1
|
Ertik O, Yanardag R. Purification and characterization of glutamate dehydrogenase from rainbow trout (Oncorhynchus mykiss) liver and molecular docking studies. Biotechnol Appl Biochem 2024. [PMID: 38689532 DOI: 10.1002/bab.2593] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2024] [Accepted: 04/16/2024] [Indexed: 05/02/2024]
Abstract
Glutamate dehydrogenase (GDH) participates in the energy metabolism of proteins and the synthesis of metabolites important for the organism. In this study, GDH enzyme was purified from the liver of rainbow trout (Oncorhynchus mykiss) by 2',5'-ADP Sepharose 4B affinity chromatography in one step. As a result of this purification process, GDH enzyme was purified 171-fold with 5.83 U/mg protein-specific activity. The characterization experiments presented that the storage stability of the purified GDH enzyme was determined as -80°C; optimum temperature 40°C; it was determined that the optimum ionic strength was 100 mM phosphate buffer and the optimum pH was 8.00. Sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS-PAGE) and PAGE studies showed that the natural molar mass of the purified GDH enzyme was 346.74 kDa, and the molar mass of its subunits was 53.71 kDa. Km and Vmax values for substrates and coenzymes of GDH enzyme purified from rainbow trout liver were calculated, and the lowest Km value was found in NAD+ (1.86 mM) and the highest Vmax value in NH4 + (1.79 U/mL). The effects of some metal ions, vitamins, and solvents on the activity of the purified GDH enzyme were investigated and also IC50 values and inhibition types. The metal ion with the lowest IC50 value is Ag+ (8.65 ± 1.68 μM), and the vitamin is B6 (0.77 ± 0.04 mM). The binding affinities of inhibitors were investigated with molecular docking, based on the conformational state of GDH.
Collapse
Affiliation(s)
- Onur Ertik
- Department of Chemistry, Faculty of Engineering, Istanbul University-Cerrahpaşa, Avcilar, Istanbul, Turkey
| | - Refiye Yanardag
- Department of Chemistry, Faculty of Engineering, Istanbul University-Cerrahpaşa, Avcilar, Istanbul, Turkey
| |
Collapse
|
2
|
Oz Tuncay F, Cakmak U, Kolcuoglu Y. Aqueous two-phase extraction and characterization of thermotolerant alkaliphilic Cladophora hutchinsiae xylanase: biochemical properties and potential applications in fruit juice clarification and fish feed supplementation. Prep Biochem Biotechnol 2024; 54:553-563. [PMID: 37668166 DOI: 10.1080/10826068.2023.2253469] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/06/2023]
Abstract
Xylanase finds extensive applications in diverse biotechnological fields such as biofuel production, pulp and paper industry, baking and brewing industry, food and feed industry, and deinking of waste paper. Here, polyethylene glycol (PEG)-phosphate aqueous two-phase system (ATPS) was applied for the purification of an alkaline active and thermotolerant xylanase from a marine source, Cladophora hutchinsiae (C. hutchinsiae). In the purification process, the effects of some experimental factors such as PEG concentration and PEG molar mass, potassium phosphate(K2HP04) concentration, and pH on xylanase distribution were systematically investigated. Relative enzymatic activity and purification factor obtained were 93.21% and 7.18, respectively. A single protein band of 28 kDa was observed on SDS-PAGE. The optimum temperature and pH of xylanase with beechwood xylan were 30 °C and 9.0, respectively. The Lineweaver-Burk graph was utilized to determine the Km (4.5 ± 0.8 mg/mL), Vmax (0.04 ± 0.01 U) and kcat (0.001 s-1) values of the enzyme. It was observed that the purified xylanase maintained 70% of its activity at 4 °C and was found stable at pH 4.0 by retaining almost all of its activity. Enzymatic activity was slightly enhanced with Na+, K+, Ca2+ and acetone. The highest increase in the reducing sugar amount was 53.6 ± 3.8, for orange juice at 50 U/mL enzyme concentration.
Collapse
Affiliation(s)
- Fulya Oz Tuncay
- Department of Chemistry, Karadeniz Technical University, Trabzon, Turkey
| | - Ummuhan Cakmak
- Department of Chemistry, Karadeniz Technical University, Trabzon, Turkey
| | - Yakup Kolcuoglu
- Department of Chemistry, Karadeniz Technical University, Trabzon, Turkey
| |
Collapse
|
3
|
Gerni S, Özdemir H. Development of a new affinity chromatography method for purification of horseradish peroxidase enzyme. Biotechnol Appl Biochem 2024; 71:202-212. [PMID: 37904288 DOI: 10.1002/bab.2532] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2023] [Accepted: 10/15/2023] [Indexed: 11/01/2023]
Abstract
In this study, benzohydroxamic acid molecules were synthesized from methyl 4-amino-2-methoxy, methyl 4-amino-3-nitro, methyl 4-amino-3-methyl, and methyl 4-amino-3-chloro benzoate molecules, and the horseradish peroxidase (HRP) enzyme was purified in one step using the affinity chromatography technique for the first time. The IC50 and Ki values for the 4-amino 3-methyl benzohydroxamic acid molecule were 0.136 and 0.132 ± 0.054 μM, respectively, while the IC50 and Ki values for the 4-amino-3-nitro benzohydroxamic acid molecule were 56.00 and 51.90 ± 9.90 μM, respectively. It was found that the IC50 and Ki values for the 4-amino-3-chloro benzohydroxamic acid molecule were 218.33 and 175.67 ± 43.78 μM, respectively, whereas the IC50 and Ki values for the 4-amino-2-methoxy benzohydroxamic acid molecule were 306.00 and 218.00 ± 68.80 μM, respectively. The HRP enzyme was synthesized from 4-amino-2-methoxy hydroxamic acid column with a 35.97% yield 601.13 times, 4-amino-3-nitro hydroxamic acid column, with a 14.00% yield 404.11 times, 4-amino-3-methyl hydroxamic acid column with an 8.70% yield 394.88 times, and 4-amino-3-chloro hydroxamic acid column with a 4.48% yield 284.85 times. Thus, the HRP enzyme was purified in a single step with hydroxamic acids, and its molecular weight was found to be 44 kDa. The optimum pH was 8.0, the optimum temperature was 15°C, and the optimum ionic strength was 0.4 M for the purified HRP enzyme.
Collapse
Affiliation(s)
- Serpil Gerni
- Department of Chemistry, Faculty of Science, Ataturk University, Erzurum, Turkey
| | - Hasan Özdemir
- Department of Chemistry, Faculty of Science, Ataturk University, Erzurum, Turkey
| |
Collapse
|
4
|
Işık K, Soydan E. Purification and characterisation of glutathione reductase from scorpionfish (scorpaena porcus) and investigation of heavy metal ions inhibition. J Enzyme Inhib Med Chem 2023; 38:2167078. [PMID: 36938699 PMCID: PMC10035961 DOI: 10.1080/14756366.2023.2167078] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/21/2023] Open
Abstract
In the current study, glutathione reductase was purified from Scorpion fish (Scorpaena porcus) liver tissue and the effects of heavy metal ions on the enzyme activity were determined. The purification process consisted of three stages; preparation of the homogenate, ammonium sulphate precipitation and affinity chromatography purification. At the end of these steps, the enzyme was purified 25.9-fold with a specific activity of 10.479 EU/mg and a yield of 28.3%. The optimum pH was found to be 6.5, optimum substrate concentration was 2 mM NADPH and optimum buffer was 300 mM KH2PO4. After purification, inhibition effects of Mn+2, Cd+2, Ni+2, and Cr3+, as heavy metal ions were investigated. IC50 values of the heavy metals were calculated as 2.4 µM, 30 µM, 135 µM and 206 µM, respectively.
Collapse
Affiliation(s)
- Kübra Işık
- Department of Agricultural Biotechnology, Faculty of Agriculture, Ondokuz Mayıs University, Samsun, Turkey
| | - Ercan Soydan
- Department of Agricultural Biotechnology, Faculty of Agriculture, Ondokuz Mayıs University, Samsun, Turkey
| |
Collapse
|
5
|
Rivera-Morán MA, Sampedro JG. Isolation of the Sarcoplasmic Reticulum Ca 2+-ATPase from Rabbit Fast-Twitch Muscle. Methods Protoc 2023; 6:102. [PMID: 37888034 PMCID: PMC10608927 DOI: 10.3390/mps6050102] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2023] [Revised: 10/13/2023] [Accepted: 10/17/2023] [Indexed: 10/28/2023] Open
Abstract
The sarcoendoplasmic reticulum Ca2+-ATPase (SERCA) is a membrane protein that is destabilized during purification in the absence of calcium ions. The disaccharide trehalose is a protein stabilizer that accumulates in the yeast cytoplasm when under stress. In the present work, SERCA was purified by including trehalose in the purification protocol. The purified SERCA showed high protein purity (~95%) and ATPase activity. ATP hydrolysis was dependent on the presence of Ca2+ and the enzyme kinetics showed a hyperbolic dependence on ATP (Km = 12.16 ± 2.25 μM ATP). FITC labeling showed the integrity of the ATP-binding site and the identity of the isolated enzyme as a P-type ATPase. Circular dichroism (CD) spectral changes at a wavelength of 225 nm were observed upon titration with ATP, indicating α-helical rearrangements in the nucleotide-binding domain (N-domain), which correlated with ATP affinity (Km). The presence of Ca2+ did not affect FITC labeling or the ATP-mediated structural changes at the N-domain. The use of trehalose in the SERCA purification protocol stabilized the enzyme. The isolated SERCA appears to be suitable for structural and ligand binding studies, e.g., for testing newly designed or natural inhibitors. The use of trehalose is recommended for the isolation of unstable enzymes.
Collapse
Affiliation(s)
| | - José G. Sampedro
- Instituto de Física, Universidad Autónoma de San Luis Potosí, Avenida Chapultepec 1570, Privadas del Pedregal, San Luis Potosí 78295, Mexico
| |
Collapse
|
6
|
Baltacı A, Cıkrıkcı K, Gençer N. Investigation of the effects of some pesticides on carbonic anhydrase isoenzymes. J Mol Recognit 2023; 36:e3048. [PMID: 37551992 DOI: 10.1002/jmr.3048] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2023] [Revised: 06/25/2023] [Accepted: 07/20/2023] [Indexed: 08/09/2023]
Abstract
The aim of this study was to investigate the inhibitory effects of some pesticides known to have harmful effects on human health on carbonic anhydrase isoenzymes. Therefore, carbonic anhydrase isoenzymes (hCA I and II) were purified from human erythrocytes. The isoenzymes were purified from human erythrocytes by using an affinity column that has the chemical structure of Sepharose-4B-4-(6-amino-hexyloxy)-benzenesulfonamide. The purity of the isoenzymes was checked by sodium dodecyl sulphate polyacrylamide gel electrophoresis (SDSPAGE). It was determined that the pesticides used in this study inhibit hCA I and hCA II isoenzymes at different levels in vitro. It was determined that the strongest inhibitor for the hCA I enzyme was Carbofuran (IC50 :6.52 μM; Ki : 3.58 μM) and the weakest one was 1-Naphtol (IC50 :16.55 μM; Ki : 14.4 μM) among these pesticides. It was also found that the strongest inhibitor for the hCA II enzyme was coumatetralil (IC50 :5.06 μM; Ki : 1.62 μM) and the weakest one was Dimethachlor (IC50 14.6 μM; Ki : 8.44 μM).
Collapse
Affiliation(s)
- Aybike Baltacı
- Department of Chemistry, Faculty of Art and Sciences, Balikesir University, Balikesir, Turkey
| | - Kubra Cıkrıkcı
- Department of Chemistry, Faculty of Art and Sciences, Balikesir University, Balikesir, Turkey
| | - Nahit Gençer
- Department of Chemistry, Faculty of Art and Sciences, Balikesir University, Balikesir, Turkey
| |
Collapse
|
7
|
Narita T, Tobisawa Y, Bobkov A, Jackson M, Ohyama C, Irie F, Yamaguchi Y. TMEM2 is a bona fide hyaluronidase possessing intrinsic catalytic activity. J Biol Chem 2023; 299:105120. [PMID: 37527776 PMCID: PMC10474455 DOI: 10.1016/j.jbc.2023.105120] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2023] [Revised: 07/25/2023] [Accepted: 07/27/2023] [Indexed: 08/03/2023] Open
Abstract
Transmembrane protein 2 (TMEM2) was originally identified as a membrane-anchored protein of unknown function. We previously demonstrated that TMEM2 can degrade hyaluronan (HA). Furthermore, we showed that induced global knockout of Tmem2 in adult mice results in rapid accumulation of incompletely degraded HA in bodily fluids and organs, supporting the identity of TMEM2 as a cell surface hyaluronidase. In spite of these advances, no direct evidence has been presented to demonstrate the intrinsic hyaluronidase activity of TMEM2. Here, we directly establish the catalytic activity of TMEM2. The ectodomain of TMEM2 (TMEM2ECD) was expressed as a His-tagged soluble protein and purified by affinity and size-exclusion chromatography. Both human and mouse TMEM2ECD robustly degrade fluorescein-labeled HA into 5 to 10 kDa fragments. TMEM2ECD exhibits this HA-degrading activity irrespective of the species of TMEM2 origin and the position of epitope tag insertion. The HA-degrading activity of TMEM2ECD is more potent than that of HYAL2, a hyaluronidase which, like TMEM2, has been implicated in cell surface HA degradation. Finally, we show that TMEM2ECD can degrade not only fluorescein-labeled HA but also native high-molecular weight HA. In addition to these core findings, our study reveals hitherto unrecognized confounding factors, such as the quality of reagents and the choice of assay systems, that could lead to erroneous conclusions regarding the catalytic activity of TMEM2. In conclusion, our results demonstrate that TMEM2 is a legitimate functional hyaluronidase. Our findings also raise cautions regarding the choice of reagents and methods for performing degradation assays for hyaluronidases.
Collapse
Affiliation(s)
- Takuma Narita
- Human Genetics Program, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, California, USA
| | - Yuki Tobisawa
- Human Genetics Program, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, California, USA; Department of Urology, Hirosaki University Graduate School of Medicine, Hirosaki, Japan
| | - Andrey Bobkov
- Conrad Prebys Center for Chemical Genomics, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, California, USA
| | - Michael Jackson
- Conrad Prebys Center for Chemical Genomics, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, California, USA
| | - Chikara Ohyama
- Department of Urology, Hirosaki University Graduate School of Medicine, Hirosaki, Japan
| | - Fumitoshi Irie
- Human Genetics Program, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, California, USA
| | - Yu Yamaguchi
- Human Genetics Program, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, California, USA.
| |
Collapse
|
8
|
Ahmad MS, Shah N, Akbar Z, Khan T, Ali A. Simple two-step purification and characterisation of peroxidase from Citrullus colocynthis. Nat Prod Res 2023:1-10. [PMID: 37621192 DOI: 10.1080/14786419.2023.2248644] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/26/2023]
Abstract
Peroxidase is a biotechnologically important enzyme. The purification of peroxidase from the root of Citrullus colocynthis was carried out in a simple two-step process with maximum purity level. The sample was extracted in a high salt buffer, and the enzyme was partially purified with a Q-Sepharose anion exchange column. Final purification was carried out with HighLoad 16/600 Superdex G-75 column. The purified protein was analysed with SDS gel electrophoresis, which suggested a single band of approximately 35 kDa. Further, the enzyme was identified with the help of Mass spectrometric analysis using an ESI-QTOF Mass spectrometer. The study will be helpful for the isolation and its commercial uses in biotechnology.
Collapse
Affiliation(s)
- Malik Shoaib Ahmad
- Dr. Panjwani Center for Molecular Medicine and Drug Research, International Center for Chemical and Biological Sciences, University of Karachi, Karachi, Pakistan
- H. E. J. Research Institute of Chemistry, International Center for Chemical and Biological Sciences, University of Karachi, Karachi, Pakistan
| | - Nayab Shah
- Dr. Panjwani Center for Molecular Medicine and Drug Research, International Center for Chemical and Biological Sciences, University of Karachi, Karachi, Pakistan
| | - Zeeshan Akbar
- H. E. J. Research Institute of Chemistry, International Center for Chemical and Biological Sciences, University of Karachi, Karachi, Pakistan
| | - Tajwali Khan
- Dr. Panjwani Center for Molecular Medicine and Drug Research, International Center for Chemical and Biological Sciences, University of Karachi, Karachi, Pakistan
| | - Arslan Ali
- Dr. Panjwani Center for Molecular Medicine and Drug Research, International Center for Chemical and Biological Sciences, University of Karachi, Karachi, Pakistan
- H. E. J. Research Institute of Chemistry, International Center for Chemical and Biological Sciences, University of Karachi, Karachi, Pakistan
| |
Collapse
|
9
|
Pinmanee P, Sompinit K, Jantimaporn A, Khongkow M, Haltrich D, Nimchua T, Sukyai P. Purification and Immobilization of Superoxide Dismutase Obtained from Saccharomyces cerevisiae TBRC657 on Bacterial Cellulose and Its Protective Effect against Oxidative Damage in Fibroblasts. Biomolecules 2023; 13:1156. [PMID: 37509191 PMCID: PMC10377281 DOI: 10.3390/biom13071156] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2023] [Revised: 07/13/2023] [Accepted: 07/19/2023] [Indexed: 07/30/2023] Open
Abstract
Superoxide dismutase (SOD) is an essential enzyme that eliminates harmful reactive oxygen species (ROS) generating inside living cells. Due to its efficacities, SOD is widely applied in many applications. In this study, the purification of SOD produced from Saccharomyces cerevisiae TBRC657 was conducted to obtain the purified SOD that exhibited specific activity of 513.74 U/mg with a purification factor of 10.36-fold. The inhibitory test revealed that the purified SOD was classified as Mn-SOD with an estimated molecular weight of 25 kDa on SDS-PAGE. After investigating the biochemical characterization, the purified SOD exhibited optimal activity under conditions of pH 7.0 and 35 °C, which are suitable for various applications. The stability test showed that the purified SOD rapidly decreased in activity under high temperatures. To overcome this, SOD was successfully immobilized on bacterial cellulose (BC), resulting in enhanced stability under those conditions. The immobilized SOD was investigated for its ability to eliminate ROS in fibroblasts. The results indicated that the immobilized SOD released and retained its function to regulate the ROS level inside the cells. Thus, the immobilized SOD on BC could be a promising candidate for application in many industries that require antioxidant functionality under operating conditions.
Collapse
Affiliation(s)
- Phitsanu Pinmanee
- Biotechnology of Biopolymers and Bioactive Compounds Special Research Unit, Department of Biotechnology, Faculty of Agro-Industry, Kasetsart University, Bangkok 10900, Thailand
- Enzyme Technology Research Team, National Center of Genetic Engineering and Biotechnology (BIOTEC), Pathum Thani 12120, Thailand
| | - Kamonwan Sompinit
- Enzyme Technology Research Team, National Center of Genetic Engineering and Biotechnology (BIOTEC), Pathum Thani 12120, Thailand
| | - Angkana Jantimaporn
- Nanomedicine and Veterinary Research Team, National Center of Nanotechnology (NANOTEC), Pathum Thani 12120, Thailand
| | - Mattaka Khongkow
- Nanomedicine and Veterinary Research Team, National Center of Nanotechnology (NANOTEC), Pathum Thani 12120, Thailand
| | - Dietmar Haltrich
- Department for Food Science and Food Technology, University of Natural Resources and Life Sciences (BOKU), 1190 Vienna, Austria
| | - Thidarat Nimchua
- Enzyme Technology Research Team, National Center of Genetic Engineering and Biotechnology (BIOTEC), Pathum Thani 12120, Thailand
| | - Prakit Sukyai
- Biotechnology of Biopolymers and Bioactive Compounds Special Research Unit, Department of Biotechnology, Faculty of Agro-Industry, Kasetsart University, Bangkok 10900, Thailand
| |
Collapse
|
10
|
Zhou Y, Syed JH, Semchonok DA, Wright E, Kyrilis FL, Hamdi F, Kastritis PL, Bruce BD, Reynolds TB. Solubilization, purification, and characterization of the hexameric form of phosphatidylserine synthase from Candida albicans. J Biol Chem 2023:104756. [PMID: 37116705 DOI: 10.1016/j.jbc.2023.104756] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2022] [Revised: 04/17/2023] [Accepted: 04/18/2023] [Indexed: 04/30/2023] Open
Abstract
Phosphatidylserine (PS) synthase from Candida albicans, encoded by the CHO1 gene, has been identified as a potential drug target for new antifungals against systemic candidiasis. Rational drug design or small molecule screening are effective ways to identify specific inhibitors of Cho1, but both will be facilitated by protein purification. Due to the transmembrane nature of Cho1, methods were needed to solubilize and purify the native form of Cho1. Here, we used six non-ionic detergents and three styrene maleic acids (SMAs) to solubilize an HA-tagged Cho1 protein from the total microsomal fractions. Blue native PAGE (BN-PAGE) and immunoblot analysis revealed a single band corresponding to Cho1 in all detergent-solubilized fractions, while two bands were present in the SMA2000-solubilized fraction. Our enzymatic assay suggests that digitonin- or DDM-solubilized enzyme has the most PS synthase activity. Pull-downs of HA-tagged Cho1 in the digitonin-solubilized fraction reveal an apparent MW of Cho1 consistent with a hexamer. Furthermore, negative-staining electron microscopy analysis and AlphaFold2 structure prediction modeling suggest the hexamer is composed of a trimer of dimers. We purified Cho1 protein to near-homogeneity as a hexamer using affinity chromatography and TEV protease treatment, and optimized Cho1 enzyme activity for manganese and detergent concentrations, temperature (24°C), and pH (8.0). The purified Cho1 has a Km for its substrate CDP-diacylglycerol of 72.20 μM with a Vmax of 0.079 nmol/(μg*min) while exhibiting a sigmoidal kinetic curve for its other substrate serine, indicating cooperative binding. Purified hexameric Cho1 can potentially be used in downstream structure determination and small drug screening.
Collapse
Affiliation(s)
- Yue Zhou
- Department of Microbiology, University of Tennessee at Knoxville, Knoxville, TN, United States
| | - Jawhar H Syed
- Department of Biochemistry Cellular and Molecular Biology, University of Tennessee Knoxville, Knoxville, TN, United States
| | - Dmitry A Semchonok
- Interdisciplinary Research Center HALOmem & Institute of Biochemistry and Biotechnology, Martin Luther University Halle-Wittenberg, Halle, Germany
| | - Edward Wright
- Department of Biochemistry Cellular and Molecular Biology, University of Tennessee Knoxville, Knoxville, TN, United States
| | - Fotis L Kyrilis
- Interdisciplinary Research Center HALOmem & Institute of Biochemistry and Biotechnology, Martin Luther University Halle-Wittenberg, Halle, Germany
| | - Farzad Hamdi
- Interdisciplinary Research Center HALOmem & Institute of Biochemistry and Biotechnology, Martin Luther University Halle-Wittenberg, Halle, Germany
| | - Panagiotis L Kastritis
- Interdisciplinary Research Center HALOmem & Institute of Biochemistry and Biotechnology, Martin Luther University Halle-Wittenberg, Halle, Germany
| | - Barry D Bruce
- Department of Microbiology, University of Tennessee at Knoxville, Knoxville, TN, United States; Department of Biochemistry Cellular and Molecular Biology, University of Tennessee Knoxville, Knoxville, TN, United States
| | - Todd B Reynolds
- Department of Microbiology, University of Tennessee at Knoxville, Knoxville, TN, United States
| |
Collapse
|
11
|
Miao L, Sun S, Ma T, Abdelrahman Yousif Abdellah Y, Wang Y, Mi Y, Yan H, Sun G, Hou N, Zhao X, Li C, Zang H. A Novel Estrone Degradation Gene Cluster and Catabolic Mechanism in Microbacterium oxydans ML-6. Appl Environ Microbiol 2023; 89:e0148922. [PMID: 36847539 PMCID: PMC10057884 DOI: 10.1128/aem.01489-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Accepted: 02/05/2023] [Indexed: 03/01/2023] Open
Abstract
Global-scale estrone (E1) contamination of soil and aquatic environments results from the widespread use of animal manure as fertilizer, threatening both human health and environmental security. A detailed understanding of the degradation of E1 by microorganisms and the associated catabolic mechanism remains a key challenge for the bioremediation of E1-contaminated soil. Here, Microbacterium oxydans ML-6, isolated from estrogen-contaminated soil, was shown to efficiently degrade E1. A complete catabolic pathway for E1 was proposed via liquid chromatography-tandem mass spectrometry (LC-MS/MS), genome sequencing, transcriptomic analysis, and quantitative reverse transcription-PCR (qRT-PCR). In particular, a novel gene cluster (moc) associated with E1 catabolism was predicted. The combination of heterologous expression, gene knockout, and complementation experiments demonstrated that the 3-hydroxybenzoate 4-monooxygenase (MocA; a single-component flavoprotein monooxygenase) encoded by the mocA gene was responsible for the initial hydroxylation of E1. Furthermore, to demonstrate the detoxification of E1 by strain ML-6, phytotoxicity tests were performed. Overall, our findings provide new insight into the molecular mechanism underlying the diversity of E1 catabolism in microorganisms and suggest that M. oxydans ML-6 and its enzymes have potential applications in E1 bioremediation to reduce or eliminate E1-related environmental pollution. IMPORTANCE Steroidal estrogens (SEs) are mainly produced by animals, while bacteria are major consumers of SEs in the biosphere. However, the understanding of the gene clusters that participate in E1 degradation is still limited, and the enzymes involved in the biodegradation of E1 have not been well characterized. The present study reports that M. oxydans ML-6 has effective SE degradation capacity, which facilitates the development of strain ML-6 as a broad-spectrum biocatalyst for the production of certain desired compounds. A novel gene cluster (moc) associated with E1 catabolism was predicted. The 3-hydroxybenzoate 4-monooxygenase (MocA; a single-component flavoprotein monooxygenase) identified in the moc cluster was found to be necessary and specific for the initial hydroxylation of E1 to generate 4-OHE1, providing new insight into the biological role of flavoprotein monooxygenase.
Collapse
Affiliation(s)
- Lei Miao
- College of Resources and Environment, Northeast Agricultural University, Harbin, People’s Republic of China
| | - Shanshan Sun
- College of Resources and Environment, Northeast Agricultural University, Harbin, People’s Republic of China
| | - Tian Ma
- College of Resources and Environment, Northeast Agricultural University, Harbin, People’s Republic of China
| | | | - Yue Wang
- College of Resources and Environment, Northeast Agricultural University, Harbin, People’s Republic of China
| | - Yaozu Mi
- College of Resources and Environment, Northeast Agricultural University, Harbin, People’s Republic of China
| | - Haohao Yan
- College of Resources and Environment, Northeast Agricultural University, Harbin, People’s Republic of China
| | - Guanjun Sun
- College of Resources and Environment, Northeast Agricultural University, Harbin, People’s Republic of China
| | - Ning Hou
- College of Resources and Environment, Northeast Agricultural University, Harbin, People’s Republic of China
| | - Xinyue Zhao
- College of Resources and Environment, Northeast Agricultural University, Harbin, People’s Republic of China
| | - Chunyan Li
- College of Resources and Environment, Northeast Agricultural University, Harbin, People’s Republic of China
| | - Hailian Zang
- College of Resources and Environment, Northeast Agricultural University, Harbin, People’s Republic of China
| |
Collapse
|
12
|
Eneva R, Engibarov S, Gocheva Y, Mitova S, Arsov A, Petrov K, Abrashev R, Lazarkevich I, Petrova P. Safe Sialidase Production by the Saprophyte Oerskovia paurometabola: Gene Sequence and Enzyme Purification. Molecules 2022; 27:molecules27248922. [PMID: 36558051 PMCID: PMC9782813 DOI: 10.3390/molecules27248922] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2022] [Revised: 12/01/2022] [Accepted: 12/14/2022] [Indexed: 12/23/2022] Open
Abstract
Sialidase preparations are applied in structural and functional studies on sialoglycans, in the production of sialylated therapeutic proteins and synthetic substrates for use in biochemical research, etc. They are obtained mainly from pathogenic microorganisms; therefore, the demand for apathogenic producers of sialidase is of exceptional importance for the safe production of this enzyme. Here, we report for the first time the presence of a sialidase gene and enzyme in the saprophytic actinomycete Oerskovia paurometabola strain O129. An electrophoretically pure, glycosylated enzyme with a molecular weight of 70 kDa was obtained after a two-step chromatographic procedure using DEAE cellulose and Q-sepharose. The biochemical characterization showed that the enzyme is extracellular, inductive, and able to cleave α(2→3,6,8) linked sialic acids with preference for α(2→3) bonds. The enzyme production was strongly induced by glycomacropeptide (GMP) from milk whey, as well as by sialic acid. Investigation of the deduced amino acid sequence revealed that the protein molecule has the typical six-bladed β-propeller structure and contains all features of bacterial sialidases, i.e., an YRIP motif, five Asp-boxes, and the conserved amino acids in the active site. The presence of an unusual signal peptide of 40 amino acids was predicted. The sialidase-producing O. paurometabola O129 showed high and constant enzyme production. Together with its saprophytic nature, this makes it a reliable producer with high potential for industrial application.
Collapse
Affiliation(s)
- Rumyana Eneva
- Institute of Microbiology, Bulgarian Academy of Sciences, 1113 Sofia, Bulgaria
- Correspondence:
| | - Stephan Engibarov
- Institute of Microbiology, Bulgarian Academy of Sciences, 1113 Sofia, Bulgaria
| | - Yana Gocheva
- Institute of Microbiology, Bulgarian Academy of Sciences, 1113 Sofia, Bulgaria
| | - Simona Mitova
- Institute of Microbiology, Bulgarian Academy of Sciences, 1113 Sofia, Bulgaria
| | - Alexander Arsov
- Institute of Microbiology, Bulgarian Academy of Sciences, 1113 Sofia, Bulgaria
| | - Kaloyan Petrov
- Institute of Chemical Engineering, Bulgarian Academy of Sciences, 1113 Sofia, Bulgaria
| | - Radoslav Abrashev
- Institute of Microbiology, Bulgarian Academy of Sciences, 1113 Sofia, Bulgaria
| | - Irina Lazarkevich
- Institute of Microbiology, Bulgarian Academy of Sciences, 1113 Sofia, Bulgaria
| | - Penka Petrova
- Institute of Microbiology, Bulgarian Academy of Sciences, 1113 Sofia, Bulgaria
| |
Collapse
|
13
|
Ahmed S, Miller WT. The noncatalytic regions of the tyrosine kinase Tnk1 are important for activity and substrate specificity. J Biol Chem 2022; 298:102664. [PMID: 36334623 DOI: 10.1016/j.jbc.2022.102664] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2022] [Revised: 10/24/2022] [Accepted: 10/27/2022] [Indexed: 11/29/2022] Open
Abstract
Human Tnk1 (thirty-eight negative kinase 1) is a member of the Ack family of nonreceptor tyrosine kinases. Tnk1 contains a sterile alpha motif, a tyrosine kinase catalytic domain, an SH3 (Src homology 3) domain, and a large C-terminal region that contains a ubiquitin association domain. However, specific physiological roles for Tnk1 have not been characterized in depth. Here, we expressed and purified Tnk1 from Sf9 insect cells and established an in vitro assay system using a peptide substrate derived from the Wiskott-Aldrich Syndrome Protein (WASP). By Tnk1 expression in mammalian cells, we found that the N-terminal SAM domain is important for self-association and kinase activity. We also studied a fusion protein, originally discovered in a Hodgkin's Lymphoma cell line, that contains an unrelated sequence from the C17ORF61 gene fused to the C-terminus of Tnk1. Cells expressing the fusion protein showed increased tyrosine phosphorylation of cellular substrates relative to cells expressing WT Tnk1. A truncated Tnk1 construct (residues 1-465) also showed enhanced phosphorylation, indicating that the C17ORF61 sequence was dispensable for the effect. Additionally, in vitro kinase assays with the WASP peptide substrate showed no increase in intrinsic Tnk1 activity in C-terminally truncated constructs, suggesting that the truncations did not simply remove an autoinhibitory element. Fluorescence microscopy experiments demonstrated that the C-terminus of Tnk1 plays an important role in the subcellular localization of the kinase. Taken together, our data suggest that the noncatalytic regions of Tnk1 play important roles in governing activity and substrate phosphorylation.
Collapse
|
14
|
Biasoto HP, Hebeda CB, Farsky SHP, Pessoa A, Costa-Silva TA, Monteiro G. Extracellular expression of Saccharomyces cerevisiae's L-asparaginase II in Pichia pastoris results in novel enzyme with better parameters. Prep Biochem Biotechnol 2022; 53:511-522. [PMID: 35981094 DOI: 10.1080/10826068.2022.2111582] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/15/2022]
Abstract
L-asparaginase (ASNase) is an efficient inhibitor of tumor development, used in chemotherapy sessions against acute lymphoblastic leukemia (ALL) tumor cells; its use results in 80% complete remission of the disease in treated patients. Saccharomyces cerevisiae's L-asparaginase II (ScASNaseII) has a high potential to substitute bacteria ASNase in patients that developed hypersensitivity, but the endogenous production of it results in hypermannosylated immunogenic enzyme. Here we describe the genetic process to acquire the ScASNaseII expressed in the extracellular medium. Our strategy involved a fusion of mature sequence of protein codified by ASP3 (amino acids 26-362) with the secretion signal sequence of Pichia pastoris acid phosphatase enzyme; in addition, this DNA construction was integrated in P. pastoris Glycoswitch® strain genome, which has the cellular machinery to express and secrete high quantity of enzymes with humanized glycosylation. Our data show that the DNA construction and strain employed can express extracellular asparaginase with specific activity of 218.2 IU mg-1. The resultant enzyme is 40% more stable than commercially available Escherichia coli's ASNase (EcASNaseII) when incubated with human serum. In addition, ScASNaseII presents 50% lower cross-reaction with anti-ASNase antibody produced against EcASNaseII when compared with ASNase from Dickeya chrysanthemi.
Collapse
Affiliation(s)
- Henrique P Biasoto
- Departamento de Tecnologia Bioquímico-Farmacêutica, Faculdade de Ciências Farmacêuticas, Universidade de São Paulo, São Paulo, Brazil
| | - Cristina B Hebeda
- Departamento de Análises Clínicas e Toxicológicas, Faculdade de Ciências Farmacêuticas, Universidade de São Paulo, São Paulo, Brazil
| | - Sandra H P Farsky
- Departamento de Análises Clínicas e Toxicológicas, Faculdade de Ciências Farmacêuticas, Universidade de São Paulo, São Paulo, Brazil
| | - Adalberto Pessoa
- Departamento de Tecnologia Bioquímico-Farmacêutica, Faculdade de Ciências Farmacêuticas, Universidade de São Paulo, São Paulo, Brazil
| | - Tales A Costa-Silva
- Centro de Ciencias Naturais e Humanas, Universidade Federal do ABC, Santo André, SP, Brazil
| | - Gisele Monteiro
- Departamento de Tecnologia Bioquímico-Farmacêutica, Faculdade de Ciências Farmacêuticas, Universidade de São Paulo, São Paulo, Brazil
| |
Collapse
|
15
|
Jäckel L, Schnabel A, Stellmach H, Klauß U, Matschi S, Hause G, Vogt T. The terminal enzymatic step in piperine biosynthesis is co-localized with the product piperine in specialized cells of black pepper (Piper nigrum L.). Plant J 2022; 111:731-747. [PMID: 35634755 DOI: 10.1111/tpj.15847] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/15/2022] [Revised: 05/18/2022] [Accepted: 05/26/2022] [Indexed: 06/15/2023]
Abstract
Piperine (1-piperoyl piperidine) is responsible for the pungent perception of dried black pepper (Piper nigrum) fruits and essentially contributes to the aromatic properties of this spice in combination with a blend of terpenoids. The final step in piperine biosynthesis involves piperine synthase (PS), which catalyzes the reaction of piperoyl CoA and piperidine to the biologically active and pungent amide. Nevertheless, experimental data on the cellular localization of piperine and the complete biosynthetic pathway are missing. Not only co-localization of enzymes and products, but also potential transport of piperamides to the sink organs is a possible alternative. This work, which includes purification of the native enzyme, immunolocalization, laser microdissection, fluorescence microscopy, and electron microscopy combined with liquid chromatography electrospray ionization tandem mass spectrometry (LC-ESI-MS/MS), provides experimental evidence that piperine and PS are co-localized in specialized cells of the black pepper fruit perisperm. PS accumulates during early stages of fruit development and its level declines before the fruits are fully mature. The product piperine is co-localized to PS and can be monitored at the cellular level by its strong bluish fluorescence. Rising piperine levels during fruit maturation are consistent with the increasing numbers of fluorescent cells within the perisperm. Signal intensities of individual laser-dissected cells when monitored by LC-ESI-MS/MS indicate molar concentrations of this alkaloid. Significant levels of piperine and additional piperamides were also detected in cells distributed in the cortex of black pepper roots. In summary, the data provide comprehensive experimental evidence of and insights into cell-specific biosynthesis and storage of piperidine alkaloids, specific and characteristic for the Piperaceae. By a combination of fluorescence microscopy and LC-MS/MS analysis we localized the major piperidine alkaloids to specific cells of the fruit perisperm and the root cortex. Immunolocalization of native piperine and piperamide synthases shows that enzymes are co-localized with high concentrations of products in these idioblasts.
Collapse
Affiliation(s)
- Luise Jäckel
- Department of Cell and Metabolic Biology, Leibniz Institute of Plant Biochemistry, Weinberg 3, D-06120, Halle (Saale), Germany
| | - Arianne Schnabel
- Department of Cell and Metabolic Biology, Leibniz Institute of Plant Biochemistry, Weinberg 3, D-06120, Halle (Saale), Germany
| | - Hagen Stellmach
- Department of Cell and Metabolic Biology, Leibniz Institute of Plant Biochemistry, Weinberg 3, D-06120, Halle (Saale), Germany
| | - Ulrike Klauß
- Department of Cell and Metabolic Biology, Leibniz Institute of Plant Biochemistry, Weinberg 3, D-06120, Halle (Saale), Germany
| | - Susanne Matschi
- Department of Biochemistry of Plant Interactions, Leibniz Institute of Plant Biochemistry, Weinberg 3, D-06120, Halle (Saale), Germany
| | - Gerd Hause
- Electron Microscopy Lab, Biocenter, Martin-Luther-University Halle-Wittenberg, Weinbergweg 22, D-06120, Halle (Saale), Germany
| | - Thomas Vogt
- Department of Cell and Metabolic Biology, Leibniz Institute of Plant Biochemistry, Weinberg 3, D-06120, Halle (Saale), Germany
| |
Collapse
|
16
|
Sun S, Bi X, Yang B, Zhang W, Zhang X, Sun S, Xiao J, Yang Y, Huang Z. Nitrite removal by Acinetobacter sp.TX: a candidate of curbing N 2O emission. Environmental Technology 2022; 43:2300-2309. [PMID: 33427603 DOI: 10.1080/09593330.2021.1874543] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/18/2020] [Accepted: 01/01/2021] [Indexed: 06/12/2023]
Abstract
The nitrite removal pathway in Acinetobacter sp. TX5 was explored through the key gene identification and the corresponding enzyme purification, after which the capability to reduce nitrite by immobilized beads was investigated in a fixed-bed reactor. Results revealed that a nosZ gene encoding nitrous oxide reductase (N2OR) exists in TX5 cells, and a N2OR responsible for the reduction of N2O to N2 was purified successfully with a molecular weight of 70.05 kDa, a purification fold of 16.30 and a recovery rate of 5.17%. For TX5 immobilization, the optimal values of polyvinyl alcohol (PVA), spent mushroom substrate (SMS) and Aci (TX5) obtained by response surface methodology (RSM) were 6.32%, 2.92% and 4.57%, respectively. In a fixed-bed reactor packed with immobilized TX5, the removal efficiency (RE) achieved 90% (at 50 h) for NO2--N and 85% (at 96 h) for total nitrogen (TN). On the basis of these results, a nitrite removal pathway in TX5 was proposed. Overall, Acinetobacter sp. TX5 might be a promising candidate for nitrite removal with an ability to suppress N2O accumulation.
Collapse
Affiliation(s)
- Shuqian Sun
- College of Life Science, Fujian Agriculture and Forestry University, Fuhzou, People's Republic of China
| | - Xiaohui Bi
- College of Life Science, Fujian Agriculture and Forestry University, Fuhzou, People's Republic of China
| | - Bin Yang
- College of Life Science, Fujian Agriculture and Forestry University, Fuhzou, People's Republic of China
| | - Weihong Zhang
- College of Life Science, Fujian Agriculture and Forestry University, Fuhzou, People's Republic of China
| | - Xinyu Zhang
- College of Life Science, Fujian Agriculture and Forestry University, Fuhzou, People's Republic of China
| | - Shujing Sun
- College of Life Science, Fujian Agriculture and Forestry University, Fuhzou, People's Republic of China
| | - Jibo Xiao
- College of Life and Environmental Science, Wenzhou University, Wenzhou, People's Republic of China
- Wenzhou Chuangyuan Environment Technology Co. Ltd., Wenzhou, People's Republic of China
| | - Yunlong Yang
- College of Life and Environmental Science, Wenzhou University, Wenzhou, People's Republic of China
| | - Zhida Huang
- Wenzhou Institute of Industry & Science, Wenzhou, People's Republic of China
| |
Collapse
|
17
|
Ramírez-Silva L, Hernández-Alcántara G, Guerrero-Mendiola C, González-Andrade M, Rodríguez-Romero A, Rodríguez-Hernández A, Lugo-Munguía A, Gómez-Coronado PA, Rodríguez-Méndez C, Vega-Segura A. The K +-Dependent and -Independent Pyruvate Kinases Acquire the Active Conformation by Different Mechanisms. Int J Mol Sci 2022; 23:1347. [PMID: 35163274 DOI: 10.3390/ijms23031347] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2021] [Revised: 01/15/2022] [Accepted: 01/17/2022] [Indexed: 12/10/2022] Open
Abstract
Eukarya pyruvate kinases possess glutamate at position 117 (numbering of rabbit muscle enzyme), whereas bacteria have either glutamate or lysine. Those with E117 are K+-dependent, whereas those with K117 are K+-independent. In a phylogenetic tree, 80% of the sequences with E117 are occupied by T113/K114/T120 and 77% of those with K117 possess L113/Q114/(L,I,V)120. This work aims to understand these residues’ contribution to the K+-independent pyruvate kinases using the K+-dependent rabbit muscle enzyme. Residues 117 and 120 are crucial in the differences between the K+-dependent and -independent mutants. K+-independent activity increased with L113 and Q114 to K117, but L120 induced structural differences that inactivated the enzyme. T120 appears to be key in folding the protein and closure of the lid of the active site to acquire its active conformation in the K+-dependent enzymes. E117K mutant was K+-independent and the enzyme acquired the active conformation by a different mechanism. In the K+-independent apoenzyme of Mycobacterium tuberculosis, K72 (K117) flips out of the active site; in the holoenzyme, K72 faces toward the active site bridging the substrates through water molecules. The results provide evidence that two different mechanisms have evolved for the catalysis of this reaction.
Collapse
|
18
|
Abstract
Colistin (polymyxin E) and polymyxin B have been used as last-resort agents for treating infections caused by multidrug-resistant Gram-negative bacteria. However, their efficacy has been challenged by the emergence of the mobile colistin resistance gene mcr-1, which encodes a transmembrane phosphoethanolamine (PEA) transferase enzyme, MCR-1. The enzyme catalyzes the transfer of the cationic PEA moiety of phosphatidylethanolamine (PE) to lipid A, thereby neutralizing the negative charge of lipid A and blocking the binding of positively charged polymyxins. This study aims to facilitate understanding of the mechanism of the MCR-1 enzyme by investigating its active-site sequence requirements. For this purpose, 23 active-site residues of MCR-1 protein were randomized by constructing single-codon randomization libraries. The libraries were individually selected for supporting Escherichia coli cell growth in the presence of colistin or polymyxin B. Deep sequencing of the polymyxin-resistant clones revealed that wild-type residues predominates at 17 active-site residue positions, indicating these residues play critical roles in MCR-1 function. These residues include Zn2+-chelating residues as well as residues that may form a hydrogen bond network with the PEA moiety or make hydrophobic interactions with the acyl chains of PE. Any mutations at these residues significantly decrease polymyxin resistance levels and the PEA transferase activity of the MCR-1 enzyme. Therefore, deep sequencing of the randomization libraries of MCR-1 enzyme identifies active-site residues that are essential for its polymyxin resistance function. Thus, these residues may be utilized as targets to develop inhibitors to circumvent MCR-1-mediated polymyxin resistance.
Collapse
|
19
|
Öztürk C, Bayrak S, Demir Y, Aksoy M, Alım Z, Özdemir H, İrfan Küfrevioglu Ö. Some indazoles as alternative inhibitors for potato polyphenol oxidase. Biotechnol Appl Biochem 2021; 69:2249-2256. [PMID: 34775655 DOI: 10.1002/bab.2283] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2021] [Accepted: 11/09/2021] [Indexed: 01/12/2023]
Abstract
Fresh-cut vegetables and fruits have gained attention among consumers because of their fresh appearance, lack of pollution, nutrition, and convenience. However, in fresh-cut foods, enzymatic browning is the main problem. Polyphenol oxidase (PPO) is a vital enzyme involved in the process of enzymatic browning. In this study, PPO was purified from potato using Sepharose 4B-l-tyrosine-p-aminobenzoic acid affinity chromatography and the effect of some indazoles on the enzyme was determined. The enzyme was purified with a specific activity of 52,857.14 EU/mg protein and 21.26-purification fold. Indazoles exhibited inhibitor properties for PPO with IC50 values in the range of 0.11-1.12 mM and Ki values in the range of 0.15 ± 0.04-3.55 ± 0.88 mM. Among these compounds, 7-chloro-1H-indazole was shown as the most potent PPO inhibitor (Ki : 0.15 ± 0.04 mM). Determination of the enzyme's inhibition kinetics will simplify the testing of candidate PPO inhibitors.
Collapse
Affiliation(s)
- Cansu Öztürk
- Department of Chemistry, Faculty of Sciences, Atatürk University, Erzurum, Turkey
| | - Songül Bayrak
- Department of Chemistry, Faculty of Sciences, Atatürk University, Erzurum, Turkey
| | - Yeliz Demir
- Department of Pharmacy Services, Nihat Delibalta Göle Vocational High School, Ardahan University, Ardahan, Turkey
| | - Mine Aksoy
- Department of Chemistry, Faculty of Sciences, Atatürk University, Erzurum, Turkey
| | - Zuhal Alım
- Department of Chemistry, Faculty of Science and Arts, Ahievran University, Kırşehir, Turkey
| | - Hasan Özdemir
- Department of Chemistry, Faculty of Sciences, Atatürk University, Erzurum, Turkey
| | | |
Collapse
|
20
|
Fenice M, Khare SK, Gorrasi S. Editorial: Mining, Designing, Mechanisms and Applications of Extremophilic Enzymes. Front Microbiol 2021; 12:709377. [PMID: 34759895 PMCID: PMC8573210 DOI: 10.3389/fmicb.2021.709377] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2021] [Accepted: 09/29/2021] [Indexed: 11/13/2022] Open
Affiliation(s)
- Massimiliano Fenice
- Dipartimento di Scienze Biologiche ed Ecologiche, University of Tuscia, Viterbo, Italy
| | - Sunil Kumar Khare
- Department of Chemistry, Indian Institute of Technology Delhi, New Delhi, India
| | - Susanna Gorrasi
- Dipartimento di Scienze Biologiche ed Ecologiche, University of Tuscia, Viterbo, Italy
| |
Collapse
|
21
|
Sharma C, Osmolovskiy A, Singh R. Microbial Fibrinolytic Enzymes as Anti-Thrombotics: Production, Characterisation and Prodigious Biopharmaceutical Applications. Pharmaceutics 2021; 13:1880. [PMID: 34834294 PMCID: PMC8625737 DOI: 10.3390/pharmaceutics13111880] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2021] [Revised: 10/23/2021] [Accepted: 10/29/2021] [Indexed: 12/19/2022] Open
Abstract
Cardiac disorders such as acute myocardial infarction, embolism and stroke are primarily attributed to excessive fibrin accumulation in the blood vessels, usually consequential in thrombosis. Numerous methodologies including the use of anti-coagulants, anti-platelet drugs, surgical operations and fibrinolytic enzymes are employed for the dissolution of fibrin clots and hence ameliorate thrombosis. Microbial fibrinolytic enzymes have attracted much more attention in the management of cardiovascular disorders than typical anti-thrombotic strategies because of the undesirable after-effects and high expense of the latter. Fibrinolytic enzymes such as plasminogen activators and plasmin-like proteins hydrolyse thrombi with high efficacy with no significant after-effects and can be cost effectively produced on a large scale with a short generation time. However, the hunt for novel fibrinolytic enzymes necessitates complex purification stages, physiochemical and structural-functional attributes, which provide an insight into their mechanism of action. Besides, strain improvement and molecular technologies such as cloning, overexpression and the construction of genetically modified strains for the enhanced production of fibrinolytic enzymes significantly improve their thrombolytic potential. In addition, the unconventional applicability of some fibrinolytic enzymes paves their way for protein hydrolysis in addition to fibrin/thrombi, blood pressure regulation, anti-microbials, detergent additives for blood stain removal, preventing dental caries, anti-inflammatory and mucolytic expectorant agents. Therefore, this review article encompasses the production, biochemical/structure-function properties, thrombolytic potential and other surplus applications of microbial fibrinolytic enzymes.
Collapse
Affiliation(s)
- Chhavi Sharma
- Amity Institute of Microbial Technology, Amity University Uttar Pradesh, Noida 201313, India;
| | - Alexander Osmolovskiy
- Department of Microbiology, Faculty of Biology, Lomonosov Moscow State University, 119991 Moscow, Russia
| | - Rajni Singh
- Amity Institute of Microbial Technology, Amity University Uttar Pradesh, Noida 201313, India;
| |
Collapse
|
22
|
Yakasai HM, Rahman MF, Manogaran M, Yasid NA, Syed MA, Shamaan NA, Shukor MY. Microbiological Reduction of Molybdenum to Molybdenum Blue as a Sustainable Remediation Tool for Molybdenum: A Comprehensive Review. Int J Environ Res Public Health 2021; 18:5731. [PMID: 34071757 PMCID: PMC8198738 DOI: 10.3390/ijerph18115731] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/14/2021] [Revised: 04/07/2021] [Accepted: 04/08/2021] [Indexed: 11/19/2022]
Abstract
Molybdenum (Mo) microbial bioreduction is a phenomenon that is beginning to be recognized globally as a tool for the remediation of molybdenum toxicity. Molybdenum toxicity continues to be demonstrated in many animal models of spermatogenesis and oogenesis, particularly those of ruminants. The phenomenon has been reported for more than 100 years without a clear understanding of the reduction mechanism, indicating a clear gap in the scientific knowledge. This knowledge is not just fundamentally important-it is specifically important in applications for bioremediation measures and the sustainable recovery of metal from industrial or mine effluent. To date, about 52 molybdenum-reducing bacteria have been isolated globally. An increasing number of reports have also been published regarding the assimilation of other xenobiotics. This phenomenon is likely to be observed in current and future events in which the remediation of xenobiotics requires microorganisms capable of degrading or transforming multi-xenobiotics. This review aimed to comprehensively catalogue all of the characterizations of molybdenum-reducing microorganisms to date and identify future opportunities and improvements.
Collapse
Affiliation(s)
- Hafeez Muhammad Yakasai
- Department of Biochemistry, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, Serdang 43400, Malaysia; (H.M.Y.); (M.F.R.); (M.M.); (N.A.Y.); (M.A.S.)
- Department of Biochemistry, Faculty of Basic Medical Sciences, College of Health Science, Bayero University, Kano PMB 3011, Nigeria
| | - Mohd Fadhil Rahman
- Department of Biochemistry, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, Serdang 43400, Malaysia; (H.M.Y.); (M.F.R.); (M.M.); (N.A.Y.); (M.A.S.)
| | - Motharasan Manogaran
- Department of Biochemistry, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, Serdang 43400, Malaysia; (H.M.Y.); (M.F.R.); (M.M.); (N.A.Y.); (M.A.S.)
| | - Nur Adeela Yasid
- Department of Biochemistry, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, Serdang 43400, Malaysia; (H.M.Y.); (M.F.R.); (M.M.); (N.A.Y.); (M.A.S.)
| | - Mohd Arif Syed
- Department of Biochemistry, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, Serdang 43400, Malaysia; (H.M.Y.); (M.F.R.); (M.M.); (N.A.Y.); (M.A.S.)
| | - Nor Aripin Shamaan
- Faculty of Medicine and Health Sciences, Universiti Sains Islam Malaysia, Kuala Lumpur 55100, Malaysia;
| | - Mohd Yunus Shukor
- Department of Biochemistry, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, Serdang 43400, Malaysia; (H.M.Y.); (M.F.R.); (M.M.); (N.A.Y.); (M.A.S.)
| |
Collapse
|
23
|
Anand G, Leibman-Markus M, Elkabetz D, Bar M. Method for the Production and Purification of Plant Immuno-Active Xylanase from Trichoderma. Int J Mol Sci 2021; 22:4214. [PMID: 33921693 PMCID: PMC8073006 DOI: 10.3390/ijms22084214] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Revised: 04/12/2021] [Accepted: 04/15/2021] [Indexed: 11/18/2022] Open
Abstract
Plants lack a circulating adaptive immune system to protect themselves against pathogens. Therefore, they have evolved an innate immune system based upon complicated and efficient defense mechanisms, either constitutive or inducible. Plant defense responses are triggered by elicitors such as microbe-associated molecular patterns (MAMPs). These components are recognized by pattern recognition receptors (PRRs) which include plant cell surface receptors. Upon recognition, PRRs trigger pattern-triggered immunity (PTI). Ethylene Inducing Xylanase (EIX) is a fungal MAMP protein from the plant-growth-promoting fungi (PGPF)-Trichoderma. It elicits plant defense responses in tobacco (Nicotiana tabacum) and tomato (Solanum lycopersicum), making it an excellent tool in the studies of plant immunity. Xylanases such as EIX are hydrolytic enzymes that act on xylan in hemicellulose. There are two types of xylanases: the endo-1, 4-β-xylanases that hydrolyze within the xylan structure, and the β-d-xylosidases that hydrolyze the ends of the xylan chain. Xylanases are mainly synthesized by fungi and bacteria. Filamentous fungi produce xylanases in high amounts and secrete them in liquid cultures, making them an ideal system for xylanase purification. Here, we describe a method for cost- and yield-effective xylanase production from Trichoderma using wheat bran as a growth substrate. Xylanase produced by this method possessed xylanase activity and immunogenic activity, effectively inducing a hypersensitive response, ethylene biosynthesis, and ROS burst.
Collapse
Affiliation(s)
- Gautam Anand
- Department of Plant Pathology and Weed Research, Plant Protection Institute, Agricultural Research Organization, Volcani Institute, Rishon LeZion 50250, Israel; (G.A.); (M.L.-M.); (D.E.)
| | - Meirav Leibman-Markus
- Department of Plant Pathology and Weed Research, Plant Protection Institute, Agricultural Research Organization, Volcani Institute, Rishon LeZion 50250, Israel; (G.A.); (M.L.-M.); (D.E.)
| | - Dorin Elkabetz
- Department of Plant Pathology and Weed Research, Plant Protection Institute, Agricultural Research Organization, Volcani Institute, Rishon LeZion 50250, Israel; (G.A.); (M.L.-M.); (D.E.)
- Department of Plant Pathology and Microbiology, Faculty of Agriculture, Hebrew University of Jerusalem, Rehovot 91905, Israel
| | - Maya Bar
- Department of Plant Pathology and Weed Research, Plant Protection Institute, Agricultural Research Organization, Volcani Institute, Rishon LeZion 50250, Israel; (G.A.); (M.L.-M.); (D.E.)
| |
Collapse
|
24
|
Karagöz FP, Demir Y, Kotan MŞ, Dursun A, Beydemir Ş, Dikbaş N. Purification of the phytase enzyme from Lactobacillus plantarum: The effect on pansy growth and macro-micro element content. Biotechnol Appl Biochem 2020; 68:1067-1075. [PMID: 32919432 DOI: 10.1002/bab.2026] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
In the present study, the phytase enzyme was purified from Lactobacillus plantarum with a 3.08% recovery, 9.57-purification fold, and with a specific activity of 278.82 EU/mg protein. Then, the effects of the 5 EU and 10 EU purified phytase was determined on the plant growth, quality, the macro-micro nutrient content of pansy (Viola × wittrockiana), which is of great importance in ornamental plants industry. The research was established under greenhouse conditions with natural light in 2017. The pansy seeds were coated with phytase enzyme solution, sown in a peat environment, and transferred to pots at the seedling period. In general, the 5 EU and 10 EU applications increase plant height, the number of leaves per plant, the number of side branches per plant, and flower height parameters compared to control. Also, micro- and macronutrient values in soil and plant samples were examined. According to the results, the phytase application on pansy cultivation positively affected the properties and yielded high quality of plants.
Collapse
Affiliation(s)
| | - Yeliz Demir
- Department of Pharmacy Services, Nihat Delibalta Göle Vocational High School, Ardahan University, Ardahan, Turkey
| | - Merve Şenol Kotan
- Department of Agricultural Biotechnology, Faculty of Agriculture, Ataturk University, Erzurum, Turkey
| | - Atilla Dursun
- Department of Horticulture, Faculty of Agriculture, Atatürk University, Erzurum, Turkey
| | - Şükrü Beydemir
- Department Biochemistry, Faculty Pharmacy, Anadolu University, Eskişehir, Turkey.,The Rectorate of Bilecik Şeyh Edebali University, Bilecik, Turkey
| | - Neslihan Dikbaş
- Department of Agricultural Biotechnology, Faculty of Agriculture, Ataturk University, Erzurum, Turkey
| |
Collapse
|
25
|
Kalin R, Köksal Z, Bayrak S, Gerni S, Ozyürek IN, Usanmaz H, Karaman M, Atasever A, Özdemir H, Gülçin İ. Molecular docking and inhibition profiles of some antibiotics on lactoperoxidase enzyme purified from bovine milk. J Biomol Struct Dyn 2020; 40:401-410. [PMID: 32856529 DOI: 10.1080/07391102.2020.1814416] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
Antibiotics are generally used for human and veterinary applications to preserve and to control microbial diseases. Milk has a biologically significant enzyme known as lactoperoxidase (LPO) that is a member of peroxidase family. In metabolism, LPO has ability to catalyze the transformation of thiocyanate (SCN-) to hypothiocyanite (OSCN-) that is an antibacterial agent and the reaction occurs with hydrogen peroxide. In this work, LPO inhibition effects of some antibiotics including cefazolin, oxytetracycline, flunixin meglumine, cefuroxime, tylosin, vancomycin, chloramphenicol and lincomycin were tested. Among the antibiotics cefazolin was indicated the strongest inhibitory efficacy. The half maximal inhibitory concentration (IC50) and the inhibition constant (Ki) values of cefazolin were found as 8.19 and 34.66 µM, respectively. It was shown competitive inhibition. 5-Methyl-1,3,4-thiadiazol-2-yl moiety activity plays a key role in the inhibition mechanism of cefazolin.Communicated by Ramaswamy H. Sarma.
Collapse
Affiliation(s)
- Ramazan Kalin
- Department of Basic Science, Faculty of Science, Erzurum Technical University, Erzurum, Turkey
| | - Zeynep Köksal
- Department of Chemistry, Faculty of Engineering and Natural Sciences, İstanbul Medeniyet University, İstanbul, Turkey
| | - Songül Bayrak
- Department of Chemistry, Faculty of Science, Atatürk University, Erzurum, Turkey
| | - Serpil Gerni
- Department of Chemistry, Faculty of Science, Atatürk University, Erzurum, Turkey
| | - Işıl Nihan Ozyürek
- Department of Chemistry, Faculty of Science, Atatürk University, Erzurum, Turkey
| | - Hande Usanmaz
- Department of Bioengineering, Faculty of Engineering and Architecture, Sinop University, Sinop, Turkey
| | - Muhammet Karaman
- Department of Molecular Biology and Genetics, Faculty of Arts and Science, Kilis 7 Aralik University, Kilis, Turkey
| | - Ali Atasever
- Ispir Hamza Polat Vocational Training School, Ataturk University, Erzurum, Turkey
| | - Hasan Özdemir
- Department of Chemistry, Faculty of Science, Atatürk University, Erzurum, Turkey
| | - İlhami Gülçin
- Department of Chemistry, Faculty of Science, Atatürk University, Erzurum, Turkey
| |
Collapse
|
26
|
Martinelli L, Adamopoulos A, Johansson P, Wan PT, Gunnarsson J, Guo H, Boyd H, Zelcer N, Sixma TK. Structural analysis of the LDL receptor-interacting FERM domain in the E3 ubiquitin ligase IDOL reveals an obscured substrate-binding site. J Biol Chem 2020; 295:13570-13583. [PMID: 32727844 PMCID: PMC7521653 DOI: 10.1074/jbc.ra120.014349] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2020] [Revised: 07/21/2020] [Indexed: 12/31/2022] Open
Abstract
Hepatic abundance of the low-density lipoprotein receptor (LDLR) is a critical determinant of circulating plasma LDL cholesterol levels and hence development of coronary artery disease. The sterol-responsive E3 ubiquitin ligase inducible degrader of the LDLR (IDOL) specifically promotes ubiquitination and subsequent lysosomal degradation of the LDLR and thus controls cellular LDL uptake. IDOL contains an extended N-terminal FERM (4.1 protein, ezrin, radixin, and moesin) domain, responsible for substrate recognition and plasma membrane association, and a second C-terminal RING domain, responsible for the E3 ligase activity and homodimerization. As IDOL is a putative lipid-lowering drug target, we investigated the molecular details of its substrate recognition. We produced and isolated full-length IDOL protein, which displayed high autoubiquitination activity. However, in vitro ubiquitination of its substrate, the intracellular tail of the LDLR, was low. To investigate the structural basis for this, we determined crystal structures of the extended FERM domain of IDOL and multiple conformations of its F3ab subdomain. These reveal the archetypal F1-F2-F3 trilobed FERM domain structure but show that the F3c subdomain orientation obscures the target-binding site. To substantiate this finding, we analyzed the full-length FERM domain and a series of truncated FERM constructs by small-angle X-ray scattering (SAXS). The scattering data support a compact and globular core FERM domain with a more flexible and extended C-terminal region. This flexibility may explain the low activity in vitro and suggests that IDOL may require activation for recognition of the LDLR.
Collapse
Affiliation(s)
- Luca Martinelli
- Division of Biochemistry, Netherlands Cancer Institute, Amsterdam, The Netherlands; Department of Medical Biochemistry, Amsterdam UMC, Amsterdam Cardiovascular Sciences and Gastroenterology and Metabolism, University of Amsterdam, Amsterdam, the Netherlands
| | | | - Patrik Johansson
- IMED Biotech Unit, Discovery Sciences, AstraZeneca, Mölndal, Sweden
| | - Paul T Wan
- IMED Biotech Unit, Discovery Sciences, AstraZeneca, Mölndal, Sweden
| | - Jenny Gunnarsson
- IMED Biotech Unit, Discovery Sciences, AstraZeneca, Mölndal, Sweden
| | - Hongwei Guo
- IMED Biotech Unit, Discovery Sciences, AstraZeneca, Mölndal, Sweden
| | - Helen Boyd
- IMED Biotech Unit, Discovery Sciences, AstraZeneca, Mölndal, Sweden
| | - Noam Zelcer
- Department of Medical Biochemistry, Amsterdam UMC, Amsterdam Cardiovascular Sciences and Gastroenterology and Metabolism, University of Amsterdam, Amsterdam, the Netherlands.
| | - Titia K Sixma
- Division of Biochemistry, Netherlands Cancer Institute, Amsterdam, The Netherlands; Oncode Institute, Utrecht, The Netherlands.
| |
Collapse
|
27
|
Linde D, Olmedo A, González-Benjumea A, Estévez M, Renau-Mínguez C, Carro J, Fernández-Fueyo E, Gutiérrez A, Martínez AT. Two New Unspecific Peroxygenases from Heterologous Expression of Fungal Genes in Escherichia coli. Appl Environ Microbiol 2020; 86:e02899-19. [PMID: 31980430 DOI: 10.1128/AEM.02899-19] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2019] [Accepted: 01/17/2020] [Indexed: 12/22/2022] Open
Abstract
UPOs catalyze regio- and stereoselective oxygenations of both aromatic and aliphatic compounds. Similar reactions were previously described for cytochrome P450 monooxygenases, but UPOs have the noteworthy biotechnological advantage of being stable enzymes requiring only H2O2 to be activated. Both characteristics are related to the extracellular nature of UPOs as secreted proteins. In the present study, the limited repertoire of UPO enzymes available for organic synthesis and other applications is expanded with the description of two new ascomycete UPOs obtained by Escherichia coli expression of the corresponding genes as soluble and active enzymes. Moreover, directed mutagenesis in E. coli, together with enzyme molecular modeling, provided relevant structure-function information on aromatic substrate oxidation by these two new biocatalysts. Unspecific peroxygenases (UPOs) constitute a new family of fungal heme-thiolate enzymes in which there is high biotechnological interest. Although several thousand genes encoding hypothetical UPO-type proteins have been identified in sequenced fungal genomes and other databases, only a few UPO enzymes have been experimentally characterized to date. Therefore, gene screening and heterologous expression from genetic databases are a priority in the search for ad hoc UPOs for oxyfunctionalization reactions of interest. Very recently, Escherichia coli production of a previously described basidiomycete UPO (as a soluble and active enzyme) has been reported. Here, we explored this convenient heterologous expression system to obtain the protein products from available putative UPO genes. In this way, two UPOs from the ascomycetes Collariella virescens (syn., Chaetomium virescens) and Daldinia caldariorum were successfully obtained, purified, and characterized. Comparison of their kinetic constants for oxidation of model substrates revealed 10- to 20-fold-higher catalytic efficiency of the latter enzyme in oxidizing simple aromatic compounds (such as veratryl alcohol, naphthalene, and benzyl alcohol). Homology molecular models of these enzymes showed three conserved and two differing residues in the distal side of the heme (the latter representing two different positions of a phenylalanine residue). Interestingly, replacement of the C. virescens UPO Phe88 by the homologous residue in the D. caldariorum UPO resulted in an F88L variant with 5- to 21-fold-higher efficiency in oxidizing these aromatic compounds. IMPORTANCE UPOs catalyze regio- and stereoselective oxygenations of both aromatic and aliphatic compounds. Similar reactions were previously described for cytochrome P450 monooxygenases, but UPOs have the noteworthy biotechnological advantage of being stable enzymes requiring only H2O2 to be activated. Both characteristics are related to the extracellular nature of UPOs as secreted proteins. In the present study, the limited repertoire of UPO enzymes available for organic synthesis and other applications is expanded with the description of two new ascomycete UPOs obtained by Escherichia coli expression of the corresponding genes as soluble and active enzymes. Moreover, directed mutagenesis in E. coli, together with enzyme molecular modeling, provided relevant structure-function information on aromatic substrate oxidation by these two new biocatalysts.
Collapse
|
28
|
Stomberski CT, Anand P, Venetos NM, Hausladen A, Zhou HL, Premont RT, Stamler JS. AKR1A1 is a novel mammalian S-nitroso-glutathione reductase. J Biol Chem 2019; 294:18285-18293. [PMID: 31649033 DOI: 10.1074/jbc.ra119.011067] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2019] [Revised: 10/16/2019] [Indexed: 12/11/2022] Open
Abstract
Oxidative modification of Cys residues by NO results in S-nitrosylation, a ubiquitous post-translational modification and a primary mediator of redox-based cellular signaling. Steady-state levels of S-nitrosylated proteins are largely determined by denitrosylase enzymes that couple NAD(P)H oxidation with reduction of S-nitrosothiols, including protein and low-molecular-weight (LMW) S-nitrosothiols (S-nitroso-GSH (GSNO) and S-nitroso-CoA (SNO-CoA)). SNO-CoA reductases require NADPH, whereas enzymatic reduction of GSNO can involve either NADH or NADPH. Notably, GSNO reductase (GSNOR, Adh5) accounts for most NADH-dependent GSNOR activity, whereas NADPH-dependent GSNOR activity is largely unaccounted for (CBR1 mediates a minor portion). Here, we de novo purified NADPH-coupled GSNOR activity from mammalian tissues and identified aldo-keto reductase family 1 member A1 (AKR1A1), the archetypal mammalian SNO-CoA reductase, as a primary mediator of NADPH-coupled GSNOR activity in these tissues. Kinetic analyses suggested an AKR1A1 substrate preference of SNO-CoA > GSNO. AKR1A1 deletion from murine tissues dramatically lowered NADPH-dependent GSNOR activity. Conversely, GSNOR-deficient mice had increased AKR1A1 activity, revealing potential cross-talk among GSNO-dependent denitrosylases. Molecular modeling and mutagenesis of AKR1A1 identified Arg-312 as a key residue mediating the specific interaction with GSNO; in contrast, substitution of the SNO-CoA-binding residue Lys-127 minimally affected the GSNO-reducing activity of AKR1A1. Together, these findings indicate that AKR1A1 is a multi-LMW-SNO reductase that can distinguish between and metabolize the two major LMW-SNO signaling molecules GSNO and SNO-CoA, allowing for wide-ranging control of protein S-nitrosylation under both physiological and pathological conditions.
Collapse
Affiliation(s)
- Colin T Stomberski
- Department of Biochemistry, Case Western Reserve University School of Medicine, Cleveland, Ohio 44106; Institute for Transformative Molecular Medicine, Case Western Reserve University School of Medicine, Cleveland, Ohio 44016
| | - Puneet Anand
- Institute for Transformative Molecular Medicine, Case Western Reserve University School of Medicine, Cleveland, Ohio 44016
| | - Nicholas M Venetos
- Department of Biochemistry, Case Western Reserve University School of Medicine, Cleveland, Ohio 44106; Institute for Transformative Molecular Medicine, Case Western Reserve University School of Medicine, Cleveland, Ohio 44016
| | - Alfred Hausladen
- Institute for Transformative Molecular Medicine, Case Western Reserve University School of Medicine, Cleveland, Ohio 44016
| | - Hua-Lin Zhou
- Department of Biochemistry, Case Western Reserve University School of Medicine, Cleveland, Ohio 44106; Institute for Transformative Molecular Medicine, Case Western Reserve University School of Medicine, Cleveland, Ohio 44016
| | - Richard T Premont
- Institute for Transformative Molecular Medicine, Case Western Reserve University School of Medicine, Cleveland, Ohio 44016; Harrington Discovery Institute, University Hospitals Cleveland Medical Center, Cleveland, Ohio 44016
| | - Jonathan S Stamler
- Institute for Transformative Molecular Medicine, Case Western Reserve University School of Medicine, Cleveland, Ohio 44016; Harrington Discovery Institute, University Hospitals Cleveland Medical Center, Cleveland, Ohio 44016; Department of Medicine, Case Western Reserve University School of Medicine, Cleveland, Ohio 44016.
| |
Collapse
|
29
|
Gökçe B, Sarıoğlu N, Gençer N, Arslan O. Association of human serum paraoxonase-1 with some respiratory drugs. J Biochem Mol Toxicol 2019; 33:e22407. [PMID: 31581362 DOI: 10.1002/jbt.22407] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2018] [Revised: 09/16/2019] [Accepted: 09/20/2019] [Indexed: 01/31/2023]
Abstract
In this study, we investigated the effects of certain respiratory drugs, which are mainly used on human serum paraoxonase-1 (hPON1; EC 3.1.8.1). hPON1 was purified from human serum, with 354.91 fold and 45% yield by using two simple step procedures including, first, ammonium sulfate precipitation, then, Sepharose-4B-l-tyrosine-1-naphthylamine hydrophobic interaction chromatography. SDS-polyacrylamide gel electrophoresis showed a single protein band belonging to hPON1 with 43 kDa. All the pharmaceutical compounds inhibited the PON1 enzyme highly at the micromolar level. The obtained IC50 values for nine different pharmaceutics ranged from 0.219 μM (salbutamol sulfate) to 67.205 μM (montelukast sodium). So, all drugs could be considered as potent hPON1 inhibitors. Ki values and inhibition types were determined by Lineweaver-Burk graphs. While varenicline tartrate and moxifloxacin hydrochloride inhibited the enzyme in a noncompetitive manner, others inhibited it in a mixed manner.
Collapse
Affiliation(s)
- Başak Gökçe
- Department of Biochemistry, Faculty of Pharmacy, Suleyman Demirel University, Isparta, Turkey
| | - Nurhan Sarıoğlu
- Department of Pulmonary Diseases, Faculty of Medicine, Balikesir University, Balikesir, Turkey
| | - Nahit Gençer
- Department of Chemistry, Faculty of Art and Science, Balikesir University, Balikesir, Turkey
| | - Oktay Arslan
- Department of Chemistry, Faculty of Art and Science, Balikesir University, Balikesir, Turkey
| |
Collapse
|
30
|
Yin L, Harwood CS. Functional divergence of annotated l-isoaspartate O-methyltransferases in an α-proteobacterium. J Biol Chem 2019; 294:2854-2861. [PMID: 30578298 DOI: 10.1074/jbc.ra118.006546] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2018] [Revised: 12/14/2018] [Indexed: 12/28/2022] Open
Abstract
Spontaneous formation of isoaspartates (isoDs) often causes protein damage. l-Isoaspartate O-methyltransferase (PIMT) repairs isoD residues by catalyzing the formation of an unstable l-isoaspartyl methyl ester that spontaneously converts to an l-aspartyl residue. PIMTs are widely distributed in all three domains of life and have been studied most intensively in connection with their role in protein repair and aging in plants and animals. Studies of bacterial PIMTs have been limited to Escherichia coli, which has one PIMT. The α-proteobacterium Rhodopseudomonas palustris has three annotated PIMT genes, one of which (rpa2580) has been found to be important for cellular longevity in a growth-arrested state. However, the biochemical activities of these three R. palustris PIMTs are unknown. Here, we expressed and characterized all three annotated PIMT proteins, finding that two of them, RPA0376 and RPA2838, had PIMT activity, whereas RPA2580 did not. RPA0376 and RPA2838 single- and double-deletion mutants did not differ in longevity from WT R. palustris and did not exhibit elevated levels of isoD residues in aged cells. Comparative sequence analyses revealed that RPA2580 belongs to a separate phylogenetic group of annotated PIMT proteins present in the α-proteobacteria. Our results suggest that this group of proteins is not involved in repair of protein isoD residues. In addition, the bona fide bacterial PIMT enzymes may play a different or subtler role in bacterial physiology than previously suggested.
Collapse
Affiliation(s)
- Liang Yin
- From the Department of Microbiology, University of Washington, Seattle, Washington 98195
| | - Caroline S Harwood
- From the Department of Microbiology, University of Washington, Seattle, Washington 98195
| |
Collapse
|
31
|
Baldin SM, Shcherbakova TA, Švedas VK. Isolation, Purification and Characterization of L,D-transpeptidase 2 from Mycobacterium tuberculosis. Acta Naturae 2019; 11:23-28. [PMID: 31024745 PMCID: PMC6475871] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022] Open
Abstract
L,D-transpeptidase 2 from Mycobacterium tuberculosis plays a key role in the formation of nonclassical 3-3 peptidoglycan cross-links in a pathogen's cell wall making it resistant to a broad range of penicillin antibiotics. The conditions of cultivation, isolation, and purification of recombinant L,D-transpeptidase 2 from M. tuberculosis have been optimized in this study. Oxidation of the free SH groups of catalytic cysteine Cys354 is an important factor causing the inactivation of the enzyme, which occurs during both the expression and storage of enzyme preparations. The biochemical characteristics of purified L,D-transpeptidase 2 and L,D-transpeptidase 2 lacking domain A were determined; the kinetic constants of enzyme-catalyzed nitrocefin transformation were evaluated.
Collapse
Affiliation(s)
- S. M. Baldin
- Lomonosov Moscow State University, Belozersky Institute of Physicochemical Biology, Leninskie gory 1, bldg. 40, 119991, Moscow, Russia ,Lomonosov Moscow State University, Faculty of Chemistry, Leninskie gory 1, bldg. 3, 119991, Moscow, Russia
| | - T. A. Shcherbakova
- Lomonosov Moscow State University, Belozersky Institute of Physicochemical Biology, Leninskie gory 1, bldg. 40, 119991, Moscow, Russia
| | - V. K. Švedas
- Lomonosov Moscow State University, Belozersky Institute of Physicochemical Biology, Leninskie gory 1, bldg. 40, 119991, Moscow, Russia
| |
Collapse
|
32
|
Lee CJ, Rana MS, Bae C, Li Y, Banerjee A. In vitro reconstitution of Wnt acylation reveals structural determinants of substrate recognition by the acyltransferase human Porcupine. J Biol Chem 2018; 294:231-245. [PMID: 30420431 DOI: 10.1074/jbc.ra118.005746] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2018] [Revised: 10/30/2018] [Indexed: 11/06/2022] Open
Abstract
Wnt proteins regulate a large number of processes, including cellular growth, differentiation, and tissue homeostasis, through the highly conserved Wnt signaling pathway in metazoans. Porcupine (PORCN) is an endoplasmic reticulum (ER)-resident integral membrane enzyme that catalyzes posttranslational modification of Wnts with palmitoleic acid, an unsaturated lipid. This unique form of lipidation with palmitoleic acid is a vital step in the biogenesis and secretion of Wnt, and PORCN inhibitors are currently in clinical trials for cancer treatment. However, PORCN-mediated Wnt lipidation has not been reconstituted in vitro with purified enzyme. Here, we report the first successful purification of human PORCN and confirm, through in vitro reconstitution with the purified enzyme, that PORCN is necessary and sufficient for Wnt acylation. By systematically examining a series of substrate variants, we show that PORCN intimately recognizes the local structure of Wnt around the site of acylation. Our in vitro assay enabled us to examine the activity of PORCN with a range of fatty acyl-CoAs with varying length and unsaturation. The selectivity of human PORCN across a spectrum of fatty acyl-CoAs suggested that the kink in the unsaturated acyl chain is a key determinant of PORCN-mediated catalysis. Finally, we show that two putative PORCN inhibitors that were discovered with cell-based assays indeed target human PORCN. Together, these results provide discrete, high-resolution biochemical insights into the mechanism of PORCN-mediated Wnt acylation and pave the way for further detailed biochemical and structural studies.
Collapse
Affiliation(s)
- Chul-Jin Lee
- Cell Biology and Neurobiology Branch, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland 20892
| | - Mitra S Rana
- Cell Biology and Neurobiology Branch, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland 20892
| | - Chanhyung Bae
- Molecular Physiology and Biophysics Section, Porter Neuroscience Research Center, NINDS, National Institutes of Health, Bethesda, Maryland 20892
| | - Yan Li
- Protein/Peptide Sequencing Facility, NINDS, National Institutes of Health, Bethesda, Maryland 20892
| | - Anirban Banerjee
- Cell Biology and Neurobiology Branch, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland 20892.
| |
Collapse
|
33
|
Kytidou K, Beekwilder J, Artola M, van Meel E, Wilbers RHP, Moolenaar GF, Goosen N, Ferraz MJ, Katzy R, Voskamp P, Florea BI, Hokke CH, Overkleeft HS, Schots A, Bosch D, Pannu N, Aerts JMFG. Nicotiana benthamiana α-galactosidase A1.1 can functionally complement human α-galactosidase A deficiency associated with Fabry disease. J Biol Chem 2018; 293:10042-10058. [PMID: 29674318 PMCID: PMC6028973 DOI: 10.1074/jbc.ra118.001774] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2018] [Revised: 04/17/2018] [Indexed: 11/06/2022] Open
Abstract
α-Galactosidases (EC 3.2.1.22) are retaining glycosidases that cleave terminal α-linked galactose residues from glycoconjugate substrates. α-Galactosidases take part in the turnover of cell wall-associated galactomannans in plants and in the lysosomal degradation of glycosphingolipids in animals. Deficiency of human α-galactosidase A (α-Gal A) causes Fabry disease (FD), a heritable, X-linked lysosomal storage disorder, characterized by accumulation of globotriaosylceramide (Gb3) and globotriaosylsphingosine (lyso-Gb3). Current management of FD involves enzyme-replacement therapy (ERT). An activity-based probe (ABP) covalently labeling the catalytic nucleophile of α-Gal A has been previously designed to study α-galactosidases for use in FD therapy. Here, we report that this ABP labels proteins in Nicotiana benthamiana leaf extracts, enabling the identification and biochemical characterization of an N. benthamiana α-galactosidase we name here A1.1 (gene accession ID GJZM-1660). The transiently overexpressed and purified enzyme was a monomer lacking N-glycans and was active toward 4-methylumbelliferyl-α-d-galactopyranoside substrate (Km = 0.17 mm) over a broad pH range. A1.1 structural analysis by X-ray crystallography revealed marked similarities with human α-Gal A, even including A1.1's ability to hydrolyze Gb3 and lyso-Gb3, which are not endogenous in plants. Of note, A1.1 uptake into FD fibroblasts reduced the elevated lyso-Gb3 levels in these cells, consistent with A1.1 delivery to lysosomes as revealed by confocal microscopy. The ease of production and the features of A1.1, such as stability over a broad pH range, combined with its capacity to degrade glycosphingolipid substrates, warrant further examination of its value as a potential therapeutic agent for ERT-based FD management.
Collapse
Affiliation(s)
| | - Jules Beekwilder
- the Plant Sciences Group, Wageningen University and Research, Droevendaalsesteeg 1, 6708 PB Wageningen, and
| | | | | | - Ruud H P Wilbers
- the Plant Sciences Group, Wageningen University and Research, Droevendaalsesteeg 1, 6708 PB Wageningen, and
| | - Geri F Moolenaar
- Cloning and Protein Purification Facility, Leiden Institute of Chemistry, Einsteinweg 55, 2333 CC Leiden
| | - Nora Goosen
- Cloning and Protein Purification Facility, Leiden Institute of Chemistry, Einsteinweg 55, 2333 CC Leiden
| | | | | | | | | | - Cornelis H Hokke
- the Department of Parasitology, Centre of Infectious Diseases, Leiden University Medical Center, Albinusdreef 2, 2333 ZA Leiden, The Netherlands
| | | | - Arjen Schots
- the Plant Sciences Group, Wageningen University and Research, Droevendaalsesteeg 1, 6708 PB Wageningen, and
| | - Dirk Bosch
- the Plant Sciences Group, Wageningen University and Research, Droevendaalsesteeg 1, 6708 PB Wageningen, and
| | | | | |
Collapse
|
34
|
Skotnicová P, Sobotka R, Shepherd M, Hájek J, Hrouzek P, Tichý M. The cyanobacterial protoporphyrinogen oxidase HemJ is a new b-type heme protein functionally coupled with coproporphyrinogen III oxidase. J Biol Chem 2018; 293:12394-12404. [PMID: 29925590 DOI: 10.1074/jbc.ra118.003441] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2018] [Revised: 06/14/2018] [Indexed: 12/27/2022] Open
Abstract
Protoporphyrinogen IX oxidase (PPO), the last enzyme that is common to both chlorophyll and heme biosynthesis pathways, catalyzes the oxidation of protoporphyrinogen IX to protoporphyrin IX. PPO has several isoforms, including the oxygen-dependent HemY and an oxygen-independent enzyme, HemG. However, most cyanobacteria encode HemJ, the least characterized PPO form. We have characterized HemJ from the cyanobacterium Synechocystis sp. PCC 6803 (Synechocystis 6803) as a bona fide PPO; HemJ down-regulation resulted in accumulation of tetrapyrrole precursors and in the depletion of chlorophyll precursors. The expression of FLAG-tagged Synechocystis 6803 HemJ protein (HemJ.f) and affinity isolation of HemJ.f under native conditions revealed that it binds heme b The most stable HemJ.f form was a dimer, and higher oligomeric forms were also observed. Using both oxygen and artificial electron acceptors, we detected no enzymatic activity with the purified HemJ.f, consistent with the hypothesis that the enzymatic mechanism for HemJ is distinct from those of other PPO isoforms. The heme absorption spectra and distant HemJ homology to several membrane oxidases indicated that the heme in HemJ is redox-active and involved in electron transfer. HemJ was conditionally complemented by another PPO, HemG from Escherichia coli. If grown photoautotrophically, the complemented strain accumulated tripropionic tetrapyrrole harderoporphyrin, suggesting a defect in enzymatic conversion of coproporphyrinogen III to protoporphyrinogen IX, catalyzed by coproporphyrinogen III oxidase (CPO). This observation supports the hypothesis that HemJ is functionally coupled with CPO and that this coupling is disrupted after replacement of HemJ by HemG.
Collapse
Affiliation(s)
- Petra Skotnicová
- From the Czech Academy of Sciences, Institute of Microbiology, Centre Algatech, 379 81 Třeboň, Czech Republic.,the Faculty of Science, University of South Bohemia, 370 05 České Budějovice, Czech Republic, and
| | - Roman Sobotka
- From the Czech Academy of Sciences, Institute of Microbiology, Centre Algatech, 379 81 Třeboň, Czech Republic.,the Faculty of Science, University of South Bohemia, 370 05 České Budějovice, Czech Republic, and
| | - Mark Shepherd
- the School of Biosciences, RAPID Group, University of Kent, Canterbury CT2 7NZ,United Kingdom
| | - Jan Hájek
- From the Czech Academy of Sciences, Institute of Microbiology, Centre Algatech, 379 81 Třeboň, Czech Republic.,the Faculty of Science, University of South Bohemia, 370 05 České Budějovice, Czech Republic, and
| | - Pavel Hrouzek
- From the Czech Academy of Sciences, Institute of Microbiology, Centre Algatech, 379 81 Třeboň, Czech Republic.,the Faculty of Science, University of South Bohemia, 370 05 České Budějovice, Czech Republic, and
| | - Martin Tichý
- From the Czech Academy of Sciences, Institute of Microbiology, Centre Algatech, 379 81 Třeboň, Czech Republic, .,the Faculty of Science, University of South Bohemia, 370 05 České Budějovice, Czech Republic, and
| |
Collapse
|
35
|
Shaw JA, Henard CA, Liu L, Dieckman LM, Vázquez-Torres A, Bourret TJ. Salmonella enterica serovar Typhimurium has three transketolase enzymes contributing to the pentose phosphate pathway. J Biol Chem 2018; 293:11271-11282. [PMID: 29848552 DOI: 10.1074/jbc.ra118.003661] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2018] [Revised: 05/23/2018] [Indexed: 11/06/2022] Open
Abstract
The genus Salmonella is responsible for many illnesses in humans and other vertebrate animals. We report here that Salmonella enterica serovar Typhimurium harbors three transketolases that support the non-oxidative branch of the pentose phosphate pathway. BLAST analysis identified two genes, STM14_2885 and STM14_2886, that together encode a putative transketolase (TktC) with 46-47% similarity to the known TktA and TktB isoforms. Assessing the mRNA and protein expression for each of the three transketolases, we determined that all are expressed in WT cells and regulated to varying extents by the alternative sigma factor RpoS. Enzyme assays with lysates from WT and transketolase-knockout strains established that TktA is responsible for >88% of the transketolase activity in WT cells. We purified recombinant forms of each isoenzyme to assess the kinetics for canonical transketolase reactions. TktA and TktB had comparable values for Vmax (539-1362 μm NADH consumed/s), Km (80-739 μm), and catalytic efficiency (1.02 × 108-1.06 × 109 m-1/s) for each substrate tested. The recombinant form of TktC had lower Km values (23-120 μm), whereas the Vmax (7.8-16 μm NADH consumed/s) and catalytic efficiency (5.58 × 106 to 6.07 × 108 m-1/s) were 10-100-fold lower. Using a murine model of Salmonella infection, we showed that a strain lacking all three transketolases is avirulent in C57BL/6 mice. These data provide evidence that S Typhimurium possesses three transketolases that contribute to pathogenesis.
Collapse
Affiliation(s)
- Jeff A Shaw
- Department of Medical Microbiology and Immunology, Creighton University School of Medicine, Omaha, Nebraska 68178
| | - Calvin A Henard
- Department of Immunology and Microbiology, University of Colorado School of Medicine, Aurora, Colorado 80011
| | - Lin Liu
- Department of Immunology and Microbiology, University of Colorado School of Medicine, Aurora, Colorado 80011
| | - Lynne M Dieckman
- Department of Chemistry, Creighton University, Omaha, Nebraska 68178
| | - Andrés Vázquez-Torres
- Department of Immunology and Microbiology, University of Colorado School of Medicine, Aurora, Colorado 80011; Veterans Affairs Eastern Colorado Health Care System, Denver, Colorado 80220
| | - Travis J Bourret
- Department of Medical Microbiology and Immunology, Creighton University School of Medicine, Omaha, Nebraska 68178.
| |
Collapse
|
36
|
Langenegger N, Koua D, Schürch S, Heller M, Nentwig W, Kuhn-Nentwig L. Identification of a precursor processing protease from the spider Cupiennius salei essential for venom neurotoxin maturation. J Biol Chem 2018; 293:2079-2090. [PMID: 29269415 PMCID: PMC5808768 DOI: 10.1074/jbc.m117.810911] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2017] [Revised: 12/13/2017] [Indexed: 12/12/2022] Open
Abstract
Spider venom neurotoxins and cytolytic peptides are expressed as elongated precursor peptides, which are post-translationally processed by proteases to yield the active mature peptides. The recognition motifs for these processing proteases, first published more than 10 years ago, include the processing quadruplet motif (PQM) and the inverted processing quadruplet motif (iPQM). However, the identification of the relevant proteases was still pending. Here we describe the purification of a neurotoxin precursor processing protease from the venom of the spider Cupiennius salei The chymotrypsin-like serine protease is a 28-kDa heterodimer with optimum activity at venom's pH of 6.0. We designed multiple synthetic peptides mimicking the predicted cleavage sites of neurotoxin precursors. Using these peptides as substrates, we confirm the biochemical activity of the protease in propeptide removal from neurotoxin precursors by cleavage C-terminal of the PQM. Furthermore, the PQM protease also cleaves the iPQM relevant for heterodimerization of a subgroup of neurotoxins. An involvement in the maturing of cytolytic peptides is very likely, due to high similarity of present protease recognition motifs. Finally, bioinformatics analysis, identifying sequences of homolog proteins from 18 spiders of 9 families, demonstrate the wide distribution and importance of the isolated enzyme for spiders. In summary, we establish the first example of a PQM protease, essential for maturing of spider venom neurotoxins. In the future, the here described protease may be established as a powerful tool for production strategies of recombinant toxic peptides, adapted to the maturing of spider venom toxins.
Collapse
Affiliation(s)
- Nicolas Langenegger
- From the Institute of Ecology and Evolution, University of Bern, Baltzerstrasse 6, CH-3012 Bern, Switzerland
| | - Dominique Koua
- From the Institute of Ecology and Evolution, University of Bern, Baltzerstrasse 6, CH-3012 Bern, Switzerland
- the Institut National Polytechnique Félix Houphouet-Boigny, BP 1093 Yamoussoukro, Côte d'Ivoire
| | - Stefan Schürch
- the Department of Chemistry and Biochemistry, University of Bern, Freiestrasse 3, CH-3012 Bern, Switzerland, and
| | - Manfred Heller
- the Department of Clinical Research, Proteomics and Mass Spectrometry Core Facility, University of Bern, Freiburgstrasse 15, CH-3010 Bern, Switzerland
| | - Wolfgang Nentwig
- From the Institute of Ecology and Evolution, University of Bern, Baltzerstrasse 6, CH-3012 Bern, Switzerland
| | - Lucia Kuhn-Nentwig
- From the Institute of Ecology and Evolution, University of Bern, Baltzerstrasse 6, CH-3012 Bern, Switzerland,
| |
Collapse
|
37
|
Partovi SE, Mus F, Gutknecht AE, Martinez HA, Tripet BP, Lange BM, DuBois JL, Peters JW. Coenzyme M biosynthesis in bacteria involves phosphate elimination by a functionally distinct member of the aspartase/fumarase superfamily. J Biol Chem 2018; 293:5236-5246. [PMID: 29414784 DOI: 10.1074/jbc.ra117.001234] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2017] [Revised: 01/23/2018] [Indexed: 11/06/2022] Open
Abstract
For nearly 30 years, coenzyme M (CoM) was assumed to be present solely in methanogenic archaea. In the late 1990s, CoM was reported to play a role in bacterial propene metabolism, but no biosynthetic pathway for CoM has yet been identified in bacteria. Here, using bioinformatics and proteomic approaches in the metabolically versatile bacterium Xanthobacter autotrophicus Py2, we identified four putative CoM biosynthetic enzymes encoded by the xcbB1, C1, D1, and E1 genes. Only XcbB1 was homologous to a known CoM biosynthetic enzyme (ComA), indicating that CoM biosynthesis in bacteria involves enzymes different from those in archaea. We verified that the ComA homolog produces phosphosulfolactate from phosphoenolpyruvate (PEP), demonstrating that bacterial CoM biosynthesis is initiated similarly as the phosphoenolpyruvate-dependent methanogenic archaeal pathway. The bioinformatics analysis revealed that XcbC1 and D1 are members of the aspartase/fumarase superfamily (AFS) and that XcbE1 is a pyridoxal 5'-phosphate-containing enzyme with homology to d-cysteine desulfhydrases. Known AFS members catalyze β-elimination reactions of succinyl-containing substrates, yielding fumarate as the common unsaturated elimination product. Unexpectedly, we found that XcbC1 catalyzes β-elimination on phosphosulfolactate, yielding inorganic phosphate and a novel metabolite, sulfoacrylic acid. Phosphate-releasing β-elimination reactions are unprecedented among the AFS, indicating that XcbC1 is an unusual phosphatase. Direct demonstration of phosphosulfolactate synthase activity for XcbB1 and phosphate β-elimination activity for XcbC1 strengthened their hypothetical assignment to a CoM biosynthetic pathway and suggested functions also for XcbD1 and E1. Our results represent a critical first step toward elucidating the CoM pathway in bacteria.
Collapse
Affiliation(s)
- Sarah E Partovi
- From the Department of Chemistry and Biochemistry, Montana State University, Bozeman, Montana 59717 and
| | | | - Andrew E Gutknecht
- From the Department of Chemistry and Biochemistry, Montana State University, Bozeman, Montana 59717 and
| | - Hunter A Martinez
- From the Department of Chemistry and Biochemistry, Montana State University, Bozeman, Montana 59717 and
| | - Brian P Tripet
- From the Department of Chemistry and Biochemistry, Montana State University, Bozeman, Montana 59717 and
| | - Bernd Markus Lange
- the Institute of Biological Chemistry and.,M. J. Murdock Metabolomics Laboratory, Washington State University, Pullman, Washington 99164
| | - Jennifer L DuBois
- From the Department of Chemistry and Biochemistry, Montana State University, Bozeman, Montana 59717 and
| | | |
Collapse
|
38
|
Schwander T, McLean R, Zarzycki J, Erb TJ. Structural basis for substrate specificity of methylsuccinyl-CoA dehydrogenase, an unusual member of the acyl-CoA dehydrogenase family. J Biol Chem 2017; 293:1702-1712. [PMID: 29275330 PMCID: PMC5798300 DOI: 10.1074/jbc.ra117.000764] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2017] [Revised: 12/20/2017] [Indexed: 11/13/2022] Open
Abstract
(2S)-methylsuccinyl-CoA dehydrogenase (MCD) belongs to the family of FAD-dependent acyl-CoA dehydrogenase (ACD) and is a key enzyme of the ethylmalonyl-CoA pathway for acetate assimilation. It catalyzes the oxidation of (2S)-methylsuccinyl-CoA to α,β-unsaturated mesaconyl-CoA and shows only about 0.5% activity with succinyl-CoA. Here we report the crystal structure of MCD at a resolution of 1.37 Å. The enzyme forms a homodimer of two 60-kDa subunits. Compared with other ACDs, MCD contains an ∼170-residue-long N-terminal extension that structurally mimics a dimer–dimer interface of these enzymes that are canonically organized as tetramers. MCD catalyzes the unprecedented oxidation of an α-methyl branched dicarboxylic acid CoA thioester. Substrate specificity is achieved by a cluster of three arginines that accommodates the terminal carboxyl group and a dedicated cavity that facilitates binding of the C2 methyl branch. MCD apparently evolved toward preventing the nonspecific oxidation of succinyl-CoA, which is a close structural homolog of (2S)-methylsuccinyl-CoA and an essential intermediate in central carbon metabolism. For different metabolic engineering and biotechnological applications, however, an enzyme that can oxidize succinyl-CoA to fumaryl-CoA is sought after. Based on the MCD structure, we were able to shift substrate specificity of MCD toward succinyl-CoA through active-site mutagenesis.
Collapse
Affiliation(s)
- Thomas Schwander
- From the Department of Biochemistry and Synthetic Metabolism, Max-Planck-Institute for Terrestrial Microbiology Marburg, Karl-von-Frisch-Strasse 10, D-35043 Marburg, Germany and
| | - Richard McLean
- From the Department of Biochemistry and Synthetic Metabolism, Max-Planck-Institute for Terrestrial Microbiology Marburg, Karl-von-Frisch-Strasse 10, D-35043 Marburg, Germany and
| | - Jan Zarzycki
- From the Department of Biochemistry and Synthetic Metabolism, Max-Planck-Institute for Terrestrial Microbiology Marburg, Karl-von-Frisch-Strasse 10, D-35043 Marburg, Germany and
| | - Tobias J Erb
- From the Department of Biochemistry and Synthetic Metabolism, Max-Planck-Institute for Terrestrial Microbiology Marburg, Karl-von-Frisch-Strasse 10, D-35043 Marburg, Germany and .,the LOEWE Center for Synthetic Microbiology (SYNMIKRO), D-35043 Marburg, Germany
| |
Collapse
|
39
|
Köksal Z, Kalin R, Camadan Y, Usanmaz H, Almaz Z, Gülçin İ, Gokcen T, Gören AC, Ozdemir H. Secondary Sulfonamides as Effective Lactoperoxidase Inhibitors. Molecules 2017; 22:molecules22060793. [PMID: 28538675 PMCID: PMC6152724 DOI: 10.3390/molecules22060793] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2017] [Revised: 04/27/2017] [Accepted: 05/09/2017] [Indexed: 01/26/2023] Open
Abstract
Secondary sulfonamides (4a–8h) incorporating acetoxybenzamide, triacetoxybenzamide, hydroxybenzamide, and trihydroxybenzamide and possessing thiazole, pyrimidine, pyridine, isoxazole and thiadiazole groups were synthesized. Lactoperoxidase (LPO, E.C.1.11.1.7), as a natural antibacterial agent, is a peroxidase enzyme secreted from salivary, mammary, and other mucosal glands. In the present study, the in vitro inhibitory effects of some secondary sulfonamide derivatives (4a–8h) were examined against LPO. The obtained results reveal that secondary sulfonamide derivatives (4a–8h) are effective LPO inhibitors. The Ki values of secondary sulfonamide derivatives (4a–8h) were found in the range of 1.096 × 10−3 to 1203.83 µM against LPO. However, the most effective inhibition was found for N-(sulfathiazole)-3,4,5-triacetoxybenzamide (6a), with Ki values of 1.096 × 10−3 ± 0.471 × 10−3 µM as non-competitive inhibition.
Collapse
Affiliation(s)
- Zeynep Köksal
- Department of Chemistry, Faculty of Sciences, İstanbul Medeniyet University, 34730 İstanbul, Turkey.
| | - Ramazan Kalin
- Department of Chemistry, Faculty of Science, Ataturk University, 25240 Erzurum, Turkey.
- Department of Basic Science, Faculty of Science, Erzurum Technical University, 25240 Erzurum, Turkey.
| | - Yasemin Camadan
- Pharmacy Services Program, Vocational School of Health Services, Artvin Coruh University, 08000 Artvin, Turkey.
| | - Hande Usanmaz
- Department of Bioengineering, Faculty of Engineering and Architecture, Sinop University, 57000 Sinop, Turkey.
| | - Züleyha Almaz
- Department of Molecular Biology and Genetics, Faculty of Sciences and Arts, Muş Alparslan University, 49250 Muş, Turkey.
| | - İlhami Gülçin
- Department of Chemistry, Faculty of Science, Ataturk University, 25240 Erzurum, Turkey.
| | - Taner Gokcen
- TUBITAK UME, Chemistry Group Laboratories, P.O. Box: 54, 41470 Gebze Kocaeli, Turkey.
- Department of Organic Chemistry, Faculty of Science, Istanbul Technical University, 34469 Istanbul, Turkey.
| | - Ahmet Ceyhan Gören
- TUBITAK UME, Chemistry Group Laboratories, P.O. Box: 54, 41470 Gebze Kocaeli, Turkey.
| | - Hasan Ozdemir
- Department of Chemistry, Faculty of Science, Ataturk University, 25240 Erzurum, Turkey.
| |
Collapse
|
40
|
Kumar K, Belur PD. New extracellular thermostable oxalate oxidase produced from endophytic Ochrobactrum intermedium CL6: Purification and biochemical characterization. Prep Biochem Biotechnol 2017; 46:734-9. [PMID: 26796139 DOI: 10.1080/10826068.2015.1135458] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
Oxalate oxidase (EC 1.2.3.4) catalyzes the oxidative cleavage of oxalate to carbon dioxide with the reduction of molecular oxygen to hydrogen peroxide. Oxalate oxidase found its application in clinical assay for oxalate in blood and urine. This study describes the purification and biochemical characterization of an oxalate oxidase produced from an endophytic bacterium, Ochrobactrum intermedium CL6. The cell-free fermentation broth was subjected to two-step enzyme purification, which resulted in a 58.74-fold purification with 83% recovery. Specific activity of the final purified enzyme was 26.78 U mg(-1) protein. The enzyme displayed an optimum pH and temperature of 3.8 and 80°C, respectively, and high stability at 4-80°C for 6 h. The enzymatic activity was not influenced by metal ions and chemical agents (K(+), Na(+), Zn(2+), Fe(3+), Mn(2+), Mg(2+), glucose, urea, lactate) commonly found in serum and urine, with Cu(2+) being the exception. The enzyme appears to be a metalloprotein stimulated by Ca(2+) and Fe(2+). Its Km and Kcat for oxalate were found to be 0.45 mM and 85 s(-1), respectively. This enzyme is the only known oxalate oxidase which did not show substrate inhibition up to a substrate concentration of 50 mM. Thermostability, kinetic properties, and the absence of substrate inhibition make this enzyme an ideal candidate for clinical applications.
Collapse
Affiliation(s)
- Kunal Kumar
- a Department of Chemical Engineering , National Institute of Technology Karnataka , Mangalore , Karnataka , India
| | - Prasanna D Belur
- a Department of Chemical Engineering , National Institute of Technology Karnataka , Mangalore , Karnataka , India
| |
Collapse
|
41
|
Ravindran R, Jaiswal AK. Microbial Enzyme Production Using Lignocellulosic Food Industry Wastes as Feedstock: A Review. Bioengineering (Basel) 2016; 3:E30. [PMID: 28952592 PMCID: PMC5597273 DOI: 10.3390/bioengineering3040030] [Citation(s) in RCA: 49] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2016] [Revised: 11/09/2016] [Accepted: 11/11/2016] [Indexed: 11/17/2022] Open
Abstract
Enzymes are of great importance in the industry due to their substrate and product specificity, moderate reaction conditions, minimal by-product formation and high yield. They are important ingredients in several products and production processes. Up to 30% of the total production cost of enzymes is attributed to the raw materials costs. The food industry expels copious amounts of processing waste annually, which is mostly lignocellulosic in nature. Upon proper treatment, lignocellulose can replace conventional carbon sources in media preparations for industrial microbial processes, such as enzyme production. However, wild strains of microorganisms that produce industrially important enzymes show low yield and cannot thrive on artificial substrates. The application of recombinant DNA technology and metabolic engineering has enabled researchers to develop superior strains that can not only withstand harsh environmental conditions within a bioreactor but also ensure timely delivery of optimal results. This article gives an overview of the current complications encountered in enzyme production and how accumulating food processing waste can emerge as an environment-friendly and economically feasible solution for a choice of raw material. It also substantiates the latest techniques that have emerged in enzyme purification and recovery over the past four years.
Collapse
Affiliation(s)
- Rajeev Ravindran
- School of Food Science and Environmental Health, College of Sciences and Health, Dublin Institute of Technology, Cathal Brugha Street, Dublin D01 HV58, Ireland.
| | - Amit K Jaiswal
- School of Food Science and Environmental Health, College of Sciences and Health, Dublin Institute of Technology, Cathal Brugha Street, Dublin D01 HV58, Ireland.
| |
Collapse
|
42
|
Genç H, Kalin R, Köksal Z, Sadeghian N, Kocyigit UM, Zengin M, Gülçin İ, Özdemir H. Discovery of Potent Carbonic Anhydrase and Acetylcholinesterase Inhibitors: 2-Aminoindan β-Lactam Derivatives. Int J Mol Sci 2016; 17:E1736. [PMID: 27775608 DOI: 10.3390/ijms17101736] [Citation(s) in RCA: 59] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2016] [Revised: 10/02/2016] [Accepted: 10/10/2016] [Indexed: 12/11/2022] Open
Abstract
β-Lactams are pharmacologically important compounds because of their various biological uses, including antibiotic and so on. β-Lactams were synthesized from benzylidene-inden derivatives and acetoxyacetyl chloride. The inhibitory effect of these compounds was examined for human carbonic anhydrase I and II (hCA I, and II) and acetylcholinesterase (AChE). The results reveal that β-lactams are inhibitors of hCA I, II and AChE. The Ki values of β-lactams (2a–k) were 0.44–6.29 nM against hCA I, 0.93–8.34 nM against hCA II, and 0.25–1.13 nM against AChE. Our findings indicate that β-lactams (2a–k) inhibit both carbonic anhydrases (CA) isoenzymes and AChE at low nanomolar concentrations.
Collapse
|
43
|
Maalcke WJ, Reimann J, de Vries S, Butt JN, Dietl A, Kip N, Mersdorf U, Barends TRM, Jetten MSM, Keltjens JT, Kartal B. Characterization of Anammox Hydrazine Dehydrogenase, a Key N2-producing Enzyme in the Global Nitrogen Cycle. J Biol Chem 2016; 291:17077-92. [PMID: 27317665 PMCID: PMC5016112 DOI: 10.1074/jbc.m116.735530] [Citation(s) in RCA: 72] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2016] [Revised: 06/07/2016] [Indexed: 11/06/2022] Open
Abstract
Anaerobic ammonium-oxidizing (anammox) bacteria derive their energy for growth from the oxidation of ammonium with nitrite as the electron acceptor. N2, the end product of this metabolism, is produced from the oxidation of the intermediate, hydrazine (N2H4). Previously, we identified N2-producing hydrazine dehydrogenase (KsHDH) from the anammox organism Kuenenia stuttgartiensis as the gene product of kustc0694 and determined some of its catalytic properties. In the genome of K. stuttgartiensis, kustc0694 is one of 10 paralogs related to octaheme hydroxylamine (NH2OH) oxidoreductase (HAO). Here, we characterized KsHDH as a covalently cross-linked homotrimeric octaheme protein as found for HAO and HAO-related hydroxylamine-oxidizing enzyme kustc1061 from K. stuttgartiensis Interestingly, the HDH trimers formed octamers in solution, each octamer harboring an amazing 192 c-type heme moieties. Whereas HAO and kustc1061 are capable of hydrazine oxidation as well, KsHDH was highly specific for this activity. To understand this specificity, we performed detailed amino acid sequence analyses and investigated the catalytic and spectroscopic (electronic absorbance, EPR) properties of KsHDH in comparison with the well defined HAO and kustc1061. We conclude that HDH specificity is most likely derived from structural changes around the catalytic heme 4 (P460) and of the electron-wiring circuit comprising seven His/His-ligated c-type hemes in each subunit. These nuances make HDH a globally prominent N2-producing enzyme, next to nitrous oxide (N2O) reductase from denitrifying microorganisms.
Collapse
Affiliation(s)
- Wouter J Maalcke
- From the Department of Microbiology, Institute for Water and Wetland Research, Radboud University Nijmegen, 6525 AJ Nijmegen, The Netherlands
| | - Joachim Reimann
- From the Department of Microbiology, Institute for Water and Wetland Research, Radboud University Nijmegen, 6525 AJ Nijmegen, The Netherlands
| | - Simon de Vries
- the Department of Biotechnology, Delft University of Technology, 2628 BC Delft, The Netherlands
| | - Julea N Butt
- the Centre for Molecular and Structural Biochemistry, School of Chemistry and School of Biological Sciences, University of East Anglia, Norwich NR4 7TJ, United Kingdom, and
| | - Andreas Dietl
- the Department of Biomolecular Mechanisms, Max Planck Institute for Medical Research, 69120 Heidelberg, Germany
| | - Nardy Kip
- From the Department of Microbiology, Institute for Water and Wetland Research, Radboud University Nijmegen, 6525 AJ Nijmegen, The Netherlands
| | - Ulrike Mersdorf
- the Department of Biomolecular Mechanisms, Max Planck Institute for Medical Research, 69120 Heidelberg, Germany
| | - Thomas R M Barends
- the Department of Biomolecular Mechanisms, Max Planck Institute for Medical Research, 69120 Heidelberg, Germany
| | - Mike S M Jetten
- From the Department of Microbiology, Institute for Water and Wetland Research, Radboud University Nijmegen, 6525 AJ Nijmegen, The Netherlands, the Department of Biotechnology, Delft University of Technology, 2628 BC Delft, The Netherlands
| | - Jan T Keltjens
- From the Department of Microbiology, Institute for Water and Wetland Research, Radboud University Nijmegen, 6525 AJ Nijmegen, The Netherlands
| | - Boran Kartal
- From the Department of Microbiology, Institute for Water and Wetland Research, Radboud University Nijmegen, 6525 AJ Nijmegen, The Netherlands,
| |
Collapse
|
44
|
Dela Seña C, Sun J, Narayanasamy S, Riedl KM, Yuan Y, Curley RW, Schwartz SJ, Harrison EH. Substrate Specificity of Purified Recombinant Chicken β-Carotene 9',10'-Oxygenase (BCO2). J Biol Chem 2016; 291:14609-19. [PMID: 27143479 DOI: 10.1074/jbc.m116.723684] [Citation(s) in RCA: 57] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2016] [Indexed: 11/06/2022] Open
Abstract
Provitamin A carotenoids are oxidatively cleaved by β-carotene 15,15'-dioxygenase (BCO1) at the central 15-15' double bond to form retinal (vitamin A aldehyde). Another carotenoid oxygenase, β-carotene 9',10'-oxygenase (BCO2) catalyzes the oxidative cleavage of carotenoids at the 9'-10' bond to yield an ionone and an apo-10'-carotenoid. Previously published substrate specificity studies of BCO2 were conducted using crude lysates from bacteria or insect cells expressing recombinant BCO2. Our attempts to obtain active recombinant human BCO2 expressed in Escherichia coli were unsuccessful. We have expressed recombinant chicken BCO2 in the strain E. coli BL21-Gold (DE3) and purified the enzyme by cobalt ion affinity chromatography. Like BCO1, purified recombinant chicken BCO2 catalyzes the oxidative cleavage of the provitamin A carotenoids β-carotene, α-carotene, and β-cryptoxanthin. Its catalytic activity with β-carotene as substrate is at least 10-fold lower than that of BCO1. In further contrast to BCO1, purified recombinant chicken BCO2 also catalyzes the oxidative cleavage of 9-cis-β-carotene and the non-provitamin A carotenoids zeaxanthin and lutein, and is inactive with all-trans-lycopene and β-apocarotenoids. Apo-10'-carotenoids were detected as enzymatic products by HPLC, and the identities were confirmed by LC-MS. Small amounts of 3-hydroxy-β-apo-8'-carotenal were also consistently detected in BCO2-β-cryptoxanthin reaction mixtures. With the exception of this activity with β-cryptoxanthin, BCO2 cleaves specifically at the 9'-10' bond to produce apo-10'-carotenoids. BCO2 has been shown to function in preventing the excessive accumulation of carotenoids, and its broad substrate specificity is consistent with this.
Collapse
Affiliation(s)
- Carlo Dela Seña
- From the Department of Human Nutrition, Ohio State Biochemistry Program
| | - Jian Sun
- From the Department of Human Nutrition
| | | | | | - Yan Yuan
- From the Department of Human Nutrition
| | - Robert W Curley
- Ohio State Biochemistry Program, College of Pharmacy, The Ohio State University, Columbus, Ohio 43210
| | | | - Earl H Harrison
- From the Department of Human Nutrition, Ohio State Biochemistry Program,
| |
Collapse
|
45
|
Kunishima M, Yamauchi Y, Mizutani M, Kuse M, Takikawa H, Sugimoto Y. Identification of (Z)-3:(E)-2-Hexenal Isomerases Essential to the Production of the Leaf Aldehyde in Plants. J Biol Chem 2016; 291:14023-14033. [PMID: 27129773 DOI: 10.1074/jbc.m116.726687] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2016] [Indexed: 11/06/2022] Open
Abstract
The green odor of plants is characterized by green leaf volatiles (GLVs) composed of C6 compounds. GLVs are biosynthesized from polyunsaturated fatty acids in thylakoid membranes by a series of enzymes. A representative member of GLVs (E)-2-hexenal, known as the leaf aldehyde, has been assumed to be produced by isomerization from (Z)-3-hexenal in the biosynthesis pathway; however, the enzyme has not yet been identified. In this study, we purified the (Z)-3:(E)-2-hexenal isomerase (HI) from paprika fruits and showed that various plant species have homologous HIs. Purified HI is a homotrimeric protein of 110 kDa composed of 35-kDa subunits and shows high activity at acidic and neutral pH values. Phylogenetic analysis showed that HIs belong to the cupin superfamily, and at least three catalytic amino acids (His, Lys, Tyr) are conserved in HIs of various plant species. Enzymatic isomerization of (Z)-3-hexenal in the presence of deuterium oxide resulted in the introduction of deuterium at the C4 position of (E)-2-hexenal, and a suicide substrate 3-hexyn-1-al inhibited HI irreversibly, suggesting that the catalytic mode of HI is a keto-enol tautomerism reaction mode mediated by a catalytic His residue. The gene expression of HIs in Solanaceae plants was enhanced in specific developmental stages and by wounding treatment. Transgenic tomato plants overexpressing paprika HI accumulated (E)-2-hexenal in contrast to wild-type tomato plants mainly accumulating (Z)-3-hexenal, suggesting that HI plays a key role in the production of (E)-2-hexenal in planta.
Collapse
Affiliation(s)
- Mikiko Kunishima
- Graduate School of Agricultural Science, Kobe University, 1-1 Rokkodai, Nada, Kobe 657-8501, Japan
| | - Yasuo Yamauchi
- Graduate School of Agricultural Science, Kobe University, 1-1 Rokkodai, Nada, Kobe 657-8501, Japan.
| | - Masaharu Mizutani
- Graduate School of Agricultural Science, Kobe University, 1-1 Rokkodai, Nada, Kobe 657-8501, Japan
| | - Masaki Kuse
- Graduate School of Agricultural Science, Kobe University, 1-1 Rokkodai, Nada, Kobe 657-8501, Japan
| | - Hirosato Takikawa
- Graduate School of Agricultural Science, Kobe University, 1-1 Rokkodai, Nada, Kobe 657-8501, Japan
| | - Yukihiro Sugimoto
- Graduate School of Agricultural Science, Kobe University, 1-1 Rokkodai, Nada, Kobe 657-8501, Japan
| |
Collapse
|
46
|
Zhang Y, Halder S, Kerr RA, Parrell D, Ruotolo B, Kroos L. Complex Formed between Intramembrane Metalloprotease SpoIVFB and Its Substrate, Pro-σK. J Biol Chem 2016; 291:10347-62. [PMID: 26953342 DOI: 10.1074/jbc.m116.715508] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2016] [Indexed: 11/06/2022] Open
Abstract
Intramembrane metalloproteases (IMMPs) are conserved from bacteria to humans and control many important signaling pathways, but little is known about how IMMPs interact with their substrates. SpoIVFB is an IMMP that cleaves Pro-σ(K) during Bacillus subtilis endospore formation. When catalytically inactive SpoIVFB was coexpressed with C-terminally truncated Pro-σ(K)(1-126) (which can be cleaved by active SpoIVFB) in Escherichia coli, the substrate dramatically improved solubilization of the enzyme from membranes with mild detergents. Both the Pro(1-20) and σ(K)(21-126) parts contributed to improving SpoIVFB solubilization from membranes, but only the σ(K) part was needed to form a stable complex with SpoIVFB in a pulldown assay. The last 10 residues of SpoIVFB were required for improved solubilization from membranes by Pro-σ(K)(1-126) and for normal interaction with the substrate. The inactive SpoIVFB·Pro-σ(K)(1-126)-His6 complex was stable during affinity purification and gel filtration chromatography. Disulfide cross-linking of the purified complex indicated that it resembled the complex formed in vivo Ion mobility-mass spectrometry analysis resulted in an observed mass consistent with a 4:2 SpoIVFB·Pro-σ(K)(1-126)-His6 complex. Stepwise photobleaching of SpoIVFB fused to a fluorescent protein supported the notion that the enzyme is tetrameric during B. subtilis sporulation. The results provide the first evidence that an IMMP acts as a tetramer, give new insights into how SpoIVFB interacts with its substrate, and lay the foundation for further biochemical analysis of the enzyme·substrate complex and future structural studies.
Collapse
Affiliation(s)
- Yang Zhang
- From the Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan 48824 and
| | - Sabyasachi Halder
- From the Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan 48824 and
| | - Richard A Kerr
- the Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109
| | - Daniel Parrell
- From the Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan 48824 and
| | - Brandon Ruotolo
- the Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109
| | - Lee Kroos
- From the Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan 48824 and
| |
Collapse
|
47
|
Acer Ö, Bekler FM, Pirinççioğlu H, Güven RG, Güven K. Purification and Characterization of Thermostable and Detergent-Stable α-Amylase from Anoxybacillus sp. AH1. Food Technol Biotechnol 2016; 54:70-77. [PMID: 27904395 PMCID: PMC5105632 DOI: 10.17133/ftb.54.01.16.4122] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2015] [Accepted: 09/11/2015] [Indexed: 09/29/2022] Open
Abstract
A thermostable and detergent-stable α-amylase from a newly isolated Anoxybacillus sp. AH1 was purified and characterized. Maximum enzyme production (1874.8 U/mL) was obtained at 24 h of incubation. The amylase was purified by using Sephadex G-75 gel filtration, after which an 18-fold increase in specific activity and a yield of 9% were achieved. The molecular mass of the purified enzyme was estimated at 85 kDa by sodium dodecyl sulphate-polyacrylamide gel electrophoresis (SDS-PAGE). The optimum pH and temperature values of the enzyme were 7.0 and 60 °C, respectively. The enzyme was highly stable in the presence of 30% glycerol, retaining 85% of its original activity at 60 °C within 120 min. Km and vmax values were 0.102 µmol and 0.929 µmol/min, respectively, using Lineweaver-Burk plot. The enzyme activity was increased by various detergents, but it was significantly inhibited in the presence of urea. Mg2+ and Ca2+ also significantly activated α-amylase, while Zn2+, Cu2+ and metal ion chelators ethylenediaminetetraacetic acid (EDTA) and 1,10-phenanthroline (phen) greatly inhibited the enzyme activity. α-Amylase activity was enhanced by β-mercaptoethanol (β-ME) and dithiothreitol (DTT) to a great extent, but inhibited by p-chloromercuribenzoic acid (PCMB). Iodoacetamide (IAA) and N-ethylmaleimide (NEM) had a slight, whereas phenylmethylsulfonyl fluoride (PMSF) had a strong inhibitory effect on the amylase activity.
Collapse
Affiliation(s)
- Ömer Acer
- Molecular Biology and Genetic Department, Faculty of Science, Dicle University, TR-21280 Diyarbakır, Turkey
| | - Fatma Matpan Bekler
- Molecular Biology and Genetic Department, Faculty of Science, Dicle University, TR-21280 Diyarbakır, Turkey
| | - Hemşe Pirinççioğlu
- Molecular Biology and Genetic Department, Faculty of Science, Dicle University, TR-21280 Diyarbakır, Turkey
| | - Reyhan Gül Güven
- Division of Science Teaching, Ziya Gökalp Faculty of Education, Dicle University, TR-21280 Diyarbakır, Turkey
| | - Kemal Güven
- Molecular Biology and Genetic Department, Faculty of Science, Dicle University, TR-21280 Diyarbakır, Turkey
| |
Collapse
|
48
|
Şirin S, Aydaş SB, Aslım B. Biochemical Evaluation of Phenylalanine Ammonia Lyase from Endemic Plant Cyathobasis fruticulosa (Bunge) Aellen. for the Dietary Treatment of Phenylketonuria. Food Technol Biotechnol 2016; 54:296-303. [PMID: 27956861 DOI: 10.17113/ftb.54.03.16.4519] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Enzyme substitution therapy with the phenylalanine ammonia lyase (PAL) is a new approach to the treatment of patients with phenylketonuria (PKU). This enzyme is responsible for the conversion of phenylalanine to trans-cinnamic acid. We assessed the PAL enzyme of the endemic plant Cyathobasis fruticulosa (Bunge) Aellen. for its possible role in the dietary treatment of PKU. The enzyme was found to have a high activity of (64.9±0.1) U/mg, with the optimum pH, temperature and buffer (Tris-HCl and l-phenylalanine) concentration levels of pH=8.8, 37 °C and 100 mM, respectively. Optimum enzyme activity was achieved at pH=4.0 and 7.5, corresponding to pH levels of gastric and intestinal juice, and NaCl concentration of 200 mM. The purification of the enzyme by 1.87-fold yielded an activity of 98.6 U/mg. PAL activities determined by HPLC analyses before and after purification were similar. Two protein bands, one at 70 and the other at 23 kDa, were determined by Western blot analysis of the enzyme. This enzyme is a potential candidate for serial production of dietary food and biotechnological products.
Collapse
Affiliation(s)
- Seda Şirin
- Gazi University, Faculty of Science, Department of Biology, TR-06500 Teknikokullar, Ankara, Turkey
| | - Selcen Babaoğlu Aydaş
- Gazi University, Vocational High School of Health Services, TR-06830 Gölbaşı, Ankara, Turkey
| | - Belma Aslım
- Gazi University, Faculty of Science, Department of Biology, TR-06500 Teknikokullar, Ankara, Turkey
| |
Collapse
|
49
|
Bhat R, Kaur T, Khajuria M, Vyas R, Vyas D. Purification and Characterization of a Novel Redox-Regulated Isoform of Myrosinase (β-Thioglucoside Glucohydrolase) from Lepidium latifolium L. J Agric Food Chem 2015; 63:10218-10226. [PMID: 26527478 DOI: 10.1021/acs.jafc.5b04468] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Myrosinase (ExPASy entry EC 3.2.1.147) is involved in the hydrolysis of glucosinolates to isothiocyanates, nitriles, and thiocyanates that are responsible for various ecological and health benefits. Myrosinase was purified from the leaves of Lepidium latifolium, a high-altitude plant, to homogeneity in a three-step purification process. Purified enzyme exists as dimer in native form (∼160 kDa) with a subunit size of ∼70 kDa. The enzyme exhibited maximum activity at pH 6.0 and 50 °C. With sinigrin as substrate, the enzyme showed Km and Vmax values of 171 ± 23 μM and 0.302 μmol min(-1) mg(-1), respectively. The enzyme was found to be redox-regulated, with an increase in Vmax and Kcat in the presence of GSH. Reduced forms of the enzyme were found to be more active. This thiol-regulated kinetic behavior of myrosinase signifies enzyme's strategy to fine-tune its activity in different redox environments, thus regulating its biological effects.
Collapse
Affiliation(s)
- Rohini Bhat
- Biodiversity and Applied Botany Division, ‡Formulation and Drug Development Division, and §Academy of Scientific and Innovative Research, Indian Institute of Integrative Medicine (CSIR) , Canal Road, Jammu, Jammu and Kashmir 180001, India
| | - Tarandeep Kaur
- Biodiversity and Applied Botany Division, ‡Formulation and Drug Development Division, and §Academy of Scientific and Innovative Research, Indian Institute of Integrative Medicine (CSIR) , Canal Road, Jammu, Jammu and Kashmir 180001, India
| | - Manu Khajuria
- Biodiversity and Applied Botany Division, ‡Formulation and Drug Development Division, and §Academy of Scientific and Innovative Research, Indian Institute of Integrative Medicine (CSIR) , Canal Road, Jammu, Jammu and Kashmir 180001, India
| | - Ruchika Vyas
- Biodiversity and Applied Botany Division, ‡Formulation and Drug Development Division, and §Academy of Scientific and Innovative Research, Indian Institute of Integrative Medicine (CSIR) , Canal Road, Jammu, Jammu and Kashmir 180001, India
| | - Dhiraj Vyas
- Biodiversity and Applied Botany Division, ‡Formulation and Drug Development Division, and §Academy of Scientific and Innovative Research, Indian Institute of Integrative Medicine (CSIR) , Canal Road, Jammu, Jammu and Kashmir 180001, India
| |
Collapse
|
50
|
Gao Y, Jin L, Shi H, Chu Z. Characterization of a Novel Butachlor Biodegradation Pathway and Cloning of the Debutoxylase (Dbo) Gene Responsible for Debutoxylation of Butachlor in Bacillus sp. hys-1. J Agric Food Chem 2015; 63:8381-8390. [PMID: 26368393 DOI: 10.1021/acs.jafc.5b03326] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Bacillus sp. strain hys-1, which was isolated from active sludge, could degrade >90% butachlor at a concentration of 100 mg/L within 7 days. The present work revealed that strain hys-1 could mineralize butachlor via the following pathway: butachlor was initially metabolized to 2-chloro-N-(2,6-diethylphenyl)-N-methylacetamide by debutoxylation and then transformed to form 2-chloro-N-(2,6-diethylphenyl)acetamide by N-demethylation. Subsequently, it was converted to 2,6-diethylaniline and further mineralized into CO2 and H2O. In addition, the catalytic efficiency of crude cell extracts descended as follows: alachlor > acetochlor > butachlor. Furthermore, a novel 744 bp gene responsible for transforming butachlor into 2-chloro-N-(2,6-diethylphenyl)-N-methylacetamide was cloned from strain hys-1 and the encoding debutoxylase was designated Dbo. Then Dbo was expressed in Escherichia coli BL21 (DE3) and purified using Ni-nitrilotriacetic acid affinity chromatography. Dbo displayed the highest activity against butachlor at pH 6.5 and 30 °C. Metal ions played an important role in Dbo activity. To the best of the authors' knowledge, this is the first report that strain hys-1 can mineralize butachlor by a novel metabolic mechanism and the first identification of a gene encoding butachlor debutoxylase.
Collapse
Affiliation(s)
- Yang Gao
- Zhejiang Ocean University , Zhoushan 316000, China
| | - Lei Jin
- Zhejiang Ocean University , Zhoushan 316000, China
- Marine Fishery Research Institute of Zhejiang Province , Zhoushan 316021, China
| | - Hui Shi
- Marine Fishery Research Institute of Zhejiang Province , Zhoushan 316021, China
| | - Zhangjie Chu
- Zhejiang Ocean University , Zhoushan 316000, China
| |
Collapse
|