparative analyses reveal remarkable diversity in the number and classes of OYE among fungi. Quantitative real-time PCR (qRT-PCR) of Ascochyta rabiei OYEs indicates differential expression of OYE genes during oxidative stress and plant infection. This study shows relationship of OYE with fungal ecology and lifestyle, and provides a foundation for future functional analysis and characterization of OYE gene family.
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Affiliation(s)
- Shadab Nizam
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi-110067, India
| | - Sandhya Verma
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi-110067, India
| | - Nilam Nayan Borah
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi-110067, India
| | - Rajesh Kumar Gazara
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi-110067, India
| | - Praveen Kumar Verma
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi-110067, India
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26
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Litthauer S, Gargiulo S, van Heerden E, Hollmann F, Opperman D. Heterologous expression and characterization of the ene-reductases from Deinococcus radiodurans and Ralstonia metallidurans. ACTA ACUST UNITED AC 2014. [DOI: 10.1016/j.molcatb.2013.10.020] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
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27
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Hunter WJ. A Rhizobium selenitireducens protein showing selenite reductase activity. Curr Microbiol 2013; 68:311-6. [PMID: 24474405 DOI: 10.1007/s00284-013-0474-7] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2013] [Accepted: 08/28/2013] [Indexed: 10/26/2022]
Abstract
Biobarriers remove, via precipitation, the metalloid selenite (SeO₃⁻²) from groundwater; a process that involves the biological reduction of soluble SeO₃⁻² to insoluble elemental red selenium (Se⁰). The enzymes associated with this reduction process are poorly understood. In Rhizobium selenitireducens at least two enzymes are potentially involved; one, a nitrite reductase reduces SeO₃⁻² to Se⁰ but another protein may also be involved which is investigated in this study. Proteins from R. selenitireducens cells were precipitated with ammonium sulfate and run on native electrophoresis gels. When these gels were incubated with NADH and SeO₃⁻² a band of precipitated Se⁰ developed signifying the presence of a SeO₃⁻² reducing protein. Bands were cut from the gel and analyzed for peptides via LCMSMS. The amino acid sequences associated with the bands indicated the presence of an NADH:flavin oxidoreductase that resembles YP_001326930 from Sinorhizobium medicae. The protein is part of a protein family termed old-yellow-enzymes (OYE) that contain a flavin binding domain. OYE enzymes are often involved in protecting cells from oxidative stress and, due in part to an active site that has a highly accessible binding pocket, are generally active on a wide range of substrates. This report is the first of an OYE enzyme being involved in SeO₃⁻² reduction.
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Affiliation(s)
- W J Hunter
- United States Department of Agriculture-Agricultural Research Service, 2150-D Centre Avenue, Fort Collins, CO, 80526-8119, USA,
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Wang L, Li Y, Duan J. Biodegradation of 2-methylquinoline by Enterobacter aerogenes TJ-D isolated from activated sludge. J Environ Sci (China) 2013; 25:1310-1318. [PMID: 24218841 DOI: 10.1016/s1001-0742(12)60192-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
Bacterial strain Enterobacter aerogenes TJ-D capable of utilizing 2-methylquinoline as the sole carbon and energy source was isolated from acclimated activated sludge under denitrifying conditions. The ability to degrade 2-methylquinoline by E. aerogenes TJ-D was investigated under denitrifying conditions. Under optimal conditions of temperature (35 degrees C) and initial pH 7, 2-methylquinoline of 100 mg/L was degraded within 176 hr. The degradation of 2-methylquinoline by E. aerogenes TJ-D could be well described by the Haldane model (R2 > 0.91). During the degradation period of 2-methylquinoline (initial concentration 100 mg/L), nitrate was almost completely consumed (the removal efficiency was 98.5%), while nitrite remained at low concentration (< 0.62 mg/L) during the whole denitrification period. 1,2,3,4-Tetrahydro-2-methylquinoline, 4-ethyl-benzenamine, N-butyl-benzenamine, N-ethyl-benzenamine and 2,6-diethyl-benzenamine were metabolites produced during the degradation. The degradation pathway of 2-methylquinoline by E. aerogenes TJ-D was proposed. 2-Methylquinoline is initially hydroxylated at C-4 to form 2-methyl-4-hydroxy-quinoline, and then forms 2-methyl-4-quinolinol as a result of tautomerism. Hydrogenation of the heterocyclic ring at positions 2 and 3 produces 2,3-dihydro-2-methyl-4-quinolinol. The carbon-carbon bond at position 2 and 3 in the heterocyclic ring may cleave and form 2-ethyl-N-ethyl-benzenamine. Tautomerism may result in the formation of 2,6-diethyl-benzenamine and N-butyl-benzenamine. 4-Ethyl-benzenamine and N-ethyl-benzenamine were produced as a result of losing one ethyl group from the above molecules.
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Affiliation(s)
- Lin Wang
- State Key Laboratory of Pollution Control and Resource Reuse, Tongji University, Shanghai 200092, China
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Tuo BH, Yan JB, Fan BA, Yang ZH, Liu JZ. Biodegradation characteristics and bioaugmentation potential of a novel quinoline-degrading strain of Bacillus sp. isolated from petroleum-contaminated soil. BIORESOURCE TECHNOLOGY 2012; 107:55-60. [PMID: 22243925 DOI: 10.1016/j.biortech.2011.12.114] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/13/2011] [Revised: 12/06/2011] [Accepted: 12/06/2011] [Indexed: 05/11/2023]
Abstract
Quinoline and its derivatives are widely considered to be environmental pollutants. In this study, the biodegradation characteristics and bioaugmentation potential for a novel strain were described. The strain, named Q2, which could utilize quinoline as the sole carbon, nitrogen and energy source, was isolated and identified as a Bacillus sp. The optimum temperature, initial pH and shaker rotary speed for quinoline degradation were 30°C, pH 8-10 and 100-200 rpm, respectively. During the biodegradation process, the quinoline-N was released as ammonium and the culture broth became yellow, pink and brown in turn, which indicated that several intermediates were generated. GC/MS analysis showed that 2(1H)-quinolinone and 8-hydroxycoumarin were produced. Furthermore, the bioaugmentation of Q2 into the sludge consortium, which was taken from refinery wastewater treatment plant, to degrade quinoline was investigated. The results showed that it could coexist with the other microbes and the remarkably enhanced quinoline biodegradation ability was achieved.
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Affiliation(s)
- Bao-hua Tuo
- College of Chemical Engineering and Technology, Wuhan University of Science and Technology, Wuhan 430081, People's Republic of China
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Lapalikar GV, Taylor MC, Warden AC, Scott C, Russell RJ, Oakeshott JG. F420H2-dependent degradation of aflatoxin and other furanocoumarins is widespread throughout the actinomycetales. PLoS One 2012; 7:e30114. [PMID: 22383957 PMCID: PMC3288000 DOI: 10.1371/journal.pone.0030114] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2011] [Accepted: 12/09/2011] [Indexed: 11/18/2022] Open
Abstract
Two classes of F420-dependent reductases (FDR-A and FDR-B) that can reduce aflatoxins and thereby degrade them have previously been isolated from Mycobacterium smegmatis. One class, the FDR-A enzymes, has up to 100 times more activity than the other. F420 is a cofactor with a low reduction potential that is largely confined to the Actinomycetales and some Archaea and Proteobacteria. We have heterologously expressed ten FDR-A enzymes from diverse Actinomycetales, finding that nine can also use F420H2 to reduce aflatoxin. Thus FDR-As may be responsible for the previously observed degradation of aflatoxin in other Actinomycetales. The one FDR-A enzyme that we found not to reduce aflatoxin belonged to a distinct clade (herein denoted FDR-AA), and our subsequent expression and analysis of seven other FDR-AAs from M. smegmatis found that none could reduce aflatoxin. Certain FDR-A and FDR-B enzymes that could reduce aflatoxin also showed activity with coumarin and three furanocoumarins (angelicin, 8-methoxysporalen and imperatorin), but none of the FDR-AAs tested showed any of these activities. The shared feature of the compounds that were substrates was an α,β-unsaturated lactone moiety. This moiety occurs in a wide variety of otherwise recalcitrant xenobiotics and antibiotics, so the FDR-As and FDR-Bs may have evolved to harness the reducing power of F420 to metabolise such compounds. Mass spectrometry on the products of the FDR-catalyzed reduction of coumarin and the other furanocoumarins shows their spontaneous hydrolysis to multiple products.
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Affiliation(s)
- Gauri V Lapalikar
- Ecosystem Sciences, Commonwealth Science and Industrial Research Organisation, Canberra, Australian Capital Territory, Australia
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31
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Lapalikar GV, Taylor MC, Warden AC, Onagi H, Hennessy JE, Mulder RJ, Scott C, Brown SE, Russell RJ, Easton CJ, Oakeshott JG. Cofactor promiscuity among F420-dependent reductases enables them to catalyse both oxidation and reduction of the same substrate. Catal Sci Technol 2012. [DOI: 10.1039/c2cy20129a] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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32
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Durchschein K, Fabian WMF, Macheroux P, Zangger K, Trimmel G, Faber K. Reductive biotransformation of nitroalkenes via nitroso-intermediates to oxazetes catalyzed by xenobiotic reductase A (XenA). Org Biomol Chem 2011; 9:3364-9. [DOI: 10.1039/c0ob01216e] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
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33
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Yanto Y, Yu HH, Hall M, Bommarius AS. Characterization of xenobiotic reductase A (XenA): study of active site residues, substrate spectrum and stability. Chem Commun (Camb) 2010; 46:8809-11. [PMID: 20959917 DOI: 10.1039/c0cc02354j] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Xenobiotic reductase A (XenA) has broad catalytic activity and reduces various α,β-unsaturated and nitro compounds with moderate to excellent stereoselectivity. Single mutants C25G and C25V are able to reduce nitrobenzene, a non-active substrate for the wild type, to produce aniline. Total turnover is dominated by chemical rather than thermal instability.
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Affiliation(s)
- Yanto Yanto
- School of Chemical and Biomolecular Engineering, Parker H. Petit Institute of Bioengineering and Biosciences, Georgia Institute of Technology, 315 Ferst Drive, Atlanta, GA, USA
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34
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Stueckler C, Winkler CK, Bonnekessel M, Faber K. Asymmetric Synthesis of (R)-3-Hydroxy-2-methylpropanoate (‘Roche Ester’) and Derivatives via Biocatalytic CC-Bond Reduction. Adv Synth Catal 2010. [DOI: 10.1002/adsc.201000522] [Citation(s) in RCA: 52] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
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Spiegelhauer O, Werther T, Mende S, Knauer SH, Dobbek H. Determinants of substrate binding and protonation in the flavoenzyme xenobiotic reductase A. J Mol Biol 2010; 403:286-98. [PMID: 20826164 DOI: 10.1016/j.jmb.2010.08.047] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2010] [Revised: 08/17/2010] [Accepted: 08/26/2010] [Indexed: 10/19/2022]
Abstract
Xenobiotic reductase A (XenA) from Pseudomonas putida 86 catalyzes the NAD(P)H-dependent reduction of various α,β-unsaturated carbonyl compounds and is a member of the old yellow enzyme family. The reaction of XenA follows a ping-pong mechanism, implying that its active site has to accommodate and correctly position the various substrates to be oxidized (NADH/NADPH) and to be reduced (different α,β-unsaturated carbonyl compounds) to enable formal hydride transfers between the substrate and the isoalloxazine ring. The active site of XenA is lined by two tyrosine (Tyr27, Tyr183) and two tryptophan (Trp302, Trp358) residues, which were proposed to contribute to substrate binding. We analyzed the individual contributions of the four residues, using site-directed mutagenesis, steady-state and transient kinetics, redox potentiometry and crystal structure analysis. The Y183F substitution decreases the affinity of XenA for NADPH and reduces the rate of the oxidative half-reaction by two to three orders of magnitude, the latter being in agreement with its function as a proton donor in the oxidative half-reaction. Upon reduction of the flavin, Trp302 swings into the active site of XenA (in-conformation) and decreases the extent of the substrate-binding pocket. Its exchange against alanine induces substrate inhibition at elevated NADPH concentrations, indicating that the in-conformation of Trp302 helps to disfavor the nonproductive NADPH binding in the reduced state of XenA. Our analysis shows that while the principal catalytic mechanism of XenA, for example, type of proton donor, is analogous to that of other members of the old yellow enzyme family, its strategy to correctly position and accommodate different substrates is unprecedented.
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Affiliation(s)
- Olivia Spiegelhauer
- AG Bioanorganische Chemie, Universität Bayreuth, Universitätsstrasse 30, 95447 Bayreuth, Germany
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36
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Stenuit BA, Agathos SN. Microbial 2,4,6-trinitrotoluene degradation: could we learn from (bio)chemistry for bioremediation and vice versa? Appl Microbiol Biotechnol 2010; 88:1043-64. [DOI: 10.1007/s00253-010-2830-x] [Citation(s) in RCA: 64] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2010] [Revised: 08/06/2010] [Accepted: 08/08/2010] [Indexed: 12/11/2022]
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37
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Toogood H, Gardiner J, Scrutton N. Biocatalytic Reductions and Chemical Versatility of the Old Yellow Enzyme Family of Flavoprotein Oxidoreductases. ChemCatChem 2010. [DOI: 10.1002/cctc.201000094] [Citation(s) in RCA: 250] [Impact Index Per Article: 17.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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38
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Jakob RP, Zierer BK, Weininger U, Hofmann SD, Lorenz SH, Balbach J, Dobbek H, Schmid FX. Elimination of a cis-Proline-Containing Loop and Turn Optimization Stabilizes a Protein and Accelerates Its Folding. J Mol Biol 2010; 399:331-46. [DOI: 10.1016/j.jmb.2010.04.007] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2010] [Revised: 03/31/2010] [Accepted: 04/02/2010] [Indexed: 10/19/2022]
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Spiegelhauer O, Mende S, Dickert F, Knauer SH, Ullmann GM, Dobbek H. Cysteine as a modulator residue in the active site of xenobiotic reductase A: a structural, thermodynamic and kinetic study. J Mol Biol 2010; 398:66-82. [PMID: 20206186 DOI: 10.1016/j.jmb.2010.02.044] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2009] [Revised: 02/20/2010] [Accepted: 02/24/2010] [Indexed: 11/18/2022]
Abstract
Xenobiotic reductase A (XenA) from Pseudomonas putida 86 catalyzes the NADH/NADPH-dependent reduction of various substrates, including 2-cyclohexenone and 8-hydroxycoumarin. XenA is a member of the old yellow enzyme (OYE) family of flavoproteins and is structurally and functionally similar to other bacterial members of this enzyme class. A characteristic feature of XenA is the presence of a cysteine residue (Cys25) in the active site, where in most members of the OYE family a threonine residue is found that modulates the reduction potential of the FMN/FMNH(-) couple. We investigated the role of Cys25 by studying two variants in which the residue has been exchanged for a serine and an alanine residue. While the exchange against alanine has a remarkably small effect on the reduction potential, the reactivity and the structure of XenA, the exchange against serine increases the reduction potential by +82 mV, increases the rate constant of the reductive half-reaction and decreases the rate constant in the oxidative half-reaction. We determined six crystal structures at high to true atomic resolution (d(min) 1.03-1.80 A) of the three XenA variants with and without the substrate coumarin bound in the active site. The atomic resolution structure of XenA in complex with coumarin reveals a compressed active site geometry in which the isoalloxazine ring is sandwiched between coumarin and the protein backbone. The structures further reveal that the conformation of the active site and substrate interactions are preserved in the two variants, indicating that the observed changes are due to local effects only. We propose that Cys25 and the residues in its place determine which of the two half-reactions is rate limiting, depending on the substrate couple. This might help to explain why the genome of Pseudomonas putida encodes multiple xenobiotic reductases containing either cysteine, threonine or alanine in the active site.
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Affiliation(s)
- Olivia Spiegelhauer
- Bioinorganic Chemistry, Universität Bayreuth, Universitätsstrasse 30, 95447 Bayreuth, Germany
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40
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Crystal structure of a thermostable Old Yellow Enzyme from Thermus scotoductus SA-01. Biochem Biophys Res Commun 2010; 393:426-31. [DOI: 10.1016/j.bbrc.2010.02.011] [Citation(s) in RCA: 66] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2010] [Accepted: 02/03/2010] [Indexed: 11/20/2022]
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41
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Yanto Y, Hall M, Bommarius AS. Nitroreductase from Salmonella typhimurium: characterization and catalytic activity. Org Biomol Chem 2010; 8:1826-32. [DOI: 10.1039/b926274a] [Citation(s) in RCA: 62] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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42
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Spiegelhauer O, Dickert F, Mende S, Niks D, Hille R, Ullmann M, Dobbek H. Kinetic characterization of xenobiotic reductase A from Pseudomonas putida 86. Biochemistry 2009; 48:11412-20. [PMID: 19839648 DOI: 10.1021/bi901370u] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Xenobiotic reductase A (XenA) from Pseudomonas putida is a member of the old-yellow-enzyme family of flavin-containing enzymes and catalyzes the NADH/NADPH-dependent reduction of various substrates, including 8-hydroxycoumarin and 2-cyclohexenone. Here we present a kinetic and thermodynamic analysis of XenA. In the reductive half-reaction, complexes of oxidized XenA with NADH or NADPH form charge-transfer (CT) intermediates with increased absorption around 520-560 nm, which occurs with a second-order rate constant of 9.4 x 10(5) M(-1) s(-1) with NADH and 6.4 x 10(5) M(-1) s(-1) with NADPH, while its disappearance is controlled by a rate constant of 210-250 s(-1) with both substrates. Transfer of hydride from NADPH proceeds 24 times more rapidly than from NADH. This modest kinetic preference of XenA for NADPH is unlike the typical discrimination between NADH and NADPH by binding affinity. Docking studies combined with electrostatic energy calculations indicate that the 2'-phosphate group attached to the adenine moiety of NADPH is responsible for this difference. The reductions of 2-cyclohexenone and coumarin in the oxidative half-reaction are both concentration-dependent under the assay conditions and reveal a more than 50-fold larger limiting rate constant for the reduction of 2-cyclohexenone compared to that of coumarin. Our work corroborates the link between XenA and other members of the old-yellow-enzyme family but demonstrates several differences in the reactivity of these enzymes.
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Subfunctionality of hydride transferases of the old yellow enzyme family of flavoproteins of Pseudomonas putida. Appl Environ Microbiol 2008; 74:6703-8. [PMID: 18791012 DOI: 10.1128/aem.00386-08] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
To investigate potential complementary activities of multiple enzymes belonging to the same family within a single microorganism, we chose a set of Old Yellow Enzyme (OYE) homologs of Pseudomonas putida. The physiological function of these enzymes is not well established; however, an activity associated with OYE family members from different microorganisms is their ability to reduce nitroaromatic compounds. Using an in silico approach, we identified six OYE homologs in P. putida KT2440. Each gene was subcloned into an expression vector, and each corresponding gene product was purified to homogeneity prior to in vitro analysis for its catalytic activity against 2,4,6-trinitrotoluene (TNT). One of the enzymes, called XenD, lacked in vitro activity, whereas the other five enzymes demonstrated type I hydride transferase activity and reduced the nitro groups of TNT to hydroxylaminodinitrotoluene derivatives. XenB has the additional ability to reduce the aromatic ring of TNT to produce Meisenheimer complexes, defined as type II hydride transferase activity. The condensations of the primary products of type I and type II hydride transferases react with each other to yield diarylamines and nitrite; the latter can be further reduced to ammonium and serves as a nitrogen source for microorganisms in vivo.
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Jackson CJ, Taylor MC, Tattersall DB, French NG, Carr PD, Ollis DL, Russell RJ, Oakeshott JG. Cloning, expression, purification, crystallization and preliminary X-ray studies of a pyridoxine 5'-phosphate oxidase from Mycobacterium smegmatis. Acta Crystallogr Sect F Struct Biol Cryst Commun 2008; 64:435-7. [PMID: 18453720 DOI: 10.1107/s1744309108011512] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2008] [Accepted: 04/22/2008] [Indexed: 11/10/2022]
Abstract
Pyridoxine 5'-phosphate oxidases (PNPOxs) are known to catalyse the terminal step in pyridoxal 5'-phosphate biosynthesis in a flavin mononucleotide-dependent manner in humans and Escherichia coli. Recent reports of a putative PNPOx from Mycobacterium tuberculosis, Rv1155, suggest that the cofactor or catalytic mechanism may differ in Mycobacterium species. To investigate this, a putative PNPOx from M. smegmatis, Msmeg_3380, has been cloned. This enzyme has been recombinantly expressed in E. coli and purified to homogeneity. Good-quality crystals of selenomethionine-substituted Msmeg_3380 were obtained by the hanging-drop vapour-diffusion technique and diffracted to 1.2 A using synchrotron radiation.
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A novel chromate reductase from Thermus scotoductus SA-01 related to old yellow enzyme. J Bacteriol 2008; 190:3076-82. [PMID: 18263719 DOI: 10.1128/jb.01766-07] [Citation(s) in RCA: 105] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Bacteria can reduce toxic and carcinogenic Cr(VI) to insoluble and less toxic Cr(III). Thermus scotoductus SA-01, a South African gold mine isolate, has been shown to be able to reduce a variety of metals, including Cr(VI). Here we report the purification to homogeneity and characterization of a novel chromate reductase. The oxidoreductase is a homodimeric protein, with a monomer molecular mass of approximately 36 kDa, containing a noncovalently bound flavin mononucleotide cofactor. The chromate reductase is optimally active at a pH of 6.3 and at 65 degrees C and requires Ca(2+) or Mg(2+) for activity. Enzyme activity was also dependent on NADH or NADPH, with a preference for NADPH, coupling the oxidation of approximately 2 and 1.5 mol NAD(P)H to the reduction of 1 mol Cr(VI) under aerobic and anaerobic conditions, respectively. The K(m) values for Cr(VI) reduction were 3.5 and 8.4 microM for utilizing NADH and NADPH as electron donors, respectively, with corresponding V(max) values of 6.2 and 16.0 micromol min(-1) mg(-1). The catalytic efficiency (k(cat)/K(m)) of chromate reduction was 1.14 x 10(6) M(-1) s(-1), which was >50-fold more efficient than that of the quinone reductases and >180-fold more efficient than that of the nitroreductases able to reduce Cr(VI). The chromate reductase was identified to be encoded by an open reading frame of 1,050 bp, encoding a single protein of 38 kDa under the regulation of an Escherichia coli sigma(70)-like promoter. Sequence analysis shows the chromate reductase to be related to the old yellow enzyme family, in particular the xenobiotic reductases involved in the oxidative stress response.
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